Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005265.1 Kokia drynarioides strain JFW-HI SEQ_119176, 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: 37096
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:392 original size:14 final size:15
Alignment explanation
Indices: 361--400 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
351 TATCTTTATC
361 TTATTTATATTCTATT
1 TTATTTAT-TTCTATT
377 TTATTTATTTCT-TT
1 TTATTTATTTCTATT
*
391 TTTTTTATTT
1 TTATTTATTT
401 ATCCATCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.48
15 4 0.17
16 8 0.35
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (15 bp):
TTATTTATTTCTATT
Found at i:812 original size:14 final size:14
Alignment explanation
Indices: 793--824 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
783 TATGGAGGGA
793 AATGTTGAATCTGC
1 AATGTTGAATCTGC
807 AATGTTGAATCTGC
1 AATGTTGAATCTGC
821 AATG
1 AATG
825 ACGAACCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (14 bp):
AATGTTGAATCTGC
Found at i:1255 original size:40 final size:40
Alignment explanation
Indices: 1167--1242 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
1157 TACAATCATC
1167 CAATCTTTTACCCTAATCAGAGAGCAAATTGAAGACCTTT
1 CAATCTTTTACCCTAATCAGAGAGCAAATTGAAGACCTTT
* *
1207 CAATCTTTTACCCTAATCAGAGGGCAGATTGAAGAC
1 CAATCTTTTACCCTAATCAGAGAGCAAATTGAAGAC
1243 TATTAGATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (40 bp):
CAATCTTTTACCCTAATCAGAGAGCAAATTGAAGACCTTT
Found at i:1335 original size:40 final size:40
Alignment explanation
Indices: 1255--1724 Score: 368
Period size: 40 Copynumber: 11.8 Consensus size: 40
1245 TTAGATCTTT
* ** *** *
1255 TTGAAGACCATCCAATCTTTTACCCTAATTAAAAGACAGA
1 TTGAAGACCATCCAATCTCTTACCCTAACCATGGGGCAGA
* * * **
1295 TTAAAGATCATTCAATCTCTTACCCCGACCATGGGGCAGA
1 TTGAAGACCATCCAATCTCTTACCCTAACCATGGGGCAGA
* * **
1335 TTGAAG-CAATCCAATCTTTTACCCTAACCAAAGGGCAGA
1 TTGAAGACCATCCAATCTCTTACCCTAACCATGGGGCAGA
* * * ** ** *
1374 TTAAAAATCATCCAATCTCTTACCCCGACCATGGGAAAAA
1 TTGAAGACCATCCAATCTCTTACCCTAACCATGGGGCAGA
* *
1414 TTGAAG-CCATCTAATCTCTTACCCTAACCA-GAGGGCAAA
1 TTGAAGACCATCCAATCTCTTACCCTAACCATG-GGGCAGA
* * ** * *
1453 TTGAAGATCATCCGATCTCTTACCCCGACCATGGGGAAAA
1 TTGAAGACCATCCAATCTCTTACCCTAACCATGGGGCAGA
* *
1493 TTGAAG-CCATCCAATCTCTTACCCTAACCATGTGACAGA
1 TTGAAGACCATCCAATCTCTTACCCTAACCATGGGGCAGA
* * *
1532 TTAAAG-CAATCCAATCTTTTACCCTAACCA-GAGGGCAGA
1 TTGAAGACCATCCAATCTCTTACCCTAACCATG-GGGCAGA
* * *
1571 TTGAAGACCATCCAATCTTTTACCCTAACTA-GAGGGTAGA
1 TTGAAGACCATCCAATCTCTTACCCTAACCATG-GGGCAGA
* *
1611 TTGAAGACCAT-CAGATCTTTTACCCTAACCA-GTAGGCAGA
1 TTGAAGACCATCCA-ATCTCTTACCCTAACCATG-GGGCAGA
* * *
1651 TTGAAGACCAACCAATCTCTTA-CCTCGACCATGGGGTAGA
1 TTGAAGACCATCCAATCTCTTACCCT-AACCATGGGGCAGA
* **
1691 TTGAAGATCATCGGATCTCTTACCCCT-ACCATGG
1 TTGAAGACCATCCAATCTCTTA-CCCTAACCATGG
1725 ATTAAAACAA
Statistics
Matches: 341, Mismatches: 77, Indels: 24
0.77 0.17 0.05
Matches are distributed among these distances:
38 2 0.01
39 127 0.37
40 205 0.60
41 4 0.01
42 3 0.01
