Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007405.1 Corchorus capsularis cultivar CVL-1 contig07426, 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: 89578
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:267 original size:22 final size:22
Alignment explanation
Indices: 214--399 Score: 104
Period size: 22 Copynumber: 8.5 Consensus size: 22
204 AGATTTGTGC
** * *
214 TTATCAAAATTTCCTAGGGAGA
1 TTATCAAAATTTTATAGGTAGG
*
236 TTAACAAAATTTTATAGGTAGG
1 TTATCAAAATTTTATAGGTAGG
258 TTATGC-AAATTTTATAGAG-AGG
1 TTAT-CAAAATTTTATAG-GTAGG
* * *
280 TTATCGAAATTTCAT-GGTGTGG
1 TTATCAAAATTTTATAGGT-AGG
302 TTATCAAAATTTTAT--G-AGG
1 TTATCAAAATTTTATAGGTAGG
*
321 TTATCAAAATTTTCATA-GTGCGG
1 TTATCAAAATTTT-ATAGGT-AGG
* *
344 TTA-C-CAATTTTATTTAGTGT-GA
1 TTATCAAAATTTTA--TAG-GTAGG
* * *
366 TTATTAAAATTTTATAGGCAGA
1 TTATCAAAATTTTATAGGTAGG
388 TTATCAAAATTT
1 TTATCAAAATTT
400 CACACTGAGA
Statistics
Matches: 130, Mismatches: 18, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
19 15 0.12
20 4 0.03
21 11 0.08
22 84 0.65
23 7 0.05
24 9 0.07
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGTAGG
Found at i:310 original size:66 final size:67
Alignment explanation
Indices: 240--509 Score: 229
Period size: 66 Copynumber: 4.1 Consensus size: 67
230 GGGAGATTAA
* *
240 CAAAATTTTATAGGTAGGTTATGC-AAATTTT-ATAGAGAGGTTATCGAAATTTCATGGTGTGGT
1 CAAAATTTTATAGGTAGGTTAT-CAAAATTTTCATAGTGAGGTTATCGAAATTTCATAGTGTGGT
303 TAT
65 TAT
* * * *
306 CAAAATTTTAT--G-AGGTTATCAAAATTTTCATAGTGCGGTTA-C-CAATTTTATTTAGTGTGA
1 CAAAATTTTATAGGTAGGTTATCAAAATTTTCATAGTGAGGTTATCGAAATTTCA--TAGTGTGG
366 TTAT
64 TTAT
* * * * * * * * * *
370 TAAAATTTTATAGGCAGATTATCAAAA-TTTCACACTGAGATAATCAAAAATTCATAGTGCGGTT
1 CAAAATTTTATAGGTAGGTTATCAAAATTTTCATAGTGAGGTTATCGAAATTTCATAGTGTGGTT
*
434 AC
66 AT
* * * * *
436 CAAAATTTCACAGTGT-GGTTATC-AAATTTTCATAGGGAGGTTATCGAAATTTCATAATGAGGT
1 CAAAATTTTATAG-GTAGGTTATCAAAATTTTCATAGTGAGGTTATCGAAATTTCATAGTGTGGT
499 TAT
65 TAT
502 C-AAATTTT
1 CAAAATTTT
510 CAAAATGTGG
Statistics
Matches: 158, Mismatches: 35, Indels: 23
0.73 0.16 0.11
Matches are distributed among these distances:
62 7 0.04
63 15 0.09
64 31 0.20
65 9 0.06
66 78 0.49
67 13 0.08
68 5 0.03
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (67 bp):
CAAAATTTTATAGGTAGGTTATCAAAATTTTCATAGTGAGGTTATCGAAATTTCATAGTGTGGTT
AT
Found at i:410 original size:22 final size:22
Alignment explanation
Indices: 366--532 Score: 129
Period size: 22 Copynumber: 7.6 Consensus size: 22
356 TTTAGTGTGA
* * *
366 TTATTAAAATTTTATAG-GCAGA
1 TTATCAAAATTTCATAGTG-AGG
* * *
388 TTATCAAAATTTCACACTGAGA
1 TTATCAAAATTTCATAGTGAGG
* * *
410 TAATCAAAAATTCATAGTGCGG
1 TTATCAAAATTTCATAGTGAGG
* * *
432 TTACCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
454 TTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
476 TTATCGAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
498 TTATCAAATTTTCAAAATGTGG
1 TTATCAAAATTTCATAGTGAGG
*
520 TTATCAATATTTC
1 TTATCAAAATTTC
533 CACATTGGAG
Statistics
