Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 170 of 190
Found at i:27925061 original size:122 final size:117
Alignment explanation
Indices: 27924846--27925090 Score: 266
Period size: 122 Copynumber: 2.0 Consensus size: 117
27924836 TTTGTCAATG
* * *
27924846 ATTTTCATAAAATAAAATTTTCAAAAAAAATATTTTTGGAAAAAGGTTGAAAATATCAATTTTTC
1 ATTTTCATAAAATAAAAGTTTCAAAAAAAATATTTTTGGAAAAAGATTGAAAATACCAATTTTTC
* **
27924911 TTAAAAATAAATTTTTTTTTAAAAATA-TTTTT-GAAGAAAAGTTAAAAGTATCA
66 TTAAAAATAAA-TTATTTAAAAAAATATTTTTTAGAA-AAAA-TTAAAAGTATCA
* *
27924964 ATTTTCTTAAAAATAAAAGTTT-AAAAAATATATACATTTTTGAGAAAAA-ATTGAAAGTACCAA
1 ATTTTCAT-AAAATAAAAGTTTCAAAAAA-A-AT--ATTTTTG-GAAAAAGATTGAAAATACCAA
* *
27925027 TTTTTCTTAAAAGTAAA-TATTTAAAAATATATATTTTTTAGAAAAAATTGAAAGTATCA
60 TTTTTCTTAAAAATAAATTATTTAAAAA-A-ATATTTTTTAGAAAAAATTAAAAGTATCA
27925086 ATTTT
1 ATTTT
27925091 TCTTGTATAA
Statistics
Matches: 107, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
118 13 0.12
119 13 0.12
120 9 0.08
121 1 0.01
122 53 0.50
123 15 0.14
124 3 0.03
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (117 bp):
ATTTTCATAAAATAAAAGTTTCAAAAAAAATATTTTTGGAAAAAGATTGAAAATACCAATTTTTC
TTAAAAATAAATTATTTAAAAAAATATTTTTTAGAAAAAATTAAAAGTATCA
Found at i:27925078 original size:60 final size:60
Alignment explanation
Indices: 27924854--27925094 Score: 221
Period size: 60 Copynumber: 4.0 Consensus size: 60
27924844 TGATTTTCAT
* * * *
27924854 AAAATAAA-ATTTTCAAAAA-AAATA-TTTTTGGAAAAAGGTTGAAAATATCAATTTTTCTTA
1 AAAATAAATA-TTT-AAAAATATATATTTTTTAGAAAAA-ATTGAAAGTATCAATTTTTCTTA
* ** *
27924914 AAAATAAATTTTTTTTTAAA-A-ATA-TTTTT-GAAGAAAAGTTAAAAGTATCAA-TTTTCTTA
1 AAAATAAA--TATTTAAAAATATATATTTTTTAGAA-AAAA-TTGAAAGTATCAATTTTTCTTA
* *
27924973 AAAATAAA-AGTTTAAAAAATATATACATTTTTGAGAAAAAATTGAAAGTACCAATTTTTCTTA
1 AAAATAAATA-TTT-AAAAATATAT--ATTTTTTAGAAAAAATTGAAAGTATCAATTTTTCTTA
*
27925036 AAAGTAAATATTTAAAAATATATATTTTTTAGAAAAAATTGAAAGTATCAATTTTTCTT
1 AAAATAAATATTTAAAAATATATATTTTTTAGAAAAAATTGAAAGTATCAATTTTTCTT
27925095 GTATAAAAGC
Statistics
Matches: 151, Mismatches: 15, Indels: 30
0.77 0.08 0.15
Matches are distributed among these distances:
57 3 0.02
58 3 0.02
59 20 0.13
60 66 0.44
61 4 0.03
62 25 0.17
63 26 0.17
64 4 0.03
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (60 bp):
AAAATAAATATTTAAAAATATATATTTTTTAGAAAAAATTGAAAGTATCAATTTTTCTTA
Found at i:27932444 original size:42 final size:42
Alignment explanation
Indices: 27932394--27932484 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
27932384 AGATTACCCC
* * *
27932394 TGAAGCCAGAATGTAAGTCAGTCTAGTAAAAATTGAGGTGAA
1 TGAAGCCAGAATGTAAGCCAGTCTAGTAAAAACTAAGGTGAA
*
27932436 TGGAGCCAGAATGTAAGCCAGTCTAGTAAAAACTAAGGTGAA
1 TGAAGCCAGAATGTAAGCCAGTCTAGTAAAAACTAAGGTGAA
27932478 TGAAGCC
1 TGAAGCC
27932485 TGAAATGCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (42 bp):
TGAAGCCAGAATGTAAGCCAGTCTAGTAAAAACTAAGGTGAA
Found at i:27934774 original size:13 final size:13
Alignment explanation
Indices: 27934756--27934783 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
27934746 GTGATAATAG
27934756 ATTACTTCACGAA
1 ATTACTTCACGAA
27934769 ATTACTTCACGAA
1 ATTACTTCACGAA
27934782 AT
1 AT
27934784 GAGTAGAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.32
Consensus pattern (13 bp):
ATTACTTCACGAA
Found at i:27936287 original size:16 final size:16
Alignment explanation
Indices: 27936266--27936306 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
27936256 CATTTGCATA
27936266 GCATGCATTGAATTAC
1 GCATGCATTGAATTAC
* *
27936282 GCATGCATTGTATTTC
1 GCATGCATTGAATTAC
27936298 GCATAGCAT
1 GCAT-GCAT
27936307 ATACTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (16 bp):
GCATGCATTGAATTAC
Found at i:27936756 original size:88 final size:88
Alignment explanation
Indices: 27936570--27936898 Score: 357
Period size: 88 Copynumber: 3.8 Consensus size: 88
27936560 TCATGTAGCC
*
27936570 TTGTTTATTTTTTAAAAGTTGTTGAGCAT-T-TGATTATAG-A-AGCTTTATTTATTTTTC-AAA
1 TTGTTTATTTTTTCAAAGTTGTTGA--ATCTCTG-TT-TAGAAGAGCTTTATTTATTTTTCAAAA
* * *
27936630 GTTGTTGAA-CCTTTGTTTAGAGCAGCT
62 GTTGTT-AAGCCTCTGATTAGAGGAGCT
* * *
27936657 TTGTTTTTTTTTTCAAAGTTGTTGAATCTCTGTTTAGAAGAGCCTTCTTTATTTTTCAAAAGTTG
1 TTGTTTATTTTTTCAAAGTTGTTGAATCTCTGTTTAGAAGAGCTTTATTTATTTTTCAAAAGTTG
*
27936722 TTAAGCCTCTGATTAAAGGAGCT
66 TTAAGCCTCTGATTAGAGGAGCT
* ** *
27936745 TTGTTTATTTTTTCGAAGTTGTTGAGCCTCTGTTTAGAAGAGCTTTATTTATTTTTCAAAAGTTA
1 TTGTTTATTTTTTCAAAGTTGTTGAATCTCTGTTTAGAAGAGCTTTATTTATTTTTCAAAAGTTG
*
27936810 TTGAGCCTCTGATTAGAGGAGCT
66 TTAAGCCTCTGATTAGAGGAGCT
* * * * * * * * *
27936833 TTATTTATTTTTTCAAAATTGTT-AAGCCTCCGTTTAGATGAGTTTTGTTTATTCTTCAAAAATT
1 TTGTTTATTTTTTCAAAGTTGTTGAA-TCTCTGTTTAGAAGAGCTTTATTTATTTTTCAAAAGTT
27936897 GT
65 GT
27936899 GAATCTCCGC
Statistics
Matches: 207, Mismatches: 28, Indels: 13
0.83 0.11 0.05
Matches are distributed among these distances:
85 5 0.02
86 4 0.02
87 43 0.21
88 155 0.75
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (88 bp):
TTGTTTATTTTTTCAAAGTTGTTGAATCTCTGTTTAGAAGAGCTTTATTTATTTTTCAAAAGTTG
TTAAGCCTCTGATTAGAGGAGCT
Found at i:27936840 original size:132 final size:132
Alignment explanation
Indices: 27936566--27936885 Score: 360
Period size: 132 Copynumber: 2.4 Consensus size: 132
27936556 ATTTTCATGT
* * * * * * * *
27936566 AGCCTTGTTTATTTTTTAAAAGTTGTTGAGCATTTGATTATAGAAGCTTTATTTA-TTTTTCAAA
1 AGCCTTATTTATTTTTCAAAAGTTGTTAAGCCTCTGATTAAAGGAGCTTTGTTTATTTTTTCAAA
* * * * * *
27936630 GTTGTTGAACCTTTGTTTAGAGCAGCTTTGTTTTTTTTTTCAAAGTTGTTGAATCTCTGTTTAGA
66 GTTGTTGAACCTCTGTTTAGAGCAGCTTTGATTTATTTTTCAAAGTTATTGAACCTCTGATTAGA
27936695 AG
131 AG
* *
27936697 AGCCTTCTTTATTTTTCAAAAGTTGTTAAGCCTCTGATTAAAGGAGCTTTGTTTATTTTTTCGAA
1 AGCCTTATTTATTTTTCAAAAGTTGTTAAGCCTCTGATTAAAGGAGCTTTGTTTATTTTTTCAAA
* *
27936762 GTTGTTGAGCCTCTGTTTAGAAG-AGCTTT-ATTTATTTTTCAAAAGTTATTGAGCCTCTGATTA
66 GTTGTTGAACCTCTGTTTAG-AGCAGCTTTGATTTATTTTTC-AAAGTTATTGAACCTCTGATTA
*
27936825 GAGG
129 GAAG
* * * * * *
27936829 AGCTTTATTTATTTTTTCAAAA-TTGTTAAGCCTCCGTTTAGATGAGTTTTGTTTATT
1 AGCCTTATTTA-TTTTTCAAAAGTTGTTAAGCCTCTGATTAAAGGAGCTTTGTTTATT
27936886 CTTCAAAAAT
Statistics
Matches: 160, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
131 56 0.35
132 92 0.57
133 12 0.08
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (132 bp):
AGCCTTATTTATTTTTCAAAAGTTGTTAAGCCTCTGATTAAAGGAGCTTTGTTTATTTTTTCAAA
GTTGTTGAACCTCTGTTTAGAGCAGCTTTGATTTATTTTTCAAAGTTATTGAACCTCTGATTAGA
AG
Found at i:27936870 original size:44 final size:43
Alignment explanation
Indices: 27936573--27936898 Score: 269
Period size: 44 Copynumber: 7.4 Consensus size: 43
27936563 TGTAGCCTTG
* * * * * * *
27936573 TTTATTTTTTAAAAGTTGTTGAGCATTTGATTATAGAAGCTTTA
1 TTTATTTTTCAAAA-TTGTTAAGCCTCTGTTTAGAGGAGCTTTA
* * * *
27936617 TTTATTTTTCAAAGTTGTTGAA-CCTTTGTTTAGAGCAGCTTTGT
1 TTTATTTTTCAAAATTGTT-AAGCCTCTGTTTAGAGGAGCTTT-A
* * * * * *
27936661 TTTTTTTTTCAAAGTTGTTGAA-TCTCTGTTTAGAAGAGCCTTC
1 TTTATTTTTCAAAATTGTT-AAGCCTCTGTTTAGAGGAGCTTTA
* * *
27936704 TTTATTTTTCAAAAGTTGTTAAGCCTCTGATTAAAGGAGCTTTG
1 TTTATTTTTCAAAA-TTGTTAAGCCTCTGTTTAGAGGAGCTTTA
* * * *
27936748 TTTATTTTTTCGAAGTTGTTGAGCCTCTGTTTAGAAGAGCTTTA
1 TTTA-TTTTTCAAAATTGTTAAGCCTCTGTTTAGAGGAGCTTTA
* * *
27936792 TTTATTTTTCAAAAGTTATTGAGCCTCTGATTAGAGGAGCTTTA
1 TTTATTTTTCAAAA-TTGTTAAGCCTCTGTTTAGAGGAGCTTTA
* * * *
27936836 TTTATTTTTTCAAAATTGTTAAGCCTCCGTTTAGATGAGTTTTG
1 TTTA-TTTTTCAAAATTGTTAAGCCTCTGTTTAGAGGAGCTTTA
*
27936880 TTTATTCTTCAAAAATTGT
1 TTTATTTTTC-AAAATTGT
27936899 GAATCTCCGC
Statistics
Matches: 231, Mismatches: 43, Indels: 16
0.80 0.15 0.06
Matches are distributed among these distances:
43 48 0.21
44 165 0.71
45 18 0.08
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.48
Consensus pattern (43 bp):
TTTATTTTTCAAAATTGTTAAGCCTCTGTTTAGAGGAGCTTTA
Found at i:27937134 original size:17 final size:16
Alignment explanation
Indices: 27937112--27937150 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
27937102 TTGGGCTTAA
27937112 TTATTTATTCATTTAT
1 TTATTTATTCATTTAT
*
27937128 GTTATTTATTGATTTAT
1 -TTATTTATTCATTTAT
27937145 TTATTT
1 TTATTT
27937151 GTTTTTCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (16 bp):
TTATTTATTCATTTAT
Found at i:27937136 original size:4 final size:4
Alignment explanation
Indices: 27937112--27937150 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
27937102 TTGGGCTTAA
* *
27937112 TTAT TTAT TCAT TTAT GTTAT TTAT TGAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TT
27937151 GTTTTTCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:27938158 original size:16 final size:16
Alignment explanation
Indices: 27938137--27938167 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27938127 TGAAAGTATC
27938137 AATTTTCTTTAAAAAT
1 AATTTTCTTTAAAAAT
*
27938153 AATTTTTTTTAAAAA
1 AATTTTCTTTAAAAA
27938168 AAAATATTTT
