Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008888.1 Hibiscus syriacus cultivar Beakdansim tig00112153_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: 1025554
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:429872 original size:20 final size:20
Alignment explanation
Indices: 429696--429872 Score: 94
Period size: 20 Copynumber: 9.5 Consensus size: 20
429686 GTGATTCTCT
* **
429696 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
* *
429716 CATTGCGATAGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
429736 CATTGCGATAGTCATTTGT-G
1 CGTTGCGATTGTCATTT-TCG
* *
429756 CATTGCGATAGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
429776 CGTAGCGATT-T--TGTT--
1 CGTTGCGATTGTCATTTTCG
*
429791 -GTTGCGATTTTCA-TTTCG
1 CGTTGCGATTGTCATTTTCG
* * *
429809 CATTGC-A-----ATTCTCT
1 CGTTGCGATTGTCATTTTCG
*
429823 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
*
429843 CGTTGCGATTGTCATTTTTG
1 CGTTGCGATTGTCATTTTCG
429863 CGTTGCGATT
1 CGTTGCGATT
429873 TTAAGTTTCA
Statistics
Matches: 125, Mismatches: 17, Indels: 30
0.73 0.10 0.17
Matches are distributed among these distances:
13 1 0.01
14 16 0.13
15 2 0.02
16 2 0.02
17 3 0.02
18 1 0.01
19 6 0.05
20 93 0.74
21 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:432064 original size:33 final size:33
Alignment explanation
Indices: 432001--432064 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
431991 TCATTTTTGC
* ** *
432001 ATTGCGATTCACTCGTTGCGCTTTTTATTTCGT
1 ATTGCGATTCACTCGTTGCGATAGTCATTTCGT
*
432034 ATTGCGATTCTCTCGTTGCGATAGTCATTTC
1 ATTGCGATTCACTCGTTGCGATAGTCATTTC
432065 CGCGTTACGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (33 bp):
ATTGCGATTCACTCGTTGCGATAGTCATTTCGT
Found at i:432075 original size:20 final size:20
Alignment explanation
Indices: 432047--432140 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
432037 GCGATTCTCT
432047 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
432067 CGTTACGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
432087 CGTTGCGATAGTCATTTACG
1 CGTTGCGATAGTCATTTCCG
*
432107 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
432127 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
432141 AATGAATGTC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 64 0.97
21 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:435485 original size:20 final size:20
Alignment explanation
Indices: 435469--435555 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
435459 CAGAATCTCG
435469 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
*
435489 TTGCGATTTACGTAATCACA
1 TTGCGATTTACGTAATCGCA
* ** *
435509 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTACGTAA-TCGCA
*
435530 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
435550 TTGCGA
1 TTGCGA
435556 ATTAGGAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 41 0.75
21 14 0.25
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:435493 original size:61 final size:61
Alignment explanation
Indices: 435428--435558 Score: 144
Period size: 61 Copynumber: 2.1 Consensus size: 61
435418 AGAAATCGAG
* *
435428 TTGCGAATTT-GAAATTCAGTATTGCGATAGT-CAGAA-TCTCGTTGCGATTTACGTAATCGCA
1 TTGCGAATTTAGAAA-TCA-CATTGCGATAGTCCA-AATTCGCGTTGCGATTTACGTAATCGCA
* ** *
435489 TTGCG-ATTTACGTAATCACATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGAATTTA-GAAATCACATTGCGATAGTCCAAATTCGCGTTGCGATTTACGTAATCGCA
435550 TTGCGAATT
1 TTGCGAATT
435559 AGGAAAATCG
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
60 15 0.25
61 38 0.64
62 6 0.10
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (61 bp):
TTGCGAATTTAGAAATCACATTGCGATAGTCCAAATTCGCGTTGCGATTTACGTAATCGCA
Found at i:436209 original size:2 final size:2
Alignment explanation
Indices: 436202--436237 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
436192 AAATTAATGT
436202 TA TA TA TA TA TA TA TA TA TA T- TA T- TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
436238 TAACATAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:437497 original size:2 final size:2
Alignment explanation
Indices: 437486--437518 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
437476 TTAATAATAA
437486 AT AT -T 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
437519 TAAATTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:443623 original size:21 final size:21
Alignment explanation
Indices: 443599--443657 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
443589 TATTTATATC
443599 TGCCTTTGTGGCTATTATCTA
1 TGCCTTTGTGGCTATTATCTA
*
443620 TGCCTTTGAGGCTATTATCTA
1 TGCCTTTGTGGCTATTATCTA
443641 TGCCTTTGTGGCATATT
1 TGCCTTTGTGGC-TATT
443658 TTTCATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 31 0.89
22 4 0.11
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.46
Consensus pattern (21 bp):
TGCCTTTGTGGCTATTATCTA
Found at i:444301 original size:173 final size:173
Alignment explanation
Indices: 444012--444362 Score: 702
Period size: 173 Copynumber: 2.0 Consensus size: 173
444002 AGTTTTAATG
444012 TTATTAGAGAAGCCCAAATCATGTATTTAGTTTATGGTGATAGTTATAAACTCTTATTATAATTT
1 TTATTAGAGAAGCCCAAATCATGTATTTAGTTTATGGTGATAGTTATAAACTCTTATTATAATTT
444077 TAGATATTTTCATTTTTTTAATAATGCTAGTGGCTTTTTCAATGGAAACACCTCGATGACCTTCG
66 TAGATATTTTCATTTTTTTAATAATGCTAGTGGCTTTTTCAATGGAAACACCTCGATGACCTTCG
444142 TCACCGATGATTGTTTTGGTGGCGTTTCACTTTTTTAATCTTA
131 TCACCGATGATTGTTTTGGTGGCGTTTCACTTTTTTAATCTTA
444185 TTATTAGAGAAGCCCAAATCATGTATTTAGTTTATGGTGATAGTTATAAACTCTTATTATAATTT
1 TTATTAGAGAAGCCCAAATCATGTATTTAGTTTATGGTGATAGTTATAAACTCTTATTATAATTT
444250 TAGATATTTTCATTTTTTTAATAATGCTAGTGGCTTTTTCAATGGAAACACCTCGATGACCTTCG
66 TAGATATTTTCATTTTTTTAATAATGCTAGTGGCTTTTTCAATGGAAACACCTCGATGACCTTCG
444315 TCACCGATGATTGTTTTGGTGGCGTTTCACTTTTTTAATCTTA
131 TCACCGATGATTGTTTTGGTGGCGTTTCACTTTTTTAATCTTA
444358 TTATT
1 TTATT
444363 GAGGACCCGA
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
173 178 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.44
Consensus pattern (173 bp):
TTATTAGAGAAGCCCAAATCATGTATTTAGTTTATGGTGATAGTTATAAACTCTTATTATAATTT
TAGATATTTTCATTTTTTTAATAATGCTAGTGGCTTTTTCAATGGAAACACCTCGATGACCTTCG
TCACCGATGATTGTTTTGGTGGCGTTTCACTTTTTTAATCTTA
Found at i:444529 original size:24 final size:23
Alignment explanation
Indices: 444502--444554 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
444492 ATAATGAACA
*
444502 AAATAATTGT-TTAAATATCACATT
1 AAATAATT-TATTAAATAT-ACATG
*
444526 AAATACTTTATTAAATATACATG
1 AAATAATTTATTAAATATACATG
444549 AAATAA
1 AAATAA
444555 AATATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.38
Consensus pattern (23 bp):
AAATAATTTATTAAATATACATG
Found at i:445303 original size:24 final size:24
Alignment explanation
Indices: 445276--445329 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
445266 ATCATTTATA
*
445276 TATTTTTTGTTTTAATAAAATTTT
1 TATTATTTGTTTTAATAAAATTTT
445300 TATTATTTGTTTTAATAAAATTTT
1 TATTATTTGTTTTAATAAAATTTT
445324 TATTAT
1 TATTAT
445330 CAAATAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TATTATTTGTTTTAATAAAATTTT
Found at i:446552 original size:42 final size:43
Alignment explanation
Indices: 446455--446563 Score: 168
Period size: 42 Copynumber: 2.6 Consensus size: 43
446445 TGAGAACAAA
*
446455 AAACGCCGCAAAATGTCGAGATCTATAGCGCTATTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGCTATTTTTGGAAC
*
446498 AAACGCCGCAAAAGGTCGAGATCTATAGCGGC-A-TTTTGGAAT
1 AAACGCCGCAAAAGGTCGAGATCTATAGC-GCTATTTTTGGAAC
*
446540 AAACGCCACAAAAGGTCGAGATCT
1 AAACGCCGCAAAAGGTCGAGATCT
446564 TTTGCTAAGA
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
42 31 0.50
43 29 0.47
44 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCGCTATTTTTGGAAC
Found at i:449798 original size:41 final size:41
Alignment explanation
Indices: 449750--449871 Score: 176
Period size: 41 Copynumber: 3.0 Consensus size: 41
449740 AAGAAGCTAT
*
449750 TAAAGTACTACG-TTTTAGCGCCGTTTGT-TGAAAAACGCCAC
1 TAAAGTACTA-GATTTTAGCGCCGTTTGTCT-AAAAACACCAC
*
449791 TAAAGTACTAGATTTTAGCGGCGTTTGTCTAAAAACACCAC
1 TAAAGTACTAGATTTTAGCGCCGTTTGTCTAAAAACACCAC
* *
449832 TAAAGTACTAGATTTTAGCGGCTTTTGTCTAAAAACACCA
1 TAAAGTACTAGATTTTAGCGCCGTTTGTCTAAAAACACCA
449872 TGATATATGT
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
40 1 0.01
41 74 0.97
42 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (41 bp):
TAAAGTACTAGATTTTAGCGCCGTTTGTCTAAAAACACCAC
Found at i:452190 original size:39 final size:39
Alignment explanation
Indices: 452074--452190 Score: 132
Period size: 39 Copynumber: 3.0 Consensus size: 39
452064 TTTGTATTCA
* * *
452074 TAATTT-TTAAAATATTTCATTCTAACATTCTAAATTCT
1 TAATTTCTTAAATTATTTCACTCTAACATTCTAAATTAT
* *
452112 TAATTTCTTAAATTTTTTCAC-CTTAATC-TTCTAACTTAT
1 TAATTTCTTAAATTATTTCACTC-TAA-CATTCTAAATTAT
* *
452151 TAATTTCTTAAATTATTTCACTCTAACAATGTAAATTAT
1 TAATTTCTTAAATTATTTCACTCTAACATTCTAAATTAT
452190 T
1 T
452191 TCTCAAATTA
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
38 8 0.12
39 55 0.85
40 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.01, T:0.50
Consensus pattern (39 bp):
TAATTTCTTAAATTATTTCACTCTAACATTCTAAATTAT
Found at i:452251 original size:14 final size:13
Alignment explanation
Indices: 452227--452272 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
452217 ATATTTTAAA
452227 TTTAA-TTTATTT
1 TTTAATTTTATTT
452239 CTTTAATTTTA-TT
1 -TTTAATTTTATTT
*
452252 TTTAAGTTTTATAT
1 TTTAA-TTTTATTT
452266 TTTAATT
1 TTTAATT
452273 ATATAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 5 0.17
13 14 0.48
14 10 0.34
