Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021155.1 Corchorus olitorius cultivar O-4 contig21188, 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: 48430
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:551 original size:30 final size:32
Alignment explanation
Indices: 497--562 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
487 GACTAAATAT
*
497 CAAAAAAATCCCTTATATTTTTCTTT-TGGGA
1 CAAAAAAATCCCTTATAGTTTTCTTTATGGGA
*
528 CAAAATAATCCCTTAT-GTTTTCTTTATGGGA
1 CAAAAAAATCCCTTATAGTTTTCTTTATGGGA
559 CAAA
1 CAAA
563 TTAGTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (32 bp):
CAAAAAAATCCCTTATAGTTTTCTTTATGGGA
Found at i:4643 original size:3 final size:3
Alignment explanation
Indices: 4635--4693 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
4625 AATTATATTG
4635 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4683 TAA TAA TAA TA
1 TAA TAA TAA TA
4694 CACTTGGATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:9677 original size:24 final size:24
Alignment explanation
Indices: 9625--9678 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
9615 ATAAATGTTG
*
9625 TTGATAA-TCTTCTCTTTTATCTC
1 TTGATAATTCTTCTCTTTTATCAC
9648 -TGATAATTC-TCTCTATTTATCAC
1 TTGATAATTCTTCTCT-TTTATCAC
9671 TTGATAAT
1 TTGATAAT
9679 ATCTAGCCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 11 0.41
23 9 0.33
24 7 0.26
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.52
Consensus pattern (24 bp):
TTGATAATTCTTCTCTTTTATCAC
Found at i:9989 original size:118 final size:121
Alignment explanation
Indices: 9859--10081 Score: 296
Period size: 121 Copynumber: 1.8 Consensus size: 121
9849 TTAAACCCAT
* *
9859 TGTCTTCTGGACAAATGT-AA-C-ATGTGCTCTTATTGCCTCATTAAAAACTTTAAGTCGGAAAA
1 TGTCTTCTGGAC-AAT-TCAATCAATGTGCTATTATTGCCTCATTAAAAACCTTAAGTCGGAAAA
*
9921 CCCAGT-GG-AAACCGAACAGAAGGGAAAAAGAGTGCAGAGCAATTAAATCCATGTAA
64 CCCAGTAGGAAAACCGAACAGAAGGAAAAAAGAGTGCAGAGCAATTAAATCCATGTAA
*
9977 TGTCTT-TAGGACAATTCAATCTAGATGTGCTATTGTTGCCTCATTAAAAACCTTAAGTCGGAAA
1 TGTCTTCT-GGACAATTCAATC-A-ATGTGCTATTATTGCCTCATTAAAAACCTTAAGTCGGAAA
*
10041 ACCTAGTAGGATAAAACCGAACAGAAGGAAAAAAGAGTGCA
63 ACCCAGTAGG--AAAACCGAACAGAAGGAAAAAAGAGTGCA
10082 ACGCACTTTA
Statistics
Matches: 90, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
116 1 0.01
117 6 0.07
118 11 0.12
121 43 0.48
122 2 0.02
125 27 0.30
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (121 bp):
TGTCTTCTGGACAATTCAATCAATGTGCTATTATTGCCTCATTAAAAACCTTAAGTCGGAAAACC
CAGTAGGAAAACCGAACAGAAGGAAAAAAGAGTGCAGAGCAATTAAATCCATGTAA
Found at i:10464 original size:16 final size:15
Alignment explanation
Indices: 10443--10472 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
10433 TTTTCAGAAG
10443 AAGAAAAAAGAAAAAT
1 AAGAAAAAA-AAAAAT
10459 AAGAAAAAAAAAAA
1 AAGAAAAAAAAAAA
10473 CAAAAACGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (15 bp):
AAGAAAAAAAAAAAT
Found at i:13520 original size:2 final size:2
Alignment explanation
Indices: 13513--13545 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
13503 CTAATCATCT
13513 TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13546 TAATATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13546 original size:10 final size:10
