Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012005.1 Corchorus capsularis cultivar CVL-1 contig12026, 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: 4731
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:1909 original size:26 final size:24
Alignment explanation
Indices: 1854--1911 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
1844 ATATATTTCT
*
1854 AAATTTCTATTATTAAAATTTAGTA
1 AAATTT-TATTATTAAAATTAAGTA
* *
1879 TAATTTTATTATTTAAAAATTAATTA
1 AAATTTTATTA-TT-AAAATTAAGTA
1905 AAATTTT
1 AAATTTT
1912 CAATTTAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 5 0.19
25 7 0.26
26 15 0.56
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
AAATTTTATTATTAAAATTAAGTA
Found at i:2216 original size:22 final size:22
Alignment explanation
Indices: 2188--2371 Score: 144
Period size: 22 Copynumber: 8.3 Consensus size: 22
2178 TGTCTCTATG
*
2188 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
2210 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
2233 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
2254 TGGTTA-CAAAAATTTCATATGGA
1 TGGTTATC-AAAATTTCATA-GGA
*
2277 -AGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* * *
2298 TGCTTACCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
2320 TTAGTTATTAAAATTTCTTAGGT
1 -TGGTTATCAAAATTTCATAGGA
* *
2343 TGGTTATTAAAAATTTCATAGGG
1 TGGTTA-TCAAAATTTCATAGGA
2366 TGGTTA
1 TGGTTA
2372 ATTATAACAA
Statistics
Matches: 127, Mismatches: 23, Indels: 23
0.73 0.13 0.13
Matches are distributed among these distances:
21 5 0.04
22 83 0.65
23 39 0.31
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.40
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:2336 original size:23 final size:23
Alignment explanation
Indices: 2306--2363 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
2296 TGTGCTTACC
2306 AAAATTTCATATGATTAGTTATT-
1 AAAATTTCATA-GATTAGTTATTA
* * *
2329 AAAATTTCTTAGGTTGGTTATTA
1 AAAATTTCATAGATTAGTTATTA
2352 AAAATTTCATAG
1 AAAATTTCATAG
2364 GGTGGTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 9 0.30
23 21 0.70
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (23 bp):
AAAATTTCATAGATTAGTTATTA
Found at i:2432 original size:22 final size:22
Alignment explanation
Indices: 2407--2751 Score: 111
Period size: 22 Copynumber: 15.6 Consensus size: 22
2397 ATCAAAGAGA
*
2407 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
2429 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
*
2451 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGCGAGG
*
2473 TTA-CTAATATTTCAT-GCGGAGG
1 TTATC-AAAATTTCATAGC-GAGG
*
2495 TTATCAAAATTTCATATG-AAGG
1 TTATCAAAATTTCATA-GCGAGG
* * **
2517 GTAT-AAAAGTCTCAATTTC-ATGAG
1 TTATCAAAA-TTTC-ATAGCGA-G-G
* * * *
2541 -TACCAAAATTTGAAAG-AAGG
1 TTATCAAAATTTCATAGCGAGG
* * * *
2561 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGCGAGG
* * **
2582 TTATCGAAATTTCATAGAGATCAAA
1 TTATCAAAATTTCATAGCG---AGG
* *
2607 TTATCAAAATTT-ATTG-GAAGA
1 TTATCAAAATTTCATAGCG-AGG
* **
2628 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGCGAGG
* *
2650 TAATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* ** * *
2672 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGCGAGG
* *
2694 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGCGAGG
* * * **
2716 TCAACAAAATTTTATAATGAGG
1 TTATCAAAATTTCATAGCGAGG
*
2738 TTATCAAATTTTCA
1 TTATCAAAATTTCA
2752 AAATGAGATT
Statistics
Matches: 236, Mismatches: 63, Indels: 48
0.68 0.18 0.14
Matches are distributed among these distances:
20 10 0.04
21 32 0.14
22 158 0.67
23 15 0.06
24 9 0.04
25 12 0.05
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:2616 original size:25 final size:22
Alignment explanation
Indices: 2581--2644 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
2571 TCATAGAGTG
*
2581 ATTATCGAAATTTCATAGAGATCAA
1 ATTATCAAAATTTCATAG-GA--AA
* *
2606 ATTATCAAAATTT-ATTGGAAG
1 ATTATCAAAATTTCATAGGAAA
2627 ATTATCAAAATTTCATAG
1 ATTATCAAAATTTCATAG
2645 TGTTGTAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 14 0.41
22 3 0.09
23 2 0.06
24 3 0.09
25 12 0.35
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (22 bp):
ATTATCAAAATTTCATAGGAAA
Found at i:2724 original size:66 final size:66
Alignment explanation
