Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016273.1 Corchorus olitorius cultivar O-4 contig16306, 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: 120246
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3382 original size:16 final size:15
Alignment explanation
Indices: 3358--3417 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
3348 GGCAATTGGA
*
3358 CGGGTTCGGGCTTTTT
1 CGGGCTCGGG-TTTTT
**
3374 CGGGCTCGGGTTAAGT
1 CGGGCTCGGGTT-TTT
*
3390 CGGGTTCGGGTATTTT
1 CGGGCTCGGGT-TTTT
3406 CGGGCTCGGGTT
1 CGGGCTCGGGTT
3418 ATGTCGGGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 3 0.09
16 31 0.89
17 1 0.03
ACGTcount: A:0.05, C:0.18, G:0.42, T:0.35
Consensus pattern (15 bp):
CGGGCTCGGGTTTTT
Found at i:3399 original size:32 final size:32
Alignment explanation
Indices: 3358--3447 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 32
3348 GGCAATTGGA
3358 CGGGTTCGGGCT-TTTTCGGGCTCGGGTTAAGT
1 CGGGTTCGGG-TATTTTCGGGCTCGGGTTAAGT
*
3390 CGGGTTCGGGTATTTTCGGGCTCGGGTTATGT
1 CGGGTTCGGGTATTTTCGGGCTCGGGTTAAGT
* * *
3422 CGGGTTCGAGTATTTTTGGGTTCGGG
1 CGGGTTCGGGTATTTTCGGGCTCGGG
3448 CTCGGGTTCG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 1 0.02
32 52 0.98
ACGTcount: A:0.07, C:0.16, G:0.41, T:0.37
Consensus pattern (32 bp):
CGGGTTCGGGTATTTTCGGGCTCGGGTTAAGT
Found at i:3424 original size:16 final size:16
Alignment explanation
Indices: 3373--3425 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
3363 TCGGGCTTTT
*
3373 TCGGGCTCGGGTTAAG
1 TCGGGCTCGGGTTATG
* *
3389 TCGGGTTCGGG-TATTT
1 TCGGGCTCGGGTTA-TG
3405 TCGGGCTCGGGTTATG
1 TCGGGCTCGGGTTATG
3421 TCGGG
1 TCGGG
3426 TTCGAGTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 2 0.07
16 26 0.87
17 2 0.07
ACGTcount: A:0.08, C:0.17, G:0.43, T:0.32
Consensus pattern (16 bp):
TCGGGCTCGGGTTATG
Found at i:3603 original size:13 final size:12
Alignment explanation
Indices: 3580--3626 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
3570 AAATTTATTG
3580 ATAATATATAAT
1 ATAATATATAAT
3592 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
3605 ATAACAT-TATT
1 ATAATATATAAT
3616 ATCAATATATA
1 AT-AATATATA
3627 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:5427 original size:10 final size:10
Alignment explanation
Indices: 5412--5442 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5402 ATTTTGCAAA
5412 AAAAAAAAAG
1 AAAAAAAAAG
5422 AAAAAAAAAG
1 AAAAAAAAAG
*
5432 AAAAAGAAAG
1 AAAAAAAAAG
5442 A
1 A
5443 GTAAAGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:5430 original size:16 final size:16
Alignment explanation
Indices: 5409--5440 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5399 TTTATTTTGC
5409 AAAAAAAAAAAAGAAA
1 AAAAAAAAAAAAGAAA
*
5425 AAAAAAGAAAAAGAAA
1 AAAAAAAAAAAAGAAA
5441 GAGTAAAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAGAAA
Found at i:22196 original size:16 final size:15
Alignment explanation
Indices: 22158--22199 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
22148 ACAGAGATTG
*
22158 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
22173 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
22188 ACTAGAAAACAA
1 AC-AGAAAACAA
22200 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:27914 original size:405 final size:405
Alignment explanation
Indices: 27163--27979 Score: 1501
Period size: 405 Copynumber: 2.0 Consensus size: 405
27153 ATCGCTCTTG
*
