Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013172.1 Corchorus olitorius cultivar O-4 contig13205, 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: 19228
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3850 original size:19 final size:18
Alignment explanation
Indices: 3817--3852 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3807 TGGAAATTAT
3817 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
3835 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
3853 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:4594 original size:67 final size:67
Alignment explanation
Indices: 4480--4615 Score: 209
Period size: 67 Copynumber: 2.0 Consensus size: 67
4470 ATAGCTCGAC
** *
4480 AATCAACACACATTCTCCAAGTTCCATCCTTCTTTGGAGTAACCAACACGGGAACAACACATGGA
1 AATCAACACACATTCTCCAAGTTCCATCCTTCTTTGGAACAACCAACACAGGAACAACACATGGA
4545 GA
66 GA
* * * *
4547 AATCAACATACATTCTCCAAGTTCCATCCTTTTTTGGAACAAGCAACACAGGAACAACACATGGG
1 AATCAACACACATTCTCCAAGTTCCATCCTTCTTTGGAACAACCAACACAGGAACAACACATGGA
4612 GA
66 GA
4614 AA
1 AA
4616 GGCTTTCTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (67 bp):
AATCAACACACATTCTCCAAGTTCCATCCTTCTTTGGAACAACCAACACAGGAACAACACATGGA
GA
Found at i:10035 original size:22 final size:22
Alignment explanation
Indices: 10008--10899 Score: 604
Period size: 22 Copynumber: 40.7 Consensus size: 22
9998 GGCTATCAAA
*
10008 GAGGTTATAAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* * * *
10030 GTGGTTATCGAATTTTCATAGG
1 GAGGTTATCAAAATTTCATAGT
10052 GAGGTTATCAAAATTTCACT-GT
1 GAGGTTATCAAAATTTCA-TAGT
* * *
10074 GTGGTTATCAAAATTTTATAGG
1 GAGGTTATCAAAATTTCATAGT
*
10096 GAGGTTATTAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* *
10118 GAGGCTATCAACATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* * *
10140 GCGGTTATCAAAAGTTCATTCG-
1 GAGGTTATCAAAATTTCA-TAGT
* *
10162 GAGG-TACCAAAATTTTCGTAGT
1 GAGGTTATCAAAA-TTTCATAGT
*
10184 GTGGTTATCAAAATTTCATA-T
1 GAGGTTATCAAAATTTCATAGT
* * *
10205 GGTGGTTATCAAGATTTCATAGA
1 -GAGGTTATCAAAATTTCATAGT
* *
10228 GAGATTATCAAAATTTCATTGT
1 GAGGTTATCAAAATTTCATAGT
* *
10250 GTGGTTATCAAAATTTAATACG-
1 GAGGTTATCAAAATTTCATA-GT
*
10272 GAGGTTATCAAAATTTCATTGT
1 GAGGTTATCAAAATTTCATAGT
* * *
10294 GTGGTTATCAAAATTTAATAGG
1 GAGGTTATCAAAATTTCATAGT
* *
10316 GAGTTTATCAAAATTTCATTGT
1 GAGGTTATCAAAATTTCATAGT
* * *
10338 GTGGTTATCAAAATTTAATAGG
1 GAGGTTATCAAAATTTCATAGT
*
10360 GAGTTTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* * * * *
10382 GTGATTATCAAAATTTTATTGG
1 GAGGTTATCAAAATTTCATAGT
* *
10404 GAGG-TACCAAAAGTTC-TAAGT
1 GAGGTTATCAAAATTTCAT-AGT
* *
10425 GTA-GTTATCAAAATTTCATTGG
1 G-AGGTTATCAAAATTTCATAGT
* * **
10447 GAGGTTTAGCGAAATTTTTTACG-
1 GAGG-TTATCAAAATTTCATA-GT
* *
10470 GAGATTATCAAAATTTCATTGT
1 GAGGTTATCAAAATTTCATAGT
* *
10492 -ATGTTATCAAAATTTCATAGG
1 GAGGTTATCAAAATTTCATAGT
*
10513 GATGTTA-CTAAAATTTCATAAG-
1 GAGGTTATC-AAAATTTCAT-AGT
* * **
10535 AAGGTTATCAAAATTTTATAAA
1 GAGGTTATCAAAATTTCATAGT
* **
10557 GAGATTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAGT
* *
10579 AAGGTTTATCAAAATTTAATAAG-
1 GAGG-TTATCAAAATTTCAT-AGT
* *
10602 GAGATTATCACAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* *
10624 GTGGTTATCACAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* * * *
10646 GTGATTATC-GAATTTTATAGT
1 GAGGTTATCAAAATTTCATAGT
* * * * * * *
10667 GTGGTCACCAACATTTTATCGG
1 GAGGTTATCAAAATTTCATAGT
* * *
10689 GAGGATTATCAAAATTTTACAGG
1 GAGG-TTATCAAAATTTCATAGT
10712 GAGGTTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* * *