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTAATTTTATTT
Found at i:452277 original size:13 final size:13
Alignment explanation
Indices: 452227--452289 Score: 58
Period size: 14 Copynumber: 4.8 Consensus size: 13
452217 ATATTTTAAA
*
452227 TTTAA-TTTATTT
1 TTTAATTTTATAT
452239 CTTTAATTTTAT-T
1 -TTTAATTTTATAT
452252 TTTAAGTTTTATAT
1 TTTAA-TTTTATAT
*
452266 TTTAATTATATAAT
1 TTTAATTTTAT-AT
*
452280 TTAAATTTTA
1 TTTAATTTTA
452290 AAATTTTATG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
12 5 0.12
13 17 0.40
14 21 0.49
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (13 bp):
TTTAATTTTATAT
Found at i:452281 original size:14 final size:14
Alignment explanation
Indices: 452240--452297 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
452230 AATTTATTTC
452240 TTTAATTTTAT--T
1 TTTAATTTTATAAT
452252 TTTAAGTTTTAT-AT
1 TTTAA-TTTTATAAT
*
452266 TTTAATTATATAAT
1 TTTAATTTTATAAT
* *
452280 TTAAATTTTAAAAT
1 TTTAATTTTATAAT
452294 TTTA
1 TTTA
452298 TGAGTGAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
12 5 0.13
13 11 0.29
14 22 0.58
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTTAATTTTATAAT
Found at i:454884 original size:23 final size:21
Alignment explanation
Indices: 454837--454890 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
454827 ACACGTGTAC
*
454837 ACATAAAAATAGATAGAATTA
1 ACATAAAAATAAATAGAATTA
454858 ACATAATAAATAAATA-AATATGA
1 ACATAA-AAATAAATAGAAT-T-A
*
454881 ACATACAAAT
1 ACATAAAAAT
454891 TTAAATGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.32
22 13 0.46
23 6 0.21
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.24
Consensus pattern (21 bp):
ACATAAAAATAAATAGAATTA
Found at i:457480 original size:18 final size:18
Alignment explanation
Indices: 457457--457500 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
457447 AGCCATAGTG
457457 GGGTTTTAGAGATGTTTT
1 GGGTTTTAGAGATGTTTT
457475 GGGTTTTAGAGATGTTTT
1 GGGTTTTAGAGATGTTTT
457493 GGGTTTTA
1 GGGTTTTA
457501 AGGCTCTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (18 bp):
GGGTTTTAGAGATGTTTT
Found at i:458578 original size:125 final size:127
Alignment explanation
Indices: 458422--458678 Score: 322
Period size: 125 Copynumber: 2.0 Consensus size: 127
458412 AATATTAAAC
* * * *
458422 AAATCATATGATAAGCATAAAAACATTATGAAGTAAAAATTTCACCAGACTTATGCTTTTGTTTG
1 AAATCATATGATAAGCATAAAAACATTATGAAGTAAAAACTCCACAACACTTATGCTTTTGTTTG
* * *
458487 ATAC-CTGAGAAATGAT-GACAC-CCGGTTACTTGTGTATGACAACCATCTACATTATACAAG
66 ATACTC-AAGAAATGATAGACACACCGGTTACTTATGCATGACAACCATCTACATTATACAAG
* * * *
458547 AAATCGTATGATAAGCATAAGAACATTATGAAGTAAGAACTCCATAACACTTATGCTTTTGTTTG
1 AAATCATATGATAAGCATAAAAACATTATGAAGTAAAAACTCCACAACACTTATGCTTTTGTTTG
** * * * *
458612 ATACTCAAGAAATGATAGGACACATGGGTTACTTATGCATGACGATCGTCTACTTTATACAAG
66 ATACTCAAGAAATGATA-GACACACCGGTTACTTATGCATGACAACCATCTACATTATACAAG
458675 AAAT
1 AAAT
458679 ATCTAGATAT
Statistics
Matches: 111, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
125 70 0.63
126 1 0.01
127 5 0.05
128 35 0.32
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (127 bp):
AAATCATATGATAAGCATAAAAACATTATGAAGTAAAAACTCCACAACACTTATGCTTTTGTTTG
ATACTCAAGAAATGATAGACACACCGGTTACTTATGCATGACAACCATCTACATTATACAAG
Found at i:461466 original size:42 final size:45
Alignment explanation
Indices: 461419--461502 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 45
461409 TATGCAAAAG
461419 ATATAATATAA-AAATATTT-TTCGA-TT-TAAAA-TTTTAAAGATT
1 ATATAAT-TAATAAATATTTATT-GATTTATAAAACTTTTAAAGATT
461461 ATATAATTAATAAATATTTATTGATTTATAAAACTTTTAAAG
1 ATATAATTAATAAATATTTATTGATTTATAAAACTTTTAAAG
461503 TTAAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
41 3 0.08
42 17 0.46
43 4 0.11
44 5 0.14
45 8 0.22
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (45 bp):
ATATAATTAATAAATATTTATTGATTTATAAAACTTTTAAAGATT
Found at i:462526 original size:60 final size:60
Alignment explanation
Indices: 462459--462600 Score: 194
Period size: 60 Copynumber: 2.4 Consensus size: 60
462449 ATAACTAGAT
* * * ** *
462459 GACTATTTTATAACTTTTAATAGCTAAGAAAATCAACAAAGTAGGGCCCTCTGATTGAGA
1 GACTATTTTGTAACTTTTAATAGCCAAGAAAATCAACAAAGTAGAGCCCTAGGACTGAGA
* * * *
462519 GACTATTTTGTAACTTTTAATAGCCATGAAACTCAACAAATTAGAGTCCTAGGACTGAGA
1 GACTATTTTGTAACTTTTAATAGCCAAGAAAATCAACAAAGTAGAGCCCTAGGACTGAGA
462579 GACTATTTTGTAACTTTTAATA
1 GACTATTTTGTAACTTTTAATA
462601 ATTGGAGATA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (60 bp):
GACTATTTTGTAACTTTTAATAGCCAAGAAAATCAACAAAGTAGAGCCCTAGGACTGAGA
Found at i:470345 original size:30 final size:31
Alignment explanation
Indices: 470311--470370 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
470301 GAAGACAAAG
470311 AATAT-TTTTTTCAAGTGGCCAGTTGTATTT
1 AATATATTTTTTCAAGTGGCCAGTTGTATTT
470341 AATATATTTTTTCAAGTGGCCAGTTGTATT
1 AATATATTTTTTCAAGTGGCCAGTTGTATT
470371 CCAACAAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (31 bp):
AATATATTTTTTCAAGTGGCCAGTTGTATTT
Found at i:473108 original size:19 final size:20
Alignment explanation
Indices: 473093--473130 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
473083 TCCAAGATTA
473093 TATTGC-ACTACCAAGACCT
1 TATTGCAACTACCAAGACCT
473112 TATTGCAACTACCAAGACC
1 TATTGCAACTACCAAGACC
473131 ATACTACATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.34, C:0.32, G:0.11, T:0.24
Consensus pattern (20 bp):
TATTGCAACTACCAAGACCT
Found at i:479371 original size:32 final size:32
Alignment explanation
Indices: 479323--479396 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
479313 GTGTATGAGT
* * * * *
479323 CACAACGGAGTCAATATTGCATTTAGATAATG
1 CACAACAGAGTCAATATGGAATTCAGATAATA
*
479355 CACAACAGAGTTAATATGGAATTCAGATAATA
1 CACAACAGAGTCAATATGGAATTCAGATAATA
*
479387 CACAATAGAG
1 CACAACAGAG
479397 CTAGTAATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (32 bp):
CACAACAGAGTCAATATGGAATTCAGATAATA
Found at i:486768 original size:84 final size:82
Alignment explanation
Indices: 486680--486959 Score: 296
Period size: 84 Copynumber: 3.3 Consensus size: 82
486670 TCAGGGCTTA
*
486680 AATTATAAAAAGTAAAAAATGGGATTGAAAAATTAGGGACTTAAATTATAGAA-GTAAAAAGTGA
1 AATTAT-AAAAGTAAAAAGTGGGATTGAAAAATTAGGG-CTT-AATTATA-AAGGTAAAAAGTGA
*
486744 GATT-AAAAAGTTAGGGCCTC
62 GATTAAAAAAATTAGGGCCTC
* * * * *
486764 AATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAGGGCATCAATTATAAAGGTATAAAGTGAG
1 AATTATAAAAGTAAAAAGTGGGATTG--AAAAATTAGGGC-TTAATTATAAAGGTAAAAAGTGAG
*
486829 ATTAAAAAATTTAGGGCCTC
63 ATTAAAAAAATTAGGGCCTC
* * * *
486849 AATTAT-AAAGCTAAAAATTGGGATTGAAAAACTAGGGGCTCTAATTATAAATGTAAAAAGTGGG
1 AATTATAAAAG-TAAAAAGTGGGATTGAAAAATTA-GGGCT-TAATTATAAAGGTAAAAAGTGAG
* * *
486913 GTTGAAAAAAATTAGAGACATC
63 ATT-AAAAAAATTAG-GGCCTC
486935 AATTATAAAAGTAAAAAGTGGGATT
1 AATTATAAAAGTAAAAAGTGGGATT
486960 ACAGCCTACT
Statistics
Matches: 164, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
83 26 0.16
84 56 0.34
85 55 0.34
86 23 0.14
87 4 0.02
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (82 bp):
AATTATAAAAGTAAAAAGTGGGATTGAAAAATTAGGGCTTAATTATAAAGGTAAAAAGTGAGATT
AAAAAAATTAGGGCCTC
Found at i:486809 original size:43 final size:43
Alignment explanation
Indices: 486680--486959 Score: 254
Period size: 42 Copynumber: 6.6 Consensus size: 43
486670 TCAGGGCTTA
* * * * *
486680 AATTATAAAAAGTAAAAAATGGGATTG--AAAAATTAGGGACTTA
1 AATTAT-AAAGGTAAAAAGTGAGATTGAAAAAAATTAGGG-CATC
* *
486723 AATTATAGAA-GTAAAAAGTGAGATT--AAAAAGTTAGGGCCTC
1 AATTATA-AAGGTAAAAAGTGAGATTGAAAAAAATTAGGGCATC
*
486764 AATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAGGGCATC
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGCATC
* * *
486807 AATTATAAAGGTATAAAGTGAGATT-AAAAAATTTAGGGCCTC
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGCATC
* * * *
486849 AATTATAAAGCTAAAAATTGGGATTG--AAAAACTAGGGGC-TC
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTA-GGGCATC
* * * *
486890 TAATTATAAATGTAAAAAGTGGGGTTGAAAAAAATTAGAGACATC
1 -AATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAG-GGCATC
* *
486935 AATTATAAAAGTAAAAAGTGGGATT
1 AATTATAAAGGTAAAAAGTGAGATT
486960 ACAGCCTACT
Statistics
Matches: 200, Mismatches: 25, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
40 2 0.01
41 31 0.16
42 86 0.43
43 47 0.23
44 32 0.16
45 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (43 bp):
AATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGCATC
Found at i:486853 original size:85 final size:81
Alignment explanation
Indices: 486680--486959 Score: 292
Period size: 85 Copynumber: 3.3 Consensus size: 81
486670 TCAGGGCTTA
* * *
486680 AATTATAAAAAGTAAAAAATGGGATTGAAAAATTAGGGACTTAAATTATAGAAGTAAAAAGTGAG
1 AATTAT-AAAGGTAAAAAGTGGGATTGAAAAATTAGGG-C-TCAATTATA-AAGTAAAAAGTGAG
*
486745 ATT-AAAAAGTTAGGGCCTC
62 ATTAAAAAAATTAGGGCCTC
* * *
486764 AATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAGGGCATCAATTATAAAGGTATAAAGTGAG
1 AATTATAAAGGTAAAAAGTGGGATTG--AAAAATTAGGGC-TCAATTATAAA-GTAAAAAGTGAG
*
486829 ATTAAAAAATTTAGGGCCTC
62 ATTAAAAAAATTAGGGCCTC
* * * * *
486849 AATTATAAAGCTAAAAATTGGGATTGAAAAACTAGGGGCTCTAATTATAAATGTAAAAAGTGGGG
1 AATTATAAAGGTAAAAAGTGGGATTGAAAAATTA-GGGCTC-AATTATAAA-GTAAAAAGTGAGA
* *
486914 TTGAAAAAAATTAGAGACATC
63 TT-AAAAAAATTAG-GGCCTC
*
486935 AATTATAAAAGTAAAAAGTGGGATT
1 AATTATAAAGGTAAAAAGTGGGATT
486960 ACAGCCTACT
Statistics
Matches: 165, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
83 27 0.16
84 54 0.33
85 58 0.35
86 26 0.16
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (81 bp):
AATTATAAAGGTAAAAAGTGGGATTGAAAAATTAGGGCTCAATTATAAAGTAAAAAGTGAGATTA
AAAAAATTAGGGCCTC
