Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004234.1 Hibiscus syriacus cultivar Beakdansim tig00009277_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: 230063
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:629 original size:31 final size:30
Alignment explanation
Indices: 572--640 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
562 TAAAAAAATT
*
572 AAATTAAAAAATTAGAGTGATTAAATTAGAA
1 AAATTAAAAAATTAGAGTAATTAAATTA-AA
*
603 ATAATTTAAAAATTA-AGTAATTAAATTAAA
1 A-AATTAAAAAATTAGAGTAATTAAATTAAA
633 AAATTAAA
1 AAATTAAA
641 TTTCAATGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.18
30 3 0.09
31 13 0.38
32 12 0.35
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (30 bp):
AAATTAAAAAATTAGAGTAATTAAATTAAA
Found at i:2980 original size:113 final size:111
Alignment explanation
Indices: 2832--3048 Score: 337
Period size: 113 Copynumber: 1.9 Consensus size: 111
2822 CCATAACATG
* * *
2832 CTGCTATATTTTGATGGTTTATGTTCCTTTTCTCACAC-TGAATGAATTAGTCCATGCATGCACA
1 CTGCTATATTCTGATGGTGTATGTTCCTTTTCTCACACATGAATGAATAAGTCCATGCATGCAC-
* *
2896 AGAATGTCAACTACGAAACTGATTGATCATGTACAGATAGTCTGGAAGC
65 A-AATATC-ACTACGAAACTGATTGACCATGTACAGATAGTCTGGAAGC
2945 CTGCTATATTCTGATGGTGTATGTTCCTTTTCTCACACATGAATGAATAAGTCCATGCATGCACA
1 CTGCTATATTCTGATGGTGTATGTTCCTTTTCTCACACATGAATGAATAAGTCCATGCATGCACA
**
3010 AATATCACTATTAAACTGATTGACCATGTACAGATAGTC
66 AATATCACTACGAAACTGATTGACCATGTACAGATAGTC
3049 ACGGCAAACC
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
111 30 0.31
112 5 0.05
113 37 0.39
114 24 0.25
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (111 bp):
CTGCTATATTCTGATGGTGTATGTTCCTTTTCTCACACATGAATGAATAAGTCCATGCATGCACA
AATATCACTACGAAACTGATTGACCATGTACAGATAGTCTGGAAGC
Found at i:12035 original size:60 final size:60
Alignment explanation
Indices: 11931--12048 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
11921 ATGGGTCCTT
* *
11931 AAACTATAATTTTCATTTTAAATTAACCTTTAAACTTTTAAATATT-TCAATTTCATCCAA
1 AAACTATAAATCTCATTTTAAATTAACCTTTAAACTTTTAAATATTCT-AATTTCATCCAA
* * * *
11991 AAACTATAAATCTCATTTTAAATTAGTCC-TTCAATTTTTTAATATTCTAATTTCATCC
1 AAACTATAAATCTCATTTTAAATTA-ACCTTTAAACTTTTAAATATTCTAATTTCATCC
12049 CTACACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 47 0.94
61 3 0.06
ACGTcount: A:0.37, C:0.16, G:0.01, T:0.46
Consensus pattern (60 bp):
AAACTATAAATCTCATTTTAAATTAACCTTTAAACTTTTAAATATTCTAATTTCATCCAA
Found at i:12693 original size:44 final size:44
Alignment explanation
Indices: 12645--12752 Score: 191
Period size: 44 Copynumber: 2.5 Consensus size: 44
12635 TATCGTCTTA
12645 TAAAATTCATATTTCTCAATCTTTAATATAATCTTTCAGATAAC
1 TAAAATTCATATTTCTCAATCTTTAATATAATCTTTCAGATAAC
* *
12689 TAAAATTCATATTTCTCGATCTTTAATATAATCTTTTAGATAAC
1 TAAAATTCATATTTCTCAATCTTTAATATAATCTTTCAGATAAC
12733 TAAAATTCATA-TTCTCAATC
1 TAAAATTCATATTTCTCAATC
12753 ATAATGACTC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
43 8 0.13
44 53 0.87
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.44
Consensus pattern (44 bp):
TAAAATTCATATTTCTCAATCTTTAATATAATCTTTCAGATAAC
Found at i:17587 original size:2 final size:2
Alignment explanation
Indices: 17582--17606 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17572 TTTTTACAGT
17582 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17607 GACTATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18639 original size:11 final size:11
Alignment explanation
Indices: 18623--18653 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
18613 ATTTTTCAAT
*
18623 CCACCATCCGC
1 CCACCACCCGC
18634 CCACCACCCGC
1 CCACCACCCGC
18645 CCACCACCC
1 CCACCACCC
18654 ATGATAGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.71, G:0.06, T:0.03
Consensus pattern (11 bp):
CCACCACCCGC
Found at i:21541 original size:16 final size:16
Alignment explanation
Indices: 21520--21551 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21510 ACAATGTCAC
*
21520 ATCATACTTCTACAAT
1 ATCATACTTATACAAT
21536 ATCATACTTATACAAT
1 ATCATACTTATACAAT
21552 CTTTATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATACTTATACAAT
Found at i:24834 original size:124 final size:123
Alignment explanation
Indices: 24701--24927 Score: 328
Period size: 124 Copynumber: 1.8 Consensus size: 123
24691 GACCTATTTC
* * * * * * * *
24701 CTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGTTCTTCTTATTTTGAACTTCTTCTTTCTTT
1 CTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC-TTCCTC
* * *
24766 TTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTA
65 TTCAAATAAGTTCGTCTTATTATGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTA
* *
24825 CTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAATTTCTTCTTCCTCT
1 CTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
24890 TCAAATAAGTTCGTCTTATTATGAACTTTCTCTGGAAA
66 TCAAATAAGTTCGTCTTATTATGAACTTTCTCTGGAAA
24928 TGTTGATCCA
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
123 40 0.44
124 50 0.56
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (123 bp):
CTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
TCAAATAAGTTCGTCTTATTATGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTA
Found at i:25060 original size:113 final size:113
Alignment explanation
Indices: 24843--25367 Score: 759
Period size: 113 Copynumber: 4.7 Consensus size: 113
24833 ATAGAATTAT
* * * * * *
24843 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAATTTCTTCTTCC-TCTTCAAATAAGTTCGTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
24907 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
* * * *
24955 ACAAAAGGTTAAACAAGTTCTTCTCATTATGAATTTTTTCTTCCTTCTTCAGATGAATTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** * *
25020 ATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGGTTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
* *
25068 GCATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
25133 ATTATGAACTTTCTCTGGCAAAGCTAATCTATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
* * *
25181 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
25246 ATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
* *
25294 GCAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTT-CTCTCTTCAGATGAGTTCTTCT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCT-TCTTCAGATGAGTTCTTCT
25357 CATTATGAACT
65 CATTATGAACT
25368 CTAACTGACA
Statistics
Matches: 372, Mismatches: 39, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
111 2 0.01
112 99 0.27
113 271 0.73
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
Found at i:25389 original size:338 final size:342
Alignment explanation
Indices: 24723--25374 Score: 897
Period size: 338 Copynumber: 1.9 Consensus size: 342
24713 AGTCATTCAA
* * * * * * *
24723 AAGGTTGAATAAGTTCTTCTTATTTTGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTTATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
24788 TGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTACTTCTGTGATAGAATTATGCAAAAGGTT
66 TGAACTTTCTCTGGAAA----TATGCTAATCTATCTA---CAGTGATAGAATTATGCAAAAGGTT
* *
24853 GAACAAGCTCTTCTCATTGTGAATTTCTTCTTCCTCTTCAAATAAGTTCGTCTTATTATGAACTT
124 GAACAAACTCTTCTCATTATGAATTTCTTCTTCCTCTTCAAATAAGTTCGTCTTATTATGAACTT
* *
24918 TCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAGTTCTTCTCATT
189 TCTCTGGAAATGCTAATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAGTTCTTCTCATT
* *
24983 ATGAATTTTTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTAACTGGAAAAGCTGAT
254 ATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTAACTGGAAAAGCTGAT
25048 CCATCAAGTGATGGGTTTGAGCAT
319 CCATCAAGTGATGGGTTTGAGCAT
*
25072 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
25137 TGAACTTTCTCTGGCAA-A-GCTAATCTATC-A-AGTGATGGATTTGA-GCAAAAGGTTGAACAA
66 TGAACTTTCTCTGGAAATATGCTAATCTATCTACAGTGATAGAATT-ATGCAAAAGGTTGAACAA
* * * * *
25197 ATTCTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGAGTTCTTCTTATTATGAACTTTCTCT
130 ACTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAAATAAGTTCGTCTTATTATGAACTTTCTCT
* * * *
25262 GGCAAA-GCTAATCCATCAAGTGATGGATTTGAGCAAAA-GTTGAACAAGTTCTTCTTATTATGA
194 GG-AAATGCTAATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAGTTCTTCTCATTATGA
*
25325 ACTTCTTCTT-CTCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
258 ACTTCTTCTTCCT-TCTTCAGATGAATTCTTCTCATTATGAACTCTAACTG
25375 ACACTGTTGA
Statistics
Matches: 271, Mismatches: 28, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
337 2 0.01
338 117 0.43
339 63 0.23
340 3 0.01
342 1 0.00
343 11 0.04
344 1 0.00
349 73 0.27
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (342 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAATATGCTAATCTATCTACAGTGATAGAATTATGCAAAAGGTTGAACAAA
CTCTTCTCATTATGAATTTCTTCTTCCTCTTCAAATAAGTTCGTCTTATTATGAACTTTCTCTGG
AAATGCTAATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAA
GTGATGGGTTTGAGCAT
Found at i:25869 original size:95 final size:95
Alignment explanation
Indices: 25706--25899 Score: 370
Period size: 95 Copynumber: 2.0 Consensus size: 95
25696 ATGTTAATTA
