Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007171.1 Corchorus capsularis cultivar CVL-1 contig07192, 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: 11675
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:467 original size:2 final size:2
Alignment explanation
Indices: 462--491 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
452 CTATATAAAC
462 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
492 CTCATTAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:738 original size:30 final size:30
Alignment explanation
Indices: 689--763 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
679 TACAAAATCT
*
689 ATTAATATCTACC---TTTTTTTAAGAATA
1 ATTAATATCTACCAATTTTTTTTAAGAACA
* *
716 ATTAATATCTACCAATTTTTTTTAGGCACA
1 ATTAATATCTACCAATTTTTTTTAAGAACA
746 ATTAATATCTACCAATTT
1 ATTAATATCTACCAATTT
764 AATTACAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 13 0.31
30 29 0.69
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (30 bp):
ATTAATATCTACCAATTTTTTTTAAGAACA
Found at i:6216 original size:33 final size:33
Alignment explanation
Indices: 6179--6250 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
6169 TTCATTTAGT
*
6179 AATTTAGTATTTTTAATGAGGTAGTTTAAGTTC
1 AATTTAGTATTTTTAATCAGGTAGTTTAAGTTC
6212 AATTTAGTATTTTTAATCAGGTAGTTTAAGTTC
1 AATTTAGTATTTTTAATCAGGTAGTTTAAGTTC
6245 AATTTA
1 AATTTA
6251 CTTCATTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (33 bp):
AATTTAGTATTTTTAATCAGGTAGTTTAAGTTC
Found at i:9750 original size:68 final size:67
Alignment explanation
Indices: 9617--10007 Score: 410
Period size: 66 Copynumber: 5.9 Consensus size: 67
9607 TTCATTTACG
* * *
9617 AAAA-TACCCTTTCGGTGGAAGGGTCATTTTCTTCTTTTGCATTTGAGTTTAGTATTTTCTTTTC
1 AAAAGTACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATTTTCTTTTC
9681 CC
66 CC
* *
9683 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCCTTTCGCATTTAAGTTTAGTATTTTCTTTT
1 AAAAGTACCCTTTCGGTCGAAGGGTCATTTTCGT-CTTTTGCATTTAAGTTTAGTATTTTCTTTT
9748 CCC
65 CCC
* * * *
9751 AAAAGAACCCTTTCGGTGGAAGGGTCATTTTCATC---T-CATTTAAGTTTAGTATCTT-TTTTC
1 AAAAGTACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATTTTCTTTTC
9811 CC
66 CC
* * * * * ** *
9813 AAAAATACCCTTTCGGTCAAAGGGTCAGTGTT-GTCTTTTGCATTCAAGTTTAGCATTCCCATTT
1 AAAAGTACCCTTTCGGTCGAAGGGTCA-TTTTCGTCTTTTGCATTTAAGTTTAGTATTTTCTTTT
9877 -CC
65 CCC
** * * * *
9879 ATGAGTACCCTTTCGGTCAAAGGGTCAGTGTT-GTCTTTTACATTCAAGTTTAGTATTTT-TATT
1 AAAAGTACCCTTTCGGTCGAAGGGTCA-TTTTCGTCTTTTGCATTTAAGTTTAGTATTTTCT-TT
9942 T-CC
64 TCCC
* * *
9945 AAAAATACCCTTCCGGTCGAAGGGTCATTTTCGTCTTTTTGCATCTAAGTTTAGT-TTTATCTT
1 AAAAGTACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTAGTATTT-TCTT