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (40 bp):
TTGAAGACCATCCAATCTCTTACCCTAACCATGGGGCAGA
Found at i:1504 original size:118 final size:118
Alignment explanation
Indices: 1382--1595 Score: 311
Period size: 118 Copynumber: 1.8 Consensus size: 118
1372 GATTAAAAAT
* * * *
1382 CATCCAATCTCTTACCCCGACCATGGGAAAAATTGAAGCCATCTAATCTCTTACCCTAACCAGAG
1 CATCCAATCTCTTACCCCAACCATGGGAAAAATTAAAGCAATCCAATCTCTTACCCTAACCAGAG
* *
1447 GGCAAATTGAAGATCATCCGATCTCTTACCCCGACCATGGGGAAAATTGAAGC
66 GGCAAATTGAAGACCATCCAATCTCTTACCCCGACCATGGGGAAAATTGAAGC
* * * * *
1500 CATCCAATCTCTTACCCTAACCATGTGACAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAG
1 CATCCAATCTCTTACCCCAACCATGGGAAAAATTAAAGCAATCCAATCTCTTACCCTAACCAGAG
* *
1565 GGCAGATTGAAGACCATCCAATCTTTTACCC
66 GGCAAATTGAAGACCATCCAATCTCTTACCC
1596 TAACTAGAGG
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
118 83 1.00
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.24
Consensus pattern (118 bp):
CATCCAATCTCTTACCCCAACCATGGGAAAAATTAAAGCAATCCAATCTCTTACCCTAACCAGAG
GGCAAATTGAAGACCATCCAATCTCTTACCCCGACCATGGGGAAAATTGAAGC
Found at i:1612 original size:79 final size:78
Alignment explanation
Indices: 1255--1724 Score: 396
Period size: 79 Copynumber: 5.9 Consensus size: 78
1245 TTAGATCTTT
* ** * * * *
1255 TTGAAGACCATCCAATCTTTTACCCTAATTAAAAGACAGATTAAAGATCATTCAATCTCTTACCC
1 TTGAAG-CCATCCAATCTCTTACCCTAACCAGAGGGCAGATTAAAGA-CATCCAATCTCTTACCC
1320 CGACCATGGGGCAGA
64 CGACCATGGGGCAGA
* * * *
1335 TTGAAGCAATCCAATCTTTTACCCTAACCAAAGGGCAGATTAAAAATCATCCAATCTCTTACCCC
1 TTGAAGCCATCCAATCTCTTACCCTAACCAGAGGGCAGATTAAAGA-CATCCAATCTCTTACCCC
** *
1400 GACCATGGGAAAAA
65 GACCATGGGGCAGA
* * * *
1414 TTGAAGCCATCTAATCTCTTACCCTAACCAGAGGGCAAATTGAAGATCATCCGATCTCTTACCCC
1 TTGAAGCCATCCAATCTCTTACCCTAACCAGAGGGCAGATTAAAGA-CATCCAATCTCTTACCCC
* *
1479 GACCATGGGGAAAA
65 GACCATGGGGCAGA
* * *
1493 TTGAAGCCATCCAATCTCTTACCCTAACCATG-TGACAGATTAAAG-CAATCCAATCTTTTACCC
1 TTGAAGCCATCCAATCTCTTACCCTAACCA-GAGGGCAGATTAAAGAC-ATCCAATCTCTTACCC
**
1556 TAACCA-GAGGGCAGA
64 CGACCATG-GGGCAGA
* * * * *
1571 TTGAAGACCATCCAATCTTTTACCCTAACTAGAGGGTAGATTGAAGACCAT-CAGATCTTTTACC
1 TTGAAG-CCATCCAATCTCTTACCCTAACCAGAGGGCAGATTAAAGA-CATCCA-ATCTCTTACC
** *
1635 CTAACCA-GTAGGCAGA
63 CCGACCATG-GGGCAGA
* * * * **
1651 TTGAAGACCAACCAATCTCTTA-CCTCGACCATG-GGGTAGATTGAAGATCATCGGATCTCTTAC
1 TTGAAG-CCATCCAATCTCTTACCCT-AACCA-GAGGGCAGATTAAAGA-CATCCAATCTCTTAC
*
1714 CCCTACCATGG
62 CCCGACCATGG
1725 ATTAAAACAA
Statistics
Matches: 329, Mismatches: 49, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
77 2 0.01
78 30 0.09
79 207 0.63
80 87 0.26
81 3 0.01
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (78 bp):
TTGAAGCCATCCAATCTCTTACCCTAACCAGAGGGCAGATTAAAGACATCCAATCTCTTACCCCG
ACCATGGGGCAGA
Found at i:1654 original size:158 final size:158
Alignment explanation
Indices: 1255--1674 Score: 465
Period size: 158 Copynumber: 2.7 Consensus size: 158
1245 TTAGATCTTT
* * * * *
1255 TTGAAGACCATCCAATCTTTTACCCTAATTAAAAGACAGATTAAAGATCATTCA-ATCTCTTACC
