Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005719.1 Corchorus capsularis cultivar CVL-1 contig05737, 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: 11500
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:948 original size:196 final size:195
Alignment explanation
Indices: 367--948 Score: 751
Period size: 196 Copynumber: 3.0 Consensus size: 195
357 TTTTGTTGGC
* * * *
367 TCCCCAGTGGAGTCGCCAGAAAATGTGGGAGCCTTTTTGTGCGAAAGGTAGGCCTGACCCGGCTC
1 TCCCCAGCGGAGTCGCCATAAAATGTGGGAGCCTTTTTGTGCGAAAGGTAAGCCTGACCCAGCTC
* * * ** * * * *
432 -AAGGGGTGGA-TCCTAGCCAGCCCC-AACTTCC-CAAAAGAAGAATTGGGTTTCTAAAGATGGG
66 GATGAGTTGGATTCAAAGCCAGCCCCAAACTTCCTCAGAAGAAGAAATGGGTTTCTGAAGATGGT
* *
493 GGCAAGGAGGAATGAGGAAATTCTGCGGTGATTGGATGAGACTTGCAATAGAAAAAGTAACTCTT
131 GGCAAGGAGGAATGAGGAAATTCTGCGGTGATTGGATGAGACTTGCAACAGGAAAA-TAACTCTT
558 G
195 G
* * * *
559 TCCCTAGCGGAGTCACCATAAATTGTAGGAGCCTTTTTGTGCGAAAGGTAAGCCTGACCCAGCTC
1 TCCCCAGCGGAGTCGCCATAAAATGTGGGAGCCTTTTTGTGCGAAAGGTAAGCCTGACCCAGCTC
* * *
624 GATGAATTGGATTCAAAGCCAGCCCCAAACTTCCTCAGAAGAAGAAGTGGGTTTTTGAAGATGGT
66 GATGAGTTGGATTCAAAGCCAGCCCCAAACTTCCTCAGAAGAAGAAATGGGTTTCTGAAGATGGT
* * * * * * *
689 GACCAGGAGGAATGAGGAAATTTTACGGTGATTGGATGAGACATGCAGCAAGGAAAGTAACTCTT
131 GGCAAGGAGGAATGAGGAAATTCTGCGGTGATTGGATGAGACTTGCAAC-AGGAAAATAACTCTT
754 G
195 G
* * * *
755 TCCCCGGCGGAGTCGCCATAAAATGTGGGAGTCTTTTTGTGTGAAAGGTAAGCCTGGCCCAGCTC
1 TCCCCAGCGGAGTCGCCATAAAATGTGGGAGCCTTTTTGTGCGAAAGGTAAGCCTGACCCAGCTC
*
820 GATGAGTTGGATTCAAAGCCGGCCCCAAACTTCCTCAGAAGAAGAAATGGGTTTCTGAAGATGGT
66 GATGAGTTGGATTCAAAGCCAGCCCCAAACTTCCTCAGAAGAAGAAATGGGTTTCTGAAGATGGT
* * * *
885 GGCAAGGTGGAAT-AGGGAAATCCCGCGGTGATTGGATGAGACTTGTAACAGGGAAAATAACTCT
131 GGCAAGGAGGAATGA-GGAAATTCTGCGGTGATTGGATGAGACTTGCAACA-GGAAAATAACTCT
949 CTTCTCAATG
Statistics
Matches: 332, Mismatches: 51, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
192 57 0.17
193 6 0.02
194 12 0.04
195 9 0.03
196 243 0.73
197 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.23
Consensus pattern (195 bp):
TCCCCAGCGGAGTCGCCATAAAATGTGGGAGCCTTTTTGTGCGAAAGGTAAGCCTGACCCAGCTC
GATGAGTTGGATTCAAAGCCAGCCCCAAACTTCCTCAGAAGAAGAAATGGGTTTCTGAAGATGGT
GGCAAGGAGGAATGAGGAAATTCTGCGGTGATTGGATGAGACTTGCAACAGGAAAATAACTCTTG
Found at i:7139 original size:2 final size:2
Alignment explanation
Indices: 7132--7174 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
7122 ATCAATGCCA
*
7132 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT TT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
7174 A
1 A
7175 AAAGTAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7236 original size:31 final size:31
Alignment explanation
Indices: 7195--7260 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
7185 AATTTTATAT
* *
7195 TTTCCGATTGTATCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
*
7226 TTTCCAATTGTACCCTTTTCTTTGAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
7257 TTTC
1 TTTC
7261 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Found at i:7774 original size:22 final size:22
Alignment explanation
Indices: 7746--7886 Score: 74
Period size: 22 Copynumber: 6.3 Consensus size: 22
7736 TGTCTCTATG
7746 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
7768 TGGTTATTATAATTTGATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
7791 T-GTTATCAAAATTCCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
* *
7810 TGTGTTTACCAAAATTTCATAGGA
1 TG-G-TTATCAAAATTTCATAAGA
* * * *
7834 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
* **
7858 TGATTATTGAAATTTCAT-AGA
1 TGGTTATCAAAATTTCATAAGA
7879 GTGGTTAT
1 -TGGTTAT
7887 AAATCATCAC
Statistics
Matches: 88, Mismatches: 22, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 2 0.02
22 60 0.68
23 5 0.06
24 17 0.19
25 1 0.01
26 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:8047 original size:22 final size:21
Alignment explanation
Indices: 7999--8283 Score: 148
Period size: 22 Copynumber: 12.8 Consensus size: 21
7989 TTTCATGGGG
* *
7999 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
8021 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
*
8043 AGGTTAT-AAAAGTTTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* *
8068 AGGAGTATCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
8090 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
*
8109 AGTGATTATCGAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
