Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010457.1 Corchorus capsularis cultivar CVL-1 contig10478, 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: 22653
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Found at i:1147 original size:12 final size:12
Alignment explanation
Indices: 1130--1168 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1120 GTACAGATAT
1130 CGGATATATCGA
1 CGGATATATCGA
1142 CGGATATATCGA
1 CGGATATATCGA
1154 -GG---TATCGA
1 CGGATATATCGA
1162 CGGATAT
1 CGGATAT
1169 TTAATTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:3364 original size:3 final size:3
Alignment explanation
Indices: 3356--3381 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3346 ACCACTCCCG
3356 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
3382 ATTTTTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:4466 original size:2 final size:2
Alignment explanation
Indices: 4459--4496 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4449 ATAAGATAAG
4459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4497 TGACTTGGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4960 original size:14 final size:14
Alignment explanation
Indices: 4943--4970 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4933 CTTAATCTTG
4943 AATTGATAATTTAA
1 AATTGATAATTTAA
4957 AATTGATAATTTAA
1 AATTGATAATTTAA
4971 TTCAAGGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
AATTGATAATTTAA
Found at i:5066 original size:44 final size:41
Alignment explanation
Indices: 4956--5045 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
4946 TGATAATTTA
4956 AAATTGATAATTTAATTCAAGGGTCTCGATGACTTGTTCTT
1 AAATTGATAATTTAATTCAAGGGTCTCGATGACTTGTTCTT
4997 AAATTGATAATTTAATTCAAGGGTCTCGATGACTTGTTCTT
1 AAATTGATAATTTAATTCAAGGGTCTCGATGACTTGTTCTT
*
5038 GAATTGAT
1 AAATTGAT
5046 GATAATTTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (41 bp):
AAATTGATAATTTAATTCAAGGGTCTCGATGACTTGTTCTT
Found at i:5383 original size:16 final size:16
Alignment explanation
Indices: 5362--5396 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5352 ATCTGAAATA
*
5362 CTTCAGAGCTTTTCTG
1 CTTCAGAACTTTTCTG
5378 CTTCAGAACTTTTCTG
1 CTTCAGAACTTTTCTG
5394 CTT
1 CTT
5397 TCTGAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.26, G:0.14, T:0.46
Consensus pattern (16 bp):
CTTCAGAACTTTTCTG
Found at i:6910 original size:32 final size:32
Alignment explanation
Indices: 6832--6938 Score: 178
Period size: 32 Copynumber: 3.3 Consensus size: 32
6822 TTTTCATGGT
6832 GAAGCCGCCCCATGAGGGCGGCCTGCCGTGGC
1 GAAGCCGCCCCATGAGGGCGGCCTGCCGTGGC
* *
6864 AAAGCCCGCCCCATGAGGGCGGCCTGCCGTGGT
1 GAAG-CCGCCCCATGAGGGCGGCCTGCCGTGGC
*
6897 GAAGCCGCCCCATGAGGACGGCCTGCCGTGGC
1 GAAGCCGCCCCATGAGGGCGGCCTGCCGTGGC
6929 GAAGCCGCCC
1 GAAGCCGCCC
6939 TCTCCGCCGT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
32 39 0.57
33 30 0.43
ACGTcount: A:0.15, C:0.38, G:0.37, T:0.09
Consensus pattern (32 bp):
GAAGCCGCCCCATGAGGGCGGCCTGCCGTGGC
