Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 69 of 204
Found at i:20507382 original size:22 final size:21
Alignment explanation
Indices: 20507357--20507415 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
20507347 GAAATTTGGA
*
20507357 AGGAATTTGAGAGTAAATTGAG
1 AGGAATTTGAGAG-AAAATGAG
20507379 AGGATATTTTGAG-GAAAATGAG
1 AGGA-A-TTTGAGAGAAAATGAG
*
20507401 ATGAAATTTGAGAGA
1 A-GGAATTTGAGAGA
20507416 TGATTAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 6 0.19
22 15 0.48
23 4 0.13
24 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (21 bp):
AGGAATTTGAGAGAAAATGAG
Found at i:20508631 original size:17 final size:18
Alignment explanation
Indices: 20508609--20508655 Score: 80
Period size: 17 Copynumber: 2.7 Consensus size: 18
20508599 TTTTTCACAT
20508609 AAAAAATATAAATTATC-
1 AAAAAATATAAATTATCA
20508626 AAAAAATA-AAATTATCA
1 AAAAAATATAAATTATCA
20508643 AAAAAATATAAAT
1 AAAAAATATAAAT
20508656 ATTATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.29
17 16 0.57
18 4 0.14
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAAATATAAATTATCA
Found at i:20508634 original size:15 final size:16
Alignment explanation
Indices: 20508609--20508647 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
20508599 TTTTTCACAT
20508609 AAAAAATATAAATTATC
1 AAAAAATA-AAATTATC
20508626 AAAAAATAAAATTATC
1 AAAAAATAAAATTATC
20508642 AAAAAA
1 AAAAAA
20508648 ATATAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAATAAAATTATC
Found at i:20508711 original size:9 final size:9
Alignment explanation
Indices: 20508699--20508813 Score: 74
Period size: 9 Copynumber: 12.2 Consensus size: 9
20508689 AAACTCTAAT
20508699 AAATTATAA
1 AAATTATAA
20508708 AAATTAT-A
1 AAATTATAA
20508716 AAATTCATAA
1 AAATT-ATAA
20508726 AATATT-TAA
1 AA-ATTATAA
*
20508735 AATTTTATAA
1 AA-ATTATAA
*
20508745 AAATGCATTAA
1 AAAT-TA-TAA
*
20508756 AATTCTATAA
1 AAAT-TATAA
*
20508766 AAATCATAA
1 AAATTATAA
*
20508775 AAA-TATTA
1 AAATTATAA
20508783 AAATTAATATA
1 AAATT-ATA-A
*
20508794 AACTTATAA
1 AAATTATAA
*
20508803 AAAATATAA
1 AAATTATAA
20508812 AA
1 AA
20508814 TAAATCAGTC
Statistics
Matches: 83, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
8 12 0.14
9 36 0.43
10 20 0.24
11 15 0.18
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (9 bp):
AAATTATAA
Found at i:20508746 original size:19 final size:18
Alignment explanation
Indices: 20508702--20508814 Score: 86
Period size: 19 Copynumber: 6.0 Consensus size: 18
20508692 CTCTAATAAA
20508702 TTATAAAAATTATAAAAT
1 TTATAAAAATTATAAAAT
*
20508720 TCATAAAATATT-TAAAATT
1 TTATAAAA-ATTATAAAA-T
*
20508739 TTATAAAAATGCATTAAAAT
1 TTATAAAAAT-TA-TAAAAT
*
20508759 TCTATAAAAATCATAAAA-
1 T-TATAAAAATTATAAAAT
* * *
20508777 ATATTAAAATTAATATAAAC
1 TTATAAAAATT-ATA-AAAT
*
20508797 TTATAAAAAATATAAAAT
1 TTATAAAAATTATAAAAT
20508815 AAATCAGTCA
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
17 8 0.11
18 20 0.26
19 22 0.29
20 12 0.16
21 14 0.18
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (18 bp):
TTATAAAAATTATAAAAT
Found at i:20508777 original size:20 final size:20
Alignment explanation
Indices: 20508703--20508778 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 20
20508693 TCTAATAAAT
*
20508703 TATAAAAATTA-TAAAATTC
1 TATAAAAATCATTAAAATTC
*
20508722 -AT-AAAAT-ATTTAAAATTT
1 TATAAAAATCA-TTAAAATTC
20508740 TATAAAAATGCATTAAAATTC
1 TATAAAAAT-CATTAAAATTC
*
20508761 TATAAAAATCATAAAAAT
1 TATAAAAATCATTAAAAT
20508779 ATTAAAATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
16 1 0.02
17 5 0.10
18 9 0.19
19 2 0.04
20 13 0.27
21 17 0.35
22 1 0.02
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (20 bp):
TATAAAAATCATTAAAATTC
Found at i:20508802 original size:28 final size:28
Alignment explanation
Indices: 20508703--20508814 Score: 88
Period size: 28 Copynumber: 3.9 Consensus size: 28
20508693 TCTAATAAAT
*
20508703 TATAAAAATTATAAAATTCA-TAAAA-TA
1 TATAAAAATTATAAAAAT-ATTAAAATTA
* * *
20508730 TTTAAAATTTTATAAAAATGCATTAAAATTC
1 TATAAAA-ATTATAAAAAT--ATTAAAATTA
*
20508761 TATAAAAATCATAAAAATATTAAAATTA
1 TATAAAAATTATAAAAATATTAAAATTA
*
20508789 -ATATAAACTTATAAAAA-ATATAAAAT
1 TATA-AAAATTATAAAAATAT-TAAAAT
20508815 AAATCAGTCA
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
27 11 0.16
28 35 0.51
29 2 0.03
30 14 0.20
31 7 0.10
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (28 bp):
TATAAAAATTATAAAAATATTAAAATTA
Found at i:20510954 original size:5 final size:5
Alignment explanation
Indices: 20510946--20510985 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
20510936 TTCTTTTTAG
* * *
20510946 AATTT AATTT AATTT AATTT AATTT GATTT GATTT GATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
20510986 TACTTTGTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:20518624 original size:27 final size:27
Alignment explanation
Indices: 20518594--20518651 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
20518584 TCTCTTAGGG
* *
20518594 GTATAACATTCATTTTACCCTATGGGA
1 GTATAACAGTCATTCTACCCTATGGGA
** *
20518621 GTATTTCAGTCATTCTACCCTATGGGG
1 GTATAACAGTCATTCTACCCTATGGGA
20518648 GTAT
1 GTAT
20518652 TGATATAGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (27 bp):
GTATAACAGTCATTCTACCCTATGGGA
Found at i:20520054 original size:27 final size:27
Alignment explanation
Indices: 20520028--20520118 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
20520018 TTACCATATG
*
20520028 GGGGTATTTCGGTTAATTTTTCCTAT-
1 GGGGTATTTCGATTAATTTTTCCTATA
* * **
20520054 GAGGGTATTTTGATCAATTTACCCTATA
1 G-GGGTATTTCGATTAATTTTTCCTATA
*
20520082 GGGGTATTTCGATT-ATTTTATCGTATA
1 GGGGTATTTCGATTAATTTT-TCCTATA
20520109 GGGGTATTTC
1 GGGGTATTTC
20520119 AATCATTTAT
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
26 5 0.10
27 46 0.88
28 1 0.02
ACGTcount: A:0.21, C:0.11, G:0.23, T:0.45
Consensus pattern (27 bp):
GGGGTATTTCGATTAATTTTTCCTATA
Found at i:20520068 original size:54 final size:54
Alignment explanation
Indices: 20520004--20520126 Score: 151
Period size: 54 Copynumber: 2.3 Consensus size: 54
20519994 CTCGTATCAA
* *
20520004 GTATTTTGATCATTTTACCATATGGGGGTATTTCGGTTAATTTT-TCCTAT-GAGG
1 GTATTTTGATCATTTTACCATATAGGGGTATTTCGATT-ATTTTATCCTATAG-GG
* * *
20520058 GTATTTTGATCAATTTACCCTATAGGGGTATTTCGATTATTTTATCGTATAGGG
1 GTATTTTGATCATTTTACCATATAGGGGTATTTCGATTATTTTATCCTATAGGG
**
20520112 GTATTTCAATCATTT
1 GTATTTTGATCATTT
20520127 ATCGACCTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 5 0.08
54 53 0.90
55 1 0.02
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (54 bp):
GTATTTTGATCATTTTACCATATAGGGGTATTTCGATTATTTTATCCTATAGGG
Found at i:20520126 original size:27 final size:26
Alignment explanation
Indices: 20520078--20520130 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
20520068 CAATTTACCC
* *
20520078 TATAGGGGTATTTCGATTATTTTATCG
1 TATAGGGGTATTTCAATCA-TTTATCG
20520105 TATAGGGGTATTTCAATCATTTATCG
1 TATAGGGGTATTTCAATCATTTATCG
20520131 ACCTCTCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (26 bp):
TATAGGGGTATTTCAATCATTTATCG
Found at i:20520662 original size:24 final size:25
Alignment explanation
Indices: 20520626--20520672 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
20520616 CCCAAATCTC
*
20520626 AATATTCTCTCCTCAAATCTCTCCA
1 AATATCCTCTCCTCAAATCTCTCCA
20520651 AATATCCT-TCCTCAAATCTCTC
1 AATATCCTCTCCTCAAATCTCTC
20520673 TATGACCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (25 bp):
AATATCCTCTCCTCAAATCTCTCCA
Found at i:20522697 original size:53 final size:54
Alignment explanation
Indices: 20522640--20522751 Score: 165
Period size: 53 Copynumber: 2.1 Consensus size: 54
20522630 ATAACAATCT
* *
20522640 TTTTACCCTATAAGGGTATTTCGGTC-ATTCTACCCTAT-GGGGTATTTCGGTCA
1 TTTTACCCTATAAGGGTATTTCGGTCAATT-TACACTATGGGGGTATTTCGATCA
* *
20522693 TTTTACCTTATGAGGGTATTTCGGTCAATTTACACTATGGGGGTATTTCGATCA
1 TTTTACCCTATAAGGGTATTTCGGTCAATTTACACTATGGGGGTATTTCGATCA
20522747 TTTTA
1 TTTTA
20522752 TCGTGTGGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
53 31 0.58
54 22 0.42
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (54 bp):
TTTTACCCTATAAGGGTATTTCGGTCAATTTACACTATGGGGGTATTTCGATCA
Found at i:20522761 original size:26 final size:27
Alignment explanation
Indices: 20522640--20522775 Score: 150
Period size: 27 Copynumber: 5.1 Consensus size: 27
20522630 ATAACAATCT
**
20522640 TTTTACCCTATAAGGGTATTTCGGTCA
1 TTTTACCCTATGGGGGTATTTCGGTCA
*
20522667 TTCTACCCTAT-GGGGTATTTCGGTCA
1 TTTTACCCTATGGGGGTATTTCGGTCA
* *
20522693 TTTTACCTTATGAGGGTATTTCGGTCA
1 TTTTACCCTATGGGGGTATTTCGGTCA
* * *
20522720 ATTTACACTATGGGGGTATTTCGATCA
1 TTTTACCCTATGGGGGTATTTCGGTCA
* * * *
20522747 TTTTATCGTGTGGGGGTA-TTCGATCA
1 TTTTACCCTATGGGGGTATTTCGGTCA
20522773 TTT
1 TTT
20522776 ATTGACCTCT
Statistics
Matches: 93, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
26 34 0.37
27 59 0.63
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (27 bp):
TTTTACCCTATGGGGGTATTTCGGTCA
Found at i:20522764 original size:54 final size:53
Alignment explanation
Indices: 20522640--20522774 Score: 157
Period size: 53 Copynumber: 2.5 Consensus size: 53
20522630 ATAACAATCT
* * * *
20522640 TTTTACCCTATAAGGGTATTTCGGTCATTCTACCCTATGGGGTATTTCGGTCA
1 TTTTACCGTATGAGGGTATTTCGGTCATTCTACACTATGGGGTATTTCGATCA
*
20522693 TTTTACCTTATGAGGGTATTTCGGTCAATT-TACACTATGGGGGTATTTCGATCA
1 TTTTACCGTATGAGGGTATTTCGGTC-ATTCTACACTAT-GGGGTATTTCGATCA
* * * *
20522747 TTTTATCGTGTGGGGGTA-TTCGATCATT
1 TTTTACCGTATGAGGGTATTTCGGTCATT
20522775 TATTGACCTC
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
52 3 0.04
53 37 0.52
54 31 0.44
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.41
Consensus pattern (53 bp):
TTTTACCGTATGAGGGTATTTCGGTCATTCTACACTATGGGGTATTTCGATCA
Found at i:20528485 original size:44 final size:44
Alignment explanation
Indices: 20528422--20528512 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
