Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 43
Found at i:2956524 original size:13 final size:13
Alignment explanation
Indices: 2956506--2956548 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
2956496 GTCACAACCC
2956506 GACCCGACCCGTT
1 GACCCGACCCGTT
2956519 GACCCGACCCGTT
1 GACCCGACCCGTT
*
2956532 GACCCGACTCGTT
1 GACCCGACCCGTT
2956545 GACC
1 GACC
2956549 GTTGACCGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2962442 original size:24 final size:24
Alignment explanation
Indices: 2962410--2962465 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
2962400 ATGTTTCTTC
2962410 ATCACCTCTATAATAATAACATAT
1 ATCACCTCTATAATAATAACATAT
2962434 ATCACCTCTATAATAATAACATAT
1 ATCACCTCTATAATAATAACATAT
2962458 ATCACCTC
1 ATCACCTC
2962466 AATTTAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (24 bp):
ATCACCTCTATAATAATAACATAT
Found at i:2962620 original size:22 final size:22
Alignment explanation
Indices: 2962573--2962620 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2962563 GAAATATTAA
*
2962573 TTAAATTTATAAAATTTTAGAG
1 TTAAATTAATAAAATTTTAGAG
*
2962595 -TAAATTAAATAATATTTTAG-G
1 TTAAATT-AATAAAATTTTAGAG
2962616 TTAAA
1 TTAAA
2962621 ATGAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (22 bp):
TTAAATTAATAAAATTTTAGAG
Found at i:2966098 original size:2 final size:2
Alignment explanation
Indices: 2966091--2966120 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2966081 ATTGAGATAA
2966091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2966121 TGTTGTACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2969186 original size:18 final size:17
Alignment explanation
Indices: 2969156--2969189 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2969146 CTTTCTAACT
*
2969156 GTGCTATATCTCGTGTG
1 GTGCTATACCTCGTGTG
2969173 GTGCATATACCTCGTGT
1 GTGC-TATACCTCGTGT
2969190 TTTCAAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (17 bp):
GTGCTATACCTCGTGTG
Found at i:2979605 original size:18 final size:18
Alignment explanation
Indices: 2979570--2979628 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
2979560 ACTTCGCATG
2979570 AAGAAAGAAAAA--AAATA
1 AAGAAA-AAAAATGAAATA
2979587 AA-AAATAAAAATGAAATA
1 AAGAAA-AAAAATGAAATA
*
2979605 AAGAAAGAAAATGAAATA
1 AAGAAAAAAAATGAAATA
2979623 AAGAAA
1 AAGAAA
2979629 GGAAAAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
16 8 0.22
17 2 0.05
18 24 0.65
19 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (18 bp):
AAGAAAAAAAATGAAATA
Found at i:2979629 original size:18 final size:19
Alignment explanation
Indices: 2979594--2979639 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
2979584 ATAAAAAATA
2979594 AAAATGAAATAAAGAAA-G
1 AAAATGAAATAAAGAAAGG
2979612 AAAATGAAATAAAGAAAGG
1 AAAATGAAATAAAGAAAGG
*
2979631 AAAAAGAAA
1 AAAATGAAA
2979640 GATAGATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (19 bp):
AAAATGAAATAAAGAAAGG
Found at i:2979666 original size:8 final size:8
Alignment explanation
Indices: 2979649--2979683 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
2979639 AGATAGATAG
*
2979649 AAAGAAAA
1 AAAGAGAA
2979657 AAAGAGAA
1 AAAGAGAA
2979665 AAAGAGAA
1 AAAGAGAA
2979673 AAAGAGAA
1 AAAGAGAA
2979681 AAA
1 AAA
2979684 AAAAAGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAGAGAA
Found at i:2979668 original size:16 final size:16
Alignment explanation
Indices: 2979626--2979688 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 16
2979616 TGAAATAAAG
*
2979626 AAAG-GAAAAAGAAAG
1 AAAGAGAAAAAGAAAA
* * *
2979641 ATAGATAGAAAGAAAA
1 AAAGAGAAAAAGAAAA
*
2979657 AAAGAGAAAAAGAGAA
1 AAAGAGAAAAAGAAAA
2979673 AAAGAGAAAAA-AAAA
1 AAAGAGAAAAAGAAAA
2979688 A
1 A
2979689 GAATAAACAA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
15 7 0.18
16 31 0.82
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AAAGAGAAAAAGAAAA
Found at i:2979755 original size:45 final size:45
Alignment explanation
Indices: 2979701--2979787 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
2979691 ATAAACAAAA
* *
2979701 GAGGTTCAAGATGAAAACCCGTAAAGGGTGTCTTGA-AATTGAAT
1 GAGGTTCAAGATGAAAACCCGTAAAGGGCGACTTGAGAATTGAAT
*
2979745 GAGGTCTCAAGTTGAAAACCCGTAAAGGGCGACTTGAGAATTG
1 GAGGT-TCAAGATGAAAACCCGTAAAGGGCGACTTGAGAATTG
2979788 TGTAAATTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 5 0.13
45 28 0.74
46 5 0.13
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (45 bp):
GAGGTTCAAGATGAAAACCCGTAAAGGGCGACTTGAGAATTGAAT
Found at i:2981161 original size:134 final size:133
Alignment explanation
Indices: 2980917--2981487 Score: 648
Period size: 134 Copynumber: 4.3 Consensus size: 133
2980907 ATCGAACTCA
** ** *
2980917 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATATTTCCAGATATGATTTTCGCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTC-CTCAAGAA
* * * * * * * * *
2980982 GAAGCGGAACAAATCACTCTCTTTCAAGATTTTATCTTTCATGAGTAACAGTGGAATAAATATGC
65 AAAGCGAAACAAATCACTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGC
*
2981047 CTCA
130 CTCG
* * * *
2981051 ATTTAATATTCCCTG-AGTAACAGTGGAATGAATCAACGCCCCCAGATCTGATTTTCCTTTAAGA
1 ATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCC-TCAAGA
* * *
2981115 AAAAGTGAAACAAATCCCTCTCTTTCAAAATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG
64 AAAAGCGAAACAAATCACTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG
2981180 CCTCG
129 CCTCG
* * * * ** * *
2981185 ATTCAATCTTCCATGAAGAACAATGAAATGAATCAAAGTCCTTAGATCTGATTTTTCCACACGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGA-TTTTCCTCAAGAA
* * *
2981250 GAAGCGAAATAGATCACTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCT-GAACAAGTCTG
65 AAAGCGAAACAAATCACTCTCTTTCAAGATTTGATATTCCCTGAGTAACAG-TGGAACAAGTCTG
2981314 CCTCG
129 CCTCG
* * * *
2981319 ATTCAATCTTCCCTG-AGTAACAGTGGAACGAATCAA-GTCCCCAAATCTAATTTCCCTCAAGAA
1 ATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCTCAAGAA
* * * * *
2981382 AAAACGAAACATATC-CATCTCTTTCAAGATTTGATATTCCCTTAGTGACAGTGGAACAAGTCTA
65 AAAGCGAAACAAATCAC-TCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG
2981446 CCTCG
129 CCTCG
* *
2981451 ATTCAATCTTCCTTGAAGAACAGTGGAATGAGTCAAC
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAAC
2981488 TTTTCTTGAT
Statistics
Matches: 366, Mismatches: 61, Indels: 21
0.82 0.14 0.05
Matches are distributed among these distances:
131 2 0.01
132 98 0.27
133 17 0.05
134 240 0.66
135 9 0.02
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (133 bp):
ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCTCAAGAAA
AAGCGAAACAAATCACTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCC
TCG
Found at i:2981680 original size:3 final size:3
Alignment explanation
Indices: 2981672--2981731 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
2981662 CTTATCTTTA
* *
2981672 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAA TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2981719 TTT TAT TAT TAT T
1 TAT TAT TAT TAT T
2981732 TTCATATTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2990328 original size:2 final size:2
Alignment explanation
Indices: 2990321--2990352 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2990311 TGTATTCTAA
2990321 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2990353 AGGCATAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2992507 original size:38 final size:38
Alignment explanation
Indices: 2992450--2992549 Score: 155
Period size: 38 Copynumber: 2.6 Consensus size: 38
2992440 TGGCATTTCA
* *
2992450 TGTTGCATTGCATGTTAAATAGTTAAATAATTAGTGTG
1 TGTTACATTGCATGTTAAATAGTTAAATAACTAGTGTG
* *
2992488 TGTTATATTGCATGTTAAATAATTAAATAACTAGTGTG
1 TGTTACATTGCATGTTAAATAGTTAAATAACTAGTGTG
*
2992526 TGTTACATTGCATGTTATATAGTT
1 TGTTACATTGCATGTTAAATAGTT
2992550 TGTATATATT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (38 bp):
TGTTACATTGCATGTTAAATAGTTAAATAACTAGTGTG
Found at i:2992681 original size:16 final size:17
Alignment explanation
Indices: 2992650--2992682 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2992640 CAAAAAAAAA
*
2992650 ATAGGTTCATTTACATT
1 ATAGGTCCATTTACATT
2992667 ATAGGTCCA-TTACATT
1 ATAGGTCCATTTACATT
2992683 TGTTTTACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
ATAGGTCCATTTACATT
Found at i:2993338 original size:80 final size:80
Alignment explanation
Indices: 2993189--2993348 Score: 250
Period size: 82 Copynumber: 2.0 Consensus size: 80
2993179 GTCCAAAAAT
** *
2993189 GTATTAATTTAGGCTTTAAATTTTATTTATTTCAATTTGATCCTAAGAATTTTATAATTTAATAT
1 GTATTAATTTAGGAATTAAATTTTATTTATTTCAATTTGATCCTAAGAATTTTACAATTTAATAT
2993254 ATATA-ACTATATAAC
66 ATATATA-TATATAAC
*
2993269 GTATTAATTTAGGAATTAAATTTTTATTTTATTTCAATTTGATCCTACGAATTTTACAATTTAAT
1 GTATTAATTTAGGAATTAAA-TTTTA-TTTATTTCAATTTGATCCTAAGAATTTTACAATTTAAT
2993334 ATATATATATATATA
64 ATATATATATATATA
2993349 TATATATATA
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
80 18 0.25
81 5 0.07
82 49 0.67
83 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (80 bp):
GTATTAATTTAGGAATTAAATTTTATTTATTTCAATTTGATCCTAAGAATTTTACAATTTAATAT
ATATATATATATAAC
Found at i:2993339 original size:2 final size:2
Alignment explanation
Indices: 2993332--2993358 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2993322 TTACAATTTA
2993332 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2993359 ATGTATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2993365 original size:92 final size:93
Alignment explanation
Indices: 2993250--2993427 Score: 288
Period size: 93 Copynumber: 1.9 Consensus size: 93
2993240 TTATAATTTA
2993250 ATATATATAACTATATAACGTATTAATTTAGGAATTAAATTTTT-ATTTTATTTCAATTTGATCC
1 ATATATATAACTATATAACGTATTAATTTAGGAATTAAATTTTTAATTTTATTTCAATTTGATCC
2993314 TACGAATTTTACAATTTAATATATATAT
66 TACGAATTTTACAATTTAATATATATAT
* ** *
2993342 ATATATATATA-TATATAATGTATTAATTTAGGCTTTAAATTTTTAATTTTATTTCAATTTGTTC
1 ATATATATA-ACTATATAACGTATTAATTTAGGAATTAAATTTTTAATTTTATTTCAATTTGATC
*
2993406 CTACGAATTTTATAATTTAATA
65 CTACGAATTTTACAATTTAATA
2993428 AATGTAACTC
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
92 39 0.49
93 40 0.51
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.50
Consensus pattern (93 bp):
ATATATATAACTATATAACGTATTAATTTAGGAATTAAATTTTTAATTTTATTTCAATTTGATCC
TACGAATTTTACAATTTAATATATATAT
Found at i:2993500 original size:22 final size:21
Alignment explanation
Indices: 2993472--2993601 Score: 110
Period size: 22 Copynumber: 6.1 Consensus size: 21
2993462 GTATTGTATA
2993472 TTTATATTATATAGTTTAATAC
1 TTTATATTATATA-TTTAATAC
2993494 TTTATA-TATATACTTT-ATA-
1 TTTATATTATATA-TTTAATAC
* *
2993513 TTTAATATT-TTTATTTCTATAC
1 TTT-ATATTATATATTT-AATAC
2993535 TTTAATACTT-TATATTTAATAC
1 TTT-ATA-TTATATATTTAATAC
2993557 -TTATATTATATAGTTTAATAC
1 TTTATATTATATA-TTTAATAC
* *
2993578 TTTATAGTGTATACTTTAATAC
1 TTTATATTATATA-TTTAATAC
2993600 TT
1 TT
2993602 ATAACTTATC
Statistics
Matches: 92, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
19 8 0.09
20 16 0.17
21 23 0.25
22 37 0.40
23 8 0.09
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTATATTATATATTTAATAC
Found at i:2993511 original size:35 final size:35
Alignment explanation
Indices: 2993438--2993514 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
2993428 AATGTAACTC
*
2993438 TATATGTATATACTTTAATACTCTGTATTGTATATT
1 TATAT-TATATACTTTAATACTCTGTATTATATATT
*
2993474 TATATTATATAGTTTAATACT-T-TATATATATACTT
1 TATATTATATACTTTAATACTCTGTAT-TATATA-TT
2993509 TATATT
1 TATATT
2993515 TAATATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 3 0.08
34 6 0.16
35 23 0.62
36 5 0.14
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (35 bp):
TATATTATATACTTTAATACTCTGTATTATATATT
Found at i:2993581 original size:35 final size:36
Alignment explanation
Indices: 2993503--2993583 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 36
2993493 CTTTATATAT
* * *
2993503 ATACTTTATATTTAATATTTTTATTTCTATACTTTA
1 ATACTTTATATTTAATACTTATATTTATATACTTTA
*
2993539 ATACTTTATATTTAATACTTATA-TTATATAGTTTA
1 ATACTTTATATTTAATACTTATATTTATATACTTTA
2993574 ATACTTTATA
1 ATACTTTATA
2993584 GTGTATACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 20 0.49
36 21 0.51
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (36 bp):
ATACTTTATATTTAATACTTATATTTATATACTTTA
Found at i:2993653 original size:8 final size:8
Alignment explanation
Indices: 2993640--2994067 Score: 105
Period size: 8 Copynumber: 57.1 Consensus size: 8
2993630 ATAGTTTGTA
2993640 TATATACT
1 TATATACT
2993648 TATATACT
1 TATATACT
2993656 T-TATA-T
1 TATATACT
2993662 TATATAC-
1 TATATACT
2993669 TA-ATACT
1 TATATACT
*
2993676 T-TATAGT
1 TATATACT
2993683 T-TATA-T
1 TATATACT
*
2993689 AAT-TA-T
1 TATATACT
2993695 ATATATACT
1 -TATATACT
*
2993704 TATAT-TT
1 TATATACT
*
2993711 TATAGT-TT
1 TATA-TACT
2993719 ATATATAC-
1 -TATATACT
2993727 T-TATACTT
1 TATATAC-T
***
2993735 TATATGGA
1 TATATACT
2993743 TATATACT
1 TATATACT
* *
2993751 TTTATAGT
1 TATATACT
2993759 ATATATACT
1 -TATATACT
2993768 TATATACT
1 TATATACT
2993776 T-TATA-T
1 TATATACT
2993782 TATATACT
1 TATATACT
2993790 TATATACT
1 TATATACT
2993798 T-TAGT-CT
1 TATA-TACT
*
2993805 T-TATA-A
1 TATATACT
2993811 T-TATACTT
1 TATATAC-T
2993819 TATATA-T
1 TATATACT
*
2993826 ACATATA-T
1 -TATATACT
*
2993834 AATATAC-
1 TATATACT
2993841 T-TATACT
1 TATATACT
2993848 TCATATTA-T
1 T-ATA-TACT
2993857 TATATA-T
1 TATATACT
2993864 GTATATATTCT
1 -TATATA--CT
2993875 T-TATAC-
1 TATATACT
*
2993881 TA-AAACT
1 TATATACT
2993888 T-TATA--
1 TATATACT
2993893 TATATA--
1 TATATACT
2993899 TATATATCT
1 TATATA-CT
*
2993908 ATATATTCT
1 -TATATACT
2993917 T-TATAC-
1 TATATACT
*
2993923 TA-AAACT
1 TATATACT
2993930 T-TATA-T
1 TATATACT
2993936 ATATATA-T
1 -TATATACT
2993944 ATATATA-T
1 -TATATACT
2993952 ATATATA-T
1 -TATATACT
2993960 CTAT-TA--
1 -TATATACT
2993966 TATATA-T
1 TATATACT
2993973 ATATATA-T
1 -TATATACT
*
2993981 ATATATATT
1 -TATATACT
*
2993990 TATA-ATT
1 TATATACT
*
2993997 TATAT-GT
1 TATATACT
2994004 ATATATACT
1 -TATATACT
*
2994013 TTTATAC-
1 TATATACT
*
2994020 TATATAGTT
1 TATATA-CT
2994029 TATATACT
1 TATATACT
2994037 T-TATA-T
1 TATATACT
2994043 TATATACT
1 TATATACT
2994051 TATATACT
1 TATATACT
2994059 TATATACT
1 TATATACT
2994067 T
1 T
2994068 TAGTCTTTAT
Statistics
Matches: 331, Mismatches: 33, Indels: 112
0.70 0.07 0.24
Matches are distributed among these distances:
5 4 0.01
6 51 0.15
7 89 0.27
8 142 0.43
9 36 0.11
10 8 0.02
11 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (8 bp):
TATATACT
Found at i:2993703 original size:34 final size:36
