Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013170.1 Corchorus olitorius cultivar O-4 contig13203, 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: 11145
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Found at i:74 original size:30 final size:30
Alignment explanation
Indices: 1--1180 Score: 1420
Period size: 30 Copynumber: 39.1 Consensus size: 30
* * * *
1 AAGCAATGATCCTTAACCAAGATTAGAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * * *
31 AAGCAAGTGATCCTCAAACAAGACTAAAATG
1 AAGCAA-TGATCCTCAACCAGGATTAAAATA
*
62 AAGCAATGATCCTCAGA-CAGGATTAAAATG
1 AAGCAATGATCCTCA-ACCAGGATTAAAATA
* *
92 AACCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
122 AAGCAACGATCCTACAACCTAGGATTAAAATA
1 AAGCAATGATCCT-CAACC-AGGATTAAAATA
* * *
154 AGGCAAAGATCCTCAACCAGGGTTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
184 AAGCAATGATCCTTAACCAAGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * * * *
214 AAGCAGTGATCCTCAAACAAGACTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
244 AAGCAATGATCCTCAGA-CAGGATTAACTTATA
1 AAGCAATGATCCTCA-ACCAGGATTAA--AATA
276 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
306 AAGCAACGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
336 AAGCAAAGATCCTCAACCAGGAATAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
366 AAGCAATGATCCTTAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
396 ATGCAAAT-ATCCTCCACCAGGATTAAAATA
1 AAGC-AATGATCCTCAACCAGGATTAAAATA
* *
426 AAG-AAGCGATCCTCAACTAGGATTAAAATA
1 AAGCAA-TGATCCTCAACCAGGATTAAAATA
* *
456 AAGCAACGATCCTCAACCATGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
486 AAGCAACGATCTTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
516 AAGCAAAGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
546 AAGCAATGATCCTTAACTAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
576 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
606 AAGCAATGATCCTTAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
636 ATGCAAAT-ATCCTCCACCAGGATTAAAATA
1 AAGC-AATGATCCTCAACCAGGATTAAAATA
** *
666 AAGCAGCGATCCTCAACTAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
696 AAGCAACGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
726 AAGCAACGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * * * *
756 AAGCAGTGATCCTCAAACAAGACTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
786 AAGCAATGATCCTCAGA-CAGGATTAAAATG
1 AAGCAATGATCCTCA-ACCAGGATTAAAATA
* *
816 AACCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
846 AAGCAACGATCCTCAACCTAGGATTAAAATA
1 AAGCAATGATCCTCAACC-AGGATTAAAATA
* * *
877 AGGCAAAGATCCTCAACCAGGGTTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
907 AAGCAATGATCCTTAACCAAGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * * * *
937 AAGCAGTGATCCTCAAACAAGACTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
967 AAGCAATGATCCTCAGA-CAGGATTAACTTATA
1 AAGCAATGATCCTCA-ACCAGGATTAA--AATA
* *
999 AAGCAATGATCTTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1029 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1059 AAACAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1089 AAGCAAAGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
1119 AAGGAATGATCCTCAAACAAGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* **
1149 AAGCAATGATCCTCAAACATTATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1179 AA
1 AA
1181 TTGACAAAGT
Statistics
Matches: 1006, Mismatches: 122, Indels: 44
0.86 0.10 0.04
Matches are distributed among these distances:
28 2 0.00
29 3 0.00
30 850 0.84
31 77 0.08
32 74 0.07
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.20
