Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012287.1 Corchorus olitorius cultivar O-4 contig12320, 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: 18247
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:200 original size:30 final size:29
Alignment explanation
Indices: 157--213 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
147 TTAGGATTAG
157 TTATTTATGCTTTAATTTGCAA-TTTCCT
1 TTATTTATGCTTTAATTTGCAAGTTTCCT
*
185 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTAT-TTATG-CTTTAATTTGCAAGTTTC
214 ATTAATAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 5 0.20
30 12 0.48
31 4 0.16
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.58
Consensus pattern (29 bp):
TTATTTATGCTTTAATTTGCAAGTTTCCT
Found at i:1759 original size:19 final size:18
Alignment explanation
Indices: 1735--1770 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1725 TGAAGATTTA
1735 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
1754 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
1771 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:5877 original size:19 final size:21
Alignment explanation
Indices: 5850--5892 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
5840 ATTTTAATTA
5850 TTTTTTTGT-GT-GTTT-ATG
1 TTTTTTTGTGGTGGTTTGATG
5868 TTTTTATTGTGGTGGTTTGATG
1 TTTTT-TTGTGGTGGTTTGATG
5890 TTT
1 TTT
5893 AAAGTGATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.24
19 4 0.19
20 2 0.10
21 4 0.19
22 6 0.29
ACGTcount: A:0.07, C:0.00, G:0.26, T:0.67
Consensus pattern (21 bp):
TTTTTTTGTGGTGGTTTGATG
Found at i:9231 original size:41 final size:41
Alignment explanation
Indices: 9124--9404 Score: 280
Period size: 41 Copynumber: 6.7 Consensus size: 41
9114 TCTTCGTCCC
* *
9124 CAAAGTCCCCAAACACATTTATAACACAGGGGCAAT-TATCTCT
1 CAAAGTCCCCAAACACATTTATAACACAGAGGC-ATCTA--TAT
*
9167 CTAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATAT
1 C-AAAGTCCCCAAACACATTTATAACACAGAGGCATCTATAT
* * * * *
9209 CAAAGTCCCCAAACACAATTATAACATAGGGGCAATTCTCTTT
1 CAAAGTCCCCAAACACATTTATAACACAGAGGC-A-TCTATAT
* ** *
9252 AAAAGTCCTTAAGCACATTTATAACACAGAGGCATCTATAT
1 CAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATAT
* * * *
9293 CAAAGTCTCCAAGCACAATTATAACACAGAGGCACCTCTATTT
1 CAAAGTCCCCAAACACATTTATAACACAGAGGCA--TCTATAT
* *
9336 CAAAGTCCTCAAGCACATTTATAACACAGAGGCATCTATA-
1 CAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATAT
*
9376 CTAAAGTCCCTAAACA-ATATTATAACACA
1 C-AAAGTCCCCAAACACAT-TTATAACACA
9405 AGGGCAATTT
Statistics
Matches: 199, Mismatches: 31, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
40 3 0.02
41 88 0.44
42 5 0.03
43 71 0.36
44 32 0.16
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.25
Consensus pattern (41 bp):
CAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATAT
Found at i:9291 original size:84 final size:83
Alignment explanation
Indices: 9124--9413 Score: 395
Period size: 84 Copynumber: 3.4 Consensus size: 83
9114 TCTTCGTCCC
* * *
9124 CAAAGTCCCCAAACACATTTATAACACAGGGGCAATTATCTCTCTAAAGTCCTCAAACACATTTA
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAA-T-TCTCTTTAAAGTCCTCAAGCACATTTA
9189 TAACACAGAGGCATCTATAT
64 TAACACAGAGGCATCTATAT
* *
9209 CAAAGTCCCCAAACACAATTATAACATAGGGGCAATTCTCTTTAAAAGTCCTTAAGCACATTTAT
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTT-AAAGTCCTCAAGCACATTTAT
9274 AACACAGAGGCATCTATAT
65 AACACAGAGGCATCTATAT
* * * ** *
9293 CAAAGTCTCCAAGCACAATTATAACACAGAGGCACCTCTATTTCAAAGTCCTCAAGCACATTTAT
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTT-AAAGTCCTCAAGCACATTTAT
9358 AACACAGAGGCATCTATA-
65 AACACAGAGGCATCTATAT
* *
9376 CTAAAGTCCCTAAACA-ATATTATAACACAAGGGCAATT
1 C-AAAGTCCCCAAACACA-ATTATAACACAGGGGCAATT
9414 TCTATATGGC
Statistics
Matches: 181, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
83 8 0.04
84 140 0.77
85 33 0.18
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.24
Consensus pattern (83 bp):
CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTTAAAGTCCTCAAGCACATTTATA
ACACAGAGGCATCTATAT
Found at i:13358 original size:72 final size:72
Alignment explanation
Indices: 13233--13438 Score: 270
Period size: 72 Copynumber: 2.9 Consensus size: 72
13223 CCCATGGTCC
* *
13233 TCTTCTTCATTGCGATTGTAGCCGAGGCATTTCCCACATTTGGCGGTCCTTCGCACAATCCTTAC
1 TCTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
13298 ATAATCA
66 ATAATCA
* * * *
13305 TCTTCTTCATTGCGATTGTAGCCAAGGCAGTTCTCGCATTTGGCAGTCTTTCGCACAATCCTTAC
1 TCTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
*
13370 ATGATCA
66 ATAATCA
* * * * * * *
13377 TCCTTC-TCGTTGTGATTTTAGCTGAGGCAGTTCCCACATTTGGTAATCCTTCGCATAATCCT
1 T-CTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCT
13439 CACTACTAGT
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
72 111 0.97
73 4 0.03
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.35
Consensus pattern (72 bp):
TCTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
ATAATCA
Found at i:13924 original size:14 final size:15
Alignment explanation
Indices: 13898--13927 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
13888 CTAAGTCCAA
13898 TCCTTGCTTATTTAT
1 TCCTTGCTTATTTAT
13913 TCCTTG-TTATTTAT
1 TCCTTGCTTATTTAT
13927 T
1 T
13928 TTTCCTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (15 bp):
TCCTTGCTTATTTAT
Found at i:15518 original size:15 final size:17
Alignment explanation
Indices: 15485--15519 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
15475 CTTATTATCT
15485 ATTGCTTTTCTATTTTA
1 ATTGCTTTTCTATTTTA
15502 ATTG-TTTTCTA-TTTA
1 ATTGCTTTTCTATTTTA
15517 ATT
1 ATT
15520 TACTTTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 7 0.39
17 4 0.22
ACGTcount: A:0.20, C:0.09, G:0.06, T:0.66
Consensus pattern (17 bp):
ATTGCTTTTCTATTTTA
Found at i:17946 original size:6 final size:6
Alignment explanation
Indices: 17929--17969 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
17919 ATACTTTTAT
17929 ATATAG -TATAG ATATAG ATATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
17970 GTATTCCCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
ATATAG
Done.