Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 40 of 332
Found at i:12172631 original size:78 final size:78
Alignment explanation
Indices: 12172527--12172680 Score: 281
Period size: 78 Copynumber: 2.0 Consensus size: 78
12172517 AGGGGGCCCA
*
12172527 GGGCCTCTGCCAGCCCCGTATATATATATTGCACCTATTTTCTCACTTCATCTTCATCTTCATCA
1 GGGCCTCTGCCAGCCCCGTAAATATATATTGCACCTATTTTCTCACTTCATCTTCATCTTCATCA
12172592 ACCACTTGTTTCT
66 ACCACTTGTTTCT
* *
12172605 GGGCCTCTGCCAGCCCTGTAAATATATATTGCACCTATTTTCTCTCTTCATCTTCATCTTCATCA
1 GGGCCTCTGCCAGCCCCGTAAATATATATTGCACCTATTTTCTCACTTCATCTTCATCTTCATCA
12172670 ACCACTTGTTT
66 ACCACTTGTTT
12172681 TTCTTTCTCT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.19, C:0.31, G:0.10, T:0.39
Consensus pattern (78 bp):
GGGCCTCTGCCAGCCCCGTAAATATATATTGCACCTATTTTCTCACTTCATCTTCATCTTCATCA
ACCACTTGTTTCT
Found at i:12184154 original size:31 final size:31
Alignment explanation
Indices: 12184116--12184174 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
12184106 GTCGTGTGGG
* *
12184116 CCACACGGGTATGT-GGACCCATACGAGTGAA
1 CCACACGGGCATGTAGG-CCCACACGAGTGAA
12184147 CCACACGGGCATGTAGGCCCACACGAGT
1 CCACACGGGCATGTAGGCCCACACGAGT
12184175 TATAACACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.27, C:0.31, G:0.29, T:0.14
Consensus pattern (31 bp):
CCACACGGGCATGTAGGCCCACACGAGTGAA
Found at i:12191082 original size:27 final size:26
Alignment explanation
Indices: 12191047--12191141 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 26
12191037 AGCATGGCTG
* *
12191047 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
12191073 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
12191101 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
*
12191128 CCAGATCAGATAAT
1 CCAGAACAGATAAT
12191142 TTGTGGTATA
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.11
27 39 0.62
28 17 0.27
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:12191155 original size:28 final size:28
Alignment explanation
Indices: 12191047--12191158 Score: 115
Period size: 27 Copynumber: 4.1 Consensus size: 28
12191037 AGCATGGCTG
* * *
12191047 CCAGAACAGATAA--TGTGACAGAGTCA
1 CCAGATCAGATAATTTGTGGCAGAGCCA
*
12191073 CCAGATACAGATAA-TCGTGGCAGAGCCA
1 CCAGAT-CAGATAATTTGTGGCAGAGCCA
* *
12191101 CCAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGATCAGATAATTTGTGGCAGAGCCA
* *
12191128 CCAGATCAGATAATTTGTGGTATAGCCA
1 CCAGATCAGATAATTTGTGGCAGAGCCA
12191156 CCA
1 CCA
12191159 AGACGCTTCC
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
26 6 0.08
27 34 0.48
28 31 0.44
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (28 bp):
CCAGATCAGATAATTTGTGGCAGAGCCA
Found at i:12192288 original size:15 final size:15
Alignment explanation
Indices: 12192233--12192289 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
12192223 TTTATATTAC
*
12192233 AAAATATTTGTTATT
1 AAAATATTTATTATT
* *
12192248 AATATATTTATAATTGT
1 AAAATATTTATTA-T-T
12192265 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
12192282 AAAATATT
1 AAAATATT
12192290 AGTATTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:12192353 original size:13 final size:14
Alignment explanation
Indices: 12192322--12192363 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
12192312 ATGTGAAGAA
12192322 TATTATTTAAAATTAT
1 TATT-TTTAAAA-TAT
12192338 TATTTTTAAAAT-T
1 TATTTTTAAAATAT
*
12192351 TATTGTTAAAATA
1 TATTTTTAAAATA
12192364 AAATTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
15 7 0.29
16 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
TATTTTTAAAATAT
Found at i:12192463 original size:25 final size:25
Alignment explanation
Indices: 12192427--12192476 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
12192417 TTATTATATA
12192427 AATAAATGTAAATAAATAT-ATATTT
1 AATAAATGTAAA-AAATATAATATTT
*
12192452 AATAATAT-TAAAAATTATAATATTT
1 AATAA-ATGTAAAAAATATAATATTT
12192477 TTATTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 5 0.23
25 15 0.68
26 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AATAAATGTAAAAAATATAATATTT
Found at i:12192496 original size:9 final size:9
Alignment explanation
Indices: 12192482--12192510 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
12192472 TATTTTTATT
12192482 AATATTTTA
1 AATATTTTA
12192491 AATATTTTA
1 AATATTTTA
12192500 AATATTTTA
1 AATATTTTA
12192509 AA
1 AA
12192511 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
AATATTTTA
Found at i:12192695 original size:19 final size:20
Alignment explanation
Indices: 12192649--12192695 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
12192639 AAAAATAATT
12192649 TATTTTCTATTGACCTGTAAGC
1 TATTTTCTATTGACC--TAAGC
12192671 TATTTTCTATTGACC-AAGC
1 TATTTTCTATTGACCTAAGC
*
12192690 TGTTTT
1 TATTTT
12192696 TTTTTTTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 9 0.38
22 15 0.62
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (20 bp):
TATTTTCTATTGACCTAAGC
Found at i:12195632 original size:14 final size:15
Alignment explanation
Indices: 12195603--12195632 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12195593 CAAAATTAAG
12195603 ACATGATACTTTCAC
1 ACATGATACTTTCAC
12195618 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
12195632 A
1 A
12195633 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:12199650 original size:18 final size:19
Alignment explanation
Indices: 12199615--12199653 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
12199605 ATATATAGCT
*
12199615 AAAATTTTAGAAAGTTAAA
1 AAAATTTGAGAAAGTTAAA
*
12199634 AAAATTTGA-AAATTTAAA
1 AAAATTTGAGAAAGTTAAA
12199652 AA
1 AA
12199654 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (19 bp):
AAAATTTGAGAAAGTTAAA
Found at i:12199666 original size:18 final size:19
Alignment explanation
Indices: 12199645--12199683 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12199635 AAATTTGAAA
12199645 ATTT-AAAAATAAAAAAAT
1 ATTTAAAAAATAAAAAAAT
*
12199663 ATTTAAAAAATAAAAATAT
1 ATTTAAAAAATAAAAAAAT
12199682 AT
1 AT
12199684 ATTTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTTAAAAAATAAAAAAAT
Found at i:12199670 original size:25 final size:24
Alignment explanation
Indices: 12199630--12199680 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
12199620 TTTAGAAAGT
**
12199630 TAAAAAAATTTGAAAATTTAAAAA
1 TAAAAAAATTTGAAAAAATAAAAA
*
12199654 TAAAAAAATATTTAAAAAATAAAAA
1 TAAAAAAAT-TTGAAAAAATAAAAA
12199679 TA
1 TA
12199681 TATATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
TAAAAAAATTTGAAAAAATAAAAA
Found at i:12199853 original size:26 final size:27
Alignment explanation
Indices: 12199824--12199884 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
12199814 TATTTTGAAC
*
12199824 TTTCTTAAATTTTTA-T-ATTTTTTTA
1 TTTCTTAAAATTTTACTAATTTTTTTA
12199849 TTT-TCTAAAATTTTACCTAATTTTTTTA
1 TTTCT-TAAAATTTTA-CTAATTTTTTTA
12199877 TTTCTTAA
1 TTTCTTAA
12199885 CTTATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 1 0.03
25 12 0.40
27 1 0.03
28 15 0.50
29 1 0.03
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTCTTAAAATTTTACTAATTTTTTTA
Found at i:12204344 original size:28 final size:28
Alignment explanation
Indices: 12204304--12204382 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
12204294 GCAATCAAAT
* * *
12204304 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
12204332 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
12204360 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
12204383 CAAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:12204645 original size:41 final size:40
Alignment explanation
Indices: 12204555--12204702 Score: 145
Period size: 41 Copynumber: 3.6 Consensus size: 40
12204545 CGGGCTTCGG
* *
12204555 GCCTAGCAGGCTATAATGCTGGTGAAATGATATCAGGCTTCAA
1 GCCTAGCAGGCTA-AATGCCGGTG-AATGAT-TCAGGCTTAAA
* *
12204598 GCCTAGCAGGCGAAATGCCGGTGAATGAGTTCAGACTTAAA
1 GCCTAGCAGGCTAAATGCCGGTGAATGA-TTCAGGCTTAAA
* *** * *
12204639 GTCTAGCAGGCTTCGTGCCGGTG-ATGAATTCGGGTTTAAA
1 GCCTAGCAGGCTAAATGCCGGTGAATG-ATTCAGGCTTAAA
*
12204679 ACCTAGCAGGCTAAATGCCGGTGA
1 GCCTAGCAGGCTAAATGCCGGTGA
12204703 TTTGATAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
40 30 0.35
41 33 0.39
42 10 0.12
43 12 0.14
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (40 bp):
GCCTAGCAGGCTAAATGCCGGTGAATGATTCAGGCTTAAA
Found at i:12204698 original size:40 final size:40
Alignment explanation
Indices: 12204556--12204703 Score: 118
Period size: 40 Copynumber: 3.6 Consensus size: 40
12204546 GGGCTTCGGG
* * * *
12204556 CCTAGCAGGCTATAATGCTGGTGAAATG-ATATCAGGCTTCAAG
1 CCTAGCAGGCTA-AATGCCGGTG--ATGAAT-TCAGACTTAAAA
* * *
12204599 CCTAGCAGGCGAAATGCCGGTGAATGAGTTCAGACTTAAAG
1 CCTAGCAGGCTAAATGCCGGTG-ATGAATTCAGACTTAAAA
* *** * **
12204640 TCTAGCAGGCTTCGTGCCGGTGATGAATTCGGGTTTAAAA
1 CCTAGCAGGCTAAATGCCGGTGATGAATTCAGACTTAAAA
12204680 CCTAGCAGGCTAAATGCCGGTGAT
1 CCTAGCAGGCTAAATGCCGGTGAT
12204704 TTGATAAAAG
Statistics
Matches: 85, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
40 33 0.39
41 31 0.36
42 10 0.12
43 11 0.13
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (40 bp):
CCTAGCAGGCTAAATGCCGGTGATGAATTCAGACTTAAAA
Found at i:12210945 original size:15 final size:15
Alignment explanation
Indices: 12210925--12210958 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
12210915 GGTTCATGAT
12210925 TGTTCCTCTCAATAA
1 TGTTCCTCTCAATAA
*
12210940 TGTTCCTTTCAATAA
1 TGTTCCTCTCAATAA
12210955 TGTT
1 TGTT
12210959 TTTTCCAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.47
Consensus pattern (15 bp):
TGTTCCTCTCAATAA
Found at i:12215946 original size:38 final size:37
Alignment explanation
Indices: 12215904--12215976 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
12215894 TCTCAACAGT
*
12215904 TAGATTCTAG-TTCTGTCAAATTGTAACATTTTAAAAGC
1 TAGATT-TAGATTCTGTCAAATTGTAAC-TGTTAAAAGC
* *
