Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012196.1 Corchorus capsularis cultivar CVL-1 contig12217, 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: 6511
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Found at i:662 original size:199 final size:199
Alignment explanation
Indices: 22--1163 Score: 1394
Period size: 199 Copynumber: 5.7 Consensus size: 199
12 CGGGACGTCT
* * *
22 AGTCTGCTAAACTCGACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATGCAATACAC
1 AGTCTGCTAAACTCCACTGACGGTATATAGTATAATTTTTCTTATAGGATTATTATACAATACAC
* * * *
87 AT-TCAGTGTAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTCACACATACCTCATTTCATATT
66 -TGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAAT
* *
151 TAATAAAATATTTAATAATAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCATGCA
130 TAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCA
* **
216 TGCAC
195 CGTGC
* * * * * * * * *
221 AGTCTACTAAACTCCACTAATGGTGTATTGTATAATTGTTCTTCTAGGAATATTATACAATAAAC
1 AGTCTGCTAAACTCCACTGACGGTATATAGTATAATTTTTCTTATAGGATTATTATACAATACAC
* *
286 TGTCAATGCAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATT
66 TGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATT
* * *
351 AATTAAATATATTTAATAATAATACATA-TCCCTTAAGGGGACATACGTCAACCCTTAAA-CCTC
131 AA-TAAA-ATATTTAATATTAATACATATTCCC-TAAGGGGACACATGTCAACCCTTAAACCCT-
414 GCACGTGC
192 GCACGTGC
* * *
422 AGTTTGCTAAACTCGACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATACAC
1 AGTCTGCTAAACTCCACTGACGGTATATAGTATAATTTTTCTTATAGGATTATTATACAATACA-
* * * * *
487 CT-TTAATGTAAATTTTGAACTCAATAAGCGGGTTAAGAAGTTGACACAGACCTCATTTCACAAT
65 CTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAAT
551 TAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCA
130 TAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCA
*
616 CGTTC
195 CGTGC
* * *
621 AGTCTGCTAAACTCCATTGACGGTATATTGTATAGTTTTTCTTATAGGATTATTATACAATACAC
1 AGTCTGCTAAACTCCACTGACGGTATATAGTATAATTTTTCTTATAGGATTATTATACAATACAC
* * * * *
686 TGTCAAAGTAAATTTTGGACTCCATAAGCGGGTTTAGAAGTTGACATATATCTCATTTCATCATT
66 TGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATT
* * *
751 AATTAAATATATAATATTAATACATA---CCTAAGGGGACACATGTCAACCCTTAAACCCTGGAC
131 AATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCAC
**
813 GTTT
196 GTGC
* * *
817 AGTCTGTTAAACTCCACTTACGGTACTGTATAATATAATTTTTCTTATAGGATTATTATACAATA
1 AGTCTGCTAAACTCCACTGACGGTA---TATAGTATAATTTTTCTTATAGGATTATTATACAATA
* * * * *
882 CACTGTCAGTGTAAAATTTGGACTCCATGCA-CGGGTTAAGAAGTTGACATATACCCCATTTCAT
63 CACTGTCAATGTAAATTTTGGACTCCAT-AAGCGGGTTAAGAAGTTGACACATACCTCATTTCAT
* * *
946 AATTAATTAGATATTTAATATTAATACATCTTCCCTAAGGGGACACATGTCAACCCTTAAATCCC
127 AATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA-CCC
1011 -GCACGTGC
191 TGCACGTGC
* * * * * *
1019 AGTCCGCTAAAATCCATTTACGGTATATTA-TATAATTTTTCTTATAGGATTATTATACAACACG
1 AGTCTGCTAAACTCCACTGACGGTATA-TAGTATAATTTTTCTTATAGGATTATTATACAATACA
* * * * * * * * *
1083 CTATCAGTATAAATTTTTGACTCTATAAGTGGGTTAAGAA---CACACAAACCTCATTTCATCAT
