Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 4 of 290
Found at i:1138151 original size:38 final size:37
Alignment explanation
Indices: 1138088--1138174 Score: 126
Period size: 38 Copynumber: 2.4 Consensus size: 37
1138078 TGTAAGTTAT
1138088 GTAAGTTATG--A-TATGATATACATTTATGTATTAC
1 GTAAGTTATGTAAGTATGATATACATTTATGTATTAC
* *
1138122 GTAAGTTATGTCAAGTATGATATATATTTATGTATTAT
1 GTAAGTTATGT-AAGTATGATATACATTTATGTATTAC
1138160 GTAAGTTATGTAAGT
1 GTAAGTTATGTAAGT
1138175 TTTGTAAGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
34 10 0.21
37 5 0.11
38 32 0.68
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.45
Consensus pattern (37 bp):
GTAAGTTATGTAAGTATGATATACATTTATGTATTAC
Found at i:1138426 original size:15 final size:14
Alignment explanation
Indices: 1138412--1138472 Score: 59
Period size: 15 Copynumber: 4.2 Consensus size: 14
1138402 GGAAAAAAAT
1138412 TTATTTTAATTAAA
1 TTATTTTAATTAAA
* *
1138426 TAATATTTAAATAAA
1 TTAT-TTTAATTAAA
*
1138441 TTATTTTAGTTAAA
1 TTATTTTAATTAAA
* *
1138455 TAATATTTAAGTAAA
1 TTAT-TTTAATTAAA
1138470 TTA
1 TTA
1138473 ATCCAAATTA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
14 14 0.39
15 22 0.61
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TTATTTTAATTAAA
Found at i:1138447 original size:29 final size:29
Alignment explanation
Indices: 1138412--1138472 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1138402 GGAAAAAAAT
1138412 TTATTTTAATTAAATAATATTTAAATAAA
1 TTATTTTAATTAAATAATATTTAAATAAA
* *
1138441 TTATTTTAGTTAAATAATATTTAAGTAAA
1 TTATTTTAATTAAATAATATTTAAATAAA
1138470 TTA
1 TTA
1138473 ATCCAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
TTATTTTAATTAAATAATATTTAAATAAA
Found at i:1138587 original size:195 final size:194
Alignment explanation
Indices: 1138237--1138637 Score: 687
Period size: 195 Copynumber: 2.1 Consensus size: 194
1138227 ATTATTTCCC
* * *
1138237 TTTAAA-AAATTGTTTTAATTAAATAATATTTAAATTAATTAATCCAAATTATGTAATTTAAAAA
1 TTTAAATAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAA
*
1138301 ATTGTGTATAAAAAGTTGAAAATCGTATAAGATGAAATGTCAACTTTGTTACATGAAAAAGAAAT
66 ATTGTGTATAAAAAGTTGAAAACCGTATAAGATGAAATGTCAACTTTGTTACATGAAAAAGAAAT
*
1138366 AATAAACATAAAATTTGACGATGTGGAAAATCACATGGAAAAAAATTTATTTTAATTAAATAATA
131 AATAAAAATAAAATTTGACGATGTGGAAAATCACATGGAAAAAAA-TTATTTTAATTAAATAATA
* *
1138431 TTTAAATAAATTATTTTAGTTAAATAATATTTAAGTAAATTAATCCAAATTATATAATTTAAAAA
1 TTTAAATAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAA
*
1138496 ATTGTGTATAAAAAGTTGAAAACCGTATAAGATGAAATGTCAACTTTGTTCCATGAAAAAGAAAT
66 ATTGTGTATAAAAAGTTGAAAACCGTATAAGATGAAATGTCAACTTTGTTACATGAAAAAGAAAT
* * *
1138561 AATAAAAATAAAATTTGATGATGTGGAAAATCACATGGAAATAAATTATTTTAATTAAATGATA
131 AATAAAAATAAAATTTGACGATGTGGAAAATCACATGGAAAAAAATTATTTTAATTAAATAATA
1138625 TTTAAATAAATTA
1 TTTAAATAAATTA
1138638 ATACAAAATA
Statistics
Matches: 195, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
194 37 0.19
195 158 0.81
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.35
Consensus pattern (194 bp):
TTTAAATAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAA
ATTGTGTATAAAAAGTTGAAAACCGTATAAGATGAAATGTCAACTTTGTTACATGAAAAAGAAAT
AATAAAAATAAAATTTGACGATGTGGAAAATCACATGGAAAAAAATTATTTTAATTAAATAATA
Found at i:1138770 original size:14 final size:14
Alignment explanation
Indices: 1138751--1138781 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1138741 CTTGTTTTAA
*
1138751 TATGGTAATGGCAT
1 TATGGTAATGACAT
1138765 TATGGTAATGACAT
1 TATGGTAATGACAT
1138779 TAT
1 TAT
1138782 CGACTAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (14 bp):
TATGGTAATGACAT
Found at i:1139045 original size:24 final size:24
Alignment explanation
Indices: 1139013--1139059 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1139003 TTAACTTAAA
*
1139013 TGATAAAATGGATGATAATATTTG
1 TGATAAAATGGATGAGAATATTTG
1139037 TGATAAAATGGATGAGAATATTT
1 TGATAAAATGGATGAGAATATTT
1139060 CAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (24 bp):
TGATAAAATGGATGAGAATATTTG
Found at i:1141654 original size:17 final size:19
Alignment explanation
Indices: 1141618--1141654 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
1141608 ATAAAATTTG
*
1141618 AAATCTTGAGAATTATTTA
1 AAATCTTGAGAATTAATTA
1141637 AAAT-TTGA-AATTAATTA
1 AAATCTTGAGAATTAATTA
1141654 A
1 A
1141655 TATATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (19 bp):
AAATCTTGAGAATTAATTA
Found at i:1141801 original size:7 final size:7
Alignment explanation
Indices: 1141791--1141877 Score: 86
Period size: 7 Copynumber: 12.0 Consensus size: 7
1141781 AACCCCTGTC
1141791 CCCTTAA
1 CCCTTAA
1141798 CCCTTAAA
1 CCCTT-AA
*
1141806 CCCCTAA
1 CCCTTAA
* *
1141813 CCCATAT
1 CCCTTAA
1141820 CCCATTAA
1 CCC-TTAA
*
1141828 CCCCTAAA
1 -CCCTTAA
1141836 CCCTTAA
1 CCCTTAA
1141843 CCCTTAA
1 CCCTTAA
1141850 CCCTTAA
1 CCCTTAA
1141857 CCAC-TAA
1 CC-CTTAA
1141864 CCCTTAA
1 CCCTTAA
*
1141871 CCTTTAA
1 CCCTTAA
1141878 ATCCTAAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
6 1 0.01
7 51 0.76
8 12 0.18
9 3 0.04
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.25
Consensus pattern (7 bp):
CCCTTAA
Found at i:1141815 original size:30 final size:30
Alignment explanation
Indices: 1141767--1141872 Score: 92
Period size: 30 Copynumber: 3.6 Consensus size: 30
1141757 CTAAACCTTA
* * * * *
1141767 AACCCC-AAACTCCAAACCCCTGTCCCCTT
1 AACCCCTAAACCCCTAACCCATATCCCATT
*
1141796 AACCCTTAAACCCCTAACCCATATCCCATT
1 AACCCCTAAACCCCTAACCCATATCCCATT
* * *
1141826 AACCCCTAAACCCTTAACCCTTAACCC-TT
1 AACCCCTAAACCCCTAACCCATATCCCATT
* *
1141855 AACCACT-AACCCTTAACC
1 AACCCCTAAACCCCTAACC
1141873 TTTAAATCCT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
28 11 0.17
29 13 0.20
30 41 0.63
ACGTcount: A:0.32, C:0.46, G:0.01, T:0.21
Consensus pattern (30 bp):
AACCCCTAAACCCCTAACCCATATCCCATT
Found at i:1141832 original size:22 final size:21
Alignment explanation
Indices: 1141795--1141872 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 21
1141785 CCTGTCCCCT
1141795 TAACCCTTAAACCCCTAACCCA
1 TAACCCTT-AACCCCTAACCCA
* *
1141817 TATCCCATTAACCCCTAAACCCT
1 TAACCC-TTAACCCCT-AACCCA
*
1141840 TAACCCTTAACCCTTAA-CCA
1 TAACCCTTAACCCCTAACCCA
1141860 CTAACCCTTAACC
1 -TAACCCTTAACC
1141873 TTTAAATCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
20 2 0.04
21 14 0.29
22 20 0.42
23 12 0.25
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (21 bp):
TAACCCTTAACCCCTAACCCA
Found at i:1141902 original size:8 final size:7
Alignment explanation
Indices: 1141829--1141908 Score: 63
Period size: 7 Copynumber: 11.1 Consensus size: 7
1141819 TCCCATTAAC
1141829 CCCTAAA
1 CCCTAAA
*
1141836 CCCTTAA
1 CCCTAAA
*
1141843 CCCTTAA
1 CCCTAAA
*
1141850 CCCTTAA
1 CCCTAAA
1141857 CCACT-AA
1 CC-CTAAA
*
1141864 CCCTTAA
1 CCCTAAA
*
1141871 CCTTTAAA
1 CC-CTAAA
*
1141879 TCCTAAA
1 CCCTAAA
*
1141886 TCCTAAA
1 CCCTAAA
1141893 CCCATAAA
1 CCC-TAAA
1141901 CCCTAAA
1 CCCTAAA
1141908 C
1 C
1141909 TATAATGATA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
6 2 0.03
7 48 0.76
8 13 0.21
ACGTcount: A:0.38, C:0.39, G:0.00, T:0.24
Consensus pattern (7 bp):
CCCTAAA
Found at i:1142152 original size:14 final size:15
Alignment explanation
Indices: 1142123--1142161 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1142113 CCCAACCAAT
1142123 AACCCCTAAACTTTA
1 AACCCCTAAACTTTA
*
1142138 AACCCC-AACCTTTA
1 AACCCCTAAACTTTA
1142152 AA-CCCTAAAC
1 AACCCCTAAAC
1142162 CCATAATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 3 0.14
14 12 0.57
15 6 0.29
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCCTAAACTTTA
Found at i:1142578 original size:40 final size:40
Alignment explanation
Indices: 1142528--1142621 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 40
1142518 CGCTTTGTCA
* *
1142528 GCTCAATCTATAG-TGGAGTTTTTCAAAAAGCACCGCTAAT
1 GCTCGATCTATAGCTGCA-TTTTTCAAAAAGCACCGCTAAT
* * *
1142568 GCTCGATCTATAGCTGCATTTTTCAGAAAGCGCTGCTAAT
1 GCTCGATCTATAGCTGCATTTTTCAAAAAGCACCGCTAAT
* *
1142608 GCTTGATCTGTAGC
1 GCTCGATCTATAGC
1142622 ACCGCTAATG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
40 43 0.93
41 3 0.07
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (40 bp):
GCTCGATCTATAGCTGCATTTTTCAAAAAGCACCGCTAAT
Found at i:1142725 original size:40 final size:40
Alignment explanation
Indices: 1142681--1142786 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 40
1142671 TTTTTTTGTG
* *
1142681 GCATTTTTAAAAAAGCACCGCTAATGGTCGAGCTATAGCA
1 GCATTTTTAAAAAAGCGCCGCTAATGCTCGAGCTATAGCA
** * * * *
1142721 GCATTTTTTGAAAAGCGCCGGTAGTGCTCGATCTATAGCG
1 GCATTTTTAAAAAAGCGCCGCTAATGCTCGAGCTATAGCA
* *
1142761 GCATTTTTCAAAAAGTGCCGCTAATG
1 GCATTTTTAAAAAAGCGCCGCTAATG
1142787 ACACTAAAGC
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (40 bp):
GCATTTTTAAAAAAGCGCCGCTAATGCTCGAGCTATAGCA
Found at i:1145413 original size:21 final size:22
Alignment explanation
Indices: 1145385--1145435 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
1145375 TTGAAATGGC
1145385 AAAT-ATGAGAAATG-AATATG
1 AAATGATGAGAAATGAAATATG
1145405 AGAA-GATGAGAAATGAAATATG
1 A-AATGATGAGAAATGAAATATG
1145427 AAATGATGA
1 AAATGATGA
1145436 AATAAGATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.04
21 14 0.52
22 12 0.44
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.22
Consensus pattern (22 bp):
AAATGATGAGAAATGAAATATG
Found at i:1152589 original size:19 final size:19
Alignment explanation
Indices: 1152542--1152602 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
1152532 TTGTAATGCA
* *
1152542 AATAAAGGCACCGAAGTAC
1 AATAGAGGCACCGAAGTGC
* *
