Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 45 of 106
Found at i:17047097 original size:7 final size:7
Alignment explanation
Indices: 17047084--17047122 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
17047074 TGTACTCTGC
17047084 ATTTAAA
1 ATTTAAA
*
17047091 GTTTAAA
1 ATTTAAA
*
17047098 GTTTAAA
1 ATTTAAA
17047105 ATTTAAA
1 ATTTAAA
*
17047112 ATTTAAT
1 ATTTAAA
17047119 ATTT
1 ATTT
17047123 CAACAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (7 bp):
ATTTAAA
Found at i:17050511 original size:56 final size:56
Alignment explanation
Indices: 17050435--17050545 Score: 177
Period size: 56 Copynumber: 2.0 Consensus size: 56
17050425 AATTTTATTA
* *
17050435 AGTCAATAATTTTGCTTCTAAGTGACATGATTAAGCAAAAAAAATTTCTTTTCCTT
1 AGTCAATAATTTTGCATCTAAGTAACATGATTAAGCAAAAAAAATTTCTTTTCCTT
* * *
17050491 AGTCAATAATTTTGCATCTAAGTAATATGATTAAGCCAAAAAATTTTCTTTTCCT
1 AGTCAATAATTTTGCATCTAAGTAACATGATTAAGCAAAAAAAATTTCTTTTCCT
17050546 AGAAGCCATA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (56 bp):
AGTCAATAATTTTGCATCTAAGTAACATGATTAAGCAAAAAAAATTTCTTTTCCTT
Found at i:17052755 original size:28 final size:28
Alignment explanation
Indices: 17052701--17052770 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
17052691 TGAATAATAA
* *
17052701 AAACATATTATAAACAAATAAATTACA-C
1 AAACATA-AATAAACAAATAAACTACATC
* *
17052729 TAAACATAAATAAGCAAATACACTACATC
1 -AAACATAAATAAACAAATAAACTACATC
*
17052758 AAATATAAATAAA
1 AAACATAAATAAA
17052771 ATTTCAATCT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 26 0.76
29 8 0.24
ACGTcount: A:0.61, C:0.14, G:0.01, T:0.23
Consensus pattern (28 bp):
AAACATAAATAAACAAATAAACTACATC
Found at i:17062489 original size:2 final size:2
Alignment explanation
Indices: 17062484--17062537 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
17062474 TGATATATCA
17062484 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17062526 AT AT AT AT AT AT
1 AT AT AT AT AT AT
17062538 CTAAGGCAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17079260 original size:18 final size:18
Alignment explanation
Indices: 17079221--17079267 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
17079211 TGATATTCTC
*
17079221 AATATATTTTTTAATAAT
1 AATATATATTTTAATAAT
17079239 -ATATATATTTTAA-AGAT
1 AATATATATTTTAATA-AT
17079256 AATATATATTTT
1 AATATATATTTT
17079268 TTACGTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 14 0.54
18 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
AATATATATTTTAATAAT
Found at i:17079542 original size:21 final size:22
Alignment explanation
Indices: 17079496--17079542 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
17079486 GCTATTGATA
* *
17079496 CATATCGTTTTTTATTAATATG
1 CATATCGTTTTATATGAATATG
*
17079518 -ATATCGTTTTATATGCAT-TG
1 CATATCGTTTTATATGAATATG
17079538 CATAT
1 CATAT
17079543 TGTACGACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51
Consensus pattern (22 bp):
CATATCGTTTTATATGAATATG
Found at i:17085406 original size:28 final size:28
Alignment explanation
Indices: 17085375--17085473 Score: 101
Period size: 28 Copynumber: 3.6 Consensus size: 28
17085365 TATCATGACG
*
17085375 TATAACAACTACATTTTTCAACATAACA
1 TATAACAACTATATTTTTCAACATAACA
* * * * * *
17085403 TATAATAATTA-AATTTTCAATATGACG
1 TATAACAACTATATTTTTCAACATAACA
* *
17085430 TGTAACAATTATATTTTTCAACATAACA
1 TATAACAACTATATTTTTCAACATAACA
*
17085458 TGTAACAACTATATTT
1 TATAACAACTATATTT
17085474 ACAATATGAT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 21 0.37
28 36 0.63
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.38
Consensus pattern (28 bp):
TATAACAACTATATTTTTCAACATAACA
Found at i:17085436 original size:55 final size:55
Alignment explanation
Indices: 17085369--17085482 Score: 156
Period size: 55 Copynumber: 2.1 Consensus size: 55
17085359 CTTTTTTATC
* * *
17085369 ATGACGTATAACAACTACATTTTTCAACATAACATATAATAATTAAATTTTCAAT
1 ATGACGTATAACAACTACATTTTTCAACATAACATATAACAACTAAATTTACAAT
* * * * *
17085424 ATGACGTGTAACAATTATATTTTTCAACATAACATGTAACAACTATATTTACAAT
1 ATGACGTATAACAACTACATTTTTCAACATAACATATAACAACTAAATTTACAAT
17085479 ATGA
1 ATGA
17085483 TTTTTTATAG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (55 bp):
ATGACGTATAACAACTACATTTTTCAACATAACATATAACAACTAAATTTACAAT
Found at i:17085439 original size:27 final size:27
Alignment explanation
Indices: 17085389--17085482 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
17085379 ACAACTACAT
* * * *
17085389 TTTTCAACATAACATATAATAATTAAA
1 TTTTCAATATGACATGTAACAATTAAA
* *
17085416 TTTTCAATATGACGTGTAACAATTATAT
1 TTTTCAATATGACATGTAACAATTA-AA
* * * *
17085444 TTTTCAACATAACATGTAACAACTATA
1 TTTTCAATATGACATGTAACAATTAAA
*
17085471 TTTACAATATGA
1 TTTTCAATATGA
17085483 TTTTTTATAG
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
27 29 0.57
28 22 0.43
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (27 bp):
TTTTCAATATGACATGTAACAATTAAA
Found at i:17091585 original size:12 final size:12
Alignment explanation
Indices: 17091568--17091597 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17091558 TTTTCAACGA
17091568 AAAATTCCGTTG
1 AAAATTCCGTTG
*
17091580 AAAATTCTGTTG
1 AAAATTCCGTTG
17091592 AAAATT
1 AAAATT
17091598 TGACATTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (12 bp):
AAAATTCCGTTG
Found at i:17091893 original size:12 final size:12
Alignment explanation
Indices: 17091871--17091924 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
17091861 AAAAAGTAAC
17091871 TTTCTAACGAAAT
1 TTTC-AACGAAAT
17091884 TTTCAACGAAAT
1 TTTCAACGAAAT
** *
17091896 TTTCCATTGAAAA
1 TTT-CAACGAAAT
*
17091909 TTCCAACGAAAT
1 TTTCAACGAAAT
17091921 TTTC
1 TTTC
17091925 CGTTGGAAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
12 20 0.62
13 12 0.38
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (12 bp):
TTTCAACGAAAT
Found at i:17094206 original size:2 final size:2
Alignment explanation
Indices: 17094193--17094245 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
17094183 NNNNNNNNNN
*
17094193 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17094235 TA TA TA TA TA T
1 TA TA TA TA TA T
17094246 CGATTATGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17094778 original size:12 final size:12
Alignment explanation
Indices: 17094761--17094798 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
17094751 CTTGAATAAG
17094761 ATACGTGAGGAA
1 ATACGTGAGGAA
*
17094773 ATACGTGGGGAA
1 ATACGTGAGGAA
*
17094785 ATACGTGAAGAA
1 ATACGTGAGGAA
17094797 AT
1 AT
17094799 GAGAAATGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.32, T:0.18
Consensus pattern (12 bp):
ATACGTGAGGAA
Found at i:17098338 original size:30 final size:30
Alignment explanation
Indices: 17098302--17098358 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
17098292 GGTCAAAATA
*
17098302 TTTCCAACGGAAAATTTCGTTGGAAATATT
1 TTTCCAACAGAAAATTTCGTTGGAAATATT
*
17098332 TTTCCAACAGAAATTTTCGTTGGAAAT
1 TTTCCAACAGAAAATTTCGTTGGAAAT
17098359 CCTAAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (30 bp):
TTTCCAACAGAAAATTTCGTTGGAAATATT
Found at i:17101572 original size:20 final size:21
Alignment explanation
Indices: 17101544--17101591 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
17101534 AAATTTATTC
*
17101544 ATAGTTAG-CTAGATCTATCA
1 ATAGATAGCCTAGATCTATCA
* **
17101564 ATAGATAGCCTCGATCTATTG
1 ATAGATAGCCTAGATCTATCA
17101585 ATAGATA
1 ATAGATA
17101592 ATGCCATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
ATAGATAGCCTAGATCTATCA
Found at i:17102912 original size:79 final size:78
Alignment explanation
Indices: 17102703--17102913 Score: 230
Period size: 77 Copynumber: 2.7 Consensus size: 78
17102693 CTTTAGACTC
* * *
17102703 GGTGTGGGGGTAAGAATACCACAAGGTTAAGCTTGGACAACGTACCACTTTTTTCCCTTGTATGT
1 GGTGTGGGGGTAAGAATACCATAAAGTTAAGCTTGGACAACGTACCACTTTTTCCCCTTGTATGT
*
17102768 TGGCTCTAGTCTT
66 TGCCTCTAGTCTT
* * * * ** *
17102781 GGTGT-GAGGTAAGAATACCATAAAGATAAGCTTGGCCAATGTGTCACCTTTTCCCCTTTTGTAT
1 GGTGTGGGGGTAAGAATACCATAAAGTTAAGCTTGGACAACGTACCACTTTTTCCCC--TTGTAT
*
17102845 GTTGCCTCTAGTTTT
64 GTTGCCTCTAGTCTT
* * * *
17102860 GGTGTGGGGGTAAGAATACTATAACGTTAAG-TTGGGCATA-ATACCACTTTTTCC
1 GGTGTGGGGGTAAGAATACCATAAAGTTAAGCTTGGACA-ACGTACCACTTTTTCC
17102914 TTCTTTATGA
Statistics
Matches: 108, Mismatches: 21, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
77 41 0.38
78 5 0.05
79 40 0.37
80 22 0.20
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (78 bp):
GGTGTGGGGGTAAGAATACCATAAAGTTAAGCTTGGACAACGTACCACTTTTTCCCCTTGTATGT
TGCCTCTAGTCTT
Found at i:17106127 original size:531 final size:530
Alignment explanation
Indices: 17105120--17106169 Score: 1401
Period size: 531 Copynumber: 2.0 Consensus size: 530
17105110 TTAATGGGTA
* *
17105120 TTGTGTTGTTTATTTCAAATCTATGCTTATTGCTTCTAATTGCTTGATCAACAATTAGATTGATT
1 TTGTGTTGTTTATTTCAAATCAATGCTTATTGCTTCTAATTGCTTGATCAACAATTAGATTGAGT
* * ** * * * * *
17105185 TGGGTCTCTTAATGCAACTTGATGAAGAGAGTTTAGAATAGACCAATGGTTTGAATAGCATGTGT
66 TGGATCTCTAAATGCAACTTGAAAAAGAGAATTTAAAATAGACCAAAGGTTTAAATAACATGTGT
* * *
17105250 TCATTTCACTTAGAGTTTAGGTGATTTGATTAGTATTTATAATAGAAATATACCTAAATACCATA
131 TCACTTCACTTAGAGCTTAGGTGATTTGATTAGTATTTAGAATAGAAATATACCTAAATACCATA
* * ** *** *
17105315 TGTAGCCAAATTTAGAGCCTAAGCTTAGTGAACCTTCCTTAACTAATTTACATAGACATATGGAG
196 TGCAGCCAAATTTAGAGCATAAGCTTAGTGAACCTTAATTAACTAATTTACATAGACATACAAAA
* * * * *
17105380 AATTAATTATGAGAGGTATGCTCACGAGCATCTTGACAAAGACTTGTAGACAAATTTGGACTTTA
261 AATAAATTAAGAGAGGTATGCTCACGAACATCTTGACAAAGAATTGTAGACAAATTTGGACTCTA
* * * * * * *
17105445 GGTTAGCAACCAACCTATTGATTTAAGTATAAAAAGAGAAATTAAATTCAAATGAAAGGTTGAGT
