Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012808.1 Corchorus olitorius cultivar O-4 contig12841, 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: 66904
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4807 original size:19 final size:18
Alignment explanation
Indices: 4774--4809 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4764 TTGAAATTAT
4774 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
4792 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
4810 TAAATCTTCA
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:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:9909 original size:30 final size:30
Alignment explanation
Indices: 9849--9909 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
9839 GAAGTTCGTG
*
9849 ATTGAAGATTAATTGAAAATAATGTGAAGA
1 ATTGAAGATTAATTGAAAATAATGTCAAGA
* *
9879 ATTGAAGATTAA-TGAAGAATTATTTCAAGA
1 ATTGAAGATTAATTGAA-AATAATGTCAAGA
9909 A
1 A
9910 GAAAGAATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (30 bp):
ATTGAAGATTAATTGAAAATAATGTCAAGA
Found at i:11135 original size:21 final size:21
Alignment explanation
Indices: 11094--11135 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11084 TAGGACTTGA
* *
11094 CAACCTTGCCTAGGCATGGCC
1 CAACCTTGCCCAGGCACGGCC
*
11115 CAACCTTGCCCAGGCGCGGCC
1 CAACCTTGCCCAGGCACGGCC
11136 TACCCCAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.43, G:0.26, T:0.14
Consensus pattern (21 bp):
CAACCTTGCCCAGGCACGGCC
Found at i:20842 original size:12 final size:12
Alignment explanation
Indices: 20825--20855 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
20815 CCCTTGCCTA
20825 AAAAACTAGAAG
1 AAAAACTAGAAG
20837 AAAAACTAGAAG
1 AAAAACTAGAAG
20849 AATAAAC
1 AA-AAAC
20856 CTAAAACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.68, C:0.10, G:0.13, T:0.10
Consensus pattern (12 bp):
AAAAACTAGAAG
Found at i:26329 original size:24 final size:24
Alignment explanation
Indices: 26263--26329 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
26253 TTTTTTTACC
*
26263 TACCTATTTAT-TCATTTATCTCTA
1 TACCTATTTATCT-ATTTATCTATA
* *
26287 TACCTCTTTATCTAATTATCTATA
1 TACCTATTTATCTATTTATCTATA
*
26311 TACCTATTTATCTTTTTAT
1 TACCTATTTATCTATTTAT
26330 TTATCTAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
24 35 0.97
25 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.55
Consensus pattern (24 bp):
TACCTATTTATCTATTTATCTATA
Found at i:26332 original size:12 final size:12
Alignment explanation
Indices: 26315--26375 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 12
26305 TCTATATACC
26315 TATTTATCTTTT
1 TATTTATCTTTT
26327 TATTTATCTAATATTTT
1 TATTTATC-----TTTT
26344 TATTTAT-TTTT
1 TATTTATCTTTT
26355 CTATTTAT-TTTT
1 -TATTTATCTTTT
26367 TATTTATCT
1 TATTTATCT
26376 ATTACTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
11 11 0.26
12 20 0.48
17 11 0.26
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTATCTTTT
Found at i:26370 original size:23 final size:23
Alignment explanation
Indices: 26340--26398 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
26330 TTATCTAATA
26340 TTTTTATTTATTTTTCTA-TTTAT
1 TTTTTATTTATTTTT-TACTTTAT
* *
26363 TTTTTATTTATCTATTACTTTAT
1 TTTTTATTTATTTTTTACTTTAT
*
26386 TTTAT-TTTATTTT
1 TTTTTATTTATTTT
26399 AATAATTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 8 0.27
23 22 0.73
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTATTTATTTTTTACTTTAT
Found at i:26374 original size:40 final size:41
Alignment explanation