Consensus pattern (30 bp):
AAGCAATGATCCTCAACCAGGATTAAAATA
Found at i:1534 original size:69 final size:69
Alignment explanation
Indices: 1446--1621 Score: 307
Period size: 69 Copynumber: 2.6 Consensus size: 69
1436 AAGTAAAGCT
* *
1446 TGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTAAATGGCTTGGATGGAACCAAGGCTT
1511 AAAC
66 AAAC
* *
1515 TGATTCGTATGGAAACGAGTTTGGTTTGTGGAAAAGCCTAAATGGCTTGGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTAAATGGCTTGGATGGAACCAAGGCTT
*
1580 GAAC
66 AAAC
1584 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1622 AAAGCATTCG
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 100 1.00
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.27
Consensus pattern (69 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTAAATGGCTTGGATGGAACCAAGGCTT
AAAC
Found at i:1823 original size:26 final size:26
Alignment explanation
Indices: 1785--1838 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
1775 GTCTACTGAA
1785 ATAAACTACAGAAAAGATCGCCATGG
1 ATAAACTACAGAAAAGATCGCCATGG
*
1811 ATAAACTGA-AGAAAAGATCGCCCTGG
1 ATAAACT-ACAGAAAAGATCGCCATGG
1837 AT
1 AT
1839 CCATTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (26 bp):
ATAAACTACAGAAAAGATCGCCATGG
Found at i:1958 original size:35 final size:35
Alignment explanation
Indices: 1875--2254 Score: 355
Period size: 35 Copynumber: 11.0 Consensus size: 35
1865 GCCCTAGGTC
* * * *
1875 AACTGAAATAAAGATCACCCTAGATCAACTGAAGT-
1 AACTG-AAGAAAGATCGCCCTGGATCAACTGAAATG
* * * *
1910 AATTGAGGAAAGATCGCCCTGGATCAATTAAAATG
1 AACTGAAGAAAGATCGCCCTGGATCAACTGAAATG
*
1945 AACTGAAGAAAGATCGCCCTGGATCAACTGAAATA
1 AACTGAAGAAAGATCGCCCTGGATCAACTGAAATG
* *
1980 AACTGAATAAAAGATCGCCCTGGATCAACTGAAATA
1 AACTGAA-GAAAGATCGCCCTGGATCAACTGAAATG
* * * *
2016 AACTGGAGAAAGACCGCCCTGGGTCAA--GTAA-G
1 AACTGAAGAAAGATCGCCCTGGATCAACTGAAATG
* * *
2048 --CTGAAGAAAAGATCGCCCTGGATCCATTAAAATG
1 AACTGAAG-AAAGATCGCCCTGGATCAACTGAAATG
* * * * *
2082 AATTGAAGAAGGACCGCCCTGGGTCAACTGAAGT-
1 AACTGAAGAAAGATCGCCCTGGATCAACTGAAATG
* *
2116 AACTGAATAAAAGATCGCCCTGGATCAACTGAAGT-
1 AACTGAA-GAAAGATCGCCCTGGATCAACTGAAATG
* * * *
2151 AATTGAGGAAAGATCGCCCTGGATCAATTAAAATG
1 AACTGAAGAAAGATCGCCCTGGATCAACTGAAATG
* *
2186 AACTGAAGAAAGATCGCCCTGGATTAGCTGAAAT-
1 AACTGAAGAAAGATCGCCCTGGATCAACTGAAATG
* *
2220 AAATGAAGGAAAGATCGCTCTGGATCAACTGAAAT
1 AACTGAA-GAAAGATCGCCCTGGATCAACTGAAAT
2255 AAATCTTCAG
Statistics
Matches: 279, Mismatches: 55, Indels: 22
0.78 0.15 0.06
Matches are distributed among these distances:
30 5 0.02
31 16 0.06
33 5 0.02
34 58 0.21
35 157 0.56
36 38 0.14
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.19
Consensus pattern (35 bp):
AACTGAAGAAAGATCGCCCTGGATCAACTGAAATG
Found at i:2193 original size:104 final size:103
Alignment explanation
Indices: 1875--2252 Score: 390
Period size: 104 Copynumber: 3.7 Consensus size: 103
1865 GCCCTAGGTC
* * * * * *
1875 AACTGAAATAAAGATCACCCTAGATCAACTGAAGTAATTG-AGGAAAGATCGCCCTGGATCAATT
1 AACTG-AAGAAAGATCGCCCTGGATCAACTGAAATAACTGAAGGAAAGATCGCCCTGGATCAACT
* * * * *
1939 AAAATGAACTGAAGAAAGATCGCCCTGGATCAACTGAAATA
65 GAAGTGAA-TG-AGAAAGATCGCCCTGGATCAATTAAAATG
* * * * *
1980 AACTGAATAAAAGATCGCCCTGGATCAACTGAAATAAACTGGA-GAAAGACCGCCCTGGGTCAAG
1 AACTGAA-GAAAGATCGCCCTGGATCAACTGAAAT-AACTGAAGGAAAGATCGCCCTGGATCAAC
*
2044 T-AAGCTGAA-GA-AAAGATCGCCCTGGATCCATTAAAATG
64 TGAAG-TGAATGAGAAAGATCGCCCTGGATCAATTAAAATG
* * * * * **
2082 AATTGAAGAAGGACCGCCCTGGGTCAACTGAAGTAACTGAATAAAAGATCGCCCTGGATCAACTG
1 AACTGAAGAAAGATCGCCCTGGATCAACTGAAATAACTGAAGGAAAGATCGCCCTGGATCAACTG
2147 AAGT-AATTGAGGAAAGATCGCCCTGGATCAATTAAAATG
66 AAGTGAA-TGA-GAAAGATCGCCCTGGATCAATTAAAATG
