Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015419.1 Corchorus olitorius cultivar O-4 contig15452, 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: 61479
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3328 original size:55 final size:56
Alignment explanation
Indices: 3226--3330 Score: 142
Period size: 55 Copynumber: 1.9 Consensus size: 56
3216 TGATTTTTGA
* *
3226 TTGATTGATTGATCAGATCACAAACTCCGAAAATGGTTTTATTGGGTTTATGTTTT
1 TTGAATGATTGATCAGATCACAAACTCCGAAAATGGTTTTATGGGGTTTATGTTTT
* **
3282 TTGAATGATTGAT-TGATCACAAACT-CGATGATGGTTTTAATGGGGTTTA
1 TTGAATGATTGATCAGATCACAAACTCCGAAAATGGTTTT-ATGGGGTTTA
3331 GGGGAAGAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
54 11 0.26
55 20 0.47
56 12 0.28
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.41
Consensus pattern (56 bp):
TTGAATGATTGATCAGATCACAAACTCCGAAAATGGTTTTATGGGGTTTATGTTTT
Found at i:4346 original size:37 final size:39
Alignment explanation
Indices: 4256--4361 Score: 171
Period size: 39 Copynumber: 2.7 Consensus size: 39
4246 CTAGAGAATA
*
4256 TGCTAATACATTGGCTTCCTAATTACAAAGTGTTATGTG
1 TGCTAATACATTGGCTTCCTAATTACAAAGTGTTATATG
4295 TGCTAATACATTGGCTTCCTAATTACAAAGTG-TA-ATG
1 TGCTAATACATTGGCTTCCTAATTACAAAGTGTTATATG
*
4332 TGCTAATACGTTGGCTTCCATAATTACAAA
1 TGCTAATACATTGGCTTCC-TAATTACAAA
4362 TTGGAACGTA
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
37 20 0.31
38 12 0.19
39 32 0.50
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (39 bp):
TGCTAATACATTGGCTTCCTAATTACAAAGTGTTATATG
Found at i:4944 original size:14 final size:14
Alignment explanation
Indices: 4925--4957 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
4915 TCTTAGCAAA
4925 AAAATAATAATAAT
1 AAAATAATAATAAT
4939 AAAATAATAATAAT
1 AAAATAATAATAAT
4953 AAAAT
1 AAAAT
4958 GAAAGCATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:4947 original size:17 final size:17
Alignment explanation
Indices: 4922--4954 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4912 CTTTCTTAGC
4922 AAAAAAATAATAATAAT
1 AAAAAAATAATAATAAT
*
4939 AAAATAATAATAATAA
1 AAAAAAATAATAATAA
4955 AATGAAAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAAAATAATAATAAT
Found at i:16308 original size:16 final size:16
Alignment explanation
Indices: 16287--16320 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
16277 ACAATTGAAC
16287 ATTTAAAGTGAAATTG
1 ATTTAAAGTGAAATTG
16303 ATTTAAAGTGAAATTG
1 ATTTAAAGTGAAATTG
16319 AT
1 AT
16321 AGAGTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (16 bp):
ATTTAAAGTGAAATTG
Found at i:18740 original size:22 final size:20
Alignment explanation
Indices: 18696--18737 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
18686 TACTATTCTT
18696 AAGAGTTAACCAATTAAAAA
1 AAGAGTTAACCAATTAAAAA
18716 AAGAGTTAACCAATTAAAAA
1 AAGAGTTAACCAATTAAAAA
18736 AA
1 AA
18738 AAGTCAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.19
Consensus pattern (20 bp):
AAGAGTTAACCAATTAAAAA
Found at i:21978 original size:2 final size:2
Alignment explanation
Indices: 21971--22002 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21961 GTAGAGTTTT
21971 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
22003 ACAATTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31194 original size:50 final size:50
Alignment explanation
Indices: 31130--31224 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
31120 CAGCGATTGA
*
31130 AACGATTAACCTCCATTTGACCCAAAACGATGACGAAACGATCAAATAGT
1 AACGATTAACCTCCATTTGACCCAAAACAATGACGAAACGATCAAATAGT
* *
31180 AACGGTTAACCTCCATTTGACCCAAAATAATGACGAAACGATCAA
1 AACGATTAACCTCCATTTGACCCAAAACAATGACGAAACGATCAA
31225 TAATGGTGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (50 bp):
AACGATTAACCTCCATTTGACCCAAAACAATGACGAAACGATCAAATAGT
Found at i:33398 original size:60 final size:61
Alignment explanation
Indices: 33305--33463 Score: 236
Period size: 60 Copynumber: 2.7 Consensus size: 61
33295 CTAATTGCTT
* *
33305 AAATAAGGCCCTAACGTGT-TCCAAAATGCTCAAATAAGGGGCC-GATATTTTAATTTGACC
1 AAATAAGGGCCTAACGT-TATCGAAAATGCTCAAATAAGGGGCCTGATATTTTAATTTGACC
*
33365 AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAA-GGGCCTGATATTTTATTTTGACC
1 AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGGCCTGATATTTTAATTTGACC
* *
33425 AAATAA-GGCCTAATGTTATCGAAAATGTTCAAATAAGGG
