Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019931.1 Corchorus olitorius cultivar O-4 contig19964, 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: 6992
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:313 original size:27 final size:27
Alignment explanation
Indices: 282--338 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
272 TTTTTCATTT
282 ATATTTCTAA-ATTGCCATTATT-AAATA
1 ATATTT-TAATATT-CCATTATTAAAATA
309 ATATTTTAATTATTCCATTATTAAAATA
1 ATATTTTAA-TATTCCATTATTAAAATA
337 AT
1 AT
339 GGAAACTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 3 0.11
27 14 0.52
28 10 0.37
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (27 bp):
ATATTTTAATATTCCATTATTAAAATA
Found at i:3041 original size:22 final size:22
Alignment explanation
Indices: 3015--3087 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 22
3005 CAAAAATTAT
*
3015 AGGGAGATTAACAAAATCTCAC
1 AGGGAGGTTAACAAAATCTCAC
* *
3037 AGGGAGGTTATCAAAA-CTCAT
1 AGGGAGGTTAACAAAATCTCAC
* * *
3058 AGGCAGGTT-ACAAAATTTCAT
1 AGGGAGGTTAACAAAATCTCAC
*
3079 AGGAAGGTT
1 AGGGAGGTT
3088 TATTAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 5 0.12
21 24 0.56
22 14 0.33
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (22 bp):
AGGGAGGTTAACAAAATCTCAC
Found at i:3071 original size:42 final size:43
Alignment explanation
Indices: 3002--3087 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 43
2992 CATACTATAG
* * *
3002 TATCAAAAATTATAGGGAGATTAACAAAATCTCACAGGGAGGT
1 TATCAAAAATCATAGGCAGATTAACAAAATCTCACAGGAAGGT
* * * *
3045 TATCAAAACTCATAGGCAGGTT-ACAAAATTTCATAGGAAGGT
1 TATCAAAAATCATAGGCAGATTAACAAAATCTCACAGGAAGGT
3087 T
1 T
3088 TATTAAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 18 0.50
43 18 0.50
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.26
Consensus pattern (43 bp):
TATCAAAAATCATAGGCAGATTAACAAAATCTCACAGGAAGGT
Found at i:3111 original size:44 final size:44
Alignment explanation
Indices: 3002--3166 Score: 140
Period size: 44 Copynumber: 3.8 Consensus size: 44
2992 CATACTATAG
* * * * * * * *
3002 TATCAAAAATT-ATAGGGAGATTAACAAAATCTCACAGGGAGGT
1 TATCAAAATTTCATAGGTAGGTTATCAAAATTTCATATGGAGTT
* *
3045 TATCAAAA-CTCATAGGCAGGTTA-CAAAATTTCATA-GGAAGGTT
1 TATCAAAATTTCATAGGTAGGTTATCAAAATTTCATATGG-A-GTT
* * *
3088 TATTAAAATTTCATAGTTAGGTTATCAAAGTTTCATATGGAGTT
1 TATCAAAATTTCATAGGTAGGTTATCAAAATTTCATATGGAGTT
* **
3132 TATCACAATTTCATAGGTAAATTATCAAAATTTCA
1 TATCAAAATTTCATAGGTAGGTTATCAAAATTTCA
3167 GAGCGTGGTT
Statistics
Matches: 99, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
41 2 0.02
42 12 0.12
43 27 0.27
44 44 0.44
45 12 0.12
46 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (44 bp):
TATCAAAATTTCATAGGTAGGTTATCAAAATTTCATATGGAGTT
Found at i:3121 original size:22 final size:22
Alignment explanation
Indices: 3002--3166 Score: 124
Period size: 22 Copynumber: 7.6 Consensus size: 22
2992 CATACTATAG
* * *
3002 TATCAAAAATT-ATAGGGAGAT
1 TATCAAAATTTCATAGGAAGGT
* * * *
3023 TAACAAAATCTCACAGGGAGGT
1 TATCAAAATTTCATAGGAAGGT
* *
3045 TATCAAAA-CTCATAGGCAGGT
1 TATCAAAATTTCATAGGAAGGT
3066 TA-CAAAATTTCATAGGAAGGTT
1 TATCAAAATTTCATAGGAAGG-T
* **
3088 TATTAAAATTTCATAGTTAGGT
1 TATCAAAATTTCATAGGAAGGT
* *
3110 TATCAAAGTTTCATATGG-AGTT
1 TATCAAAATTTCATA-GGAAGGT
* *
3132 TATCACAATTTCATAGGTAA-AT
1 TATCAAAATTTCATAGG-AAGGT
3154 TATCAAAATTTCA
1 TATCAAAATTTCA
3167 GAGCGTGGTT
Statistics
Matches: 116, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
20 5 0.04
21 33 0.28
22 61 0.53
23 17 0.15
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAAGGT
Found at i:6378 original size:2 final size:2
Alignment explanation
Indices: 6371--6395 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6361 AGATTGAATG
6371 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6396 GGGTAATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.