Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013816.1 Kokia drynarioides strain JFW-HI SEQ_128844, 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: 164580
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 113 characters in sequence are not A, C, G, or T
Found at i:18 original size:6 final size:6
Alignment explanation
Indices: 5--34 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1 GGTG
*
5 GGAGGT GGGGGT GGAGGT GGAGGT GGAGGT
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT
35 TCTAATGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.70, T:0.17
Consensus pattern (6 bp):
GGAGGT
Found at i:2696 original size:21 final size:21
Alignment explanation
Indices: 2670--2711 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2660 TTTATAGCCT
2670 TCAAAAGAGGAAACAAAACAA
1 TCAAAAGAGGAAACAAAACAA
2691 TCAAAAGAGGAAACAAAACAA
1 TCAAAAGAGGAAACAAAACAA
2712 GAACAAATAA
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:0.67, C:0.14, G:0.14, T:0.05
Consensus pattern (21 bp):
TCAAAAGAGGAAACAAAACAA
Found at i:17378 original size:29 final size:30
Alignment explanation
Indices: 17321--17386 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
17311 ATGATTTGTG
* * *
17321 AAAATTGAATTAAATTAAAATTGTATGTAT
1 AAAATTGAATAAAATCAAAATTGCATGTAT
*
17351 AAAATTGCATAAAATCAAAATT-CATGTAT
1 AAAATTGAATAAAATCAAAATTGCATGTAT
*
17380 AACATTG
1 AAAATTG
17387 TACCAAACTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (30 bp):
AAAATTGAATAAAATCAAAATTGCATGTAT
Found at i:33283 original size:12 final size:12
Alignment explanation
Indices: 33244--33284 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
33234 GATATGGAGA
*
33244 ATATATACACAT
1 ATATATATACAT
*
33256 ATACATATACAT
1 ATATATATACAT
*
33268 ATATATATGCAT
1 ATATATATACAT
33280 ATATA
1 ATATA
33285 CACGTAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (12 bp):
ATATATATACAT
Found at i:36242 original size:2 final size:2
Alignment explanation
Indices: 36235--36267 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36225 TTTTATTCAT
36235 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36268 TAGGTAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37506 original size:59 final size:59
Alignment explanation
Indices: 37414--37532 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
37404 TTTTATGCAG
37414 TGCAACATGCTCTCAGCTTCCATCCTTTCCCGACTAGACCGTATAAATCGAAACTTTCT
1 TGCAACATGCTCTCAGCTTCCATCCTTTCCCGACTAGACCGTATAAATCGAAACTTTCT
*
37473 TGCAACATGCTCTCAGCTTCCATCCTTTCCCGACTAGATCGTATAAATCGAAACTTTCT
1 TGCAACATGCTCTCAGCTTCCATCCTTTCCCGACTAGACCGTATAAATCGAAACTTTCT
37532 T
1 T
37533 TGGGACGGCT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (59 bp):
TGCAACATGCTCTCAGCTTCCATCCTTTCCCGACTAGACCGTATAAATCGAAACTTTCT
Found at i:49146 original size:13 final size:14
Alignment explanation
Indices: 49123--49151 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
49113 TTGGTTATTT
49123 TTTATTATTTTTAA
1 TTTATTATTTTTAA
49137 TTTA-TATTTTTAA
1 TTTATTATTTTTAA
49150 TT
1 TT
49152 AATAACTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTATTTTTAA
Found at i:49585 original size:3 final size:3
Alignment explanation
Indices: 49579--49608 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
49569 AATATTTGAA
49579 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49609 TTAATATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:50044 original size:7 final size:7
Alignment explanation
Indices: 50034--50063 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
50024 TCTTTATAAT
50034 TTTTAAA
1 TTTTAAA
50041 TTTTAAA
1 TTTTAAA
50048 TTTTAAA
1 TTTTAAA
*
50055 ATTTAAA
1 TTTTAAA
50062 TT
1 TT
50064 CAATTGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTTTAAA
Found at i:55658 original size:17 final size:18
Alignment explanation
Indices: 55638--55673 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
55628 TATACGATAA
*
55638 TAATATTTATA-TTAATT
1 TAATAATTATATTTAATT
55655 TAATAATTATATTTAATT
1 TAATAATTATATTTAATT
55673 T
1 T
55674 TTTATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATAATTATATTTAATT
Found at i:62263 original size:41 final size:41
Alignment explanation
Indices: 62202--62322 Score: 154
Period size: 41 Copynumber: 2.9 Consensus size: 41
62192 GAGGAAACGC
* * * *
62202 CAGAGCATTAGCAACTTTTATTAGAAAACGCCGCTAAATGT
1 CAGAGCATTAGCAGCGTTTATTAGAAAACGCAGCTAAAAGT
* *
62243 CAGAGCATTAGCAGCGTTTATTAGAAAACACTGCTAAAAGT
1 CAGAGCATTAGCAGCGTTTATTAGAAAACGCAGCTAAAAGT
*
62284 AAGAGCATTAGCAGCGTTTA-TAGGAAAAACGCAGCTAAA
1 CAGAGCATTAGCAGCGTTTATTA-G-AAAACGCAGCTAAA
62323 GATTAGGAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 2 0.03
41 56 0.80
42 12 0.17
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (41 bp):
CAGAGCATTAGCAGCGTTTATTAGAAAACGCAGCTAAAAGT
Found at i:62644 original size:31 final size:29
Alignment explanation
Indices: 62609--62731 Score: 88
Period size: 31 Copynumber: 4.0 Consensus size: 29
62599 ATGATAATTA
62609 AATCAAAATTAAAGTTTCATGTATATATGTG
1 AATCAAAATTAAAG-TTCATGTATATAT-TG
* * *
62640 AATCATAATTAGAAATTCATGTGTATAATTG
1 AATCAAAATTA-AAGTTCATGTATAT-ATTG
* *
62671 CA-CCAAATTAAAGTTCATGTATATAATTG
1 AATCAAAATTAAAGTTCATGTATAT-ATTG
* * *
62700 CACAT-TAAATCAATGTTCATGTATAATATTG
1 -A-ATCAAAATTAAAGTTCATGTAT-ATATTG
62731 A
1 A
62732 GATTTATCCA
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
29 17 0.23
30 7 0.09
31 44 0.59
32 6 0.08
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (29 bp):
AATCAAAATTAAAGTTCATGTATATATTG
Found at i:62690 original size:29 final size:29
Alignment explanation
Indices: 62614--62702 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
62604 AATTAAATCA
* *
62614 AAATTAAAGTTTCATGTATAT-ATGTGAATC
1 AAATTAAAG-TTCATGTATATAAT-TGCACC
* *
62644 ATAATTAGAAATTCATGTGTATAATTGCACC
1 A-AATTA-AAGTTCATGTATATAATTGCACC
62675 AAATTAAAGTTCATGTATATAATTGCAC
1 AAATTAAAGTTCATGTATATAATTGCAC
62703 ATTAAATCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 20 0.40
30 6 0.12
31 20 0.40
32 4 0.08
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (29 bp):
AAATTAAAGTTCATGTATATAATTGCACC
Found at i:62724 original size:29 final size:27
Alignment explanation
Indices: 62661--62726 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
62651 GAAATTCATG
*
62661 TGTATAATTGCACCAAATTAAAGTTCA
1 TGTATAATTGCACCAAATCAAAGTTCA
* *
62688 TGTATATAATTGCACATTAAATCAATGTTCA
1 TG--TATAATTGCAC--CAAATCAAAGTTCA
62719 TGTATAAT
1 TGTATAAT
62727 ATTGAGATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 2 0.06
29 17 0.53
31 13 0.41
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAGTTCA
Found at i:64083 original size:41 final size:40
Alignment explanation
Indices: 64033--64124 Score: 94
Period size: 41 Copynumber: 2.2 Consensus size: 40
64023 AAAAAATTAG
* * *
64033 AGGTTAAGCAATAACGACATTTATGAGAAAAACATCGCAAA
1 AGGTAAAGCAATAACGACATCTATGAG-AAAACACCGCAAA
* * * *
64074 AGGTAAAGCATTAGCGGCGTCTATGAGAAAACACCGCAAA
1 AGGTAAAGCAATAACGACATCTATGAGAAAACACCGCAAA
*
64114 AGATAAGAGCA
1 AGGTAA-AGCA
64125 TTAGCAAAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 17 0.40
41 25 0.60
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (40 bp):
AGGTAAAGCAATAACGACATCTATGAGAAAACACCGCAAA
Found at i:64133 original size:19 final size:19
Alignment explanation
Indices: 64109--64148 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
64099 AGAAAACACC
64109 GCAAAAGATAAGAGCATTA
1 GCAAAAGATAAGAGCATTA
*
64128 GCAAAAGGTAAGAGCATTA
1 GCAAAAGATAAGAGCATTA
