Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 52 of 198
Found at i:15553952 original size:19 final size:19
Alignment explanation
Indices: 15553930--15553967 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
15553920 AATTTAATTT
*
15553930 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
15553949 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
15553968 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:15554319 original size:21 final size:20
Alignment explanation
Indices: 15554287--15554324 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
15554277 ATATATTTTT
15554287 ATTTTTTATTTTTAAAATAA
1 ATTTTTTATTTTTAAAATAA
15554307 ATTTTTTATTTTTAAAAT
1 ATTTTTTATTTTTAAAAT
15554325 TTTTTGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTTTATTTTTAAAATAA
Found at i:15555421 original size:19 final size:18
Alignment explanation
Indices: 15555378--15555421 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
15555368 GATTTGATAT
* *
15555378 TAAAAGGTTGTTAATAAA
1 TAAAATGTTATTAATAAA
15555396 TAAAAATGTTATTAATATAA
1 T-AAAATGTTATTAATA-AA
15555416 TAAAAT
1 TAAAAT
15555422 AAAACTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 18 0.82
20 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (18 bp):
TAAAATGTTATTAATAAA
Found at i:15555508 original size:26 final size:24
Alignment explanation
Indices: 15555455--15555513 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 24
15555445 GTGATCATAG
*
15555455 AAAATGAAATATTTTTATTTTAATAA
1 AAAAT-AAATATTTTTATTCT-ATAA
15555481 AAAATAAATATTTATTATGTCTA-AA
1 AAAATAAATATTT-TTAT-TCTATAA
15555506 AAAATAAA
1 AAAATAAA
15555514 AAAAAGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 18 0.60
26 10 0.33
27 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (24 bp):
AAAATAAATATTTTTATTCTATAA
Found at i:15559607 original size:23 final size:23
Alignment explanation
Indices: 15559581--15559627 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
15559571 AGGATCGACG
*
15559581 TCACGACGAGGA-ATGTTGTGTGA
1 TCACGAC-AGGATATATTGTGTGA
*
15559604 TCACGACATGATATATTGTGTGA
1 TCACGACAGGATATATTGTGTGA
15559627 T
1 T
15559628 TGAACCATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (23 bp):
TCACGACAGGATATATTGTGTGA
Found at i:15560509 original size:23 final size:23
Alignment explanation
Indices: 15560481--15560527 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
15560471 TTTCAAGTGC
*
15560481 GCTAGTGATAGTGGCACTTCGGT
1 GCTAGTGACAGTGGCACTTCGGT
15560504 GCTAGTGACAGTGGCACTTCGGT
1 GCTAGTGACAGTGGCACTTCGGT
15560527 G
1 G
15560528 TCGTTTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.19, G:0.36, T:0.28
Consensus pattern (23 bp):
GCTAGTGACAGTGGCACTTCGGT
Found at i:15563002 original size:18 final size:19
Alignment explanation
Indices: 15562981--15563021 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
15562971 TTAATTTTTG
15562981 TTTATTTATTTA-TTTATT
1 TTTATTTATTTAGTTTATT
* *
15562999 TTTATTTGTTTAGTTTCTT
1 TTTATTTATTTAGTTTATT
15563018 TTTA
1 TTTA
15563022 ATTCTTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTATTTATTTAGTTTATT
Found at i:15572702 original size:14 final size:14
Alignment explanation
Indices: 15572683--15572710 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15572673 TTGTGTAAAT
15572683 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
15572697 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
15572711 TATAAACATA
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:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGAAA
Found at i:15572769 original size:39 final size:39
Alignment explanation
Indices: 15572682--15572806 Score: 162
Period size: 39 Copynumber: 3.1 Consensus size: 39
15572672 TTTGTGTAAA
* *
15572682 TAAAAAGAAAAGAAAAAAAAGAAAAGAAATATAAACATAGTCAA-
1 TAAAAAGAAAAGAAGAAAAAGTAAAGAAATAT----ATA-T-AAG
*
15572726 TAAAAATAAAAGAAGAAAAAGTAAAGAAATATATATAAG
1 TAAAAAGAAAAGAAGAAAAAGTAAAGAAATATATATAAG
15572765 TAAAAAGAAAAGAAGAAAAAGTAAAGAAATATATATAAG
1 TAAAAAGAAAAGAAGAAAAAGTAAAGAAATATATATAAG
15572804 TAA
1 TAA
15572807 GTATGTTAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
38 2 0.03
39 42 0.55
40 3 0.04
44 29 0.38
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.15
Consensus pattern (39 bp):
TAAAAAGAAAAGAAGAAAAAGTAAAGAAATATATATAAG
Found at i:15583587 original size:29 final size:29
Alignment explanation
Indices: 15583545--15583606 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
15583535 ATCTAGTTAC
15583545 CATGGAATGTTTTTCCGAATATTATTAAG
1 CATGGAATGTTTTTCCGAATATTATTAAG
*
15583574 CATGGAATGTTTTTCTGAATATTATTAAG
1 CATGGAATGTTTTTCCGAATATTATTAAG
15583603 CATG
1 CATG
15583607 ATGATAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.42
Consensus pattern (29 bp):
CATGGAATGTTTTTCCGAATATTATTAAG
Found at i:15589757 original size:20 final size:20
Alignment explanation
Indices: 15589720--15589757 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15589710 GTTTTTCTAG
*
15589720 TTTAAATTATTTTGTTAAAT
1 TTTAAATTATTTTATTAAAT
15589740 TTTAAATT-TTTATATTAA
1 TTTAAATTATTT-TATTAA
15589758 TAAAGAGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTAAATTATTTTATTAAAT
Found at i:15593155 original size:37 final size:38
Alignment explanation
Indices: 15593069--15593158 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 38
15593059 AAAGAAAATG
* * * *
15593069 AATAAAGATCAAAGAGAAGTTTGCTCAAATCTTGGAAA
1 AATAAAGAGCAAAGAAAAGATTGCTCAAATCTTGCAAA
*
15593107 AAAATAAGAGCAAAGAAAAGATTGCTCAAAT-TCT-CAAA
1 AATA-AAGAGCAAAGAAAAGATTGCTCAAATCT-TGCAAA
15593145 AATAAAGAGCAAAG
1 AATAAAGAGCAAAG
15593159 TTTGCTCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
37 10 0.23
38 10 0.23
39 24 0.55
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (38 bp):
AATAAAGAGCAAAGAAAAGATTGCTCAAATCTTGCAAA
Found at i:15593615 original size:15 final size:16
Alignment explanation
Indices: 15593595--15593625 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15593585 ATAAAAAATA
15593595 TTTTTGA-GCATGATT
1 TTTTTGATGCATGATT
15593610 TTTTTGATGCATGATT
1 TTTTTGATGCATGATT
15593626 ATTTGTGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.55
Consensus pattern (16 bp):
TTTTTGATGCATGATT
Found at i:15596637 original size:45 final size:45
Alignment explanation
Indices: 15596588--15596718 Score: 172
Period size: 45 Copynumber: 2.9 Consensus size: 45
15596578 TTTGTCTGAT
* * * * *
15596588 TCATGATACCATGACGTCTTTCAATTCTGGTCTTACTCGTTAGAA
1 TCATGATGCCATAACGTCTTTCAACTATGGTCTTACTCGTTAAAA
* * * *
15596633 TCATGTTGCCATAACGTCTTTCAGCTATGGTCTTACTTGCTAAAA
1 TCATGATGCCATAACGTCTTTCAACTATGGTCTTACTCGTTAAAA
*
15596678 TCGTGATGCCATAACGTCTTTCAACTATGGTCTTACTCGTT
1 TCATGATGCCATAACGTCTTTCAACTATGGTCTTACTCGTT
15596719 TCCGGTATGG
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (45 bp):
TCATGATGCCATAACGTCTTTCAACTATGGTCTTACTCGTTAAAA
Found at i:15596804 original size:45 final size:46
Alignment explanation
Indices: 15596684--15596810 Score: 161
Period size: 45 Copynumber: 2.8 Consensus size: 46
15596674 AAAATCGTGA
* * * *
15596684 TGCCATAACGTCTTTCAACTATGGTCTTA-CTCGTTTCCGGTATGG
1 TGCCATAATGTCTTTCAACTATGGTCTTATTTAGTTTCCGGTATAG
* * * *
15596729 TGCCATAGTTTCTTTCAACTACGGTCTTATTTAG-TTCTGGTATAG
1 TGCCATAATGTCTTTCAACTATGGTCTTATTTAGTTTCCGGTATAG
15596774 TGCCATAATGTCTTTCAACTATGGTCTTATTT-GTTTC
1 TGCCATAATGTCTTTCAACTATGGTCTTATTTAGTTTC
15596811 ATTCAAACCA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 1 0.01
45 66 0.96
46 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.43
Consensus pattern (46 bp):
TGCCATAATGTCTTTCAACTATGGTCTTATTTAGTTTCCGGTATAG
Found at i:15598763 original size:42 final size:42
Alignment explanation
Indices: 15598704--15598786 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
15598694 TTGTTGTGTT
15598704 ATGCCATGATAGGGAACTAATTTT-CATAATGATTTGTATATG
1 ATGCCATGATAGGGAACT-ATTTTGCATAATGATTTGTATATG
15598746 ATGCCATGATAGGGAACTATTTTGCATAATGATTTGTATAT
1 ATGCCATGATAGGGAACTATTTTGCATAATGATTTGTATAT
15598787 TTGTTAATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 5 0.12
42 35 0.88
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (42 bp):
ATGCCATGATAGGGAACTATTTTGCATAATGATTTGTATATG
Found at i:15599070 original size:46 final size:46
Alignment explanation
Indices: 15599017--15599196 Score: 137
Period size: 46 Copynumber: 3.9 Consensus size: 46
15599007 GTTCTTGCCC
*
15599017 AGGTTCCCAATTCCTACATATGTTGCGGACTGGAGAATACAGATTT
1 AGGTTCCCAACTCCTACATATGTTGCGGACTGGAGAATACAGATTT
* * * ** * * *
15599063 AGGTTCCCAATTCCTATATATGTAGCAAACTAGAGAATACAAATTC
1 AGGTTCCCAACTCCTACATATGTTGCGGACTGGAGAATACAGATTT
** * * * * * *
15599109 AAATTTCTAGCTCTTCCATATGTTGTGGACTGGAGAATACATG-TTT
1 AGGTTCCCAACTCCTACATATGTTGCGGACTGGAGAATACA-GATTT
* * * ** *
15599155 AGTTTCCCAGCTCTTGTATATGTTGCGGATTGGAGAATACAG
1 AGGTTCCCAACTCCTACATATGTTGCGGACTGGAGAATACAG
15599197 TAATATTAAA
Statistics
Matches: 102, Mismatches: 31, Indels: 3
0.75 0.23 0.02
Matches are distributed among these distances:
45 1 0.01
46 101 0.99
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (46 bp):
AGGTTCCCAACTCCTACATATGTTGCGGACTGGAGAATACAGATTT
Found at i:15606550 original size:49 final size:49
Alignment explanation
Indices: 15606497--15606728 Score: 134
Period size: 50 Copynumber: 4.7 Consensus size: 49
15606487 CAAAGCTATG
* * *
15606497 TCCCAGACATAGTCTTACATTGGATGTTTTCTGTA-C-TGCCAATGTCATA
1 TCCCAGACATAGTCTTACATGGGA-GTTCTC-ATACCGTGCCAATGTCATA
* * * *
15606546 TCCCAGATATTGTCTTACATGGGAGTTCTCATACCGGTGCCCATGTCATG
1 TCCCAGACATAGTCTTACATGGGAGTTCTCATACC-GTGCCAATGTCATA
* ** * * *
15606596 TCCCAGACATGGTCTTACGA-GGGACCTCTCAT-CTCGGTGCCAACGCCATG
1 TCCCAGACATAGTCTTAC-ATGGGAGTTCTCATAC-C-GTGCCAATGTCATA
* * ** ** *
15606646 TCCCAGACATGGTCTTACATGGAACCTCTCA-ACTCGATGCCAA-CACTATG
1 TCCCAGACATAGTCTTACATGGGAGTTCTCATAC-CG-TGCCAATGTC-ATA
* **
15606696 TCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TCCCAGACATAGTCTTACATGGGAGTTCTCATA
15606729 ATCTGAATGA
Statistics
Matches: 155, Mismatches: 18, Indels: 18
0.81 0.09 0.09
Matches are distributed among these distances:
