Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014592.1 Corchorus olitorius cultivar O-4 contig14625, 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: 42265
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:632 original size:5 final size:5
Alignment explanation
Indices: 622--667 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
612 TTTTCAATCT
622 AAAA- AAAA- AAAA- AAAA- AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
668 TTCCACTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 16 0.39
5 25 0.61
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:1401 original size:55 final size:55
Alignment explanation
Indices: 1342--1451 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
1332 ATCCTCCATC
1342 CTGATGGTATAAATTTCTTCACACCATCAGAACTAATTTCTACATCCTGATGGTA
1 CTGATGGTATAAATTTCTTCACACCATCAGAACTAATTTCTACATCCTGATGGTA
*
1397 CTGATGGTATAAATTTCTTCACACCATCAGAACTAATTTCTTCATCCTGATGGTA
1 CTGATGGTATAAATTTCTTCACACCATCAGAACTAATTTCTACATCCTGATGGTA
1452 TAAATTTCTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (55 bp):
CTGATGGTATAAATTTCTTCACACCATCAGAACTAATTTCTACATCCTGATGGTA
Found at i:1438 original size:23 final size:23
Alignment explanation
Indices: 1408--1528 Score: 67
Period size: 23 Copynumber: 5.3 Consensus size: 23
1398 TGATGGTATA
1408 AATTTCTTCACACCATCAGAACT
1 AATTTCTTCACACCATCAGAACT
* * *
1431 AATTTCTTCATC-CTGAT-GGTA-T
1 AATTTCTTCA-CAC-CATCAGAACT
*
1453 AAATTTC-TCACACCATCAGAACC
1 -AATTTCTTCACACCATCAGAACT
** * *
1476 AATTTCTTCATCATGAT-GGTA-T
1 AATTTCTTCA-CACCATCAGAACT
*
1498 AAATTTC-TCACACCATCAGAACC
1 -AATTTCTTCACACCATCAGAACT
1521 AATTTCTT
1 AATTTCTT
1529 TATCCTGATG
Statistics
Matches: 69, Mismatches: 17, Indels: 24
0.63 0.15 0.22
Matches are distributed among these distances:
21 7 0.10
22 24 0.35
23 31 0.45
24 7 0.10
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (23 bp):
AATTTCTTCACACCATCAGAACT
Found at i:1480 original size:45 final size:45
Alignment explanation
Indices: 1397--1721 Score: 463
Period size: 45 Copynumber: 7.4 Consensus size: 45
1387 CCTGATGGTA
*
1397 CTGATGGTATAAATTTCTTCACACCATCAGAACTAATTTCTTCATC
1 CTGATGGTATAAATTTC-TCACACCATCAGAACCAATTTCTTCATC
1443 CTGATGGTATAAATTTCTCACACCATCAGAACCAATTTCTTCATC
1 CTGATGGTATAAATTTCTCACACCATCAGAACCAATTTCTTCATC
* *
1488 ATGATGGTATAAATTTCTCACACCATCAGAACCAATTTCTTTATC
1 CTGATGGTATAAATTTCTCACACCATCAGAACCAATTTCTTCATC
* *
1533 CTGATGGTATAAATTTCTCACACCATCAGAACCGATTTCTTTATC
1 CTGATGGTATAAATTTCTCACACCATCAGAACCAATTTCTTCATC
*
1578 CTGATGGTATAAATTTCTCACACCATCAGAACCGA----TT--T-
1 CTGATGGTATAAATTTCTCACACCATCAGAACCAATTTCTTCATC
* * *
1616 C---TGGTATAAGTTTCTCACACCATCATAACCAATTTCTTTATC
1 CTGATGGTATAAATTTCTCACACCATCAGAACCAATTTCTTCATC
* *
1658 CTGATGGTATAAATTTCTTCACACCATCAGAACTAATTTCTCCATC
1 CTGATGGTATAAATTTC-TCACACCATCAGAACCAATTTCTTCATC
1704 CTGATGGTATAAATTTCT
1 CTGATGGTATAAATTTCT
1722 TCTTTTTTAT
Statistics
Matches: 255, Mismatches: 13, Indels: 23
0.88 0.04 0.08
Matches are distributed among these distances:
