Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015032.1 Corchorus capsularis cultivar CVL-1 contig15053, 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: 91407
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1254 original size:130 final size:130
Alignment explanation
Indices: 894--1675 Score: 929
Period size: 130 Copynumber: 6.0 Consensus size: 130
884 GTGGAACGAC
* * * ** * * * *
894 TTATAAAGTTGTTTCG-ATAGATTATGATTTCGCAACAACTTTAAGAATCTGTTGTTATGAATAT
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTT--GTTTTTGTTGTTACGAAAAC
* ** * * * * * *
958 TGCAAATATTGGCAACAACTAAAAAGGTGTTGTATAAAATACCATCAAGATCATTTTGACAACGT
64 TGTAAGCATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGT
1023 TT
129 TT
* * * ** *** *
1025 TTATAAAGTTGTTACGAATAGCTTAAT-AGTTTCGCAGCAACCTAAGAAGTTGTTGTTACGAATA
1 TTATAAAGTTGTTACGAATAG-TTTATGA-TTTCGCAACGA-CTTTGTTTTTGTTGTTACGAAAA
* * * *
1089 CTGTAAACATTGGTAACAACTAAAAAAATGTTGTGTAAAATACCATCAAAATCACTTAGACAACG
63 CTGTAAGCATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACG
1154 TTT
128 TTT
* *
1157 TTATGAAGTTGTTACGAATAGTTTGTGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTG
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTG
* * * *
1222 TAAGCATTGACAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAGATCATTTTGGCAACGTTT
66 TAAGCATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTTT
* * ** * *
1287 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTCAGAATTTGTTGTTACGAATATT
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTT-TGTTTTTGTTGTTACGAAAACT
* *
1352 GTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAACCACTTAGGCAACGTT
65 GTAAGCATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTT
1417 T
130 T
* * *
1418 TTATGAAGTTGTTACGAATAGTTTGTGATTTGGCAACGACTTTGTTTTTGTTGTTACGAAAACTG
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTG
* * * **
1483 TAAGTATCGGCAACAACTAAAAAAATGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGACT
66 TAAGCATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTTT
* * * * *
1548 TTATAAAATTGTTACAAATAGATTATGATTTCGCAACGGCTTTCTTTTTGTTGTTACGAAAACTG
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTG
* * * *
1613 TAAGCATTGGCAACAATTAAAAAAGTCGTTGGGTAAAATACCATCAAAATCACTAAGCCAACG
66 TAAGCATTGGCAACAACTAAAAAAGT-GTTGTGTAAAATACCATCAAAATCACTTAGGCAACG
1676 ACTTTTAATT
Statistics
Matches: 561, Mismatches: 83, Indels: 14
0.85 0.13 0.02
Matches are distributed among these distances:
130 271 0.48
131 175 0.31
132 100 0.18
133 13 0.02
134 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (130 bp):
TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTG
TAAGCATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTTT
Found at i:1416 original size:261 final size:261
Alignment explanation
Indices: 965--1675 Score: 1041
Period size: 261 Copynumber: 2.7 Consensus size: 261
955 TATTGCAAAT
* * *
965 ATTGGCAACAACTAAAAAGGTGTTGTATAAAATACCATCAAGATCATTTTGACAACGTTTTTATA
1 ATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAGATCATTTTGGCAACGTTTTTATA
* * * * *
1030 AAGTTGTTACGAATAGCTTAAT-AGTTTCGCAGCAACCTAAGAAGTTGTTGTTACGAATACTGTA
66 AAGTTGTTACGAATAG-TTTATGA-TTTCGCAACAACTTCAGAATTTGTTGTTACGAATACTGTA
* *
1094 AACATTGGTAACAACTAAAAAAATGTTGTGTAAAATACCATCAAAATCACTTAGACAACGTTTTT
129 AACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGACAACGTTTTT
1159 ATGAAGTTGTTACGAATAGTTTGTGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTGTA
194 ATGAAGTTGTTACGAATAGTTTGTGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTGTA
1224 AGC
259 AGC
*
1227 ATTGACAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAGATCATTTTGGCAACGTTTTTATA
1 ATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAGATCATTTTGGCAACGTTTTTATA
*
1292 AAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTCAGAATTTGTTGTTACGAATATTGTAAA
66 AAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTCAGAATTTGTTGTTACGAATACTGTAAA
* *
1357 CATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAACCACTTAGGCAACGTTTTTAT
131 CATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGACAACGTTTTTAT
*
1422 GAAGTTGTTACGAATAGTTTGTGATTTGGCAACGACTTTGTTTTTGTTGTTACGAAAACTGTAAG
196 GAAGTTGTTACGAATAGTTTGTGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTGTAAG
*
1487 T
261 C
* * * * * **
1488 ATCGGCAACAACTAAAAAAATGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGACTTTATA
1 ATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAGATCATTTTGGCAACGTTTTTATA
* * * ** ** *
1553 AAATTGTTACAAATAGATTATGATTTCGCAACGGCTTTC--TTTTTGTTGTTACGAAAACTGTAA
66 AAGTTGTTACGAATAGTTTATGATTTCGCAACAAC-TTCAGAATTTGTTGTTACGAATACTGTAA
* * * * *
1616 GCATTGGCAACAATTAAAAAAGTCGTTGGGTAAAATACCATCAAAATCACTAAGCCAACG
130 ACATTGGCAACAACTAAAAAAGT-GTTGTGTAAAATACCATCAAAATCACTTAGACAACG
1676 ACTTTTAATT
Statistics
Matches: 407, Mismatches: 39, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
260 41 0.10
261 285 0.70
262 81 0.20
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (261 bp):
ATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAGATCATTTTGGCAACGTTTTTATA
AAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTCAGAATTTGTTGTTACGAATACTGTAAA
CATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGACAACGTTTTTAT
GAAGTTGTTACGAATAGTTTGTGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTGTAAG
C
Found at i:7460 original size:2 final size:2
Alignment explanation
Indices: 7453--7477 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7443 TTTCTAATTA
7453 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
7478 ACATATTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:16943 original size:67 final size:67
Alignment explanation
Indices: 16777--16992 Score: 269
Period size: 67 Copynumber: 3.2 Consensus size: 67
16767 ATGTGTTGGG
*
16777 TTCCAAATGCGTTTTTC-TGATGGTCACTTTAGGTTCCAATTGATCTGGAGTCAA-TTAGAATGT
1 TTCCAAATGCGTTTTTCAT-ATGGTCACTTTAGGTTCCAATTGATCTGGAGTCAATTTA-TATGT
16840 CGG-
64 CGGA
* * * * * *
16843 TTTCAAATGTGTTTTTTCA-ATGGTCACTTTAGGTTTCGATTGATCTTGAGTCAATTTATATGTT
1 TTCCAAATGCG-TTTTTCATATGGTCACTTTAGGTTCCAATTGATCTGGAGTCAATTTATATGTC
16907 GGA
65 GGA
* * * * *
16910 TTCCAAATGTGTTTTTCATATGGTCACTTTAGGTTCCAATTGATCCGGTGTCAATTAATATGTCA
1 TTCCAAATGCGTTTTTCATATGGTCACTTTAGGTTCCAATTGATCTGGAGTCAATTTATATGTCG
16975 GA
66 GA
16977 TTCCAAATGCGTTTTT
1 TTCCAAATGCGTTTTT
16993 TCGATTCCAA
Statistics
Matches: 128, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
66 54 0.42
67 74 0.58
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (67 bp):
TTCCAAATGCGTTTTTCATATGGTCACTTTAGGTTCCAATTGATCTGGAGTCAATTTATATGTCG
GA
Found at i:20702 original size:43 final size:43
Alignment explanation
Indices: 20654--20736 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
20644 AGCTTAGACT
*