1152561 AAACAGAGGCATCGAAGTGC
1 -AATAGAGGCACCGAAGTGC
1152581 AATAGAGGCACCGAAGTGC
1 AATAGAGGCACCGAAGTGC
1152600 AAT
1 AAT
1152603 CCTGTACAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.43, C:0.20, G:0.26, T:0.11
Consensus pattern (19 bp):
AATAGAGGCACCGAAGTGC
Found at i:1153551 original size:17 final size:18
Alignment explanation
Indices: 1153517--1153552 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1153507 TGAATTTCTA
1153517 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
1153535 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
1153552 T
1 T
1153553 AACTCACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:1163515 original size:43 final size:42
Alignment explanation
Indices: 1163447--1163584 Score: 134
Period size: 43 Copynumber: 3.2 Consensus size: 42
1163437 AACGTCCCTA
* * *
1163447 ACGTGGTCTTACATGTAATCTCATATCGATGCCACTATCCCAG
1 ACGTGGTCTTACACGTAAACACATATCGATGCCAC-ATCCCAG
* * * *
1163490 ACAG-GGTCTTACTCTTAAACACATATTGATGCCAACGTCCCAG
1 AC-GTGGTCTTACACGTAAACACATATCGATGCC-ACATCCCAG
* * * *
1163533 ACGTGGTCTTACACGTAATCACATATCGATGCCAACGTTCCGG
1 ACGTGGTCTTACACGTAAACACATATCGATGCC-ACATCCCAG
1163576 ACGTGGTCT
1 ACGTGGTCT
1163585 AATACATGAT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 1 0.01
43 75 0.95
44 3 0.04
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (42 bp):
ACGTGGTCTTACACGTAAACACATATCGATGCCACATCCCAG
Found at i:1165006 original size:43 final size:43
Alignment explanation
Indices: 1164945--1165268 Score: 450
Period size: 43 Copynumber: 7.5 Consensus size: 43
1164935 TAGTTTATCA
* *
1164945 TGGTCTTATACGTAATCACATATCGATGCCAATGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
** * *
1164988 TGGTCTTATGCGTAATCACATATCGATGCCAACGTCCCAAACT
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* * * *
1165031 TGGTCTTACAAGTAATAACATATCGATGCCAACATCCCAGATG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
** * *
1165074 TGGTCTTATGCTTAATCACATATTGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
*
1165117 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGAAG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* *
1165160 TGGTCTTACGCGTAATCACATATCGATGCCAATGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* * * *
1165203 TGGCCTTACGCGTAATCACATGTCGATGCGAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
*
1165246 TAGTCTTACACGTAATCACATAT
1 TGGTCTTACACGTAATCACATAT
1165269 TGATATCTCA
Statistics
Matches: 245, Mismatches: 36, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 245 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
Found at i:1167643 original size:46 final size:46
Alignment explanation
Indices: 1167593--1167764 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
1167583 TGGTTGAGCA
*
1167593 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACG
* * * * *
1167639 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAA--A--CG
* *
1167686 TCCGAACTCGTTGAGTTGAGT-TCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCT-GAGTTCACTTATGGATGCAAACG
* *
1167732 CCCGAGCTCGTTGAGTTGAGTC-GAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTA
1167765 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 15, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
43 6 0.06
45 13 0.13
46 48 0.47
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACG
Found at i:1167749 original size:93 final size:92
Alignment explanation
Indices: 1167590--1167759 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 92
1167580 GGATGGTTGA
* *
1167590 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
1167655 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGT-CGAGTTCGTGAGATGTAACTAG
* * *
1167683 GCATCCGAACTCGTTGAGTTGAGT-TCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCT-GAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
1167747 TTGAGTCGAGTTC
65 TTGAGTCGAGTTC
1167760 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
92 8 0.11
93 63 0.89
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCGAGTTCGTGAGATGTAACTAG
Found at i:1176783 original size:46 final size:46
Alignment explanation
Indices: 1176733--1176905 Score: 167
Period size: 46 Copynumber: 3.7 Consensus size: 46
1176723 TGCTTGAGCA
* *
1176733 TCCGAACTCGTTGAGTAGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
1176779 TCCGAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAA--A--CG
* * *
1176826 TCCAAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
1176872 -CCTAAGCTCGTTGAGTTGAGTTCGAGTTCACTTA
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
1176906 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 13, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
45 6 0.06
46 52 0.50
47 25 0.24
48 2 0.02
50 5 0.05
51 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:1176889 original size:93 final size:93
Alignment explanation
Indices: 1176730--1176899 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
1176720 GGATGCTTGA
* *
1176730 GCATCCGAACTCGTTGAGTAGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTAGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
1176795 TGAGTCCGAGTTTGTGAGATGTAACTAG
66 TGAGTCCGAGTTTGTGAGATGTAACTAG
* * * *
1176823 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG-CCTAAGCTCGTTGAG
1 GCATCCAAACTCGTTGAGTAGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAA-CTCGTTGAG
*
1176887 TTGAGTTCGAGTT
65 TTGAGTCCGAGTT
1176900 CACTTAGGGG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
92 4 0.06
93 65 0.94
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTAGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTTGTGAGATGTAACTAG
Found at i:1180130 original size:26 final size:26
Alignment explanation
Indices: 1180101--1180150 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1180091 CATAGTGTCT
*
1180101 GTACCTCGTTCGGAAAGCAGTCTTCC
1 GTACCTCGTTCGAAAAGCAGTCTTCC
1180127 GTACCTCGTTCGAAAAGCAGTCTT
1 GTACCTCGTTCGAAAAGCAGTCTT
1180151 TGGCACATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (26 bp):
GTACCTCGTTCGAAAAGCAGTCTTCC
Found at i:1183396 original size:204 final size:204
Alignment explanation
Indices: 1183046--1183452 Score: 814
Period size: 204 Copynumber: 2.0 Consensus size: 204
1183036 GCATTTAACA
1183046 AACACATACCTGAACTTTTTAGCTCGATTACACATTCAATCATAACTTATCATTGCTCGTTTAAC
1 AACACATACCTGAACTTTTTAGCTCGATTACACATTCAATCATAACTTATCATTGCTCGTTTAAC
1183111 CATTCAGAATTAATAAGATATTCAGATAATCACATATTTTGTACAATGCTAACGTCCTAGACATG
66 CATTCAGAATTAATAAGATATTCAGATAATCACATATTTTGTACAATGCTAACGTCCTAGACATG
1183176 GTCTTACATGTAATCTCATATCGATATCACTATCCCAGACAGGGTCTTACTCTTAAACACATATC
131 GTCTTACATGTAATCTCATATCGATATCACTATCCCAGACAGGGTCTTACTCTTAAACACATATC
1183241 GATGCCAAT
196 GATGCCAAT
1183250 AACACATACCTGAACTTTTTAGCTCGATTACACATTCAATCATAACTTATCATTGCTCGTTTAAC
1 AACACATACCTGAACTTTTTAGCTCGATTACACATTCAATCATAACTTATCATTGCTCGTTTAAC
1183315 CATTCAGAATTAATAAGATATTCAGATAATCACATATTTTGTACAATGCTAACGTCCTAGACATG
66 CATTCAGAATTAATAAGATATTCAGATAATCACATATTTTGTACAATGCTAACGTCCTAGACATG
1183380 GTCTTACATGTAATCTCATATCGATATCACTATCCCAGACAGGGTCTTACTCTTAAACACATATC
131 GTCTTACATGTAATCTCATATCGATATCACTATCCCAGACAGGGTCTTACTCTTAAACACATATC
1183445 GATGCCAA
196 GATGCCAA
1183453 CGTCCCAGAC
Statistics
Matches: 203, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 203 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.33
Consensus pattern (204 bp):
AACACATACCTGAACTTTTTAGCTCGATTACACATTCAATCATAACTTATCATTGCTCGTTTAAC
CATTCAGAATTAATAAGATATTCAGATAATCACATATTTTGTACAATGCTAACGTCCTAGACATG
GTCTTACATGTAATCTCATATCGATATCACTATCCCAGACAGGGTCTTACTCTTAAACACATATC
GATGCCAAT
Found at i:1183522 original size:43 final size:43
Alignment explanation
Indices: 1183358--1183524 Score: 158
Period size: 43 Copynumber: 3.9 Consensus size: 43
1183348 ATATTTTGTA
* * * * * *
1183358 CAATGCTAACGTCCTAGACATGGTCTTACATGTAATCTCATAT
1 CAATGCCAACATCCCAGACGTGGTCTTACACGTAATCACATAT
* ** * * *
1183401 CGATATC-ACTATCCCAGACAG-GGTCTTACTCTTAAACACATAT
1 CAATGCCAAC-ATCCCAGAC-GTGGTCTTACACGTAATCACATAT
* *
1183444 CGATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATAT
1 CAATGCCAACATCCCAGACGTGGTCTTACACGTAATCACATAT
**
1183487 CAATGCCAACATCCTGGACGTGGTCTTACACGTAATCA
1 CAATGCCAACATCCCAGACGTGGTCTTACACGTAATCA
1183525 ACTTTCACTT
Statistics
Matches: 98, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
42 3 0.03
43 93 0.95
44 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (43 bp):
CAATGCCAACATCCCAGACGTGGTCTTACACGTAATCACATAT
Found at i:1191100 original size:18 final size:20
Alignment explanation
Indices: 1191062--1191101 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1191052 AGGACTTGTC
*
1191062 TACTGCATTATTTGATGCTG
1 TACTGCATTATTTGATACTG
1191082 TACTG-ATTA-TTGATACTG
1 TACTGCATTATTTGATACTG
1191100 TA
1 TA
1191102 ATGGGTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.45
Consensus pattern (20 bp):
TACTGCATTATTTGATACTG
Found at i:1193632 original size:40 final size:40
Alignment explanation
Indices: 1193554--1193734 Score: 276
Period size: 40 Copynumber: 4.5 Consensus size: 40
1193544 ACCCAAGTAT
* *
1193554 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
1193593 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1193633 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
1193673 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1193713 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
1193735 CATCCGAATA
Statistics
Matches: 130, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 11 0.08
40 118 0.91
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:1201811 original size:40 final size:40