25706 TGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGTTCTT
1 TGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGTTCTT
*
25771 TTAATACCGAGAAATCTTGAATTCTGATTC
66 TTAATACCGAGAAATCTTGAATTATGATTC
*
25801 TGATAACAACTCATCTGATTATGAAGTGATCTTTCAATATGATTTCACAGATATCGATAGTTCTT
1 TGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGTTCTT
25866 TTAATACCGAGAAATCTTGAATTATGATTC
66 TTAATACCGAGAAATCTTGAATTATGATTC
25896 TGAT
1 TGAT
25900 GAGGAGAATA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (95 bp):
TGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGTTCTT
TTAATACCGAGAAATCTTGAATTATGATTC
Found at i:26322 original size:92 final size:87
Alignment explanation
Indices: 26220--26454 Score: 302
Period size: 92 Copynumber: 2.7 Consensus size: 87
26210 GTTCTGGGTT
* * * *
26220 TTATATCAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATG-ATATTAGCACATTCCTC
1 TTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCA-ATGAGCACATTCCTC
26284 TTCCAAATTCAATAACTGGTTCTGTGG
65 TTCCAAATTC---AA-TGGTTCTGTGG
26311 TTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCAATGAGCACATTCCTC
1 TT-ATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCAATGAGCACATTCCTC
*
26376 TTCCAAATTCAAT-GAT-TGAT--
65 TTCCAAATTCAATGGTTCTG-TGG
* *
26396 TT-TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGAACATT
1 TTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCAATGAGCACATT
26455 ATTTGTTCCA
Statistics
Matches: 134, Mismatches: 7, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
83 55 0.41
85 2 0.01
86 2 0.01
87 3 0.02
88 1 0.01
89 2 0.01
91 2 0.01
92 66 0.49
93 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (87 bp):
TTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCAATGAGCACATTCCTCT
TCCAAATTCAATGGTTCTGTGG
Found at i:27685 original size:1 final size:1
Alignment explanation
Indices: 27681--27737 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
27671 TTGACCCCCC
* * * * * * *
27681 TTTTTTCTTTTTTCTTTCTTTTTTCTTTTTTTTTTCTTTCTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27738 CTCTTCAAGC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:27700 original size:11 final size:11
Alignment explanation
Indices: 27684--27742 Score: 82
Period size: 11 Copynumber: 5.2 Consensus size: 11
27674 ACCCCCCTTT
27684 TTTCTTTTTTC
1 TTTCTTTTTTC
27695 TTTCTTTTTTC
1 TTTCTTTTTTC
*
27706 TTTTTTTTTTC
1 TTTCTTTTTTC
*
27717 TTTCTTTTTTTT
1 TTTC-TTTTTTC
27729 TTTCTTTTTCTC
1 TTTCTTTTT-TC
27741 TT
1 TT
27743 CAAGCATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
11 29 0.69
12 13 0.31
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:27701 original size:18 final size:17
Alignment explanation
Indices: 27680--27742 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 17
27670 CTTGACCCCC
27680 CTTTTTTCTTTTTTCTTT
1 CTTTTTTCTTTTTT-TTT
27698 CTTTTTTCTTTTTTTTTT
1 CTTTTTTC-TTTTTTTTT
*
27716 CTTTCTT-TTTTTTTTT
1 CTTTTTTCTTTTTTTTT
27732 CTTTTTCTCTT
1 CTTTTT-TCTT
27743 CAAGCATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
16 14 0.35
17 1 0.03
18 19 0.47
19 6 0.15
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
CTTTTTTCTTTTTTTTT
Found at i:27716 original size:22 final size:21
Alignment explanation
Indices: 27681--27739 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 21
27671 TTGACCCCCC
*
27681 TTTTTTCTTTTTTCTTTCTTT
1 TTTTTTTTTTTTTCTTTCTTT
27702 TTTCTTTTTTTTTTCTTTCTTT
1 TTT-TTTTTTTTTTCTTTCTTT
27724 TTTTTTTTCTTTTTCT
1 TTTTTTTT-TTTTTCT
27740 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 8 0.23
22 27 0.77
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTTTTTTTTTTCTTTCTTT
Found at i:35091 original size:15 final size:15
Alignment explanation
Indices: 35068--35099 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35058 TGAAATGAAT
35068 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
35083 AATGCATGTATGCAA
1 AATGAATGTATGCAA
35098 AA
1 AA
35100 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:38406 original size:25 final size:22
Alignment explanation
Indices: 38378--38434 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
38368 ATGAAATATT
38378 AATAATATATATAAATACTATAAAA
1 AATAATATATAT--ATA-TATAAAA
*
38403 AATAATATGTATATATATAAAA
1 AATAATATATATATATATAAAA
*
38425 AAGAAT-TATA
1 AATAATATATA
38435 AATTAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 3 0.10
22 12 0.41
23 3 0.10
25 11 0.38
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
AATAATATATATATATATAAAA
Found at i:40446 original size:3 final size:3
Alignment explanation
Indices: 40423--40467 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
40413 TTGGGTTTTG
*
40423 TAA TAT TAA TAAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40468 ATTTTAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:41117 original size:9 final size:10
Alignment explanation
Indices: 41101--41146 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
41091 TAATTACAAG
41101 TAATTAAACT
1 TAATTAAACT
*
41111 T-ATTAAATT
1 TAATTAAACT
*
41120 TAATTAATAAT
1 TAATTAA-ACT
41131 TAATTAAAC-
1 TAATTAAACT
41140 TAATTAA
1 TAATTAA
41147 TGACCTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 15 0.48
10 7 0.23
11 9 0.29
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (10 bp):
TAATTAAACT
Found at i:46671 original size:11 final size:11
Alignment explanation
Indices: 46655--46684 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
46645 ACGTTCAAAG
46655 GAAACTGGAAA
1 GAAACTGGAAA
46666 GAAACTGGAAA
1 GAAACTGGAAA
46677 GAAACTGG
1 GAAACTGG
46685 GGGATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.30, T:0.10
Consensus pattern (11 bp):
GAAACTGGAAA
Found at i:48757 original size:21 final size:21
Alignment explanation
Indices: 48731--48783 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
48721 ATTCTGACTA
48731 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
48752 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
48773 TCGCAATGCGA
1 TCGCATTGCGA
48784 ATACGTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:48802 original size:20 final size:20
Alignment explanation
Indices: 48773--48845 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
48763 TTTTCCTAAT
48773 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
48793 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
48813 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
48833 TCGCAATGTGAAT
1 TCGCAATGCGAAT
48846 CTGACTATCG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:49419 original size:20 final size:20
Alignment explanation
Indices: 49390--49441 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
49380 TAGTTTCGAG
49390 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGCGGA
*
49410 AATGAGAATCGCAACGC-GA
1 AATGAAAATCGCAACGCGGA
**
49429 AACCAAAATCGCA
1 AATGAAAATCGCA
49442 TTGCGATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGGA
Found at i:49438 original size:19 final size:20
Alignment explanation
Indices: 49394--49441 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
49384 TTCGAGAATG
**
49394 AAAATCGCAACGCGGAAATG
1 AAAATCGCAACGCGGAAACC
*
49414 AGAATCGCAACGC-GAAACC
1 AAAATCGCAACGCGGAAACC
49433 AAAATCGCA
1 AAAATCGCA
49442 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAACC
Found at i:49459 original size:19 final size:19
Alignment explanation
Indices: 49437--49596 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
49427 GAAACCAAAA
*
49437 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
49456 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
49475 TCGCATTGCGATTCTCTCATTGCGATT
1 TCGCGTTGCGA---T-T--TT-C-ATT
*
49502 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
49522 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* ** *
49536 TCTCGTTGCGATAGTCCTT
1 TCGCGTTGCGATTTTCATT
49555 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
49575 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
49595 TC
1 TC
49597 AACCAAAAGA
Statistics
Matches: 113, Mismatches: 12, Indels: 32
0.72 0.08 0.20
Matches are distributed among these distances:
14 10 0.09
16 2 0.02
17 3 0.03
19 41 0.36
20 34 0.30
21 2 0.02
22 3 0.03
23 1 0.01
24 1 0.01
25 3 0.03
26 1 0.01
27 3 0.03
28 9 0.08
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:49531 original size:47 final size:51
Alignment explanation
Indices: 49457--49588 Score: 173
Period size: 47 Copynumber: 2.6 Consensus size: 51
49447 ATTTTCATTT
*
49457 CGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGAT-T-C-T-
1 CGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATATCCTTC
* *
49504 CTCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCCTTTC
1 CGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATA-TCC-TTC
*
49557 CGCGTTGCGATTTTCATTCTCTCGTTGCGATT
1 CGCGTTGCGATTTTCATT-TCGCGTTGCGATT
49589 TTCATTTCAA
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
47 41 0.56
49 1 0.01
50 1 0.01
52 1 0.01
53 17 0.23
54 12 0.16
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (51 bp):
CGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATATCCTTC
Found at i:49544 original size:14 final size:14
Alignment explanation
Indices: 49480--49547 Score: 73
Period size: 14 Copynumber: 4.5 Consensus size: 14
49470 TCATTTCGCA
*
49480 TTGCGATTCTCTCA
1 TTGCGATTCTCTCG
49494 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
49508 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
49527 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
49541 TTGCGAT
1 TTGCGAT
49548 AGTCCTTTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 30 0.65
16 3 0.07
17 3 0.07
19 10 0.22
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:50024 original size:12 final size:12
Alignment explanation
Indices: 49999--50035 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
49989 GCCCCGATTA
49999 CCCGAATACCCGG
1 CCCG-ATACCCGG
*
50012 CCCGATACTCGG
1 CCCGATACCCGG
50024 CCCGATACCCGG
1 CCCGATACCCGG
50036 GTATTCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.19, C:0.46, G:0.24, T:0.11
Consensus pattern (12 bp):
CCCGATACCCGG
Found at i:51682 original size:21 final size:21
Alignment explanation
Indices: 51656--51709 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
51646 AATTTAGATT
51656 TGTTACTAAATGTGAAATTAG
1 TGTTACTAAATGTGAAATTAG
51677 TGTTACTAAATGTGAAATTAG
1 TGTTACTAAATGTGAAATTAG
51698 TGTTACTAAATG
1 TGTTACTAAATG
51710 GTTAATATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.39
Consensus pattern (21 bp):
TGTTACTAAATGTGAAATTAG
Found at i:53342 original size:14 final size:14
Alignment explanation
Indices: 53323--53358 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
53313 ATTGTTTAAT
53323 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
53337 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
53351 TGATTTGT
1 TGATTTGT
53359 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:53523 original size:26 final size:25
Alignment explanation
Indices: 53483--53533 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
53473 GCGAAATGAA
*
53483 AATTGCAACGTGAAACTAAAATCGC
1 AATTGCAACGCGAAACTAAAATCGC
*
53508 AATTCGCAACGCGAAACTAAATTCGC
1 AATT-GCAACGCGAAACTAAAATCGC
53534 GTTGCGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.20
Consensus pattern (25 bp):
AATTGCAACGCGAAACTAAAATCGC
Found at i:53551 original size:19 final size:19
Alignment explanation
Indices: 53529--53679 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
53519 CGAAACTAAA
53529 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
53548 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
53563 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
53581 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
53596 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
53614 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
53629 -TCTCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
** **
53647 TTCGTATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
53666 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
53680 AGATATTAAG
Statistics
Matches: 92, Mismatches: 24, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 24 0.26
16 9 0.10
17 9 0.10
19 41 0.45
20 9 0.10
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:53575 original size:33 final size:33
Alignment explanation
Indices: 53533--53659 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
53523 ACTAAATTCG
* *
53533 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
53566 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
53599 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
53632 CGTTGCAATTTTCATTTCGTATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
53660 AGTCATTTCC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:53725 original size:20 final size:20
Alignment explanation
Indices: 53643--53725 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
53633 GTTGCAATTT
*
53643 TCATTT-CGTATTGCGATAG
1 TCATTTCCGTGTTGCGATAG
*
53662 TCATTTCCGCGTTGCGATAG
1 TCATTTCCGTGTTGCGATAG
**
53682 --ATATTAAGATGATTGCGA-ATG
1 TCAT-TTCCG-TG-TTGCGATA-G
53703 TCATTTCCGTGTTGCGATAG
1 TCATTTCCGTGTTGCGATAG
53723 TCA
1 TCA
53726 AATGAATACC
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
18 2 0.04
19 9 0.18
20 23 0.47
21 10 0.20
22 3 0.06
23 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
TCATTTCCGTGTTGCGATAG
Found at i:56230 original size:24 final size:24
Alignment explanation
Indices: 56196--56249 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
56186 CTGAAAAATC
56196 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
56220 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
56244 ATCAAA
1 ATCAAA
56250 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:56263 original size:24 final size:24
Alignment explanation
Indices: 56196--56263 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
56186 CTGAAAAATC
* * *
56196 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
56220 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
56244 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
56264 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:57134 original size:20 final size:20
Alignment explanation
Indices: 57111--57314 Score: 210
Period size: 21 Copynumber: 10.2 Consensus size: 20
57101 AGAATCTCGT
57111 TGCGATTTAC-TAAATCGCAA
1 TGCGA-TTACGTAAATCGCAA
57131 TGCGATTACGTAAATCG-AA
1 TGCGATTACGTAAATCGCAA
* * *
57150 GTGCGAATTAGGAAAATCGTAA
1 -TGCG-ATTACGTAAATCGCAA
57172 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
57192 TGCGAATTA-GTAAAATCGCAA
1 TGCG-ATTACGT-AAATCGCAA
57213 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
57233 TGCGAATTA-GTAAAATCGCAA
1 TGCG-ATTACGT-AAATCGCAA
57254 TGCGATTACGTAAAT--C--
1 TGCGATTACGTAAATCGCAA
*
57270 -GCGATTACGTAAATCGTAA
1 TGCGATTACGTAAATCGCAA
* *
57289 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
*
57310 CGCGA
1 TGCGA
57315 ATTTGGGAAA
Statistics
Matches: 158, Mismatches: 10, Indels: 32
0.79 0.05 0.16
Matches are distributed among these distances:
15 14 0.09
18 1 0.01
19 6 0.04
20 66 0.42
21 69 0.44
22 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:57174 original size:41 final size:41
Alignment explanation
Indices: 57122--57271 Score: 257
Period size: 41 Copynumber: 3.7 Consensus size: 41
57112 GCGATTTACT
57122 AAATCGCAATGCGATTACGTAAATCG-AAGTGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAA-TGCGAATTAGGA
* *
57163 AAATCGTAATGCGATTACGTAAATCGCAATGCGAATTAGTA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
*
57204 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGTA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
57245 AAATCGCAATGCGATTACGTAAATCGC
1 AAATCGCAATGCGATTACGTAAATCGC
57272 GATTACGTAA
Statistics
Matches: 105, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
41 103 0.98
42 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (41 bp):
AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
Found at i:57275 original size:15 final size:15
Alignment explanation
Indices: 57255--57285 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
57245 AAATCGCAAT
57255 GCGATTACGTAAATC
1 GCGATTACGTAAATC
57270 GCGATTACGTAAATC
1 GCGATTACGTAAATC
57285 G
1 G
57286 TAATGCGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (15 bp):
GCGATTACGTAAATC
Found at i:59582 original size:19 final size:19
Alignment explanation
Indices: 59536--59574 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
59526 GAGAGGAGTT
59536 GGGACAACTGATTGTGTCA
1 GGGACAACTGATTGTGTCA
59555 GGGACAACTGATTGTGTCA
1 GGGACAACTGATTGTGTCA
59574 G
1 G
59575 TGTCAACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (19 bp):
GGGACAACTGATTGTGTCA
Found at i:68072 original size:18 final size:18
Alignment explanation
Indices: 68049--68084 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
68039 GATGATAGCC
68049 GTTGGCTGGTTCAAGGAG
1 GTTGGCTGGTTCAAGGAG
68067 GTTGGCTGGTTCAAGGAG
1 GTTGGCTGGTTCAAGGAG
68085 ATGATTGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.44, T:0.28
Consensus pattern (18 bp):
GTTGGCTGGTTCAAGGAG
Found at i:72499 original size:35 final size:36
Alignment explanation
Indices: 72459--72529 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
72449 AAAAAACGTC
72459 TTATTGGTT-AAAGATAGTATTGTACATTCTCTTAA
1 TTATTGGTTAAAAGATAGTATTGTACATTCTCTTAA
72494 TTATTGGTTAAAAGATAGTATTGTACATTCTCTTAA
1 TTATTGGTTAAAAGATAGTATTGTACATTCTCTTAA
72530 AAAATTTAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 9 0.26
36 26 0.74
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.45
Consensus pattern (36 bp):
TTATTGGTTAAAAGATAGTATTGTACATTCTCTTAA
Found at i:74395 original size:14 final size:14
Alignment explanation
Indices: 74372--74410 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
74362 TAGATAATAT
*
74372 ATATTAAAAATTAA
1 ATATTTAAAATTAA
74386 ATATTTAAAATTAA
1 ATATTTAAAATTAA
*
74400 AAATATTAAAA
1 ATAT-TTAAAA
74411 AAAAATGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATTTAAAATTAA
Found at i:74649 original size:261 final size:268
Alignment explanation
