Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016877.1 Corchorus olitorius cultivar O-4 contig16910, 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: 12664
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:903 original size:10 final size:10
Alignment explanation
Indices: 888--953 Score: 105
Period size: 10 Copynumber: 6.6 Consensus size: 10
878 AATTTAATAT
888 GGATATTTAC
1 GGATATTTAC
898 GGATATTTAC
1 GGATATTTAC
*
908 AGATATTTAC
1 GGATATTTAC
* *
918 GGATACTGAC
1 GGATATTTAC
928 GGATATTTAC
1 GGATATTTAC
938 GGATATTTAC
1 GGATATTTAC
948 GGATAT
1 GGATAT
954 ATCGAGAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 50 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (10 bp):
GGATATTTAC
Found at i:1271 original size:14 final size:14
Alignment explanation
Indices: 1252--1283 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1242 AGGGAATAAT
1252 CCTTAACCATATCG
1 CCTTAACCATATCG
1266 CCTTAACCATATCG
1 CCTTAACCATATCG
1280 CCTT
1 CCTT
1284 TCTCTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.38, G:0.06, T:0.31
Consensus pattern (14 bp):
CCTTAACCATATCG
Found at i:4476 original size:25 final size:25
Alignment explanation
Indices: 4425--4476 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
4415 AATAAATATC
*
4425 AAATTAATTTGTAATATAATATGAA
1 AAATTAATTTGTAAAATAATATGAA
* *
4450 AAATTAATTTTTATAAATCATAT-AA
1 AAATTAATTTGTA-AAATAATATGAA
4475 AA
1 AA
4477 TAAAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
AAATTAATTTGTAAAATAATATGAA
Found at i:7758 original size:24 final size:24
Alignment explanation
Indices: 7731--7777 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
7721 CTCTCTCAAT
7731 TGACTAAATGGAAGTAAAAAAGTG
1 TGACTAAATGGAAGTAAAAAAGTG
*
7755 TGACTAAATTGAAGTAAAAAAGT
1 TGACTAAATGGAAGTAAAAAAGT
7778 AGAAAGACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.04, G:0.21, T:0.23
Consensus pattern (24 bp):
TGACTAAATGGAAGTAAAAAAGTG
Found at i:8289 original size:16 final size:16
Alignment explanation
Indices: 8268--8318 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
8258 TCTTTTCTAT
8268 AATTTAATGTGTTTAA
1 AATTTAATGTGTTTAA
*
8284 AATTTAATG-ATTT--
1 AATTTAATGTGTTTAA
8297 --TTTAA-GTGTTTAA
1 AATTTAATGTGTTTAA
8310 AATTTAATG
1 AATTTAATG
8319 ATAATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
10 1 0.04
11 8 0.30
15 8 0.30
16 10 0.37
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (16 bp):
AATTTAATGTGTTTAA
Found at i:8306 original size:26 final size:27
Alignment explanation
Indices: 8270--8320 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
8260 TTTTCTATAA
8270 TTTAATGTGTTTAAAATTTAATGATTT
1 TTTAATGTGTTTAAAATTTAATGATTT
8297 TTTAA-GTGTTTAAAATTTAATGAT
1 TTTAATGTGTTTAAAATTTAATGAT
8321 AATTAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (27 bp):
TTTAATGTGTTTAAAATTTAATGATTT
Found at i:10747 original size:70 final size:70
Alignment explanation
Indices: 10656--10797 Score: 239
Period size: 70 Copynumber: 2.0 Consensus size: 70
10646 CACGTGCTTG
* * *
10656 CACGTGATCCATCCTGCTTTTAGTAGATAATAAATTTAAGAATTAAGCATTAAAAAATATAAGGC
1 CACGTGACCCATCCTGCTTTTAGTAAATAATAAATTTAAGAATTAAACATTAAAAAATATAAGGC
10721 CGACC
66 CGACC
* *
10726 CACGTGACCCATCCTGTTTTTAGTAAATAATAAATTTAAGAATTAAACTTTAAAAAATATAAGGC
1 CACGTGACCCATCCTGCTTTTAGTAAATAATAAATTTAAGAATTAAACATTAAAAAATATAAGGC
10791 CGACC
66 CGACC
10796 CA
1 CA
10798 ATTGATTCTA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.29
Consensus pattern (70 bp):
CACGTGACCCATCCTGCTTTTAGTAAATAATAAATTTAAGAATTAAACATTAAAAAATATAAGGC
CGACC
Found at i:12286 original size:43 final size:43
Alignment explanation
Indices: 12152--12480 Score: 381
Period size: 41 Copynumber: 7.8 Consensus size: 43
