Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 43 of 187
Found at i:12601721 original size:41 final size:41
Alignment explanation
Indices: 12601621--12601945 Score: 499
Period size: 41 Copynumber: 8.0 Consensus size: 41
12601611 TTGAGTTTTG
*
12601621 GGGCCTTTAGCGACGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
12601662 -TGCCTTTAGCGGCTTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
12601702 GGGCCTTTAGCGGCATTTTTGAAGAAGTGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
12601743 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
12601784 GGGCCTTTAGCGCCGTTTTTGAAGAAGCGCCGCCAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
12601825 TGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* * * **
12601866 GGACCTTTAGCGGCGTTTTTAAAGAAGCACTTCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
12601907 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
12601946 CCGTTTTTGA
Statistics
Matches: 256, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 37 0.14
41 219 0.86
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
Found at i:12602326 original size:14 final size:14
Alignment explanation
Indices: 12602309--12602345 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12602299 GGGTTTAATA
12602309 TATATGGTTTAGGG
1 TATATGGTTTAGGG
*
12602323 TATATGATTTAGGG
1 TATATGGTTTAGGG
12602337 TATATGGTT
1 TATATGGTT
12602346 AATTTAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:12602591 original size:20 final size:19
Alignment explanation
Indices: 12602566--12602604 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
12602556 TAAGGTGTAG
12602566 GGGTTAGGGGTTAGGGATTT
1 GGGTTAGGGGTTA-GGATTT
*
12602586 GGGTTAGGGTTTAGGATTT
1 GGGTTAGGGGTTAGGATTT
12602605 AGGATTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (19 bp):
GGGTTAGGGGTTAGGATTT
Found at i:12602671 original size:7 final size:7
Alignment explanation
Indices: 12602659--12602703 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
12602649 TAAATAAGAT
12602659 TTAGGGG
1 TTAGGGG
12602666 TTAGGGG
1 TTAGGGG
*
12602673 TTAGGAG
1 TTAGGGG
12602680 TTAGGGG
1 TTAGGGG
*
12602687 TTAGAGG
1 TTAGGGG
*
12602694 TTAGAGG
1 TTAGGGG
12602701 TTA
1 TTA
12602704 AGAGTTAGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:12602682 original size:14 final size:14
Alignment explanation
Indices: 12602659--12602711 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
12602649 TAAATAAGAT
*
12602659 TTAGGGGTTAGGGG
1 TTAGGAGTTAGGGG
12602673 TTAGGAGTTAGGGG
1 TTAGGAGTTAGGGG
*
12602687 TTA-GAGGTTAGAGG
1 TTAGGA-GTTAGGGG
*
12602701 TTAAGAGTTAG
1 TTAGGAGTTAG
12602712 TGATTTAGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 2 0.06
14 31 0.89
15 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.45, T:0.30
Consensus pattern (14 bp):
TTAGGAGTTAGGGG
Found at i:12603206 original size:13 final size:13
Alignment explanation
Indices: 12603188--12603214 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12603178 ATAAATAAAT
12603188 AAATTAATGTAAC
1 AAATTAATGTAAC
12603201 AAATTAATGTAAC
1 AAATTAATGTAAC
12603214 A
1 A
12603215 GATTGACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
AAATTAATGTAAC
Found at i:12603830 original size:20 final size:20
Alignment explanation
Indices: 12603792--12603830 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12603782 CTTTGCATTT
*
12603792 AATCTCCAAAACCCATTTTA
1 AATCTCCAAAAACCATTTTA
12603812 AATCTCCCAAAAACC-TTTT
1 AATCT-CCAAAAACCATTTT
12603831 CTTTTATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (20 bp):
AATCTCCAAAAACCATTTTA
Found at i:12604007 original size:30 final size:30
Alignment explanation
Indices: 12603954--12604010 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
12603944 CTGCAGAAGA
* **
12603954 AGAAGAAACAACTGTTGTTGAACAAGAACG
1 AGAAGAAACAACTGTCGCCGAACAAGAACG
12603984 AGAAGAAACAACTGTCGCCGAACAAGA
1 AGAAGAAACAACTGTCGCCGAACAAGA
12604011 GTCTGTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (30 bp):
AGAAGAAACAACTGTCGCCGAACAAGAACG
Found at i:12607295 original size:43 final size:43
Alignment explanation
Indices: 12607199--12607432 Score: 281
Period size: 43 Copynumber: 5.3 Consensus size: 43
12607189 AGGTTATATT
* *
12607199 TTTAGCGGCGTTTTTGCG-AGAAGCGCCGCTATACTAAGGTCATGGTC
1 TTTAGCGGCGTTTGTG-GTAAAAGCGCCGC--TA--AAGGTCATGGTC
* * *
12607246 TATAGCGGCGTTTGTGGTAAAAGTGCCGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGGTC
* * * * **
12607289 TATAGCGGCGTTTGTGGGATAGGCGCCGCTAAAGGTCATGACC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGGTC
* *
12607332 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGGTC
*
12607375 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGGTC
*
12607418 TTTAGCGGCATTTGT
1 TTTAGCGGCGTTTGT
12607433 TTCGAAAAAC
Statistics
Matches: 165, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
43 139 0.84
45 2 0.01
46 1 0.01
47 23 0.14
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:12621894 original size:20 final size:20
Alignment explanation
Indices: 12621852--12621894 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
12621842 ACATAATACA
*
12621852 TTAAAAATACTAAAAATATT
1 TTAAAAATACTAAAAAAATT
*
12621872 TTAAAAAT-TTAAAAAAATCT
1 TTAAAAATACTAAAAAAAT-T
12621892 TTA
1 TTA
12621895 TACTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAAAATACTAAAAAAATT
Found at i:12626433 original size:45 final size:45
Alignment explanation
Indices: 12626371--12626531 Score: 225
Period size: 45 Copynumber: 3.6 Consensus size: 45
12626361 AACACATAGC
* * * *
12626371 ACCACCTTTATAGTCAATGATACTCGGTGGAATCAGCACATAGCA
1 ACCACCTTTATAATCAATGATACCCGGTGGAATCAGCACACAACA
* **
12626416 ACCACCTTCATAATCAAT-AGTACCCATTGGAATCAGCACACAACA
1 ACCACCTTTATAATCAATGA-TACCCGGTGGAATCAGCACACAACA
*
12626461 ACTACCTTTATAATCAATGATACCCGGTGGAATCAGCACACAACA
1 ACCACCTTTATAATCAATGATACCCGGTGGAATCAGCACACAACA
*
12626506 ACCACCTTTATAATCAATGGTACCCG
1 ACCACCTTTATAATCAATGATACCCG
12626532 ATACACATAG
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.01
45 99 0.98
46 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (45 bp):
ACCACCTTTATAATCAATGATACCCGGTGGAATCAGCACACAACA
Found at i:12630081 original size:22 final size:21
Alignment explanation
Indices: 12630056--12630119 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 21
12630046 TTCTTATTCC
12630056 TAATTTAAAACACATTAAATT
1 TAATTTAAAACACATTAAATT
** * * * *
12630077 ATAATACAATATACATGCATATT
1 -TAATTTAAAACACAT-TAAATT
12630100 TAATTTAAAACACATTAAAT
1 TAATTTAAAACACATTAAAT
12630120 ATATTAATGC
Statistics
Matches: 29, Mismatches: 12, Indels: 3
0.66 0.27 0.07
Matches are distributed among these distances:
21 3 0.10
22 22 0.76
23 4 0.14
