Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017840.1 Corchorus olitorius cultivar O-4 contig17873, 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: 68743
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--40 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41 TCCATGGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:575 original size:2 final size:2
Alignment explanation
Indices: 570--636 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
560 TATATATATA
570 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
612 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
637 ATCCTTTTCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2559 original size:35 final size:35
Alignment explanation
Indices: 2512--2650 Score: 118
Period size: 35 Copynumber: 3.7 Consensus size: 35
2502 ATTAGTAGGG
* *
2512 TCATATAGTTGCATATTTAGTAGGGGACATCTGCA
1 TCATATAATTGCATATTCAGTAGGGGACATCTGCA
** *
2547 TCATATAATTGCATATTCAGTAGGACATCATATAGC-
1 TCATATAATTGCATATTCAGTAGGGGA-CATCT-GCA
*
2583 TCATATTGTCATGTAGTTGCATATTCAGTTGGGGACATCTGCA
1 TCATA---T-A---A-TTGCATATTCAGTAGGGGACATCTGCA
*
2626 TCATATAGTTGCATATTCAGTAGGG
1 TCATATAATTGCATATTCAGTAGGG
2651 TCATATAGTT
Statistics
Matches: 82, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
35 39 0.48
36 9 0.11
37 2 0.02
39 2 0.02
40 2 0.02
42 2 0.02
43 10 0.12
44 16 0.20
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (35 bp):
TCATATAATTGCATATTCAGTAGGGGACATCTGCA
Found at i:2654 original size:25 final size:25
Alignment explanation
Indices: 2626--2677 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
2616 GACATCTGCA
*
2626 TCATATAGTTGCATATTCAGTAGGG
1 TCATATAGTTACATATTCAGTAGGG
2651 TCATATAGTTACATATTCAGTAGGG
1 TCATATAGTTACATATTCAGTAGGG
2676 TC
1 TC
2678 GTCTGCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (25 bp):
TCATATAGTTACATATTCAGTAGGG
Found at i:2660 original size:60 final size:58
Alignment explanation
Indices: 2590--2706 Score: 144
Period size: 60 Copynumber: 2.0 Consensus size: 58
2580 AGCTCATATT
* * * * *
2590 GTCATGTAGTTGCATATTCAGTTGGGGACATCTGCATCATATAGTTGCATATTCAGTAGG
1 GTCATATAGTTACATATTCAG-TAGGGACATCTGCATAATATA-TTACATATTCAGTAGG
* * *
2650 GTCATATAGTTACATATTCAGTAGGGTCGTCTGCATAATATATTACATTTTCAGTAG
1 GTCATATAGTTACATATTCAGTAGGGACATCTGCATAATATATTACATATTCAGTAG
2707 ATTAACATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 13 0.27
59 17 0.35
60 19 0.39
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (58 bp):
GTCATATAGTTACATATTCAGTAGGGACATCTGCATAATATATTACATATTCAGTAGG
Found at i:3349 original size:16 final size:16
Alignment explanation
Indices: 3328--3361 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3318 TGAGCGTTTT
*
3328 TTTTTTGGCGATAGGC
1 TTTTTTGGCGATAAGC
3344 TTTTTTGGCGATAAGC
1 TTTTTTGGCGATAAGC
3360 TT
1 TT
3362 AAGTGAGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.26, T:0.47
Consensus pattern (16 bp):
TTTTTTGGCGATAAGC
Found at i:3798 original size:26 final size:26
Alignment explanation
Indices: 3769--3823 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
3759 TTCATAATTT
*
3769 TATTTAATTAAATAATAATATAAAAA
1 TATTAAATTAAATAATAATATAAAAA
*
3795 TATTAAATTAAATAATAATATACAAA
1 TATTAAATTAAATAATAATATAAAAA
3821 TAT
1 TAT
3824 AGAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
TATTAAATTAAATAATAATATAAAAA
Found at i:3833 original size:10 final size:10
Alignment explanation
Indices: 3818--3842 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3808 AATAATATAC
3818 AAATATAGAA
1 AAATATAGAA
3828 AAATATAGAA
1 AAATATAGAA
3838 AAATA
1 AAATA
3843 AATTTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (10 bp):
AAATATAGAA
Found at i:4913 original size:40 final size:41
Alignment explanation
Indices: 4847--4926 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 41
4837 TAATGTCCTA
4847 CAATCCTGAAGAAAAATAGGAAAAGAAGAAGAAGAAGGAAG
1 CAATCCTGAAGAAAAATAGGAAAAGAAGAAGAAGAAGGAAG
4888 CAATCCTGAAG-AAAATAGGAAAAGAAGAAGAAGAAGGAA
1 CAATCCTGAAGAAAAATAGGAAAAGAAGAAGAAGAAGGAA
4927 ATAGGCGGCG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
40 28 0.72
41 11 0.28
ACGTcount: A:0.59, C:0.07, G:0.26, T:0.07
Consensus pattern (41 bp):
CAATCCTGAAGAAAAATAGGAAAAGAAGAAGAAGAAGGAAG
Found at i:4927 original size:18 final size:18
Alignment explanation
Indices: 4864--4927 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
4854 GAAGAAAAAT
4864 AGGAAAAGAAGAAGAAGA
1 AGGAAAAGAAGAAGAAGA
*** *
4882 AGGAAGCAATCCTGAAGAAAA
1 AGGAA--AA-GAAGAAGAAGA
4903 TAGGAAAAGAAGAAGAAGA
1 -AGGAAAAGAAGAAGAAGA
4922 AGGAAA
1 AGGAAA
4928 TAGGCGGCGC
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
18 11 0.32
19 7 0.21
20 4 0.12
21 7 0.21
22 5 0.15
ACGTcount: A:0.61, C:0.05, G:0.30, T:0.05
Consensus pattern (18 bp):
AGGAAAAGAAGAAGAAGA
Found at i:6224 original size:330 final size:326
Alignment explanation
Indices: 5494--6362 Score: 1003
Period size: 330 Copynumber: 2.6 Consensus size: 326
5484 GATGTTTCAT
* *
5494 GCCAAGACTCATTGAAATATCTATATTCATCTAATCAAATCTCAGCTATATTGGATTTAAAGATT
1 GCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGC-ATATTGGATTTAAAGATT
* * ** * * ****
5559 TGTTTTTACGAGCATCTGAATCATGTTTTTATTTAATTAGAAATAAATTTTTTAAAAAAGTAAAA
65 TGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTATTAGAAATTAATTGGAAAAAAAAG-AAAA
* ** * ** * *
5624 AAATATTAGAAACGTGAAAAGTCCTTCAATATTTTTGGTATTGAATT-TATATTTTTATGAGTAT