12215942 TAGATTTTGATTTTGTCAAATTGTAACTGTTAAAA
1 TAGATTTAGATTCTGTCAAATTGTAACTGTTAAAA
12215977 AATATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 9 0.29
38 22 0.71
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (37 bp):
TAGATTTAGATTCTGTCAAATTGTAACTGTTAAAAGC
Found at i:12220659 original size:26 final size:25
Alignment explanation
Indices: 12220614--12220676 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
12220604 CCTTCGAACA
* * *
12220614 ACTCAAAGTCAAAGGTCCTCGGACCC
1 ACTCAAACTCAAAAGACCTCGGA-CC
*
12220640 ACTCAAACTCAAAAGACCTCTGACC
1 ACTCAAACTCAAAAGACCTCGGACC
12220665 ATCTC-AACTCAA
1 A-CTCAAACTCAA
12220677 TCTCTCTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 10 0.31
26 22 0.69
ACGTcount: A:0.37, C:0.35, G:0.11, T:0.17
Consensus pattern (25 bp):
ACTCAAACTCAAAAGACCTCGGACC
Found at i:12221228 original size:20 final size:20
Alignment explanation
Indices: 12221203--12221250 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
12221193 TGCAACTATG
12221203 TTTCACCAAGCCCAAACATA
1 TTTCACCAAGCCCAAACATA
12221223 TTTCACCAAGCCCAAACATA
1 TTTCACCAAGCCCAAACATA
12221243 TTTCACCA
1 TTTCACCA
12221251 TATTGACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.35, G:0.04, T:0.23
Consensus pattern (20 bp):
TTTCACCAAGCCCAAACATA
Found at i:12222370 original size:16 final size:16
Alignment explanation
Indices: 12222349--12222383 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
12222339 TCCCATGCAT
12222349 AATACTACCTTAGCCG
1 AATACTACCTTAGCCG
12222365 AATACTACCTTAGCCG
1 AATACTACCTTAGCCG
12222381 AAT
1 AAT
12222384 GCTCCCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (16 bp):
AATACTACCTTAGCCG
Found at i:12225282 original size:46 final size:46
Alignment explanation
Indices: 12225215--12225528 Score: 450
Period size: 46 Copynumber: 6.8 Consensus size: 46
12225205 AGTGTGCTCT
* *
12225215 CTGATATGGAATGTATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
12225261 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
12225307 CTGATATGAAATGTGTAAGACCATGGTTGAAACATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
12225353 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
12225399 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** **
12225445 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
12225492 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
12225529 TATGACATCA
Statistics
Matches: 250, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 208 0.83
47 42 0.17
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:12228555 original size:38 final size:38
Alignment explanation
Indices: 12228504--12228576 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
12228494 CTCAATAGCC
* *
12228504 AGATTCTGGTTTTGTCAAATCGTAACCGTTTAAAAGTT
1 AGATTCTGATTTTGTCAAATCATAACCGTTTAAAAGTT
* **
12228542 AGATTCTGATTTTGTTAAATCATAATTGTTTAAAA
1 AGATTCTGATTTTGTCAAATCATAACCGTTTAAAA
12228577 ATATTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (38 bp):
AGATTCTGATTTTGTCAAATCATAACCGTTTAAAAGTT
Found at i:12231529 original size:31 final size:31
Alignment explanation
Indices: 12231491--12231554 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
12231481 GAGATAATTT
12231491 TTGCTACCGTGTTTTCAAGCTTGCTGCACTC
1 TTGCTACCGTGTTTTCAAGCTTGCTGCACTC
12231522 TTGCTACCGTGTTTTCAAGCTTGCTGCACTC
1 TTGCTACCGTGTTTTCAAGCTTGCTGCACTC
12231553 TT
1 TT
12231555 TCGATATTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.12, C:0.28, G:0.19, T:0.41
Consensus pattern (31 bp):
TTGCTACCGTGTTTTCAAGCTTGCTGCACTC
Found at i:12234150 original size:22 final size:22
Alignment explanation
Indices: 12234123--12234193 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
12234113 TTTGATGAGA
12234123 ATTTAAATTTCACCATATGTAT
1 ATTTAAATTTCACCATATGTAT
** ***
12234145 ATTTAAATTAAAGTTTGATGTGA-
1 ATTTAAATTTCACCAT-ATGT-AT
*
12234168 GTTTAAATTTCACCATATGTAT
1 ATTTAAATTTCACCATATGTAT
12234190 ATTT
1 ATTT
12234194 TTATCTGTTT
Statistics
Matches: 34, Mismatches: 12, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
21 1 0.03
22 18 0.53
23 14 0.41
24 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (22 bp):
ATTTAAATTTCACCATATGTAT
Found at i:12234153 original size:45 final size:45
Alignment explanation
Indices: 12234103--12234193 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
12234093 AGTTGAATGG
12234103 TAAATTAAAGTTTGATGAGAATTTAAATTTCACCATATGTATATT
1 TAAATTAAAGTTTGATGAGAATTTAAATTTCACCATATGTATATT
* *
12234148 TAAATTAAAGTTTGATGTGAGTTTAAATTTCACCATATGTATATT
1 TAAATTAAAGTTTGATGAGAATTTAAATTTCACCATATGTATATT
12234193 T
1 T
12234194 TTATCTGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (45 bp):
TAAATTAAAGTTTGATGAGAATTTAAATTTCACCATATGTATATT
Found at i:12235200 original size:26 final size:26
Alignment explanation
Indices: 12235171--12235256 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
12235161 GACTAATTAT
12235171 AAAATTAAAATATAAAGATTGAATTG
1 AAAATTAAAATATAAAGATTGAATTG
* ** ** *
12235197 AAAA-TAGAAATTTAATCATTTTTATGTAA
1 AAAATTA-AAATATAAAGA-TTGAAT-T-G
12235226 AAAATTAAAATATAAAGATTGAATTG
1 AAAATTAAAATATAAAGATTGAATTG
12235252 AAAAT
1 AAAAT
12235257 AGAAATTTAA
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
25 2 0.05
26 17 0.40
27 5 0.12
28 5 0.12
29 12 0.28
30 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.09, T:0.34
Consensus pattern (26 bp):
AAAATTAAAATATAAAGATTGAATTG
Found at i:12254736 original size:16 final size:16
Alignment explanation
Indices: 12254686--12254737 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
12254676 TCGTGTACTC
*
12254686 TTTTTTCCTTCATTAGG
1 TTTTTTCC-TCATAAGG
12254703 TTTTTATCC-CATAA-G
1 TTTTT-TCCTCATAAGG
*
12254718 TTTTTTCCTAATAAGG
1 TTTTTTCCTCATAAGG
12254734 TTTT
1 TTTT
12254738 AACGAAGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
16 9 0.30
17 5 0.17
18 3 0.10
ACGTcount: A:0.19, C:0.15, G:0.10, T:0.56
Consensus pattern (16 bp):
TTTTTTCCTCATAAGG
Found at i:12259663 original size:27 final size:27
Alignment explanation
Indices: 12259633--12259694 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
12259623 ATTAAATCTT
12259633 TTTAATAATTA-AT-AAATTATTTGTAAA
1 TTTAATAATTACATGAAA-TATTT-TAAA
*
12259660 TTTAATTA-TACATGAAATATTTTAAA
1 TTTAATAATTACATGAAATATTTTAAA
*
12259686 TATAATAAT
1 TTTAATAAT
12259695 AAACAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 12 0.41
27 14 0.48
28 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
TTTAATAATTACATGAAATATTTTAAA
Found at i:12264585 original size:43 final size:41
Alignment explanation
Indices: 12264536--12264650 Score: 126
Period size: 42 Copynumber: 2.7 Consensus size: 41
12264526 AGATATCGTG
* *
12264536 TAAGACCGTGTCTGGGACACAGGCCTCGAT-TGATATTTACGTA
1 TAAGACCATGTCTGGGACACAGGCATCGATCTGAT-TTT--GTA
*
12264579 TAAGACCATGTCTGGGACATC-GGCATCGTATCTGATTTTGTG
1 TAAGACCATGTCTGGGACA-CAGGCATCG-ATCTGATTTTGTA
* *
12264621 TAAGACCCTGTCTGGGACAGAGGCATCGAT
1 TAAGACCATGTCTGGGACACAGGCATCGAT
12264651 ATTAAATTAC
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
41 2 0.03
42 27 0.43
43 24 0.38
44 6 0.10
45 4 0.06
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (41 bp):
TAAGACCATGTCTGGGACACAGGCATCGATCTGATTTTGTA
Found at i:12266052 original size:11 final size:11
Alignment explanation
Indices: 12266038--12266092 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
12266028 AGATAAATAT
12266038 TATTTTATTAA
1 TATTTTATTAA
*
12266049 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
12266062 TATTTT-TTAT
1 TATTTTATTAA
*
12266072 TATTTTATTAT
1 TATTTTATTAA
12266083 TATTTTATTA
1 TATTTTATTA
12266093 GTATATAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 6 0.16
11 22 0.58
12 3 0.08
13 7 0.18
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:12268267 original size:46 final size:46
Alignment explanation
Indices: 12268214--12268579 Score: 527
Period size: 46 Copynumber: 8.0 Consensus size: 46
12268204 AGTGTGCTCT
*
12268214 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
12268260 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
12268306 CTGATATGAAATGTGTAAGACTATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
12268352 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
12268398 CTGATATGAAATGTGTAAGACTATGGTTAAAAGATACCATGACAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
12268444 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
12268490 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
12268536 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
12268580 TCATGTCAAA
Statistics
Matches: 294, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
45 1 0.00
46 293 1.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:12274854 original size:18 final size:18
Alignment explanation
Indices: 12274831--12274866 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12274821 ATTTGGGTAA
12274831 AACCGAAATAATTCGGTT
1 AACCGAAATAATTCGGTT
*
12274849 AACCGAATTAATTCGGTT
1 AACCGAAATAATTCGGTT
12274867 GGGGGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (18 bp):
AACCGAAATAATTCGGTT
Found at i:12275175 original size:9 final size:9
Alignment explanation
Indices: 12275161--12275235 Score: 89
Period size: 9 Copynumber: 8.4 Consensus size: 9
12275151 TTTATACAAA
12275161 TAATTCGGT
1 TAATTCGGT
*
12275170 TAATTCAGT
1 TAATTCGGT
*
12275179 TAATTCGAT
1 TAATTCGGT
* *
12275188 TAATTTGGA
1 TAATTCGGT
*
12275197 TAATTAGG-
1 TAATTCGGT
12275205 TAATTCGGT
1 TAATTCGGT
*
12275214 TAATTCGAT
1 TAATTCGGT
12275223 TAATTCGGT
1 TAATTCGGT
12275232 TAAT
1 TAAT
12275236 CTTATACTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
8 7 0.13
9 48 0.87
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:12275210 original size:35 final size:36
Alignment explanation
Indices: 12275160--12275227 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
