Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010171.1 Corchorus capsularis cultivar CVL-1 contig10192, 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: 10236
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:754 original size:31 final size:31
Alignment explanation
Indices: 719--785 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 31
709 AACTTTATGT
*
719 TTTCCGATTATATCCTTAT-TTTT-AAAATATA
1 TTTCCAATTATA-CCTT-TCTTTTAAAAATATA
*
750 TTTCCAATTGTACCTTTCTTTTAAAAAATATA
1 TTTCCAATTATACCTTTCTTTT-AAAAATATA
782 TTTC
1 TTTC
786 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 1 0.03
30 8 0.26
31 10 0.32
32 12 0.39
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (31 bp):
TTTCCAATTATACCTTTCTTTTAAAAATATA
Found at i:2036 original size:19 final size:20
Alignment explanation
Indices: 2009--2046 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1999 TACTATTATT
2009 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
2029 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
2047 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:2239 original size:22 final size:22
Alignment explanation
Indices: 2211--2395 Score: 124
Period size: 22 Copynumber: 8.3 Consensus size: 22
2201 TTGTCTCTAC
2211 ATGGTTATCAAAATTTCATAAG
1 ATGGTTATCAAAATTTCATAAG
* * *
2233 ATGGTTATTATAATTTCATGAGG
1 ATGGTTATCAAAATTTCAT-AAG
*
2256 A-GGTTATCAAAATTCCAT-AG
1 ATGGTTATCAAAATTTCATAAG
* * *
2276 TGTGGTTACCAAAATCTCATAAG
1 -ATGGTTATCAAAATTTCATAAG
**
2299 AAAGTTATCAAAATTTCAT-AG
1 ATGGTTATCAAAATTTCATAAG
* * *
2320 TGTGGTTACCAAAATTTCATAGG
1 -ATGGTTATCAAAATTTCATAAG
* * *
2343 ATTAGGTTATTAAAATTTCTTAGG
1 A-T-GGTTATCAAAATTTCATAAG
* ** *
2367 TTGGTTATTGAAATTTCATAGG
1 ATGGTTATCAAAATTTCATAAG
*
2389 GTGGTTA
1 ATGGTTA
2396 ATTATCAAAA
Statistics
Matches: 126, Mismatches: 29, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 98 0.78
23 8 0.06
24 17 0.13
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
ATGGTTATCAAAATTTCATAAG
Found at i:2327 original size:66 final size:66
Alignment explanation
Indices: 2212--2341 Score: 163
Period size: 66 Copynumber: 2.0 Consensus size: 66
2202 TGTCTCTACA
* * ** * * *
2212 TGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCATAGT
1 TGGTTACCAAAATCTCATAAGAAAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTCCATAGT
2277 G
66 G
* *
2278 TGGTTACCAAAATCTCATAAGAAAGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCATAG
1 TGGTTACCAAAATCTCATAAGAAAGTTATCAAAATTTCATGAG-GAGGTTACCAAAATTCCATAG
2342 GATTAGGTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 2 0.04
66 52 0.96
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (66 bp):
TGGTTACCAAAATCTCATAAGAAAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTCCATAGT
G
Found at i:2372 original size:46 final size:44
Alignment explanation
Indices: 2213--2388 Score: 169
Period size: 44 Copynumber: 4.0 Consensus size: 44
2203 GTCTCTACAT
* ** *
2213 GGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCATGAGG-A
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAT-AGGAA
* * *
2257 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATCTCATAAGAA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGAA
*
2301 AGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATTA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGA--A
