Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008299.1 Hibiscus syriacus cultivar Beakdansim tig00110985_pilon, 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: 147011
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:1435 original size:353 final size:340
Alignment explanation
Indices: 814--1499 Score: 777
Period size: 353 Copynumber: 2.0 Consensus size: 340
804 TTTAAAAATA
*
814 AATTAATTTAATTTAAAAATAAATTATATAAAAATATTAAATAATATTAGAATAATTTAAATTAT
1 AATTAATTTAATTTAAAAATAAATTATATAAAAATATTAAATAATATTAGAATAATTTAAATAAT
* * *
879 TTATGTTAAGAACATATTAATATATTTAAATATTAATATTATATAGGGCATCTAATTATACCGTG
66 TTATATTAAGAACATACTAATATATTTAAATATTAATATTATATAGGGCATCCAATTATACCGTG
* * ** * * *
944 TGAAACTCTTTTAGTTTATACCATTTTAAGACCAGTAGATGGGAAATTAAAGAGTGAAATTATCG
131 TAAAACTCTTTTAATTTATACCATTTTAAGACCAGTAGATGAAAAATTAAAGACTGAAATTACCA
* *
1009 TGAAAATGAAAAGATATTCACTAAAAACGATTAATCTCAATCTTTGATTTATCTTAATCCAATGG
196 TGAAAATGAAAAGATATTCACTAAAAACGATTAATCTCAACCTTTGATTTATCTCAATCCAATGG
* *
1074 CTCTAAAAATG-TGTAAAAC-AAAAGAGTTTT-C-C-ATAGTAAG-GATCCTAATCCTTATTATA
261 CACTAAAAA-GATGCAAAACTAAAAGAGTTTTACACAATA-TAAGTGATCCTAAT-CTTATTATA
1133 TTTAAAAATTATATAATT
323 TTTAAAAATTATATAATT
* *
1151 AATTAATTTAATTTAAGAAT-AATTATATAAAAATATT-AATAATATTATAATAATTTAAATCAA
1 AATTAATTTAATTTAAAAATAAATTATATAAAAATATTAAATAATATTAGAATAATTTAAAT-AA
*
1214 TTTA-ATTAAGAATATACTAATATAATTTAAATTGTAATTTAAATTTATTATTATATTGGGGGCA
65 TTTATATTAAGAACATACTAATAT-ATTTAAA---T-A-TT-AA--TATTA-TATA----GGGC-
** * * * *
1278 AATCCAATTATAGTGTGTAAAACTC-TTTAATTT-TATCATTTTAGGACCATTTGATGAAAGAAT
115 -ATCCAATTATACCGTGTAAAACTCTTTTAATTTATACCATTTTAAGACCAGTAGATGAAA-AAT
* *
1341 TAAAGACT-AGATTAACCATGGAAAATGAACAGATATTCACTAAAAAACGAATTAATCTCAACCT
178 TAAAGACTGAAATT-ACCAT-GAAAATGAAAAGATATTCACT-AAAAACG-ATTAATCTCAACCT
* *
1405 TTGATTTCTCTCAATCCAATGAG-ACTAAAAAGATGCAAACCTAAAAGAGTTTTACACAATATAA
239 TTGATTTATCTCAATCCAATG-GCACTAAAAAGATGCAAAACTAAAAGAGTTTTACACAATATAA
* *
1469 GTGATCCTAATTTTATTATATTTATAAATTA
303 GTGATCCTAATCTTATTATATTTAAAAATTA
1500 ATTAATTTAA
Statistics
Matches: 290, Mismatches: 30, Indels: 39
0.81 0.08 0.11
Matches are distributed among these distances:
335 38 0.13
336 29 0.10
337 19 0.07
339 1 0.00
340 1 0.00
341 2 0.01
342 2 0.01
344 5 0.02
345 4 0.01
349 28 0.10
350 20 0.07
351 40 0.14
352 8 0.03
353 45 0.16
354 12 0.04
355 1 0.00
356 23 0.08
357 12 0.04
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (340 bp):
AATTAATTTAATTTAAAAATAAATTATATAAAAATATTAAATAATATTAGAATAATTTAAATAAT
TTATATTAAGAACATACTAATATATTTAAATATTAATATTATATAGGGCATCCAATTATACCGTG
TAAAACTCTTTTAATTTATACCATTTTAAGACCAGTAGATGAAAAATTAAAGACTGAAATTACCA
TGAAAATGAAAAGATATTCACTAAAAACGATTAATCTCAACCTTTGATTTATCTCAATCCAATGG
CACTAAAAAGATGCAAAACTAAAAGAGTTTTACACAATATAAGTGATCCTAATCTTATTATATTT
AAAAATTATATAATT
Found at i:5569 original size:15 final size:17
Alignment explanation
Indices: 5545--5581 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
5535 TAATCTGATC
*
5545 CAAATGTAAAAA-AATT
1 CAAATATAAAAATAATT
5561 -AAATATAAAAATAATT
1 CAAATATAAAAATAATT
5577 CAAAT
1 CAAAT
5582 GCATCGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 10 0.56
16 4 0.22
17 4 0.22
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (17 bp):
CAAATATAAAAATAATT
Found at i:7832 original size:26 final size:26
Alignment explanation
Indices: 7802--7852 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
7792 TTAAGAATAA
7802 ATTATCCAAATCAAACAATGATAATC
1 ATTATCCAAATCAAACAATGATAATC
*
7828 ATTATCCAAATGAAACAATGATAAT
1 ATTATCCAAATCAAACAATGATAAT
7853 TTAATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (26 bp):
ATTATCCAAATCAAACAATGATAATC
Found at i:14106 original size:15 final size:15
Alignment explanation
Indices: 14086--14114 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14076 GTTCTTGCTG
14086 AAACTGCTCACTGCA
1 AAACTGCTCACTGCA
14101 AAACTGCTCACTGC
1 AAACTGCTCACTGC
14115 GTCTGTTCTA
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:0.31, C:0.34, G:0.14, T:0.21
Consensus pattern (15 bp):
AAACTGCTCACTGCA
Found at i:15076 original size:14 final size:14
Alignment explanation
Indices: 15057--15085 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15047 CAAATATATA
15057 ATAATTTATAGTTT
1 ATAATTTATAGTTT
15071 ATAATTTATAGTTT
1 ATAATTTATAGTTT
15085 A
1 A
15086 AATATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
ATAATTTATAGTTT
Found at i:15799 original size:4 final size:4
Alignment explanation
Indices: 15790--15815 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
15780 ATATATGCAG
15790 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
15816 GGGATAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:17844 original size:21 final size:20
Alignment explanation
Indices: 17747--17844 Score: 58
Period size: 21 Copynumber: 4.6 Consensus size: 20
17737 CTATATAAAC
*
17747 AATATAATTTAAGAATAAATT
1 AATATAATTTAAGAA-ATATT
*
17768 AATTTAATTTAA-AAATATAT
1 AATATAATTTAAGAAATAT-T
*
17788 AA-ATAATATT-AGAATTATTT
1 AATATAAT-TTAAGAAATA-TT
*
17808 AAATTATTTATGTTAAGAACATATT
1 -AA-TA-TAAT-TTAAGAA-ATATT
17833 AATATAATTTAA
1 AATATAATTTAA
17845 ATCTATAATT
Statistics
Matches: 59, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
19 8 0.14
20 12 0.20
21 18 0.31
22 3 0.05
23 3 0.05
24 7 0.12
25 6 0.10
26 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (20 bp):
AATATAATTTAAGAAATATT
Found at i:17853 original size:13 final size:13
Alignment explanation
Indices: 17835--17859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17825 AACATATTAA
17835 TATAATTTAAATC
1 TATAATTTAAATC
17848 TATAATTTAAAT
1 TATAATTTAAAT
17860 ATTAATGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATTTAAATC
Found at i:21038 original size:13 final size:13
Alignment explanation
Indices: 21020--21045 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21010 TATTATTATT
21020 ATTATATAAATAA
1 ATTATATAAATAA
21033 ATTATATAAATAA
1 ATTATATAAATAA
21046 TTTTATTTAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTATATAAATAA
Found at i:21303 original size:4 final size:4
Alignment explanation
Indices: 21294--21319 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
21284 ATATATGCAG
21294 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
21320 GGGATAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:22190 original size:17 final size:17
Alignment explanation
Indices: 22165--22197 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22155 ACCTAAATTC
22165 TTATGATATTTATAATA
1 TTATGATATTTATAATA
*
22182 TTATTATATTTATAAT
1 TTATGATATTTATAAT
22198 CTATATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATGATATTTATAATA
Found at i:22305 original size:21 final size:22
Alignment explanation
Indices: 22208--22305 Score: 66
Period size: 21 Copynumber: 4.5 Consensus size: 22
22198 CTATATAAAC
*
22208 AATATAATTTAAGAATA-AATT
1 AATATAATTTAAGAATATATTT
*
22229 AATTTAATTTAA-AA-ATATTT
1 AATATAATTTAAGAATATATTT
22249 AA-ATAATATT-AGAATA-ATTT
1 AATATAAT-TTAAGAATATATTT
* *
22269 AAATTATTTATGTTAAGAACATA-TT
1 -AA-TA-TAAT-TTAAGAATATATTT
22294 AATATAATTTAA
1 AATATAATTTAA
22306 ATCTATAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
19 6 0.10
20 15 0.25
21 18 0.30
22 3 0.05
23 3 0.05
24 7 0.12
25 7 0.12
26 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (22 bp):
AATATAATTTAAGAATATATTT
Found at i:22626 original size:19 final size:20
Alignment explanation
Indices: 22598--22640 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
22588 AATTTAAGAA
*
22598 TAAATTATATAAAAAT-ATT
1 TAAATAATATAAAAATAATT
* *
22617 TAAATAATATTATAATAATT
1 TAAATAATATAAAAATAATT
22637 TAAA
1 TAAA
22641 CAATTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATAATATAAAAATAATT
Found at i:22683 original size:13 final size:14
Alignment explanation
