Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011657.1 Corchorus olitorius cultivar O-4 contig11690, 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: 1892
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.21
Found at i:1341 original size:20 final size:20
Alignment explanation
Indices: 1311--1892 Score: 524
Period size: 20 Copynumber: 31.9 Consensus size: 20
1301 GTCCGAGTGT
1311 CAAG-GCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1330 CAAGTCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
* *
1350 CAACTCCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
*
1364 CAAG-GCCTAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1383 CAAGTCGCCGAGTGCCA----
1 CAAGT-GCCGAGTGCCATCGG
*
1400 -AAG-GCCTAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1418 CAAGTGCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1438 CAAGTCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1458 CAAGTGCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1478 CAAGTGCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
1492 CAAG-GCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1511 CAAGTCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1531 CAA-TCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
* *
1550 CAACTCCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
*
1564 CAAG-GCCTAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1583 CAAGTGCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
*
1597 CAAG-GCCTAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1616 CAAGTGCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1636 CAAGTGTCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1656 CAAGTCCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
1670 CAAG-GCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1689 CAAGT-CTCGAGTGCCATCGG
1 CAAGTGC-CGAGTGCCATCGG
*
1709 CAAGTCCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
1723 CAAG-GCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1742 CAAGTCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1762 CAAGTCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1782 CAAGTCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
* *
1802 CAACTCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
* *
1822 CAACTCCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
*
1836 CAAG-GCCTAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1855 CAAGTGCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1875 CAAGTGTCGAGTGCCATC
1 CAAGTGCCGAGTGCCATC
Statistics
Matches: 474, Mismatches: 29, Indels: 119
0.76 0.05 0.19
Matches are distributed among these distances:
13 47 0.10
14 35 0.07
16 10 0.02
17 7 0.01
19 55 0.12
20 309 0.65
21 11 0.02
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (20 bp):
CAAGTGCCGAGTGCCATCGG
Found at i:1368 original size:53 final size:53
Alignment explanation
Indices: 1290--1892 Score: 347
Period size: 53 Copynumber: 11.1 Consensus size: 53
1280 GTTGCCAAGC
*
1290 GCCATCGGCAAGT-CCGAGTGTCAAGGCCGAGTGCCATCGGCAAGTCCCGAGT
1 GCCATCGGCAAGTGCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCCCGAGT
* * *
1342 GCCATCGGCAACTCCCGAGTGCCAAGGCCTAGTGCCATCGGCAAGTCGCCGAGT
1 GCCATCGGCAAGTGCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTC-CCGAGT
** * *
1396 GCCAAAGGCCTAGTGCC-A-TCGGCAAGTGCCGAGTGCCATCGGCAAGTCCCGAGT
1 GCCATCGG-CAAGTGCCGAGT-GCCAAG-GCCGAGTGCCATCGGCAAGTCCCGAGT
* * * *
1450 GCCATCGGCAAGTGCCGAGTGCCATCGG-CAAGTGCCGAGT-GCCAAG-GCCGAGT
1 GCCATCGGCAAGTGCCGAGTGCCA-AGGCCGAGTGCC-A-TCGGCAAGTCCCGAGT
* * *
1503 GCCATCGGCAAGTCCCGAGTGCCATCGGCAATCCCGAGTGCCATCGGCAACTCCCGAGT
1 GCCATCGGCAAGTGCCGAGTGCCA-AGG-----CCGAGTGCCATCGGCAAGTCCCGAGT
* * * * *
1562 GCCA-AGGCCTAGTGCC-A-TCGGCAAGTGCCGAGTG----C--CAAG-GCCTAGT
1 GCCATCGG-CAAGTGCCGAGT-GCCAAG-GCCGAGTGCCATCGGCAAGTCCCGAGT
*
1608 GCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTGTCGAGTGCCATCGGCAAGTCCCGAGT
1 GCCATCGGCAAGTGCCGAGTG----C--CAAG-GCCGAGTGCCATCGGCAAGTCCCGAGT
* * * *
1668 GCCA-AGGCCGAGTGCC-A-TCGGCAAGTCTCGAGTGCCATCGGCAAGTCCCGAGT
1 GCCATCGG-CAAGTGCCGAGT-GCCAAGGC-CGAGTGCCATCGGCAAGTCCCGAGT
* * * *
1721 GCCA-AGGCCGAGTGCC-A-TCGGCAAGTCCCGAGTGCCATCGGCAAGTCCCGAGT
1 GCCATCGG-CAAGTGCCGAGT-GCCAAG-GCCGAGTGCCATCGGCAAGTCCCGAGT
* * *
1774 GCCATCGGCAAGTCCCGAGTGCCATCGGCAACTCCCGAGTGCCATCGGCAACTCCCGAGT
1 GCCATCGGCAAGTGCCGAGTGCCA-AGG------CCGAGTGCCATCGGCAAGTCCCGAGT
* * * **
1834 GCCA-AGGCCTAGTGCC-A-TCGGCAAGTGCCGAGTGCCATCGGCAAGTGTCGAGT
1 GCCATCGG-CAAGTGCCGAGT-GCCAAG-GCCGAGTGCCATCGGCAAGTCCCGAGT
1887 GCCATC
1 GCCATC
Statistics
Matches: 437, Mismatches: 59, Indels: 108
0.72 0.10 0.18
Matches are distributed among these distances:
46 16 0.04
47 7 0.02
48 1 0.00
49 1 0.00
52 12 0.03
53 214 0.49
54 48 0.11
55 30 0.07
57 4 0.01
58 15 0.03
59 38 0.09
60 51 0.12
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (53 bp):
GCCATCGGCAAGTGCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCCCGAGT
Found at i:1399 original size:34 final size:34
Alignment explanation
Indices: 1339--1433 Score: 158
Period size: 35 Copynumber: 2.8 Consensus size: 34
1329 GCAAGTCCCG
*
1339 AGTGCCATCGGCAACTC-CCGAGTGCCAAGGCCT
1 AGTGCCATCGGCAAGTCGCCGAGTGCCAAGGCCT
1372 AGTGCCATCGGCAAGTCGCCGAGTGCCAAAGGCCT
1 AGTGCCATCGGCAAGTCGCCGAGTGCC-AAGGCCT
1407 AGTGCCATCGGCAAGT-GCCGAGTGCCA
1 AGTGCCATCGGCAAGTCGCCGAGTGCCA
1434 TCGGCAAGTC
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
33 17 0.29
34 19 0.32
35 23 0.39
ACGTcount: A:0.22, C:0.33, G:0.31, T:0.15
Consensus pattern (34 bp):
AGTGCCATCGGCAAGTCGCCGAGTGCCAAGGCCT
Found at i:1484 original size:33 final size:33
Alignment explanation
Indices: 1447--1880 Score: 188
Period size: 33 Copynumber: 12.1 Consensus size: 33
1437 GCAAGTCCCG
*
1447 AGTGCCATCGGCAAGTGCCGAGTGCCATCGGCA
1 AGTGCCATCGGCAAGTCCCGAGTGCCATCGGCA
* *
1480 AGTGCCGAGT-GCCAAG-GCCGAGTGCCATCGGCAA
1 AGTGCC-A-TCGGCAAGTCCCGAGTGCCATCGGC-A
1514 GTCCCGAGTGCCATCGGCAA-TCCCGAGTGCCATCGGCA
1 ------AGTGCCATCGGCAAGTCCCGAGTGCCATCGGCA
* * * * *
1552 ACTCCCGAGT-GCCAAG-GCCTAGTGCCATCGGCA
1 AGTGCC-A-TCGGCAAGTCCCGAGTGCCATCGGCA
* * *
1585 AGTGCCGAGT-GCCAAG-GCCTAGTGCCATCGGCAA
1 AGTGCC-A-TCGGCAAGTCCCGAGTGCCATCGGC-A
**
1619 GTGCCGAGTGCCATCGGCAAGTGTCGAGTGCCATCGGCA
1 ------AGTGCCATCGGCAAGTCCCGAGTGCCATCGGCA
* * *
1658 AGTCCCGAGT-GCCAAG-GCCGAGTGCCATCGGCAA
1 AGTGCC-A-TCGGCAAGTCCCGAGTGCCATCGGC-A
* *
1692 GTCTCGAGTGCCATCGGCAAGTCCCGAGTGCCA-AGGCCG