129 CAATATTAGAAGTGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTAAGACTAT
* * * * * *
5688 TATGGCAAAAAATTTAGGAAAAAGGTTTCGGTTCAATTTTTACAAAATTTTAGCCGAAATTATGT
194 TGTGGCAAAAAATTGAGGAAAAAAGTTTCGGGTAAATTTTTACAAAATTTTAGCCGAAATCATGT
** *
5753 ACTATCTCCACGGTTTTTGGCTAAAAACGTGTTGTGGGACACCGCCTCAGTTTTGCAAGATTTTT
259 ACTATCTCCACGGTTTTTGGCTAAAAACGTGTTCAGGGACACCGCCTCAGATTTGCAAGATTTTT
*
5818 GGC
324 AGC
* * * * * *
5821 GCTAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACAATT-GTTTTAAAAAC
1 GCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAG-CA-TATTGGATTTAAAGAT
* *
5885 TTATTTTTACGAGCGTCAGAATCTTGTTTCGATTTTATTAGAAATTAATTAGGAAAAAAAAGAAA
64 TTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTATTAGAAATTAATT-GGAAAAAAAAGAAA
* *
5950 ACGATATTAGAAGTGTGAAAAGCCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTAAGACT
128 ACAATATTAGAAGTGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATA-TTTTTAAGACT
* ** *
6015 ATTGTGGCAAAAAATTGAGGAAACAAATTTTCGGGTAAATTTTTGTAAAATTTTAGCCGAAATCG
192 ATTGTGGCAAAAAATTGAGGAAA-AAAGTTTCGGGTAAATTTTTACAAAATTTTAGCCGAAATCA
* * **
6080 TGTATTAT-TCATCACGGTTTTTGGCTAAAAACGTGTTCCAGGG-C-CCGGCTCAGATTTGCGTG
256 TGTACTATCTC--CACGGTTTTTGGCTAAAAACGTGTT-CAGGGACACCGCCTCAGATTTGCAAG
6142 ATTTTTAGC
318 ATTTTTAGC
* * * * *
6151 GCCAAAACTCCTTGAAAAATCTCTATTCATCTAACCAAGTTTCAGTCATATTGGATTTAAAGATT
1 GCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAG-CATATTGGATTTAAAGATT
* * * *
6216 TGTTTTTACGAGAATCATAATCTTGTTTCGATTTTA-TAGGAAATTAATTCGGAAAAATTAGGAA
65 TGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTATTA-GAAATTAATT-GGAAAAA-AAAGAA
* * *
6280 AACAATATTAGAAGTTTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATACTTTTTACGAC
127 AACAATATTAGAAGTGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATA-TTTTTAAGAC
* *
6345 TACTGTGGCGAAAAATTG
191 TATTGTGGCAAAAAATTG
6363 GCCAAAATCG
Statistics
Matches: 456, Mismatches: 74, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
327 135 0.30
328 15 0.03
329 37 0.08
330 160 0.35
331 106 0.23
332 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (326 bp):
GCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCATATTGGATTTAAAGATTT
GTTTTTACGAGCATCAGAATCTTGTTTCGATTTTATTAGAAATTAATTGGAAAAAAAAGAAAACA
ATATTAGAAGTGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTAAGACTATTG
TGGCAAAAAATTGAGGAAAAAAGTTTCGGGTAAATTTTTACAAAATTTTAGCCGAAATCATGTAC
TATCTCCACGGTTTTTGGCTAAAAACGTGTTCAGGGACACCGCCTCAGATTTGCAAGATTTTTAG
C
Found at i:6962 original size:627 final size:623
Alignment explanation
Indices: 5798--7595 Score: 1756
Period size: 607 Copynumber: 2.9 Consensus size: 623
5788 GGGACACCGC
* *
5798 CTCAGTTTTGCA-AGATTTTTGGCGCTAAGACTCCTTGAAATATCTATATTTATCTAACCAAATC
1 CTCAGTTTTGCATA-ATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATC
* ** * * *
5862 TCAGCCACAATTGTTTTAAAAACTTATTTTTACGAGCGTCAGAATCTTGTTTCGATTTTATTAGA
65 TCAGCCAC-ATTGATTTAAGGATTTGTTTTTACGAGCATCAGAATC-T-TTTCGA-TTTATTAGA
* * * * * *
5927 AATTAATTAGGAAAAAAAAG-AAAACGATATTAGAAGT-GTGAAAAGCCCTTCAATTTTTTTGGC
126 AATCAATTA-GAAAAAAAGGAAAAACGAAATTAGAA-TCGTGAAATGCCCATCAATCTTTTTGGC
* * * * *
5990 GTTGAATTATATATTTTTTAAGACTATTGTGGCAAAAAATTGAGGAAACAA-ATTTTCGGGTAAA
189 -TTAAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAA-AATA-TTTCGGGTCAG
* *
6054 TTTTTGTAAAATTTTAGCCGAAATCGTGTATTATTCATCACGGTTTTTGGCTAAAAACGTG-TTC
251 TTTTTGCAAAATTTTAGCCGAAATCGTGTA-TA-TCATCACGGTTTTTGGCCAAAAACGTGTTTC
* * * * * * * *
6118 CAGGGCCCGGCTCAGATTTGCGTGATTTTTA-GCGCCAAAACTCCTTGAAAAATCTCTATTCATC
314 GAGGGCCCGGATCAGTTTTGCATGA-TTTTAGGCTCCAACACTCCTTGAAATATCTATATTCATC
* * * * * * * *
6182 TAACCAAGTTTCAGTCA-TATTGGATTTAAAGATTTGTTTTTACGAGAATCATAATCTTGTTTCG
378 TAACCAAATCTCAGCCACAATT-TATTTAAGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCG
*
6246 ATTTTA-TAGGAAATTAATTCGGAAAAATTAGGAAAACAATATTAGAAGTT-TGAAAAGCCCTTC
442 ATTTTATTA-GAAATTAATTCGGAAAAAATAGGAAAACAATATTAGAA-TTGTGAAAAGCCCTTC
* * **
6309 AATCTTTTTGGCGTTGAATTATATACTTTTTACGACTACTGTGGCGAAAAATT-GG-CCAAAA-T
505 AATCTTTTTGGCGTTGAATTATATACTTTTTACGACTATTGTGGCCAAAAATTAGGAAAAAAATT
* * * * * *
6371 CGTGTACTAA-CCAT-CACAGTTTTTGG-TT-AAA-AACGAGTTTCGTAACCCAGA
570 CGGGT--TAAGCCATGCAAAATTTTCGGTTTCAAATAACGAGTTCCGGAACCCAGA
* ** *
6422 -TCAGTTTTGCATAATTTTTGGGGCCAAGACTGATTGAAATATCTATATTCATCTAACTAAATCT
1 CTCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCT
*
6486 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATATTTCGATTTAATTAGAA
66 CAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCAGAATC-T-TTTCGATTT-ATTAGAA
* **
6551 ATCAATTTAGAAAAAAAGGGAAAAACGAAATTAGAATCGTGAAATGCCCCTCAATCTTTTTCACT
127 ATCAA-TTAGAAAAAAA-GGAAAAACGAAATTAGAATCGTGAAATGCCCATCAATCTTTTTGGCT
* * *
6616 TAAAACTGTATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAGTTT
190 T-AAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAATATTTCGGGTCAGTTT
*
6681 TTGCAAAACTTTTAGCCGAAATCGTGTACTATCCATCACGGTCTTTTGGCGAAAAACGTGTTTCG
254 TTGCAAAA-TTTTAGCCGAAATCGTGTA-TAT-CATCACGGT-TTTTGGCCAAAAACGTGTTTCG
* * * * * *
6746 A-GGCTACGGATCAGTTTTGCATGATTTTAGGCTCCAACAGTCCTTGCATTATTTATATCCATCT
315 AGGGC-CCGGATCAGTTTTGCATGATTTTAGGCTCCAACACTCCTTGAAATATCTATATTCATCT
* *
6810 AACCAAATCTCAGCCACAATTTATTTAAGGATTTGCTTTTACAAGCATCAGAATCTTGTTTCGAT
379 AACCAAATCTCAGCCACAATTTATTTAAGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGAT
* * *
6875 TTTATTAGAAATTAGTTCGGAAAAAATAGTAAAACAATAGTAGAATTGTGAAAAGCCCTTCAATC
