Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011936.1 Corchorus capsularis cultivar CVL-1 contig11957, 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: 12078
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Found at i:868 original size:21 final size:21
Alignment explanation
Indices: 842--881 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
832 AGCACAAGTG
842 ACCGGCCATGCGACTTGGACA
1 ACCGGCCATGCGACTTGGACA
863 ACCGGCCATGCGACTTGGA
1 ACCGGCCATGCGACTTGGA
882 GATGCCTGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.15
Consensus pattern (21 bp):
ACCGGCCATGCGACTTGGACA
Found at i:905 original size:33 final size:33
Alignment explanation
Indices: 863--1008 Score: 131
Period size: 33 Copynumber: 4.4 Consensus size: 33
853 GACTTGGACA
* *
863 ACCGGCCATGCGACTTGGAGATG-CCTGCGCAAC
1 ACCGGCCATGCGACATGGAGATGCCCGGC-CAAC
*
896 ACCGGCCATGCGACATGGAGATGCCCGGCCATC
1 ACCGGCCATGCGACATGGAGATGCCCGGCCAAC
* **
929 ACCGGCCACGCGACATGGCCATGCCCGGCC-AC
1 ACCGGCCATGCGACATGGAGATGCCCGGCCAAC
* **
961 ACCCGGCCACT-TGAC-TCGGCCATGCCCGGCC-AC
1 A-CCGGCCA-TGCGACAT-GGAGATGCCCGGCCAAC
994 AACCGGCCATGCGAC
1 -ACCGGCCATGCGAC
1009 CCTTTGTATA
Statistics
Matches: 97, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
32 4 0.04
33 88 0.91
34 5 0.05
ACGTcount: A:0.20, C:0.41, G:0.28, T:0.11
Consensus pattern (33 bp):
ACCGGCCATGCGACATGGAGATGCCCGGCCAAC
Found at i:7731 original size:75 final size:75
Alignment explanation
Indices: 7538--7718 Score: 258
Period size: 75 Copynumber: 2.4 Consensus size: 75
7528 TTATGTAGAC
* * *
7538 TGTGAGCAAAGGAACGATGGGTTTTAATCAAAAAAAGTTTC-AAATCAGTTTCAATCAAAGCAAT
1 TGTGAGCAAAAGAATGATGAGTTTTAATCAAAAAAAGTTTCAAAATCAGTTTCAATCAAAGCAAT
*
7602 GGTTTCGAGG
66 GGTTTCAAGG
* * * *
7612 TGTGGGCAAAAGAATCATGAGTTTTAATCAAAACAGGTTTCAAAATCAGTTTCAATCAAAGCAAT
1 TGTGAGCAAAAGAATGATGAGTTTTAATCAAAAAAAGTTTCAAAATCAGTTTCAATCAAAGCAAT
7677 GGTTTCAAGG
66 GGTTTCAAGG
*
7687 TGTGAGCAAATA-AGTGATGAGTTTTAATCAAA
1 TGTGAGCAAA-AGAATGATGAGTTTTAATCAAA
7719 GGATGTTTCA
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
74 34 0.36
75 59 0.63
76 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.28
Consensus pattern (75 bp):
TGTGAGCAAAAGAATGATGAGTTTTAATCAAAAAAAGTTTCAAAATCAGTTTCAATCAAAGCAAT
GGTTTCAAGG
Found at i:8544 original size:14 final size:15
Alignment explanation
Indices: 8525--8562 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
8515 GATGAAAAAG
8525 AAAGAAGAA-AAGGA
1 AAAGAAGAAGAAGGA
8539 AAAGAA-AAGAAGGA
1 AAAGAAGAAGAAGGA
*
8553 AAAAAAGAAG
1 AAAGAAGAAG
8563 TGAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 16 0.76
15 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAGAAGAAGAAGGA
Found at i:8916 original size:16 final size:16
Alignment explanation
Indices: 8897--8934 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
8887 TGAAAAAATG
8897 AAAGAAAAAGAAAAAA
1 AAAGAAAAAGAAAAAA
*
8913 AAAGAAAAAGAGAAAA
1 AAAGAAAAAGAAAAAA
*
8929 AGAGAA
1 AAAGAA
8935 TGAAGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAAAAAA
Found at i:9273 original size:50 final size:50
