Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 60 of 132
Found at i:16774906 original size:26 final size:26
Alignment explanation
Indices: 16774865--16774917 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
16774855 TTCTGGGCGT
16774865 AATTTTGGACACGTTCATGCAGCGAC
1 AATTTTGGACACGTTCATGCAGCGAC
* *
16774891 AATTTTGGATATGTTCATGCAGCGAC
1 AATTTTGGACACGTTCATGCAGCGAC
16774917 A
1 A
16774918 TTTCTCGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (26 bp):
AATTTTGGACACGTTCATGCAGCGAC
Found at i:16774948 original size:37 final size:38
Alignment explanation
Indices: 16774907--16774994 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
16774897 GGATATGTTC
* *
16774907 ATGCAGCGACATTTCTCGG-TGCAA-TTGAAGAGTACTT
1 ATGCAGCGACAGTTCT-GGATGCAATTTGAAGAATACTT
* *
16774944 ATGCAGCGATAGTTCTGGATGCAATTTGAAGAATATTT
1 ATGCAGCGACAGTTCTGGATGCAATTTGAAGAATACTT
*
16774982 ATGCAGCGTCAGT
1 ATGCAGCGACAGT
16774995 CTTGGGTGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
36 2 0.05
37 19 0.44
38 22 0.51
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (38 bp):
ATGCAGCGACAGTTCTGGATGCAATTTGAAGAATACTT
Found at i:16776645 original size:24 final size:24
Alignment explanation
Indices: 16776613--16776693 Score: 99
Period size: 24 Copynumber: 3.4 Consensus size: 24
16776603 AATCTTCCAG
*
16776613 TTAAACTCTATTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
* *
16776637 TTAAACTCTGTTTATTTATTACAA
1 TTAAACTCTGTTTATTTGTTTCAA
* * *
16776661 CTAAACTTTGTTTATTTGTTTCAG
1 TTAAACTCTGTTTATTTGTTTCAA
*
16776685 TCAAACTCT
1 TTAAACTCT
16776694 TATTAGTCTA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:16784728 original size:21 final size:21
Alignment explanation
Indices: 16784704--16784757 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
16784694 GAAATTTAAA
*
16784704 ACAAGCATAATGAGGAAAGTT
1 ACAAACATAATGAGGAAAGTT
* *
16784725 ACAAAACATTATGAGGAGAGTT
1 AC-AAACATAATGAGGAAAGTT
16784747 ACAAACATAAT
1 ACAAACATAAT
16784758 ATTTTGTAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.50, C:0.11, G:0.19, T:0.20
Consensus pattern (21 bp):
ACAAACATAATGAGGAAAGTT
Found at i:16793616 original size:11 final size:11
Alignment explanation
Indices: 16793600--16793635 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
16793590 GTATATAAAA
16793600 AATTTAAATTT
1 AATTTAAATTT
16793611 AATTTAAATTT
1 AATTTAAATTT
*
16793622 AATAATAAATTT
1 AAT-TTAAATTT
16793634 AA
1 AA
16793636 AACAAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:16794019 original size:21 final size:21
Alignment explanation
Indices: 16793995--16794049 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
16793985 GAAATTTAAA
16793995 ACAAACATAATGAGAAAAGTT
1 ACAAACATAATGAGAAAAGTT
* * * *
16794016 ACAAAACATTACGAGGAGAGTT
1 AC-AAACATAATGAGAAAAGTT
16794038 ACAAACATAATG
1 ACAAACATAATG
16794050 TTTTGTAGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (21 bp):
ACAAACATAATGAGAAAAGTT
Found at i:16797645 original size:25 final size:25
Alignment explanation
Indices: 16797613--16797792 Score: 189
Period size: 25 Copynumber: 7.2 Consensus size: 25
16797603 CAACTTGGTG
16797613 GAGCGATATTCTGTCTGGCTCGTAA
1 GAGCGATATTCTGTCTGGCTCGTAA
* * * *
16797638 GAGCGATATTCTGTATGGTTCATTA
1 GAGCGATATTCTGTCTGGCTCGTAA
* *
16797663 GAGCGATATTTTGTCTTGCTCGTAA
1 GAGCGATATTCTGTCTGGCTCGTAA
* *
16797688 GAGCGATATTCTATCTGGCTCATAA
1 GAGCGATATTCTGTCTGGCTCGTAA
* * *
16797713 GAGCAATATTCTATCTGGCTCGTTA
1 GAGCGATATTCTGTCTGGCTCGTAA
* *
16797738 GAGCGATATCCTGTTTGGCTCGTAA
1 GAGCGATATTCTGTCTGGCTCGTAA
** * * *
16797763 GAGTTAAACTCTGTCTAGGCTCGTAT
1 GAGCGATATTCTGTCT-GGCTCGTAA
16797789 GAGC
1 GAGC
16797793 TAAATTTCTA
Statistics
Matches: 124, Mismatches: 30, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
25 113 0.91
26 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (25 bp):
GAGCGATATTCTGTCTGGCTCGTAA
Found at i:16797739 original size:75 final size:75
Alignment explanation
Indices: 16797613--16797765 Score: 209
Period size: 75 Copynumber: 2.0 Consensus size: 75
16797603 CAACTTGGTG
* * * * * **
16797613 GAGCGATATTCTGTCTGGCTCGTAAGAGCGATATTCTGTATGGTTCATTAGAGCGATATTTTGTC
1 GAGCGATATTCTATCTGGCTCATAAGAGCAATATTCTATATGGCTCATTAGAGCGATATCCTGT-
16797678 TT-GCTCGTAA
65 TTGGCTCGTAA
* *
16797688 GAGCGATATTCTATCTGGCTCATAAGAGCAATATTCTATCTGGCTCGTTAGAGCGATATCCTGTT
1 GAGCGATATTCTATCTGGCTCATAAGAGCAATATTCTATATGGCTCATTAGAGCGATATCCTGTT
16797753 TGGCTCGTAA
66 TGGCTCGTAA
16797763 GAG
1 GAG
16797766 TTAAACTCTG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 2 0.03
75 66 0.97
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (75 bp):
GAGCGATATTCTATCTGGCTCATAAGAGCAATATTCTATATGGCTCATTAGAGCGATATCCTGTT
TGGCTCGTAA
Found at i:16801555 original size:52 final size:52
Alignment explanation
Indices: 16801470--16801656 Score: 302
Period size: 52 Copynumber: 3.6 Consensus size: 52
16801460 TAAATGCAAA
* *
16801470 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
* *
16801522 AGGTCCAATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATA
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
* * *
16801574 AGGTCCGATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTACG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
*
16801626 AGGTCTGATGACTATGTGTCATCATGAGTAT
1 AGGTCCGATGACTATGTGTCATCATGAGTAT
16801657 CAAATGAGAA
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 123 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
Found at i:16805690 original size:20 final size:19
Alignment explanation
Indices: 16805644--16805812 Score: 115
Period size: 20 Copynumber: 8.5 Consensus size: 19
16805634 AAAGTGTAAA
* *
16805644 CAGGGGAACTGAAGTACATT
1 CAGGGGCAC-GAAGTGCATT
16805664 CAGGGGCACGAAAGTGCATT
1 CAGGGGCACG-AAGTGCATT
* * * **
16805684 CAGGGGCATCAAATTGAAAA
1 CAGGGGCA-CGAAGTGCATT
* *
16805704 CGGGGGCACCGAAATGCATT
1 CAGGGGCA-CGAAGTGCATT
* * *
16805724 CAAGTGCACTGAAGTGCA-A
1 CAGGGGCAC-GAAGTGCATT
*
16805743 CAAGGGCAACGAAGTGCATT
1 CAGGGGC-ACGAAGTGCATT
**
16805763 CAGGGGCACTGAAGTGCAAA
1 CAGGGGCAC-GAAGTGCATT
*
16805783 CAAGGGCATCGAAGTGCATT
1 CAGGGGCA-CGAAGTGCATT
16805803 CAGGGGCACG
1 CAGGGGCACG
16805813 GATGTGTGTT
Statistics
Matches: 114, Mismatches: 28, Indels: 15
0.73 0.18 0.10
Matches are distributed among these distances:
19 20 0.18
20 92 0.81
21 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.32, T:0.15
Consensus pattern (19 bp):
CAGGGGCACGAAGTGCATT
Found at i:16805761 original size:39 final size:40
Alignment explanation
Indices: 16805707--16805811 Score: 149
Period size: 39 Copynumber: 2.6 Consensus size: 40
16805697 TTGAAAACGG
* * *
16805707 GGGCACCGAAATGCATTCAAGTGCACTGAAGTGC-AACAA
1 GGGCAACGAAGTGCATTCAAGGGCACTGAAGTGCAAACAA
*
16805746 GGGCAACGAAGTGCATTCAGGGGCACTGAAGTGCAAACAA
1 GGGCAACGAAGTGCATTCAAGGGCACTGAAGTGCAAACAA
* *
16805786 GGGCATCGAAGTGCATTCAGGGGCAC
1 GGGCAACGAAGTGCATTCAAGGGCAC
16805812 GGATGTGTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
39 30 0.50
40 30 0.50
ACGTcount: A:0.32, C:0.22, G:0.31, T:0.14
Consensus pattern (40 bp):
GGGCAACGAAGTGCATTCAAGGGCACTGAAGTGCAAACAA
Found at i:16805796 original size:40 final size:40
Alignment explanation
Indices: 16805617--16805811 Score: 171
Period size: 40 Copynumber: 4.9 Consensus size: 40
16805607 CCATCATAAA
* * ** *
16805617 TGCAAGACAAGGGCATCAAAGTGTAAACAGGGGAACTGAAG
1 TGCAA-ACAAGGGCATCGAAGTGCATTCAGGGGCACTGAAG
* ** * * *
16805658 TACATTCAGGGGCA-CGAAAGTGCATTCAGGGGCA-TCAAAT
1 TGCAAACAAGGGCATCG-AAGTGCATTCAGGGGCACT-GAAG
* ** * * * *
16805698 TGAAAACGGGGGCACCGAAATGCATTCAAGTGCACTGAAG
1 TGCAAACAAGGGCATCGAAGTGCATTCAGGGGCACTGAAG
*
16805738 TGC-AACAAGGGCAACGAAGTGCATTCAGGGGCACTGAAG
1 TGCAAACAAGGGCATCGAAGTGCATTCAGGGGCACTGAAG
16805777 TGCAAACAAGGGCATCGAAGTGCATTCAGGGGCAC
1 TGCAAACAAGGGCATCGAAGTGCATTCAGGGGCAC
16805812 GGATGTGTGT
Statistics
Matches: 120, Mismatches: 29, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
39 35 0.29
40 79 0.66
41 6 0.05
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.15
Consensus pattern (40 bp):
TGCAAACAAGGGCATCGAAGTGCATTCAGGGGCACTGAAG
Found at i:16823607 original size:23 final size:23
Alignment explanation
Indices: 16823566--16823620 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
16823556 TAAATGAAGT
* * *
16823566 AAGCATAAACGTATCATGCTGAC
1 AAGCGTAAACATATAATGCTGAC
*
16823589 GAGCGTAAACATATAATGCTGAC
1 AAGCGTAAACATATAATGCTGAC
16823612 AAGCGTAAA
1 AAGCGTAAA
16823621 TGTACTTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (23 bp):
AAGCGTAAACATATAATGCTGAC
Found at i:16846183 original size:17 final size:16
Alignment explanation
Indices: 16846171--16846203 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16846161 CCAAACTTTA
16846171 AAACAATCAAAACTCT
1 AAACAATCAAAACTCT
*
16846187 AAACAACCAAAAC-CT
1 AAACAATCAAAACTCT
16846202 AA
1 AA
16846204 CCCTAACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.61, C:0.27, G:0.00, T:0.12
Consensus pattern (16 bp):
AAACAATCAAAACTCT
Found at i:16846910 original size:19 final size:20
Alignment explanation
Indices: 16846886--16846927 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16846876 ATTATATATT
*
16846886 ATTAA-TTCGGTTAATTTTG
1 ATTAATTTCGATTAATTTTG
*
16846905 ATTAATTTTGATTAATTTTG
1 ATTAATTTCGATTAATTTTG
16846925 ATT
1 ATT
16846928 TGATTAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (20 bp):
ATTAATTTCGATTAATTTTG
Found at i:16846911 original size:10 final size:10
Alignment explanation
Indices: 16846896--16846927 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
16846886 ATTAATTCGG
16846896 TTAATTTTGA
1 TTAATTTTGA
16846906 TTAATTTTGA
1 TTAATTTTGA
16846916 TTAATTTTGA
1 TTAATTTTGA
16846926 TT
1 TT
16846928 TGATTAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (10 bp):
TTAATTTTGA
Found at i:16847733 original size:31 final size:31
Alignment explanation
Indices: 16847666--16847734 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
16847656 TATAAATGAT
*** *
16847666 CAATTTATTTTTTAATTTAATGCACAAAGAA
1 CAATTTATTTTTTAAGAGAATGAACAAAGAA
*
16847697 TAATTTATTTTTTAAGAGAATGAACAAA-ATA
1 CAATTTATTTTTTAAGAGAATGAACAAAGA-A
16847728 CAATTTA
1 CAATTTA
16847735 ACTATTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (31 bp):
CAATTTATTTTTTAAGAGAATGAACAAAGAA
Found at i:16853275 original size:22 final size:23
Alignment explanation
Indices: 16853236--16853283 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
16853226 ATAACGGTTC
* *
16853236 AAAAATTTTCTTTTCATTTAATA
1 AAAAATTTTCTCTGCATTTAATA
*
16853259 AAAAATTTTC-CTGCATTTATTA
1 AAAAATTTTCTCTGCATTTAATA
16853281 AAA
1 AAA
16853284 CTATGTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (23 bp):
AAAAATTTTCTCTGCATTTAATA
Found at i:16856314 original size:15 final size:16
Alignment explanation
Indices: 16856284--16856314 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16856274 TATGTTTTCA
16856284 ACAAATTTTCTTTTGC
1 ACAAATTTTCTTTTGC
16856300 ACAAATTTT-TTTTGC
1 ACAAATTTTCTTTTGC
16856315 TTTTTGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (16 bp):
ACAAATTTTCTTTTGC
Found at i:16872056 original size:121 final size:121
Alignment explanation
Indices: 16871913--16872145 Score: 439
Period size: 121 Copynumber: 1.9 Consensus size: 121
16871903 AATCTATTAG
16871913 ACAATAGGTAGTATATAAAAAATATAAATATAATTTAAATTTAACAGTAAACTTAAAAACAAATA
1 ACAATAGGTAGTATATAAAAAATATAAATATAATTTAAATTTAACAGTAAACTTAAAAACAAATA