Found at i:490520 original size:7 final size:7
Alignment explanation
Indices: 490508--490538 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
490498 TTTGGTCATT
490508 AAAGGTC
1 AAAGGTC
490515 AAAGGTC
1 AAAGGTC
490522 AAAGGTC
1 AAAGGTC
490529 AAAGGTC
1 AAAGGTC
490536 AAA
1 AAA
490539 TAGGTCATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.48, C:0.13, G:0.26, T:0.13
Consensus pattern (7 bp):
AAAGGTC
Found at i:491155 original size:20 final size:20
Alignment explanation
Indices: 491130--491184 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
491120 AGATTTCTAT
491130 AAGGGTATCGATACCTTAGG
1 AAGGGTATCGATACCTTAGG
*
491150 AAGGGTACCGATACCTTAGG
1 AAGGGTATCGATACCTTAGG
*
491170 GAGGGTATCGATACC
1 AAGGGTATCGATACC
491185 CCCTAAAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (20 bp):
AAGGGTATCGATACCTTAGG
Found at i:492128 original size:25 final size:25
Alignment explanation
Indices: 492070--492119 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
492060 CAGTCTTATA
*
492070 TGGCACTACGGTGC-AA-TTCTACG
1 TGGCACTTCGGTGCAAATTTCTACG
492093 TGGCACTTCGGTGCAAATTTCTACG
1 TGGCACTTCGGTGCAAATTTCTACG
492118 TG
1 TG
492120 ATCCTTCGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 13 0.54
24 2 0.08
25 9 0.38
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (25 bp):
TGGCACTTCGGTGCAAATTTCTACG
Found at i:492767 original size:22 final size:23
Alignment explanation
Indices: 492737--492787 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
492727 AAATTTAACA
* *
492737 TTCAGTACTGTTCA-CGGTATTG
1 TTCATTACTGTTCAGCGGTACTG
492759 TTCATTACTGTTCATGCGGTACTG
1 TTCATTACTGTTCA-GCGGTACTG
492783 TTCAT
1 TTCAT
492788 ACCATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.52
24 12 0.48
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.43
Consensus pattern (23 bp):
TTCATTACTGTTCAGCGGTACTG
Found at i:508614 original size:91 final size:91
Alignment explanation
Indices: 508451--508810 Score: 594
Period size: 91 Copynumber: 3.9 Consensus size: 91
508441 AAGGAGGTGG
*
508451 ATCAACATTTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
1 ATCAACA-TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
508516 TAATGAGAAGAACTTGTTCAACCTTGC
65 TAATGAGAAGAACTTGTTCAACCTTGC
* * *
508543 ATCAACATTTCCAGTAGAGAGTTCATGATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
* *
508608 AATGAGAATAACTTGTTCAACCTTGG
66 AATGAGAAGAACTTGTTCAACCTTGC
* *
508634 TTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
508699 AATGAGAAGAACTTGTTCAACCTTGC
66 AATGAGAAGAACTTGTTCAACCTTGC
* * * * *
508725 ATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACCCATCCGATGAGGGAGAATAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
508790 AATGAGAAGAACTTGTTCAAC
66 AATGAGAAGAACTTGTTCAAC
508811 TTGGGTGATT
Statistics
Matches: 248, Mismatches: 20, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
91 241 0.97
92 7 0.03
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (91 bp):
ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTGC
Found at i:511718 original size:28 final size:28
Alignment explanation
Indices: 511685--511740 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
511675 TACTCTTGGC
511685 ATGCCAACTATACCTCTAGCTCTCATGA
1 ATGCCAACTATACCTCTAGCTCTCATGA
511713 ATGCCAACTATACCTCTAGCTCTCATGA
1 ATGCCAACTATACCTCTAGCTCTCATGA
511741 CAGATAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.29
Consensus pattern (28 bp):
ATGCCAACTATACCTCTAGCTCTCATGA
Found at i:514472 original size:13 final size:13
Alignment explanation
Indices: 514454--514513 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
514444 AACTGTAAAA
514454 AAATAAAATAATT
1 AAATAAAATAATT
*
514467 AAATAAAAT-ACT
1 AAATAAAATAATT
*
514479 AAA-AAAATTATGT
1 AAATAAAATAAT-T
*
514492 -AATACAATAATT
1 AAATAAAATAATT
514504 AAATAAAATA
1 AAATAAAATA
514514 CTAACAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
11 5 0.13
12 9 0.24
13 24 0.63
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:514473 original size:21 final size:21
Alignment explanation
Indices: 514449--514488 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
514439 TTTATAACTG
*
514449 TAAAAAAATAAAATAATTAAA
1 TAAAAAAATAAAAAAATTAAA
* *
514470 TAAAATACTAAAAAAATTA
1 TAAAAAAATAAAAAAATTA
514489 TGTAATACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAAAAATAAAAAAATTAAA
Found at i:514541 original size:17 final size:18
Alignment explanation
Indices: 514509--514542 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
514499 TAATTAAATA
514509 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
514527 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
514543 ACCTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:514591 original size:10 final size:10
Alignment explanation
Indices: 514576--514618 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
514566 ATATTTGTTT
*
514576 TTTGAGATGA
1 TTTGAGAAGA
514586 TTTGAG-AGAA
1 TTTGAGAAG-A
*
514596 TTAGAGAAGA
1 TTTGAGAAGA
514606 TTTGAGAAGA
1 TTTGAGAAGA
514616 TTT
1 TTT
514619 AGTGTGGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 1 0.04
10 25 0.89
11 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.28, T:0.35
Consensus pattern (10 bp):
TTTGAGAAGA
Found at i:515471 original size:43 final size:42
Alignment explanation
Indices: 515424--515541 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 42
515414 TCCTTTGATA
* * *
515424 ATCTCCTGTTTCTTCTATTTTCACTGCAATTGGTCTCTTAATC
1 ATCTCCTGTTTCTGCCATTTT-ACTGCAATTGGTCTCTTAAGC
* * * *
515467 ATCT-CTGATTTATGCCATTTATGCTGCATTTAGTCTCTTAAGC
1 ATCTCCTG-TTTCTGCCATTT-TACTGCAATTGGTCTCTTAAGC
* *
515510 ACCTCTTGTTTCTGCCATTTTTACTGCAATTG
1 ATCTCCTGTTTCTGCCA-TTTTACTGCAATTG
515542 AGCTAATTGT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
42 3 0.05
43 49 0.84
44 6 0.10
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.47
Consensus pattern (42 bp):
ATCTCCTGTTTCTGCCATTTTACTGCAATTGGTCTCTTAAGC
Found at i:520873 original size:36 final size:36
Alignment explanation
Indices: 520593--520872 Score: 425
Period size: 36 Copynumber: 7.8 Consensus size: 36
520583 ATGCGCTACA
* *
520593 TCCTTCCGTTCAACTTGAATCGGAAGTACCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
*
520629 TCCTTCCGTTTGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
*
520665 TCCTTCCGTTCGACTTGAATCGAAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
** *
520701 TCCTTCCGTTCCTCTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
* *
520737 TCCTTCCGTTCGACTTGAATTGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
* * * *
520773 TCCTTCCGTTCGACTTGAATCGAAAGTGTCGGTGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
* *
520809 TCCTTCCGTTCGACTTAAATCGGAAGTGTCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
520845 TCCTTCCGTTCGACTTGAATCGGAAGTG
1 TCCTTCCGTTCGACTTGAATCGGAAGTG
520873 TAGATGAAAT
Statistics
Matches: 223, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 223 1.00
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
Found at i:522502 original size:9 final size:9
Alignment explanation
Indices: 522488--522535 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
522478 TAATCATGAT
522488 TATTTTAAA
1 TATTTTAAA
522497 TATTTTAAA
1 TATTTTAAA
* *
522506 TAATTAAAA
1 TATTTTAAA
* *
522515 TATATAAAA
1 TATTTTAAA
522524 TATATTTAAA
1 TAT-TTTAAA
522534 TA
1 TA
522536 CAACTTGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 26 0.81
10 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TATTTTAAA
Found at i:522718 original size:20 final size:20
Alignment explanation
Indices: 522693--522749 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
522683 TTTTTAAAAA
522693 TAATTTTAAAAAGGAAAAGT
1 TAATTTTAAAAAGGAAAAGT
*
522713 TAATTTT-GAAAGGAAAAAGT
1 TAATTTTAAAAAGG-AAAAGT
522733 TAATTTTGAAAAAGGAA
1 TAATTTT-AAAAAGGAA
522750 TTTCAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 5 0.16
20 20 0.62
21 2 0.06
22 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.30
Consensus pattern (20 bp):
TAATTTTAAAAAGGAAAAGT
Found at i:522921 original size:28 final size:28
Alignment explanation
Indices: 522889--523126 Score: 141
Period size: 28 Copynumber: 8.6 Consensus size: 28
522879 CGAATAAAAG
522889 AATTAATTCCGAAACAGGA-ATTCTTAAA
1 AATTAATTCCGAAACAGGACATT-TTAAA
*
522917 AATTAACTT-CGAAACAGGACATTTTAGA
1 AATTAA-TTCCGAAACAGGACATTTTAAA
* ** *
522945 AATTACTTCTTAAA-TGGA-ATATTTAAA
1 AATTAATTCCGAAACAGGACAT-TTTAAA
* * * *
522972 AATTAATTCCGACACAAGACGTCTT-AA
1 AATTAATTCCGAAACAGGACATTTTAAA
* * * *
522999 AATTAATTCAG-AATAGGACATTTTGAT
1 AATTAATTCCGAAACAGGACATTTTAAA
* * *
523026 AATTAATTCC-AAGAAAGGATATTTTAAT
1 AATTAATTCCGAA-ACAGGACATTTTAAA
* * * * *
523054 AATTAGTTCTGAAACCGGAGATTTTAAT
1 AATTAATTCCGAAACAGGACATTTTAAA
*** * *
523082 AATTAATTTAAAAACAGGACATCTTAAT
1 AATTAATTCCGAAACAGGACATTTTAAA
*
523110 AATTAATTCAG-AACAGG
1 AATTAATTCCGAAACAGG
523127 GGATATTTAC
Statistics
Matches: 161, Mismatches: 39, Indels: 21
0.73 0.18 0.10
Matches are distributed among these distances:
26 10 0.06
27 49 0.30
28 94 0.58
29 8 0.05
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (28 bp):
AATTAATTCCGAAACAGGACATTTTAAA
Found at i:523141 original size:56 final size:54
Alignment explanation
Indices: 522993--523143 Score: 144
Period size: 56 Copynumber: 2.7 Consensus size: 54
522983 ACACAAGACG
* * * *
522993 TCTTAA-AATTAATTCAGAATAGGACATTTTGATAATTAATTCCAAGAAAGGATA
1 TCTTAATAATTAATTCAGAACAGGAGATTTT-ATAATTAATTCCAAAAAAGGACA
* * * * *
523047 TTTTAATAATTAGTTCTGAAACCGGAGATTTTAATAATTAATT-TAAAAACAGGACA
