Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007862.1 Hibiscus syriacus cultivar Beakdansim tig00110229_pilon, whole genome shotgun sequence
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: 338149
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:2593 original size:8 final size:8
Alignment explanation
Indices: 2580--2607 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2570 AAAAGAAGAT
2580 ATATATAC
1 ATATATAC
2588 ATATATAC
1 ATATATAC
2596 ATATATAC
1 ATATATAC
2604 ATAT
1 ATAT
2608 GGGAGAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:18311 original size:21 final size:21
Alignment explanation
Indices: 18287--18328 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
18277 AGTGGTCTTT
18287 GACTATTTTTTGGATTTTGTA
1 GACTATTTTTTGGATTTTGTA
18308 GACTATTTTTTGGATTTTGTA
1 GACTATTTTTTGGATTTTGTA
18329 TGAACTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57
Consensus pattern (21 bp):
GACTATTTTTTGGATTTTGTA
Found at i:19843 original size:11 final size:11
Alignment explanation
Indices: 19827--19851 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19817 AATCTTATTC
19827 TTTCTCTCTAT
1 TTTCTCTCTAT
19838 TTTCTCTCTAT
1 TTTCTCTCTAT
19849 TTT
1 TTT
19852 ATAGTTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTCTCTCTAT
Found at i:21119 original size:3 final size:3
Alignment explanation
Indices: 21111--21136 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
21101 TGTGCATTAC
21111 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
21137 GTTTAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:21166 original size:16 final size:16
Alignment explanation
Indices: 21123--21174 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
21113 ATAATAATAA
21123 TAATA-ATAATAATAGTT
1 TAATATATAA-AATA-TT
*
21140 TAATTTGATAAAATATT
1 TAATAT-ATAAAATATT
*
21157 TAATATATAAATTATT
1 TAATATATAAAATATT
21173 TA
1 TA
21175 TAATTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 11 0.37
17 11 0.37
18 4 0.13
19 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
TAATATATAAAATATT
Found at i:22701 original size:14 final size:14
Alignment explanation
Indices: 22682--22708 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22672 TAGTAGCACA
22682 TGAAATTCAATAAT
1 TGAAATTCAATAAT
22696 TGAAATTCAATAA
1 TGAAATTCAATAA
22709 ATCCAAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (14 bp):
TGAAATTCAATAAT
Found at i:23510 original size:20 final size:21
Alignment explanation
Indices: 23472--23512 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
23462 CCACAAAATC
* *
23472 ATTTTTCAAAATTTCATTTTG
1 ATTTTTCAAAATCTAATTTTG
23493 ATTTTT-AAAATCTAATTTTG
1 ATTTTTCAAAATCTAATTTTG
23513 CTTTCAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (21 bp):
ATTTTTCAAAATCTAATTTTG
Found at i:28906 original size:32 final size:32
Alignment explanation
Indices: 28869--29017 Score: 165
Period size: 32 Copynumber: 4.7 Consensus size: 32
28859 ACTAGTCAAG
*
28869 GTGCATTC-TAATAATACACATTATGGTTAGGT
1 GTGCATTCAT-ATAATGCACATTATGGTTAGGT
28901 GTGCATTCATATAATGCACATTATGGTTAGGT
1 GTGCATTCATATAATGCACATTATGGTTAGGT
* * * *
28933 TTGCATTCATATAATGCATAGTATGGCTAGGT
1 GTGCATTCATATAATGCACATTATGGTTAGGT
* * * * *
28965 TTGCATTCAAATAATGCATAGTATGGTCAGGT
1 GTGCATTCATATAATGCACATTATGGTTAGGT
* * *
28997 TTACATTCAGATAATGCACAT
1 GTGCATTCATATAATGCACAT
29018 GAGTATCAGT
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
32 103 0.99
33 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (32 bp):
GTGCATTCATATAATGCACATTATGGTTAGGT
Found at i:31188 original size:21 final size:21
Alignment explanation
Indices: 31162--31320 Score: 234
Period size: 21 Copynumber: 7.6 Consensus size: 21
31152 TTTGACTGGA
31162 AGTATCGATACTGCCAAAGGT
1 AGTATCGATACTGCCAAAGGT
31183 AGTATCGATACTGCC-AAGAGT
1 AGTATCGATACTGCCAAAG-GT
*
31204 AGTATCGATACTGCCAAGGGT
1 AGTATCGATACTGCCAAAGGT
31225 AGTATCGATACTGCC-AAGAGT
1 AGTATCGATACTGCCAAAG-GT
*
31246 AGTATCGATACTGCCAAGGGT
1 AGTATCGATACTGCCAAAGGT
31267 AGTATCGATACTGCC-AAGAGT
1 AGTATCGATACTGCCAAAG-GT
*
31288 AGTATCGATACTGCCAAGGGT
1 AGTATCGATACTGCCAAAGGT
*
31309 AGTATTGATACT
1 AGTATCGATACT
31321 ACCCCTGCAG
Statistics
Matches: 126, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.06
21 113 0.90
22 6 0.05
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (21 bp):
AGTATCGATACTGCCAAAGGT
Found at i:31226 original size:42 final size:42
Alignment explanation
Indices: 31162--31320 Score: 300
Period size: 42 Copynumber: 3.8 Consensus size: 42
31152 TTTGACTGGA
*
31162 AGTATCGATACTGCCAAAGGTAGTATCGATACTGCCAAGAGT
1 AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
31204 AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
1 AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
31246 AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
1 AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
*
31288 AGTATCGATACTGCCAAGGGTAGTATTGATACT
1 AGTATCGATACTGCCAAGGGTAGTATCGATACT
31321 ACCCCTGCAG
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 115 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (42 bp):
AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
Found at i:31261 original size:63 final size:63
Alignment explanation
Indices: 31162--31320 Score: 266
Period size: 63 Copynumber: 2.5 Consensus size: 63
31152 TTTGACTGGA
*
31162 AGTATCGATACTGCCAA-AGGTAGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGGGT
1 AGTATCGATACTGCCAAGA-GTAGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGAGT
*
31225 AGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
1 AGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGAGT
* *
31288 AGTATCGATACTGCCAAGGGTAGTATTGATACT
1 AGTATCGATACTGCCAAGAGTAGTATCGATACT
31321 ACCCCTGCAG
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
63 90 0.99
64 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (63 bp):
AGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGAGT
Found at i:32497 original size:31 final size:32
Alignment explanation
Indices: 32412--32502 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 32
32402 GAATGACCTA
*
32412 TCCATATGT-TCCAAAGAACATAGGTAACACTG
1 TCCATATGTCTCAAAAG-ACATAGGTAACACTG
* ** * *
32444 TCAATATGTCTTGAAGGGCATAGGTAA-ACTG
1 TCCATATGTCTCAAAAGACATAGGTAACACTG
32475 TCCATATGTCTCAAAAGACATAGGTAAC
1 TCCATATGTCTCAAAAGACATAGGTAAC
32503 TCTCGACTCT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
31 26 0.55
32 17 0.36
33 4 0.09
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (32 bp):
TCCATATGTCTCAAAAGACATAGGTAACACTG
Found at i:35555 original size:13 final size:13
Alignment explanation
Indices: 35534--35563 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35524 TTATTATATA
*
35534 TTTATTATTTTAT
1 TTTACTATTTTAT
35547 TTTACTATTTTAT
1 TTTACTATTTTAT
35560 TTTA
1 TTTA
35564 TTACTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTACTATTTTAT
Found at i:36595 original size:21 final size:21
Alignment explanation
Indices: 36547--36596 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
36537 ATTACTATCA
36547 CAATGCGATTTTCCAATTTCG
1 CAATGCGATTTTCCAATTTCG
**
36568 CGTTGCGATTTTCCCAA-TTCG
1 CAATGCGATTTT-CCAATTTCG
*
36589 TAATGCGA
1 CAATGCGA
36597 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (21 bp):
CAATGCGATTTTCCAATTTCG
Found at i:36652 original size:41 final size:41
Alignment explanation
Indices: 36604--36768 Score: 156
Period size: 41 Copynumber: 4.0 Consensus size: 41
36594 CGAATAAGTA
* *
36604 AATCGCAATGCGGAT-TTGGAAAATCGCAATGCGATACTGAC
1 AATCGCAATGC-GATAATAGAAAATCGCAATGCGATACTGAC
* * * *
36645 AACCGCAATGCGATAATATAAAATCGCAATGCGA-ATTTGGAA
1 AATCGCAATGCGATAATAGAAAATCGCAATGCGATA-CT-GAC
* * *
36687 AATCGCAATGCGA-ATTTGGAAAATCGTAATGCGATACTGAC
1 AATCGCAATGCGATA-ATAGAAAATCGCAATGCGATACTGAC
* * * *
36728 TATCGCAACGCGATAATACAAAATCGCAACGCGATACTGAC
1 AATCGCAATGCGATAATAGAAAATCGCAATGCGATACTGAC
36769 TTTCGCAACG
Statistics
Matches: 98, Mismatches: 20, Indels: 12
0.75 0.15 0.09
Matches are distributed among these distances:
40 4 0.04
41 62 0.63
42 31 0.32
43 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (41 bp):
AATCGCAATGCGATAATAGAAAATCGCAATGCGATACTGAC
Found at i:36693 original size:83 final size:83