Indices: 22665--22693 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
22655 AATATATTAA
22665 TATAATTTAAA-AT
1 TATAATTTAAATAT
22678 TATAATTTAAATAT
1 TATAATTTAAATAT
22692 TA
1 TA
22694 ATATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAATTTAAATAT
Found at i:22932 original size:370 final size:369
Alignment explanation
Indices: 22238--22940 Score: 952
Period size: 370 Copynumber: 1.9 Consensus size: 369
22228 TAATTTAATT
**
22238 TAAAAATATTTAAATAATATTAGAATAATTTAAATTATTTATGTTAAGAACATATTAATATAATT
1 TAAAAATATTTAAATAATATTAGAATAATTTAAACAATTTATGTTAAGAACATATTAATATAATT
* ** *
22303 TAAATCTATAATTTGAATATTAATATTATTATATAGGGCAGGATCTAATTATACTGTGTAAAACT
66 TAAATCTATAATTTAAATATTAATATTATTATATAGGGCAAAATCCAATTATACTGTGTAAAACT
* * ** * ***
22368 CTTTTAGTTTATACCATTTTAAGACCAGTAGATGGGAGAAATTAAAGAGTGAAATTAATTGTGGA
131 CTTTAAGTTTACACCATTTTAAGACCAGTAGATGAAAGAAATTAAAGACTGAAATTAACCATGGA
** *
22433 AAATGAAAAGATATTCACTAAAAATGAATTAATCTCAATCTTTGATTTATCTCAATCCAATGGCT
196 AAATGAAAAGATATTCACTAAAAAACAATTAATCTCAATCTTTGATTTATCTCAATCCAATGGCA
** * * *
22498 CTAAAAATGTGTAAAACTAAAAGAGTTTTACATACTATAAATGGATCCTAATCCTTATTATATTT
261 CTAAAAAACTGCAAAACTAAAAGAGTTTTACACAATATAAATGGATCCTAATCCTTATTATATTT
22563 AAAAATTATATAAATTAATTAATTTAATTTAAGAATAAATTATA
326 AAAAATTATATAAATTAATTAATTTAATTTAAGAATAAATTATA
* *
22607 TAAAAATATTTAAATAATATTATAATAATTTAAACAATTTAAT-TTAAGAATATATTAATATAAT
1 TAAAAATATTTAAATAATATTAGAATAATTTAAACAATTT-ATGTTAAGAACATATTAATATAAT
* *
22671 TTAAAAT-TATAATTTAAATATTAATATTATTATATGGGGGCAAAATCCAATTATAGTGTGTAAA
65 TT-AAATCTATAATTTAAATATTAATATTATTATAT-AGGGCAAAATCCAATTATACTGTGTAAA
* * * * * *
22735 ACTCTTTAATTTTACATCATTTTAGGATCATTGGATGAAAGAAATTAAAGACT-AAGATTAACCA
128 ACTCTTTAAGTTTACACCATTTTAAGACCAGTAGATGAAAGAAATTAAAGACTGAA-ATTAACCA
* *
22799 TGGAAAATGAACAGATATAT-ACTAAAAAACATATTAATCTC-ATCCTTTGATTTCTCTCAATCC
192 TGGAAAATGAAAAGATAT-TCACTAAAAAACA-ATTAATCTCAAT-CTTTGATTTATCTCAATCC
* *
22862 AATGAG-ACTAAAAAACTGCAAACCTAAAAGAGTTTTACACAATATAAGTGGATCCTAATCCTTA
254 AATG-GCACTAAAAAACTGCAAAACTAAAAGAGTTTTACACAATATAAATGGATCCTAATCCTTA
*
22926 -TATATTTATAAATTA
318 TTATATTTAAAAATTA
22941 ATTAATTTAA
Statistics
Matches: 289, Mismatches: 37, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
369 88 0.30
370 118 0.41
371 82 0.28
372 1 0.00
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (369 bp):
TAAAAATATTTAAATAATATTAGAATAATTTAAACAATTTATGTTAAGAACATATTAATATAATT
TAAATCTATAATTTAAATATTAATATTATTATATAGGGCAAAATCCAATTATACTGTGTAAAACT
CTTTAAGTTTACACCATTTTAAGACCAGTAGATGAAAGAAATTAAAGACTGAAATTAACCATGGA
AAATGAAAAGATATTCACTAAAAAACAATTAATCTCAATCTTTGATTTATCTCAATCCAATGGCA
CTAAAAAACTGCAAAACTAAAAGAGTTTTACACAATATAAATGGATCCTAATCCTTATTATATTT
AAAAATTATATAAATTAATTAATTTAATTTAAGAATAAATTATA
Found at i:26416 original size:15 final size:17
Alignment explanation
Indices: 26397--26434 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
26387 CTAAATGATC
26397 CAAATGTAAAAA-AATT
1 CAAATGTAAAAATAATT
*
26413 -AAATATAAAAATAATT
1 CAAATGTAAAAATAATT
26429 CAAATG
1 CAAATG
26435 CATCGCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
15 10 0.56
16 4 0.22
17 4 0.22
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (17 bp):
CAAATGTAAAAATAATT
Found at i:28586 original size:26 final size:26
Alignment explanation
Indices: 28557--28611 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
28547 CACAATTCAC
* * *
28557 ATCATAATTCGAATCAAACAATGATA
1 ATCATAATCCAAATCAAACAATAATA
* *
28583 ATCATTATCCAAATCAAACATTAATA
1 ATCATAATCCAAATCAAACAATAATA
28609 ATC
1 ATC
28612 CGAGTTTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (26 bp):
ATCATAATCCAAATCAAACAATAATA
Found at i:28676 original size:26 final size:26
Alignment explanation
Indices: 28646--28696 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
28636 TTAAGAATAA
28646 ATTATCCAAATCAAACAATGATAATC
1 ATTATCCAAATCAAACAATGATAATC
*
28672 ATTATCCAAATGAAACAATGATAAT
1 ATTATCCAAATCAAACAATGATAAT
28697 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (26 bp):
ATTATCCAAATCAAACAATGATAATC
Found at i:29336 original size:28 final size:27
Alignment explanation
Indices: 29282--29338 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
29272 TAATATTATA
*
29282 ATAATTTAAATTTAAGAATTTATTAAT
1 ATAATTTAAATTTAAGAATTTAATAAT
*
29309 ATAATTTTAAATTT-ATAATTTAAATAAT
1 ATAA-TTTAAATTTAAGAATTT-AATAAT
29337 AT
1 AT
29339 TATATGGGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
ATAATTTAAATTTAAGAATTTAATAAT
Found at i:32041 original size:60 final size:59
Alignment explanation
Indices: 31971--32093 Score: 237
Period size: 60 Copynumber: 2.1 Consensus size: 59
31961 CAATTGTATT
31971 AAAGACTAAACTATCATCGCCAAAACAGAAAATCAAGGGGGAAAGTGTAAGTACTATCAA
1 AAAGACTAAACTATCATCGCCAAAACAGAAAATCAAGGGGG-AAGTGTAAGTACTATCAA
32031 AAAGACTAAACTATCATCGCCAAAACAGAAAATCAAGGGGGAAGTGTAAGTACTATCAA
1 AAAGACTAAACTATCATCGCCAAAACAGAAAATCAAGGGGGAAGTGTAAGTACTATCAA
32090 AAAG
1 AAAG
32094 GAATGAGCAG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 22 0.35
60 41 0.65
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (59 bp):
AAAGACTAAACTATCATCGCCAAAACAGAAAATCAAGGGGGAAGTGTAAGTACTATCAA
Found at i:42198 original size:11 final size:11
Alignment explanation
Indices: 42182--42212 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
42172 AAATTCTTTA
42182 AAATAAAAAAG
1 AAATAAAAAAG
42193 AAAT-AAAAAG
1 AAATAAAAAAG
42203 AAATAAAAAA
1 AAATAAAAAA
42213 TATTCTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (11 bp):
AAATAAAAAAG
Found at i:42699 original size:82 final size:83
Alignment explanation
Indices: 42595--42774 Score: 283
Period size: 82 Copynumber: 2.2 Consensus size: 83
42585 AATAATATTT
* * * * *
42595 TTTA-AATGATTAAATCTGAGAGTTTTACTCTAACAAAAACTCTTTTAATATCTAAATTTAAACA
1 TTTATAAT-ATTAAACCTAAGAGTTTTACTCCAACAAAAACTCTTTTAATATATAAATTTAAAAA
42659 AATTATAATAT-TTTTAAA
65 AATTATAATATCTTTTAAA
*
42677 TTTATAATATTAAACCTAAGAGTTTTACTCCAACCAAAACTCTTTTAATATATAAATTTAAAAAA
1 TTTATAATATTAAACCTAAGAGTTTTACTCCAACAAAAACTCTTTTAATATATAAATTTAAAAAA
42742 ATTATAATATCTTTTAAA
66 ATTATAATATCTTTTAAA
42760 TTTATAATATTAAAC
1 TTTATAATATTAAAC
42775 ACATATTTCC
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
82 65 0.72
83 25 0.28
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (83 bp):
TTTATAATATTAAACCTAAGAGTTTTACTCCAACAAAAACTCTTTTAATATATAAATTTAAAAAA
ATTATAATATCTTTTAAA
Found at i:44631 original size:26 final size:25
Alignment explanation
Indices: 44567--44631 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
44557 AAAAAGCATA
* *
44567 AAATCAAA-ATTCATATCATAGTCC
1 AAATCAAACATTAATATCATAATCC
* * *
44591 ATATCAACCAATAATAATCATAATCC
1 AAATCAAACATTAAT-ATCATAATCC
44617 AAATCAAACATTAAT
1 AAATCAAACATTAAT
44632 CAGTCCTAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
24 6 0.19
25 4 0.13
26 21 0.68
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.28
Consensus pattern (25 bp):
AAATCAAACATTAATATCATAATCC
Found at i:46071 original size:26 final size:26
Alignment explanation
Indices: 46037--46089 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
46027 TTTAAGAATA
46037 TATTATCCAAATCAAAAAATGATAAT
1 TATTATCCAAATCAAAAAATGATAAT
*
46063 TATTATCCAAATCAAACAATGATAAT
1 TATTATCCAAATCAAAAAATGATAAT
46089 T
1 T
46090 TAAATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (26 bp):
TATTATCCAAATCAAAAAATGATAAT
Found at i:46202 original size:30 final size:28
Alignment explanation
Indices: 46166--46228 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 28
46156 ATTTATAATT
**
46166 TAAATATTATTATTATATTAATAAATTATA
1 TAAATATTATTATT-TAAGAATAAATTA-A
*
46196 TAAATATTTTTATTTAAGAATAAATTAA
1 TAAATATTATTATTTAAGAATAAATTAA
46224 TAAAT
1 TAAAT
46229 CAGAGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 6 0.20
29 11 0.37
30 13 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TAAATATTATTATTTAAGAATAAATTAA
