Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015128.1 Corchorus olitorius cultivar O-4 contig15161, 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: 7626
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:389 original size:27 final size:28
Alignment explanation
Indices: 331--404 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
321 GCGTGAACTT
* *
331 AAAATGACCAAAATACCCCCGAATGTGC
1 AAAATGACCAAAATGCCCCCGAATGTGA
*
359 AAAATGACCAAAATGCCCCTGAATGT-A
1 AAAATGACCAAAATGCCCCCGAATGTGA
386 AAAATGACCGAAAAATGCC
1 AAAATGACC--AAAATGCC
405 ACTATGTGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 9 0.22
28 24 0.59
29 8 0.20
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCCGAATGTGA
Found at i:938 original size:30 final size:30
Alignment explanation
Indices: 902--1449 Score: 717
Period size: 30 Copynumber: 18.2 Consensus size: 30
892 CAATAATCTG
902 ATAAAGCAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
932 ATAAAGCAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * * *
962 ACAAAACAACGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
992 ATGATGCAATGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
1022 ACAAATCAATGATCCTCAACCAGGATCAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
1052 ACAAAAGCAATGATCCTCAACCAGGACTAAA
1 A-TAAAGCAATGATCCTCAACCAGGATTAAA
*
1083 ACAAAGCAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
1113 ATAAAGCAACGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
1143 ATGATGCAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
1173 ATAAAGCAAAT-ATCCTCAATCAGGATTAAA
1 ATAAAGC-AATGATCCTCAACCAGGATTAAA
**
1203 ATGGAGCAAAT-ATCCTCAACCAGGATTAAA
1 ATAAAGC-AATGATCCTCAACCAGGATTAAA
*
1233 ATAAAGCAAAT-ATCCTCAATCAGGATTAAA
1 ATAAAGC-AATGATCCTCAACCAGGATTAAA
**
1263 ATGGAGCAAAT-ATCCTCAACCAGGATTAAA
1 ATAAAGC-AATGATCCTCAACCAGGATTAAA
* **
1293 ATAAAGCAATGATCTTCAATTAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
1323 ACAAAGCAATGATCCTCAAACAGGATTAAC
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
1353 GTAAAGCAATGATCCTCAAACAGGATTAAC
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
1383 ATAAAGCAATGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
1413 ATAAAGCAATGATCATCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
1443 ATAAAGC
1 ATAAAGC
1450 TGATAAAGCA
Statistics
Matches: 459, Mismatches: 56, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
29 3 0.01
30 427 0.93
31 29 0.06
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.20
Consensus pattern (30 bp):
ATAAAGCAATGATCCTCAACCAGGATTAAA
Found at i:1836 original size:31 final size:31
Alignment explanation
Indices: 1789--1857 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1779 GGATTAATTA
* * * *
1789 AAATGAACTGAAGAAAATATCGCCCTGGATC
1 AAATAAACCGAAGAAAAGATCGCCCTCGATC
*
1820 AAATAAACCGAAGAAAAGATCTCCCTCGATC
1 AAATAAACCGAAGAAAAGATCGCCCTCGATC
*
1851 AACTAAA
1 AAATAAA
1858 ATAACTTGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.22, G:0.14, T:0.17
Consensus pattern (31 bp):
AAATAAACCGAAGAAAAGATCGCCCTCGATC
Found at i:2083 original size:31 final size:31
Alignment explanation
Indices: 2048--2158 Score: 134
Period size: 31 Copynumber: 3.5 Consensus size: 31
2038 AATTGAGGAG
2048 AGATCACCCTGGATCAACTGACATTGAATGA
1 AGATCACCCTGGATCAACTGACATTGAATGA
* * * *
2079 AGATCACCCTGGATTAATTGAAATAAACT-AAAGAA
1 AGATCACCCTGGATCAACTGACAT----TGAATG-A
2114 AGATCACCCTGGATCAACTGACATTGAATGA
1 AGATCACCCTGGATCAACTGACATTGAATGA
2145 AGATCACCCTGGAT
1 AGATCACCCTGGAT
2159 TAATTGAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
31 37 0.56
32 3 0.05
34 3 0.05
35 23 0.35
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.23
Consensus pattern (31 bp):
AGATCACCCTGGATCAACTGACATTGAATGA
Found at i:2118 original size:66 final size:66
Alignment explanation
Indices: 1872--2203 Score: 342
Period size: 66 Copynumber: 4.9 Consensus size: 66
1862 CTTGAAGTAG
* * * *
1872 GATCACCCTGGATCAATTGAAATGAATTGAAGAAAGATCGCCCTGGGTCTACTGAAATAACTTGA
1 GATCACCCTGGATCAATTGAAATAAATTGAAGAAAGATCACCCTGGATCAACTG--A-AA-TTGA
1937 A-GAA
62 ATGAA
* * * * * *