Indices: 2625--2774 Score: 171
Period size: 66 Copynumber: 2.3 Consensus size: 66
2615 ATTTATTGGA
* ** *
2625 AGATTATCAAAATTTCATAGTGTTGTAATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAA
1 AGATTATCAAAATTTCATAGAGGGGTAATCAAAATTTCATAA-CGAGGTTATCAAAATTACAAAA
2689 TG
65 TG
* * * * *
2691 TGATTATCAAAATTTCATAGAGGGGTCAA-CAAAATTTTATAATGAGGTTATCAAATTTTCAAAA
1 AGATTATCAAAATTTCATAGAGGGGT-AATCAAAATTTCATAACGAGGTTATCAAAATTACAAAA
2755 TG
65 TG
2757 AGATTA-CAAAAATTTCAT
1 AGATTATC-AAAATTTCAT
2775 GGTGGTATTT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
65 1 0.01
66 66 0.93
67 4 0.06
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (66 bp):
AGATTATCAAAATTTCATAGAGGGGTAATCAAAATTTCATAACGAGGTTATCAAAATTACAAAAT
G
Found at i:2746 original size:21 final size:21
Alignment explanation
Indices: 2722--2766 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2712 GGGGTCAACA
* *
2722 AAATTTT-ATAATGAGGTTATC
1 AAATTTTCAAAATGAGATTA-C
2743 AAATTTTCAAAATGAGATTAC
1 AAATTTTCAAAATGAGATTAC
2764 AAA
1 AAA
2767 AATTTCATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.36
Consensus pattern (21 bp):
AAATTTTCAAAATGAGATTAC
Found at i:2772 original size:22 final size:22
Alignment explanation
Indices: 2625--2773 Score: 79
Period size: 22 Copynumber: 6.8 Consensus size: 22
2615 ATTTATTGGA
* *
2625 AGATTATCAAAATTTCATAGTG
1 AGATTATCAAAATTTCAAAATG
* * **
2647 TTG-TAATCAAAATTTCAAAGCG
1 -AGATTATCAAAATTTCAAAATG
* * *
2669 AGGTTATCAAAATTACATAATG
1 AGATTATCAAAATTTCAAAATG
* *
2691 TGATTATCAAAATTTCATAGA-G
1 AGATTATCAAAATTTCA-AAATG
* * * * * *
2713 GGGTCAACAAAATTTTATAATG
1 AGATTATCAAAATTTCAAAATG
* *
2735 AGGTTATCAAATTTTCAAAATG
1 AGATTATCAAAATTTCAAAATG
2757 AGATTA-CAAAAATTTCA
1 AGATTATC-AAAATTTCA
2774 TGGTGGTATT
Statistics
Matches: 92, Mismatches: 30, Indels: 9
0.70 0.23 0.07
Matches are distributed among these distances:
21 3 0.03
22 87 0.95
23 2 0.02
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (22 bp):
AGATTATCAAAATTTCAAAATG
Found at i:2906 original size:22 final size:22
Alignment explanation
Indices: 2876--3266 Score: 141
Period size: 22 Copynumber: 18.0 Consensus size: 22
2866 TCAGGGAGGA
*
2876 TATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGTTGAGT
* *
2898 TTTCAAAATTTCATAAG-TGGGT
1 TATCAAAATTTCAT-AGTTGAGT
2920 TATCAAAATTTCATAGTATGTAG-
1 TATCAAAATTTCATAGT-TG-AGT
*
2943 -ATCAAAATTTCATA-ATGAGGT
1 TATCAAAATTTCATAGTTGA-GT
** *
2964 TATCAAAAAATCATAG-GGATGT
1 TATCAAAATTTCATAGTTGA-GT
2986 TATCAAAA-TT--T-G-T-AGT
1 TATCAAAATTTCATAGTTGAGT
* **
3002 TATCAAGATTTCATAAG-AAAGT
1 TATCAAAATTTCAT-AGTTGAGT
* *
3024 TATCAAAATTTTATA-TGGAGGTT
1 TATCAAAATTTCATAGTTGA-G-T
* ** *
3047 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATA-GTTGAGT
*
3070 TATCAAAATTTCATAG-CGAGGT
1 TATCAAAATTTCATAGTTGA-GT
*
3092 TATCACAATTTCATAGTGTGA-T
1 TATCAAAATTTCATAGT-TGAGT
3114 TATCAAAATTTCAGT-GTATGA-T
1 TATCAAAATTTCA-TAGT-TGAGT
*
3136 TA-CTAACAA-TTCATA-TGGAGGT
1 TATC-AA-AATTTCATAGTTGA-GT
* * * *
3158 TTTTAAATTTTCATAATGTG-GT
1 TATCAAAATTTCATAGT-TGAGT
* *
3180 TATCAATATATCATA--TGAAGGT
1 TATCAAAATTTCATAGTTG-A-GT
* *
3202 TATCAACATCTCATAGTGTTG-GT
1 TATCAAAATTTCATA--GTTGAGT
* *
3225 TATCAAAATTTCATTG-GGAAGT
1 TATCAAAATTTCATAGTTG-AGT
3247 TATCAAAATTTCATA-TTGAG
1 TATCAAAATTTCATAGTTGAG
3267 GTCTCCAAAA
Statistics
Matches: 281, Mismatches: 46, Indels: 85
0.68 0.11 0.21
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 1 0.00
19 5 0.02
20 6 0.02
21 15 0.05
22 181 0.64
23 53 0.19
24 4 0.01
25 2 0.01
26 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (22 bp):
TATCAAAATTTCATAGTTGAGT
Found at i:3051 original size:23 final size:22
Alignment explanation
Indices: 3023--3124 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 22
3013 CATAAGAAAG
3023 TTATCAAAATTTTATATGGAGGT
1 TTATCAAAATTTTATA-GGAGGT
*
3046 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGG-AGGT
*
3069 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAG-GAGGT
* * * *
3091 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAG-GAGGT
3113 TTATCAAAATTT
1 TTATCAAAATTT
3125 CAGTGTATGA
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.01
22 30 0.43
23 37 0.54
24 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGAGGT
Done.