20528412 TTTTAAACTC
*
20528422 TATCCTTGAATTGTTCTTTATGTTTATTCTTTTCATTAAGTTTA
1 TATCCTTGAATTGTTCTTTATGTTCATTCTTTTCATTAAGTTTA
20528466 TATCCTTGAATTGTTCTTTATGTTCATTCTTTTCATTAAGTTTA
1 TATCCTTGAATTGTTCTTTATGTTCATTCTTTTCATTAAGTTTA
20528510 TAT
1 TAT
20528513 TGTTTAGATC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (44 bp):
TATCCTTGAATTGTTCTTTATGTTCATTCTTTTCATTAAGTTTA
Found at i:20531263 original size:40 final size:40
Alignment explanation
Indices: 20531032--20531256 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
20531022 TTGAATGATG
* * * *
20531032 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
20531072 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
20531112 TCCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
20531151 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
** *
20531191 TTTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
20531232 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20531257 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
39 34 0.21
40 117 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:20539370 original size:16 final size:17
Alignment explanation
Indices: 20539347--20539384 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
20539337 AATAAACAAT
20539347 TAAA-TAAATT-GGAAA
1 TAAATTAAATTGGGAAA
20539362 TAAATTAAATTGGGAAA
1 TAAATTAAATTGGGAAA
20539379 TAAATT
1 TAAATT
20539385 TGGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.19
16 6 0.29
17 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (17 bp):
TAAATTAAATTGGGAAA
Found at i:20545202 original size:21 final size:20
Alignment explanation
Indices: 20545172--20545237 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
20545162 CTTAGACCAA
20545172 GTGGGGGTCAACACGCCCGT
1 GTGGGGGTCAACACGCCCGT
**
20545192 GTGGGAGGTCAAC-CGCTCATT
1 GTGGG-GGTCAACACGC-CCGT
* *
20545213 TTCGGGGTCAACACGCCCGT
1 GTGGGGGTCAACACGCCCGT
20545233 GTGGG
1 GTGGG
20545238 AGTACGTACA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.15, C:0.27, G:0.38, T:0.20
Consensus pattern (20 bp):
GTGGGGGTCAACACGCCCGT
Found at i:20549535 original size:29 final size:28
Alignment explanation
Indices: 20549503--20549675 Score: 220
Period size: 29 Copynumber: 6.0 Consensus size: 28
20549493 GGCTATCGAT
*
20549503 TATGAAAAGGGATGGTGAGGACCATCAA
1 TATGAAAAGGGATGGTGACGACCATCAA
20549531 CTATGAAAAGGGATGGTGACGACCATCAAA
1 -TATGAAAAGGGATGGTGACGACCATC-AA
20549561 TATGAAAAGGGATGGTGACGACCATCGAA
1 TATGAAAAGGGATGGTGACGACCATC-AA
* * *
20549590 TATGAAAAGGGATGGTGACAACTATCGAT
1 TATGAAAAGGGATGGTGACGACCATC-AA
**
20549619 TAATGAAAAGGGATGGTTTCGACCATCGAA
1 T-ATGAAAAGGGATGGTGACGACCATC-AA
* *
20549649 TATGAAAAGGGACGGTTACGACCATCA
1 TATGAAAAGGGATGGTGACGACCATCA
20549676 TTTAGCACAC
Statistics
Matches: 130, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
28 1 0.01
29 103 0.79
30 26 0.20
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (28 bp):
TATGAAAAGGGATGGTGACGACCATCAA
Found at i:20549644 original size:59 final size:58
Alignment explanation
Indices: 20549495--20549660 Score: 244
Period size: 58 Copynumber: 2.8 Consensus size: 58
20549485 ATAGCTTCGG
* *
20549495 CTATCGATTATGAAAAGGGATGGTGAGGACCATC-AACTATGAAAAGGGATGGTGACGA
1 CTATCGATTATGAAAAGGGATGGTGACGACCATCGAA-TATGAAAAGGGATGGTGACAA
* * *
20549553 CCATCAAATATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGATGGTGACAA
1 CTATCGATTATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGATGGTGACAA
**
20549611 CTATCGATTAATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGA
1 CTATCGATT-ATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGA
20549661 CGGTTACGAC
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
58 56 0.58
59 40 0.42
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (58 bp):
CTATCGATTATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGATGGTGACAA
Found at i:20549658 original size:88 final size:87
Alignment explanation
Indices: 20549497--20549674 Score: 248
Period size: 88 Copynumber: 2.0 Consensus size: 87
20549487 AGCTTCGGCT
* **
20549497 ATCGATTATGAAAAGGGATGGTGAGGACCATCAACTATGAAAAGGGATGGTGACGACCATCAAAT
1 ATCGAATATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGATGGTGACGACCATCAAAT
*
20549562 ATGAAAAGGGATGGTGACGACC
66 ATGAAAAGGGACGGTGACGACC
* * * ** *
20549584 ATCGAATATGAAAAGGGATGGTGACAACTATCGATTAATGAAAAGGGATGGTTTCGACCATCGAA
1 ATCGAATATGAAAAGGGATGGTGACAACCATCAACT-ATGAAAAGGGATGGTGACGACCATCAAA
*
20549649 TATGAAAAGGGACGGTTACGACC
65 TATGAAAAGGGACGGTGACGACC
20549672 ATC
1 ATC
20549675 ATTTAGCACA
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
87 30 0.38
88 49 0.62
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (87 bp):
ATCGAATATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGATGGTGACGACCATCAAAT
ATGAAAAGGGACGGTGACGACC
Found at i:20564636 original size:16 final size:16
Alignment explanation
Indices: 20564617--20564656 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
20564607 AAACATATTT
*
20564617 AAACTAATTTAACTAA
1 AAACTAAATTAACTAA
*
20564633 AAACCAAATTAACTAA
1 AAACTAAATTAACTAA
20564649 ATAACTAA
1 A-AACTAA
20564657 CTAGACCGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (16 bp):
AAACTAAATTAACTAA
Found at i:20571680 original size:20 final size:20
Alignment explanation
Indices: 20571647--20571691 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
20571637 TAAATTCACA
20571647 TAATTAAAACAAGACAC-AAT
1 TAATTAAAACAAGAC-CTAAT
**
20571667 TAATTAAATTAAGACCTAAT
1 TAATTAAAACAAGACCTAAT
20571687 TAATT
1 TAATT
20571692 CGATTAGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (20 bp):
TAATTAAAACAAGACCTAAT
Found at i:20573249 original size:26 final size:24
Alignment explanation
Indices: 20573220--20573270 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
20573210 TGTCCAAACC
*
20573220 AAAACATAATTAAACTAAATTAACTA
1 AAAACAGAATT-AACTAAA-TAACTA
*
20573246 AAAACCGAATTAACTAAATAACTA
1 AAAACAGAATTAACTAAATAACTA
20573270 A
1 A
20573271 CTAGACTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 7 0.30
26 9 0.39
ACGTcount: A:0.61, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAACAGAATTAACTAAATAACTA
Found at i:20573250 original size:16 final size:16
Alignment explanation
Indices: 20573231--20573270 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
20573221 AAACATAATT
20573231 AAACTAAATTAACTAA
1 AAACTAAATTAACTAA
**
20573247 AAACCGAATTAACTAA
1 AAACTAAATTAACTAA
20573263 ATAACTAA
1 A-AACTAA
20573271 CTAGACTGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.60, C:0.15, G:0.03, T:0.23
Consensus pattern (16 bp):
AAACTAAATTAACTAA
Found at i:20576658 original size:20 final size:20
Alignment explanation
Indices: 20576612--20576658 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
20576602 AGCTCGTTTC
*
20576612 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
20576632 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
20576652 CAGCTCA
1 CAGCTCA
20576659 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:20578070 original size:11 final size:12
Alignment explanation
Indices: 20578047--20578086 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
20578037 AAAAAAATCG
20578047 AAATTCAAAAAA
1 AAATTCAAAAAA
20578059 AAATTCAAAAAA
1 AAATTCAAAAAA
* *
20578071 AAAGTGAAAAAA
1 AAATTCAAAAAA
20578083 AAAT
1 AAAT
20578087 CGAGCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:20578095 original size:14 final size:13
Alignment explanation
Indices: 20578064--20578125 Score: 56
Period size: 14 Copynumber: 4.8 Consensus size: 13
20578054 AAAAAAAATT
* *
20578064 CAAAAAAAAAGTG
1 CAAAAAAAATGAG
*
20578077 AAAAAAAAATCGAG
1 CAAAAAAAAT-GAG
*
20578091 CAAAAAAAA-AAG
1 CAAAAAAAATGAG
20578103 -AAAAAAAAGTGAG
1 CAAAAAAAA-TGAG
20578116 CAAAAAAAAT
1 CAAAAAAAAT
20578126 CAAGTTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
11 8 0.21
12 2 0.05
13 11 0.28
14 18 0.46
ACGTcount: A:0.74, C:0.06, G:0.13, T:0.06
Consensus pattern (13 bp):
CAAAAAAAATGAG
Found at i:20578095 original size:26 final size:25
Alignment explanation
Indices: 20578064--20578124 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
20578054 AAAAAAAATT
*
20578064 CAAAAAAAAAGTGAAAAAAAAATCGAG
1 CAAAAAAAAA-AGAAAAAAAAAT-GAG
*
20578091 CAAAAAAAAAAGAAAAAAAAGTGAG
1 CAAAAAAAAAAGAAAAAAAAATGAG
20578116 CAAAAAAAA
1 CAAAAAAAA
20578125 TCAAGTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 12 0.38
26 10 0.31
27 10 0.31
ACGTcount: A:0.75, C:0.07, G:0.13, T:0.05
Consensus pattern (25 bp):
CAAAAAAAAAAGAAAAAAAAATGAG
Found at i:20578136 original size:39 final size:37
Alignment explanation
Indices: 20578066--20578139 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
20578056 AAAAAATTCA
*
20578066 AAAAAAAAGTGAAAAAAAAATCGAGCAAAAAAAAAAG
1 AAAAAAAAGTGAAAAAAAAATCAAGCAAAAAAAAAAG
**
20578103 AAAAAAAAGTGAGCAAAAAAAATCAAGTTAAAAAAAA
1 AAAAAAAAGTGA--AAAAAAAATCAAGCAAAAAAAAA
20578140 GTGAAAAGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 12 0.38
39 20 0.62
ACGTcount: A:0.74, C:0.05, G:0.12, T:0.08
Consensus pattern (37 bp):
AAAAAAAAGTGAAAAAAAAATCAAGCAAAAAAAAAAG
Found at i:20579211 original size:13 final size:12
Alignment explanation
Indices: 20579181--20579214 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
20579171 AGAGAGGGTC
20579181 TGAAAAAGAGTT
1 TGAAAAAGAGTT
*
20579193 TGAAAAATAGTT
1 TGAAAAAGAGTT
20579205 TGAAAAAGAG
1 TGAAAAAGAG
20579215 AAGAGTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
TGAAAAAGAGTT
Found at i:20580905 original size:20 final size:20
Alignment explanation
Indices: 20580859--20580905 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
20580849 AGCTCGTTTC
*
20580859 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
20580879 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
20580899 CAGCTCA
1 CAGCTCA
