Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024231.1 Corchorus olitorius cultivar O-4 contig24264, 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: 18522
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:954 original size:10 final size:10
Alignment explanation
Indices: 939--985 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
929 AATTTAACGC
*
939 TTAATTTGTT
1 TTAATTTGTA
949 TTAATTTGTA
1 TTAATTTGTA
*
959 ATAATTTAGTA
1 TTAATTT-GTA
*
970 TTAATTAGTA
1 TTAATTTGTA
980 TTAATT
1 TTAATT
986 AATTAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 24 0.75
11 8 0.25
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (10 bp):
TTAATTTGTA
Found at i:956 original size:31 final size:31
Alignment explanation
Indices: 885--966 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
875 GTTTATCAAC
*
885 TTTTAATTTGTTTAATTTAAGTCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGTCTTTAATTT
** *
916 TAATGATTTGTTTAATTTAACG-C-TTAATTT
1 TTTTAATTTGTTTAATTTAA-GTCTTTAATTT
*
946 GTTTTAATTTGTAATAATTTA
1 -TTTTAATTTGT-TTAATTTA
967 GTATTAATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
30 6 0.15
31 26 0.65
32 8 0.20
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.59
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGTCTTTAATTT
Found at i:975 original size:21 final size:20
Alignment explanation
Indices: 940--985 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
930 ATTTAACGCT
* *
940 TAATTTGTTTTAATTTGTAA
1 TAATTTGTATTAATTAGTAA
*
960 TAATTTAGTATTAATTAGTAT
1 TAATTT-GTATTAATTAGTAA
981 TAATT
1 TAATT
986 AATTAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
TAATTTGTATTAATTAGTAA
Found at i:1457 original size:16 final size:15
Alignment explanation
Indices: 1433--1491 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
1423 CCAACCCGAG
1433 ACCGAACCCGAAAAT
1 ACCGAACCCGAAAAT
* *
1448 ACCTGAACCCGACATAG
1 ACC-GAACCCGA-AAAT
*
1465 ACCGAACCAGAAAAT
1 ACCGAACCCGAAAAT
1480 ACCCGAACCCGA
1 A-CCGAACCCGA
1492 CAGAGCCCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 6 0.17
16 24 0.69
17 5 0.14
ACGTcount: A:0.42, C:0.36, G:0.15, T:0.07
Consensus pattern (15 bp):
ACCGAACCCGAAAAT
Found at i:1471 original size:32 final size:32
Alignment explanation
Indices: 1430--1523 Score: 127
Period size: 32 Copynumber: 2.9 Consensus size: 32
1420 AGCCCAACCC
*
1430 GAGACCGAACCCGAAAATACCTGAACCCGACA
1 GAGACCGAACCCGAAAATACCCGAACCCGACA
* *
1462 TAGACCGAACCAGAAAATACCCGAACCCGACA
1 GAGACCGAACCCGAAAATACCCGAACCCGACA
* *
1494 GAGCCCGAACCCGAATGA-ACCCGAACCCGA
1 GAGACCGAACCCGAA-AATACCCGAACCCGA
1524 ATAAGCCCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 53 0.98
33 1 0.02
ACGTcount: A:0.39, C:0.36, G:0.19, T:0.05
Consensus pattern (32 bp):
GAGACCGAACCCGAAAATACCCGAACCCGACA
Found at i:1500 original size:16 final size:16
Alignment explanation
Indices: 1480--1538 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
1470 ACCAGAAAAT
1480 ACCCGAACCCGACA-GA
1 ACCCGAACCCGA-ATGA
*
1496 GCCCGAACCCGAATGA
1 ACCCGAACCCGAATGA
1512 ACCCGAACCCGAAT-A
1 ACCCGAACCCGAATGA
*
1527 AGCCCTAACCCG
1 A-CCCGAACCCG
1539 CCCAAGCCCG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 3 0.08
16 35 0.92
ACGTcount: A:0.34, C:0.42, G:0.19, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCGAATGA
Found at i:1683 original size:27 final size:27
Alignment explanation
Indices: 1649--1700 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1639 CCAAAAGCAA
* *
1649 ATCAATTTCCTGTAGACCTACATAATC
1 ATCAATTTCCCGTACACCTACATAATC
*
1676 ATCAATTTCCCGTACACCTATATAA
1 ATCAATTTCCCGTACACCTACATAA
