Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014387.1 Corchorus olitorius cultivar O-4 contig14420, 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: 39440
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1554 original size:120 final size:118
Alignment explanation
Indices: 1281--1636 Score: 615
Period size: 118 Copynumber: 3.0 Consensus size: 118
1271 TATTGTTAAC
1281 GCGTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGT
1 GCGTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGT
1346 GGAAAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
66 GGAAAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
* * * *
1399 GCGTTTGGGACCTAAAAATTAAGGAGTAATTTATACTATTTTCAATGGAAGAGTTGGTTTGAAGT
1 GCGTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGT
*
1464 GGAAAATTTAAGGACTTGAGAAATTCCTCAAAACAATATTAATGGTTGTGGTGGA
66 GGAAAATTTAAGGACTT--GAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
**
1519 GCGTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAAA
1 GCGTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGT
1584 GG-AAATTTGAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
66 GGAAAATTT-AAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
1637 TGTTCTTCCA
Statistics
Matches: 223, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
118 113 0.51
119 6 0.03
120 104 0.47
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.34
Consensus pattern (118 bp):
GCGTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGT
GGAAAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
Found at i:2577 original size:29 final size:31
Alignment explanation
Indices: 2522--2593 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 31
2512 ACAAAGTTGC
*
2522 AAGTAGAGGGACTAAATTGACAGTTTT-TAT
1 AAGTAGAGGGACTAAATTGACACTTTTGTAT
** *
2552 -AGTAGAGGGA-TCAAATTGATTCTTTTGTGT
1 AAGTAGAGGGACT-AAATTGACACTTTTGTAT
2582 AAGTAGAGGGAC
1 AAGTAGAGGGAC
2594 CTGTGGAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 1 0.03
29 21 0.62
30 2 0.06
31 10 0.29
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.32
Consensus pattern (31 bp):
AAGTAGAGGGACTAAATTGACACTTTTGTAT
Found at i:3161 original size:28 final size:28
Alignment explanation
Indices: 3085--3162 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 28
3075 TTTTTTTTTT
3085 TCATCAAAATCATAAATTATGGCAAAAA
1 TCATCAAAATCATAAATTATGGCAAAAA
** * *
3113 AAATCATAA--ATAGATTA----AAAAA
1 TCATCAAAATCATAAATTATGGCAAAAA
3135 TCATCAAAATCATAAATTATGGCAAAAA
1 TCATCAAAATCATAAATTATGGCAAAAA
3163 AGAAAAAATC
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
22 11 0.31
24 7 0.19
26 7 0.19
28 11 0.31
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (28 bp):
TCATCAAAATCATAAATTATGGCAAAAA
Found at i:3310 original size:54 final size:56
Alignment explanation
Indices: 3211--3320 Score: 154
Period size: 54 Copynumber: 2.0 Consensus size: 56
3201 AATTTTTTTC
** * *
3211 CATCAAAATCATAAATTATGGCAAAAAAAAATCATAAATAGATAAA-A-ATAAAAT
1 CATCAAAATCATAAATTATGGCAAAAAAAAAAAAAAAATACATAAATACATAAAAT
3265 CATCAAAATCATAAATTATGGCAAAAAAGAAAAAAAAAAT-CATAAATACATAAAAT
1 CATCAAAATCATAAATTATGGCAAAAAA-AAAAAAAAAATACATAAATACATAAAAT
3321 TGAACCAACT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
54 33 0.67
55 9 0.18
56 7 0.14
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (56 bp):
CATCAAAATCATAAATTATGGCAAAAAAAAAAAAAAAATACATAAATACATAAAAT
Found at i:5066 original size:54 final size:54
Alignment explanation
Indices: 4978--5105 Score: 199
Period size: 54 Copynumber: 2.4 Consensus size: 54
4968 GCTCTGAGAA
* *
4978 ATAATTCATAAAAACAAATAAATAAATATAATAAATCACATATTAATTTGTAAT
1 ATAAATCATAAAAATAAATAAATAAATATAATAAATCACATATTAATTTGTAAT