Found at i:48298 original size:14 final size:14
Alignment explanation
Indices: 48279--48306 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48269 CAAATATATA
48279 ATAATTTATAGTTT
1 ATAATTTATAGTTT
48293 ATAATTTATAGTTT
1 ATAATTTATAGTTT
48307 CAATATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
ATAATTTATAGTTT
Found at i:50944 original size:17 final size:18
Alignment explanation
Indices: 50914--50950 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
50904 ATTATACCTA
50914 AATTCTTATGATATTTAT
1 AATTCTTATGATATTTAT
*
50932 AATT-TTATTATATTTAT
1 AATTCTTATGATATTTAT
50949 AA
1 AA
50951 ACTATATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
AATTCTTATGATATTTAT
Found at i:51001 original size:16 final size:16
Alignment explanation
Indices: 50982--51023 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
50972 AAGAATAAAT
*
50982 TAATTTAATTTAAAAA
1 TAATTTAATATAAAAA
50998 TAATTT-ATATAAAAA
1 TAATTTAATATAAAAA
51013 T-ATTTAA-ATAA
1 TAATTTAATATAA
51024 TATTAGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.33
15 10 0.42
16 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATTTAATATAAAAA
Found at i:51017 original size:14 final size:15
Alignment explanation
Indices: 50982--51023 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
50972 AAGAATAAAT
*
50982 TAATTTAATTTAAAAA
1 TAATTTAA-ATAAAAA
*
50998 TAATTTATATAAAAA
1 TAATTTAAATAAAAA
51013 T-ATTTAAATAA
1 TAATTTAAATAA
51024 TATTAGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 9 0.39
15 7 0.30
16 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATTTAAATAAAAA
Found at i:51083 original size:13 final size:13
Alignment explanation
Indices: 51065--51089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51055 AACATATTAA
51065 TATAATTTAAATC
1 TATAATTTAAATC
51078 TATAATTTAAAT
1 TATAATTTAAAT
51090 ATCAATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATTTAAATC
Found at i:51437 original size:13 final size:14
Alignment explanation
Indices: 51421--51449 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
51411 AATATATTAA
51421 TATAATTTAAA-AT
1 TATAATTTAAATAT
51434 TATAATTTAAATAT
1 TATAATTTAAATAT
51448 TA
1 TA
51450 ATATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAATTTAAATAT
Found at i:51438 original size:26 final size:25
Alignment explanation
Indices: 51380--51439 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 25
51370 ATATAAAAAT
51380 ATTATAATAATTTAAATCAATTTAA
1 ATTATAATAATTTAAATCAATTTAA
*
51405 TTTAATAAT-ATATTAATAT-AATTTAAA
1 ATT-ATAATAAT-TTAA-ATCAATTT-AA
51432 ATTATAAT
1 ATTATAAT
51440 TTAAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
25 4 0.14
26 19 0.66
27 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATAATAATTTAAATCAATTTAA
Found at i:54273 original size:19 final size:20
Alignment explanation
Indices: 54245--54288 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
54235 AATTTAAAAA
*
54245 TAAATTATATAAAAAT-ATT
1 TAAATAATATAAAAATAATT
* *
54264 TAAATAATATTAGAATAATT
1 TAAATAATATAAAAATAATT
54284 TAAAT
1 TAAAT
54289 TATTTATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAATAATATAAAAATAATT
Found at i:54636 original size:11 final size:11
Alignment explanation
Indices: 54609--54639 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
54599 GAATAAATTA
*
54609 TATAAAAATAT
1 TATAATAATAT
54620 TATAATAATAT
1 TATAATAATAT
54631 TATAATAAT
1 TATAATAAT
54640 TTAAATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATAATAATAT
Found at i:54924 original size:372 final size:357
Alignment explanation
Indices: 54221--54946 Score: 904
Period size: 372 Copynumber: 2.0 Consensus size: 357
54211 TATAATTTAA
54221 AAATAAATTAATTTAATTTAAAAATAAATTATATAAAAATATTTAAATAATATTAGAATAATTTA
1 AAATAAATTAATTTAATTTAAAAATAAATTATATAAAAATATTTAAATAATATTAGAATAATTTA
* **
54286 AATTATTTATGTTAAGAACATATTAATATAATTTAAATATTAATATTATTATATAGGGCATGATC
66 AATAATTTATGTTAAGAACATATTAATATAATTTAAATATTAATATTATTATATAGGGCAAAATC
* * * **
54351 TAATTATACCGTGTGAAACTCTTTTAGTTTATACCATTTTAAGACCAGTAGATGGGAGAAATTAA
131 CAATTATACCGTGTAAAACTCTTTAAGTTTATACCATTTTAAGACCAGTAGATGAAAGAAATTAA
* * * *
54416 AGAGTGAAATTAATCGTGAAAAATGAAAAGATATTCACTAAAAAACGAATTAATCTCAATCTTTG
196 AGACTGAAATTAACCATGAAAAATGAAAAGATATTCACTAAAAAACGAATTAATCTCAACCTTTG
* * * * *
54481 ATTTATCTTAATCCAATGGCTCTAAAAATGTGTAAAACTAAAAGAGTTTTACATAGTATAAATGG
261 ATTTATCTCAATCCAATGGCACTAAAAATGTGCAAAACTAAAAGAGTTTTACACAATATAAATGG
54546 ATCCTAATCCTTATTATATTTAAAAATTATAT
326 ATCCTAATCCTTATTATATTTAAAAATTATAT
* * *
54578 AAATTAATTAATTTAATTTAAGAATAAATTATATAAAAATA-TTATAATAATATTATAATAATTT
1 AAATAAATTAATTTAATTTAAAAATAAATTATATAAAAATATTTA-AATAATATTAGAATAATTT
*
54642 AAATCAATTTAAT-TTAAGAATATACTAATATAATTTAAAATTGTAATTTAAATATTAATATTAT
65 AAAT-AATTT-ATGTTAAG---A-AC----AT-A-TT--AA-TATAATTTAAATATTAATATTAT
* ** * * * *
54706 TATATGGGGGCAAAATCCAATTATAGTGTGTAAAACTCTTTAATTTTATATCATTTTAGGACCAT
115 TATAT-AGGGCAAAATCCAATTATACCGTGTAAAACTCTTTAAGTTTATACCATTTTAAGACCAG
* * *
54771 TTGATGAAAGAAATTAAAGACT-AAGATTAACCATGGAAAATGAACAGATATTCACTAAAAAACG
179 TAGATGAAAGAAATTAAAGACTGAA-ATTAACCATGAAAAATGAAAAGATATTCACTAAAAAACG
* *
54835 AATTAATCTCAACCTTTGATTTCTCTCAATCCAATGAG-ACTAAAAA-GATGCAAACCTAAAAGA
243 AATTAATCTCAACCTTTGATTTATCTCAATCCAATG-GCACTAAAAATG-TGCAAAACTAAAAGA
* ** *
54898 GTTTTACACAATATAAGTGGATCCTAATTTTTATTATATTTATAAATTA
306 GTTTTACACAATATAAATGGATCCTAATCCTTATTATATTTAAAAATTA
54947 ATTAATTTAA
Statistics
Matches: 312, Mismatches: 37, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
356 3 0.01
357 61 0.20
358 9 0.03
359 2 0.01
361 1 0.00
362 2 0.01
366 2 0.01
367 1 0.00
368 2 0.01
370 2 0.01
371 30 0.10
372 196 0.63
373 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (357 bp):
AAATAAATTAATTTAATTTAAAAATAAATTATATAAAAATATTTAAATAATATTAGAATAATTTA
AATAATTTATGTTAAGAACATATTAATATAATTTAAATATTAATATTATTATATAGGGCAAAATC
CAATTATACCGTGTAAAACTCTTTAAGTTTATACCATTTTAAGACCAGTAGATGAAAGAAATTAA
AGACTGAAATTAACCATGAAAAATGAAAAGATATTCACTAAAAAACGAATTAATCTCAACCTTTG
ATTTATCTCAATCCAATGGCACTAAAAATGTGCAAAACTAAAAGAGTTTTACACAATATAAATGG
ATCCTAATCCTTATTATATTTAAAAATTATAT
Found at i:54955 original size:25 final size:26
Alignment explanation
Indices: 54927--54997 Score: 60
Period size: 25 Copynumber: 2.8 Consensus size: 26
54917 GATCCTAATT
54927 TTTATTATATTTATAAATTAA-TTAA
1 TTTATTATATTTATAAATTAATTTAA
**
54952 TTTAAATTA-A-GAATAAATTAATTTAA
1 TTT--ATTATATTTATAAATTAATTTAA
* *
54978 TTTATAATATTT-TAATTTAA
1 TTTATTATATTTATAAATTAA
54998 ATAAATAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
24 3 0.09
25 20 0.57
26 8 0.23
27 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
TTTATTATATTTATAAATTAATTTAA
Found at i:54971 original size:21 final size:21
Alignment explanation
Indices: 54946--54999 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
54936 TTTATAAATT
54946 AATTAATTTAAATTAAGAATA
1 AATTAATTTAAATTAAGAATA
* *
54967 AATTAATTT-AATTTATAATA
1 AATTAATTTAAATTAAGAATA
**
54987 TTTTAATTTAAAT
1 AATTAATTTAAAT
55000 AAATAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AATTAATTTAAATTAAGAATA
Found at i:54986 original size:20 final size:20
Alignment explanation
Indices: 54935--54997 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
54925 TTTTTATTAT
*
54935 ATTTATAAATTAATTAATTTAA
1 ATTTAT-AATAAATTAATTT-A
* *
54957 ATTAAGAATAAATTAATTTA
1 ATTTATAATAAATTAATTTA
**
54977 ATTTATAATATTTTAATTTA
1 ATTTATAATAAATTAATTTA
54997 A
1 A
54998 ATAAATAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 18 0.53
21 12 0.35
22 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTATAATAAATTAATTTA
Found at i:55007 original size:21 final size:21
Alignment explanation
Indices: 54948--55009 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
54938 TATAAATTAA
* **
54948 TTAATTTAAATTAAGAATAAA
1 TTAATTTAAATTAATAATATT
*
54969 TTAATTT-AATTTATAATATT
