Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016619.1 Corchorus olitorius cultivar O-4 contig16652, 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: 12332
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--68 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
49 AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AA
69 AAAAAATGGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1326 original size:13 final size:12
Alignment explanation
Indices: 1296--1351 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
1286 GTTGAGGAAC
*
1296 TGTTTTATTAAC
1 TGTTTTATTAAA
1308 TGTTTTATTAATA
1 TGTTTTATTAA-A
1321 TGTTTTA-TAAA
1 TGTTTTATTAAA
*
1332 TGGTTTTAATAAA
1 T-GTTTTATTAAA
1345 TTGTTTT
1 -TGTTTT
1352 GGGTGCATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
11 2 0.05
12 20 0.51
13 16 0.41
14 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.59
Consensus pattern (12 bp):
TGTTTTATTAAA
Found at i:1349 original size:25 final size:25
Alignment explanation
Indices: 1296--1351 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
1286 GTTGAGGAAC
* *
1296 TGTTTTATTAACTGTTTTATTAATA
1 TGTTTTATTAAATGTTTTATAAATA
1321 TGTTTTA-TAAATGGTTTTAATAAAT-
1 TGTTTTATTAAAT-GTTTT-ATAAATA
1346 TGTTTT
1 TGTTTT
1352 GGGTGCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.59
Consensus pattern (25 bp):
TGTTTTATTAAATGTTTTATAAATA
Found at i:3443 original size:25 final size:23
Alignment explanation
Indices: 3378--3444 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 23
3368 TAATTAAATG
3378 ATAATAAATC-AATTAAATTTAA
1 ATAATAAATCAAATTAAATTTAA
* * *
3400 ATTAATAAGTTAAAATTAACTTGTAA
1 A-TAATAA-ATCAAATTAAATT-TAA
3426 ATAATAAATCAAAGTTAAA
1 ATAATAAATCAAA-TTAAA
3445 AAAATAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
22 1 0.03
23 6 0.18
24 5 0.15
25 18 0.53
26 4 0.12
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (23 bp):
ATAATAAATCAAATTAAATTTAA
Found at i:8388 original size:28 final size:28
Alignment explanation
Indices: 8356--8536 Score: 222
Period size: 28 Copynumber: 6.5 Consensus size: 28
8346 CTTTGCTTCT
* *
8356 CATTTTGGTCATTTTTCATGACCAAGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
8384 CATTTTGGTCATTTCTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
* * * *
8412 TATTTTGGTCATTCTACAGGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
* *
8440 CATTTTGGTCATTCTAT-AGGTCCAGGGG
1 CATTTTGGTCATT-TTTCATGTCCAGGGG
* *
8468 CATTGTGGTCATTATTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
8496 CATTTTGGTCA-TTTGCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
8523 TATTTTGGTCATTT
1 CATTTTGGTCATTT
8537 GCACGTCCGG
Statistics
Matches: 130, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 25 0.19
28 105 0.81
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (28 bp):
CATTTTGGTCATTTTTCATGTCCAGGGG
Found at i:8554 original size:27 final size:28
Alignment explanation
Indices: 8356--8560 Score: 220
Period size: 28 Copynumber: 7.4 Consensus size: 28
8346 CTTTGCTTCT
* * * *
8356 CATTTTGGTCATTTTTCATGACCAAGGG
1 CATTTTGGTCATTCTACATGTCCAGGGG
8384 CATTTTGGTCATTTCT-CATGTCCAGGGG
1 CATTTTGGTCA-TTCTACATGTCCAGGGG
* *
8412 TATTTTGGTCATTCTACAGGTCCAGGGG
1 CATTTTGGTCATTCTACATGTCCAGGGG
* *
8440 CATTTTGGTCATTCTATAGGTCCAGGGG
1 CATTTTGGTCATTCTACATGTCCAGGGG
* * *
8468 CATTGTGGTCATTATTCATGTCCAGGGG
1 CATTTTGGTCATTCTACATGTCCAGGGG
*
8496 CATTTTGGTCATT-TGCATGTCCAGGGG
1 CATTTTGGTCATTCTACATGTCCAGGGG
* * *
8523 TATTTTGGTCATT-TGCACGTCC-GGGG
1 CATTTTGGTCATTCTACATGTCCAGGGG
*
8549 ACATTTTAGTCA
1 -CATTTTGGTCA
8561 ATTCATGCAC
Statistics
Matches: 156, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
26 4 0.03
27 46 0.29
28 103 0.66
29 3 0.02
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.38
Consensus pattern (28 bp):
CATTTTGGTCATTCTACATGTCCAGGGG
Done.