Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 128 of 187
Found at i:38869616 original size:14 final size:14
Alignment explanation
Indices: 38869597--38869624 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38869587 CCAATTTATT
38869597 AATGAATTATTAAA
1 AATGAATTATTAAA
38869611 AATGAATTATTAAA
1 AATGAATTATTAAA
38869625 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:38874424 original size:169 final size:170
Alignment explanation
Indices: 38874145--38874480 Score: 629
Period size: 169 Copynumber: 2.0 Consensus size: 170
38874135 ACCATAAAAC
*
38874145 TTCAAGAACAACTCAAACTCATCAATGGAATAATCTATAACATTTAATAGTTTTACAAATTAGTC
1 TTCAAGAACAACTCAAACTCATCAATGGAATAATCTATAACATTTAACAGTTTTACAAATTAGTC
38874210 CCCAGGTTAGCTAAATCAAGATAATACGAGCTCAAAAACATAAAAATTACTAAAA-CGAGATCAA
66 CCCAGGTTAGCTAAATCAAGATAATACGAGCTCAAAAACATAAAAATTACTAAAATCGAGATCAA
38874274 GGATCACTTACATACCCCAACCCTAGCTTGACCAAAATTT
131 GGATCACTTACATACCCCAACCCTAGCTTGACCAAAATTT
38874314 TTCAAGAACAACTCAAACTCATCAATGGAATAATCTATAACATTTAACAGTTTTACAAATTAGTC
1 TTCAAGAACAACTCAAACTCATCAATGGAATAATCTATAACATTTAACAGTTTTACAAATTAGTC
* * *
38874379 CCCAGGTTAGCTAAATCAAGATAATAGGAGCTCAAAAACATAAAAATTACTAAAATCGGGATCGA
66 CCCAGGTTAGCTAAATCAAGATAATACGAGCTCAAAAACATAAAAATTACTAAAATCGAGATCAA
38874444 GGATCACTTACATACCCCAACCCTAGCTTGACCAAAA
131 GGATCACTTACATACCCCAACCCTAGCTTGACCAAAA
38874481 CTTTCTTCTC
Statistics
Matches: 162, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
169 118 0.73
170 44 0.27
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (170 bp):
TTCAAGAACAACTCAAACTCATCAATGGAATAATCTATAACATTTAACAGTTTTACAAATTAGTC
CCCAGGTTAGCTAAATCAAGATAATACGAGCTCAAAAACATAAAAATTACTAAAATCGAGATCAA
GGATCACTTACATACCCCAACCCTAGCTTGACCAAAATTT
Found at i:38876150 original size:38 final size:39
Alignment explanation
Indices: 38876099--38876175 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 39
38876089 GTGAGCCTGA
38876099 CTACGTGGGCCTTTGATTGGG-CAAAACTCAATTCTCTT
1 CTACGTGGGCCTTTGATTGGGCCAAAACTCAATTCTCTT
*
38876137 CTACGTGGGCCTTTGATTGGGCCAAGACTCAATTCTCTT
1 CTACGTGGGCCTTTGATTGGGCCAAAACTCAATTCTCTT
38876176 TCTTTATTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 21 0.57
39 16 0.43
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (39 bp):
CTACGTGGGCCTTTGATTGGGCCAAAACTCAATTCTCTT
Found at i:38884851 original size:12 final size:12
Alignment explanation
Indices: 38884834--38884858 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38884824 TCTATATCAA
38884834 GCCTAGCACACG
1 GCCTAGCACACG
38884846 GCCTAGCACACG
1 GCCTAGCACACG
38884858 G
1 G
38884859 ACGTGTGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.28, T:0.08
Consensus pattern (12 bp):
GCCTAGCACACG
Found at i:38891520 original size:50 final size:49
Alignment explanation
Indices: 38891414--38891521 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 49
38891404 TGTTTATATA
* * *
38891414 ATTATTT-TTTAGATTTGATGTTTTAAATAAATATAAATATTTATTTAT
1 ATTATTTGTTTAGATCTGATGTTTTAAACAAATATAAATATTTAGTTAT
* * * *
38891462 -TTATTTTGTTTAGATCTGGTGTTTTTACACAAATATAGATATTTGGTTAT
1 ATTA-TTTGTTTAGATCTGATG-TTTTAAACAAATATAAATATTTAGTTAT
38891512 ATTATTTGTT
1 ATTATTTGTT
38891522 CAAGATATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
47 3 0.06
48 3 0.06
49 11 0.22
50 29 0.59
51 3 0.06
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.56
Consensus pattern (49 bp):
ATTATTTGTTTAGATCTGATGTTTTAAACAAATATAAATATTTAGTTAT
Found at i:38891824 original size:82 final size:81
Alignment explanation
Indices: 38891720--38891955 Score: 280
Period size: 82 Copynumber: 2.9 Consensus size: 81
38891710 TTATTGTCGT
* * *
38891720 TCAATAGACTTTATTCCT-TTTTTATTTTGTTTCCAAACAAGAATTAATTGAATAATTCTATTTC
1 TCAACAGATTTTATT-CTATTTTTATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTC
*
38891784 AGAATTTATTCTC-ACAGC
65 AG-ATTTATTCCCGACA-C
* *
38891802 TCAACAGATTTTATTCTATTTTTATTTTGTTTCCAAACAATAATTAAATAAATAATTCTATTTCT
1 TCAACAGATTTTATTCTATTTTTATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTC-
* *
38891867 AGATTTATTCCCGCCAT
65 AGATTTATTCCCGACAC
* * * * *
38891884 TTAACAGATTTTATT-TGATTTTGATTTTGTTTCCAAACAAGATTTAATTAAATAATTTTGTTTC
1 TCAACAGATTTTATTCT-ATTTTTATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTC
38891948 AGGATTTA
65 A-GATTTA
38891956 ATCCTGTCGG
Statistics
Matches: 134, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
81 4 0.03
82 126 0.94
83 4 0.03
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (81 bp):
TCAACAGATTTTATTCTATTTTTATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTCA
GATTTATTCCCGACAC
Found at i:38892078 original size:12 final size:13
Alignment explanation
Indices: 38892061--38892091 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
38892051 TTTTTTATTT
38892061 ATTGTGGCTTT-A
1 ATTGTGGCTTTAA
38892073 ATTGTGGCTTTAA
1 ATTGTGGCTTTAA
38892086 ATTGTG
1 ATTGTG
38892092 AAAGCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.48
Consensus pattern (13 bp):
ATTGTGGCTTTAA
Found at i:38892098 original size:28 final size:29
Alignment explanation
Indices: 38892067--38892121 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
38892057 ATTTATTGTG
* * *
38892067 GCTTTAATTGTGGCTTTAAA-TTGTGAAA
1 GCTTAAATTGTAGCTTCAAACTTGTGAAA
38892095 GCTTAAATTGTAGCTTCAAACTTGTGA
1 GCTTAAATTGTAGCTTCAAACTTGTGA
38892122 CATCAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (29 bp):
GCTTAAATTGTAGCTTCAAACTTGTGAAA
Found at i:38896393 original size:40 final size:40
Alignment explanation
Indices: 38896309--38896452 Score: 105
Period size: 40 Copynumber: 3.6 Consensus size: 40
38896299 ATTTGGATAA
***
38896309 AAAACGCTGCTAAAAATCAAGCAATAGCAGCGTTTTTTTT
1 AAAACGCTGCTAAAAATCAAGCAATAGCAGCGTTTTTCGG
* * * *
38896349 AAAACGCTGCTAAAGATCCAA-TATTAGCGGCGTTTTTCGG
1 AAAACGCTGCTAAAAAT-CAAGCAATAGCAGCGTTTTTCGG
* * * **
38896389 AAAACGCCG-TAAAAAAT-GAGCATTAGCAGCGTTTTTCAA
1 AAAACGCTGCT-AAAAATCAAGCAATAGCAGCGTTTTTCGG
* *
38896428 AAAAGCGCCGCAAAAAATCTAAGCA
1 AAAA-CGCTGCTAAAAATC-AAGCA
38896453 CAACGATGTC
Statistics
Matches: 81, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
38 1 0.01
39 20 0.25
40 53 0.65
41 3 0.04
42 4 0.05
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (40 bp):
AAAACGCTGCTAAAAATCAAGCAATAGCAGCGTTTTTCGG
Found at i:38896553 original size:41 final size:41
Alignment explanation
Indices: 38896482--38896797 Score: 271
Period size: 41 Copynumber: 7.5 Consensus size: 41
38896472 GTTTTTGGGC
* * * *
38896482 CTTTAGCGGCGTTTTTTAAAAAACGCCGCTAATGTTCGAGG
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGAGG
* * *
38896523 CTTTAGCGGCGTTTTTGAAGAAGCGTCGCTAATCCTCGGGG
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGAGG
* *
38896564 CTTTAGCGACGTTTTTGAAGAAGCGCCGCTAATGCTCTG-GT
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC-GAGG
* * *
38896605 CTTTAGCGGCATTTTTTAAGAAGCGCCGCTAATGCTCTAGGCTTGCTCTGGG
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG--CT---C--G----AGG
* **
38896657 CTTTAGCGGCGTTTTTGGAA-AAACGCCGCTAATAATCGAGG
1 CTTTAGCGGCGTTTTT-GAAGAAGCGCCGCTAATGCTCGAGG
* * *
38896698 CTTTAGCGGCTTTTTTGAAGAAGCGCCGCTAATGCTCTA-T
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGAGG
* * * * *
38896738 TTTTAGCGGCTTTTTTTAAGAAGCGCCGCTAATGCTTTG-GT
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC-TCGAGG
38896779 CTTTAGCGGCGTTTTTGAA
1 CTTTAGCGGCGTTTTTGAA
38896798 AAAAGCACCG
Statistics
Matches: 225, Mismatches: 34, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
40 36 0.16
41 150 0.67
42 1 0.00
43 2 0.01
45 1 0.00
46 1 0.00
47 3 0.01
50 1 0.00
52 28 0.12
53 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGAGG
Found at i:38896699 original size:52 final size:52
Alignment explanation
Indices: 38896596--38896700 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 52
38896586 GCGCCGCTAA
* * * ** *
38896596 TGCTCTGGTCTTTAGCGGCATTTTTTAAGAAGCGCCGCTAATGCTCTAGGCT
1 TGCTCTGGGCTTTAGCGGCATTTTTGAAGAAACGCCGCTAATAATCGAGGCT
*
38896648 TGCTCTGGGCTTTAGCGGCGTTTTTGGAA-AAACGCCGCTAATAATCGAGGCT
1 TGCTCTGGGCTTTAGCGGCATTTTT-GAAGAAACGCCGCTAATAATCGAGGCT
38896700 T
1 T
38896701 TAGCGGCTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 43 0.96
53 2 0.04
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (52 bp):
TGCTCTGGGCTTTAGCGGCATTTTTGAAGAAACGCCGCTAATAATCGAGGCT
Found at i:38896720 original size:93 final size:93
Alignment explanation
Indices: 38896561--38896736 Score: 259
Period size: 93 Copynumber: 1.9 Consensus size: 93
38896551 CTAATCCTCG
* ** *
38896561 GGGCTTTAGCGACGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCATTTTTTAAGA
1 GGGCTTTAGCGACGTTTTTGAAGAAACGCCGCTAATAATCTGGGCTTTAGCGGCATTTTTTAAGA
38896626 AGCGCCGCTAATGCTCTAGGCTTGCTCT
66 AGCGCCGCTAATGCTCTAGGCTTGCTCT
*
38896654 GGGCTTTAGCGGCGTTTTTGGAA-AAACGCCGCTAATAATC-GAGGCTTTAGCGGC-TTTTTTGA
1 GGGCTTTAGCGACGTTTTT-GAAGAAACGCCGCTAATAATCTG-GGCTTTAGCGGCATTTTTT-A
38896716 AGAAGCGCCGCTAATGCTCTA
63 AGAAGCGCCGCTAATGCTCTA
38896737 TTTTTAGCGG
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
92 7 0.09
93 65 0.87
94 3 0.04
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (93 bp):
GGGCTTTAGCGACGTTTTTGAAGAAACGCCGCTAATAATCTGGGCTTTAGCGGCATTTTTTAAGA
AGCGCCGCTAATGCTCTAGGCTTGCTCT
Found at i:38897280 original size:13 final size:13
Alignment explanation
Indices: 38897264--38897301 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
38897254 CGAAATCCGG
*
38897264 GAGTTGAATCCTA
1 GAGTTGAATCCAA
38897277 GAGTTGAAATCCAA
1 GAGTTG-AATCCAA
38897291 GAGTTGAATCC