Alignment explanation
Indices: 2993647--2993772 Score: 116
Period size: 34 Copynumber: 3.4 Consensus size: 36
2993637 GTATATATAC
*
2993647 TTATATACTTTATATTATATACTAATACTTTATAGT
1 TTATATACATTATATTATATACTAATACTTTATAGT
* *
2993683 TTATATA-ATTATA-TATATACTTATATTTTATAGT
1 TTATATACATTATATTATATACTAATACTTTATAGT
*
2993717 TTATATATACTTATACTTTATATGGA-TATATACTTTTATAGT
1 TTATATACA-TTATA--TTATAT--ACTA-ATAC-TTTATAGT
*
2993759 ATATATAC-TTATAT
1 TTATATACATTATAT
2993773 ACTTTATATT
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
34 26 0.35
35 6 0.08
36 12 0.16
38 1 0.01
39 5 0.07
40 6 0.08
41 4 0.05
42 14 0.19
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (36 bp):
TTATATACATTATATTATATACTAATACTTTATAGT
Found at i:2993748 original size:17 final size:18
Alignment explanation
Indices: 2993728--2993773 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
2993718 TATATATACT
2993728 TATACTTTATAT-GGATA
1 TATACTTTATATAGGATA
*
2993745 TATACTTT-TATAGTATA
1 TATACTTTATATAGGATA
2993762 TATAC-TTATATA
1 TATACTTTATATA
2993774 CTTTATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (18 bp):
TATACTTTATATAGGATA
Found at i:2993763 original size:25 final size:24
Alignment explanation
Indices: 2993751--2994446 Score: 101
Period size: 22 Copynumber: 31.2 Consensus size: 24
2993741 GATATATACT
* *
2993751 TTTATAGTATATATACTTATATAC
1 TTTATACTATATATACATATATAC
*
2993775 TTTATA-T-TATATACTTATATAC
1 TTTATACTATATATACATATATAC
2993797 TTTAGT-CT-T-TATA-AT-TATAC
1 TTTA-TACTATATATACATATATAC
* *
2993817 TTTATA-TATACATATATAATATAC
1 TTTATACTATATATACAT-ATATAC
*
2993841 -TTATACT-TCATATTA-TTATATA-
1 TTTATACTAT-ATA-TACATATATAC
* * * *
2993863 TGTATATATTCTTTATAC-TA-AAAC
1 T-T-TATACTATATATACATATATAC
2993887 TTTATA-TATATAT--ATATAT-C
1 TTTATACTATATATACATATATAC
* * * * *
2993907 TATATATTCTTTATAC-TA-AAAC
1 TTTATACTATATATACATATATAC
*
2993929 TTTATA-TATATATATATATATA-
1 TTTATACTATATATACATATATAC
* * *
2993951 TATATA-TATCTAT-TATATATA-
1 TTTATACTATATATACATATATAC
* * * *
2993972 TATATA-TATATATATATTTATAA
1 TTTATACTATATATACATATATAC
* * *
2993995 TTTATATGTATATATACTTTTATAC
1 TTTATA-CTATATATACATATATAC
* * * *
2994020 TATATAGTTTATATAC-TTTATA-
1 TTTATACTATATATACATATATAC
*
2994042 TTATATACT-TATATACTTATATAC
1 TT-TATACTATATATACATATATAC
2994066 TTTAGT-CT-T-TATA-AT-TATA-
1 TTTA-TACTATATATACATATATAC
*
2994085 -TTATA-TATATATATATAATATAC
1 TTTATACTATATATACAT-ATATAC
* ** *
2994108 -TTATACTTTATATGTATATATAG
1 TTTATACTATATATACATATATAC
* * * ** *
2994131 TTTATACGAAAAACTTTATACATAC
1 TTTATACTATATA-TACATATATAC
** *
2994156 ATACATACATATATATAC-TTTATA-
1 -TTTATAC-TATATATACATATATAC
* *
2994180 GTT-TA-TATATATACTTATATAC
1 TTTATACTATATATACATATATAC
* *
2994202 -TT-TA-TAT-TATGCTTATATAC
1 TTTATACTATATATACATATATAC
* *
2994222 TTT-T--T-TTTATAA-T-TATAC
1 TTTATACTATATATACATATATAC
*
2994240 TTTATA-TATATATATATAATATAC
1 TTTATACTATATATACAT-ATATAC
* * * *
2994264 -TTATACT-TTTTTATATATGTA-
1 TTTATACTATATATACATATATAC
* * * *
2994285 TATATACTTTAAATACTTATATAC
1 TTTATACTATATATACATATATAC
*
2994309 TTTATTCT-T-TATA-AT-TATAC
1 TTTATACTATATATACATATATAC
*
2994329 TTTATA-TATATATATA-ATATAC
1 TTTATACTATATATACATATATAC
* *
2994351 -TTATACTTTATATTA-TTATATAC
1 TTTATACTATATA-TACATATATAC
* * * * *
2994374 -GTATA-TATGCTTTATATGTATA-
1 TTTATACTAT-ATATACATATATAC
* * *
2994396 TATATA-TATATATA-ATTTATAG
1 TTTATACTATATATACATATATAC
*
2994418 TTTATA-TATATATACTTATATAC
1 TTTATACTATATATACATATATAC
2994441 TTTATA
1 TTTATA
2994447 TTTAAACTAT
Statistics
Matches: 509, Mismatches: 92, Indels: 143
0.68 0.12 0.19
Matches are distributed among these distances:
17 2 0.00
18 12 0.02
19 10 0.02
20 61 0.12
21 79 0.16
22 120 0.24
23 113 0.22
24 62 0.12
25 40 0.08
26 7 0.01
27 3 0.01
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTATACTATATATACATATATAC
Found at i:2993916 original size:42 final size:42
Alignment explanation
Indices: 2993836--2993955 Score: 181
Period size: 42 Copynumber: 2.9 Consensus size: 42
2993826 ACATATATAA
* * * *
2993836 TATACTTATACTTCATAT-TAT-TATATATGTATATATTCTT
1 TATACTAAAACTTTATATATATATATATATATATATATTCTT
*
2993876 TATACTAAAACTTTATATATATATATATATCTATATATTCTT
1 TATACTAAAACTTTATATATATATATATATATATATATTCTT
2993918 TATACTAAAACTTTATATATATATATATATATATATAT
1 TATACTAAAACTTTATATATATATATATATATATATAT
2993956 ATATCTATTA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 15 0.21
41 3 0.04
42 55 0.75
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (42 bp):
TATACTAAAACTTTATATATATATATATATATATATATTCTT
Found at i:2994356 original size:65 final size:64
Alignment explanation
Indices: 2994287--2994445 Score: 157
Period size: 65 Copynumber: 2.4 Consensus size: 64
2994277 TATATGTATA
*
2994287 TATACTTTAAATACTTATATACTTTATTCTTTATAAT-TATACTTTATATATATATATAA-TATA
1 TATACTTTAAATACTTATATACTTTATGCTTTAT-ATGTATA---TATATATATATATAATTATA
2994350 -CT
62 GCT
*
2994352 TATACTTTATATTA-TTATATACGTATATATGCTTTATATGTATATATATATATATATAATTTAT
1 TATACTTTA-AATACTTATATAC-T-T-TATGCTTTATATGTATATATATATATATATAA-TTAT
*
2994416 AGTT
61 AGCT
* *
2994420 TATA-TATATATACTTATATACTTTAT
1 TATACTTTAAATACTTATATACTTTAT
2994446 ATTTAAACTA
Statistics
Matches: 79, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
64 3 0.04
65 33 0.42
66 7 0.09
67 18 0.23
68 18 0.23
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (64 bp):
TATACTTTAAATACTTATATACTTTATGCTTTATATGTATATATATATATATATAATTATAGCT
Found at i:2994486 original size:11 final size:11
Alignment explanation
Indices: 2994472--2994553 Score: 64
Period size: 11 Copynumber: 7.8 Consensus size: 11
2994462 CTATACATAG
2994472 TATATATAATT
1 TATATATAATT
*
2994483 TATA-ATTATT
1 TATATATAATT
* *
2994493 CATA-AT-ATA
1 TATATATAATT
* *
2994502 TAAATATAAGT
1 TATATATAATT
**
2994513 TGCATAT-ATT
1 TATATATAATT
*
2994523 TAAATATAATT
1 TATATATAATT
2994534 TATATATAATT
1 TATATATAATT
2994545 TATATATAA
1 TATATATAA
2994554 ACTATATAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
9 4 0.07
10 19 0.35
11 32 0.58
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (11 bp):
TATATATAATT
Found at i:2994550 original size:243 final size:238
Alignment explanation
Indices: 2993984--2994535 Score: 518
Period size: 243 Copynumber: 2.3 Consensus size: 238
2993974 TATATATATA
* * ** * * * *
2993984 TATATTTATAATTTATATGTATATATACTTTTATAC-TATATAGTT-TATATACTTTATATTATA
1 TATAATTATAATTTATATATATATATA-TAATATACTTATACAGTTGCATATA-TGTA-AATATA
* *
2994047 TACTTATATACTTATATACTTTAGTCTTTATAATTATATTATATATATATATATAATATACTTAT
63 -ATTTAAATACTTATATACTTTAGTCTTTATAATTATATTATATATATATATATAATATACTTAT
* *
2994112 ACTTTATATGTATATATAGTTTATACGAAAAACTTTATACATACATACATACATATATATACTTT
127 ACTTTATATGTATATATAGTATATACG----ACTTTATA-ATACATACATACATATATATAATTT
** * ** **
2994177 ATAGTTTATATATATACTTATATACTTTATATTATGCTTATATACTTTTTTT
187 ATAGTTTATATATATACTTATATACTTTATATTAAACTTATAAACTTCATAG
* ** ** * *
2994229 TATAATTATACTTTATATATATATATATAATATACTTATACTTTTTTATATATGTATATATACTT
1 TATAATTATAATTTATATATATATATATAATATACTTATACAGTTGCATATATGTAAATATAATT
*
2994294 TAAATACTTATATACTTTATTCTTTATAATTATACTT-TATATATATATATAATATACTTATACT
66 TAAATACTTATATACTTTAGTCTTTATAATTATA-TTATATATATATATATAATATACTTATACT
* ** * *
2994358 TTATAT-TATTATATACGTATATATG-CTTTAT-ATGTATATATATATATATATAATTTATAGTT
130 TTATATGTA-TATATA-GTATATACGACTTTATAATACATACATACATATATATAATTTATAG-T
2994420 TATATATATATACTTATATACTTTATATTTAAACTATATAAACTATACATAG
192 T-TATATATATACTTATATACTTTATA-TTAAACT-TATAAACT-T-CATAG
*
2994472 TAT-A-TATAATTTATA-AT-TAT-TCATAATATA-TAAATATA-AGTTGCATATATTTAAATAT
1 TATAATTATAATTTATATATATATAT-ATAATATACT---TATACAGTTGCATATATGTAAATAT
2994530 AATTTA
62 AATTTA
2994536 TATATAATTT
Statistics
Matches: 255, Mismatches: 37, Indels: 35
0.78 0.11 0.11
Matches are distributed among these distances:
237 24 0.09
238 4 0.02
239 42 0.16
240 26 0.10
241 21 0.08
242 4 0.02
243 76 0.30
244 19 0.07
245 33 0.13
246 6 0.02
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (238 bp):
TATAATTATAATTTATATATATATATATAATATACTTATACAGTTGCATATATGTAAATATAATT
TAAATACTTATATACTTTAGTCTTTATAATTATATTATATATATATATATAATATACTTATACTT
TATATGTATATATAGTATATACGACTTTATAATACATACATACATATATATAATTTATAGTTTAT
ATATATACTTATATACTTTATATTAAACTTATAAACTTCATAG
Found at i:2994564 original size:31 final size:30
Alignment explanation
Indices: 2994420--2994677 Score: 118
Period size: 29 Copynumber: 8.3 Consensus size: 30
2994410 ATTTATAGTT
* * *
2994420 TATATATATATACTTATATACTTTATATTTAA
1 TATATATATAAAC-TATATA-TATATATATAA
* *
2994452 -A-CTATATAAACTATACATAGTATATATAA
1 TATATATATAAACTATATATA-TATATATAA
* * * *
2994481 TTTATA-AT-TATTCATAATATATAAATATAA
1 TATATATATAAACT-AT-ATATATATATATAA
* *
2994511 GTTGCATATATTTAAA-TATA-ATTTATATATAA
1 --T--ATATATATAAACTATATATATATATATAA
* *
2994543 TTTATATATAAACTATATA-ATTTATACTAAA
1 TATATATATAAACTATATATATATATA-T-AA
* * * *
2994574 CTATATAGTTTATATTATATATATATACA-AA
1 -TATATA-TATAAACTATATATATATATATAA
* *
2994605 TACAAATATAAACTATATATATATATATATA
1 TATATATATAAACTATATATATATATATA-A
* *
2994636 TATATACAATATAACTATATATATATATATAG
1 TATATA-TATA-AACTATATATATATATATAA
*
2994668 TTTATATATA
1 TATATATATA
2994678 GTTTATACAT
Statistics
Matches: 166, Mismatches: 38, Indels: 45
0.67 0.15 0.18
Matches are distributed among these distances:
28 10 0.06
29 41 0.25
30 28 0.17
31 19 0.11
32 24 0.14
33 30 0.18
34 11 0.07
35 2 0.01
36 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.45
Consensus pattern (30 bp):
TATATATATAAACTATATATATATATATAA
Found at i:2994638 original size:25 final size:25
Alignment explanation
Indices: 2994610--2994715 Score: 83
Period size: 25 Copynumber: 4.2 Consensus size: 25
2994600 ACAAATACAA
2994610 ATATAAACTATATATATATATATAT
1 ATATAAACTATATATATATATATAT
* *
2994635 ATATATACAATATA-ACTATATATAT
1 ATATAAACTATATATA-TATATATAT
* * * * *
2994660 ATATATAGTTTATATATAGTTTATAC
1 ATATAAACTATATATATA-TATATAT
*
2994686 ATATATAACTTTATAT-TATATACT-T
1 ATATA-AACTATATATATATATA-TAT
2994711 ATATA
1 ATATA
2994716 CTTTACTCTT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
24 1 0.02
25 42 0.65
26 14 0.22
27 8 0.12
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (25 bp):
ATATAAACTATATATATATATATAT
Found at i:2994640 original size:27 final size:27
Alignment explanation
Indices: 2994590--2994666 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
2994580 AGTTTATATT
* * * *
2994590 ATATATATATACAAATACAAATATA-A
1 ATATATATATATATATATATATATACA
2994616 ACTATATATATATATATATATATATACA
1 A-TATATATATATATATATATATATACA
2994644 ATATA-ACTATATATATATATATA
1 ATATATA-TATATATATATATATA
2994667 GTTTATATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
26 2 0.05
27 40 0.91
28 2 0.05
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (27 bp):
ATATATATATATATATATATATATACA
Found at i:2994674 original size:27 final size:27
Alignment explanation
Indices: 2993638--2994701 Score: 149
Period size: 28 Copynumber: 40.2 Consensus size: 27
2993628 TTATAGTTTG
2993638 TATATATACT-TATATACT-T-TATATT
1 TATATATACTATATATA-TATATATATT
* *
2993663 ATATACTAATACTTTATAGTTTATATA-ATT
1 -TATA-T-ATACTATATA-TATATATATATT
2993693 ATATATATACT-TATAT-T-T-TATAGTT
1 -TATATATACTATATATATATATATA-TT
*
2993718 TATATATACTTATACTTTATATGGATATATACT
1 TATATATAC-TATA---TATAT--ATATATATT
*
2993751 T-T-TATAGTATATATACT-TATATACTT
1 TATATATACTATATATA-TATATATA-TT
* *
2993777 TATAT-TA-TATACTTATATACTTTAGTCTT
1 TATATATACTATA--TATATA-TATA-TATT
* * *
2993806 TATAATTATACTTTATATATACATATATAA
1 TAT-A-TATACTATATATATATATATAT-T
*
2993836 TATACTTATACT-TCATAT-TATTATATATG
1 TATA--TATACTAT-ATATATA-TATATATT
*
2993865 TATATATTCT-T-TATACTA-A-A-ACTT
1 TATATATACTATATATA-TATATATA-TT
*
2993889 TATATATA-TATATATATCTATATATT
1 TATATATACTATATATATATATATATT
* *
2993915 CT-T-TATACTA-A-A-ACTTTATATATA
1 -TATATATACTATATATA-TATATATATT
*
2993939 TATATATA-TATATATATATATCTA-T
1 TATATATACTATATATATATATATATT
2993964 TATATATA-TATATATATATATATATT
1 TATATATACTATATATATATATATATT
* *
2993990 TATA-AT--T-TATATGTATATATACT
1 TATATATACTATATATATATATATATT
*
2994013 T-T-TATACTATATAGTTTATATACT-TT
1 TATATATACTATATA-TATATATA-TATT
2994039 ATATTATATACT-TATATACT-TATATACTT
1 -TA-TATATACTATATATA-TATATATA-TT
* * *
2994068 TAGTCTTTA-TA-AT-TATATTATATATA
1 TA-TATATACTATATATATA-TATATATT
* * *
2994094 TATATATAATATACT-TATACTTTATATG
1 TATATATACTATA-TATATA-TATATATT
* * * * * * *
2994122 TATATATAGTTTATACGAAAAACTTTATA
1 TATATATACTATATA-TATATA-TATATT
* * * *
2994151 CATACATAC-ATACATATATATA-CTT
1 TATATATACTATATATATATATATATT
*
2994176 TATAGTTTA-TATATATACT-TATATACTT
1 TATA-TATACTATATATA-TATATATA-TT
* *
2994204 TATATTATGCT-TATATACT-T-T-TTTT
1 TATA-TATACTATATATA-TATATATATT
*
2994229 TATAATTATACT-T-TATATATATATATA
1 TAT-A-TATACTATATATATATATATATT
* * *
2994256 TA-ATATACT-TATACTTTTTTATATATG
1 TATATATACTATATA--TATATATATATT
* * *
2994283 TATATATACTTTAAATACT-TATATACT
1 TATATATACTATATATA-TATATATATT
2994310 T-TAT-T-CT-T-TATA-AT-TATACTT
1 TATATATACTATATATATATATATA-TT
2994331 TATATATA-TATATA-ATATACTTATACTT
1 TATATATACTATATATATATA--TATA-TT
* ** *
2994359 TATAT-TATTATATACGTATATATGCTT
1 TATATATACTATATATATATATAT-ATT
*
2994386 TATATGTA-TATATATATATATATAATT
1 TATATATACTATATATATATATAT-ATT
*
2994413 TATAGTTTA-TATATATATACTTATATACTT
1 TATA-TATACTATATATATA--TATATA-TT
* * * *
2994443 TATATTTAAACTATATAAACTATACATA-G
1 TATA--TATACTATATATA-TATATATATT
2994472 TATATATA--AT-T-TATA-AT-TATT
1 TATATATACTATATATATATATATATT
* *
2994493 CATA-ATA-TATAAATATAAGTTGCATATATT
1 TATATATACTATATATAT-A--T--ATATATT
*
2994523 TA-A-ATA-TA-AT-T-TATATATAAT
1 TATATATACTATATATATATATATATT
*
2994544 T-TATATA-TA-A-A-CTATATA-ATT
1 TATATATACTATATATATATATATATT
* * *
2994565 TATACTAAACTATATAGTTTATAT-TATA
1 TATA-TATACTATATA-TATATATATATT
* * * **
2994593 TATATATAC-AAATACAAATATA-AAC
1 TATATATACTATATATATATATATATT
*
2994618 TATATATA-TATATATATATATATA-C
1 TATATATACTATATATATATATATATT
*
2994643 AATATA-ACTATATATATATATATAGTT
1 TATATATACTATATATATATATATA-TT
* * *
2994670 TATATATAGTTTATACATATATA-ACTT
1 TATATATACTATATATATATATATA-TT
2994697 TATAT
1 TATAT
2994702 TATATACTTA
Statistics
Matches: 776, Mismatches: 120, Indels: 283
0.66 0.10 0.24
Matches are distributed among these distances:
20 9 0.01
21 20 0.03
22 25 0.03
23 32 0.04
24 53 0.07
25 134 0.17
26 79 0.10
27 118 0.15
28 135 0.17
29 68 0.09
30 61 0.08
31 20 0.03
32 10 0.01
33 8 0.01
34 4 0.01
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (27 bp):
TATATATACTATATATATATATATATT
Found at i:2994675 original size:11 final size:11
Alignment explanation
Indices: 2994659--2994684 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2994649 ACTATATATA