Found at i:8984 original size:197 final size:196
Alignment explanation
Indices: 8451--9845 Score: 1660
Period size: 199 Copynumber: 7.1 Consensus size: 196
8441 TCAAATCACT
* * * * * * *
8451 TTATATAATTTTTCTTATAAGATTATTATACAATACACTTTTCAGTGTAAATTTAACACTCCCTA
1 TTATATAATTTTTCTTATAGGATTATTATACAACACGC-TGTCAGTGTAAATTTTAGACT--TTA
* *
8516 AACGGGTTAAGAAATTGACACAATACCCCATTTCATAGTCAATTAAATATTTAATATTAATACAT
63 AA-GGGTTAAGAAGTTGACAC-ATACCCCATTTCATAATCAATTAAATATTTAATATTAATACAT
* * * * * * *
8581 ATTCCTTAAGGGGATACATGTCAACCCTTAAACCCTGCACATGTAGTCTGCTAAATTCGACTGAC
126 ATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGAC
*
8646 --AGTA
191 GGTGTA
* * ** * **
8650 TAATATAATTTTTCTTATAAGATTATTATACAATC-CATTGTCAGTGTAAATTTTGGAC--TCCA
1 TTATATAATTTTTCTTATAGGATTATTATACAA-CACGCTGTCAGTGTAAATTTTAGACTTTAAA
* *
8712 ----TAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATA-TC
65 GGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATTC
* *
8772 TTCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAAATCCACTGACGGT
130 -CCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGT
8837 GTA
194 GTA
*
8840 TTATATAATTTCTCTTATAGGATTATTATACAACACGCTGTCAGTGTAAATTTTAGACTTTAAGA
1 TTATATAATTTTTCTTATAGGATTATTATACAACACGCTGTCAGTGTAAATTTTAGACTTTAA-A
* * * * *
8905 GGGTTAAAAAGTTGACACATACCTCATTTCATCATCAATTAAATATATAATATTAATAAATATTC
65 GGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATTC
** * * * * *
8970 CCTAAGATGACACATGTCAACTCTTAAACCCCACACGTGTAGTCTGCTAAACTCGAGTGACGGTG
130 CCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTG
9035 TA
195 TA
* * * * * *
9037 -TAGAATAATTTTTCTTAAAGGATTATCATACGATACACG--GTCAGTATAAATTTTGGACTACA
1 TTA-TATAATTTTTCTTATAGGATTATTATAC-A-ACACGCTGTCAGTGTAAATTTTAGACT--T
* * *
9099 TAAACGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATAAAATATTTAATATTAGTACA
61 TAAA-GGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACA
* *
9164 TATTCCCTAAGAGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAAATCCACTGA
125 TATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGA
9229 CGGTGTA
190 CGGTGTA
*
9236 TTATATAATTTTTCTTATAGGATTATTATACAACACGCTGTCTGTGTAAATTTTAGACTTTATAA
1 TTATATAATTTTTCTTATAGGATTATTATACAACACGCTGTCAGTGTAAATTTTAGACTTTA-AA
* * * * *
9301 GCGGGTTAAGAAGTTGATACATACCTCATTTCATCATCATTTAAATATATAATATTAATACATAT
65 --GGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATAT
*
9366 TCCCTAAGGGGACACGTGTCAATCCC-TAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACG
128 TCCCTAAGGGGACACATGTCAA-CCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACG
9430 GTGTA
192 GTGTA
* * * * ** **
9435 TTGTATAATTGTTCTTATATGATTATTATACAATAAACTG-CAAAGTAAATTTT-GCACTCCATT
1 TTATATAATTTTTCTTATAGGATTATTATACAACACGCTGTCAGTGTAAATTTTAG-ACT---TT
* * * *
9498 AACGGGTTGAGAAGTTGACACATACCCCATTTCATAATTAATTAAGTATTTAATATTAATACATA
62 AAAGGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATA
* * * * *
9563 TTCCTTAAGGGGACACATGTCAACCCTTAAAGCCGGCATGTGCAGTCTGCTAAACTCTACTGACG
