Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019673.1 Corchorus olitorius cultivar O-4 contig19706, 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: 81308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2505 original size:23 final size:23
Alignment explanation
Indices: 2448--2496 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2438 TTTTACCCCA
2448 TAATAAATCGACCTTACCATGTC
1 TAATAAATCGACCTTACCATGTC
2471 TAATAAATCGACCTTACCATGTC
1 TAATAAATCGACCTTACCATGTC
2494 TAA
1 TAA
2497 AGTCACGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (23 bp):
TAATAAATCGACCTTACCATGTC
Found at i:4203 original size:2 final size:2
Alignment explanation
Indices: 4198--4294 Score: 185
Period size: 2 Copynumber: 48.5 Consensus size: 2
4188 TACTATATAT
*
4198 AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4240 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4282 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
4295 TATATATATA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 93 1.00
ACGTcount: A:0.51, C:0.48, G:0.00, T:0.01
Consensus pattern (2 bp):
AC
Found at i:15861 original size:2 final size:2
Alignment explanation
Indices: 15854--15896 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
15844 GTTTGAGTGG
15854 TA TA TA TA TA 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 TA TA
15896 T
1 T
15897 GAAGAAACCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33296 original size:36 final size:36
Alignment explanation
Indices: 33249--33338 Score: 180
Period size: 36 Copynumber: 2.5 Consensus size: 36
33239 GTTTGAATGG
33249 TTCTCCCTATTTCAATTGGGATTTTAAGTATCCCTT
1 TTCTCCCTATTTCAATTGGGATTTTAAGTATCCCTT
33285 TTCTCCCTATTTCAATTGGGATTTTAAGTATCCCTT
1 TTCTCCCTATTTCAATTGGGATTTTAAGTATCCCTT
33321 TTCTCCCTATTTCAATTG
1 TTCTCCCTATTTCAATTG
33339 TTAATTTGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (36 bp):
TTCTCCCTATTTCAATTGGGATTTTAAGTATCCCTT
Found at i:38177 original size:30 final size:30
Alignment explanation
Indices: 38133--38208 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
38123 GGATCCTGCA
*
38133 GTAAATAAACTGTTGACTTTGAATCACACT
1 GTAAATACACTGTTGACTTTGAATCACACT
* * * *
38163 GTTAATACACTGTTGACTTTGGATCTCGCT
1 GTAAATACACTGTTGACTTTGAATCACACT
*
38193 GTAAATACATTGTTGA
1 GTAAATACACTGTTGA
38209 TGTTGATAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (30 bp):
GTAAATACACTGTTGACTTTGAATCACACT
Found at i:46792 original size:85 final size:86
Alignment explanation
Indices: 46649--46820 Score: 328
Period size: 85 Copynumber: 2.0 Consensus size: 86
46639 GAATTATGCC
46649 TGGTTCTCTGAGCTTGATCTTTATATGTTGAAAACGATAGATAAATGTCTTCTAAGGTCTTTCAC
1 TGGTTCTCTGAGCTTGATCTTTATATGTTGAAAACGATAGATAAATGTCTTCTAAGGTCTTTCAC
46714 ATGATTTTTATTATTG-TGTT
66 ATGATTTTTATTATTGTTGTT
*
46734 TGGTTCTCTGAGCTTGATCTTTATATGTTGAAAACGATAGATACATGTCTTCTAAGGTCTTTCAC
1 TGGTTCTCTGAGCTTGATCTTTATATGTTGAAAACGATAGATAAATGTCTTCTAAGGTCTTTCAC
46799 ATGATTTTTATTATTGTTGTT
66 ATGATTTTTATTATTGTTGTT
46820 T
1 T
46821 AAATGTGTTT
Statistics
Matches: 85, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 80 0.94
86 5 0.06
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (86 bp):
TGGTTCTCTGAGCTTGATCTTTATATGTTGAAAACGATAGATAAATGTCTTCTAAGGTCTTTCAC
ATGATTTTTATTATTGTTGTT
Found at i:58509 original size:3 final size:3
Alignment explanation
Indices: 58501--58532 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
58491 GATCATTGCC
58501 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
58533 TAGCCAAACT
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:0.34, C:0.34, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:58644 original size:13 final size:13
Alignment explanation
Indices: 58626--58652 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58616 CATAAATAAT