1 TCTTAATAATTAATTCAG-AACAGGAGATTTT-ATAATTAATTCCAAAAA-AGGACA
*
523103 TCTTAATAATTAATTCAGAACAGGGGATATTTACTAATTAA
1 TCTTAATAATTAATTCAGAACAGGAGAT-TTTA-TAATTAA
523144 ATCTACTTAT
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
54 5 0.06
55 22 0.29
56 50 0.65
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (54 bp):
TCTTAATAATTAATTCAGAACAGGAGATTTTATAATTAATTCCAAAAAAGGACA
Found at i:523252 original size:29 final size:29
Alignment explanation
Indices: 523217--523511 Score: 98
Period size: 29 Copynumber: 10.3 Consensus size: 29
523207 ATTGACTTCA
523217 TAATAATTAATTCGGAACACTGGATATCT
1 TAATAATTAATTCGGAACACTGGATATCT
* *
523246 TAATAATTAATT-GAGAACA-TCGAATATTT
1 TAATAATTAATTCG-GAACACT-GGATATCT
* * *
523275 TACTAATTAA-TC-GACCTA-TGGATATTT
1 TAATAATTAATTCGGAAC-ACTGGATATCT
** * *
523302 TGCTAATTAGTTCAGGAA-A-TGCAT-T-T
1 TAATAATTAATTC-GGAACACTGGATATCT
* * * * *
523328 TCATAATTAATT-GGCAATACTGAACATCG
1 TAATAATTAATTCGG-AACACTGGATATCT
* *
523357 TAATAATTAATTCGGAACAAATAGATATCT
1 TAATAATTAATTCGGAAC-ACTGGATATCT
* * *
523387 TACTAATTAATTC--AACTTACTGGGTATTT
1 TAATAATTAATTCGGAAC--ACTGGATATCT
* * * * ** * *
523416 TACTAATTAGTTTAGG-ATACTATATGTTT
1 TAATAATTA-ATTCGGAACACTGGATATCT
* *
523445 TCATAATTAATT-GGAAACAGTGGATAT-T
1 TAATAATTAATTCGG-AACACTGGATATCT
* *
523473 ATAATAATTAATTCGGAAAACTGTATATCT
1 -TAATAATTAATTCGGAACACTGGATATCT
*
523503 TTATAATTA
1 TAATAATTA
523512 TTTTAGAATG
Statistics
Matches: 195, Mismatches: 48, Indels: 46
0.67 0.17 0.16
Matches are distributed among these distances:
24 2 0.01
25 2 0.01
26 11 0.06
27 24 0.12
28 19 0.10
29 109 0.56
30 27 0.14
31 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
TAATAATTAATTCGGAACACTGGATATCT
Found at i:523424 original size:141 final size:139
Alignment explanation
Indices: 523102--523402 Score: 358
Period size: 140 Copynumber: 2.2 Consensus size: 139
523092 AAAACAGGAC
* ** * * * *
523102 ATCTTAATAATTAATTCAGAACAGGGGATA-TTTACTAATTAAATCTACTTATTGATATATTGCT
1 ATCTTAATAATTAATT-ACAACATCGAATATTTTACTAATT-AATCGACCTATGGATATATTGCT
* * *
523166 AATTAGTTCAGGAAACTGATATTTTCATAATTATTGACAACATTGACTTCATAATAATTAATTCG
64 AATTAGTTCAGGAAACTGACATTTTCATAATTATTGACAACACTGACATCATAATAATTAATTCG
* *
523231 GAACACTGGAT
129 GAACAATAGAT
* *
523242 ATCTTAATAATTAATTGAGAACATCGAATATTTTACTAATTAATCGACCTATGGATATTTTGCTA
1 ATCTTAATAATTAATT-ACAACATCGAATATTTTACTAATTAATCGACCTATGGATATATTGCTA
* * *
523307 ATTAGTTCAGGAAA-TG-CATTTTCATAATTAATTGGCAATACTGAACATCGTAATAATTAATTC
65 ATTAGTTCAGGAAACTGACATTTTCATAATT-ATTGACAACACTG-ACATCATAATAATTAATTC
523370 GGAACAAATAGAT
128 GGAAC-AATAGAT
*
523383 ATCTTACTAATTAATT-CAAC
1 ATCTTAATAATTAATTACAAC
523403 TTACTGGGTA
Statistics
Matches: 139, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
138 12 0.09
139 15 0.11
140 82 0.59
141 30 0.22
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.37
Consensus pattern (139 bp):
ATCTTAATAATTAATTACAACATCGAATATTTTACTAATTAATCGACCTATGGATATATTGCTAA
TTAGTTCAGGAAACTGACATTTTCATAATTATTGACAACACTGACATCATAATAATTAATTCGGA
ACAATAGAT
Found at i:523902 original size:29 final size:28
Alignment explanation
Indices: 523870--523925 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
523860 ATATGTTAGT
*
523870 AATTAATTCCGGACACTGGATATCATAAA
1 AATTAATTCCGAACACTGG-TATCATAAA
* *
523899 AATTAATTCTGAACACTGGTATTATAA
1 AATTAATTCCGAACACTGGTATCATAA
523926 TAGTTAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (28 bp):
AATTAATTCCGAACACTGGTATCATAAA
Found at i:524256 original size:28 final size:29
Alignment explanation
Indices: 524216--524322 Score: 112
Period size: 28 Copynumber: 3.8 Consensus size: 29
524206 AATAAAAGAA
** *
524216 TTAATTCCAAAAC-GGACCTTTTAAAAAT
1 TTAATTCTGAAACAGGACATTTTAAAAAT
* * *
524244 TTAATTTTGAAACAGGATATTTTATAAA-
1 TTAATTCTGAAACAGGACATTTTAAAAAT
*
524272 TTAATTCTGAAACATGACATTTT-AAAAT
1 TTAATTCTGAAACAGGACATTTTAAAAAT
* *
524300 TTAATTCCGAAACAAGACATTTT
1 TTAATTCTGAAACAGGACATTTT
524323 GGAAATAAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
27 3 0.05
28 51 0.78
29 11 0.17
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (29 bp):
TTAATTCTGAAACAGGACATTTTAAAAAT
Found at i:524276 original size:56 final size:55
Alignment explanation
Indices: 524214--524353 Score: 145
Period size: 56 Copynumber: 2.5 Consensus size: 55
524204 ACAATAAAAG
* * ** * * *
524214 AATTAATTCCAAAACGGACCTTTTAAAAATTTAATTTTGAAACAGGATATTTTATA
1 AATTAATTCCGAAACGGACATTTT-AAAATTTAATTCCGAAACAAGACATTTTAGA
* * *
524270 AATTAATTCTGAAACATGACATTTTAAAATTTAATTCCGAAACAAGACATTTTGGA
1 AATTAATTCCGAAAC-GGACATTTTAAAATTTAATTCCGAAACAAGACATTTTAGA
* * *
524326 AATAAATTCCGAAACGAAAATTTTAAAA
1 AATTAATTCCGAAACGGACATTTTAAAA
524354 AAATTCCTAC
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
55 10 0.15
56 51 0.75
57 7 0.10
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (55 bp):
AATTAATTCCGAAACGGACATTTTAAAATTTAATTCCGAAACAAGACATTTTAGA
Found at i:524333 original size:28 final size:27
Alignment explanation
Indices: 524214--524353 Score: 106
Period size: 28 Copynumber: 5.1 Consensus size: 27
524204 ACAATAAAAG
* * *
524214 AATTAATTCCAAAAC-GGACCTTTTAAA
1 AATTAATTCCGAAACAAGACATTTT-AA
** * *
524241 AATTTAATTTTGAAACAGGATATTTTATA
1 AA-TTAATTCCGAAACAAGACATTTTA-A
* *
524270 AATTAATTCTGAAACATGACATTTTAA
1 AATTAATTCCGAAACAAGACATTTTAA
*
524297 AATTTAATTCCGAAACAAGACATTTTGGA
1 AA-TTAATTCCGAAACAAGACATTTT-AA
*
524326 AATAAATTCCGAAACGAA-A-ATTTTAA
1 AATTAATTCCGAAAC-AAGACATTTTAA
524352 AA
1 AA
524354 AAATTCCTAC
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
26 3 0.03
27 10 0.11
28 66 0.70
29 15 0.16
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (27 bp):
AATTAATTCCGAAACAAGACATTTTAA
Found at i:529775 original size:16 final size:17
Alignment explanation
Indices: 529754--529789 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
529744 CGTCACCTTG
529754 AAAAGG-GTTACAACAT
1 AAAAGGAGTTACAACAT
*
529770 AAAAGGAGTTACAACCT
1 AAAAGGAGTTACAACAT
529787 AAA
1 AAA
529790 TGTGGTGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.53, C:0.14, G:0.17, T:0.17
Consensus pattern (17 bp):
AAAAGGAGTTACAACAT
Found at i:529829 original size:17 final size:17
Alignment explanation
Indices: 529781--529861 Score: 67
Period size: 18 Copynumber: 4.7 Consensus size: 17
529771 AAAGGAGTTA
529781 CAACCT-AAATGTGGTG
1 CAACCTAAAATGTGGTG
* *
529797 CAACTTGAAAAAGTGGTG
1 CAACCT-AAAATGTGGTG
*
529815 CAACCTAAAATGTGGCG
1 CAACCTAAAATGTGGTG
* *
529832 CCACCATAAAATAG-GTTG
1 CAACC-TAAAAT-GTGGTG
*
529850 CAACTTAAAATG
1 CAACCTAAAATG
529862 GCAACCATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
16 6 0.12
17 19 0.37
18 25 0.49
19 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (17 bp):
CAACCTAAAATGTGGTG
Found at i:530364 original size:15 final size:15
Alignment explanation
Indices: 530344--530373 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
530334 CAAATTATAT
530344 CTCTAAATTAGGAAA
1 CTCTAAATTAGGAAA
*
530359 CTCTAAGTTAGGAAA
1 CTCTAAATTAGGAAA
530374 GATACTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (15 bp):
CTCTAAATTAGGAAA
Found at i:531830 original size:12 final size:12
Alignment explanation
Indices: 531810--531843 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
531800 TAATTTTAAG
*
531810 ATTTGAAAATCA
1 ATTTTAAAATCA
531822 ATTTTAAAATCA
1 ATTTTAAAATCA
*
531834 ATTTTGAAAT
1 ATTTTAAAAT
531844 TGAAAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (12 bp):
ATTTTAAAATCA
Found at i:554990 original size:34 final size:34
Alignment explanation
Indices: 554952--555033 Score: 155
Period size: 34 Copynumber: 2.4 Consensus size: 34
554942 GAGATTACTA
554952 AGTGTTCGAGAGAATATCTAAGTAGCACATCCTT
1 AGTGTTCGAGAGAATATCTAAGTAGCACATCCTT
554986 AGTGTTCGAGAGAATATCTAAGTAGCACATCCTT
1 AGTGTTCGAGAGAATATCTAAGTAGCACATCCTT
*
555020 AATGTTCGAGAGAA
1 AGTGTTCGAGAGAA
555034 ACTAGGGAGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (34 bp):
AGTGTTCGAGAGAATATCTAAGTAGCACATCCTT
Found at i:559892 original size:169 final size:168
Alignment explanation
Indices: 559611--559949 Score: 653
Period size: 169 Copynumber: 2.0 Consensus size: 168
559601 ACCTTAAAAT
559611 TCAATATTACTTTATTTGTTATATCGAAACATCAAAGTTTTCAACACATGTTAAACTGGGTTCTT
1 TCAATATTACTTTATTTGTTATATCGAAACATCAAAGTTTTCAACACATGTTAAACTGGGTTCTT
559676 GGGAATCTGATGATAGCTTGATTATCACACAAAACTTTAAAGTGATCCTTGCGATTAGTGTCAAG
66 GGGAATCTGATGATAGCTTGATTATCACACAAAACTTTAAAGTGATCCTTGCGATTAGTGTCAAG
559741 TTCTTTTAGTAGTTT-AGTAGCCAAATTCCTTCACATA
131 TTCTTTTAGTAGTTTAAGTAGCCAAATTCCTTCACATA
559778 TCAATATTACTTTATTTGTTATATCGAAACATCAAATGTTTTCAACACATGTTAAACTGGGTTCT
1 TCAATATTACTTTATTTGTTATATCGAAACATCAAA-GTTTTCAACACATGTTAAACTGGGTTCT
559843 TGGGAATCTGAATGATAGCTTGATTATCACACAAAACTTTAAAGTGATCCTTGCGATTAGTGTCA
65 TGGGAATCTG-ATGATAGCTTGATTATCACACAAAACTTTAAAGTGATCCTTGCGATTAGTGTCA
559908 AGTTCTTTTAGTAGTTTAAGTAGCCAAATTCCTTCACATA
129 AGTTCTTTTAGTAGTTTAAGTAGCCAAATTCCTTCACATA
559948 TC
1 TC
559950 CATTCCTTCA
Statistics
Matches: 169, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
167 36 0.21
168 38 0.22
169 71 0.42
170 24 0.14
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (168 bp):
TCAATATTACTTTATTTGTTATATCGAAACATCAAAGTTTTCAACACATGTTAAACTGGGTTCTT
GGGAATCTGATGATAGCTTGATTATCACACAAAACTTTAAAGTGATCCTTGCGATTAGTGTCAAG
TTCTTTTAGTAGTTTAAGTAGCCAAATTCCTTCACATA
Found at i:564074 original size:15 final size:15
Alignment explanation
Indices: 564054--564083 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
564044 CAAATTATAT
564054 CTCTAAATTAGGAAA
1 CTCTAAATTAGGAAA
*
564069 CTCTAAGTTAGGAAA