5032 CATAAATCATAAAAATAAA-AAATAAATATAATAAATCACATATTAATTTGTAAT
1 -ATAAATCATAAAAATAAATAAATAAATATAATAAATCACATATTAATTTGTAAT
5086 AT-AA-CATAAAAATAATATAA
1 ATAAATCATAAAAATAA-ATAA
5106 TTTTCGTCTT
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
51 11 0.16
52 3 0.04
53 4 0.06
54 35 0.51
55 16 0.23
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (54 bp):
ATAAATCATAAAAATAAATAAATAAATATAATAAATCACATATTAATTTGTAAT
Found at i:7900 original size:20 final size:19
Alignment explanation
Indices: 7866--7903 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
7856 ATGATTACTA
*
7866 AAAACAATTAGAGGTTATC
1 AAAACAATTAAAGGTTATC
7885 AAAACAATTATAAGGTTAT
1 AAAACAATTA-AAGGTTAT
7904 TAATAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAACAATTAAAGGTTATC
Found at i:9651 original size:116 final size:116
Alignment explanation
Indices: 9525--9761 Score: 447
Period size: 116 Copynumber: 2.0 Consensus size: 116
9515 TAATGTCTAA
9525 AAAAATGTACTTTAACGTAAAAATAATTAGTATTATCTTAGACTTTTAAAATATGGAAATAAAAT
1 AAAAATGTACTTTAACGTAAAAATAATTAGTATTATCTTAGACTTTTAAAATATGGAAATAAAAT
* *
9590 CTGGTTGGATTACATATTAATCCTTAAAAATATAAATAAAATTTTAAAATT
66 CTGATTGGATTACATATTAATCCTTAAAAATATAAATAAAATTATAAAATT
*
9641 AAAAATGTACTTTAACGTAAAAATAATTAGTATTATCTTAGACTTTTTAAATATGGAAATAAAAT
1 AAAAATGTACTTTAACGTAAAAATAATTAGTATTATCTTAGACTTTTAAAATATGGAAATAAAAT
9706 CTGATTGGATTACATATTAATCCTTAAAAATATAAATAAAATTATAAAATT
66 CTGATTGGATTACATATTAATCCTTAAAAATATAAATAAAATTATAAAATT
9757 AAAAA
1 AAAAA
9762 GGGTATTTTA
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 118 1.00
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (116 bp):
AAAAATGTACTTTAACGTAAAAATAATTAGTATTATCTTAGACTTTTAAAATATGGAAATAAAAT
CTGATTGGATTACATATTAATCCTTAAAAATATAAATAAAATTATAAAATT
Found at i:11449 original size:23 final size:22
Alignment explanation
Indices: 11383--11494 Score: 113
Period size: 22 Copynumber: 5.1 Consensus size: 22
11373 AAAAAAAACC
* *
11383 TCATAGGGAGGTTATCAAAA-A
1 TCATAGGAAGGTTATCAAAATT
11404 TCATAGGAAGGTTA-CAAAATT
1 TCATAGGAAGGTTATCAAAATT
*
11425 TCATAGGAAGGTTTATTAAAATT
1 TCATAGGAAGG-TTATCAAAATT
** *
11448 TCATAGTTAGGTTATCAAAAGT
1 TCATAGGAAGGTTATCAAAATT
* *
11470 TCATATGG-AGTTTATCACAATT
1 TCATA-GGAAGGTTATCAAAATT
11492 TCA
1 TCA
11495 ATAGTAACTA
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
20 5 0.07
21 24 0.32
22 31 0.41
23 16 0.21
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (22 bp):
TCATAGGAAGGTTATCAAAATT
Found at i:11699 original size:22 final size:22
Alignment explanation
Indices: 11641--11717 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 22
11631 AATAACGATA
* ** *
11641 TTATGAAATTTCGAGAACCTTT
1 TTATGAAATTTTGTTAACCTTC
*
11663 TTAT--AATTTTTTTAACCTTC
1 TTATGAAATTTTGTTAACCTTC
*
11683 TTATGAAATTTTGTTAACCTCC
1 TTATGAAATTTTGTTAACCTTC
* *
11705 TTAAGGAATTTTG
1 TTATGAAATTTTG
11718 AAGACCTCAC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 15 0.34
22 29 0.66
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (22 bp):
TTATGAAATTTTGTTAACCTTC
Found at i:11876 original size:22 final size:22
Alignment explanation
Indices: 11838--11897 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
11828 AAGACCTCCA
*
11838 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* *
11860 TCTGAAATTTTGATAATCACAC
1 TATGAAATTGTGATAATCACAC
11882 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
11898 CTTTGCTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:11965 original size:23 final size:22
Alignment explanation
Indices: 11903--11966 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
11893 GATAACTTTG
* *
11903 CTATGAAATTTTAGTAAACCTTC