326 GGCTAGCAACCAACCCATTGATATAAGTATAAAAAGAGAAATTAAATCCAAATAAAAAGTAGAGT
* * * * * * *
17105510 AATTCCACAATCCTAGGCCTCAATACATTGATTCTCTAGCAATTTTTAGCATTAGCTCCTTAGTA
391 AATTCCACAATCCTAGGCCTCAATACACTAAGTCTCTAGAAATTTTTAGCATCAACTCATTAGTA
* *
17105575 TAGCTTTGTTACTTAAATTTTATTTTTAATTAATTTTCAAATTTGATTTACTTAGATAAGATTAG
456 TAGCTTTGTTACTTAAATTTTAGTTTTAATTAA-TTTCAAATTAGATTTACTTAGATAAGATTAG
17105640 TGAGCCCAATT
520 TGAGCCCAATT
17105651 TTGTGTTGTTTATTTCAAATCAATGCTTATTGCTTCTAATTGCTTGATCAACAATTAGATTGAGT
1 TTGTGTTGTTTATTTCAAATCAATGCTTATTGCTTCTAATTGCTTGATCAACAATTAGATTGAGT
17105716 TGGATCTCTAAATGCAACTTGAAAAA-AGGAATTTAAAATAGACCAAAGGTTTAAATAACATGTG
66 TGGATCTCTAAATGCAACTTGAAAAAGA-GAATTTAAAATAGACCAAAGGTTTAAATAACATGTG
* *
17105780 TTCACTTCACTTAGAGCTTAGGTGATTTGATTAGTATTTAGGATAGAAATATACCTATATACCAT
130 TTCACTTCACTTAGAGCTTAGGTGATTTGATTAGTATTTAGAATAGAAATATACCTAAATACCAT
* * *
17105845 GTGCAGCCAAATTTAGAGCATAAGCTTAGTGAACC-TAATTAAATTAATTTTCATAGACATACAA
195 ATGCAGCCAAATTTAGAGCATAAGCTTAGTGAACCTTAATT-AACTAATTTACATAGACATACAA
* * * * * *
17105909 AAAATAAATTAAGATAGGTATGTTTAC-AATATCTTGACAGAGAATTGTAGATAAATTTGGACTC
259 AAAATAAATTAAGAGAGGTATGCTCACGAACATCTTGACAAAGAATTGTAGACAAATTTGGACTC
* * * *
17105973 TAGGCTAGCAACTAACCCATTGATATAAGTATAACGAA-TGAAATTAAATCCAACTAAAAAGTAG
324 TAGGCTAGCAACCAACCCATTGATATAAGTATAA-AAAGAGAAATTAAATCCAAATAAAAAGTAG
** * * * *
17106037 AGTAATTCCACAATTTTAGG-CTCTATTTCACTAAGTCTCTAGAAATTTCTTAGCATCAATTTAT
388 AGTAATTCCACAATCCTAGGCCTC-AATACACTAAGTCTCTAGAAATTT-TTAGCATCAACTCAT
* *
17106101 TAGCT-TAGCTTTGTTACTTCAATTTTAGTTTTAATTAATTTCAAATTAGATTTACTTGGATAAG
451 TAG-TATAGCTTTGTTACTTAAATTTTAGTTTTAATTAATTTCAAATTAGATTTACTTAGATAAG
17106165 ATTAG
515 ATTAG
17106170 GGTGCCAAAT
Statistics
Matches: 447, Mismatches: 66, Indels: 13
0.85 0.13 0.02
Matches are distributed among these distances:
529 3 0.01
530 150 0.34
531 293 0.66
532 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (530 bp):
TTGTGTTGTTTATTTCAAATCAATGCTTATTGCTTCTAATTGCTTGATCAACAATTAGATTGAGT
TGGATCTCTAAATGCAACTTGAAAAAGAGAATTTAAAATAGACCAAAGGTTTAAATAACATGTGT
TCACTTCACTTAGAGCTTAGGTGATTTGATTAGTATTTAGAATAGAAATATACCTAAATACCATA
TGCAGCCAAATTTAGAGCATAAGCTTAGTGAACCTTAATTAACTAATTTACATAGACATACAAAA
AATAAATTAAGAGAGGTATGCTCACGAACATCTTGACAAAGAATTGTAGACAAATTTGGACTCTA
GGCTAGCAACCAACCCATTGATATAAGTATAAAAAGAGAAATTAAATCCAAATAAAAAGTAGAGT
AATTCCACAATCCTAGGCCTCAATACACTAAGTCTCTAGAAATTTTTAGCATCAACTCATTAGTA
TAGCTTTGTTACTTAAATTTTAGTTTTAATTAATTTCAAATTAGATTTACTTAGATAAGATTAGT
GAGCCCAATT
Found at i:17108283 original size:32 final size:32
Alignment explanation
Indices: 17108247--17108309 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
17108237 CATGTTAGTG
* *
17108247 TGTGATGGTGATGTAGTAGTGCCACATCAACA
1 TGTGAGGGTGACGTAGTAGTGCCACATCAACA
*
17108279 TGTGAGGGTGACGTGGTAGTGCCACATCAAC
1 TGTGAGGGTGACGTAGTAGTGCCACATCAAC
17108310 GTTGACCTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.25
Consensus pattern (32 bp):
TGTGAGGGTGACGTAGTAGTGCCACATCAACA
Found at i:17112355 original size:25 final size:25
Alignment explanation
Indices: 17112327--17112404 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
17112317 TCGCAATGAA
17112327 GTATATCAACTCGTGGCCTAGCCAC
1 GTATATCAACTCGTGGCCTAGCCAC
* * * *
17112352 GTATAACGACTTGTGGCCTTGCCAC
1 GTATATCAACTCGTGGCCTAGCCAC
17112377 GTATAATCACAAAC-CGTGGCCTAGCCAC
1 GTAT-AT--C-AACTCGTGGCCTAGCCAC
17112405 ATCTAATAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
25 25 0.61
26 1 0.02
28 13 0.32
29 2 0.05
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.23
Consensus pattern (25 bp):
GTATATCAACTCGTGGCCTAGCCAC
Found at i:17114588 original size:17 final size:15
Alignment explanation
Indices: 17114568--17114606 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
17114558 TACCTTTGTA
17114568 TTTTCTTTTCTTCCTTG
1 TTTTCTTTTCTT--TTG
17114585 TTTTCTTTTCTTTTG
1 TTTTCTTTTCTTTTG
17114600 TTTTCTT
1 TTTTCTT
17114607 GCTCTTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 10 0.45
17 12 0.55
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (15 bp):
TTTTCTTTTCTTTTG
Found at i:17117308 original size:2 final size:2
Alignment explanation
Indices: 17117303--17117327 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17117293 TATATGGTAA
17117303 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 A
17117328 CACGTATGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17117453 original size:36 final size:36
Alignment explanation
Indices: 17117356--17117480 Score: 146
Period size: 36 Copynumber: 3.5 Consensus size: 36
17117346 CTCACCCAGC
* *
17117356 TCATGTGCACTCCCACATCGTGCATAACTAATACCA
1 TCATGTGCACTCCCACATCGTGCACAGCTAATACCA
* *
17117392 TCATGTGCACCCCCACATCGTGCACAGCTAATGCCA
1 TCATGTGCACTCCCACATCGTGCACAGCTAATACCA
* * * *
17117428 TCATGTGCACTCCGACATTGCGCACAGGC-AATATCA
1 TCATGTGCACTCCCACATCGTGCACA-GCTAATACCA
17117464 TCAT-TGCCACTCCCACA
1 TCATGTG-CACTCCCACA
17117481 CCACACATGC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
35 2 0.03
36 72 0.95
37 2 0.03
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.22
Consensus pattern (36 bp):
TCATGTGCACTCCCACATCGTGCACAGCTAATACCA
Found at i:17127563 original size:2 final size:2
Alignment explanation
Indices: 17127551--17127589 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
17127541 ATAGGCCTAG
*
17127551 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17127590 TATGTTGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:17133963 original size:35 final size:35
Alignment explanation
Indices: 17133937--17134192 Score: 232
Period size: 35 Copynumber: 7.3 Consensus size: 35
17133927 CTTAATTGTT
*
17133937 TAATTTAATCAATTAGACCCAATAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * * * *
17133972 CAATTTAATTAATTAAGTCCAACAATTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* *
17134007 CAATTTTAATCAATTAGGCCCAATGACTTAATTAAA
1 TAA-TTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * ***
17134043 CAAAGTTAATCAATTAGGCCTAATAACTTAATTGTT
1 -TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* *
17134079 TAATTTAATTAATTAGGCCC-ATGACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * *
17134113 TAATTTAATTAATTAGGCCCAATGATTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * *
17134148 TAATTTATTTAATTTGG--C-ACAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
*
17134180 CAATTTTAATCAA
1 TAA-TTTAATCAA
17134193 GTGCTTGAGA
Statistics
Matches: 180, Mismatches: 37, Indels: 10
0.79 0.16 0.04
Matches are distributed among these distances:
32 13 0.07
33 8 0.04
34 30 0.17
35 75 0.42
36 52 0.29
37 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (35 bp):
TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
Found at i:17136072 original size:21 final size:20
Alignment explanation
Indices: 17136046--17136085 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
17136036 ACTACATTAT
17136046 ATTGATATATATATGTTGTGC
1 ATTGATATATA-ATGTTGTGC
17136067 ATTGATGA-ATAATGTTGTG
1 ATTGAT-ATATAATGTTGTG
17136086 TAATGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 9 0.50
22 1 0.06
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.45
Consensus pattern (20 bp):
ATTGATATATAATGTTGTGC
Found at i:17136141 original size:42 final size:42
Alignment explanation
Indices: 17136095--17136235 Score: 135
Period size: 42 Copynumber: 3.4 Consensus size: 42
17136085 GTAATGATAT
* * *
17136095 TGACCCAGCTATGTGCTAGTAGGAGTGTGCATACGCCGATGA
1 TGACCCAGCTATGTGCGAGTAGGAGTGAGCATAAGCCGATGA
** *
17136137 TGACCTGGTTATGTGCGAGT-GAGAGTGCA-CATAAGCCGATGA
1 TGACCCAGCTATGTGCGAGTAG-GAGTG-AGCATAAGCCGATGA
* * * *
17136179 TGACCCGGCTATGTTCGAGTAGGAGTGAGCATAAGTCG-TGC
1 TGACCCAGCTATGTGCGAGTAGGAGTGAGCATAAGCCGATGA
* *
17136220 TGACCCAACCATGTGC
1 TGACCCAGCTATGTGC
17136236 TAGTGGGGAG
Statistics
Matches: 80, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
41 16 0.20
42 63 0.79
43 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.23
Consensus pattern (42 bp):
TGACCCAGCTATGTGCGAGTAGGAGTGAGCATAAGCCGATGA
Found at i:17136984 original size:10 final size:9
Alignment explanation
Indices: 17136964--17136988 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17136954 AGGAATTAAT
17136964 AAAATAAAA
1 AAAATAAAA
17136973 AAAATAAAA
1 AAAATAAAA
17136982 AAAATAA
1 AAAATAA
17136989 TATTTTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAAAA
Found at i:17137338 original size:19 final size:19
Alignment explanation
Indices: 17137300--17137339 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
17137290 GCGTGGCCTA
*
17137300 AGTTAAGTTAAGTTAAGTT
1 AGTTAAGTTAAGTCAAGTT
*
17137319 AGTTAAGTTAAGTCAGGTT
1 AGTTAAGTTAAGTCAAGTT
17137338 AG
1 AG
17137340 GTAGAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38
Consensus pattern (19 bp):
AGTTAAGTTAAGTCAAGTT
Found at i:17137341 original size:5 final size:5
Alignment explanation
Indices: 17137298--17137331 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
17137288 CTGCGTGGCC
17137298 TAAGT TAAGT TAAGT TAAGT T-AGT TAAGT TAAGT
1 TAAGT TAAGT TAAGT TAAGT TAAGT TAAGT TAAGT
17137332 CAGGTTAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (5 bp):
TAAGT
Found at i:17142083 original size:13 final size:13
Alignment explanation
Indices: 17142065--17142089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17142055 AGAGAAATTG
17142065 TGATTTTATAAAA
1 TGATTTTATAAAA
17142078 TGATTTTATAAA
1 TGATTTTATAAA
17142090 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:17143301 original size:2 final size:2
Alignment explanation
Indices: 17143294--17143332 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
17143284 TGATGATGGG
* * *
