Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013070.1 Kokia drynarioides strain JFW-HI SEQ_128088, 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: 153997
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:179 original size:69 final size:69
Alignment explanation
Indices: 101--238 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
91 AATAATTGAA
101 GAAAAAATACAATTTGCTCACATTTATAATAACATTTTGAAAAGAAAATGTGAGCAAAAACACGA
1 GAAAAAATACAATTTGCTCACATTTATAATAACATTTTGAAAAGAAAATGTGAGCAAAAACACGA
166 GAAC
66 GAAC
170 GAAAAAATACAATTTGCTCACATTTATAATAACATTTTGAAAAGAAAATGTGAGCAAAAACACGA
1 GAAAAAATACAATTTGCTCACATTTATAATAACATTTTGAAAAGAAAATGTGAGCAAAAACACGA
235 GAAC
66 GAAC
239 CACGAAATCT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (69 bp):
GAAAAAATACAATTTGCTCACATTTATAATAACATTTTGAAAAGAAAATGTGAGCAAAAACACGA
GAAC
Found at i:11951 original size:62 final size:62
Alignment explanation
Indices: 11854--11979 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
11844 AACATTTTTG
11854 CAACCTAAGCACAGTGTCAAACTGGATGCAGGGAAAACAAAGCCAGAGTGGAACCTCTATAT
1 CAACCTAAGCACAGTGTCAAACTGGATGCAGGGAAAACAAAGCCAGAGTGGAACCTCTATAT
11916 CAACCTAAGCACAGTGTCAAACTGGATGCAGGGAAAACAAAGCCAGAGTGGAACCTCTATAT
1 CAACCTAAGCACAGTGTCAAACTGGATGCAGGGAAAACAAAGCCAGAGTGGAACCTCTATAT
11978 CA
1 CA
11980 TTGAAACAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (62 bp):
CAACCTAAGCACAGTGTCAAACTGGATGCAGGGAAAACAAAGCCAGAGTGGAACCTCTATAT
Found at i:17060 original size:14 final size:14
Alignment explanation
Indices: 17041--17069 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17031 GCCAAGGTTA
17041 GAATCATATCAAAG
1 GAATCATATCAAAG
17055 GAATCATATCAAAG
1 GAATCATATCAAAG
17069 G
1 G
17070 CTACTTTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (14 bp):
GAATCATATCAAAG
Found at i:24479 original size:118 final size:119
Alignment explanation
Indices: 24269--24511 Score: 398
Period size: 118 Copynumber: 2.0 Consensus size: 119
24259 TTCTTCTTGA
*
24269 TTTTTGTGGAGAGGGAGCAATCATACTTACGTAACTAGCCATGCTTGTCTTTATGCCTATAAGCA
1 TTTTTGTGGAGAGAGAGCAATCATACTTACGTAACTAGCCATGCTTGTCTTTATGCCTATAAGCA
*
24334 GAGCCTAGAACTCAAACTAATTAATGCATTAATTGCCCAAAGCAGACATTG-CT
66 GACCCTAGAACTCAAACTAATTAATGCATTAATTGCCCAAAGCAGACATTGACT
* *
24387 TTTTTGTGGGGAGAGAGCAATCATACTTATGTAACTAGCCATGCTTGTCTTTATGCCTATAAGCA
1 TTTTTGTGGAGAGAGAGCAATCATACTTACGTAACTAGCCATGCTTGTCTTTATGCCTATAAGCA
* * * *
24452 GACCCTCGAATTCAAACTAATTGATGCATTAATTGCCTAAAGCAGACATTGATCT
66 GACCCTAGAACTCAAACTAATTAATGCATTAATTGCCCAAAGCAGACATTGA-CT
24507 TTTTT
1 TTTTT
24512 TCTTTTTCTT
Statistics
Matches: 115, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
118 108 0.94
120 7 0.06
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (119 bp):
TTTTTGTGGAGAGAGAGCAATCATACTTACGTAACTAGCCATGCTTGTCTTTATGCCTATAAGCA
GACCCTAGAACTCAAACTAATTAATGCATTAATTGCCCAAAGCAGACATTGACT
Found at i:65203 original size:27 final size:28
Alignment explanation
Indices: 65155--65211 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
65145 TCTCTCTTGT
*
65155 GCCAAATTACAGAATATCGCTCTTTCGA
1 GCCAAATTACAGAATATCGCTCTTACGA
65183 GCCAAA-TACAGAATTAT-GCTCTTACGA
1 GCCAAATTACAGAA-TATCGCTCTTACGA
65210 GC
1 GC
65212 TAGAGTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (28 bp):
GCCAAATTACAGAATATCGCTCTTACGA
Found at i:65256 original size:28 final size:28
Alignment explanation