20654 AATCAGCCCCATCCATCCATAGTTATATAAGGTGATGACTTCA
1 AATCAGCCCCATCCATCCATAGTTATAGAAGGTGATGACTTCA
* *
20697 AATCAGCCCCATCCGTCCGTAGTTATAGAAGGTGATGACT
1 AATCAGCCCCATCCATCCATAGTTATAGAAGGTGATGACT
20737 CCATCTAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
AATCAGCCCCATCCATCCATAGTTATAGAAGGTGATGACTTCA
Found at i:23229 original size:28 final size:28
Alignment explanation
Indices: 23158--23229 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 28
23148 CCAAATTAGT
23158 CCCTTAACTATCTATTTTGGGACAAATTGAC
1 CCCTTAACT-T-T-TTTTGGGACAAATTGAC
23189 CCCTTAACTTTTTTTGGGGACAAATTGAC
1 CCCTTAACTTTTTTT-GGGACAAATTGAC
23218 CCCTTAACTTTT
1 CCCTTAACTTTT
23230 AAAAACGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 4 0.10
29 26 0.65
30 1 0.03
31 9 0.22
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (28 bp):
CCCTTAACTTTTTTTGGGACAAATTGAC
Found at i:23941 original size:31 final size:29
Alignment explanation
Indices: 23871--23950 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
23861 TCTCGTTTTT
* * *
23871 AAAAGTTAAAGGGTCAATTTGTCCCCAAA
1 AAAAGTTAAGGGGCCAATTTATCCCCAAA
23900 AAAAGTTAAGGGGCCAATTTAT-CCCAAA
1 AAAAGTTAAGGGGCCAATTTATCCCCAAA
23928 ATGAATAGTTAAGGGGCCAATTT
1 A--AA-AGTTAAGGGGCCAATTT
23951 GGGTATTAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 7 0.16
29 19 0.42
30 2 0.04
31 17 0.38
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTATCCCCAAA
Found at i:25813 original size:21 final size:21
Alignment explanation
Indices: 25773--25813 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25763 AAGGGGGTTA
*
25773 CTAAATACCGTCCTAGTTTTG
1 CTAAATACCGTCCCAGTTTTG
*
25794 CTAAATACCGTCCCATTTTT
1 CTAAATACCGTCCCAGTTTT
25814 TACACTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (21 bp):
CTAAATACCGTCCCAGTTTTG
Found at i:25904 original size:33 final size:33
Alignment explanation
Indices: 25859--25946 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 33
25849 CTTTTACATT
* * **
25859 GAGCCTCTCCACTAGGACGGCTCAGCCACGGTG
1 GAGCCTCCCCACTAGGACGGCTCAACCACGACG
*
25892 GAGTCTCCCCACTAGGGA-GGCTCAACCACGACG
1 GAGCCTCCCCACTA-GGACGGCTCAACCACGACG
* *
25925 GAGCCTCCCCACTGGGGCGGCT
1 GAGCCTCCCCACTAGGACGGCT
25947 AGACCATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
32 2 0.04
33 40 0.89
34 3 0.07
ACGTcount: A:0.18, C:0.38, G:0.31, T:0.14
Consensus pattern (33 bp):
GAGCCTCCCCACTAGGACGGCTCAACCACGACG
Found at i:28167 original size:29 final size:27
Alignment explanation
Indices: 28124--28197 Score: 112
Period size: 29 Copynumber: 2.7 Consensus size: 27
28114 TTTATAAAAA
*
28124 AAAAAAAAAACTATTTCTTAGTTGGCC
1 AAAAAAAAAACTATTTATTAGTTGGCC
28151 AAGAAAAAAAAACTATTTATTAGTTGGCC
1 -A-AAAAAAAAACTATTTATTAGTTGGCC
*
28180 AAAACAAAAACTATTTAT
1 AAAAAAAAAACTATTTAT
28198 AAATAGTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 16 0.37
28 2 0.05
29 25 0.58
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.28
Consensus pattern (27 bp):
AAAAAAAAAACTATTTATTAGTTGGCC
Found at i:33183 original size:135 final size:135
Alignment explanation
Indices: 32899--33171 Score: 329
Period size: 135 Copynumber: 2.0 Consensus size: 135
32889 TTTTCTAATT
* * *
32899 AATATATTCTATAAATATGATCCCAAATACTTTTTAATTAGTTGATTTAGTCTCTCAAGATTTGA
1 AATAGATTCTATAAATATGATCCCAAATACTTTTTAATTAGTCGATTTAGTCCCTCAAGATTTGA
* * * * * * * *
32964 TTCTATGCAATTTAGTCCTTCACCTTTTTTTCTTGTATATTTTTTTAATATTTCTTTTTAATTTT
