Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014196.1 Corchorus olitorius cultivar O-4 contig14229, 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: 39594
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:3145 original size:51 final size:52
Alignment explanation
Indices: 3044--3145 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
3034 GTTCATCAAA
* **
3044 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
* *
3096 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
3146 CTTCATTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.05
51 36 0.84
52 5 0.12
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
Found at i:4295 original size:24 final size:24
Alignment explanation
Indices: 4263--4310 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
4253 CTGCGGGCTT
4263 TTCACGGTTGATAAAGTGTCTGCC
1 TTCACGGTTGATAAAGTGTCTGCC
4287 TTCACGGTTGATAAAGTGTCTGCC
1 TTCACGGTTGATAAAGTGTCTGCC
4311 ATTATGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (24 bp):
TTCACGGTTGATAAAGTGTCTGCC
Found at i:4676 original size:54 final size:54
Alignment explanation
Indices: 4594--4700 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
4584 ATACTCTTAG
4594 TTCTGCTCTCAAATAAGTCATTCACAAATAGTTCACAAATAAGTATTGTTTCAA
1 TTCTGCTCTCAAATAAGTCATTCACAAATAGTTCACAAATAAGTATTGTTTCAA
4648 TTCTGCTCTCAAATAAGTCATTCACAAATAGTTCACAAATAAGTATTGTTTCA
1 TTCTGCTCTCAAATAAGTCATTCACAAATAGTTCACAAATAAGTATTGTTTCA
4701 GCAAAGTTGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (54 bp):
TTCTGCTCTCAAATAAGTCATTCACAAATAGTTCACAAATAAGTATTGTTTCAA
Found at i:4691 original size:26 final size:26
Alignment explanation
Indices: 4603--4691 Score: 90
Period size: 26 Copynumber: 3.3 Consensus size: 26
4593 GTTCTGCTCT
4603 CAAATAAGTCATTCACAAATAGTTCA
1 CAAATAAGTCATTCACAAATAGTTCA
** * * * *
4629 CAAATAAGT-ATTGTTTCAATTCTGCTCT
1 CAAATAAGTCA-T-TCACAAAT-AGTTCA
4657 CAAATAAGTCATTCACAAATAGTTCA
1 CAAATAAGTCATTCACAAATAGTTCA
4683 CAAATAAGT
1 CAAATAAGT
4692 ATTGTTTCAG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
25 1 0.02
26 22 0.47
27 10 0.21
28 13 0.28
29 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (26 bp):
CAAATAAGTCATTCACAAATAGTTCA
Found at i:8361 original size:22 final size:22
Alignment explanation
Indices: 8328--8370 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
8318 TACAGAGATG
*
8328 AAATGAAGAGAGGAAGAAAATT
1 AAATGAAGAGAGAAAGAAAATT
*
8350 AAATG-AGAAGAGAAAGGAAAT
1 AAATGAAG-AGAGAAAGAAAAT
8371 GAAAACATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (22 bp):
AAATGAAGAGAGAAAGAAAATT
Found at i:10301 original size:45 final size:45
Alignment explanation
Indices: 10216--10301 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
10206 ATTAAATATC
* * * ** *
10216 AATAACCAAAGCAAACTGAAATTAACAACTACCCTTTCCAACATT
1 AATAACCAAACCAAACTAAAACTAACAACTAAACTCTCCAACATT
*
10261 AATAATCAAACCAAACTAAAACTAACAACTAAACTCTCCAA
1 AATAACCAAACCAAACTAAAACTAACAACTAAACTCTCCAA
10302 ACATCCACCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.51, C:0.27, G:0.02, T:0.20
Consensus pattern (45 bp):
AATAACCAAACCAAACTAAAACTAACAACTAAACTCTCCAACATT
Found at i:10747 original size:435 final size:433
Alignment explanation
Indices: 10204--11075 Score: 1640
Period size: 432 Copynumber: 2.0 Consensus size: 433
10194 AATCAAACTA
10204 AAAT-TAAATATCAATAACCAAAGCAAACTGAAATTAACAACTACCCTTTCCAACATTAATAATC
1 AAATGTAAATATCAATAACCAAAGCAAACTGAAATTAACAACTACCCTTTCCAACATTAATAATC
*
10268 AAACCAAACTAAAACTAACAACTAAACTCTCCAAACATCCACCTCTCTAAATACCAAGCAACATC
66 AAACCAAACTAAAACTAACAACTAAACTCTCCAAACACCCACCTCTCTAAATACCAAGCAACATC
10333 AAATAATGGCCAAAGTTGACAAAAAAAAAATTGACATGAAGCCTCAAGGGGACAAAAAATGACAT
131 AAATAATGGCCAAAGTT-A-AAAAAAAAAA-TGACATGAAGCCTCAAGGGGACAAAAAATGACAT