2994659 TATATATAGTT
1 TATATATAGTT
2994670 TATATATAGTT
1 TATATATAGTT
2994681 TATA
1 TATA
2994685 CATATATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
TATATATAGTT
Found at i:2994705 original size:13 final size:13
Alignment explanation
Indices: 2994674--2994972 Score: 89
Period size: 13 Copynumber: 22.8 Consensus size: 13
2994664 ATAGTTTATA
*
2994674 TATAGTTTATACAT
1 TATACTTTATAC-T
*
2994688 ATATAACTTTATATT
1 -TAT-ACTTTATACT
2994703 ATATACTTATATACT
1 -TATACTT-TATACT
*
2994718 T-TACTCTTAATAAT
1 TATACT-TT-ATACT
2994732 TATACTTTATACTT
1 TATACTTTATAC-T
2994746 TATA-TTTAATACT
1 TATACTTT-ATACT
2994759 TATACTTTATA-T
1 TATACTTTATACT
*
2994771 TAT-C-ATATA--
1 TATACTTTATACT
2994780 TATACTTTATACT
1 TATACTTTATACT
* * *
2994793 AAAAGTTTATA--
1 TATACTTTATACT
*
2994804 TATA-TATATACTT
1 TATACTTTATAC-T
*
2994817 TATAGTTTATA-T
1 TATACTTTATACT
2994829 ATATACTTT-TACTT
1 -TATACTTTATAC-T
*
2994843 TATAGTTTATA-T
1 TATACTTTATACT
*
2994855 ATATA-TATATATACA
1 -TATACT-T-TATACT
*
2994870 CATAC-TTATACTT
1 TATACTTTATAC-T
*
2994883 TATA-TGTATA--
1 TATACTTTATACT
*
2994893 TATACTCTATATACA
1 TATACT-T-TATACT
* *
2994908 TAAACTTTATATT
1 TATACTTTATACT
*
2994921 ATATACTTATGTACT
1 -TATACTT-TATACT
*
2994936 T-TAGTCTTTATAAT
1 TATA--CTTTATACT
2994950 TATACTTTATA-T
1 TATACTTTATACT
*
2994962 TACACTTTATA
1 TATACTTTATA
2994973 TGTATATATA
Statistics
Matches: 216, Mismatches: 31, Indels: 77
0.67 0.10 0.24
Matches are distributed among these distances:
9 3 0.01
10 14 0.06
11 8 0.04
12 25 0.12
13 75 0.35
14 53 0.25
15 31 0.14
16 7 0.03
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (13 bp):
TATACTTTATACT
Found at i:2994706 original size:17 final size:16
Alignment explanation
Indices: 2994669--2994925 Score: 67
Period size: 15 Copynumber: 15.4 Consensus size: 16
2994659 TATATATAGT
*
2994669 TTATATATAGTTTATA
1 TTATATATACTTTATA
*
2994685 -CATATATAACTTTATA
1 TTATATAT-ACTTTATA
2994701 -T-TATATAC-TTATA
1 TTATATATACTTTATA
2994714 -TACT-T-TACTCTTAATAA
1 TTA-TATATACT-TT-AT-A
2994731 TTATACTTTATACTTTATA
1 TTATA---TATACTTTATA
2994750 TTTAATACTTATACTTTATA
1 -TT-ATA--TATACTTTATA
*
2994770 TTATCATATA-TATACT-
1 TTAT-ATATACTTTA-TA
* *
2994786 TTATACTAAAAGTTTATA
1 TTATA-T-ATACTTTATA
2994804 TATATATATACTTTATA
1 T-TATATATACTTTATA
2994821 GTTTATATATATACTTT-TA
1 ---T-TATATATACTTTATA
* *
2994840 CT-T-TATAGTTTATA
1 TTATATATACTTTATA
*
2994854 -TATATATA-TATATA
1 TTATATATACTTTATA
**
2994868 CACATACTTATACTTTATA
1 -TTATA--TATACTTTATA
*
2994887 TGTATATATACTCTATA
1 T-TATATATACTTTATA
* *
2994904 -TACATAAACTTTATA
1 TTATATATACTTTATA
2994919 TTATATA
1 TTATATA
2994926 CTTATGTACT
Statistics
Matches: 185, Mismatches: 21, Indels: 70
0.67 0.08 0.25
Matches are distributed among these distances:
13 17 0.09
14 12 0.06
15 32 0.17
16 25 0.14
17 28 0.15
18 13 0.07
19 18 0.10
20 30 0.16
21 6 0.03
22 4 0.02
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (16 bp):
TTATATATACTTTATA
Found at i:2994707 original size:2 final size:2
Alignment explanation
Indices: 2993889--2994692 Score: 177
Period size: 2 Copynumber: 401.0 Consensus size: 2
2993879 ACTAAAACTT
* * * * *
2993889 TA TA TA TA TA TA TA TA TC TA TA TA T- TC TT TA TA CTA -A AA CTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
*
2993931 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
2993972 TA TA TA TA TA TA TA TA TT TA TA -A TT TA TA TG TA TA TA TA CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
2994013 TT TA TA CTA TA TA GTT TA TA TA CTT TA TA T- TA TA TA CT- TA TA
1 TA TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* * *
2994055 TA CT- TA TA TA CTT TA GTC TT TA TA -A T- TA TA T- TA TA TA TA
1 TA -TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
2994094 TA TA TA TA -A TA TA CT- TA TA CTT TA TA TG TA TA TA TA GTT TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* * * * * * * * *
2994135 TA CGA AA AA CTT TA TA CA TA CA TA CA TA CA TA TA TA TA CTT TA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
2994178 TA GTT TA TA TA TA TA CT- TA TA TA CTT TA TA T- TA TGC T- TA TA
1 TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA T-A TA TA TA
* * * *
2994219 TA CT- TT TT TT TA TA -A T- TA TA CTT TA TA TA TA TA TA TA TA -A
1 TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * *
2994259 TA TA CT- TA TA CT- TT TT TA TA TA TG TA TA TA TA CTT TA AA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
2994300 CT- TA TA TA CTT TA T- TC TT TA TA -A T- TA TA CTT TA TA TA TA
1 -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* **
2994339 TA TA TA -A TA TA CT- TA TA CTT TA TA T- TA T- TA TA TA CG TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
2994379 TA TGC TT TA TA TG TA TA TA TA TA TA TA TA TA -A TT TA TA GTT TA
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
2994422 TA TA TA TA TA CT- TA TA TA CTT TA TA TT TA AA CTA TA TA AA CTA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA
* *
2994465 TA CA TA GTA TA TA TA -A TT TA TA -A T- TA T- TCA TA -A TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * * * * *
2994504 AA TA TA -A GT- TG CA TA TA TT TA AA TA TA -A TT TA TA TA TA -A
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
2994543 TT TA TA TA TA AA CTA TA TA -A TT TA TA CTA AA CTA TA TA GTT TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA -TA TA TA -TA TA
* * * * *
2994586 TA T- TA TA TA TA TA TA CA AA TA CA AA TA TA AA CTA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
2994628 TA TA TA TA TA TA TA CA -A TA TA -A CTA TA TA TA TA TA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA
* *
2994670 TA TA TA TA GTT TA TA CA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA
2994693 ACTTTATATT
Statistics
Matches: 580, Mismatches: 130, Indels: 184
0.65 0.15 0.21
Matches are distributed among these distances:
1 45 0.08
2 487 0.84
3 48 0.08
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2994734 original size:22 final size:23
Alignment explanation
Indices: 2994687--2994735 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
2994677 AGTTTATACA
*
2994687 TATATAACTTTATATTATATACT
1 TATATAACTTTATATTATATAAT
*
2994710 TATAT-ACTTTACTCTTA-ATAAT
1 TATATAACTTTA-TATTATATAAT
2994732 TATA
1 TATA
2994736 CTTTATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATAACTTTATATTATATAAT
Found at i:2994743 original size:7 final size:7
Alignment explanation
Indices: 2994674--2994853 Score: 83
Period size: 7 Copynumber: 25.6 Consensus size: 7
2994664 ATAGTTTATA
*
2994674 TATAGTT
1 TATACTT
*
2994681 TATACATA
1 TATAC-TT
2994689 TATAACTT
1 TAT-ACTT
2994697 TATA-TT
1 TATACTT
2994703 ATATACTT
1 -TATACTT
2994711 ATATACTT
1 -TATACTT
2994719 TACT-CTT
1 TA-TACTT
* *
2994726 AATA-AT
1 TATACTT
2994732 TATACTT
1 TATACTT
2994739 TATACTT
1 TATACTT
2994746 TATA-TT
1 TATACTT
2994752 TAATAC-T
1 T-ATACTT
2994759 TATACTT
1 TATACTT
2994766 TATA-TT
1 TATACTT
*
2994772 ATCATA-TA
1 -T-ATACTT
2994780 TATACTT
1 TATACTT
2994787 TATAC-T
1 TATACTT
* * *
2994793 AAAAGTT
1 TATACTT
*
2994800 TATATATAT
1 TATA-CT-T
2994809 ATATACTT
1 -TATACTT
*
2994817 TATAGTT
1 TATACTT
*
2994824 TATA-TA
1 TATACTT
2994830 TATACTT
1 TATACTT
2994837 T-TACTT
1 TATACTT
*
2994843 TATAGTT
1 TATACTT
2994850 TATA
1 TATA
2994854 TATATATATA
Statistics
Matches: 134, Mismatches: 20, Indels: 38
0.70 0.10 0.20
Matches are distributed among these distances:
6 33 0.25
7 68 0.51
8 25 0.19
9 4 0.03
10 4 0.03
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (7 bp):
TATACTT
Found at i:2994745 original size:27 final size:27
Alignment explanation
Indices: 2994704--2994769 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
2994694 CTTTATATTA
2994704 TATACTTATATACTTTACT-CTTAATAAT
1 TATACTT-TATACTTTA-TACTTAATAAT
* *
2994732 TATACTTTATACTTTATATTTAATACT
1 TATACTTTATACTTTATACTTAATAAT
2994759 TATACTTTATA
1 TATACTTTATA
2994770 TTATCATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 1 0.03
27 27 0.77
28 7 0.20
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (27 bp):
TATACTTTATACTTTATACTTAATAAT
Found at i:2994829 original size:26 final size:26
Alignment explanation
Indices: 2994732--2994865 Score: 118
Period size: 26 Copynumber: 5.2 Consensus size: 26
2994722 TCTTAATAAT
* *
2994732 TATACTTTATACTTTATATTTA-ATA
1 TATACTTTATAGTTTATATATATATA
*
2994757 CTTATACTTTATA-TTATCATATATATACTT
1 --TATACTTTATAGTT-T-ATATATATA-TA
* *
2994787 TATAC-TAAAAG-TT-TATATATATA
1 TATACTTTATAGTTTATATATATATA
2994810 TATACTTTATAGTTTATATATATACT-
1 TATACTTTATAGTTTATATATATA-TA
*
2994836 TTTACTTTATAGTTTATATATATATA
1 TATACTTTATAGTTTATATATATATA
2994862 TATA
1 TATA
2994866 TACACATACT
Statistics
Matches: 88, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
23 6 0.07
24 12 0.14
25 3 0.03
26 37 0.42
27 17 0.19
28 11 0.12
29 1 0.01
30 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (26 bp):
TATACTTTATAGTTTATATATATATA
Found at i:2994936 original size:22 final size:20
Alignment explanation
Indices: 2994911--2994963 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
2994901 ATATACATAA
*
2994911 ACTTTATATTATATACTTATGT
1 ACTTTATATTATATAATTA--T
*
2994933 ACTTTAGTCTT-TATAATTAT
1 ACTTTA-TATTATATAATTAT
2994953 ACTTTATATTA
1 ACTTTATATTA
2994964 CACTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.12
20 7 0.27
22 13 0.50
23 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.55
Consensus pattern (20 bp):
ACTTTATATTATATAATTAT
Found at i:2995290 original size:26 final size:27
Alignment explanation
Indices: 2995261--2995313 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
2995251 ATAAACCCTT
2995261 TATAATTATA-TTATATATATATATAA
1 TATAATTATACTTATATATATATATAA
* *
2995287 TATACTTATACTTTATATGTATATATA
1 TATAATTATAC-TTATATATATATATA
2995314 GTTTATACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
28 14 0.61
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (27 bp):
TATAATTATACTTATATATATATATAA
Found at i:2995521 original size:87 final size:87
Alignment explanation
Indices: 2995365--2995648 Score: 303
Period size: 87 Copynumber: 3.2 Consensus size: 87
2995355 TATATATATA
* * * *
2995365 TATATATATATATATATATATACTTTATAGTTTATATATATATATACTTATCTTATATATGCTTA
1 TATATATATATATATATATATACTTTATATTTTATATATGTATATA--TA-CTT-TAAATACTTA
2995430 TATACTTTATTTTTATAATTATACTT
62 TATACTTTATTTTTATAATTATACTT
*
2995456 TATATATATATATATATATATAC-TTATACTTTTTTATATGTATATATACTTTAAATACTTATAT
1 TATATATATATATATATATATACTTTATA-TTTTATATATGTATATATACTTTAAATACTTATAT
2995520 ACTTTATTCTTTATAATTATACTT
65 ACTTTATT-TTTATAATTATACTT
* * *
2995544 TATATATATA-ATA-ACT-TATACTTTATATTATTATATACGTATATATGCTTTATATGTA-TAT
1 TATATATATATATATA-TATATACTTTATATT-TTATATATGTATATATACTTTA-A-ATACT-T
* * * *
2995605 ATATA-TATATATATATAATTATAGTT
61 ATATACTTTATTTTTATAATTATACTT
2995631 TATATATATACT-TATATA
1 TATATATATA-TATATATA
2995649 CTTTATTTTA
Statistics
Matches: 168, Mismatches: 13, Indels: 26
0.81 0.06 0.13
Matches are distributed among these distances:
86 8 0.05
87 70 0.42
88 37 0.22
89 11 0.07
90 5 0.03
91 37 0.22
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (87 bp):
TATATATATATATATATATATACTTTATATTTTATATATGTATATATACTTTAAATACTTATATA
CTTTATTTTTATAATTATACTT
Found at i:2995594 original size:27 final size:29
Alignment explanation
Indices: 2995564--2995618 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2995554 ATAACTTATA
*
2995564 CTTTATAT-TAT-TATATACGTATATATG
1 CTTTATATGTATATATATACATATATATG
*
2995591 CTTTATATGTATATATATATATATATAT
1 CTTTATATGTATATATATACATATATAT
2995619 ATAATTATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
28 3 0.12
29 13 0.54
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (29 bp):
CTTTATATGTATATATATACATATATATG
Found at i:2995694 original size:11 final size:11
Alignment explanation
Indices: 2995680--2995761 Score: 64
Period size: 11 Copynumber: 7.8 Consensus size: 11
2995670 CTATACATAG
2995680 TATATATAATT
1 TATATATAATT
*
2995691 TATA-ATTATT
1 TATATATAATT
* *
2995701 CATA-AT-ATA
1 TATATATAATT
* *
2995710 TAAATATAAGT
1 TATATATAATT
**
2995721 TGCATAT-ATT
1 TATATATAATT
*
2995731 TAAATATAATT
1 TATATATAATT
2995742 TATATATAATT
1 TATATATAATT
2995753 TATATATAA
1 TATATATAA
2995762 ACTATATAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
9 4 0.07
10 19 0.35
11 32 0.58
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (11 bp):
TATATATAATT
Found at i:2995802 original size:11 final size:11
Alignment explanation
Indices: 2995786--2995909 Score: 63
Period size: 10 Copynumber: 12.2 Consensus size: 11
2995776 ACTAATAAAC
*
2995786 TATATAGTTTA
1 TATATAGTATA
2995797 TATATAGTATA
1 TATATAGTATA
2995808 TA-ATA--ATA
1 TATATAGTATA
* * * *
2995816 CAAATA-CAAA
1 TATATAGTATA
* *
2995826 TATAAACTATA
1 TATATAGTATA
2995837 TATATA-TATA
1 TATATAGTATA
2995847 TATATA-TATA
1 TATATAGTATA
*
2995857 TATACA--A-A
1 TATATAGTATA
* *
2995865 TATAAACTATA
1 TATATAGTATA
2995876 TATATA-TATA
1 TATATAGTATA
2995886 TATATAGGT-TA
1 TATATA-GTATA
*
2995897 TATATAGTTTA
1 TATATAGTATA
2995908 TA
1 TA
2995910 CATATATAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
8 10 0.11
9 4 0.04
10 40 0.43
11 37 0.40
12 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (11 bp):
TATATAGTATA
Found at i:2995862 original size:39 final size:39
Alignment explanation
Indices: 2995795--2995891 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
2995785 CTATATAGTT
2995795 TATATATAGTATATA-ATA-ATACAAATACAAATATAAAC
1 TATATATA-TATATATATATATACAAATACAAATATAAAC
* *
2995833 TATATATATATATATATATATATATATACAAATATAAAC
1 TATATATATATATATATATATACAAATACAAATATAAAC
2995872 TATATATATATATATATATA
1 TATATATATATATATATATA
2995892 GGTTATATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
37 6 0.11
38 11 0.20
39 38 0.69
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (39 bp):
TATATATATATATATATATATACAAATACAAATATAAAC
Found at i:2995902 original size:2 final size:2
Alignment explanation
Indices: 2995352--2995891 Score: 138
Period size: 2 Copynumber: 271.5 Consensus size: 2
2995342 ACATACATAC
*
2995352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT TT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
* * *
2995396 TT AT AT AT AT AT AT ACT -T AT CT -T AT AT AT GCT -T AT AT ACT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT -AT AT AT AT A-T
* * * *
2995436 TT AT TT TT AT A- AT -T AT ACT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * * *
2995477 ACT -T AT ACT -T TT TT AT AT GT AT AT AT ACT TT AA AT ACT -T AT
