Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 69 of 161
Found at i:21443384 original size:50 final size:53
Alignment explanation
Indices: 21443272--21443420 Score: 171
Period size: 50 Copynumber: 2.8 Consensus size: 53
21443262 ATTTGGGTAA
* * * *
21443272 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGACTATG
1 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCATCA-CGAGA--ATG
*
21443328 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-CGAG-ATG
1 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGAATG
* *
21443378 AGAGGTCCCT-CGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AGAGGT-CCTATGTAAGACCATGTCTGGGACATGGCATTGGCAT
21443421 GTTATTATCA
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
50 39 0.46
51 3 0.04
53 3 0.04
55 1 0.01
56 38 0.45
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.24
Consensus pattern (53 bp):
AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGAATG
Found at i:21447628 original size:18 final size:19
Alignment explanation
Indices: 21447591--21447628 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
21447581 AATACTAAAA
*
21447591 TTCACATATTTGACATTTT
1 TTCACATATTTGACACTTT
*
21447610 TTCA-ATATTTTACACTTT
1 TTCACATATTTGACACTTT
21447628 T
1 T
21447629 ACCGTAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.26, C:0.16, G:0.03, T:0.55
Consensus pattern (19 bp):
TTCACATATTTGACACTTT
Found at i:21452440 original size:27 final size:27
Alignment explanation
Indices: 21452410--21452587 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
21452400 ATATTGAGTC
* * *
21452410 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
21452437 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
21452464 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
21452492 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* * **
21452519 TGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
21452546 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
21452573 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
21452588 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:21461660 original size:27 final size:27
Alignment explanation
Indices: 21461630--21461761 Score: 178
Period size: 27 Copynumber: 4.9 Consensus size: 27
21461620 GGTTATAACA
21461630 ATCATTTTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
21461657 ATCATTTTATCCTATAGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
**
21461684 ATCATTTTACCCTATGAAGGTATTTC-
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
21461710 AGTCATTTTACCTTATGGGGGTATTTTG
1 A-TCATTTTACCCTATGGGGGTATTTCG
*
21461738 GTCA-TTTACCCTATGGGGGTATTT
1 ATCATTTTACCCTATGGGGGTATTT
21461762 TGGTGCAGAT
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
26 20 0.22
27 71 0.78
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (27 bp):
ATCATTTTACCCTATGGGGGTATTTCG
Found at i:21461675 original size:54 final size:54
Alignment explanation
Indices: 21461617--21461733 Score: 139
Period size: 54 Copynumber: 2.2 Consensus size: 54
21461607 TTTCATCTCC
* **
21461617 TAGGGTTATAACAATCATTTTACCCTATGGGGGTATTTC-GATCATTTTATCCTA
1 TAGGGGTATAACAATCATTTTACCCTATGAAGGTATTTCAG-TCATTTTATCCTA
** *
21461671 TAGGGGTATTTCGATCATTTTACCCTATGAAGGTATTTCAGTCATTTTA-CCTTA
1 TAGGGGTATAACAATCATTTTACCCTATGAAGGTATTTCAGTCATTTTATCC-TA
*
21461725 TGGGGGTAT
1 TAGGGGTAT
21461734 TTTGGTCATT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 2 0.04
54 51 0.94
55 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (54 bp):
TAGGGGTATAACAATCATTTTACCCTATGAAGGTATTTCAGTCATTTTATCCTA
Found at i:21464174 original size:21 final size:21
Alignment explanation
Indices: 21464146--21464191 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
21464136 CTAATAAGAT
21464146 AAAA-TTATAAT-AAAAACTTC
1 AAAATTTATAATCAAAAAC-TC
* *
21464166 AAAATTTATTATCAAACACTC
1 AAAATTTATAATCAAAAACTC
21464187 AAAAT
1 AAAAT
21464192 CTGCATGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATTTATAATCAAAAACTC
Found at i:21464584 original size:21 final size:21
Alignment explanation
Indices: 21464560--21464600 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21464550 CATTTTGTTT
*
21464560 GTGTTTGTGTTAATTTGCTTG
1 GTGTTTGTGTTAATTAGCTTG
* *
21464581 GTGTTTTTTTTAATTAGCTT
1 GTGTTTGTGTTAATTAGCTT
21464601 TCTTCACTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.05, G:0.22, T:0.61
Consensus pattern (21 bp):
GTGTTTGTGTTAATTAGCTTG
Found at i:21464703 original size:17 final size:18
Alignment explanation
Indices: 21464665--21464703 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21464655 ATTATTGCTC
* *
21464665 TTATGTGTATTGTATTGC
1 TTATGTATATTGTATTGA
21464683 TTATGTATATT-TATTGA
1 TTATGTATATTGTATTGA
21464700 TTAT
1 TTAT
21464704 TTGTCGTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.59
Consensus pattern (18 bp):
TTATGTATATTGTATTGA
Found at i:21466557 original size:19 final size:19
Alignment explanation
Indices: 21466533--21466579 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
21466523 AACGTCTCTT
*
21466533 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
21466552 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
21466571 TATGCATTA
1 TTTGCATTA
21466580 AAGTCCACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:21469331 original size:12 final size:12
Alignment explanation
Indices: 21469294--21469358 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 12
21469284 AGTAGAGGAC
21469294 AAAA-AAAACAAA
1 AAAACAAAAC-AA
21469306 AAAACAAAGGACAA
1 AAAACAAA--ACAA
21469320 AAAACAAAACAA
1 AAAACAAAACAA
*
21469332 AGAACAAAACTAA
1 AAAACAAAAC-AA
*
21469345 AAAA-GAAACAA
1 AAAACAAAACAA
21469356 AAA
1 AAA
21469359 CCTCTACTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
11 5 0.11
12 21 0.46
13 8 0.17
14 10 0.22
15 2 0.04
ACGTcount: A:0.80, C:0.12, G:0.06, T:0.02
Consensus pattern (12 bp):
AAAACAAAACAA
Found at i:21469347 original size:19 final size:18
Alignment explanation
Indices: 21469303--21469340 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
21469293 CAAAAAAAAC
*
21469303 AAAAAAACAAAGGACAAA
1 AAAAAAACAAAGAACAAA
21469321 AAACAAAACAAAGAACAAA
1 AAA-AAAACAAAGAACAAA
21469340 A
1 A
21469341 CTAAAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAGAACAAA
Found at i:21469822 original size:50 final size:52
Alignment explanation
Indices: 21469697--21469836 Score: 158
Period size: 52 Copynumber: 2.7 Consensus size: 52
21469687 TCACCTAAAG
*
21469697 AAGGAGAAGGGACCAAGGTAAAAACCCGCAAAGGGCACTTTAAGTCCTAAAAAA
1 AAGGAGAA--GACCAAGGTGAAAACCCGCAAAGGGCACTTTAAGTCCTAAAAAA
* * *** *
21469751 AATGAGACGACCAAGGTGAAAACCCGCAAAGGGTGTTTTGAGTCCT-AAAAA
1 AAGGAGAAGACCAAGGTGAAAACCCGCAAAGGGCACTTTAAGTCCTAAAAAA
* **
21469802 AAGGA-AAGGCCAAGGTGAAAACCCAAAAAGGGCAC
1 AAGGAGAAGACCAAGGTGAAAACCCGCAAAGGGCAC
21469837 CTTGAAAACA
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
50 23 0.32
51 9 0.13
52 33 0.46
54 6 0.08
ACGTcount: A:0.44, C:0.19, G:0.26, T:0.11
Consensus pattern (52 bp):
AAGGAGAAGACCAAGGTGAAAACCCGCAAAGGGCACTTTAAGTCCTAAAAAA
Found at i:21480380 original size:50 final size:51
Alignment explanation
Indices: 21480256--21480422 Score: 221
Period size: 51 Copynumber: 3.3 Consensus size: 51
21480246 GGTCATTACA
* * *
21480256 TGTTTAATGTTGTCCAAGATTTTTCTCAGTTAATGTTTTTTAATAATTAGT
1 TGTTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAATAATTAGT
* * * *
21480307 TATTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAGTCATTTGT
1 TGTTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAATAATTAGT
* * *
21480358 TGTTT-ATGTTGTCCAAGATTTTGCCCAATTGATGTTGTTTAATTATTA-T
1 TGTTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAATAATTAGT
21480407 CTGTTTAATGTTGTCC
1 -TGTTTAATGTTGTCC
21480423 GAGGTTTTTC
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
49 1 0.01
50 43 0.43
51 57 0.56
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (51 bp):
TGTTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAATAATTAGT
Found at i:21480454 original size:51 final size:50
Alignment explanation
Indices: 21480256--21480456 Score: 138
Period size: 51 Copynumber: 4.0 Consensus size: 50
21480246 GGTCATTACA
* * * * * * *
21480256 TGTTTAATGTTGTCCAAGATTTTTCTCAGTTAATGTTTTTTAATAATTAGT-
1 TGTTT-ATGTTGTCCAAGATTTTGCCCAATTGATGCTATTTAATTATTA-TC
* * * * * * * *
21480307 TATTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAGTCATT-TGT
1 TGTTT-ATGTTGTCCAAGATTTTGCCCAATTGATGCTATTTAATTATTAT-C
* *
21480358 TGTTTATGTTGTCCAAGATTTTGCCCAATTGATGTTGTTTAATTATTATC
1 TGTTTATGTTGTCCAAGATTTTGCCCAATTGATGCTATTTAATTATTATC
* * * *
21480408 TGTTTAATGTTGTCCGAGGTTTTTCACC-ATTGATGCTATTTTATTATTA
1 TGTTT-ATGTTGTCCAAGATTTTGC-CCAATTGATGCTATTTAATTATTA
21480457 ATTGTTCGAT
Statistics
Matches: 127, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
49 1 0.01
50 43 0.34
51 81 0.64
52 2 0.02
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.51
Consensus pattern (50 bp):
TGTTTATGTTGTCCAAGATTTTGCCCAATTGATGCTATTTAATTATTATC
Found at i:21487140 original size:51 final size:51
Alignment explanation
Indices: 21487044--21487143 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
21487034 GTGTGGAAAT
* * *
21487044 CTACTCGCCCGTGTGTGATAGCTCCAGTCCCCACACGTATATGTCACTTAC
1 CTACACGCCCGTGTGTGATAGCTCCAGTCCCCACACGAACATGTCACTTAC
* * *
21487095 CTACACGCCTGTGTGTGATAGCTCTAGTCCCCACAC-AACCGTGTCACTT
1 CTACACGCCCGTGTGTGATAGCTCCAGTCCCCACACGAA-CATGTCACTT
21487144 TCCCACACAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 1 0.02
51 41 0.98
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (51 bp):
CTACACGCCCGTGTGTGATAGCTCCAGTCCCCACACGAACATGTCACTTAC
Found at i:21501398 original size:17 final size:18
Alignment explanation
Indices: 21501378--21501411 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21501368 TTAATGCATG
21501378 TTATTA-ATGTGTTAATT
1 TTATTACATGTGTTAATT
*