1 CTCTAAATTAGGAAA
564084 TATACTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (15 bp):
CTCTAAATTAGGAAA
Found at i:570622 original size:29 final size:28
Alignment explanation
Indices: 570590--570653 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
570580 AGATTATCGA
*
570590 TTTATATAAA-AATTATTAAATATTAATAT
1 TTTATATAAATAATAATT-AATA-TAATAT
* *
570619 TTTATTTAAATAATAATTAATATAATCT
1 TTTATATAAATAATAATTAATATAATAT
570647 TTT-TATA
1 TTTATATA
570654 CTTTTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 3 0.10
28 8 0.27
29 13 0.43
30 6 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTATATAAATAATAATTAATATAATAT
Found at i:576344 original size:45 final size:45
Alignment explanation
Indices: 576283--576403 Score: 188
Period size: 45 Copynumber: 2.7 Consensus size: 45
576273 TATTTTTTTG
* * *
576283 TTGATAATGTATCCATATGCATTTCAACTATTGTATACTCTTCTA
1 TTGATAATGTACCCATATACATTTCAACTATAGTATACTCTTCTA
* * *
576328 TTGATACTGTACCCATATACATTTCAACTATAGTATACTTTTCTG
1 TTGATAATGTACCCATATACATTTCAACTATAGTATACTCTTCTA
576373 TTGATAATGTACCCATATACATTTCAACTAT
1 TTGATAATGTACCCATATACATTTCAACTAT
576404 GGCATCCTTC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (45 bp):
TTGATAATGTACCCATATACATTTCAACTATAGTATACTCTTCTA
Found at i:576436 original size:90 final size:90
Alignment explanation
Indices: 576266--576440 Score: 210
Period size: 90 Copynumber: 1.9 Consensus size: 90
576256 CACTTTAAAT
* * * * * * **
576266 TATAATATATTTTTTTGTTGATAATGTATCCATATGCATTTCAACTATTGTATACTCTTCTATTG
1 TATAATATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATGGCATACTCTTCTACCG
* *
576331 ATACTGTACCCATATACATTTCAAC
66 ATAATGCACCCATATACATTTCAAC
*
576356 TATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATGGCAT-C-CTTCCATAC
1 TATAATATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATGGCATACTCTT-C-TAC
*
576419 CGATAATGCACCTATATACATT
64 CGATAATGCACCCATATACATT
576441 ATTATTTTCA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
88 3 0.04
89 2 0.03
90 66 0.93
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (90 bp):
TATAATATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATGGCATACTCTTCTACCG
ATAATGCACCCATATACATTTCAAC
Found at i:576728 original size:83 final size:83
Alignment explanation
Indices: 576589--576754 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
576579 ATTTTCATCT
576589 AGATTGCATACAAGAAATGTACTCACCTGACTTTCCTTGATAAGTGTCTAAAAAGTAAGGATGAT
1 AGATTGCATACAAGAAATGTACTCACCTGACTTTCCTTGATAAGTGTCTAAAAAGTAAGGATGAT
576654 TACTCCGGGAATTTGCCC
66 TACTCCGGGAATTTGCCC
576672 AGATTGCATACAAGAAATGTACTCACCTGACTTTCCTTGATAAGTGTCTAAAAAGTAAGGATGAT
1 AGATTGCATACAAGAAATGTACTCACCTGACTTTCCTTGATAAGTGTCTAAAAAGTAAGGATGAT
576737 TACTCCGGGAATTTGCCC
66 TACTCCGGGAATTTGCCC
576755 TTTCCCTTAG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (83 bp):
AGATTGCATACAAGAAATGTACTCACCTGACTTTCCTTGATAAGTGTCTAAAAAGTAAGGATGAT
TACTCCGGGAATTTGCCC
Found at i:576970 original size:20 final size:21
Alignment explanation
Indices: 576947--576986 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
576937 ATCGATTCTA
*
576947 CTACCCTA-GTACCGATACTT
1 CTACACTAGGTACCGATACTT
576967 CTACACTAGGGTACCGATAC
1 CTACACTA-GGTACCGATAC
576987 CCCTTCCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (21 bp):
CTACACTAGGTACCGATACTT
Found at i:577072 original size:22 final size:21
Alignment explanation
Indices: 577026--577084 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
577016 TTCGATGTTT
577026 CATGGTATCGATAC-CCTTAA
1 CATGGTATCGATACTCCTTAA
*
577046 CATGGTATCGATACTACCTT-G
1 CATGGTATCGATACT-CCTTAA
*
577067 CTATGGTACCGATACTCC
1 C-ATGGTATCGATACTCC
577085 CCTTACGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 14 0.41
21 3 0.09
22 17 0.50
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (21 bp):
CATGGTATCGATACTCCTTAA
Found at i:577121 original size:96 final size:96
Alignment explanation
Indices: 576976--577157 Score: 264
Period size: 97 Copynumber: 1.9 Consensus size: 96
576966 TCTACACTAG
* *
576976 GGTACCGATACCCCTTCCTGGTATTGATACCAAAATTAGGTTCGATGTTT-CATGGTATCGATAC
1 GGTACCGATACCCCTTACTGGTATCGATACCAAAATTAGGTTCGATGTTTGCATGGTATCGATAC
577040 CCTTA-ACATGGTATCGATACTACCTTGCTAT
66 CCTTACA-ATGGTATCGATACTACCTTGCTAT
* *
577071 GGTACCGATACTCCCCTTAC-GGTATCGATACCGAAATT-GGATTCGATGTTTGCTTGGTATCGA
1 GGTACCGATA--CCCCTTACTGGTATCGATACCAAAATTAGG-TTCGATGTTTGCATGGTATCGA
577134 TACCCTTACAATGGTATCGATACT
63 TACCCTTACAATGGTATCGATACT
577158 GTCTCAACGG
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
95 12 0.15
96 26 0.33
97 39 0.50
98 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (96 bp):
GGTACCGATACCCCTTACTGGTATCGATACCAAAATTAGGTTCGATGTTTGCATGGTATCGATAC
CCTTACAATGGTATCGATACTACCTTGCTAT
Found at i:581532 original size:10 final size:10
Alignment explanation
Indices: 581517--581543 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
581507 TTTTATTATT
581517 TCGGGTTGGG
1 TCGGGTTGGG
581527 TCGGGTTGGG
1 TCGGGTTGGG
581537 TCGGGTT
1 TCGGGTT
581544 TCTAAGTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.56, T:0.33
Consensus pattern (10 bp):
TCGGGTTGGG
Found at i:582946 original size:18 final size:19
Alignment explanation
Indices: 582923--582958 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
582913 ATATCCTAAA
582923 TTTACATATTAA-ATTAAT
1 TTTACATATTAACATTAAT
*
582941 TTTACATCTTAACATTAA
1 TTTACATATTAACATTAA
582959 AAAATATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTACATATTAACATTAAT
Found at i:583016 original size:29 final size:29
Alignment explanation
Indices: 582984--583207 Score: 166
Period size: 30 Copynumber: 7.6 Consensus size: 29
582974 TTAAATTATT
* * *
582984 AAATATATTTTGTTCTTGTCTTAACCTAA
1 AAATATATTTTATTCTTATCTTAACTTAA
583013 AAATATATTTTATTCTTAT-TCTAACTTAA
1 AAATATATTTTATTCTTATCT-TAACTTAA
* * *
583042 ATATATATTTTAATCTTTATCTAAACTTAA
1 AAATATATTTTATTC-TTATCTTAACTTAA
*
583072 AAATATATTTTATTCTTATCTTAACTTATT
1 AAATATATTTTATTCTTATCTTAACTTA-A
* * * * * *
583102 ACATAAATTATATTCTTAACTTAAGTTATT
1 AAATATATTTTATTCTTATCTTAACTTA-A
** * * *
583132 AAATATATGCTATTCTTACCTTAAATTATT
1 AAATATATTTTATTCTTATCTTAACTTA-A
* * *
583162 AAATATA-ATTAGTTTTTATTTTAACTT-A
1 AAATATATTTTA-TTCTTATCTTAACTTAA
* *
583190 AAACATCTTTTATTCTTA
1 AAATATATTTTATTCTTA
583208 AAAATATATT
Statistics
Matches: 157, Mismatches: 32, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
28 11 0.07
29 54 0.34
30 91 0.58
31 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (29 bp):
AAATATATTTTATTCTTATCTTAACTTAA
Found at i:583071 original size:30 final size:28
Alignment explanation
Indices: 582984--583099 Score: 142
Period size: 29 Copynumber: 4.0 Consensus size: 28
582974 TTAAATTATT
* * *
582984 AAATATATTTTGTTCTTGTCTTAACCTAA
1 AAATATATTTTATTCTTATC-TAACTTAA
583013 AAATATATTTTATTCTTATTCTAACTTAA
1 AAATATATTTTATTCTTA-TCTAACTTAA
* *
583042 ATATATATTTTAATCTTTATCTAAACTTAA
1 AAATATATTTTATTC-TTATCT-AACTTAA
583072 AAATATATTTTATTCTTATCTTAACTTA
1 AAATATATTTTATTCTTATC-TAACTTA
583100 TTACATAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
29 50 0.66
30 26 0.34
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (28 bp):
AAATATATTTTATTCTTATCTAACTTAA
Found at i:583118 original size:30 final size:30
Alignment explanation
Indices: 582946--583189 Score: 125
Period size: 30 Copynumber: 8.4 Consensus size: 30
582936 TTAATTTTAC
582946 ATCTTAAC--ATTAAA-AAA-TATATT-TT
1 ATCTTAACTTATTAAATAAATTATATTCTT
* * * * *
582971 ATATTAAATTATTAAATATATTTTGTTCTT
1 ATCTTAACTTATTAAATAAATTATATTCTT
* * * * *
583001 GTCTTAACCTA-AAAATATATTTTATTCTT
1 ATCTTAACTTATTAAATAAATTATATTCTT
* * *
583030 AT-TCTAACTTA--AATATATATTTTAATCTTT
1 ATCT-TAACTTATTAA-ATAAATTATATTC-TT
* * * *
583060 ATCTAAACTTA-AAAATATATTTTATTCTT
1 ATCTTAACTTATTAAATAAATTATATTCTT
*
583089 ATCTTAACTTATTACATAAATTATATTCTT
1 ATCTTAACTTATTAAATAAATTATATTCTT
* * * **
583119 AACTTAAGTTATTAAATATATGCTATTCTT
1 ATCTTAACTTATTAAATAAATTATATTCTT
* *
583149 ACCTTAAATTATTAAATATAATTAGT-TT-TT
1 ATCTTAACTTATTAAATA-AATTA-TATTCTT
*
583179 ATTTTAACTTA
1 ATCTTAACTTA
583190 AAACATCTTT
Statistics
Matches: 171, Mismatches: 35, Indels: 21
0.75 0.15 0.09
Matches are distributed among these distances:
25 6 0.04
27 6 0.04
28 5 0.03
29 51 0.30
30 95 0.56
31 7 0.04
32 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (30 bp):
ATCTTAACTTATTAAATAAATTATATTCTT
Found at i:583225 original size:25 final size:25
Alignment explanation
Indices: 583197--583257 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
583187 TTAAAACATC
583197 TTTTATTCTTAAAAATATATTTT-T
1 TTTTATTCTTAAAAATATATTTTAT
* *
583221 ATTTTA-ACTACAAAAATATATTTTAT
1 -TTTTATTCT-TAAAAATATATTTTAT
583247 TTTTATT-TTAA
1 TTTTATTCTTAA
583258 CTACAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
24 4 0.14
25 24 0.83
26 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTATTCTTAAAAATATATTTTAT
Found at i:583248 original size:30 final size:30
Alignment explanation
Indices: 583212--583287 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
583202 TTCTTAAAAA
583212 TATATTTTTATTTTAACTACAAAAATATAT
1 TATATTTTTATTTTAACTACAAAAATATAT
*
583242 TTTATTTTTATTTTAACTACAAAAATATAT
1 TATATTTTTATTTTAACTACAAAAATATAT
*
583272 TATATTTTTATCTTAA
1 TATATTTTTATTTTAA
583288 ATATAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (30 bp):
TATATTTTTATTTTAACTACAAAAATATAT
Found at i:583355 original size:31 final size:28
Alignment explanation
Indices: 583320--583468 Score: 106
Period size: 30 Copynumber: 5.1 Consensus size: 28
583310 AATATAAATA
583320 TTTAAGTTAAGATAATAATAAATTATATTTT
