Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000186.1 Hibiscus syriacus cultivar Beakdansim tig00000329_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: 3152351
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 14 of 17
Found at i:2445930 original size:84 final size:84
Alignment explanation
Indices: 2445812--2445981 Score: 243
Period size: 84 Copynumber: 2.0 Consensus size: 84
2445802 GAGTCGGCTA
* * * *
2445812 GAGGTGATGGATCTCGGTGTTAAGGTGTATAATCGACTCGATAAGGTGATAAATCTCGGTGTCAA
1 GAGGTGATGGATCTCAGTGTGAAGGTGGAGAATCGACTCGATAAGGTGATAAATCTCGGTGTCAA
*
2445877 AGTGGAGAATCGACTCGAT
66 AGTGGAGAATCAACTCGAT
* * **
2445896 GAGGTGATGGATCTCAGTGTCGAA-GTGGAGAATCGACTCGATGAGGTGATGAATCTCGGTGTTG
1 GAGGTGATGGATCTCAGTGT-GAAGGTGGAGAATCGACTCGATAAGGTGATAAATCTCGGTGTCA
2445960 AAGTGGAGAATCAACTCGAT
65 AAGTGGAGAATCAACTCGAT
2445980 GA
1 GA
2445982 AAAAGTAAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
84 74 0.97
85 2 0.03
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.26
Consensus pattern (84 bp):
GAGGTGATGGATCTCAGTGTGAAGGTGGAGAATCGACTCGATAAGGTGATAAATCTCGGTGTCAA
AGTGGAGAATCAACTCGAT
Found at i:2445949 original size:21 final size:21
Alignment explanation
Indices: 2445883--2445950 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
2445873 TCAAAGTGGA
2445883 GAATCGACTCGATGAGGTGAT
1 GAATCGACTCGATGAGGTGAT
* * * *
2445904 GGATCTCAGT-G-TCGAAGTGGA-
1 GAATC-GACTCGAT-GAGGT-GAT
2445925 GAATCGACTCGATGAGGTGAT
1 GAATCGACTCGATGAGGTGAT
2445946 GAATC
1 GAATC
2445951 TCGGTGTTGA
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
20 5 0.15
21 23 0.70
22 5 0.15
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.24
Consensus pattern (21 bp):
GAATCGACTCGATGAGGTGAT
Found at i:2447362 original size:14 final size:14
Alignment explanation
Indices: 2447343--2447400 Score: 107
Period size: 14 Copynumber: 4.1 Consensus size: 14
2447333 AAAATTAAAT
2447343 TCGCAACACGAAAA
1 TCGCAACACGAAAA
2447357 TCGCAACACGAAAA
1 TCGCAACACGAAAA
2447371 TCGCAACACGAAAA
1 TCGCAACACGAAAA
*
2447385 TCGCAACTCGAAAA
1 TCGCAACACGAAAA
2447399 TC
1 TC
2447401 AAAATTCGCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.47, C:0.29, G:0.14, T:0.10
Consensus pattern (14 bp):
TCGCAACACGAAAA
Found at i:2447412 original size:35 final size:34
Alignment explanation
Indices: 2447367--2447434 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 34
2447357 TCGCAACACG
*
2447367 AAAATCGCAACACGAAAATCGCAACTCGAAAATC
1 AAAATCGCAACACAAAAATCGCAACTCGAAAATC
* *
2447401 AAAATTCGCAACACAAAAATTGTAACTCGAAAAT
1 AAAA-TCGCAACACAAAAATCGCAACTCGAAAAT
2447435 GAAATTTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 4 0.13
35 26 0.87
ACGTcount: A:0.51, C:0.22, G:0.10, T:0.16
Consensus pattern (34 bp):
AAAATCGCAACACAAAAATCGCAACTCGAAAATC
Found at i:2447419 original size:21 final size:20
Alignment explanation
Indices: 2447381--2447420 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2447371 TCGCAACACG
* *
2447381 AAAATCGCAACTCGAAAATC
1 AAAATCGCAACACAAAAATC
2447401 AAAATTCGCAACACAAAAAT
1 AAAA-TCGCAACACAAAAAT
2447421 TGTAACTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.23, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACAAAAATC
Found at i:2447503 original size:20 final size:20
Alignment explanation
Indices: 2447480--2447537 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2447470 AATTTCTTTA
2447480 TCGAGTTGCGATTTTCGTTT
1 TCGAGTTGCGATTTTCGTTT
* *
2447500 TCGAGTTGCGAATTTCATTT
1 TCGAGTTGCGATTTTCGTTT
*
2447520 TCAAGTTGCGATTTTCGT
1 TCGAGTTGCGATTTTCGT
2447538 GTTATGAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.47
Consensus pattern (20 bp):
TCGAGTTGCGATTTTCGTTT
Found at i:2447512 original size:40 final size:35
Alignment explanation
Indices: 2447467--2447582 Score: 130
Period size: 34 Copynumber: 3.2 Consensus size: 35
2447457 AATTCGTAAC
*
2447467 TCGAATTTC-TTTATCGAGTTGCGATTTTCGTTTTCGA
1 TCGAATTTCATTT-TCGAGTTGCGATTTTCGTGTT--A
*
2447504 GTTGCGAATTTCATTTTCAAGTTGCGATTTTCGTGTTA
1 --T-CGAATTTCATTTTCGAGTTGCGATTTTCGTGTTA
*
2447542 T-GAATTTCATTTTCGAGTTGCGATTTTCGTGTTG
1 TCGAATTTCATTTTCGAGTTGCGATTTTCGTGTTA
2447576 T-GAATTT
1 TCGAATTT
2447583 AAGTTTCTTG
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
34 38 0.54
36 1 0.01
38 1 0.01
39 1 0.01
40 27 0.38
41 3 0.04
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.49
Consensus pattern (35 bp):
TCGAATTTCATTTTCGAGTTGCGATTTTCGTGTTA
Found at i:2447952 original size:22 final size:22
Alignment explanation
Indices: 2447924--2447978 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2447914 GATGAAGGGG
2447924 GTCACCGGAGATGGGGACGGAT
1 GTCACCGGAGATGGGGACGGAT
*
2447946 GTCACCGAAGATGGGGACGGAT
1 GTCACCGGAGATGGGGACGGAT
*
2447968 GTCGCCGGAGA
1 GTCACCGGAGA
2447979 GAGTGAGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.44, T:0.13
Consensus pattern (22 bp):
GTCACCGGAGATGGGGACGGAT
Found at i:2448181 original size:60 final size:60
Alignment explanation
Indices: 2448111--2448233 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
2448101 TTCGTGTTGT
* * * * *
2448111 GAATTCTAAAATCGAGTTGCGAAAATGAAATTCGCGTTGAGAAATTAAAACTCGCTTTGC
1 GAATTATAAAATCGAGTTGCGAAAACGAAACTCGCGTTGAGAAATTAAAAATCGATTTGC
* * *
2448171 GAATTATAAAATCGAGTTGCGAAAACGAAACTCGTGTTGCGAATTTAAAAATCGATTTGC
1 GAATTATAAAATCGAGTTGCGAAAACGAAACTCGCGTTGAGAAATTAAAAATCGATTTGC
2448231 GAA
1 GAA
2448234 AAAGAAATTC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (60 bp):
GAATTATAAAATCGAGTTGCGAAAACGAAACTCGCGTTGAGAAATTAAAAATCGATTTGC
Found at i:2448192 original size:20 final size:20
Alignment explanation
Indices: 2448087--2448233 Score: 77
Period size: 20 Copynumber: 7.3 Consensus size: 20
2448077 AAAAACTAAT
* * *
2448087 TTGCGAATTTTAAATTCGTG
1 TTGCGAATTATAAAATCGAG
* *
2448107 TTGTGAATTCTAAAATCGAG
1 TTGCGAATTATAAAATCGAG
* * *
2448127 TTGCGAA-AATGAAATTCGCG
1 TTGCGAATTAT-AAAATCGAG
* * **
2448147 TTGAGAAATTA-AAACTCGCT
1 TTGCG-AATTATAAAATCGAG
2448167 TTGCGAATTATAAAATCGAG
1 TTGCGAATTATAAAATCGAG
* * * *
2448187 TTGCGAA-AACGAAACTCGTG
1 TTGCGAATTA-TAAAATCGAG
*
2448207 TTGCGAATT-TAAAAATCGAT
1 TTGCGAATTAT-AAAATCGAG
2448227 TTGCGAA
1 TTGCGAA
2448234 AAAGAAATTC
Statistics
Matches: 94, Mismatches: 26, Indels: 14
0.70 0.19 0.10
Matches are distributed among these distances:
19 7 0.07
20 84 0.89
21 2 0.02
22 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (20 bp):
TTGCGAATTATAAAATCGAG
Found at i:2448202 original size:40 final size:40
Alignment explanation
Indices: 2448158--2448272 Score: 135
Period size: 40 Copynumber: 2.8 Consensus size: 40
2448148 TGAGAAATTA
*
2448158 AAACTCGCT-TTGCGAA-TTATAAAATCGAGTTGCGAAAACG
1 AAACTCG-TGTTGCGAATTTA-AAAATCGAGTTGCGAAAAAG
*
2448198 AAACTCGTGTTGCGAATTTAAAAATCGATTTGCGAAAAAG
1 AAACTCGTGTTGCGAATTTAAAAATCGAGTTGCGAAAAAG
* * *
2448238 AAATTCGTGTTGCGAAATTGTCAAATTCGAGTTGC
1 AAACTCGTGTTGCG-AATT-TAAAAATCGAGTTGC
2448273 AAATTCGTCT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
39 1 0.02
40 45 0.69
41 7 0.11
42 12 0.18
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (40 bp):
AAACTCGTGTTGCGAATTTAAAAATCGAGTTGCGAAAAAG
Found at i:2448250 original size:20 final size:19
Alignment explanation
Indices: 2448179--2448254 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 19
2448169 GCGAATTATA
* *
2448179 AAATCGAGTTGCGAAAACG
1 AAATCGTGTTGCGAAAAAG
*
2448198 AAACTCGTGTTGCGAATTTAA-
1 AAA-TCGTGTTGCGAA--AAAG
2448219 AAATCGAT-TTGCGAAAAAG
1 AAATCG-TGTTGCGAAAAAG
2448238 AAATTCGTGTTGCGAAA
1 AAA-TCGTGTTGCGAAA
2448255 TTGTCAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
18 2 0.04
19 7 0.15
20 32 0.70
21 4 0.09
22 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.25
Consensus pattern (19 bp):
AAATCGTGTTGCGAAAAAG
Found at i:2448250 original size:60 final size:60
Alignment explanation
Indices: 2448118--2448254 Score: 166
Period size: 60 Copynumber: 2.3 Consensus size: 60
2448108 TGTGAATTCT
* * * * ** *
2448118 AAAATCGAGTTGCGAAAATGAAATTCGCGTTGAGAAATTAAAACTCGCTTTGCGAATTAT
1 AAAATCGAGTTGCGAAAACGAAACTCGCGTTGAGAAATTAAAAATCGATTTGCGAAAAAG
* * *
2448178 AAAATCGAGTTGCGAAAACGAAACTCGTGTTGCGAATTTAAAAATCGATTTGCGAAAAAG
1 AAAATCGAGTTGCGAAAACGAAACTCGCGTTGAGAAATTAAAAATCGATTTGCGAAAAAG
* *
2448238 AAATTCGTGTTGCGAAA
1 AAAATCGAGTTGCGAAA
2448255 TTGTCAAATT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (60 bp):
AAAATCGAGTTGCGAAAACGAAACTCGCGTTGAGAAATTAAAAATCGATTTGCGAAAAAG
Found at i:2448316 original size:21 final size:20
Alignment explanation
Indices: 2448291--2448335 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2448281 CTTGTGTGTC
2448291 CGAATTC-CAAATTCTGTGTTG
1 CGAATTCGCAAA--CTGTGTTG
*
2448312 CGAATTCGGAAACTGTGTTG
1 CGAATTCGCAAACTGTGTTG
2448332 CGAA
1 CGAA
2448336 ATTGGCTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 7 0.32
22 3 0.14
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (20 bp):
CGAATTCGCAAACTGTGTTG
Found at i:2449680 original size:28 final size:28
Alignment explanation
Indices: 2449636--2449714 Score: 131
Period size: 28 Copynumber: 2.8 Consensus size: 28
2449626 ATGATGACAC
* *
2449636 ATGTCACTAGTGTCACGTGTCATGTCAT
1 ATGTCACTAGTGCCACGTGTCATGCCAT
2449664 ATGTCACTAGTGCCACGTGTCATGCCAT
1 ATGTCACTAGTGCCACGTGTCATGCCAT
*
2449692 ATGTCACTAGTGCCACATGTCAT
1 ATGTCACTAGTGCCACGTGTCAT
2449715 TGGTGACATG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (28 bp):
ATGTCACTAGTGCCACGTGTCATGCCAT
Found at i:2450490 original size:26 final size:26
Alignment explanation
Indices: 2450455--2450557 Score: 102
Period size: 26 Copynumber: 3.9 Consensus size: 26
2450445 TTAAACTAAT
2450455 AATATTTTATATATTTAAATTTTAAA
1 AATATTTTATATATTTAAATTTTAAA
* *
2450481 AATATTTTATATATACT-AACTTTAAA