1701 AATTGAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.33
Consensus pattern (27 bp):
ATCAATTTCCCGTACACCTACATAATC
Found at i:3471 original size:19 final size:19
Alignment explanation
Indices: 3424--3471 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
3414 TTGGGTTAAT
* *
3424 TAGATTTGGGATTGAGGGG
1 TAGATTTGGAATTGAGGGC
3443 TAGAATTTGGAAATTGA-GGC
1 TAG-ATTTGG-AATTGAGGGC
3463 TAGATTTGG
1 TAGATTTGG
3472 GTTCGAGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 9 0.36
20 11 0.44
21 5 0.20
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (19 bp):
TAGATTTGGAATTGAGGGC
Found at i:7016 original size:32 final size:32
Alignment explanation
Indices: 6978--7042 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
6968 CACTTTCCCT
6978 TTGAATTTAGAAATTTAGCCCAATTCACCCCC
1 TTGAATTTAGAAATTTAGCCCAATTCACCCCC
* * *
7010 TTGAATTTGGAAATTTAGGCCAATTTACCCCC
1 TTGAATTTAGAAATTTAGCCCAATTCACCCCC
7042 T
1 T
7043 AACATGACGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (32 bp):
TTGAATTTAGAAATTTAGCCCAATTCACCCCC
Found at i:9826 original size:13 final size:13
Alignment explanation
Indices: 9805--9928 Score: 61
Period size: 13 Copynumber: 8.8 Consensus size: 13
9795 ACGCCACTAT
9805 ATATAATTTCTAA
1 ATATAATTTCTAA
*
9818 ATATGATTTTCTAA
1 ATAT-AATTTCTAA
9832 ATATAATTTCATTACA
1 ATATAATTTC--TA-A
* * *
9848 TTTATTATTTCTAT
1 -ATATAATTTCTAA
9862 ATACT-ATTTCTAA
1 ATA-TAATTTCTAA
*
9875 ATGTAATTTCATTACA
1 ATATAATTTC--TA-A
* *
9891 TTTATTATTTCTAA
1 -ATATAATTTCTAA
*
9905 ATACTATTTTCTAA
1 ATA-TAATTTCTAA
*
9919 ATGTAATTTC
1 ATATAATTTC
9929 ATTACATTTA
Statistics
Matches: 83, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
12 1 0.01
13 33 0.40
14 24 0.29
15 8 0.10
16 2 0.02
17 15 0.18
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.52
Consensus pattern (13 bp):
ATATAATTTCTAA
Found at i:9830 original size:14 final size:14
Alignment explanation
Indices: 9805--9840 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
9795 ACGCCACTAT
9805 ATATAA-TTTCTAA
1 ATATAATTTTCTAA
*
9818 ATATGATTTTCTAA
1 ATATAATTTTCTAA
9832 ATATAATTT
1 ATATAATTT
9841 CATTACATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (14 bp):
ATATAATTTTCTAA
Found at i:9874 original size:43 final size:44
Alignment explanation
Indices: 9810--9971 Score: 222
Period size: 44 Copynumber: 3.7 Consensus size: 44
9800 ACTATATATA
*
9810 ATTTCTAAATA-TGATTTTCTAAATATAATTTCATTACATTTATT
1 ATTTCTAAATACT-ATTTTCTAAATGTAATTTCATTACATTTATT
*
9854 ATTTCTATATACTA-TTTCTAAATGTAATTTCATTACATTTATT
1 ATTTCTAAATACTATTTTCTAAATGTAATTTCATTACATTTATT
*
9897 ATTTCTAAATACTATTTTCTAAATGTAATTTCATTACATTTATA
1 ATTTCTAAATACTATTTTCTAAATGTAATTTCATTACATTTATT
* * * *
9941 AGTTGC-AAATATTATTTTGTAAATATAATTT
1 A-TTTCTAAATACTATTTTCTAAATGTAATTT
9972 ACAAATATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
43 41 0.38
44 62 0.58
45 4 0.04
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (44 bp):
ATTTCTAAATACTATTTTCTAAATGTAATTTCATTACATTTATT
Found at i:9957 original size:87 final size:88
Alignment explanation
Indices: 9810--9971 Score: 222
Period size: 87 Copynumber: 1.9 Consensus size: 88
9800 ACTATATATA
* * *
9810 ATTTCTAAATATGATTTTCTAAATATAATTTCATTACATTTATTATTTCTATATACTA-TTTCTA
1 ATTTCTAAATATGATTTTCTAAATATAATTTCATTACATTTATAATTGCTAAATACTATTTTCTA
*
9874 AATGTAATTTCATTACATTTATT
66 AATATAATTTCATTACATTTATT
* * *
9897 ATTTCTAAATACT-ATTTTCTAAATGTAATTTCATTACATTTATAAGTTGC-AAATATTATTTTG
1 ATTTCTAAATA-TGATTTTCTAAATATAATTTCATTACATTTATAA-TTGCTAAATACTATTTTC
9960 TAAATATAATTT
64 TAAATATAATTT
9972 ACAAATATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
87 47 0.72
88 18 0.28
