Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014043.1 Corchorus capsularis cultivar CVL-1 contig14064, 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: 10770
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1464 original size:194 final size:194
Alignment explanation
Indices: 1135--1527 Score: 777
Period size: 194 Copynumber: 2.0 Consensus size: 194
1125 TATAGTATTA
*
1135 GTATTTATGTAATGATCAGATAGATAAGCTTGCTAATTACCATGAAATGGTTGCTGCTGCGATTG
1 GTATTTATGTAATGATCAGATAGATAAGATTGCTAATTACCATGAAATGGTTGCTGCTGCGATTG
1200 CTAGCGCTTTCTTTTACGCTTGTGAGTCTTGAGTTGCTTGATTAAGTACTCAATGATCTCCTTCA
66 CTAGCGCTTTCTTTTACGCTTGTGAGTCTTGAGTTGCTTGATTAAGTACTCAATGATCTCCTTCA
1265 GACTGGCTTTCCTTCCCTCCTTCAAGTTCCATATCTCATCAACTGGGTACCTTCCACTTGGATT
131 GACTGGCTTTCCTTCCCTCCTTCAAGTTCCATATCTCATCAACTGGGTACCTTCCACTTGGATT
1329 GTATTTATGTAATGATCAGATAGATAAGATTGCTAATTACCATGAAATGGTTGCTGCTGCGATTG
1 GTATTTATGTAATGATCAGATAGATAAGATTGCTAATTACCATGAAATGGTTGCTGCTGCGATTG
1394 CTAGCGCTTTCTTTTACGCTTGTGAGTCTTGAGTTGCTTGATTAAGTACTCAATGATCTCCTTCA
66 CTAGCGCTTTCTTTTACGCTTGTGAGTCTTGAGTTGCTTGATTAAGTACTCAATGATCTCCTTCA
1459 GACTGGCTTTCCTTCCCTCCTTCAAGTTCCATATCTCATCAACTGGGTACCTTCCACTTGGATT
131 GACTGGCTTTCCTTCCCTCCTTCAAGTTCCATATCTCATCAACTGGGTACCTTCCACTTGGATT
1523 GTATT
1 GTATT
1528 CATTCATTTC
Statistics
Matches: 198, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
194 198 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (194 bp):
GTATTTATGTAATGATCAGATAGATAAGATTGCTAATTACCATGAAATGGTTGCTGCTGCGATTG
CTAGCGCTTTCTTTTACGCTTGTGAGTCTTGAGTTGCTTGATTAAGTACTCAATGATCTCCTTCA
GACTGGCTTTCCTTCCCTCCTTCAAGTTCCATATCTCATCAACTGGGTACCTTCCACTTGGATT
Found at i:3221 original size:33 final size:33
Alignment explanation
Indices: 3178--3292 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
3168 CGATGCAACT
* * *
3178 TAGTCTTCTCATGCATCAACTCATCATGGAACA
1 TAGTCTTCTCATGCATAAACTCATCATGCATCA
*
3211 TAGTCCTCTCATGCATAAACTCATCATGCATCA
1 TAGTCTTCTCATGCATAAACTCATCATGCATCA
*
3244 TAGTCTTCTCATGCATAAACTCAGCATGCATCA
1 TAGTCTTCTCATGCATAAACTCATCATGCATCA
3277 TAGTCTTCTCATGCAT
1 TAGTCTTCTCATGCAT
3293 TAGCTGCCTC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (33 bp):
TAGTCTTCTCATGCATAAACTCATCATGCATCA
Found at i:3237 original size:15 final size:15
Alignment explanation
Indices: 3219--3274 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
3209 CATAGTCCTC
3219 TCATGCATAAACTCA
1 TCATGCATAAACTCA
*
3234 TCATGCATCATAGTCTTC-
1 TCATGCAT-A-A-AC-TCA
3252 TCATGCATAAACTCA
1 TCATGCATAAACTCA
*
3267 GCATGCAT
1 TCATGCAT
3275 CATAGTCTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 2 0.06
15 16 0.48
16 2 0.06
17 2 0.06
18 9 0.27
19 2 0.06
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (15 bp):
TCATGCATAAACTCA
Found at i:7512 original size:186 final size:186
Alignment explanation
Indices: 7192--7752 Score: 980
Period size: 186 Copynumber: 3.0 Consensus size: 186
7182 GTATTGATTC
* * * *
7192 CTTACGAGCATCTAGGAGCTCTTGATTAGTTAAGCTTTCTTTGACAGTCAGGCAATTGCAACGGC
1 CTTACAAGCATCTAGGAGCTCTTGATTAGTTAAGTTTTCTTTGACAATCAGGCAATTGCAACTGC
* *
7257 TTCGCAAATCTTCCAATTCTTCTGACTTTTCCTCCAACTCTTTCCTTAGAGCAGATATCTCAGCA
66 TCCACAAATCTTCCAATTCTTCTGACTTTTCCTCCAACTCTTTCCTTAGAGCAGATATCTCAGCA
7322 CTTGAAGCTTTGTCAACTTCAACAGGAACTTCAACAAGATCCTGACAAGGCAAATT
131 CTTGAAGCTTTGTCAACTTCAACAGGAACTTCAACAAGATCCTGACAAGGCAAATT
* *
