Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 95 of 141
Found at i:30951948 original size:16 final size:16
Alignment explanation
Indices: 30951927--30951958 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30951917 AAAAATAAGG
*
30951927 AATCATGGGAATTAGA
1 AATCATGGAAATTAGA
30951943 AATCATGGAAATTAGA
1 AATCATGGAAATTAGA
30951959 TTAAGGTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (16 bp):
AATCATGGAAATTAGA
Found at i:30952954 original size:425 final size:424
Alignment explanation
Indices: 30952139--30952984 Score: 1370
Period size: 425 Copynumber: 2.0 Consensus size: 424
30952129 TCTCTCCTCT
* *
30952139 TTTCTCTTCAATTTTCTTTCTTTTTCCCATGTGTGTTGCCGCCCAAGCCACCAAAATTCACCATT
1 TTTCTCTTCAACTTTCTTTCTTTTTCCCATGTGTGCTGCCGCCCAAGCCACCAAAATTCACCATT
*
30952204 AATTTCTCTTCTTTTTACAGTGGGTTCTTGCACCATTCTCTTCATCTTCTTGCTATCATTTTATC
66 AATTTCTCTTCTTTTTACAGCGGGTTCTTGCACCATTCTCTTCATCTTCTTGCTATCATTTTATC
* * * * **
30952269 ATAAAATTTCCAGCCTTAAATCTAAAATTTTATCAATCAAAATTGACCTCCATTGTTGCCCCAAA
131 ATAAAACTTCCAGCCTTAAATCTAAAATTTTAGCAATCAAAATCGACCTCCACTAATGCCCCAAA
* * * *
30952334 AGAAATCCATTGCCGCCCATATCTTCTTGCTTGAGTAGGTGTCATTTTCTTTCAATTTTCTTGAT
196 AGAAATCCATTACCACCCATATCTTCTTACTTGAATAGGTGTCATTTTCTTTCAATTTTCTTGAT
*
30952399 GGATCTTTCAATAAAATAACCAATTTTATAGATCTAGAATTGGGATAATATTTAAAGATTTAATA
261 GGATCTTTCAATAAAATAACCAATTTTATAGATCTAAAATTGGGATAATATTTAAAGATTTAATA
* *
30952464 ATTATTTTTCTAGCCTTTAAAGCAATTTTAAATGTTGTTTTAAATTAGCCCCAATTTGGCCACCG
326 ATTATATTTCTAGCCTTTAAAGCAATTTTAAATGTTGTTTTAAATCAGCCCCAATTTGGCCACCG
*
30952529 TTGGTGGTGGTGTGTGCGCCTAAGGGCTAGATTC
391 TTGGTGGTGGTGTGTGCGCCTAAAGGCTAGATTC
* *
30952563 TTTCTTTTCAACTTTCTTTCATTTTTCCCTTGTGTGCTGCCGCCCAAGCCACCAAAATTCACCAT
1 TTTCTCTTCAACTTTCTTTC-TTTTTCCCATGTGTGCTGCCGCCCAAGCCACCAAAATTCACCAT
* * * *
30952628 TAATTTCTTTTCTTTTTACAGCGTGTTCTTGCACCATTCTTTTCATCTTCTTGCTATCGTTTTAT
65 TAATTTCTCTTCTTTTTACAGCGGGTTCTTGCACCATTCTCTTCATCTTCTTGCTATCATTTTAT
* * *
30952693 CATAAAACTTCCAGCCTTAAATCTGAAATTTTAGCACTCAAAATCGACCTCCACTAATGCCCTGA
130 CATAAAACTTCCAGCCTTAAATCTAAAATTTTAGCAATCAAAATCGACCTCCACTAATGCCC-CA
* * * *
30952758 AAA-AAATCCATTACTACCCCTATTTTCTTACTTGAATAGGTGTCATTTTCTTTCATTTTTCTTG
194 AAAGAAATCCATTACCACCCATATCTTCTTACTTGAATAGGTGTCATTTTCTTTCAATTTTCTTG
* *
30952822 ATGGATCTTTCAATAAAATAACCAATTTTATAGATCTAAAATTGGGGTAATTTTTAAAGATTTAA
259 ATGGATCTTTCAATAAAATAACCAATTTTATAGATCTAAAATTGGGATAATATTTAAAGATTTAA
*
30952887 TAATTATATTTCTAGCCTTTAAAGCAATTTTAAATGTTGTTTTAAATCAGCCCCAATTTGTCCAC
324 TAATTATATTTCTAGCCTTTAAAGCAATTTTAAATGTTGTTTTAAATCAGCCCCAATTTGGCCAC
30952952 CGTTGGTGGTGGTGTGTGCGCCTAAAGGCTAGA
389 CGTTGGTGGTGGTGTGTGCGCCTAAAGGCTAGA
30952985 AAAGGGGTTT
Statistics
Matches: 387, Mismatches: 33, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
424 18 0.05
425 365 0.94
426 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (424 bp):
TTTCTCTTCAACTTTCTTTCTTTTTCCCATGTGTGCTGCCGCCCAAGCCACCAAAATTCACCATT
AATTTCTCTTCTTTTTACAGCGGGTTCTTGCACCATTCTCTTCATCTTCTTGCTATCATTTTATC
ATAAAACTTCCAGCCTTAAATCTAAAATTTTAGCAATCAAAATCGACCTCCACTAATGCCCCAAA
AGAAATCCATTACCACCCATATCTTCTTACTTGAATAGGTGTCATTTTCTTTCAATTTTCTTGAT
GGATCTTTCAATAAAATAACCAATTTTATAGATCTAAAATTGGGATAATATTTAAAGATTTAATA
ATTATATTTCTAGCCTTTAAAGCAATTTTAAATGTTGTTTTAAATCAGCCCCAATTTGGCCACCG
TTGGTGGTGGTGTGTGCGCCTAAAGGCTAGATTC
Found at i:30968650 original size:19 final size:19
Alignment explanation
Indices: 30968626--30968921 Score: 368
Period size: 19 Copynumber: 15.8 Consensus size: 19
30968616 AATCTTCAGG
30968626 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
30968645 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
30968664 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
30968683 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
30968702 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* ** *
30968721 AATATATAATATTAGATAT
1 GATATGCAATCTTAGATAT
30968740 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
30968759 GACATATAATC-T---TA-
1 GATATGCAATCTTAGATAT
30968773 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
30968792 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* * **
30968811 AACATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
30968830 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* ** *
30968849 AATATATAATATTAGATAT
1 GATATGCAATCTTAGATAT
30968868 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
** *
30968887 GATATATAATATTAGATAT
1 GATATGCAATCTTAGATAT
30968906 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
30968922 NNNNNNNNNN
Statistics
Matches: 230, Mismatches: 42, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
14 8 0.03
15 3 0.01
18 3 0.01
19 216 0.94
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:30968810 original size:14 final size:14
Alignment explanation
Indices: 30968740--30968792 Score: 61
Period size: 14 Copynumber: 3.4 Consensus size: 14
30968730 TATTAGATAT
30968740 GATATGCAATCTTA
1 GATATGCAATCTTA
30968754 GATATGACATATAATCTTA
1 GATATG-C----AATCTTA
30968773 GATATGCAATCTTA
1 GATATGCAATCTTA
30968787 GATATG
1 GATATG
30968793 ATATGCAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
18 1 0.03
19 13 0.38
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (14 bp):
GATATGCAATCTTA
Found at i:30970138 original size:19 final size:19
Alignment explanation
Indices: 30970114--30970224 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
30970104 AATCTTCAGG
30970114 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
30970133 GATATGCAATGTTAGATAT
1 GATATGCAATCTTAGATAT
* ** *
30970152 AATATATAATCATAGATAT
1 GATATGCAATCTTAGATAT
30970171 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
30970190 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
30970209 AATATGCAATCTTAGA
1 GATATGCAATCTTAGA
30970225 AGATATGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:30971578 original size:30 final size:30
Alignment explanation
Indices: 30971510--30971581 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
30971500 ATCGACGACC
**
30971510 ATCAAATTATGAAAAGGGATGGCTTCAGCA
1 ATCAAATTATGAAAAGGGATAACTTCAGCA
* * * *
30971540 ATCGAATTATGTAAAGGGATAACTTCGGCT
1 ATCAAATTATGAAAAGGGATAACTTCAGCA
30971570 ATCAAATTATGA
1 ATCAAATTATGA
30971582 TAGTGAAAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (30 bp):
ATCAAATTATGAAAAGGGATAACTTCAGCA
Found at i:30971682 original size:29 final size:30
Alignment explanation
Indices: 30971585--30971714 Score: 124
Period size: 30 Copynumber: 4.4 Consensus size: 30
30971575 ATTATGATAG
* *
30971585 TGAAAAGGGATGGTGACGACCATCAAATTA
1 TGAAAAGGGATGGTGACTACCATCAAAATA
* * ** *
30971615 TGAAAATGGATGGCTTTGGCT---ATTGAATTA
1 TGAAAAGGGATGG---TGACTACCATCAAAATA
* *
30971645 TGAATAGGGATGGTGACTACCATCAACA-A
1 TGAAAAGGGATGGTGACTACCATCAAAATA
30971674 TGAAAAGGGATGGTGACTACCATCAAAATA
1 TGAAAAGGGATGGTGACTACCATCAAAATA
30971704 TGAAAAGGGAT
1 TGAAAAGGGAT
30971715 AACTTCGACT
Statistics
Matches: 79, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
27 4 0.05
29 27 0.34
30 45 0.57
33 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (30 bp):
TGAAAAGGGATGGTGACTACCATCAAAATA
Found at i:30971756 original size:89 final size:89
Alignment explanation
Indices: 30971585--30971757 Score: 213
Period size: 89 Copynumber: 1.9 Consensus size: 89
30971575 ATTATGATAG
* * ** * * ** * *
30971585 TGAAAAGGGATGGTGACGACCATCAAATTATGAAAATGGATGGCTTTGGCTATTGAATTATGAAT
1 TGAAAAGGGATGGTGACGACCATCAAAATATGAAAAGGGATAACTTCGACTACCGAACTATGAAA
* *
30971650 AGGGATGGTGACTACCATCAACAA
66 AGGGATGGTAACAACCATCAACAA
*
30971674 TGAAAAGGGATGGTGACTACCATCAAAATATGAAAAGGGATAACTTCGACTACCGAACTATGAAA
1 TGAAAAGGGATGGTGACGACCATCAAAATATGAAAAGGGATAACTTCGACTACCGAACTATGAAA
30971739 ATGGG-TGGTAACAACCATC
66 A-GGGATGGTAACAACCATC
30971758 GTGATTTTTC
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
89 67 0.96
90 3 0.04
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.23
Consensus pattern (89 bp):
TGAAAAGGGATGGTGACGACCATCAAAATATGAAAAGGGATAACTTCGACTACCGAACTATGAAA
AGGGATGGTAACAACCATCAACAA
Found at i:30985783 original size:16 final size:17
Alignment explanation
Indices: 30985762--30985809 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
30985752 CTCATATCCA
30985762 ATTATAGTAAAAATAG-
1 ATTATAGTAAAAATAGC
*
30985778 ATTATAGTATTACAA-AGC
1 ATTATAGTA--AAAATAGC
30985796 ATTATAGTAAAAAT
1 ATTATAGTAAAAAT
30985810 GTAACTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
16 12 0.46
17 2 0.08
18 12 0.46
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.33
Consensus pattern (17 bp):
ATTATAGTAAAAATAGC
Found at i:30987030 original size:60 final size:59
Alignment explanation
Indices: 30986966--30987082 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 59
30986956 AAGCCTACTA
* *
30986966 GGCACAGAGCCTAAATAACACCGGCATAAAGCCTGCTAGGCACAAAGCCTAAATAACACC
1 GGCACAAAGCCTAAATAACACCGGCAT-AAGCCTGCTAGGCACAAAGCATAAATAACACC
* * * * *
30987026 GGCACAAAGCCTGAATAACATCGGCATAAGCCTGCTAGGTAGAAAGCATGAATAACA
1 GGCACAAAGCCTAAATAACACCGGCATAAGCCTGCTAGGCACAAAGCATAAATAACA
30987083 TTATACTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 26 0.52
60 24 0.48
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (59 bp):
GGCACAAAGCCTAAATAACACCGGCATAAGCCTGCTAGGCACAAAGCATAAATAACACC
Found at i:30987038 original size:38 final size:38
Alignment explanation
Indices: 30986929--30987038 Score: 166
Period size: 38 Copynumber: 2.9 Consensus size: 38
30986919 TAATACACCA
* * * *
30986929 GCACAAAGCCTGAATAACACTGACACAAAGCCTACTAG
1 GCACAAAGCCTAAATAACACCGGCACAAAGCCTGCTAG
* *
30986967 GCACAGAGCCTAAATAACACCGGCATAAAGCCTGCTAG
1 GCACAAAGCCTAAATAACACCGGCACAAAGCCTGCTAG
30987005 GCACAAAGCCTAAATAACACCGGCACAAAGCCTG
1 GCACAAAGCCTAAATAACACCGGCACAAAGCCTG
30987039 AATAACATCG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.40, C:0.30, G:0.18, T:0.12
Consensus pattern (38 bp):
GCACAAAGCCTAAATAACACCGGCACAAAGCCTGCTAG
Found at i:30987058 original size:21 final size:22
Alignment explanation
Indices: 30986923--30987059 Score: 84
Period size: 22 Copynumber: 6.8 Consensus size: 22
30986913 AAATTTTAAT
*
30986923 ACACCAGCACAAAGCCTGAATA
1 ACACCGGCACAAAGCCTGAATA
* * *
30986945 ACACTGACACAAAGCCT-ACT-
1 ACACCGGCACAAAGCCTGAATA
* *
30986965 --A--GGCACAGAGCCTAAATA
1 ACACCGGCACAAAGCCTGAATA
* *
30986983 ACACCGGCATAAAGCCTG-CT-
1 ACACCGGCACAAAGCCTGAATA
*
30987003 --A--GGCACAAAGCCTAAATA
1 ACACCGGCACAAAGCCTGAATA
30987021 ACACCGGCACAAAGCCTGAATA
1 ACACCGGCACAAAGCCTGAATA
* *
30987043 ACATCGGCA-TAAGCCTG
1 ACACCGGCACAAAGCCTG
30987060 CTAGGTAGAA
Statistics
Matches: 86, Mismatches: 17, Indels: 25
0.67 0.13 0.20
Matches are distributed among these distances:
16 21 0.24
17 3 0.03
18 2 0.02
20 2 0.02
21 10 0.12
22 48 0.56
ACGTcount: A:0.40, C:0.30, G:0.18, T:0.12
Consensus pattern (22 bp):
ACACCGGCACAAAGCCTGAATA
Found at i:30989187 original size:18 final size:19
Alignment explanation
Indices: 30989150--30989187 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
30989140 AAAGTTAGGA
* *
30989150 AAAAGATTATATTCTTTCC
1 AAAAGAATATAATCTTTCC
30989169 AAAAGAATATAAT-TTTCC
1 AAAAGAATATAATCTTTCC
30989187 A
1 A
30989188 TGTCCTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (19 bp):
AAAAGAATATAATCTTTCC
Found at i:30994432 original size:1 final size:1
Alignment explanation
Indices: 30994426--30994455 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
30994416 ACACACACAC
30994426 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30994456 CCTATTACGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30995390 original size:16 final size:16
Alignment explanation
Indices: 30995356--30995390 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30995346 AGTATTACGA
*
30995356 TAACATTTCAAACATT
1 TAACATTTCAAACAAT
*
30995372 TAACATTTCATACAAT
1 TAACATTTCAAACAAT
30995388 TAA