12275150 TTTTATACAA
*
12275160 ATAATTCGGTTAATTCAGTTAATTCGATTAATTTGG
1 ATAATTAGGTTAATTCAGTTAATTCGATTAATTTGG
*
12275196 ATAATTAGG-TAATTCGGTTAATTCGATTAATT
1 ATAATTAGGTTAATTCAGTTAATTCGATTAATT
12275228 CGGTTAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 22 0.73
36 8 0.27
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.44
Consensus pattern (36 bp):
ATAATTAGGTTAATTCAGTTAATTCGATTAATTTGG
Found at i:12276462 original size:42 final size:41
Alignment explanation
Indices: 12276360--12276500 Score: 133
Period size: 43 Copynumber: 3.3 Consensus size: 41
12276350 ATCTGAGATA
* *
12276360 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCGATTGATATT
1 TCGTGTAAGACCATGTCTGGGACACAGGCATCGATTGA-ATT
* *
12276402 TACGTATAAGACCATGTCTGGGACATC-GGTATCGTATCTG-ATT
1 T-CGTGTAAGACCATGTCTGGGACA-CAGGCATCG-AT-TGAATT
* *
12276445 TCGTGTAAGACCCTGTCTGGGACAAAGGCATCGATATTGAATT
1 TCGTGTAAGACCATGTCTGGGACACAGGCATCG--ATTGAATT
* *
12276488 ACATGTAAGACCA
1 TCGTGTAAGACCA
12276501 CGTTAGGAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
42 30 0.37
43 46 0.57
44 3 0.04
45 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
TCGTGTAAGACCATGTCTGGGACACAGGCATCGATTGAATT
Found at i:12277088 original size:15 final size:16
Alignment explanation
Indices: 12277063--12277092 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12277053 GGTTTTGGTG
12277063 TATGTTTCTAATGTGC
1 TATGTTTCTAATGTGC
12277079 TATG-TTCTAATGTG
1 TATGTTTCTAATGTG
12277093 ATTTTGTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (16 bp):
TATGTTTCTAATGTGC
Found at i:12280896 original size:97 final size:97
Alignment explanation
Indices: 12280730--12280989 Score: 394
Period size: 97 Copynumber: 2.7 Consensus size: 97
12280720 ACACCTGATT
* * * * * *
12280730 GCTAAACCCTAAATTTGAAATAGATTGGAGAAAAATTAGTCGGTTTCTGTTGATTTAAATGCGTT
1 GCTAAATCCTGAATTTGAAACAGATTCGAGAAAAATTAGTCGATTTCTGTTGATTTAAATGTGTT
* *
12280795 GAAAGCCTTAATAGTTCTTTGCGAACATAATG
66 GAAAGCCTTAATAATTCTTAGCGAACATAATG
*
12280827 GCTAAATCCTGAATTTGAAACAGATTCGAGAAAAATTAGTCGATTTCTGTTGCTTTAAATGTGTT
1 GCTAAATCCTGAATTTGAAACAGATTCGAGAAAAATTAGTCGATTTCTGTTGATTTAAATGTGTT
*
12280892 GAAAGCCTTAATAATTCTTAGCGAACTTAATG
66 GAAAGCCTTAATAATTCTTAGCGAACATAATG
* * * *
12280924 GCTAAATCCTGAATTTGAAACACATTCGAGAAAAGTTAGCCGTTTTCTGTTGATTTAAATGTGTT
1 GCTAAATCCTGAATTTGAAACAGATTCGAGAAAAATTAGTCGATTTCTGTTGATTTAAATGTGTT
12280989 G
66 G
12280990 TGATATCGAT
Statistics
Matches: 148, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 148 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (97 bp):
GCTAAATCCTGAATTTGAAACAGATTCGAGAAAAATTAGTCGATTTCTGTTGATTTAAATGTGTT
GAAAGCCTTAATAATTCTTAGCGAACATAATG
Found at i:12288452 original size:18 final size:18
Alignment explanation
Indices: 12288431--12288465 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12288421 TTTATTTTCA
12288431 TAATAAAATTAATTAATT
1 TAATAAAATTAATTAATT
**
12288449 TAATATCATTAATTAAT
1 TAATAAAATTAATTAAT
12288466 CTAAGTATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATAAAATTAATTAATT
Found at i:12294082 original size:5 final size:5
Alignment explanation
Indices: 12294072--12294174 Score: 52
Period size: 5 Copynumber: 19.4 Consensus size: 5
12294062 TAAGATAAAC
* *
12294072 ATTAA ATTAA ATTAAA TATTAA ATCT-T ATTAA ATT-A ATAAAA TATTAA
1 ATTAA ATTAA ATT-AA -ATTAA AT-TAA ATTAA ATTAA AT-TAA -ATTAA
* *
12294120 ATTAA ATTTAA TATTAA ATT-A A-TAA ATTACT ATTAA GATTAGT ATTAA
1 ATTAA A-TTAA -ATTAA ATTAA ATTAA ATTA-A ATTAA -ATTA-A ATTAA
12294168 ATTAA AT
1 ATTAA AT
12294175 ATATTAAAAC
Statistics
Matches: 76, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
3 1 0.01
4 8 0.11
5 33 0.43
6 28 0.37
7 6 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (5 bp):
ATTAA
Found at i:12294134 original size:17 final size:17
Alignment explanation
Indices: 12294034--12294141 Score: 67
Period size: 16 Copynumber: 6.9 Consensus size: 17
12294024 AAGCTTATAC
12294034 TTTAATATTAAATT-AA
1 TTTAATATTAAATTAAA
* *
12294050 TATAATATT-TATTAAGA
1 TTTAATATTAAATTAA-A
* *
12294067 -TAAACATTAAATTAAA
1 TTTAATATTAAATTAAA
12294083 -TTAA-A-T--ATTAAA
1 TTTAATATTAAATTAAA
*
12294095 TCT--TATTAAATT-AA
1 TTTAATATTAAATTAAA
**
12294109 TAAAATATTAAATTAAA
1 TTTAATATTAAATTAAA
12294126 TTTAATATTAAATTAA
1 TTTAATATTAAATTAA
12294142 TAAATTACTA
Statistics
Matches: 69, Mismatches: 12, Indels: 21
0.68 0.12 0.21
Matches are distributed among these distances:
12 7 0.10
13 2 0.03
14 4 0.06
15 7 0.10
16 27 0.39
17 22 0.32
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAATATTAAATTAAA
Found at i:12294155 original size:31 final size:32
Alignment explanation
Indices: 12294035--12294172 Score: 96
Period size: 31 Copynumber: 4.5 Consensus size: 32
12294025 AGCTTATACT
* * *
12294035 TTAATATTAAATTAATATAATATTTATTAAGA
1 TTAATATTAAATTAATAAAATACTAATTAAGA
* * *
12294067 TAAACATTAAATTAA-ATTAA-A-T-ATTAA-A
1 TTAATATTAAATTAATA-AAATACTAATTAAGA
*
12294095 TCT--TATTAAATTAATAAAATATTAAATTAA-A
1 T-TAATATTAAATTAATAAAATACT-AATTAAGA
*
12294126 TTTAATATTAAATTAATAAATTACT-ATTAAGA
1 -TTAATATTAAATTAATAAAATACTAATTAAGA
*
12294158 TTAGTATTAAATTAA
1 TTAATATTAAATTAA
12294173 ATATATTAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
27 12 0.14
28 4 0.05
29 6 0.07
30 1 0.01
31 28 0.32
32 18 0.21
33 18 0.21
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (32 bp):
TTAATATTAAATTAATAAAATACTAATTAAGA
Found at i:12294167 original size:43 final size:42
Alignment explanation
Indices: 12294072--12294176 Score: 122
Period size: 43 Copynumber: 2.5 Consensus size: 42
12294062 TAAGATAAAC
* *
12294072 ATTAAATTAAATTAAATATTAAATCTTATTAAATTAATAAAAT
1 ATTAAATTAAATTAAATATTAAA-CTTAATAAATTAATAAAAG
* * *
12294115 ATTAAATTAAATTTAATATTAAA-TTAATAAATTACTATTAAG
1 ATTAAATTAAATTAAATATTAAACTTAATAAATTAATA-AAAG
*
12294157 ATTAGTATTAAATTAAATAT
1 ATTA-AATTAAATTAAATAT
12294177 ATTAAAACAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 12 0.23
42 6 0.11
43 35 0.66
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (42 bp):
ATTAAATTAAATTAAATATTAAACTTAATAAATTAATAAAAG
Found at i:12299590 original size:20 final size:20
Alignment explanation
Indices: 12299565--12299603 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12299555 GGGACAATTG
*
12299565 AATCAATTTGATTAAAATCA
1 AATCAAATTGATTAAAATCA
*
12299585 AATCAAATTGATTAGAATC
1 AATCAAATTGATTAAAATC
12299604 TAATTCAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (20 bp):
AATCAAATTGATTAAAATCA
Found at i:12300956 original size:15 final size:15
Alignment explanation
Indices: 12300938--12300968 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12300928 GACGATTCCG
12300938 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
12300953 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
12300968 T
1 T
12300969 ACTGATACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
TGTGCTCTGATTCAT
Found at i:12301750 original size:22 final size:23
Alignment explanation
Indices: 12301690--12301774 Score: 79
Period size: 22 Copynumber: 3.8 Consensus size: 23
12301680 CTAAACAGAT
*
12301690 AAGTGCTAAGAAAAGAGCATCGA
1 AAGTGCTAAGCAAAGAGCATCGA
* ** *
12301713 AA-TGCTGATTAGAGAGCA-CGA
1 AAGTGCTAAGCAAAGAGCATCGA
12301734 AAGTGCTAAGCAAAGAGCATCG-
1 AAGTGCTAAGCAAAGAGCATCGA
*
12301756 AAGTGTTCAA-CAAAGAGCA
1 AAGTGCT-AAGCAAAGAGCA
12301775 CCAAAGTACT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
21 5 0.10
22 39 0.78
23 6 0.12
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (23 bp):
AAGTGCTAAGCAAAGAGCATCGA
Found at i:12301773 original size:44 final size:44
Alignment explanation
Indices: 12301690--12301786 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
12301680 CTAAACAGAT
* ** * *
12301690 AAGTGCTAAGAAAAGAGCATCGAAATGCTGATTAGAGAGCACGA
1 AAGTGCTAAGAAAAGAGCATCGAAATGCTCAACAAAGAGCACCA
* * *
12301734 AAGTGCTAAGCAAAGAGCATCGAAGTGTTCAACAAAGAGCACCA
1 AAGTGCTAAGAAAAGAGCATCGAAATGCTCAACAAAGAGCACCA
*
12301778 AAGTACTAA
1 AAGTGCTAA
12301787 ACTAGTACAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.15
Consensus pattern (44 bp):
AAGTGCTAAGAAAAGAGCATCGAAATGCTCAACAAAGAGCACCA
Found at i:12301781 original size:22 final size:22
Alignment explanation
Indices: 12301690--12301786 Score: 63
Period size: 22 Copynumber: 4.4 Consensus size: 22
12301680 CTAAACAGAT
* *
12301690 AAGTGCTAAGAAAAGAGCATCGA
1 AAGTGCTAAGCAAAGAGCA-CCA
* ** * *
12301713 AA-TGCTGATTAGAGAGCACGA
1 AAGTGCTAAGCAAAGAGCACCA
* *
12301734 AAGTGCTAAGCAAAGAGCATCG
1 AAGTGCTAAGCAAAGAGCACCA
*
12301756 AAGTGTTCAA-CAAAGAGCACCA
1 AAGTGCT-AAGCAAAGAGCACCA
*
12301778 AAGTACTAA
1 AAGTGCTAA
12301787 ACTAGTACAC
Statistics
Matches: 56, Mismatches: 16, Indels: 6
0.72 0.21 0.08
Matches are distributed among these distances:
21 7 0.12
22 45 0.80
23 4 0.07
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.15
Consensus pattern (22 bp):
AAGTGCTAAGCAAAGAGCACCA
Found at i:12311254 original size:26 final size:26
Alignment explanation
Indices: 12311233--12311297 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
12311223 AAATCGCAAT
* *
12311233 AAAGCTGCCAGTAATAGTATCGCAGC
1 AAAGCTGCCAGTAACAATATCGCAGC
* * *
12311259 AAAGCTGTCAATAACAATAACGCAGC
1 AAAGCTGCCAGTAACAATATCGCAGC
12311285 AAAGCTGCCAGTA
1 AAAGCTGCCAGTA
12311298 TCAGGCTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (26 bp):
AAAGCTGCCAGTAACAATATCGCAGC
Found at i:12318493 original size:16 final size:16
Alignment explanation
Indices: 12318472--12318506 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
12318462 TTACCTAATC
12318472 AACTGATAAAGGGGTA
1 AACTGATAAAGGGGTA
12318488 AACTGATAAAGGGGTA
1 AACTGATAAAGGGGTA
12318504 AAC
1 AAC
12318507 GCAATAGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.09, G:0.29, T:0.17
Consensus pattern (16 bp):
AACTGATAAAGGGGTA
Found at i:12325265 original size:45 final size:44
