Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 23 of 214
Found at i:6457555 original size:13 final size:13
Alignment explanation
Indices: 6457517--6457594 Score: 60
Period size: 13 Copynumber: 6.3 Consensus size: 13
6457507 AGCACTTAAA
*
6457517 ATTTATGCATTTT
1 ATTTATACATTTT
*
6457530 ATTT-T-TA-TTT
1 ATTTATACATTTT
6457540 ATTTATACATTTT
1 ATTTATACATTTT
*
6457553 ATTT-TATCAATTT
1 ATTTATA-CATTTT
*
6457566 A-CTATATCA-TTT
1 ATTTATA-CATTTT
6457578 ATTTATACATTTT
1 ATTTATACATTTT
6457591 ATTT
1 ATTT
6457595 TTATTTTATC
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 7 0.13
11 2 0.04
12 11 0.21
13 33 0.62
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (13 bp):
ATTTATACATTTT
Found at i:6457565 original size:22 final size:23
Alignment explanation
Indices: 6457516--6457566 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
6457506 TAGCACTTAA
* *
6457516 AATTTATGCATTTTATTTTTATT
1 AATTTATACATTTTATTTTTATC
*
6457539 TATTTATACATTTTA-TTTTATC
1 AATTTATACATTTTATTTTTATC
6457561 AATTTA
1 AATTTA
6457567 CTATATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (23 bp):
AATTTATACATTTTATTTTTATC
Found at i:6457799 original size:16 final size:15
Alignment explanation
Indices: 6457780--6457809 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6457770 TCTTCATCTA
6457780 TTTATTTATTCATTTG
1 TTTATTTA-TCATTTG
6457796 TTTATTTATCATTT
1 TTTATTTATCATTT
6457810 AAACGTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTATTTATCATTTG
Found at i:6461342 original size:6 final size:6
Alignment explanation
Indices: 6461331--6461365 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
6461321 CTTCAGCTTT
*
6461331 TTTTTC TTTTTC TTTTTC TTTTTT TTTTGTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT-TC TTTT
6461366 AGAGGTCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:6461353 original size:13 final size:12
Alignment explanation
Indices: 6461328--6461365 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
6461318 CATCTTCAGC
6461328 TTTTTTTTCTTT
1 TTTTTTTTCTTT
*
6461340 TTCTTTTTCTTT
1 TTTTTTTTCTTT
6461352 TTTTTTTGTCTTT
1 TTTTTTT-TCTTT
6461365 T
1 T
6461366 AGAGGTCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.87
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:6463163 original size:9 final size:9
Alignment explanation
Indices: 6463149--6463190 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
6463139 TTGTTATAAT
6463149 AATTAATAC
1 AATTAATAC
6463158 AATTAATAC
1 AATTAATAC
6463167 AATT-A-AC
1 AATTAATAC
6463174 AATTAATAC
1 AATTAATAC
6463183 AATTAATA
1 AATTAATA
6463191 ATTTGATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.19
8 2 0.06
9 23 0.74
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (9 bp):
AATTAATAC
Found at i:6463175 original size:16 final size:16
Alignment explanation
Indices: 6463156--6463193 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
6463146 AATAATTAAT
6463156 ACAATTAATACAATTA
1 ACAATTAATACAATTA
6463172 ACAATTAATACAATTA
1 ACAATTAATACAATTA
*
6463188 ATAATT
1 ACAATT
6463194 TGATAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
ACAATTAATACAATTA
Found at i:6470135 original size:44 final size:44
Alignment explanation
Indices: 6470033--6470135 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
6470023 TCTTATCTCT
* * * *
6470033 CTGAAGTTACAGTGGAACGAGATGAAGTTACAAGTCCTATATCC
1 CTGAAGTTACAGTGGAACAAGATGAAGCTACAAATCCTATACCC
* ** *
6470077 CAGAAGTTGTAGTGGAACAAGATGAAGCTATAAATCCTATACCC
1 CTGAAGTTACAGTGGAACAAGATGAAGCTACAAATCCTATACCC
6470121 CTGAAGTTACAGTGG
1 CTGAAGTTACAGTGG
6470136 GTTGGAATGA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.24
Consensus pattern (44 bp):
CTGAAGTTACAGTGGAACAAGATGAAGCTACAAATCCTATACCC
Found at i:6471487 original size:31 final size:28
Alignment explanation
Indices: 6471443--6471509 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 28
6471433 GTCCCTTCAC
* *
6471443 TTTTTTTTCTTTTTAATTTTGTCCTATTTCA
1 TTTTATTT-TTTTTAATTTTATCCT-TTT-A
*
6471474 TCTTTATTTTTTTTATTTTTATCCTTTTA
1 T-TTTATTTTTTTTAATTTTATCCTTTTA
6471503 TTTTATT
1 TTTTATT
6471510 CTTGTGCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 6 0.19
29 2 0.06
30 3 0.09
31 15 0.47
32 6 0.19
ACGTcount: A:0.13, C:0.10, G:0.01, T:0.75
Consensus pattern (28 bp):
TTTTATTTTTTTTAATTTTATCCTTTTA
Found at i:6472703 original size:27 final size:27
Alignment explanation
Indices: 6472664--6472716 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
6472654 GTTACCGTTT
6472664 TTGGGCGTCATGAAGGCACTTAGGTTG
1 TTGGGCGTCATGAAGGCACTTAGGTTG
*
6472691 TTGGGCGTTATGAAGGCACTTAGGTT
1 TTGGGCGTCATGAAGGCACTTAGGTT
6472717 TTAACCCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.13, G:0.36, T:0.32
Consensus pattern (27 bp):
TTGGGCGTCATGAAGGCACTTAGGTTG
Found at i:6473029 original size:45 final size:45
Alignment explanation
Indices: 6472975--6473066 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
6472965 AAATTGATTA
6472975 TTATTTAGTTCTATGTTAATTGAGCTTGAACAGTTAAATTCATAG
1 TTATTTAGTTCTATGTTAATTGAGCTTGAACAGTTAAATTCATAG
6473020 TTATTTAGTTCTATGTTAATTGAGCTTGAACAGTTAAATTCATAG
1 TTATTTAGTTCTATGTTAATTGAGCTTGAACAGTTAAATTCATAG
6473065 TT
1 TT
6473067 TGACAATAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (45 bp):
TTATTTAGTTCTATGTTAATTGAGCTTGAACAGTTAAATTCATAG
Found at i:6479094 original size:18 final size:18
Alignment explanation
Indices: 6479073--6479118 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
6479063 TAATTTAGCC
*
6479073 ATTTTTATTTCTATTATA
1 ATTTTTATTTCTAGTATA
6479091 ATTTTTATTTCTAGTATA
1 ATTTTTATTTCTAGTATA
6479109 ATTTTTATTT
1 ATTTTTATTT
6479119 TGTTTTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTTATTTCTAGTATA
Found at i:6479128 original size:23 final size:23
Alignment explanation
Indices: 6479093--6479138 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6479083 CTATTATAAT
6479093 TTTTATTTCTAGTATAATTTTTA
1 TTTTATTTCTAGTATAATTTTTA
* * *
6479116 TTTTGTTTTTAGTTTAATTTTTA
1 TTTTATTTCTAGTATAATTTTTA
6479139 CATTCTAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.70
Consensus pattern (23 bp):
TTTTATTTCTAGTATAATTTTTA
Found at i:6483035 original size:6 final size:6
Alignment explanation
Indices: 6483026--6483092 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
6483016 TTTATTTTCT
* * * *
6483026 TTTTAG TTTTAG TTTTA- TTTTA- TGTCTA- TGATTAT TTTTAT TTTTAG
1 TTTTAG TTTTAG TTTTAG TTTTAG T-TTTAG T-TTTAG TTTTAG TTTTAG
6483073 TTTTAG TTTTAG TTTTAG TT
1 TTTTAG TTTTAG TTTTAG TT
6483093 GTTTTAGTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
5 6 0.11
6 47 0.87
7 1 0.02
ACGTcount: A:0.18, C:0.01, G:0.12, T:0.69
Consensus pattern (6 bp):
TTTTAG
Found at i:6484718 original size:22 final size:23
Alignment explanation
Indices: 6484692--6484738 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
6484682 TTCCTAATTA
* *
6484692 ATGGCTCTC-TGAGCTTCCCGAT
1 ATGGCTCGCTTGAACTTCCCGAT
6484714 ATGGCTCGCTTGAACTTCCCGAT
1 ATGGCTCGCTTGAACTTCCCGAT
6484737 AT
1 AT
6484739 ATGGTTATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.32
Consensus pattern (23 bp):
ATGGCTCGCTTGAACTTCCCGAT
Found at i:6488030 original size:30 final size:30
Alignment explanation
Indices: 6487942--6488030 Score: 142
Period size: 30 Copynumber: 3.0 Consensus size: 30
6487932 AGCTTCAGGG
* * *
6487942 GCCACACGGGTTGGGCACATGCCCATGTAA
1 GCCACACGGGCTGGCCACATGCCCATGTGA
*
6487972 GCCACACGGGCTGGCCATATGCCCATGTGA
1 GCCACACGGGCTGGCCACATGCCCATGTGA
6488002 GCCACACGGGCTGGCCACATGCCCATGTG
1 GCCACACGGGCTGGCCACATGCCCATGTG
6488031 CCAGCCTGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.20, C:0.34, G:0.30, T:0.16
Consensus pattern (30 bp):
GCCACACGGGCTGGCCACATGCCCATGTGA
Found at i:6498167 original size:14 final size:14
Alignment explanation
Indices: 6498148--6498174 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6498138 ACCTAAACTA
6498148 TTTATAGAAGAAAT
1 TTTATAGAAGAAAT
6498162 TTTATAGAAGAAA
1 TTTATAGAAGAAA
6498175 ATCCTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (14 bp):
TTTATAGAAGAAAT
Found at i:6499716 original size:14 final size:14
Alignment explanation
Indices: 6499695--6499728 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6499685 TGGTATGGGT
6499695 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
6499708 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
6499722 TTATAGG
1 TTATAGG
6499729 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:6509042 original size:9 final size:10
Alignment explanation
Indices: 6509020--6509053 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
6509010 TAGATTTTTA
6509020 AAAAAAATTGT
1 AAAAAAATT-T
6509031 AAAAAAA-TT
1 AAAAAAATTT
6509040 AAAAAAATTT
1 AAAAAAATTT
6509050 AAAA
1 AAAA
6509054 TTTTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.36
10 7 0.32
11 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:6509053 original size:27 final size:27
Alignment explanation
Indices: 6509023--6509078 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
6509013 ATTTTTAAAA
*
6509023 AAAATTGTAAAAAAATTAAAAAAATTT
1 AAAATTGTAAAAAAATCAAAAAAATTT
* * *
6509050 AAAATTTTATAAAAATCATAAAAATTT
1 AAAATTGTAAAAAAATCAAAAAAATTT
6509077 AA
1 AA
6509079 CGACCCCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAATTGTAAAAAAATCAAAAAAATTT
Found at i:6509925 original size:19 final size:20
Alignment explanation
Indices: 6509901--6509960 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 20
6509891 ATTCTTTACA
6509901 TTTTATAATTTTTTAC-AAT
1 TTTTATAATTTTTTACTAAT
6509920 TTTTATAATTTTTT-CTAAT
1 TTTTATAATTTTTTACTAAT
* *
6509939 TTTTAATAACTTTTTAATAAT
1 TTTT-ATAATTTTTTACTAAT
6509960 T
1 T
6509961 GAATTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.03
19 21 0.58
20 9 0.25
21 5 0.14
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTTTACTAAT
Found at i:6509933 original size:11 final size:10
Alignment explanation
Indices: 6509901--6509960 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
6509891 ATTCTTTACA
6509901 TTTTATAATT
1 TTTTATAATT
*
6509911 TTTTACAA-T
1 TTTTATAATT
6509920 TTTTATAATT
1 TTTTATAATT
*
6509930 TTTTCTAATT
1 TTTTATAATT
*
6509940 TTTAATAACTT
1 TTTTATAA-TT
*
6509951 TTTAATAATT
1 TTTTATAATT
6509961 GAATTTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
9 8 0.19
10 25 0.58
11 10 0.23
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:6513292 original size:27 final size:26
Alignment explanation
Indices: 6513262--6513317 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
6513252 AGGCTATCCC
6513262 TTCATAATT-CACCACAAAGGCATTCAT
1 TTCAT-ATTGCACCACAAAGGCATTC-T
* *
6513289 TTCATATTGCGCCACAAAGGCTTTCT
1 TTCATATTGCACCACAAAGGCATTCT
6513315 TTC
1 TTC
6513318 TTTCCTGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (26 bp):
TTCATATTGCACCACAAAGGCATTCT
Found at i:6514341 original size:61 final size:61
Alignment explanation
Indices: 6514266--6514393 Score: 256
Period size: 61 Copynumber: 2.1 Consensus size: 61
6514256 ATTACTAAAT
6514266 TATCTTATCAAAAGTTTACAACTTCCAAGAAACCTAATTTAATATCCCCTTATCTTTTAAC
1 TATCTTATCAAAAGTTTACAACTTCCAAGAAACCTAATTTAATATCCCCTTATCTTTTAAC
6514327 TATCTTATCAAAAGTTTACAACTTCCAAGAAACCTAATTTAATATCCCCTTATCTTTTAAC
1 TATCTTATCAAAAGTTTACAACTTCCAAGAAACCTAATTTAATATCCCCTTATCTTTTAAC
6514388 TATCTT
1 TATCTT
6514394 GGTTCACATT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (61 bp):
TATCTTATCAAAAGTTTACAACTTCCAAGAAACCTAATTTAATATCCCCTTATCTTTTAAC
Found at i:6517486 original size:22 final size:22
Alignment explanation
Indices: 6517443--6517486 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
6517433 TATATAAATT
* **
6517443 AAGTTAAAATTATTGTGGGTCA
1 AAGTCAAAATTATCATGGGTCA
*
6517465 AAGTCAAAATTATCATGTGTCA
1 AAGTCAAAATTATCATGGGTCA
6517487 TAATTAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (22 bp):
AAGTCAAAATTATCATGGGTCA
Found at i:6520887 original size:12 final size:12
Alignment explanation
Indices: 6520870--6520912 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
6520860 TAAGGGAAGA
6520870 GAGCCCAAGCAT
1 GAGCCCAAGCAT
*
6520882 GAGCCCAAGTAT
1 GAGCCCAAGCAT
6520894 GAGCCCAAGCAT
1 GAGCCCAAGCAT
6520906 GAGCCCA
1 GAGCCCA
6520913 GGTATGTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.33, C:0.33, G:0.26, T:0.09
Consensus pattern (12 bp):
GAGCCCAAGCAT
Found at i:6520902 original size:24 final size:24
Alignment explanation
Indices: 6520870--6520918 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
6520860 TAAGGGAAGA
6520870 GAGCCCAAGCATGAGCCCAAGTAT
1 GAGCCCAAGCATGAGCCCAAGTAT
*
6520894 GAGCCCAAGCATGAGCCCAGGTAT
1 GAGCCCAAGCATGAGCCCAAGTAT
6520918 G
1 G
6520919 TCGCCTTTCA
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:0.29, G:0.29, T:0.12
Consensus pattern (24 bp):
GAGCCCAAGCATGAGCCCAAGTAT
Found at i:6527474 original size:19 final size:22
Alignment explanation
Indices: 6527436--6527484 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
6527426 AAATAGTGAG
*
6527436 AATT-TATTTTCTAAGTAT-A-
1 AATTCTATTTTCTAAGAATAAC
6527455 AATTCTATTTTCT-AGAATAAC
1 AATTCTATTTTCTAAGAATAAC
6527476 AATTCTATT
1 AATTCTATT
6527485 GGTTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 8 0.31
20 9 0.35
21 9 0.35
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (22 bp):
AATTCTATTTTCTAAGAATAAC
Found at i:6530042 original size:17 final size:17
Alignment explanation
Indices: 6530011--6530043 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6530001 TAGAATTGAG
6530011 TTGAGATAATTATTTAA
1 TTGAGATAATTATTTAA
6530028 TTGAG-TAATTAATTTA
1 TTGAGATAATT-ATTTA
6530044 GTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
TTGAGATAATTATTTAA
Found at i:6530051 original size:13 final size:13
Alignment explanation
Indices: 6530024--6530065 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
6530014 AGATAATTAT
*
6530024 TTAATTGAG-TAA
1 TTAATTTAGTTAA
6530036 TTAATTTAGTTAA
1 TTAATTTAGTTAA
* *
6530049 TTAAATTAATTAA
1 TTAATTTAGTTAA
6530062 TTAA
1 TTAA
6530066 ATAATATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
TTAATTTAGTTAA
Found at i:6530066 original size:13 final size:13
Alignment explanation
Indices: 6530033--6530067 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
6530023 TTTAATTGAG
* *
6530033 TAATTAATTTAGT
1 TAATTAAATTAAT
6530046 TAATTAAATTAAT
1 TAATTAAATTAAT
6530059 TAATTAAAT
1 TAATTAAAT
6530068 AATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:6531488 original size:15 final size:16
Alignment explanation
Indices: 6531458--6531491 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6531448 ACATGTGTGC
*
6531458 ATAAAACAACAAATTT
1 ATAAAACAAAAAATTT
6531474 ATAAAA-AAAAAATTT
1 ATAAAACAAAAAATTT
6531489 ATA
1 ATA
6531492 GCAAGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAACAAAAAATTT
Found at i:6533662 original size:19 final size:19
Alignment explanation
Indices: 6533632--6533681 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
6533622 AAAATATAGA
6533632 AAAAGTAAAAAGTA-AAAAT
1 AAAAG-AAAAAGTACAAAAT
6533651 AAGAAGAAAAAGTACAAAAT
1 AA-AAGAAAAAGTACAAAAT
*
6533671 AAAAGCAAAAG
1 AAAAGAAAAAG
6533682 CCTTATGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.72, C:0.04, G:0.14, T:0.10
Consensus pattern (19 bp):
AAAAGAAAAAGTACAAAAT
Found at i:6540339 original size:26 final size:27
Alignment explanation
Indices: 6540278--6540336 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
6540268 GTCAGGAAAT
*
6540278 GAAGCCTTTGTGGATAACTTTAAAAAG
1 GAAGCCTTTGTGGATAACTCTAAAAAG
* *
6540305 AAAGCCTTTGTGGCTAACTCTAAAAAG
1 GAAGCCTTTGTGGATAACTCTAAAAAG
6540332 GAAGC
1 GAAGC
6540337 TTTCAAGGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.25
Consensus pattern (27 bp):
GAAGCCTTTGTGGATAACTCTAAAAAG
Found at i:6540452 original size:28 final size:28
Alignment explanation
Indices: 6540386--6540452 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
6540376 TTGTAATAGG
*
6540386 ATAGCCTTTGTGGCGCAATGTAAAAGGA
1 ATAGCCTTTGTGGCGCAATGTAAAAAGA
* *
6540414 ACA-CCTGTGTGGCG-AAT-TATGAAAAGA
1 ATAGCCTTTGTGGCGCAATGTA--AAAAGA
6540441 ATAGCCTTTGTG
1 ATAGCCTTTGTG
6540453 ATGGATTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 2 0.06
26 3 0.10
27 17 0.55
28 9 0.29
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (28 bp):
ATAGCCTTTGTGGCGCAATGTAAAAAGA
Found at i:6542533 original size:11 final size:11
Alignment explanation
Indices: 6542517--6542542 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6542507 TAGAAGAGAC
6542517 GAAACAGGGGA
1 GAAACAGGGGA
6542528 GAAACAGGGGA
1 GAAACAGGGGA
6542539 GAAA
1 GAAA
6542543 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:6543218 original size:3 final size:3
Alignment explanation
Indices: 6543198--6543233 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
6543188 GTGCGGTAAG
* *
6543198 TAT TAA TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6543234 GAGTGGGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:6549511 original size:10 final size:10
Alignment explanation
Indices: 6549496--6549528 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
6549486 AATATAAAGT
6549496 AAATGAAATA
1 AAATGAAATA
6549506 AAATGAAATA
1 AAATGAAATA
6549516 AAATGAAATA
1 AAATGAAATA
6549526 AAA
1 AAA
6549529 ACAAAGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (10 bp):
AAATGAAATA
Found at i:6549584 original size:11 final size:11
Alignment explanation
Indices: 6549568--6549595 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
6549558 TAGAAGAGAC
6549568 GAAACAGGGGA
1 GAAACAGGGGA
6549579 GAAACAGGGGA
1 GAAACAGGGGA
6549590 GAAACA
1 GAAACA
6549596 AGAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.11, G:0.39, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:6550672 original size:37 final size:39
Alignment explanation
Indices: 6550622--6550713 Score: 109
Period size: 39 Copynumber: 2.4 Consensus size: 39
6550612 CGGATAGATT
* *
6550622 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-ACTTTGC
1 CGATGAGGCACTGGGTACCAACTATTGCTTCGAACTAT-C
* **
6550659 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTACCAACTATTGCTTCGAACTATC
6550698 CGATGAGGCACTGGGT
1 CGATGAGGCACTGGGT
6550714 GTCATACTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 21 0.46
40 4 0.09
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGGCACTGGGTACCAACTATTGCTTCGAACTATC
Found at i:6556257 original size:125 final size:125
Alignment explanation
Indices: 6556014--6556580 Score: 645
Period size: 126 Copynumber: 4.5 Consensus size: 125
6556004 GATAAAATTA
* * * * * *
6556014 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
6556079 AGGTCCTGGGAAAATAATTTCGACTTGATGTTTTTGAGCAAATAGTTTAAAAAACATTTC
66 AGGTCCTAGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAAACACTTC
* ** *
6556139 AAGCAGGATGCTTTGTGAGAAGAATTTGTGAAATCGCGCCGTCGTGGACGCGCTTTTACTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
6556204 TGGTCCTAGAAGAAATAATTTCGAGTTGATGTTTTTGAGCAAATAGTTTAAAAAACGCTTC
66 AGGTCCTAGAA-AAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAAACACTTC
* * * * *
6556265 AAACAGGATGCTTTATAAGAAGAATTTGTGAAGTCGTGCCCACGTGGATGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * * * * *
6556330 AGGTCCTAAAAAAATAATTTTGAGTTAACGTTTCTGAGCAAATAATATAAAACAACGCTGC
66 AGGTCCTAGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAA-AACACTTC
* * * * * * *
6556391 AAGTAGCATGCTATT-TGAGAAGAATTTGTGAAATTGTGCCCTCGTGAACGTGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * * * *
6556455 TTGGTCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAATAGTAT-AAAATCGA-TTC
65 TAGGTCCTAGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAAAC-ACTTC
* * *