Indices: 74184--74716 Score: 954
Period size: 261 Copynumber: 2.0 Consensus size: 268
74174 ATAATATTTG
*
74184 TTTGGCGTGGTGAAGGGAGGGCTCCAATTAGTAGAAAAAAACCCGCAACCCCTTGGGTATCCTGC
1 TTTGGCGTGGTGAAGGGAGGGCTCCAATTAGTAGAAAAAAACCCGCAACCCCTTGAGTATCCTGC
74249 ACTTGGAAAAAGTAGAAAAATAATAAATATAACGATAATTTGATTCTTCGTCGTCGTAGTAAATA
66 ACTTGGAAAAAGTAGAAAAATAATAAATATAACGATAATTTGATTCTTCGTCGTCGTAGTAAATA
*
74314 GGAGAGAAAATTTCTTTCTTCGTCTTTACAAAAATAAAAAACAAAAAATAGATAAT---ATATAT
131 GGAGAGAAAATTTCTTTCTTCGTCTTTACAAAAACAAAAAACAAAAAATAGATAATAGAATATAT
74376 -T-AAAAATTAAATATTTAAAATTAAAAATATT-AAAAAAAAATGGGCGAACGACGGGAATTGAA
196 ATAAAAAATTAAATATTTAAAATTAAAAATATTAAAAAAAAAATGGGCGAACGACGGGAATTGAA
74438 CCCGCGCA
261 CCCGCGCA
74446 TTTGGCGTGGTGAAGGGAGGGCTCCAATTAGTAG-AAAAAACCCGCAACCCCTTGAGTATCCTGC
1 TTTGGCGTGGTGAAGGGAGGGCTCCAATTAGTAGAAAAAAACCCGCAACCCCTTGAGTATCCTGC
74510 ACTTGGAAAAAGTAGAAAAATAATAAATATAACGATAATTTGATTCTTCGTCGTCGTAGTAAATA
66 ACTTGGAAAAAGTAGAAAAATAATAAATATAACGATAATTTGATTCTTCGTCGTCGTAGTAAATA
*
74575 GGAGAGAAAATTTCTTTCTTCGTCTTTACAAAAACAAAAAACCAAAAATAGATAATAGATAATAT
131 GGAGAGAAAATTTCTTTCTTCGTCTTTACAAAAACAAAAAACAAAAAATAGATAATAG--AATAT
*
74640 ATATTAAATAATTAAATATTTAAAATTAAAAATATTAAAAAAAAAATGGGCGAACGACGGGAATT
194 ATA-TAAAAAATTAAATATTTAAAATTAAAAATATTAAAAAAAAAATGGGCGAACGACGGGAATT
74705 GAACCCGCGCA
258 GAACCCGCGCA
74716 T
1 T
74717 GGTGGATGCG
Statistics
Matches: 258, Mismatches: 4, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
261 148 0.57
262 34 0.13
266 6 0.02
268 1 0.00
269 29 0.11
270 40 0.16
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (268 bp):
TTTGGCGTGGTGAAGGGAGGGCTCCAATTAGTAGAAAAAAACCCGCAACCCCTTGAGTATCCTGC
ACTTGGAAAAAGTAGAAAAATAATAAATATAACGATAATTTGATTCTTCGTCGTCGTAGTAAATA
GGAGAGAAAATTTCTTTCTTCGTCTTTACAAAAACAAAAAACAAAAAATAGATAATAGAATATAT
ATAAAAAATTAAATATTTAAAATTAAAAATATTAAAAAAAAAATGGGCGAACGACGGGAATTGAA
CCCGCGCA
Found at i:76367 original size:23 final size:23
Alignment explanation
Indices: 76341--76400 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
76331 AGAAGGAGAA
*
76341 AAATATGTCATAAAGACAAAAAT
1 AAATATGTCACAAAGACAAAAAT
* * *
76364 AAATGTGTCACAAAGGCAAAGAT
1 AAATATGTCACAAAGACAAAAAT
* *
76387 AAACAAGTCACAAA
1 AAATATGTCACAAA
76401 TGCAAAATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (23 bp):
AAATATGTCACAAAGACAAAAAT
Found at i:88457 original size:15 final size:15
Alignment explanation
Indices: 88437--88468 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
88427 AAAATCTTTC
*
88437 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
88452 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
88467 TT
1 TT
88469 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:93841 original size:30 final size:30
Alignment explanation
Indices: 93785--93841 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
93775 ATTTGGATTC
*
93785 AAATTTAATCAAAATTTTACTATAGTCCCT
1 AAATTTAATCAAAATTTTAATATAGTCCCT
* *
93815 AAATTTAATTAAAATTTTAATTTAGTC
1 AAATTTAATCAAAATTTTAATATAGTC
93842 ATTGGAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATTTAATCAAAATTTTAATATAGTCCCT
Found at i:98609 original size:20 final size:22
Alignment explanation
Indices: 98584--98641 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
98574 TTCCCCTTGA
98584 AGTGCATCGATGCATTC-TA-C
1 AGTGCATCGATGCATTCTTAGC
98604 AGTGCATCGATGCATTCTTTAGC
1 AGTGCATCGATGCATTC-TTAGC
98627 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
98642 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 2 0.06
23 2 0.06
24 13 0.38
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAGC
Found at i:98702 original size:64 final size:63
Alignment explanation
Indices: 98629--98769 Score: 178
Period size: 64 Copynumber: 2.2 Consensus size: 63
98619 TCTTTAGCAT
* *
98629 GTGCATCGATGCACTACC-CATGCATCAATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACT-CCTCATGCATCAATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
98692 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTACATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCAATACACAAATTACATTCGATGTTTCATCTTTAAAGA
98756 GTGCATCGATGCAC
1 GTGCATCGATGCAC
98770 ATTGAATATG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 21 0.31
64 47 0.69
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCAATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:99942 original size:14 final size:14
Alignment explanation
Indices: 99923--99955 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
99913 CTAATGAACT
99923 TGACGTCATAGACC
1 TGACGTCATAGACC
99937 TGACGTCATAGACC
1 TGACGTCATAGACC
99951 TGACG
1 TGACG
99956 CTCACACCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.21
Consensus pattern (14 bp):
TGACGTCATAGACC
Found at i:100472 original size:23 final size:24
Alignment explanation
Indices: 100445--100491 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
100435 AAACTTTCAT
*
100445 TAAATAAAATTAGTT-ATTTTACA
1 TAAATAAAACTAGTTGATTTTACA
* *
100468 TAAATTAAACTATTTGATTTTACA
1 TAAATAAAACTAGTTGATTTTACA
100492 AAACCTATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (24 bp):
TAAATAAAACTAGTTGATTTTACA
Found at i:101207 original size:18 final size:18
Alignment explanation
Indices: 101180--101214 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
101170 CCACTATAAA
101180 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
*
101198 ATGTCTCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
101215 GTAGACCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:101594 original size:20 final size:20
Alignment explanation
Indices: 101565--101602 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
101555 ATATTATTCA
*
101565 TTATGTCAATATCACATAAT
1 TTATGCCAATATCACATAAT
101585 TTATGCCAATATCACATA
1 TTATGCCAATATCACATA
101603 TGCTCATGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (20 bp):
TTATGCCAATATCACATAAT
Found at i:101809 original size:2 final size:2
Alignment explanation
Indices: 101802--101845 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
101792 TACGATATGC
101802 AT AT AT AT AT AT 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 AT AT AT AT AT AT
101844 AT
1 AT
101846 CAAAAAATCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104071 original size:31 final size:31
Alignment explanation
Indices: 104028--104100 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
104018 AGTTATTTCA
*
104028 GGGACTATATTGTAAACAAACTAAATATTGG
1 GGGACTATATTGTAAACAAACTAAATATTAG
* * *
104059 GGGATTATATTGTAAACAGACTAAATGTTAG
1 GGGACTATATTGTAAACAAACTAAATATTAG
*
104090 GGGACTGTATT
1 GGGACTATATT
104101 ACAAGTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (31 bp):
GGGACTATATTGTAAACAAACTAAATATTAG
Found at i:105061 original size:41 final size:41
Alignment explanation
Indices: 104943--105274 Score: 208
Period size: 41 Copynumber: 8.1 Consensus size: 41
104933 TTTTTCTTAA
* *
104943 AAATGCCGCTATAGAGTAGTACTTTAGTGCCGTTTTTATAC
1 AAATGCCGCAATAGAGTAGTACTTTAGTGGCGTTTTTATAC
* * * *
104984 AAACGCCGCAATAG-GT--TCATTTATAGCGGC-TTTTTTTCAAC
1 AAATGCCGCAATAGAGTAGT-ACTT-TAGTGGCGTTTTTAT--AC
* * *
105025 AAATGCCGCAACAGAGTAGTACTTTAGTGGCATTTTTATAT
1 AAATGCCGCAATAGAGTAGTACTTTAGTGGCGTTTTTATAC
* * *
105066 AAATGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
1 AAATGCCGCAATAGAGTAGTACTTTAGTGGCGTTTTTATAC
*** * * * *
105107 AAACATCGCTATAGACTAATACTTTAGTGGCGTTTTTATAT
1 AAATGCCGCAATAGAGTAGTACTTTAGTGGCGTTTTTATAC
* ** * * * * * *
105148 AAACGCCGTTATACAATTGTACTTTAGTGGCATTTGTGTTTAT
1 AAATGCCGCAATAGAGTAGTACTTTAGTGGCGTTT-T-TATAC
* * * * *
105191 AAACGCCGCTAA-AGACTTGTAATTTAGTGGCGTTTATATAC
1 AAATGCCGC-AATAGAGTAGTACTTTAGTGGCGTTTTTATAC
* * * * * *
105232 AAACGCCGCTATACACTTGTACTTTGGTGGCG-TTTTATAC
1 AAATGCCGCAATAGAGTAGTACTTTAGTGGCGTTTTTATAC
105272 AAA
1 AAA
105275 CACCGCAAAT
Statistics
Matches: 232, Mismatches: 47, Indels: 25
0.76 0.15 0.08
Matches are distributed among these distances:
38 1 0.00
39 9 0.04
40 18 0.08
41 153 0.66
42 9 0.04
43 40 0.17
44 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (41 bp):
AAATGCCGCAATAGAGTAGTACTTTAGTGGCGTTTTTATAC
Found at i:105102 original size:82 final size:81
Alignment explanation
Indices: 104939--105282 Score: 257
Period size: 82 Copynumber: 4.2 Consensus size: 81
104929 GCGTTTTTTC
* * * * * ***
104939 TTAA-AAATGCCGCTATAGAGTAGTACTTTAGTGCCGTTTTTATACAAACGCCGCAATAGGTTC-
1 TTAACAAACGCCGCAATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATACACTCG
* * *
105002 -ATTTATAGCGGCTTTTT
66 TACTT-TAGTGGC-GTTT
* * * * * * *
105019 TTCAACAAATGCCGCAACAGAGTAGTACTTTAGTGGCATTTTTATATAAATGCCGCTATAGACTC
1 TT-AACAAACGCCGCAATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATACACTC
105084 GTACTTTAGTGGCGTTT
65 GTACTTTAGTGGCGTTT
** * * * * * *
105101 TTATACAAACATCGCTATAGACTAATACTTTAGTGGCGTTTTTATATAAACGCCGTTATACAATT
1 TTA-ACAAACGCCGCAATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATACACTC
*
105166 GTACTTTAGTGGCATTTGT
65 GTACTTTAGTGGC-GTT-T
* * * * *
105185 GTTTATAAACGCCGCTAA-AGACTTGTAATTTAGTGGCGTTTATATACAAACGCCGCTATACACT