27163 ATTAGGGCACCACTCGAGGGCACTGATCCCTAGGATGATGATCTGCAAGACAAGGAACACCTGAG
1 ATTAGGGCACCACTCGAGAGCACTGATCCCTAGGATGATGATCTGCAAGACAAGGAACACCTGAG
*
27228 TGGCAGGGGGATGCCCTGCGTTAGCACTCCGATGTTTAAGTCAGATTCCCTTAAAGGTAAGGAAT
66 TGGCAGGGGGATGCCCTGCGTTAGCACTCCGATGCTTAAGTCAGATTCCCTTAAAGGTAAGGAAT
* *
27293 AACAGGATTCAGTGCTGTAAAGTAGTGGGGTCAGAAATCATACCTCCAAATAGGATAATCCGAGG
131 AACAGGATTCAATGCTGTAAAGTAGTAGGGTCAGAAATCATACCTCCAAATAGGATAATCCGAGG
* *
27358 GTATTTATAGGGTGTGAAAGGCGGTTACCTTCACACGTGGGAGCAGTCGGGCTGCTAGACCCGCG
196 GTATTTATAAGGTGTGAAAGGCGGTTACCTTCACACGTGGGAGCAGTCGGGCTGCTAAACCCGCG
* *
27423 CGTTGACCTGCTTAGGGTCCGAAGCGTGTGGCATTGGAGTGCGTGAGGCCTAATGTATGGGCTTT
261 CGTTGACCCGCTTAGGGTCCGAAGCGTGTGGCATTGGAGTGCGTGAAGCCTAATGTATGGGCTTT
* ** *
27488 GGCTTTGATGGGCCCTGTAGGGTCGTTTGGCCCATATTGGCTCCTGGGGCCTTATGGCTATGTCC
326 GGCTTTGATGGGCCATGTAGGGTCGTCCGGCCCATATTGGCTCCTGGGGCCTTATGGCTATATCC
27553 TTTGAGTTTGCTTTC
391 TTTGAGTTTGCTTTC
27568 ATTAGGGCACCACTCGAGAGCACTGATCCCTAGGATGATGATCTGCAAGACAAGGAACACCTGAG
1 ATTAGGGCACCACTCGAGAGCACTGATCCCTAGGATGATGATCTGCAAGACAAGGAACACCTGAG
27633 TGGCAGGGGGATGCCCTGCGTTAGCACTCCGATGCTTAAGTCAGATTCCCTTAAAGGTAAGGAAT
66 TGGCAGGGGGATGCCCTGCGTTAGCACTCCGATGCTTAAGTCAGATTCCCTTAAAGGTAAGGAAT
*
27698 AACAGGATTCAATGCTGTAAAGTAGTAGGGTCAGAAATCATACCTCCAAATAGGGTAATCCGAGG
131 AACAGGATTCAATGCTGTAAAGTAGTAGGGTCAGAAATCATACCTCCAAATAGGATAATCCGAGG
27763 GTATTTATAAGGTGTGAAAGGCGGTTACCTTCACACGTGGGAGCAGTCGGGCTGCTAAACCCGCG
196 GTATTTATAAGGTGTGAAAGGCGGTTACCTTCACACGTGGGAGCAGTCGGGCTGCTAAACCCGCG
*
27828 CGTTGACCCGCTTAGGGTCCGAAGCGTGTGGCATTGGAGTGTGTGAAGCCTAATGTATGGGCTTT
261 CGTTGACCCGCTTAGGGTCCGAAGCGTGTGGCATTGGAGTGCGTGAAGCCTAATGTATGGGCTTT
27893 GGCTTTGATGGGCCATGTAGGGTCGTCCGGCCCATATTGGCTCCTGGGGCCTTATGGCTATATCC
326 GGCTTTGATGGGCCATGTAGGGTCGTCCGGCCCATATTGGCTCCTGGGGCCTTATGGCTATATCC
27958 TTTGAGTTTGCTTTC
391 TTTGAGTTTGCTTTC
27973 -TTAGGGC
1 ATTAGGGC
27980 CTTTAGTTAG
Statistics
Matches: 398, Mismatches: 14, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
404 7 0.02
405 391 0.98
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (405 bp):
ATTAGGGCACCACTCGAGAGCACTGATCCCTAGGATGATGATCTGCAAGACAAGGAACACCTGAG
TGGCAGGGGGATGCCCTGCGTTAGCACTCCGATGCTTAAGTCAGATTCCCTTAAAGGTAAGGAAT
AACAGGATTCAATGCTGTAAAGTAGTAGGGTCAGAAATCATACCTCCAAATAGGATAATCCGAGG
GTATTTATAAGGTGTGAAAGGCGGTTACCTTCACACGTGGGAGCAGTCGGGCTGCTAAACCCGCG
CGTTGACCCGCTTAGGGTCCGAAGCGTGTGGCATTGGAGTGCGTGAAGCCTAATGTATGGGCTTT
GGCTTTGATGGGCCATGTAGGGTCGTCCGGCCCATATTGGCTCCTGGGGCCTTATGGCTATATCC
TTTGAGTTTGCTTTC
Found at i:29900 original size:107 final size:105
Alignment explanation
Indices: 29673--29934 Score: 368
Period size: 107 Copynumber: 2.5 Consensus size: 105
29663 AATTTTTCTA
* ** * * *
29673 ACCCTTAAAATAAAATTTTAATTTTAATTT-AGACTAAATTTAATGAAA-TAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
29736 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* * *
29776 ACCCTTAAAATAAAAATAAAATTTAAATTTGAGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* *
29841 TTTCTAAAATCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
29883 ACCCTTAAAATAAAAATAAAATTTTAATTTG-GGACTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGG-CTAAACTTAGTGAAATTA
29935 AGGCTAAACT
Statistics
Matches: 141, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
103 26 0.18
104 15 0.11
105 33 0.23
106 2 0.01
107 65 0.46
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:31781 original size:56 final size:56
Alignment explanation
