Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010271.1 Corchorus capsularis cultivar CVL-1 contig10292, 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: 17748
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2418 original size:30 final size:31
Alignment explanation
Indices: 2354--2418 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
2344 AATTTTATGT
* * *
2354 TTTCCGATTATACCCTTATTTTTAAAATATA
1 TTTCCAATTATACCCTTATTTTAAAAACATA
*
2385 TTTCCAATTGTACCCTT-TTTTAAAAACATA
1 TTTCCAATTATACCCTTATTTTAAAAACATA
2415 TTTC
1 TTTC
2419 TAAATTGCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.31, C:0.18, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTCCAATTATACCCTTATTTTAAAAACATA
Found at i:2425 original size:31 final size:31
Alignment explanation
Indices: 2364--2425 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
2354 TTTCCGATTA
* * *
2364 TACCCTTATTTTTAAAATATATTTCCAATTG
1 TACCCTTATTTTAAAAACATATTTCAAATTG
2395 TACCCTT-TTTTAAAAACATATTTCTAAATTG
1 TACCCTTATTTTAAAAACATATTTC-AAATTG
2426 CCATTAGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (31 bp):
TACCCTTATTTTAAAAACATATTTCAAATTG
Found at i:2488 original size:15 final size:15
Alignment explanation
Indices: 2444--2494 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
2434 AAATAATATT
2444 TTAATTATTCCATTA
1 TTAATTATTCCATTA
** *
2459 TT--TT-TTTAATCA
1 TTAATTATTCCATTA
2471 TTAATTATTCCATTA
1 TTAATTATTCCATTA
2486 TTAATTATT
1 TTAATTATT
2495 AGATTATAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 2 0.07
15 16 0.59
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAATTATTCCATTA
Found at i:2500 original size:15 final size:15
Alignment explanation
Indices: 2444--2501 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 15
2434 AAATAATATT
*
2444 TTAATTATTCCATTA
1 TTAATTATTACATTA
* *
2459 TT--TTTTTA-ATCA
1 TTAATTATTACATTA
*
2471 TTAATTATTCCATTA
1 TTAATTATTACATTA
*
2486 TTAATTATTAGATTA
1 TTAATTATTACATTA
2501 T
1 T
2502 AGAATACGTA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
12 5 0.16
13 4 0.12
14 4 0.12
15 19 0.59
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAATTATTACATTA
Found at i:3132 original size:20 final size:20
Alignment explanation
Indices: 3095--3133 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3085 TACTATTATT
3095 TTTTGAATTTAATATTTAAC
1 TTTTGAATTTAATATTTAAC
*
3115 TTTT-AATTTCAATTTTTAA
1 TTTTGAATTT-AATATTTAA
3134 ATATCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTGAATTTAATATTTAAC
Found at i:3313 original size:22 final size:22
Alignment explanation
Indices: 3266--3319 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3256 AAGAGTAGGT
* *
3266 GGTTATCAAAATTTTATAGTGT
1 GGTTATCAAAATTTCATAGTGA
3288 GGTTATCAAAATTTCATA-TGAA
1 GGTTATCAAAATTTCATAGTG-A
3310 GGTTAT-AAAA
1 GGTTATCAAAA
3320 GTCTCAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGA
Found at i:3418 original size:25 final size:22
Alignment explanation
Indices: 3342--3487 Score: 81
Period size: 22 Copynumber: 6.6 Consensus size: 22
3332 TAAGGAGTAC
*
3342 CAAAATTTGATAGAAG--GTTAT
1 CAAAATTTCATAG-AGTTGTTAT
* * * *
3363 C-AAATCTCATAGAGTTATAAA
1 CAAAATTTCATAGAGTTGTTAT
*
3384 CGAAATTTCATAGAGATTAGATTAT
1 CAAAATTTCATAGAG-TT-G-TTAT
*
3409 CAAAATTTCATAGTGTTGTTAT
1 CAAAATTTCATAGAGTTGTTAT
*
3431 CAAAATTTCAAAACGAG--GTTAT
1 CAAAATTTC-ATA-GAGTTGTTAT
* *
3453 CAAAATTACATA-A-TATGATAT
1 CAAAATTTCATAGAGT-TGTTAT
*
3474 CAGAATTTCATAGA
1 CAAAATTTCATAGA
3488 AGGGTCAACA
Statistics
Matches: 95, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.03
20 9 0.09
21 20 0.21
22 39 0.41
23 5 0.05
24 4 0.04
25 15 0.16
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGAGTTGTTAT
Found at i:3451 original size:22 final size:22
Alignment explanation
Indices: 3405--3896 Score: 147
Period size: 22 Copynumber: 22.5 Consensus size: 22
3395 AGAGATTAGA
** **
3405 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
3427 TTATCAAAATTTCA-AAACGAGG
1 TTATCAAAATTTCATAAA-GAGG
* * *
3449 TTATCAAAATTACAT-AATATG
1 TTATCAAAATTTCATAAAGAGG
* *
3470 ATATCAGAATTTCATAGAAG-GG
1 TTATCAAAATTTCATA-AAGAGG
* * *
3492 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
* *
3514 TTATCTACATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
* * * *
3536 TTATCAAATTTTCAAAAAGTGA
1 TTATCAAAATTTCATAAAGAGG
** **
3558 TTA-CAAAAATTTCATAGTGGTATT
