Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015157.1 Corchorus olitorius cultivar O-4 contig15190, 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: 18271
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:2312 original size:2 final size:2
Alignment explanation
Indices: 2305--2330 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2295 CCTTGCTAAT
2305 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2331 GGCCGCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6418 original size:51 final size:51
Alignment explanation
Indices: 6347--6449 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
6337 TATTTCTGAA
* **
6347 AGAGAAACACGAATACAGTGTTTTTATGTCCGGAGACAAGAT-TGAAACAAG
1 AGAGAAACACGAAAACAGTGTTTGGATGTCCGGAGACAAGATCT-AAACAAG
* * * *
6398 AGAGAAACACTAAAAGAGTGTTTGGGTGTCCTGAGACAAGATCTAAACAAG
1 AGAGAAACACGAAAACAGTGTTTGGATGTCCGGAGACAAGATCTAAACAAG
6449 A
1 A
6450 AAAATATGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (51 bp):
AGAGAAACACGAAAACAGTGTTTGGATGTCCGGAGACAAGATCTAAACAAG
Found at i:11716 original size:2 final size:2
Alignment explanation
Indices: 11709--11743 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11699 ACAGACATAC
11709 AT AT AT 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 AT AT AT A
11744 ATAAGTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15594 original size:22 final size:22
Alignment explanation
Indices: 15567--15754 Score: 82
Period size: 22 Copynumber: 8.5 Consensus size: 22
15557 ATTACACTAT
*
15567 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
15589 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** * *
15611 TTTTAATAACGATACTATGGAA
1 TTTTGATAACCTTCCTATGAAA
* * * * *
15633 TTTCGAGAACCTT-TTCAT-TAT
1 TTTTGATAACCTTCCT-ATGAAA
** *
15654 TTTTTTTAACCTTCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* * *
15676 TTTTGTTAACC-TCTCTAAGGAA
1 TTTTGATAACCTTC-CTATGAAA
*
15698 TTTTGA-AGGCC-TCACTATGAAA
1 TTTTGATA-ACCTTC-CTATGAAA
* *
15720 TTTTGATATAACTTCCCAATGAAA
1 TTTTGATA-ACCTT-CCTATGAAA
*
15744 TTCTGATAACC
1 TTTTGATAACC
15755 AACACTATGA
Statistics
Matches: 122, Mismatches: 35, Indels: 17
0.70 0.20 0.10
Matches are distributed among these distances:
21 16 0.13
22 83 0.68
23 7 0.06
24 15 0.12
25 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:16220 original size:22 final size:20
Alignment explanation
Indices: 16195--16234 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16185 GAAGGTTATC
16195 AAATCTCATACAGTGATTATTG
1 AAATCTCAT--AGTGATTATTG
*
16217 AAATTTCATAGTGATTAT
1 AAATCTCATAGTGATTAT
16235 CAAAATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (20 bp):
AAATCTCATAGTGATTATTG
Found at i:16231 original size:20 final size:20
Alignment explanation
Indices: 16206--16293 Score: 68
Period size: 20 Copynumber: 4.2 Consensus size: 20
16196 AATCTCATAC
**
16206 AGTGATTATTGAAATTTCAT
1 AGTGATTATCAAAATTTCAT
16226 AGTGATTATCAAAATTTCAT
1 AGTGATTATCAAAATTTCAT
** * * *
16246 AAAGAAGTTATCAAATTTTAAAA
1 AGTG-A-TTATCAAAATTT-CAT
*
16269 ATGTGATTACCAAAATTTCAT
1 A-GTGATTATCAAAATTTCAT
16290 AGTG
1 AGTG
16294 GTATTTATGC
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
20 23 0.45
21 3 0.06
22 21 0.41
23 3 0.06