17143294 TA TA TA TA TA TA TA TA TA TA CA TA TA CA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17143333 GTGTGTTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:17145953 original size:21 final size:21
Alignment explanation
Indices: 17145929--17145968 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17145919 AGATTTAAGA
17145929 CTTTTAGTT-GCATTAAAATCT
1 CTTTT-GTTAGCATTAAAATCT
*
17145950 CTTTTGTTAGCTTTAAAAT
1 CTTTTGTTAGCATTAAAAT
17145969 TATTATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (21 bp):
CTTTTGTTAGCATTAAAATCT
Found at i:17147387 original size:66 final size:66
Alignment explanation
Indices: 17147279--17147435 Score: 212
Period size: 66 Copynumber: 2.4 Consensus size: 66
17147269 CCATTATTGT
*
17147279 AGGTTGTGGTTGAGCCTTTGAAAAACCACTTTGAGTTTTAGTTTAACCCGTGAAAAACAAGT-G-
1 AGGTTGTGGTTGAGCC-TTGAAAAACCACTTTGAGTTTTAGTTGAACCCGTGAAAAACAA-TCGC
17147342 TAAA
64 T-AA
* * * *
17147346 AGGTTGTGGTTGAGCCTTGAAAAATCACTTTGGGTTTTAGTTGATCCCGTGAAAAACCATCGCTA
1 AGGTTGTGGTTGAGCCTTGAAAAACCACTTTGAGTTTTAGTTGAACCCGTGAAAAACAATCGCTA
17147411 A
66 A
17147412 AGGTTGTGGTTGAG-CTTGCAAAAA
1 AGGTTGTGGTTGAGCCTTG-AAAAA
17147436 GCCATTGTAA
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
65 5 0.06
66 60 0.73
67 17 0.21
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (66 bp):
AGGTTGTGGTTGAGCCTTGAAAAACCACTTTGAGTTTTAGTTGAACCCGTGAAAAACAATCGCTA
A
Found at i:17149001 original size:19 final size:19
Alignment explanation
Indices: 17148977--17149020 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
17148967 TTCCAAAAGG
17148977 AACTTTATGCAACGAGACT
1 AACTTTATGCAACGAGACT
17148996 AACTTTATGCAACGAGACT
1 AACTTTATGCAACGAGACT
17149015 AACTTT
1 AACTTT
17149021 CAAGGATCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (19 bp):
AACTTTATGCAACGAGACT
Found at i:17158216 original size:19 final size:19
Alignment explanation
Indices: 17158189--17158226 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17158179 GCATTTGACT
17158189 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
* *
17158208 TATTGGAGTATGTTTTGAG
1 TATTAGAGTATGATTTGAG
17158227 GTTTAGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:17160812 original size:42 final size:43
Alignment explanation
Indices: 17160685--17160812 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 43
17160675 TTGATGTGGA
* * * *
17160685 CTCGGCTATGTGGGAGTAGGAGTGCGCACACGCCGATGATGA-
1 CTCGGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGATGAC
* *
17160727 CTCGGCTATGTGCGAGTAAGAGTGCGCATAAGCCAATTATGAC
1 CTCGGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGATGAC
* *
17160770 CT-GGCTATGTGCGAGTAAGAGTGCGCATAAGTCGATGCTGAC
1 CTCGGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGATGAC
17160812 C
1 C
17160813 CAGCCATGTG
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
42 73 0.97
43 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (43 bp):
CTCGGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGATGAC
Found at i:17160884 original size:2 final size:2
Alignment explanation
Indices: 17160877--17160921 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
17160867 ATGATGATGG
* *
17160877 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AC AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17160918 AT AT
1 AT AT
17160922 GTGTCATGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:17163250 original size:66 final size:66
Alignment explanation
Indices: 17163134--17163290 Score: 228
Period size: 66 Copynumber: 2.4 Consensus size: 66
17163124 CCATTGTTGT
* *
17163134 AGGTTGTGGTTGAGCCTTTGAAAAACCACTTTGGGTTTTAGTTTAGCCCGTGAAAAACTAGTG-T
1 AGGTTGTGGTTGAGCC-TTGAAAAACCACTTTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGCT
17163198 AAA
65 -AA
* * *
17163201 AGGTTGTGGTTGAGCCTTGAAAAACCACTTTGGGTTTTGGTTGATCCCGTGAAAAACCATTGCTA
1 AGGTTGTGGTTGAGCCTTGAAAAACCACTTTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGCTA
17163266 A
66 A
17163267 AGGTTGTGGTTGAG-CTTGAGAAAA
1 AGGTTGTGGTTGAGCCTTGA-AAAA
17163291 GCCATTGTAA
Statistics
Matches: 83, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
65 5 0.06
66 61 0.73
67 17 0.20
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.32
Consensus pattern (66 bp):
AGGTTGTGGTTGAGCCTTGAAAAACCACTTTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGCTA
A
Found at i:17165930 original size:4 final size:4
Alignment explanation
Indices: 17165857--17165974 Score: 137
Period size: 4 Copynumber: 29.5 Consensus size: 4
17165847 TGTTTGATAG
* * * * * * *
17165857 ATAT ATAT ATAT ATAG ATAT CTAG ATAT ATCT AGAT ATAT CTAT AGAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
17165905 ATAT CTAT AGAT AGAT AGAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
17165953 ATAT ATAT ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT AT
17165975 NNNNNNNNNN
Statistics
Matches: 96, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 96 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:17165972 original size:10 final size:10
Alignment explanation
Indices: 17165857--17165974 Score: 137
Period size: 10 Copynumber: 11.8 Consensus size: 10
17165847 TGTTTGATAG
17165857 ATATATATAT
1 ATATATATAT
*
17165867 ATATAGATAT
1 ATATATATAT
* *
17165877 CTAGATATAT
1 ATATATATAT
* *
17165887 CTAGATATAT
1 ATATATATAT
* *
17165897 CTATAGATAT
1 ATATATATAT
* *
17165907 ATCTATAGAT
1 ATATATATAT
* *
17165917 AGATAGATAT
1 ATATATATAT
17165927 ATATATATAT
1 ATATATATAT
17165937 ATATATATAT
1 ATATATATAT
17165947 ATATATATAT
1 ATATATATAT
17165957 ATATATATAT
1 ATATATATAT
17165967 ATATATAT
1 ATATATAT
17165975 NNNNNNNNNN
Statistics
Matches: 92, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 92 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (10 bp):
ATATATATAT
Found at i:17173311 original size:22 final size:21
Alignment explanation
Indices: 17173286--17173326 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
17173276 ACCTTTTTTT
*
17173286 CACTTGTTTCCTTGAATTTTCA
1 CACTT-TTCCCTTGAATTTTCA
17173308 CACTTTTCCCTTGAATTTT
1 CACTTTTCCCTTGAATTTT
17173327 TCCACTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (21 bp):
CACTTTTCCCTTGAATTTTCA
Found at i:17173327 original size:22 final size:21
Alignment explanation
Indices: 17173281--17173333 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
17173271 ATCTTACCTT
* *
17173281 TTTTTCACTTGTTTCCTTGAA
1 TTTTCCACTTGTTCCCTTGAA
17173302 TTTTCACACTT-TTCCCTTGAA
1 TTTTC-CACTTGTTCCCTTGAA
17173323 TTTTTCCACTT
1 -TTTTCCACTT
17173334 AGGGTTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.15, C:0.25, G:0.06, T:0.55
Consensus pattern (21 bp):
TTTTCCACTTGTTCCCTTGAA
Found at i:17175963 original size:2 final size:2
Alignment explanation
Indices: 17175956--17175989 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17175946 AAATAAATAA
17175956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17175990 TAGCATCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17179235 original size:55 final size:55
Alignment explanation
Indices: 17179158--17179288 Score: 235
Period size: 55 Copynumber: 2.4 Consensus size: 55
17179148 AACCACCTGC
*
17179158 TCATCAGCTCATGTGCACTCCCACACCACATATAGTTGGAATCATCATCCACCGG
1 TCATCAGCTCATGTGCACTCCCACACCACATATAGTTGGAATCATCATCCACAGG
* *
17179213 TCATCAGCTCATGTGCACTCCCACACCGCATGTAGTTGGAATCATCATCCACAGG
1 TCATCAGCTCATGTGCACTCCCACACCACATATAGTTGGAATCATCATCCACAGG
17179268 TCATCAGCTCATGTGCACTCC
1 TCATCAGCTCATGTGCACTCC
17179289 ACATCGCAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 73 1.00
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.24
Consensus pattern (55 bp):
TCATCAGCTCATGTGCACTCCCACACCACATATAGTTGGAATCATCATCCACAGG
Found at i:17182269 original size:30 final size:30
Alignment explanation
Indices: 17182233--17182289 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17182223 TCATTGACCG
*
17182233 GAGTAATCTCTCGAT-AGTCAACATCACCCA
1 GAGTAATCTCCCGATGAGT-AACATCACCCA
17182263 GAGTAATCTCCCGATGAGTAACATCAC
1 GAGTAATCTCCCGATGAGTAACATCAC
17182290 AGCACTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (30 bp):
GAGTAATCTCCCGATGAGTAACATCACCCA
Found at i:17185244 original size:2 final size:2
Alignment explanation
Indices: 17185231--17185318 Score: 151
Period size: 2 Copynumber: 44.5 Consensus size: 2
17185221 TTTATTTATG
* *
17185231 TA TA TA TG TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17185273 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17185314 TA TA T
1 TA TA T
17185319 GTTTGTGAAA
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
1 1 0.01
2 80 0.99
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17186269 original size:2 final size:2
Alignment explanation
Indices: 17186262--17186291 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17186252 GTTGCAAACA
17186262 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17186292 TTTGATGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17192741 original size:21 final size:21
Alignment explanation
Indices: 17192717--17192757 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17192707 AATAACACAT
17192717 TGTCATAAACAACCCATCAGA
1 TGTCATAAACAACCCATCAGA
* *
17192738 TGTCATTAACAATCCATCAG
1 TGTCATAAACAACCCATCAG
17192758 CAATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (21 bp):
TGTCATAAACAACCCATCAGA
Found at i:17192749 original size:58 final size:58
Alignment explanation
Indices: 17192675--17192790 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
17192665 TTCTTAGCAT
* *
17192675 TCAGATGTCATTAACAATCCATTAGCAATTAAAATAACACATTGTCATAAACAACCCA
1 TCAGATGTCATTAACAATCCATCAGCAATTAAAATAACACATTATCATAAACAACCCA
*
