Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009973.1 Corchorus olitorius cultivar O-4 contig10005, 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: 6767
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Found at i:632 original size:58 final size:58
Alignment explanation
Indices: 562--1100 Score: 686
Period size: 58 Copynumber: 9.2 Consensus size: 58
552 TCACATGAAT
* * ** * *
562 TGTCTTCAGATCCATTTGTGGGCTGTCTTCA-CACCCATTCTTTAAAAT-TTGTAGGAAC
1 TGTCTTCAGATCCATCTGTGAGCTGTCTTCAGC-CTTAATC-TTAAAATCTTTTAGGAAC
* * *
620 TGTCTTCAGATCCATCTGTGTGCTGTCTTCAGCCTTAATTTTAAAATTTTTTAGGAAC
1 TGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAAC
* * * *
678 TGTCTTCAGATCCATTTCTGTGAGCTGTCTTCAGTCTCAATTTTAAAAAATATTTTAGGAAC
1 TGTCTTCAGATCCA--TCTGTGAGCTGTCTTCAGCCTTAATCTT--AAAATCTTTTAGGAAC
* * * *
740 TGTCTTCAAAACCATCTGTGAGCCGTCTTCAGCCTTAATCTTAAAATCTCTTAGGAAC
1 TGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAAC
* *
798 TGCCTTCAGATCCATCTGTGAGCTGTCTTCAGCTTTAATCTTAAAATCTTTTAGGAAC
1 TGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAAC
* * * *
856 TGTCCTCATATCCATTTGTGAGCTGTCTTCAGCCTTAATCTTAAAGTCTTTTAGGAAC
1 TGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAAC
* *
914 TGTCTTCAGATCCATCTGTAAGCTGTCTTCAGCCTTAATCTTAAAATCTTTTTGGAAC
1 TGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAAC
* * * **** **
972 TGTCTTCAGATCTATCTGTGAGCTGTCTTCAGTCTCAAAAAAAAAAAATTTTAGGAAC
1 TGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAAC
* *
1030 TGTCTTCAGATCCATCCGTGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTAAGGAAC
1 TGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAAC
1088 TGTCTTCAGATCC
1 TGTCTTCAGATCC
1101 GTCTCTGATG
Statistics
Matches: 416, Mismatches: 59, Indels: 12
0.85 0.12 0.02
Matches are distributed among these distances:
57 7 0.02
58 332 0.80
59 1 0.00
60 49 0.12
62 27 0.06
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (58 bp):
TGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAAC
Found at i:2240 original size:22 final size:23
Alignment explanation
Indices: 2215--2267 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
2205 TTTAGGCTAA
* *
2215 ATTTTTTTATTTTTTTTA-ATTT
1 ATTTTTTTATTTTTTATATATAT
*
2237 ATTTATTTATTTTTTATATATAT
1 ATTTTTTTATTTTTTATATATAT
2260 ATTTTTTT
1 ATTTTTTT
2268 CGGGCGTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (23 bp):
ATTTTTTTATTTTTTATATATAT
Found at i:2557 original size:1 final size:1
Alignment explanation
Indices: 2542--2607 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
2532 TTTGTTTGTG
* * * * * * * * *
2542 TTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTGTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2607 T
1 T
2608 GCGACCCGGT
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (1 bp):
T
Found at i:2607 original size:6 final size:6
Alignment explanation
Indices: 2525--2604 Score: 114
Period size: 6 Copynumber: 13.8 Consensus size: 6
2515 CCTGTCGCAA
*
2525 TTTTTG -TTTTG TTTGTG -TTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
2571 TTTTTG TTTTTG TTTTTG TTGTTT- TTTTT- TTTTT
1 TTTTTG TTTTTG TTTTTG TT-TTTG TTTTTG TTTTT
2605 TTTGCGACCC
Statistics
Matches: 69, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
5 17 0.25
6 49 0.71
7 3 0.04
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:6480 original size:41 final size:41
Alignment explanation
Indices: 6435--6721 Score: 255
Period size: 41 Copynumber: 6.9 Consensus size: 41
6425 TAAAATCTTT
* *
6435 GATGGGATCTTTCCCTTAATTGAAAACTTCGAAAAAGACTA
1 GATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGACTA
* *
6476 GATGGGATCTTTCCCTAAATTGAAAATTTTGAAGAAGACTA
1 GATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGACTA
** ** * *
6517 GATGGGATCTTTCCCTAAATT-AAAGGTTTTTGAAAACTATTT
1 GATGGGATCTTTCCCTAAATTGAAA--ACTTTGAAAAAGACTA
* * *
6559 GAAGGGATCTTTCCCTATA-TGAAAATCTTTGTAAAAAATACTTTA
1 GATGGGATCTTTCCCTAAATTGAAAA-CTTTG--AAAAAGAC--TA
* *
6604 G-TGGGATCTTTCCCTAATCTTGAAATCTTTGAAGAAAATGACTA
1 GATGGGATCTTTCCCTAA-ATTGAAAACTTTG-A-AAAA-GACTA
*
6648 GATGGGATCTTTCCCTAAATT-AAAACTTCTG-AAAA-ACTT
1 GATGGGATCTTTCCCTAAATTGAAAACTT-TGAAAAAGACTA
* *
6687 GATGGGATCTTTCCCTGAATT-AAAACTTCGAAAAA
1 GATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAA
6722 TACTTTGGCG
Statistics
Matches: 204, Mismatches: 27, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
38 1 0.00
39 34 0.17
40 3 0.01
41 67 0.33
42 30 0.15
43 12 0.06
44 23 0.11
45 27 0.13
46 7 0.03
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (41 bp):
GATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGACTA
Done.