Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018574.1 Corchorus olitorius cultivar O-4 contig18607, 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: 40687
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:2401 original size:18 final size:18
Alignment explanation
Indices: 2378--2419 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
2368 CAACTAAAAT
2378 GGTTTTCAAAAGAGTC-AA
1 GGTTTTCAAAAGA-TCTAA
2396 GGTTTTCAAAAGATCTAA
1 GGTTTTCAAAAGATCTAA
2414 GGTTTT
1 GGTTTT
2420 TGAAACTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (18 bp):
GGTTTTCAAAAGATCTAA
Found at i:4499 original size:22 final size:22
Alignment explanation
Indices: 4452--4616 Score: 206
Period size: 22 Copynumber: 7.5 Consensus size: 22
4442 GTTTTAAACA
*
4452 TCTCAGGGCAGACTTTTAA-CG
1 TCTCAGGGCAGACTTTCAAGCG
* * *
4473 TCTCAGGGTAGGCTTCCAAGCG
1 TCTCAGGGCAGACTTTCAAGCG
4495 TCTCAGGGCAGACTTTCAAGCG
1 TCTCAGGGCAGACTTTCAAGCG
* *
4517 TCTTAGAGCAGACTTTCAAGCG
1 TCTCAGGGCAGACTTTCAAGCG
* *
4539 TCTCAGGGCAGGCTTCCAAGCG
1 TCTCAGGGCAGACTTTCAAGCG
* ** *
4561 TCTCAAGGTGGACTATCAAGCG
1 TCTCAGGGCAGACTTTCAAGCG
*
4583 TCTCAGGGTAGACTTTCAAGCG
1 TCTCAGGGCAGACTTTCAAGCG
4605 TCTCAGGGCAGA
1 TCTCAGGGCAGA
4617 TTCTCTTCAG
Statistics
Matches: 120, Mismatches: 23, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
21 15 0.12
22 105 0.88
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (22 bp):
TCTCAGGGCAGACTTTCAAGCG
Found at i:4564 original size:66 final size:66
Alignment explanation
Indices: 4452--4615 Score: 231
Period size: 66 Copynumber: 2.5 Consensus size: 66
4442 GTTTTAAACA
* * * * *
4452 TCTCAGGGCAGACTTTTAA-CGTCTCAGGGTAGGCTTCCAAGCGTCTCAGGGCAGACTTTCAAGC
1 TCTCAGAGCAGACTTTCAAGCGTCTCAGGGCAGGCTTCCAAGCGTCTCAAGGCAGACTATCAAGC
4516 G
66 G
* **
4517 TCTTAGAGCAGACTTTCAAGCGTCTCAGGGCAGGCTTCCAAGCGTCTCAAGGTGGACTATCAAGC
1 TCTCAGAGCAGACTTTCAAGCGTCTCAGGGCAGGCTTCCAAGCGTCTCAAGGCAGACTATCAAGC
4582 G
66 G
* *
4583 TCTCAGGGTAGACTTTCAAGCGTCTCAGGGCAG
1 TCTCAGAGCAGACTTTCAAGCGTCTCAGGGCAG
4616 ATTCTCTTCA
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
65 16 0.18
66 71 0.82
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.24
Consensus pattern (66 bp):
TCTCAGAGCAGACTTTCAAGCGTCTCAGGGCAGGCTTCCAAGCGTCTCAAGGCAGACTATCAAGC
G
Found at i:4661 original size:27 final size:27
Alignment explanation
Indices: 4605--4695 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
4595 CTTTCAAGCG
* * **
4605 TCTCAGGGCAGATTCTCTTCAGTGGCA
1 TCTCAGGGTAGATTCGCTTCAGTGATA
4632 TCTCAGGGTAGATTCGCTTCAGTGATA
1 TCTCAGGGTAGATTCGCTTCAGTGATA
* *
4659 TCTC-GAGGTAGATTCGCTTTAGTAATA
1 TCTCAG-GGTAGATTCGCTTCAGTGATA
4686 TCTCAGGGTA
1 TCTCAGGGTA
4696 AGTTCAGCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.02
27 54 0.96
28 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (27 bp):
TCTCAGGGTAGATTCGCTTCAGTGATA
Found at i:4814 original size:36 final size:35