Alignment explanation
Indices: 1201738--1201922 Score: 309
Period size: 40 Copynumber: 4.7 Consensus size: 40
1201728 AACCCAAGTA
* **
1201738 CCTTCGGGATTTAG-CCGGATATAACAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
1201777 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1201817 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
1201857 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
1201897 CCTTCGGGACTTAACCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGT
1201923 CACTGTGACA
Statistics
Matches: 139, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 13 0.09
40 126 0.91
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:1203950 original size:40 final size:40
Alignment explanation
Indices: 1203731--1203943 Score: 281
Period size: 40 Copynumber: 5.3 Consensus size: 40
1203721 TGGCTAAGTC
* *
1203731 CCGAAGGC-TTTGTGCTAAGTGACTAAATCCGGACTAAGAT
1 CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGACTAAGAT
* *
1203771 CCGAAGGCATTCGTACGAGTTACTAAATCCGGACTAAGAT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
*
1203811 CCGAAGGTATTTGTGCGAGTTACTAAATCCGGACTAAGAT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
**
1203851 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-T
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
* *
1203890 CCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATG-T
1 -CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGACTAAGAT
1203930 CCCGAAGGCATTTG
1 -CCGAAGGCATTTG
1203944 AACGAGTAGC
Statistics
Matches: 158, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
39 1 0.01
40 150 0.95
41 7 0.04
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
Found at i:1207676 original size:50 final size:50
Alignment explanation
Indices: 1207601--1207700 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1207591 TCGGTGACTC
1207601 GGTTTAGTGGTCCCGAAACCACTTTTCGACTAGGGTCAATTTAGGGCTGT
1 GGTTTAGTGGTCCCGAAACCACTTTTCGACTAGGGTCAATTTAGGGCTGT
1207651 GGTTTAGTGGTCCCGAAACCACTTTTCGACTAGGGTCAATTTAGGGCTGT
1 GGTTTAGTGGTCCCGAAACCACTTTTCGACTAGGGTCAATTTAGGGCTGT
1207701 CACAGAACTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (50 bp):
GGTTTAGTGGTCCCGAAACCACTTTTCGACTAGGGTCAATTTAGGGCTGT
Found at i:1210168 original size:24 final size:24
Alignment explanation
Indices: 1210141--1210220 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 24
1210131 TTTCATACTC
* *
1210141 ATCTTCATGTCGACCCTTGTCTTT
1 ATCTTCATCTCCACCCTTGTCTTT
1210165 ATCTTCATCTCCACCCTTGTCTTT
1 ATCTTCATCTCCACCCTTGTCTTT
* * * * * *
1210189 GTCTTCGTCTCTATCGTTGTCTTC
1 ATCTTCATCTCCACCCTTGTCTTT
1210213 ATCTTCAT
1 ATCTTCAT
1210221 TGTCGTCTTC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.11, C:0.31, G:0.10, T:0.47
Consensus pattern (24 bp):
ATCTTCATCTCCACCCTTGTCTTT
Found at i:1210210 original size:18 final size:18
Alignment explanation
Indices: 1210187--1210241 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
1210177 ACCCTTGTCT
1210187 TTGTCTTCGTCTCTATCG
1 TTGTCTTCGTCTCTATCG
* *
1210205 TTGTCTTCATCT-TCATTG
1 TTGTCTTCGTCTCT-ATCG
* *
1210223 TCGTCTTCGTCTCCATCG
1 TTGTCTTCGTCTCTATCG
1210241 T
1 T
1210242 CTTCCTCCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 1 0.03
18 28 0.97
ACGTcount: A:0.07, C:0.29, G:0.15, T:0.49
Consensus pattern (18 bp):
TTGTCTTCGTCTCTATCG
Found at i:1214208 original size:21 final size:21
Alignment explanation
Indices: 1214184--1214230 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
1214174 TGTGGATAGG
1214184 GGACACA-TCCGTGTGACTATA
1 GGACACACT-CGTGTGACTATA
*
1214205 GGACACACTCGTGTGACTATG
1 GGACACACTCGTGTGACTATA
1214226 GGACA
1 GGACA
1214231 TGCCCGTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (21 bp):
GGACACACTCGTGTGACTATA
Found at i:1216955 original size:16 final size:17
Alignment explanation
Indices: 1216936--1216968 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1216926 GTATAAATGG
1216936 AATTAAGTAAT-GAATA
1 AATTAAGTAATCGAATA
*
1216952 AATTATGTAATCGAATA
1 AATTAAGTAATCGAATA
1216969 TTGATGAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (17 bp):
AATTAAGTAATCGAATA
Found at i:1218574 original size:46 final size:45
Alignment explanation
Indices: 1218474--1218576 Score: 116
Period size: 46 Copynumber: 2.3 Consensus size: 45
1218464 AGAGCCCTTT
* * *
1218474 TTAGTAACAGAATAATTTGGGCCTTAGCCCATTACAGCAACAGAA
1 TTAGTAATAGAATAATGTGGGCCTAAGCCCATTACAGCAACAGAA
* * * ** *
1218519 TCAGAAATAGAATACATGTGGGCCTAAGCCCATTATAGTGACAGTA
1 TTAGTAATAGAATA-ATGTGGGCCTAAGCCCATTACAGCAACAGAA
1218565 TTAGTAATAGAA
1 TTAGTAATAGAA
1218577 ATGCAACAGT
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
45 11 0.24
46 35 0.76
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (45 bp):
TTAGTAATAGAATAATGTGGGCCTAAGCCCATTACAGCAACAGAA
Found at i:1218797 original size:32 final size:32
Alignment explanation
Indices: 1218747--1218809 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1218737 CACGGCTTAC
* *
1218747 AGCCATCAGTAGTGGTAATTTGATCAGCACAA
1 AGCCATCAATAGTGGTAATATGATCAGCACAA
*
1218779 AGCCATCAATAGCT-GTAATATGATCGGCACA
1 AGCCATCAATAG-TGGTAATATGATCAGCACA
1218810 CAGTCATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (32 bp):
AGCCATCAATAGTGGTAATATGATCAGCACAA
Found at i:1219345 original size:27 final size:27
Alignment explanation
Indices: 1219301--1219375 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
1219291 CAAAACAGTC
* *
1219301 ATTTTACCCTACAGGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
*
1219328 ATTTTACACTATAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
*
1219355 ATTTTACACTACAAGTGTATT
1 ATTTTACACTACAAGGGTATT
1219376 AACGACCCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:1222275 original size:26 final size:25
Alignment explanation
Indices: 1222173--1222286 Score: 115
Period size: 25 Copynumber: 4.6 Consensus size: 25
1222163 ATACATGTAT
*
1222173 GCTCATACGAGC-GATAAACGGTAA
1 GCTCATACGAGCTGAGAAACGGTAA
** *
1222197 GCTCATATAAGCTGA-ATAATGGTAA
1 GCTCATACGAGCTGAGA-AACGGTAA
* * * *
1222222 GCTCCTCCGAGTTGAGTAACGGTAA
1 GCTCATACGAGCTGAGAAACGGTAA
*
1222247 GCTCTTACGAGCTGAGAAATCGGTAA
1 GCTCATACGAGCTGAGAAA-CGGTAA
1222273 GCTCATACGAGCTG
1 GCTCATACGAGCTG
1222287 CGGTGAGTTC
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
24 11 0.15
25 41 0.58
26 19 0.27
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTGAGAAACGGTAA
Found at i:1225027 original size:25 final size:24
Alignment explanation
Indices: 1224979--1225027 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1224969 ATGTAATTTA
*
1224979 ATTTTAGAAAAATTATTTGATATC
1 ATTTTAGAAAAATTATCTGATATC
1225003 ATTTTAGAAGAAATATATCTG-TATC
1 ATTTTAGAA-AAAT-TATCTGATATC
1225028 TTATTGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 8 0.36
26 5 0.23
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (24 bp):
ATTTTAGAAAAATTATCTGATATC
Found at i:1226023 original size:14 final size:14
Alignment explanation
Indices: 1226004--1226030 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1225994 AACGAAGAAA
1226004 CAGCTAAGCAAAAC
1 CAGCTAAGCAAAAC
1226018 CAGCTAAGCAAAA
1 CAGCTAAGCAAAA
1226031 GCTTTTCGCT
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:0.26, G:0.15, T:0.07
Consensus pattern (14 bp):
CAGCTAAGCAAAAC
Found at i:1226090 original size:2 final size:2
Alignment explanation
Indices: 1226085--1226113 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1226075 TTTTTTCCTC
1226085 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1226114 CCCAAATCCC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1227558 original size:80 final size:79
Alignment explanation
Indices: 1227462--1227652 Score: 224
Period size: 83 Copynumber: 2.4 Consensus size: 79
1227452 TGCTGAGCTC
* *
1227462 GTTTTTATTTGTTCAGTAACGGTAGTTTCTGTTCTCCAATTATGCTTGG-TCGTG-CTTCTAAAA
1 GTTTTTATTTGTTCAGTGACGGTAGTTTCTATTCTCCAATTATGCTTGGCT-GTGCCTT-TAAAA
1227525 AGTTGCTGAGATTGTT
64 AGTTGCTGAGATTGTT
* * * * * *
1227541 GTTTTTAATTTGTTCAGTGACAGTAATTGCTTCTATTCTTCATTTGTGCTTGGCTTTGCCTTTAA
1 GTTTTT-ATTTGTTCAGTGACGGT-A--GTTTCTATTCTCCAATTATGCTTGGCTGTGCCTTTAA
1227606 AAAGTTGCTGAGATTGTT
62 AAAGTTGCTGAGATTGTT
*
1227624 GTTTATCATTTGTTCAGTGACGGTAGTTT
1 GTTT-TTATTTGTTCAGTGACGGTAGTTT
1227653 TACAAATCCA
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
79 6 0.06
80 18 0.19
81 1 0.01
82 1 0.01
83 63 0.67
84 5 0.05
ACGTcount: A:0.19, C:0.13, G:0.21, T:0.47
Consensus pattern (79 bp):
GTTTTTATTTGTTCAGTGACGGTAGTTTCTATTCTCCAATTATGCTTGGCTGTGCCTTTAAAAAG
TTGCTGAGATTGTT
Found at i:1227873 original size:3 final size:3
Alignment explanation
Indices: 1227867--1227911 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1227857 ACAACCACAA
1227867 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
1227912 TTCTTGCATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1232087 original size:17 final size:17
Alignment explanation
Indices: 1232062--1232094 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1232052 AAAATTACAA
1232062 AATAAATTTTAAAATTC
1 AATAAATTTTAAAATTC
*
1232079 AATATATTTTAAAATT
1 AATAAATTTTAAAATT
1232095 TTCAAAATTT
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAAATTTTAAAATTC
Found at i:1232117 original size:25 final size:25
Alignment explanation
Indices: 1232065--1232116 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1232055 ATTACAAAAT
1232065 AAATTTTAAAATTCAATATATTTTA
1 AAATTTTAAAATTCAATATATTTTA
*
1232090 AAATTTTCAAAATT-TATAT-TTTTA
1 AAATTTT-AAAATTCAATATATTTTA
1232114 AAA
1 AAA
1232117 AAATCATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 8 0.32