1 TTAATTTAAATTAATAATATT
*
54989 TTAATTTAAATAAATAATATT
1 TTAATTTAAATTAATAATATT
55010 ATAGTAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAATTTAAATTAATAATATT
Found at i:59043 original size:15 final size:17
Alignment explanation
Indices: 59019--59055 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
59009 TAATCTGATC
*
59019 CAAATGTAAAAA-AATT
1 CAAATATAAAAATAATT
59035 -AAATATAAAAATAATT
1 CAAATATAAAAATAATT
59051 CAAAT
1 CAAAT
59056 GCATCGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 10 0.56
16 4 0.22
17 4 0.22
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (17 bp):
CAAATATAAAAATAATT
Found at i:61310 original size:26 final size:26
Alignment explanation
Indices: 61280--61330 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
61270 TTAAGAATAA
61280 ATTATCCAAATCAAACAATGATAATC
1 ATTATCCAAATCAAACAATGATAATC
*
61306 ATTATCCAAATGAAACAATGATAAT
1 ATTATCCAAATCAAACAATGATAAT
61331 TTAATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (26 bp):
ATTATCCAAATCAAACAATGATAATC
Found at i:67591 original size:15 final size:15
Alignment explanation
Indices: 67571--67599 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
67561 GTTCTTGCTG
67571 AAACTGCTCACTGCA
1 AAACTGCTCACTGCA
67586 AAACTGCTCACTGC
1 AAACTGCTCACTGC
67600 GTCTGTTCTA
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:0.31, C:0.34, G:0.14, T:0.21
Consensus pattern (15 bp):
AAACTGCTCACTGCA
Found at i:68561 original size:14 final size:14
Alignment explanation
Indices: 68542--68570 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
68532 CAAATATATA
68542 ATAATTTATAGTTT
1 ATAATTTATAGTTT
68556 ATAATTTATAGTTT
1 ATAATTTATAGTTT
68570 A
1 A
68571 AATATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
ATAATTTATAGTTT
Found at i:69284 original size:4 final size:4
Alignment explanation
Indices: 69275--69300 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
69265 ATATATGCAG
69275 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
69301 GGGATAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:71333 original size:21 final size:20
Alignment explanation
Indices: 71236--71333 Score: 58
Period size: 21 Copynumber: 4.6 Consensus size: 20
71226 CTATATAAAC
*
71236 AATATAATTTAAGAATAAATT
1 AATATAATTTAAGAA-ATATT
*
71257 AATTTAATTTAA-AAATATAT
1 AATATAATTTAAGAAATAT-T
*
71277 AA-ATAATATT-AGAATTATTT
1 AATATAAT-TTAAGAAATA-TT
*
71297 AAATTATTTATGTTAAGAACATATT
1 -AA-TA-TAAT-TTAAGAA-ATATT
71322 AATATAATTTAA
1 AATATAATTTAA
71334 ATCTATAATT
Statistics
Matches: 59, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
19 8 0.14
20 12 0.20
21 18 0.31
22 3 0.05
23 3 0.05
24 7 0.12
25 6 0.10
26 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (20 bp):
AATATAATTTAAGAAATATT
Found at i:71342 original size:13 final size:13
Alignment explanation
Indices: 71324--71348 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71314 AACATATTAA
71324 TATAATTTAAATC
1 TATAATTTAAATC
71337 TATAATTTAAAT
1 TATAATTTAAAT
71349 ATTAATGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATTTAAATC
Found at i:74527 original size:13 final size:13
Alignment explanation
Indices: 74509--74534 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
74499 TATTATTATT
74509 ATTATATAAATAA
1 ATTATATAAATAA
74522 ATTATATAAATAA
1 ATTATATAAATAA
74535 TTTTATTTAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTATATAAATAA
Found at i:74792 original size:4 final size:4
Alignment explanation
Indices: 74783--74808 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
74773 ATATATGCAG
74783 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
74809 GGGATAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:75677 original size:17 final size:17
Alignment explanation
Indices: 75652--75684 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
75642 ACCTAAATTC
75652 TTATGATATTTATAATA
1 TTATGATATTTATAATA
*
75669 TTATTATATTTATAAT
1 TTATGATATTTATAAT
75685 CTATATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATGATATTTATAATA
Found at i:75712 original size:11 final size:10
Alignment explanation
Indices: 75698--75758 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
75688 TATAAACAAT
75698 ATAATTTAAGA
1 ATAATTTAA-A
* *
75709 ATAAATTAAT
1 ATAATTTAAA
*
75719 TTAATTTAAA
1 ATAATTTAAA
*
75729 AAAATTT-AA
1 ATAATTTAAA
*
75738 ATAATATTAGA
1 ATAAT-TTAAA
75749 ATAATTTAAA
1 ATAATTTAAA
75759 TTATTTATGT
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
9 6 0.16
10 18 0.47
11 14 0.37
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
ATAATTTAAA
Found at i:76114 original size:19 final size:20
Alignment explanation
Indices: 76086--76128 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
76076 AATTTAAGAA
*
76086 TAAATTATATAAAAAT-ATT
1 TAAATAATATAAAAATAATT
* *
76105 TAAATAATATTATAATAATT
1 TAAATAATATAAAAATAATT
76125 TAAA
1 TAAA
76129 CAATTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATAATATAAAAATAATT
Found at i:76171 original size:13 final size:14
Alignment explanation
Indices: 76153--76181 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
76143 AATATATTAA
76153 TATAATTTAAA-AT
1 TATAATTTAAATAT
76166 TATAATTTAAATAT
1 TATAATTTAAATAT
76180 TA
1 TA
76182 ATATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAATTTAAATAT
Found at i:76352 original size:371 final size:369
Alignment explanation
Indices: 75725--76428 Score: 945
Period size: 371 Copynumber: 1.9 Consensus size: 369
75715 TAATTTAATT
**
75725 TAAAAAAATTTAAATAATATTAGAATAATTTAAATTATTTATGTTAAGAACATATTAATATAATT
1 TAAAAAAATTTAAATAATATTAGAATAATTTAAACAATTTATGTTAAGAACATATTAATATAATT
* ** *
75790 TAAATCTATAATTTGAATATTAATATTATTATATAGGGCAGGATCTAATTATACTGTGTAAAACT
66 TAAATCTATAATTTAAATATTAATATTATTATATAGGGCAAAATCCAATTATACTGTGTAAAACT
* * ** * ***
75855 CTTTTAGTTTATACCATTTTAAGACCAGTAGATGGGAGAAATTAAAGAGTGAAATTAATTGTGGA
131 CTTTAAGTTTACACCATTTTAAGACCAGTAGATGAAAGAAATTAAAGACTGAAATTAACCATGGA
*
75920 AAATGAAAAGATATTCACTAAAAAATGAATTAATCTCAATCTTTGATTTATCTCAATCCAATG-G
196 AAATGAAAAGATATTCACTAAAAAATCAATTAATCTCAATCTTTGATTTATCTCAATCCAATGAG
* ** * * *
75984 CTCTAAAAATGTGTAAAACTAAAAGAGTTTTACATACTATAAATGGATCCTAATCCTTATTATAT
261 -ACTAAAAAACTGCAAAACTAAAAGAGTTTTACACAATATAAATGGATCCTAATCCTTA-TATAT
76049 TTAAAAATTATATAAATTAATTAATTTAATTTAAGAATAAATTATA
324 TTAAAAATTATATAAATTAATTAATTTAATTTAAGAATAAATTATA
* * *
76095 TAAAAATATTTAAATAATATTATAATAATTTAAACAATTTAAT-TTAAGAATATATTAATATAAT
1 TAAAAAAATTTAAATAATATTAGAATAATTTAAACAATTT-ATGTTAAGAACATATTAATATAAT
* *
76159 TTAAAAT-TATAATTTAAATATTAATATTATTATATGGGGGCAAAATCCAATTATAGTGTGTAAA
65 TT-AAATCTATAATTTAAATATTAATATTATTATAT-AGGGCAAAATCCAATTATACTGTGTAAA
* * * * * *
76223 ACTCTTTAATTTTACATCATTTTAGGATCATTGGATGAAAGAAATTAAAGACT-AAGATTAACCA
128 ACTCTTTAAGTTTACACCATTTTAAGACCAGTAGATGAAAGAAATTAAAGACTGAA-ATTAACCA
* *
76287 TGGAAAATGAACAGATATAT-ACTAAAAAA-CATATTAATCTC-ATCCTTTGATTTCTCTCAATC
192 TGGAAAATGAAAAGATAT-TCACTAAAAAATCA-ATTAATCTCAAT-CTTTGATTTATCTCAATC
* *
76349 CAATGAGACTAAAAAACTGCAAACCTAAAAGAGTTTTACACAATATAAGTGGATCCTAATCCTTA
254 CAATGAGACTAAAAAACTGCAAAACTAAAAGAGTTTTACACAATATAAATGGATCCTAATCCTTA
*
76414 TATATTTATAAATTA
319 TATATTTAAAAATTA
76429 ATTAATTTAA
Statistics
Matches: 289, Mismatches: 37, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
370 104 0.36
371 183 0.63
372 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (369 bp):
TAAAAAAATTTAAATAATATTAGAATAATTTAAACAATTTATGTTAAGAACATATTAATATAATT
TAAATCTATAATTTAAATATTAATATTATTATATAGGGCAAAATCCAATTATACTGTGTAAAACT
CTTTAAGTTTACACCATTTTAAGACCAGTAGATGAAAGAAATTAAAGACTGAAATTAACCATGGA
AAATGAAAAGATATTCACTAAAAAATCAATTAATCTCAATCTTTGATTTATCTCAATCCAATGAG
ACTAAAAAACTGCAAAACTAAAAGAGTTTTACACAATATAAATGGATCCTAATCCTTATATATTT
AAAAATTATATAAATTAATTAATTTAATTTAAGAATAAATTATA
Found at i:79905 original size:15 final size:17