Indices: 26314--26393 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
26304 ATCTATATAC
*
26314 CTATTTATCTTTTTATTTATCTAATA-TTTTTATTTATTTTT
1 CTATTTATCTTTTTATTTATCTAATACTTTAT-TTTATTTTT
*
26355 CTATTTAT-TTTTTATTTATCTATTACTTTATTTTATTTT
1 CTATTTATCTTTTTATTTATCTAATACTTTATTTTATTTT
26394 ATTTTAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 24 0.67
41 12 0.33
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (41 bp):
CTATTTATCTTTTTATTTATCTAATACTTTATTTTATTTTT
Found at i:30915 original size:54 final size:54
Alignment explanation
Indices: 30847--31462 Score: 749
Period size: 54 Copynumber: 11.4 Consensus size: 54
30837 ATGAAATAGT
* * *
30847 TGTGCGGTATTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATAACCT
1 TGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
* * *
30901 TGTGCGGTCATTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATAACCC
1 TGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
* * * * *
30955 --TGCGATCTTTCCTAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAAATGACCA
1 TGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
* * * * *
31007 TGTGCGGTCTTTCATAGAAATTTTCATAGGTTCAAGTTGATCTTCAAATGACCC
1 TGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
*
31061 TGTGTGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
1 TGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
* * * *
31115 TATGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTCCAGATAACCC
1 TGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
* *
31169 TGTGCGGTCTTTCATAGAAGTTTTAAGAGGTTTAAGTTGATCTTCAGATGACCC
1 TGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
* *
31223 TTTGCGGTCTTTCATAGAAGTTTTCAAAGATTTAAGTTGATCTTCAGATGACCC
1 TGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
** * *
31277 TGTGCGGTCTTTTGTAGAAGTTTTCAGAGATCTAAGTTGAT-TTTATGATGACCC
1 TGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCA-GATGACCC
* * * * * *
31331 TGTGCGGACTTTCAAAAAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACTC
1 TGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
* ** * * ** *
31385 GGTGTTGTCTTTCATTA-AAGTTTTTAGAGA-TCAGAGTTGATCCCCAGATGATCC
1 TGTGCGGTCTTTCA-TAGAAGTTTTCAGAGATTTA-AGTTGATCTTCAGATGACCC
* *
31439 AGTGCGATCATTTCA-AGAAGTTTT
1 TGTGCGGTC-TTTCATAGAAGTTTT
31463 GAATGATCAG
Statistics
Matches: 488, Mismatches: 66, Indels: 16
0.86 0.12 0.03
Matches are distributed among these distances:
52 46 0.09
53 5 0.01
54 428 0.88
55 9 0.02
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (54 bp):
TGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
Found at i:31471 original size:54 final size:54
Alignment explanation
Indices: 31413--32011 Score: 603
Period size: 54 Copynumber: 11.2 Consensus size: 54
31403 AGTTTTTAGA
* * *
31413 GATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTTCAAGAAGTTTTGAAT
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
* * * * *
31467 GATCAGAGTTGATCCCCAAATGATCTAGTGTGAT-ATT-TAAGAAGTTTTCAAT
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
* * ** * **
31519 GATCAGAGTTGATCCCTAGATGATCCCGTATGGTCATTCCAAGTAGTTTTCTTT
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
* * * * **
31573 GATCAGAGTTGAT-CCAAGATGACCCAGTGCGGTCATTCCAAGTAGTTCTCTTT
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
* *
31626 GTTCAGAGTTGAT-CCCAGATGA-CCTAGTGCGGTCATTCCAAGAAGTTTTTAGA-
1 GATCAGAGTTGATCCCCAGATGATCC-AGTGCGGTCATTCCAAGAAGTTTTCA-AT
* * *
31679 GATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCCTTCCAAAAAGTTTTCGAA-