Alignment explanation
Indices: 36603--36761 Score: 255
Period size: 83 Copynumber: 1.9 Consensus size: 83
36593 GCGAATAAGT
* * *
36603 AAATCGCAATGCGGATTTGGAAAATCGCAATGCGATACTGACAACCGCAATGCGATAATATAAAA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACAACCGCAACGCGATAATACAAAA
*
36668 TCGCAATGCGAATTTGGA
66 TCGCAACGCGAATTTGGA
* * *
36686 AAATCGCAATGCGAATTTGGAAAATCGTAATGCGATACTGACTATCGCAACGCGATAATACAAAA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACAACCGCAACGCGATAATACAAAA
36751 TCGCAACGCGA
66 TCGCAACGCGA
36762 TACTGACTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 69 1.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (83 bp):
AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACAACCGCAACGCGATAATACAAAA
TCGCAACGCGAATTTGGA
Found at i:36720 original size:21 final size:21
Alignment explanation
Indices: 36603--36720 Score: 127
Period size: 21 Copynumber: 5.7 Consensus size: 21
36593 GCGAATAAGT
*
36603 AAATCGCAATGCGGATTTGGA
1 AAATCGCAATGCGAATTTGGA
*
36624 AAATCGCAATGCG-ATACT-GA
1 AAATCGCAATGCGAAT-TTGGA
* * *
36644 CAACCGCAATGCGATAATAT--A
1 AAATCGCAATGCG--AATTTGGA
36665 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
36686 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
*
36707 AAATCGTAATGCGA
1 AAATCGCAATGCGA
36721 TACTGACTAT
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
19 4 0.05
20 15 0.18
21 61 0.73
22 1 0.01
23 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTGGA
Found at i:36740 original size:20 final size:20
Alignment explanation
Indices: 36717--36863 Score: 152
Period size: 20 Copynumber: 7.3 Consensus size: 20
36707 AAATCGTAAT
*
36717 GCGATACTGACTATCGCAAC
1 GCGATACTGACTTTCGCAAC
* **
36737 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TTTCGCAAC
36758 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
* *
36778 GTGATACTGACTTTTGCAAC
1 GCGATACTGACTTTCGCAAC
*
36798 GCGATTCTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
* *
36818 GCGATTCCGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
* * *
36838 GAGATTCTGACTATCGCAAC
1 GCGATACTGACTTTCGCAAC
*
36858 GAGATA
1 GCGATA
36864 ATACAGAATC
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 90 0.83
21 15 0.14
22 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (20 bp):
GCGATACTGACTTTCGCAAC
Found at i:36769 original size:41 final size:41
Alignment explanation
Indices: 36623--36883 Score: 147
Period size: 41 Copynumber: 6.4 Consensus size: 41
36613 GCGGATTTGG
* * * *
36623 AAAATCGCAATGCGATACTGACAACCGCAATGCGATAATAT
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* ** * * **
36664 AAAATCGCAATGCGA-ATTTGGAAAATCGCAATGCGA-ATTTGG
1 AAAATCGCAATGCGATA-CT-GACTATCGCAACGCGATA-ATAC
*
36706 AAAATCGTAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* * * *
36747 AAAATCGCAACGCGATACTGACTTTCGCAACGTGATACTGAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT-AC
** * * * * *
36789 --TTTTGCAACGCGATTCTGACTTTCGCAACGCGAT--TCC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
*** * * * *
36826 GACTTTCGCAACGAGATTCTGACTATCGCAACGAGATAATAC
1 -AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* *
36868 AGAATCTCAATGCGAT
1 AAAATCGCAATGCGAT
36884 TTTCAAAGTT
Statistics
Matches: 173, Mismatches: 36, Indels: 22
0.75 0.16 0.10
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
40 60 0.35
41 75 0.43
42 35 0.20
43 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
Found at i:37630 original size:24 final size:24
Alignment explanation
Indices: 37603--37656 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
37593 GTATTCGAAA
*
37603 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
37627 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
37651 TTTGAT
1 TTTGAT
37657 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:40197 original size:19 final size:20
Alignment explanation
Indices: 40155--40198 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
40145 CAATCATCTT
*
40155 AATGTCTATCGCAATGCGGA
1 AATGACTATCGCAATGCGGA
40175 AATGACTATCGCAATGC-GA
1 AATGACTATCGCAATGCGGA
40194 AATGA
1 AATGA
40199 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (20 bp):
AATGACTATCGCAATGCGGA
Found at i:40204 original size:19 final size:19
Alignment explanation
Indices: 40162--40269 Score: 74
Period size: 19 Copynumber: 6.2 Consensus size: 19
40152 CTTAATGTCT
**
40162 ATCGCAATGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
40182 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40201 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
* *
40215 ATCGTAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
40234 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
40248 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
40267 ATC
1 ATC
40270 ACAACGAGGG
Statistics
Matches: 67, Mismatches: 11, Indels: 21
0.68 0.11 0.21
Matches are distributed among these distances:
14 17 0.25
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 28 0.42
20 10 0.15
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40229 original size:33 final size:33
Alignment explanation
Indices: 40182--40308 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
40172 GGAAATGACT
40182 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
40215 ATCGTAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
40248 ATCGTAATGCGAAATGAAAATCACAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
40281 ATCACAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
40309 CGAATTTAGT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:40364 original size:33 final size:33
Alignment explanation
Indices: 40322--40386 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
40312 ATTTAGTTTC
* *
40322 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTT
1 GCGTTGCGATTCTCTCGTTGCGATTTTCATTTT
40355 GCGTTGCGATTCTCTCGTTGCGATTTTCATTT
1 GCGTTGCGATTCTCTCGTTGCGATTTTCATTT
40387 CGCATTGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.09, C:0.18, G:0.23, T:0.49
Consensus pattern (33 bp):
GCGTTGCGATTCTCTCGTTGCGATTTTCATTTT
Found at i:40523 original size:14 final size:14
Alignment explanation
Indices: 40504--40540 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
40494 CATCAATTAA
*
40504 ACAAATTAACTTTT
1 ACAAATCAACTTTT
*
40518 ACAAATCATCTTTT
1 ACAAATCAACTTTT
40532 ACAAATCAA
1 ACAAATCAA
40541 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:41956 original size:21 final size:21
Alignment explanation
Indices: 41890--41956 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
41880 GTGAATCGGG
*
41890 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
41910 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
41932 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
41953 CTCT
1 CTCT
41957 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:41975 original size:42 final size:41
Alignment explanation
Indices: 41890--42012 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
41880 GTGAATCGGG
* * * *
41890 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
41932 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * * *
41974 CTATTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
42013 CGATTCGGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 4 0.06
42 56 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:42562 original size:94 final size:94
Alignment explanation
Indices: 42401--42705 Score: 512
Period size: 94 Copynumber: 3.3 Consensus size: 94
42391 GAATAGTTTC
*
42401 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
42466 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
42495 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
*
42560 ACATTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
42589 AATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTT
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTT
*
42653 CACAGTGTT----AATAAACAGTTTAGCAG
65 CACAGTGTTAAAGAATACACAGTTTAGCAG
* *
42679 TATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAACAAATTTACT
42706 AAGCAATCTA
Statistics
Matches: 203, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
90 41 0.20
93 19 0.09
94 143 0.70