1 ------AGTGCCATCGGCAAGTCCCGAGTGCCATCGG-CA
1731 AGTGCCATCGGCAAGTCCCGAGTGCCATCGGCAA
1 AGTGCCATCGGCAAGTCCCGAGTGCCATCGGC-A
1765 GTCCCGAGTGCCATCGGCAAGTCCCGAGTGCCATCGGCAA
1 ------AGTGCCATCGGCAAGTCCCGAGTGCCATCGGC-A
* * *
1805 CTCCCGAGTGCCATCGGCAACTCCCGAGTGCCA-AGGCCT
1 ------AGTGCCATCGGCAAGTCCCGAGTGCCATCGG-CA
*
1844 AGTGCCATCGGCAAGTGCCGAGTGCCATCGGCA
1 AGTGCCATCGGCAAGTCCCGAGTGCCATCGGCA
1877 AGTG
1 AGTG
1881 TCGAGTGCCA
Statistics
Matches: 325, Mismatches: 31, Indels: 90
0.73 0.07 0.20
Matches are distributed among these distances:
32 4 0.01
33 150 0.46
34 20 0.06
35 2 0.01
38 4 0.01
39 37 0.11
40 108 0.33
ACGTcount: A:0.21, C:0.33, G:0.32, T:0.15
Consensus pattern (33 bp):
AGTGCCATCGGCAAGTCCCGAGTGCCATCGGCA
Found at i:1499 original size:13 final size:14
Alignment explanation
Indices: 1478--1506 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1468 GTGCCATCGG
1478 CAAGTGCCGAGTGC
1 CAAGTGCCGAGTGC
1492 CAAG-GCCGAGTGC
1 CAAGTGCCGAGTGC
1505 CA
1 CA
1507 TCGGCAAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.24, C:0.31, G:0.34, T:0.10
Consensus pattern (14 bp):
CAAGTGCCGAGTGC
Found at i:1505 original size:73 final size:74
Alignment explanation
Indices: 1372--1892 Score: 421
Period size: 73 Copynumber: 7.1 Consensus size: 74
1362 GCCAAGGCCT
** * *
1372 AGTGCCATCGGCAAGTCGCCGAGTGCCAAAGGCCTAGTGCC-A-TCGGCAAGTGCCGAGTGCCAT
1 AGTGCCATCGGCAAGT-GCCGAGTGCCATCGG-CAAGTGCCGAGT-GCCAAGTGCCGAGTGCCAT
1435 CGGCAAGTCCCG
63 CGGCAAGTCCCG
1447 AGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTGCCGAGTGCCAAG-GCCGAGTGCCATCGG
1 AGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTGCCGAGTGCCAAGTGCCGAGTGCCATCGG
1511 CAAGTCCCG
66 CAAGTCCCG
* * * *
1520 AGTGCCATCGGCAA-TCCCGAGTGCCATCGGCAACTCCCGAGTGCCAAG-GCCTAGTGCCATCGG
1 AGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTGCCGAGTGCCAAGTGCCGAGTGCCATCGG
*
1583 CAAGTGCCG
66 CAAGTCCCG
* *
1592 AGTG----C--CAAG-GCCTAGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTGTCGAGTGC
1 AGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTGCCGAGTG----C--CAAGTGCCGAGTGC
1650 CATCGGCAAGTCCCG
60 CATCGGCAAGTCCCG
* * *
1665 AGTG----C--CAAG-GCCGAGTGCCATCGGCAAGT-CTCGAGTGCC-A-TCGGCAAGTCCCGAG
1 AGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTGC-CGAGTGCCAAGT-GCCGAGTGCC-A-
* *
1720 T-GCCAAG-GCCG
62 TCGGCAAGTCCCG
* * *
1731 AGTGCCATCGGCAAGTCCCGAGTGCCATCGGCAAGTCCCGAGTGCCATCGGCAAGTCCCGAGTGC
1 AGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTGCCGAGTG----C--CAAGTGCCGAGTGC
*
1796 CATCGGCAACTCCCG
60 CATCGGCAAGTCCCG
* * * * *
1811 AGTGCCATCGGCAACTCCCGAGTGCCA-AGGCCTAGTGCC-A-TCGGCAAGTGCCGAGTGCCATC
1 AGTGCCATCGGCAAGTGCCGAGTGCCATCGG-CAAGTGCCGAGT-GCCAAGTGCCGAGTGCCATC
**
1873 GGCAAGTGTCG
64 GGCAAGTCCCG
1884 AGTGCCATC
1 AGTGCCATC
Statistics
Matches: 373, Mismatches: 39, Indels: 70
0.77 0.08 0.15
Matches are distributed among these distances:
65 1 0.00
66 42 0.11
67 7 0.02
68 2 0.01
69 1 0.00
70 2 0.01
72 66 0.18
73 159 0.43
74 20 0.05
75 17 0.05
77 1 0.00
78 2 0.01
79 10 0.03
80 42 0.11
81 1 0.00
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (74 bp):
AGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTGCCGAGTGCCAAGTGCCGAGTGCCATCGG
CAAGTCCCG
Done.