64147 GC
1 GC
64149 GGCGTTTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.15
Consensus pattern (19 bp):
GCAAAAGATAAGAGCATTA
Found at i:64162 original size:60 final size:59
Alignment explanation
Indices: 64069--64187 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 59
64059 GAAAAACATC
*
64069 GCAAAAGGTAAAGCATTAGCGGCGTCTATGAGAAAACACCGCAAAAGATAAGAGCATTA
1 GCAAAAGGTAAAGCATTAGCGGCGTCTAGGAGAAAACACCGCAAAAGATAAGAGCATTA
* * *
64128 GCAAAAGGTAAGAGCATTAGCGGCGTTTAGGAGAAAACGCCGCAAAAGGTAAGAGCATTA
1 GCAAAAGGTAA-AGCATTAGCGGCGTCTAGGAGAAAACACCGCAAAAGATAAGAGCATTA
64188 ACAGCGTTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
59 11 0.20
60 44 0.80
ACGTcount: A:0.42, C:0.16, G:0.27, T:0.15
Consensus pattern (59 bp):
GCAAAAGGTAAAGCATTAGCGGCGTCTAGGAGAAAACACCGCAAAAGATAAGAGCATTA
Found at i:64185 original size:41 final size:41
Alignment explanation
Indices: 64128--64205 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
64118 AAGAGCATTA
* *
64128 GCAAAAGGTAAGAGCATTAGCGGCGTTTA-GGAGAAAACGCC
1 GCAAAAGGTAAGAGCATTAACAGCGTTTATGG-GAAAACGCC
64169 GCAAAAGGTAAGAGCATTAACAGCGTTTATGGGAAAA
1 GCAAAAGGTAAGAGCATTAACAGCGTTTATGGGAAAA
64206 ACATCGCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (41 bp):
GCAAAAGGTAAGAGCATTAACAGCGTTTATGGGAAAACGCC
Found at i:65135 original size:42 final size:43
Alignment explanation
Indices: 65084--65164 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 43
65074 TATTAGTAGT
*
65084 GTTTGTGAGAAAAGCGCCGCTAAAGACCATGTT-TTTAGTGAC
1 GTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTTTAGTGAC
**
65126 GTTTGTGAGAAAAGCGCCACTAAAGGTCATGTTCTTTAG
1 GTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTTTAG
65165 CGGTTTAGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 30 0.86
43 5 0.14
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (43 bp):
GTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTTTAGTGAC
Found at i:65295 original size:43 final size:42
Alignment explanation
Indices: 65202--65318 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 42
65192 GCCGCTAAAA
*
65202 CGCTAAAGACCATGTTCTTTTAGCGGCGTTTATGGAAAAAGCT
1 CGCTAAAGACCATGTTC-TTTAGCGGCATTTATGGAAAAAGCT
* * *
65245 CTCCTAAAGACCATGTTCTTTAGCGGCATTTGTGGGAGAAGAG-T
1 C-GCTAAAGACCATGTTCTTTAGCGGCATTTAT-GGA-AAAAGCT
*
65289 CGCTAAAGACCATGTTCTATAGCGGCATTT
1 CGCTAAAGACCATGTTCTTTAGCGGCATTT
65319 TTCTGCAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
43 41 0.63
44 20 0.31
45 4 0.06
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (42 bp):
CGCTAAAGACCATGTTCTTTAGCGGCATTTATGGAAAAAGCT
Found at i:67201 original size:10 final size:10
Alignment explanation
Indices: 67186--67258 Score: 62
Period size: 10 Copynumber: 7.2 Consensus size: 10
67176 TCCATGTAAG
67186 ATTTTATAAT
1 ATTTTATAAT
*
67196 ATTTTA-ATT
1 ATTTTATAAT
*
67205 ATTTTTTATAT
1 ATTTTATA-AT
67216 ATTTTAGTTAAAT
1 ATTTTA--T-AAT
67229 ATTTTA-AA-
1 ATTTTATAAT
*
67237 ATTTTATAAG
1 ATTTTATAAT
67247 ATTTTATAAT
1 ATTTTATAAT
67257 AT
1 AT
67259 CCATTTTGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
8 6 0.12
9 11 0.22
10 18 0.35
11 6 0.12
13 9 0.18
14 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (10 bp):
ATTTTATAAT
Found at i:67768 original size:29 final size:32
Alignment explanation
Indices: 67716--67790 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 32
67706 TTTTTAAATT
*
67716 AATAATATTAAAATTACATATTAATCT-TTTAA
1 AATAATATAAAAATTACATATTAAT-TATTTAA
67748 AATAATA-AAAAATTA-AT-TTAATTATTTAA
1 AATAATATAAAAATTACATATTAATTATTTAA
*
67777 AATATTATAAAAAT
1 AATAATATAAAAAT
67791 ATAAATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 1 0.03
29 16 0.41
30 8 0.21
31 7 0.18
32 7 0.18
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (32 bp):
