Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011834.1 Corchorus olitorius cultivar O-4 contig11867, 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: 3645
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Found at i:249 original size:76 final size:73
Alignment explanation
Indices: 109--255 Score: 197
Period size: 76 Copynumber: 2.0 Consensus size: 73
99 ATCTGGACTA
*
109 TGAACAAAGGAATGATGAGTTTTAATCAAAGTTTTCAAAAAATCAGTCTTAATCAAAACTATGAT
1 TGAACAAAGGAATGATGAGTTTTAATCAAAGTTTTC-AAAAATCAGTCTTAATCAAAACAATGAT
174 TTCGAGTTG
65 TTCGAGTTG
* * **
183 TGAACAAAGGAATGATGGTGTTTTAATCAAAAGATGTTTC-AAAATCAGTTTTGGTCAAAACAAT
1 TGAACAAAGGAATGAT-GAGTTTTAATC-AAAG-T-TTTCAAAAATCAGTCTTAATCAAAACAAT
247 GATTTCGAG
62 GATTTCGAG
256 GTAACCGAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
74 16 0.25
75 10 0.16
76 33 0.52
77 1 0.02
78 4 0.06
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.32
Consensus pattern (73 bp):
TGAACAAAGGAATGATGAGTTTTAATCAAAGTTTTCAAAAATCAGTCTTAATCAAAACAATGATT
TCGAGTTG
Found at i:672 original size:15 final size:14
Alignment explanation
Indices: 652--681 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
642 AAAAAAAATG
652 AATGAAAATTGAAAA
1 AATGAAAA-TGAAAA
667 AATGAAAATGAAAA
1 AATGAAAATGAAAA
681 A
1 A
682 GGAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (14 bp):
AATGAAAATGAAAA
Found at i:686 original size:21 final size:19
Alignment explanation
Indices: 644--687 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
634 AAATCAATAA
**
644 AAAAAATGAATGAAAATTG
1 AAAAAATGAATGAAAAAGG
663 AAAAAATGAAAATGAAAAAGG
1 AAAAAATG--AATGAAAAAGG
684 AAAA
1 AAAA
688 TAAAGGCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
21 13 0.62
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (19 bp):
AAAAAATGAATGAAAAAGG
Found at i:1080 original size:5 final size:5
Alignment explanation
Indices: 1072--1118 Score: 60
Period size: 5 Copynumber: 9.0 Consensus size: 5
1062 AAAAAAAAAC
1072 TCAAA TCAAA GTC-AA TCAAA TCAAAA TCAAA TCAAA TCAAAA TCAAA
1 TCAAA TCAAA -TCAAA TCAAA TC-AAA TCAAA TCAAA TC-AAA TCAAA
1119 AGAGAATCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 2 0.05
5 24 0.63
6 12 0.32
ACGTcount: A:0.60, C:0.19, G:0.02, T:0.19
Consensus pattern (5 bp):
TCAAA
Found at i:1090 original size:31 final size:31
Alignment explanation
Indices: 1055--1117 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
1045 AGTCCACTCC
*
1055 ATCAAA-AAAAAAAAAACTCAAATCAAAGTCA
1 ATCAAATAAAAAAAAAA-TCAAATCAAAATCA
* **
1086 ATCAAATCAAAATCAAATCAAATCAAAATCA
1 ATCAAATAAAAAAAAAATCAAATCAAAATCA
1117 A
1 A
1118 AAGAGAATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.65, C:0.17, G:0.02, T:0.16
Consensus pattern (31 bp):
ATCAAATAAAAAAAAAATCAAATCAAAATCA
Found at i:1099 original size:11 final size:11
Alignment explanation
Indices: 1085--1119 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1075 AATCAAAGTC
1085 AATCAAATCAA
1 AATCAAATCAA
1096 AATCAAATC-A
1 AATCAAATCAA
1106 AATCAAAATCAA
1 AATC-AAATCAA
1118 AA
1 AA
1120 GAGAATCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.23
11 14 0.64
12 3 0.14
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (11 bp):
AATCAAATCAA
Found at i:1106 original size:16 final size:16
Alignment explanation
Indices: 1072--1118 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
1062 AAAAAAAAAC
*
1072 TCAAATCAAAGTC-AA
1 TCAAATCAAAATCAAA
1087 TCAAATCAAAATCAAA
1 TCAAATCAAAATCAAA
1103 TCAAATCAAAATCAAA
1 TCAAATCAAAATCAAA
1119 AGAGAATCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.60, C:0.19, G:0.02, T:0.19
Consensus pattern (16 bp):
TCAAATCAAAATCAAA
Found at i:1764 original size:50 final size:50
Alignment explanation
Indices: 1698--1848 Score: 194
Period size: 50 Copynumber: 3.0 Consensus size: 50
1688 GAAGTTTTAC
* * * *
1698 AATAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTTGCTTTTCAA
1 AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTCGCTTTTCAA
** * *
1748 GGTAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAGTTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTCGCTTTTCAA
* * * *
1798 AATAAGTTTGCATTCCATTTATGAGACCAAGATCAAAGTTCGCTGTTCAA
1 AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTCGCTTTTCAA
1848 A
1 A
1849 GGGCATTTTA
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (50 bp):
AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTCGCTTTTCAA
Found at i:2510 original size:50 final size:50
Alignment explanation
Indices: 2434--2664 Score: 374
Period size: 50 Copynumber: 4.6 Consensus size: 50
2424 AATGCTTTGA
* *
2434 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACACAGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACAGG
*
2484 TTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACAGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACAGG
*
2534 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACAGG
* * *
2584 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTAAATTATCAGCACATG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACAGG
*
2634 CTTTTCCACAAGCCACA-TCCGTTTCCATACG
1 CTTTTCCACAAGCCAAACT-CGTTTCCATACG
2665 GTGCATTATC
Statistics
Matches: 170, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
49 1 0.01
50 169 0.99
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (50 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACAGG
Found at i:2747 original size:27 final size:27
Alignment explanation
Indices: 2717--2797 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
2707 GATAAGCGGA
2717 AGACGGTCCTTTCAAGATTGAATTGGT
1 AGACGGTCCTTTCAAGATTGAATTGGT
* ** *
2744 AGACAG----TTCAAAGGA-T-AAGCGGA
1 AGACGGTCCTTTC-AA-GATTGAATTGGT
2767 AGACGGTCCTTTCAAGATTGAATTGGT
1 AGACGGTCCTTTCAAGATTGAATTGGT
2794 AGAC
1 AGAC
2798 AGTTCAAAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 16
0.61 0.13 0.26
Matches are distributed among these distances:
23 12 0.32
24 3 0.08
25 4 0.11
26 3 0.08
27 16 0.42
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (27 bp):
AGACGGTCCTTTCAAGATTGAATTGGT
Found at i:2748 original size:50 final size:50
Alignment explanation
Indices: 2673--2855 Score: 289
Period size: 50 Copynumber: 3.7 Consensus size: 50
2663 CGGTGCATTA
* * *
2673 TCCTTTTAAGATCGAATTGGTAGACAATTCAAAGGATAAGCGGAAGACGG
1 TCCTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGG
2723 TCCTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGG
1 TCCTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGG
2773 TCCTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGG
1 TCCTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGG
* * *
2823 -CCTTTTAATATTAAATTGG-AGAACAGTTCAAAG
1 TCCTTTCAAGATTGAATTGGTAG-ACAGTTCAAAG
2856 AAATTGATCG
Statistics
Matches: 126, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
48 2 0.02
49 27 0.21
50 97 0.77
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.26
Consensus pattern (50 bp):
TCCTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGG
Found at i:2930 original size:57 final size:57
Alignment explanation
Indices: 2842--2956 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
2832 ATTAAATTGG
2842 AGAACAGTTCAAAGAAATTGATCGGGAGACGATCCATTTCGAAGTAAAAAGAAAAGT
1 AGAACAGTTCAAAGAAATTGATCGGGAGACGATCCATTTCGAAGTAAAAAGAAAAGT
2899 AGAACAGTTCAAAGAAATTGATCGGGAGACGATCCATTTCGAAGTAAAAAGAAAAGT
1 AGAACAGTTCAAAGAAATTGATCGGGAGACGATCCATTTCGAAGTAAAAAGAAAAGT
2956 A
1 A
2957 AATGTCCGAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.46, C:0.12, G:0.23, T:0.19
Consensus pattern (57 bp):
AGAACAGTTCAAAGAAATTGATCGGGAGACGATCCATTTCGAAGTAAAAAGAAAAGT
Found at i:3251 original size:27 final size:27
Alignment explanation
Indices: 3167--3255 Score: 124
Period size: 27 Copynumber: 3.3 Consensus size: 27
3157 GGAATTTTGG
3167 GGTCATTTGCATGTTCAGGGGCATTTT
1 GGTCATTTGCATGTTCAGGGGCATTTT
* *
3194 AGTCATTTGCATGTCCAGGGGCATTTT
1 GGTCATTTGCATGTTCAGGGGCATTTT
* * * *
3221 GGTCATTTGCACGTTCAAGGGCATCTC
1 GGTCATTTGCATGTTCAGGGGCATTTT
3248 GGTCATTT
1 GGTCATTT
3256 TAAGCACTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (27 bp):
GGTCATTTGCATGTTCAGGGGCATTTT
Done.