444 TTTATTAGAAATTAATTCGGAAAAAATAGGAAAACAATATTAGAATTGTGAAAAGCCCTTCAATC
* *
6940 TTTTTGGCGTTGAATAATATAC-TTTTACGTCTATTGTGGCCAAAAATTGAGGAAAAAAAATTTC
509 TTTTTGGCGTTGAATTATATACTTTTTACGACTATTGTGGCCAAAAATT-AGG-AAAAAAA-TTC
*** * * *
7004 GGGTTAAGTTTTGCAAAATTTTCGGTTTTTGCCAAAATAACGTGTTCCGGAGCCCCGA
571 GGGTTAAGCCATGCAAAATTTTCGG--TTT--C-AAATAACGAGTTCCGGAACCCAGA
* * * * * * *
7062 CTCTGTTTTGCATGATTTTT-GTGCCAAGACACCTCGAAAAATCTATATTCATATAACCAAATCT
1 CTCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCT
* * *
7126 TAGTCACTTTAGATTTAAGGATTTGTTTTTACGAGCATCAGAATC--TT-G-----TT-----TC
66 CAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCAGAATCTTTTCGATTTATTAGAAATC
* * * *
7178 GATT----AAAAAGGAAAAACGAAATTAGAAGCATGAAAAT-CCCATCGATCTTTTTGGCTTTAA
130 AATTAGAAAAAAAGGAAAAACGAAATTAGAATCGTG-AAATGCCCATCAATCTTTTTGGC-TTAA
* * * *
7238 ATTATATATTCTTTATGAGTATTGTGGCAAAAAATTG-GGGAAAATAATTTCAGGTCAGTATTTG
193 ATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAAT-ATTTCGGGTCAGTTTTTG
* * *
7302 CAAAAATTTTAGCCGAAATCGTG----------CGGTTTTCTTGGCCAAAAACGCGTTCCGATGC
257 C-AAAATTTTAGCCGAAATCGTGTATATCATCACGG-TTT-TTGGCCAAAAACGTGTTTCGA-GG
* * **
7357 CCCCAGATCAGTTTTGCATGATATTT-GGCTCC-ACACTCCTAAAAATATCTATATTCATCTAAC
318 GCCCGGATCAGTTTTGCATGAT-TTTAGGCTCCAACACTCCTTGAAATATCTATATTCATCTAAC
* * * * **
7420 TAAATCTTAGCCACAATTTAATTATGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTAA
382 CAAATCTCAGCCACAATTTATTTAAGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTT
* *
7485 ATTAGAAATTAATTCGGAAAAAATAGGAAAACGATATTAGAATTGTGAAAAGCCGTTCAATCTTT
447 ATTAGAAATTAATTCGGAAAAAATAGGAAAACAATATTAGAATTGTGAAAAGCCCTTCAATCTTT
** * * *
7550 TTGATGATGAATTATATACTTTTTATGACTATTTTGGCCAAAAATT
512 TTGGCGTTGAATTATATACTTTTTACGACTATTGTGGCCAAAAATT
7596 TTGGGTCAGT
Statistics
Matches: 986, Mismatches: 143, Indels: 106
0.80 0.12 0.09
Matches are distributed among these distances:
606 5 0.01
607 175 0.18
608 47 0.05
609 4 0.00
617 7 0.01
618 104 0.11
619 15 0.02
622 6 0.01
623 118 0.12
624 33 0.03
625 105 0.11
626 49 0.05
627 171 0.17
628 7 0.01
629 2 0.00
630 7 0.01
631 1 0.00
632 14 0.01
635 3 0.00
636 2 0.00
639 3 0.00
640 91 0.09
641 17 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (623 bp):
CTCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCT
CAGCCACATTGATTTAAGGATTTGTTTTTACGAGCATCAGAATCTTTTCGATTTATTAGAAATCA
ATTAGAAAAAAAGGAAAAACGAAATTAGAATCGTGAAATGCCCATCAATCTTTTTGGCTTAAATT
ATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAATATTTCGGGTCAGTTTTTGCAAA
ATTTTAGCCGAAATCGTGTATATCATCACGGTTTTTGGCCAAAAACGTGTTTCGAGGGCCCGGAT
CAGTTTTGCATGATTTTAGGCTCCAACACTCCTTGAAATATCTATATTCATCTAACCAAATCTCA
GCCACAATTTATTTAAGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTATTAGAAAT
TAATTCGGAAAAAATAGGAAAACAATATTAGAATTGTGAAAAGCCCTTCAATCTTTTTGGCGTTG
AATTATATACTTTTTACGACTATTGTGGCCAAAAATTAGGAAAAAAATTCGGGTTAAGCCATGCA
AAATTTTCGGTTTCAAATAACGAGTTCCGGAACCCAGA
Found at i:9184 original size:332 final size:333
Alignment explanation
Indices: 8010--9754 Score: 2624
Period size: 333 Copynumber: 5.3 Consensus size: 333
8000 AAACGAGTTC
8010 AGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTCCTGAATTAATTTCTAATGAAATCGA
1 AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCCTGAATTAATTTCTAATGAAATCGA
* * *
8074 AACAAGATTCAAATGCTCGTAAAAACAAATCATTAAATGCAATGTGACTAAGTTTTTATTAGATG
66 AACAAGATTCAAATGCTCGTGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATG
* *
8139 AATATAGATATTTCAAGGAGTCCGGACGCCAAAAATCATGCAAAATTGAGCCGGGACCCCGAAAC
131 AATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAAC
* * *
8204 GCATCTTTAGCCAAAAACC------G-T-G---ACGATTTTGGCTAAAATTTTGCTAAAAATGAC
196 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGAC
* * *
8258 CGCGAAAATTTTTTCCTCAATTTTGGGATAAAATAATCATAAAATATATACAATGTAACGCCAAA
261 CGCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAA
8323 AGAGATTGG
326 A-AGATTGG
*
8332 AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCCTGAATTAATTTATAATGAAATCGA
1 AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCCTGAATTAATTTCTAATGAAATCGA
*
8397 AACAAGATTCAAATGCTCGGGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATG
66 AACAAGATTCAAATGCTCGTGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATG
* * ** * *
8462 AATATAGTTATTTTAAGGAAACCTAATGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAAC
131 AATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAAC
* *
8527 GCGTTTTTAGCCAAAAACCGTGATTGTTAGTACACGATTTTGGCTAAAATTTTCCAAAAAATGAC
196 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGAC
* * * *
8592 TGCGAAATATTTTCCCTCAATTTTTGGATAAAATACTCATAAAATATATAC-ATGTAAAGCCAAA
261 CGCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAA
8656 AAGATTGG
326 AAGATTGG
* *
8664 AGGACTTTTCACGCTTTTAATATTGTTTTTCATATTTTTCCTGAATTAATTTTGTAATGAAATCG
1 AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCCTGAATTAA-TTTCTAATGAAATCG
* **
8729 AAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTAACTAAGTTTTTATTAGAT
65 AAACAAGATTCAAATGCTCGTGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGAT
* *
8794 GAATATAGATATTTCAAGGAGTCCTGACGCAAAAAATCATGCAAAACTTAGCCGGGACCCCGAAA
130 GAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAA
* *
8859 CGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTTTGCTAAAATTTTGCAAAAAATGA
195 CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGA
*