* * ***
2347 GGTTATTAAAATTTCTTAG-GTTGGTTATTGAAATTTCATAGG
1 GGTTATCAAAATTTCATAGTG-TGGTTACCAAAATTTCATAGG
2389 GTGGTTAATT
Statistics
Matches: 110, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
43 4 0.04
44 70 0.64
45 1 0.01
46 35 0.32
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.38
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGAA
Found at i:2498 original size:22 final size:22
Alignment explanation
Indices: 2473--2564 Score: 64
Period size: 22 Copynumber: 4.2 Consensus size: 22
2463 TATATAGTGT
2473 GGTTAACAAAATTTCATTAGAA
1 GGTTAACAAAATTTCATTAGAA
* * *
2495 GGTT-ACTAATATTTCATGAGGA
1 GGTTAAC-AAAATTTCATTAGAA
* * * *
2517 GGTTATCAAAATTTTATATTG-T
1 GGTTAACAAAATTTCAT-TAGAA
*
2539 GGTTATCAAAATTTCA-TATGAA
1 GGTTAACAAAATTTCATTA-GAA
2561 GGTT
1 GGTT
2565 TATAAAAGTC
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
20 1 0.02
21 3 0.06
22 47 0.89
23 2 0.04
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (22 bp):
GGTTAACAAAATTTCATTAGAA
Found at i:2646 original size:22 final size:23
Alignment explanation
Indices: 2594--2821 Score: 119
Period size: 22 Copynumber: 10.4 Consensus size: 23
2584 TAAGGAGTAC
* *
2594 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
2615 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
2636 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
*
2661 CAAAATTT-ATAG-GAAGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
2682 CAAAATTTCATA-ATGTTG-TTAT
1 CAAAATTTCATAGA-GATGATTAT
* * *
2704 CAAAATTTCAAAGCGA-GGTTA-
1 CAAAATTTCATAGAGATGATTAT
*
2725 CAAAAATTACATA-ATG-TGATTAT
1 C-AAAATTTCATAGA-GATGATTAT
* * * * *
2748 CAGAATTTCATAGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* *
2770 CAAAATTTTATAAAGATG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
2792 CAAAATTTAATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
2814 C-AAATTTC
1 CAAAATTTC
2822 CAAAATGTGA
Statistics
Matches: 160, Mismatches: 29, Indels: 36
0.71 0.13 0.16
Matches are distributed among these distances:
20 10 0.06
21 30 0.19
22 95 0.59
23 8 0.05
24 4 0.03
25 13 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:2678 original size:21 final size:24
Alignment explanation
Indices: 2630--2693 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 24
2620 CTCATAGAGT
*
2630 GATTATCGAAATTTCATAGAGATCA
1 GATTATCAAAATTTCATAGAGA-CA
2655 GATTATCAAAATTT-ATAG-GA-A
1 GATTATCAAAATTTCATAGAGACA
2676 GATTATCAAAATTTCATA
1 GATTATCAAAATTTCATA
2694 ATGTTGTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 15 0.41
22 3 0.08
23 2 0.05
24 4 0.11
25 13 0.35
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (24 bp):
GATTATCAAAATTTCATAGAGACA
Found at i:2810 original size:88 final size:88
Alignment explanation
Indices: 2682--2848 Score: 205
Period size: 88 Copynumber: 1.9 Consensus size: 88
2672 GGAAGATTAT
* * ** *
2682 CAAAATTTCATAATGTTGTTATCAAAATTTCAAAGCGAGGTTA-CAAAAATTACATAATGTGATT
1 CAAAATTTCATAAAGATGTTATCAAAATTTCAAAAAGAGGTTATC-AAAATTACAAAATGTGATT
*
2746 ATC-AGAATTTCATAGAGGGGTCAA
65 A-CAAAAATTTCATAGAGGGGTCAA
* * *
2770 CAAAATTTTATAAAGATGTTATCAAAATTT-AATAAAGAGGTTATCAAATTTCCAAAATGTGATT
1 CAAAATTTCATAAAGATGTTATCAAAATTTCAA-AAAGAGGTTATCAAAATTACAAAATGTGATT
2834 ACAAAAATTTCATAG
65 ACAAAAATTTCATAG
2849 TGGTATTTCT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
87 3 0.04