17192733 TCAGATGTCATTAACAATCCATCAGCAATTAAAATAACACATTATCATAAACAGCCCA
1 TCAGATGTCATTAACAATCCATCAGCAATTAAAATAACACATTATCATAAACAACCCA
17192791 GCATCATCAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (58 bp):
TCAGATGTCATTAACAATCCATCAGCAATTAAAATAACACATTATCATAAACAACCCA
Found at i:17196018 original size:22 final size:21
Alignment explanation
Indices: 17195993--17196033 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17195983 AAGGAATAAA
17195993 AGAAAGAAAACAAAGGGAAACT
1 AGAAA-AAAACAAAGGGAAACT
**
17196015 AGAAAAATTCAAAGGGAAA
1 AGAAAAAAACAAAGGGAAA
17196034 TTCGCGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.63, C:0.07, G:0.22, T:0.07
Consensus pattern (21 bp):
AGAAAAAAACAAAGGGAAACT
Found at i:17206536 original size:52 final size:52
Alignment explanation
Indices: 17206381--17206536 Score: 267
Period size: 52 Copynumber: 3.0 Consensus size: 52
17206371 NNNNNNNNNN
* **
17206381 TGATAGTGGTGTGCTGTGTGAGTGCACACACAGATGATATATGCCATGTGTA
1 TGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCG
* *
17206433 TGATAGTGGTGTGCTGTGTGAGTGCACTCACTGATGATATATACCATGTGCG
1 TGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCG
17206485 TGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCG
1 TGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCG
17206537 ATGTGGGAGT
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 97 1.00
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.31
Consensus pattern (52 bp):
TGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCG
Found at i:17206560 original size:36 final size:35
Alignment explanation
Indices: 17206493--17206625 Score: 124
Period size: 36 Copynumber: 3.7 Consensus size: 35
17206483 CGTGATAGTG
* *
17206493 GTGTGCTGTGTGAGTGCACACACTGATGATATATGCCAT
1 GTGTGGTGTGGGAGTG--CACA-TGATGATAT-TGCCAT
* * *
17206532 GTGCGATGTGGGAGTGCACATGATGATATTGCCTT
1 GTGTGGTGTGGGAGTGCACATGATGATATTGCCAT
* * *
17206567 TTGTGGTGTGGGAGTGCACAAGATGAT-TCTAGCTAT
1 GTGTGGTGTGGGAGTGCACATGATGATAT-T-GCCAT
*
17206603 GTGTGGTGTGGAAGTGCACATGA
1 GTGTGGTGTGGGAGTGCACATGA
17206626 GCTAGTGAGA
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
34 1 0.01
35 29 0.37
36 32 0.41
37 4 0.05
39 13 0.16
ACGTcount: A:0.22, C:0.14, G:0.34, T:0.31
Consensus pattern (35 bp):
GTGTGGTGTGGGAGTGCACATGATGATATTGCCAT
Found at i:17206581 original size:35 final size:36
Alignment explanation
Indices: 17206493--17206625 Score: 119
Period size: 35 Copynumber: 3.6 Consensus size: 36
17206483 CGTGATAGTG
* * *
17206493 GTGTGCTGTGTGAGTGCACACACTGATGATATATGCCAT
1 GTGTGGTGTGGGAGTG--CACA-TGATGATATATGCCTT
* *
17206532 GTGCGATGTGGGAGTGCACATGATGATAT-TGCCTT
1 GTGTGGTGTGGGAGTGCACATGATGATATATGCCTT
* * *
17206567 TTGTGGTGTGGGAGTGCACAAGATGAT-TCTAG-CTAT
1 GTGTGGTGTGGGAGTGCACATGATGATATAT-GCCT-T
*
17206603 GTGTGGTGTGGAAGTGCACATGA
1 GTGTGGTGTGGGAGTGCACATGA
17206626 GCTAGTGAGA
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
34 1 0.01
35 31 0.39
36 31 0.39
37 4 0.05
39 13 0.16
ACGTcount: A:0.22, C:0.14, G:0.34, T:0.31
Consensus pattern (36 bp):
GTGTGGTGTGGGAGTGCACATGATGATATATGCCTT
Found at i:17206944 original size:73 final size:73
Alignment explanation
Indices: 17206839--17207153 Score: 252
Period size: 73 Copynumber: 4.3 Consensus size: 73
17206829 CGTTGCAAGG
* *
17206839 AGAAACTCTCGAGTGTTGGGGGCTTGACTAGCCTAGAATTTCGTTACAGCAAAAATGCATTCTCG
1 AGAAACTCTCGGGTGTTGGGGGCTTGACTAGCCTAGAATTTCGTTACAGCAAAAATGCATTCTCA
17206904 TTGTAGCA
66 TTGTAGCA
* * * * * * * * * * *
17206912 AGAAACTCTCGGGTGCTAGGGGCTTAAGTAGCCCAAAATTTTGCTGCAGCGAAAATGCATTCTTA
1 AGAAACTCTCGGGTGTTGGGGGCTTGACTAGCCTAGAATTTCGTTACAGCAAAAATGCATTCTCA
*
17206977 TTGTAGCG
66 TTGTAGCA
* * * * * *
17206985 AGAAACTCTCAGGTGTTGGGGGCTGGACTAGCCTAGAATTTCATTCCAACAAAAAGGCATTCTCA
1 AGAAACTCTCGGGTGTTGGGGGCTTGACTAGCCTAGAATTTCGTTACAGCAAAAATGCATTCTCA
* ** *
17207050 CTACAGCG
66 TTGTAGCA
** * * * * ** * * *
17207058 TTAAACTCTCAGCTGTTGAGGGTTTGACTAGCCTAGAATTTTCACTGCAGCGAAAATGCATTCTT
1 AGAAACTCTCGGGTGTTGGGGGCTTGACTAGCCTAGAA-TTTCGTTACAGCAAAAATGCATTCTC
** * *
17207123 GCTGCAACA
65 ATTGTAGCA
17207132 AGAAACTCTCGGGGTGGTTGGG
1 AGAAACTCTC-GGGT-GTTGGG
17207154 TTAAATGCCT
Statistics
Matches: 185, Mismatches: 54, Indels: 3
0.76 0.22 0.01
Matches are distributed among these distances:
73 145 0.78
74 33 0.18
75 2 0.01
76 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (73 bp):
AGAAACTCTCGGGTGTTGGGGGCTTGACTAGCCTAGAATTTCGTTACAGCAAAAATGCATTCTCA
TTGTAGCA
Found at i:17207090 original size:146 final size:147
Alignment explanation
Indices: 17206838--17207122 Score: 342
Period size: 146 Copynumber: 1.9 Consensus size: 147
17206828 TCGTTGCAAG
* * * *
17206838 GAGAAACTCTCGAGTGTTGGGGGCTTGACTAGCCTAGAATTTCGTTACAGCAAAAATGCATTCTC
1 GAGAAACTCTCGAGTGTTGGGGGCTGGACTAGCCTAGAATTTCATTACAACAAAAAGGCATTCTC
** ** * * * *
17206903 GTTGTAGCAAGAAACTCTCGGGTGCTAGGGGCTTAAGTAGCCCAAAATTTT-GCTGCAGCGAAAA
66 ACTACAGCAAGAAACTCTCAGCTGCTAGGGGCTTAACTAGCCCAAAATTTTCACTGCAGCGAAAA
17206967 TGCATTCTTATTGTAGC
131 TGCATTCTTATTGTAGC
*
17206984 GAGAAACTCTC-AGGTGTTGGGGGCTGGACTAGCCTAGAATTTCATTCCAACAAAAAGGCATTCT
1 GAGAAACTCTCGA-GTGTTGGGGGCTGGACTAGCCTAGAATTTCATTACAACAAAAAGGCATTCT
*** * * * * *
17207048 CACTACAGCGTTAAACTCTCAGCTG-TTGAGGGTTTGACTAGCCTAGAATTTTCACTGCAGCGAA
65 CACTACAGCAAGAAACTCTCAGCTGCTAG-GGGCTTAACTAGCCCAAAATTTTCACTGCAGCGAA
17207112 AATGCATTCTT
129 AATGCATTCTT
17207123 GCTGCAACAA
Statistics
Matches: 115, Mismatches: 21, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
145 3 0.03
146 91 0.79
147 21 0.18
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (147 bp):
GAGAAACTCTCGAGTGTTGGGGGCTGGACTAGCCTAGAATTTCATTACAACAAAAAGGCATTCTC
ACTACAGCAAGAAACTCTCAGCTGCTAGGGGCTTAACTAGCCCAAAATTTTCACTGCAGCGAAAA
TGCATTCTTATTGTAGC
Found at i:17214074 original size:34 final size:34
Alignment explanation
Indices: 17214036--17214102 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
17214026 TGGAATTCCT
* *
17214036 AAGCTC-CCACCAAGCTTTTACAATGGCTTTTCAC
1 AAGCTCACCA-CAACCTTTAACAATGGCTTTTCAC
*
17214070 AAGCTCAGCCACAACCTTTAACAATGGTTTTTC
1 AAGCTCA-CCACAACCTTTAACAATGGCTTTTC
17214103 CTGAGATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 6 0.21
35 19 0.68
36 3 0.11
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (34 bp):
AAGCTCACCACAACCTTTAACAATGGCTTTTCAC
Found at i:17214611 original size:15 final size:17
Alignment explanation
Indices: 17214586--17214625 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
17214576 TATTTTTATA
17214586 ATTTTAGTTAAT-AAATT
1 ATTTTA-TTAATAAAATT
17214603 -TTTTATTAATAAAATT
1 ATTTTATTAATAAAATT
17214619 ATTTTAT
1 ATTTTAT
17214626 GATTTAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.24
16 10 0.48
17 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTATTAATAAAATT
Found at i:17214751 original size:22 final size:22
Alignment explanation
Indices: 17214704--17214759 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
17214694 AAGTAATATT
*
17214704 ATTA-ATAATTAAATTATTAAT
1 ATTATATAATTAAATTATTAAA
*
17214725 TTTATATAATTAAA-TATATAAA
1 ATTATATAATTAAATTAT-TAAA
17214747 ATTAT-TAAATTAA
1 ATTATAT-AATTAA
17214760 TTAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTATATAATTAAATTATTAAA
Found at i:17214756 original size:8 final size:8
Alignment explanation
Indices: 17214701--17214764 Score: 53
Period size: 8 Copynumber: 8.1 Consensus size: 8
17214691 AATAAGTAAT
17214701 ATTATT-A
1 ATTATTAA
*
17214708 ATAATTAA
1 ATTATTAA
17214716 ATTATT-A
1 ATTATTAA
*
17214723 ATT-TTAT
1 ATTATTAA
*
17214730 ATAATTAA
1 ATTATTAA
*
17214738 ATATATAAA
1 AT-TATTAA
17214747 ATTATTAA
1 ATTATTAA
17214755 ATTAATTAA
1 ATT-ATTAA
17214764 A
1 A
17214765 AAAAAATTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
6 2 0.05
7 11 0.25
8 19 0.43
9 12 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
ATTATTAA
Found at i:17223406 original size:18 final size:18
Alignment explanation
Indices: 17223366--17223403 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
17223356 TACAAGCTCA
*
17223366 TTTAATTTTATTCAAATT
1 TTTAATTTTATTAAAATT
*
17223384 CTTAATTTT-TTAAAATT
1 TTTAATTTTATTAAAATT
17223401 TTT
1 TTT
17223404 TAAATTTCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 1
0.81 0.14 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAATTTTATTAAAATT
Found at i:17223519 original size:24 final size:24
Alignment explanation
Indices: 17223472--17223544 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
17223462 AAAAATTAAA
* *
17223472 ATTTTTATTTAATT-TTTTCTATTT
1 ATTTTTA-TTAATTATATTATATTT
17223496 ATATTATTATT-ATTAT-TTATATTT
1 AT-TT-TTATTAATTATATTATATTT
*
17223520 ATTTTTTTTAATTATATTATATTT
1 ATTTTTATTAATTATATTATATTT
17223544 A
1 A
17223545 CTCATATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
22 4 0.10
23 7 0.17
24 23 0.55
25 5 0.12
26 3 0.07
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (24 bp):
ATTTTTATTAATTATATTATATTT
Found at i:17239584 original size:21 final size:21
Alignment explanation
Indices: 17239560--17239615 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
17239550 AGAGAAAATG
*
17239560 AGGATAGAGAGACAAAGGAGA
1 AGGAGAGAGAGACAAAGGAGA
*
17239581 AGGAGA-AGGAGAAGAAAGGAGA
1 AGGAGAGA-GAG-ACAAAGGAGA
17239603 AGAGAGAGAGAGA
1 AG-GAGAGAGAGA
17239616 AGGGAGTGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 1 0.03
21 8 0.28
22 12 0.41
23 7 0.24
24 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.43, T:0.02
Consensus pattern (21 bp):
AGGAGAGAGAGACAAAGGAGA
Found at i:17239585 original size:6 final size:6
Alignment explanation
Indices: 17239574--17239618 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
17239564 TAGAGAGACA