AATAATATAAAAATTACATATTAATTATTTAA
Found at i:72921 original size:4 final size:4
Alignment explanation
Indices: 72914--72956 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
72904 CACACACATA
*
72914 TATG TATG TATG TATG TATG TATG TATG TATG CATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
72957 ATGTTATTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:75331 original size:18 final size:15
Alignment explanation
Indices: 75295--75324 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
75285 TCTGAATTAA
75295 ATTATTTATTTTTAT
1 ATTATTTATTTTTAT
75310 ATTATTTATTTTTAT
1 ATTATTTATTTTTAT
75325 GATATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTATTTATTTTTAT
Found at i:78999 original size:17 final size:17
Alignment explanation
Indices: 78979--79014 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
78969 TTTTGAACAA
78979 TTTAATTTTTTTTATTT
1 TTTAATTTTTTTTATTT
* *
78996 TTTACTTTTTTTTGTTT
1 TTTAATTTTTTTTATTT
79013 TT
1 TT
79015 CCTTTTTTTT
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:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTAATTTTTTTTATTT
Found at i:79021 original size:17 final size:16
Alignment explanation
Indices: 78979--79025 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
78969 TTTTGAACAA
*
78979 TTTAATTTTTTTTATTT
1 TTTACTTTTTTTT-TTT
*
78996 TTTACTTTTTTTTGTT
1 TTTACTTTTTTTTTTT
*
79012 TTTCCTTTTTTTTT
1 TTTACTTTTTTTTT
79026 CATATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.09, C:0.06, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTACTTTTTTTTTTT
Found at i:79198 original size:21 final size:22
Alignment explanation
Indices: 79183--79225 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
79173 TAAAAGAGAT
79183 GGAGAAA-AAAAGAAAACAAAA
1 GGAGAAACAAAAGAAAACAAAA
*
79204 GGAGAAACAAAAGAAAATAAAA
1 GGAGAAACAAAAGAAAACAAAA
79226 AAAAAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.74, C:0.05, G:0.19, T:0.02
Consensus pattern (22 bp):
GGAGAAACAAAAGAAAACAAAA
Found at i:98990 original size:17 final size:17
Alignment explanation
Indices: 98957--98990 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
98947 ATTATATTAC
* *
98957 TATTATTTTGTTGTTGT
1 TATTATTTTGATATTGT
98974 TATTATTTTGATATTGT
1 TATTATTTTGATATTGT
98991 ATAACTCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (17 bp):
TATTATTTTGATATTGT
Found at i:101452 original size:25 final size:25
Alignment explanation
Indices: 101424--101473 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
101414 TAAAGAAGAT
*
101424 TTCAACTTTTTATTAAATGAGTAAA
1 TTCAACTTTTTATTAAATGAATAAA
101449 TTCAACTTTTTATTAAATGAATAAA
1 TTCAACTTTTTATTAAATGAATAAA
101474 CAAACGAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (25 bp):
TTCAACTTTTTATTAAATGAATAAA
Found at i:103801 original size:9 final size:10
Alignment explanation
Indices: 103771--103805 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
103761 AAAAAATCAT
103771 AAAATATATA
1 AAAATATATA
103781 AAAATATATA
1 AAAATATATA
*
103791 AAAATGT-TA
1 AAAATATATA
103800 AAAATA
1 AAAATA
103806 AAAAATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (10 bp):
AAAATATATA
Found at i:104013 original size:17 final size:17
Alignment explanation
Indices: 103993--104045 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
103983 ACTTATAGAA
103993 AATATA-AAAAAATTAT
1 AATATATAAAAAATTAT
104009 GAATACTATAAAAATATTA-
1 -AATA-TATAAAAA-ATTAT
*
104028 AATATATAATAAATTAT
1 AATATATAAAAAATTAT
104045 A
1 A
104046 TTTTTTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 6 0.19
19 5 0.16
20 4 0.13
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
AATATATAAAAAATTAT
Found at i:104023 original size:18 final size:17
Alignment explanation
