Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014782.1 Corchorus olitorius cultivar O-4 contig14815, 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: 22678
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2079 original size:22 final size:22
Alignment explanation
Indices: 2041--2256 Score: 161
Period size: 22 Copynumber: 9.8 Consensus size: 22
2031 AGATTTGAGA
*
2041 AGGTTATC-AAATCTCATAGAG
1 AGGTTATCAAAATTTCATAGAG
* *
2062 TGGTTATCGAAATTTCATAGAG
1 AGGTTATCAAAATTTCATAGAG
*
2084 ATCAGATTATCAAAATTT-ATA-AG
1 ---AGGTTATCAAAATTTCATAGAG
* * *
2107 AAGATTATCAAAATTTTATAGTG
1 -AGGTTATCAAAATTTCATAGAG
*** * *
2130 TTATTATCAAAATTTCAAAGCG
1 AGGTTATCAAAATTTCATAGAG
*
2152 AGGTTATCAAAATTACATA-ATG
1 AGGTTATCAAAATTTCATAGA-G
* * *
2174 TGATTATCAAAATTTTATAGAG
1 AGGTTATCAAAATTTCATAGAG
* * * *
2196 GGGTCAACAAAATTTTATAGAG
1 AGGTTATCAAAATTTCATAGAG
*
2218 AGGTTATCAAAATTTCATAAAG
1 AGGTTATCAAAATTTCATAGAG
*
2240 AGGTTATCAAATTTTCA
1 AGGTTATCAAAATTTCA
2257 AAATGTGATT
Statistics
Matches: 155, Mismatches: 32, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
21 22 0.14
22 114 0.74
23 4 0.03
24 3 0.02
25 12 0.08
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGAG
Found at i:2180 original size:44 final size:45
Alignment explanation
Indices: 2044--2976 Score: 249
Period size: 44 Copynumber: 21.2 Consensus size: 45
2034 TTTGAGAAGG
* * *
2044 TTATC-AAATCTCAT-AGAGTGGTTATCGAAATTTCATAGA-GATCAGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATA-ATG-T--GA
* * * *
2090 TTATCAAAATTT-ATAAGA-AGATTATCAAAATTTTATAGTGTTA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* *
2133 TTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * * * *
2177 TTATCAAAATTTTAT-AGAGGGGTCAACAAAATTTTATAGA-GAGG
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATA-ATGTGA
* *
2221 TTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * *
2265 TTACCAAAATTTCATAGTGGTATTTCTGGGGAGGTTATCAAAATTTCATAGTATGG
1 TTATCAAAATTTCATA-----A------GAGAGGTTATCAAAATTTCATAATGTGA
* * * * * *
2321 TTA-CCAAA--T--TAGGA-AGGTTATTAAACTTTTATTATG-GA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * * *
2359 GTAATTAAAATTTC---AG-GCATGATATCAAAATTTCAT-ATGAAGG
1 -TTATCAAAATTTCATAAGAG-AGGTTATCAAAATTTCATAATG-TGA
* * *
2402 TTATCAAAATTTCATATGA-AGGTTATCAAAATTTCAT-ATGAAGG
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATG-TGA
** * *
2446 TTATCAAAATTTCAT-AGTTTA-GTTTTCAAAATTTCATAA-GAGGA
1 TTATCAAAATTTCATAAG-AGAGGTTATCAAAATTTCATAATG-TGA
* * ** *
2490 TTATCAAAATTTCAT-AGGGAGATTAAAAAAATTTCATAATGAGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
** *
2534 TTATCAAAAAATCATAAG-GAGGTTATCAAAATTT-GT-A---G-
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * ** * *
2572 TTATCAAGATTTCATAAG-TAGGTTATCAAAATTTTATAGCGAGGT
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATG-TGA
* * * ** * *
2617 TTATCAAAATTTTATAGGA-ATGTTTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAAGAGA-GGTTATCAAAATTTCATAATGTGA
* * * * * * *
2662 TTATCACAATTTCAT-AGTGTGATTATCAAAATTTTAGAGTGTGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * * * *
2706 TTA-CTAATAA-TTCATATGA-ATGTTTTTAAATTTTCATAACGTGG
1 TTATC-AA-AATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * ** * * *
2750 TTATCAATATATCATATG-GAAGTTATCAACGTCTC--AGTGTTGG
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATG-TGA
* * * * *
2793 TTATCAAAATTTCATTAGA-AAGTTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * *
2837 TCT-TCAAAATTTCTTACG-GAGGTTAACAAAATTTCATAA-GAAGG
1 T-TATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATG-TGA
* * * * * * * *
2881 TTA-AAAAATTTTATAA-AAAGGTTCTCGAAATTTTATAGTATCG-
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGT-GA
* * * *
2924 TTATTAAAATTTCATAAGA-AGATTATCAAAATTTCATAAGGAGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
*
2968 TCATCAAAA
1 TTATCAAAA
2977 ATAGTGTAAT
Statistics
Matches: 650, Mismatches: 167, Indels: 142
0.68 0.17 0.15
Matches are distributed among these distances:
38 31 0.05
39 20 0.03
40 4 0.01
41 4 0.01
42 28 0.04
43 83 0.13
44 349 0.54
45 49 0.08
46 42 0.06
47 8 0.01
49 1 0.00
51 2 0.00
53 1 0.00
55 4 0.01
56 24 0.04
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (45 bp):
TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
Found at i:2190 original size:66 final size:66
Alignment explanation
Indices: 2090--2278 Score: 186
Period size: 66 Copynumber: 2.9 Consensus size: 66
2080 AGAGATCAGA
* * * *
2090 TTATCAAAATT-TAT-AAGAAGATTATCAAAATTTTATAGTGTTATTATCAAAATTTCAAAGCGA
1 TTATCAAAATTACATAAAG-AGATTATCAAAATTTTATAGTGTGATTAACAAAATTTCAAAGAGA