Alignment explanation
Indices: 12325196--12325736 Score: 228
Period size: 45 Copynumber: 12.2 Consensus size: 44
12325186 AGTTACAGGA
*
12325196 AGCAGACTTAAAGTTAC-AGATCTTATCTCCATGTATCGGCTATGG
1 AGCAGA-TTAAAATTACGAG-TCTTATCTCCATGTATCGGCTATGG
** *
12325241 AGCAGATTGAAAATGGCGAGTCTTATCTACATGTATCGGCTATGG
1 AGCAGATT-AAAATTACGAGTCTTATCTCCATGTATCGGCTATGG
** *** * * * *
12325286 AGCAGATTTTAGCCACCAGCCTTATCTCTC-TG-AGGT-AGC-AAGAG
1 AGCAGATTAAAATTACGAGTCTTATCTC-CATGTA--TCGGCTATG-G
* * * *
12325330 AGCAGGTTGAAGATATA-G-GTCTTATCTTCC-TGAAGT-TG-TA-GG
1 AGCAGATT-AAAAT-TACGAGTCTTATC-TCCATGTA-TCGGCTATGG
* *
12325372 AAGCAGACTAAAAATTAC-AGATCTTATCTCCATGTATTGGCTATGG
1 -AGCAGA-TTAAAATTACGAG-TCTTATCTCCATGTATCGGCTATGG
* * ** *
12325418 AGCATATCAGAAATGGCGAGTCTTATCTCCATGTATTGGCTATGG
1 AGCAGATTA-AAATTACGAGTCTTATCTCCATGTATCGGCTATGG
* * ** *** * *
12325463 AGAAAATTTTAGCCACAAGTCTTATCTTCCTAAAGT-T--GC-A-GG
1 AGCAGATTAAAATTACGAGTCTTATC-TCC--ATGTATCGGCTATGG
* *
12325505 AAGCAGACTGAAAATTAC-AGATCTTATCTCTATGTATCGGCTATGG
1 -AGCAGA-TTAAAATTACGAG-TCTTATCTCCATGTATCGGCTATGG
* *
12325551 AGCAGATCAGAAATGACGAGTCTTATCTCCATGTATCGGCTATGG
1 AGCAGATTA-AAATTACGAGTCTTATCTCCATGTATCGGCTATGG
** *** * * *
12325596 AGCAGATTTTAGCCACAAGTCTTATCTTCC-TGAAGT-TGC-A-GG
1 AGCAGATTAAAATTACGAGTCTTATC-TCCATGTA-TCGGCTATGG
* *
12325638 AAGCAGACTGAAAATTAC-AGATCTTATCTCCATATATCGGCTATGG
1 -AGCAGA-TTAAAATTACGAG-TCTTATCTCCATGTATCGGCTATGG
* *
12325684 AGCAGATTAGAAATTGCGAGTCTTATCTCCATGTATCAGCTATGG
1 AGCAGATTA-AAATTACGAGTCTTATCTCCATGTATCGGCTATGG
12325729 AGCAGATT
1 AGCAGATT
12325737 TTAACCACAA
Statistics
Matches: 370, Mismatches: 80, Indels: 92
0.68 0.15 0.17
Matches are distributed among these distances:
41 3 0.01
42 8 0.02
43 40 0.11
44 115 0.31
45 185 0.50
46 16 0.04
47 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (44 bp):
AGCAGATTAAAATTACGAGTCTTATCTCCATGTATCGGCTATGG
Found at i:12325510 original size:133 final size:133
Alignment explanation
Indices: 12325348--12325801 Score: 764
Period size: 133 Copynumber: 3.4 Consensus size: 133
12325338 GAAGATATAG
* * *
12325348 GTCTTATCTTCCTGAAGTTGTAGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGTATTGGC
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
* * * *
12325413 TATGGAGCATATCAGAAATGGCGAGTCTTATCTCCATGTATTGGCTATGGAGAAAATTTTAGCCA
66 TATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
12325478 CAA
131 CAA
* *
12325481 GTCTTATCTTCCTAAAGTTGCAGGAAGCAGACTGAAAATTACAGATCTTATCTCTATGTATCGGC
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
*
12325546 TATGGAGCAGATCAGAAATGACGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
66 TATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
12325611 CAA
131 CAA
*
12325614 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATATATCGGC
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
* * * *
12325679 TATGGAGCAGATTAGAAATTGCGAGTCTTATCTCCATGTATCAGCTATGGAGCAGATTTTAACCA
66 TATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
12325744 CAA
131 CAA
*
12325747 GTCTTATCTTCCTGAAGTTACAGGAAGCAGACTGAAAATTACAGATCTTATCTCC
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAGATCTTATCTCC
12325802 TAAGTAGTAG
Statistics
Matches: 302, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 302 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (133 bp):
GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
TATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
CAA
Found at i:12325533 original size:177 final size:177
Alignment explanation
Indices: 12325036--12325489 Score: 685
Period size: 177 Copynumber: 2.6 Consensus size: 177
12325026 TGAAAGTTGA
* ** * *
12325036 AGATCTTATCTCCATGTGTCGGCTATGGAGTGGATCGAAAATGGCCAGTCTTATCTCCATATATC
1 AGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTCCATGTATC
* * *
12325101 GACTATGGATCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGTAGGTTGAAGA
66 GGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGA
* *
12325166 TACAGGTCTTATCTTCCTGAAGTTACAGGAAGCAGACTTAAAGTTAC
131 TACAGGTCTTATCTTCCTGAAGTTACAGGAAGCAGACTAAAAATTAC
* *
12325213 AGATCTTATCTCCATGTATCGGCTATGGAGCAGATTGAAAATGGCGAGTCTTATCTACATGTATC
1 AGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTCCATGTATC
*
12325278 GGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGA
66 GGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGA
* **
12325343 TATAGGTCTTATCTTCCTGAAGTTGTAGGAAGCAGACTAAAAATTAC
131 TACAGGTCTTATCTTCCTGAAGTTACAGGAAGCAGACTAAAAATTAC
* *
12325390 AGATCTTATCTCCATGTATTGGCTATGGAGCATATC-AGAAATGGCGAGTCTTATCTCCATGTAT
1 AGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGA-AAATGGCGAGTCTTATCTCCATGTAT
* * * * *
12325454 TGGCTATGGAGAAAATTTTAGCCACAAGTCTTATCT
65 CGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCT
12325490 TCCTAAAGTT
Statistics
Matches: 251, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
176 1 0.00
177 250 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (177 bp):
AGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTCCATGTATC
GGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGA
TACAGGTCTTATCTTCCTGAAGTTACAGGAAGCAGACTAAAAATTAC
Found at i:12331454 original size:24 final size:24
Alignment explanation
Indices: 12331427--12331481 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
12331417 CCTAAAATCT
*
12331427 CTCCATAATACTCT-CATTGATTTC
1 CTCCACAATACTCTAC-TTGATTTC
* *
12331451 CTCCCCAATCCTCTACTTGATTTC
1 CTCCACAATACTCTACTTGATTTC
12331475 CTCCACA
1 CTCCACA
12331482 TAACACTCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.22, C:0.38, G:0.04, T:0.36
Consensus pattern (24 bp):
CTCCACAATACTCTACTTGATTTC
Found at i:12333093 original size:55 final size:54
Alignment explanation
Indices: 12333006--12333260 Score: 251
Period size: 55 Copynumber: 4.8 Consensus size: 54
12332996 ATTAGGGTTT
*
12333006 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * * * *
12333061 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGGC
* ** *
12333116 AAAGG-TCCCATGTAAGACCATGCCAAGGGATGGC-ATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGGC
* *
12333169 AATGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
* ** *
12333218 AAGGATACCACGTAAGACCATGAAAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
12333261 GTACCCGCGT
Statistics
Matches: 167, Mismatches: 26, Indels: 20
0.78 0.12 0.09
Matches are distributed among these distances:
49 38 0.23
52 6 0.04
53 40 0.24
54 12 0.07
55 67 0.40
56 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:12333212 original size:108 final size:110
Alignment explanation
Indices: 12333013--12333213 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
12333003 TTTAAGGATA
*
12333013 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
12333078 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * * *
12333123 CCATGTAAGACCATGCCAAGGGATGGC-ATTGGTGA-G-TTCATAAGGCAATGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
12333185 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
12333214 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.57
109 7 0.08
110 26 0.31
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:12333473 original size:16 final size:16
Alignment explanation
Indices: 12333452--12333482 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12333442 ATAAATTTGA
12333452 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
12333468 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
12333483 AGTGAATAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:12341481 original size:213 final size:213
Alignment explanation
Indices: 12340572--12341558 Score: 1132
Period size: 211 Copynumber: 4.7 Consensus size: 213
12340562 TTTTTTTTAA
* * * *
12340572 TATTCCAGGAAGCT-C--CTCAGAATAAAAAACCTGTAGTTTCTAAAAATGGCCCTGTTCCAGCT
1 TATTCCAGGAAGCTCCTGCTCAGAAGAAAAAACCTGTAGTTGCTAAAACTGGCTCTGTTCCAGCT
* * *
12340634 GCCAAGACAGTGAAAGCTGATAGTAGTTCTGAGTCTAGCAGTGAGGAAGATTCATCCTCTGACGA
66 GCTAAGACAGTGAAAGCTGATAGTAGTTCTGAGTCTAGTAGTGAGGAAGATTCATCCTCTGATGA
* * * *
12340699 AGTGAGTATCATGCTCATGCTTGTAATA-TAGCATGGTTGGTAATATTCTTTT-CTATGATTTTT
131 AGTGAGTATTATGCTCATGCTTATAATATTAGCATGGTTGGGAATATTCTTTTGC-ATGATTGTT
12340762 GATGTTCAATATTTTGTTT
195 GATGTTCAATATTTTGTTT
* ** *
12340781 TA-TCCAGGAAGCTCCTGCTCAGAAGAAAAATCCTGTAGTTGCTAAAAAGGGCTGTGTTCCAGCT
1 TATTCCAGGAAGCTCCTGCTCAGAAGAAAAAACCTGTAGTTGCTAAAACTGGCTCTGTTCCAGCT
* * *
12340845 GCCAAGACAGTGAAAGCTGATAGCAGTTCT---TCAAGTAGTGAGGAAGATTCATCCTCTGATGA
66 GCTAAGACAGTGAAAGCTGATAGTAGTTCTGAGTCTAGTAGTGAGGAAGATTCATCCTCTGATGA
* * * * ** * * *
12340907 AGTGAGTATTATGCTCTTGCTAGTTAAAACATTCGCATAATT-GG-ACATTCTTTTGTATAATTG
131 AGTGAGTATTATGCTCATGC---TTATAATATTAGCATGGTTGGGAATATTCTTTTGCATGATTG
*
12340970 TTAATGTTCAAT-TTTT-TTT
193 TTGATGTTCAATATTTTGTTT
* * * * *
12340989 T-TT-CAGGAAGCTCCTGCTCAGAATAAAAAACCTGTAGCTGCAAAAACTGGCTCTATTCCGGCT
1 TATTCCAGGAAGCTCCTGCTCAGAAGAAAAAACCTGTAGTTGCTAAAACTGGCTCTGTTCCAGCT
* * * * *
12341052 GCTAAGACTGTTAAAGCTGGTAGTAGTTCTGAGTCTAGTAGTGAAGAAGACTCATCCTCTGATGA
66 GCTAAGACAGTGAAAGCTGATAGTAGTTCTGAGTCTAGTAGTGAGGAAGATTCATCCTCTGATGA
* * * * * *
12341117 AGTGAGTAATATG-T-ATGTTTATATTTTTAGTATGGTTGGGAGTATTCTTTTGCATGATTGTTG
131 AGTGAGTATTATGCTCATGCTTATAATATTAGCATGGTTGGGAATATTCTTTTGCATGATTGTTG
*
12341180 ATGTTCAATATTTTGTCT
196 ATGTTCAATATTTTGTTT
* * * * *** ** *
12341198 TATCCCAGGAAGCTACTGCACAGAA-TAAAAACTCTGTAGCCACTAAAACTGTATCTGTTCCAGA
1 TATTCCAGGAAGCTCCTGCTCAGAAGAAAAAAC-CTGTAGTTGCTAAAACTGGCTCTGTTCCAGC
* * * *
12341262 TGCTAAGGCTGTGAAAGCTGATAGTAGTTCTGAGTCTAGTAGTGAGGAAGGTTCATCCTCTGACG
65 TGCTAAGACAGTGAAAGCTGATAGTAGTTCTGAGTCTAGTAGTGAGGAAGATTCATCCTCTGATG
* *
12341327 AAGTGAGTATTATACTCATGCTTATAATATTATCATGGTTGGGAATATTCTTTTGCATGATTGTT
130 AAGTGAGTATTATGCTCATGCTTATAATATTAGCATGGTTGGGAATATTCTTTTGCATGATTGTT
12341392 -ATTGTTCAAT-TGTTTGTTT
