Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020911.1 Corchorus olitorius cultivar O-4 contig20944, 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: 3556
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Found at i:645 original size:17 final size:18
Alignment explanation
Indices: 606--645 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
596 ATTTAGAGAT
606 AGAAAAAAGAAAAAATCC
1 AGAAAAAAGAAAAAATCC
624 A-AAAAAATG-AAAAAT-C
1 AGAAAAAA-GAAAAAATCC
640 AGAAAA
1 AGAAAA
646 TCAAAAGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.10
17 16 0.80
18 2 0.10
ACGTcount: A:0.75, C:0.07, G:0.10, T:0.07
Consensus pattern (18 bp):
AGAAAAAAGAAAAAATCC
Found at i:1392 original size:36 final size:36
Alignment explanation
Indices: 1334--1874 Score: 617
Period size: 36 Copynumber: 15.4 Consensus size: 36
1324 GTGGTCCTAT
*
1334 TTCAGTTTATTTCAGTTTGATCCAGGGTGATCTTTTC
1 TTCAGTTTATTTCAG-TTGATCCAGGGCGATCTTTTC
* * *
1371 TTCATTTTACTTCAGTTGATCCAGGGCGATCCTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
** * * * * *
1407 TTCAGTTTATTTTTGTTGACCCAGGGTGGTCCTAT-
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
*
1442 TTCAG-----TT-A---GATCCAGGGTGATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* *
1469 TTCATTTTACTTT-AGTTGATCCAGGGCGATCCTTTC
1 TTCAGTTTA-TTTCAGTTGATCCAGGGCGATCTTTTC
* * *
1505 TTCAGTTTATTT-ATGTTGACCCAGGGCGGTTTTTTC
1 TTCAGTTTATTTCA-GTTGATCCAGGGCGATCTTTTC
*
1541 TTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* * *
1577 TTCAGTTTATTTCAGTTGACCCATGGCGGTC-TTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
1612 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* *
1648 TTCAGTTTATTTCAATTGATCCAGGGCGGTC-TTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* *
1683 TTCAATTTATTTCAGTTGATCTAGGGCGATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* * *
1719 TTCAATTTATTTCAATTGATGCAGGGCGATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
*
1755 TTCAGTTTATTTCACTTGATCCAGGGCGATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* *
1791 TTCAGTTTATTTCAATTGATCCAGGACGATC-TTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* * * * *
1826 CTCAATTTACTTCAGTAGATCCAGGGCGATCTTCTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
*
1862 TGCAGTTTATTTC
1 TTCAGTTTATTTC
1875 GATTGACTGC
Statistics
Matches: 429, Mismatches: 60, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
26 14 0.03
27 4 0.01
30 2 0.00
33 3 0.01
35 101 0.24
36 291 0.68
37 14 0.03
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (36 bp):
TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
Found at i:1472 original size:98 final size:100
Alignment explanation
Indices: 1340--1834 Score: 394
Period size: 107 Copynumber: 4.8 Consensus size: 100
1330 CTATTTCAGT
1340 TTATTTCAGTTTGATCCAGGGTGATCTTTTCTTCATTTTACTTCAGTTGATCCAGGGCGATCCTT
1 TTATTTCAG-TTGATCCAGGGTGATCTTTTCTTCATTTTACTTCAGTTGATCCAGGGCGATCCTT
* *
1405 TCTTCAGTTTATTTTTGTTGACCCAGGGTGG-TC-C
65 TCTTCAGTTTATTTATGTTGACCCAGGGCGGTTCTC
*
1439 -TATTTCAGTTAGATCCAGGGTGATCTTTTCTTCATTTTACTTTAGTTGATCCAGGGCGATCCTT
1 TTATTTCAGTT-GATCCAGGGTGATCTTTTCTTCATTTTACTTCAGTTGATCCAGGGCGATCCTT
1503 TCTTCAGTTTATTTATGTTGACCCAGGGCGGTTTTTTCTTC
65 TCTTCAGTTTATTTATGTTGACCCAGGGCGG----TTC-TC
* * * * * * *
1544 AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCATGGCGGT-C
1 ---TTATTTCAGTTGATCCAGGGTGATCTTTTCTTCATTTTACTTCAGTTGATCCAGGGCGATCC
* *
1608 TTTCTTCAGTTTATTTCA-GTTGATCCAGGGCGATCTTTTCTTC
63 TTTCTTCAGTTTATTT-ATGTTGACCCAGGGCG----GTTC-TC
* * * * * * *
1651 AGTTTATTTCAATTGATCCAGGGCGGTC-TTTCTTCAATTTATTTCAGTTGATCTAGGGCGATCT
1 ---TTATTTCAGTTGATCCAGGGTGATCTTTTCTTCATTTTACTTCAGTTGATCCAGGGCGATCC
* * ** *
1715 TTTCTTCAATTTATTTCA-ATTGATGCAGGGCGATCTTTTCTTC
63 TTTCTTCAGTTTATTT-ATGTTGACCCAGGGCG----GTTC-TC
* * * * * *
1758 AGTTTATTTCACTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGACGAT-C
1 ---TTATTTCAGTTGATCCAGGGTGATCTTTTCTTCATTTTACTTCAGTTGATCCAGGGCGATCC
* *
1822 TTTCCTCAATTTA
63 TTTCTTCAGTTTA
1835 CTTCAGTAGA
Statistics
Matches: 345, Mismatches: 32, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
97 2 0.01
98 89 0.26
103 2 0.01
105 1 0.00
106 29 0.08
107 140 0.41
108 72 0.21
109 10 0.03