21501395 TTATTACATGTTTTAAT
1 TTATTACATGTGTTAAT
21501412 GATGTCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (18 bp):
TTATTACATGTGTTAATT
Found at i:21501404 original size:27 final size:27
Alignment explanation
Indices: 21501355--21501412 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
21501345 TTTTGTGATA
* *
21501355 AATGTGTTTTATTTTAATGCATGTTATT
1 AATGTGTTTAATTTTAATACATGTT-TT
*
21501383 AATGTG-TTAATTTTATTACATGTTTT
1 AATGTGTTTAATTTTAATACATGTTTT
21501409 AATG
1 AATG
21501413 ATGTCCAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 6 0.22
27 15 0.56
28 6 0.22
ACGTcount: A:0.28, C:0.03, G:0.14, T:0.55
Consensus pattern (27 bp):
AATGTGTTTAATTTTAATACATGTTTT
Found at i:21502341 original size:20 final size:21
Alignment explanation
Indices: 21502311--21502368 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
21502301 ACATCATAGA
21502311 TGCATAACAGGGGCACCGAA-G
1 TGCA-AACAGGGGCACCGAATG
* * *
21502332 TGGAAACAGGGGTA-CAAATG
1 TGCAAACAGGGGCACCGAATG
21502352 TGCAAACAGGGGCACCG
1 TGCAAACAGGGGCACCG
21502369 TAGCACGAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.34, C:0.21, G:0.34, T:0.10
Consensus pattern (21 bp):
TGCAAACAGGGGCACCGAATG
Found at i:21509904 original size:27 final size:27
Alignment explanation
Indices: 21509871--21510415 Score: 668
Period size: 27 Copynumber: 20.2 Consensus size: 27
21509861 GAGTTAAAAA
* *
21509871 TCATTTTACCCTAT-GGGGGTCTTTCGG
1 TCATTTTACCCT-TCGAGGGTATTTCGG
* **
21509898 TCATTTTACCTTTCGAGGGTATTTTAG
1 TCATTTTACCCTTCGAGGGTATTTCGG
*
21509925 TCATTTTACCCTTCGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCGG
**
21509952 TCATTTTACCCTTC-AGGGGTATTTCTA
1 TCATTTTACCCTTCGA-GGGTATTTCGG
* ** * *
21509979 TCTTTTTA-CCTTTTAAGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* **
21510005 TCATTTTACCTTTCGAGGGTATTTTAG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* *
21510032 TCATTTTACCCTTCGAGGTTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* *
21510059 TCATTTTACCCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGG
21510086 TCATTTTACCCTTC-AGGGGTATTTCGG
1 TCATTTTACCCTTCGA-GGGTATTTCGG
* **
21510113 TCATTTTATCCTTCGAGGGTATTTTAG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* * *
21510140 TCATTTTACCTTTTGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* **
21510167 TCATTTTACCGTTCGAGGGTATTAGGG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* *
21510194 TCATTTTACCCTTCGAAGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* *
21510221 TCATTTTACCCTTCGAGCGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCGG
21510248 TCATTTTACCCTTC-AGGGGTATTTCGG
1 TCATTTTACCCTTCGA-GGGTATTTCGG
*
21510275 TCATTTTACCCTTCGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* * *
21510302 TTATTTTATCCTTCGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGG
*
21510329 TCATTTTACCCTTCAAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGG
*
21510356 TCATTTTACCCTTCGAGTGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGG
21510383 TCATTTTACCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGG
21510410 TCATTT
1 TCATTT
21510416 GTCCATAACT
Statistics
Matches: 446, Mismatches: 64, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
26 21 0.05
27 423 0.95
28 2 0.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCGG
Found at i:21519241 original size:2 final size:2
Alignment explanation
Indices: 21519234--21519281 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
21519224 AATAAAGCTT
21519234 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
21519276 TC TC TC
1 TC TC TC
21519282 CTTTTATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:21521443 original size:32 final size:32
Alignment explanation
Indices: 21521388--21521498 Score: 186
Period size: 32 Copynumber: 3.5 Consensus size: 32
21521378 AAATGGCTAC
*
21521388 AAGCCATCAATAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
21521420 AAGCCATCAGTAAGGGTACTATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*
21521452 AAGCCATCAGTAACAGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
21521484 AAGCCATCAGTAACG
1 AAGCCATCAGTAACG
21521499 TCGTAGTAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.18
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:21521765 original size:27 final size:27
Alignment explanation
Indices: 21521741--21521905 Score: 224
Period size: 27 Copynumber: 6.1 Consensus size: 27
21521731 TCGAGGGTCG
21521741 TTACGGTCATTTTA-CCTACAGGGGTA
1 TTACGGTCATTTTACCCTACAGGGGTA
*
21521767 TTACAGTCATTTTACCCTACAGGGGTA
1 TTACGGTCATTTTACCCTACAGGGGTA
*
21521794 TTACGGTCATTTTACCTTACAGGGGTA
1 TTACGGTCATTTTACCCTACAGGGGTA
**
21521821 TTACGGTCATTTTACCCTATGGGGGTA
1 TTACGGTCATTTTACCCTACAGGGGTA
* * **
21521848 TTACAGTCATTTTATCCTATGGGGGTA
1 TTACGGTCATTTTACCCTACAGGGGTA
* **
21521875 TTACGGTCATTTTATCCTATGGGGGTA
1 TTACGGTCATTTTACCCTACAGGGGTA
21521902 TTAC
1 TTAC
21521906 AGTTATTATA
Statistics
Matches: 129, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
26 13 0.10
27 116 0.90
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (27 bp):
TTACGGTCATTTTACCCTACAGGGGTA
Found at i:21521833 original size:54 final size:53
Alignment explanation
Indices: 21521741--21521919 Score: 250
Period size: 54 Copynumber: 3.3 Consensus size: 53
21521731 TCGAGGGTCG
* **
21521741 TTACGGTCATTTTACCTACAGGGGTATTACAGTCATTTTACCCTACAGGGGTA
1 TTACGGTCATTTTACCTACAGGGGTATTACGGTCATTTTACCCTATGGGGGTA
21521794 TTACGGTCATTTTACCTTACAGGGGTATTACGGTCATTTTACCCTATGGGGGTA
1 TTACGGTCATTTTACC-TACAGGGGTATTACGGTCATTTTACCCTATGGGGGTA
* ** *
21521848 TTACAGTCATTTTATCCTATGGGGGTATTACGGTCATTTTATCCTATGGGGGTA
1 TTACGGTCATTTTA-CCTACAGGGGTATTACGGTCATTTTACCCTATGGGGGTA
* * *
21521902 TTACAGTTATTATACCTA
1 TTACGGTCATTTTACCTA
21521920 TTTTAGGGTT
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
53 20 0.17
54 93 0.81
55 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (53 bp):
TTACGGTCATTTTACCTACAGGGGTATTACGGTCATTTTACCCTATGGGGGTA
Found at i:21526678 original size:14 final size:14
Alignment explanation
Indices: 21526655--21526691 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
21526645 GTTAATTACT
21526655 AACA-AAAAAAATA
1 AACATAAAAAAATA
21526668 AACATAAAAAAATA
1 AACATAAAAAAATA
*
21526682 AGCATAAAAA
1 AACATAAAAA
21526692 TATATGTGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.78, C:0.08, G:0.03, T:0.11
Consensus pattern (14 bp):
AACATAAAAAAATA
Found at i:21527268 original size:35 final size:35
Alignment explanation
Indices: 21527228--21527297 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
21527218 TTAATATAAA
* * *
21527228 AATAATTATATTAAGAATTTTATTAAATTA-TATTT
1 AATAATAATATTAA-AATATGATTAAATTATTATTT
21527263 AATAATAATATTAAAATATGATTAAATTATTATTT
1 AATAATAATATTAAAATATGATTAAATTATTATTT
21527298 TTTATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 13 0.42
35 18 0.58
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (35 bp):
AATAATAATATTAAAATATGATTAAATTATTATTT
Found at i:21527274 original size:23 final size:22
Alignment explanation
Indices: 21527231--21527287 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
21527221 ATATAAAAAT
**
21527231 AATTATATTAAGAATTTTATTA
1 AATTATATTAAGAATAATATTA
*
21527253 AATTATATTTAATAATAATATTA
1 AATTATA-TTAAGAATAATATTA
*
21527276 AAATATGATTAA
1 AATTAT-ATTAA
21527288 ATTATTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 7 0.24
23 21 0.72
24 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
AATTATATTAAGAATAATATTA
Found at i:21529705 original size:23 final size:23
Alignment explanation
Indices: 21529675--21529720 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
21529665 ATGTTATAAC
*
21529675 TTTTTTTATTTACTAAAATATAT
1 TTTTTTTATTTACCAAAATATAT
21529698 TTTTTTTATTTACCAAAATATAT
1 TTTTTTTATTTACCAAAATATAT
21529721 AATAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTTTTATTTACCAAAATATAT
Found at i:21529810 original size:27 final size:27
Alignment explanation
Indices: 21529774--21529847 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
21529764 CCTTGGTCAC
*
21529774 GCCAAAGCCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
*
21529801 GCCAATGCCATTAGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
21529828 GCCATACTG--ATTGGCGGCAC
1 GCCA-A-TGCCATTGGCGGCAC
21529848 TACTCGTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 39 0.93
28 1 0.02
29 2 0.05
ACGTcount: A:0.24, C:0.30, G:0.28, T:0.18
Consensus pattern (27 bp):
GCCAATGCCATTGGCGGCACCAATGGT
Found at i:21530004 original size:19 final size:21
Alignment explanation
Indices: 21529966--21530004 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
21529956 AATAATTGAT
*
21529966 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
21529987 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
21530005 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:21530472 original size:42 final size:43
Alignment explanation
Indices: 21530396--21530481 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
21530386 ACATCGCTAA
*
21530396 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-AGAAAAAAACGCCGCTAAAGATCATGTT
* * *
21530440 CTTTAGCGGCGCTT-AGGAAAAAACGTCGCTAAAGATTATGTT
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTT
21530482 GTCTAGCGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 25 0.66
44 13 0.34
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:21530588 original size:43 final size:42
Alignment explanation
Indices: 21530499--21530644 Score: 170
Period size: 42 Copynumber: 3.5 Consensus size: 42
21530489 GCCGTTTATC
*
21530499 ATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCT-AAAGATC
1 ATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAAG-TA
*
21530541 ATGTTCTTTAGCAGCGCTTAGGAAGAAAACGCCGCTAAAAGTA
1 ATGTTCTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAAGTA
* * * * *