Indices: 31693--31806 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
31683 TATCCATTTC
* *
31693 CTTTCATACAATAAATGTTATAATAAACCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAACCCTATCCCCATATCTCTACTTAATTATT
*
31749 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAACCCTATCCCCATATCTCTACTTAATTATT
31805 CT
1 CT
31807 ATAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAACCCTATCCCCATATCTCTACTTAATTATT
Found at i:45003 original size:2 final size:2
Alignment explanation
Indices: 44996--45025 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44986 AACCGTCCAA
44996 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
45026 TCAATAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55682 original size:15 final size:15
Alignment explanation
Indices: 55662--55694 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
55652 AGAGATGAGG
55662 ATTCTCCAGCAAGGC
1 ATTCTCCAGCAAGGC
55677 ATTCTCCAGCAAGGC
1 ATTCTCCAGCAAGGC
55692 ATT
1 ATT
55695 AATGTCTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (15 bp):
ATTCTCCAGCAAGGC
Found at i:82114 original size:28 final size:28
Alignment explanation
Indices: 82082--82137 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
82072 GGTTTGAAGT
* *
82082 CAATTTGTTTAAAATATGATTGCAAAAA
1 CAATTTGTTTAAAACATGATTACAAAAA
82110 CAATTTGTTTAAAACATGATTACAAAAA
1 CAATTTGTTTAAAACATGATTACAAAAA
82138 ATGACGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (28 bp):
CAATTTGTTTAAAACATGATTACAAAAA
Found at i:86037 original size:19 final size:22
Alignment explanation
Indices: 86013--86052 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
86003 GCTCTACTTT
86013 TTACTT-G-CCTTTTA-CATTC
1 TTACTTGGCCCTTTTATCATTC
86032 TTACTTGGCCCTTTTATCATT
1 TTACTTGGCCCTTTTATCATT
86053 GCATTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 7 0.39
22 4 0.22
ACGTcount: A:0.15, C:0.25, G:0.07, T:0.53
Consensus pattern (22 bp):
TTACTTGGCCCTTTTATCATTC
Found at i:92079 original size:6 final size:6
Alignment explanation
Indices: 92064--92120 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
92054 TAATAGGTTC
* *
92064 ACCATT ACCCTT ACCCTT ACCATT ACCATT ACCATT ACCATT ACCATT
1 ACCATT ACCATT ACCATT ACCATT ACCATT ACCATT ACCATT ACCATT
92112 ACCATT ACC
1 ACCATT ACC
92121 CCCGAAAGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.30, C:0.39, G:0.00, T:0.32
Consensus pattern (6 bp):
ACCATT
Found at i:103226 original size:29 final size:31
Alignment explanation
Indices: 103141--103239 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 31
103131 TAGAGGGGTC
* * * * * *
103141 AATGTCTTGAATATGGAATTTCACGGGTCAC
1 AATGTCCTGAATTTGGAAGTTCAAGGGGCAA
*
103172 GATGTCCTGAATTTGGAAGTTCAAGGGGCAA
1 AATGTCCTGAATTTGGAAGTTCAAGGGGCAA
* *
103203 AATGTCCTG-ATTT-GAAGTTTAAGGGGCAG
1 AATGTCCTGAATTTGGAAGTTCAAGGGGCAA
*
103232 AACGTCCT
1 AATGTCCT
103240 TGACGCAATC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 21 0.37
30 4 0.07
31 32 0.56
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (31 bp):
AATGTCCTGAATTTGGAAGTTCAAGGGGCAA
Found at i:107154 original size:22 final size:22
Alignment explanation
Indices: 107126--107168 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
107116 TTTTTCCCTT
107126 GAACATGTAGCGTTTGGACATG
1 GAACATGTAGCGTTTGGACATG
107148 GAACATGTAGCGTTTGGACAT
1 GAACATGTAGCGTTTGGACAT
107169 TTTACCCCTA
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:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (22 bp):