1 -TTAACAAACGCCGC-AATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATACACT
* *
105249 TGTACTTTGGTGGCG-TT
64 CGTACTTTAGTGGCGTTT
*
105266 TTATACAAACACCGCAA
1 TTA-ACAAACGCCGCAA
105283 ATTTATAATT
Statistics
Matches: 211, Mismatches: 43, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
80 6 0.03
81 13 0.06
82 117 0.55
83 8 0.04
84 64 0.30
85 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (81 bp):
TTAACAAACGCCGCAATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATACACTCG
TACTTTAGTGGCGTTT
Found at i:105242 original size:125 final size:122
Alignment explanation
Indices: 105043--105275 Score: 322
Period size: 125 Copynumber: 1.9 Consensus size: 122
105033 CAACAGAGTA
* * * *
105043 GTACTTTAGTGGCATTTTTATATAAATGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACA
1 GTACTTTAGTGGCATTTTTATATAAACGCCGCTAAAGACTCGTAATTTAGTGGCGTTTATATACA
* * *
105108 AACATCGCTATAGACTAATACTTTAGTGGCGTTTTTATATAAACGCCGTTATACAATT
66 AACACCGCTATACACTAATACTTTAGTGGCG-TTTTATACAAACGCCGTTATACAATT
* *
105166 GTACTTTAGTGGCATTTGTGTTTATAAACGCCGCTAAAGACTTGTAATTTAGTGGCGTTTATATA
1 GTACTTTAGTGGCATTT-T-TATATAAACGCCGCTAAAGACTCGTAATTTAGTGGCGTTTATATA
* ** *
105231 CAAACGCCGCTATACACTTGTACTTTGGTGGCGTTTTATACAAAC
64 CAAACACCGCTATACACTAATACTTTAGTGGCGTTTTATACAAAC
105276 ACCGCAAATT
Statistics
Matches: 95, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
123 17 0.18
124 12 0.13
125 66 0.69
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (122 bp):
GTACTTTAGTGGCATTTTTATATAAACGCCGCTAAAGACTCGTAATTTAGTGGCGTTTATATACA
AACACCGCTATACACTAATACTTTAGTGGCGTTTTATACAAACGCCGTTATACAATT
Found at i:107541 original size:43 final size:43
Alignment explanation
Indices: 107483--107712 Score: 212
Period size: 43 Copynumber: 5.6 Consensus size: 43
107473 AACGGAGTGC
* * *
107483 TAGATCTGACCTTTTGCGACGTTTGTATCCAAAAACGCTGCTA
1 TAGATCTGACATTTTGCGGCGTTTGTATCCAAAAACGCCGCTA
* *
107526 TAGATCTGACATTTTGCGTCGTTTGTATGCAAAAACGCCGCTA
1 TAGATCTGACATTTTGCGGCGTTTGTATCCAAAAACGCCGCTA
* * * * *
107569 TAGAACTG--A-----C--CTTTTGTATCAAAAAATGCTGCTA
1 TAGATCTGACATTTTGCGGCGTTTGTATCCAAAAACGCCGCTA
* *
107603 TAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAATGCCGCTA
1 TAGATCTGACATTTTGCGGCGTTTGTATCCAAAAACGCCGCTA
* * * *
107646 TAGATATGACATTTTTCGGCGTTTGT-TCTAAAAACGCCGCAA
1 TAGATCTGACATTTTGCGGCGTTTGTATCCAAAAACGCCGCTA
*
107688 TAGATCTTGATC-TATTGCGGCGTTT
1 TAGATC-TGA-CATTTTGCGGCGTTT
107713 TTTGTTCTCA
Statistics
Matches: 152, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
34 26 0.17
36 1 0.01
41 2 0.01
42 18 0.12
43 104 0.68
44 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (43 bp):
TAGATCTGACATTTTGCGGCGTTTGTATCCAAAAACGCCGCTA
Found at i:107594 original size:34 final size:34
Alignment explanation
Indices: 107547--107618 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
107537 TTTTGCGTCG
107547 TTTGTATGCAAAAACGCCGCTATAGAACTGACCT
1 TTTGTATGCAAAAACGCCGCTATAGAACTGACCT
* * *
107581 TTTGTAT-CAAAAAATGCTGCTATAGATCTGACCT
1 TTTGTATGC-AAAAACGCCGCTATAGAACTGACCT
107615 TTTG
1 TTTG
107619 CGGCGTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 1 0.03
34 33 0.97
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (34 bp):
TTTGTATGCAAAAACGCCGCTATAGAACTGACCT
Found at i:107636 original size:77 final size:77
Alignment explanation
Indices: 107504--107649 Score: 238
Period size: 77 Copynumber: 1.9 Consensus size: 77
107494 TTTTGCGACG
* * *
107504 TTTGTATCCAAAAACGCTGCTATAGATCTGACATTTTGCGTCGTTTGTATGCAAAAACGCCGCTA
1 TTTGTATCAAAAAACGCTGCTATAGATCTGACATTTTGCGGCGTTTGTATCCAAAAACGCCGCTA
107569 TAGAACTGACCT
66 TAGAACTGACCT
* * *
107581 TTTGTATCAAAAAATGCTGCTATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAATGCCGCTA
1 TTTGTATCAAAAAACGCTGCTATAGATCTGACATTTTGCGGCGTTTGTATCCAAAAACGCCGCTA
107646 TAGA
66 TAGA
107650 TATGACATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 63 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (77 bp):
TTTGTATCAAAAAACGCTGCTATAGATCTGACATTTTGCGGCGTTTGTATCCAAAAACGCCGCTA
TAGAACTGACCT
Found at i:110519 original size:20 final size:20
Alignment explanation
Indices: 110490--110532 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
110480 ATTTCACCAC
*
110490 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
110510 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
110530 ATG
1 ATG
110533 GGCTCTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:119783 original size:20 final size:20
Alignment explanation
Indices: 119754--119796 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
119744 ATTTCACCAC
*
119754 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
119774 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
119794 ATG
1 ATG
119797 GGCTCTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:120330 original size:31 final size:30
Alignment explanation
Indices: 120295--120352 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
120285 CTTTTAAAAC
120295 TTGCAATACAGTCCCCCAACATTTAGTCCGT
1 TTGCAATACAGT-CCCCAACATTTAGTCCGT
**
120326 TTGCAATATGGTCCCCAACATTTAGTC
1 TTGCAATACAGTCCCCAACATTTAGTC
120353 TGCTTACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (30 bp):
TTGCAATACAGTCCCCAACATTTAGTCCGT
Found at i:120344 original size:30 final size:30
Alignment explanation
Indices: 120308--120371 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
120298 CAATACAGTC
* *
120308 CCCCAACATTTAGTCCGTTTGCAATATGGT
1 CCCCAACATTTAGTCCGCTTACAATATGGT
*
120338 CCCCAACATTTAGTCTGCTTACAATATGGT
1 CCCCAACATTTAGTCCGCTTACAATATGGT
120368 CCCC
1 CCCC
120372 GAAGTAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (30 bp):
CCCCAACATTTAGTCCGCTTACAATATGGT
Found at i:120593 original size:12 final size:12
Alignment explanation
Indices: 120573--120648 Score: 71
Period size: 12 Copynumber: 5.8 Consensus size: 12
120563 GATAGATGAT
120573 ATAAATCTATTA
1 ATAAATCTATTA
*
120585 ATAATTCTATCTAAA
1 ATAAATCTAT-T--A
120600 ATAAATCTATTA
1 ATAAATCTATTA
*
120612 ATAATTCTATCTAA
1 ATAAATCTAT-T-A
120626 AGTAAATCTATTA
1 A-TAAATCTATTA
*
120639 ATAATTCTAT
1 ATAAATCTAT
120649 CTAAAGGTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
12 27 0.51
13 4 0.08
14 4 0.08
15 18 0.34
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (12 bp):
ATAAATCTATTA
Found at i:120654 original size:27 final size:27
Alignment explanation
Indices: 120574--120654 Score: 153
Period size: 27 Copynumber: 3.0 Consensus size: 27
120564 ATAGATGATA
*
120574 TAAATCTATTAATAATTCTATCTAAAA
1 TAAATCTATTAATAATTCTATCTAAAG
120601 TAAATCTATTAATAATTCTATCTAAAG
1 TAAATCTATTAATAATTCTATCTAAAG
120628 TAAATCTATTAATAATTCTATCTAAAG
1 TAAATCTATTAATAATTCTATCTAAAG
120655 GTTTTAGTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (27 bp):
TAAATCTATTAATAATTCTATCTAAAG
Found at i:130148 original size:15 final size:15
Alignment explanation
Indices: 130128--130157 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
130118 TCCCCCAATC
*
130128 ATTCTTATAATTATT
1 ATTCTTATAACTATT
130143 ATTCTTATAACTATT
1 ATTCTTATAACTATT
130158 TTTTGGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTCTTATAACTATT
Found at i:132711 original size:18 final size:17
Alignment explanation
Indices: 132684--132717 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
132674 GTTATGTAGT
132684 ATTAAATTATGGTTGTA
1 ATTAAATTATGGTTGTA
132701 ATTATAATTATGGTTGT
1 ATTA-AATTATGGTTGT
132718 GGTGTTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (17 bp):
ATTAAATTATGGTTGTA
Found at i:142853 original size:29 final size:30
Alignment explanation
Indices: 142798--142858 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
142788 CATTTCGAGT
* *
142798 AACGGAATGAAACGTTAGGCACCAAACTGG
1 AACGAAATGAAACGTTAGACACCAAACTGG
*
142828 AACGAAAT-AAACGTTAGACACTAAACTGG
1 AACGAAATGAAACGTTAGACACCAAACTGG
142857 AA
1 AA
142859 AACGGGCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (30 bp):
AACGAAATGAAACGTTAGACACCAAACTGG
Found at i:146359 original size:27 final size:28
Alignment explanation
Indices: 146319--146377 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
146309 TATTTGGTTA
* *
146319 TTATTAGAAAATCA-ACTTATTAGCATT
1 TTATTAGAAAATCATAATTATGAGCATT
* * *
146346 TTATTAGGAGATCATAATTATGAGTATT
1 TTATTAGAAAATCATAATTATGAGCATT
146374 TTAT
1 TTAT
146378 ACTATTAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (28 bp):
TTATTAGAAAATCATAATTATGAGCATT
Found at i:147412 original size:34 final size:34
Alignment explanation
Indices: 147349--147419 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
147339 TATTAATTAA
*
147349 CCTGAATTACATAAGATACAAAATGCACTCAAAC
1 CCTGAATTACATAAGATACAAAATACACTCAAAC
** * *
147383 CCTGAATTACATAAGATACGCATTACACTCTAAC
1 CCTGAATTACATAAGATACAAAATACACTCAAAC
147417 CCT
1 CCT
147420 CCTTGATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (34 bp):
CCTGAATTACATAAGATACAAAATACACTCAAAC
Found at i:154999 original size:271 final size:271
Alignment explanation
Indices: 154516--155057 Score: 1057
Period size: 271 Copynumber: 2.0 Consensus size: 271
154506 GCTTGCTTAG
154516 GGATCTCGATTCTATGTGGCTTGTTGGTGTAGGAGCTTAGAATCTGAGTTAGTGGTAGAGGAATT
