Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011411.1 Corchorus capsularis cultivar CVL-1 contig11432, 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: 11128
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Found at i:6573 original size:31 final size:32
Alignment explanation
Indices: 6538--6601 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
6528 AACTTTATGT
* *
6538 TTTCCGATTGTACCCTTATT-TTTAAAATATA
1 TTTCCAATTGTACCCTTATTATTTAAAACATA
* *
6569 TTTCCAATTGTACCTTTTTTATTTAAAACATA
1 TTTCCAATTGTACCCTTATTATTTAAAACATA
6601 T
1 T
6602 CTCTAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.50
Consensus pattern (32 bp):
TTTCCAATTGTACCCTTATTATTTAAAACATA
Found at i:6892 original size:22 final size:21
Alignment explanation
Indices: 6838--6967 Score: 80
Period size: 22 Copynumber: 5.9 Consensus size: 21
6828 CTCTATGTGA
*
6838 TTATCAAAATTTCATAAGATGG
1 TTATCAAAATTTCATAGGA-GG
* *
6860 TTATTATAATTTCATGAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* **
6882 TTATCAAAATTCCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
* * *
6904 TTACCAAAATTTCATACTGTGG
1 TTATCAAAATTTCATA-GGAGG
* *
6926 TTACCAAAGTTTCATAGGATCAGG
1 TTATCAAAATTTCATAGG---AGG
* *
6950 TTATTAAAATTTCTTAGG
1 TTATCAAAATTTCATAGG
6968 TTGAGTATTG
Statistics
Matches: 83, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
21 3 0.04
22 61 0.73
23 3 0.04
24 16 0.19
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:6962 original size:24 final size:22
Alignment explanation
Indices: 6935--6989 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
6925 GTTACCAAAG
6935 TTTCATAGGATCAGGTTATTAAAA
1 TTTCATAGGATCA-G-TATTAAAA
* * * *
6959 TTTCTTAGGTTGAGTATTGAAA
1 TTTCATAGGATCAGTATTAAAA
6981 TTTCATAGG
1 TTTCATAGG
6990 GTGGTTAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 15 0.58
23 1 0.04
24 10 0.38
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (22 bp):
TTTCATAGGATCAGTATTAAAA
Found at i:7167 original size:22 final size:21
Alignment explanation
Indices: 7032--7420 Score: 134
Period size: 22 Copynumber: 17.7 Consensus size: 21
7022 ATCAAAGAGA
* *
7032 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-AAGG
* **
7054 TTAT-AAGAATTTCGTAGTGTGG
1 TTATCAA-AATTTCATAG-AAGG
* *
7076 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGAAGG
* * *
7098 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGAAGG
* **
7120 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAG-AAGG
7142 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GAAGG
* *
7164 TTAT-AAAAGTCTCAATTTCATAAGG
1 TTATCAAAA-TTTC-A--T-AGAAGG
*
7189 --AGT-AAAATTTGATAGAAGG
1 TTA-TCAAAATTTCATAGAAGG
*
7208 TTATC-AAATCTCATAG-AGTG
1 TTATCAAAATTTCATAGAAG-G
*
7228 ATTATCTAAATTTCATAGAGATCGG
1 -TTATCAAAATTTCATAGA-A--GG
*
7253 ATTATCAAAATTT-ATAGGAAGA
1 -TTATCAAAATTTCATA-GAAGG
*
7275 TTATCAAAATTTCATAG-TGTTG
1 TTATCAAAATTTCATAGAAG--G
* * *
7297 TTATCAAAATTTCAAAGCGAGA
1 TTATCAAAATTTCATAG-AAGG
* *
7319 TTATCAAAATTACATA-ATGTG
1 TTATCAAAATTTCATAGAAG-G
* * *
7340 ATTATCATAAGTTCATAGAGGGG
1 -TTATCAAAATTTCATAGA-AGG
* * * *
7363 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGA-AGG
*
7385 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGA-AGG
*
7407 TTATCAAATTTTCA
1 TTATCAAAATTTCA
7421 AAATGTGATT
Statistics
Matches: 282, Mismatches: 51, Indels: 68
0.70 0.13 0.17
Matches are distributed among these distances:
19 7 0.02
20 14 0.05
21 28 0.10
22 186 0.66
23 13 0.05
24 12 0.04
25 20 0.07
26 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGAAGG
Found at i:7307 original size:68 final size:64
Alignment explanation
Indices: 7192--7329 Score: 156
Period size: 68 Copynumber: 2.1 Consensus size: 64
7182 CATAAGGAGT
* *
7192 AAAATTTGATAGAAGGTTATCAAATCTCATAGAGTGATTATCTAAATTTCATAGAGATCG-GATT
1 AAAATTTGATAGAAGATTATCAAATCTCATAGAGTGATTATCAAAATTTCA-A-AG--CGAGATT
7256 ATC
62 ATC
* *
7259 AAAATTT-ATAGGAAGATTATCAAAATTTCATAGTGTTG-TTATCAAAATTTCAAAGCGAGATTA
1 AAAATTTGATA-GAAGATTATC-AAATCTCATAGAG-TGATTATCAAAATTTCAAAGCGAGATTA
7322 TC
63 TC
7324 AAAATT
1 AAAATT
7330 ACATAATGTG
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
64 2 0.03
65 13 0.21
66 5 0.08
67 17 0.27
68 24 0.38
69 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (64 bp):