24 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (20 bp):
AGTGATTATCAAAATTTCAT
Found at i:16460 original size:22 final size:21
Alignment explanation
Indices: 16389--16936 Score: 126
Period size: 22 Copynumber: 25.3 Consensus size: 21
16379 TCAGGGACGA
* * *
16389 TATCAAAGTTTGATAAGAAGGT
1 TATCAAAATTTCATATG-AGGT
*
16411 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA--TGAGGT
*
16433 TTTCAAAATTTCATATGAGGAT
1 TATCAAAATTTCATATGAGG-T
*
16455 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATG-AGGT
* * *
16476 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATA-TGAGGT
*
16499 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCAT-ATGAGGT
** *
16521 TATCAAAAAATCATA-GGGTTGT
1 TATCAAAATTTCATATGAG--GT
*
16543 TATCAAAA-TT--TGT-A-GT
1 TATCAAAATTTCATATGAGGT
* *
16559 TATTAAGATTTC--A---GGT
1 TATCAAAATTTCATATGAGGT
* * *
16575 TATCAAAATTTTATAGGGACGTT
1 TATCAAAATTTCATA-TGA-GGT
* *
16598 TATCAAACTTTTATA-GAAAGGTT
1 TATCAAAATTTCATATG--AGG-T
*
16621 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATA-TGAGGT
* * * *
16643 TATCACAATTTCAGAGTGTGAT
1 TATCAAAATTTCATA-TGAGGT
*
16665 TA-CTAACAA-TTCATATGGAGAAT
1 TATC-AA-AATTTCATAT-GAG-GT
* * * *
16688 T-TTAAATTTTCATAACGTGGT
1 TATCAAAATTTCAT-ATGAGGT
* *
16709 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATAT-GAGGT
* * * *
16731 TATCAACATCTCATAGTGTTGCT
1 TATCAAAATTTCATA-TG-AGGT
* *
16754 TATTAAAATTTCAT-TGGGAAGT
1 TATCAAAATTTCATAT--GAGGT
16776 TATCAAAATTTCATAGTGAGGT
1 TATCAAAATTTCATA-TGAGGT
* * *
16798 CATCAAAATTTCTTAGAGAGGT
1 TATCAAAATTTCATA-TGAGGT
* *
16820 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATG-AGGT
** * **
16842 TAAAAAAATTTTATAAAAAGGT
1 TATCAAAATTTCAT-ATGAGGT
* * *
16864 TCTCAATATTCCATA-GTAGCGT
1 TATCAAAATTTCATATG-AG-GT
* * *
16886 TATTAAAATTTCATAAGAAGAT
1 TATCAAAATTTCATATG-AGGT
* *
16908 TATCAAAATCTCATAAGGAGGT
1 TATCAAAATTTCAT-ATGAGGT
*
16930 CATCAAA
1 TATCAAA
16937 GATAGTGTAA
Statistics
Matches: 387, Mismatches: 91, Indels: 96
0.67 0.16 0.17
Matches are distributed among these distances:
16 19 0.05
17 2 0.01
18 1 0.00
19 1 0.00
20 4 0.01
21 18 0.05
22 273 0.71
23 66 0.17
24 2 0.01
25 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (21 bp):
TATCAAAATTTCATATGAGGT
Found at i:16526 original size:44 final size:44
Alignment explanation
Indices: 16410--16936 Score: 185
Period size: 44 Copynumber: 11.7 Consensus size: 44
16400 GATAAGAAGG
* * * *
16410 TTATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATA-TGAGGA
1 TTATCAAAATTTCATA-ATGAGGTTATCAAAATTTCATAGGGA-GA
* * *
16454 TTATCAAAATTTCATAGT-ATGTAGATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAATGAGGT-TATCAAAATTTCATAGGGAGA
* ** *
16498 TTAACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGTTG-
1 TTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGGG-AGA
* * * *
16542 TTATCAAAATTTGTAGTTATTAAGATTTCAGGTTATCAAAATTTTATAGGGACGT
1 TTATCAAAA--T-T--TCA-T-A-A--TGAGGTTATCAAAATTTCATAGGGA-GA
* * * * *
16597 TTATCAAACTTTTATAGA-AAGGTTTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATA-ATGAGG-TTATCAAAATTTCATAGGGAGA
* * * * * *
16642 TTATCACAATTTCAGAGTGTGATTA-CTAACAA-TTCATATGGAGAA
1 TTATCAAAATTTCATAATGAGGTTATC-AA-AATTTCATAGGGAG-A
* * * * * * * *