1 TTTAAGTTAAGATAA-AATAAA-TATA-TTT
* * *
583351 TTTAATTTGAGATAAAATTAACATTTATTT
1 TTTAAGTTAAGATAAAA-TAA-ATATATTT
* *
583381 TTTAAATTGAAAATAAAAATAAATATA-TT
1 TTTAAGTT-AAGAT-AAAATAAATATATTT
* * *
583410 TTTAGGTTACGAAAATAATAAAATATATTT
1 TTTAAGTTAAGATAA-AAT-AAATATATTT
**
583440 AATAAGTTAAGAT-AAA-AAATATATTT
1 TTTAAGTTAAGATAAAATAAATATATTT
583466 TTT
1 TTT
583469 GATGAGAACA
Statistics
Matches: 92, Mismatches: 19, Indels: 19
0.71 0.15 0.15
Matches are distributed among these distances:
26 11 0.12
27 2 0.02
28 7 0.08
29 16 0.17
30 26 0.28
31 25 0.27
32 5 0.05
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.44
Consensus pattern (28 bp):
TTTAAGTTAAGATAAAATAAATATATTT
Found at i:583384 original size:30 final size:30
Alignment explanation
Indices: 583331--583412 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
583321 TTAAGTTAAG
* * *
583331 ATAATAATAAATTATATTTTTTTAATTTG-AG
1 ATAAAAATAAA-TATA-TTTTTTAAATTGAAA
* *
583362 ATAAAATTAACATTTATTTTTTAAATTGAAA
1 ATAAAAATAA-ATATATTTTTTAAATTGAAA
583393 ATAAAAATAAATATATTTTT
1 ATAAAAATAAATATATTTTT
583413 AGGTTACGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
30 20 0.48
31 21 0.50
32 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.48
Consensus pattern (30 bp):
ATAAAAATAAATATATTTTTTAAATTGAAA
Found at i:584109 original size:11 final size:11
Alignment explanation
Indices: 584078--584106 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
584068 AGAAAAATAT
584078 ATTAAATTAAA
1 ATTAAATTAAA
584089 ATTAAATTAAA
1 ATTAAATTAAA
584100 A-TAAATT
1 ATTAAATT
584107 TAATCGTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTAAATTAAA
Found at i:584471 original size:24 final size:23
Alignment explanation
Indices: 584427--584471 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
584417 TTTACCCTTT
*
584427 ATTTTTAAATAATTTACCATTAA
1 ATTTTTAAATAATTTAACATTAA
*
584450 ATTTTTAACTAATTTATACATT
1 ATTTTTAAATAATTTA-ACATT
584472 GAGCCCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTTAAATAATTTAACATTAA
Found at i:587523 original size:20 final size:20
Alignment explanation
Indices: 587498--587553 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
587488 ATTCGCGTTG
*
587498 CATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTC
587518 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
*
587538 CAGTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
587554 AGTTGAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:587662 original size:20 final size:20
Alignment explanation
Indices: 587639--587735 Score: 113
Period size: 20 Copynumber: 4.8 Consensus size: 20
587629 ATTCGCATTG
*
587639 CATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTC
*
587659 CATTTGGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* * *
587679 CAGTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* **
587700 AAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
587720 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
587736 AGTCTACAGT
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:587681 original size:141 final size:141
Alignment explanation
Indices: 587427--587707 Score: 508
Period size: 141 Copynumber: 2.0 Consensus size: 141
587417 TGGATTTGCG
*
587427 AAAATGACCAACAAAATCGCAATGCAATCTCTAATTCGCATTGCGATCTCCACAATCGTAAATTC
1 AAAATGACCAACAAAATCGCAATGCAATCTCTAATTCGCATTGCGATCTCCACAATCGCAAATTC
*
587492 GCGTTGCATTTCGCGTTGCGATTTTTCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
66 GCATTGCATTTCGCGTTGCGATTTTTCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
587557 TGAAAATCGCA
131 TGAAAATCGCA
* * *
587568 AAAATGACCAACAAAATCTCAATGCGATCTCTAATTCGCATTGCGATCTCCACTATCGCAAATTC
1 AAAATGACCAACAAAATCGCAATGCAATCTCTAATTCGCATTGCGATCTCCACAATCGCAAATTC
*
587633 GCATTGCATTTCGCGTTGCGATTTTTCATTTGGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
66 GCATTGCATTTCGCGTTGCGATTTTTCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
587698 TGAAAATCGC
131 TGAAAATCGC
587708 GTTGCGATTT
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
141 134 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (141 bp):
AAAATGACCAACAAAATCGCAATGCAATCTCTAATTCGCATTGCGATCTCCACAATCGCAAATTC
GCATTGCATTTCGCGTTGCGATTTTTCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
TGAAAATCGCA
Found at i:587755 original size:22 final size:22
Alignment explanation
Indices: 587727--587812 Score: 97
Period size: 22 Copynumber: 4.0 Consensus size: 22
587717 TTCCATTTCG
587727 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
587749 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
*
587768 CGTTGCTATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
587790 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
587812 C
1 C
587813 AAAATTCTTG
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
19 9 0.18
20 5 0.10
21 5 0.10
22 30 0.61
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:587772 original size:41 final size:41
Alignment explanation
Indices: 587666--587798 Score: 146
Period size: 41 Copynumber: 3.2 Consensus size: 41
587656 TTTCATTTGG
* * * *
587666 CGTTGCGATTTTCCAGTTCGCGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCT-ACAGTTGT
*
587707 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTACAGTTGT
*
587749 CGTTGCGATTTTCCAAATT-CGTTGCTATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-AATTCCGTTGCGATAGTCTACAGTTGT
*
587790 TGTTGCGAT
1 CGTTGCGAT
587799 AGTCTACAGT
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
41 64 0.78
42 15 0.18
43 3 0.04
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCCAATTCCGTTGCGATAGTCTACAGTTGT
Found at i:588578 original size:21 final size:22
Alignment explanation
Indices: 588533--588583 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
588523 AATTTGGAAA
*
588533 ATCGCAACGACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
588555 ATCGCAACAACAACTGTA-ACT
1 ATCGCAACAACAACTGTAGACT
588576 ATCGCAAC
1 ATCGCAAC
588584 GCGAAATGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (22 bp):
ATCGCAACAACAACTGTAGACT
Found at i:588601 original size:20 final size:20
Alignment explanation
Indices: 588576--588669 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
588566 AACTGTAACT
588576 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
588596 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
588617 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
588637 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
588657 ATCGCAACGCGAA
1 ATCGCAACGCGAA
588670 TTTGCGATAG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 48 0.76
21 15 0.24
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:588676 original size:28 final size:28
Alignment explanation
Indices: 588645--588699 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
588635 AAATCGCAAC
588645 GCGA-AATGGAAAATCGCAACGCGAATTT
1 GCGATAATGG-AAATCGCAACGCGAATTT
* * *
588673 GCGATAGTGGAGATCGCAATGCGAATT
1 GCGATAATGGAAATCGCAACGCGAATT
588700 AGAGATCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (28 bp):
GCGATAATGGAAATCGCAACGCGAATTT
Found at i:594897 original size:2 final size:2
Alignment explanation
Indices: 594890--594921 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
594880 AATAATTATT
594890 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
594922 TAATAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:594942 original size:24 final size:26
Alignment explanation
Indices: 594891--594975 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 26
594881 ATAATTATTT
* * * *
594891 ATATATATATATATATATATATATATA
1 ATATAAATATATATTTA-ATTTAAATA
*
594918 ATATTAATA-A-ATTTAATTTAAATA
1 ATATAAATATATATTTAATTTAAATA
594942 A-A-AAATATATATTTAATTTAAAT-
1 ATATAAATATATATTTAATTTAAATA
*
594965 ATATATATATA
1 ATATAAATATA
594976 CCCGGCCTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
22 4 0.09
23 3 0.06
24 22 0.47
25 10 0.21
26 1 0.02
27 7 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATAAATATATATTTAATTTAAATA
Found at i:594957 original size:19 final size:19
Alignment explanation
Indices: 594933--594972 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
594923 AATAAATTTA
594933 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
594952 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
594971 AT
1 AT
594973 ATACCCGGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:595000 original size:23 final size:23
Alignment explanation
Indices: 594973--595024 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
594963 ATATATATAT
* *
594973 ATACCCGGCCTAATA-CGGACCCA
1 ATACCCGACCCAATACCGG-CCCA
594996 ATACCCGACCCAATACCCGGCCCA
1 ATACCCGACCCAATA-CCGGCCCA
595020 ATACC
1 ATACC
595025 TGTTTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.52
24 9 0.36
25 3 0.12
ACGTcount: A:0.31, C:0.44, G:0.13, T:0.12
Consensus pattern (23 bp):
ATACCCGACCCAATACCGGCCCA
Found at i:595005 original size:12 final size:12
Alignment explanation
Indices: 594990--595024 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
594980 GCCTAATACG
594990 GACCCAATACCC
1 GACCCAATACCC
595002 GACCCAATACCC
1 GACCCAATACCC
*
595014 GGCCCAATACC
1 GACCCAATACC
595025 TGTTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.31, C:0.49, G:0.11, T:0.09
Consensus pattern (12 bp):
GACCCAATACCC
Found at i:596812 original size:65 final size:65
Alignment explanation
Indices: 596708--596838 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
596698 ACATTCTATA
596708 ACATAATCTGAGTGCCAATTGGGATGTCTTCTTACACGATCTGATTGACGAGTTGTTGGAGCTTC