1 GAGTTGAATCC
38897302 CTTATAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (13 bp):
GAGTTGAATCCAA
Found at i:38900826 original size:43 final size:43
Alignment explanation
Indices: 38900758--38901028 Score: 400
Period size: 43 Copynumber: 6.3 Consensus size: 43
38900748 GTAGAAACGC
* * * * *
38900758 CTTTAGTGGCGTTTTTAGGAAAAGCGTCGCTAAAGGTCATGGC
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
*
38900801 CTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
*
38900844 CTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
* *
38900887 CTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
* * *
38900930 CTTTAGCGGCGTTTTTGGG-AAAGCGCCGTTAAAGGCCATGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
* *
38900972 CTTTAGCGGAGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
*
38901015 CTTTAGTGGCGTTT
1 CTTTAGCGGCGTTT
38901029 ATTTCTAAAA
Statistics
Matches: 208, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
42 36 0.17
43 172 0.83
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
Found at i:38902643 original size:42 final size:43
Alignment explanation
Indices: 38902534--38902803 Score: 332
Period size: 43 Copynumber: 6.3 Consensus size: 43
38902524 TTTTAGAAAT
* *
38902534 AAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
*
38902577 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGC-TTTCCCAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
38902619 AAATGCCGCTAAAAACCA-GAACCTTTAGCGGCACTTTTTCCAC
1 AAACGCCGCTAAAGACCATG-ACCTTTAGCGGCGCTTTTCCCAC
** *
38902662 AAACGCCGCTAAAGACCAAAACC-TTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
38902704 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAT
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
38902747 AAACGCCGCTATAAG-CCATGACCTTTAGCGACTCTTTTCCCAA
1 AAACGCCGCTA-AAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
38902790 AAACTCCACTAAAG
1 AAACGCCGCTAAAG
38902804 GCGTTTCTAC
Statistics
Matches: 195, Mismatches: 27, Indels: 11
0.84 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 73 0.37
43 119 0.61
44 2 0.01
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:38902657 original size:85 final size:86
Alignment explanation
Indices: 38902534--38902803 Score: 350
Period size: 85 Copynumber: 3.2 Consensus size: 86
38902524 TTTTAGAAAT
*
38902534 AAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCATGAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCATGAC
38902599 CTTTAGCGGCGC-TTTCCCAA
66 CTTTAGCGGCGCTTTTCCCAA
* * * **
38902619 AAATGCCGCTAAAAACCA-GAACCTTTAGCGGCACTTTTTCCACAAACGCCGCTAAAGACCAAAA
1 AAACGCCGCTAAAGACCATG-ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCATGA
* *
38902683 CC-TTAGCGGCGCTTTTCTCAC
65 CCTTTAGCGGCGCTTTTCCCAA
* * * *
38902704 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCATAAACGCCGCTATAAG-CCATGA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTA-AAGACCATGA
* *
38902768 CCTTTAGCGACTCTTTTCCCAA
65 CCTTTAGCGGCGCTTTTCCCAA
* *
38902790 AAACTCCACTAAAG
1 AAACGCCGCTAAAG
38902804 GCGTTTCTAC
Statistics
Matches: 156, Mismatches: 24, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
84 11 0.07
85 115 0.74
86 30 0.19
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.23
Consensus pattern (86 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCATGAC
CTTTAGCGGCGCTTTTCCCAA
Found at i:38907350 original size:21 final size:22
Alignment explanation
Indices: 38907318--38907359 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
38907308 AGGATACCAA
38907318 TTTTAGGGGGGGAAATTAGGGG
1 TTTTAGGGGGGGAAATTAGGGG
38907340 TTTTA-GGGGGGAAATTAGGG
1 TTTTAGGGGGGGAAATTAGGG
38907360 AAAAAAAGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.48, T:0.29
Consensus pattern (22 bp):
TTTTAGGGGGGGAAATTAGGGG
Found at i:38907769 original size:8 final size:8
Alignment explanation
Indices: 38907756--38907799 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
38907746 TTATAAAACA
*
38907756 TAAACCCT
1 TAAACCCC
38907764 TAAACCCC
1 TAAACCCC
38907772 T-AACCCC
1 TAAACCCC
*
38907779 TAAA-TCC
1 TAAACCCC
38907786 TAAACCCC
1 TAAACCCC
38907794 TAAACC
1 TAAACC
38907800 TTAAACCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
7 13 0.42
8 18 0.58
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.18
Consensus pattern (8 bp):
TAAACCCC
Found at i:38907776 original size:15 final size:15
Alignment explanation
Indices: 38907773--38907820 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
38907763 TTAAACCCCT
38907773 AACCCCTAAATCC-TA
1 AACCCCTAAA-CCTTA
38907788 AACCCCTAAACCTTA
1 AACCCCTAAACCTTA
* *
38907803 AACCTC-AACCCTTA
1 AACCCCTAAACCTTA
38907817 AACC
1 AACC
38907821 ATAAATCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCCCTAAACCTTA
Found at i:38907846 original size:14 final size:14
Alignment explanation
Indices: 38907829--38907868 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
38907819 CCATAAATCA
38907829 TAAACAATAATCCC
1 TAAACAATAATCCC
*
38907843 TAAACCCATAATCCC
1 TAAA-CAATAATCCC
*
38907858 TAAACTATAAT
1 TAAACAATAAT
38907869 GATAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACAATAATCCC
Found at i:38909236 original size:41 final size:41
Alignment explanation
Indices: 38909191--38909463 Score: 253
Period size: 41 Copynumber: 6.1 Consensus size: 41
38909181 TAAAATATTT
* *
38909191 TAAAGACCAAAGCATTAGCGGCGCTTCTTCAAAAACGCCAC
1 TAAAGACCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGC
38909232 TAAAGACCAGAGCATTAGCGGCGCTT-TTCCAAAAACGCCGC
1 TAAAGACCAGAGCATTAGCGGCGCTTCTT-CAAAAACGCCGC
38909273 TAAAGCCCAGAGCAAGCCTAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGC
1 T--A----A-AG--A-CC-AGAGCATTAGCGGCGCTTCTTCAAAAACGCCGC
* *
38909325 TAAAGCCCAAAGCATTAGCGGCGCTT-TTCCAAAAACGCCGC
1 TAAAGACCAGAGCATTAGCGGCGCTTCTT-CAAAAACGCCGC
38909366 TAAATCCCAGAGCAAGCCTAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGC
1 T--A----A-AG--A-CC-AGAGCATTAGCGGCGCTTCTTCAAAAACGCCGC
* * *
38909418 TAAAGCCCAGATCATTAGCGGCGCTTCTTAAAAAACGCCGC
1 TAAAGACCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGC
38909459 TAAAG
1 TAAAG
38909464 GTCCAAAAAC
Statistics
Matches: 197, Mismatches: 9, Indels: 52
0.76 0.03 0.20
Matches are distributed among these distances:
40 4 0.02
41 103 0.52
42 4 0.02
43 2 0.01
45 4 0.02
46 2 0.01
47 2 0.01
48 4 0.02
50 3 0.02
51 4 0.02
52 61 0.31
53 4 0.02
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.17
Consensus pattern (41 bp):
TAAAGACCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGC
Found at i:38909318 original size:52 final size:52
Alignment explanation
Indices: 38909240--38909428 Score: 260
Period size: 52 Copynumber: 3.8 Consensus size: 52
38909230 ACTAAAGACC
38909240 AGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCAGAGCAAGCCT
1 AGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCAGAGCAAGCCT
38909292 AGAGCATTAGCGGCGCTTCTT-CAAAAACGCCGCTAAAG-CC----C-A----
1 AGAGCATTAGCGGCGCTT-TTCCAAAAACGCCGCTAAAGCCCAGAGCAAGCCT
*
38909334 A-AGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAATCCCAGAGCAAGCCT
1 AGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCAGAGCAAGCCT
38909385 AGAGCATTAGCGGCGCTTCTT-CAAAAACGCCGCTAAAGCCCAGA
1 AGAGCATTAGCGGCGCTT-TTCCAAAAACGCCGCTAAAGCCCAGA
38909429 TCATTAGCGG
Statistics
Matches: 121, Mismatches: 2, Indels: 28
0.80 0.01 0.19
Matches are distributed among these distances:
40 2 0.02
41 32 0.26
42 3 0.02
46 2 0.02
47 2 0.02
51 3 0.02
52 73 0.60
53 4 0.03
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (52 bp):
AGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCAGAGCAAGCCT
Found at i:38909360 original size:93 final size:93
Alignment explanation
Indices: 38909201--38909463 Score: 456
Period size: 93 Copynumber: 2.8 Consensus size: 93
38909191 TAAAGACCAA
* *
38909201 AGCATTAGCGGCGCTTCTTCAAAAACGCCACTAAAGACCAGAGCATTAGCGGCGCTTTTCCAAAA
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTTTCCAAAA
38909266 ACGCCGCTAAAGCCCAGAGCAAGCCTAG
66 ACGCCGCTAAAGCCCAGAGCAAGCCTAG
*
38909294 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCAAAGCATTAGCGGCGCTTTTCCAAAA
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTTTCCAAAA
*
38909359 ACGCCGCTAAATCCCAGAGCAAGCCTAG
66 ACGCCGCTAAAGCCCAGAGCAAGCCTAG
* *
38909387 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCAGATCATTAGCGGCGCTTCTT-AAAA
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCGCTT-TTCCAAA
38909451 AACGCCGCTAAAG
65 AACGCCGCTAAAG
38909464 GTCCAAAAAC
Statistics
Matches: 161, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
93 159 0.99
94 2 0.01
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.17
Consensus pattern (93 bp):
AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTTTCCAAAA
ACGCCGCTAAAGCCCAGAGCAAGCCTAG
Found at i:38909588 original size:40 final size:39
Alignment explanation
Indices: 38909507--38909621 Score: 140
Period size: 40 Copynumber: 2.9 Consensus size: 39
38909497 CGCTTATTGG
* * *
38909507 AAAACGCCGCTAATGCTCATTTTTAGCGGCGTTTTCCAA
1 AAAACGCCGCTAATGTTGATTTTTAGCGGCGTTTTACAA
* *
38909546 AAAACGCCGCTAATGTTGGATCTTTAGCGGCGTTTTAGAA
1 AAAACGCCGCTAATGTT-GATTTTTAGCGGCGTTTTACAA
* * *
38909586 AAAACGCTGCTATTGCTTGATTTTTAGCAGCGTTTT
1 AAAACGCCGCTAATG-TTGATTTTTAGCGGCGTTTT
38909622 TTATCCGAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 16 0.25
40 47 0.72
41 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (39 bp):
AAAACGCCGCTAATGTTGATTTTTAGCGGCGTTTTACAA
Found at i:38912768 original size:6 final size:6