1 GGATCTCGATTCTATGTGGCTTGTTGGTGTAGGAGCTTAGAATCTGAGTTAGTGGTAGAGGAATT
*
154581 TGGGTTCTTAGAGGTGTGTTTGGGTTAGGTGGTAAGTATAGCGTGGACCAAAGATTTAAATTGCG
66 TGGGTTCTTAGAGGTGTGTTTGGGTTAGGTGGTAAGTATAACGTGGACCAAAGATTTAAATTGCG
154646 GTTGCGTAATGTTAATTGGACCTTCAATTTGTTCATCCGAATGAAATCCGGTGTCAACACATATA
131 GTTGCGTAATGTTAATTGGACCTTCAATTTGTTCATCCGAATGAAATCCGGTGTCAACACATATA
* *
154711 TTGACTATTGACCCCTAGATCAAAATTGTTTGTAGTTTATAAAACCTTTTCTTAGCTGTTACATA
196 TTGACTATTGACCCCTAGATCAAAATTATTTGTAGTTTATAAAACCTTTTCTTAGCTGCTACATA
154776 AAGATACCCAT
261 AAGATACCCAT
154787 GGATCTCGATTCTATGTGGCTTGTTGGTGTAGGAGCTTAGAATCTGAGTTAGTGGTAGAGGAATT
1 GGATCTCGATTCTATGTGGCTTGTTGGTGTAGGAGCTTAGAATCTGAGTTAGTGGTAGAGGAATT
154852 TGGGTTCTTAGAGGTGTGTTTGGGTTAGGTGGTAAGTATAACGTGGACCAAAGATTTAAATTGCG
66 TGGGTTCTTAGAGGTGTGTTTGGGTTAGGTGGTAAGTATAACGTGGACCAAAGATTTAAATTGCG
154917 GTTGCGTAATGTTAATTGGACCTTCAATTTGTTCATCCGAATGAAATCCGGTGTCAACACATATA
131 GTTGCGTAATGTTAATTGGACCTTCAATTTGTTCATCCGAATGAAATCCGGTGTCAACACATATA
154982 TTGACTATTGACCCCTAGATCAAAATTATTTGTAGTTTATAAAACCTTTTCTTAGCTGCTACATA
196 TTGACTATTGACCCCTAGATCAAAATTATTTGTAGTTTATAAAACCTTTTCTTAGCTGCTACATA
155047 AAGATACCCAT
261 AAGATACCCAT
155058 AAATCAATAG
Statistics
Matches: 268, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
271 268 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (271 bp):
GGATCTCGATTCTATGTGGCTTGTTGGTGTAGGAGCTTAGAATCTGAGTTAGTGGTAGAGGAATT
TGGGTTCTTAGAGGTGTGTTTGGGTTAGGTGGTAAGTATAACGTGGACCAAAGATTTAAATTGCG
GTTGCGTAATGTTAATTGGACCTTCAATTTGTTCATCCGAATGAAATCCGGTGTCAACACATATA
TTGACTATTGACCCCTAGATCAAAATTATTTGTAGTTTATAAAACCTTTTCTTAGCTGCTACATA
AAGATACCCAT
Found at i:156192 original size:2 final size:2
Alignment explanation
Indices: 156180--156209 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
156170 CTACATAATA
*
156180 AT AT GT 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
156210 GATTATAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:163451 original size:18 final size:17
Alignment explanation
Indices: 163428--163464 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
163418 TTCATATACT
*
163428 TTAATTATCTTTTTTATA
1 TTAATTAT-TTTATTATA
163446 TTAATTATTTTATTATA
1 TTAATTATTTTATTATA
163463 TT
1 TT
163465 TTAAAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTAATTATTTTATTATA
Found at i:163960 original size:31 final size:33
Alignment explanation
Indices: 163925--164011 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 33
163915 AAACGTGTGT
*
163925 TTTTTAAAAACGATATTGAAAAC-AT-ATATAG
1 TTTTTAAAAACAATATTGAAAACTATAATATAG
* * * *
163956 TTTTTTAAAATAATTTTGAACACTTATAATATAG
1 TTTTTAAAAACAATATTGAAAAC-TATAATATAG
* *
163990 TTTTT-AAAATAATTTTGAAAAC
1 TTTTTAAAAACAATATTGAAAAC
164012 GTGTATAACT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 18 0.38
33 18 0.38
34 11 0.23
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.43
Consensus pattern (33 bp):
TTTTTAAAAACAATATTGAAAACTATAATATAG
Found at i:164008 original size:64 final size:64
Alignment explanation
Indices: 163940--164076 Score: 152
Period size: 64 Copynumber: 2.1 Consensus size: 64
163930 AAAAACGATA
** * * *
163940 TTGAAAACATATATAGTTTTTTAAAATAATTTTGAACACTTAT-A-ATATAGTTTTTAAAATAAT
1 TTGAAAACATATATA--ACTTTAAAACAATTTTGAAAACGTATAATATATAGTTTTTAAAATAAT
164003 T
64 T
* * * **
164004 TTGAAAACGTGTATAACTTTAAAACAGTTTTGAAAACGTATAATATATAGTTTTTAAAATGGTT
1 TTGAAAACATATATAACTTTAAAACAATTTTGAAAACGTATAATATATAGTTTTTAAAATAATT
164068 TTGAAAACA
1 TTGAAAACA
164077 GTTTTTTTCA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
62 20 0.33
63 1 0.02
64 39 0.65
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (64 bp):
TTGAAAACATATATAACTTTAAAACAATTTTGAAAACGTATAATATATAGTTTTTAAAATAATT
Found at i:164133 original size:31 final size:31
Alignment explanation
Indices: 164089--164175 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
164079 TTTTTTCAAA
*
164089 AATATATTA-ATATATTATATAGTTTTTGAG
1 AATATAATATATATATTATATAGTTTTTGAG
*
164119 AATATAATATATATATTATATAGTTTTCGAG
1 AATATAATATATATATTATATAGTTTTTGAG
*
164150 AATAT-A-ATATATATTATATAATTTTT
1 AATATAATATATATATTATATAGTTTTT
164176 ATTATTTATG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
29 18 0.35
30 9 0.17
31 25 0.48
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (31 bp):
AATATAATATATATATTATATAGTTTTTGAG
Found at i:164229 original size:15 final size:15
Alignment explanation
Indices: 164181--164231 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
164171 TTTTTATTAT
164181 TTATGTTATTTA-TTA
1 TTAT-TTATTTATTTA
*
164196 TTATTTTAGGTTATATTA
1 TTA-TTTA-TTTAT-TTA
164214 TTATTTATTTATTTA
1 TTATTTATTTATTTA
164229 TTA
1 TTA
164232 AATTTTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 12 0.40
16 8 0.27
17 4 0.13
18 6 0.20
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
TTATTTATTTATTTA
Found at i:164669 original size:189 final size:190
Alignment explanation
Indices: 164348--164695 Score: 495
Period size: 189 Copynumber: 1.8 Consensus size: 190
164338 ATAGAGTTTC
* * *
164348 ACAAATCAAGCTCAACGCTGCACCAGATCAACGACTGAGATCGAAGTAAAATAGGGTTGCAAACC
1 ACAAATCAAGCTCAACGCTGCACCAGATCAACGACTGAGATCGAAGAAAAATAGAGTTGCAAAAC
* * * *
164413 CCTAATCATATGAAGCCAAACACCGTACGAAAGGAAGCAAGTAGCACGAGTGAAGGCCACGCGCC
66 CCTAATCATATAAAGCCAAACACCGCACGAAAGGAAGCAAGCAGCACGAGTGAAGACCACGCGCC
*
164478 AACAAGTTGGCCGAAAC-TTTCGGTCGAACGCCTGGGACCAGCCTATATGCAAAATAGGG
131 AACAAGTTGGCCAAAACTTTTCGGTCGAACGCCTGGGACCAGCCTATATGCAAAATAGGG
* * *
164537 ACAAATCAAGCTCAATG-TAGCACCATATCAACGGCTGAGATCGAAGAAAAATAGAGTTGCAAAA
1 ACAAATCAAGCTCAACGCT-GCACCAGATCAACGACTGAGATCGAAGAAAAATAGAGTTGCAAAA
* * * * * * *
164601 CCTTAATCATATAAAGCCAAGCGCCGCACGAGAGGAAGTAAGCAGCACGCA-TGGAGACCACTCG
65 CCCTAATCATATAAAGCCAAACACCGCACGAAAGGAAGCAAGCAGCACG-AGTGAAGACCACGCG
164665 CCAACAAGTTGGCCAAAACTTTTCGGTCGAA
129 CCAACAAGTTGGCCAAAACTTTTCGGTCGAA
164696 TGCTTGGACT
Statistics
Matches: 138, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
188 1 0.01
189 125 0.91
190 12 0.09
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.16
Consensus pattern (190 bp):
ACAAATCAAGCTCAACGCTGCACCAGATCAACGACTGAGATCGAAGAAAAATAGAGTTGCAAAAC
CCTAATCATATAAAGCCAAACACCGCACGAAAGGAAGCAAGCAGCACGAGTGAAGACCACGCGCC
AACAAGTTGGCCAAAACTTTTCGGTCGAACGCCTGGGACCAGCCTATATGCAAAATAGGG
Found at i:166801 original size:30 final size:30
Alignment explanation
Indices: 166767--166826 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
166757 TATATAACAT
166767 GAATCCTATAAGAAAATTTTAATATTAAAC
1 GAATCCTATAAGAAAATTTTAATATTAAAC
*
166797 GAATCCTATAAGCAAATTTTAATATTAAAC
1 GAATCCTATAAGAAAATTTTAATATTAAAC
166827 TAAAATAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (30 bp):
GAATCCTATAAGAAAATTTTAATATTAAAC
Found at i:167285 original size:14 final size:15
Alignment explanation
Indices: 167266--167298 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
167256 TTTAATATTT
167266 AAATAAATAAT-TAA
1 AAATAAATAATATAA
167280 AAAT-AATAATATAA
1 AAATAAATAATATAA
167294 AAATA
1 AAATA
167299 CTAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAAATAATATAA
Found at i:170214 original size:60 final size:60
Alignment explanation
Indices: 170061--170215 Score: 159
Period size: 60 Copynumber: 2.6 Consensus size: 60
170051 TTTAGGGATA
* * ** * * *
170061 AAATTGAAATATTCAAAAGTTTGGGGACTAATTTAGAAAGAAGGTCATAATTTAGGGATG
1 AAATTAAAATATTTAAAAGTTTAAGGACTAATTTAGAAAGAAGATCATAATTTAAGAATG
* * * * * *
170121 AAATTATAATGTTTAAAAGCTCAATGACTAATTTAG-AATAAGATACATAATTTAAGAATG
1 AAATTAAAATATTTAAAAGTTTAAGGACTAATTTAGAAAGAAGAT-CATAATTTAAGAATG
* *
170181 AAATTAAAATATTTAAAAATTTAAGGACCAATTTA
1 AAATTAAAATATTTAAAAGTTTAAGGACTAATTTA
170216 AACTGAGGAT
Statistics
Matches: 74, Mismatches: 20, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
59 6 0.08
60 68 0.92
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (60 bp):
AAATTAAAATATTTAAAAGTTTAAGGACTAATTTAGAAAGAAGATCATAATTTAAGAATG
Found at i:171400 original size:67 final size:67
Alignment explanation
Indices: 171321--171456 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
171311 GCTTCTTTCT
*
171321 AAACGCGTCAAATGGTCAGAATATTTCTTACTAACATTATAACATTCATAATATTTTAACAAAAA
1 AAACGAGTCAAATGGTCAGAATATTTCTTACTAACATTATAACATTCATAATATTTTAACAAAAA
171386 AA
66 AA
171388 AAACGAGTCAAATGGTCAGAATATTTCTTACTAACATTATAACATTCATAATATTTTAACAAAAA
1 AAACGAGTCAAATGGTCAGAATATTTCTTACTAACATTATAACATTCATAATATTTTAACAAAAA
171453 AA
66 AA
171455 AA
1 AA
171457 TTCTGAGCCA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (67 bp):
AAACGAGTCAAATGGTCAGAATATTTCTTACTAACATTATAACATTCATAATATTTTAACAAAAA
AA
Found at i:177993 original size:23 final size:24
Alignment explanation
Indices: 177949--177993 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
177939 AGCTTTTCTT
*
177949 TTTTTTTTGTACGAACTTCTCTGG
1 TTTTTTTTGTACGAACTACTCTGG
177973 TTTTTTTT-TACCGAA-TACTCT
1 TTTTTTTTGTA-CGAACTACTCT
177994 CGTTCTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.56
Consensus pattern (24 bp):
TTTTTTTTGTACGAACTACTCTGG
Found at i:178586 original size:3 final size:3