16871978 ATAGGTATACTTTACATAGTATTTGTAGATGGATTGTAAAAAAAAATAATAGGTAT
66 ATAGGTATACTTTACATAGTATTTGTAGATGGATTGTAAAAAAAAATAATAGGTAT
16872034 ACAATAGGTAGTATATAAAAAATATAAATATAATTTAAATTTAACAGTAAACTTAAAAACAAATA
1 ACAATAGGTAGTATATAAAAAATATAAATATAATTTAAATTTAACAGTAAACTTAAAAACAAATA
* * *
16872099 ATATGTATACTTTACGTAGTATTTGTAGATGGATTGTAAATAAAAAT
66 ATAGGTATACTTTACATAGTATTTGTAGATGGATTGTAAAAAAAAAT
16872146 CCGTTGAGGC
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 109 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (121 bp):
ACAATAGGTAGTATATAAAAAATATAAATATAATTTAAATTTAACAGTAAACTTAAAAACAAATA
ATAGGTATACTTTACATAGTATTTGTAGATGGATTGTAAAAAAAAATAATAGGTAT
Found at i:16873987 original size:16 final size:16
Alignment explanation
Indices: 16873952--16873987 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16873942 TGTCTTCGAA
*
16873952 TTTGAATTATTTCAGT
1 TTTGAATTATTTCAGG
*
16873968 TTTGAATTATTTTAGG
1 TTTGAATTATTTCAGG
16873984 TTTG
1 TTTG
16873988 GATTCAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.58
Consensus pattern (16 bp):
TTTGAATTATTTCAGG
Found at i:16884570 original size:18 final size:18
Alignment explanation
Indices: 16884519--16884570 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
16884509 TTTTAATTTT
16884519 CAATTTCATCTTCTTCCC
1 CAATTTCATCTTCTTCCC
*
16884537 C-A-TT-AT-TTCTTTCC
1 CAATTTCATCTTCTTCCC
16884551 CAATTTCATCTTCTTCCC
1 CAATTTCATCTTCTTCCC
16884569 CA
1 CA
16884571 TTTTTCCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.29
15 3 0.11
16 4 0.14
17 3 0.11
18 10 0.36
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (18 bp):
CAATTTCATCTTCTTCCC
Found at i:16884573 original size:17 final size:17
Alignment explanation
Indices: 16884521--16884573 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
16884511 TTAATTTTCA
16884521 ATTTCATCTTCTTCCCC
1 ATTTCATCTTCTTCCCC
*
16884538 A-TT-AT-TTCTTTCCCA
1 ATTTCATCTTC-TTCCCC
16884553 ATTTCATCTTCTTCCCC
1 ATTTCATCTTCTTCCCC
16884570 ATTT
1 ATTT
16884574 TTCCATCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 3 0.10
15 8 0.27
16 4 0.13
17 12 0.40
18 3 0.10
ACGTcount: A:0.15, C:0.34, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTCATCTTCTTCCCC
Found at i:16884780 original size:99 final size:99
Alignment explanation
Indices: 16884658--16884855 Score: 342
Period size: 99 Copynumber: 2.0 Consensus size: 99
16884648 TTTTGAACCA
* * *
16884658 AACCATGGCTACTTCTCCACTTGGATTCTGAACCAAATCATGGCTTCTTCTTTTTCCATCACTCT
1 AACCATGGCTACTTCTCCACTTGGATTCTGAACCAAACCATGGCTTCTTCTTCTTCCACCACTCT
* *
16884723 TCCAACCCTTCAAGGTTCTTTATTTCAATCTCAT
66 CCCAACCCTTCAAGGTTCTCTATTTCAATCTCAT
*
16884757 AACCATGGCTACTTCTCCACTTGGATTCTGAATCAAACCATGGCTTCTTCTTCTTCCACCACTCT
1 AACCATGGCTACTTCTCCACTTGGATTCTGAACCAAACCATGGCTTCTTCTTCTTCCACCACTCT
16884822 CCCAACCCTTCAAGGTTCTCTATTTCAATCTCAT
66 CCCAACCCTTCAAGGTTCTCTATTTCAATCTCAT
16884856 TTCTTAGGAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 93 1.00
ACGTcount: A:0.22, C:0.32, G:0.09, T:0.36
Consensus pattern (99 bp):
AACCATGGCTACTTCTCCACTTGGATTCTGAACCAAACCATGGCTTCTTCTTCTTCCACCACTCT
CCCAACCCTTCAAGGTTCTCTATTTCAATCTCAT
Found at i:16885508 original size:11 final size:11
Alignment explanation
Indices: 16885476--16885557 Score: 63
Period size: 11 Copynumber: 7.9 Consensus size: 11
16885466 AATATTTTAA
*
16885476 AAAATAATTTC
1 AAAATAATTTT
*
16885487 AAATTAATTTT
1 AAAATAATTTT
16885498 AAAATAATTTT
1 AAAATAATTTT
16885509 --AATAATTTT
1 AAAATAATTTT
16885518 ---AT-ATTTT
1 AAAATAATTTT
16885525 GAAAATATAATTTT
1 --AAA-ATAATTTT
16885539 --AATAATTTT
1 AAAATAATTTT
16885548 AAAATAATTT
1 AAAATAATTT
16885558 GCTAACGTGG
Statistics
Matches: 59, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.08
8 2 0.03
9 17 0.29
10 1 0.02
11 27 0.46
13 2 0.03
14 5 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:16885514 original size:51 final size:50
Alignment explanation
Indices: 16885445--16885557 Score: 165
Period size: 51 Copynumber: 2.2 Consensus size: 50
16885435 GATTAAAATA
*
16885445 TTAAAATAAATTTAATAATTTAATATTTT-AAAAAATAATTTCAAATTAATT
1 TTAAAATAATTTTAATAATTTAATATTTTGAAAAAATAATTT-AAA-TAATT
* * *
16885496 TTAAAATAATTTTAATAATTTTATATTTTGAAAATATAATTTTAATAATT
1 TTAAAATAATTTTAATAATTTAATATTTTGAAAAAATAATTTAAATAATT
16885546 TTAAAATAATTT
1 TTAAAATAATTT
16885558 GCTAACGTGG
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
50 17 0.30
51 29 0.51
52 11 0.19
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (50 bp):
TTAAAATAATTTTAATAATTTAATATTTTGAAAAAATAATTTAAATAATT
Found at i:16885536 original size:21 final size:22
Alignment explanation
Indices: 16885510--16885553 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
16885500 AATAATTTTA
16885510 ATAATTTT-AT-ATTTTGAAAAT
1 ATAATTTTAATAATTTT-AAAAT
16885531 ATAATTTTAATAATTTTAAAAT
1 ATAATTTTAATAATTTTAAAAT
16885553 A
1 A
16885554 ATTTGCTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATAATTTTAATAATTTTAAAAT
Found at i:16897360 original size:18 final size:18
Alignment explanation
Indices: 16897339--16897381 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
16897329 GGCTACATAC
*
16897339 GAGCATGTGATTGCATCT
1 GAGCATGTGACTGCATCT
16897357 GAGCATGTGACTGCATCT
1 GAGCATGTGACTGCATCT
*
16897375 GATCATG
1 GAGCATG
16897382 ATGTGCCTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (18 bp):
GAGCATGTGACTGCATCT
Found at i:16899789 original size:17 final size:18
Alignment explanation
Indices: 16899752--16899791 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
16899742 TAACAAAATG
16899752 ATGCAGTGACAAAATAAA
1 ATGCAGTGACAAAATAAA
* *
16899770 ATGCAGTGATAATA-AAA
1 ATGCAGTGACAAAATAAA
16899787 ATGCA
1 ATGCA
16899792 TTAAAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (18 bp):
ATGCAGTGACAAAATAAA
Found at i:16914537 original size:17 final size:17
Alignment explanation
Indices: 16914481--16914538 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
16914471 AATATATATT
*
16914481 GAAATGCAATGACAAAT
1 GAAATGCAATGACAAAA
* *
16914498 GCAGATGTAATGACAATAA
1 G-AAATGCAATGACAA-AA
*
16914517 -AAATGCAAGGACAAAA
1 GAAATGCAATGACAAAA
16914533 GAAATG
1 GAAATG
16914539 TGATGACAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
16 2 0.06
17 17 0.53
18 12 0.38
19 1 0.03
ACGTcount: A:0.53, C:0.10, G:0.21, T:0.16
Consensus pattern (17 bp):
GAAATGCAATGACAAAA
Found at i:16924740 original size:51 final size:51
Alignment explanation
Indices: 16924659--16924895 Score: 350
Period size: 51 Copynumber: 4.6 Consensus size: 51
16924649 GCTATAAACG
* *
16924659 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATTACGGATT
* *
16924711 AAAGGTCCGGTGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATTACGGATT
* * *
16924762 AAAGGTCTGATGACTAAATGCCATCGTGAGTAAATGAATCCATTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATTACGGATT
* *
16924813 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATTACGGATT
* *
16924864 CAAGGTCCGATGAC-AATATGTCATCGTGAGTA
1 AAAGGTCCGATGACTAA-GTGTCATCGTGAGTA
16924896 TTAAATGAAA
Statistics
Matches: 170, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
50 2 0.01
51 164 0.96
52 4 0.02
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATTACGGATT
Found at i:16932027 original size:51 final size:51
Alignment explanation
Indices: 16931947--16932175 Score: 316
Period size: 51 Copynumber: 4.5 Consensus size: 51
16931937 CGAAAGAGTC
16931947 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTT
* * * *
16931998 CGGTGACTAAGTGTCATCGTGAGTGAATGAATCCTTTACAGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTT
* *
16932049 CGATGACTAAATGTCATCGTGAGTAAATGAACCCTTTACGGATTAAAGGTT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTT
* * * * * *
16932100 CGATGACTAAGTGTCATCATGTGTAAATGAATCCATGACGAATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTT
* *
16932151 CGATGAC-AATATGTCATCTTGAGTA
1 CGATGACTAA-GTGTCATCGTGAGTA
16932176 TTAAATGAAA
Statistics
Matches: 156, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
50 2 0.01
51 154 0.99
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (51 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTT
Found at i:16932129 original size:102 final size:102
Alignment explanation
Indices: 16931939--16932175 Score: 352
Period size: 102 Copynumber: 2.3 Consensus size: 102
16931929 GCTATAAACG
* * *
16931939 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTTCGGTGA
1 AAAG-GTCCGATGACTAAATGTCATCGTGAGTAAATGAACCCTTTACGGATTAAAGGTTCGATGA
* * * *
16932004 CTAAGTGTCATCGTGAGTGAATGAATCCTTTAC-AGATT
65 CTAAGTGTCATCATGAGTAAATGAATCCATGACGA-ATT
16932042 AAAGGTCCGATGACTAAATGTCATCGTGAGTAAATGAACCCTTTACGGATTAAAGGTTCGATGAC
1 AAAGGTCCGATGACTAAATGTCATCGTGAGTAAATGAACCCTTTACGGATTAAAGGTTCGATGAC
*
16932107 TAAGTGTCATCATGTGTAAATGAATCCATGACGAATT
66 TAAGTGTCATCATGAGTAAATGAATCCATGACGAATT
*
16932144 AAAGGTCCGATGAC-AATATGTCATCTTGAGTA
1 AAAGGTCCGATGACTAA-ATGTCATCGTGAGTA
16932176 TTAAATGAAA
Statistics
Matches: 123, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
101 2 0.02
102 116 0.94
103 5 0.04
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (102 bp):
AAAGGTCCGATGACTAAATGTCATCGTGAGTAAATGAACCCTTTACGGATTAAAGGTTCGATGAC
TAAGTGTCATCATGAGTAAATGAATCCATGACGAATT
Found at i:16932899 original size:21 final size:21
Alignment explanation
Indices: 16932875--16932921 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
16932865 GTTTTTAGTT
* *
16932875 TCGGTAGATACATGACTTGTA
1 TCGGTAGAAACATCACTTGTA
**
16932896 TCGGTAGAAATTTCACTTGTA
1 TCGGTAGAAACATCACTTGTA
16932917 TCGGT
1 TCGGT
16932922 TGAACTAGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TCGGTAGAAACATCACTTGTA
Found at i:16937914 original size:3 final size:3
Alignment explanation
Indices: 16937908--16937957 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
16937898 TAATAATAAG
*
16937908 AAC AAC AAC AAC AAC GAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
16937956 AA
1 AA
16937958 TAATAATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.66, C:0.32, G:0.02, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:16943934 original size:57 final size:57
Alignment explanation
Indices: 16943803--16943926 Score: 146
Period size: 57 Copynumber: 2.2 Consensus size: 57
16943793 GATGATAAAT
* ** *
16943803 TGAGTCATAAAGCTGTTCAAAATAAGGTTATTCAAGCTGTTTATATTGATGTTTAAC
1 TGAGTCATAAAGCTGTCCAAAATAAGGTTATTCAAGCTGTCCATATTGATATTTAAC
* *
16943860 TGAGTCA-AAATGCTGTCCAAATTAAGGTTATTCATGCTGTCCAT-TTGGATATCTTAA-
1 TGAGTCATAAA-GCTGTCCAAAATAAGGTTATTCAAGCTGTCCATATT-GATAT-TTAAC
16943917 TGAGTCATAA
1 TGAGTCATAA
16943927 GGTTGTCCTA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
56 5 0.09
57 46 0.81
58 6 0.11
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (57 bp):
TGAGTCATAAAGCTGTCCAAAATAAGGTTATTCAAGCTGTCCATATTGATATTTAAC
Found at i:16944243 original size:26 final size:27
Alignment explanation
Indices: 16944187--16944243 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
16944177 AACGAGATGT
* *
16944187 TGTTGTATAATAAAGTTACAATAATTG
1 TGTTGTATAATAAAGTTACAATAAATA
* * *
16944214 TGTTTTAT-ATAAAGTTGCATTAAATA
1 TGTTGTATAATAAAGTTACAATAAATA
16944240 TGTT
1 TGTT
16944244 AGAAATGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.46
Consensus pattern (27 bp):
TGTTGTATAATAAAGTTACAATAAATA
Found at i:16948053 original size:79 final size:79
Alignment explanation
Indices: 16947918--16948116 Score: 267
Period size: 79 Copynumber: 2.5 Consensus size: 79