6556515 TAGAAGGATGCTTTATGAGAAGAATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
6556580 A
66 A
6556581 ACATGTTTGG
Statistics
Matches: 374, Mismatches: 63, Indels: 11
0.83 0.14 0.02
Matches are distributed among these distances:
123 2 0.01
124 57 0.15
125 101 0.27
126 212 0.57
127 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTAGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAAACACTTC
Found at i:6556473 original size:251 final size:251
Alignment explanation
Indices: 6556012--6556580 Score: 714
Period size: 251 Copynumber: 2.3 Consensus size: 251
6556002 AAGATAAAAT
* * * * *
6556012 TAAAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTACA
1 TAAA-CAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACA
*** * * * * * * *
6556077 GTAGGTCCTGGGAAAATAATTTCGACTTGATGTTTTTGAGCAAATAGTTTAAAAAACATTTCAAG
65 GTAGGTCCTAAAAAAATAATTTCGACTTAACGTTTCTGAGCAAATAATATAAAAAACACTGCAAG
* * *
6556142 CAGGATGCTTTGTGAGAAGAATTTGTGAAATCGCGCCGTCGTGGACGCGCTTTTACTACAGTTGG
130 CAGCATGCTTTGTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACGCGCTTTTACTACAGTTGG
* * * * *
6556207 TCCTAGAAGAAATAATTTCGAGTTGATGTTTTTGAGCAAATAGTTTAAAAAACGCTTC
195 TCCTAGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTAT-AAAAACGATTC
* *
6556265 -AAACAGGATGCTTTATAAGAAGAATTTGTGAAGTCGTGCCCACGTGGATGCGCTTTTGCTACAG
1 TAAACAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * *
6556329 TAGGTCCTAAAAAAATAATTTTGAGTTAACGTTTCTGAGCAAATAATATAAAACAACGCTGCAAG
66 TAGGTCCTAAAAAAATAATTTCGACTTAACGTTTCTGAGCAAATAATATAAAA-AACACTGCAAG
* * * * *
6556394 TAGCATGCTATT-TGAGAAGAATTTGTGAAATTGTGCCCTCGTGAACGTGCTTTTGCTACAGTTG
130 CAGCATGCT-TTGTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACGCGCTTTTACTACAGTTG
* * *
6556458 GTCCTGGAA-AAATAATTTTGACTTGACGTTTCTGAGCAAATAGTATAAAATCGATTC
194 GTCCTAGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAACGATTC
* * * *
6556515 TAGA-AGGATGCTTTATGAGAAGAATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAG
1 TAAACAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAG
6556579 TA
66 TA
6556581 ACATGTTTGG
Statistics
Matches: 271, Mismatches: 42, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
250 66 0.24
251 131 0.48
252 72 0.27
253 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (251 bp):
TAAACAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAG
TAGGTCCTAAAAAAATAATTTCGACTTAACGTTTCTGAGCAAATAATATAAAAAACACTGCAAGC
AGCATGCTTTGTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACGCGCTTTTACTACAGTTGGT
CCTAGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAACGATTC
Found at i:6559747 original size:21 final size:21
Alignment explanation
Indices: 6559721--6560967 Score: 1176
Period size: 21 Copynumber: 57.8 Consensus size: 21
6559711 TCAAATTATA
6559721 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
6559742 TTTAAGTTAAGGGTTAAGGGTTAAGGAT
1 TTTAAGTTAAGGGTT-AGGG-T-----T
6559770 TTTAAAGTTAAGGGTCTAGGGTT
1 TTT-AAGTTAAGGGT-TAGGGTT
* * *
6559793 TTAAAGTTAAGGATTTATGGTT
1 TTTAAGTTAAGG-GTTAGGGTT
*
6559815 TTTAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * **
6559836 TTTAGGTTTAGGGTTTATAGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
6559858 TTTAATTTAAGGGTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
6559879 TTTAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* *
6559901 TTAAAGTTAATGGTTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTT
*
6559923 TTAAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
6559944 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
6559966 TTTAAGTTAAGGGTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTT
6559987 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
6560009 TTAAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* * *
6560031 TTAAAGTTAAGGTTTAAGG--
1 TTTAAGTTAAGGGTTAGGGTT
*
6560050 TTTAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* * *
6560072 TTAAAGTTAAGGTTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6560093 TTTAGGTTAAGGGTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6560114 TTTAGGTTAAGGTTTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTT
*
6560134 TTTAATTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6560155 TTTAAGTTAAAGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6560176 TTCAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6560197 TTTAGGTTAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * * *
6560218 TTTAATTTAATGATTAGGATT
1 TTTAAGTTAAGGGTTAGGGTT
*
6560239 TTTAAGTTAAGCGTTTAGGGTT
1 TTTAAGTTAAG-GGTTAGGGTT
*
6560261 TTTAAGTTAATGGGTCTAAGGTT
1 TTTAAGTTAA-GGGT-TAGGGTT
* *
6560284 TTAAAGTTAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6560305 TTCAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6560326 TTTAGGTTAAAGGTTTAGGG-T
1 TTTAAGTT-AAGGGTTAGGGTT
* *
6560347 TTTAATTTAAGGGTTAAGGTTT
1 TTTAAGTTAAGGGTT-AGGGTT
6560369 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
6560391 TTTAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* * *
6560413 TTAAAGTTAAGGTTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6560434 TTCAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6560455 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
6560477 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
6560499 TTAAAGTTAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
** *
6560520 TTTGGGTTAAGAGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
6560541 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
6560563 TTTAATTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
6560584 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
6560606 TCTAAGTTAAGGGTCTAGGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
** * *
6560628 TAAAAGTTAAAGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
6560649 TTTCAGGTTAAGGGTTAGGG-T
1 TTT-AAGTTAAGGGTTAGGGTT
* **
6560670 TTTAGGTTAAAGATTTAGGGTT
1 TTTAAGTT-AAGGGTTAGGGTT
* * * *
6560692 TTAAATTTAAGGATTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTT
6560713 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGG-TTAGGGTT
*
6560734 TTTAAGTTAAGGGTCTAAGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* *
6560756 TTAAAGTTAAGGGTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
6560777 TTTAGGTTTAGGGGTTATGGTT
1 TTTAAG-TTAAGGGTTAGGGTT
* *
6560799 TTTAATTTAAGGGTTTAGGTTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
6560821 TTTAATTTAAAAGTTTAGGGTTT
1 TTTAAGTT-AAGGGTTAGGG-TT
*
6560844 TTTAAGTTAAGGGTTTAAGG-T
1 TTTAAGTTAAGGG-TTAGGGTT
* *
6560865 TTTAAGGTTAATGGTTAAGGTT
1 TTTAA-GTTAAGGGTTAGGGTT
*
6560887 TTTAGGTTAAGGGGTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTT
* *
6560909 TTAAAGTTAATGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6560930 TTTAGGTTAATGGTTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTT
* *
6560952 TTAAAGTTAAAGGTTA
1 TTTAAGTTAAGGGTTA
6560968 ATGAGTTAGG
Statistics
Matches: 1023, Mismatches: 156, Indels: 94
0.80 0.12 0.07
Matches are distributed among these distances:
19 12 0.01
20 33 0.03
21 467 0.46
22 447 0.44
23 43 0.04
28 5 0.00
29 15 0.01
30 1 0.00
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.44
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:6559760 original size:28 final size:29
Alignment explanation
Indices: 6559726--6559792 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
6559716 TTATATTTAA
* *
6559726 GTTAAGGGTT-AGGGTTTTTAAGTTAAGG
1 GTTAAGGGTTAAGGATTTTAAAGTTAAGG
6559754 GTTAAGGGTTAAGGATTTTAAAGTTAAGG
1 GTTAAGGGTTAAGGATTTTAAAGTTAAGG
6559783 GTCT-AGGGTT
1 GT-TAAGGGTT
6559793 TTAAAGTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 10 0.29
29 24 0.69
30 1 0.03
ACGTcount: A:0.27, C:0.01, G:0.34, T:0.37
Consensus pattern (29 bp):
GTTAAGGGTTAAGGATTTTAAAGTTAAGG
Found at i:6559779 original size:22 final size:22
Alignment explanation
Indices: 6559754--6560968 Score: 981
Period size: 22 Copynumber: 56.5 Consensus size: 22
6559744 TAAGTTAAGG
* *
6559754 GTTAAGGGTTAAGGATTTTAAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6559776 GTTAAGGGTCT-AGGGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* * * *
6559798 GTTAAGGATTTATGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6559820 GTTAAGGGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
* * **
6559841 GTTTAGGGTTTATAGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6559863 TTTAAGGGTT-ATGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6559884 GTTAAGGGTCT-ATGGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* * *
6559906 GTTAATGGTTTAGGGTTTTAAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6559928 GTTAAGGGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6559949 GTTAAGGGTTTAGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
6559971 GTTAAGGGTTAA-GGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6559992 GTTAAGGGTTTAGGGTTTTAAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6560014 GTTAAGGGTCT-ATGGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
*
6560036 GTTAAGGTTTAA-GG--TTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6560055 GTTAAGGGTCT-ATGGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* *
6560077 GTTAAGGTTTAA-GGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6560098 GTTAAGGGTT-ATGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560119 GTTAA-GGTTTAGGG-TTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560139 TTTAAGGGTT-AGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* * * *
6560160 GTTAA-AGTTTAGGGTTTTCAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560181 GTTAAGGGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560202 GTTAA-GGTTTAGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* * * *
6560223 TTTAATGATT-AGGATTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6560244 GTTAAGCGTTTAGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560266 GTTAATGGGTCTAA-GGTTTTAAA