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.36
Consensus pattern (21 bp):
TAATTTAAAACACATTAAATT
Found at i:12630551 original size:29 final size:29
Alignment explanation
Indices: 12630517--12630619 Score: 138
Period size: 29 Copynumber: 3.6 Consensus size: 29
12630507 GTGAATAAAG
12630517 TGAAATGAATATGAAATGAAAATAAAATA
1 TGAAATGAATATGAAATGAAAATAAAATA
* * *
12630546 TGAAATGAATTTGACATGAAACTAAAATA
1 TGAAATGAATATGAAATGAAAATAAAATA
* *
12630575 TTAAATGAATATGAAATGAAAATAAAGTA
1 TGAAATGAATATGAAATGAAAATAAAATA
12630604 T-AAATTGAA-ATGAAAT
1 TGAAA-TGAATATGAAAT
12630620 AAATTACAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.15
29 55 0.85
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (29 bp):
TGAAATGAATATGAAATGAAAATAAAATA
Found at i:12630727 original size:12 final size:12
Alignment explanation
Indices: 12630710--12630791 Score: 64
Period size: 12 Copynumber: 6.8 Consensus size: 12
12630700 CAAATTTAGA
*
12630710 TGAAATGCAATG
1 TGAAATGAAATG
12630722 TGAAATGAAATG
1 TGAAATGAAATG
* *
12630734 AGAAATGAAA-A
1 TGAAATGAAATG
*
12630745 TGAAATG-AATT
1 TGAAATGAAATG
12630756 TAGAAATGAAAAT-
1 T-GAAATG-AAATG
12630769 TGAAAATTGAAAT-
1 TG-AAA-TGAAATG
12630782 TGAAATGAAA
1 TGAAATGAAA
12630792 AAAGAAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
10 2 0.03
11 12 0.20
12 30 0.51
13 10 0.17
14 5 0.08
ACGTcount: A:0.55, C:0.01, G:0.20, T:0.24
Consensus pattern (12 bp):
TGAAATGAAATG
Found at i:12630792 original size:18 final size:17
Alignment explanation
Indices: 12630709--12630792 Score: 66
Period size: 18 Copynumber: 4.7 Consensus size: 17
12630699 ACAAATTTAG
*
12630709 ATGAAATG-CAATGTGAA
1 ATGAAATGAAAAT-TGAA
12630726 ATGAAATGAGAAA-TGAAA
1 ATGAAATGA-AAATTG-AA
*
12630744 ATGAAATG-AATTTAGAA
1 ATGAAATGAAAATT-GAA
12630761 ATGAAAATTGAAAATTGAA
1 ATG-AAA-TGAAAATTGAA
12630780 ATTGAAATGAAAA
1 A-TGAAATGAAAA
12630793 AAGAAAAATT
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
16 2 0.04
17 16 0.29
18 20 0.36
19 11 0.20
20 6 0.11
ACGTcount: A:0.56, C:0.01, G:0.19, T:0.24
Consensus pattern (17 bp):
ATGAAATGAAAATTGAA
Found at i:12631109 original size:19 final size:20
Alignment explanation
Indices: 12631073--12631110 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12631063 GAATACTAGA
*
12631073 AAAAAAATAAATTTAAATGG
1 AAAAAAATAAATTGAAATGG
*
12631093 AAAAAAATTAA-TGAAATG
1 AAAAAAATAAATTGAAATG
12631111 AAATGAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (20 bp):
AAAAAAATAAATTGAAATGG
Found at i:12631263 original size:21 final size:21
Alignment explanation
Indices: 12631237--12631290 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
12631227 TAATATGAAA
*
12631237 AAAATTGAAATGAGAAAAAAT
1 AAAATTTAAATGAGAAAAAAT
*
12631258 TAAATTTAAATG-GAAAAAAT
1 AAAATTTAAATGAGAAAAAAT
12631278 AAAATTTAAATGA
1 AAAATTTAAATGA
12631291 AATGAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (21 bp):
AAAATTTAAATGAGAAAAAAT
Found at i:12631275 original size:20 final size:20
Alignment explanation
Indices: 12631238--12631311 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 20
12631228 AATATGAAAA
*
12631238 AAATTGAAATGAGAAAAAATT
1 AAATTTAAATG-GAAAAAATT
*
12631259 AAATTTAAATGGAAAAAATA
1 AAATTTAAATGGAAAAAATT
12631279 AAATTTAAAT-GAAATGAAATTT
1 AAATTTAAATGGAAA--AAA-TT
*
12631301 AAATGTAAATG
1 AAATTTAAATG
12631312 TAAATGTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.09
20 18 0.40
21 13 0.29
22 10 0.22
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.28
Consensus pattern (20 bp):
AAATTTAAATGGAAAAAATT
Found at i:12631304 original size:6 final size:6
Alignment explanation
Indices: 12631279--12631367 Score: 100
Period size: 6 Copynumber: 15.8 Consensus size: 6
12631269 GGAAAAAATA
* *
12631279 AAATTT AAATG- AAATG- AAATTT AAATGT AAATGT AAATGT AAATGT
1 AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT
* *
12631325 AAATGT AAATG- AAATG- AAATG- AAATGG AAATGG AAATG- AAATG
1 AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATG
12631368 AAAAAAAATT
Statistics
Matches: 78, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
5 29 0.37
6 49 0.63
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.28
Consensus pattern (6 bp):
AAATGT
Found at i:12631336 original size:181 final size:181
Alignment explanation
Indices: 12631013--12631338 Score: 425
Period size: 181 Copynumber: 1.8 Consensus size: 181
12631003 AATGATAAAT
12631013 TGAAAAAAAAATTGAAATGAAACTACTTGTGATTAATATGAAAAAAAATTGAATACTAGAAAAAA
1 TGAAAAAAAAATTGAAATGAAACTACTTGTGATTAATATGAAAAAAAATTGAATACTAGAAAAAA
* * *
12631078 AATAAATTTAAATGGAAAAAAATTAATGAAATGAAATGAATTTGTAATGATTATGAAATGAAATG
66 AATAAATTTAAATGGAAAAAAATAAATGAAATGAAATGAATTTGAAATGATAATGAAATGAAATG
* *
12631143 ATAGTTTAAATGAAAATAAATTATAAATTGAAATGAAAACAAAAACTGAAA
131 ATAATGTAAATGAAAATAAATTATAAATTGAAATGAAAACAAAAACTGAAA
* * * *
12631194 TGAAAAAATAATTTAAATGAGACTACTTGTTATTAATATG-AAAAAAATTGAA-A-T-GAGAAAA
1 TGAAAAAAAAATTGAAATGAAACTACTTGTGATTAATATGAAAAAAAATTGAATACTAGA-AAAA
* *
12631255 AATTAAATTTAAATGG-AAAAAATAAAATTTAAATGAAATGAAATTT-AAATG-TAAATGTAAAT
65 AAATAAATTTAAATGGAAAAAAAT-AAA-TGAAATGAAATG-AATTTGAAATGAT-AATG-AAAT
12631317 GTAAATG-TAAATGTAAATGAAA
125 G-AAATGAT-AATGTAAATGAAA
12631339 TGAAATGAAA
Statistics
Matches: 126, Mismatches: 11, Indels: 16
0.82 0.07 0.10
Matches are distributed among these distances:
177 9 0.07
178 23 0.18
179 19 0.15
180 23 0.18
181 52 0.41
ACGTcount: A:0.57, C:0.02, G:0.13, T:0.29
Consensus pattern (181 bp):
TGAAAAAAAAATTGAAATGAAACTACTTGTGATTAATATGAAAAAAAATTGAATACTAGAAAAAA
AATAAATTTAAATGGAAAAAAATAAATGAAATGAAATGAATTTGAAATGATAATGAAATGAAATG
ATAATGTAAATGAAAATAAATTATAAATTGAAATGAAAACAAAAACTGAAA
Found at i:12631376 original size:27 final size:27
Alignment explanation
Indices: 12631319--12631376 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
12631309 ATGTAAATGT
* * **
12631319 AAATGTAAATGTAAATGAAATGAAATG
1 AAATGGAAATGGAAATGAAATGAAAAA
12631346 AAATGGAAATGGAAATGAAATGAAAAA
1 AAATGGAAATGGAAATGAAATGAAAAA
12631373 AAAT
1 AAAT
12631377 TAAAAGGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (27 bp):
AAATGGAAATGGAAATGAAATGAAAAA
Found at i:12634155 original size:90 final size:90
Alignment explanation
Indices: 12634042--12634369 Score: 471
Period size: 90 Copynumber: 3.6 Consensus size: 90
12634032 ATTCTAGAAT
* * * * * *
12634042 ATTAATACACAAAAATATAAAATTCAAACAACAAATAACACGGACTAAATTAAATTTAAACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACCC
12634107 AACAAACTACAAACAGATGGATAAA
66 AACAAACTACAAACAGATGGATAAA
*
12634132 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGGCTAAATTAAATTTAAACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACCC
* * *
12634197 AAGAAACTAAAAACAGATGGGTAAA