1 AATATTTTATATAT-TTAAATTTTAAA
* *
2450507 AATATTTTATTTTTATTTTAATTTATAAA
1 AATATTTTA--TATATTTAAATTT-TAAA
* *
2450536 TATATTTT-TATATTAAAATTTT
1 AATATTTTATATATTTAAATTTT
2450558 TTGAAGTTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
25 1 0.02
26 41 0.65
27 2 0.03
28 8 0.13
29 11 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
AATATTTTATATATTTAAATTTTAAA
Found at i:2450671 original size:33 final size:31
Alignment explanation
Indices: 2450620--2450732 Score: 122
Period size: 31 Copynumber: 3.6 Consensus size: 31
2450610 ATATATTTAG
* *
2450620 TAAATTAAGATAAAATATATATTTTGAAAAGT
1 TAAAATAAAATAAAATATATATTTT-AAAAGT
2450652 TAAAATAATAATAAAATATAT-TTTTAAAAGT
1 TAAAATAA-AATAAAATATATATTTTAAAAGT
* * * *
2450683 TTAGATAAGCATAAAATATATATTTTTAAA-T
1 TAAAATAA-AATAAAATATATATTTTAAAAGT
2450714 TAAAATTAAAATAAAATAT
1 TAAAA-TAAAATAAAATAT
2450733 TTCTTAATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
31 36 0.53
32 21 0.31
33 11 0.16
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (31 bp):
TAAAATAAAATAAAATATATATTTTAAAAGT
Found at i:2450780 original size:25 final size:25
Alignment explanation
Indices: 2450719--2450781 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 25
2450709 TAAATTAAAA
* *
2450719 TTAAAATAAAATATTTCTTAATTAAG
1 TTAATATAAAA-ATTTATTAATTAAG
2450745 -TAATA-ATAAAATTTATGTAA-TAAG
1 TTAATATA-AAAATTTAT-TAATTAAG
2450769 TTAATATAAAAAT
1 TTAATATAAAAAT
2450782 ATTTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
24 10 0.32
25 20 0.65
26 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.40
Consensus pattern (25 bp):
TTAATATAAAAATTTATTAATTAAG
Found at i:2451156 original size:28 final size:28
Alignment explanation
Indices: 2451116--2451171 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2451106 ATTATTCATA
* *
2451116 TATTCAATTGAATAGTGACATGTGACAT
1 TATTCAACTGAATAGTGACACGTGACAT
*
2451144 TATTCAACTGAATGGTGACACGTGACAT
1 TATTCAACTGAATAGTGACACGTGACAT
2451172 CTTTACTCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (28 bp):
TATTCAACTGAATAGTGACACGTGACAT
Found at i:2454111 original size:13 final size:14
Alignment explanation
Indices: 2454089--2454123 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2454079 TAAACAGGGG
2454089 TAAATAAACAAA-A
1 TAAATAAACAAAGA
*
2454102 TAACTAAACAAAGA
1 TAAATAAACAAAGA
2454116 TAAATAAA
1 TAAATAAA
2454124 TAAATACATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.17
Consensus pattern (14 bp):
TAAATAAACAAAGA
Found at i:2454557 original size:2 final size:2
Alignment explanation
Indices: 2454550--2454593 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2454540 ACCATTTAAA
2454550 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
2454592 AT
1 AT
2454594 TACCCATCAC
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:2461842 original size:26 final size:26
Alignment explanation
Indices: 2461813--2461864 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2461803 TAATGATGAT
2461813 CCTATTAGTAAACAAAATTACTACCA
1 CCTATTAGTAAACAAAATTACTACCA
2461839 CCTATTAGTAAACAAAATTACTACCA
1 CCTATTAGTAAACAAAATTACTACCA
2461865 GATTTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (26 bp):
CCTATTAGTAAACAAAATTACTACCA
Found at i:2464054 original size:17 final size:17
Alignment explanation
Indices: 2464029--2464061 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2464019 ATTAAACCTG
2464029 AAGGCCCAATTACAACC
1 AAGGCCCAATTACAACC
*
2464046 AAGGTCCAATTACAAC
1 AAGGCCCAATTACAAC
2464062 AAAACCCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.30, G:0.12, T:0.15
Consensus pattern (17 bp):
AAGGCCCAATTACAACC
Found at i:2467668 original size:17 final size:17
Alignment explanation
Indices: 2467646--2467680 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2467636 CACGTGAGGA
*
2467646 TTATTTTTCTTCTTATT
1 TTATTTATCTTCTTATT
*
2467663 TTATTTATCTTTTTATT
1 TTATTTATCTTCTTATT
2467680 T
1 T
2467681 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTATCTTCTTATT
Found at i:2477459 original size:17 final size:16
Alignment explanation
Indices: 2477428--2477461 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2477418 CACGTGAGGA
2477428 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
2477444 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
2477461 T
1 T
2477462 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:2484723 original size:307 final size:308
Alignment explanation
Indices: 2484151--2484767 Score: 1177
Period size: 306 Copynumber: 2.0 Consensus size: 308
2484141 CAAGAAAAAT
2484151 AGTGAGATCGAGAATGGCCCCACCCCCAGATAGAGTTTCGAACGTTTCCAAACATCCAAAGTAGA
1 AGTGAGATCGAGAATGGCCCCACCCCCAGATAGAGTTTCGAACGTTTCCAAACATCCAAAGTAGA
2484216 GGCACGGTTCAAAACCATTCAGCTACGCCAAGTCTATTTGGAAGATGGATTCGTTTTTCCAGCCG
66 GGCACGGTTCAAAACCATTCAGCTACGCCAAGTCTATTTGGAAGATGGATTCGTTTTTCCAGCCG
2484281 AAAGAGAAGAGCAGTTTGGCCCTGAGGTGATGGACGTCATAAAGAAGCATAACTGGAGAAGTTTG
131 AAAGAGAAGAGCAGTTTGGCCCTGAGGTGATGGACGTCATAAAGAAGCATAACTGGAGAAGTTTG
2484346 CTCGTAATCCTAACGCTGTAGCAACCAGAAATGTGAGGGAGTTCTATGCCCACCTCGCAGACACC
196 CTCGTAATCCTAACGCTGTAGCAACCAGAAATGTGAGGGAGTTCTATGCCCACCTCGCAGACACC
2484411 TCCAACCACAC-ATATGTTCGAGGAAAACTCATTCGCTTTTCCCCTTC
261 TCCAACCACACAATATGTTCGAGGAAAACTCATTCGCTTTTCCCCTTC
2484458 AGTGAGATCGAGAATGGCCCCA-CCCCAGATAGAGTTTCGAACGTTTCCAAACATCCAAAGTAGA
1 AGTGAGATCGAGAATGGCCCCACCCCCAGATAGAGTTTCGAACGTTTCCAAACATCCAAAGTAGA
2484522 GGCACGGTTCAAAACCATTCAGCTACGCCAAGTCTATTTGGAAGATGGATTCGTTTTTCCAGCCG
66 GGCACGGTTCAAAACCATTCAGCTACGCCAAGTCTATTTGGAAGATGGATTCGTTTTTCCAGCCG
2484587 AAAGAGAAGAGCAGTTTGGCCCTGAGGTGATGGACGTCATAAAGAAGCATAACTGGGAGAAGTTT
131 AAAGAGAAGAGCAGTTTGGCCCTGAGGTGATGGACGTCATAAAGAAGCATAACT-GGAGAAGTTT
2484652 GCTCGTAATCCTAACGCTGTAGC-ACCAGAAATGGTGAGGGAGTTCTATGCCCACCTCGCAGACA
195 GCTCGTAATCCTAACGCTGTAGCAACCAGAAAT-GTGAGGGAGTTCTATGCCCACCTCGCAGACA
2484716 CCTCCAACCACACAGTATATGTTCGAGGAAAACTCATTCGCTTTTCCCCTTC
259 CCTCCAACCACACA--ATATGTTCGAGGAAAACTCATTCGCTTTTCCCCTTC
2484768 TGCACTTAAC
Statistics
Matches: 305, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
306 170 0.56
307 99 0.32
310 36 0.12
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (308 bp):
AGTGAGATCGAGAATGGCCCCACCCCCAGATAGAGTTTCGAACGTTTCCAAACATCCAAAGTAGA
GGCACGGTTCAAAACCATTCAGCTACGCCAAGTCTATTTGGAAGATGGATTCGTTTTTCCAGCCG
AAAGAGAAGAGCAGTTTGGCCCTGAGGTGATGGACGTCATAAAGAAGCATAACTGGAGAAGTTTG
CTCGTAATCCTAACGCTGTAGCAACCAGAAATGTGAGGGAGTTCTATGCCCACCTCGCAGACACC
TCCAACCACACAATATGTTCGAGGAAAACTCATTCGCTTTTCCCCTTC
Found at i:2496015 original size:63 final size:64
Alignment explanation
Indices: 2495876--2496037 Score: 168
Period size: 63 Copynumber: 2.5 Consensus size: 64
2495866 ATTATTCAAG
* * * * * *
2495876 GTGTATTGATGCACATGAAGTGCATTGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
* * ** *
2495940 GTGTACCGATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAACATCGAATGGGATTTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCA-TCA
* *
2496004 -TGTATCGATGCA-TAGATAGTACATCGATGCACCC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCC
2496038 GTCAAGGGAT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
62 2 0.02
63 46 0.56
64 34 0.41
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:2496746 original size:23 final size:23
Alignment explanation
Indices: 2496703--2496746 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2496693 ATTTTATACA
*
2496703 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTATACGTG
*
2496726 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCAATTATACG
2496747 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
GCACTTCGGTGCAATTATACGTG
Found at i:2505063 original size:14 final size:14
Alignment explanation
Indices: 2505052--2505079 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2505042 GTAAAATATG
2505052 GTATGAACAATACC
1 GTATGAACAATACC
2505066 GTATGAACAATACC
1 GTATGAACAATACC
2505080 AAAATGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
GTATGAACAATACC
Found at i:2505734 original size:31 final size:31
Alignment explanation
Indices: 2505686--2505927 Score: 320
Period size: 31 Copynumber: 8.0 Consensus size: 31
2505676 CCCGAAGGAC
* * *
2505686 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
2505717 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
2505748 CAGTCCAAATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2505779 CAGT-CATA-GT-CCGAAGAACATAAGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2505807 CAGT-CATATGT-CCGAAGAAAATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2505836 CAGTCCATATGT-CCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2505866 CAGTCCATATGTCCCAAAG-ACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
2505896 AAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2505927 C
1 C
2505928 CTCGAGCCTT
Statistics
Matches: 188, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
28 24 0.13
29 24 0.13
30 66 0.35
31 73 0.39
32 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2505847 original size:30 final size:30
Alignment explanation
Indices: 2505698--2505927 Score: 315
Period size: 30 Copynumber: 7.7 Consensus size: 30
2505688 GTCCATAGAT
* * *
2505698 TCCGAAGAACCTAGGTAATCAGTCTATATG
1 TCCGAAGAACATAGGTAAACAGTCCATATG
*
2505728 TCCCGAAGAACATAGGTAAACAGTCCAAATG
1 T-CCGAAGAACATAGGTAAACAGTCCATATG
2505759 TCTCGAAGAACATAGGTAAACAGT-CATA-G
1 TC-CGAAGAACATAGGTAAACAGTCCATATG
*
2505788 TCCGAAGAACATAAGTAAACAGT-CATATG
1 TCCGAAGAACATAGGTAAACAGTCCATATG
*
2505817 TCCGAAGAAAATAGGTAAACAGTCCATATG
1 TCCGAAGAACATAGGTAAACAGTCCATATG
2505847 TCCGAAGAACATAGGTAAACAGTCCATATG
1 TCCGAAGAACATAGGTAAACAGTCCATATG
* * *
2505877 TCCCAA-AGACATAGGTAAAAAATCCATATG
1 TCCGAAGA-ACATAGGTAAACAGTCCATATG