8924 CCGCGAAAAATTTTTCCTCAATTTTTTGAT-AAATACTCATAAAATATATACAATGTAACGCCAA
260 CCGCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAA
*
8988 AAAAATTGG
325 AAAGATTGG
* *
8997 AGTACTTTTCACGTTTTTAATATCGTTTTTCATATTTTTCCTGAATTAATTTCTAATGAAATCGA
1 AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCCTGAATTAATTTCTAATGAAATCGA
*
9062 AACAAGATTCAAATGCTCGGGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATG
66 AACAAGATTCAAATGCTCGTGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATG
* *** *
9127 AATATAGATATTTCAAGGAGTCTTGACATAAAAAATCATGCAAAACTGAGCCGGGACCCAGAAAC
131 AATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAAC
*
9192 GCGTTTTTAGCCAAAAACCCTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGAC
196 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGAC
* * *
9257 CGCGAAAATTTTTTTCCTTAATTTTTGGATAAAATACTCCTAAAATATATACAATGTAACGCCAA
261 CGCGAAAA-ATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAA
* *
9322 AAAGAATGA
325 AAAGATTGG
* * * *
9331 AGGACTTTCCACTCTTTTAATAT-TTGTTTTCATA-TTTTCCTGAATTAATTTCTAATTAAATCG
1 AGGACTTTTCACGCTTTTAATATCGT-TTTTCATATTTTTCCTGAATTAATTTCTAATGAAATCG
* * *
9394 AAATAAGATTCAAATGCTCGTGAAAACAAATCCTTAAATGTAATATGGCTAAGTTTTTATTAGAT
65 AAACAAGATTCAAATGCTCGTGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGAT
* * *
9459 GAATATATATATATATTTCATGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGAGG-CCC
130 G---A-ATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCG-GGACCC
* * *
9523 CAAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGTCTAAAAATTTGCAAAA
190 CGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAA
** * * * * *
9588 AATGATTGCGAAAAATATTTCCTCAATTTTTGGATAAAATACTCATAAAATACATAAAATTTAAT
255 AATGACCGCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAAC
*
9653 GTCAAAAAGATTGG
320 GCCAAAAAGATTGG
* *
9667 AGGACTTTTCACACTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCTAATGAAATCG
1 AGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCCTGAATTAATTTCTAATGAAATCG
9732 AAACAAGATTCAAATGCTCGTGA
65 AAACAAGATTCAAATGCTCGTGA
9755 TTGAGCCAAA
Statistics
Matches: 1288, Mismatches: 110, Indels: 34
0.90 0.08 0.02
Matches are distributed among these distances:
322 34 0.03
323 164 0.13
329 1 0.00
330 1 0.00
331 1 0.00
332 282 0.22
333 406 0.32
334 141 0.11
336 84 0.07
337 123 0.10
338 51 0.04
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (333 bp):
AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCCTGAATTAATTTCTAATGAAATCGA
AACAAGATTCAAATGCTCGTGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATG
AATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAAC
GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGAC
CGCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAA
AAGATTGG
Found at i:9394 original size:665 final size:662
Alignment explanation
Indices: 8010--9751 Score: 2652
Period size: 665 Copynumber: 2.6 Consensus size: 662
8000 AAACGAGTTC
*
8010 AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTCCTGAATTAATTTCTAATGAAATCGAA
1 AGGACTTTTCACGCTTTTAATATTGTTTTTCATATTTTCCTGAATTAATTTCTAATGAAATCGAA
*
8075 ACAAGATTCAAATGCTCGTAAAAACAAATCATTAAATGCAATGTGACTAAGTTTTTATTAGATGA
66 ACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGACTAAGTTTTTATTAGATGA
*
8140 ATATAGATATTTCAAGGAGTCCGGACGCCAAAAATCATGCAAAA-TTGAGCCGGGACCCCGAAAC
131 ATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTT-AGCCGGGACCCCGAAAC
* * * * *
8204 GCATCTTTAGCCAAAAAC-----CG-T-G---ACGATTTTGGCTAAAATTTTGCTAAAAATGACC
195 GCGTTTTTAGCCAAAAACGTGATGGTTAGTACACGATTTTTGCTAAAATTTTGCAAAAAATGACC
* * *
8259 GCGAAAATTTTTTCCTCAATTTTGGGATAAAATAATCATAAAATATATACAATGTAACGCCAAAA
260 GCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAAA
*
8324 GAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCCTGAATTAATTTATAAT
325 -AGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCCTGAATTAATTTCTAAT
8389 GAAATCGAAACAAGATTCAAATGCTCGGGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTT
389 GAAATCGAAACAAGATTCAAATGCTCGGGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTT
* * *
8454 ATTAGATGAATATAGTTATTTTAAGGAAACCTAATGCCAAAAATCATGCAAAACTGAGCCGGGAC
454 ATTAGATGAATATAGATATTTCAAGGAAACCTAAT-CAAAAAATCATGCAAAACTGAGCCGGGAC
* * *
8519 CCCGAAACGCGTTTTTAGCCAAAAACCGTGATTGTTAGTACACGATTTTGGCTAAAATTTTCCAA
518 CCAGAAACGCGTTTTTAGCCAAAAACCCTGATGGTTAGTACACGATTTTGGCTAAAATTTTCCAA
*
8584 AAAATGACTGCGAAATATTTTCCCTCAATTTTTGGATAAAATACTCATAAAATATATACATGTAA
583 AAAATGACCGCGAAATATTTTCCCTCAATTTTTGGATAAAATACTCATAAAATATATACATGTAA
* *
8649 AGCCAAAAAGATTGG
648 AGCCAAAAAGAATGA
*
8664 AGGACTTTTCACGCTTTTAATATTGTTTTTCATATTTTTCCTGAATTAATTTTGTAATGAAATCG
1 AGGACTTTTCACGCTTTTAATATTGTTTTTCATA-TTTTCCTGAATTAA-TTTCTAATGAAATCG
*
8729 AAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTAACTAAGTTTTTATTAGAT
64 AAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGACTAAGTTTTTATTAGAT
*
8794 GAATATAGATATTTCAAGGAGTCCTGACGCAAAAAATCATGCAAAACTTAGCCGGGACCCCGAAA
129 GAATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTTAGCCGGGACCCCGAAA
8859 CGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTTTGCTAAAATTTTGCAAAAAATGA
194 CGCGTTTTTAGCCAAAAA-CGTGATGGTTAGTACACGATTTTTGCTAAAATTTTGCAAAAAATGA
*
8924 CCGCGAAAAATTTTTCCTCAATTTTTTGAT-AAATACTCATAAAATATATACAATGTAACGCCAA
258 CCGCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAA
* * *
8988 AAAAATTGGAGTACTTTTCACGTTTTTAATATCGTTTTTCATATTTTTCCTGAATTAATTTCTAA