1 TTGAAGACCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGATCA-TCAGATCTCTTACC
* * *
1319 CCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAAAGGGCAGATTAAAAATCA
65 CCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCTAACCAAAGGACAGATTAAAAA-CA
*
1384 TCCAATCTCTTACCCCGACCATGGGAAAAA
129 TCCAATCTCTTACCCCAACCATGGGAAAAA
* * * * *
1414 TTGAAG-CCATCTAATCTCTTACCCTAACCAGAGGGCAAATTGAAGATCATCCGATCTCTTACCC
1 TTGAAGACCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGATCATCAGATCTCTTACCC
* * * *
1478 CGACCATGGGGAAAATTGAAGCCATCCAATCTCTTACCCTAACC-ATGTGACAGATT-AAAGCAA
66 CGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCTAACCAAAG-GACAGATTAAAAAC-A
* * ** *
1541 TCCAATCTTTTACCCTAACCA-GAGGGCAGA
129 TCCAATCTCTTACCCCAACCATG-GGAAAAA
* * *
1571 TTGAAGACCATCCAATCTTTTACCCTAACTAGAGGGTAGATTGAAGACCATCAGATCTTTTACCC
1 TTGAAGACCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGATCATCAGATCTCTTACCC
** * *
1636 TAACCA-GTAGGCAGATTGAAGACCAACCAATCTCTTACC
66 CGACCATG-GGGCAGATTGAAG-CCATCCAATCTCTTACC
1675 TCGACCATGG
Statistics
Matches: 217, Mismatches: 37, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
156 2 0.01
157 37 0.17
158 156 0.72
159 22 0.10
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.25
Consensus pattern (158 bp):
TTGAAGACCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGATCATCAGATCTCTTACCC
CGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCTAACCAAAGGACAGATTAAAAACATC
CAATCTCTTACCCCAACCATGGGAAAAA
Found at i:2354 original size:4 final size:4
Alignment explanation
Indices: 2347--2382 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
2337 TTATTATTTT
*
2347 ATAA ATAA ATAA AAAA ATAA ATAA ATAA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
2383 ATTAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:3321 original size:30 final size:30
Alignment explanation
Indices: 3258--3323 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
3248 AAATTTAGTT
* * ***
3258 TTTGACCCCTAAATTTTTTAAAAATTTTGA
1 TTTGACCCCTAAAGTTTTCAAAAATTCAAA
*
3288 TTTGACCCTTAAAGTTTTCAAAAATTCAAA
1 TTTGACCCCTAAAGTTTTCAAAAATTCAAA
3318 TTTGAC
1 TTTGAC
3324 TCAGTTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (30 bp):
TTTGACCCCTAAAGTTTTCAAAAATTCAAA
Found at i:4269 original size:26 final size:26
Alignment explanation
Indices: 4237--4287 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
4227 CAATGTTTAA
4237 AACTTCAATACAAGTACCCTAAATAC
1 AACTTCAATACAAGTACCCTAAATAC
4263 AACTTCAATACAAGTACCCTAAATA
1 AACTTCAATACAAGTACCCTAAATA
4288 TAATATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.24
Consensus pattern (26 bp):
AACTTCAATACAAGTACCCTAAATAC
Found at i:7216 original size:32 final size:31
Alignment explanation
Indices: 7171--7243 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 31
7161 TTTTTAGAGG
*
7171 TTGATTAGAACAAA-TCCTTGAAGAAACTAGAA
1 TTGATTA-AACAAACT-CTTAAAGAAACTAGAA
* * *
7203 TTGATTAATACAAACTTTTAAAGAAATTAGGA
1 TTGATTAA-ACAAACTCTTAAAGAAACTAGAA
7235 TTGATTAAA
1 TTGATTAAA
7244 AATTTAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 2 0.06