16947908 CCAATGATCA
* * * * ** *
16947918 TGGCACCTAGTGCCTAGTGGATAAACCGCAAGTGTGAGCCTAGCTCTAGTTTGATTAACCAACAA
1 TGGCACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAAATCTAGTTGGATTAACCAACAA
16947983 TGTCCGTCAAATCC
66 TGTCCGTCAAATCC
* *
16947997 TGGCACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCCAAATTTAGTTGGATTAACCAACAA
1 TGGCACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAAATCTAGTTGGATTAACCAACAA
* *
16948062 TGTCTGTCAAATCT
66 TGTCCGTCAAATCC
*
16948076 TGGCTCCCAGTGCCTAGC-GATTAAACCGC-AATGTGAGCCCA
1 TGGCACCCAGTGCCTAGCGGA-TAAACCGCAAATGTGAGCCCA
16948117 GCTCTAGTCA
Statistics
Matches: 106, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
78 13 0.12
79 93 0.88
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (79 bp):
TGGCACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAAATCTAGTTGGATTAACCAACAA
TGTCCGTCAAATCC
Found at i:16948561 original size:2 final size:2
Alignment explanation
Indices: 16948554--16948581 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16948544 ACACATACTC
16948554 AT 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 AT
16948582 TTCCTATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16949040 original size:26 final size:25
Alignment explanation
Indices: 16949010--16949058 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
16949000 ATGGAGCTTC
16949010 TTCTTATTCTTTTGTTTCTAATTTCT
1 TTCTTATTCTTTT-TTTCTAATTTCT
* *
16949036 TTCTTCTTCTTTTTTTCTTATTT
1 TTCTTATTCTTTTTTTCTAATTT
16949059 TGTGAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.08, C:0.16, G:0.02, T:0.73
Consensus pattern (25 bp):
TTCTTATTCTTTTTTTCTAATTTCT
Found at i:16953194 original size:5 final size:5
Alignment explanation
Indices: 16953180--16953232 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
16953170 GTTGTAGATA
* * * *
16953180 TTATT CTATT TTATT CTATT TTATT TTATT TATTTT TTATT TTTTCT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT T-TATT TTATT TTAT-T TTATT
16953232 T
1 T
16953233 AATTAATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 30 0.79
6 8 0.21
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:16962330 original size:51 final size:51
Alignment explanation
Indices: 16962250--16962373 Score: 162
Period size: 51 Copynumber: 2.4 Consensus size: 51
16962240 TCATTTAATG
* * * *
16962250 CTCACGATGACA-TATTGTCAGT-GGGCCTTTAATTCGTCATGGATTCATTTA
1 CTCACGATGACACT-TAGTCA-TCGGGCCTTTAATCCGTAAAGGATTCATTTA
*
16962301 CTCACGATGACACTTAGTCATCGGTCCTTTAATCCGTAAAGGATTCATTTA
1 CTCACGATGACACTTAGTCATCGGGCCTTTAATCCGTAAAGGATTCATTTA
*
16962352 CTCACGATGACACTTAGACATC
1 CTCACGATGACACTTAGTCATC
16962374 AAATCAGCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 1 0.02
51 63 0.97
52 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (51 bp):
CTCACGATGACACTTAGTCATCGGGCCTTTAATCCGTAAAGGATTCATTTA
Found at i:16964328 original size:21 final size:21
Alignment explanation
Indices: 16964281--16964333 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
16964271 TTGTACTAGT
* *
16964281 TCTACCGATACAAGTGAAATT
1 TCTACCGATACAAGTCAAATA
* **
16964302 TTTACCGATACAAGTCATGTA
1 TCTACCGATACAAGTCAAATA
*
16964323 TCTACCAATAC
1 TCTACCGATAC
16964334 TAAAAACTCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (21 bp):
TCTACCGATACAAGTCAAATA
Found at i:16965104 original size:51 final size:51
Alignment explanation
Indices: 16965031--16965267 Score: 318
Period size: 51 Copynumber: 4.6 Consensus size: 51
16965021 TTTCATTTAA
* * * * *
16965031 TACTCACGATGACA-TATTGTCATCGGACCTTTAATTCATCATGGATTCATT
1 TACTCACGATGACACT-TAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
16965082 TACTCACGATGACACTTAGTCATCGGACCTTTCATCCGTAAATGG-TTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAA-GGATTCATT
* * *
16965133 TACTCATGATGACATTTAGTCATCGGACCTTTAATCCGTAAAAGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
16965184 TACTCACGATGACACTTAGTCA-CTAGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATC-GGACCTTTAATCCGTAAAGGATTCATT
*
16965235 TACTCACGATGATACTTAGTCATCGGACTCTTT
1 TACTCACGATGACACTTAGTCATCGGAC-CTTT
16965268 CGTTTATAGC
Statistics
Matches: 164, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
50 2 0.01
51 154 0.94
52 8 0.05
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:16971123 original size:23 final size:23
Alignment explanation
Indices: 16971080--16971131 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
16971070 TGATCTAAAC
** *
16971080 AAAATTACAAACGGTTAGGATAT
1 AAAATTACAAACAATTAGGATAA
*
16971103 AAAATTACAAACAATTTGGATAA
1 AAAATTACAAACAATTAGGATAA
16971126 AAAATT
1 AAAATT
16971132 GAGAGAAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.12, T:0.27
Consensus pattern (23 bp):
AAAATTACAAACAATTAGGATAA
Found at i:16971615 original size:65 final size:65
Alignment explanation
Indices: 16971531--16971666 Score: 263
Period size: 65 Copynumber: 2.1 Consensus size: 65
16971521 ATGGGGAAAT
16971531 CTTTGGTAATCAAACTGATTGGATGGGGTATCGGTTTCAATGCTCTTCTCAATAGGATTCAGCTG
1 CTTTGGTAATCAAACTGATTGGATGGGGTATCGGTTTCAATGCTCTTCTCAATAGGATTCAGCTG
*
16971596 CTTTGGTAATCAAATTGATTGGATGGGGTATCGGTTTCAATGCTCTTCTCAATAGGATTCAGCTG
1 CTTTGGTAATCAAACTGATTGGATGGGGTATCGGTTTCAATGCTCTTCTCAATAGGATTCAGCTG
16971661 CTTTGG
1 CTTTGG
16971667 AAACAAAGTC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 70 1.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (65 bp):
CTTTGGTAATCAAACTGATTGGATGGGGTATCGGTTTCAATGCTCTTCTCAATAGGATTCAGCTG
Found at i:16989177 original size:15 final size:13
Alignment explanation
Indices: 16989153--16989191 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
16989143 TGCATATGCA
16989153 TACATGCATTCAT
1 TACATGCATTCAT
16989166 TAGCATTGCATTTCAT
1 TA-CA-TGCA-TTCAT
16989182 TACATGCATT
1 TACATGCATT
16989192 AAATTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 6 0.26
16 7 0.30
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (13 bp):
TACATGCATTCAT
Found at i:17000867 original size:11 final size:11
Alignment explanation
Indices: 17000840--17000869 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
17000830 AACTCGTGCA
17000840 TCCAAAAACAC
1 TCCAAAAACAC
17000851 TCCCAAAAACAC
1 T-CCAAAAACAC
17000863 TCCAAAA
1 TCCAAAA
17000870 CCTTCATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.37, G:0.00, T:0.10
Consensus pattern (11 bp):
TCCAAAAACAC
Found at i:17002625 original size:18 final size:19
Alignment explanation
Indices: 17002599--17002636 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17002589 CGGTTGGTTC
17002599 GAGGGGCAA-GAAAAGAAA
1 GAGGGGCAAGGAAAAGAAA
* *
17002617 GAGGTGCAAGGGAAAGAAA
1 GAGGGGCAAGGAAAAGAAA
17002636 G
1 G
17002637 TGAAGAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.50, C:0.05, G:0.42, T:0.03
Consensus pattern (19 bp):
GAGGGGCAAGGAAAAGAAA
Found at i:17005111 original size:20 final size:20
Alignment explanation
Indices: 17005074--17005114 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17005064 GTCTATCAAC
*
17005074 TATACTTGCATCGACGTGTG
1 TATACTTGCATCAACGTGTG
17005094 TATACTTGCAT-AATCGTGTG
1 TATACTTGCATCAA-CGTGTG
17005114 T
1 T
17005115 CGTAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (20 bp):
TATACTTGCATCAACGTGTG
Found at i:17006089 original size:49 final size:49
Alignment explanation
Indices: 17006035--17006489 Score: 328
Period size: 49 Copynumber: 9.3 Consensus size: 49
17006025 AACGGCATAC
* * * *
17006035 CTAACACCATAAAATCGAAGAGGGATAGATTGAAGCAGTAATGGCAAAT
1 CTAACACCTTAAAATCGAAGAGGGATAGATTGAAGCAGTAACGGTAGAT
* * * * *
17006084 TTAACACCCTAAAATCGAAGAGGGAAAGATTGAAGCCGTAACGGTGGAT
1 CTAACACCTTAAAATCGAAGAGGGATAGATTGAAGCAGTAACGGTAGAT
* * * * * * * *
17006133 CTTACACCTTAAAATTGAAGAGGAATAGGTTGAAGCTGTAACGATGGAC
1 CTAACACCTTAAAATCGAAGAGGGATAGATTGAAGCAGTAACGGTAGAT
* * * * * * **
17006182 CTAAAACCTTAAAACCAAAGAGGGAAAGATCGAAGTCA-CAACAATAGAT
1 CTAACACCTTAAAATCGAAGAGGGATAGATTGAAG-CAGTAACGGTAGAT
* * * * * *
17006231 CTTACACCTTAAAATTGAAGAGGGATAGGTTGAAGC-GATAATGGCAGAC
1 CTAACACCTTAAAATCGAAGAGGGATAGATTGAAGCAG-TAACGGTAGAT
* * *
17006280 CTAACACCTTAAAACCAAAGAGGGATAGATTGAAGCCGTAACGGT-GAAT
1 CTAACACCTTAAAATCGAAGAGGGATAGATTGAAGCAGTAACGGTAG-AT
* * * * * * **
17006329 CTAACACCCTAAAATCAAAAAGAGGA-AGATTGAAACCACT-ATGACAGAT
1 CTAACACCTTAAAATCGAAGAG-GGATAGATTG-AAGCAGTAACGGTAGAT
* * * * * *
17006378 CTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGTC-GCAACGATAAAC
1 CTAACACCTTAAAATCGAAGAGGGATAGATTGAAG-CAGTAACGGTAGAT
* ** * * *
17006427 CTAACACCCTAAAATTAAAGAGGGATAGATTGAAGCTGTAATGGTGGAT
1 CTAACACCTTAAAATCGAAGAGGGATAGATTGAAGCAGTAACGGTAGAT
17006476 CTAACACCTTAAAA
1 CTAACACCTTAAAA
17006490 CAAAAAAGAG
Statistics
Matches: 307, Mismatches: 87, Indels: 24
0.73 0.21 0.06
Matches are distributed among these distances:
48 8 0.03
49 289 0.94
50 10 0.03
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.20
Consensus pattern (49 bp):
CTAACACCTTAAAATCGAAGAGGGATAGATTGAAGCAGTAACGGTAGAT
Found at i:17006195 original size:98 final size:98
Alignment explanation
Indices: 17006035--17006636 Score: 460
Period size: 98 Copynumber: 6.1 Consensus size: 98
17006025 AACGGCATAC
* * * **** ** *
17006035 CTAACACCATAAAATCGAAGAGGGATAGATTGAAGCAGTAATGGCAAATTTAACACCCTAAAATC
1 CTAACACCTTAAAATTGAAGAGGGATAGGTTGAAGCAGTAATGATGGACCTAACACCTTAAAATC
* ** *
17006100 GAAGAGGGAAAGATTGAAGCCGTAACGGTGGAT
66 AAAGAGGGAAAGATTGAAGCCACAACGATGGAT
* * * * * *
17006133 CTTACACCTTAAAATTGAAGAGGAATAGGTTGAAGCTGTAACGATGGACCTAAAACCTTAAAACC
1 CTAACACCTTAAAATTGAAGAGGGATAGGTTGAAGCAGTAATGATGGACCTAACACCTTAAAATC
* * * *
17006198 AAAGAGGGAAAGATCGAAGTCACAACAATAGAT
66 AAAGAGGGAAAGATTGAAGCCACAACGATGGAT
* *** *
17006231 CTTACACCTTAAAATTGAAGAGGGATAGGTTGAAGC-GATAATGGCAGACCTAACACCTTAAAAC
1 CTAACACCTTAAAATTGAAGAGGGATAGGTTGAAGCAG-TAATGATGGACCTAACACCTTAAAAT
* ** * *
17006295 CAAAGAGGGATAGATTGAAGCCGTAACGGTGAAT
65 CAAAGAGGGAAAGATTGAAGCCACAACGATGGAT
* ** * * * * ** * *
17006329 CTAACACCCTAAAATCAAAAAGAGGA-AGATTGAAACCACT-ATGACAGATCTTACACCTTAAAA
1 CTAACACCTTAAAATTGAAGAG-GGATAGGTTG-AAGCAGTAATGATGGACCTAACACCTTAAAA
* * * * * ** *
17006392 TCGAAGAGGGATAGGTTGAAGTCGCAACGATAAAC
64 TCAAAGAGGGAAAGATTGAAGCCACAACGATGGAT
* * * * * *
17006427 CTAACACCCTAAAATTAAAGAGGGATAGATTGAAGCTGTAATGGTGGATCTAACACCTTAAAA-C
1 CTAACACCTTAAAATTGAAGAGGGATAGGTTGAAGCAGTAATGATGGACCTAACACCTTAAAATC
* * * * * *
17006491 AAAAAAGAGAGAGATTAAAGCCACAATGACGGAT
66 -AAAGAGGGAAAGATTGAAGCCACAACGATGGAT
* * * * * *
17006525 CTTACAACTTAAAATTGAAGAGGGATAAGTTAAAGCCAG-AATGATGAACTTAACACCTTAAAAT
1 CTAACACCTTAAAATTGAAGAGGGATAGGTTGAAG-CAGTAATGATGGACCTAACACCTTAAAAT
*
17006589 CAAATAGGGATAA-ATTGAAGCCACAACGATGGAT
65 CAAAGAGGGA-AAGATTGAAGCCACAACGATGGAT
17006623 CTAACACCTTAAAA
1 CTAACACCTTAAAA
17006637 CCAATGAGTG
Statistics
Matches: 394, Mismatches: 100, Indels: 20
0.77 0.19 0.04
Matches are distributed among these distances:
97 9 0.02
98 374 0.95
99 11 0.03
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (98 bp):
CTAACACCTTAAAATTGAAGAGGGATAGGTTGAAGCAGTAATGATGGACCTAACACCTTAAAATC
AAAGAGGGAAAGATTGAAGCCACAACGATGGAT
Found at i:17006287 original size:147 final size:147
Alignment explanation
Indices: 17006035--17006682 Score: 563
Period size: 147 Copynumber: 4.4 Consensus size: 147
17006025 AACGGCATAC
* * * * * * * * *
17006035 CTAACACCATAAAATCGAAGAGGGATAGATTGAAG-CAGTAATGGCAAAT-TTAACACCCTAAAA
1 CTAACACCTTAAAACCAAAAAGGGAAAGATTGAAGCCA-CAATGACAGATCTT-ACACCTTAAAA
