Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022114.1 Corchorus olitorius cultivar O-4 contig22147, 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: 33105
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:2170 original size:27 final size:27
Alignment explanation
Indices: 2130--2206 Score: 145
Period size: 27 Copynumber: 2.9 Consensus size: 27
2120 CATTTTGCAC
2130 ACTCAGGGGCATTTTGGTCATTTATGT
1 ACTCAGGGGCATTTTGGTCATTTATGT
*
2157 ACTCAGGGGTATTTTGGTCATTTATGT
1 ACTCAGGGGCATTTTGGTCATTTATGT
2184 ACTCAGGGGCATTTTGGTCATTT
1 ACTCAGGGGCATTTTGGTCATTT
2207 TGCATGCTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.18, C:0.14, G:0.26, T:0.42
Consensus pattern (27 bp):
ACTCAGGGGCATTTTGGTCATTTATGT
Found at i:4192 original size:17 final size:18
Alignment explanation
Indices: 4170--4203 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4160 ATCCAACGAA
*
4170 AACTGAATAA-GAAAATT
1 AACTGAAAAAGGAAAATT
4187 AACTGAAAAAGGAAAAT
1 AACTGAAAAAGGAAAAT
4204 AAAAAGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.06, G:0.15, T:0.18
Consensus pattern (18 bp):
AACTGAAAAAGGAAAATT
Found at i:18990 original size:19 final size:18
Alignment explanation
Indices: 18957--18992 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18947 TGGAAATAAT
18957 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
18975 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
18993 CAAGTCTTCA
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:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:20215 original size:120 final size:118
Alignment explanation
Indices: 20083--20465 Score: 628
Period size: 120 Copynumber: 3.2 Consensus size: 118
20073 CCCTTTCTGC
*
20083 TTTT-AAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTCAATTCAAAAATCTTGTTTTGTTTTT
1 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAG-TTTTCAATTC-AAAATCTTGTCTTGTTTTT
*
20147 AAAATCCTGTTGAAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGCCTTGT
64 AAAATCCTGTTGAAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGTCTTGT
20202 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAA
1 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAA
*
20267 AATCCTGATCG-AGGTCTCTGGTAGAGAGTTTTTCAATTCAAAAATCTTGTCTTGT
66 AATCCTG-TTGAAGGTCTCTGGTAGAGAGTTTTT-AATTC-AAAATCTTGTCTTGT
* * *
20322 TTTTAAAATCGTGATCGAGGTCTTTGTTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAA
1 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAA
*
20387 AATCCTGTTCGAA-GTCTCTGGTAGAGAGTTTTTATTTCAAAATCTTGTCTTGT
66 AATCCTGTT-GAAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGTCTTGT
20440 TTTTAAAATCCTGATCGAGGTCTCTG
1 TTTTAAAATCCTGATCGAGGTCTCTG
20466 ATTGAGACAA
Statistics
Matches: 248, Mismatches: 10, Indels: 13
0.92 0.04 0.05
Matches are distributed among these distances:
118 88 0.35
119 26 0.10
120 133 0.54
121 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (118 bp):
TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAA
AATCCTGTTGAAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGTCTTGT
Found at i:20223 original size:59 final size:59
Alignment explanation
Indices: 20083--20465 Score: 608
Period size: 59 Copynumber: 6.4 Consensus size: 59
20073 CCCTTTCTGC
*
20083 TTTT-AAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTCAATTCAAAAATCTTGTTTTGT
1 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTT-AATTC-AAAATCTTGTCTTGT
* *
20143 TTTTAAAATCCTG-TTGAAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGCCTTGT
1 TTTTAAAATCCTGATCG-AGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGTCTTGT
*
20202 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGT
1 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGTCTTGT
20261 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTCAATTCAAAAATCTTGTCTTGT
1 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTT-AATTC-AAAATCTTGTCTTGT
* * * *
20322 TTTTAAAATCGTGATCGAGGTCTTTGTTAGAGAGTTTTCAATTCAAAATCTTGTCTTGT
1 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGTCTTGT
* * *
20381 TTTTAAAATCCTGTTCGAAGTCTCTGGTAGAGAGTTTTTATTTCAAAATCTTGTCTTGT
1 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGTCTTGT
20440 TTTTAAAATCCTGATCGAGGTCTCTG
1 TTTTAAAATCCTGATCGAGGTCTCTG
20466 ATTGAGACAA
Statistics
Matches: 298, Mismatches: 20, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
59 195 0.65
60 23 0.08
61 80 0.27
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (59 bp):
TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGTCTTGT
Found at i:20387 original size:179 final size:179
Alignment explanation