Alignment explanation
Indices: 9215--9366 Score: 225
Period size: 50 Copynumber: 3.0 Consensus size: 50
9205 GAAGTTTTAT
*
9215 AAATAAGATTGCATTCCATCTGTGAGGT-CAATATCAAAATTCGATTTTCA
1 AAATAAGATTGCATTCCATTTGTGA-GTCCAATATCAAAATTCGATTTTCA
* * *
9265 AAATAAGATTGCATTTCATTTATGAGTCCAATATCAAAATTCGATTTTCG
1 AAATAAGATTGCATTCCATTTGTGAGTCCAATATCAAAATTCGATTTTCA
* * *
9315 AGATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCA
1 AAATAAGATTGCATTCCATTTGTGAGTCCAATATCAAAATTCGATTTTCA
9365 AA
1 AA
9367 GGGCATTTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 2 0.02
50 88 0.98
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (50 bp):
AAATAAGATTGCATTCCATTTGTGAGTCCAATATCAAAATTCGATTTTCA
Found at i:9756 original size:70 final size:70
Alignment explanation
Indices: 9673--10589 Score: 1230
Period size: 70 Copynumber: 13.2 Consensus size: 70
9663 AATGTTTTGA
*
9673 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATCCAAGCATG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAG-TCAGTTCAAGCTTTGGTTCCATCCAAGCATG
9737 CAGGGG
65 CAGGGG
* *** *
9743 CTTTTCCATAAGCCAAACTCGTTTCCATA-GACAGAGTTCAAGCTTTGGTTCCATCCAAAGCATT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCC-AAGCATG
9807 CAGGGG
65 CAGGGG
** * *
9813 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGAGAGTTCAAGTTTTGGTTCCATCCAAAGCATT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCC-AAGCATG
9878 CAGGGG
65 CAGGGG
* *
9884 CTTTTCCACAAGCCAAACTCGTTTCAATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCATGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
9949 AGGGG
66 AGGGG
* * ** *
9954 CTTTTCCATAAGCCAAACTCGTTTCCATATGAGAGAGTTCAAGCTTTGGTTCCATCCAAACATGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
10019 AGGGG
66 AGGGG
* *
10024 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAACA-GC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
*
10088 AGCGG
66 AGGGG
* * *
10093 CTTTTCCACAAGCCAAACTCGTTT-CATACGAGTCAGTTCAAACTTTGGTTCCATCCAAGTATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
10157 AGGGG
66 AGGGG
* * * * *
10162 CTTTTCCACAAGCCATACTCGTTTCCATACGAATCAGTTCAAACTTTGGTTCCATCCAAGTATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
10227 AGGGG
66 AGGGG
* * * *
10232 CTCTTT-CACAAGCCAAACTCGTATCCATACGAGTCAGTTCAAACTTTGGTTCCATCCAAGTATT
1 CT-TTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATG
10296 CAGGGG
65 CAGGGG
* * * *
10302 CTTTTCCACAAGCCAAACTCGTTTCCATACGAATCAGTTCAAACTTTGGTTCCATCCAAGTATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
10367 AGGGG
66 AGGGG
* * * *
10372 CTTTTTCACAAGCCAAACTTGTTTCCATACAAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
10436 AGGGG
66 AGGGG
* * * *
10441 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATT-TAGCCTTGGTTCCATCCAAGCA-GC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
*
10504 AAGGG
66 AGGGG
* * * * * * *
10509 CTTTTCCACTAGCCAAGCTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCC-A--AT-T
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
10569 AGGGG
66 AGGGG
*
10574 CTTTTCCATAAGCCAA
1 CTTTTCCACAAGCCAA
10590 GTTCATTTCC