47 2 0.01
48 6 0.04
49 25 0.16
50 120 0.77
51 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (49 bp):
TCCCAGACATAGTCTTACATGGGAGTTCTCATACCGTGCCAATGTCATA
Found at i:15606601 original size:50 final size:50
Alignment explanation
Indices: 15606533--15606775 Score: 240
Period size: 50 Copynumber: 4.7 Consensus size: 50
15606523 TTTTCTGTAC
* * * **
15606533 TGCCAATGTCATATCCCAGATATTGTCTTACATGGGAGTTCTCATAC-CGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-CTCGG
*
15606583 TGCCCATGTCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCTCGG
* * * * *
15606633 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGAACCTCTCAACTCGA
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** *
15606683 TGCCAA-CACTATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTGAATG
1 TGCCAATGTC-ATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-CTC-G---G
* *
15606738 ATGCCAATGTCGTGTCCTAGACATGGTCTTACATGGGA
1 -TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
15606776 TCTCATTCCC
Statistics
Matches: 160, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
49 3 0.02
50 121 0.76
51 3 0.02
52 1 0.01
56 31 0.19
57 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:15617026 original size:20 final size:19
Alignment explanation
Indices: 15616962--15617027 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
15616952 TGTTTTTTAG
*
15616962 TATTGTGATATATGCTTGAA
1 TATTATGAT-TATGCTTGAA
* *
15616982 TATTATGTGATTAT--ATGAT
1 TATTA--TGATTATGCTTGAA
15617001 TATTATGATCTATGCTTGAA
1 TATTATGAT-TATGCTTGAA
15617021 TATTATG
1 TATTATG
15617028 CGATTATATG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
17 4 0.11
18 3 0.08
19 8 0.22
20 14 0.39
21 3 0.08
22 4 0.11
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.48
Consensus pattern (19 bp):
TATTATGATTATGCTTGAA
Found at i:15617026 original size:39 final size:39
Alignment explanation
Indices: 15616960--15617087 Score: 159
Period size: 39 Copynumber: 3.3 Consensus size: 39
15616950 CATGTTTTTT
*
15616960 AGTATTGTGATATATGCTTGAATATTATGTGATTATATG
1 AGTATTGTGATCTATGCTTGAATATTATGTGATTATATG
* * *
15616999 ATTATTATGATCTATGCTTGAATATTATGCGATTATATG
1 AGTATTGTGATCTATGCTTGAATATTATGTGATTATATG
* * *
15617038 AGTATTGTGATAC-ATGCTTAAACATTAGGTGATTATATG
1 AGTATTGTGAT-CTATGCTTGAATATTATGTGATTATATG
* *
15617077 TGTAATGTGAT
1 AGTATTGTGAT
15617088 ACAAGCTTAA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
39 75 0.99
40 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (39 bp):
AGTATTGTGATCTATGCTTGAATATTATGTGATTATATG
Found at i:15626155 original size:22 final size:23
Alignment explanation
Indices: 15626127--15626171 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
15626117 AATATAATAA
*
15626127 ATTTCATATTTA-TAAATTAAAT
1 ATTTCATAATTATTAAATTAAAT
*
15626149 ATTTCATAATTATTCAATTAAAT
1 ATTTCATAATTATTAAATTAAAT
15626172 GCAATGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTCATAATTATTAAATTAAAT
Found at i:15627494 original size:15 final size:17
Alignment explanation
Indices: 15627474--15627505 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
15627464 ACAAAATGAG
15627474 AATAA-TTAAT-ACAAA
1 AATAATTTAATCACAAA
15627489 AATAATTTAATCACAAA
1 AATAATTTAATCACAAA
15627506 TAAACCAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAATTTAATCACAAA
Found at i:15627698 original size:19 final size:20
Alignment explanation
Indices: 15627665--15627704 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
15627655 TAAAAAAAAG
*
15627665 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
15627685 AATTT-AAATGATGTGGATA
1 AATTTAAAATAATGTGGATA
15627704 A
1 A
15627705 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:15629754 original size:44 final size:44
Alignment explanation
Indices: 15629701--15630134 Score: 185
Period size: 44 Copynumber: 9.9 Consensus size: 44
15629691 CCTTTATTTT
* * *
15629701 AATCCACTCCACTGTAATCTTAAGGAGATAGGATTACCAGCTTC
1 AATCTACTCCACTGTAATCTCAAGGAGATAAGATTACCAGCTTC
* * * *
15629745 AATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTGA-AATTCTTC
1 AATCTACTCCACTGTAATCTCAAGGAGATAAGA-TT-ACCA-GCTTC
** * * * * *
15629791 GGTCTATTCCACTGTAATCTCAGGGAGATAAG---ACCTGATGC
1 AATCTACTCCACTGTAATCTCAAGGAGATAAGATTACCAGCTTC
* * * ** * *
15629832 GATCTACTCTACTGTAA-CTTCATA-GAGATAAGATCATTTA-TTTT
1 AATCTACTCCACTGTAATC-TCA-AGGAGATAAGATTA-CCAGCTTC
** * *
15629876 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTC
1 AATCTACTCCACTGTAATCTCAAGGAGATAAGATTACCAGCTTC
* * *
15629920 AATCTACTCCGCTGTAATCTC-AGAGAGATAAGATCTGA-AATTCTTC
1 AATCTACTCCACTGTAATCTCAAG-GAGATAAGAT-T-ACCA-GCTTC
** * * * * *
15629966 GGTCTATTCCACTGTAATCTCAGGGAGATAAG---ACCTGATAC
1 AATCTACTCCACTGTAATCTCAAGGAGATAAGATTACCAGCTTC
* * * ** * ** * *
15630007 GATCTATTCTACTGTAA-CTTTAGAGAGATAAGATCATTTA-TTTT
1 AATCTACTCCACTGTAATCTCAAG-GAGATAAGATTA-CCAGCTTC
* * * *
15630051 AATCCACTCCACTGTAATCTCAGGGAGATAGGATTACCAACTTC
1 AATCTACTCCACTGTAATCTCAAGGAGATAAGATTACCAGCTTC
* * *
15630095 AATCTGCTCCGCTGTAATCTCAAGGAGATAGGATTCACCA
1 AATCTACTCCACTGTAATCTCAAGGAGATAAGATT-ACCA
15630135 TCTTTGATCT
Statistics
Matches: 281, Mismatches: 82, Indels: 53
0.68 0.20 0.13
Matches are distributed among these distances:
40 4 0.01
41 54 0.19
43 3 0.01
44 143 0.51
45 13 0.05
46 63 0.22
47 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (44 bp):
AATCTACTCCACTGTAATCTCAAGGAGATAAGATTACCAGCTTC
Found at i:15629808 original size:46 final size:46
Alignment explanation
Indices: 15629741--15629998 Score: 182
Period size: 46 Copynumber: 5.8 Consensus size: 46
15629731 GGATTACCAG
* *
15629741 CTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTGAAATT
1 CTTCGATCTACTCCACTGTAATCTCAGGGAGATAAGATTTGAAATT
* * **
15629787 CTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTG--A--
1 CTTCGATCTACTCCACTGTAATCTCAGGGAGATAAGATTTGAAATT
* * ** *
15629829 -TGCGATCTACTCTACTGTAA-CTTCATAGAGATAAGATCATT--TATT
1 CTTCGATCTACTCCACTGTAATC-TCAGGGAGATAAGAT--TTGAAATT
* ** * * *
15629874 -TT-AATCCGCTCCACTGTAATCTCAGGGAGATAGGA-TT-ACCA-G
1 CTTCGATCTACTCCACTGTAATCTCAGGGAGATAAGATTTGA-AATT
* * * *
15629916 CTTCAATCTACTCCGCTGTAATCTCAGAGAGATAAGATCTGAAATT
1 CTTCGATCTACTCCACTGTAATCTCAGGGAGATAAGATTTGAAATT
* *
15629962 CTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGA
1 CTTCGATCTACTCCACTGTAATCTCAGGGAGATAAGA
15629999 CCTGATACGA
Statistics
Matches: 161, Mismatches: 37, Indels: 28
0.71 0.16 0.12
Matches are distributed among these distances:
40 1 0.01
41 30 0.19
43 5 0.03
44 53 0.33
45 4 0.02
46 68 0.42
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (46 bp):
CTTCGATCTACTCCACTGTAATCTCAGGGAGATAAGATTTGAAATT
Found at i:15629820 original size:175 final size:175
Alignment explanation
Indices: 15629593--15630124 Score: 902
Period size: 175 Copynumber: 3.0 Consensus size: 175
15629583 TACTATTTAC
* * * * *
15629593 GGAGACAAGATCTGTAATTCTTCGGTTTATTCCACTGTAATCTCATGGAGATAAGACCTGACGCG
1 GGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCG
* *
15629658 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTTA
66 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTGTAATCTCA
*
15629723 AGGAGATAGGATTACCAGCTTCAATCTACTCCGCTGTAATCTCAG
131 GGGAGATAGGATTACCAGCTTCAATCTACTCCGCTGTAATCTCAG
*
15629768 GGAGATAAGATTTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCG
1 GGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCG
* *
15629833 ATCTACTCTACTGTAACTTCATAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCA
66 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTGTAATCTCA
15629898 GGGAGATAGGATTACCAGCTTCAATCTACTCCGCTGTAATCTCAG
131 GGGAGATAGGATTACCAGCTTCAATCTACTCCGCTGTAATCTCAG
* *
15629943 AGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATACG
1 GGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCG
* *
15630008 ATCTATTCTACTGTAACTTTAGAGAGATAAGATCATTTATTTTAATCCACTCCACTGTAATCTCA
66 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTGTAATCTCA
* * *
15630073 GGGAGATAGGATTACCAACTTCAATCTGCTCCGCTGTAATCTCAA
131 GGGAGATAGGATTACCAGCTTCAATCTACTCCGCTGTAATCTCAG
15630118 GGAGATA
1 GGAGATA
15630125 GGATTCACCA
Statistics
Matches: 335, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 335 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (175 bp):
GGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCG
ATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTGTAATCTCA
GGGAGATAGGATTACCAGCTTCAATCTACTCCGCTGTAATCTCAG
Found at i:15638690 original size:19 final size:19
Alignment explanation
Indices: 15638666--15638711 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
15638656 AATAATCTTA
* *
15638666 AATGCATATG-ATGACATG
1 AATGCAAATGCATGAAATG
15638684 TAATGCAAATGCATGAAATG
1 -AATGCAAATGCATGAAATG
15638704 AATGCAAA
1 AATGCAAA
15638712 AAAGAGCGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.24
Consensus pattern (19 bp):
AATGCAAATGCATGAAATG
Found at i:15642608 original size:19 final size:20
Alignment explanation
Indices: 15642575--15642614 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
15642565 TAAAAAAAAG
*
15642575 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
15642595 AATTT-AAATGATGTGGATA
1 AATTTAAAATAATGTGGATA
15642614 A
1 A
15642615 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:15648574 original size:25 final size:25
Alignment explanation
Indices: 15648528--15648583 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
15648518 CAGCTCTCTT
***
15648528 GAGCTTCCCAATATTTGGCTCACAA
1 GAGCTTCCCAATATTCAACTCACAA
* *
15648553 GAGCTTCCCATTATTCAACTCACAT
1 GAGCTTCCCAATATTCAACTCACAA
15648578 GAGCTT
1 GAGCTT
15648584 TCCGTTATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (25 bp):
GAGCTTCCCAATATTCAACTCACAA
Found at i:15673183 original size:43 final size:43
Alignment explanation
Indices: 15673127--15673898 Score: 629
Period size: 43 Copynumber: 18.0 Consensus size: 43
15673117 CCGACACAAT
* * * * *
15673127 TATACTAGTACACACAGTGCATCATTGGATATACCGAAGCAAC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
** * * *
15673170 TATACAAGCACACACAGTGCATTATAGGATATACTC-AAGTAAC
