Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018923.1 Corchorus olitorius cultivar O-4 contig18956, 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: 5959
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Found at i:2131 original size:19 final size:20
Alignment explanation
Indices: 2104--2141 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2094 TACTATTATT
2104 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
2124 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
2142 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:2335 original size:22 final size:22
Alignment explanation
Indices: 2307--2491 Score: 153
Period size: 22 Copynumber: 8.3 Consensus size: 22
2297 TGTCTCTGTT
*
2307 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* * *
2329 TGGTTATTATAATTTCAGGAGGA
1 TGGTTATCAAAATTTCA-TAGGA
*
2352 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
2373 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* *
2396 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAGGA
**
2417 AAGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
2439 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* **
2461 TCAGGTTATTAAAATTTTTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
*
2485 AGGTTAT
1 TGGTTAT
2492 TGAAATTTTA
Statistics
Matches: 131, Mismatches: 22, Indels: 20
0.76 0.13 0.12
Matches are distributed among these distances:
21 6 0.05
22 103 0.79
23 5 0.04
24 17 0.13
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:2504 original size:66 final size:65
Alignment explanation
Indices: 2353--2509 Score: 183
Period size: 66 Copynumber: 2.4 Consensus size: 65
2343 TCAGGAGGAG
* *
2353 GTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATGGGAA
1 GTTATCAAAATT-TATAGTGTGGTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATAGGAA
2418 A
65 A
* **
2419 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA-GGATCAGGTTATTAAAATTTTTTAG
1 GTTATCAAAATTT-ATAGTGTGGTTACCAAAATTTCATATGGA--A-GTTATCAAAATTTCATAG
*
2483 GAAG
62 GAAA
**
2487 GTTATTGAAATTT-TAGTGTGGTT
1 GTTATCAAAATTTATAGTGTGGTT
2510 TTCACAATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
65 3 0.04
66 47 0.59
67 1 0.01
68 28 0.35
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (65 bp):
GTTATCAAAATTTATAGTGTGGTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATAGGAAA
Found at i:2567 original size:22 final size:22
Alignment explanation
Indices: 2542--2608 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
2532 ATCAAAGAGA
*
2542 TTATCAAAATGTCATAACGAGG
1 TTATCAAAATTTCATAACGAGG
** *
2564 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAACGAGG
* *
2586 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATAACGAGG
2608 T
1 T
2609 AAGGAGGTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (22 bp):
TTATCAAAATTTCATAACGAGG
Found at i:2683 original size:22 final size:22
Alignment explanation
Indices: 2613--2941 Score: 87
Period size: 22 Copynumber: 14.8 Consensus size: 22
2603 GGAGGTAAGG
*
2613 AGGTTATCAAATTTTCATA-GTA
1 AGGTTATCAAAATTTCATATG-A
* * **
2635 TGGTTATTAAAATTTTTTAGTG-
1 AGGTTATCAAAATTTCATA-TGA
*
2657 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
* *
2679 AGGTTAT-AAAAGCCTTAATTTCAT-A
1 AGGTTATCAAAA--TTTCA--T-ATGA
* * *
2704 AGGAGTACCAAAATTTGATA-GA