Indices: 103992--104045 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
103982 AACTTATAGA
*
103992 AAATATAAAAAAATTAT
1 AAATATATAAAAATTAT
*
104009 GAATACTATAAAAA-TATT
1 AAATA-TATAAAAATTA-T
104027 AAATATATAATAAATTAT
1 AAATATATAA-AAATTAT
104045 A
1 A
104046 TTTTTTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 11 0.37
18 17 0.57
19 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATATATAAAAATTAT
Found at i:104671 original size:19 final size:18
Alignment explanation
Indices: 104644--104708 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 18
104634 TGAGTGTTAT
*
104644 TAATATTATAATTTTTTA
1 TAATTTTATAATTTTTTA
104662 TAATCTTTAT-A-TTTTTA
1 TAAT-TTTATAATTTTTTA
*
104679 TGATATTTATAAGATTTATTTA
1 TAAT-TTTAT-A-ATTT-TTTA
104701 TAATTTTA
1 TAATTTTA
104709 ATAAATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
17 14 0.38
18 5 0.14
19 4 0.11
20 1 0.03
21 6 0.16
22 7 0.19
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (18 bp):
TAATTTTATAATTTTTTA
Found at i:124503 original size:2 final size:2
Alignment explanation
Indices: 124492--124533 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
124482 ACAAAGACAA
124492 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
124533 A
1 A
124534 AGGGTTATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:131489 original size:22 final size:22
Alignment explanation
Indices: 131464--131526 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
131454 CACAAAAAAG
131464 TTAAATTTATTAAATATTAAAT
1 TTAAATTTATTAAATATTAAAT
* * *
131486 TTAAAATAATATAAATA-TATAT
1 TTAAATTTAT-TAAATATTAAAT
131508 TTAAAATTT-TTAAA-ATTAA
1 TT-AAATTTATTAAATATTAA
131527 TATAAAAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
20 1 0.03
21 6 0.19
22 15 0.47
23 10 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAATTTATTAAATATTAAAT
Found at i:137724 original size:34 final size:35
Alignment explanation
Indices: 137686--137771 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 35
137676 ATCTGGCGTC
*
137686 AACAAATAATTCAAAAATTATAAAA-ACAAAAAGT
1 AACAAATAATTCAAAAATTAAAAAATACAAAAAGT
* *
137720 AACAAAATAATTCAAAATTTAAAAAATATAAAAAGT
1 AAC-AAATAATTCAAAAATTAAAAAATACAAAAAGT
*
137756 AATAAA-AATTCAAAAA
1 AACAAATAATTCAAAAA
137772 AAAAAAAGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
34 12 0.27
35 23 0.51
36 10 0.22
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (35 bp):
AACAAATAATTCAAAAATTAAAAAATACAAAAAGT
Found at i:138813 original size:20 final size:20
Alignment explanation
Indices: 138761--138827 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
138751 CTATAAAAAA
**
138761 TAAAAATAAATAAAATTTA-
1 TAAAAATATTTAAAATTTAG
* *
138780 TAAAAACTA-CTAAATTTTAG
1 TAAAAA-TATTTAAAATTTAG
*
138800 TAAAAATATTTAAAATTTAT
1 TAAAAATATTTAAAATTTAG
138820 TAAAAATA
1 TAAAAATA
138828 AATTTTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.40
20 24 0.60
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (20 bp):
TAAAAATATTTAAAATTTAG
Found at i:139119 original size:38 final size:38
Alignment explanation
Indices: 139075--139170 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 38
139065 TTTAGTAAAA
*
139075 TAATTTTTATAATTTTTTTACGAATTTTAT-ATTTCTT-
1 TAATTTTTATAATATTTTTACG-ATTTTATGATTTCTTC
* * *
139112 TACATTTTTTTTATAATTTTTATGATTTTATGATTTCTTC
1 TA-ATTTTTATAAT-ATTTTTACGATTTTATGATTTCTTC
139152 TAATTTTTA-AATATTTTTA
1 TAATTTTTATAATATTTTTA
139171 TACTTTTCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
37 9 0.18
38 18 0.37
39 20 0.41
40 2 0.04
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (38 bp):
TAATTTTTATAATATTTTTACGATTTTATGATTTCTTC
Found at i:153806 original size:19 final size:20
Alignment explanation
Indices: 153784--153828 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
