Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017264.1 Corchorus olitorius cultivar O-4 contig17297, 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: 34848
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3355 original size:19 final size:18
Alignment explanation
Indices: 3322--3357 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3312 TTGAAATAAT
3322 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
3340 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
3358 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:3365 original size:11 final size:10
Alignment explanation
Indices: 3322--3368 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
3312 TTGAAATAAT
3322 TCTTCAATGA
1 TCTTCAATGA
3332 TCTTCAA--A
1 TCTTCAATGA
*
3340 TCTTCAAATTA
1 TCTTC-AATGA
3351 TCTTCAATGA
1 TCTTCAATGA
3361 GTCTTCAA
1 -TCTTCAA
3369 ACACGAGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:14060 original size:17 final size:17
Alignment explanation
Indices: 14038--14073 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
14028 ATCGCTCAAA
14038 TATATTTACGTTAGGTT
1 TATATTTACGTTAGGTT
14055 TATATTTACGTTAGGTT
1 TATATTTACGTTAGGTT
14072 TA
1 TA
14074 GGATGATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.53
Consensus pattern (17 bp):
TATATTTACGTTAGGTT
Found at i:14257 original size:48 final size:48
Alignment explanation
Indices: 14186--14377 Score: 303
Period size: 48 Copynumber: 3.9 Consensus size: 48
14176 CCACTTAAAT
*
14186 AGTGGTGGGATCAGTTTGCTGAACCAATCGTGTAACAACACATTTTTA
1 AGTGGTGGGACCAGTTTGCTGAACCAATCGTGTAACAACACATTTTTA
* **
14234 AGTGGTGGGACCAATTTGCTGAACCAATCGTGTAACAACACATCCACTTAAA
1 AGTGGTGGGACCAGTTTGCTGAACCAATCGTGTAACAACACAT----TTTTA
14286 TAGTGGTGGGACCAGTTTGCTGAACCAATCGTGTAACAACACATTTTTA
1 -AGTGGTGGGACCAGTTTGCTGAACCAATCGTGTAACAACACATTTTTA
14335 AGTGGTGGGACCAGTTTGCTGAACCAATCGTGTAACAACACAT
1 AGTGGTGGGACCAGTTTGCTGAACCAATCGTGTAACAACACAT
14378 CATGGAGGAC
Statistics
Matches: 132, Mismatches: 7, Indels: 10
0.89 0.05 0.07
Matches are distributed among these distances:
48 84 0.64
49 3 0.02
52 3 0.02
53 42 0.32
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (48 bp):
AGTGGTGGGACCAGTTTGCTGAACCAATCGTGTAACAACACATTTTTA
Found at i:14353 original size:101 final size:101
Alignment explanation
Indices: 14176--14378 Score: 388
Period size: 101 Copynumber: 2.0 Consensus size: 101
14166 TATAAAAAGC
*
14176 CCACTTAAATAGTGGTGGGATCAGTTTGCTGAACCAATCGTGTAACAACACATTTTTAAGTGGTG
1 CCACTTAAATAGTGGTGGGACCAGTTTGCTGAACCAATCGTGTAACAACACATTTTTAAGTGGTG
14241 GGACCAATTTGCTGAACCAATCGTGTAACAACACAT
66 GGACCAATTTGCTGAACCAATCGTGTAACAACACAT
14277 CCACTTAAATAGTGGTGGGACCAGTTTGCTGAACCAATCGTGTAACAACACATTTTTAAGTGGTG
1 CCACTTAAATAGTGGTGGGACCAGTTTGCTGAACCAATCGTGTAACAACACATTTTTAAGTGGTG
*
14342 GGACCAGTTTGCTGAACCAATCGTGTAACAACACAT
66 GGACCAATTTGCTGAACCAATCGTGTAACAACACAT
14378 C
1 C
14379 ATGGAGGACC
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (101 bp):
CCACTTAAATAGTGGTGGGACCAGTTTGCTGAACCAATCGTGTAACAACACATTTTTAAGTGGTG
GGACCAATTTGCTGAACCAATCGTGTAACAACACAT
Found at i:20525 original size:19 final size:17
Alignment explanation
Indices: 20484--20535 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
20474 GGGTAACCTA
20484 AGAACAGAGAGATAAATT
1 AGAA-AGAGAGATAAATT
*
20502 AGAAAGAGAGCTACAATT
1 AGAAAGAGAGATA-AATT
20520 AGGAAA-AGAGTATAAA
1 A-GAAAGAGAG-ATAAA
20536 GCTTAAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 8 0.28
18 15 0.52
19 6 0.21
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (17 bp):
AGAAAGAGAGATAAATT
Found at i:23158 original size:9 final size:10
Alignment explanation
Indices: 23144--23177 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
23134 TTGAAAAATC
23144 GAAAAATTTT
1 GAAAAATTTT
23154 GAAAAATTTT
1 GAAAAATTTT
23164 GAAAAATTTT
1 GAAAAATTTT
23174 -AAAA
1 GAAAA
23178 TTTGTTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (10 bp):
GAAAAATTTT
Found at i:26245 original size:21 final size:21
Alignment explanation
Indices: 26221--26270 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
26211 ACAAAAATAG
26221 AAAACAAAAATACGAT-AAAAC
1 AAAACAAAAA-ACGATAAAAAC
* * *
26242 AAAACTATAAAGGATAAAAAC
1 AAAACAAAAAACGATAAAAAC
26263 AAAACAAA
1 AAAACAAA
26271 TGAGTTCCCC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.72, C:0.12, G:0.06, T:0.10
Consensus pattern (21 bp):
AAAACAAAAAACGATAAAAAC
Found at i:32072 original size:21 final size:21
Alignment explanation
Indices: 32047--32096 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
32037 ACAAAAACAA
32047 AAAACAAAAATACGAT-AAAAC
1 AAAACAAAAA-ACGATAAAAAC
* * *
32068 AAAACTATAAAGGATAAAAAC
1 AAAACAAAAAACGATAAAAAC
32089 AAAACAAA
1 AAAACAAA
32097 TGAGATCCCA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.72, C:0.12, G:0.06, T:0.10
Consensus pattern (21 bp):
AAAACAAAAAACGATAAAAAC
Found at i:34125 original size:13 final size:13
Alignment explanation
Indices: 34107--34132 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34097 TTATCGCCCC
34107 GTTTTAGTAATTT
1 GTTTTAGTAATTT
34120 GTTTTAGTAATTT
1 GTTTTAGTAATTT
34133 ATCATGTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
GTTTTAGTAATTT
Done.