1 ACATAATCTGAGTGCCAATTGGGATGTCTTCTTACACGATCTGATTGACGAGTTGTTGGAGCTTC
596773 ACATAATCTGAGTGCCAATTGGGATGTCTTCTTACACGATCTGATTGACGAGTTGTTGGAGCTTC
1 ACATAATCTGAGTGCCAATTGGGATGTCTTCTTACACGATCTGATTGACGAGTTGTTGGAGCTTC
596838 A
1 A
596839 GAACTCTCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (65 bp):
ACATAATCTGAGTGCCAATTGGGATGTCTTCTTACACGATCTGATTGACGAGTTGTTGGAGCTTC
Found at i:601961 original size:16 final size:16
Alignment explanation
Indices: 601940--601980 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
601930 CAATGAACAT
601940 TGAGCTTAACGAGTAA
1 TGAGCTTAACGAGTAA
601956 TGAGCTTAACGAGTAA
1 TGAGCTTAACGAGTAA
601972 TGAGCTTAA
1 TGAGCTTAA
601981 TGAGCAACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (16 bp):
TGAGCTTAACGAGTAA
Found at i:608363 original size:21 final size:23
Alignment explanation
Indices: 608319--608364 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
608309 TGGTGGTTGG
608319 TTTAATGGATGTTTAAACTTTAT
1 TTTAATGGATGTTTAAACTTTAT
*
608342 TTTAATGG-TGTTT-AAGTTTAT
1 TTTAATGGATGTTTAAACTTTAT
608363 TT
1 TT
608365 GGTTCTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 5 0.23
23 8 0.36
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (23 bp):
TTTAATGGATGTTTAAACTTTAT
Found at i:609583 original size:196 final size:197
Alignment explanation
Indices: 609249--609642 Score: 781
Period size: 196 Copynumber: 2.0 Consensus size: 197
609239 AATTTGAGTT
609249 CCCCCATAGGTAATGACAAAGACCCTGATGAGGTTCAGGATTAGCTTCCGATTATACCAAATCTG
1 CCCCCATAGGTAATGACAAAGACCCTGATGAGGTTCAGGATTAGCTTCCGATTATACCAAATCTG
609314 AGTTTATTGAGGGAGTTTGGTCGTCTAAAATCCAATCAAATTCATTGCGATATGGATATTCGAGA
66 AGTTTATTGAGGGAGTTTGGTCGTCTAAAATCCAATCAAATTCATTGCGATATGGATATTCGAGA
609379 AAGATCTAGACAAGACAGAAGATGTGGGCATTGTAGAAACCCATGACACACTA-AAAAACATGTT
131 AAGATCTAGACAAGACAGAAGATGTGGGCATTGTAGAAACCCATGACACACTAGAAAAACATGTT
609443 CA
196 CA
609445 CCCCCATAGGTAATGACAAAGACCCTGATGAGGTTCAGGATTAGCTTCCGATTATACCAAATCTG
1 CCCCCATAGGTAATGACAAAGACCCTGATGAGGTTCAGGATTAGCTTCCGATTATACCAAATCTG
609510 AGTTTATTGAGGGAGTTTGGTCGTCTAAAATCCAATCAAATTCATTGCGATATGGATATTCGAGA
66 AGTTTATTGAGGGAGTTTGGTCGTCTAAAATCCAATCAAATTCATTGCGATATGGATATTCGAGA
609575 AAGATCTAGACAAGACAGAAGATGTGGGCATTGTAGAAACCCATGACACACTAGAAAAACATGTT
131 AAGATCTAGACAAGACAGAAGATGTGGGCATTGTAGAAACCCATGACACACTAGAAAAACATGTT
609640 CA
196 CA
609642 C
1 C
609643 TTATGTTGTC
Statistics
Matches: 197, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
196 183 0.93
197 14 0.07
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (197 bp):
CCCCCATAGGTAATGACAAAGACCCTGATGAGGTTCAGGATTAGCTTCCGATTATACCAAATCTG
AGTTTATTGAGGGAGTTTGGTCGTCTAAAATCCAATCAAATTCATTGCGATATGGATATTCGAGA
AAGATCTAGACAAGACAGAAGATGTGGGCATTGTAGAAACCCATGACACACTAGAAAAACATGTT
CA
Found at i:612145 original size:17 final size:16
Alignment explanation
Indices: 612119--612173 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
612109 AATTAAATAC
*
612119 AATATTAAATAATTTA
1 AATATTAAATAAATTA
612135 AATACTTAAATAAATTA
1 AATA-TTAAATAAATTA
* *
612152 AATATAAAATATAATAA
1 AATATTAAATA-AATTA
612169 AATAT
1 AATAT
612174 ACCTTAAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 10 0.29
17 24 0.71
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATTAAATAAATTA
Found at i:612174 original size:17 final size:16
Alignment explanation
Indices: 612112--612174 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
612102 AAAATTTAAT
* *
612112 TAAATACAATATTAAA
1 TAAATAAAATATAAAA
* * *
612128 TAATTTAAATACTTAAA
1 TAAATAAAATA-TAAAA
*
612145 TAAATTAAATATAAAA
1 TAAATAAAATATAAAA
612161 TATAATAAAATATA
1 TA-AATAAAATATA
612175 CCTTAAACAG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
16 14 0.36
17 25 0.64
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAATAAAATATAAAA
Found at i:612215 original size:10 final size:10
Alignment explanation
Indices: 612200--612236 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
612190 ATAAAAGTAT
*
612200 TTGAGAGAGG
1 TTGAGAGAAG
*
612210 TTGAGAGAAT
1 TTGAGAGAAG
612220 TTGAGAGAAG
1 TTGAGAGAAG
612230 TTGAGAG
1 TTGAGAG
612237 GATTTGGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.41, T:0.24
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:612221 original size:20 final size:20
Alignment explanation
Indices: 612198--612242 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
612188 ATATAAAAGT
*
612198 ATTTGAGAGAGGTTGAGAGA
1 ATTTGAGAGAAGTTGAGAGA
*
612218 ATTTGAGAGAAGTTGAGAGG
1 ATTTGAGAGAAGTTGAGAGA
612238 ATTTG
1 ATTTG
612243 GTGTGATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.29
Consensus pattern (20 bp):
ATTTGAGAGAAGTTGAGAGA
Found at i:619262 original size:30 final size:31
Alignment explanation
Indices: 619190--619267 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 31
619180 ATCAGATTAG
*
619190 CACTATAGTGTGTAAGGACACTTAATACAGT
1 CACTATAGTGTGTAAGGACACTTAATACAAT
* *
619221 -ACTATAATGTGTAAGGACACTTAGTA-AAT
1 CACTATAGTGTGTAAGGACACTTAATACAAT
*
619250 CACTGTAGTGTGTAAGGA
1 CACTATAGTGTGTAAGGA
619268 TGCACAGGGC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 2 0.05
30 39 0.95
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (31 bp):
CACTATAGTGTGTAAGGACACTTAATACAAT
Found at i:620930 original size:20 final size:20
Alignment explanation
Indices: 620905--620951 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
620895 CCTCTAGATT
*
620905 GAGATGTAGAAATTGAAATA
1 GAGATGTAAAAATTGAAATA
620925 GAGATGTAAAAATTGAAATA
1 GAGATGTAAAAATTGAAATA
*
620945 AAGATGT
1 GAGATGT
620952 TTTAAGGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (20 bp):
GAGATGTAAAAATTGAAATA
Found at i:625617 original size:34 final size:34
Alignment explanation
Indices: 625567--625683 Score: 152
Period size: 34 Copynumber: 3.6 Consensus size: 34
625557 TATCACTAAA
* *
625567 GTGTGTAAGAAAACTTAGTTCATATGGTACTATG
1 GTGTGTAAGGACACTTAGTTCATATGGTACTATG
* *
625601 GTGTGTAAGGACACTTAGTGCATATGGTAATATG
1 GTGTGTAAGGACACTTAGTTCATATGGTACTATG
* *
625635 GTGTGTAAGGACACTTAG-T-ACAT--TACTATA
1 GTGTGTAAGGACACTTAGTTCATATGGTACTATG
625665 GTGTGTAAGGACACTTAGT
1 GTGTGTAAGGACACTTAGT
625684 ATAGCACTGT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
30 23 0.31
32 3 0.04
34 48 0.65
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (34 bp):
GTGTGTAAGGACACTTAGTTCATATGGTACTATG
Found at i:625671 original size:30 final size:30
Alignment explanation
Indices: 625561--625709 Score: 136
Period size: 34 Copynumber: 4.7 Consensus size: 30
625551 TCAGATTATC
* * *
625561 ACTAAAGTGTGTAAGAAAACTTAGTTCATATGGT
1 ACTATAGTGTGTAAGGACACTTAG-T-ATAT--T
*
625595 ACTATGGTGTGTAAGGACACTTAGTGCATATGGT
1 ACTATAGTGTGTAAGGACACTTAGT--ATAT--T
* * *
625629 AATATGGTGTGTAAGGACACTTAGTACATT
1 ACTATAGTGTGTAAGGACACTTAGTATATT
**
625659 ACTATAGTGTGTAAGGACACTTAGTATAGC
1 ACTATAGTGTGTAAGGACACTTAGTATATT
*
625689 ACTGTAGTGTGTAAGGACACT
1 ACTATAGTGTGTAAGGACACT
625710 CAGTGCAACA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
30 46 0.45
32 3 0.03
33 1 0.01
34 52 0.51
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (30 bp):
ACTATAGTGTGTAAGGACACTTAGTATATT
Found at i:625729 original size:30 final size:30
Alignment explanation
Indices: 625633--625774 Score: 149
Period size: 30 Copynumber: 4.7 Consensus size: 30
625623 TATGGTAATA
* * ** *
625633 TGGTGTGTAAGGACACTTAGTACATTACTA
1 TGGTGTGTAAGGACACTCAGTGCAACACTG
* * ** *
625663 TAGTGTGTAAGGACACTTAGTATAGCACTG
1 TGGTGTGTAAGGACACTCAGTGCAACACTG
* *
625693 TAGTGTGTAAGGACACTCAGTGCAACATTG
1 TGGTGTGTAAGGACACTCAGTGCAACACTG
*
625723 TGGTGTGTTAGGACACTCAGTGCAACACTG
1 TGGTGTGTAAGGACACTCAGTGCAACACTG
* *
625753 TGCTGTGTTAGGACACTCAGTG
1 TGGTGTGTAAGGACACTCAGTG
625775 TATATGGTAA
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 98 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (30 bp):
TGGTGTGTAAGGACACTCAGTGCAACACTG
Found at i:629675 original size:61 final size:61
Alignment explanation
Indices: 629610--629765 Score: 224
Period size: 61 Copynumber: 2.6 Consensus size: 61
629600 GAAACTACAC
* * *
629610 CTAAAGTCTTTGAATT-AAAGGCTAAAGTTATAATAAATAACAAACTGAAAGAATTTAAAAT
1 CTAAAGGCTTT-AATTAAAAGACTAAAGTTATAATAAATAACAAACTAAAAGAATTTAAAAT
* * *
629671 CTAAAGGCTCTAATTAAAAGACTAAAGTTATAGTAAATAGCAAACTAAAAGAATTTAAAAT
1 CTAAAGGCTTTAATTAAAAGACTAAAGTTATAATAAATAACAAACTAAAAGAATTTAAAAT
* *
629732 CGAAAGGCTTTAATTAAAAGACTAAAGTTCTAAT
1 CTAAAGGCTTTAATTAAAAGACTAAAGTTATAAT
629766 TTTAAAGTCT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 4 0.05
61 80 0.95
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (61 bp):
CTAAAGGCTTTAATTAAAAGACTAAAGTTATAATAAATAACAAACTAAAAGAATTTAAAAT
Found at i:631296 original size:16 final size:17
Alignment explanation
Indices: 631264--631303 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
631254 AAAATTATAT
*
631264 AATGTGTTTATTTTGTA
1 AATGTATTTATTTTGTA
631281 AATGTATTTA-TTTGTA
1 AATGTATTTATTTTGTA
631297 ATATGTA
1 A-ATGTA
631304 CATGGGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (17 bp):
AATGTATTTATTTTGTA
Found at i:631380 original size:25 final size:23
Alignment explanation
Indices: 631351--631396 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
631341 TTTATTTACT
*
631351 TAAAATAGTTTGGATTTATATAATA
1 TAAAATA-TTTGAATTTA-ATAATA
631376 TAAAATATTTGAATTTAATAA
1 TAAAATATTTGAATTTAATAA
631397 CATGGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 9 0.45
25 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (23 bp):
TAAAATATTTGAATTTAATAATA
Found at i:631424 original size:11 final size:11
Alignment explanation