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC-AAT
* * * * *
31733 GATCAGAGTTGATCTCTAGATGATCCGGTGCGGTCTTTTCAAGAAGTTTTCGAA-
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC-AAT
* * *
31787 GATCAGAGTTGATCTCCAGATGATCC-G-GTGGTCATTCCAAAAAGTTTTCAAT
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
* * * *
31839 GATCAGAATTGATCTCCATATGATCTAGTGCGGTCCA-TCCAAGAAGGTTTTTCGAA-
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGT-CATTCCAAGAA-G-TTTTC-AAT
* * * *
31895 GATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCGTTTCAAGAAGTTTTCAAA
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
* * * * *
31949 GATCAAAGTTGATCTCCAGATGAT-CTGATGCGGTCATTTCAAGAAGTTTTCGAT
1 GATCAGAGTTGATCCCCAGATGATCCAG-TGCGGTCATTCCAAGAAGTTTTCAAT
32003 GATCAGAGT
1 GATCAGAGT
32012 AGTTCTCGAA
Statistics
Matches: 469, Mismatches: 59, Indels: 34
0.83 0.10 0.06
Matches are distributed among these distances:
51 2 0.00
52 84 0.18
53 100 0.21
54 230 0.49
55 8 0.02
56 43 0.09
57 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (54 bp):
GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
Found at i:31533 original size:106 final size:108
Alignment explanation
Indices: 31413--32011 Score: 619
Period size: 106 Copynumber: 5.6 Consensus size: 108
31403 AGTTTTTAGA
* *
31413 GATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTTCAAGAAGTTTT-GAATGATCAGAGTT
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGAA-GATCAGAGTT
* * * * *
31477 GATCCCCAAATGATCTAGTGTGAT-ATT-TAAGAAGTTTTCAAT
65 GATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
* * ** * ***
31519 GATCAGAGTTGATCCCTAGATGATCCCGTATGGTCATTCCAAGTAGTTTTCTTTGATCAGAGTTG
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGAAGATCAGAGTTG
* * * * **
31584 AT-CCAAGATGACCCAGTGCGGTCATTCCAAGTAGTTCTCTTT
66 ATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
* *
31626 GTTCAGAGTTGAT-CCCAGATGA-CCTAGTGCGGTCATTCCAAGAAGTTTT-TAGAGATCAGAGT
1 GATCAGAGTTGATCCCCAGATGATCC-AGTGCGGTCATTCCAAGAAGTTTTCGA-AGATCAGAGT
* * *
31688 TGATCCCTAGATGATCCAGTGCGGTCCTTCCAAAAAGTTTTCGAA-
64 TGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC-AAT
* * * * *
31733 GATCAGAGTTGATCTCTAGATGATCCGGTGCGGTCTTTTCAAGAAGTTTTCGAAGATCAGAGTTG
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGAAGATCAGAGTTG
* * *
31798 ATCTCCAGATGATCC-G-GTGGTCATTCCAAAAAGTTTTCAAT
66 ATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
* * * *
31839 GATCAGAATTGATCTCCATATGATCTAGTGCGGTCCA-TCCAAGAAGGTTTTTCGAAGATCAGAG
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGT-CATTCCAAGAA-G-TTTTCGAAGATCAGAG
* * * *
31903 TTGATCTCCAGATGATCCAGTGCGGTCGTTTCAAGAAGTTTTCAAA
63 TTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
* * * * *
31949 GATCAAAGTTGATCTCCAGATGAT-CTGATGCGGTCATTTCAAGAAGTTTTCGATGATCAGAGT
1 GATCAGAGTTGATCCCCAGATGATCCAG-TGCGGTCATTCCAAGAAGTTTTCGAAGATCAGAGT
32012 AGTTCTCGAA
Statistics
Matches: 408, Mismatches: 67, Indels: 34
0.80 0.13 0.07
Matches are distributed among these distances:
105 19 0.05
106 156 0.38
107 68 0.17
108 103 0.25
109 8 0.02
110 54 0.13
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (108 bp):
GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGAAGATCAGAGTTG
ATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAT
Found at i:31674 original size:160 final size:161
Alignment explanation
Indices: 31095--32011 Score: 671
Period size: 162 Copynumber: 5.7 Consensus size: 161
31085 CAGAGATTTA
