Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016451.1 Corchorus capsularis cultivar CVL-1 contig16472, 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: 31764
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1341 original size:15 final size:15
Alignment explanation
Indices: 1321--1358 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1311 GGTGGGCGTC
1321 GGTCGGTTTCGGTCA
1 GGTCGGTTTCGGTCA
1336 GGTCGGTTTCGGTCA
1 GGTCGGTTTCGGTCA
1351 GGTCGGTT
1 GGTCGGTT
1359 GGAAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.05, C:0.18, G:0.42, T:0.34
Consensus pattern (15 bp):
GGTCGGTTTCGGTCA
Found at i:2436 original size:15 final size:15
Alignment explanation
Indices: 2403--2470 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
2393 TTTTAGTTAT
* *
2403 ATATATATCTAAATT
1 ATATATATATAAATA
*
2418 ATATATATATATATA
1 ATATATATATAAATA
* *
2433 ATATAAATATAAAAA
1 ATATATATATAAATA
* *
2448 ATAT-TAATATTATTA
1 ATATAT-ATATAAATA
2463 ATATATAT
1 ATATATAT
2471 TCGGTCTGTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
15 40 0.98
16 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATATATATAAATA
Found at i:4641 original size:219 final size:218
Alignment explanation
Indices: 4262--4699 Score: 815
Period size: 219 Copynumber: 2.0 Consensus size: 218
4252 CCCTGCATAT
4262 GTAAACAATTTTGCAACCTGAAGTCCTGAAAGAAGTTGGCAATGAATTAAAAGGGTCGTGCGTAG
1 GTAAACAATTTTGCAACCTGAAGTCCTGAAAGAAGTTGGCAATGAATTAAAAGGGTCGTGCGTAG
*
4327 CCGCGAGCGGGCCTTTACGGTCCCGATTGTCGACGCCTTGTGCAGCATCAAACTCAATGAAGGGA
66 CCGCGAGCGGGACTTTACGGTCCCGATTGTCGACGCCTTGTGCAGCATCAAACTCAATGAAGGGA
*
4392 ACAACATCATGCGGCGACTTTGTGAGCAAAGGGCTGGTTGAGTCATCGTATTGGGACCTTGTAAC
131 ACAACATCATGCGGCGACTTTGTGAGCAAAGGGCTGGTTGAGTCATCATATTGGGACCTTGTAAC
4457 AATGGCGTAAAGCAAGGGCCCTGA
196 AATGGCG-AAAGCAAGGGCCCTGA
4481 GTAAACAATTTTGCAACCTGAAGTCCTGAAAGAAGTTGGCAATGAATTAAAAGGG-CTGTGCGTA
1 GTAAACAATTTTGCAACCTGAAGTCCTGAAAGAAGTTGGCAATGAATTAAAAGGGTC-GTGCGTA
*
4545 GCCGCGAGCGGGACTTTACGGTCCCGATTGTCGACGCCTTGTGCAGCATCAAGCTCAATGAAGGG
65 GCCGCGAGCGGGACTTTACGGTCCCGATTGTCGACGCCTTGTGCAGCATCAAACTCAATGAAGGG
4610 AACAACATCATGCGGCGACTTTGTGAGCAAAGGGCTGGTTGAGTCATCATATTGGGACCTTGTAA
130 AACAACATCATGCGGCGACTTTGTGAGCAAAGGGCTGGTTGAGTCATCATATTGGGACCTTGTAA
*
4675 CAATGGCGAAAGCAAGGGCCTTGA
195 CAATGGCGAAAGCAAGGGCCCTGA
4699 G
1 G
4700 CCAAGTCGCA
Statistics
Matches: 214, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
218 17 0.08
219 197 0.92
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (218 bp):
GTAAACAATTTTGCAACCTGAAGTCCTGAAAGAAGTTGGCAATGAATTAAAAGGGTCGTGCGTAG
CCGCGAGCGGGACTTTACGGTCCCGATTGTCGACGCCTTGTGCAGCATCAAACTCAATGAAGGGA
ACAACATCATGCGGCGACTTTGTGAGCAAAGGGCTGGTTGAGTCATCATATTGGGACCTTGTAAC
AATGGCGAAAGCAAGGGCCCTGA
Found at i:8766 original size:166 final size:166