20580906 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:20585117 original size:14 final size:14
Alignment explanation
Indices: 20585098--20585129 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20585088 ATTATGCCAG
20585098 AATTAAAAACACAT
1 AATTAAAAACACAT
20585112 AATT-AAAACACAT
1 AATTAAAAACACAT
20585125 -ATTAA
1 AATTAA
20585130 TGATATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (14 bp):
AATTAAAAACACAT
Found at i:20585204 original size:39 final size:38
Alignment explanation
Indices: 20585108--20585222 Score: 149
Period size: 39 Copynumber: 3.0 Consensus size: 38
20585098 AATTAAAAAC
*
20585108 ACATAATTAAAACACATATTAATGATATTCAAACTAAG
1 ACATAATTAAAACACATATTAATGATGTTCAAACTAAG
*
20585146 ACATAATTAAAAACGCATATTAATGATGTTCAAACTAAG
1 ACATAATT-AAAACACATATTAATGATGTTCAAACTAAG
* * ** *
20585185 ACATAATTAAGGACTCATATTAGCGGTGTTCAAACTAA
1 ACATAATTAA-AACACATATTAATGATGTTCAAACTAA
20585223 AATAACTAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 10 0.15
39 58 0.85
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (38 bp):
ACATAATTAAAACACATATTAATGATGTTCAAACTAAG
Found at i:20585231 original size:9 final size:9
Alignment explanation
Indices: 20585217--20585242 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
20585207 GCGGTGTTCA
20585217 AACTAAAAT
1 AACTAAAAT
20585226 AACTAAAAT
1 AACTAAAAT
20585235 AACTAAAA
1 AACTAAAA
20585243 ATGGATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
AACTAAAAT
Found at i:20585396 original size:36 final size:36
Alignment explanation
Indices: 20585333--20585405 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
20585323 CACGGAGTGC
* * * *
20585333 CTGCCCAAGCTTAATGAATTAGTCCCGTGATAGCTT
1 CTGCCCAAACTTAATCAATGAGACCCGTGATAGCTT
* * *
20585369 CTGCCCAAACTTGATCAATGAGACCCGTTATGGCTT
1 CTGCCCAAACTTAATCAATGAGACCCGTGATAGCTT
20585405 C
1 C
20585406 CTTGAACTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (36 bp):
CTGCCCAAACTTAATCAATGAGACCCGTGATAGCTT
Found at i:20593534 original size:50 final size:50
Alignment explanation
Indices: 20593477--20593571 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
20593467 GTTTCTTATA
* * *
20593477 TCGGTGCCCATGCCATGTCTCAGACATGGTCTTACGA-GGGACCTCTCATC
1 TCGGTGCCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATC
20593527 TCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
1 TCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
20593572 ATTCCCTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
49 1 0.02
50 40 0.98
ACGTcount: A:0.19, C:0.33, G:0.24, T:0.24
Consensus pattern (50 bp):
TCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
Found at i:20594310 original size:78 final size:78
Alignment explanation
Indices: 20594181--20594341 Score: 279
Period size: 78 Copynumber: 2.1 Consensus size: 78
20594171 ACCATAAAAT
*
20594181 ATCAAAATAAACATATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGGTTAAATTATTG-
1 ATCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGGTTAAATTATTGC
*
20594245 TTAGAATGAGCTAA
66 TT-GAATAAGCTAA
20594259 ATCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGGTTAAATTATTGC
1 ATCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGGTTAAATTATTGC
*
20594324 TTGAATAAGTTAA
66 TTGAATAAGCTAA
20594337 ATCAA
1 ATCAA
20594342 GTGATCGGGA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
78 77 0.97
79 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (78 bp):
ATCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGGTTAAATTATTGC
TTGAATAAGCTAA
Found at i:20595198 original size:29 final size:29
Alignment explanation
Indices: 20595172--20595385 Score: 119
Period size: 29 Copynumber: 7.3 Consensus size: 29
20595162 TCGTAACCGA
*
20595172 CCCTTTTCATATTTGATGGTTGAAACCAT
1 CCCTTTTCATATTTGATGGTCGAAACCAT
* * * **
20595201 CCCTTTTCATTAATCGATGCTCGTCACCAT
1 CCCTTTTCA-TATTTGATGGTCGAAACCAT
* *
20595231 CCCTTTTCATATTTGATGGTC-ATCACTAT
1 CCCTTTTCATATTTGATGGTCGA-AACCAT
* * * * * *
20595260 CCCTTTTCATAATCGAT-ATCCGTAGCTAT
1 CCCTTTTCATATTTGATGGT-CGAAACCAT
* * * *
20595289 CCCTTTTCATATTCGATAG-CTGAAGCTAT
1 CCCTTTTCATATTTGATGGTC-GAAACCAT
* * **
20595318 CACTTTTCATATTCGATGGTCGTCACCAT
1 CCCTTTTCATATTTGATGGTCGAAACCAT
* * * * * *
20595347 CCCTTTTCATAATCGATAGCCGAAGCTAT
1 CCCTTTTCATATTTGATGGTCGAAACCAT
20595376 CCCTTTTCAT
1 CCCTTTTCAT
20595386 TGGCCAATGA
Statistics
Matches: 144, Mismatches: 34, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
28 2 0.01
29 118 0.82
30 24 0.17
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (29 bp):
CCCTTTTCATATTTGATGGTCGAAACCAT
Found at i:20595363 original size:58 final size:58
Alignment explanation
Indices: 20595156--20595385 Score: 227
Period size: 58 Copynumber: 3.9 Consensus size: 58
20595146 GTGTGCTAAA
* * * * * *
20595156 CGATGATCGTAACCGA-CCCTTTTCATATTTGATGGTTGAAACCATCCCTTTTCATTAAT
1 CGATGATCGTCACC-ATCCCTTTTCATATTCGATAGCTGAAGCTATCCCTTTTCA-TAAT
* * * *
20595215 CGATGCTCGTCACCATCCCTTTTCATATTTGATGGTCAT-CA-CTATCCCTTTTCATAAT
1 CGATGATCGTCACCATCCCTTTTCATATTCGATAG-C-TGAAGCTATCCCTTTTCATAAT
* * *
20595273 CGAT-ATCCGT-AGCTATCCCTTTTCATATTCGATAGCTGAAGCTATCACTTTTCATATT
1 CGATGAT-CGTCA-CCATCCCTTTTCATATTCGATAGCTGAAGCTATCCCTTTTCATAAT
* * *
20595331 CGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCAT
1 CGATGATCGTCACCATCCCTTTTCATATTCGATAGCTGAAGCTATCCCTTTTCAT
20595386 TGGCCAATGA
Statistics
Matches: 145, Mismatches: 17, Indels: 19
0.80 0.09 0.10
Matches are distributed among these distances:
56 1 0.01
57 4 0.03
58 93 0.64
59 45 0.31
60 1 0.01
61 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (58 bp):
CGATGATCGTCACCATCCCTTTTCATATTCGATAGCTGAAGCTATCCCTTTTCATAAT
Found at i:20598330 original size:42 final size:42
Alignment explanation
Indices: 20598250--20598331 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
20598240 CGTTTTCTCT
* **
20598250 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGTCCAACCATGGTCTTACACATATGCACATATTG
*
20598292 ATGCCATAGTCCAGCCATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGTCCAACCATGGTCTTACACA-TATGCACATAT
20598332 CACACCGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATAGTCCAACCATGGTCTTACACATATGCACATATTG
Found at i:20600913 original size:23 final size:22
Alignment explanation
Indices: 20600870--20600913 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
20600860 TTCTAAGCCG
20600870 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
20600893 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
20600914 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:20601024 original size:45 final size:45
Alignment explanation
Indices: 20600960--20601046 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
20600950 TAGATACTCA
* *
20600960 GTGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTCCG
1 GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTCCG
*
20601005 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
20601047 TCAGTTCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (45 bp):
GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTCCG
Found at i:20601115 original size:51 final size:51
Alignment explanation
Indices: 20601053--20601193 Score: 167
Period size: 51 Copynumber: 2.8 Consensus size: 51
20601043 ATGTTCAGTT
* * *
20601053 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTTGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCTGATA
** * * * *
20601104 CATGTAGTAGCCTGCACATAGTATTACACACGTGATCGA-AACTATCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACCATCTGATA
* *
20601155 CGCATAGTAGCCTGCACATAGTACTACACACATGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
20601194 CACTTTCACT
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
50 2 0.03
51 69 0.95
52 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCTGATA
Found at i:20601212 original size:51 final size:50
Alignment explanation
Indices: 20601054--20601223 Score: 127
Period size: 51 Copynumber: 3.3 Consensus size: 50
20601044 TGTTCAGTTC
* *
20601054 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTAC--CA-TTTGAT
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACTTCACTTT--T
* * **
20601103 ACATGTAGTAGCCTGCACATAGTATTACACACGTGATCGA-AAC-T-ATCTGGT
1 ACA--TAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACTTCA-CTTTT
* *
20601154 ACGCATAGTAGCCTGCACATAGTACTACACACATGACCATCACTTTCACTTTT
1 A--CATAGTAGCCTGCACATAGTACTACACACGTGACCATAAC-TTCACTTTT
* *
20601207 ACATAGTGGCCTACACA
1 ACATAGTAGCCTGCACA
20601224 CAATACGTGC
Statistics
Matches: 95, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
49 3 0.03
50 2 0.02
51 79 0.83
52 2 0.02
53 8 0.08
54 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (50 bp):
ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACTTCACTTTT
Found at i:20607287 original size:92 final size:93
Alignment explanation
Indices: 20607128--20607308 Score: 274
Period size: 92 Copynumber: 2.0 Consensus size: 93
20607118 ACAAACTTGG
* * * * *
20607128 ACCTAAACTTAGAAACTGTAATTCAGTTTGATATTTTTTTTAGATACCTGACTAACTATCGTTAA
1 ACCTAAACTTAGAAACTGTAAGTCAATTTAATATTTTTTTTAAATACCTGACTAACTATCCTTAA
*
20607193 ATTATTATTTTCATCGAATCATATCAAT
66 ATTATTATTTTCATCCAATCATATCAAT
* * *
20607221 ACCTAAATTTAGAAATTGTAAGTCAATTTAATA-TTTTTTTAAATACCTGACTAACTGTCCTTAA
1 ACCTAAACTTAGAAACTGTAAGTCAATTTAATATTTTTTTTAAATACCTGACTAACTATCCTTAA
20607285 ATTATTATTTTCATCCAATCATAT
66 ATTATTATTTTCATCCAATCATAT
20607309 TGACACCACG
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
92 51 0.65
93 28 0.35
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (93 bp):
ACCTAAACTTAGAAACTGTAAGTCAATTTAATATTTTTTTTAAATACCTGACTAACTATCCTTAA
ATTATTATTTTCATCCAATCATATCAAT
Found at i:20617134 original size:32 final size:32
Alignment explanation
Indices: 20617098--20617158 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
20617088 TTTATACCAC
20617098 TAAACAAGACGGATATACTCCACCAACAATTG
1 TAAACAAGACGGATATACTCCACCAACAATTG