25 11 0.44
26 6 0.24
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATTTTAAAATTCAATATATTTTA
Found at i:1232682 original size:26 final size:26
Alignment explanation
Indices: 1232635--1232684 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1232625 CACCGAAATA
* ** *
1232635 AAGCAGAAGCAAACTCTCAAGTCAAG
1 AAGCAAAAGCAAACAATAAAGTCAAG
1232661 AAGCAAAAGCAAACAATAAAGTCA
1 AAGCAAAAGCAAACAATAAAGTCA
1232685 CAAGAAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.54, C:0.20, G:0.16, T:0.10
Consensus pattern (26 bp):
AAGCAAAAGCAAACAATAAAGTCAAG
Found at i:1234981 original size:28 final size:26
Alignment explanation
Indices: 1234943--1235066 Score: 140
Period size: 28 Copynumber: 4.5 Consensus size: 26
1234933 AATTTTTCTC
*
1234943 GCACACTTAGTGCTCAATAACCGATTT
1 GCACACTTAGTGCTCAA-AACCAATTT
*
1234970 CGCACACTTAGTGCTCGGAAATCCAATTT
1 -GCACACTTAGTGCTC--AAAACCAATTT
* *
1234999 GCACACTTAGTGCTTAAAACCAACTT
1 GCACACTTAGTGCTCAAAACCAATTT
* *
1235025 GCACACTTAGTGCTCAATGACCGATTTT
1 GCACACTTAGTGCTCAA-AACC-AATTT
1235053 GCACACTTAGTGCT
1 GCACACTTAGTGCT
1235067 TGGTATCAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
26 25 0.30
27 3 0.04
28 46 0.55
29 7 0.08
30 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (26 bp):
GCACACTTAGTGCTCAAAACCAATTT
Found at i:1235054 original size:54 final size:55
Alignment explanation
Indices: 1234943--1235067 Score: 150
Period size: 54 Copynumber: 2.3 Consensus size: 55
1234933 AATTTTTCTC
* * *
1234943 GCACACTTAGTGCTCAATAACCGATTTCGCACACTTAGTGCTCGGAAATCCAATTT
1 GCACACTTAGTGCTTAATAACCAACTTCGCACACTTAGTGCTC-GAAATCCAATTT
*
1234999 GCACACTTAGTGCTTAA-AACCAACTT-GCACACTTAGTGCTC--AATGACCGATTTT
1 GCACACTTAGTGCTTAATAACCAACTTCGCACACTTAGTGCTCGAAAT--CC-AATTT
1235053 GCACACTTAGTGCTT
1 GCACACTTAGTGCTT
1235068 GGTATCAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
51 3 0.05
53 2 0.03
54 34 0.55
55 7 0.11
56 16 0.26
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (55 bp):
GCACACTTAGTGCTTAATAACCAACTTCGCACACTTAGTGCTCGAAATCCAATTT
Found at i:1245608 original size:51 final size:51
Alignment explanation
Indices: 1245533--1245634 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
1245523 CGCTCTGGGC
* *
1245533 AGTCCCTGAGAATGTGGTCGAGAGATCTACATATGAAACATGCACCGCTCT
1 AGTCCCTGAGAAAGTGGTCAAGAGATCTACATATGAAACATGCACCGCTCT
* * * *
1245584 AGTCCCTGAGAAAGTGGTCAAGAGATCTTCATCTGAAACATGTACTGCTCT
1 AGTCCCTGAGAAAGTGGTCAAGAGATCTACATATGAAACATGCACCGCTCT
1245635 TCACTCAGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (51 bp):
AGTCCCTGAGAAAGTGGTCAAGAGATCTACATATGAAACATGCACCGCTCT
Found at i:1249930 original size:23 final size:22
Alignment explanation
Indices: 1249899--1249943 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1249889 AATATAGTCC
* *
1249899 TTTATTTATTTATTTTTTATTCA
1 TTTACTTATCTATTTTTT-TTCA
*
1249922 TTTACTTATCTCTTTTTTTTCA
1 TTTACTTATCTATTTTTTTTCA
1249944 CCATCTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTACTTATCTATTTTTTTTCA
Found at i:1250247 original size:21 final size:22
Alignment explanation
Indices: 1250207--1250248 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1250197 TACCTTCATT
* *
1250207 ATTATTGATTTTTTTGTTATCC
1 ATTATTGATTATTTTATTATCC
1250229 ATTATT-ATTATTTTATTATC
1 ATTATTGATTATTTTATTATC
1250249 ATCTATTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (22 bp):
ATTATTGATTATTTTATTATCC
Found at i:1250336 original size:3 final size:3
Alignment explanation
Indices: 1250323--1250375 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
1250313 CTTGTACATA
* *
1250323 TAT TGT TAT TAT TAT TAC TAT TAT TAT T-T TAT CTAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
1250367 TAT T-T TAT T
1 TAT TAT TAT T
1250376 TATATCTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 6 0.14
3 33 0.79
4 3 0.07
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1250348 original size:15 final size:16
Alignment explanation
Indices: 1250328--1250367 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
1250318 ACATATATTG
1250328 TTATTATTATTA-CTA
1 TTATTATTATTATCTA
1250343 TTATTATT-TTATCTA
1 TTATTATTATTATCTA
1250358 TTATTATTAT
1 TTATTATTAT
1250368 ATTTTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.13
15 19 0.83
16 1 0.04
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATTATTATCTA
Found at i:1255830 original size:27 final size:26
Alignment explanation
Indices: 1255800--1255890 Score: 71
Period size: 26 Copynumber: 3.4 Consensus size: 26
1255790 CAATTTCCTT
1255800 CTTATTACATTTGCTATCTTTGATTAA
1 CTTATT-CATTTGCTATCTTTGATTAA
* * **
1255827 CTTATTCATTT-CGAGTTAATTTCCTT--
1 CTTATTCATTTGCTA--T-CTTTGATTAA
1255853 CTTATTACATTTGCTATCTTTGATTAA
1 CTTATT-CATTTGCTATCTTTGATTAA
*
1255880 TTTATTCATTT
1 CTTATTCATTT
1255891 CGAGCTATGC
Statistics
Matches: 48, Mismatches: 9, Indels: 15
0.67 0.12 0.21
Matches are distributed among these distances:
25 7 0.15
26 17 0.35
27 17 0.35
28 7 0.15
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (26 bp):
CTTATTCATTTGCTATCTTTGATTAA
Found at i:1255871 original size:53 final size:53
Alignment explanation
Indices: 1255791--1255894 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
1255781 ACTCCAAATC
1255791 AATTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCATTTCGAGTT
1 AATTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCATTTCGAGTT
*
1255844 AATTTCCTTCTTATTACATTTGCTATCTTTGATTAATTTATTCATTTCGAG
1 AATTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCATTTCGAG
1255895 CTATGCTCCA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.23, C:0.16, G:0.08, T:0.53
Consensus pattern (53 bp):
AATTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCATTTCGAGTT
Found at i:1256364 original size:46 final size:46
Alignment explanation
Indices: 1256305--1256438 Score: 196
Period size: 46 Copynumber: 2.9 Consensus size: 46
1256295 AAAGAAAGCT
* * * * *
1256305 CAAATCCTGTACCCCTAAGCTGTAGTGGAATGGATTGAAGAAGATA
1 CAAATCCTATACCCCTGAGTTGCAGTGGGATGGATTGAAGAAGATA
*
1256351 CAAATCCTATACCCCTGAGTTGCAGTGGGATGGATTGAAGATGATA
1 CAAATCCTATACCCCTGAGTTGCAGTGGGATGGATTGAAGAAGATA
* *
1256397 CAAATCCTATACCCTTGAGTTGCAGTGGGATGGATGGAAGAA
1 CAAATCCTATACCCCTGAGTTGCAGTGGGATGGATTGAAGAA
1256439 ACCAAATTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (46 bp):
CAAATCCTATACCCCTGAGTTGCAGTGGGATGGATTGAAGAAGATA
Found at i:1258198 original size:20 final size:20
Alignment explanation
Indices: 1258173--1258215 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1258163 CTTTGATCAA
1258173 ACCTCTAGAAGACACTAATC
1 ACCTCTAGAAGACACTAATC
*
1258193 ACCTCTAGAGGACACTAATC
1 ACCTCTAGAAGACACTAATC
1258213 ACC
1 ACC
1258216 AAAAGAAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.33, G:0.12, T:0.19
Consensus pattern (20 bp):
ACCTCTAGAAGACACTAATC
Found at i:1260124 original size:34 final size:34
Alignment explanation
Indices: 1260053--1260124 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
1260043 CGTATCCTAG
*
1260053 CTACAGTCTCAGTCTTCTAAAGTTTTCAGTTTTCC
1 CTACAGTCTCAGTCTTCTAAAG-TTTCAGTTTACC
*
1260088 CTACTGTCTCAGT-TTCTACAA-TTTCAGTATTACC
1 CTACAGTCTCAGTCTTCTA-AAGTTTCAGT-TTACC
1260122 CTA
1 CTA
1260125 ACTACAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 7 0.21
34 12 0.36
35 14 0.42
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (34 bp):
CTACAGTCTCAGTCTTCTAAAGTTTCAGTTTACC
Found at i:1263837 original size:142 final size:142
Alignment explanation
Indices: 1263579--1264103 Score: 685
Period size: 143 Copynumber: 3.7 Consensus size: 142
1263569 GAATCCATAA
* * * * * * *
1263579 ATCTTATCTTCTTGAAGTTGTAGTGGAGAAGATTAAAGCCATCAGCCTTATTTTCCTGAAGTTGT
1 ATCTTATCTTCTTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
* *
1263644 AGTGGAGCAGACTGAAGATAGCGAATCTTAATTCCCTGACATTGTAGTGGAACAAATTAAAGCTA
66 AGTGGAGCAGACTGAAGACAGCGAATCTT-ATTCCCTGACGTTGTAGTGGAACAAATTAAAGCTA
*
1263709 CAAATTATGGTGG
130 CAAATTATGGAGG
* * *
1263722 ATCTTATCTTCCTGAGGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTCATCTCCCTGAAGTTG-
1 ATCTTATCTTCTTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
* * * *
1263786 AGTGGAGCAAACTGAAGACAGCGAATCTTACTTTCCTGACGTTGTAGTGGAATAGATTAAAGCTA
66 AGTGGAGCAGACTGAAGACAGCGAATCTTA-TTCCCTGACGTTGTAGTGGAACAAATTAAAGCTA
1263851 CAAATTATGGAGG
130 CAAATTATGGAGG
* * * * *
1263864 ATCTTATCTTCTTGAAGTTG-TGACGGAGTAGATTGAAGCCACCGGCCTTATCTCCTTGAAGTTA
1 ATCTTATCTTCTTGAAGTTGCAG-TGGAGTAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTG
* ** * *
1263928 CAGTGGAGCAGGCTGAAGACAAAGAATCTTATCTCCCTGAAGTTGTAGTGGAACAAATTGAAGCT
65 CAGTGGAGCAGACTGAAGACAGCGAATCTTAT-TCCCTGACGTTGTAGTGGAACAAATTAAAGCT
* *
1263993 ACAAATTATGGCGA
129 ACAAATTATGGAGG
* * * * * *
1264007 ATCTTATCTTCTTGAAGTTACAGTGGAGCAGATTTAAGCCATCAACCTTATCTCTCTGAAGTTGC
1 ATCTTATCTTCTTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
1264072 AGTGGAGCAGACTGAAGACAGCGAATCTTATT
66 AGTGGAGCAGACTGAAGACAGCGAATCTTATT
1264104 TCCTTGAAGC
Statistics
Matches: 328, Mismatches: 49, Indels: 11
0.85 0.13 0.03
Matches are distributed among these distances:
141 2 0.01
142 125 0.38
143 200 0.61
144 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (142 bp):
ATCTTATCTTCTTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
AGTGGAGCAGACTGAAGACAGCGAATCTTATTCCCTGACGTTGTAGTGGAACAAATTAAAGCTAC
AAATTATGGAGG
Found at i:1264197 original size:96 final size:96
Alignment explanation
Indices: 1264050--1264235 Score: 214
Period size: 96 Copynumber: 1.9 Consensus size: 96
1264040 TTAAGCCATC
* * * **
1264050 AACCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCTTGAAGCT
1 AACCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGACAGCCAATCTTACCTCCTTGAAGCT
*
1264115 GCACCAGAATAGATTGAAGCTACAAGTGGCA
66 CCACCAGAATAGATTGAAGCTACAAGTGGCA
* * *
1264146 AACCTTATCTCCCTGAGGTTACAGTGGAGCAGGCTGAA-ATTA-CCAATTCTTACCTCCTTGAAG
1 AACCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGA-CAGCCAA-TCTTACCTCCTTGAAG
* * * * *
1264209 TTCCAGCGGAGTAGATTGAAGTTACAA
64 CTCCACCAGAATAGATTGAAGCTACAA
1264236 ATCTCTTCTC
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
95 4 0.05
96 70 0.95
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (96 bp):
AACCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGACAGCCAATCTTACCTCCTTGAAGCT
CCACCAGAATAGATTGAAGCTACAAGTGGCA
Found at i:1264380 original size:45 final size:45
Alignment explanation
Indices: 1264149--1264389 Score: 202
Period size: 44 Copynumber: 5.4 Consensus size: 45
1264139 AGTGGCAAAC
* **
1264149 CTTATCTCCCTGAGGTTACAGTGGAGCAGGCTGAAATTACCAATT
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAATTACCAATT
* * * * * * *
1264194 CTTACCTCCTTGAAGTTCCAGCGGAGTAGATTGAAGTTA-CAAAT
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAATTACCAATT
* * ** *
1264238 CTCT-TCTCCCTGAAATTACATTGGAGCAGATTGAAGCTA-CAATC
1 CT-TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAATTACCAATT
** * * * * * **
1264282 CTTATCTTTCTGGAGTTGCAGTAGAGCAGGA-TAAAAATACACAAAC
1 CTTATCTCCCTGAAGTTACAGTGGAGCA-GATTGAAATTAC-CAATT
1264328 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAATTACCAATT
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAATTACCAATT
*
1264373 CTTATCTCCTTGAAGTT
1 CTTATCTCCCTGAAGTT
1264390 TTAGCGGAGT
Statistics
Matches: 149, Mismatches: 41, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
43 1 0.01
44 60 0.40
45 54 0.36
46 34 0.23
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAATTACCAATT
Found at i:1264485 original size:179 final size:179
Alignment explanation
Indices: 1264144--1264485 Score: 463
Period size: 179 Copynumber: 1.9 Consensus size: 179
1264134 CTACAAGTGG
* *
1264144 CAAACCTTATCTCCCTGAGGTTACAGTGGAGCAGGCTGAAATTACCAATTCTTACCTCCTTGAAG
1 CAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAATTACCAATTCTTACCTCCTTGAAG
* ** * *
1264209 TTCCAGCGGAGTAGATTGAAGTTACAAATCTCTTCTCCCTGAAATTACATTGGAGCAGATTGAAG
66 TTCCAGCGGAGTAGATCGAAACTACAAATCTCTTCTCCCTGAAATTACATCGGAGCAGATCGAAG
* * * ** * *
1264274 CTACAATCCTTATCTTTCTGGAGTTGCAGTAGAGCAGGATAAAAATACA
131 CGACAATCCTTAACCTTCTAAAGATACAGTAGAGCAGGATAAAAATACA
* *
1264323 CAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAATTACCAATTCTTATCTCCTTGAAG
1 CAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAATTACCAATTCTTACCTCCTTGAAG
** * *
1264388 TTTTAGCGGAGTAGATCGAAACTACAAATCTCTTTTCCCTGAAATTACATCGGAGCGGATCGAAG
66 TTCCAGCGGAGTAGATCGAAACTACAAATCTCTTCTCCCTGAAATTACATCGGAGCAGATCGAAG
*
1264453 CGCCAATTCC-TACACCTT-TAAAGATACAGTAGA
131 CGACAA-TCCTTA-ACCTTCTAAAGATACAGTAGA
1264486 TTGGAACGAG
Statistics
Matches: 140, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
179 134 0.96
180 6 0.04
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (179 bp):
CAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAATTACCAATTCTTACCTCCTTGAAG
TTCCAGCGGAGTAGATCGAAACTACAAATCTCTTCTCCCTGAAATTACATCGGAGCAGATCGAAG
CGACAATCCTTAACCTTCTAAAGATACAGTAGAGCAGGATAAAAATACA
Found at i:1265870 original size:17 final size:17
Alignment explanation
Indices: 1265848--1265881 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1265838 AATATAGTCC
* *
1265848 TTTATTTATTTATTTAT
1 TTTATTCATTTACTTAT
1265865 TTTATTCATTTACTTAT
1 TTTATTCATTTACTTAT
1265882 CTATTGTTTT
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:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTCATTTACTTAT
Found at i:1266196 original size:21 final size:22
Alignment explanation
Indices: 1266156--1266196 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1266146 ACCTTCATTA
1266156 TTATTGATTTTTTAATTATCCG
1 TTATTGATTTTTTAATTATCCG
1266178 TTATT-ATTATTTT-ATTATC
1 TTATTGATT-TTTTAATTATC
1266197 ATTATCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (22 bp):
TTATTGATTTTTTAATTATCCG
Found at i:1266289 original size:12 final size:13
Alignment explanation
Indices: 1266274--1266317 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
1266264 ATATTGTTCA
*
1266274 TATTATTACTAT-
1 TATTATTATTATC
1266286 TATTATT-TTATC
1 TATTATTATTATC
1266298 TATTATTATTATC
1 TATTATTATTATC
*
1266311 TTTTATT
1 TATTATT
1266318 TATATATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 3 0.11
12 14 0.50
13 11 0.39
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTATTATTATC
Found at i:1266319 original size:24 final size:24
Alignment explanation
Indices: 1266273--1266325 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1266263 TATATTGTTC
1266273 ATATTATTACTATTATTATTTTAT
1 ATATTATTACTATTATTATTTTAT
* * *
1266297 CTATTATTATTATCTTTTA-TTTAT
1 ATATTATTACTAT-TATTATTTTAT
1266321 ATATT
1 ATATT
1266326 TCACTACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (24 bp):
ATATTATTACTATTATTATTTTAT
Found at i:1266717 original size:19 final size:17
Alignment explanation
Indices: 1266684--1266718 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1266674 TGATATTATT
1266684 CAAAAAAGGAAGGTTTC
1 CAAAAAAGGAAGGTTTC
1266701 CAAAATAAGGCAAGGTTT
1 CAAAA-AAGG-AAGGTTT
1266719 TGAACTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (17 bp):
CAAAAAAGGAAGGTTTC
Found at i:1269661 original size:27 final size:27
Alignment explanation
Indices: 1269631--1269718 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
1269621 AGGTTATCCC
*
1269631 TTCATATTTCGCCACAAAGGCTACTCT
1 TTCATATTTCGCCACAAAGGATACTCT
* *
1269658 TTCATATTTTGCAACAAAGGATACTCT
1 TTCATATTTCGCCACAAAGGATACTCT
* * * *
1269685 TACATATTGCACCACAAAGGAGTTC-CT
1 TTCATATTTCGCCACAAAGGA-TACTCT
1269712 TTCATAT
1 TTCATAT
1269719 CGCACTACAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 48 0.96
28 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (27 bp):
TTCATATTTCGCCACAAAGGATACTCT
Found at i:1271005 original size:39 final size:39
Alignment explanation
Indices: 1270951--1271028 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
1270941 ATTTCATTTG
*
1270951 AAACTAGACTCATTAAGGAGTCTAAGCATATCAATTTTA
1 AAACTAGACTCATTAAGGAGTCTAAGCATATAAATTTTA
1270990 AAACTAGACTCATTAAGGAGTCTAAGCATATAAATTTTA
1 AAACTAGACTCATTAAGGAGTCTAAGCATATAAATTTTA
1271029 TCTTATAACC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (39 bp):
AAACTAGACTCATTAAGGAGTCTAAGCATATAAATTTTA
Found at i:1271890 original size:26 final size:26
Alignment explanation
Indices: 1271861--1271920 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
1271851 TTCCTTTGAA
* * *
1271861 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
1271887 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
1271915 ACATTC
1 TCATTC
1271921 TCAATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:1271936 original size:28 final size:28
Alignment explanation
Indices: 1271868--1271937 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
1271858 GAATCATTCG
*
1271868 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTTGCACACTAAGTGACATTCTCA
* *
1271896 ATATCTCGCACACTAAGTGACATTCTCA
1 ATATTTTGCACACTAAGTGACATTCTCA
*
1271924 ATATTTTGTACACT
1 ATATTTTGCACACT
1271938 GAGTACCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (28 bp):
ATATTTTGCACACTAAGTGACATTCTCA
Found at i:1276994 original size:57 final size:57
Alignment explanation
Indices: 1276864--1276994 Score: 181
Period size: 57 Copynumber: 2.3 Consensus size: 57
1276854 TGATCTCATT
** * * * * *
1276864 TCACACACTTAGTGCCCCAACAACTGATCTTGCACACACAGTGCTTGGTTACGAAAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAATGCTCGGTTACGAAAC
* *
1276921 TCGCACACACAGTGCCTCAACAACCGATCTCGCACACACAATGCTCGGTTACGGAAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAATGCTCGGTTACGAAAC
1276978 TCACACACACAGTGCCT
1 TCACACACACAGTGCCT
1276995 ATGTTCACTT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.30, C:0.35, G:0.16, T:0.19
Consensus pattern (57 bp):
TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAATGCTCGGTTACGAAAC
Found at i:1277751 original size:12 final size:12
Alignment explanation
Indices: 1277734--1277759 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1277724 AAGGGGGGTA
1277734 AGCTTTACGCTT
1 AGCTTTACGCTT
1277746 AGCTTTACGCTT
1 AGCTTTACGCTT
1277758 AG
1 AG
1277760 TAAGTTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (12 bp):
AGCTTTACGCTT
Found at i:1278905 original size:61 final size:61
Alignment explanation
Indices: 1278810--1278931 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
1278800 ATTATAAAGT
1278810 CGTCTCATAAACAATACATATAATATAGCATGTACACCTGTTCACTTTGCTCTATTTAATC
1 CGTCTCATAAACAATACATATAATATAGCATGTACACCTGTTCACTTTGCTCTATTTAATC
1278871 CGTCTCATAAACAATACATATAATATAGCATGTACACCTGTTCACTTTGCTCTATTTAATC
1 CGTCTCATAAACAATACATATAATATAGCATGTACACCTGTTCACTTTGCTCTATTTAATC
1278932 ATTCAATCAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (61 bp):
CGTCTCATAAACAATACATATAATATAGCATGTACACCTGTTCACTTTGCTCTATTTAATC
Found at i:1278992 original size:26 final size:26
Alignment explanation
Indices: 1278963--1279022 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
1278953 TCCCTTTGAA
* * *
1278963 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
1278989 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
1279017 CCATTC
1 TCATTC
1279023 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:1279008 original size:28 final size:28
Alignment explanation
Indices: 1278977--1279038 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