* * * * * ** * *
17006098 TCGAAGAGGGAAAGATTGAAGCCGTAACGGTGGATCTTACACCTTAAAATTGAAGAGGAATAGGT
64 TCGAAGAGGGATAGGTTGAAGCCGTAACGGTAGACCTAACACCTTAAAATCAAAGAGGGATAGAT
* *
17006163 TGAAGCTGTAACGATGGAC
129 TGAAGCCGTAACGATGGAT
* * * * ** * *
17006182 CTAAAACCTTAAAACCAAAGAGGGAAAGATCGAAGTCACAACAATAGATCTTACACCTTAAAATT
1 CTAACACCTTAAAACCAAAAAGGGAAAGATTGAAGCCACAATGACAGATCTTACACCTTAAAATC
* * *
17006247 GAAGAGGGATAGGTTGAAG-CGATAATGGCAGACCTAACACCTTAAAACCAAAGAGGGATAGATT
66 GAAGAGGGATAGGTTGAAGCCG-TAACGGTAGACCTAACACCTTAAAATCAAAGAGGGATAGATT
* *
17006311 GAAGCCGTAACGGTGAAT
130 GAAGCCGTAACGATGGAT
* * * *
17006329 CTAACACCCTAAAATCAAAAAGAGG-AAGATTGAAACCACTATGACAGATCTTACACCTTAAAAT
1 CTAACACCTTAAAACCAAAAAG-GGAAAGATTGAAGCCACAATGACAGATCTTACACCTTAAAAT
* * * * * *
17006393 CGAAGAGGGATAGGTTGAAGTCGCAACGATAAACCTAACACCCTAAAATTAAAGAGGGATAGATT
65 CGAAGAGGGATAGGTTGAAGCCGTAACGGTAGACCTAACACCTTAAAATCAAAGAGGGATAGATT
* * *
17006458 GAAGCTGTAATGGTGGAT
130 GAAGCCGTAACGATGGAT
* * * * * * *
17006476 CTAACACCTTAAAACAAAAAAGAGAGAGATTAAAGCCACAATGACGGATCTTACAACTTAAAATT
1 CTAACACCTTAAAACCAAAAAGGGAAAGATTGAAGCCACAATGACAGATCTTACACCTTAAAATC
* * * * * * *
17006541 GAAGAGGGATAAGTTAAAGCCAG-AATGAT-GAACTTAACACCTTAAAATCAAATAGGGATAAAT
66 GAAGAGGGATAGGTTGAAGCC-GTAACGGTAG-ACCTAACACCTTAAAATCAAAGAGGGATAGAT
**
17006604 TGAAGCCACAACGATGGAT
129 TGAAGCCGTAACGATGGAT
** * ** *
17006623 CTAACACCTTAAAACCAATGAGTGAATAGATTGAAGCTGCAATGGC-GAATCTTACACCTT
1 CTAACACCTTAAAACCAAAAAGGGAA-AGATTGAAGCCACAATGACAG-ATCTTACACCTT
17006683 TTGAAAAAAA
Statistics
Matches: 402, Mismatches: 89, Indels: 19
0.79 0.17 0.04
Matches are distributed among these distances:
146 3 0.01
147 364 0.91
148 35 0.09
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (147 bp):
CTAACACCTTAAAACCAAAAAGGGAAAGATTGAAGCCACAATGACAGATCTTACACCTTAAAATC
GAAGAGGGATAGGTTGAAGCCGTAACGGTAGACCTAACACCTTAAAATCAAAGAGGGATAGATTG
AAGCCGTAACGATGGAT
Found at i:17006525 original size:49 final size:46
Alignment explanation
Indices: 17006472--17006637 Score: 134
Period size: 49 Copynumber: 3.4 Consensus size: 46
17006462 CTGTAATGGT
* *
17006472 GGATCTAACACCTTAAAACAAAAAAGAGAGAGATTAAAGCCACAATGA
1 GGATCTAACACCTTAAAAC-AAAAAGGGATA-ATTAAAGCCACAATGA
* * ** * *
17006520 CGGATCTTACAACTTAAAATTGAAGAGGGATAAGTTAAAGCCAGAATGA
1 -GGATCTAACACCTTAAAA-CAAAAAGGGATAA-TTAAAGCCACAATGA
* * * * *
17006569 TGAACTTAACACCTTAAAATCAAATAGGGATAAATTGAAGCCACAACGA
1 GGATC-TAACACCTTAAAA-CAAAAAGGGAT-AATTAAAGCCACAATGA
17006618 TGGATCTAACACCTTAAAAC
1 -GGATCTAACACCTTAAAAC
17006638 CAATGAGTGA
Statistics
Matches: 92, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
48 5 0.05
49 82 0.89
50 5 0.05
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (46 bp):
GGATCTAACACCTTAAAACAAAAAGGGATAATTAAAGCCACAATGA
Found at i:17006974 original size:42 final size:42
Alignment explanation
Indices: 17006915--17007271 Score: 301
Period size: 42 Copynumber: 8.5 Consensus size: 42
17006905 TTACATCATC
* *
17006915 CCATCCAATCTTTTACCCTAACCAGAGGGCAGATTAAAGACA
1 CCATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACA
* **
17006957 CCATCCAATCTCTTACCCCGACCATG-GGGCAAATTGAAG---
1 CCATCCAATCTTTTACCCTAACCA-GAGGGCAAATTGAAGACA
* *
17006996 CCATCCAATCTTTTACCCTAACCGGAAGGCAAATTGAAGACA
1 CCATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACA
* * * *
17007038 CCATCCAATCTCTTACCATGACCATG-GGACAAATTG-A-A-A
1 CCATCCAATCTTTTACCCTAACCA-GAGGGCAAATTGAAGACA
*
17007077 CCATCCAATCTTTTACCCTAACCAGAGGTCAAATTGAAGACA
1 CCATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACA
* * * *
17007119 CCATCCAATCTCTTACCCTGACCATG-GGGCAGA-T--AGAAA
1 CCATCCAATCTTTTACCCTAACCA-GAGGGCAAATTGAAGACA
* * *
17007158 CCAACCAGTCTTTTACCCCTAATCCAGAAGGGCAGATTGAAG-CAA
1 CCATCCAATCTTTTA-CCCTAA-CCAG-AGGGCAAATTGAAGAC-A
* *
17007203 CCATTCAATCTTTTACCTCTAATCCAGAGGG-ATAGATTGAAGTCA
1 CCATCCAATCTTTTACC-CTAA-CCAGAGGGCA-A-ATTGAAGACA
17007248 CCAAATCCAATCTTTTATCCCTAA
1 CC--ATCCAATCTTTTA-CCCTAA
17007272 ATCCAAGGGG
Statistics
Matches: 254, Mismatches: 35, Indels: 47
0.76 0.10 0.14
Matches are distributed among these distances:
38 2 0.01
39 79 0.31
40 8 0.03
41 6 0.02
42 95 0.37
43 5 0.02
44 6 0.02
45 34 0.13
46 1 0.00
47 16 0.06
48 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (42 bp):
CCATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACA
Found at i:17007050 original size:81 final size:81
Alignment explanation
Indices: 17006915--17007219 Score: 416
Period size: 81 Copynumber: 3.7 Consensus size: 81
17006905 TTACATCATC
* * * *
17006915 CCATCCAATCTTTTACCCTAACCAGAGGGCAGATTAAAGACACCATCCAATCTCTTACCCCGACC
1 CCATCCAATCTTTTACCCTAACCAGAAGGCAAATTGAAGACACCATCCAATCTCTTACCCTGACC
*
17006980 ATGGGGCAAATTGAAG
66 ATGGGGCAAATTGAAA
* *
17006996 CCATCCAATCTTTTACCCTAACCGGAAGGCAAATTGAAGACACCATCCAATCTCTTACCATGACC
1 CCATCCAATCTTTTACCCTAACCAGAAGGCAAATTGAAGACACCATCCAATCTCTTACCCTGACC
*
17007061 ATGGGACAAATTGAAA
66 ATGGGGCAAATTGAAA
17007077 CCATCCAATCTTTTACCCTAACCAG-AGGTCAAATTGAAGACACCATCCAATCTCTTACCCTGAC
1 CCATCCAATCTTTTACCCTAACCAGAAGG-CAAATTGAAGACACCATCCAATCTCTTACCCTGAC
* *
17007141 CATGGGGCAGATAGAAA
65 CATGGGGCAAATTGAAA
* * * * *
17007158 CCAACCAGTCTTTTACCCCTAATCCAGAAGGGCAGATTGAAG-CAACCATTCAATCTTTTACC
1 CCATCCAATCTTTTA-CCCTAA-CCAGAA-GGCAAATTGAAGAC-ACCATCCAATCTCTTACC
17007220 TCTAATCCAG
Statistics
Matches: 200, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
80 3 0.01
81 158 0.79
82 6 0.03
83 5 0.03
84 26 0.13
85 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (81 bp):
CCATCCAATCTTTTACCCTAACCAGAAGGCAAATTGAAGACACCATCCAATCTCTTACCCTGACC
ATGGGGCAAATTGAAA
Found at i:17008016 original size:24 final size:26
Alignment explanation
Indices: 17007969--17008016 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
17007959 TTTTATTATT
17007969 ATTTATATTTAGTTGTTTATTTTGAC
1 ATTTATATTTAGTTGTTTATTTTGAC
17007995 ATTTA-ATTTA-TTGATTT-TTTTG
1 ATTTATATTTAGTTG-TTTATTTTG
17008017 TTGATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.23, C:0.02, G:0.10, T:0.65
Consensus pattern (26 bp):
ATTTATATTTAGTTGTTTATTTTGAC
Found at i:17008119 original size:12 final size:13
Alignment explanation
Indices: 17008097--17008138 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
17008087 TCTTTTAGCA
17008097 TTTTATT-TTTAT
1 TTTTATTATTTAT
17008109 TTTT-TTATTTAT
1 TTTTATTATTTAT
17008121 CTTGTTATTATTTAT
1 -TT-TTATTATTTAT
17008136 TTT
1 TTT
17008139 CATGCCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.08
12 9 0.35
13 3 0.12
14 4 0.15
15 8 0.31
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:17009029 original size:16 final size:16
Alignment explanation
Indices: 17009004--17009034 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17008994 CGAGCTTTTT
*
17009004 ATTTTCAATAATTAAG
1 ATTTTAAATAATTAAG
17009020 ATTTTAAATAATTAA
1 ATTTTAAATAATTAA
17009035 TTAGGTACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
ATTTTAAATAATTAAG
Found at i:17010548 original size:42 final size:40
Alignment explanation
Indices: 17010496--17010574 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 40
17010486 GGAGTTTTTA
** *
17010496 GTATCAGTAGATGTATAACTTGTTTCGATAGAAGAGTCTCTT
1 GTATCAGTAGAACTATAACTTGTATCGATA-AA-AGTCTCTT
* *
17010538 GTATCGGTAGAACTATCACTTGTATCGATAAAAGTCT
1 GTATCAGTAGAACTATAACTTGTATCGATAAAAGTCT
17010575 GCATTGTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 5 0.16
41 2 0.06
42 25 0.78
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35
Consensus pattern (40 bp):
GTATCAGTAGAACTATAACTTGTATCGATAAAAGTCTCTT
Found at i:17017089 original size:35 final size:36
Alignment explanation
Indices: 17017024--17017096 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 36
17017014 TAGGCATGGT
17017024 CTTCGGGTCAACAAGGAGTAAAATGAGCATCATGAC
1 CTTCGGGTCAACAAGGAGTAAAATGAGCATCATGAC
17017060 CTTCGGGTCAAC-AGGAAG-AAAATGAGCATCATGAC
1 CTTCGGGTCAACAAGG-AGTAAAATGAGCATCATGAC
17017095 CT
1 CT
17017097 CAAGGTCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 22 0.61
36 14 0.39
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (36 bp):
CTTCGGGTCAACAAGGAGTAAAATGAGCATCATGAC
Found at i:17017104 original size:35 final size:35
Alignment explanation
Indices: 17017024--17017120 Score: 108
Period size: 35 Copynumber: 2.7 Consensus size: 35
17017014 TAGGCATGGT
*
17017024 CTTCGGGTCAACAAGG-AGTAAAATGAGCATCATGAC
1 CTTCAGGTCAAC-AGGAAG-AAAATGAGCATCATGAC
*
17017060 CTTCGGGTCAACAGGAAGAAAATGAGCATCATGAC
1 CTTCAGGTCAACAGGAAGAAAATGAGCATCATGAC
* *
17017095 C-TCAAGGTCAATAGGGAATAAAATGA
1 CTTC-AGGTCAACA-GGAAGAAAATGA
17017121 ATAACGATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
34 2 0.04
35 28 0.51
36 25 0.45
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.19
Consensus pattern (35 bp):
CTTCAGGTCAACAGGAAGAAAATGAGCATCATGAC
Found at i:17017504 original size:3 final size:3
Alignment explanation
Indices: 17017496--17017560 Score: 103
Period size: 3 Copynumber: 21.3 Consensus size: 3
17017486 AAAGGCCCAA
* *
17017496 ATT ATT ATT ATC ATT ACT ATT ATT ATT AATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
17017542 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
17017561 GGGTTTCATG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:17018458 original size:144 final size:147
Alignment explanation
Indices: 17017979--17018621 Score: 797
Period size: 144 Copynumber: 4.4 Consensus size: 147
17017969 GATTTTGGAA
* * * * * * *
17017979 AAAGTTTTGATTTTTTTAAACAAATTCAAAATTAAAGCTTT-GATTTTTAAGTAAAATAGTGATT
1 AAAGTTTTTATTTTTTTTAACTATTTCGAAATAAAAG-TTTAGATTTTTAAGTAAAGTAGTGATT
** * *
17018043 TTTTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAAT-TG----TT--TT-TTTT-AGAA
65 TTCATTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAAA
* *
17018099 AAGTTTAAATTTTCAAAC
130 AAATTTAAATTTTTAAAC
*
17018117 AAAGTTTTTATTTTTTTTAACTATTTCGAAATAAAAATTTAGA-TTTTAAG-AAAGTAGTGATTT
1 AAAGTTTTTATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTT
* *
17018180 TCATTAAAAAAAAGAATGTTTATATTTATTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGA
66 TCATTAAAAAAAAGAAAGTTTAGATTT-TTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAA-A
17018245 AAAAGTTTAAATTTTTAAAC
129 AAAA-TTTAAATTTTTAAAC
*
17018265 --AGTTTTTA-TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTT
1 AAAGTTTTTATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTT
* *
17018327 TCATTAAAAAAAAGAAATTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTT-AAAAA
66 TCATTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAAAA
*
17018391 AA-TTAAATTTTTAAAT
131 AATTTAAATTTTTAAAC
** *
17018407 AATTTTTTTA-TTTTTTTAACTACTTCGAAATGAAAA-TTTAGATTTTTAAGTAAAGTAGTGATT
1 AAAGTTTTTATTTTTTTTAACTATTTCGAAAT-AAAAGTTTAGATTTTTAAGTAAAGTAGTGATT
* * *
17018470 TTCATT-AAAAAAATAAAGTTTAGATTTTTAAAAAATAAAAATCTATTTTTTAGTGATTTTAAAG
65 TTCATTAAAAAAAAGAAAGTTTAGATTTTT-AAAAATAAAAATCTGTTTTTTAGTTATTTT--A-
17018534 AAAAAAATTTAAATTTTTAAAC
126 AAAAAAATTTAAATTTTTAAAC
* *
17018556 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTCTT-GATTTTGAAGTAAAGTAGTGATT
1 AAAGTTTTTATTTTTTTTAACTATTTCGAAATAAAAGT-TTAGATTTTTAAGTAAAGTAGTGATT
17018620 TT
65 TT
17018622 GTTTTAATCA
Statistics
Matches: 442, Mismatches: 36, Indels: 42
0.85 0.07 0.08
Matches are distributed among these distances:
136 34 0.08
137 24 0.05
138 34 0.08
142 15 0.03
143 20 0.05
144 93 0.21
145 40 0.09
146 48 0.11
147 42 0.10
148 21 0.05
149 24 0.05
150 45 0.10
151 2 0.00