10734 AAAGTTATCAAAATTTCTATAAT
1 GAGGTTATCAAAATTTC-ATAGT
* * *
10757 AAGGTTATCAAAATTTCGTAAT
1 GAGGTTATCAAAATTTCATAGT
* * **
10779 GTGTTTATCAAAA-TGAACT-GT
1 GAGGTTATCAAAATTTCA-TAGT
*
10800 GTGGTTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
10822 GAGGTTATCAAAA-TT-ATAAG-
1 GAGGTTATCAAAATTTCAT-AGT
* * *
10842 AAGGTTATCAAAATTTTAAAG-
1 GAGGTTATCAAAATTTCATAGT
* *
10863 GTATG-TATCAAAATTT-AAAGT
1 G-AGGTTATCAAAATTTCATAGT
*
10884 GTGGTTATCAAAATTT
1 GAGGTTATCAAAATTT
10900 GATATGAATA
Statistics
Matches: 679, Mismatches: 153, Indels: 77
0.75 0.17 0.08
Matches are distributed among these distances:
20 20 0.03
21 109 0.16
22 466 0.69
23 82 0.12
24 2 0.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGT
Found at i:10821 original size:155 final size:155
Alignment explanation
Indices: 10539--10822 Score: 333
Period size: 155 Copynumber: 1.8 Consensus size: 155
10529 CATAAGAAGG
* *
10539 TTATCAAAATTTTATAAAGAGATTATCAAAATTTCATAAAAAGGTTTATCAAAATTTAATAAGGA
1 TTATCAAAATTTTACAAAGAGATTATCAAAATTTCATAAAAAGGTTTATCAAAATTTAATAAGAA
* * * ** * *
10604 GATTATCACAATTTCATAGTGTGGTTATCACAATTTCATAGTGTGATTATCGAATTTTATAGTGT
66 GATTATCAAAATTTCATAATGTGGTTATCAAAATAACATAGTGTGATTATCAAATTTCATAGTGT
10669 GGTCACCAACATTTTATCGGGAGGA
131 GGTCACCAACATTTTATCGGGAGGA
** * * * *
10694 TTATCAAAATTTTACAGGGAGGTTATCAAAATTTCATAGTAAA-G-TTATCAAAATTTCTATAAT
1 TTATCAAAATTTTACAAAGAGATTATCAAAATTTCATA-AAAAGGTTTATCAAAATTT-AATAAG
* * * *
10757 AAGGTTATCAAAATTTCGTAATGTGTTTATCAAAATGAAC-T-GTGTGGTTATCAAAATTTCATA
64 AAGATTATCAAAATTTCATAATGTGGTTATCAAAAT-AACATAGTGTGATTATC-AAATTTCATA
10820 GTG
127 GTG
10823 AGGTTATCAA
Statistics
Matches: 106, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
154 22 0.21
155 80 0.75
156 4 0.04
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (155 bp):
TTATCAAAATTTTACAAAGAGATTATCAAAATTTCATAAAAAGGTTTATCAAAATTTAATAAGAA
GATTATCAAAATTTCATAATGTGGTTATCAAAATAACATAGTGTGATTATCAAATTTCATAGTGT
GGTCACCAACATTTTATCGGGAGGA
Found at i:10830 original size:43 final size:44
Alignment explanation
Indices: 10713--10857 Score: 129
Period size: 43 Copynumber: 3.3 Consensus size: 44
10703 TTTTACAGGG
* * **
10713 AGGTTATCAAAATTTCATAGTAAAGTTATCAAAATTTCTATAAT
1 AGGTTATCAAAATTTCATAGTGAGGTTATCAAAATAACTATAAT
* * * * * *
10757 AAGGTTATCAAAATTTCGTAATGTGTTTATCAAAATGAACTGT-GT
1 -AGGTTATCAAAATTTCATAGTGAGGTTATCAAAAT-AACTATAAT
*
10802 -GGTTATCAAAATTTCATAGTGAGGTTATCAAAAT---TATAAGA
1 AGGTTATCAAAATTTCATAGTGAGGTTATCAAAATAACTATAA-T
10843 AGGTTATCAAAATTT
1 AGGTTATCAAAATTT
10858 TAAAGGTATG
Statistics
Matches: 79, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
39 2 0.03
42 14 0.18
43 30 0.38
45 30 0.38
46 3 0.04
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.37
Consensus pattern (44 bp):
AGGTTATCAAAATTTCATAGTGAGGTTATCAAAATAACTATAAT
Found at i:17286 original size:41 final size:43
Alignment explanation
Indices: 17219--17339 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 43
17209 GCCATATAGA
* * * * *
17219 AATTGCCCTTGTGTTATAATTATGTTTATGGACTTTAG-TATAG
1 AATTGCCCCTGTGTTATAAATGTGTTTA-GGACTTTAGAGAGAG
*
17262 -A-TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAGAGAG
1 AATTGCCCCTGTGTTATAAATGTGTTT-AGGACTTTAGAGAGAG
*
17304 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
1 AATTGCCCCTGTGTTATAAATGTGTTT-AGGACTTT
17340 GGGGAGGGAG
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
41 29 0.44
42 5 0.08
43 1 0.02
44 31 0.47
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (43 bp):
AATTGCCCCTGTGTTATAAATGTGTTTAGGACTTTAGAGAGAG
Done.