35 28 0.11
38 1 0.00
39 3 0.01
41 3 0.01
42 1 0.00
45 161 0.63
46 58 0.23
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (45 bp):
CTGATGGTATAAATTTCTCACACCATCAGAACCAATTTCTTCATC
Found at i:1482 original size:22 final size:22
Alignment explanation
Indices: 1454--1527 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
1444 TGATGGTATA
1454 AATTTCTCACACCATCAGAACC
1 AATTTCTCACACCATCAGAACC
** * * **
1476 AATTTCTTCATCATGAT-GGTATA
1 AATTTC-TCA-CACCATCAGAACC
1499 AATTTCTCACACCATCAGAACC
1 AATTTCTCACACCATCAGAACC
1521 AATTTCT
1 AATTTCT
1528 TTATCCTGAT
Statistics
Matches: 37, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
21 4 0.11
22 18 0.49
23 11 0.30
24 4 0.11
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (22 bp):
AATTTCTCACACCATCAGAACC
Found at i:1630 original size:35 final size:35
Alignment explanation
Indices: 1582--1652 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1572 TTTATCCTGA
*
1582 TGGTATAAATTTCTCACACCATCAGAACCGATTTC
1 TGGTATAAATTTCTCACACCATCAGAACCAATTTC
* *
1617 TGGTATAAGTTTCTCACACCATCATAACCAATTTC
1 TGGTATAAATTTCTCACACCATCAGAACCAATTTC
1652 T
1 T
1653 TTATCCTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (35 bp):
TGGTATAAATTTCTCACACCATCAGAACCAATTTC
Found at i:1670 original size:80 final size:81
Alignment explanation
Indices: 1537--1690 Score: 274
Period size: 80 Copynumber: 1.9 Consensus size: 81
1527 TTTATCCTGA
*
1537 TGGTATAAATTTCTCACACCATCAGAACCGATTTCTTTATCCTGATGGTATAAATTTC-TCACAC
1 TGGTATAAATTTCTCACACCATCAGAACCAATTTCTTTATCCTGATGGTATAAATTTCTTCACAC
1601 CATCAGAACCGATTTC
66 CATCAGAACCGATTTC
* *
1617 TGGTATAAGTTTCTCACACCATCATAACCAATTTCTTTATCCTGATGGTATAAATTTCTTCACAC
1 TGGTATAAATTTCTCACACCATCAGAACCAATTTCTTTATCCTGATGGTATAAATTTCTTCACAC
1682 CATCAGAAC
66 CATCAGAAC
1691 TAATTTCTCC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
80 55 0.79
81 15 0.21
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (81 bp):
TGGTATAAATTTCTCACACCATCAGAACCAATTTCTTTATCCTGATGGTATAAATTTCTTCACAC
CATCAGAACCGATTTC
Found at i:1696 original size:46 final size:46
Alignment explanation
Indices: 1617--1723 Score: 162
Period size: 46 Copynumber: 2.3 Consensus size: 46
1607 AACCGATTTC
* * **
1617 TGGTATAAGTTTC-TCACACCATCATAACCAATTTCTTTATCCTGA
1 TGGTATAAATTTCTTCACACCATCAGAACCAATTTCTCCATCCTGA
*
1662 TGGTATAAATTTCTTCACACCATCAGAACTAATTTCTCCATCCTGA
1 TGGTATAAATTTCTTCACACCATCAGAACCAATTTCTCCATCCTGA
1708 TGGTATAAATTTCTTC
1 TGGTATAAATTTCTTC
1724 TTTTTTATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 12 0.21
46 44 0.79
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.38
Consensus pattern (46 bp):
TGGTATAAATTTCTTCACACCATCAGAACCAATTTCTCCATCCTGA
Found at i:4840 original size:21 final size:21
Alignment explanation
Indices: 4807--4860 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
4797 CTCAACCTGG
*
4807 GCACCCACATGG-TTGCCTTGA
1 GCACCCACGTGGTTTG-CTTGA
*
4828 GCACCCATGTGGTTTGCTTGA
1 GCACCCACGTGGTTTGCTTGA
* *
4849 GGACCCAGGTGG
1 GCACCCACGTGG
