Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 88 of 226
Found at i:31089645 original size:18 final size:17
Alignment explanation
Indices: 31089619--31089657 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
31089609 ATTTTCCTTC
31089619 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
31089636 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
31089654 CACA
1 CACA
31089658 AGTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:31107826 original size:6 final size:6
Alignment explanation
Indices: 31107815--31107841 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31107805 GGCTTTAACT
31107815 AAAACG AAAACG AAAACG AAAACG AAA
1 AAAACG AAAACG AAAACG AAAACG AAA
31107842 TCTCATAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAACG
Found at i:31111729 original size:28 final size:29
Alignment explanation
Indices: 31111673--31111728 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
31111663 ATGTTATCTT
31111673 TTTTATTTATTTACCAAAATATTATAAAA
1 TTTTATTTATTTACCAAAATATTATAAAA
*
31111702 TTTT-TTTATTTACTAAAATA-TATAAAA
1 TTTTATTTATTTACCAAAATATTATAAAA
31111729 AACAAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 7 0.27
28 15 0.58
29 4 0.15
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (29 bp):
TTTTATTTATTTACCAAAATATTATAAAA
Found at i:31112263 original size:19 final size:19
Alignment explanation
Indices: 31112239--31112301 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
31112229 AAGCAATAGT
31112239 TTATTAAAGTAAAATAGAG
1 TTATTAAAGTAAAATAGAG
*** ** * *
31112258 TTATTACTTTTTAATAAAC
1 TTATTAAAGTAAAATAGAG
31112277 TTATTAAAGTAAAATAGAG
1 TTATTAAAGTAAAATAGAG
31112296 TTATTA
1 TTATTA
31112302 CTTAATTAGA
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (19 bp):
TTATTAAAGTAAAATAGAG
Found at i:31113103 original size:28 final size:30
Alignment explanation
Indices: 31113072--31113137 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
31113062 TTTTTGGTAT
*
31113072 ATTTTGGTAAAT-A-AAAAAAAGGGATAAC
1 ATTTTGGTAAATAATAAAAAAAAGGATAAC
31113100 ATTTTGGTAAATAATAAAAAAAAGGATAAC
1 ATTTTGGTAAATAATAAAAAAAAGGATAAC
31113130 ATTTTGGT
1 ATTTTGGT
31113138 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 12 0.34
29 1 0.03
30 22 0.63
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (30 bp):
ATTTTGGTAAATAATAAAAAAAAGGATAAC
Found at i:31113309 original size:9 final size:9
Alignment explanation
Indices: 31113297--31113327 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31113287 GTTAAACGAG
31113297 TCGAGTTAT
1 TCGAGTTAT
*
31113306 TCGAGTTAA
1 TCGAGTTAT
31113315 TCGAGTTAT
1 TCGAGTTAT
31113324 TCGA
1 TCGA
31113328 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:31113398 original size:9 final size:9
Alignment explanation
Indices: 31113381--31113417 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31113371 TGAGTTTTCG
31113381 AATTCGAAT
1 AATTCGAAT
*
31113390 AACTCGAAT
1 AATTCGAAT
31113399 AATTCGAAT
1 AATTCGAAT
31113408 AATTCGAAT
1 AATTCGAAT
31113417 A
1 A
31113418 TCAAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:31114824 original size:20 final size:19
Alignment explanation
Indices: 31114799--31114836 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
31114789 AATTCTATTT
31114799 TTTTAATTTTATAACATATA
1 TTTTAATTTTATAA-ATATA
31114819 TTTTAATTTTATAAATAT
1 TTTTAATTTTATAAATAT
31114837 TTTATGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTAATTTTATAAATATA
Found at i:31115868 original size:94 final size:96
Alignment explanation
Indices: 31115770--31115998 Score: 248
Period size: 104 Copynumber: 2.3 Consensus size: 96
31115760 TTGGTGGCAT
*
31115770 ATTTGGTGAAGCAATCTTGAATAGGTGAAATA-C-T-TGGGAAGAAAATTTGGAAAAGCCAGATT
1 ATTTGGTGAAGCAATCTTGAATAGGTGAAATAGCATATGGGAAGAAAATTTGGAAAAGCCAGACT
*
31115832 AAATAGGCAAAATAAAATTTCCTAAAAGGTAA
66 AAATAGGCAAAATAAAATGT-CTAAAAGGTAA
* * *
31115864 ATTTGGTGAAACAATCTTGAATAGGTGAAATATAATGCAAATACTTGGAAGCAAATTTGGAAAAG
1 ATTTGGTGAAGCAATCTTGAATAGGTG-AA-AT-A-GC--ATA-TGGGAAGAAAATTTGGAAAAG
* * * *
31115929 TCAGACTAAATAGGCAAAATAAGATGTCTTAGAGGTAA
59 CCAGACTAAATAGGCAAAATAAAATGTCTAAAAGGTAA
** * *
31115967 ATTTGACGAAGCAGTCTTGAAGAGGTGAAATA
1 ATTTGGTGAAGCAATCTTGAATAGGTGAAATA
31115999 TAATGCCTTG
Statistics
Matches: 111, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
94 26 0.23
95 2 0.02
96 2 0.02
97 1 0.01
99 1 0.01
100 1 0.01
101 2 0.02
102 3 0.03
103 31 0.28
104 42 0.38
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (96 bp):
ATTTGGTGAAGCAATCTTGAATAGGTGAAATAGCATATGGGAAGAAAATTTGGAAAAGCCAGACT
AAATAGGCAAAATAAAATGTCTAAAAGGTAA
Found at i:31116004 original size:103 final size:105
Alignment explanation
Indices: 31115797--31116004 Score: 294
Period size: 103 Copynumber: 2.0 Consensus size: 105
31115787 TGAATAGGTG
* *
31115797 AAATACTTGGGAAGAAAATTTGGAAAAGCCAGATTAAATAGGCAAAATAAAATTTCCTAAAAGGT
1 AAATACTTGGGAAGAAAATTTGGAAAAGCCAGACTAAATAGGCAAAATAAAATGTCCTAAAAGGT
** *
31115862 AAATTTGGTGAAACAATCTTGAATAGGTGAAATATAATGC
66 AAATTTGACGAAACAATCTTGAAGAGGTGAAATATAATGC
* * * * *
31115902 AAATACTT-GGAAGCAAATTTGGAAAAGTCAGACTAAATAGGCAAAATAAGATGT-CTTAGAGGT
1 AAATACTTGGGAAGAAAATTTGGAAAAGCCAGACTAAATAGGCAAAATAAAATGTCCTAAAAGGT
* *
31115965 AAATTTGACGAAGCAGTCTTGAAGAGGTGAAATATAATGC
66 AAATTTGACGAAACAATCTTGAAGAGGTGAAATATAATGC
31116005 CTTGGAGGTA
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
103 42 0.46
104 41 0.45
105 8 0.09
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (105 bp):
AAATACTTGGGAAGAAAATTTGGAAAAGCCAGACTAAATAGGCAAAATAAAATGTCCTAAAAGGT
AAATTTGACGAAACAATCTTGAAGAGGTGAAATATAATGC
Found at i:31116380 original size:74 final size:74
Alignment explanation
Indices: 31116241--31116381 Score: 178
Period size: 74 Copynumber: 1.9 Consensus size: 74
31116231 ATAAGAGTAG
* * * * *
31116241 ATATATAATTAACTCTCCAAAGAAGGGGTTTGCCTAAATGAAAGAACTCTGTAATAGTAGATATA
1 ATATATAATGAACTCTCCAAAGAAGGAGTTTACCTAAATGAAAGAACTCCGAAATAGTAGATATA
31116306 TATATATAT
66 TATATATAT
** *
31116315 ATATATAATGAACTCTCCAATA-AAGGAGTTTACCTAAATGAGTGAACTCCGAAAGT-GTAGGTA
1 ATATATAATGAACTCTCCAA-AGAAGGAGTTTACCTAAATGAAAGAACTCCGAAA-TAGTAGATA
31116378 TATA
64 TATA
31116382 ATGAACTCTC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
74 55 0.96
75 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (74 bp):
ATATATAATGAACTCTCCAAAGAAGGAGTTTACCTAAATGAAAGAACTCCGAAATAGTAGATATA
TATATATAT
Found at i:31116410 original size:60 final size:60
Alignment explanation
Indices: 31116315--31116447 Score: 187
Period size: 60 Copynumber: 2.2 Consensus size: 60
31116305 ATATATATAT
* * * *
31116315 ATATATAATGAACTCTCCAATAAAGGAGTTTACCTAAATGAGTGAACTCCGAAAGTGTAG
1 ATATATAATGAACTCTCCAATAAAGAAGTTCACCTAAATGAGTGAACACCGAAAGAGTAG
* *
31116375 GTATATAATGAACTCTCCAATGAAA-AAGTTCACCTAAATGAGTGAACACCGTAAGAGTAG
1 ATATATAATGAACTCTCCAAT-AAAGAAGTTCACCTAAATGAGTGAACACCGAAAGAGTAG
*
31116435 ACATATAATGAAC
1 ATATATAATGAAC
31116448 GGTTCACTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 61 0.95
61 3 0.05
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (60 bp):
ATATATAATGAACTCTCCAATAAAGAAGTTCACCTAAATGAGTGAACACCGAAAGAGTAG
Found at i:31116463 original size:47 final size:47
Alignment explanation
Indices: 31116402--31116494 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 47
31116392 CAATGAAAAA
*
31116402 GTTCACCTAAATGAGTGAACACCGTAAGAGTAGACATATAATGAACG
1 GTTCACCTAAATGAGTGAACACCATAAGAGTAGACATATAATGAACG
* * ** *
31116449 GTTCACTTGAATGAGTGAACTTCATAAGAGTAGATATATAATGAAC
1 GTTCACCTAAATGAGTGAACACCATAAGAGTAGACATATAATGAAC
31116495 TCTCTAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (47 bp):
GTTCACCTAAATGAGTGAACACCATAAGAGTAGACATATAATGAACG
Found at i:31132836 original size:57 final size:60
Alignment explanation
Indices: 31132737--31132874 Score: 169
Period size: 57 Copynumber: 2.3 Consensus size: 60
31132727 GGATTACTCG
* *
31132737 TCCGGGCTAAATCCATTTTCCACATATTCTTCGGGGGTGCTATATC-A-A-GATCACCCA
1 TCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGGGTGCTATATCGATAGGATCACCCA
* *
31132794 TCCGGGCTAGAT-CTTTTTCACACATATTCTTTGGGAGG-GCTATATCAGGATAGGATCACCCG
1 TCCGGGCTAGATCCTTTTTC-CACATATTCTTCGGG-GGTGCTATATC--GATAGGATCACCCA
31132856 TCCGGGCTAGATCCTTTTT
1 TCCGGGCTAGATCCTTTTT
31132875 ACCGTCAATT
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
56 6 0.09
57 33 0.48
58 2 0.03
60 1 0.01
61 1 0.01
62 20 0.29
63 6 0.09
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (60 bp):
TCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGGGTGCTATATCGATAGGATCACCCA
Found at i:31136117 original size:20 final size:20
Alignment explanation
Indices: 31136094--31136131 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31136084 GTGAAAACAA
31136094 AGGCA-AAAATGTGCAATCAG
1 AGGCACAAAA-GTGCAATCAG
*
31136114 AGGCACCAAAGTGCAATC
1 AGGCACAAAAGTGCAATC
31136132 TCGTACAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (20 bp):
AGGCACAAAAGTGCAATCAG
Found at i:31140137 original size:33 final size:32
Alignment explanation
Indices: 31140060--31140139 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
31140050 CGACATGCCC
* ** * *
31140060 GTGTGGCCCACACGGCCTACTTGCCCTAGCTT
1 GTGTGGCTCACACGGCCTACTACCCCCAGCCT
31140092 GTGTGG-TCCACACGGCCTACCTACCCCCAGCCT
1 GTGTGGCT-CACACGGCCTA-CTACCCCCAGCCT
31140125 GTGTGGCTCACACGG
1 GTGTGGCTCACACGG
31140140 TCTGGTACAC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 17 0.43
33 22 0.55
34 1 0.03
ACGTcount: A:0.14, C:0.39, G:0.26, T:0.21
Consensus pattern (32 bp):
GTGTGGCTCACACGGCCTACTACCCCCAGCCT
Found at i:31141853 original size:50 final size:51
Alignment explanation
Indices: 31141787--31141965 Score: 265
Period size: 50 Copynumber: 3.6 Consensus size: 51