66 AACAAACTACAAACAGATGGATAAA
* * * *
12634222 ATTAATGCACGAAAATTTTAAAGTCAAACTATATATAATACAGG-CTAAATTAAATTTAAACACT
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATAC-GGACTAAATTAAATTTAAACACC
*
12634286 CAACAAACTACAAACCGAT-GAGTAAA
65 CAACAAACTACAAACAGATGGA-TAAA
* *
12634312 ATTAATACACGAAAATTTTCAATTCAAACTACATATAATACGGATTAAATTAAATTTA
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTA
12634370 CAGATATAAA
Statistics
Matches: 212, Mismatches: 23, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
89 3 0.01
90 207 0.98
91 2 0.01
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (90 bp):
ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACCC
AACAAACTACAAACAGATGGATAAA
Found at i:12634459 original size:180 final size:177
Alignment explanation
Indices: 12633999--12634435 Score: 495
Period size: 180 Copynumber: 2.4 Consensus size: 177
12633989 AGTACACAAC
* *
12633999 AAATTAAATTTACAAATATAATAAAATACAAACATTCTAGAATATTAATACACAAAAATATAAAA
1 AAATTAAATTTACAAATATAAAAAAATACAAACATTCTAGAA-ATTAATACACGAAAATATAAAA
*** *
12634064 TTCAAACAACAAATAACACGGACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGGAT
65 -TCAAACCTTAAATAACACAGACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGGAT
*
12634129 AAAATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGGCT
129 AAAATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACT
*** * * * ** * *
12634178 AAATTAAATTTA-AACACCCAAGAAACTAAAAACAGATGGGTA-AAATTAATGCACGAAAATTTT
1 AAATTAAATTTACAA-ATATAAAAAAATACAAAC--AT-TCTAGAAATTAATACACGAAAA-TAT
* * * * * *
12634241 AAAGTCAAA-CTATATATAATACAGGCTAAATTAAATTTAAACACTCAACAAACTACAAACCGAT
61 AAAATCAAACCT-TAAATAACACAGACTAAATTAAATTTAAACACCCAACAAACTACAAACAGAT
* *
12634305 -GAGTAAAATTAATACACGAAAATTTTCAATTCAAACTACATATAATACGGATT
125 GGA-TAAAATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACT
* *
12634358 AAATTAAATTTACAGATATAAAAAAATACAAACATTCTAAGAAATTAATACATGAAAATATAATA
1 AAATTAAATTTACAAATATAAAAAAATACAAACATTCT-AGAAATTAATACACGAAAATATAA-A
*
12634423 ATGAAACCTTAAA
64 ATCAAACCTTAAA
12634436 CCCTAAACGA
Statistics
Matches: 207, Mismatches: 39, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
177 1 0.00
178 9 0.04
179 49 0.24
180 136 0.66
181 10 0.05
182 2 0.01
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (177 bp):
AAATTAAATTTACAAATATAAAAAAATACAAACATTCTAGAAATTAATACACGAAAATATAAAAT
CAAACCTTAAATAACACAGACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGGATAA
AATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACT
Found at i:12634813 original size:26 final size:25
Alignment explanation
Indices: 12634734--12634803 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 25
12634724 AATTCGGTTG
***
12634734 TACACTACAAAAAACTCCCATATGCAA
1 TACACTACAAAAAACTCATTTATG--A
*
12634761 TTCACTACAAAAAACTCATTTGATGA
1 TACACTACAAAAAACTCATTT-ATGA
*
12634787 TACACTACAAAACACTC
1 TACACTACAAAAAACTC
12634804 TCATTTTGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 16 0.44
27 17 0.47
28 3 0.08
ACGTcount: A:0.46, C:0.27, G:0.04, T:0.23
Consensus pattern (25 bp):
TACACTACAAAAAACTCATTTATGA
Found at i:12640594 original size:74 final size:73
Alignment explanation
Indices: 12640473--12640618 Score: 238
Period size: 74 Copynumber: 2.0 Consensus size: 73
12640463 AGATTTTAAA
* * * *
12640473 AAAAAAAGGGATCATGCCCAGTGAGTTAGGACATGATCTTTTCTTAATTCCCGAGATCGTTTAAA
1 AAAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCAGAGATCGTTT-AA
12640538 AATTTGAGG
65 AATTTGAGG
*
12640547 AAAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTTCAGAGATCGTTTAAA
1 AAAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCAGAGATCGTTTAAA
12640612 ATTTGAG
66 ATTTGAG
12640619 TTTGAAAAGA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
73 10 0.15
74 57 0.85
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (73 bp):
AAAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCAGAGATCGTTTAAA
ATTTGAGG
Found at i:12642095 original size:19 final size:19
Alignment explanation
Indices: 12642071--12642116 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
12642061 TAGTATTTCG
*
12642071 AAATAAAAATAAATGTAAA
1 AAATAAAAATAAATATAAA
*
12642090 AAATAAATATAAATATAAA
1 AAATAAAAATAAATATAAA
*
12642109 AAAGAAAA
1 AAATAAAA
12642117 CACCTTTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (19 bp):
AAATAAAAATAAATATAAA
Found at i:12642154 original size:20 final size:18
Alignment explanation
Indices: 12642121--12642157 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
12642111 AGAAAACACC
12642121 TTTTGTTTTTTTTTTGAG
1 TTTTGTTTTTTTTTTGAG
12642139 TTTTAGTTTTTCTTTTTGA
1 TTTT-GTTTTT-TTTTTGA
12642158 ACCTTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.08, C:0.03, G:0.14, T:0.76
Consensus pattern (18 bp):
TTTTGTTTTTTTTTTGAG
Found at i:12646743 original size:45 final size:45
Alignment explanation
Indices: 12646665--12646785 Score: 134
Period size: 45 Copynumber: 2.7 Consensus size: 45
12646655 ATTGTTCAAG
* * * * * *
12646665 AATGTCATAGCGTCTTTCAGCCACGGTCCTATTTATTTTCGACAT
1 AATGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTTCGACAT
***
12646710 AATGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTTTTTCAT
1 AATGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTTCGACAT
** *
12646755 GTTGCCATAGTATCTTTCAACTATGGTCTTA
1 AATGCCATAGTGTCTTTCAACTATGGTCTTA
12646786 ACCGTTTTTC
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (45 bp):
AATGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTTCGACAT
Found at i:12654894 original size:16 final size:16
Alignment explanation
Indices: 12654873--12654904 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12654863 ATTTTGTTGC
*
12654873 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
12654889 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
12654905 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:12655555 original size:78 final size:78
Alignment explanation
Indices: 12655425--12655581 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 78
12655415 CTCACATTAT
*
12655425 TCAATCCAGTCCAAAAATCATATTTTGGAAAAATTACATTTTTGCCCCTAAAGTTTCACAAAATT
1 TCAATCCAGTCCAAAAATCATATTTTGGAAAAATTACATTTTTGCCCATAAAGTTTCACAAAATT
*
12655490 ATGATTTTGCCCC
66 ACGATTTTGCCCC
12655503 TCAATCCAGTCCAAAAATCATA-TTTGGAAAAAATTACATTTTTGCCCATAAAGTTTCACAAAAT
1 TCAATCCAGTCCAAAAATCATATTTTGG-AAAAATTACATTTTTGCCCATAAAGTTTCACAAAAT
12655567 TACGATTTTGCCCC
65 TACGATTTTGCCCC
12655581 T
1 T
12655582 AGGCTCAAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 5 0.07
78 71 0.93
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.34
Consensus pattern (78 bp):
TCAATCCAGTCCAAAAATCATATTTTGGAAAAATTACATTTTTGCCCATAAAGTTTCACAAAATT
ACGATTTTGCCCC
