Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014664.1 Corchorus olitorius cultivar O-4 contig14697, 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: 47719
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--41 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 ATC
4 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42 TAGAAGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1444 original size:15 final size:15
Alignment explanation
Indices: 1424--1455 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1414 TTAAGTTTCC
1424 ATCGAAGTAGTAGTG
1 ATCGAAGTAGTAGTG
1439 ATCGAAGTAGTAGTG
1 ATCGAAGTAGTAGTG
1454 AT
1 AT
1456 GGGTGGGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.28
Consensus pattern (15 bp):
ATCGAAGTAGTAGTG
Found at i:16444 original size:7 final size:7
Alignment explanation
Indices: 16432--16457 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16422 CACCAAAGGG
16432 GAAGACT
1 GAAGACT
16439 GAAGACT
1 GAAGACT
16446 GAAGACT
1 GAAGACT
16453 GAAGA
1 GAAGA
16458 GGGAGACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.31, T:0.12
Consensus pattern (7 bp):
GAAGACT
Found at i:21755 original size:5 final size:5
Alignment explanation
Indices: 21745--21770 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21735 TCCCTCCCTC
21745 TCCTT TCCTT TCCTT TCCTT TCCTT T
1 TCCTT TCCTT TCCTT TCCTT TCCTT T
21771 AAAAACTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TCCTT
Found at i:22899 original size:10 final size:10
Alignment explanation
Indices: 22884--22929 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
22874 ATTTAATACA
*
22884 TAATTTGTTT
1 TAATTTGTAT
*
22894 TAATTTGTAA
1 TAATTTGTAT
22904 TAATTTAGTAT
1 TAATTT-GTAT
*
22915 TAATTAGTAT
1 TAATTTGTAT
22925 TAATT
1 TAATT
22930 AATTTAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 23 0.74
11 8 0.26
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (10 bp):
TAATTTGTAT
Found at i:22900 original size:31 final size:31
Alignment explanation
Indices: 22829--22910 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 31
22819 GTCTATCAGC
* *
22829 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTATAATTT
** * *
22860 TAATGATTTGTTTAATTTAATAC-ATAATTT
1 TTTTAATTTGTTTAATTTAAGACTATAATTT
*
22890 GTTTTAATTTGTAATAATTTA
1 -TTTTAATTTGT-TTAATTTA
22911 GTATTAATTA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
30 5 0.13
31 27 0.69
32 7 0.18
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.57
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTATAATTT
Found at i:22919 original size:21 final size:20
Alignment explanation
Indices: 22860--22929 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
22850 ACTTTCATTT
* *
22860 TAATGATTTGT-TTAATTTAA
1 TAATAATTTGTATTAA-TTAG
* *
22880 TACATAATTTGTTTTAATTTG
1 TA-ATAATTTGTATTAATTAG
22901 TAATAATTTAGTATTAATTAG
1 TAATAATTT-GTATTAATTAG
*
22922 TATTAATT
1 TAATAATT
22930 AATTTAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 9 0.22
21 28 0.68
22 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.09, T:0.54
Consensus pattern (20 bp):
TAATAATTTGTATTAATTAG
Found at i:28985 original size:27 final size:27
Alignment explanation
Indices: 28955--29137 Score: 251
Period size: 27 Copynumber: 6.8 Consensus size: 27
28945 TTAGGGTCAC
* *
28955 CTAGGGGCATTTTAGTCATTTGCACGT
1 CTAGGGGCATTTTGGTCATTTGCATGT
28982 CTAGGGGCATTTTGGTCATTTGCATGT
1 CTAGGGGCATTTTGGTCATTTGCATGT
* * **
29009 TTAGGGGCATTTTAGTCATTTGCACAT
1 CTAGGGGCATTTTGGTCATTTGCATGT
*
29036 CCAGGGGCATTTTGGTCATTTGCATGT
1 CTAGGGGCATTTTGGTCATTTGCATGT
* *
29063 TTAGGGGCATTTTAGTCATTTGCATGT
1 CTAGGGGCATTTTGGTCATTTGCATGT
* *
29090 CCAGGGGTATTTTGGTCATTTGCATGT
1 CTAGGGGCATTTTGGTCATTTGCATGT
29117 -TCAGGGGCATTTTGGTCATTT
1 CT-AGGGGCATTTTGGTCATTT
29138 TAGATTTACT
Statistics
Matches: 135, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
27 135 1.00
ACGTcount: A:0.17, C:0.15, G:0.27, T:0.40
Consensus pattern (27 bp):
CTAGGGGCATTTTGGTCATTTGCATGT
Found at i:29019 original size:54 final size:54
Alignment explanation
Indices: 28956--29137 Score: 310
Period size: 54 Copynumber: 3.4 Consensus size: 54
28946 TAGGGTCACC
*
28956 TAGGGGCATTTTAGTCATTTGCACGTCTAGGGGCATTTTGGTCATTTGCATGTT
1 TAGGGGCATTTTAGTCATTTGCACGTCCAGGGGCATTTTGGTCATTTGCATGTT
*
29010 TAGGGGCATTTTAGTCATTTGCACATCCAGGGGCATTTTGGTCATTTGCATGTT
1 TAGGGGCATTTTAGTCATTTGCACGTCCAGGGGCATTTTGGTCATTTGCATGTT
* *
29064 TAGGGGCATTTTAGTCATTTGCATGTCCAGGGGTATTTTGGTCATTTGCATGTT
1 TAGGGGCATTTTAGTCATTTGCACGTCCAGGGGCATTTTGGTCATTTGCATGTT
* *
29118 CAGGGGCATTTTGGTCATTT
1 TAGGGGCATTTTAGTCATTT
29138 TAGATTTACT
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 121 1.00
ACGTcount: A:0.17, C:0.15, G:0.27, T:0.41
Consensus pattern (54 bp):