32 32 0.91
33 1 0.03
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.32
Consensus pattern (31 bp):
TTGATTAAACAAACTCTTAAAGAAACTAGAA
Found at i:9252 original size:31 final size:31
Alignment explanation
Indices: 9191--9254 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
9181 ATGGAAGTTA
9191 TTTGATTTCTTTTATAACTACAATAAATATT
1 TTTGATTTCTTTTATAACTACAATAAATATT
* *
9222 TTTGTATTT-TTTTA-AACTATTAATATATATT
1 TTTG-ATTTCTTTTATAACTA-CAATAAATATT
9253 TT
1 TT
9255 AATTAAAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 20 0.69
32 4 0.14
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTGATTTCTTTTATAACTACAATAAATATT
Found at i:9736 original size:17 final size:17
Alignment explanation
Indices: 9714--9756 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
9704 TTGTAATATT
*
9714 TATTTATATAGTTTAGA
1 TATTTAAATAGTTTAGA
**
9731 TATTTAAATCTTTTAGA
1 TATTTAAATAGTTTAGA
9748 TATTTAAAT
1 TATTTAAAT
9757 CTTTACATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (17 bp):
TATTTAAATAGTTTAGA
Found at i:9757 original size:17 final size:17
Alignment explanation
Indices: 9725--9760 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
9715 ATTTATATAG
9725 TTTAGATATTTAAATCT
1 TTTAGATATTTAAATCT
9742 TTTAGATATTTAAATCT
1 TTTAGATATTTAAATCT
9759 TT
1 TT
9761 ACATTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAGATATTTAAATCT
Found at i:9995 original size:20 final size:21
Alignment explanation
Indices: 9969--10018 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
9959 GGATTATGTA
9969 ATTTGGATTTAT-AACTTTAT
1 ATTTGGATTTATAAACTTTAT
* * *
9989 GTTTGGATTTTTAAATTTTAT
1 ATTTGGATTTATAAACTTTAT
10010 ATTTGGATT
1 ATTTGGATT
10019 ATATTATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:10277 original size:20 final size:20
Alignment explanation
Indices: 10235--10277 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
10225 ATAAAAATAT
**
10235 AATAAAAAAATAAATATTTA
1 AATAAAAAAATAAATATCAA
* *
10255 AATAAAAAAATACATGTCAA
1 AATAAAAAAATAAATATCAA
10275 AAT
1 AAT
10278 TTTAAGATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (20 bp):
AATAAAAAAATAAATATCAA
Found at i:11440 original size:41 final size:39
Alignment explanation
Indices: 11370--11486 Score: 119
Period size: 41 Copynumber: 2.9 Consensus size: 39
11360 TTATTTTAAG
* **
11370 TTTTTTTAAAATTTTAAATTTTATTATATATTTTTTAGA
1 TTTTTTTAAAATTTTAAATTTAAAAATATATTTTTTAGA
**
11409 TTTTTTTAAAATTTTATAATTTAAAAAATATAAATTTTAGAA
1 TTTTTTTAAAATTTTA-AATTT-AAAAATATATTTTTTAG-A
* * *
11451 TTTTTATAAATATTTTGAATTTTAAAAT-TATTTTTT
1 TTTTTTTAAA-ATTTTAAATTTAAAAATATATTTTTT
11487 TGTAATTTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
39 16 0.25
40 11 0.17
41 17 0.27
42 15 0.23
43 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (39 bp):
TTTTTTTAAAATTTTAAATTTAAAAATATATTTTTTAGA
Found at i:11484 original size:18 final size:20
Alignment explanation
Indices: 11361--11473 Score: 58
Period size: 19 Copynumber: 5.7 Consensus size: 20
11351 ACACAATTAT
* *
