Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015561.1 Corchorus olitorius cultivar O-4 contig15594, 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: 7702
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:500 original size:10 final size:10
Alignment explanation
Indices: 479--507 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
469 TTAAAAAAGG
479 AAATAAAA-T
1 AAATAAAATT
488 AAATAAAATT
1 AAATAAAATT
498 AAATAAAATT
1 AAATAAAATT
508 GTTAATATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATAAAATT
Found at i:3258 original size:123 final size:123
Alignment explanation
Indices: 3039--3286 Score: 496
Period size: 123 Copynumber: 2.0 Consensus size: 123
3029 TCACCGCAAA
3039 AGGCAAGTCAACCTTAATAGCTAATTTTTAGGTGTTTTTGCGTTTCAAAAGTGCTTTTGGATATT
1 AGGCAAGTCAACCTTAATAGCTAATTTTTAGGTGTTTTTGCGTTTCAAAAGTGCTTTTGGATATT
3104 AAATTACTAAAATCACTTAAATATTTTCTCTCTTTCTATTTTAATTAGTACCCTTTTT
66 AAATTACTAAAATCACTTAAATATTTTCTCTCTTTCTATTTTAATTAGTACCCTTTTT
3162 AGGCAAGTCAACCTTAATAGCTAATTTTTAGGTGTTTTTGCGTTTCAAAAGTGCTTTTGGATATT
1 AGGCAAGTCAACCTTAATAGCTAATTTTTAGGTGTTTTTGCGTTTCAAAAGTGCTTTTGGATATT
3227 AAATTACTAAAATCACTTAAATATTTTCTCTCTTTCTATTTTAATTAGTACCCTTTTT
66 AAATTACTAAAATCACTTAAATATTTTCTCTCTTTCTATTTTAATTAGTACCCTTTTT
3285 AG
1 AG
3287 ACATTTTATC
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 125 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.45
Consensus pattern (123 bp):
AGGCAAGTCAACCTTAATAGCTAATTTTTAGGTGTTTTTGCGTTTCAAAAGTGCTTTTGGATATT
AAATTACTAAAATCACTTAAATATTTTCTCTCTTTCTATTTTAATTAGTACCCTTTTT
Found at i:6087 original size:22 final size:22
Alignment explanation
Indices: 6057--6151 Score: 67
Period size: 22 Copynumber: 4.5 Consensus size: 22
6047 CTTTGTAGAT
*
6057 TATCGAAATTTCATAGTGTAGC
1 TATCAAAATTTCATAGTGTAGC
* * *
6079 TATCAAAATTTCATAATGTGGT
1 TATCAAAATTTCATAGTGTAGC
*
6101 TA-CAAAAATTTCAAAG-GTA--
1 TATC-AAAATTTCATAGTGTAGC
* *
6120 -ATCAAATTTTCATATTGT-GC
1 TATCAAAATTTCATAGTGTAGC
6140 TTATCAAAATTT
1 -TATCAAAATTT
6152 TATTGTTAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
18 10 0.18
19 3 0.05
21 3 0.05
22 39 0.71
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTAGC
Found at i:6198 original size:22 final size:22
Alignment explanation
Indices: 6170--6212 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6160 GATTAACGAA
6170 ATTCTATAGGGAAGTTATCAAC
1 ATTCTATAGGGAAGTTATCAAC
*
6192 ATTCTATAGGGAGGTTATCAA
1 ATTCTATAGGGAAGTTATCAA
6213 AATTTCATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (22 bp):
ATTCTATAGGGAAGTTATCAAC
Found at i:6222 original size:22 final size:22
Alignment explanation
Indices: 6175--6244 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
6165 ACGAAATTCT
* *
6175 ATAGGGAAGTTATCAACA-TTC
1 ATAGGGAGGTTATCAAAATTTC
6196 TATAGGGAGGTTATCAAAATTTC
1 -ATAGGGAGGTTATCAAAATTTC
* *
6219 ATA-GTATGGTTATCCAAATTTC
1 ATAGGGA-GGTTATCAAAATTTC
6241 ATAG
1 ATAG
6245 TGTACCAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.05
22 36 0.88
23 3 0.07
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (22 bp):
ATAGGGAGGTTATCAAAATTTC
Found at i:6245 original size:22 final size:22
Alignment explanation
Indices: 6204--6245 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
6194 TCTATAGGGA
6204 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
*
6226 GGTTATCCAAATTTCATAGT
1 GGTTATCAAAATTTCATAGT
6246 GTACCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAT
Found at i:6374 original size:21 final size:22
Alignment explanation
Indices: 6307--6442 Score: 125
Period size: 22 Copynumber: 6.2 Consensus size: 22
6297 GGTCATCAAA
*
6307 AAAATTTTCATATAGAGGTTATC
1 AAAA-TTTCATAGAGAGGTTATC
* * * * *
6330 ACAGTTTTATAGTGTGGTTATC
1 AAAATTTCATAGAGAGGTTATC
6352 AAAATTTCATAG-GATGG-TATC
1 AAAATTTCATAGAGA-GGTTATC
* *
6373 AAAATTTCATAGTGTGGTTATC
1 AAAATTTCATAGAGAGGTTATC
* *
6395 AAAGTTTCACAG-GAGGTTATC
1 AAAATTTCATAGAGAGGTTATC
* *
6416 ACAATTTCTTAGAGAGGTTATC
1 AAAATTTCATAGAGAGGTTATC
6438 AAAAT
1 AAAAT
6443 AATATAACAA
Statistics
Matches: 90, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
21 35 0.39
22 53 0.59
23 2 0.02
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAGAGAGGTTATC
Found at i:6385 original size:43 final size:43
Alignment explanation
Indices: 6321--6472 Score: 148
Period size: 43 Copynumber: 3.5 Consensus size: 43
6311 TTTTCATATA
* * * *
6321 GAGGTTATCACAGTTTTATAGTGTGGTTATCAAAATTTCATAG
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAG
*
6364 GATGG-TATCAAAATTTCATAGTGTGGTTATCAAAGTTTCACAG
1 GA-GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAG
* * * * *
6407 GAGGTTATCACAATTTCTTAGAGAGGTTATCAAAATAATATAACA-
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAAT--T-TCACAG
*
6452 -AGATTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
6473 AAGTAGGAGA
Statistics
Matches: 89, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 2 0.02
43 63 0.71
44 19 0.21
45 1 0.01
46 4 0.04
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (43 bp):
GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAG
Found at i:6611 original size:17 final size:18
Alignment explanation
Indices: 6589--6625 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6579 AATGGAAATC
*
6589 TTAAAA-GTTTACTCATT
1 TTAAAACGTGTACTCATT
6606 TTAAAACGTGTACTCATT
1 TTAAAACGTGTACTCATT
6624 TT
1 TT
6626 CATAGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (18 bp):
TTAAAACGTGTACTCATT
Found at i:7414 original size:2 final size:2
Alignment explanation
Indices: 7407--7436 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
7397 CATTTTCTTT
7407 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7437 CTTTTAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.