1 GTTAA-GGGT-TAAGGGTTTTTAA
* * *
6560289 GTTAA-GGTTTAGGGTTTTCAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560310 GTTAAGGGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6560331 GTTAAAGGTTTAGGG-TTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6560352 TTTAAGGGTTAAGGTTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560374 GTTAAGGGTTTAGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6560396 GTTAAGGGTCT-ATGGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* * * *
6560418 GTTAA-GGTTTATGGTTTTCAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560439 GTTAAGGGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6560460 GTTAAGGGTTTATGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560482 GTTAAGGGTTTAA-GGTTTTAAA
1 GTTAAGGG-TTAAGGGTTTTTAA
* **
6560504 GTTAA-GGTTTAGGGTTTTTGG
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6560525 GTTAAGAGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560546 GTTAAGGGTTTAGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560568 TTTAAGGGTT-AGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6560589 GTTAAGGGTTTAGGGTTTCTAA
1 GTTAAGGGTTAAGGGTTTTTAA
**
6560611 GTTAAGGGTCT-AGGGTTTAAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* * *
6560633 GTTAA-AGTTTAGGGTTTTTCAG
1 GTTAAGGGTTAAGGGTTTTT-AA
*
6560655 GTTAAGGGTT-AGGG-TTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
* * * *
6560675 GTTAAAGATTTAGGGTTTTAAA
1 GTTAAGGGTTAAGGGTTTTTAA
* * *
6560697 TTTAAGGATT-AGTGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560718 GTTAAGGGTTTAGGG-TTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560739 GTTAAGGGTCTAA-GGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* *
6560761 GTTAAGGGTT-ATGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6560782 GTTTAGGGGTT-ATGGTTTTTAA
1 G-TTAAGGGTTAAGGGTTTTTAA
* * *
6560804 TTTAAGGGTTTAGGTTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* ** *
6560826 TTTAAAAGTTTAGGGTTTTTTAA
1 GTTAAGGGTTAAGGG-TTTTTAA
6560849 GTTAAGGGTTTAA-GG-TTTTAA
1 GTTAAGGG-TTAAGGGTTTTTAA
* *
6560870 GGTTAATGGTTAA-GGTTTTTAG
1 -GTTAAGGGTTAAGGGTTTTTAA
*
6560892 GTTAAGGGGTT-AGGGTTTTAAA
1 GTTAA-GGGTTAAGGGTTTTTAA
* *
6560914 GTTAATGGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
* * *
6560935 GTTAATGGTTTAGGGTTTTAAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6560957 GTTAAAGGTTAA
1 GTTAAGGGTTAA
6560969 TGAGTTAGGG
Statistics
Matches: 1000, Mismatches: 136, Indels: 114
0.80 0.11 0.09
Matches are distributed among these distances:
19 13 0.01
20 46 0.05
21 435 0.44
22 461 0.46
23 40 0.04
24 5 0.00
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.44
Consensus pattern (22 bp):
GTTAAGGGTTAAGGGTTTTTAA
Found at i:6559853 original size:43 final size:42
Alignment explanation
Indices: 6559721--6560967 Score: 1176
Period size: 43 Copynumber: 28.9 Consensus size: 42
6559711 TCAAATTATA
6559721 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAAGGGTTAAGGAT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTT-AGGG-T-----T
* * *
6559770 TTTAAAGTTAAGGGTCTAGGGTTTTAAAGTTAAGGATTTATGGTT
1 TTT-AAGTTAAGGGT-TAGGGTTTTTAAGTTAAGG-GTTAGGGTT
* * * **
6559815 TTTAGGTTAAGGGTTAGGGTTTTTAGGTTTAGGGTTTATAGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTT
* * *
6559858 TTTAATTTAAGGGTTATGGTTTTTAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT-TAGGGTT
* * *
6559901 TTAAAGTTAATGGTTTAGGGTTTTAAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* *
6559944 TTTAGGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* *
6559987 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGT-TAGGGTT
* * * *
6560031 TTAAAGTTAAGGTTTAAGG--TTTAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT-TAGGGTT
* * * * *
6560072 TTAAAGTTAAGGTTTAAGGTTTTTAGGTTAAGGGTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* * *
6560114 TTTAGGTTAAGGTTTAGGG-TTTTAATTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* * * *
6560155 TTTAAGTTAAAGTTTAGGGTTTTCAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* * * * * *
6560197 TTTAGGTTAAGGTTTAGGGTTTTTAATTTAATGATTAGGATT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* *
6560239 TTTAAGTTAAGCGTTTAGGGTTTTTAAGTTAATGGGTCTAAGGTT
1 TTTAAGTTAAG-GGTTAGGGTTTTTAAGTTAA-GGGT-TAGGGTT
* * * *
6560284 TTAAAGTTAAGGTTTAGGGTTTTCAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* * * *
6560326 TTTAGGTTAAAGGTTTAGGG-TTTTAATTTAAGGGTTAAGGTTT
1 TTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTT-AGGGTT
*
6560369 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGT-TAGGGTT
* * * * *
6560413 TTAAAGTTAAGGTTTATGGTTTTCAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* * *
6560455 TTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGG-TTAGGGTT
* * ** *
6560499 TTAAAGTTAAGGTTTAGGGTTTTTGGGTTAAGAGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* *
6560541 TTTAGGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTAGGGTT
*
6560584 TTTAAGTTAAGGGTTTAGGGTTTCTAAGTTAAGGGTCTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGT-TAGGGTT
** * * *
6560628 TAAAAGTTAAAGTTTAGGGTTTTTCAGGTTAAGGGTTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTTTTT-AAGTTAAGGGTTAGGGTT
* ** * * * *
6560670 TTTAGGTTAAAGATTTAGGGTTTTAAATTTAAGGATTAGTGTT
1 TTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
*
6560713 TTTAAGTTAAGGGTTTAGGG-TTTTAAGTTAAGGGTCTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGT-TAGGGTT
* * * * *
6560756 TTAAAGTTAAGGGTTATGGTTTTTAGGTTTAGGGGTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAG-TTAAGGGTTAGGGTT
* * * * *
6560799 TTTAATTTAAGGGTTTAGGTTTTTTAATTTAAAAGTTTAGGGTTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTT-AAGGGTTAGGG-TT
* * *
6560844 TTTAAGTTAAGGGTTTAAGG-TTTTAAGGTTAATGGTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAA-GTTAAGGGTTAGGGTT
* * *
6560887 TTTAGGTTAAGGGGTTAGGGTTTTAAAGTTAATGGTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* * * *
6560930 TTTAGGTTAATGGTTTAGGGTTTTAAAGTTAAAGGTTA
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGTTA
6560968 ATGAGTTAGG
Statistics
Matches: 1005, Mismatches: 157, Indels: 78
0.81 0.13 0.06
Matches are distributed among these distances:
41 76 0.08
42 189 0.19
43 474 0.47
44 187 0.19
45 41 0.04
49 3 0.00
50 12 0.01
51 21 0.02
52 2 0.00
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.44
Consensus pattern (42 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
Found at i:6560049 original size:7 final size:7
Alignment explanation
Indices: 6560037--6560135 Score: 55
Period size: 7 Copynumber: 14.3 Consensus size: 7
6560027 GGTTTTAAAG
6560037 TTAAGGT
1 TTAAGGT
6560044 TTAAGGT
1 TTAAGGT
6560051 TTAA-G-
1 TTAAGGT
6560056 TTAAGGGT
1 TTAA-GGT
* *
6560064 CTATGGTT
1 TTAAGG-T
*
6560072 TTAAAG-
1 TTAAGGT
6560078 TTAAGGT
1 TTAAGGT
6560085 TTAAGGTT
1 TTAAGG-T
*
6560093 TTTAGG-
1 TTAAGGT
*
6560099 TTAAGGG
1 TTAAGGT
*
6560106 TTATGGTT
1 TTAAGG-T
*
6560114 TTTAGG-
1 TTAAGGT
6560120 TTAAGGT
1 TTAAGGT
*
6560127 TTAGGGT
1 TTAAGGT
6560134 TT
1 TT
6560136 TAATTTAAGG
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
5 4 0.06
6 16 0.23
7 33 0.48
8 16 0.23
ACGTcount: A:0.24, C:0.01, G:0.29, T:0.45
Consensus pattern (7 bp):
TTAAGGT
Found at i:6561275 original size:21 final size:21
Alignment explanation
Indices: 6561250--6561312 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
6561240 TCCAGCTTTT
*
6561250 GGCGGCGATTATAGTTCTTCC
1 GGCGGCGATTATGGTTCTTCC
* *
6561271 GGCGGCGGTTGTGGTTCTTCC
1 GGCGGCGATTATGGTTCTTCC
* *
6561292 GGCGGGGATTCTGGTTCTTCC
1 GGCGGCGATTATGGTTCTTCC
6561313 AGTAGGGCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.06, C:0.24, G:0.37, T:0.33
Consensus pattern (21 bp):
GGCGGCGATTATGGTTCTTCC
Found at i:6561595 original size:18 final size:18
Alignment explanation
Indices: 6561569--6561611 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
6561559 GACTCGAAAA
* *
6561569 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
6561587 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
6561605 AGGAAAC
1 AGGAAAC
6561612 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:6562416 original size:20 final size:20
Alignment explanation
Indices: 6562379--6562416 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6562369 TTTATTTTTA
*
6562379 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
6562399 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
6562417 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:6569834 original size:26 final size:26
Alignment explanation
Indices: 6569804--6569855 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
6569794 CACCACTGAA
*
6569804 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
6569830 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
6569856 CTTTTTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:6570026 original size:104 final size:103
Alignment explanation
Indices: 6569782--6570141 Score: 580
Period size: 104 Copynumber: 3.5 Consensus size: 103
6569772 CGGTAGATCC
*
6569782 CGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGGAATCAGCACA
1 CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACA
6569846 TAGCAACCCCCTTTTTCATTTCAAAGATACGGTGGATAT
66 TAGCAACCCCC-TTTTCATTTCAAAGATACGGTGGATAT
* * *
6569885 TGCACTTAGCATCACCAATGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACA
1 CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACA
*
6569950 TAACAACCCCCTTTTCATTTCAAAGATACGGTGGATAT
66 TAGCAACCCCCTTTTCATTTCAAAGATACGGTGGATAT
6569988 CGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCAC
1 CGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCAC
* *
6570053 ATAGCAACCCCCTTTCACATTTCAAAGATATGGTGGATCA-