20617130 TAAACAAGACGGATATACTCCACCAACAA
1 TAAACAAGACGGATATACTCCACCAACAA
20617159 ATTAAGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.16
Consensus pattern (32 bp):
TAAACAAGACGGATATACTCCACCAACAATTG
Found at i:20618605 original size:29 final size:29
Alignment explanation
Indices: 20618560--20618616 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
20618550 AGGGGAGAGA
* *
20618560 CTCGAGGCTGTTTAGCTGGTGTGGGTAAC
1 CTCGAGGCTGTTGAGCTGGTGCGGGTAAC
*
20618589 CTCGAGTCTGTTGAGCTGGTGCGGGTAA
1 CTCGAGGCTGTTGAGCTGGTGCGGGTAA
20618617 TTTAGATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.18, G:0.39, T:0.30
Consensus pattern (29 bp):
CTCGAGGCTGTTGAGCTGGTGCGGGTAAC
Found at i:20618770 original size:21 final size:20
Alignment explanation
Indices: 20618746--20618794 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
20618736 TTTACTATAT
20618746 TATTAAATTAATATTTAAAAA
1 TATTAAATTAAT-TTTAAAAA
* *
20618767 TATTTAAAATTTATTTTAAGAA
1 TA-TT-AAATTAATTTTAAAAA
20618789 TATTAA
1 TATTAA
20618795 TTATAGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 2 0.08
21 4 0.17
22 11 0.46
23 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TATTAAATTAATTTTAAAAA
Found at i:20618774 original size:22 final size:22
Alignment explanation
Indices: 20618750--20618792 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
20618740 CTATATTATT
20618750 AAATTAATATTTAAAAATATTTA
1 AAATTAAT-TTTAAAAATATTTA
* *
20618773 AAATTTATTTTAAGAATATT
1 AAATTAATTTTAAAAATATT
20618793 AATTATAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATTAATTTTAAAAATATTTA
Found at i:20639132 original size:12 final size:12
Alignment explanation
Indices: 20639115--20639149 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
20639105 TAAGTTTCTC
*
20639115 TTTTCATTTTCA
1 TTTTCATTTCCA
20639127 TTTTCATTTCCA
1 TTTTCATTTCCA
*
20639139 TTTCCATTTCC
1 TTTTCATTTCC
20639150 GTTTCGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTCATTTCCA
Found at i:20643358 original size:59 final size:60
Alignment explanation
Indices: 20643286--20643405 Score: 224
Period size: 59 Copynumber: 2.0 Consensus size: 60
20643276 TTATTCTCGT
*
20643286 ACCACGAGCTGCTTCAAGTGTGGGCTCGAACCAATTGAACCAAAACATAGAACTA-AAAA
1 ACCACGAACTGCTTCAAGTGTGGGCTCGAACCAATTGAACCAAAACATAGAACTATAAAA
20643345 ACCACGAACTGCTTCAAGTGTGGGCTCGAACCAATTGAACCAAAACATAGAACTATAAAA
1 ACCACGAACTGCTTCAAGTGTGGGCTCGAACCAATTGAACCAAAACATAGAACTATAAAA
20643405 A
1 A
20643406 GTTTTCTTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 54 0.92
60 5 0.08
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (60 bp):
ACCACGAACTGCTTCAAGTGTGGGCTCGAACCAATTGAACCAAAACATAGAACTATAAAA
Found at i:20646239 original size:41 final size:41
Alignment explanation
Indices: 20646179--20646261 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
20646169 ATATGGAAGT
*
20646179 ATGTTAGGATTTAGTTTTTGACATGTTCTTCAATAAAAGAA
1 ATGTTAGGATTTAGGTTTTGACATGTTCTTCAATAAAAGAA
*
20646220 ATGTTAGGATTTAGGTTTTGACGTGTTCTTCAATAAAAGAA
1 ATGTTAGGATTTAGGTTTTGACATGTTCTTCAATAAAAGAA
20646261 A
1 A
20646262 GAATTCAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (41 bp):
ATGTTAGGATTTAGGTTTTGACATGTTCTTCAATAAAAGAA
Found at i:20649943 original size:39 final size:40
Alignment explanation
Indices: 20649898--20650122 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
20649888 GCTCCTCGTT
* * * *
20649898 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
20649938 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
20649977 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
20650017 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
20650057 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
20650098 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
20650123 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:20650131 original size:41 final size:41
Alignment explanation
Indices: 20650054--20650131 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
20650044 CTTGTATCTC
* * *
20650054 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
20650095 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
20650132 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:20713444 original size:27 final size:27
Alignment explanation
Indices: 20713407--20713611 Score: 223
Period size: 27 Copynumber: 7.6 Consensus size: 27
20713397 TAAATTGTAC
*
20713407 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
20713434 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
20713461 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20713487 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
20713515 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
20713542 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
20713570 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
20713597 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
20713612 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 0.84
28 24 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:20713468 original size:54 final size:54
Alignment explanation
Indices: 20713408--20713611 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
20713398 AAATTGTACA
* * *
20713408 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
** ** * *
20713462 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
**
20713516 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
20713571 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
20713612 GACTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Found at i:20718434 original size:18 final size:18
Alignment explanation
Indices: 20718389--20718434 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
20718379 GGAGGAATTC
*
20718389 TTTTTCTTTA-GTTTTTAT
1 TTTTTC-TTAGGTGTTTAT
20718407 TTCTTT-TTAGGTGTTTAT
1 TT-TTTCTTAGGTGTTTAT
20718425 TTTTTCTTAG
1 TTTTTCTTAG
20718435 TTAGTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 6 0.25
18 15 0.62
19 3 0.12
ACGTcount: A:0.11, C:0.07, G:0.11, T:0.72
Consensus pattern (18 bp):
TTTTTCTTAGGTGTTTAT
Found at i:20724965 original size:43 final size:43
Alignment explanation
Indices: 20724907--20725098 Score: 164
Period size: 43 Copynumber: 4.5 Consensus size: 43
20724897 TCTAAAGGTC
*
20724907 GTTGCTAAGTACTGATTCCACCGTATATTTGATTGTGAAAGGG
1 GTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGG
* * * * * *
20724950 GTTGCTATGTGCTGATT-CTCCATATCA-CTGAATAT-AAAGGTG
1 GTTGCTAAGTGCTGATTCCACCGTAT-ATTTGATTGTGAAAGG-G
* *
20724992 GTTTCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGG
1 GTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGG
** * * *
20725035 GTTGCTATCTGCTGATTCC-CCGTATCA-CTGAATT-T-AATGTG
1 GTTGCTAAGTGCTGATTCCACCGTAT-ATTTG-ATTGTGAAAGGG
*
20725076 GTTGCTAAGTGCTGAATCCACCG
1 GTTGCTAAGTGCTGATTCCACCG
20725099 AGTAACGGAT
Statistics
Matches: 116, Mismatches: 25, Indels: 17
0.73 0.16 0.11
Matches are distributed among these distances:
41 25 0.22
42 39 0.34
43 47 0.41
44 5 0.04
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (43 bp):
GTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGG
Found at i:20725007 original size:85 final size:84
Alignment explanation
Indices: 20724899--20725098 Score: 301
Period size: 85 Copynumber: 2.4 Consensus size: 84
20724889 TTATTGGTTC
* * *
20724899 TAAAGGTCGTTGCTAAGTACTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGCTG
1 TAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATCTGCTG
*
20724964 ATTCTCCATATCACTGAAT
66 ATTCCCCATATCACTGAAT
* *
20724983 ATAAAGGTGGTTTCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTATCTGCT
1 -TAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATCTGCT
*
20725048 GATTCCCCGTATCACTGAAT
65 GATTCCCCATATCACTGAAT
* * *
20725068 TTAATGTGGTTGCTAAGTGCTGAATCCACCG
1 TAAAGGTGGTTGCTAAGTGCTGATTCCACCG
20725099 AGTAACGGAT
Statistics
Matches: 104, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
84 27 0.26
85 77 0.74
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (84 bp):
TAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATCTGCTG
ATTCCCCATATCACTGAAT
Found at i:20728060 original size:28 final size:28
Alignment explanation
Indices: 20728018--20728096 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 28
20728008 AGGTTATCCC
*
20728018 TTCATAATTCGCCACAAAGGCTTTTTCT
1 TTCATATTTCGCCACAAAGGCTTTTTCT
* **
20728046 TTCATATTTCACCACAAA-GAATTTTCT
1 TTCATATTTCGCCACAAAGGCTTTTTCT
* *
20728073 TTCATGTTTCGCCACAAAGACTTT
1 TTCATATTTCGCCACAAAGGCTTT
20728097 CCTTTCTTGA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
27 23 0.56
28 18 0.44
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (28 bp):
TTCATATTTCGCCACAAAGGCTTTTTCT
Found at i:20736059 original size:47 final size:47
Alignment explanation
Indices: 20736008--20736128 Score: 181
Period size: 47 Copynumber: 2.6 Consensus size: 47
20735998 GTCCAACTAA
20736008 GGTCTTACACGGAATCACATATCACACCGATGTC-ATATCCCAGATAT
1 GGTCTTACACGGAATCACATATCACACCGATG-CGATATCCCAGATAT
* * *
20736055 GGTCTTACACAGTAGCACATATCACACCGATGCGATATCCCAGATAT
1 GGTCTTACACGGAATCACATATCACACCGATGCGATATCCCAGATAT
*
20736102 GGTCTTACACGAAAATCACATATCACA
1 GGTCTTACACG-GAATCACATATCACA
20736129 TATTGCCATG
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
46 1 0.02
47 52 0.80
48 12 0.18
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (47 bp):
GGTCTTACACGGAATCACATATCACACCGATGCGATATCCCAGATAT
Found at i:20737420 original size:22 final size:22
Alignment explanation
Indices: 20737387--20737455 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
20737377 TATGCACTAT
* *
20737387 TAAATAGAGAGCACTAAAGTGT
1 TAAACAGAGAGCACTAAAGTGC
* *
20737409 TATACAGAGAGCA-TGAATGTGC
1 TAAACAGAGAGCACT-AAAGTGC
*
20737431 TAAACAGAGAGCACTAATGTGC
1 TAAACAGAGAGCACTAAAGTGC
20737453 TAA
1 TAA
20737456 TAATCAAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (22 bp):