127 TTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACG
9628 GTGTA
192 GTGTA
* * *
9633 TTGTATAATTGTTCTTATAGGATTA-T-TACAACACGCTGTCTGTGTAAATTTTAGACTTTATAA
1 TTATATAATTTTTCTTATAGGATTATTATACAACACGCTGTCAGTGTAAATTTTAGACTTTA-AA
* * *
9696 GCGGGTTAAGAAGTTGACACATACCACATTTCATCATCAATTAAATATATAATATTAATACATAT
65 --GGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATAT
* *
9761 TCCCTAAGGAGACACATGTCAA-CCTTAAACCCCGCACGTGCAGTCTGCTAAACTCGACTGACGG
128 TCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGG
9825 TGTA
193 TGTA
9829 TTGA-ATAATTTTTCTTA
1 TT-ATATAATTTTTCTTA
9846 AGTTATACCA
Statistics
Matches: 1028, Mismatches: 132, Indels: 75
0.83 0.11 0.06
Matches are distributed among these distances:
187 2 0.00
188 95 0.09
189 13 0.01
190 53 0.05
192 1 0.00
193 1 0.00
194 5 0.00
195 1 0.00
196 67 0.07
197 253 0.25
198 175 0.17
199 353 0.34
200 6 0.01
201 3 0.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (196 bp):
TTATATAATTTTTCTTATAGGATTATTATACAACACGCTGTCAGTGTAAATTTTAGACTTTAAAG
GGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATTCC
CTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGT
A
Found at i:12303 original size:2 final size:2
Alignment explanation
Indices: 12296--12337 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
12286 CCGAATCATC
*
12296 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12337 A
1 A
12338 ATAAATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:13510 original size:8 final size:10
Alignment explanation
Indices: 13481--13511 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
13471 ATTTAATCTA
13481 ATTTAAATAT
1 ATTTAAATAT
13491 ATTTAAATAT
1 ATTTAAATAT
13501 ATTTAAATAT
1 ATTTAAATAT
13511 A
1 A
13512 ACTATATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTTAAATAT
Found at i:14516 original size:40 final size:40
Alignment explanation
Indices: 14470--14548 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
14460 TTTCTTGAAG
14470 GATATTTAAGAATATACTTTTTAAAGGATTTATTTTTAAT
1 GATATTTAAGAATATACTTTTTAAAGGATTTATTTTTAAT
* * *
14510 GATATTTAAGACTGTATTTTTTAAAGGATTTATTTTTAA
1 GATATTTAAGAATATACTTTTTAAAGGATTTATTTTTAA
14549 AGGATATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (40 bp):
GATATTTAAGAATATACTTTTTAAAGGATTTATTTTTAAT
Found at i:14545 original size:15 final size:15
Alignment explanation
Indices: 14527--14558 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
14517 AAGACTGTAT
*
14527 TTTTTAAAGGATTTA
1 TTTTTAAAGGATATA
14542 TTTTTAAAGGATATA
1 TTTTTAAAGGATATA
14557 TT
1 TT
14559 ATGATGATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
TTTTTAAAGGATATA
Found at i:18283 original size:27 final size:26
Alignment explanation
Indices: 18239--18433 Score: 167
Period size: 27 Copynumber: 7.2 Consensus size: 26
18229 TATTTCTTGA
*
18239 TTACTAATTACCATTTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
* *
18265 GTACTGATTACCATATTTTACTCTTTT
1 TTACTGATTACCATTTTTTACTC-TTT
* *