1 TATACTGGCACACACAGTGCATCATCGGATAAAC-CGAAGTAAC
* * * ** **
15673213 TATAATGGCACACACAATGCATCATCAGATAAATTGAAGTATG
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* * * * *
15673256 TATACTGGCACATACAGTGCATCATTC-AACT-AACCAAAGAAAA
1 TATACTGGCACACACAGTGCATCA-TCGGA-TAAACCGAAGTAAC
* * * ** * *
15673299 TATACTAGAACACACAGTGCATCACCGGATAAATTGAACTAGC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* * * * *
15673342 TATACTAGCACACACAGTGCATCATCGGATAAATCAAAGAAAA
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* * *
15673385 TATACCT-GCACACATAGTGCATCATCGGATAAACTGAA-TAAAA
1 TATA-CTGGCACACACAGTGCATCATCGGATAAACCGAAGT-AAC
* * * ** * *
15673428 TATACTGGCACACATATTACATCATCAAATAAACTGAAGTATC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* ***
15673471 TATACTGGCACATACAGTGCATCATCGGATAAATTAAAGTAAC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* * * *
15673514 TATGCTGGCATACATAGTGCATCATCGGATAAACCGAAGTATC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* * * * **
15673557 TATACTGGCACACACAATGTACCATCGAATAAATTGAAGTAAC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* * * * *
15673600 TATACTTGCACACATAGTGCATCATCAGATAAACCGAAATATC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* * *
15673643 TATACTGGCACATATAGTGCATCATCGGATAAATCGAAGTAAC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* * *
15673686 TATATTGGCACACACAGTGCATCATCAGATAAACTGAAGTAAC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* * * * *
15673729 TATACTCGCACACATAGTGCATCATCAGATAAACCAAAGTATC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* * * * ** *
15673772 TATACTGACACATATAGTACATCATTAGATAAATCGAAGTAAC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
* * * ** *
15673815 TATACTAGCATACCCAGTGCATCA-CTAAATAAACCAAAGTAAC
1 TATACTGGCACACACAGTGCATCATC-GGATAAACCGAAGTAAC
* * * *
15673858 TATACCGACACATATAGTGCATCATCGGATAAACCGAAGTA
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTA
15673899 TAACCTGTAT
Statistics
Matches: 574, Mismatches: 143, Indels: 24
0.77 0.19 0.03
Matches are distributed among these distances:
42 4 0.01
43 562 0.98
44 8 0.01
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (43 bp):
TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGTAAC
Found at i:15683400 original size:146 final size:143
Alignment explanation
Indices: 15683137--15683424 Score: 414
Period size: 146 Copynumber: 2.0 Consensus size: 143
15683127 GTTACATAGA
* * * **
15683137 CATTTAACCTCTAAAAATGTATTAGAAGTTTTCTCCTCATACGGCTCGAGAAAAAAAGATCAATT
1 CATTTAACCCCTAAAAATGTATAAGAAATTTTCTCCTCATACAACTCGAGAAAAAAAGATCAATT
* **
15683202 AAAATTTATGTCTATGTATGAAATTATAATGTATGAAATTAAAATATAAAAAAGATCCATATTTC
66 AAAAGTTATGTCTATGTATGAAATTATAATGTATGAAATTAAAATAT-AAAAA-ATCCATAAATC
15683267 AACAAATCAATTAGG
129 AACAAATCAATTAGG
* * * * *
15683282 CATTTAACCCCTAGAAATGTATAATAAATTTTTTCCTCATACAACTTGAGAAAAAAAAGATTAAT
1 CATTTAACCCCTAAAAATGTATAAGAAATTTTCTCCTCATACAACTCGAG-AAAAAAAGATCAAT
* *
15683347 TAAAAGTTATGTCTATGTATGAAATTATAATGTATGGAATTAGAATATAAAAAATCCATAAATCA
65 TAAAAGTTATGTCTATGTATGAAATTATAATGTATGAAATTAAAATATAAAAAATCCATAAATCA
15683412 ACAAATCAATTAG
130 ACAAATCAATTAG
15683425 CCTTTCAAGA
Statistics
Matches: 127, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
144 23 0.18
145 46 0.36
146 58 0.46
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.32
Consensus pattern (143 bp):
CATTTAACCCCTAAAAATGTATAAGAAATTTTCTCCTCATACAACTCGAGAAAAAAAGATCAATT
AAAAGTTATGTCTATGTATGAAATTATAATGTATGAAATTAAAATATAAAAAATCCATAAATCAA
CAAATCAATTAGG
Found at i:15683672 original size:91 final size:91
Alignment explanation
Indices: 15683576--15683745 Score: 256
Period size: 91 Copynumber: 1.9 Consensus size: 91
15683566 CCAATTTAGT
* *
15683576 CCTTG-CAGTTAATTAACATAATCAATTAAGCCCCTTT-GTTAACTA-AATCCGCGGTTGACCAC
1 CCTTGCCA-TTAATTAAAATAATCAATCAAG-CCCTTTCGTTAAC-AGAATCCGCGGTTGACCAC
15683638 ATTGACTGTTAAAATAAGCCCAATTGAAC
63 ATTGACTGTTAAAATAAGCCCAATTGAAC
* *
15683667 CCTTGCCATTAATTAAAATAATCAATCAAGCCTTTTCGTTAACAGAATCCGTGGTTGACCACATT
1 CCTTGCCATTAATTAAAATAATCAATCAAGCCCTTTCGTTAACAGAATCCGCGGTTGACCACATT
15683732 GACTGTTAAAATAA
66 GACTGTTAAAATAA
15683746 ATTGACTGAC
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
90 6 0.08
91 64 0.89
92 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.31
Consensus pattern (91 bp):
CCTTGCCATTAATTAAAATAATCAATCAAGCCCTTTCGTTAACAGAATCCGCGGTTGACCACATT
GACTGTTAAAATAAGCCCAATTGAAC
Found at i:15683878 original size:20 final size:20
Alignment explanation
Indices: 15683804--15683892 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
15683794 TAATATTTTT
*
15683804 TTATAAAAAA-TA-AAAAAA
1 TTATAAAAAATTAGAAAATA
* * *
15683822 TCATACAAAA-TAGAAAAAAA
1 TTATAAAAAATTAG-AAAATA
* *
15683842 TTATAAAAAAATGGAAAATA
1 TTATAAAAAATTAGAAAATA
*
15683862 TTATTAAAAATTAG-AAATA
1 TTATAAAAAATTAGAAAATA
15683881 TTA-AAAAAATTA
1 TTATAAAAAATTA
15683893 AAATTGATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
18 18 0.31
19 8 0.14
20 30 0.52
21 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (20 bp):
TTATAAAAAATTAGAAAATA
Found at i:15683879 original size:19 final size:17
Alignment explanation
Indices: 15683845--15683896 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
15683835 AAAAAAATTA
*
15683845 TAAAAAAATGGAAAATAT
1 TAAAAAAAT-TAAAATAT
*
15683863 TATTAAAAATTAGAAATAT
1 TA-AAAAAATTA-AAATAT
15683882 TAAAAAAATTAAAAT
1 TAAAAAAATTAAAAT
15683897 TGATATAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 4 0.14
18 11 0.38
19 14 0.48
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAAAAAAATTAAAATAT
Found at i:15684062 original size:20 final size:22
Alignment explanation
Indices: 15684037--15684082 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
15684027 AAATTTTATA
*
15684037 AAAAACATAT-ACAAATTC-TT
1 AAAAACATATAACAAAATCATT
*
15684057 AAAAACTTATAACAAAATCATT
1 AAAAACATATAACAAAATCATT
15684079 AAAA
1 AAAA
15684083 TATAAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 7 0.32
22 6 0.27
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAACATATAACAAAATCATT
Found at i:15684125 original size:17 final size:18
Alignment explanation
Indices: 15684070--15684127 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
15684060 AACTTATAAC
*
15684070 AAAATCATTAAA-ATATA
1 AAAATAATTAAATATATA
* * *
15684087 AAAGTTATTAAAAATCATA
1 AAAATAATTAAATAT-ATA
15684106 AAAATAATTAAATATA-A
1 AAAATAATTAAATATATA
15684123 AAAAT
1 AAAAT
15684128 GTTAAAATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 16 0.47
18 3 0.09
19 15 0.44
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAATAATTAAATATATA
Found at i:15684173 original size:10 final size:11
Alignment explanation
Indices: 15684150--15684183 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
15684140 ATACACTTAT
*
15684150 AAAAATTATAA
1 AAAAATCATAA
15684161 AAAAATCATAA
1 AAAAATCATAA
15684172 AAAAAT-ATAA
1 AAAAATCATAA
15684182 AA
1 AA
15684184 TTTATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAATCATAA
Found at i:15684228 original size:17 final size:17
Alignment explanation
Indices: 15684173--15684227 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
15684163 AAATCATAAA
15684173 AAAATATAAAATTTA-T
1 AAAATATAAAATTTATT
* ** *
15684189 ATAATATAAAAAATATA
1 AAAATATAAAATTTATT
*
15684206 AAAATCTAAAATTTATT
1 AAAATATAAAATTTATT
15684223 AAAAT
1 AAAAT
15684228 CATTTATAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATATAAAATTTATT
Found at i:15684248 original size:21 final size:21
Alignment explanation
Indices: 15684212--15684253 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
15684202 TATAAAAATC
*
15684212 TAAAATTTATTAAAATCATTTA
1 TAAAATTTAATAAAAT-ATTTA
15684234 TAAAA-TTAATAAAATATTTA
1 TAAAATTTAATAAAATATTTA
15684254 AATTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAATTTAATAAAATATTTA
Found at i:15684285 original size:10 final size:9
Alignment explanation
Indices: 15683804--15684349 Score: 126
Period size: 9 Copynumber: 58.0 Consensus size: 9
15683794 TAATATTTTT
15683804 TTATAAAAA
1 TTATAAAAA
* *
15683813 ATAAAAAAA
1 TTATAAAAA
*
15683822 TCATACAAAA
1 TTATA-AAAA
* *
15683832 TAGAAAAAAA
1 T-TATAAAAA
15683842 TTATAAAAA
1 TTATAAAAA
*
15683851 -AATGGAAAATA
1 TTAT--AAAA-A
15683862 TTATTAAAAA
1 TTA-TAAAAA
* *
15683872 TTAGAAATA
1 TTATAAAAA
15683881 TTA-AAAAA
1 TTATAAAAA
*
15683889 --ATTAAAA
1 TTATAAAAA
**
15683896 TTGATATAATC
1 TT-ATA-AAAA
15683907 TTATAAAAA
1 TTATAAAAA
15683916 -TATAAAAA
1 TTATAAAAA
*
15683924 ATATTAGAAAA
1 TTA-TA-AAAA
*
15683935 TAATAAAAA
1 TTATAAAAA
*
15683944 CCTTATAAATA
1 --TTATAAAAA
*
15683955 CTATAAAAA
1 TTATAAAAA
*
15683964 ATATAAAAGA
1 TTATAAAA-A
15683974 TT-TAATAAA
1 TTATAA-AAA
*
15683983 TTGTAATAAA
1 TTATAA-AAA
15683993 TT-TAAAAA
1 TTATAAAAA
15684001 TTAATGAAACATA
1 TT-AT-AAA-A-A
*
15684014 TT-TAAAACG
1 TTATAAAA-A
*
15684023 TT-TAAAATT
1 TTATAAAA-A
15684032 TTATAAAAAA
1 TTAT-AAAAA
* *
15684042 CATATACAAA
1 -TTATAAAAA
*
15684052 TTCTTAAAAA
1 TT-ATAAAAA
15684062 CTTATAACAAAA
1 -TTAT-A-AAAA
* *
15684074 TCATTAAAA
1 TTATAAAAA
*
15684083 -TATAAAAG
1 TTATAAAAA
15684091 TTATTAAAAA
1 TTA-TAAAAA
*
15684101 TCATAAAAA
1 TTATAAAAA
* *
15684110 TAAT-TAAA
1 TTATAAAAA
15684118 -TATAAAAA
1 TTATAAAAA
* * *
15684126 ATGTTAAAA
1 TTATAAAAA
* *
15684135 TTGATATACAC
1 TT-ATA-AAAA
15684146 TTATAAAAA
1 TTATAAAAA
15684155 TTATAAAAAAA
1 TTAT--AAAAA
*
15684166 TCATAAAAAA
1 TTAT-AAAAA
* *
15684176 ATATAAAAT
1 TTATAAAAA
*
15684185 TTAT-ATAA
1 TTATAAAAA
15684193 -TATAAAAA
1 TTATAAAAA
*
15684201 ATATAAAAA
1 TTATAAAAA
* *
15684210 -TCTAAAAT
1 TTATAAAAA
15684218 TTATTAAAATCA
1 TTA-TAAAA--A
15684230 TT-TATAAAA
1 TTATA-AAAA
15684239 TTAATAAAATA
1 TT-ATAAAA-A
**
15684250 TT-TAAATT
1 TTATAAAAA
15684258 TTATAAAAA
1 TTATAAAAA
*
15684267 CGTAT-AAAA
1 -TTATAAAAA
15684276 TTAGTAAAAA
1 TTA-TAAAAA
15684286 TTATAAAAA
1 TTATAAAAA
15684295 -TATAAAAAA
1 TTAT-AAAAA
*
15684304 TTCTAATAAA
1 TTATAA-AAA
15684314 TTTATAAAAA
1 -TTATAAAAA
* *
15684324 ATATTAACAA
1 TTA-TAAAAA
15684334 -T-TAAAAA
1 TTATAAAAA
15684341 TTATAAAAA
1 TTATAAAAA
15684350 AACTATTTAA
Statistics
