Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013036.1 Corchorus capsularis cultivar CVL-1 contig13057, 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: 20639
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35 GAAACCAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2325 original size:21 final size:21
Alignment explanation
Indices: 2299--2343 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2289 CAAAATGACA
2299 TAATTTACT-AAATATGTATTT
1 TAATTTACTCAAAT-TGTATTT
* *
2320 TAATTTATTCAAATTGTGTTT
1 TAATTTACTCAAATTGTATTT
2341 TAA
1 TAA
2344 GGCCCTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (21 bp):
TAATTTACTCAAATTGTATTT
Found at i:3064 original size:73 final size:74
Alignment explanation
Indices: 2939--3095 Score: 244
Period size: 73 Copynumber: 2.1 Consensus size: 74
2929 TGGTCTTTTC
* *
2939 ACACTTTTCGGGTGACTAAAAAGCCCCTCTATGAGTTTCCCATATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCACATTCCTTTTCCTTCTACCCTTT
3004 TTCGTAATT
66 TTCGTAATT
* * * *
3013 ACACTTTTCGGATGACTAAAAAG-TCCTTTATGAGTTTCCCCCATTCCTTTTCCTTTTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCACATTCCTTTTCCTTCTACCCTTT
3077 TTCGTAATT
66 TTCGTAATT
3086 ACACATTTTC
1 ACAC-TTTTC
3096 TTCCTTAATT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
73 49 0.64
74 27 0.36
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.42
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCACATTCCTTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:4887 original size:2 final size:2
Alignment explanation
Indices: 4882--4915 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4872 ACACACACAG
4882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4916 AAGATGTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8813 original size:30 final size:31
Alignment explanation
Indices: 8777--8846 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
8767 GGCGAAAATG
*
8777 CAATTCAGGATACACCGTTACCA-CTTGTGT
1 CAATTCAGGATACAACGTTACCAGCTTGTGT
* * *
8807 CAATTCAGGATATAACGTTATCAGGTTGTGT
1 CAATTCAGGATACAACGTTACCAGCTTGTGT
8838 CAATTCAGG
1 CAATTCAGG
8847 CAAAAAACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 20 0.57
31 15 0.43
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (31 bp):
CAATTCAGGATACAACGTTACCAGCTTGTGT
Found at i:8927 original size:23 final size:23
Alignment explanation
Indices: 8897--8941 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
8887 AAAAAATCGC
*
8897 GTTGAACGGTACACGTGTAATTT
1 GTTGAACGGTACACGCGTAATTT
*
8920 GTTGAACGTTACACGCGTAATT
1 GTTGAACGGTACACGCGTAATT
8942 AATTGGACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (23 bp):
GTTGAACGGTACACGCGTAATTT
Found at i:16041 original size:19 final size:20
Alignment explanation
Indices: 16017--16063 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
16007 ATGCATATGG
16017 ATTTTGT-CACTTTATGTGA
1 ATTTTGTCCACTTTATGTGA
*
16036 ATTTTGTGCCCCTTTATGTGA
1 ATTTTGT-CCACTTTATGTGA
*
16057 TTTTTGT
1 ATTTTGT
16064 AAGTTTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
21 17 0.71
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.55
Consensus pattern (20 bp):
ATTTTGTCCACTTTATGTGA
Found at i:16385 original size:30 final size:32
Alignment explanation
Indices: 16331--16396 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
16321 AACTTTATAT
*
16331 TTTCCGATTGTACCCTTATTTTT-AAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
*
16362 TTTCCAATTGTATCCTT-TTTTTAAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
16393 TTTC
1 TTTC
16397 TAAATTACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (32 bp):
TTTCCAATTGTACCCTTATTTTTAAAAACATA
Found at i:16563 original size:22 final size:22
Alignment explanation
Indices: 16536--16920 Score: 171
Period size: 22 Copynumber: 17.6 Consensus size: 22
16526 TAGTATGTAG
16536 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGATT
* **
16558 AACAAAATTTCATAATGAGATT
1 ATCAAAATTTCATAGGGAGATT
** *
16580 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGATT
*
16602 ATCAAAA-TT--T--GTAG-TT
1 ATCAAAATTTCATAGGGAGATT
* * *
16618 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGATT
* *
16640 ATCAAAATTTTATAGGGACATTT
1 ATCAAAATTTCATAGGGAGA-TT
* * *
16663 ATCAAAATTTTATAGGAAAGTTT
1 ATCAAAATTTCATAGG-GAGATT
* **
16686 ATCAAAATTTCACAGCAATG-TT
1 ATCAAAATTTCATAGGGA-GATT
* * *
16708 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGATT
* * *
16730 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGATT
* * * *
16752 ACTGACAA-TTCATATGGAGGTT
1 A-TCAAAATTTCATAGGGAGATT
* * * * ** * *
16774 TTTAAATTTTCAAAACGTGGTT
1 ATCAAAATTTCATAGGGAGATT
* * *
16796 ATCAATATATCATATGGAGATT
1 ATCAAAATTTCATAGGGAGATT
* ** *
16818 ATCAACATCTT-ATAGTGTTGGTT
1 ATCAAAAT-TTCATAG-GGAGATT
**
16841 ATCAAAATTTCATTTGGA-AGTT
1 ATCAAAATTTCATAGGGAGA-TT
*
16863 ATCAAAATTTCATAGTGAGATCT
1 ATCAAAATTTCATAGGGAGAT-T