Alignment explanation
Indices: 38912757--38912814 Score: 116
Period size: 6 Copynumber: 9.7 Consensus size: 6
38912747 ATAAGAATTG
38912757 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC
38912805 TCTCCC TCTC
1 TCTCCC TCTC
38912815 AGTCGAAGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
TCTCCC
Found at i:38916749 original size:22 final size:23
Alignment explanation
Indices: 38916714--38916757 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
38916704 AAATAATGGT
38916714 TTAAAACATGTAAAACATTTTTC
1 TTAAAACATGTAAAACATTTTTC
* *
38916737 TTAAAAC-TTTAAAATATTTTT
1 TTAAAACATGTAAAACATTTTT
38916758 AAATTACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (23 bp):
TTAAAACATGTAAAACATTTTTC
Found at i:38917676 original size:17 final size:18
Alignment explanation
Indices: 38917647--38917681 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
38917637 TTATATTTAT
38917647 TTTAAAAATAATAAAAAA
1 TTTAAAAATAATAAAAAA
38917665 TTTAAAAA-AATAAAAAA
1 TTTAAAAATAATAAAAAA
38917682 GGCATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TTTAAAAATAATAAAAAA
Found at i:38917815 original size:15 final size:12
Alignment explanation
Indices: 38917780--38917821 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 12
38917770 AATTTTTTTG
38917780 AAAT-TTTAGAA
1 AAATATTTAGAA
38917791 AAATATTTAGAA
1 AAATATTTAGAA
38917803 AAATAGAATTTAGAA
1 AAAT---ATTTAGAA
38917818 AAAT
1 AAAT
38917822 TATAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.15
12 11 0.41
15 12 0.44
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (12 bp):
AAATATTTAGAA
Found at i:38917829 original size:10 final size:10
Alignment explanation
Indices: 38917816--38917874 Score: 64
Period size: 10 Copynumber: 5.6 Consensus size: 10
38917806 TAGAATTTAG
38917816 AAAAATTATAA
1 AAAAATTAT-A
*
38917827 AAAAATCATA
1 AAAAATTATA
38917837 AAAAATTATA
1 AAAAATTATA
* *
38917847 AATATAATTTTT
1 AA-A-AATTATA
38917859 AAAAATTATA
1 AAAAATTATA
38917869 AAAAAT
1 AAAAAT
38917875 GGAAATATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 23 0.57
11 10 0.25
12 7 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:38917933 original size:23 final size:25
Alignment explanation
Indices: 38917856--38917939 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 25
38917846 AAATATAATT
* *
38917856 TTTAAAAATTATAAAAAATGGAAAT-A
1 TTTAAAAA-TA-AAATAATAGAAATCA
38917882 -TTAAAATATTAAAATAATAGAAATCA
1 TTTAAAA-A-TAAAATAATAGAAATCA
38917908 TTTAGAAAATAAAAT-ATA-AAAT-A
1 TTTA-AAAATAAAATAATAGAAATCA
38917931 TTTAAAAAT
1 TTTAAAAAT
38917940 TATAAAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
22 5 0.10
23 5 0.10
24 4 0.08
25 20 0.38
26 11 0.21
27 4 0.08
28 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (25 bp):
TTTAAAAATAAAATAATAGAAATCA
Found at i:38917945 original size:18 final size:17
Alignment explanation
Indices: 38917918--38917956 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
38917908 TTTAGAAAAT
*
38917918 AAAATATAAAATATTTA
1 AAAATATAAAAAATTTA
38917935 AAAATTATAAAAAATTTA
1 AAAA-TATAAAAAATTTA
38917953 AAAA
1 AAAA
38917957 ATTAGATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATATAAAAAATTTA
Found at i:38917952 original size:41 final size:42
Alignment explanation
Indices: 38917859--38917958 Score: 107
Period size: 43 Copynumber: 2.4 Consensus size: 42
38917849 TATAATTTTT
*
38917859 AAAAATTATAAAAAATGGAAATATTAAAATATTAAAATAATAG
1 AAAAATT-TAAAAAATGAAAATATTAAAATATTAAAATAATAG
* * *
38917902 AAATCATTTAGAAAAT-AAAATA-TAAAATATTTAAAAATTATA-
1 AAA-AATTTAAAAAATGAAAATATTAAAATA-TT-AAAATAATAG
38917944 AAAAATTTAAAAAAT
1 AAAAATTTAAAAAAT
38917959 TAGATATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
41 17 0.35
42 10 0.21
43 18 0.38
44 3 0.06
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (42 bp):
AAAAATTTAAAAAATGAAAATATTAAAATATTAAAATAATAG
Found at i:38917957 original size:9 final size:9
Alignment explanation
Indices: 38917918--38917959 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
38917908 TTTAGAAAAT
*
38917918 AAAATATAA
1 AAAATTTAA
*
38917927 AATATTT-A
1 AAAATTTAA
38917935 AAAATTATAA
1 AAAATT-TAA
38917945 AAAATTTAA
1 AAAATTTAA
38917954 AAAATT
1 AAAATT
38917960 AGATATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.21
9 15 0.54
10 7 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATTTAA
Found at i:38922693 original size:30 final size:31
Alignment explanation
Indices: 38922636--38922695 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
38922626 ATAAATGCCA
* *
38922636 AAAAAAATTACGTGAATAGATCAATTTTTTT
1 AAAAAAATTACGGGAATAGAGCAATTTTTTT
* *
38922667 AAAAAAATTATGGGAATA-AGCTATTTTTT
1 AAAAAAATTACGGGAATAGAGCAATTTTTT
38922696 GGAAATCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (31 bp):
AAAAAAATTACGGGAATAGAGCAATTTTTTT
Found at i:38922794 original size:41 final size:41
Alignment explanation
Indices: 38922749--38922886 Score: 138
Period size: 41 Copynumber: 3.4 Consensus size: 41
38922739 GCATGTTGTA
*
38922749 TTGAAAACGCTTTCAACTAGAATCGCTTTTTGCTAAGTCAC
1 TTGAAAACGCTTCCAACTAGAATCGCTTTTTGCTAAGTCAC
* * * * *
38922790 TTGAAAATGCTTCCAACTGGAAGCG-TTTTCAGC-ATATTGCA-
1 TTGAAAACGCTTCCAACTAGAATCGCTTTT-TGCTA-AGT-CAC
* * *
38922831 TGGAAAACGCTTCCATCTAGAATCGCTTTCTGCTAAGTCAC
1 TTGAAAACGCTTCCAACTAGAATCGCTTTTTGCTAAGTCAC
*
38922872 TTGAAAATGCTTCCA
1 TTGAAAACGCTTCCA
38922887 GTTGGAAGTG
Statistics
Matches: 75, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
40 7 0.09
41 62 0.83
42 6 0.08
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (41 bp):
TTGAAAACGCTTCCAACTAGAATCGCTTTTTGCTAAGTCAC
Found at i:38922837 original size:82 final size:82
Alignment explanation
Indices: 38922725--38922900 Score: 262
Period size: 82 Copynumber: 2.1 Consensus size: 82
38922715 CAGGAAAACT
* * * * * *
38922725 TGGAAGCGTTTTTAGCATGTTGTATTGAAAACGCTTTCAACTAGAATCGCTTTTTGCTAAGTCAC
1 TGGAAGCGTTTTCAGCATATTGCATGGAAAACGCTTCCAACTAGAATCGCTTTCTGCTAAGTCAC
38922790 TTGAAAATGCTTCCAAC
66 TTGAAAATGCTTCCAAC
*
38922807 TGGAAGCGTTTTCAGCATATTGCATGGAAAACGCTTCCATCTAGAATCGCTTTCTGCTAAGTCAC
1 TGGAAGCGTTTTCAGCATATTGCATGGAAAACGCTTCCAACTAGAATCGCTTTCTGCTAAGTCAC
**
38922872 TTGAAAATGCTTCCAGT
66 TTGAAAATGCTTCCAAC
*
38922889 TGGAAGTGTTTT
1 TGGAAGCGTTTT
38922901 TCCCCCCAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (82 bp):
TGGAAGCGTTTTCAGCATATTGCATGGAAAACGCTTCCAACTAGAATCGCTTTCTGCTAAGTCAC
TTGAAAATGCTTCCAAC
Found at i:38923275 original size:34 final size:32
Alignment explanation
Indices: 38923226--38923302 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 32
38923216 AATGATAATA
*
38923226 ATATTTCTTATTATATTTTAATGTTGCATAATTTT-T
1 ATATTT-TT-TTATATTTGAAT-TT--ATAATTTTGT
*
38923262 ATATTTTTTTATATTTGAATTTATTATTTTGT
1 ATATTTTTTTATATTTGAATTTATAATTTTGT
38923294 ATATTTTTT
1 ATATTTTTT
38923303 CCTTAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 7 0.18
32 10 0.26
33 2 0.05
34 11 0.29
35 2 0.05
36 6 0.16
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (32 bp):
ATATTTTTTTATATTTGAATTTATAATTTTGT
Found at i:38925803 original size:20 final size:18
Alignment explanation
Indices: 38925753--38925804 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
38925743 CTACAAGATA
38925753 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
38925770 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
*
38925790 GATATTAAATTAATA
1 AATATTAAATTAATA
38925805 AAATATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.38
18 1 0.03
19 3 0.10
20 14 0.48
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:38925863 original size:68 final size:71
Alignment explanation
Indices: 38925720--38925864 Score: 154
Period size: 68 Copynumber: 2.1 Consensus size: 71
38925710 TATTAAATCT
* * *
38925720 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAATATTAAGATAATC
1 TATTAAATTAATAAAATATTTATCTA-AAGATAAATATCAAATGAAATTTAATATTAAGATAATC
*** *
38925785 ACTTTGA
65 AAAATAA
* * *
38925792 TATTAAATTAATAAAATA-TTAT-T-AAGATAAGTATCAAATGAAATTTAATATTAA-ATCTATT
1 TATTAAATTAATAAAATATTTATCTAAAGATAAATATCAAATGAAATTTAATATTAAGAT-AATC
38925853 AAAATAA
65 AAAATAA
38925860 TATTA
1 TATTA
38925865 TTATTTTAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
67 2 0.03
68 38 0.61
70 1 0.02
71 4 0.06
72 17 0.27
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (71 bp):
TATTAAATTAATAAAATATTTATCTAAAGATAAATATCAAATGAAATTTAATATTAAGATAATCA
AAATAA
Found at i:38929455 original size:89 final size:89
Alignment explanation
Indices: 38929299--38929476 Score: 284
Period size: 89 Copynumber: 2.0 Consensus size: 89
38929289 GCTGAAGCTT
** *
38929299 CCTCTCGAGCACAGATCGCATAAGCTTTAGTCGGCACTGGTGCCTCAAATCTCACAGTAGAGCCT
1 CCTCTCGAGCACAGATCGCATAAGCTTTAGTCAACACTGGTGCCTCAAATCTCACAGCAGAGCCT
38929364 TTCATTCCACTACGACTATTACCC
66 TTCATTCCACTACGACTATTACCC
* * * *
38929388 CCTCTCGAGCACGGATCGCATGAGCTTTAGTCAACACTGGTGCCTCAGATCTCACAGCAGAGTCT
1 CCTCTCGAGCACAGATCGCATAAGCTTTAGTCAACACTGGTGCCTCAAATCTCACAGCAGAGCCT
*
38929453 TTCGTTCCACTACGACTATTACCC
66 TTCATTCCACTACGACTATTACCC
38929477 GCATTACCAG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 81 1.00
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.26
Consensus pattern (89 bp):
CCTCTCGAGCACAGATCGCATAAGCTTTAGTCAACACTGGTGCCTCAAATCTCACAGCAGAGCCT
TTCATTCCACTACGACTATTACCC
Found at i:38936489 original size:26 final size:26
Alignment explanation
Indices: 38936426--38936495 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
38936416 CTTTACATTG
* *
38936426 TTGCTCACACGAGCTGGGAAATAGGC