31141777 AAATCTCATA
* ** * *
31141787 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCTC-ATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCTCAACGCCATG
** *
31141837 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGGTG-TCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCTCAACGCCATG
31141887 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGC-CAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCTCAACGCCATG
31141937 TCCCAGACATGGTCTTACATGGGACCTCT
1 TCCCAGACATGGTCTTACATGGGACCTCT
31141966 TTACCCAAAT
Statistics
Matches: 116, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
49 2 0.02
50 114 0.98
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (51 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCTCAACGCCATG
Found at i:31146767 original size:15 final size:15
Alignment explanation
Indices: 31146749--31146778 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31146739 TTAAAATAAT
*
31146749 TTTTTAACTTTTTAG
1 TTTTTAAATTTTTAG
31146764 TTTTTAAATTTTTAG
1 TTTTTAAATTTTTAG
31146779 AAAACAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (15 bp):
TTTTTAAATTTTTAG
Found at i:31148415 original size:19 final size:19
Alignment explanation
Indices: 31148391--31148429 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
31148381 ATAAGTAAAT
31148391 ACACATATCACTTCAATTC
1 ACACATATCACTTCAATTC
31148410 ACACATATCACTTCAATTC
1 ACACATATCACTTCAATTC
31148429 A
1 A
31148430 TCCATCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (19 bp):
ACACATATCACTTCAATTC
Found at i:31148976 original size:22 final size:22
Alignment explanation
Indices: 31148951--31149021 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
31148941 CCATAGTGTC
31148951 TTTCAACTATGGCCTTATACGT
1 TTTCAACTATGGCCTTATACGT
*
31148973 TTTCGATA-TAAT-GCC--ATAGTGT
1 TTTC-A-ACT-ATGGCCTTATA-CGT
31148995 CTTTCAACTATGGCCTTATACGT
1 -TTTCAACTATGGCCTTATACGT
31149018 TTTC
1 TTTC
31149022 GATATAGTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
21 6 0.16
22 15 0.39
23 11 0.29
24 6 0.16
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (22 bp):
TTTCAACTATGGCCTTATACGT
Found at i:31149003 original size:45 final size:45
Alignment explanation
Indices: 31148835--31149102 Score: 288
Period size: 45 Copynumber: 5.9 Consensus size: 45
31148825 ATCTTATTTA
* * * *
31148835 TTTTCGACATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCA
1 TTTTCGATATAATGCCATAGTGTCTTTCAACTATGGTCTTATACG
** * ***
31148880 TTTTCCG-TCATGTTGCCATAGTGTCTTTCAACCATGGTCTTATTTA
1 TTTT-CGAT-ATAATGCCATAGTGTCTTTCAACTATGGTCTTATACG
** * *
31148926 TTTTCTG-TCATGTTTCCATAGTGTCTTTCAACTATGGCCTTATACG
1 TTTTC-GAT-ATAATGCCATAGTGTCTTTCAACTATGGTCTTATACG
*
31148972 TTTTCGATATAATGCCATAGTGTCTTTCAACTATGGCCTTATACG
1 TTTTCGATATAATGCCATAGTGTCTTTCAACTATGGTCTTATACG
* * *
31149017 TTTTCGATATAGTGCCATAGTGTCTTTCAACTATGGTCTTACATG
1 TTTTCGATATAATGCCATAGTGTCTTTCAACTATGGTCTTATACG
** * *
31149062 TTTTTTATATAATGTCATAGTGCCTTTCAACTATGGTCTTA
1 TTTTCGATATAATGCCATAGTGTCTTTCAACTATGGTCTTA
31149103 CATGTTTGAA
Statistics
Matches: 197, Mismatches: 22, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
45 117 0.59
46 80 0.41
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.44
Consensus pattern (45 bp):
TTTTCGATATAATGCCATAGTGTCTTTCAACTATGGTCTTATACG
Found at i:31149126 original size:45 final size:44
Alignment explanation
Indices: 31148842--31149170 Score: 224
Period size: 45 Copynumber: 7.3 Consensus size: 44
31148832 TTATTTTCGA
31148842 CATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCAT-TTTCCG-T
1 CATGATGCCATAGTGTCTTTCAACTATGGTCTTA--CATGTTT--GAT
* * * *
31148888 CATGTTGCCATAGTGTCTTTCAACCATGGTCTTATTTATTTTCTG-T
1 CATGATGCCATAGTGTCTTTCAACTATGGTCTTA--CATGTT-TGAT
* * * * *
31148934 CATGTTTCCATAGTGTCTTTCAACTATGGCCTTATACGTTTTCGAT
1 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACATG-TTT-GAT
* * * *
31148980 -ATAATGCCATAGTGTCTTTCAACTATGGCCTTATACGTTTTCGAT
1 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACATG-TTT-GAT
*
31149025 -AT-AGTGCCATAGTGTCTTTCAACTATGGTCTTACATGTTTTTTAT
1 CATGA-TGCCATAGTGTCTTTCAACTATGGTCTTACATG--TTTGAT
* * *
31149070 -ATAATGTCATAGTGCCTTTCAACTATGGTCTTACATGTTTGAAT
1 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACATGTTTG-AT
* * * * * * * *
31149114 CGTGATGCCATAGCGTATTTTAGCTATAGTCTTAC-TCTTTTAATT
1 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACAT-GTTTGA-T
31149159 CATGATGCCATA
1 CATGATGCCATA
31149171 ACGCCTTTCA
Statistics
Matches: 241, Mismatches: 30, Indels: 25
0.81 0.10 0.08
Matches are distributed among these distances:
43 3 0.01
44 8 0.03
45 152 0.63
46 75 0.31
47 2 0.01
48 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (44 bp):
CATGATGCCATAGTGTCTTTCAACTATGGTCTTACATGTTTGAT
Found at i:31153631 original size:19 final size:19
Alignment explanation
Indices: 31153593--31153631 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31153583 AAATAGCAAG
*
31153593 AATTTATTTTCTAAGTATA
1 AATTTATTTTCTAAGGATA
31153612 AATTCTATTTTCT-AGGATA
1 AATT-TATTTTCTAAGGATA
31153631 A
1 A
31153632 CAATTCTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (19 bp):
AATTTATTTTCTAAGGATA
Found at i:31155013 original size:60 final size:61
Alignment explanation
Indices: 31154895--31155027 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 61
31154885 ATTAGCCTAA
* * *
31154895 TAACAAATTTAGTCCTCCAATGTTTACACATTTTATTAATTTGATGCTAAATCT-AAAAAT
1 TAACAAATTTAGTCCTCCAATGTTTACAAAATTTATTAATTTAATGCTAAATCTAAAAAAT
* * ** *
31154955 TCAACAAATTTAGT-CTTCAATGTTTACAAAATTTA-TCATTTAATTTTAATTCTAAAAAAAT
1 T-AACAAATTTAGTCCTCCAATGTTTACAAAATTTATTAATTTAATGCTAAATCT-AAAAAAT
*
31155016 TAATAAATTTAG
1 TAACAAATTTAG
31155028 CCCTAAAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
59 13 0.21
60 29 0.48
61 19 0.31
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (61 bp):
TAACAAATTTAGTCCTCCAATGTTTACAAAATTTATTAATTTAATGCTAAATCTAAAAAAT
Found at i:31155803 original size:52 final size:52
Alignment explanation
Indices: 31155668--31155877 Score: 267
Period size: 52 Copynumber: 4.0 Consensus size: 52
31155658 TGGGTCTCGA
*
31155668 AATTTTTTTGGGGTTTTGGGACATTGATGGTCGACACCAACTTTATCAGATT
1 AATTTTTTTGGGGTTTTGGGACATTGATGGCCGACACCAACTTTATCAGATT
* ** * *
31155720 AAAAATTTTTTGGGGGTTTTGGGACATTGATGATCGATACCAACTGTATCAGATT
1 ---AATTTTTTTGGGGTTTTGGGACATTGATGGCCGACACCAACTTTATCAGATT
** * *
31155775 AATTTTTTTTTGGTTTTGGGACACTGATGGCCAACACCAACTTTATCAGATT
1 AATTTTTTTGGGGTTTTGGGACATTGATGGCCGACACCAACTTTATCAGATT
*** *
31155827 AATTTTTTTTTTGTTTTAGGACATTGATGGCCGACACCAACTTTATCAGAT
1 AATTTTTTTGGGGTTTTGGGACATTGATGGCCGACACCAACTTTATCAGAT
31155878 ATATATAGGT
Statistics
Matches: 138, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
52 90 0.65
55 48 0.35
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (52 bp):
AATTTTTTTGGGGTTTTGGGACATTGATGGCCGACACCAACTTTATCAGATT
Found at i:31155836 original size:107 final size:104
Alignment explanation
Indices: 31155668--31155877 Score: 267
Period size: 107 Copynumber: 2.0 Consensus size: 104
31155658 TGGGTCTCGA
* * *
31155668 AATTTTTTTGGGGTTTTGGGACATTGATGGTCGACACCAACTTTATCAGATTAAAAATTTTTTGG
1 AATTTTTTTGGGGTTTTGGGACACTGATGGCCAACACCAACTTTATCAGATTAAAAATTTTTT--
* * *
31155733 GGGTTTTGGGACATTGATGATCGATACCAACTGTATCAGATT
64 -GGTTTTAGGACATTGATGACCGACACCAACTGTATCAGATT
** *** *
31155775 AATTTTTTTTTGGTTTTGGGACACTGATGGCCAACACCAACTTTATCAGATTAATTTTTTTTTTG
1 AATTTTTTTGGGGTTTTGGGACACTGATGGCCAACACCAACTTTATCAGATTAAAAATTTTTTGG
* *
31155840 TTTTAGGACATTGATGGCCGACACCAACTTTATCAGAT
66 TTTTAGGACATTGATGACCGACACCAACTGTATCAGAT
31155878 ATATATAGGT
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
104 34 0.38
107 55 0.62
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (104 bp):
AATTTTTTTGGGGTTTTGGGACACTGATGGCCAACACCAACTTTATCAGATTAAAAATTTTTTGG
TTTTAGGACATTGATGACCGACACCAACTGTATCAGATT
Found at i:31161196 original size:6 final size:6
Alignment explanation
Indices: 31161185--31161289 Score: 124
Period size: 6 Copynumber: 17.7 Consensus size: 6
31161175 AATATATAAA
* * * *
31161185 AAATTG AAATTG AAAGTTG -TATTG -AATTG AAATTC AATTTG AAATTA
1 AAATTG AAATTG AAA-TTG AAATTG AAATTG AAATTG AAATTG AAATTG
* * *
31161232 AAATAG GAATTA AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG
31161280 AAATTG AAAT
1 AAATTG AAAT
31161290 GAATTTATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
5 7 0.08
6 73 0.88
7 3 0.04
ACGTcount: A:0.50, C:0.01, G:0.15, T:0.34
Consensus pattern (6 bp):
AAATTG
Found at i:31161569 original size:18 final size:17
Alignment explanation
Indices: 31161523--31161562 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
31161513 TGGAATGAAA
*
31161523 TTAAAATGAAATTATAT
1 TTAAAATGAAAATATAT
31161540 TTAAAATGAAAATATAT
1 TTAAAATGAAAATATAT
31161557 TTAAAA
1 TTAAAA
31161563 AAGAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
TTAAAATGAAAATATAT
Found at i:31161574 original size:18 final size:17
Alignment explanation
Indices: 31161536--31161574 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
31161526 AAATGAAATT
* *
31161536 ATATTTAAAATGAAAAT
1 ATATTTAAAAAGAAAAA
31161553 ATATTTAAAAAAGAAAAA
1 ATATTT-AAAAAGAAAAA
31161571 ATAT
1 ATAT
31161575 ATTGATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
ATATTTAAAAAGAAAAA
Found at i:31162008 original size:23 final size:23
Alignment explanation
Indices: 31161957--31162002 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
31161947 TTTGGGGTAG
* *
31161957 CTGTAATATCCCGAAAATTACTA
1 CTGTAATACCCCGAAAATTAATA
31161980 CTGTAATACCCCGAAAATTAATA
1 CTGTAATACCCCGAAAATTAATA
31162003 TAGTAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (23 bp):
CTGTAATACCCCGAAAATTAATA