18292 TTACTGATTACCCCTTTTCTTACTGTTT
1 TTACTGATTA-CCATTTT-TTACTCTTT
* * *
18320 TTACTGAATATCACTTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
* * *
18346 TTATTTAATTACCATTTCTTACTCTTT
1 TTA-CTGATTACCATTTTTTACTCTTT
* *
18373 ATTACTAATTACTC-TCTTTTACTCTTTT
1 -TTACTGATTAC-CATTTTTTACTC-TTT
* *
18401 TTACTGATCACCACTTTTTACTCATTT
1 TTACTGATTACCATTTTTTACTC-TTT
18428 CTTACT
1 -TTACT
18434 CTTTTTACTG
Statistics
Matches: 134, Mismatches: 26, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
26 32 0.24
27 68 0.51
28 29 0.22
29 5 0.04
ACGTcount: A:0.21, C:0.22, G:0.03, T:0.54
Consensus pattern (26 bp):
TTACTGATTACCATTTTTTACTCTTT
Found at i:18326 original size:55 final size:53
Alignment explanation
Indices: 18239--18405 Score: 162
Period size: 55 Copynumber: 3.1 Consensus size: 53
18229 TATTTCTTGA
* *
18239 TTACTAATTACCATTTT-TTACTCTTTGTACTGATTACCATATTTTACTCTTTT
1 TTACTAATTACCCTTTTCTTACTCTTTTTACTGATTACCAT-TTTTACTCTTTT
* * * *
18292 TTACTGATTACCCCTTTTCTTACTGTTTTTACTGAATATCACTTTTTACTC-TTT
1 TTACTAATTA-CCCTTTTCTTACTCTTTTTACTGATTACCA-TTTTTACTCTTTT
* * *
18346 TTATTTAATTA-CCATTTCTTACTCTTTATTACTAATTACTC-TCTTTTACTCTTTT
1 TTA-CTAATTACCCTTTTCTTACTCTTT-TTACTGATTAC-CAT-TTTTACTCTTTT
18401 TTACT
1 TTACT
18406 GATCACCACT
Statistics
Matches: 92, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
53 24 0.26
54 29 0.32
55 38 0.41
56 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.03, T:0.56
Consensus pattern (53 bp):
TTACTAATTACCCTTTTCTTACTCTTTTTACTGATTACCATTTTTACTCTTTT
Found at i:18496 original size:22 final size:21
Alignment explanation
Indices: 18469--18549 Score: 56
Period size: 22 Copynumber: 3.7 Consensus size: 21
18459 TTGAATTTAA
18469 TTACTGACTATCATTTTACTCT
1 TTACTGACTATCATTTTACT-T
* **
18491 TTACTGATTATTTTTTTACTTTT
1 TTACTGACTATCATTTTAC--TT
* * *
18514 TTATTGATTA-CTATTTCACTT
1 TTACTGACTATC-ATTTTACTT
*
18535 TTACTGACTACCATT
1 TTACTGACTATCATT
18550 ACTTTTTGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
21 13 0.28
22 17 0.37
23 15 0.33
24 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.05, T:0.56
Consensus pattern (21 bp):
TTACTGACTATCATTTTACTT
Found at i:18534 original size:23 final size:23
Alignment explanation
Indices: 18490--18536 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
18480 CATTTTACTC
* * *
18490 TTTACTGATTATTTTTTTACTTT
1 TTTACTGATTACTATTTCACTTT
*
18513 TTTATTGATTACTATTTCACTTT
1 TTTACTGATTACTATTTCACTTT
18536 T
1 T
18537 ACTGACTACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.19, C:0.11, G:0.04, T:0.66
Consensus pattern (23 bp):
TTTACTGATTACTATTTCACTTT
Found at i:18651 original size:69 final size:67
Alignment explanation
Indices: 18527--18653 Score: 157
Period size: 69 Copynumber: 1.9 Consensus size: 67
18517 TTGATTACTA
* * * *
18527 TTTCACTTTTACTGACTACCATTACTTTTTGAACTTGAACACTGATTACCTTTTTACTTTTCTTC
1 TTTCACTTCTACTGACTACCATTACTCTTTGAACTTGAACACTGACTACCATTTTACTTTTCTTC
18592 AT
66 AT
* * *