Alignment explanation
Indices: 4739--4864 Score: 189
Period size: 36 Copynumber: 3.5 Consensus size: 35
4729 TTCGGGATTA
*
4739 AGTTAGGATGGTCGAGGGTGATCTTCCAATCAGTTTG
1 AGTTAGGATGATCG-GGGTGATCTTCC-ATCAGTTTG
4776 AGTTAGGATGATCAGGGGTGATCTTCCATCAGTTTG
1 AGTTAGGATGATC-GGGGTGATCTTCCATCAGTTTG
* *
4812 AGTTAGGATGATCGGGTGTGATCTTTCTTCAGTTTG
1 AGTTAGGATGATCGGG-GTGATCTTCCATCAGTTTG
4848 AGTTAGGATGATCGGGG
1 AGTTAGGATGATCGGGG
4865 GTGACGCAGG
Statistics
Matches: 84, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
35 4 0.05
36 55 0.65
37 24 0.29
38 1 0.01
ACGTcount: A:0.21, C:0.12, G:0.33, T:0.34
Consensus pattern (35 bp):
AGTTAGGATGATCGGGGTGATCTTCCATCAGTTTG
Found at i:5318 original size:21 final size:20
Alignment explanation
Indices: 5280--5318 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5270 TTAGCAATTC
*
5280 TAGCTAATTATGAGTTGTTT
1 TAGCTAATTATAAGTTGTTT
*
5300 TAGCTAGATTATAATTTGT
1 TAGCTA-ATTATAAGTTGT
5319 GTTTGTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (20 bp):
TAGCTAATTATAAGTTGTTT
Found at i:5886 original size:36 final size:36
Alignment explanation
Indices: 5804--6132 Score: 392
Period size: 36 Copynumber: 9.2 Consensus size: 36
5794 TCATCTTCAA
* * * *
5804 TCAGTTTGACTTAGGATGATCGAGGGTGATC-TCCA
1 TCAGTTTGAGTTAGGATGATCGGGGGTGATCTTTCT
*
5839 TCAGTTTGAGTTAGGACGATCGGGGGTGATCTTTCT
1 TCAGTTTGAGTTAGGATGATCGGGGGTGATCTTTCT
* * *
5875 TCAGTTTGAGTTAGGATTATCAGGGGTGATCTTCCAT
1 TCAGTTTGAGTTAGGATGATCGGGGGTGATCTTTC-T
* * *
5912 T-AGTTTGAGTTAGGATGAGCGGGGGTGATCTTCCA
1 TCAGTTTGAGTTAGGATGATCGGGGGTGATCTTTCT
5947 TCAGTTTGAGTTAGGATGATCGGGGGTGATCTTTCT
1 TCAGTTTGAGTTAGGATGATCGGGGGTGATCTTTCT
** * * *
5983 TCAGCCTAAGTCAGGATGATCAGGGGTGATCTTTCT
1 TCAGTTTGAGTTAGGATGATCGGGGGTGATCTTTCT
* * * *
6019 TTAGTTTAAGTCAGGATGATCGGGGGTGGTCTTTCT
1 TCAGTTTGAGTTAGGATGATCGGGGGTGATCTTTCT
* * *
6055 TCAGTTGGAGTCAGGATGATCGGGGGTGGTCTTTCT
1 TCAGTTTGAGTTAGGATGATCGGGGGTGATCTTTCT
* * * *
6091 TCAGTTTGAGTCAGGATGATCGAGGGTGGTATTTCT
1 TCAGTTTGAGTTAGGATGATCGGGGGTGATCTTTCT
6127 TCAGTT
1 TCAGTT
6133 CAATTCACGA
Statistics
Matches: 259, Mismatches: 32, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
35 29 0.11
36 228 0.88
37 2 0.01
ACGTcount: A:0.19, C:0.14, G:0.32, T:0.35
Consensus pattern (36 bp):
TCAGTTTGAGTTAGGATGATCGGGGGTGATCTTTCT
Found at i:5984 original size:108 final size:108
Alignment explanation
Indices: 5796--6116 Score: 437
Period size: 108 Copynumber: 3.0 Consensus size: 108
5786 AAAGCAACTC
* * * * *
5796 ATCTTCAATCAGTTTGACTTAGGATGATCGAGGGTGATC-TCCATCAGTTTGAGTTAGGACGATC
1 ATCTTCCATTAGTTTGAGTTAGGATGATCGGGGGTGATCTTCCATCAGTTTGAGTTAGGATGATC
* *
5860 GGGGGTGATCTTTCTTCAGTTTGAGTTAGGATTATCAGGGGTG
66 GGGGGTGATCTTTCTTCAGTTTGAGTCAGGATGATCAGGGGTG
*
5903 ATCTTCCATTAGTTTGAGTTAGGATGAGCGGGGGTGATCTTCCATCAGTTTGAGTTAGGATGATC
1 ATCTTCCATTAGTTTGAGTTAGGATGATCGGGGGTGATCTTCCATCAGTTTGAGTTAGGATGATC