Alignment explanation
Indices: 13516--13551 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
13506 ATCATCTTAT
13516 ATATATATATA
1 ATATATAT-TA
13527 TATATATATTA
1 -ATATATATTA
13538 ATATATATTA
1 ATATATATTA
13548 ATAT
1 ATAT
13552 TAATATTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 2 0.08
12 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATATATTA
Found at i:13551 original size:16 final size:18
Alignment explanation
Indices: 13520--13557 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
13510 TCTTATATAT
13520 ATATATATATATATATTA
1 ATATATATATATATATTA
13538 ATATATAT-TA-ATATTA
1 ATATATATATATATATTA
13554 ATAT
1 ATAT
13558 TATGATCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 2 0.10
18 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATATATATATTA
Found at i:21100 original size:40 final size:40
Alignment explanation
Indices: 21038--21117 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
21028 AACTAATGAC
* *
21038 TTTCTTTTCTTAACTAAATTTTCTTAAAAGCACTTATAAA
1 TTTCATTTCTTAACTAAATTTTCTTAAAAGAACTTATAAA
* *
21078 TTTCATTTCTTAACTGAGTTTTCTTAAAAGAACTTATAAA
1 TTTCATTTCTTAACTAAATTTTCTTAAAAGAACTTATAAA
21118 ATAAAACAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (40 bp):
TTTCATTTCTTAACTAAATTTTCTTAAAAGAACTTATAAA
Found at i:21393 original size:128 final size:130
Alignment explanation
Indices: 21153--21407 Score: 347
Period size: 128 Copynumber: 2.0 Consensus size: 130
21143 GAACTTCTAG
* * *
21153 TAATATATGATTTTATGGTCAATAATGTGTTTACATTGAACTGGTTAAAAACCCTTGTAATTATT
1 TAATATATGATTTTATGGTCAATAATGTGTTCACATTCAACTGGTCAAAAACCCTTGTAA-TATT
21218 AAAAAAAAAAGGGCCAGAGGAAAAAGGAATGGTCAGAAACTAATTGAGGGCATTCTTAGTAAATA
65 -AAAAAAAAAGGGCCAGAGGAAAAAGGAATGGTCAGAAACTAATTGAGGGCATTCTTAGTAAATA
21283 AA
129 AA
21285 TAATATATGATTTTATGGTCAATAAATGCT-TTCACATTCAACTGGTCAAAAACCCTTGT-A-AT
1 TAATATATGATTTTATGGTCAAT-AATG-TGTTCACATTCAACTGGTCAAAAACCCTTGTAATAT
* ** * * * * *
21347 T-ACAAAAAAGGGCTGGAGGAGAAGGGAATTGTGAGAAACTAATTGAGGGCCTTCTTAGTAA
64 TAAAAAAAAAGGGCCAGAGGAAAAAGGAATGGTCAGAAACTAATTGAGGGCATTCTTAGTAA
21408 TTAACCAAGT
Statistics
Matches: 110, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
128 52 0.47
130 3 0.03
132 24 0.22
133 30 0.27
134 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (130 bp):
TAATATATGATTTTATGGTCAATAATGTGTTCACATTCAACTGGTCAAAAACCCTTGTAATATTA
AAAAAAAAGGGCCAGAGGAAAAAGGAATGGTCAGAAACTAATTGAGGGCATTCTTAGTAAATAAA
Found at i:23035 original size:29 final size:30
Alignment explanation
Indices: 22963--23028 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
22953 AGATTCGAAG
*
22963 TTCATGAT-TGAAGATTTATTGAAGATAAT
1 TTCAAGATATGAAGATTTATTGAAGATAAT
*
22992 TTCAAGATATGAAGA-TTATTGAAGAATTAT
1 TTCAAGATATGAAGATTTATTGAAG-ATAAT
23022 TTCAAGA
1 TTCAAGA
23029 AGTAAGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.38
Consensus pattern (30 bp):
TTCAAGATATGAAGATTTATTGAAGATAAT
Found at i:24336 original size:21 final size:19
Alignment explanation
Indices: 24307--24350 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
24297 ATAGTTTAGA
*
24307 TTTAATTTAGTTTGCCTTTTT
1 TTTAATTTA-ATTG-CTTTTT