1 TAA
30995391 ATATTCAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (16 bp):
TAACATTTCAAACAAT
Found at i:30996847 original size:69 final size:68
Alignment explanation
Indices: 30996724--30996970 Score: 273
Period size: 69 Copynumber: 3.6 Consensus size: 68
30996714 ATATAAAGAG
* * * * *
30996724 TGTGCCCAACACTAGTCAGATAAATTGAGAGAAGTTGCACCCAGCGCTAGTCGGATAACCGACGA
1 TGTG-CCAGCACTAGTAAGATAAACTGACAGAAGTTGCACCTAGCGCTAGTCGGATAACCGACGA
30996789 TGGT
65 TGGT
* * * * * *
30996793 TCTGCTCAGCACTAGTAAGATGAACTAACAGATGTTGCACCTAGCACTAGTCGGATAACCGACAA
1 TGTGC-CAGCACTAGTAAGATAAACTGACAGAAGTTGCACCTAGCGCTAGTCGGATAACCGACGA
30996858 TGGT
65 TGGT
* * **
30996862 TGTGCCCAGCACTAGTCAA-ATAAACTGACAAAAGTTG-AGCCTAGCGCTAGTCGAATAACTAAC
1 TGTG-CCAGCACTAGT-AAGATAAACTGACAGAAGTTGCA-CCTAGCGCTAGTCGGATAACCGAC
*
30996925 GATAGT
63 GATGGT
*
30996931 TGTGCCTAGCACTAGTTAGATAAACTGACAGAAGTTGCAC
1 TGTGCC-AGCACTAGTAAGATAAACTGACAGAAGTTGCAC
30996971 TGGTTGTGCC
Statistics
Matches: 147, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
68 5 0.03
69 138 0.94
70 4 0.03
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (68 bp):
TGTGCCAGCACTAGTAAGATAAACTGACAGAAGTTGCACCTAGCGCTAGTCGGATAACCGACGAT
GGT
Found at i:30996912 original size:35 final size:35
Alignment explanation
Indices: 30996832--30996967 Score: 114
Period size: 34 Copynumber: 3.9 Consensus size: 35
30996822 AGATGTTGCA
** * ** *
30996832 CCTAGCACTAGTCGGAT-AACCGACAATGGTTGTG
1 CCTAGCACTAGTCAAATAAACTGACAAAAGTTGAG
*
30996866 CCCAGCACTAGTCAAATAAACTGACAAAAGTTGAG
1 CCTAGCACTAGTCAAATAAACTGACAAAAGTTGAG
* * * * * *
30996901 CCTAGCGCTAGTCGAAT-AACTAACGATAGTTGTG
1 CCTAGCACTAGTCAAATAAACTGACAAAAGTTGAG
* * *
30996935 CCTAGCACTAGTTAGATAAACTGACAGAAGTTG
1 CCTAGCACTAGTCAAATAAACTGACAAAAGTTG
30996968 CACTGGTTGT
Statistics
Matches: 78, Mismatches: 22, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
34 40 0.51
35 38 0.49
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (35 bp):
CCTAGCACTAGTCAAATAAACTGACAAAAGTTGAG
Found at i:30996995 original size:44 final size:44
Alignment explanation
Indices: 30996929--30997014 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
30996919 ACTAACGATA
*
30996929 GTTGTGCCTAGCACTAGTTAGATAAACTGACAGAAGTTGCACTG
1 GTTGTGCCCAGCACTAGTTAGATAAACTGACAGAAGTTGCACTG
* *
30996973 GTTGTGCCCAGCACT-GTGTAGATAAATTGATAGAAGTTGCAC
1 GTTGTGCCCAGCACTAGT-TAGATAAACTGACAGAAGTTGCAC
30997015 CAAGCGCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 2 0.05
44 36 0.95
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (44 bp):
GTTGTGCCCAGCACTAGTTAGATAAACTGACAGAAGTTGCACTG
Found at i:30997070 original size:113 final size:113
Alignment explanation
Indices: 30996858--30997080 Score: 270
Period size: 113 Copynumber: 2.0 Consensus size: 113
30996848 TAACCGACAA
* *
30996858 TGGTTGTGCCCAGCACTAGTCAAATAAACTGACAAAAGTTGAGCCTAGCGCTAGTCGAATAACTA
1 TGGTTGTGCCCAGCACTAGTCAAATAAACTGACAAAAGTTGAGCCAAGCGCTAGTCGAATAACCA
* * * * *
30996923 ACGATAGTTGTGCCTAGCACTAGTTAGATAAACTGACAGAAGTTGCAC
66 ACGATAGTTGTGCCCAACACCAGTCAGAGAAACTGACAGAAGTTGCAC
* * * * * *
30996971 TGGTTGTGCCCAGCACT-GTGTAGATAAATTGATAGAAGTTGCA-CCAAGCGCTAGTCGGATAAC
1 TGGTTGTGCCCAGCACTAGT-CAAATAAACTGACAAAAGTTG-AGCCAAGCGCTAGTCGAATAAC
* * *
30997034 CGACGATGGTTGTGCCCAACACCAGTCAGAGGAACTGACAGAAGTTG
64 CAACGATAGTTGTGCCCAACACCAGTCAGAGAAACTGACAGAAGTTG
30997081 TGCCCAGCGC
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
112 2 0.02
113 89 0.97
114 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (113 bp):
TGGTTGTGCCCAGCACTAGTCAAATAAACTGACAAAAGTTGAGCCAAGCGCTAGTCGAATAACCA
ACGATAGTTGTGCCCAACACCAGTCAGAGAAACTGACAGAAGTTGCAC
Found at i:30997090 original size:69 final size:69
Alignment explanation
Indices: 30997004--30997166 Score: 236
Period size: 69 Copynumber: 2.4 Consensus size: 69
30996994 ATAAATTGAT
* * *
30997004 AGAAGTTGCACCAAGCGCTAGTCGGATAACCGACGATGGTTGTGCCCAACACCAGTCAGAGGAAC
1 AGAAGTTGCGCCCAGCGCTAGTCGGATAACCGACAATGGTTGTGCCCAACACCAGTCAGAGGAAC
*
30997069 TGAC
66 TAAC
* * * * *
30997073 AGAAGTTGTGCCCAGCGCTAGTCGGATAACCGACAATGGTTGTGCCCAGCACTAGTTAGATGAAC
1 AGAAGTTGCGCCCAGCGCTAGTCGGATAACCGACAATGGTTGTGCCCAACACCAGTCAGAGGAAC
30997138 TAAC
66 TAAC
*
30997142 AGAAGTTGCGCCCAGCGTTAGTCGG
1 AGAAGTTGCGCCCAGCGCTAGTCGG
30997167 GTGAACCAAC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 83 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (69 bp):
AGAAGTTGCGCCCAGCGCTAGTCGGATAACCGACAATGGTTGTGCCCAACACCAGTCAGAGGAAC
TAAC
Found at i:30997233 original size:20 final size:20
Alignment explanation
Indices: 30997208--30997255 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
30997198 AGTCCATAAA
30997208 ATCACATTTCACAACCCAAT
1 ATCACATTTCACAACCCAAT
* *
30997228 ATCACATTTCATAACTCAAT
1 ATCACATTTCACAACCCAAT
30997248 ATCACATT
1 ATCACATT
30997256 CACTTCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (20 bp):
ATCACATTTCACAACCCAAT
Found at i:31001527 original size:18 final size:18
Alignment explanation
Indices: 31001504--31001539 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
31001494 GCTGCAAGGA
31001504 TAGGTTTTTGAATAATAG
1 TAGGTTTTTGAATAATAG
31001522 TAGGTTTTTGAATAATAG
1 TAGGTTTTTGAATAATAG
31001540 CAGGATATAT
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (18 bp):
TAGGTTTTTGAATAATAG
Found at i:31003298 original size:23 final size:24
Alignment explanation
Indices: 31003271--31003317 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
31003261 ATTCCATGTT
31003271 CATATAGCAT-TATC-TCATATTTC
1 CATATAGCATGTATCATCAT-TTTC
*
31003294 CATATATCATGTATCATCATTTTC
1 CATATAGCATGTATCATCATTTTC
31003318 ATGTATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 8 0.38
25 4 0.19
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (24 bp):
CATATAGCATGTATCATCATTTTC
Found at i:31003539 original size:26 final size:25
Alignment explanation
Indices: 31003510--31003565 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
31003500 ATCCTCTCTC
31003510 GAGCCATATAA-AAGGAAGCTCACAAA
1 GAGCCAT-TAACAA-GAAGCTCACAAA
31003536 GAGCCATTAATCAAGAAGCTCACAAA
1 GAGCCATTAA-CAAGAAGCTCACAAA
31003562 GAGC
1 GAGC
31003566 ATTTCAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 3 0.11
26 23 0.82
27 2 0.07
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (25 bp):
GAGCCATTAACAAGAAGCTCACAAA
Found at i:31003847 original size:64 final size:64
Alignment explanation
Indices: 31003746--31003866 Score: 190
Period size: 64 Copynumber: 1.9 Consensus size: 64
31003736 GAGCCATATT
* *
31003746 AGGACGCTCACAAAGAACTGCGGTATGTCCGCAACACATGCAAGACCACTACCGATCATATAAC
1 AGGACGCTCACAAAGAACTACGGTATGTCCGCAACACATCCAAGACCACTACCGATCATATAAC
* *
31003810 AGGACGCTCACAAA-AAGCTATGGTATGTCCGCAACACATCCAGGACCACTACCGATC
1 AGGACGCTCACAAAGAA-CTACGGTATGTCCGCAACACATCCAAGACCACTACCGATC
31003867 GGGATGCTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 2 0.04
64 50 0.96
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.16
Consensus pattern (64 bp):
AGGACGCTCACAAAGAACTACGGTATGTCCGCAACACATCCAAGACCACTACCGATCATATAAC
Found at i:31010359 original size:26 final size:25
Alignment explanation
Indices: 31010330--31010386 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
31010320 ATCCTCTCTC
*
31010330 GAGCCATATAA-AAGGAAGCTTACAAA
1 GAGCCAT-TAACAA-GAAGCTCACAAA
31010356 GAGCCATTAATCAAGAAGCTCACAAA
1 GAGCCATTAA-CAAGAAGCTCACAAA
31010382 GAGCC
1 GAGCC
31010387 TTTCAGGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 3 0.11
26 23 0.82
27 2 0.07
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (25 bp):
GAGCCATTAACAAGAAGCTCACAAA
Found at i:31010466 original size:26 final size:26
Alignment explanation
Indices: 31010417--31010503 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 26
31010407 ATGTATAACG
* **
31010417 GGAAGCTCACACAGAG-CCATAATCA
1 GGAAGCTCACAAAGAGTCTTTAATCA
* *
31010442 GGAAGTTTACAAAGAAGT-TTTAATCA
1 GGAAGCTCACAAAG-AGTCTTTAATCA
* *
31010468 GGAAGCTCACAAAGAGTCTTTAAACG
1 GGAAGCTCACAAAGAGTCTTTAATCA
31010494 GGAAGCTCAC
1 GGAAGCTCAC
31010504 GAAAAGCCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
25 14 0.28
26 36 0.72
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGTCTTTAATCA
Found at i:31014100 original size:76 final size:76
Alignment explanation
Indices: 31014002--31014169 Score: 275
Period size: 76 Copynumber: 2.2 Consensus size: 76
31013992 ACGCCCTGCG
* * *
31014002 CTAGCCAGATGAACTGATAGATATAAAGAGTGTGCGTAGCTCTAGTTAGATAAACTGACAGAAGT
1 CTAGTCAGATGAACCGATAGATATAAAGAGTGTGCGTAGCTCTAGTAAGATAAACTGACAGAAGT
31014067 TGCACCCAGTA
66 TGCACCCAGTA
*
31014078 CTAGTCAGATGAACCGATAGATATAAAGAGTGTGCGTAGCTCTAGTAAGATAAACTGACAGAATT
1 CTAGTCAGATGAACCGATAGATATAAAGAGTGTGCGTAGCTCTAGTAAGATAAACTGACAGAAGT
*
31014143 TGCACCCAGTG
66 TGCACCCAGTA
*
31014154 CTAGTCGGAT-AACCGA
1 CTAGTCAGATGAACCGA
31014170 CGATGGTTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
75 6 0.07
76 80 0.93
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (76 bp):
CTAGTCAGATGAACCGATAGATATAAAGAGTGTGCGTAGCTCTAGTAAGATAAACTGACAGAAGT
TGCACCCAGTA
Found at i:31014220 original size:35 final size:35
Alignment explanation
Indices: 31014119--31014447 Score: 194
Period size: 35 Copynumber: 9.5 Consensus size: 35
31014109 GTGCGTAGCT
* * * * **
31014119 CTAGTAAGATAAACTGACAGAATTTGCACCCAGTG
1 CTAGTCAGATGAACTGACAGAAGTTGCGCCCAGCA
* * * *
31014154 CTAGTCGGAT-AACCGAC-GATGGTTGTGCCCAGCA
1 CTAGTCAGATGAACTGACAGA-AGTTGCGCCCAGCA
* *
31014188 CTAGTCAGATGAACTGATAGAAGTTGCGCCCAGCG
1 CTAGTCAGATGAACTGACAGAAGTTGCGCCCAGCA
* * *
31014223 CTAGTCAGAT-AA-TCGA-TGATAGTTGGGCCTAGCA
1 CTAGTCAGATGAACT-GACAGA-AGTTGCGCCCAGCA
* * *
31014257 CTAGTCAGATAAACTAACAGAAGTTGCGCCCAGCG
1 CTAGTCAGATGAACTGACAGAAGTTGCGCCCAGCA
* * * *
31014292 CTAGTCGGAT-AACCGAC-GATGGTTGAGCCCAGCA
1 CTAGTCAGATGAACTGACAGA-AGTTGCGCCCAGCA
* * * * *
31014326 CTAGTCATATGAACTAACAGAAGTTGCTCCTAGCG
1 CTAGTCAGATGAACTGACAGAAGTTGCGCCCAGCA
* * * * * *
31014361 CTAATCGGAT-AACCGACATG--GTTGTGCCTAACA
1 CTAGTCAGATGAACTGACA-GAAGTTGCGCCCAGCA
* *
31014394 CTAGTCAGATGAACTAACAGAAGTTGAGCCCAAG-A
1 CTAGTCAGATGAACTGACAGAAGTTGCGCCC-AGCA
* *
31014429 CTAGTCGGATGAACCGACA
1 CTAGTCAGATGAACTGACA
31014448 ATATCAATTA
Statistics
Matches: 220, Mismatches: 58, Indels: 32
0.71 0.19 0.10
Matches are distributed among these distances:
33 25 0.11
34 84 0.38
35 103 0.47
36 8 0.04
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (35 bp):
CTAGTCAGATGAACTGACAGAAGTTGCGCCCAGCA
Found at i:31014220 original size:69 final size:69
Alignment explanation
Indices: 31014119--31014446 Score: 408
Period size: 69 Copynumber: 4.8 Consensus size: 69
31014109 GTGCGTAGCT
* * * * * *
31014119 CTAGTAAGATAAACTGACAGAATTTGCACCCAGTGCTAGTCGGATAACCGACGATGGTTGTGCCC
1 CTAGTCAGATGAACTAACAGAAGTTGCGCCCAGCGCTAGTCGGATAACCGACGATGGTTGTGCCC
31014184 AGCA
66 AGCA
* * * * * * * *
31014188 CTAGTCAGATGAACTGATAGAAGTTGCGCCCAGCGCTAGTCAGATAATCGATGATAGTTGGGCCT
1 CTAGTCAGATGAACTAACAGAAGTTGCGCCCAGCGCTAGTCGGATAACCGACGATGGTTGTGCCC
31014253 AGCA
66 AGCA
* *
31014257 CTAGTCAGATAAACTAACAGAAGTTGCGCCCAGCGCTAGTCGGATAACCGACGATGGTTGAGCCC
1 CTAGTCAGATGAACTAACAGAAGTTGCGCCCAGCGCTAGTCGGATAACCGACGATGGTTGTGCCC
31014322 AGCA
66 AGCA
* * * * *
31014326 CTAGTCATATGAACTAACAGAAGTTGCTCCTAGCGCTAATCGGATAACCGAC-ATGGTTGTGCCT
1 CTAGTCAGATGAACTAACAGAAGTTGCGCCCAGCGCTAGTCGGATAACCGACGATGGTTGTGCCC
*
31014390 AACA
66 AGCA
* *
31014394 CTAGTCAGATGAACTAACAGAAGTTGAGCCCAAG-ACTAGTCGGATGAACCGAC
1 CTAGTCAGATGAACTAACAGAAGTTGCGCCC-AGCGCTAGTCGGAT-AACCGAC
31014447 AATATCAATT
Statistics
Matches: 222, Mismatches: 35, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
68 49 0.22
69 173 0.78
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (69 bp):
CTAGTCAGATGAACTAACAGAAGTTGCGCCCAGCGCTAGTCGGATAACCGACGATGGTTGTGCCC
AGCA
Found at i:31014517 original size:20 final size:20
Alignment explanation