TAAACAGAGAGCACTAAAGTGC
Found at i:20737495 original size:25 final size:25
Alignment explanation
Indices: 20737435--20737585 Score: 188
Period size: 25 Copynumber: 6.3 Consensus size: 25
20737425 ATGTGCTAAA
* *
20737435 CAGAGAGCACTAATGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAATAAT
*
20737460 CA-A-AG-A--G-CGTGCTAGTAAT
1 CAGAGAGCACTGACGTGCTAATAAT
*
20737479 TAGAGAGCACTGACGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAATAAT
20737504 CAGAGAGCACTGACGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAATAAT
* * *
20737529 TAGAGAGCACTGATGTGCAAATAAT
1 CAGAGAGCACTGACGTGCTAATAAT
*
20737554 CAGAGAGCACGGACGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAATAAT
20737579 CAGAGAG
1 CAGAGAG
20737586 TACGCTAAAC
Statistics
Matches: 107, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
19 11 0.10
20 1 0.01
21 2 0.02
22 2 0.02
23 2 0.02
24 2 0.02
25 87 0.81
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (25 bp):
CAGAGAGCACTGACGTGCTAATAAT
Found at i:20742440 original size:6 final size:6
Alignment explanation
Indices: 20742428--20742495 Score: 91
Period size: 6 Copynumber: 11.2 Consensus size: 6
20742418 TAGGTTTCTC
* * * *
20742428 AAAATG GAAATG GAAATG GAAATG GAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
20742476 AAAATG AAAATG AGAAATG A
1 AAAATG AAAATG A-AAATG A
20742496 TACATTTGCA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
6 53 0.90
7 6 0.10
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:20746765 original size:18 final size:18
Alignment explanation
Indices: 20746744--20746778 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20746734 TTATTTTTTG
20746744 ATTTCTTTCTCTTTTTCA
1 ATTTCTTTCTCTTTTTCA
20746762 ATTTCTTTCTCTTTTTC
1 ATTTCTTTCTCTTTTTC
20746779 TTCTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTCTTTCTCTTTTTCA
Found at i:20746779 original size:30 final size:29
Alignment explanation
Indices: 20746745--20746826 Score: 73
Period size: 30 Copynumber: 2.9 Consensus size: 29
20746735 TATTTTTTGA
20746745 TTTCTTTCTCTTTTTCAATTTCTTTCTCTT
1 TTTCTTTCTCTTTTTCAATTTCTTTCT-TT
**
20746775 TTTC--T-TCTTTTTCTTTTTC-TTCTTT
1 TTTCTTTCTCTTTTTCAATTTCTTTCTTT
* *
20746800 TTCTTTTTCTTCTTTTTCAATCTCTTT
1 TT-TCTTTC-TCTTTTTCAATTTCTTT
20746827 TTCGAGTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
25 4 0.10
26 5 0.12
27 12 0.30
28 2 0.05
30 15 0.38
31 2 0.05
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTCTTTCTCTTTTTCAATTTCTTTCTTT
Found at i:20746784 original size:15 final size:15
Alignment explanation
Indices: 20746746--20746814 Score: 93
Period size: 15 Copynumber: 4.4 Consensus size: 15
20746736 ATTTTTTGAT
20746746 TTCTTTCTCTTTTTC
1 TTCTTTCTCTTTTTC
20746761 AATTTCTTTCTCTTTTTC
1 ---TTCTTTCTCTTTTTC
*
20746779 TTCTTTTTCTTTTTC
1 TTCTTTCTCTTTTTC
*
20746794 TTCTTTTTCTTTTTC
1 TTCTTTCTCTTTTTC
20746809 TTCTTT
1 TTCTTT
20746815 TTCAATCTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
15 35 0.70
18 15 0.30
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (15 bp):
TTCTTTCTCTTTTTC
Found at i:20746785 original size:9 final size:9
Alignment explanation
Indices: 20746767--20746850 Score: 56
Period size: 9 Copynumber: 9.4 Consensus size: 9
20746757 TTTCAATTTC
20746767 TTTC-TCTT
1 TTTCTTCTT
20746775 TTTCTTC--
1 TTTCTTCTT
20746782 TTT-TTCTT
1 TTTCTTCTT
20746790 TTTCTTC--
1 TTTCTTCTT
20746797 TTT-TTCTT
1 TTTCTTCTT
20746805 TTTCTTCTT
1 TTTCTTCTT
20746814 TTTCAATCTCTT
1 TTTC--T-TCTT
20746826 TTTCGAGTTCTT
1 TTTC---TTCTT
*
20746838 TTCCTTCTT
1 TTTCTTCTT
20746847 TTTC
1 TTTC
20746851 GAGTTTATTA
Statistics
Matches: 62, Mismatches: 3, Indels: 21
0.72 0.03 0.24
Matches are distributed among these distances:
6 6 0.10
7 6 0.10
8 10 0.16
9 22 0.35
11 1 0.02
12 15 0.24
13 2 0.03
ACGTcount: A:0.04, C:0.23, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:20746789 original size:21 final size:21
Alignment explanation
Indices: 20746753--20746810 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
20746743 GATTTCTTTC
**
20746753 TCTTTTTCAATTTCTTTCTCT
1 TCTTTTTCTTTTTCTTTCTCT
*
20746774 T-TTTCTTCTTTTTCTTTTTCT
1 TCTTT-TTCTTTTTCTTTCTCT
20746795 TCTTTTTCTTTTTCTT
1 TCTTTTTCTTTTTCTT
20746811 CTTTTTCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 3 0.09
21 26 0.81
22 3 0.09
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (21 bp):
TCTTTTTCTTTTTCTTTCTCT
Found at i:20746825 original size:15 final size:15
Alignment explanation
Indices: 20746764--20746817 Score: 99
Period size: 15 Copynumber: 3.6 Consensus size: 15
20746754 CTTTTTCAAT
*
20746764 TTCTTTCTCTTTTTC
1 TTCTTTTTCTTTTTC
20746779 TTCTTTTTCTTTTTC
1 TTCTTTTTCTTTTTC
20746794 TTCTTTTTCTTTTTC
1 TTCTTTTTCTTTTTC
20746809 TTCTTTTTC
1 TTCTTTTTC
20746818 AATCTCTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTCTTTTTCTTTTTC
Found at i:20747335 original size:16 final size:18
Alignment explanation
Indices: 20747303--20747336 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20747293 TTATTTACTG
20747303 AAAATAAGAAAAGTTAAA
1 AAAATAAGAAAAGTTAAA
20747321 AAAAT-AGAAAA-TTAAA
1 AAAATAAGAAAAGTTAAA
20747337 TACCTCACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (18 bp):
AAAATAAGAAAAGTTAAA
Found at i:20752187 original size:26 final size:26
Alignment explanation
Indices: 20752151--20752216 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
20752141 TCTGACCCAC
* *
20752151 AGCTCATGTGAGCAGGCCCATTTT-AT
1 AGCTCGTGTGAGCAGACCC-TTTTCAT
* * *
20752177 AGCTTGTGTGAGCATACTCTTTTCAT
1 AGCTCGTGTGAGCAGACCCTTTTCAT
20752203 AGCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
20752217 TATATGTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 4 0.12
26 29 0.88
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (26 bp):
AGCTCGTGTGAGCAGACCCTTTTCAT
Found at i:20754661 original size:22 final size:21
Alignment explanation
Indices: 20754630--20754670 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
20754620 GAACATATAG
20754630 CCACTAATGTTGCGACAACCA
1 CCACTAATGTTGCGACAACCA
20754651 CCACTCAATGTTGCGACAAC
1 CCACT-AATGTTGCGACAAC
20754671 GAACTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.20
Consensus pattern (21 bp):
CCACTAATGTTGCGACAACCA
Found at i:20756233 original size:41 final size:42
Alignment explanation
Indices: 20756158--20756281 Score: 182
Period size: 40 Copynumber: 3.0 Consensus size: 42
20756148 ACCAAAAATT
20756158 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAA-AAAAATTAAAAAAAGTATTTTAAAAA
20756202 TATTTTAAAATTAAAAAAAAATT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAAATTAAAAAAAGTATTTTAAAAA
* * *
20756243 -AATTTAAAATT-TAAAAAATTTAAAAAAAGTATTTTAAAA
1 TATTTTAAAATTAAAAAAAAATTAAAAAAAGTATTTTAAAA
20756282 TTAAAAAAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
39 8 0.11
40 27 0.36
41 18 0.24
42 7 0.09
43 10 0.13
44 6 0.08
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (42 bp):
TATTTTAAAATTAAAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:20756247 original size:11 final size:10
Alignment explanation
Indices: 20756208--20756270 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
20756198 AAAATATTTT
*
20756208 AAAATTAAAA
1 AAAATTTAAA
*
20756218 AAAAATTAAA
1 AAAATTTAAA
20756228 AAAGTATTTTAAA
1 AAA--A-TTTAAA
20756241 AAAATTT---
1 AAAATTTAAA
20756248 AAAATTT-AA
1 AAAATTTAAA
20756257 AAAATTTAAA
1 AAAATTTAAA
20756267 AAAA
1 AAAA
20756271 GTATTTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
7 7 0.16
9 7 0.16
10 20 0.45
11 1 0.02
12 1 0.02
13 8 0.18
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:20756251 original size:29 final size:29
Alignment explanation
Indices: 20756219--20756291 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
20756209 AAATTAAAAA
*
20756219 AAAATTAAAAAAGTATTTTAAAAAA-A-TTT
1 AAAATTAAAAAA--ATTTAAAAAAAGATTTT
*
20756248 AAAATTTAAAAAATTTAAAAAAAGTATTTT
1 AAAATTAAAAAAATTTAAAAAAAG-ATTTT
20756278 AAAATTAAAAAAAT
1 AAAATTAAAAAAAT
20756292 AAAAATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 10 0.26
29 12 0.32
30 16 0.42
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTAAAAAAATTTAAAAAAAGATTTT
Found at i:20759114 original size:19 final size:19
Alignment explanation
Indices: 20759075--20759131 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
20759065 ATATTTAAAA
*
20759075 TATTAAAATTGATATAAACT
1 TATTAAAATT-ATAAAAACT
20759095 TATTAAAATTATAAAAACT
1 TATTAAAATTATAAAAACT
20759114 TA-TAAATATTATAAAAAC
1 TATTAAA-ATTATAAAAAC
20759132 ATAAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
18 4 0.11
19 21 0.60
20 10 0.29
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (19 bp):
TATTAAAATTATAAAAACT
Found at i:20759187 original size:10 final size:10
Alignment explanation
Indices: 20759046--20759273 Score: 80
Period size: 9 Copynumber: 23.9 Consensus size: 10
20759036 CAATTATAAA
20759046 TATATATAAAT
1 TATATA-AAAT
* *
20759057 AATATTAAA-
1 TATATAAAAT
*
20759066 TATTTAAAA-
1 TATATAAAAT
20759075 TAT-TAAAAT
1 TATATAAAAT
*
20759084 TGATATAAACT
1 T-ATATAAAAT
20759095 TAT-TAAAAT
1 TATATAAAAT
20759104 TATA-AAAACT
1 TATATAAAA-T
*
20759114 TATA-AATAT
1 TATATAAAAT
*
20759123 TATA-AAAACA
1 TATATAAAA-T
* *
20759133 TAAAAAAAAT
1 TATATAAAAT
*
20759143 CTA-A-GAAAT
1 -TATATAAAAT
20759152 TATA-AAAA-
1 TATATAAAAT
20759160 -ATATAAAAT
1 TATATAAAAT
20759169 TA-ATAAAAT
1 TATATAAAAT
*
20759178 TATTTAAAAT
1 TATATAAAAT
* *
20759188 TATAAAAAAA
1 TATATAAAAT
** *
20759198 CGTATGAGAAT
1 TATAT-AAAAT
* *
20759209 TTTTTAAAA-
1 TATATAAAAT
*
20759218 TAGTATAATAT
1 TA-TATAAAAT
20759229 TATA-AAAA-
1 TATATAAAAT
20759237 TAT-TAAAAT
1 TATATAAAAT
*
20759246 TGATATAAACT
1 T-ATATAAAAT
20759257 TATA-AAAAT
1 TATATAAAAT
20759266 TAT-TAAAA
1 TATATAAAA
20759274 ACAAACATAA
Statistics
Matches: 163, Mismatches: 33, Indels: 44
0.68 0.14 0.18
Matches are distributed among these distances:
7 3 0.02
8 18 0.11
9 63 0.39
