Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015299.1 Corchorus olitorius cultivar O-4 contig15332, 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: 12241
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:908 original size:27 final size:27
Alignment explanation
Indices: 871--969 Score: 144
Period size: 27 Copynumber: 3.7 Consensus size: 27
861 AGTGAGCTTA
* * *
871 AAATGACCAAAATGCCCCTGAATATGT
1 AAATGACAAAAATGCCCCTGAATGTGC
*
898 AAATGACCAAAATGCCCCTGAATGTGC
1 AAATGACAAAAATGCCCCTGAATGTGC
* *
925 AAATGACAAAAATGCCCCTGGACGTGC
1 AAATGACAAAAATGCCCCTGAATGTGC
952 AAATGACAAAAATGCCCC
1 AAATGACAAAAATGCCCC
970 ATAGATGACC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.17
Consensus pattern (27 bp):
AAATGACAAAAATGCCCCTGAATGTGC
Found at i:1701 original size:11 final size:13
Alignment explanation
Indices: 1674--1705 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
1664 AAAACCATTT
1674 ATAAAACATATTA
1 ATAAAACATATTA
1687 ATAAAACA-A-TA
1 ATAAAACATATTA
1698 ATAAAACA
1 ATAAAACA
1706 GTTCCTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAAAACATATTA
Found at i:3295 original size:7 final size:6
Alignment explanation
Indices: 3274--3324 Score: 68
Period size: 6 Copynumber: 8.3 Consensus size: 6
3264 AATCCTAACC
*
3274 TTTCTCT TTTCTT TTTCTT TTTCTT TTTCTT TTT-TCT TTTCAT TTTCTT
1 TTTCT-T TTTCTT TTTCTT TTTCTT TTTCTT TTTCT-T TTTCTT TTTCTT
3323 TT
1 TT
3325 ACTACTTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 1 0.03
6 34 0.85
7 5 0.12
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:3319 original size:13 final size:13
Alignment explanation
Indices: 3274--3313 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
3264 AATCCTAACC
*
3274 TTTCTCTTTTCTT
1 TTTCTTTTTTCTT
3287 TTTC-TTTTTCTT
1 TTTCTTTTTTCTT
3299 TTTCTTTTTTCTT
1 TTTCTTTTTTCTT
3312 TT
1 TT
3314 CATTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTCTTTTTTCTT
Found at i:6164 original size:21 final size:21
Alignment explanation
Indices: 6135--6178 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
6125 GTTTGGCTAC
6135 TGGAATGGGTGTTTATAACAG
1 TGGAATGGGTGTTTATAACAG
* *
6156 TGGATTGGGTGTTTATGACAG
1 TGGAATGGGTGTTTATAACAG
6177 TG
1 TG
6179 CGTAGTGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.36, T:0.36
Consensus pattern (21 bp):
TGGAATGGGTGTTTATAACAG
Found at i:7822 original size:20 final size:20
Alignment explanation
Indices: 7793--7838 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7783 GATCCTGCAG
* *
7793 ATGC-AAATGTGAGATTAAT
1 ATGCAAAATGTGACATAAAT
7812 ATGCAAAATGTGACATAAAT
1 ATGCAAAATGTGACATAAAT
7832 ATGCAAA
1 ATGCAAA
7839 GGAACACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (20 bp):
ATGCAAAATGTGACATAAAT
Found at i:8333 original size:23 final size:23
Alignment explanation
Indices: 8307--8381 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
8297 TTAAAGGACC
8307 GTCTTCCGCTTATCCTTTGAATT
1 GTCTTCCGCTTATCCTTTGAATT
** * * **
8330 GTCTTCCAATTCAT-CTTAAAGGACC
1 GTCTTCCGCTT-ATCCTT--TGAATT
8355 GTCTTCCGCTTATCCTTTGAATT
1 GTCTTCCGCTTATCCTTTGAATT
8378 GTCT
1 GTCT
8382 ACCAATTCAA
Statistics
Matches: 36, Mismatches: 12, Indels: 8
0.64 0.21 0.14
Matches are distributed among these distances:
23 18 0.50
24 4 0.11
25 14 0.39