1278967 TCGATATTTT
*
1278977 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
1279005 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
1279033 GTACAC
1 GCACAC
1279039 AGTACCATAT
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:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:1290501 original size:42 final size:42
Alignment explanation
Indices: 1290442--1290546 Score: 151
Period size: 42 Copynumber: 2.5 Consensus size: 42
1290432 TAGGGTTACA
*
1290442 GAGACTATGTGTAAGACCATATCTGGG-ATATGGCATCAATGT
1 GAGACTATGTGTAAGACCATATC-GGGAATATGGCATCAATAT
*
1290484 GAGACTATGTGTAAGACCATATCGGGAATATGGCATCGATAT
1 GAGACTATGTGTAAGACCATATCGGGAATATGGCATCAATAT
*
1290526 GAGACT-TCATGTAAGACCATA
1 GAGACTAT-GTGTAAGACCATA
1290547 CTTGGGCTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
41 4 0.07
42 54 0.93
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (42 bp):
GAGACTATGTGTAAGACCATATCGGGAATATGGCATCAATAT
Found at i:1290604 original size:43 final size:42
Alignment explanation
Indices: 1290452--1290605 Score: 111
Period size: 42 Copynumber: 3.6 Consensus size: 42
1290442 GAGACTATGT
* ***
1290452 GTAAGACCATATCTGGGATATGGCATCA-ATGTGAGAC-T-ATG
1 GTAAGACCATATCTGGAATATGGCAT-AGATACAAGACTTCA-G
* * ** *
1290493 TGTAAGACCATATCGGGAATATGGCATCGATATGAGACTTCAT
1 -GTAAGACCATATCTGGAATATGGCATAGATACAAGACTTCAG
**
1290536 GTAAGACCATA-CTTGGGCTATTGGCATAGATTACAAGA-TTACAG
1 GTAAGACCATATC-TGGAATA-TGGCATAGA-TACAAGACTT-CAG
1290580 GTAAGACCATATCTGGAATATGGCAT
1 GTAAGACCATATCTGGAATATGGCAT
1290606 TGGTACGGTA
Statistics
Matches: 90, Mismatches: 14, Indels: 15
0.76 0.12 0.13
Matches are distributed among these distances:
41 1 0.01
42 47 0.52
43 17 0.19
44 24 0.27
45 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (42 bp):
GTAAGACCATATCTGGAATATGGCATAGATACAAGACTTCAG
Found at i:1293038 original size:24 final size:24
Alignment explanation
Indices: 1292989--1293039 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1292979 TGCTTTGTTT
**
1292989 TAATTTAATTAAACTTTTATTTTA
1 TAATTTAATTAAACTTTTATAATA
**
1293013 TAATTTAATTAATGTTTTATAATA
1 TAATTTAATTAAACTTTTATAATA
1293037 TAA
1 TAA
1293040 AAACATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TAATTTAATTAAACTTTTATAATA
Found at i:1299609 original size:41 final size:41
Alignment explanation
Indices: 1299547--1299747 Score: 215
Period size: 41 Copynumber: 4.9 Consensus size: 41
1299537 GATTCAGAAT
* * *
1299547 TACCAAAGT-CTAAACAAGGGCACGTATGTGCAATTTAGGCG
1 TACCAAAGTAC-AAACAGGGGCACGTATGTGCAATTCAGGGG
* * * * * *
1299588 TATCAAAGTATAAATAGGGGCATGCATGTGCAATTAAGGGG
1 TACCAAAGTACAAACAGGGGCACGTATGTGCAATTCAGGGG
* *
1299629 TACCGAAGTACAAACAGGGGCACATATGTGCAATTCAGGGG
1 TACCAAAGTACAAACAGGGGCACGTATGTGCAATTCAGGGG
** * * * *
1299670 TACTGAAGTACAAATAGAGGCATGTATGTGTAATTCAGGGG
1 TACCAAAGTACAAACAGGGGCACGTATGTGCAATTCAGGGG
* *
1299711 TACCAAAGTACAAACATGGGCACGTACGTGCAATTCA
1 TACCAAAGTACAAACAGGGGCACGTATGTGCAATTCA
1299748 ACAATATTCT
Statistics
Matches: 129, Mismatches: 30, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
41 129 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.22
Consensus pattern (41 bp):
TACCAAAGTACAAACAGGGGCACGTATGTGCAATTCAGGGG
Found at i:1299660 original size:82 final size:82
Alignment explanation
Indices: 1299547--1299747 Score: 253
Period size: 82 Copynumber: 2.5 Consensus size: 82
1299537 GATTCAGAAT
* * *
1299547 TACCAAAGT-CTAAACAAGGGCACGTATGTGCAATTTAGGCGTA-TCAAAGTATAAATAGGGGCA
1 TACCAAAGTAC-AAACAAGGGCACGTATGTGCAATTCAGGCGTACT-AAAGTACAAATAGAGGCA
1299610 TGCATGTGCAATTAAGGGG
64 TGCATGTGCAATTAAGGGG
* * * * *
1299629 TACCGAAGTACAAACAGGGGCACATATGTGCAATTCAGGGGTACTGAAGTACAAATAGAGGCATG
1 TACCAAAGTACAAACAAGGGCACGTATGTGCAATTCAGGCGTACTAAAGTACAAATAGAGGCATG
* * *
1299694 TATGTGTAATTCAGGGG
66 CATGTGCAATTAAGGGG
* *
1299711 TACCAAAGTACAAACATGGGCACGTACGTGCAATTCA
1 TACCAAAGTACAAACAAGGGCACGTATGTGCAATTCA
1299748 ACAATATTCT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
82 100 0.98
83 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.22
Consensus pattern (82 bp):
TACCAAAGTACAAACAAGGGCACGTATGTGCAATTCAGGCGTACTAAAGTACAAATAGAGGCATG
CATGTGCAATTAAGGGG
Found at i:1302392 original size:16 final size:16
Alignment explanation
Indices: 1302371--1302404 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1302361 GGTTCTTCAC
*
1302371 TTATTTGTTCACTTAT
1 TTATTTATTCACTTAT
1302387 TTATTTATTCACTTAT
1 TTATTTATTCACTTAT
1302403 TT
1 TT
1302405 GTTATTCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.12, G:0.03, T:0.65
Consensus pattern (16 bp):
TTATTTATTCACTTAT
Found at i:1304662 original size:23 final size:23
Alignment explanation
Indices: 1304632--1304680 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1304622 AAATTATATA
*
1304632 AATAAAGGGTCAGTAGGCACTCT
1 AATAAAGGGACAGTAGGCACTCT
1304655 AATAAAGGGACAGTAGGCACTCT
1 AATAAAGGGACAGTAGGCACTCT
1304678 AAT
1 AAT
1304681 GCTAAGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (23 bp):
AATAAAGGGACAGTAGGCACTCT
Found at i:1305899 original size:104 final size:104
Alignment explanation
Indices: 1305719--1305927 Score: 391
Period size: 104 Copynumber: 2.0 Consensus size: 104
1305709 GTTAGATAAA
* *
1305719 CAACTATTGTAAAGAGATTTTTGATGAAATTGTCAATTAGGGACTTAATTGAAAAATAAAAAAAT
1 CAACTATTATAAAGAGATTTTTGATGAAATTGTCAATTAGGGACTAAATTGAAAAATAAAAAAAT
1305784 ACATGGTGAAATTGTGAAATAAATGAAACATAGGCCATG
66 ACATGGTGAAATTGTGAAATAAATGAAACATAGGCCATG
*
1305823 CAACTATTATAAAGAGATTTTTGATGAAATTGTCAATTAGGGACTAAATTGAAAAATAAAAAATT
1 CAACTATTATAAAGAGATTTTTGATGAAATTGTCAATTAGGGACTAAATTGAAAAATAAAAAAAT
1305888 ACATGGTGAAATTGTGAAATAAATGAAACATAGGCCATG
66 ACATGGTGAAATTGTGAAATAAATGAAACATAGGCCATG
1305927 C
1 C
1305928 TAGGGACCTA
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (104 bp):
CAACTATTATAAAGAGATTTTTGATGAAATTGTCAATTAGGGACTAAATTGAAAAATAAAAAAAT
ACATGGTGAAATTGTGAAATAAATGAAACATAGGCCATG
Found at i:1306483 original size:25 final size:25
Alignment explanation
Indices: 1306410--1306475 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
1306400 TCCACCACTC
* *
1306410 GTGAGAGCATACTAATTTATAGATT
1 GTGAGAGCATACTGATTTATAGCTT
*
1306435 GTGAAAGCATACTGATTTATAGCTT
1 GTGAGAGCATACTGATTTATAGCTT
1306460 GTGAGAGCATACTGAT
1 GTGAGAGCATACTGAT
1306476 CTGCAGCTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (25 bp):
GTGAGAGCATACTGATTTATAGCTT
Found at i:1311798 original size:43 final size:43
Alignment explanation
Indices: 1311737--1311854 Score: 191
Period size: 43 Copynumber: 2.7 Consensus size: 43
1311727 ACCGTGTGTT
* * *
1311737 CCTACTTCAAATTCCCACATGGCTTGAGACACGACTGTTTGTC
1 CCTACTTCAAATGCCCACATGGCCTGAGACACGACTGTTTCTC
1311780 CCTACTTCAAATGCCCACATGGCCTGAGACACGACTGTTTCTC
1 CCTACTTCAAATGCCCACATGGCCTGAGACACGACTGTTTCTC
* *
1311823 CCTACTTCAAATGCCCACACGACCTGAGACAC
1 CCTACTTCAAATGCCCACATGGCCTGAGACAC
1311855 AGGCGTGTCT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (43 bp):
CCTACTTCAAATGCCCACATGGCCTGAGACACGACTGTTTCTC
Found at i:1322253 original size:58 final size:58
Alignment explanation
Indices: 1322178--1322293 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
1322168 GATGGTGGAA
*
1322178 CCAAACTACATAAAACTGTTGAAAATTGCTGAAGTAGCTTGTGTAGTTGCTAAGTTAC
1 CCAAACTACAGAAAACTGTTGAAAATTGCTGAAGTAGCTTGTGTAGTTGCTAAGTTAC
*
1322236 CCAAACTGCAGAAAACTGTTGAAAATTGCTGAAGTAGCTTGTGTAGTTGCTAAGTTAC
1 CCAAACTACAGAAAACTGTTGAAAATTGCTGAAGTAGCTTGTGTAGTTGCTAAGTTAC
1322294 GAGAATTACC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (58 bp):
CCAAACTACAGAAAACTGTTGAAAATTGCTGAAGTAGCTTGTGTAGTTGCTAAGTTAC
Found at i:1338970 original size:38 final size:37
Alignment explanation
Indices: 1338905--1338982 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 37
1338895 ATATTTGATG
* * *
1338905 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCAGGTTAAATCCAGCAAGCTTCGTGCTGGT-T
**
1338943 TATATCCAGGTTTTATCCAGCAAGCTTCGTGCTGGTT
1 TATATCCAGGTTAAATCCAGCAAGCTTCGTGCTGGTT
1338980 TAT
1 TAT
1338983 CCCGCAGGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 4 0.11
38 31 0.89
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (37 bp):
TATATCCAGGTTAAATCCAGCAAGCTTCGTGCTGGTT
Found at i:1338984 original size:24 final size:24
Alignment explanation
Indices: 1338954--1339007 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1338944 ATATCCAGGT
*
1338954 TTTATCCAGCAAGCTTCGTGCTGG
1 TTTATCCAGCAAGCTTCATGCTGG
* *
1338978 TTTATCCCGCAGGCTTCATGCTGG
1 TTTATCCAGCAAGCTTCATGCTGG
1339002 TATTAT
1 T-TTAT
1339008 ATCCGGGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (24 bp):
TTTATCCAGCAAGCTTCATGCTGG
Found at i:1339037 original size:62 final size:63
Alignment explanation
Indices: 1338919--1339045 Score: 184
Period size: 62 Copynumber: 2.0 Consensus size: 63
1338909 TCCGGGTTAA
* ** *
1338919 ATCCCGCAGGCTTCGTGCTGGTATTATATCCAGGTTTTATCCAGCAAGCTTCGTGCTGGT-TT
1 ATCCCGCAGGCTTCATGCTGGTATTATATCCAGGTTAAATCCAGCAAGCTTAGTGCTGGTATT
* * *
1338981 ATCCCGCAGGCTTCATGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTATT
1 ATCCCGCAGGCTTCATGCTGGTATTATATCCAGGTTAAATCCAGCAAGCTTAGTGCTGGTATT
1339044 AT
1 AT
1339046 ATTCGAGCTT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
62 53 0.93
63 4 0.07
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (63 bp):
ATCCCGCAGGCTTCATGCTGGTATTATATCCAGGTTAAATCCAGCAAGCTTAGTGCTGGTATT
Found at i:1339080 original size:40 final size:38
Alignment explanation
Indices: 1338981--1339068 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
1338971 GTGCTGGTTT
*
1338981 ATCCCGCAGGCTTCA-TGCTGGTATTATATCCGGGTTAA
1 ATCCCGCAGGCTT-AGTGCTGGTATTATATCCGGCTTAA
