Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013370.1 Corchorus capsularis cultivar CVL-1 contig13391, 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: 87753
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2203 original size:3 final size:3
Alignment explanation
Indices: 2195--2226 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2185 ATTTACTTTT
2195 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2227 TCTCAGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4384 original size:28 final size:27
Alignment explanation
Indices: 4331--4403 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
4321 AACAAAACTC
4331 AATTATTTATTATTATTATCTCAAAAAA
1 AATTATTTATTATTATTATCTC-AAAAA
* * * *
4359 AATTATTTATTATTGCTT-TTTTAAAAG
1 AATTATTTATTATT-ATTATCTCAAAAA
4386 AA-TATTTATTATTATTAT
1 AATTATTTATTATTATTAT
4404 TATTATTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 2 0.05
26 12 0.32
27 6 0.16
28 16 0.42
29 2 0.05
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (27 bp):
AATTATTTATTATTATTATCTCAAAAA
Found at i:4399 original size:3 final size:3
Alignment explanation
Indices: 4391--4425 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4381 AAAAGAATAT
4391 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4426 GTTTTGGCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4644 original size:29 final size:29
Alignment explanation
Indices: 4607--4666 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
4597 AAAATAAAGC
* *
4607 TACCCATTTTAGATAAAAACTACCCATTA
1 TACCAATTTTAGAAAAAAACTACCCATTA
4636 TACCAATTTTAGAAAAAAACTACCCATTA
1 TACCAATTTTAGAAAAAAACTACCCATTA
4665 TA
1 TA
4667 AGATAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (29 bp):
TACCAATTTTAGAAAAAAACTACCCATTA
Found at i:4688 original size:13 final size:13
Alignment explanation
Indices: 4670--4700 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
4660 CATTATAAGA
4670 TAAATATAATATT
1 TAAATATAATATT
4683 TAAATATAATATT
1 TAAATATAATATT
4696 TAAAT
1 TAAAT
4701 TTATTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATATAATATT
Found at i:4947 original size:51 final size:51
Alignment explanation
Indices: 4871--4968 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
4861 CTCACTACAA
*
4871 TCTATACTAATTATAATGCTAAAACCTGAGGTTGTCTCACGAGTTGACTCG
1 TCTATACTAATTATAATGCCAAAACCTGAGGTTGTCTCACGAGTTGACTCG
*
4922 TCTATACTAATTATAATGCCAAAACCTGAGTTTGTCTCACGAGTTGA
1 TCTATACTAATTATAATGCCAAAACCTGAGGTTGTCTCACGAGTTGA
4969 TTCGGAGACA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (51 bp):
TCTATACTAATTATAATGCCAAAACCTGAGGTTGTCTCACGAGTTGACTCG
Found at i:5265 original size:37 final size:37
Alignment explanation
Indices: 5218--5291 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
5208 TCTACAGAAA
*
5218 CTACATAAACTATCTTCATCTTTCTCATTCCATATTT
1 CTACAGAAACTATCTTCATCTTTCTCATTCCATATTT
5255 CTACAGAAACTATCTTCATCTTTCTCATTCCATATTT
1 CTACAGAAACTATCTTCATCTTTCTCATTCCATATTT
5292 TGGGAGACAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.01, T:0.45
Consensus pattern (37 bp):
CTACAGAAACTATCTTCATCTTTCTCATTCCATATTT
Found at i:12342 original size:15 final size:15
Alignment explanation
Indices: 12322--12353 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12312 AACTTACTAA
*
12322 AAAGAATAAAAATAG
1 AAAGAAGAAAAATAG
12337 AAAGAAGAAAAATAG
1 AAAGAAGAAAAATAG
12352 AA
1 AA
12354 GACACGTGGT
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:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (15 bp):