12142 CAATAACCAA
* * *
12152 AAAGTCCCCAAACACATATATAACACAGGGGCA-ATTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTT-TATTAC
* *
12195 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATA-T-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCACCTTTATTAC
* *
12237 CAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTTTATTAC
* *
12280 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTTTATTAC
** *
12322 -AAGTCCCCAAACACATATATAACACTTAGGCA-ATTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTT-TATTAC
* *
12364 AAAGTCCTCAAACACATATATAACACAGA-GC-CATTTA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTTTATTA-C
* *
12405 AAAGTCCCCAAACACATATATAACACATG-GGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACA-GAGGCACCTTTATTAC
* *
12448 AAAGTTCTCAAACACATATATAACACAGAGGCA
1 AAAGTCCCCAAACACATATATAACACAGAGGCA
12481 TTTCTCCTTA
Statistics
Matches: 246, Mismatches: 26, Indels: 27
0.82 0.09 0.09
Matches are distributed among these distances:
40 3 0.01
41 97 0.39
42 13 0.05
43 97 0.39
44 35 0.14
45 1 0.00
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCACCTTTATTAC
Found at i:12311 original size:84 final size:84
Alignment explanation
Indices: 12153--12480 Score: 507
Period size: 84 Copynumber: 3.9 Consensus size: 84
12143 AATAACCAAA
*
12153 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC-AAAGTCCTCAAACACATATATA
12218 ACACAGAGGCACCTATATCC
65 ACACAGAGGCACCTATATCC
*
12238 AAGTCCCCAAACACATATATAACACAGGGGCACCTT-TATTACAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCA-ATTCTATTACAAAGTCCTCAAACACATATATA
*
12302 ACACAGAGGCACCTATATTC
65 ACACAGAGGCACCTATATCC
***
12322 AAGTCCCCAAACACATATATAACACTTAGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
* ** *
12387 CACAGAGCCATTTATATCA
66 CACAGAGGCACCTATATCC
* *
12406 AAGTCCCCAAACACATATATAACACATGGGC-ATCTCTATTACAAAGTTCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTACAAAGTCCTCAAACACATATATA
12470 ACACAGAGGCA
65 ACACAGAGGCA
12481 TTTCTCCTTA
Statistics
Matches: 224, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
83 4 0.02
84 181 0.81
85 37 0.17
86 2 0.01
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.22
Consensus pattern (84 bp):
AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
CACAGAGGCACCTATATCC
Found at i:12481 original size:43 final size:43
Alignment explanation
Indices: 12152--12481 Score: 385
Period size: 43 Copynumber: 7.8 Consensus size: 43
12142 CAATAACCAA
* * *
12152 AAAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTCC
1 AAAGTCCTCAAACACATATATAACACAGAGGC-ATCTCTATTAC
12195 AAAAGTCCTCAAACACATATATAACACAGAGGCA-C-CTA-TATC
1 -AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTA-C
* * * * *
12237 CAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
12280 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATT-C
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
* **
12322 -AAGTCCCCAAACACATATATAACACTTAGGCAAT-TCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGAGGC-ATCTCTATTAC
*
12364 AAAGTCCTCAAACACATATATAACACAGAGCCAT-T-TA-TATC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTA-C
*
12405 AAAGTCCCCAAACACATATATAACACATG-GGCATCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACA-GAGGCATCTCTATTAC
*
12448 AAAGTTCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCTCAAACACATATATAACACAGAGGCAT
12482 TTCTCCTTAT
Statistics
Matches: 248, Mismatches: 24, Indels: 29
0.82 0.08 0.10
Matches are distributed among these distances:
40 2 0.01
41 97 0.39
42 14 0.06
43 101 0.41
44 34 0.14
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (43 bp):
AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
Done.