Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003216.1 Hibiscus syriacus cultivar Beakdansim tig00006770_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: 127059
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1405 original size:30 final size:30
Alignment explanation
Indices: 1365--1432 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
1355 CTGCATAAAT
* **
1365 AAATTCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
1395 AAATGCATCATTTATAACACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
1425 ATATGCAT
1 AAATGCAT
1433 TCAAATTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:7992 original size:10 final size:10
Alignment explanation
Indices: 7977--8023 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
7967 TACACTTGAA
7977 GAAAAAAAAT
1 GAAAAAAAAT
7987 GAAAAAAAAT
1 GAAAAAAAAT
7997 G---AAAAAT
1 GAAAAAAAAT
*
8004 GAAAAAAAAA
1 GAAAAAAAAT
*
8014 GAAAATAAAT
1 GAAAAAAAAT
8024 AAATAAATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
7 7 0.23
10 24 0.77
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (10 bp):
GAAAAAAAAT
Found at i:8003 original size:17 final size:17
Alignment explanation
Indices: 7981--8018 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
7971 CTTGAAGAAA
*
7981 AAAAATGAAAAAAAATG
1 AAAAATGAAAAAAAAAG
7998 AAAAATGAAAAAAAAAG
1 AAAAATGAAAAAAAAAG
8015 AAAA
1 AAAA
8019 TAAATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.08
Consensus pattern (17 bp):
AAAAATGAAAAAAAAAG
Found at i:8017 original size:27 final size:28
Alignment explanation
Indices: 7977--8033 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
7967 TACACTTGAA
* *
7977 GAAAAAAAATGAAAAAAAATGAA-AAAT
1 GAAAAAAAAAGAAAAAAAATAAATAAAT
*
8004 GAAAAAAAAAGAAAATAAATAAATAAAT
1 GAAAAAAAAAGAAAAAAAATAAATAAAT
8032 GA
1 GA
8034 GGGTTCAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (28 bp):
GAAAAAAAAAGAAAAAAAATAAATAAAT
Found at i:9503 original size:3 final size:3
Alignment explanation
Indices: 9495--9574 Score: 108
Period size: 3 Copynumber: 26.7 Consensus size: 3
9485 TATTTCTATA
* *
9495 TAT TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
9543 TAT TAT TAT TAT TCT T-T TCAT TTT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA
9575 ATATAAATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.03
3 64 0.94
4 2 0.03
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:11443 original size:2 final size:2
Alignment explanation
Indices: 11436--11514 Score: 151
Period size: 2 Copynumber: 40.0 Consensus size: 2
11426 TGATTATGTG
11436 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11515 ATACATTATG
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 75 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11664 original size:20 final size:20
Alignment explanation
Indices: 11639--11676 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11629 TAACAAATTA
11639 TTACTGTTACACCTTTTTTT
1 TTACTGTTACACCTTTTTTT
*
11659 TTACTGTTATACCTTTTT
1 TTACTGTTACACCTTTTT
11677 ATTCACTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.05, T:0.61
Consensus pattern (20 bp):
TTACTGTTACACCTTTTTTT
Found at i:15115 original size:31 final size:30
Alignment explanation
Indices: 15076--15187 Score: 100
Period size: 31 Copynumber: 3.7 Consensus size: 30
15066 TGAAAAATAA
* **
15076 TTTACGTAAAATAGATTATTTGAAAATTGT
1 TTTACGTAAAATAAATTACATGAAAATTGT
15106 TTTCACGTAAAATAAATTACATGAAAATTGT
1 TTT-ACGTAAAATAAATTACATGAAAATTGT
* * * * * *
15137 TTTACGAAAAAAAAGATTACCT-TAAACTAT
1 TTTACGTAAAATAA-ATTACATGAAAATTGT
* *
15167 TTTACGTAGAATGAATTACAT
1 TTTACGTAAAATAAATTACAT
15188 TTTTTGGAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
29 6 0.09
30 27 0.41
31 33 0.50
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (30 bp):
TTTACGTAAAATAAATTACATGAAAATTGT
Found at i:15621 original size:19 final size:18
Alignment explanation
Indices: 15549--15639 Score: 60
Period size: 17 Copynumber: 4.9 Consensus size: 18
15539 ATATTACTAA
*
15549 ATTAAAAATATCATATCAT
1 ATTAAAAATATAATAT-AT
**
15568 A-TATTAATATAATATAT
1 ATTAAAAATATAATATAT
* * *
15585 CTGAATAGATATTAATATAGT
1 ATTAA-AAATA-TAATATA-T
15606 ATTAAAAATATAATAT-T
1 ATTAAAAATATAATATAT
* *
15623 ATTAAAATTATATTATA
1 ATTAAAAATATAATATA
15640 ATAATATTAA
Statistics
Matches: 54, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
17 17 0.31
18 12 0.22
19 10 0.19
20 11 0.20
21 4 0.07
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAAAAATATAATATAT
Found at i:15716 original size:46 final size:49
Alignment explanation
Indices: 15621--15721 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 49
15611 AAATATAATA
* * **
15621 TTATTAAAATTATATTATAATAATATTAAATATTTTAATAATTAATTTT
1 TTATTAAAATGATATTATAATAATATTAAATAATAAAATAATTAATTTT
*
15670 TTATTAAAATGATA-T-TAA-AATATTAAATAAATAAAATAA-TACTTTT
1 TTATTAAAATGATATTATAATAATATTAAAT-AATAAAATAATTAATTTT
15716 TTATTA
1 TTATTA
15722 TTTATAGTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
46 22 0.48
47 10 0.22
48 1 0.02
49 13 0.28
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (49 bp):
TTATTAAAATGATATTATAATAATATTAAATAATAAAATAATTAATTTT
Found at i:15948 original size:22 final size:22
Alignment explanation
Indices: 15922--15964 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
15912 ATTTTCTACA
15922 AAAATT-AAACACACTCTTACTG
1 AAAATTCAAACACACT-TTACTG
*
15944 AAAATTCAAACTCACTTTACT
1 AAAATTCAAACACACTTTACT
15965 CTAATGACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATTCAAACACACTTTACTG
Found at i:17232 original size:11 final size:11
Alignment explanation
Indices: 17218--17242 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17208 TTATCTTAAA
17218 ATATTTTTTTT
1 ATATTTTTTTT
17229 ATATTTTTTTT
1 ATATTTTTTTT
17240 ATA
1 ATA
17243 GTTTAAGTGA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
ATATTTTTTTT
Found at i:20363 original size:14 final size:14
Alignment explanation
Indices: 20344--20413 Score: 113
Period size: 14 Copynumber: 5.0 Consensus size: 14
20334 GTTTTCTTCA
20344 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
20358 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
* *
20372 TGTAGAAAACAAAA
1 TGTAGAAAACAGAC
*
20386 TGTAGAAAATAGAC
1 TGTAGAAAACAGAC
20400 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
20414 AAGTCTGTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 50 1.00
ACGTcount: A:0.53, C:0.11, G:0.20, T:0.16
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:25139 original size:14 final size:14
Alignment explanation
Indices: 25120--25161 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
25110 CCTGATATCA
25120 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
*
25134 TGTAGAAAACAGAA
1 TGTAGAAAACAGAC
25148 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
25162 AAGTCTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.52, C:0.12, G:0.21, T:0.14
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:53770 original size:18 final size:18
Alignment explanation
Indices: 53743--53778 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
53733 CACCGGTCAA
*
53743 CGGGTCGGGTCAACGGGT
1 CGGGTAGGGTCAACGGGT
53761 CGGGTAGGGTCAACGGGT
1 CGGGTAGGGTCAACGGGT
53779 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.19, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTAGGGTCAACGGGT
Found at i:53779 original size:13 final size:13
Alignment explanation
Indices: 53737--53765 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53727 GAATAGCACC
53737 GGTCAACGGGTCG
1 GGTCAACGGGTCG
53750 GGTCAACGGGTCG
1 GGTCAACGGGTCG
53763 GGT
1 GGT
53766 AGGGTCAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:53811 original size:10 final size:10
Alignment explanation
Indices: 53791--53841 Score: 61
Period size: 9 Copynumber: 5.2 Consensus size: 10
53781 ACGGGTCGTG
53791 ACCGGTC-AA
1 ACCGGTCAAA
53800 ACCGGTCAAA
1 ACCGGTCAAA
53810 ACCGGTTCAAA
1 ACCGG-TCAAA
* *
53821 ATCGGT-TAA
1 ACCGGTCAAA
53830 ACCGGTCAAA
1 ACCGGTCAAA
53840 AC
1 AC
53842 TGGTTTCCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 14 0.40
10 12 0.34
11 9 0.26
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:53821 original size:11 final size:11
Alignment explanation
Indices: 53798--53846 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 11
53788 GTGACCGGTC
53798 AAACCGG-TCA
1 AAACCGGTTCA
53808 AAACCGGTTCA
1 AAACCGGTTCA
*
53819 AAATCGGTT--
1 AAACCGGTTCA
53828 AAACCGG-TCA
1 AAACCGGTTCA
*
53838 AAACTGGTT
1 AAACCGGTT
53847 TCCAGCGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
8 1 0.03
9 6 0.19
10 13 0.41
11 12 0.38
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (11 bp):
AAACCGGTTCA
Found at i:60933 original size:29 final size:29
Alignment explanation
Indices: 60873--60966 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
60863 ATTTTACACA
** * *
60873 AATAGCACCC-TTT-TAAAAAATTACCAA
1 AATAGCACCCATTTCTAATTAATTCCCAG
60900 AATAGCACCCATTTCTAATTAATTCCCAG
1 AATAGCACCCATTTCTAATTAATTCCCAG
***
60929 AATAGCA-CCAAAACTGAATTAATTCCCAG
1 AATAGCACCCATTTCT-AATTAATTCCCAG
60958 AATAGCACC
1 AATAGCACC
60967 GGTCAACGGT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
27 10 0.18
28 8 0.14
29 37 0.66
30 1 0.02
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (29 bp):
AATAGCACCCATTTCTAATTAATTCCCAG
Found at i:61001 original size:13 final size:13
Alignment explanation
Indices: 60985--61015 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
60975 GTCAACGGGT
*
60985 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
60998 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
61011 CGGGT
1 CGGGT
61016 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:61050 original size:10 final size:10
Alignment explanation
Indices: 61035--61082 Score: 71
Period size: 10 Copynumber: 4.8 Consensus size: 10
61025 GTGACCAGTG
61035 AAACCGGTCA
1 AAACCGGTCA
61045 AAACCGGTTCA
1 AAACCGG-TCA
*
61056 AAACCGGT-T
1 AAACCGGTCA
61065 AAACCGGTCA
1 AAACCGGTCA
61075 AAACCGGT
1 AAACCGGT
61083 TTCCAGCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 8 0.24
10 16 0.47
11 10 0.29
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.15
Consensus pattern (10 bp):
AAACCGGTCA
Found at i:65562 original size:20 final size:20
Alignment explanation
Indices: 65533--65588 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
65523 AGTTGTTGGG
* *
65533 CAAGAGTATCGATACTCTTT
1 CAAGAATATCGAAACTCTTT
65553 CAAGAATATCGAAACTCTTT
1 CAAGAATATCGAAACTCTTT
*
65573 CAAGAATATCAAAACT
1 CAAGAATATCGAAACT
65589 TTGGGTCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (20 bp):
CAAGAATATCGAAACTCTTT
Found at i:66228 original size:15 final size:15
Alignment explanation
Indices: 66208--66238 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
66198 CAGAACAAAC
66208 CAGTAGACTAGATAG
1 CAGTAGACTAGATAG
*
66223 CAGTAGACTTGATAG
1 CAGTAGACTAGATAG
66238 C
1 C
66239 TTGGACATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (15 bp):
CAGTAGACTAGATAG