1 TTGCTCACACGAGCTGTGAAATAGGA
* * * * *
38936452 CTGCTTATACGAGTTGTGAAATGGGA
1 TTGCTCACACGAGCTGTGAAATAGGA
38936478 TTGCTCACACGAGCTGTG
1 TTGCTCACACGAGCTGTG
38936496 GGTCAAAATG
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (26 bp):
TTGCTCACACGAGCTGTGAAATAGGA
Found at i:38939821 original size:5 final size:5
Alignment explanation
Indices: 38939813--38939867 Score: 76
Period size: 5 Copynumber: 11.0 Consensus size: 5
38939803 TTTAAAAACA
* *
38939813 CATAT CATAT TATAT CATAT CA-AT ACATAT CATAT CATAT CATAC CATAT
1 CATAT CATAT CATAT CATAT CATAT -CATAT CATAT CATAT CATAT CATAT
38939863 CATAT
1 CATAT
38939868 AATAAATATG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
4 2 0.05
5 40 0.91
6 2 0.05
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (5 bp):
CATAT
Found at i:38945756 original size:20 final size:18
Alignment explanation
Indices: 38945707--38945756 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
38945697 CAATATAAAC
38945707 ATTAAATTA-AATTTAAT
1 ATTAAATTATAATTTAAT
*
38945724 ATTAAGATAATAACTTTAAT
1 ATTAA-ATTATAA-TTTAAT
38945744 ATTAAATTTATAA
1 ATTAAA-TTATAA
38945757 AATACTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 5 0.19
18 3 0.11
19 3 0.11
20 16 0.59
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTAAATTATAATTTAAT
Found at i:38953286 original size:38 final size:38
Alignment explanation
Indices: 38953236--38953340 Score: 147
Period size: 39 Copynumber: 2.7 Consensus size: 38
38953226 TTATCGAAAT
* * *
38953236 CATTGTTATAATTGTTGTAATTATAATTTACGATCGAA
1 CATTATTATAATTATTGTAATTATAATTTACGATCAAA
* *
38953274 TATTATTATAATTATTGTAATTATAAATTTTCGATCAAA
1 CATTATTATAATTATTGTAATTAT-AATTTACGATCAAA
*
38953313 CATTATTATAATTATGGTAATTATAATT
1 CATTATTATAATTATTGTAATTATAATT
38953341 ATTACATTCG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 25 0.42
39 34 0.58
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.48
Consensus pattern (38 bp):
CATTATTATAATTATTGTAATTATAATTTACGATCAAA
Found at i:38954367 original size:29 final size:29
Alignment explanation
Indices: 38954335--38954396 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
38954325 ACTGGAAGTG
* *
38954335 TTTTCCAAAAAAT-GGTCTATTCCCGTAAA
1 TTTTCC-AAAAATCGGCCTATTCACGTAAA
* *
38954364 TTTTCCTAAAATCGGCCTATTCACGTAAT
1 TTTTCCAAAAATCGGCCTATTCACGTAAA
38954393 TTTT
1 TTTT
38954397 TTGACATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (29 bp):
TTTTCCAAAAATCGGCCTATTCACGTAAA
Found at i:38960189 original size:26 final size:26
Alignment explanation
Indices: 38960156--38960216 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
38960146 TATCCGGAGC
* *
38960156 TCCTGATTAAAGGCTCTTCGTGAGCT
1 TCCTGATTAAAAGCTCTTCGTGAACT
* * *
38960182 TCTTGATTAAAAGTTCTTTGTGAACT
1 TCCTGATTAAAAGCTCTTCGTGAACT
38960208 TCCTGATTA
1 TCCTGATTA
38960217 TTACTCTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (26 bp):
TCCTGATTAAAAGCTCTTCGTGAACT
Found at i:38961080 original size:2 final size:2
Alignment explanation
Indices: 38961073--38961101 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38961063 CCTATTTCAG
38961073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38961102 GGTAAATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38963726 original size:11 final size:11
Alignment explanation
Indices: 38963710--38963734 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38963700 TGGGTTCTGC
38963710 ATGGTAATTGG
1 ATGGTAATTGG
38963721 ATGGTAATTGG
1 ATGGTAATTGG
38963732 ATG
1 ATG
38963735 TGGGGAATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.36, T:0.36
Consensus pattern (11 bp):
ATGGTAATTGG
Found at i:38981013 original size:46 final size:45
Alignment explanation
Indices: 38980903--38981036 Score: 128
Period size: 46 Copynumber: 2.9 Consensus size: 45
38980893 CAGGTGAAAG
* * * ** *
38980903 TAATAGTGCCCGGTTACCCGTTTGGGTTAAACCTACACGAATAATGAA
1 TAATAGTGCCTGGTCACCTGTAAGGGTTGAACCTACAC--A-AATGAA
* *
38980951 TCATAGTGTCTGGTCACCTGTAAGGGTTGAACCTACACAAATCGAA
1 TAATAGTGCCTGGTCACCTGTAAGGGTTGAACCTACACAAAT-GAA
38980997 TAATAGTGCCTGGTCACCCAT-TAA-GGTTGAACCTACACAA
1 TAATAGTGCCTGGTCA-CC-TGTAAGGGTTGAACCTACACAA
38981037 CAAATTGTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
45 3 0.04
46 34 0.47
47 5 0.07
48 31 0.42
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (45 bp):
TAATAGTGCCTGGTCACCTGTAAGGGTTGAACCTACACAAATGAA
Found at i:38984958 original size:36 final size:36
Alignment explanation
Indices: 38984906--38984982 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
38984896 AATCCCAATA
*
38984906 AAAATCTAATAATAATTA-AAAATTAAAAATGTTAAT
1 AAAATCTAATAATAATTATAAAA-TAAAAACGTTAAT
* *
38984942 GAAAATCTCA-AATAATTATAAAATAATAACGTTAAT
1 -AAAATCTAATAATAATTATAAAATAAAAACGTTAAT
38984978 AAAAT
1 AAAAT
38984983 TTTAAAATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 5 0.14
36 19 0.53
37 12 0.33
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (36 bp):
AAAATCTAATAATAATTATAAAATAAAAACGTTAAT
Found at i:38985956 original size:22 final size:22
Alignment explanation
Indices: 38985931--38985974 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
38985921 CTTCTTCAAA
*
38985931 AAAGAAAAGATCTTTTCCAGAT
1 AAAGAAAAAATCTTTTCCAGAT
38985953 AAAGAAAAAATCTTTTCCAGAT
1 AAAGAAAAAATCTTTTCCAGAT
38985975 TTATTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (22 bp):
AAAGAAAAAATCTTTTCCAGAT
Found at i:38986534 original size:20 final size:19
Alignment explanation
Indices: 38986509--38986567 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
38986499 AAACCCAATA
38986509 AAAATAAAAATGTAAATAAT
1 AAAATAAAAATGT-AATAAT
*
38986529 AAAATAATAATGT--TAAT
1 AAAATAAAAATGTAATAAT
*
38986546 AAATATAAAATTGTAATAAT
1 AAA-ATAAAAATGTAATAAT
38986566 AA
1 AA
38986568 TTAAAAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.21
18 8 0.24
20 18 0.55
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAATAAAAATGTAATAAT
Found at i:38986806 original size:19 final size:19
Alignment explanation
Indices: 38986744--38986807 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
38986734 GGCCTTCGCT
*
38986744 TCGCCTCCTCATCTCTGGC
1 TCGCCTCCTCATCTCTGCC
** *
38986763 TCTGTCCGTCCGTCGGCTTTGCC
1 TC-G-CC-TCC-TCATCTCTGCC
38986786 TCGCCTCCTCATCTCTGCC
1 TCGCCTCCTCATCTCTGCC
38986805 TCG
1 TCG
38986808 TTCTTTGTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 13 0.38
20 4 0.12
21 4 0.12
22 4 0.12
23 9 0.26
ACGTcount: A:0.03, C:0.45, G:0.19, T:0.33
Consensus pattern (19 bp):
TCGCCTCCTCATCTCTGCC
Found at i:38996535 original size:18 final size:18
Alignment explanation
Indices: 38996509--38996546 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
38996499 AAATAATTTT
*
38996509 AATATTAAATAATTAATG
1 AATAGTAAATAATTAATG
38996527 AATAGTAAATAATTAATG
1 AATAGTAAATAATTAATG
38996545 AA
1 AA
38996547 AAACATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (18 bp):
AATAGTAAATAATTAATG
Found at i:39003314 original size:39 final size:40
Alignment explanation
Indices: 39003236--39003311 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
39003226 GCAATAACAC
* *
39003236 AAATTAAAAATAAAAACAAGAAATATTTTTGGATTTTTGA
1 AAATTAAAAAAAAAAACAAGAAATATTTTTGAATTTTTGA
* *
39003276 AAATTAAAAAAAAAAAGAA-AACT-TTTTTGAATTTTT
1 AAATTAAAAAAAAAAACAAGAAATATTTTTGAATTTTT
39003312 TGATTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 12 0.38
39 3 0.09
40 17 0.53
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (40 bp):
AAATTAAAAAAAAAAACAAGAAATATTTTTGAATTTTTGA
Found at i:39009161 original size:15 final size:15
Alignment explanation
Indices: 39009141--39009172 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39009131 CATTTCACTA
*
39009141 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
39009156 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
39009171 TT
1 TT
39009173 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:39010308 original size:15 final size:14
Alignment explanation
Indices: 39010280--39010306 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39010270 GAATTTTCTT
39010280 GAAAAATTAATTTG
1 GAAAAATTAATTTG
39010294 GAAAAATTAATTT
1 GAAAAATTAATTT
39010307 TGATCAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
GAAAAATTAATTTG
Found at i:39011101 original size:26 final size:26
Alignment explanation
Indices: 39011050--39011100 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
39011040 AGTTGTAGAG
*
39011050 AGAAAATTCTCTGAAGAGATTATTTT
1 AGAAAATTCTCTAAAGAGATTATTTT
* *
39011076 AGAAAATT-TCTAAAGATATTTTTTT
1 AGAAAATTCTCTAAAGAGATTATTTT
39011101 TGATTTACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTATTTT
Found at i:39013165 original size:22 final size:21
Alignment explanation
Indices: 39013116--39013169 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
39013106 ACTAATATTT
* *
39013116 TTTTTTCATTTTTTAAAAATTA
1 TTTTTT-ATTTTTAAAAAATCA
*
39013138 TCTTTTATTTTTAAAAAATACA
1 TTTTTTATTTTTAAAAAAT-CA
39013160 TTTTTTATTT
1 TTTTTTATTT
39013170 CTCAAGATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTTATTTTTAAAAAATCA
Found at i:39015741 original size:2 final size:2
Alignment explanation
Indices: 39015734--39015762 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39015724 TCGCAAATCA
39015734 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
39015763 TGACGACGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39021428 original size:25 final size:26
Alignment explanation
Indices: 39021376--39021443 Score: 111
