Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008797.1 Corchorus capsularis cultivar CVL-1 contig08818, 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: 35245
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:859 original size:22 final size:22
Alignment explanation
Indices: 775--863 Score: 92
Period size: 22 Copynumber: 4.0 Consensus size: 22
765 CTAATCCCTG
* *
775 TGAAACTTTGACACCCACACTA
1 TGAAACTTTGATAACCACACTA
797 TGAAA-TTTCGATAACCATC-CTA
1 TGAAACTTT-GATAACCA-CACTA
* * * *
819 TGAAATTTTGATTATCACATTA
1 TGAAACTTTGATAACCACACTA
841 TGAAACTTTGATAACCACACTA
1 TGAAACTTTGATAACCACACTA
863 T
1 T
864 AAAATAGTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
21 4 0.07
22 46 0.85
23 4 0.07
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (22 bp):
TGAAACTTTGATAACCACACTA
Found at i:984 original size:22 final size:22
Alignment explanation
Indices: 958--999 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
948 GATTTGGTAC
958 ACTATGAAATTTGGATAACCAT
1 ACTATGAAATTTGGATAACCAT
*
980 ACTATGAAATTTTGATAACC
1 ACTATGAAATTTGGATAACC
1000 TCCCTAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
ACTATGAAATTTGGATAACCAT
Found at i:1148 original size:22 final size:22
Alignment explanation
Indices: 1030--1173 Score: 107
Period size: 22 Copynumber: 6.6 Consensus size: 22
1020 TTCCCTATAG
* *
1030 AATTTTGTTAAT-ATCACTATGA
1 AATTTTGATAATCA-CATTATGA
* ** *
1052 AATTTTGATAAGCACAACATCA
1 AATTTTGATAATCACATTATGA
* *
1074 AATTTTGATTA-C-CTTCTATGA
1 AATTTTGATAATCACAT-TATGA
*
1095 AATTTTTG-TAACCACATTATGA
1 AA-TTTTGATAATCACATTATGA
** *
1117 AATTAGGATAATTACATTATGA
1 AATTTTGATAATCACATTATGA
* *
1139 AATTTTGATAGTCACACTATGA
1 AATTTTGATAATCACATTATGA
1161 AATTTTGATAATC
1 AATTTTGATAATC
1174 TGCAAAGTGA
Statistics
Matches: 94, Mismatches: 22, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
20 1 0.01
21 11 0.12
22 79 0.84
23 3 0.03
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
AATTTTGATAATCACATTATGA
Found at i:1639 original size:29 final size:31
Alignment explanation
Indices: 1606--1669 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1596 TAGTAGTTTA
1606 GAAATATGTTTT-AAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
1635 GAAATATGTTTTAAAAATAAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
1666 GAAA
1 GAAA
1670 ATATAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 12 0.36
30 4 0.12
31 17 0.52
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATTG
Found at i:1721 original size:5 final size:5
Alignment explanation
Indices: 1698--1742 Score: 65
Period size: 5 Copynumber: 9.0 Consensus size: 5
1688 GTACTTTTAT
*
1698 ATATA GTATA GATAT- ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1743 TTTAGATAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 4 0.11
5 29 0.81
6 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:1771 original size:11 final size:12
Alignment explanation
Indices: 1698--1772 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 12
1688 GTACTTTTAT
1698 ATATAG-TATAG
1 ATATAGATATAG
1709 ATAT--ATATA-
1 ATATAGATATAG
1718 ATATA-ATATA-
1 ATATAGATATAG
1728 ATATA-ATATA-
1 ATATAGATATAG
* *
1738 ATATATTTAGATAG
1 ATATA--GATATAG
1752 ATATAGATATAG
1 ATATAGATATAG
1764 AT-TAGATAT
1 ATATAGATAT
1773 TTTTGCCCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
9 4 0.07
10 24 0.44
11 11 0.20
12 7 0.13
13 4 0.07
14 5 0.09
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (12 bp):
ATATAGATATAG
Found at i:6642 original size:52 final size:53
Alignment explanation
Indices: 6497--6661 Score: 156
Period size: 52 Copynumber: 3.0 Consensus size: 53
6487 CAAGGACATT
* * * *
6497 TATAAGTCCCTAAACACAGAGGCAATTCTATATTAAAAGTCCTCAAACACAAGGGCATT
1 TATAAGTCCCTAAACACAGAGGC-A--CTCT-CTCAAAGTCCTCAAACACAAGGG--TA
6556 TATAAGTCCCTAAACACAGAGGCACCTCTCTCAAAGTCCTCAAACACAAGGGTA
1 TATAAGTCCCTAAACACAGAGGCA-CTCTCTCAAAGTCCTCAAACACAAGGGTA
* * * *
6610 T-TCA-TCCCTAAGCACATAGGCA-TCTACATCAAAGTCCTCAAGCACAAGGGTA
1 TATAAGTCCCTAAACACAGAGGCACTCT-C-TCAAAGTCCTCAAACACAAGGGTA
6662 CCTACATTAA
Statistics
Matches: 95, Mismatches: 9, Indels: 11
0.83 0.08 0.10
Matches are distributed among these distances:
50 3 0.03
51 1 0.01
52 39 0.41
53 2 0.02
54 2 0.02
56 21 0.22
57 3 0.03
58 1 0.01
59 23 0.24