* * * * *
31095 AGTTGATCTTCAGATGACCCTA-TGCGGTC-TTTCATAGAAGTTTTCAGAGGTTTA-AGTTGATC
1 AGTTGATCTCCAGATGATCC-AGTGCGGTCATTTCA-AGAAGTTTTCA-AAGATCAGAGTTGATC
* * * * * * *
31157 TCCAGATAACCCTGTGCGGTC-TTTCATAGAAGTTTTAAGAGGTTTA-AGTTGAT-CTTCAGATG
63 TCCAGATGA-CCTGTGCGGTCATTCCA-AGAAGTTTTCA-ATGATCAGAGTTGATCCCT-AGATG
* ** * * *
31219 ACCCTTTGCGGTC-TTTCATAGAAGTTTTCAAAGATTTA-
124 ATCCAGTGCGGTCATTCCA-AGAAGTTTTCGAAGA-TCAG
* * * * ** * *
31257 AGTTGATCTTCAGATGACCCTGTGCGGTCTTTTGTAGAAGTTTTCAGAGATCTA-AGTTGAT-TT
1 AGTTGATCTCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAAAGATC-AGAGTTGATCTC
* * * * * * *
31320 TATGATGACCCTGTGCGGACTTTCAAAAAAGCTTTCAGA-GATCTA-AGTTGAT-CTTCAGATGA
65 CA-GATGA-CCTGTGCGGTCATTCCAAGAAGTTTTCA-ATGATC-AGAGTTGATCCCT-AGATGA
* ** * *
31382 -CTCGGTGTTGTC-TTTCATTA-AAGTTTT-TAGAGATCAG
125 TC-CAGTGCGGTCATTCCA--AGAAGTTTTCGA-AGATCAG
* * * * *
31419 AGTTGATCCCCAGATGATCCAGTGCGATCATTTCAAGAAGTTTTGAATGATCAGAGTTGATCCCC
1 AGTTGATCTCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAAAGATCAGAGTTGATCTCC
* * * * * *
31484 AAATGATCTAGTGTGAT-ATT-TAAGAAGTTTTCAATGATCAGAGTTGATCCCTAGATGATCCCG
66 AGATGACCT-GTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCTAGATGATCCAG
** * ***
31547 TATGGTCATTCCAAGTAGTTTTCTTTGATCAG
130 TGCGGTCATTCCAAGAAGTTTTCGAAGATCAG
* * * * * *** *
31579 AGTTGATC-CAAGATGACCCAGTGCGGTCATTCCAAGTAGTTCTCTTTGTTCAGAGTTGATC-CC
1 AGTTGATCTCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAAAGATCAGAGTTGATCTCC
*
31642 AGATGACCTAGTGCGGTCATTCCAAGAAGTTTTTAGA-GATCAGAGTTGATCCCTAGATGATCCA
66 AGATGACCT-GTGCGGTCATTCCAAGAAGTTTTCA-ATGATCAGAGTTGATCCCTAGATGATCCA
* *
31706 GTGCGGTCCTTCCAAAAAGTTTTCGAAGATCAG
129 GTGCGGTCATTCCAAGAAGTTTTCGAAGATCAG
* * * *
31739 AGTTGATCTCTAGATGATCCGGTGCGGTCTTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCC
1 AGTTGATCTCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAAAGATCAGAGTTGATCTCC
* * * * *
31804 AGATGATCC-G-GTGGTCATTCCAAAAAGTTTTCAATGATCAGAATTGATCTCC-ATATGATCTA
66 AGATGA-CCTGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC-CCTAGATGATCCA
31866 GTGCGGTCCA-TCCAAGAAGGTTTTTCGAAGATCAG
129 GTGCGGT-CATTCCAAGAA-G-TTTTCGAAGATCAG
* *
31901 AGTTGATCTCCAGATGATCCAGTGCGGTCGTTTCAAGAAGTTTTCAAAGATCAAAGTTGATCTCC
1 AGTTGATCTCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAAAGATCAGAGTTGATCTCC
* * *
31966 AGATGATCTGATGCGGTCATTTCAAGAAGTTTTCGATGATCAGAGT
66 AGATGACCTG-TGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGT
32012 AGTTCTCGAA
Statistics
Matches: 611, Mismatches: 110, Indels: 66
0.78 0.14 0.08
Matches are distributed among these distances:
158 15 0.02
159 50 0.08
160 179 0.29
161 72 0.12
162 255 0.42
163 11 0.02
164 29 0.05
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (161 bp):
AGTTGATCTCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAAAGATCAGAGTTGATCTCC
AGATGACCTGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCTAGATGATCCAGT
GCGGTCATTCCAAGAAGTTTTCGAAGATCAG
Found at i:33432 original size:4 final size:4
Alignment explanation
Indices: 33413--33479 Score: 52
Period size: 4 Copynumber: 17.5 Consensus size: 4
33403 TTTTTATAGC
* * *
33413 TATT TATC TA-T TATT TATT TA-C TATT TATCT T-TT TATT TATT AATT
1 TATT TATT TATT TATT TATT TATT TATT TAT-T TATT TATT TATT TATT
**
33459 TAGC TA-T TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TA
33480 CTATTATCTA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
3 8 0.16
4 39 0.80
5 2 0.04
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (4 bp):