Indices: 20083--20465 Score: 644
Period size: 179 Copynumber: 2.1 Consensus size: 179
20073 CCCTTTCTGC
*
20083 TTTT-AAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTCAATTCAAAAATCTTGTTTTGTTTTT
1 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTCAATTCAAAAATCTTGTCTTGTTTTT
* *
20147 AAAATCCTGTTGAAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGCCTTGTTTTTAAAATC
66 AAAATCCTGTCGAAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGCCTTGTTTTTAAAATC
*
20212 CTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGT
131 CTGATCGAAGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGT
20261 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTCAATTCAAAAATCTTGTCTTGTTTTT
1 TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTCAATTCAAAAATCTTGTCTTGTTTTT
* * * *
20326 AAAATCGTGATCG-AGGTCTTTGTTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAAT
66 AAAATCCTG-TCGAAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGCCTTGTTTTTAAAAT
* * *
20390 CCTGTTCGAAGTCTCTGGTAGAGAGTTTTTATTTCAAAATCTTGTCTTGT
130 CCTGATCGAAGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGT
20440 TTTTAAAATCCTGATCGAGGTCTCTG
1 TTTTAAAATCCTGATCGAGGTCTCTG
20466 ATTGAGACAA
Statistics
Matches: 192, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
178 4 0.02
179 186 0.97
180 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (179 bp):
TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTTCAATTCAAAAATCTTGTCTTGTTTTT
AAAATCCTGTCGAAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGCCTTGTTTTTAAAATC
CTGATCGAAGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGT
Found at i:21345 original size:11 final size:11
Alignment explanation
Indices: 21329--21354 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21319 AGATAATTTC
21329 TTTTCTTCTAG
1 TTTTCTTCTAG
21340 TTTTCTTCTAG
1 TTTTCTTCTAG
21351 TTTT
1 TTTT
21355 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:22134 original size:15 final size:15
Alignment explanation
Indices: 22104--22145 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
22094 TTACTTTGCT
22104 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
22120 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
22135 TTGCTTTCTGT
1 TTGTTTTCTGT
22146 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:22450 original size:59 final size:59
Alignment explanation
Indices: 22303--22439 Score: 204
Period size: 59 Copynumber: 2.3 Consensus size: 59
22293 CGACCGATCA
* *
22303 GTCTCTGGTAGAGAGTTTTCAATTCAAAATCATGTCTTGTTTTTAAAATCCTAATCGAG
1 GTCTCTGGTAGAGAGTTTTCAATTCAAAATCATATCTTGCTTTTAAAATCCTAATCGAG
* * *
22362 GTCTCTGGTAGACAGTTTTCAATTCAAAATCCTATCTTGCTTTT-AAATCCTATTCGAG
1 GTCTCTGGTAGAGAGTTTTCAATTCAAAATCATATCTTGCTTTTAAAATCCTAATCGAG
* *
22420 GTCTTTGGTAAAGAGTTTTC
1 GTCTCTGGTAGAGAGTTTTC
22440 TATTTTAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 30 0.43
59 40 0.57
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (59 bp):
GTCTCTGGTAGAGAGTTTTCAATTCAAAATCATATCTTGCTTTTAAAATCCTAATCGAG
Found at i:22934 original size:17 final size:15
Alignment explanation
Indices: 22899--22940 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
22889 TGGACTTTCT
22899 AAAA-TAAAATAAAA
1 AAAATTAAAATAAAA
22913 AAAATTAAAAGTAAAA
1 AAAATTAAAA-TAAAA
*
22929 ACAAATTTAAAT
1 A-AAATTAAAAT
22941 TTTTTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.17
15 5 0.21
16 7 0.29
17 8 0.33
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATTAAAATAAAA
Found at i:24722 original size:28 final size:27
Alignment explanation
Indices: 24689--24784 Score: 124
Period size: 27 Copynumber: 3.6 Consensus size: 27
24679 TGTTTCTTAA
*
24689 TTGGTCATTT-TGCACACTTAGGGGCATT
1 TTGGTCATTTATG--CACTCAGGGGCATT
* *
24717 TGGGTCATTTATGCACTGAGGGGCATT
1 TTGGTCATTTATGCACTCAGGGGCATT
*
24744 TTGGTCATTTGTGCACTCAGGGGCATT
1 TTGGTCATTTATGCACTCAGGGGCATT
24771 TTGGTCATTT-TGCA
1 TTGGTCATTTATGCA
24785 TGCTCTAGGT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
26 4 0.06
27 47 0.76
28 9 0.15
29 2 0.03
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (27 bp):
TTGGTCATTTATGCACTCAGGGGCATT
Found at i:29850 original size:23 final size:23
Alignment explanation
Indices: 29796--29850 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
29786 ACACTTTAAT
*
29796 TTCTATTTTTAATTTGTTCTATC
1 TTCTATTTTTAATTTGTTCGATC
*
29819 TTTTATTTTT-ATTTCGTTCGATC
1 TTCTATTTTTAATTT-GTTCGATC
*
29842 TTCTCTTTT
1 TTCTATTTT
29851 CTTTGATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.13, C:0.15, G:0.05, T:0.67
Consensus pattern (23 bp):
TTCTATTTTTAATTTGTTCGATC
Done.