Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007347.1 Corchorus capsularis cultivar CVL-1 contig07368, 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: 20572
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:887 original size:20 final size:21
Alignment explanation
Indices: 839--889 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
829 ATTTAGGGGT
839 TTTTTCCGTTGACTGGAAGAA
1 TTTTTCCGTTGACTGGAAGAA
* *
860 TATTTTCCGTTGACTTG-AGCA
1 T-TTTTCCGTTGACTGGAAGAA
881 TTTTTCCGT
1 TTTTTCCGT
890 AAGCCAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 8 0.30
21 5 0.19
22 14 0.52
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.45
Consensus pattern (21 bp):
TTTTTCCGTTGACTGGAAGAA
Found at i:1358 original size:43 final size:43
Alignment explanation
Indices: 1297--1384 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
1287 ACAAATTTGA
*
1297 TATGTTGCATATTTTAACTTTATAATTCTCCATCAATCAATCT
1 TATGTTGCATAGTTTAACTTTATAATTCTCCATCAATCAATCT
*
1340 TATGTTGCATAGTTTAACTTTATAATTCTTCATCAATCAATCT
1 TATGTTGCATAGTTTAACTTTATAATTCTCCATCAATCAATCT
1383 TA
1 TA
1385 CACCACCGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (43 bp):
TATGTTGCATAGTTTAACTTTATAATTCTCCATCAATCAATCT
Found at i:2706 original size:15 final size:15
Alignment explanation
Indices: 2683--2712 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2673 ATGACCTGTA
*
2683 TCAATTGGGCAACAG
1 TCAAGTGGGCAACAG
2698 TCAAGTGGGCAACAG
1 TCAAGTGGGCAACAG
2713 CTGAAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.17
Consensus pattern (15 bp):
TCAAGTGGGCAACAG
Found at i:6236 original size:14 final size:14
Alignment explanation
Indices: 6217--6247 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
6207 ATTGTCCATC
6217 TAGTGCCTCATTAT
1 TAGTGCCTCATTAT
6231 TAGTGCCTCATTAT
1 TAGTGCCTCATTAT
6245 TAG
1 TAG
6248 ACACAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (14 bp):
TAGTGCCTCATTAT
Found at i:7037 original size:14 final size:14
Alignment explanation
Indices: 7018--7046 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
7008 TTACCACTAC
7018 ACAGCAGGTGCGCT
1 ACAGCAGGTGCGCT
7032 ACAGCAGGTGCGCT
1 ACAGCAGGTGCGCT
7046 A
1 A
7047 ATTCACTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (14 bp):
ACAGCAGGTGCGCT
Found at i:7203 original size:20 final size:20
Alignment explanation
Indices: 7178--7219 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
7168 TTCTCATATG
7178 AATCCAATGAATGAAAAATA
1 AATCCAATGAATGAAAAATA
7198 AATCCAATGAATGAAAAATA
1 AATCCAATGAATGAAAAATA
7218 AA
1 AA
7220 GGCTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.19
Consensus pattern (20 bp):
AATCCAATGAATGAAAAATA
Found at i:8470 original size:22 final size:22
Alignment explanation
Indices: 8445--8628 Score: 81
Period size: 22 Copynumber: 8.3 Consensus size: 22
8435 TGTTTCTATG
8445 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
8467 TGGTTATTATAATTTCACAAGGA
1 TGGTTATCAAAATTTCATAA-GA
*
8490 -GGTTATCAAAA-TTC-TATAGCG
1 TGGTTATCAAAATTTCATA-AG-A
* *
8511 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* * *
8534 -AGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* * **
8555 TGGTTACCAAATTTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
8577 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
8601 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
8623 TGGTTA
1 TGGTTA
8629 ATTTTCACAA
Statistics
Matches: 121, Mismatches: 30, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.02
21 4 0.03
22 88 0.73
23 6 0.05
24 20 0.17
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:8515 original size:44 final size:43
Alignment explanation
Indices: 8446--8571 Score: 128
Period size: 44 Copynumber: 2.9 Consensus size: 43
8436 GTTTCTATGT
* ** *
8446 GGTTATCAAAATT-TCATAAGATGGTTATTATAATTTCACAAGGA
1 GGTTATCAAAATTCT-AT-AGGTGGTTACCAAAATTTCACAAGGA
* *
8490 GGTTATCAAAATTCTATAGCGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTCTATAG-GTGGTTACCAAAATTTCACAAGGA
* * *
8534 AGTTATCAAAATTCCATAGTGTGGTTACCAAATTTTCA
1 GGTTATCAAAATTCTATAG-GTGGTTACCAAAATTTCA
8572 TGGGATCAGG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.03
44 67 0.96
45 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTCTATAGGTGGTTACCAAAATTTCACAAGGA
Found at i:8741 original size:22 final size:22
Alignment explanation
Indices: 8664--9611 Score: 193
Period size: 22 Copynumber: 43.1 Consensus size: 22
8654 ATCAAATAGA
* *
8664 TTATCAAAATGTCATAACGAGG
1 TTATCAAAATTTCATAAGGAGG
*
8686 TTAT-AAGAATTTCATTAGGAGG
1 TTATCAA-AATTTCATAAGGAGG
* **
8708 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAAGGAGG
* *
8730 TTATCAAAATTTTAT-AGTGTGG
1 TTATCAAAATTTCATAAG-GAGG
*
8752 TTATCAAAATTTTATAAGGA-G
1 TTATCAAAATTTCATAAGGAGG
* * * *
8773 -TACCAAAATTTGAT-AGAAGT
1 TTATCAAAATTTCATAAGGAGG
*
8793 TTATC-AAATCTCAT-A-GAGTG
1 TTATCAAAATTTCATAAGGAG-G
* * **
8813 ATTATCGAAATTTCATAGAGATCAAA
1 -TTATCAAAATTTCATA-AG--GAGG
* * *
8839 TTATC-AAAATTTAT-AGGAAGA
1 TTATCAAAATTTCATAAGG-AGG
* **
8860 TTATCAAAATTTCATAATGTTG
1 TTATCAAAATTTCATAAGGAGG
*
8882 TTATCAAAATTCCA-AAGCGAGG
1 TTATCAAAATTTCATAAG-GAGG
* * * *
8904 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAGGAGG
*
8926 TTATCAGAATTTCATAGAGG-GG
1 TTATCAAAATTTCATA-AGGAGG
* * * *
8948 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAAGGAGG
* *
8970 TTATCAAAATTTCAGAAAGAGG
1 TTATCAAAATTTCATAAGGAGG
* * * * *
8992 TTATCAAATTTTCAGAATGTGA
1 TTATCAAAATTTCATAAGGAGG
*
9014 TTA-CAAAAATTTCAT-A-GTGG
1 TTATC-AAAATTTCATAAGGAGG
* **
9034 TATTTCTGGGAAGGTTATCA-AA--A--
1 T-TATC----AAAATT-TCATAAGGAGG
* *
9057 TT-TCATAGTATGGTTATCAAATTAGGAAGG
1 TTATCA-A--A--ATT-TC--ATAAGG-AGG
* * * *
9087 TTATTAAACTTTTATTATGGAGG
1 TTATCAAAATTTCA-TAAGGAGG
*
9110 ATATCAAAATTTC--AAGGAGG
1 TTATCAAAATTTCATAAGGAGG
* *
9130 ATATCAAAATTTCAT-AGTTTA-G
1 TTATCAAAATTTCATAAG--GAGG
*
9152 TTTTCAAAATTTCATAA-GAGGG
1 TTATCAAAATTTCATAAGGA-GG
* *
9174 TTATCAAAATTTCAT-AGTATGC
1 TTATCAAAATTTCATAAGGA-GG
* * *
9196 ATATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAAGGAGG
* *
9218 TTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAAGGAGG
** *
9240 TTATCAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATAAGGAGG
*
9262 TTATCAAAA-TT--T--GTA-G
1 TTATCAAAATTTCATAAGGAGG
* * *
9278 TTATCAAGATTTCATAAGAAAG
1 TTATCAAAATTTCATAAGGAGG
* *
9300 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATAAGGAGG
* * * *
9322 TTTATCAAAATTTTATATGAAGAT
1 -TTATCAAAATTTCATAAGGAG-G
* * * *
9346 TTATCAAAATTTTATATGAAGAT
1 TTATCAAAATTTCATAAGGAG-G
*
9369 TTATCAAAATTTTAT-AGCGAGG
1 TTATCAAAATTTCATAAG-GAGG
* *
9391 TTATCAAAATTT--TATGGTGTG
1 TTATCAAAATTTCATAAGGAG-G
* * *
9412 ATTATCAAAATTTCA-GAGTATGA
1 -TTATCAAAATTTCATAAGGA-GG
*
9435 TTA-CTAACAA-TTCATATGGAGG
1 TTATC-AA-AATTTCATAAGGAGG
* * * * *
9457 TTTTTAAATTTTCATAATGTGG
1 TTATCAAAATTTCATAAGGAGG
* * *
9479 TTATCAATATATCAT-ATGA--
1 TTATCAAAATTTCATAAGGAGG
* * * * *
9498 TAACCAACATCTCAT-AGTGTTGG
1 TTATCAAAATTTCATAAG-G-AGG
** *
9521 TTATCAAAATTTCATTGGGAAG
1 TTATCAAAATTTCATAAGGAGG
**
9543 TTATCAAAATTTCATACTGAGG
1 TTATCAAAATTTCATAAGGAGG
* * * * *
9565 TTTTCAAAATTCCTTAGGGAAG
1 TTATCAAAATTTCATAAGGAGG
* * *
9587 TTAACAAAATTTCTTAAGAAGG
1 TTATCAAAATTTCATAAGGAGG
9609 TTA
1 TTA
9612 AAAAAAAATT
Statistics
Matches: 678, Mismatches: 168, Indels: 160
0.67 0.17 0.16
Matches are distributed among these distances:
16 9 0.01
17 5 0.01
18 1 0.00
19 19 0.03
20 48 0.07
21 41 0.06
22 411 0.61
23 105 0.15
24 14 0.02
25 11 0.02
26 6 0.01
27 1 0.00
28 2 0.00
30 3 0.00
31 2 0.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGAGG
Found at i:8848 original size:25 final size:22
Alignment explanation
Indices: 8813--8875 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 22
8803 TCATAGAGTG
*
8813 ATTATCGAAATTTCATAGAGATCAA