2153 GG
65 GG
* * * * * * * *
2155 TTATCAAAATTACATAATGTGATTATCAAAATTTTATAGAGGGGTCAACAAAATTTTATAGAGAG
1 TTATCAAAATTACATAAAGAGATTATCAAAATTTTATAGTGTGATTAACAAAATTTCAAAGAGAG
2220 G
66 G
* * * * *
2221 TTATCAAAATTTCATAAAGAGGTTATC-AAATTTTCAAAATGTGATTACCAAAATTTCA
1 TTATCAAAATTACATAAAGAGATTATCAAAATTTT-ATAGTGTGATTAACAAAATTTCA
2279 TAGTGGTATT
Statistics
Matches: 97, Mismatches: 24, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
65 18 0.19
66 77 0.79
67 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (66 bp):
TTATCAAAATTACATAAAGAGATTATCAAAATTTTATAGTGTGATTAACAAAATTTCAAAGAGAG
G
Found at i:2409 original size:22 final size:22
Alignment explanation
Indices: 2381--3027 Score: 281
Period size: 22 Copynumber: 29.9 Consensus size: 22
2371 TCAGGCATGA
2381 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
2403 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
2425 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
2447 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* *
2469 TTTCAAAATTTCATAAG-AGGAT
1 TATCAAAATTTCATATGAAGG-T
* * *
2491 TATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATGAAGGT
** *
2513 TAAAAAAATTTCATAATG-AGAT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
2535 TATCAAAAAATCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
2557 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
2573 TATCAAGATTTCATAAGTAGGT
1 TATCAAAATTTCATATGAAGGT
* *
2595 TATCAAAATTTTATA-GCGAGGTT
1 TATCAAAATTTCATATG-AAGG-T
* * *
2618 TATCAAAATTTTATAGGAATGTT
1 TATCAAAATTTCATATGAA-GGT
*
2641 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
2663 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
2685 TATCAAAATTTTAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
2707 TA-CTAATAA-TTCATATGAATGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
2729 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* *
2751 TATCAATATATCATATGGAA-GT
1 TATCAAAATTTCATAT-GAAGGT
** * * **
2773 TATCAACGTCTCA-GTGTTGGT
1 TATCAAAATTTCATATGAAGGT
*
2794 TATCAAAATTTCAT-TAGAAAGT
1 TATCAAAATTTCATAT-GAAGGT
2816 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
2838 CT-TCAAAATTTCTTACGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
2860 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
2882 TA-AAAAATTTTATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
2903 TCTCGAAATTTTATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* * *
2925 TATTAAAATTTCATAAGAAGAT
1 TATCAAAATTTCATATGAAGGT
* * *
2947 TATCAAAATTTCATAAGGAGAT
1 TATCAAAATTTCATATGAAGGT
*
2969 CATCAAAA----ATAGTGTAA--T
1 TATCAAAATTTCATA-TG-AAGGT
* * *
2987 TATCATAATTTAATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
*
3009 TATCATAATTTCATATGAA
1 TATCAAAATTTCATATGAA
3028 TATTTCATTT
Statistics
Matches: 481, Mismatches: 98, Indels: 92
0.72 0.15 0.14
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 12 0.02
19 1 0.00
20 7 0.01
21 46 0.10
22 354 0.74
23 46 0.10
24 4 0.01
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:2624 original size:23 final size:23
Alignment explanation
Indices: 2594--2697 Score: 115
Period size: 23 Copynumber: 4.6 Consensus size: 23
2584 CATAAGTAGG
2594 TTATCAAAATTTTATAGCGAGGT
1 TTATCAAAATTTTATAGCGAGGT
*
2617 TTATCAAAATTTTATAG-GAATGT
1 TTATCAAAATTTTATAGCG-AGGT
*
2640 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGCGAGGT
* * * * *
2662 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGCGAGGT
2684 TTATCAAAATTTTA
1 TTATCAAAATTTTA
2698 GAGTGTGATT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
21 1 0.01
22 30 0.43
23 38 0.54
24 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGCGAGGT
Found at i:3669 original size:11 final size:11
Alignment explanation
Indices: 3645--3679 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3635 TTGACAGCGC
3645 AACAAAAACAA
1 AACAAAAACAA
* *
3656 AACGAAAACGA
1 AACAAAAACAA
3667 AACAAAAACAA
1 AACAAAAACAA
3678 AA
1 AA
3680 AAACAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:8883 original size:2 final size:2
Alignment explanation
Indices: 8876--8916 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
8866 CTTCCCTATT
8876 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
8917 TATAATTAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:20982 original size:3 final size:3
Alignment explanation
Indices: 20974--21005 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20964 TTTCTCTAGG
20974 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
21006 AGAAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.