11361 TATTTTA-AGTTTTTTTAAA
1 TATTTTAGAATTTTTATAAA
*
11380 -ATTTTA-AATTTTATTATATA
1 TATTTTAGAA-TTT-TTATAAA
* *
11400 TTTTTTAG-ATTTTTTTAAA
1 TATTTTAGAATTTTTATAAA
* ** *
11419 -ATTTTATAATTTAAAAAATA
1 TATTTTAGAATTTTTATAA-A
11439 TAAATTTTAGAATTTTTATAAA
1 T--ATTTTAGAATTTTTATAAA
11461 TATTTT-GAATTTT
1 TATTTTAGAATTTT
11474 AAAATTATTT
Statistics
Matches: 69, Mismatches: 16, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
18 12 0.17
19 21 0.30
20 14 0.20
21 6 0.09
22 2 0.03
23 14 0.20
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TATTTTAGAATTTTTATAAA
Found at i:11578 original size:9 final size:9
Alignment explanation
Indices: 11564--11594 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
11554 TACCAATTTG
11564 TTATTCAAA
1 TTATTCAAA
*
11573 TTATTCGAA
1 TTATTCAAA
11582 TTATTCAAA
1 TTATTCAAA
11591 TTAT
1 TTAT
11595 AAAATTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (9 bp):
TTATTCAAA
Found at i:18959 original size:14 final size:14
Alignment explanation
Indices: 18940--18970 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
18930 ATCCAAACAA
18940 TAACAACAAAATAG
1 TAACAACAAAATAG
*
18954 TAACAACATAATAG
1 TAACAACAAAATAG
18968 TAA
1 TAA
18971 AATAGTAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (14 bp):
TAACAACAAAATAG
Found at i:19007 original size:32 final size:32
Alignment explanation
Indices: 18938--19036 Score: 85
Period size: 32 Copynumber: 3.1 Consensus size: 32
18928 ATATCCAAAC
* * * *
18938 AATAACAACAAAATAGT-AACAACATAATAGTAA
1 AATAGCAACAAAATACTAAAAAAAATAA-AG-AA
* *
18971 AATAGTAGCAAAATACTGAAAAAAAA-AAAGAA
1 AATAGCAACAAAATACT-AAAAAAAATAAAGAA
* *
19003 AATAGCAACAAAATAGTAAAAAAAATCAAGAA
1 AATAGCAACAAAATACTAAAAAAAATAAAGAA
19035 AA
1 AA
19037 CAAAAAAAAC
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
31 8 0.15
32 23 0.43
33 15 0.28
34 2 0.04
35 5 0.09
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.14
Consensus pattern (32 bp):
AATAGCAACAAAATACTAAAAAAAATAAAGAA
Found at i:21322 original size:18 final size:18
Alignment explanation
Indices: 21281--21329 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
21271 AAACTAATAT
*
21281 ATTTTCTATAATATGAAA
1 ATTTTCTATTATATGAAA
* * *
21299 AATTTCTATTATTTGAGA
1 ATTTTCTATTATATGAAA
21317 ATTTTCTATTATA
1 ATTTTCTATTATA
21330 ATATTTAGAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
ATTTTCTATTATATGAAA
Found at i:21618 original size:14 final size:14
Alignment explanation
Indices: 21580--21611 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
21570 TCCTAGACCC
21580 TGAACATTAAACCT
1 TGAACATTAAACCT
*
21594 TGAACATTAAACGT
1 TGAACATTAAACCT
21608 TGAA
1 TGAA
21612 TCTTAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (14 bp):
TGAACATTAAACCT
Found at i:21668 original size:21 final size:21
Alignment explanation
Indices: 21642--21686 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
21632 AATCAACCTG
21642 AACCTTGGACCTTGAACATTA
1 AACCTTGGACCTTGAACATTA
21663 AACCTTGGACCTTGAACATTA
1 AACCTTGGACCTTGAACATTA
21684 AAC
1 AAC