16687 TT-TTAAATTTTCATAACGTGGTTATCAATATATCATATGGAGG
1 TTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGGGAGA
* * * * * * *
16730 TTATCAACATCTCATAGTGTTGCTTATTAAAATTTCATTGGGA-A
1 TTATCAAAATTTCATAATG-AGGTTATCAAAATTTCATAGGGAGA
* * * * *
16774 GTTATCAAAATTTCATAGTGAGGTCATCAAAATTTCTTAGAGAGG
1 -TTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGGGAGA
* ** * *** *
16819 TTAACAAAATTTCATAA-GAAGGTTAAAAAAATTTTATAAAAAGG
1 TTATCAAAATTTCATAATG-AGGTTATCAAAATTTCATAGGGAGA
* * * * * * *
16863 TTCTCAATATTCCATAGT-AGCGTTATTAAAATTTCATAAGAAGA
1 TTATCAAAATTTCATAATGAG-GTTATCAAAATTTCATAGGGAGA
* * *
16907 TTATCAAAATCTCATAAGGAGGTCATCAAA
1 TTATCAAAATTTCATAATGAGGTTATCAAA
16937 GATAGTGTAA
Statistics
Matches: 357, Mismatches: 94, Indels: 64
0.69 0.18 0.12
Matches are distributed among these distances:
42 1 0.00
43 10 0.03
44 219 0.61
45 64 0.18
46 19 0.05
47 1 0.00
48 3 0.01
49 3 0.01
50 4 0.01
51 1 0.00
52 2 0.01
53 1 0.00
54 21 0.06
55 8 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGGGAGA
Found at i:16548 original size:66 final size:65
Alignment explanation
Indices: 16409--16553 Score: 161
Period size: 66 Copynumber: 2.2 Consensus size: 65
16399 TGATAAGAAG
** ** **
16409 GTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATATGAGGATTATCAAAATTTCATAGTAT
1 GTTATCAAAATTTCATAGTGGAGTTAACAAAATTTCATATGAGGATTATCAAAAAATCATAGTAT
*
16474 GTAGATCAAAATTTCATAG-GGAGATTAACAAAATTTCATAATGAGG-TTATCAAAAAATCATAG
1 GT-TATCAAAATTTCATAGTGGAG-TTAACAAAATTTCAT-ATGAGGATTATCAAAAAATCATA-
16537 GGT-T
62 -GTAT
16541 GTTATCAAAATTT
1 GTTATCAAAATTT
16554 GTAGTTATTA
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
65 4 0.06
66 52 0.78
67 9 0.13
68 2 0.03
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (65 bp):
GTTATCAAAATTTCATAGTGGAGTTAACAAAATTTCATATGAGGATTATCAAAAAATCATAGTAT
Found at i:16604 original size:23 final size:22
Alignment explanation
Indices: 16574--16653 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
16564 AGATTTCAGG
*
16574 TTATCAAAATTTTATAGGGACGT
1 TTATCAAAATTTTATAGAGA-GT
* *
16597 TTATCAAACTTTTATAGAAAGGT
1 TTATCAAAATTTTATAGAGA-GT
* * *
16620 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTTATAGAGAGT
*
16642 TTATCACAATTT
1 TTATCAAAATTT
16654 CAGAGTGTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 12 0.26
23 35 0.74
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTTATAGAGAGT
Found at i:17432 original size:19 final size:19
Alignment explanation
Indices: 17370--17433 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
17360 TGAGTTTAGT
*
17370 ATTTCTTAATTTACAAAGA
1 ATTTCTTAATTTACAGAGA
*
17389 ATTTTCTATGATTTGAGTC-GAGA
1 A-TTTCT-TAATTT-A--CAGAGA
17412 ATTTCTTAATTTACAGAGA
1 ATTTCTTAATTTACAGAGA
17431 ATT
1 ATT
17434 CTCAAGGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
18 1 0.03
19 8 0.22
20 6 0.17
21 10 0.28
22 6 0.17
23 4 0.11
24 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (19 bp):
ATTTCTTAATTTACAGAGA
Found at i:18230 original size:2 final size:2
Alignment explanation
Indices: 18223--18268 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
18213 TTAAAACTAG
18223 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18265 TA TA
1 TA TA
18269 CTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.