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGTTAAAGAATACACAGTTTAGCAG
Found at i:44307 original size:25 final size:25
Alignment explanation
Indices: 44279--44343 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
44269 ATACCAAGTT
44279 AGATATACCAAAAACTACATTGTGA
1 AGATATACCAAAAACTACATTGTGA
44304 AGATATACCAAAAACTACATTGTGA
1 AGATATACCAAAAACTACATTGTGA
44329 AGATATACCAAAAAC
1 AGATATACCAAAAAC
44344 AATAAACATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.22
Consensus pattern (25 bp):
AGATATACCAAAAACTACATTGTGA
Found at i:44435 original size:20 final size:20
Alignment explanation
Indices: 44410--44472 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
44400 TTTTGGTTGA
44410 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
44430 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
** *
44449 AAATGACTATCGCAATGAGAG
1 -AATGAAAATCGCAACGAGAG
44470 AAT
1 AAT
44473 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 34 0.94
21 1 0.03
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:44536 original size:14 final size:14
Alignment explanation
Indices: 44513--44601 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
44503 TTTGGTTTCG
*
44513 CGTTGAGATTATCT
1 CGTTGCGATTATCT
*
44527 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
44546 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
44560 CGTTGCGATTTTTATTTCG
1 CGTTGCGA---TTA--TCT
*
44579 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
44593 CGTTGCGAT
1 CGTTGCGAT
44602 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 28 0.47
16 5 0.08
17 6 0.10
19 20 0.34
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:44545 original size:33 final size:33
Alignment explanation
Indices: 44497--44622 Score: 171
Period size: 33 Copynumber: 3.8 Consensus size: 33
44487 AAAATCGCAA
** *
44497 TGCGATTTTGGTTTCGCGTTGAGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
44530 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
* *
44563 TGCGATTTTTATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
** *
44596 TGCGATAGTCATTTCCACGTTGCGATT
1 TGCGATTTTCATTT-CGCGTTGCGATT
44623 TTCATTCTCG
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 72 0.87
34 11 0.13
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:44551 original size:19 final size:18
Alignment explanation
Indices: 44527--44588 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 18
44517 GAGATTATCT
44527 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTT-ATTTCG
*
44546 CGTTGCGA--TTA--TCT
1 CGTTGCGATTTTATTTCG
44560 CGTTGCGATTTTTATTTCG
1 CGTTGCGA-TTTTATTTCG
44579 CGTTGCGATT
1 CGTTGCGATT
44589 CTCTCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.28
16 1 0.03
17 5 0.14
18 2 0.06
19 18 0.50
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (18 bp):
CGTTGCGATTTTATTTCG
Found at i:45227 original size:21 final size:20
Alignment explanation
Indices: 45181--45254 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
45171 ATTCGCATTG
*
45181 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
45201 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
45221 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
45242 ATTCGCATTGCGA
1 ATTCGCATTGCGA
45255 ATTATGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 30 0.62
21 18 0.38
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:45238 original size:41 final size:41
Alignment explanation
Indices: 45181--45377 Score: 161
Period size: 41 Copynumber: 4.8 Consensus size: 41
45171 ATTCGCATTG
* * *
45181 ATTCGCATTACGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAA
*
45222 ATTCGCATTGCGATTTACGTATTCGCATTGCGAATTAT-GAA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCCAA
* ** * * * ***
45263 AATCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAAA
1 ATTCGCATTGCGATTTACGT-ATTCGCATTGCG-ATTATCCAA
* *
45305 ATT-GCATTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGAT-TTAC-GTATTCGCATTGCGATTATCCAA
* *
45345 ATTCGCATTGTGATTTACTTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
45378 ATTGGGAAAA
Statistics
Matches: 123, Mismatches: 24, Indels: 18
0.75 0.15 0.11
Matches are distributed among these distances:
40 16 0.13
41 94 0.76
42 10 0.08
43 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAA
Found at i:45275 original size:21 final size:21
Alignment explanation
Indices: 45251--45306 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
45241 TATTCGCATT
*
45251 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
45272 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
45292 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
45307 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:45315 original size:21 final size:21
Alignment explanation
Indices: 45244--45316 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
45234 ATTTACGTAT
* *
45244 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
45265 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
45285 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
45306 TTGCATTGCGA
1 TCGCAATGCGA
45317 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:45352 original size:21 final size:20
Alignment explanation
Indices: 45326--45377 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
45316 ATAGTCAGTA
*
45326 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
* **
45347 TCGCATTGTGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
45367 TCGCATTGCGA
1 TCGCATTGCGA
45378 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:45419 original size:21 final size:22
Alignment explanation
Indices: 45367--45419 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
45357 ATTTACTTAT
45367 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
45388 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
45409 TCGCATTGCGA
1 TCGCATTGCGA
45420 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:57159 original size:24 final size:24
Alignment explanation
Indices: 57130--57185 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
57120 TTGAAGTTCG
57130 ATTGAAGCCTAAAATTCGAGCTCA
1 ATTGAAGCCTAAAATTCGAGCTCA
*
57154 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTCGAGCTCA
57178 ATTGAAGC
1 ATTGAAGC
57186 GAAAGAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTCGAGCTCA
Found at i:59196 original size:20 final size:20
Alignment explanation
Indices: 59173--59223 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
59163 TGCGATTTTC
*
59173 CAAATTCGCAACACATAAGT
1 CAAATTCGCAACACAGAAGT
59193 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
59213 CAAATTCGCAA
1 CAAATTCGCAA
59224 AGCGCGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:59290 original size:19 final size:19
Alignment explanation
Indices: 59266--59308 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
59256 TTCGAATTCA
59266 AAACACAATATTTATTTCG
1 AAACACAATATTTATTTCG
59285 AAACACAATATTTATTTCG
1 AAACACAATATTTATTTCG
59304 AAACA
1 AAACA
59309 TAAATGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (19 bp):
AAACACAATATTTATTTCG
Found at i:59806 original size:20 final size:20
Alignment explanation
Indices: 59783--59865 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
59773 ATTCGTAACA
59783 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAACG
59803 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAACG
*
59823 CGAAAATGAAAATCGCAACC
1 CGAAAATGAAAATCGCAACG
59843 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAACG
59863 CGA
1 CGA
59866 TTTTAGTTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.10
Consensus pattern (20 bp):
CGAAAATGAAAATCGCAACG
Found at i:59897 original size:20 final size:19
Alignment explanation
Indices: 59862--59909 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
59852 AAATCGCAAC
59862 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
59881 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
59901 GCAATTTTA
1 GCGATTTTA
59910 AATTTCAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:59915 original size:20 final size:20
Alignment explanation
Indices: 59872--59915 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
59862 GCGATTTTAG
* * *