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:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTTCTTTAAAAAT
Found at i:27938224 original size:63 final size:62
Alignment explanation
Indices: 27938087--27938420 Score: 389
Period size: 62 Copynumber: 5.4 Consensus size: 62
27938077 TGATTTTCCT
*
27938087 AAAATAAAA-TTTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTTA
1 AAAATAAAATTTTTTAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTA
** *
27938148 AAAATAATTTTTTTTAAAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTA
1 AAAATAAAATTTTTTAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTA
* *
27938210 AAAATAAAATTTTTT--AAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTG
1 AAAATAAAATTTTTTAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTA
* * * * * *
27938270 AAAATAAAA--GTTTAAAAAATATATACATTTTTGAGGAAAAGTTGGAATTACCATTTTTTTCTT
1 AAAATAAAATTTTTTAAAAAA-A-A-ATATTTTTGAGGAAAAGTTGAAAGTATCA-ATTTTTCTT
27938333 A
62 A
** *
27938334 AAAATAAAGATTTTTT-TTAAAAAATATTTTTTAGGAAAAGTT-AATAGTATCAATTTTTCTTA
1 AAAATAAA-ATTTTTTAAAAAAAAATATTTTTGAGGAAAAGTTGAA-AGTATCAATTTTTCTTA
*
27938396 AAAATAAAA-TTTCTAAAATAAAAAT
1 AAAATAAAATTTTTTAAAA-AAAAAT
27938421 TTTCAAAAAT
Statistics
Matches: 230, Mismatches: 29, Indels: 27
0.80 0.10 0.09
Matches are distributed among these distances:
58 3 0.01
60 59 0.26
61 10 0.04
62 82 0.36
63 51 0.22
64 17 0.07
65 2 0.01
66 3 0.01
67 3 0.01
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.40
Consensus pattern (62 bp):
AAAATAAAATTTTTTAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTA
Found at i:27938445 original size:72 final size:72
Alignment explanation
Indices: 27938348--27938497 Score: 196
Period size: 72 Copynumber: 2.1 Consensus size: 72
27938338 TAAAGATTTT
* * *
27938348 TTTTAAAAAATATTTTTTAGGAAAAG-TT-AATAGTATCAATTTTTCTTAAAAATAAAATTTCTA
1 TTTTAAAAAATAGTTTTAAGGAAAAGTTTGAA-AGTATCAATTTTCCTTAAAAATAAAATTTCTA
27938411 AAATAAAAA
65 AAA-AAAAA
* * * * *
27938420 TTTTCAAAAATAGTTTTAAGGAAAAGTTTGAAAGTATCAATTTTCCTTGAAATTAAAATTTTTTA
1 TTTTAAAAAATAGTTTTAAGGAAAAGTTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCTAA
27938485 AAAAAAA
66 AAAAAAA
27938492 TTTTAA
1 TTTTAA
27938498 GGAAAAGTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
72 33 0.49
73 32 0.48
74 2 0.03
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (72 bp):
TTTTAAAAAATAGTTTTAAGGAAAAGTTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCTAA
AAAAAAA
Found at i:27938479 original size:58 final size:59
Alignment explanation
Indices: 27938411--27938522 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
27938401 AAAATTTCTA
* * *
27938411 AAATAAAAA-TTTTCAAAAATAGTTTTAAGGAAAAGTTTGAAAGTATC-AATTTTCCTTG
1 AAATAAAAATTTTTCAAAAAAAATTTTAAGGAAAAG-TTGAAAATATCTAATTTTCCTTG
* *
27938469 AAATTAAAATTTTTTAAAAAAAATTTTAAGGAAAAGTTGAAAATATCTAATTTT
1 AAATAAAAATTTTTCAAAAAAAATTTTAAGGAAAAGTTGAAAATATCTAATTTT
27938523 TTAAAAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 18 0.38
59 29 0.62
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (59 bp):
AAATAAAAATTTTTCAAAAAAAATTTTAAGGAAAAGTTGAAAATATCTAATTTTCCTTG
Found at i:27939134 original size:20 final size:21
Alignment explanation
Indices: 27939106--27939144 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
27939096 CAAAATTTTT
*
27939106 TATTCTTTT-TAATATAAAAG
1 TATTATTTTATAATATAAAAG
*
27939126 TATTATTTTATATTATAAA
1 TATTATTTTATAATATAAA
27939145 TATAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTATTTTATAATATAAAAG
Found at i:27939251 original size:29 final size:29
Alignment explanation
Indices: 27939194--27939278 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 29
27939184 TAGTTATTTA
* *
27939194 TTATTTTAGTCATAT-T-TTTGTATATAT
1 TTATATTAGTCATATATATTCGTATATAT
* * * * *
27939221 TTATGTTAGTCGTGTATGTTCGTGTATAT
1 TTATATTAGTCATATATATTCGTATATAT
*
27939250 TTGTATTAGTCATATATATTCGTATATAT
1 TTATATTAGTCATATATATTCGTATATAT
27939279 CCCATATTTA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
27 12 0.27
28 1 0.02
29 32 0.71
ACGTcount: A:0.25, C:0.06, G:0.14, T:0.55
Consensus pattern (29 bp):
TTATATTAGTCATATATATTCGTATATAT
Found at i:27939757 original size:31 final size:31
Alignment explanation
Indices: 27939688--27939757 Score: 72
Period size: 31 Copynumber: 2.2 Consensus size: 31
27939678 AAACAAAAAA
*
27939688 AAATATTTTATATTTTCGTATAGACATAAATT
1 AAATA-TTTATATTTTCGTATAAACATAAATT
*
27939720 ATAATATTTA-ATTTTCGTGTAAAACAT-AATAT
1 A-AATATTTATATTTTCGTAT-AAACATAAAT-T
27939752 AAATAT
1 AAATAT
27939758 ACAAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
31 17 0.52
32 12 0.36
33 4 0.12
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
AAATATTTATATTTTCGTATAAACATAAATT
Found at i:27943731 original size:28 final size:29
Alignment explanation
Indices: 27943699--27943778 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 29
27943689 ATTATTACAC
*
27943699 TATTTAACAATATACATATCATATTAA-A
1 TATTTAACAATATAAATATCATATTAATA
*
27943727 TATTTTAA-ATTATAAATATCATATTAATA
1 TA-TTTAACAATATAAATATCATATTAATA
*
27943756 TATTT-ACATATATATATAT-ATAT
1 TATTTAACA-ATATAAATATCATAT
27943779 ATATAATACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 1 0.02
28 27 0.61
29 16 0.36
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.46
Consensus pattern (29 bp):
TATTTAACAATATAAATATCATATTAATA
Found at i:27944344 original size:3 final size:3
Alignment explanation
Indices: 27944336--27944373 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
27944326 ATTTGTCTCA
*
27944336 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27944374 CAACGTCACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27945825 original size:3 final size:3
Alignment explanation
Indices: 27945817--27945854 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
27945807 ATTAGATGTT
27945817 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 TA
27945855 TAGTTAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27952763 original size:26 final size:27
Alignment explanation
Indices: 27952728--27952793 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
27952718 AAGGAGTAAG
27952728 AGACTAAGAGGGAA-TAGTTGAGCAAA
1 AGACTAAGAGGGAAGTAGTTGAGCAAA
27952754 AGACTAAGAGGGAAGTAGTTGAGCAAA
1 AGACTAAGAGGGAAGTAGTTGAGCAAA
27952781 AGACTAAGAGGGA
1 AGACTAAGAGGGA
27952794 GGCAAAGATG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
26 14 0.36
27 25 0.64
ACGTcount: A:0.45, C:0.08, G:0.33, T:0.14
Consensus pattern (27 bp):
AGACTAAGAGGGAAGTAGTTGAGCAAA
Found at i:27952806 original size:27 final size:27
Alignment explanation
Indices: 27952728--27952810 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
27952718 AAGGAGTAAG
* **
27952728 AGACTAAGAGGGAA-TAGTTGAGCAAA
1 AGACTAAGAGGGAAGCAGAAGAGCAAA
* **
27952754 AGACTAAGAGGGAAGTAGTTGAGCAAA
1 AGACTAAGAGGGAAGCAGAAGAGCAAA
*
27952781 AGACTAAGAGGGAGGCA-AAGATGCAAA
1 AGACTAAGAGGGAAGCAGAAGA-GCAAA
27952808 AGA
1 AGA
27952811 TTGAAGGGGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 16 0.31
27 35 0.69
ACGTcount: A:0.47, C:0.08, G:0.33, T:0.12
Consensus pattern (27 bp):
AGACTAAGAGGGAAGCAGAAGAGCAAA
Found at i:27953133 original size:20 final size:19
Alignment explanation
Indices: 27953096--27953135 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
27953086 ATTAAAAACT
* *
27953096 AAAAAAAAAGAAATATCAA
1 AAAAAAAAAAAAAAATCAA
27953115 AAAAAAAAAAAACAAATCAA
1 AAAAAAAAAAAA-AAATCAA
27953135 A
1 A
27953136 TCAAGACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.82, C:0.07, G:0.03, T:0.07
Consensus pattern (19 bp):
AAAAAAAAAAAAAAATCAA
Found at i:27956118 original size:9 final size:9
Alignment explanation
Indices: 27956099--27956136 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
27956089 TTTGAATAAT
27956099 TTTTTACTTA
1 TTTTTA-TTA
27956109 TTTTTATTA
1 TTTTTATTA
27956118 --TTTATTA
1 TTTTTATTA
27956125 TTTTTATTA
1 TTTTTATTA
27956134 TTT
1 TTT
27956137 GAATATTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.27
9 13 0.50
10 6 0.23
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTATTA
Found at i:27956127 original size:16 final size:17
Alignment explanation
Indices: 27956101--27956136 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
27956091 TGAATAATTT
27956101 TTTACTTATTTTTATTA
1 TTTACTTATTTTTATTA
27956118 TTTA-TTATTTTTATTA
1 TTTACTTATTTTTATTA
27956134 TTT
1 TTT
27956137 GAATATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTACTTATTTTTATTA
Found at i:27956972 original size:129 final size:124
Alignment explanation
Indices: 27956683--27957038 Score: 451
Period size: 129 Copynumber: 2.9 Consensus size: 124
27956673 ATTATTATTG
* * * *
27956683 TTATTTTGTGTTTGAAAAACTTCTAAAATATTTCTAACACTTTTAGAATATTTGAGAAAATT-AT
1 TTATTTTATGTTTGAAAAAATTCTAAAATATTTCTAACACTTTTAGAATATTTTAAAAAATTCAT
* * *
27956747 TTTATGTAA-ATTTTCAATAAAATCACCACTTGTGATTTTA--TTTTTTATTAATAAAGT
66 TGTAT-AAATATTTTTAATAAAATCACCACTTGTGATTTTATTTTTTTTATTAATAAAGT