21530584 ATGTTCTATAGCGACG-TTTGGTCAAAAACGCCGCTAATAGTA
1 ATGTTCTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAAAAGTA
* *
21530626 GTCTTCTTTAGCGGCGCTT
1 ATGTTCTTTAGCGGCGCTT
21530645 TTTTCACAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
42 56 0.64
43 28 0.32
44 4 0.05
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (42 bp):
ATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAAGTA
Found at i:21531105 original size:12 final size:12
Alignment explanation
Indices: 21531085--21531140 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
21531075 GAACCTCTAA
*
21531085 TTCTATCGCTGC
1 TTCTCTCGCTGC
21531097 TTCTCTCGCTGC
1 TTCTCTCGCTGC
*
21531109 TTCTCTTGCTGC
1 TTCTCTCGCTGC
**
21531121 GGC-CT--CTGC
1 TTCTCTCGCTGC
21531130 TTCTCTCGCTG
1 TTCTCTCGCTG
21531141 TAGCCTATGC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 5 0.14
10 2 0.06
11 2 0.06
12 26 0.74
ACGTcount: A:0.02, C:0.38, G:0.20, T:0.41
Consensus pattern (12 bp):
TTCTCTCGCTGC
Found at i:21531129 original size:21 final size:21
Alignment explanation
Indices: 21531105--21531173 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
21531095 GCTTCTCTCG
*
21531105 CTGCTTCTCTTGCTGCGGCCT
1 CTGCTTCTCTTGCTGCAGCCT
* *
21531126 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTTGCTGCAGCCT
* *
21531147 ATGCTTC-CTTTGCTGCCGCCT
1 CTGCTTCTC-TTGCTGCAGCCT
21531168 CTGCTT
1 CTGCTT
21531174 TAAGTTGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 1 0.03
21 38 0.97
ACGTcount: A:0.03, C:0.38, G:0.20, T:0.39
Consensus pattern (21 bp):
CTGCTTCTCTTGCTGCAGCCT
Found at i:21536660 original size:9 final size:9
Alignment explanation
Indices: 21536643--21537026 Score: 249
Period size: 9 Copynumber: 44.9 Consensus size: 9
21536633 AAGTTATACA
21536643 TTATGTAAG
1 TTATGTAAG
*
21536652 TTGTGTAAG
1 TTATGTAAG
21536661 TTATGTAAG
1 TTATGTAAG
*
21536670 TTGTGTAAG
1 TTATGTAAG
21536679 TTATGTAAG
1 TTATGTAAG
*
21536688 TTGTGTAAG
1 TTATGTAAG
*
21536697 TTGTGTAAG
1 TTATGTAAG
**
21536706 TTGCGTAAG
1 TTATGTAAG
*
21536715 TTGTGT-A-
1 TTATGTAAG
* *
21536722 TTATGAAAC
1 TTATGTAAG
21536731 TTATGTAAG
1 TTATGTAAG
*
21536740 TTATGT--C
1 TTATGTAAG
21536747 TTATGTAAG
1 TTATGTAAG
* *
21536756 TTATGCAAA
1 TTATGTAAG
*
21536765 TTCTGT-A-
1 TTATGTAAG
21536772 TTATGTAAG
1 TTATGTAAG
21536781 TTATGTAAG
1 TTATGTAAG
*
21536790 TTGTGT-A-
1 TTATGTAAG
*
21536797 TTATATAAG
1 TTATGTAAG
21536806 TTATGTAAG
1 TTATGTAAG
*
21536815 TTGTGT-A-
1 TTATGTAAG
21536822 TTATGTAAG
1 TTATGTAAG
21536831 TTATGTAAG
1 TTATGTAAG
* **
21536840 TTTTTGT-TT
1 -TTATGTAAG
*
21536849 TTGTGT-A-
1 TTATGTAAG
*
21536856 TTATGTAAC
1 TTATGTAAG
21536865 TTATGTAAG
1 TTATGTAAG
*
21536874 TTATGTAGG
1 TTATGTAAG
*
21536883 GTATGTATTA-
1 TTATGTA--AG
*
21536893 TTATGTAAC
1 TTATGTAAG
* *
21536902 TTATTTAAT
1 TTATGTAAG
*
21536911 TTATGTAGG
1 TTATGTAAG
*
21536920 GTATGTAAG
1 TTATGTAAG
21536929 TTATGTAAG
1 TTATGTAAG
*
21536938 TTGTGT-A-
1 TTATGTAAG
*
21536945 TTATTTACA-
1 TTATGTA-AG
*
21536954 -CATGTAAG
1 TTATGTAAG
*
21536962 TTGTGT-A-
1 TTATGTAAG
21536969 TTATGTAAG
1 TTATGTAAG
*
21536978 TTATGCAAG
1 TTATGTAAG
21536987 TTATGT-A-
1 TTATGTAAG
* *
21536994 TTAAGTAGG
1 TTATGTAAG
21537003 TTATGTAAG
1 TTATGTAAG
21537012 TTATGT-A-
1 TTATGTAAG
21537019 TTATGTAA
1 TTATGTAA
21537027 ATTAATATAT
Statistics
Matches: 293, Mismatches: 57, Indels: 51
0.73 0.14 0.13
Matches are distributed among these distances:
7 50 0.17
8 25 0.09
9 207 0.71
10 11 0.04
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:21536661 original size:25 final size:25
Alignment explanation
Indices: 21536642--21537026 Score: 304
Period size: 25 Copynumber: 15.4 Consensus size: 25
21536632 TAAGTTATAC
* *
21536642 ATTATGTAAGTTGTGTAAGTTATGT
1 ATTATGTAAGTTATGTAAGTTGTGT
*
21536667 AAGTTGTGTAAGTTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAGTTGTGT
* **
21536694 AAGTTGTGTAAGTTGCGTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAGTTGTGT
* * *
21536721 ATTATGAAACTTATGTAAGTTATGT
1 ATTATGTAAGTTATGTAAGTTGTGT
* * * *
21536746 CTTATGTAAGTTATGCAAATTCTGT
1 ATTATGTAAGTTATGTAAGTTGTGT
21536771 ATTATGTAAGTTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTAAGTTGTGT
*
21536796 ATTATATAAGTTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTAAGTTGTGT
*
21536821 ATTATGTAAGTTATGTAAGTTTTTGT
1 ATTATGTAAGTTATGTAAG-TTGTGT
* * * *
21536847 -TTTTGTGTA-TTATGTAACTTATGT
1 ATTATGT-AAGTTATGTAAGTTGTGT
* *
21536871 AAGTTATGTAGGGTATGT-A----T-T
1 -A-TTATGTAAGTTATGTAAGTTGTGT
* * * *
21536892 ATTATGTAACTTATTTAATTTATGT
1 ATTATGTAAGTTATGTAAGTTGTGT
*
21536917 AGGGTATGTAAGTTATGTAAGTTGTGT
1 A--TTATGTAAGTTATGTAAGTTGTGT
* *
21536944 ATTATTTACA--CATGTAAGTTGTGT
1 ATTATGTA-AGTTATGTAAGTTGTGT
* *
21536968 ATTATGTAAGTTATGCAAGTTATGT
1 ATTATGTAAGTTATGTAAGTTGTGT
* * *
21536993 ATTAAGTAGGTTATGTAAGTTATGT
1 ATTATGTAAGTTATGTAAGTTGTGT
21537018 ATTATGTAA
1 ATTATGTAA
21537027 ATTAATATAT
Statistics
Matches: 288, Mismatches: 53, Indels: 37
0.76 0.14 0.10
Matches are distributed among these distances:
19 11 0.04
20 2 0.01
21 1 0.00
22 1 0.00
23 1 0.00
24 26 0.09
25 160 0.56
26 10 0.03
27 76 0.26
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.47
Consensus pattern (25 bp):
ATTATGTAAGTTATGTAAGTTGTGT
Found at i:21536749 original size:16 final size:16
Alignment explanation
Indices: 21536730--21536760 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21536720 TATTATGAAA
21536730 CTTATGTAAGTTATGT
1 CTTATGTAAGTTATGT
21536746 CTTATGTAAGTTATG
1 CTTATGTAAGTTATG
21536761 CAAATTCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (16 bp):
CTTATGTAAGTTATGT
Found at i:21536810 original size:34 final size:36
Alignment explanation
Indices: 21536643--21537026 Score: 249
Period size: 34 Copynumber: 11.2 Consensus size: 36
21536633 AAGTTATACA
* *
21536643 TTATGTAAGTTGTGTAAGTTATGTAAGTTGTGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAG
* * **
21536679 TTATGTAAGTTGTGTAAGTTGTGTAAGTTGCGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAG
* * * *
21536715 TTGTGT-A-TTATGAAACTTATGTAAGTTATGT--C
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAG
* * *
21536747 TTATGTAAGTTATGCAAATTCTGT-A-TTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAG
* *
21536781 TTATGTAAGTTGTGT-A-TTATATAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAG
* * **
21536815 TTGTGT-A-TTATGTAAGTTATGTAAGTTTTTGT-TT
1 TTATGTAAGTTATGTAAGTTATGTAAG-TTATGTAAG
* * *
21536849 TTGTGT-A-TTATGTAACTTATGTAAGTTATGTAGG
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAG
* * * * *
21536883 GTATGTATTA-TTATGTAACTTATTTAATTTATGTAGG
1 TTATGTA--AGTTATGTAAGTTATGTAAGTTATGTAAG
* * *
21536920 GTATGTAAGTTATGTAAGTTGTGT-A-TTATTTACA-
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA-AG
* * *
21536954 -CATGTAAGTTGTGT-A-TTATGTAAGTTATGCAAG
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAG
* *
21536987 TTATGT-A-TTAAGTAGGTTATGTAAGTTATGT-A-
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAG
21537019 TTATGTAA
1 TTATGTAA
21537027 ATTAATATAT
Statistics
Matches: 278, Mismatches: 48, Indels: 47
0.75 0.13 0.13
Matches are distributed among these distances:
31 5 0.02
32 33 0.12
33 31 0.11
34 117 0.42
35 8 0.03
36 51 0.18
37 33 0.12
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.47
Consensus pattern (36 bp):
TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAG
Found at i:21536904 original size:37 final size:37
Alignment explanation
Indices: 21536854--21536926 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
21536844 TGTTTTTGTG
21536854 TATTATGTAACTTATGTAAGTTATGTAGGGTATGTAT
1 TATTATGTAACTTATGTAAGTTATGTAGGGTATGTAT
* *
21536891 TATTATGTAACTTATTTAATTTATGTAGGGTATGTA
1 TATTATGTAACTTATGTAAGTTATGTAGGGTATGTA
21536927 AGTTATGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (37 bp):
TATTATGTAACTTATGTAAGTTATGTAGGGTATGTAT
Found at i:21537262 original size:41 final size:41
Alignment explanation
Indices: 21537217--21537354 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 41
21537207 TTAATAAAAT
21537217 TTAAATATAGCTTACATCTGTAAATTAATATATGTATAATA
1 TTAAATATAGCTTACATCTGTAAATTAATATATGTATAATA
* * *
21537258 TTAAAAATATAG-TAATACTTATTTAAGTTATCAATTTAT-TAT-TAATAAAA
1 TT--AAATATAGCT--TAC--ATCT--G-TA--AATTAATATATGT-ATAATA
21537308 TTTAAATATAGCTTACATCTGTAAATTAATATATGTATAATA
1 -TTAAATATAGCTTACATCTGTAAATTAATATATGTATAATA
21537350 TTAAA
1 TTAAA
21537355 AATATAGTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 32
0.66 0.05 0.28
Matches are distributed among these distances:
41 13 0.17
42 9 0.12
43 11 0.15
44 4 0.05
46 6 0.08
48 4 0.05
49 11 0.15
50 9 0.12
51 8 0.11
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (41 bp):
TTAAATATAGCTTACATCTGTAAATTAATATATGTATAATA
Found at i:21537266 original size:43 final size:43
Alignment explanation
Indices: 21537219--21537361 Score: 132
Period size: 43 Copynumber: 3.2 Consensus size: 43
21537209 AATAAAATTT
21537219 AAATATAGCTTACATCTGTAAATTAATATATGTATAATATTAA
1 AAATATAGCTTACATCTGTAAATTAATATATGTATAATATTAA
* * * *
21537262 AAATATAG-TAATACTTATTTAAGTTATCAATTTAT-TAT-TAATAAAATT-T
1 AAATATAGCT--TAC--ATCT--G-TA--AATTAATATATGT-ATAATATTAA
21537311 AAATATAGCTTACATCTGTAAATTAATATATGTATAATATTAA
1 AAATATAGCTTACATCTGTAAATTAATATATGTATAATATTAA
21537354 AAATATAG
1 AAATATAG
21537362 TAATACTTAT
Statistics
Matches: 78, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
41 6 0.08
42 11 0.14
43 19 0.24
44 4 0.05
46 6 0.08
48 4 0.05
49 11 0.14
50 11 0.14
51 6 0.08
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (43 bp):
AAATATAGCTTACATCTGTAAATTAATATATGTATAATATTAA
Found at i:21537306 original size:92 final size:92
Alignment explanation
Indices: 21537202--21537417 Score: 432
Period size: 92 Copynumber: 2.3 Consensus size: 92
21537192 TATGTTTAAA
21537202 TATTATTAATAAAATTTAAATATAGCTTACATCTGTAAATTAATATATGTATAATATTAAAAATA
1 TATTATTAATAAAATTTAAATATAGCTTACATCTGTAAATTAATATATGTATAATATTAAAAATA