Matches: 114, Mismatches: 30, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
22 113 0.99
23 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:504 original size:88 final size:88
Alignment explanation
Indices: 278--505 Score: 229
Period size: 88 Copynumber: 2.6 Consensus size: 88
268 TTTATAGAGA
* *
278 GGTTATCGAAA-TTTCAT-GGTGTGGTTATCAAAATTT--T-ATGAGGTTATCAAAATTTTCATA
1 GGTTATC-AAATTTTCATAGG-GAGGTTATCAAAATTTCATAATGAGGTTATCAAAATATTCATA
* *
338 GTGCGGTTACCAATTTTATTTAGTGT
64 GTGCGGTTACCAATTTCA-TCAGTGT
* * * * * * * *
364 GATTATTAAAATTTT-ATAGGCAGATTATCAAAATTTCACACTGAGATAATCAAAA-ATTCATAG
1 GGTTA-TCAAATTTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTTATCAAAATATTCATAG
427 TGCGGTTACCAAAATTTCA-CAGTGT
65 TGCGGTTACC--AATTTCATCAGTGT
*
452 GGTTATCAAATTTTCATAGGGAGGTTATCGAAATTTCATAATGAGGTTATCAAA
1 GGTTATCAAATTTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTTATCAAA
506 TTTTCAAAAT
Statistics
Matches: 112, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
86 22 0.20
87 14 0.12
88 58 0.52
89 12 0.11
90 6 0.05
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (88 bp):
GGTTATCAAATTTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTTATCAAAATATTCATAGT
GCGGTTACCAATTTCATCAGTGT
Found at i:510 original size:44 final size:44
Alignment explanation
Indices: 214--511 Score: 159
Period size: 44 Copynumber: 6.8 Consensus size: 44
204 AGATTTGTGC
* ** * * *
214 TTATCAAAATTTCCTAGGGAGATTAACAAAATTTT-ATAGGTAGG
1 TTATCAAAATTTCATAATGAGGTTATC-AAATTTTCATAGGGAGG
* *
258 TTATGC-AAATTTTATAGA-GAGGTTATCGAAA-TTTCAT-GGTGTGG
1 TTAT-CAAAATTTCATA-ATGAGGTTATC-AAATTTTCATAGG-GAGG
* *
302 TTATCAAAATTT--T-ATGAGGTTATCAAAATTTTCATAGTGCGG
1 TTATCAAAATTTCATAATGAGGTTATC-AAATTTTCATAGGGAGG
* * * * * * * *
344 TTA-C-CAATTTTATTTAGTGTGATTATTAAAATTTT-ATAGGCAGA
1 TTATCAAAATTTCA--TAATGAGGTTA-TCAAATTTTCATAGGGAGG
* * * * ** * *
388 TTATCAAAATTTCACACTGAGATAATCAAAAATTCATAGTGCGG
1 TTATCAAAATTTCATAATGAGGTTATCAAATTTTCATAGGGAGG
* * * *
432 TTACCAAAATTTCACAGTGTGGTTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCATAATGAGGTTATCAAATTTTCATAGGGAGG
*
476 TTATCGAAATTTCATAATGAGGTTATCAAATTTTCA
1 TTATCAAAATTTCATAATGAGGTTATCAAATTTTCA
512 AAATGTGGTT
Statistics
Matches: 190, Mismatches: 47, Indels: 34
0.70 0.17 0.13
Matches are distributed among these distances:
40 6 0.03
41 13 0.07
42 13 0.07
43 13 0.07
44 123 0.65
45 15 0.08
46 7 0.04
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCATAATGAGGTTATCAAATTTTCATAGGGAGG
Found at i:3058 original size:33 final size:33
Alignment explanation
Indices: 3016--3144 Score: 179
Period size: 33 Copynumber: 3.9 Consensus size: 33
3006 TTACACTAGT
*
3016 CTCCCCACTAGGACGGCTTCACCATGGCGGAGC
1 CTCCCCACTAGGACGGCTCCACCATGGCGGAGC
3049 CTCCCCACTAGGACGGCTCCACCATGGCGGAGC
1 CTCCCCACTAGGACGGCTCCACCATGGCGGAGC
** * **
3082 CTCCCCACTAGGACGGCTCCGGCTTACCGGAGC
1 CTCCCCACTAGGACGGCTCCACCATGGCGGAGC
*
3115 CTCCCCTCTAGGACGGCT-CAGCCATGGCGG
1 CTCCCCACTAGGACGGCTCCA-CCATGGCGG
3145 GCGGCTAGTC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