66 TTATATGCAATTTAGTCATTCACCTTTATTTCTTATATATGTTTTTAATATTGCTTATTAATATT
* *
33029 GCTTC
131 GATTA
** * *
33034 TTTAGATTCTATAAATGTGATCTCAAATACTTTTCT-ATTAGTCGATTTAGTCCCTCAAGCATTT
1 AATAGATTCTATAAATATGATCCCAAATACTTTT-TAATTAGTCGATTTAGTCCCTCAAG-ATTT
*
33098 GATTATATGCAATTTAGTCATTCACCTTTATTTCTTATA-ATGTTTTT-ATGTTGCTTATTAATA
64 GATTATATGCAATTTAGTCATTCACCTTTATTTCTTATATATGTTTTTAATATTGCTTATTAATA
33161 TT-ATATA
129 TTGAT-TA
33168 AATA
1 AATA
33172 TGATCTAATA
Statistics
Matches: 115, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
133 1 0.01
134 17 0.15
135 57 0.50
136 40 0.35
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (135 bp):
AATAGATTCTATAAATATGATCCCAAATACTTTTTAATTAGTCGATTTAGTCCCTCAAGATTTGA
TTATATGCAATTTAGTCATTCACCTTTATTTCTTATATATGTTTTTAATATTGCTTATTAATATT
GATTA
Found at i:35458 original size:30 final size:30
Alignment explanation
Indices: 35424--35483 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
35414 CCAACCACAC
*
35424 TTTCAATCATAGAACAAAGTGCATTAGATG
1 TTTCAATCATAGAACAAAGTGCACTAGATG
*
35454 TTTCAATCTTAGAACAAAGTGCACTAGATG
1 TTTCAATCATAGAACAAAGTGCACTAGATG
35484 GAGGCATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (30 bp):
TTTCAATCATAGAACAAAGTGCACTAGATG
Found at i:37974 original size:2 final size:2
Alignment explanation
Indices: 37967--37993 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37957 TTGAAGTTTA
37967 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
37994 GGTTCCTCAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39759 original size:29 final size:31
Alignment explanation
Indices: 39718--39792 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 31
39708 TTTATTTTTG
* *
39718 ACAAATTGCATAGG-CACACTCT-GATTGAA
1 ACAAATTGTATAGGCCACACTCTCCATTGAA
*
39747 ACAAATTGTATAGGGCCATACTCTCCATTGAA
1 ACAAATTGTATA-GGCCACACTCTCCATTGAA
39779 ACAAATTGTATAGG
1 ACAAATTGTATAGG
39793 GTAGTCTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 11 0.28
30 2 0.05
31 9 0.22
32 18 0.45
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (31 bp):
ACAAATTGTATAGGCCACACTCTCCATTGAA
Found at i:48550 original size:84 final size:86
Alignment explanation
Indices: 48428--48592 Score: 253
Period size: 85 Copynumber: 1.9 Consensus size: 86
48418 GAAAATAACA
**
48428 AAAATCCTATGGTTAATTTAACTTACCATATATATGA-TTTTTAAAAGGGTATTGCAGTAAATTG
1 AAAATCCTATGGTTAATTTAACTTACCATATATATGATTTTTTAAAAGGGTATTGCAACAAATTG
48492 ATCCTGAAATTATGCTTAAAC
66 ATCCTGAAATTATGCTTAAAC
* * * * *
48513 AAAATCCTA-GGTTAATTTAACTTACCATATGTTTGATTTTTTTAAAGGGTATTGTAACGAATTG
1 AAAATCCTATGGTTAATTTAACTTACCATATATATGATTTTTTAAAAGGGTATTGCAACAAATTG
48577 ATCCTGAAATTATGCT
66 ATCCTGAAATTATGCT
48593 ACATGTGAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 25 0.35
85 47 0.65
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (86 bp):
AAAATCCTATGGTTAATTTAACTTACCATATATATGATTTTTTAAAAGGGTATTGCAACAAATTG
ATCCTGAAATTATGCTTAAAC
Found at i:78933 original size:2 final size:2
Alignment explanation
Indices: 78922--78968 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
78912 AACTTCAAAT
* *
78922 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TC TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
78963 TC TA TA
1 TA TA TA
78969 CCATATATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:79265 original size:109 final size:109
Alignment explanation
Indices: 79069--79343 Score: 455