* *
27956804 TT-TTTTATGTTT---AAAATT-TAAAATTTTTCTAACATTTTTAGAATATTTTAAAAAATCTCA
1 TTATTTTATGTTTGAAAAAATTCTAAAATATTTCTAACACTTTTAGAATATTTTAAAAAAT-TCA
* * *
27956864 TTGTATAAATATTTTTAATAAAATCACCACTTGTAATTTTAATTTTTTTTGTTAATAACATTT
65 TTGTATAAATATTTTTAATAAAATCACCACTTGTGATTTT-ATTTTTTTTATTAATAA-A-GT
27956927 TTATTTTATGTTTGAAAAAAATTCTAAAATATTTCTAACACTTTTAGAATATTTTAAAAAATTTC
1 TTATTTTATGTTTG-AAAAAATTCTAAAATATTTCTAACACTTTTAGAATATTTTAAAAAA-TTC
* **
27956992 TTTGGGTAAATATTTTTAATAAAATCACCACTTGTGATTTTATTTTT
64 ATTGTATAAATATTTTTAATAAAATCACCACTTGTGATTTTATTTTT
27957039 ATTTTATCAT
Statistics
Matches: 202, Mismatches: 18, Indels: 23
0.83 0.07 0.09
Matches are distributed among these distances:
116 34 0.17
117 8 0.04
118 34 0.17
119 1 0.00
120 9 0.04
121 15 0.07
122 1 0.00
123 3 0.01
124 10 0.05
128 12 0.06
129 74 0.37
130 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (124 bp):
TTATTTTATGTTTGAAAAAATTCTAAAATATTTCTAACACTTTTAGAATATTTTAAAAAATTCAT
TGTATAAATATTTTTAATAAAATCACCACTTGTGATTTTATTTTTTTTATTAATAAAGT
Found at i:27958279 original size:3 final size:3
Alignment explanation
Indices: 27958268--27958306 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
27958258 AAAAAATATA
27958268 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27958307 CTAAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27958752 original size:49 final size:49
Alignment explanation
Indices: 27958692--27958787 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 49
27958682 ATAATGAATA
** ** *
27958692 CTCCACTAAGTAAAGGTTCAATGACTTTAAACATTTTATCTTGAAAATG
1 CTCCACTAAGTAAAGACTCAACAACTTTAAAAATTTTATCTTGAAAATG
* * *
27958741 CTCCTCTAAGTAGAGACTCGACAACTTTAAAAATTTTATCTTGAAAA
1 CTCCACTAAGTAAAGACTCAACAACTTTAAAAATTTTATCTTGAAAA
27958788 AAGCTCATCA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (49 bp):
CTCCACTAAGTAAAGACTCAACAACTTTAAAAATTTTATCTTGAAAATG
Found at i:27958817 original size:49 final size:49
Alignment explanation
Indices: 27958709--27958823 Score: 124
Period size: 49 Copynumber: 2.3 Consensus size: 49
27958699 AAGTAAAGGT
* * * *
27958709 TCAATGACTTTAAACATTTTATCTTGAAAATGCTCCTCTAAGTAGAGAC
1 TCAATGACTTTAAAAATTTTATCTTGAAAAAGCTCATCAAAGTAGAGAC
* ** * *
27958758 TCGACAACTTTAAAAATTTTATCTTGAAAAAAGCTCATCAAAG-CGAGGC
1 TCAATGACTTTAAAAATTTTATCTTG-AAAAAGCTCATCAAAGTAGAGAC
*
27958807 TTAATGACTTTAAAAAT
1 TCAATGACTTTAAAAAT
27958824 CTTTTCTCGA
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
49 39 0.75
50 13 0.25
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (49 bp):
TCAATGACTTTAAAAATTTTATCTTGAAAAAGCTCATCAAAGTAGAGAC
Found at i:27965967 original size:20 final size:21
Alignment explanation
Indices: 27965925--27965964 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
27965915 TCCAAAATTA
27965925 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
27965946 ATAAAATATTATTTTTTAA
1 ATAAAATATTATTTTTTAA
27965965 TATCAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:27972577 original size:26 final size:27
Alignment explanation
Indices: 27972562--27972613 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
27972552 TTTTGATTAC
27972562 TTAACTTTCACAAATC-TGTCATCAAA
1 TTAACTTTCACAAATCTTGTCATCAAA
27972588 TTAACTTTCACAAATC-TGTCATCAAA
1 TTAACTTTCACAAATCTTGTCATCAAA
27972614 CTAATCTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (27 bp):
TTAACTTTCACAAATCTTGTCATCAAA
Found at i:27973503 original size:20 final size:21
Alignment explanation
Indices: 27973478--27973520 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
27973468 AGGACTGTAA
27973478 TTTTTTTTT-G-TTTGGGTTT
1 TTTTTTTTTGGTTTTGGGTTT
27973497 TTTTTTTTTGGTTTTGGGTTT
1 TTTTTTTTTGGTTTTGGGTTT
27973518 TTT
1 TTT
27973521 GACAGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.41
20 1 0.05
21 12 0.55
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (21 bp):
TTTTTTTTTGGTTTTGGGTTT
Found at i:27973821 original size:3 final size:3
Alignment explanation
Indices: 27973801--27973860 Score: 95
Period size: 3 Copynumber: 19.7 Consensus size: 3
27973791 TACAAAAAAA
27973801 AAT AA- AAT AAAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27973847 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
27973861 ATGAATGTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 46 0.85
4 6 0.11
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:27977471 original size:9 final size:10
Alignment explanation
Indices: 27977452--27977488 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
27977442 AATTAATTAC
27977452 AATCAAAATCA
1 AATC-AAATCA
27977463 AAT-AAATCA
1 AATCAAATCA
27977472 AATCAAATC-
1 AATCAAATCA
27977481 AATCAAAT
1 AATCAAAT
27977489 TCACTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 17 0.68
10 5 0.20
11 3 0.12
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (10 bp):
AATCAAATCA
Found at i:27977476 original size:14 final size:14
Alignment explanation
Indices: 27977452--27977488 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
27977442 AATTAATTAC
27977452 AATCAAAATCAAATA
1 AATC-AAATCAAATA
*
27977467 AATCAAATCAAATC
1 AATCAAATCAAATA
27977481 AATCAAAT
1 AATCAAAT
27977489 TCACTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (14 bp):
AATCAAATCAAATA
Found at i:27977484 original size:4 final size:5
Alignment explanation
Indices: 27977452--27977488 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
27977442 AATTAATTAC
27977452 AATCAA AATCA AAT-A AATCA AATCA AATC- AATCA AAT
1 AATC-A AATCA AATCA AATCA AATCA AATCA AATCA AAT
27977489 TCACTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
4 8 0.28
5 17 0.59
6 4 0.14
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (5 bp):
AATCA
Found at i:27985771 original size:13 final size:13
Alignment explanation
Indices: 27985753--27985778 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27985743 AAGTTTCCCT
27985753 CATATTTTGAGGC
1 CATATTTTGAGGC
27985766 CATATTTTGAGGC
1 CATATTTTGAGGC
27985779 TAAAGACCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
CATATTTTGAGGC
Found at i:27993369 original size:2 final size:2
Alignment explanation
Indices: 27993362--27993386 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27993352 ACGTGAGATT
27993362 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
27993387 TAGTTTTTTT
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:27993591 original size:26 final size:27
Alignment explanation
Indices: 27993562--27993612 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
27993552 TGTAAGATTA
*
27993562 TATTAAATAAAA-ATAAAT-TATATTTT
1 TATTAAA-AAAATAAAAATATATATTTT
27993588 TATTAAAAAAATAAAAATATATATT
1 TATTAAAAAAATAAAAATATATATT
27993613 ATTGAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TATTAAAAAAATAAAAATATATATTTT
Found at i:27993614 original size:24 final size:24
Alignment explanation
Indices: 27993570--27993615 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
27993560 TATATTAAAT
* *
27993570 AAAAATAAATTATATTTTTATTAA
1 AAAAATAAAATATATTATTATTAA
27993594 AAAAATAAAA-ATATATATTATT
1 AAAAATAAAATATAT-TATTATT
27993616 GAATGATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAAATAAAATATATTATTATTAA
Found at i:27994439 original size:21 final size:22
Alignment explanation
Indices: 27994410--27994454 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
27994400 ATTTGTAATT
*
27994410 AAAAGAAATTATCAT-ATTTAA
1 AAAAAAAATTATCATCATTTAA
* *
27994431 AAAAAAAATTCTTATCATTTAA
1 AAAAAAAATTATCATCATTTAA
27994453 AA
1 AA
27994455 GAGTTGTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAAAAATTATCATCATTTAA
Found at i:27997572 original size:21 final size:21
Alignment explanation
Indices: 27997548--27997618 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
27997538 TCAAATGAAA
27997548 TTATATTTTTTATATTTTTAT
1 TTATATTTTTTATATTTTTAT
*
27997569 TTAT-TTTTATTTTATTTTTAT
1 TTATATTTT-TTATATTTTTAT
* * * *
27997590 TTTTATTTCTTAAAATTTTAT
1 TTATATTTTTTATATTTTTAT
27997611 TT-TATTTT
1 TTATATTTT
27997619 CAATTACCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
20 9 0.22
21 29 0.71
22 3 0.07
ACGTcount: A:0.23, C:0.01, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATATTTTTTATATTTTTAT
Found at i:27997573 original size:10 final size:10
Alignment explanation
Indices: 27997551--27997591 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
27997541 AATGAAATTA
*
27997551 TATTTTT-TA
1 TATTTTTATT
27997560 TATTTTTATT
1 TATTTTTATT
27997570 TATTTTTATTT
1 TATTTTTA-TT
27997581 TATTTTTATT
1 TATTTTTATT
27997591 T
1 T
27997592 TTATTTCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 7 0.24
10 12 0.41
11 10 0.34
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TATTTTTATT
Found at i:27997575 original size:17 final size:17
Alignment explanation
Indices: 27997548--27997597 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
27997538 TCAAATGAAA