Alignment explanation
Indices: 8469--8812 Score: 458
Period size: 166 Copynumber: 2.1 Consensus size: 166
8459 TTGTCAATTA
* ** * *
8469 AGAAATGACCAAAAAATTTATTTATTTAATCCCCTCTGGAATAAAAAGTTAGGACATTTAAGTAA
1 AGAAATGACCAAAAAATTTACTTATTTAATCCCCTCAAGAATAAAAAGTTAGAACATTTAAGCAA
* * * ** * * *
8534 TCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTATCTAGCTCATTATCAATCCTTGATGGGGAT
66 TCTGCCAAGTAGGAAAAGACGAAAAAGATAAGTTATCTAGCCCAAAAGCAAGCCTTGATAGGGAT
* * *
8599 CTTTTAGTAATTCCACTACTCTATTAAAGTCCATCG
131 CTTTCAGTAATTCCACTACTCTATTAAAATCAATCG
* * *
8635 AGAAATGATC-AAAAATATTACTTATTTAATCCCCTCAAGAATCACAAGTTAGAACATTTAAGCA
1 AGAAATGACCAAAAAAT-TTACTTATTTAATCCCCTCAAGAATAAAAAGTTAGAACATTTAAGCA
* *
8699 ATCTGCCAAGTAGGAAAAGACGAAAAA-ATAAGTTCTCTAGCACCAAAAGCAAGCCTTGGTAGGG
65 ATCTGCCAAGTAGGAAAAGACGAAAAAGATAAGTTATCTAGC-CCAAAAGCAAGCCTTGATAGGG
*
8763 ATCTTTCAGTAATTCCACTACTCTATTAAAATCAATTG
129 ATCTTTCAGTAATTCCACTACTCTATTAAAATCAATCG
8801 AGAAATGACCAA
1 AGAAATGACCAA
8813 GCAAGCCTTG
Statistics
Matches: 152, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
165 18 0.12
166 133 0.88
167 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (166 bp):
AGAAATGACCAAAAAATTTACTTATTTAATCCCCTCAAGAATAAAAAGTTAGAACATTTAAGCAA
TCTGCCAAGTAGGAAAAGACGAAAAAGATAAGTTATCTAGCCCAAAAGCAAGCCTTGATAGGGAT
CTTTCAGTAATTCCACTACTCTATTAAAATCAATCG
Found at i:8851 original size:66 final size:66
Alignment explanation
Indices: 8745--8878 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
8735 CTAGCACCAA
8745 AAGCAAGCCTTGGTAGGGATCTTTCAGTAATTCCACTACTCTATTAAAATCAATTGAGAAATGAC
1 AAGCAAGCCTTGGTAGGGATCTTTCAGTAATTCCACTACTCTATTAAAATCAATTGAGAAATGAC
8810 C
66 C
* * *
8811 AAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGAC
1 AAGCAAGCCTTGGTAGGGATCTTTCAGTAATTCCACTACTCTATTAAAATCAATTGAGAAATGAC
8876 C
66 C
8877 AA
1 AA
8879 AAAGTCTAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (66 bp):
AAGCAAGCCTTGGTAGGGATCTTTCAGTAATTCCACTACTCTATTAAAATCAATTGAGAAATGAC
C
Found at i:9602 original size:48 final size:48
Alignment explanation
Indices: 9491--9649 Score: 176
Period size: 48 Copynumber: 3.3 Consensus size: 48
9481 AAAGAAAATA
* * * ** * * *
9491 TTTCAATCCCAAAATACAACCCAAAAG-AAAAAAAACTATTTGATACATT
1 TTTCAATCCCAAAAGACAAACCAAAAGTAAACAATTCTA--TGCTTCATG
* *
9540 TTTCAATCCCAAAAGGCAAACCAAAAGTAAACAATTCTTTGCTTCATG
1 TTTCAATCCCAAAAGACAAACCAAAAGTAAACAATTCTATGCTTCATG
* * *
9588 TTTCAATCCCAAAAGACAATCCAAAAGTAAACAATTCTATGCTTTATT
1 TTTCAATCCCAAAAGACAAACCAAAAGTAAACAATTCTATGCTTCATG
9636 TTTCAATCCCAAAA
1 TTTCAATCCCAAAA
9650 TGAGAAAAAA
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
48 63 0.67
49 24 0.26
50 7 0.07
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (48 bp):
TTTCAATCCCAAAAGACAAACCAAAAGTAAACAATTCTATGCTTCATG
Found at i:10460 original size:2 final size:2