88 63 0.94
89 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (88 bp):
CAAAATTTCATAAAGATGTTATCAAAATTTCAAAAAGAGGTTATCAAAATTACAAAATGTGATTA
CAAAAATTTCATAGAGGGGTCAA
Found at i:2951 original size:20 final size:20
Alignment explanation
Indices: 2926--2977 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2916 TTATGGAGTA
2926 ATCAAAATTTCAGAGAGGAT
1 ATCAAAATTTCAGAGAGGAT
* *
2946 ATCAAAATTTTAGGGAGGAT
1 ATCAAAATTTCAGAGAGGAT
2966 ATCAAAATTTCA
1 ATCAAAATTTCA
2978 TATGAATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (20 bp):
ATCAAAATTTCAGAGAGGAT
Found at i:2993 original size:22 final size:22
Alignment explanation
Indices: 2926--3458 Score: 214
Period size: 22 Copynumber: 24.6 Consensus size: 22
2916 TTATGGAGTA
* *
2926 ATCAAAATTTCAGA-G-AGGAT
1 ATCAAAATTTCATATGAAGGTT
* * *
2946 ATCAAAATTT--TAGGGAGGAT
1 ATCAAAATTTCATATGAAGGTT
*
2966 ATCAAAATTTCATATGAATGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
2988 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * *
3010 ATCAAAATATCATATGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
3032 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
** *
3054 ATCAAAAAATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
*
3076 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * *
3092 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* *
3114 ATCAAAATTT-ATAGGAAGATTT
1 ATCAAAATTTCATATGAAG-GTT
* *
3136 ATCAAAATTTCCTA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* *
3158 ATCAAAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
3180 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
*
3202 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * * * *
3224 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
* * *
3246 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
3268 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
3291 ATCAAAATTTCAT-TGGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
3313 ATCAAAATTTCATATTG-AGGTT
1 ATCAAAATTTCATA-TGAAGGTT
* * * * *
3335 TTCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* *
3357 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
** **
3379 AAAAAAAATTT-ATAAAAAGGTT
1 -ATCAAAATTTCATATGAAGGTT
* * * ***
3401 CTCGAAATTGCATA-GTATCATT
1 ATCAAAATTTCATATG-AAGGTT
* *
3423 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
3445 ATCAAAATTTCATA
1 ATCAAAATTTCATA
3459 ATGGGATCAT
Statistics
Matches: 391, Mismatches: 85, Indels: 72
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 3 0.01
19 1 0.00
20 27 0.07
21 30 0.08
22 274 0.70
23 42 0.11
24 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:5863 original size:2 final size:2
Alignment explanation
Indices: 5856--5901 Score: 67
Period size: 2 Copynumber: 22.5 Consensus size: 2
5846 CTGCGAAAAT
5856 TA TA TA TA TA GTA -A GTA 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 TA
5899 TA T
1 TA T
5902 TCTTAAATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 1 0.02
2 37 0.90
3 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:9131 original size:26 final size:26
Alignment explanation
Indices: 9095--9150 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
9085 AATCACTATA
*
9095 GGCACTTGCTGATGGCAGTTGGCCTT
1 GGCACTTGCTGATGGCACTTGGCCTT
9121 GGCACTTGCTGATGGCACTTGGCCTT
1 GGCACTTGCTGATGGCACTTGGCCTT
9147 GGCA