*
27997548 TTATATTT-TTTATATT
1 TTATATTTATTTTTATT
27997564 TT-TATTTATTTTTATT
1 TTATATTTATTTTTATT
*
27997580 TTATTTTTATTTTTATT
1 TTATATTTATTTTTATT
27997597 T
1 T
27997598 CTTAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 5 0.17
16 11 0.37
17 14 0.47
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (17 bp):
TTATATTTATTTTTATT
Found at i:27997577 original size:6 final size:6
Alignment explanation
Indices: 27997554--27997597 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
27997544 GAAATTATAT
*
27997554 TTTTTA TATTTT- TATTTA TTTTTA -TTTTA TTTTTA TTTTTA TTT
1 TTTTTA T-TTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
27997598 CTTAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 8 0.24
6 21 0.64
7 4 0.12
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:27997582 original size:11 final size:11
Alignment explanation
Indices: 27997560--27997597 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
27997550 ATATTTTTTA
27997560 TATTTTTA-TT
1 TATTTTTATTT
27997570 TATTTTTATTT
1 TATTTTTATTT
27997581 TATTTTTATTTT
1 TATTTTTA-TTT
27997593 TATTT
1 TATTT
27997598 CTTAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 8 0.31
11 10 0.38
12 8 0.31
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:28005240 original size:13 final size:14
Alignment explanation
Indices: 28005204--28005237 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
28005194 TGTTTCGTAG
*
28005204 AAAATGATTTTTAA
1 AAAATAATTTTTAA
28005218 AAAATAATTTTTAA
1 AAAATAATTTTTAA
28005232 AAAATA
1 AAAATA
28005238 TTTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
AAAATAATTTTTAA
Found at i:28005385 original size:16 final size:17
Alignment explanation
Indices: 28005343--28005442 Score: 80
Period size: 16 Copynumber: 5.8 Consensus size: 17
28005333 TTTTTTTAAA
28005343 TAATATT-AAAATTATT
1 TAATATTAAAAATTATT
*
28005359 TATTATT-AAAATTA-T
1 TAATATTAAAAATTATT
* *
28005374 TAATATTAAAAAATAAT
1 TAATATTAAAAATTATT
* *
28005391 TATATTTTAATAATAATATT
1 TA-ATATTAA-AA-ATTATT
28005411 TAATATTAAAATATTATGT
1 TAATATTAAAA-ATTAT-T
*
28005430 TAATATAAAAAAT
1 TAATATTAAAAAT
28005443 ACTTGAAATA
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
15 7 0.10
16 19 0.27
17 3 0.04
18 15 0.21
19 19 0.27
20 7 0.10
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (17 bp):
TAATATTAAAAATTATT
Found at i:28005393 original size:20 final size:19
Alignment explanation
Indices: 28005371--28005443 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 19
28005361 TTATTAAAAT
28005371 TATTAATATTAAAAAAT-A
1 TATTAATATTAAAAAATAA
* *
28005389 -ATT-ATATTTTAATAATAA
1 TATTAATA-TTAAAAAATAA
* *
28005407 TATTTAATATTAAAATATTA
1 TA-TTAATATTAAAAAATAA
*
28005427 TGTTAATA-TAAAAAATA
1 TATTAATATTAAAAAATA
28005444 CTTGAAATAA
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
16 3 0.07
17 10 0.24
18 8 0.20
19 7 0.17
20 10 0.24
21 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (19 bp):
TATTAATATTAAAAAATAA
Found at i:28005432 original size:19 final size:18
Alignment explanation
Indices: 28005343--28005443 Score: 83
Period size: 18 Copynumber: 5.9 Consensus size: 18
28005333 TTTTTTTAAA
28005343 TAATATTAAAAT--TATT
1 TAATATTAAAATAATATT
*
28005359 TATTATTAAAAT--TA-T
1 TAATATTAAAATAATATT
*
28005374 TAATATTAAAA-AATAAT
1 TAATATTAAAATAATATT
*
28005391 TATATTTTAATAATAATATT
1 TA-ATATTAA-AATAATATT
*
28005411 TAATATTAAAATATTATGT
1 TAATATTAAAATAATAT-T
28005430 TAATA-TAAAA-AATA
1 TAATATTAAAATAATA
28005444 CTTGAAATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
15 11 0.15
16 15 0.21
17 6 0.08
18 18 0.25
19 14 0.20
20 7 0.10
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (18 bp):
TAATATTAAAATAATATT
Found at i:28005511 original size:13 final size:13
Alignment explanation
Indices: 28005472--28005669 Score: 116
Period size: 15 Copynumber: 14.3 Consensus size: 13
28005462 ATCATTCTTT
28005472 ATATTATTTATTA
1 ATATTATTTATTA
*
28005485 AT-GTA-TTA-TA
1 ATATTATTTATTA
*
28005495 ATATTATTTCTTA
1 ATATTATTTATTA
28005508 ATATTATTTATTAA
1 ATATTATTTATT-A
*
28005522 TATATTATATTAATA
1 -ATATTAT-TTATTA
28005537 GTATATTATTTATTA
1 --ATATTATTTATTA
28005552 ATATATGATTTATTA
1 ATAT-T-ATTTATTA
* * * *
28005567 ATCTAATATGATTT
1 ATATTAT-TTATTA
*
28005581 AT-TTATTAATATA
1 ATATTATTTAT-TA
28005594 ATATTATTTATTAA
1 ATATTATTTATT-A
*
28005608 TATATTATATTAATAA
1 -ATATTAT-TT-ATTA
28005624 CATATTATTTATTA
1 -ATATTATTTATTA
* *
28005638 ATATAATATAATATA
1 ATATTAT-TTAT-TA
*
28005653 ATATTATCTATTA
1 ATATTATTTATTA
28005666 ATAT
1 ATAT
28005670 AATATTATTT
Statistics
Matches: 145, Mismatches: 22, Indels: 36
0.71 0.11 0.18
Matches are distributed among these distances:
10 4 0.03
11 5 0.03
12 7 0.05
13 40 0.28
14 24 0.17
15 41 0.28
16 22 0.15
17 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (13 bp):
ATATTATTTATTA
Found at i:28005550 original size:18 final size:17
Alignment explanation
Indices: 28005471--28005681 Score: 139
Period size: 18 Copynumber: 12.7 Consensus size: 17
28005461 TATCATTCTT
*
28005471 TATATTATTTATTAATG
1 TATATTATTTATTAATA
* **
28005488 TATTATAATATTATTTCT-
1 TA-TATTAT-TTATTAATA
28005506 TAATATTATTTATT-A-A
1 T-ATATTATTTATTAATA
28005522 TATATTA--TATTAATA
1 TATATTATTTATTAATA
28005537 GTATATTATTTATTAATA
1 -TATATTATTTATTAATA
*
28005555 TATGATTTATTAATCTAATA
1 TAT-A-TTATTTAT-TAATA
28005575 TGAT-TTATTTATTAATA
1 T-ATATTATTTATTAATA
28005592 TAATATTATTTATT-A-A
1 T-ATATTATTTATTAATA
28005608 TATATTA--TATTAATAA
1 TATATTATTTATTAAT-A
*
28005624 CATATTATTTATTAATA
1 TATATTATTTATTAATA
*
28005641 TA-A-TA--TAAT-ATA
1 TATATTATTTATTAATA
*
28005653 -ATATTATCTATTAATA
1 TATATTATTTATTAATA
28005669 TAATATTATTTAT
1 T-ATATTATTTAT
28005682 AAGTAAAATT
Statistics
Matches: 155, Mismatches: 13, Indels: 51
0.71 0.06 0.23
Matches are distributed among these distances:
11 1 0.01
12 4 0.03
13 13 0.08
14 2 0.01
15 18 0.12
16 21 0.14
17 21 0.14
18 53 0.34
19 14 0.09
20 6 0.04
21 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TATATTATTTATTAATA
Found at i:28005584 original size:22 final size:22
Alignment explanation
Indices: 28005559--28005646 Score: 86
Period size: 22 Copynumber: 3.8 Consensus size: 22
28005549 TTAATATATG
*
28005559 ATTTATTAATCTAATATGATTT
1 ATTTATTAATATAATATGATTT
*
28005581 ATTTATTAATATAATATTATTT
1 ATTTATTAATATAATATGATTT
* **
28005603 ATTAATATATTATATTAATAACATATT
1 ATT--TAT-TAATA-TAATATGAT-TT
28005630 ATTTATTAATATAATAT
1 ATTTATTAATATAATAT
28005647 AATATAATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
22 23 0.43
23 5 0.09
24 7 0.13
25 7 0.13
26 7 0.13
27 5 0.09
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (22 bp):
ATTTATTAATATAATATGATTT
Found at i:28005671 original size:28 final size:28
Alignment explanation
Indices: 28005506--28005674 Score: 138
Period size: 31 Copynumber: 5.9 Consensus size: 28
28005496 TATTATTTCT
28005506 TAATATTATTTATTAATATATTATATTAATA
1 TAATATTATTTATTAATATA--ATA-TAATA
*
28005537 GT-ATATTATTTATTAATATATGATTTATTAATC
1 -TAATATTATTTATTAATATA--A--TA-TAATA
*
28005570 TAATATGATTTA-T--T-T-AT-TAATA
1 TAATATTATTTATTAATATAATATAATA
28005592 TAATATTATTTATTAATATATTATATTAATA
1 TAATATTATTTATTAATATA--ATA-TAATA
28005623 -ACATATTATTTATTAATATAATATAATA
1 TA-ATATTATTTATTAATATAATATAATA
*
28005651 TAATATTATCTATTAATATAATAT
1 TAATATTATTTATTAATATAATAT
28005675 TATTTATAAG
Statistics
Matches: 117, Mismatches: 6, Indels: 32
0.75 0.04 0.21
Matches are distributed among these distances:
22 15 0.13
23 1 0.01
24 1 0.01
25 1 0.01
26 2 0.02
28 26 0.22
29 7 0.06
30 2 0.02
31 43 0.37
32 3 0.03
33 16 0.14
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TAATATTATTTATTAATATAATATAATA
Found at i:28006144 original size:16 final size:17
Alignment explanation
Indices: 28006113--28006147 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
28006103 TAGAATAATT
28006113 TTATTTATTGTTCAAAA
1 TTATTTATTGTTCAAAA
*
28006130 TTATTT-TTTTTCAAAA
1 TTATTTATTGTTCAAAA
28006146 TT
1 TT
28006148 TATATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (17 bp):
TTATTTATTGTTCAAAA
Found at i:28006150 original size:17 final size:18
Alignment explanation
Indices: 28006112--28006150 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
28006102 ATAGAATAAT
28006112 TTTATTTATTGTTCAAAA
1 TTTATTTATTGTTCAAAA
*
28006130 -TTATTT-TTTTTCAAAA
1 TTTATTTATTGTTCAAAA
28006146 TTTAT
1 TTTAT
28006151 ATAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATTTATTGTTCAAAA
Found at i:28006749 original size:23 final size:23
Alignment explanation
Indices: 28006705--28006749 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
28006695 CTCATTTTCA
* *
28006705 GATTTTTATATTATAGTTATTCG
1 GATTTTTATATTATAATCATTCG
28006728 GATTTTTATATTATAATCATTC
1 GATTTTTATATTATAATCATTC
28006750 TCGTACCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.56
Consensus pattern (23 bp):
GATTTTTATATTATAATCATTCG