Alignment explanation
Indices: 10453--10479 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10443 TAATATGTAG
10453 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
10480 TTGGTGCACC
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:14515 original size:91 final size:91
Alignment explanation
Indices: 14360--14542 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
14350 TATCAAATAA
14360 AACTTTAGTAAACATAAGACATAATACATAATAATACTAATATTGACCCAAACTACTAATAGTGT
1 AACTTTAGTAAACATAAGACATAATACATAATAATACTAATATTGACCCAAACTACTAATAGTGT
14425 CGGCATACCATGGCTCATGCCGTCCC
66 CGGCATACCATGGCTCATGCCGTCCC
14451 AACTTTAGTAAACATAAGACATAATACATAATAATACTAATATTGACCCAAACTACTAATAGTGT
1 AACTTTAGTAAACATAAGACATAATACATAATAATACTAATATTGACCCAAACTACTAATAGTGT
14516 CGGCATACCATGGCTCATGCCGTCCC
66 CGGCATACCATGGCTCATGCCGTCCC
14542 A
1 A
14543 TGAAGGCATG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (91 bp):
AACTTTAGTAAACATAAGACATAATACATAATAATACTAATATTGACCCAAACTACTAATAGTGT
CGGCATACCATGGCTCATGCCGTCCC
Found at i:14917 original size:33 final size:33
Alignment explanation
Indices: 14874--14964 Score: 119
Period size: 33 Copynumber: 2.8 Consensus size: 33
14864 AAAAATGCAT
*
14874 GTGCCGCCCTAGGAGGGCGGCATGCCATGGCTA
1 GTGCCGCCCTAGGAGGGCGGCATGCCATGGCAA
* **
14907 GTGCCACCCTAGGAGGATGGCATGCCATGGCAA
1 GTGCCGCCCTAGGAGGGCGGCATGCCATGGCAA
* * *
14940 GGGCCGCCCCAAGAGGGCGGCATGC
1 GTGCCGCCCTAGGAGGGCGGCATGC
14965 TACAGCTGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.19, C:0.31, G:0.38, T:0.12
Consensus pattern (33 bp):
GTGCCGCCCTAGGAGGGCGGCATGCCATGGCAA
Found at i:15076 original size:32 final size:32
Alignment explanation
Indices: 15028--15117 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
15018 GGGGCGGCAG
* *
15028 TAGCCATAGCAGGCCGCCCTCCTGGGGCTGCT
1 TAGCCATGGCATGCCGCCCTCCTGGGGCTGCT
15060 TAGCCATGGCATGCCGCCCTCCTGGGGCTGCT
1 TAGCCATGGCATGCCGCCCTCCTGGGGCTGCT
15092 TAGCCATGGCATGCCGCCCTCCTGGG
1 TAGCCATGGCATGCCGCCCTCCTGGG
15118 ACGGCACGCG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.11, C:0.38, G:0.31, T:0.20
Consensus pattern (32 bp):
TAGCCATGGCATGCCGCCCTCCTGGGGCTGCT
Found at i:17538 original size:30 final size:31
Alignment explanation
Indices: 17502--17572 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
17492 GGCGAAAATG
*
17502 CAATTCAGGATACACCGTTA-CGACTTGTGT
1 CAATTCAGGATACAACGTTATCGACTTGTGT
* **
17532 CAATTCAGGATATAACGTTATCGGGTTGTGT
1 CAATTCAGGATACAACGTTATCGACTTGTGT
17563 CAAATTCAGG
1 C-AATTCAGG
17573 CAAAAATAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 18 0.51
31 9 0.26
32 8 0.23
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (31 bp):
CAATTCAGGATACAACGTTATCGACTTGTGT
Found at i:18984 original size:31 final size:30
Alignment explanation