Matches: 394, Mismatches: 82, Indels: 122
0.66 0.14 0.20
Matches are distributed among these distances:
6 1 0.00
7 14 0.04
8 49 0.12
9 146 0.37
10 107 0.27
11 65 0.16
12 8 0.02
13 4 0.01
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:15684799 original size:15 final size:16
Alignment explanation
Indices: 15684781--15684814 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15684771 ATAAAACATT
15684781 AAAAATA-AAAAATAA
1 AAAAATATAAAAATAA
*
15684796 AAAAATATAAAATTAA
1 AAAAATATAAAAATAA
15684812 AAA
1 AAA
15684815 TCAGTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAATATAAAAATAA
Found at i:15685021 original size:29 final size:28
Alignment explanation
Indices: 15684980--15685071 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 28
15684970 ATGTTTTAAT
*
15684980 TTTTTATAT-TTTTTATGATTTTTATAAG
1 TTTTTAAATATTTTTAT-ATTTTTATAAG
*
15685008 TTTTTAAGA-ATTTTTATATCTTTTATAAA
1 TTTTTAA-ATATTTTTATAT-TTTTATAAG
* * *
15685037 ATTTTAAATATTTGTATTAATTTTATAAAG
1 TTTTTAAATATTTTTA-TATTTTTAT-AAG
15685067 TTTTT
1 TTTTT
15685072 CATAATTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
28 9 0.18
29 34 0.67
30 8 0.16
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (28 bp):
TTTTTAAATATTTTTATATTTTTATAAG
Found at i:15685031 original size:20 final size:19
Alignment explanation
Indices: 15684980--15685041 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
15684970 ATGTTTTAAT
*
15684980 TTTTTATATTTTTTATG-A
1 TTTTTATATTTTTTAAGAA
*
15684998 TTTTTATAAGTTTTTAAGAA
1 TTTTTAT-ATTTTTTAAGAA
15685018 TTTTTATATCTTTTATAA-AA
1 TTTTTATAT-TTTT-TAAGAA
15685038 TTTT
1 TTTT
15685042 AAATATTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.19
19 9 0.24
20 18 0.49
21 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTATATTTTTTAAGAA
Found at i:15685139 original size:9 final size:9
Alignment explanation
Indices: 15684980--15685218 Score: 90
Period size: 9 Copynumber: 25.8 Consensus size: 9
15684970 ATGTTTTAAT
*
15684980 TTTTTATAT
1 TTTTTATAA
*
15684989 TTTTTATGA
1 TTTTTATAA
15684998 TTTTTATAA
1 TTTTTATAA
*
15685007 GTTTTTAAGAA
1 -TTTTT-ATAA
15685018 TTTTTAT-A
1 TTTTTATAA
15685026 TCTTTTATAAA
1 T-TTTTAT-AA
*
15685037 ATTTTA-AA
1 TTTTTATAA
15685045 TATTTGTATTAA
1 T-TTT-TA-TAA
15685057 -TTTTATAAA
1 TTTTTAT-AA
15685066 GTTTTTCATAA
1 -TTTTT-ATAA
*
15685077 TTTATTAGAA
1 TTT-TTATAA
15685087 --TTT-T-A
1 TTTTTATAA
15685092 TTTTTATAA
1 TTTTTATAA
* *
15685101 TATTTACAA
1 TTTTTATAA
* *
15685110 GTTTTAATTA
1 -TTTTTATAA
15685120 TTTAATTATAA
1 TTT--TTATAA
15685131 TTTTTATAA
1 TTTTTATAA
*
15685140 GTTTATATCAA
1 -TTTTTAT-AA
15685151 -TTTTAGT-A
1 TTTTTA-TAA
15685159 TTTTTAT--
1 TTTTTATAA
15685166 TTTTTAATAA
1 TTTTT-ATAA
*
15685176 -TTATATAA
1 TTTTTATAA
15685184 TATTTTATAA
1 T-TTTTATAA
*
15685194 TTTTTCT-A
1 TTTTTATAA
*
15685202 TTTTTAATCA
1 TTTTT-ATAA
15685212 TTTTTAT
1 TTTTTAT
15685219 GGGAAAATAT
Statistics
Matches: 175, Mismatches: 23, Indels: 64
0.67 0.09 0.24
Matches are distributed among these distances:
5 1 0.01
7 10 0.06
8 21 0.12
9 66 0.38
10 52 0.30
11 21 0.12
12 4 0.02
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:15685568 original size:18 final size:18
Alignment explanation
Indices: 15685517--15685568 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
15685507 ATGTAATACT
* *
15685517 TAAAATTCCTTAAAAATA
1 TAAAAATCCATAAAAATA
*
15685535 TAAAAAAATTCATAAAAATA
1 T--AAAAATCCATAAAAATA
*
15685555 TAAAAATCCCTAAA
1 TAAAAATCCATAAA
15685569 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 12 0.44
20 15 0.56
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAAAATCCATAAAAATA
Found at i:15701903 original size:132 final size:129
Alignment explanation
Indices: 15701685--15701945 Score: 290
Period size: 132 Copynumber: 2.0 Consensus size: 129
15701675 CATTTATGGT
* * * ** * * * *
15701685 TATTACTGGACTTTTCAATTAAGAGGCATGTTTGCTTGATGGTAGTGTTTCATTATGTATGATTC
1 TATTACTGGACATTTCAATTAAGAGGCATGTTTGCTTGACGCTAGTGCGTCACTAAGCATAATTC
* * * *
15701750 TTCCTCGAATTTGCTTGTGTTGCTTTAATACTATTATTCATTGTGTATATATATCCTTGATCTTT
66 TTCCTCGAATTTGCTTGTGTTGCTTGAAAACTATTA-TCAAT-TG-ATATATATCCTTGATCCTT
15701815 TA
128 TA
* *
15701817 TATTACTGGACATTTCAATTAATAGGCATGTTTGCTTGACGCTAGTGCGTCCCTAAGCATAATTC
1 TATTACTGGACATTTCAATTAAGAGGCATGTTTGCTTGACGCTAGTGCGTCACTAAGCATAATTC
** * * * *
15701882 TT-CTATTAGTTTTCTTTTGTTGCTTGAAAACTATTATCAATTGCTATATATCCTTGATCCTTTA
66 TTCCT-CGAATTTGCTTGTGTTGCTTGAAAACTATTATCAATTGATATATATCCTTGATCCTTTA
15701946 GGTTTTTATG
Statistics
Matches: 107, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
129 19 0.18
130 2 0.02
131 6 0.06
132 80 0.75
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (129 bp):
TATTACTGGACATTTCAATTAAGAGGCATGTTTGCTTGACGCTAGTGCGTCACTAAGCATAATTC
TTCCTCGAATTTGCTTGTGTTGCTTGAAAACTATTATCAATTGATATATATCCTTGATCCTTTA
Found at i:15711693 original size:39 final size:38
Alignment explanation
Indices: 15711633--15711838 Score: 268
Period size: 39 Copynumber: 5.3 Consensus size: 38
15711623 CAACTCTCAA
* * *
15711633 TAGAACCAGTGGGTATGGCTCAATTGAGCATACTTTTAG
1 TAGAATCAGTAGGTAT-GCTCGATTGAGCATACTTTTAG
* *
15711672 TAGAATCAGTAGGTAATGCTCAATTAAGCATACTTTTAG
1 TAGAATCAGTAGGT-ATGCTCGATTGAGCATACTTTTAG
15711711 TAGAATCAGTAGGTATGACTCGATTGAGCATACTTTTAG
1 TAGAATCAGTAGGTATG-CTCGATTGAGCATACTTTTAG
* * *
15711750 TAGAATCAGTGGGTATGACTCGATTGAGCATACTTTCAT
1 TAGAATCAGTAGGTATG-CTCGATTGAGCATACTTTTAG
* * *
15711789 TAGAATCAGTAGATATGGCTCGATTGAGCATACTTTCAA
1 TAGAATCAGTAGGTAT-GCTCGATTGAGCATACTTTTAG
15711828 TAGAATCAGTA
1 TAGAATCAGTA
15711839 TCCCATTTTT
Statistics
Matches: 153, Mismatches: 11, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
38 3 0.02
39 147 0.96
40 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (38 bp):
TAGAATCAGTAGGTATGCTCGATTGAGCATACTTTTAG
Found at i:15718565 original size:19 final size:19
Alignment explanation
Indices: 15718524--15718579 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
15718514 TTTAAAATAG
* *
15718524 TTTTAACTCGATTGAAA-A
1 TTTTAACTCTATTAAAACA
15718542 TATTTAACTCTATTAAAACCA
1 T-TTTAACTCTATTAAAA-CA
15718563 TTTTAACT-TGATTAAAA
1 TTTTAACTCT-ATTAAAA
15718580 GTTGATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 1 0.03
19 15 0.47
20 14 0.44
21 2 0.06
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTTAACTCTATTAAAACA
Found at i:15734932 original size:18 final size:18
Alignment explanation
Indices: 15734891--15734936 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
15734881 TTTTATTGAA
*
15734891 AAATTAATTTAGTTAATT
1 AAATTAATTTAGTTAAAT
*
15734909 TAATTAATTTA-TTAAAT
1 AAATTAATTTAGTTAAAT
15734926 AATATTAATTT
1 AA-ATTAATTT
15734937 TAGGAAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
AAATTAATTTAGTTAAAT
Found at i:15735631 original size:22 final size:21
Alignment explanation
Indices: 15735597--15735640 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
15735587 TTCAAAATTA
*
15735597 AATTATTAATATATTGAATTTT
1 AATTATTAATATAAT-AATTTT
**
15735619 AATTATTTTTATAATAATTTT
1 AATTATTAATATAATAATTTT
15735640 A
1 A
15735641 CACAAATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
AATTATTAATATAATAATTTT
Found at i:15739384 original size:15 final size:14
Alignment explanation
Indices: 15739366--15739406 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
15739356 TAAGGTCTTG
15739366 TTAATTAAAGTTTAA
1 TTAATT-AAGTTTAA
* *
15739381 TTAATTAATTTTTA
1 TTAATTAAGTTTAA
15739395 TTAATTAAGTTT
1 TTAATTAAGTTT
15739407 TGAACTAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
TTAATTAAGTTTAA
Found at i:15745461 original size:17 final size:17
Alignment explanation
Indices: 15745439--15745473 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15745429 CTAGATATGT
15745439 GTAAAAGATGATG-TGGA
1 GTAAAAGAT-ATGATGGA
15745456 GTAAAAGATATGATGGA
1 GTAAAAGATATGATGGA
15745473 G
1 G
15745474 ATATCACTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (17 bp):
GTAAAAGATATGATGGA
Found at i:15745642 original size:69 final size:69
Alignment explanation
Indices: 15745538--15745685 Score: 199
Period size: 69 Copynumber: 2.1 Consensus size: 69
15745528 TCTACGGAGA
* * * *
15745538 CCTTGGTGTGGTGGAGGGATGATATTTTATCTGATACGATATTGTGCCTACGAGCTTTACACTAT
1 CCTTGGTGTGATGGAGGGATGATATGTTATATGATACGATATTGTGCCTACGAGCTTTACACTAC
*
15745603 GGTG
66 AGTG
* * **
15745607 CCTTGGTGTGATGGAGGGATGAT-TCGTTATATGATATGTTATTGTGCCTACGAGCTTTGGACTA
1 CCTTGGTGTGATGGAGGGATGATAT-GTTATATGATACGATATTGTGCCTACGAGCTTTACACTA
15745671 CAGTG
65 CAGTG
15745676 CCTTGGTGTG
1 CCTTGGTGTG
15745686 GTGTAGTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 1 0.01
69 68 0.99
ACGTcount: A:0.19, C:0.14, G:0.30, T:0.36
Consensus pattern (69 bp):
CCTTGGTGTGATGGAGGGATGATATGTTATATGATACGATATTGTGCCTACGAGCTTTACACTAC
AGTG
Found at i:15750680 original size:17 final size:18
Alignment explanation
Indices: 15750640--15750681 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
15750630 GCAATTCAAG
* *
15750640 AGTTTCCCTACAGTTTCT
1 AGTTTTCCTACAGTCTCT
15750658 AGTTTTCCTACAGTCTC-
1 AGTTTTCCTACAGTCTCT
15750675 AGTTTTC
1 AGTTTTC
15750682 TCTAATTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.17, C:0.26, G:0.12, T:0.45
Consensus pattern (18 bp):
AGTTTTCCTACAGTCTCT
Found at i:15751519 original size:30 final size:30
Alignment explanation
Indices: 15751483--15751571 Score: 119
Period size: 28 Copynumber: 3.0 Consensus size: 30
15751473 TAGCAGTATA
*
15751483 GTGTGGGCCTTAGCCCATTACAGTAACAGT
1 GTGTGGGCCTTAGCCCAATACAGTAACAGT
* * *
15751513 GTGTGGGCCTTAGCCTAATAAAGTAATA--
1 GTGTGGGCCTTAGCCCAATACAGTAACAGT
15751541 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
1 GTGTGGGCCTTAGCCCAATACAGTAA-CAGT
15751572 ACAATGCAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 24 0.49
29 1 0.02
30 24 0.49
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (30 bp):
GTGTGGGCCTTAGCCCAATACAGTAACAGT
Found at i:15751750 original size:26 final size:26
Alignment explanation
Indices: 15751676--15751752 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
15751666 ACACCAATAT
* *
15751676 CGCAACAAAGCTGCCAGTAATAATAA