Found at i:12658908 original size:15 final size:15
Alignment explanation
Indices: 12658855--12658911 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
12658845 TTTAATAGAT
*
12658855 TTAATATTAAATTTAA
1 TTAATATTATA-TTAA
* *
12658871 TCTAATATTTATCTTGA
1 T-TAATA-TTATATTAA
*
12658888 TAAATATTATATTAA
1 TTAATATTATATTAA
12658903 TTAATATTA
1 TTAATATTA
12658912 AAGTGATTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 15 0.47
16 5 0.16
17 9 0.28
18 3 0.09
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAATATTATATTAA
Found at i:12661836 original size:30 final size:31
Alignment explanation
Indices: 12661797--12661856 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
12661787 GGAGGTGGGA
*
12661797 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
12661828 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
12661857 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:12666999 original size:18 final size:17
Alignment explanation
Indices: 12666960--12667004 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
12666950 AAACCAAATG
*
12666960 TTAATTTAATTATAAAA
1 TTAATTTAATTACAAAA
12666977 TTAATTTATATTACATAAA
1 TTAATTTA-ATTACA-AAA
12666996 -TAATTTAAT
1 TTAATTTAAT
12667005 GAAAAACCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATTTAATTACAAAA
Found at i:12673098 original size:6 final size:6
Alignment explanation
Indices: 12673087--12673116 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
12673077 TAAAATATAT
*
12673087 TATTTA TATTTA TATTTG TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA
12673117 ATTAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:12686335 original size:41 final size:41
Alignment explanation
Indices: 12686280--12686358 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
12686270 CCTAATTGGG
12686280 AAAACAATTCCCTTATTCTAATAAACTACTAAAAGATAAGA
1 AAAACAATTCCCTTATTCTAATAAACTACTAAAAGATAAGA
*
12686321 AAAATAATTCCCTTATTCTAATAAACTACTAAAAGATA
1 AAAACAATTCCCTTATTCTAATAAACTACTAAAAGATA
12686359 GAATAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.29
Consensus pattern (41 bp):
AAAACAATTCCCTTATTCTAATAAACTACTAAAAGATAAGA
Found at i:12686421 original size:19 final size:19
Alignment explanation
Indices: 12686397--12686437 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
12686387 TGATTTATTC
12686397 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
*
12686416 TAAGATTTATTTACCTAAA
1 TAAGATTTATCTACCTAAA
12686435 TAA
1 TAA
12686438 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:12696918 original size:54 final size:54
Alignment explanation
Indices: 12696832--12696937 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 54
12696822 GTGTACCTGA
* *
12696832 TTCAATTGATTCTCCTAAAACGGAAATCTGTGAGAAGGATTTATCTACAAGTGT
1 TTCAATTGATTCTCCTAAAAAGGAAATCTGTGAGAAGGATCTATCTACAAGTGT
* * *
12696886 TTCAATTGATTCTCCTAAAAAGGAACTTTGTGAGAAGGATCTATCTAGAAGT
1 TTCAATTGATTCTCCTAAAAAGGAAATCTGTGAGAAGGATCTATCTACAAGT
12696938 TTTGAACTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (54 bp):
TTCAATTGATTCTCCTAAAAAGGAAATCTGTGAGAAGGATCTATCTACAAGTGT
Found at i:12700820 original size:6 final size:6
Alignment explanation
Indices: 12700811--12700839 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12700801 TTTCACAATA
12700811 TACTAT TACTAT TACTAT TACTAT TACTA
1 TACTAT TACTAT TACTAT TACTAT TACTA
12700840 GTATGGCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (6 bp):
TACTAT
Found at i:12714166 original size:18 final size:18
Alignment explanation
Indices: 12714121--12714172 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
12714111 CCAGGTGAAT
* *
12714121 ATTTTGTAACCTTAGGAG
1 ATTTTGTAATCTTAGAAG
12714139 ATTTTGTAATCTTAGAAG
1 ATTTTGTAATCTTAGAAG
*
12714157 ATTTTGTAATATTAGA
1 ATTTTGTAATCTTAGA
12714173 GGATCTTGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (18 bp):
ATTTTGTAATCTTAGAAG
Found at i:12716621 original size:27 final size:25
Alignment explanation
Indices: 12716591--12716676 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 25
12716581 AACACATTAG
12716591 GAAAGAAATGCCTATGTGGCGTAATAT
1 GAAAGAAA-GCCTATGTGGCG-AATAT
* *
12716618 GAAATGAACA-CATATGTGGCACAATAT
1 GAAA-GAA-AGCCTATGTGGC-GAATAT
*
12716645 GAAAGAAACGCCTTTGTGGCGAATCAT
1 GAAAGAAA-GCCTATGTGGCGAAT-AT
12716672 GAAAG
1 GAAAG
12716677 GATAACCTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 37 0.77
28 3 0.06
29 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (25 bp):
GAAAGAAAGCCTATGTGGCGAATAT
Found at i:12724537 original size:12 final size:12
Alignment explanation
Indices: 12724520--12724545 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12724510 CAATTCGATT
12724520 ATAAAAAATTGA
1 ATAAAAAATTGA
12724532 ATAAAAAATTGA
1 ATAAAAAATTGA
12724544 AT
1 AT
12724546 TTTGAATTAT
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:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (12 bp):
ATAAAAAATTGA
Found at i:12730297 original size:43 final size:43
Alignment explanation
Indices: 12730184--12730297 Score: 106
Period size: 43 Copynumber: 2.7 Consensus size: 43
12730174 AGTGTTTTCC
* * * * * *
12730184 TGTAAGACCATGTCTGGGACGTTGTCATCGACTTGTGTTTTCG
1 TGTAAGACCATGTCTGGGACGTTGGCGTCGACTCGTGATTACA
* * *
12730227 TGTAAGACCTTGTCAGGGACAG-CGGCGTCGA-TCCGTGATTACA
1 TGTAAGACCATGTCTGGGAC-GTTGGCGTCGACT-CGTGATTACA
*
12730270 TGTAAGACCACGTCTGGGACGTTGGCGT
1 TGTAAGACCATGTCTGGGACGTTGGCGT
12730298 TGTACGAATC
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
42 2 0.04
43 52 0.95
44 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACGTTGGCGTCGACTCGTGATTACA
Found at i:12732345 original size:23 final size:23
Alignment explanation
Indices: 12732319--12732391 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
12732309 CTGGTGGAAG
*
12732319 CATTTTGGCATTACGGTGCAATT
1 CATTTTGGCATTACAGTGCAATT
* * * *
12732342 CATTTTGCCACTACTGTGCAACT
1 CATTTTGGCATTACAGTGCAATT
* *
12732365 CATTCTAGCACTT-CAGTGCAATT
1 CATTTTGGCA-TTACAGTGCAATT
12732388 CATT
1 CATT
12732392 CTATGGAGTG
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (23 bp):
CATTTTGGCATTACAGTGCAATT
Found at i:12732392 original size:23 final size:24
Alignment explanation
Indices: 12732334--12732394 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
12732324 TGGCATTACG
* *
12732334 GTGCAATTCATT-TTGCCACTACT
1 GTGCAATTCATTCTAGCCACTACA
* *
12732357 GTGCAACTCATTCTAG-CACTTCA
1 GTGCAATTCATTCTAGCCACTACA
12732380 GTGCAATTCATTCTA
1 GTGCAATTCATTCTA
12732395 TGGAGTGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 30 0.94
24 2 0.06
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (24 bp):
GTGCAATTCATTCTAGCCACTACA
Found at i:12738363 original size:23 final size:24
Alignment explanation