*
1339019 ATCCCGCAGGCTTAGTGCTGGTATTATATTCGAGCTTAA
1 ATCCCGCAGGCTTAGTGCTGGTATTATATCCG-GCTTAA
*
1339058 AGTTCCGCAGG
1 A-TCCCGCAGG
1339069 TTCTGTGCTG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 1 0.02
38 29 0.66
39 6 0.14
40 8 0.18
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (38 bp):
ATCCCGCAGGCTTAGTGCTGGTATTATATCCGGCTTAA
Found at i:1343779 original size:24 final size:24
Alignment explanation
Indices: 1343747--1343802 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1343737 GTCGAGAATC
1343747 AACAGGTGTTGTCCCTTGCGCGGG
1 AACAGGTGTTGTCCCTTGCGCGGG
1343771 AACAGGTGTTGTCCCTTGCGCGGG
1 AACAGGTGTTGTCCCTTGCGCGGG
*
1343795 AGCAGGTG
1 AACAGGTG
1343803 CTATACCCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.14, C:0.23, G:0.39, T:0.23
Consensus pattern (24 bp):
AACAGGTGTTGTCCCTTGCGCGGG
Found at i:1344055 original size:18 final size:18
Alignment explanation
Indices: 1344034--1344068 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1344024 GAGGCATTAT
1344034 CAAACAAAAACACATTTC
1 CAAACAAAAACACATTTC
**
1344052 CAAACAACCACACATTT
1 CAAACAAAAACACATTT
1344069 ATACAAGTCA
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:0.51, C:0.31, G:0.00, T:0.17
Consensus pattern (18 bp):
CAAACAAAAACACATTTC
Found at i:1345700 original size:56 final size:56
Alignment explanation
Indices: 1345637--1345769 Score: 239
Period size: 56 Copynumber: 2.4 Consensus size: 56
1345627 TCCCAGACAG
*
1345637 GGTCTTACTCACACACATATATCGGAGTCACATATCAATGCCAACGTATAAAACAT
1 GGTCTTACTCACACACATATATCGAAGTCACATATCAATGCCAACGTATAAAACAT
*
1345693 GGTCTTACTCACACACATATATCGAAGTCACATATCGATGCCAACGTATAAAACAT
1 GGTCTTACTCACACACATATATCGAAGTCACATATCAATGCCAACGTATAAAACAT
*
1345749 GGTCTTACTCGCACACATATA
1 GGTCTTACTCACACACATATA
1345770 ACGATGCCAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (56 bp):
GGTCTTACTCACACACATATATCGAAGTCACATATCAATGCCAACGTATAAAACAT
Found at i:1347984 original size:22 final size:21
Alignment explanation
Indices: 1347959--1347999 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1347949 CCGAATTGGT
1347959 CACACGAGCATGTTGCCCCTCC
1 CACACGAGCATG-TGCCCCTCC
* *
1347981 CACACGGGCGTGTGCCCCT
1 CACACGAGCATGTGCCCCT
1348000 ATGTCTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.15, C:0.44, G:0.24, T:0.17
Consensus pattern (21 bp):
CACACGAGCATGTGCCCCTCC
Found at i:1360820 original size:27 final size:27
Alignment explanation
Indices: 1360789--1360966 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
1360779 TAAATTGTAC
1360789 AGCACTAAGTGTGCGATTTGACTATAT
1 AGCACTAAGTGTGCGATTTGACTATAT
* ** *
1360816 TGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTAT-AT
* * **
1360844 -GCACTAAGTGTGCGAATTGACCATGC
1 AGCACTAAGTGTGCGATTTGACTATAT
* *
1360870 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATAT
* **
1360898 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATAT
* *
1360925 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATAT
*
1360952 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
1360967 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 104 0.81
28 25 0.19
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATAT
Found at i:1360904 original size:82 final size:81
Alignment explanation
Indices: 1360790--1360945 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
1360780 AAATTGTACA
* *
1360790 GCACTAAGTGTGCGATTTGACTATATTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATATAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
1360854 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
1360871 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATATAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
1360936 TGCGAGTTGA
65 TGCGAATTGA
1360946 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATATAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:1360957 original size:82 final size:81
Alignment explanation
Indices: 1360786--1360966 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
1360776 GATTAAATTG
* *
1360786 TACAGCACTAAGTGTGCGATTTGACTATATTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATATAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
1360851 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
1360867 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATATAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
1360931 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
1360949 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
1360967 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATATAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:1366534 original size:18 final size:18
Alignment explanation
Indices: 1366462--1366534 Score: 92
Period size: 18 Copynumber: 4.1 Consensus size: 18
1366452 CTTGGTCCAT
*
1366462 TGCAGTAACAGTAAACAG
1 TGCAGTAACAGTAAATAG
* *
1366480 TGCAGTAACAATAACTAG
1 TGCAGTAACAGTAAATAG
* * *
1366498 TGTAGTAATAGTAATTAG
1 TGCAGTAACAGTAAATAG
1366516 TGCAGTAACAGTAAATAG
1 TGCAGTAACAGTAAATAG
1366534 T
1 T
1366535 ATGCAAATCC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (18 bp):
TGCAGTAACAGTAAATAG
Found at i:1366908 original size:27 final size:27
Alignment explanation
Indices: 1366854--1367057 Score: 163
Period size: 27 Copynumber: 7.5 Consensus size: 27
1366844 AATATACACA
*
1366854 TACATCATATATGGGCAAAA-TAATCATTT
1 TACATCATA-A-GGGCAAAACT-TTCATTT
*
1366883 TACATCATAAGGGAAAAACTTTCATTT
1 TACATCATAAGGGCAAAACTTTCATTT
* * *
1366910 TACCTCATAAGGG-AAAAATCGTCATTT
1 TACATCATAAGGGCAAAACT-TTCATTT
*
1366937 TATCA-CATAAGGGCAAAACAGTT-ATTTT
1 TA-CATCATAAGGGCAAAAC-TTTCA-TTT
* **
1366965 TCCAT-ATAAGGGCAAAACCGTCATTT
1 TACATCATAAGGGCAAAACTTTCATTT
*
1366991 TACCTCATAAGGGCAAAA-TCTTCATTT
1 TACATCATAAGGGCAAAACT-TTCATTT
*
1367018 TATCA-CATAAGGGCAAAACTATCATTT
1 TA-CATCATAAGGGCAAAACTTTCATTT
1367045 TATC-TCATAAGGG
1 TA-CATCATAAGGG
1367058 TTCAGGTACG
Statistics
Matches: 144, Mismatches: 18, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
26 12 0.08
27 109 0.76
28 14 0.10
29 9 0.06
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (27 bp):
TACATCATAAGGGCAAAACTTTCATTT
Found at i:1366936 original size:54 final size:54
Alignment explanation
Indices: 1366877--1367057 Score: 187
Period size: 54 Copynumber: 3.4 Consensus size: 54
1366867 GGCAAAATAA
* *
1366877 TCATTTTA-CATCATAAGGGAAAAACTTTCATTTTACCTCATAAGGGAAAAATCG
1 TCATTTTATCATCATAAGGGCAAAACTTTCATTTTACCTCATAAGGGCAAAA-CG
* *
1366931 TCATTTTATCA-CATAAGGGCAAAACAGTT-ATTTTTCCAT-ATAAGGGCAAAACCG
1 TCATTTTATCATCATAAGGGCAAAAC-TTTCATTTTACC-TCATAAGGGCAAAA-CG
* * * *
1366985 TCATTTTA-CCTCATAAGGGCAAAA-TCTTCATTTTATCACATAAGGGCAAAACTA
1 TCATTTTATCATCATAAGGGCAAAACT-TTCATTTTACCTCATAAGGGCAAAAC-G
1367039 TCATTTTATC-TCATAAGGG
1 TCATTTTATCATCATAAGGG
1367058 TTCAGGTACG
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
53 4 0.04
54 97 0.91
55 6 0.06
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.32
Consensus pattern (54 bp):
TCATTTTATCATCATAAGGGCAAAACTTTCATTTTACCTCATAAGGGCAAAACG
Found at i:1367001 original size:81 final size:82
Alignment explanation
Indices: 1366880--1367036 Score: 253
Period size: 81 Copynumber: 1.9 Consensus size: 82
1366870 AAAATAATCA
**
1366880 TTTTACATCATAAGGGAAAAACTTTCATTTTACCTCATAAGGGAAAAATCGTCATTTTATCACAT
1 TTTTACATCATAAGGGAAAAACCGTCATTTTACCTCATAAGGGAAAAATCGTCATTTTATCACAT
1366945 AAGGGCAAAACAGTTAT
66 AAGGGCAAAACAGTTAT
* * * *
1366962 TTTTCCAT-ATAAGGGCAAAACCGTCATTTTACCTCATAAGGGCAAAATCTTCATTTTATCACAT
1 TTTTACATCATAAGGGAAAAACCGTCATTTTACCTCATAAGGGAAAAATCGTCATTTTATCACAT
1367026 AAGGGCAAAAC
66 AAGGGCAAAAC
1367037 TATCATTTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 62 0.90
82 7 0.10
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (82 bp):
TTTTACATCATAAGGGAAAAACCGTCATTTTACCTCATAAGGGAAAAATCGTCATTTTATCACAT
AAGGGCAAAACAGTTAT
Found at i:1367045 original size:81 final size:82
Alignment explanation
Indices: 1366857--1367057 Score: 252
Period size: 81 Copynumber: 2.5 Consensus size: 82
1366847 ATACACATAC
* * **
1366857 ATCATATATGGGCAAAA-TAATCA-TTTTACATCATAAGGGAAAAACTTTCATTTTACCTCATAA
1 ATCACATAAGGGCAAAACT-ATCATTTTTACATCATAAGGGAAAAACCGTCATTTTACCTCATAA
1366920 GGGAAAAATCGTCATTTT
65 GGGAAAAATCGTCATTTT
* * *
1366938 ATCACATAAGGGCAAAAC-AGTTATTTTTCCAT-ATAAGGGCAAAACCGTCATTTTACCTCATAA
1 ATCACATAAGGGCAAAACTA-TCATTTTTACATCATAAGGGAAAAACCGTCATTTTACCTCATAA
* *
1367001 GGGCAAAATCTTCATTTT
65 GGGAAAAATCGTCATTTT
1367019 ATCACATAAGGGCAAAACTATCA-TTTTATC-TCATAAGGG
1 ATCACATAAGGGCAAAACTATCATTTTTA-CATCATAAGGG
1367058 TTCAGGTACG
Statistics
Matches: 103, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
80 6 0.06
81 89 0.86
82 8 0.08
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (82 bp):
ATCACATAAGGGCAAAACTATCATTTTTACATCATAAGGGAAAAACCGTCATTTTACCTCATAAG
GGAAAAATCGTCATTTT
Found at i:1370413 original size:27 final size:27
Alignment explanation
Indices: 1370381--1370574 Score: 230
Period size: 27 Copynumber: 7.2 Consensus size: 27
1370371 ACATACATCA
1370381 CATAAGGGCAAAATAGTCATTTTACCT
1 CATAAGGGCAAAATAGTCATTTTACCT
* *
1370408 CATAAGGGAAAAATCGTCATTTTACCT
1 CATAAGGGCAAAATAGTCATTTTACCT
* *
1370435 CATAAGGGCAAAATTA-TCATTTTATCA
1 CATAAGGGCAAAA-TAGTCATTTTACCT
* *
1370462 CATAAGGGCAAAACAATCATTTTACCAT
1 CATAAGGGCAAAATAGTCATTTTACC-T
**
1370490 -ATAAGGGCAAAACCGTCATTTTACCT
1 CATAAGGGCAAAATAGTCATTTTACCT
* * * *
1370516 CATAAGCGCAAAATCGTCATTTTATCA
1 CATAAGGGCAAAATAGTCATTTTACCT
* *
1370543 CATAAGGGCAAAACAGTCATTTTATCT
1 CATAAGGGCAAAATAGTCATTTTACCT
1370570 CATAA
1 CATAA
1370575 AGGTTCAGGT
Statistics