1 CTATAAAATTTTA-TAAACCTCC
11926 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTT-ATAAACCTCC
11949 CTATAAAATTTCTATAAA
1 CTATAAAATTT-TATAAA
11967 ATTTTGATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 35 0.95
24 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.38
Consensus pattern (22 bp):
CTATAAAATTTTATAAACCTCC
Found at i:11990 original size:22 final size:22
Alignment explanation
Indices: 11965--12121 Score: 141
Period size: 22 Copynumber: 7.4 Consensus size: 22
11955 AATTTCTATA
11965 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCCTTATG
* *
11987 AAATCTTGATAA----C-TA-C
1 AAATTTTGATAACCTCCTTATG
*
12003 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCCTTATG
** *
12025 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCTTATG
* * *
12047 AAATTTTGCTAATCTCCCTATG
1 AAATTTTGATAACCTCCTTATG
* *
12069 AAATTTTGATCAACATAC-TATG
1 AAATTTTGAT-AACCTCCTTATG
12091 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CTTATG
12113 AAATTTTGA
1 AAATTTTGA
12122 AAACTAAACT
Statistics
Matches: 106, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
16 11 0.10
17 2 0.02
18 1 0.01
20 1 0.01
21 6 0.06
22 81 0.76
23 4 0.04
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTCCTTATG
Found at i:12037 original size:38 final size:38
Alignment explanation
Indices: 11931--12025 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 38
11921 CCTTCCTATA
* *
11931 AAATTTTGATAAACCTCCCTATAAAAT-TT-CT-A-TA-
1 AAATTTTGAT-AACCTCCCTATGAAATCTTGATAACTAC
*
11965 AAATTTTGATAACCTCCTTATGAAATCTTGATAACTAC
1 AAATTTTGATAACCTCCCTATGAAATCTTGATAACTAC
12003 AAATTTTGATAACCTCCCTATGA
1 AAATTTTGATAACCTCCCTATGA
12026 TTTTTTGATA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
33 14 0.27
34 12 0.23
35 1 0.02
36 1 0.02
37 2 0.04
38 22 0.42
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (38 bp):
AAATTTTGATAACCTCCCTATGAAATCTTGATAACTAC
Found at i:12066 original size:44 final size:44
Alignment explanation
Indices: 11960--12144 Score: 172
Period size: 44 Copynumber: 4.3 Consensus size: 44
11950 TATAAAATTT
* * *
11960 CTATAAAATTTTGATAACCTCCTTATGAAATCTTGAT-AAC-TA
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATCAACATA
** *
12002 C----AAATTTTGATAACCTCCCTATGATTTTTTGAT-AACCTCA
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATCAACAT-A
* * *
12042 TTATGAAATTTTGCTAATCTCCCTATGAAATTTTGATCAACATA
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATCAACATA
* * *
12086 CTATGAAATTTTGATAACC-CTCTTATGAAATTTTGA-AAACTAAA
1 CTATGAAATTTTGATAACCTC-CCTATGAAATTTTGATCAAC-ATA
12130 CTATGAAATTTTGAT
1 CTATGAAATTTTGAT
12145 TACTCCATAA
Statistics
Matches: 118, Mismatches: 16, Indels: 16
0.79 0.11 0.11
Matches are distributed among these distances:
38 31 0.26
39 1 0.01
40 1 0.01
42 1 0.01
43 4 0.03
44 76 0.64
45 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATCAACATA
Found at i:12134 original size:22 final size:21
Alignment explanation
Indices: 12064--12143 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 21
12054 GCTAATCTCC
* *
12064 CTATGAAATTTTGATCAACATA
1 CTATGAAATTTTGA-AAACAAA
* ***
12086 CTATGAAATTTTGATAACCCT
1 CTATGAAATTTTGAAAACAAA
12107 CTTATGAAATTTTGAAAACTAAA
1 C-TATGAAATTTTGAAAAC-AAA
12130 CTATGAAATTTTGA
1 CTATGAAATTTTGA
12144 TTACTCCATA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.08
22 43 0.90
23 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
CTATGAAATTTTGAAAACAAA
Found at i:12275 original size:22 final size:22
Alignment explanation
Indices: 12250--12818 Score: 250
Period size: 22 Copynumber: 25.7 Consensus size: 22
12240 AATCACATTT
* *
12250 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