8132 GATCGGATTATCAAAATTT-ATAGAA
1 -A--GG-TTATCAAAATTTCATAG-A
* * *
8157 AGATTATCAAAATTTCAAAGCG
1 AGGTTATCAAAATTTCATAG-A
*
8179 AGGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* * *
8199 TGTGATTATTAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
8222 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
*
8244 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
8266 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
8284 ATATGTGATT
Statistics
Matches: 205, Mismatches: 37, Indels: 42
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.01
20 11 0.05
21 26 0.13
22 122 0.60
23 5 0.02
24 7 0.03
25 20 0.10
26 8 0.04
27 4 0.02
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:8155 original size:46 final size:44
Alignment explanation
Indices: 7988--8308 Score: 178
Period size: 44 Copynumber: 7.2 Consensus size: 44
7978 TTCATTAAAT
* * ** * *
7988 ATTTCATGGGGAGGTTATCAAAATTTTATAGTGTGGTTATCAAA
1 ATTTCATAGAGAGGTTATCAAAATTACATAGAGTGATTATCAAA
*
8032 ATTTCATATGA-AGGTTAT-AAAAGTTTCAATTTCATA-AG-GAGTATCAAA
1 ATTTCATA-GAGAGGTTATCAAAA--TT--A---CATAGAGTGATTATCAAA
* *
8080 ATTTGATAGA-AGGTTATC-AAATCT-CATAGAGTGATTATCGAA
1 ATTTCATAGAGAGGTTATCAAAAT-TACATAGAGTGATTATCAAA
* **
8122 ATTTCATAGAGATCGGATTATCAAAATT-TATAGAAAGATTATCAAA
1 ATTTCATAGAGA--GG-TTATCAAAATTACATAGAGTGATTATCAAA
* * * *
8168 ATTTCAAAGCGAGGTTATCAAAATTACATA-ATGTGATTATTAGA
1 ATTTCATAGAGAGGTTATCAAAATTACATAGA-GTGATTATCAAA
* * * ** * * *
8212 ATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAA
1 ATTTCATAGAGAGGTTATCAAAATTACATAGAGTGATTATCAAA
* * * *
8256 ATTTCATAAAGAGGTTATCAAATTTTCAATA-TGTGATTA-CAAAA
1 ATTTCATAGAGAGGTTATCAAAATTAC-ATAGAGTGATTATC-AAA
8300 ATTTCATAG
1 ATTTCATAG
8309 TGGTATTTCT
Statistics
Matches: 212, Mismatches: 43, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
40 4 0.02
41 2 0.01
42 17 0.08
43 18 0.08
44 95 0.45
45 10 0.05
46 31 0.15
47 16 0.08
48 15 0.07
49 1 0.00
50 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (44 bp):
ATTTCATAGAGAGGTTATCAAAATTACATAGAGTGATTATCAAA
Found at i:8252 original size:88 final size:87
Alignment explanation
Indices: 8143--8308 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 87
8133 ATCGGATTAT
*
8143 CAAAATTTATAGAAAGATTATCAAAATTTCA-AAGCGAGGTTATCAAAATTAC-ATAATGTGATT
1 CAAAATTTATAGAAAGATTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAT-ATGTGATT
** *
8206 ATTAGAATTTCATAGAGGGGTCAA
64 ACAAAAATTTCATAGAGGGGTCAA
* * *
8230 CAAAATTTTATA-AAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAATATGTGATT
1 CAAAA-TTTATAGAA-AGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAATATGTGATT
8294 ACAAAAATTTCATAG
64 ACAAAAATTTCATAG
8309 TGGTATTTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
87 7 0.10
88 57 0.84
89 4 0.06
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (87 bp):
CAAAATTTATAGAAAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAATATGTGATTAC
AAAAATTTCATAGAGGGGTCAA
Found at i:8442 original size:22 final size:22
Alignment explanation
Indices: 8395--8929 Score: 173
Period size: 22 Copynumber: 24.6 Consensus size: 22
8385 TTATGGAGTA
* *
8395 ATCAAAATTTCA-A-GGAGGAT
1 ATCAAAATTTCATATGAAGGTT
8415 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* **
8437 ATCAAATTTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * * *
8459 TTCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
* *
8481 AACAAAATTTCATAATG-AGATT
1 ATCAAAATTTCAT-ATGAAGGTT
*
8503 ATCAAAA-ATCATAGTG-AGGTT
1 ATCAAAATTTCATA-TGAAGGTT
* *
8524 ATTAAAA-TT--TGT-AA--TT
1 ATCAAAATTTCATATGAAGGTT
* * *
8540 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
8562 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* * *
8585 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATGAAG-GTT
* *
8608 ATTAAAATCTCATA-GCAAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
8630 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
8652 ATCAAAATTTCAGA-GTATGATT
1 ATCAAAATTTCATATG-AAGGTT
* *
8674 A-CTAACAA-TTCATATGGAGATT
1 ATC-AA-AATTTCATATGAAGGTT
* * * * *
8696 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
* * *
8718 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
8740 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
8763 ATCAAAATTTCAT-TGGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
8785 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
* * * *