AAAGAAGAAAAATAG
Found at i:14697 original size:2 final size:2
Alignment explanation
Indices: 14690--14726 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
14680 TTAACTAAAT
14690 TA TA TA TA TA -A T- TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14727 ATTAAAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14704 original size:12 final size:12
Alignment explanation
Indices: 14687--14730 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 12
14677 CAATTAACTA
14687 AATTATATATAT
1 AATTATATATAT
14699 AATTATATATAT
1 AATTATATATAT
14711 ATATATATATTATAT
1 A-AT-TATA-TATAT
14726 AATTA
1 AATTA
14731 AAGATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 13 0.45
13 4 0.14
14 6 0.21
15 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTATATATAT
Found at i:14707 original size:8 final size:9
Alignment explanation
Indices: 14692--14730 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
14682 AACTAAATTA
14692 TATATATAAT
1 TATATAT-AT
14702 TATATATAT
1 TATATATAT
14711 ATATATATAT
1 -TATATATAT
14721 TATATA-AT
1 TATATATAT
14729 TA
1 TA
14731 AAGATAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.14
9 8 0.29
10 16 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TATATATAT
Found at i:14968 original size:42 final size:43
Alignment explanation
Indices: 14898--14980 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
14888 CTTAAACGTG
*
14898 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC
*
14941 TTAATCGTGTC-CGACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATTAC-GACACGAAACACGATAA
14981 GCCAAACACG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 1 0.03
42 25 0.68
43 11 0.30
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC
Found at i:27323 original size:17 final size:17
Alignment explanation
Indices: 27301--27361 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
27291 CGTCTGCCTA
*
27301 TTTTCTTTTTTCTTTTC
1 TTTTCTTTTTCCTTTTC
27318 TTTTCTTTTTCCTTTTTC
1 TTTTCTTTTTCC-TTTTC
* * *
27336 TCTTTC-TCTCCCTTTTT
1 T-TTTCTTTTTCCTTTTC
27353 TTTTCTTTT
1 TTTTCTTTT
27362 AAGTTTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
16 4 0.11
17 18 0.50
18 10 0.28
19 4 0.11
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCTTTTTCCTTTTC
Found at i:36449 original size:2 final size:2
Alignment explanation
Indices: 36442--36474 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36432 ATTCTCTGTA
36442 TG TG TG TG 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 TG TG TG TG T
36475 CTGTCTGTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:37701 original size:78 final size:78
Alignment explanation
Indices: 37572--37729 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
37562 GTGACTAGTT
37572 TTAACCATATTGGCTGTGTCAGCAAGAGAGAAGTTGCTAAAACCTCAGTGGAGATTATTTGGACT
1 TTAACCATATTGGCTGTGTCAGCAAGAGAGAAGTTGCTAAAACCTCAGTGGAGATTATTTGGACT
37637 TTGTAGGTTATTG
66 TTGTAGGTTATTG
37650 TTAACCATATTGGCTGTGTCAGCAAGAGAGAAGTTGCTAAAACCTCAGTGGAGATTATTTGGACT
1 TTAACCATATTGGCTGTGTCAGCAAGAGAGAAGTTGCTAAAACCTCAGTGGAGATTATTTGGACT
37715 TTGTAGGTTATTG
66 TTGTAGGTTATTG
37728 TT
1 TT
37730 GACTACGTCT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (78 bp):
TTAACCATATTGGCTGTGTCAGCAAGAGAGAAGTTGCTAAAACCTCAGTGGAGATTATTTGGACT
TTGTAGGTTATTG
Found at i:38382 original size:181 final size:181
Alignment explanation
Indices: 38078--38425 Score: 635
Period size: 181 Copynumber: 1.9 Consensus size: 181