Alignment explanation
Indices: 79886--79923 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
79876 CTAAATGATC
79886 CAAATGTAAAAA-AATT
1 CAAATGTAAAAATAATT
*
79902 -AAATATAAAAATAATT
1 CAAATGTAAAAATAATT
79918 CAAATG
1 CAAATG
79924 CATCGCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
15 10 0.56
16 4 0.22
17 4 0.22
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (17 bp):
CAAATGTAAAAATAATT
Found at i:82076 original size:26 final size:26
Alignment explanation
Indices: 82047--82101 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
82037 CACAATTCAC
* * *
82047 ATCATAATTCGAATCAAACAATGATA
1 ATCATAATCCAAATCAAACAATAATA
* *
82073 ATCATTATCCAAATCAAACATTAATA
1 ATCATAATCCAAATCAAACAATAATA
82099 ATC
1 ATC
82102 CGAGTTTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (26 bp):
ATCATAATCCAAATCAAACAATAATA
Found at i:82166 original size:26 final size:26
Alignment explanation
Indices: 82136--82186 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
82126 TTAAGAATAA
82136 ATTATCCAAATCAAACAATGATAATC
1 ATTATCCAAATCAAACAATGATAATC
*
82162 ATTATCCAAATGAAACAATGATAAT
1 ATTATCCAAATCAAACAATGATAAT
82187 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (26 bp):
ATTATCCAAATCAAACAATGATAATC
Found at i:82824 original size:28 final size:27
Alignment explanation
Indices: 82770--82826 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
82760 TAATATTATA
*
82770 ATAATTTAAATTTAAGAATTTATTAAT
1 ATAATTTAAATTTAAGAATTTAATAAT
*
82797 ATAATTTTAAATTT-ATAATTTAAATAAT
1 ATAA-TTTAAATTTAAGAATTT-AATAAT
82825 AT
1 AT
82827 TATTATATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
ATAATTTAAATTTAAGAATTTAATAAT
Found at i:85532 original size:60 final size:60
Alignment explanation
Indices: 85462--85585 Score: 248
Period size: 60 Copynumber: 2.1 Consensus size: 60
85452 CAATTGTATT
85462 AAAGACTAAACTATCATCGCCAAAACAGAAAATCAAGGGGGAAAGTGTAAGTACTATCAA
1 AAAGACTAAACTATCATCGCCAAAACAGAAAATCAAGGGGGAAAGTGTAAGTACTATCAA
85522 AAAGACTAAACTATCATCGCCAAAACAGAAAATCAAGGGGGAAAGTGTAAGTACTATCAA
1 AAAGACTAAACTATCATCGCCAAAACAGAAAATCAAGGGGGAAAGTGTAAGTACTATCAA
85582 AAAG
1 AAAG
85586 GAATGAGCAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (60 bp):
AAAGACTAAACTATCATCGCCAAAACAGAAAATCAAGGGGGAAAGTGTAAGTACTATCAA
Found at i:102957 original size:23 final size:23
Alignment explanation
Indices: 102930--102975 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
102920 AAATAAACGA
102930 AAATAATAAATAAATATATAAAT
1 AAATAATAAATAAATATATAAAT
* * *
102953 AAATAATATATATATGTATAAAT
1 AAATAATAAATAAATATATAAAT
102976 GAGTAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATAATAAATAAATATATAAAT
Found at i:102975 original size:19 final size:16
Alignment explanation
Indices: 102934--102966 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
102924 AAACGAAAAT
102934 AATAAATAAATATATA
1 AATAAATAAATATATA
102950 AATAAATAATATATATA
1 AATAAATAA-ATATATA
102967 TGTATAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAATAAATATATA
Found at i:103057 original size:12 final size:12
Alignment explanation
Indices: 103032--103073 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
103022 TATATAAAAA
* *
103032 ATAAAGATAAAT
1 ATAAATATATAT
103044 ATAAATATATAT
1 ATAAATATATAT
*
103056 ATATATATATAT
1 ATAAATATATAT
103068 A-AAATA
1 ATAAATA
103074 ATTTGTAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (12 bp):
ATAAATATATAT
Found at i:103122 original size:16 final size:16
Alignment explanation
Indices: 103101--103133 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
103091 AAGAGTCATA
103101 AAATAAGAATAA-AAAT
1 AAATAA-AATAAGAAAT
103117 AAATAAAATAAGAAAT
1 AAATAAAATAAGAAAT
103133 A
1 A
103134 TATATATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (16 bp):
AAATAAAATAAGAAAT
Found at i:104593 original size:21 final size:20
Alignment explanation
Indices: 104560--104603 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
104550 AAATTACGCA
*
104560 TTTAGTTTATAAACTATCAAT
1 TTTAGTTCATAAACT-TCAAT
* *
104581 TTTAGTTCCTAAACTTTAAT
1 TTTAGTTCATAAACTTCAAT
104601 TTT
1 TTT
104604 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTAGTTCATAAACTTCAAT
Found at i:105335 original size:31 final size:30
Alignment explanation
Indices: 105261--105335 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
105251 ACTAAAGTTT
*
105261 AATTTTTTTAATTTAATTACTTAACTTTCA
1 AATTTTTTTAATTTAATCACTTAACTTTCA
* ** *
105291 AATTACTCCTAATTTAATCACTCTGACTTTCA
1 AATT-TTTTTAATTTAATCACT-TAACTTTCA
*
105323 ACTTTTTTTAATT
1 AATTTTTTTAATT
105336 ACATATTAAC
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
30 4 0.12
31 19 0.56
32 11 0.32
ACGTcount: A:0.31, C:0.16, G:0.01, T:0.52
Consensus pattern (30 bp):
AATTTTTTTAATTTAATCACTTAACTTTCA
Found at i:108540 original size:16 final size:17
Alignment explanation
Indices: 108516--108548 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
108506 ATTAGTATTT
*
108516 TTCATTTAAAT-TTAAA
1 TTCAATTAAATCTTAAA
108532 TTCAATTAAATCTTAAA
1 TTCAATTAAATCTTAAA
108549 AATTGATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
TTCAATTAAATCTTAAA
Found at i:120086 original size:22 final size:22
Alignment explanation
Indices: 120058--120111 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
120048 GGTATGTTAG
120058 GTTCGTTTATGTTCACGAACAA
1 GTTCGTTTATGTTCACGAACAA
120080 GTTCGTTTATGTTCACGAACAA
1 GTTCGTTTATGTTCACGAACAA
120102 GTTCGTTTAT
1 GTTCGTTTAT
120112 TGACTTGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (22 bp):
GTTCGTTTATGTTCACGAACAA
Found at i:121079 original size:9 final size:8
Alignment explanation
Indices: 121054--121078 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
121044 TTGGTTTCCC
121054 TATTTTTT
1 TATTTTTT
121062 TATTTTTT
1 TATTTTTT
121070 TATTTTTT
1 TATTTTTT
121078 T
1 T
121079 TTCTACGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TATTTTTT
Found at i:121762 original size:21 final size:21
Alignment explanation
Indices: 121738--121777 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
121728 ATTGTGGACT
*
121738 GTCACATCAGTACCGTGAATC
1 GTCACATCAGTAACGTGAATC
*
121759 GTCACGTCAGTAACGTGAA
1 GTCACATCAGTAACGTGAA
121778 CTACTACATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (21 bp):
GTCACATCAGTAACGTGAATC
Found at i:124656 original size:21 final size:20
Alignment explanation
Indices: 124570--124726 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
124560 AAATGACCAA
**
124570 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
124589 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
124609 CATAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
124629 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
124650 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
124671 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
124691 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
124712 GAAAATCGCAACGCG
1 CAAAATCGCAACGCG
124727 TATGGGTAAA
Statistics
Matches: 103, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 47 0.46
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:124737 original size:20 final size:20
Alignment explanation
Indices: 124694--124827 Score: 144
Period size: 20 Copynumber: 6.7 Consensus size: 20
124684 CGATTTTCCA
* ** *
124694 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
**
124714 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
124734 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
124754 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
124774 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
124794 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
124815 AAATCGCAACGCG
1 AAATCGCAACGCG
124828 ATATTTAAAG
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.01
20 78 0.82
21 15 0.16