2505907 TCCCGAAGAACATAGGTAAAC
1 T-CCGAAGAACATAGGTAAAC
2505928 CTCGAGCCTT
Statistics
Matches: 179, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
28 24 0.13
29 26 0.15
30 66 0.37
31 62 0.35
32 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.20
Consensus pattern (30 bp):
TCCGAAGAACATAGGTAAACAGTCCATATG
Found at i:2505850 original size:59 final size:61
Alignment explanation
Indices: 2505698--2505927 Score: 319
Period size: 59 Copynumber: 3.8 Consensus size: 61
2505688 GTCCATAGAT
* * * *
2505698 TCCGAAGAACCTAGGTAATCAGTCTATATGTCCCGAAGAACATAGGTAAACAGTCCAAATG
1 TCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATG
*
2505759 TCTCGAAGAACATAGGTAAACAGT-CATA-GT-CCGAAGAACATAAGTAAACAGT-CATATG
1 TC-CGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATG
*
2505817 TCCGAAGAAAATAGGTAAACAGTCCATATGT-CCGAAGAACATAGGTAAACAGTCCATATG
1 TCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATG
* * *
2505877 TCCCAA-AGACATAGGTAAAAAATCCATATGTCCCGAAGAACATAGGTAAAC
1 TCCGAAGA-ACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAAC
2505928 CTCGAGCCTT
Statistics
Matches: 152, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
57 20 0.13
58 11 0.07
59 45 0.30
60 33 0.22
61 24 0.16
62 19 0.12
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.20
Consensus pattern (61 bp):
TCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATG
Found at i:2506494 original size:19 final size:19
Alignment explanation
Indices: 2506470--2506528 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
2506460 TTTTTATTTA
2506470 AGGGGGAATCGATACCCCC
1 AGGGGGAATCGATACCCCC
*
2506489 AGGGGGAATCTG-T--TCCC
1 AGGGGGAATC-GATACCCCC
2506506 --GGGGAATCGATACCCCC
1 AGGGGGAATCGATACCCCC
2506523 AGGGGG
1 AGGGGG
2506529 GAATTGTCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 1 0.03
15 9 0.28
17 6 0.19
19 15 0.47
20 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.37, T:0.14
Consensus pattern (19 bp):
AGGGGGAATCGATACCCCC
Found at i:2510095 original size:31 final size:31
Alignment explanation
Indices: 2510057--2510395 Score: 551
Period size: 31 Copynumber: 11.0 Consensus size: 31
2510047 CCCGAATGGC
* * *
2510057 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
2510088 CAGTCCATATATCCCGAAGAACATAGGTAAG
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2510119 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2510150 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2510181 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2510212 CAGTCCATATGTCCCGAAG-ACA-GGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2510241 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2510272 CAGTCCATATGTCCCGAAGAACATAGGT-AA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2510302 CAGTCCATATGTCCCGAAGAACAAAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
2510333 TAGTCCATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2510364 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2510395 C
1 C
2510396 CCTCGACCCT
Statistics
Matches: 288, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
29 25 0.09
30 35 0.12
31 228 0.79
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2510365 original size:152 final size:153
Alignment explanation
Indices: 2510082--2510383 Score: 534
Period size: 152 Copynumber: 2.0 Consensus size: 153
2510072 GAAGAACCTA
* * *
2510082 GGTAATCAGTCCATATATCCCGAAGAACATAGGTAAGCAGTCTATATGTCCCGAAGAACATAGGT
1 GGTAAACAGTCCATATATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGT
*
2510147 AAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
66 AAACAGTCCATATGTCCCGAAGAACAAAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
2510212 CAGTCCATATGTCCCGAAGACAG
131 CAGTCCATATGTCCCGAAGACAG
*
2510235 GGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGT
1 GGTAAACAGTCCATATATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGT
* *
2510300 -AACAGTCCATATGTCCCGAAGAACAAAGGTAAATAGTCCATATGTCTCGAAGAACATAGGTAAA
66 AAACAGTCCATATGTCCCGAAGAACAAAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
2510364 CAGTCCATATGTCCCGAAGA
131 CAGTCCATATGTCCCGAAGA
2510384 ACATAGGTAA
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
152 81 0.57
153 61 0.43
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (153 bp):
GGTAAACAGTCCATATATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGT
AAACAGTCCATATGTCCCGAAGAACAAAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
CAGTCCATATGTCCCGAAGACAG
Found at i:2510366 original size:183 final size:184
Alignment explanation
Indices: 2510057--2510395 Score: 583
Period size: 183 Copynumber: 1.8 Consensus size: 184
2510047 CCCGAATGGC
* * *
2510057 CAGTCCATAGATTCCGAAGAACCTAGGTAATCAGTCCATATATCCCGAAGAACATAGGTAAGCAG
1 CAGTCCATAGATCCCGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACATAGGTAAGCAG
* *
2510122 TCTATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCC
66 TCCATATGTCCCGAAGAACAAAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCC
2510187 ATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGACAGGGTAAA
131 ATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGACAGGGTAAA
*
2510241 CAGTCCATATG-TCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA-CA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACATAGGTAAGCA
* *
2510304 GTCCATATGTCCCGAAGAACAAAGGTAAATAGTCCATATGTCTCGAAGAACATAGGTAAACAGTC
65 GTCCATATGTCCCGAAGAACAAAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTC
2510369 CATATGTCCCGAAGAACATAGGTAAAC
130 CATATGTCCCGAAGAACATAGGTAAAC
2510396 CCTCGACCCT
Statistics
Matches: 146, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
183 90 0.62
184 55 0.38
185 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (184 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACATAGGTAAGCAG
TCCATATGTCCCGAAGAACAAAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCC
ATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGACAGGGTAAA
Found at i:2510996 original size:35 final size:35
Alignment explanation
Indices: 2510950--2511018 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
2510940 TTTATTTAGG
2510950 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCT
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCT
2510985 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCC
2511019 CCCTGCACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.29, G:0.32, T:0.19
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCT
Found at i:2511021 original size:20 final size:20
Alignment explanation
Indices: 2510949--2511012 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
2510939 TTTTATTTAG
2510949 GGGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
*
2510969 GGGGGAATCTG-T----TCC-
1 GGGGGAATC-GATACCCCCCA
*
2510984 TGGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
2511004 GGGGGAATC
1 GGGGGAATC
2511013 TGTTCCCCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
14 1 0.03
15 9 0.27
16 2 0.06
19 2 0.06
20 18 0.55
21 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.34, T:0.16
Consensus pattern (20 bp):
GGGGGAATCGATACCCCCCA
Found at i:2517151 original size:2 final size:2
Alignment explanation
Indices: 2517146--2517193 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2517136 TGTGTGTGTG
2517146 TA 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 TA
2517188 TA TA TA
1 TA TA TA
2517194 ATTAGGTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2517235 original size:15 final size:15
Alignment explanation
Indices: 2517212--2517243 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2517202 AAATAACTTA
*
2517212 TTTAGTCATTTATAT
1 TTTAATCATTTATAT
2517227 TTTAATCATTTATAT
1 TTTAATCATTTATAT
2517242 TT
1 TT
2517244 ATATCCCATA
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:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTAATCATTTATAT
Found at i:2520311 original size:46 final size:46
Alignment explanation
Indices: 2520244--2520347 Score: 172
Period size: 46 Copynumber: 2.2 Consensus size: 46
2520234 CATGTAGGAG
*
2520244 TAAGTAAAATTCGATTTGACTAGAAAAATTAATTTTTTAATCGATT
1 TAAGTAAAATTCGAATTGACTAGAAAAATTAATTTTTTAATCGATT
*
2520290 TAAGTAAAATTCGAATTGACTAGAAAAATTGATTTTTTAATCGATT
1 TAAGTAAAATTCGAATTGACTAGAAAAATTAATTTTTTAATCGATT
*
2520336 TAATTAGAAATT
1 TAAGTA-AAATT
2520348 TTTTTTATTC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 49 0.91
47 5 0.09
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (46 bp):
TAAGTAAAATTCGAATTGACTAGAAAAATTAATTTTTTAATCGATT
Found at i:2520465 original size:21 final size:20
Alignment explanation
Indices: 2520429--2520472 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
2520419 TCGAGTTGTA
2520429 AAATAGAACTCTAATAACTC
1 AAATAGAACTCTAATAACTC
*
2520449 AAATAGTAACT-TGAATAATTC
1 AAATAG-AACTCT-AATAACTC
2520470 AAA
1 AAA
2520473 AATTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.27
Consensus pattern (20 bp):
AAATAGAACTCTAATAACTC
Found at i:2520862 original size:23 final size:23
Alignment explanation
Indices: 2520836--2520883 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2520826 ATAAAGTACA
*
2520836 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
2520859 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
2520882 AT
1 AT
2520884 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2521398 original size:23 final size:23
Alignment explanation
Indices: 2521359--2521431 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
2521349 ATACTTTACA
* *
2521359 ATATAAGCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
2521382 ATATAAACGCTATCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