Found at i:31166288 original size:89 final size:92
Alignment explanation
Indices: 31166188--31166393 Score: 265
Period size: 93 Copynumber: 2.3 Consensus size: 92
31166178 AATATGCAAC
* * * *
31166188 AAATTAAATTTATAGAT-ATAAGAA-A-ACACAAACATTCTAAAATATTAATACACGAAAATATA
1 AAATTAAATTTACAGATAAAAAAAATATACACAAACATTCTAAAAAATTAATACACGAAAATATA
**
31166250 AAATTCAAACAACAAACAATATGGACT
66 AAATTCAAACAACAAACAATACAGACT
* *
31166277 AAATTAAATTTACAGATACAAAAAAATATATATAAACATTCTAAAAAATTAATACACGAAAATAT
1 AAATTAAATTTACAGATA-AAAAAAATATACACAAACATTCTAAAAAATTAATACACGAAAATAT
* *
31166342 AAAATTCGAACAACAAATAATACAGACT
65 AAAATTCAAACAACAAACAATACAGACT
** *
31166370 AAATTTGATTTACAGATACAAAAA
1 AAATTAAATTTACAGATAAAAAAA
31166394 TTTTGAATAG
Statistics
Matches: 100, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
89 16 0.16
91 5 0.05
92 6 0.06
93 73 0.73
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (92 bp):
AAATTAAATTTACAGATAAAAAAAATATACACAAACATTCTAAAAAATTAATACACGAAAATATA
AAATTCAAACAACAAACAATACAGACT
Found at i:31166420 original size:93 final size:93
Alignment explanation
Indices: 31166217--31166393 Score: 291
Period size: 93 Copynumber: 1.9 Consensus size: 93
31166207 AAGAAAACAC
* **
31166217 AAACATTCTAAAATATTAATACACGAAAATATAAAATTCAAACAACAAACAATATGGACTAAATT
1 AAACATTCTAAAAAATTAATACACGAAAATATAAAATTCAAACAACAAACAATACAGACTAAATT
31166282 AAATTTACAGATACAAAAAAATATATAT
66 AAATTTACAGATACAAAAAAATATATAT
* *
31166310 AAACATTCTAAAAAATTAATACACGAAAATATAAAATTCGAACAACAAATAATACAGACTAAATT
1 AAACATTCTAAAAAATTAATACACGAAAATATAAAATTCAAACAACAAACAATACAGACTAAATT
**
31166375 TGATTTACAGATACAAAAA
66 AAATTTACAGATACAAAAA
31166394 TTTTGAATAG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (93 bp):
AAACATTCTAAAAAATTAATACACGAAAATATAAAATTCAAACAACAAACAATACAGACTAAATT
AAATTTACAGATACAAAAAAATATATAT
Found at i:31173418 original size:3 final size:3
Alignment explanation
Indices: 31173410--31173456 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
31173400 TCGAAAAACT
31173410 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
31173457 GTCAAAACCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:31174367 original size:13 final size:13
Alignment explanation
Indices: 31174349--31174373 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31174339 CAACAAACAA
31174349 ATAAAGAAAAAAT
1 ATAAAGAAAAAAT
31174362 ATAAAGAAAAAA
1 ATAAAGAAAAAA
31174374 GCGCATAATA
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
ATAAAGAAAAAAT
Found at i:31174435 original size:15 final size:17
Alignment explanation
Indices: 31174415--31174481 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 17
31174405 AAACTATAAA
31174415 ATTTATATA-A-AAAAT
1 ATTTATATATATAAAAT
*
31174430 ATTTATATATATAATAT
1 ATTTATATATATAAAAT
* *
31174447 ATTTATGAGA-ATAAAAA
1 ATTTAT-ATATATAAAAT
*
31174464 ATATATATATATAGAAAT
1 ATTTATATATATA-AAAT
31174482 TATAAAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
15 9 0.22
16 3 0.08
17 23 0.57
18 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (17 bp):
ATTTATATATATAAAAT
Found at i:31174440 original size:17 final size:17
Alignment explanation
Indices: 31174418--31174476 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
31174408 CTATAAAATT
31174418 TATATAAAAAATATTTA
1 TATATAAAAAATATTTA
* *
31174435 TATATATAATATATTTA
1 TATATAAAAAATATTTA
* *
31174452 TGAGAATAAAAAATATATA
1 T-A-TATAAAAAATATTTA
31174471 TATATA
1 TATATA
31174477 GAAATTATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 19 0.58
18 2 0.06
19 12 0.36
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TATATAAAAAATATTTA
Found at i:31174605 original size:20 final size:20
Alignment explanation
Indices: 31174577--31174623 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31174567 GCATATATAT
*
31174577 ATATATATAGAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
31174597 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
31174617 ATATATA
1 ATATATA
31174624 CGTACATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:31174638 original size:54 final size:53
Alignment explanation
Indices: 31174466--31174639 Score: 164
Period size: 54 Copynumber: 3.2 Consensus size: 53
31174456 AATAAAAAAT
31174466 ATATATATATAGAAATTATAAAAATATGGATAGAAAGTATAATATATATATACGTAC
1 ATATATATATAGAAATTAT-AAAATAT-GATAGAAAGTAT-A-ATATATATACGTAC
* * * *
31174523 ATATATATGT--AAGTTA-ATAAATATAGATCATAAAG-ATAATGAT-TGCATA--TAT
1 ATATATATATAGAAATTATA-AAATAT-GAT-AGAAAGTATAAT-ATAT--ATACGTAC
31174575 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATACGTAC
1 ATATATATATAGAAATTATAAAATATG-ATAGAAAGTATAATATATATACGTAC
31174629 ATATATATATA
1 ATATATATATA
31174640 TATATAAGGT
Statistics
Matches: 95, Mismatches: 9, Indels: 29
0.71 0.07 0.22
Matches are distributed among these distances:
52 17 0.18
53 12 0.13
54 46 0.48
55 11 0.12
57 9 0.09
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (53 bp):
ATATATATATAGAAATTATAAAATATGATAGAAAGTATAATATATATACGTAC
Found at i:31175678 original size:18 final size:18
Alignment explanation
Indices: 31175655--31175690 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
31175645 TTCGATTTAC
31175655 GAATCTTTGATTTTCTTT
1 GAATCTTTGATTTTCTTT
31175673 GAATCTTTGATTTTCTTT
1 GAATCTTTGATTTTCTTT
31175691 CTATCTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (18 bp):
GAATCTTTGATTTTCTTT
Found at i:31175696 original size:18 final size:18
Alignment explanation
Indices: 31175656--31175699 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
31175646 TCGATTTACG
*
31175656 AATCTTTGATTTTCTTTG
1 AATCTTTGATTTTCTTTC
31175674 AATCTTTGATTTTCTTTC
1 AATCTTTGATTTTCTTTC
*
31175692 TATCTTTG
1 AATCTTTG
31175700 CTGTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (18 bp):
AATCTTTGATTTTCTTTC
Found at i:31176308 original size:45 final size:45
Alignment explanation
Indices: 31176258--31176395 Score: 183
Period size: 44 Copynumber: 3.1 Consensus size: 45
31176248 CTACATCTTT
* ** *
31176258 AGGGAGATAGGATTTGTTTA-CTTTCAACCTATTCCATTGCTGACC
1 AGGGAGATAGGATTTCTCAATC-TTCAACCTATTCCACTGCTGACC
31176303 AGGGAGATAGGA-TTCTCAATCTTCAACCTATTCCACTGCTGACC
1 AGGGAGATAGGATTTCTCAATCTTCAACCTATTCCACTGCTGACC
* * *
31176347 AGGGAGATAGGA-TTCACAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAGGATTTCTCAATCTTCAACCTATTCCACTGCTGACC
31176391 AGGGA
1 AGGGA
31176396 AGTAGAATTA
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
44 72 0.85
45 13 0.15
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (45 bp):
AGGGAGATAGGATTTCTCAATCTTCAACCTATTCCACTGCTGACC
Found at i:31176337 original size:44 final size:44
Alignment explanation
Indices: 31176280--31176395 Score: 196
Period size: 44 Copynumber: 2.6 Consensus size: 44
31176270 TTTGTTTACT
* *
31176280 TTCAACCTATTCCATTGCTGACCAGGGAGATAGGATTCTCAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
31176324 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
31176368 TTCAATCTATTCCACTGCTGCCCAGGGA
1 TTCAACCTATTCCACTGCTGACCAGGGA
31176396 AGTAGAATTA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
Found at i:31176483 original size:132 final size:131
Alignment explanation
Indices: 31176347--31176999 Score: 925
Period size: 132 Copynumber: 4.9 Consensus size: 131
31176337 ACTGCTGACC
* * * * *
31176347 AGGGAGATAGGAT-TCACAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGTC
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTG-C
* ** * * *
31176411 TTCAATGTATTCCGTTGTAACCATAGGGAGGTAAAATTCGTCATCTTCGATCTACTCCGCTACTG
64 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCGCTACTG
31176476 CTT
129 CTT
* * * *
31176479 AGGGAGATAATATCTGAAATCTTCAACCTACTCCACTATTGTCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACT-GCT
*
31176544 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAA-TCTGCCATCTTCGATCTGCTCCGCTACTA
65 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTC-GCCATCTTCGATCTGCTCCGCTACTG
31176608 CTT
129 CTT
* * * * *
31176611 GGGGAGATAAGATCTGAAATCTTTAATCTATTCCACTGTTGTCCAGGAAAGTAGAATTATTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACT-GCT
* * * * *
31176676 TCAATGTACTCTATTGTAACCACAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
65 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCGCTACTGC
31176741 TT
130 TT
*
31176743 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACT-GCT
* *
31176808 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCGCTACTGC
65 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCGCTACTGC
31176873 TT
130 TT
*
31176875 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAAGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACT-GCT
* *
31176940 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAA-TCTGTCATCTTCGATCTGCTTCGCT
65 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTC-GCCATCTTCGATCTGCTCCGCT
31177000 GTCGGCGCAA
Statistics
Matches: 465, Mismatches: 51, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
131 3 0.01
132 458 0.98
133 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (131 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGCTT
CAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCGCTACTGCT
T
Found at i:31177109 original size:44 final size:44
Alignment explanation
Indices: 31177054--31177197 Score: 119
Period size: 44 Copynumber: 3.3 Consensus size: 44
31177044 CGCTGTAACC
*
31177054 CAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCAGCA
1 CAGGAAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCAGCA
* * * * * * * * *
31177098 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTGGTGTCTTTGATCTGCTTCGCTGTCAGCA
* * * * * **
31177142 CAGGGAGGCAAGGCTGGTGTCTTCGATATGCTTCGCTATCGGTG