323 AAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCCTGAATTAATTTCTAA
9053 TGAAATCGAAACAAGATTCAAATGCTCGGGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTT
388 TGAAATCGAAACAAGATTCAAATGCTCGGGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTT
** *
9118 TATTAGATGAATATAGATATTTCAAGGAGTCTTGACAT-AAAAAATCATGCAAAACTGAGCCGGG
453 TATTAGATGAATATAGATATTTCAAGGAAACCT-A-ATCAAAAAATCATGCAAAACTGAGCCGGG
*
9182 ACCCAGAAACGCGTTTTTAGCCAAAAACCCTGATGGTTAGTACACGATTTTGGCTAAAATTTTGC
516 ACCCAGAAACGCGTTTTTAGCCAAAAACCCTGATGGTTAGTACACGATTTTGGCTAAAATTTTCC
* * * *
9247 AAAAAATGACCGCGAAAATTTTTTTCCTTAATTTTTGGATAAAATACTCCTAAAATATATACAAT
581 AAAAAATGACCGCG-AAATATTTTCCCTCAATTTTTGGATAAAATACTCATAAAATATATAC-AT
*
9312 GTAACGCCAAAAAGAATGA
644 GTAAAGCCAAAAAGAATGA
* * *
9331 AGGACTTTCCACTCTTTTAATATT-TGTTTTCATATTTTCCTGAATTAATTTCTAATTAAATCGA
1 AGGACTTTTCACGCTTTTAATATTGT-TTTTCATATTTTCCTGAATTAATTTCTAATGAAATCGA
* * * * *
9395 AATAAGATTCAAATGCTCGTGAAAACAAATCCTTAAATGTAATATGGCTAAGTTTTTATTAGATG
65 AACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGACTAAGTTTTTATTAGATG
* * * *
9460 AATATATATATATATTTCATGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGAGG-CCCC
130 ---A-ATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTTAGCCG-GGACCCC
* *
9524 AAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA-TTTTGTCTAAAAATTTGCAAAA
190 GAAACGCGTTTTTAGCCAAAAA-CGTGATGGTTAGTACACGATTTTTG-CTAAAATTTTGCAAAA
** * * * * *
9588 AATGATTGCGAAAAATATTTCCTCAATTTTTGGATAAAATACTCATAAAATACATAAAATTTAAT
253 AATGACCGCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAAC
* * *
9653 GTCAAAAAGATTGGAGGACTTTTCACACTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAAT
318 GCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCCTGAATTAAT
9718 TTCTAATGAAATCGAAACAAGATTCAAATGCTCG
382 TTCTAATGAAATCGAAACAAGATTCAAATGCTCG
9752 TGATTGAGCC
Statistics
Matches: 992, Mismatches: 69, Indels: 37
0.90 0.06 0.03
Matches are distributed among these distances:
654 33 0.03
655 14 0.01
656 153 0.15
657 3 0.00
662 1 0.00
663 1 0.00
664 1 0.00
665 324 0.33
666 94 0.09
667 106 0.11
668 6 0.01
669 137 0.14
670 70 0.07
671 49 0.05
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (662 bp):
AGGACTTTTCACGCTTTTAATATTGTTTTTCATATTTTCCTGAATTAATTTCTAATGAAATCGAA
ACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGACTAAGTTTTTATTAGATGA
ATATAGATATTTCAAGGAGTCCTGACGCCAAAAATCATGCAAAACTTAGCCGGGACCCCGAAACG
CGTTTTTAGCCAAAAACGTGATGGTTAGTACACGATTTTTGCTAAAATTTTGCAAAAAATGACCG
CGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAAAA
GATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCCTGAATTAATTTCTAATGA
AATCGAAACAAGATTCAAATGCTCGGGAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTAT
TAGATGAATATAGATATTTCAAGGAAACCTAATCAAAAAATCATGCAAAACTGAGCCGGGACCCA
GAAACGCGTTTTTAGCCAAAAACCCTGATGGTTAGTACACGATTTTGGCTAAAATTTTCCAAAAA
ATGACCGCGAAATATTTTCCCTCAATTTTTGGATAAAATACTCATAAAATATATACATGTAAAGC
CAAAAAGAATGA
Found at i:12936 original size:333 final size:331
Alignment explanation
Indices: 11451--13206 Score: 2567
Period size: 333 Copynumber: 5.3 Consensus size: 331
11441 CGACCGATCA
*
11451 GCTCGTAAAAACAAATCCTTAAATGCAATGTGACTAAGTTTTTATTAGATGAATATAGATATTTC
1 GCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAATATAGATATTTC
* * **
11516 AAGGAGTCCTGACGCCAAAAATCCTGCAAAACTGAGTTGGGACCCCGAAACGCGTTTTTAGCAAA
66 AAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAACGCGTTTTTAGC-AA
*
11581 AAACCGTGATGGTTAGTACTCGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTT
130 AAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTT
* * *
11646 CCTCAATTTTTTGGATAAAATACTCTTAAAATGTATACAATGTAACGGCAAAAAGATTGGAGGAC
195 CCTCAA-TTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAAAAGATTGGAGGAC
* * *
11711 TTTTCACGCTTTTAATATCGTTTATCATATTTTTCCTAAATTAATTTTTAATGAAATCGAAACAA
259 TTTTCACGCTTTTAATATCGTTTTTCATA-TTTTCCTGAATTAATTTCTAATGAAATCGAAACAA
11776 GATTCAAAT
323 GATTCAAAT
* * * *
11785 GCTCGTAAAAACAAATCCTTAAATTCAATGTGGCCAAGTTCTTAATAGATGAATATAGATATTTC
1 GCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAATATAGATATTTC
* ** * * *
11850 AAGGAGTATTGAC-AAAAAAATTGATGCAAAACTGAGTCGGGACCCCGTAACGCGTTTTTAGCCA
66 AAGGAGTCTTGACGCCAAAAA-TCATGCAAAACTGAGCCGGGACCCCGAAACGCGTTTTTAG-CA
11914 AAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGA-CGTCGAAAAATTT
129 AAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCG-CGAAAAATTT
* * * * * *
11978 TTCCTCATTTTTTTGATAAAATACTAATAAAATATATACAATTTAACACCAAAAAGGTTGGAGGA
193 TTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAAAAGATTGGAGGA
** *
12043 CTTTTCATACTTTTAATATCATTTTTCATATTTTCCTGAATTAATTTCTAATGAAATCGAAACAA
258 CTTTTCACGCTTTTAATATCGTTTTTCATATTTTCCTGAATTAATTTCTAATGAAATCGAAACAA
12108 G----AAAT
323 GATTCAAAT
* * *
12113 GCTCGTAAAAAAAAATCCTTAAATGCAATGTGACTAAGTTTTTATTATATGAATATAGATATTTC
1 GCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAATATAGATATTTC
* * * * * * *
12178 ATGGAATATGGATGCCAAAAATCATGCAAAACTGAGCCGGTACCCCGAAACGTGTTTTTAGTCAA
66 AAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAACGCGTTTTTAG-CAA
*
12243 AAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAGTTTTT
130 AAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTT
* *
12308 CCTCAGTTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAAAATATTGGAGGACT
195 CCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAAAAGATTGGAGGACT
*