GAACATGTAGCGTTTGGACATG
Found at i:107419 original size:30 final size:30
Alignment explanation
Indices: 107364--107421 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
107354 TAGGCCGATG
*
107364 GGGCAAAACATCCTAAAATTAAAGTTCATT
1 GGGCAAAACATCCTAAAACTAAAGTTCATT
*
107394 GGGCAAAACATCC-AAAGCTACAAGTTCA
1 GGGCAAAACATCCTAAAACTA-AAGTTCA
107422 AGGGAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.21
Consensus pattern (30 bp):
GGGCAAAACATCCTAAAACTAAAGTTCATT
Found at i:108514 original size:31 final size:30
Alignment explanation
Indices: 108451--108523 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
108441 CGTCAGAAAA
*
108451 GGGCTTATTTGATTTTTTTAAAGAGTTCAG
1 GGGCTTATTTGATTTTTATAAAGAGTTCAG
108481 GGGCTTATTTGACTATTTTATATAA-A-TTCAG
1 GGGCTTATTTGA-T-TTTTATA-AAGAGTTCAG
108512 GGGCCTT-TTTGA
1 GGG-CTTATTTGA
108524 GCAATAAACC
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 12 0.32
31 14 0.37
32 10 0.26
33 2 0.05
ACGTcount: A:0.23, C:0.10, G:0.22, T:0.45
Consensus pattern (30 bp):
GGGCTTATTTGATTTTTATAAAGAGTTCAG
Found at i:108895 original size:19 final size:19
Alignment explanation
Indices: 108875--108911 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
108865 AATTAATTAT
108875 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
108893 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
108912 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:108922 original size:19 final size:19
Alignment explanation
Indices: 108881--108922 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
108871 TTATTTTAAT
* * *
108881 ATTATATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
108900 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
108919 ATTA
1 ATTA
108923 CTCCTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:109045 original size:19 final size:19
Alignment explanation
Indices: 108997--109035 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
108987 ATTATACAAG
*
108997 TTAATTTTAATTTATTCAT
1 TTAATTTTAATCTATTCAT
109016 TTAATTTTAATCTATTCAT
1 TTAATTTTAATCTATTCAT
109035 T
1 T
109036 ATTATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAATTTTAATCTATTCAT
Found at i:113656 original size:27 final size:27
Alignment explanation
Indices: 113622--113693 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
113612 CGGCAAATAA
113622 GGGCAAAACTGTAATTTAG-TCAACCAG
1 GGGCAAAACTGTAATTTAGCT-AACCAG
* *
113649 GGGTAAAA-TGGTAATTTTAGCTGACCAG
1 GGGCAAAACT-GTAA-TTTAGCTAACCAG
*
113677 GGGCAAAACAGTAATTT
1 GGGCAAAACTGTAATTT
113694 CGACATCGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 1 0.03
27 14 0.38
28 21 0.57
29 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (27 bp):
GGGCAAAACTGTAATTTAGCTAACCAG
Found at i:114629 original size:17 final size:17
Alignment explanation
Indices: 114603--114638 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
114593 AATTTTCTTA
114603 TTTTCCTTTTCTCTTCC
1 TTTTCCTTTTCTCTTCC
* *
114620 TTTTCTTTTTCTTTTCC
1 TTTTCCTTTTCTCTTCC
114637 TT
1 TT
114639 ATCTCAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTCCTTTTCTCTTCC
Found at i:114768 original size:23 final size:22
Alignment explanation
Indices: 114729--114780 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
114719 TCCTTTTTCC
* *
114729 TTTCTTATTCTTCTTTCTTTTT
1 TTTCTTTTTCTTCTTTCATTTT
*
114751 TTTCTTTTTTTTCATTTCATTTT
1 TTTCTTTTTCTTC-TTTCATTTT