1 CAGGAAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCAGCA
31177186 CAGGAAGGCAAG
1 CAGGAAGGCAAG
31177198 ATCTGCTATT
Statistics
Matches: 72, Mismatches: 26, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
43 16 0.22
44 37 0.51
45 19 0.26
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCAGCA
Found at i:31177157 original size:88 final size:88
Alignment explanation
Indices: 31176982--31177209 Score: 348
Period size: 88 Copynumber: 2.6 Consensus size: 88
31176972 AAATCTGTCA
* *
31176982 TCTTCGATCTGCTTCGCTGTCGGCGCAAGAAGGCAAGATCTGCTATTTTTTTTAACCTGTTCCGC
1 TCTTCGATCTGCTTCGCTGTCGGCGCAGGAAGGCAAGATCTGCTA---TTTTTAACCTGCTCCGC
*
31177047 TGTAACCCAGGGAGGCAAGGCTGGTG
63 TGCAACCCAGGGAGGCAAGGCTGGTG
* * *
31177073 TCTTTGATCTGCTTCGCTGTCAGCACAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGC
1 TCTTCGATCTGCTTCGCTGTCGGCGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGC
31177138 AACCCAGGGAGGCAAGGCTGGTG
66 AACCCAGGGAGGCAAGGCTGGTG
* * *
31177161 TCTTCGATATGCTTCGCTATCGGTGCAGGAAGGCAAGATCTGCTATTTT
1 TCTTCGATCTGCTTCGCTGTCGGCGCAGGAAGGCAAGATCTGCTATTTT
31177210 CACTGATCTG
Statistics
Matches: 125, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
88 84 0.67
91 41 0.33
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (88 bp):
TCTTCGATCTGCTTCGCTGTCGGCGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGC
AACCCAGGGAGGCAAGGCTGGTG
Found at i:31185650 original size:22 final size:20
Alignment explanation
Indices: 31185610--31185650 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
31185600 ATTAACTTAC
*
31185610 TTATATTATATGTATTTATT
1 TTATATTATATATATTTATT
31185630 TTATATTATAAATATATTTAT
1 TTATATTAT--ATATATTTAT
31185651 AATAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATATTATATATATTTATT
Found at i:31185675 original size:29 final size:29
Alignment explanation
Indices: 31185641--31185701 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
31185631 TATATTATAA
31185641 ATATATTTATAATA-ACTAAAAATAATACT
1 ATATATTTATAATATACTAAAAATAATA-T
* *
31185670 ATATATTTATTATATATTAAAAATAATAT
1 ATATATTTATAATATACTAAAAATAATAT
31185699 ATA
1 ATA
31185702 GATAAATCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATATTTATAATATACTAAAAATAATAT
Found at i:31187933 original size:43 final size:43
Alignment explanation
Indices: 31187885--31188156 Score: 356
Period size: 43 Copynumber: 6.4 Consensus size: 43
31187875 AGCGTTTACA
* *
31187885 GAAAAAAACGCCGCTAAAGCTCATGTCCTTTAGCGGCGCTTAG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* *
31187928 GAAAAAAACGCCGCTAATGATCATGTTCTTTAGCGGTGCTT-G
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * * *
31187970 GGAAAAAACGCCGCTAAAGGA-CATGATCTTTAGCAGCGCTTTG
1 GAAAAAAACGCCGCTAAA-GATCATGTTCTTTAGCGGCGCTTAG
* * *
31188013 GTAAAAAACGCCACTAATGATCATGTTCTTTAGCGGCGCTT-G
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
*
31188055 G-GAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * * *
31188097 GAAAAAAACGCCACTAAAAATAATGTTCTTTAGCGGCGCATAG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
31188140 G-AAAAAACGCCGCTAAA
1 GAAAAAAACGCCGCTAAA
31188157 AGTAGTGTTC
Statistics
Matches: 201, Mismatches: 23, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
41 36 0.18
42 55 0.27
43 110 0.55
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (43 bp):
GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
Found at i:31187987 original size:85 final size:84
Alignment explanation
Indices: 31187887--31188156 Score: 391
Period size: 85 Copynumber: 3.2 Consensus size: 84
31187877 CGTTTACAGA
* *
31187887 AAAAAACGCCGCTAAAGCTCATGTCCTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAATGATCAT
1 AAAAAACGCCGCTAAAGATCATGT-CTTTAGCGGCGCTTAGGAAAAAAACGCCACTAATGATCAT
*
31187952 GTTCTTTAGCGGTGCTTGGG
65 GTTCTTTAGCGGCGCTTGGG
* * *
31187972 AAAAAACGCCGCTAAAGGA-CATGATCTTTAGCAGCGCTTTGGTAAAAAACGCCACTAATGATCA
1 AAAAAACGCCGCTAAA-GATCATG-TCTTTAGCGGCGCTTAGGAAAAAAACGCCACTAATGATCA
31188036 TGTTCTTTAGCGGCGCTTGGG
64 TGTTCTTTAGCGGCGCTTGGG
** *
31188057 -AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACGCCACTAAAAATAAT
1 AAAAAACGCCGCTAAAGATCATG-TCTTTAGCGGCGCTTAGGAAAAAAACGCCACTAATGATCAT
* *
31188121 GTTCTTTAGCGGCGCATAGG
65 GTTCTTTAGCGGCGCTTGGG
31188141 AAAAAACGCCGCTAAA
1 AAAAAACGCCGCTAAA
31188157 AGTAGTGTTC
Statistics
Matches: 166, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
83 2 0.01
84 72 0.43
85 90 0.54
86 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (84 bp):
AAAAAACGCCGCTAAAGATCATGTCTTTAGCGGCGCTTAGGAAAAAAACGCCACTAATGATCATG
TTCTTTAGCGGCGCTTGGG
Found at i:31188636 original size:21 final size:21
Alignment explanation
Indices: 31188612--31188683 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
31188602 TTCTTTTGAA
*
31188612 CCTCTGCTTCTCTCGCTGCGG
1 CCTCTGCTTCTCTCGCTGCAG
*
31188633 CCTCTGCTTCTCTTGCTGCAG
1 CCTCTGCTTCTCTCGCTGCAG
* *
31188654 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCTCTCGCTGCAG
31188675 CCTCTGCTT
1 CCTCTGCTT
31188684 TAAGTTGTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.01, C:0.44, G:0.19, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCAG
Found at i:31204794 original size:9 final size:9
Alignment explanation
Indices: 31204777--31205027 Score: 170
Period size: 9 Copynumber: 28.8 Consensus size: 9
31204767 TATGTATTAA
*
31204777 GTAAATTAT
1 GTAAGTTAT
31204786 GTAAGTTAT
1 GTAAGTTAT
*
31204795 GTACGTGTA-
1 GTAAGT-TAT
31204804 -TAAGTTAT
1 GTAAGTTAT
31204812 GTAAGTTAT
1 GTAAGTTAT
*
31204821 GTATGTTAT
1 GTAAGTTAT
31204830 GTAAG-T-T
1 GTAAGTTAT
31204837 GTAAGTTAT
1 GTAAGTTAT
*
31204846 G-CA-TTAT
1 GTAAGTTAT
**
31204853 GTAACCTAT
1 GTAAGTTAT
31204862 GTAAGTTAT
1 GTAAGTTAT
** *
31204871 CAAAGTAAT
1 GTAAGTTAT
*
31204880 GTATGTTAT
1 GTAAGTTAT
31204889 GTAAG-T-T
1 GTAAGTTAT
*
31204896 GTAGGTTAT
1 GTAAGTTAT
*
31204905 -TATGTATTAT
1 GTAAG--TTAT
31204915 GTAAGTTAT
1 GTAAGTTAT
*
31204924 GTAAGTTGT
1 GTAAGTTAT
*
31204933 GTAAGATAT
1 GTAAGTTAT
*
31204942 TTAAGTTAT
1 GTAAGTTAT
*
31204951 GTAAGTTTT
1 GTAAGTTAT
31204960 GT-A-TTAT
1 GTAAGTTAT
31204967 GTAAGTTAT
1 GTAAGTTAT
* *
31204976 GTATGCTAT
1 GTAAGTTAT
31204985 GT-A-TTAT
1 GTAAGTTAT
31204992 GTAAGTTGTTAT
1 GTAA---GTTAT
*
31205004 GTTA-TTAT
1 GTAAGTTAT
31205012 GTAAGTTAT
1 GTAAGTTAT
*
31205021 GCAAGTT
1 GTAAGTT
31205028 TAACCACAAG
Statistics
Matches: 186, Mismatches: 36, Indels: 40
0.71 0.14 0.15
Matches are distributed among these distances:
7 28 0.15
8 23 0.12
9 119 0.64
10 6 0.03
11 3 0.02
12 7 0.04
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:31204794 original size:25 final size:26
Alignment explanation
Indices: 31204766--31204870 Score: 78
Period size: 25 Copynumber: 4.2 Consensus size: 26
31204756 TTTACATAAT
31204766 TTATGTA-TTAAGTAAATTATGTAAG
1 TTATGTAGTTAAGTAAATTATGTAAG
*
31204791 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA-GT-TAAGTAAATTATGTAAG
* *
31204817 TTATGTATGTTATGT-AAGT-TGTAAG
1 TTATGTA-GTTAAGTAAATTATGTAAG
* * **
31204842 TTATGCA-TTATGTAACCTATGTAAG
1 TTATGTAGTTAAGTAAATTATGTAAG
31204867 TTAT
1 TTAT
31204871 CAAAGTAATG
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
23 6 0.09
24 2 0.03
25 30 0.46
26 23 0.35
27 3 0.05
28 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (26 bp):
TTATGTAGTTAAGTAAATTATGTAAG
Found at i:31204923 original size:16 final size:16
Alignment explanation
Indices: 31204904--31205021 Score: 86
Period size: 16 Copynumber: 7.3 Consensus size: 16
31204894 TTGTAGGTTA
31204904 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
*
31204920 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
* *
31204938 ATATTTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
*
31204956 TTTTGTATTATGTAAG
1 TTATGTATTATGTAAG
31204972 TTATGTATGCTATGT-A-
1 TTATGTAT--TATGTAAG
*
31204988 TTATGTA--A-GT-TG
1 TTATGTATTATGTAAG
31205000 TTATGTTATTATGTAAG
1 TTATG-TATTATGTAAG
31205017 TTATG
1 TTATG
31205022 CAAGTTTAAC
Statistics
Matches: 82, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
11 2 0.02
12 6 0.07
13 2 0.02
15 1 0.01
16 31 0.38
17 9 0.11
18 31 0.38
ACGTcount: A:0.29, C:0.01, G:0.20, T:0.50
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:31204950 original size:62 final size:58
Alignment explanation
Indices: 31204804--31204957 Score: 173
Period size: 62 Copynumber: 2.6 Consensus size: 58
31204794 TGTACGTGTA
31204804 TAAGTTATGTAAGTTATGTATGTTATGTAAGTTGTAAGTTATGCATTATGTAACCTATG
1 TAAGTTATGTAAG-TATGTATGTTATGTAAGTTGTAAGTTATGCATTATGTAACCTATG
** * * **
31204863 TAAGTTATCAAAGTAATGTATGTTATGTAAGTTGTAGGTTATTATGTATTATGTAAGTTATG
1 TAAGTTATGTAAGT-ATGTATGTTATGTAAGTTGTAAG---TTATGCATTATGTAACCTATG
* * *
31204925 TAAGTTGTGTAAGATATTTAAGTTATGTAAGTT
1 TAAGTTATGTAAG-TATGTATGTTATGTAAGTT
31204958 TTGTATTATG
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
58 1 0.01
59 33 0.42
62 44 0.56
63 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (58 bp):
TAAGTTATGTAAGTATGTATGTTATGTAAGTTGTAAGTTATGCATTATGTAACCTATG
Found at i:31204977 original size:25 final size:25
Alignment explanation
Indices: 31204781--31204998 Score: 149
Period size: 25 Copynumber: 8.5 Consensus size: 25
31204771 TATTAAGTAA
* *
31204781 ATTATGTAAGTTATGTACGTGTAT-A
1 ATTATGTAAGTTATGTAAGT-TATGT
*
31204806 AGTTATGTAAGTTATGTATGTTATGT
1 A-TTATGTAAGTTATGTAAGTTATGT
* *
31204832 AAGT-TGTAAGTTATG-CA-TTATGT
1 -ATTATGTAAGTTATGTAAGTTATGT
* ** *
31204855 AACCTATGTAAGTTATCAAAGTAATGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
* *
31204882 ATGTTATGTAAGTTGTAGGTTA-TTATGT
1 A--TTATGTAAG-T-TATGTAAGTTATGT
*
31204910 ATTATGTAAGTTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTAAGTTATGT
* * *
31204935 AAGATATTTAAGTTATGTAAGTTTTGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