1 AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
33464 ACTGACATCA
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
59 34 0.37
60 57 0.63
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (61 bp):
AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGGCCTGATATTTTAATTTGACC
Found at i:33546 original size:31 final size:30
Alignment explanation
Indices: 33508--33672 Score: 129
Period size: 31 Copynumber: 5.5 Consensus size: 30
33498 CGACGTCAGG
* * *
33508 CCCTTATTTGAGCATTTTGGCAAACGTTGGA
1 CCCTTATTTGAGCATTTT-ACAAACATTAGA
** * ** *
33539 CCCTTATTTG-GCCAAATTA-AAAGACCAGG
1 CCCTTATTTGAG-CATTTTACAAACATTAGA
* *
33568 CCCTTATTTGAGCATTTTGGCAAACGTTAGA
1 CCCTTATTTGAGCATTTT-ACAAACATTAGA
* ** * *
33599 CCCTTATTTGACCAAATTA-AAAAATCAGA
1 CCCTTATTTGAGCATTTTACAAACATTAGA
33628 CCCTTATTTGAGCATTTTTACAAACATTAGA
1 CCCTTATTTGAGCA-TTTTACAAACATTAGA
33659 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
33673 ATTAACCCTC
Statistics
Matches: 99, Mismatches: 29, Indels: 12
0.71 0.21 0.09
Matches are distributed among these distances:
29 38 0.38
30 5 0.05
31 56 0.57
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTACAAACATTAGA
Found at i:33577 original size:60 final size:60
Alignment explanation
Indices: 33504--33677 Score: 260
Period size: 60 Copynumber: 2.9 Consensus size: 60
33494 TTTTCGACGT
* * *
33504 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTGGACCCTTATTTGGCCAAATTAAAAGAC
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGACCAAATTAAAAAAC
*
33564 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGACCAAATTAAAAAAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGACCAAATTAAAAAAC
* ** * *
33624 CAGACCCTTATTTGAGCATTTTTACAAACATTAGACCCTTATTTGAGC-AATTAA
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGACCAAATTAA
33678 CCCTCTTTGT
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 6 0.06
60 99 0.94
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGACCAAATTAAAAAAC
Found at i:33635 original size:29 final size:29
Alignment explanation
Indices: 33537--33638 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
33527 GCAAACGTTG
* * *
33537 GACCCTTATTTGGCCAAATTAAAAGACCA
1 GACCCTTATTTGACCAAATTAAAAAATCA
* * ** * ** *
33566 GGCCCTTATTTGAGCATTTTGGCAAACGTTA
1 GACCCTTATTTGACCAAATT--AAAAAATCA
33597 GACCCTTATTTGACCAAATTAAAAAATCA
1 GACCCTTATTTGACCAAATTAAAAAATCA
33626 GACCCTTATTTGA
1 GACCCTTATTTGA
33639 GCATTTTTAC
Statistics
Matches: 53, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
29 33 0.62
31 20 0.38
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (29 bp):
GACCCTTATTTGACCAAATTAAAAAATCA
Found at i:35948 original size:57 final size:57
Alignment explanation
Indices: 35860--35974 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
35850 TTGATTCATC
*
35860 TTCGAATTCGGATTAGTCGGATCCAATATGATTATCTGAAGATAATATAAAATCAAA
1 TTCGAATTCGGATTAGTCGGATCCAATATGATTATCTGAAGATAATATAAAACCAAA
* *
35917 TTCGAATTTGGATTAGTCGGGTCCAATATGATTATCTGAAGATAATATAAAACCAAA
1 TTCGAATTCGGATTAGTCGGATCCAATATGATTATCTGAAGATAATATAAAACCAAA
35974 T
1 T
35975 GAAGTTTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (57 bp):
TTCGAATTCGGATTAGTCGGATCCAATATGATTATCTGAAGATAATATAAAACCAAA
Found at i:50984 original size:60 final size:60
Alignment explanation
Indices: 50891--51021 Score: 244
Period size: 60 Copynumber: 2.2 Consensus size: 60
50881 AGAATGAGAA
*
50891 CACACAAAGTCAACAAGAGATAAGCCCGGGCGAAGGAACGCAAGGTTTACCAGAGACAAG
1 CACACAAAGTCAACAAGAGATAAGCCCGGGCGAAGGAACACAAGGTTTACCAGAGACAAG
*
50951 CACACAAAGTCAACAAGAGATAAGCCCGGGCGAAGGAACACAAGGTTTACCTGAGACAAG
1 CACACAAAGTCAACAAGAGATAAGCCCGGGCGAAGGAACACAAGGTTTACCAGAGACAAG
51011 CACACAAAGTC
1 CACACAAAGTC
51022 CACAGGACAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.09
Consensus pattern (60 bp):
CACACAAAGTCAACAAGAGATAAGCCCGGGCGAAGGAACACAAGGTTTACCAGAGACAAG
Found at i:54379 original size:17 final size:16
Alignment explanation
Indices: 54327--54375 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
54317 CACCCCCCAT
*
54327 ATCACTAGTGATCTAAG
1 ATCACCAGTGATC-AAG
54344 ATCACCAGTGATGCAAG
1 ATCACCAGTGAT-CAAG
*
54361 ATCACCGGTGATCAA
1 ATCACCAGTGATCAA
54376 AGATTACATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (16 bp):
ATCACCAGTGATCAAG
Done.