58626 TATACAAAAAAAA
1 TATACAAAAAAAA
58639 TATACAAAAAAAA
1 TATACAAAAAAAA
58652 T
1 T
58653 TAAAATGTTT
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:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (13 bp):
TATACAAAAAAAA
Found at i:59386 original size:4 final size:4
Alignment explanation
Indices: 59377--59414 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
59367 AGTATAATAA
*
59377 TCTT TCTT TCTT TCTT T-TT T-TT TTTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
59415 GGTCTATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
3 6 0.19
4 26 0.81
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TCTT
Found at i:60282 original size:29 final size:29
Alignment explanation
Indices: 60216--60295 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
60206 ACGTGGCATG
* *
60216 CCACGTGTACCAAAAAGCGATATATGGCACG
1 CCACGTGTACCAAAAAGTG--ATATGGCACA
* *
60247 CTACGTGTACCAAAAAGTGATGTGGCACA
1 CCACGTGTACCAAAAAGTGATATGGCACA
*
60276 CCACGTGTACAAAAAAGTGA
1 CCACGTGTACCAAAAAGTGA
60296 CACGTATCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 26 0.60
31 17 0.40
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (29 bp):
CCACGTGTACCAAAAAGTGATATGGCACA
Found at i:64238 original size:20 final size:20
Alignment explanation
Indices: 64213--64252 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
64203 CTAGGTAATA
64213 ATAATGCATGGTCCAAGAAT
1 ATAATGCATGGTCCAAGAAT
64233 ATAATGCATGGTCCAAGAAT
1 ATAATGCATGGTCCAAGAAT
64253 GCTTGATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (20 bp):
ATAATGCATGGTCCAAGAAT
Found at i:66452 original size:19 final size:18
Alignment explanation
Indices: 66398--66452 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 18
66388 ATTGAACTAT
66398 AATTATGTTTATTTC-AA
1 AATTATGTTTATTTCTAA
*
66415 CAATT-T-TTTCTTTCTAA
1 -AATTATGTTTATTTCTAA
66432 AATTATGTTTATTTACTAA
1 AATTATGTTTATTT-CTAA
66451 AA
1 AA
66453 CCAGTTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 11 0.35
17 4 0.13
18 10 0.32
19 6 0.19
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.53
Consensus pattern (18 bp):
AATTATGTTTATTTCTAA
Found at i:75065 original size:2 final size:2
Alignment explanation
Indices: 75058--75096 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
75048 GCACTTTACC
75058 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
75097 AGTCAACCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:77485 original size:82 final size:83
Alignment explanation
Indices: 77356--77523 Score: 257
Period size: 82 Copynumber: 2.0 Consensus size: 83
77346 AATTAGTTAA
* *
77356 AAAAAAATTGGATATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCAGTG
1 AAAAAAATTGGATATGTGTCAACTCCACAACCCGCTTGTAGAATCCAAAATTTACACCGCCAGTG
77421 TATCAAATAATTACCCAT
66 TATCAAATAATTACCCAT
* * * * *
77439 AAAAAAA-TGGGTATGTGTCAACTCCTCACCCCGCTTGTAGAATCCAAATTTTACACCGTCAGTG
1 AAAAAAATTGGATATGTGTCAACTCCACAACCCGCTTGTAGAATCCAAAATTTACACCGCCAGTG
*
77503 TATCAAATAATTACTCAT
66 TATCAAATAATTACCCAT
77521 AAA
1 AAA
77524 GTAATAGGAA
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
82 70 0.91
83 7 0.09
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
AAAAAAATTGGATATGTGTCAACTCCACAACCCGCTTGTAGAATCCAAAATTTACACCGCCAGTG
TATCAAATAATTACCCAT
Found at i:78697 original size:31 final size:29
Alignment explanation
Indices: 78643--78707 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 29
78633 TATGGGGTTT
78643 ATTTGTCCCAAAGAAAAGTTAAGGGGCCA
1 ATTTGTCCCAAAGAAAAGTTAAGGGGCCA
* * *
78672 ATTTGTCCCAAAATGGATAGTTAAGGGGCTA
1 ATTTGTCCC-AAA-GAAAAGTTAAGGGGCCA
78703 ATTTG
1 ATTTG
78708 GGTATTAAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 9 0.29
30 3 0.10
31 19 0.61
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (29 bp):
ATTTGTCCCAAAGAAAAGTTAAGGGGCCA
Done.