1 AGG-TTATCAAAATTTCATATGA
*
2726 AGGTTATC-AAATCTCATA-G-
1 AGGTTATCAAAATTTCATATGA
* *
2745 AGTGATTATCGAAATTTCATAAAGA
1 AG-G-TTATCAAAATTTCAT-ATGA
* *
2770 TCGGATTAT-AGAAATTT-ATAGGA
1 -AGG-TTATCA-AAATTTCATATGA
*
2793 AGATTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** * *
2815 TTGTTATCAAAATTTCA-AAGCG
1 AGGTTATCAAAATTTCATATG-A
* *
2837 AGGTTATCCAAATTACATAATGA
1 AGGTTATCAAAATTTCAT-ATGA
**
2860 A-AATATCAAAATTTCATA-GA
1 AGGTTATCAAAATTTCATATGA
* * *
2880 GAGGTCAACAAAATTTTATA-GA
1 -AGGTTATCAAAATTTCATATGA
* *
2902 GAGGCTATCAAAATTTCAT-TAA
1 -AGGTTATCAAAATTTCATATGA
*
2924 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
2942 GAATGTGATT
Statistics
Matches: 226, Mismatches: 52, Indels: 58
0.67 0.15 0.17
Matches are distributed among these distances:
19 2 0.01
20 13 0.06
21 27 0.12
22 139 0.62
23 10 0.04
24 6 0.03
25 20 0.09
26 5 0.02
27 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:3523 original size:22 final size:22
Alignment explanation
Indices: 3066--3618 Score: 173
Period size: 22 Copynumber: 25.4 Consensus size: 22
3056 TCAGGGAGGA
* *
3066 TATCAAAATTCCATATGAAGGT
1 TATCAAAATTTCATAAGAAGGT
* *
3088 TATCAAAATTCCAT-AGTTTA-GT
1 TATCAAAATTTCATAAG--AAGGT
* * *
3110 TTTCCAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAAGAAGGT
* * *
3132 TATCAAAATCTCAT-AGTATGT
1 TATCAAAATTTCATAAGAAGGT
* * * *
3153 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAAGAAGGT
*
3176 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCATAA-GAAGGT
** ** *
3198 TATCAAAAAATCATTGGGAGGT
1 TATCAAAATTTCATAAGAAGGT
*
3220 TATC-AAATTT--T--GTA-GT
1 TATCAAAATTTCATAAGAAGGT
* *
3236 TATCAAGATTTCATAAGGAGGT
1 TATCAAAATTTCATAAGAAGGT
* * *
3258 TATCAAAATTTTATAAGGAGATT
1 TATCAAAATTTCATAAGAAG-GT
*
3281 TATCAAAATTTTAT-AGCAAGGT
1 TATCAAAATTTCATAAG-AAGGT
* * *
3303 TATCACAATTTCATAATG-TGAT
1 TATCAAAATTTCATAA-GAAGGT
* *
3325 TATCAAAATTTCA-AAGTATGAT
1 TATCAAAATTTCATAAG-AAGGT
*
3347 TA-CTAATAA-TTCA-AATGGAGGT
1 TATC-AA-AATTTCATAA-GAAGGT
* * *
3369 TCT-TAAATTCTCATAACG-TGGT
1 TATCAAAATT-TCATAA-GAAGGT
* * * *
3391 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATAAGAAGGT
* * ** **
3413 TATCAACATCTCATCGTGTTGGT
1 TATCAAAATTTCAT-AAGAAGGT
**
3436 TATCAAAATTTCATTCGGAA-GT
1 TATCAAAATTTCA-TAAGAAGGT
3458 TATCAAAATTTCATAATG-AGGT
1 TATCAAAATTTCATAA-GAAGGT
* * * * *
3480 TTTCAAAATTCCTTAGGGAGGT
1 TATCAAAATTTCATAAGAAGGT
3502 TATCAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATAAGAAGGT
**
3524 TAAAAAAATTT-ATAA-AATGGT
1 TATCAAAATTTCATAAGAA-GGT
* * ***
3545 TCTCGAAA-TTCA-ATAGTATTAT
1 TATCAAAATTTCATA-AG-AAGGT
* * *
3567 TATTAAAGTTTCATAGGAAGGT
1 TATCAAAATTTCATAAGAAGGT
* * *
3589 TATTAAAATTTTATAAGGAGGT
1 TATCAAAATTTCATAAGAAGGT
3611 TATCAAAA
1 TATCAAAA
3619 ATAGTGTAAT
Statistics
Matches: 390, Mismatches: 100, Indels: 82
0.68 0.17 0.14
Matches are distributed among these distances:
16 6 0.02
17 7 0.02
19 2 0.01
20 8 0.02
21 34 0.09
22 273 0.70
23 57 0.15
24 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAAGAAGGT
Found at i:5925 original size:2 final size:2
Alignment explanation
Indices: 5918--5959 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5908 ACTATAATTT
5918 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
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.