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:125227 original size:33 final size:33
Alignment explanation
Indices: 125188--125258 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
125178 TTCACTTAGA
*
125188 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
125221 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
125254 TTTCA
1 TTTCA
125259 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:125364 original size:21 final size:21
Alignment explanation
Indices: 125338--125434 Score: 151
Period size: 21 Copynumber: 4.7 Consensus size: 21
125328 TGCAGAAGAG
*
125338 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
125359 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
125379 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
125400 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
125421 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
125435 TCGCAACGCG
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.25
21 51 0.75
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.11
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:125395 original size:41 final size:42
Alignment explanation
Indices: 125336--125434 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 42
125326 TTTGCAGAAG
* *
125336 AGTCGCAACGAGATAAATGAAAATCGCAACGAGAG-AATGAC
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAATGAA
*
125377 TGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAATGAA
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAATGAA
*
125419 AATCGCAACGAGAGAA
1 AGTCGCAACGAGAGAA
125435 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
41 33 0.63
42 19 0.37
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.11
Consensus pattern (42 bp):
AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAATGAA
Found at i:125438 original size:14 final size:14
Alignment explanation
Indices: 125419--125475 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
125409 GAGAAATGAA
125419 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
125433 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
125452 AATCGCAACGAGAG
1 AATCGCAACGAGAG
125466 AATCGCAACG
1 AATCGCAACG
125476 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:125453 original size:33 final size:33
Alignment explanation
Indices: 125411--125491 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
125401 CGCAACGAGA
125411 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
125444 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
125477 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
125492 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:125509 original size:19 final size:19
Alignment explanation
Indices: 125487--125584 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
125477 GAAACCAAAA
*
125487 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
125506 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
125520 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
125539 TTGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
125553 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
125572 TCGCGTTGCGATT
1 TCGCGTTGCGATT
125585 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
16 5 0.08
17 6 0.10
19 31 0.51
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:125528 original size:14 final size:14
Alignment explanation
Indices: 125509--125598 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
125499 TTTCATTTCG
125509 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
125523 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TTC--TCT
125541 GCGTTGCGATTCTCT
1 -CGTTGCGATTCTCT
*
125556 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
125575 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
125589 CGTTGCGATT
1 CGTTGCGATT
125599 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 3 0.05
16 5 0.08
17 5 0.08
18 3 0.05
19 18 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:125534 original size:33 final size:33
Alignment explanation
Indices: 125492--125606 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
125482 CAAAATCGCA
125492 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
125525 TTGCGATTTTCATTTTGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
125558 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
125591 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
125607 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:127455 original size:93 final size:93
Alignment explanation
Indices: 127296--127948 Score: 1276
Period size: 93 Copynumber: 7.1 Consensus size: 93
127286 TAGATTGCTT
*
127296 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127361 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
127389 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127454 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
127481 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127546 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
127574 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127639 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
127666 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127731 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
127759 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127824 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
127852 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127917 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
127944 AGTAA
1 AGTAA
127949 TGCAATCCAT
Statistics
Matches: 557, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
92 190 0.34
93 367 0.66
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:127526 original size:185 final size:186
Alignment explanation
Indices: 127296--127948 Score: 1276
Period size: 185 Copynumber: 3.5 Consensus size: 186
127286 TAGATTGCTT
*
127296 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127361 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
127426 GTGTATTCTTTAACACTGTGAAATAGTA-TTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
127481 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127546 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
127611 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG-TTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
127666 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127731 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
127796 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
127852 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127917 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
127949 TGCAATCCAT
Statistics
Matches: 465, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
185 348 0.75
186 117 0.25
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:127793 original size:278 final size:278
Alignment explanation
Indices: 127296--127948 Score: 1274
Period size: 278 Copynumber: 2.4 Consensus size: 278
127286 TAGATTGCTT
*
127296 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127361 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
127426 GTGTATTCTTTAACACTGTGAAATAGTATTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATAGTATTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
127491 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
127556 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
127574 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127639 TTTGTCTTTG-TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
127703 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
131 GTGTATTCTTTAACACTGTGAAATAGTA-TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
127768 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
195 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