17239574 AAGGAG AAGGAG AAGGAG AA-GA- AAGGAG AA-GAG AGAGAGAG AAGG
1 AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG A-AG-GAG AAGG
17239619 GAGTGGGGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
4 2 0.06
5 8 0.24
6 18 0.53
7 2 0.06
8 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AAGGAG
Found at i:17243309 original size:7 final size:7
Alignment explanation
Indices: 17243289--17243354 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
17243279 TATTAATTAA
17243289 AAAAAAT
1 AAAAAAT
* *
17243296 CATAAAT
1 AAAAAAT
17243303 AAAAAAT
1 AAAAAAT
17243310 AAAAATGAT
1 AAAAA--AT
17243319 AAAAAAT
1 AAAAAAT
17243326 ---AAAT
1 AAAAAAT
*
17243330 TAAAAAT
1 AAAAAAT
17243337 AAAAAAAT
1 -AAAAAAT
17243345 AAAAAA-
1 AAAAAAT
17243351 AAAA
1 AAAA
17243355 GAAGAAGAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
4 4 0.08
6 4 0.08
7 27 0.56
8 6 0.12
9 7 0.15
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (7 bp):
AAAAAAT
Found at i:17243315 original size:20 final size:20
Alignment explanation
Indices: 17243290--17243354 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
17243280 ATTAATTAAA
*
17243290 AAAAATCATAAATAAAAAAT
1 AAAAATAATAAATAAAAAAT
*
17243310 AAAAATGATAAA-AAATAAATT
1 AAAAATAATAAATAAA-AAA-T
*
17243331 AAAAATAAAAAAATAAAAAA-
1 AAAAAT-AATAAATAAAAAAT
17243351 AAAA
1 AAAA
17243355 GAAGAAGAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.08
20 18 0.47
21 7 0.18
22 7 0.18
23 3 0.08
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (20 bp):
AAAAATAATAAATAAAAAAT
Found at i:17243351 original size:27 final size:27
Alignment explanation
Indices: 17243297--17243350 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
17243287 AAAAAAAATC
*
17243297 ATAAATAAAAAATAAAAATGATAAAAA
1 ATAAATAAAAAATAAAAATAATAAAAA
*
17243324 ATAAATTAAAAATAAAAA-AATAAAAA
1 ATAAATAAAAAATAAAAATAATAAAAA
17243350 A
1 A
17243351 AAAAGAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.19
Consensus pattern (27 bp):
ATAAATAAAAAATAAAAATAATAAAAA
Found at i:17244119 original size:106 final size:106
Alignment explanation
Indices: 17243941--17244133 Score: 253
Period size: 106 Copynumber: 1.8 Consensus size: 106
17243931 TGACTGCCGG
* * * * *
17243941 TTGTTGGTGCTGCCGACCATCGTGCCACCAGATCCGGCGAAAGGTAGCCCACAGCAAAGAAGGAG
1 TTGTTGGTGCTACCGACCATCGCGCCACCAGATCCGGCGAAAAGCAACCCACAGCAAAGAAGGAG
* *
17244006 AGGGAACGCCGCCGAAGGGAGGAAGCTTGAGTAGCAACCGC
66 AGAGAACGCCGACGAAGGGAGGAAGCTTGAGTAGCAACCGC
** * * *
17244047 TTGTTGGTGCTATTGACCATTGCGCCACCAGATCTGGCGAAAAGCAACCCACAGCAAGGTAAGG-
1 TTGTTGGTGCTACCGACCATCGCGCCACCAGATCCGGCGAAAAGCAACCCACAGCAAAG-AAGGA
*
17244111 GAGAGAACGTCGACGAAGGGAGG
65 GAGAGAACGCCGACGAAGGGAGG
17244134 TTCGGTTGTG
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
106 69 0.95
107 4 0.05
ACGTcount: A:0.28, C:0.24, G:0.33, T:0.14
Consensus pattern (106 bp):
TTGTTGGTGCTACCGACCATCGCGCCACCAGATCCGGCGAAAAGCAACCCACAGCAAAGAAGGAG
AGAGAACGCCGACGAAGGGAGGAAGCTTGAGTAGCAACCGC
Found at i:17250213 original size:126 final size:125
Alignment explanation
Indices: 17250022--17250272 Score: 484
Period size: 126 Copynumber: 2.0 Consensus size: 125
17250012 GGTCACACAC
17250022 ATCACCATGTATTGCAGAAGGATGGCTGCATATGCCCATGATGACAAGCTCTTGATACATTGCTT
1 ATCACCATGTATTGCAGAAGGATGGCTGCATATGCCCATGATGACAAGCTCTTGATACATTGCTT
17250087 CCAAGATAGCCTCACTAGTTCTGCAGCAAAGTGGTACGTCCAACTGGACCGCAATAGAAT
66 CCAAGATAGCCTCACTAGTTCTGCAGCAAAGTGGTACGTCCAACTGGACCGCAATAGAAT
17250147 NATCACCATGTATTGCAGAAGGATGGCTGCATATGCCCATGATGACAAGCTCTTGATACATTGCT
1 -ATCACCATGTATTGCAGAAGGATGGCTGCATATGCCCATGATGACAAGCTCTTGATACATTGCT
*
17250212 TCCAAGATAGCCTCACTAGTTCTGCAGCAAAGTGGTACGTCCAACTGGACCGCAATCGAAT
65 TCCAAGATAGCCTCACTAGTTCTGCAGCAAAGTGGTACGTCCAACTGGACCGCAATAGAAT
17250273 CCACACATGG
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 124 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (125 bp):
ATCACCATGTATTGCAGAAGGATGGCTGCATATGCCCATGATGACAAGCTCTTGATACATTGCTT
CCAAGATAGCCTCACTAGTTCTGCAGCAAAGTGGTACGTCCAACTGGACCGCAATAGAAT
Found at i:17257957 original size:37 final size:37
Alignment explanation
Indices: 17257902--17258168 Score: 200
Period size: 37 Copynumber: 7.1 Consensus size: 37
17257892 TAGTTTCAAG
* * * *
17257902 ATTTCTAAAGTCTCGTTGCCTTAGTTTTGAGGAGTCC
1 ATTTTTAAAGTCTTGTTGCCTCAGTTTTGAGGAGTTC
*
17257939 ATTTTTAAAGTCTTGTTGCCTCAGTTTTGAAGAGTTC
1 ATTTTTAAAGTCTTGTTGCCTCAGTTTTGAGGAGTTC
* ** * *
17257976 ATTTTAAAAGTCTCATGGCCTCAGCTTTGAGGAGTTC
1 ATTTTTAAAGTCTTGTTGCCTCAGTTTTGAGGAGTTC
* * * *** *
17258013 ATTTTTATAGTCATGTTACCTCAACATTGAGGAG-CC
1 ATTTTTAAAGTCTTGTTGCCTCAGTTTTGAGGAGTTC
* * *
17258049 ATATTTTTAAAGT-TATGTTGCCTCAGTTTTGGGGGGTTTT
1 --ATTTTTAAAGTCT-TGTTGCCTCAGTTTTGAGGAG-TTC
** *
17258089 ATTTTTAAAAGT-TTCGTAACCTCAATTTTGAGGAGTTC
1 ATTTTT-AAAGTCTT-GTTGCCTCAGTTTTGAGGAGTTC
* **
17258127 ATTTGTAAAGT-TTCGTTGCCTCAACTTTGAGGAGTCTC
1 ATTTTTAAAGTCTT-GTTGCCTCAGTTTTGAGGAGT-TC
17258165 ATTT
1 ATTT
17258169 AAAAAAAAAA
Statistics
Matches: 181, Mismatches: 41, Indels: 15
0.76 0.17 0.06
Matches are distributed among these distances:
36 1 0.01
37 114 0.63
38 45 0.25
39 21 0.12
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (37 bp):
ATTTTTAAAGTCTTGTTGCCTCAGTTTTGAGGAGTTC
Found at i:17258149 original size:114 final size:112
Alignment explanation
Indices: 17257939--17258160 Score: 259
Period size: 114 Copynumber: 2.0 Consensus size: 112
17257929 TGAGGAGTCC
** *
17257939 ATTTTTAAAGTCTTGTTGCCTCAGTTTTGAAGAGTTCATTTTAAAAGTCTCATGGCCTCAGCTTT
1 ATTTTTAAAGTCTTGTTGCCTCAGTTTTGAAGAGTTCATTTTAAAAGTCTCATAACCTCAACTTT
* *
17258004 GAGGAGTTCATTTTTATAGTCATGTTACCTCAACATTGAGGAGCCAT
66 GAGGAGTTCATTTGTAAAGTCATGTTACCTCAACATTGAGGAGCCAT
** * * * * *
17258051 ATTTTTAAAGT-TATGTTGCCTCAGTTTTGGGGGGTTTTATTTTTAAAAGTTTCGTAACCTCAAT
1 ATTTTTAAAGTCT-TGTTGCCTCAGTTTTGAAGAG-TTCA-TTTTAAAAGTCTCATAACCTCAAC
* * *
17258115 TTTGAGGAGTTCATTTGTAAAGT-TTCGTTGCCTCAACTTTGAGGAG
63 TTTGAGGAGTTCATTTGTAAAGTCAT-GTTACCTCAACATTGAGGAG
17258161 TCTCATTTAA
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
111 1 0.01
112 29 0.32
113 4 0.04
114 57 0.63
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (112 bp):
ATTTTTAAAGTCTTGTTGCCTCAGTTTTGAAGAGTTCATTTTAAAAGTCTCATAACCTCAACTTT
GAGGAGTTCATTTGTAAAGTCATGTTACCTCAACATTGAGGAGCCAT
Found at i:17258372 original size:20 final size:16
Alignment explanation
Indices: 17258355--17258393 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
17258345 AACAAAAATG
17258355 ATAAAAAATGAATTAAAA
1 ATAAAAAA--AATTAAAA
17258373 ATAAAAAAAATTAAAA
1 ATAAAAAAAATTAAAA
17258389 A-AAAA
1 ATAAAA
17258394 GAATAAGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 9 0.43
18 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
ATAAAAAAAATTAAAA
Found at i:17258932 original size:44 final size:44
Alignment explanation
Indices: 17258883--17258971 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
17258873 ATTTTGAGAG
* *
17258883 AGAGAGCTGAAGCTTTGGGCTCACCGCCGGCGAAAGGAAAAAGC
1 AGAGAGCTGAAGCTTCGGGCTCACCGCCGGCGAAAAGAAAAAGC
* ** * *
17258927 AGAGAGCTGGAGCTTCGGGCTTGCTGTCGGCGAAAAGAAAAAGC
1 AGAGAGCTGAAGCTTCGGGCTCACCGCCGGCGAAAAGAAAAAGC
17258971 A
1 A
17258972 AGGAAGCCCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.31, C:0.20, G:0.35, T:0.13
Consensus pattern (44 bp):
AGAGAGCTGAAGCTTCGGGCTCACCGCCGGCGAAAAGAAAAAGC
Found at i:17259177 original size:106 final size:106
Alignment explanation
Indices: 17258994--17259186 Score: 278
Period size: 106 Copynumber: 1.8 Consensus size: 106
17258984 TGATCGTCGA
* * * *
17258994 TTGTTGGTGCTGCCGACCATCGTGCCACCAGATCCGACGAAAGGCAGCCCACAATAAGGAATGAG
1 TTGTTGGTGCTGCCGACCATCGTGCCACCAGATCCGACAAAAAGCAGCCCACAACAAGGAAGGAG
*
17259059 AAGGAACACCGGCGAAGGGAGGAAGCCCGAGTAGTAGCCGC
66 AAAGAACACCGGCGAAGGGAGGAAGCCCGAGTAGTAGCCGC
* * * * *
17259100 TTGTTGGTGCTGCCGACCATTGTGCCACCAGATCTGGCAAAAAGCAGCCCACAACAAGGTAGGGG
1 TTGTTGGTGCTGCCGACCATCGTGCCACCAGATCCGACAAAAAGCAGCCCACAACAAGGAAGGAG
* *
17259165 AAAGAACGCCGGCGAATGGAGG
66 AAAGAACACCGGCGAAGGGAGG
17259187 TCAGGTTGTG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 75 1.00
ACGTcount: A:0.29, C:0.25, G:0.32, T:0.13
Consensus pattern (106 bp):
TTGTTGGTGCTGCCGACCATCGTGCCACCAGATCCGACAAAAAGCAGCCCACAACAAGGAAGGAG
AAAGAACACCGGCGAAGGGAGGAAGCCCGAGTAGTAGCCGC
Found at i:17260464 original size:8 final size:8
Alignment explanation
Indices: 17260430--17260516 Score: 76
Period size: 8 Copynumber: 11.2 Consensus size: 8
17260420 AAATATAGGG
17260430 AAAAT-AT
1 AAAATAAT
17260437 AAAAT-AT
1 AAAATAAT
17260444 AAAA-AA-
1 AAAATAAT
17260450 AATAATAAT
1 AA-AATAAT
*
17260459 AAAATAAA
1 AAAATAAT
17260467 AAAAT-AT
1 AAAATAAT
* *
17260474 GATAATAAA
1 -AAAATAAT
17260483 AAAATAAT
1 AAAATAAT
*
17260491 AAAATAAA
1 AAAATAAT
*
17260499 AAAATAAA
1 AAAATAAT
17260507 AAAATAAT
1 AAAATAAT
17260515 AA
1 AA
17260517 TAAATGACCA
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
6 2 0.03
7 15 0.23
8 46 0.70
9 3 0.05
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (8 bp):
AAAATAAT
Found at i:17260465 original size:62 final size:59
Alignment explanation
Indices: 17260398--17260520 Score: 158
Period size: 62 Copynumber: 2.0 Consensus size: 59
17260388 TGTGTAAAAG
* * *
17260398 AAATAAAAAAATAT-ATCAAGAAAAATATAGGGAAAATATAAAATATAAAAAAAATAATAATA
1 AAATAAAAAAATATGAT-AAGAAAAAAATA-AGAAAATA-AAAAAAT-AAAAAAATAATAATA
* *
17260460 AAATAAAAAAATATGATAATAAAAAAATAATAAAATAAAAAAATAAAAAAATAATAATA
1 AAATAAAAAAATATGATAAGAAAAAAATAAGAAAATAAAAAAATAAAAAAATAATAATA
17260519 AA
1 AA
17260521 TGACCAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
59 17 0.31
60 6 0.11
61 6 0.11
62 24 0.44