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.21
Consensus pattern (53 bp):
TATAAGTCCCTAAACACAGAGGCACTCTCTCAAAGTCCTCAAACACAAGGGTA
Found at i:6655 original size:30 final size:31
Alignment explanation
Indices: 6614--6681 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
6604 AGGGTATTCA
*
6614 TCCCT-AAGCACATA-GGCATCTACATCAAAG
1 TCCCTCAAGCACA-AGGGCACCTACATCAAAG
* *
6644 T-CCTCAAGCACAAGGGTACCTACATTAAAG
1 TCCCTCAAGCACAAGGGCACCTACATCAAAG
6674 TCCCTCAA
1 TCCCTCAA
6682 TACAGAGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 4 0.12
30 22 0.69
31 6 0.19
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.21
Consensus pattern (31 bp):
TCCCTCAAGCACAAGGGCACCTACATCAAAG
Found at i:6831 original size:2 final size:2
Alignment explanation
Indices: 6792--6822 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6782 AATATTCCAT
6792 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 T
6823 GCATATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14303 original size:7 final size:7
Alignment explanation
Indices: 14291--14374 Score: 105
Period size: 7 Copynumber: 11.0 Consensus size: 7
14281 TCATACATAC
14291 CCAAATA
1 CCAAATA
14298 CCAAATA
1 CCAAATA
14305 TCCAAATA
1 -CCAAATA
14313 TCCAAATA
1 -CCAAATA
14321 CCAAATA
1 CCAAATA
14328 TCCAAATA
1 -CCAAATA
14336 CCAAAATATA
1 CC--AA-ATA
14346 CCAAATA
1 CCAAATA
14353 CCAAATA
1 CCAAATA
14360 CCAAATA
1 CCAAATA
14367 TCCAAATA
1 -CCAAATA
14375 TTCAAATACT
Statistics
Matches: 71, Mismatches: 0, Indels: 11
0.87 0.00 0.13
Matches are distributed among these distances:
7 33 0.46
8 31 0.44
9 2 0.03
10 5 0.07
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (7 bp):
CCAAATA
Found at i:14309 original size:8 final size:8
Alignment explanation
Indices: 14291--14382 Score: 122
Period size: 8 Copynumber: 11.9 Consensus size: 8
14281 TCATACATAC
14291 CCAAATA-
1 CCAAATAT
14298 CCAAATAT
1 CCAAATAT
14306 CCAAATAT
1 CCAAATAT
14314 CCAAATA-
1 CCAAATAT
14321 CCAAATAT
1 CCAAATAT
14329 CCAAATA-
1 CCAAATAT
14336 CCAAAATAT
1 CC-AAATAT
14345 ACCAAATA-
1 -CCAAATAT
14353 CCAAATA-
1 CCAAATAT
14360 CCAAATAT
1 CCAAATAT
14368 CCAAATAT
1 CCAAATAT
*
14376 TCAAATA
1 CCAAATA
14383 CTCAGCAAAT
Statistics
Matches: 78, Mismatches: 1, Indels: 11
0.87 0.01 0.12
Matches are distributed among these distances:
7 30 0.38
8 41 0.53
9 5 0.06
10 2 0.03
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.21
Consensus pattern (8 bp):
CCAAATAT
Found at i:14318 original size:23 final size:22
Alignment explanation
Indices: 14291--14383 Score: 125
Period size: 23 Copynumber: 4.0 Consensus size: 22
14281 TCATACATAC
14291 CCAAATACCAAATATCCAAATA
1 CCAAATACCAAATATCCAAATA
14313 TCCAAATACCAAATATCCAAATA
1 -CCAAATACCAAATATCCAAATA
14336 CCAAAATATACCAAATA-CCAAATA
1 CC--AA-ATACCAAATATCCAAATA
*
14360 CCAAATATCCAAATATTCAAATA
1 CCAAATA-CCAAATATCCAAATA
14383 C
1 C
14384 TCAGCAAATT
Statistics
Matches: 64, Mismatches: 1, Indels: 10
0.85 0.01 0.13
Matches are distributed among these distances:
21 3 0.05
22 11 0.17
23 29 0.45
24 11 0.17
25 10 0.16
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (22 bp):
CCAAATACCAAATATCCAAATA
Found at i:19319 original size:55 final size:52
Alignment explanation
Indices: 19252--19354 Score: 125
Period size: 52 Copynumber: 1.9 Consensus size: 52
19242 CATTTATAAG
* *
19252 TCCCTAAACACAGAGGCAATTCTATATTAAAAGTTCTCAAACACAAGGGTATTCA
1 TCCCTAAACACAGAGGC-A-TCTACA-TAAAAGTCCTCAAACACAAGGGTATTCA
* * * *
19307 TCCCTAAGCACAGATGCATCTACATCAAAGTCCTCAAGCACAAGGGTA
1 TCCCTAAACACAGAGGCATCTACATAAAAGTCCTCAAACACAAGGGTA
19355 CCTACATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
52 21 0.50
53 5 0.12
54 1 0.02
55 15 0.36
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (52 bp):
TCCCTAAACACAGAGGCATCTACATAAAAGTCCTCAAACACAAGGGTATTCA
Found at i:19396 original size:30 final size:30
Alignment explanation
Indices: 19362--19436 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
19352 GTACCTACAT
19362 TAAAGTCCCCAAACATAGAGGCATCTATAC
1 TAAAGTCCCCAAACATAGAGGCATCTATAC
19392 TAAAGTCCCCAAACATAGAGGCATCTATAC
1 TAAAGTCCCCAAACATAGAGGCATCTATAC
19422 TAAAGTCCCCAAACA
1 TAAAGTCCCCAAACA
19437 CATATAACAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (30 bp):
TAAAGTCCCCAAACATAGAGGCATCTATAC
Done.