Found at i:68020 original size:2 final size:2
Alignment explanation
Indices: 68002--68034 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
67992 AAATTATTAT
68002 TA TA T- TA TA TCA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T
68035 GTGTGTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68698 original size:2 final size:2
Alignment explanation
Indices: 68691--68722 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
68681 ATAAGAAGAA
68691 AT AT 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 AT AT
68723 TGTATATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70050 original size:48 final size:49
Alignment explanation
Indices: 69955--70053 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
69945 GCTGATGTGT
69955 CTATGCTTAAAAAATATATAGTATAAAAATTATAAAACTTTTATGGGCC
1 CTATGCTTAAAAAATATATAGTATAAAAATTATAAAACTTTTATGGGCC
*
70004 CTATGCTTAAAAAATATATATTATAAAAATTATAAAAC-TTTATGGGCC
1 CTATGCTTAAAAAATATATAGTATAAAAATTATAAAACTTTTATGGGCC
70052 CT
1 CT
70054 GGGCGGGCGC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 12 0.24
49 37 0.76
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.35
Consensus pattern (49 bp):
CTATGCTTAAAAAATATATAGTATAAAAATTATAAAACTTTTATGGGCC
Found at i:71030 original size:29 final size:29
Alignment explanation
Indices: 70952--71020 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
70942 AAAAATTGCA
**
70952 AAACTTTGAACCATGCACCATTCGGTGCC
1 AAACTTTGAACCATGCATAATTCGGTGCC
70981 AAACTTTGAACCATGCATAATTCGGTGCC
1 AAACTTTGAACCATGCATAATTCGGTGCC
71010 AAACTTTGAAC
1 AAACTTTGAAC
71021 TTTCAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (29 bp):
AAACTTTGAACCATGCATAATTCGGTGCC
Found at i:77427 original size:48 final size:48
Alignment explanation
Indices: 77365--77470 Score: 149
Period size: 48 Copynumber: 2.2 Consensus size: 48
77355 TAACATCAAC
* *
77365 ATTCGCAATTACTAAAACACTCGAAATCACAAATTAATAACCTTTAAT
1 ATTCACAATTACTAAAACACTCGAAATCACAAAATAATAACCTTTAAT
* * * *
77413 ATTCACAATTACTAACATACTTGAAATCATAAAATAATAACCTTTAAT
1 ATTCACAATTACTAAAACACTCGAAATCACAAAATAATAACCTTTAAT
*
77461 ATTTACAATT
1 ATTCACAATT
77471 TAAGACCTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (48 bp):
ATTCACAATTACTAAAACACTCGAAATCACAAAATAATAACCTTTAAT
Found at i:79879 original size:11 final size:11
Alignment explanation
Indices: 79863--79888 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
79853 TGATTTGGAC
79863 ATTTTTTATTT
1 ATTTTTTATTT
79874 ATTTTTTATTT
1 ATTTTTTATTT
79885 ATTT
1 ATTT
79889 CTGAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
ATTTTTTATTT
Found at i:80315 original size:41 final size:41
Alignment explanation
Indices: 80270--80367 Score: 187
Period size: 41 Copynumber: 2.4 Consensus size: 41
80260 ATTCGCGTTG
80270 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
80311 CATTTCGCGTTGCGACAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
80352 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
80368 TTTCCATTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:80320 original size:20 final size:20
Alignment explanation
Indices: 80295--80387 Score: 123
Period size: 20 Copynumber: 4.6 Consensus size: 20
80285 TAGTTGAAAA
80295 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
** ** **
80315 TCGCGTTGCGACAGTTGAAAA
1 TCGCGTTGCGA-TTTTCCATT
80336 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
80356 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
80376 TCGCGTTGCGAT
1 TCGCGTTGCGAT
80388 AGTCTACAGT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:80548 original size:5 final size:6
Alignment explanation
Indices: 80509--80545 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
80499 GACACGTATT
80509 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
80546 CGAGAGTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.30, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:81545 original size:18 final size:19
Alignment explanation
Indices: 81477--81563 Score: 104
Period size: 19 Copynumber: 4.5 Consensus size: 19
81467 CAACGAATTT
81477 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
81496 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
81518 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
81537 TCG-AACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
81555 TCGCAACGA
1 TCGCAACGA
81564 CAACTGTAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
18 18 0.32
19 21 0.38
20 2 0.04
21 2 0.04
22 13 0.23
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:81555 original size:59 final size:60
Alignment explanation
Indices: 81477--81624 Score: 212
Period size: 59 Copynumber: 2.5 Consensus size: 60
81467 CAACGAATTT
*
81477 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAA-CGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACCGAA-ATGGAAAA
*
81537 TCG-AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATTGCAACGCGAAATGGAAAA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAAC-CGAAATGGAAAA
*
81597 TCGCAACGCGAA-ATGGAAAATCGCAACG
1 TCGCAA--CGAATTTGGAAAATCGCAACG
81625 CGATTTTCAA
Statistics
Matches: 80, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
59 42 0.52
60 13 0.16
61 6 0.08
62 15 0.19
63 4 0.05
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.18
Consensus pattern (60 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACCGAAATGGAAAA
Found at i:81604 original size:20 final size:20
Alignment explanation