2521405 ATATTAACGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
2521428 ATAT
1 ATAT
2521432 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:2521432 original size:23 final size:23
Alignment explanation
Indices: 2521368--2521432 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
2521358 AATATAAGCA
*
2521368 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATTAACG
*
2521391 CTATCTATTACATTATATTAACG
1 CTACCTATTACATTATATTAACG
*
2521414 CTACCTATTACATCATATT
1 CTACCTATTACATTATATT
2521433 TTTACCTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (23 bp):
CTACCTATTACATTATATTAACG
Found at i:2521878 original size:489 final size:489
Alignment explanation
Indices: 2520960--2521881 Score: 1776
Period size: 489 Copynumber: 1.9 Consensus size: 489
2520950 TAATATGTTG
2520960 AAAGTGTCTATACTTTTTTATAAAAAAAGATCGATACTTTTTTAAAGTTATGTAATTTATGTTTC
1 AAAGTGTCTATACTTTTTTATAAAAAAAGATCGATACTTTTTTAAAGTTATGTAATTTATGTTTC
2521025 AATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAA
66 AATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAA
2521090 AAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAAC
2521155 CAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATACATCG
196 CAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATACATCG
2521220 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
261 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
2521285 AGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGATAGA
326 AGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGATAGA
2521350 TACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTATCTATTACATTATATTAACGC
391 TACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTATCTATTACATTATATTAACGC
2521415 TACCTATTACATCATATTTTTACCTATTATATTA
456 TACCTATTACATCATATTTTTACCTATTATATTA
*
2521449 AAAGTGTCTATAC-TTTTTAT-AAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
1 AAAGTGTCTATACTTTTTTATAAAAAAAGATCGATAC-TTTTTTAAAGTTATGTAATTTATGTTT
2521512 CAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
65 CAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
*
2521577 ATAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTA
129 AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTA
*
2521642 ACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATAT
194 ACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATACAT
*
2521707 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCTCTCA
259 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
2521772 AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGATA
324 AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGATA
2521837 GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCT
389 GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCT
2521882 TACAGACTTC
Statistics
Matches: 427, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
487 14 0.03
488 37 0.09
489 376 0.88
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (489 bp):
AAAGTGTCTATACTTTTTTATAAAAAAAGATCGATACTTTTTTAAAGTTATGTAATTTATGTTTC
AATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAA
AAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAAC
CAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATACATCG
TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
AGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGATAGA
TACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTATCTATTACATTATATTAACGC
TACCTATTACATCATATTTTTACCTATTATATTA
Found at i:2523540 original size:20 final size:20
Alignment explanation
Indices: 2523509--2523557 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2523499 TCTGGTAACG
*
2523509 TTTTACCGGTTTTATCAT-T
1 TTTTACCTGTTTTATCATAT
*
2523528 TTGTTACCTGTTTTATTATAT
1 TT-TTACCTGTTTTATCATAT
2523549 TTTTACCTG
1 TTTTACCTG
2523558 GTATATCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.16, C:0.14, G:0.10, T:0.59
Consensus pattern (20 bp):
TTTTACCTGTTTTATCATAT
Found at i:2523599 original size:181 final size:181
Alignment explanation
Indices: 2523295--2523767 Score: 608
Period size: 181 Copynumber: 2.6 Consensus size: 181
2523285 CGTACTTACG
* * * * * *
2523295 AAAGTATCGATACTTTCAATATATCCGATATCATTTTACCGGTTTAATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCTGTTT
* ** * *
2523360 TATCATATTTTTACATGTTATATAATTGTGGATCGATATATTTTTTTAAAATATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTTAAAATATCGACACATTAT
*
2523425 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
2523476 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGTTACCTGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCTGTTT
* * *
2523541 TATTATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAA-TATCGACACATTAT
** * * *
2523606 AGGATTTAAAATTGCTTCTCTTTTAAATTCACGAAGTGTCGCTCCTTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * **
2523658 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATA-CTGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCT-GTT
* * * *
2523722 TTGTCATAGTTTTACCTGTTATATCGTTTTGGACCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
2523768 AATTTGGATC
Statistics
Matches: 252, Mismatches: 37, Indels: 5
0.86 0.13 0.02
Matches are distributed among these distances:
180 10 0.04
181 149 0.59
182 93 0.37
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCTGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAATATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:2526709 original size:6 final size:6
Alignment explanation
Indices: 2526698--2526728 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2526688 TATAAAGGCA
2526698 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG A
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG A
2526729 ATGTGATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:2528084 original size:32 final size:32
Alignment explanation
Indices: 2528040--2528100 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
2528030 TATAAGAGGA
2528040 TATTTTATTGAGTCCATCGATTATTAAAAGTT
1 TATTTTATTGAGTCCATCGATTATTAAAAGTT
*
2528072 TATTTTGA-TGAGTTCATCGATTATTAAAA
1 TATTTT-ATTGAGTCCATCGATTATTAAAA
2528101 ATTATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (32 bp):
TATTTTATTGAGTCCATCGATTATTAAAAGTT
Found at i:2532637 original size:25 final size:26
Alignment explanation
Indices: 2532566--2532638 Score: 62
Period size: 25 Copynumber: 2.8 Consensus size: 26
2532556 CCTATTAATT
*
2532566 ATATCTTTTTCAA-ATTTCAATTAAAAG
1 ATATCATTTT-AATATTT-AATTAAAAG
* **
2532593 ATA-CGAATTTAATAAATAATTAAAA-
1 ATATC-ATTTTAATATTTAATTAAAAG
2532618 ATATCATTTTAATATTTAATT
1 ATATCATTTTAATATTTAATT
2532639 TTGTTAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
25 16 0.44
26 12 0.33
27 8 0.22
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.44
Consensus pattern (26 bp):
ATATCATTTTAATATTTAATTAAAAG
Found at i:2534694 original size:33 final size:33
Alignment explanation
Indices: 2534632--2534694 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
2534622 ATTATTACCC
* *
2534632 TAATCAAATTGCTCGAATCATATCCTGCTATCA
1 TAATCAAATTGCTCAAATCATAGCCTGCTATCA
2534665 TAAT-AAAGTTGCTCAAATCAT-GCCTTGCTA
1 TAATCAAA-TTGCTCAAATCATAGCC-TGCTA
2534695 CCAAGTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 5 0.19
33 21 0.81
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (33 bp):
TAATCAAATTGCTCAAATCATAGCCTGCTATCA
Found at i:2534710 original size:27 final size:26
Alignment explanation
Indices: 2534670--2534742 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
2534660 TATCATAATA
* *
2534670 AAGTTGCTCAAATCATGCCTTGCTACC
1 AAGTTGTTCGAATCATGCC-TGCTACC
*
2534697 AAGTTGTTCGAATCATGTCCTGCTATC
1 AAGTTGTTCGAATCATG-CCTGCTACC
* *
2534724 AAGTTGTTTGAACCATGCC
1 AAGTTGTTCGAATCATGCC
2534743 CTGTTACCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
26 2 0.05
27 36 0.90
28 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (26 bp):
AAGTTGTTCGAATCATGCCTGCTACC
Found at i:2534745 original size:27 final size:27
Alignment explanation
Indices: 2534683--2534750 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
2534673 TTGCTCAAAT
* *
2534683 CATGCCTTGCTACCAAGTTGTTCGAAT
1 CATGCCCTGCTACCAAGTTGTTCGAAC
* * *
2534710 CATGTCCTGCTATCAAGTTGTTTGAAC
1 CATGCCCTGCTACCAAGTTGTTCGAAC
*
2534737 CATGCCCTGTTACC
1 CATGCCCTGCTACC
2534751 CTGACACTAC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.34
Consensus pattern (27 bp):
CATGCCCTGCTACCAAGTTGTTCGAAC
Found at i:2535032 original size:24 final size:24
Alignment explanation
Indices: 2535000--2535048 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2534990 TAGCAGGAAG
*
2535000 AACAATTTGTAGTGTTAGGGTAGC
1 AACAATTTGTAGTGTCAGGGTAGC
2535024 AACAATTTGTAGTGTCAGGGTAGC
1 AACAATTTGTAGTGTCAGGGTAGC
2535048 A
1 A
2535049 TGGCATGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.31
Consensus pattern (24 bp):
AACAATTTGTAGTGTCAGGGTAGC
Found at i:2536298 original size:21 final size:22
Alignment explanation
Indices: 2536256--2536304 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
2536246 TATTGAGTTA
* * *
2536256 TCTTCTCTCTTTTTTGTTTGAT
1 TCTTTTCTCTTTTATGTGTGAT
2536278 TCTTTTCTCTTTTATG-GTGAT
1 TCTTTTCTCTTTTATGTGTGAT
*
2536299 TTTTTT
1 TCTTTT
2536305 GCTTTTTCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.06, C:0.14, G:0.10, T:0.69
Consensus pattern (22 bp):
TCTTTTCTCTTTTATGTGTGAT
Found at i:2538667 original size:65 final size:64
Alignment explanation
Indices: 2538530--2538691 Score: 168
Period size: 65 Copynumber: 2.5 Consensus size: 64
2538520 ATTGTTCAGA
* * * * * *
2538530 GTGTATCGATGCACAGGAAGTGCATCAATGCA-CCCATTAAAAATGGAAACATCGAATGCAGTTG
1 GTGTATCGATGCATAGGAA-TGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGGAAATTG
* *