Matches: 144, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.01
27 141 0.98
28 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.29
Consensus pattern (27 bp):
CATAAGGGCAAAATAGTCATTTTACCT
Found at i:1370471 original size:81 final size:81
Alignment explanation
Indices: 1370377--1370574 Score: 308
Period size: 81 Copynumber: 2.4 Consensus size: 81
1370367 ATATACATAC
* * *
1370377 ATCACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGAAAAATCGTCATTTTACCTCATAAGG
1 ATCACATAAGGGCAAAACAGTCATTTTACCTCATAAGGGAAAAACCGTCATTTTACCTCATAAGC
*
1370442 GCAAAATTATCATTTT
66 GCAAAATCATCATTTT
* *
1370458 ATCACATAAGGGCAAAACAATCATTTTACCAT-ATAAGGGCAAAACCGTCATTTTACCTCATAAG
1 ATCACATAAGGGCAAAACAGTCATTTTACC-TCATAAGGGAAAAACCGTCATTTTACCTCATAAG
*
1370522 CGCAAAATCGTCATTTT
65 CGCAAAATCATCATTTT
*
1370539 ATCACATAAGGGCAAAACAGTCATTTTATCTCATAA
1 ATCACATAAGGGCAAAACAGTCATTTTACCTCATAA
1370575 AGGTTCAGGT
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
80 1 0.01
81 104 0.98
82 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.29
Consensus pattern (81 bp):
ATCACATAAGGGCAAAACAGTCATTTTACCTCATAAGGGAAAAACCGTCATTTTACCTCATAAGC
GCAAAATCATCATTTT
Found at i:1374973 original size:3 final size:3
Alignment explanation
Indices: 1374965--1374994 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1374955 GGCATTCGGC
1374965 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1374995 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1376365 original size:40 final size:40
Alignment explanation
Indices: 1376307--1376405 Score: 162
Period size: 40 Copynumber: 2.5 Consensus size: 40
1376297 GATAGATAAT
* * *
1376307 GTAAAATATATCCAGGTTAAATCCCGTAGGCTTTGTGCTG
1 GTAAAATATATCCGGGTTAAATCCCGCAAGCTTTGTGCTG
1376347 GTAAAATATATCCGGGTTAAATCCCGCAAGCTTTGTGCTG
1 GTAAAATATATCCGGGTTAAATCCCGCAAGCTTTGTGCTG
*
1376387 GTAAAATATATCTGGGTTA
1 GTAAAATATATCCGGGTTA
1376406 TAAACCTAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (40 bp):
GTAAAATATATCCGGGTTAAATCCCGCAAGCTTTGTGCTG
Found at i:1377429 original size:27 final size:27
Alignment explanation
Indices: 1377399--1377595 Score: 191
Period size: 27 Copynumber: 7.3 Consensus size: 27
1377389 ACATACATCA
* * *
1377399 CATAGGGGCAAAACAGACATTTTAACT
1 CATAAGGGCAAAACAGTCATTTTACCT
*
1377426 CATAAGGGCAAAACTA-TCATTTTGCCT
1 CATAAGGGCAAAAC-AGTCATTTTACCT
** * *
1377453 CATAAGGGCAAAATTGTTATTTTATCAT
1 CATAAGGGCAAAACAGTCATTTTA-CCT
* *
1377481 -ATAAGGGCAAAACAGTCATTTTGCCA
1 CATAAGGGCAAAACAGTCATTTTACCT
* *
1377507 CATAAGGGTAAAACCGTCATTTTACCT
1 CATAAGGGCAAAACAGTCATTTTACCT
* ** * *
1377534 CGTAAGGGCAAAACCTTCATTTTATCA
1 CATAAGGGCAAAACAGTCATTTTACCT
* *
1377561 CATAAGGGCAAAACAATCATTTTATCT
1 CATAAGGGCAAAACAGTCATTTTACCT
1377588 CATAAGGG
1 CATAAGGG
1377596 TTCAGGTATG
Statistics
Matches: 138, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
26 1 0.01
27 134 0.97
28 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (27 bp):
CATAAGGGCAAAACAGTCATTTTACCT
Found at i:1377596 original size:81 final size:81
Alignment explanation
Indices: 1377395--1377596 Score: 246
Period size: 81 Copynumber: 2.5 Consensus size: 81
1377385 ATACACATAC
* * * *
1377395 ATCACATAGGGGCAAAACAGA-CATTTTAACTCATAAGGGCAAAACTATCATTTTGCCTCATAAG
1 ATCACATAAGGGCAAAACA-ATCATTTTAACTCATAAGGGTAAAACCATCATTTTACCTCATAAG
* *
1377459 GGCAAAATTGTTATTTT
65 GGCAAAACTGTCATTTT
* * ** * * *
1377476 ATCATATAAGGGCAAAACAGTCATTTTGCCACATAAGGGTAAAACCGTCATTTTACCTCGTAAGG
1 ATCACATAAGGGCAAAACAATCATTTTAACTCATAAGGGTAAAACCATCATTTTACCTCATAAGG
1377541 GCAAAACCT-TCATTTT
66 GCAAAA-CTGTCATTTT
*
1377557 ATCACATAAGGGCAAAACAATCATTTTATCTCATAAGGGT
1 ATCACATAAGGGCAAAACAATCATTTTAACTCATAAGGGT
1377597 TCAGGTATGC
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
81 100 0.99
82 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (81 bp):
ATCACATAAGGGCAAAACAATCATTTTAACTCATAAGGGTAAAACCATCATTTTACCTCATAAGG
GCAAAACTGTCATTTT
Found at i:1379557 original size:77 final size:77
Alignment explanation
Indices: 1379426--1379607 Score: 258
Period size: 77 Copynumber: 2.4 Consensus size: 77
1379416 GTAAGTTATA
* * * *
1379426 CGAAGGACTATTATCATGGCCTGAAGCCAAACAATCCAATATGCATGTCCCGAAGCCAAATCGGT
1 CGAAGTACTATTATCATGGCCCGAAGCCAAACAATCCAATATGCATGGCCCGAAGCCAAATCAGT
1379491 ATAATACACA-C
66 ATAATACACAGC
* * * * *
1379502 TCGAAGTGCTATTATCATGGCCCAAAGCCAAACCATCCGATATGCATGGCTCGAAGCCAAATCAG
1 -CGAAGTACTATTATCATGGCCCGAAGCCAAACAATCCAATATGCATGGCCCGAAGCCAAATCAG
1379567 TATAATACACAGC
65 TATAATACACAGC
*
1379580 CGAAGTACTAATATCATGGCCCGAAGCC
1 CGAAGTACTATTATCATGGCCCGAAGCC
1379608 TAATCAACAT
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
77 91 0.99
78 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (77 bp):
CGAAGTACTATTATCATGGCCCGAAGCCAAACAATCCAATATGCATGGCCCGAAGCCAAATCAGT
ATAATACACAGC
Found at i:1385734 original size:43 final size:42
Alignment explanation
Indices: 1385684--1385777 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
1385674 TCCCGGACGT
* * *
1385684 GGTCTTACATGTAGTCAAATATCGATACCACTGTCCCAGACAG
1 GGTCTTACATGAAATCAAATA-CGATACCAATGTCCCAGACAG
* * * *
1385727 GGTCTTACATGAAATCATATACGATGCCAATGTCCCAGTCAT
1 GGTCTTACATGAAATCAAATACGATACCAATGTCCCAGACAG
1385769 GGTCTTACA
1 GGTCTTACA
1385778 CATAAGTCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 26 0.59
43 18 0.41
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (42 bp):
GGTCTTACATGAAATCAAATACGATACCAATGTCCCAGACAG
Found at i:1385773 original size:42 final size:43
Alignment explanation
Indices: 1385665--1385821 Score: 131
Period size: 43 Copynumber: 3.7 Consensus size: 43
1385655 AGCTCGTTCA
* * * * *
1385665 ATGCCAACGTCCCGGACGTGGTCTTACATGTAGTCAAATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCAAATATCG
* * * *
1385708 ATACCACTGTCCCAGACAGGGTCTTACATGAAATCATATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCAAATATCG
* * *
1385750 ATGCCAATGTCCCAGTCATGGTCTTACACAT-AAGTCATAA-ATTG
1 ATGCCAATGTCCCAGACATGGTCTT--ACATGAAATCA-AATATCG
* **
1385794 ATGCCAATGTCCCAAATGTGGTCTTACA
1 ATGCCAATGTCCCAGACATGGTCTTACA
1385822 CGATAACACA
Statistics
Matches: 90, Mismatches: 20, Indels: 9
0.76 0.17 0.08
Matches are distributed among these distances:
42 26 0.29
43 37 0.41
44 27 0.30
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGAAATCAAATATCG
Found at i:1387548 original size:12 final size:12
Alignment explanation
Indices: 1387528--1387557 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1387518 TTAAGCTATT
*
1387528 ACACGGCCTAGC
1 ACACAGCCTAGC
1387540 ACACAGCCTAGC
1 ACACAGCCTAGC
1387552 ACACAG
1 ACACAG
1387558 GTGTGTGAGG
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:0.33, C:0.40, G:0.20, T:0.07
Consensus pattern (12 bp):
ACACAGCCTAGC
Found at i:1394753 original size:29 final size:29
Alignment explanation
Indices: 1394711--1394792 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1394701 TATATATGTG
*
1394711 AATTATCGAGCACTAAGTGTGTGAAGTAA
1 AATTATCGAGCACTAAGTGTGCGAAGTAA
1394740 AATTATCGAGCACTAAGTGTGCGAAGTAA
1 AATTATCGAGCACTAAGTGTGCGAAGTAA
* *
1394769 AACTATCGAGCACTAAGCGTGCGA
1 AATTATCGAGCACTAAGTGTGCGA
1394793 TCTCATTGCA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (29 bp):
AATTATCGAGCACTAAGTGTGCGAAGTAA
Found at i:1405568 original size:21 final size:21
Alignment explanation
Indices: 1405544--1405608 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 21
1405534 GGAAGAGAAT
*
1405544 TGAAACTTCCTAAATGATGAA
1 TGAAACTTCCTGAATGATGAA
1405565 TG-AAC-TCCTTGAAT-A-GAA
1 TGAAACTTCC-TGAATGATGAA
1405583 GTGAAACTTCCTGAATGATGAA
1 -TGAAACTTCCTGAATGATGAA
1405605 TGAA
1 TGAA
1405609 CTCCTTGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
18 3 0.08
19 6 0.16
20 15 0.41
21 10 0.27
22 3 0.08
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (21 bp):
TGAAACTTCCTGAATGATGAA
Found at i:1405600 original size:40 final size:40
Alignment explanation
Indices: 1405539--1405618 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
1405529 AGATAGGAAG
*
1405539 AGAATTGAAACTTCCTAAATGATGAATGAACTCCTTGAAT
1 AGAAGTGAAACTTCCTAAATGATGAATGAACTCCTTGAAT
*
1405579 AGAAGTGAAACTTCCTGAATGATGAATGAACTCCTTGAAT
1 AGAAGTGAAACTTCCTAAATGATGAATGAACTCCTTGAAT
1405619 TGGAGTTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (40 bp):
AGAAGTGAAACTTCCTAAATGATGAATGAACTCCTTGAAT
Found at i:1405617 original size:20 final size:20
Alignment explanation
Indices: 1405556--1405618 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 20
1405546 AAACTTCCTA
1405556 AATGATGAATGAACTCCTTG
1 AATGATGAATGAACTCCTTG
1405576 AAT-A-GAAGTGAAACTTCC-TG
1 AATGATGAA-TG-AAC-TCCTTG
1405596 AATGATGAATGAACTCCTTG
1 AATGATGAATGAACTCCTTG
1405616 AAT
1 AAT
1405619 TGGAGTTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
18 3 0.08
19 6 0.16
20 19 0.51
21 6 0.16
22 3 0.08
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (20 bp):
AATGATGAATGAACTCCTTG
Found at i:1408188 original size:18 final size:18
Alignment explanation
Indices: 1408165--1408202 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1408155 AATATATATT
1408165 AACCCAAGTACCCAACCC
1 AACCCAAGTACCCAACCC
*
1408183 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
1408201 AA
1 AA
1408203 TCATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.47, G:0.03, T:0.08
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:1408195 original size:13 final size:13
Alignment explanation
Indices: 1408179--1408203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1408169 CAAGTACCCA
1408179 ACCCAACCCAATT
1 ACCCAACCCAATT
1408192 ACCCAACCCAAT
1 ACCCAACCCAAT
1408204 CATAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Done.