Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024773.1 Corchorus olitorius cultivar O-4 contig24806, 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: 39399
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:3486 original size:2 final size:2
Alignment explanation
Indices: 3481--3516 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3471 ATATTCAAAG
3481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3517 GGTGTTACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6258 original size:64 final size:59
Alignment explanation
Indices: 6180--6302 Score: 201
Period size: 64 Copynumber: 2.0 Consensus size: 59
6170 AAGTAATAAG
6180 TATCAGACAAAAGAAGCACACCACATAATAACAGAGATATATAATAAAAATAAAAAACTGTGTC
1 TATCAGACAAAAGAAGCACACCACATAATAACAGAG----ATAATAAAAAT-AAAAACTGTGTC
6244 TATCAGACAAAAGAAGCACACCACATAATAACAGAGATAATAAAAATAAAAACTGTGTC
1 TATCAGACAAAAGAAGCACACCACATAATAACAGAGATAATAAAAATAAAAACTGTGTC
6303 CTTTGAAGGG
Statistics
Matches: 59, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
59 12 0.20
60 11 0.19
64 36 0.61
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.18
Consensus pattern (59 bp):
TATCAGACAAAAGAAGCACACCACATAATAACAGAGATAATAAAAATAAAAACTGTGTC
Found at i:17324 original size:41 final size:43
Alignment explanation
Indices: 17222--17551 Score: 397
Period size: 41 Copynumber: 7.8 Consensus size: 43
17212 CCAATAACCA
* * *
17222 AAAGTTCCCAAACACATATATAACACATG-GGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACA-GAGGCATCTATATTAC
* *
17265 AAAAGTCCTCAAACACATATATAACACAGAGACATCTATATT-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
* * *
17308 -AAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
*
17350 AAAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
* * *
17392 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
* * * * *
17435 AAAGTCCTCAAACACATATTTAACATAAAGACATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
*
17476 AAAGTCCCCAAACACATATATAACACA-AGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGA-GGCATCTATATTAC
*
17519 AAAGTCCTCAAACACATATATAACACAGAGGCA
1 AAAGTCCCCAAACACATATATAACACAGAGGCA
17552 CTTCTCCTTA
Statistics
Matches: 245, Mismatches: 31, Indels: 21
0.82 0.10 0.07
Matches are distributed among these distances:
40 1 0.00
41 103 0.42
42 5 0.02
43 66 0.27
44 70 0.29
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
Found at i:17581 original size:84 final size:85
Alignment explanation
Indices: 17222--17548 Score: 525
Period size: 85 Copynumber: 3.9 Consensus size: 85
17212 CCAATAACCA
* * *
17222 AAAGTTCCCAAACACATATATAACACATGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
17287 AACACAGAGACATCTATATTC
66 AACACAGAGACATCTATA-TC
* *
17308 -AAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTACAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
*
17372 AACACAGAGGCATCTATATC
66 AACACAGAGACATCTATATC
* *
17392 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATTT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
* *
17456 AACATAAAGACATCTATATC
66 AACACAGAGACATCTATATC
*
17476 AAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTAC-AAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
17540 AACACAGAG
66 AACACAGAG
17549 GCACTTCTCC
Statistics
Matches: 223, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
84 107 0.48
85 116 0.52
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (85 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
AACACAGAGACATCTATATC
Found at i:21157 original size:3 final size:3
Alignment explanation
Indices: 21149--21233 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
21139 ACAGATTTAT
21149 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21197 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
21234 AAGTATAAAC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:22291 original size:13 final size:14
Alignment explanation
Indices: 22271--22307 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
22261 ATTATCAATA
22271 TGTA-TTATTATGT
1 TGTATTTATTATGT
*
22284 T-TATTTATAATGT
1 TGTATTTATTATGT
22297 TGTATTTATTA
1 TGTATTTATTA
22308 ATATTAGTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 2 0.10
13 10 0.50
14 8 0.40
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (14 bp):
TGTATTTATTATGT
Found at i:24935 original size:40 final size:40
Alignment explanation
Indices: 24852--24940 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
24842 TCCCTCCAAC
* * *
24852 TTAACCCTCCCAATAATTAAGGAAATAAATTAAATCCAGGT
1 TTAACCC-CCTAATAATTAAGGAAAGAAATTAAATCCACGT
* * * *
24893 TTAGCCCCCTAATAATTAAGGTAGGAAATTAAATCTACGT
1 TTAACCCCCTAATAATTAAGGAAAGAAATTAAATCCACGT
24933 TTAACCCC
1 TTAACCCC
24941 TAGTTATAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 34 0.85
41 6 0.15
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.28
Consensus pattern (40 bp):
TTAACCCCCTAATAATTAAGGAAAGAAATTAAATCCACGT
Found at i:25058 original size:13 final size:13
Alignment explanation
Indices: 25040--25069 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25030 TGGCACGTCA
25040 GGAGAGACAAATT
1 GGAGAGACAAATT
*
25053 GGAGAGACAAGTT
1 GGAGAGACAAATT
25066 GGAG
1 GGAG
25070 GGTCATCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.40, T:0.13
Consensus pattern (13 bp):
GGAGAGACAAATT
Found at i:25758 original size:20 final size:21
Alignment explanation
Indices: 25717--25760 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
25707 TTATGACTTA
25717 TTACTTAGCAAATTGAAAATT
1 TTACTTAGCAAATTGAAAATT
*
25738 TTACTTTGCAAATTG-AAATT
1 TTACTTAGCAAATTGAAAATT
25758 TTA
1 TTA
25761 TTAAGTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (21 bp):
TTACTTAGCAAATTGAAAATT
Found at i:31249 original size:29 final size:29
Alignment explanation
Indices: 31192--31248 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
31182 TTTTGTCTCC
31192 TGAACTTCAATTTTGGACATTTTACCCCT
1 TGAACTTCAATTTTGGACATTTTACCCCT
* *
31221 TGAATTTCAATTTTGGGACGTTTTACCC
1 TGAACTTCAATTTT-GGACATTTTACCC
31249 TCTCAACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (29 bp):
TGAACTTCAATTTTGGACATTTTACCCCT
Found at i:34669 original size:46 final size:45
Alignment explanation
Indices: 34616--34710 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 45
34606 ATAAATAAAC
34616 TACATACCTACCAAATAAACAAACAAATTACAAACAAAATCTCAAT
1 TACATACCTACCAAATAAACAAACAAATTACAAACAAAATCTC-AT
34662 TACATACCTACCAAATAAACAAACAAATTACAAACAAAATCTCAT
1 TACATACCTACCAAATAAACAAACAAATTACAAACAAAATCTCAT
34707 TACA
1 TACA
34711 ATTCAAATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 6 0.12
46 43 0.88
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (45 bp):
TACATACCTACCAAATAAACAAACAAATTACAAACAAAATCTCAT
Done.