1 ATTATCAAAATTTCATAG-GA--AA
*
8838 ATTATCAAAATTT-ATAGGAAG
1 ATTATCAAAATTTCATAGGAAA
8859 ATTATCAAAATTTCATA
1 ATTATCAAAATTTCATA
8876 ATGTTGTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 14 0.40
22 3 0.09
23 2 0.06
24 4 0.11
25 12 0.34
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (22 bp):
ATTATCAAAATTTCATAGGAAA
Found at i:9330 original size:23 final size:23
Alignment explanation
Indices: 9278--9405 Score: 145
Period size: 23 Copynumber: 5.7 Consensus size: 23
9268 AAATTTGTAG
* * * *
9278 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
9300 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
*
9323 TTATCAAAATTTTATATGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
9346 TTATCAAAATTTTATATGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
9369 TTATCAAAATTTTATAGCG-AG-G
1 TTATCAAAATTTTATAG-GAAGAT
9391 TTATCAAAATTTTAT
1 TTATCAAAATTTTAT
9406 GGTGTGATTA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
22 31 0.33
23 61 0.66
24 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:9612 original size:22 final size:22
Alignment explanation
Indices: 9569--9617 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
9559 CTGAGGTTTT
*
9569 CAAAATTCCTTAGGGAAGTTAA
1 CAAAATTCCTTAGAGAAGTTAA
*
9591 CAAAATTTCTTA-AGAAGGTTAA
1 CAAAATTCCTTAGAGAA-GTTAA
*
9613 AAAAA
1 CAAAA
9618 AATTTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (22 bp):
CAAAATTCCTTAGAGAAGTTAA
Found at i:9835 original size:2 final size:2
Alignment explanation
Indices: 9830--9859 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9820 AAAAAAGATA
9830 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
9860 GAAAATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11390 original size:54 final size:53
Alignment explanation
Indices: 11326--11434 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 53
11316 AAGTTAAATT
*
11326 AATACAATAACCCATTCAATATTTTTCCAGATGGAAGTTTTCA-GTATTCTTATG
1 AATACAATAACCCATTCAATATTCTTCCAGATGGAA-TTTT-AGGTATTCTTATG
*
11380 AATACAATAACCCATTCAATATTCTTCGAGATGGAATTTTAGTGTATTCTTATG
1 AATACAATAACCCATTCAATATTCTTCCAGATGGAATTTTAG-GTATTCTTATG
11434 A
1 A
11435 GGTAATTTGG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
52 1 0.02
53 4 0.08
54 46 0.90
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.39
Consensus pattern (53 bp):
AATACAATAACCCATTCAATATTCTTCCAGATGGAATTTTAGGTATTCTTATG
Found at i:11725 original size:71 final size:73
Alignment explanation
Indices: 11599--11739 Score: 241
Period size: 71 Copynumber: 1.9 Consensus size: 73
11589 GTTCAAAACA
*
11599 AATTTCATTATGATGACGAAAAAACAAACAAACATATACATACGGATGGAGATGTTAATAAACAA
1 AATTTCATTATGATGACG--AAAACAAACAAACATATACATACGGATAGAGATGTTAATAAACAA
11664 AATTTTACCG
64 AATTTTACCG
11674 AATTTCATTATGATGACG-AAA-AAACAAACATATACATACGGATAGAGATGTTAATAAACAAAA
1 AATTTCATTATGATGACGAAAACAAACAAACATATACATACGGATAGAGATGTTAATAAACAAAA
11737 TTT
66 TTT
11740 CTCAGAAATA
Statistics
Matches: 65, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
71 44 0.68
72 3 0.05
75 18 0.28
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (73 bp):
AATTTCATTATGATGACGAAAACAAACAAACATATACATACGGATAGAGATGTTAATAAACAAAA
TTTTACCG
Found at i:14910 original size:19 final size:19
Alignment explanation
Indices: 14886--14925 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
14876 AAAATTGTTC
14886 GTTATTTATTTGTGTATTT
1 GTTATTTATTTGTGTATTT
14905 GTTATTTATTTGTGTATTT
1 GTTATTTATTTGTGTATTT
14924 GT
1 GT
14926 GTAACTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.17, T:0.68
Consensus pattern (19 bp):
GTTATTTATTTGTGTATTT
Found at i:20542 original size:2 final size:2
Alignment explanation
Indices: 20535--20563 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20525 AGCATACTTC
20535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20564 CTTACTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.