Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005454.1 Corchorus capsularis cultivar CVL-1 contig05472, 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: 4938
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1664 original size:156 final size:156
Alignment explanation
Indices: 1277--1670 Score: 440
Period size: 156 Copynumber: 2.5 Consensus size: 156
1267 CATCTTGGCT
* * * *
1277 AAGTTTCATCTCAAACGGGCTTA-AGATGAAAAACTTATGCATGTTTTTCAGTTAAGGACGGTTT
1 AAGTTTCATCTCAATCGGACTTAGA-ATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTT
* * * * * * * *
1341 GGGGTGTCAAACCAACTTCACTATGAAAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATAGTTT
65 GGGGTGTGAAACCAAGTTCACTATCAAAGGGAGTTCAGTTTCACTTAGAATTTTTCCCACAGTCT
*
1406 TATGGAGATAATCTAAGCCTACTGGTGGA
130 TATGGAGATAATCTAAGCC-ACT-GTGCA
* * * * * *
1435 AA--TTCAGCTCTATTGGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAAGACAGTTTA
1 AAGTTTCATCTCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTG
* * *
1498 GGGAGAGAAACCAAGTTCACTATCAAGGGGA-TCTCAGTTTCACTTAGAATTTTTCCCACAGTCT
66 GGGTGTGAAACCAAGTTCACTATCAAAGGGAGT-TCAGTTTCACTTAGAATTTTTCCCACAGTCT
*
1562 TGTGGAGATAATCTAAGTCC-CT-TGACA
130 TATGGAGATAATCTAAG-CCACTGTG-CA
* * * *
1589 AAGTTTCATCTCAATCAGACTTAGAATGAAAAACTTATGCTTGTTTTTCATTTAAGGAAAGTGTG
1 AAGTTTCATCTCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTG
*
1654 GGGTGTGAAACCTAGTT
66 GGGTGTGAAACCAAGTT
1671 TACCATGAAG
Statistics
Matches: 194, Mismatches: 36, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
153 2 0.01
154 3 0.02
155 3 0.02
156 181 0.93
157 3 0.02
158 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (156 bp):
AAGTTTCATCTCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTG
GGGTGTGAAACCAAGTTCACTATCAAAGGGAGTTCAGTTTCACTTAGAATTTTTCCCACAGTCTT
ATGGAGATAATCTAAGCCACTGTGCA
Found at i:2059 original size:28 final size:28
Alignment explanation
Indices: 2000--2064 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
1990 GCCATGTGAT
* *
2000 ACATCATAGGGAAGATTTTCCACTTGAT
1 ACATCAGAGGGAAGATTTTCCACTTGAC
2028 ACATCAGAGGGAAGAATTTTCGC-C-TGAC
1 ACATCAGAGGGAAG-ATTTTC-CACTTGAC
2056 ACATCAGAG
1 ACATCAGAG
2065 AGAGATAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 25 0.76
29 7 0.21
30 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (28 bp):
ACATCAGAGGGAAGATTTTCCACTTGAC
Found at i:2414 original size:26 final size:27
Alignment explanation
Indices: 2383--2446 Score: 107
Period size: 26 Copynumber: 2.5 Consensus size: 27
2373 AATATGTAAA
2383 ATATATTAT-TAAATAAGAATATATAT
1 ATATATTATGTAAATAAGAATATATAT
2409 ATATA-TATGTAAATAAGAATATATAT
1 ATATATTATGTAAATAAGAATATATAT
2435 ATATA-TATGTAA
1 ATATATTATGTAA
2447 GACTTTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 3 0.08
26 34 0.92
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (27 bp):
ATATATTATGTAAATAAGAATATATAT
Found at i:2480 original size:18 final size:17
Alignment explanation
Indices: 2453--2490 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2443 GTAAGACTTT
2453 TATTTTAATATATAATA
1 TATTTTAATATATAATA
*
2470 TATTATTAATATGTAATA
1 TATT-TTAATATATAATA
2488 TAT
1 TAT
2491 ATATATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTTAATATATAATA
Found at i:2490 original size:20 final size:20
Alignment explanation
Indices: 2367--2492 Score: 59
Period size: 20 Copynumber: 6.2 Consensus size: 20
2357 AAATCATTTT
*
2367 TATT-TTAATATGTAAAATA
1 TATTATTAATATGTAATATA
*
2386 TATTATTAAATAAG-AATATA
1 TATTATT-AATATGTAATATA
*
2406 TA-TA-TATATATGTAAATAAGAA
1 TATTATTA-ATATGT-AAT-A-TA
* *
2428 TATATATATATATATGTAAGACTTT
1 TAT-TAT-TA-ATATGTAATA--TA
*
2453 TATT-TTAATATAT-A-ATA
1 TATTATTAATATGTAATATA
2470 TATTATTAATATGTAATATA
1 TATTATTAATATGTAATATA
2490 TAT
1 TAT
2493 ATATATGTGT
Statistics
Matches: 81, Mismatches: 11, Indels: 29
0.67 0.09 0.24
Matches are distributed among these distances:
17 6 0.07
18 13 0.16
19 8 0.10
20 19 0.23
21 11 0.14
22 5 0.06
23 1 0.01
24 4 0.05
25 5 0.06
26 9 0.11
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.46
Consensus pattern (20 bp):
TATTATTAATATGTAATATA
Found at i:3453 original size:27 final size:27
Alignment explanation
Indices: 3423--3493 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
3413 AACTGAACTA
3423 ACTCAAACATCCAAGATCTATAGGGAG
1 ACTCAAACATCCAAGATCTATAGGGAG
3450 ACTCAAACATCCAAGATCTATAGGGAG
1 ACTCAAACATCCAAGATCTATAGGGAG
3477 ACTCAAACATCCAAGAT
1 ACTCAAACATCCAAGAT
3494 ATCTGGAGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.18
Consensus pattern (27 bp):
ACTCAAACATCCAAGATCTATAGGGAG
Done.