Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019896.1 Corchorus olitorius cultivar O-4 contig19929, 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: 9868
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Found at i:165 original size:36 final size:36
Alignment explanation
Indices: 118--187 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
108 TTCAATAACC
* *
118 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
154 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
188 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:1012 original size:204 final size:201
Alignment explanation
Indices: 674--1083 Score: 739
Period size: 204 Copynumber: 2.0 Consensus size: 201
664 GCTTATTAAC
674 TTTATCAATGATGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGATGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
* * *
739 ATACAACACATTATTATTATATATAAAACTATACCAAAAAAATTTAGTTGAACATTAGTGGTTGA
66 ATACAACACATTACTATTATATATAAAACTATACAAAAAAAAATTAGTTGAACATTAGTGGTTGA
804 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
131 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
869 GATTTA
196 GATTTA
* * *
875 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTACTATCAAAGTTGTAGTGAATAA
1 TTTATCAATGATGAATGTTATTAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
940 GATACAACACATTACTATTATATATATAGAACTATACAAAAAAAAATTAGTTGAACATTAGTGGT
65 GATACAACACATTACTATTATATATA-A-AACTATACAAAAAAAAATTAGTTGAACATTAGTGGT
1005 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
128 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
1070 TCCGATTTA
193 TCCGATTTA
1079 TTTAT
1 TTTAT
1084 TATTAAGGAA
Statistics
Matches: 200, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
201 23 0.12
202 63 0.31
203 1 0.00
204 113 0.56
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (201 bp):
TTTATCAATGATGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
ATACAACACATTACTATTATATATAAAACTATACAAAAAAAAATTAGTTGAACATTAGTGGTTGA
TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
GATTTA
Found at i:1500 original size:12 final size:13
Alignment explanation
Indices: 1476--1504 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1466 GTTTAGACTT
1476 ATATAGTATATAG
1 ATATAGTATATAG
1489 ATATAG-ATATAG
1 ATATAGTATATAG
1501 ATAT
1 ATAT
1505 GGACGTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (13 bp):
ATATAGTATATAG
Found at i:8038 original size:22 final size:21
Alignment explanation
Indices: 8010--8225 Score: 136
Period size: 22 Copynumber: 10.0 Consensus size: 21
8000 CTTATAGGGA
*
8010 GGTTATCGAAATTTCATGATGT
1 GGTTATCAAAATTTCAT-ATGT
*
8032 GGTTATCAAAATTTTCATAGTGC
1 GGTTATCAAAA-TTTCATA-TGT
* *
8055 GGTTA-C-CAATTTTAT-TGT
1 GGTTATCAAAATTTCATATGT
* *
8073 GTGATTATCAAAATTTCACATTT
1 G-G-TTATCAAAATTTCATATGT
*
8096 AGATTATCAAAATTTCATAGTGT
1 -GGTTATCAAAATTTCATA-TGT
*
8119 GGTTATCAAAATTTCACAATGT
1 GGTTATCAAAATTTCA-TATGT
*
8141 GGTTATCAAATTTTCATAT-T
1 GGTTATCAAAATTTCATATGT
** * *
8161 AGGTTATTGAAATTTCATAACGA
1 -GGTTATCAAAATTTCAT-ATGT
* * *
8184 AGTTATCAAATTTTCACAGTGT
1 GGTTATCAAAATTTCATA-TGT
* *
8206 GGTCATCAATATTTC-TATGT
1 GGTTATCAAAATTTCATATGT
8226 TAGCATGAAA
Statistics
Matches: 147, Mismatches: 33, Indels: 30
0.70 0.16 0.14
Matches are distributed among these distances:
18 3 0.02
19 1 0.01
20 12 0.08
21 21 0.14
22 91 0.62
23 18 0.12
24 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (21 bp):
GGTTATCAAAATTTCATATGT
Found at i:8152 original size:65 final size:66
Alignment explanation
Indices: 8072--8220 Score: 158
Period size: 65 Copynumber: 2.3 Consensus size: 66
8062 AATTTTATTG
* ** **
8072 TGTGATTATCAAAATTTCACAT-TTAGATTATCAAAATTTCATAGTGTGGTTATCAAAATTTCAC
1 TGTGGTTATC-AAATTTCACATATTAGATTATCAAAATTTCATAACGAAGTTATCAAAATTTCAC
8136 AA
65 AA
* * ** *
8138 TGTGGTTATCAAATTT-TCATATTAGGTTATTGAAATTTCATAACGAAGTTATCAAATTTTCACA
1 TGTGGTTATCAAATTTCACATATTAGATTATCAAAATTTCATAACGAAGTTATCAAAATTTCACA
*
8202 G
66 A
*
8203 TGTGGTCATCAATATTTC
1 TGTGGTTATCAA-ATTTC
8221 TATGTTAGCA
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
64 3 0.04
65 52 0.76
66 13 0.19
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (66 bp):
TGTGGTTATCAAATTTCACATATTAGATTATCAAAATTTCATAACGAAGTTATCAAAATTTCACA
A
Found at i:8166 original size:43 final size:44
Alignment explanation
Indices: 8010--8220 Score: 166
Period size: 43 Copynumber: 4.8 Consensus size: 44
8000 CTTATAGGGA
* * *
8010 GGTTATCGAAA-TTTCAT-GATGTGGTTATCAAAATTTTCATAGTGC
1 GGTTATC-AAATTTTCATAG-TGTGGTTATCAAAA-TTTCACAATGT
* * * *
8055 GGTTA-CCAATTTT-ATTGTGTGATTATCAAAATTTCAC-ATTT
1 GGTTATCAAATTTTCATAGTGTGGTTATCAAAATTTCACAATGT
* *
8096 AGATTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAATGT
1 -GGTTATCAAATTTTCATAGTGTGGTTATCAAAATTTCACAATGT
** * * *
8141 GGTTATCAAATTTTCATA-T-TAGGTTATTGAAATTTCATAACGA
1 GGTTATCAAATTTTCATAGTGT-GGTTATCAAAATTTCACAATGT
* * * *
8184 AGTTATCAAATTTTCACAGTGTGGTCATCAATATTTC
1 GGTTATCAAATTTTCATAGTGTGGTTATCAAAATTTC
8221 TATGTTAGCA
Statistics
Matches: 132, Mismatches: 25, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
41 1 0.01
42 10 0.08
43 57 0.43
44 55 0.42
45 9 0.07
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (44 bp):
GGTTATCAAATTTTCATAGTGTGGTTATCAAAATTTCACAATGT
Found at i:8563 original size:49 final size:49
Alignment explanation
Indices: 8502--8596 Score: 190
Period size: 49 Copynumber: 1.9 Consensus size: 49
8492 TGGGCTAGCC
8502 AAAAAAAACTTTCTTCAAAACCTAAAACTTGAACTTCACGATTTTGAAA
1 AAAAAAAACTTTCTTCAAAACCTAAAACTTGAACTTCACGATTTTGAAA
8551 AAAAAAAACTTTCTTCAAAACCTAAAACTTGAACTTCACGATTTTG
1 AAAAAAAACTTTCTTCAAAACCTAAAACTTGAACTTCACGATTTTG
8597 CATGTTTGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.29
Consensus pattern (49 bp):
AAAAAAAACTTTCTTCAAAACCTAAAACTTGAACTTCACGATTTTGAAA
Done.