59872 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCAATTTTAAA
59892 TTTCGCGTTGCAATTTTAAA
1 TTTCGCGTTGCAATTTTAAA
59912 TTTC
1 TTTC
59916 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCAATTTTAAA
Found at i:61591 original size:21 final size:21
Alignment explanation
Indices: 61564--61613 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
61554 GATATGGGAG
*
61564 TTACGTGATGAGGTCAATACT
1 TTACGTGAGGAGGTCAATACT
* **
61585 TTGCGTGAGGAGGTCGGTACT
1 TTACGTGAGGAGGTCAATACT
61606 TTACGTGA
1 TTACGTGA
61614 AGACAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:62051 original size:21 final size:22
Alignment explanation
Indices: 62023--62128 Score: 94
Period size: 21 Copynumber: 5.0 Consensus size: 22
62013 GATTCACCTA
*
62023 TCATCGTTCAAGAGGCCTCTCC
1 TCATCGTTCAAGAGGCCCCTCC
* *
62045 T-ATCGTTTAAGAGGCCCCT-A
1 TCATCGTTCAAGAGGCCCCTCC
*
62065 TCATCCTTCAAGAGGCCCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
* * * * *
62087 -CACCATTTAAGAGGCTCCT-G
1 TCATCGTTCAAGAGGCCCCTCC
*
62107 TCATCGTTCAAGAGGTCCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
62129 CACCGTTTGA
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
20 1 0.02
21 61 0.97
22 1 0.02
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.26
Consensus pattern (22 bp):
TCATCGTTCAAGAGGCCCCTCC
Found at i:62066 original size:42 final size:42
Alignment explanation
Indices: 62019--62141 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
62009 GCCTGATTCA
* * * *
62019 CCTATCATCGTTCAAGAGGCCTCTCCTATCGTTTAAGAGGCC
1 CCTATCATCGTTCAAGAGGCCCCTCCCACCATTTAAGAGGCC
* *
62061 CCTATCATCCTTCAAGAGGCCCCTCCCACCATTTAAGAGGCT
1 CCTATCATCGTTCAAGAGGCCCCTCCCACCATTTAAGAGGCC
* * * *
62103 CCTGTCATCGTTCAAGAGGTCCCTCCCACCGTTTGAGAG
1 CCTATCATCGTTCAAGAGGCCCCTCCCACCATTTAAGAG
62142 CCCGATTCAC
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (42 bp):
CCTATCATCGTTCAAGAGGCCCCTCCCACCATTTAAGAGGCC
Found at i:63559 original size:64 final size:64
Alignment explanation
Indices: 63482--63630 Score: 237
Period size: 64 Copynumber: 2.3 Consensus size: 64
63472 AAATTGATGT
*
63482 ATTTGTACAAGTTGATTTGTTTAATTGATGAGGAAATAAGA-ATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAA-ATATTATTTTTTGCTTGTTTAATTG
* * *
63546 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAAATCTTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAATATTATTTTTTGCTTGTTTAATTG
*
63610 ATTTTTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
63631 GTTTTAAATT
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
63 1 0.01
64 78 0.99
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAATATTATTTTTTGCTTGTTTAATTG
Found at i:63972 original size:18 final size:18
Alignment explanation
Indices: 63949--63984 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
63939 AAGCCGGTTG
63949 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
**
63967 TGATTGTTATTTTGATTT
1 TGATTGGGATTTTGATTT
63985 CCTTTTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.22, T:0.61
Consensus pattern (18 bp):
TGATTGGGATTTTGATTT
Found at i:66279 original size:24 final size:24
Alignment explanation
Indices: 66252--66322 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
66242 CAAAATCCGA
66252 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
66276 GTATTGACCAAGATCAAAGTCCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
66300 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
66323 AATACTGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:66464 original size:12 final size:12
Alignment explanation
Indices: 66443--66476 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
66433 TGTTGTGGGT
*
66443 TTTGAGATTGTG
1 TTTGATATTGTG
66455 TTTGATATTGTG
1 TTTGATATTGTG
*
66467 TTTGGTATTG
1 TTTGATATTG
66477 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:67288 original size:20 final size:19
Alignment explanation
Indices: 67244--67370 Score: 80
Period size: 20 Copynumber: 6.4 Consensus size: 19
67234 CAAAACATTT
*
67244 GTGTTGCGAAACTAAAA-C
1 GTGTTGCGAAATTAAAATC
*
67262 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
67282 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
* **
67302 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAA-TC
*
67322 GCGTTGCG-AATTCAGAAATC
1 GTGTTGCGAAATT-A-AAATC
* * *
67342 GAGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATT-AAAATC
67362 AGTGTTGCG
1 -GTGTTGCG
67371 GATTTGGAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
18 15 0.18
19 10 0.12
20 40 0.47
21 20 0.24
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:67390 original size:20 final size:20
Alignment explanation
Indices: 67320--67421 Score: 98
Period size: 20 Copynumber: 5.0 Consensus size: 20
67310 AAAACAAAAT
**
67320 TCGCGTTGCGAATTCAGAAA
1 TCGCGTTGCGAATTTGGAAA
*
67340 TCGAGTTGCGAATTT-GAAA
1 TCGCGTTGCGAATTTGGAAA
* *
67359 TTCAGTGTTGCGGATTTGGAAA
1 -TC-GCGTTGCGAATTTGGAAA
67381 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGG-AAA
** *
67402 TCGCAATGCGTATTTGGAAA
1 TCGCGTTGCGAATTTGGAAA
67422 CTGAGTTGTG
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
19 4 0.06
20 31 0.45
21 30 0.43
22 4 0.06
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGGAAA
Found at i:67396 original size:41 final size:40
Alignment explanation
Indices: 67264--67392 Score: 159
Period size: 40 Copynumber: 3.2 Consensus size: 40
67254 ACTAAAACCT
*
67264 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGGAAATCGA
** * *
67304 GTTGCGAAAACAAAATTCGCGTTGCGAATTCAGAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGGAAATCGA
* * * * *
67344 GTTGCGAATTTGAAATTCAGTGTTGCGGATTTGGAAATCGC
1 GTTGCGAAATTAAAATTC-GTGTTGCGAATTCGGAAATCGA
67385 GTTGCGAA
1 GTTGCGAA
67393 TTTGGAAAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
40 49 0.66
41 25 0.34
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCGGAAATCGA
Found at i:67404 original size:21 final size:21
Alignment explanation
Indices: 67315--67421 Score: 94
Period size: 21 Copynumber: 5.1 Consensus size: 21
67305 TTGCGAAAAC
**
67315 AAAATTCGCGTTGCGAATTCAG
1 AAAA-TCGCGTTGCGAATTTGG
*
67337 -AAATCGAGTTGCGAATTT-G
1 AAAATCGCGTTGCGAATTTGG
* * *
67356 AAATTCAGTGTTGCGGATTTGG
1 AAAATC-GCGTTGCGAATTTGG
67378 -AAATCGCGTTGCGAATTTGG
1 AAAATCGCGTTGCGAATTTGG
** *
67398 AAAATCGCAATGCGTATTTGG
1 AAAATCGCGTTGCGAATTTGG
67419 AAA
1 AAA
67422 CTGAGTTGTG
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
19 1 0.01
20 30 0.43
21 38 0.54
22 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (21 bp):
AAAATCGCGTTGCGAATTTGG
Found at i:67417 original size:41 final size:41
Alignment explanation
Indices: 67336--67439 Score: 104
Period size: 41 Copynumber: 2.5 Consensus size: 41
67326 TGCGAATTCA
* ***
67336 GAAATCGAGTTGCGAATTTGAAATTCAGTGTTGCGGATTTG
1 GAAATCGAGTTGCGAATTTGAAAATCAGCAATGCGGATTTG
* *
67377 GAAATCGCGTTGCGAATTTGGAAAATC-GCAATGCGTATTTG
1 GAAATCGAGTTGCGAATTT-GAAAATCAGCAATGCGGATTTG
* *
67418 GAAA-CTGAGTTGTGAAATTGAA
1 GAAATC-GAGTTGCGAATTTGAA
67440 GTTCGAACTT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
40 4 0.08
41 42 0.81
42 6 0.12
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (41 bp):
GAAATCGAGTTGCGAATTTGAAAATCAGCAATGCGGATTTG
Found at i:75238 original size:13 final size:13
Alignment explanation
Indices: 75220--75254 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
75210 ATGATATGTG
75220 GTTTATACAGATT
1 GTTTATACAGATT
75233 GTTTATACAGATT
1 GTTTATACAGATT
*
75246 GTTCATACA
1 GTTTATACA
75255 TTATGCCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (13 bp):
GTTTATACAGATT
Found at i:76006 original size:12 final size:12
Alignment explanation
Indices: 75991--76053 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
75981 ATGATTTATG
75991 AGGGACTTGTAA
1 AGGGACTTGTAA
* * *
76003 AGGGAGTCGTATG
1 AGGGACTTGTA-A
76016 AGGGACTTGTAA
1 AGGGACTTGTAA
* *
76028 AGGGAGTCGTATA
1 AGGGACTTGTA-A
76041 AGGGACTTG-AA
1 AGGGACTTGTAA
76052 AG
1 AG
76054 CTTAAATAGC
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
11 3 0.08
12 19 0.49
13 17 0.44
ACGTcount: A:0.32, C:0.08, G:0.38, T:0.22
Consensus pattern (12 bp):
AGGGACTTGTAA
Found at i:76021 original size:25 final size:25
Alignment explanation
Indices: 75987--76053 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