65 ATAGCAACCCCCTTT-TCATTTCAAAGATACGGTGGAT-AT
* **
6570093 CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
6570142 TTTATATACA
Statistics
Matches: 239, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
103 91 0.38
104 108 0.45
105 39 0.16
106 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.19
Consensus pattern (103 bp):
CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACA
TAGCAACCCCCTTTTCATTTCAAAGATACGGTGGATAT
Found at i:6570509 original size:30 final size:30
Alignment explanation
Indices: 6570475--6570532 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
6570465 CCACCCAACT
*
6570475 TTTTGAAAAATTATAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
6570505 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
6570533 GCTCGGAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:6576103 original size:15 final size:15
Alignment explanation
Indices: 6576085--6576129 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
6576075 AATATATATA
*
6576085 TCAATTCCATCCAAT
1 TCAATTCAATCCAAT
6576100 TCAATTCAATCCAAT
1 TCAATTCAATCCAAT
*
6576115 TCAATTCAATTCAAT
1 TCAATTCAATCCAAT
6576130 AATCAATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.36
Consensus pattern (15 bp):
TCAATTCAATCCAAT
Found at i:6576106 original size:5 final size:5
Alignment explanation
Indices: 6576085--6576129 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
6576075 AATATATATA
* * *
6576085 TCAAT TCCAT CCAAT TCAAT TCAAT CCAAT TCAAT TCAAT TCAAT
1 TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT
6576130 AATCAATACA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.36
Consensus pattern (5 bp):
TCAAT
Found at i:6577436 original size:37 final size:36
Alignment explanation
Indices: 6577394--6577738 Score: 336
Period size: 37 Copynumber: 9.2 Consensus size: 36
6577384 CTTGAACAAC
* * *
6577394 TTTCAGTATATTCAATAGACATTGCTCTTTTGAGCA
1 TTTCAGTATAATCAGTAGATATTGCTCTTTTGAGCA
*
6577430 TGTTCAGTATAATTAGTAGATATTGCT-TATTTGAGCAA
1 T-TTCAGTATAATCAGTAGATATTGCTCT-TTTGAGC-A
* *
6577468 CTTTCAATATAATCAGTAGATATTGCTCTTTTAAGCACA
1 -TTTCAGTATAATCAGTAGATATTGCTCTTTTGAG--CA
6577507 TTT-AGTATAATCAGTAGATATTGCT-TATTTGAGCAA
1 TTTCAGTATAATCAGTAGATATTGCTCT-TTTGAGC-A
* * **
6577543 CTTTCAGTATAATCAATAGACATTATTCTTTTGAGCA
1 -TTTCAGTATAATCAGTAGATATTGCTCTTTTGAGCA
* * *
6577580 CGTTCAATATAATCAGTAGATATTGCTCGTTTGAGCAA
1 -TTTCAGTATAATCAGTAGATATTGCTCTTTTGAGC-A
*
6577618 CTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCA
1 -TTTCAGTATAATCAGTAGATATTGCTCTTTTGAGCA
* * * * *
6577655 CGTCCAATATAATCAGAAGATATTGCTCGTTTGAGCA
1 -TTTCAGTATAATCAGTAGATATTGCTCTTTTGAGCA
* * *
6577692 CATTCAGTATAATAAGTAGATATTGCTCATTTGAGCA
1 -TTTCAGTATAATCAGTAGATATTGCTCTTTTGAGCA
6577729 TATTCAGTAT
1 T-TTCAGTAT
6577739 TTAATCGATT
Statistics
Matches: 258, Mismatches: 37, Indels: 27
0.80 0.11 0.08
Matches are distributed among these distances:
35 1 0.00
36 4 0.02
37 158 0.61
38 90 0.35
39 4 0.02
40 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (36 bp):
TTTCAGTATAATCAGTAGATATTGCTCTTTTGAGCA
Found at i:6577515 original size:75 final size:75
Alignment explanation
Indices: 6577385--6577738 Score: 458
Period size: 75 Copynumber: 4.7 Consensus size: 75
6577375 TATCGTTCGC
* * * * *
6577385 TTGAACAACTTTCAGTATATTCAATAGACATTGCTCTTTTGAGCATGTTCAGTATAATTAGTAGA
1 TTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAGTAGA
*
6577450 TATTGCTTAT
66 TATTGCTCAT
* * * * *
6577460 TTGAGCAACTTTCAATATAATCAGTAGATATTGCTCTTTTAAGCACATTTAGTATAATCAGTAGA
1 TTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAGTAGA
*
6577525 TATTGCTTAT
66 TATTGCTCAT
* ** *
6577535 TTGAGCAACTTTCAGTATAATCAATAGACATTATTCTTTTGAGCACGTTCAATATAATCAGTAGA
1 TTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAGTAGA
*
6577600 TATTGCTCGT
66 TATTGCTCAT
* * *
6577610 TTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTCCAATATAATCAGAAGA
1 TTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAGTAGA
*
6577675 TATTGCTCGT
66 TATTGCTCAT
* * * * **
6577685 TTGAGC-ACATTCAGTATAATAAGTAGATATTGCTCATTTGAGCATATTCAGTAT
1 TTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTAT
6577739 TTAATCGATT
Statistics
Matches: 245, Mismatches: 34, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
74 40 0.16
75 205 0.84
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (75 bp):
TTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAGTAGA
TATTGCTCAT
Found at i:6577595 original size:112 final size:110
Alignment explanation
Indices: 6577398--6577738 Score: 353
Period size: 112 Copynumber: 3.0 Consensus size: 110
6577388 AACAACTTTC
* * * * * * * * * **
6577398 AGTATATTCAATAGACATTGCTCTTTTGAGCATGTTCAGTATAATTAGTAGATATTGCTTATTTG
1 AGTATAATCAGTAGACATTGCTCTTTTGAGCACGTCCAATATAATCAGAAGACATTACTCGTTTG
* * *
6577463 AGCAACTTTCAATATAATCAGTAGATATTGCTCTTTTAAGCACATTT
66 AGC-ACATTCAATATAATCAGTAGATATTGCTCATTTGAGCA-ATTT
* * * * * *
6577510 AGTATAATCAGTAGATATTGCT-TATTTGAGCAACTTTCAGTATAATCA-ATAGACATTATTCTT
1 AGTATAATCAGTAGACATTGCTCT-TTTGAGC-ACGTCCAATATAATCAGA-AGACATTACTCGT
* *
6577573 TTGAGCACGTTCAATATAATCAGTAGATATTGCTCGTTTGAGCAACTTT
63 TTGAGCACATTCAATATAATCAGTAGATATTGCTCATTTGAGCAA-TTT
* *
6577622 CAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTCCAATATAATCAGAAGATATTGCTCGTTT
1 -AGTATAATCAGTAGACATTGCTCTTTTGAGCACGTCCAATATAATCAGAAGACATTACTCGTTT
* * *
6577687 GAGCACATTCAGTATAATAAGTAGATATTGCTCATTTGAGCATATTC
65 GAGCACATTCAATATAATCAGTAGATATTGCTCATTTGAGCA-ATTT
6577734 AGTAT
1 AGTAT
6577739 TTAATCGATT
Statistics
Matches: 193, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
111 7 0.04
112 128 0.66
113 57 0.30
114 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38
Consensus pattern (110 bp):
AGTATAATCAGTAGACATTGCTCTTTTGAGCACGTCCAATATAATCAGAAGACATTACTCGTTTG
AGCACATTCAATATAATCAGTAGATATTGCTCATTTGAGCAATTT
Found at i:6581595 original size:62 final size:59
Alignment explanation
Indices: 6581526--6581642 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
6581516 AGTGATTATC
* * * * *
6581526 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATATAATATTTATC-T-TA-ATAAACATTATATTAATTTAATAAGAT
6581588 TTAATATTAAATTTAATATAATATTTATCTTAATAAACATTATATTAATTTAATA
1 TTAATATTAAATTTAATATAATATTTATCTTAATAAACATTATATTAATTTAATA
6581643 TTAAAGTCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
60 2 0.04
61 1 0.02
62 27 0.54
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTTAATATAATATTTATCTTAATAAACATTATATTAATTTAATAAGAT
Found at i:6581611 original size:17 final size:17
Alignment explanation
Indices: 6581589--6581647 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
6581579 TAATAAGATT
6581589 TAATATTAAATTTAATA
1 TAATATTAAATTTAATA
*
6581606 TAATATT-TATCTTAATA
1 TAATATTAAAT-TTAATA
* * *
6581623 -AACATTATA-TTAATT
1 TAATATTAAATTTAATA
6581638 TAATATTAAA
1 TAATATTAAA
6581648 GTCATTAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 5 0.15
16 14 0.41
17 15 0.44
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTAAATTTAATA
Found at i:6585052 original size:45 final size:45
Alignment explanation
Indices: 6584983--6585082 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 45
6584973 GATGTGTTCG
* *
6584983 TATAACAGGTTTGGATATCGTAAATGAGCTTACACACGTCCAACC
1 TATAACAGATTTGGATATCATAAATGAGCTTACACACGTCCAACC
* * *
6585028 TATAACAGATTTGGATATCATAAATGGGCTTGCACATGTCCAACC
1 TATAACAGATTTGGATATCATAAATGAGCTTACACACGTCCAACC
6585073 TATAACAGAT
1 TATAACAGAT
6585083 CACTCTTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (45 bp):
TATAACAGATTTGGATATCATAAATGAGCTTACACACGTCCAACC
Found at i:6585700 original size:25 final size:25
Alignment explanation
Indices: 6585661--6585717 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
6585651 TGCAAATTTT
6585661 TTAAGAATTACAAAAAGTTAT-AAAAA
1 TTAA-AATTAC-AAAAGTTATCAAAAA
* *
6585687 TTAAAATTATAAAATTTATCAAAAA
1 TTAAAATTACAAAAGTTATCAAAAA
*
6585712 TAAAAA
1 TTAAAA
6585718 ATGTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 8 0.30
25 15 0.56
26 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (25 bp):
TTAAAATTACAAAAGTTATCAAAAA
Found at i:6585754 original size:17 final size:18
Alignment explanation
Indices: 6585700--6585754 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
6585690 AAATTATAAA
*
6585700 ATTTATCAAAAATAAAAAAT
1 ATTTAT-AAAAA-ATAAAAT
* *
6585720 GTTTATAAAAAAT-TAAT
1 ATTTATAAAAAATAAAAT
6585737 ATTT-TAAAAAATAAAAT
1 ATTTATAAAAAATAAAAT
6585754 A
1 A
6585755 AATATAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 8 0.28
17 10 0.34
18 1 0.03
19 5 0.17
20 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
ATTTATAAAAAATAAAAT
Found at i:6586549 original size:21 final size:21
Alignment explanation
Indices: 6586523--6586562 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6586513 AATAAATACC
6586523 AAAAATTTATTTTAAAAATTA
1 AAAAATTTATTTTAAAAATTA
6586544 AAAAATTTATTTTAAAAAT
1 AAAAATTTATTTTAAAAAT
6586563 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAATTTATTTTAAAAATTA
Found at i:6586567 original size:11 final size:11
Alignment explanation
Indices: 6586551--6586611 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
6586541 TTAAAAAATT
6586551 TATTTTAAAAA
1 TATTTTAAAAA
6586562 TATTTT--AAA
1 TATTTTAAAAA
6586571 -A--TTAAAAA
1 TATTTTAAAAA
* * *
6586579 AAATTAAAAAA
1 TATTTTAAAAA
6586590 GTATTTTAAAAA
1 -TATTTTAAAAA
6586602 TATTTTAAAA
1 TATTTTAAAA
6586612 TTAAATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
6 2 0.05
8 4 0.10
9 4 0.10
11 22 0.55
12 8 0.20
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:6586595 original size:40 final size:41
Alignment explanation
Indices: 6586536--6586616 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 41
6586526 AATTTATTTT
*
6586536 AAAAATTAAAAAATTTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAATGTATTTTAAAAATATTTTAAAATTAAA