Indices: 65213--65282 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
65203 CTTACGAGCT
*
65213 AGAGTTATGCTCTTAC-AAACAAGAATAC
1 AGAGTTATACTCTTACGAAACAA-AATAC
* **
65241 AGAGTTATACTTTTACGAGCCAAAATAC
1 AGAGTTATACTCTTACGAAACAAAATAC
*
65269 AGAG-TATGCTCTTA
1 AGAGTTATACTCTTA
65283 TGACCCAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
27 8 0.23
28 23 0.66
29 4 0.11
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (28 bp):
AGAGTTATACTCTTACGAAACAAAATAC
Found at i:68589 original size:45 final size:45
Alignment explanation
Indices: 68523--68614 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
68513 ACAAAAGTGG
*
68523 GAACTAGTGATGCAATTGAAATCGTGAATTATATGGTAAGGCAAA
1 GAACTAGTGATGCAATCGAAATCGTGAATTATATGGTAAGGCAAA
68568 GAACTAGTGATGCAATCGAAATCGTGAATTATATGGTAAGGCAAA
1 GAACTAGTGATGCAATCGAAATCGTGAATTATATGGTAAGGCAAA
68613 GA
1 GA
68615 CCATAACAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (45 bp):
GAACTAGTGATGCAATCGAAATCGTGAATTATATGGTAAGGCAAA
Found at i:83109 original size:2 final size:2
Alignment explanation
Indices: 83102--83128 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
83092 AGTATCTATT
83102 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 T
83129 CTTTTTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:84937 original size:6 final size:6
Alignment explanation
Indices: 84926--84975 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
84916 TTTATATTTT
**
84926 ATATTA ATATTA ATATTA ATATTAA ATAAAA ATAATT- ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATT-A ATATTA AT-ATTA ATATTA ATATTA
84975 A
1 A
84976 ATAAAAAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 3 0.08
6 29 0.78
7 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
ATATTA
Found at i:97346 original size:25 final size:25
Alignment explanation
Indices: 97318--97426 Score: 154
Period size: 23 Copynumber: 4.5 Consensus size: 25
97308 AACACGTCTC
97318 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
97343 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
* *
97368 GTGCTCTCTG--ATTAGTACTTTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
**
97391 GCACTCTCTG-T-TTAGCACTGTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
97414 GTGCTCTCTGTTA
1 GTGCTCTCTGTTA
97427 GTACTTTGGT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
23 37 0.51
24 1 0.01
25 35 0.48
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (25 bp):
GTGCTCTCTGTTATTAGCACTGTGT
Found at i:97423 original size:23 final size:23
Alignment explanation
Indices: 97297--97447 Score: 146
Period size: 23 Copynumber: 6.5 Consensus size: 23
97287 ACACTAGCGC
* *
97297 GCTCTCTGTTTAACAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
97320 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
97345 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* * * *
97370 GCTCTCTGATTAGTACTTTGTGC
1 GCTCTCTGTTTAGCACTGTGTGT
*
97393 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
97416 GCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGTTTAGCACTGTGTGT
*
97437 ACTCTCTGTTT
1 GCTCTCTGTTT
97448 GTTCCGTATA
Statistics
Matches: 109, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
21 9 0.08
22 11 0.10
23 44 0.40
24 1 0.01
25 41 0.38
26 3 0.03
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:98886 original size:12 final size:12