195 GA-TGTTCAATAT-TTTGTTT
* ** * * *
12341411 TATTCCAGGAAGTTCCTGCTCAGAAGAAAAAACCCATAGTTGCTAAAAGTGGCTCTATACCAGCT
1 TATTCCAGGAAGCTCCTGCTCAGAAGAAAAAACCTGTAGTTGCTAAAACTGGCTCTGTTCCAGCT
* * *
12341476 GCTAAGACAGTGAAGGCTGATAGTAGTTCAGAGTCTAGTAGTGAGGAAGATTCATCCTCCGATGA
66 GCTAAGACAGTGAAAGCTGATAGTAGTTCTGAGTCTAGTAGTGAGGAAGATTCATCCTCTGATGA
*
12341541 AGTAAGTATTATGCTCAT
131 AGTGAGTATTATGCTCAT
12341559 ATTATATTAA
Statistics
Matches: 643, Mismatches: 111, Indels: 44
0.81 0.14 0.06
Matches are distributed among these distances:
205 11 0.02
206 2 0.00
207 102 0.16
208 69 0.11
209 11 0.02
210 73 0.11
211 187 0.29
212 10 0.02
213 172 0.27
214 6 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (213 bp):
TATTCCAGGAAGCTCCTGCTCAGAAGAAAAAACCTGTAGTTGCTAAAACTGGCTCTGTTCCAGCT
GCTAAGACAGTGAAAGCTGATAGTAGTTCTGAGTCTAGTAGTGAGGAAGATTCATCCTCTGATGA
AGTGAGTATTATGCTCATGCTTATAATATTAGCATGGTTGGGAATATTCTTTTGCATGATTGTTG
ATGTTCAATATTTTGTTT
Found at i:12348686 original size:12 final size:12
Alignment explanation
Indices: 12348669--12348702 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12348659 CGACTCGCCC
12348669 ATATTAATTTTT
1 ATATTAATTTTT
*
12348681 ATATTATTTTTT
1 ATATTAATTTTT
12348693 ATA-TAATTTT
1 ATATTAATTTT
12348703 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:12354210 original size:53 final size:52
Alignment explanation
Indices: 12354138--12354265 Score: 141
Period size: 51 Copynumber: 2.5 Consensus size: 52
12354128 ATACCGATGT
* * * *
12354138 CATATCCCAAATATGGTCTTATACGGGATCACATTATCACATCACACCAACGC
1 CATAGCCCAACTATGGTCTTATACGGGAACAC-GTATCACATCACACCAACGC
* ** ** *
12354191 CATAGCTCAACTATGGTCTTATA-GGGAACACGTATCACATTGCACTGATGC
1 CATAGCCCAACTATGGTCTTATACGGGAACACGTATCACATCACACCAACGC
*
12354242 CATAGCCCAGCTATGGTCTTATAC
1 CATAGCCCAACTATGGTCTTATAC
12354266 AAGTGCACAT
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
51 35 0.56
52 7 0.11
53 20 0.32
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (52 bp):
CATAGCCCAACTATGGTCTTATACGGGAACACGTATCACATCACACCAACGC
Found at i:12358931 original size:262 final size:262
Alignment explanation
Indices: 12358456--12358936 Score: 748
Period size: 262 Copynumber: 1.8 Consensus size: 262
12358446 AATTAAATGG
* * *
12358456 GCCATTAACCTCAATTTAATATTTTTTCTTTTAATTCCAAGCAGAATTTGAAGAGATAAGCTTTG
1 GCCATTAACATCAATTTAATATTTGTCCTTTTAATTCCAAGCAGAATTTGAAGAGATAAGCTTTG
* *
12358521 CTGAGAAAAATAAAATTACATATTAGGCTAAAATATCCGCAAGCCTAAAAGAGCTTGACATTTTG
66 CTAAGAAAAATAAAATTACATATTAAGCTAAAATATCCGCAAGCCTAAAAGAGCTTGACATTTTG
* * * * *
12358586 CATCGCCCATGTCGTTGATCATTGTGGTCGTGCTATTGCCCTACTCATCCCATTGTTGTATATCT
131 CATCGCCCATGTCATTGATCACTATAGTCGTGCTACTGCCCTACTCATCCCATTGTTGTATATCT
*
12358651 TTTCCTGCAAATTATTTGGTTTTAGAAATTTTGACTAATGGAGCTAATAACATCTGTGAATTAAG
196 TTTCCTGCAAACTATTTGGTTTTAGAAATTTTGACTAATGGAGCTAATAACATCTGTGAATTAAG
12358716 GA
261 GA
12358718 GCCATTAACATCAATTTAATATTTGTCCTTTTAATTCCAAGCAGAATTTGAAGAGATAAG-TTCT
1 GCCATTAACATCAATTTAATATTTGTCCTTTTAATTCCAAGCAGAATTTGAAGAGATAAGCTT-T
* ** *
12358782 GCTAAGGAAAATAAAATTACATATTAAGCTAAAATATTTGCAAGCCTAAAAGGGCTTGACATTTT
65 GCTAAGAAAAATAAAATTACATATTAAGCTAAAATATCCGCAAGCCTAAAAGAGCTTGACATTTT
* * * * *
12358847 GTATCGCTCATGTCATTGATCACTATAGTCGTGCTACTGCCGTACTCATCTCATTGTTGTGTATC
130 GCATCGCCCATGTCATTGATCACTATAGTCGTGCTACTGCCCTACTCATCCCATTGTTGTATATC
* *
12358912 TTTTCCTGTAGACTATTTGGTTTTA
195 TTTTCCTGCAAACTATTTGGTTTTA
12358937 AATAAAATTA
Statistics
Matches: 196, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
261 2 0.01
262 194 0.99
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (262 bp):
GCCATTAACATCAATTTAATATTTGTCCTTTTAATTCCAAGCAGAATTTGAAGAGATAAGCTTTG
CTAAGAAAAATAAAATTACATATTAAGCTAAAATATCCGCAAGCCTAAAAGAGCTTGACATTTTG
CATCGCCCATGTCATTGATCACTATAGTCGTGCTACTGCCCTACTCATCCCATTGTTGTATATCT
TTTCCTGCAAACTATTTGGTTTTAGAAATTTTGACTAATGGAGCTAATAACATCTGTGAATTAAG
GA
Found at i:12359295 original size:316 final size:315
Alignment explanation
Indices: 12358707--12359643 Score: 1455
Period size: 316 Copynumber: 3.0 Consensus size: 315
12358697 ATAACATCTG
* *
12358707 TGAATTAAGGAGCCATTAACATCAATTTAATATTTGTCCTTTTAATTCCAAGCAGAATTTGAAGA
1 TGAATTAATGAGCCTTTAACATCAATTTAATATTTGTCCTTTTAATTCCAAGCAGAATTTGAAGA
* * **
12358772 GATAAGTTCTGCTAAGGAAAATAAAATTACATATTAAGCTAAAATATTTGCAAGCCTAAAAGGGC
66 GATAAGTTCTGCTGAGGAAAATAAAATTACATATTAGGCTAAAATATCCGCAAGCCTAAAAGGGC
* * * *
12358837 TTGACATTTTGTATCGCTCATGTCATTGATCACTATAGTCGTGCTACTGCCGTACTCATCTCATT
131 TTGACATTTTGTATCGCCCATGTCATTGATCACTGTAGTCGTGCTTCTGCCGTGCTCATCTCATT
* * * * *
12358902 GTTGTGTATCTTTTCCTGTAGACTATTTGGTTTTAAATAAAATTAAAAAATTAAAAGAACTTTTG
196 GTTGTATATCTTTTCCTGCATATTATTTGGTTTTAAATAAAATTCAAAAATTAAAAGAACTTTTG
* * * *
12358967 GAAATTTTGACTAATTGAGCTAATAACATTTGTGAATTAAGGAGTCATTAGCTTC
261 AAAATTTTGACTAATTGAGCTAATAACATCTGTGAATTAAGGAGCCATTAACTTC
12359022 TGAATTAAATGAGCCTTTAACATCAATTTAATATTTGTCCTTTTAATTCCAAGCAGAATTTGAAG
1 TGAATT-AATGAGCCTTTAACATCAATTTAATATTTGTCCTTTTAATTCCAAGCAGAATTTGAAG
** * *
12359087 AGATAAACTCTGCTGAGGAAAATAAAATTACATATTAGGCTAAAATATCCACAAGCCTAAAAGAG
65 AGATAAGTTCTGCTGAGGAAAATAAAATTACATATTAGGCTAAAATATCCGCAAGCCTAAAAGGG
* * * * * * *
12359152 CTTGACATTTTGCATCGCCCACGTCGTTGGTCATTGTAGTCGTGCTTCTGCCGTGTTTATCTCAT
130 CTTGACATTTTGTATCGCCCATGTCATTGATCACTGTAGTCGTGCTTCTGCCGTGCTCATCTCAT
12359217 TGTTGTATATCTTTTCCTGCATATTATTTGGTTTTAAATAAAATTCAAAAATTAAAAGAACTTTT
195 TGTTGTATATCTTTTCCTGCATATTATTTGGTTTTAAATAAAATTCAAAAATTAAAAGAACTTTT
*
12359282 GAAAATTTTGACTAATGGAGCTAATAACATCTGTGAATTAAGGAGCCATTAACTTC
260 GAAAATTTTGACTAATTGAGCTAATAACATCTGTGAATTAAGGAGCCATTAACTTC
*
12359338 TGAAATTAATGAG-CTATTAACTTCAATTTAATATTTGTCCTTTTAATTCCAAGCAGAATTTGAA
1 TG-AATTAATGAGCCT-TTAACATCAATTTAATATTTGTCCTTTTAATTCCAAGCAGAATTTGAA
*
12359402 GAGATAAGTTTTGCTGAGGAAAATAAAATTACATATTAGGCTAAAATATCCGCAAGCCTAAAAGG
64 GAGATAAGTTCTGCTGAGGAAAATAAAATTACATATTAGGCTAAAATATCCGCAAGCCTAAAAGG
* * * *
12359467 GCTTGACATTTTGTGTCACCCATGTCATTGATCACTGTAGTCATGC-TATGCCGTGCTCATCTCA
129 GCTTGACATTTTGTATCGCCCATGTCATTGATCACTGTAGTCGTGCTTCTGCCGTGCTCATCTCA
* *
12359531 TTATTGTATATCTTTTCCTACATATTATTTGGTTTTAAATAAAATTCAAAAATTAAAAGAACTTT
194 TTGTTGTATATCTTTTCCTGCATATTATTTGGTTTTAAATAAAATTCAAAAATTAAAAGAACTTT
* * *
12359596 TGAAAATATTGACTAATTGAGCTAATAACATCTATGAATTAAGAAGCC
259 TGAAAATTTTGACTAATTGAGCTAATAACATCTGTGAATTAAGGAGCC
12359644 TTTATTTCAA
Statistics
Matches: 565, Mismatches: 54, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
315 130 0.23
316 431 0.76
317 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (315 bp):
TGAATTAATGAGCCTTTAACATCAATTTAATATTTGTCCTTTTAATTCCAAGCAGAATTTGAAGA
GATAAGTTCTGCTGAGGAAAATAAAATTACATATTAGGCTAAAATATCCGCAAGCCTAAAAGGGC
TTGACATTTTGTATCGCCCATGTCATTGATCACTGTAGTCGTGCTTCTGCCGTGCTCATCTCATT
GTTGTATATCTTTTCCTGCATATTATTTGGTTTTAAATAAAATTCAAAAATTAAAAGAACTTTTG
AAAATTTTGACTAATTGAGCTAATAACATCTGTGAATTAAGGAGCCATTAACTTC
Found at i:12359334 original size:25 final size:24
Alignment explanation
Indices: 12359306--12359358 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
12359296 ATGGAGCTAA
*
12359306 TAACATCTGTGAATTAAGGAGCCAT
1 TAACATCTG-AAATTAAGGAGCCAT
* * *
12359331 TAACTTCTGAAATTAATGAGCTAT
1 TAACATCTGAAATTAAGGAGCCAT
12359355 TAAC
1 TAAC
12359359 TTCAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (24 bp):
TAACATCTGAAATTAAGGAGCCAT
Found at i:12361550 original size:19 final size:19
Alignment explanation
Indices: 12361526--12361567 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
12361516 GAACTTTTTA
*
12361526 TTTTATTTTATTTTTTATT
1 TTTTATTATATTTTTTATT
*
12361545 TTTTATTATATTTTTTGTT
1 TTTTATTATATTTTTTATT
12361564 TTTT
1 TTTT
12361568 TTTCATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTATTATATTTTTTATT
Found at i:12361551 original size:24 final size:22
Alignment explanation
Indices: 12361521--12361570 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
12361511 CTCCAGAACT
* *
12361521 TTTTATTTTATTTTATTTTTTATT
1 TTTTATTATATTTT-TTGTTT-TT
12361545 TTTTATTATATTTTTTGTTTTT
1 TTTTATTATATTTTTTGTTTTT
12361567 TTTT
1 TTTT
12361571 CATGAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 5 0.21
24 13 0.54
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTTATTATATTTTTTGTTTTT
Found at i:12368128 original size:15 final size:15
Alignment explanation
Indices: 12368080--12368141 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
12368070 TTAACGGCTC
12368080 AATAACTAAAATATTA
1 AATAACTAAAATA-TA
*
12368096 CAAT-AC-AACAACATA
1 -AATAACTAA-AATATA
*
12368111 AATAATTAAAATATA
1 AATAACTAAAATATA
12368126 AATAACTAAAATATA
1 AATAACTAAAATATA
12368141 A
1 A
12368142 TCTAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 3 0.08
15 25 0.66
16 7 0.18
17 3 0.08
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAACTAAAATATA
Found at i:12386459 original size:46 final size:46
Alignment explanation
Indices: 12386403--12386497 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
12386393 TAAATAGATG
*
12386403 ATTGCCATGAAACATGAATAGTATGATGTTAATAGTATATGGTATA
1 ATTGCCATGAAACATGAATAGTATGATGTAAATAGTATATGGTATA
12386449 ATTGCCATGAAACATGAATAGTATGATGTAAATAGTATATGGTATA
1 ATTGCCATGAAACATGAATAGTATGATGTAAATAGTATATGGTATA
12386495 ATT
1 ATT
12386498 ACATAAATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (46 bp):
ATTGCCATGAAACATGAATAGTATGATGTAAATAGTATATGGTATA
Found at i:12389653 original size:316 final size:313
Alignment explanation
Indices: 12389081--12389661 Score: 726
Period size: 316 Copynumber: 1.8 Consensus size: 313
12389071 ATTTGTCGTC
*
12389081 TCATAGATGAAATGAAATAGCAACAAGTTTTTTCGAATATTAATCTTTTATCTATTGTTTGGCTT
1 TCATAGATGAAATGAAATAGCAACAAGTTTTTTCGAATATGAATCTTTTATCTATTGTTTGGCTT
** * * * * *
12389146 TGAACATATATACCTTTGGGATATCTGTTGTTTGACTTCCATTGTATATGCTGCTGGTCTTGAGT
66 CCAACATACATACCTTCGAGATATC--TTGTTTGACTTCCAATCTATATGCTGCTGGTCTTGAGT
* * * *
