Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024841.1 Corchorus olitorius cultivar O-4 contig24874, 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: 14492
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:689 original size:16 final size:15
Alignment explanation
Indices: 651--698 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
641 CTCCATTTAC
*
651 TTTTTCTTTGCATTG-
1 TTTTGCTTTG-ATTGA
666 TTTTGCTTTGATTGA
1 TTTTGCTTTGATTGA
*
681 TTATTGCTTCGATTGA
1 TT-TTGCTTTGATTGA
697 TT
1 TT
699 GCTTATCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 4 0.14
15 11 0.38
16 14 0.48
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.60
Consensus pattern (15 bp):
TTTTGCTTTGATTGA
Found at i:8460 original size:36 final size:36
Alignment explanation
Indices: 8420--8537 Score: 175
Period size: 37 Copynumber: 3.2 Consensus size: 36
8410 AATAAAAAAA
8420 AAAAAAAAAAACTGGACCTAAAATAGAGAGAGGTCG
1 AAAAAAAAAAACTGGACCTAAAATAGAGAGAGGTCG
8456 AAAAAGAAAAAACTGGACCTAAAATAGAGAGAGGTCG
1 AAAAA-AAAAAACTGGACCTAAAATAGAGAGAGGTCG
* *
8493 AAAAAGAAAAACTTGG-CCTAAAATAGAAAGAGGTCAG
1 AAAAAAAAAAAC-TGGACCTAAAATAGAGAGAGGTC-G
*
8530 AGAAAAAA
1 AAAAAAAA
8538 GAAATAAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
36 29 0.39
37 46 0.61
ACGTcount: A:0.57, C:0.10, G:0.22, T:0.11
Consensus pattern (36 bp):
AAAAAAAAAAACTGGACCTAAAATAGAGAGAGGTCG
Found at i:9469 original size:59 final size:59
Alignment explanation
Indices: 9400--9998 Score: 476
Period size: 59 Copynumber: 10.2 Consensus size: 59
9390 TTTTAAAGCA
* * * *
9400 TGTTCGAGGTCTCTAGTAGAGAGTTTTTAATCCAAAACCTTGTCTTGTTTTTAAAATCC
1 TGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCC
* ** *
9459 TGGTCGAGGTCTCTGGTAGAGAGTTTTCTGCTT-TAAATCTTGT-TT-TTTTTAAAAAAAAAAAT
1 TGTTCGAGGTCTCTGGTAGAGAGTTTTC-AATTCAAAATCTTGTCTTGTTTTT-------AAAAT
**
9521 AT
58 CC
* * * * *
9523 TGTTCAAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTGGTCTTATTTTTAAATTCT
1 TGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCC
* * * *
9582 TGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTTGTCTCGTTTTCAAAGTCC
1 TGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCC
* * * * *
9641 TGTTTGAGGTCTCTGGTAGAGAGTTTTCTATTTTAAAAT-AT-TCTTCCTTTTT--AATCC
1 TGTTCGAGGTCTCTGGTAGAGAGTTTTC-AATTCAAAATCTTGTCTT-GTTTTTAAAATCC
* * * * * * * * *
9698 TGTTTGAGATCTCTAGTAGAGAGTTTTCAGCTTTAAGAT-AT-TCTTCCTTTTT-AAATCG
1 TGTTCGAGGTCTCTGGTAGAGAGTTTTCA-ATTCAAAATCTTGTCTT-GTTTTTAAAATCC
* * ** *
9756 TGGTCGAGGTCTCTGGTAGGGAGTTTTCTGCTTTAAAA-----TCTTGTTTTTAAAATCC
1 TGTTCGAGGTCTCTGGTAGAGAGTTTTC-AATTCAAAATCTTGTCTTGTTTTTAAAATCC
** *
9811 TGTTCGAGGTCTCTAATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTCTTAAAATCC
1 TGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCC
* * * *
9870 TGTTCGAGGTCTCTGGTAGAGAGTTCTTAAATCCAAAACCTTATCTTGTTTTTAAAATCC