75977 TTTTATGATT
75987 TATGAGGGACTTGTAAAGGGAGTCG
1 TATGAGGGACTTGTAAAGGGAGTCG
76012 TATGAGGGACTTGTAAAGGGAGTCG
1 TATGAGGGACTTGTAAAGGGAGTCG
*
76037 TATAAGGGACTTG-AAAG
1 TATGAGGGACTTGTAAAG
76054 CTTAAATAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
24 4 0.10
25 37 0.90
ACGTcount: A:0.31, C:0.07, G:0.37, T:0.24
Consensus pattern (25 bp):
TATGAGGGACTTGTAAAGGGAGTCG
Found at i:76045 original size:13 final size:13
Alignment explanation
Indices: 76002--76045 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
75992 GGGACTTGTA
76002 AAGGGAGTCGTAT
1 AAGGGAGTCGTAT
* * *
76015 GAGGGACTTGTA-
1 AAGGGAGTCGTAT
76027 AAGGGAGTCGTAT
1 AAGGGAGTCGTAT
76040 AAGGGA
1 AAGGGA
76046 CTTGAAAGCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.32, C:0.07, G:0.41, T:0.20
Consensus pattern (13 bp):
AAGGGAGTCGTAT
Found at i:78572 original size:21 final size:21
Alignment explanation
Indices: 78548--78600 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
78538 AATACAAAGA
78548 AGTATTGATACTACTTCATGT
1 AGTATTGATACTACTTCATGT
78569 AGTATTGATACTACTTCATGT
1 AGTATTGATACTACTTCATGT
*
78590 AGTATCGATAC
1 AGTATTGATAC
78601 CATATGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
AGTATTGATACTACTTCATGT
Found at i:79194 original size:33 final size:33
Alignment explanation
Indices: 79148--79211 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
79138 AAGAGGTTTT
*
79148 GGTTCTAGCTTAGCCTGCT-AAAAACTAGGGAAA
1 GGTTCTAGCTTAGCCCG-TAAAAAACTAGGGAAA
*
79181 GGTTCTAGTTTAGCCCGTAAAAAACTAGGGA
1 GGTTCTAGCTTAGCCCGTAAAAAACTAGGGA
79212 GTTTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (33 bp):
GGTTCTAGCTTAGCCCGTAAAAAACTAGGGAAA
Found at i:88598 original size:4 final size:4
Alignment explanation
Indices: 88589--88622 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
88579 GAGTGCAAAG
88589 AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
88623 GGTAAAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:94926 original size:18 final size:18
Alignment explanation
Indices: 94903--94950 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
94893 GTTGGCTACT
94903 TCATCTTCT-TCATTGGAG
1 TCATCTT-TATCATTGGAG
*
94921 TCATCTTTATCATTGGAT
1 TCATCTTTATCATTGGAG
94939 TCATCTTTATCA
1 TCATCTTTATCA
94951 CTTCAAGCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 1 0.04
18 27 0.96
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (18 bp):
TCATCTTTATCATTGGAG
Found at i:96988 original size:5 final size:5
Alignment explanation
Indices: 96980--97063 Score: 145
Period size: 5 Copynumber: 17.0 Consensus size: 5
96970 CAAAAACGCT
96980 ATATA ATAT- A-ATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
97028 ATATAA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATAT-A ATATA ATATA ATATA ATATA ATATA ATATA
97064 TTGAAAATTT
Statistics
Matches: 76, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 67 0.88
6 5 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:98380 original size:81 final size:82
Alignment explanation
Indices: 98224--98380 Score: 253
Period size: 82 Copynumber: 1.9 Consensus size: 82
98214 TTAGGGTGTG
* *
98224 TTTGGTTCACGGAATGTAAGATTATCAGTAAGAGTAAAAGATTATCAGGGAATAAGATTACTGAG
1 TTTGGTTCACAGAATGTAAGATTATCAGTAAGAGTAAAAGATTATCAGAGAATAAGATTACTGAG
*
98289 TATATTGTATTTTATGT
66 AATATTGTATTTTATGT
** *
98306 TTTGGTTCACAGAATGTAAGATTATCAGTGGGAGTAAAAGATT-TCAGAGAATAAGATTACTGGG
1 TTTGGTTCACAGAATGTAAGATTATCAGTAAGAGTAAAAGATTATCAGAGAATAAGATTACTGAG
98370 AATATTGTATT
66 AATATTGTATT
98381 CTGTGTTTGG
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 29 0.42
82 40 0.58
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (82 bp):
TTTGGTTCACAGAATGTAAGATTATCAGTAAGAGTAAAAGATTATCAGAGAATAAGATTACTGAG
AATATTGTATTTTATGT
Found at i:98584 original size:37 final size:39
Alignment explanation
Indices: 98504--98582 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 39
98494 AACAAGTTAG
*
98504 AAAATATATATATATTTTCTTTAAAAAAATTAAATTCAT
1 AAAATATATATATATTTTCTTTAAAAAAATTAAAATCAT
* *
98543 AAAATTTATATA-ATTTT-TTT-ACAAAATTAAAAAT-AT
1 AAAATATATATATATTTTCTTTAAAAAAATT-AAAATCAT
98579 AAAA
1 AAAA
98583 ATGTTTAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 13 0.36
37 7 0.19
38 5 0.14
39 11 0.31
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (39 bp):
AAAATATATATATATTTTCTTTAAAAAAATTAAAATCAT
Found at i:100496 original size:18 final size:18
Alignment explanation
Indices: 100473--100520 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
100463 ATGAAGATTC
100473 TGAAAATAAAACCGAAAA
1 TGAAAATAAAACCGAAAA
* **
100491 TGAAAA-AGAAAACGAAGC
1 TGAAAATA-AAACCGAAAA
100509 TGAAAATAAAAC
1 TGAAAATAAAAC
100521 TAACCAACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.65, C:0.10, G:0.15, T:0.10
Consensus pattern (18 bp):
TGAAAATAAAACCGAAAA
Found at i:102152 original size:21 final size:21
Alignment explanation
Indices: 102110--102152 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
102100 GTAGAAGTTA
* * *
102110 TTTTATATTGCTTTTTATAAC
1 TTTTATATTGCATATTAAAAC
*
102131 TTTTCTATTGCATATTAAAAC
1 TTTTATATTGCATATTAAAAC
102152 T
1 T
102153 GTTAAATATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTATATTGCATATTAAAAC
Found at i:103444 original size:4 final size:4
Alignment explanation
Indices: 103437--103462 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
103427 TTTTGGATGA
103437 GAGG GAGG GAGG GAGG GAGG GAGG GA
1 GAGG GAGG GAGG GAGG GAGG GAGG GA
103463 AATTTAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:108824 original size:19 final size:19
Alignment explanation
Indices: 108800--108836 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
108790 CTTTAAGTTT
108800 AATATTTTATTTTTATATG
1 AATATTTTATTTTTATATG
*
108819 AATATTTTCTTTTTATAT
1 AATATTTTATTTTTATAT
108837 TTTGATGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
AATATTTTATTTTTATATG
Found at i:109248 original size:22 final size:22
Alignment explanation
Indices: 109212--109256 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
109202 AATTTCTGAG
109212 TAAAAAAATTAAGAGAAGAAAAA
1 TAAAAAAATTAAGAGAA-AAAAA
*
109235 TAAAAAAA-TGAGAGAAAAAAA
1 TAAAAAAATTAAGAGAAAAAAA
109256 T
1 T
109257 GAGAGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 7 0.33
23 8 0.38
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (22 bp):
TAAAAAAATTAAGAGAAAAAAA
Found at i:109254 original size:13 final size:14
Alignment explanation
Indices: 109236--109270 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
109226 GAAGAAAAAT
109236 AAAAAAATGAGA-G
1 AAAAAAATGAGAGG
109249 AAAAAAATGAGAGG
1 AAAAAAATGAGAGG
109263 AAAAAAAT
1 AAAAAAAT
109271 TTAACCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (14 bp):
AAAAAAATGAGAGG
Found at i:112863 original size:25 final size:28
Alignment explanation
Indices: 112808--112863 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 28
112798 TTCCAAGTAA
* *
112808 ATCTTAGTGTTATTTGCTTTTATTTTTCG
1 ATCTTAGTGTTATTTGC-TTTATGTTCCG
112837 ATCTT-GT-TTATTTG-TTTATGTTCCG
1 ATCTTAGTGTTATTTGCTTTATGTTCCG
112862 AT
1 AT
112864 ATTATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 11 0.44
27 7 0.28
28 2 0.08
29 5 0.20
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.61
Consensus pattern (28 bp):
ATCTTAGTGTTATTTGCTTTATGTTCCG
Found at i:125391 original size:21 final size:21
Alignment explanation
Indices: 125317--125392 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
125307 ATTACGACTA
125317 TCGCAATGCGATAGTCCAAGT
1 TCGCAATGCGATAGTCCAAGT
** * * *
125338 TCGCGTTGCAATTTATTCCAAAT
1 TCGCAATGCGA--TAGTCCAAGT
*
125361 TCG--TTGCGATAGTCCAAGT
1 TCGCAATGCGATAGTCCAAGT
125380 TCGCAATGCGATA
1 TCGCAATGCGATA
125393 AAATCGCAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
19 11 0.26
21 20 0.48
23 11 0.26
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (21 bp):
TCGCAATGCGATAGTCCAAGT
Found at i:126270 original size:19 final size:19
Alignment explanation
Indices: 126246--126339 Score: 107
Period size: 21 Copynumber: 4.7 Consensus size: 19
126236 CGTTGTGATT
126246 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
* *
126265 TTGGACTATCACAACGAAT
1 TTGGACTATCGCAACGAAC