21537267 TAGTAATACTTATTTAAGTTATCAATT
66 TAGTAATACTTATTTAAGTTATCAATT
21537294 TATTATTAATAAAATTTAAATATAGCTTACATCTGTAAATTAATATATGTATAATATTAAAAATA
1 TATTATTAATAAAATTTAAATATAGCTTACATCTGTAAATTAATATATGTATAATATTAAAAATA
21537359 TAGTAATACTTATTTAAGTTATCAATT
66 TAGTAATACTTATTTAAGTTATCAATT
21537386 TATTATTAATAAAATTTAAATATAGCTTACAT
1 TATTATTAATAAAATTTAAATATAGCTTACAT
21537418 AAGCAATCTT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 124 1.00
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (92 bp):
TATTATTAATAAAATTTAAATATAGCTTACATCTGTAAATTAATATATGTATAATATTAAAAATA
TAGTAATACTTATTTAAGTTATCAATT
Found at i:21537400 original size:43 final size:43
Alignment explanation
Indices: 21537261--21537400 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 43
21537251 TATAATATTA
21537261 AAAATATAGTAATACTTATTTAAGTTATCAATTTATTATTAAT
1 AAAATATAGTAATACTTATTTAAGTTATCAATTTATTATTAAT
* * * *
21537304 AAAATTTA-AATATAGCTTACATCTGTAAATTAAT-ATATGTATAATATT-A-
1 AAAATATAGTA-ATA-CTT--AT-T-TAAGTT-ATCA-AT-T-TATTATTAAT
21537353 AAAATATAGTAATACTTATTTAAGTTATCAATTTATTATTAAT
1 AAAATATAGTAATACTTATTTAAGTTATCAATTTATTATTAAT
21537396 AAAAT
1 AAAAT
21537401 TTAAATATAG
Statistics
Matches: 75, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
41 6 0.08
42 3 0.04
43 19 0.25
44 9 0.12
45 1 0.01
46 4 0.05
47 1 0.01
48 9 0.12
49 14 0.19
50 3 0.04
51 6 0.08
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (43 bp):
AAAATATAGTAATACTTATTTAAGTTATCAATTTATTATTAAT
Found at i:21537517 original size:121 final size:121
Alignment explanation
Indices: 21537386--21537660 Score: 541
Period size: 121 Copynumber: 2.3 Consensus size: 121
21537376 GTTATCAATT
21537386 TATTATTAATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCACT
1 TATTATTAATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCACT
21537451 GAATTATGGGTGGAGAGGTATATGTGTTACTGATTTGGCAACAAAATATGTTTAAA
66 GAATTATGGGTGGAGAGGTATATGTGTTACTGATTTGGCAACAAAATATGTTTAAA
21537507 TATTATTAATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCACT
1 TATTATTAATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCACT
21537572 GAATTATGGGTGGAGAGGTATATGTGTTACTGATTTGGCAACAAAATATGTTTAAA
66 GAATTATGGGTGGAGAGGTATATGTGTTACTGATTTGGCAACAAAATATGTTTAAA
*
21537628 TATTATTAATAAAATTTAAATATAGTTTACATA
1 TATTATTAATAAAATTTAAATATAGCTTACATA
21537661 CGTAAATTAA
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 153 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (121 bp):
TATTATTAATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCACT
GAATTATGGGTGGAGAGGTATATGTGTTACTGATTTGGCAACAAAATATGTTTAAA
Found at i:21541011 original size:23 final size:23
Alignment explanation
Indices: 21540987--21541032 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
21540977 ATATATGTAT
21540987 AATT-TAAATATAATCAACATTATA
1 AATTATAAAT-TAATCAA-ATTATA
*
21541011 AATTATAAATTATTCAAATTAT
1 AATTATAAATTAATCAAATTAT
21541033 TCAAATAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (23 bp):
AATTATAAATTAATCAAATTATA
Found at i:21541148 original size:27 final size:28
Alignment explanation
Indices: 21541104--21541163 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
21541094 TAACTAACAC
* * *
21541104 AATAT-TAATATATTTATAT-GTTTCAT
1 AATATATAACATATATATATCGTTGCAT
21541130 AATATATAACATATATATATCGTTGCAT
1 AATATATAACATATATATATCGTTGCAT
21541158 -ATATAT
1 AATATAT
21541164 CTTTTTCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 5 0.17
27 18 0.62
28 6 0.21
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (28 bp):
AATATATAACATATATATATCGTTGCAT
Found at i:21541436 original size:7 final size:7
Alignment explanation
Indices: 21541424--21541449 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21541414 TCATTAACGC
21541424 TAAACCA
1 TAAACCA
21541431 TAAACCA
1 TAAACCA
21541438 TAAACCA
1 TAAACCA
21541445 TAAAC
1 TAAAC
21541450 ATCATGCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCA
Found at i:21542272 original size:42 final size:41
Alignment explanation
Indices: 21542226--21542322 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
21542216 ATGACCAAGT
* * *
21542226 CATTAGTGGAGCTTATTAAAAAAACGCCTCTAAAGGCCAGAG
1 CATTAGTGGCGCTTA-TAAAAAAACACCGCTAAAGGCCAGAG
* * * *
21542268 CATTAGCGGCGCTTATAAGAAAACATCGCTAAAGGCTAGAG
1 CATTAGTGGCGCTTATAAAAAAACACCGCTAAAGGCCAGAG
21542309 CATTAGTGGCGCTT
1 CATTAGTGGCGCTT
21542323 TACGAAAATC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 34 0.72
42 13 0.28
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (41 bp):
CATTAGTGGCGCTTATAAAAAAACACCGCTAAAGGCCAGAG
Found at i:21542339 original size:41 final size:41
Alignment explanation
Indices: 21542245--21542386 Score: 126
Period size: 41 Copynumber: 3.4 Consensus size: 41
21542235 AGCTTATTAA
* * * *
21542245 AAAAACGCCTCTAAAGGCCAGAGCATTAGCGGCGCTTATAAG
1 AAAATCGCCGCTAAAGGCTAGAGCATTAGCGGCGCTT-TACG
** *
21542287 AAAA-CATCGCTAAAGGCTAGAGCATTAGTGGCGCTTTACG
1 AAAATCGCCGCTAAAGGCTAGAGCATTAGCGGCGCTTTACG
* * * * * *
21542327 AAAATCGCCGCTAAAAGGTTGGAGAATTAGCGGCGATTTGTCA
1 AAAATCGCCGCT-AAAGGCTAGAGCATTAGCGGCGCTTT-ACG
21542370 AAAAT-GCCGCTAAAGGC
1 AAAATCGCCGCTAAAGGC
21542387 CCAAAAATAT
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
40 7 0.09
41 37 0.46
42 31 0.38
43 6 0.07
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (41 bp):
AAAATCGCCGCTAAAGGCTAGAGCATTAGCGGCGCTTTACG
Found at i:21543267 original size:18 final size:18
Alignment explanation
Indices: 21543244--21543281 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
21543234 GGTTGGTGGT
21543244 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
*
21543262 GAAGAAGAAGGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
21543280 GA
1 GA
21543282 TCATTGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.08, G:0.47, T:0.11
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:21549117 original size:4 final size:4
Alignment explanation
Indices: 21549101--21549231 Score: 90
Period size: 4 Copynumber: 31.0 Consensus size: 4
21549091 CTCATTTCCT
*
21549101 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTCC TTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C TTTC T-TTC
* * *
21549147 -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCC TTTTC TTTTC TTCTT
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC -TTTC TT-TC
*
21549194 TTTC TTTC TTTCC TCTAC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC
21549232 CCTCTCCTTC
Statistics
Matches: 104, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
3 9 0.09
4 64 0.62
5 24 0.23
6 7 0.07
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:21549153 original size:45 final size:42
Alignment explanation
Indices: 21549068--21549209 Score: 185
Period size: 40 Copynumber: 3.6 Consensus size: 42
21549058 CCTTCCCTCC
*
21549068 TCTTCTTC-TTCTTT-TTTTCTCTTCTCATTTCCTTTTC-TT
1 TCTTCTTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTCTTT
*
21549107 TC--CTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTC--T
1 TCTTCTTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTCTTT
21549145 TCTTCTTTCTTTCTTT-TTTTCTCTTCTCCTTTCCTTTTCTTT
1 TCTTC-TTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTCTTT
*
21549187 TCTTCTT-TTTCTTTCTTTCCTCT
1 TCTTCTTCTTTCTTTCTTTTCTCT
21549210 ACTTTCTTTC
Statistics
Matches: 91, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
37 4 0.04
38 9 0.10
39 23 0.25
40 30 0.33
41 19 0.21
42 6 0.07
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.70
Consensus pattern (42 bp):
TCTTCTTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTCTTT
Found at i:21549167 original size:74 final size:73
Alignment explanation
Indices: 21549040--21549230 Score: 202
Period size: 74 Copynumber: 2.7 Consensus size: 73
21549030 ATTACATTTT
* * *
21549040 TTTTCTTT-TTTTTTCCTTCCTTCCCTCCTCTTCTTC-TTCTTT-TTTTCTCTTCTCATT-TCCT
1 TTTTCTTTCTTTTTTCTTTCCTTTCCTCTTCTTCTTCTTTCTTTCTTTTCTCTTCTC-TTCTCCT
*
21549101 TTTCTTTCC
65 TTCCTTTCC
*
21549110 TTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTCTTCTTTCTTTCTTTT-T-TTCTCTTCTC
1 -T-TTTCTTTCTTTTTTCTT-TCCTTTCCTCTTCTTCTTCTTTCTTTCTTTTCTCTTCTCTTCTC
*
21549173 CTTTCCTTTTC
63 CTTTCCTTTCC
*
21549184 TTTTC-TTC-TTTTTCTTT-CTTTCCTCTACTTTCTTTCTTTCTTTCTTT
1 TTTTCTTTCTTTTTTCTTTCCTTTCCTCTTC-TTC-TTCTTTCTTTCTTT
21549231 CCCTCTCCTT
Statistics
Matches: 104, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
68 9 0.09
69 4 0.04
70 22 0.21
71 4 0.04
72 11 0.11
73 11 0.11
74 32 0.31
75 7 0.07
76 4 0.04
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (73 bp):
TTTTCTTTCTTTTTTCTTTCCTTTCCTCTTCTTCTTCTTTCTTTCTTTTCTCTTCTCTTCTCCTT
TCCTTTCC
Found at i:21549181 original size:40 final size:40
Alignment explanation
Indices: 21549068--21549231 Score: 181
Period size: 40 Copynumber: 4.3 Consensus size: 40
21549058 CCTTCCCTCC
*
21549068 TCTTC-TTC-TTCTTTTTTTCTCTTCTCATTTCCTTTTCTT
1 TCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTC-T
21549107 TCCTTCTTTCTTTC--TTTTT-TCTTCTCCTTTCCTTTTCT
1 T-CTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCT
21549145 TCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCT
1 TCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCT
* * *
21549185 T-TTCTTCTTTTTCTTTCTTTC-C-TCTACTTT-C-TTTC-
1 TCTTCTT-TCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCT
21549220 T-TTCTTTCTTTC
1 TCTTCTTTCTTTC
21549232 CCTCTCCTTC
Statistics
Matches: 113, Mismatches: 5, Indels: 19
0.82 0.04 0.14
Matches are distributed among these distances:
34 5 0.04
35 6 0.05
36 4 0.04
37 13 0.12
38 9 0.08
39 29 0.26
40 41 0.36
41 3 0.03
42 3 0.03
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (40 bp):
TCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCT
Found at i:21549321 original size:27 final size:27
Alignment explanation
Indices: 21549272--21549324 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