2538594 GTGCATCGATGCATTAGGAATGCATCGATGCACCCCCCTT-AAAATGAAAACATCGAAGGTAAAT
1 GTGTATCGATGCA-TAGGAATGCATCGATGCA-CCCCATTAAAAATGAAAACATCGAAGG-AAAT
2538658 T-
63 TG
* *
2538659 GTGTATCGATGCATGGGTAGTGCATCGATGCAC
1 GTGTATCGATGCATAGG-AATGCATCGATGCAC
2538692 ATGTTAAAGA
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
64 27 0.33
65 47 0.57
66 8 0.10
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (64 bp):
GTGTATCGATGCATAGGAATGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGGAAATTG
Found at i:2540222 original size:23 final size:23
Alignment explanation
Indices: 2540162--2540214 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
2540152 CATGGCATTA
* *
2540162 CGGTGCATTTCTACGCGGTATTT
1 CGGTGCATTTCTACGCGGCACTT
2540185 CGGTGCATTTCTACGCGGCACTT
1 CGGTGCATTTCTACGCGGCACTT
2540208 CGGTGCA
1 CGGTGCA
2540215 ATTATACGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.32
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGGCACTT
Found at i:2542976 original size:11 final size:11
Alignment explanation
Indices: 2542960--2542984 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2542950 AGTTTTAATA
2542960 TTAAAACAATT
1 TTAAAACAATT
2542971 TTAAAACAATT
1 TTAAAACAATT
2542982 TTA
1 TTA
2542985 TAACGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAAACAATT
Found at i:2548955 original size:23 final size:23
Alignment explanation
Indices: 2548913--2548997 Score: 127
Period size: 23 Copynumber: 3.7 Consensus size: 23
2548903 ATAGGGCATA
* * *
2548913 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAT
2548935 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAT
*
2548958 GGAAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAT
2548981 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
2548998 AGGGGAATCG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 14 0.25
23 43 0.75
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAT
Found at i:2551250 original size:16 final size:17
Alignment explanation
Indices: 2551216--2551250 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2551206 TAACAAAAAG
2551216 GGGGAGAAGTGTTTTAAA
1 GGGGAGAAGTG-TTTAAA
2551234 GGGGAGAAGTG-TTAAA
1 GGGGAGAAGTGTTTAAA
2551250 G
1 G
2551251 TAAGGGGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
18 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.43, T:0.23
Consensus pattern (17 bp):
GGGGAGAAGTGTTTAAA
Found at i:2560716 original size:31 final size:31
Alignment explanation
Indices: 2560673--2560749 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
2560663 AAAATTTAAA
*
2560673 AGTTTAGGTATTAAAACATACTAAAACTGAT
1 AGTTTAGATATTAAAACATACTAAAACTGAT
* *
2560704 AGTTTAGATATTAAAATATACTAAAATTGAT
1 AGTTTAGATATTAAAACATACTAAAACTGAT
*
2560735 AGTTTAGATACTAAA
1 AGTTTAGATATTAAA
2560750 CCCTTTATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (31 bp):
AGTTTAGATATTAAAACATACTAAAACTGAT
Found at i:2562862 original size:20 final size:21
Alignment explanation
Indices: 2562839--2562879 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2562829 TATTATATGT
**
2562839 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
2562859 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
2562880 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:2564302 original size:11 final size:11
Alignment explanation
Indices: 2564279--2564310 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
2564269 ATGTAATTAT
2564279 TATTTATATATA
1 TATTTA-ATATA
2564291 TATTTAATATA
1 TATTTAATATA
2564302 TATTTAATA
1 TATTTAATA
2564311 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:2564314 original size:3 final size:3
Alignment explanation
Indices: 2564306--2564376 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
2564296 AATATATATT
*
2564306 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2564354 TAA TAA TAA TAT TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
2564377 TGGATAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2564657 original size:114 final size:117
Alignment explanation
Indices: 2564571--2565274 Score: 965
Period size: 114 Copynumber: 6.1 Consensus size: 117
2564561 GGGGATGATG
*
2564571 ATCCATCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTT
* * *
2564635 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT-GCAATGTTG
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
* *
2564686 ATCCATCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
1 ATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTT
2564750 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
* * * *
2564802 ATCCATTAACTTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTT
2564867 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
* * *
2564919 ATCCATCAACTTGATGAATTC-AGAAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1 ATCCATCAACATGATGAATTCAAG-CAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCT
* * *
2564983 TCCTTCTTCAGAT-A--AGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGACTG
65 TCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGA-TA
* ** * *
2565034 ATCCATCAA-ATGATGGATTCGGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTT
* * *
2565098 CCTTCTTCA-A--ATGAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATA
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATA
** * * * *
2565147 ATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAAAAAATTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTT
* *
2565212 CCTTCTTCA-A--ATGAGTTCTTCTCATTATGAACTTTACCTGGCAAAGATA
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
2565261 ATCCATCAA-ATGAT
1 ATCCATCAACATGAT
2565275 AGATTTGAAT
Statistics
Matches: 549, Mismatches: 29, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
112 1 0.00
113 17 0.03
114 223 0.41
115 118 0.21
116 16 0.03
117 174 0.32
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (117 bp):
ATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTT
CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
Found at i:2566198 original size:84 final size:84
Alignment explanation
Indices: 2566006--2566474 Score: 825
Period size: 84 Copynumber: 5.6 Consensus size: 84
2565996 CCTACTGAAT
* * * *
2566006 CAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTA-TGAACACATTCATCTTTTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
*
2566070 ATGATT-GTTCTGTCCAAC
66 ATGATTGGTTTTGTCCAAC
2566088 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
2566153 ATGATTGGTTTTGTCCAAC
66 ATGATTGGTTTTGTCCAAC
2566172 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
*
2566237 ATGATTGGTTCTGTCCAAC
66 ATGATTGGTTTTGTCCAAC
2566256 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
2566321 ATGATTGGTTTTGTCCAAC
66 ATGATTGGTTTTGTCCAAC
* * *
2566340 CAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATATTTTCTAAATTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT-CATCTTCTAAATTC
2566405 AATGATTGGTTTTGTCCAAC
65 AATGATTGGTTTTGTCCAAC
*
2566425 CAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT
2566475 ATATTTGTTC
Statistics
Matches: 374, Mismatches: 10, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
82 38 0.10
83 28 0.07
84 226 0.60
85 82 0.22
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (84 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
ATGATTGGTTTTGTCCAAC
Found at i:2566452 original size:253 final size:250
Alignment explanation
Indices: 2566006--2566474 Score: 830
Period size: 253 Copynumber: 1.9 Consensus size: 250
2565996 CCTACTGAAT
* *
2566006 CAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTATGAACACATTCATCTTTTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
*
2566071 TGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACA
66 TGATTGTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACA
*
2566136 TTCATCTTCTAAATTCAATGATTGGTTTTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
131 TTCATCTTCTAAATTCAATGATTGGTTTTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCA
2566201 GAAGATGCTATTGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
196 GAAGATGCTATTGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
* *
2566256 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTAAACTCA
*
2566321 ATGATTGGTTTTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCA
65 ATGATT-GTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCA
* *
2566386 CATTATATTTTCTAAATTCAATGATTGGTTTTGTCCAACCAAATCAGATAACTCAAAGAACACTT
129 CATT-CATCTTCTAAATTCAATGATTGGTTTTGTCCAACCAAATCAGATAACTCAAAGAACACTT
2566451 CCAGAAGATGCTATTGAGCACATT
193 CCAGAAGATGCTATTGAGCACATT
2566475 ATATTTGTTC
Statistics
Matches: 207, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
250 38 0.18
251 28 0.14
252 60 0.29
253 81 0.39
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (250 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
TGATTGTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACA
TTCATCTTCTAAATTCAATGATTGGTTTTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCA
GAAGATGCTATTGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAAC
Found at i:2567635 original size:7 final size:7
Alignment explanation
Indices: 2567613--2567696 Score: 66
Period size: 7 Copynumber: 11.9 Consensus size: 7
2567603 CTTGACCCCC
2567613 TTTCTTTT
1 TTTC-TTT
2567621 TCTTCTTT
1 T-TTCTTT
2567629 TTTCTTT
1 TTTCTTT
*
2567636 TTTTTCTT
1 TTTCT-TT
*
2567644 TTTC-AT
1 TTTCTTT
2567650 TTTCTATT
1 TTTCT-TT
*
2567658 TTT-TCT
1 TTTCTTT
*
2567664 TCTCTTT
1 TTTCTTT
2567671 TTT-TTT
1 TTTCTTT
*
2567677 CTTCTTT
1 TTTCTTT
2567684 TTTCTTT
1 TTTCTTT
2567691 TTTCTT
1 TTTCTT
2567697 CAAGCATAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
6 13 0.22
7 30 0.50
8 14 0.23
