Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015533.1 Corchorus olitorius cultivar O-4 contig15566, 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: 43489
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:661 original size:10 final size:10
Alignment explanation
Indices: 646--674 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
636 CCATATTAAC
646 AATTTTATTT
1 AATTTTATTT
656 AATTTTATTT
1 AATTTTATTT
666 -ATTTTATTT
1 AATTTTATTT
675 CCTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
AATTTTATTT
Found at i:10256 original size:13 final size:13
Alignment explanation
Indices: 10238--10265 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
10228 ATGAAAGTTA
10238 ATTGAAATTTTGG
1 ATTGAAATTTTGG
10251 ATTGAAATTTTGG
1 ATTGAAATTTTGG
10264 AT
1 AT
10266 CGGATCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.46
Consensus pattern (13 bp):
ATTGAAATTTTGG
Found at i:18366 original size:4 final size:4
Alignment explanation
Indices: 18357--18400 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
18347 GAGCACTGAC
18357 ATTA ATTA ATTA ATTA ATTA A-TA ATTA ATT- ATTA ATT- ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
18401 GCCAACATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 9 0.24
4 28 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:18383 original size:11 final size:11
Alignment explanation
Indices: 18357--18399 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
18347 GAGCACTGAC
18357 ATTAATTAATTA
1 ATTAATTAA-TA
18369 ATTAATTAATA
1 ATTAATTAATA
*
18380 ATTAATTATTA
1 ATTAATTAATA
18391 ATT-ATTAAT
1 ATTAATTAAT
18400 TGCCAACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 5 0.17
11 15 0.52
12 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTAATTAATA
Found at i:18400 original size:7 final size:7
Alignment explanation
Indices: 18357--18400 Score: 61
Period size: 7 Copynumber: 6.0 Consensus size: 7
18347 GAGCACTGAC
18357 ATTAATT
1 ATTAATT
18364 AATTAATT
1 -ATTAATT
*
18372 AATTAATA
1 -ATTAATT
18380 ATTAATT
1 ATTAATT
18387 ATTAATT
1 ATTAATT
18394 ATTAATT
1 ATTAATT
18401 GCCAACATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
7 20 0.59
8 14 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
ATTAATT
Found at i:28961 original size:75 final size:76
Alignment explanation
Indices: 28879--29031 Score: 202
Period size: 81 Copynumber: 2.0 Consensus size: 76
28869 CTAAAAGACC
* * *
28879 CAACTGATCAAATTCTG-CAAAAAAA-CCATATACCCATTTGGTCTAGAAGGGAAGTTTCAGCCA
1 CAACTGATCAAATTCTGAAAAAAAAACCCATATACCCATTTGGTCTAGAACGG-AGTTTCACCCA
28942 TTGTTGATAACT
65 TTGTTGATAACT
*
28954 CAACTGATTAAATTCTGAAAAAAAAAAAAAACCCATATACCCATTTGGTCTAGAACGGAGTTTCA
1 CAACTGATCAAATTCTG-----AAAAAAAAACCCATATACCCATTTGGTCTAGAACGGAGTTTCA
29019 CCCATTGTTGATA
61 CCCATTGTTGATA
29032 GTGAAAGAGC
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
75 16 0.24
81 26 0.39
82 25 0.37
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (76 bp):
CAACTGATCAAATTCTGAAAAAAAAACCCATATACCCATTTGGTCTAGAACGGAGTTTCACCCAT
TGTTGATAACT
Found at i:29054 original size:11 final size:11
Alignment explanation
Indices: 29038--29062 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29028 GATAGTGAAA
29038 GAGCTTTTAAG
1 GAGCTTTTAAG
29049 GAGCTTTTAAG
1 GAGCTTTTAAG
29060 GAG
1 GAG
29063 TTTCACCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.32, T:0.32
Consensus pattern (11 bp):
GAGCTTTTAAG
Found at i:32053 original size:231 final size:231
Alignment explanation
Indices: 31269--32093 Score: 1368
Period size: 232 Copynumber: 3.6 Consensus size: 231
31259 GGAACTTCTT
31269 CACACCAAAATGGATCTCTCCA-TAAAGCATCAAGATAATAGGATGCACCGCATGAATCTTCTGG
1 CACACCAAAATGGATCTCT-CAGTAAAGCATCAAGATAATAGGATGCACCGCATGAATCTTCTGG
* * *
31333 CTCAGAAAAAAGCTAAAAGGGCATCATCTTCAAGGCCTAAGGCCGATACAGGTTGTGCTTCTGAA
65 CTCAGAAAAAAGCTCAAAGGCCATCATCTTCAACGCCTAAGGCCGATACAGGTTGTGCTTCTGAA