* *
31204962 ATTATGTAAGTTATGTATGCTATGT
1 ATTATGTAAGTTATGTAAGTTATGT
31204987 ATTATGTAAGTT
1 ATTATGTAAGTT
31204999 GTTATGTTAT
Statistics
Matches: 153, Mismatches: 27, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
23 8 0.05
24 6 0.04
25 62 0.41
26 32 0.21
27 35 0.23
28 7 0.05
29 3 0.02
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.46
Consensus pattern (25 bp):
ATTATGTAAGTTATGTAAGTTATGT
Found at i:31205125 original size:16 final size:16
Alignment explanation
Indices: 31205101--31205155 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
31205091 TATAAAAATT
*
31205101 TTATATAAGTTATGTA
1 TTATGTAAGTTATGTA
31205117 TTATGTAAG----GTA
1 TTATGTAAGTTATGTA
**
31205129 ACATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
31205145 TTATGTAAGTT
1 TTATGTAAGTT
31205156 TACATATAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
12 10 0.33
16 20 0.67
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.45
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:31205138 original size:28 final size:28
Alignment explanation
Indices: 31205103--31205172 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
31205093 TAAAAATTTT
31205103 ATATAAGTTATGTATTATGTAAGGTAAC
1 ATATAAGTTATGTATTATGTAAGGTAAC
* * *
31205131 ATGTAAGTTATGTATTATGTAAGTTTAC
1 ATATAAGTTATGTATTATGTAAGGTAAC
31205159 ATATAAGTTTATGT
1 ATATAAG-TTATGT
31205173 GATAGTTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 31 0.84
29 6 0.16
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (28 bp):
ATATAAGTTATGTATTATGTAAGGTAAC
Found at i:31205377 original size:13 final size:13
Alignment explanation
Indices: 31205359--31205400 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
31205349 TAAATTTTAG
*
31205359 TAAGTAATGTATT
1 TAAGTAATATATT
*
31205372 TAAGTAACATATT
1 TAAGTAATATATT
*
31205385 TAAGTAATAAATT
1 TAAGTAATATATT
31205398 TAA
1 TAA
31205401 CCAAATTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:31208995 original size:2 final size:2
Alignment explanation
Indices: 31208988--31209021 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31208978 ATAGTAACTA
31208988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31209022 GGGATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31209953 original size:40 final size:41
Alignment explanation
Indices: 31209909--31210003 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
31209899 GCGCTTAAAC
* *
31209909 AAAAACGCCGCTAAAACACCTAG-ATTAGCGGCGATTTTCA
1 AAAAACGCCACTAAAACACCTAGCATTAGCGGCGATTTACA
* ** * * *
31209949 AAAAACGCCATTAAAAGTCTTAGCCTTAGCGGCGCTTTACA
1 AAAAACGCCACTAAAACACCTAGCATTAGCGGCGATTTACA
31209990 AAAAACGCCACTAA
1 AAAAACGCCACTAA
31210004 TTCCCCCGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 18 0.40
41 27 0.60
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (41 bp):
AAAAACGCCACTAAAACACCTAGCATTAGCGGCGATTTACA
Found at i:31210782 original size:30 final size:31
Alignment explanation
Indices: 31210748--31210807 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
31210738 AAACCTTTTA
*
31210748 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* * *
31210778 TTTTCCGCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
31210808 TCCCACCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.02, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:31210925 original size:17 final size:16
Alignment explanation
Indices: 31210891--31210921 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31210881 CCTATTTACT
*
31210891 TTCCCTAAAACTTTTA
1 TTCCCCAAAACTTTTA
31210907 TTCCCCAAAACTTTT
1 TTCCCCAAAACTTTT
31210922 TATTTTTCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (16 bp):
TTCCCCAAAACTTTTA
Found at i:31214829 original size:2 final size:2
Alignment explanation
Indices: 31214822--31214855 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31214812 ATATTTGTTT
31214822 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31214856 ATACCTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31217870 original size:12 final size:12
Alignment explanation
Indices: 31217853--31217885 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
31217843 AATAGGATCA
31217853 ATATATGTATTT
1 ATATATGTATTT
*
31217865 ATATATATATTT
1 ATATATGTATTT
31217877 ATATATGTA
1 ATATATGTA
31217886 GTTGAGAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (12 bp):
ATATATGTATTT
Found at i:31219268 original size:8 final size:8
Alignment explanation
Indices: 31219255--31219279 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
31219245 CTAAAGTGAT
31219255 TTTTCATA
1 TTTTCATA
31219263 TTTTCATA
1 TTTTCATA
31219271 TTTTCATA
1 TTTTCATA
31219279 T
1 T
31219280 CGCTTTGTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTCATA
Found at i:31219401 original size:2 final size:2
Alignment explanation
Indices: 31219394--31219418 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31219384 TGTAAAATTT
31219394 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
31219419 TAATATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31242126 original size:29 final size:30
Alignment explanation
Indices: 31242073--31242129 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
31242063 TCCGAGCCTT
31242073 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGTAAAAGTTTA
* *
31242103 GGGGCAAAATTGTAATTTTG-AAAAGTT
1 GGGGCAAAAATGTAATTATGTAAAAGTT
31242130 AGAGTCAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGTAAAAGTTTA
Found at i:31242360 original size:13 final size:13
Alignment explanation
Indices: 31242342--31242372 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
31242332 TTCCAGCAAC
31242342 TATGAATTTATTT
1 TATGAATTTATTT
31242355 TATGAATTTATTT
1 TATGAATTTATTT
*
31242368 GATGA
1 TATGA
31242373 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:31242581 original size:50 final size:50
Alignment explanation
Indices: 31242467--31242708 Score: 286
Period size: 50 Copynumber: 4.7 Consensus size: 50
31242457 ATTTGGGTAA
* * *
31242467 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
* *
31242523 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
31242573 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
31242623 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
31242673 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
31242709 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 92 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:31242659 original size:100 final size:103
Alignment explanation
Indices: 31242467--31242716 Score: 353
Period size: 100 Copynumber: 2.4 Consensus size: 103
31242457 ATTTGGGTAA
31242467 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCC
* * *
31242532 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * * *
31242573 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
*
31242635 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
31242673 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
31242717 GTTATTATCA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 50 0.38
101 39 0.30
105 2 0.02
106 40 0.31
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:31252527 original size:50 final size:50
Alignment explanation
Indices: 31252469--31252654 Score: 255
Period size: 50 Copynumber: 3.7 Consensus size: 50
31252459 TAAGATCAAA
** * *
31252469 AGAGGTCCCCCGTAAGACCATGTCTGGGACCTGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
* *
31252519 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
* * * *
31252569 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
**
31252619 AGAAAATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
31252655 TTTGGCATGT
Statistics
Matches: 119, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
50 90 0.76
51 29 0.24
ACGTcount: A:0.26, C:0.25, G:0.31, T:0.18
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
Found at i:31258036 original size:24 final size:22
Alignment explanation
Indices: 31257989--31258038 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
31257979 TCATCCTTAG
*
31257989 AAAATTAAGAAAAGAAAATGAT
1 AAAATTAAGAAAAGAAAATAAT
31258011 AAAATT-AGAAAGATGATAAATAAT
1 AAAATTAAGAAA-A-GA-AAATAAT
31258035 AAAA
1 AAAA
31258039 CCAAACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 7 0.29
23 2 0.08
24 10 0.42
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (22 bp):
AAAATTAAGAAAAGAAAATAAT
Found at i:31259033 original size:26 final size:26
Alignment explanation
Indices: 31259004--31259069 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
31258994 TCGTTATATA
31259004 GCTCTTCATGAGCTTCCCGATTAAAG
1 GCTCTTCATGAGCTTCCCGATTAAAG
* * * *
31259030 GCTCTTTATGAGCTTTCTGATTAATG
1 GCTCTTCATGAGCTTCCCGATTAAAG
*
31259056 GCTCTCCA-GAGCTT
1 GCTCTTCATGAGCTT
31259070 TCCAATATGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 6 0.18
26 28 0.82
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (26 bp):
GCTCTTCATGAGCTTCCCGATTAAAG
Found at i:31261362 original size:16 final size:15
Alignment explanation
Indices: 31261329--31261371 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
31261319 TTTTAATAAG
31261329 ATTTAATATTAAATTA
1 ATTTAATATT-AATTA
31261345 ATTTAATATTAATGTA
1 ATTTAATATTAAT-TA
31261361 A-TTAAT-TTAAT
1 ATTTAATATTAAT
31261372 CATAGTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.19
15 8 0.31
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTAATATTAATTA
Found at i:31268005 original size:17 final size:17
Alignment explanation
Indices: 31267983--31268027 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
31267973 AAATTTTAGA
*
31267983 CCCACACGCCCTTGTGG
1 CCCACACGCCCGTGTGG
31268000 CCCACACGCCCGTGTGG
