Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021292.1 Corchorus olitorius cultivar O-4 contig21325, 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: 27307
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:1083 original size:154 final size:154
Alignment explanation
Indices: 554--1188 Score: 1065
Period size: 154 Copynumber: 4.1 Consensus size: 154
544 GATTCGTATC
* * * *
554 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGTTATATTAGTCCTATCGGGGCC
1 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
* ** *
619 CGTTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTAT
66 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
684 GGCCTAACTATAATCATTTTGGTG
131 GGCCTAACTATAATCATTTTGGTG
** * *
708 AGATTAGTCCACTGTGAAGTACTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTC
1 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
* *
773 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCGTT-TTTAT
66 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
*
837 GGACTAACTATAATCATTTTGGTG
131 GGCCTAACTATAATCATTTTGGTG
*
861 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTC
1 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
* * *
926 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAACGCCTTTCTTTCCATTTTTTAT
66 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
*
991 GGTCTAACTATAATCATTTTGGTG
131 GGCCTAACTATAATCATTTTGGTG
* *
1015 AGATTAGCCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCC
1 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
1080 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
66 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
1145 GGCCTAACTATAATCATTTTGGTG
131 GGCCTAACTATAATCATTTTGGTG
1169 AGATTAGTCCACTGTGAAGT
1 AGATTAGTCCACTGTGAAGT
1189 ACTTTAGATT
Statistics
Matches: 450, Mismatches: 30, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
153 146 0.32
154 304 0.68
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (154 bp):
AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
GGCCTAACTATAATCATTTTGGTG
Found at i:1108 original size:307 final size:308
Alignment explanation
Indices: 554--1188 Score: 1065
Period size: 307 Copynumber: 2.1 Consensus size: 308
544 GATTCGTATC
*
554 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGTTATATTAGTCCTATCGGGGCC
1 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGTTATATTAGGCCTATCGGGGCC
* ** * *
619 CGTTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTAT
66 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAACGCCTTTCTTTCCATTGTTTAT
* *
684 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTACTTAACTCATTTGGAACACT
131 GGCCTAACTATAATCATTTTGGTGAGATTAGCCCACTGTGAAGTACTTAACTCATTTAGAACACT
*
749 TGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC
196 TGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC
*
814 AAAGCTTTTCTTTCCGTT-TTTATGGACTAACTATAATCATTTTGGTG
261 AAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTG
* * * *
861 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTC
1 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGTTATATTAGGCCTATCGGGGCC
* *
926 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAACGCCTTTCTTTCCATTTTTTAT
66 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAACGCCTTTCTTTCCATTGTTTAT
* ** *
991 GGTCTAACTATAATCATTTTGGTGAGATTAGCCCACTGTGAAGTTTTTAGCTCATTTAGAACACT
131 GGCCTAACTATAATCATTTTGGTGAGATTAGCCCACTGTGAAGTACTTAACTCATTTAGAACACT
1056 TGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC
196 TGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC
* *
1121 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTG
261 AAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTG
1169 AGATTAGTCCACTGTGAAGT
1 AGATTAGTCCACTGTGAAGT
1189 ACTTTAGATT
Statistics
Matches: 305, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
307 257 0.84
308 48 0.16
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (308 bp):
AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGTTATATTAGGCCTATCGGGGCC
CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAACGCCTTTCTTTCCATTGTTTAT