21687 GTTGAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (21 bp):
AACCTTGGACCTTGAACATTA
Found at i:27158 original size:14 final size:14
Alignment explanation
Indices: 27139--27185 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
27129 TCTCAAATTG
27139 TAATAAATATGATA
1 TAATAAATATGATA
27153 TAATAAAT-TG---
1 TAATAAATATGATA
*
27163 TAATAAACATGATA
1 TAATAAATATGATA
27177 TAATAAATA
1 TAATAAATA
27186 AATCATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
10 7 0.26
11 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.34
Consensus pattern (14 bp):
TAATAAATATGATA
Found at i:27161 original size:24 final size:24
Alignment explanation
Indices: 27133--27184 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
27123 GATTAGTCTC
*
27133 AAATTGTAATAAATATGATATAAT
1 AAATTGTAATAAACATGATATAAT
27157 AAATTGTAATAAACATGATATAAT
1 AAATTGTAATAAACATGATATAAT
27181 AAAT
1 AAAT
27185 AAATCATAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
AAATTGTAATAAACATGATATAAT
Found at i:28149 original size:22 final size:22
Alignment explanation
Indices: 28124--28171 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
28114 ACGAATTTAA
*
28124 AATTGAATTGA-TACAATAATTT
1 AATTGAATTAATTA-AATAATTT
*
28146 AATTGAATTAATTAATTAATTT
1 AATTGAATTAATTAAATAATTT
28168 AATT
1 AATT
28172 TGATAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (22 bp):
AATTGAATTAATTAAATAATTT
Found at i:28445 original size:23 final size:24
Alignment explanation
Indices: 28414--28458 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
28404 TATAAATAGA
28414 AACTATAAGATGATTTAATTGCTC
1 AACTATAAGATGATTTAATTGCTC
28438 AACT-TAAGATGATTTAATTGC
1 AACTATAAGATGATTTAATTGC
28459 AAAATTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (24 bp):
AACTATAAGATGATTTAATTGCTC
Found at i:32043 original size:103 final size:102
Alignment explanation
Indices: 31864--32074 Score: 377
Period size: 103 Copynumber: 2.1 Consensus size: 102
31854 AGAGAGGGAG
31864 ATGGGTATTCGGTTTACTGTAAAAAAGGGAGGAGAGAGGCCATGGAAGATAGGTTCTCAGCTTCA
1 ATGGGTATTCGGTTTACTGTAAAAAAGGGAGGAGAGAGGCCATGGAAGATAGGTTCTCAGCTTCA
*
31929 GCTGAACTTCAAGGAGATTCCAAGCAGGTATTTTTTTT
66 GCTGAACTTCAAGGAGATTCCAAGCAAGTA-TTTTTTT
* * *
31967 ATGGGTATTCGGTTTACTGTAAAAGAGGTAGGAGAGAGGCTATGGAAGATAGGTTCTCAGCTTCA
1 ATGGGTATTCGGTTTACTGTAAAAAAGGGAGGAGAGAGGCCATGGAAGATAGGTTCTCAGCTTCA
32032 GCTGAACTTCAAGGAGATTCCAAGCAAGTATTTTTTT
66 GCTGAACTTCAAGGAGATTCCAAGCAAGTATTTTTTT
32069 ATGGGT
1 ATGGGT
32075 CAAATTATAA
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 13 0.12
103 91 0.88
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (102 bp):
ATGGGTATTCGGTTTACTGTAAAAAAGGGAGGAGAGAGGCCATGGAAGATAGGTTCTCAGCTTCA
GCTGAACTTCAAGGAGATTCCAAGCAAGTATTTTTTT
Found at i:35654 original size:9 final size:10
Alignment explanation
Indices: 35640--35665 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
35630 TTTTATAAAG
35640 AAAAAAATAA
1 AAAAAAATAA
35650 AAAAAAATAA
1 AAAAAAATAA
35660 AAAAAA
1 AAAAAA
35666 GGGCATAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Done.