1 A-T AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT
* * * *
2995518 AT ACT TT AT -T CT TT AT A- AT -T AT ACT TT AT AT AT AT A- AT A-
1 AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * * *
2995557 ACT -T AT ACT TT AT AT -T AT -T AT AT AC GT AT AT AT GCT TT AT
1 A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
* *
2995597 AT GT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AGT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * * *
2995638 AT ACT -T AT AT ACT TT AT -T TT AA ACT AT AT AA ACT AT AC AT AGT
1 AT A-T AT AT AT A-T AT AT AT AT AT A-T AT AT AT A-T AT AT AT A-T
* *
2995681 AT AT AT A- AT TT AT A- AT -T AT -T CAT A- AT AT AT AA AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
** * * * *
2995718 AGT -T GC AT AT AT TT AA AT AT A- AT TT AT AT AT A- AT TT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
2995758 AT AA ACT AT AT A- AT TT AT ACT A- AT AA ACT AT AT AGT TT AT AT
1 AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT AT A-T AT AT AT
* * * * *
2995800 AT AGT AT AT A- AT A- AT AC AA AT AC AA AT AT AA ACT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
2995842 AT AT AT AT AT AT AT AT AT AC AA AT AT AA ACT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
2995885 AT AT AT A
1 AT AT AT A
2995892 GGTTATATAT
Statistics
Matches: 392, Mismatches: 83, Indels: 126
0.65 0.14 0.21
Matches are distributed among these distances:
1 33 0.08
2 328 0.84
3 31 0.08
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2995972 original size:9 final size:9
Alignment explanation
Indices: 2995958--2996000 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 9
2995948 TCTTAATAAT
2995958 TATACTTTA
1 TATACTTTA
2995967 TATAC-TT-
1 TATACTTTA
2995974 TATA-TTTA
1 TATACTTTA
2995982 -ATAC-TTA
1 TATACTTTA
2995989 TATACTTTA
1 TATACTTTA
2995998 TAT
1 TAT
2996001 TATCATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
7 12 0.41
8 6 0.21
9 11 0.38
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (9 bp):
TATACTTTA
Found at i:2996057 original size:26 final size:26
Alignment explanation
Indices: 2995987--2996099 Score: 124
Period size: 26 Copynumber: 4.2 Consensus size: 26
2995977 ATTTAATACT
2995987 TATATACTTTATA-TTATCATATATATA
1 TATATACTTTATAGTT-T-ATATATATA
* *
2996014 TACTTTATAC-TAAAAGTTTATATATATA
1 TA---TATACTTTATAGTTTATATATATA
2996042 TATATACTTTATAGTTTATATATATA
1 TATATACTTTATAGTTTATATATATA
*
2996068 CT-TTTACTTTATAGTTTATATATATA
1 -TATATACTTTATAGTTTATATATATA
2996094 TATATA
1 TATATA
2996100 TACACATACT
Statistics
Matches: 73, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
25 6 0.08
26 42 0.58
27 3 0.04
28 11 0.15
29 4 0.05
30 7 0.10
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (26 bp):
TATATACTTTATAGTTTATATATATA
Found at i:2996067 original size:52 final size:54
Alignment explanation
Indices: 2995987--2996099 Score: 160
Period size: 52 Copynumber: 2.1 Consensus size: 54
2995977 ATTTAATACT
*
2995987 TATATACTTTATATTATCATATATATATACTTTATAC-TAAAAGTTTATATATATA
1 TATATACTTTATAGTAT-ATATATATATACTTT-TACTTAAAAGTTTATATATATA
* *
2996042 TATATACTTTATAGT-T-TATATATATACTTTTACTTTATAGTTTATATATATA
1 TATATACTTTATAGTATATATATATATACTTTTACTTAAAAGTTTATATATATA
2996094 TATATA
1 TATATA
2996100 TACACATACT
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
51 3 0.06
52 36 0.67
54 1 0.02
55 14 0.26
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (54 bp):
TATATACTTTATAGTATATATATATATACTTTTACTTAAAAGTTTATATATATA
Found at i:2996087 original size:20 final size:20
Alignment explanation
Indices: 2995895--2996252 Score: 129
Period size: 22 Copynumber: 18.1 Consensus size: 20
2995885 ATATATAGGT
*
2995895 TATATATAGTTTATAC---A
1 TATATATACTTTATACTTTA
*
2995912 TATATAAACTTTATA-TTATA
1 TATATATACTTTATACTT-TA
*
2995932 TACTTATATACTTTACT-CTTAA
1 TA--TATATACTTTA-TACTTTA
2995954 TA-ATTATACTTTATATACTTTA
1 TATA-TATAC-TT-TATACTTTA
*
2995976 TATTTAATACTTATATACTTTA
1 TATAT-ATACTT-TATACTTTA
2995998 TATTATCATA-TATATATACTTTA
1 TA-TAT-ATACT-T-TATACTTTA
* * *
2996021 TACTA-AAAGTTTATA-TATA
1 TA-TATATACTTTATACTTTA
*
2996040 TATATATACTTTATAGTTTA
1 TATATATACTTTATACTTTA
2996060 TATATATACTTT-TACTTTA
1 TATATATACTTTATACTTTA
* *
2996079 TAGTTTATATA-TATATA-TATA
1 TA---TATATACTTTATACTTTA
* *
2996100 TACACATAC-TTATACTTTA
1 TATATATACTTTATACTTTA
* *
2996119 TATGTATA---TATACTCTA
1 TATATATACTTTATACTTTA
*
2996136 TATACATA----A-ACTTTA
1 TATATATACTTTATACTTTA
*
2996151 TATTATATACTTATGTACTTTA
1 TA-TATATACTT-TATACTTTA
* * *
2996173 GTCTTTATA-ATTATACTTTA
1 -TATATATACTTTATACTTTA
* *
2996193 TAT-TACACTTTATA-TGTA
1 TATATATACTTTATACTTTA
* *
2996211 TATATA-A-GTTATAATTTA
1 TATATATACTTTATACTTTA
*
2996229 TCTATATACTTATATACTTTA
1 TATATATACTT-TATACTTTA
2996250 TAT
1 TAT
2996253 TTAAATTATA
Statistics
Matches: 258, Mismatches: 44, Indels: 74
0.69 0.12 0.20
Matches are distributed among these distances:
15 7 0.03
16 6 0.02
17 32 0.12
18 28 0.11
19 40 0.16
20 36 0.14
21 24 0.09
22 57 0.22
23 28 0.11
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (20 bp):
TATATATACTTTATACTTTA
Found at i:2998236 original size:148 final size:148
Alignment explanation
Indices: 2998079--2998383 Score: 592
Period size: 148 Copynumber: 2.1 Consensus size: 148
2998069 AAATATAAAT
*
2998079 TATATAGTTTAATTTATGTAAAGAAAATTTATCTAACAATTATAAGATATATAAAACATAATATA
1 TATATAGTTTAAATTATGTAAAGAAAATTTATCTAACAATTATAAGATATATAAAACATAATATA
*
2998144 AAAGATAAATTCATATTAATAATTCTCATCACCCATTTTATTGGGGTGGTGACACGTGGCGGTTT
66 AAAGATAAATTCATATTAATAATTCTCATCACCCATTTTATTCGGGTGGTGACACGTGGCGGTTT
2998209 GTAATATATAATATATGA
131 GTAATATATAATATATGA
2998227 TATATAGTTTAAATTATGTAAAGAAAATTTATCTAACAATTATAAGATATATAAAACATAATATA
1 TATATAGTTTAAATTATGTAAAGAAAATTTATCTAACAATTATAAGATATATAAAACATAATATA
2998292 AAAGATAAATTCATATTAATAATTCTCATCACCCATTTTATTCGGGTGGTGACACGTGGCGGTTT
66 AAAGATAAATTCATATTAATAATTCTCATCACCCATTTTATTCGGGTGGTGACACGTGGCGGTTT
2998357 GTAATATATAATATATGA
131 GTAATATATAATATATGA
2998375 TATATAGTT
1 TATATAGTT
2998384 AGTACATATA
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 155 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (148 bp):
TATATAGTTTAAATTATGTAAAGAAAATTTATCTAACAATTATAAGATATATAAAACATAATATA
AAAGATAAATTCATATTAATAATTCTCATCACCCATTTTATTCGGGTGGTGACACGTGGCGGTTT
GTAATATATAATATATGA
Found at i:2998637 original size:38 final size:38
Alignment explanation
Indices: 2998580--2998679 Score: 155
Period size: 38 Copynumber: 2.6 Consensus size: 38
2998570 TGGCATTTCA
* *
2998580 TGTTGCATTGCATGTTAAATAGTTAAATAATTAGTGTG
1 TGTTACATTGCATGTTAAATAGTTAAATAACTAGTGTG
* *
2998618 TGTTATATTGCATGTTAAATAATTAAATAACTAGTGTG
1 TGTTACATTGCATGTTAAATAGTTAAATAACTAGTGTG
*
2998656 TGTTACATTGCATGTTATATAGTT
1 TGTTACATTGCATGTTAAATAGTT
2998680 TGTATATATT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (38 bp):
TGTTACATTGCATGTTAAATAGTTAAATAACTAGTGTG
Found at i:2999442 original size:82 final size:81
Alignment explanation
Indices: 2999321--2999573 Score: 269
Period size: 93 Copynumber: 3.0 Consensus size: 81
2999311 GTCCAAAAAT
* *
2999321 GTATTAATTTAGG-ATTTATATTTTA-TTTATTTCAATTTGATCCTAAGAATTTTATAATTTAAT
1 GTATTAATTTAGGCA-TTAAATTTTATTTTATTTCAATTTGATCCTACGAATTTTATAATTTAAT
2999384 ATATATAACTATATAAC
65 ATATATAACTATATAAC
2999401 GTATTAATTTAGGCATTAAACTTTTATTTTATTTCAATTTGATCCTACGAATTTTACAATTTAAT
1 GTATTAATTTAGGCATTAAA-TTTTATTTTATTTCAATTTGATCCTACGAATTTT---A--TAAT
*
2999466 ATATATATATATATATA-TATTTATAAT
60 -T-TA-ATATATATA-ACTA--TATAAC
* * *
2999493 GTAATAATTTAGGCTTTAAATTTTTAATTTTATTTCAATTTGTTCCTACGAATTTTATAATTTAA
1 GTATTAATTTAGGCATTAAA-TTTT-ATTTTATTTCAATTTGATCCTACGAATTTTATAATTTAA
* * *
2999558 TAAATGTAACTCTATA
64 TATATATAACTATATA
2999574 TGTATATACT
Statistics
Matches: 147, Mismatches: 10, Indels: 29
0.79 0.05 0.16
Matches are distributed among these distances:
80 17 0.12
81 6 0.04
82 27 0.18
83 4 0.03
84 1 0.01
85 9 0.06
86 2 0.01
87 5 0.03
88 5 0.03
89 2 0.01
90 12 0.08
91 1 0.01
92 27 0.18
93 29 0.20
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (81 bp):
GTATTAATTTAGGCATTAAATTTTATTTTATTTCAATTTGATCCTACGAATTTTATAATTTAATA
TATATAACTATATAAC
Found at i:2999502 original size:92 final size:93
Alignment explanation
Indices: 2999382--2999559 Score: 270
Period size: 93 Copynumber: 1.9 Consensus size: 93
2999372 TTATAATTTA
*
2999382 ATATATATAACTATATAACGTATTAATTTAGGCATTAAACTTTT-ATTTTATTTCAATTTGATCC
1 ATATATATAACTATATAACGTAATAATTTAGGCATTAAACTTTTAATTTTATTTCAATTTGATCC
2999446 TACGAATTTTACAATTTAATATATATAT
66 TACGAATTTTACAATTTAATATATATAT
* * * * *
2999474 ATATATATATA-TTTATAATGTAATAATTTAGGCTTTAAATTTTTAATTTTATTTCAATTTGTTC
1 ATATATATA-ACTATATAACGTAATAATTTAGGCATTAAACTTTTAATTTTATTTCAATTTGATC
*
2999538 CTACGAATTTTATAATTTAATA
65 CTACGAATTTTACAATTTAATA
2999560 AATGTAACTC
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
92 37 0.48
93 40 0.52
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (93 bp):
ATATATATAACTATATAACGTAATAATTTAGGCATTAAACTTTTAATTTTATTTCAATTTGATCC
TACGAATTTTACAATTTAATATATATAT
Found at i:2999632 original size:22 final size:21
Alignment explanation
Indices: 2999604--2999733 Score: 110
Period size: 22 Copynumber: 6.1 Consensus size: 21
2999594 GTATTGTATA
2999604 TTTATATTATATAGTTTAATAC
1 TTTATATTATATA-TTTAATAC
2999626 TTTATA-TATATACTTT-ATA-
1 TTTATATTATATA-TTTAATAC
* *
2999645 TTTAATATT-TTTATTTCTATAC
1 TTT-ATATTATATATTT-AATAC
2999667 TTTAATACTT-TATATTTAATAC
1 TTT-ATA-TTATATATTTAATAC
2999689 -TTATATTATATAGTTTAATAC
1 TTTATATTATATA-TTTAATAC
* *
2999710 TTTATAGTGTATACTTTAATAC
1 TTTATATTATATA-TTTAATAC
2999732 TT
1 TT
2999734 ATAACTTATC
Statistics
Matches: 92, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
19 8 0.09
20 16 0.17
21 23 0.25
22 37 0.40
23 8 0.09
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTATATTATATATTTAATAC
Found at i:2999643 original size:35 final size:35
Alignment explanation
Indices: 2999570--2999646 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
2999560 AATGTAACTC
*
2999570 TATATGTATATACTTTAATACTCTGTATTGTATATT
1 TATAT-TATATACTTTAATACTCTGTATTATATATT
*
2999606 TATATTATATAGTTTAATACT-T-TATATATATACTT
1 TATATTATATACTTTAATACTCTGTAT-TATATA-TT
2999641 TATATT
1 TATATT
2999647 TAATATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 3 0.08
34 6 0.16
35 23 0.62
36 5 0.14
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (35 bp):
TATATTATATACTTTAATACTCTGTATTATATATT
Found at i:2999678 original size:36 final size:35
Alignment explanation
Indices: 2999635--2999715 Score: 117
Period size: 36 Copynumber: 2.3 Consensus size: 35
2999625 CTTTATATAT
* * *
2999635 ATACTTTATATTTAATATTTTTATTTCTATACTTTA
1 ATACTTTATATTTAATACTTATA-TTATATACTTTA
*
2999671 ATACTTTATATTTAATACTTATATTATATAGTTTA
1 ATACTTTATATTTAATACTTATATTATATACTTTA
2999706 ATACTTTATA
1 ATACTTTATA
2999716 GTGTATACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 20 0.49
36 21 0.51
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (35 bp):
ATACTTTATATTTAATACTTATATTATATACTTTA
Found at i:2999713 original size:35 final size:36
Alignment explanation
Indices: 2999635--2999993 Score: 121
Period size: 35 Copynumber: 9.9 Consensus size: 36
2999625 CTTTATATAT
* * *
2999635 ATACTTTATATTTAATATTTTTATTTCTATACTTTA
1 ATACTTTATATTTAATACTTATATTTATATACTTTA
*
2999671 ATACTTTATATTTAATACTTATA-TTATATAGTTTA
1 ATACTTTATATTTAATACTTATATTTATATACTTTA
* *
2999706 ATACTTTATAGTGT-ATACTTTAATACTTATA-AC-TT-
1 ATACTTTATA-TTTAATAC-TT-ATATTTATATACTTTA
* *
2999741 AT-CTATATATATATATACTTTATAGTTTGTATATA-TACTTA
1 ATACTTTATATTTA-ATAC-TTATA--TT-TATATACT--TTA
* * *
2999782 TATACTTTATA-TTATATACTAATACTT-TATAGTTTA
1 -ATACTTTATATTTA-ATACTTATATTTATATACTTTA
* * *
2999818 TATA-ATTATATAT-ATACTTATATTT-TATAGTTT-
1 -ATACTTTATATTTAATACTTATATTTATATACTTTA
* * *
2999851 ATA---TATACTT-ATACTTTATATGGATATATACTTTT
1 ATACTTTATATTTAATAC-TTATAT--TTATATACTTTA
* * * * *
2999886 ATAGTATATATATATATACTTATACTTTATAT-GTATA
1 ATACTTTATATTTA-ATACTTATA-TTTATATACTTTA
*
2999923 TATATTTTATATACTTATATACTT-TATATTATATAC-TTA
1 -ATACTTTATAT--TTA-ATACTTATAT-TTATATACTTTA
* *
2999962 ATACTTTAGTCTTT-ATAATTATACTTTATATA
1 ATACTTTA-TATTTAATACTTATA-TTTATATA
2999994 TATATATATA
Statistics
Matches: 251, Mismatches: 35, Indels: 74
0.70 0.10 0.21
Matches are distributed among these distances:
30 9 0.04
31 6 0.02
32 3 0.01
33 3 0.01
34 34 0.14
35 46 0.18
36 45 0.18
37 17 0.07
38 35 0.14
39 18 0.07
40 16 0.06
41 4 0.02
42 9 0.04
43 6 0.02
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (36 bp):
ATACTTTATATTTAATACTTATATTTATATACTTTA
Found at i:2999764 original size:28 final size:28
Alignment explanation
Indices: 2999719--2999870 Score: 76
Period size: 28 Copynumber: 5.6 Consensus size: 28
2999709 CTTTATAGTG
*
2999719 TATACTTTAATAC-TTATAACTTATCTATA
1 TATACTAT-ATACTTTATAACTT-TCTATA
* *
2999748 TATA-TATATACTTTAT-AGTTTGTATA
1 TATACTATATACTTTATAACTTTCTATA
*
2999774 TATACTTATATACTTTAT-A--TTATATA
1 TATAC-TATATACTTTATAACTTTCTATA
* * * *
2999800 CTAATACTTTATAGTTTATATA-ATTATATA
1 -T-ATACTATATACTTTATA-ACTTTCTATA
* *
2999830 TATACT-TATATTTTAT-A-GTT-TATA
1 TATACTATATACTTTATAACTTTCTATA
2999854 TATACT-TATACTTTATA
1 TATACTATATACTTTATA
2999871 TGGATATATA
Statistics
Matches: 105, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
24 19 0.18
25 3 0.03
26 15 0.14
27 27 0.26
28 28 0.27
29 6 0.06
30 7 0.07
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (28 bp):
TATACTATATACTTTATAACTTTCTATA
Found at i:2999773 original size:20 final size:21
Alignment explanation
Indices: 2999748--3001137 Score: 200
Period size: 20 Copynumber: 67.8 Consensus size: 21
2999738 CTTATCTATA
*
2999748 TATATATATACTT-TATAGTT
1 TATATATATACTTATATACTT
*
2999768 TGTATATATACTTATATACTT
1 TATATATATACTTATATACTT
2999789 TATATTATATAC-TA-ATACTT
1 TATA-TATATACTTATATACTT
*
2999809 TATAGTTTATATAATTATATA---
1 TATA---TATATACTTATATACTT
* *
2999830 TATACT-TATA-TTTTATA-GT
1 TATA-TATATACTTATATACTT
2999849 T-TATATATAC-T-TATACTTT
1 TATATATATACTTATATAC-TT
* *
2999868 ATATGGATATATACTTTTATAGTAT
1 -TAT--ATATATACTTATATACT-T
2999893 ATATATATATAC-T-TATAC-T
1 -TATATATATACTTATATACTT
*
2999912 T-TATATGTA--TATATA-TT
1 TATATATATACTTATATACTT
2999929 T-TATAT--ACTTATATACTT
1 TATATATATACTTATATACTT
2999947 TATATTATATACTTA-ATACTT
1 TATA-TATATACTTATATACTT
* * *
2999968 TAGTCTTTATA-AT-TATACTT
1 TA-TATATATACTTATATACTT
*
2999988 TATATATATA--TATATA--A
1 TATATATATACTTATATACTT
3000005 TATACT-TATACTTCATAT--TAT
1 TATA-TATATACTT-ATATACT-T
* *
3000026 TATATAT-GA-TTATATTCTT
1 TATATATATACTTATATACTT