114774 TTTCTTT
1 TTTCTTT
114781 GGGCCAAGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTCTTCTTTCATTTT
Found at i:118430 original size:331 final size:328
Alignment explanation
Indices: 117221--119132 Score: 1656
Period size: 333 Copynumber: 5.8 Consensus size: 328
117211 CGGATCGTAG
* * * **
117221 AACGTGTTTTTAGCCAAATATCGTGATGATTAACACACGATTTCGGCTAAAATTTTGCAAAAAAT
1 AACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGC-AAAAAT
* * * * * * * * * *
117286 TAACCCGAAAGATATCTCCTCAATTTTTAG-TCATAATACTTATAAAAACTATATAATTCAACGT
65 TGACTCGAAAAATATTTCCTCAATTTATGGCT-AAAATACTCATAAAAAATATATAATTCAACGC
* * * * * *
117350 CAAAAAGATTGAAGGGCTTTTCACGCGTATAATATCATTTTTCATATTTTTTCTGAATTAATTTC
129 CAAAAAGATTGGAGAGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCT-AATTAATGTC
* * * * *
117415 TAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAA-AAATCCTTAAATGCAATGTGGCTAAGA
193 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGACTGAGA
* * * ** * * *
117479 TTTTATTAGATGAATGTAGATATTTCAAGGACTGCCGGCACCAAAAA-CAATTCAAAACTGAGTC
258 TTTGATTAGATGAATATAGATATTTCAAGGAGTATCGG-ACTAAAAATC-ATGCAAAA-T-AGCC
*
117543 GGGGCCCCGA
319 AGGGCCCCGA
* * * * *
117553 AACGCGTTTTTAGCCAAAAAAAAAACAGTGATGGTTAGTACACGATTTAGGTTAAAATTTTACAA
1 AACGCGTTTTTAGCC-----AAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAA
* * * * * *
117618 AAAATGAC-CAGAAAAATA-TTCTCTCAATTTTTAGCCACAATACTGATAAAAAATATATAATTC
61 AAATTGACTC-GAAAAATATTTC-CTCAATTTATGGCTAAAATACTCATAAAAAATATATAATTC
* * * * * *
117681 AATGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTC-T-TTTTTTCCGAATTA
124 AACGCCAAAAAGATTGGAGAGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTT-CTAATTA
* * * * * * *
117744 ATTTCTAATTAAAACGAAACATGATTCAAATGTTTGT---AA-AAA--C---AAT--GAT-TG--
188 ATGTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGAC
* * * * * * *
117795 -G-GATTTGGTTAGATGAATGTAGATATTTCAAGGATTCTCAGTG-CCAAAAATCATTCAAAATT
253 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTATC-G-GACTAAAAATCATGCAAAATA
* ** *
117857 G-AATCGGGCCATGG
316 GCCA--GGGCCCCGA
* *
117871 AACGCGTTTTTAGCCAAAAATCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATT
1 AACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATT
* * * * * **
117936 GACCCGAAAGATATCTCCTCAATTTTTAG-TCATGATACTCATAAAAAA-ATATAATTCAACGCC
66 GACTCGAAAAATATTTCCTCAATTTATGGCT-AAAATACTCATAAAAAATATATAATTCAACGCC
* * * * * *
117999 AAAAAGATTGTAGGGCTTTTCACGCTTGTAATATCGTTTTTCATATTTTTTATGAATTAATTTCC
130 AAAAAGATTGGAGAGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCT-AATTAATGTCT
* * * * * *
118064 AATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATGCAATGTGTCTAAAAC
194 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGACTGAGA-
* *
118129 TTT-ATTAGATGAATATAGATATTTCAAGGAGTGTCGGCACTAAAAACCATGCAAAACTGAGCCA
258 TTTGATTAGATGAATATAGATATTTCAAGGAGTATCGG-ACTAAAAATCATGCAAAA-T-AGCCA
118193 GGGCCCCGA
320 GGGCCCCGA
* * * ** *
118202 AACGCGTTTTTAACCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACATTGCAAAAAA
1 AACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCT-AAAATTTTGCAAAAAT
* * * * * * * * *
118267 TGATTCGAAAAATGTTTCCCCTATTTATGGATAAAATACTCATAAAATATATATAATTTAATGGC
65 TGACTCGAAAAATATTTCCTCAATTTATGGCTAAAATACTCATAAAAAATATATAATTCAACGCC
* * * * *
118332 AAAAAGATTGGAGAACTTTTCACGTTTTTAATATCATTTTTCATA-TTTTTCTGATTAATTTCTA
130 AAAAAGATTGGAGAGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAATTAATGTCTA
* * * * * * *
118396 ATCAAATCGAAACAGGATACAGATACTTGTAAAAACAAATTCTTAAATCGAATGTGGCTGAGATT
195 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGACTGAGATT
* * * * *
118461 TGATTAGATGAATATGGATATCTCAAGGAGTCT-TGACGTCAAAAATCATGCAAAA-AGCCAGTG
260 TGATTAGATGAATATAGATATTTCAAGGAGTATCGGAC-T-AAAAATCATGCAAAATAGCCAGGG
118524 CCCC-A
323 CCCCGA
* * * * *
118529 TAACGCATTTTTAGCCAAAAACTGTGATGATTATTACACGATTTTGGCTAAAATTTTGTAAAAAT
1 -AACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAAT
* * * * *
118594 TAATTAGAAAAATATTTCCACAATTTATGGCTAAAATACTCGTAAAAAATATATAATTCAACGCC
65 TGACTCGAAAAATATTTCCTCAATTTATGGCTAAAATACTCATAAAAAATATATAATTCAACGCC
* * * *
118659 AAAAAGATTGAAGAGCTTTTGACG-TTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATGTC
130 AAAAAGATTGGAGAGCTTTTCACGCTTT-TAATATCGTTTTTCATATTTTTT-CTAATTAATGTC
* *
118723 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTT---TCCAATTTGAATGAGA
193 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGACTGAGA
* * * * *
118785 TTTGATTAAATGAATTTAGATATTTCAAGTAGTATCGGAGCCAAAAATCATGCAAAATTAAGCTA
258 TTTGATTAGATGAATATAGATATTTCAAGGAGTATCGGA-CTAAAAATCATGCAAAA-T-AGCCA
* *
118850 GGTCCCCGG
320 GGGCCCCGA
* * * * *
118859 AACGCGTTGTTAGGCAAAAACTGTGATGGTTTGTTAGTACACGATTTCGGCTAAAATTTTGTAAA
1 AACGCGTTTTTAGCCAAAAACCGTGAT-G---ATTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * * *
118924 AATTGACAC-AAAAGAT-TTCTCCTCTATTTTTGGCTAATATACTCATAAAAAATATATAATTCA
62 AATTGACTCGAAAA-ATATT-TCCTCAATTTATGGCTAAAATACTCATAAAAAATATATAATTCA
* * * * * * *
118987 ACGCCAAAATGATTGGAGGGCTTTTTACGCTTTTAATATCGTATTTCTTACTTTTTCTAAATTTA
125 ACGCCAAAAAGATTGGAGAGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCT-AATTAA
119052 TGTCTAATTAAATCGAAACAAGATTCTA-ATGCTCGTAAAAA-AAATTCTTAAATCCAATGTTG-
189 TGTCTAATTAAATCGAAACAAGATTC-AGATGCTCGTAAAAACAAATTCTTAAATCCAATG-TGA
* *
119114 TTGAGATTTGGTTAGATGA
252 CTGAGATTTGATTAGATGA
119133 TGTAAAGTAT
Statistics
Matches: 1295, Mismatches: 214, Indels: 139
0.79 0.13 0.08
Matches are distributed among these distances:
312 53 0.04
313 79 0.06
314 43 0.03
317 3 0.00
318 25 0.02
319 48 0.04
320 3 0.00
321 1 0.00
323 5 0.00
324 2 0.00
325 2 0.00
326 64 0.05
327 105 0.08
328 61 0.05
329 87 0.07
330 49 0.04
331 161 0.12
332 84 0.06
333 218 0.17
334 46 0.04
335 27 0.02
336 95 0.07
337 34 0.03
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (328 bp):
AACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATT
GACTCGAAAAATATTTCCTCAATTTATGGCTAAAATACTCATAAAAAATATATAATTCAACGCCA
AAAAGATTGGAGAGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAATTAATGTCTAA
TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGACTGAGATTT
GATTAGATGAATATAGATATTTCAAGGAGTATCGGACTAAAAATCATGCAAAATAGCCAGGGCCC
CGA
Found at i:118753 original size:660 final size:651
Alignment explanation
Indices: 117012--119132 Score: 2162
Period size: 660 Copynumber: 3.2 Consensus size: 651
117002 ACGCGTTTTT
* * * *
117012 TAAAAAATATATAATTAAATGCCAAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTT
1 TAAAAAATATATAATTCAATGCC-AAAAAGATTGGAGGGCTTTTCACGCTTTTAATATCGTTTTT
* ** * * * *
117077 C-CTTTTTCTTTTTCCAATTTCTAATTAAAACGAAAGATGATTCAAATGTTTGT---AAAAA--C
65 CTATTTTTCTGATT--AATTTCTAATTAAATCGAAACAAGATTC-AATGCTTGTAAAAAAAATTC
* *
117136 ---AAT-G---GT-TGGGATTTGGTTAGATGAAATATAGATATTTCAAGGAGTCTCAGTGCCAAA
127 TTAAATCGAATGTGTGAGATTTGGTTAGATG-AATATAGATATCTCAAGGAGTCTCAGT-CCAAA
* * * *** * ** * **