10008 ACAAAAATGC
Statistics
Matches: 276, Mismatches: 36, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
62 32 0.12
63 21 0.08
65 4 0.01
66 105 0.38
67 50 0.18
68 64 0.23
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (67 bp):
AAAAGTACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATTTTCTTTTC
CC
Found at i:10015 original size:197 final size:194
Alignment explanation
Indices: 9603--10031 Score: 440
Period size: 197 Copynumber: 2.2 Consensus size: 194
9593 AGGTCATTAG
* * * * **
9603 AGTTTTCATTTACGAAAATACCCTTTCGGTGGAAGGGTCATTTTCTTCTTTTGCATTTGAGTTTA
1 AGTTTT-ATTTACAAAAATACCCTTTCGGTGAAAGGGTCATGTTCGTCTTTTGCATTCAAGTTTA
* ** * ** * * *
9668 GTATTTTCTTTTCCCAAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCCTTTCGCATTTAAGT
65 GCATTCCCATTTCCCAAAAGTACCCTTTCGGTCAAAGGGTCATGTTCGTCCTTTCACATTCAAGT
* * *
9733 TTAGTATTTTCTTTTCCCAAAAGAACCCTTTCGGTGGAAGGGTCATTTTCATCTCATTTAAGTTT
130 TTAGTATTTTCTTTTCCCAAAAGAACCCTTCCGGTCGAAGGGTCATTTTCATCTCATCTAAGTTT
* * *
9798 AGTATCTTTTTTCCCAAAAATACCCTTTCGGTCAAAGGGTCAGTGTT-GTCTTTTGCATTCAAGT
1 AGT-T-TTATTT-ACAAAAATACCCTTTCGGTGAAAGGGTCA-TGTTCGTCTTTTGCATTCAAGT
** *
9862 TTAGCATTCCCATTT-CCATGAGTACCCTTTCGGTCAAAGGGTCAGTGTT-GT-CTTTTACATTC
62 TTAGCATTCCCATTTCCCAAAAGTACCCTTTCGGTCAAAGGGTCA-TGTTCGTCCTTTCACATTC
*
9924 AAGTTTAGTATTTT-TATTT-CCAAAA-ATACCCTTCCGGTCGAAGGGTCATTTTCGTCTTTTTG
126 AAGTTTAGTATTTTCT-TTTCCCAAAAGA-ACCCTTCCGGTCGAAGGGTCATTTTCATC----T-
9986 CATCTAAGTTT
184 CATCTAAGTTT
* *
9997 AGTTTTATCTTACAAAAATGCCCCTTCGGTGAAAG
1 AGTTTTAT-TTACAAAAATACCCTTTCGGTGAAAG
10032 TTTAGTTTCT
Statistics
Matches: 191, Mismatches: 30, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
193 1 0.01
194 33 0.17
195 28 0.15
196 31 0.16
197 78 0.41
198 7 0.04
199 13 0.07
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (194 bp):
AGTTTTATTTACAAAAATACCCTTTCGGTGAAAGGGTCATGTTCGTCTTTTGCATTCAAGTTTAG
CATTCCCATTTCCCAAAAGTACCCTTTCGGTCAAAGGGTCATGTTCGTCCTTTCACATTCAAGTT
TAGTATTTTCTTTTCCCAAAAGAACCCTTCCGGTCGAAGGGTCATTTTCATCTCATCTAAGTTT
Found at i:10022 original size:132 final size:125
Alignment explanation
Indices: 9617--10031 Score: 340
Period size: 131 Copynumber: 3.2 Consensus size: 125
9607 TTCATTTACG
* * **
9617 AAAAT-ACCCTTTCGGTGGAAGGGTCATTTTCTTCTTTTGCATTTGAGTTTAGTATTTTCTTTTC
1 AAAATGACCCTTTCGGTGAAAGGGTCATTTTCATC---T-CATTCAAGTTTAGTATTTT-TTTT-
* * *
9681 CCAAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCCTTTCGCATTTAAGTTTAGTATTT-TCT
60 CCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGT-CTTTTGCA-TTAAGTTTAGT-TTTATC-
*
9745 TTTCCC
121 -TTCCA
* * *
9751 AAAA-GAACCCTTTCGGTGGAAGGGTCATTTTCATCTCATTTAAGTTTAGTATCTTTTTTCCCAA