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (147 bp):
AAAGTTTTTATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTT
TCATTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAAAA
AATTTAAATTTTTAAAC
Found at i:17018513 original size:290 final size:284
Alignment explanation
Indices: 17017980--17018621 Score: 864
Period size: 283 Copynumber: 2.2 Consensus size: 284
17017970 ATTTTGGAAA
* * * * *
17017980 AAGTTTTGATTTTTTTAAACAAATTCAAAATTAAAGCTTTGATTTTTAAGTAAAATAGTGATTTT
1 AAGTTTTGATTTTTTT-AACTATTTCGAAATAAAAG-TTTGATTTTTAAGTAAAGTAGTGATTTT
** * * **
17018045 TTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATTGTTTTTTTTAGAAAAGTTTAAATT
64 CATTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATTGTTTTTTTTAAAAAAAATTAAATT
*
17018110 TTCAAACAAAGTTTTTATTTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTAAGAAAGTAGT
129 TTCAAACAAAGTTTTTATTTTTTTTAACTACTTCGAAATAAAAATTTAGATTTTAAGAAAGTAGT
* * *
17018175 GATTTTCATTAAAAAAAAGAATGTTTATATTTATTAAAAATAAAAATCTGTTTTTTAGTTATTTT
194 GATTTTCATTAAAAAAAAGAATGTTTAGATTTATTAAAAATAAAAATCTATTTTTTAGTGATTTT
*
17018240 AAAG-AAAAAGTTTAAATTTTTAAAC
259 AAAGAAAAAAATTTAAATTTTTAAAC
*
17018265 -AGTTTTTATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTTC
1 AAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTT-GATTTTTAAGTAAAGTAGTGATTTTC
* *
17018329 ATTAAAAAAAAGAAATTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAAAAAT
65 ATTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAAT-TGTTTTTT--TTA----AAAAAAAT
* * ** *
17018394 TAAATTTTTAAATAATTTTTTTA-TTTTTTTAACTACTTCGAAATGAAAATTTAGATTTTTAAGT
123 TAAATTTTCAAACAAAGTTTTTATTTTTTTTAACTACTTCGAAATAAAAATTTAGA-TTTTAAG-
17018458 AAAGTAGTGATTTTCATTAAAAAAATA-AA-GTTTAGATTT-TTAAAAAATAAAAATCTATTTTT
186 AAAGTAGTGATTTTCATTAAAAAAA-AGAATGTTTAGATTTATT-AAAAATAAAAATCTATTTTT
17018520 TAGTGATTTTAAAGAAAAAAATTTAAATTTTTAAAC
249 TAGTGATTTTAAAGAAAAAAATTTAAATTTTTAAAC
*
17018556 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTCTTGATTTTGAAGTAAAGTAGTGATTT
1 -AAGTTTTGA-TTTTTTTAACTATTTCGAAATAAAAGT-TTGATTTTTAAGTAAAGTAGTGATTT
17018621 T
63 T
17018622 GTTTTAATCA
Statistics
Matches: 314, Mismatches: 26, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
282 3 0.01
283 74 0.24
284 22 0.07
286 3 0.01
289 32 0.10
290 72 0.23
291 47 0.15
292 1 0.00
293 7 0.02
294 51 0.16
295 2 0.01
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.45
Consensus pattern (284 bp):
AAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGATTTTTAAGTAAAGTAGTGATTTTCA
TTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATTGTTTTTTTTAAAAAAAATTAAATTTT
CAAACAAAGTTTTTATTTTTTTTAACTACTTCGAAATAAAAATTTAGATTTTAAGAAAGTAGTGA
TTTTCATTAAAAAAAAGAATGTTTAGATTTATTAAAAATAAAAATCTATTTTTTAGTGATTTTAA
AGAAAAAAATTTAAATTTTTAAAC
Found at i:17020086 original size:240 final size:238
Alignment explanation
Indices: 17019665--17020142 Score: 794
Period size: 240 Copynumber: 2.0 Consensus size: 238
17019655 AAAATTATAA
17019665 TAATGATAAAAGATCGAATAAGTTGTAGATCAATTTTAATATTTCTCTTAATTCATTAGTAACTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATCAATTTTAATATTTCTCTTAATTCATTAGTAACTT
* *
17019730 TTAGGTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATGTATTTTACTAGAATC
66 TTAAGTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATC
* *
17019795 ATTTAAGTATCTTTTAGGACTCTCGTTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
131 ATTTAAGTATCCTTTAGGACTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
**
17019860 AGTTTGGTGAACATGTCTTAGTCAAGTTACAAGTAAATCGGAG
196 AGTTTGGTGAACACATCTTAGTCAAGTTACAAGTAAATCGGAG
* **
17019903 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTATTTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATCAATTTTAATATTTCTCTTAATTCATTAGTA--AC
*
17019968 TTTTAAGTTTTTTTTAGGATTTTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAA
64 TTTTAAGTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAA
* ** * *
17020033 TTATTTAAGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGA
129 TCATTTAAGTATCCTTTAGGACTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGA
*
17020098 TAAGTTTGGTGAACACATCTTAGTCAAGTTACAAGTAAATTGGAG
194 TAAGTTTGGTGAACACATCTTAGTCAAGTTACAAGTAAATCGGAG
17020143 GCATTTTTTA
Statistics
Matches: 222, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
238 60 0.27
240 162 0.73
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (238 bp):
TAATGATAAAAGATCGAATAAGTTGTAGATCAATTTTAATATTTCTCTTAATTCATTAGTAACTT
TTAAGTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATC
ATTTAAGTATCCTTTAGGACTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
AGTTTGGTGAACACATCTTAGTCAAGTTACAAGTAAATCGGAG
Found at i:17023445 original size:4 final size:4
Alignment explanation
Indices: 17023436--17023499 Score: 65
Period size: 4 Copynumber: 16.0 Consensus size: 4
17023426 GTGCCCCAAT
* * * * * * *
17023436 TTCA TTCA TTCA CTCA CTCA CTCA CTCA TTGA TTCA TTGA TTCA TTGA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
17023484 TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA
17023500 CTTATACACT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.25, C:0.27, G:0.05, T:0.44
Consensus pattern (4 bp):
TTCA
Found at i:17023721 original size:12 final size:12
Alignment explanation
Indices: 17023704--17023729 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17023694 TAGAGGAACA
17023704 GATGGAAATGAT
1 GATGGAAATGAT
17023716 GATGGAAATGAT
1 GATGGAAATGAT
17023728 GA
1 GA
17023730 CTACAATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (12 bp):
GATGGAAATGAT
Found at i:17032266 original size:42 final size:42
Alignment explanation
Indices: 17032206--17032770 Score: 785
Period size: 42 Copynumber: 13.5 Consensus size: 42
17032196 AAGGAAAGCA
17032206 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
17032248 TTCATTGTATTTAAAGGCCCAAGTATGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
17032290 TTCATTGTATTTAGAGGCCCATGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
17032332 TTCATTGCATTTATAGGCCCAGATGTTGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
17032374 TTCATTGCATTTAGAGGCCCAAGTGTGGAGG-CCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCC-ATTTACTT
*
17032416 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTAC-T
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
17032457 TTCATTACATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** *
17032499 TTCATTGCATTTTAGAGGCCCAGGTGTATAGGCCCATTTACTT
1 TTCATTGCA-TTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* ** *
17032542 TTCATTGTATTTAGAGGCCCAGGTGCAGAGG-CCTATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCC-ATTTACTT
* * * *
17032584 TTCATTACATTTAGAGGCCGAGGTGTGAAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
17032626 TTCATTGTATTTAGAGGCCCAAGTGTGCAAGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
17032668 TTAATTGCATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
17032710 TTCATTGGATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
17032752 TTCATTGCATTTAGAGGCC
1 TTCATTGCATTTAGAGGCC
17032771 TATTTACTTT
Statistics
Matches: 465, Mismatches: 52, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
41 42 0.09
42 380 0.82
43 43 0.09
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:17032777 original size:28 final size:28
Alignment explanation
Indices: 17032744--17032798 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
17032734 GTGGAGGTCC
17032744 ATTTACTTTTCATTGCATTTAGAGGCCT
1 ATTTACTTTTCATTGCATTTAGAGGCCT
* *
17032772 ATTTACTTTTTATTTCATTTAGAGGCC
1 ATTTACTTTTCATTGCATTTAGAGGCC
17032799 GAGGTGTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (28 bp):
ATTTACTTTTCATTGCATTTAGAGGCCT
Found at i:17033276 original size:3 final size:3
Alignment explanation
Indices: 17033268--17033313 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
17033258 AAAGGCCCAA
* *
17033268 ATT ATT ATT ATC ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
17033314 GGGTTTCATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:17033906 original size:52 final size:51
Alignment explanation
Indices: 17033840--17034075 Score: 173
Period size: 52 Copynumber: 4.6 Consensus size: 51
17033830 GGTTTTTTAG
*
17033840 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAAT
1 AAAAGTTTAAATTTTTAAA-AAAGTATTGATTTTTTTTAACTATTTCAAAAT
* * * ** *
17033892 AAAAGTTTATATTTTTAAGAAAGTAGTGATTTTCATTAA--A----AAAAGA
1 AAAAGTTTAAATTTTTAAAAAAGTATTGATTTTTTTTAACTATTTCAAAA-T
* * *** ** *
17033938 AAAAGTTTATATTTTTTAAAAA-TAAAAATCTGTTTTTTAGTTATTTTAAAGA-
1 AAAAGTTTAAATTTTTAAAAAAGTATTGAT-T-TTTTTTAACTATTTCAAA-AT
* *
17033990 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTACTTCAAAAT
1 AAAAGTTTAAATTTTTAAA-AAAGTATTGATTTTTTTTAACTATTTCAAAAT
* * *
17034042 AAAAGTTTGAATTTTTAAGTAAAGTAGTGATTTT
1 AAAAGTTTAAATTTTTAA-AAAAGTATTGATTTT
17034076 CATTAAAAAA
Statistics
Matches: 141, Mismatches: 29, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
45 8 0.06
46 21 0.15
47 5 0.04
49 2 0.01
51 17 0.12
52 77 0.55
53 7 0.05
54 4 0.03
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (51 bp):
AAAAGTTTAAATTTTTAAAAAAGTATTGATTTTTTTTAACTATTTCAAAAT
Found at i:17033973 original size:138 final size:140
Alignment explanation
Indices: 17033720--17033977 Score: 371
Period size: 138 Copynumber: 1.9 Consensus size: 140
17033710 ATTTTGGAAA
* *
17033720 AAAGTTTTGGTTTTTTTAAACAATTTCGAAATAAAAAGCTTTGATTTTTAAGTAAAATACTGATT
1 AAAGTTTTGATTTTTTTAAACAATTTCAAAATAAAAAGCTTTGATTTTTAAGTAAAATACTGATT
* * *
17033785 TTCTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATTTGGTTTTTTAGAAAAGTTTAA
66 TTCATTAAAAAAAGAAAAAGTTTAGATTTTTAAAAATAAAAATCTGGTTTTTTAGAAAAGTTTAA
17033850 ATTTTTAAAC
131 ATTTTTAAAC
* * * * *
17033860 AAAGTTTTGATTTTTTTTAACTATTTCAAAAT-AAAAG-TTTATATTTTTAAG-AAAGTAGTGAT
1 AAAGTTTTGATTTTTTTAAACAATTTCAAAATAAAAAGCTTT-GATTTTTAAGTAAAATACTGAT
*
17033922 TTTCATTAAAAAAAGAAAAAGTTTATATTTTTTAAAAATAAAAATCT-GTTTTTTAG
65 TTTCATTAAAAAAAGAAAAAGTTTAGA-TTTTTAAAAATAAAAATCTGGTTTTTTAG
17033978 TTATTTTAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
138 45 0.43
139 32 0.30
140 28 0.27
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.43
Consensus pattern (140 bp):
AAAGTTTTGATTTTTTTAAACAATTTCAAAATAAAAAGCTTTGATTTTTAAGTAAAATACTGATT
TTCATTAAAAAAAGAAAAAGTTTAGATTTTTAAAAATAAAAATCTGGTTTTTTAGAAAAGTTTAA
ATTTTTAAAC
Found at i:17034178 original size:52 final size:50
Alignment explanation
Indices: 17033840--17034183 Score: 163
Period size: 52 Copynumber: 6.8 Consensus size: 50
17033830 GGTTTTTTAG
* * * *
17033840 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAA-A
1 AAAAGTTTAAATTTTTAAATAAAATTTTGA--TTTTTTAATTATTTTAAAGA
* * * ** * ***
17033891 TAAAAGTTTATATTTTT-AAGAAAGTAGTGA--TTTTCATTA-AAAAAAGA
1 -AAAAGTTTAAATTTTTAAATAAAATTTTGATTTTTTAATTATTTTAAAGA
* * * *
17033938 AAAAGTTTATATTTTTTAAAAATAAAAATCTG-TTTTTTAGTTATTTTAAAGA
1 AAAAGTTTA-AATTTTT--AAATAAAATTTTGATTTTTTAATTATTTTAAAGA
* * * *
17033990 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTACTTCAAA-A
1 AAAAGTTTAAATTTTTAAATAAAATTTTGA--TTTTTTAATTATTTTAAAGA
* * * ** * **
17034041 TAAAAGTTTGAATTTTTAAGTAAAGTAGTGA--TTTTCATTA--AAAAAGAA
1 -AAAAGTTTAAATTTTTAAATAAAATTTTGATTTTTTAATTATTTTAAAG-A
* * * **
17034089 AGAAAGTTTATATTTTTAAAAAATAAAAATCTG-TTTTTTCGTTATTTTAAAGA
1 A-AAAGTTTAAATTTTT---AAATAAAATTTTGATTTTTTAATTATTTTAAAGA
17034142 AAAAGTTTAAATTTTTAAATAAAATTTTGATTTTTTTAATTA
1 AAAAGTTTAAATTTTTAAATAAAATTTTGA-TTTTTTAATTA