*
10398 GACATGACACCTAAATCCTAACCATGAAATGACAAACCCTAAGTGAGATGAATGGTAAATCCCAA
193 GACATGACACCTAAATCCTAACCATGAAATGACAAACCCTAAGTGAGATGAATGGTAAACCCCAA
10463 CCATGACATGAAAACCAAACCCTAACATGTCATCCAAAGTGAAGGGC-AAAAAGAATTGGAATGC
258 CCATGACATGAAAACCAAACCCTAACATGTCATCCAAAGTGAAGGGCAAAAAAGAATTGGAATGC
10527 CCAAATTATCCTCAAAGCTTATATTAAATGCCAAAATTACCCTCGAGACTTATACGAAATAACAA
323 CCAAATTATCCTCAAAGCTTATATTAAATGCCAAAATTACCCTCGAGACTTATACGAAATAACAA
10592 AAGAACCAATGGCAAAAATACCAAAAAACCATGCAAATAGTACCCC
388 AAGAACCAATGGCAAAAATACCAAAAAACCATGCAAATAGTACCCC
10638 AAATGTAAATATCAATAACCAAAGCAAACTGAAATTAACAACTACCCTTTCCAACATTAATAATC
1 AAATGTAAATATCAATAACCAAAGCAAACTGAAATTAACAACTACCCTTTCCAACATTAATAATC
* *
10703 AAACTAAACTAAAATTAACAACTAAACTCTCCAAACACCCACCTCTCTAAATACCAAGCAACATC
66 AAACCAAACTAAAACTAACAACTAAACTCTCCAAACACCCACCTCTCTAAATACCAAGCAACATC
*
10768 AAATAATGGCCAAAGTTAACAAAAAAAATGACATGAAGCCTCAAGGGGACAAAAAATGACATGAC
131 AAATAATGGCCAAAGTTAAAAAAAAAAATGACATGAAGCCTCAAGGGGACAAAAAATGACATGAC
10833 ATGACACCTAAATCCTAACCATGAAATGACAAACCCTAAGTGAGATGAATGGTAAACCCCAACCA
196 ATGACACCTAAATCCTAACCATGAAATGACAAACCCTAAGTGAGATGAATGGTAAACCCCAACCA
10898 TGACATGAAAACCAAACCCTAACATGTCATCCAAAGTGAAGGGCAAAAAAGAATTGGAATGCCCA
261 TGACATGAAAACCAAACCCTAACATGTCATCCAAAGTGAAGGGCAAAAAAGAATTGGAATGCCCA
*
10963 AATTATCCTCAAAGCTTATATTAGATGCCAAAATTACCCTCGAGACTTATACGAAATAACAAAAG
326 AATTATCCTCAAAGCTTATATTAAATGCCAAAATTACCCTCGAGACTTATACGAAATAACAAAAG
*
11028 AACCAATGGCAAAAATACTAAAAAACCATGCAAATAGTACCCC
391 AACCAATGGCAAAAATACCAAAAAACCATGCAAATAGTACCCC
11071 AAATG
1 AAATG
11076 AATGTGGTGA
Statistics
Matches: 429, Mismatches: 7, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
432 145 0.34
433 140 0.33
434 5 0.01
435 139 0.32
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.19
Consensus pattern (433 bp):
AAATGTAAATATCAATAACCAAAGCAAACTGAAATTAACAACTACCCTTTCCAACATTAATAATC
AAACCAAACTAAAACTAACAACTAAACTCTCCAAACACCCACCTCTCTAAATACCAAGCAACATC
AAATAATGGCCAAAGTTAAAAAAAAAAATGACATGAAGCCTCAAGGGGACAAAAAATGACATGAC
ATGACACCTAAATCCTAACCATGAAATGACAAACCCTAAGTGAGATGAATGGTAAACCCCAACCA
TGACATGAAAACCAAACCCTAACATGTCATCCAAAGTGAAGGGCAAAAAAGAATTGGAATGCCCA
AATTATCCTCAAAGCTTATATTAAATGCCAAAATTACCCTCGAGACTTATACGAAATAACAAAAG
AACCAATGGCAAAAATACCAAAAAACCATGCAAATAGTACCCC
Found at i:11182 original size:2 final size:2
Alignment explanation
Indices: 11138--11174 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11128 ATTGTTTGTT
11138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11175 CAATATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11959 original size:22 final size:22
Alignment explanation
Indices: 11884--11983 Score: 87
Period size: 21 Copynumber: 4.6 Consensus size: 22
11874 TCATAGTTAG
* *
11884 GTTATCAAAAGTTTCATATGGAA
1 GTTATCAAAA-TTTTATATGGTA
* *
11907 TTTATCACAATTTTATA-GGTA
1 GTTATCAAAATTTTATATGGTA
* * *
11928 ATTATTAAAATTTTATATGGTG
1 GTTATCAAAATTTTATATGGTA
* *
11950 GTTATCAAAATTTAATAAGGTA
1 GTTATCAAAATTTTATATGGTA
*
11972 -ATATCAAAATTT
1 GTTATCAAAATTT
11984 CATAAAAATA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
21 28 0.45
22 26 0.42
23 8 0.13
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (22 bp):
GTTATCAAAATTTTATATGGTA
Found at i:11988 original size:21 final size:22
Alignment explanation
Indices: 11863--11988 Score: 89
Period size: 22 Copynumber: 5.8 Consensus size: 22
11853 ATAGGAAAGT
* * *
11863 TTATTAAAATTTCAT-AGTTAGG
1 TTATCAAAATTTCATAAGGTA-A
*
11885 TTATCAAAAGTTTCATATGG-AA
1 TTATCAAAA-TTTCATAAGGTAA
* *
11907 TTTATCACAATTTTAT-AGGTAA
1 -TTATCAAAATTTCATAAGGTAA
* * * **
11929 TTATTAAAATTTTATATGGTGG
1 TTATCAAAATTTCATAAGGTAA
*
11951 TTATCAAAATTTAATAAGGTAA
1 TTATCAAAATTTCATAAGGTAA