38068 TGGGTTACCA
* * *
38078 GGGTTTTATGCTTCTGTTTTAAACTCAAACAATTCTGTTTTGCCTGTGCTAGGCTGTAAAAGCTT
1 GGGTTTTATGCTTCTGCTTTAAACTCAAACAATTCTGCTTTGCCTGTGCTAGGCAGTAAAAGCTT
*
38143 TTCAGGTTTTCAGTTTGTACTTTGACCTTACTAATATAGAGCATACATTATTGGTCAAGAGGTTT
66 TTCAGGTTTTCACTTTGTACTTTGACCTTACTAATATAGAGCATACATTATTGGTCAAGAGGTTT
*
38208 CATTATGTTTTAACTTTGGGAGGGTACAATTTTGTCAAGAGAGGTTATTGG
131 CATTATGTTTCAACTTTGGGAGGGTACAATTTTGTCAAGAGAGGTTATTGG
38259 GGGTTTTATGCTTCTGCTTTAAACTCAAACAATTCTGCTTTGCCTGTGCTAGGCAGTAAAAGCTT
1 GGGTTTTATGCTTCTGCTTTAAACTCAAACAATTCTGCTTTGCCTGTGCTAGGCAGTAAAAGCTT
38324 TTCAGGTTTTCACTTTGTACTTTGACCTTACTAATATAGAGCATACATTCA-TGGTCAAGAGGTT
66 TTCAGGTTTTCACTTTGTACTTTGACCTTACTAATATAGAGCATACATT-ATTGGTCAAGAGGTT
38388 TCATTATGTTTCAACTTTGGGAGGGTACAATTTTGTCA
130 TCATTATGTTTCAACTTTGGGAGGGTACAATTTTGTCA
38426 CATCGAGTTG
Statistics
Matches: 161, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
181 160 0.99
182 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (181 bp):
GGGTTTTATGCTTCTGCTTTAAACTCAAACAATTCTGCTTTGCCTGTGCTAGGCAGTAAAAGCTT
TTCAGGTTTTCACTTTGTACTTTGACCTTACTAATATAGAGCATACATTATTGGTCAAGAGGTTT
CATTATGTTTCAACTTTGGGAGGGTACAATTTTGTCAAGAGAGGTTATTGG
Found at i:38892 original size:27 final size:27
Alignment explanation
Indices: 38830--38894 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
38820 CAGAGTATTC
* *
38830 CATTTTCCCCAATCGCTTTAGTGTAGT
1 CATTTTCCTCTATCGCTTTAGTGTAGT
38857 CATTTTCCTCTATCGCTTTAGTGTAGT
1 CATTTTCCTCTATCGCTTTAGTGTAGT
38884 CATTTTCCTCT
1 CATTTTCCTCT
38895 TTCTTTGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.15, C:0.26, G:0.12, T:0.46
Consensus pattern (27 bp):
CATTTTCCTCTATCGCTTTAGTGTAGT
Found at i:40370 original size:2 final size:2
Alignment explanation
Indices: 40363--40389 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40353 AGTTTAATTA
40363 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
40390 GCATCAGCAT
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:42181 original size:2 final size:2
Alignment explanation
Indices: 42169--42207 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
42159 AAAATAATTG
42169 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42208 GACATATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:50090 original size:2 final size:2
Alignment explanation
Indices: 50048--50074 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50038 AATTTAATTA
50048 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
50075 AAACAAAATA
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:56763 original size:28 final size:28
Alignment explanation
Indices: 56728--56782 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
56718 TGTTATATTG
*
56728 ATGCATCTTAA-CTTTTCTGTTTTATTAT
1 ATGCATCTTAACCTTTT-TATTTTATTAT
56756 ATGCATCTTAACCTTTTTATTTTATTA
1 ATGCATCTTAACCTTTTTATTTTATTA
56783 CATTCCTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (28 bp):
ATGCATCTTAACCTTTTTATTTTATTAT
Found at i:59635 original size:3 final size:3
Alignment explanation
Indices: 59627--59666 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
59617 CTTTCTTTCT
59627 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
59667 TTTTTTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:59669 original size:9 final size:9
Alignment explanation
Indices: 59622--59679 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
59612 GTGTTCTTTC
59622 TTTCTTTCTT
1 TTTC-TTCTT
*
59632 CTTCTTCTT