Indices: 12738337--12738383 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12738327 GAGTTACCTG
*
12738337 TTAAGCTC-AATGAGCTTCTTGTT
1 TTAAACTCTAATGAGCTTCTTGTT
* *
12738360 TTAAACTCTTATGAGTTTCTTGTT
1 TTAAACTCTAATGAGCTTCTTGTT
12738384 ATAGCCCAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (24 bp):
TTAAACTCTAATGAGCTTCTTGTT
Found at i:12744536 original size:27 final size:27
Alignment explanation
Indices: 12744506--12744648 Score: 92
Period size: 28 Copynumber: 5.2 Consensus size: 27
12744496 GATCAGAGAT
* * *
12744506 AGTCTATTGGGACAGTAAACACAGGTG
1 AGTCTATCGAGACAGTAAACACAGGTA
*
12744533 AGTCTGTCGAGACAGTAAACACAGGTA
1 AGTCTATCGAGACAGTAAACACAGGTA
* * *
12744560 AGTCTA-CGGGGATAGTACACACGAGGTA
1 AGTCTATC-GAGACAGTAAACAC-AGGTA
* * * *
12744588 TGT-TCACCGAGATAGTAAACATGAGGTA
1 AGTCT-ATCGAGACAGTAAACA-CAGGTA
* * * *
12744616 AGTCCACCAAGACAGTAATCACGAGGTA
1 AGTCTATCGAGACAGTAAACAC-AGGTA
12744644 AGTCT
1 AGTCT
12744649 GATGGGATGC
Statistics
Matches: 90, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
26 1 0.01
27 40 0.44
28 48 0.53
29 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (27 bp):
AGTCTATCGAGACAGTAAACACAGGTA
Found at i:12749494 original size:13 final size:12
Alignment explanation
Indices: 12749478--12749516 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
12749468 AAATAAAATG
12749478 TTAAAAATTAGAA
1 TTAAAAATTA-AA
12749491 TTAAAAATTAATA
1 TTAAAAATTAA-A
12749504 TTAAGAAATTAAA
1 TTAA-AAATTAAA
12749517 ATTAGGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 16 0.67
14 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (12 bp):
TTAAAAATTAAA
Found at i:12749497 original size:27 final size:27
Alignment explanation
Indices: 12749467--12749520 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
12749457 AGTAATAAAT
* *
12749467 AAAATAAAATGTTAA-AAATTAGAATTA
1 AAAAT-AAATATTAAGAAATTAAAATTA
*
12749494 AAAATTAATATTAAGAAATTAAAATTA
1 AAAATAAATATTAAGAAATTAAAATTA
12749521 GGTGTTCAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (27 bp):
AAAATAAATATTAAGAAATTAAAATTA
Found at i:12750965 original size:23 final size:23
Alignment explanation
Indices: 12750913--12751021 Score: 91
Period size: 23 Copynumber: 4.7 Consensus size: 23
12750903 TCACTTTTTG
* *
12750913 GGTTGTGTTTGAAGGCTATACT-T
1 GGTTGTGTTTGGAGGGTATA-TAT
12750936 -GTATGTGTTTGGAGGGTATATAT
1 GGT-TGTGTTTGGAGGGTATATAT
* *
12750959 GGTTGTGTTTGGTGGAG-ATATTT
1 GGTTGTGTTTGGAGG-GTATATAT
*
12750982 GGTTGTGTTTAGAGGGTATA-AT
1 GGTTGTGTTTGGAGGGTATATAT
* *
12751004 CGATTGTGATTGGAGGGT
1 -GGTTGTGTTTGGAGGGT
12751022 GATAGCTTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
22 5 0.07
23 62 0.89
24 3 0.04
ACGTcount: A:0.18, C:0.03, G:0.37, T:0.42
Consensus pattern (23 bp):
GGTTGTGTTTGGAGGGTATATAT
Found at i:12752092 original size:16 final size:16
Alignment explanation
Indices: 12752071--12752102 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12752061 AGTCCTTAAC
12752071 TGCATGATTAAGTATT
1 TGCATGATTAAGTATT
12752087 TGCATGATTAAGTATT
1 TGCATGATTAAGTATT
12752103 GTATGGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (16 bp):
TGCATGATTAAGTATT
Found at i:12754555 original size:27 final size:27
Alignment explanation
Indices: 12754525--12754577 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
12754515 AACTCCTCTG
*
12754525 TGGCGCAATATGAAAGGAAAGCCTTTT
1 TGGCGCAATATGAAAAGAAAGCCTTTT
*
12754552 TGGCGCAATATGAAAAGAACGCCTTT
1 TGGCGCAATATGAAAAGAAAGCCTTT
12754578 GGGCGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (27 bp):
TGGCGCAATATGAAAAGAAAGCCTTTT
Found at i:12754589 original size:26 final size:27
Alignment explanation
Indices: 12754526--12754591 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
12754516 ACTCCTCTGT
* *
12754526 GGCGCAATATGAAAGGAAAGCCTTTTT
1 GGCGCAATATGAAAAGAAAGCCTTTTG
*
12754553 GGCGCAATATGAAAAGAACGCC-TTTG
1 GGCGCAATATGAAAAGAAAGCCTTTTG
12754579 GGCG-AATTATGAA
1 GGCGCAA-TATGAA
12754592 GGGATAGCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.06
26 13 0.37
27 20 0.57
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (27 bp):
GGCGCAATATGAAAAGAAAGCCTTTTG
Found at i:12755939 original size:41 final size:42
Alignment explanation
Indices: 12755861--12755960 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 42
12755851 CTATATGATT
* * *
12755861 AGCACTAAGTGTGCG-AATTAAATGATGAGGTTGAATAA-CG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACCG
* *
12755901 AGCACTAAGTGTCCGAAACTAAATAATGATGTTAAATAACCG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACCG
12755943 -GCACTAAGTGTGCGAAAC
1 AGCACTAAGTGTGCGAAAC
12755961 CGAGATCAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
40 14 0.27
41 36 0.69
42 2 0.04
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (42 bp):
AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACCG
Found at i:12761462 original size:25 final size:25
Alignment explanation
Indices: 12761407--12761462 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
12761397 CATAGATCAC
12761407 ATGAGCTTCCCATTATATGGCTCGA
1 ATGAGCTTCCCATTATATGGCTCGA
*
12761432 AAGAGCTTCCCATT-TATGTGCTC-A
1 ATGAGCTTCCCATTATATG-GCTCGA
12761456 TATGAGC
1 -ATGAGC
12761463 ATTCTTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (25 bp):
ATGAGCTTCCCATTATATGGCTCGA
Found at i:12762534 original size:13 final size:13
Alignment explanation
Indices: 12762516--12762541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12762506 ATCCACACGG
12762516 CCTAATTAATGCA
1 CCTAATTAATGCA
12762529 CCTAATTAATGCA
1 CCTAATTAATGCA
12762542 AGTCAATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
CCTAATTAATGCA
Found at i:12764781 original size:15 final size:16
Alignment explanation
Indices: 12764761--12764790 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12764751 GAGAGAAGCC
12764761 ATAATAA-TCAACAAT
1 ATAATAACTCAACAAT
12764776 ATAATAACTCAACAA
1 ATAATAACTCAACAA
12764791 ACATGAAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (16 bp):
ATAATAACTCAACAAT
Found at i:12785637 original size:26 final size:27
Alignment explanation
Indices: 12785571--12785625 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
12785561 TTAGGTAAAT
*
12785571 ACAATAGATAAATTTTTTAGACATCCA
1 ACAATAGATAATTTTTTTAGACATCCA
12785598 ACAATAGATAATTTTTTTAGACATCCA
1 ACAATAGATAATTTTTTTAGACATCCA
12785625 A
1 A
12785626 AGTAAGAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.35
Consensus pattern (27 bp):
ACAATAGATAATTTTTTTAGACATCCA
Found at i:12786038 original size:10 final size:10
Alignment explanation
Indices: 12786008--12786041 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
12785998 AGTCTTAATT
12786008 TAAAAAAATA
1 TAAAAAAATA
* *
12786018 GATAAAAATA