11973 -TATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
11989 AAATATTTAA
Statistics
Matches: 81, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
21 30 0.37
22 35 0.43
23 15 0.19
24 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGTAA
Found at i:12225 original size:20 final size:19
Alignment explanation
Indices: 12200--12241 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
12190 GAAGGAAAAC
12200 AAATTTATATTTCAAGATAT
1 AAATTTAT-TTTCAAGATAT
*
12220 AAATTTGTTTTCAAGATAT
1 AAATTTATTTTCAAGATAT
12239 AAA
1 AAA
12242 ATCATCTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (19 bp):
AAATTTATTTTCAAGATAT
Found at i:13487 original size:2 final size:2
Alignment explanation
Indices: 13482--13521 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
13472 TTTTTTCAAG
13482 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
13522 CCTTGTACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23757 original size:57 final size:58
Alignment explanation
Indices: 23635--23757 Score: 171
Period size: 57 Copynumber: 2.2 Consensus size: 58
23625 CCTTTCACAC
* *
23635 AATAAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATTCTTTCA
1 AATAAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTACA
* * *
23693 CA-CAATAAATGTTATAATAAATCATAT-TCCCCTATCTCTACTTAATTATTC-TACAA
1 AATAAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTAC-A
23749 AATAAATAA
1 AATAAATAA
23758 TATTTTCTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
55 2 0.04
56 25 0.45
57 28 0.50
58 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (58 bp):
AATAAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTACA
Found at i:23870 original size:42 final size:42
Alignment explanation
Indices: 23811--23890 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
23801 AAGGATCAGA
23811 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATG
1 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATG
*
23853 ATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
23891 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (42 bp):
ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATG
Found at i:24898 original size:55 final size:55
Alignment explanation
Indices: 24811--24977 Score: 298
Period size: 55 Copynumber: 3.0 Consensus size: 55
24801 TCTGTTTCCT
* *
24811 TTCACACAATAAATGTTATAATAAATCTTATCCCCCAATCTCTACTTAATTATTC
1 TTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATTC
24866 TTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATTC
1 TTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATTC
*
24921 TTCACACAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATTC
1 TTCACACAATAAATGTTATAATAAATCATAT-CCCCCTATCTCTACTTAATTATTC
24977 T
1 T
24978 ACAAAACATA
Statistics
Matches: 108, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
55 83 0.77
56 25 0.23
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (55 bp):
TTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATTC
Found at i:25349 original size:42 final size:42
Alignment explanation
Indices: 25290--25370 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
25280 TAAGGATCAG
*
25290 GATTTGAGTTGAGTATTTCTTAATTTAGAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
25332 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
25371 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:39245 original size:21 final size:22
Alignment explanation
Indices: 39207--39249 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
39197 ATAATAAAAT
39207 AATATATTATTATATTATTAAA
1 AATATATTATTATATTATTAAA
* *
39229 AATAT-TTTTTATCTTATTAAA
1 AATATATTATTATATTATTAAA
39250 TGAAAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATATTATTATATTATTAAA
Done.