6586577 AAAAATTAAAAAA-GTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAATGTATTTTAAAAATATTTTAAAATTAAA
6586617 TTTTTTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 26 0.67
41 13 0.33
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (41 bp):
AAAAATTAAAAAATGTATTTTAAAAATATTTTAAAATTAAA
Found at i:6593810 original size:11 final size:11
Alignment explanation
Indices: 6593791--6593823 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
6593781 TTAATATAAA
6593791 TAATAAATAATT
1 TAAT-AATAATT
6593803 TAATAATAATT
1 TAATAATAATT
6593814 TAA-AATAATT
1 TAATAATAATT
6593824 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 10 0.48
12 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATT
Found at i:6593844 original size:24 final size:21
Alignment explanation
Indices: 6593768--6593879 Score: 79
Period size: 22 Copynumber: 5.1 Consensus size: 21
6593758 GTTATTAAAT
6593768 TTTAATAAGATTATTAATATAA
1 TTTAATAA-ATTATTAATATAA
* *
6593790 -ATAATAAATAATTTAATAATAA
1 TTTAATAAATTA-TTAAT-ATAA
6593812 TTTAAAATAATTATTATTAAATATAA
1 TTT--AATAA--ATTATT-AATATAA
*
6593838 TTTAATAAA--AAT-ATATAA
1 TTTAATAAATTATTAATATAA
*
6593856 TTTAATAAAATTCTTAATATAA
1 TTTAAT-AAATTATTAATATAA
6593878 TT
1 TT
6593880 ATTCTTATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 24
0.70 0.07 0.24
Matches are distributed among these distances:
18 12 0.17
19 3 0.04
20 5 0.07
21 12 0.17
22 13 0.18
23 1 0.01
24 5 0.07
25 5 0.07
26 9 0.13
27 6 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (21 bp):
TTTAATAAATTATTAATATAA
Found at i:6593857 original size:55 final size:55
Alignment explanation
Indices: 6593786--6593902 Score: 148
Period size: 55 Copynumber: 2.1 Consensus size: 55
6593776 GATTATTAAT
6593786 ATAAATAATAAATAATTTAATAATAA-T-TTAAAATAATTATTATTAAATATAATTTA
1 ATAAA-AATAAATAATTTAATAA-AATTCTTAAAATAATTATTATTAAAT-TAATTTA
* * * *
6593842 ATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATTAATTTA
1 ATAAAAATAAATAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAATTTA
*
6593897 CTAAAA
1 ATAAAA
6593903 TCATAATATA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 2 0.04
55 29 0.54
56 23 0.43
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (55 bp):
ATAAAAATAAATAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAATTTA
Found at i:6593917 original size:55 final size:56
Alignment explanation
Indices: 6593786--6593918 Score: 132
Period size: 55 Copynumber: 2.4 Consensus size: 56
6593776 GATTATTAAT
* *
6593786 ATAAATAATAAATAATTTAATAATAA-T-TTAAAATAATTATTATTAAATATAATTTA
1 ATAAA-AATATATAATATAATAA-AATTCTTAAAATAATTATTATTAAATATAATTTA
* * * *
6593842 ATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTTATAT-TAATTTA
1 ATAAAAATATATAATATAATAAAATTCTTAAAATAATTATTATTAAATATAATTTA
*
6593897 CT-AAAATCATA-ATATATAATAA
1 ATAAAAAT-ATATA-ATATAATAA
6593919 TATAAAAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
54 8 0.12
55 36 0.54
56 23 0.34
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (56 bp):
ATAAAAATATATAATATAATAAAATTCTTAAAATAATTATTATTAAATATAATTTA
Found at i:6594329 original size:77 final size:76
Alignment explanation
Indices: 6594202--6594362 Score: 295
Period size: 77 Copynumber: 2.1 Consensus size: 76
6594192 ATTTTTTGTC
6594202 CACTTTAATAATTAAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTAAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAA-T
*
6594267 TTATTGACATAA
65 TTATTAACATAA
*
6594279 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTAAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
6594344 TATTAACATAA
66 TATTAACATAA
6594355 CACTTTAA
1 CACTTTAA
6594363 GATTGTCTCA
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
76 20 0.24
77 62 0.76
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (76 bp):
CACTTTAATAATTAAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
TATTAACATAA
Found at i:6609312 original size:21 final size:21
Alignment explanation
Indices: 6609287--6609333 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
6609277 AAAAAATAAA
6609287 ATATTAAAA-ATATATTATTTT
1 ATATTAAAATATATA-TATTTT
* *
6609308 ATATTAATATTTATATATTTT
1 ATATTAAAATATATATATTTT
6609329 ATATT
1 ATATT
6609334 TAAACTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTAAAATATATATATTTT
Found at i:6609548 original size:29 final size:31
Alignment explanation
Indices: 6609516--6609580 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
6609506 AAAATTTTAA
* *
6609516 GTATAAATTTATACA-TA-ATCAAAGTTCAT
1 GTATAAAATTACACATTAGATCAAAGTTCAT
* *
6609545 GTATAAAATTGCACATTAGATCAAATTTCAT
1 GTATAAAATTACACATTAGATCAAAGTTCAT
6609576 GTATA
1 GTATA
6609581 TTTTTGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 12 0.40
30 2 0.07
31 16 0.53
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (31 bp):
GTATAAAATTACACATTAGATCAAAGTTCAT
Found at i:6609662 original size:20 final size:21
Alignment explanation
Indices: 6609620--6609663 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
6609610 GTATGTTTTA
* *
6609620 ATATTTACATTGTAATACTAT
1 ATATTTAAATTGTAATACAAT
*
6609641 ATATTTAAATT-TTATACAAT
1 ATATTTAAATTGTAATACAAT
6609661 ATA
1 ATA
6609664 AAATACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATTTAAATTGTAATACAAT
Found at i:6612455 original size:16 final size:16
Alignment explanation
Indices: 6612434--6612466 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6612424 TGAGGTAAAG
6612434 TTGTTACACTACTTCA
1 TTGTTACACTACTTCA
6612450 TTGTTACACTACTTCA
1 TTGTTACACTACTTCA
6612466 T
1 T
6612467 AAAAACTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGTTACACTACTTCA
Found at i:6629850 original size:11 final size:11
Alignment explanation
Indices: 6629827--6629864 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
6629817 GTAAGATGGC
6629827 TTTTCTT-TCT
1 TTTTCTTCTCT
6629837 TTTTCTTCTCT
1 TTTTCTTCTCT
*
6629848 TTTTTTTCT-T
1 TTTTCTTCTCT
6629858 TTTTCTT
1 TTTTCTT
6629865 TTTTCTGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 14 0.56
11 11 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTCTCT
Found at i:6629855 original size:14 final size:13
Alignment explanation
Indices: 6629828--6629870 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
6629818 TAAGATGGCT
6629828 TTTCTTTCTTTTTC
1 TTTCTTT-TTTTTC
6629842 TTCTCTTTTTTTTC
1 TT-TCTTTTTTTTC
*
6629856 TTTTTTCTTTTTTC
1 TTTCTT-TTTTTTC
6629870 T
1 T
6629871 GTAGTTGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 3 0.12
14 18 0.69
15 5 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:6632209 original size:12 final size:12
Alignment explanation
Indices: 6632192--6632221 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6632182 ACAAAATTCG
6632192 AATTTAATTTCC
1 AATTTAATTTCC
*
6632204 AATTTAATTTCT
1 AATTTAATTTCC
6632216 AATTTA
1 AATTTA
6632222 TTTATGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:6637297 original size:12 final size:12
Alignment explanation
Indices: 6637280--6637312 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
6637270 ACAAAATCCG
6637280 AATTTAATTTCC
1 AATTTAATTTCC
*
6637292 AATTTAATTTCT
1 AATTTAATTTCC
6637304 AATTTAATT
1 AATTTAATT
6637313 AATTAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:6637736 original size:6 final size:6
Alignment explanation
Indices: 6637725--6637749 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6637715 GCTTTTTTAT
6637725 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
6637750 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:6637760 original size:6 final size:6
Alignment explanation
Indices: 6637751--6637775 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6637741 TATTAATATA
6637751 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
6637776 TTATTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:6638069 original size:30 final size:29
Alignment explanation
Indices: 6638006--6638069 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
6637996 TAATCTTGTT
* *
6638006 TAGTTGGATGACCAATTTAAAAAAATTCA
1 TAGTTGGATGACAAATTTAAAAAAATCCA
* * *
6638035 TAGTTGGGTGACAAATTTGAGACAAATCCA
1 TAGTTGGATGACAAATTT-AAAAAAATCCA
6638065 TAGTT
1 TAGTT
6638070 AGGTAATCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (29 bp):
TAGTTGGATGACAAATTTAAAAAAATCCA
Found at i:6638721 original size:13 final size:13
Alignment explanation
Indices: 6638703--6638728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6638693 CATGCAAGAC
6638703 AACGTGGTTGAGA
1 AACGTGGTTGAGA
6638716 AACGTGGTTGAGA
1 AACGTGGTTGAGA
6638729 GCAAGGCAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.38, T:0.23
Consensus pattern (13 bp):
AACGTGGTTGAGA
Found at i:6639542 original size:18 final size:18
Alignment explanation
Indices: 6639515--6639549 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6639505 AGCACCAAAG
6639515 CTTTCATCCTCCTCCTCA
1 CTTTCATCCTCCTCCTCA
* *
6639533 CTTTCTTCCTCTTCCTC
1 CTTTCATCCTCCTCCTC
6639550 TTCTTCATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.49, G:0.00, T:0.46
Consensus pattern (18 bp):
CTTTCATCCTCCTCCTCA
Found at i:6644432 original size:14 final size:16
Alignment explanation
Indices: 6644413--6644444 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
6644403 CCAATATTTT
6644413 ATTTTT-TAAAAT-TA
1 ATTTTTATAAAATATA
6644427 ATTTTTATAAAATATA
1 ATTTTTATAAAATATA
6644443 AT
1 AT
6644445 GCACTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTTATAAAATATA
Found at i:6644987 original size:21 final size:21
Alignment explanation
Indices: 6644922--6644992 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
6644912 GTTTTTAGGG
6644922 TTAAGGTTTTGTTAAAATAAT
1 TTAAGGTTTTGTTAAAATAAT
* ** *
6644943 TTAGGGTTAGGTT--TATAAGGT
1 TTAAGGTTTTGTTAAAATAA--T
6644964 TTAAGGTTTTGTTAAAATAAT
1 TTAAGGTTTTGTTAAAATAAT
*
6644985 TTAGGGTT
1 TTAAGGTT