12389211 TTCCACTTTGTATAACAGAGATTAGAGGAAGGCCATTCTGCTGCTGATGTTCTTTTCGGTTCTAA
129 TTCCACTTTGTATAACAGAGATTAAAGGAAGGCCATGCTGCTGATGATGTTCTCTTCGGTTCTAA
* * * *
12389276 CTATTGATGGTTTTTCAGTCCAGATGCTCCTAAGATAAGGCCATTAAAATGTACCGAACTCTCAC
194 CTATTGATGGTTTTTCAGTCCAGATGCTCCCAAGACAAGGCCATTAAAACGCACCGAACTCTCAC
12389341 AGAGGCCATTAAAAATGTCCCAATGATGTCCTTGGTTCTGACTATTGATGATTTG
259 AGAGGCCATTAAAAATGTCCCAATGATGTCCTTGGTTCTGACTATTGATGATTTG
* * *
12389396 TCATAGATGAAATGAAATAGCAACATGTTTTTTCGAATATGAATCTTTTTATGTGTTGTTTGGCT
1 TCATAGATGAAATGAAATAGCAACAAGTTTTTTCGAATATGAATC-TTTTATCTATTGTTTGGCT
* * * * * *
12389461 TCCATCGTACATGCCTTCGAGATATC-TGTTTGGCTT-TAATCTATGTG-T-CATCGGTCTTGAG
65 TCCAACATACATACCTTCGAGATATCTTGTTTGACTTCCAATCTATATGCTGC-T-GGTCTTGAG
* * *
12389522 TTTCCACTTTGTACTAATAATAGTAGTGATTAAAGGAAGGCCCTGCTGTTGATGATG-TC-CTT-
128 TTTCCACTTTG---T-ATAACAG-A--GATTAAAGGAAGGCCATGCTGCTGATGATGTTCTCTTC
* * *
12389584 GGTTTTAACTATTGATGGTTTTTCAGTGCAGATGTTCCCAAGACAAGGCCATTAAAACGCACCGA
186 GGTTCTAACTATTGATGGTTTTTCAGTCCAGATGCTCCCAAGACAAGGCCATTAAAACGCACCGA
12389649 ACTCTCACAGAGG
251 ACTCTCACAGAGG
12389662 TTGAAGGATT
Statistics
Matches: 225, Mismatches: 31, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
310 1 0.00
311 2 0.01
312 27 0.12
313 9 0.04
315 44 0.20
316 112 0.50
317 3 0.01
318 2 0.01
319 25 0.11
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (313 bp):
TCATAGATGAAATGAAATAGCAACAAGTTTTTTCGAATATGAATCTTTTATCTATTGTTTGGCTT
CCAACATACATACCTTCGAGATATCTTGTTTGACTTCCAATCTATATGCTGCTGGTCTTGAGTTT
CCACTTTGTATAACAGAGATTAAAGGAAGGCCATGCTGCTGATGATGTTCTCTTCGGTTCTAACT
ATTGATGGTTTTTCAGTCCAGATGCTCCCAAGACAAGGCCATTAAAACGCACCGAACTCTCACAG
AGGCCATTAAAAATGTCCCAATGATGTCCTTGGTTCTGACTATTGATGATTTG
Found at i:12391333 original size:21 final size:20
Alignment explanation
Indices: 12391298--12391347 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
12391288 ATATACACAT
* *
12391298 TAAAAATATAAAAATAGAAA
1 TAAATATATAAAAATACAAA
*
12391318 TAAATATATAAAAAATTCAAA
1 TAAATATAT-AAAAATACAAA
*
12391339 AAAATATAT
1 TAAATATAT
12391348 TTAAAATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAATATATAAAAATACAAA
Found at i:12391352 original size:23 final size:23
Alignment explanation
Indices: 12391321--12391403 Score: 59
Period size: 23 Copynumber: 3.6 Consensus size: 23
12391311 ATAGAAATAA
*
12391321 ATATATAAAAAATTCAAAAAAAT
1 ATATTTAAAAAATTCAAAAAAAT
12391344 ATATTT--AAAA-TCTAAAAAAAT
1 ATATTTAAAAAATTC-AAAAAAAT
*
12391365 ATAAATTATAAAAAATTTTAAAATAAA-
1 AT--ATT-TAAAAAA-TTCAAAA-AAAT
12391392 AT-TTTAAAAAAT
1 ATATTTAAAAAAT
12391404 ACGATAATTG
Statistics
Matches: 49, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
20 2 0.04
21 14 0.29
22 1 0.02
23 15 0.31
24 3 0.06
26 4 0.08
27 6 0.12
28 4 0.08
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATTTAAAAAATTCAAAAAAAT
Found at i:12391353 original size:21 final size:21
Alignment explanation
Indices: 12391319--12391367 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
12391309 AAATAGAAAT
12391319 AAATATATAAAAAAT-TCAAAA
1 AAATATATAAAAAATCT-AAAA
**
12391340 AAATATATTTAAAATCTAAAA
1 AAATATATAAAAAATCTAAAA
12391361 AAATATA
1 AAATATA
12391368 AATTATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATATATAAAAAATCTAAAA
Found at i:12391404 original size:15 final size:13
Alignment explanation
Indices: 12391376--12391400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12391366 TAAATTATAA
12391376 AAAATTTTAAAAT
1 AAAATTTTAAAAT
12391389 AAAATTTTAAAA
1 AAAATTTTAAAA
12391401 AATACGATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATTTTAAAAT
Found at i:12391469 original size:18 final size:18
Alignment explanation
Indices: 12391446--12391483 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12391436 ATATTATTAC
12391446 AAAAATGA-AGAAAAATGT
1 AAAAATGATA-AAAAATGT
*
12391464 AAAAATTATAAAAAATGT
1 AAAAATGATAAAAAATGT
12391482 AA
1 AA
12391484 TTTCTTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (18 bp):
AAAAATGATAAAAAATGT
Found at i:12391559 original size:19 final size:20
Alignment explanation
Indices: 12391532--12391583 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
12391522 TAAAATACTT
12391532 TTTTTAATTTTTATA-A-CA
1 TTTTTAATTTTTATATATCA
*
12391550 TTTTTCAATTTTTATATATTA
1 TTTTT-AATTTTTATATATCA
12391571 TTTTTAATTTTTA
1 TTTTTAATTTTTA
12391584 AAATTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 5 0.17
19 10 0.33
20 9 0.30
21 6 0.20
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAATTTTTATATATCA
Found at i:12391562 original size:20 final size:20
Alignment explanation
Indices: 12391532--12391583 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
12391522 TAAAATACTT
12391532 TTTTTAA-TTTT-TATAACA
1 TTTTTAATTTTTATATAACA
**
12391550 TTTTTCAATTTTTATATATTA
1 TTTTT-AATTTTTATATAACA
12391571 TTTTTAATTTTTA
1 TTTTTAATTTTTA
12391584 AAATTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 5 0.17
19 2 0.07
20 12 0.41
21 10 0.34
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAATTTTTATATAACA
Found at i:12391591 original size:20 final size:20
Alignment explanation
Indices: 12391532--12391591 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
12391522 TAAAATACTT
* *
12391532 TTTTTAATTTTTATAA--CA
1 TTTTTAATTTTTAAAATTTA
*
12391550 TTTTTCAATTTTT-ATATATTA
1 TTTTT-AATTTTTAAAAT-TTA
12391571 TTTTTAATTTTTAAAATTTA
1 TTTTTAATTTTTAAAATTTA
12391591 T
1 T
12391592 AATTATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 6 0.18
19 7 0.21
20 11 0.33
21 9 0.27
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTAATTTTTAAAATTTA
Found at i:12391938 original size:11 final size:11
Alignment explanation
Indices: 12391924--12391948 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12391914 TATAAAAAAG
12391924 TTTAAAAATAA
1 TTTAAAAATAA
12391935 TTTAAAAATAA
1 TTTAAAAATAA
12391946 TTT
1 TTT
12391949 TTTATAAAAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTAAAAATAA
Found at i:12407448 original size:13 final size:14
Alignment explanation
Indices: 12407429--12407470 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
12407419 AAAACTATCG
12407429 AGAGAGAAAAAGAT
1 AGAGAGAAAAAGAT
*
12407443 -GAGAG-AAAACAT
1 AGAGAGAAAAAGAT
12407455 AGAGAGAAAATAGAT
1 AGAGAGAAAA-AGAT
12407470 A
1 A
12407471 AATTGTAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
12 6 0.26
13 10 0.43
14 3 0.13
15 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.26, T:0.10
Consensus pattern (14 bp):
AGAGAGAAAAAGAT
Found at i:12407721 original size:22 final size:22
Alignment explanation
Indices: 12407693--12407737 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
12407683 TAACTCGTAC
12407693 CAAGCTTATTCAAGTTCTCTAA
1 CAAGCTTATTCAAGTTCTCTAA
12407715 CAAGCTTATTCAAGTTCTCTAA
1 CAAGCTTATTCAAGTTCTCTAA
12407737 C
1 C
12407738 TTTGAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (22 bp):
CAAGCTTATTCAAGTTCTCTAA
Found at i:12408210 original size:97 final size:97
Alignment explanation
Indices: 12408081--12408261 Score: 267
Period size: 97 Copynumber: 1.9 Consensus size: 97
12408071 CCTTACATAG
* *
12408081 TGGTTTCAAGATAGGAAAGAAAAGACAATTTCACTCGGCTTTGACACATGTCTTTTATATATCAT
1 TGGTTTCAAGATAGGAAAGAAAAGACAATTTCACCCGGCTTTGACACATGTCATTTATA-AT-AT
*
12408146 ATAAATATTTTTATTTTAAAAGTTCCCCCTTGTA
64 AAAAATATTTTTATTTTAAAAGTTCCCCCTTGTA
* * * *
12408180 TGGTTTCAAGATA-TAAA-AAAAGACAGTTTCACCCGGCTTTGACACGTGTCATTTCTAATATAA
1 TGGTTTCAAGATAGGAAAGAAAAGACAATTTCACCCGGCTTTGACACATGTCATTTATAATATAA
12408243 AAATATTTTTATTTTAAAA
66 AAATATTTTTATTTTAAAA
12408262 AATGCCCTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
95 22 0.29
96 2 0.03
97 35 0.47
98 3 0.04
99 13 0.17
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (97 bp):
TGGTTTCAAGATAGGAAAGAAAAGACAATTTCACCCGGCTTTGACACATGTCATTTATAATATAA
AAATATTTTTATTTTAAAAGTTCCCCCTTGTA
Found at i:12410041 original size:49 final size:49
Alignment explanation
Indices: 12409988--12410085 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
12409978 TTCAACAAGT
12409988 AAGTAAAAGAAATGACATGGTATCTATACAAACGAAATGGTTCATGATC
1 AAGTAAAAGAAATGACATGGTATCTATACAAACGAAATGGTTCATGATC
*
12410037 AAGTAAAGGAAATGACATGGTATCTATACAAACGAAATGGTTCATGATC
1 AAGTAAAAGAAATGACATGGTATCTATACAAACGAAATGGTTCATGATC
12410086 TTATGAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.24
Consensus pattern (49 bp):
AAGTAAAAGAAATGACATGGTATCTATACAAACGAAATGGTTCATGATC
Found at i:12410074 original size:25 final size:25
Alignment explanation
Indices: 12409996--12410075 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
12409986 GTAAGTAAAA
12409996 GAAATGACATGGTATCTATACAAAC
1 GAAATGACATGGTATCTATACAAAC
* * *
12410021 GAAATGGTTCAT-G-ATC-A-AGTAAAG
1 GAAAT-G-ACATGGTATCTATA-CAAAC
12410045 GAAATGACATGGTATCTATACAAAC
1 GAAATGACATGGTATCTATACAAAC
12410070 GAAATG
1 GAAATG
12410076 GTTCATGATC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
22 3 0.07
23 3 0.07
24 12 0.29
25 18 0.43
26 3 0.07
27 3 0.07
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (25 bp):
GAAATGACATGGTATCTATACAAAC
Found at i:12410086 original size:25 final size:25
Alignment explanation
Indices: 12410009--12410086 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
12409999 ATGACATGGT
12410009 ATCTATACAAACGAAATGGTTCATG
1 ATCTATACAAACGAAATGGTTCATG
* * *
12410034 ATC-A-AGTAAAGGAAAT-G-ACATGG
1 ATCTATA-CAAACGAAATGGTTCAT-G
12410057 TATCTATACAAACGAAATGGTTCATG
1 -ATCTATACAAACGAAATGGTTCATG
12410083 ATCT
1 ATCT
12410087 TATGAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 3 0.08
23 3 0.08
24 12 0.30
25 16 0.40
26 3 0.08
27 3 0.08
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (25 bp):
ATCTATACAAACGAAATGGTTCATG
Found at i:12416301 original size:7 final size:7
Alignment explanation
Indices: 12416289--12416315 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12416279 AATCTGAGTA
