Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017613.1 Corchorus olitorius cultivar O-4 contig17646, 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: 22978
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:938 original size:28 final size:31
Alignment explanation
Indices: 886--942 Score: 84
Period size: 28 Copynumber: 1.9 Consensus size: 31
876 GTATCTCTTA
*
886 ATTATATATATAAATAAATTATATTATATAT
1 ATTATATATATAAATAAATAATATTATATAT
917 ATTAT-TATAT-AAT-AATAATATTATAT
1 ATTATATATATAAATAAATAATATTATAT
943 TAGTAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 12 0.48
29 3 0.12
30 5 0.20
31 5 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
ATTATATATATAAATAAATAATATTATATAT
Found at i:3224 original size:27 final size:27
Alignment explanation
Indices: 3186--3258 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
3176 CAAAACACAC
*
3186 AAACAGGAACTCAAAATCAGCCACTA-A
1 AAACAGGAACTCAAAA-CAACCACTACA
*
3213 AAACAGAAACTCAAAACAACCACTACA
1 AAACAGGAACTCAAAACAACCACTACA
3240 AAACAGGAACTTCAAAACA
1 AAACAGGAAC-TCAAAACA
3259 GTAACACAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 8 0.20
27 25 0.61
28 8 0.20
ACGTcount: A:0.56, C:0.26, G:0.08, T:0.10
Consensus pattern (27 bp):
AAACAGGAACTCAAAACAACCACTACA
Found at i:3255 original size:14 final size:13
Alignment explanation
Indices: 3186--3259 Score: 58
Period size: 14 Copynumber: 5.5 Consensus size: 13
3176 CAAAACACAC
*
3186 AAACAGGAACTCA
1 AAACAGCAACTCA
* *
3199 AAATCAGCCACTAA
1 AAA-CAGCAACTCA
*
3213 AAACAGAAACTCA
1 AAACAGCAACTCA
* *
3226 AAACAACCACTACA
1 AAACAGCAACT-CA
*
3240 AAACAGGAACTTCA
1 AAACAGCAAC-TCA
3254 AAACAG
1 AAACAG
3260 TAACACAGAA
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
13 18 0.39
14 27 0.59
15 1 0.02
ACGTcount: A:0.55, C:0.26, G:0.09, T:0.09
Consensus pattern (13 bp):
AAACAGCAACTCA
Found at i:3292 original size:135 final size:136
Alignment explanation
Indices: 3103--3395 Score: 414
Period size: 135 Copynumber: 2.2 Consensus size: 136
3093 CATGAACCCA
* *
3103 AAAAACAGGAA-TTGTAAAACAATAAAACAGAAATTGAAAAAAAATTGTACATCAACCCAAAAAA
1 AAAAACAGGAACTT-CAAAACAATAAAACAGAAATTGAAAAAAAATTCTACATCAACCCAAAAAA
* * *
3167 CAGAAACTGCAAAACACACAAACAGGAACTCAAAATCAGCCACTAAAA-ACAGAAACT-CAAAAC
65 CAGAAACTGCAAAACAAAAAAACAGGAACTCAAAATCAGCCACTAAAATACAGAAACTAAAAAAC
3230 AACCACT
130 AACCACT
* * ** *
3237 ACAAAACAGGAACTTCAAAACAGTAACACAGAAATTGAAAACAGGA-TCTACATCAACCGAAAAA
1 A-AAAACAGGAACTTCAAAACAATAAAACAGAAATTGAAAA-AAAATTCTACATCAACCCAAAAA
*
3301 ACAGAAAGTGCAAAACAAAAAAACAGGAACTCAAAATCAGCCACTAAAATACAGAAACTAAAAAA
64 ACAGAAACTGCAAAACAAAAAAACAGGAACTCAAAATCAGCCACTAAAATACAGAAACTAAAAAA
*
3366 CAGCCACT
129 CAACCACT
3374 AAAAATCAGGAACTTCAAAACA
1 AAAAA-CAGGAACTTCAAAACA
3396 CGAAATCAAA
Statistics
Matches: 141, Mismatches: 12, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
134 1 0.01
135 95 0.67
136 17 0.12
137 28 0.20
ACGTcount: A:0.57, C:0.21, G:0.10, T:0.12
Consensus pattern (136 bp):
AAAAACAGGAACTTCAAAACAATAAAACAGAAATTGAAAAAAAATTCTACATCAACCCAAAAAAC
AGAAACTGCAAAACAAAAAAACAGGAACTCAAAATCAGCCACTAAAATACAGAAACTAAAAAACA
ACCACT
Found at i:3393 original size:28 final size:28
Alignment explanation
Indices: 3318--3395 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
3308 GTGCAAAACA
*
3318 AAAAAACAGGAAC-TCAAAATCAGCCACT