65 CTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAAT
* *
1145 TAATTAAATATAT-ATATTA
130 TAATAAAATATTTAATATTA
1164 CATATTATTT
Statistics
Matches: 821, Mismatches: 103, Indels: 42
0.85 0.11 0.04
Matches are distributed among these distances:
195 6 0.01
196 88 0.11
198 4 0.00
199 479 0.58
200 24 0.03
201 161 0.20
202 56 0.07
203 3 0.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (199 bp):
AGTCTGCTAAACTCCACTGACGGTATATAGTATAATTTTTCTTATAGGATTATTATACAATACAC
TGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATT
AATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCAC
GTGC
Found at i:1044 original size:398 final size:395
Alignment explanation
Indices: 1--1163 Score: 1504
Period size: 400 Copynumber: 2.9 Consensus size: 395
*
1 CCCTTAAACCCCGGGACGTCTAGTCTGCTAAACTCGACTGACGGTGTATAGTATAATTTTTCTTA
1 CCCTTAAA-CCCTGGACGTCTAGTCTGCTAAACTCGACTGACGGTGTATAGTATAATTTTTCTTA
*
66 TAGGATTATTATGCAATACACATTCAGTGTAAATTTTGGACTCCATAAGCA--GGTTAAGAAGTT
65 TAGGATTATTATACAATACAC-TTCAGTGTAAATTTTGGACTCCAT--GCACGGGTTAAGAAGTT
* * *
129 CACACATACCTCATTTCATATTTAATAAAATATTTAATAATAATACATATTCCCTAAGGGGACAC
127 GACACATACCTCATTTCATAATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACAC
* * * * * * * *
194 ATGTCAACCCTTAAACCATGCATGCACAGTCTACTAAACTCCACTAATGGTGTATTGTATAATTG
192 ATGTCAACCCTTAAACC-CGCACGTACAGTCTGCTAAACTCCATTAACGGTATATTGTATAATTT
* * * * *
259 TTCTTCTAGGAATATTATACAATAAACTGTCAATGCAAATTTTGGACTCCATAAGCGGGTTAAGA
256 TTCTTATAGGATTATTATACAATACACTGTCAAAGTAAATTTTGGACTCCATAAGCGGGTTAAGA
* * *
324 AGTTGACACATACCCCATTTCATAATTAATTAAATATATTTAATAATAATACATATCCCTTAAGG
321 AGTTGACACATACCTCATTTCATCATTAATTAAATATA--TAATATTAATACATA-CCCTTAAGG
*
389 GGACATACGTCAA
383 GGACACACGTCAA
* *
402 CCCTTAAA-CCTCGCACGTGC-AGTTTGCTAAACTCGACTGACGGTGTATAGTATAATTTTTCTT
1 CCCTTAAACCCT-GGACGT-CTAGTCTGCTAAACTCGACTGACGGTGTATAGTATAATTTTTCTT
* * * * *
465 ATAGGATTATTATACAATACACCTTTAATGTAAATTTTGAACTCAAT-AAGCGGGTTAAGAAGTT
64 ATAGGATTATTATACAATACA-CTTCAGTGTAAATTTTGGACTCCATGCA-CGGGTTAAGAAGTT
* *
529 GACACAGACCTCATTTCACAATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACAC
127 GACACATACCTCATTTCATAATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACAC
* * *
594 ATGTCAACCCTTAAACCCTGCACGTTCAGTCTGCTAAACTCCATTGACGGTATATTGTATAGTTT
192 ATGTCAACCCTTAAACCC-GCACGTACAGTCTGCTAAACTCCATTAACGGTATATTGTATAATTT
*
659 TTCTTATAGGATTATTATACAATACACTGTCAAAGTAAATTTTGGACTCCATAAGCGGGTTTAGA
256 TTCTTATAGGATTATTATACAATACACTGTCAAAGTAAATTTTGGACTCCATAAGCGGGTTAAGA
* *
724 AGTTGACATATATCTCATTTCATCATTAATTAAATATATAATATTAATACATA-CC-TAAGGGGA
321 AGTTGACACATACCTCATTTCATCATTAATTAAATATATAATATTAATACATACCCTTAAGGGGA
*
787 CACATGTCAA
386 CACACGTCAA
* * * * *
797 CCCTTAAACCCTGGACGTTTAGTCTGTTAAACTCCACTTACGGTACTGTATAATATAATTTTTCT
1 CCCTTAAACCCTGGACGTCTAGTCTGCTAAACTCGACTGACGG---TGTATAGTATAATTTTTCT
*
862 TATAGGATTATTATACAATACACTGTCAGTGTAAAATTTGGACTCCATGCACGGGTTAAGAAGTT
63 TATAGGATTATTATACAATACACT-TCAGTGTAAATTTTGGACTCCATGCACGGGTTAAGAAGTT
* * * * *
927 GACATATACCCCATTTCATAATTAATTAGATATTTAATATTAATACATCTTCCCTAAGGGGACAC
127 GACACATACCTCATTTCATAATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACAC
* * * * *
992 ATGTCAACCCTTAAATCCCGCACGTGCAGTCCGCTAAAATCCATTTACGGTATATTATATAATTT
192 ATGTCAACCCTTAAA-CCCGCACGTACAGTCTGCTAAACTCCATTAACGGTATATTGTATAATTT
* * * * * * *
1057 TTCTTATAGGATTATTATACAACACGCTATCAGTA-TAAATTTTTGACTCTATAAGTGGGTTAAG
256 TTCTTATAGGATTATTATACAATACACTGTCA-AAGTAAATTTTGGACTCCATAAGCGGGTTAAG
* *
1121 AA---CACACAAACCTCATTTCATCATTAATTAAATATAT-ATATTA
320 AAGTTGACACATACCTCATTTCATCATTAATTAAATATATAATATTA
1164 CATATTATTT
Statistics
Matches: 670, Mismatches: 76, Indels: 39
0.85 0.10 0.05
Matches are distributed among these distances:
394 6 0.01
395 79 0.12
396 5 0.01
397 3 0.00
398 255 0.38
399 7 0.01
400 305 0.46
401 10 0.01
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (395 bp):
CCCTTAAACCCTGGACGTCTAGTCTGCTAAACTCGACTGACGGTGTATAGTATAATTTTTCTTAT
AGGATTATTATACAATACACTTCAGTGTAAATTTTGGACTCCATGCACGGGTTAAGAAGTTGACA
CATACCTCATTTCATAATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGT
CAACCCTTAAACCCGCACGTACAGTCTGCTAAACTCCATTAACGGTATATTGTATAATTTTTCTT
ATAGGATTATTATACAATACACTGTCAAAGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTG
ACACATACCTCATTTCATCATTAATTAAATATATAATATTAATACATACCCTTAAGGGGACACAC
GTCAA
Found at i:1389 original size:10 final size:10
Alignment explanation
Indices: 1374--1407 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1364 CATTCATCAT
1374 TAAAACACAC
1 TAAAACACAC
*
1384 TAAAACACAAT
1 TAAAACAC-AC
1395 TAAAACACAC
1 TAAAACACAC
1405 TAA
1 TAA
1408 TTGACAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.15
Consensus pattern (10 bp):
TAAAACACAC
Found at i:2527 original size:198 final size:195
Alignment explanation
Indices: 2179--2617 Score: 587
Period size: 198 Copynumber: 2.2 Consensus size: 195
2169 TCCACTTGTA
* * * * *
2179 TAATATTAATACATATTCCCTCAGGGGACACATGTCAACCATTGAACCTTGCACCTGCAGTATGC
1 TAATATCAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCTTGAACCTGCAGTATGC
* *
2244 TAAACTCCACTGACGGTTCATTGTATAATTGTTCTTATAGGATTATTATACAATACACTGTCAAT
66 TAAAATCCACTGACGGTTCATTGTATAATTGTTCTTATAGGATCATTATACAATACACTGTCAAT
* * * * **
2309 GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGGCACATACTTCATTTCATAATTAATTAAA
131 ATAAATTTTGAACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTC---A-TAATTAAA
2374 TATT
192 TATT
* * * * *
2378 TGATATGAATACATATTCCCTAAGGGGACACATCTCAACCCTTAAATCC-TGAACGTGCAGTCTG
1 TAATATCAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA-CCTTGAACCTGCAGTATG
* * *
2442 CTAAAATCCACTGAC-GTGT-ATTGTATAATTTTTCTTATAGGATCATTATATAATACATTGTCA
65 CTAAAATCCACTGACGGT-TCATTGTATAATTGTTCTTATAGGATCATTATACAATACACTGTCA
*
2505 GTATAAATTTTGAACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTCATAATTAAATA
129 ATATAAATTTTGAACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTCATAATTAAATA
2570 TT
194 TT
* *
2572 TAATATCAATACGTATTCCCTAAGGGTACACATGTCAACCCTTAAA
1 TAATATCAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA
2618 GTGAAACCTC
Statistics
Matches: 212, Mismatches: 26, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