32 1 0.01
33 82 0.99
ACGTcount: A:0.16, C:0.41, G:0.28, T:0.15
Consensus pattern (33 bp):
CTCCCCACTAGGACGGCTCCACCATGGCGGAGC
Found at i:3243 original size:33 final size:33
Alignment explanation
Indices: 3201--3282 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
3191 TAGCCGAGCC
*
3201 GCCCCAGTGGGGCGGCCTGCCCATGGTGAAGCT
1 GCCCCAGTGGGGCGGCCTACCCATGGTGAAGCT
3234 GCCCCAGTGGGGCGGCCTACCCATGGTGAAGCT
1 GCCCCAGTGGGGCGGCCTACCCATGGTGAAGCT
3267 GCCCCAGTGGGGCGGC
1 GCCCCAGTGGGGCGGC
3283 TTGAGCCATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.12, C:0.34, G:0.40, T:0.13
Consensus pattern (33 bp):
GCCCCAGTGGGGCGGCCTACCCATGGTGAAGCT
Found at i:4513 original size:6 final size:6
Alignment explanation
Indices: 4502--4531 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
4492 ACAAGGCAAT
*
4502 AGATGG AGATGG GGATGG AGATGG AGATGG
1 AGATGG AGATGG AGATGG AGATGG AGATGG
4532 CATGGACCCG
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:0.30, C:0.00, G:0.53, T:0.17
Consensus pattern (6 bp):
AGATGG
Found at i:12970 original size:3 final size:3
Alignment explanation
Indices: 12962--12992 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12952 GTACTTGTTA
12962 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12993 TAAGAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13549 original size:31 final size:31
Alignment explanation
Indices: 13514--13585 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 31
13504 CATATCTAAC
*
13514 TCTTGTCTCTGCTGGAACACTTGCATTTATT
1 TCTTGTATCTGCTGGAACACTTGCATTTATT
13545 TCTTGTATCTGCTGG-A-AC--GC-TTTCATT
1 TCTTGTATCTGCTGGAACACTTGCATTT-ATT
13572 TCTTGTATCTGCTG
1 TCTTGTATCTGCTG
13586 TATCCTTTAC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 3 0.08
27 19 0.49
29 2 0.05
30 1 0.03
31 14 0.36
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (31 bp):
TCTTGTATCTGCTGGAACACTTGCATTTATT
Found at i:28956 original size:62 final size:62
Alignment explanation
Indices: 28859--28982 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
28849 TGCTAATATA
28859 ATCTATTTCAGCTTCAAAGTTTGGAGCAATATATATTCATCAACTTTTTAGTATCTAGCACT
1 ATCTATTTCAGCTTCAAAGTTTGGAGCAATATATATTCATCAACTTTTTAGTATCTAGCACT
28921 ATCTATTTCAGCTTCAAAGTTTGGAGCAATATATATTCATCAACTTTTTAGTATCTAGCACT
1 ATCTATTTCAGCTTCAAAGTTTGGAGCAATATATATTCATCAACTTTTTAGTATCTAGCACT
28983 CATTTACTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (62 bp):
ATCTATTTCAGCTTCAAAGTTTGGAGCAATATATATTCATCAACTTTTTAGTATCTAGCACT
Found at i:29926 original size:21 final size:21
Alignment explanation
Indices: 29900--29941 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29890 AGATTTGGAT
29900 TTAGTGGGTGCTTACTTGAAA
1 TTAGTGGGTGCTTACTTGAAA
29921 TTAGTGGGTGCTTACTTGAAA
1 TTAGTGGGTGCTTACTTGAAA
29942 GTAGGTTTTC
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:0.24, C:0.10, G:0.29, T:0.38
Consensus pattern (21 bp):
TTAGTGGGTGCTTACTTGAAA
Found at i:35258 original size:77 final size:77
Alignment explanation
Indices: 35131--35285 Score: 292