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (100 bp):
TTATTTCAGTTGATCCAGGGTGATCTTTTCTTCATTTTACTTCAGTTGATCCAGGGCGATCCTTT
CTTCAGTTTATTTATGTTGACCCAGGGCGGTTCTC
Found at i:1636 original size:107 final size:107
Alignment explanation
Indices: 1439--1874 Score: 572
Period size: 107 Copynumber: 4.1 Consensus size: 107
1429 AGGGTGGTCC
* * *
1439 TATTTCAGTTAGATCCAGGGTGATCTTTTCTTCATTTTACTTT-AGTTGATCCAGGGCGATCCTT
1 TATTTCAGTT-GATCCAGGGCGATCCTTTCTTCAGTTTA-TTTCAGTTGATCCAGGGCGAT-CTT
* * * *
1503 TCTTCAGTTTATTT-ATGTTGACCCAGGGCGGTTTTTTCTTCAGTT
63 TCTTCAATTTATTTCA-GTTGATCCAGGGCGATCTTTTCTTCAGTT
* * *
1548 TATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCATGGCGGTCTTTCT
1 TATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTCT
*
1613 TCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTT
66 TCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTT
* * * *
1655 TATTTCAATTGATCCAGGGCGGT-CTTTCTTCAATTTATTTCAGTTGATCTAGGGCGATCTTTTC
1 TATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATC-TTTC
* *
1719 TTCAATTTATTTCAATTGATGCAGGGCGATCTTTTCTTCAGTT
65 TTCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTT
* * * * *
1762 TATTTCACTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGACGATCTTTCC
1 TATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTCT
* * * *
1827 TCAATTTACTTCAGTAGATCCAGGGCGATCTTCTCTGCAGTT
66 TCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTT
1869 TATTTC
1 TATTTC
1875 GATTGACTGC
Statistics
Matches: 290, Mismatches: 33, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
106 31 0.11
107 178 0.61
108 71 0.24
109 10 0.03
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (107 bp):
TATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTCT
TCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTT
Found at i:1653 original size:71 final size:71
Alignment explanation
Indices: 1439--1880 Score: 573
Period size: 71 Copynumber: 6.2 Consensus size: 71
1429 AGGGTGGTCC
* * * * *
1439 TATTTCAGTTAGATCCAGGGTGATCTTTTCTTCATTTTACTTT-AGTTGATCCAGGGCGATCCTT
1 TATTTCAATT-GATCCAGGGCGGTC-TTTCTTCAGTTTA-TTTCAGTTGATCCAGGGCGATCTTT
1503 TCTTCAGTT
63 TCTTCAGTT
* * * *
1512 TATTT-ATGTTGACCCAGGGCGGTTTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTT
1 TATTTCA-ATTGATCCAGGGCGG-TCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
1576 CTTCAGTT
64 CTTCAGTT
* * *
1584 TATTTCAGTTGACCCATGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCT
1 TATTTCAATTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCT
1649 TCAGTT
66 TCAGTT
* *
1655 TATTTCAATTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGATCTAGGGCGATCTTTTCT
1 TATTTCAATTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCT
*
1720 TCAATT
66 TCAGTT
* * *
1726 TATTTCAATTGATGCAGGGCGATCTTTTCTTCAGTTTATTTCACTTGATCCAGGGCGATCTTTTC
1 TATTTCAATTGATCCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
1791 TTCAGTT
65 TTCAGTT
* * * * * * *
1798 TATTTCAATTGATCCAGGACGATCTTTCCTCAATTTACTTCAGTAGATCCAGGGCGATCTTCTCT
1 TATTTCAATTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCT
*
1863 GCAGTT
66 TCAGTT
*
1869 TATTTCGATTGA
1 TATTTCAATTGA
1881 CTGCAAAATG
Statistics
Matches: 334, Mismatches: 30, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
71 188 0.56
72 136 0.41
73 10 0.03
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (71 bp):
TATTTCAATTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCT
TCAGTT
Found at i:1755 original size:143 final size:143
Alignment explanation
Indices: 1439--1880 Score: 602
Period size: 143 Copynumber: 3.1 Consensus size: 143
1429 AGGGTGGTCC
* * * *
1439 TATTTCAGTTAGATCCAGGGTGATCTTTTCTTCATTTTACTTT-AGTTGATCCAGGGCGATCCTT
1 TATTTCAATT-GATCCAGGGCGATCTTTTCTTCAGTTTA-TTTCAGTTGATCCAGGGCGATCTTT
* * * *
1503 TCTTCAGTTTATTT-ATGTTGACCCAGGGCGGTTTTTTCTTCAGTTTATTTCAGTTGATCCAGGG
64 TCTTCAGTTTATTTCA-ATTGATCCAGGGCGG-TCTTTCTTCAATTTATTTCAGTTGATCCAGGG
*
1567 CGATCCTTTCTTCAGTT
127 CGATCTTTTCTTCAGTT
* * * *
1584 TATTTCAGTTGACCCATGGCGGTC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
1 TATTTCAATTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
*
1648 TTCAGTTTATTTCAATTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGATCTAGGGCGAT
66 TTCAGTTTATTTCAATTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGATCCAGGGCGAT
*
1713 CTTTTCTTCAATT
131 CTTTTCTTCAGTT
* *
1726 TATTTCAATTGATGCAGGGCGATCTTTTCTTCAGTTTATTTCACTTGATCCAGGGCGATCTTTTC
1 TATTTCAATTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* * * * *
1791 TTCAGTTTATTTCAATTGATCCAGGACGATCTTTCCTCAATTTACTTCAGTAGATCCAGGGCGAT
66 TTCAGTTTATTTCAATTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGATCCAGGGCGAT
* *
1856 CTTCTCTGCAGTT
131 CTTTTCTTCAGTT
*
1869 TATTTCGATTGA
1 TATTTCAATTGA
1881 CTGCAAAATG
Statistics
Matches: 265, Mismatches: 29, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
142 66 0.25
143 178 0.67
144 11 0.04
145 10 0.04
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (143 bp):
TATTTCAATTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
TTCAGTTTATTTCAATTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGATCCAGGGCGAT
CTTTTCTTCAGTT
Found at i:2185 original size:30 final size:30
Alignment explanation
Indices: 2144--2981 Score: 953
Period size: 30 Copynumber: 28.1 Consensus size: 30
2134 TTTTATCAGT
* *
2144 TTTATTCTAATCCTGTTTGAGGATCATT-A
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
2173 TCTTATGTTAATCCTGCTTGAGGATCATTGC
1 T-TTATTTTAATCCTGTTTGAGGATCATTGC
* *
2204 TTTATTTTAATCCTGTTTGAGGAGCACTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * *
2234 TTTGTGTTAATCCTGTTTGGGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
2264 TTTATGTTAATCCTCG-TTGAGGATCGTTGC
1 TTTATTTTAATCCT-GTTTGAGGATCATTGC
* *
2294 -----TTT-ATCCTGTTTGAGGATCAATCC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
2318 TTAATTTTAATCATGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * *
2348 TTCATTTTAATCCTGGTTGAGGATCAATGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
2378 TTTATTTTAATTCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
2408 TTCATTTTTAATCCTGTTTGAGGATCATTGC
1 TTTA-TTTTAATCCTGTTTGAGGATCATTGC
* * * *
2439 TTCATTTTAATCCTGGTTGACGATCAATGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
2469 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
2499 TTTATGTTAATCCTGTTTAAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * * *
2529 TTCATGTTAATCCTGGTTGAGGATCAATGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
2559 TTTATTTTAATCCTGTTTGAGAATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
2589 TTTATTTTAATCCTGTTTGAGGATCATTAC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
2619 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
2649 TTTATTGTAATCGTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
2679 TTTATGTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * **
2709 TTTATTCTAATCCTGGTTGAGGATCATCAC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
2739 TTCATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
2769 TTTATTTTAATCCTGGTTAAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
2799 TTCATTTTAATCCTGATTGAGGAT-ATTCGC
1 TTTATTTTAATCCTGTTTGAGGATCATT-GC
** * *
2829 TCCATTTTAATCTTGGTTGAGGAT-ATTTGC
1 TTTATTTTAATCCTGTTTGAGGATCA-TTGC
* * * **
2859 ATCATTTTAATCCTGGTTGAGGATTGTTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * * *
2889 TTTATTTTAATCATGGTTGAAGACCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
2919 TTTATTTTAATCCT-TGTTGAGGATCATCGC
1 TTTATTTTAATCCTGT-TTGAGGATCATTGC
* * * *
2949 TATATTTTTATCCTGATTT-AGGATTATTAC
1 TTTATTTTAATCCTG-TTTGAGGATCATTGC
2979 TTT
1 TTT
2982 GGTTTATTTG
Statistics
Matches: 694, Mismatches: 98, Indels: 33
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.00
24 16 0.02
25 2 0.00
29 7 0.01
30 632 0.91
31 35 0.05
32 1 0.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (30 bp):
TTTATTTTAATCCTGTTTGAGGATCATTGC
Found at i:3481 original size:27 final size:26
Alignment explanation
Indices: 3443--3499 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
3433 TTTCCAAAAA
*
3443 TTCAGGGGCATTTTGGTCATTTGTACG
1 TTCAGGGGCATTTAGGTCATTT-TACG
*
3470 TTCAGGGGCATTTAGGTCATTTTAGG
1 TTCAGGGGCATTTAGGTCATTTTACG
3496 TTCA
1 TTCA
3500 CTTTTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.18, C:0.14, G:0.28, T:0.40
Consensus pattern (26 bp):
TTCAGGGGCATTTAGGTCATTTTACG
Done.