Alignment explanation
Indices: 98871--98897 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
98861 TAATAAGTTT
98871 TTACAAATATAA
1 TTACAAATATAA
98883 TTACAAATATAA
1 TTACAAATATAA
98895 TTA
1 TTA
98898 TAAGTGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
TTACAAATATAA
Found at i:101693 original size:20 final size:19
Alignment explanation
Indices: 101668--101720 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 19
101658 TTCCCATAAA
101668 AATTTTAAAAATTTAAAAAT
1 AATTTTAAAAATTT-AAAAT
101688 AATTTTTAAAAATTTAAAAT
1 AA-TTTTAAAAATTTAAAAT
* *
101708 AGTTTTTAAAATT
1 AATTTTAAAAATT
101721 CAAATGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 10 0.33
20 8 0.27
21 12 0.40
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTTTAAAAATTTAAAAT
Found at i:101696 original size:21 final size:20
Alignment explanation
Indices: 101670--101718 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
101660 CCCATAAAAA
101670 TTTTAAAAATTTAAAAATAAT
1 TTTTAAAAATTT-AAAATAAT
*
101691 TTTTAAAAATTTAAAATAGT
1 TTTTAAAAATTTAAAATAAT
101711 TTTTAAAA
1 TTTTAAAA
101719 TTCAAATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TTTTAAAAATTTAAAATAAT
Found at i:101743 original size:19 final size:19
Alignment explanation
Indices: 101670--101744 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
101660 CCCATAAAAA
* *
101670 TTTTAAAAATTTAAAAATAAT
1 TTTTAAAAATTT-CAAAT-AG
*
101691 TTTTAAAAATTTAAAATAG
1 TTTTAAAAATTTCAAATAG
*
101710 TTTTTAAAA-TTCAAAT-G
1 TTTTAAAAATTTCAAATAG
101727 TTTGTAAAAATTTCAAAT
1 TTT-TAAAAATTTCAAAT
101745 TTTATATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.08
18 11 0.23
19 16 0.33
20 5 0.10
21 12 0.25
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (19 bp):
TTTTAAAAATTTCAAATAG
Found at i:103478 original size:21 final size:21
Alignment explanation
Indices: 103448--103487 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
103438 ACAGCCTTAG
*
103448 GAGGCTGCGGTGGAGGCGACT
1 GAGGCAGCGGTGGAGGCGACT
103469 GAGGCAGCGGTGGAGGCGA
1 GAGGCAGCGGTGGAGGCGA
103488 TGCTGCTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.55, T:0.10
Consensus pattern (21 bp):
GAGGCAGCGGTGGAGGCGACT
Found at i:107228 original size:29 final size:30
Alignment explanation
Indices: 107186--107244 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
107176 ATATGAATTA
* *
107186 TGTGTAATTATATATATG-AATTTTGATTT
1 TGTGTAATTATATACATGAAATTTCGATTT
*
107215 TGTGTAATTTTATACATGAAATTTCGATTT
1 TGTGTAATTATATACATGAAATTTCGATTT
107245 GATCCGATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGTAATTATATACATGAAATTTCGATTT
Found at i:117893 original size:21 final size:24
Alignment explanation
Indices: 117857--117902 Score: 71
Period size: 21 Copynumber: 2.0 Consensus size: 24
117847 TATGTAATCT
117857 TTAGAAGATATGATTTTGTA-ATA
1 TTAGAAGATATGATTTTGTAGATA
117880 TTAG-AGAT-TGATTTTGTAGATA
1 TTAGAAGATATGATTTTGTAGATA
117902 T
1 T
117903 CTTTTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 8 0.36
23 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.46
Consensus pattern (24 bp):
TTAGAAGATATGATTTTGTAGATA
Found at i:122985 original size:21 final size:24
Alignment explanation
Indices: 122941--122989 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 24
122931 GTATTTGATA
122941 TGTAATCTTTAGAAAATATGATTT
1 TGTAATCTTTAGAAAATATGATTT
*