21549262 CCCTATTATA
**
21549272 CATTGGTGCCGCCAAAGGTATTGGCAC
1 CATTGGTGCCGCCAAAGCCATTGGCAC
* *
21549299 CATTGGTGCTGCCAATGCCATTGGCA
1 CATTGGTGCCGCCAAAGCCATTGGCA
21549325 TGACCAGTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (27 bp):
CATTGGTGCCGCCAAAGCCATTGGCAC
Found at i:21549438 original size:23 final size:23
Alignment explanation
Indices: 21549389--21549442 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
21549379 TTTTTGATAT
*
21549389 ATTTTGGTAAATAAAATATATAT
1 ATTTTGGTAAATAAAATATATAC
* *
21549412 ATTTTGGTAAA-AAATTTTATAAC
1 ATTTTGGTAAATAAAATATAT-AC
21549435 ATTTTGGT
1 ATTTTGGT
21549443 TATTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (23 bp):
ATTTTGGTAAATAAAATATATAC
Found at i:21549729 original size:15 final size:14
Alignment explanation
Indices: 21549702--21549728 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21549692 GTTTAGAGTT
21549702 TTTTAGGGTTTTTA
1 TTTTAGGGTTTTTA
21549716 TTTTAGGGTTTTT
1 TTTTAGGGTTTTT
21549729 TTAGATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.22, T:0.67
Consensus pattern (14 bp):
TTTTAGGGTTTTTA
Found at i:21549824 original size:20 final size:20
Alignment explanation
Indices: 21549801--21549848 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
21549791 AAATATATAA
*
21549801 ATTTTGAAATTTTTATAAA-T
1 ATTTTGAAA-TTTTAAAAATT
21549821 ATTTTG-AATTTTAAAAATT
1 ATTTTGAAATTTTAAAAATT
21549840 ATTTTGAAA
1 ATTTTGAAA
21549849 ATTGTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (20 bp):
ATTTTGAAATTTTAAAAATT
Found at i:21551960 original size:15 final size:15
Alignment explanation
Indices: 21551940--21551970 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21551930 ACTGTATTAA
21551940 AATAGAAATAAGTTC
1 AATAGAAATAAGTTC
21551955 AATAGAAATAAGTTC
1 AATAGAAATAAGTTC
21551970 A
1 A
21551971 GTTAGCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (15 bp):
AATAGAAATAAGTTC
Found at i:21552550 original size:40 final size:40
Alignment explanation
Indices: 21552506--21552592 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
21552496 TGTACTTTGG
* *
21552506 TACCCTTAAATGCACATTTATGCCCCTGTTTGAACTTCGA
1 TACCCCTAAATGCACATCTATGCCCCTGTTTGAACTTCGA
* * * *
21552546 TACCCCTAAATGCACATCTGTGCTCCTTTTTGCACTTCGA
1 TACCCCTAAATGCACATCTATGCCCCTGTTTGAACTTCGA
*
21552586 TGCCCCT
1 TACCCCT
21552593 GATCGTATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (40 bp):
TACCCCTAAATGCACATCTATGCCCCTGTTTGAACTTCGA
Found at i:21564250 original size:33 final size:33
Alignment explanation
Indices: 21564213--21564283 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
21564203 CTGATTTAGT
21564213 CTTCTCCTCATCTCCCTCTAGTCCTGTTGTGGC
1 CTTCTCCTCATCTCCCTCTAGTCCTGTTGTGGC
* * *
21564246 CTTCTCCTTATCTCCCTCTGGTCCTTTTGTGGC
1 CTTCTCCTCATCTCCCTCTAGTCCTGTTGTGGC
21564279 CTTCT
1 CTTCT
21564284 TCATAGTGGC
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:0.04, C:0.38, G:0.14, T:0.44
Consensus pattern (33 bp):
CTTCTCCTCATCTCCCTCTAGTCCTGTTGTGGC
Found at i:21566669 original size:36 final size:36
Alignment explanation
Indices: 21566614--21566709 Score: 140
Period size: 36 Copynumber: 2.7 Consensus size: 36
21566604 AATTATCACT
* * *
21566614 CTTA-AATATCACAACTATATCATTAGCCCGAATAA
1 CTTATAATATCACAAGTATATCAATAGCCCAAATAA
* *
21566649 CTTATAATATCACAAGTATATCAATAGGCCAAATCA
1 CTTATAATATCACAAGTATATCAATAGCCCAAATAA
21566685 CTTATAATATCACAAGTATATCAAT
1 CTTATAATATCACAAGTATATCAAT
21566710 TCAAATATAC
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 4 0.07
36 51 0.93
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (36 bp):
CTTATAATATCACAAGTATATCAATAGCCCAAATAA
Found at i:21575255 original size:26 final size:26
Alignment explanation
Indices: 21575199--21575255 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
21575189 TTACCGAAAT
* * *
21575199 AGGGTAAATTACCGAAATACCCTCGA
1 AGGGTAAATCACCGAAATACCCCCAA
* *
21575225 TGGGTAAATCACTGAAATACCCCCAA
1 AGGGTAAATCACCGAAATACCCCCAA
21575251 AGGGT
1 AGGGT
21575256 CGAATGACCG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (26 bp):
AGGGTAAATCACCGAAATACCCCCAA
Found at i:21575464 original size:27 final size:27
Alignment explanation
Indices: 21575426--21575477 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
21575416 ATTGAGGAAG
*
21575426 TACTGTTACTGGTGGCTCTGCCACAAA
1 TACTATTACTGGTGGCTCTGCCACAAA
21575453 TACTATTACTGGTGGCTCTGCCACA
1 TACTATTACTGGTGGCTCTGCCACA
21575478 TATATTGCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (27 bp):
TACTATTACTGGTGGCTCTGCCACAAA
Found at i:21578330 original size:91 final size:90
Alignment explanation
Indices: 21578168--21578343 Score: 228
Period size: 91 Copynumber: 1.9 Consensus size: 90
21578158 CATAATTTAA
* * * * * * *
21578168 AGTCATTCAGACCACATTTATTGACATCTAAACAACAATTTACTGCTGCTTTAATACACCAAACA
1 AGTCATTCAGACAACATTAATTAACAACTAAACAACAATTTACTACTGCATTAATACAACAAACA
*
21578233 ATAGTCCTTAAAACAACATAAATAC
66 ACAGTCCTTAAAACAACATAAATAC
* *
21578258 AGTCACTT-AGACAACATTAATTAACAACTAAACAAGAATTTTTCTACTGCATTAATACAACAAA
1 AGTCA-TTCAGACAACATTAATTAACAACTAAACAACAA-TTTACTACTGCATTAATACAACAAA
*
21578322 CAACAGTCCTTAAAATAACATA
64 CAACAGTCCTTAAAACAACATA
21578344 TTTTTCTGCT
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
90 30 0.41
91 43 0.59
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.27
Consensus pattern (90 bp):
AGTCATTCAGACAACATTAATTAACAACTAAACAACAATTTACTACTGCATTAATACAACAAACA
ACAGTCCTTAAAACAACATAAATAC
Found at i:21578350 original size:48 final size:48
Alignment explanation
Indices: 21578287--21578391 Score: 140
Period size: 48 Copynumber: 2.2 Consensus size: 48
21578277 ATTAACAACT
* **
21578287 AAACAAGA-ATTTTTCTACTGCATTAATACAACAAACAACAGTCCTTA
1 AAACAACATATTTTTCTACTAAATTAATACAACAAACAACAGTCCTTA
* * * *
21578334 AAATAACATATTTTTCTGCTAAATTAATACACCAAACATCAGTCCTTA
1 AAACAACATATTTTTCTACTAAATTAATACAACAAACAACAGTCCTTA
21578382 AAACAACATA
1 AAACAACATA
21578392 AATACACCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 6 0.12
48 43 0.88
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.29
Consensus pattern (48 bp):
AAACAACATATTTTTCTACTAAATTAATACAACAAACAACAGTCCTTA
Found at i:21580151 original size:30 final size:30
Alignment explanation
Indices: 21580125--21580184 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
21580115 TTACACGGTT
21580125 GTATGACACACACAACTTGGCGACACGACC
1 GTATGACACACACAACTTGGCGACACGACC
* * *
21580155 GTGTGACAGACACAACTTGGTGACACGACC
1 GTATGACACACACAACTTGGCGACACGACC
21580185 ATTTGTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (30 bp):
GTATGACACACACAACTTGGCGACACGACC
Found at i:21589299 original size:14 final size:15
Alignment explanation
Indices: 21589280--21589309 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
21589270 AAAATGAAAG
21589280 AAGGAGGAG-AAGAA
1 AAGGAGGAGAAAGAA
21589294 AAGGAGGAGAAAGAA
1 AAGGAGGAGAAAGAA
21589309 A
1 A
21589310 CATCGTGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (15 bp):
AAGGAGGAGAAAGAA
Found at i:21589443 original size:17 final size:17
Alignment explanation
Indices: 21589421--21589453 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21589411 ATAAGTACGC
*
21589421 ATTGTCATTGCATTTTT
1 ATTGTCATTACATTTTT
21589438 ATTGTCATTACATTTT
1 ATTGTCATTACATTTT
21589454 CATGTTAGTG
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:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (17 bp):
ATTGTCATTACATTTTT
Found at i:21589521 original size:19 final size:19
Alignment explanation
Indices: 21589497--21589541 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
21589487 AGTTTAGGGG
21589497 AATGCACATGGGGCTTAGA
1 AATGCACATGGGGCTTAGA
*
21589516 AATGCACATGGGGCTTTGA
1 AATGCACATGGGGCTTAGA
21589535 AATGCAC
1 AATGCAC
21589542 CCACATTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (19 bp):
AATGCACATGGGGCTTAGA
Found at i:21591884 original size:31 final size:31
Alignment explanation
Indices: 21591846--21591906 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
21591836 TTTTGCTCGC
** *
21591846 ATAATATATTTCATATAAAACCTTGTCCTTT
1 ATAATATATCACATAGAAAACCTTGTCCTTT
*
21591877 ATAATATATCACATGGAAAACCTTGTCCTT
1 ATAATATATCACATAGAAAACCTTGTCCTT
21591907 CCTTTTCCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (31 bp):
ATAATATATCACATAGAAAACCTTGTCCTTT
Found at i:21593778 original size:50 final size:50
Alignment explanation
Indices: 21593667--21594015 Score: 274
Period size: 50 Copynumber: 6.9 Consensus size: 50
21593657 CATTTGGGTA
* * *
21593667 AAGAGATCCCATTTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA-T
* * *
21593721 ATGAGAGGTCCCAAGTCAGACCATGTCTGGGGCATGGCATTGGCACCGAGAT
1 A--AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* * *
21593773 AAGAGGTCCCATGTAAGACCACGTCTGGGACATGGCGTTGGGACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* * * * *
21593823 GAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCAAGCT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* **** * *
21593873 GAGAGGTCCCCCAAAAGACCATGTCTTGGGACATGGCA-TGAGCACCTATAT
1 AAGAGGTCCCATGTAAGACCATGTC-TGGGACATGGCATTG-GCACCGAGAT
* ** * * * * * *
21593924 GAGAACTCTCATGTAAGACCATATCTGGGATATGGCATTAGCAGTACAAGA-
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCGAGAT
* * * *
21593975 AACA--TCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
21594016 TGTTATATTC
Statistics
Matches: 239, Mismatches: 49, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
49 30 0.13
50 124 0.52
51 37 0.15
52 5 0.02
53 4 0.02
54 1 0.00
55 1 0.00
56 37 0.15
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:21595819 original size:21 final size:21
Alignment explanation
Indices: 21595793--21595837 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
21595783 GTGATGTAGG
21595793 GAAAGCAGAATTTTGGCTTGA
1 GAAAGCAGAATTTTGGCTTGA
21595814 GAAAGCAGAATTTTGGCTTGA
1 GAAAGCAGAATTTTGGCTTGA
21595835 GAA
1 GAA