17034184 CTTCGGAATA
Statistics
Matches: 216, Mismatches: 52, Indels: 49
0.68 0.16 0.15
Matches are distributed among these distances:
46 15 0.07
47 14 0.06
48 21 0.10
49 21 0.10
50 7 0.03
51 41 0.19
52 91 0.42
53 2 0.01
54 4 0.02
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (50 bp):
AAAAGTTTAAATTTTTAAATAAAATTTTGATTTTTTAATTATTTTAAAGA
Found at i:17034207 original size:151 final size:149
Alignment explanation
Indices: 17033840--17034375 Score: 756
Period size: 152 Copynumber: 3.6 Consensus size: 149
17033830 GGTTTTTTAG
* *
17033840 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAATAAAAGTTTATATT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTACTTCAAAATAAAAGTTT-GATT
*
17033905 TTTAAG-AAAGTAGTGATTTTCATTAAAAAAAGAAAAAGTTTATATTTTTTAAAAATAAAAATCT
65 TTTAAGTAAAGTAGTGATTTTCATTAAAAAAA-AAAAAGTTTATATTTTTAAAAAATAAAAATCT
17033969 GTTTTTTAGTTATTTTAAAGA
129 GTTTTTTAGTTATTTTAAAGA
*
17033990 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTACTTCAAAATAAAAGTTTGAATT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTACTTCAAAATAAAAGTTTG-ATT
17034055 TTTAAGTAAAGTAGTGATTTTCATTAAAAAAGAAAGAAAGTTTATATTTTTAAAAAATAAAAATC
65 TTTAAGTAAAGTAGTGATTTTCATTAAAAAA-AAA-AAAGTTTATATTTTTAAAAAATAAAAATC
*
17034120 TGTTTTTTCGTTATTTTAAAGA
128 TGTTTTTTAGTTATTTTAAAGA
* * * ** *
17034142 AAAAGTTTAAATTTTTAAATAAAATTTTGA-TTTTTTTAATTACTTCGGAATAAAAATTTAGATT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTACTTCAAAATAAAAGTTT-GATT
* * * * * *
17034206 TTCAAGTAAAGTAGTGATTTTTATT--AAAAAAAAAAGTTTAGATTTTTAAAAAGTAAAAAACTA
65 TTTAAGTAAAGTAGTGATTTTCATTAAAAAAAAAAAAGTTTATATTTTTAAAAAATAAAAATCTG
* *
17034269 TTTTTTAGTAATTTTCAAGGA
130 TTTTTTAGTTATTTT-AAAGA
* * *
17034290 AAAGGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTCTTGATT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTACTTCAAAATAAAAGT-TTGATT
* *
17034355 TTAAAGTAAAATAGTGATTTT
65 TTTAAGTAAAGTAGTGATTTT
17034376 GTTTTAATCA
Statistics
Matches: 350, Mismatches: 28, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
147 40 0.11
148 34 0.10
149 50 0.14
150 69 0.20
151 77 0.22
152 80 0.23
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.44
Consensus pattern (149 bp):
AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTACTTCAAAATAAAAGTTTGATTT
TTAAGTAAAGTAGTGATTTTCATTAAAAAAAAAAAAGTTTATATTTTTAAAAAATAAAAATCTGT
TTTTTAGTTATTTTAAAGA
Found at i:17035814 original size:237 final size:238
Alignment explanation
Indices: 17035398--17035867 Score: 784
Period size: 237 Copynumber: 2.0 Consensus size: 238
17035388 AAAATCATAA
* *
17035398 TAATGATAAAAGATTGAATAAATTGTAGATGAATTTTAATATTTCTCTTAATTTATTAGTAACTT
1 TAATGATAAAAGATCGAATAAATTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
*
17035463 TTAAGTTGTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTTACTAGAATC
66 TTAAGTTGTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATC
*
17035528 ATTTAAGTATCTTTTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
131 ATTTAAGTATCCTTTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
*
17035593 AGTTTGGTGAACACGTCTTAGTCAAGTTATAAGTAAATCGAAG
196 AGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATCGAAG
* * *
17035636 TAATGATAAAATATCGAATAATTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGT-ATTT
1 TAATGATAAAAGATCGAATAAATTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
*
17035700 TTAAGGTT-TTTTTAGGATTCTAAAATAGATTTAATTTTAAGAATTGAAAGTATTTTACTAGAA-
66 TTAA-GTTGTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAAT
* * * *
17035763 CTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGA
130 C-ATTTAAGTATCCTTTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGA
17035828 TAAGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAAT
194 TAAGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAAT
17035868 TGGAGGCATT
Statistics
Matches: 217, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
236 1 0.00
237 157 0.72
238 59 0.27
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (238 bp):
TAATGATAAAAGATCGAATAAATTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
TTAAGTTGTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATC
ATTTAAGTATCCTTTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
AGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATCGAAG
Found at i:17042887 original size:7 final size:7
Alignment explanation
Indices: 17042871--17042902 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
17042861 AGTCAATTAT
17042871 AACCCTA
1 AACCCTA
*
17042878 AACTCTA
1 AACCCTA
17042885 AACCCTA
1 AACCCTA
17042892 AACCCTA
1 AACCCTA
17042899 AACC
1 AACC
17042903 AAAAATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.16
Consensus pattern (7 bp):
AACCCTA
Found at i:17054628 original size:56 final size:57
Alignment explanation
Indices: 17054547--17054653 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 57
17054537 TTAATATAAC
* * *
17054547 ATTTGGTATTTTAACTTGATATTTTTT-TAATTTAG-TACTTAAATTTTTTTAATCCA
1 ATTTGATATTTGAACTTGATATTTTTTCTAACTT-GTTACTTAAATTTTTTTAATCCA
* *
17054603 ATTTGATATTTGAACTTGATGTTTTTTCTAACTTGTTATTTAAATTTTTTT
1 ATTTGATATTTGAACTTGATATTTTTTCTAACTTGTTACTTAAATTTTTTT
17054654 TAACACAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
56 25 0.57
57 19 0.43
ACGTcount: A:0.26, C:0.07, G:0.08, T:0.59
Consensus pattern (57 bp):
ATTTGATATTTGAACTTGATATTTTTTCTAACTTGTTACTTAAATTTTTTTAATCCA
Found at i:17054950 original size:27 final size:27
Alignment explanation
Indices: 17054889--17054984 Score: 84
Period size: 27 Copynumber: 3.4 Consensus size: 27
17054879 TAAATTAGAG
*
17054889 AAAAAAATCAAATTTAAATACTAAATT
1 AAAAAAATAAAATTTAAATACTAAATT
*** *
17054916 ACCTAAATAAAATTTAAATATTAAATT
1 AAAAAAATAAAATTTAAATACTAAATT
* * *
17054943 AAAAAAATACGAAATTTGAGTACCAAATT
1 AAAAAAATA--AAATTTAAATACTAAATT
17054972 GAATAAAAATAAA
1 -AA-AAAAATAAA
17054985 TGGTTTTATA
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
27 28 0.53
29 16 0.30
30 2 0.04
31 7 0.13
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAAAAATAAAATTTAAATACTAAATT
Found at i:17055428 original size:30 final size:29
Alignment explanation
Indices: 17055350--17055429 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 29
17055340 TCAATAAAAC
* * * *
17055350 ATAAAAATAATAATAATTAAGTTCTCATA
1 ATAAAAATATTATTAATTTAGATCTCATA
* *
17055379 AAAAAAAT-TTCATCTAATTTAGATCTTATCA
1 ATAAAAATATT-AT-TAATTTAGATCTCAT-A
17055410 ATAAAAATATTATTAATTTA
1 ATAAAAATATTATTAATTTA
17055430 ACCTTTTCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
28 1 0.03
29 8 0.20
30 19 0.47
31 10 0.25
32 2 0.05
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (29 bp):
ATAAAAATATTATTAATTTAGATCTCATA
Found at i:17055728 original size:30 final size:29
Alignment explanation
Indices: 17055671--17055729 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
17055661 TAAAATATTG
17055671 TTTTTTTATATTTAAATTTAAATAAAACA
1 TTTTTTTATATTTAAATTTAAATAAAACA
17055700 TTTTTTTATAGTTCTAAATTTAAA-AAAACA
1 TTTTTTTATA-TT-TAAATTTAAATAAAACA
17055730 CAAAAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 10 0.36
30 8 0.29
31 10 0.36
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (29 bp):
TTTTTTTATATTTAAATTTAAATAAAACA
Found at i:17057330 original size:29 final size:30
Alignment explanation
Indices: 17057207--17057342 Score: 186
Period size: 30 Copynumber: 4.5 Consensus size: 30
17057197 TTAAAACTGA
* *
17057207 GTCACATTTGAATTTTTGGAAAGTTTCAAGG
1 GTCAAATTTGAATTTTTGGAAAG-TTCGAGG
* * *
17057238 GTTAAATTAGAATTTTTGGAAAGTT-TAGGG
1 GTCAAATTTGAATTTTTGGAAAGTTCGA-GG
17057268 GTCAAATTTGAATTTTTGGAAAGTTCGAGG
1 GTCAAATTTGAATTTTTGGAAAGTTCGAGG
*
17057298 GTCAAATTTGAATGTTTGG-AAGTTCGAGG
1 GTCAAATTTGAATTTTTGGAAAGTTCGAGG
17057327 GTCAAATTTGAATTTT
1 GTCAAATTTGAATTTT
17057343 AAAAAATTTG
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
29 26 0.28
30 47 0.50
31 21 0.22
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.39
Consensus pattern (30 bp):
GTCAAATTTGAATTTTTGGAAAGTTCGAGG
Found at i:17057355 original size:29 final size:28
Alignment explanation
Indices: 17057207--17057361 Score: 132
Period size: 30 Copynumber: 5.2 Consensus size: 28
17057197 TTAAAACTGA
* *
17057207 GTCACATTTGAATTTTTGGAAAGTTTCAAGG
1 GTCAAATTTGAA-TTTT-GAAAG-TTCGAGG
* * *
17057238 GTTAAATTAGAATTTTTGGAAAGTT-TAGGG
1 GTCAAATTTGAA-TTTT-GAAAGTTCGA-GG
17057268 GTCAAATTTGAATTTTTGGAAAGTTCGAGG
1 GTCAAATTTGAA-TTTT-GAAAGTTCGAGG
*
17057298 GTCAAATTTGAATGTTTGGAAGTTCGAGG
1 GTCAAATTTGAAT-TTTGAAAGTTCGAGG
* * *
17057327 GTCAAATTTGAATTTTAAAAAATTTGAGG
1 GTCAAATTTGAATTTT-GAAAGTTCGAGG
17057356 GTCAAA
1 GTCAAA
17057362 ACATAATTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
28 3 0.03
29 40 0.37
30 44 0.41
31 21 0.19
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.37
Consensus pattern (28 bp):
GTCAAATTTGAATTTTGAAAGTTCGAGG
Found at i:17059212 original size:40 final size:38
Alignment explanation
Indices: 17059144--17059278 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
17059134 ACCAGAATGG
* *
17059144 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
17059184 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
17059221 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
17059262 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
17059279 ACTCAAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:17059276 original size:41 final size:38
Alignment explanation
Indices: 17059176--17059279 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
17059166 TTCGAAGCAA
* *
17059176 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
17059213 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
17059251 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
17059280 CTCAAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:17059407 original size:6 final size:6
Alignment explanation
Indices: 17059382--17059426 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
17059372 ACAATTCATG
* * *
17059382 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
17059427 ATTTTGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:17059902 original size:29 final size:29
Alignment explanation
Indices: 17059866--17059929 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
17059856 TACAGAGATC
17059866 AAAT-GATGTTCCCGTCTATTTCTTTTGA
1 AAATAGATGTTCCCGTCTATTTCTTTTGA
17059894 AAATAGATGTTCCCGTCTATTTCTTTTGA
1 AAATAGATGTTCCCGTCTATTTCTTTTGA
17059923 AAATAGA
1 AAATAGA
17059930 CTCATTAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.11
29 31 0.89
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (29 bp):
AAATAGATGTTCCCGTCTATTTCTTTTGA
Found at i:17062278 original size:40 final size:40
Alignment explanation
Indices: 17062234--17062321 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
17062224 CCCATGGTTG
* * *
17062234 GGGTAAGACATCAGATGGTCTTCAGTCTGCCTTCTAATTA
1 GGGTAAAACATCAGATGGTCTTCAATCTGCCCTCTAATTA
* **
17062274 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAATTA
1 GGGTAAAACATCAGATGGTCTTCAATCTGCCCTCTAATTA
17062314 GGGTAAAA
1 GGGTAAAA
17062322 GACTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (40 bp):
GGGTAAAACATCAGATGGTCTTCAATCTGCCCTCTAATTA
Found at i:17062322 original size:40 final size:40
Alignment explanation
Indices: 17062247--17062323 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
17062237 TAAGACATCA
* *
17062247 GATGGTCTTCAGTCTGCCTTCTAATTAGGGTAAAAGATTG