1 TAAAAAAATA
12786028 TAAAAAAATA
1 TAAAAAAATA
12786038 TAAA
1 TAAA
12786042 TTTATCAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:12787678 original size:13 final size:13
Alignment explanation
Indices: 12787654--12787700 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
12787644 GTGTTAACTT
12787654 TTTTATTTTATTAC
1 TTTTA-TTTATTAC
12787668 TTTTATTTATTA-
1 TTTTATTTATTAC
*
12787680 TTTT-TTTATTTC
1 TTTTATTTATTAC
*
12787692 ATTTATTTA
1 TTTTATTTA
12787701 CCTTGTTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 6 0.21
12 7 0.24
13 11 0.38
14 5 0.17
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTATTTATTAC
Found at i:12799942 original size:7 final size:7
Alignment explanation
Indices: 12799932--12799977 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
12799922 AGAATGATGA
*
12799932 ATGAGAG
1 ATGAGGG
*
12799939 ATGAGTG
1 ATGAGGG
*
12799946 TTGAGGG
1 ATGAGGG
12799953 ATGAGGG
1 ATGAGGG
12799960 ATGAGGG
1 ATGAGGG
*
12799967 ATGAAGG
1 ATGAGGG
12799974 ATGA
1 ATGA
12799978 TTTGAGAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.48, T:0.20
Consensus pattern (7 bp):
ATGAGGG
Found at i:12804962 original size:36 final size:36
Alignment explanation
Indices: 12804906--12805012 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
12804896 AGAAAATATT
* *
12804906 CATTACTTACATTTTATATCACCAATGAACGATTTA
1 CATTTCTTACATTTTATATCATCAATGAACGATTTA
* * * *
12804942 CATTTCTTCCATTTTATATCATCAGTGGACGATCTA
1 CATTTCTTACATTTTATATCATCAATGAACGATTTA
** *
12804978 CACCTCTTGCATTTTATATCATCAATGAACGATTT
1 CATTTCTTACATTTTATATCATCAATGAACGATTT
12805013 TGCACCGCTT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.40
Consensus pattern (36 bp):
CATTTCTTACATTTTATATCATCAATGAACGATTTA
Found at i:12813285 original size:26 final size:25
Alignment explanation
Indices: 12813247--12813296 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
12813237 AATCAAATAT
*
12813247 TAAAAATATATTTATATTAATATTC
1 TAAAAATAAATTTATATTAATATTC
* *
12813272 TAAAAATTAAATTTATTTTTATATT
1 TAAAAA-TAAATTTATATTAATATT
12813297 TAATTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TAAAAATAAATTTATATTAATATTC
Found at i:12813902 original size:20 final size:21
Alignment explanation
Indices: 12813858--12813902 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
12813848 AACCATGTTG
* *
12813858 TTTTGTTGTTGTTTTTCCATG
1 TTTTGTTGTTGTTTTCCCATC
12813879 TTTTGTTGTTGTTTTCCCA-C
1 TTTTGTTGTTGTTTTCCCATC
12813899 TTTT
1 TTTT
12813903 TATCATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.04, C:0.13, G:0.16, T:0.67
Consensus pattern (21 bp):
TTTTGTTGTTGTTTTCCCATC
Found at i:12813903 original size:21 final size:21
Alignment explanation
Indices: 12813856--12813897 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12813846 GAAACCATGT
*
12813856 TGTTTTGTTGTTGTTTTTCCA
1 TGTTTTGTTGTTGTTTTCCCA
12813877 TGTTTTGTTGTTGTTTTCCCA
1 TGTTTTGTTGTTGTTTTCCCA
12813898 CTTTTTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.12, G:0.19, T:0.64
Consensus pattern (21 bp):
TGTTTTGTTGTTGTTTTCCCA
Found at i:12815319 original size:14 final size:14
Alignment explanation
Indices: 12815267--12815333 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
12815257 ATTATTTTAT
**
12815267 CTTAAACCTCAAAC
1 CTTAAACCTTGAAC
*
12815281 CCTAAACCTTGAA-
1 CTTAAACCTTGAAC
*
12815294 -TTCAAACATTGAAC
1 CTT-AAACCTTGAAC
12815308 CTTAAACCTTGAAC
1 CTTAAACCTTGAAC
*
12815322 CTCAAACCTTGA
1 CTTAAACCTTGA
12815334 GGTTCGAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
12 1 0.02
13 9 0.21
14 31 0.72
15 2 0.05
ACGTcount: A:0.39, C:0.30, G:0.06, T:0.25
Consensus pattern (14 bp):
CTTAAACCTTGAAC
Found at i:12815364 original size:27 final size:27
Alignment explanation
Indices: 12815334--12815386 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
12815324 CAAACCTTGA
12815334 GGTTCGAGATTTAAGGTTCAAGGGTTG
1 GGTTCGAGATTTAAGGTTCAAGGGTTG
* * * *
12815361 GGTTTGGGGTTTAAGGTTCAATGGTT
1 GGTTCGAGATTTAAGGTTCAAGGGTT
12815387 TGGAGTTACG
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:0.19, C:0.06, G:0.38, T:0.38
Consensus pattern (27 bp):
GGTTCGAGATTTAAGGTTCAAGGGTTG
Found at i:12819842 original size:75 final size:74
Alignment explanation
Indices: 12819686--12820069 Score: 264
Period size: 75 Copynumber: 5.1 Consensus size: 74
12819676 AGTCGGTTAA
* * ** * *
12819686 ATACTGAATGTGCTCAAATGAGCAATACCTACTAATTATGCTGAATG-TGCTCATACAAGCAATA
1 ATACTGAATGTGCTCAAA-GAGCAATGCCTACTGATTATATTGAAAGTTGCTCAAACAAGCAATA
12819750 TCTACTGATT
65 TCTACTGATT
* * *
12819760 ATACTGAATGTTCTCAGAAGAGCAATGCCTACTGATTGTATTGAAAGTTTCTCAAACAAGCAATA
1 ATACTGAATGTGCTCA-AAGAGCAATGCCTACTGATTATATTGAAAGTTGCTCAAACAAGCAATA
* *
12819825 TCTAGTGGTT
65 TCTACTGATT
* * * * *
12819835 ATACTGAAAGTGCTCAAAAGAGCAATGTCTACTGAATATATTGAAAGTTGCTCAAACGAGCTATA
1 ATACTGAATGTGCTC-AAAGAGCAATGCCTACTGATTATATTGAAAGTTGCTCAAACAAGCAATA
* *
12819900 CCCACTGATT
65 TCTACTGATT
* * *
12819910 TTATTGAATGT--T-AAACGAGCGATAT-CC-ACTGATTATACT-AAATGTTTGCTCAAACAAGC
1 ATACTGAATGTGCTCAAA-GAGC-A-ATGCCTACTGATTATATTGAAA-G-TTGCTCAAACAAGC
* *
12819969 GATATCCACAT-ATT
61 AATATCTAC-TGATT
* * * * * ** * * *
12819983 ATACTAAATGTTTGCACAAACAAGCAATATCC-ACTGGTCGTACTGAATGTTTGCTCAAACGAGC
1 ATACTGAATG--TGCTCAAA-GAGCAAT-GCCTACTGATTATATTGAAAG-TTGCTCAAACAAGC
* *
12820047 GATATCCACTGATT
61 AATATCTACTGATT
12820061 ATACTGAAT
1 ATACTGAAT
12820070 AATATCTTTC
Statistics
Matches: 249, Mismatches: 43, Indels: 32
0.77 0.13 0.10
Matches are distributed among these distances:
71 6 0.02
72 15 0.06
73 33 0.13
74 40 0.16
75 95 0.38
76 3 0.01
77 2 0.01
78 53 0.21
79 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (74 bp):
ATACTGAATGTGCTCAAAGAGCAATGCCTACTGATTATATTGAAAGTTGCTCAAACAAGCAATAT
CTACTGATT
Found at i:12819954 original size:34 final size:35
Alignment explanation
Indices: 12819886--12820065 Score: 121
Period size: 39 Copynumber: 4.8 Consensus size: 35
12819876 TGAAAGTTGC
* * * * *
12819886 TCAAACGAGCTATACCCACTGATTTTATTGAATGT
1 TCAAACGAGCGATATCCACTGATTATACTAAATGT
12819921 T-AAACGAGCGATATCCACTGATTATACTAAATGTTT
1 TCAAACGAGCGATATCCACTGATTATACTAAATG--T
*
12819957 GCTCAAACAAGCGATATCCACAT-ATTATACTAAATGTT
1 --TCAAACGAGCGATATCCAC-TGATTATACTAAATG-T
* * * ** *
12819995 TGCACAAACAAGCAATATCCACTGGTCGTACTGAATGTTT
1 T---CAAACGAGCGATATCCACTGATTATACTAAATG--T
12820035 GCTCAAACGAGCGATATCCACTGATTATACT
1 --TCAAACGAGCGATATCCACTGATTATACT
12820066 GAATAATATC
Statistics
Matches: 116, Mismatches: 16, Indels: 22
0.75 0.10 0.14
Matches are distributed among these distances:
34 27 0.23
35 1 0.01
36 2 0.02
38 4 0.03
39 78 0.67
40 3 0.03
42 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (35 bp):
TCAAACGAGCGATATCCACTGATTATACTAAATGT
