Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016027.1 Corchorus olitorius cultivar O-4 contig16060, 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: 22293
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1670 original size:22 final size:22
Alignment explanation
Indices: 1642--1684 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1632 TTTCCCGCAA
*
1642 CAAGTCCTAGG-CAGGAGTTGTC
1 CAAGTCCT-GGACAGGACTTGTC
1664 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCTGGACAGGACTTGT
1685 TCTGAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAGGACTTGTC
Found at i:1738 original size:50 final size:50
Alignment explanation
Indices: 1663--1784 Score: 190
Period size: 50 Copynumber: 2.4 Consensus size: 50
1653 CAGGAGTTGT
*
1663 CCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTCCGTCTTTCAACAAA
1 CCAAGTCCTGGACAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAAA
* * *
1713 CCAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTCCGTCTTTCAACAGA
1 CCAAGTCCTGGACAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAAA
* *
1763 CCAGGTCCTGGACAGGCGTTGT
1 CCAAGTCCTGGACAGGAGTTGT
1785 CAAGTCCTGG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (50 bp):
CCAAGTCCTGGACAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAAA
Found at i:3502 original size:55 final size:55
Alignment explanation
Indices: 3414--3524 Score: 143
Period size: 55 Copynumber: 2.0 Consensus size: 55
3404 GATCAAACTT
* * * * *
3414 TCATTTGATTAGTGTTCTCATCTATTTGCGTCTTCGATTTATTTTTAATCCTAGA
1 TCATTTCATTAGTGTTCTAATATATTTGAGTCTTCGATTTATTTCTAATCCTAGA
* *
3469 TCATTTCATTAGTGTTGC-AATATATTTGAGTCTTGGATTTATTTCTAATTCTAGA
1 TCATTTCATTAGTGTT-CTAATATATTTGAGTCTTCGATTTATTTCTAATCCTAGA
3524 T
1 T
3525 GTTTGAATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
55 47 0.98
56 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (55 bp):
TCATTTCATTAGTGTTCTAATATATTTGAGTCTTCGATTTATTTCTAATCCTAGA
Found at i:10069 original size:17 final size:17
Alignment explanation
Indices: 10044--10085 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
10034 ACCAGACCTT
*
10044 AGCTACTGACAGTTGAA
1 AGCTGCTGACAGTTGAA
10061 AGCTGCTGACAGTTGAA
1 AGCTGCTGACAGTTGAA
10078 AGCTGCTG
1 AGCTGCTG
10086 CTAATTGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (17 bp):
AGCTGCTGACAGTTGAA
Found at i:13252 original size:128 final size:129
Alignment explanation
Indices: 13028--13296 Score: 330
Period size: 128 Copynumber: 2.1 Consensus size: 129
13018 CATTATTTAA
* *
13028 ACTTTTATAATCTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCAAATATCTATATAAT
1 ACTTTTATAATCTTAATCAACTAAAAACTCTATTTTTATATAATT-AAT-AAATATCTATATAAC
* * * *
13093 TATTTAATTTTTACCATTTTACTATTTTAATTTAAAAA-ATTATATATATTAGAATTTTTTAAAT
64 TATTTAATTTTTACCATTTTACTAATTTAA-TTAAAAAGATTAAATATATTAGAAATTTTAAAAT
13157 AT
128 AT
* * * *
13159 ACTTTTATAGTTTTAATCAACTAAAAACTCTATTTTTTATTTAATT-AT-AATATCCT-TATACC
1 ACTTTTATAATCTTAATCAACTAAAAACTCTA-TTTTTATATAATTAATAAATAT-CTATATAAC
* * *
13221 TATTTTATTTTTATCATTTTACTAATTTAATTAAAAAGCTTAAATATATTAGAAATTTTAAAATA
64 TATTTAATTTTTACCATTTTACTAATTTAATTAAAAAGATTAAATATATTAGAAATTTTAAAATA
13286 T
129 T
*
13287 ATTTCTTATA
1 ACTT-TTATA
13297 TGACATTGTT
Statistics
Matches: 120, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
127 7 0.06
128 63 0.52
129 7 0.06
130 2 0.02
131 29 0.24
132 12 0.10
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.49
Consensus pattern (129 bp):
ACTTTTATAATCTTAATCAACTAAAAACTCTATTTTTATATAATTAATAAATATCTATATAACTA
TTTAATTTTTACCATTTTACTAATTTAATTAAAAAGATTAAATATATTAGAAATTTTAAAATAT