4861 GCAGTGTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.17, C:0.28, G:0.31, T:0.24
Consensus pattern (21 bp):
GCACCCACGTGGTTTGCTTGA
Found at i:8319 original size:157 final size:157
Alignment explanation
Indices: 8006--8306 Score: 575
Period size: 157 Copynumber: 1.9 Consensus size: 157
7996 CTCTTCAGGA
* *
8006 TATGGAGTGTGAAAAGCAGGTCTACCCGTCCTTCTGAGTTCAGGACCAAGCATCTCTTGAACTAT
1 TATGGAGTGTGAAAAGCAGGTCTACCCGTCCTTCTGAGTCCAGGACCAAGCATCTCTTAAACTAT
*
8071 ATCTATGATCTGATTGCGATCGAGCCCTGGAACTTCCTGTCTGAATACTTCAGCACGATCGTGGG
66 ATCTATGATCTAATTGCGATCGAGCCCTGGAACTTCCTGTCTGAATACTTCAGCACGATCGTGGG
8136 GGCGCACCTGTGCTCTAGGAGCGTGGC
131 GGCGCACCTGTGCTCTAGGAGCGTGGC
8163 TATGGAGTGTGAAAAGCAGGTCTACCCGTCCTTCTGAGTCCAGGACCAAGCATCTCTTAAACTAT
1 TATGGAGTGTGAAAAGCAGGTCTACCCGTCCTTCTGAGTCCAGGACCAAGCATCTCTTAAACTAT
8228 ATCTATGATCTAATTGCGATCGAGCCCTGGAACTTCCTGTCTGAATACTTCAGCACGATCGTGGG
66 ATCTATGATCTAATTGCGATCGAGCCCTGGAACTTCCTGTCTGAATACTTCAGCACGATCGTGGG
8293 GGCGCACCTGTGCT
131 GGCGCACCTGTGCT
8307 TTGGGAGTGT
Statistics
Matches: 141, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 141 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (157 bp):
TATGGAGTGTGAAAAGCAGGTCTACCCGTCCTTCTGAGTCCAGGACCAAGCATCTCTTAAACTAT
ATCTATGATCTAATTGCGATCGAGCCCTGGAACTTCCTGTCTGAATACTTCAGCACGATCGTGGG
GGCGCACCTGTGCTCTAGGAGCGTGGC
Found at i:13373 original size:15 final size:16
Alignment explanation
Indices: 13353--13382 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13343 AATATTAAAA
13353 TTTTGA-ATTTCATTC
1 TTTTGAGATTTCATTC
13368 TTTTGAGATTTCATT
1 TTTTGAGATTTCATT
13383 TGGATATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (16 bp):
TTTTGAGATTTCATTC
Found at i:13595 original size:5 final size:5
Alignment explanation
Indices: 13585--13619 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
13575 TTATTAGATA
13585 TTATT TTATT TTATT TTATGT TTATT TTATT TTAT
1 TTATT TTATT TTATT TTAT-T TTATT TTATT TTAT
13620 GTAATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:13608 original size:16 final size:16
Alignment explanation
Indices: 13585--13621 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
13575 TTATTAGATA
13585 TTAT-TTTATTTTATT
1 TTATGTTTATTTTATT
13600 TTATGTTTATTTTATT
1 TTATGTTTATTTTATT
13616 TTATGT
1 TTATGT
13622 AATATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (16 bp):
TTATGTTTATTTTATT
Found at i:20667 original size:20 final size:17
Alignment explanation
Indices: 20642--20685 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
20632 TTATATAATC
20642 AAATATATGTTAAACATTAT
1 AAATATATG--AAA-ATTAT
20662 AAATATTATGAAAATTAT
1 AAATA-TATGAAAATTAT
20680 AAATAT
1 AAATAT
20686 TTAGTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 10 0.43
19 3 0.13
20 5 0.22
21 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (17 bp):
AAATATATGAAAATTAT
Found at i:21457 original size:21 final size:23
Alignment explanation
Indices: 21411--21457 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
21401 TGATAATTTA