63 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (59 bp):
AAATAAAAAAATATGATAAGAAAAAAATAAGAAAATAAAAAAATAAAAAAATAATAATA
Found at i:17260478 original size:24 final size:22
Alignment explanation
Indices: 17260435--17260519 Score: 99
Period size: 21 Copynumber: 4.0 Consensus size: 22
17260425 TAGGGAAAAT
17260435 ATAAAATATAAAAAA-AATAATA
1 ATAAAATA-AAAAAATAATAATA
*
17260457 ATAAAATAAAAAAAT-ATGATA
1 ATAAAATAAAAAAATAATAATA
*
17260478 AT-AAA-AAAATAATAA-AATA
1 ATAAAATAAAAAAATAATAATA
*
17260497 AAAAAATAAAAAAATAATAATA
1 ATAAAATAAAAAAATAATAATA
17260519 A
1 A
17260520 ATGACCAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
19 11 0.21
20 7 0.13
21 22 0.42
22 13 0.25
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (22 bp):
ATAAAATAAAAAAATAATAATA
Found at i:17260494 original size:32 final size:33
Alignment explanation
Indices: 17260442--17260519 Score: 110
Period size: 32 Copynumber: 2.5 Consensus size: 33
17260432 AATATAAAAT
17260442 ATAAAAAAAATAATAATAAAATAAAAAAATATG
1 ATAAAAAAAATAATAATAAAATAAAAAAATATG
*
17260475 ATAATAAAAA-AATAATAAAATAAAAAAATA--
1 ATAAAAAAAATAATAATAAAATAAAAAAATATG
*
17260505 A-AAAAATAATAATAA
1 ATAAAAAAAATAATAA
17260520 ATGACCAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 6 0.15
30 6 0.15
32 20 0.49
33 9 0.22
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (33 bp):
ATAAAAAAAATAATAATAAAATAAAAAAATATG
Found at i:17260511 original size:16 final size:16
Alignment explanation
Indices: 17260437--17260513 Score: 97
Period size: 16 Copynumber: 4.9 Consensus size: 16
17260427 GGGAAAATAT
17260437 AAAAT-ATAAAA-AAA
1 AAAATAATAAAATAAA
*
17260451 ATAATAATAAAATAAA
1 AAAATAATAAAATAAA
*
17260467 AAAAT-ATGATAATAAA
1 AAAATAAT-AAAATAAA
17260483 AAAATAATAAAATAAA
1 AAAATAATAAAATAAA
*
17260499 AAAATAAAAAAATAA
1 AAAATAATAAAATAA
17260514 TAATAAATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
14 4 0.07
15 8 0.15
16 40 0.74
17 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.19
Consensus pattern (16 bp):
AAAATAATAAAATAAA
Found at i:17260529 original size:27 final size:24
Alignment explanation
Indices: 17260437--17260516 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
17260427 GGGAAAATAT
* *
17260437 AAAAT-ATAAAA-AAAATAATAAT
1 AAAATAATAAAATAAAAAAATAAA
* ** *
17260459 AAAATAAAAAAATATGATAATAAA
1 AAAATAATAAAATAAAAAAATAAA
17260483 AAAATAATAAAATAAAAAAATAAA
1 AAAATAATAAAATAAAAAAATAAA
17260507 AAAATAATAA
1 AAAATAATAA
17260517 TAAATGACCA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 5 0.10
23 5 0.10
24 38 0.79
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.20
Consensus pattern (24 bp):
AAAATAATAAAATAAAAAAATAAA
Found at i:17262174 original size:29 final size:30
Alignment explanation
Indices: 17262117--17262183 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
17262107 AATCAAAAGG
* *
17262117 ACTTAATTGATTCAAAATAAAAATTTAAAA
1 ACTTAATTGATACAAAATAAAAATATAAAA
* *
17262147 ACTTAATTGA-ACACAATAAAAATATAAAG
1 ACTTAATTGATACAAAATAAAAATATAAAA
17262176 ACTTAATT
1 ACTTAATT
17262184 AACTTTTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 23 0.70
30 10 0.30
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.31
Consensus pattern (30 bp):
ACTTAATTGATACAAAATAAAAATATAAAA
Found at i:17262228 original size:2 final size:2
Alignment explanation
Indices: 17262217--17262258 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
17262207 AACTTATTAA
17262217 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17262258 A
1 A
17262259 AAAGAGAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17270017 original size:19 final size:20
Alignment explanation
Indices: 17269993--17270047 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
17269983 AGGAAATGAA
*
17269993 AATATATTAAATATTATT-T
1 AATATATTAAATATTATTCC
17270012 AATATATT-AATATTATTCC
1 AATATATTAAATATTATTCC
* *
17270031 ACTATAATAAATATTAT
1 AATATATTAAATATTAT
17270048 AAAACATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.29
19 14 0.45
20 8 0.26
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATATTAAATATTATTCC
Found at i:17270380 original size:22 final size:22
Alignment explanation
Indices: 17270348--17270422 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
17270338 AACTATCTTC
17270348 TAATACAAAATATTATTAAATTA
1 TAATA-AAAATATTATTAAATTA
** *
17270371 TAATAAAAATA-TATTTGTATTT
1 TAATAAAAATATTA-TTAAATTA
* * *
17270393 TGATGAAAATATTATTTAATTA
1 TAATAAAAATATTATTAAATTA
*
17270415 TAGTAAAA
1 TAATAAAA
17270423 GTTATTTTGA
Statistics
Matches: 39, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
21 2 0.05
22 30 0.77
23 7 0.18
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (22 bp):
TAATAAAAATATTATTAAATTA
Found at i:17270482 original size:158 final size:163
Alignment explanation
Indices: 17270145--17270490 Score: 499
Period size: 163 Copynumber: 2.1 Consensus size: 163
17270135 CTTTTAGTAT
*
17270145 TAAATATTATTTAATTATAATAAAAGAATTAATTATCTTCTAATACAAAATATTATTAAATTATA
1 TAAAT-TT-TTTAATTATAATAAAAGAATTAACTATCTTCTAATACAAAATATTATTAAATTATA
* *
17270210 TAAAAATATATTGTTTTTTGATGAAAATATTATTTAATTATAGTAAAAAGGTATTTTGATTTTAT
64 TAAAAATATATTGTATTTTGATGAAAATATTATTTAATTATAGTAAAAAGGTATTTTGATTTGAT
* *
17270275 TAACTATTATTATAGTATTTTTATCTTTTAACAAAA
129 TAAC-ATCATGATAGTATTTTTATCTTTTAACAAAA
* **
17270311 TAAATTTTTTAATT-NAATAAAAGGTTTAACTATCTTCTAATACAAAATATTATTAAATTATAAT
1 TAAATTTTTTAATTATAATAAAAGAATTAACTATCTTCTAATACAAAATATTATTAAATTAT-AT
*
17270375 AAAAATATATTTGTATTTTGATGAAAATATTATTTAATTATAGT-AAAAGTTATTTTGATTTGAT
65 AAAAATATA-TTGTATTTTGATGAAAATATTATTTAATTATAGTAAAAAGGTATTTTGATTTGAT
*
17270439 T-GC-TCA-GA-A-TATTTTTATCTTTTAACAAAA
129 TAACATCATGATAGTATTTTTATCTTTTAACAAAA
*
17270469 TAAATTTTTTAATTTTAATAAA
1 TAAATTTTTTAATTATAATAAA
17270491 GAGTATTTAT
Statistics
Matches: 166, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
158 35 0.21
159 7 0.04
160 1 0.01
161 2 0.01
163 44 0.27
164 37 0.22
165 35 0.21
166 5 0.03
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (163 bp):
TAAATTTTTTAATTATAATAAAAGAATTAACTATCTTCTAATACAAAATATTATTAAATTATATA
AAAATATATTGTATTTTGATGAAAATATTATTTAATTATAGTAAAAAGGTATTTTGATTTGATTA
ACATCATGATAGTATTTTTATCTTTTAACAAAA
Found at i:17271247 original size:19 final size:19
Alignment explanation
Indices: 17271210--17271248 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17271200 AGTACTTTTA
*
17271210 GAAGAACATGTTTTGTATG
1 GAAGAACATGTTGTGTATG
17271229 GAAGAACATGCTTGT-TATG
1 GAAGAACATG-TTGTGTATG
17271248 G
1 G
17271249 GTATAGCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (19 bp):
GAAGAACATGTTGTGTATG
Found at i:17272838 original size:27 final size:28
Alignment explanation
Indices: 17272808--17272863 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
17272798 ATAGTGGATT
*
17272808 TAATATGCTGATATATATATA-TATATA
1 TAATATGCTGAGATATATATACTATATA
* *
17272835 TAATATGTTGAGATATCTATACTATATA
1 TAATATGCTGAGATATATATACTATATA
17272863 T
1 T
17272864 TAAAGGTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (28 bp):
TAATATGCTGAGATATATATACTATATA
Found at i:17273116 original size:23 final size:21
Alignment explanation
Indices: 17273064--17273116 Score: 52
Period size: 24 Copynumber: 2.4 Consensus size: 21
17273054 CTTTTTCCAC
17273064 TGCTCTTTTCTTTCTTTTATT
1 TGCTCTTTTCTTTCTTTTATT
* * *
17273085 TGGTGCTTTTTTGTTCATTTTCTT
1 TGCT-CTTTTCT-TTC-TTTTATT
17273109 TGCTCTTT
1 TGCTCTTT
17273117 GATTTGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 6 0.24
23 7 0.28
24 9 0.36
ACGTcount: A:0.04, C:0.17, G:0.11, T:0.68
Consensus pattern (21 bp):
TGCTCTTTTCTTTCTTTTATT
Found at i:17283384 original size:14 final size:15
Alignment explanation
Indices: 17283338--17283376 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
17283328 TTCGAATATG
17283338 AAAACATGAAGTTTA
1 AAAACATGAAGTTTA
17283353 AAAACATGAAGTTTA
1 AAAACATGAAGTTTA
17283368 AAAACATGA
1 AAAACATGA
17283377 GTATAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.13, T:0.23
Consensus pattern (15 bp):
AAAACATGAAGTTTA
Found at i:17286490 original size:81 final size:84
Alignment explanation
Indices: 17286391--17286594 Score: 333
Period size: 84 Copynumber: 2.5 Consensus size: 84
17286381 CTCATGTCTA
* *
17286391 TTACAACATGAATTAGAGAAAATTGAACCTGATTTTTAGTTATTTAGTTTA-TTTT-TT-ATTAA
1 TTACAACATGAATTAGAGAAAATTGAACCTGATTTTTAGTTATTCAATTTATTTTTCTTAATTAA
*
17286453 ATATTTTTTACATTAGTAC
66 ATATTTTTTACATTAATAC
*
17286472 TTACAACATGAATTAGAGAAAATTGAACCTGATTTTTAGTTATTCAATTTATTTTTCTTAATTGA
1 TTACAACATGAATTAGAGAAAATTGAACCTGATTTTTAGTTATTCAATTTATTTTTCTTAATTAA
17286537 ATATTTTTTACATTAATAC
66 ATATTTTTTACATTAATAC
* *
17286556 TTACAACATGAATTAGACAAAATTGAATCTGATTTTTAG
1 TTACAACATGAATTAGAGAAAATTGAACCTGATTTTTAG
17286595 ATAATGAAAT
Statistics
Matches: 114, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
81 49 0.43
82 4 0.04
83 2 0.02
84 59 0.52
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (84 bp):
TTACAACATGAATTAGAGAAAATTGAACCTGATTTTTAGTTATTCAATTTATTTTTCTTAATTAA
ATATTTTTTACATTAATAC
Found at i:17286810 original size:31 final size:31
Alignment explanation
Indices: 17286775--17286835 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
17286765 GTCTTTATAT
17286775 AATTCATAACATACTATCATTGACCAAATTA
1 AATTCATAACATACTATCATTGACCAAATTA
* *
17286806 AATTCATAGCATACTATCATTGGCCAAATT
1 AATTCATAACATACTATCATTGACCAAATT
17286836 GATGCTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.33
Consensus pattern (31 bp):
AATTCATAACATACTATCATTGACCAAATTA
Found at i:17291219 original size:67 final size:68
Alignment explanation
Indices: 17291111--17291261 Score: 205
Period size: 67 Copynumber: 2.2 Consensus size: 68
17291101 GCTTTTACAA