1 CGCAACAAAGCTGCCAGTAACAGTAA
*
15751702 CGCAACAAAGCTTCCAGTAACAGTAA
1 CGCAACAAAGCTGCCAGTAACAGTAA
*
15751728 CGCAACAAAGCTGCTAGTAACAGTA
1 CGCAACAAAGCTGCCAGTAACAGTA
15751753 TATGTGGCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.16
Consensus pattern (26 bp):
CGCAACAAAGCTGCCAGTAACAGTAA
Found at i:15751974 original size:27 final size:27
Alignment explanation
Indices: 15751915--15752121 Score: 124
Period size: 27 Copynumber: 7.7 Consensus size: 27
15751905 TTCCACTCCT
** * *
15751915 AGGGGTATAACAGTTATTTTACCCTATG
1 AGGGGTATTTCAGTCATTTTACCCT-TC
15751943 A-GGGTATTTCAGTCATTTTACCCTTC
1 AGGGGTATTTCAGTCATTTTACCCTTC
*
15751969 AGGGGTATTTC-GATCATTTTACCCTTT
1 AGGGGTATTTCAG-TCATTTTACCCTTC
* *
15751996 GGGGGTATTTCAATCATTTTACCCTTC
1 AGGGGTATTTCAGTCATTTTACCCTTC
* * * *
15752023 -GAGGTTATTT-TGATCATCTTACCCATC
1 AG-GGGTATTTCAG-TCATTTTACCCTTC
* **
15752050 -GAGCGTATTTTGGTCATTTTACCCATT-
1 AG-GGGTATTTCAGTCATTTTACCC-TTC
** *
15752077 AATGGTATTTCGGGT-ATTTTACCCTTC
1 AGGGGTATTTC-AGTCATTTTACCCTTC
*
15752104 -GAGGGTATTTCGGTCATT
1 AG-GGGTATTTCAGTCATT
15752122 AGCCCACGAA
Statistics
Matches: 143, Mismatches: 24, Indels: 25
0.74 0.12 0.13
Matches are distributed among these distances:
26 9 0.06
27 128 0.90
28 6 0.04
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (27 bp):
AGGGGTATTTCAGTCATTTTACCCTTC
Found at i:15751988 original size:54 final size:55
Alignment explanation
Indices: 15751930--15752121 Score: 191
Period size: 54 Copynumber: 3.6 Consensus size: 55
15751920 TATAACAGTT
15751930 ATTTTACCCTAT-GAGGGTATTTCAGTCATTTTACCCTTCAGGGGTATTTCGATC
1 ATTTTACCCTATCGAGGGTATTTCAGTCATTTTACCCTTCAGGGGTATTTCGATC
* * * * *
15751984 ATTTTACCCT-TTGGGGGTATTTCAATCATTTTACCCTTC-GAGGTTATTTTGATC
1 ATTTTACCCTATCGAGGGTATTTCAGTCATTTTACCCTTCAG-GGGTATTTCGATC
* * ** ** *
15752038 ATCTTACCC-ATCGAGCGTATTTTGGTCATTTTACCCATT-AATGGTATTTCGGGT-
1 ATTTTACCCTATCGAGGGTATTTCAGTCATTTTACCC-TTCAGGGGTATTTC-GATC
*
15752092 ATTTTACCCT-TCGAGGGTATTTCGGTCATT
1 ATTTTACCCTATCGAGGGTATTTCAGTCATT
15752122 AGCCCACGAA
Statistics
Matches: 112, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
53 2 0.02
54 106 0.95
55 4 0.04
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (55 bp):
ATTTTACCCTATCGAGGGTATTTCAGTCATTTTACCCTTCAGGGGTATTTCGATC
Found at i:15752045 original size:81 final size:82
Alignment explanation
Indices: 15751929--15752113 Score: 191
Period size: 81 Copynumber: 2.3 Consensus size: 82
15751919 GTATAACAGT
* * *
15751929 TATTTTACCCTAT-GAGGGTA-TTTCAGTCATTTTACCCTTC-AGGGGTATTTCGATCATTTTAC
1 TATTTTACCCT-TCGAGGGTATTTTCAGTCATCTTACCCATCGA-GCGTATTTCGATCATTTTAC
* **
15751991 CCTTTGGGGGTATTTC-AA
64 CCATTAAGGGTATTTCGAA
* * * *
15752009 TCATTTTACCCTTCGAGGTTATTTTGA-TCATCTTACCCATCGAGCGTATTTTGGTCATTTTACC
1 T-ATTTTACCCTTCGAGGGTATTTTCAGTCATCTTACCCATCGAGCGTATTTCGATCATTTTACC
* **
15752073 CATTAATGGTATTTCGGG
65 CATTAAGGGTATTTCGAA
15752091 TATTTTACCCTTCGAGGGTATTT
1 TATTTTACCCTTCGAGGGTATTT
15752114 CGGTCATTAG
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
80 2 0.02
81 78 0.91
82 6 0.07
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.43
Consensus pattern (82 bp):
TATTTTACCCTTCGAGGGTATTTTCAGTCATCTTACCCATCGAGCGTATTTCGATCATTTTACCC
ATTAAGGGTATTTCGAA
Found at i:15758805 original size:9 final size:9
Alignment explanation
Indices: 15758764--15758806 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
15758754 ACCCAAAAAA
*
15758764 TATTATTTT
1 TATTTTTTT
*
15758773 TATTTTATT
1 TATTTTTTT
*
15758782 TATTTTTTG
1 TATTTTTTT
15758791 TATTTTTTT
1 TATTTTTTT
*
15758800 TGTTTTT
1 TATTTTT
15758807 GCACTTTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (9 bp):
TATTTTTTT
Found at i:15773081 original size:17 final size:17
Alignment explanation
Indices: 15773051--15773084 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
15773041 TTTTTTCCCA
15773051 AATTAAAATAAAATAAC
1 AATTAAAATAAAATAAC
15773068 AATTATAAAT-AAATAAC
1 AATTA-AAATAAAATAAC
15773085 TGACTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
AATTAAAATAAAATAAC
Found at i:15792522 original size:50 final size:50
Alignment explanation
Indices: 15792424--15792911 Score: 631
Period size: 50 Copynumber: 9.7 Consensus size: 50
15792414 ATGTGAGCCA
15792424 ATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATGAGAGGTCCC
15792480 ATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCC
* * *
15792530 ATGTAAGACCATGTCTGGTACATGGCATTGGCACCGAGATGAGAGGACCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCC
*
15792580 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCC
* *
15792630 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCTC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCC
* *
15792680 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCC
* *
15792730 ATGTAAGACCATGTCTGGGACATGGCGTTGGCAC-CAGGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACTGA-GATGAGAGGTCCC
** * * **
15792780 CCGTAAGACCATGTCTGGGACATGGCATGGGCA-TCGATATGAGAACTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACT-GAGATGAGAGGTCCC
* * * * * * * ** *
15792830 ATGTAAGACCATATCTGAGATATGGCATTGGCAGT-ATAGGAAACATCTC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCC
* *
15792879 ATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA
15792912 TGTTATTATC
Statistics
Matches: 389, Mismatches: 39, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
49 38 0.10
50 311 0.80
51 2 0.01
53 4 0.01
55 1 0.00
56 33 0.08
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (50 bp):
ATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCC
Found at i:15797340 original size:19 final size:19
Alignment explanation
Indices: 15797318--15797355 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
15797308 TCCATCATCC
15797318 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCACTCTCTCA
*
15797337 CTCATTCATCACTCTCTCA
1 CTCATCCATCACTCTCTCA
15797356 ACTCCTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.34
Consensus pattern (19 bp):
CTCATCCATCACTCTCTCA
Found at i:15807195 original size:22 final size:20
Alignment explanation
Indices: 15807170--15807222 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 20
15807160 ATTTATTTAA
*
15807170 TTATTTTTAGGTATTTAGGAAT
1 TTATTTTTA-GTAATTA-GAAT
15807192 TTATTTCTTTAGTAATTAGAAT
1 TTA-TT-TTTAGTAATTAGAAT
15807214 TTAATTTTT
1 TT-ATTTTT
15807223 GCAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 3 0.11
22 11 0.41
23 9 0.33
24 4 0.15
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.58
Consensus pattern (20 bp):
TTATTTTTAGTAATTAGAAT
Found at i:15807220 original size:23 final size:25
Alignment explanation
Indices: 15807164--15807220 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
15807154 CTTGTTATTT
* *
15807164 ATTTAATTATTTTTAGGTATTTAGGA
1 ATTTAATT-TCTTTAGGTAATTAGGA
15807190 ATTT-ATTTCTTTA-GTAATTA-GA
1 ATTTAATTTCTTTAGGTAATTAGGA
15807212 ATTTAATTT
1 ATTTAATTT
15807221 TTGCAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 6 0.21
23 10 0.36
24 5 0.18
25 3 0.11
26 4 0.14
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.56
Consensus pattern (25 bp):
ATTTAATTTCTTTAGGTAATTAGGA
Found at i:15814912 original size:20 final size:20
Alignment explanation
Indices: 15814887--15814930 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
15814877 CAAAAACTAG
*
15814887 AAATTGATTAAAATCAAATC
1 AAATTGATTAAAATCAAATA
**
15814907 AAATTGATTGGAATCAAATA
1 AAATTGATTAAAATCAAATA
15814927 AAAT
1 AAAT
15814931 CAGGTCATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.30
Consensus pattern (20 bp):
AAATTGATTAAAATCAAATA
Found at i:15830111 original size:44 final size:44
Alignment explanation
Indices: 15830063--15830247 Score: 114
Period size: 44 Copynumber: 4.2 Consensus size: 44
15830053 AAGATTGTAG
15830063 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGCGA
* * ** ** *
15830107 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAAATCGAAGACGGCGA
* * * * * *
15830150 AGCCTTGTCTCCCTGAGCAGTAGTGGAG-AAGGTTGAAGA-GTG-TA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAA-ATCGAAGACG-GCGA
* *
15830194 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGCGA
*
15830239 TTCTTATCT
1 ATCTTATCT
15830248 TTCCAAGATA
Statistics
Matches: 102, Mismatches: 25, Indels: 28
0.66 0.16 0.18
Matches are distributed among these distances:
42 4 0.04
43 11 0.11
44 73 0.72
45 10 0.10
46 4 0.04
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGCGA
Found at i:15830251 original size:132 final size:132
Alignment explanation
Indices: 15830014--15831366 Score: 2260
Period size: 132 Copynumber: 10.2 Consensus size: 132
15830004 CAGATCGGTA
15830014 ACCAAGCCTTGTC-CCTCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 ACCAAGCCTTGTCTCC-CTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
15830078 GCAGTAGTGGAGCAAATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
65 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
15830143 GCC
130 GCC
* * *
15830146 ACCAAGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGAGTGTAGATCTTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* *
15830211 CAGTAGTGGAGCAGATCGAAGACGGTGATTCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
15830276 CC
131 CC
15830278 ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* * *
15830343 TAGTAGTGGAGCAGATCGACGACGGCGAATCTTATCTTTCCAAAATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
15830408 CC
131 CC
* * * *
15830410 ACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTTAATAGTGTAGATCTTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* *
15830475 CAGTAGTGGAGCAGATCGACGACGGCGAATCTTATCTTTCCAAGATAGTGAGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
15830540 CC
131 CC
* * * *
15830542 ACCAAGCCTTGTCTCCCTAAGCAGTAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAA
1 ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* * *
15830607 CAGTAGCGGAGCAGATCTAAGACGGCGAATCTTATTTTTCCAAGATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
15830672 CC
131 CC
* *
15830674 ACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAGATATTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