* * *
16886 -TCAAAATTCCTTATGGAGATT
1 ATCAAAATTTCATAGGGAGATT
*
16907 AACAAAATTTCATA
1 ATCAAAATTTCATA
16921 AGGTTAAAAA
Statistics
Matches: 266, Mismatches: 78, Indels: 38
0.70 0.20 0.10
Matches are distributed among these distances:
16 8 0.03
17 5 0.02
19 2 0.01
21 9 0.03
22 187 0.70
23 54 0.20
24 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGATT
Found at i:16584 original size:44 final size:44
Alignment explanation
Indices: 16536--16920 Score: 211
Period size: 44 Copynumber: 8.8 Consensus size: 44
16526 TAGTATGTAG
* *
16536 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGATT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGATT
** *
16580 ATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GT-AG-TT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGATT
* * * * * *
16618 ATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGACATTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGA-TT
* * * * **
16663 ATCAAAATTTTATAGGAAAGTTTATCAAAATTTCACAGCAATG-TT
1 ATCAAAATTTCATAGG-GAGATTATCAAAATTTCATAGTGA-GATT
* * * * *
16708 ATCACAATTTCATAGTGTGATTATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGATT
* * * * * * * *
16752 ACTGACAA-TTCATATGGAGGTTTTTAAATTTTCAAAACGTG-G-TT
1 A-TCAAAATTTCATAGGGAGATTATCAAAATTTC-ATA-GTGAGATT
* * * * * *
16796 ATCAATATATCATATGGAGATTATCAACATCTT-ATAGTGTTGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAAT-TTCATAGTG-AGATT
**
16841 ATCAAAATTTCATTTGGA-AGTTATCAAAATTTCATAGTGAGATCT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGAT-T
* * * *
16886 -TCAAAATTCCTTATGGAGATTAACAAAATTTCATA
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATA
16921 AGGTTAAAAA
Statistics
Matches: 259, Mismatches: 60, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
38 27 0.10
39 4 0.02
40 1 0.00
41 2 0.01
42 4 0.02
43 9 0.03
44 117 0.45
45 74 0.29
46 21 0.08
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGATT
Found at i:16666 original size:23 final size:23
Alignment explanation
Indices: 16638--16695 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 23
16628 CATAAGGAGG
*
16638 TTATCAAAATTTTATAGGGACA-T
1 TTATCAAAATTTTATA-GGAAAGT
16661 TTATCAAAATTTTATAGGAAAGT
1 TTATCAAAATTTTATAGGAAAGT
16684 TTATCAAAATTT
1 TTATCAAAATTT
16696 CACAGCAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 4 0.12
23 29 0.88
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAAGT
Found at i:16878 original size:45 final size:45
Alignment explanation
Indices: 16791--16879 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
16781 TTTCAAAACG
* *
16791 TGGTTATCAATATATCATATGGAGATTATCAACATCTTATAGTGT
1 TGGTTATCAAAATATCATATGGAGATTATCAAAATCTTATAGTGT
* *
16836 TGGTTATCAAAATTTCATTTGGA-AGTTATCAAAAT-TTCATAGTG
1 TGGTTATCAAAATATCATATGGAGA-TTATCAAAATCTT-ATAGTG
16880 AGATCTTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 3 0.08
45 35 0.92
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAGATTATCAAAATCTTATAGTGT
Found at i:17140 original size:44 final size:44
Alignment explanation
Indices: 17058--17141 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
17048 CATAGTATCG
* * * *
17058 TTATGGAAGTTATCAAAATTTTATAGTGAAGTCTTCAAAATTCC
1 TTATGGAAGTTAACAAAATTTCATAGAGAAGTCATCAAAATTCC
17102 TTATGG-AGATTAACAAAATTTCATA-AGAAGGTCATCAAAA
1 TTATGGAAG-TTAACAAAATTTCATAGAGAA-GTCATCAAAA
17142 AATTTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
43 5 0.15
44 29 0.85
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (44 bp):
TTATGGAAGTTAACAAAATTTCATAGAGAAGTCATCAAAATTCC
Found at i:17234 original size:40 final size:40
Alignment explanation
Indices: 17185--17278 Score: 179
Period size: 40 Copynumber: 2.4 Consensus size: 40
17175 ATCGAAGGTC
*
17185 ATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATT
1 ATCATAATTTCATAAGGACGTCATAAAAAATAGTGTAATT
17225 ATCATAATTTCATAAGGACGTCATAAAAAATAGTGTAATT
1 ATCATAATTTCATAAGGACGTCATAAAAAATAGTGTAATT
17265 ATCATAATTTCATA
1 ATCATAATTTCATA
17279 GTAAGATTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (40 bp):
ATCATAATTTCATAAGGACGTCATAAAAAATAGTGTAATT
Found at i:17280 original size:62 final size:61
Alignment explanation
Indices: 17213--17358 Score: 186
Period size: 62 Copynumber: 2.3 Consensus size: 61
17203 CGTCATAAAA
*
17213 AATAGTGTAATTATCATAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCATAATTT
1 AATAGTG-AATTATCATAATTTCATAAGAACGTCATAAAAAATAGTGTAATTATCATAATTT
* * * * * *
17275 CATAGTAAGATTATCAAAATTTCATAAGAATGTCATCAAAATTAGTGTAATTATCATAATTT
1 AATAGTGA-ATTATCATAATTTCATAAGAACGTCATAAAAAATAGTGTAATTATCATAATTT
17337 AATAG-GAATGTTATCATAATTT
1 AATAGTGAA--TTATCATAATTT
17359 TGTATGACTA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
60 1 0.01
61 2 0.03
62 68 0.96
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (61 bp):
AATAGTGAATTATCATAATTTCATAAGAACGTCATAAAAAATAGTGTAATTATCATAATTT
Done.