Found at i:28011255 original size:18 final size:17
Alignment explanation
Indices: 28011217--28011258 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 17
28011207 TAATTATACA
28011217 TAAATATAATATTTTAT
1 TAAATATAATATTTTAT
28011234 TAAAT-TAATATTTTAAAT
1 TAAATATAATATTTT--AT
28011252 TAAATAT
1 TAAATAT
28011259 TAAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.41
17 5 0.23
18 7 0.32
19 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATATAATATTTTAT
Found at i:28011259 original size:14 final size:13
Alignment explanation
Indices: 28011233--28011273 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
28011223 TAATATTTTA
28011233 TTAAATTAATATT
1 TTAAATTAATATT
*
28011246 TTAAATTAA-ATA
1 TTAAATTAATATT
28011258 TTAAA-TAATAATT
1 TTAAATTAAT-ATT
28011271 TTA
1 TTA
28011274 TTAATATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 3 0.12
12 7 0.29
13 14 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAAATTAATATT
Found at i:28011272 original size:41 final size:39
Alignment explanation
Indices: 28011195--28011277 Score: 105
Period size: 41 Copynumber: 2.1 Consensus size: 39
28011185 AAAATTAATA
*
28011195 TAAATTATATTTTAATTATACATAAATATAATATTTTAT
1 TAAATTATATTTTAATTAAACATAAATATAATATTTTAT
* *
28011234 TAAATTAATATTTTAAATTAAATATTAA-ATAATAATTTTAT
1 TAAATT-ATATTTT-AATTAAACATAAATATAAT-ATTTTAT
28011275 TAA
1 TAA
28011278 TATAACACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 6 0.16
40 12 0.32
41 20 0.53
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (39 bp):
TAAATTATATTTTAATTAAACATAAATATAATATTTTAT
Found at i:28018916 original size:24 final size:23
Alignment explanation
Indices: 28018885--28018930 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
28018875 GATTGTTCTT
*
28018885 TTTTTGTTTTATTTCATTTTTTCC
1 TTTTTGTTTT-TTTAATTTTTTCC
28018909 TTTTTGTTTTTTTAATTTTTTC
1 TTTTTGTTTTTTTAATTTTTTC
28018931 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTTTGTTTTTTTAATTTTTTCC
Found at i:28020240 original size:26 final size:26
Alignment explanation
Indices: 28020191--28020240 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
28020181 AATACTCCTT
28020191 TTAACATAATTACTAAAATATATTTA
1 TTAACATAATTACTAAAATATATTTA
28020217 TTAACATAATTGACTAAAAT-TATT
1 TTAACATAATT-ACTAAAATATATT
28020241 ATAATATCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (26 bp):
TTAACATAATTACTAAAATATATTTA
Found at i:28020356 original size:6 final size:6
Alignment explanation
Indices: 28020333--28020385 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
28020323 TTATATCTTT
* * *
28020333 TTTTAC TTTTTC ATTCTTAC TCTT-C TTTTAC TTTTAC TTTTAC TTTTAA
1 TTTTAC TTTTAC -TT-TTAC TTTTAC TTTTAC TTTTAC TTTTAC TTTTAC
28020382 TTTT
1 TTTT
28020386 TTTTTTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
5 4 0.10
6 29 0.74
7 3 0.08
8 3 0.08
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAC
Found at i:28028407 original size:27 final size:28
Alignment explanation
Indices: 28028374--28028426 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
28028364 TCAACAATCA
*
28028374 TTTAA-TTTATTAAT-AAAATATTAAAAT
1 TTTAATTTTATAAATCAAAAT-TTAAAAT
28028401 TTTAATTTTATAAATCAAAATTTAAA
1 TTTAATTTTATAAATCAAAATTTAAA
28028427 TTTAAACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.22
28 13 0.57
29 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTAATTTTATAAATCAAAATTTAAAAT
Found at i:28040711 original size:16 final size:16
Alignment explanation
Indices: 28040677--28040709 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
28040667 CTTTATCTTC
28040677 TTTCCTTTTTTCTTTT
1 TTTCCTTTTTTCTTTT
28040693 TTT-CTTTTTT-TTTT
1 TTTCCTTTTTTCTTTT
28040707 TTT
1 TTT
28040710 TTTGCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 7 0.41
16 3 0.18
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTCCTTTTTTCTTTT
Found at i:28040712 original size:8 final size:8
Alignment explanation
Indices: 28040677--28040710 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
28040667 CTTTATCTTC
*
28040677 TTTCCTTT
1 TTTCTTTT
28040685 TTTCTTTT
1 TTTCTTTT
28040693 TTTCTTTT
1 TTTCTTTT
28040701 TTT-TTTT
1 TTTCTTTT
28040708 TTT
1 TTT
28040711 TTGCAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTCTTTT
Found at i:28041724 original size:14 final size:14
Alignment explanation
Indices: 28041704--28041765 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
28041694 TAAATTTTAA
28041704 TTTTAATAAAATTT
1 TTTTAATAAAATTT
*
28041718 ATTTAATATAAA-TT
1 TTTTAATA-AAATTT
*
28041732 TTTT-ATTAAATTT
1 TTTTAATAAAATTT
*
28041745 TTTTATTAAAATTT
1 TTTTAATAAAATTT
28041759 TTTTAAT
1 TTTTAAT
28041766 TATAAAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 3 0.08
13 8 0.21
14 25 0.64
15 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAATAAAATTT
Found at i:28041734 original size:27 final size:26
Alignment explanation
Indices: 28041704--28041760 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
28041694 TAAATTTTAA
28041704 TTTTAATAAAATTTATTTAATATAAAT
1 TTTTAATAAAATTTATTTAATA-AAAT
* * * *
28041731 TTTTTATTAAATTTTTTTATTAAAAT
1 TTTTAATAAAATTTATTTAATAAAAT
28041757 TTTT
1 TTTT
28041761 TTAATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTAATAAAATTTATTTAATAAAAT
Found at i:28041748 original size:13 final size:13
Alignment explanation
Indices: 28041712--28041763 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
28041702 AATTTTAATA
*
28041712 AAATTTATTTAATAT
1 AAATTT-TTTTAT-T
28041727 AAA-TTTTTTATT
1 AAATTTTTTTATT
28041739 AAATTTTTTTATT
1 AAATTTTTTTATT
28041752 AAAATTTTTTTA
1 -AAATTTTTTTA
28041764 ATTATAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
12 4 0.12
13 14 0.41
14 13 0.38
15 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AAATTTTTTTATT
Found at i:28046960 original size:20 final size:21
Alignment explanation
Indices: 28046935--28046975 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28046925 GAAAGACGGG
*
28046935 GAAGCCC-AACGAGGCTACCA
1 GAAGCCCTAACCAGGCTACCA
*
28046955 GAAGCCCTAACCAGGTTACCA
1 GAAGCCCTAACCAGGCTACCA
28046976 TAACTAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.34, C:0.34, G:0.22, T:0.10
Consensus pattern (21 bp):
GAAGCCCTAACCAGGCTACCA
Found at i:28048512 original size:70 final size:70
Alignment explanation
Indices: 28048382--28048520 Score: 208
Period size: 70 Copynumber: 2.0 Consensus size: 70
28048372 ACATGTGATG
* * *
28048382 GGGGCCTTTTAAAGTGGGTTATCCCACATCTAATAAATTTTTAACATGCTATAGTTTTATATTCA
1 GGGGCCTTTTAAAGTGGGTTATCCCACATCTAATAAATTTTCAACATGCTATAATCTTATATTCA
28048447 GGTTA
66 GGTTA
* * *
28048452 GGGGCCTTTTAAAGTGGGTTATCTCACATCTAATAAATTTTCAACAT-CTTGTAATCTTATATTT
1 GGGGCCTTTTAAAGTGGGTTATCCCACATCTAATAAATTTTCAACATGC-TATAATCTTATATTC
28048516 AGGTT
65 AGGTT
28048521 GAGCTCCTCC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
69 1 0.02
70 61 0.98
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (70 bp):
GGGGCCTTTTAAAGTGGGTTATCCCACATCTAATAAATTTTCAACATGCTATAATCTTATATTCA
GGTTA
Found at i:28050197 original size:2 final size:2
Alignment explanation
Indices: 28050192--28050216 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28050182 ATATATATAT
28050192 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
28050217 AAATATATAT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:28055193 original size:14 final size:13
Alignment explanation
Indices: 28055165--28055190 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28055155 TAAAAACAGT
28055165 TTTCCCAATAAAA
1 TTTCCCAATAAAA
28055178 TTTCCCAATAAAA
1 TTTCCCAATAAAA
28055191 ATTATCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
TTTCCCAATAAAA
Found at i:28055334 original size:11 final size:11
Alignment explanation
Indices: 28055316--28055349 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
28055306 TTAAAATCAA
28055316 ATAAAATTTAT
1 ATAAAATTTAT
28055327 CA-AAAATTTAT
1 -ATAAAATTTAT
28055338 ATAAAATTTAT
1 ATAAAATTTAT
28055349 A
1 A
28055350 CTTACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 19 0.90
12 1 0.05
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
ATAAAATTTAT
Found at i:28056266 original size:2 final size:2
Alignment explanation
Indices: 28056255--28056289 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
28056245 CATGAATTGC
28056255 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28056290 AAATTCTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28057327 original size:2 final size:2
Alignment explanation
Indices: 28057310--28057348 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
28057300 AGTCAAATGT
* *
28057310 TG TG TC TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
28057349 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.03, G:0.44, T:0.51
Consensus pattern (2 bp):
TG
Found at i:28063598 original size:9 final size:9
Alignment explanation