117193 AATCATTCAAAATTGAACCGGATCGTAGAACGTGTTTTTAGCCAAATATCGTGATGATTAACACA
190 AATCATGCAAAATAGAATCGCCCCAT-GAACGCATTTTTAGCCAAAAATCGTGATGATTATTACA
117258 CGATTTCGGCTAAAATTTTGCAAAAAATTAACCCGAAAGATATCTCCTCAATTTTTAGTCATAAT
254 CGATTTCGGCTAAAATTTTG-AAAAAATTAACCCGAAAGATATCTCCTCAATTTTTAGTCATAAT
* * * * *
117323 ACTTATAAAAACTATATAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCGTATAATATCAT
318 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTATAATATCGT
117388 TTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAA-
383 TTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAC
* * * * *
117452 AAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAATGTAGATATTTCAAGGACTGCCGG
448 AAATTCTTAAATGCAATGTGACTAAGA-TTTATTAGATGAATATAGATATTTCAAGGAGTGTCGG
* * * *
117517 CACCAAAAACAATTCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAAAAAAACAGT
512 CACCAAAAACCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAGCC-----AAAAACAGT
* * * * *
117582 GATGGTTAGTACACGATTTAGGTTAAAATTTTACAAAAAATGACCAGAAAAATATTCTCTCAATT
572 GATGGTTAGTACACGATTTAGGCTAAAATTTTGCAAAAAATGAAC-GAAAAATTTTC-CTCTATT
* * * *
117647 TTTAGCCACAATACTGA
635 TTTGGCTAAAATACTCA
* * *
117664 TAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTC
1 TAAAAAATATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTTTAATATCGTTTTTC
* * * * *
117729 TTTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTCAAATGTTTGT---AAAAA--C--
66 TATTTTTCTG-ATTAATTTCTAATTAAATCGAAACAAGATTC-AATGCTTGTAAAAAAAATTCTT
* * *
117787 -AAT-G-AT-TG-G-GATTTGGTTAGATGAATGTAGATATTTCAAGGATTCTCAGTGCCAAAAAT
129 AAATCGAATGTGTGAGATTTGGTTAGATGAATATAGATATCTCAAGGAGTCTCAGT-CCAAAAAT
* * ** *
117846 CATTCAAAATTGAATCGGGCCATGGAACGCGTTTTTAGCCAAAAATCGTGATGATTATTACACGA
193 CATGCAAAATAGAATCGCCCCAT-GAACGCATTTTTAGCCAAAAATCGTGATGATTATTACACGA
* * *
117911 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATCTCCTCAATTTTTAGTCATGATACTC
257 TTTCGGCTAAAATTTTGAAAAAATTAACCCGAAAGATATCTCCTCAATTTTTAGTCATAATACTC
* *
117976 ATAAAAAA-ATATAATTCAACGCCAAAAAGATTGTAGGGCTTTTCACGCTTGTAATATCGTTTTT
322 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTATAATATCGTTTTT
* * *
118040 CATATTTTTTATGAATTAATTTCCAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAAT
387 CATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAAT
* * *
118105 TCTTAAATGCAATGTGTCTAAAACTTTATTAGATGAATATAGATATTTCAAGGAGTGTCGGCACT
452 TCTTAAATGCAATGTGACTAAGA-TTTATTAGATGAATATAGATATTTCAAGGAGTGTCGGCACC
* *
118170 AAAAACCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAACCAAAAACCGTGATGGTTAG
516 AAAAACCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGTTAG
* ** * * * *
118235 TACACGATTTTGGCTAAAAACATTGCAAAAAATGATTCGAAAAATGTTTCCCCTATTTATGGATA
581 TACACGATTTAGGCT-AAAATTTTGCAAAAAATGA-ACGAAAAAT-TTTCCTCTATTTTTGGCTA
118300 AAATACTCA
643 AAATACTCA
* * * ** * *
118309 TAAAATATATATAATTTAATGGCAAAAAGATTGGAGAACTTTTCACGTTTTTAATATCATTTTTC
1 TAAAAAATATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTTTAATATCGTTTTTC
* * * *
118374 ATATTTTTCTGATTAATTTCTAATCAAATCGAAACAGGATACAGATACTTGTAAAAACAAATTCT
66 -TATTTTTCTGATTAATTTCTAATTAAATCGAAACAAGATTCA-ATGCTTGTAAAAA-AAATTCT
* * *
118439 TAAATCGAATGTGGCTGAGATTTGATTAGATGAATATGGATATCTCAAGGAGTCTTGACGT-CAA
128 TAAATCGAATGT-G-TGAGATTTGGTTAGATGAATATAGATATCTCAAGGAGTC-TCA-GTCCAA
*
118503 AAATCATGCAAAA-AGCCAGT-GCCCCAT-AACGCATTTTTAGCCAAAAA-CTGTGATGATTATT
189 AAATCATGCAAAATAG--AATCGCCCCATGAACGCATTTTTAGCCAAAAATC-GTGATGATTATT