12416289 TAACATT
1 TAACATT
12416296 TAACATT
1 TAACATT
12416303 TAACATT
1 TAACATT
12416310 TAACAT
1 TAACAT
12416316 GTTTTGTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (7 bp):
TAACATT
Found at i:12417062 original size:32 final size:32
Alignment explanation
Indices: 12417026--12417153 Score: 220
Period size: 32 Copynumber: 4.0 Consensus size: 32
12417016 TATAACTATA
12417026 CTACTTTTTTATATGTAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
*
12417058 CTACTTTTTTATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
12417090 CAACTTTTTTATATGTAAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
*
12417122 CTATTTTTTTATATGTAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
12417154 ATTTTTTGTG
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 89 1.00
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.46
Consensus pattern (32 bp):
CTACTTTTTTATATGTAAAACTAATGTATGAT
Found at i:12419173 original size:21 final size:21
Alignment explanation
Indices: 12419149--12419200 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
12419139 CATTGTTTCT
*
12419149 AATCTCACCGTTACAGTATCC
1 AATCTCACCGTTACAGTAACC
*
12419170 AATCTCACCGTTACAGTAACT
1 AATCTCACCGTTACAGTAACC
12419191 AATCTCACCG
1 AATCTCACCG
12419201 CCACCGCTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.33, G:0.10, T:0.27
Consensus pattern (21 bp):
AATCTCACCGTTACAGTAACC
Found at i:12420931 original size:30 final size:30
Alignment explanation
Indices: 12420895--12420953 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
12420885 TACAATTTCA
* *
12420895 TTTTATTTTTATTTTAATTTGGACCTAATC
1 TTTTATTTTTATTTCAATTTAGACCTAATC
* *
12420925 TTTTATTTTTGTTTCAATTTAGTCCTAAT
1 TTTTATTTTTATTTCAATTTAGACCTAAT
12420954 GGCCATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.22, C:0.10, G:0.07, T:0.61
Consensus pattern (30 bp):
TTTTATTTTTATTTCAATTTAGACCTAATC
Found at i:12421203 original size:17 final size:19
Alignment explanation
Indices: 12421183--12421226 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
12421173 GTAAAAATAG
*
12421183 TATATATTATTTTTA-T-T
1 TATATATTATTTATATTAT
12421200 TATATATTATTTATATTAT
1 TATATATTATTTATATTAT
12421219 TATATATT
1 TATATATT
12421227 CTATTTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 14 0.58
18 1 0.04
19 9 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TATATATTATTTATATTAT
Found at i:12421224 original size:21 final size:19
Alignment explanation
Indices: 12421183--12421268 Score: 63
Period size: 20 Copynumber: 4.5 Consensus size: 19
12421173 GTAAAAATAG
12421183 TATATATTA-TTTTTATT-
1 TATATATTATTTTTTATTA
12421200 TATATATTATTTATATTATTA
1 TATATATTATTT-T-TTATTA
** *
12421221 TATAT-TCTATTTATAAATTT
1 TATATAT-TATTT-TTTATTA
*
12421241 TAT-TATATATCTTTTATTA
1 TATATAT-TATTTTTTATTA
12421260 TATATATTA
1 TATATATTA
12421269 ACCCCTACAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
17 9 0.17
18 2 0.04
19 11 0.20
20 20 0.37
21 12 0.22
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATATTATTTTTTATTA
Found at i:12421231 original size:12 final size:12
Alignment explanation
Indices: 12421193--12421264 Score: 62
Period size: 14 Copynumber: 6.1 Consensus size: 12
12421183 TATATATTAT
12421193 TTTTATT-TATA
1 TTTTATTATATA
*
12421204 TATTATT-TATA
1 TTTTATTATATA
12421215 --TTATTATATA
1 TTTTATTATATA
* *
12421225 TTCTATTTATAAA
1 TTTTA-TTATATA
12421238 TTTTATTATATA
1 TTTTATTATATA
12421250 TCTTTTATTATATA
1 --TTTTATTATATA
12421264 T
1 T
12421265 ATTAACCCCT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
9 5 0.10
10 4 0.08
11 10 0.20
12 9 0.18
13 10 0.20
14 12 0.24
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTATTATATA
Found at i:12421232 original size:32 final size:30
Alignment explanation
Indices: 12421196--12421268 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 30
12421186 ATATTATTTT
12421196 TATTTATATATTATTTATATTATTATATATTC
1 TATTTATATATTATTT-TATTA-TATATATTC
* *
12421228 TATTTATA-A--ATTTTATTATATATCTTT
1 TATTTATATATTATTTTATTATATATATTC
12421255 TATTATATATATTA
1 TATT-TATATATTA
12421269 ACCCCTACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 11 0.31
28 9 0.26
29 5 0.14
31 2 0.06
32 8 0.23
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TATTTATATATTATTTTATTATATATATTC
Found at i:12421267 original size:23 final size:24
Alignment explanation
Indices: 12421210--12421268 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
12421200 TATATATTAT
12421210 TTATATTATTATATATTCTATTTA
1 TTATATTATTATATATTCTATTTA
* *
12421234 TAAATTTTATTATATA-TCT-TTTA
1 T-TATATTATTATATATTCTATTTA
12421257 TTATATATATTA
1 TTATAT-TATTA
12421269 ACCCCTACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
22 3 0.10
23 10 0.34
24 4 0.14
25 12 0.41
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATATTATTATATATTCTATTTA
Found at i:12421304 original size:15 final size:15
Alignment explanation
Indices: 12421284--12421318 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
12421274 TACATTATTT
12421284 TTATTTTATTATATA
1 TTATTTTATTATATA
*
12421299 TTATTTTATTATTTA
1 TTATTTTATTATATA
12421314 TTATT
1 TTATT
12421319 AGTATATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTTTATTATATA
Found at i:12421772 original size:14 final size:14
Alignment explanation
Indices: 12421753--12421779 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12421743 TTTGCATAAA
12421753 ATATTGTTATATTT
1 ATATTGTTATATTT
12421767 ATATTGTTATATT
1 ATATTGTTATATT
12421780 CATTGTTTTC
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:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
ATATTGTTATATTT
Found at i:12421844 original size:64 final size:62
Alignment explanation
Indices: 12421768--12421888 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 62
12421758 GTTATATTTA
* * *
12421768 TATTGTTATATTCATTGTTTTCCATGTTATATTTTGCATGAAATGTTATTATGTATGTAATCAG
1 TATTATTATATTCATTGTTTTCCATGATATATCTTGCATGAAATGTTA--ATGTATGTAATCAG
* *
12421832 TATTATTATATTCATTGTTTTCTATGATGTATCTTGCATGAAATGTTAATGTATGTA
1 TATTATTATATTCATTGTTTTCCATGATATATCTTGCATGAAATGTTAATGTATGTA
12421889 TATTTAGGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
62 9 0.17
64 43 0.83
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.51
Consensus pattern (62 bp):
TATTATTATATTCATTGTTTTCCATGATATATCTTGCATGAAATGTTAATGTATGTAATCAG
Found at i:12426513 original size:5 final size:5
Alignment explanation
Indices: 12426503--12426534 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
12426493 AATTTGTGAA
12426503 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
12426535 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:12426528 original size:9 final size:9
Alignment explanation
Indices: 12426504--12426534 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
12426494 ATTTGTGAAA
12426504 AAATAAAAT
1 AAATAAAAT
12426513 AAAATAAAAT
1 -AAATAAAAT
12426523 AAATAAAAT
1 AAATAAAAT
12426532 AAA
1 AAA
12426535 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:12429604 original size:29 final size:30
Alignment explanation
Indices: 12429554--12429635 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 30
12429544 TTTTAATAGT
* *
12429554 CTATACTTTTATAATTTTTTAAAAGAT-TAAA
1 CTATAATTTTAT--TTTTTTAAAAGATCAAAA
*
12429585 CTA-AATTTTTATTTTTTTAAGAGATCAAAA
1 CTATAA-TTTTATTTTTTTAAAAGATCAAAA
*
12429615 GTATAATTTTATTTTTATTAA
1 CTATAATTTTATTTTT-TTAA
12429636 TTTAAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
29 12 0.28
30 16 0.37
31 15 0.35
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (30 bp):
CTATAATTTTATTTTTTTAAAAGATCAAAA
Found at i:12430969 original size:4 final size:4
Alignment explanation
Indices: 12430960--12430993 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
12430950 GCTTTATGTC
12430960 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
12430994 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:12433311 original size:117 final size:117
Alignment explanation
Indices: 12433105--12433343 Score: 442
Period size: 117 Copynumber: 2.0 Consensus size: 117
12433095 ATAATGCATG
* * *
12433105 GGCACCTTCATCTGGTGTTCTTCCAAACGGGGTTCCTATAGGAGATGATACACCTAATGAGGGAT
1 GGCACCTTCATCTGGTGTTCTTCCAAACAGGGTTCCTATAGCAAATGATACACCTAATGAGGGAT
*
12433170 TTGGTGATTCAGATGAACATAGTAATGAGAATGAAGGTATTCCTCCTAATGA
66 TTGGTGATTCAGATGAACATAGTAATGAGAATGAAGATATTCCTCCTAATGA
12433222 GGCACCTTCATCTGGTGTTCTTCCAAACAGGGTTCCTATAGCAAATGATACACCTAATGAGGGAT
1 GGCACCTTCATCTGGTGTTCTTCCAAACAGGGTTCCTATAGCAAATGATACACCTAATGAGGGAT
12433287 TTGGTGATTCAGATGAACATAGTAATGAGAATGAAGATATTCCTCCTAATGA
66 TTGGTGATTCAGATGAACATAGTAATGAGAATGAAGATATTCCTCCTAATGA
12433339 GGCAC
1 GGCAC
12433344 TATCAAGCCC
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (117 bp):
GGCACCTTCATCTGGTGTTCTTCCAAACAGGGTTCCTATAGCAAATGATACACCTAATGAGGGAT
TTGGTGATTCAGATGAACATAGTAATGAGAATGAAGATATTCCTCCTAATGA
Found at i:12437929 original size:90 final size:90
Alignment explanation
Indices: 12437763--12437929 Score: 214
Period size: 90 Copynumber: 1.9 Consensus size: 90
12437753 ATGTAAATCA
*** * * *
12437763 ATTTTAGTCCATATTATTTGTTGGTTGAAATTTATAATTTTGTATATCAGTTTTGTAAATTTTTG
1 ATTTTAGTCCATATTATTTACCGGTTGAAATTTATAATTTTGTATACCAGTTTTGAAAATGTTTG
*
12437828 TATTATTTTTTGGATCCGTAAAAAT
66 TATTATATTTTGGATCCGTAAAAAT
*
12437853 ATTTTAGTCCATATTATTTACCGGTTGAATTTTAT-ATTTTAGTATACCAAGTTTCT-AAAATGT
1 ATTTTAGTCCATATTATTTACCGGTTGAAATTTATAATTTT-GTATACC-AGTTT-TGAAAATGT
12437916 TTGTATTA-ATTTTG
63 TTGTATTATATTTTG
12437930 TATATACATA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
89 5 0.08
90 42 0.64
91 18 0.27
92 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (90 bp):
ATTTTAGTCCATATTATTTACCGGTTGAAATTTATAATTTTGTATACCAGTTTTGAAAATGTTTG
TATTATATTTTGGATCCGTAAAAAT
Found at i:12446408 original size:22 final size:20
Alignment explanation