Period size: 77 Copynumber: 2.0 Consensus size: 77
35121 ACCCACTAAC
*
35131 AAATATCATAATCCAAGGGGCATGAACCAAATATATATCAGATTACTTTAATGGCTCAAAACAAA
1 AAATAGCATAATCCAAGGGGCATGAACCAAATATATATCAGATTACTTTAATGGCTCAAAACAAA
35196 CAAAAATCATCA
66 CAAAAATCATCA
*
35208 AAATAGCATAATCCAGGGGGCATGAACCAAATATATATCAGATTACTTTAATGGCTCAAAACAAA
1 AAATAGCATAATCCAAGGGGCATGAACCAAATATATATCAGATTACTTTAATGGCTCAAAACAAA
35273 CAAAAATCATCA
66 CAAAAATCATCA
35285 A
1 A
35286 GTGTGAATTG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.23
Consensus pattern (77 bp):
AAATAGCATAATCCAAGGGGCATGAACCAAATATATATCAGATTACTTTAATGGCTCAAAACAAA
CAAAAATCATCA
Found at i:43917 original size:39 final size:39
Alignment explanation
Indices: 43862--43945 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 39
43852 GAAAAGAGGA
43862 TCAAATTTCCAAAAGATTTGTCATCTAATTATTAATTGG
1 TCAAATTTCCAAAAGATTTGTCATCTAATTATTAATTGG
* *
43901 TCAAATTTGCATAAGATTTGTCATCTAATTATTAATTGG
1 TCAAATTTCCAAAAGATTTGTCATCTAATTATTAATTGG
43940 -CAAATT
1 TCAAATT
43946 ATACAATACA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
38 6 0.14
39 37 0.86
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.42
Consensus pattern (39 bp):
TCAAATTTCCAAAAGATTTGTCATCTAATTATTAATTGG
Found at i:44358 original size:17 final size:17
Alignment explanation
Indices: 44326--44359 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44316 TAACAAGTCC
*
44326 CGGGTCTTAATGGATCA
1 CGGGTCTTAATAGATCA
*
44343 CGGGTCTTAGTAGATCA
1 CGGGTCTTAATAGATCA
44360 GATAGAATCG
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:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (17 bp):
CGGGTCTTAATAGATCA
Found at i:45504 original size:30 final size:28
Alignment explanation
Indices: 45454--45517 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 28
45444 ATAATTTGCC
45454 ATACTTTTTTTTGATGATTTATTCAACAT
1 ATAC-TTTTTTTGATGATTTATTCAACAT
*
45483 ATACTTTTTTTGATAATATTTATTCAACAT
1 ATACTTTTTTTGAT--GATTTATTCAACAT
45513 ATACT
1 ATACT
45518 GACTTGAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 10 0.31
29 4 0.12
30 18 0.56
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.53
Consensus pattern (28 bp):
ATACTTTTTTTGATGATTTATTCAACAT
Found at i:48212 original size:20 final size:20
Alignment explanation
Indices: 48187--48226 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
48177 TATTGTAAAG
48187 GTATTAATTATATCAATAGT
1 GTATTAATTATATCAATAGT
*
48207 GTATTAATTATATCTATAGT
1 GTATTAATTATATCAATAGT
48227 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (20 bp):
GTATTAATTATATCAATAGT
Found at i:49269 original size:179 final size:181
Alignment explanation
Indices: 48955--49317 Score: 599
Period size: 179 Copynumber: 2.0 Consensus size: 181
48945 TTCATGAAAG
* *
48955 TTGTAGACCATGGAATTACCTTTAAATAGACACTTTGAATTACCTTGATCAGTCAAATAGAAAAA
1 TTGTAGACCATGGAATTACCTTTAAATAGACACTCTGAATCACCTTGATCAGTCAAATAG-AAAA
* * *
49020 AAATAAAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCATAATTGTAAGTGATTAAATAGTA
65 AAATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAGAA
49085 TAAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAGATGA
130 TAAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAA-ATGA
* *
49138 TTGTAGACCATGGAATTACCTTTAAATAGACAC-CTGAATCACTTTGATCGGTCAAATAG-AAAA
1 TTGTAGACCATGGAATTACCTTTAAATAGACACTCTGAATCACCTTGATCAGTCAAATAGAAAAA
*
49201 AA-AAAACAATTAAAGCCGAAACATTCAATCGTCCAACATATAATTGTAAG-GATTAAATAGCAA
66 AATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAG-AA
49264 TAAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAATGA
130 TAAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAATGA
49316 TT
1 TT
49318 TGTTTATGGA
Statistics
Matches: 171, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
178 16 0.09
179 94 0.55
180 6 0.04
182 22 0.13
183 33 0.19
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.27
Consensus pattern (181 bp):
TTGTAGACCATGGAATTACCTTTAAATAGACACTCTGAATCACCTTGATCAGTCAAATAGAAAAA
AATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAGAAT
AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAATGA
Found at i:52790 original size:20 final size:17
Alignment explanation
Indices: 52768--52811 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
52758 TTTCTTCTTC
* *
52768 TTCTTCTTCTTCCCCTA
1 TTCTTCTTCATCTCCTA
52785 TTCTTCTTCATCTCCTA
1 TTCTTCTTCATCTCCTA
52802 TTCTTCTTCA
1 TTCTTCTTCA
52812 ACAAAATGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.09, C:0.36, G:0.00, T:0.55
Consensus pattern (17 bp):
TTCTTCTTCATCTCCTA
Found at i:53441 original size:14 final size:14
Alignment explanation
Indices: 53422--53448 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53412 TTCCCCGTCG
53422 TAGGGGAAGAAGAA
1 TAGGGGAAGAAGAA
53436 TAGGGGAAGAAGA
1 TAGGGGAAGAAGA
53449 TGGGAGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.07
Consensus pattern (14 bp):
TAGGGGAAGAAGAA
Found at i:64004 original size:76 final size:76
Alignment explanation
Indices: 63878--64030 Score: 200
Period size: 76 Copynumber: 2.0 Consensus size: 76
63868 TAAGTATCTC
** * * *
63878 ATTTTTTTTTATATTCACAAGTTAACCTTGTTCGAGTCGGGTAGACCCACTATG-GGGATAAAAC
1 ATTTTTTGGTATATTCACAAATTAACCTTGTTCGAGTCGGATAGACCCACTATGCGAG-TAAAAC
*
63942 TTTCCCAACAAT
65 TCTCCCAACAAT
* * **
63954 ATTTTTTGGTATATTTACAAATTAACCTTGTTCGAGTCGGATTGGTCCACTATGCGAGTAAAACT
1 ATTTTTTGGTATATTCACAAATTAACCTTGTTCGAGTCGGATAGACCCACTATGCGAGTAAAACT
64019 CTCCCAACAAT
66 CTCCCAACAAT
64030 A
1 A
64031 GTATCTCCTT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
76 64 0.97
77 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (76 bp):
ATTTTTTGGTATATTCACAAATTAACCTTGTTCGAGTCGGATAGACCCACTATGCGAGTAAAACT
CTCCCAACAAT
Found at i:83996 original size:10 final size:10
Alignment explanation
Indices: 83981--84006 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
83971 GAGGACTCTA
83981 GAATTTTCTG
1 GAATTTTCTG
83991 GAATTTTCTG
1 GAATTTTCTG
84001 GAATTT
1 GAATTT
84007 AGCAGCAACT
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:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Done.