Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012446.1 Corchorus olitorius cultivar O-4 contig12479, 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: 36240
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:483 original size:19 final size:19
Alignment explanation
Indices: 459--497 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
449 AAAGGGTAAT
*
459 TAAAAAAAAATTGTTTTCA
1 TAAAAAAAAAGTGTTTTCA
478 TAAAAAAAAAGTGTTTTCA
1 TAAAAAAAAAGTGTTTTCA
497 T
1 T
498 GATAGAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (19 bp):
TAAAAAAAAAGTGTTTTCA
Found at i:7088 original size:37 final size:37
Alignment explanation
Indices: 7036--7108 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
7026 ATGAGTTAAA
*
7036 AAAAAACTGGACCTAAAACAGAAAGAGGTCAGAAAAG
1 AAAAAACAGGACCTAAAACAGAAAGAGGTCAGAAAAG
*
7073 AAAAAACAGGGCCTAAAACAGAAAGAGGTCAGAAAA
1 AAAAAACAGGACCTAAAACAGAAAGAGGTCAGAAAA
7109 AAGAAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.58, C:0.14, G:0.22, T:0.07
Consensus pattern (37 bp):
AAAAAACAGGACCTAAAACAGAAAGAGGTCAGAAAAG
Found at i:7113 original size:18 final size:18
Alignment explanation
Indices: 7050--7114 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
7040 AACTGGACCT
*
7050 AAAACAGAAAGAGGTCAG
1 AAAAAAGAAAGAGGTCAG
* * * **
7068 AAAAGAAAAAACAGGGCCT
1 AAAA-AAGAAAGAGGTCAG
*
7087 AAAACAGAAAGAGGTCAG
1 AAAAAAGAAAGAGGTCAG
7105 AAAAAAGAAA
1 AAAAAAGAAA
7115 TAAATAAAAG
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
18 21 0.64
19 12 0.36
ACGTcount: A:0.62, C:0.11, G:0.23, T:0.05
Consensus pattern (18 bp):
AAAAAAGAAAGAGGTCAG
Found at i:9802 original size:59 final size:59
Alignment explanation
Indices: 9733--10191 Score: 649
Period size: 59 Copynumber: 7.7 Consensus size: 59
9723 ATTCCCCTTT
9733 TTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATC
1 TTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATC
9792 TTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATC
1 TTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATC
* *
9851 TTGTTTTTAAAATCATGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTT-AGT-
1 TTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT-TTCA-TC
* * *
9910 TTGTTTTTAAAATCCTGTTCGAGGTCTCTTTTATAGAATTTTCAATTCAAAATTTCATC
1 TTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATC
9969 TTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATC
1 TTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATC
* * * * * *
10028 TTGTTTTTAAAAATCATGTTCGAGGTCTTTGGTAGAGAGTTTTAAATTCCAAATCTT-GTC
1 TTGTTTTT-AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT-TTCATC
* **
10088 TTGTCTTTTAAAATCCTGATT-GAGGTCTCTAG-TAGAGAGTTTTTCGATTCAAAATCGCATC
1 TTGT-TTTTAAAATCCTG-TTCGAGGTCTCT-GTTAGAGAG-TTTTCAATTCAAAATTTCATC
* * * *
10149 TTGCTTTTAAAACCCTGTTCGAGGTCTGTGGTAGAGAGTTTTC
1 TTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTC
10192 TTTTTTTAAA
Statistics
Matches: 360, Mismatches: 27, Indels: 26
0.87 0.07 0.06
Matches are distributed among these distances:
58 3 0.01
59 232 0.64
60 99 0.28
61 26 0.07
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (59 bp):
TTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATC
Found at i:10028 original size:177 final size:177
Alignment explanation
Indices: 9732--10191 Score: 717
Period size: 177 Copynumber: 2.6 Consensus size: 177