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (88 bp):
ATTTCTAAATATGATTTTCTAAATATAATTTCATTACATTTATAATTGCTAAATACTATTTTCTA
AATATAATTTCATTACATTTATT
Found at i:9976 original size:27 final size:27
Alignment explanation
Indices: 9937--9998 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
9927 TCATTACATT
* * *
9937 TATAAGTTGCAAATATTATTTTGTAAA-
1 TATAATTTACAAATATTATTTT-CAAAG
9964 TATAATTTACAAATATTATTTTCAAAG
1 TATAATTTACAAATATTATTTTCAAAG
9991 TATAATTT
1 TATAATTT
9999 CAAGAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (27 bp):
TATAATTTACAAATATTATTTTCAAAG
Found at i:10272 original size:134 final size:133
Alignment explanation
Indices: 10046--10329 Score: 462
Period size: 134 Copynumber: 2.1 Consensus size: 133
10036 TTTACAAAAG
10046 AAAAACGCCACTATTTGCAAAACCTCAAAATTGGGCATGCCCGCGCGTGGCCAAGGTTTGGCCCG
1 AAAAACGCCACTATTTGCAAAACCTCAAAATTGGGCATGCCCGCGCGTGGCCAAGGTTTGGCCCG
*
10111 CGCGCAGCTTATCCCAGGCTGTTCACTTCAATTCAACTTGGTTATTGTATATGGCGGCGTTTAGT
66 CGCGCAGCTTATCCCAGGCTGTTCACTTCAATTCAACTTGGTTATTGTATATGGCGGCGTTT-GG
10176 TTAC
130 TTAC
* *
10180 AAAAACGCCACTATTTGCAAAACCTCAAAATTGGGCCTGCCCGCGCGTGGCCAAGTTTTGGCCCG
1 AAAAACGCCACTATTTGCAAAACCTCAAAATTGGGCATGCCCGCGCGTGGCCAAGGTTTGGCCCG
* * *
10245 CGCGC-GACTTATCCTAGGCTGTTCACTTCAATTCAACTTGGTTATTGTATATGGTGGTGTTTGG
66 CGCGCAG-CTTATCCCAGGCTGTTCACTTCAATTCAACTTGGTTATTGTATATGGCGGCGTTTGG
*
10309 TTAT
130 TTAC
* *
10313 AGAAACACCACTATTTG
1 AAAAACGCCACTATTTG
10330 ATACATTGAA
Statistics
Matches: 140, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
133 20 0.14
134 120 0.86
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.29
Consensus pattern (133 bp):
AAAAACGCCACTATTTGCAAAACCTCAAAATTGGGCATGCCCGCGCGTGGCCAAGGTTTGGCCCG
CGCGCAGCTTATCCCAGGCTGTTCACTTCAATTCAACTTGGTTATTGTATATGGCGGCGTTTGGT
TAC
Found at i:11353 original size:27 final size:27
Alignment explanation
Indices: 11299--11373 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
11289 GTTAGGTTGG
* *
11299 TTTTGGACTTGCACTTGGACATTATAGC
1 TTTT-GACTTGCATTTGGACCTTATAGC
*
11327 TTTTGACTTGCATTTGGACCTTTTAGC
1 TTTTGACTTGCATTTGGACCTTATAGC
* * * *
11354 CTTGGATTTGCTTTTGGACC
1 TTTTGACTTGCATTTGGACC
11374 ATAATGGAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (27 bp):
TTTTGACTTGCATTTGGACCTTATAGC
Found at i:15693 original size:44 final size:42
Alignment explanation
Indices: 15633--15729 Score: 126
Period size: 44 Copynumber: 2.3 Consensus size: 42
15623 ATATCCATTG
*
15633 ATATATG-TCATACATCC-TTCATGCATGGTCCATGTCTTTGTAT
1 ATATATGTTCATACATCCATT-ATGCATGATCCAT-TCTTT-TAT
* *
15676 ATATATGTTCATACATCCATTATGCATTATCCATTCTTTTGT
1 ATATATGTTCATACATCCATTATGCATGATCCATTCTTTTAT
15718 ATATATGTTCAT
1 ATATATGTTCAT
15730 GCATAGGTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
42 14 0.29
43 12 0.24
44 21 0.43
45 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (42 bp):
ATATATGTTCATACATCCATTATGCATGATCCATTCTTTTAT
Found at i:15743 original size:42 final size:43
Alignment explanation
Indices: 15633--15753 Score: 129
Period size: 42 Copynumber: 2.8 Consensus size: 43
15623 ATATCCATTG
* * **
15633 ATATATG-TCATACATCCTTCATGCATGGTCCATGTCTTTGTAT
1 ATATATGTTCATACATACATCATGCATTATCCAT-TCTTTGTAT
* * *
15676 ATATATGTTCATACATCCATTATGCATTATCCATTCTTT-TGT
1 ATATATGTTCATACATACATCATGCATTATCCATTCTTTGTAT
* **
15718 ATATATGTTCATGCATAGGTCATGCATTATCCATTC
1 ATATATGTTCATACATACATCATGCATTATCCATTC
15754 ATTACTCCAT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 33 0.49
43 12 0.18
44 22 0.33
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.43
Consensus pattern (43 bp):
ATATATGTTCATACATACATCATGCATTATCCATTCTTTGTAT
Done.