12373 TTTCACACTTTTAATATCGTTTTTCATATTTTCCTGAATTAATTTCTAATGAAATCGAAACAAGA
260 TTTCACGCTTTTAATATCGTTTTTCATATTTTCCTGAATTAATTTCTAATGAAATCGAAACAAGA
12438 TTCAAAT
325 TTCAAAT
12445 GCTCGGT-AAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAATATAGATATTT
1 GCTC-GTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAATATAGATATTT
* *** * * *
12509 CAAGGAGTGTTGACATAAAAAATAATGCAAAACTGAGCCGGGACCTCGTAACGCGTTTTTAGCAA
65 CAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAACGCGTTTTTAGC-A
* *
12574 AAAACTGTGATGGTTAGTATACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATATT
129 AAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAAT-TT
* *
12639 TT-CTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGCCAAAAAGATTGGAGGA
193 TTCCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAAAAGATTGGAGGA
* * * * *
12703 CTTATCACGCTTTTAATATAGTTTTTCATATTTTTTCTAAATTAATTTCTAGTGAAATCGAAACA
258 CTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTCCTGAATTAATTTCTAATGAAATCGAAACA
* *
12768 CGATTAAAAT
322 AGATTCAAAT
* * *
12778 ACTCGTAAAAACAAATCCTTAAATGCAATGTTGCTAAGTTTTTATTATATGAATATAGATATTTC
1 GCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAATATAGATATTTC
* * * * *
12843 ATGGAGTCTTGATGCCAAAAATCATGCAAAACTGAACCAGGACCCCGAAACGTGTTTTTAGTCAA
66 AAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAACGCGTTTTTAG-CAA
* * *
12908 AAACCGTGATGGTTAGTACACAATTTTGGCTAAAATTTTGCAAAAAGTGACCGCGAAAAGTTTTT
130 AAACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTT
* *
12973 CCTCAATTTTTGGATAAAATAATCATAAAATATATGCAATGTAACGCCAAAAAAGATTGGAGGAC
195 CCTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCC-AAAAAGATTGGAGGAC
* * *
13038 TTTACACGCTTATAATATCGTTTTTCATATTTTACTGAATTAATTTCTAATGAAATCGAAACAAG
259 TTTTCACGCTTTTAATATCGTTTTTCATATTTTCCTGAATTAATTTCTAATGAAATCGAAACAAG
13103 ATTCAAAT
324 ATTCAAAT
* *
13111 GCTCGGGAAAAA-AAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAATTTAGATATTT
1 GCTC-GTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAATATAGATATTT
* * *
13175 CCAGGAATCCTGACGCCAAAAATCATGCAAAA
65 CAAGGAGTCTTGACGCCAAAAATCATGCAAAA
13207 TTTTTCGGGT
Statistics
Matches: 1272, Mismatches: 132, Indels: 37
0.88 0.09 0.03
Matches are distributed among these distances:
328 290 0.23
329 7 0.01
331 1 0.00
332 296 0.23
333 454 0.36
334 223 0.18
335 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (331 bp):
GCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAATATAGATATTTC
AAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAACGCGTTTTTAGCAAA
AACCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTTC
CTCAATTTTTGGATAAAATACTCATAAAATATATACAATGTAACGCCAAAAAGATTGGAGGACTT
TTCACGCTTTTAATATCGTTTTTCATATTTTCCTGAATTAATTTCTAATGAAATCGAAACAAGAT
TCAAAT
Found at i:14126 original size:35 final size:36
Alignment explanation
Indices: 14087--14158 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
14077 GCCACATCTT
* * * *
14087 CTGTTGATCGAG-CCACTTGCCACGTCATCAGTTGA
1 CTGTTGACCGAGTCAACCTGCCACATCATCAGTTGA
*
14122 CTGTTGACCGAGTCAACCTGCCACATCATCCGTTGA
1 CTGTTGACCGAGTCAACCTGCCACATCATCAGTTGA
14158 C
1 C
14159 CAAGTCAACC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 11 0.35
36 20 0.65
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (36 bp):
CTGTTGACCGAGTCAACCTGCCACATCATCAGTTGA
Found at i:14186 original size:29 final size:29
Alignment explanation
Indices: 14125--14189 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
14115 CAGTTGACTG
* *
14125 TTGACCGAGTCAACCTGCCACATCATCCG
1 TTGACCAAGTCAACCTGCCACATCATCCA
* * *
14154 TTGACCAAGTCAACCTGCCACGTTATCTA
1 TTGACCAAGTCAACCTGCCACATCATCCA
14183 TTGACCA
1 TTGACCA
14190 CCCCTCTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.25
Consensus pattern (29 bp):
TTGACCAAGTCAACCTGCCACATCATCCA
Found at i:15103 original size:28 final size:29
Alignment explanation
Indices: 15071--15132 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
15061 CAGTTGAGCA
*
15071 TTGACCA-GCCAACCTACCATATTATCCG
1 TTGACCAGGCCAACCTACCACATTATCCG
* * *
15099 TTGACCAGGTCAACCTGCCACGTTATCCG
1 TTGACCAGGCCAACCTACCACATTATCCG
15128 TTGAC
1 TTGAC
15133 TGTTAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (29 bp):
TTGACCAGGCCAACCTACCACATTATCCG
Found at i:15230 original size:29 final size:29
Alignment explanation
Indices: 15197--15257 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
15187 ATCAGTTGAG
* *
15197 CGTTGACCGAGCCAACCTACCATATTATC
1 CGTTGACCAAGCCAACCTACCACATTATC
* * *
15226 CGTTGACCAAGTCAACCTGCCACGTTATC
1 CGTTGACCAAGCCAACCTACCACATTATC
15255 CGT
1 CGT
15258 AGACTGTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (29 bp):
CGTTGACCAAGCCAACCTACCACATTATC
Found at i:15278 original size:65 final size:65
Alignment explanation
Indices: 15050--15454 Score: 374
Period size: 65 Copynumber: 6.3 Consensus size: 65
15040 TCGAGCCACT
* * *
15050 TGCCACGTTATCAGTTGAGCATTGACC-AGCCAACCTACCATATTATCCGTTGACCAGGTCAACC
1 TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATTATCCGTTGACCAAGTCAACC
* * *** * * * * * * * *
15114 TGCCACGTTATCCGTTGA-CTGTTAATTAAGTCAACCCGGCACA-TCTCCTGTTGATCGAG-CCA
1 TGCCACGTTATCAGTTGAGC-GTTGACCGAGCCAACCTGCCATATTATCC-GTTGACCAAGTCAA
*
15176 CT
64 CC
*
15178 TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTACCATATTATCCGTTGACCAAGTCAACC
1 TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATTATCCGTTGACCAAGTCAACC
* * * *** * * * * * * * *