9722 AATTCCCCTT
* *
9732 TTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATCTTGTT
1 TTTGTTTTTAAAATCCTGTTCGAGGTCTCTATTAGAGAATTTTCAATTCAAAATTTCATCTTGTT
9797 TTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATCTTGTTTTT-AA
66 TTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATCTTGTTTTTAAA
*
9861 AATCATGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTAG
131 AATCATGTTCGAGGTCTCTGGTAGAGAGTTTTAAATTCAAAATCTT-G
* *
9909 TTTGTTTTTAAAATCCTGTTCGAGGTCTCTTTTATAGAATTTTCAATTCAAAATTTCATCTTGTT
1 TTTGTTTTTAAAATCCTGTTCGAGGTCTCTATTAGAGAATTTTCAATTCAAAATTTCATCTTGTT
9974 TTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATCTTGTTTTTAAA
66 TTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATCTTGTTTTTAAA
* *
10039 AATCATGTTCGAGGTCTTTGGTAGAGAGTTTTAAATTCCAAATCTTG
131 AATCATGTTCGAGGTCTCTGGTAGAGAGTTTTAAATTCAAAATCTTG
* * * **
10086 TCTTGTCTTTTAAAATCCTGATT-GAGGTCTCTAGTAGAGAGTTTTTCGATTCAAAATCGCATCT
1 T-TTGT-TTTTAAAATCCTG-TTCGAGGTCTCTATTAGAGA-ATTTTCAATTCAAAATTTCATCT
* * * *
10150 TGCTTTTAAAACCCTGTTCGAGGTCTGTGGTAGAGAGTTTTC
62 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTC
10192 TTTTTTTAAA
Statistics
Matches: 261, Mismatches: 17, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
177 126 0.48
178 49 0.19
179 27 0.10
180 59 0.23
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (177 bp):
TTTGTTTTTAAAATCCTGTTCGAGGTCTCTATTAGAGAATTTTCAATTCAAAATTTCATCTTGTT
TTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTCATCTTGTTTTTAAA
AATCATGTTCGAGGTCTCTGGTAGAGAGTTTTAAATTCAAAATCTTG
Found at i:10515 original size:29 final size:29
Alignment explanation
Indices: 10473--10690 Score: 285
Period size: 29 Copynumber: 7.5 Consensus size: 29
10463 TTATTTCTTA
*
10473 ATTGGTCATTTTTGCACATTCAAGGGCAT
1 ATTGGTCATTTTTGCACATTCAGGGGCAT
10502 ATTGGTCATTTTTGCACATTCAGGGGCAT
1 ATTGGTCATTTTTGCACATTCAGGGGCAT
10531 ATTGGTCATTTTTGCACATTCAGGGGCAT
1 ATTGGTCATTTTTGCACATTCAGGGGCAT
* **
10560 ATTGGTCATTTTTGCACATCCAGGGATAT
1 ATTGGTCATTTTTGCACATTCAGGGGCAT
* * *
10589 TTTGGTCATTTTTTGCATATCCAGGGGCAT
1 ATTGGTCA-TTTTTGCACATTCAGGGGCAT
* * **
10619 TTTGGTCTTTTTTGCACATTCAACGGCAT
1 ATTGGTCATTTTTGCACATTCAGGGGCAT
* *
10648 TTTGGTCATTTTTGCACTTTCAGGGGCACT
1 ATTGGTCATTTTTGCACATTCAGGGGCA-T
*
10678 -CTGGTCATTTTTG
1 ATTGGTCATTTTTG
10691 AATGCTCTAG
Statistics
Matches: 169, Mismatches: 18, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
29 143 0.85
30 26 0.15
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (29 bp):
ATTGGTCATTTTTGCACATTCAGGGGCAT
Found at i:10639 original size:88 final size:87
Alignment explanation
Indices: 10473--10690 Score: 280
Period size: 88 Copynumber: 2.5 Consensus size: 87
10463 TTATTTCTTA
*
10473 ATTGGTCATTTTTGCACATTCAAGGGCATATTGGTCATTTTTGCACATTCAGGGGCATATTGGTC
1 ATTGGTCATTTTTGCACATTCAAGGGCATATTGGTCATTTTTGCACATCCAGGGGCATATTGGTC
**
10538 ATTTTTGCACATTCAGGGGCAT
66 ATTTTTGCACATTCAACGGCAT
* * *
10560 ATTGGTCATTTTTGCACA-TCCAGGG-ATATTTTGGTCATTTTTTGCATATCCAGGGGCATTTTG
1 ATTGGTCATTTTTGCACATTCAAGGGCATA--TTGGTCA-TTTTTGCACATCCAGGGGCATATTG
*
10623 GTCTTTTTTGCACATTCAACGGCAT
63 GTCATTTTTGCACATTCAACGGCAT
* * * *
10648 TTTGGTCATTTTTGCACTTTCAGGGGCACT-CTGGTCATTTTTG
1 ATTGGTCATTTTTGCACATTCAAGGGCA-TATTGGTCATTTTTG
10691 AATGCTCTAG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
85 3 0.03
86 6 0.05
87 31 0.27
88 66 0.58
89 5 0.04
90 1 0.01