18594 TTTCTCTTCTACTGACTACCATTTTACTCTTTGAACTT-AATTACTGACTATCATTTTACT
1 TTTCACTTCTACTGACTACCA--TTACTCTTTGAACTTGAA-CACTGACTACCATTTTACT
18654 CTTTACTGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
67 19 0.38
68 2 0.04
69 29 0.58
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (67 bp):
TTTCACTTCTACTGACTACCATTACTCTTTGAACTTGAACACTGACTACCATTTTACTTTTCTTC
AT
Found at i:18662 original size:22 final size:22
Alignment explanation
Indices: 18634--18883 Score: 167
Period size: 22 Copynumber: 11.5 Consensus size: 22
18624 TTGAACTTAA
* *
18634 TTACTGACTATCATTTTACTCT
1 TTACTGATTACCATTTTACTCT
** *
18656 TTACTGATTA-TTTCTTTACTTTT
1 TTACTGATTACCAT-TTTAC-TCT
* * * *
18679 TTATTAATTACTACTTTACTC-
1 TTACTGATTACCATTTTACTCT
*
18700 TTACTGATT-CC-TATTACTCT
1 TTACTGATTACCATTTTACTCT
* *
18720 TTACTGATTATCACTTTACTCT
1 TTACTGATTACCATTTTACTCT
* * * * *
18742 ATACTAATTACCATTGTACCCA
1 TTACTGATTACCATTTTACTCT
* * *
18764 TTACTGACTACCTTTTTACTTTT
1 TTACTGATTACCATTTTAC-TCT
*
18787 TTACTGATTGCCA--TTACT-T
1 TTACTGATTACCATTTTACTCT
* *
18806 CTTACTGATTACCATATTGCTCT
1 -TTACTGATTACCATTTTACTCT
*
18829 TTACTAATTACCATTTTAC-CTT
1 TTACTGATTACCATTTTACTC-T
18851 TTACTGATTACCATTTTAC-CTT
1 TTACTGATTACCATTTTACTC-T
18873 TTACTGATTAC
1 TTACTGATTAC
18884 ATTATTATAT
Statistics
Matches: 175, Mismatches: 41, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
19 7 0.04
20 23 0.13
21 14 0.08
22 104 0.59
23 26 0.15
24 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.50
Consensus pattern (22 bp):
TTACTGATTACCATTTTACTCT
Found at i:18768 original size:64 final size:64
Alignment explanation
Indices: 18649--18770 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 64
18639 GACTATCATT
** * * * * *
18649 TTACTCTTTACTGATTATTTCTTTACTTTTTTATTAATTACTACTTTACTCTTACTGATTCCTA
1 TTACTCTTTACTGATTATCACTTTACTTCTATACTAATTACCACTTTACCCTTACTGATTCCTA
18713 TTACTCTTTACTGATTATCACTTTAC-TCTATACTAATTACCA-TTGTACCCATTACTGA
1 TTACTCTTTACTGATTATCACTTTACTTCTATACTAATTACCACTT-TACCC-TTACTGA
18771 CTACCTTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
62 2 0.04
63 16 0.33
64 31 0.63
ACGTcount: A:0.25, C:0.21, G:0.04, T:0.50
Consensus pattern (64 bp):
TTACTCTTTACTGATTATCACTTTACTTCTATACTAATTACCACTTTACCCTTACTGATTCCTA
Found at i:18811 original size:87 final size:86
Alignment explanation
Indices: 18700--18881 Score: 226
Period size: 87 Copynumber: 2.1 Consensus size: 86
18690 TACTTTACTC
*
18700 TTACTGATTCCTATTACTCTTTACTGATTATCACT-TTACTCTATACTAATTACCATTGTACCCA
1 TTACTGATTCCTATTACTCTTTACTGATTACCA-TATTACTCTATACTAATTACCATTGTACCCA
* *
18764 TTACTGACTACCTTTTTACTTTT
65 TTACTGACTACCATTTTAC-CTT
* * * *
18787 TTACTGATTGCC-ATTACT-TCTTACTGATTACCATATTGCTCTTTACTAATTACCATTTTACCT
1 TTACTGATT-CCTATTACTCT-TTACTGATTACCATATTACTCTATACTAATTACCATTGTACCC
* *
18850 TTTACTGATTACCATTTTACCTT
64 ATTACTGACTACCATTTTACCTT
18873 TTACTGATT
1 TTACTGATT
18882 ACATTATTAT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
86 13 0.16
87 68 0.82
88 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.05, T:0.48