10 50 0.31
11 29 0.18
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (10 bp):
TATATAAAAT
Found at i:20759195 original size:19 final size:19
Alignment explanation
Indices: 20759066--20759195 Score: 58
Period size: 19 Copynumber: 6.9 Consensus size: 19
20759056 TAATATTAAA
*
20759066 TATTTAAAA-TATTAAAAT
1 TATTTAAAATTATAAAAAT
* * *
20759084 TGATATAAACTTATTAAAAT
1 T-ATTTAAAATTATAAAAAT
* *
20759104 TA-TAAAAACTTATAAATAT
1 TATTTAAAA-TTATAAAAAT
** *
20759123 TA--TAAAAACATAAAAAA
1 TATTTAAAATTATAAAAAT
* *
20759140 AATCTAAGAAATTATAAAAA-
1 TAT-TTA-AAATTATAAAAAT
*
20759160 -ATATAAAATTA-ATAAAAT
1 TATTTAAAATTATA-AAAAT
20759178 TATTTAAAATTATAAAAA
1 TATTTAAAATTATAAAAA
20759196 AACGTATGAG
Statistics
Matches: 82, Mismatches: 19, Indels: 21
0.67 0.16 0.17
Matches are distributed among these distances:
16 1 0.01
17 17 0.21
18 9 0.11
19 33 0.40
20 12 0.15
21 10 0.12
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
TATTTAAAATTATAAAAAT
Found at i:20759554 original size:6 final size:7
Alignment explanation
Indices: 20759533--20759575 Score: 50
Period size: 7 Copynumber: 5.6 Consensus size: 7
20759523 CAGTTCAATT
20759533 AAATAAA
1 AAATAAA
20759540 AAATAAA
1 AAATAAA
20759547 AAATAAA
1 AAATAAA
20759554 AACATATTAA
1 AA-ATA--AA
20759564 AAATAGAA
1 AAATA-AA
20759572 AAAT
1 AAAT
20759576 TGGTTCAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
7 16 0.50
8 9 0.28
9 3 0.09
10 4 0.12
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (7 bp):
AAATAAA
Found at i:20759835 original size:10 final size:10
Alignment explanation
Indices: 20759751--20759934 Score: 68
Period size: 10 Copynumber: 18.7 Consensus size: 10
20759741 TTTTTACAAA
20759751 ATTTTA-AAT
1 ATTTTATAAT
*
20759760 ATTTTACATAT
1 ATTTTATA-AT
*
20759771 ATTCTAT-AT
1 ATTTTATAAT
20759780 -TTTTATAAT
1 ATTTTATAAT
*
20759789 -TTATTAGAAT
1 ATT-TTATAAT
*
20759799 TTTTTATAAT
1 ATTTTATAAT
*
20759809 A-TCTATAAT
1 ATTTTATAAT
20759818 ATTTTTATAAT
1 A-TTTTATAAT
20759829 ATTTTAT-A-
1 ATTTTATAAT
**
20759837 GGTTTAT-AT
1 ATTTTATAAT
* *
20759846 CAATTT-TCAT
1 -ATTTTATAAT
*
20759856 ATTTTAAAAT
1 ATTTTATAAT
*
20759866 ATATTTTTAAT
1 AT-TTTATAAT
20759877 A-TTTAGTAAT
1 ATTTTA-TAAT
*
20759887 -TTATAT-AT
1 ATTTTATAAT
*
20759895 ATTTTTAAATAT
1 A-TTTTATA-AT
*
20759907 ATTTTAAAAT
1 ATTTTATAAT
*
20759917 ATTTAATAAT
1 ATTTTATAAT
20759927 AATTTTAT
1 -ATTTTAT
20759935 CAAATCAAAC
Statistics
Matches: 132, Mismatches: 24, Indels: 36
0.69 0.12 0.19
Matches are distributed among these distances:
8 13 0.10
9 30 0.23
10 49 0.37
11 37 0.28
12 3 0.02
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.57
Consensus pattern (10 bp):
ATTTTATAAT
Found at i:20759869 original size:12 final size:12
Alignment explanation
Indices: 20759854--20759918 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
20759844 ATCAATTTTC
20759854 ATATTTTAAAAT
1 ATATTTTAAAAT
*
20759866 ATATTTTTAATATTT
1 ATA-TTTTAA-A-AT
* *
20759881 AGTAATTT-ATAT
1 A-TATTTTAAAAT
*
20759893 ATATTTTTAAAT
1 ATATTTTAAAAT
20759905 ATATTTTAAAAT
1 ATATTTTAAAAT
20759917 AT
1 AT
20759919 TTAATAATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 5 0.12
12 21 0.51
13 6 0.15
14 2 0.05
15 5 0.12
16 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
ATATTTTAAAAT
Found at i:20763502 original size:28 final size:28
Alignment explanation
Indices: 20763464--20763519 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
20763454 TAAAAGCCTG
*
20763464 ACACTCTGGTCAAAAACCATATGATCAC
1 ACACTCTGGTCAAAAACCACATGATCAC
*
20763492 ACACTCTGGTCGAAAACCACATGATCAC
1 ACACTCTGGTCAAAAACCACATGATCAC
20763520 TCTTATAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (28 bp):
ACACTCTGGTCAAAAACCACATGATCAC
Found at i:20765478 original size:33 final size:33
Alignment explanation
Indices: 20765435--20765497 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
20765425 ACTGAGTTTG
* *
20765435 CCAAATAGGAAGATGATGACCCGCTCACATTTT
1 CCAAACAGGAAGATGATGACCCACTCACATTTT
20765468 CCAAACAGGAAGATGATGACCCACTCACAT
1 CCAAACAGGAAGATGATGACCCACTCACAT
20765498 ATGACGAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (33 bp):
CCAAACAGGAAGATGATGACCCACTCACATTTT
Found at i:20768655 original size:27 final size:27
Alignment explanation
Indices: 20768625--20768798 Score: 197
Period size: 27 Copynumber: 6.4 Consensus size: 27
20768615 TGAGTCCGCT
* * * *
20768625 CACTCAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* *
20768652 CACTTAGTGCTACGTAATCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
20768679 CACTTAGTGCTACATAGTCAAACTCGCA
1 CACTTAGTGCTACATAGTCAAA-TCGCA
** * *
20768707 CACTTAGTGCCGCATGGTCAATTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* **
20768734 CACTTAGTGC-ATCATATTCATTTCGCA
1 CACTTAGTGCTA-CATAGTCAAATCGCA
*
20768761 CACTTAGTGCAACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
20768788 CACTTAGTGCT
1 CACTTAGTGCT
20768799 GTCCAATTTA
Statistics
Matches: 126, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 102 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CACTTAGTGCTACATAGTCAAATCGCA
Found at i:20768767 original size:82 final size:81
Alignment explanation
Indices: 20768642--20768797 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
20768632 TGCTATATAA
* *
20768642 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
20768707 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
20768724 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
20768788 CACTTAGTGC
65 CACTTAGTGC
20768798 TGTCCAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:20776667 original size:27 final size:27
Alignment explanation
Indices: 20776637--20776810 Score: 197
Period size: 27 Copynumber: 6.4 Consensus size: 27
20776627 TGAGTCCGCT
* * * *
20776637 CACTCAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* *
20776664 CACTTAGTGCTACGTAATCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
20776691 CACTTAGTGCTACATAGTCAAACTCGCA
1 CACTTAGTGCTACATAGTCAAA-TCGCA
** * *
20776719 CACTTAGTGCCGCATGGTCAATTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* **
20776746 CACTTAGTGC-ATCATATTCATTTCGCA
1 CACTTAGTGCTA-CATAGTCAAATCGCA
*
20776773 CACTTAGTGCAACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
20776800 CACTTAGTGCT
1 CACTTAGTGCT
20776811 GTACAATTTA
Statistics
Matches: 126, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 102 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CACTTAGTGCTACATAGTCAAATCGCA
Found at i:20776779 original size:82 final size:81
Alignment explanation
Indices: 20776654--20776809 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
20776644 TGCTATATAA
* *
20776654 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
20776719 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
20776736 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
20776800 CACTTAGTGC
65 CACTTAGTGC
20776810 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:20781616 original size:37 final size:37
Alignment explanation
Indices: 20781547--20781732 Score: 227
Period size: 37 Copynumber: 5.1 Consensus size: 37
20781537 AGTACACAAG
* *
20781547 TAATCCAACCGA-AGCACGTCAAATGCTCATAAGAGC
1 TAATCCAACCGATAACACGCCAAATGCTCATAAGAGC
*
20781583 TAATCCAACCGATAACACGCCGAATGCTCATAAGAGC
1 TAATCCAACCGATAACACGCCAAATGCTCATAAGAGC
* * ** * *
20781620 TAATCCAACTGAT-ACTTCATCGAATGATCATAAGAGC
1 TAATCCAACCGATAAC-ACGCCAAATGCTCATAAGAGC
20781657 TAATCCAACC-ATAAACACGCCAAATGCTCATAAGAGC
1 TAATCCAACCGAT-AACACGCCAAATGCTCATAAGAGC
*
20781694 TAATCCAACCG-TAAACACACCAAATGCTCATAAGAGC
1 TAATCCAACCGAT-AACACGCCAAATGCTCATAAGAGC
20781731 TA
1 TA
20781733 TACACCCACC
Statistics
Matches: 130, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
36 16 0.12
37 112 0.86
38 2 0.02
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.19
Consensus pattern (37 bp):
TAATCCAACCGATAACACGCCAAATGCTCATAAGAGC
Found at i:20781725 original size:74 final size:73
Alignment explanation
Indices: 20781547--20781732 Score: 257
Period size: 74 Copynumber: 2.5 Consensus size: 73
20781537 AGTACACAAG
* * *
20781547 TAATCCAACCGAAGCACGTCAAATGCTCATAAGAGCTAATCCAACCGATAACACGCCGAATGCTC
1 TAATCCAACCGAAACACATCAAATGCTCATAAGAGCTAATCCAACCGATAACACGCCAAATGCTC
20781612 ATAAGAGC
66 ATAAGAGC
* * * * *
20781620 TAATCCAACTGATACTTCATCGAATGATCATAAGAGCTAATCCAACC-ATAAACACGCCAAATGC
1 TAATCCAACCGAAAC-ACATCAAATGCTCATAAGAGCTAATCCAACCGAT-AACACGCCAAATGC
20781684 TCATAAGAGC
64 TCATAAGAGC
*
20781694 TAATCCAACCGTAAACACACCAAATGCTCATAAGAGCTA
1 TAATCCAACCG-AAACACATCAAATGCTCATAAGAGCTA
20781733 TACACCCACC
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
73 14 0.15
74 79 0.82
75 3 0.03
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.19
Consensus pattern (73 bp):
TAATCCAACCGAAACACATCAAATGCTCATAAGAGCTAATCCAACCGATAACACGCCAAATGCTC
ATAAGAGC
Found at i:20782260 original size:37 final size:38
Alignment explanation
Indices: 20782210--20782371 Score: 215
Period size: 37 Copynumber: 4.4 Consensus size: 38
20782200 ATAACACGTG
* *
20782210 GCTCATAAGAGCTAATCCAATCGAT-AACACGCCAAAT
1 GCTCATAAGAGCTAATCCAACCGATAAACACACCAAAT
* * ** *
20782247 GCTCATAAGAGCTAATGCAACCGAT-ACCTTATCAAAT
1 GCTCATAAGAGCTAATCCAACCGATAAACACACCAAAT
*
20782284 GATCATAAGAGCTAATCCAACC-ATAAACACACCAAAT
1 GCTCATAAGAGCTAATCCAACCGATAAACACACCAAAT
*
20782321 GCTCATAAGAGCTAATCCAACCG-TAAACACGCCAAAT
1 GCTCATAAGAGCTAATCCAACCGATAAACACACCAAAT
20782358 GCTCATAAGAGCTA
1 GCTCATAAGAGCTA
20782372 TACATCCGCC
Statistics
Matches: 108, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
36 2 0.02
37 106 0.98
ACGTcount: A:0.41, C:0.27, G:0.13, T:0.19
Consensus pattern (38 bp):
GCTCATAAGAGCTAATCCAACCGATAAACACACCAAAT
Found at i:20796021 original size:30 final size:30
Alignment explanation
Indices: 20795925--20796087 Score: 147
Period size: 30 Copynumber: 5.5 Consensus size: 30
20795915 TCATCGACGA
* * *
20795925 ATAAAAAGGAATAGCTTCGGCTATCGAT-T