* *
31398 CAATTTGTTCTCCTTGATATAGTCTTACTCTTATCCATCAAATAATGTTTGTGTTGAATTCTTTT
130 CAATTTGTTCTCCTTGATATAGTCTTACTCTTATCCATCAAATAATGTTTGTGATGAATTC-GTT
* *
31463 TTTTTTTTCTTTTTCTTATAACAGATCCATTTTGTCTG
194 TTTTTTTTCTTTTTCTTTTGACAGATCCATTTTGTCTG
* *
31501 CACACCAAAATGGATCTCTCAGTAAAGCATCGAGATAATAGGATGCACCGCATGAAGCTTCTGGC
1 CACACCAAAATGGATCTCTCAGTAAAGCATCAAGATAATAGGATGCACCGCATGAATCTTCTGGC
* *
31566 TCAGAAAAAAGCTCAAAGGCCATCATCTTTAACGCCTAAGGCCAATACAGGTTGTGCTTCTGAAC
66 TCAGAAAAAAGCTCAAAGGCCATCATCTTCAACGCCTAAGGCCGATACAGGTTGTGCTTCTGAAC
31631 AATTTGTTCTCCTTGATATAGTCTTACTCTTATCCATCAAATAATGTTTGTGATGAATTCGTTTT
131 AATTTGTTCTCCTTGATATAGTCTTACTCTTATCCATCAAATAATGTTTGTGATGAATTCGTTTT
31696 ATTTTTTCTTTTTCTTTTGACAGATCCATTTTGTCTG
196 -TTTTTTCTTTTTCTTTTGACAGATCCATTTTGTCTG
*
31733 CACACCAAAATGGATCTCTCAGTAAAGCATCAAGATAATAGGATGTACCGCATGAATCTTCTGGC
1 CACACCAAAATGGATCTCTCAGTAAAGCATCAAGATAATAGGATGCACCGCATGAATCTTCTGGC
* * * *
31798 TCAGAGAAAAGCTCAAAGGCCATCATCTTTAACGCAC-AAGGCTGATACAGGTTGTGCTCCTGAA
66 TCAGAAAAAAGCTCAAAGGCCATCATCTTCAACGC-CTAAGGCCGATACAGGTTGTGCTTCTGAA
*
31862 CAATTTGTTCTCCTTGATATAGTCTTACTCTTATCCATCTAATAATGTTTGTGATGAATTCGTTT
130 CAATTTGTTCTCCTTGATATAGTCTTACTCTTATCCATCAAATAATGTTTGTGATGAATTCGTTT
* * *
31927 TCTTTTTCTTTTTCTTTTGACAGATCCTTTTTTTCTG
195 TTTTTTTCTTTTTCTTTTGACAGATCCATTTTGTCTG
*
31964 CACACCAAAATGGATCTCTCAGTAAAGCATCGAA-ATAATAGGATGTACCGCATGAATCTTCTGG
1 CACACCAAAATGGATCTCTCAGTAAAGCATC-AAGATAATAGGATGCACCGCATGAATCTTCTGG
* * *
32028 CTCAAAAAAAAGCTCAAAGGCCATCATCTTCAACACCTATGGCCGATACAGGTTGTGCTTCTGAA
65 CTCAGAAAAAAGCTCAAAGGCCATCATCTTCAACGCCTAAGGCCGATACAGGTTGTGCTTCTGAA
32093 C
130 C
32094 GACCTAAGGC
Statistics
Matches: 559, Mismatches: 29, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
230 1 0.00
231 157 0.28
232 400 0.72
233 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (231 bp):
CACACCAAAATGGATCTCTCAGTAAAGCATCAAGATAATAGGATGCACCGCATGAATCTTCTGGC
TCAGAAAAAAGCTCAAAGGCCATCATCTTCAACGCCTAAGGCCGATACAGGTTGTGCTTCTGAAC
AATTTGTTCTCCTTGATATAGTCTTACTCTTATCCATCAAATAATGTTTGTGATGAATTCGTTTT
TTTTTTCTTTTTCTTTTGACAGATCCATTTTGTCTG
Found at i:32105 original size:33 final size:33
Alignment explanation
Indices: 32062--32192 Score: 217
Period size: 33 Copynumber: 4.0 Consensus size: 33
32052 CATCTTCAAC
*
32062 ACCTATGGCCGATACAGGTTGTGCTTCTGAACG
1 ACCTAAGGCCGATACAGGTTGTGCTTCTGAACG
*
32095 ACCTAAGGCCGATACAGGTTGTGCTTCTGATCG
1 ACCTAAGGCCGATACAGGTTGTGCTTCTGAACG
* *
32128 ACCTAAGGTCGATACAGGTTGTGCTTCTGAACA
1 ACCTAAGGCCGATACAGGTTGTGCTTCTGAACG
*
32161 ACCTAAGGCTGATACAGGTTGTGCTTCTGAAC
1 ACCTAAGGCCGATACAGGTTGTGCTTCTGAAC
32193 AATTTGTTCT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (33 bp):
ACCTAAGGCCGATACAGGTTGTGCTTCTGAACG
Found at i:40045 original size:32 final size:32
Alignment explanation
Indices: 40007--40075 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
39997 GGATCCGATC
40007 TTTTGGTTATGTTTGCTAACATTCATAAGCTT
1 TTTTGGTTATGTTTGCTAACATTCATAAGCTT
40039 TTTTGGTTATGTTTGCTAACATTCATAAGCTT
1 TTTTGGTTATGTTTGCTAACATTCATAAGCTT
40071 TTTTG
1 TTTTG
40076 AGGAAAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (32 bp):
TTTTGGTTATGTTTGCTAACATTCATAAGCTT
Found at i:42628 original size:17 final size:17
Alignment explanation
Indices: 42606--42640 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42596 ATTCTGTGAA
42606 TCTTTTTAACATTAATG
1 TCTTTTTAACATTAATG
42623 TCTTTTTAACATTAATG
1 TCTTTTTAACATTAATG
42640 T
1 T
42641 GAAACAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (17 bp):
TCTTTTTAACATTAATG
Found at i:43273 original size:20 final size:17
Alignment explanation
Indices: 43231--43264 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43221 TTACTTTTCT
43231 TAATTATTTTTAGATTA
1 TAATTATTTTTAGATTA
*
43248 TAATTATTTTTTGATTA
1 TAATTATTTTTAGATTA
43265 AAATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TAATTATTTTTAGATTA
Done.