Indices: 28063584--28063609 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28063574 TCATTTGCAT
28063584 TTTTATTTA
1 TTTTATTTA
28063593 TTTTATTTA
1 TTTTATTTA
28063602 TTTTATTT
1 TTTTATTT
28063610 TGTAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTATTTA
Found at i:28069165 original size:18 final size:17
Alignment explanation
Indices: 28069125--28069171 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
28069115 AACCTAAAAT
*
28069125 TTTTACAAACTTGAAAC
1 TTTTGCAAACTTGAAAC
*
28069142 TTTTGCGAAACTTGGAA-
1 TTTTGC-AAACTTGAAAC
28069159 TTCTTGCAAACTT
1 TT-TTGCAAACTT
28069172 TTGTAAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (17 bp):
TTTTGCAAACTTGAAAC
Found at i:28076147 original size:31 final size:31
Alignment explanation
Indices: 28076109--28076200 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
28076099 AATTAACCAA
28076109 GCATATAGAATTAAAAGTTAGGAATAAGGGG
1 GCATATAGAATTAAAAGTTAGGAATAAGGGG
28076140 GCATATAGAATTAAAAGTTAGGAATAAGGGG
1 GCATATAGAATTAAAAGTTAGGAATAAGGGG
28076171 GCATATAGAATTAAAAGTTAGGAAT-AGGGG
1 GCATATAGAATTAAAAGTTAGGAATAAGGGG
28076201 AGATTGAAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 5 0.08
31 56 0.92
ACGTcount: A:0.45, C:0.03, G:0.29, T:0.23
Consensus pattern (31 bp):
GCATATAGAATTAAAAGTTAGGAATAAGGGG
Found at i:28086189 original size:2 final size:2
Alignment explanation
Indices: 28086182--28086207 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28086172 GGGTCTCCAC
28086182 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
28086208 CTTGATTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28089225 original size:118 final size:118
Alignment explanation
Indices: 28089038--28089269 Score: 401
Period size: 118 Copynumber: 2.0 Consensus size: 118
28089028 TGATTTCGCT
*
28089038 TCCGCTGGTGTGATTGGATTGGAGGCTTTTAGCCCAACAAAATTTGTTGGGATTTGCCTTGAATT
1 TCCGCTGGTGTGATTGGATTGGAGGCTTTTAGCCCAACAAAATTTGTTGGGATTTGCCTTGAATC
* *
28089103 TCATAATCCTACATCGAAAGTTAGTAAGTTTTGAATTTGTCCAGTATCCAGTA
66 TCATAATCCCACATCGAAAGTTAGTAAGTTTTAAATTTGTCCAGTATCCAGTA
* * *
28089156 TCCGCTGGTGTGATTGGATTGGAGGCTTTTAGCCTAATAAAATTTGTTGGGATTTGCTTTGAATC
1 TCCGCTGGTGTGATTGGATTGGAGGCTTTTAGCCCAACAAAATTTGTTGGGATTTGCCTTGAATC
*
28089221 TCATAATCCCACATCGAAAGTTAGTGAGTTTTAAATTTGTCCAGTATCC
66 TCATAATCCCACATCGAAAGTTAGTAAGTTTTAAATTTGTCCAGTATCC
28089270 CACATCGAAG
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 107 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (118 bp):
TCCGCTGGTGTGATTGGATTGGAGGCTTTTAGCCCAACAAAATTTGTTGGGATTTGCCTTGAATC
TCATAATCCCACATCGAAAGTTAGTAAGTTTTAAATTTGTCCAGTATCCAGTA
Found at i:28092088 original size:31 final size:30
Alignment explanation
Indices: 28092047--28092146 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 30
28092037 AGGCTTTTAG
* * *
28092047 CCCAATAAATGGTATCAGAGTCGTGATGTTC
1 CCCAACAAATGGTATCAGAAT-ATGATGTTC
* *
28092078 CCCAACAAATGGTATCAGAATTATGGTGATC
1 CCCAACAAATGGTATCAGAA-TATGATGTTC
* *
28092109 TCCAACAAATGATATCAGAAATATGATGTTC
1 CCCAACAAATGGTATCAG-AATATGATGTTC
28092140 CCCAACA
1 CCCAACA
28092147 TTTTTGAGTG
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 54 0.95
32 3 0.05
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (30 bp):
CCCAACAAATGGTATCAGAATATGATGTTC
Found at i:28092460 original size:11 final size:11
Alignment explanation
Indices: 28092446--28092475 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28092436 ATATTTTAAA
28092446 ATTATTAAATT
1 ATTATTAAATT
28092457 ATTATTAAATT
1 ATTATTAAATT
28092468 ATT-TTAAA
1 ATTATTAAA
28092476 ATCAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:28105880 original size:19 final size:19
Alignment explanation
Indices: 28105852--28105889 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28105842 GCTAAGAAAC
*
28105852 GACAACAACTTGCATTATG
1 GACAACAACTTGCACTATG
*
28105871 GACAATAACTTGCACTATG
1 GACAACAACTTGCACTATG
28105890 AGATGTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (19 bp):
GACAACAACTTGCACTATG
Found at i:28106819 original size:3 final size:3
Alignment explanation
Indices: 28106811--28106850 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
28106801 TTTATAGCAT
28106811 TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28106851 TTACTTAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:28106833 original size:20 final size:20
Alignment explanation
Indices: 28106810--28106853 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
28106800 TTTTATAGCA
28106810 TTTATTATTATTATTATTAT
1 TTTATTATTATTATTATTAT
28106830 TTTATTATTATTATTATTAT
1 TTTATTATTATTATTATTAT
28106850 TTTA
1 TTTA
28106854 CTTAGGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATTATTATTATTATTAT
Found at i:28106836 original size:17 final size:17
Alignment explanation
Indices: 28106814--28106847 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28106804 ATAGCATTTA
28106814 TTATTATTATTATTATT
1 TTATTATTATTATTATT
28106831 TTATTATTATTATTATT
1 TTATTATTATTATTATT
28106848 ATTTTACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTATTATTATTATT
Found at i:28107187 original size:12 final size:12
Alignment explanation
Indices: 28107172--28107199 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28107162 TTTATTTAAT
28107172 TTTTATTATTTA
1 TTTTATTATTTA
28107184 TTTTATTATTTA
1 TTTTATTATTTA
28107196 TTTT
1 TTTT
28107200 TGTTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:28107525 original size:11 final size:11
Alignment explanation
Indices: 28107509--28107533 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28107499 TATATAACAA
28107509 AAATAAAAATT
1 AAATAAAAATT
28107520 AAATAAAAATT
1 AAATAAAAATT
28107531 AAA
1 AAA
28107534 AAACAAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAAAATT
Found at i:28108198 original size:34 final size:32
Alignment explanation
Indices: 28108155--28108236 Score: 128
Period size: 34 Copynumber: 2.5 Consensus size: 32
28108145 TGTTGTGTGT
*
28108155 TTTTTTTTTTGTTTTTTTTAGTAGACTAAGAAGA
1 TTTTTTTTTT-TTTTTTTTAGTAAACTAAGAA-A
28108189 TTTTTTTTTTTGTTTTTTTAGTAAACTAAGAAA
1 TTTTTTTTTTT-TTTTTTTAGTAAACTAAGAAA
28108222 TTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTT
28108237 CAACCAAAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
32 4 0.09
33 13 0.28
34 29 0.63
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (32 bp):
TTTTTTTTTTTTTTTTTTAGTAAACTAAGAAA
Found at i:28108313 original size:20 final size:20
Alignment explanation
Indices: 28108269--28108316 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
28108259 TTTGGCAAAA
*
28108269 CTTTTTTTTTTGTTTAGTTT
1 CTTTTTTTTTTGTTTAGGTT
* *
28108289 TTTTTTTTTTTGTTTGGGTT
1 CTTTTTTTTTTGTTTAGGTT
28108309 CTTTTTTT
1 CTTTTTTT
28108317 ATCCCTTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.81
Consensus pattern (20 bp):
CTTTTTTTTTTGTTTAGGTT
Found at i:28108883 original size:40 final size:41
Alignment explanation
Indices: 28108837--28108920 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
28108827 ATAATTTTTT
*
28108837 AAAATT-AAAAACTCCTCTATACAAAGGCTCGACAACTTTG
1 AAAATTAAAAAACTCCTCTAAACAAAGGCTCGACAACTTTG
* * *
28108877 AAAATTAAAAAACTCCTTTAAACAAAGGTTTGACAACTTTG
1 AAAATTAAAAAACTCCTCTAAACAAAGGCTCGACAACTTTG
28108918 AAA
1 AAA
28108921 TTTTAAAAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 6 0.15
41 33 0.85
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (41 bp):
AAAATTAAAAAACTCCTCTAAACAAAGGCTCGACAACTTTG
Found at i:28108960 original size:42 final size:42
Alignment explanation
Indices: 28108909--28109183 Score: 201
Period size: 43 Copynumber: 6.5 Consensus size: 42
28108899 CAAAGGTTTG
* * * * *
28108909 ACAACTTTGAAATTTTAAAAGGCTAATCTAATTAGAGGCTTA
1 ACAATTTTGAAAATTTAAAAGGCTCATCTAAGTAGAGGCTCA
* * * *
28108951 ATAATTTTGAAAAATTTAAAAGACTCCTCTAAGTGGAAGG-TCA
1 ACAATTTTG-AAAATTTAAAAGGCTCATCTAAGTAG-AGGCTCA
* * * * * * * *
28108994 AGAACTTTGAAATTTTAAAAAGCTCCTCTAAGCAGAAGCTTA
1 ACAATTTTGAAAATTTAAAAGGCTCATCTAAGTAGAGGCTCA
* * * * * * * *
28109036 ATAACTTTAAAAATTTAAAAGACTCATTTGAGTAGAAGCTCG
1 ACAATTTTGAAAATTTAAAAGGCTCATCTAAGTAGAGGCTCA
* *
28109078 ACAATTTTAAAAACTTTAAAAGGCTCATCTAAATAGAGGCTCA
1 ACAATTTTGAAAA-TTTAAAAGGCTCATCTAAGTAGAGGCTCA
* * * * *
28109121 ACAATTTTGAAAACTTTAAAAGGCTTATTTAAGCAAAGGTTCA
1 ACAATTTTGAAAA-TTTAAAAGGCTCATCTAAGTAGAGGCTCA
* *
28109164 ACAACTTTGAAAAATTAAAA
1 ACAATTTTGAAAATTTAAAA
28109184 TATTCTACCT
Statistics
Matches: 183, Mismatches: 46, Indels: 8
0.77 0.19 0.03
Matches are distributed among these distances:
41 2 0.01
42 78 0.43
43 100 0.55
44 3 0.02
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (42 bp):
ACAATTTTGAAAATTTAAAAGGCTCATCTAAGTAGAGGCTCA
Found at i:28109000 original size:85 final size:85
Alignment explanation
Indices: 28108909--28109175 Score: 268
Period size: 85 Copynumber: 3.1 Consensus size: 85
28108899 CAAAGGTTTG
* *
28108909 ACAACTTTGAAATTTTAAAAGGCTAATCTAATTAGAGGCTTAATAATTTTGAAAAATTTAAAAGA