Indices: 31014488--31014525 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31014478 ATCGTATGTC
31014488 ATAACCCAATATCACATTTT
1 ATAACCCAATATCACATTTT
* *
31014508 ATAACTCAATATTACATT
1 ATAACCCAATATCACATT
31014526 CACTTCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAACCCAATATCACATTTT
Found at i:31019640 original size:762 final size:759
Alignment explanation
Indices: 31017475--31019750 Score: 3239
Period size: 751 Copynumber: 3.0 Consensus size: 759
31017465 TTTACTATTT
* *
31017475 CTGCTTGAGCCACCCAGGTGGTGGAGCTTGGATGGGTTTCGAATTCTGTGGGAAATCTGATAGAA
1 CTGCTTGAGCCACCCAGGTGGT-GAGTTTGGATGGGTTTCGAATTCTATGGGAAATCTGATAGAA
* *
31017540 GTGAGTACCTAATATGGTGGAGTTAGTAGGGGAAATGGTTAGTGGTTTTTTTAAAAAAAAAGAAA
65 GTGGGTACCTAATTTGGTGGAGTTAGTAGGGGAAATGGTTAGTGGTTTTTTT----AAAAAGAAA
*
31017605 ATTTAATTA--TTTTTTTGAAATCCCCAAAAATTCTCTTTTATTTTCTAACGTCTAACGTTTTCT
126 ATTTAATTATTTTTTTTTGAAATCCCCAAAAATTCTCTTTTCTTTTCTAACGTCTAACGTTTTCT
* * *
31017668 TC-CTCCATTCTTAACCTTTGCTTTACAATTATTTCTTCTTCACACCATATTATATGTTTCTTTC
191 TCTC-CCATTCTTCATCTTTGCTTTTCAATTATTTCTTCTTCACACCATATTATATGTTTCTTTC
* * *
31017732 TTTTTGTTCCTTTCCATTTTGCTTTTACTTCTGTTTCAGTTCCCATCTTCTACACAGTCAATTGT
255 TTTTTGTTCCTTTCCCTTTT-CTTTTGCTTCTGTTTCAGTTCCCATCTTCTACACAGTCGATTGT
* * *
31017797 CGTACCTTGTTGGTAAGTGGTTGTGGTGTTTGTGTCAATGGTGGAATTATTTCCTTGTTGGTATA
319 CGTACCTTGTTGGTAAGTGGTTGTGGTGTTTTTGTCAGTGGTGGAATTATTTCCTTGTTGGTATG
**
31017862 GAGAATTATTATGTTCAGGTTGGTTGTAATTGTGGCGTAAGGTTGTTTGATTGCATTCTTTTCTG
384 GAGAATTATTATGTTCAGGTTGGTTGTAATTGTGGCGTAAGGTTGTTTGATTGGGTTCTTTTCTG
* * * * * *
31017927 TTATTAGGAGAAGATCGTGAAGCATTC-GACAACCCACAAGCAAATTAAATGTGGGTGATGACTG
449 TTATTAGGAGAAGACCGTGAAGCTTTCAG-CGACCCACAAGCAAATTAAGTGTGGGTGGTGGCTG
* *
31017991 TTCGTTTGGGTAAGTGATCGAACACCC-AAAAGGGGTTGAATTTCGGTTTAGTAAGGTGTATGTT
513 TTCGTTTGGGTAAGTGATCGAACACCCAAAAAGGGGTAGAATTTTGGTTTAGTAAGGTGTATGTT
** * *
31018055 AGTGTTTTTAATCATAAGTGTTAATTGGAATTAGTAAATTATTGCTAATTTGGAGGATTAATTAA
578 AGCATTTTTAATCATAAGTGTTAATTGGAATTAGTAAATCATTGCTAATTTGGAGGATTAATTGA
* * *
31018120 TGTTTTTAGGTTCTAGAAGCCTCATGGATGGATTCGCATAAAAAAAGCCAAGGTGTGTAACAAAA
643 TGTTTTTAGGTTCTGGAAGCCTCGTGG-TGGATTCGCATAAAAAAAGCCAAGGTGTGTAACGAAA
* * * *
31018185 ACTAGAAAAATTGA-GAACGGCTAAAAGCCGAAAAATTGGACTGTTGACGCCAC
707 ACTAGAAAAA-TCACGAATGGCTGAAAGCCGAAAAATTGGACTGTCGACGCCAC
* ** * *
31018238 CTCCTTGAGCTGCCCAGGTGGTGAAGTTTGGATAGGTTTCGAATTATATGGGAAATCTGATAGAA
1 CTGCTTGAGCCACCCAGGTGGTG-AGTTTGGATGGGTTTCGAATTCTATGGGAAATCTGATAGAA
* * *
31018303 GTGGGCACCTAATTTGGTGGAGTTAGTGGGGGAAATGGTTAATGGTTTTCTTTAAAAAGAAAATT
65 GTGGGTACCTAATTTGGTGGAGTTAGTAGGGGAAATGGTTAGTGGTTTT-TTTAAAAAGAAAATT
* * ** * *
31018368 TAGTAATTATTTTTTTGAAAT-CCTTAAAATT-TCTGTTCTTGTT-TTACGTCTAACGTTTTCTT
129 TAATTATT-TTTTTTTGAAATCCCCAAAAATTCTCTTTTCTT-TTCTAACGTCTAACGTTTTCTT
* * *
31018430 -TCCCCATTCTTCATCTTTGCTTTTCAATTTTTTCTTCTTTACACCATATTATTTGTTTCTTTCT
192 CT-CCCATTCTTCATCTTTGCTTTTCAATTATTTCTTCTTCACACCATATTATATGTTTCTTTCT
* * * *
31018494 TTTTGTTTCTTT-CC----CTTTTGCTTTTGTTTCAG-T----TCTTCTACATAGTCGATTGTTG
256 TTTTGTTCCTTTCCCTTTTCTTTTGCTTCTGTTTCAGTTCCCATCTTCTACACAGTCGATTGTCG
*
31018549 TACCTTGTTGGTAAGTGGTTGTGGTGTTTGTTGTCAGTGGTGGAATTATTTCCTTATTGGTATGG
321 TACCTTGTTGGTAAGTGGTTGTGGTGTTT-TTGTCAGTGGTGGAATTATTTCCTTGTTGGTATGG
* *
31018614 AGAATTATTATGTTCAGGTTGGTTGTAATTATGGTGTAAGGTTGTTTGATTGGGTT-TTTTCTGT
385 AGAATTATTATGTTCAGGTTGGTTGTAATTGTGGCGTAAGGTTGTTTGATTGGGTTCTTTTCTGT
* * * * * *
31018678 TACTAGGAGAAGACCGTGAAGTTTTCAGTGACCCACTAGCAAATTAAGTATGGGTGGTGGTTGTT
450 TATTAGGAGAAGACCGTGAAGCTTTCAGCGACCCACAAGCAAATTAAGTGTGGGTGGTGGCTGTT
* * *
31018743 CGTTTGGGCAAGTGATCGAACACCCAAAAAAGGGTAGAATTTTGGTTAAGTAAGGTGTATGTTAG
515 CGTTTGGGTAAGTGATCGAACACCCAAAAAGGGGTAGAATTTTGGTTTAGTAAGGTGTATGTTAG
* *
31018808 CATTTTTAATCATAAGTGTTAATTGGAATTAGTAAATCATTGATAATTTGGAGGATTAATTGACG
580 CATTTTTAATCATAAGTGTTAATTGGAATTAGTAAATCATTGCTAATTTGGAGGATTAATTGATG
*
31018873 TTTTTAGGTTCTGGAAGCCTCGTGAGTGGATTCGGATAAAAAAAGCCAAGGTGTGTAACGAAAAC
645 TTTTTAGGTTCTGGAAGCCTCGTG-GTGGATTCGCATAAAAAAAGCCAAGGTGTGTAACGAAAAC
* *
31018938 TAGAAAAATCACGAATGGCTGAAAGCCAAAAAATTGGATTGTCGACGCCAC
709 TAGAAAAATCACGAATGGCTGAAAGCCGAAAAATTGGACTGTCGACGCCAC
* * *
31018989 CTGCTTGAGCCACCTAGGTGGTAGAGTTTGCATGGGTTTCGAATTCTATGGGAAATCTAATAGAA
1 CTGCTTGAGCCACCCAGGTGGT-GAGTTTGGATGGGTTTCGAATTCTATGGGAAATCTGATAGAA
* * *
31019054 GTGGGTACCTAATTTGGTGAAGTTAGTAGGGGAAATGGTTAGTGGTTTTTTTAGAAAAGTAATTT
65 GTGGGTACCTAATTTGGTGGAGTTAGTAGGGGAAATGGTTAGTGGTTTTTTTA-AAAAGAAAATT
* * *
31019119 TAATTATTTTTTTTTGAAATCCCCAAAAATTCACTTTTCTTTTCTGACGTCTAATGTTTTCTTCT
129 TAATTATTTTTTTTTGAAATCCCCAAAAATTCTCTTTTCTTTTCTAACGTCTAACGTTTTCTTCT
** *
31019184 CCCATTCTTCATCTTCACTTTTCAATTATTCCTTCTTCACACCATATTATATGTTT-TTTCTTTT
194 CCCATTCTTCATCTTTGCTTTTCAATTATTTCTTCTTCACACCATATTATATGTTTCTTTCTTTT
31019248 TGTTCCTTTCCCTTTTTCTTTTGCTTCTGTTTCAGTTCCCATCTTCTACACAGTCGATTGTCGTA
259 TGTTCCTTTCCC-TTTTCTTTTGCTTCTGTTTCAGTTCCCATCTTCTACACAGTCGATTGTCGTA
* * *
31019313 GCTTGTTAGTAAGTGGTTTTGGTGTTTTTGTCAGTGGTGGAATTATTTCCTTGTTGGTATGGAGA
323 CCTTGTTGGTAAGTGGTTGTGGTGTTTTTGTCAGTGGTGGAATTATTTCCTTGTTGGTATGGAGA
* * *
31019378 ATTATTATGTTTAGGTTGGTTGTAATTGTGACGTAAGATTGTTTGATTGGGTTCTTTTCTGTTAT
388 ATTATTATGTTCAGGTTGGTTGTAATTGTGGCGTAAGGTTGTTTGATTGGGTTCTTTTCTGTTAT
* * * *
31019443 TAGGAGAAAACCATGAAGCTTTCAGCGACCTACCAGCAAATTAAGTGTGGGTGGTGGCTGTTCGT
453 TAGGAGAAGACCGTGAAGCTTTCAGCGACCCACAAGCAAATTAAGTGTGGGTGGTGGCTGTTCGT
*
31019508 TTGGGTAAGTGATCGAACACCCAAAAAGGGGTAGAATTTTGGTTTAGTAAGGTGTATGTTTGCAT
518 TTGGGTAAGTGATCGAACACCCAAAAAGGGGTAGAATTTTGGTTTAGTAAGGTGTATGTTAGCAT
* * * *
31019573 TTTTAATCATAAGTATTACTTGGAATTAATAAATCATTGCTAATTTAGATGG-TTAATTGATGTT
583 TTTTAATCATAAGTGTTAATTGGAATTAGTAAATCATTGCTAATTTGGA-GGATTAATTGATGTT
* *
31019637 TTTAGGTTTTGGAAGCCTCGTGGGTGGATTCGCATAAAAAAAACCAAGGTGTGTAACGAAAACTA
647 TTTAGGTTCTGGAAGCCTCGT-GGTGGATTCGCATAAAAAAAGCCAAGGTGTGTAACGAAAACTA
* * * *
31019702 GAAAAATCACAAATGGCTGAAAGCTGAAAAACTGGACTGTCGACACCAC
711 GAAAAATCACGAATGGCTGAAAGCCGAAAAATTGGACTGTCGACGCCAC
31019751 ATGACCGTGT
Statistics
Matches: 1338, Mismatches: 142, Indels: 67
0.86 0.09 0.04
Matches are distributed among these distances:
750 149 0.11
751 420 0.31
752 78 0.06
753 1 0.00
754 1 0.00
755 16 0.01
757 17 0.01
758 1 0.00
760 17 0.01
761 176 0.13
762 344 0.26
763 115 0.09
764 3 0.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (759 bp):
CTGCTTGAGCCACCCAGGTGGTGAGTTTGGATGGGTTTCGAATTCTATGGGAAATCTGATAGAAG
TGGGTACCTAATTTGGTGGAGTTAGTAGGGGAAATGGTTAGTGGTTTTTTTAAAAAGAAAATTTA
ATTATTTTTTTTTGAAATCCCCAAAAATTCTCTTTTCTTTTCTAACGTCTAACGTTTTCTTCTCC
CATTCTTCATCTTTGCTTTTCAATTATTTCTTCTTCACACCATATTATATGTTTCTTTCTTTTTG
TTCCTTTCCCTTTTCTTTTGCTTCTGTTTCAGTTCCCATCTTCTACACAGTCGATTGTCGTACCT
TGTTGGTAAGTGGTTGTGGTGTTTTTGTCAGTGGTGGAATTATTTCCTTGTTGGTATGGAGAATT
ATTATGTTCAGGTTGGTTGTAATTGTGGCGTAAGGTTGTTTGATTGGGTTCTTTTCTGTTATTAG
GAGAAGACCGTGAAGCTTTCAGCGACCCACAAGCAAATTAAGTGTGGGTGGTGGCTGTTCGTTTG
GGTAAGTGATCGAACACCCAAAAAGGGGTAGAATTTTGGTTTAGTAAGGTGTATGTTAGCATTTT
TAATCATAAGTGTTAATTGGAATTAGTAAATCATTGCTAATTTGGAGGATTAATTGATGTTTTTA
GGTTCTGGAAGCCTCGTGGTGGATTCGCATAAAAAAAGCCAAGGTGTGTAACGAAAACTAGAAAA
ATCACGAATGGCTGAAAGCCGAAAAATTGGACTGTCGACGCCAC
Found at i:31022205 original size:25 final size:26
Alignment explanation
Indices: 31022171--31022242 Score: 92
Period size: 27 Copynumber: 2.8 Consensus size: 26
31022161 TCTTGTACAT
31022171 GTATGCTCACACAAGCTGTG-AATCG
1 GTATGCTCACACAAGCTGTGAAATCG
* * *
31022196 GTATGCTCACACGAGCTATGAAAATGG
1 GTATGCTCACACAAGCTGTG-AAATCG
*
31022223 GTCTGCTCACACAAGCTGTG
1 GTATGCTCACACAAGCTGTG
31022243 GGTCAAAACG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 18 0.46
27 21 0.54
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (26 bp):
GTATGCTCACACAAGCTGTGAAATCG
Found at i:31023307 original size:22 final size:23
Alignment explanation
Indices: 31023282--31023330 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
31023272 CATACTTTGA
*
31023282 TTTTT-TTAGATGT-TTCTGTTGT
1 TTTTTCTTA-ATGTATTCTGGTGT
*
31023304 TTTTTCTTAATGTATTGTGGTGT
1 TTTTTCTTAATGTATTCTGGTGT
31023327 TTTT
1 TTTT
31023331 ATTTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.10, C:0.04, G:0.18, T:0.67
Consensus pattern (23 bp):
TTTTTCTTAATGTATTCTGGTGT
Found at i:31026924 original size:17 final size:18
Alignment explanation
Indices: 31026902--31026939 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
31026892 TTTGGGCCGA
*
31026902 GTGGG-CCACACGGGCGT
1 GTGGGCCCACACAGGCGT
*
31026919 GTGGGCCCACATAGGCGT
1 GTGGGCCCACACAGGCGT
31026937 GTG
1 GTG
31026940 AGTCCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.13, C:0.26, G:0.45, T:0.16
Consensus pattern (18 bp):
GTGGGCCCACACAGGCGT
Found at i:31032247 original size:24 final size:24
Alignment explanation
Indices: 31032215--31032263 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
31032205 GGTCCAATCT
31032215 ACTACAACGAATTGTGGCAGATCA
1 ACTACAACGAATTGTGGCAGATCA
31032239 ACTACAACGAATTGTGGCAGATCA
1 ACTACAACGAATTGTGGCAGATCA
31032263 A
1 A
31032264 ATTCCCACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (24 bp):
ACTACAACGAATTGTGGCAGATCA
Found at i:31035819 original size:33 final size:33
Alignment explanation
Indices: 31035782--31035848 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
31035772 TAGATCACAT
31035782 TGTTTCTCCCTATTCCACTCTGATTTTACAAAA
1 TGTTTCTCCCTATTCCACTCTGATTTTACAAAA
* *
31035815 TGTTTCTCTCTATTTCACTCTGATTTTACAAAA
1 TGTTTCTCCCTATTCCACTCTGATTTTACAAAA
31035848 T
1 T
31035849 CACTGTTACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.46
Consensus pattern (33 bp):
TGTTTCTCCCTATTCCACTCTGATTTTACAAAA
Found at i:31044971 original size:27 final size:27
Alignment explanation
Indices: 31044941--31044993 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
31044931 TCCTTTTAAC
31044941 TTAATTACGATATATTTTCCACATAAT
1 TTAATTACGATATATTTTCCACATAAT
* * *
31044968 TTAATTATGGTATATTTTCCATATAA
1 TTAATTACGATATATTTTCCACATAA
31044994 ACCATTGTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (27 bp):
TTAATTACGATATATTTTCCACATAAT
Found at i:31053809 original size:17 final size:18
Alignment explanation
Indices: 31053774--31053812 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
31053764 GAAATCCTAC
*
31053774 CCATCCAGCCTCTACACT
1 CCATCCAGCCTCAACACT
31053792 CCATCCAGCC-CAACACT
1 CCATCCAGCCTCAACACT
31053809 CCAT
1 CCAT
31053813 GTGGGGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.26, C:0.51, G:0.05, T:0.18
Consensus pattern (18 bp):
CCATCCAGCCTCAACACT
Found at i:31057670 original size:9 final size:9
Alignment explanation
Indices: 31057658--31057693 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
31057648 AATTTTAAAT
31057658 ATTTAATCA
1 ATTTAATCA
31057667 ATTTAATCA
1 ATTTAATCA
31057676 ATTTAATC-
1 ATTTAATCA
*
31057684 ATTTACTCA
1 ATTTAATCA
31057693 A
1 A
31057694 AAACTAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTTAATCA
Found at i:31057679 original size:18 final size:17
Alignment explanation
Indices: 31057658--31057693 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31057648 AATTTTAAAT
31057658 ATTTAATCAATTTAATCA
1 ATTTAATC-ATTTAATCA
*
31057676 ATTTAATCATTTACTCA
1 ATTTAATCATTTAATCA
31057693 A
1 A
31057694 AAACTAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAATCATTTAATCA
Found at i:31058501 original size:43 final size:43
Alignment explanation
Indices: 31058438--31058639 Score: 219
Period size: 43 Copynumber: 4.7 Consensus size: 43
31058428 ATATTTTGGT
* *
31058438 ATATTCGATGATGCACTGTGTGTACCAGTATAGTTACTTCGAA
1 ATATCCGATGATGCACTGTGTGTACCAGTATAGTTACTTCGAG
* * * * *
31058481 ATATCTGATGATGCA-T-TGTGTGCCAATATAGTTACTTTGGG
1 ATATCCGATGATGCACTGTGTGTACCAGTATAGTTACTTCGAG
* * * *
31058522 ATATCCGATGATGCACTATTTGTGCCAGTATAGTTGCTTCGAG
1 ATATCCGATGATGCACTGTGTGTACCAGTATAGTTACTTCGAG
* ** * * * *