Found at i:12819984 original size:39 final size:39
Alignment explanation
Indices: 12819922--12820065 Score: 200
Period size: 39 Copynumber: 3.7 Consensus size: 39
12819912 ATTGAATGTT
*
12819922 AAACGAGCGATATCCACTGATTATACTAAATGTTTGCTC
1 AAACAAGCGATATCCACTGATTATACTAAATGTTTGCTC
*
12819961 AAACAAGCGATATCCACAT-ATTATACTAAATGTTTGCAC
1 AAACAAGCGATATCCAC-TGATTATACTAAATGTTTGCTC
* * ** *
12820000 AAACAAGCAATATCCACTGGTCGTACTGAATGTTTGCTC
1 AAACAAGCGATATCCACTGATTATACTAAATGTTTGCTC
*
12820039 AAACGAGCGATATCCACTGATTATACT
1 AAACAAGCGATATCCACTGATTATACT
12820066 GAATAATATC
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
38 1 0.01
39 88 0.98
40 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (39 bp):
AAACAAGCGATATCCACTGATTATACTAAATGTTTGCTC
Found at i:12820066 original size:39 final size:38
Alignment explanation
Indices: 12819686--12820069 Score: 288
Period size: 37 Copynumber: 10.2 Consensus size: 38
12819676 AGTCGGTTAA
* *
12819686 ATACTGAATG-TGCTCAAATGAGCAATA-CCTACTAATT
1 ATACTGAATGTTGCTCAAACGAGCAATATCC-ACTGATT
* * * *
12819723 ATGCTGAATG-TGCTCATACAAGCAATATCTACTGATT
1 ATACTGAATGTTGCTCAAACGAGCAATATCCACTGATT
*
12819760 ATACTGAATGTT-CTCAGAA-GAGCAAT-GCCTACTGATT
1 ATACTGAATGTTGCTCA-AACGAGCAATATCC-ACTGATT
* * * * * * * *
12819797 GTATTGAAAGTTTCTCAAACAAGCAATATCTAGTGGTT
1 ATACTGAATGTTGCTCAAACGAGCAATATCCACTGATT
* * * * *
12819835 ATACTGAAAG-TGCTCAAAAGAGCAATGTCTACTGAAT
1 ATACTGAATGTTGCTCAAACGAGCAATATCCACTGATT
* * * *
12819872 ATATTGAAAGTTGCTCAAACGAGCTATACCCACTGATT
1 ATACTGAATGTTGCTCAAACGAGCAATATCCACTGATT
* * *
12819910 TTATTGAATG-T--T-AAACGAGCGATATCCACTGATT
1 ATACTGAATGTTGCTCAAACGAGCAATATCCACTGATT
* * *
12819944 ATACTAAATGTTTGCTCAAACAAGCGATATCCACAT-ATT
1 ATACTGAATG-TTGCTCAAACGAGCAATATCCAC-TGATT
* * * * *
12819983 ATACTAAATGTTTGCACAAACAAGCAATATCCACTGGTC
1 ATACTGAATG-TTGCTCAAACGAGCAATATCCACTGATT
* *
12820022 GTACTGAATGTTTGCTCAAACGAGCGATATCCACTGATT
1 ATACTGAATG-TTGCTCAAACGAGCAATATCCACTGATT
12820061 ATACTGAAT
1 ATACTGAAT
12820070 AATATCTTTC
Statistics
Matches: 277, Mismatches: 55, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
34 27 0.10
35 1 0.00
36 2 0.01
37 96 0.35
38 57 0.21
39 93 0.34
40 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (38 bp):
ATACTGAATGTTGCTCAAACGAGCAATATCCACTGATT
Found at i:12824976 original size:37 final size:38
Alignment explanation
Indices: 12824926--12825311 Score: 330
Period size: 39 Copynumber: 10.2 Consensus size: 38
12824916 CAGTTAAATC
* * *
12824926 CTGAATG-TGCTCAAACGAGCAATATCTATTAATTATA
1 CTGAATGTTGCTCAAACGAGCAATATCCACTGATTATA
* * *
12824963 CTGAATG-TGCTCAAACGAGAAATATCTATTGATTATA
1 CTGAATGTTGCTCAAACGAGCAATATCCACTGATTATA
* * *
12825000 CTGAATG-TGCTCAAAAGAGCAATGTCTACTGATTATA
1 CTGAATGTTGCTCAAACGAGCAATATCCACTGATTATA
* * * * *
12825037 CTGAAAGTTTCTCAAACGAGTAATATCTACTGATTATT
1 CTGAATGTTGCTCAAACGAGCAATATCCACTGATTATA
* * * * * * *
12825075 CTGAACG-TGCTCAAAAGAGAAATGTCTATTGAATATA
1 CTGAATGTTGCTCAAACGAGCAATATCCACTGATTATA
* * * * ** * *
12825112 CTAAAAGTTGCTTAAATGAGCGGTGTCCACTTATTATA
1 CTGAATGTTGCTCAAACGAGCAATATCCACTGATTATA
* * *
12825150 CTGAATGTTTGCTCAAATGAGCGATATCCACTAATTATA
1 CTGAATG-TTGCTCAAACGAGCAATATCCACTGATTATA
* * * *
12825189 CTGAATGTTTGCTCAAATGAGCGATATCCACTCATCATA
1 CTGAATG-TTGCTCAAACGAGCAATATCCACTGATTATA
* * *
12825228 CTGAATGTTTTCTCCAACGAGCGATATCCACTGATTATA
1 CTGAATG-TTGCTCAAACGAGCAATATCCACTGATTATA
* **
12825267 CTGAATGTTTTCTCAAACGAGTGATATCCACTGATTATA
1 CTGAATG-TTGCTCAAACGAGCAATATCCACTGATTATA
12825306 CTGAAT
1 CTGAAT
12825312 ATGATCTTTC
Statistics
Matches: 300, Mismatches: 46, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
37 102 0.34
38 57 0.19
39 141 0.47
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (38 bp):
CTGAATGTTGCTCAAACGAGCAATATCCACTGATTATA
Found at i:12826761 original size:76 final size:76
Alignment explanation
Indices: 12826633--12826776 Score: 202
Period size: 76 Copynumber: 1.9 Consensus size: 76
12826623 TAGCTCGGTT
* *
12826633 GAGTAACCGGATGTGTCATTATAAAGGTTTAGCTCGAAAGGGTAACTCGATATATATATGTATAC
1 GAGTAACCGGATGTGTCATTACAAAGGTTTAGCTCGAAAGAGTAACTCGATATATATATGTATAC
12826698 TAAACTCTGCC
66 TAAACTCTGCC
* * * *
12826709 GAGTAACTC-GATGTGTCATTGCAAAGGTTTAGCTTGGACGAGTAAC-CTGATATATATATGTAT
1 GAGTAAC-CGGATGTGTCATTACAAAGGTTTAGCTCGAAAGAGTAACTC-GATATATATATGTAT
12826772 ACTAA
64 ACTAA
12826777 GCTCAGATGA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
75 1 0.02
76 58 0.97
77 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (76 bp):
GAGTAACCGGATGTGTCATTACAAAGGTTTAGCTCGAAAGAGTAACTCGATATATATATGTATAC
TAAACTCTGCC
Found at i:12830082 original size:3 final size:3
Alignment explanation
Indices: 12830074--12830147 Score: 132
Period size: 3 Copynumber: 25.0 Consensus size: 3
12830064 AGTTGTATCT
*
12830074 AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
12830122 AGA AGA AGA AGA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
12830148 TAATTTATGG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 66 0.97
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12840469 original size:21 final size:21
Alignment explanation
Indices: 12840443--12840485 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12840433 GGGGTGACTA
12840443 AGGAAAAAAATTTAAAAAATT
1 AGGAAAAAAATTTAAAAAATT
12840464 AGGAAAAAAATTTAAAAAATT
1 AGGAAAAAAATTTAAAAAATT
12840485 A
1 A
12840486 TTTTGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (21 bp):
AGGAAAAAAATTTAAAAAATT
Found at i:12848868 original size:15 final size:16
Alignment explanation
Indices: 12848842--12848874 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
12848832 ATCGACTAGG
12848842 AAAATAAAAAATATTT
1 AAAATAAAAAATATTT
12848858 AAAAT-AAAAATATTT
1 AAAATAAAAAATATTT
12848873 AA
1 AA
12848875 TTAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATAAAAAATATTT
Found at i:12859543 original size:185 final size:185
Alignment explanation
Indices: 12859224--12859595 Score: 699
Period size: 185 Copynumber: 2.0 Consensus size: 185
12859214 CCTCCTTCGA
12859224 GAAAGATGGCTTAGGGAACCGAGACAGATTGGTGGAATCCCTTCCCATTATGCACGTTTCTGATA
1 GAAAGATGGCTTAGGGAACCGAGACAGATTGGTGGAATCCCTTCCCATTATGCACGTTTCTGATA
* *
12859289 ATGAGAAAGAAGAGGACTCAAGGGACATTGAGGAATGTATGCGAAGGATTGATAGCCTAGTCAAG
66 ATGAGAAAGAAGAAGACTCAAGGGACATTGAAGAATGTATGCGAAGGATTGATAGCCTAGTCAAG
*
12859354 GGTGACTTTATTGCTAGTCAAGAGGCGCCTACTGTTGAGGAGGAAGTTGATGTAG
131 GGTGACTTTATCGCTAGTCAAGAGGCGCCTACTGTTGAGGAGGAAGTTGATGTAG
12859409 GAAAGATGGCTTAGGGAACCGAGACAGATTGGTGGAATCCCTTCCCATTATGCACGTTTCTGATA
1 GAAAGATGGCTTAGGGAACCGAGACAGATTGGTGGAATCCCTTCCCATTATGCACGTTTCTGATA
* *
12859474 ATGAGAAAGAAGAAGACTCAAGGGGCATTGAAGAATGTATGCGAAGGATTGATAGCCTAGTCGAG