Period size: 109 Copynumber: 2.5 Consensus size: 109
79059 ACTATTATAG
* *
79069 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
79134 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
79183 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
79248 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
79292 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
79344 TAAGTTTTTT
Statistics
Matches: 157, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 7 0.04
109 124 0.79
110 3 0.02
111 2 0.01
114 21 0.13
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:82355 original size:14 final size:14
Alignment explanation
Indices: 82338--82377 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
82328 GAACTAGAGA
82338 GGGAGAGGGAGAAG
1 GGGAGAGGGAGAAG
82352 GGGAGAGGGAGAAG
1 GGGAGAGGGAGAAG
82366 GGGAGAGAGGAG
1 GGGAGAG-GGAG
82378 CTCTCAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (14 bp):
GGGAGAGGGAGAAG
Found at i:84716 original size:93 final size:93
Alignment explanation
Indices: 84589--84768 Score: 252
Period size: 93 Copynumber: 1.9 Consensus size: 93
84579 AATATAGAAT
* **
84589 TTTTGACAAGTTAATCAATTGAGGGTGAACATTTAGGACCAAATAAGGATGGGTACCATGTAAAA
1 TTTTGACAAGTTAATCAATTGAGGGTGAACATTTAGGACCAAATAAGGATAGACACCATGTAAAA
84654 TTACATACAAAATAATAAGAAATGGACA
66 TTACATACAAAATAATAAGAAATGGACA
* * ** * *
84682 TTTTGACGAGTTAATTAATTGAGGGTGGGCATTTAGGACCATATAAGGGTAGACACCATGTAAAA
1 TTTTGACAAGTTAATCAATTGAGGGTGAACATTTAGGACCAAATAAGGATAGACACCATGTAAAA
* **
84747 TTACATAGAAAATGTTAAGAAA
66 TTACATACAAAATAATAAGAAA
84769 GTTGAAGGTT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (93 bp):
TTTTGACAAGTTAATCAATTGAGGGTGAACATTTAGGACCAAATAAGGATAGACACCATGTAAAA
TTACATACAAAATAATAAGAAATGGACA
Found at i:87130 original size:2 final size:2
Alignment explanation
Indices: 87125--87149 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
87115 AGTGTGTGTG
87125 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 T
87150 GCTTGCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88840 original size:18 final size:18
Alignment explanation
Indices: 88819--88874 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
88809 GGATACGGAT
88819 ACGGAGAGGGAGACCGAG
1 ACGGAGAGGGAGACCGAG
**
88837 ACGGAGAGGGAGAGGGAG
1 ACGGAGAGGGAGACCGAG
* **
88855 ACGAAGACCGAGACCGAG
1 ACGGAGAGGGAGACCGAG
88873 AC
1 AC
88875 TCCATCTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.46, T:0.00
Consensus pattern (18 bp):
ACGGAGAGGGAGACCGAG
Found at i:88862 original size:24 final size:23
Alignment explanation
Indices: 88803--88873 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
88793 TTCTGAATCT
* *
88803 GGAGACGGATACGGATACGGAGAG
1 GGAGAC-GAGACGGAGACGGAGAG
*
88827 GGAGACCGAGACGGAGAGGGAGAG
1 GGAGA-CGAGACGGAGACGGAGAG
* *
88851 GGAGACGAAGACCGAGACCGAGA
1 GGAGACG-AGACGGAGACGGAGA
88874 CTCCATCTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 2 0.05
24 36 0.92
25 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.46, T:0.03
Consensus pattern (23 bp):
GGAGACGAGACGGAGACGGAGAG
Found at i:90244 original size:13 final size:13
Alignment explanation
Indices: 90226--90252 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
90216 TGGATCCAGG
90226 ACTAAATAAGGAA
1 ACTAAATAAGGAA
90239 ACTAAATAAGGAA
1 ACTAAATAAGGAA
90252 A
1 A
90253 AGCTCCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (13 bp):
ACTAAATAAGGAA
Done.