**
126284 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
*
126305 TTCGACTATCGCAACGAGAAC
1 TTGGACTATCGCAAC--GAAC
126326 TTGGACTATCGCAA
1 TTGGACTATCGCAA
126340 TGCGATAGTC
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 29 0.48
21 32 0.52
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:128833 original size:22 final size:23
Alignment explanation
Indices: 128792--128840 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
128782 AAGTTGTGGT
*
128792 TAAAATAAAAAATAAGAATTAAA
1 TAAAAGAAAAAATAAGAATTAAA
*
128815 TAAAAGAAAAAA-AATAATTAAA
1 TAAAAGAAAAAATAAGAATTAAA
128837 TAAA
1 TAAA
128841 CAAATTAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
TAAAAGAAAAAATAAGAATTAAA
Found at i:130580 original size:29 final size:28
Alignment explanation
Indices: 130537--130633 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
130527 CTACTGTGTA
*
130537 TTTTTCTGCATTGTTCGAACCAAATCAG
1 TTTTTCTGCACTGTTCGAACCAAATCAG
** *
130565 TTTCTTCTGCACTGTTCTG-TTCGAAT---
1 TTT-TTCTGCACTGTTC-GAACCAAATCAG
* *
130591 TTTTTCTGCACAGTTCGAACCAAGTCAG
1 TTTTTCTGCACTGTTCGAACCAAATCAG
130619 TTTTTCTGCACTGTT
1 TTTTTCTGCACTGTT
130634 TTTTTCGTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
24 1 0.02
25 15 0.28
26 3 0.06
28 17 0.32
29 16 0.30
30 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (28 bp):
TTTTTCTGCACTGTTCGAACCAAATCAG
Found at i:130767 original size:20 final size:21
Alignment explanation
Indices: 130728--130775 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
130718 AGTTCGCTAA
130728 AAAAATAAAAAAAAATAAAAC
1 AAAAATAAAAAAAAATAAAAC
* *
130749 GAAAATAAAAAAATA-AAAAC
1 AAAAATAAAAAAAAATAAAAC
130769 AAAAATA
1 AAAAATA
130776 TAACGAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.10
Consensus pattern (21 bp):
AAAAATAAAAAAAAATAAAAC
Found at i:130773 original size:31 final size:29
Alignment explanation
Indices: 130725--130783 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 29
130715 TAAAGTTCGC
130725 TAAAAAAATAAAAAAAAATAAAACGAAAA
1 TAAAAAAATAAAAAAAAATAAAACGAAAA
*
130754 TAAAAAAATAAAAACAAAAATATAACGAAA
1 TAAAAAAAT-AAAA-AAAAATAAAACGAAA
130784 TGGGTTGCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 9 0.33
30 4 0.15
31 14 0.52
ACGTcount: A:0.80, C:0.05, G:0.03, T:0.12
Consensus pattern (29 bp):
TAAAAAAATAAAAAAAAATAAAACGAAAA
Found at i:137172 original size:75 final size:76
Alignment explanation
Indices: 137105--137268 Score: 224
Period size: 76 Copynumber: 2.2 Consensus size: 76
137095 AAAAAATTAT
* *
137105 ATAATATTCTAAATCCTAATTAAAATACT-AAAACATATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACATATTTAAACTAAAATACAAAGATAAAGAT
137169 AAAATATAAAA
66 AAAATATAAAA
* * *
137180 ATAATATCCTAAAACTTAATTAAAATGCTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACATATTTAAACTAAAATACAAAGATAAAGAT
* * *
137244 ATAATGTTTAAA
66 AAAAT-ATAAAA
*
137256 ATATTATCCTAAA
1 ATAATATCCTAAA
137269 TTTAAGTTTA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 31 0.40
76 47 0.60
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAAACATATTTAAACTAAAATACAAAGATAAAGAT
AAAATATAAAA
Found at i:138837 original size:23 final size:23
Alignment explanation
Indices: 138807--138853 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
138797 AACATTTATT
138807 TCCCATAAAATCTACCTTCGGTG
1 TCCCATAAAATCTACCTTCGGTG
*
138830 TCCCATAAAATTTACCTTCGGTG
1 TCCCATAAAATCTACCTTCGGTG
138853 T
1 T
138854 ATCAAGTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.34
Consensus pattern (23 bp):
TCCCATAAAATCTACCTTCGGTG
Found at i:144922 original size:21 final size:21
Alignment explanation
Indices: 144896--144938 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
144886 CTATACTTAG
144896 ATAATTTAGTTTTTGTGCTTT
1 ATAATTTAGTTTTTGTGCTTT
144917 ATAATTTAGTTTTTGTGCTTT
1 ATAATTTAGTTTTTGTGCTTT
144938 A
1 A
144939 ACTTAACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.05, G:0.14, T:0.60
Consensus pattern (21 bp):
ATAATTTAGTTTTTGTGCTTT
Found at i:145928 original size:15 final size:15
Alignment explanation
Indices: 145908--145936 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
145898 ACCAACAACT
145908 GCAGGAACTCCAGTC
1 GCAGGAACTCCAGTC
145923 GCAGGAACTCCAGT
1 GCAGGAACTCCAGT
145937 TTTGGAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.14
Consensus pattern (15 bp):
GCAGGAACTCCAGTC
Found at i:149246 original size:25 final size:24
Alignment explanation
Indices: 149199--149249 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
149189 GCAGTGTTGG
*
149199 AAGTCAAAGTTGAGGCTGTAAATC
1 AAGTCAAAGTTGAGGCTGGAAATC
*
149223 AAGTCAAATTTGGAGGCTGGAAATC
1 AAGTCAAAGTT-GAGGCTGGAAATC
149248 AA
1 AA
149250 AGCTGGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (24 bp):
AAGTCAAAGTTGAGGCTGGAAATC
Found at i:154501 original size:19 final size:19
Alignment explanation
Indices: 154477--154526 Score: 72
Period size: 15 Copynumber: 2.8 Consensus size: 19
154467 TAATAAGGTT
154477 ATTTATTTTAAAATAAATA
1 ATTTATTTTAAAATAAATA
154496 ATTTATTTT---A-AAATA
1 ATTTATTTTAAAATAAATA
154511 ATTTATTTTAAAATAA
1 ATTTATTTTAAAATAA
154527 TTTATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 14 0.52
16 1 0.04
18 1 0.04
19 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATTTTAAAATAAATA
Found at i:154509 original size:15 final size:15
Alignment explanation
Indices: 154491--154645 Score: 143
Period size: 15 Copynumber: 9.8 Consensus size: 15
154481 ATTTTAAAAT
154491 AAATAATTTATTTTA
1 AAATAATTTATTTTA
154506 AAATAATTTATTTTA
1 AAATAATTTATTTTA
*
154521 AAATAATTTATTATA
1 AAATAATTTATTTTA
*
154536 AAATAATTTACTTTA
1 AAATAATTTATTTTA
* *
154551 AAATAAATTATTATAA
1 AAATAATTTATT-TTA
154567 AATATGGATTGATTTATTTTA
1 AA-AT--A---ATTTATTTTA
154588 AAATAATTTATTTT-
1 AAATAATTTATTTTA
*
154602 AAATAATTTATTAGTATG
1 AAATAATTTATT--T-TA
* *
154620 AATTGATTTATTTT-
1 AAATAATTTATTTTA
154634 AAATAATTTATT
1 AAATAATTTATT
154646 AGTATGGATT
Statistics
Matches: 117, Mismatches: 12, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
14 22 0.19
15 62 0.53
16 6 0.05
17 3 0.03
18 11 0.09
19 1 0.01
20 2 0.02
21 4 0.03
22 6 0.05
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (15 bp):
AAATAATTTATTTTA
Found at i:154600 original size:19 final size:19
Alignment explanation
Indices: 154475--154518 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
154465 TTTAATAAGG
154475 TTATTTATTTTAAAATAAA
1 TTATTTATTTTAAAATAAA
* *
154494 TAATTTATTTTAAAATAAT
1 TTATTTATTTTAAAATAAA
154513 TTATTT
1 TTATTT
154519 TAAAATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTTATTTTAAAATAAA
Found at i:154630 original size:18 final size:18
Alignment explanation
Indices: 154607--154663 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
154597 ATTTTAAATA
154607 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
154625 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
154639 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
154657 ATTTATT
1 ATTTATT
154664 TTAAAATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:154632 original size:32 final size:32
Alignment explanation
Indices: 154593--154668 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
154583 TTTTAAAATA
154593 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
154625 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
154657 ATTTATTTTAAA
1 ATTTATTTTAAA
154669 ATATAGATTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:154741 original size:32 final size:32
Alignment explanation
Indices: 154698--154802 Score: 122
Period size: 32 Copynumber: 3.6 Consensus size: 32
154688 TGTAGTTGTG
154698 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
*
154730 TAGATTGATTTA-TTT---TAA---A--A-TA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
154752 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
*
154784 TGTATTGATTTATTTTAAA
1 TGGATTGATTTATTTTAAA
154803 ATATGAATTG
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
22 13 0.22
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.07
32 31 0.52
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
TGGATTGATTTATTTTAAATAATTTATTAGTA
Found at i:154798 original size:22 final size:22
Alignment explanation
Indices: 154782--154890 Score: 200