1 GATGGTCTTCAATCTGCCCTCTAATTAGGGTAAAAGATTG
17062287 GATGGTCTTCAATCTGCCCTCTAATTAGGGTAAAAGA
1 GATGGTCTTCAATCTGCCCTCTAATTAGGGTAAAAGA
17062324 CTCAGGGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (40 bp):
GATGGTCTTCAATCTGCCCTCTAATTAGGGTAAAAGATTG
Found at i:17075299 original size:30 final size:30
Alignment explanation
Indices: 17075227--17075433 Score: 155
Period size: 29 Copynumber: 7.1 Consensus size: 30
17075217 AGGAAAAAAA
17075227 AGGGGTCAAAAATG-AAGTTTTA-AAGAA-TTT
1 AGGGGT-AAAAATGTAA-TTTTAGAA-AAGTTT
*
17075257 A-GGGT-TAAATGTAATTTTAGAAAAGTTT
1 AGGGGTAAAAATGTAATTTTAGAAAAGTTT
* *
17075285 AGGGGTAAAAATGTAATTTTAGGAAATTTT
1 AGGGGTAAAAATGTAATTTTAGAAAAGTTT
* * * *
17075315 A-GGGTTAAAATGTGATTTTAGAGAACTTT
1 AGGGGTAAAAATGTAATTTTAGAAAAGTTT
* *
17075344 -GAGGTCAAAATGTAATTTT-GAAAAAGTTT
1 AGGGGTAAAAATGTAATTTTAG-AAAAGTTT
* * * *
17075373 AAGGGTTAAAATGTAATCTTGGAAAAGTTT
1 AGGGGTAAAAATGTAATTTTAGAAAAGTTT
* * *
17075403 -GGGGTCAAAATGTGATTTCTTG-AAAGTTT
1 AGGGGTAAAAATGTAATTT-TAGAAAAGTTT
17075432 AG
1 AG
17075434 AAATATGATT
Statistics
Matches: 143, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
27 12 0.08
28 9 0.06
29 73 0.51
30 48 0.34
31 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (30 bp):
AGGGGTAAAAATGTAATTTTAGAAAAGTTT
Found at i:17075378 original size:59 final size:58
Alignment explanation
Indices: 17075228--17075420 Score: 207
Period size: 59 Copynumber: 3.3 Consensus size: 58
17075218 GGAAAAAAAA
17075228 GGGGTCAAAAATG-AAGTTTTA-AAGAATTT-AGGGTT-AAATGTAATTTTAGAAAAGTTT
1 GGGGTC-AAAATGTAA-TTTTAGAA-AATTTAAGGGTTAAAATGTAATTTTAGAAAAGTTT
* * * * * *
17075285 AGGGGTAAAAATGTAATTTTAGGAAATTTTAGGGTTAAAATGTGATTTTAGAGAACTTT
1 -GGGGTCAAAATGTAATTTTAGAAAATTTAAGGGTTAAAATGTAATTTTAGAAAAGTTT
* * *
17075344 GAGGTCAAAATGTAATTTT-GAAAAAGTTTAAGGGTTAAAATGTAATCTTGGAAAAGTTT
1 GGGGTCAAAATGTAATTTTAG-AAAA-TTTAAGGGTTAAAATGTAATTTTAGAAAAGTTT
*
17075403 GGGGTCAAAATGTGATTT
1 GGGGTCAAAATGTAATTT
17075421 CTTGAAAGTT
Statistics
Matches: 113, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
57 17 0.15
58 34 0.30
59 62 0.55
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
GGGGTCAAAATGTAATTTTAGAAAATTTAAGGGTTAAAATGTAATTTTAGAAAAGTTT
Found at i:17084064 original size:22 final size:22
Alignment explanation
Indices: 17084039--17084080 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17084029 AAAATAAACT
*
17084039 AAAAAAAATTATAAAAATGTAA
1 AAAAAAAATTAGAAAAATGTAA
**
17084061 AAAAAAGGTTAGAAAAATGT
1 AAAAAAAATTAGAAAAATGT
17084081 GACCAGGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (22 bp):
AAAAAAAATTAGAAAAATGTAA
Found at i:17092903 original size:53 final size:52
Alignment explanation
Indices: 17092818--17092989 Score: 222
Period size: 53 Copynumber: 3.3 Consensus size: 52
17092808 CGGCCTTGTG
* *
17092818 TCAAAGATTAAAGGTCCAATGACTCTTTGTCATCGTGAGTTATATGAATCCTA
1 TCAAGGATTAAAGGTCCAATGACT-TGTGTCATCGTGAGTTATATGAATCCTA
*
17092871 TCATGGATTAAAGGTCCAATGACTATGTGTCATCGTGAGTTATATGAATCCTA
1 TCAAGGATTAAAGGTCCAATGACT-TGTGTCATCGTGAGTTATATGAATCCTA
* * * * * * *
17092924 TTACGGATTAAAGGTCCGATGAC-TGTGTCATCGTGATTTACACGAA-CCCA
1 TCAAGGATTAAAGGTCCAATGACTTGTGTCATCGTGAGTTATATGAATCCTA
17092974 TCAAGGATTAAAGGTC
1 TCAAGGATTAAAGGTC
17092990 TGATTTACAC
Statistics
Matches: 106, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
50 17 0.16
51 20 0.19
53 69 0.65
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (52 bp):
TCAAGGATTAAAGGTCCAATGACTTGTGTCATCGTGAGTTATATGAATCCTA
Found at i:17093713 original size:21 final size:21
Alignment explanation
Indices: 17093697--17093743 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
17093687 ATTTGTTTCA
*
17093697 GTAGAAGAGTCACTTGTATCG
1 GTAGAACAGTCACTTGTATCG
*
17093718 GTAGAACTGTCACTTGTATCG
1 GTAGAACAGTCACTTGTATCG
17093739 GTAGA
1 GTAGA
17093744 GGTCTGCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
GTAGAACAGTCACTTGTATCG
Found at i:17094880 original size:26 final size:26
Alignment explanation
Indices: 17094820--17094926 Score: 90
Period size: 26 Copynumber: 4.1 Consensus size: 26
17094810 AATTTTGGGC
* * * *
17094820 ACAATTCTAGACATGCTCATACAGCG
1 ACAATTCTGGACATGTTCATGCAACG
*
17094846 ACAACTCTGGACATGTTCATGCAACG
1 ACAATTCTGGACATGTTCATGCAACG
** * *
17094872 ATTATTCTGGACAAGTTTC-TGCGACG
1 ACAATTCTGGACATG-TTCATGCAACG
* * *
17094898 ACAATGCTGGACATGCTCATGCAGCG
1 ACAATTCTGGACATGTTCATGCAACG
17094924 ACA
1 ACA
17094927 TTAGTAGTAA
Statistics
Matches: 62, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
25 2 0.03
26 57 0.92
27 3 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (26 bp):
ACAATTCTGGACATGTTCATGCAACG
Found at i:17101520 original size:19 final size:19
Alignment explanation
Indices: 17101489--17101528 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
17101479 GCTACTGTCA
17101489 AAAGAAAGAAAAGAAGAAG
1 AAAGAAAGAAAAGAAGAAG
*
17101508 AAAGAGAAG-AAAGATGAAG
1 AAAGA-AAGAAAAGAAGAAG
17101527 AA
1 AA
17101529 TTGGCTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (19 bp):
AAAGAAAGAAAAGAAGAAG
Found at i:17111211 original size:34 final size:34
Alignment explanation
Indices: 17111117--17111212 Score: 138
Period size: 34 Copynumber: 2.8 Consensus size: 34
17111107 GTTACAGTGT
* *
17111117 TTTGGTGTGTTGGATAGACTAGCTCTTATGAGCA
1 TTTGGTGTGTTGGATGGATTAGCTCTTATGAGCA
* *
17111151 TTTGGTGTGATGGATGAATTAGCTCTTATGAGCA
1 TTTGGTGTGTTGGATGGATTAGCTCTTATGAGCA
* *
17111185 TTTGGTGTGTTGGTTGGATTAACTCTTA
1 TTTGGTGTGTTGGATGGATTAGCTCTTA
17111213 CAAGACCATG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 54 1.00
ACGTcount: A:0.20, C:0.09, G:0.29, T:0.42
Consensus pattern (34 bp):
TTTGGTGTGTTGGATGGATTAGCTCTTATGAGCA
Found at i:17112281 original size:18 final size:18
Alignment explanation
Indices: 17112258--17112295 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
17112248 TAATATAATT
17112258 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
17112276 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
17112294 TT
1 TT
17112296 CGAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:17112359 original size:30 final size:32
Alignment explanation
Indices: 17112298--17112361 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
17112288 TTCGAATTCG
*
17112298 AAAATTTAACTCGATTCGAACTTGAAATTCGAAA
1 AAAATTCAACTCGATTCGAAC-T-AAATTCGAAA
17112332 AAAATTCAACTCGATTCGAA-T-AATTCGAAA
1 AAAATTCAACTCGATTCGAACTAAATTCGAAA
17112362 TTCGAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 9 0.31
32 1 0.03
34 19 0.66
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (32 bp):
AAAATTCAACTCGATTCGAACTAAATTCGAAA
Found at i:17114390 original size:23 final size:23
Alignment explanation
Indices: 17114342--17114397 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
17114332 TAATTGAGTA
* * *
17114342 AATTAAGTAAATTTATTTTAGTT
1 AATTAAATAAATATATTTTAGAT
17114365 AATTAAATAAATAATATTTT-GAT
1 AATTAAATAAAT-ATATTTTAGAT
17114388 AA-TAAA-AAAT
1 AATTAAATAAAT
17114398 TAGTTATTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.14
22 4 0.14
23 15 0.52
24 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
AATTAAATAAATATATTTTAGAT
Found at i:17116070 original size:21 final size:21
Alignment explanation
Indices: 17116044--17116093 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
17116034 AGGTAAAATC
17116044 TCTTCTGTTGTTTCATACCCA
1 TCTTCTGTTGTTTCATACCCA
*
17116065 TCTTCTGCTGTTTCATACCCA
1 TCTTCTGTTGTTTCATACCCA
17116086 TCTTCTGT
1 TCTTCTGT
17116094 ACTTGGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.12, C:0.30, G:0.10, T:0.48
Consensus pattern (21 bp):
TCTTCTGTTGTTTCATACCCA
Found at i:17119966 original size:28 final size:27
Alignment explanation
Indices: 17119930--17119982 Score: 63
Period size: 26 Copynumber: 1.9 Consensus size: 27
17119920 TAAAAATGAT
* *
17119930 ATTTGACCATTTATGTTGTTTTTTTTTTA
1 ATTTGACCA-ATATG-TGTTATTTTTTTA
17119959 ATTT-ACCAATATGTGTTATTTTTT
1 ATTTGACCAATATGTGTTATTTTTT
17119983 GATAGAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 10 0.45
27 4 0.18
28 4 0.18
29 4 0.18
ACGTcount: A:0.21, C:0.08, G:0.09, T:0.62
Consensus pattern (27 bp):
ATTTGACCAATATGTGTTATTTTTTTA
Found at i:17122739 original size:5 final size:5
Alignment explanation
Indices: 17122729--17122753 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
17122719 TATAGTTAAA
17122729 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
17122754 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:17125970 original size:28 final size:28
Alignment explanation
Indices: 17125938--17125996 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
17125928 AAAAAGGGAA
17125938 GTCTGCCAAGGACTATCTTAAGTAGAAT
1 GTCTGCCAAGGACTATCTTAAGTAGAAT
* * *
17125966 GTCTGCTAAGGACTATCTTAGGTGGAAT
1 GTCTGCCAAGGACTATCTTAAGTAGAAT
17125994 GTC
1 GTC
17125997 CTCTAGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (28 bp):
GTCTGCCAAGGACTATCTTAAGTAGAAT
Found at i:17127997 original size:21 final size:21
Alignment explanation
Indices: 17127968--17128022 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
17127958 GAAAATAAAA
17127968 CCCTGTATTGCACTATAGTGC
1 CCCTGTATTGCACTATAGTGC
* * * *
17127989 CCCTATATTACA-TTTGGTGC
1 CCCTGTATTGCACTATAGTGC
17128009 CCCTGTATTGCACT
1 CCCTGTATTGCACT
17128023 TCGGTGCCCC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.36
Consensus pattern (21 bp):
CCCTGTATTGCACTATAGTGC
Found at i:17128010 original size:20 final size:21
Alignment explanation
Indices: 17127985--17128033 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
17127975 TTGCACTATA
*
17127985 GTGCCCCTATATTACA-TTTG
1 GTGCCCCTATATTACACTTCG
* *
17128005 GTGCCCCTGTATTGCACTTCG
1 GTGCCCCTATATTACACTTCG
17128026 GTGCCCCT
1 GTGCCCCT
17128034 GCGTGTTACG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (21 bp):
GTGCCCCTATATTACACTTCG
Found at i:17128030 original size:21 final size:20
Alignment explanation
Indices: 17127968--17128034 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 20
17127958 GAAAATAAAA
*
17127968 CCCTGTATTGCACTATAGTGC
1 CCCTGTATTGCACT-TGGTGC
* * *
17127989 CCCTATATTACATTTGGTGC
1 CCCTGTATTGCACTTGGTGC
17128009 CCCTGTATTGCACTTCGGTGC
1 CCCTGTATTGCACTT-GGTGC
17128030 CCCTG
1 CCCTG
17128035 CGTGTTACGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.45
21 21 0.55
ACGTcount: A:0.15, C:0.31, G:0.19, T:0.34
Consensus pattern (20 bp):
CCCTGTATTGCACTTGGTGC
Found at i:17129853 original size:195 final size:194
Alignment explanation
Indices: 17129521--17129955 Score: 515
Period size: 195 Copynumber: 2.2 Consensus size: 194
17129511 CAATGGTTGG
* * * * * * *
17129521 GGTACCGCATATGTTACGAGT-TTTCGATAACTCGTGTGAGTAGCATCGTGAGTCAGAAAAGAGA
1 GGTACCGCATATGTTGCGAGTCCTT-GACAACTCGTGTGAGCAGCATCGTAAATCAAAAAAGAGA
* * **
17129585 TATGAAATCCTAAAATGGATTACAGGCCCTACGATGGCTGGGATTTATACTTGAATGCATATTCT
65 TATGAAATCCTAAAATGGATTACAGGCCCTACGATGGCTGGGACTTATACATGAATGCATAACCT
* * * * *
17129650 CGACAGCTCGTGTGAGCAGCATCGTTAGG-GAACAG-TTATATGCACAGATACCGTATCGA-TGA
130 CGACAGCTCGTGTGAGCAGCATCGTTAGGAG-ACAGTTTATA-G-ACAAACACCATACCGACAG-
17129712 CTAA
191 CTAA
* *
17129716 GGTACCGCATATGTTGCGAGTCCTTGACAGCTCGTGTGAGCAGTATCGTAAATCAAAAAAAGAGA
1 GGTACCGCATATGTTGCGAGTCCTTGACAACTCGTGTGAGCAGCATCGTAAATC-AAAAAAGAGA
* * * * *
17129781 TATG-GATCCTAGAATGGATTATAGGCCCTACGGTGGCTGGGACTTATGCAT-AAGTGCATACAC
65 TATGAAATCCTAAAATGGATTACAGGCCCTACGATGGCTGGGACTTATACATGAA-TGCATA-AC
*