Consensus pattern (86 bp):
TTACTGATTCCTATTACTCTTTACTGATTACCATATTACTCTATACTAATTACCATTGTACCCAT
TACTGACTACCATTTTACCTT
Found at i:18897 original size:109 final size:106
Alignment explanation
Indices: 18694--18890 Score: 243
Period size: 109 Copynumber: 1.8 Consensus size: 106
18684 AATTACTACT
* *
18694 TTACTCTTACTGATTCCTATTACTCTTTACTGATTATCACTTTACTCTATACTAATTACCATTGT
1 TTACTCTTACTGATTCCTATTACTCTTTACTAATTACCACTTTACTCTATACTAATTACCATTGT
* *
18759 ACCCATTACTGACTACCTTTTTACTTTTTTACTGATTGCCA
66 ACCCATTACTGACTACATTATTACTTTTTTACTGATTGCCA
* * * *
18800 TTACTTCTTACTGATTACCATATTGCTCTTTACTAATTACCATTTTAC-CTTTTACTGATTACCA
1 TTAC-TCTTACTGATT-CC-TATTACTCTTTACTAATTACCACTTTACTC-TATACTAATTACCA
* ** *
18864 TTTTACCTTTTACTGATTACATTATTA
62 TTGTACCCATTACTGACTACATTATTA
18891 TATTTTTTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
106 4 0.05
107 11 0.15
108 3 0.04
109 57 0.76
ACGTcount: A:0.24, C:0.23, G:0.05, T:0.48
Consensus pattern (106 bp):
TTACTCTTACTGATTCCTATTACTCTTTACTAATTACCACTTTACTCTATACTAATTACCATTGT
ACCCATTACTGACTACATTATTACTTTTTTACTGATTGCCA
Found at i:18918 original size:15 final size:14
Alignment explanation
Indices: 18871--18933 Score: 58
Period size: 15 Copynumber: 4.5 Consensus size: 14
18861 CCATTTTACC
*
18871 TTTTACTGATTACA
1 TTTTACTGATTATA
* *
18885 TTATTA-T-ATTTTT
1 TT-TTACTGATTATA
18898 TTTTACTGATTACTA
1 TTTTACTGATTA-TA
*
18913 TTTTACTGATTATC
1 TTTTACTGATTATA
18927 TTTTACT
1 TTTTACT
18934 TTACTGATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
12 3 0.08
13 6 0.15
14 14 0.36
15 16 0.41
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.60
Consensus pattern (14 bp):
TTTTACTGATTATA
Found at i:18957 original size:20 final size:19
Alignment explanation
Indices: 18915--19159 Score: 148
Period size: 20 Copynumber: 13.3 Consensus size: 19
18905 GATTACTATT
*
18915 TTACTGATTATCTTTTACT-
1 TTACTGATTA-CCTTTACTC
18934 TTACTGATTATCCTTTACTC
1 TTACTGATTA-CCTTTACTC
*
18954 TTACTGATCACCTTTCACTC
1 TTACTGATTACCTTT-ACTC
18974 TTACTGATTA---TT--T-
1 TTACTGATTACCTTTACTC
* * *
18987 TTGCTAATTACCCTTTGCTC
1 TTACTGATTA-CCTTTACTC
19007 TTACTGATTA---TT--T-
1 TTACTGATTACCTTTACTC
* * *
19020 TTGCTAATTACCCTTTGCTC
1 TTACTGATTA-CCTTTACTC
19040 TTACTGATTACCTTTTACTC
1 TTACTGATTACC-TTTACTC
* *
19060 TTATTGATTACC----CAC
1 TTACTGATTACCTTTACTC
*
19075 -TAGCTGATTACCTTTTACTT
1 TTA-CTGATTACC-TTTACTC
* *
19095 TTACTGATTACTTTTTGCTC
1 TTACTGATTAC-CTTTACTC
19115 TTACTGATTACCTCTTACTC
1 TTACTGATTACCT-TTACTC
19135 TTACTGATTACCTTTTACTC
1 TTACTGATTACC-TTTACTC
19155 TTACT
1 TTACT
19160 AGTCATCTTT
Statistics
Matches: 177, Mismatches: 22, Indels: 53
0.70 0.09 0.21
Matches are distributed among these distances:
13 16 0.09
14 4 0.02
15 10 0.06
16 2 0.01
17 6 0.03
19 28 0.16
20 108 0.61
21 3 0.02
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.50
Consensus pattern (19 bp):
TTACTGATTACCTTTACTC
Found at i:19008 original size:33 final size:33
Alignment explanation