Period size: 25 Copynumber: 2.6 Consensus size: 26
39021366 AAATAAAAAA
*
39021376 TTACCAAAATGTTATAACTTTTTTTAT
1 TTACCAAAAT-ATATAACTTTTTTTAT
39021403 TTACCAAAATATATAA-TTTTTTTAT
1 TTACCAAAATATATAACTTTTTTTAT
39021428 TTACCAAAATATATAA
1 TTACCAAAATATATAA
39021444 AAAACAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 25 0.62
26 5 0.12
27 10 0.25
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.47
Consensus pattern (26 bp):
TTACCAAAATATATAACTTTTTTTAT
Found at i:39021528 original size:27 final size:27
Alignment explanation
Indices: 39021498--39021564 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
39021488 AGGGAAGCAG
39021498 GTTGGCGGCACCAAACAAGGGAACCCT
1 GTTGGCGGCACCAAACAAGGGAACCCT
*
39021525 GTTGGCGGCACCAAACAAGGGATCCCT
1 GTTGGCGGCACCAAACAAGGGAACCCT
39021552 GTTGGCGGCACCA
1 GTTGGCGGCACCA
39021565 GTCCTGCCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.25, C:0.30, G:0.31, T:0.13
Consensus pattern (27 bp):
GTTGGCGGCACCAAACAAGGGAACCCT
Found at i:39021865 original size:3 final size:3
Alignment explanation
Indices: 39021857--39021941 Score: 163
Period size: 3 Copynumber: 28.7 Consensus size: 3
39021847 AATTTTATAG
39021857 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39021904 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
39021942 AGATGTTACT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 79 0.98
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39022700 original size:18 final size:18
Alignment explanation
Indices: 39022672--39022716 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
39022662 TTGATATGGT
* *
39022672 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
*
39022690 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
39022708 TGGTGGCGA
1 TGGTGGCGA
39022717 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:39026229 original size:17 final size:17
Alignment explanation
Indices: 39026207--39026246 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
39026197 TTAGTGTGTT
*
39026207 TTTTTTCTATTTTTTTA
1 TTTTTTCTATTTTTTAA
* *
39026224 TTTTTTTTGTTTTTTAA
1 TTTTTTCTATTTTTTAA
39026241 TTTTTT
1 TTTTTT
39026247 TGATATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.10, C:0.03, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTTCTATTTTTTAA
Found at i:39026236 original size:16 final size:16
Alignment explanation
Indices: 39026217--39026248 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39026207 TTTTTTCTAT
*
39026217 TTTTTTATTTTTTTTG
1 TTTTTTAATTTTTTTG
39026233 TTTTTTAATTTTTTTG
1 TTTTTTAATTTTTTTG
39026249 ATATATTTTG
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:0.09, C:0.00, G:0.06, T:0.84
Consensus pattern (16 bp):
TTTTTTAATTTTTTTG
Found at i:39026279 original size:25 final size:27
Alignment explanation
Indices: 39026249--39026318 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 27
39026239 AATTTTTTTG
39026249 ATATATTTTGGTAAAT-AAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAGTTAT
39026274 ATATATTTTGGTAAATACAAAAAAAGTTAT
1 ATATATTTTGGTAAAT---AAAAAAGTTAT
39026304 A-ATATTTTGGTAAAT
1 ATATATTTTGGTAAAT
39026319 TTTTTGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
25 16 0.40
29 19 0.47
30 5 0.12
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (27 bp):
ATATATTTTGGTAAATAAAAAAGTTAT
Found at i:39026377 original size:19 final size:18
Alignment explanation
Indices: 39026353--39026389 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
39026343 TATAAAACCC
39026353 ATAATAAAACATTACAAAA
1 ATAATAAAACATTA-AAAA
*
39026372 ATAATAAAATATTAAAAA
1 ATAATAAAACATTAAAAA
39026390 TACCAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAATAAAACATTAAAAA
Found at i:39026390 original size:17 final size:17
Alignment explanation
Indices: 39026353--39026402 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
39026343 TATAAAACCC
*
39026353 ATAATAAAACATTACAAAA
1 ATAATAAAATATT--AAAA
39026372 ATAATAAAATATTAAAA
1 ATAATAAAATATTAAAA
**
39026389 ATACCAAAATATTA
1 ATAATAAAATATTA
39026403 TATATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 16 0.57
19 12 0.43
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAATAAAATATTAAAA
Found at i:39027162 original size:10 final size:10
Alignment explanation
Indices: 39027121--39027247 Score: 79
Period size: 10 Copynumber: 12.8 Consensus size: 10
39027111 NTTCTTCTTC
*
39027121 TTTCTTTCTT
1 TTTCTTTCCT
*
39027131 TTTTTTTCCT
1 TTTCTTTCCT
39027141 CTTCTCCTTTCCT
1 -TT-T-CTTTCCT
39027154 TTTCTTTCCT
1 TTTCTTTCCT
39027164 TATT-TTT-C-
1 T-TTCTTTCCT
39027172 TTTCTTTCCT
1 TTTCTTTCCT
***
39027182 CCCCTTTCCT
1 TTTCTTTCCT
39027192 TTTCTTTCCT
1 TTTCTTTCCT
39027202 TCTT-TTT-C-
1 T-TTCTTTCCT
39027210 TTTCTTTCC-
1 TTTCTTTCCT
*
39027219 TCTCATTTCCT
1 TTTC-TTTCCT
* *
39027230 TTTCCTTCTT
1 TTTCTTTCCT
39027240 TTTCTTTC
1 TTTCTTTC
39027248 TTCCTTTCTT
Statistics
Matches: 91, Mismatches: 14, Indels: 24
0.71 0.11 0.19
Matches are distributed among these distances:
7 4 0.04
8 8 0.09
9 7 0.08
10 53 0.58
11 10 0.11
12 3 0.03
13 6 0.07
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTCTTTCCT
Found at i:39027170 original size:33 final size:37
Alignment explanation
Indices: 39027121--39027233 Score: 126
Period size: 38 Copynumber: 3.1 Consensus size: 37
39027111 NTTCTTCTTC
* *
39027121 TTTCTTTCTTTTTTTTTC-CTC-TT-CT-CCTTTCCT
1 TTTCTTTCCTTATTTTTCTCTCTTTCCTCCCTTTCCT
*
39027154 TTTCTTTCCTTATTTTTCTTTCTTTCCTCCCCTTTCCT
1 TTTCTTTCCTTATTTTTCTCTCTTTCCT-CCCTTTCCT
* * *
39027192 TTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCATTTCCT
1 TTTCTTTCCTTATTTTTCTCTCTTTCCTC-CCTTTCCT
39027230 TTTC
1 TTTC
39027234 CTTCTTTTTC
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
33 16 0.23
34 2 0.03
35 2 0.03
36 2 0.03
37 1 0.01
38 46 0.67
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (37 bp):
TTTCTTTCCTTATTTTTCTCTCTTTCCTCCCTTTCCT
Found at i:39027177 original size:18 final size:18
Alignment explanation
Indices: 39027154--39027264 Score: 95
Period size: 18 Copynumber: 6.1 Consensus size: 18
39027144 CTCCTTTCCT
*
39027154 TTTCTTTCCTTATTTTTC
1 TTTCTTTCCTTCTTTTTC
* * *
39027172 TTTCTTTCCTCCCCTTTCC
1 TTTCTTTCCT-TCTTTTTC
39027191 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTTCTTTTTC
*
39027210 TTTCTTTCC-TCTCATTTC
1 TTTCTTTCCTTCT-TTTTC
*
39027228 -CT-TTTCCTTCTTTTTC
1 TTTCTTTCCTTCTTTTTC
39027244 TTTC-TTCCTTTCTTTCTTC
1 TTTCTTTCC-TTCTTT-TTC
39027263 TT
1 TT
39027265 CTTCCCCTCT
Statistics
Matches: 74, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
16 9 0.12
17 12 0.16
18 29 0.39
19 14 0.19
20 10 0.14
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTCTTTCCTTCTTTTTC
Found at i:39027195 original size:38 final size:38
Alignment explanation
Indices: 39027146--39027255 Score: 150
Period size: 38 Copynumber: 2.9 Consensus size: 38
39027136 TTCCTCTTCT
39027146 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
1 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
* *
39027184 CCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCT
1 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
* * * *
39027222 CATTTCCTTTTCCTT-CTTTTTCTTTCTTCCTTTC
1 CCTTTCCTTTTCTTTCCTTATT-TTTCTTTCTTTC
39027256 TTTCTTCTTC
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 5 0.08
38 60 0.92
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.65
Consensus pattern (38 bp):
CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
Found at i:39027234 original size:34 final size:36
Alignment explanation
Indices: 39027175--39027249 Score: 100
Period size: 34 Copynumber: 2.1 Consensus size: 36
39027165 ATTTTTCTTT
*
39027175 CTTTCCTCCCCTTTCCTTTTCTTTCCTTCTTTTTCTTT
1 CTTTCCTCCCATTTCC--TTCTTTCCTTCTTTTTCTTT
*
39027213 CTTTCCTCTCATTTCC-T-TTTCCTTCTTTTTCTTT
1 CTTTCCTCCCATTTCCTTCTTTCCTTCTTTTTCTTT
39027247 CTT
1 CTT
39027250 CCTTTCTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 20 0.57
35 1 0.03
38 14 0.40
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (36 bp):
CTTTCCTCCCATTTCCTTCTTTCCTTCTTTTTCTTT
Found at i:39027248 original size:10 final size:10
Alignment explanation
Indices: 39027196--39027267 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
39027186 TTTCCTTTTC
*
39027196 TTTCCTTCTT
1 TTTCTTTCTT
39027206 TTTCTTTCTT
1 TTTCTTTCTT
*
39027216 TCCTCTCATTTCCT
1 T--T-TC-TTTCTT
*
39027230 TTTCCTTCTT
1 TTTCTTTCTT
39027240 TTTCTTTCTT
1 TTTCTTTCTT
39027250 CCTTTCTTTCTT
1 --TTTCTTTCTT
*
39027262 CTTCTT
1 TTTCTT
39027268 CCCCTCTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:39027265 original size:28 final size:29
Alignment explanation
Indices: 39027185--39027267 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 29
39027175 CTTTCCTCCC
39027185 CTTTCCTTTTCTTTC--CTTCTTTTTCTTT
1 CTTTCC-TTTCTTTCTTCTTCTTTTTCTTT
*
39027213 CTTTCCTCTCATTTCCTTTTCCTTCTTTTTCTTT
1 CTTTCCTTTC-TTT-C--TT-CTTCTTTTTCTTT
39027247 C-TTCCTTTCTTTCTTCTTCTT
1 CTTTCCTTTCTTTCTTCTTCTT
39027268 CCCCTCTCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
27 3 0.07
28 15 0.33
29 3 0.07
31 1 0.02
32 3 0.07
33 7 0.15
34 14 0.30
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67
Consensus pattern (29 bp):
CTTTCCTTTCTTTCTTCTTCTTTTTCTTT
Found at i:39027393 original size:19 final size:18
Alignment explanation
Indices: 39027369--39027414 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 18
39027359 TCAGTTCAGG
39027369 TTTTTTTTTCTGTTTTTT
1 TTTTTTTTTCTGTTTTTT
39027387 ATTTTTTTTTCTGTTTTTT
1 -TTTTTTTTTCTGTTTTTT
39027406 TGTTTTTTT
1 T-TTTTTTT