* * *** * * * * * *
118564 ACACGATTTTGGCTAAAATTTTGTAAAAATTAATTAGAAAAATATTTCCACAATTTAT-GGCTAA
251 ACACGATTTCGGCTAAAATTTTGAAAAAATTAACCCGAAAGATATCTCCTCAATTTTTAGTC-AT
* * * * *
118628 AATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTGACGTTTCTAATAT
315 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTATAATAT
* ** * *
118693 CGTTTTTCCTATTTTTTCCAAATTAATGTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
380 CGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAA
* * * * * * * *
118758 AACAAATTCTT---TCCAATTTGAATGAGATTTGATTAAATGAATTTAGATATTTCAAGTAGTAT
445 AACAAATTCTTAAATGCAATGTGACTAAGATTT-ATTAGATGAATATAGATATTTCAAGGAGTGT
* * * * * * * * *
118820 CGG-AGCCAAAAATCATGCAAAATTAAGCTAGGTCCCCGGAACGCGTTGTTAGGCAAAAACTGTG
509 CGGCA-CCAAAAACCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAGCCAAAAACAGTG
* * *
118884 ATGGTTTGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACAC-AAAAGATTTCTCCTC
573 AT-G---GTTAGTACACGATTTAGGCTAAAATTTTGCAAAAAATGA-ACGAAAA-ATTT-TCCTC
*
118948 TATTTTTGGCTAATATACTCA
631 TATTTTTGGCTAAAATACTCA
* * * *
118969 TAAAAAATATATAATTCAACGCCAAAATGATTGGAGGGCTTTTTACGCTTTTAATATCGTATTTC
1 TAAAAAATATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTTTAATATCGTTTTTC
* * * *
119034 TTACTTTTTCTAAATTTATGTCTAATTAAATCGAAACAAGATTCTAATGCTCGTAAAAAAAATTC
66 -TA-TTTTTCT-GATTAATTTCTAATTAAATCGAAACAAGATTC-AATGCTTGTAAAAAAAATTC
*
119099 TTAAATCCAATGTTGTTGAGATTTGGTTAGATGA
127 TTAAATCGAATG-TG-TGAGATTTGGTTAGATGA
119133 TGTAAAGTAT
Statistics
Matches: 1252, Mismatches: 171, Indels: 83
0.83 0.11 0.06
Matches are distributed among these distances:
644 31 0.02
645 127 0.10
646 12 0.01
648 110 0.09
649 157 0.13
650 107 0.09
651 104 0.08
652 30 0.02
653 2 0.00
654 3 0.00
655 1 0.00
656 6 0.00
657 91 0.07
658 5 0.00
659 99 0.08
660 210 0.17
661 112 0.09
662 42 0.03
663 3 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (651 bp):
TAAAAAATATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTTTAATATCGTTTTTC
TATTTTTCTGATTAATTTCTAATTAAATCGAAACAAGATTCAATGCTTGTAAAAAAAATTCTTAA
ATCGAATGTGTGAGATTTGGTTAGATGAATATAGATATCTCAAGGAGTCTCAGTCCAAAAATCAT
GCAAAATAGAATCGCCCCATGAACGCATTTTTAGCCAAAAATCGTGATGATTATTACACGATTTC
GGCTAAAATTTTGAAAAAATTAACCCGAAAGATATCTCCTCAATTTTTAGTCATAATACTCATAA
AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTATAATATCGTTTTTCATA
TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTT
AAATGCAATGTGACTAAGATTTATTAGATGAATATAGATATTTCAAGGAGTGTCGGCACCAAAAA
CCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACAC
GATTTAGGCTAAAATTTTGCAAAAAATGAACGAAAAATTTTCCTCTATTTTTGGCTAAAATACTC
A
Found at i:119500 original size:15 final size:16
Alignment explanation
Indices: 119482--119511 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
119472 ATAAATAATA
119482 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
119497 ATATTATAATCTAAA
1 ATATTATAATCTAAA
119512 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:119682 original size:13 final size:13
Alignment explanation
Indices: 119651--119688 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
119641 TTTTATATAG
119651 TAGTAAGATAA-A
1 TAGTAAGATAAGA
119663 -A-TAAGATAAGA
1 TAGTAAGATAAGA
119674 TAGTAAGATAAGA
1 TAGTAAGATAAGA
119687 TA
1 TA
119689 TAATTTCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.35
11 2 0.09
12 1 0.04
13 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (13 bp):
TAGTAAGATAAGA
Done.