1 CCCACACGCCCGTGTGG
*
31268017 CCCATACGCCC
1 CCCACACGCCC
31268028 AATCTTGGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.13, C:0.51, G:0.22, T:0.13
Consensus pattern (17 bp):
CCCACACGCCCGTGTGG
Found at i:31269302 original size:21 final size:21
Alignment explanation
Indices: 31269250--31269304 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
31269240 CCTCGAAAGC
**
31269250 TGAACAGAAGGTCATAAGAGT
1 TGAACAGAAACTCATAAGAGT
* * *
31269271 TTAATACAAACTCATAAGAGT
1 TGAACAGAAACTCATAAGAGT
31269292 TGAACAGAAACTC
1 TGAACAGAAACTC
31269305 GAAAGAGCTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (21 bp):
TGAACAGAAACTCATAAGAGT
Found at i:31271278 original size:30 final size:30
Alignment explanation
Indices: 31271236--31271296 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
31271226 GGGGGTGGGA
31271236 TGGGAGGGGAGTAAAAGTTTTGGGGGGAAAG
1 TGGGAGGGGAGTAAAAGTTTT-GGGGGAAAG
31271267 TGGGA-GGGAGTAAAAGTTTTGGGGGAAAG
1 TGGGAGGGGAGTAAAAGTTTTGGGGGAAAG
31271296 T
1 T
31271297 AAAGAGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.33
30 15 0.50
31 5 0.17
ACGTcount: A:0.30, C:0.00, G:0.49, T:0.21
Consensus pattern (30 bp):
TGGGAGGGGAGTAAAAGTTTTGGGGGAAAG
Found at i:31272915 original size:27 final size:27
Alignment explanation
Indices: 31272877--31272936 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
31272867 GCAAAATTTC
*
31272877 AAAACAGTTGGTGGGTACTCCTTACTT
1 AAAACAGTTGGTGGGTACTCCTTACCT
31272904 AAAACAGTTGGTGGGTACTCCTTACCT
1 AAAACAGTTGGTGGGTACTCCTTACCT
31272931 AAAACA
1 AAAACA
31272937 TATTTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (27 bp):
AAAACAGTTGGTGGGTACTCCTTACCT
Found at i:31282271 original size:19 final size:20
Alignment explanation
Indices: 31282232--31282272 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31282222 CTTAAGATAG
*
31282232 TAAAATATATTTGGAATAAT
1 TAAAATATATTTAGAATAAT
*
31282252 TAAAATATTTTTAG-ATAAT
1 TAAAATATATTTAGAATAAT
31282271 TA
1 TA
31282273 TTTAATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
TAAAATATATTTAGAATAAT
Found at i:31289722 original size:2 final size:2
Alignment explanation
Indices: 31289715--31289743 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31289705 CCACCAACTC
31289715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31289744 AAGTAGATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31289882 original size:13 final size:13
Alignment explanation
Indices: 31289864--31289915 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
31289854 GAATGAAAAT
31289864 ATTTATATATGAA
1 ATTTATATATGAA
31289877 A-TT-TATATGAA
1 ATTTATATATGAA
*
31289888 ATTTTTATAT-AA
1 ATTTATATATGAA
*
31289900 AATTATATATCGAA
1 ATTTATATAT-GAA
31289914 AT
1 AT
31289916 ATTTTTGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 9 0.28
12 14 0.44
13 6 0.19
14 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (13 bp):
ATTTATATATGAA
Found at i:31289889 original size:26 final size:27
Alignment explanation
Indices: 31289860--31289920 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 27
31289850 ATATGAATGA
*
31289860 AAATATTTATATATGAAATT-TATAT-G
1 AAATATTT-TATATAAAATTATATATCG
31289886 AAAT-TTTTATATAAAATTATATATCG
1 AAATATTTTATATAAAATTATATATCG
31289912 AAATATTTT
1 AAATATTTT
31289921 TGTTTAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 10 0.32
25 8 0.26
26 9 0.29
27 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (27 bp):
AAATATTTTATATAAAATTATATATCG
Found at i:31290710 original size:21 final size:21
Alignment explanation
Indices: 31290686--31290730 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31290676 CTCGTGTAAC
*
31290686 AATTAACATATACTTCATAAA
1 AATTAACAAATACTTCATAAA
* *
31290707 AATTCAGAAATACTTCATAAA
1 AATTAACAAATACTTCATAAA
31290728 AAT
1 AAT
31290731 ATATATCCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (21 bp):
AATTAACAAATACTTCATAAA
Found at i:31295912 original size:12 final size:12
Alignment explanation
Indices: 31295895--31295924 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31295885 GGACACACGG
31295895 CCGTGTCCTAAC
1 CCGTGTCCTAAC
*
31295907 CCGTGTCCTCAC
1 CCGTGTCCTAAC
31295919 CCGTGT
1 CCGTGT
31295925 AACTCACTGA
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:0.10, C:0.43, G:0.20, T:0.27
Consensus pattern (12 bp):
CCGTGTCCTAAC
Found at i:31301959 original size:20 final size:21
Alignment explanation
Indices: 31301926--31301966 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
31301916 TTCTATTATT
31301926 TTAATAAGATTTAATATTAAA
1 TTAATAAGATTTAATATTAAA
31301947 TTAATAA-ATTTAATATTAAA
1 TTAATAAGATTTAATATTAAA
31301967 GTGATTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAATAAGATTTAATATTAAA
Found at i:31306429 original size:19 final size:19
Alignment explanation
Indices: 31306387--31306430 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
31306377 AATCCATATG
** *
31306387 TATTTTATGCTCTTTTTTA
1 TATTTTATGAACTTTTATA
*
31306406 AATTTTATGAACTTTTATA
1 TATTTTATGAACTTTTATA
31306425 TATTTT
1 TATTTT
31306431 TTAAAATTTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (19 bp):
TATTTTATGAACTTTTATA
Found at i:31312903 original size:29 final size:30
Alignment explanation
Indices: 31312870--31312928 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
31312860 ACTTAACAAG
*
31312870 CAAATACCTCTAAAATAGTAAC-AAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
31312899 CAAATATCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
31312929 TAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:31315862 original size:15 final size:15
Alignment explanation
Indices: 31315844--31315875 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31315834 GAGAGAGGAA
31315844 AATAGAAAAAACAAG
1 AATAGAAAAAACAAG
*
31315859 AATAGAAAAAAGAAG
1 AATAGAAAAAACAAG
31315874 AA
1 AA
31315876 GATGAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.06
Consensus pattern (15 bp):
AATAGAAAAAACAAG
Found at i:31319633 original size:26 final size:29
Alignment explanation
Indices: 31319580--31319633 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 29
31319570 TTCTTTCTCT
*
31319580 TTTCCTTTTCTTTTCATTTTTAGTTTAGG
1 TTTCCTTTTCTTTTCATTTTTAGGTTAGG
31319609 TTTCC-TTTC-TTTC-TTTTTAGGTTAG
1 TTTCCTTTTCTTTTCATTTTTAGGTTAG
31319634 ATCTTAGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 11 0.46
27 4 0.17
28 4 0.17
29 5 0.21
ACGTcount: A:0.09, C:0.15, G:0.11, T:0.65
Consensus pattern (29 bp):
TTTCCTTTTCTTTTCATTTTTAGGTTAGG
Found at i:31320436 original size:25 final size:25
Alignment explanation
Indices: 31320379--31320450 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
31320369 ACACAATTAC
* *
31320379 CCACTTGACAATCCTTTGGGTTTGA
1 CCACTTGGCAATCCTTTGGGTTCGA
31320404 CCACTTGGCAATCCTTTGGGTTCGA
1 CCACTTGGCAATCCTTTGGGTTCGA
* * *
31320429 CCATTTGG-AATACTTTGTGTTC
1 CCACTTGGCAATCCTTTGGGTTC
31320451 CATCAAAACT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 12 0.29
25 30 0.71
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.38
Consensus pattern (25 bp):
CCACTTGGCAATCCTTTGGGTTCGA
Found at i:31324186 original size:15 final size:16
Alignment explanation
Indices: 31324155--31324186 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31324145 AAGAGAGGAA
31324155 AATAGAAAAAAACAAG
1 AATAGAAAAAAACAAG
31324171 AATAGAAAAAAA-AAG
1 AATAGAAAAAAACAAG
31324186 A
1 A
31324187 TGAAGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.06
Consensus pattern (16 bp):
AATAGAAAAAAACAAG
Found at i:31327246 original size:6 final size:6
Alignment explanation
Indices: 31327235--31327266 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
31327225 TTTTGTTTGC
31327235 AAAATT AAAATT AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AA
31327267 CAGTGTACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:31327392 original size:25 final size:25
Alignment explanation
Indices: 31327345--31327392 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
31327335 TAGTCTTTTC
*
31327345 TTTTATTAATAATAATATAAAATAT
1 TTTTATTAATAATAAAATAAAATAT
*
31327370 TTTTATTAA-AATTAAAATTAAAT
1 TTTTATTAATAA-TAAAATAAAAT
31327393 TTTAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTTATTAATAATAAAATAAAATAT
Found at i:31329562 original size:21 final size:22
Alignment explanation
Indices: 31329537--31329577 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31329527 TCAAAATCTT
* *
31329537 GAATTT-AAATATTTTAATTGC
1 GAATTTCAAAAATTTAAATTGC
31329558 GAATTTCAAAAATTTAAATT
1 GAATTTCAAAAATTTAAATT
31329578 CAAATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (22 bp):
GAATTTCAAAAATTTAAATTGC
Found at i:31336801 original size:22 final size:23
Alignment explanation
Indices: 31336748--31336803 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
31336738 CCCGTTTTTA
* * *
31336748 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
31336771 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
31336793 ATTAAAATTAA
1 ATTAAAATTAA
31336804 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:31336816 original size:16 final size:16
Alignment explanation
Indices: 31336779--31336818 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
31336769 TTAATAAAAT
* *
31336779 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
31336795 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
31336811 TAAAATTA
1 TAAAATTA
31336819 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:31336924 original size:9 final size:9
Alignment explanation
Indices: 31336891--31336918 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
31336881 TTTATCAAAT
31336891 TATTAATTG
1 TATTAATTG
31336900 TATTAATTG
1 TATTAATTG