153774 TAATATAAAA
*
153784 ATTTTGAAATTTT-ATAATT
1 ATTTTGAAATTTTAAAAATT
*
153803 ATTTT-TAATTTTAAAAATT
1 ATTTTGAAATTTTAAAAATT
153822 ATTTTGA
1 ATTTTGA
153829 TTCTTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
ATTTTGAAATTTTAAAAATT
Found at i:154223 original size:14 final size:15
Alignment explanation
Indices: 154201--154234 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
154191 CATGTGTCTT
*
154201 ATTTATTTAATTTTA
1 ATTTATTTAAATTTA
154216 ATTT-TTTAAATTTA
1 ATTTATTTAAATTTA
154230 ATTTA
1 ATTTA
154235 AAGATACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTATTTAAATTTA
Found at i:154350 original size:18 final size:19
Alignment explanation
Indices: 154308--154351 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 19
154298 CTCTATTTGT
154308 TAAAA-AAAATATTTAATA
1 TAAAATAAAATATTTAATA
*
154326 T--ATTAAAATA-TTAATA
1 TAAAATAAAATATTTAATA
154342 TAAAATAAAA
1 TAAAATAAAA
154352 ACAGTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 6
0.72 0.07 0.21
Matches are distributed among these distances:
16 8 0.38
17 6 0.29
18 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAATAAAATATTTAATA
Found at i:154577 original size:33 final size:32
Alignment explanation
Indices: 154526--154589 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
154516 TACTATAATC
154526 TTTATTTATTTTTTTAATTCGTAAAGTGTGAT
1 TTTATTTATTTTTTTAATTCGTAAAGTGTGAT
* *
154558 TTTATTTTTATTTTTTAATTGGTAAAGTGTGA
1 TTTATTTAT-TTTTTTAATTCGTAAAGTGTGA
154590 GTCTTTTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 8 0.28
33 21 0.72
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (32 bp):
TTTATTTATTTTTTTAATTCGTAAAGTGTGAT
Found at i:157492 original size:20 final size:19
Alignment explanation
Indices: 157456--157502 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
157446 GAACTTTAAT
157456 TTAACAAAATAATTTTAATAA
1 TTAA-AAAATAATTTTAA-AA
157477 TTAAAAAAT-ATGTTTAAAA
1 TTAAAAAATAAT-TTTAAAA
*
157496 ATAAAAA
1 TTAAAAA
157503 TACACAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.42
20 10 0.42
21 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
TTAAAAAATAATTTTAAAA
Found at i:161134 original size:27 final size:27
Alignment explanation
Indices: 161093--161161 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
161083 AAAAATACCT
*
161093 GACACTCAATAGAGGAACATAAAGT-GA
1 GACAC-CAATGGAGGAACATAAAGTGGA
161120 CGACACCAATGGAGGAACATAAAGTGGA
1 -GACACCAATGGAGGAACATAAAGTGGA
*
161148 GGCACCAATGGAGG
1 GACACCAATGGAGG
161162 GTTTTTAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 31 0.82
28 7 0.18
ACGTcount: A:0.42, C:0.17, G:0.29, T:0.12
Consensus pattern (27 bp):
GACACCAATGGAGGAACATAAAGTGGA
Found at i:164223 original size:28 final size:26
Alignment explanation
Indices: 164147--164229 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 26
164137 CCCTCCTTAA
164147 TCAA-TCTAGTGTTTACGATTTAGAGTT
1 TCAAGTCTAGTGTTTACG-TTTAG-GTT
*
164174 TCAAGTCTAGTGTTTATGGTTTAAGGTT
1 TCAAGTCTAGTGTTTA-CGTTT-AGGTT
*
164202 TCAAGTCTAGGGTTTACAGTTTAGGTT
1 TCAAGTCTAGTGTTTAC-GTTTAGGTT
164229 T
1 T
164230 TAGGGTTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
27 10 0.20
28 36 0.73
29 3 0.06
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (26 bp):
TCAAGTCTAGTGTTTACGTTTAGGTT
Found at i:164488 original size:20 final size:21
Alignment explanation
Indices: 164463--164504 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
164453 GTCCATTTGC
164463 CTCGG-AGGAGTAGAGTATTG
1 CTCGGAAGGAGTAGAGTATTG
164483 CTCGGAAGGAGTAGAGTATTG
1 CTCGGAAGGAGTAGAGTATTG
164504 C
1 C
164505 GGTGGCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.26, C:0.12, G:0.38, T:0.24
Consensus pattern (21 bp):
CTCGGAAGGAGTAGAGTATTG
Done.