15243 TGCCACGTTATCCGTAGA-CTGTTAATTAAGTCAACCCGGCACA-TCTCCTGTTGATCGAG-CCA
1 TGCCACGTTATCAGTTGAGC-GTTGACCGAGCCAACCTGCCATATTATCC-GTTGACCAAGTCAA
*
15305 CT
64 CC
* * *
15307 TGCCATGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCAACC
1 TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATTATCCGTTGACCAAGTCAACC
* *
15372 TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCAACC
1 TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATTATCCGTTGACCAAGTCAACC
*
15437 TGCCACGTTATCCGTTGA
1 TGCCACGTTATCAGTTGA
15455 CCACCCTTCC
Statistics
Matches: 263, Mismatches: 67, Indels: 21
0.75 0.19 0.06
Matches are distributed among these distances:
63 1 0.00
64 111 0.42
65 151 0.57
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.26
Consensus pattern (65 bp):
TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATTATCCGTTGACCAAGTCAACC
Found at i:15359 original size:29 final size:29
Alignment explanation
Indices: 15326--15457 Score: 115
Period size: 29 Copynumber: 4.3 Consensus size: 29
15316 ATCAGTTGAG
15326 CGTTGACC-GAGCCAACCTGCCATATCATC
1 CGTTGACCAG-GCCAACCTGCCATATCATC
* *
15355 CGTTGACCAGGTCAACCTGCCACGTTATCAGTTGAG
1 CGTTGACCAGGCCAACCTGCCA---TATCA--T--C
15391 CGTTGACC-GAGCCAACCTGCCATATCATC
1 CGTTGACCAG-GCCAACCTGCCATATCATC
* ** *
15420 CGTTGACCAGGTCAACCTGCCACGTTATC
1 CGTTGACCAGGCCAACCTGCCATATCATC
15449 CGTTGACCA
1 CGTTGACCA
15458 CCCTTCCTAG
Statistics
Matches: 85, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
29 51 0.60
30 2 0.02
31 1 0.01
32 5 0.06
33 5 0.06
34 1 0.01
35 1 0.01
36 19 0.22
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (29 bp):
CGTTGACCAGGCCAACCTGCCATATCATC
Found at i:15360 original size:36 final size:36
Alignment explanation
Indices: 15292--15425 Score: 115
Period size: 36 Copynumber: 3.9 Consensus size: 36
15282 CACATCTCCT
* * * *
15292 GTTGATCGAGCC-ACTTGCCATGTTATCAGTTGAGC
1 GTTGACCGAGCCAACCTGCCATATCATCAGTTGAGC
15327 GTTGACCGAGCCAACCTGCCATATCATC-------C
1 GTTGACCGAGCCAACCTGCCATATCATCAGTTGAGC
* ** *
15356 GTTGACC-AGGTCAACCTGCCACGTTATCAGTTGAGC
1 GTTGACCGA-GCCAACCTGCCATATCATCAGTTGAGC
*
15392 GTTGACCGAGCCAACCTGCCATATCATCCGTTGA
1 GTTGACCGAGCCAACCTGCCATATCATCAGTTGA
15426 CCAGGTCAAC
Statistics
Matches: 76, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
28 1 0.01
29 23 0.30
35 11 0.14
36 40 0.53
37 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.25
Consensus pattern (36 bp):
GTTGACCGAGCCAACCTGCCATATCATCAGTTGAGC
Found at i:15425 original size:129 final size:129
Alignment explanation
Indices: 15000--15389 Score: 683
Period size: 129 Copynumber: 3.0 Consensus size: 129
14990 TGTCATCCCA
* * *
15000 TTGACCGTTAATTAAGTTAACCCGGCACATCTCTTGTTGATCGAGCCACTTGCCACGTTATCAGT
1 TTGACTGTTAATTAAGTCAACCCGGCACATCTCCTGTTGATCGAGCCACTTGCCACGTTATCAGT
*
15065 TGAGCATTGACC-AGCCAACCTACCATATTATCCGTTGACCAGGTCAACCTGCCACGTTATCCG
66 TGAGCGTTGACCGAGCCAACCTACCATATTATCCGTTGACCAGGTCAACCTGCCACGTTATCCG
15128 TTGACTGTTAATTAAGTCAACCCGGCACATCTCCTGTTGATCGAGCCACTTGCCACGTTATCAGT
1 TTGACTGTTAATTAAGTCAACCCGGCACATCTCCTGTTGATCGAGCCACTTGCCACGTTATCAGT
*
15193 TGAGCGTTGACCGAGCCAACCTACCATATTATCCGTTGACCAAGTCAACCTGCCACGTTATCCG
66 TGAGCGTTGACCGAGCCAACCTACCATATTATCCGTTGACCAGGTCAACCTGCCACGTTATCCG
* *
15257 TAGACTGTTAATTAAGTCAACCCGGCACATCTCCTGTTGATCGAGCCACTTGCCATGTTATCAGT
1 TTGACTGTTAATTAAGTCAACCCGGCACATCTCCTGTTGATCGAGCCACTTGCCACGTTATCAGT
* * *
15322 TGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCAACCTGCCACGTTATCAG
66 TGAGCGTTGACCGAGCCAACCTACCATATTATCCGTTGACCAGGTCAACCTGCCACGTTATCCG
15386 TTGA
1 TTGA
15390 GCGTTGACCG
Statistics
Matches: 249, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
128 73 0.29
129 176 0.71
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (129 bp):
TTGACTGTTAATTAAGTCAACCCGGCACATCTCCTGTTGATCGAGCCACTTGCCACGTTATCAGT
TGAGCGTTGACCGAGCCAACCTACCATATTATCCGTTGACCAGGTCAACCTGCCACGTTATCCG
Found at i:15655 original size:36 final size:35
Alignment explanation
Indices: 15615--15721 Score: 93
Period size: 36 Copynumber: 3.2 Consensus size: 35
15605 TGTATAGACT
*
15615 TGCCATGTTATTAGTTGAGCGTTGATCGAGCCAACC
1 TGCCATGTTATCAGTTGAGCGTTGA-CGAGCCAACC
* * *
15651 TGCCA---TATCA--T--CCGTTGACCAGGTCAACC
1 TGCCATGTTATCAGTTGAGCGTTGACGA-GCCAACC
*
15680 TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACC
1 TGCCATGTTATCAGTTGAGCGTTGA-CGAGCCAACC
15716 TGCCAT
1 TGCCAT
15722 ATCATCCGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
28 2 0.04
29 17 0.31
31 1 0.02
32 5 0.09
33 4 0.07
34 1 0.02
36 22 0.41
37 2 0.04
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (35 bp):
TGCCATGTTATCAGTTGAGCGTTGACGAGCCAACC
Found at i:15667 original size:29 final size:28
Alignment explanation
Indices: 15634--15763 Score: 89
Period size: 29 Copynumber: 4.2 Consensus size: 28
15624 ATTAGTTGAG
15634 CGTTGATCGAGCCAACCTGCCATATCATC
1 CGTTGA-CGAGCCAACCTGCCATATCATC
* * *
15663 CGTTGACCAGGTCAACCTGCCACGTTATCAGTTGAG
1 CGTTGACGA-GCCAACCTGCCA---TATCA--T--C
15699 CGTTGACCGAGCCAACCTGCCATATCATC
1 CGTTGA-CGAGCCAACCTGCCATATCATC
* * ** *
15728 CGTTGACCAGGTCAACCTGCCACGTTATC
1 CGTTGACGA-GCCAACCTGCCATATCATC
15757 CGTTGAC
1 CGTTGAC
15764 CACCCTTCCT
Statistics
Matches: 80, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
28 4 0.05
29 45 0.56
31 1 0.01
32 5 0.06
33 5 0.06
34 1 0.01
36 17 0.21
37 2 0.03
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.24
Consensus pattern (28 bp):
CGTTGACGAGCCAACCTGCCATATCATC