Indices: 18949--19021 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
18939 ATTTGCAATT
* *
18949 TATCCTGAATTGTCACAACCCGATAACGTTA
1 TATCCTGAATTGACACAACCC-ATAACGGTA
* ** *
18980 TATCCTAAATTGACACAAGTCATAACGGTG
1 TATCCTGAATTGACACAACCCATAACGGTA
19010 TATCCTGAATTG
1 TATCCTGAATTG
19022 CATTTTCACC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 18 0.51
31 17 0.49
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (30 bp):
TATCCTGAATTGACACAACCCATAACGGTA
Found at i:19554 original size:27 final size:27
Alignment explanation
Indices: 19513--19565 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
19503 TTATTACAAT
19513 AAGAAATCATATTCCAGTATCTTATTC
1 AAGAAATCATATTCCAGTATCTTATTC
* *
19540 AAGAAATCATTTTCCAGTTTCTTATT
1 AAGAAATCATATTCCAGTATCTTATT
19566 GCCATCTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (27 bp):
AAGAAATCATATTCCAGTATCTTATTC
Found at i:22233 original size:35 final size:35
Alignment explanation
Indices: 22152--22725 Score: 678
Period size: 35 Copynumber: 16.6 Consensus size: 35
22142 TTTACTAAAT
* *
22152 TTAATTACCCTGAATTAAGTTGCTTA-TTACTTAC
1 TTAATTACCCTGAATTAAGTTGATTACTGACTTAC
* *
22186 TTAATTATCCTGAATTAAGTTGATTACTGACTCAC
1 TTAATTACCCTGAATTAAGTTGATTACTGACTTAC
*
22221 TTAATTACCCTGAATTAAAGTTGATTA-TAGACTCAC
1 TTAATTACCCTGAATT-AAGTTGATTACT-GACTTAC
*
22257 TTAATTACCCTGAATTAAGTTTATTACTGACTTAC
1 TTAATTACCCTGAATTAAGTTGATTACTGACTTAC
* * *
22292 TTAATTACCCTAAATTAAGTTGGTTACCGACTTAC
1 TTAATTACCCTGAATTAAGTTGATTACTGACTTAC
*
22327 TTAATTACCTTGAATTAAGTTGATTACTGACTTAC
1 TTAATTACCCTGAATTAAGTTGATTACTGACTTAC
22362 TTAATTACCCTGAATTAAGTTGATTACTGACTTAC
1 TTAATTACCCTGAATTAAGTTGATTACTGACTTAC
* *
22397 TTAATTACCCTGAATTATGTTGATTACTGACTCAC
1 TTAATTACCCTGAATTAAGTTGATTACTGACTTAC
* *
22432 TTAATTACCCTGAATTAAGTTGATTGCTGACTCAC
1 TTAATTACCCTGAATTAAGTTGATTACTGACTTAC
* * *
22467 TTAATTACCCTAAATTAAAGTTAATTACTGACTCAC
1 TTAATTACCCTGAATT-AAGTTGATTACTGACTTAC
*
22503 TTAATTACCCTGAATTAAAGTTGATTACTGACTCAC
1 TTAATTACCCTGAATT-AAGTTGATTACTGACTTAC
* *
22539 TTAATTACCCTGAATTAAGTT-ACTCATTGAAC-TAC
1 TTAATTACCCTGAATTAAGTTGA-TTACTG-ACTTAC
*
22574 TTAATTACCCTGAATTAAGCT-ACTTACTG----AC
1 TTAATTACCCTGAATTAAGTTGA-TTACTGACTTAC
* * *
22605 TTAATTACCCTAAATTAAGTT-ACCTA-TTACTTAC
1 TTAATTACCCTGAATTAAGTTGA-TTACTGACTTAC
22639 TTAATTA-CCTGAATTAAGTTG----CTGACTTAC
1 TTAATTACCCTGAATTAAGTTGATTACTGACTTAC
* *
22669 TTAATTTCCCTGAATTAAAGTTG-TTCACTGGCTTAC
1 TTAATTACCCTGAATT-AAGTTGATT-ACTGACTTAC
* * *
22705 CTAATTGCCCTTAATTAAGTT
1 TTAATTACCCTGAATTAAGTT
22726 ACTTATTACT
Statistics
Matches: 479, Mismatches: 42, Indels: 37
0.86 0.08 0.07
Matches are distributed among these distances:
30 14 0.03
31 33 0.07
32 6 0.01
33 12 0.03
34 34 0.07
35 256 0.53
36 124 0.26
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (35 bp):
TTAATTACCCTGAATTAAGTTGATTACTGACTTAC