AAAATTTGATAGAAGATTATCAAATCTCATAGAGTGATTATCAAAATTTCAAAGCGAGATTATC
Found at i:7576 original size:22 final size:22
Alignment explanation
Indices: 7526--8082 Score: 163
Period size: 22 Copynumber: 25.6 Consensus size: 22
7516 TTATGGAGTA
* *
7526 ATCAAAATTTCA-A-GGAGGAT
1 ATCAAAATTTCATATGAAGGTT
*
7546 AGCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* *
7568 ATCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
7590 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
*
7612 ATCAAAATTTCATA-GAGAGATT
1 ATCAAAATTTCATATGA-AGGTT
*
7634 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
** * * *
7656 ATCAAAAAATCATAGGGAGCTT
1 ATCAAAATTTCATATGAAGGTT
*
7678 ATCAAAA---C-T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * * **
7694 ATCAAGATTCCATAAGAAAATT
1 ATCAAAATTTCATATGAAGGTT
* * *
7716 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* * *
7739 ATCAAAATTTTATAGGAAGACTT
1 ATCAAAATTTCATATGAAG-GTT
*
7762 ATCAAAATTTCATA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * * *
7784 ATCATAATTTTATA-G-CGTGATC
1 ATCAAAATTTCATATGAAG-G-TT
* * * *
7806 ATCAAATTTTCAGAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
*
7828 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * * * *
7850 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
* * *
7872 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
7894 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
*
7917 ATCAAAATTTCAT-TGAAAAGTT
1 ATCAAAATTTCATATG-AAGGTT
7939 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
* * * *
7962 -TCAAAATTCCTTAAGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* ** *
7983 AACAAAATTTCATAAAAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * ** *
8005 -TAAAAAATT-ATAAAAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
8025 CTCAAAATTCCATA-GTATCGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
8047 ATTAAAATTTCACAGGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
8069 ATCAAAATTTCATA
1 ATCAAAATTTCATA
8083 ATAAGATCAT
Statistics
Matches: 396, Mismatches: 103, Indels: 74
0.69 0.18 0.13
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 1 0.00
19 2 0.01
20 24 0.06
21 31 0.08
22 261 0.66
23 62 0.16
24 5 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:7744 original size:23 final size:22
Alignment explanation
Indices: 7714--7798 Score: 107
Period size: 23 Copynumber: 3.8 Consensus size: 22
7704 CATAAGAAAA
7714 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
* *
7736 TTTATCAAAATTTTATAGGAAGAC
1 -TTATCAAAATTTTATAGGGAG-G
* *
7760 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTTATAGGGAGG
*
7782 TTATCATAATTTTATAG
1 TTATCAAAATTTTATAG
7799 CGTGATCATC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 15 0.28
23 38 0.72
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGG
Found at i:9605 original size:22 final size:22
Alignment explanation
Indices: 9579--9625 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
9569 ATTTATTCAT
9579 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
9601 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
9623 TAT
1 TAT
9626 AGTATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:9621 original size:11 final size:11
Alignment explanation
Indices: 9579--9621 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
9569 ATTTATTCAT
*
9579 TATTAATTAAC
1 TATTAATTAGC
*
9590 TATTAATTAGA
1 TATTAATTAGC
9601 TATTAATTAGC
1 TATTAATTAGC
9612 TATTAATTAG
1 TATTAATTAG
9622 ATATAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:9773 original size:2 final size:2
Alignment explanation
Indices: 9760--9801 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
9750 GACAAAAATA
9760 AT AT AT AGT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9802 TTAATCTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9801 original size:17 final size:17
Alignment explanation
Indices: 9760--9802 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
9750 GACAAAAATA
*
9760 ATATATAGTATATATAT
1 ATATATATTATATATAT
9777 ATATATATTATATATAT
1 ATATATATTATATATAT
9794 ATATATATT
1 ATATATATT
9803 TAATCTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATATATATTATATATAT
Done.