* * * *
17291111 TGGCTTTTCACAGGTTCAACCATAACCTTTCACAATAGTTTTTCACGAGATCAACCAAAATCC-A
1 TGGCTTTTCAAAGGCTCAACCATAACCTTTAACAATAGTTTTTCACGAGATCAACCAAAACCCAA
17291175 AAC
66 AAC
* * * *
17291178 TGGCTTTTCAAAGGCTCAATCGTAACCTTTAACAATGGTTTTTCACGGGATCAACCAAAACCCAA
1 TGGCTTTTCAAAGGCTCAACCATAACCTTTAACAATAGTTTTTCACGAGATCAACCAAAACCCAA
17291243 AAC
66 AAC
**
17291246 TAACTTTTCAAAGGCT
1 TGGCTTTTCAAAGGCT
17291262 AAGTTAGAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
67 55 0.75
68 18 0.25
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (68 bp):
TGGCTTTTCAAAGGCTCAACCATAACCTTTAACAATAGTTTTTCACGAGATCAACCAAAACCCAA
AAC
Found at i:17293034 original size:52 final size:46
Alignment explanation
Indices: 17292913--17293023 Score: 213
Period size: 46 Copynumber: 2.4 Consensus size: 46
17292903 CCCGCCACAC
17292913 TCAGCTCATGTGCACTCCCTACATGCACAATGCAATATCATCATCA
1 TCAGCTCATGTGCACTCCCTACATGCACAATGCAATATCATCATCA
17292959 TCAGCTCATGTGCACTCCCTACATGCACAATGCAATATCATCATCA
1 TCAGCTCATGTGCACTCCCTACATGCACAATGCAATATCATCATCA
*
17293005 TCAGCTCTTGTGCACTCCC
1 TCAGCTCATGTGCACTCCC
17293024 ACACCGTACA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.27, C:0.34, G:0.12, T:0.27
Consensus pattern (46 bp):
TCAGCTCATGTGCACTCCCTACATGCACAATGCAATATCATCATCA
Found at i:17293046 original size:43 final size:43
Alignment explanation
Indices: 17292999--17293091 Score: 141
Period size: 43 Copynumber: 2.2 Consensus size: 43
17292989 TGCAATATCA
* * * *
17292999 TCATCATCAGCTCTTGTGCACTCCCACACCGTACATAGTTGGG
1 TCATCATCAACTCATGTGCACTACCACACCGCACATAGTTGGG
17293042 TCATCATCAACTCATGTGCACTACCACACCGCACATAGTTGGG
1 TCATCATCAACTCATGTGCACTACCACACCGCACATAGTTGGG
*
17293085 TCCTCAT
1 TCATCAT
17293092 TATCACACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (43 bp):
TCATCATCAACTCATGTGCACTACCACACCGCACATAGTTGGG
Found at i:17303860 original size:19 final size:20
Alignment explanation
Indices: 17303823--17303860 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
17303813 TCATTATGGG
*
17303823 ATTTTAAATTTCTCAATTTC
1 ATTTTAAATATCTCAATTTC
*
17303843 ATTTTAAA-ATCTCTATTT
1 ATTTTAAATATCTCAATTT
17303861 GGATTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTAAATATCTCAATTTC
Found at i:17304400 original size:27 final size:27
Alignment explanation
Indices: 17304345--17304478 Score: 76
Period size: 27 Copynumber: 4.9 Consensus size: 27
17304335 TTTTTTTAAC
* * *
17304345 AAATTATTAATATTT-TAAATTAATTAA
1 AAATTATTAATATTTAAAAAATAA-AAA
17304372 AAATTATTAATATTTAAAAAATAAAAA
1 AAATTATTAATATTTAAAAAATAAAAA
* * * **
17304399 AAATAAATTTTAAT-TATATATTATAAAAA
1 AAAT---TATTAATATTTAAAAAATAAAAA
* * **
17304428 AAA-TATCTAAAATTTAAAAATTAATTA
1 AAATTAT-TAATATTTAAAAAATAAAAA
* *
17304455 AAATTATTAATATTTGAAACATAA
1 AAATTATTAATATTTAAAAAATAA
17304479 TAAATTTAAA
Statistics
Matches: 79, Mismatches: 21, Indels: 14
0.69 0.18 0.12
Matches are distributed among these distances:
25 2 0.03
26 3 0.04
27 45 0.57
28 9 0.11
29 14 0.18
30 6 0.08
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (27 bp):
AAATTATTAATATTTAAAAAATAAAAA
Found at i:17304509 original size:41 final size:43
Alignment explanation
Indices: 17304453--17304561 Score: 129
Period size: 41 Copynumber: 2.6 Consensus size: 43
17304443 AAAAATTAAT
17304453 TAAAATTATTAATATTTGAAACATAATAAAT-TTAAATTATAAA
1 TAAAA-TATTAATATTTGAAACATAATAAATATTAAATTATAAA
* * *
17304496 T-AAATATTGATATTTGAAA-AT-ATTAATGATTAAATTATGAA
1 TAAAATATTAATATTTGAAACATAATAAAT-ATTAAATTATAAA
17304537 TAAAATATTAATATTT-AAACGATAA
1 TAAAATATTAATATTTGAAAC-ATAA
17304562 ATTATTAATG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
39 5 0.09
40 2 0.04
41 29 0.52
42 16 0.29
43 3 0.05
44 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (43 bp):
TAAAATATTAATATTTGAAACATAATAAATATTAAATTATAAA
Found at i:17306934 original size:21 final size:21
Alignment explanation
Indices: 17306908--17306994 Score: 81
Period size: 21 Copynumber: 4.2 Consensus size: 21
17306898 AAATTGCTTC
17306908 AATGATCTTTCAACTTGTTTG
1 AATGATCTTTCAACTTGTTTG
*
17306929 AATGATC-CTCGAACTTGTTTG
1 AATGATCTTTC-AACTTGTTTG
*
17306950 AATGAT-TTTGC-ATTTGTTTG
1 AATGATCTTT-CAACTTGTTTG
** * *
17306970 GGTGATCCTTGAACTTGTTTG
1 AATGATCTTTCAACTTGTTTG
17306991 AATG
1 AATG
17306995 TGTTTTTGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
20 14 0.27
21 36 0.71
22 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.21, T:0.45
Consensus pattern (21 bp):
AATGATCTTTCAACTTGTTTG
Found at i:17307145 original size:22 final size:21
Alignment explanation
Indices: 17307117--17307185 Score: 84
Period size: 22 Copynumber: 3.2 Consensus size: 21
17307107 TTTTGACTTA
*
17307117 TTTTTGAAGTTGTTTGAATGAG
1 TTTTTGAACTTGTTTGAAT-AG
17307139 TTTTTGAACTTGTTTGAATAG
1 TTTTTGAACTTGTTTGAATAG
* * *
17307160 TTTTTAAACTTATTTAAATAAG
1 TTTTTGAACTTGTTTGAAT-AG
17307182 TTTT
1 TTTT
17307186 GAAGATCCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.43
22 24 0.57
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.54
Consensus pattern (21 bp):
TTTTTGAACTTGTTTGAATAG
Found at i:17307238 original size:21 final size:21
Alignment explanation
Indices: 17307212--17307280 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
17307202 TCCATGTAAA
*
17307212 AAGTTTTAAAATTGCTTGAAT
1 AAGTTTTGAAATTGCTTGAAT
*
17307233 AAGTTTTGAAATTACTTGAAT
1 AAGTTTTGAAATTGCTTGAAT
* * *
17307254 AATTTTTGAACTTGTTTGAAT
1 AAGTTTTGAAATTGCTTGAAT
17307275 -AGTTTT
1 AAGTTTT
17307281 TAAACTTGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 5 0.12
21 36 0.88
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.48
Consensus pattern (21 bp):
AAGTTTTGAAATTGCTTGAAT
Found at i:17307281 original size:21 final size:21
Alignment explanation
Indices: 17307215--17307300 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
17307205 ATGTAAAAAG
* *
17307215 TTTTAAAATTGCTTGAATAAGT
1 TTTTAAACTTGTTTGAAT-AGT
* ** *
17307237 TTTGAAA-TTACTTGAATAAT
1 TTTTAAACTTGTTTGAATAGT
*
17307257 TTTTGAACTTGTTTGAATAGT
1 TTTTAAACTTGTTTGAATAGT
*
17307278 TTTTAAACTTGTTTAAATTAGT
1 TTTTAAACTTGTTTGAA-TAGT
17307300 T
1 T
17307301 ATAAATCTCT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
20 7 0.13
21 34 0.65
22 11 0.21
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.50
Consensus pattern (21 bp):
TTTTAAACTTGTTTGAATAGT
Found at i:17307305 original size:21 final size:21
Alignment explanation
Indices: 17307262--17307305 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17307252 ATAATTTTTG
* *
17307262 AACTTGTTTGAATAGTTTTTA
1 AACTTGTTTAAATAGTTTATA
17307283 AACTTGTTTAAATTAG-TTATA
1 AACTTGTTTAAA-TAGTTTATA
17307304 AA
1 AA
17307306 TCTCTCTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (21 bp):
AACTTGTTTAAATAGTTTATA
Found at i:17307470 original size:21 final size:21
Alignment explanation
Indices: 17307446--17307507 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
17307436 TGGTTCTACC
17307446 CAAAATGTATAGATACATTTT
1 CAAAATGTATAGATACATTTT
* * *
17307467 CAAAATGTATCGATATA-GTT
1 CAAAATGTATAGATACATTTT
* *
17307487 CAAAATATATTGATACATTTT
1 CAAAATGTATAGATACATTTT
17307508 GATACATTCC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (21 bp):
CAAAATGTATAGATACATTTT
Found at i:17307490 original size:20 final size:21
Alignment explanation
Indices: 17307446--17307504 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
17307436 TGGTTCTACC
*
17307446 CAAAATGTATAGATACATTTT
1 CAAAATGTATAGATACATGTT
* *
17307467 CAAAATGTATCGATATA-GTT
1 CAAAATGTATAGATACATGTT
* *
17307487 CAAAATATATTGATACAT
1 CAAAATGTATAGATACAT
17307505 TTTGATACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
CAAAATGTATAGATACATGTT
Found at i:17308072 original size:28 final size:28
Alignment explanation
Indices: 17308023--17308089 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
17308013 AGTGTGTAAA
* *
17308023 GGTTGTGCTTGAACTTTAAAAAAACAAT
1 GGTTATGCTTGAACCTTAAAAAAACAAT
* * **
17308051 GGTTATGCTTGATCCTTGAAAAGGCAAT
1 GGTTATGCTTGAACCTTAAAAAAACAAT
*
17308079 AGTTATGCTTG
1 GGTTATGCTTG
17308090 GACATTTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (28 bp):
GGTTATGCTTGAACCTTAAAAAAACAAT
Found at i:17308100 original size:28 final size:28
Alignment explanation
Indices: 17308047--17308104 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
17308037 TTTAAAAAAA
* *
17308047 CAATGGTTATGCTTGATCCTTGAAAAGG
1 CAATAGTTATGCTTGATCATTGAAAAGG
*
17308075 CAATAGTTATGCTTGGA-CATTTAAAAGG
1 CAATAGTTATGCTT-GATCATTGAAAAGG
17308103 CA
1 CA
17308105 TTGTATTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (28 bp):
CAATAGTTATGCTTGATCATTGAAAAGG
Found at i:17308322 original size:84 final size:84
Alignment explanation
Indices: 17308213--17308371 Score: 230
Period size: 84 Copynumber: 1.9 Consensus size: 84
17308203 GCATTTTCTC
* * * * *
17308213 TTTATTCTTCACTATTTACATTTGTGCATTTCACTTTACTTTGAAGAGTTTTGAAAATTTGT-TC
1 TTTACTCTTCACTATTTACACTTGTGCATTTCACATTACCTTGAAGAGTTTTGAAAATTTATCT-
17308277 TTAACTTGTTTGTTCTTTGA
65 TTAACTTGTTTGTTCTTTGA
* * *
17308297 TTTACTCTTCATTATTTATACTTGTGCATTTTACATTACCTTGAAGAGTTTTGAAAATTTATCTT
1 TTTACTCTTCACTATTTACACTTGTGCATTTCACATTACCTTGAAGAGTTTTGAAAATTTATCTT
17308362 TAACTTGTTT
66 TAACTTGTTT
17308372 ATGCATTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
84 65 0.98
85 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.53
Consensus pattern (84 bp):
TTTACTCTTCACTATTTACACTTGTGCATTTCACATTACCTTGAAGAGTTTTGAAAATTTATCTT
TAACTTGTTTGTTCTTTGA
Found at i:17310505 original size:100 final size:100
Alignment explanation
Indices: 17310317--17310516 Score: 276
Period size: 100 Copynumber: 2.0 Consensus size: 100
17310307 TTCAACGGAT