31058565 ATATCTGATTTTGCATTGTGTGTACCAGTATAATTGCTTCGAT
1 ATATCCGATGATGCACTGTGTGTACCAGTATAGTTACTTCGAG
*
31058608 ATATCCGATGATGCACTGTGTGTGCCAGTATA
1 ATATCCGATGATGCACTGTGTGTACCAGTATA
31058640 CATGATTTGG
Statistics
Matches: 130, Mismatches: 27, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
41 34 0.26
42 2 0.02
43 94 0.72
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (43 bp):
ATATCCGATGATGCACTGTGTGTACCAGTATAGTTACTTCGAG
Found at i:31058573 original size:84 final size:85
Alignment explanation
Indices: 31058432--31058639 Score: 274
Period size: 84 Copynumber: 2.4 Consensus size: 85
31058422 CATGTTATAT
* *
31058432 TTTGGTATATTCGATGATGCACTGTGTGTACCAGTATAGTTACTTCGAAATATCTGATGATGCAT
1 TTTGGTATATCCGATGATGCACTGTGTGTGCCAGTATAGTTACTTCGAAATATCTGATGATGCAT
*
31058497 TGTGTG-CCAATATAGTTAC
66 TGTGTGACCAATATAATTAC
* * * * * **
31058516 TTTGGGATATCCGATGATGCACTATTTGTGCCAGTATAGTTGCTTCGAGATATCTGATTTTGCAT
1 TTTGGTATATCCGATGATGCACTGTGTGTGCCAGTATAGTTACTTCGAAATATCTGATGATGCAT
* *
31058581 TGTGTGTACCAGTATAATTGC
66 TGTGTG-ACCAATATAATTAC
* *
31058602 TTCGATATATCCGATGATGCACTGTGTGTGCCAGTATA
1 TTTGGTATATCCGATGATGCACTGTGTGTGCCAGTATA
31058640 CATGATTTGG
Statistics
Matches: 105, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
84 62 0.59
86 43 0.41
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (85 bp):
TTTGGTATATCCGATGATGCACTGTGTGTGCCAGTATAGTTACTTCGAAATATCTGATGATGCAT
TGTGTGACCAATATAATTAC
Found at i:31060892 original size:2 final size:2
Alignment explanation
Indices: 31060885--31060941 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
31060875 GGTATTAGCA
*
31060885 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31060927 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
31060942 AAAGGATAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:31063927 original size:18 final size:18
Alignment explanation
Indices: 31063904--31063948 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
31063894 CTTAATGGAT
*
31063904 TTACAAGATCATCTAAGA
1 TTACAAAATCATCTAAGA
* *
31063922 TTACAAAATCTTCTAATA
1 TTACAAAATCATCTAAGA
31063940 TTACAAAAT
1 TTACAAAAT
31063949 ATTCACCCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (18 bp):
TTACAAAATCATCTAAGA
Found at i:31065031 original size:25 final size:25
Alignment explanation
Indices: 31064968--31065031 Score: 58
Period size: 25 Copynumber: 2.6 Consensus size: 25
31064958 GATTTAACCG
* * * *
31064968 ATTCATTCTATTATGTTATTTATTG
1 ATTCAATCTATTATGGTATTGATTA
* *
31064993 ATTTAATC-ATTTATGGTCTTGATTA
1 ATTCAATCTA-TTATGGTATTGATTA
31065018 ATTCAATCTATTAT
1 ATTCAATCTATTAT
31065032 TGTTTATAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
24 1 0.03
25 28 0.93
26 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.08, T:0.55
Consensus pattern (25 bp):
ATTCAATCTATTATGGTATTGATTA
Found at i:31068497 original size:13 final size:13
Alignment explanation
Indices: 31068446--31068510 Score: 87
Period size: 13 Copynumber: 5.1 Consensus size: 13
31068436 AGTTCTTCAT
31068446 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
31068459 TG-TTTTGAAAAG
1 TGCTTTTGAAAAG
* *
31068471 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
31068484 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
31068497 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
31068510 T
1 T
31068511 TTGGTTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
12 12 0.27
13 32 0.73
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:31069887 original size:13 final size:13
Alignment explanation
Indices: 31069869--31069945 Score: 109
Period size: 13 Copynumber: 5.9 Consensus size: 13
31069859 AGTTCTTCAT
*
31069869 TGCTTTTGAGAAG
1 TGCTTTTCAGAAG
31069882 TGCTTTTCAGAAG
1 TGCTTTTCAGAAG
*
31069895 TGTTTTTCAGAAG
1 TGCTTTTCAGAAG
*
31069908 TGTTTTTCAGAAG
1 TGCTTTTCAGAAG
* *
31069921 TACTTTTGAGAAG
1 TGCTTTTCAGAAG
31069934 TGCTTTTCAGAA
1 TGCTTTTCAGAA
31069946 ATTTGAGTGT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 57 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (13 bp):
TGCTTTTCAGAAG
Found at i:31070168 original size:104 final size:104
Alignment explanation
Indices: 31069988--31070193 Score: 385
Period size: 104 Copynumber: 2.0 Consensus size: 104
31069978 CTTTTGAAGA
* *
31069988 ATAAAATGTCCATTTTAGACATGGGATTGTAAAGTAACAAATATGTATTTAAATAATGTTCAAAT
1 ATAAAATGTCCATTTTAGACATGAGATTATAAAGTAACAAATATGTATTTAAATAATGTTCAAAT
31070053 TAGTTAATATTATGATATTTTAGCAAAAATATAAAAAGG
66 TAGTTAATATTATGATATTTTAGCAAAAATATAAAAAGG
31070092 ATAAAATGTCCATTTTAGACATGAGATTATAAAGTAACAAATATGTATTTAAATAATGTTCAAAT
1 ATAAAATGTCCATTTTAGACATGAGATTATAAAGTAACAAATATGTATTTAAATAATGTTCAAAT
*
31070157 TAGTTAATATTATTATATTTTAGCAAAAATATAAAAA
66 TAGTTAATATTATGATATTTTAGCAAAAATATAAAAA
31070194 AATAATTTAT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (104 bp):
ATAAAATGTCCATTTTAGACATGAGATTATAAAGTAACAAATATGTATTTAAATAATGTTCAAAT
TAGTTAATATTATGATATTTTAGCAAAAATATAAAAAGG
Found at i:31070197 original size:51 final size:51
Alignment explanation
Indices: 31070038--31070199 Score: 123
Period size: 51 Copynumber: 3.1 Consensus size: 51
31070028 ATATGTATTT
*
31070038 AAATAATGTTCAAATTAGTTAATATTATGATATTTTAGCAAAAATATAAAA
1 AAATAATGTTCAAATTAGTTAATATTATTATATTTTAGCAAAAATATAAAA
* * ** * *** * * * ***
31070089 AGGATAAAATGTCCATTTTAG--ACATGA-GATTATAAAGTAACAAATATGTATTT
1 A--A-ATAATGTTCAAATTAGTTA-AT-ATTATTATATTTTAGCAAAAATATAAAA
31070142 AAATAATGTTCAAATTAGTTAATATTATTATATTTTAGCAAAAATATAAAA
1 AAATAATGTTCAAATTAGTTAATATTATTATATTTTAGCAAAAATATAAAA
31070193 AAATAAT
1 AAATAAT
31070200 TTATTATAAC
Statistics
Matches: 74, Mismatches: 29, Indels: 16
0.62 0.24 0.13
Matches are distributed among these distances:
50 13 0.18
51 27 0.36
52 2 0.03
53 19 0.26
54 13 0.18
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.36
Consensus pattern (51 bp):
AAATAATGTTCAAATTAGTTAATATTATTATATTTTAGCAAAAATATAAAA
Found at i:31073079 original size:14 final size:13
Alignment explanation
Indices: 31073055--31073112 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 13
31073045 AATGAAAATA
*
31073055 TTTTTAATTTAAT
1 TTTTTATTTTAAT
31073068 TTATTTATTTTAAT
1 TT-TTTATTTTAAT
31073082 TTTTTAATTTT-AT
1 TTTTT-ATTTTAAT
*
31073095 CTTTT-TTTTAAT
1 TTTTTATTTTAAT
*
31073107 ATTTTA
1 TTTTTA
31073113 CTATACCTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 4 0.11
12 6 0.16
13 11 0.29
14 17 0.45
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTATTTTAAT
Found at i:31073091 original size:27 final size:25
Alignment explanation
Indices: 31073055--31073112 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
31073045 AATGAAAATA
*
31073055 TTTTTAATTTAATTTATTTATTTTAAT
1 TTTTTAATTTAATCT-TTT-TTTTAAT
*
31073082 TTTTTAATTTTATCTTTTTTTTAAT
1 TTTTTAATTTAATCTTTTTTTTAAT
*
31073107 ATTTTA
1 TTTTTA
31073113 CTATACCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 12 0.43
26 3 0.11
27 13 0.46
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTTAATTTAATCTTTTTTTTAAT
Found at i:31076005 original size:4 final size:4
Alignment explanation
Indices: 31075996--31076031 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
31075986 TGAATTTTGA
31075996 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
31076032 ATCATCTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:31077697 original size:23 final size:22
Alignment explanation
Indices: 31077654--31077711 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
31077644 AAAGGGTATC
* *
31077654 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
31077675 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
31077698 TGCATATCATATCT
1 TACAAATCATATCT
31077712 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:31078365 original size:44 final size:45
Alignment explanation
Indices: 31078317--31078436 Score: 136
Period size: 47 Copynumber: 2.7 Consensus size: 45
31078307 CTTCGATCTG
* * * ** *
31078317 CTCCACTACTGCTTAGAGAGATAAGATCT-GTAATTTTCAACCTA
1 CTCCACTGCTGCTCAGGGAGATAAGATCTAACAATCTTCAACCTA
* *
31078361 CTCCATTGCTGCTCAGGGAGATAAGGTCTACAACAATCTTCAACCTA
1 CTCCACTGCTGCTCAGGGAGATAAGATCT--AACAATCTTCAACCTA
31078408 CTCCACTGCTGCTCAGGGAGATAAG-TCTA
1 CTCCACTGCTGCTCAGGGAGATAAGATCTA
31078437 GTGGCTTAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
44 25 0.39
46 3 0.05
47 36 0.56
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (45 bp):
CTCCACTGCTGCTCAGGGAGATAAGATCTAACAATCTTCAACCTA
Found at i:31078540 original size:179 final size:177
Alignment explanation
Indices: 31078239--31078606 Score: 537
Period size: 179 Copynumber: 2.1 Consensus size: 177
31078229 TTTTCAACCT
* * *
31078239 ACTCAGGGAGATAAGACTAGTGGTTTAAATCTTCTTCCCTACTACCTTTGGAAGATAAGATTCGC
1 ACTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACCTTTGGAAGATAAGACTCGC
* *
31078304 CGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAATTTTCAACCTACTCCATTG
66 CGTATTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAATTTTCAACCTACTCCACTG
*
31078369 CTGCTCAGGGAGATAAGG-TCTACAACAATCTTCAACCTACTCCACTGCTG
131 CTGCTCAGAGAGAT-AGGAT-T-C-ACAATCTTCAACCTACTCCACTGCTG
*
31078419 -CTCAGGGAGATAAGTCTAGTGGCTTAAATCTGCTTCCCTACTACC-TTGAGAAGATAAGACTCG
1 ACTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACCTTTG-GAAGATAAGACTCG
* ** * * *
31078482 CCGTATTCGATTTTTTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCTACT
65 CCGTATTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAATTTTCAACCTACTCCACT
*
31078547 GCTGCTCAGAGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTG
130 GCTGCTCAGAGAGATAGGATTCACAATCTTCAACCTACTCCACTGCTG
31078595 AC-CAGGGAGATA
1 ACTCAGGGAGATA
31078607 GGANNNNNNN
Statistics
Matches: 171, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
176 35 0.20
177 2 0.01
178 7 0.04
179 127 0.74
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (177 bp):
ACTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACCTTTGGAAGATAAGACTCGC
CGTATTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAATTTTCAACCTACTCCACTG
CTGCTCAGAGAGATAGGATTCACAATCTTCAACCTACTCCACTGCTG
Found at i:31080395 original size:44 final size:44
Alignment explanation
Indices: 31080332--31080967 Score: 988
Period size: 44 Copynumber: 14.9 Consensus size: 44
31080322 NNNNNNNNNN
31080332 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
31080376 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
31080420 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
31080464 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
31080508 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATA-G--
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
31080549 ----AA--TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
** * *
31080586 TTGCAATCCTCAACCTATTCCACTGCTGACTAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
31080630 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
31080674 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
31080718 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
*
31080762 TCACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGG--
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
31080804 -----A--TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
* * *
31080840 TTACAATCTTCAACCTATTCCACTGCTGACTAGGGAGATAGGAT
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
* * *
31080884 TCACAATCTTTAACCTATTCCACTGCTGACCAGAGAGGTAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
* * * * *
31080928 TTATAATGTTCAACCTATTCCACTACTGACTAGGGAGATA
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATA
31080968 AAGCTTTGTG
Statistics
Matches: 548, Mismatches: 24, Indels: 40
0.90 0.04 0.07
Matches are distributed among these distances:
34 57 0.10
35 7 0.01
37 3 0.01
41 3 0.01
43 6 0.01
44 472 0.86
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (44 bp):
TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