Indices: 12446383--12446422 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12446373 CCTTCTCCAT
12446383 TTTCAGTTTTTAATTAAATTTA
1 TTTCA-TTTTT-ATTAAATTTA
*
12446405 TTTCATTTTTTTTAAATT
1 TTTCATTTTTATTAAATT
12446423 AGCCTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 5 0.29
22 5 0.29
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (20 bp):
TTTCATTTTTATTAAATTTA
Found at i:12446564 original size:26 final size:25
Alignment explanation
Indices: 12446500--12446566 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
12446490 ATATATAATT
*
12446500 TATTTATTTTAAAAAACTATACATA
1 TATTTATATTAAAAAACTATACATA
**
12446525 TA-TTATTATTAAAAATACTATTTATA
1 TATTTA-TATTAAAAA-ACTATACATA
*
12446551 TATTTATATAAAAAAA
1 TATTTATATTAAAAAA
12446567 TTTATTTATC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 3 0.09
25 11 0.31
26 18 0.51
27 3 0.09
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTTATATTAAAAAACTATACATA
Found at i:12446585 original size:14 final size:14
Alignment explanation
Indices: 12446568--12446708 Score: 83
Period size: 14 Copynumber: 9.9 Consensus size: 14
12446558 ATAAAAAAAT
*
12446568 TTATTTATCATATA
1 TTATTTATTATATA
12446582 TTATTT-TCCTATATA
1 TTATTTAT--TATATA
* * *
12446597 TT-TATATTAGATT
1 TTATTTATTATATA
* *
12446610 TTATTATATAACAT-
1 TTATT-TATTATATA
* *
12446624 TTATTATATTTTTTA
1 TTATT-TATTATATA
12446639 TT-TTTATTATATA
1 TTATTTATTATATA
*
12446652 TTACTTATTATATA
1 TTATTTATTATATA
*
12446666 TTTTTTATTATATA
1 TTATTTATTATATA
**
12446680 TTATGTATATCGTATA
1 TTAT-T-TATTATATA
*
12446696 TTATCTATTATAT
1 TTATTTATTATAT
12446709 TATTTATGTT
Statistics
Matches: 96, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
13 16 0.17
14 52 0.54
15 17 0.18
16 11 0.11
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (14 bp):
TTATTTATTATATA
Found at i:12446642 original size:7 final size:7
Alignment explanation
Indices: 12446624--12446715 Score: 51
Period size: 7 Copynumber: 12.1 Consensus size: 7
12446614 TATATAACAT
12446624 TTATTATA
1 TTATT-TA
*
12446632 TTTTTTA
1 TTATTTA
12446639 TT-TTTA
1 TTATTTA
*
12446645 TTATATA
1 TTATTTA
*
12446652 TTACTTA
1 TTATTTA
*
12446659 TTATATA
1 TTATTTA
*
12446666 TTTTTTA
1 TTATTTA
*
12446673 TTATATA
1 TTATTTA
12446680 TTATGTATA
1 TTAT-T-TA
12446689 TCGTATATTA
1 T--TAT-TTA
12446699 TCTATTATA
1 T-TATT-TA
12446708 TTATTTA
1 TTATTTA
12446715 T
1 T
12446716 GTTTTATATT
Statistics
Matches: 65, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
6 6 0.09
7 34 0.52
8 9 0.14
9 9 0.14
10 3 0.05
11 4 0.06
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.64
Consensus pattern (7 bp):
TTATTTA
Found at i:12446649 original size:32 final size:33
Alignment explanation
Indices: 12446608--12446688 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 33
12446598 TTATATTAGA
12446608 TTTTATTATATA-ACAT-TTATTATATTTTTTAT
1 TTTTATTATATATACATATTA-TATATTTTTTAT
*
12446640 TTTTATTATATATTACTTATTATATATTTTTTAT
1 TTTTATTATATA-TACATATTATATATTTTTTAT
* *
12446674 TATATATTATGTATA
1 T-TTTATTATATATA
12446689 TCGTATATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 12 0.29
34 18 0.43
35 12 0.29
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.64
Consensus pattern (33 bp):
TTTTATTATATATACATATTATATATTTTTTAT
Found at i:12446833 original size:14 final size:15
Alignment explanation
Indices: 12446803--12446840 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
12446793 ATTATATACA
12446803 TATTTCATTATTATT
1 TATTTCATTATTATT
12446818 TATTT-ATTATGT-TT
1 TATTTCATTAT-TATT
12446832 TATTTCATT
1 TATTTCATT
12446841 TTAAATTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (15 bp):
TATTTCATTATTATT
Found at i:12452413 original size:28 final size:28
Alignment explanation
Indices: 12452373--12452465 Score: 152
Period size: 28 Copynumber: 3.3 Consensus size: 28
12452363 ATGTACTAGA
12452373 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
12452401 ATACCCCTATGTATGTAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
12452429 ATACCCCTATGTATGCAAAATGACC-TCT
1 ATACCCCTATGTATGCAAAATTACCAT-T
12452457 ATACCCCTA
1 ATACCCCTA
12452466 GGGTTAATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 1 0.02
28 60 0.98
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:12452629 original size:27 final size:28
Alignment explanation
Indices: 12452571--12452652 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
12452561 AGGAAGCGTC
*
12452571 CTGGTGGCTATGCCACAAATTATCTGTT
1 CTGGTGGCCATGCCACAAATTATCTGTT
* *
12452599 CTGGTGGCCCTGCCACATA-TATCTGTT
1 CTGGTGGCCATGCCACAAATTATCTGTT
* *
12452626 CTGGTGG-CATTGCCATAAAATATCTGT
1 CTGGTGGCCA-TGCCACAAATTATCTGT
12452653 ATTTGGTGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 22 0.48
28 23 0.50
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (28 bp):
CTGGTGGCCATGCCACAAATTATCTGTT
Found at i:12452679 original size:55 final size:56
Alignment explanation
Indices: 12452571--12452685 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 56
12452561 AGGAAGCGTC
* *
12452571 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * * * *
12452626 CTGGTGGC-ATTGCCATAAAATATCTGTATTTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
12452682 CTGG
1 CTGG
12452686 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.58
56 20 0.40
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:12453694 original size:16 final size:15
Alignment explanation
Indices: 12453675--12453736 Score: 51
Period size: 16 Copynumber: 4.3 Consensus size: 15
12453665 AAATAGATAT
12453675 TTATTTAAATATTATA
1 TTATTT-AATATTATA
* *
12453691 TTATTT-CTATAATTA
1 TTATTTAATATTA-TA
*
12453706 TTAATTAATATTA-A
1 TTATTTAATATTATA
12453720 -TA-TTAATATTATA
1 TTATTTAATATTATA
12453733 TTAT
1 TTAT
12453737 ATTATGAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
12 9 0.25
13 3 0.08
14 7 0.19
15 7 0.19
16 10 0.28
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATTTAATATTATA
Found at i:12453719 original size:10 final size:11
Alignment explanation
Indices: 12453682--12453741 Score: 58
Period size: 10 Copynumber: 5.7 Consensus size: 11
12453672 TATTTATTTA
12453682 AATATTATATT
1 AATATTATATT
*
12453693 -AT-TTCTA-T
1 AATATTATATT
12453701 AATTATTA-ATT
1 AA-TATTATATT
12453712 AATATTAATATT
1 AATATT-ATATT
12453724 AATATTATATT
1 AATATTATATT
12453735 -ATATTAT
1 AATATTAT
12453742 GAAATAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
8 1 0.02
9 5 0.12
10 15 0.37
11 11 0.27
12 9 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
AATATTATATT
Found at i:12453720 original size:6 final size:6
Alignment explanation
Indices: 12453709--12453740 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
12453699 ATAATTATTA
12453709 ATTAAT ATTAAT ATTAAT ATT-AT ATT-AT ATTA
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTA
12453741 TGAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTAAT
Found at i:12453738 original size:16 final size:15
Alignment explanation
Indices: 12453683--12453740 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
12453673 ATTTATTTAA
12453683 ATATTATATT-ATTT
1 ATATTATATTAATTT
* * *
12453697 CTATAATTATTAATTA
1 ATATTA-TATTAATTT
12453713 ATATTAATATTAATATT
1 ATATT-ATATTAAT-TT
12453730 ATATTATATTA
1 ATATTATATTA
12453741 TGAAATAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 4 0.12
15 4 0.12
16 19 0.56
17 7 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTATATTAATTT
Found at i:12453900 original size:31 final size:32
Alignment explanation
Indices: 12453859--12453921 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
12453849 TTAATTATAA
*
12453859 AAGATATTTAT-TAATTAAATAT-TTATATTAT
1 AAGATATTTATGTAA-TAAATATATTAAATTAT
*
12453890 AAGATTTTTATGTAATAAATATATTAAATTAT
1 AAGATATTTATGTAATAAATATATTAAATTAT
12453922 GACAAGTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (32 bp):
AAGATATTTATGTAATAAATATATTAAATTAT
Found at i:12454046 original size:15 final size:16
Alignment explanation
Indices: 12454021--12454073 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 16
12454011 AAAGTAAAAC
12454021 AAAAGAAAAAGAAATG
1 AAAAGAAAAAGAAATG
*
12454037 AAAA-AAAAAGATA-G
1 AAAAGAAAAAGAAATG
*
12454051 AAAAGAAACAG-AATG
1 AAAAGAAAAAGAAATG
*
12454066 AAACGAAA
1 AAAAGAAA
12454074 CAGAGAGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 6 0.19
15 21 0.68
16 4 0.13
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAAGAAATG
Found at i:12455498 original size:20 final size:21
Alignment explanation
Indices: 12455475--12455523 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
12455465 AATTATATTG
12455475 AATTGAAAAAAAATAT-AATT
1 AATTGAAAAAAAATATGAATT
**
12455495 AATT-AATTAAAATATGAATT
1 AATTGAAAAAAAATATGAATT
12455515 AATTGAAAA
1 AATTGAAAA
12455524 CTGAAAAGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 9 0.39
20 12 0.52
21 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (21 bp):
AATTGAAAAAAAATATGAATT
Found at i:12455918 original size:18 final size:18
Alignment explanation
Indices: 12455889--12455955 Score: 89
Period size: 18 Copynumber: 3.7 Consensus size: 18
12455879 AAAGATCGAC
12455889 TGTTACTGAATAACTGAT
1 TGTTACTGAATAACTGAT
* * *
12455907 TATTATTGAATAATTGAT
1 TGTTACTGAATAACTGAT
* *
12455925 TGTTACCGAATAACTGAC
1 TGTTACTGAATAACTGAT
12455943 TGTTACTGAATAA
1 TGTTACTGAATAA
12455956 ATAATCGTTC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (18 bp):
TGTTACTGAATAACTGAT
Found at i:12457163 original size:14 final size:16
Alignment explanation
Indices: 12457144--12457180 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
12457134 CGATGTCCTT
12457144 TTTGCAT-TCAT-GCA
1 TTTGCATCTCATAGCA
12457158 TTTGCATCTCATAGCA
1 TTTGCATCTCATAGCA
12457174 TTT-CATC
1 TTTGCATC
12457181 GCATCGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (16 bp):
TTTGCATCTCATAGCA
Done.