ACGTcount: A:0.17, C:0.27, G:0.13, T:0.43
Consensus pattern (23 bp):
GTCTTCCGCTTATCCTTTGAATT
Found at i:8368 original size:48 final size:50
Alignment explanation
Indices: 8222--8495 Score: 376
Period size: 50 Copynumber: 5.5 Consensus size: 50
8212 CAATCAACTT
* * * * *
8222 CTTTGAATTATCTTCCAATCCAATATTAAAAGGACTGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * *
8272 GTTTGAACTGTTTTCCAATTGC-ATATT-AAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATT-CAATCTTAAAAGGACCGTCTTCCGCTTATC
*
8321 CTTTGAATTGTCTTCCAATTC-ATCTT-AAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * *
8369 CTTTGAATTGTCTACCAATTCAATCTTAAAAGGACCGCCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
8419 TTTTGAACTGTCTACCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
8470 CTTTGAACTGTCTTCCAATTCAATCT
1 CTTTGAACTGTCTTCCAATTCAATCT
8496 CGAGAAAACC
Statistics
Matches: 203, Mismatches: 17, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
48 47 0.23
49 43 0.21
50 66 0.33
51 47 0.23
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.38
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:8522 original size:101 final size:97
Alignment explanation
Indices: 8250--8495 Score: 280
Period size: 101 Copynumber: 2.5 Consensus size: 97
8240 TCCAATATTA
* * * * * **
8250 AAAGGACTGTCTTCCGCTTATCGTTTGAACTGTTTTCCAATTGCATAT-T-AAAGGACCGTCTTC
1 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATT-CA-ATCTGAAAAGACCACCTTC
* * * *
8313 CGCTTATCCTTTGAATTGTCTTCCAATTCATCTT
64 CGCATATCTTTTGAACTGTCTACCAATTCATCTT
* * *
8347 AAAGGACCGTCTTCCGCTTATCCTTTGAATTGTCTACCAATTCAATCTTAAAAGGACCGCCTTCC
1 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTGAAAA-GACCACCTTCC
*
8412 GCTTATCTTTTGAACTGTCTACCAATTCAATCTT
65 GCATATCTTTTGAACTGTCTACCAATTC-ATCTT
*
8446 AAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCT
1 --AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
8496 CGAGAAAACC
Statistics
Matches: 131, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
95 2 0.02
96 3 0.02
97 40 0.31
98 35 0.27
99 5 0.04
101 46 0.35
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (97 bp):
AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTGAAAAGACCACCTTCCG
CATATCTTTTGAACTGTCTACCAATTCATCTT
Found at i:8806 original size:65 final size:64
Alignment explanation
Indices: 8727--8851 Score: 205
Period size: 65 Copynumber: 1.9 Consensus size: 64
8717 AGTGCATCTC
* * *
8727 TTAATAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTCGAGAAACTATCTTCTGGTGTACTTT
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAAAT-TTCGAGAAACCATCTTCTGGTGTACTTT
*
8792 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAAATTTTGAGAAACCATCTTCTGGTGTA
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAAATTTCGAGAAACCATCTTCTGGTGTA
8852 ATCCTTAATG
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
64 22 0.39
65 34 0.61
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (64 bp):
TTAACAAGATCGTCTTCCGATCAACTTCTGAAAAATTTCGAGAAACCATCTTCTGGTGTACTTT
Found at i:8924 original size:67 final size:67
Alignment explanation
Indices: 8726--9118 Score: 442
Period size: 67 Copynumber: 5.9 Consensus size: 67
8716 CAGTGCATCT
* * * * * ** *
8726 CTTAATAAGATCGTCTTCCGATCAAC-TTCTGAAAACTC-TTCGAG-AAACTATCTTCTGGTGTA