Found at i:22720 original size:212 final size:206
Alignment explanation
Indices: 22152--22725 Score: 625
Period size: 211 Copynumber: 2.8 Consensus size: 206
22142 TTTACTAAAT
* * * *
22152 TTAATTACCCTGAATTAAGTTGCTTATTACT-TACTTAATTATCCTGAATTAAGTTGATTACTGA
1 TTAATTACCCTGAATTAA---GCTGATTACTGTACTTAATTACCCTAAATTAAGTTGACTACTGA
* * *
22216 CTCACTTAATTACCCTGAATTAAAGTTGATT-ATAGACTCACTTAATTACCCTGAATT-AAGTTT
63 CTCACTTAATTACCCTGAATT-AA--TGATTGCT-GACTCACTTAATTACCCTAAATTAAAGTTA
* * * *
22279 ATTACTGACTTACTTAATTACCCTAAATTAAGTTGGTTACCGACTTACTTAATTACCTTGAATTA
124 ATTACTGACTCACTTAATTACCCTAAATTAAGTTGATTACCGACTCACTTAATTACCCTGAATTA
*
22344 AGTTGATTACTGACTTAC
189 AGTTGATCACTGACTTAC
* * * *
22362 TTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTACCCTGAATTATGTTGATTACTGA
1 TTAATTACCCTGAATTAAGCTGATTACTG---TACTTAATTACCCTAAATTAAGTTGACTACTGA
22427 CTCACTTAATTACCCTGAATTAAGTTGATTGCTGACTCACTTAATTACCCTAAATTAAAGTTAAT
63 CTCACTTAATTACCCTGAATTAA--TGATTGCTGACTCACTTAATTACCCTAAATTAAAGTTAAT
* *
22492 TACTGACTCACTTAATTACCCTGAATTAAAGTTGATTACTGACTCACTTAATTACCCTGAATTAA
126 TACTGACTCACTTAATTACCCTAAATT-AAGTTGATTACCGACTCACTTAATTACCCTGAATTAA
*
22557 GTT-ACTCATTGAAC-TAC
190 GTTGA-TCACTG-ACTTAC
*
22574 TTAATTACCCTGAATTAAGCT-ACTTACTG-ACTTAATTACCCTAAATTAAGTT-ACCTA-TTAC
1 TTAATTACCCTGAATTAAGCTGA-TTACTGTACTTAATTACCCTAAATTAAGTTGA-CTACTGAC
* * * * *
22635 TTACTTAATTA-CCTGAATTAA-G-TTGCTGACTTACTTAATTTCCCTGAATTAAAGTT-GTTCA
64 TCACTTAATTACCCTGAATTAATGATTGCTGACTCACTTAATTACCCTAAATTAAAGTTAATT-A
* * * * *
22696 CTGGCTTACCTAATTGCCCTTAATTAAGTT
128 CTGACTCACTTAATTACCCTAAATTAAGTT
22726 ACTTATTACT
Statistics
Matches: 322, Mismatches: 30, Indels: 33
0.84 0.08 0.09
Matches are distributed among these distances:
201 7 0.02
202 52 0.16
203 1 0.00
206 10 0.03
207 22 0.07
208 23 0.07
210 49 0.15
211 87 0.27
212 69 0.21
213 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (206 bp):
TTAATTACCCTGAATTAAGCTGATTACTGTACTTAATTACCCTAAATTAAGTTGACTACTGACTC
ACTTAATTACCCTGAATTAATGATTGCTGACTCACTTAATTACCCTAAATTAAAGTTAATTACTG
ACTCACTTAATTACCCTAAATTAAGTTGATTACCGACTCACTTAATTACCCTGAATTAAGTTGAT
CACTGACTTAC
Found at i:26376 original size:2 final size:2
Alignment explanation
Indices: 26369--26410 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
26359 TAGCGAAAGA
26369 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
26411 ATTATAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29420 original size:19 final size:21
Alignment explanation
Indices: 29384--29425 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
29374 TTTCTTCTAT
29384 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
29404 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
29424 TT
1 TT
29426 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Done.