194 53 0.25
195 1 0.00
198 89 0.42
199 67 0.32
200 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (195 bp):
TAATATCAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCTTGAACCTGCAGTATGC
TAAAATCCACTGACGGTTCATTGTATAATTGTTCTTATAGGATCATTATACAATACACTGTCAAT
ATAAATTTTGAACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTCATAATTAAATATT
Found at i:2665 original size:198 final size:194
Alignment explanation
Indices: 2179--2671 Score: 564
Period size: 198 Copynumber: 2.5 Consensus size: 194
2169 TCCACTTGTA
* * * * * * *
2179 TAATATTAATACATATTCCCTCAGGGGACACATGTCAACCATTGAA-CCTTGC-ACCTGCAGTAT
1 TAATATCAATACATATTCCCTAAGGGGACACATCTCAACCCTTAAATCC-T-CAACGTGCAGTCT
* * *
2242 GCTAAACTCCACTGACGGTTCATTGTATAATTGTTCTTATAGGATTATTATACAATACACTGTCA
64 GCTAAACT---CTGACGGTGCATTGTATAATTTTTCTTATAGGATCATTATACAATACACTGTCA
* * * * **
2307 ATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGGCACATACTTCATTTCATAATTAATTA
126 ATATAAATTTTGAACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTC--AATTAATTA
2372 AATATT
189 AATATT
* * *
2378 TGATATGAATACATATTCCCTAAGGGGACACATCTCAACCCTTAAATCCTGAACGTGCAGTCTGC
1 TAATATCAATACATATTCCCTAAGGGGACACATCTCAACCCTTAAATCCTCAACGTGCAGTCTGC
* * * * *
2443 TAAAATCCACTGAC-GTGTATTGTATAATTTTTCTTATAGGATCATTATATAATACATTGTCAGT
66 T-AAA--CTCTGACGGTGCATTGTATAATTTTTCTTATAGGATCATTATACAATACACTGTCAAT
2507 ATAAATTTTGAACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTC-A-TAATTAAATA
128 ATAAATTTTGAACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTCAATTAATTAAATA
2570 TT
193 TT
* * *
2572 TAATATCAATACGTATTCCCTAAGGGTACACATGTCAACCCTTAAAGTGAAACCTCACACGTGCA
1 TAATATCAATACATATTCCCTAAGGGGACACATCTCAACCCTTAAA-T----CCTCA-ACGTGCA
2637 GTCTGCTAAACTCTGACGGTGCATTGTATAATTTT
60 GTCTGCTAAACTCTGACGGTGCATTGTATAATTTT
2672 CTTCCCCCCT
Statistics
Matches: 251, Mismatches: 31, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
194 53 0.21
195 2 0.01
197 6 0.02
198 105 0.42
199 65 0.26
200 19 0.08
202 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (194 bp):
TAATATCAATACATATTCCCTAAGGGGACACATCTCAACCCTTAAATCCTCAACGTGCAGTCTGC
TAAACTCTGACGGTGCATTGTATAATTTTTCTTATAGGATCATTATACAATACACTGTCAATATA
AATTTTGAACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTCAATTAATTAAATATT
Found at i:3331 original size:12 final size:13
Alignment explanation
Indices: 3316--3349 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3306 AATCTAAATC
3316 TAAAGCAAATT-A
1 TAAAGCAAATTAA
*
3328 TAAAACAAATTAA
1 TAAAGCAAATTAA
3341 TAAAGCAAA
1 TAAAGCAAA
3350 CAATAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.65, C:0.09, G:0.06, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:3337 original size:23 final size:23
Alignment explanation
Indices: 3294--3337 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3284 AAAATAAAGC
* *
3294 AAAGCAAATCTAAATCTAAATCT
1 AAAGCAAATATAAAACTAAATCT
3317 AAAGCAAATTATAAAAC-AAAT
1 AAAGCAAA-TATAAAACTAAAT
3338 TAATAAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.23
Consensus pattern (23 bp):
AAAGCAAATATAAAACTAAATCT
Done.