91 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (87 bp):
ATTGGTCATTTTTGCACATTCAAGGGCATATTGGTCATTTTTGCACATCCAGGGGCATATTGGTC
ATTTTTGCACATTCAACGGCAT
Found at i:10683 original size:117 final size:116
Alignment explanation
Indices: 10474--10690 Score: 319
Period size: 117 Copynumber: 1.9 Consensus size: 116
10464 TATTTCTTAA
* **
10474 TTGGTCATTTTTGCACATTCAAGGGCATATTGGTCATTTTTGCACATTCAGGGGCATATTGGTCA
1 TTGGTCATTTTTGCACATCCAAGGGCATATTGGTCATTTTTGCACATTCAACGGCATATTGGTCA
*
10539 TTTTTGCACATTCAGGGGCATATTGGTCATTTTTGCACATCCAGGGATATT
66 TTTTTGCACATTCAGGGGCATACTGGTCATTTTTGCACATCCAGGGATATT
* * * * *
10590 TTGGTCATTTTTTGCATATCCAGGGGCATTTTGGTCTTTTTTGCACATTCAACGGCATTTTGGTC
1 TTGGTCA-TTTTTGCACATCCAAGGGCATATTGGTCATTTTTGCACATTCAACGGCATATTGGTC
*
10655 ATTTTTGCACTTTCAGGGGCACT-CTGGTCATTTTTG
65 ATTTTTGCACATTCAGGGGCA-TACTGGTCATTTTTG
10691 AATGCTCTAG
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
116 7 0.08
117 81 0.91
118 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (116 bp):
TTGGTCATTTTTGCACATCCAAGGGCATATTGGTCATTTTTGCACATTCAACGGCATATTGGTCA
TTTTTGCACATTCAGGGGCATACTGGTCATTTTTGCACATCCAGGGATATT
Found at i:19934 original size:30 final size:30
Alignment explanation
Indices: 19894--19991 Score: 133
Period size: 30 Copynumber: 3.3 Consensus size: 30
19884 GGCTGACTCC
* * *
19894 TCAAACTCTTCTTCGGGATCCTCATTCAGG
1 TCAAAATCTTCTTCGGGATCCTCATCCGGG
19924 TCAAAATCTTCTTCGGGATCCTCATCCGGG
1 TCAAAATCTTCTTCGGGATCCTCATCCGGG
* ** *
19954 TCAAAATCATCTTTAGGATCCACATCCGGG
1 TCAAAATCTTCTTCGGGATCCTCATCCGGG
19984 TCAAAATC
1 TCAAAATC
19992 ATCCTCATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.30
Consensus pattern (30 bp):
TCAAAATCTTCTTCGGGATCCTCATCCGGG
Found at i:24456 original size:3 final size:3
Alignment explanation
Indices: 24448--24472 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
24438 TTTTCTTTCT
24448 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
24473 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:24787 original size:20 final size:20
Alignment explanation
Indices: 24762--24813 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
24752 TACTTATATC
*
24762 ATTTGGGTTTTAGGGTTAGT-
1 ATTTGGGTTTTAGAGTTA-TA
24782 ATTTGGGTTTTAGAGTTATA
1 ATTTGGGTTTTAGAGTTATA
*
24802 ACTTGGGTTTTA
1 ATTTGGGTTTTA
24814 TTAGTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (20 bp):
ATTTGGGTTTTAGAGTTATA
Found at i:28627 original size:34 final size:35
Alignment explanation
Indices: 28571--28668 Score: 162
Period size: 34 Copynumber: 2.8 Consensus size: 35
28561 CGGCAAAGAA
*
28571 AAAGTGGAGAATTACATATTGCAAAACCTGAATTT
1 AAAGTGGAGAATTACATCTTGCAAAACCTGAATTT
*
28606 AAAGTGGAG-ATTACATCTTGCAAAACATGAATTT
1 AAAGTGGAGAATTACATCTTGCAAAACCTGAATTT
*
28640 ATAGTGGAGAATTACATCTTGCAAAACCT
1 AAAGTGGAGAATTACATCTTGCAAAACCT
28669 TTAAACATTC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
34 31 0.53
35 27 0.47
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (35 bp):
AAAGTGGAGAATTACATCTTGCAAAACCTGAATTT
Found at i:28991 original size:12 final size:12
Alignment explanation
Indices: 28960--28995 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
28950 GGAGCCAAAA
* *
28960 ATACATACATAC
1 ATACATATATAT
28972 ATACATATATAT
1 ATACATATATAT
28984 ATACATATATAT
1 ATACATATATAT
28996 GTATTTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (12 bp):
ATACATATATAT
Done.