1 ATAAAAAGGGATGGCTTCGGCTATCAATCT
* * *
20795954 ATGAAAAGGGATGG-TGAT-GACCATCGAA-CT
1 ATAAAAAGGGATGGCT--TCGGCTATC-AATCT
*
20795984 ATGAAAAGGGATGGCTTCGGCTATCAATCT
1 ATAAAAAGGGATGGCTTCGGCTATCAATCT
*
20796014 ATAAAAAGGGATGGCTTTGGCTATCAATCT
1 ATAAAAAGGGATGGCTTCGGCTATCAATCT
* * *
20796044 ATGAAAAGAGATAGCTTCGGCTATCAAAT-T
1 ATAAAAAGGGATGGCTTCGGCTATC-AATCT
*
20796074 ATAAAAAGGAATGG
1 ATAAAAAGGGATGG
20796088 TGACACCATC
Statistics
Matches: 108, Mismatches: 18, Indels: 15
0.77 0.13 0.11
Matches are distributed among these distances:
28 1 0.01
29 19 0.18
30 84 0.78
31 4 0.04
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (30 bp):
ATAAAAAGGGATGGCTTCGGCTATCAATCT
Found at i:20796048 original size:60 final size:59
Alignment explanation
Indices: 20795928--20796114 Score: 218
Period size: 60 Copynumber: 3.2 Consensus size: 59
20795918 TCGACGAATA
* * *
20795928 AAAAGGAATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGATGACCATCGAACTATG
1 AAAAGGGATAGCTTCGGCTATCAATTATAAAAAGGGATGGTGATGACCATCGAACTATG
* * * *
20795987 AAAAGGGATGGCTTCGGCTATCAATCTATAAAAAGGGATGGCT-TTGGCTATC-AATCTATG
1 AAAAGGGATAGCTTCGGCTATCAAT-TATAAAAAGGGATGG-TGATGACCATCGAA-CTATG
* * * *
20796047 AAAAGAGATAGCTTCGGCTATCAAATTATAAAAAGGAATGGTGA-CACCATCAAACTATG
1 AAAAGGGATAGCTTCGGCTATC-AATTATAAAAAGGGATGGTGATGACCATCGAACTATG
20796106 AAAAGGGAT
1 AAAAGGGAT
20796115 GGTGACGACT
Statistics
Matches: 107, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
59 42 0.39
60 61 0.57
61 4 0.04
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (59 bp):
AAAAGGGATAGCTTCGGCTATCAATTATAAAAAGGGATGGTGATGACCATCGAACTATG
Found at i:20796099 original size:29 final size:30
Alignment explanation
Indices: 20796066--20796141 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 30
20796056 AGCTTCGGCT
*
20796066 ATCAAATTATAAAAAGGAATGGTGAC-ACC
1 ATCAAATTATGAAAAGGAATGGTGACGACC
* * *
20796095 ATCAAACTATGAAAAGGGATGGTGACGACT
1 ATCAAATTATGAAAAGGAATGGTGACGACC
20796125 ATCAAATTATGAAAAGG
1 ATCAAATTATGAAAAGG
20796142 GATAACTTCG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 23 0.56
30 18 0.44
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (30 bp):
ATCAAATTATGAAAAGGAATGGTGACGACC
Found at i:20796136 original size:30 final size:29
Alignment explanation
Indices: 20795951--20796144 Score: 133
Period size: 30 Copynumber: 6.5 Consensus size: 29
20795941 TCGGCTATCG
* * *
20795951 ATTATGAAAAGGGATGGTGATGACCATCGA
1 ATTATGAAAAGGGATGGT-ACGACTATCAA
* * *
20795981 ACTATGAAAAGGGATGGCTTCGGCTATC-A
1 ATTATGAAAAGGGATGG-TACGACTATCAA
* ** *
20796010 ATCTATAAAAAGGGATGGCTTTGGCTATC-A
1 AT-TATGAAAAGGGATGG-TACGACTATCAA
* * * *
20796040 ATCTATGAAAAGAGATAGCTTCGGCTATCAA
1 AT-TATGAAAAGGGAT-GGTACGACTATCAA
* * *
20796071 ATTATAAAAAGGAATGGTGAC-ACCATCAA
1 ATTATGAAAAGGGATGGT-ACGACTATCAA
*
20796100 ACTATGAAAAGGGATGGTGACGACTATCAA
1 ATTATGAAAAGGGATGGT-ACGACTATCAA
20796130 ATTATGAAAAGGGAT
1 ATTATGAAAAGGGAT
20796145 AACTTCGGTT
Statistics
Matches: 134, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
29 28 0.21
30 101 0.75
31 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (29 bp):
ATTATGAAAAGGGATGGTACGACTATCAA
Found at i:20796165 original size:119 final size:120
Alignment explanation
Indices: 20795935--20796193 Score: 294
Period size: 119 Copynumber: 2.2 Consensus size: 120
20795925 ATAAAAAGGA
* * * * *
20795935 ATAGCTTCGGCTATC-GATTATGAAAAGGGATGGTGATGACCATCGAACTATGAAAAGGGATGGC
1 ATAGCTTCGGCTATCAAATTATAAAAAGGAATGGTGATCACCATCAAACTATGAAAAGGGATGGC
* * ** * *
20795999 TTCGGCTATCAATCTATAAAAAGGGATGGCTTTGGCTATCAATCTATGAAAAGAG
66 TACGACTATCAATCTATAAAAAGGGATAACTTCGGCTATCAAACTATGAAAAGAG
20796054 ATAGCTTCGGCTATCAAATTATAAAAAGGAATGGTGA-CACCATCAAACTATGAAAAGGGATGG-
1 ATAGCTTCGGCTATCAAATTATAAAAAGGAATGGTGATCACCATCAAACTATGAAAAGGGATGGC
* * * *
20796117 TGACGACTATCAAAT-TATGAAAAGGGATAACTTCGGTTGT-AGAACTATGAAAAGGG
66 T-ACGACTATC-AATCTATAAAAAGGGATAACTTCGGCTATCA-AACTATGAAAAGAG
* * *
20796173 ATAACTTCAGTTATCAAATTA
1 ATAGCTTCGGCTATCAAATTA
20796194 CGAAAAGGGA
Statistics
Matches: 118, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
118 2 0.02
119 95 0.81
120 21 0.18
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (120 bp):
ATAGCTTCGGCTATCAAATTATAAAAAGGAATGGTGATCACCATCAAACTATGAAAAGGGATGGC
TACGACTATCAATCTATAAAAAGGGATAACTTCGGCTATCAAACTATGAAAAGAG
Found at i:20796199 original size:30 final size:30
Alignment explanation
Indices: 20796124--20796204 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
20796114 TGGTGACGAC
*
20796124 TATCAAATTATGAAAAGGGATAACTTCGGT
1 TATCAAATTATGAAAAGGGATAACTTCAGT
* *
20796154 TGT-AGAACTATGAAAAGGGATAACTTCAGT
1 TATCA-AATTATGAAAAGGGATAACTTCAGT
*
20796184 TATCAAATTACGAAAAGGGAT
1 TATCAAATTATGAAAAGGGAT
20796205 GTGTCAACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (30 bp):
TATCAAATTATGAAAAGGGATAACTTCAGT
Found at i:20807724 original size:101 final size:102
Alignment explanation
Indices: 20807600--20807890 Score: 433
Period size: 101 Copynumber: 2.9 Consensus size: 102
20807590 ACTTTTATCA
* * * * * * *** *
20807600 TTCGATACACGTAGTGGCCTTCACATAGTACTACACACGTGATCAAGTTTTA-CGGTTCACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
*
20807664 TAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
*
20807701 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCAATT-ACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
20807765 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
* * *
20807802 CTCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATTGATTCACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
20807867 TAGCCTTCACACAGTACTACACAC
66 TAGCCTTCACACAGTACTACACAC
20807891 ATGTTCATCG
Statistics
Matches: 172, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
101 139 0.81
102 33 0.19
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (102 bp):
TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
Found at i:20807737 original size:51 final size:51
Alignment explanation
Indices: 20807600--20807890 Score: 290
Period size: 51 Copynumber: 5.7 Consensus size: 51
20807590 ACTTTTATCA
* * *
20807600 TTCGATACACGTAGTGGCCTTCACATAGTACTACACACGTGATC-AAG-TT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
*
20807649 TTACGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
1 TT-CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * *
20807701 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGC-TT
** * *
20807751 TATCAAT-TACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * * * *
20807802 CTCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGC-TT
* * * *
20807852 TATTGATTCACGTAGTAGCCTTCACACAGTACTACACAC
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACAC
20807891 ATGTTCATCG
Statistics
Matches: 196, Mismatches: 36, Indels: 18
0.78 0.14 0.07
Matches are distributed among these distances:
49 6 0.03
50 78 0.40
51 106 0.54
52 6 0.03
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (51 bp):
TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
Found at i:20807868 original size:152 final size:150
Alignment explanation
Indices: 20807608--20807889 Score: 361
Period size: 152 Copynumber: 1.9 Consensus size: 150
20807598 CATTCGATAC
* * * * * *
20807608 ACGTAGTGGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCACGTAGTAGCCTTCA
1 ACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAGTTCTACGGTACACATAGTAGCCTTCA
* **
20807673 CATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACTTAGTACTACACA
66 CATAGTACTACACACGTGACCAAA-CTTTTCGATACACATAGTAGCCTTCACACAGTACTACACA
20807738 TGTGACCATCATTTATCAATT
130 TGTGACCATCATTTATCAATT
*
20807759 ACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTACACATTGTAGCCTT
1 ACGTAGTAGCCTTCACACAGTACTACACACGTGACC-AAG-TTCTACGGTACACATAGTAGCCTT
* * * * * *
20807823 CACTTAGTACTACACATGTGACC-ATCATTTATTGATTCACGTAGTAGCCTTCACACAGTACTAC
64 CACATAGTACTACACACGTGACCAAAC-TTT-TCGATACACATAGTAGCCTTCACACAGTACTAC
20807887 ACA
127 ACA
20807890 CATGTTCATC
Statistics
Matches: 111, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
150 1 0.01
151 37 0.33
152 70 0.63
153 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (150 bp):
ACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAGTTCTACGGTACACATAGTAGCCTTCA
CATAGTACTACACACGTGACCAAACTTTTCGATACACATAGTAGCCTTCACACAGTACTACACAT
GTGACCATCATTTATCAATT
Found at i:20809487 original size:27 final size:26
Alignment explanation
Indices: 20809431--20809514 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 26
20809421 TACAGAACCG
* **
20809431 TTCCTTCAAAGTTCGCCATATGTACAA
1 TTCCTTCAAAGTTCACCATACATAC-A
20809458 TTCCTTCAAAGTTCACCATACATATCA
1 TTCCTTCAAAGTTCACCATACATA-CA
* * *
20809485 TT-CTATCAGAGTTTACCATACCTACCA
1 TTCCT-TCAAAGTTCACCATACATA-CA
20809512 TTC
1 TTC
20809515 TTTAGATTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
26 2 0.04
27 44 0.94
28 1 0.02
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.35
Consensus pattern (26 bp):
TTCCTTCAAAGTTCACCATACATACA
Found at i:20820541 original size:31 final size:31
Alignment explanation
Indices: 20820494--20820939 Score: 410
Period size: 31 Copynumber: 14.5 Consensus size: 31
20820484 AACTTATCTT
** * *
20820494 CATATACAAACCAATTTCGATAATGTATAAC
1 CATATACAAATTAATTTCAACAATGTATAAC
* * * * *
20820525 CATAGACAAATAAATTTCAGCAATTTACAAC
1 CATATACAAATTAATTTCAACAATGTATAAC
* * *
20820556 CATATACGAATTAA-TTCAGCAACT-TATATC
1 CATATACAAATTAATTTCAACAA-TGTATAAC
20820586 CATATAC-AATTCAATTTCAACAATGTATAAC
1 CATATACAAATT-AATTTCAACAATGTATAAC
* *
20820617 CATATACAAATTAATTTCAGCAATGTATAAT
1 CATATACAAATTAATTTCAACAATGTATAAC
* ** ***
20820648 TATATACAAATTAA-TTCGGCAACT-TATCTT
1 CATATACAAATTAATTTCAACAA-TGTATAAC
* * * *
20820678 TATATACAAATCAAATTCAATAATGTATAAC
1 CATATACAAATTAATTTCAACAATGTATAAC
* * *
20820709 CATATACAAATAAATTTCAGCAATGTACAAC
1 CATATACAAATTAATTTCAACAATGTATAAC
*