** *
5968 GGGGGTGATCTTTCTTCAGCCTAAGTCAGGATGATCAGGGGTG
66 GGGGGTGATCTTTCTTCAGTTTGAGTCAGGATGATCAGGGGTG
* * * * * * * * *
6011 ATCTTTCTTTAGTTTAAGTCAGGATGATCGGGGGTGGTCTTTCTTCAGTTGGAGTCAGGATGATC
1 ATCTTCCATTAGTTTGAGTTAGGATGATCGGGGGTGATCTTCCATCAGTTTGAGTTAGGATGATC
*
6076 GGGGGTGGTCTTTCTTCAGTTTGAGTCAGGATGATCGAGGG
66 GGGGGTGATCTTTCTTCAGTTTGAGTCAGGATGATC-AGGG
6117 TGGTATTTCT
Statistics
Matches: 187, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
107 34 0.18
108 149 0.80
109 4 0.02
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (108 bp):
ATCTTCCATTAGTTTGAGTTAGGATGATCGGGGGTGATCTTCCATCAGTTTGAGTTAGGATGATC
GGGGGTGATCTTTCTTCAGTTTGAGTCAGGATGATCAGGGGTG
Found at i:16033 original size:72 final size:72
Alignment explanation
Indices: 15902--16047 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 72
15892 GCTGGTTGGA
* * * * *
15902 ATTCCTGTATAGACTTGACAGATTGCATAGATAGTTTAATGAATTAAATTCCAATTTAGAATCAA
1 ATTCCCGTATAGACTTGACAAATTGCATAGATAATTTAATGAATCAAATTCCAACTTAGAATCAA
15967 TTTGATC
66 TTTGATC
* * * ** *
15974 ATTCCCGTGTAGACTTGACAAATTGCATAGATAATTTAGTGAATCCAATTTGAACTTAGAATCAT
1 ATTCCCGTATAGACTTGACAAATTGCATAGATAATTTAATGAATCAAATTCCAACTTAGAATCAA
16039 TTTGATC
66 TTTGATC
16046 AT
1 AT
16048 ATATTGAAAC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (72 bp):
ATTCCCGTATAGACTTGACAAATTGCATAGATAATTTAATGAATCAAATTCCAACTTAGAATCAA
TTTGATC
Found at i:23417 original size:15 final size:14
Alignment explanation
Indices: 23391--23432 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
23381 AGGATTAGGG
*
23391 AAAAAA-AAAAAGT
1 AAAAAACAAAAAGA
*
23404 AAGAAACGAAAAAGA
1 AAAAAAC-AAAAAGA
23419 AAAAAACAAAAAGA
1 AAAAAACAAAAAGA
23433 GAGGACTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 5 0.21
14 7 0.29
15 12 0.50
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (14 bp):
AAAAAACAAAAAGA
Found at i:23923 original size:27 final size:27
Alignment explanation
Indices: 23885--23937 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
23875 TCGGGTTTTT
*
23885 GGGTTCGGATCAAATTCAAGTCAGGTC
1 GGGTTCGAATCAAATTCAAGTCAGGTC
*
23912 GGGTTCGAATCAATTTCAAGTCAGGT
1 GGGTTCGAATCAAATTCAAGTCAGGT
23938 TTTTCGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GGGTTCGAATCAAATTCAAGTCAGGTC
Found at i:24310 original size:19 final size:19
Alignment explanation
Indices: 24288--24330 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
24278 CAAGGGTTGA
24288 AATTAATTAATTAAATAAT
1 AATTAATTAATTAAATAAT
* * *
24307 AATTATTTTATTGAATAAT
1 AATTAATTAATTAAATAAT
*
24326 TATTA
1 AATTA
24331 TCAAAAGTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
AATTAATTAATTAAATAAT
Found at i:37167 original size:13 final size:13
Alignment explanation
Indices: 37149--37174 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37139 CTTGGCATGA
37149 GTGATGATTTTTG
1 GTGATGATTTTTG
37162 GTGATGATTTTTG
1 GTGATGATTTTTG