Indices: 81579--81627 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
81569 GTAGACTATT
81579 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
81599 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
81619 GCAACGCGA
1 GCAACGCGA
81628 TTTTCAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.22, G:0.27, T:0.08
Consensus pattern (20 bp):
GCAACGCGAAATGGAAAATC
Found at i:82601 original size:20 final size:20
Alignment explanation
Indices: 82578--82631 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
82568 GCATTAAGAT
*
82578 TTTCCAAATTCG-TGTTGCGA
1 TTTCCAAATTCGCAG-TGCGA
82598 TTTCCAAATTCGCAGTGCGA
1 TTTCCAAATTCGCAGTGCGA
82618 TTTCCAAATTCGCA
1 TTTCCAAATTCGCA
82632 ACACTGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (20 bp):
TTTCCAAATTCGCAGTGCGA
Found at i:82647 original size:41 final size:41
Alignment explanation
Indices: 82597--82734 Score: 147
Period size: 40 Copynumber: 3.4 Consensus size: 41
82587 TCGTGTTGCG
*
82597 ATTTCCAAATTCGC-AGTGCGATTTCCAAATTCGCAACACTGA
1 ATTT-CAAATTCGCAACT-CGATTTCCAAATTCGCAACACTGA
**
82639 ATTTCAAATTCGCAACTCGATTTCTGAATTCGCAACA-TGA
1 ATTTCAAATTCGCAACTCGATTTCCAAATTCGCAACACTGA
**** *
82679 ATTTTGTTTTCGCAACTCGATTTTCAAATTCGCAACAC-GA
1 ATTTCAAATTCGCAACTCGATTTCCAAATTCGCAACACTGA
* *
82719 ATTTTAATTTCGCAAC
1 ATTTCAAATTCGCAAC
82735 AGGTTTTAGT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 49 0.60
41 27 0.33
42 6 0.07
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (41 bp):
ATTTCAAATTCGCAACTCGATTTCCAAATTCGCAACACTGA
Found at i:82691 original size:40 final size:40
Alignment explanation
Indices: 82615--82734 Score: 152
Period size: 40 Copynumber: 3.0 Consensus size: 40
82605 ATTCGCAGTG
* * *
82615 CGATTTCCAAATTCGCAACACTGAATTTCAAATTCGCAACT
1 CGATTTCTAAATTCGCAACA-TGAATTTTAATTTCGCAACT
* **
82656 CGATTTCTGAATTCGCAACATGAATTTTGTTTTCGCAACT
1 CGATTTCTAAATTCGCAACATGAATTTTAATTTCGCAACT
*
82696 CGATTT-TCAAATTCGCAACACGAATTTTAATTTCGCAAC
1 CGATTTCT-AAATTCGCAACATGAATTTTAATTTCGCAAC
82735 AGGTTTTAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 49 0.72
41 18 0.26
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (40 bp):
CGATTTCTAAATTCGCAACATGAATTTTAATTTCGCAACT
Found at i:82735 original size:20 final size:19
Alignment explanation
Indices: 82626--82754 Score: 91
Period size: 20 Copynumber: 6.5 Consensus size: 19
82616 GATTTCCAAA
* *
82626 TTCGCAACACTGAATTTCAAA
1 TTCGCAACAC-G-ATTTTAAT
*
82647 TTCGCAACTCGATTTCTGAA-
1 TTCGCAACACGATTT-T-AAT
* **
82667 TTCGCAACATGAATTTTGTT
1 TTCGCAACACG-ATTTTAAT
* *
82687 TTCGCAACTCGATTTTCAAA
1 TTCGCAACACGATTTT-AAT
82707 TTCGCAACACGAATTTTAAT
1 TTCGCAACACG-ATTTTAAT
* *
82727 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGATTTTAAT
82745 TTCGCAACAC
1 TTCGCAACAC
82755 AAATGTTTTG
Statistics
Matches: 86, Mismatches: 15, Indels: 16
0.74 0.13 0.14
Matches are distributed among these distances:
18 15 0.17
19 10 0.12
20 41 0.48
21 20 0.23
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.35
Consensus pattern (19 bp):
TTCGCAACACGATTTTAAT
Found at i:83529 original size:12 final size:12
Alignment explanation
Indices: 83508--83541 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
83498 ACCACATTTC
*
83508 CAATACCAAACA
1 CAATATCAAACA
83520 CAATATCAAACA
1 CAATATCAAACA
*
83532 CAATCTCAAA
1 CAATATCAAA
83542 ACCCACAACC
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:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:86137 original size:20 final size:20
Alignment explanation
Indices: 86114--86160 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
86104 AAACGCAAAA
86114 TCGCAACGCGAATTTGACTT
1 TCGCAACGCGAATTTGACTT
**
86134 TCGCATTGCGAATTTGACTT
1 TCGCAACGCGAATTTGACTT
86154 TCGCAAC
1 TCGCAAC
86161 CATCGTAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (20 bp):
TCGCAACGCGAATTTGACTT
Found at i:86383 original size:63 final size:64
Alignment explanation
Indices: 86268--86400 Score: 205
Period size: 63 Copynumber: 2.1 Consensus size: 64
86258 ATTTAAAACA
86268 ACAAATCAATTAAACAAACAAAAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTT
1 ACAAATCAATTAAACAAACAAAAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTT
* *** * *
86332 ACAAATCAATTAAACAACCAAAAAA-AATTCTTATTTCCTCATCAATTAAACAAATCAACTTTT
1 ACAAATCAATTAAACAAACAAAAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTT
86395 ACAAAT
1 ACAAAT
86401 ACGTCAATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
63 39 0.62
64 24 0.38
ACGTcount: A:0.53, C:0.18, G:0.01, T:0.28
Consensus pattern (64 bp):
ACAAATCAATTAAACAAACAAAAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTT
Found at i:87776 original size:21 final size:21
Alignment explanation
Indices: 87752--87857 Score: 133
Period size: 21 Copynumber: 5.0 Consensus size: 21
87742 GAACGGTTGA
*
87752 AGGGACCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
**
87773 AGGGGCCTCTTGAACGATGGG
1 AGGGGCCTCTTGAACGATGAC
* *
87794 AGGGGCCTCTTGAAGGATGAT
1 AGGGGCCTCTTGAACGATGAC
*
87815 AGGGGCCTCTTGAACGAT-ATG
1 AGGGGCCTCTTGAACGATGA-C
*
87836 AGAGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
87857 A
1 A
87858 AGTGAATCGG
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.01
21 71 0.97
22 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:87804 original size:42 final size:42
Alignment explanation
Indices: 87752--87857 Score: 158
Period size: 42 Copynumber: 2.5 Consensus size: 42
87742 GAACGGTTGA
* *
87752 AGGGACCTCTTGAACGATGACAGGGGCCTCTTGAACGATGGG