1 ACAACTTTGAAATTTTAAAAGGCTCATCTAAATAGAGGCTTAATAATTTTGAAAAATTTAAAAGA
* * *
28108974 CTCCTCTAAGTGGAAGGTCA
66 CTCATCTAAGTAGAAGCTCA
* * * ** * *
28108994 AGAACTTTGAAATTTTAAAAAGCTCCTCTAAGCAGAAGCTTAATAACTTT-AAAAATTTAAAAGA
1 ACAACTTTGAAATTTTAAAAGGCTCATCTAAATAGAGGCTTAATAATTTTGAAAAATTTAAAAGA
* * *
28109058 CTCATTTGAGTAGAAGCTCG
66 CTCATCTAAGTAGAAGCTCA
* * * * * *
28109078 ACAATTTTAAAAACTTTAAAAGGCTCATCTAAATAGAGGCTCAACAATTTTGAAAACTTTAAAAG
1 ACAACTTT-GAAATTTTAAAAGGCTCATCTAAATAGAGGCTTAATAATTTTGAAAAATTTAAAAG
* * * * *
28109143 GCTTATTTAAGCA-AAGGTTCA
65 ACTCATCTAAGTAGAA-GCTCA
28109164 ACAACTTTGAAA
1 ACAACTTTGAAA
28109176 AATTAAAATA
Statistics
Matches: 144, Mismatches: 35, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
84 34 0.24
85 79 0.55
86 31 0.22
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (85 bp):
ACAACTTTGAAATTTTAAAAGGCTCATCTAAATAGAGGCTTAATAATTTTGAAAAATTTAAAAGA
CTCATCTAAGTAGAAGCTCA
Found at i:28109182 original size:85 final size:85
Alignment explanation
Indices: 28108873--28109183 Score: 256
Period size: 85 Copynumber: 3.7 Consensus size: 85
28108863 GCTCGACAAC
* * * ** ** *
28108873 TTTG-AAAA-TTAAAAAACTCCTTTAAACAAAGGTTTGACAACTTTGAAATTTTAAAAGGCTAAT
1 TTTGAAAAATTTAAAAGACTCATTTAAGCAAAGGTTCAACAACTTTGAAAAATTAAAAGGCTCAT
*
28108936 CTAATTAGAGGCTTAATAAT
66 CTAAATAGAGGCTTAATAAT
* * ** * ** * *
28108956 TTTGAAAAATTTAAAAGACTCCTCTAAGTGGAAGG-TCAAGAACTTTGAAATTTTAAAAAGCTCC
1 TTTGAAAAATTTAAAAGACTCATTTAAG-CAAAGGTTCAACAACTTTGAAAAATTAAAAGGCTCA
** * *
28109020 TCTAAGCAGAAGCTTAATAAC
65 TCTAAATAGAGGCTTAATAAT
* * * * *
28109041 TTT-AAAAATTTAAAAGACTCATTTGAGTAGAA-GCTCGACAA-TTTTAAAAACTTTAAAAGGCT
1 TTTGAAAAATTTAAAAGACTCATTTAAGCA-AAGGTTCAACAACTTTGAAAAA--TTAAAAGGCT
* *
28109103 CATCTAAATAGAGGCTCAACAAT
63 CATCTAAATAGAGGCTTAATAAT
* * *
28109126 TTTGAAAACTTTAAAAGGCTTATTTAAGCAAAGGTTCAACAACTTTGAAAAATTAAAA
1 TTTGAAAAATTTAAAAGACTCATTTAAGCAAAGGTTCAACAACTTTGAAAAATTAAAA
28109184 TATTCTACCT
Statistics
Matches: 177, Mismatches: 41, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
83 11 0.06
84 32 0.18
85 94 0.53
86 32 0.18
87 8 0.05
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (85 bp):
TTTGAAAAATTTAAAAGACTCATTTAAGCAAAGGTTCAACAACTTTGAAAAATTAAAAGGCTCAT
CTAAATAGAGGCTTAATAAT
Found at i:28109329 original size:119 final size:122
Alignment explanation
Indices: 28109164--28109417 Score: 295
Period size: 119 Copynumber: 2.1 Consensus size: 122
28109154 CAAAGGTTCA
* * * *
28109164 ACAAC-TTTGAAAAATTAAAATATTCTACCTAGAGGACTTACGAATCTAGATAATGAAAGCTCTT
1 ACAACTTTTGAAAAATTAAAATATTATACCTAGAGGACTTACAAATCTAGATAATGAAAGCACCT
* * * * *
28109228 CTAAGTAGAGGCTCAACAAC-TT-AAAAA-AAAAAAACTCCTCTAAGTAGAGGCTTT
66 CTAAGCAAAAGCTCAACAACTTTAAAAAATAAAAAAACTCCTCTAAGTAGAAGCTCT
* * ** * * *
28109282 ACAACTTTTGAAGATTTAAAATATTATATTTAGAGGATTTACAAATCTTGATAATGAATGCACCT
1 ACAACTTTTGAAAAATTAAAATATTATACCTAGAGGACTTACAAATCTAGATAATGAAAGCACCT
*
28109347 CTAAGCAAAAGCTTAACAACTTTAAAAAAGTTAAAAAAACTCCTCTAAGTAGAAGCTCT
66 CTAAGCAAAAGCTCAACAACTTTAAAAAA--TAAAAAAACTCCTCTAAGTAGAAGCTCT
28109406 ACAA-TTTT-AAAA
1 ACAACTTTTGAAAA
28109418 TTCTCATTTT
Statistics
Matches: 112, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
118 5 0.04
119 64 0.57
120 2 0.02
121 5 0.04
122 3 0.03
123 4 0.04
124 29 0.26
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (122 bp):
ACAACTTTTGAAAAATTAAAATATTATACCTAGAGGACTTACAAATCTAGATAATGAAAGCACCT
CTAAGCAAAAGCTCAACAACTTTAAAAAATAAAAAAACTCCTCTAAGTAGAAGCTCT
Found at i:28121064 original size:3 final size:3
Alignment explanation
Indices: 28121056--28121111 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
28121046 TTTATAACAT
28121056 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28121104 TTA TTA TT
1 TTA TTA TT
28121112 TACTTAAGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28121439 original size:22 final size:22
Alignment explanation
Indices: 28121414--28121455 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28121404 ATTTTCTAGA
*
28121414 TTTTTTATTGTTGGTTTTATCC
1 TTTTTTATTATTGGTTTTATCC
*
28121436 TTTTTTATTATTTGTTTTAT
1 TTTTTTATTATTGGTTTTAT
28121456 TATTTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.74
Consensus pattern (22 bp):
TTTTTTATTATTGGTTTTATCC
Found at i:28125801 original size:160 final size:154
Alignment explanation
Indices: 28125610--28125905 Score: 443
Period size: 160 Copynumber: 1.9 Consensus size: 154
28125600 CATAAAAATT
*
28125610 AAAAAAAAAAAAAGGTTTAGAGATAGAAAGAGAAAGTGAAAGGGTATGC-CTGCACATTGCAGCT
1 AAAAAAAAAAAAAGGTTTAGAGATAGAAAGAGAAAGTGAAAGAGTATGCTC-GCACATTGCAGCT
* * *
28125674 GTCTCCAGCCCATTTCCCTCCCCTTCCCGACCCTCCCTCTAACCCCATT-CCTTCTTTATATACT
65 GCCTCCAGCCCATTTCCCTCCCC-TCCC--CCCT-CC-CTAACCCCATTCCCCTCTTCATATACT
28125738 ATTCTTAATCCCATAAAAATTAAAAACAAA
125 ATTCTTAATCCCATAAAAATTAAAAACAAA
28125768 AAAAAAACAAAAAGAGGTTTAGAGATAGAAAGAGAAAGTGAAAGAGTATGCTCGCACATTGCAGC
1 AAAAAAA-AAAAA-AGGTTTAGAGATAGAAAGAGAAAGTGAAAGAGTATGCTCGCACATTGCAGC
* * *
28125833 TGCCTCCAGCGCATTTCCCTCCCCTCCCCTCTCCCTAACCCCATTCCCCTCTTCATATCCTATTC
64 TGCCTCCAGCCCATTTCCCTCCCCTCCCCCCTCCCTAACCCCATTCCCCTCTTCATATACTATTC
28125898 TTAATCCC
129 TTAATCCC
28125906 CCACTTCTCT
Statistics
Matches: 127, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
155 11 0.09
156 26 0.20
157 3 0.02
158 7 0.06
159 9 0.07
160 70 0.55
161 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.25
Consensus pattern (154 bp):
AAAAAAAAAAAAAGGTTTAGAGATAGAAAGAGAAAGTGAAAGAGTATGCTCGCACATTGCAGCTG
CCTCCAGCCCATTTCCCTCCCCTCCCCCCTCCCTAACCCCATTCCCCTCTTCATATACTATTCTT
AATCCCATAAAAATTAAAAACAAA
Found at i:28131121 original size:40 final size:40
Alignment explanation
Indices: 28131077--28131154 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
28131067 AATGTAATGA
28131077 AATAAATTCATACAAGAAATTGAATCCCAAACATTTCAAT
1 AATAAATTCATACAAGAAATTGAATCCCAAACATTTCAAT
*
28131117 AATAAATTCATACAAGAAATTGAATCCCAAACGTTTCA
1 AATAAATTCATACAAGAAATTGAATCCCAAACATTTCA
28131155 TTCCGTTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27
Consensus pattern (40 bp):
AATAAATTCATACAAGAAATTGAATCCCAAACATTTCAAT
Found at i:28134174 original size:21 final size:18
Alignment explanation
Indices: 28134148--28134186 Score: 51
Period size: 21 Copynumber: 2.0 Consensus size: 18
28134138 ACAATTATTT
28134148 TTTTAAGAATATTTTAATTAA
1 TTTTAA-AA-ATTTT-ATTAA
28134169 TTTTAAAAATTTTATTAA
1 TTTTAAAAATTTTATTAA
28134187 AATAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 2 0.11
21 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTTAAAAATTTTATTAA
Found at i:28138781 original size:57 final size:56
Alignment explanation
Indices: 28138709--28138823 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 56
28138699 ATGAGAAAAA
28138709 GATAATTTTTATTATCAAGAAAGACCTTTATCATTACAAGTTGATGCTATTTGGATT
1 GATAATTTTTATTATCAAGAAAGACCTTTATCATTACAAGTTGATGCTA-TTGGATT
*
28138766 GATAATTTTTATTATCGAGAAAGACCTTTATCATTACAAGTTGATGCTATTGGATT
1 GATAATTTTTATTATCAAGAAAGACCTTTATCATTACAAGTTGATGCTATTGGATT
28138822 GA
1 GA
28138824 AGAACGCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 9 0.16
57 48 0.84
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (56 bp):
GATAATTTTTATTATCAAGAAAGACCTTTATCATTACAAGTTGATGCTATTGGATT
Found at i:28150274 original size:34 final size:34
Alignment explanation
Indices: 28150191--28150285 Score: 91
Period size: 39 Copynumber: 2.6 Consensus size: 34
28150181 ATCGTCAGGC
*
28150191 AAATGTATCTATTATTATGTGTCAAACTTACATA
1 AAATGTATCTATTATTATGTGTCAAACCTACATA
* * * *
28150225 AAATATAAAAAATCTATTCTTTTGTGTCAAACCTACGTA
1 AAATGT-----ATCTATTATTATGTGTCAAACCTACATA
*
28150264 AAATGTATCTATTAGTATGTGT
1 AAATGTATCTATTATTATGTGT
28150286 TTCTAAAAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
34 18 0.38
39 29 0.62
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (34 bp):
AAATGTATCTATTATTATGTGTCAAACCTACATA
Found at i:28150477 original size:21 final size:21
Alignment explanation
Indices: 28150451--28150490 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28150441 ATTTAAAAGT
* *
28150451 GCAATTCGGATTTATTTAAGG
1 GCAATTAGGATGTATTTAAGG
28150472 GCAATTAGGATGTATTTAA
1 GCAATTAGGATGTATTTAA
28150491 CTATTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.38
Consensus pattern (21 bp):
GCAATTAGGATGTATTTAAGG
Found at i:28151179 original size:51 final size:51
Alignment explanation
Indices: 28151124--28151221 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
28151114 GAAAAATACT
*
28151124 ATAGAATGTATTCATTCAAATACCAAGATCAAACATGTAATGACAAGTACC
1 ATAGAATGTATTCATTCAAATACCAAGATCAAACAAGTAATGACAAGTACC
*
28151175 ATAGAATGTATTCGTTCAAATACCAAGATCAAACAAGTAATGACAAG
1 ATAGAATGTATTCATTCAAATACCAAGATCAAACAAGTAATGACAAG
28151222 CACTAAGCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.24
Consensus pattern (51 bp):
ATAGAATGTATTCATTCAAATACCAAGATCAAACAAGTAATGACAAGTACC
Found at i:28152988 original size:14 final size:14
Alignment explanation