39027415 GATATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 1 0.04
19 25 0.96
ACGTcount: A:0.02, C:0.04, G:0.07, T:0.87
Consensus pattern (18 bp):
TTTTTTTTTCTGTTTTTT
Found at i:39027394 original size:20 final size:19
Alignment explanation
Indices: 39027368--39027414 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
39027358 ATCAGTTCAG
39027368 GTTTTTTTTTCTGTTTTTT
1 GTTTTTTTTTCTGTTTTTT
*
39027387 ATTTTTTTTTCTGTTTTTTT
1 GTTTTTTTTTCTG-TTTTTT
39027407 GTTTTTTT
1 GTTTTTTT
39027415 GATATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (19 bp):
GTTTTTTTTTCTGTTTTTT
Found at i:39027448 original size:27 final size:29
Alignment explanation
Indices: 39027416--39027484 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 29
39027406 TGTTTTTTTG
39027416 ATATATTTTGGTAAAT-AAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
39027443 ATATATTTTGGTAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
39027472 A-ACATTTTGGTAA
1 ATATATTTTGGTAA
39027485 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 16 0.41
28 18 0.46
29 5 0.13
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:39038915 original size:18 final size:18
Alignment explanation
Indices: 39038894--39038932 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
39038884 AAAGGAAGAC
39038894 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
39038912 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
39038930 AGA
1 AGA
39038933 GCAAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:39040736 original size:33 final size:34
Alignment explanation
Indices: 39040699--39040770 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
39040689 GAGTTAGTTT
39040699 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
* *
39040732 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
39040766 ATTAA
1 ATTAA
39040771 TTTGTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:39048844 original size:21 final size:20
Alignment explanation
Indices: 39048805--39048844 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39048795 AATTTTAAAG
*
39048805 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATACATTTTT
*
39048825 TATTTTTAAAATACAATTTT
1 TATTTTTAAAATACATTTTT
39048845 AGTGTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTAAAATACATTTTT
Found at i:39049769 original size:24 final size:24
Alignment explanation
Indices: 39049741--39049789 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
39049731 ATATTAAAAA
39049741 ATAAATATCATAATGAACACAAGT
1 ATAAATATCATAATGAACACAAGT
39049765 ATAAATATCATAATGAACACAAGT
1 ATAAATATCATAATGAACACAAGT
39049789 A
1 A
39049790 AGCTAGAAAA
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:0.55, C:0.12, G:0.08, T:0.24
Consensus pattern (24 bp):
ATAAATATCATAATGAACACAAGT
Found at i:39053632 original size:41 final size:42
Alignment explanation
Indices: 39053534--39053649 Score: 155
Period size: 41 Copynumber: 2.8 Consensus size: 42
39053524 AGCCCGTACA
* *
39053534 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATG-AATCAAATATCG
* *
39053577 ATGCCACTGTCCCAGGCAGGGTCTTACATGAATCAAATA-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGAATCAAATATCG
*
39053618 ATGCCAATGTCCCAGACATGGTCTTACATGAA
1 ATGCCAATGTCCCAGACAGGGTCTTACATGAA
39053650 AACACATATC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 31 0.48
42 8 0.12
43 25 0.38
44 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATGAATCAAATATCG
Found at i:39053834 original size:2 final size:2
Alignment explanation
Indices: 39053827--39053872 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
39053817 TCATGTAACC
39053827 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39053869 TA TA
1 TA TA
39053873 GTCAAATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39054621 original size:15 final size:14
Alignment explanation
Indices: 39054584--39054627 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
39054574 TTTTATTATA
39054584 ATAACTTTATAATAT
1 ATAACTTTATAAT-T
*
39054599 ATAA-TTTATTATT
1 ATAACTTTATAATT
39054612 ATAACCTTTATAATT
1 ATAA-CTTTATAATT
39054627 A
1 A
39054628 ATATAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAACTTTATAATT
Found at i:39056713 original size:22 final size:22
Alignment explanation
Indices: 39056685--39056739 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
39056675 CTGCTCTCTA
*
39056685 TGTTGCGACATTGGTCTTTTTG
1 TGTTGCGACATTGGTCTTTCTG
39056707 TGTTGCGACATTGGTCTTTCTG
1 TGTTGCGACATTGGTCTTTCTG
39056729 TGTTGCGACAT
1 TGTTGCGACAT
39056740 AGCGACCAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.27, T:0.45
Consensus pattern (22 bp):
TGTTGCGACATTGGTCTTTCTG
Found at i:39059076 original size:20 final size:20
Alignment explanation
Indices: 39059051--39059089 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39059041 AAAGATGCAT
39059051 AACAGAGGCATCGAA-GTGCG
1 AACAGAGGCA-CGAATGTGCG
39059071 AACAGAGGCACGAATGTGC
1 AACAGAGGCACGAATGTGC
39059090 AGGTAGAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.36, C:0.21, G:0.33, T:0.10
Consensus pattern (20 bp):
AACAGAGGCACGAATGTGCG
Found at i:39073057 original size:44 final size:44
Alignment explanation
Indices: 39072990--39073103 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 44
39072980 ATGGAGTCTT
* * *
39072990 TCATCCATGGTCTTACTCATTATACTTGGTTA-CCATAGCATCAC
1 TCATCCATGGTCTTACTCCTTATAC-CGGGTAGCCATAGCATCAC
* * **
39073034 TCATCTATGGTCTTACTCCTTATACCGGGTAGCCATGGCATCTT
1 TCATCCATGGTCTTACTCCTTATACCGGGTAGCCATAGCATCAC
* *
39073078 TCATCCATGGTCTTACACCATATACC
1 TCATCCATGGTCTTACTCCTTATACC
39073104 TTTACCTTGT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 4 0.07
44 55 0.93
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.35
Consensus pattern (44 bp):
TCATCCATGGTCTTACTCCTTATACCGGGTAGCCATAGCATCAC
Found at i:39081158 original size:21 final size:21
Alignment explanation
Indices: 39081133--39081184 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
39081123 TGCATCTATG
*
39081133 GGCCTTAAAATGGGCTTACGA
1 GGCCTTAAAATGGGATTACGA
* *
39081154 GGCCTTACAATGGGATTATGA
1 GGCCTTAAAATGGGATTACGA
39081175 GGCCTTAAAA
1 GGCCTTAAAA
39081185 ATAGTTAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (21 bp):
GGCCTTAAAATGGGATTACGA
Found at i:39082564 original size:20 final size:18
Alignment explanation
Indices: 39082534--39082594 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 18
39082524 ATAGATGTAT
*
39082534 AACAGAAGCACCAAAGTGC
1 AACAGAGGCA-CAAAGTGC
39082553 AGACAGAGGCACAAATGTGC
1 A-ACAGAGGCACAAA-GTGC
39082573 AAGCAGAGGCACAGAAGTGC
1 AA-CAGAGGCACA-AAGTGC
39082593 AA
1 AA
39082595 ACAAAGCACG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 6 0.16
20 29 0.78
21 2 0.05
ACGTcount: A:0.44, C:0.21, G:0.28, T:0.07
Consensus pattern (18 bp):
AACAGAGGCACAAAGTGC
Found at i:39088247 original size:32 final size:32
Alignment explanation
Indices: 39088211--39088311 Score: 79
Period size: 32 Copynumber: 3.2 Consensus size: 32
39088201 CCCATTACAT
39088211 GCTATGTTAGTCCTAGAATCGACTAAATCGTA
1 GCTATGTTAGTCCTAGAATCGACTAAATCGTA
* *
39088243 GCTATGATA-CCACTA-AAT-G--TAACACCTC-TAA
1 GCTATGTTAGTC-CTAGAATCGACTAA-A--TCGT-A
*
39088274 CTCTATGTTAGTCCTAGAATCGACTAAATCGTA
1 -GCTATGTTAGTCCTAGAATCGACTAAATCGTA
39088307 GCTAT
1 GCTAT
39088312 TATACCACTA
Statistics
Matches: 51, Mismatches: 6, Indels: 24
0.63 0.07 0.30
Matches are distributed among these distances:
28 3 0.06
29 1 0.02
30 2 0.04
31 7 0.14
32 25 0.49
33 7 0.14
34 2 0.04
35 1 0.02
36 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (32 bp):
GCTATGTTAGTCCTAGAATCGACTAAATCGTA
Found at i:39088317 original size:64 final size:64
Alignment explanation
Indices: 39088212--39088340 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
39088202 CCATTACATG
39088212 CTATGTTAGTCCTAGAATCGACTAAATCGTAGCTATGATACCACTAAATGTAACACCTCTAACT
1 CTATGTTAGTCCTAGAATCGACTAAATCGTAGCTATGATACCACTAAATGTAACACCTCTAACT
*
39088276 CTATGTTAGTCCTAGAATCGACTAAATCGTAGCTATTATACCACTAAATGTAACACCTCTAACT
1 CTATGTTAGTCCTAGAATCGACTAAATCGTAGCTATGATACCACTAAATGTAACACCTCTAACT
39088340 C
1 C
39088341 GTATTCATTG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (64 bp):
CTATGTTAGTCCTAGAATCGACTAAATCGTAGCTATGATACCACTAAATGTAACACCTCTAACT
Found at i:39089479 original size:13 final size:13
Alignment explanation
Indices: 39089458--39089487 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39089448 CAAACTGAAC
*
39089458 TTCTTTCCTTATT
1 TTCTATCCTTATT
39089471 TTCTATCCTTATT
1 TTCTATCCTTATT
39089484 TTCT
1 TTCT
39089488 TAAAGTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (13 bp):
TTCTATCCTTATT
Found at i:39093177 original size:48 final size:48
Alignment explanation
Indices: 39093102--39093271 Score: 214
Period size: 48 Copynumber: 3.5 Consensus size: 48
39093092 TGGGTCACGT
*
39093102 GTGGCATGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
*
39093150 GTGGCACGGACTGTGTGCAGGCTACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
* * * * * ** * *
39093198 GTGGCACGGATTATGTGCAGGCCACCGAGAGTCTGTTATTACACAAAG
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
* * *
39093246 GTGGTACAGACTGTGTGTAGGCCACC
1 GTGGCACGGACTGTGTGCAGGCCACC
39093272 GAGAAATCTA
Statistics
Matches: 105, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 105 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (48 bp):
GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
Found at i:39093343 original size:2 final size:2
Alignment explanation