* *
3000045 TATACTA-AAACTTTATATA-TA
1 TATA-TATATAC-TTATATACTT
*
3000066 TATATATATA-TAATATA-TAT
1 TATATATATACTTATATACT-T
3000086 TATATATA-A-TATATATA-TT
1 TATATATATACT-TATATACTT
* *
3000105 TATACTTTATATGTATATATACTT
1 TATA-TATATA-CT-TATATACTT
*
3000129 TATACTATATAGTTTATATACTT
1 TATA-TATATA-CTTATATACTT
3000152 TATATTATATAC-TATATACTT
1 TATA-TATATACTTATATACTT
* * * *
3000173 TAGTCT-TATAATTATATTAATA
1 TA-TATATATACTTATA-TACTT
3000195 TATATATATA--T-TATACTT
1 TATATATATACTTATATACTT
* * *
3000213 ATGTATATATAGTTTATACGAAAACTT
1 -TATATATATA-CTTAT----ATACTT
* * * *
3000240 TATACATACATACATACATAC-A
1 TAT--ATATATACTTATATACTT
*
3000262 TATATATATA--TATATA-TA
1 TATATATATACTTATATACTT
* *
3000280 TATATATATA-TAATATA-TA
1 TATATATATACTTATATACTT
*
3000299 TATATATATACTT-TATAGTT
1 TATATATATACTTATATACTT
3000319 TATATATATAC-TATATAC-T
1 TATATATATACTTATATACTT
*
3000338 T-TATATATGCTTATATACTT
1 TATATATATACTTATATACTT
* * * *
3000358 TAGTTTTTATA-AT-TAGACTT
1 TA-TATATATACTTATATACTT
*
3000378 TATATATATA-TAATATAC-T
1 TATATATATACTTATATACTT
3000397 TATACT-T-T--TTATATA-TT
1 TATA-TATATACTTATATACTT
*
3000414 TATATA-CT--TTATATACTT
1 TATATATATACTTATATACTT
* * *
3000432 ATATACTTTATTCTT-TATA-AT
1 -TATA-TATATACTTATATACTT
*
3000453 TATACTTTATA-TTATATA-TT
1 TATA-TATATACTTATATACTT
*
3000473 ATATTATATATATCTATATATA-TA
1 -TA-TATATATA-CT-TATATACTT
*
3000497 TATATATATATTTATATA-TT
1 TATATATATACTTATATACTT
3000517 ATACTTATATATACTT-TATA-TT
1 -TA--TATATATACTTATATACTT
* * * * *
3000539 TAAACTATAAAGCTATACATAGTA
1 TATA-TATATA-CT-TATATACTT
* *
3000563 TATA-ATTTA-TAAT-TA-TT
1 TATATATATACTTATATACTT
* ** *
3000580 CATATATATAAATATA-AGCTG
1 TATATATATACTTATATA-CTT
* * * *
3000601 CATATATTTA--AATATAATT
1 TATATATATACTTATATACTT
* *
3000620 TATATATA-ATTTATATTAAACTA
1 TATATATATACTTATA-T--ACTT
* *
3000643 TATA-ATTATA-TTAATAAACTA
1 TATATA-TATACTT-ATATACTT
* **
3000664 TATAGT-TTTA-TATATATACAAA
1 TATA-TATATACT-TATATAC-TT
* *
3000686 TATAAACTATA-TTATATA-TA
1 TATATA-TATACTTATATACTT
* *
3000706 TATATATATAATATATATA-TA
1 TATATATATACT-TATATACTT
* *
3000727 TATAGTTTATACATATATAAAACTT
1 TATA-TATATAC-T-TAT-ATACTT
* *
3000752 TATATTAGATTCTTATATACTT
1 TATA-TATATACTTATATACTT
3000774 TACTTAATAATTATACTT-TATACTT
1 TA--T-AT-A-TATACTTATATACTT
*
3000799 TATATTTAATAC-T-TATACTT
1 TATATAT-ATACTTATATACTT
3000819 TATATATATA--TATATACTT
1 TATATATATACTTATATACTT
* *
3000838 TATACTAAATA--TATATA-TA
1 TATA-TATATACTTATATACTT
*
3000857 TATATATAT-C-TATATA-TA
1 TATATATATACTTATATACTT
*
3000875 TATATATATA-TATATATA-TA
1 TATATATATACT-TATATACTT
*
3000895 TATATATATA-TATATACTTAGTT
1 TATATATATACT-TATA--TACTT
3000918 TATATATATACTT-T-TACTT
1 TATATATATACTTATATACTT
* *
3000937 TATAGTTTATA-TATATATAC-A
1 TATA-TATATACT-TATATACTT
* *
3000958 CATACT-TATACTT-TATA-TG
1 TATA-TATATACTTATATACTT
3000977 TATATATACT-CTATATACATAAACTT
1 TATATATA-TACT-TAT--AT--ACTT
*
3001003 TATATTATATACTTATGTACTT
1 TATA-TATATACTTATATACTT
* * *
3001025 TAGTCTTTATA-AT-TATACTT
1 TA-TATATATACTTATATACTT
* *
3001045 TATAT-TACACTT-TATA-TG
1 TATATATATACTTATATACTT
*
3001063 TATATATA-AGTTATA-A-TT
1 TATATATATACTTATATACTT
* *
3001081 TATCTATATATTTATATACTT
1 TATATATATACTTATATACTT
* * ***
3001102 TATATTTA-AATTATATAAGC
1 TATATATATACTTATATACTT
3001122 TATATATATA-TTATAT
1 TATATATATACTTATAT
3001138 TTATATATAT
Statistics
Matches: 1050, Mismatches: 152, Indels: 336
0.68 0.10 0.22
Matches are distributed among these distances:
15 1 0.00
16 2 0.00
17 66 0.06
18 102 0.10
19 173 0.16
20 240 0.23
21 142 0.14
22 114 0.11
23 105 0.10
24 40 0.04
25 30 0.03
26 16 0.02
27 13 0.01
28 6 0.01
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
TATATATATACTTATATACTT
Found at i:2999776 original size:22 final size:23
Alignment explanation
Indices: 2999746--3000537 Score: 200
Period size: 23 Copynumber: 35.2 Consensus size: 23
2999736 AACTTATCTA
*
2999746 TATATATATATACTT-TATA-GT
1 TATATATATATACTTATATACTT
*
2999767 T-TGTATATATACTTATATACTT
1 TATATATATATACTTATATACTT
2999789 TATAT-TATATAC-TA-ATACTT
1 TATATATATATACTTATATACTT
* *
2999809 TATAGTTTATATAATTATATA---
1 TATA-TATATATACTTATATACTT
*
2999830 TATACT-TATAT--TT-TATA-GT
1 TATA-TATATATACTTATATACTT
2999849 T-TATAT--ATAC-T-TATACTTT
1 TATATATATATACTTATATAC-TT
** * * *
2999868 ATATGGATATATACTTTTATAGTA
1 -TATATATATATACTTATATACTT
2999892 TATATATATATAC-T-TATACTT
1 TATATATATATACTTATATACTT
*
2999913 TATATGTATATATATTTTATATAC-T
1 TATA--TATATATA-CTTATATACTT
*
2999938 TATATACTTTATA-TTATATACTT
1 TATATA-TATATACTTATATACTT
* * * *
2999961 AATACTTTAGTCTTTA-TAATTATACTT
1 --TA-TATA-TATATACTTA-TATACTT
2999988 TATATATATATA-TATAATATAC-T
1 TATATATATATACT-T-ATATACTT
3000011 TATACT-TCATATTA-TTATATA-TGAT
1 TATA-TAT-ATA-TACTTATATACT--T
* * *
3000036 TATATTCTTTATAC-TA-AAACTT
1 TATA-TATATATACTTATATACTT
* *
3000058 TATATATATATA-TATATATAATA
1 TATATATATATACT-TATATACTT
*
3000081 TATATTATATATAATATATATA-TT
1 TATA-TATATATACT-TATATACTT
* *
3000105 TATACTTTATAT-GTATATATACTT
1 TATA-TATATATACT-TATATACTT
3000129 TATACTATATAGT--TTATATACTT
1 TATA-TATATA-TACTTATATACTT
3000152 TATAT-TATATAC-TATATACTT
1 TATATATATATACTTATATACTT
* *
3000173 TAGTCTTATAATTATA-TTA-ATA-TA
1 TA-T-ATAT-A-TATACTTATATACTT
*
3000197 TATATATATTATACTTATGTA---
1 TATATATA-TATACTTATATACTT
* * *
3000218 TATATAGTTTATAC-GA-AAACTT
1 TATATA-TATATACTTATATACTT
* * * *
3000240 TATACATACATACATACATACATAT
1 TATATATATATACTTATATAC-T-T
*
3000265 ATATATATATATA-TATATATA-TA
1 -TATATATATATACT-TATATACTT
3000288 TATAATATATATA-TATATATACTT
1 TAT-ATATATATACT-TATATACTT
3000312 TATAGT-T-TATA--TATATACTAT
1 TATA-TATATATACTTATATACT-T
* *
3000333 ATACTTTATATATGCTTATATACTT
1 -TA-TATATATATACTTATATACTT
* * *
3000358 TAGT-T-TTTATA-AT-TAGACTT
1 TA-TATATATATACTTATATACTT
*
3000378 TATATATATATAATATACTTATACTT
1 TATATATATATACT-TA--TATACTT
3000404 T-T-TATATAT--TTATATACTT
1 TATATATATATACTTATATACTT
*
3000423 TATATACTTATATACTT-TATTCTT
1 TATATA--TATATACTTATATACTT
3000447 TATA-AT-TATACTT-TATA--T
1 TATATATATATACTTATATACTT
3000465 TATATAT-TATA-TTATATA-TAT
1 TATATATATATACTTATATACT-T
3000486 CTATATATATATA-TATATATA-TT
1 -TATATATATATACT-TATATACTT
3000509 TATATAT-TATACTTATATATACTT
1 TATATATATATAC-T-TATATACTT
3000533 TATAT
1 TATAT
3000538 TTAAACTATA
Statistics
Matches: 600, Mismatches: 69, Indels: 201
0.69 0.08 0.23
Matches are distributed among these distances:
16 2 0.00
17 10 0.02
18 12 0.02
19 22 0.04
20 58 0.10
21 85 0.14
22 75 0.12
23 126 0.21
24 108 0.18
25 44 0.07
26 51 0.09
27 7 0.01
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.52
Consensus pattern (23 bp):
TATATATATATACTTATATACTT
Found at i:2999827 original size:112 final size:103
Alignment explanation
Indices: 2999576--2999942 Score: 244
Period size: 103 Copynumber: 3.7 Consensus size: 103
2999566 ACTCTATATG
* * * * *
2999576 TATATACTTTAATACTCTGTATTGTATATTTATA-TTATATAGTTTA-ATACTTTATATATATAC
1 TATATACTTT-ATACTTTATATTATATACTTATACTT-TATAGTTTATATACATTATATATATAC
* * *
2999639 TTTATATTTAATA-TTTTTAT-TTC-TATACTTTA-AT--A
64 -TTATATTTAATAGTCTATATATACTTATACTTTATATGGA
* * *
2999674 CTTTATA-TTTAATAC-TTATATTATATAGTTTAATACTTTATAG--TGTATAC--T-T-TA-AT
1 -TATATACTTT-ATACTTTATATTATATA-CTT-ATACTTTATAGTTTATATACATTATATATAT
** *
2999730 ACTTATAACT--TA-TCTATATATA-TATATACTTTATAGTTTGTA
62 ACTTATATTTAATAGTCTATATATACT-TATACTTTATA---TGGA
*
2999772 TATATACTTATATACTTTATATTATATACTAATACTTTATAGTTTATATA-ATTATATATATACT
1 TATATACTT-TATACTTTATATTATATACTTATACTTTATAGTTTATATACATTATATATATACT
* *
2999836 TATATTTTATAGTTTATATATACTTATACTTTATATGGA
65 TATATTTAATAGTCTATATATACTTATACTTTATATGGA
* * * *
2999875 TATATACTTTTATAGTATATATATATATACTTATACTTTATA-TGTATATATATT-T-TATATAC
1 TATATAC-TTTATACTTTATAT-TATATACTTATACTTTATAGTTTATATACATTATATATATAC
2999937 TTATAT
64 TTATAT
2999943 ACTTTATATT
Statistics
Matches: 216, Mismatches: 22, Indels: 57
0.73 0.07 0.19
Matches are distributed among these distances:
90 7 0.03
91 1 0.00
92 15 0.07
93 5 0.02
94 2 0.01
95 1 0.00
96 2 0.01
97 26 0.12
98 23 0.11
99 31 0.14
100 3 0.01
101 1 0.00
102 15 0.07
103 38 0.18
104 23 0.11
105 2 0.01
106 20 0.09
107 1 0.00
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (103 bp):
TATATACTTTATACTTTATATTATATACTTATACTTTATAGTTTATATACATTATATATATACTT
ATATTTAATAGTCTATATATACTTATACTTTATATGGA
Found at i:2999935 original size:9 final size:8
Alignment explanation
Indices: 2999744--3000156 Score: 71
Period size: 8 Copynumber: 50.6 Consensus size: 8
2999734 ATAACTTATC
*
2999744 TATATATA
1 TATATATT
2999752 TATATACTT
1 TATATA-TT
2999761 TATAGT-TT
1 TATA-TATT
2999769 GTATATATACT
1 -TATATAT--T
2999780 TATATACTT
1 TATATA-TT
*
2999789 TATATTATA
1 TATA-TATT
2999798 TACTAATACTT
1 TA-T-ATA-TT
*
2999809 TATA-GTT
1 TATATATT
*
2999816 TATATAAT
1 TATATATT
*
2999824 TATATATA
1 TATATATT
2999832 TACTTATATT
1 TA--TATATT
2999842 T-TATAGTT
1 TATATA-TT
2999850 TATATATACT
1 TATATAT--T
*
2999860 TATA-CTT
1 TATATATT
***
2999867 TATATGGA
1 TATATATT
2999875 TATATACTT
1 TATATA-TT
*
2999884 T-TATA-G
1 TATATATT
*
2999890 TATATATA
1 TATATATT
*
2999898 TATATACT
1 TATATATT
*
2999906 TATA-CTT
1 TATATATT
* *
2999913 TATATGTA
1 TATATATT
2999921 TATATATTT
1 TATATA-TT
*
2999930 TATATACT
1 TATATATT
*
2999938 TATATACT
1 TATATATT
2999946 T-TATA-T
1 TATATATT
*
2999952 TATATACT
1 TATATATT
2999960 TA-ATACTT
1 TATATA-TT
* *
2999968 TA-GTCTT
1 TATATATT
2999975 TATA-A-T
1 TATATATT
*
2999981 TATA-CTT
1 TATATATT
*
2999988 TATATATA
1 TATATATT
2999996 TATATA-T
1 TATATATT
* *
3000003 AATATACT
1 TATATATT
*
3000011 TATA-CTT
1 TATATATT
*
3000018 CATAT-TAT
1 TATATAT-T
3000026 TATATATGAT
1 TATATAT--T
*
3000036 TATATTCTT
1 TATA-TATT
3000045 TATACTAAAACTT
1 TATA-T---A-TT
3000058 TATATA--
1 TATATATT
*
3000064 TATATATA
1 TATATATT
*
3000072 TATATA-A
1 TATATATT
3000079 TATATATT
1 TATATATT
*
3000087 ATATATAATA
1 -TATAT-ATT
3000097 TATATATT
1 TATATATT
*
3000105 TATA-CTT
1 TATATATT
* *
3000112 TATATGTA
1 TATATATT
*
3000120 TATATACT
1 TATATATT
*
3000128 T-TATA-C
1 TATATATT
3000134 TATATAGTT
1 TATATA-TT
3000143 TATATACTT
1 TATATA-TT
3000152 TATAT
1 TATAT
3000157 TATATACTAT
Statistics
Matches: 299, Mismatches: 57, Indels: 97
0.66 0.13 0.21
Matches are distributed among these distances:
6 15 0.05
7 75 0.25
8 99 0.33
9 63 0.21
10 32 0.11
11 8 0.03
12 1 0.00
13 6 0.02
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (8 bp):
TATATATT
Found at i:3000170 original size:37 final size:34
Alignment explanation
Indices: 2999600--3001013 Score: 293
Period size: 34 Copynumber: 41.5 Consensus size: 34
2999590 CTCTGTATTG
* * *
2999600 TATA-TTTATATTATATAGTTTA-ATACTTTATATA
1 TATACTTTATATTATATA-TATATATA-TATATTTA
* * * *
2999634 TATACTTTATATTTAATATTTTTATTTCTATACTTTA
1 TATACTTTATA-TT-ATATATATATATATATA-TTTA
2999671 -ATACTTTATATT-TA-ATACTTATATTATATAGTTTA
1 TATACTTTATATTATATATA--TATA-TATATA-TTTA
* * * *
2999706 -ATACTTTATAGTGTATA-CT-T-TA-ATACTTA
1 TATACTTTATATTATATATATATATATATATTTA
* * *
2999735 TA-ACTTATCTATATATATATATACTTTATAGTTTGTATA
1 TATACTT-TATAT-TATATATATA-TATATA-TAT-T-TA
*
2999774 TATACTTATATACTT-TATAT-TATATACTAATACTT-
1 TATACTT-TATA-TTATATATATATATA-T-ATATTTA
* *
2999809 TATAGTTTATATAAT-TATATATATACTTATATTT-
1 TATACTTTATATTATATATATATATA--TATATTTA
* * ***
2999843 TATAGTTTATA-TATACT-TATACTTTATATGGATA
1 TATACTTTATATTATA-TATATA-TATATATATTTA
* *
2999877 TATACTTT-TA-TA-GTATATATATATATA-CT-
1 TATACTTTATATTATATATATATATATATATTTA
* *
2999906 TATACTTTATATGTATATATAT-TTTATATACTTA
1 TATACTTTATAT-TATATATATATATATATATTTA
* *
2999940 TATACTTTATATTATATA-CT-TA-ATA-CTTTA
1 TATACTTTATATTATATATATATATATATATTTA
* * *
2999970 -GT-CTTTATAATTATACTTTATATATATATATATAA
1 TATACTTTAT-ATTATA-TATATATATATATAT-TTA
3000005 TATAC-TTATACTTCATAT-TAT-TATATATGA-TTA
1 TATACTTTATA-TT-ATATATATATATATAT-ATTTA
* * * * *
3000038 TATTCTTTATACTAAAACTTTATATATATATATATA
1 TATACTTTATA-TTATA-TATATATATATATATTTA
* *
3000074 TATAATATATATTATATATA-ATATATATA-TT-
1 TATACTTTATATTATATATATATATATATATTTA
3000105 TATACTTTATATGTATATATACTTTATACTATATAGTTTA
1 TATACTTTATAT-TATATATA---TATA-TATATA-TTTA
3000145 TATACTTTATATTATATACTATATACT-T-TAGTCTTA
1 TATACTTTATATTATATA-TATATA-TATATA-T-TTA
*
3000181 TA-A--TTATATTAATATATATATATATTATACTTA
1 TATACTTTATATT-ATATATATATATA-TATATTTA
* * * * * **
3000214 TGTA-TATATAGTT-TATACGA-AAACTTTATACATA
1 TATACTTTATA-TTATATA-TATATA-TATATATTTA
* * * * *
3000248 CATAC-ATACA-TACATATATATATATATATATA
1 TATACTTTATATTATATATATATATATATATTTA
* * *
3000280 TATA-TATATATAATATATATATATATATACTT-
1 TATACTTTATATTATATATATATATATATATTTA
* *
3000312 TATAGTTTATATATATACTATATACTTTATATATGCTTA
1 TATACTTTATAT-TATA-TATATA-TATATATAT--TTA
* * * *
3000351 TATACTTTAGTTTTTATAATTAGACTTTATATATATATAA
1 TATACTTTA--TATTAT-A-TATA-TATATATATAT-TTA
* *
3000391 TATAC-TTATACTT-TTTATATATTTATATACTTTA
1 TATACTTTATA-TTATATATATATATATATA-TTTA
*
3000425 TATACTTATATACTT-TAT-TCT-T-TATA-A--T-
1 TATACTT-TATA-TTATATATATATATATATATTTA
*
3000453 TATACTTTATATTATATATTATATTATATATATCTA
1 TATACTTTATATTATATA-TATA-TATATATATTTA
* *
3000489 TATA-TATATATATATATATTTATATATTATACTTATA
1 TATACTTTATAT-TATATATATATATA-TATA-TT-TA
* * * *
3000526 TATACTTTATATT-TAAACTATAAAGCTATACATAGTA
1 TATACTTTATATTATATA-TATATA--TATATAT-TTA
* * **
3000563 TATAATTTATAATTATTCATATATATAAATATAAGCTGCA
1 TATACTTTAT-ATTA-T-ATATATATATATAT-A--TTTA
* *
3000603 TATA-TTTA-AATATA-ATTTATATATA-ATTTA
1 TATACTTTATATTATATATATATATATATATTTA
*** * **
3000633 TATTAAACTATATAAT-TATAT-TA-ATA-AACTA
1 TA-TACTTTATATTATATATATATATATATATTTA
* * * *
3000664 TATAGTTT-TATATATATACAAATATAAACTATATTA
1 TATACTTTATAT-TATATATATATATATA-TAT-TTA
* *
3000700 TATA-TATATATATATAATATATATATATATAGTT-
1 TATACTTTATAT-TAT-ATATATATATATATATTTA
* * * * *
3000734 TATAC-ATATATAAAACTTTATAT-TAGAT-TCTTA
1 TATACTTTATATTATA-TATATATATATATAT-TTA
* * *
3000767 TATACTTTACTTAATAATTATACTTTATACTTTATATTTA
1 TATACTTTA--T-ATTA-TATA-TATATA-TATATATTTA
*
3000807 -ATAC-TTATACTT-TATATATATATATATACTT-
1 TATACTTTATA-TTATATATATATATATATATTTA
* *
3000838 TATAC--TA-AATATATATATATATATATATCTA
1 TATACTTTATATTATATATATATATATATATTTA
* *
3000869 TATA-TATATA-TATATATATATATATATATATA
1 TATACTTTATATTATATATATATATATATATTTA
* * *
3000901 TATA-TATATACTTA-GT-T-TATATATATACTT-
1 TATACTTTATA-TTATATATATATATATATATTTA
* * *
3000931 T-TACTTTATAGTT-TATATATATATACACATACT-
1 TATACTTTATA-TTATATATATATATATATAT-TTA
* *
3000964 TATACTTTATATGTATATATACTCTATATACA--TA
1 TATACTTTATAT-TATATATA-TATATATATATTTA
3000998 -A-ACTTTATATTATATA
1 TATACTTTATATTATATA
3001014 CTTATGTACT
Statistics
Matches: 1035, Mismatches: 178, Indels: 337
0.67 0.11 0.22
Matches are distributed among these distances:
26 2 0.00
27 7 0.01
28 13 0.01
29 31 0.03
30 50 0.05
31 66 0.06
32 131 0.13
33 131 0.13
34 164 0.16
35 108 0.10
36 116 0.11
37 73 0.07
38 32 0.03
39 40 0.04
40 51 0.05
41 19 0.02
42 1 0.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (34 bp):
TATACTTTATATTATATATATATATATATATTTA
Found at i:3000216 original size:98 final size:99
Alignment explanation
Indices: 2999890--3000547 Score: 330
Period size: 98 Copynumber: 6.8 Consensus size: 99
2999880 ACTTTTATAG
* * * ** *
2999890 TATATATATATATACTTATACTT-TATATGTATATATATTTTATATA-CTTATATACTTTATATT
1 TATATATATATATACTTATACTTATGTATATATATTTATACTATATAGATTATATACTTTATATT
2999953 ATATACT-TAATACTTTAGTCTTTATAATTATACTTTA
66 ATATACTAT-ATACTTTAGTC-TTATAATTATA--TTA
* *
2999990 TATATATATATATA-ATATACTTA--TACT-TCATA-TTAT--TATATATGATTATATTCTTTAT
1 TATATATATATATACTTATACTTATGTA-TAT-ATATTTATACTATATA-GATTATATACTTTAT
* * *
3000048 ACTA-AAACTTTATATA-TATATA-TATATATAATATATATTA
63 ATTATATAC--TATATACT-T-TAGTCT-TATAAT-TATATTA
* *
3000088 TATATAATATATATATTTATACTTTATATGTATATATACTTTATACTATATAGTTTATATACTTT
1 TATAT-ATATATATACTTATAC--T-TATGTATATATA-TTTATACTATATAGATTATATACTTT
3000153 ATATTATATACTATATACTTTAGTCTTATAATTATATTA
61 ATATTATATACTATATACTTTAGTCTTATAATTATATTA
* * *
3000192 -ATATATATATATA-TTATACTTATGTATATATAGTTTATACGA-A-A-ACTT-TATAC-ATACA
1 TATATATATATATACTTATACTTATGTATATATA-TTTATACTATATAGA-TTATATACTTTATA
* * * *
3000250 -TACATAC-ATACA-TATA-T-ATAT-A-TATA-TA
64 TTATATACTATATACTTTAGTCTTATAATTATATTA
* * * *
3000278 TATATATATATATA-ATATA--TATATATATATACTTTATAGTTTATATATATACTATATAC-TT
1 TATATATATATATACTTATACTTATGTATATATA-TTTATA--CTATATAGAT--TATATACTTT
* * *
3000339 -TA-TATATGCTTATATACTTTAGTTTTTATAATTAGACTTTA
61 ATATTATATAC-TATATACTTTAG-TCTTATAATTATA--TTA
* * *
3000380 TATATATATAATATACTTATACTT-TTTATATAT-TTATATACTTTATATACTTATATACTTTAT
1 TATATATAT-ATATACTTATACTTATGTATATATATT-TATACTATATAGA-TTATATACTTTAT
* * *
3000443 -TCTTTATAAT-TATACTTTA-TATTATATATTATATTA
63 AT-TATATACTATATACTTTAGTCTTATA-ATTATATTA
* **
3000479 TATATATCTATATA--TATA--TA--TATATATATTTATA-TATTATACTTATATATACTTTATA
1 TATATATATATATACTTATACTTATGTATATATATTTATACTA-TATAGAT-TATATACTTTATA
*
3000537 TT-TAAACTATA
64 TTATATACTATA
3000548 AAGCTATACA
Statistics
Matches: 443, Mismatches: 50, Indels: 137
0.70 0.08 0.22
Matches are distributed among these distances:
85 17 0.04
86 2 0.00
87 22 0.05
88 2 0.00
89 5 0.01
90 2 0.00
91 10 0.02
92 16 0.04
93 40 0.09
94 10 0.02
95 5 0.01
96 14 0.03
97 7 0.02
98 57 0.13
99 47 0.11
100 32 0.07
101 18 0.04
102 39 0.09
103 16 0.04
104 23 0.05
105 19 0.04
106 14 0.03
107 17 0.04
108 9 0.02
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.52
Consensus pattern (99 bp):
TATATATATATATACTTATACTTATGTATATATATTTATACTATATAGATTATATACTTTATATT
ATATACTATATACTTTAGTCTTATAATTATATTA
Found at i:3000644 original size:19 final size:21
Alignment explanation
Indices: 3000622--3000667 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3000612 ATATAATTTA
*
3000622 TATATAATT-TA-TATTAAAC
1 TATATAATTATATTAATAAAC
3000641 TATATAATTATATTAATAAAC
1 TATATAATTATATTAATAAAC
3000662 TATATA
1 TATATA
3000668 GTTTTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 9 0.38
20 2 0.08
21 13 0.54
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TATATAATTATATTAATAAAC
Found at i:3000644 original size:21 final size:23
Alignment explanation
Indices: 3000620--3000667 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 23
3000610 AAATATAATT
*
3000620 TATATATAATT-TA-TATTAAAC
1 TATATATAATTATATTAATAAAC
3000641 --TATATAATTATATTAATAAAC
1 TATATATAATTATATTAATAAAC
3000662 TATATA
1 TATATA
3000668 GTTTTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
19 9 0.41
20 2 0.09
21 7 0.32
23 4 0.18
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TATATATAATTATATTAATAAAC
Found at i:3000927 original size:2 final size:2
Alignment explanation
Indices: 3000058--3000910 Score: 271
Period size: 2 Copynumber: 430.0 Consensus size: 2
3000048 ACTAAAACTT
3000058 TA TA TA TA TA TA TA TA TA TA -A TA TA TA T- TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
3000097 TA TA TA TT TA TA CTT TA TA TG TA TA TA TA CTT TA TA CTA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
3000140 GTT TA TA TA CTT TA TA T- TA TA TA CTA TA TA CTT TA GTC T- TA TA
1 -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA -TA TA TA TA
*
3000183 -A T- TA TA T- TA -A TA TA TA TA TA TA T- TA TA CT- TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * * * * * *
3000220 TA TA GTT TA TA CGA -A AA CTT TA TA CA TA CA TA CA TA CA TA CA
1 TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
3000262 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
3000303 TA TA TA CTT TA TA GTT TA TA TA TA TA CTA TA TA CTT TA TA TA TGC
1 TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA T-A
* * * * *
3000348 T- TA TA TA CTT TA GTT TT TA TA -A T- TA GA CTT TA TA TA TA TA
1 TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
3000388 TA -A TA TA CT- TA TA CTT TT TA TA TA TT TA TA TA CTT TA TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
3000429 CT- TA TA TA CTT TA T- TC TT TA TA -A T- TA TA CTT TA TA T- TA
1 -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
*
3000467 TA TA T- TA TA T- TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
3000507 TT TA TA TA T- TA TA CT- TA TA TA TA CTT TA TA TT TA AA CTA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA -TA TA
* ** * *
3000548 AA GC TA TA CA TA GTA TA TA -A TT TA TA -A T- TA T- TCA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
* ** * * * * *
3000588 TA AA TA TA -A GC TG CA TA TA TT TA AA TA TA -A TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3000628 -A TT TA TA T- TA AA CTA TA TA -A T- TA TA T- TA -A TA AA CTA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
3000666 TA GT- TT TA TA TA TA TA CA AA TA TA AA CTA TA T- TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
3000708 TA TA TA TA -A TA TA TA TA TA TA TA GTT TA TA CA TA TA TA -A AA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
3000749 CTT TA TA T- TA GA T- TC T- TA TA TA CTT TA CT- TA -A TA -A T-
1 -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA
* * * *
3000785 TA TA CTT TA TA CTT TA TA TT TA -A TA CT- TA TA CTT TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * *
3000827 TA TA TA TA CTT TA TA CTA AA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3000871 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3000911 CTTAGTTTAT
Statistics
Matches: 624, Mismatches: 130, Indels: 194
0.66 0.14 0.20
Matches are distributed among these distances:
1 52 0.08
2 525 0.84
3 47 0.08
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3000938 original size:19 final size:17
Alignment explanation
Indices: 3000794--3000940 Score: 60
Period size: 16 Copynumber: 8.5 Consensus size: 17
3000784 TTATACTTTA
*
3000794 TACTTTATATTTAATACTT
1 TACTTTATATAT-ATAC-T
*
3000813 ATACTTTATATATATATAT
1 -TACTTTATATATATA-CT
*
3000832 ATACTTTATACTAAATA--
1 -TACTTTATA-TATATACT
*
3000849 TA-TATATATATATA--
1 TACTTTATATATATACT
*
3000863 TATCTATATATATATA-T
1 TA-CTTTATATATATACT
*
3000880 ATA-TATATATATATA-T
1 -TACTTTATATATATACT
*
3000896 ATA-TATATATATATACT
1 -TACTTTATATATATACT
*
3000913 TAGTTTATATATATACTTT
1 TACTTTATATATATAC--T
3000932 TACTTTATA
1 TACTTTATA
3000941 GTTTATATAT
Statistics
Matches: 110, Mismatches: 7, Indels: 21
0.80 0.05 0.15
Matches are distributed among these distances:
14 7 0.06
15 5 0.05
16 44 0.40
17 13 0.12
18 2 0.02
19 23 0.21
20 16 0.15
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (17 bp):
TACTTTATATATATACT
Found at i:3001024 original size:22 final size:20
Alignment explanation
Indices: 3000999--3001051 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
3000989 ATATACATAA
*
3000999 ACTTTATATTATATACTTATGT
1 ACTTTATATTATATAATTA--T
*
3001021 ACTTTAGTCTT-TATAATTAT
1 ACTTTA-TATTATATAATTAT
3001041 ACTTTATATTA
1 ACTTTATATTA
3001052 CACTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.12
20 7 0.27
22 13 0.50
23 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.55
Consensus pattern (20 bp):
ACTTTATATTATATAATTAT
Found at i:3001145 original size:48 final size:45
Alignment explanation
Indices: 3001032--3001146 Score: 110
Period size: 48 Copynumber: 2.5 Consensus size: 45
3001022 CTTTAGTCTT
* *
3001032 TATA-ATTATACTTTATATTACACTTTATATGTATATATAAGTTATA
1 TATATATTATA-TTTATA-TATACTTTATATGTATATATAAGCTATA
* *
3001078 -ATTTATCTATATATT-TATATACTTTATATTTAAATTATATAAGCTATA
1 TATATAT-TATAT-TTATATATACTTTATATGT--A-TATATAAGCTATA
3001126 TATATATTATATTTATATATA
1 TATATATTATATTTATATATA
3001147 TACAGAAGCT
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
45 14 0.25
46 5 0.09
47 9 0.16
48 23 0.41
49 5 0.09
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (45 bp):
TATATATTATATTTATATATACTTTATATGTATATATAAGCTATA
Found at i:3002015 original size:17 final size:17
Alignment explanation
Indices: 3001979--3002017 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3001969 GTGTAAAACT
*
3001979 GTTGACCATTGACCTAC
1 GTTGACCATTGACCGAC
* *
3001996 GTTGACCGTTGACCGGC
1 GTTGACCATTGACCGAC
3002013 GTTGA
1 GTTGA
3002018 GCACAGTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (17 bp):
GTTGACCATTGACCGAC
Found at i:3003359 original size:38 final size:38
Alignment explanation
Indices: 3003301--3003400 Score: 139
Period size: 38 Copynumber: 2.6 Consensus size: 38
3003291 TTGGCATTCA
* *
3003301 TGTTGCATTGCATGTTAAATAGTTAAATAATTAGTGTG
1 TGTTACATTGCATGTTAAATAGTTAAATAACTAGTGTG
* *
3003339 TGTTTA-TTTGCATGTTAAATAATTAAATAACTAGTGTG
1 TG-TTACATTGCATGTTAAATAGTTAAATAACTAGTGTG
*
3003377 TGTTACATTGCATGTTATATAGTT
1 TGTTACATTGCATGTTAAATAGTT
3003401 TGTATATTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 3 0.06
38 48 0.91
39 2 0.04
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (38 bp):
TGTTACATTGCATGTTAAATAGTTAAATAACTAGTGTG
Found at i:3004132 original size:82 final size:83
Alignment explanation
Indices: 3004000--3004161 Score: 260
Period size: 82 Copynumber: 2.0 Consensus size: 83
3003990 GTCCAAAAAT
*
3004000 GTATTAATTTAGGCTTTAAA-TTTTA-TTTATTTCAATTTGATCCTAAGAATTTTATAATTTAAT
1 GTATTAATTTAGGCTTTAAATTTTTATTTTATTTCAATTTGATCCTACGAATTTTATAATTTAAT
3004063 ATATATAACTATATA-AC
66 ATATATAACTATATATAC
* *
3004080 GTATTAATTTAGGCATTAAATTTTTATTTTATTTCAATTTGATCCTACGAATTTTACAATTTAAT
1 GTATTAATTTAGGCTTTAAATTTTTATTTTATTTCAATTTGATCCTACGAATTTTATAATTTAAT
3004145 ATATATATA-TATATATA
66 ATATATA-ACTATATATA
3004162 TATATTTATA
Statistics
Matches: 75, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
80 19 0.25
81 5 0.07
82 49 0.65
83 2 0.03
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.49
Consensus pattern (83 bp):
GTATTAATTTAGGCTTTAAATTTTTATTTTATTTCAATTTGATCCTACGAATTTTATAATTTAAT
ATATATAACTATATATAC
Found at i:3004178 original size:94 final size:95
Alignment explanation
Indices: 3004061--3004240 Score: 292
Period size: 95 Copynumber: 1.9 Consensus size: 95
3004051 TTATAATTTA
3004061 ATATATATAACTATATAACGTATTAATTTAGGCATTAAATTTTT-ATTTTATTTCAATTTGATCC
1 ATATATATAACTATATAACGTATTAATTTAGGCATTAAATTTTTAATTTTATTTCAATTTGATCC
3004125 TACGAATTTTACAATTTAATATATATATAT
66 TACGAATTTTACAATTTAATATATATATAT
* * * *
3004155 ATATATATATA-TTTATAATGTATTAATTTAGGCTTTAAATTTTTAATTTTATTTCAATTTGTTC
1 ATATATATA-ACTATATAACGTATTAATTTAGGCATTAAATTTTTAATTTTATTTCAATTTGATC
*
3004219 CTACGAATTTTATAATTTAATA
65 CTACGAATTTTACAATTTAATA
3004241 AATGTAACTC
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
94 39 0.49
95 40 0.51
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.51
Consensus pattern (95 bp):
ATATATATAACTATATAACGTATTAATTTAGGCATTAAATTTTTAATTTTATTTCAATTTGATCC
TACGAATTTTACAATTTAATATATATATAT
Found at i:3004321 original size:36 final size:33
Alignment explanation
Indices: 3004281--3004402 Score: 106
Period size: 34 Copynumber: 3.5 Consensus size: 33
3004271 CTCTGTATTG
3004281 TATATTT-ATATTATAGTTTAATACTTATATATACTT
1 TATATTTAATATTATA-TTT-ATACTT-TA-ATACTT
*
3004317 TATATTTAATATTTTTATTTATACTTTAATACTT
1 TATATTTAATA-TTATATTTATACTTTAATACTT
* *
3004351 TATATTTAATATATATATAGTT-TACTTT-ATAGTG
1 TATATTTAATAT-TATAT--TTATACTTTAATACTT
3004385 TATACTTTAATAGTTATA
1 TATA-TTTAATA-TTATA
3004403 ACTTATCTAT
Statistics
Matches: 75, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
33 1 0.01
34 29 0.39
35 19 0.25
36 16 0.21
37 6 0.08
38 4 0.05
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (33 bp):
TATATTTAATATTATATTTATACTTTAATACTT
Found at i:3004328 original size:7 final size:6
Alignment explanation
Indices: 3004276--3004368 Score: 57
Period size: 7 Copynumber: 14.5 Consensus size: 6
3004266 TAATACTCTG
*
3004276 TATTGTA TATTTA TA-TTA TAGTTTAA TACTTA TA--TA TACTTTA TATTTAA
1 TATT-TA TATTTA TATTTA TA-TTT-A TATTTA TATTTA TA-TTTA TATTT-A
* *
3004326 TATTTT TATTTA TACTTTAA TACTTTA TATTTAA TATATA TAT
1 TATTTA TATTTA TA-TTT-A TA-TTTA TATTT-A TATTTA TAT
3004369 AGTTTACTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
4 4 0.06
5 5 0.07
6 24 0.33
7 29 0.40
8 10 0.14
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (6 bp):
TATTTA
Found at i:3004339 original size:19 final size:21
Alignment explanation
Indices: 3004285--3004358 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
3004275 GTATTGTATA
*
3004285 TTTATA-TTATAGTTTAATAC
1 TTTATATTTATACTTTAATAC
3004305 TTATATATACTTTATA-TTTAATA-
1 -T-T-TATA-TTTATACTTTAATAC
*
3004328 TTTTTATTTATACTTTAATAC
1 TTTATATTTATACTTTAATAC
3004349 TTTATATTTA
1 TTTATATTTA
3004359 ATATATATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
19 6 0.13
20 10 0.22
21 11 0.24
22 2 0.04
23 4 0.09
24 7 0.16
25 5 0.11
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.59
Consensus pattern (21 bp):
TTTATATTTATACTTTAATAC
Found at i:3004339 original size:26 final size:27
Alignment explanation
Indices: 3004305--3004367 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 27
3004295 AGTTTAATAC
3004305 TTATATATACTTT-ATA-TTTAATATTT
1 TTATATATACTTTAATACTTT-ATATTT
*
3004331 TTATTTATACTTTAATACTTTATATTT
1 TTATATATACTTTAATACTTTATATTT
*
3004358 AATATATATA
1 -TTATATATA
3004368 TAGTTTACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 12 0.39
27 9 0.29
28 10 0.32
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (27 bp):
TTATATATACTTTAATACTTTATATTT
Found at i:3004416 original size:48 final size:47
Alignment explanation
Indices: 3004336--3004434 Score: 114
Period size: 48 Copynumber: 2.1 Consensus size: 47