Found at i:31080706 original size:210 final size:212
Alignment explanation
Indices: 31080339--31080967 Score: 958
Period size: 210 Copynumber: 3.0 Consensus size: 212
31080329 NNNTCACAAT
*
31080339 CTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTG
1 CTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACT-GCAATC-TCAACCTATTCCACTGCTG
31080404 ACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACA
64 ACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACA
31080469 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGC
129 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGC
31080534 TGACCAGGGAGATA-G-AA
194 TGACCAGGGAGATAGGCAA
31080551 -TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGACTTGCAATCCTCAACCTATTCCACTGCTG
1 CTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC-TGCAAT-CTCAACCTATTCCACTGCTG
*
31080614 ACTAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACA
64 ACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACA
31080679 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGC
129 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGC
31080744 TGACCAGGGAGATAGGACTCACAA
194 TGACCAGGGAGATAGG-----CAA
*
31080768 TCTTCAACCTATTCCACTACTGACCAGGGAGATA-G---G--AT-TC-ACCTATTCCACTGCTGA
1 -CTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTGCAATCTCAACCTATTCCACTGCTGA
* * *
31080825 CCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACTAGGGAGATAGGATTCACAA
65 CCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAA
* * * * * * *
31080890 TCTTTAACCTATTCCACTGCTGACCAGAGAGGTAGGACTTATAATGTTCAACCTATTCCACTACT
130 TCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCT
*
31080955 GACTAGGGAGATA
195 GACCAGGGAGATA
31080968 AAGCTTTGTG
Statistics
Matches: 390, Mismatches: 15, Indels: 26
0.90 0.03 0.06
Matches are distributed among these distances:
210 346 0.89
211 8 0.02
213 2 0.01
215 1 0.00
217 2 0.01
219 4 0.01
220 27 0.07
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (212 bp):
CTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTGCAATCTCAACCTATTCCACTGCTGAC
CAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAAT
CTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTG
ACCAGGGAGATAGGCAA
Found at i:31080793 original size:254 final size:254
Alignment explanation
Indices: 31080334--31080967 Score: 1142
Period size: 254 Copynumber: 2.5 Consensus size: 254
31080324 NNNNNNNNTC
*
31080334 ACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCAC
1 ACAATCTTCAACCTATTCCACTGCTGACTAGGGAGATAGGACTCACAATCTTCAACCTATTCCAC
31080399 TGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
66 TGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
31080464 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCC
131 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCC
*
31080529 ACTGCTGACCAGGGAGATAGAATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTT
196 ACTACTGACCAGGGAGATAGAATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTT
* *
31080588 GCAATCCTCAACCTATTCCACTGCTGACTAGGGAGATAGGACTCACAATCTTCAACCTATTCCAC
1 ACAATCTTCAACCTATTCCACTGCTGACTAGGGAGATAGGACTCACAATCTTCAACCTATTCCAC
31080653 TGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
66 TGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
31080718 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCC
131 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCC
*
31080783 ACTACTGACCAGGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTT
196 ACTACTGACCAGGGAGATAGAATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTT
* *
31080842 ACAATCTTCAACCTATTCCACTGCTGACTAGGGAGATAGGATTCACAATCTTTAACCTATTCCAC
1 ACAATCTTCAACCTATTCCACTGCTGACTAGGGAGATAGGACTCACAATCTTCAACCTATTCCAC
* * * * * * *
31080907 TGCTGACCAGAGAGGTAGGACTTATAATGTTCAACCTATTCCACTACTGACTAGGGAGATA
66 TGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATA
31080968 AAGCTTTGTG
Statistics
Matches: 364, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
254 364 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (254 bp):
ACAATCTTCAACCTATTCCACTGCTGACTAGGGAGATAGGACTCACAATCTTCAACCTATTCCAC
TGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCC
ACTACTGACCAGGGAGATAGAATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTT
Found at i:31080837 original size:34 final size:34
Alignment explanation
Indices: 31080774--31080838 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
31080764 ACAATCTTCA
31080774 ACCTATTCCACTACTGACCAGGGAGATAGGATTC
1 ACCTATTCCACTACTGACCAGGGAGATAGGATTC
*
31080808 ACCTATTCCACTGCTGACCAGGGAGATAGGA
1 ACCTATTCCACTACTGACCAGGGAGATAGGA
31080839 CTTACAATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (34 bp):
ACCTATTCCACTACTGACCAGGGAGATAGGATTC
Found at i:31080926 original size:122 final size:122
Alignment explanation
Indices: 31080686--31080926 Score: 419
Period size: 122 Copynumber: 2.0 Consensus size: 122
31080676 ACAATCTTCA
31080686 ACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAG
*
31080751 GGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGGATTC
66 GGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACCAGAGAGATAGGATTC
* *
31080808 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACTAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAG
* * * *
31080873 GGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGACCAGAGAGGTAGGA
66 GGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACCAGAGAGATAGGA
31080927 CTTATAATGT
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
122 112 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (122 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAG
GGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACCAGAGAGATAGGATTC
Found at i:31086862 original size:23 final size:22
Alignment explanation
Indices: 31086836--31086880 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31086826 AGATTAAATC
31086836 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
31086859 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
31086881 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:31087413 original size:23 final size:23
Alignment explanation
Indices: 31087382--31087432 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
31087372 ACCTACTTCC
* * *
31087382 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTATCGGGATA
31087405 TTACAGTAGTAATTATCGGGATA
1 TTACAGTAGTAATTATCGGGATA
31087428 TTACA
1 TTACA
31087433 CGGTGTACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (23 bp):
TTACAGTAGTAATTATCGGGATA
Found at i:31089325 original size:21 final size:21
Alignment explanation
Indices: 31089301--31089343 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
31089291 AAACCCAACC
31089301 CAATAAAACTAAAACTAAAGT
1 CAATAAAACTAAAACTAAAGT
31089322 CAATAAAACTAAAACTAAAGT
1 CAATAAAACTAAAACTAAAGT
31089343 C
1 C
31089344 TACCCAATTA
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:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (21 bp):
CAATAAAACTAAAACTAAAGT
Found at i:31089536 original size:17 final size:17
Alignment explanation
Indices: 31089516--31089578 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
31089506 TAATTTCAAG
31089516 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
31089533 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
31089551 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
31089570 AATTATGTA
1 AATTATGTA
31089579 GTGATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:31089540 original size:37 final size:37
Alignment explanation
Indices: 31089513--31089587 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
31089503 TGTTAATTTC
* *
31089513 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
* *
31089550 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
31089587 A
1 A
31089588 TTCGGGTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
Found at i:31092241 original size:16 final size:16
Alignment explanation
Indices: 31092220--31092259 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
31092210 TTTGGTTCGC
31092220 TGTAATAGAATAGAGG
1 TGTAATAGAATAGAGG
* *
31092236 TGTAATGGAATATAGG
1 TGTAATAGAATAGAGG
*
31092252 CGTAATAG
1 TGTAATAG
31092260 GTAATCCTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.40, C:0.03, G:0.30, T:0.28
Consensus pattern (16 bp):
TGTAATAGAATAGAGG
Found at i:31092333 original size:44 final size:46
Alignment explanation
Indices: 31092239--31092334 Score: 133
Period size: 44 Copynumber: 2.1 Consensus size: 46
31092229 ATAGAGGTGT
* * *
31092239 AATGGAATATAGGCGTAATAGGTAATCCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATCCATGTGTTTGGTTGAATGG
* *
31092285 AATGGAATAGAGGCGTAATA-GT-ATTCATGTGTTTTGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATCCATGTGTTTGGTTGAATGG
31092329 AATGGA
1 AATGGA
31092335 GTTGTAATAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
44 24 0.53
45 2 0.04
46 19 0.42
ACGTcount: A:0.30, C:0.05, G:0.29, T:0.35
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATCCATGTGTTTGGTTGAATGG
Found at i:31094443 original size:49 final size:49
Alignment explanation
Indices: 31094366--31094465 Score: 148
Period size: 49 Copynumber: 2.0 Consensus size: 49
31094356 AAAAATAAAC
* * **
31094366 TAAAATTAAGTTTATATCATGAATTCAAAAGGTGGACACTTTATAAAAT
1 TAAAATTAAGTTAATATCATGAATTCAAAAGCTCAACACTTTATAAAAT
31094415 TAAAATTAAGTTCAATATCATGAA-TCAAAAGCTCAACACTTTATAAAAT
1 TAAAATTAAGTT-AATATCATGAATTCAAAAGCTCAACACTTTATAAAAT
31094464 TA
1 TA
31094466 TAACACATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 36 0.78
50 10 0.22
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (49 bp):
TAAAATTAAGTTAATATCATGAATTCAAAAGCTCAACACTTTATAAAAT
Found at i:31096177 original size:30 final size:30
Alignment explanation
Indices: 31096143--31096214 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
31096133 AACTGTGAGT
31096143 AGAGGAAACAATCGAACAAGCCAAAGAAGA
1 AGAGGAAACAATCGAACAAGCCAAAGAAGA
31096173 AGAGGAAACAATCGAACAAGCCAAAGAAGA
1 AGAGGAAACAATCGAACAAGCCAAAGAAGA
*
31096203 AGAGGAAGCAAT
1 AGAGGAAACAAT
31096215 AACACACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.56, C:0.15, G:0.25, T:0.04
Consensus pattern (30 bp):
AGAGGAAACAATCGAACAAGCCAAAGAAGA
Found at i:31096567 original size:19 final size:19
Alignment explanation
Indices: 31096486--31096649 Score: 118
Period size: 19 Copynumber: 8.1 Consensus size: 19
31096476 TTTACTTTCT
*
31096486 TTTTTAGTGATAATTATAA
1 TTTTTAGTGTTAATTATAA
*
31096505 TTTTTGTAATGTTAATTATAA
1 -TTTT-TAGTGTTAATTATAA
*
31096526 TTGTTGTAGCAT-TTGA-T-TAA
1 TT-TT-TAG--TGTTAATTATAA
31096546 TTTTTAGTGTTAATTATAA
1 TTTTTAGTGTTAATTATAA
31096565 TTTTTAGTGTTAATTATAA
1 TTTTTAGTGTTAATTATAA
*** *
31096584 TTACAATTGTTGTAGCATTTGATTAA
1 TTTTTAGTG-T-TA--A-TT-A-TAA
31096610 TTTTTAGTGTTAATTATAA
1 TTTTTAGTGTTAATTATAA
*
31096629 TTTTTAGTGCTAATTATAA
1 TTTTTAGTGTTAATTATAA
31096648 TT
1 TT
31096650 ATAATGTTTG
Statistics
Matches: 116, Mismatches: 14, Indels: 29
0.73 0.09 0.18
Matches are distributed among these distances:
16 1 0.01
17 3 0.03
18 4 0.03
19 52 0.45
20 13 0.11
21 23 0.20
22 4 0.03
23 2 0.02
24 4 0.03
25 2 0.02
26 8 0.07
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.54
Consensus pattern (19 bp):
TTTTTAGTGTTAATTATAA
Found at i:31096604 original size:64 final size:63
Alignment explanation
Indices: 31096486--31096673 Score: 287
Period size: 64 Copynumber: 3.0 Consensus size: 63
31096476 TTTACTTTCT
*
31096486 TTTTTAGTGATAATTATAA-TTTT--TGTAATGT-TAATTATAATTGTTGTAGCATTTGATTAA
1 TTTTTAGTGTTAATTATAATTTTTAGTGTAAT-TATAATTATAATTGTTGTAGCATTTGATTAA
*
31096546 TTTTTAGTGTTAATTATAATTTTTAGTGTTAATTATAATTACAATTGTTGTAGCATTTGATTAA
1 TTTTTAGTGTTAATTATAATTTTTAGTG-TAATTATAATTATAATTGTTGTAGCATTTGATTAA
31096610 TTTTTAGTGTTAATTATAATTTTTAGTGCTAATTATAATTATAA-TGTTTGTAGCATTTGATTAA