TATT
Found at i:33433 original size:15 final size:15
Alignment explanation
Indices: 33413--33492 Score: 60
Period size: 15 Copynumber: 5.3 Consensus size: 15
33403 TTTTTATAGC
33413 TATTTATCTATTATT
1 TATTTATCTATTATT
33428 TATTTA-CTATTTATCT
1 TATTTATCTA-TTAT-T
*
33444 T-TTTATTTATTAATT
1 TATTTATCTATT-ATT
**
33459 TAGCTAT-TATTTATT
1 TATTTATCTA-TTATT
*
33474 TATTTA-CTATTATC
1 TATTTATCTATTATT
33488 TATTT
1 TATTT
33493 TTTTTACCTA
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
14 12 0.23
15 29 0.56
16 11 0.21
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.65
Consensus pattern (15 bp):
TATTTATCTATTATT
Found at i:33454 original size:27 final size:27
Alignment explanation
Indices: 33413--33479 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
33403 TTTTTATAGC
* *
33413 TATTTATCTA-TTATTTATTTA-CTATT
1 TATTTATTTATTTATTAATTTAGCTA-T
33439 TATCTT-TTTATTTATTAATTTAGCTAT
1 TAT-TTATTTATTTATTAATTTAGCTAT
33466 TATTTATTTATTTA
1 TATTTATTTATTTA
33480 CTATTATCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 8 0.23
27 24 0.69
28 3 0.09
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (27 bp):
TATTTATTTATTTATTAATTTAGCTAT
Found at i:33517 original size:8 final size:8
Alignment explanation
Indices: 33412--33600 Score: 92
Period size: 8 Copynumber: 24.6 Consensus size: 8
33402 TTTTTTATAG
33412 CTATTTAT
1 CTATTTAT
33420 CTA-TTAT
1 CTATTTAT
*
33427 TTATTTA-
1 CTATTTAT
33434 CTATTTAT
1 CTATTTAT
*
33442 CTTTTTAT
1 CTATTTAT
* *
33450 TTATTAAT
1 CTATTTAT
* **
33458 TTAGCTAT
1 CTATTTAT
33466 -TATTTAT
1 CTATTTAT
*
33473 TTATTTA-
1 CTATTTAT
33480 CTA-TTAT
1 CTATTTAT
*
33487 CTATTTTTT
1 CTA-TTTAT
* ** *
33496 TTACCTAC
1 CTATTTAT
33504 CTATTTAT
1 CTATTTAT
33512 CTATTTAT
1 CTATTTAT
* * *
33520 CTCTATAC
1 CTATTTAT
*
33528 CTCTTTAT
1 CTATTTAT
*
33536 CTAATTAT
1 CTATTTAT
* *
33544 CTATATAC
1 CTATTTAT
33552 CTATTTAT
1 CTATTTAT
33560 -T-TTT-T
1 CTATTTAT
33565 -TATTTAT
1 CTATTTAT
*
33572 -TTTTCTAT
1 CTATT-TAT
33580 CTATTTAT
1 CTATTTAT
*
33588 TTATTTAT
1 CTATTTAT
33596 CTATT
1 CTATT
33601 ACTTTTTTTT
Statistics
Matches: 133, Mismatches: 38, Indels: 20
0.70 0.20 0.10
Matches are distributed among these distances:
5 2 0.02
6 9 0.07
7 27 0.20
8 87 0.65
9 8 0.06
ACGTcount: A:0.24, C:0.13, G:0.01, T:0.62
Consensus pattern (8 bp):
CTATTTAT
Found at i:33570 original size:4 final size:4
Alignment explanation
Indices: 33553--33600 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
33543 TCTATATACC
* * *
33553 TATT TATT TTTT TATT TATT T-TT CTATC TATT TATT TATT TATC TATT
1 TATT TATT TATT TATT TATT TATT -TATT TATT TATT TATT TATT TATT
33601 ACTTTTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 2 0.06
4 33 0.92
5 1 0.03
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:33570 original size:12 final size:12
Alignment explanation
Indices: 33553--33595 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
33543 TCTATATACC
33553 TATTTATTTTTT
1 TATTTATTTTTT
*
33565 TATTTATTTTTC
1 TATTTATTTTTT
* *
33577 TATCTATTTATT
1 TATTTATTTTTT
33589 TATTTAT
1 TATTTAT
33596 CTATTACTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (12 bp):
TATTTATTTTTT
Found at i:38204 original size:3 final size:3
Alignment explanation
Indices: 38196--38251 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
38186 ACAATTCATA
38196 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38244 TAT ATAT T
1 TAT -TAT T
38252 TATATAACAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:38255 original size:6 final size:7