Statistics
Matches: 776, Mismatches: 63, Indels: 21
0.90 0.07 0.02
Matches are distributed among these distances:
65 19 0.02
67 1 0.00
68 110 0.14
69 125 0.16
70 427 0.55
71 94 0.12
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (70 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
AGGGG
Found at i:10317 original size:348 final size:349
Alignment explanation
Indices: 9673--10537 Score: 1253
Period size: 348 Copynumber: 2.5 Consensus size: 349
9663 AATGTTTTGA
* *
9673 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATCCAAGCATG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAG-TCAGTTCAAGCCTTGGTTCCATCCAAGCA-G
* ***
9737 CAGGGGCTTTTCCATAAGCCAAACTCGTTTCCATA-GACAGAGTTCAAGCTTTGGTTCCATCCAA
64 CAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCC-A
* **
9801 AGCATTCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGAGAGTTCAAGTTTTGGTTCC
128 AGCATTCAGGGGCTTTTCCACAAGCC-AACTCGTTTCCATACGAGACAGTTCAAACTTTGGTTCC
* *
9866 ATCCAAAGCATTCAGGGGCTTTTCCACAAGCCAAACTCGTTTCAATACGAGTCAGTTCAAGCCTT
192 ATCCAAAGCATTCAGGGGCTTTTCCACAAGCCAAACTCGTATCAATACGAGTCAGTTCAAACCTT
* * *
9931 GGTTCCATCCAAGCATGCAGGGGCTTTTCCATAAGCCAAACTCGTTTCCATATGAGA-GAGTTCA
257 GGTTCCATCCAAGCATGCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGA-ATCAGTTCA
*
9995 AGCTTTGGTTCCATCCAAACATGCAGGGG
321 AACTTTGGTTCCATCCAAACATGCAGGGG
*
10024 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAACAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* * *
10089 GCGGCTTTTCCACAAGCCAAACTCGTTT-CATACGAGTCAGTTCAAACTTTGGTTCCATCCAAGT
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGC
10153 ATTCAGGGGCTTTTCCACAAGCCATACTCGTTTCCATACGA-ATCAGTTCAAACTTTGGTTCCAT
131 ATTCAGGGGCTTTTCCACAAGCCA-ACTCGTTTCCATACGAGA-CAGTTCAAACTTTGGTTCCAT
* * *
10217 CC-AAGTATTCAGGGGCTCTTT-CACAAGCCAAACTCGTATCCATACGAGTCAGTTCAAACTTTG
194 CCAAAGCATTCAGGGGCT-TTTCCACAAGCCAAACTCGTATCAATACGAGTCAGTTCAAACCTTG
* *
10280 GTTCCATCCAAGTATTCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAATCAGTTCAAA
258 GTTCCATCCAAGCATGCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAATCAGTTCAAA
** *
10345 CTTTGGTTCCATCCAAGTATTCAGGGG
323 CTTTGGTTCCATCCAAACATGCAGGGG
* * *
10372 CTTTTTCACAAGCCAAACTTGTTTCCATACAAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* * * *
10437 GGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATT-TAGCCTTGGTTCCATCCAAGC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGC
* * *
10501 A-GCAAGGGCTTTTCCACTAGCCAAGCTCGTTTCCATA
131 ATTCAGGGGCTTTTCCACAAGCCAA-CTCGTTTCCATA
10538 TGAGTTAGTT
Statistics
Matches: 465, Mismatches: 41, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
346 1 0.00
347 32 0.07
348 241 0.52
349 81 0.17
350 53 0.11
351 57 0.12
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (349 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGC
ATTCAGGGGCTTTTCCACAAGCCAACTCGTTTCCATACGAGACAGTTCAAACTTTGGTTCCATCC
AAAGCATTCAGGGGCTTTTCCACAAGCCAAACTCGTATCAATACGAGTCAGTTCAAACCTTGGTT
CCATCCAAGCATGCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAATCAGTTCAAACTT
TGGTTCCATCCAAACATGCAGGGG
Done.