1 AGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGG
* * *
87794 AGGGGCCTCTTGAAGGATGATAGGGGCCTCTTGAACGATATG
1 AGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGG
*
87836 AGAGGCCTCTTGAACGATGACA
1 AGGGGCCTCTTGAACGATGACA
87858 AGTGAATCGG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (42 bp):
AGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGG
Found at i:89984 original size:20 final size:20
Alignment explanation
Indices: 89961--90004 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
89951 AAATCGCAAC
89961 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
89981 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
90001 GCGA
1 GCGA
90005 ATTTAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:90015 original size:20 final size:20
Alignment explanation
Indices: 89972--90015 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
89962 CGATTTTCAT
* * *
89972 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
*
89992 TTTCGTGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
90012 TTTC
1 TTTC
90016 AAATAGTCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:90372 original size:22 final size:22
Alignment explanation
Indices: 90344--90400 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
90334 GATGGAGATA
* *
90344 GACGGATTTTGCCGGATATGGG
1 GACGGATTTCGCCGGAGATGGG
*
90366 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
90388 GACGGATGTCGCC
1 GACGGATTTCGCC
90401 ATAGAGAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.18, G:0.42, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:93509 original size:18 final size:18
Alignment explanation
Indices: 93486--93520 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
93476 AATTATTTAA
93486 ATTTAAA-ATCTAAAAACT
1 ATTTAAATAT-TAAAAACT
93504 ATTTAAATATTAAAAAC
1 ATTTAAATATTAAAAAC
93521 AAATAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTTAAATATTAAAAACT
Found at i:95071 original size:18 final size:18
Alignment explanation
Indices: 95044--95094 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
95034 ACTGAATATT
*
95044 TGTCCCGAAGGATCACTA
1 TGTCCCGAAGGACCACTA
* *
95062 TGTCCTGAAGTACCACTA
1 TGTCCCGAAGGACCACTA
**
95080 TGTTTCGAAGGACCA
1 TGTCCCGAAGGACCA
95095 ATGTTAATCC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:99388 original size:20 final size:19
Alignment explanation
Indices: 99365--99401 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
99355 AGAACCCCAG
*
99365 GGGGGTATCGATTCCCCTA
1 GGGGGAATCGATTCCCCTA
*
99384 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
99402 TCAAATGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.27, G:0.35, T:0.24
Consensus pattern (19 bp):
GGGGGAATCGATTCCCCTA
Found at i:103288 original size:22 final size:21
Alignment explanation
Indices: 103246--103285 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
103236 GAGTTTATTT
103246 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTGAAACA
103267 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
103286 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAACA
Found at i:105640 original size:20 final size:20
Alignment explanation
Indices: 105612--105649 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
105602 TATCTTTTAG
105612 ATTCATATAATT-TCATATTT
1 ATTCATAT-ATTATCATATTT
*
105632 ATTCTTATATTATCATAT
1 ATTCATATATTATCATAT
105650 AACTTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTCATATATTATCATATTT
Found at i:110765 original size:20 final size:20
Alignment explanation
Indices: 110737--110774 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
110727 TATCTTTTAG
110737 ATTCATATAATT-TCATATCT
1 ATTCATAT-ATTATCATATCT
*
110757 ATTCTTATATTATCATAT
1 ATTCATATATTATCATAT
110775 AACTTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTCATATATTATCATATCT
Found at i:117384 original size:30 final size:30
Alignment explanation
Indices: 117350--117455 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 30
117340 AGAAGTTAGT
117350 TGGGATGTTCTTCTATGTTTCTTAGCCATG
1 TGGGATGTTCTTCTATGTTTCTTAGCCATG
* * * * *
117380 TGGGATTGTTTTGTTCTCATATTTTTACTCTTTAGACTTT
1 TGGGA-TG--TT-CT-TC-TA-TGTT--TC-TTAGCCATG
117420 TGGGATGTTCTTCTATGTTTCTTAGCCATG
1 TGGGATGTTCTTCTATGTTTCTTAGCCATG
117450 TGGGAT
1 TGGGAT
117456 TGTTTTTTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 20
0.65 0.12 0.23
Matches are distributed among these distances:
30 17 0.30
31 4 0.07
33 5 0.09
34 3 0.05
35 4 0.07
36 3 0.05
37 5 0.09
39 4 0.07
40 11 0.20
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.50
Consensus pattern (30 bp):
TGGGATGTTCTTCTATGTTTCTTAGCCATG
Found at i:117395 original size:36 final size:36
Alignment explanation
Indices: 117355--117461 Score: 84
Period size: 36 Copynumber: 3.0 Consensus size: 36
117345 TTAGTTGGGA
117355 TGTTCTTCTATGTTTCTTAGCCATGTGGGATTGTTT
1 TGTTCTTCTATGTTTCTTAGCCATGTGGGATTGTTT
* ** *
117391 TGTTC-TC-ATATTT-TTA-CTC-T-TTAGACTT-TTGGGA
1 TGTTCTTCTATGTTTCTTAGC-CATGTGGGA-TTGTT---T
117425 TGTTCTTCTATGTTTCTTAGCCATGTGGGATTGTTT
1 TGTTCTTCTATGTTTCTTAGCCATGTGGGATTGTTT
117461 T
1 T
117462 TTAAAAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 24
0.61 0.10 0.29
Matches are distributed among these distances:
31 5 0.10
32 4 0.08
33 4 0.08
34 10 0.20
35 4 0.08
36 11 0.22
37 4 0.08
38 4 0.08
39 5 0.10
ACGTcount: A:0.13, C:0.14, G:0.20, T:0.53
Consensus pattern (36 bp):
TGTTCTTCTATGTTTCTTAGCCATGTGGGATTGTTT
Found at i:118377 original size:2 final size:2
