Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017460.1 Corchorus olitorius cultivar O-4 contig17493, 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: 25445
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1220 original size:21 final size:20
Alignment explanation
Indices: 1178--1227 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
1168 GATTATGTAA
**
1178 ATGCAAAATGTGAAATTCAT
1 ATGCAAAATGTGAAATGAAT
*
1198 ATGCGAAAATGTGATATGAAT
1 ATGC-AAAATGTGAAATGAAT
1219 ATGCAAAAT
1 ATGCAAAAT
1228 AACATAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (20 bp):
ATGCAAAATGTGAAATGAAT
Found at i:1389 original size:27 final size:28
Alignment explanation
Indices: 1323--1395 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
1313 GATGAAGTAG
1323 AAATGACCAAAATGCCCCTGGACATGCA
1 AAATGACCAAAATGCCCCTGGACATGCA
* * *
1351 AAATGACTAAAATACCCCT-GA-ATGCGC
1 AAATGACCAAAATGCCCCTGGACATGC-A
1378 AAATGACCAAAATGCCCC
1 AAATGACCAAAATGCCCC
1396 ATAGATGACC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 4 0.10
27 18 0.46
28 17 0.44
ACGTcount: A:0.41, C:0.29, G:0.15, T:0.15
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGCA
Found at i:5732 original size:9 final size:9
Alignment explanation
Indices: 5708--5747 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
5698 TCAAAGCATA
5708 AAAACAAT-
1 AAAACAATC
5716 -AAAC-ATC
1 AAAACAATC
5723 AAAACAATC
1 AAAACAATC
*
5732 AAAACAAAC
1 AAAACAATC
5741 AAAACAA
1 AAAACAA
5748 AGCAACCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
6 2 0.07
7 4 0.14
8 4 0.14
9 18 0.64
ACGTcount: A:0.72, C:0.20, G:0.00, T:0.07
Consensus pattern (9 bp):
AAAACAATC
Found at i:7522 original size:41 final size:41
Alignment explanation
Indices: 7506--7695 Score: 242
Period size: 41 Copynumber: 4.6 Consensus size: 41
7496 AAATAGTAAG
* * *
7506 TATTAACTTCAATCAAGGACG-AAATTGAACCAATTAAAAGA
1 TATTAACATCAATC-AGGAGGCAAATCGAACCAATTAAAAGA
* *
7547 TAATAACCTCAATCAGG-GAGCAAATCGAACCAATTAAAAGA
1 TATTAACATCAATCAGGAG-GCAAATCGAACCAATTAAAAGA
*
7588 TATTAACATCAATCAGGGGGCAAATCGAACCAATTAAAAGA
1 TATTAACATCAATCAGGAGGCAAATCGAACCAATTAAAAGA
* *
7629 TATTAACATCAATCAGGGGGCAAATCGAACCAATTAAAAAA
1 TATTAACATCAATCAGGAGGCAAATCGAACCAATTAAAAGA
* *
7670 TATCAACCTCAATCAGG-GTGCAAATC
1 TATTAACATCAATCAGGAG-GCAAATC
7696 AAAGAAGAAA
Statistics
Matches: 136, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
40 5 0.04
41 130 0.96
42 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (41 bp):
TATTAACATCAATCAGGAGGCAAATCGAACCAATTAAAAGA
Found at i:9713 original size:87 final size:87
Alignment explanation
Indices: 9592--9812 Score: 273
Period size: 87 Copynumber: 2.5 Consensus size: 87
9582 TAAAGCATTC
* * *
9592 AAAATGCCCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCTTGGATGTGCAAAGATCA
1 AAAATGACCAAAATGCCCTTGAATGTGCAAAAATGACCAAAATGCCCTTGGATGTGCAAACATCA
* *
9657 TCAAAATGCTCCT-AGACATGCA
66 TAAAAATG-TCATGAGACATGCA
* * * * *
9679 AAAATGACCATAGTGTCCTTGAATGTGCAAAAATGACCAAAATGCCCTTGGATGTGTAAACATGA
1 AAAATGACCAAAATGCCCTTGAATGTGCAAAAATGACCAAAATGCCCTTGGATGTGCAAACATCA
* *
9744 TAAAAATGTCATGGGACGTGCA
66 TAAAAATGTCATGAGACATGCA
* * * * *
9766 AATATGATCAAAATGCCCTGGGATGTGCAAAAATGACCAGAATGCCC
1 AAAATGACCAAAATGCCCTTGAATGTGCAAAAATGACCAAAATGCCC
9813 CTGAGTAAGC
Statistics
Matches: 113, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
86 3 0.03
87 110 0.97
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (87 bp):
AAAATGACCAAAATGCCCTTGAATGTGCAAAAATGACCAAAATGCCCTTGGATGTGCAAACATCA
TAAAAATGTCATGAGACATGCA
Found at i:9853 original size:29 final size:29
Alignment explanation
Indices: 9592--9863 Score: 226
Period size: 29 Copynumber: 9.4 Consensus size: 29
9582 TAAAGCATTC
* * *
9592 AAAATGCCCAAAATGCCCCTGAATGTGCA
1 AAAATGACCAAAATGCCCTTGGATGTGCA
9621 AAAATGACCAAAATGCCCTTGGATGTGCA
1 AAAATGACCAAAATGCCCTTGGATGTGCA
* * * * **
9650 AAGATCATCAAAATGCTCC-TAGACATGCA
1 AAAATGACCAAAATGC-CCTTGGATGTGCA
* * * *
9679 AAAATGACCATAGTGTCCTTGAATGTGCA
1 AAAATGACCAAAATGCCCTTGGATGTGCA