8808 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * * *
8829 AACCAAATTTCATAAGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
** **
8851 AAAAAAATTT-ATAAAAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * * **
8872 CTCGAAATTCCATA-GTATCGTT
1 ATCAAAATTTCATATG-AAGGTT
* *
8894 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
8916 ATCAAAATTTCATA
1 ATCAAAATTTCATA
8930 ATGGGATCAT
Statistics
Matches: 383, Mismatches: 93, Indels: 76
0.69 0.17 0.14
Matches are distributed among these distances:
16 7 0.02
17 2 0.01
18 2 0.01
19 2 0.01
20 16 0.04
21 41 0.11
22 246 0.64
23 65 0.17
24 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:8508 original size:44 final size:44
Alignment explanation
Indices: 8395--8929 Score: 244
Period size: 44 Copynumber: 12.3 Consensus size: 44
8385 TTATGGAGTA
* * * *
8395 ATCAAAATTTCA-AG-GAGGATATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
* * *
8437 ATCAAATTTTCATAGTTTA-GTTTTCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAG-TGAGGTTATCAAAATTTCATAGGGAGATT
* * * * * *
8481 AACAAAATTTCATAATGAGATTATCAAAA-ATCATAGTGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
* * * * *
8524 ATTAAAA-TT--T-GT-A-ATTATCAAGATTTCATA-AGAAAGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGA-TT
* * * *
8562 ATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGTGAGG-TTATCAAAATTTCATAGGGAGA-TT
* * ** * * *
8608 ATTAAAATCTCATAGCAAGGTTATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
* * *
8652 ATCAAAATTTCAGAGT-ATGATTA-CTAACAA-TTCATATGGAGATT
1 ATCAAAATTTCATAGTGA-GGTTATC-AA-AATTTCATAGGGAGATT
* * * ** * * * * *
8696 TTTAAATTTTCATAACGTGGTTATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
* * * *
8740 ATCAACATCTCATAGTGTTGGTTATCAAAATTTCATTGGGA-AGTT
1 ATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATAGGGAGA-TT
* * * *
8785 ATCAAAATTTCATATTGAGGTCT-TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAGGGAGATT
* * ** *** *
8829 AACCAAATTTCATAAG-GAGGTTAAAAAAATTT-ATAAAAAGGTT
1 ATCAAAATTTCAT-AGTGAGGTTATCAAAATTTCATAGGGAGATT
* * * * * * *
8872 CTCGAAATTCCATAGT-ATCGTTATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGTGA-GGTTATCAAAATTTCATAGGGAGATT
8916 ATCAAAATTTCATA
1 ATCAAAATTTCATA
8930 ATGGGATCAT
Statistics
Matches: 359, Mismatches: 105, Indels: 56
0.69 0.20 0.11
Matches are distributed among these distances:
37 11 0.03
38 14 0.04
39 3 0.01
40 1 0.00
41 1 0.00
42 17 0.05
43 52 0.14
44 169 0.47
45 72 0.20
46 19 0.05
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
Found at i:8588 original size:23 final size:23
Alignment explanation
Indices: 8538--8615 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
8528 AAATTTGTAA
* * * *
8538 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
8560 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
8583 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
8606 TTATTAAAAT
1 TTATCAAAAT
8616 CTCATAGCAA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 16 0.35
23 30 0.65
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:8622 original size:23 final size:23
Alignment explanation
Indices: 8538--8644 Score: 65
Period size: 23 Copynumber: 4.7 Consensus size: 23
8528 AAATTTGTAA
* * * *
8538 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATCTCATAGGAAGAT
* * * *
8560 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATCTCATAGGAAGAT
* *
8583 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATCTCATAGGAAGAT
* * *
8606 TTATTAAAATCTCATAGCAAG-G
1 TTATCAAAATCTCATAGGAAGAT
* *
8628 TTATCACAATTTCATAG
1 TTATCAAAATCTCATAG
8645 TGTGATTATC
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
22 30 0.44
23 38 0.56
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (23 bp):
TTATCAAAATCTCATAGGAAGAT
Found at i:8786 original size:45 final size:45
Alignment explanation
Indices: 8713--8798 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
8703 TTTCATAACG
* * *
8713 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
8758 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
8799 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:11079 original size:2 final size:2
Alignment explanation
Indices: 11072--11109 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11062 TGTACTCTTT
11072 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
11110 ATCAGATTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.