Alignment explanation
Indices: 118370--118404 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
118360 AATAAAACTT
*
118370 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
118405 AAAAGGATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:120554 original size:2 final size:2
Alignment explanation
Indices: 120547--120581 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
120537 TACAAAGGTC
120547 AT AT AT AT -T 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 AT AT AT AT
120582 GTGTGTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:121177 original size:20 final size:21
Alignment explanation
Indices: 121152--121194 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
121142 AATAATAAAT
121152 TATTTAAAA-AAATCAATCCA
1 TATTTAAAATAAATCAATCCA
121172 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
121193 TA
1 TA
121195 CTAATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (21 bp):
TATTTAAAATAAATCAATCCA
Found at i:121210 original size:32 final size:31
Alignment explanation
Indices: 121172--121548 Score: 187
Period size: 32 Copynumber: 12.7 Consensus size: 31
121162 AATCAATCCA
121172 TATTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAAT-CATACTAATAAAT
*
121204 TATTT-AAATAAATCAATCA-A-TTATAAAT
1 TATTTAAAATAAATCAATCATACTAATAAAT
121232 TATTTAAAA-AAATCAATC---C--AT--A-
1 TATTTAAAATAAATCAATCATACTAATAAAT
*
121254 T-TTTAAAATAAATAAATCTATACTAATAAAT
1 TATTTAAAATAAATCAATC-ATACTAATAAAT
121285 TATTTAAAATAAATCAAT--T-C--AT--A-
1 TATTTAAAATAAATCAATCATACTAATAAAT
121308 T-TTTAAAATAAATCAATCATACTAATAAAT
1 TATTTAAAATAAATCAATCATACTAATAAAT
121338 TATTTAAAATAAATCAATCCATAC-AACTACAA-
1 TATTTAAAATAAATCAAT-CATACTAA-TA-AAT
* * ** *
121370 TA-AT-AAATCAATCCATATTTTA-AAATAAAT
1 TATTTAAAATAAAT-CA-ATCATACTAATAAAT
* * * * * * * * *
121400 CAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 -TAT--TTA-AAATAAATCAATCATACT-AATAAAT
121436 CCATATTTTAAAATAAATCAATTCATACTAATAAAT
1 ---TA-TTTAAAATAAATCAA-TCATACTAATAAAT
121472 TATTTAAAATAAATCAATC---C--AT--A-
1 TATTTAAAATAAATCAATCATACTAATAAAT
121495 T-TTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAAT-CATACTAATAAAT
121526 TATTTAAAATAAATCAATTCATA
1 TATTTAAAATAAATCAA-TCATA
121549 TTTTATAATA
Statistics
Matches: 267, Mismatches: 26, Indels: 104
0.67 0.07 0.26
Matches are distributed among these distances:
21 7 0.03
22 41 0.15
23 4 0.01
24 3 0.01
25 3 0.01
26 6 0.02
27 2 0.01
28 27 0.10
29 8 0.03
30 14 0.05
31 42 0.16
32 65 0.24
33 5 0.02
34 5 0.02
35 1 0.00
36 26 0.10
37 6 0.02
38 1 0.00
39 1 0.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.36
Consensus pattern (31 bp):
TATTTAAAATAAATCAATCATACTAATAAAT
Found at i:121230 original size:80 final size:82
Alignment explanation
Indices: 121141--121543 Score: 298
Period size: 80 Copynumber: 5.0 Consensus size: 82
121131 CATACAACTA
*
121141 CAATAATAAATTATTTAAAAAAATCAATCCATA-TTTAAAATAAATCAATCCATACTAATAAATT
1 CAATAATAAATTATTTAAAAAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATT
121205 ATTT-AAATAAATCAAT
66 ATTTAAAATAAATCAAT
* *
121221 CAATTATAAATTATTTAAAAAAATCAATCCATATTTTAAAATAAATAAATCTATACTAATAAATT
1 CAATAATAAATTATTTAAAAAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATT
121286 ATTTAAAATAAATCAAT
66 ATTTAAAATAAATCAAT
* *
121303 ---TCAT--A-T-TTTAAAATAAATCAATCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 CAATAATAAATTATTTAAAA-AAATCAATC---C--AT--A-T-TTTAAAATAAATAAATCCATA
*
121361 C-AACTACA--A--T--AATAAATCAAT
56 CTAA-TAAATTATTTAAAATAAATCAAT
* * * ** * ** ** **
121382 C---CAT--ATT-TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCA
1 CAATAATAAATTATTTAAAAAAATCAATCCATA-TTTTAAAATAAAT-AAATCCATACTAATAAA
121439 -TATTTTAAAATAAATCAATT
64 TTA-TTTAAAATAAATCAA-T
*
121459 CATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAA
1 CA-A-TAATAAATTATTTAAAA-AAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAA
121524 ATTATTTAAAATAAATCAAT
63 ATTATTTAAAATAAATCAAT
121544 TCATATTTTA
Statistics
Matches: 256, Mismatches: 32, Indels: 65
0.73 0.09 0.18
Matches are distributed among these distances:
70 3 0.01
71 11 0.04
72 7 0.03
74 3 0.01
75 7 0.03
76 21 0.08
77 3 0.01
79 28 0.11
80 38 0.15
81 36 0.14
82 14 0.05
83 2 0.01
84 11 0.04
85 38 0.15
86 32 0.12
87 2 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (82 bp):
CAATAATAAATTATTTAAAAAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATT
ATTTAAAATAAATCAAT
Found at i:121245 original size:24 final size:27
Alignment explanation
Indices: 121198--121356 Score: 77
Period size: 28 Copynumber: 5.9 Consensus size: 27
121188 ATCCATACTA
121198 ATAAATTATTTAAATAAATCAATCAATT
1 ATAAATTATTTAAATAAA-CAATCAATT
*
121226 ATAAATTATTTAAAAAAATCAATCCATATT
1 ATAAATTATTTAAATAAA-CAAT-CA-ATT
* * * *
121256 TTAAA--A--TAAATAAATCTAT-ACTA
1 ATAAATTATTTAAATAAA-CAATCAATT
*
121279 ATAAATTATTTAAA-ATA-AATCAATT
1 ATAAATTATTTAAATAAACAATCAATT
* *
121304 CAT--ATT-TTAAAATAAATCAATCATACTA
1 -ATAAATTATTTAAATAAA-CAATCA-A-TT
121332 ATAAATTATTTAAAATAAATCAATC
1 ATAAATTATTT-AAATAAA-CAATC
121357 CATACAACTA
Statistics
Matches: 99, Mismatches: 15, Indels: 31
0.68 0.10 0.21
Matches are distributed among these distances:
23 10 0.10
24 8 0.08
25 3 0.03
26 20 0.20
27 7 0.07
28 24 0.24
29 5 0.05
30 9 0.09
31 13 0.13
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (27 bp):
ATAAATTATTTAAATAAACAATCAATT
Found at i:121285 original size:81 final size:81
Alignment explanation
Indices: 121141--121543 Score: 293