122965 TGTAAT-TTTAG-AGAT-TGATTT
1 TGTAATCTTTAGAAAATATGATTT
122986 TGTA
1 TGTA
122990 GATAGCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 5 0.21
24 6 0.25
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (24 bp):
TGTAATCTTTAGAAAATATGATTT
Found at i:132370 original size:113 final size:112
Alignment explanation
Indices: 132232--132435 Score: 297
Period size: 113 Copynumber: 1.8 Consensus size: 112
132222 CATTATAATT
* * *
132232 ATTTTTTATTAATTTATTATATAAAAGAACG-AAAACAT-TCTCATAAAAAATATAACTTAATTT
1 ATTTTTTATTAATTTATTAGATAAAAAAAAGAAAAAC-TCTCTCAT-AAAAATATAACTTAATTT
132295 GA-ATATGAAAATATATTTTAATAATTTCAATTTCAAATCTCATGAGATAA
64 -ATATATGAAAA-ATATTTTAATAATTTCAATTTCAAATCTCATGAGATAA
* * *
132345 ATTTTTTATTGATTTATTAGATAAAAAAAATAAAAACTCTCTCATAAAAATATAACTTGATTTAT
1 ATTTTTTATTAATTTATTAGATAAAAAAAAGAAAAACTCTCTCATAAAAATATAACTTAATTTAT
132410 ATATGAAAAATATTTTAATAATTTCA
66 ATATGAAAAATATTTTAATAATTTCA
132436 TAATTGAATT
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
112 18 0.22
113 53 0.65
114 11 0.13
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (112 bp):
ATTTTTTATTAATTTATTAGATAAAAAAAAGAAAAACTCTCTCATAAAAATATAACTTAATTTAT
ATATGAAAAATATTTTAATAATTTCAATTTCAAATCTCATGAGATAA
Found at i:134090 original size:6 final size:6
Alignment explanation
Indices: 134081--134114 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
134071 ATAATATATC
* *
134081 ATTTTC ATTTTA ATTTTA ATTTTA ATTTCA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTT
134115 CAATGGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:142834 original size:19 final size:20
Alignment explanation
Indices: 142797--142840 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
142787 AAGAGTTACG
*
142797 AGAAAGTATCAAAACTTATA
1 AGAAAGTATCAAAAATTATA
* *
142817 AGAATGTAT-AAAAATTATG
1 AGAAAGTATCAAAAATTATA
142836 AGAAA
1 AGAAA
142841 TGCAAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.25
Consensus pattern (20 bp):
AGAAAGTATCAAAAATTATA
Found at i:142842 original size:20 final size:20
Alignment explanation
Indices: 142796--142852 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
142786 CAAGAGTTAC
*
142796 GAGAAA-GTATCAAAACTTAT
1 GAGAAATGTAT-AAAAATTAT
*
142816 AAG-AATGTATAAAAATTAT
1 GAGAAATGTATAAAAATTAT
* *
142835 GAGAAATGCAAAAAAATT
1 GAGAAATGTATAAAAATT
142853 CGAGGAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.25
Consensus pattern (20 bp):
GAGAAATGTATAAAAATTAT
Found at i:143431 original size:26 final size:26
Alignment explanation
Indices: 143373--143424 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
143363 AACAATCAAT
**
143373 AACTTTTATATGCCTTTATATTCAAA
1 AACTTTTATATGCCTTTATATAAAAA
143399 AACTTTTATATGCCTTT-T-TAAAAA
1 AACTTTTATATGCCTTTATATAAAAA
143423 AA
1 AA
143425 TATTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.25
25 1 0.04
26 17 0.71
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (26 bp):
AACTTTTATATGCCTTTATATAAAAA
Found at i:148079 original size:87 final size:84
Alignment explanation
Indices: 147936--148106 Score: 288
Period size: 87 Copynumber: 2.0 Consensus size: 84
147926 AAAAATACCT
* *
147936 GACACCCAATGGAAGGACACAANGCGGCATTGAAGGAGAGATTTAAAGTGGTGGCACTAAGGGGT
1 GACACCCAATGGAAGGACACAAGGCGGCATTGAAGGAGAGATTTAAAGTGGCGGCACTAAGGGGT
148001 ATTTTGCCACTTGGCAGCA
66 ATTTTGCCACTTGGCAGCA
148020 GACACCCAATGGAAGGACACAAAGTGGCGGCATTGAAGGAGAGATTTAAAGTGGCGGCACTAAGG
