Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019958.1 Corchorus olitorius cultivar O-4 contig19991, 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: 23953
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:683 original size:18 final size:19
Alignment explanation
Indices: 647--684 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
637 GTAGTTTCTT
647 ATTTTGTATAGATTAATTC
1 ATTTTGTATAGATTAATTC
666 ATTTGTGTATA-ATT-ATTC
1 ATTT-TGTATAGATTAATTC
684 A
1 A
685 AACTTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (19 bp):
ATTTTGTATAGATTAATTC
Found at i:4800 original size:1 final size:1
Alignment explanation
Indices: 4794--4819 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4784 TGTGTTGCTA
4794 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
4820 ATAGTGTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13647 original size:21 final size:21
Alignment explanation
Indices: 13621--13664 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
13611 ACTGAAATGG
*
13621 TGAGATTAAACATTGTACAGA
1 TGAGATTAAACACTGTACAGA
* *
13642 TGAGATTAGATACTGTACAGA
1 TGAGATTAAACACTGTACAGA
13663 TG
1 TG
13665 GGAATATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (21 bp):
TGAGATTAAACACTGTACAGA
Found at i:14099 original size:15 final size:16
Alignment explanation
Indices: 14079--14114 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
14069 CGTTTTTGAT
14079 AAAAAGC-AAAAAAAA
1 AAAAAGCTAAAAAAAA
14094 AAAAAGCTAAAAAAAA
1 AAAAAGCTAAAAAAAA
14110 AAAAA
1 AAAAA
14115 AAAAAGGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.86, C:0.06, G:0.06, T:0.03
Consensus pattern (16 bp):
AAAAAGCTAAAAAAAA
Found at i:14628 original size:27 final size:28
Alignment explanation
Indices: 14597--14655 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 28
14587 TTTTTTCAAA
14597 AATATTTCTAAATTA-T-CATTATT-AAAT
1 AATATTT-T-AATTATTCCATTATTAAAAT
14624 AATATTTTAATTATTCCATTATTAAAAT
1 AATATTTTAATTATTCCATTATTAAAAT
14652 AATA
1 AATA
14656 AAAATCTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.17
26 2 0.07
27 14 0.48
28 8 0.28
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (28 bp):
AATATTTTAATTATTCCATTATTAAAAT
Found at i:16364 original size:21 final size:23
Alignment explanation
Indices: 16338--16384 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
16328 AAAATCATAT
16338 ATAGGAAGG-TTA-CAAAATTTC
1 ATAGGAAGGTTTATCAAAATTTC
*
16359 ATAGGAAGGTTTATTAAAATTTC
1 ATAGGAAGGTTTATCAAAATTTC
16382 ATA
1 ATA
16385 ATTAGGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
23 11 0.48
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (23 bp):
ATAGGAAGGTTTATCAAAATTTC
Found at i:16397 original size:22 final size:23
Alignment explanation
Indices: 16351--16406 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
16341 GGAAGGTTAC
*
16351 AAAATTTCATAGGAAGGTTTATT
1 AAAATTTCATAAGAAGGTTTATT
**
16374 AAAATTTCATAATTAGG-TTATT
1 AAAATTTCATAAGAAGGTTTATT
*
16396 AAAGTTTCATA
1 AAAATTTCATA
16407 TGGAATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (23 bp):
AAAATTTCATAAGAAGGTTTATT
Found at i:16416 original size:22 final size:21
Alignment explanation
Indices: 16391--16450 Score: 50
Period size: 22 Copynumber: 2.7 Consensus size: 21
16381 CATAATTAGG
*
16391 TTATTAAAGTTTCATATGG-AAT