3004326 TATTTTTATT
*
3004336 TATACTTTAATACTTTATATTTAATATATATATAGTTTACTTTATAG-TG
1 TATACTTTAATACTTTATACTTAATATATATATAG---ACTTTATAGTTG
* *
3004385 TATACTTTAATA-GTTATAACTT-ATCTATATATAGACTTTATAGTTG
1 TATACTTTAATACTTTAT-ACTTAATATATATATAGACTTTATAGTTG
3004431 TATA
1 TATA
3004435 TATACTTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
45 9 0.20
46 6 0.13
48 15 0.33
49 15 0.33
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (47 bp):
TATACTTTAATACTTTATACTTAATATATATATAGACTTTATAGTTG
Found at i:3004516 original size:23 final size:21
Alignment explanation
Indices: 3004476--3004518 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3004466 TTATAGATAA
3004476 TTATATAACTTATATTATAGT
1 TTATATAACTTATATTATAGT
3004497 TTATATATACTTATACTTATAG
1 TTATATA-ACTTATA-TTATAG
3004519 GATATATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (21 bp):
TTATATAACTTATATTATAGT
Found at i:3004524 original size:23 final size:21
Alignment explanation
Indices: 3004477--3004526 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
3004467 TATAGATAAT
**
3004477 TATATAACTTATATTATAGTT
1 TATATAACTTATATTATAGGA
3004498 TATATATACTTATACTTATAGGA
1 TATATA-ACTTATA-TTATAGGA
3004521 TATATA
1 TATATA
3004527 CTTTTAGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.24
22 7 0.28
23 12 0.48
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (21 bp):
TATATAACTTATATTATAGGA
Found at i:3004538 original size:21 final size:21
Alignment explanation
Indices: 3004499--3004538 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3004489 ATTATAGTTT
*
3004499 ATATATACTTATACTTATAGG
1 ATATATACTTATACGTATAGG
* *
3004520 ATATATACTTTTAGGTATA
1 ATATATACTTATACGTATA
3004539 TACTTATACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (21 bp):
ATATATACTTATACGTATAGG
Found at i:3004540 original size:14 final size:15
Alignment explanation
Indices: 3004508--3004546 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
3004498 TATATATACT
3004508 TATACTTATAGGATA
1 TATACTTATAGGATA
*
3004523 TATACTTTTAGG-TA
1 TATACTTATAGGATA
3004537 TATACTTATA
1 TATACTTATA
3004547 CTTATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (15 bp):
TATACTTATAGGATA
Found at i:3004554 original size:8 final size:7
Alignment explanation
Indices: 3004535--3005119 Score: 116
Period size: 6 Copynumber: 88.9 Consensus size: 7
3004525 TACTTTTAGG
3004535 TATATAC
1 TATATAC
3004542 T-TATAC
1 TATATAC
3004548 T-TATA-
1 TATATAC
3004553 TATATAC
1 TATATAC
* *
3004560 TTTCTA-
1 TATATAC
*
3004566 GATTATA-
1 TA-TATAC
3004573 TATATA-
1 TATATAC
3004579 TATATAC
1 TATATAC
3004586 T-TATAC
1 TATATAC
*
3004592 TTATATATT
1 -TATATA-C
3004601 TATATA-
1 TATATAC
*
3004607 TATTATAT
1 TA-TATAC
3004615 TATATAC
1 TATATAC
3004622 TTATATAC
1 -TATATAC
3004630 T-T-TAC
1 TATATAC
* *
3004635 TCT-T-T
1 TATATAC
*
3004640 TAAATAC
1 TATATAC
3004647 TTTATATA-
1 --TATATAC
*
3004655 TAAATAC
1 TATATAC
3004662 T-TATAC
1 TATATAC
*
3004668 TTCATATTAT
1 -T-ATA-TAC
3004678 TGATATA-
1 T-ATATAC
*
3004685 TATATTC
1 TATATAC
*
3004692 TTTATAC
1 TATATAC
*
3004699 TA-AAAC
1 TATATAC
3004705 T-TATA-
1 TATATAC
3004710 TATATA-
1 TATATAC
*
3004716 TATAGA-
1 TATATAC
3004722 TATATA-
1 TATATAC
*
3004728 TATATAT
1 TATATAC
3004735 TATATA-
1 TATATAC
3004741 TAT-TA-
1 TATATAC
3004746 TATATA-
1 TATATAC
*
3004752 TATATAT
1 TATATAC
*
3004759 TATATATG
1 TATATA-C
3004767 TATATAC
1 TATATAC
*
3004774 TTTTATAC
1 -TATATAC
*
3004782 TATATAGT
1 TATATA-C
3004790 TATATAC
1 TATATAC
* *
3004797 TTTATAT
1 TATATAC
3004804 TATATAC
1 TATATAC
3004811 -ATATAC
1 TATATAC
3004817 TATATAC
1 TATATAC
*
3004824 TTTAGT-C
1 TATA-TAC
* *
3004831 TTTATAA
1 TATATAC
*
3004838 T-TATAT
1 TATATAC
3004844 TATATA-
1 TATATAC
3004850 TATATA-
1 TATATAC
3004856 -ATATAC
1 TATATAC
3004862 T-TATAC
1 TATATAC
*
3004868 TTTTATTA-
1 -TATA-TAC
*
3004876 TATATAG
1 TATATAC
*
3004883 TTTATAC
1 TATATAC
* * *
3004890 GAAAAAC
1 TATATAC
*
3004897 TTTATAC
1 TATATAC
*
3004904 -ATACA-
1 TATATAC
*
3004909 TACATAC
1 TATATAC
3004916 ATATATA-
1 -TATATAC
3004923 TATATA-
1 TATATAC
3004929 TATATA-
1 TATATAC
3004935 TATATAC
1 TATATAC
* *
3004942 TTTATAG
1 TATATAC
*
3004949 TTTATA-
1 TATATAC
3004955 TATATAC
1 TATATAC
3004962 T-TATAC
1 TATATAC
3004968 T-T-TA-
1 TATATAC
*
3004972 TATATGC
1 TATATAC
3004979 TATATAC
1 TATATAC
* **
3004986 T-TTTTT
1 TATATAC
*
3004992 TATA-AT
1 TATATAC
3004998 TATATA-
1 TATATAC
3005004 TATATA-
1 TATATAC
3005010 T-TATA-
1 TATATAC
3005015 -ATATAC
1 TATATAC
3005021 T-TATAC
1 TATATAC
* *
3005027 TTTATAT
1 TATATAC
3005034 TATATAC
1 TATATAC
*
3005041 GTATATGC
1 -TATATAC
3005049 T-T-TA-
1 TATATAC
3005053 TATATA-
1 TATATAC
3005059 TATATA-
1 TATATAC
*
3005065 TATATAA
1 TATATAC
* *
3005072 TTTATAGT
1 TATATA-C
3005080 TATATA-
1 TATATAC
3005086 TATATAC
1 TATATAC
3005093 TTATATAC
1 -TATATAC
*
3005101 TTTATA-
1 TATATAC
* *
3005107 TTTAAAC
1 TATATAC
3005114 TATATA
1 TATATA
3005120 AACTATACAT
Statistics
Matches: 441, Mismatches: 76, Indels: 122
0.69 0.12 0.19
Matches are distributed among these distances:
4 2 0.00
5 30 0.07
6 194 0.44
7 135 0.31
8 65 0.15
9 13 0.03
10 2 0.00
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (7 bp):
TATATAC
Found at i:3005082 original size:29 final size:29
Alignment explanation
Indices: 3005050--3005106 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
3005040 CGTATATGCT
3005050 TTATATATATATA-TATATATAATTTATAG
1 TTATATATATATACT-TATATAATTTATAG
*
3005079 TTATATATATATACTTATATACTTTATA
1 TTATATATATATACTTATATAATTTATA
3005107 TTTAAACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (29 bp):
TTATATATATATACTTATATAATTTATAG
Found at i:3005099 original size:2 final size:2
Alignment explanation
Indices: 3004706--3005091 Score: 141
Period size: 2 Copynumber: 193.0 Consensus size: 2
3004696 TACTAAAACT
*
3004706 TA TA TA TA TA TA TA GA TA TA TA TA TA TA T- TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3004746 TA TA TA TA TA TA T- TA TA TA TG TA TA TA CT- TT TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA
* * * *
3004788 GT- TA TA TA CTT TA TA T- TA TA TA CA TA TA CTA TA TA CTT TA GTC
1 -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA -TA
*
3004831 TT TA TA -A T- TA TA T- TA TA TA TA TA TA -A TA TA CT- TA TA CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * * * * * *
3004869 TT TA T- TA TA TA TA GTT TA TA CGA AA AA CTT TA TA CA TA CA TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* * * *
3004911 CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA CTT TA TA GTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * * *
3004955 TA TA TA CT- TA TA CTT TA TA TA TGC TA TA TA CTT TT TT TA TA -A
1 TA TA TA -TA TA TA -TA TA TA TA T-A TA TA TA -TA TA TA TA TA TA
*
3004997 T- TA TA TA TA TA TA T- TA TA -A TA TA CT- TA TA CTT TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
** * * *
3005036 TA TA CG TA TA TGC TT TA TA TA TA TA TA TA TA TA TA -A TT TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3005078 GT- TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA
3005092 CTTATATACT
Statistics
Matches: 289, Mismatches: 51, Indels: 88
0.68 0.12 0.21
Matches are distributed among these distances:
1 22 0.08
2 244 0.84
3 23 0.08
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3005126 original size:29 final size:28
Alignment explanation
Indices: 3005056--3005126 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
3005046 TGCTTTATAT
*
3005056 ATATATATA-TATATAATTTATAGTTAT
1 ATATATATACTATATAATTTATAGTTAA
* *
3005083 ATATATATACTTATATACTTTATATTTAA
1 ATATATATAC-TATATAATTTATAGTTAA
*
3005112 ACTATATAAACTATA
1 A-TATATATACTATA
3005127 CATAGTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.24
29 20 0.54
30 8 0.22
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (28 bp):
ATATATATACTATATAATTTATAGTTAA
Found at i:3005147 original size:74 final size:75
Alignment explanation
Indices: 3004990--3005149 Score: 172
Period size: 74 Copynumber: 2.1 Consensus size: 75
3004980 ATATACTTTT
* * * *
3004990 TTTATAATTATATATATATATTATAATATACTTATACTTTATATTATATACGTATATGCTTTATA
1 TTTATAATTATATATATATATTATAATATACTTATACTTTATATTATAAACGTATATACTATACA
3005055 TATATATATA
66 TATATATATA
*
3005065 TATATAATT-TATAGT-TATA-TAT-ATATACTTATATACTTTATATT-TAAAC-TATATAAACT
1 TTTATAATTATATA-TATATATTATAATATAC-T-TATACTTTATATTATAAACGTATAT--ACT
3005124 ATACATAGTATATA-A
61 ATACATA-TATATATA
3005139 TTTATAATTAT
1 TTTATAATTAT
3005150 TCATAATATA
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
72 11 0.15
73 8 0.11
74 37 0.51
75 16 0.22
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (75 bp):
TTTATAATTATATATATATATTATAATATACTTATACTTTATATTATAAACGTATATACTATACA
TATATATATA
Found at i:3005278 original size:26 final size:26
Alignment explanation
Indices: 3005248--3005302 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
3005238 AATAATACAA
3005248 ATACAAATATAAAACTATATATA-TAT
1 ATACAAATAT-AAACTATATATATTAT
3005274 ATACAAATATAAACTATATATATTAT
1 ATACAAATATAAACTATATATATTAT
3005300 ATA
1 ATA
3005303 GTTATATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (26 bp):
ATACAAATATAAACTATATATATTAT
Found at i:3005301 original size:32 final size:31
Alignment explanation
Indices: 3005226--3005302 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
3005216 ATAAAATATG
*
3005226 TATATAGTATATAATAATACAAATACAAATA
1 TATATATTATATAATAATACAAATACAAATA
* * *
3005257 TA-AAACTATATATATATATACAAATATAAACTA
1 TATATATTATATA-ATA-ATACAAATACAAA-TA
3005290 TATATATTATATA
1 TATATATTATATA
3005303 GTTATATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
30 8 0.22
31 5 0.14
32 12 0.32
33 4 0.11
34 8 0.22
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.36
Consensus pattern (31 bp):
TATATATTATATAATAATACAAATACAAATA
Found at i:3005325 original size:41 final size:40
Alignment explanation
Indices: 3005263--3005341 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 40
3005253 AATATAAAAC
3005263 TATATATATATATACAAATATAAACTATATATATTATATAGT
1 TATATATATATATACAAATATAAACT-T-TATATTATATAGT
* *
3005305 TATATATGT-TATACATATATAAACTTTATATTATATA
1 TATATATATATATACAAATATAAACTTTATATTATATA
3005342 TCTTTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
39 11 0.31
40 1 0.03
41 15 0.43
42 8 0.23
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (40 bp):
TATATATATATATACAAATATAAACTTTATATTATATAGT
Found at i:3005492 original size:16 final size:18
Alignment explanation
Indices: 3005445--3005494 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
3005435 TATATACTTT
*
3005445 ACTTTATAGTTATATATA
1 ACTTTATACTTATATATA
** *
3005463 TGTTTATACATATATA-A
1 ACTTTATACTTATATATA
3005480 ACTTTATA-TTATATA
1 ACTTTATACTTATATA
3005495 CTTATATACT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
16 6 0.24
17 7 0.28
18 12 0.48
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (18 bp):
ACTTTATACTTATATATA
Found at i:3005509 original size:13 final size:13
Alignment explanation
Indices: 3005480--3005664 Score: 55
Period size: 13 Copynumber: 13.8 Consensus size: 13
3005470 ACATATATAA
*
3005480 ACTTTATATTATAT
1 ACTTTATACT-TAT
3005494 ACTTATATACTT-T
1 ACTT-TATACTTAT
*
3005507 ACTCTTAATAATTAT
1 ACT-TT-ATACTTAT
*
3005522 ACTTTATATTTAAT
1 ACTTTATACTT-AT
3005536 ACTTATATACTTTAT
1 ACTT-TATAC-TTAT
* *
3005551 ATTATTATATATATAT
1 ACT-TTATA-CT-TAT
* * *
3005567 ACTTCATACTAAA
1 ACTTTATACTTAT
**
3005580 AGGTTATA--TAT
1 ACTTTATACTTAT
*
3005591 A-TATATACTTTAT
1 ACTTTATAC-TTAT
*
3005604 AGTTTATA-TATAT
1 ACTTTATACT-TAT
3005617 ACTTT-TACTTTAT
1 ACTTTATAC-TTAT
*
3005630 AGTTTATA-TATAT
1 ACTTTATACT-TAT
*
3005643 A-TATATACTTAT
1 ACTTTATACTTAT
3005655 AC-TTATACTT
1 ACTTTATACTT
3005665 TTTATGTATA
Statistics
Matches: 127, Mismatches: 23, Indels: 44
0.65 0.12 0.23
Matches are distributed among these distances:
10 4 0.03
11 2 0.02
12 20 0.16
13 39 0.31
14 28 0.22
15 26 0.20
16 8 0.06
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (13 bp):
ACTTTATACTTAT
Found at i:3005550 original size:22 final size:20
Alignment explanation
Indices: 3005409--3005759 Score: 123
Period size: 20 Copynumber: 16.4 Consensus size: 20
3005399 ATACTAAAAG
3005409 TTTATATATATATAC-TTATA
1 TTTATAT-TATATACTTTATA
*
3005429 TTTATA-TATATACTTTA-C
1 TTTATATTATATACTTTATA
*
3005447 TTTATAGTTATATA---TATG
1 TTTATA-TTATATACTTTATA
*
3005465 TTTATACATATATAAACTTTATA
1 TTTAT--AT-TATATACTTTATA
*
3005488 TTATATACTTATATACTTTACTC
1 TT-TATA-TTATATACTTTA-TA
* *
3005511 TTAATAAT-TATACTTTATA
1 TTTATATTATATACTTTATA
3005530 TTTAATACTTATATACTTTATA
1 TTT-ATA-TTATATACTTTATA
3005552 TTATTATATATATATACTTCATACTAAAA
1 -T-TTATAT-TATATACTT--TA-T---A
3005581 GGTTATATATATATATACTTTATA
1 --TT-TATAT-TATATACTTTATA
3005605 GTTTATA-TATATACTTT-TA
1 -TTTATATTATATACTTTATA
3005624 CTTTATAGTTTATATA-TATATATA
1 -TTTATA--TTATATACT-T-TATA
* *
3005648 TACTTATACT-TATACTTTTTA
1 T--TTATATTATATACTTTATA
* * *
3005669 TGTATATATAAGTTATAATTTATC
1 T-T-TATATTA--TATACTTTATA
*
3005693 TATATACTTATATACTTTATA
1 TTTATA-TTATATACTTTATA
* ***
3005714 TTTAAATTATATAAGCTATA
1 TTTATATTATATACTTTATA
* *
3005734 TATATATTATATA-TATATA
1 TTTATATTATATACTTTATA
*
3005753 TATATAT
1 TTTATAT
3005760 ACATACATAC
Statistics
Matches: 256, Mismatches: 34, Indels: 83
0.69 0.09 0.22
Matches are distributed among these distances:
17 2 0.01
18 18 0.07
19 26 0.10
20 63 0.25
21 24 0.09
22 46 0.18
23 31 0.12
24 17 0.07
25 7 0.03
26 1 0.00
27 1 0.00
28 2 0.01
29 2 0.01
30 16 0.06
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (20 bp):
TTTATATTATATACTTTATA
Found at i:3005609 original size:7 final size:7
Alignment explanation
Indices: 3005594--3005665 Score: 57
Period size: 6 Copynumber: 11.1 Consensus size: 7
3005584 TATATATATA
3005594 TATACTT
1 TATACTT
*
3005601 TATAGTT
1 TATACTT
*
3005608 TATA-TA
1 TATACTT
3005614 TATACTT
1 TATACTT
3005621 T-TACTT
1 TATACTT
*
3005627 TATAGTT
1 TATACTT
*
3005634 TATA-TA
1 TATACTT
*
3005640 TATA-TA
1 TATACTT
3005646 TATAC-T
1 TATACTT
3005652 TATAC-T
1 TATACTT
3005658 TATACTT
1 TATACTT
3005665 T
1 T
3005666 TTATGTATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
6 33 0.60
7 22 0.40
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (7 bp):
TATACTT
Found at i:3005691 original size:81 final size:82
Alignment explanation
Indices: 3005514--3005726 Score: 240
Period size: 81 Copynumber: 2.6 Consensus size: 82
3005504 TTTACTCTTA
* *
3005514 ATAATTATACTTTATATTTAATACTTATATACTTTATA-TTAT-TATATATATATACTTCATACT