6644993 CTTGGTTTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
19 4 0.11
21 29 0.78
23 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (21 bp):
TTAAGGTTTTGTTAAAATAAT
Found at i:6645142 original size:34 final size:33
Alignment explanation
Indices: 6645037--6645142 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
6645027 TTTAGTGTTC
* *
6645037 TTTTTT-AAAAATTAATTAAATTAGGGTTTAGG
1 TTTTTTAAAAAATTAATTAAATTTGGGTTTAGT
** *
6645069 AGTTTTAAATTAATTAATTAAATTTGGGTTTAGT
1 TTTTTTAAA-AAATTAATTAAATTTGGGTTTAGT
*
6645103 GTTTTTAAGAAAATTAATTAAATTTGGGTTTAGT
1 TTTTTTAA-AAAATTAATTAAATTTGGGTTTAGT
6645137 TTTTTT
1 TTTTTT
6645143 TAAAGGCATA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 4 0.06
33 2 0.03
34 55 0.89
35 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (33 bp):
TTTTTTAAAAAATTAATTAAATTTGGGTTTAGT
Found at i:6647179 original size:125 final size:127
Alignment explanation
Indices: 6647032--6647551 Score: 755
Period size: 126 Copynumber: 4.1 Consensus size: 127
6647022 GATTTTAGTT
* * * * * * *
6647032 TTTTTCTACGGTAGTTCCTGAAAAAATAATTTTGAGAAGATGATTCTCAACAAATAGTCTTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
* *
6647097 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACT-AAAAAAACTCCCACGTGGA-AGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACA-CTC
* * * *
6647157 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTAAGAAGACGGTTCTAAATAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
* *
6647222 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCTACGTGGACACTT
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
* *
6647283 TTTTTCTACAGTAGTTCGTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
* * * *
6647348 ACCCTTCAAGTAGGATGCACTGTCAACAAAATTGA-AGAAAAAAGCTCCCACGTGGACACTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
* *
6647409 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGTTTCTGAATAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
*
6647474 ACACTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACACTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
* *
6647535 TTTTTTTACAGCAGTTC
1 TTTTTCTACAGTAGTTC
6647552 ATGTTTGGCC
Statistics
Matches: 356, Mismatches: 35, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
125 90 0.25
126 265 0.74
127 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (127 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
Found at i:6647743 original size:28 final size:28
Alignment explanation
Indices: 6647712--6647773 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
6647702 CGGCGTTATT
* *
6647712 TTTTTATCGGAGAATACAACGCGAATAA
1 TTTTTATCAGAGAACACAACGCGAATAA
*
6647740 TTTTTATCAGAGAACACAACGCGAATTA
1 TTTTTATCAGAGAACACAACGCGAATAA
6647768 TTTTTA
1 TTTTTA
6647774 ACTAGACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (28 bp):
TTTTTATCAGAGAACACAACGCGAATAA
Found at i:6650156 original size:20 final size:20
Alignment explanation
Indices: 6650131--6650168 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
6650121 ACAACCTATG
6650131 GTGTACACCTGATAAATATC
1 GTGTACACCTGATAAATATC
6650151 GTGTACACCTGATAAATA
1 GTGTACACCTGATAAATA
6650169 AGACTTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (20 bp):
GTGTACACCTGATAAATATC
Found at i:6651084 original size:18 final size:18
Alignment explanation
Indices: 6651053--6651096 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
6651043 GACTGGGAAA
* *
6651053 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
* *
6651071 ATGATACATGTAAGGGCT
1 AGGATACATATAAGGGCT
6651089 AGGATACA
1 AGGATACA
6651097 CACCTGGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.27, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:6652864 original size:30 final size:30
Alignment explanation
Indices: 6652830--6652898 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
6652820 ATTAATTAAA
6652830 GAGAGTTTTGAGAAATTTAAGGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAGGAGAAATTT
* *
6652860 GAGAGCTTTGAGAAATTTAGGGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAGGAGAAATTT
*
6652890 GAAAGTTTT
1 GAGAGTTTT
6652899 TTTGCTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.38, C:0.01, G:0.28, T:0.33
Consensus pattern (30 bp):
GAGAGTTTTGAGAAATTTAAGGAGAAATTT
Found at i:6653973 original size:20 final size:20
Alignment explanation
Indices: 6653950--6654011 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
6653940 TATTTTTCTA
6653950 GATTAGTTCAGATTTAAATT
1 GATTAGTTCAGATTTAAATT
** *** *
6653970 GATT--TTCTTATTTTTCTA
1 GATTAGTTCAGATTTAAATT
6653988 GATTAGTTCAGATTTAAATT
1 GATTAGTTCAGATTTAAATT
6654008 GATT
1 GATT
6654012 TTTATACATT
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
18 12 0.43
20 16 0.57
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (20 bp):
GATTAGTTCAGATTTAAATT
Found at i:6653989 original size:38 final size:38
Alignment explanation
Indices: 6653938--6654013 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
6653928 ATTATATGTG
6653938 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
1 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
6653976 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
1 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
6654014 TATACATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (38 bp):
CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
Found at i:6668298 original size:49 final size:49
Alignment explanation
Indices: 6668243--6668388 Score: 222
Period size: 49 Copynumber: 3.0 Consensus size: 49
6668233 TTCGTTTTCT
* *
6668243 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGTCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
* * *
6668292 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTAC
1 CGATGCCATAGTCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
6668341 CGATGCCATA-TCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGT-CCAGCTATGGTCTTACACGGAATCACA-AATCACAT
6668389 GTTCACATGT
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
49 81 0.93
50 6 0.07
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (49 bp):
CGATGCCATAGTCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
Found at i:6669384 original size:37 final size:37
Alignment explanation
Indices: 6669314--6669422 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
6669304 TACGTATGAT
* * *
6669314 CACTTATCAC-TTG-TCCCTGATCAGATAAATGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
6669349 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
6669386 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
6669423 TAAAGCTATC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 10 0.15
36 3 0.04
37 55 0.81
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:6669465 original size:52 final size:52
Alignment explanation
Indices: 6669386--6669594 Score: 279
Period size: 52 Copynumber: 4.1 Consensus size: 52
6669376 TAAGTGTAGC
* * *
6669386 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
6669439 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAA-CTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCC-AAAGCTATCACTTAT
* * *
6669491 CAC---T---TTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
* *
6669537 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
6669589 CACTTT
1 CACTTT
6669595 CCACATAAGT
Statistics
Matches: 139, Mismatches: 9, Indels: 17
0.84 0.05 0.10
Matches are distributed among these distances:
45 2 0.01
46 39 0.28
49 1 0.01
52 85 0.61
53 12 0.09
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
Found at i:6669496 original size:98 final size:98
Alignment explanation
Indices: 6669386--6669697 Score: 489
Period size: 98 Copynumber: 3.3 Consensus size: 98
6669376 TAAGTGTAGC
** *
6669386 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTT
*
6669451 GTCACTTGATCAGATAAGTGTAGCCGAAACTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
6669484 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTT
6669549 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
6669582 CACTTATCAC-TT-TC-C---A-C--ATAAGTGTAGCCGAAGCCATCACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTT
6669638 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
6669671 CACCTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCTCTTGATCAGA
6669698 AGTACTCAAA
Statistics
Matches: 197, Mismatches: 8, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
89 79 0.40
90 2 0.01
91 3 0.02
92 2 0.01
95 2 0.01
96 3 0.02
97 2 0.01
98 104 0.53
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33
Consensus pattern (98 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:6669609 original size:37 final size:37
Alignment explanation
Indices: 6669562--6669635 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
6669552 ACTTGATCAG
*
6669562 ATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCAC
1 ATAAGTGTAGCCGAAGCCATCACTTATCACTTTCCAC
6669599 ATAAGTGTAGCCGAAGCCATCACTTATCACTTTCCAC
1 ATAAGTGTAGCCGAAGCCATCACTTATCACTTTCCAC
6669636 TTGTCACTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (37 bp):
ATAAGTGTAGCCGAAGCCATCACTTATCACTTTCCAC
Found at i:6669663 original size:89 final size:89
Alignment explanation
Indices: 6669510--6669683 Score: 321
Period size: 89 Copynumber: 2.0 Consensus size: 89
6669500 TCTTGATCAG
*
6669510 ATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCG
1 ATAAGTATAGCCGAAGCCATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCG
*
6669575 AAGCTATCACTTATCACTTTCCAC
66 AAGCTATCACCTATCACTTTCCAC
*
6669599 ATAAGTGTAGCCGAAGCCATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCG
1 ATAAGTATAGCCGAAGCCATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCG
6669664 AAGCTATCACCTATCACTTT
66 AAGCTATCACCTATCACTTT
