Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021801.1 Corchorus olitorius cultivar O-4 contig21834, 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: 51668
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2667 original size:17 final size:17
Alignment explanation
Indices: 2627--2667 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2617 TATTTTGGTA
2627 TATTTACAAAATTTCAT
1 TATTTACAAAATTTCAT
2644 TATTTTA-AAGAATTTCAT
1 TA-TTTACAA-AATTTCAT
2662 TATTTA
1 TATTTA
2668 TACTTAACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (17 bp):
TATTTACAAAATTTCAT
Found at i:3622 original size:42 final size:42
Alignment explanation
Indices: 3568--3650 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
3558 TACTCTTTTC
*
3568 TTCATATGGAAATGAAAGGCCTGAAAAGAGGTTACAATTCTT
1 TTCATATGGAAATGAAAGGCCCGAAAAGAGGTTACAATTCTT
**
3610 TTCATATGGAAATGAAAGGCCCGAGGAGAGGTTACAATTCT
1 TTCATATGGAAATGAAAGGCCCGAAAAGAGGTTACAATTCT
3651 AGATAATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (42 bp):
TTCATATGGAAATGAAAGGCCCGAAAAGAGGTTACAATTCTT
Found at i:6284 original size:19 final size:19
Alignment explanation
Indices: 6247--6284 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6237 GGGGTTTCCT
6247 AGTAGGTTAGTTAAGCTGC
1 AGTAGGTTAGTTAAGCTGC
*
6266 AGTAGTGTTTGTTAA-CTGC
1 AGTAG-GTTAGTTAAGCTGC
6285 TACTACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.24, C:0.11, G:0.29, T:0.37
Consensus pattern (19 bp):
AGTAGGTTAGTTAAGCTGC
Found at i:12698 original size:62 final size:62
Alignment explanation
Indices: 12626--12751 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
12616 CAAGTTTTAA
*
12626 ATATTTCAATCTAGTCCCTAGAGGACACATGTCACCCTTCAGGATCGTATGTGTAGTCTGCT
1 ATATTTCAATCTAGTCCCTAAAGGACACATGTCACCCTTCAGGATCGTATGTGTAGTCTGCT
12688 ATATTTCAATCTAGTCCCTAAAGGACACATGTCACCCTTCAGGATCGTATGTGTAGTCTGCT
1 ATATTTCAATCTAGTCCCTAAAGGACACATGTCACCCTTCAGGATCGTATGTGTAGTCTGCT
12750 AT
1 AT
12752 CCACTGACGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (62 bp):
ATATTTCAATCTAGTCCCTAAAGGACACATGTCACCCTTCAGGATCGTATGTGTAGTCTGCT
Found at i:12841 original size:51 final size:51
Alignment explanation
Indices: 12784--12888 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
12774 TTAGCCTTAA
12784 ATAATTGCTAGAATTTAACCATATTAGGAGGATATATATTATATAGGGTTT
1 ATAATTGCTAGAATTTAACCATATTAGGAGGATATATATTATATAGGGTTT
12835 ATAATTGCTAGAATTTAACCATATTAGGAGGATATATATTATATAGGGTTT
1 ATAATTGCTAGAATTTAACCATATTAGGAGGATATATATTATATAGGGTTT
12886 ATA
1 ATA
12889 TATAATATAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (51 bp):
ATAATTGCTAGAATTTAACCATATTAGGAGGATATATATTATATAGGGTTT
Found at i:16280 original size:46 final size:45
Alignment explanation
Indices: 16228--16368 Score: 187
Period size: 46 Copynumber: 3.1 Consensus size: 45
16218 AAAATAGACC
* *
16228 AAAATAGTTATCTAAATTAAACTAGAATAGACCAAAATAGTTATCT
1 AAAATAGTTATCTAAATTAAA-TAGAACAAACCAAAATAGTTATCT
* *
16274 AAAATAGTCATCTAAATTAAAATAGACCAAACCAAAATAGTTATCT
1 AAAATAGTTATCTAAATT-AAATAGAACAAACCAAAATAGTTATCT
*
16320 AAAATAG-TCTCTAAATTAAGATA-AACCAAACCAAAATAGTTATCT
1 AAAATAGTTATCTAAATTAA-ATAGAA-CAAACCAAAATAGTTATCT
16365 AAAA
1 AAAA
16369 CAGTCTCTAA
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
44 3 0.04
45 34 0.40
46 45 0.53
47 3 0.04
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.27
Consensus pattern (45 bp):
AAAATAGTTATCTAAATTAAATAGAACAAACCAAAATAGTTATCT
Found at i:16348 original size:45 final size:45
Alignment explanation
Indices: 16258--16379 Score: 208
Period size: 45 Copynumber: 2.7 Consensus size: 45
16248 ACTAGAATAG
*
16258 ACCAAAATAGTTATCTAAAATAGTCATCTAAATTAAAATAGACCAA
1 ACCAAAATAGTTATCTAAAATAGTC-TCTAAATTAAAATAAACCAA
*
16304 ACCAAAATAGTTATCTAAAATAGTCTCTAAATTAAGATAAACCAA
1 ACCAAAATAGTTATCTAAAATAGTCTCTAAATTAAAATAAACCAA
*
16349 ACCAAAATAGTTATCTAAAACAGTCTCTAAA
1 ACCAAAATAGTTATCTAAAATAGTCTCTAAA
16380 CTAATAGTCG
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 48 0.66
46 25 0.34
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (45 bp):
ACCAAAATAGTTATCTAAAATAGTCTCTAAATTAAAATAAACCAA
Found at i:16485 original size:24 final size:23
Alignment explanation
Indices: 16458--16506 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
16448 TAAAAAATTA
16458 AAAATACAAATT-TGATCCTCTCAT
1 AAAATACAAATTCT-ATCCTC-CAT
*
16482 AAAATACATATTCTATCCTCCAT
1 AAAATACAAATTCTATCCTCCAT
16505 AA
1 AA
16507 TGGGCTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.22