Indices: 39093336--39093361 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39093326 TGAATGATGA
39093336 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
39093362 GTGGATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39100237 original size:48 final size:48
Alignment explanation
Indices: 39100107--39100225 Score: 159
Period size: 48 Copynumber: 2.5 Consensus size: 48
39100097 CGCATATGCA
*
39100107 GCACGGAC-AGTGTGCAGGCCACCAATATTCTATTAACATACAAGGGTG
1 GCACGGACTA-TGTGCAGGCCACCAATATTCTGTTAACATACAAGGGTG
* * * * *
39100155 GCACGGATTGTGTACAGGCCACCAATATTCTGTTAAGATACAAGGGTT
1 GCACGGACTATGTGCAGGCCACCAATATTCTGTTAACATACAAGGGTG
*
39100203 GCACGGACTATGTGCTGGCCACC
1 GCACGGACTATGTGCAGGCCACC
39100226 GAGAGTCTGT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (48 bp):
GCACGGACTATGTGCAGGCCACCAATATTCTGTTAACATACAAGGGTG
Found at i:39108497 original size:18 final size:18
Alignment explanation
Indices: 39108473--39108515 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39108463 AAACCTATAA
39108473 AAAATAAATAC-ACTAAGT
1 AAAATAAA-ACTACTAAGT
*
39108491 TAAATAAAACTACTAAGT
1 AAAATAAAACTACTAAGT
39108509 AAAATAA
1 AAAATAA
39108516 CCAAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.63, C:0.09, G:0.05, T:0.23
Consensus pattern (18 bp):
AAAATAAAACTACTAAGT
Found at i:39112437 original size:20 final size:20
Alignment explanation
Indices: 39112414--39112468 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
39112404 ACATGCAGAA
* *
39112414 AAAGGCACAAATTTGCAAGC
1 AAAGGCACAAATGTGCAAAC
39112434 AAAGGCACCAAA-GTGCAAAC
1 AAAGGCA-CAAATGTGCAAAC
*
39112454 AAATGCACAAATGTG
1 AAAGGCACAAATGTG
39112469 GGATCAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (20 bp):
AAAGGCACAAATGTGCAAAC
Found at i:39117551 original size:32 final size:32
Alignment explanation
Indices: 39117515--39117578 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
39117505 CCCAGCATGA
39117515 TTGTTGCTACCTTTTTATATGTTGCAAAATAG
1 TTGTTGCTACCTTTTTATATGTTGCAAAATAG
39117547 TTGTTGCTACCTTTTTATATGTTGCAAAATAG
1 TTGTTGCTACCTTTTTATATGTTGCAAAATAG
39117579 CCATACTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (32 bp):
TTGTTGCTACCTTTTTATATGTTGCAAAATAG
Found at i:39119256 original size:201 final size:201
Alignment explanation
Indices: 39118908--39119309 Score: 768
Period size: 201 Copynumber: 2.0 Consensus size: 201
39118898 TATACAACTC
39118908 ACGATGTTGGGACAATGATGATCTCAAGTCTGAGGATCATATACATAGTTATCACTTTGAGTAAT
1 ACGATGTTGGGACAATGATGATCTCAAGTCTGAGGATCATATACATAGTTATCACTTTGAGTAAT
*
39118973 GTTGTGACTATTACATAATAATCCAAGAAACAAACTCATAGTGAGTCAGTCCAATATGTTGTTCT
66 GTTGTGACTATTACATAATAATCCAAGAAACAAACTCATAGCGAGTCAGTCCAATATGTTGTTCT
*
39119038 TTAACACATATTCATGTATTGATTTTGACATCTCTATGCCAATGACAACACTTTGTCATCAATCA
131 TTAACACATACTCATGTATTGATTTTGACATCTCTATGCCAATGACAACACTTTGTCATCAATCA
39119103 ACTATA
196 ACTATA
39119109 ACGATGTTGGGACAATGATGATCTCAAGTCTGAGGATCATATACATAGTTATCACTTTGAGTAAT
1 ACGATGTTGGGACAATGATGATCTCAAGTCTGAGGATCATATACATAGTTATCACTTTGAGTAAT
*
39119174 GTTGTGACTATTACATAATAATCCAAGAAACATACTCATAGCGAGTCAGTCCAATATGTTGTTCT
66 GTTGTGACTATTACATAATAATCCAAGAAACAAACTCATAGCGAGTCAGTCCAATATGTTGTTCT
*
39119239 TTAACACATACTCATGTATTGATTTTGACATCTCTATGTCAATGACAACACTTTGTCATCAATCA
131 TTAACACATACTCATGTATTGATTTTGACATCTCTATGCCAATGACAACACTTTGTCATCAATCA
39119304 ACTATA
196 ACTATA
39119310 CATTAGTCTT
Statistics
Matches: 197, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
201 197 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (201 bp):
ACGATGTTGGGACAATGATGATCTCAAGTCTGAGGATCATATACATAGTTATCACTTTGAGTAAT
GTTGTGACTATTACATAATAATCCAAGAAACAAACTCATAGCGAGTCAGTCCAATATGTTGTTCT
TTAACACATACTCATGTATTGATTTTGACATCTCTATGCCAATGACAACACTTTGTCATCAATCA
ACTATA
Found at i:39121756 original size:17 final size:18
Alignment explanation
Indices: 39121717--39121757 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
39121707 TGAATGAATG
39121717 AATAAATAGATTATAAAA
1 AATAAATAGATTATAAAA
*
39121735 CATAAATA-ATTA-AAACA
1 AATAAATAGATTATAAA-A
39121752 AATAAA
1 AATAAA
39121758 ACTTAGTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.15
17 10 0.50
18 7 0.35
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAATAGATTATAAAA
Found at i:39126170 original size:23 final size:24
Alignment explanation
Indices: 39126144--39126189 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
39126134 TGCTAACTAA
*
39126144 ATGAAGGGGA-AAATGAAAGGTTT
1 ATGAAGGAGAGAAATGAAAGGTTT
* *
39126167 ATGAATGAGAGAAATGAGAGGTT
1 ATGAAGGAGAGAAATGAAAGGTT
39126190 AGTGAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.43, C:0.00, G:0.35, T:0.22
Consensus pattern (24 bp):
ATGAAGGAGAGAAATGAAAGGTTT
Found at i:39128319 original size:17 final size:17
Alignment explanation
Indices: 39128290--39128322 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39128280 TATCGTTTGT
39128290 TTATCTTTCTTATTTAG
1 TTATCTTTCTTATTTAG
39128307 TTAT-TTTCATTATTTA
1 TTATCTTTC-TTATTTA
39128323 TTTTTATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.67
Consensus pattern (17 bp):
TTATCTTTCTTATTTAG
Found at i:39129662 original size:61 final size:58
Alignment explanation
Indices: 39129591--39129704 Score: 174
Period size: 61 Copynumber: 1.9 Consensus size: 58
39129581 AGTGATTATC
* *
39129591 TTAATGTTAAATTTAATTTAATATTTATCTTGTAGATAAATATTATATTAATTTAATAGAT
1 TTAATATTAAATTTAATATAATATTTATC-T-T-GATAAATATTATATTAATTTAATAGAT
*
39129652 TTAATATTAAATTTAATATAATATTTATCTTGATAAGTATTATATTAATTTAA
1 TTAATATTAAATTTAATATAATATTTATCTTGATAAATATTATATTAATTTAA
39129705 CATCAAAGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
58 21 0.42
59 1 0.02
60 1 0.02
61 27 0.54
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (58 bp):
TTAATATTAAATTTAATATAATATTTATCTTGATAAATATTATATTAATTTAATAGAT
Found at i:39129719 original size:58 final size:61
Alignment explanation
Indices: 39129597--39129726 Score: 153
Period size: 58 Copynumber: 2.2 Consensus size: 61
39129587 TATCTTAATG
* * **
39129597 TTAAATTTAATTTAATATTTATCTTGTAGATAAATATTATATTAATTTAATAGATTTAATA
1 TTAAATTTAATATAATATTTATCTTGTAGATAAATATTATATTAATTTAATACATCAAATA
*
39129658 TTAAATTTAATATAATATTTATC-T-T-GATAAGTATTATATTAATTT-A-ACATCAAAGTGA
1 TTAAATTTAATATAATATTTATCTTGTAGATAAATATTATATTAATTTAATACATCAAA-T-A
*
39129716 TTAAGTTTAAT
1 TTAAATTTAAT
39129727 TATAGTTGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
56 5 0.08
57 2 0.03
58 30 0.49
59 1 0.02
60 1 0.02
61 22 0.36
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (61 bp):
TTAAATTTAATATAATATTTATCTTGTAGATAAATATTATATTAATTTAATACATCAAATA
Found at i:39133336 original size:259 final size:259
Alignment explanation
Indices: 39132877--39134174 Score: 2227
Period size: 259 Copynumber: 5.0 Consensus size: 259
39132867 ATTTGGTATA
* * * * *
39132877 GATACCTTGGCTCGAGTATCAATACTCGGGGAAGAAAAATTGATACTTTATCCGATGGTATCGAT
1 GATACCTTGGCTCGAGTATCAATACTCGGGGAAGAAATATCGATACTTTATTCGGTGGTACCGAT
* * *
39132942 ATTTTTTGATAGTTGGGCTTTTACTCGAGAAACAGTATGCTCATTTGGTATCGTTTTTCCAAGTG
66 ATTTTTTGATAGTTGGGTTTTTAATCGAGAAACAGTATGCTCATTTGGTATCGTGTTTCCAAGTG
* * *
39133007 GTATCGAAACCACTTAAGGAAAATATGGATAACTAGATATCAATATCAATACCTACGGACATTTT
131 GTATCGATACCACTTAAGGAAAATATCGATAACTGGATATCAATATCAATACCTACGGACATTTT
* *
39133072 TATGAAATTTTGCTAATTAGCCCTTATGCATGATGCTGGCAATATGTATGATCAATTAACAAAT
196 TATGAAATTTTGCTAATTAGCCCTTATGCATGATGCTGGCAGTATGTATGACCAATTAACAAAT
*
39133136 GATACCTTGGCTCGAGTATCAATACTCGGGGAAGAAATATCGATACTTTATTCGGTGGTACCAAT
1 GATACCTTGGCTCGAGTATCAATACTCGGGGAAGAAATATCGATACTTTATTCGGTGGTACCGAT
* * * *
39133201 ATTTTTTGATAGTTGGGTTTTTAATTGACAAACAGTATGCTCATTTGGTATTGTTTTTCCAAGTG
66 ATTTTTTGATAGTTGGGTTTTTAATCGAGAAACAGTATGCTCATTTGGTATCGTGTTTCCAAGTG
*
39133266 GTATCGATACCACTTAAGGAAAATATCGATAACTGGATATCAATATCAATCCCTACGGACATTTT
131 GTATCGATACCACTTAAGGAAAATATCGATAACTGGATATCAATATCAATACCTACGGACATTTT
* *
39133331 TATGAAATTTTGCTAATTAGCCCTTAAGCATGATGCTGGCAGTATGTATGATCAATTAACAAAT
196 TATGAAATTTTGCTAATTAGCCCTTATGCATGATGCTGGCAGTATGTATGACCAATTAACAAAT
* * * *
39133395 GATACCTTGGCTTGAGTATCAATACTCGAGGAAGAAATATCGATACTTTACTCGGTGGTATCGAT
1 GATACCTTGGCTCGAGTATCAATACTCGGGGAAGAAATATCGATACTTTATTCGGTGGTACCGAT
* *
39133460 ATTTCTTGATAGTTGGGTTTTTAATCGAGAAATAGTATGCTCATTTGGTATCGTGTTTCCAAGTG
66 ATTTTTTGATAGTTGGGTTTTTAATCGAGAAACAGTATGCTCATTTGGTATCGTGTTTCCAAGTG
*
39133525 GTATCGATACCACTTAAGGAAAATATCGATAACTGGATATCAATATCAATACCTATGGACATTTT
131 GTATCGATACCACTTAAGGAAAATATCGATAACTGGATATCAATATCAATACCTACGGACATTTT
* * *
39133590 TATGAAATTTTGCTAACTAGCCCTTATGCATGATGTTGGCAGTATGTATGACCGATTAACAAAT
196 TATGAAATTTTGCTAATTAGCCCTTATGCATGATGCTGGCAGTATGTATGACCAATTAACAAAT
39133654 GATACCTTGGCTCGAGTATCAATACTCGGGGAAGAAATATCGATACTTTATTCGGTGGTACCGAT
1 GATACCTTGGCTCGAGTATCAATACTCGGGGAAGAAATATCGATACTTTATTCGGTGGTACCGAT
*
39133719 ATTTTTTTATAGTTGGGTTTTTAATCGAGAAACAGTATGCTCATTTGGTATCGTGTTTCCAAGTG
66 ATTTTTTGATAGTTGGGTTTTTAATCGAGAAACAGTATGCTCATTTGGTATCGTGTTTCCAAGTG
**
39133784 GTATCGATACCACTTAAGGAAAATATCGATAACTGGATATCAATATCAATACCTACAAACATTTT
131 GTATCGATACCACTTAAGGAAAATATCGATAACTGGATATCAATATCAATACCTACGGACATTTT
*
39133849 TATGAAATTTTGCTAATTAGCCCTTATGCATGATGCTGGCAGTATGTATGACCGATTAACAAAT
196 TATGAAATTTTGCTAATTAGCCCTTATGCATGATGCTGGCAGTATGTATGACCAATTAACAAAT
* **
39133913 GATACCTTGGCTCGAGTATCAATACTCAGGGAAGAAATATCGATACTTTATTCGGTGGTACTAAT
1 GATACCTTGGCTCGAGTATCAATACTCGGGGAAGAAATATCGATACTTTATTCGGTGGTACCGAT
*
39133978 ATTTTTTGATAGTTGGGTTTTTAATCGAGAAACAATATGCTCATTTGGTATCGTGTTTCCAAGTG
66 ATTTTTTGATAGTTGGGTTTTTAATCGAGAAACAGTATGCTCATTTGGTATCGTGTTTCCAAGTG
*