1 GGCA
9151 TCGGCACTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.12, C:0.25, G:0.34, T:0.29
Consensus pattern (26 bp):
GGCACTTGCTGATGGCACTTGGCCTT
Found at i:9157 original size:32 final size:32
Alignment explanation
Indices: 9095--9368 Score: 329
Period size: 32 Copynumber: 8.7 Consensus size: 32
9085 AATCACTATA
*
9095 GGCACTTGCTGATGGCAGTTGGCC-T----T-
1 GGCACTTGCTGATGGCACTTGGCCTTGGCATC
9121 GGCACTTGCTGATGGCACTTGGCCTTGGCATC
1 GGCACTTGCTGATGGCACTTGGCCTTGGCATC
* * *
9153 GGCACTTGCTGATGACACTTGGGCTTAGCATC
1 GGCACTTGCTGATGGCACTTGGCCTTGGCATC
*
9185 GGGCACTTGCTGATGACACTTGGCCTTGGCATC
1 -GGCACTTGCTGATGGCACTTGGCCTTGGCATC
9218 GGCA-TT-CTCCGATGGCACTTGGCCTTGGCATC
1 GGCACTTGCT--GATGGCACTTGGCCTTGGCATC
*
9250 GGGACTTGCTGATGGCACTTGGCCTTGGCATC
1 GGCACTTGCTGATGGCACTTGGCCTTGGCATC
9282 GGCA-TT-CTCCGATGGCACTTGGCCTTGGCATC
1 GGCACTTGCT--GATGGCACTTGGCCTTGGCATC
*
9314 GGGACTTGCTGATGGCACTTGGCCTTGGCATC
1 GGCACTTGCTGATGGCACTTGGCCTTGGCATC
*
9346 AGCA-TT-CTCCGATGGCACTTGGC
1 GGCACTTGCT--GATGGCACTTGGC
9369 GATCTAATCA
Statistics
Matches: 219, Mismatches: 12, Indels: 28
0.85 0.05 0.11
Matches are distributed among these distances:
26 23 0.11
27 1 0.00
30 6 0.03
31 7 0.03
32 144 0.66
33 34 0.16
34 4 0.02
ACGTcount: A:0.14, C:0.27, G:0.31, T:0.28
Consensus pattern (32 bp):
GGCACTTGCTGATGGCACTTGGCCTTGGCATC
Found at i:9286 original size:64 final size:64
Alignment explanation
Indices: 9124--9368 Score: 404
Period size: 64 Copynumber: 3.8 Consensus size: 64
9114 TGGCCTTGGC
* * *
9124 ACTTGCTGATGGCACTTGGCCTTGGCATCGGCACTTGCT--GATGACACTTGGGCTTAGCATCGG
1 ACTTGCTGATGGCACTTGGCCTTGGCATCGGCA-TT-CTCCGATGGCACTTGGCCTTGGCATCGG
9187 G
64 G
*
9188 CACTTGCTGATGACACTTGGCCTTGGCATCGGCATTCTCCGATGGCACTTGGCCTTGGCATCGGG
1 -ACTTGCTGATGGCACTTGGCCTTGGCATCGGCATTCTCCGATGGCACTTGGCCTTGGCATCGGG
9253 ACTTGCTGATGGCACTTGGCCTTGGCATCGGCATTCTCCGATGGCACTTGGCCTTGGCATCGGG
1 ACTTGCTGATGGCACTTGGCCTTGGCATCGGCATTCTCCGATGGCACTTGGCCTTGGCATCGGG
*
9317 ACTTGCTGATGGCACTTGGCCTTGGCATCAGCATTCTCCGATGGCACTTGGC
1 ACTTGCTGATGGCACTTGGCCTTGGCATCGGCATTCTCCGATGGCACTTGGC
9369 GATCTAATCA
Statistics
Matches: 172, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
63 2 0.01
64 116 0.67
65 54 0.31
ACGTcount: A:0.14, C:0.28, G:0.30, T:0.28
Consensus pattern (64 bp):
ACTTGCTGATGGCACTTGGCCTTGGCATCGGCATTCTCCGATGGCACTTGGCCTTGGCATCGGG
Found at i:9857 original size:115 final size:115
Alignment explanation
Indices: 9653--9868 Score: 319
Period size: 115 Copynumber: 1.9 Consensus size: 115
9643 GAATTTGAGA
* *
9653 CAGTTTTTTGAGTTTCAGTTTGTTTTTTTAGTCTGTTTTTTTTATTTTATCCAATCTTACAATAA
1 CAGTTTTTTGAGTTTCAGTTTGTTTTCTTAGTCTGTTTTTTTTATTTAATCCAATCTTAC-A-AA
9718 TAGACTGAGAATTGTTAATTATATTGGGATGAATAGACTAAGAATTGTTAGT
64 TAGACTGAGAATTGTTAATTATATTGGGATGAATAGACTAAGAATTGTTAGT
* ***
9770 CAGTTTTTTGAGTTTCAGTTTG-TTTCTTAGTCAGTTTTTTTTTTATTTAATTTGATCTTAC-AA
1 CAGTTTTTTGAGTTTCAGTTTGTTTTCTTAGTC--TGTTTTTTTTATTTAATCCAATCTTACAAA
*
9833 TAGACTGAGGATTGTTAATTATATTGGGATGAATAG
64 TAGACTGAGAATTGTTAATTATATTGGGATGAATAG
9869 CGGAATTTTG
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
115 37 0.41
116 9 0.10
117 22 0.24
118 22 0.24
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (115 bp):
CAGTTTTTTGAGTTTCAGTTTGTTTTCTTAGTCTGTTTTTTTTATTTAATCCAATCTTACAAATA
GACTGAGAATTGTTAATTATATTGGGATGAATAGACTAAGAATTGTTAGT
Done.