1 AAAATG-ACCCTTTCGGTGAAAGGGTCATTTTCATCTCATTCAAGTTTAGTAT-TTTTTTTCCAA
* * **
9815 AAATACCCTTTCGGTCAAAGGGTCAGTGTT-GTCTTTTGCATTCAAGTTTAGCATTCCCAT-TTC
64 AAATACCCTTTCGGTCGAAGGGTCA-TTTTCGTCTTTTGCATT-AAGTTTAG--TT-TTATCTTC
9878 CA
124 CA
** * * * *
9880 TGAGT-ACCCTTTCGGTCAAAGGGTCAGTGTTGTCTTTTACATTCAAGTTTAGTATTTTTATTTC
1 AAAATGACCCTTTCGGTGAAAGGGTCA-T-TT-TCATCT-CATTCAAGTTTAGTATTTTT-TTTC
* *
9944 CAAAAATACCCTTCCGGTCGAAGGGTCATTTTCGTCTTTTTGCATCTAAGTTTAGTTTTATCTTA
61 CAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCAT-TAAGTTTAGTTTTATCTTC
10009 CA
124 CA
*
10011 AAAATG-CCCCTTCGGTGAAAG
1 AAAATGACCCTTTCGGTGAAAG
10032 TTTAGTTTCT
Statistics
Matches: 230, Mismatches: 31, Indels: 43
0.76 0.10 0.14
Matches are distributed among these distances:
128 21 0.09
129 21 0.09
130 33 0.14
131 54 0.23
132 52 0.23
133 16 0.07
134 5 0.02
135 28 0.12
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (125 bp):
AAAATGACCCTTTCGGTGAAAGGGTCATTTTCATCTCATTCAAGTTTAGTATTTTTTTTCCAAAA
ATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTAAGTTTAGTTTTATCTTCCA
Found at i:10174 original size:6 final size:6
Alignment explanation
Indices: 10163--10189 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10153 AAAATACAAA
10163 AAGATT AAGATT AAGATT AAGATT AAG
1 AAGATT AAGATT AAGATT AAGATT AAG
10190 CATTTAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.30
Consensus pattern (6 bp):
AAGATT
Found at i:11601 original size:21 final size:22
Alignment explanation
Indices: 11572--11621 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
11562 AATTTTGAGT
* *
11572 TGATGACCTCCCTATG-AATTC
1 TGATAACCTCCATATGAAATTC
*
11593 TGATAACCTCCATATGAAATTT
1 TGATAACCTCCATATGAAATTC
11615 TGATAAC
1 TGATAAC
11622 TGTCTATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (22 bp):
TGATAACCTCCATATGAAATTC
Found at i:11618 original size:22 final size:22
Alignment explanation
Indices: 11488--11621 Score: 78
Period size: 22 Copynumber: 6.0 Consensus size: 22
11478 AAACCTAATA
*
11488 TCCATATGAAATTTTGATTA-C
1 TCCATATGAAATTTTGATAACC
* * *
11509 T-AATCTATGACATTTTGATAACT
1 TCCA--TATGAAATTTTGATAACC
* * *
11532 TCCCT-TGAAATTTTGAGAGCC
1 TCCATATGAAATTTTGATAACC
* *
11553 GCCTTATGAAATTTTGAGTTGATGACC
1 TCCATATGAAATTTTGA--T-A--ACC
* *
11580 TCCCTATG-AATTCTGATAACC
1 TCCATATGAAATTTTGATAACC
11601 TCCATATGAAATTTTGATAAC
1 TCCATATGAAATTTTGATAAC
11622 TGTCTATTCT
Statistics
Matches: 83, Mismatches: 19, Indels: 21
0.67 0.15 0.17
Matches are distributed among these distances:
20 1 0.01
21 26 0.31
22 37 0.45
23 2 0.02
24 1 0.01
25 1 0.01
26 7 0.08
27 8 0.10
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (22 bp):
TCCATATGAAATTTTGATAACC
Done.