Alignment explanation
Indices: 178578--178626 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
178568 ATGTAAATTA
* *
178578 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
178626 A
1 A
178627 TACAAAAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:179068 original size:122 final size:126
Alignment explanation
Indices: 178831--179139 Score: 371
Period size: 122 Copynumber: 2.4 Consensus size: 126
178821 GTGACATGGT
* *
178831 TCCTACGTGATGAGGAATCT-AGTC-GAGGGATGACACTGCTCATACATGATGAAGAGTTCTTGG
1 TCCTACGTGATGAGG-ATCTGA-TCTG-GGGATGACACGGCTCATAC--G-TGATGAGTTCTTGG
* *
178894 CCATCTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGGGGACGACTGGTTATCTATGGTTGAC
60 CCATCTTA-GAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTATGGTTGAC
178959 A-C
124 AGC
178961 TCCTACGTGATGAGGATCTGATCTGGGGAATGACACGGCTCATACGTGATGAGTTC-TGGCCATC
1 TCCTACGTGATGAGGATCTGATCTGGGG-ATGACACGGCTCATACGTGATGAGTTCTTGGCCATC
*
179025 -TA-AA-GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
65 TTAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTATGGTTGACA--GC
* * * * *
179086 TCCTACGTGATGAGGAGATCTGGTCTGGTGATGACACGGTTCCTACATGATGAG
1 TCCTACGTGATGA-G-GATCTGATCTGGGGATGACACGGCTCATACGTGATGAG
179140 GACGGCTGGC
Statistics
Matches: 161, Mismatches: 10, Indels: 20
0.84 0.05 0.10
Matches are distributed among these distances:
122 50 0.31
123 2 0.01
125 16 0.10
126 30 0.19
127 21 0.13
128 1 0.01
129 9 0.06
130 32 0.20
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (126 bp):
TCCTACGTGATGAGGATCTGATCTGGGGATGACACGGCTCATACGTGATGAGTTCTTGGCCATCT
TAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTATGGTTGACAGC
Found at i:179083 original size:43 final size:39
Alignment explanation
Indices: 179036--179148 Score: 122
Period size: 40 Copynumber: 2.8 Consensus size: 39
179026 AAAGGTGATA
179036 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT-TG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG---TC--TGGTATG
* *
179079 ACACGGCTCCTACGTGATGAGGA-GATCTGGTCTGGTGATG
1 ACACGGTTCCTACGTGATGAGGACG-GCTGGTCTGGT-ATG
*
179119 ACACGGTTCCTACATGATGAGGACGGCTGG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG
179149 CCATCTTTAG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
38 4 0.07
40 29 0.48
41 1 0.02
42 1 0.02
43 26 0.43
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (39 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGTCTGGTATG
Found at i:179322 original size:28 final size:28
Alignment explanation
Indices: 179290--179369 Score: 133
Period size: 28 Copynumber: 2.8 Consensus size: 28
179280 AGACAAAATT
179290 CGTTTTAAGGGAAACGACTCAAAGACGA
1 CGTTTTAAGGGAAACGACTCAAAGACGA
179318 CGTTTTAAGGGAAACGACTCAAAGACGA
1 CGTTTTAAGGGAAACGACTCAAAGACGA
* *
179346 CGTTTAAAGGGAAACTGTCTCAAA
1 CGTTTTAAGGGAAAC-GACTCAAA
179370 TGAGACAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 42 0.86
29 7 0.14
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (28 bp):
CGTTTTAAGGGAAACGACTCAAAGACGA
Found at i:179424 original size:92 final size:93
Alignment explanation
Indices: 179266--179435 Score: 220
Period size: 92 Copynumber: 1.8 Consensus size: 93
179256 TTTTAAAAGC
* *
179266 AACTGTCTCAAAAGAGACAAAATTCGTTTTAAGGGAAACGACTCAAAGACGACGTTTTAAGGGAA
1 AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGACGACGTTTTAAGAGAA
*
179331 AC-GACTCAAAGACGACGTTTAAAGGGA
66 ACAAACTCAAAGACGACGTTTAAAGGGA
* ** ** *
179358 AACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAATTGATCTCAAAGATTA-GTGTTT-CGAG
1 AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAACGA-CTCAAAGACGACGT-TTTAAGAG
179421 AAACAAACTCAAAGA
64 AAACAAACTCAAAGA
179436 TGTTTTTTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
92 45 0.68
93 21 0.32
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (93 bp):
AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGACGACGTTTTAAGAGAA
ACAAACTCAAAGACGACGTTTAAAGGGA
Found at i:179805 original size:15 final size:15
Alignment explanation
Indices: 179781--179824 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
179771 AAGATGATCT
*
179781 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
179796 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
179811 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
179825 CAAACTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:180009 original size:29 final size:28
Alignment explanation
Indices: 179972--180170 Score: 136
Period size: 29 Copynumber: 6.8 Consensus size: 28
179962 TCTCGAGAGA
*
179972 CAAA-ATTTTGTTTCAAAGGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
* ****
180000 CAAAGATTTTTTCCAAAAGAAATTGTCTT
1 CAAAGATTTTTTTCAAAAGAAACAAAC-T
* *
180029 TAAGAGATAAAATTTTGTTTCAAAAGAAACAGACT
1 CAA-AGAT----TTTT-T-TCAAAAGAAACAAACT
180064 CAAAGA--TTTTTCAAAAGAAAC-AACT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
* *
180089 CAAAGATATTTATTCAAAAGGAACAAACT
1 CAAAGAT-TTTTTTCAAAAGAAACAAACT
* * *
180118 CCAAGATTTTTATTCTAAAGGAACAAACT
1 CAAAGATTTTT-TTCAAAAGAAACAAACT
*
180147 CAAAGATTTTTTTTCAAGAGAAAC
1 CAAAGA-TTTTTTTCAAAAGAAAC
180171 TGTCTCAAGA
Statistics
Matches: 134, Mismatches: 22, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
25 9 0.07
26 11 0.08
27 1 0.01
28 34 0.25
29 48 0.36
30 9 0.07
34 7 0.05
35 4 0.03
36 11 0.08
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:180018 original size:63 final size:62
Alignment explanation
Indices: 179946--180083 Score: 197
Period size: 64 Copynumber: 2.2 Consensus size: 62
179936 AATGTGGGTA
* * *
179946 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGA-T
* * *
180008 TTTTCCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTT-CAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
180071 TTTTCAAAAGAAA
1 TTTTCAAAAGAAA
180084 CAACTCAAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
62 13 0.19
63 18 0.26
64 37 0.54
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (62 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:180822 original size:34 final size:35
Alignment explanation
Indices: 180784--180877 Score: 147
Period size: 34 Copynumber: 2.7 Consensus size: 35
180774 AAAGGGAAAA
**
180784 TGTCTCAAATGAGACAAAATTTGTTTG-AATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTGAAATAAAT
*
180818 TGTCTCAAGCGAGACAAAATGT-TTTGAAATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTGAAATAAAT
180852 TGTCTCAAGCGAGACAAAATTTGTTT
1 TGTCTCAAGCGAGACAAAATTTGTTT
180878 TTAGAAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
33 4 0.07
34 47 0.87
35 3 0.06
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTGAAATAAAT
Found at i:181237 original size:4 final size:4
Alignment explanation
Indices: 181228--181313 Score: 104
Period size: 4 Copynumber: 22.0 Consensus size: 4
181218 TTTATGTATC
* *
181228 ATGT ATGT A--T ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGG ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
181274 ATGT ATAT ATGT ATGT ATGT GTAT ACGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
181314 GTATATTCTT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.03
4 66 0.97
ACGTcount: A:0.28, C:0.01, G:0.23, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:181260 original size:20 final size:20
Alignment explanation
Indices: 181235--181319 Score: 116
Period size: 20 Copynumber: 4.2 Consensus size: 20
181225 ATCATGTATG
181235 TATATGTATGTATGTATGTA
1 TATATGTATGTATGTATGTA
*
181255 TATATGTATGTATGGATGTA
1 TATATGTATGTATGTATGTA
* * *
181275 TGTATATATGTATGTATGTG
1 TATATGTATGTATGTATGTA
* *
181295 TATACGTATGTATGTATGTG
1 TATATGTATGTATGTATGTA
181315 TATAT
1 TATAT
181320 TCTTCTCGAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.28, C:0.01, G:0.22, T:0.48
Consensus pattern (20 bp):
TATATGTATGTATGTATGTA
Found at i:182507 original size:12 final size:11
Alignment explanation
Indices: 182485--182605 Score: 66
Period size: 12 Copynumber: 10.5 Consensus size: 11
182475 TTTGTCCTCT
182485 TTTTGTTCTTTG
1 TTTT-TTCTTTG
182497 CTTTTTTCTTTG
1 -TTTTTTCTTTG
* *
182509 ACTTTTGCTTTG
1 -TTTTTTCTTTG
*
182521 -ATTTTCTTTG
1 TTTTTTCTTTG
*
182531 TTTTTGCTTTG
1 TTTTTTCTTTG
* *
182542 ATTTTTT-TCTC
1 -TTTTTTCTTTG
* **
182553 TCTGCTCTTTG
1 TTTTTTCTTTG
182564 TTTTTTTCTTTG
1 -TTTTTTCTTTG
182576 CTCTTTTCTCTTTG
1 -T-TTTT-TCTTTG
*
182590 ATTTTTCTTTG
1 TTTTTTCTTTG
182601 TTTTT
1 TTTTT
182606 GATTGGATCT
Statistics
Matches: 81, Mismatches: 21, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
10 11 0.14
11 22 0.27
12 34 0.42
13 8 0.10
14 6 0.07
ACGTcount: A:0.03, C:0.15, G:0.11, T:0.71
Consensus pattern (11 bp):
TTTTTTCTTTG
Found at i:182525 original size:11 final size:11
Alignment explanation
Indices: 182499--182546 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
182489 GTTCTTTGCT
*
182499 TTTTTCTTTGA
1 TTTTGCTTTGA
182510 CTTTTGCTTTGA
1 -TTTTGCTTTGA
*
182522 TTTT-CTTTGT
1 TTTTGCTTTGA
182532 TTTTGCTTTGA
1 TTTTGCTTTGA
182543 TTTT
1 TTTT
182547 TTTCTCTCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.28
11 13 0.41
12 10 0.31
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.71