1 AAAAATCAGGAACTTCAAAA-CAGCCACT
* **
3346 -AAAATACAGAAACTAAAAAACAGCCACT
1 AAAAAT-CAGGAACTTCAAAACAGCCACT
3374 AAAAATCAGGAACTTCAAAACA
1 AAAAATCAGGAACTTCAAAACA
3396 CGAAATCAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
27 4 0.10
28 27 0.68
29 9 0.22
ACGTcount: A:0.58, C:0.22, G:0.09, T:0.12
Consensus pattern (28 bp):
AAAAATCAGGAACTTCAAAACAGCCACT
Found at i:9054 original size:2 final size:2
Alignment explanation
Indices: 9047--9072 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9037 TTTAGTATTT
9047 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
9073 CTAGTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9160 original size:22 final size:22
Alignment explanation
Indices: 9135--9191 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
9125 TGTTTTTATG
* *
9135 AAATTTTGATAATCACCCTATT
1 AAATTTTGATAATCACCATATC
*
9157 AAATTTTGATAACCACCATATC
1 AAATTTTGATAATCACCATATC
9179 AAATTTTGATAAT
1 AAATTTTGATAAT
9192 TACCTACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAATCACCATATC
Found at i:9219 original size:43 final size:44
Alignment explanation
Indices: 9135--9233 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 44
9125 TGTTTTTATG
** * * *
9135 AAATTTTGATAATCACCCTATTAAATTTTGATAACCACCATATC
1 AAATTTTGATAATCACCCTACAAAATTGTGATAAACACCATAAC
* * *
9179 AAATTTTGATAATTA-CCTACAAAATTGTGATAAACTCCATAAG
1 AAATTTTGATAATCACCCTACAAAATTGTGATAAACACCATAAC
*
9222 AAACTTTGATAA
1 AAATTTTGATAA
9234 CCTAACTATG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 32 0.70
44 14 0.30
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.34
Consensus pattern (44 bp):
AAATTTTGATAATCACCCTACAAAATTGTGATAAACACCATAAC
Found at i:9815 original size:18 final size:18
Alignment explanation
Indices: 9792--9834 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
9782 CCCTTTTCGG
*
9792 CATTCATGGC-ATATCTCT
1 CATTCAT-GCAATATCTCC
9810 CATTCATGCAATATCTCC
1 CATTCATGCAATATCTCC
9828 CATTCAT
1 CATTCAT
9835 CTCACAAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (18 bp):
CATTCATGCAATATCTCC
Found at i:13135 original size:22 final size:22
Alignment explanation
Indices: 13107--13149 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13097 TTTCCCGTAA
* *
13107 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCCTGGACAGGACTTGTC
13129 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCTGGACAGGACTTGT
13150 TCTGGATTTT
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:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAGGACTTGTC
Found at i:13203 original size:50 final size:50
Alignment explanation
Indices: 13128--13249 Score: 174
Period size: 50 Copynumber: 2.4 Consensus size: 50
13118 CAGGAGTTGT
* * *
13128 CCAAGTCCTGGACAGGACTTGTTCTGGA-TTTTCTTCCGTCTTTCAACATA
1 CCAAGTCCTGGGCAGGAGTTGTTCT-GATTTTTCTTCCGTCTTTCAACAGA
*
13178 CCAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTCTGTCTTTCAACAGA
1 CCAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTCCGTCTTTCAACAGA
* *
13228 CCAGGTCTTGGGCAGGAGTTGT
1 CCAAGTCCTGGGCAGGAGTTGT
13250 CAAGTCCTGG
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 2 0.03
50 63 0.97
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (50 bp):
CCAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTCCGTCTTTCAACAGA
Done.