6669684 GTCACTTGAT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 82 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (89 bp):
ATAAGTATAGCCGAAGCCATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCG
AAGCTATCACCTATCACTTTCCAC
Found at i:6672953 original size:17 final size:17
Alignment explanation
Indices: 6672920--6672953 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6672910 TTGTGTTTTG
*
6672920 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
6672937 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
6672954 GTTAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:6673950 original size:41 final size:41
Alignment explanation
Indices: 6673888--6674007 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
6673878 TGATCGAATG
* *
6673888 TAATACAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
*
6673929 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGATA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
* * * * * * *
6673970 CATTTCGGACTATAGGTCTAGCAGGCTAAAAGCCGGTG
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTG
6674008 TACTGAATCA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
Found at i:6674392 original size:25 final size:25
Alignment explanation
Indices: 6674361--6674435 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
6674351 TGTATATACA
6674361 TATTCGAATGTATGTATTAGCTATG
1 TATTCGAATGTATGTATTAGCTATG
*
6674386 TATTCGAA--TATGTA-TA--TATA
1 TATTCGAATGTATGTATTAGCTATG
6674406 TATTCGAATGTATGTATTAGCTATG
1 TATTCGAATGTATGTATTAGCTATG
6674431 TATTC
1 TATTC
6674436 AGGTATAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
20 11 0.26
22 8 0.19
23 8 0.19
25 16 0.37
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (25 bp):
TATTCGAATGTATGTATTAGCTATG
Found at i:6674395 original size:45 final size:45
Alignment explanation
Indices: 6674346--6674435 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
6674336 TGTATATGAT
6674346 GAATATGTATATACATATTCGAATGTATGTATTAGCTATGTATTC
1 GAATATGTATATACATATTCGAATGTATGTATTAGCTATGTATTC
*
6674391 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
1 GAATATGTATATACATATTCGAATGTATGTATTAGCTATGTATTC
6674436 AGGTATAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (45 bp):
GAATATGTATATACATATTCGAATGTATGTATTAGCTATGTATTC
Found at i:6674411 original size:20 final size:20
Alignment explanation
Indices: 6674346--6674414 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 20
6674336 TGTATATGAT
*
6674346 GAATATGTATATACATATTC
1 GAATATGTATATATATATTC
*
6674366 GAATGTATGTATTAGCTATGTATTC
1 GAA--TATGTA-TA--TATATATTC
6674391 GAATATGTATATATATATTC
1 GAATATGTATATATATATTC
6674411 GAAT
1 GAAT
6674415 GTATGTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
20 15 0.37
22 8 0.20
23 8 0.20
25 10 0.24
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (20 bp):
GAATATGTATATATATATTC
Found at i:6678777 original size:37 final size:37
Alignment explanation
Indices: 6678727--6678800 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
6678717 ATGAAAGAAA
6678727 AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
1 AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
6678764 AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
1 AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
6678801 TAATAAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (37 bp):
AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
Found at i:6680139 original size:14 final size:14
Alignment explanation
Indices: 6680120--6680147 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6680110 ACCCTAGTAG
6680120 TAATTAACAAGAAA
1 TAATTAACAAGAAA
6680134 TAATTAACAAGAAA
1 TAATTAACAAGAAA
6680148 GTCGCTAGAT
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:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
TAATTAACAAGAAA
Found at i:6685781 original size:17 final size:17
Alignment explanation
Indices: 6685756--6685803 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
6685746 TGATGTGTTC
*
6685756 TTCAGTAAAAGAAAGAA
1 TTCAATAAAAGAAAGAA
6685773 TTCAATAAAAGAAAGAA
1 TTCAATAAAAGAAAGAA
*
6685790 TTCGATAAAAGAAA
1 TTCAATAAAAGAAA
6685804 AGTAGGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (17 bp):
TTCAATAAAAGAAAGAA
Found at i:6692329 original size:38 final size:38
Alignment explanation
Indices: 6692276--6692352 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
6692266 AAATACTAAG
6692276 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
1 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
** **
6692314 TGATAAATTTGTTTAGCATGCTTGTTTTTAACTCTTAT
1 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
6692352 T
1 T
6692353 TTTGTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (38 bp):
TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
Found at i:6694292 original size:17 final size:18
Alignment explanation
Indices: 6694270--6694306 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
6694260 CAAAACTAAG
6694270 GTTCATTTGGTGTT-CAT
1 GTTCATTTGGTGTTCCAT
6694287 GTTCATTTGGTGTTCCAT
1 GTTCATTTGGTGTTCCAT
6694305 GT
1 GT
6694307 CAGGATGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.11, C:0.14, G:0.24, T:0.51
Consensus pattern (18 bp):
GTTCATTTGGTGTTCCAT
Found at i:6705239 original size:77 final size:76
Alignment explanation
Indices: 6705112--6705333 Score: 245
Period size: 77 Copynumber: 2.9 Consensus size: 76
6705102 CAATTCTCCA
* *
6705112 CATGGTATCAAATGTTTTTGGTTCTTTCCTTATAAGTGTTTTTTTTCTGGTCGAACTCTTGCTTC
1 CATGGTATCAGATGTTTTTGGTTCTTT-CTTATAAGTGTTTTTTTTCTGGTCGAAATCTTGCTTC
*
6705177 TCATGTTTAGTC
65 TCATGTTCAGTC
* *
6705189 CATGGTATCAGATGTTTTTGGTT-TTT-TTCCTAAGTGTTTTCTTTTCCTGGTTGAAATCTTGCT
1 CATGGTATCAGATGTTTTTGGTTCTTTCTT-ATAAGTGTTTT-TTTT-CTGGTCGAAATCTTGCT
* *
6705252 TCTCTTGTTCATTC
63 TCTCATGTTCAGTC
* * * *
6705266 CATGGTATCAGAT-TTTTCTGGTTCCTTAC-TATGAAGAGTTTTTTTTCTTGGTCGAATTATTGC
1 CATGGTATCAGATGTTTT-TGGTT-CTTTCTTAT-AAGTGTTTTTTTTC-TGGTCGAAATCTTGC
6705329 TTCTC
62 TTCTC
6705334 CTATTCTATT
Statistics
Matches: 123, Mismatches: 13, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
74 2 0.02
75 10 0.08
76 11 0.09
77 67 0.54
78 22 0.18
79 11 0.09
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (76 bp):
CATGGTATCAGATGTTTTTGGTTCTTTCTTATAAGTGTTTTTTTTCTGGTCGAAATCTTGCTTCT
CATGTTCAGTC
Found at i:6707580 original size:4 final size:4
Alignment explanation
Indices: 6707571--6707604 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
6707561 AAGTTTTATT
6707571 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
6707605 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:6707612 original size:22 final size:22
Alignment explanation
Indices: 6707554--6707613 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
6707544 AAGTGGCCCA
*
6707554 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
6707578 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
6707599 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
6707614 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:6709964 original size:18 final size:18
Alignment explanation
Indices: 6709943--6709981 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6709933 GATTGAGAGT
* *
6709943 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
6709961 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
6709979 GAA
1 GAA
6709982 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:6711363 original size:17 final size:17
Alignment explanation
Indices: 6711341--6711374 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6711331 TTGAAAATCA
6711341 GGCCAAA-TTGTTAAAGT
1 GGCCAAAGTTG-TAAAGT
6711358 GGCCAAAGTTGTAAAGT
1 GGCCAAAGTTGTAAAGT
6711375 TTTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (17 bp):
GGCCAAAGTTGTAAAGT
Found at i:6711390 original size:4 final size:4
Alignment explanation
Indices: 6711381--6711414 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
6711371 AAGTTTTATT
6711381 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
6711415 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:6711422 original size:22 final size:22
Alignment explanation
Indices: 6711364--6711423 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
6711354 AAGTGGCCAA
*
6711364 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
6711388 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
6711409 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
6711424 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:6723644 original size:36 final size:30
Alignment explanation
Indices: 6723576--6723635 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
6723566 GCTCAATAAG
6723576 AATCTTAAATATTAATATTGATACTAAGTT
1 AATCTTAAATATTAATATTGATACTAAGTT
*
6723606 AATCTTAAATATTAATATTGATATTAAGTT
1 AATCTTAAATATTAATATTGATACTAAGTT
6723636 TAAATTAATT
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:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (30 bp):
AATCTTAAATATTAATATTGATACTAAGTT
Found at i:6723715 original size:31 final size:27
Alignment explanation
Indices: 6723677--6723738 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 27
6723667 AAATAATCAT
6723677 TCAACTATGATAGTGTTTTTATTTTAGTCA
1 TCAACTAT-A-AGTGTTTTTA-TTTAGTCA
* *
6723707 CTCAACTATAATTTTTTTTATTTAGTCA
1 -TCAACTATAAGTGTTTTTATTTAGTCA
6723735 TCAA
1 TCAA
6723739 AGTTTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.14
28 8 0.28
29 8 0.28
30 1 0.03
31 8 0.28
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (27 bp):
TCAACTATAAGTGTTTTTATTTAGTCA
Found at i:6728226 original size:2 final size:2
Alignment explanation
Indices: 6728221--6728246 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6728211 ACACACACAG
6728221 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
6728247 GCTTAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.