21595838 TACTATCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.29, T:0.27
Consensus pattern (21 bp):
GAAAGCAGAATTTTGGCTTGA
Found at i:21600618 original size:50 final size:50
Alignment explanation
Indices: 21600513--21600854 Score: 380
Period size: 50 Copynumber: 6.7 Consensus size: 50
21600503 GGTAAAAAGA
* * *
21600513 TCCCATGTAA-ACCATGTCTGGGACATGTCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATGAGAGG
* *
21600568 TCCCATGTAGGACCATGTCTGGGACATGCCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
* * * *
21600618 TCCCATGTAAGGCCATGTCTAGGACATGCCGTTGGCACCGAGATGAGACG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
* * *
21600668 TCCCATGAAAGACCATGTCTAGGACATGGCGTTGGCACCGAGAAGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
* * *
21600718 TCCCATATAAGACCATGTCTGAGACATGGCGTTGGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
** * * * * **
21600768 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
* * * *
21600818 TCTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
21600855 GAACAAGAAA
Statistics
Matches: 251, Mismatches: 35, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
50 214 0.85
53 3 0.01
55 10 0.04
56 24 0.10
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
Found at i:21600829 original size:100 final size:100
Alignment explanation
Indices: 21600560--21600903 Score: 368
Period size: 100 Copynumber: 3.5 Consensus size: 100
21600550 CATTGAGATT
* *
21600560 ATGAGAGGTCCCATGTAGGACCATGTCTGGGACATGCCGTTGGCACCGAGATGAGAGGTCCCATG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATG
* * *
21600625 TAAGGCCATGTCT-AGGACATGCCGTTGGCACCGAG
66 TAAGACCATGTCTGA-GACATGGCGTTGGCACCAAG
* * * * *
21600660 ATGAGACGTCCCATGAAAGACCATGTCTAGGACATGGCGTTGGCACCGAGAAGAGAGGTCCCATA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATG
21600725 TAAGACCATGTCTGAGACATGGCGTTGGCACCAAG
66 TAAGACCATGTCTGAGACATGGCGTTGGCACCAAG
** * * * * ** *
21600760 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAACTCTCATG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATG
* * * * * *
21600825 TAAGACCATATCTGGGATATGGCATTGGCA-GAAC
66 TAAGACCATGTCTGAGACATGGCGTTGGCACCAAG
* * ** * * * *
21600859 AAGAAACATCCCATGTAAGACTATGTCTGGGGCATAGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
21600904 TGTTATATTC
Statistics
Matches: 202, Mismatches: 41, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
99 36 0.18
100 165 0.82
101 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.21
Consensus pattern (100 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATG
TAAGACCATGTCTGAGACATGGCGTTGGCACCAAG
Found at i:21608354 original size:33 final size:33
Alignment explanation
Indices: 21608316--21608388 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
21608306 CTGATTTAGT
*
21608316 CTTCTCCTCATCTCCCTCTGGTCCTGTTGTGGC
1 CTTCTCCTCATCTCCCTCTGGCCCTGTTGTGGC
* * *
21608349 CTTCTCATTATCTCCCTCTGGCCCTTTTGTGGC
1 CTTCTCCTCATCTCCCTCTGGCCCTGTTGTGGC
21608382 CTTCTCC
1 CTTCTCC
21608389 ATAGTGGCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.04, C:0.40, G:0.15, T:0.41
Consensus pattern (33 bp):
CTTCTCCTCATCTCCCTCTGGCCCTGTTGTGGC
Found at i:21610250 original size:56 final size:56
Alignment explanation
Indices: 21610164--21610395 Score: 437
Period size: 56 Copynumber: 4.1 Consensus size: 56
21610154 ACAAGGGATG
21610164 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
21610220 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
21610276 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
21610332 ATGGGCAAAACATGTCATCAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
21610388 ATGGGCAA
1 ATGGGCAA
21610396 TAAACTAATA
Statistics
Matches: 172, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 172 1.00
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:21617065 original size:47 final size:47
Alignment explanation
Indices: 21616999--21617660 Score: 1270
Period size: 47 Copynumber: 14.1 Consensus size: 47
21616989 GAAATGATAG
21616999 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617046 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617093 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617140 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617187 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617234 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617281 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617328 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617375 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617422 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617469 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617516 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617563 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * *
21617610 CAAGGCCTAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21617657 TAAG
1 TAAG
21617661 TCCCGAAGGG
Statistics
Matches: 608, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 608 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:21617835 original size:37 final size:37
Alignment explanation
Indices: 21617779--21617857 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
21617769 CCGAGCTCTA
* * *
21617779 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
21617816 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
21617853 AAGAC
1 AAGAC
21617858 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:21627996 original size:11 final size:11
Alignment explanation
Indices: 21627980--21628019 Score: 80
Period size: 11 Copynumber: 3.6 Consensus size: 11
21627970 CTAGCAATAC
21627980 ATCACCATTAT
1 ATCACCATTAT
21627991 ATCACCATTAT
1 ATCACCATTAT
21628002 ATCACCATTAT
1 ATCACCATTAT
21628013 ATCACCA
1 ATCACCA
21628020 ATACAAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.38, C:0.30, G:0.00, T:0.33
Consensus pattern (11 bp):
ATCACCATTAT
Found at i:21630401 original size:19 final size:18
Alignment explanation
Indices: 21630362--21630401 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21630352 TTTAACCATT
*
21630362 ACAATGCTTTTGGCTCTC
1 ACAATGCTTTTGGCACTC
*
21630380 ACAATGCTTTTGTTCACTC
1 ACAATGCTTTTG-GCACTC
21630399 ACA
1 ACA
21630402 TTTCTCATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.38
Consensus pattern (18 bp):
ACAATGCTTTTGGCACTC
Found at i:21633494 original size:27 final size:27
Alignment explanation
Indices: 21633452--21633512 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
21633442 TAAGAGTTTG
* *
21633452 AGGCCTGGTGAACTGGTGTTCGCCAGA
1 AGGCCTGATGAACTGGGGTTCGCCAGA
* *
21633479 AGGCCTGATGAGCTGGGGTTTGCCAGA
1 AGGCCTGATGAACTGGGGTTCGCCAGA
21633506 AGGCCTG
1 AGGCCTG
21633513 TAGAACAGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.18, C:0.21, G:0.39, T:0.21
Consensus pattern (27 bp):
AGGCCTGATGAACTGGGGTTCGCCAGA
Found at i:21633523 original size:27 final size:27
Alignment explanation
Indices: 21633452--21633524 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
21633442 TAAGAGTTTG
* * * *
21633452 AGGCCTGGTGAACTGGTGTTCGCCAGA
1 AGGCCTGATGAACAGGGGTTTGCCAGA
* *
21633479 AGGCCTGATGAGCTGGGGTTTGCCAGA
1 AGGCCTGATGAACAGGGGTTTGCCAGA
21633506 AGGCCTG-TAGAACAGGGGT
1 AGGCCTGAT-GAACAGGGGT
21633525 CACTAGTGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.21, C:0.19, G:0.40, T:0.21
Consensus pattern (27 bp):
AGGCCTGATGAACAGGGGTTTGCCAGA
Found at i:21633622 original size:25 final size:26
Alignment explanation
Indices: 21633554--21633624 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
21633544 CTATGATCGT
21633554 TAGTGGGCTTGGTGCAG-TAGGGATTGC
1 TAGTGGGCTTGGTG-AGCT-GGGATTGC
* *
21633581 TAGTGGGCTTGGGGAGCTGGGGTTGC
1 TAGTGGGCTTGGTGAGCTGGGATTGC
*
21633607 -AGTGGGCCTGGTGAGCTG
1 TAGTGGGCTTGGTGAGCTG
21633625 TGATCACTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 16 0.41
26 9 0.23
27 14 0.36
ACGTcount: A:0.11, C:0.13, G:0.49, T:0.27
Consensus pattern (26 bp):
TAGTGGGCTTGGTGAGCTGGGATTGC
Found at i:21637741 original size:37 final size:37
Alignment explanation
Indices: 21637700--21637899 Score: 160
Period size: 37 Copynumber: 5.2 Consensus size: 37
21637690 ACACCCAGTG
21637700 TCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTT
1 TCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTT
* * * *
21637737 TCTCATC-A-AATCTATCCGAAGAAA-TATAGTGACACCCAGTG
1 TCTCATCGACAA---AGCCGAAGAAAGT-T-G-G-TACCCTGTT
21637778 TCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTT
1 TCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTT
* * * *
21637815 TCTCATC-A-AATCTATCCGAAGAAA-TATAGTGACACCCAGTG
1 TCTCATCGACAA---AGCCGAAGAAAGT-T-G-G-TACCCTGTT
21637856 TCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTT
1 TCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTT
21637893 TCTCATC
1 TCTCATC
21637900 AAATCTATCC
Statistics
Matches: 127, Mismatches: 16, Indels: 40
0.69 0.09 0.22
Matches are distributed among these distances:
35 4 0.03
36 2 0.02
37 35 0.28
38 24 0.19
39 4 0.03
40 24 0.19
41 28 0.22
42 2 0.02
43 4 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (37 bp):
TCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTT
Found at i:21637817 original size:78 final size:78
Alignment explanation
Indices: 21637683--21637939 Score: 505
Period size: 78 Copynumber: 3.3 Consensus size: 78
21637673 GTTCAAAGCA
21637683 ATAGTTGACACCCAGTGTCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTTTCTCATCAAAT
1 ATAG-TGACACCCAGTGTCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTTTCTCATCAAAT
21637748 CTATCCGAAGAAAT
65 CTATCCGAAGAAAT
21637762 ATAGTGACACCCAGTGTCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATC
1 ATAGTGACACCCAGTGTCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATC
21637827 TATCCGAAGAAAT
66 TATCCGAAGAAAT
21637840 ATAGTGACACCCAGTGTCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATC
1 ATAGTGACACCCAGTGTCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATC
21637905 TATCCGAAGAAAT
66 TATCCGAAGAAAT
21637918 ATAGTGACACCCAGTGTCTCAT
1 ATAGTGACACCCAGTGTCTCAT
21637940 TGACTCGAGG
Statistics
Matches: 178, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 174 0.98
79 4 0.02
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (78 bp):
ATAGTGACACCCAGTGTCTCATCGACAAAGCCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATC
TATCCGAAGAAAT
Found at i:21637838 original size:38 final size:38
Alignment explanation
Indices: 21637714--21637916 Score: 170
Period size: 38 Copynumber: 5.2 Consensus size: 38
21637704 ATCGACAAAG
21637714 CCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATCTAT
1 CCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATCTAT
* * * *
21637752 CCGAAGAAA-TATAGTGACACCCAGTGTCTCATCGACAA---AG
1 CCGAAGAAAGT-T-G-G-TACCCTGTTTCTCATC-A-AATCTAT
21637792 CCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATCTAT
1 CCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATCTAT
* * * *
21637830 CCGAAGAAA-TATAGTGACACCCAGTGTCTCATCGACAA---AG
1 CCGAAGAAAGT-T-G-G-TACCCTGTTTCTCATC-A-AATCTAT
21637870 CCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATCTAT
1 CCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATCTAT
21637908 CCGAAGAAA
1 CCGAAGAAA
21637917 TATAGTGACA
Statistics
Matches: 129, Mismatches: 16, Indels: 40
0.70 0.09 0.22
Matches are distributed among these distances:
35 4 0.03
36 2 0.02
37 28 0.22
38 33 0.26
39 4 0.03
40 24 0.19
41 28 0.22
42 2 0.02
43 4 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (38 bp):
CCGAAGAAAGTTGGTACCCTGTTTCTCATCAAATCTAT
Found at i:21638871 original size:16 final size:16
Alignment explanation
Indices: 21638852--21638882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21638842 ATGGTCTCTG
*
21638852 TTTCTTTTCTTCTTTA
1 TTTCTTTTATTCTTTA
21638868 TTTCTTTTATTCTTT
1 TTTCTTTTATTCTTT
21638883 TACTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTTATTCTTTA
Found at i:21645509 original size:22 final size:22
Alignment explanation
Indices: 21645481--21645530 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
21645471 TCCACACATA
21645481 TATTCATCATTCGATTGAATTT
1 TATTCATCATTCGATTGAATTT
21645503 TATTCATCATTCGATTGAATTT
1 TATTCATCATTCGATTGAATTT
*
21645525 TTTTCA
1 TATTCA
21645531 ACTTAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.52
Consensus pattern (22 bp):
TATTCATCATTCGATTGAATTT
Found at i:21646538 original size:25 final size:25
Alignment explanation
Indices: 21646488--21646538 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
21646478 TTCGACGCAC
* ** *
21646488 AGCTTGTGTGAGCATATTGATTTAT
1 AGCTTGTGAGAGCATACCGATCTAT
21646513 AGCTTGTGAGAGCATACCGATCTAT
1 AGCTTGTGAGAGCATACCGATCTAT
21646538 A
1 A
21646539 ACTCGAGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (25 bp):
AGCTTGTGAGAGCATACCGATCTAT
Found at i:21658623 original size:20 final size:20
Alignment explanation
Indices: 21658598--21658638 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
21658588 CTCTATTATC
*
21658598 TTGCATTGTTTTTAGGTTTA
1 TTGCATAGTTTTTAGGTTTA
21658618 TTGCATAGTTTTTAGGTTTA
1 TTGCATAGTTTTTAGGTTTA
21658638 T
1 T
21658639 GTGATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.59
Consensus pattern (20 bp):
TTGCATAGTTTTTAGGTTTA
Found at i:21658961 original size:16 final size:15
Alignment explanation
Indices: 21658906--21658966 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
21658896 TTCATTCAAA
21658906 CATTTAGATCATTTG
1 CATTTAGATCATTTG
* * *
21658921 CACTTAGATTTAATTG
1 CATTTAGA-TCATTTG
**
21658937 CATAGAGATCATCTTG
1 CATTTAGATCAT-TTG
*
21658953 CATTTAGATAATTT
1 CATTTAGATCATTT
21658967 AATTTAATCA
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
15 11 0.33
16 22 0.67
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (15 bp):
CATTTAGATCATTTG
Found at i:21659238 original size:7 final size:7
Alignment explanation
Indices: 21659226--21659252 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
21659216 ACATTACTAA
21659226 TTTATTC
1 TTTATTC
21659233 TTTATTC
1 TTTATTC
21659240 TTTATTC
1 TTTATTC
21659247 TTTATT
1 TTTATT
21659253 TGTGATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTATTC
Found at i:21667254 original size:12 final size:12
Alignment explanation
Indices: 21667237--21667262 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21667227 GGAAAATATG
21667237 ATAAATATGTTA
1 ATAAATATGTTA
21667249 ATAAATATGTTA
1 ATAAATATGTTA
21667261 AT
1 AT
21667263 GTTACCACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
ATAAATATGTTA
Found at i:21671907 original size:27 final size:27
Alignment explanation
Indices: 21671876--21671935 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
21671866 CCGTTGGGAT
* * *
21671876 AGTAAATACGAAGTAGTCTATTGGAAC
1 AGTAAAAACGAAGTAGTCTATCGAAAC
* **
21671903 AGTAAAAATGGGGTAGTCTATCGAAAC
1 AGTAAAAACGAAGTAGTCTATCGAAAC
21671930 AGTAAA
1 AGTAAA
21671936 CACAGAGTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.23
Consensus pattern (27 bp):
AGTAAAAACGAAGTAGTCTATCGAAAC
Found at i:21671945 original size:27 final size:27
Alignment explanation
Indices: 21671887--21671946 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
21671877 GTAAATACGA
* * **
21671887 AGTAGTCTATTGGAACAGTAAAAATGG
1 AGTAGTCTATCGAAACAGTAAAAACAG
* *
21671914 GGTAGTCTATCGAAACAGTAAACACAG
1 AGTAGTCTATCGAAACAGTAAAAACAG
21671941 AGTAGT
1 AGTAGT
21671947 TCGTTGGGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (27 bp):
AGTAGTCTATCGAAACAGTAAAAACAG
Found at i:21681648 original size:18 final size:18
Alignment explanation
Indices: 21681611--21681654 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
21681601 CATTGTTTGG
*
21681611 CAAATTAATATAGTTCAC
1 CAAATTAATACAGTTCAC
*
21681629 CATATTAATACAGATT-AC
1 CAAATTAATACAG-TTCAC
21681647 CAAATTAA
1 CAAATTAA
21681655 CACAATTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.32
Consensus pattern (18 bp):
CAAATTAATACAGTTCAC
Found at i:21682049 original size:27 final size:28
Alignment explanation
Indices: 21682019--21682086 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 28
21682009 ATACCAAAAT
* *
21682019 CCATTAATATATACTATGTAA-ATAAAG
1 CCATGAATATATACTATATAAGATAAAG
* * *
21682046 CCATGCATATATATTATATAAGATAAAA
1 CCATGAATATATACTATATAAGATAAAG
* *
21682074 TCATGCATATATA
1 CCATGAATATATA
21682087 TAATATATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 17 0.50
28 17 0.50
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (28 bp):
CCATGAATATATACTATATAAGATAAAG
Found at i:21682078 original size:28 final size:27
Alignment explanation
Indices: 21682025--21682093 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
21682015 AAATCCATTA
* * *
21682025 ATATATACTATGTAAATAAAGCCATGC
1 ATATATATTATATAAATAAAACCATGC
*
21682052 ATATATATTATATAAGATAAAATCATGC
1 ATATATATTATATAA-ATAAAACCATGC
*
21682080 ATATATATAATATA
1 ATATATATTATATA
21682094 TGTATAACCA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 13 0.36
28 23 0.64
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (27 bp):
ATATATATTATATAAATAAAACCATGC
Found at i:21682132 original size:26 final size:24
Alignment explanation
Indices: 21682082--21682151 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 24
21682072 AATCATGCAT
* *
21682082 ATATATAATATATGTATAACCACCC
1 ATATAT-ATATATATATAACAACCC
* *
21682107 ACGTGTATATATATATATCACAACCC
1 A--TATATATATATATATAACAACCC
21682133 ATATATATATAATATATAA
1 ATATATATAT-ATATATAA
21682152 GATGCATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
24 8 0.22
25 8 0.22
26 16 0.44
27 4 0.11
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (24 bp):
ATATATATATATATATAACAACCC
Found at i:21687834 original size:54 final size:55
Alignment explanation
Indices: 21687771--21687904 Score: 148
Period size: 54 Copynumber: 2.5 Consensus size: 55
21687761 AGTGGCAATT
* *
21687771 GAAGACCATATAGTGTAAGCCCTAGTCGTT-GACTATGGCATCAAATGGGGAAA-A
1 GAAGACCATATAGTGTAAGACCTAGTCATTAG-CTATGGCATCAAATGGGGAAACA
* ** * *
21687825 GAAGACCATATAGTCTAAGGTCTAGCCATTAGCTATGGCATCATATGGGGAAACA
1 GAAGACCATATAGTGTAAGACCTAGTCATTAGCTATGGCATCAAATGGGGAAACA
* * *
21687880 -AAGGCCACATTGTGTAAGACCTAGT
1 GAAGACCATATAGTGTAAGACCTAGT
21687905 TTGAGACTAT
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
54 63 0.97
55 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (55 bp):
GAAGACCATATAGTGTAAGACCTAGTCATTAGCTATGGCATCAAATGGGGAAACA
Found at i:21688434 original size:30 final size:30
Alignment explanation
Indices: 21688362--21688440 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
21688352 TGAATGAATT
* * *
21688362 TGGATGCCCTTGTTGCTATCTAATGATGTG
1 TGGATGCCTTTGTGGCTATCTAATGATGTA
***
21688392 TGGGCACCTTTGTGGCTATCTAATGATGTA
1 TGGATGCCTTTGTGGCTATCTAATGATGTA
*
21688422 TGGATGCGTTTGTGGCTAT
1 TGGATGCCTTTGTGGCTAT
21688441 TTAAGTCAAG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.16, C:0.15, G:0.29, T:0.39
Consensus pattern (30 bp):
TGGATGCCTTTGTGGCTATCTAATGATGTA
Found at i:21692235 original size:20 final size:20
Alignment explanation
Indices: 21692212--21692288 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
21692202 AAGATGATGA
21692212 ACCATTTCATTTACTTACTT
1 ACCATTTCATTTACTTACTT
*
21692232 ACCATTCCATTTACTTACTCT
1 ACCATTTCATTTACTTACT-T
* *
21692253 -TCACTTT-ATCTACTTACTT
1 ACCA-TTTCATTTACTTACTT
*
21692272 TCCATTTCATTTACTTA
1 ACCATTTCATTTACTTA
21692289 GCATAAGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 4 0.09
20 40 0.85
21 3 0.06
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.49
Consensus pattern (20 bp):
ACCATTTCATTTACTTACTT
Found at i:21697476 original size:31 final size:31
Alignment explanation
Indices: 21697433--21697503 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
21697423 TGCAAAATGT
21697433 TTGGTCATGAATGGTAGGAATTGGTTTAGATC