Found at i:15719 original size:65 final size:65
Alignment explanation
Indices: 15615--15762 Score: 260
Period size: 65 Copynumber: 2.3 Consensus size: 65
15605 TGTATAGACT
* * *
15615 TGCCATGTTATTAGTTGAGCGTTGATCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCAACC
1 TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCAACC
15680 TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCAACC
1 TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCAACC
*
15745 TGCCACGTTATCCGTTGA
1 TGCCACGTTATCAGTTGA
15763 CCACCCTTCC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 79 1.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (65 bp):
TGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCAACC
Found at i:15862 original size:308 final size:308
Alignment explanation
Indices: 15304--15916 Score: 1190
Period size: 308 Copynumber: 2.0 Consensus size: 308
15294 TGATCGAGCC
15304 ACTTGCCATGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCA
1 ACTTGCCATGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCA
15369 ACCTGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCA
66 ACCTGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCA
15434 ACCTGCCACGTTATCCGTTGACCACCCTTCCTAGCTTAATTTTAATCTGAGTTTATCTCAACAAA
131 ACCTGCCACGTTATCCGTTGACCACCCTTCCTAGCTTAATTTTAATCTGAGTTTATCTCAACAAA
15499 AACCGGCCATAAAATGACCGAAGTACCCCTTATGATTTGTTGTTACATTTGTGTGTGCAACCCTT
196 AACCGGCCATAAAATGACCGAAGTACCCCTTATGATTTGTTGTTACATTTGTGTGTGCAACCCTT
15564 TCATGGACAAATCGGTAATGTTGAATTCAATGTTAATGTGTTGTATAG
261 TCATGGACAAATCGGTAATGTTGAATTCAATGTTAATGTGTTGTATAG
* *
15612 ACTTGCCATGTTATTAGTTGAGCGTTGATCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCA
1 ACTTGCCATGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCA
15677 ACCTGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCA
66 ACCTGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCA
*
15742 ACCTGCCACGTTATCCGTTGACCACCCTTCCTAGCTTAATTTTAATCTGAGTTTATCTCAACAGA
131 ACCTGCCACGTTATCCGTTGACCACCCTTCCTAGCTTAATTTTAATCTGAGTTTATCTCAACAAA
*
15807 AACCGGCCATAAAATGACCGAAGTACCCTTTATGATTTGTTGTTACATTTGTGTGTGCAACCCTT
196 AACCGGCCATAAAATGACCGAAGTACCCCTTATGATTTGTTGTTACATTTGTGTGTGCAACCCTT
15872 TCATGGACAAATCGGTAATGTTGAATTCAATGTTAATGTGTTGTA
261 TCATGGACAAATCGGTAATGTTGAATTCAATGTTAATGTGTTGTA
15917 CAGATGTGTT
Statistics
Matches: 301, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
308 301 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (308 bp):
ACTTGCCATGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCA
ACCTGCCACGTTATCAGTTGAGCGTTGACCGAGCCAACCTGCCATATCATCCGTTGACCAGGTCA
ACCTGCCACGTTATCCGTTGACCACCCTTCCTAGCTTAATTTTAATCTGAGTTTATCTCAACAAA
AACCGGCCATAAAATGACCGAAGTACCCCTTATGATTTGTTGTTACATTTGTGTGTGCAACCCTT
TCATGGACAAATCGGTAATGTTGAATTCAATGTTAATGTGTTGTATAG
Found at i:30036 original size:13 final size:13
Alignment explanation
Indices: 30018--30043 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30008 ATGACAGTCT
30018 TATAAGATCTACA
1 TATAAGATCTACA
30031 TATAAGATCTACA
1 TATAAGATCTACA
30044 ATTTGAAGGG
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TATAAGATCTACA
Found at i:43488 original size:35 final size:35
Alignment explanation
Indices: 43442--43512 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
43432 ATGTTTCCTG
43442 CACCCGAATATTTGACTCAATGATTAATATATGCT
1 CACCCGAATATTTGACTCAATGATTAATATATGCT
43477 CACCCGAATATTTGACTCAATGATTAATATATGCT
1 CACCCGAATATTTGACTCAATGATTAATATATGCT
43512 C
1 C
43513 GGTAGTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (35 bp):
CACCCGAATATTTGACTCAATGATTAATATATGCT
Found at i:49699 original size:3 final size:3
Alignment explanation
Indices: 49648--49680 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
49638 TATAAAGATC
*
49648 TTG TTG TTG TTG TTG TTG TTG TTC TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
49681 GCGTTGGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.30, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:53428 original size:7 final size:7
Alignment explanation
Indices: 53418--53446 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
53408 AAAGAGAAGA
53418 GGTTTGG
1 GGTTTGG
53425 GGTTTGG
1 GGTTTGG
53432 GGTTTGG
1 GGTTTGG
53439 GGTTTGG
1 GGTTTGG
53446 G
1 G
53447 CGTGAGAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.59, T:0.41
Consensus pattern (7 bp):
GGTTTGG
Found at i:55628 original size:15 final size:15
Alignment explanation
Indices: 55610--55638 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55600 TATATTTGCA
55610 TTATATATAATATTT
1 TTATATATAATATTT
55625 TTATATATAATATT
1 TTATATATAATATT
55639 AATAATCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATATAATATTT
Found at i:56968 original size:6 final size:6
Alignment explanation
Indices: 56959--56985 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
56949 CAGCTGCTGC
56959 TCTCTT TCTCTT TCTCTT TCTCTT TCT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCT
56986 GTCTGTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TCTCTT
Found at i:57599 original size:17 final size:17
Alignment explanation
Indices: 57574--57614 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
57564 TTTTATTTTA
* *
57574 TAATT-TTTTTTAAGAT
1 TAATTATTTTATAAAAT
57590 TAATTATTTTATAAAAT
1 TAATTATTTTATAAAAT
57607 T-ATTATTT
1 TAATTATTT
57615 CTATCGGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TAATTATTTTATAAAAT
Done.