*
15830739 CAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
15830804 CC
131 CC
*
15830806 ACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
15830871 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
15830936 CC
131 CC
* * * *
15830938 ACCAAGCCTTGTCTCCCTAAGCAGCAGTGGAGAAGGTTGAAGATTATAGATCTCATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
*
15831003 CAGTAGTGGAGCAGATCTAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
15831068 CC
131 CC
* * * * * *
15831070 ACCTAGCCTTGTCTCCCAGAGTAGCAGTGGAGAAGGTTGAAGATTATAGATCTCATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* *
15831135 CAGTAGTGGAGCAGATCTAAGACGGTGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
15831200 CC
131 CC
* *
15831202 ACCAAGCCTTGTCTCCCTGAGTAGTAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* * *
15831267 CAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTAAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
15831332 CC
131 CC
* *
15831334 ACCAAACCTTGTCTCCCTG-GACAGCAGCAGAGA
1 ACCAAGCCTTGTCTCCCTGAG-CAGCAGCGGAGA
15831367 TAATTAAAGC
Statistics
Matches: 1147, Mismatches: 72, Indels: 4
0.94 0.06 0.00
Matches are distributed among these distances:
131 1 0.00
132 1144 1.00
133 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (132 bp):
ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
CC
Found at i:15835302 original size:18 final size:20
Alignment explanation
Indices: 15835265--15835308 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
15835255 GCTCGCTCTT
*
15835265 TTACTTTTTACTTTATTCAA
1 TTACTTTTTACTTGATTCAA
15835285 TTACTTTTT-C-TGATTCAA
1 TTACTTTTTACTTGATTCAA
15835303 TTACTT
1 TTACTT
15835309 GGATTGACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
19 1 0.04
20 9 0.39
ACGTcount: A:0.23, C:0.16, G:0.02, T:0.59
Consensus pattern (20 bp):
TTACTTTTTACTTGATTCAA
Found at i:15835364 original size:4 final size:4
Alignment explanation
Indices: 15835349--15835423 Score: 143
Period size: 4 Copynumber: 19.0 Consensus size: 4
15835339 TGTATCCATA
15835349 TATG TATG -ATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
15835396 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
15835424 AAGTTGGTGT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 3 0.04
4 67 0.96
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:15844534 original size:34 final size:35
Alignment explanation
Indices: 15844479--15844545 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
15844469 CAAACACCAG
*
15844479 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
15844514 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
15844546 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:15846738 original size:20 final size:20
Alignment explanation
Indices: 15846696--15846739 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
15846686 TAATACATTA
* *
15846696 AATTTAAAAAAATAACTCTT
1 AATTTAAAAAAATAACACGT
15846716 AATTTAAATAAAATAA-ACGT
1 AATTTAAA-AAAATAACACGT
15846736 AATT
1 AATT
15846740 ATCTAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (20 bp):
AATTTAAAAAAATAACACGT
Found at i:15860030 original size:34 final size:34
Alignment explanation
Indices: 15859987--15860055 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
15859977 TGAAGATAAC
15859987 ATTGAGGATTCGTTTACTAAGACTCTTGTAACTA
1 ATTGAGGATTCGTTTACTAAGACTCTTGTAACTA
15860021 ATTGAGGATTCGTTTACTAAGACTCTTGTAACTA
1 ATTGAGGATTCGTTTACTAAGACTCTTGTAACTA
15860055 A
1 A
15860056 GTGTTTTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (34 bp):
ATTGAGGATTCGTTTACTAAGACTCTTGTAACTA
Found at i:15872064 original size:9 final size:9
Alignment explanation
Indices: 15872050--15872134 Score: 73
Period size: 9 Copynumber: 9.4 Consensus size: 9
15872040 TTTGGTTAAA
15872050 AATTAACCG
1 AATTAACCG
*
15872059 AATTAATCG
1 AATTAACCG
* *
15872068 AATTGACTG
1 AATTAACCG
**
15872077 AATTAACTA
1 AATTAACCG
* *
15872086 AACTACCCG
1 AATTAACCG
15872095 AATTAACCG
1 AATTAACCG
*
15872104 AATT-ACTCA
1 AATTAAC-CG
*
15872113 AATTACCCG
1 AATTAACCG
15872122 AATTAACCG
1 AATTAACCG
15872131 AATT
1 AATT
15872135 GAATCCCTAC
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
8 2 0.03
9 55 0.95
10 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:15872096 original size:27 final size:27
Alignment explanation
Indices: 15872066--15872134 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
15872056 CCGAATTAAT
* *
15872066 CGAATTGACTGAATTAACT-AAACTACC
1 CGAATTAACCGAATT-ACTCAAACTACC
*
15872093 CGAATTAACCGAATTACTCAAATTACC
1 CGAATTAACCGAATTACTCAAACTACC
15872120 CGAATTAACCGAATT
1 CGAATTAACCGAATT
15872135 GAATCCCTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 3 0.08
27 35 0.92
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (27 bp):
CGAATTAACCGAATTACTCAAACTACC
Found at i:15872278 original size:6 final size:6
Alignment explanation
Indices: 15872174--15872262 Score: 178
Period size: 6 Copynumber: 14.8 Consensus size: 6
15872164 ACTTTTAGAC
15872174 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT
15872222 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
15872263 AATTTTATTT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:15872286 original size:20 final size:20
Alignment explanation
Indices: 15872174--15872275 Score: 139
Period size: 18 Copynumber: 5.5 Consensus size: 20
15872164 ACTTTTAGAC
15872174 TTTAGTTTTAGTTTTAG--T
1 TTTAGTTTTAGTTTTAGAAT
15872192 TTTAGTTTTAGTTTTAG--T
1 TTTAGTTTTAGTTTTAGAAT
15872210 TTTAGTTTTAGTTTTAG--T
1 TTTAGTTTTAGTTTTAGAAT
15872228 TTTAGTTTTAGTTTTAG--T
1 TTTAGTTTTAGTTTTAGAAT
15872246 TTTAGTTTTAGTTTTAGAAT
1 TTTAGTTTTAGTTTTAGAAT
*
15872266 TTTATTTTTA
1 TTTAGTTTTA
15872276 TTTATTAAAT
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
18 71 0.88
20 10 0.12
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.67
Consensus pattern (20 bp):
TTTAGTTTTAGTTTTAGAAT
Found at i:15872343 original size:18 final size:18
Alignment explanation
Indices: 15872303--15872346 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
15872293 AATTTTTATG
**
15872303 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
15872321 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
15872339 CTTGGGTT
1 ATTGGGTT
15872347 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:15872549 original size:18 final size:18
Alignment explanation
Indices: 15872509--15872551 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
15872499 ACCGAAAAAA
15872509 TTCGGTTAACCGAATTCT
1 TTCGGTTAACCGAATTCT
* *
15872527 GTCGGTTAACCGAATTTT
1 TTCGGTTAACCGAATTCT
15872545 TTCGGTT
1 TTCGGTT
15872552 TTACCCGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (18 bp):
TTCGGTTAACCGAATTCT
Found at i:15875638 original size:20 final size:20
Alignment explanation
Indices: 15875603--15875651 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
15875593 ATCATGGTCT
*
15875603 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
15875622 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
15875642 TTGCTTACTT
1 TTGCTTACTT
15875652 AAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:15875921 original size:50 final size:50
Alignment explanation
Indices: 15875854--15875999 Score: 186
Period size: 50 Copynumber: 2.9 Consensus size: 50
15875844 GATAATAACA
* **
15875854 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * *
15875904 TGCCCATGCCATGTCCCAGACATGGTCTTACGA-GGAACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATATCGG
* *
15875954 TGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTGTCATA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
15876000 ACCTCAATAA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
50 80 0.99
51 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:15878807 original size:35 final size:36
Alignment explanation
Indices: 15878767--15878845 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
15878757 AATATAAGCT
* * *
15878767 CTATCATATTGCATGAA-AACATATCCACATATTTA
1 CTATCACATGGCATGAATAACATACCCACATATTTA
* *
15878802 CTATCACATGGCATGAATAACATACCCTCATATTCA
1 CTATCACATGGCATGAATAACATACCCACATATTTA
*
15878838 CTTTCACA
1 CTATCACA
15878846 ACGGTCATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 15 0.41
36 22 0.59
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (36 bp):
CTATCACATGGCATGAATAACATACCCACATATTTA
Found at i:15879827 original size:17 final size:18
Alignment explanation
Indices: 15879805--15879838 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15879795 AGAAATTAAG
*
15879805 AATTGG-AGACCAAAAGC
1 AATTGGAAGAACAAAAGC
15879822 AATTGGAAGAACAAAAG
1 AATTGGAAGAACAAAAG
15879839 GAGAGCAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.12, G:0.24, T:0.12
Consensus pattern (18 bp):
AATTGGAAGAACAAAAGC
Found at i:15883567 original size:36 final size:35
Alignment explanation
Indices: 15883496--15883567 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 35
15883486 TCTCTATCAT
* *
15883496 ATGGCATGAAAACATATCCACATATTTATTGTCAC
1 ATGGCATCAAAACATATCCACATATTCATTGTCAC
15883531 ATGGCATCAATAACATA-CCATCATATTCACTT-TCAC
1 ATGGCATCAA-AACATATCCA-CATATTCA-TTGTCAC
15883567 A
1 A
15883568 ACGATCATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 12 0.38
36 18 0.56
37 2 0.06
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.31
Consensus pattern (35 bp):
ATGGCATCAAAACATATCCACATATTCATTGTCAC
Found at i:15884552 original size:17 final size:18
Alignment explanation
Indices: 15884530--15884563 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15884520 AGGGATTAGG
*
15884530 AATTGG-AGATCAAAAGC
1 AATTGGAAGAACAAAAGC
15884547 AATTGGAAGAACAAAAG
1 AATTGGAAGAACAAAAG
15884564 GAGAGCAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.09, G:0.24, T:0.15
Consensus pattern (18 bp):
AATTGGAAGAACAAAAGC
Found at i:15885291 original size:18 final size:18
Alignment explanation
Indices: 15885258--15885310 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
15885248 ATTCACCTAA
*
15885258 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
