Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007467.1 Corchorus capsularis cultivar CVL-1 contig07488, 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: 32371
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--61 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
62 ATATATATAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:66 original size:2 final size:2
Alignment explanation
Indices: 61--85 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51 TCTCTCTCTC
61 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 T
86 CCAAACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2639 original size:16 final size:16
Alignment explanation
Indices: 2620--2650 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2610 AACTGAAAAA
2620 GACCCAAACCAAAATT
1 GACCCAAACCAAAATT
*
2636 GACCCAAACCCAAAT
1 GACCCAAACCAAAAT
2651 AACCCGACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.35, G:0.06, T:0.10
Consensus pattern (16 bp):
GACCCAAACCAAAATT
Found at i:4308 original size:29 final size:28
Alignment explanation
Indices: 4275--4401 Score: 114
Period size: 29 Copynumber: 4.4 Consensus size: 28
4265 TAGGATCAGG
4275 AGGTCAAACAGGCAGAACACAGGACCCG-A
1 AGGTCAAACAGGCAGAA-ACAGGA-CCGAA
** * *
4304 AGGTCAAACATACGGAAAAATGGATCC-AA
1 AGGTCAAACAGGCAGAAACA-GGA-CCGAA
* * *
4333 ATGTCAAATAGGCAGAAAACGGGACCGAA
1 AGGTCAAACAGGCAG-AAACAGGACCGAA
*
4362 AGGTCAAACAGGCAGTAAACATGACCGAA
1 AGGTCAAACAGGCAG-AAACAGGACCGAA
4391 AGGTCAAACAG
1 AGGTCAAACAG
4402 AGCGGAATAT
Statistics
Matches: 77, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
28 4 0.05
29 70 0.91
30 3 0.04
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.09
Consensus pattern (28 bp):
AGGTCAAACAGGCAGAAACAGGACCGAA
Found at i:14228 original size:22 final size:22
Alignment explanation
Indices: 14158--14321 Score: 103
Period size: 22 Copynumber: 7.5 Consensus size: 22
14148 AGGAGATTAA
* *
14158 CAAAATCTCACAGAGAGG-TTAT
1 CAAAATTTCATAGA-AGGTTTAT
* *
14180 CAAAA-ATCATAGGAAGG-ATA-
1 CAAAATTTCATA-GAAGGTTTAT
14200 CAAAATTTCATAGAAGGTTTAT
1 CAAAATTTCATAGAAGGTTTAT
* *
14222 TAAAATTTCATAGTTAGG-TTAT
1 CAAAATTTCATAG-AAGGTTTAT
* *
14244 CAAAGTTTCATATGGA-GTTTAT
1 CAAAATTTCATA-GAAGGTTTAT
* *
14266 CAAAATTTCATA-ATGTGATTAT
1 CAAAATTTCATAGAAG-GTTTAT
*
14288 CAAAATTTAATAG--GGTAGTTAT
1 CAAAATTTCATAGAAGGT--TTAT
14310 CAAAATTTCATA
1 CAAAATTTCATA
14322 AAAATATTCA
Statistics
Matches: 113, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
20 11 0.10
21 18 0.16
22 80 0.71
23 4 0.04
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGAAGGTTTAT
Found at i:14264 original size:44 final size:45
Alignment explanation
Indices: 14216--14322 Score: 130
Period size: 44 Copynumber: 2.4 Consensus size: 45
14206 TTCATAGAAG
* * * * * *
14216 GTTTATTAAAATTTCATAGT-TAGGTTATCAAAGTTTCATATGG-A
1 GTTTATCAAAATTTCATAATGT-GATTATCAAAATTTAATAGGGTA
14260 GTTTATCAAAATTTCATAATGTGATTATCAAAATTTAATAGGGTA
1 GTTTATCAAAATTTCATAATGTGATTATCAAAATTTAATAGGGTA
14305 G-TTATCAAAATTTCATAA
1 GTTTATCAAAATTTCATAA
14323 AAATATTCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
44 52 0.95
45 3 0.05
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.41
Consensus pattern (45 bp):
GTTTATCAAAATTTCATAATGTGATTATCAAAATTTAATAGGGTA
Found at i:14577 original size:15 final size:15
Alignment explanation
Indices: 14553--14583 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14543 TAAATTCTAT
*
14553 AAATCTCTATAAAGA
1 AAATCACTATAAAGA
14568 AAATCACTATAAAGA
1 AAATCACTATAAAGA
14583 A
1 A
14584 GATTTAGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (15 bp):
AAATCACTATAAAGA
Found at i:17947 original size:13 final size:13
Alignment explanation
Indices: 17931--17956 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17921 AATATTAGTT
17931 TTATAAATTAATA
1 TTATAAATTAATA
17944 TTATAAATTAATA
1 TTATAAATTAATA
17957 CTGTGACGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTATAAATTAATA
Found at i:25406 original size:51 final size:51
Alignment explanation
Indices: 25330--25433 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
25320 TTCTCAATCA
*
25330 ATTGCCCTTGACTGATTTGAGTGGTTGGAGGAGGGATTCGATGAGATCCCG
1 ATTGCCCTTGACTGATTTGAGTGGTTGGAGGAGGGATTCAATGAGATCCCG
25381 ATTGCCCTTGACTGATTTGAGTGGTTGGAGGAGGGATTCAATGAGATCCCG
1 ATTGCCCTTGACTGATTTGAGTGGTTGGAGGAGGGATTCAATGAGATCCCG
25432 AT
1 AT
25434 GAAATTCGGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (51 bp):
ATTGCCCTTGACTGATTTGAGTGGTTGGAGGAGGGATTCAATGAGATCCCG
Found at i:25468 original size:31 final size:31
Alignment explanation
Indices: 25430--25492 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
25420 AATGAGATCC
25430 CGATGAAATTCGGTGCGGAAGTTTTGGGCGG
1 CGATGAAATTCGGTGCGGAAGTTTTGGGCGG
25461 CGATGAAATTCGGTGCGGAAGTTTTGGGCGG
1 CGATGAAATTCGGTGCGGAAGTTTTGGGCGG
25492 C
1 C
25493 TTGAGTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.14, G:0.41, T:0.25
Consensus pattern (31 bp):
CGATGAAATTCGGTGCGGAAGTTTTGGGCGG
Done.