1 CTTAATGAGATTGTCTTCCAATCAACATT-TGAAAATTCTTTCTAGCAAACCGTCTTCTGGTGTT
*
8788 CTT
65 CTC
* ** * * * * * *
8791 TTTAACAAGATCGTCTTCCGATCAAC-TTCTGAAAAAT-TTT-GAG-AAACCATCTTCTGGTGTA
1 CTTAATGAGATTGTCTTCCAATCAACATT-TGAAAATTCTTTCTAGCAAACCGTCTTCTGGTGTT
*
8852 ATC
65 CTC
* * *
8855 CTTAATGAGATTGTCTTTCAATCAACATTTGAAAATTCTTTCTGGCAAACCGTCTTCTGGTGTCC
1 CTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCTGGTGTTC
8920 TC
66 TC
* *
8922 CTTAGTGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTTC
1 CTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCTGGTGTTC
8987 TC
66 TC
8989 CTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCT-GTGTT
1 CTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTT-CTGGTGTT
9053 CTC
65 CTC
* * * * *
9056 CTTAATGAGATTGCCTTCCAATCATCTTTTGAAAATTCTTTCTATCAAACCGTCTTCCGGTGT
1 CTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCTGGTGT
9119 ACTTCTAAAA
Statistics
Matches: 291, Mismatches: 30, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
64 48 0.16
65 41 0.14
66 2 0.01
67 199 0.68
68 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (67 bp):
CTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCTGGTGTTC
TC
Found at i:10972 original size:23 final size:23
Alignment explanation
Indices: 10948--10991 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
10938 CATTTTAGCT
*
10948 TTTGA-TTCACTTTGATTTGAAC
1 TTTGATTTCAATTTGATTTGAAC
*
10970 TTTGATTTGAATTTGATTTGAA
1 TTTGATTTCAATTTGATTTGAA
10992 TTACTTAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (23 bp):
TTTGATTTCAATTTGATTTGAAC
Found at i:10973 original size:12 final size:12
Alignment explanation
Indices: 10956--10991 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
10946 CTTTTGATTC
10956 ACTTTGATTTGA
1 ACTTTGATTTGA
10968 ACTTTGATTTGA
1 ACTTTGATTTGA
10980 A-TTTGATTTGA
1 ACTTTGATTTGA
10991 A
1 A
10992 TTACTTAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.50
Consensus pattern (12 bp):
ACTTTGATTTGA
Found at i:10986 original size:11 final size:11
Alignment explanation
Indices: 10958--10993 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
10948 TTTGATTCAC
10958 TTTGATTTGAA
1 TTTGATTTGAA
10969 CTTTGATTTGAA
1 -TTTGATTTGAA
10981 TTTGATTTGAA
1 TTTGATTTGAA
10992 TT
1 TT
10994 ACTTAACGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.56
Consensus pattern (11 bp):
TTTGATTTGAA
Found at i:11303 original size:14 final size:13
Alignment explanation
Indices: 11278--11336 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 13
11268 TAAAAGACTC
11278 AAAACC-TTTTTG
1 AAAACCTTTTTTG
11290 AAAACCTATTTTTG
1 AAAACCT-TTTTTG
11304 AAAACCTTTTCTTG
1 AAAACCTTTT-TTG
*
11318 AAAACAATTTTCTTG
1 AAAAC-CTTTT-TTG
11333 AAAA
1 AAAA
11337 ACATGTCTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
12 6 0.14
13 3 0.07
14 21 0.50
15 12 0.29
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (13 bp):
AAAACCTTTTTTG
Found at i:11339 original size:16 final size:15
Alignment explanation
Indices: 11301--11336 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
11291 AAACCTATTT
*
11301 TTGAAAAC-CTTTTC
1 TTGAAAACAATTTTC
11315 TTGAAAACAATTTTC
1 TTGAAAACAATTTTC
11330 TTGAAAA
1 TTGAAAA
11337 ACATGTCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (15 bp):
TTGAAAACAATTTTC
Done.