31336909 TATTAATTG
1 TATTAATTG
31336918 T
1 T
31336919 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:31336929 original size:68 final size:68
Alignment explanation
Indices: 31336807--31337016 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
31336797 AAATTAATTG
* *
31336807 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTCTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
31336870 TGA
66 TGA
31336873 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
31336938 TGA
66 TGA
*
31336941 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
31337006 TGA
66 TGA
31337009 TTAGTAAA
1 TTAGTAAA
31337017 ACAAACTTGA
Statistics
Matches: 139, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
66 26 0.19
68 113 0.81
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:31336971 original size:9 final size:9
Alignment explanation
Indices: 31336959--31336986 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
31336949 TTTATCAAAT
31336959 TATTAATTG
1 TATTAATTG
31336968 TATTAATTG
1 TATTAATTG
31336977 TATTAATTG
1 TATTAATTG
31336986 T
1 T
31336987 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:31337130 original size:23 final size:24
Alignment explanation
Indices: 31337083--31337128 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
31337073 AAATAAACTT
31337083 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
31337107 AAAATAAAAAA-TATATATATTT
1 AAAATAAAAAACTAT-TATATTT
31337129 AATATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:31337882 original size:33 final size:31
Alignment explanation
Indices: 31337825--31337898 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 31
31337815 CAAACTAATC
* *
31337825 TTCTCTCAAATTTCCTCAATTTCC-TCTAAAT
1 TTCTCTC-AATTTCCTCAAATTCCTTCCAAAT
31337856 TTCCTCTCAATTTGCTCTCAAATTCCTTCCAAAT
1 TT-CTCTCAATTT-C-CTCAAATTCCTTCCAAAT
31337890 TTCTCTCAA
1 TTCTCTCAA
31337899 ATCCATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
31 7 0.19
32 6 0.16
33 16 0.43
34 8 0.22
ACGTcount: A:0.24, C:0.31, G:0.01, T:0.43
Consensus pattern (31 bp):
TTCTCTCAATTTCCTCAAATTCCTTCCAAAT
Found at i:31337899 original size:11 final size:11
Alignment explanation
Indices: 31337825--31337900 Score: 72
Period size: 11 Copynumber: 7.0 Consensus size: 11
31337815 CAAACTAATC
31337825 TTCTCTCAAAT
1 TTCTCTCAAAT
31337836 TTC-CTC-AAT
1 TTCTCTCAAAT
31337845 TTC-CTCTAAAT
1 TTCTCTC-AAAT
31337856 TTCCTCTC-AAT
1 TT-CTCTCAAAT
31337867 TTGCTCTCAAAT
1 TT-CTCTCAAAT
*
31337879 TCCT-TCCAAAT
1 TTCTCT-CAAAT
31337890 TTCTCTCAAAT
1 TTCTCTCAAAT
31337901 CCATATTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
9 9 0.16
10 4 0.07
11 33 0.60
12 6 0.11
13 3 0.05
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.43
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:31339147 original size:7 final size:7
Alignment explanation
Indices: 31339135--31339160 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31339125 TAGTCGATTG
31339135 GTATTTA
1 GTATTTA
31339142 GTATTTA
1 GTATTTA
31339149 GTATTTA
1 GTATTTA
31339156 GTATT
1 GTATT
31339161 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:31339538 original size:17 final size:17
Alignment explanation
Indices: 31339516--31339551 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
31339506 GTTCCGGAGT
31339516 TAGCGTGCGTTCCAGAA
1 TAGCGTGCGTTCCAGAA
*
31339533 TAGCGTTCGTTCCAGAA
1 TAGCGTGCGTTCCAGAA
31339550 TA
1 TA
31339552 CATGCCATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (17 bp):
TAGCGTGCGTTCCAGAA
Found at i:31340369 original size:25 final size:25
Alignment explanation
Indices: 31340341--31340596 Score: 197
Period size: 25 Copynumber: 10.8 Consensus size: 25
31340331 TATTTTGATA
31340341 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
31340366 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
31340391 TTATTTGATGTAATAAAATAGAATT
1 TTATTTGATGTAATAAAATAGAAGT
* ** *
31340416 TTTTTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
*
31340435 ATTATTTGATGTAATAAAATAGAAAT
1 -TTATTTGATGTAATAAAATAGAAGT
* ** *
31340461 TTTTTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
*
31340480 ATTATTTGATGTAATAAAATATAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
* *
31340506 TTATTTGATGTAATAAAATATAATTT
1 TTATTTGATGTAATAAAATAGAA-GT
* ** *
31340532 TTTTTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
31340551 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
31340577 TTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATA
31340597 TAAATTTTTT
Statistics
Matches: 181, Mismatches: 28, Indels: 44
0.72 0.11 0.17
Matches are distributed among these distances:
19 3 0.02
20 23 0.13
21 13 0.07
22 4 0.02
23 4 0.02
24 12 0.07
25 111 0.61
26 11 0.06
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:31340377 original size:70 final size:70
Alignment explanation
Indices: 31340296--31340637 Score: 444
Period size: 70 Copynumber: 4.9 Consensus size: 70
31340286 TATTTTGATA
*
31340296 TTATTTTATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
31340361 GAAGT
66 GAAGT
* * ** * * *
31340366 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATTTTTTTTGA-GT--T-
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGA-GT--T-ATTTTG-ATATTATTTGATGTAATA
** *
31340427 ATTTTG-A-T
61 AAATAGAAGT
31340435 ATTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAAT
1 -TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAAT
*
31340500 ATAAGT
65 AGAAGT
* *
31340506 TTATTTGATGTAATAAAATATAATTTTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAAT
1 TTATTTGATGTAATAAAATAGAA-ATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAAT
31340571 AGAAGT
65 AGAAGT
*
31340577 TTATTTGATGTAATAAAATATAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAA
31340638 CATGAGATTA
Statistics
Matches: 233, Mismatches: 26, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
65 9 0.04
66 5 0.02
67 1 0.00
68 1 0.00
69 5 0.02
70 122 0.52
71 74 0.32
72 1 0.00
73 1 0.00
74 5 0.02
75 9 0.04
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (70 bp):
TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
GAAGT
Found at i:31340500 original size:115 final size:116
Alignment explanation
Indices: 31340366--31340584 Score: 395
Period size: 116 Copynumber: 1.9 Consensus size: 116
31340356 AAATAGAAGT
31340366 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAA-TTTTTTTTGAGTTATT
1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATTTTTTTTTGAGTTATT
*
31340430 TTGATATTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATA
66 TTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGTTATTTTGATA
* *
31340481 TTATTTGATGTAATAAAATATAAGTTTATTTGATGTAATAAAATATAATTTTTTTTTGAGTTATT
1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATTTTTTTTTGAGTTATT
*
31340546 TTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
66 TTGATATTATTTGATGTAATAAAATAGAAATTTATTTGA
31340585 TGTAATAAAA
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
115 46 0.46
116 53 0.54
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (116 bp):
TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATTTTTTTTTGAGTTATT
TTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGTTATTTTGATA
Found at i:31340513 original size:45 final size:45
Alignment explanation
Indices: 31340279--31340500 Score: 313
Period size: 45 Copynumber: 4.8 Consensus size: 45
31340269 TGTACAAATA
*
31340279 TTTTGA-TTATTTTGATATTATTTTATGTAATAAAATAGAAATTT
1 TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAATTT
*
31340323 TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTT
1 TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAATTT
* ** * *
31340368 ATTTGATGTAATAAAATAGA-AGTTTATTTGATGTAATAAAATAGAATTTT
1 TTTTGA-GT--T-ATTTTGATA--TTATTTGATGTAATAAAATAGAAATTT
31340418 TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAATTT
1 TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAATTT
31340463 TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
31340501 TAAGTTTATT
Statistics
Matches: 158, Mismatches: 12, Indels: 15
0.85 0.06 0.08
Matches are distributed among these distances:
44 6 0.04
45 105 0.66
46 6 0.04
47 2 0.01
48 2 0.01
49 6 0.04
50 31 0.20
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (45 bp):
TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAATTT
Found at i:31344189 original size:125 final size:125
Alignment explanation
Indices: 31343813--31344190 Score: 589
Period size: 125 Copynumber: 3.0 Consensus size: 125
31343803 TCCAAACATG
*
31343813 CTACTGTAGCAAAAGCGCGTCCATGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
31343878 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* * *
31343938 CAACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTCA-AATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * * * * * * **
31344002 CTTGAAGCGTTTTTTATACTATTTGTTCAGAAGCGTCAACTCAAAATAATTT-TTTTAGGAC
65 GTAGAAGCG-ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
*
31344063 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTAACAAATTCTTCTCATAAAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
*
31344128 TAAAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
31344188 CTA
1 CTA
31344191 AAAAGCCTGA
Statistics
Matches: 222, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
124 39 0.18
125 144 0.65
126 39 0.18
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
Found at i:31347210 original size:41 final size:43
Alignment explanation
Indices: 31347039--31347240 Score: 281
Period size: 42 Copynumber: 4.8 Consensus size: 43
31347029 AAACAAAAAC
* *
31347039 GCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTCCTAAGT
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACTAAAT
* **
31347081 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT-CTAAGC
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACTAAAT
31347123 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTAC-AAAT
1 GCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTTACTAAAT
31347166 GCCGCTAAAGAACATGTT-TTGTAGCGGC-TTTTTTTAC-AAAT
1 GCCGCTAAAGAACATGTTCTT-TAGCGGCGTTTTTTTACTAAAT
**
31347207 GCCGCTAAAGAACATGTTCTTTAGTAGCGTTTTT
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
31347241 ATACAAAAAA
Statistics
Matches: 147, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
41 36 0.24
42 70 0.48
43 40 0.27
44 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (43 bp):
GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACTAAAT
Found at i:31347608 original size:21 final size:21
Alignment explanation
Indices: 31347546--31347616 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
31347536 TTTTGGTCTG
* *
31347546 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCCGC
*
31347567 CTCAGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCCGC
* *
31347588 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCCGC
31347609 CTCTGCTT
1 CTCTGCTT
31347617 TAAGTTGTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.03, C:0.48, G:0.18, T:0.31
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCCGC
Found at i:31349351 original size:21 final size:21
Alignment explanation
Indices: 31349326--31349368 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
31349316 TTTGTTCTGG
31349326 AAAGGGCAAAGTTACTGATCT
1 AAAGGGCAAAGTTACTGATCT
31349347 AAAGGGCAAAGTTACTGATCT
1 AAAGGGCAAAGTTACTGATCT
31349368 A
1 A
31349369 TCGTCGATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (21 bp):
AAAGGGCAAAGTTACTGATCT
Found at i:31353389 original size:51 final size:51
Alignment explanation
Indices: 31353172--31353598 Score: 705
Period size: 51 Copynumber: 8.3 Consensus size: 51
31353162 TATGTAAGTT
*
31353172 ATGTAAGTTATGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTAAATGTATA
1 ATGTAAG-T-TGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATA
* *
31353224 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTAAGTGTATA
1 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATA
*
31353274 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATTATGTAAG-TTGTAAGTTAAATGTATA
* * *
31353326 ATGTAAGTTGTAAGTTATTATGTATTATGTTAGTTGTTAGTTAAGTGTATA
1 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATA
*
31353377 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATA
*
31353428 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAGTGTATA
1 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATA
*
31353479 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATTATGTAAG-TTGTAAGTTAAATGTATA
*
31353531 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATA
31353582 ATGTAAGTTGTAAGTTA
1 ATGTAAGTTGTAAGTTA
31353599 AGTGTATAAT
Statistics
Matches: 356, Mismatches: 16, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
50 58 0.16
51 194 0.54
52 104 0.29
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (51 bp):
ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATA
Found at i:31353485 original size:205 final size:203
Alignment explanation
Indices: 31353172--31353605 Score: 760
Period size: 205 Copynumber: 2.1 Consensus size: 203
31353162 TATGTAAGTT
31353172 ATGTAAGTTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTATAATGTAAGTTGTAA
1 ATGTAAG-T-TGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTATAATGTAAGTTGTAA
31353237 GTTAAATGTATTATGTAAGTTGTAAGTTAAGTGTATAATGTAAGTTGTAAGTTATTATGTATTAT
64 GTTAAATGTATTATGTAAGTTGTAAGTTAAGTGTATAATGTAAGTTGTAAGTTATTATGTATTAT
* *
31353302 GTAAGTTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTTAGTTGTTAGT
129 GTAAGTTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGT
*
31353367 TAAGTGTATA
194 TAAATGTATA
* *
31353377 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAG
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTAAATGTATAATGTAAGTTGTAAG
*
31353442 TTATTATGTATTATGTAAGTTGTAAGTTAAGTGTATAATGTAAGTTGTAAGTTATTATGTATTAT
65 TTA-AATGTATTATGTAAGTTGTAAGTTAAGTGTATAATGTAAGTTGTAAGTTATTATGTATTAT
31353507 GTAAGTTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGT
129 GTAAGTTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGT
*
31353572 TAAATGTATT
194 TAAATGTATA
*
31353582 ATGTAAGTTGTAAGTTAAGTGTAT
1 ATGTAAGTTGTAAGTTAAATGTAT
31353606 AATGNNNNNN
Statistics
Matches: 218, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
203 9 0.04
204 54 0.25
205 155 0.71
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.46
Consensus pattern (203 bp):
ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTATAATGTAAGTTGTAAGT
TAAATGTATTATGTAAGTTGTAAGTTAAGTGTATAATGTAAGTTGTAAGTTATTATGTATTATGT
AAGTTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTA
AATGTATA
Found at i:31354802 original size:31 final size:32
Alignment explanation
Indices: 31354736--31354821 Score: 113
Period size: 31 Copynumber: 2.7 Consensus size: 32
31354726 GAGCTATTTC
* *
31354736 CCAT-TTAGCAGCAGAAATCAATAGAAGCGGTA
1 CCATCTTAGCAGCAAAAACCAATAGAA-CGGTA
*
31354768 CCATCTTAGCAGCAAAAACCAGTAGAA-GGTA
1 CCATCTTAGCAGCAAAAACCAATAGAACGGTA
*
31354799 CCATCTTAGCTGCAAAAACCAAT
1 CCATCTTAGCAGCAAAAACCAAT
31354822 TATAATTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 25 0.52
32 4 0.08
33 19 0.40
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (32 bp):
CCATCTTAGCAGCAAAAACCAATAGAACGGTA
Found at i:31356742 original size:22 final size:23
Alignment explanation
Indices: 31356695--31356756 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
31356685 TATCTCTTGT
*
31356695 ATATTTAATTTAA-ATTTTACATTA
1 ATATTT-A-TTAATATTTTACAGTA
31356719 ATATTTATTAATATTTTA-AGTA
1 ATATTTATTAATATTTTACAGTA
31356741 ATATTT-TTAAGTATTT
1 ATATTTATTAA-TATTT
31356757 AATATAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 4 0.11
22 18 0.51
23 7 0.20
24 6 0.17
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (23 bp):
ATATTTATTAATATTTTACAGTA
Found at i:31357616 original size:39 final size:40
Alignment explanation
Indices: 31357553--31357629 Score: 106
Period size: 39 Copynumber: 1.9 Consensus size: 40
31357543 AACCCATAAC
31357553 CCTAAATCCCCCTTAACCCTTAAAGCATAAA-CCCTAAACT
1 CCTAAATCCCCCTTAACCCTTAAAGCA-AAACCCCTAAACT
*
31357593 CCTAAATCTCCC-TAATCCC-TAAAGCAAAACCCCTAAA
1 CCTAAATCCCCCTTAA-CCCTTAAAGCAAAACCCCTAAA
31357630 AAATTTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
38 3 0.09
39 17 0.50
40 14 0.41
ACGTcount: A:0.39, C:0.38, G:0.03, T:0.21
Consensus pattern (40 bp):
CCTAAATCCCCCTTAACCCTTAAAGCAAAACCCCTAAACT
Found at i:31358583 original size:114 final size:112
Alignment explanation
Indices: 31358374--31358591 Score: 253
Period size: 114 Copynumber: 1.9 Consensus size: 112
31358364 NNNNNNNATA
* *
31358374 ATTAGCGGCGCTTCCTATAAAGCGCCACTAAATCCCTGAAAGCTGGCGAGACGATGTCGTTGCGC
1 ATTAGCGGCGCTT-CTATAAAGCGCCACTAAATCCCTGAAAGCTGGCGAAACGACGTCGTTGCGC
* *
31358439 TAGATTTTTTTACGGCGCTTTCCCAGAAACGCCGCTAAAGACCTAAGC
65 TAGATTTTTTTACGGCGCTTTCACACAAACGCCGCTAAAGACCTAAGC
* * * *
31358487 ATTAGCGGCGCTT-TATAGGAAGCGCCGCTAATTCCGTGAATAGCTCGG-GAAACGGCGTCGTTG
1 ATTAGCGGCGCTTCTATA--AAGCGCCACTAAATCCCTGAA-AGCT-GGCGAAACGACGTCGTTG
* * * *
31358550 CGTTTAG-TTTTTTTGCGGCGCTTTTATACAAACGCCGCTAAA
62 CG-CTAGATTTTTTTACGGCGCTTTCACACAAACGCCGCTAAA
31358592 TCCCCAAAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
111 4 0.05
113 31 0.35
114 48 0.55
115 5 0.06
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.27
Consensus pattern (112 bp):
ATTAGCGGCGCTTCTATAAAGCGCCACTAAATCCCTGAAAGCTGGCGAAACGACGTCGTTGCGCT
AGATTTTTTTACGGCGCTTTCACACAAACGCCGCTAAAGACCTAAGC
Found at i:31358633 original size:73 final size:71
Alignment explanation
Indices: 31358535--31358714 Score: 215
Period size: 72 Copynumber: 2.5 Consensus size: 71
31358525 AATAGCTCGG
* * *
31358535 GAAACGGCGTCGTTGCGTTTAGTTTTTTTGCGGCGCTT-TTATACAAACGCCGCTAAATCCCCAA
1 GAAACGGCGTCGTTGCGCTTAGGTTTTTTGCGGCGCTTATTA-A-AAACGCCGCTAAATCACC-A
31358599 AAT-CTC-A
63 AATGCTCTA
* * *
31358606 GAAACGGTGTCGTTGGGCTTAGGGTTTTTAGCGGCGCTTACTTAAAAACGCCGCTAAATCACCAA
1 GAAACGGCGTCGTTGCGCTTA-GGTTTTTTGCGGCGCTTA-TTAAAAACGCCGCTAAATCACCAA
*
31358671 ATGCTCTT
64 ATGCTCTA
*
31358679 GAAACGGCGTCGTTGCGC-TAGGTTTTTTGTGGCGCT
1 GAAACGGCGTCGTTGCGCTTAGGTTTTTTGCGGCGCT
31358715 GTACCTAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
71 36 0.39
72 37 0.40
73 17 0.18
74 3 0.03
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (71 bp):
GAAACGGCGTCGTTGCGCTTAGGTTTTTTGCGGCGCTTATTAAAAACGCCGCTAAATCACCAAAT
GCTCTA
Found at i:31358655 original size:72 final size:72
Alignment explanation
Indices: 31358535--31358729 Score: 222
Period size: 71 Copynumber: 2.7 Consensus size: 72
31358525 AATAGCTCGG
* * *
31358535 GAAACGGCGTCGTTGCGTTTAGTTTTTTTGCGGCGCTT--TTATACAAACGCCGCTAAATCCCCA
1 GAAACGGCGTCGTTGCGCTTAGGTTTTTTGCGGCGCTTACTTA-A-AAACGCCGCTAAATCACC-
31358598 AAAT-CTC-A
63 AAATGCTCTA
* * *
31358606 GAAACGGTGTCGTTGGGCTTAGGGTTTTTAGCGGCGCTTACTTAAAAACGCCGCTAAATCACCAA
1 GAAACGGCGTCGTTGCGCTTA-GGTTTTTTGCGGCGCTTACTTAAAAACGCCGCTAAATCACCAA
*
31358671 ATGCTCTT
65 ATGCTCTA
* *
31358679 GAAACGGCGTCGTTGCGC-TAGGTTTTTTGTGGCGCTGTACCT-AAAACGCCG
1 GAAACGGCGTCGTTGCGCTTAGGTTTTTTGCGGCGCT-TACTTAAAAACGCCG
31358730 GTAATGTTTA
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
71 45 0.42
72 41 0.39
73 17 0.16
74 3 0.03
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.29
Consensus pattern (72 bp):
GAAACGGCGTCGTTGCGCTTAGGTTTTTTGCGGCGCTTACTTAAAAACGCCGCTAAATCACCAAA
TGCTCTA
Done.