37175 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:37546 original size:19 final size:19
Alignment explanation
Indices: 37524--37566 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
37514 CAAGGGCTGA
37524 AATTAATTAATTAAATAAT
1 AATTAATTAATTAAATAAT
* * *
37543 AATTATTTTATTGAATAAT
1 AATTAATTAATTAAATAAT
*
37562 TATTA
1 AATTA
37567 TCAAAAGTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
AATTAATTAATTAAATAAT
Found at i:39518 original size:27 final size:30
Alignment explanation
Indices: 39480--40132 Score: 217
Period size: 31 Copynumber: 20.6 Consensus size: 30
39470 ATAATGGTGT
39480 AGACAGGTC-TT-TC-TCAATTCTGACCTC
1 AGACAGGTCTTTATCTTCAATTCTGACCTC
*
39507 AGACAGGTCTTTATCTTTCAATTCCGACCTC
1 AGACAGGTCTTTATC-TTCAATTCTGACCTC
39538 AGACAGGTCTTTATCTTTCAATTCCTG-CCTC
1 AGACAGGTCTTTATC-TTCAATT-CTGACCTC
* * *
39569 AGACAGGCCTTTCTTAGT-TTTATTTC-GACCTC
1 AGACAGG--TCT-TTA-TCTTCAATTCTGACCTC
* * *
39601 AGACATGTCTTTATCTTTCAATTCCGGCCTC
1 AGACAGGTCTTTATC-TTCAATTCTGACCTC
* * **
39632 AAACAGGTCTTTCTCAGTTTTATT-TCGACCTC
1 AGACAGGTCTTTATC--TTCAATTCT-GACCTC
* *
39664 AGACATGTCTTTATCTTTTAAATTC-GACCTC
1 AGACAGGTCTTTATC--TTCAATTCTGACCTC
* * **
39695 AAACAGGTCTTTCTCAGTTTTATT-TCGACCTC
1 AGACAGGTCTTTATC--TTCAATTCT-GACCTC
* * * *
39727 AGACATGTCTTTATCTTTCAACTCCAGGCCTC
1 AGACAGGTCTTTATC-TTCAA-TTCTGACCTC
* * *
39759 AGACAGGTTTTTCTCAGCTTTTAATT-TCGACCTC
1 AGACAGG-TCTT-T-ATC-TTCAATTCT-GACCTC
* * *
39793 AGACAGGTCTTTATCTTTCAACTCCAGGCCTC
1 AGACAGGTCTTTATC-TTCAA-TTCTGACCTC
* *
39825 AGAACAGGTCTTTCTCAGCTTTTAATT-TCGACCTC
1 AG-ACAGGTC-TT-T-ATC-TTCAATTCT-GACCTC
* * *
39860 AGACAGGTCTTTATCTTTCAACTCCAGGCCTC
1 AGACAGGTCTTTATC-TTCAA-TTCTGACCTC
* * *
39892 AGAACAAGTCTTTCTCAGCTTTTAATT-TCGACCTC
1 AG-ACAGGTC-TT-T-ATC-TTCAATTCT-GACCTC
*
39927 AGACAGGTCTTTATCTTTCAATTC-CAGCCTC
1 AGACAGGTCTTTATC-TTCAATTCTGA-CCTC
* * * * *
39958 AGACAGGCCTTTCTCAGTCTTATTAC-GACATC
1 AGACAGGTCTTTATC-TTC-AATT-CTGACCTC
* * * *
39990 AGACATGTCTTTATCTTTCAATTCCGGCCTG
1 AGACAGGTCTTTATC-TTCAATTCTGACCTC
* *
40021 AGACAGGTCTTTCTTAGT-TTTATTTC-GACCTC
1 AGACAGGTC--T-TTA-TCTTCAATTCTGACCTC
* *
40053 AGACAGGTCTTTATCTTTTAAATTC-CACCTC
1 AGACAGGTCTTTATC--TTCAATTCTGACCTC
* * **
40084 AGATAGGTCTTTCTCAGTTTTATT-TCGACCTC
1 AGACAGGTCTTTATC--TTCAATTCT-GACCTC
40116 AGACAGGTCTTTATCTT
1 AGACAGGTCTTTATCTT
40133 TAACCTCAAA
Statistics
Matches: 467, Mismatches: 107, Indels: 101
0.69 0.16 0.15
Matches are distributed among these distances:
27 9 0.02
28 4 0.01
29 8 0.02
30 13 0.03
31 176 0.38
32 140 0.30
33 39 0.08
34 37 0.08
35 27 0.06
36 14 0.03
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (30 bp):
AGACAGGTCTTTATCTTCAATTCTGACCTC
Found at i:39612 original size:63 final size:63
Alignment explanation
Indices: 39493--40190 Score: 896
Period size: 63 Copynumber: 11.0 Consensus size: 63
39483 CAGGTCTTTC
* * * * *