1 TTTTTAGTGTTAATTATAATTTTTAGTG-TAATTATAATTATAATTG-TTGTAGCATTTGATTAA
31096674 AAAAAATTTT
Statistics
Matches: 118, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
60 18 0.15
61 4 0.03
63 5 0.04
64 91 0.77
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.53
Consensus pattern (63 bp):
TTTTTAGTGTTAATTATAATTTTTAGTGTAATTATAATTATAATTGTTGTAGCATTTGATTAA
Found at i:31096799 original size:47 final size:48
Alignment explanation
Indices: 31096725--31096815 Score: 148
Period size: 47 Copynumber: 1.9 Consensus size: 48
31096715 TAGTGTTAAT
* *
31096725 TATAATTTTTCTATCAAACAATATAAGTAATATAAAACATTGTTCAAA
1 TATAATTTTTCAATCAAAAAATATAAGTAATATAAAACATTGTTCAAA
*
31096773 TATAATTTTT-AATCAAAAAATTTAAGTAATATAAAACATTGTT
1 TATAATTTTTCAATCAAAAAATATAAGTAATATAAAACATTGTT
31096816 TGAAGACCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 30 0.75
48 10 0.25
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (48 bp):
TATAATTTTTCAATCAAAAAATATAAGTAATATAAAACATTGTTCAAA
Found at i:31096929 original size:17 final size:17
Alignment explanation
Indices: 31096907--31096942 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31096897 GTTTTAAATG
31096907 AAACATATCGAAAATAA
1 AAACATATCGAAAATAA
* *
31096924 AAACATATTGAAACTAA
1 AAACATATCGAAAATAA
31096941 AA
1 AA
31096943 TATAACCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.11, G:0.06, T:0.19
Consensus pattern (17 bp):
AAACATATCGAAAATAA
Found at i:31097216 original size:10 final size:10
Alignment explanation
Indices: 31097201--31097239 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
31097191 CGTGGGATAC
31097201 CATACAGAAA
1 CATACAGAAA
31097211 CATACAGAAA
1 CATACAGAAA
* *
31097221 CATATAGAGA
1 CATACAGAAA
31097231 CATACAGAA
1 CATACAGAA
31097240 TATTAACATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.56, C:0.18, G:0.13, T:0.13
Consensus pattern (10 bp):
CATACAGAAA
Found at i:31097298 original size:25 final size:25
Alignment explanation
Indices: 31097218--31097308 Score: 110
Period size: 25 Copynumber: 3.6 Consensus size: 25
31097208 AAACATACAG
* *
31097218 AAACATATAGAGACATACAGAATAT
1 AAACATACAGAAACATACAGAATAT
* * *
31097243 TAACATACAGAAACGTAAATTGAATAT
1 AAACATACAGAAACATACA--GAATAT
*
31097270 AAACATATAGAAACATACAGAATAT
1 AAACATACAGAAACATACAGAATAT
31097295 AAACATACAGAAAC
1 AAACATACAGAAAC
31097309 CATTTCCACT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
25 33 0.61
27 21 0.39
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (25 bp):
AAACATACAGAAACATACAGAATAT
Found at i:31098950 original size:12 final size:12
Alignment explanation
Indices: 31098911--31098951 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
31098901 CAAAATAATT
31098911 ACAAAGATGCAA
1 ACAAAGATGCAA
*
31098923 ACAAACCAT-C-A
1 ACAAA-GATGCAA
31098934 ACAAAGATGCAA
1 ACAAAGATGCAA
31098946 ACAAAG
1 ACAAAG
31098952 CTGATGTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 2 0.08
11 7 0.29
12 13 0.54
13 2 0.08
ACGTcount: A:0.59, C:0.22, G:0.12, T:0.07
Consensus pattern (12 bp):
ACAAAGATGCAA
Found at i:31100945 original size:233 final size:231
Alignment explanation
Indices: 31100534--31101235 Score: 1145
Period size: 233 Copynumber: 3.0 Consensus size: 231
31100524 TCCGGAGAAT
* * **
31100534 ATTAACGAAGGTCGGATCAAGATAGGCTGGTTACGAGACACATTCCCTGAGCTAGATGATGATTC
1 ATTAACGGAGGTCGGATCGAGATAGGCTGGTTACGAGACACATT-CCTGAGCCGGATGATGATTC
*
31100599 TACCGAACTAGAAAGAATCCGATATGCTCGAGCATACATTCTTGAGATCATTGGAGGTTATTTGA
65 TACCGAACTAGAAAGAATCTGATATGCTCGA-CATACATTCTTGAGATCATTGGAGGTTATTTGA
*
31100664 TGTTGGACTTGTCACGGAACCTTGTACATCTGAGATGGCTATTGAAACTTGTTGATTTTAGAGCA
129 TGTCGGACTTGTCACGGAACCTTGTACATCTGAGATGGCTATTGAAACTTGTTGATTTTAGAGCA
31100729 GCTGGTGAATTTAGTTAGGGGTCTGCCGTGTTGGCAAC
194 GCTGGTGAATTTAGTTAGGGGTCTGCCGTGTTGGCAAC
*
31100767 ATTAACGGAGGTCAGATCGAGATAGGCTGGTTACGAGACACATTCCTGGAGCCGGATGATGATTC
1 ATTAACGGAGGTCGGATCGAGATAGGCTGGTTACGAGACACATTCCT-GAGCCGGATGATGATTC
* *
31100832 TACCAAACTAGAAAGAATCTGATATGCTCAGACATACATTCTTGAGATTATTGGAGGTTATTTGA
65 TACCGAACTAGAAAGAATCTGATATGCTC-GACATACATTCTTGAGATCATTGGAGGTTATTTGA
*
31100897 TGTCGGACTTGTCACGGAACCTTGTACATCTGAGATGGCTACTGAAACTTGTTGATTTTAGAGCA
129 TGTCGGACTTGTCACGGAACCTTGTACATCTGAGATGGCTATTGAAACTTGTTGATTTTAGAGCA
* * *
31100962 GCTAGTGAATTTAGTTAGGGGTCTACCATGTTGGCAAC
194 GCTGGTGAATTTAGTTAGGGGTCTGCCGTGTTGGCAAC
* * *
31101000 ATTAACGGAGGTTGGATCGAGATAGGCTGGTTATGAGACACATTCTCAGAGCCGGATGATGATTC
1 ATTAACGGAGGTCGGATCGAGATAGGCTGGTTACGAGACACATTC-CTGAGCCGGATGATGATTC
* * * *
31101065 TACCGAACTAGAAAGAAT-TCGATATGCTCGGGCATACATCCTTGAGATCATTAGAGGTTATTTA
65 TACCGAACTAGAAAGAATCT-GATATGCTC-GACATACATTCTTGAGATCATTGGAGGTTATTTG
31101129 ATGTCGGACTTGTCACGGAACCTTGTACATCTGAGATGGCTATTGAAACTTGTTGATTTTAGAGC
128 ATGTCGGACTTGTCACGGAACCTTGTACATCTGAGATGGCTATTGAAACTTGTTGATTTTAGAGC
*
31101194 AGCTGGTGAATTTAGTTAGGGGCCTGCCGTGTTGGCAAC
193 AGCTGGTGAATTTAGTTAGGGGTCTGCCGTGTTGGCAAC
31101233 ATT
1 ATT
31101236 GTATTTGGAG
Statistics
Matches: 436, Mismatches: 29, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
232 4 0.01
233 429 0.98
234 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (231 bp):
ATTAACGGAGGTCGGATCGAGATAGGCTGGTTACGAGACACATTCCTGAGCCGGATGATGATTCT
ACCGAACTAGAAAGAATCTGATATGCTCGACATACATTCTTGAGATCATTGGAGGTTATTTGATG
TCGGACTTGTCACGGAACCTTGTACATCTGAGATGGCTATTGAAACTTGTTGATTTTAGAGCAGC
TGGTGAATTTAGTTAGGGGTCTGCCGTGTTGGCAAC
Found at i:31101598 original size:7 final size:7
Alignment explanation
Indices: 31101586--31101618 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
31101576 TAGTCGATTC
31101586 GTATTTA
1 GTATTTA
31101593 GTATTTA
1 GTATTTA
31101600 GTATTTA
1 GTATTTA
31101607 GTATTTA
1 GTATTTA
31101614 GTATT
1 GTATT
31101619 ATGTATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:31104648 original size:126 final size:125
Alignment explanation
Indices: 31104423--31104839 Score: 683
Period size: 126 Copynumber: 3.3 Consensus size: 125
31104413 CAGGCCAAAT
* * *
31104423 AAGAACTACTGTAGCAAAATAGCGTTCACGTGGGAGCTTCTTTCAGTACTTTTGTTGACAAAGCA
1 AAGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAC-AAGCA
31104488 TCCTACTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTC
65 TCCTACTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTC
* * *
31104549 AAGAACTACTGTAGCAAAAGAACGTCCACGTGAGAGCTTCTTTCAGTACTTTTGCTGACAGAGCT
1 AAGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACA-AGCA
*
31104614 TCCTACTTAAAGCGTTTTTAACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTC
65 TCCTACTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTC
* * *
31104675 AGGAACTACTGTAGCAAAAGAGCTTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACAATGCA
1 AAGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAA-GCA
*
31104740 TCCTACTTAAAGCGTTTTTGACACTATTTACTCAGAAACGTCTTCTCGAAATTATTTTTT-
65 TCCTACTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTC
*
31104800 TAGTAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
1 AAG-AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
31104840 TTTTAAATTA
Statistics
Matches: 270, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
125 3 0.01
126 267 0.99
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (125 bp):
AAGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAGCAT
CCTACTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTC
Found at i:31105011 original size:96 final size:96
Alignment explanation
Indices: 31104882--31105179 Score: 429
Period size: 96 Copynumber: 3.1 Consensus size: 96
31104872 CATAAACTCC
* * *
31104882 AAACCCTAATTTATTTTAGTTTGTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTTT
1 AAACCCTAATTTATTTGAGTTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAA-TTTTTA
31104947 AAAATTTATAATTAATTTACTCAAGTAACCCT
65 AAAATTTATAATTAATTTACTCAAGTAACCCT
* *
31104979 AAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCTT-AACCCTAAACCCTAATCTGATTTTTA
1 AAACCCTAATTTATTTGAGTTTTTCCTTAAAAA-CCTTAAACACTAAACCCTAATCTAATTTTTA
31105042 AAAATTTATAATTAATTTACTCAAGTAACCCT
65 AAAATTTATAATTAATTTACTCAAGTAACCCT
* * * * * *
31105074 AAACCCTAATTTAATTGATTTTTTCCTTAAAAACCATAAACACGAATCCCTAATCTAATTTTAAA
1 AAACCCTAATTTATTTGAGTTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTAA
* * * *
31105139 AAATTTATAATTAATTTAATTAAGAAACACT
66 AAATTTATAATTAATTTACTCAAGTAACCCT
31105170 AAACCCTAAT
1 AAACCCTAAT
31105180 CCCTTATTTA
Statistics
Matches: 182, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
95 57 0.31
96 104 0.57
97 21 0.12
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (96 bp):
AAACCCTAATTTATTTGAGTTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTAA
AAATTTATAATTAATTTACTCAAGTAACCCT
Found at i:31105239 original size:6 final size:6
Alignment explanation
Indices: 31105230--31105263 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
31105220 AAAACTCAAA
*
31105230 AACCCT AACCCT AAACCCT AACCTT AACCCT AAC
1 AACCCT AACCCT -AACCCT AACCCT AACCCT AAC
31105264 GCAAAGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (6 bp):
AACCCT
Found at i:31106269 original size:18 final size:17
Alignment explanation
Indices: 31106233--31106271 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
31106223 TAATGTATGA
31106233 TATTTAAAATTGTTTAT
1 TATTTAAAATTGTTTAT
* *
31106250 TATTTAGAATTTTATTAT
1 TATTTAAAATTGT-TTAT
31106268 TATT
1 TATT
31106272 AATGACAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
TATTTAAAATTGTTTAT
Found at i:31106956 original size:25 final size:25
Alignment explanation
Indices: 31106910--31106957 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
31106900 TCAAGAACTT
*
31106910 TAAAATATTTTTATTATTTTAAATA
1 TAAAATATTTTTATTATATTAAATA
*
31106935 TAAAATATTTATTTTTA-ATTAAA
1 TAAAATATTT-TTATTATATTAAA
31106958 AAAAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAAAATATTTTTATTATATTAAATA
Found at i:31106960 original size:21 final size:21
Alignment explanation
Indices: 31106926--31106969 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
31106916 ATTTTTATTA
* * *
31106926 TTTTAAATATAAAATATTTAT
1 TTTTAAATAAAAAAAATTAAT
*
31106947 TTTTAATTAAAAAAAATTAAT
1 TTTTAAATAAAAAAAATTAAT
31106968 TT
1 TT
31106970 AATTTCAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTAAATAAAAAAAATTAAT
Found at i:31107688 original size:27 final size:25
Alignment explanation
Indices: 31107646--31107697 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
31107636 CTCAATTATT
* **
31107646 AAAAAATTTCATTTTAGGCACCCAA
1 AAAAAATTTCAATTTAAACACCCAA
31107671 AAAAAAGTTTACAATTTAAACACCCAA
1 AAAAAA-TTT-CAATTTAAACACCCAA
31107698 GTTACATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 13 0.59
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (25 bp):
AAAAAATTTCAATTTAAACACCCAA
Found at i:31109323 original size:22 final size:22
Alignment explanation
Indices: 31109298--31109341 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
31109288 GAGGAAGATA
31109298 GACGATGAGGGA-AGGGAGAGGG
1 GACGATGAGGGAGAGGGA-AGGG
* *
31109320 GACGGTGGGGGAGAGGGAAGGG
1 GACGATGAGGGAGAGGGAAGGG
31109342 ACAGTGACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.27, C:0.05, G:0.64, T:0.05
Consensus pattern (22 bp):
GACGATGAGGGAGAGGGAAGGG
Found at i:31111748 original size:29 final size:30
Alignment explanation
Indices: 31111705--31111771 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
31111695 ATAAAGAGAT
31111705 TAAATT-TTTAAAAATACAAATACAA-AGAC
1 TAAATTCTTTAAAAATACAAATACAAGA-AC
* * *
31111734 TAAATTCTTT-AAAATATAATTACATGAAC
1 TAAATTCTTTAAAAATACAAATACAAGAAC
31111763 TAAATTCTT
1 TAAATTCTT
31111772 AAATTTCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (30 bp):
TAAATTCTTTAAAAATACAAATACAAGAAC
Found at i:31113216 original size:13 final size:13
Alignment explanation
Indices: 31113200--31113226 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31113190 CTTAAGTTTG