Period size: 22 Copynumber: 5.0 Consensus size: 22
154772 AATTTATTAG
*
154782 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
154804 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
154826 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
154848 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
154870 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
154891 TAATTTATTA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 85 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:154908 original size:32 final size:32
Alignment explanation
Indices: 154870--154954 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
154860 TATTTTAAAA
154870 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
154902 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
154934 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
154955 ATATGGATTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:155020 original size:80 final size:83
Alignment explanation
Indices: 154846--155034 Score: 287
Period size: 80 Copynumber: 2.3 Consensus size: 83
154836 TTTATTTTAA
*
154846 AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 AATATGGATTGATTTATTTTAAAATATGGATTGATTTA-TTT-AAT-ATGTATTAGTATGGATTG
154911 ATTTATTTTAAATAATTTATT
63 ATTTATTTTAAATAATTTATT
**
154932 TGTATGGATTGATTTATTTTAAAATATGGATTGATTTA-TT-AT-TGTAGTT-GTATGGATTGAT
1 AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTAATATGTA-TTAGTATGGATTGAT
154993 TTATTTTAAATAATTTATT
65 TTATTTTAAATAATTTATT
155012 AATATGGATTGATTTATTTTAAA
1 AATATGGATTGATTTATTTTAAA
155035 TAATTTATTA
Statistics
Matches: 97, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
80 55 0.57
81 2 0.02
82 2 0.02
84 2 0.02
86 36 0.37
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (83 bp):
AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTAATATGTATTAGTATGGATTGATT
TATTTTAAATAATTTATT
Found at i:155023 original size:32 final size:32
Alignment explanation
Indices: 154982--155066 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
154972 ATTGTAGTTG
154982 TATGGATTGATTTATTTTAAATAATTTATTAA
1 TATGGATTGATTTATTTTAAATAATTTATTAA
*
155014 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAA
*
155046 TATGGATTGAATTATTTTAAA
1 TATGGATTGATTTATTTTAAA
155067 ATATGAATTG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAA
Found at i:155071 original size:22 final size:22
Alignment explanation
Indices: 155046--155110 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
155036 AATTTATTAG
*
155046 TATGGATTGAATTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
155068 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
155090 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
155111 TAATTTATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.49
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:155118 original size:14 final size:14
Alignment explanation
Indices: 155099--155152 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
155089 ATATGGATTG
155099 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
155113 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
155131 ATTTATTTTAAATA
1 ATTTATTTTAAATA
155145 ATTTATTT
1 ATTTATTT
155153 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:155132 original size:32 final size:32
Alignment explanation
Indices: 155094--155174 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
155084 TTAAAATATG
155094 GATTGATTTATTTTAAATAATTTATTAGTATA
1 GATTGATTTATTTTAAATAATTTATTAGTATA
* *
155126 GATTGATTTATTTTAAATAATTTATTTGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATA
155158 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
155175 ATATGGATTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (32 bp):
GATTGATTTATTTTAAATAATTTATTAGTATA
Found at i:155216 original size:80 final size:80
Alignment explanation
Indices: 155068--155351 Score: 419
Period size: 80 Copynumber: 3.5 Consensus size: 80
155058 TATTTTAAAA
* *
155068 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTAT-AGATTG
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTATGA-ATTG
*
155131 ATTTATTTTAAATAATTTATTTG
58 ATTTATTTTAAATAATTTATTAG
155154 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTT
155219 TAAATAATTTATTAG
66 TAAATAATTTATTAG
* *
155234 TATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATGGATTGATTTATTT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTT
155299 TAAATAATTTATTAG
66 TAAATAATTTATTAG
* *
155314 CATGGATTGATTTATTTTTAAATATGGATTGATTTATT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT
155352 TTAAATAATT
Statistics
Matches: 188, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
80 146 0.78
81 3 0.02
82 2 0.01
84 2 0.01
86 35 0.19
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTT
TAAATAATTTATTAG
Found at i:155240 original size:220 final size:220
Alignment explanation
Indices: 154593--155254 Score: 849
Period size: 220 Copynumber: 3.1 Consensus size: 220
154583 TTTTAAAATA
*
154593 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G-A---ATTGA
* * *
154658 TTTATTTTAAAATATAGATTGATTTA--TT--AT--TGTAGTT-GTGTGGATTGATTTATTTTAA
56 TTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAA
* * *
154716 ATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TT
120 ATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT
*
154780 AGTATGTATTGATTTATTTT-AA-AA--TA-T-G-A---ATTG
179 -GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTG
*
154813 ATTTA-TTT---TAA---A--A-TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAA
154868 AATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTT
66 AATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTT
*
154933 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
131 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATT
*
154998 TTAAATAATTTATTAATATGGATTG
196 TTAAATAATTTATTAGTATGGATTG
*
155023 ATTTATTTTAAATAATTTATTAGTATGGATTGAATTATTTTAAAATATGAATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAA
*
155088 AATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTT
66 AATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTT
155153 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATT
131 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATT
155218 TTAAATAATTTATTAGTATGGATTG
196 TTAAATAATTTATTAGTATGGATTG
155243 ATTTATTTTAAA
1 ATTTATTTTAAA
155255 ATATGAATTG
Statistics
Matches: 399, Mismatches: 15, Indels: 56
0.85 0.03 0.12
Matches are distributed among these distances:
200 51 0.13
201 4 0.01
202 6 0.02
204 7 0.02
205 4 0.01
206 71 0.18
207 1 0.00
208 2 0.01
209 2 0.01
210 26 0.07
211 4 0.01
213 1 0.00
214 3 0.01
216 3 0.01
217 1 0.00
219 4 0.01
220 209 0.52
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (220 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAA
AATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTT
GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATT
TTAAATAATTTATTAGTATGGATTG
Found at i:155355 original size:21 final size:22
Alignment explanation
Indices: 155315--155358 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
155305 ATTTATTAGC
155315 ATGGATTGATTTATTTTTAAAT
1 ATGGATTGATTTATTTTTAAAT
155337 ATGGATTGATTTA-TTTTAAAT
1 ATGGATTGATTTATTTTTAAAT
155358 A
1 A
155359 ATTTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
ATGGATTGATTTATTTTTAAAT
Found at i:155416 original size:31 final size:31
Alignment explanation
Indices: 155381--155439 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
155371 AGTTGTATGG
* *
155381 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
155412 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
155440 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:155478 original size:16 final size:16
Alignment explanation
Indices: 155457--155499 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
155447 GTTTAAAAAA
155457 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
155473 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
* *
155489 TTAGTTCATTT
1 TCAGTTTATTT
155500 TAGCAGTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (16 bp):
TCAGTTTATTTATATT
Found at i:163800 original size:21 final size:21