1941 TGAGCGCCCTGGATCAATTGAAATACATTGGAGGAAAGATCGCCCTGGATCGACTGAAATAAATT
1 -GATCACCCTGGATCAATTGAAATAAATT-GAAGAAAGATCACCCTGGATCAACTG----AAATT
*
2006 GAATAAAA
60 GAAT-GAA
** * * * *
2014 GATCACCCTGGATCAAGCGAAGTAAATTGAGGAGAGATCACCCTGGATCAACTGACATTGAATGA
1 GATCACCCTGGATCAATTGAAATAAATTGAAGAAAGATCACCCTGGATCAACTGAAATTGAATGA
2079 A
66 A
* * * *
2080 GATCACCCTGGATTAATTGAAATAAACTAAAGAAAGATCACCCTGGATCAACTGACATTGAATGA
1 GATCACCCTGGATCAATTGAAATAAATTGAAGAAAGATCACCCTGGATCAACTGAAATTGAATGA
2145 A
66 A
* * *
2146 GATCACCCTGGATTAATTGAAATAAACTAAAGAAAGATCACCCTGGATCAACTGAAAT
1 GATCACCCTGGATCAATTGAAATAAATTGAAGAAAGATCACCCTGGATCAACTGAAAT
2204 AAAGTGAAGA
Statistics
Matches: 228, Mismatches: 29, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
66 117 0.51
67 8 0.04
70 24 0.11
71 51 0.22
72 24 0.11
73 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (66 bp):
GATCACCCTGGATCAATTGAAATAAATTGAAGAAAGATCACCCTGGATCAACTGAAATTGAATGA
A
Found at i:2311 original size:35 final size:35
Alignment explanation
Indices: 1714--2311 Score: 390
Period size: 35 Copynumber: 17.3 Consensus size: 35
1704 TTTGTGGTCT
* * * *
1714 ACTGAAATAAACTGCAGAAAAGATCACCATGGATAA
1 ACTGAAATAAACTGAAG-AAAGATCGCCCTGGATCA
* * *
1750 ACTG-AAGAAACTTAAGAAAAGATCGCCCTGGATTA
1 ACTGAAATAAACTGAAG-AAAGATCGCCCTGGATCA
* * * *
1785 ATTAAAATGAACTGAAGAAAATATCGCCCTGGAT--
1 ACTGAAATAAACTGAAG-AAAGATCGCCCTGGATCA
* * *
1819 -C--AAATAAACCGAAGAAAAGATCTCCCTCGATCA
1 ACTGAAATAAACTGAAG-AAAGATCGCCCTGGATCA
* * * *
1852 ACTAAAAT-AACTTGAAGTAGGATCACCCTGGATCA
1 ACTGAAATAAAC-TGAAGAAAGATCGCCCTGGATCA
* * * * *
1887 ATTGAAATGAATTGAAGAAAGATCGCCCTGGGTCT
1 ACTGAAATAAACTGAAGAAAGATCGCCCTGGATCA
* *
1922 ACTGAAAT-AACTTGAAGAATGAGCGCCCTGGATCA
1 ACTGAAATAAAC-TGAAGAAAGATCGCCCTGGATCA
* * * * *
1957 ATTGAAATACATTGGAGGAAAGATCGCCCTGGATCG
1 ACTGAAATAAACT-GAAGAAAGATCGCCCTGGATCA
* * *
1993 ACTGAAATAAATTGAATAAAAGATCACCCTGGATCA
1 ACTGAAATAAACTGAA-GAAAGATCGCCCTGGATCA
* * * * *
2029 AGC-GAAGTAAATTGAGGAGAGATCACCCTGGATCA
1 A-CTGAAATAAACTGAAGAAAGATCGCCCTGGATCA
* * *
2064 ACTGACAT----TGAATG-AAGATCACCCTGGATTA
1 ACTGAAATAAACTGAA-GAAAGATCGCCCTGGATCA
* * *
2095 ATTGAAATAAACTAAAGAAAGATCACCCTGGATCA
1 ACTGAAATAAACTGAAGAAAGATCGCCCTGGATCA
* * *
2130 ACTGACAT----TGAATG-AAGATCACCCTGGATTA
1 ACTGAAATAAACTGAA-GAAAGATCGCCCTGGATCA
* * *
2161 ATTGAAATAAACTAAAGAAAGATCACCCTGGATCA
1 ACTGAAATAAACTGAAGAAAGATCGCCCTGGATCA
* * * *
2196 ACTGAAATAAAGTGAAGAAAGACCGCCCTGGGTCG
1 ACTGAAATAAACTGAAGAAAGATCGCCCTGGATCA
* * * * *
2231 ATTGAAATAAA-TTAACGAAGGACCGCCCTGGGTCA
1 ACTGAAATAAACTGAA-GAAAGATCGCCCTGGATCA
* *
2266 ACTAAAATAAACTGAATAAAGATCGCCCTGGATCA
1 ACTGAAATAAACTGAAGAAAGATCGCCCTGGATCA
*
2301 ACTAAAATAAA
1 ACTGAAATAAA
2312 ATTTAGCAAC
Statistics
Matches: 445, Mismatches: 89, Indels: 57
0.75 0.15 0.10
Matches are distributed among these distances:
31 74 0.17
32 2 0.00
34 9 0.02
35 259 0.58
36 100 0.22
37 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (35 bp):
ACTGAAATAAACTGAAGAAAGATCGCCCTGGATCA
Found at i:3538 original size:24 final size:25
Alignment explanation
Indices: 3494--3548 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
3484 CAGTCATTTT
*
3494 CTTTCCTTTTTCTTCAATTTC-TTA
1 CTTTTCTTTTTCTTCAATTTCATTA
*
3518 CTTTTCTTTTTCTTTC-TTTTCAATTA
1 CTTTTCTTTTTC-TTCAATTTC-ATTA
3544 CTTTT
1 CTTTT
3549 TGATTTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 15 0.58
25 3 0.12
26 8 0.31
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (25 bp):
CTTTTCTTTTTCTTCAATTTCATTA
Found at i:4250 original size:2 final size:2
Alignment explanation
Indices: 4243--4272 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4233 GAACGGTAGA
4243 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
4273 GCATAATGGA
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:7228 original size:22 final size:22
Alignment explanation
Indices: 7186--7228 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
7176 AAATAAGAAA
*
7186 ACAAGGAAATAAGTTAGTAACC
1 ACAAGGAAATAAGTTAATAACC
7208 ACAAGGAAATTAAG-TAATAAC
1 ACAAGGAAA-TAAGTTAATAAC
7229 TGAAAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (22 bp):
ACAAGGAAATAAGTTAATAACC
Done.