9 3 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTCTTT
Found at i:2567645 original size:15 final size:15
Alignment explanation
Indices: 2567613--2567692 Score: 74
Period size: 15 Copynumber: 5.2 Consensus size: 15
2567603 CTTGACCCCC
*
2567613 TTTCTTTTTCTTCTTT
1 TTTCTTTTTTTTC-TT
2567629 TTTCTTTTTTTTCTT
1 TTTCTTTTTTTTCTT
* *
2567644 TTTCATTTTCTAT-TT
1 TTTC-TTTTTTTTCTT
*
2567659 TTTCTTCTCTTTT-TT
1 TTTCTT-TTTTTTCTT
2567674 TTTCTTCTTTTTTCTT
1 TTTCTT-TTTTTTCTT
2567690 TTT
1 TTT
2567693 TCTTCAAGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
14 2 0.04
15 29 0.54
16 23 0.43
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTCTTTTTTTTCTT
Found at i:2567666 original size:12 final size:12
Alignment explanation
Indices: 2567631--2567689 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
2567621 TCTTCTTTTT
2567631 TCTTTTTT-TTC
1 TCTTTTTTCTTC
2567642 T-TTTTCATT-TTC
1 TCTTTT--TTCTTC
*
2567654 TATTTTTTCTTC
1 TCTTTTTTCTTC
*
2567666 TCTTTTTTTTTC
1 TCTTTTTTCTTC
2567678 TTCTTTTTTCTT
1 -TCTTTTTTCTT
2567690 TTTTCTTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 4 0.10
11 3 0.08
12 19 0.47
13 14 0.35
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (12 bp):
TCTTTTTTCTTC
Found at i:2579070 original size:20 final size:21
Alignment explanation
Indices: 2579047--2579087 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2579037 TATTATATGT
**
2579047 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
2579067 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
2579088 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:2579999 original size:21 final size:20
Alignment explanation
Indices: 2579968--2580009 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
2579958 GTTTAGTTTT
2579968 TGTTTTTTTTTTTCTTTCTC
1 TGTTTTTTTTTTTCTTTCTC
*
2579988 TGTTTGTTTTTTTTTTTTCTC
1 TGTTT-TTTTTTTTCTTTCTC
2580009 T
1 T
2580010 CTCCGGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (20 bp):
TGTTTTTTTTTTTCTTTCTC
Found at i:2580004 original size:25 final size:24
Alignment explanation
Indices: 2579966--2580012 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
2579956 TGGTTTAGTT
*
2579966 TTTGTTTTTTTTTTTCTTTCTCTG
1 TTTGTTTTTTTTTTTCTCTCTCTG
2579990 TTTGTTTTTTTTTTTTCTCTCTC
1 TTTG-TTTTTTTTTTTCTCTCTC
2580013 CGGTTCTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (24 bp):
TTTGTTTTTTTTTTTCTCTCTCTG
Found at i:2580510 original size:11 final size:11
Alignment explanation
Indices: 2580494--2580518 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2580484 TTATTTATAT
2580494 ATATATATTTA
1 ATATATATTTA
2580505 ATATATATTTA
1 ATATATATTTA
2580516 ATA
1 ATA
2580519 ATAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATATTTA
Found at i:2580522 original size:3 final size:3
Alignment explanation
Indices: 2580514--2580588 Score: 123
Period size: 3 Copynumber: 24.7 Consensus size: 3
2580504 AATATATATT
*
2580514 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2580562 TAA TAAA TAA TAT TAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TA
2580589 TGGATAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
3 64 0.96
4 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2580686 original size:44 final size:45
Alignment explanation
Indices: 2580636--2580725 Score: 164
Period size: 44 Copynumber: 2.0 Consensus size: 45
2580626 TATAGTGGAT
2580636 AATTGGACAAATTTTGTAAGCATTGCC-GGGGGGTGGGGTTAGGC
1 AATTGGACAAATTTTGTAAGCATTGCCGGGGGGGTGGGGTTAGGC
*
2580680 AATTGGACAAATTTTGTAAGCTTTGCCGGGGGGGTGGGGTTAGGC
1 AATTGGACAAATTTTGTAAGCATTGCCGGGGGGGTGGGGTTAGGC
2580725 A
1 A
2580726 CATGGATTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 26 0.59
45 18 0.41
ACGTcount: A:0.22, C:0.11, G:0.39, T:0.28
Consensus pattern (45 bp):
AATTGGACAAATTTTGTAAGCATTGCCGGGGGGGTGGGGTTAGGC
Found at i:2582588 original size:2 final size:2
Alignment explanation
Indices: 2582581--2582620 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2582571 ATATTAAAAT
2582581 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
2582621 AATTATGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2582994 original size:2 final size:2
Alignment explanation
Indices: 2582987--2583059 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
2582977 TAAAATGTTA
2582987 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
2583029 AT AT 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 AT AT A
2583060 ACATTTACCG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2583506 original size:4 final size:4
Alignment explanation
Indices: 2583499--2583528 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
2583489 TTTGTACAAA
2583499 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
2583529 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:2587068 original size:27 final size:27
Alignment explanation
Indices: 2587013--2587068 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
2587003 TTATTATTTC
* *
2587013 TACCAATTTTATTATTGTTAGATATTT
1 TACCAATTTTATTATTATTAGATACTT
*
2587040 TACCGATTTTATTATTATT-GATCACTT
1 TACCAATTTTATTATTATTAGAT-ACTT
2587067 TA
1 TA
2587069 TCAGAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.54
Consensus pattern (27 bp):
TACCAATTTTATTATTATTAGATACTT
Found at i:2587358 original size:12 final size:12
Alignment explanation
Indices: 2587341--2587365 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2587331 CTCAAACAGA
2587341 GAGAATGAACGT
1 GAGAATGAACGT
2587353 GAGAATGAACGT
1 GAGAATGAACGT
2587365 G
1 G
2587366 TTGCATGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:2587427 original size:29 final size:29
Alignment explanation
Indices: 2587394--2587449 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
2587384 TCCCAACACA
2587394 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
2587423 TAGGTCGCCATGCCCTCTGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
2587450 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.11, C:0.38, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:2593399 original size:21 final size:21
Alignment explanation
Indices: 2593382--2593431 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2593372 TTTAAAATAT
2593382 AAAAATGATGTTTCAAAATTG
1 AAAAATGATGTTTCAAAATTG
2593403 AAAAATGATGTTTCAAAATTG
1 AAAAATGATGTTTCAAAATTG
2593424 AAAAATGA
1 AAAAATGA
2593432 AAATAAACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (21 bp):
AAAAATGATGTTTCAAAATTG
Found at i:2600026 original size:20 final size:20
Alignment explanation
Indices: 2599997--2600036 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2599987 AGTATGCTCG
2599997 GAGGGAACCGATTCCCCCCA
1 GAGGGAACCGATTCCCCCCA
*
2600017 GAGGGTACCGATTCCCCCCA
1 GAGGGAACCGATTCCCCCCA
2600037 CTGTTCAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.40, G:0.25, T:0.12
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCCA
Found at i:2604915 original size:28 final size:27
Alignment explanation
Indices: 2604862--2604916 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
2604852 AATATAAGAG
*
2604862 TGCACAAAAAATATGAATATCCGATTT
1 TGCACAAAAAATATGAATATCAGATTT
2604889 TGCACAAAAAATATTCGAA-ATCAGATTT
1 TGCACAAAAAATA-T-GAATATCAGATTT
2604917 AGGAAAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 13 0.52
28 9 0.36
29 3 0.12
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (27 bp):
TGCACAAAAAATATGAATATCAGATTT
Found at i:2607310 original size:21 final size:21
Alignment explanation
Indices: 2607286--2607327 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2607276 AGTTTATTTT
2607286 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
* *
2607307 TAAACTTTGTTTTAATTATCG
1 TAAACTTTATTTCAATTATCG
2607328 AACTTGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:2607364 original size:33 final size:32
Alignment explanation
Indices: 2607320--2607392 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 32
2607310 ACTTTGTTTT
* * *
2607320 AATTATCGAACTTGGAAGTTTTTAAGTATTTG
1 AATTATCGAACTTGAAAGTATTTAAGTATTTC
2607352 AATTTATCGAACTTGAAAGTATTTAAGTATTTC
1 AA-TTATCGAACTTGAAAGTATTTAAGTATTTC
2607385 AATTATCG
1 AATTATCG
2607393 TAAACTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 8 0.22
33 29 0.78
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.42
Consensus pattern (32 bp):
AATTATCGAACTTGAAAGTATTTAAGTATTTC
Found at i:2608872 original size:15 final size:15
Alignment explanation
Indices: 2608852--2608898 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2608842 GACCGCTGCT
* *
2608852 CCAACTTCTTCTCCA
1 CCAACTTCCTCACCA
2608867 CCAACTTCCTCACCA
1 CCAACTTCCTCACCA
* *
2608882 CCTACTTCGTCACCA
1 CCAACTTCCTCACCA
2608897 CC
1 CC
2608899 GGCTGCTGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.21, C:0.51, G:0.02, T:0.26
Consensus pattern (15 bp):
CCAACTTCCTCACCA
Found at i:2610211 original size:2 final size:2
Alignment explanation
Indices: 2610204--2610245 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2610194 ATTTGGTTTA
2610204 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
2610246 CTTAGTACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2612170 original size:3 final size:3
Alignment explanation
Indices: 2612164--2612225 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
2612154 TTAATTTTTT
* * * *
2612164 TTA TTA TTT TTG TT- TTA TTA TTA TTA TTA TTA TTA ATA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2612211 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
2612226 AATAAAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2616376 original size:7 final size:7
Alignment explanation
Indices: 2616333--2616382 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
2616323 TTTTCATACA