Alignment explanation
Indices: 163771--163815 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
163761 AAACTACATA
163771 TTTAATATCTAAATTATTATT
1 TTTAATATCTAAATTATTATT
* *
163792 TTTAGTATCTAAATTTTTATT
1 TTTAATATCTAAATTATTATT
163813 TTT
1 TTT
163816 TTTAAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTAATATCTAAATTATTATT
Found at i:165658 original size:22 final size:22
Alignment explanation
Indices: 165628--165688 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 22
165618 CCCTATGAAG
165628 TTTT-TAAATTCTTCTCTAAAA
1 TTTTATAAATTCTTCTCTAAAA
165649 TTTTATAAA---TTCTCTAAAA
1 TTTTATAAATTCTTCTCTAAAA
*
165668 TTTTATAAATTCATCTACTAA
1 TTTTATAAATTCTTCT-CTAA
165689 CATAAAATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 19 0.56
21 4 0.12
22 7 0.21
23 4 0.12
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTATAAATTCTTCTCTAAAA
Found at i:165663 original size:19 final size:19
Alignment explanation
Indices: 165639--165684 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
165629 TTTTAAATTC
165639 TTCTCTAAAATTTTATAAA
1 TTCTCTAAAATTTTATAAA
165658 TTCTCTAAAATTTTATAAA
1 TTCTCTAAAATTTTATAAA
165677 TTCATCTA
1 TTC-TCTA
165685 CTAACATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (19 bp):
TTCTCTAAAATTTTATAAA
Found at i:176747 original size:18 final size:18
Alignment explanation
Indices: 176721--176763 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
176711 TTCAAACCCA
*
176721 AGAAGCATTGGAGATATC
1 AGAACCATTGGAGATATC
176739 AGAACCATTGGAGATATC
1 AGAACCATTGGAGATATC
176757 AGAACCA
1 AGAACCA
176764 CTTGCAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (18 bp):
AGAACCATTGGAGATATC
Found at i:177745 original size:18 final size:18
Alignment explanation
Indices: 177722--177764 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
177712 TGTCCCGAAG
*
177722 GACCACTATATCCTAAAA
1 GACCACTATATCCCAAAA
*
177740 GACCACTATGTCCCAAAA
1 GACCACTATATCCCAAAA
177758 GACCACT
1 GACCACT
177765 GATAATCCCT
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:0.40, C:0.33, G:0.09, T:0.19
Consensus pattern (18 bp):
GACCACTATATCCCAAAA
Found at i:184633 original size:18 final size:18
Alignment explanation
Indices: 184610--184644 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
184600 ACTGAATATT
184610 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
184628 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
184645 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:185220 original size:20 final size:20
Alignment explanation
Indices: 185195--185245 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
185185 TATCTAAAGT
*
185195 GGGTATCGGTATCCCATATA
1 GGGTATCGATATCCCATATA
185215 GGGTATCGATATCCCATATA
1 GGGTATCGATATCCCATATA
185235 GGGTATCGATA
1 GGGTATCGATA
185246 CATCCCTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (20 bp):
GGGTATCGATATCCCATATA
Found at i:185327 original size:29 final size:29
Alignment explanation
Indices: 185294--185378 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 29
185284 TTTAACCAGT
185294 GGCTAAAATATAAGTTTTAAAAGTTTAGA
1 GGCTAAAATATAAGTTTTAAAAGTTTAGA
* * *
185323 GGCTAAAGTATAAGCTTTGAAAAGTTTAGG
1 GGCTAAAATATAAG-TTTTAAAAGTTTAGA
* *
185353 GAGC-AAAATTGTAATTTTTAAAAGTT
1 G-GCTAAAA-TATAAGTTTTAAAAGTT
185379 ATATATTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 13 0.28
30 27 0.59
31 6 0.13
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (29 bp):
GGCTAAAATATAAGTTTTAAAAGTTTAGA
Found at i:185348 original size:30 final size:29
Alignment explanation
Indices: 185294--185351 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
185284 TTTAACCAGT
*
185294 GGCTAAAATATAAGTTTTAAAAGTTTAGA
1 GGCTAAAATATAAGTTTGAAAAGTTTAGA
*
185323 GGCTAAAGTATAAGCTTTGAAAAGTTTAG
1 GGCTAAAATATAAG-TTTGAAAAGTTTAG
185352 GGAGCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (29 bp):
GGCTAAAATATAAGTTTGAAAAGTTTAGA
Found at i:191848 original size:51 final size:51
Alignment explanation
Indices: 191783--191917 Score: 146
Period size: 51 Copynumber: 2.6 Consensus size: 51
191773 CACCCGTAGC
* * * *
191783 AGTAAAGCGCGCCCCCTGAACCGCGCTATATGCTGATTTGGCAT-CATGTGG
1 AGTATAGCGCGCCCCCTGAACCGCGCTATACGCTGA-CTGGCATACACGTGG
* * **
191834 AGTATAGCGCGCCCCCTGTACCTCGCTATACGCTGACTGGGTTACACGTGG
1 AGTATAGCGCGCCCCCTGAACCGCGCTATACGCTGACTGGCATACACGTGG
* * **
191885 GGTATAGCGTGCCCCCTGCCCCGCGCTATACGC
1 AGTATAGCGCGCCCCCTGAACCGCGCTATACGC
191918 CATGTAGGGG
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
50 4 0.06
51 66 0.94
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (51 bp):
AGTATAGCGCGCCCCCTGAACCGCGCTATACGCTGACTGGCATACACGTGG
Found at i:195687 original size:24 final size:24
Alignment explanation
Indices: 195658--195739 Score: 96
Period size: 24 Copynumber: 3.3 Consensus size: 24
195648 ATTAAATGAG
195658 AAATAAAAAAATTACAATTAAACA
1 AAATAAAAAAATTACAATTAAACA
*
195682 AAATAAAGTAAA-TACAAATATAATA-A
1 AAATAAA-AAAATTAC-AAT-TAA-ACA
195708 GAAATAAAAAAATTACAATTAAACA
1 -AAATAAAAAAATTACAATTAAACA
195733 AAATAAA
1 AAATAAA
195740 GTAAATACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
24 18 0.37
25 10 0.20
26 10 0.20
27 11 0.22
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (24 bp):
AAATAAAAAAATTACAATTAAACA
Found at i:195689 original size:47 final size:49
Alignment explanation
Indices: 195626--195758 Score: 180
Period size: 51 Copynumber: 2.7 Consensus size: 49
195616 AAGTCCAACA
* * * *
195626 AATTTAACAAAATAAAGTAAGT-ATTA-AATGAGAAATAAAAAAATTAC
1 AATTAAACAAAATAAAGTAAATAAATATAATAAGAAATAAAAAAATTAC
195673 AATTAAACAAAATAAAGTAAATACAAATATAATAAGAAATAAAAAAATTAC
1 AATTAAACAAAATAAAGTAAAT--AAATATAATAAGAAATAAAAAAATTAC
195724 AATTAAACAAAATAAAGTAAATACAAATATAATAA
1 AATTAAACAAAATAAAGTAAAT--AAATATAATAA
195759 TAAAAATCTA
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
47 20 0.26
50 3 0.04
51 55 0.71
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.23
Consensus pattern (49 bp):
AATTAAACAAAATAAAGTAAATAAATATAATAAGAAATAAAAAAATTAC
Found at i:195715 original size:51 final size:51
Alignment explanation
Indices: 195656--195758 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
195646 GTATTAAATG
195656 AGAAATAAAAAAATTACAATTAAACAAAATAAAGTAAATACAAATATAATA
1 AGAAATAAAAAAATTACAATTAAACAAAATAAAGTAAATACAAATATAATA
195707 AGAAATAAAAAAATTACAATTAAACAAAATAAAGTAAATACAAATATAATA
1 AGAAATAAAAAAATTACAATTAAACAAAATAAAGTAAATACAAATATAATA
195758 A
1 A
195759 TAAAAATCTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (51 bp):
AGAAATAAAAAAATTACAATTAAACAAAATAAAGTAAATACAAATATAATA
Found at i:195748 original size:24 final size:24
Alignment explanation
Indices: 195670--195749 Score: 92
Period size: 24 Copynumber: 3.2 Consensus size: 24
195660 ATAAAAAAAT
195670 TACAATTAAACAAAATAAAGTAAA
1 TACAATTAAACAAAATAAAGTAAA
*
195694 TACAAATATAATA-AGAAATAAA-AAAA
1 TAC-AAT-TAA-ACA-AAATAAAGTAAA
195720 TTACAATTAAACAAAATAAAGTAAA
1 -TACAATTAAACAAAATAAAGTAAA
195745 TACAA
1 TACAA
195750 ATATAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
24 16 0.34
25 10 0.21
26 10 0.21
27 11 0.23
ACGTcount: A:0.68, C:0.07, G:0.04, T:0.21
Consensus pattern (24 bp):
TACAATTAAACAAAATAAAGTAAA
Found at i:196228 original size:36 final size:36
Alignment explanation
Indices: 196181--196255 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
196171 CTGTGACGCT
196181 GGCAGTGGCGGGGTCATAAAACCAGGTGAAGACGGC
1 GGCAGTGGCGGGGTCATAAAACCAGGTGAAGACGGC
196217 GGCAGTGGCGGGGTCATAAAACCAGGTGAAGACGGC
1 GGCAGTGGCGGGGTCATAAAACCAGGTGAAGACGGC
196253 GGC
1 GGC
196256 GGCATCTGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.27, C:0.20, G:0.43, T:0.11
Consensus pattern (36 bp):
GGCAGTGGCGGGGTCATAAAACCAGGTGAAGACGGC
Found at i:197945 original size:111 final size:111
Alignment explanation
Indices: 197808--198029 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
197798 ATTACAAAAA
*
197808 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
197873 AATTAAAACATTAAAATGTTATCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
197919 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
197984 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
198030 ATGATTTCCA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Done.