Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013427.1 Corchorus olitorius cultivar O-4 contig13460, 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: 22091
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:14595 original size:103 final size:104
Alignment explanation
Indices: 14352--14639 Score: 343
Period size: 108 Copynumber: 2.7 Consensus size: 104
14342 TTCCTTTTCT
* * *
14352 TTATAGAGTTTTAGAAATAAAATATAAAACTAATCTCATTAAGTTTAGCCCCAAAATTAAAATTT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCC-AAATT--AATTT
* *
14417 TATTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTTATTA
63 TATTTTTATTTTAAGGGTAAATTCCAAAATCAATAA-TTATTA
* * *
14460 TTATAGGGTTTTAGAAGTAAAATACAAAACTAATTTCACTAAATTTAGCCCCAAATTAA-TTT-T
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAATTTTAT
* *
14523 TTTTATTTTAAGGGTAAATTCCATAATCAATAA-TATTG
66 TTTTATTTTAAGGGTAAATTCCAAAATCAATAATTATTA
* *
14561 TTATAGGGTTTTAGAAATAAAATATATATAACTAA-TTCACCAAGTTTAG-ACCAAATTAAAATT
1 TTATAGGGTTTTAGAAATAAAATATA-A-AACTAATTTCACTAAGTTTAGCCCCAAATT--AATT
**
14624 AAATTTTTATTTTAAG
62 TTATTTTTATTTTAAG
14640 AATTAGAAAA
Statistics
Matches: 157, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
101 35 0.22
102 13 0.08
103 39 0.25
104 4 0.03
105 15 0.10
107 5 0.03
108 46 0.29
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (104 bp):
TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAATTTTAT
TTTTATTTTAAGGGTAAATTCCAAAATCAATAATTATTA
Found at i:15132 original size:40 final size:40
Alignment explanation
Indices: 15088--15167 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
15078 TTTCACATAA
* *
15088 ATGTTATAATAAATCTTATCCCCCTTAATTATCTATAATT
1 ATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATT
15128 ATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATT
1 ATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATT
15168 GTAACCTCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (40 bp):
ATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATT
Found at i:15414 original size:26 final size:26
Alignment explanation
Indices: 15385--15438 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
15375 TCATAATACT
*
15385 TTCGAAATTTCCTACGTATCAAACAA
1 TTCGAAATTTCCTACATATCAAACAA
15411 TTCGAAATTTCCTACATATCAAACAA
1 TTCGAAATTTCCTACATATCAAACAA
15437 TT
1 TT
15439 TAATTCAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (26 bp):
TTCGAAATTTCCTACATATCAAACAA
Found at i:15853 original size:2 final size:2
Alignment explanation
Indices: 15846--15877 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15836 ACTCTTATTA
15846 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
15878 TCTTAGCTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16232 original size:14 final size:14
Alignment explanation
Indices: 16213--16242 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
16203 TGCTCTCTAA
16213 TTCTCATGTTGTAT
1 TTCTCATGTTGTAT
16227 TTCTCATGTTGTAT
1 TTCTCATGTTGTAT
16241 TT
1 TT
16243 TTTTAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60
Consensus pattern (14 bp):
TTCTCATGTTGTAT
Found at i:18120 original size:6 final size:6
Alignment explanation
Indices: 18103--18132 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
18093 AAGATGTGAC
18103 CTAGTT -TAGTT CTAGTT CTAGTT CTAGTT C
1 CTAGTT CTAGTT CTAGTT CTAGTT CTAGTT C
18133 CTAAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
CTAGTT
Found at i:18194 original size:162 final size:156
Alignment explanation
Indices: 17898--18195 Score: 506
Period size: 162 Copynumber: 1.9 Consensus size: 156
17888 AACCATGTGC
17898 AACATTTATAAGGAATTGTGACTTAGGATAAGGGACCATAAGATGTGACCTAGTTTAGTTCTAGT
1 AACATTTATAAGGAATTGTGACTTAGGATAAGGGACCATAAGATGTGACCTAGTTTAGTTCTAGT
* *
17963 TCTAGTTCCTAATTAACTTGATAATTAAATTTTATCTCTATCTTCTGATTAAGAACAAACTTAAC
66 TCTAGTTCCTAAATAACTTGATAATTAAATTTGATCTCTATCTTCTGATTAAGAACAAACTTAAC
18028 ATCATCAACCTTGGAAAATTAAATAT
131 ATCATCAACCTTGGAAAATTAAATAT
18054 AACATTTATAAGGAATTGTGACTTAGGATAAGGGACCATAAGATGTGACCTAGTTTAGTTCTAGT
1 AACATTTATAAGGAATTGTGACTTAGGATAAGGGACCATAAGATGTGACC-----TAGTT-TAGT
* *
18119 TCTAGTTCTAGTTCCTAAATAATTTGATAATTAAATTTGATCTCTATTTTCTGATTAAGAACAAA
60 TCTAGTTCTAGTTCCTAAATAACTTGATAATTAAATTTGATCTCTATCTTCTGATTAAGAACAAA
18184 CTTAACATCATC
125 CTTAACATCATC
18196 TATATATATA
Statistics
Matches: 132, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
156 50 0.38
161 5 0.04
162 77 0.58
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (156 bp):
AACATTTATAAGGAATTGTGACTTAGGATAAGGGACCATAAGATGTGACCTAGTTTAGTTCTAGT
TCTAGTTCCTAAATAACTTGATAATTAAATTTGATCTCTATCTTCTGATTAAGAACAAACTTAAC
ATCATCAACCTTGGAAAATTAAATAT
Done.