17129844 CT-GACAGCTCGTGTGAGCAGCATCGTTAGGAGACAGTTTATAGACAAACATCATACCGACAGCT
128 CTCGACAGCTCGTGTGAGCAGCATCGTTAGGAGACAGTTTATAGACAAACACCATACCGACAGCT
*
17129908 GA
193 AA
*
17129910 GGTACCGCATATGTTGCGAGTCCTCGACAACTCGTGTGAGCAGCAT
1 GGTACCGCATATGTTGCGAGTCCTTGACAACTCGTGTGAGCAGCAT
17129956 TAGGTACTGG
Statistics
Matches: 205, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
194 59 0.29
195 123 0.60
196 23 0.11
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (194 bp):
GGTACCGCATATGTTGCGAGTCCTTGACAACTCGTGTGAGCAGCATCGTAAATCAAAAAAGAGAT
ATGAAATCCTAAAATGGATTACAGGCCCTACGATGGCTGGGACTTATACATGAATGCATAACCTC
GACAGCTCGTGTGAGCAGCATCGTTAGGAGACAGTTTATAGACAAACACCATACCGACAGCTAA
Found at i:17136083 original size:17 final size:17
Alignment explanation
Indices: 17136060--17136098 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
17136050 AATATAAATA
*
17136060 TTTTTCTTT-TTTCTTT
1 TTTTTCTTTGCTTCTTT
17136076 TCTTTTCTTTGCTTCTTT
1 T-TTTTCTTTGCTTCTTT
17136094 TTTTT
1 TTTTT
17136099 ATATGTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 12 0.60
18 7 0.35
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTGCTTCTTT
Found at i:17147041 original size:34 final size:34
Alignment explanation
Indices: 17146998--17147066 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
17146988 TATGAAGTTT
17146998 TAGAAAGAGTAGGACCAGTAGCTTACCGTTTGGC
1 TAGAAAGAGTAGGACCAGTAGCTTACCGTTTGGC
17147032 TAGAAAGAGTAGGACCAGTAGCTTACCGTTTGGC
1 TAGAAAGAGTAGGACCAGTAGCTTACCGTTTGGC
17147066 T
1 T
17147067 TCACCACCAG
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:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (34 bp):
TAGAAAGAGTAGGACCAGTAGCTTACCGTTTGGC
Found at i:17149415 original size:62 final size:62
Alignment explanation
Indices: 17149329--17149446 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 62
17149319 CACACGGTCA
* *
17149329 TGTGACCCTATTTTTAGTATACACATGACCATGTGACCCTATTTCGAGTATACACAAGGCCG
1 TGTGACCCTATTTGTAGTATACACACGACCATGTGACCCTATTTCGAGTATACACAAGGCCG
*
17149391 TGTGACCCTATTTCGT-GTATACACACGACCGTGTGACCCTATTTCGAGTATACACA
1 TGTGACCCTATTT-GTAGTATACACACGACCATGTGACCCTATTTCGAGTATACACA
17149447 CCGCCTAGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
62 51 0.98
63 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (62 bp):
TGTGACCCTATTTGTAGTATACACACGACCATGTGACCCTATTTCGAGTATACACAAGGCCG
Found at i:17149447 original size:31 final size:31
Alignment explanation
Indices: 17149329--17149447 Score: 175
Period size: 31 Copynumber: 3.8 Consensus size: 31
17149319 CACACGGTCA
** * *
17149329 TGTGACCCTATTTTTAGTATACACATGACCA
1 TGTGACCCTATTTCGAGTATACACACGACCG
* *
17149360 TGTGACCCTATTTCGAGTATACACAAGGCCG
1 TGTGACCCTATTTCGAGTATACACACGACCG
*
17149391 TGTGACCCTATTTCGTGTATACACACGACCG
1 TGTGACCCTATTTCGAGTATACACACGACCG
17149422 TGTGACCCTATTTCGAGTATACACAC
1 TGTGACCCTATTTCGAGTATACACAC
17149448 CGCCTAGAAC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (31 bp):
TGTGACCCTATTTCGAGTATACACACGACCG
Found at i:17150458 original size:9 final size:9
Alignment explanation
Indices: 17150418--17150669 Score: 111
Period size: 10 Copynumber: 27.8 Consensus size: 9
17150408 ATATTTTCCC
*
17150418 ATAAAAAAT
1 ATAAAAATT
*
17150427 -TAAAAATC
1 ATAAAAATT
17150435 ATTAAAAA-T
1 A-TAAAAATT
*
17150444 AGAAAAATT
1 ATAAAAATT
17150453 ATAAAAA-T
1 ATAAAAATT
17150461 A-AAAAATT
1 ATAAAAATT
17150469 ATTAAAAA-T
1 A-TAAAAATT
*
17150478 -TAAATATT
1 ATAAAAATT
*
17150486 AAAAAAATT
1 ATAAAAATT
17150495 GATATAAAATT
1 -ATA-AAAATT
17150506 ATAAAAATT
1 ATAAAAATT
17150515 AT---AA-T
1 ATAAAAATT
*
17150520 A-AAAAATA
1 ATAAAAATT
*
17150528 ATAATAACTT
1 ATAA-AAATT
*
17150538 ATAAATATT
1 ATAAAAATT
17150547 ATAAAAA-T
1 ATAAAAATT
17150555 ATAATAAATCT
1 ATAA-AAAT-T
17150566 AT-AAAATT
1 ATAAAAATT
**
17150574 ATAAAAAAA
1 ATAAAAATT
17150583 AGTATAAAATT
1 A-TA-AAAATT
17150594 AATAAAACATAT
1 -ATAAAA-AT-T
* *
17150606 TTAAAATTTT
1 ATAAAA-ATT
17150616 ATAAAAACTT
1 ATAAAAA-TT
*
17150626 ATTAAAATTCT
1 A-TAAAAAT-T
*
17150637 AAAAAAACTT
1 ATAAAAA-TT
*
17150647 ATAAAAATC
1 ATAAAAATT
17150656 AT-AAAATT
1 ATAAAAATT
17150664 A-AAAAA
1 ATAAAAA
17150670 AAGTGATATA
Statistics
Matches: 183, Mismatches: 30, Indels: 61
0.67 0.11 0.22
Matches are distributed among these distances:
5 2 0.01
6 2 0.01
7 12 0.07
8 35 0.19
9 49 0.27
10 50 0.27
11 31 0.17
12 2 0.01
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:17150459 original size:10 final size:10
Alignment explanation
Indices: 17150459--17150743 Score: 75
Period size: 10 Copynumber: 28.7 Consensus size: 10
17150449 AATTATAAAA
17150459 ATAAAAAATT
1 ATAAAAAATT
*
17150469 ATTAAAAA-T
1 ATAAAAAATT
*
17150478 -T-AAATATT
1 ATAAAAAATT
17150486 A-AAAAAATT
1 ATAAAAAATT
*
17150495 GATATAAAATT
1 -ATAAAAAATT
*
17150506 ATAAAAATTATA
1 ATAAAAA--ATT
*
17150518 ATAAAAAATA
1 ATAAAAAATT
* *
17150528 ATAATAACTT
1 ATAAAAAATT
*
17150538 AT-AAATATT
1 ATAAAAAATT
17150547 AT-AAAAA-T
1 ATAAAAAATT
*
17150555 ATAATAAATCT
1 ATAAAAAAT-T
17150566 AT--AAAATT
1 ATAAAAAATT
*
17150574 ATAAAAAA-A
1 ATAAAAAATT
*
17150583 AGTATAAAATT
1 A-TAAAAAATT
17150594 AATAAAACATATT
1 -ATAAAA-A-ATT
**
17150607 -TAAAATTTT
1 ATAAAAAATT
*
17150616 ATAAAAACTT
1 ATAAAAAATT
*
17150626 AT-TAAAATT
1 ATAAAAAATT
*
17150635 CTAAAAAAACTT
1 AT-AAAAAA-TT
*
17150647 AT-AAAAATC
1 ATAAAAAATT
17150656 AT--AAAATT
1 ATAAAAAATT
* *
17150664 AAAAAAAAGTG
1 ATAAAAAA-TT
*
17150675 ATATAAACATT
1 ATA-AAAAATT
17150686 -TAAAAAAATT
1 AT-AAAAAATT
* *
17150696 AAAAAAAAAGTG
1 -ATAAAAAA-TT
*
17150708 ATATAAACA-T
1 ATA-AAAAATT
17150718 AT-AAAAATT
1 ATAAAAAATT
* *
17150727 TTAAAAAATC
1 ATAAAAAATT
17150737 ATAAAAA
1 ATAAAAA
17150744 TTTGGACTAG
Statistics
Matches: 198, Mismatches: 45, Indels: 64
0.64 0.15 0.21
Matches are distributed among these distances:
7 4 0.02
8 18 0.09
9 39 0.20
10 75 0.38
11 36 0.18
12 23 0.12
13 3 0.02
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:17150503 original size:11 final size:10
Alignment explanation
Indices: 17150447--17150634 Score: 63
Period size: 9 Copynumber: 19.6 Consensus size: 10
17150437 TAAAAATAGA
17150447 AAAATTATA-
1 AAAATTATAT
17150456 AAAA-TA-A-
1 AAAATTATAT
17150463 AAAATTAT-T
1 AAAATTATAT
17150472 AAAA--AT-T
1 AAAATTATAT
*
17150479 AAATATTA-AA
1 AAA-ATTATAT
17150489 AAAATTGATAT
1 AAAATT-ATAT
17150500 AAAATTATA-
1 AAAATTATAT
17150509 AAAATTATAAT
1 AAAATTAT-AT
*
17150520 AAAA-AATAAT
1 AAAATTAT-AT
17150530 AATAACTTATA-
1 AA-AA-TTATAT
*
17150541 AATATTATA-
1 AAAATTATAT
17150550 AAAA-TATA-
1 AAAATTATAT
*
17150558 ATAAA-TCTAT
1 A-AAATTATAT
17150568 AAAATTATA-
1 AAAATTATAT
**
17150577 AAAAAAAGTAT
1 AAAATTA-TAT
17150588 AAAATTA-AT
1 AAAATTATAT
* *
17150597 AAAACATATTT
1 AAAA-TTATAT
*
17150608 AAAATTTTAT
1 AAAATTATAT
17150618 AAAAACTTAT-T
1 -AAAA-TTATAT
17150629 AAAATT
1 AAAATT
17150635 CTAAAAAAAC
Statistics
Matches: 138, Mismatches: 18, Indels: 46
0.68 0.09 0.23
Matches are distributed among these distances:
7 11 0.08
8 10 0.07
9 49 0.36
10 32 0.23
11 30 0.22
12 4 0.03
13 2 0.01
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (10 bp):
AAAATTATAT
Found at i:17150524 original size:21 final size:21
Alignment explanation
Indices: 17150478--17150659 Score: 86
Period size: 21 Copynumber: 9.0 Consensus size: 21
17150468 TATTAAAAAT
* *
17150478 TAAATATTAAAAAAATTGAT-A
1 TAAAAATTATAAAAATT-ATAA
17150499 T-AAAATTATAAAAATTATAA
1 TAAAAATTATAAAAATTATAA
* * *
17150519 TAAAAA--ATAATAATAACTTA
1 TAAAAATTATAAAAATTA-TAA
*
17150539 TAAATATTATAAAAA-TATAA
1 TAAAAATTATAAAAATTATAA
17150559 T--AAATCTAT-AAAATTATAA
1 TAAAAAT-TATAAAAATTATAA
* *
17150578 AAAAAAGTAT-AAAA-T-TAA
1 TAAAAATTATAAAAATTATAA
* *
17150596 TAAAACA-TATTTAAAATT-TTA
1 TAAAA-ATTA-TAAAAATTATAA
* *
17150617 TAAAAACTTATTAAAATTCTAA
1 TAAAAA-TTATAAAAATTATAA
*
17150639 -AAAAACTTATAAAAATCATAA
1 TAAAAA-TTATAAAAATTATAA
17150660 AATTAAAAAA
Statistics
Matches: 127, Mismatches: 18, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
18 16 0.13
19 21 0.17
20 37 0.29
21 43 0.34
22 10 0.08
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (21 bp):
TAAAAATTATAAAAATTATAA
Found at i:17150557 original size:17 final size:17
Alignment explanation
Indices: 17150421--17150580 Score: 102
Period size: 17 Copynumber: 9.3 Consensus size: 17
17150411 TTTTCCCATA
*
17150421 AAAAAT-TAAAAATCATT
1 AAAAATATAAAAATTA-T
*
17150438 AAAAATAGAAAAATTAT
1 AAAAATATAAAAATTAT
17150455 AAAAATA-AAAAATTATT
1 AAAAATATAAAAATTA-T
* *
17150472 AAAAAT-TAAATATTAA
1 AAAAATATAAAAATTAT
17150488 AAAAATTGATATAAAATTAT
1 AAAAA-T-ATA-AAAATTAT
*
17150508 AAAAAT-T-ATAA-TA-
1 AAAAATATAAAAATTAT
*
17150521 AAAAATAATAATAACTTAT
1 AAAAAT-ATAA-AAATTAT
*
17150540 AAATATTATAAAAA-TAT
1 AAA-AATATAAAAATTAT
*
17150557 AATAAATCTATAAAATTAT
1 AA-AAATATA-AAAATTAT
17150576 AAAAA
1 AAAAA
17150581 AAAGTATAAA
Statistics
Matches: 113, Mismatches: 13, Indels: 33
0.71 0.08 0.21
Matches are distributed among these distances:
13 6 0.05
14 2 0.02
15 4 0.04
16 14 0.12
17 40 0.35
18 19 0.17
19 15 0.13
20 13 0.12
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (17 bp):
AAAAATATAAAAATTAT
Found at i:17150611 original size:88 final size:88
Alignment explanation
Indices: 17150461--17150744 Score: 203
Period size: 92 Copynumber: 3.2 Consensus size: 88
17150451 TTATAAAAAT
* **
17150461 AAAAAATTATTAAAAAT--TAAATATTAAAAAAATTGATATAAAATTATAAAAATTATAATAAAA
1 AAAAAACTA-TAAAAATCATAAA-ATTAAAAAAAAAG-TATAAAATTATAAAAATTATAATAAAA
*
17150524 AATAATAATAACTTA-T-AAATAT-TA
63 AATAATAAAAACTTATTAAAAT-TCTA
* *
17150548 TAAAAA-TATAATAAATCTATAAAATTATAAAAAAAAGTATAAAATTAATAAAACA-TAT-TTAA
1 AAAAAACTATAA-AAATC-ATAAAATTA-AAAAAAAAGTATAAAATT-ATAAAA-ATTATAATAA
** *
17150610 AATTTTATAAAAACTTATTAAAATTCTA
61 AAAATAATAAAAACTTATTAAAATTCTA
* *
17150638 AAAAAACTTATAAAAATCATAAAATTAAAAAAAAGTGATATAAACATTTAAAAAAATTA-AA-AA
1 AAAAAAC-TATAAAAATCATAAAATTAAAAAAAA-AG-TATAAA-A-TTATAAAAATTATAATAA
* * * * *
17150701 AAAAGTGATATAAACATATAAAAATTTTA
61 AAAA-TAATAAAAACTTATTAAAATTCTA
*
17150730 AAAAATC-ATAAAAAT
1 AAAAAACTATAAAAAT
17150745 TTGGACTAGA
Statistics
Matches: 158, Mismatches: 20, Indels: 35
0.74 0.09 0.16
Matches are distributed among these distances:
85 3 0.02
86 6 0.04
87 5 0.03
88 29 0.18
89 29 0.18
90 30 0.19
91 16 0.10
92 38 0.24
93 2 0.01
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (88 bp):
AAAAAACTATAAAAATCATAAAATTAAAAAAAAAGTATAAAATTATAAAAATTATAATAAAAAAT
AATAAAAACTTATTAAAATTCTA
Found at i:17150706 original size:33 final size:33
Alignment explanation
Indices: 17150658--17150734 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
17150648 TAAAAATCAT
*
17150658 AAAATT-AAAAAAAAGTGATATAAACATTTAAA
1 AAAATTAAAAAAAAAGTGATATAAACATATAAA
17150690 AAAATTAAAAAAAAAGTGATATAAACATATAAA
1 AAAATTAAAAAAAAAGTGATATAAACATATAAA
**
17150723 AATTTTAAAAAA
1 AAAATTAAAAAA
17150735 TCATAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 6 0.15
33 35 0.85
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (33 bp):
AAAATTAAAAAAAAAGTGATATAAACATATAAA
Found at i:17151430 original size:20 final size:20
Alignment explanation
Indices: 17151380--17151432 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
17151370 TATAAGTTTT
17151380 TTTTATAAA-ATTTTAAATA
1 TTTTATAAATATTTTAAATA
* * *
17151399 TTTTAGATATATTTT-ATTAA
1 TTTTATAAATATTTTAAAT-A
17151419 TTTTATAAATATTT
1 TTTTATAAATATTT
17151433 AATAATTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTATAAATATTTTAAATA
Done.