1 TTGG-CATGAATGGTAGGAATTGGTTTAGATC
*
21697465 TTGGCATGAATGGTAGTAATTGGTTTAGATC
1 TTGGCATGAATGGTAGGAATTGGTTTAGATC
21697496 TTGGCATG
1 TTGGCATG
21697504 GTGTTTGAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.38
Consensus pattern (31 bp):
TTGGCATGAATGGTAGGAATTGGTTTAGATC
Found at i:21701234 original size:14 final size:14
Alignment explanation
Indices: 21701215--21701241 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21701205 CATTTCTTGG
21701215 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
21701229 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
21701242 ACTGGACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:21705021 original size:30 final size:30
Alignment explanation
Indices: 21704964--21705025 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
21704954 GTTTTTTGAA
* *
21704964 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
21704994 AATATTTACAAAAAGA-GCAACCAAATTTTT
1 AATATTTACAAAAAGAGGC-ACCAAATTTTT
21705024 AA
1 AA
21705026 AAATAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:21711557 original size:14 final size:14
Alignment explanation
Indices: 21711538--21711564 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21711528 CATTTCTTGG
21711538 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
21711552 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
21711565 ACTAGACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:21720992 original size:54 final size:54
Alignment explanation
Indices: 21720878--21720999 Score: 140
Period size: 54 Copynumber: 2.3 Consensus size: 54
21720868 ACTAGCTGTT
* * **
21720878 GACTATGACATCATATGGGGAAATTAAGACAATATAGTGTAAGGTCTAGTCGTTA
1 GACTATGGCATCATATGGGGAAATGAAGACAATATAGTGTAAGACCTAGTCG-TA
* * *
21720933 G-CTATGGCATCATATGGGGAAATGAAGACCATATTGTGTAAGACCTATTC-TA
1 GACTATGGCATCATATGGGGAAATGAAGACAATATAGTGTAAGACCTAGTCGTA
*
21720985 GGACTATGGCGTCAT
1 -GACTATGGCATCAT
21721000 GTGGAAATGA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
52 2 0.04
53 1 0.02
54 53 0.93
55 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (54 bp):
GACTATGGCATCATATGGGGAAATGAAGACAATATAGTGTAAGACCTAGTCGTA
Found at i:21721186 original size:28 final size:29
Alignment explanation
Indices: 21721154--21721209 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
21721144 TTTTTGGTTG
21721154 TTCTCTGTTATA-TGAGCATTTGTGGCTT
1 TTCTCTGTTATAGTGAGCATTTGTGGCTT
*
21721182 TTCTCTGTTATATGTGAGCCTTTGTGGC
1 TTCTCTGTTATA-GTGAGCATTTGTGGC
21721210 GAAATCGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 12 0.48
30 13 0.52
ACGTcount: A:0.12, C:0.16, G:0.23, T:0.48
Consensus pattern (29 bp):
TTCTCTGTTATAGTGAGCATTTGTGGCTT
Found at i:21721206 original size:30 final size:31
Alignment explanation
Indices: 21721129--21721209 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 31
21721119 GTTGAATCTA
*
21721129 TTATATGTGAAAGCCTTTTTGG-TTGTTCTCTG
1 TTATATGTG--AGCCTTTGTGGCTTGTTCTCTG
*
21721161 TTATA--TGAGCATTTGTGGCTT-TTCTCTG
1 TTATATGTGAGCCTTTGTGGCTTGTTCTCTG
21721189 TTATATGTGAGCCTTTGTGGC
1 TTATATGTGAGCCTTTGTGGC
21721210 GAAATCGTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
28 21 0.49
29 2 0.05
30 15 0.35
32 5 0.12
ACGTcount: A:0.15, C:0.14, G:0.23, T:0.48
Consensus pattern (31 bp):
TTATATGTGAGCCTTTGTGGCTTGTTCTCTG
Found at i:21724480 original size:37 final size:37
Alignment explanation
Indices: 21724430--21724508 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
21724420 TTATTACGAA
* * *
21724430 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
21724467 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
21724504 GTCTT
1 GTCTT
21724509 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:21724705 original size:47 final size:47
Alignment explanation
Indices: 21724629--21724778 Score: 201
Period size: 47 Copynumber: 3.2 Consensus size: 47
21724619 CTTCGGGACT
* * * * *
21724629 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
* * *
21724676 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
* * *
21724723 TATCACATATATACACTTTCACATTTATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
21724770 TATCACATA
1 TATCACATA
21724779 GAATCCTAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 93 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
Found at i:21733746 original size:33 final size:33
Alignment explanation
Indices: 21733709--21733852 Score: 94
Period size: 33 Copynumber: 4.3 Consensus size: 33
21733699 ATTCCGATGA
*
21733709 TAAGACCATGATTGGGTTATGGCACTATGGACG
1 TAAGACCATGATTGGGCTATGGCACTATGGACG
* * * ** * **
21733742 TAAGACCATGGTTGGACCATGGCGGTGTTTATACG
1 TAAGACCATGATTGGGCTATGGC--ACTATGGACG
* * *
21733777 TAAGACCAT-AGTTGGGCTATGGCATTCT-GATG
1 TAAGACCATGA-TTGGGCTATGGCACTATGGACG
* * * *
21733809 ATAAGACCATAATTGGGTTATGGCACTATGAATG
1 -TAAGACCATGATTGGGCTATGGCACTATGGACG
21733843 TAAGACCATG
1 TAAGACCATG
21733853 GCAGGGCCAT
Statistics
Matches: 83, Mismatches: 22, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
32 2 0.02
33 53 0.64
34 4 0.05
35 24 0.29
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (33 bp):
TAAGACCATGATTGGGCTATGGCACTATGGACG
Found at i:21733813 original size:101 final size:101
Alignment explanation
Indices: 21733637--21733853 Score: 335
Period size: 101 Copynumber: 2.1 Consensus size: 101
21733627 AAATTATTCA
* *
21733637 AACGTAAGACCATGGTTTGACCATCGCAATGTTTATATGTAAGACCACAGCTGGGCTATGGCATT
1 AACGTAAGACCATGGTTGGACCATCGCAATGTTTATACGTAAGACCACAGCTGGGCTATGGCATT
*
21733702 CCGATGATAAGACCATGATTGGGTTATGGCACTATG
66 CCGATGATAAGACCATAATTGGGTTATGGCACTATG
* * ** * *
21733738 GACGTAAGACCATGGTTGGACCATGGCGGTGTTTATACGTAAGACCATAGTTGGGCTATGGCATT
1 AACGTAAGACCATGGTTGGACCATCGCAATGTTTATACGTAAGACCACAGCTGGGCTATGGCATT
*
21733803 CTGATGATAAGACCATAATTGGGTTATGGCACTATG
66 CCGATGATAAGACCATAATTGGGTTATGGCACTATG
*
21733839 AATGTAAGACCATGG
1 AACGTAAGACCATGG
21733854 CAGGGCCATG
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 104 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (101 bp):
AACGTAAGACCATGGTTGGACCATCGCAATGTTTATACGTAAGACCACAGCTGGGCTATGGCATT
CCGATGATAAGACCATAATTGGGTTATGGCACTATG
Found at i:21739434 original size:35 final size:35
Alignment explanation
Indices: 21739388--21739458 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
21739378 GCATTAAACA
21739388 TAGTGGAGATAATAACTTTAAATCTTATAATTTTT
1 TAGTGGAGATAATAACTTTAAATCTTATAATTTTT
21739423 TAGTGGAGATAATAACTTTAAATCTTATAATTTTT
1 TAGTGGAGATAATAACTTTAAATCTTATAATTTTT
21739458 T
1 T
21739459 TCACATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (35 bp):
TAGTGGAGATAATAACTTTAAATCTTATAATTTTT
Found at i:21739556 original size:22 final size:22
Alignment explanation
Indices: 21739531--21739616 Score: 61
Period size: 21 Copynumber: 3.9 Consensus size: 22
21739521 AAAAAAAATT
21739531 TATAATTTTAATAAATTTTATC
1 TATAATTTTAATAAATTTTATC
** *
21739553 TAT-ATTTT-ATATTTATTTATT
1 TATAATTTTAATAAAT-TTTATC
* *
21739574 TATAAATTTTAAGATATTTT-TC
1 TAT-AATTTTAATAAATTTTATC
* *
21739596 TATATTTTTTATAAAATTTTA
1 TATAATTTTAAT-AAATTTTA
21739617 ATGTTTTTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
20 4 0.08
21 19 0.40
22 13 0.27
23 8 0.17
24 4 0.08
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (22 bp):
TATAATTTTAATAAATTTTATC
Found at i:21739652 original size:19 final size:18
Alignment explanation
Indices: 21739601--21739650 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
21739591 TTTTCTATAT
*
21739601 TTTTTATAAAATTTTAATG
1 TTTTTAT-AATTTTTAATG
*
21739620 TTTTTAT-ATTTTTAGTG
1 TTTTTATAATTTTTAATG
21739637 TTTTTATAATTTTT
1 TTTTTATAATTTTT
21739651 TAAAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.54
18 6 0.21
19 7 0.25
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (18 bp):
TTTTTATAATTTTTAATG
Found at i:21740158 original size:10 final size:10
Alignment explanation
Indices: 21740118--21740181 Score: 71
Period size: 10 Copynumber: 6.5 Consensus size: 10
21740108 TTCTAGAAAA
21740118 TTTT-TAATT
1 TTTTATAATT
*
21740127 TTTTA-ACTT
1 TTTTATAATT
21740136 TCTTTATATATT
1 T-TTTATA-ATT
*
21740148 TTTTAGAATT
1 TTTTATAATT
21740158 TTTT-TAATT
1 TTTTATAATT
21740167 TTTTATAATT
1 TTTTATAATT
21740177 TTTTA
1 TTTTA
21740182 AAAAAAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
9 16 0.35
10 21 0.46
11 6 0.13
12 3 0.07
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTTATAATT
Found at i:21740167 original size:19 final size:18
Alignment explanation
Indices: 21740118--21740180 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 18
21740108 TTCTAGAAAA
*
21740118 TTTTTAATTTTTTAACTT
1 TTTTTAATTTTTTAAATT
21740136 TCTTTATATATTTTTTAGAATT
1 T-TTT-TA-ATTTTTTA-AATT
21740158 TTTTTAATTTTTTATAATT
1 TTTTTAATTTTTTA-AATT
21740177 TTTT
1 TTTT
21740181 AAAAAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.03
19 19 0.49
20 4 0.10
21 11 0.28
22 4 0.10
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTTAATTTTTTAAATT
Found at i:21740198 original size:28 final size:27
Alignment explanation
Indices: 21740167--21740227 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
21740157 TTTTTTAATT
21740167 TTTTATAATTTTTTAAAAAAAATTTAAA
1 TTTTA-AATTTTTTAAAAAAAATTTAAA
* * * *
21740195 TTTTGAATTTTTTTATAAATATTTTAAA
1 TTTT-AAATTTTTTAAAAAAAATTTAAA
21740223 TTTTA
1 TTTTA
21740228 GAAATTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.04
28 26 0.93
29 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTAAATTTTTTAAAAAAAATTTAAA
Found at i:21740226 original size:19 final size:20
Alignment explanation
Indices: 21740204--21740246 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
21740194 ATTTTGAATT
*
21740204 TTTTTATAAA-TATTTTAAA
1 TTTTTAGAAATTATTTTAAA
*
21740223 -TTTTAGAAATTATTTTGAA
1 TTTTTAGAAATTATTTTAAA
21740242 TTTTT
1 TTTTT
21740247 GTAATTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTTAGAAATTATTTTAAA
Done.