*
12272 TGAAATTTTGATAACATCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
12294 TGAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
12316 TGAAATTTTGATAACTTCGCT-
1 TGAAATTTTGATAACCTCTCTA
**
12337 TCGAAATTTTGATAA---C-AAA
1 T-GAAATTTTGATAACCTCTCTA
12356 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* *
12380 TGAAATTTTGATAAATCACTCTA
1 TGAAATTTTGAT-AACCTCTCTA
*
12403 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* *
12423 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
* * *
12443 TGAAATTGAGACTTTTATAA-CTTTCATG
1 TGAAA-T-----TTTGATAACCTCTC-TA
* *
12471 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
12493 TGAAATCTTGATAACCTGC-CCA
1 TGAAATTTTGATAACCT-CTCTA
* *
12515 TGAAATATT-AGTAAACTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* *
12537 TGAAATTTT-ATCAACCACACTA
1 TGAAATTTTGAT-AACCTCTCTA
*
12559 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCTCTA
* * * *
12581 TGACATTTTGATAATCTTTTTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
12603 TAAAATTGTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
**
12625 TGAAATTTCAATAACCT-TCTGA
1 TGAAATTTTGATAACCTCTCT-A
* * *
12647 AGAAATTTTAATAACCTAATGCTA
1 TGAAATTTTGATAACCT-CT-CTA
* * * *
12671 TGAAATTTTGGTAAGCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
12693 TGAAATTTTGATAACCT-TCCCA
1 TGAAATTTTGATAACCTCT-CTA
*
12715 TGAAATTTTGATAACTTC-CATA
1 TGAAATTTTGATAACCTCTC-TA
* ** *
12737 TGAAAGTTT-AGTAACAACACTA
1 TGAAATTTTGA-TAACCTCTCTA
* *
12759 TGGAATTTCGATAACCTC-CTCA
1 TGAAATTTTGATAACCTCTCT-A
*
12781 TGAAATTAT-ATTAACCATCT-TA
1 TGAAATTTTGA-TAACC-TCTCTA
12803 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
12819 ACACAGAGAC
Statistics
Matches: 409, Mismatches: 93, Indels: 90
0.69 0.16 0.15
Matches are distributed among these distances:
17 12 0.03
19 5 0.01
20 14 0.03
21 23 0.06
22 285 0.70
23 24 0.06
24 16 0.04
25 13 0.03
26 6 0.01
27 4 0.01
28 7 0.02
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:13023 original size:20 final size:20
Alignment explanation
Indices: 12985--13023 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12975 TATTAACATT
12985 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
13005 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
13024 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:36236 original size:30 final size:30
Alignment explanation
Indices: 36200--36592 Score: 543
Period size: 30 Copynumber: 13.0 Consensus size: 30
36190 CAATTTTTTT
* * *
36200 TCTTACAAATGACACCAGAAGTTGTCATGG
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
* *
36230 TCTTACAATTGACACCAGAAGTTGTCATGG
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
* * *
36260 TCTTACAAATGACACCAGAAGTTGTCATAA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
*
36290 TCTTGCAATTGACACCAGAAGTTGTCATGC
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
*
36320 TCTTGCAATTGACACCAGAAGTTGTCATAA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
36350 TCTTGCAATTGACACCAGAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
*
36380 TTTTGCAATTGACACCAGAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
* *
36410 TTTTGCAATTGACATCAGAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
* *
36440 TGTTGCAATTGACACCAAAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
* *
36470 TGTTGCAATTGACACCATAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
*
36500 TCTTGCAATTGACACCATAAGTTGTCATGA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
* ** * *
36530 TCTTGCAATTGATACTTGAAGATGTCATAA
1 TCTTGCAATTGACACCAGAAGTTGTCATGA
* *
36560 TTTTATTCAATTGACACCAGAAGTTGTCATGA
1 -TCT-TGCAATTGACACCAGAAGTTGTCATGA