1 TTATC-AAAATTTCATA-AAG-AGG
*
3582 TTATCAAAATTT--TATAGTATGG
1 TTATCAAAATTTCATAAAG-A-GG
* **
3604 TTA-CCAAA-TT-A-GGA-AGG
1 TTATCAAAATTTCATAAAGAGG
* * * * *
3621 TTATTAAACTTTTATTATG-GAG
1 TTATCAAAATTTCATAAAGAG-G
* **
3643 TAATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATAAAGAGG
* ***
3663 ATATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATA-AAGAGG
*
3685 TTTTCAAAATTTCAT-AAGAGGG
1 TTATCAAAATTTCATAAAGA-GG
** *
3707 TTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAAAGAGG
* *
3729 TTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAAAGAGG
** **
3751 TTATCAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATAAAGAGG
* * **
3773 TTACCAAGATTTCAT-AAGAAAA
1 TTATCAAAATTTCATAAAG-AGG
* **
3795 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATAAAGAGG
* *
3817 TTTATCAAAATTTTATAGGAAGA-T
1 -TTATCAAAATTTCATA--AAGAGG
** *
3841 TTATCAAAATTTCATAGCGTGG
1 TTATCAAAATTTCATAAAGAGG
* ** * *
3863 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAAAGAGG
3885 TTATCAAAATTT
1 TTATCAAAATTT
3897 AGAGTGTGAT
Statistics
Matches: 336, Mismatches: 104, Indels: 60
0.67 0.21 0.12
Matches are distributed among these distances:
17 5 0.01
18 3 0.01
19 2 0.01
20 18 0.05
21 31 0.09
22 226 0.67
23 38 0.11
24 10 0.03
25 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:3758 original size:66 final size:66
Alignment explanation
Indices: 3645--3896 Score: 208
Period size: 66 Copynumber: 3.8 Consensus size: 66
3635 TTATGGAGTA
* *
3645 ATCAAAATTTC--AGGGAGGA-TATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATAAGAGG
1 ATCAAAATTTCATAGGGA-GATTATCAAAATTTCATAG-TGAGGTTATCAAAATTTCATAAGAGG
3706 GTT
64 GTT
* * ** *
3709 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTTATCAAAAAATCAT-AGGGAGG
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAAGAG-GG
3773 TT
65 TT
* * * * * * * * * *
3775 ACCAAGATTTCATAAGAAAATTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGA
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGG-TTATCAAAATTTCATAAG-AGG
*
3840 TTT
64 GTT
* * * * * *
3843 ATCAAAATTTCATAGCGTGGTTATCACAATTTCATAGTGTGATTATCAAAATTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGTTATCAAAATTT
3897 AGAGTGTGAT
Statistics
Matches: 144, Mismatches: 36, Indels: 13
0.75 0.19 0.07
Matches are distributed among these distances:
64 11 0.08
65 7 0.05
66 69 0.48
67 24 0.17
68 32 0.22
69 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (66 bp):
ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAAGAGGGT
T
Found at i:3904 original size:21 final size:22
Alignment explanation
Indices: 3664--4032 Score: 132
Period size: 22 Copynumber: 16.7 Consensus size: 22
3654 TCAGGGAGGA
*
3664 TATCAAAATTTCATAGT-TTAGT
1 TATCAAAATTTCATAGTGTGA-T
* * *
3686 TTTCAAAATTTCATAAGAG-GGT
1 TATCAAAATTTCAT-AGTGTGAT
* *
3708 TATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATAGTGTGAT
* * * *
3730 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGTGTGAT
** * * *
3752 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGTGTGAT
* * ***
3774 TACCAAGATTTCATAAG-AAAAT
1 TATCAAAATTTCAT-AGTGTGAT
* * * *
3796 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGTG-TGAT
* *
3819 TATCAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGTG-TGA-T
* *
3842 TATCAAAATTTCATAGCGTGGT
1 TATCAAAATTTCATAGTGTGAT
*
3864 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
*
3886 TATCAAAATTT-AGAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
3907 TA-CTAACAA-TTCATA-TG-GAGGT
1 TATC-AA-AATTTCATAGTGTGA--T
* * * ** *
3929 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCATAGTGTGAT
* * **
3951 TATCAATATATCATA-TGAAAGT
1 TATCAAAATTTCATAGTGTGA-T
* * *
3973 TATCAACATCTCATAGTGTCGGT
1 TATCAAAATTTCATAGTGT-GAT
*
3996 TATCAAAATTTCAT--TGGGAAGT
1 TATCAAAATTTCATAGTGTG-A-T
4018 TATCAAAATTTCATA
1 TATCAAAATTTCATA
4033 TTAAAAAAAT
Statistics
Matches: 260, Mismatches: 64, Indels: 45
0.70 0.17 0.12
Matches are distributed among these distances:
20 4 0.02
21 26 0.10
22 174 0.67
23 54 0.21
24 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:15831 original size:2 final size:2
Alignment explanation
Indices: 15824--15848 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15814 TTTGCATTTT
15824 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
15849 TTTTTTTTTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.