1 ATAATTATAATTTATATAT-ATACTTATATACTTTATATTTATATATATATATATACTTCATACT
*
3005577 AAAAGGTTATATATATAT
65 AAAACGTTATATATATAT
* *
3005595 ATACTTTATAGTTTATATATATACTT-T-TACTTTATAGTTTATATATATATATATACTT-ATAC
1 ATA-ATTATAATTTATATATATACTTATATACTTTATA-TTTATATATATATATATACTTCATAC
* * * * *
3005657 TTATACTTTTTATGTATAT
64 TAAAACGTTATATATATAT
* *
3005676 ATAAGTTATAATTTATCTATATACTTATATACTTTATATTTAAAT-TATATA
1 ATAA-TTATAATTTATATATATACTTATATACTTTATATTTATATATATATA
3005727 AGCTATATAT
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
79 9 0.08
80 1 0.01
81 58 0.52
82 35 0.31
83 9 0.08
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (82 bp):
ATAATTATAATTTATATATATACTTATATACTTTATATTTATATATATATATATACTTCATACTA
AAACGTTATATATATAT
Found at i:3005717 original size:6 final size:6
Alignment explanation
Indices: 3005588--3005759 Score: 51
Period size: 6 Copynumber: 26.8 Consensus size: 6
3005578 AAAGGTTATA
* * *
3005588 TATATA TATACTT TATAGTT TATATA TATACTT T-TACTT TATAGTT TATATA
1 TATATT TATA-TT TATA-TT TATATT TATA-TT TATA-TT TATA-TT TATATT
* * * * * * *
3005640 TATATA TATACT TATACT TATACTT TTTATG TATATA TA-AGT TATAATT
1 TATATT TATATT TATATT TATA-TT TATATT TATATT TATATT TAT-ATT
* * * ** *
3005689 TATCTA TATACTT ATATACTT TATATT TAAATT ATATAAGC TATATA TATATT
1 TATATT TATA-TT -TATA-TT TATATT TATATT -TAT-ATT TATATT TATATT
* *
3005742 ATATATA TATATA TATAT
1 -TATATT TATATT TATAT
3005760 ACATACATAC
Statistics
Matches: 127, Mismatches: 28, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
5 3 0.02
6 71 0.56
7 45 0.35
8 8 0.06
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (6 bp):
TATATT
Found at i:3005735 original size:2 final size:2
Alignment explanation
Indices: 3005730--3005760 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3005720 TTATATAAGC
3005730 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3005761 CATACATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3006620 original size:17 final size:17
Alignment explanation
Indices: 3006598--3006639 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
3006588 GTGTAAAACT
*
3006598 GTTGACCATTGACCTAC
1 GTTGACCATTGACCGAC
* *
3006615 GTTGACCGTTGACCGGC
1 GTTGACCATTGACCGAC
3006632 GTTGACCA
1 GTTGACCA
3006640 CAGTTGACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (17 bp):
GTTGACCATTGACCGAC
Found at i:3010268 original size:2 final size:2
Alignment explanation
Indices: 3010261--3010387 Score: 61
Period size: 2 Copynumber: 64.0 Consensus size: 2
3010251 TTATACATGG
* * * *
3010261 TA TA TA TA GTT TA TA CA TA -A TA TA CA TA TA T- TT TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
3010302 GTA TA TA -A CA -A TA TA AA TA TA AA CTA TA TA GTT TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* *
3010343 GTA TA TA -A TA -A TA TA AA TA TA AA CTA TA TA TA TA TA TA TA T-
1 -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
3010384 TA TA
1 TA TA
3010388 ATTGTTTCAA
Statistics
Matches: 95, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
1 7 0.07
2 80 0.84
3 8 0.08
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (2 bp):
TA
Found at i:3010284 original size:20 final size:20
Alignment explanation
Indices: 3010245--3010308 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
3010235 ATATAAACTC
*
3010245 TATATTTTATACATGGTATA
1 TATATTTTATACATAGTATA
* *
3010265 TATAGTTTATACATAATATACA
1 TATATTTTATACATAGTAT--A
*
3010287 TATATTTTATATATAGTATA
1 TATATTTTATACATAGTATA
3010307 TA
1 TA
3010309 ACAATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 19 0.53
22 17 0.47
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (20 bp):
TATATTTTATACATAGTATA
Found at i:3010339 original size:41 final size:40
Alignment explanation
Indices: 3010286--3010387 Score: 159
Period size: 41 Copynumber: 2.5 Consensus size: 40
3010276 CATAATATAC
3010286 ATATATTTTATATATAGTATATAACAATATAAATATAAACT
1 ATATA-TTTATATATAGTATATAACAATATAAATATAAACT
*
3010327 ATATAGTTTATATATAGTATATAATAATATAAATATAAACT
1 ATATA-TTTATATATAGTATATAACAATATAAATATAAACT
* *
3010368 ATATATATATATATATTATA
1 ATATATTTATATATAGTATA
3010388 ATTGTTTCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 13 0.23
41 44 0.77
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (40 bp):
ATATATTTATATATAGTATATAACAATATAAATATAAACT
Found at i:3010342 original size:11 final size:11
Alignment explanation
Indices: 3010326--3010383 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
3010316 AAATATAAAC
*
3010326 TATATAGTTTA
1 TATATAGTATA
3010337 TATATAGTATA
1 TATATAGTATA
*
3010348 TA-ATAATATA
1 TATATAGTATA
* *
3010358 AATATA-AACTA
1 TATATAGTA-TA
3010369 TATATA-TATA
1 TATATAGTATA
3010379 TATAT
1 TATAT
3010384 TATAATTGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 16 0.41
11 23 0.59
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (11 bp):
TATATAGTATA
Found at i:3011436 original size:2 final size:2
Alignment explanation
Indices: 3011378--3011421 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
3011368 AAATAAAAAT
3011378 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3011419 TA T
1 TA T
3011422 GAATGTCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3015717 original size:29 final size:28
Alignment explanation
Indices: 3015650--3015717 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
3015640 ATTCTCGATT
3015650 CTGCATGGGATTTTTCTCCGTTCTGACA
1 CTGCATGGGATTTTTCTCCGTTCTGACA
* *
3015678 CTGTATAGGATTTATTC-CTCGTTCTGACA
1 CTGCATGGGATTT-TTCTC-CGTTCTGACA
*
3015707 TTGCATGGGAT
1 CTGCATGGGAT
3015718 CAACTCCCCC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.40
Consensus pattern (28 bp):
CTGCATGGGATTTTTCTCCGTTCTGACA
Found at i:3027973 original size:45 final size:45
Alignment explanation
Indices: 3027901--3027989 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
3027891 CAAAAAGAAA
** * *
3027901 GATGATTGCAATCACAAGCTTATATAAAACGAGTTCGAACATAAG
1 GATGATTAAAATCACAAGCTTACATAAAACGAGTTCAAACATAAG
* *
3027946 GATGATTAAAATCACAAG-TTCACATAAAATGATTTCAAACATAA
1 GATGATTAAAATCACAAGCTT-ACATAAAACGAGTTCAAACATAA
3027990 AATTAAAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
44 2 0.05
45 35 0.95
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (45 bp):
GATGATTAAAATCACAAGCTTACATAAAACGAGTTCAAACATAAG
Found at i:3031150 original size:15 final size:14
Alignment explanation
Indices: 3031107--3031147 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
3031097 TTCGGTCACC
*
3031107 AACCGAACTGAATT
1 AACCGAACCGAATT
*
3031121 AACCATAACCGAATT
1 AACC-GAACCGAATT
3031136 AACCGAACCGAA
1 AACCGAACCGAA
3031148 ATTTATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.46, C:0.27, G:0.12, T:0.15
Consensus pattern (14 bp):
AACCGAACCGAATT
Found at i:3035318 original size:33 final size:33
Alignment explanation
Indices: 3035276--3035342 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
3035266 AGAGTGGTTA
*
3035276 GAGATGTTGAGATATCAGCTCGAGTCAGTTAGG
1 GAGAAGTTGAGATATCAGCTCGAGTCAGTTAGG
*
3035309 GAGAAGTTGAGATATCAGCTCGAGTCCGTTAGG
1 GAGAAGTTGAGATATCAGCTCGAGTCAGTTAGG
3035342 G
1 G
3035343 TTAACTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.34, T:0.25
Consensus pattern (33 bp):
GAGAAGTTGAGATATCAGCTCGAGTCAGTTAGG
Found at i:3043609 original size:12 final size:12
Alignment explanation
Indices: 3043592--3043618 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3043582 TTAATTGCGA
3043592 AAATTAAAATTT
1 AAATTAAAATTT
3043604 AAATTAAAATTT
1 AAATTAAAATTT
3043616 AAA
1 AAA
3043619 ACATTCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:3045113 original size:19 final size:19
Alignment explanation
Indices: 3045091--3045134 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3045081 TTAATAGAAT
*
3045091 TAATAATAATTAATAATGA
1 TAATAATAAATAATAATGA
* *
3045110 TAATAATAAATAATTATTA
1 TAATAATAAATAATAATGA
3045129 TAATAA
1 TAATAA
3045135 CATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAATAATAAATAATAATGA
Found at i:3045114 original size:16 final size:16
Alignment explanation
Indices: 3045093--3045134 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3045083 AATAGAATTA
*
3045093 ATAATAATTAATAATG
1 ATAATAATAAATAATG
*
3045109 ATAATAATAAATAATT
1 ATAATAATAAATAATG
*
3045125 ATTATAATAA
1 ATAATAATAA
3045135 CATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
ATAATAATAAATAATG
Found at i:3045499 original size:85 final size:84
Alignment explanation
Indices: 3045385--3045879 Score: 511
Period size: 83 Copynumber: 5.9 Consensus size: 84
3045375 CTCTTCAGTT
* * * * *
3045385 TTTTGGTGGCAGATAGCCCTTCTTGATTTAAGTTATGCTGCAAATGATGTGCATTTGAGCTGAGT
1 TTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTCGAGCTGAGT
*
3045450 GTAATCGAACTCGAGGGTC
66 GTAATCGAACTCGAAGGTC
* * * * * *
3045469 TTTTGGATGGCAGATAGCTCTTCTCGATTTAAGCTATGCTGCAAAT-ATTGTGCCTTTGAGCTGA
1 TTTTGG-TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA-TGTGCCTTCGAGCTGA
*
3045533 GTGTAATCGAAATCGAAGGTC
64 GTGTAATCGAACTCGAAGGTC
* * * * *
3045554 --TTGGTTGGTAGATAACCCTTCTAGCCCTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAA
1 TTTTGG-TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTCGAGCTGAG
* *
3045617 CGTAGTCGAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* * * * * * *
3045637 -TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAG
1 TTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTCG-AGCTGAG
**
3045701 TGTAATCGAACTCGGGGGTC
65 TGTAATCGAACTCGAAGGTC
* * * * *
3045721 --TT--TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTCGAGCTGAGT
* *
3045782 ATAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * * *
3045801 TTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAG
1 TTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTCG-AGCTGAG
3045866 TGTAATCGAACTCG
65 TGTAATCGAACTCG
3045880 GGGGTTTTTG
Statistics
Matches: 338, Mismatches: 63, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
80 22 0.07
81 40 0.12
82 2 0.01
83 111 0.33
84 75 0.22
85 88 0.26
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (84 bp):
TTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTCGAGCTGAGT
GTAATCGAACTCGAAGGTC
Found at i:3045862 original size:165 final size:165
Alignment explanation
Indices: 3045391--3045906 Score: 653
Period size: 165 Copynumber: 3.1 Consensus size: 165
3045381 AGTTTTTTGG
* * * * * *
3045391 TGGCAGATAGCCCTTCTTGATTTAAGTTATGCTGCAAATGATGTGCATTTGAGCTGAGTGTAATC
1 TGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* * * * * ** * * *
3045456 GAACTCGAGGGTCTTTTGGATGGCAGATAGCTCTTCTCGATTTAAGCTATGCTGCAAAT-ATTGT
66 GAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA-TGT
* * * **
3045520 GCCTTTG-AGCTGAGTGTAATCGAAATCGAAGGTCTTGGT
129 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-T--T
* * * * * *
3045559 TGGTAGATAACCCTTCTAGCCCTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTC
1 TGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* *
3045624 GAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGC
66 GAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
3045688 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
131 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
* *
3045723 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTC
1 TGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
3045788 GAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGC
66 GAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
*
3045853 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTTTT
131 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
*
3045888 TGGTAGATAG-CCTTCTCGA
1 TGGCAGATAGCCCTTCTCGA
3045907 GTTGGATATC
Statistics
Matches: 304, Mismatches: 41, Indels: 10
0.86 0.12 0.03
Matches are distributed among these distances:
164 80 0.26
165 91 0.30
166 37 0.12
167 30 0.10
168 66 0.22
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (165 bp):
TGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
Found at i:3046266 original size:106 final size:106
Alignment explanation
Indices: 3046082--3047072 Score: 1698
Period size: 106 Copynumber: 9.4 Consensus size: 106
3046072 GCATTGTTCC
* * * * * * *
3046082 GAGTCTAATATCATCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
3046147 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3046188 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
3046253 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3046294 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3046359 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3046400 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAGTTGAGAA-ATGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3046464 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3046505 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AGATATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3046569 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
3046610 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3046675 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3046716 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3046781 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3046822 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3046887 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3046928 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3046993 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3047034 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
3047073 CGAGTAAAAT
Statistics
Matches: 848, Mismatches: 35, Indels: 4
0.96 0.04 0.00
Matches are distributed among these distances:
104 1 0.00
105 199 0.23
106 648 0.76
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3050654 original size:12 final size:13
Alignment explanation
Indices: 3050637--3050665 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3050627 CTTAATTGCG
3050637 AAAATTAAAA-TT
1 AAAATTAAAATTT
3050649 AAAATTAAAATTT
1 AAAATTAAAATTT
3050662 AAAA
1 AAAA
3050666 CATTCGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:3052171 original size:17 final size:18
Alignment explanation
Indices: 3052138--3052182 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
3052128 TTAATAGAAT
3052138 TAATAATAATTAATAATGA
1 TAATAATAA-TAATAATGA
*
3052157 TAATAATAA-AATAATTA
1 TAATAATAATAATAATGA
*
3052174 TTATAATAA
1 TAATAATAA
3052183 CATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
19 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TAATAATAATAATAATGA
Done.