36592 T
1 T
36593 AAATTTCCAA
Statistics
Matches: 330, Mismatches: 31, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
30 306 0.93
31 3 0.01
32 21 0.06
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (30 bp):
TCTTGCAATTGACACCAGAAGTTGTCATGA
Found at i:36572 original size:32 final size:32
Alignment explanation
Indices: 36209--36661 Score: 196
Period size: 30 Copynumber: 14.8 Consensus size: 32
36199 TTCTTACAAA
* ** *
36209 TGACACCAGAAGTTGTCATGGTCTTA--CAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* ** * *
36239 TGACACCAGAAGTTGTCATGGTCTTA--CAAA
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * *
36269 TGACACCAGAAGTTGTCATAA-TCT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* ** * *
36299 TGACACCAGAAGTTGTCAT-GCTCT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * *
36329 TGACACCAGAAGTTGTCATAA-TCT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * *
36359 TGACACCAGAAGTTGTCATGA-TTT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * *
36389 TGACACCAGAAGTTGTCATGA-TTT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * * * *
36419 TGACATCAGAAGTTGTCATGA-TGT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * * * *
36449 TGACACCAAAAGTTGTCATGA-TGT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * * * *
36479 TGACACCATAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* * * * *
36509 TGACACCATAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* **
36539 TGATACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* ** *
36571 TGACACCAGAAGTTGTCATGATAAATT-TCCAAT
1 TGACACCAGAAGATGTCAT-A-ATTTTATTCAAT
* ***
36604 AGACATTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGATGTCATAATTTTATTCAAT
* *
36636 TGACACCAGAAGTTGTCATGATTTTA
1 TGACACCAGAAGATGTCATAATTTTA
36662 CCTTTCAAAA
Statistics
Matches: 369, Mismatches: 45, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
29 1 0.00
30 294 0.80
31 5 0.01
32 46 0.12
33 20 0.05
34 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (32 bp):
TGACACCAGAAGATGTCATAATTTTATTCAAT
Found at i:36634 original size:65 final size:62
Alignment explanation
Indices: 36209--36657 Score: 310
Period size: 60 Copynumber: 7.4 Consensus size: 62
36199 TTCTTACAAA
* * * ** * ** * *
36209 TGACACCAGAAGTTGTCATGGTCTTACAATTGACACCAGAAGTTGTCATGGTCTTA--CAAA
1 TGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATTCAAT
* * * ** * ** * *
36269 TGACACCAGAAGTTGTCATAATCTTGCAATTGACACCAGAAGTTGTCAT-GCTCT-TGCAAT
1 TGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATTCAAT
* * * ** * * *
36329 TGACACCAGAAGTTGTCATAATCTTGCAATTGACACCAGAAGTTGTCATGA-TTT-TGCAAT
1 TGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATTCAAT
* * * * * * * *
36389 TGACACCAGAAGTTGTCATGATTTTGCAATTGACA-TCAGAAGTTGTCATGA-TGT-TGCAAT
1 TGACACCAGAAGTTGTCATGATCTTCCAATAGACACT-TGAAGATGTCATAATTTTATTCAAT
* * * * * * * * *
36449 TGACACCAAAAGTTGTCATGATGTTGCAATTGACACCAT-AAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATGATCTTCCAATAGACA-CTTGAAGATGTCATAATTTTATTCAAT
* * * *
36509 TGACACCATAAGTTGTCATGATCTTGCAATTGATACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATTCAAT
* *
36571 TGACACCAGAAGTTGTCATGATAAATTTCCAATAGACATTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGAT---CTTCCAATAGACACTTGAAGATGTCATAATTTTATTCAAT
36636 TGACACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
36658 TTTACCTTTC
Statistics
Matches: 345, Mismatches: 32, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
59 4 0.01
60 256 0.74
61 2 0.01
62 26 0.08
65 57 0.17
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (62 bp):
TGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATTCAAT
Done.