15885277 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
15885295 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
15885311 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:15887800 original size:41 final size:41
Alignment explanation
Indices: 15887754--15887917 Score: 211
Period size: 41 Copynumber: 4.0 Consensus size: 41
15887744 AAGAATATTG
* *
15887754 TTGAATTGCACATGCGTGCCCCTGTTTGTACTTCGATACCC
1 TTGAATTGCACATACGTGCCCCTGTTTATACTTCGATACCC
* * * *
15887795 TTGAATTGAACATGCGTGCCCCTGTTTATACTCCGGTACCC
1 TTGAATTGCACATACGTGCCCCTGTTTATACTTCGATACCC
* * * * *
15887836 TTGAATTGCACATAAGTGCCTCTATTTTTACTTCGGTACCC
1 TTGAATTGCACATACGTGCCCCTGTTTATACTTCGATACCC
* *
15887877 CTGAATTGCACATACGTGCCCCTTTTTATACTTCGATACCC
1 TTGAATTGCACATACGTGCCCCTGTTTATACTTCGATACCC
15887918 CTGGATGTAC
Statistics
Matches: 106, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 106 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (41 bp):
TTGAATTGCACATACGTGCCCCTGTTTATACTTCGATACCC
Found at i:15896821 original size:9 final size:9
Alignment explanation
Indices: 15896807--15896893 Score: 104
Period size: 9 Copynumber: 9.7 Consensus size: 9
15896797 ATGTAGTGAT
*
15896807 TTAATTTGG
1 TTAATTCGG
*
15896816 TTAATTTGG
1 TTAATTCGG
15896825 TTAATTCGG
1 TTAATTCGG
* *
15896834 GTAATTCTG
1 TTAATTCGG
*
15896843 TTAATTTTGG
1 TTAA-TTCGG
15896853 -TAATTCGG
1 TTAATTCGG
15896861 TTAATTCGG
1 TTAATTCGG
*
15896870 GTAATTCGG
1 TTAATTCGG
15896879 TTAATTCGG
1 TTAATTCGG
15896888 TTAATT
1 TTAATT
15896894 TTTAACCAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
8 4 0.06
9 60 0.90
10 3 0.04
ACGTcount: A:0.23, C:0.07, G:0.22, T:0.48
Consensus pattern (9 bp):
TTAATTCGG
Found at i:15902283 original size:19 final size:18
Alignment explanation
Indices: 15902261--15902323 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
15902251 AATACAAAAA
15902261 AAAAATCAAAATAATTTT
1 AAAAATCAAAATAATTTT
15902279 CAAAAATTCAAAATTAATTTT
1 -AAAAA-TCAAAA-TAATTTT
* *
15902300 AGAATTCAAAAT-ATTTAT
1 AAAAATCAAAATAATTT-T
15902318 AAAAAT
1 AAAAAT
15902324 TTCAAAAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
17 4 0.11
18 6 0.16
19 11 0.30
20 9 0.24
21 7 0.19
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAAATCAAAATAATTTT
Found at i:15902324 original size:19 final size:19
Alignment explanation
Indices: 15902260--15902330 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 19
15902250 AAATACAAAA
*
15902260 AAAAAATCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
15902279 CAAAAATTCAAAATTAATTTT
1 -AAAAATTCAAAA-TAATTTT
*
15902300 -AGAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
15902318 AAAAATTTCAAAA
1 AAAAA-TTCAAAA
15902331 GTTATATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
17 4 0.09
18 2 0.05
19 13 0.30
20 18 0.41
21 7 0.16
ACGTcount: A:0.58, C:0.07, G:0.01, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:15902495 original size:20 final size:19
Alignment explanation
Indices: 15902472--15902542 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 19
15902462 AAATTACAAA
15902472 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
15902491 CAAAAATTCAAAATTAATTTT
1 -AAAAATTCAAAA-TAATTTT
* *
15902512 -AGAATTCAAAATATTTTT
1 AAAAATTCAAAATAATTTT
15902530 AAAAATTCCAAAA
1 AAAAATT-CAAAA
15902543 GTTATATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
18 6 0.13
19 15 0.33
20 17 0.38
21 7 0.16
ACGTcount: A:0.55, C:0.08, G:0.01, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:15902518 original size:39 final size:41
Alignment explanation
Indices: 15902475--15902552 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 41
15902465 TTACAAAAAA
15902475 AATTCAAAATAATTTTCAAAAATT-CAAAA-TTA-ATTTTAG
1 AATTCAAAAT-ATTTTCAAAAATTCCAAAAGTTATATTTTAG
*
15902514 AATTCAAAATATTTTTAAAAATTCCAAAAGTTATATTTT
1 AATTCAAAATATTTTCAAAAATTCCAAAAGTTATATTTT
15902553 TAAAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
38 12 0.34
39 15 0.43
40 3 0.09
41 5 0.14
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (41 bp):
AATTCAAAATATTTTCAAAAATTCCAAAAGTTATATTTTAG
Found at i:15902535 original size:212 final size:210
Alignment explanation
Indices: 15902168--15902575 Score: 667
Period size: 212 Copynumber: 1.9 Consensus size: 210
15902158 ACAATTCGAA
* *
15902168 TAACTCAAATAACATATTAGTATAAATACCCCTTTGGTCCTTGTCAATTTAAAAAAATGAGCAAA
1 TAACTCAAATAACAGATTAGTATAAATACCCCTTTGGTCCCTGTCAATTTAAAAAAATGAGCAAA
*
15902233 TTAATTTCTCTTTCAACAAATACAAAAAAAAAATCAAAATAATTTTCAAAAATTCAAAATTAATT
66 TTAATCTCTCTTTCAACAAATACAAAAAAAAAATCAAAATAATTTTCAAAAATTCAAAATTAATT
* ** *
15902298 TTAGAATTCAAAATATTTATAAAAATTTCAAAAGTTATATTTTTTTTAAATATATAAAAAATTCT
131 TTAGAATTCAAAATATTTATAAAAATTCCAAAAGTTATA-TTTTTAAAAAAATATAAAAAATTCT
15902363 AAGGGGATATTTATAC
195 AAGGGGATATTTATAC
*
15902379 TAACTCAAATAACAGATTAGTATAAATACCCCTTTGGTCCCTGTCAATTT-TAAAAATGAGCAAA
1 TAACTCAAATAACAGATTAGTATAAATACCCCTTTGGTCCCTGTCAATTTAAAAAAATGAGCAAA
* *
15902443 TTAGTCTCTCTTTCAACAAAAATTAC-AAAAAAAATTCAAAATAATTTTCAAAAATTCAAAATTA
66 TTAATCTCTCTTTCAAC--AAA-TACAAAAAAAAAATCAAAATAATTTTCAAAAATTCAAAATTA
*
15902507 ATTTTAGAATTCAAAATATTTTTAAAAATTCCAAAAGTTATATTTTTAAAAAAATATAAAAAATT
128 ATTTTAGAATTCAAAATATTTATAAAAATTCCAAAAGTTATATTTTTAAAAAAATATAAAAAATT
15902572 CTAA
193 CTAA
15902576 AGACAATTTT
Statistics
Matches: 183, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
210 28 0.15
211 72 0.39
212 80 0.44
213 3 0.02
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (210 bp):
TAACTCAAATAACAGATTAGTATAAATACCCCTTTGGTCCCTGTCAATTTAAAAAAATGAGCAAA
TTAATCTCTCTTTCAACAAATACAAAAAAAAAATCAAAATAATTTTCAAAAATTCAAAATTAATT
TTAGAATTCAAAATATTTATAAAAATTCCAAAAGTTATATTTTTAAAAAAATATAAAAAATTCTA
AGGGGATATTTATAC
Found at i:15904711 original size:39 final size:39
Alignment explanation
Indices: 15904668--15904742 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
15904658 ATTTTTTAAA
15904668 ATTAAAAAATATAAAAT-TTCTTTTTAAAAATTAAAATTT
1 ATTAAAAAATATAAAATATT-TTTTTAAAAATTAAAATTT
* *
15904707 ATTAAAAAATATAAAATATTTTTTTAATATTTAAAA
1 ATTAAAAAATATAAAATATTTTTTTAAAAATTAAAA
15904743 AAATTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (39 bp):
ATTAAAAAATATAAAATATTTTTTTAAAAATTAAAATTT
Found at i:15904953 original size:29 final size:28
Alignment explanation
Indices: 15904913--15904971 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
15904903 GCATTTAATT
15904913 AATTTTTTTAAAACTAAAAAATTATTAA
1 AATTTTTTTAAAACTAAAAAATTATTAA
* **
15904941 AATTCTTTTTAAAATTTTAAAATTATTAA
1 AATT-TTTTTAAAACTAAAAAATTATTAA
15904970 AA
1 AA
15904972 ATGAAGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTTTTTTAAAACTAAAAAATTATTAA
Found at i:15905003 original size:19 final size:20
Alignment explanation
Indices: 15904979--15905019 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
15904969 AAAATGAAGA
* *
15904979 AATATTTTTTAATATTT-TT
1 AATATTTTATAAAATTTATT
15904998 AATATTTTATAAAATTTATT
1 AATATTTTATAAAATTTATT
15905018 AA
1 AA
15905020 ATGATGGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AATATTTTATAAAATTTATT
Found at i:15906226 original size:34 final size:34
Alignment explanation
Indices: 15906154--15906226 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
15906144 TTAATTTTTA
* * * **
15906154 TTTTTCGTTGGAAAATATTTTATTTAACCTAATT
1 TTTTTCGTTGGAAAATATTTGATCTAACATAACC
* *
15906188 TTTTTCGTTGGAAAATGTTTGGTCTAACATAACC
1 TTTTTCGTTGGAAAATATTTGATCTAACATAACC
15906222 TTTTT
1 TTTTT
15906227 TGTGTTGTCT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.51
Consensus pattern (34 bp):
TTTTTCGTTGGAAAATATTTGATCTAACATAACC
Found at i:15908267 original size:17 final size:18
Alignment explanation
Indices: 15908230--15908269 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
15908220 TTTATCGGAA
15908230 AAGAAAACTAAAATGATG
1 AAGAAAACTAAAATGATG
* *
15908248 AAGATAACTAAATTGA-G
1 AAGAAAACTAAAATGATG
15908265 AAGAA
1 AAGAA
15908270 CTTATTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.17
Consensus pattern (18 bp):
AAGAAAACTAAAATGATG
Found at i:15911137 original size:30 final size:28
Alignment explanation
Indices: 15911103--15911165 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
15911093 AAAAAACCCT
15911103 TTTTTAAAAAAATTTACCGAAATGGGCCA
1 TTTTT-AAAAAATTTACCGAAATGGGCCA
* ** *
15911132 CTTTTTTAATTATTTACCGGAATGGGCCA
1 -TTTTTAAAAAATTTACCGAAATGGGCCA
15911161 TTTTT
1 TTTTT
15911166 CGCGAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 5 0.17
29 19 0.66
30 5 0.17
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (28 bp):
TTTTTAAAAAATTTACCGAAATGGGCCA
Found at i:15911635 original size:125 final size:125
Alignment explanation
Indices: 15911407--15911688 Score: 435
Period size: 125 Copynumber: 2.3 Consensus size: 125
15911397 TTATTTCGAG
**
15911407 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCAGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGT
* * *
15911471 GAAATCGTGCCCTCGTGGATGCGATTTCGGTACAGTTGGTCATGTAAGAAATAAAT-TTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAAATATTTT
15911531 TTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTAT-ATGAGAAGAAATTG
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCA-GAGAAGAAATTG
* *
15911595 TGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTATTTT
64 TGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAAATATTTT
* *
15911657 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGC
15911689 GCCCTCGTGG
Statistics
Matches: 145, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
124 7 0.05
125 127 0.88
126 11 0.08
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAAATATTTT
Found at i:15912199 original size:19 final size:19
Alignment explanation
Indices: 15912175--15912212 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
15912165 TCCAGTGTTT
*
15912175 GAGATGTATACATGACCCC
1 GAGATGTATACACGACCCC
15912194 GAGATGTATACACGACCCC
1 GAGATGTATACACGACCCC
15912213 TGGCCGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (19 bp):
GAGATGTATACACGACCCC
Found at i:15913410 original size:29 final size:29
Alignment explanation