39134043 GTATCGATACCACTTAAGGAAAATATCGATAACTGGATATCAATATCAATACCTACAGACATTTT
131 GTATCGATACCACTTAAGGAAAATATCGATAACTGGATATCAATATCAATACCTACGGACATTTT
*
39134108 TATGAAAATTTGCTAATTAGCCCTTATGCATGATGCTGGCAGTATGTATGACCAATTAACAAAT
196 TATGAAATTTTGCTAATTAGCCCTTATGCATGATGCTGGCAGTATGTATGACCAATTAACAAAT
39134172 GAT
1 GAT
39134175 TTGCATGTAA
Statistics
Matches: 984, Mismatches: 55, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
259 984 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (259 bp):
GATACCTTGGCTCGAGTATCAATACTCGGGGAAGAAATATCGATACTTTATTCGGTGGTACCGAT
ATTTTTTGATAGTTGGGTTTTTAATCGAGAAACAGTATGCTCATTTGGTATCGTGTTTCCAAGTG
GTATCGATACCACTTAAGGAAAATATCGATAACTGGATATCAATATCAATACCTACGGACATTTT
TATGAAATTTTGCTAATTAGCCCTTATGCATGATGCTGGCAGTATGTATGACCAATTAACAAAT
Found at i:39134457 original size:5 final size:5
Alignment explanation
Indices: 39134438--39134481 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
39134428 TTATACTTGT
* *
39134438 TTATA ATAT- TTATA TTATA TTATA TTATA TTATA TTACA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
39134482 ATTTTGATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 3 0.09
5 31 0.91
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:39137141 original size:41 final size:42
Alignment explanation
Indices: 39137096--39137238 Score: 157
Period size: 41 Copynumber: 3.4 Consensus size: 42
39137086 TACTCGGTGA
* * *
39137096 AATCAGCACTTAGTAACCACC-TTATATTCAATGATACGGGG
1 AATCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGG
* * *
39137137 AATCAGCACATAGCAACC-CCTTTCACAATCAAGGATATGGTGG
1 AATCAGCACTTAGCAACCACCTTT-ACAATCAATGATACGG-GG
* * * *
39137180 AATTAGCACTTAGCAACCACCTTTAGAATCAATAATTC-GGG
1 AATCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGG
39137221 AATCAGCACTTAGCAACC
1 AATCAGCACTTAGCAACC
39137239 CCTCGGGGAA
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
40 2 0.02
41 37 0.44
42 13 0.15
43 27 0.32
44 5 0.06
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (42 bp):
AATCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGG
Found at i:39137196 original size:43 final size:40
Alignment explanation
Indices: 39137134--39137241 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 40
39137124 CAATGATACG
* * *
39137134 GGGAATCAGCACATAGCAACCCCTTTCACAATCAAGGATATG
1 GGGAATCAGCACTTAGCAACCCCTTT-ACAATCAAGAAT-TC
* * *
39137176 GTGGAATTAGCACTTAGCAACCACCTTTAGAATCAATAATTC
1 G-GGAATCAGCACTTAGCAACC-CCTTTACAATCAAGAATTC
39137218 GGGAATCAGCACTTAGCAACCCCT
1 GGGAATCAGCACTTAGCAACCCCT
39137242 CGGGGAAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
40 3 0.05
41 19 0.33
42 3 0.05
43 27 0.47
44 5 0.09
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (40 bp):
GGGAATCAGCACTTAGCAACCCCTTTACAATCAAGAATTC
Found at i:39137298 original size:67 final size:68
Alignment explanation
Indices: 39137180--39137306 Score: 161
Period size: 67 Copynumber: 1.9 Consensus size: 68
39137170 GATATGGTGG
*
39137180 AATTAGCACTTAGCAACCACCTTTAGAATCAATAATTCGGGAATCAGCACTTAGCAACCCCTCGG
1 AATTAGCACTTAGCAACCACCTTTAGAATCAATAATTCGGGAATCAGCACTTAACAACCCCTCGG
39137245 GGA
66 GGA
* * * * *
39137248 AATT-GCACTTAGCAACCTCTTTTTG-ATCAGTAATTTGGGGAATCTA-CACTTAACAACCC
1 AATTAGCACTTAGCAACCACCTTTAGAATCAATAA-TTCGGGAATC-AGCACTTAACAACCC
39137307 ATTTTCGATC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
66 7 0.14
67 39 0.76
68 5 0.10
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (68 bp):
AATTAGCACTTAGCAACCACCTTTAGAATCAATAATTCGGGAATCAGCACTTAACAACCCCTCGG
GGA
Found at i:39137305 original size:41 final size:41
Alignment explanation
Indices: 39137253--39137347 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
39137243 GGGGAAATTG
* * *
39137253 CACTTAGCAACCTC-TTTTTGATCAGTAATTTGGGGAATCTA
1 CACTTAGCAACC-CATTTTCGATCAATAATTCGGGGAATCTA
* * *
39137294 CACTTAACAACCCATTTTCGATCAATGATTCGGGGAATCTG
1 CACTTAGCAACCCATTTTCGATCAATAATTCGGGGAATCTA
39137335 CACTTAGCAACCC
1 CACTTAGCAACCC
39137348 CTTACATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
40 1 0.02
41 45 0.98
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (41 bp):
CACTTAGCAACCCATTTTCGATCAATAATTCGGGGAATCTA
Found at i:39140415 original size:18 final size:16
Alignment explanation
Indices: 39140381--39140448 Score: 68
Period size: 15 Copynumber: 4.2 Consensus size: 16
39140371 TAATAATAAT
39140381 AAAGAAAGAAAAAGAA
1 AAAGAAAGAAAAAGAA
*
39140397 ATAGAAAGAACAAACGAA
1 AAAGAAAGAA-AAA-GAA
* *
39140415 AAAGAAAGAAACA-TA
1 AAAGAAAGAAAAAGAA
*
39140430 AAGGAAAG-AAAAGAA
1 AAAGAAAGAAAAAGAA
39140445 AAAG
1 AAAG
39140449 GGAAGGAAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
14 3 0.07
15 12 0.29
16 9 0.22
17 5 0.12
18 12 0.29
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.03
Consensus pattern (16 bp):
AAAGAAAGAAAAAGAA
Found at i:39140458 original size:16 final size:16
Alignment explanation
Indices: 39140384--39140460 Score: 52
Period size: 16 Copynumber: 4.8 Consensus size: 16
39140374 TAATAATAAA
*
39140384 GAAAGAAAAAGAAATA-
1 GAAAG-AAAAGAAAAAG
39140400 GAAAGAACAAACGAAAAA-
1 GAAAG-A-AAA-GAAAAAG
* *
39140418 GAAAG-AAACATAAAG
1 GAAAGAAAAGAAAAAG
39140433 GAAAGAAAAGAAAAAG
1 GAAAGAAAAGAAAAAG
* *
39140449 GGAAGGAAAGAA
1 GAAAGAAAAGAA
39140461 GGAGAAAGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
14 4 0.08
15 8 0.16
16 25 0.50
17 3 0.06
18 10 0.20
ACGTcount: A:0.70, C:0.04, G:0.23, T:0.03
Consensus pattern (16 bp):
GAAAGAAAAGAAAAAG
Found at i:39141144 original size:2 final size:2
Alignment explanation
Indices: 39141139--39141194 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
39141129 TATATATATA
39141139 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 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
39141181 TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG
39141195 ATTATATGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:39142388 original size:11 final size:11
Alignment explanation
Indices: 39142368--39142401 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
39142358 ATAAAAAAAT
*
39142368 TATTTGTTTTAG
1 TATTT-TTTTAA
39142380 TATTTTTTTAA
1 TATTTTTTTAA
39142391 TATTTTTTTAA
1 TATTTTTTTAA
39142402 AAAAATAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (11 bp):
TATTTTTTTAA
Found at i:39148536 original size:29 final size:29
Alignment explanation
Indices: 39148494--39148553 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
39148484 TTTTCAAGAC
*
39148494 CTGCTTAAAAGCAATTATATTAGAGCGAA
1 CTGCTTAAAAGCAATTATATTAGAGAGAA
39148523 CTGCTTAAAAGCAATTATATTAGAGAGAA
1 CTGCTTAAAAGCAATTATATTAGAGAGAA
39148552 CT
1 CT
39148554 ACCAGATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (29 bp):
CTGCTTAAAAGCAATTATATTAGAGAGAA
Found at i:39153760 original size:43 final size:43
Alignment explanation
Indices: 39153699--39153957 Score: 344
Period size: 43 Copynumber: 6.0 Consensus size: 43
39153689 TTGCGGCGTT
* * * *
39153699 TATAGATCATGATCTTTAGCTGCACTTTTTCCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
* *
39153742 TATAGATCAGGACCTTTAGCGGCGATTTTTCCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
* *
39153785 TATAAATCAATACCTTTAGCGGCGC-TTTTCACACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTC-CACAAACGCCGC
* ***
39153828 TATAGATCAATACCTTTAGCGGCGCTTTCGACACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
* *
39153871 TATAGCTCAAGA-CTTTAGCGGCGCTTTCTCCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
*
39153913 TATAGATCAAGACCTTTAGCGGCGC-TTTTCACACAAATGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTC-CACAAACGCCGC
39153956 TA
1 TA
39153958 AAAACATATC
Statistics
Matches: 192, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
42 48 0.25
43 142 0.74
44 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.26
Consensus pattern (43 bp):
TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
Found at i:39153922 original size:85 final size:84
Alignment explanation
Indices: 39153725--39153957 Score: 335
Period size: 85 Copynumber: 2.7 Consensus size: 84
39153715 TAGCTGCACT
* *
39153725 TTTTCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCGATTTTTC-CACAAACGCCGCTATA
1 TTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCG--CTTTCACACAAACGCCGCTATA
*
39153789 AATCAATACCTTTAGCGGCGC
64 AATCAAGACCTTTAGCGGCGC
*
39153810 TTTTCACACAAACGCCGCTATAGATCAATACCTTTAGCGGCGCTTTCGACACAAACGCCGCTATA
1 TTTTC-CACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTC-ACACAAACGCCGCTATA
**
39153875 GCTCAAGA-CTTTAGCGGCGC
64 AATCAAGACCTTTAGCGGCGC
*
39153895 TTTCTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCACACAAATGCCGCTA
1 TTT-TCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTCACACAAACGCCGCTA
39153958 AAAACATATC
Statistics
Matches: 135, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
84 4 0.03
85 70 0.52
86 61 0.45
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (84 bp):
TTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTCACACAAACGCCGCTATAAA
TCAAGACCTTTAGCGGCGC
Found at i:39154285 original size:43 final size:43
Alignment explanation
Indices: 39154221--39154305 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
39154211 ATATGCAAGA
* * *
39154221 TAATAAAACATACAATGCATTTTCTTAATCAAGTAAATCTTGG
1 TAATAAAACATACAATACATTTACTTAATCAAGAAAATCTTGG
* *
39154264 TAATAAAATATATAATACATTTACTTAATCAAGAAAATCTTG
1 TAATAAAACATACAATACATTTACTTAATCAAGAAAATCTTG
39154306 TACATCATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (43 bp):
TAATAAAACATACAATACATTTACTTAATCAAGAAAATCTTGG
Done.