1 TGTTCGAGGTCTCTGGTAGAGAGTT-TTCAATTCAAAATCTTGTCTTGTTTTTAAAATCC
* ** * **
9930 TGGTCGAGGTCTCTGGTAGAGAGTTTTCTGCTTTAAAATCTTGT-TT-TTTAAAAAAATCC
1 TGTTCGAGGTCTCTGGTAGAGAGTTTTC-AATTCAAAATCTTGTCTTGTTT-TTAAAATCC
9989 TGTTCGAGGT
1 TGTTCGAGGT
9999 TGTCGAAACA
Statistics
Matches: 440, Mismatches: 75, Indels: 50
0.78 0.13 0.09
Matches are distributed among these distances:
54 11 0.03
55 33 0.08
56 1 0.00
57 55 0.12
58 42 0.10
59 180 0.41
60 70 0.16
63 2 0.00
64 39 0.09
65 2 0.00
66 5 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.42
Consensus pattern (59 bp):
TGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCC
Found at i:9980 original size:229 final size:228
Alignment explanation
Indices: 9400--9981 Score: 622
Period size: 229 Copynumber: 2.5 Consensus size: 228
9390 TTTTAAAGCA
* *
9400 TGTTCGAGGTCTCTAGTAGAGAGTTTTTAATCCAAAACCTTGTCTTGTTTTTAAAATCCTGGTCG
1 TGTTCGAGGTCTCTGGTAGAGAGTTTTTAATCCAAAACCTTATCTTGTTTTTAAAATCCTGGTCG
* *
9465 AGGTCTCTGGTAGAGAGTTTTCTGCTTT-AAATCTTGTTTTTTTTAAAAAAAAAAATATTGTTCA
66 AGGTCTCTGGTAGAGAGTTTTCTGCTTTAAAATCTTG--TTTTTT--------AAATAGTGGTCA
* *
9529 AGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTGGTCTTATTTTTAAATTCTTGTTCGAGGTCT
121 AGGTCTCTGGTAGAGAGTTTTCAATTCAAAA----GTCTTATTTTTAAAATCCTGTTCGAGGTCT
** *
9594 CTGGTAGAGAGTTTTCAATCCAAAATCTTGTCTCGTTTTCAAAGTCC
182 CTAATAGAGAGTTTTCAATCCAAAATCTTGTCTCGTTTTCAAAATCC
* * ** * *
9641 TGTTTGAGGTCTCTGGTAGAGAGTTTTCTATTTTAAAA---TATTCTTCCTTTTT--AATCCTGT
1 TGTTCGAGGTCTCTGGTAGAGAGTTTT-TAATCCAAAACCTTA-TCTT-GTTTTTAAAATCCTGG
* * * * ** * *
9701 TTGAGATCTCTAGTAGAGAGTTTTCAGCTTTAAGATATTCTTCCTTTTTAAATCGTGGTCGAGGT
63 TCGAGGTCTCTGGTAGAGAGTTTTCTGCTTTAA-A-A-TCTTGTTTTTTAAATAGTGGTCAAGGT
* ** * *
9766 CTCTGGTAGGGAGTTTTCTGCTTTAAAA-TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTAATAG
125 CTCTGGTAGAGAGTTTTC-AATTCAAAAGTCTTATTTTTAAAATCCTGTTCGAGGTCTCTAATAG
* *
9830 AGAGTTTTCAATTCAAAATCTTGTCTTGTTCTT-AAAATCC
189 AGAGTTTTCAATCCAAAATCTTGTCTCGTT-TTCAAAATCC
*
9870 TGTTCGAGGTCTCTGGTAGAGAGTTCTTAAATCCAAAACCTTATCTTGTTTTTAAAATCCTGGTC
1 TGTTCGAGGTCTCTGGTAGAGAGTT-TTTAATCCAAAACCTTATCTTGTTTTTAAAATCCTGGTC
9935 GAGGTCTCTGGTAGAGAGTTTTCTGCTTTAAAATCTTGTTTTTTAAA
65 GAGGTCTCTGGTAGAGAGTTTTCTGCTTTAAAATCTTGTTTTTTAAA
9982 AAAATCCTGT
Statistics
Matches: 283, Mismatches: 43, Indels: 42
0.77 0.12 0.11
Matches are distributed among these distances:
229 107 0.38
230 10 0.04
231 5 0.02
232 38 0.13
233 29 0.10
234 6 0.02
239 35 0.12
240 5 0.02
241 36 0.13
242 8 0.03
243 4 0.01
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (228 bp):
TGTTCGAGGTCTCTGGTAGAGAGTTTTTAATCCAAAACCTTATCTTGTTTTTAAAATCCTGGTCG
AGGTCTCTGGTAGAGAGTTTTCTGCTTTAAAATCTTGTTTTTTAAATAGTGGTCAAGGTCTCTGG
TAGAGAGTTTTCAATTCAAAAGTCTTATTTTTAAAATCCTGTTCGAGGTCTCTAATAGAGAGTTT
TCAATCCAAAATCTTGTCTCGTTTTCAAAATCC
Done.