2616333 TGCATTT
1 TGCATTT
*
2616340 T-CATTC
1 TGCATTT
2616346 TGCATCTT
1 TGCAT-TT
2616354 TGCATCTT
1 TGCAT-TT
2616362 TGCATTT
1 TGCATTT
*
2616369 TTCATTT
1 TGCATTT
2616376 TGCATTT
1 TGCATTT
2616383 ATACTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 5 0.14
7 18 0.49
8 14 0.38
ACGTcount: A:0.14, C:0.20, G:0.10, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:2616379 original size:14 final size:14
Alignment explanation
Indices: 2616333--2616382 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
2616323 TTTTCATACA
*
2616333 TGCA-TTTTCATTC
1 TGCATTTTTCATTT
*
2616346 TGCATCTTTGCATCTT
1 TGCAT-TTTTCAT-TT
2616362 TGCATTTTTCATTT
1 TGCATTTTTCATTT
2616376 TGCATTT
1 TGCATTT
2616383 ATACTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 4 0.13
14 9 0.29
15 12 0.39
16 6 0.19
ACGTcount: A:0.14, C:0.20, G:0.10, T:0.56
Consensus pattern (14 bp):
TGCATTTTTCATTT
Found at i:2618974 original size:12 final size:11
Alignment explanation
Indices: 2618954--2618982 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2618944 GCAAAGAAAG
2618954 AAGAAAAAAAA
1 AAGAAAAAAAA
2618965 AAGAAAAAAAA
1 AAGAAAAAAAA
2618976 AAGAAAA
1 AAGAAAA
2618983 TTGAATCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:2623602 original size:55 final size:54
Alignment explanation
Indices: 2623536--2623652 Score: 182
Period size: 55 Copynumber: 2.1 Consensus size: 54
2623526 ACTTTAATGA
* *
2623536 TTACGAACATCTGAGCAGAAGCCACA-AAAAAGGATGAATGTATTGTCAAAATGTT
1 TTACGAACATCTGAGCAGAAGCCACAGAAAAA-GATGAATGCACTGTC-AAATGTT
*
2623591 TTACGAACATCTGAGCAGAAGCCACAGGAAAAGATGAATGCACTGTCAAATGTT
1 TTACGAACATCTGAGCAGAAGCCACAGAAAAAGATGAATGCACTGTCAAATGTT
2623645 TTACGAAC
1 TTACGAAC
2623653 CTGTTATTCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
54 15 0.26
55 39 0.67
56 4 0.07
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (54 bp):
TTACGAACATCTGAGCAGAAGCCACAGAAAAAGATGAATGCACTGTCAAATGTT
Found at i:2624044 original size:22 final size:22
Alignment explanation
Indices: 2624015--2624069 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2624005 ATCTACACTC
*
2624015 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
2624037 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
2624059 TTCAAAGATGA
1 TTCAAAGATGA
2624070 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:2625660 original size:76 final size:76
Alignment explanation
Indices: 2624745--2625647 Score: 1689
Period size: 76 Copynumber: 11.9 Consensus size: 76
2624735 CTATTTCCCA
* *
2624745 CATCTGTAAGTCCTTCAGTACATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2624810 AGCCTTAGGGT
66 AGCCTTAGGGT
2624821 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG-CTTTTTGATGTTTTCA
2624886 AAGCCTTAGGGT
65 AAGCCTTAGGGT
2624898 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2624963 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2624974 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAC
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2625039 AGCCTTAGGGT
66 AGCCTTAGGGT
2625050 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2625115 AACCTTAGGGT
66 AGCCTTAGGGT
*
2625126 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2625191 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2625202 CATCTGTAAGTCCTTCAATGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2625267 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2625278 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2625343 AGCCTTAGGGT
66 AGCCTTAGGGT
2625354 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2625419 AACCTTAGGGT
66 AGCCTTAGGGT
*
2625430 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2625495 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2625506 CATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2625571 AGCCTTAGGGT
66 AGCCTTAGGGT
2625582 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2625647 A
66 A
2625648 CCCTCGGGGT
Statistics
Matches: 808, Mismatches: 18, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
76 733 0.91
77 75 0.09
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:2625813 original size:3 final size:3
Alignment explanation
Indices: 2625807--2625868 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
2625797 TTAATTTTTT
* * * *
2625807 TTA TTA TTT TTG TT- TTA TTA TTA TTA TTA TTA TTA ATA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2625854 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
2625869 AATAAAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2631761 original size:21 final size:23
Alignment explanation
Indices: 2631720--2631767 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
2631710 ATTAAATTCG
*
2631720 TTTATCTAATTAAACT-TTTAAT
1 TTTATCTAATTAAACTATTAAAT
2631742 TTTAT-TAATTATAA-TATTAAAT
1 TTTATCTAATTA-AACTATTAAAT
2631764 TTTA
1 TTTA
2631768 ATTTTACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTATCTAATTAAACTATTAAAT
Found at i:2633121 original size:2 final size:2
Alignment explanation
Indices: 2633114--2633142 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2633104 CCTACCATTC
2633114 AT 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 AT A
2633143 ATGCAAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2644264 original size:24 final size:24
Alignment explanation
Indices: 2644237--2644327 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
2644227 TCAAATTTGA
* * *
2644237 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATAATACTTGACCTGG
* * *
2644261 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATAATACTTGACCTGG
* *
2644284 ATTCTGATCTAATACATGACCTGG
1 ATTCTGATATAATACTTGACCTGG
2644308 ATTCTGATATAATACTTGAC
1 ATTCTGATATAATACTTGAC
2644328 TTGAATTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.35
24 37 0.65
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (24 bp):
ATTCTGATATAATACTTGACCTGG
Found at i:2644452 original size:35 final size:35
Alignment explanation
Indices: 2644405--2644479 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
2644395 TGGAGGAAGA
*
2644405 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
*
2644440 TTACTTGCAGGCTCCTCGGCTTTGTGCTTAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
2644475 TTACT
1 TTACT
2644480 ATTCGTGACG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.09, C:0.28, G:0.28, T:0.35
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
Found at i:2646497 original size:31 final size:31
Alignment explanation
Indices: 2646462--2646521 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2646452 GTCATAACCC
* * *
2646462 GACCCGACCCGACTCGTTTACTCGACCCGTT
1 GACCCGACCCGACCCGTTGACCCGACCCGTT
2646493 GACCCGACCCGACCCGTTGACCCGACCCG
1 GACCCGACCCGACCCGTTGACCCGACCCG
2646522 ACCCGTTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.15
Consensus pattern (31 bp):
GACCCGACCCGACCCGTTGACCCGACCCGTT
Found at i:2646505 original size:18 final size:18
Alignment explanation
Indices: 2646484--2646532 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
2646474 CTCGTTTACT
2646484 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
2646502 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
2646520 CGACCCGTTGACC
1 CGACCCGTTGACC
2646533 GTTGACCCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
CGACCCGTTGACCCGACC
Found at i:2649049 original size:24 final size:24
Alignment explanation
Indices: 2649022--2649112 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
2649012 TCAAATTTGA
* *
2649022 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
2649046 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
2649069 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
2649093 ATTCTGATATAATACTTGAC
1 ATTCTGATATGATACTTGAC
2649113 TTGAATTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 21 0.37
24 36 0.63
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:2649237 original size:35 final size:35
Alignment explanation
Indices: 2649190--2649264 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
2649180 TGGAGGAAGA
*
2649190 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
2649225 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
2649260 TTACT
1 TTACT
2649265 GTTCGTGACG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.09, C:0.29, G:0.28, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
Found at i:2653543 original size:18 final size:18
Alignment explanation
Indices: 2653522--2653568 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2653512 TAAAGAATTT
2653522 GAAATGACATATATTGGA
1 GAAATGACATATATTGGA
*
2653540 GAAATGACAGATATTGGA
1 GAAATGACATATATTGGA
*
2653558 GAAATGTCATA
1 GAAATGACATA
2653569 CTTCCTTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (18 bp):
GAAATGACATATATTGGA
Found at i:2655014 original size:29 final size:31
Alignment explanation
Indices: 2654977--2655034 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
2654967 TTACTAGTAT
* *
2654977 AAGAGTTAAGTTGA-TCACTTTA-ATAATTG
1 AAGAATTAAGTTGATTCAATTTATATAATTG
*
2655006 AAGAATTAATTTGATTCAATTTATATAAT
1 AAGAATTAAGTTGATTCAATTTATATAAT
2655035 AAAAATTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.50
30 7 0.29
31 5 0.21
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (31 bp):
AAGAATTAAGTTGATTCAATTTATATAATTG
Found at i:2658773 original size:21 final size:20
Alignment explanation
Indices: 2658727--2658773 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
2658717 GAATTATCTT
*
2658727 TATTTTGGATTTTATTTGGA
1 TATTTTGGATTTTATTTGAA
2658747 TAATTTTAGGA-TTTATTTGAAA
1 T-ATTTT-GGATTTTATTTG-AA
2658769 TATTT
1 TATTT
2658774 CAAATGTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (20 bp):