Period size: 85 Copynumber: 5.0 Consensus size: 81
121131 CATACAACTA
*
121141 CAATAATAAATTATTTAAAAAAATCAATCCATATTTAAAATAAATCAATCCATACTAATAAATTA
1 CAATAATAAATTATTTAAAAAAATCAATCCATATTTAAAATAAATAAATCCATACTAATAAATTA
121206 TTT-AAATAAATCAAT
66 TTTAAAATAAATCAAT
* *
121221 CAATTATAAATTATTTAAAAAAATCAATCCATATTTTAAAATAAATAAATCTATACTAATAAATT
1 CAATAATAAATTATTTAAAAAAATCAATCCATA-TTTAAAATAAATAAATCCATACTAATAAATT
121286 ATTTAAAATAAATCAATT
65 ATTTAAAATAAATCAA-T
** * ** * ** ** *
121304 CATATTTTAAAATAAAT-CAATCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTA
1 CA-ATAATAAATTATTTAAAAAAAT-C-AATCCA-TATTTAAAATAAATAAATCCATACTAA-TA
*
121367 CA--A--T--AATAAATCAAT
61 AATTATTTAAAATAAATCAAT
* * * * * ** ** **
121382 C---CAT--ATT-TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCA
1 CAATAATAAATTATTTAAAAAAATCAATCCATA-T-TTAAAATAAAT-AAATCCATACTAATAAA
121439 -TATTTTAAAATAAATCAATT
63 TTA-TTTAAAATAAATCAA-T
*
121459 CATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAA
1 CA-A-TAATAAATTATTTAAAA-AAATCAATCCATA-TTTAAAATAAATAAATCCATACTAATAA
121524 ATTATTTAAAATAAATCAAT
62 ATTATTTAAAATAAATCAAT
121544 TCATATTTTA
Statistics
Matches: 244, Mismatches: 48, Indels: 57
0.70 0.14 0.16
Matches are distributed among these distances:
69 2 0.01
70 8 0.03
71 12 0.05
72 10 0.04
74 2 0.01
76 10 0.04
77 2 0.01
78 2 0.01
79 10 0.04
80 32 0.13
81 34 0.14
82 13 0.05
83 8 0.03
84 21 0.09
85 41 0.17
86 35 0.14
87 2 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (81 bp):
CAATAATAAATTATTTAAAAAAATCAATCCATATTTAAAATAAATAAATCCATACTAATAAATTA
TTTAAAATAAATCAAT
Found at i:121313 original size:22 final size:21
Alignment explanation
Indices: 121287--121328 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
121277 TAATAAATTA
121287 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAA-TCATAT
121309 TTTAAAATAAATCAATCATA
1 TTTAAAATAAATCAATCATA
121329 CTAATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAAAATAAATCAATCATAT
Found at i:121336 original size:22 final size:22
Alignment explanation
Indices: 121289--121336 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
121279 ATAAATTATT
**
121289 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATTCATATAA
121311 TAAAATAAATCAA-TCATACTAA
1 TAAAATAAATCAATTCATA-TAA
121333 TAAA
1 TAAA
121337 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATTCATATAA
Found at i:121372 original size:54 final size:53
Alignment explanation
Indices: 121209--121360 Score: 247
Period size: 53 Copynumber: 2.9 Consensus size: 53
121199 TAAATTATTT
*
121209 AAATAAATCAATCA-A-TTATAAATTATTTAAAA-AAATCAATCCATATTTTA
1 AAATAAATCAATCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTA
* *
121259 AAATAAATAAATCTATACTAATAAATTATTTAAAATAAATCAATTCATATTTTA
1 AAATAAATCAATC-ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTA
121313 AAATAAATCAATCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 AAATAAATCAATCATACTAATAAATTATTTAAAATAAATCAATCCATA
121361 CAACTACAAT
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
50 12 0.13
51 1 0.01
52 1 0.01
53 50 0.54
54 29 0.31
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (53 bp):
AAATAAATCAATCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTA
Found at i:121379 original size:53 final size:55
Alignment explanation
Indices: 121172--121409 Score: 230
Period size: 53 Copynumber: 4.4 Consensus size: 55
121162 AATCAATCCA
* *
121172 TATTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAATAAATCAATCAATTATAAAT
1 TATTTAAAATAAATCAATCCATAC-AATTAAA--A--TAAATAAATCAAT-ACTAATAAAT
** *
121232 TATTTAAAA-AAATCAATCCATA-TTTTAAAATAAATAAATCTATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACAATTAAAATAAATAAATCAATACTAATAAAT
* ** *
121285 TATTTAAAATAAATCAATTCATA-TTTTAAAATAAATCAATC-ATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACAATTAAAATAAATAAATCAATACTAATAAAT
* * *
121338 TATTTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C-CAT--A-
1 TATTTAAAATAAATCAATCCATACAATTAAAATAAATAAATCAATACTAATAAAT
121387 T-TTTAAAATAAATCAATCCATAC
1 TATTTAAAATAAATCAATCCATAC
121410 TAATAAATTA
Statistics
Matches: 160, Mismatches: 14, Indels: 20
0.82 0.07 0.10
Matches are distributed among these distances:
48 22 0.14
49 1 0.01
50 1 0.01
52 2 0.01
53 59 0.37
54 48 0.30
56 1 0.01
58 4 0.03
59 13 0.08
60 9 0.06
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (55 bp):
TATTTAAAATAAATCAATCCATACAATTAAAATAAATAAATCAATACTAATAAAT
Found at i:121417 original size:22 final size:23
Alignment explanation
Indices: 121342--121416 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
121332 ATAAATTATT
121342 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
121364 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
121390 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
121413 TAAA
1 TAAA
121417 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:121446 original size:22 final size:22
Alignment explanation
Indices: 121420--121462 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
121410 TAATAAATTA
121420 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
121442 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
121463 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:121453 original size:54 final size:54
Alignment explanation
Indices: 121144--121559 Score: 366
Period size: 54 Copynumber: 7.8 Consensus size: 54
121134 ACAACTACAA
121144 TAATAAATTATTTAAAA-AAATCAATCCATA-TTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