* * * *
17310317 TTCCAACGAAAAAATTTTGTTGGAAAAATTTTTGGCGAGCAAAAAAAAAAAAGGAAACCATCATT
1 TTCCAACGAAAAAATTTTATTGGAAAAATTTTTGGCAAG-AAAAAAAAAAAAGGAAACCACCATG
* *
17310382 TCTGATGGAATTTCCAACAGAATTTTAGTTGGAAAA
65 TCTAACGGAATTTCCAACAGAATTTTAGTTGGAAAA
* * *
17310418 TTCCAACGAAAAATTTTTCATTGGAAAAATTTTTGGCAAG-AAAAAAAAATAGGAGACCACCATG
1 TTCCAACGAAAAAATTTT-ATTGGAAAAATTTTTGGCAAGAAAAAAAAAAAAGGAAACCACCATG
* *
17310482 TCTAACGGAATTTCCAACGGAATTTTCGTTGGAAA
65 TCTAACGGAATTTCCAACAGAATTTTAGTTGGAAA
17310517 TCTGTTAGAA
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
100 51 0.59
101 17 0.20
102 19 0.22
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (100 bp):
TTCCAACGAAAAAATTTTATTGGAAAAATTTTTGGCAAGAAAAAAAAAAAAGGAAACCACCATGT
CTAACGGAATTTCCAACAGAATTTTAGTTGGAAAA
Found at i:17310645 original size:20 final size:20
Alignment explanation
Indices: 17310615--17310666 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
17310605 ATAATTTTTA
17310615 TTTTTATTAAAATATTTA-AAT
1 TTTTTA-TAAAAT-TTTATAAT
17310636 TTTTTAT-AAATTTTATTAAT
1 TTTTTATAAAATTTTA-TAAT
*
17310656 CTTTTATAAAA
1 TTTTTATAAAA
17310667 AATTGATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.15
19 4 0.15
20 10 0.37
21 9 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTATAAAATTTTATAAT
Found at i:17311382 original size:16 final size:17
Alignment explanation
Indices: 17311363--17311394 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17311353 AAAATATATA
17311363 TTTTTGCT-TTATTATC
1 TTTTTGCTATTATTATC
17311379 TTTTTGCTATTATTAT
1 TTTTTGCTATTATTAT
17311395 TTACATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.16, C:0.09, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTTTGCTATTATTATC
Found at i:17329123 original size:21 final size:21
Alignment explanation
Indices: 17329076--17329131 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
17329066 AAAAAATAAA
17329076 AAATAAAAATTAATCAAAAAAT
1 AAAT-AAAATTAATCAAAAAAT
*
17329098 AAATAAAA-TAATCAAATAAT
1 AAATAAAATTAATCAAAAAAT
17329118 ACAATAAAAATTAA
1 A-AAT-AAAATTAA
17329132 AATTAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 8 0.27
23 3 0.10
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATAAAATTAATCAAAAAAT
Found at i:17330287 original size:2 final size:2
Alignment explanation
Indices: 17330275--17330308 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
17330265 ATAGATTTAG
*
17330275 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17330309 ATGAATGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:17332292 original size:124 final size:123
Alignment explanation
Indices: 17332052--17332295 Score: 285
Period size: 124 Copynumber: 2.0 Consensus size: 123
17332042 TTTAAATATA
* * *
17332052 ACGTGTAACAATTTTATTTTTCAACATGACACATAACTTGGTCTTTATTTTTGTATTTTACTTTG
1 ACGTGTAACAATTTTATTTTTCAACATGACACATAACTTGGTCTCTATATTTGTATTTTACTATG
* * ** *
17332117 ATATAAATTCTTAAAGTTAAACACCTTAAACATGGTATGTAATAACTTTTTTTTTAAC
66 ACATAAACTCTTAAAGTTAAACACCTTAAACATGACATGTAAGAACTTTTTTTTTAAC
* * * *** *
17332175 ACGTGTAATAACTTTTTTTTTTCAACATGGCTTGTAATTTGGTCTCTATATTTGTATTTTACTAA
1 ACGTGTAACAA-TTTTATTTTTCAACATGACACATAACTTGGTCTCTATATTTGTATTTTACT-A
* * *
17332240 T-ACATAAACTCTTAGAGTTAAACACCTTAAATATGACGTGTAAGAA-TATTTTTTTT
64 TGACATAAACTCTTAAAGTTAAACACCTTAAACATGACATGTAAGAACT-TTTTTTTT
17332296 CCAATATGAC
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
123 11 0.11
124 88 0.88
125 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (123 bp):
ACGTGTAACAATTTTATTTTTCAACATGACACATAACTTGGTCTCTATATTTGTATTTTACTATG
ACATAAACTCTTAAAGTTAAACACCTTAAACATGACATGTAAGAACTTTTTTTTTAAC
Found at i:17332311 original size:29 final size:28
Alignment explanation
Indices: 17332269--17332368 Score: 103
Period size: 29 Copynumber: 3.5 Consensus size: 28
17332259 AAACACCTTA
*
17332269 AATATGACGTGTAAGAATATTTTTTTTCC
1 AATATGACGTGTAACAATATTTTTTTT-C
** *
17332298 AATATGACGTGTAACAATA-CGTTTTTG
1 AATATGACGTGTAACAATATTTTTTTTC
* *
17332325 AACATGACGTGTAACAATATTATTTTTTA
1 AATATGACGTGTAACAATATT-TTTTTTC
* *
17332354 AACATGGCGTGTAAC
1 AATATGACGTGTAAC
17332369 TTGATCTCTA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
27 18 0.30
28 5 0.08
29 37 0.62
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (28 bp):
AATATGACGTGTAACAATATTTTTTTTC
Found at i:17342398 original size:28 final size:28
Alignment explanation
Indices: 17342337--17342400 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
17342327 TGTAATAGCC
* **
17342337 AAATTTTTTAACATGGTATGTAACAATT
1 AAATTTTTTAACATGGCATGTAACAACA
** *
17342365 GCATTTTTTAACATGGCGTGTAACAACA
1 AAATTTTTTAACATGGCATGTAACAACA
17342393 AAATTTTT
1 AAATTTTT
17342401 AATATGATAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (28 bp):
AAATTTTTTAACATGGCATGTAACAACA
Found at i:17342426 original size:83 final size:80
Alignment explanation
Indices: 17342298--17342447 Score: 183
Period size: 83 Copynumber: 1.8 Consensus size: 80
17342288 CAACATGGCG
* * * *
17342298 TGGCGTGTAACAACCTTTTTATTATGACGTGTAATAGCCAAATTTTTTAACATGGTATGTAACAA
1 TGGCGTGTAACAACATTTTTAATATGACATGTAATAGCCAAATTTTTCAACATGGTATGTAACAA
17342363 TTGCATTTTTTAACA
66 TTGCATTTTTTAACA
* * * * * *
17342378 TGGCGTGTAACAACAAAATTTTTAATATGATATGTAATAGCTACATTTTTCAATATGTTGTGTAA
1 TGGCGTGTAACAAC---ATTTTTAATATGACATGTAATAGCCAAATTTTTCAACATGGTATGTAA
17342443 CAATT
63 CAATT
17342448 AAATTGTTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
80 14 0.25
83 43 0.75
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (80 bp):
TGGCGTGTAACAACATTTTTAATATGACATGTAATAGCCAAATTTTTCAACATGGTATGTAACAA
TTGCATTTTTTAACA
Found at i:17343604 original size:16 final size:16
Alignment explanation
Indices: 17343580--17343610 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17343570 CTTAATTTTT
*
17343580 AAATGATAAAAAAATA
1 AAATCATAAAAAAATA
17343596 AAATCATAAAAAAAT
1 AAATCATAAAAAAAT
17343611 TAGTTCAATG
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:0.74, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAATCATAAAAAAATA
Found at i:17344677 original size:43 final size:43
Alignment explanation
Indices: 17344607--17344937 Score: 297
Period size: 43 Copynumber: 7.7 Consensus size: 43
17344597 TTTAAAAAAA
* * * *
17344607 AAAAGGAATGAACTCCTTATCTAGAATGAGGCTATATAACTTT
1 AAAAGGAATAAACTCCTCATTTGGAATGAGGCTATATAACTTT
* *
17344650 AAAATGAATAAACTCCTCATTTTGAATGAGGCTATATAACTTT
1 AAAAGGAATAAACTCCTCATTTGGAATGAGGCTATATAACTTT
* * * **
17344693 AAAAAGGAATAAGCTCCTTATTTGGAATAAAACTATATAA-TCTT
1 -AAAAGGAATAAACTCCTCATTTGGAATGAGGCTATATAACT-TT
* * * * * *
17344737 AAAATGAATAAATTCTTCATTTAGAATGAGACTATGTAACTTT
1 AAAAGGAATAAACTCCTCATTTGGAATGAGGCTATATAACTTT
* ** * * * * *
17344780 GAAATAAATAAACTCATCATCTAGAATGAGGCAACATAACTTT
1 AAAAGGAATAAACTCCTCATTTGGAATGAGGCTATATAACTTT
** *
17344823 AAAAGGAATAAACTCCTTGTTTGGAACGAGGCTACT-TAACTTT
1 AAAAGGAATAAACTCCTCATTTGGAATGAGGCTA-TATAACTTT
* * * * * *
17344866 GAAATGAATAAACTCCTCATATGGAATGAGACTGTGTAACTTT
1 AAAAGGAATAAACTCCTCATTTGGAATGAGGCTATATAACTTT
* *
17344909 AAAAGGAATAAATTCGTCATTTGGAATGA
1 AAAAGGAATAAACTCCTCATTTGGAATGA
17344938 TGTTACTTAC
Statistics
Matches: 229, Mismatches: 54, Indels: 10
0.78 0.18 0.03
Matches are distributed among these distances:
42 1 0.00
43 193 0.84
44 35 0.15
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (43 bp):
AAAAGGAATAAACTCCTCATTTGGAATGAGGCTATATAACTTT
Found at i:17344936 original size:129 final size:130
Alignment explanation
Indices: 17344607--17344937 Score: 362
Period size: 129 Copynumber: 2.6 Consensus size: 130
17344597 TTTAAAAAAA
* * * * * * *
17344607 AAAAGGAATGAACTCCTTATCTAGAATGAGGCTATATAACTTTAAAATGAATAAACTCCTCATTT
1 AAAATGAATAAACTCCTCATATAGAATGAGACTATGTAACTTTAAAATGAATAAACTCATCATTT
* * * * *
17344672 TGAATGAGGCTATATAACTTTAAAAAGGAATAAGCTCCTTATTTGGAATAAAACTATATAATCTT
66 AGAATGAGGCAACATAACTTTAAAAAGGAATAAACTCCTTATTTGGAACAAAACTATATAATCTT
* * * * * *
17344737 AAAATGAATAAATTCTTCATTTAGAATGAGACTATGTAACTTTGAAATAAATAAACTCATCATCT
1 AAAATGAATAAACTCCTCATATAGAATGAGACTATGTAACTTTAAAATGAATAAACTCATCATTT
* * **
17344802 AGAATGAGGCAACATAACTTT-AAAAGGAATAAACTCCTTGTTTGGAACGAGGCTACT-TAA-CT
66 AGAATGAGGCAACATAACTTTAAAAAGGAATAAACTCCTTATTTGGAACAAAACTA-TATAATC-
17344864 TT
129 TT
* * * * * *
17344866 GAAATGAATAAACTCCTCATATGGAATGAGACTGTGTAACTTTAAAAGGAATAAATTCGTCATTT
1 AAAATGAATAAACTCCTCATATAGAATGAGACTATGTAACTTTAAAATGAATAAACTCATCATTT
*
17344931 GGAATGA
66 AGAATGA
17344938 TGTTACTTAC
Statistics
Matches: 165, Mismatches: 34, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
128 1 0.01
129 92 0.56
130 72 0.44
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (130 bp):
AAAATGAATAAACTCCTCATATAGAATGAGACTATGTAACTTTAAAATGAATAAACTCATCATTT
AGAATGAGGCAACATAACTTTAAAAAGGAATAAACTCCTTATTTGGAACAAAACTATATAATCTT
Found at i:17347739 original size:25 final size:24
Alignment explanation
Indices: 17347703--17347755 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
17347693 GTTAGCCCAT
*
17347703 TTTTTAT-TTTTTTCAAAAAAATTA
1 TTTTTATATTTTAT-AAAAAAATTA
*
17347727 TTTTTATAATTTTATAATAAAATTA
1 TTTTTAT-ATTTTATAAAAAAATTA
17347752 TTTT
1 TTTT
17347756 ATGATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 13 0.52
26 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTTATATTTTATAAAAAAATTA
Found at i:17347798 original size:21 final size:22
Alignment explanation
Indices: 17347761--17347803 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
17347751 ATTTTATGAT
*
17347761 TTAATTTATAAATTAAA-ATTA
1 TTAATTTATAAAGTAAAGATTA
17347782 TTAATTTGAT-AAGTAAAGATTA
1 TTAATTT-ATAAAGTAAAGATTA
17347804 AATGCATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
TTAATTTATAAAGTAAAGATTA
Done.