GGCCTAACTATAATCATTTTGGTGAGATTAGCCCACTGTGAAGTACTTAACTCATTTAGAACACT
TGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC
AAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTG
Found at i:7011 original size:20 final size:21
Alignment explanation
Indices: 6969--7011 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6959 TCCTTTGTTG
6969 ATGATCTCCAATGGGCTTCAA
1 ATGATCTCCAATGGGCTTCAA
* *
6990 ATGATCTCCGAT-GGCTTTAA
1 ATGATCTCCAATGGGCTTCAA
7010 AT
1 AT
7012 TCTTCAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGATCTCCAATGGGCTTCAA
Found at i:15880 original size:7 final size:7
Alignment explanation
Indices: 15842--15873 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
15832 AATTCTTTTC
15842 TTTTCTT
1 TTTTCTT
15849 TTTTCTT
1 TTTTCTT
15856 TTTTCTT
1 TTTTCTT
15863 TTTTCTT
1 TTTTCTT
15870 TTTT
1 TTTT
15874 TTCTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:15880 original size:14 final size:13
Alignment explanation
Indices: 15837--15880 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
15827 AGGCAAATTC
*
15837 TTTTC-TTTTCTT
1 TTTTCTTTTTTTT
15849 TTTTCTTTTTTCTT
1 TTTTCTTTTTT-TT
15863 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
15876 CTTTT
1 -TTTT
15881 AATTTTTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 5 0.18
13 6 0.21
14 17 0.61
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:15886 original size:21 final size:21
Alignment explanation
Indices: 15842--15887 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
15832 AATTCTTTTC
**
15842 TTTTCTTTTTTCTTTTTTCTT
1 TTTTCTTTTTTCTTTTTTAAT
15863 TTTTCTTTTTT-TTCTTTTAAT
1 TTTTCTTTTTTCTT-TTTTAAT
15884 TTTT
1 TTTT
15888 GTGTGATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTCTTTTTTCTTTTTTAAT
Found at i:16087 original size:32 final size:32
Alignment explanation
Indices: 16046--16127 Score: 164
Period size: 32 Copynumber: 2.6 Consensus size: 32
16036 TTGATCCTGT
16046 ACTTGTTAATATATATATTTTTTGTGGTGCAA
1 ACTTGTTAATATATATATTTTTTGTGGTGCAA
16078 ACTTGTTAATATATATATTTTTTGTGGTGCAA
1 ACTTGTTAATATATATATTTTTTGTGGTGCAA
16110 ACTTGTTAATATATATAT
1 ACTTGTTAATATATATAT
16128 ATTCTATATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.50
Consensus pattern (32 bp):
ACTTGTTAATATATATATTTTTTGTGGTGCAA
Found at i:16788 original size:2 final size:2
Alignment explanation
Indices: 16781--16805 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16771 TGGGAGTATT
16781 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16806 TTTGAGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25353 original size:33 final size:34
Alignment explanation
Indices: 25283--25422 Score: 107
Period size: 33 Copynumber: 4.2 Consensus size: 34
25273 ATGATCAACC
** *
25283 AAAACAG-ATTT-GTTTTCATCACAATTAGCATCC-
1 AAAACAGAATTTAG-TTTCATCACAAACAACA-CCT
25316 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAGAATTTAGTTTCATCACAAACAACACCT
25349 AAAACA-AATTTAGTGTT-ATCACAAACAACA-CT
1 AAAACAGAATTTAGT-TTCATCACAAACAACACCT
** * * * *
25381 CAAATTAG-GTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGAATTTAGTTTCATCACAAACAACACCT
25415 AAAACAGA
1 AAAACAGA
25423 TTTCATGTCG
Statistics
Matches: 88, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
32 10 0.11
33 69 0.78
34 9 0.10
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (34 bp):
AAAACAGAATTTAGTTTCATCACAAACAACACCT
Found at i:25407 original size:66 final size:66
Alignment explanation
Indices: 25331--25457 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 66
25321 AGAATTTGTT
* *
25331 TCATCACAAACAACACCTAAAACAAATTT-AGTGTTATCACAAACAACACTCAAATTAGGTTTAG
1 TCATCACAAACAACACCTAAAACAAATTTCA-TGTCATCACAAACAACACTCAAATCAGGTTTAG
25395 TA
65 TA
* * * * **
25397 TCATCGCAAACAACATCTAAAACAGATTTCATGTCGTTGCAAACAACACTCAAATCAGGTT
1 TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTT
25458 CAGAATTACC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 51 0.98
67 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (66 bp):
TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTTTAGT
A
Done.