Consensus pattern (11 bp):
TTTTGCTTTGA
Found at i:182537 original size:21 final size:22
Alignment explanation
Indices: 182502--182546 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
182492 CTTTGCTTTT
182502 TTCTTTGACTTTTGCTTTGATT
1 TTCTTTGACTTTTGCTTTGATT
*
182524 TTCTTTG-TTTTTGCTTTGATT
1 TTCTTTGACTTTTGCTTTGATT
182545 TT
1 TT
182547 TTTCTCTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.07, C:0.11, G:0.13, T:0.69
Consensus pattern (22 bp):
TTCTTTGACTTTTGCTTTGATT
Found at i:182577 original size:19 final size:22
Alignment explanation
Indices: 182537--182581 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
182527 TTTGTTTTTG
182537 CTTTGATTTTTTTCTCTCTGCT
1 CTTTGATTTTTTTCTCTCTGCT
182559 CTTTG-TTTTTTTCT-T-TGCT
1 CTTTGATTTTTTTCTCTCTGCT
182578 CTTT
1 CTTT
182582 TCTCTTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 1 0.04
21 9 0.39
22 5 0.22
ACGTcount: A:0.02, C:0.20, G:0.09, T:0.69
Consensus pattern (22 bp):
CTTTGATTTTTTTCTCTCTGCT
Found at i:183281 original size:26 final size:26
Alignment explanation
Indices: 183203--183284 Score: 86
Period size: 26 Copynumber: 3.4 Consensus size: 26
183193 TTTCAAAGTG
183203 GAAAGAATGTTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
**
183229 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
183250 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
183275 GATAGAATGT
1 GAAAGAATGT
183285 CAAAAATTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
20 13 0.30
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 22 0.51
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (26 bp):
GAAAGAATGTTTCAAGGTCTCAAAGA
Found at i:183283 original size:46 final size:45
Alignment explanation
Indices: 183191--183284 Score: 134
Period size: 46 Copynumber: 2.1 Consensus size: 45
183181 ATAAATACAG
* * *
183191 TGTTTCAAAGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAAGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
* *
183236 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAAGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
183282 TGT
1 TGT
183285 CAAAAATTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 10 0.23
46 33 0.77
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (45 bp):
TGTTTCAAAGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:188835 original size:23 final size:24
Alignment explanation
Indices: 188791--188835 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
188781 AGCTTTTTCT
*
188791 TTTTTTTTGTACGAACTTCTCTGG
1 TTTTTTTTGTACGAACTACTCTGG
188815 TTTTTTTT-TACCGAA-TACTCT
1 TTTTTTTTGTA-CGAACTACTCT
188836 CTCGTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.56
Consensus pattern (24 bp):
TTTTTTTTGTACGAACTACTCTGG
Found at i:189436 original size:3 final size:3
Alignment explanation
Indices: 189428--189476 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
189418 ATGTAAATTA
* * *
189428 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAC GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
189476 A
1 A
189477 TACAAAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:190119 original size:14 final size:15
Alignment explanation
Indices: 190100--190128 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
190090 TCCTAGATTT
190100 TATTATTT-TTATTA
1 TATTATTTGTTATTA
190114 TATTATTTGTTATTA
1 TATTATTTGTTATTA
190129 GTTTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTATTTGTTATTA
Found at i:201766 original size:106 final size:106
Alignment explanation
Indices: 201582--202851 Score: 1982
Period size: 106 Copynumber: 12.0 Consensus size: 106
201572 GCATTGTTCC
* * * * *
201582 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * *
201646 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
201688 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
201753 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
201794 GAGTCCAATATTTTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
201859 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
201900 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAACTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
201965 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
202006 GAGTCCAATATCCTTCAC--T----TTGAAATTGGCTCTGAAATTGTGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
202065 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
202106 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
202171 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
202212 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
202277 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
202318 GAGTCCAATATCCTTCGCTGTGAATTTGAAATTGGATCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
202383 CTAGCGGTCCCTTCATCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
202424 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
202489 CTAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
202530 GAGTCCAATATCCTTCGCTGTGAAGTTGAAGTTGGCTCTGAAATTAGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
202595 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
202636 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
202701 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
202742 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
202807 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
202848 GAGT
1 GAGT
202852 GTTACGATAT
Statistics
Matches: 1082, Mismatches: 73, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
100 92 0.09
102 1 0.00
104 1 0.00
105 1 0.00
106 985 0.91
107 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:204477 original size:15 final size:15
Alignment explanation
Indices: 204457--204509 Score: 70
Period size: 15 Copynumber: 3.3 Consensus size: 15
204447 TTTTTTTTTA
204457 TTTTTGTTCTTTCTT
1 TTTTTGTTCTTTCTT
204472 TTTTTGTTCTTTCTTCT
1 TTTTTGTTCTTTC-T-T
204489 TTTTTGCTTCTTTTCTT
1 TTTTTG-TTC-TTTCTT
204506 TTTT
1 TTTT
204510 GTTTTTGCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 13 0.38
16 1 0.03
17 12 0.35
18 4 0.12
19 4 0.12
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (15 bp):
TTTTTGTTCTTTCTT
Found at i:204488 original size:22 final size:21
Alignment explanation
Indices: 204449--204490 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
204439 TTTGTCCATT
*
204449 TTTTTTTATTTTTGTTCTTTC
1 TTTTTTTATTTTTCTTCTTTC
*
204470 TTTTTTTGTTCTTTCTTCTTT
1 TTTTTTTATT-TTTCTTCTTT
204491 TTTGCTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (21 bp):
TTTTTTTATTTTTCTTCTTTC
Found at i:208940 original size:5 final size:5
Alignment explanation
Indices: 208930--208964 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
208920 TGAAACAAAT
208930 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
208965 TGAAGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:209086 original size:26 final size:26
Alignment explanation
Indices: 209068--209121 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
209058 TAATGAAAAT
*
209068 AAATAAATAATATAAATAAAATAATA
1 AAATAAAAAATATAAATAAAATAATA
*
209094 AAATAAAAAATATATA-AAAAT-ATA
1 AAATAAAAAATATAAATAAAATAATA
209118 AAAT
1 AAAT
209122 GTATGTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 7 0.27
25 5 0.19
26 14 0.54
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (26 bp):
AAATAAAAAATATAAATAAAATAATA
Found at i:209113 original size:17 final size:16
Alignment explanation
Indices: 209050--209121 Score: 69
Period size: 17 Copynumber: 4.5 Consensus size: 16
209040 GCAAAGAAAC
*
209050 TAAAAACATAATGAAAA
1 TAAAAA-ATAATAAAAA
*
209067 TAAATAAATAATATAAA
1 TAAA-AAATAATAAAAA
209084 T--AAAATAAT-AAAA
1 TAAAAAATAATAAAAA
209097 TAAAAAATATATAAAAA
1 TAAAAAATA-ATAAAAA
*
209114 TATAAAAT
1 TAAAAAAT
209122 GTATGTATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
13 4 0.09
14 7 0.15
15 7 0.15
16 2 0.04
17 24 0.52
18 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (16 bp):
TAAAAAATAATAAAAA
Found at i:209432 original size:2 final size:2
Alignment explanation
Indices: 209425--209457 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
209415 ATATAATTAA
*
209425 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
209458 AATAAGGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:215246 original size:6 final size:6
Alignment explanation
Indices: 215228--215257 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
215218 GAATAAATTT
215228 ATTAAA TATTAAA ATTAAA ATTAAA ATTAA
1 ATTAAA -ATTAAA ATTAAA ATTAAA ATTAA
215258 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTAAA
Found at i:227114 original size:29 final size:29
Alignment explanation
Indices: 227072--227130 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
227062 TTATCTTCTT
227072 TAATTATCTTTCCCAACTTTGATAGTTGC
1 TAATTATCTTTCCCAACTTTGATAGTTGC
*
227101 TAATTATTTTTCCCAACTTTGATAGTTGC
1 TAATTATCTTTCCCAACTTTGATAGTTGC
227130 T
1 T
227131 GATGTATGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (29 bp):
TAATTATCTTTCCCAACTTTGATAGTTGC
Done.