*
24328 TTTAGTTTAATTGCTTTTT
1 TTTAATTTAATTGCTTTTT
24347 TTTA
1 TTTA
24351 TAATTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 8 0.38
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.68
Consensus pattern (19 bp):
TTTAATTTAATTGCTTTTT
Found at i:32249 original size:15 final size:17
Alignment explanation
Indices: 32229--32266 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
32219 TGTTCAAATG
32229 TCGGGTC-A-TTTGGGT
1 TCGGGTCAATTTTGGGT
32244 TCGGGTCAATTTTGGGT
1 TCGGGTCAATTTTGGGT
32261 T-GGGTC
1 TCGGGTC
32267 GTTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 6 0.29
17 8 0.38
ACGTcount: A:0.08, C:0.13, G:0.39, T:0.39
Consensus pattern (17 bp):
TCGGGTCAATTTTGGGT
Found at i:32933 original size:1 final size:1
Alignment explanation
Indices: 32922--32952 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
32912 CTTTCAAATC
*
32922 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32953 ATTTAGGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:34910 original size:16 final size:16
Alignment explanation
Indices: 34885--34941 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
34875 TGGATTGATC
34885 GGGTTCGGGTCATTTT
1 GGGTTCGGGTCATTTT
*
34901 GGGTTTGGGTCA-TTT
1 GGGTTCGGGTCATTTT
* * *
34916 GGATTCGGGTAATTTC
1 GGGTTCGGGTCATTTT
34932 GGGTTCGGGT
1 GGGTTCGGGT
34942 ACCCAAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 12 0.35
16 22 0.65
ACGTcount: A:0.09, C:0.11, G:0.40, T:0.40
Consensus pattern (16 bp):
GGGTTCGGGTCATTTT
Found at i:34990 original size:17 final size:17
Alignment explanation
Indices: 34950--34990 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
34940 GTACCCAAAA
34950 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
34967 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
34983 TTTCGGGT
1 TTTCGGGT
34991 TGGGCAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:36939 original size:14 final size:14
Alignment explanation
Indices: 36899--36929 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
36889 TCGATTTCAA
36899 TTTT-ATTATTTTC
1 TTTTAATTATTTTC
36912 TTTTAATTATTTTC
1 TTTTAATTATTTTC
36926 TTTT
1 TTTT
36930 TCTTTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTAATTATTTTC
Found at i:44744 original size:13 final size:13
Alignment explanation
Indices: 44726--44756 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
44716 CTTTGGACAA
44726 TTCATGGTCGATC
1 TTCATGGTCGATC
44739 TTCATGGTCGATC
1 TTCATGGTCGATC
44752 TTCAT
1 TTCAT
44757 TGTCATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (13 bp):
TTCATGGTCGATC
Found at i:45287 original size:29 final size:29
Alignment explanation
Indices: 45208--45295 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
45198 CAAACCTTTG
* *
45208 ACACGAGTGCA-AACCCACACTCAAAACAA
1 ACACAAGTGCACAACCCACACT-TAAACAA
* * *
45237 TCCCAAGTGCACAACCCACACTTGAACAA
1 ACACAAGTGCACAACCCACACTTAAACAA
**
45266 ACACAAGTGCACAACCTGCACTTAAACAA
1 ACACAAGTGCACAACCCACACTTAAACAA
45295 A
1 A
45296 ATCAGAAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 38 0.79
30 10 0.21
ACGTcount: A:0.44, C:0.34, G:0.10, T:0.11
Consensus pattern (29 bp):
ACACAAGTGCACAACCCACACTTAAACAA
Done.