TATTTTGGATTTTATTTGAA
Found at i:2663986 original size:45 final size:45
Alignment explanation
Indices: 2663926--2664425 Score: 607
Period size: 45 Copynumber: 11.2 Consensus size: 45
2663916 AAACGAATGA
* * *
2663926 ATAAATAAAATGCATAATGGTGCATTATAGGCATGAAATGATGTC
1 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCC
* * * *
2663971 ATAAATGAAAAGCATAACGGTGTATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCC
* * *
2664016 ATAAATGAAATGCATAACGTTGCATTATAGGCATGAAAGGATGCT
1 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCC
2664061 ATAAATGAAATGCATAATGGTGCATTATCA-GCATGAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTAT-AGGCATGAAAGGATGCC
*** * *
2664106 ATAAATGAAATGCATAACAATGCATTATAGGCATGAAGGGATACC
1 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCC
* * *
2664151 ATAAATGAAATGC---AT--TGCATTATCGACATGAAATGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCC
* * *
2664191 ATAAATGAAATGCATAACGGTGTATTATTGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCC
* * *
2664236 ATAAATAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCA
1 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCC
**
2664281 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGTT
1 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCC
* * * * *
2664326 ATAAATGAGATGCATAAAGGTGTATTATCGGCATGAAATGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCC
* * * *
2664371 ATAAATGAAAATACATAATGATGCATTATAAGCATGAACGGATGCC
1 ATAAATG-AAATGCATAATGGTGCATTATAGGCATGAAAGGATGCC
* *
2664417 GTCAATGAA
1 ATAAATGAA
2664426 CATAAAGAAT
Statistics
Matches: 389, Mismatches: 58, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
40 33 0.08
42 1 0.00
43 1 0.00
44 1 0.00
45 318 0.82
46 35 0.09
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (45 bp):
ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCC
Found at i:2664332 original size:220 final size:220
Alignment explanation
Indices: 2663946--2664380 Score: 667
Period size: 220 Copynumber: 2.0 Consensus size: 220
2663936 TGCATAATGG
* *
2663946 TGCATTATAGGCATGAAATGATGTCATAAATGAAAAGCATAACGGTGTATTATCGGCATGAAAGG
1 TGCATTATAGACATGAAATGATGCCATAAATGAAAAGCATAACGGTGTATTATCGGCATGAAAGG
* * *
2664011 ATGCCATAAATGAAATGCATAACGTTGCATTATAGGCATGAAAGGATGCTATAAATGAAATGCAT
66 ATGCCATAAATAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCAATAAATGAAATGCAT
2664076 AATGGTGCATTATCAGCATGAAAGGATGCCATAAATGAAATGCATAACA-ATGCATTATAGGCAT
131 AATGGTGCATTATCAGCATGAAAGGATGCCATAAATGAAATGCATAA-AGATGCATTATAGGCAT
*
2664140 GAAGGGATACCATAAATGAAATGCAT
195 GAAAGGATACCATAAATGAAATGCAT
* * *
2664166 TGCATTATCGACATGAAATGATGCCATAAATGAAATGCATAACGGTGTATTATTGGCATGAAAGG
1 TGCATTATAGACATGAAATGATGCCATAAATGAAAAGCATAACGGTGTATTATCGGCATGAAAGG
* *
2664231 ATGCCATAAATAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCAATAAATGAAATGCAT
66 ATGCCATAAATAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCAATAAATGAAATGCAT
** * * * *
2664296 AATGGTGCATTAT-AGGCATGAAAGGATGTTATAAATGAGATGCATAAAGGTGTATTATCGGCAT
131 AATGGTGCATTATCA-GCATGAAAGGATGCCATAAATGAAATGCATAAAGATGCATTATAGGCAT
* *
2664360 GAAATGATGCCATAAATGAAA
195 GAAAGGATACCATAAATGAAA
2664381 ATACATAATG
Statistics
Matches: 194, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
219 2 0.01
220 192 0.99
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.26
Consensus pattern (220 bp):
TGCATTATAGACATGAAATGATGCCATAAATGAAAAGCATAACGGTGTATTATCGGCATGAAAGG
ATGCCATAAATAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCAATAAATGAAATGCAT
AATGGTGCATTATCAGCATGAAAGGATGCCATAAATGAAATGCATAAAGATGCATTATAGGCATG
AAAGGATACCATAAATGAAATGCAT
Found at i:2669064 original size:16 final size:16
Alignment explanation
Indices: 2669043--2669081 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2669033 AACATAAAAA
*
2669043 AAACATTTCCATTAAG
1 AAACATATCCATTAAG
2669059 AAACATATCCATTAAG
1 AAACATATCCATTAAG
2669075 AAACATA
1 AAACATA
2669082 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (16 bp):
AAACATATCCATTAAG
Found at i:2681481 original size:45 final size:45
Alignment explanation
Indices: 2681409--2681957 Score: 626
Period size: 45 Copynumber: 12.2 Consensus size: 45
2681399 AAACGAATGA
* * *
2681409 ATAAATGAAATGCATAACGGTGAATTATAGGCATGAAAAGATGCC
1 ATAAATGAAATGCATAACGATGCATTATAGGCATGAAAGGATGCC
* * * * *
2681454 ATAAATAAAATGCATAATGATACATTATCA-GCATGAAATGATGTC
1 ATAAATGAAATGCATAACGATGCATTAT-AGGCATGAAAGGATGCC
* *
2681499 ATAAATGAAATGCATAACGGTGCATTATATGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGATGCATTATAGGCATGAAAGGATGCC
* * *
2681544 ATAAATGAAATGCATAACGGTGCATTATCA-GCATGAAATGATGTC
1 ATAAATGAAATGCATAACGATGCATTAT-AGGCATGAAAGGATGCC
* * *
2681589 ATAAATAAAATGCATAACGGTGCATTATAGGCA-GAAATGATGCC
1 ATAAATGAAATGCATAACGATGCATTATAGGCATGAAAGGATGCC
* * *
2681633 ATAAATGAAATGAATAAC-AGTGCATTATCGGCATGAAATGATGCC
1 ATAAATGAAATGCATAACGA-TGCATTATAGGCATGAAAGGATGCC
* * * * *
2681678 ATAAATAAAATACATAACGGTGTATTATAGTCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGATGCATTATAGGCATGAAAGGATGCC
* *
2681723 ATAAATGAAATACATAAC-AGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGA-TGCATTATAGGCATGAAAGGATGCC
* *
2681768 ATAAATGAAATACATAAC-AGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGA-TGCATTATAGGCATGAAAGGATGCC
* **
2681813 ATAAATGAAATGCATAACGATGCATTATAGGCATGAAATGATGAT
1 ATAAATGAAATGCATAACGATGCATTATAGGCATGAAAGGATGCC
* ** *
2681858 ATAAATGAAATGCATAATGGCGCATTATCA-GCATGAAAGGATGTC
1 ATAAATGAAATGCATAACGATGCATTAT-AGGCATGAAAGGATGCC
* * * *
2681903 ATAAATAAAAATGCATAATGATGCATTATAAGCATGAACGGATGCC
1 ATAAAT-GAAATGCATAACGATGCATTATAGGCATGAAAGGATGCC
*
2681949 ATCAATGAA
1 ATAAATGAA
2681958 CATAAAGAAT
Statistics
Matches: 440, Mismatches: 52, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
44 40 0.09
45 359 0.82
46 41 0.09
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGATGCATTATAGGCATGAAAGGATGCC
Found at i:2683900 original size:24 final size:24
Alignment explanation
Indices: 2683873--2683960 Score: 131
Period size: 24 Copynumber: 3.5 Consensus size: 24
2683863 TTTTAATTTT
2683873 AATATTAATTTTTTAAATAAATTA
1 AATATTAATTTTTTAAATAAATTA
2683897 AATATTAATTTTTTAAATAAATTA
1 AATATTAATTTTTTAAATAAATTA
*
2683921 AATATTAATTTTTTAATATTATATTA
1 AATATTAATTTTTTAA-A-TAAATTA
2683947 TAGATATTAATTTT
1 -A-ATATTAATTTT
2683961 AATATTAATT
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
24 40 0.68
25 1 0.02
26 6 0.10
27 1 0.02
28 11 0.19
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
AATATTAATTTTTTAAATAAATTA
Found at i:2683981 original size:63 final size:65
Alignment explanation
Indices: 2683897--2684025 Score: 235
Period size: 63 Copynumber: 2.0 Consensus size: 65
2683887 AAATAAATTA
2683897 AATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA-TTAATTTT
1 AATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTTAATTTT
*
2683961 AATATTAA-TTTTTAAATAAATTAAGTATTAATTTTTTAATATTATATTATAGATATTTAATTTT
1 AATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTTAATTTT
2684025 A
1 A
2684026 TATCATATAA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
63 46 0.73
64 17 0.27
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (65 bp):
AATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTTAATTTT
Found at i:2683993 original size:23 final size:22
Alignment explanation
Indices: 2683871--2684001 Score: 112
Period size: 24 Copynumber: 5.9 Consensus size: 22
2683861 GATTTTAATT
2683871 TTAATATTAATTTTTTAAATAAA
1 TTAATATTAA-TTTTTAAATAAA
2683894 TTAAATATTAATTTTTTAAATAAA
1 TT-AATATTAA-TTTTTAAATAAA
*
2683918 TTAAATATTAATTTTTTAAT--A
1 TT-AATATTAATTTTTAAATAAA
* * *
2683939 TT-ATATTATAGATATT-AAT--T
1 TTAATATTA-A-TTTTTAAATAAA
2683959 TTAATATTAATTTTTAAATAAA
1 TTAATATTAATTTTTAAATAAA
*
2683981 TTAAGTATTAATTTTTTAATA
1 TTAA-TATTAATTTTTAAATA
2684002 TTATATTATA
Statistics
Matches: 92, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
19 9 0.10
20 10 0.11
21 12 0.13
22 4 0.04
23 25 0.27
24 32 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATATTAATTTTTAAATAAA
Found at i:2684080 original size:20 final size:19
Alignment explanation
Indices: 2684020--2684081 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
2684010 TAGATATTTA
*
2684020 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
2684039 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
2684057 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
2684077 ATTTT
1 ATTTT
2684082 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:2684587 original size:31 final size:31
Alignment explanation
Indices: 2684550--2684610 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2684540 GTAGTTGTAT
* *
2684550 AAATTATTTAAATTTCAATATTGTAAAACTA
1 AAATTATTTAAATCTCAATATTGCAAAACTA
*
2684581 AAATTATTTAAATCTCAGTATTGCAAAACT
1 AAATTATTTAAATCTCAATATTGCAAAACT
2684611 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (31 bp):
AAATTATTTAAATCTCAATATTGCAAAACTA
Found at i:2685523 original size:23 final size:25
Alignment explanation
Indices: 2685496--2685542 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2685486 ATTAATTGTG
2685496 TCCA-CTTTCGGTGCA-TTGTTTAA
1 TCCACCTTTCGGTGCATTTGTTTAA
*
2685519 TCCACCTTTCGGTGGATTTGTTTA
1 TCCACCTTTCGGTGCATTTGTTTA
2685543 GTTTTCAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (25 bp):
TCCACCTTTCGGTGCATTTGTTTAA
Found at i:2691233 original size:2 final size:2
Alignment explanation
Indices: 2691222--2691283 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
2691212 TGATTATAAA
2691222 AT AT -T 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
2691263 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
2691284 GATCTCCTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.