Indices: 15913368--15913977 Score: 681
Period size: 29 Copynumber: 20.6 Consensus size: 29
15913358 TAATTAAAAT
**
15913368 GGGTTTTTAATTAAATTAGTTTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
* ***
15913397 GGGTTTTTAATTAAAATGGGTTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
** *
15913426 GGGTTTTTAATTAAATTAGGTTAGAGTTTA
1 GGGTTTTTAATTAAATTAAATTAG-GGTTA
*
15913456 GGG-TTTTAATTAAATTAAACTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
* * ***
15913484 GGGTTTTTTATTAAAATGGGTTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
* *
15913513 GGG-TTTTGATTAAATTAAATTAGGCTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
15913541 GGG-TTTTAATTAAATTAAATTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
*
15913569 GGGTTTTTAATTAAATTAAACTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
* ***
15913598 GGGTTTTTAATTAAAATGGGTTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
* * *
15913627 GGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTA
1 GGGTT---TTTA----ATTAAATT-----AAATTAGGGTTA
15913668 GGGTTTTTAATTAAATTAAATTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
* **
15913697 GGGTTTTAAATTAAAATGGGTTAGGGTTAGGGTTA
1 GGGTTTTTAATT-AAA----TTA-AATTAGGGTTA
*
15913732 GGATTTTTAATTAAATTAAATTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
*
15913761 GGGTTTTTAATTAAATCAAATTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
*
15913790 GGGTTTTTAATTAAATTAAATTAAGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
15913819 GGGTTTTTAATTAAATTAAATTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
* * **
15913848 GGGGTTTTAATTAAAATAGGTTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
15913877 GGGTTTTTAATTAAATTAAATTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
*
15913906 GGGTTTTTAATTAAATTAAATTA-GGTTT
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
15913934 GGGTTTTTAATTAAATTAAATTA-GGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
*
15913962 GGGTTTTTAATCAAAT
1 GGGTTTTTAATTAAAT
15913978 AATATCAAAA
Statistics
Matches: 497, Mismatches: 63, Indels: 43
0.82 0.10 0.07
Matches are distributed among these distances:
28 101 0.20
29 327 0.66
30 13 0.03
32 3 0.01
34 12 0.02
35 19 0.04
36 5 0.01
38 3 0.01
41 14 0.03
ACGTcount: A:0.32, C:0.01, G:0.24, T:0.43
Consensus pattern (29 bp):
GGGTTTTTAATTAAATTAAATTAGGGTTA
Found at i:15913626 original size:6 final size:6
Alignment explanation
Indices: 15913615--15913643 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
15913605 TAATTAAAAT
15913615 GGGTTA GGGTTA GGGTTA GGGTTA GGGTT
1 GGGTTA GGGTTA GGGTTA GGGTTA GGGTT
15913644 TTTAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.52, T:0.34
Consensus pattern (6 bp):
GGGTTA
Found at i:15913647 original size:41 final size:41
Alignment explanation
Indices: 15913590--15913672 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
15913580 TAAATTAAAC
***
15913590 TAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGGTTAGGGT
1 TAGGGTTAGGGTTTTTAATTAAAATAAATTAGGGTTAGGGT
*
15913631 TAGGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGT
1 TAGGGTTAGGGTTTTTAATTAAAATAAATTAGGGTTAGGGT
15913672 T
1 T
15913673 TTTAATTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.41
Consensus pattern (41 bp):
TAGGGTTAGGGTTTTTAATTAAAATAAATTAGGGTTAGGGT
Found at i:15913649 original size:70 final size:70
Alignment explanation
Indices: 15913560--15913701 Score: 239
Period size: 70 Copynumber: 2.0 Consensus size: 70
15913550 TTAAATTAAA
***
15913560 TTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATTAAAATAAATTAGGGT
15913625 TAGGG
66 TAGGG
* *
15913630 TTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATTAAAATAAATTAGGGT
15913695 TAGGG
66 TAGGG
15913700 TT
1 TT
15913702 TTAAATTAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.30, C:0.01, G:0.27, T:0.42
Consensus pattern (70 bp):
TTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATTAAAATAAATTAGGGT
TAGGG
Found at i:15914224 original size:7 final size:7
Alignment explanation
Indices: 15914214--15914245 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
15914204 TTATATACAT
15914214 AATACTA
1 AATACTA
15914221 AATACTA
1 AATACTA
15914228 AATACTA
1 AATACTA
15914235 AATACTA
1 AATACTA
15914242 AATA
1 AATA
15914246 TCAATCCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:15915218 original size:14 final size:15
Alignment explanation
Indices: 15915201--15915234 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
15915191 AATAATTATC
15915201 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
15915215 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
15915230 TAAAA
1 TAAAA
15915235 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:15915468 original size:22 final size:23
Alignment explanation
Indices: 15915419--15915471 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
15915409 TTAAATATGG
* *
15915419 ATTTGAGA-GATTTTTTGAAGGA
1 ATTTGAGAGGATTTTTGGAAAGA
*
15915441 AATTGAGAGGA-TTTTGGAAAGA
1 ATTTGAGAGGATTTTTGGAAAGA
15915463 ATTTGAGAG
1 ATTTGAGAG
15915472 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.34
Consensus pattern (23 bp):
ATTTGAGAGGATTTTTGGAAAGA
Found at i:15915540 original size:24 final size:22
Alignment explanation
Indices: 15915476--15915531 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
15915466 TGAGAGTTTA
*
15915476 AGAGAATTTTGAAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
15915498 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
15915520 AGAGAATATTTG
1 AGAGAAT-TTTG
15915532 TTTGTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:15915791 original size:29 final size:29
Alignment explanation
Indices: 15915735--15915790 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
15915725 TTCGTAGAAT
*
15915735 TGGCCTATTCCGATAAATAATTAAAAAAG
1 TGGCCCATTCCGATAAATAATTAAAAAAG
* *
15915764 TGGCCCATTTCGATAAAT-TTTAAAAAA
1 TGGCCCATTCCGATAAATAATTAAAAAA
15915791 AAAAGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (29 bp):
TGGCCCATTCCGATAAATAATTAAAAAAG
Found at i:15918172 original size:15 final size:16
Alignment explanation
Indices: 15918152--15918181 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15918142 GGAAATGGAA
15918152 GAGAGAATG-ATGAAT
1 GAGAGAATGAATGAAT
15918167 GAGAGAATGAATGAA
1 GAGAGAATGAATGAA
15918182 AGATGAGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (16 bp):
GAGAGAATGAATGAAT
Found at i:15919081 original size:14 final size:15
Alignment explanation
Indices: 15919063--15919103 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
15919053 TTTCATTTTT
15919063 ATTTTAATAATAA-A
1 ATTTTAATAATAATA
*
15919077 TTTTTAA-AATAATA
1 ATTTTAATAATAATA
15919091 ATTTTAACTAATA
1 ATTTTAA-TAATA
15919104 TTCTTCACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 5 0.23
14 13 0.59
16 4 0.18
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTTTAATAATAATA
Found at i:15921449 original size:20 final size:20
Alignment explanation
Indices: 15921424--15921480 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
15921414 TCTGAATAAA
15921424 AAAAATTTAAAATGTTTTTT
1 AAAAATTTAAAATGTTTTTT
**
15921444 AAAAATTTAAAATAATTTTT
1 AAAAATTTAAAATGTTTTTT
*
15921464 AAAAATTCAAAATGTTT
1 AAAAATTTAAAATGTTT
15921481 ATAAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
AAAAATTTAAAATGTTTTTT
Found at i:15921485 original size:19 final size:19
Alignment explanation
Indices: 15921424--15921487 Score: 83
Period size: 20 Copynumber: 3.3 Consensus size: 19
15921414 TCTGAATAAA
15921424 AAAAATTTAAAATGTTTTTT
1 AAAAATTTAAAATG-TTTTT
*
15921444 AAAAATTTAAAATAATTTTT
1 AAAAATTTAAAAT-GTTTTT
* *
15921464 AAAAATTCAAAATGTTTAT
1 AAAAATTTAAAATGTTTTT
15921483 AAAAA
1 AAAAA
15921488 ATAAAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
19 9 0.23
20 30 0.77
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAAATTTAAAATGTTTTT
Found at i:15921532 original size:25 final size:26
Alignment explanation
Indices: 15921488--15921547 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
15921478 TTTATAAAAA
* * *
15921488 ATAAAAATAATAATTTTAAAAAAT-T
1 ATAAAAATAAAAAATCTAAAAAATAT
*
15921513 ATAAAAATAAAAAATCTAAAGAATAT
1 ATAAAAATAAAAAATCTAAAAAATAT
15921539 ATACAAAAT
1 ATA-AAAAT
15921548 TTAAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 20 0.69
26 4 0.14
27 5 0.17
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (26 bp):
ATAAAAATAAAAAATCTAAAAAATAT
Found at i:15929090 original size:2 final size:2
Alignment explanation
Indices: 15929077--15929113 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
15929067 GTGTGAAATG
*
15929077 TA TA TA TG 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 TA TA TA TA T
15929114 GAGAACCCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15929373 original size:20 final size:21
Alignment explanation
Indices: 15929345--15929396 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
15929335 ATTTATCTTG
*
15929345 ATTTTATTTAATTCCAAT-AA
1 ATTTGATTTAATTCCAATCAA
* **
15929365 ATTTGATTTGATTTTAATCAA
1 ATTTGATTTAATTCCAATCAA
15929386 A-TTGATTTAAT
1 ATTTGATTTAAT
15929397 GGATCCTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (21 bp):
ATTTGATTTAATTCCAATCAA
Found at i:15929862 original size:20 final size:21
Alignment explanation
Indices: 15929818--15929875 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
15929808 GATATTTTAA
*
15929818 ATATAAATTATTTAATTTAATTT
1 ATATAAA-TATTT-GTTTAATTT
15929841 ATATAAATATTTGTTT-ATTT
1 ATATAAATATTTGTTTAATTT
**
15929861 ATATTTATATTTGTT
1 ATATAAATATTTGTT
15929876 CGTTAACATG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.53
21 3 0.09
22 5 0.16
23 7 0.22
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
ATATAAATATTTGTTTAATTT
Found at i:15932355 original size:2 final size:2
Alignment explanation
Indices: 15932348--15932373 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15932338 CTCTTTAACA
15932348 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
15932374 CAGTGTTAAA
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
Done.