20820740 CATATACAAATTAA-TTCAACAACT-TATATC
1 CATATACAAATTAATTTCAACAA-TGTATAAC
*
20820770 CATATAC-AATTCAGTTTCAACAATGTATAAC
1 CATATACAAATT-AATTTCAACAATGTATAAC
* * *
20820801 CATATACAAATAAATTTCAGCAATGTACAAC
1 CATATACAAATTAATTTCAACAATGTATAAC
* *
20820832 CATATACGAATTAA-TTCAACAACT-TATATC
1 CATATACAAATTAATTTCAACAA-TGTATAAC
20820862 CATATAC-AATTCAATTTCAACAATGTATAAC
1 CATATACAAATT-AATTTCAACAATGTATAAC
* *
20820893 CATATACAAATTAATTTCAGCAATGTATAAT
1 CATATACAAATTAATTTCAACAATGTATAAC
* *
20820924 TATATACGAATTAATT
1 CATATACAAATTAATT
20820940 CGACAATATA
Statistics
Matches: 343, Mismatches: 54, Indels: 36
0.79 0.12 0.08
Matches are distributed among these distances:
29 12 0.03
30 88 0.26
31 232 0.68
32 11 0.03
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.32
Consensus pattern (31 bp):
CATATACAAATTAATTTCAACAATGTATAAC
Found at i:20820601 original size:92 final size:92
Alignment explanation
Indices: 20820463--20820940 Score: 677
Period size: 92 Copynumber: 5.2 Consensus size: 92
20820453 AATATATATT
* * * * ** * *
20820463 CATATACGAATCAAATTCGGCAACTTATCTTCATATACAAACCAATTTCGATAATGTATAACCAT
1 CATATACGAAT-TAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCAT
* *
20820528 AGACAAATAAATTTCAGCAATTTACAAC
65 ATACAAATAAATTTCAGCAATGTACAAC
20820556 CATATACGAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATA
1 CATATACGAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATA
* * *
20820621 TACAAATTAATTTCAGCAATGTATAAT
66 TACAAATAAATTTCAGCAATGTACAAC
* * * * ** * * *
20820648 TATATACAAATTAATTCGGCAACTTATCTTTATATACAAATCAAATTCAATAATGTATAACCATA
1 CATATACGAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATA
20820713 TACAAATAAATTTCAGCAATGTACAAC
66 TACAAATAAATTTCAGCAATGTACAAC
* * *
20820740 CATATACAAATTAATTCAACAACTTATATCCATATACAATTCAGTTTCAACAATGTATAACCATA
1 CATATACGAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATA
20820805 TACAAATAAATTTCAGCAATGTACAAC
66 TACAAATAAATTTCAGCAATGTACAAC
*
20820832 CATATACGAATTAATTCAACAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATA
1 CATATACGAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATA
* * *
20820897 TACAAATTAATTTCAGCAATGTATAAT
66 TACAAATAAATTTCAGCAATGTACAAC
*
20820924 TATATACGAATTAATTC
1 CATATACGAATTAATTC
20820941 GACAATATAT
Statistics
Matches: 344, Mismatches: 41, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
92 333 0.97
93 11 0.03
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.32
Consensus pattern (92 bp):
CATATACGAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATA
TACAAATAAATTTCAGCAATGTACAAC
Found at i:20821708 original size:17 final size:17
Alignment explanation
Indices: 20821686--20821723 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
20821676 GATAACTATG
20821686 TTTATTTACTAATTTAC
1 TTTATTTACTAATTTAC
20821703 TTTATTTACTAATTTAC
1 TTTATTTACTAATTTAC
20821720 TTTA
1 TTTA
20821724 ATGCCATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATTTACTAATTTAC
Found at i:20823072 original size:3 final size:3
Alignment explanation
Indices: 20823064--20823089 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20823054 TTTGTTTTTG
20823064 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
20823090 TCAATTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20826461 original size:12 final size:13
Alignment explanation
Indices: 20826444--20826475 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
20826434 CCCCAGTTAC
20826444 GATCACGGT-CAT
1 GATCACGGTCCAT
20826456 GATCAC-GTCCAT
1 GATCACGGTCCAT
20826468 GATCACGG
1 GATCACGG
20826476 CTACGGTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 15 0.83
13 1 0.06
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (13 bp):
GATCACGGTCCAT
Found at i:20828811 original size:17 final size:14
Alignment explanation
Indices: 20828774--20828802 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20828764 ATTCCAGAAT
20828774 GTAATAAAAAAACC
1 GTAATAAAAAAACC
20828788 GTAATAAAAAAACC
1 GTAATAAAAAAACC
20828802 G
1 G
20828803 ACTAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.14, G:0.10, T:0.14
Consensus pattern (14 bp):
GTAATAAAAAAACC
Found at i:20828967 original size:2 final size:2
Alignment explanation
Indices: 20828960--20828999 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
20828950 GATTAAGAAT
20828960 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20829000 TTAGCGTACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20829348 original size:12 final size:12
Alignment explanation
Indices: 20829318--20829367 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
20829308 AACATAATTT
20829318 TTTTAAAAATAAAA
1 TTTT-AAAA-AAAA
*
20829332 CTTTAAAAAAAA
1 TTTTAAAAAAAA
*
20829344 TTTTAACAAAAA
1 TTTTAAAAAAAA
20829356 TATTTAAAAAAA
1 T-TTTAAAAAAA
20829368 TCTGATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 15 0.48
13 13 0.42
14 3 0.10
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (12 bp):
TTTTAAAAAAAA
Found at i:20829796 original size:15 final size:15
Alignment explanation
Indices: 20829761--20829790 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
20829751 ATAATAAAAA
20829761 TATATTAAATAATTT
1 TATATTAAATAATTT
20829776 TATATT-AATAATTT
1 TATATTAAATAATTT
20829790 T
1 T
20829791 TTTATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTAAATAATTT
Found at i:20829966 original size:16 final size:15
Alignment explanation
Indices: 20829934--20829963 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20829924 GAATGTTAAA
20829934 AAAATTATTATATTT
1 AAAATTATTATATTT
*
20829949 AAAATTATTTTATTT
1 AAAATTATTATATTT
20829964 TAATTAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAAATTATTATATTT
Found at i:20832047 original size:23 final size:23
Alignment explanation
Indices: 20832021--20832071 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
20832011 AATTAACTTA
*
20832021 AAAATC-AATAAAATAAAATAATT
1 AAAATCTAACAAAATAAAATAA-T
* *
20832044 AAAATCTAACAAAATTAAATTAT
1 AAAATCTAACAAAATAAAATAAT
20832067 AAAAT
1 AAAAT
20832072 AAAATAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAATCTAACAAAATAAAATAAT
Found at i:20839358 original size:19 final size:19
Alignment explanation
Indices: 20839325--20839388 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
20839315 AATTTACATG
* *
20839325 CAAACAAAATTCCACTTAT
1 CAAACACAATTCCACTAAT
* *
20839344 CACACACAGTTCCACTAAT
1 CAAACACAATTCCACTAAT
**
20839363 CTGACACAATTCCACTAAT
1 CAAACACAATTCCACTAAT
20839382 CAAACAC
1 CAAACAC
20839389 CATTAACGAG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.42, C:0.33, G:0.03, T:0.22
Consensus pattern (19 bp):
CAAACACAATTCCACTAAT
Found at i:20841143 original size:43 final size:40
Alignment explanation
Indices: 20841095--20841175 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 40
20841085 AGGGTAAATC
* * *
20841095 CAACAACCCATGTTTATCTTCTCCTCTTTTTAAATTCTTTTTT
1 CAACAACCCAAGATTATC-T-TCCT-TTTTAAAATTCTTTTTT
20841138 CAACAACCCAAGATTATCTTCCTTTTTAAAATTCTTTT
1 CAACAACCCAAGATTATCTTCCTTTTTAAAATTCTTTT
20841176 CAAGAGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 14 0.40
41 4 0.11
42 1 0.03
43 16 0.46
ACGTcount: A:0.26, C:0.25, G:0.02, T:0.47
Consensus pattern (40 bp):
CAACAACCCAAGATTATCTTCCTTTTTAAAATTCTTTTTT
Found at i:20842425 original size:20 final size:20
Alignment explanation
Indices: 20842397--20842436 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
20842387 ATTTTGATGT
*
20842397 GTTAGAATCATTTTAACTTG
1 GTTAAAATCATTTTAACTTG
20842417 GTTAAAATCATTTTAACTTG
1 GTTAAAATCATTTTAACTTG
20842437 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
GTTAAAATCATTTTAACTTG
Found at i:20844686 original size:33 final size:33
Alignment explanation
Indices: 20844644--20844902 Score: 146
Period size: 33 Copynumber: 7.6 Consensus size: 33
20844634 AATATGAAGG
20844644 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* * *
20844677 GGTTGCTAAGTGCTGATTGCACCGTATCTTTAAATATAAAGGG
1 GGTTGCTAAGTGCTGATT-CCCCG-A-C--T-CAT-T---GGT
*
20844720 GGTTGCTAAGTGCTGATT-CCC--C-CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* *
20844747 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* * *
20844780 GGTTGCTAAGTGCTGATTCCAACGTATCTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-C--T-CAT-T---GGT
*
20844823 GGTTGCTAAGTGCTGATT-CCC--C-CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* *
20844850 GGTTGCTAAGTGCTGATTCCCCGATTCATTAGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
20844883 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
20844903 ACCATATCTT
Statistics
Matches: 174, Mismatches: 20, Indels: 64
0.67 0.08 0.25
Matches are distributed among these distances:
27 35 0.20
28 10 0.06
31 4 0.02
32 3 0.02
33 59 0.34
34 6 0.03
35 2 0.01
36 1 0.01
37 2 0.01
38 2 0.01
39 4 0.02
40 2 0.01
41 3 0.02
42 1 0.01
43 40 0.23
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
Found at i:20844822 original size:103 final size:103
Alignment explanation
Indices: 20844640--20844950 Score: 514
Period size: 103 Copynumber: 3.0 Consensus size: 103
20844630 ATTGAATATG
* *
20844640 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTGCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
20844705 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
20844743 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCAACGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
20844808 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
20844846 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGGTTGCTAAGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* ** *
20844911 TTTGAATGTGAAAAGGGTTGCTAAGTGTTGATTCCCCC
66 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
20844949 AA
1 AA
20844951 TCACTGGTGG
Statistics
Matches: 194, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 194 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
Done.