Indices: 28152945--28152986 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
28152935 TGATGAATTT
**
28152945 TTATATAAATTTTTA
1 TTATATAAA-TTAAA
28152960 TTATATAAATTAAA
1 TTATATAAATTAAA
28152974 TTATA-AAATTAAA
1 TTATATAAATTAAA
28152987 ATAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 8 0.32
14 8 0.32
15 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATATAAATTAAA
Found at i:28154135 original size:3 final size:3
Alignment explanation
Indices: 28154127--28154161 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28154117 TCTCCCAGAG
28154127 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
28154162 TTTGATCGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:28154199 original size:3 final size:3
Alignment explanation
Indices: 28154191--28154229 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
28154181 GAAAAGTTCA
28154191 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28154230 TTTGACCGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28154233 original size:68 final size:68
Alignment explanation
Indices: 28154127--28154259 Score: 257
Period size: 68 Copynumber: 2.0 Consensus size: 68
28154117 TCTCCCAGAG
*
28154127 ATAATAATAATAATAATAATAATAATAATAATAATTTTGATCGTGATAGTTGATGAAAAGTTCAA
1 ATAATAATAATAATAATAATAATAATAATAATAATTTTGACCGTGATAGTTGATGAAAAGTTCAA
28154192 ATA
66 ATA
28154195 ATAATAATAATAATAATAATAATAATAATAATAATTTTGACCGTGATAGTTGATGAAAAGTTCAA
1 ATAATAATAATAATAATAATAATAATAATAATAATTTTGACCGTGATAGTTGATGAAAAGTTCAA
28154260 TTTTGTCCTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.35
Consensus pattern (68 bp):
ATAATAATAATAATAATAATAATAATAATAATAATTTTGACCGTGATAGTTGATGAAAAGTTCAA
ATA
Found at i:28158768 original size:30 final size:30
Alignment explanation
Indices: 28158734--28158806 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
28158724 ATCACATCAG
*
28158734 AAACCAGACTCTAGGTTGTCACCAAAACAA
1 AAACCAGACTCAAGGTTGTCACCAAAACAA
* * *
28158764 AAACCGGACTCAAGGTTGTCACCACAACAG
1 AAACCAGACTCAAGGTTGTCACCAAAACAA
*
28158794 AAGCCAGACTCAA
1 AAACCAGACTCAA
28158807 TTTCACCTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.41, C:0.29, G:0.16, T:0.14
Consensus pattern (30 bp):
AAACCAGACTCAAGGTTGTCACCAAAACAA
Found at i:28159864 original size:9 final size:9
Alignment explanation
Indices: 28159850--28159880 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28159840 GAAGGAGGGT
28159850 AAAAAATAA
1 AAAAAATAA
28159859 AAAAAATAA
1 AAAAAATAA
*
28159868 TAAAAATAA
1 AAAAAATAA
28159877 AAAA
1 AAAA
28159881 TCATCCCTTT
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:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAATAA
Found at i:28160142 original size:15 final size:14
Alignment explanation
Indices: 28160115--28160150 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
28160105 ATTTGTTTGC
*
28160115 AAAAAATGATTTTT
1 AAAAAATAATTTTT
28160129 AAAAAATAATTTTT
1 AAAAAATAATTTTT
*
28160143 TAAAAATA
1 AAAAAATA
28160151 TGTAGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
AAAAAATAATTTTT
Found at i:28160364 original size:20 final size:21
Alignment explanation
Indices: 28160322--28160379 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
28160312 ATTTATTCTT
*
28160322 ATAATTATTAATA-TT-AA-A
1 ATAATAATTAATATTTAAATA
*
28160340 A-AATAATT-ATATTTTAATA
1 ATAATAATTAATATTTAAATA
*
28160359 ATAATATTTAATATTTAAATA
1 ATAATAATTAATATTTAAATA
28160380 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.09
17 8 0.25
18 3 0.09
19 2 0.06
20 6 0.19
21 10 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAATAATTAATATTTAAATA
Found at i:28160501 original size:28 final size:29
Alignment explanation
Indices: 28160428--28160538 Score: 84
Period size: 28 Copynumber: 3.8 Consensus size: 29
28160418 AATATATTAA
* ** *
28160428 AATATTATTATTAATAAAATTTTATTAAT
1 AATAATATTATTAATATTATTTTATAAAT
* *
28160457 TAT-ATATTATTACTATTATTTTATAAAT
1 AATAATATTATTAATATTATTTTATAAAT
* *
28160485 AATAATATTA-TAATATT-TATTAATATAT
1 AATAATATTATTAATATTAT-TTTATAAAT
*
28160513 AGCATAATATTATTTAATAATATTTT
1 A--ATAATATTA-TTAATATTATTTT
28160539 TATTAATATA
Statistics
Matches: 63, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
27 1 0.02
28 36 0.57
29 8 0.13
30 9 0.14
32 8 0.13
33 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (29 bp):
AATAATATTATTAATATTATTTTATAAAT
Found at i:28160575 original size:88 final size:89
Alignment explanation
Indices: 28160404--28160584 Score: 201
Period size: 88 Copynumber: 2.0 Consensus size: 89
28160394 TTATTATTCT
* * *
28160404 TTATATTATTTATTAATATATTAAAATATTATTATTAATAAAATTTTATTAATTATATATTATTA
1 TTATAATATTTATTAATATATTAAAATAATATTATTAATAAAATTTTATTAATTATATATTAATA
* *
28160469 CTATTATTTTATAAATAA-TAATA
66 CTAATATTTTATAAATAATTAAAA
** *
28160492 TTATAATATTTATTAATATA-TAGCATAATATTATTTAATAATATTTTTATTAA-TATAT-TGTA
1 TTATAATATTTATTAATATATTAAAATAATATTA-TTAATAA-AATTTTATTAATTATATAT-TA
**
28160554 ATA-TAATATTATTATTTATAATTAAAA
63 ATACTAATATT-TTATAAATAATTAAAA
28160581 TTAT
1 TTAT
28160585 GGTTAAAAGT
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
87 17 0.22
88 43 0.55
89 18 0.23
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (89 bp):
TTATAATATTTATTAATATATTAAAATAATATTATTAATAAAATTTTATTAATTATATATTAATA
CTAATATTTTATAAATAATTAAAA
Found at i:28160726 original size:22 final size:22
Alignment explanation
Indices: 28160681--28160726 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
28160671 AAAAATGATT
*
28160681 TTATTTTTTATTGACCAGTAAA
1 TTATTTTTTATTGACCAATAAA
* *
28160703 TTATTTTTTATTGATCAATCAA
1 TTATTTTTTATTGACCAATAAA
28160725 TT
1 TT
28160727 TTCTATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (22 bp):
TTATTTTTTATTGACCAATAAA
Found at i:28163567 original size:132 final size:132
Alignment explanation
Indices: 28163252--28163741 Score: 481
Period size: 132 Copynumber: 3.7 Consensus size: 132
28163242 TGTTTTTGAA
* * * * * * * * *
28163252 AAAATGCCATC-ATTTTAGCAGTGTTTCTATCTTTCAAACGTAGCTAAATTAATTACGTTTTTAT
1 AAAATGCC-TCTATATTAGCGGCGTTTGTATCTTTCAAACATATCTAATTTAGTGACGTTTTTAT
* * *
28163316 GAAAAAAATG-CAATTGCTTTGGTGGCATTTTGATACTGAAAATAC-CACTACTTTAGAGGTATT
65 GAGAAAAATGTC-ATTGCTTTGGTGGCATTTT-A-ACTG-AAA-ACGCACTACTTTAAAGGCATT
*
28163379 TGTATCTG
125 TGTATATG
* * * *
28163387 AAAACGCCTCTATATTAGCTGCGTTTGTATGTTTCAGACATTAT-TAATTTAGTGACGTTTTTAT
1 AAAATGCCTCTATATTAGCGGCGTTTGTATCTTTCAAACA-TATCTAATTTAGTGACGTTTTTAT
* * * *
28163451 GAGAAAAATGTCATTCCTTTGGTGGCGTTTATAACTGAAACCGCACTACTTTATAGGCATTTGTA
65 GAGAAAAATGTCATTGCTTTGGTGGCATTT-TAACTGAAAACGCACTACTTTAAAGGCATTTGTA
28163516 TATG
129 TATG
* * * *
28163520 -AAATGTCTCTATATTAGCGGCGTTTGTATCTTTCAAACATCTCTAATTTAGTGGCATTTTTATG
1 AAAATGCCTCTATATTAGCGGCGTTTGTATCTTTCAAACATATCTAATTTAGTGACGTTTTTATG
* * ** * *
28163584 TA-AAAAAAGTCATTGTTTTGGTGGCATTTGTAACTGAAATTGTCGCTATTTTAAAGGCATTTGT
66 -AGAAAAATGTCATTGCTTTGGTGGCATTT-TAACTGAAAACG-CACTACTTTAAAGGCATTTGT
28163648 ATATG
128 ATATG
* * *** * *
28163653 AAAATACCTTTATATTAGCGATATTTGTATCTTTCAGACATATCTAATTTAGTGGCGTTTTT-TG
1 AAAATGCCTCTATATTAGCGGCGTTTGTATCTTTCAAACATATCTAATTTAGTGACGTTTTTATG
*
28163717 AGAAAAATGCCATTGCTTTGGTGGC
66 AGAAAAATGTCATTGCTTTGGTGGC
28163742 GTTTGTATAA
Statistics
Matches: 296, Mismatches: 49, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
131 2 0.01
132 88 0.30
133 72 0.24
134 58 0.20
135 72 0.24
136 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (132 bp):
AAAATGCCTCTATATTAGCGGCGTTTGTATCTTTCAAACATATCTAATTTAGTGACGTTTTTATG
AGAAAAATGTCATTGCTTTGGTGGCATTTTAACTGAAAACGCACTACTTTAAAGGCATTTGTATA
TG
Found at i:28168891 original size:21 final size:21
Alignment explanation
Indices: 28168867--28168910 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28168857 CTTTATCACT
*
28168867 TTGAATATCAAG-ATCATCAAC
1 TTGAATAT-AAGTATCACCAAC
*
28168888 TTGAGTATAAGTATCACCAAC
1 TTGAATATAAGTATCACCAAC
28168909 TT
1 TT
28168911 ACATAATACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (21 bp):
TTGAATATAAGTATCACCAAC
Found at i:28173463 original size:10 final size:10
Alignment explanation
Indices: 28173448--28173490 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
28173438 TGCTAAACCT
28173448 TATTGTATGA
1 TATTGTATGA
28173458 TATTGTAT--
1 TATTGTATGA
* *
28173466 TATTGAATGG
1 TATTGTATGA
28173476 TATTGTATGA
1 TATTGTATGA
28173486 TATTG
1 TATTG
28173491 AGGGGCTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 7 0.25
10 21 0.75
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (10 bp):
TATTGTATGA
Found at i:28173470 original size:18 final size:18
Alignment explanation
Indices: 28173447--28173483 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28173437 TTGCTAAACC
*
28173447 TTATTGTATGATATTGTA
1 TTATTGAATGATATTGTA
*
28173465 TTATTGAATGGTATTGTA
1 TTATTGAATGATATTGTA
28173483 T
1 T
28173484 GATATTGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (18 bp):
TTATTGAATGATATTGTA
Done.