1 TTTCTTCTT
*
59641 CTTCTTCTT
1 TTTCTTCTT
*
59650 CTTCTTC-T
1 TTTCTTCTT
59658 TTTCTTCTTT
1 TTTCTTC-TT
*
59668 TTTTTTCTT
1 TTTCTTCTT
59677 TTT
1 TTT
59680 TTCCTTCAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
8 7 0.16
9 26 0.60
10 10 0.23
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:70493 original size:20 final size:20
Alignment explanation
Indices: 70469--70530 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
70459 TTAATTAAAA
70469 AAAAAACTTATAAGGTTACT
1 AAAAAACTTATAAGGTTACT
* *
70489 TAAAAAC-TATAAAAGTTA-T
1 AAAAAACTTAT-AAGGTTACT
70508 AAAAAATGCTTATAAGGTTACT
1 AAAAAA--CTTATAAGGTTACT
70530 A
1 A
70531 CAATAGAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 9 0.27
20 12 0.36
21 7 0.21
22 5 0.15
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.31
Consensus pattern (20 bp):
AAAAAACTTATAAGGTTACT
Found at i:87216 original size:22 final size:21
Alignment explanation
Indices: 87180--87361 Score: 145
Period size: 22 Copynumber: 8.3 Consensus size: 21
87170 GTTCATCTCA
*
87180 TTCATAGGG-GGTTACCAAAT
1 TTCATAGGGAGATTACCAAAT
* *
87200 TTACATGGGGAGATTACAAAAT
1 TT-CATAGGGAGATTACCAAAT
**
87222 TTCATAGTTAAGA-TACCAAATT
1 TTCATAG-GGAGATTACCAAA-T
* *
87244 TTCATAGGGAGGTTAACAAAAT
1 TTCATAGGGAGATT-ACCAAAT
* *
87266 TTCATAGGTAAGTTTACCAAATT
1 TTCATAGG-GAGATTACCAAA-T
*
87289 TTCATAGGGAGGTTACCAAAAT
1 TTCATAGGGAGATTACC-AAAT
*
87311 TTCATAGGTA-AGTTACCAAATT
1 TTCATAGGGAGA-TTACCAAA-T
*
87333 TTCATAGGGAGGTTACCAAAAT
1 TTCATAGGGAGATTACC-AAAT
87355 TTCATAG
1 TTCATAG
87362 CGTGGTAATG
Statistics
Matches: 129, Mismatches: 20, Indels: 24
0.75 0.12 0.14
Matches are distributed among these distances:
20 2 0.02
21 21 0.16
22 82 0.64
23 24 0.19
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (21 bp):
TTCATAGGGAGATTACCAAAT
Found at i:87328 original size:89 final size:88
Alignment explanation
Indices: 87191--87361 Score: 279
Period size: 89 Copynumber: 1.9 Consensus size: 88
87181 TCATAGGGGG
* *
87191 TTACCAAATTTACATGGGGAGATTACAAAATTTCATAGTTAAGATACCAAATTTTCATAGGGAGG
1 TTACCAAATTTACATAGGGAGATTACAAAATTTCATAGGTAAGATACCAAATTTTCATAGGGAGG
87256 TTAACAAAATTTCATAGGTAAGT
66 TTAACAAAATTTCATAGGTAAGT
* * *
87279 TTACCAAATTTTCATAGGGAGGTTACCAAAATTTCATAGGTAAGTTACCAAATTTTCATAGGGAG
1 TTACCAAATTTACATAGGGAGATTA-CAAAATTTCATAGGTAAGATACCAAATTTTCATAGGGAG
*
87344 GTTACCAAAATTTCATAG
65 GTTAACAAAATTTCATAG
87362 CGTGGTAATG
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 22 0.29
89 54 0.71
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (88 bp):
TTACCAAATTTACATAGGGAGATTACAAAATTTCATAGGTAAGATACCAAATTTTCATAGGGAGG
TTAACAAAATTTCATAGGTAAGT
Found at i:87342 original size:44 final size:44
Alignment explanation
Indices: 87190--87361 Score: 274
Period size: 44 Copynumber: 3.9 Consensus size: 44
87180 TTCATAGGGG
* * * *
87190 GTTACCAAATTTACATGGGGAGATTA-CAAAATTTCATAGTTAA
1 GTTACCAAATTTTCATAGGGAGGTTACCAAAATTTCATAGGTAA
* *
87233 GATACCAAATTTTCATAGGGAGGTTAACAAAATTTCATAGGTAA
1 GTTACCAAATTTTCATAGGGAGGTTACCAAAATTTCATAGGTAA
87277 GTTTACCAAATTTTCATAGGGAGGTTACCAAAATTTCATAGGTAA
1 G-TTACCAAATTTTCATAGGGAGGTTACCAAAATTTCATAGGTAA
87322 GTTACCAAATTTTCATAGGGAGGTTACCAAAATTTCATAG
1 GTTACCAAATTTTCATAGGGAGGTTACCAAAATTTCATAG
87362 CGTGGTAATG
Statistics
Matches: 120, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
43 22 0.18
44 56 0.47
45 42 0.35
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (44 bp):
GTTACCAAATTTTCATAGGGAGGTTACCAAAATTTCATAGGTAA
Done.