Alignment explanation
Indices: 38193--38256 Score: 61
Period size: 6 Copynumber: 9.9 Consensus size: 7
38183 TCAACAATTC
38193 ATATATT
1 ATATATT
38200 AT-TATT
1 ATATATT
38206 AT-TATT
1 ATATATT
38212 AT-TATT
1 ATATATT
38218 AT-TATT
1 ATATATT
38224 AT-TATT
1 ATATATT
38230 AT-TATT
1 ATATATT
38236 ATTATTATT
1 A-TA-TATT
38245 ATATATT
1 ATATATT
38252 -TATAT
1 ATATAT
38257 AACATATATA
Statistics
Matches: 54, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
6 40 0.74
7 7 0.13
8 2 0.04
9 5 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
ATATATT
Found at i:39006 original size:19 final size:19
Alignment explanation
Indices: 38982--39022 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
38972 GCCTAGCATT
*
38982 GGTTGGCCATATCAAATTA
1 GGTTGGCCATATCAAATGA
39001 GGTTGGCCATATCAAATGA
1 GGTTGGCCATATCAAATGA
39020 GGT
1 GGT
39023 AAGGATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (19 bp):
GGTTGGCCATATCAAATGA
Found at i:45656 original size:20 final size:21
Alignment explanation
Indices: 45608--45657 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
45598 TTGACAAATG
45608 AGATTTGAAAGCCAAGGGCTT
1 AGATTTGAAAGCCAAGGGCTT
*
45629 GAGATTTGAAAG-CACGGAGCTT
1 -AGATTTGAAAGCCAAGG-GCTT
45651 -GATTTGA
1 AGATTTGA
45658 TTTGCGCGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.27
21 4 0.15
22 15 0.58
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (21 bp):
AGATTTGAAAGCCAAGGGCTT
Found at i:54143 original size:19 final size:18
Alignment explanation
Indices: 54106--54145 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
54096 CTCTTGAGAT
*
54106 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
54124 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
54143 AAT
1 AAT
54146 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:57726 original size:34 final size:34
Alignment explanation
Indices: 57688--57755 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
57678 GCTCTTACAA
*
57688 CCAATGAAGTTACACGGGCATTCATCACGCCTTT
1 CCAATGAAGTTAAACGGGCATTCATCACGCCTTT
*
57722 CCAATGAAGTTAAACGGGCCTTCATCACGCCTTT
1 CCAATGAAGTTAAACGGGCATTCATCACGCCTTT
57756 ACAAGTTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (34 bp):
CCAATGAAGTTAAACGGGCATTCATCACGCCTTT
Found at i:61236 original size:18 final size:19
Alignment explanation
Indices: 61213--61252 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
61203 CTCTTGAGTT
61213 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
61231 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
61250 AAT
1 AAT
61253 AAATCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:64461 original size:15 final size:15
Alignment explanation
Indices: 64431--64472 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
64421 TTACTCTGCT
64431 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
64447 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
64462 TTGCTTTCTGT
1 TTGTTTTCTGT
64473 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:64861 original size:32 final size:31
Alignment explanation
Indices: 64798--64864 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
64788 TTTTTAATCT
* * *
64798 AAAAAAAAAGTTTTTGCGTTTTTCTAAAAAA
1 AAAAAAAAAATTTCTGCGTTTTTATAAAAAA
**
64829 AAAAAAAAAATTGTCTGCGTTTTTATTTAAAA
1 AAAAAAAAAATT-TCTGCGTTTTTATAAAAAA
64861 AAAA
1 AAAA
64865 TATATATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (31 bp):
AAAAAAAAAATTTCTGCGTTTTTATAAAAAA
Done.