Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017851.1 Corchorus olitorius cultivar O-4 contig17884, 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: 51158
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:4706 original size:27 final size:26
Alignment explanation
Indices: 4642--4709 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
4632 TATTATCGCT
*
4642 TGATGGTGGTGCGGGTGGTGATGATGA
1 TGATGGTGGTG-GGGTGGGGATGATGA
* *
4669 TGAT-TTAGGTGGAGGTGGGGATGGTGA
1 TGATGGT-GGTGG-GGTGGGGATGATGA
4696 TGATGGTGGTGGGG
1 TGATGGTGGTGGGG
4710 AGGAGTCGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
26 4 0.12
27 29 0.85
28 1 0.03
ACGTcount: A:0.15, C:0.01, G:0.54, T:0.29
Consensus pattern (26 bp):
TGATGGTGGTGGGGTGGGGATGATGA
Found at i:8285 original size:27 final size:28
Alignment explanation
Indices: 8245--8297 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
8235 CTTTAATTAA
*
8245 AAAAGATATCTTCTAAGAAACTATATAC
1 AAAAGATACCTTCTAAGAAACTATATAC
*
8273 AAAA-ATACCTTCTTAGAAACTATAT
1 AAAAGATACCTTCTAAGAAACTATAT
8298 TCACAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (28 bp):
AAAAGATACCTTCTAAGAAACTATATAC
Found at i:11662 original size:98 final size:97
Alignment explanation
Indices: 11493--11688 Score: 365
Period size: 98 Copynumber: 2.0 Consensus size: 97
11483 AAAGATATAT
11493 CAACACTAAAGGCTTAAGAATCTATTAACAGTTCAAATATTGACTCAATGTGGACTCACTAACAA
1 CAACACTAAAGGCTTAAGAATCTATTAACAGTTCAAATATTGACTCAATGTGGACTCACTAACAA
*
11558 AATCTACCTTCCTTGAGAAATCAAGAGTTATCA
66 AATCTACCTT-CTTGAGAAATCAAGAATTATCA
*
11591 CAACACTAAAGGCTTAAGAATCTATTAATAGTTCAAATATTGACTCAATGTGGACTCACTAACAA
1 CAACACTAAAGGCTTAAGAATCTATTAACAGTTCAAATATTGACTCAATGTGGACTCACTAACAA
11656 AATCTACCTTCTTGAGAAATCAAGAATTATCA
66 AATCTACCTTCTTGAGAAATCAAGAATTATCA
11688 C
1 C
11689 TTGTCAGACA
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
97 22 0.23
98 74 0.77
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (97 bp):
CAACACTAAAGGCTTAAGAATCTATTAACAGTTCAAATATTGACTCAATGTGGACTCACTAACAA
AATCTACCTTCTTGAGAAATCAAGAATTATCA
Found at i:14782 original size:21 final size:21
Alignment explanation
Indices: 14756--14806 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
14746 AGCACCTGAA
* *
14756 CTTCCTCATCATCTTCAACTT
1 CTTCCTCATCATCTGCAACAT
* * *
14777 CTTCCTCCTCTTCTGCATCAT
1 CTTCCTCATCATCTGCAACAT
14798 CTTCCTCAT
1 CTTCCTCAT
14807 TACCCGGTTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.14, C:0.41, G:0.02, T:0.43
Consensus pattern (21 bp):
CTTCCTCATCATCTGCAACAT
Found at i:16755 original size:15 final size:15
Alignment explanation
Indices: 16729--16776 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
16719 GTCAACCTCT
*
16729 TCCTCTTCATCATCC
1 TCCTCATCATCATCC
* *
16744 TCGTCATCATCATCG
1 TCCTCATCATCATCC
*
16759 TCCTCATCGTCATCC
1 TCCTCATCATCATCC
16774 TCC
1 TCC
16777 ACCCCATCCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.15, C:0.44, G:0.06, T:0.35
Consensus pattern (15 bp):
TCCTCATCATCATCC
Found at i:17127 original size:15 final size:15
Alignment explanation
Indices: 17107--17144 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
17097 CCCAGGATCA
17107 TCTTCATCATCCTCC
1 TCTTCATCATCCTCC
*
17122 TCTTCATCTTCCTCC
1 TCTTCATCATCCTCC
*
17137 TCCTCATC
1 TCTTCATC
17145 TGACTCCGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.47, G:0.00, T:0.42
Consensus pattern (15 bp):
TCTTCATCATCCTCC
Found at i:21948 original size:15 final size:15
Alignment explanation
Indices: 21924--21954 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21914 GAGAATATAT
*
21924 AGTCTTAACTCTTTA
1 AGTCTCAACTCTTTA
21939 AGTCTCAACTCTTTA
1 AGTCTCAACTCTTTA
21954 A
1 A
21955 AGGTCGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (15 bp):
AGTCTCAACTCTTTA
Found at i:22288 original size:7 final size:7
Alignment explanation
Indices: 22276--22300 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
22266 TAGCAAAAGA
22276 ATAATCT
1 ATAATCT
22283 ATAATCT
1 ATAATCT
22290 ATAATCT
1 ATAATCT
22297 ATAA
1 ATAA
22301 AACAATGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAATCT
Found at i:23573 original size:33 final size:33
Alignment explanation
Indices: 23533--23599 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
23523 CCTTTTGACC
*
23533 TTTAACAATTTTGTTTATTCCTTCTTATATCCT
1 TTTAACAATTTTGTTTATTCCTTCTTATAACCT
*
23566 TTTAACAATTTTGTTTATTCCTTTTTATAACCT
1 TTTAACAATTTTGTTTATTCCTTCTTATAACCT
23599 T
1 T
23600 ACAGGTTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.03, T:0.58
Consensus pattern (33 bp):
TTTAACAATTTTGTTTATTCCTTCTTATAACCT
Found at i:26448 original size:3 final size:3
Alignment explanation
Indices: 26440--26484 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
26430 AGATAGTATA
26440 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26485 ATATATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:45960 original size:30 final size:28
Alignment explanation
Indices: 45908--45964 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
45898 ACGTTTCCAA
*
45908 TCCCTTGTGAAAACAATTTTTATTATCAT
1 TCCCTCGTGAAAACAATTTTTA-TATCAT
45937 TCCCTCGTGAAAACAATTTTTTATATCA
1 TCCCTCGTGAAAACAA-TTTTTATATCA
45965 AAAAACAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (28 bp):
TCCCTCGTGAAAACAATTTTTATATCAT
Found at i:47105 original size:53 final size:54
Alignment explanation
Indices: 47016--47117 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 54
47006 TAAGGTCATA
* *
47016 TATAAAATACCCTAGTGAATCCTAATTTCACTATGATAAGGAAGTCTTAACTCT
1 TATAAAATACCCTAGTGAACCCTAATTTCACTATGATAAGGAACTCTTAACTCT
*
47070 TATAAAATACCCTAGT-AACCCTAATTTCATTATGATAAGGAACTCTTA
1 TATAAAATACCCTAGTGAACCCTAATTTCACTATGATAAGGAACTCTTA
47118 TTATATACTA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 29 0.64
54 16 0.36
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (54 bp):
TATAAAATACCCTAGTGAACCCTAATTTCACTATGATAAGGAACTCTTAACTCT
Done.