1 GACACCCAATGGAAGGACAC-AA--GGCGGCATTGAAGGAGAGATTTAAAGTGGCGGCACTAAGG
*
148085 GGTGTTTTGCCACTTGGCAGCA
63 GGTATTTTGCCACTTGGCAGCA
148107 CCTCATTGTG
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
84 20 0.25
85 2 0.02
87 59 0.73
ACGTcount: A:0.30, C:0.18, G:0.32, T:0.19
Consensus pattern (84 bp):
GACACCCAATGGAAGGACACAAGGCGGCATTGAAGGAGAGATTTAAAGTGGCGGCACTAAGGGGT
ATTTTGCCACTTGGCAGCA
Found at i:148306 original size:13 final size:13
Alignment explanation
Indices: 148290--148315 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
148280 AATTTGAAGG
148290 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
148303 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
148316 GAATGAAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Found at i:148334 original size:9 final size:9
Alignment explanation
Indices: 148315--148347 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
148305 AAAAGAAAGA
148315 AGAATGAAGG
1 AGAA-GAAGG
148325 AGAAGAAGG
1 AGAAGAAGG
148334 AGAAGAAGG
1 AGAAGAAGG
148343 AGAAG
1 AGAAG
148348 GAGAGGGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (9 bp):
AGAAGAAGG
Found at i:148750 original size:20 final size:21
Alignment explanation
Indices: 148709--148751 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
148699 TAATTTACTT
148709 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
*
148730 TAATTTTATTTTGTT-GTTAG
1 TAATTTAATTTTGTTAGTTAG
148750 TA
1 TA
148752 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Found at i:149315 original size:14 final size:15
Alignment explanation
Indices: 149296--149341 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
149286 AACCTAGCTA
149296 ATTAATTACCAAAAT
1 ATTAATTACCAAAAT
*
149311 A-TAATATA-AAAAAT
1 ATTAAT-TACCAAAAT
149325 AATTAATTACCAAAAT
1 -ATTAATTACCAAAAT
149341 A
1 A
149342 ATATCATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 9 0.36
15 7 0.28
16 9 0.36
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAATTACCAAAAT
Found at i:149339 original size:16 final size:16
Alignment explanation
Indices: 149294--149343 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
149284 TAAACCTAGC
149294 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
149310 T-A-TAATATA-AAAAA
1 TAATTAAT-TACCAAAA
149324 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
149340 TAAT
1 TAAT
149344 ATCATCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:150667 original size:43 final size:43
Alignment explanation
Indices: 150585--150667 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
150575 ATTAACATTT
* * *
150585 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTAAC
1 TAAATTATATTACTTGACTCGTATTAAAATGCTTGCATGTAAC
* *
150628 TAAATTATATTACTTTACTCTTATTAAAAT-CTTGACATGT
1 TAAATTATATTACTTGACTCGTATTAAAATGCTTG-CATGT
150668 TATTAATTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 3 0.09
43 31 0.91
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAAAATGCTTGCATGTAAC
Found at i:151603 original size:12 final size:12
Alignment explanation
Indices: 151586--151610 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
151576 GATAAGAATG
151586 ATATGTTTAATT
1 ATATGTTTAATT
151598 ATATGTTTAATT
1 ATATGTTTAATT
151610 A
1 A
151611 AAGCTTATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (12 bp):
ATATGTTTAATT
Done.