* * * *
2186 AACTGAAGAAAGATCGCCCTGGATTAGCTGAAATAAATGAAGGAAAGATCGCTCTGGATCAACTG
1 AACTGAAGAAAGATCGCCCTGGATCAACTGAAATAACTGAAGGAAAGATCGCCCTGGATCAACTG
2251 AA
66 AA
2253 ATAAATCTTC
Statistics
Matches: 227, Mismatches: 36, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
100 8 0.04
101 41 0.18
102 34 0.15
103 1 0.00
104 85 0.37
105 30 0.13
106 27 0.12
107 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (103 bp):
AACTGAAGAAAGATCGCCCTGGATCAACTGAAATAACTGAAGGAAAGATCGCCCTGGATCAACTG
AAGTGAATGAGAAAGATCGCCCTGGATCAATTAAAATG
Found at i:3157 original size:7 final size:7
Alignment explanation
Indices: 3147--3200 Score: 67
Period size: 7 Copynumber: 7.7 Consensus size: 7
3137 TTTTTCAATT
3147 TTTTTTG
1 TTTTTTG
3154 -TTTTTG
1 TTTTTTG
*
3160 TTTTTGTT
1 TTTTT-TG
3168 TTGTTTTG
1 TT-TTTTG
3176 TTTTTTG
1 TTTTTTG
3183 TTTTTTG
1 TTTTTTG
3190 TTTTTT-
1 TTTTTTG
3196 TTTTT
1 TTTTT
3201 GCACTTGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 11 0.26
7 22 0.52
8 6 0.14
9 3 0.07
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTTTTG
Found at i:3159 original size:6 final size:6
Alignment explanation
Indices: 3148--3201 Score: 67
Period size: 6 Copynumber: 9.0 Consensus size: 6
3138 TTTTCAATTT
*
3148 TTTTTG TTTTTG TTTTTG -TTTTG -TTTTG TTTTTTG TTTTTTG TTTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG -TTTTTG -TTTTTG TTTTTG
3196 TTTTTG
1 TTTTTG
3202 CACTTGAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 10 0.23
6 22 0.50
7 12 0.27
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:3163 original size:5 final size:5
Alignment explanation
Indices: 3145--3197 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
3135 CATTTTTCAA
3145 TTTT- TTTTG TTTTTG TTTTTG TTTTG TTTTG TTTT- TTGTT- TTTTG
1 TTTTG TTTTG -TTTTG -TTTTG TTTTG TTTTG TTTTG TT-TTG TTTTG
3190 TTTT- TTTT
1 TTTTG TTTT
3198 TTTGCACTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
4 12 0.27
5 22 0.49
6 11 0.24
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (5 bp):
TTTTG
Found at i:3163 original size:23 final size:23
Alignment explanation
Indices: 3144--3187 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3134 TCATTTTTCA
3144 ATTTT-TTTTG-TTTTTGTTTTT
1 ATTTTGTTTTGTTTTTTGTTTTT
*
3165 GTTTTGTTTTGTTTTTTGTTTTT
1 ATTTTGTTTTGTTTTTTGTTTTT
3188 TGTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 11 0.55
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (23 bp):
ATTTTGTTTTGTTTTTTGTTTTT
Found at i:3832 original size:18 final size:19
Alignment explanation
Indices: 3809--3845 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3799 TAAAAACAAA
3809 TTTTG-AAAACCATTTTTT
1 TTTTGAAAAACCATTTTTT
*
3827 TTTTGAAAAATCATTTTTT
1 TTTTGAAAAACCATTTTTT
3846 CGAAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTGAAAAACCATTTTTT
Found at i:4275 original size:2 final size:2
Alignment explanation
Indices: 4268--4313 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
4258 GAACAGTAGA
* * *
4268 AT AT AT AT AC AC AT AT -T AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4309 AT AT A
1 AT AT A
4314 ATGGAAAGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:7640 original size:20 final size:22
Alignment explanation
Indices: 7615--7654 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
7605 TTACACCTCC
7615 CAAAATCT-AAT-CAAGATGGA
1 CAAAATCTAAATGCAAGATGGA
*
7635 CAAAATGTAAATGCAAGATG
1 CAAAATCTAAATGCAAGATG
7655 CAATCTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 3 0.18
22 7 0.41
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.20
Consensus pattern (22 bp):
CAAAATCTAAATGCAAGATGGA
Done.