Found at i:14161 original size:36 final size:36
Alignment explanation
Indices: 14121--14192 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
14111 TATGAAGTGG
14121 GGGTATGTGTTCAAATAAATATTGGTTATATAATAT
1 GGGTATGTGTTCAAATAAATATTGGTTATATAATAT
14157 GGGTATGTGTTCAAATAAATATTGGTTATATAATAT
1 GGGTATGTGTTCAAATAAATATTGGTTATATAATAT
14193 CTAAATTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (36 bp):
GGGTATGTGTTCAAATAAATATTGGTTATATAATAT
Found at i:16241 original size:1 final size:1
Alignment explanation
Indices: 16200--16225 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
16190 TAGTTTAGGG
16200 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
16226 AAAAAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:19340 original size:182 final size:182
Alignment explanation
Indices: 19033--19406 Score: 705
Period size: 182 Copynumber: 2.1 Consensus size: 182
19023 TAATCTATAC
*
19033 TATATTAAAAAGTACATACTTTTGTAAAACTTTTGAATCGTCCATTATACCCTTATTTTTCGAAT
1 TATATTAAAAAGTACATACTTTTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAAT
*
19098 ATATTTCTTAAATGCCATTGTTTAAACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATT
66 ATATTTCTTAAATGCCATTGTTTAAACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATT
19163 TAATTAAATATAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTT
131 TAATTAAATATAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTT
19215 TATATTAAAAAGTACATACTTTTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAAT
1 TATATTAAAAAGTACATACTTTTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAAT
*
19280 ATATTTCTTAAATGCCATTGTTTAGACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATT
66 ATATTTCTTAAATGCCATTGTTTAAACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATT
19345 TAATTAAATATAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTT
131 TAATTAAATATAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTT
*
19397 TA-ATCAAAAA
1 TATATTAAAAA
19407 AATTATATAT
Statistics
Matches: 188, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
181 7 0.04
182 181 0.96
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (182 bp):
TATATTAAAAAGTACATACTTTTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAAT
ATATTTCTTAAATGCCATTGTTTAAACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATT
TAATTAAATATAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTT
Found at i:19501 original size:12 final size:13
Alignment explanation
Indices: 19484--19516 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
19474 AATTAAATTC
19484 AATATTTTTA-TA
1 AATATTTTTATTA
*
19496 AATATTTTTATTT
1 AATATTTTTATTA
19509 AATATTTT
1 AATATTTT
19517 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATATTTTTATTA
Found at i:19512 original size:13 final size:13
Alignment explanation
Indices: 19484--19521 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
19474 AATTAAATTC
*
19484 AATATTTTTA-TA
1 AATATTTTTATTT
19496 AATATTTTTATTT
1 AATATTTTTATTT
*
19509 AATATTTTAATTT
1 AATATTTTTATTT
19522 TAAAAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
AATATTTTTATTT
Found at i:20226 original size:21 final size:22
Alignment explanation
Indices: 20202--20242 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20192 GTTTATAATA
20202 TTCTAGGGTCA-TCGGGTTATT
1 TTCTAGGGTCATTCGGGTTATT
* *
20223 TTCTCGGGTTATTCGGGTTA
1 TTCTAGGGTCATTCGGGTTA
20243 CGAGTTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.12, C:0.15, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTAGGGTCATTCGGGTTATT
Done.