1 TTATTAAA-TTTCATA-GGTAAA
* *
16413 TTATCACAATTTTATAGGTAAA
1 TTATTA-AATTTCATAGGTAAA
16435 TTATTAAAATTTCATA
1 TTATT-AAATTTCATA
16451 AAAATATTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 2 0.07
22 25 0.83
23 3 0.10
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (21 bp):
TTATTAAATTTCATAGGTAAA
Found at i:18261 original size:11 final size:11
Alignment explanation
Indices: 18245--18373 Score: 70
Period size: 11 Copynumber: 11.8 Consensus size: 11
18235 AAAAAATTTG
18245 TTATATATATT
1 TTATATATATT
*
18256 TTATATATATC
1 TTATATATATT
* * *
18267 ATAAATATA-A
1 TTATATATATT
18277 TT-TATATATT
1 TTATATATATT
*
18287 TTACATATATT
1 TTATATATATT
*
18298 TTATATTTTATAT
1 TTATA-TATAT-T
* * *
18311 ATATCATAAATAA
1 TTAT-ATATAT-T
*
18324 TTAAATATATT
1 TTATATATATT
18335 TTATATATA--
1 TTATATATATT
* *
18344 TCATAAATA-T
1 TTATATATATT
*
18354 TTAAATATATT
1 TTATATATATT
18365 TTATATATA
1 TTATATATA
18374 ATAGCATAAT
Statistics
Matches: 86, Mismatches: 25, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
9 12 0.14
10 9 0.10
11 45 0.52
12 9 0.10
13 10 0.12
14 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TTATATATATT
Found at i:18262 original size:9 final size:9
Alignment explanation
Indices: 18248--18372 Score: 54
Period size: 9 Copynumber: 12.8 Consensus size: 9
18238 AAATTTGTTA
18248 TATATATTT
1 TATATATTT
18257 TATATATATCAT
1 TATATAT-T--T
* *
18269 AAATATAATT
1 -TATATATTT
18279 TATATATTT
1 TATATATTT
18288 TACATATATTT
1 T--ATATATTT
18299 TATAT-TTT
1 TATATATTT
**
18307 ATATATATCA
1 -TATATATTT
* *
18317 TAAATAATTA
1 TATAT-ATTT
*
18327 AATATATTT
1 TATATATTT
*
18336 TATATATATCA
1 TATATAT-T-T
*
18347 TAAATATTT
1 TATATATTT
*
18356 AAATATATTT
1 -TATATATTT
18366 TATATAT
1 TATATAT
18373 AATAGCATAA
Statistics
Matches: 86, Mismatches: 18, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
8 3 0.03
9 43 0.50
10 18 0.21
11 15 0.17
12 2 0.02
13 5 0.06
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (9 bp):
TATATATTT
Found at i:18302 original size:18 final size:19
Alignment explanation
Indices: 18271--18314 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
18261 TATATCATAA
18271 ATATAATTTATATATTTTAC
1 ATAT-ATTTATATATTTTAC
*
18291 ATATATTT-TATATTTTAT
1 ATATATTTATATATTTTAC
18309 ATATAT
1 ATATAT
18315 CATAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.65
19 4 0.17
20 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATATTTATATATTTTAC
Found at i:18335 original size:30 final size:30
Alignment explanation
Indices: 18299--18373 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
18289 ACATATATTT
18299 TATATTTTATATATATCATAAATAATTAAA
1 TATATTTTATATATATCATAAATAATTAAA
*
18329 TATATTTTATATATATCATAAATATTTAAA
1 TATATTTTATATATATCATAAATAATTAAA
18359 TATATTTTATATATA
1 TATATTTTATATATA
18374 ATAGCATAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (30 bp):
TATATTTTATATATATCATAAATAATTAAA
Found at i:23708 original size:15 final size:15
Alignment explanation
Indices: 23688--23722 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
23678 TCTTGATTGC
23688 TTTTCGGGGATATGG
1 TTTTCGGGGATATGG
23703 TTTTCGGGGATATGG
1 TTTTCGGGGATATGG
23718 TTTTC
1 TTTTC
23723 CTTATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.09, G:0.34, T:0.46
Consensus pattern (15 bp):
TTTTCGGGGATATGG
Done.