31113200 GCTTCAATGTTCA
1 GCTTCAATGTTCA
31113213 GCTTCAATGTTCA
1 GCTTCAATGTTCA
31113226 G
1 G
31113227 TTTGGTACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (13 bp):
GCTTCAATGTTCA
Found at i:31114251 original size:15 final size:16
Alignment explanation
Indices: 31114222--31114256 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
31114212 CCATGTTAGT
31114222 AAAAATAAAATAATAA
1 AAAAATAAAATAATAA
*
31114238 AAAAATCAAA-AATAA
1 AAAAATAAAATAATAA
31114253 AAAA
1 AAAA
31114257 TAATTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAATAAAATAATAA
Found at i:31114836 original size:19 final size:18
Alignment explanation
Indices: 31114754--31114844 Score: 73
Period size: 19 Copynumber: 4.9 Consensus size: 18
31114744 AAAAATGAAA
*
31114754 AAAAAGTACAAAAATATTT
1 AAAAATTACAAAAA-ATTT
31114773 AAAAATTACAAAAAATAATT
1 AAAAATTACAAAAAAT--TT
*
31114793 AAGGAAA-T--AAAAAATAT
1 AA--AAATTACAAAAAATTT
31114810 -AAAATTACAAAAAATTT
1 AAAAATTACAAAAAATTT
31114827 AAAAATTTACTAAAAAAT
1 AAAAA-TTAC-AAAAAAT
31114845 AAAAAATAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
14 3 0.05
15 1 0.02
16 1 0.02
17 9 0.15
18 6 0.10
19 24 0.41
20 11 0.19
21 1 0.02
22 3 0.05
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.25
Consensus pattern (18 bp):
AAAAATTACAAAAAATTT
Found at i:31114847 original size:18 final size:17
Alignment explanation
Indices: 31114800--31114863 Score: 64
Period size: 14 Copynumber: 3.8 Consensus size: 17
31114790 ATTAAGGAAA
31114800 TAAAAAATATAAAATTAC
1 TAAAAAATA-AAAATTAC
31114818 -AAAAAATTTAAAAATTTAC
1 TAAAAAA--TAAAAA-TTAC
31114837 TAAAAAATAAAAA--A-
1 TAAAAAATAAAAATTAC
31114851 TAAAAAATAAAAA
1 TAAAAAATAAAAA
31114864 ATATAATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
14 13 0.31
15 1 0.02
17 6 0.14
18 10 0.24
19 6 0.14
20 6 0.14
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
TAAAAAATAAAAATTAC
Found at i:31114849 original size:19 final size:19
Alignment explanation
Indices: 31114800--31114851 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
31114790 ATTAAGGAAA
*
31114800 TAAAAAATATAAAA-TTAC
1 TAAAAAATAAAAAATTTAC
*
31114818 -AAAAAATTTAAAAATTTAC
1 TAAAAAA-TAAAAAATTTAC
31114837 TAAAAAATAAAAAAT
1 TAAAAAATAAAAAAT
31114852 AAAAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 6 0.21
18 5 0.18
19 11 0.39
20 6 0.21
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAAAAATAAAAAATTTAC
Found at i:31114855 original size:6 final size:7
Alignment explanation
Indices: 31114837--31114866 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
31114827 AAAAATTTAC
31114837 TAAAAAA
1 TAAAAAA
31114844 TAAAAAA
1 TAAAAAA
31114851 TAAAAAA
1 TAAAAAA
31114858 TAAAAAA
1 TAAAAAA
31114865 TA
1 TA
31114867 TAATATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:31115073 original size:21 final size:21
Alignment explanation
Indices: 31115031--31115073 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31115021 TTTTTTACAA
*
31115031 ATTATTTAAATAATGTTATTT
1 ATTATTTAAATAATATTATTT
* *
31115052 ATTATTTAAATATTATTTTTT
1 ATTATTTAAATAATATTATTT
31115073 A
1 A
31115074 GAAATAGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTATTTAAATAATATTATTT
Found at i:31119042 original size:15 final size:15
Alignment explanation
Indices: 31119022--31119053 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
31119012 TTGGTGGTGA
31119022 TTAAGTCAAATTGGT
1 TTAAGTCAAATTGGT
31119037 TTAAGTCAAATTGGT
1 TTAAGTCAAATTGGT
31119052 TT
1 TT
31119054 TCTAAATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (15 bp):
TTAAGTCAAATTGGT
Found at i:31119175 original size:5 final size:5
Alignment explanation
Indices: 31119165--31119189 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31119155 CTTGTTATTG
31119165 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
31119190 TGCCAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:31124021 original size:21 final size:22
Alignment explanation
Indices: 31123988--31124028 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
31123978 TTTAAATTAA
*
31123988 TTTAAATTATTATTAAATATTT
1 TTTAAATTATTATAAAATATTT
31124010 TTTAAATT-TTATAAAATAT
1 TTTAAATTATTATAAAATAT
31124029 ATTCATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTAAATTATTATAAAATATTT
Found at i:31127610 original size:121 final size:121
Alignment explanation
Indices: 31127500--31127913 Score: 812
Period size: 121 Copynumber: 3.4 Consensus size: 121
31127490 CAAACTTTAG
*
31127500 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAT-TTTAAATTATATTTTATAGT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
31127564 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
66 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
31127620 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
31127685 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
66 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
31127741 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
31127806 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
66 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
31127862 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAAT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAAT
31127914 NNNNNNNNNN
Statistics
Matches: 292, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
120 44 0.15
121 248 0.85
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (121 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
Found at i:31127753 original size:37 final size:37
Alignment explanation
Indices: 31127690--31127874 Score: 106
Period size: 38 Copynumber: 4.7 Consensus size: 37
31127680 ATAGTATTAT
* *
31127690 ATATTATG-ATTTTAGTAAATTCATATAAGAATATTTA
1 ATATTAAGAATTTTATTAAATT-ATATAAGAATATTTA
**** *
31127727 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATT
1 ATATTAAGAATTTTATTAAATTATATAAGAATATT---TA
* * ***
31127767 ATATTTAATAATAATTATGTTAAAATTATAT-TTTATAGTATTA
1 ATA-TTAAGAAT--TT-TATT-AAATTATATAAGAATA-T-TTA
* *
31127810 TATATTATG-ATTTTAGTAAATTCATATAAGAATATTTA
1 -ATATTAAGAATTTTATTAAATT-ATATAAGAATATTTA
31127848 ATATTAAGAATTTTATTAAATTATATA
1 ATATTAAGAATTTTATTAAATTATATA
31127875 TTTTTATTAA
Statistics
Matches: 113, Mismatches: 20, Indels: 30
0.69 0.12 0.18
Matches are distributed among these distances:
37 28 0.25
38 32 0.28
39 7 0.06
40 9 0.08
41 7 0.06
42 2 0.02
43 6 0.05
44 11 0.10
45 10 0.09
46 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (37 bp):
ATATTAAGAATTTTATTAAATTATATAAGAATATTTA
Found at i:31128040 original size:39 final size:40
Alignment explanation
Indices: 31127997--31128101 Score: 104
Period size: 44 Copynumber: 2.5 Consensus size: 40
31127987 TTCCATTATG
31127997 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* * *** *
31128036 CTATTACGCCTATATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
31128081 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
31128102 ACACCTCTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
39 14 0.27
40 5 0.10
44 17 0.33
45 16 0.31
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:31128099 original size:45 final size:44
Alignment explanation
Indices: 31127995--31128104 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 44
31127985 TTTTCCATTA
31127995 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * * ***
31128034 TACTATTACGCCTATATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
31128079 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
31128105 CCTCTATTCC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
39 15 0.27
40 1 0.02
44 16 0.29
45 24 0.43
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:31128104 original size:16 final size:16
Alignment explanation
Indices: 31128083--31128139 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
31128073 TTGATTTGCT
31128083 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
31128099 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
31128115 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
31128131 AATACACCT
1 ATTACACCT
31128140 TTAATCCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:31128144 original size:16 final size:16
Alignment explanation
Indices: 31128085--31128152 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
31128075 GATTTGCTAT
* *
31128085 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
* *
31128101 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
31128117 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
31128133 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
31128149 TACA
1 TACA
31128153 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:31130345 original size:23 final size:23
Alignment explanation
Indices: 31130301--31130345 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
31130291 TCTTATTTTG
* *
31130301 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
31130324 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
31130346 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:31134170 original size:14 final size:15
Alignment explanation
Indices: 31134146--31134178 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
31134136 TCCCAAGCTG
*
31134146 GGAAGGACCTTATGT
1 GGAAGGACCTTATCT
31134161 GGAA-GACCTTATCT
1 GGAAGGACCTTATCT
31134175 GGAA
1 GGAA
31134179 AAGCGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (15 bp):
GGAAGGACCTTATCT
Found at i:31134279 original size:11 final size:11
Alignment explanation
Indices: 31134258--31134296 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
31134248 AAATATTAAA
31134258 AAAAAGCAAAAG
1 AAAAAG-AAAAG
31134270 AAAGAA-AAAAG
1 AAA-AAGAAAAG
31134281 AAAAAGAAAAG
1 AAAAAGAAAAG
31134292 AAAAA
1 AAAAA
31134297 TGAGAGGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 18 0.72
12 3 0.12
13 2 0.08
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:31134279 original size:17 final size:18
Alignment explanation
Indices: 31134257--31134296 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
31134247 AAAATATTAA
*
31134257 AAAAAAGCAAAAG-AAAG
1 AAAAAAGAAAAAGAAAAG
31134274 AAAAAAGAAAAAGAAAAG
1 AAAAAAGAAAAAGAAAAG
31134292 AAAAA
1 AAAAA
31134297 TGAGAGGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAGAAAAG
Found at i:31135823 original size:92 final size:92
Alignment explanation
Indices: 31135666--31135851 Score: 266
Period size: 92 Copynumber: 2.0 Consensus size: 92
31135656 ATAGTGGAAT
* * * *
31135666 AGATTGAAGCCATAACAGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTCAAGCCACAACAGCGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACGA
* *
31135731 CAGCGAATCTTGTTTCTCCAACATTGC
66 CAGCGAATCTTGGTTCCCCAACATTGC
* *
31135758 AGATTCAAGCCACAAC-GACGAATCTTACTTCTCTAGCGGTGCAGTGGAATAGATTGAAGCTACG
1 AGATTCAAGCCACAACAG-CGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACG
* *
31135822 ACGGCGAATCTTGGTTCCCCTACATTGC
65 ACAGCGAATCTTGGTTCCCCAACATTGC
31135850 AG
1 AG
31135852 TCAAATAGAT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
91 1 0.01
92 82 0.99
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (92 bp):
AGATTCAAGCCACAACAGCGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACGA
CAGCGAATCTTGGTTCCCCAACATTGC
Found at i:31136088 original size:29 final size:29
Alignment explanation
Indices: 31136032--31136088 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
31136022 GTCGAAACCG
* *
31136032 CTTTTTTGAAAACAAAAATTTAGTGTCGA
1 CTTTTTTGAAAACAAAAAATTAGAGTCGA
*
31136061 CTTTTTT-AAAACACAAAAATTGGAGTCG
1 CTTTTTTGAAAACA-AAAAATTAGAGTCG
31136089 CCACCTATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (29 bp):
CTTTTTTGAAAACAAAAAATTAGAGTCGA
Found at i:31136675 original size:14 final size:14
Alignment explanation
Indices: 31136655--31136688 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31136645 AAAAGTTAAA