121196 TAATAAATTATTT-AAATAAATCAATCAATTATAAATTATTTAAAA-AAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATC---CAT--A-T-TTTAAAATAAATCAATCCATAC
** * ** ** ** *
121254 TTTTAAAATAAAT-AAATCTATACTAATAAAT-TATTTAAAATAAATCAATTCATA-
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
** * * * * *
121308 TTTTAAAATAAATCAATCATACTAATAAAT---TA-TTTAAAATAAATCAATCCATAC
1 TAAT-AAATTATTTAA-AATA--AATCAATCCATATTTTAAAATAAATCAATCCATAC
*
121362 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
121410 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
121464 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
121518 TAATAAATTATTTAAAATAAATCAATTCATATTTTATAATAA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
121560 TTTTTTTAAA
Statistics
Matches: 302, Mismatches: 31, Indels: 60
0.77 0.08 0.15
Matches are distributed among these distances:
44 6 0.02
46 3 0.01
47 2 0.01
48 25 0.08
49 2 0.01
50 1 0.00
51 4 0.01
52 23 0.08
53 31 0.10
54 149 0.49
55 7 0.02
56 1 0.00
57 8 0.03
58 14 0.05
59 16 0.05
60 10 0.03
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:121471 original size:22 final size:22
Alignment explanation
Indices: 121422--121470 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
121412 ATAAATTATT
**
121422 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
121444 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
121467 TAAA
1 TAAA
121471 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:121500 original size:22 final size:22
Alignment explanation
Indices: 121474--121516 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
121464 TAATAAATTA
121474 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
121496 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
121517 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:121505 original size:133 final size:132
Alignment explanation
Indices: 121144--121516 Score: 546
Period size: 133 Copynumber: 2.8 Consensus size: 132
121134 ACAACTACAA
*
121144 TAATAAATTATTTAAAA-AAATCAATCCATA-TTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
*
121207 TT-AAATAAATCAAT-CA-ATTATAAATTATTTAAAAAAATCAATCCATATTTTAAAATAAATAA
66 TTAAAATAAATCAATCCATATTAT-AA--A--T-AATAAATCAATCCATATTTTAAAATAAATAA
*
121269 ATCTATAC
125 ATCCATAC
*
121277 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAA-TCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
** *
121341 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATATTA-TA-AATAATAAATCAATCCATATTTTAAAATAAATAAATCC
121406 ATAC
129 ATAC
121410 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
*
121475 TTAAAATAAATCAATCCATATT-TTAA-AATAAATCAATCCATA
66 TTAAAATAAATCAATCCATATTATAAATAATAAATCAATCCATA
121517 CTAATAAATT
Statistics
Matches: 221, Mismatches: 11, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
130 16 0.07
131 2 0.01
132 1 0.00
133 99 0.45
134 68 0.31
135 27 0.12
136 3 0.01
137 3 0.01
138 2 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (132 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
TTAAAATAAATCAATCCATATTATAAATAATAAATCAATCCATATTTTAAAATAAATAAATCCAT
AC
Found at i:121525 original size:22 final size:22
Alignment explanation
Indices: 121476--121524 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
121466 ATAAATTATT
**
121476 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
121498 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
121521 TAAA
1 TAAA
121525 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:121568 original size:36 final size:32
Alignment explanation
Indices: 121495--121605 Score: 93
Period size: 32 Copynumber: 3.4 Consensus size: 32
121485 TCAATCCATA
*
121495 TTTTAAAATAAATCAATCCATACTAATAAATT
1 TTTTAAAATAAATCAATCCATAATAATAAATT
* * *
121527 ATTTAAAATAAATCAATTCATATTTTATAATAATTT
1 TTTTAAAATAAATCAATCCATA----ATAATAAATT
* **
121563 TTTTAAAATAAAT-TAT-TTTAA-AATAAATT
1 TTTTAAAATAAATCAATCCATAATAATAAATT
121592 ATTTTAAAATAAAT
1 -TTTTAAAATAAAT
121606 TATTTTAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
29 7 0.11
30 14 0.22
32 20 0.31
34 2 0.03
35 2 0.03
36 20 0.31
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.44
Consensus pattern (32 bp):
TTTTAAAATAAATCAATCCATAATAATAAATT
Found at i:121581 original size:15 final size:15
Alignment explanation
Indices: 121547--121613 Score: 109
Period size: 15 Copynumber: 4.5 Consensus size: 15
121537 AATCAATTCA
*
121547 TATTTTATAAT-AAT
1 TATTTTAAAATAAAT
*
121561 TTTTTTAAAATAAAT
1 TATTTTAAAATAAAT
121576 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
121591 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
121606 TATTTTAA
1 TATTTTAA
121614 TAAATAACCT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
14 9 0.18
15 40 0.82
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:121626 original size:18 final size:17
Alignment explanation
Indices: 121568--121666 Score: 66
Period size: 15 Copynumber: 5.9 Consensus size: 17
121558 AATTTTTTTA
*
121568 AAATAAATTATTTT-A-
1 AAATAACTTATTTTAAT
*
121583 AAATAAATTATTTT-A-
1 AAATAACTTATTTTAAT
*
121598 AAATAAATTATTTTAAT
1 AAATAACTTATTTTAAT
*
121615 AAATAACCTTATTAAATTATT
1 AAATAA-CTTATT---TTAAT
*
121636 TAA-AA-TTATTTTAAT
1 AAATAACTTATTTTAAT
121651 AAATAACTATATTTTA
1 AAATAACT-TATTTTA
121667 TAATTGTTCT
Statistics
Matches: 70, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
15 35 0.50
16 3 0.04
17 7 0.10
18 17 0.24
20 2 0.03
21 6 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATAACTTATTTTAAT
Done.