*
9708 AAAATGACCAAAATGCCCTTGGATGTGTA
1 AAAATGACCAAAATGCCCTTGGATGTGCA
* ** * * * *
9737 AACATGATAAAAATGTCATGGGACGTGCA
1 AAAATGACCAAAATGCCCTTGGATGTGCA
* * *
9766 AATATGATCAAAATGCCCTGGGATGTGCA
1 AAAATGACCAAAATGCCCTTGGATGTGCA
* *
9795 AAAATGACCAGAATGCCCCT-GA-GTAAGCA
1 AAAATGACCAAAATGCCCTTGGATGT--GCA
* **
9824 AAAATGACCAGAATGCCCTTGGACATGCA
1 AAAATGACCAAAATGCCCTTGGATGTGCA
*
9853 AATATGACCAA
1 AAAATGACCAA
9864 TTAAGAAAAA
Statistics
Matches: 191, Mismatches: 46, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
27 2 0.01
28 4 0.02
29 180 0.94
30 4 0.02
31 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCTTGGATGTGCA
Found at i:11491 original size:2 final size:2
Alignment explanation
Indices: 11484--11513 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11474 TTAGTTGGGC
11484 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
11514 GTTCATTTGA
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:13666 original size:41 final size:41
Alignment explanation
Indices: 13621--13716 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
13611 ATTCAATCAG
** *
13621 GTCCCTAATTTA-AGCTGTTATTTATTCAATGATTTAATTTT
1 GTCCCTAATTTAGAG-TAATATTTATTCAATGATTCAATTTT
* *
13662 GTCCCTAATTTAGAGTAATATTTATTTATTGATTCAATTTT
1 GTCCCTAATTTAGAGTAATATTTATTCAATGATTCAATTTT
*
13703 GTCCCTGATTTAGA
1 GTCCCTAATTTAGA
13717 ATTTTATTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.49
Consensus pattern (41 bp):
GTCCCTAATTTAGAGTAATATTTATTCAATGATTCAATTTT
Found at i:16933 original size:18 final size:19
Alignment explanation
Indices: 16910--16946 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
16900 CACCCTAGCC
16910 CTAGAACTAGAAGA-AAAA
1 CTAGAACTAGAAGAGAAAA
16928 CTAGAACTAGAAGAGAAAA
1 CTAGAACTAGAAGAGAAAA
16947 TTATCTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.59, C:0.11, G:0.19, T:0.11
Consensus pattern (19 bp):
CTAGAACTAGAAGAGAAAA
Found at i:17566 original size:19 final size:18
Alignment explanation
Indices: 17533--17568 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17523 TCGAGATAAT
17533 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
17551 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
17569 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:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:19894 original size:17 final size:18
Alignment explanation
Indices: 19863--19896 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19853 CCTCTTGCAC
*
19863 GAAAACACTTCTTTTTAT
1 GAAAACAATTCTTTTTAT
19881 GAAAACAATT-TTTTTA
1 GAAAACAATTCTTTTTA
19897 CTACCCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (18 bp):
GAAAACAATTCTTTTTAT
Found at i:22291 original size:15 final size:16
Alignment explanation
Indices: 22257--22291 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
22247 TTTGCTTTGC
22257 ATTGTTTTCTAGTATA
1 ATTGTTTTCTAGTATA
*
22273 ATTGTTTTCT-GTTTA
1 ATTGTTTTCTAGTATA
22288 ATTG
1 ATTG
22292 CTTCCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.60
Consensus pattern (16 bp):
ATTGTTTTCTAGTATA
Found at i:22714 original size:26 final size:27
Alignment explanation
Indices: 22676--22726 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
22666 GCGCCTTTGA
22676 AAAAAAAAGAGTTTTCGT-TTTTGCGAT
1 AAAAAAAAGAGTTTT-GTGTTTTGCGAT
22703 AAAAAAAA-AGTTTTGTGTTTTGCG
1 AAAAAAAAGAGTTTTGTGTTTTGCG
22727 TCAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 2 0.09
26 13 0.57
27 8 0.35
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (27 bp):
AAAAAAAAGAGTTTTGTGTTTTGCGAT
Found at i:22773 original size:27 final size:28
Alignment explanation
Indices: 22743--22802 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
22733 AAAAAAAAAG
* *
22743 GTTTTTGCGTCATAAAA-AAATTTTTTT
1 GTTTTTGCGTCAAAAAATAAATATTTTT
*
22770 GTTTCTGCGTCAAAAAATAAATATTTTT
1 GTTTTTGCGTCAAAAAATAAATATTTTT
*
22798 CTTTT
1 GTTTT
22803 ATTTTCTGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (28 bp):
GTTTTTGCGTCAAAAAATAAATATTTTT
Done.