TAGGGGCATTTTAGTCATTTGCACGTCCAGGGGCATTTTGGTCATTTGCATGTT
Found at i:29697 original size:15 final size:15
Alignment explanation
Indices: 29677--29706 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29667 TTCTTGAAGT
29677 AGGTTTCCTTTCTCC
1 AGGTTTCCTTTCTCC
29692 AGGTTTCCTTTCTCC
1 AGGTTTCCTTTCTCC
29707 TTTAATTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.33, G:0.13, T:0.47
Consensus pattern (15 bp):
AGGTTTCCTTTCTCC
Found at i:35131 original size:25 final size:25
Alignment explanation
Indices: 35084--35134 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
35074 TATTTTGAAC
*
35084 TTATTATTTATTATTTAAAATATAT
1 TTATTATTTATTATATAAAATATAT
*
35109 TTATTATTTATT-TAATAATATATAT
1 TTATTATTTATTAT-ATAAAATATAT
35134 T
1 T
35135 ATATCTAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATTATTTATTATATAAAATATAT
Found at i:35134 original size:21 final size:21
Alignment explanation
Indices: 35054--35136 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
35044 CGTTTAGTAA
35054 TTAAATATATATTATTTATTTATT
1 TTAAA-ATATATTA-TTATTTA-T
* *
35078 TTGAACT-TATTATT-TATTAT
1 TTAAAATATATTATTAT-TTAT
35098 TTAAAATATATTTATTATTTAT
1 TTAAAATATA-TTATTATTTAT
35120 TTAATAATATA-TATTAT
1 TTAA-AATATATTATTAT
35137 ATCTAAGATA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
20 7 0.14
21 13 0.26
22 18 0.36
23 8 0.16
24 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (21 bp):
TTAAAATATATTATTATTTAT
Found at i:37527 original size:22 final size:22
Alignment explanation
Indices: 37485--37527 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
37475 TTGCCACAAT
*
37485 AAATAGCCTATATATATAGAAA
1 AAATAGCCTATATATACAGAAA
*
37507 AAATAGCCTATATATCCAGAA
1 AAATAGCCTATATATACAGAA
37528 TATCCCAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (22 bp):
AAATAGCCTATATATACAGAAA
Found at i:38037 original size:6 final size:6
Alignment explanation
Indices: 38026--38057 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
38016 CTGTATTTCC
38026 ATGGAT ATGGAT ATGGAT ATGGAT ATGGAT AT
1 ATGGAT ATGGAT ATGGAT ATGGAT ATGGAT AT
38058 ACAACTACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (6 bp):
ATGGAT
Found at i:45989 original size:3 final size:3
Alignment explanation
Indices: 45981--46028 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
45971 CTAAAATAAA
45981 TAT 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 TAT
46029 AGGATTTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:46078 original size:21 final size:21
Alignment explanation
Indices: 46052--46094 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
46042 TAAAATAGAA
*
46052 ATAAATTATTAAAATTTAGCC
1 ATAAATTAATAAAATTTAGCC
* *
46073 ATAAATTAATAGAGTTTAGCC
1 ATAAATTAATAAAATTTAGCC
46094 A
1 A
46095 CTTGGACTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (21 bp):
ATAAATTAATAAAATTTAGCC
Found at i:47143 original size:28 final size:28
Alignment explanation
Indices: 47068--47276 Score: 186
Period size: 28 Copynumber: 6.8 Consensus size: 28
47058 TTAAAATTTA
47068 ATTGACACCAGAAGTTGTCAT-ATTAAATT
1 ATTGACACCAGAAGTTGTCATGA--AAATT
47097 ATCTTGACACCAGAAGTTGTCATGAAAATT
1 A--TTGACACCAGAAGTTGTCATGAAAATT
* *
47127 ATTGACACCAGATGTTGTCATATCAAATTATT
1 ATTGACACCAGAAGTTGTC--ATGAAA--ATT
47159 ATCTTGACACCAGAAGTTGTCATGAAAATT
1 A--TTGACACCAGAAGTTGTCATGAAAATT
* *
47189 ATTGACACCAGAAGTTATCATATCAAATTATT
1 ATTGACACCAGAAGTTGTC--ATGAAA--ATT
47221 ATCTTGACACCAGAAGTTGTCATGCTGAGGAAATT
1 A--TTGACACCAGAAGTTGTCA---TGA--AAATT
47256 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
47277 CCCAATATTG
Statistics
Matches: 152, Mismatches: 8, Indels: 39
0.76 0.04 0.20
Matches are distributed among these distances:
28 34 0.22
29 1 0.01
30 21 0.14
31 20 0.13
32 15 0.10
33 19 0.12
34 34 0.22
35 6 0.04
37 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (28 bp):
ATTGACACCAGAAGTTGTCATGAAAATT
Found at i:47184 original size:62 final size:62
Alignment explanation
Indices: 47068--47276 Score: 325
Period size: 62 Copynumber: 3.3 Consensus size: 62
47058 TTAAAATTTA
*
47068 ATTGACACCAGAAGTTGTCATAT-TAA--ATTATCTTGACACCAGAAGTTGTCATGAAAATT
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
*
47127 ATTGACACCAGATGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
*
47189 ATTGACACCAGAAGTTATCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGCTGAGGAAA
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCA---TGA--AAA
47254 TT
61 TT
47256 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
47277 CCCAATATTG
Statistics
Matches: 137, Mismatches: 5, Indels: 8
0.91 0.03 0.05
Matches are distributed among these distances:
59 22 0.16
60 2 0.01
62 85 0.62
65 3 0.02
67 25 0.18
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (62 bp):
ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
Done.