39493 TCAATTCTGACCTCAGACAGGTCTTTATC--TTTCAATTCCGACCTCAGACAGGTCTTTATCTT
1 TCAATTCCGGCCTCAGACAGGTCTTTCTCAGTTT-TATTTCGACCTCAGACAGGTCTTTATCTT
* * * *
39555 TCAATTCCTGCCTCAGACAGGCCTTTCTTAGTTTTATTTCGACCTCAGACATGTCTTTATCTT
1 TCAATTCCGGCCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTT
* *
39618 TCAATTCCGGCCTCAAACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACATGTCTTTATCTTT
1 TCAATTCCGGCCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATC-TT
* * * *
39682 TAAATT-CGACCTCAAACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACATGTCTTTATCTT
1 TCAATTCCGGCCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTT
* *
39744 TCAACTCCAGGCCTCAGACAGGTTTTTCTCAGCTTTTAATTTCGACCTCAGACAGGTCTTTATCT
1 TCAATTCC-GGCCTCAGACAGGTCTTTCTCAG-TTTT-ATTTCGACCTCAGACAGGTCTTTATCT
39809 T
63 T
*
39810 TCAACTCCAGGCCTCAGAACAGGTCTTTCTCAGCTTTTAATTTCGACCTCAGACAGGTCTTTATC
1 TCAATTCC-GGCCTCAG-ACAGGTCTTTCTCAG-TTTT-ATTTCGACCTCAGACAGGTCTTTATC
39875 TT
62 TT
* *
39877 TCAACTCCAGGCCTCAGAACAAGTCTTTCTCAGCTTTTAATTTCGACCTCAGACAGGTCTTTATC
1 TCAATTCC-GGCCTCAG-ACAGGTCTTTCTCAG-TTTT-ATTTCGACCTCAGACAGGTCTTTATC
39942 TT
62 TT
* * * * * *
39944 TCAATTCCAGCCTCAGACAGGCCTTTCTCAGTCTTATTACGACATCAGACATGTCTTTATCTT
1 TCAATTCCGGCCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTT
* *
40007 TCAATTCCGGCCTGAGACAGGTCTTTCTTAGTTTTATTTCGACCTCAGACAGGTCTTTATCTTT
1 TCAATTCCGGCCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATC-TT
* * *
40071 TAAATTCC-ACCTCAGATAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTT
1 TCAATTCCGGCCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTT
*
40133 T-AA------CCTCAAACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACAGGTCTTTATCTT
1 TCAATTCCGGCCTCAGACAGGTCTTTCTCAGTTTT-ATTTCGACCTCAGACAGGTCTTTATCTT
40190 T
1 T
40191 TAATAGCGTA
Statistics
Matches: 580, Mismatches: 46, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
56 23 0.04
57 29 0.05
61 2 0.00
62 32 0.06
63 263 0.45
64 42 0.07
65 17 0.03
66 51 0.09
67 121 0.21
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.38
Consensus pattern (63 bp):
TCAATTCCGGCCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTT
Found at i:40153 original size:56 final size:57
Alignment explanation
Indices: 40079--40190 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 57
40069 TTTAAATTCC
* *
40079 ACCTCAGATAGGTCTTTCTCAGTTTT-ATTTCGACCTCAGACAGGTCTTTATCTTTA
1 ACCTCAAACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACAGGTCTTTATCTTTA
40135 ACCTCAAACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACAGGTCTTTATCTTT
1 ACCTCAAACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACAGGTCTTTATCTTT
40191 TAATAGCGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
56 24 0.45
57 29 0.55
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (57 bp):
ACCTCAAACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACAGGTCTTTATCTTTA
Done.