*
21411 AAACACGACAAATAACATGTTAC
1 AAACACGACAAATAACATGATAC
*
21434 AAACACGACACA-AA-ATGATAC
1 AAACACGACAAATAACATGATAC
21455 AAA
1 AAA
21458 AATAGTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.57, C:0.21, G:0.09, T:0.13
Consensus pattern (23 bp):
AAACACGACAAATAACATGATAC
Found at i:29975 original size:2 final size:2
Alignment explanation
Indices: 29968--29993 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29958 TAGCTAGACC
29968 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
29994 AAATCAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30749 original size:2 final size:2
Alignment explanation
Indices: 30744--30821 Score: 81
Period size: 2 Copynumber: 38.5 Consensus size: 2
30734 TTGATTTTGA
*
30744 AT AT AT AT AT AT AT AT AT -T AT AT AT AT GAT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
*
30786 GAT -T TT GA- AT AT AT AT AT AT AT AT AT GAT AT AT AT A
1 -AT AT AT -AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A
30822 ATTTGATTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
1 3 0.05
2 58 0.88
3 5 0.08
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30819 original size:41 final size:41
Alignment explanation
Indices: 30752--30831 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
30742 GAATATATAT
30752 ATATATATATTATATATATGATATATATATATTTGATTTTGA
1 ATATATATATTATATATATGATATATATA-ATTTGATTTTGA
30794 ATATATATA-TATATATATGATATATATAATTTGATTTT
1 ATATATATATTATATATATGATATATATAATTTGATTTT
30832 TCTAATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 10 0.26
41 19 0.50
42 9 0.24
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (41 bp):
ATATATATATTATATATATGATATATATAATTTGATTTTGA
Found at i:35940 original size:80 final size:80
Alignment explanation
Indices: 35802--35968 Score: 325
Period size: 80 Copynumber: 2.1 Consensus size: 80
35792 ATCTGCCCAT
35802 GAGATGAAAATACCTCATGGACATACATAGCAAGGCCCAAGTCGTCTCCCATACAGAAGAGAGGC
1 GAGA-GAAAATACCTCATGGACATACATAGCAAGGCCCAAGTCGTCTCCCATACAGAAGAGAGGC
35867 CGCCCTCTGCCCTGCA
65 CGCCCTCTGCCCTGCA
35883 GAGAGAAAATACCTCATGGACATACATAGCAAGGCCCAAGTCGTCTCCCATACAGAAGAGAGGCC
1 GAGAGAAAATACCTCATGGACATACATAGCAAGGCCCAAGTCGTCTCCCATACAGAAGAGAGGCC
35948 GCCCTCTGCCCTGCA
66 GCCCTCTGCCCTGCA
35963 GAGAGA
1 GAGAGA
35969 TATTTTTCTC
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 82 0.95
81 4 0.05
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (80 bp):
GAGAGAAAATACCTCATGGACATACATAGCAAGGCCCAAGTCGTCTCCCATACAGAAGAGAGGCC
GCCCTCTGCCCTGCA
Found at i:38849 original size:41 final size:41
Alignment explanation
Indices: 38804--38885 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
38794 TTCACCTAAA
38804 GATGAATATCAAATGCCAATAGCAGACATGCTTATTGATTC
1 GATGAATATCAAATGCCAATAGCAGACATGCTTATTGATTC
* *
38845 GATGAATATCCAATGCCAATATCAGACATGCTTATTGATTC
1 GATGAATATCAAATGCCAATAGCAGACATGCTTATTGATTC
38886 TGCTGCTGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (41 bp):
GATGAATATCAAATGCCAATAGCAGACATGCTTATTGATTC
Done.