127833 GTTTTGTCTTTTGGTTGAA
260 GTTTTGTCTTTTGGTTGAA
127852 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
127917 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
127949 TGCAATCCAT
Statistics
Matches: 372, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
277 82 0.22
278 275 0.74
279 15 0.04
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (278 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
TTTTGTCTTTTGGTTGAA
Found at i:128036 original size:19 final size:19
Alignment explanation
Indices: 127996--128124 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
127986 TAGTTTACTT
* *
127996 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
128016 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
128035 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
128054 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
128068 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
128087 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
128101 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
128120 TCGCA
1 TCGCA
128125 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:128075 original size:33 final size:32
Alignment explanation
Indices: 128032--128124 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
128022 CGCGAAACCA
**
128032 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
128064 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
128097 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
128125 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:128122 original size:52 final size:52
Alignment explanation
Indices: 127996--128124 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
127986 TAGTTTACTT
**
127996 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
128048 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
128101 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
128125 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:128142 original size:19 final size:19
Alignment explanation
Indices: 128120--128254 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
128110 GAAACCAAAA
*
128120 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
128139 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
*
128155 T--CGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
* *
128172 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
128188 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
128205 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
128224 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
128244 TCGTGTTGCGA
1 TCGCGTTGCGA
128255 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 10 0.11
17 10 0.11
19 46 0.49
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:128161 original size:14 final size:14
Alignment explanation
Indices: 128142--128198 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
128132 TTTCATTTCG
128142 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
128156 CGTTGCGATTTTTATTT
1 CGTTGCGA---TTCTTT
*
128173 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
128189 CGTTGCGATT
1 CGTTGCGATT
128199 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 7 0.20
19 6 0.17
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:128167 original size:33 final size:33
Alignment explanation
Indices: 128125--128217 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
128115 CAAAATCGCA
*
128125 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
* *
128158 TTGCGATTTTTATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
128191 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
128218 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:130199 original size:14 final size:14
Alignment explanation
Indices: 130180--130215 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
130170 ATTGTTTAAT
130180 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
130194 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
130208 TGATTTGT
1 TGATTTGT
130216 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:130338 original size:19 final size:19
Alignment explanation
Indices: 130322--130419 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
130312 AAAAATGACT
130322 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
130341 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
130360 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
130374 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
130393 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
130413 ATCGCAA
1 ATCGCAA
130420 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.54
20 16 0.23
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:130451 original size:53 final size:53
Alignment explanation
Indices: 130322--130434 Score: 210
Period size: 53 Copynumber: 2.2 Consensus size: 53
130312 AAAAATGACT
*
130322 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
130374 ATCGCAATACGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
130427 ATCGCAAT
1 ATCGCAAT
130435 GCGTTTATAA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 28 0.47
53 31 0.53
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
ATCGCAATACGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:130471 original size:14 final size:14
Alignment explanation
Indices: 130452--130506 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
130442 TAATTTCGCA
130452 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
130466 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
130483 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
130499 TTGCGATT
1 TTGCGATT
130507 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:130490 original size:19 final size:19
Alignment explanation
Indices: 130466--130663 Score: 211
Period size: 19 Copynumber: 11.4 Consensus size: 19
130456 GATTCTCTCG
130466 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
130485 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
130499 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
130518 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
130537 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
130551 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
130570 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
130589 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
130603 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
130623 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
130637 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
130656 TTGCGATT
1 TTGCGATT
130664 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 8, Indels: 42
0.75 0.04 0.21
Matches are distributed among these distances:
14 29 0.19
16 23 0.15
17 20 0.13
18 3 0.02
19 63 0.42
20 12 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:130522 original size:52 final size:52
Alignment explanation
Indices: 130466--130635 Score: 331
Period size: 52 Copynumber: 3.2 Consensus size: 52
130456 GATTCTCTCG
130466 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
130518 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
130570 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
130623 TTGCGATTTTCAT
1 TTGCGATTTTCAT
130636 GTTGGGATTT
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 100 0.85
53 17 0.15
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:130685 original size:33 final size:33
Alignment explanation
Indices: 130444--130677 Score: 278
Period size: 33 Copynumber: 6.9 Consensus size: 33
130434 TGCGTTTATA
130444 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
130477 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
130510 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