Indices: 631408--631450 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 11
631398 ATGGTTTATG
631408 TAATATGTATA
1 TAATATGTATA
631419 TAATATGGTTTATA
1 TAATAT-G--TATA
631433 TAATATGTATA
1 TAATATGTATA
631444 TAATATG
1 TAATATG
631451 GTTTATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 17 0.59
12 1 0.03
13 1 0.03
14 10 0.34
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (11 bp):
TAATATGTATA
Found at i:631427 original size:25 final size:25
Alignment explanation
Indices: 631393--631472 Score: 124
Period size: 25 Copynumber: 3.2 Consensus size: 25
631383 TTTGAATTTA
* *
631393 ATAACATGGTTTATGTAATATGTAT
1 ATAATATGGTTTATATAATATGTAT
631418 ATAATATGGTTTATATAATATGTAT
1 ATAATATGGTTTATATAATATGTAT
* *
631443 ATAATATGGTTTATATAATACGCAT
1 ATAATATGGTTTATATAATATGTAT
631468 ATAAT
1 ATAAT
631473 GAGGTCATCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (25 bp):
ATAATATGGTTTATATAATATGTAT
Found at i:631434 original size:14 final size:14
Alignment explanation
Indices: 631389--631462 Score: 81
Period size: 14 Copynumber: 5.8 Consensus size: 14
631379 AATATTTGAA
*
631389 TTTA-ATAACATGG
1 TTTATATAATATGG
*
631402 TTTATGTAATAT-G
1 TTTATATAATATGG
631415 --TATATAATATGG
1 TTTATATAATATGG
631427 TTTATATAATAT-G
1 TTTATATAATATGG
631440 --TATATAATATGG
1 TTTATATAATATGG
631452 TTTATATAATA
1 TTTATATAATA
631463 CGCATATAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
11 19 0.37
12 2 0.04
13 6 0.12
14 24 0.47
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.47
Consensus pattern (14 bp):
TTTATATAATATGG
Found at i:633175 original size:18 final size:19
Alignment explanation
Indices: 633133--633176 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
633123 TTGTTCTTCG
633133 GGTATCAATAATCAAGGCAT
1 GGTATCAATAATCAAGG-AT
633153 GGTATCAATAAT-AGAGG-T
1 GGTATCAATAATCA-AGGAT
633171 GGTATC
1 GGTATC
633177 GGTACAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.30
19 1 0.04
20 15 0.65
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (19 bp):
GGTATCAATAATCAAGGAT
Found at i:636657 original size:33 final size:28
Alignment explanation
Indices: 636579--636647 Score: 138
Period size: 28 Copynumber: 2.5 Consensus size: 28
636569 GATGTGTATA
636579 TTTCTGCACTGTTCGAATCAAATCAGTT
1 TTTCTGCACTGTTCGAATCAAATCAGTT
636607 TTTCTGCACTGTTCGAATCAAATCAGTT
1 TTTCTGCACTGTTCGAATCAAATCAGTT
636635 TTTCTGCACTGTT
1 TTTCTGCACTGTT
636648 TTGTTCGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (28 bp):
TTTCTGCACTGTTCGAATCAAATCAGTT
Found at i:636812 original size:10 final size:10
Alignment explanation
Indices: 636797--636851 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
636787 AGTTCGTTGA
636797 AAATAAAACG
1 AAATAAAACG
*
636807 AAATAAAACAA
1 AAATAAAAC-G
*
636818 AAATAAAACAA
1 AAATAAAAC-G
636829 AAATAAAACG
1 AAATAAAACG
*
636839 AAATAAAATG
1 AAATAAAACG
636849 AAA
1 AAA
636852 CGAAATGGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
10 21 0.51
11 20 0.49
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.11
Consensus pattern (10 bp):
AAATAAAACG
Found at i:636821 original size:11 final size:10
Alignment explanation
Indices: 636796--636846 Score: 66
Period size: 11 Copynumber: 4.9 Consensus size: 10
636786 AAGTTCGTTG
636796 AAAATAAAAC
1 AAAATAAAAC
*
636806 GAAATAAAAC
1 AAAATAAAAC
636816 AAAAATAAAAC
1 -AAAATAAAAC
636827 AAAAATAAAAC
1 -AAAATAAAAC
*
636838 GAAATAAAA
1 AAAATAAAA
636847 TGAAACGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
10 17 0.46
11 20 0.54
ACGTcount: A:0.78, C:0.08, G:0.04, T:0.10
Consensus pattern (10 bp):
AAAATAAAAC
Found at i:640534 original size:42 final size:43
Alignment explanation
Indices: 640482--640588 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 43
640472 TTAAAACTCT
*
640482 TAAAAGTATTTAAACTAAAATACCTAAA-AC-AAATAAAA-AA
1 TAAAACTATTTAAACTAAAATACCTAAATACTAAATAAAATAA
* * * *
640522 TAAAATACTATTTAAAATAATAT-CCTAAATCCTAATTAAAATAA
1 T-AAA-ACTATTTAAACTAAAATACCTAAATACTAAATAAAATAA
*
640566 TAAACCTATTTAAACTAAAATAC
1 TAAAACTATTTAAACTAAAATAC
640589 AAAGATAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
40 1 0.02
41 9 0.17
42 29 0.55
43 11 0.21
44 3 0.06
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.29
Consensus pattern (43 bp):
TAAAACTATTTAAACTAAAATACCTAAATACTAAATAAAATAA
Found at i:640573 original size:25 final size:24
Alignment explanation
Indices: 640524--640573 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
640514 ATAAAAAATA
* *
640524 AAATACTATTTAAAATAATATCCT
1 AAATACTAATTAAAATAATAACCT
*
640548 AAATCCTAATTAAAATAATAAACCT
1 AAATACTAATTAAAATAAT-AACCT
640573 A
1 A
640574 TTTAAACTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATACTAATTAAAATAATAACCT
Found at i:644262 original size:19 final size:19
Alignment explanation
Indices: 644238--644275 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
644228 ATAATTAGAA
644238 TAAGATACATATTTTGATC
1 TAAGATACATATTTTGATC
644257 TAAGATACATATTTTGATC
1 TAAGATACATATTTTGATC
644276 GTATTCTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (19 bp):
TAAGATACATATTTTGATC
Found at i:644517 original size:2 final size:2
Alignment explanation
Indices: 644493--644561 Score: 101
Period size: 2 Copynumber: 36.5 Consensus size: 2
644483 AAAAGTAATA
*
644493 AT AT AT A- AT AT -T AG AT AT A- AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
644531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
644562 ATTATACACC
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
1 4 0.07
2 57 0.93
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:652248 original size:85 final size:85
Alignment explanation
Indices: 652131--652301 Score: 333
Period size: 85 Copynumber: 2.0 Consensus size: 85
652121 TAATGAGGAA
652131 CAAAGTAGTAATTTACCATTGTTTGAAAAAAAGGTTGATCTCTCATTAAGATGCCTATGTCATAC
1 CAAAGTAGTAATTTACCATTGTTTGAAAAAAAGGTTGATCTCTCATTAAGATGCCTATGTCATAC
652196 GTTGGGAAGAGAAAGTCATT
66 GTTGGGAAGAGAAAGTCATT
*
652216 CAAAGTAGTAATTTATCATTGTTTGAAAAAAAGGTTGATCTCTCATTAAGATGCCTATGTCATAC
1 CAAAGTAGTAATTTACCATTGTTTGAAAAAAAGGTTGATCTCTCATTAAGATGCCTATGTCATAC
652281 GTTGGGAAGAGAAAGTCATT
66 GTTGGGAAGAGAAAGTCATT
652301 C
1 C
652302 CCCTTCCTTT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (85 bp):
CAAAGTAGTAATTTACCATTGTTTGAAAAAAAGGTTGATCTCTCATTAAGATGCCTATGTCATAC
GTTGGGAAGAGAAAGTCATT
Found at i:654638 original size:14 final size:14
Alignment explanation
Indices: 654615--654652 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
654605 AAAAGATATT
*
654615 TAAATAAATAATTAA
1 TAAATTAATAA-TAA
654630 -AAATTAATAATAA
1 TAAATTAATAATAA
654643 TAAATTAATA
1 TAAATTAATA
654653 CTGCATATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 18 0.86
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAATTAATAATAA
Found at i:677227 original size:15 final size:15
Alignment explanation
Indices: 677207--677237 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
677197 TGAGACATTA
*
677207 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
677222 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
677237 C
1 C
677238 TCACCCAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.68, G:0.16, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:679862 original size:13 final size:14
Alignment explanation
Indices: 679834--679863 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
679824 GTTTCATAAA
679834 AATTGAAAACCCCT
1 AATTGAAAACCCCT
679848 AATTGAAAA-CCCT
1 AATTGAAAACCCCT
679861 AAT
1 AAT
679864 AGATGAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (14 bp):
AATTGAAAACCCCT
Found at i:681991 original size:54 final size:54
Alignment explanation
Indices: 681909--682530 Score: 786
Period size: 54 Copynumber: 11.6 Consensus size: 54
681899 CCGAATCGAA
*
681909 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAACCGTATCAGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAGC
* * * *
681963 ACTAAGTGTACAACCCACGGGATTCATAACAAGTTTATGAACGACCGTATC-GC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAGC
* * *
682016 AACTAATTGTGCAACCCACAGAATTCATATTAAGTTTATGAACAACCGTATCAGC
1 -ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAGC
* * *
682071 ACTAAGTGTGCAA-CCATAGAATTCATAATAAGTTTATGAACGATCGTAT-AGT
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAGC
* * * *
682123 ACTAAGTGTGCACCCCACGGAATTCATAATAAGTTTATGAACTACCGTATCGGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAGC
* * * * **
682177 ACTAAATGTGCAACCCACAAAATTCATAGTAAGTTTATGAACGATCGTATTGGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAGC
* * * * *
682231 TCTAAGTGTGCAACCCACAGAATTCATAATAAGTATATGAAAGACCATATCGGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAGC
* * *
682285 ACTAAATGTGCAACCCACAGAATTCATAATAAGTTTATGAACGATCGTATCGGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAGC
* *
682339 ACTACGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGACCGTATCAGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAGC
* * **
682393 ACTAAGTGTGCAACCTACAAAATTCATAATAAGTTTATGAACGATTGTATC-GAC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAG-C
* * * * * *
682447 ACTAAGTGTGCAACCCACAGAATTTATAATGAGCTTATGAATGACTGTATCGGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAGC
* * *
682501 ACTACGTGTGCACCCCAAAGAACTT-ATAAT
1 ACTAAGTGTGCAACCCACAGAA-TTCATAAT
682531 GATTTGAAAA
Statistics
Matches: 493, Mismatches: 68, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
52 14 0.03
53 67 0.14
54 407 0.83
55 5 0.01
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (54 bp):
ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCAGC
Done.