7378 CTTACAAGCATCTAGGAGCTCTTGATTAGTCAAGTTTTCCTTGACAATCAGGCAATTGCAACTGC
1 CTTACAAGCATCTAGGAGCTCTTGATTAGTTAAGTTTTCTTTGACAATCAGGCAATTGCAACTGC
*
7443 TCCACAAATCTTCCAATTCTTCTGACTTTTCCTCCAACTCTTTCCTTAGAGCAGATATCTCATCA
66 TCCACAAATCTTCCAATTCTTCTGACTTTTCCTCCAACTCTTTCCTTAGAGCAGATATCTCAGCA
* *
7508 CTTGAAGCTTCGTCAACTTCAATAGGAACTTCAACAAGATCCTGACAAGGCAAATT
131 CTTGAAGCTTTGTCAACTTCAACAGGAACTTCAACAAGATCCTGACAAGGCAAATT
* *
7564 CTTACAAGCATCTAGGAACTGTTGATTAGTTAAGTTTTCTTTGACAATCAGGCAATTGCAACTGC
1 CTTACAAGCATCTAGGAGCTCTTGATTAGTTAAGTTTTCTTTGACAATCAGGCAATTGCAACTGC
7629 TCCACAAATCTTCCAATTCTTCTGACTTTTCCTCCAACTCTTTCCTCT-GAGCAGATATCTCAGC
66 TCCACAAATCTTCCAATTCTTCTGACTTTTCCTCCAACTCTTTCCT-TAGAGCAGATATCTCAGC
*
7693 ACTTGAAGCTTTGTCAACTTCAACAGGAACTTCAACAAGATCCTGATAAGGCAAATT
130 ACTTGAAGCTTTGTCAACTTCAACAGGAACTTCAACAAGATCCTGACAAGGCAAATT
7750 CTT
1 CTT
7753 TTTTAGCTGA
Statistics
Matches: 355, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
186 354 1.00
187 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (186 bp):
CTTACAAGCATCTAGGAGCTCTTGATTAGTTAAGTTTTCTTTGACAATCAGGCAATTGCAACTGC
TCCACAAATCTTCCAATTCTTCTGACTTTTCCTCCAACTCTTTCCTTAGAGCAGATATCTCAGCA
CTTGAAGCTTTGTCAACTTCAACAGGAACTTCAACAAGATCCTGACAAGGCAAATT
Found at i:8725 original size:33 final size:33
Alignment explanation
Indices: 8688--8782 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 33
8678 CAGCAAATTG
*
8688 ATCATGCAACTTAGTCTTCTCATGCATCAAATC
1 ATCATGCAACATAGTCTTCTCATGCATCAAATC
* * * *
8721 ATCATGAAACCTAGTTTTCTCATG-ACTCAACTC
1 ATCATGCAACATAGTCTTCTCATGCA-TCAAATC
8754 ATCATGCAACATAGTCTTCTCATGCATCA
1 ATCATGCAACATAGTCTTCTCATGCATCA
8783 GCTGCCTCAC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.02
33 51 0.96
34 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (33 bp):
ATCATGCAACATAGTCTTCTCATGCATCAAATC
Found at i:10234 original size:21 final size:21
Alignment explanation
Indices: 10208--10252 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
10198 AGAATCTGGA
10208 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
10229 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
10250 TTG
1 TTG
10253 ACGCTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:10579 original size:32 final size:32
Alignment explanation
Indices: 10531--10616 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
10521 CCCCATGAAA
** *
10531 AGGCCGCCCCACTGGGGCGGCTT-AGCCAGGGC
1 AGGCCGCCCCGGTGGGGCGGCTTCA-CCACGGC
*
10563 AGGCCGTCCCGGTGGGGCGGCTTCACCACGGC
1 AGGCCGCCCCGGTGGGGCGGCTTCACCACGGC
10595 AGGCCGCCCCGGTGGGGCGGCT
1 AGGCCGCCCCGGTGGGGCGGCT
10617 CGGCTATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 47 0.98
33 1 0.02
ACGTcount: A:0.09, C:0.37, G:0.43, T:0.10
Consensus pattern (32 bp):
AGGCCGCCCCGGTGGGGCGGCTTCACCACGGC
Found at i:10735 original size:33 final size:31
Alignment explanation
Indices: 10685--10769 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 31
10675 CCCCACCGGT
10685 GCCGTCCC-CCTGGGGCGGCTGAGCCATGGCCAA
1 GCCG-CCCTCCTGGGGCGGCT-A-CCATGGCCAA
*
10718 GCCGCCCTCCTGGGGCGGCACTACCATGGCCAG
1 GCCGCCCTCCTGGGGCGG--CTACCATGGCCAA
10751 GCCG-CCTCCCTGGGGCGGC
1 GCCGCCCT-CCTGGGGCGGC
10770 C
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
31 1 0.02
32 6 0.13
33 37 0.79
34 1 0.02
35 2 0.04
ACGTcount: A:0.09, C:0.42, G:0.36, T:0.12
Consensus pattern (31 bp):
GCCGCCCTCCTGGGGCGGCTACCATGGCCAA
Done.