130550 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
130581 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
130614 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
130648 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
130678 GTAATTTCCG
Statistics
Matches: 171, Mismatches: 16, Indels: 28
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.05
32 6 0.04
33 95 0.56
34 29 0.17
35 6 0.04
36 4 0.02
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.05
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:132975 original size:12 final size:12
Alignment explanation
Indices: 132958--132982 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
132948 TCTTCGGGGA
132958 CTTTTTCTTCTT
1 CTTTTTCTTCTT
132970 CTTTTTCTTCTT
1 CTTTTTCTTCTT
132982 C
1 C
132983 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:133196 original size:24 final size:23
Alignment explanation
Indices: 133157--133202 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
133147 CTGAAACATC
133157 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCGTGTATTGACCAAT
133180 ATCAAAGTCCG-GATATTGACCAA
1 ATCAAA-TCCGTG-TATTGACCAA
133203 GACCAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGTGTATTGACCAAT
Found at i:133913 original size:20 final size:20
Alignment explanation
Indices: 133885--134154 Score: 274
Period size: 20 Copynumber: 13.5 Consensus size: 20
133875 AAATTTCAGT
* * *
133885 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
133905 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
133925 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
133945 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
133965 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
133985 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
134005 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
134025 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
134045 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
134065 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
134085 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
134105 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
134125 GTTGCGATTTTA-ATATTCGC
1 GTTGCGA-TTTACGGATTCGC
134145 GTTGCGATTT
1 GTTGCGATTT
134155 TGGAAAATCG
Statistics
Matches: 219, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
19 3 0.01
20 211 0.96
21 5 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:133945 original size:40 final size:40
Alignment explanation
Indices: 133885--134154 Score: 307
Period size: 40 Copynumber: 6.8 Consensus size: 40
133875 AAATTTCAGT
* *
133885 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
133925 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
133965 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* * *
134005 GTTGCGATTTACGGATACGCGTTGCGATATACGGA-TA-C
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
** * *
134043 GCATTGCGATTTACCCATACGCGTTGCGATTTACGGA-TACAC
1 G--TTGCGATTTACAGATTCGCGTTGCGATTTACGGATTA-TC
* * * **
134085 GTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACG-GATTATC
*
134125 GTTGCGATTTTA-ATATTCGCGTTGCGATTT
1 GTTGCGA-TTTACAGATTCGCGTTGCGATTT
134155 TGGAAAATCG
Statistics
Matches: 207, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 195 0.94
41 6 0.03
42 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
Found at i:134155 original size:20 final size:20
Alignment explanation
Indices: 134121--134218 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
134111 ATTTATGTGT
*
134121 TCGCGTTGCGATTTTAATAT
1 TCGCGTTGCGATTTTAATAA
134141 TCGCGTTGCGATTTTGGAA-AA
1 TCGCGTTGCGATTTT--AATAA
** *
134162 TCGCAATGCGAATTTGTACT-A
1 TCGCGTTGCG-ATTT-TAATAA
* *
134183 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTT-AATAA
134204 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
134219 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 35 0.56
22 6 0.10
23 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTAATAA
Found at i:134214 original size:42 final size:43
Alignment explanation
Indices: 134121--134219 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
134111 ATTTATGTGT
* *
134121 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
** *
134162 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
134204 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
134220 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 10 0.21
42 33 0.70
43 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:134669 original size:36 final size:36
Alignment explanation
Indices: 134628--134702 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
134618 ATTTGATTAG
134628 TTATCGCTAAAGACTTAAAGTTATTAGATATTTTTA
1 TTATCGCTAAAGACTTAAAGTTATTAGATATTTTTA
134664 TTATCGCTAAAGACTTAAAGTTATTAGATATTTTTA
1 TTATCGCTAAAGACTTAAAGTTATTAGATATTTTTA
134700 TTA
1 TTA
134703 CATGTATACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (36 bp):
TTATCGCTAAAGACTTAAAGTTATTAGATATTTTTA
Found at i:135136 original size:13 final size:13
Alignment explanation
Indices: 135118--135145 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
135108 TTGACTTTCA
135118 ACATTAAGAAAGT
1 ACATTAAGAAAGT
135131 ACATTAAGAAAGT
1 ACATTAAGAAAGT
135144 AC
1 AC
135146 GTGAGGTGAG
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:0.54, C:0.11, G:0.14, T:0.21
Consensus pattern (13 bp):
ACATTAAGAAAGT
Found at i:135400 original size:6 final size:6
Alignment explanation
Indices: 135389--135413 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
135379 TCGGCTCGGC
135389 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
135414 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:142375 original size:31 final size:31
Alignment explanation
Indices: 142337--142461 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
142327 AGGGGCGAGG
142337 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
142368 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
142399 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
142430 GTTTACTTAGGTTCTTCAGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
142461 G
1 G
142462 GTACTTCAGG
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:144802 original size:2 final size:2
Alignment explanation
Indices: 144797--144834 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
144787 CAAGAATTAG
144797 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A- 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
144835 GATTATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:144817 original size:15 final size:14
Alignment explanation
Indices: 144797--144834 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
144787 CAAGAATTAG
144797 ATATATATATATA-
1 ATATATATATATAT
144810 ATATATATATATAT
1 ATATATATATATAT
144824 ATA-ATATATAT
1 ATATATATATAT
144835 GATTATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 21 0.88
14 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:144841 original size:17 final size:17
Alignment explanation
Indices: 144797--144834 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
144787 CAAGAATTAG
144797 ATATATATATATAATAT
1 ATATATATATATAATAT
144814 ATATATATATATAATAT
1 ATATATATATATAATAT
144831 ATAT
1 ATAT
144835 GATTATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATAATAT
Found at i:144846 original size:17 final size:15
Alignment explanation
Indices: 144797--144846 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
144787 CAAGAATTAG
*
144797 ATATATATATATAAT
1 ATATATATATATAAA
*
144812 ATATATATATATATA
1 ATATATATATATAAA
144827 ATATATATGATTATAAA
1 ATATATAT-A-TATAAA
144844 ATA
1 ATA
144847 CCATTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 21 0.70
16 1 0.03
17 8 0.27
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATATATATATAAA
Done.