Indices: 18971--19049 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
18961 TCACCTTTCA
18971 CTCTTACTGATTATTTTTGCTAATTACCCTTTG
1 CTCTTACTGATTATTTTTGCTAATTACCCTTTG
19004 CTCTTACTGATTATTTTTGCTAATTACCCTTTG
1 CTCTTACTGATTATTTTTGCTAATTACCCTTTG
19037 CTCTTACTGATTA
1 CTCTTACTGATTA
19050 CCTTTTACTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.19, C:0.22, G:0.09, T:0.51
Consensus pattern (33 bp):
CTCTTACTGATTATTTTTGCTAATTACCCTTTG
Found at i:19125 original size:40 final size:39
Alignment explanation
Indices: 19033--19176 Score: 138
Period size: 40 Copynumber: 3.7 Consensus size: 39
19023 CTAATTACCC
*
19033 TTTGCTCTTACTGATTACCTTTTACTCTTATTGATTAC-
1 TTTGCTCTTACTGATTACCTTTTACTCTTACTGATTACT
* * *
19071 ---CCAC-TAGCTGATTACCTTTTACTTTTACTGATTACTT
1 TTTGCTCTTA-CTGATTACCTTTTACTCTTACTGATTAC-T
*
19108 TTTGCTCTTACTGATTACCTCTTACTCTTACTGATTACCT
1 TTTGCTCTTACTGATTACCTTTTACTCTTACTGATTA-CT
* * *
19148 TTTACTCTTACT-AGTCATCTTTTACTCTT
1 TTTGCTCTTACTGA-TTACCTTTTACTCTT
19177 TATGTTTATT
Statistics
Matches: 85, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
34 2 0.02
35 28 0.33
39 1 0.01
40 51 0.60
41 3 0.04
ACGTcount: A:0.19, C:0.24, G:0.07, T:0.50
Consensus pattern (39 bp):
TTTGCTCTTACTGATTACCTTTTACTCTTACTGATTACT
Found at i:22226 original size:31 final size:31
Alignment explanation
Indices: 22188--22252 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
22178 CAAAAGCTAA
22188 TTAACCAAAATGACTCTAATGCCAATTCTAT
1 TTAACCAAAATGACTCTAATGCCAATTCTAT
*
22219 TTAACCAAAATGATTCTAATGCCAATTCTAT
1 TTAACCAAAATGACTCTAATGCCAATTCTAT
22250 TTA
1 TTA
22253 GATGTAGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.35
Consensus pattern (31 bp):
TTAACCAAAATGACTCTAATGCCAATTCTAT
Found at i:22317 original size:23 final size:23
Alignment explanation
Indices: 22290--22342 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
22280 GTCCAATTAA
*
22290 ACTAATATGAACCAAATTATATT
1 ACTAAAATGAACCAAATTATATT
22313 ACTAAAATGAACCAAATTATATT
1 ACTAAAATGAACCAAATTATATT
*
22336 ATTAAAA
1 ACTAAAA
22343 CGATTTCATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (23 bp):
ACTAAAATGAACCAAATTATATT
Found at i:22394 original size:32 final size:32
Alignment explanation
Indices: 22344--22408 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
22334 TTATTAAAAC
* *
22344 GATTTCATGTAAGTCAATGCCAAACTACTAAT
1 GATTTCATATAAGACAATGCCAAACTACTAAT
*
22376 GATTTCATATAAGACAATGCCAAACTGCTAAT
1 GATTTCATATAAGACAATGCCAAACTACTAAT
22408 G
1 G
22409 CTAATGCCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (32 bp):
GATTTCATATAAGACAATGCCAAACTACTAAT
Found at i:22434 original size:20 final size:20
Alignment explanation
Indices: 22391--22428 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22381 CATATAAGAC
*
22391 AATGCCAAACTGCTAATGCT
1 AATGCCAAACTACTAATGCT
*
22411 AATGCCTAACTACTAATG
1 AATGCCAAACTACTAATG
22429 TGAATGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (20 bp):
AATGCCAAACTACTAATGCT
Done.