24 17 0.74
25 1 0.04
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAATACAAATTCTATCCTCCAT
Found at i:16696 original size:16 final size:16
Alignment explanation
Indices: 16675--16718 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
16665 GATGCATCTC
*
16675 ATTATGTATTATTATT
1 ATTATGTATTATTAAT
16691 ATTATGTACTTATTAAT
1 ATTATGTA-TTATTAAT
*
16708 -TTATCTATTAT
1 ATTATGTATTAT
16719 GGCAGGATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 14 0.56
17 7 0.28
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (16 bp):
ATTATGTATTATTAAT
Found at i:17270 original size:3 final size:3
Alignment explanation
Indices: 17264--17294 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
17254 TGCCGCCGAT
*
17264 TTC TTC TTC TTC TTC TTC TTC CTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
17295 CCTCCACAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:21263 original size:76 final size:76
Alignment explanation
Indices: 21134--21284 Score: 214
Period size: 76 Copynumber: 2.0 Consensus size: 76
21124 GAATTTAACC
* * *
21134 AATTTCCATAAAAAATGGCTATAATTTGTCTATTTTTTACAAATTAAAGTGTGCAATTGACAATT
1 AATTTCCATAAAAAATGACTATAATTTGTCCACTTTTTACAAATTAAAGTGTGCAATTGACAATT
21199 ATGGAAGTTCT
66 ATGGAAGTTCT
** * *
21210 AATTTCCATCCAAAATGATTATAATTTGTCCACTTTTTACAAATT-CAGATGTGCAATTGACAAT
1 AATTTCCATAAAAAATGACTATAATTTGTCCACTTTTTACAAATTAAAG-TGTGCAATTGACAAT
*
21274 TTTGGAAGTTC
65 TATGGAAGTTC
21285 AAGTGGTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
75 2 0.03
76 64 0.97
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (76 bp):
AATTTCCATAAAAAATGACTATAATTTGTCCACTTTTTACAAATTAAAGTGTGCAATTGACAATT
ATGGAAGTTCT
Found at i:25047 original size:13 final size:13
Alignment explanation
Indices: 25026--25062 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
25016 GATAATTCTT
25026 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
25039 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
25052 CTTGACCCTCC
1 TTTGACCCTCC
25063 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:26338 original size:25 final size:24
Alignment explanation
Indices: 26310--26371 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
26300 GTGGATTGTA
*
26310 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
26335 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
26359 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
26372 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:29878 original size:12 final size:12
Alignment explanation
Indices: 29861--29885 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29851 TGGTCAATTC
29861 ACTCCTTTTCTG
1 ACTCCTTTTCTG
29873 ACTCCTTTTCTG
1 ACTCCTTTTCTG
29885 A
1 A
29886 GTAAGAACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.32, G:0.08, T:0.48
Consensus pattern (12 bp):
ACTCCTTTTCTG
Found at i:47312 original size:9 final size:9
Alignment explanation
Indices: 47298--47322 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
47288 GAGTCTAGTT
47298 TTTTGTTAA
1 TTTTGTTAA
47307 TTTTGTTAA
1 TTTTGTTAA
47316 TTTTGTT
1 TTTTGTT
47323 GGCAATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (9 bp):
TTTTGTTAA
Found at i:49555 original size:22 final size:21
Alignment explanation
Indices: 49526--49671 Score: 100
Period size: 22 Copynumber: 6.8 Consensus size: 21
49516 TGAATATTTT
49526 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTA-CC
* *
49548 TATTAAATTTTGATAATTACC
1 TATGAAATTTTGATAACTACC
* *
49569 TATAAAATTGTGATAAACT-CC
1 TATGAAATTTTGAT-AACTACC
* * *
49590 ATAAGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAA-CTACC
* *
49613 TATGAAATTTTAATAAACTTTCC
1 TATGAAATTTTGAT-AAC-TACC
* *
49636 TATTAAATTTTG-TAACCTTCC
1 TATGAAATTTTGATAA-CTACC
*
49657 TATG-ATTTTTGATAA
1 TATGAAATTTTGATAA
49672 TCTTTCTGTC
Statistics
Matches: 97, Mismatches: 19, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
20 6 0.06
21 30 0.31
22 46 0.47
23 15 0.15
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:49576 original size:21 final size:22
Alignment explanation
Indices: 49530--49584 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
49520 TATTTTTATG
*
49530 AAATTTTGATAACTACCCTATT
1 AAATTTTGATAACTACCCTATA
*
49552 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAACTACCCTATA
*
49573 AAATTGTGATAA
1 AAATTTTGATAA
49585 ACTCCATAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACTACCCTATA
Done.