*
31136655 AAAAAAATAAATTAG
1 AAAAAAA-AATTTAG
31136670 AAAAAAAAATTTAG
1 AAAAAAAAATTTAG
31136684 AAAAA
1 AAAAA
31136689 CGCATGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (14 bp):
AAAAAAAAATTTAG
Found at i:31136786 original size:24 final size:22
Alignment explanation
Indices: 31136735--31136788 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
31136725 TTAAACTGTA
**
31136735 TATATATTAAAAATATGCATAT
1 TATATATGGAAAATATGCATAT
*
31136757 TATATATGGAAAATATGCGTAT
1 TATATATGGAAAATATGCATAT
31136779 GTACTATATG
1 -TA-TATATG
31136789 AAAGATGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 19 0.70
23 2 0.07
24 6 0.22
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.39
Consensus pattern (22 bp):
TATATATGGAAAATATGCATAT
Found at i:31138504 original size:44 final size:44
Alignment explanation
Indices: 31138194--31138781 Score: 150
Period size: 44 Copynumber: 13.4 Consensus size: 44
31138184 CACTGCCGAC
*
31138194 CAGGGA-ATTAGAAT-TACTGGCTTCAATATACTCCACTGTAACCT
1 CAGGGAGA-TAGAATCTACTGGCTTCAATCTACTCCACTGT-ACCT
* * * *** * *
31138238 CAGAGAGGTAAAATCTACCATCTTCGATCTACTCCAC--TACTGT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGTAC-CT
* * * *
31138281 CTAGGGAGATA-AGATCTGTAAT--ATTCAATCTATTCCACTGCTGCCT
1 C-AGGGAGATAGA-ATC--TACTGGCTTCAATCTACTCCACTG-TACCT
* *
31138327 -AGGAAGATAGAAT-TACTGGCTTCAATGTACTCCACTGTAACCT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGT-ACCT
* * * *** ** *
31138370 CAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCAC--TACTGCT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGTAC--CT
* * * * * **
31138414 TAGGGAGATA-AGATCTGTAAT--CTTCAATTTATTGCACTGTTGCT
1 CAGGGAGATAGA-ATC--TACTGGCTTCAATCTACTCCACTGTACCT
*
31138458 CAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACTGTAACCT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGT-ACCT
* * ** *** * * *
31138502 CAGGGAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGCCT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACT-GTACCT
* * * *
31138547 -AGGGAGATA-AGATCTGTAAT--CTTCGATCTATTCCACTATTA-CT
1 CAGGGAGATAGA-ATC--TACTGGCTTCAATCTACTCCACT-GTACCT
* *
31138590 CAGGGAGATAAAAT-TACTGGCTTCAATGTACTCCACTGTAACCT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGT-ACCT
* * * *** * * *
31138634 CAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGCCT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACT-GTACCT
* * * **
31138679 -AGGGAGATA-AGATCTGTAAT--CTTCAATCTATTCCACTATTGCT
1 CAGGGAGATAGA-ATC--TACTGGCTTCAATCTACTCCACTGTACCT
* *
31138722 CAGGGA-AGTAGAAT-TACTGGCTTCAATGTACTCCACTGTAACCA
1 CAGGGAGA-TAGAATCTACTGGCTTCAATCTACTCCACTGT-ACCT
* *
31138766 CAGGGAGGTAAAATCT
1 CAGGGAGATAGAATCT
31138782 GCCATCTTTG
Statistics
Matches: 387, Mismatches: 106, Indels: 101
0.65 0.18 0.17
Matches are distributed among these distances:
41 12 0.03
42 6 0.02
43 79 0.20
44 205 0.53
45 75 0.19
46 8 0.02
47 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (44 bp):
CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGTACCT
Found at i:31138896 original size:127 final size:128
Alignment explanation
Indices: 31138170--31139304 Score: 1446
Period size: 127 Copynumber: 8.8 Consensus size: 128
31138160 AAATCTGCTT
* * * * * * *
31138170 TCTTCGATCGATTCCACTGCCGACCAGGGAATTAGAATTACTGGCTTCAATATACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGCAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * * * * * *
31138235 CCT-CAGAGAGGTAAAATCTACCATCTTCGATCTACTCCACTACTGTCTAGGGAGATAAGATCTG
66 -CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGA----
31138299 TAA
126 TAA
* * *
31138302 TATTCAATCTATTCCACTGCTGCCTA-GGAAGATAGAATTACTGGCTTCAATGTACTCCACTGTA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGCAG-TAGAATTACTGGCTTCAATGTACTCCACTGTA
** ** *
31138366 ACCT-CAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
65 A-CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGA---
31138430 GTAA
126 -TAA
* * * *
31138434 TCTTCAATTTATTGCACTGTTGCTCAGGG-AGATAGAATTACTGGCTTCAATGTACTCCACTGTA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGCAG-TAGAATTACTGGCTTCAATGTACTCCACTGTA
* * * *** *
31138498 ACCT-CAGGGAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGCCTAGGGAGATAAGATCT
65 A-CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGA---
31138562 GTAA
126 -TAA
* ** * * *
31138566 TCTTCGATCTATTCCACTATTACTCAGGG-AGATAAAATTACTGGCTTCAATGTACTCCACTGTA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGCAG-TAGAATTACTGGCTTCAATGTACTCCACTGTA
** * * *** *
31138630 ACCT-CAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGCCTAGGGAGATAAGATCT
65 A-CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGA---
31138694 GTAA
126 -TAA
** * *
31138698 TCTTCAATCTATTCCACTATTGCTCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGCAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
*
31138763 CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGA-AA
66 CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGATAA
* *
31138825 TCTTCAATCTATTTCACTGCTGCCCAGGGCAGTAGAATTACTGGCTTCAATGTACTCCATTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGCAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
31138890 CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGA-AA
66 CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGATAA
* *
31138952 TCTTCAATCTATTTCACTGCTGCCCAGGGCAGTAGAATTACTGGCTTCAATGTACTCCATTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGCAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
31139017 CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGA-AA
66 CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGATAA
* *
31139079 TCTTCAATCTATTTCACTGCTGCCCAGGGCAGTAGAATTACTGGCTTCAATGTACTCCATTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGCAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
31139144 CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGA-AA
66 CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGATAA
* *
31139206 TCTTCAATCTATTTCACTGCTGCCCAGGGCAGTAGAATTACTGGCTTCAATGTACTCCATTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGCAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
31139271 CTACAGGGAGGTAAAATCTGCCATCTTTGATCTG
66 CTACAGGGAGGTAAAATCTGCCATCTTTGATCTG
31139305 TTTCACTGTC
Statistics
Matches: 949, Mismatches: 50, Indels: 13
0.94 0.05 0.01
Matches are distributed among these distances:
127 475 0.50
131 5 0.01
132 465 0.49
133 4 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (128 bp):
TCTTCAATCTATTCCACTGCTGCCCAGGGCAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
CTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTATTTAGGGAGACAAGATAA
Found at i:31140689 original size:14 final size:15
Alignment explanation
Indices: 31140666--31140702 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
31140656 AGCCTCTCCA
*
31140666 TTTTCCTTTTTCAT-
1 TTTTCATTTTTCATC
31140680 TTTTCA-TTTTCATC
1 TTTTCATTTTTCATC
31140694 TTTTCATTT
1 TTTTCATTT
31140703 CTCACATCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 7 0.35
14 11 0.55
15 2 0.10
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCATTTTTCATC
Found at i:31143638 original size:13 final size:13
Alignment explanation
Indices: 31143620--31143645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31143610 GTTCAATTTT
31143620 TTTACTAGAAAAC
1 TTTACTAGAAAAC
31143633 TTTACTAGAAAAC
1 TTTACTAGAAAAC
31143646 AAATCTCTTT
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:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:31146103 original size:24 final size:22
Alignment explanation
Indices: 31146052--31146105 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
31146042 AAACTGTATA
**
31146052 TATATATTAAAAATATGCATAT
1 TATATATGGAAAATATGCATAT
*
31146074 TATATATGGAAAATATGCGTAT
1 TATATATGGAAAATATGCATAT
31146096 GTACTATATG
1 -TA-TATATG
31146106 AAAGATGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 19 0.70
23 2 0.07
24 6 0.22
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.39
Consensus pattern (22 bp):
TATATATGGAAAATATGCATAT
Found at i:31147245 original size:50 final size:50
Alignment explanation
Indices: 31147191--31147425 Score: 200
Period size: 50 Copynumber: 4.9 Consensus size: 50
31147181 TTTGGCATTA
* *
31147191 TAGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAACAGTG
1 TAGTGGAACAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAACAGTG
* * **
31147241 TAGTGGAACAGATTGAAGCTACGACGGTGAATCTTGTTTCTCC-AACA---
1 TAGTGGAACAGATTGAAGCCACAACGGTGAATCTTACTTC-CCTAACAGTG
* * *
31147288 T--T-G--CAGATTGAAGCCACAACGGTGAATCTTACTTCTCTAGCGGTG
1 TAGTGGAACAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAACAGTG
* * ** * *
31147333 TAGTGGAACAGATTGAAGCTACGACGGTGAATCTTGGTTCCCCAACATTG
1 TAGTGGAACAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAACAGTG
* ** * * **
31147383 CAGTCAAATAGATTGAAGCCAAAATAGTGAATCTTACTTCCCT
1 TAGTGGAACAGATTGAAGCCACAACGGTGAATCTTACTTCCCT
31147426 GACGTTATAG
Statistics
Matches: 141, Mismatches: 34, Indels: 20
0.72 0.17 0.10
Matches are distributed among these distances:
41 1 0.01
42 30 0.21
44 1 0.01
45 2 0.01
47 2 0.01
48 1 0.01
50 102 0.72
51 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (50 bp):
TAGTGGAACAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAACAGTG
Found at i:31147357 original size:92 final size:92
Alignment explanation
Indices: 31147200--31147385 Score: 318
Period size: 92 Copynumber: 2.0 Consensus size: 92
31147190 ATAGTGGAAT
31147200 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTAACAGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTAACAGTGTAGTGGAACAGATTGAAGCTACGA
* *
31147265 CGGTGAATCTTGTTTCTCCAACATTGC
66 CGGTGAATCTTGGTTCCCCAACATTGC
* * * *
31147292 AGATTGAAGCCACAACGGTGAATCTTACTTCTCTAGCGGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTAACAGTGTAGTGGAACAGATTGAAGCTACGA
31147357 CGGTGAATCTTGGTTCCCCAACATTGC
66 CGGTGAATCTTGGTTCCCCAACATTGC
31147384 AG
1 AG
31147386 TCAAATAGAT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (92 bp):
AGATTGAAGCCACAACGGCGAATCTTACTTCCCTAACAGTGTAGTGGAACAGATTGAAGCTACGA
CGGTGAATCTTGGTTCCCCAACATTGC
Found at i:31147673 original size:168 final size:168
Alignment explanation
Indices: 31147378--31147761 Score: 583
Period size: 168 Copynumber: 2.3 Consensus size: 168
31147368 GGTTCCCCAA
**
31147378 CATTGCAGTCAAATAGATTGAAGCCAAAATAGTGAATCTTACTTCCCTGACGTTATAGCGGAGCA
1 CATTGCAGTCAAATAGATTGAAGCCAAAACGGTGAATCTTACTTCCCTGACGTTATAGCGGAGCA
* * * * *
31147443 GGTTAAAGCTGAGGGTAGCGAATCTTATTTCCTTGGCGTTAGGACTTGAAATAGTAGAAGTGGAG
66 GATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGAAATAGTAGAAGTGGAG
* * *
31147508 CGAATTGAAGCTGTGGGCAGCGAATCCTATCTCTTTGG
131 CAAATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGG
*
31147546 CATTGCATTCAAATAGATTGAAGCCAAAACGGTGAATCTTACTTCCCTGACGTTATAGCGGAGCA
1 CATTGCAGTCAAATAGATTGAAGCCAAAACGGTGAATCTTACTTCCCTGACGTTATAGCGGAGCA
*
31147611 GATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTT-AGATTAGCT-GAAGTGG
66 GATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGA-AATAG-TAGAAGTGG
31147674 AGCAAATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGG
129 AGCAAATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGG
* ** * *
31147714 CATTACAGTGGAATAGATTGAAGCCACAACGATGAATCTTACTTCCCT
1 CATTGCAGTCAAATAGATTGAAGCCAAAACGGTGAATCTTACTTCCCT
31147762 AGCGGTGTAG
Statistics
Matches: 196, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
167 1 0.01
168 194 0.99
169 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (168 bp):
CATTGCAGTCAAATAGATTGAAGCCAAAACGGTGAATCTTACTTCCCTGACGTTATAGCGGAGCA
GATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGAAATAGTAGAAGTGGAG
CAAATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGG
Done.