66 ATGAGAAAGAAGAAGACTCAAGGGACATTGAAGAATGTATGCGAAGGATTGATAGCCTAGTCAAG
12859539 GGTGACTTTATCGCTAGTCAAGAGGCGCCTACTGTTGAGGAGGAAGTTGATGTAG
131 GGTGACTTTATCGCTAGTCAAGAGGCGCCTACTGTTGAGGAGGAAGTTGATGTAG
12859594 GA
1 GA
12859596 GAAAAGGAAG
Statistics
Matches: 182, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
185 182 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (185 bp):
GAAAGATGGCTTAGGGAACCGAGACAGATTGGTGGAATCCCTTCCCATTATGCACGTTTCTGATA
ATGAGAAAGAAGAAGACTCAAGGGACATTGAAGAATGTATGCGAAGGATTGATAGCCTAGTCAAG
GGTGACTTTATCGCTAGTCAAGAGGCGCCTACTGTTGAGGAGGAAGTTGATGTAG
Found at i:12859674 original size:15 final size:15
Alignment explanation
Indices: 12859632--12859684 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
12859622 GAACAAGAAG
* *
12859632 GCTGAGGAAGAAAAT
1 GCTGAGAAAGAATAT
* *
12859647 ACTGAGATAGAATAT
1 GCTGAGAAAGAATAT
*
12859662 GCTGAGAAAGAATCT
1 GCTGAGAAAGAATAT
*
12859677 GTTGAGAA
1 GCTGAGAA
12859685 CATTGTTAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.43, C:0.08, G:0.28, T:0.21
Consensus pattern (15 bp):
GCTGAGAAAGAATAT
Found at i:12863584 original size:22 final size:22
Alignment explanation
Indices: 12863556--12863615 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
12863546 CTATTATACT
12863556 CCCTATGTTGCAACATTCAATG
1 CCCTATGTTGCAACATTCAATG
12863578 CCCTATGTTGCAACATTCAATG
1 CCCTATGTTGCAACATTCAATG
*
12863600 CTCTATGTTGCAACAT
1 CCCTATGTTGCAACAT
12863616 AGCGACCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (22 bp):
CCCTATGTTGCAACATTCAATG
Found at i:12867646 original size:42 final size:42
Alignment explanation
Indices: 12867587--12867674 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
12867577 TACATTGATT
*
12867587 ATAGGAAGTACGTCCCTTGATTCTGGGTGATTAGAGTTAAAG
1 ATAGGAAGTACGTCCCTTGATTCAGGGTGATTAGAGTTAAAG
12867629 ATAGGAAGTACGTCCCTTGATTCAGGGTGATTAGAGTTAAAG
1 ATAGGAAGTACGTCCCTTGATTCAGGGTGATTAGAGTTAAAG
12867671 ATAG
1 ATAG
12867675 ATAATTTGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (42 bp):
ATAGGAAGTACGTCCCTTGATTCAGGGTGATTAGAGTTAAAG
Found at i:12872488 original size:49 final size:49
Alignment explanation
Indices: 12872365--12872477 Score: 163
Period size: 49 Copynumber: 2.3 Consensus size: 49
12872355 AAATACTTAT
*** *
12872365 CTTATCAAAATGGCTGAGAAACATAAAATATGTTCTTGCACTTAACGCA
1 CTTATCAAAATGGCTGAGAAACATAAAATATGTTCCAACACTTAACACA
* * *
12872414 CTTATTAGAACGGCTGAGAAACATAAAATATGTTCCAACACTTAACACA
1 CTTATCAAAATGGCTGAGAAACATAAAATATGTTCCAACACTTAACACA
12872463 CTTATCAAAATGGCT
1 CTTATCAAAATGGCT
12872478 AAGGTACATA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (49 bp):
CTTATCAAAATGGCTGAGAAACATAAAATATGTTCCAACACTTAACACA
Found at i:12875135 original size:8 final size:8
Alignment explanation
Indices: 12875122--12875146 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12875112 AACTACAATT
12875122 ATCTAACC
1 ATCTAACC
12875130 ATCTAACC
1 ATCTAACC
12875138 ATCTAACC
1 ATCTAACC
12875146 A
1 A
12875147 AAAGAGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (8 bp):
ATCTAACC
Found at i:12880377 original size:19 final size:19
Alignment explanation
Indices: 12880353--12880403 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
12880343 GAAAAAGGAT
*
12880353 ATGCAATCTTAGATATGAC
1 ATGCAATCTTAGATAAGAC
*
12880372 ATGCAATCTTAGATAAGAT
1 ATGCAATCTTAGATAAGAC
12880391 ATGCAATCTTAGA
1 ATGCAATCTTAGA
12880404 AAATAAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (19 bp):
ATGCAATCTTAGATAAGAC
Found at i:12881295 original size:24 final size:24
Alignment explanation
Indices: 12881266--12881380 Score: 96
Period size: 23 Copynumber: 4.9 Consensus size: 24
12881256 GTATTGTATA
*
12881266 TTATTATTTTAGATTTATCATGTT
1 TTATTATTTTAAATTTATCATGTT
* *
12881290 TTATTATTTGT-AATTTATCA-ATA
1 TTATTATTT-TAAATTTATCATGTT
*
12881313 TTATTATTTTAAATTCAT--TGTT
1 TTATTATTTTAAATTTATCATGTT
**
12881335 AACATTATTTTAAATTTATCATG-T
1 -TTATTATTTTAAATTTATCATGTT
* *
12881359 ATATCTATTTCAAATTTATCAT
1 TTAT-TATTTTAAATTTATCAT
12881381 TAATATTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
22 2 0.03
23 34 0.47
24 34 0.47
25 3 0.04
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (24 bp):
TTATTATTTTAAATTTATCATGTT
Found at i:12881342 original size:70 final size:69
Alignment explanation
Indices: 12881267--12881429 Score: 186
Period size: 70 Copynumber: 2.3 Consensus size: 69
12881257 TATTGTATAT
* ** *
12881267 TATTATTTTAGATTTATCATGTTTTAT-TATTTGTAATTTATCAATATTATTATTTTAAATTCAT
1 TATTATTTTAGATTTATCATG-TATATCTATTTCAAATTTATCAATAATA-T-TTTTAAATTCAT
* *
12881331 TGTTAAC
63 TATAAAC
* * *
12881338 -ATTATTTTAAATTTATCATGTATATCTATTTCAAATTTATCATTAATATTTTTAAATTTATTAT
1 TATTATTTTAGATTTATCATGTATATCTATTTCAAATTTATCAATAATATTTTTAAATTCATTAT
12881402 AAAC
66 AAAC
* *
12881406 TATTATTTTGGATTTATCACGTAT
1 TATTATTTTAGATTTATCATGTAT
12881430 GATTATTCTA
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
68 16 0.21
69 25 0.32
70 37 0.47
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (69 bp):
TATTATTTTAGATTTATCATGTATATCTATTTCAAATTTATCAATAATATTTTTAAATTCATTAT
AAAC
Found at i:12881386 original size:24 final size:23
Alignment explanation
Indices: 12881222--12881424 Score: 119
Period size: 24 Copynumber: 8.7 Consensus size: 23
12881212 ATGTTTATAC
*
12881222 TTATTATTAAATTAATCATTAATA
1 TTATT-TTAAATTTATCATTAATA
* * * ** *
12881246 TTA-TCTAAGTGTATTGTATATTA
1 TTATTTTAAATTTATCAT-TAATA
* **
12881269 TTATTTTAGATTTATCATGTTTTA
1 TTATTTTAAATTTATCAT-TAATA
* *
12881293 TTATTTGT-AATTTATCAATATTA
1 TTATTT-TAAATTTATCATTAATA
* ** *
12881316 TTATTTTAAATTCATTGTTAACA
1 TTATTTTAAATTTATCATTAATA
12881339 TTATTTTAAATTTATCATGT-ATA
1 TTATTTTAAATTTATCAT-TAATA
*
12881362 TCTATTTCAAATTTATCATTAATA
1 T-TATTTTAAATTTATCATTAATA
* *
12881386 -T-TTTTAAATTTATTATAAACTA
1 TTATTTTAAATTTATCATTAA-TA
**
12881408 TTATTTTGGATTTATCA
1 TTATTTTAAATTTATCA
12881425 CGTATGATTA
Statistics
Matches: 134, Mismatches: 35, Indels: 20
0.71 0.19 0.11
Matches are distributed among these distances:
21 15 0.11
22 11 0.08
23 47 0.35
24 60 0.45
25 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (23 bp):
TTATTTTAAATTTATCATTAATA
Found at i:12883172 original size:16 final size:16
Alignment explanation
Indices: 12883147--12883181 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12883137 TTATGTTTTG
*
12883147 TTTTGGCTGCATGACA
1 TTTTGACTGCATGACA
*
12883163 TTTTGACTGCATGGCA
1 TTTTGACTGCATGACA
12883179 TTT
1 TTT
12883182 CATCATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (16 bp):
TTTTGACTGCATGACA
Found at i:12885775 original size:6 final size:6
Alignment explanation
Indices: 12885766--12885837 Score: 55
Period size: 6 Copynumber: 12.7 Consensus size: 6
12885756 AAAAATCAAA
* *
12885766 AAAATG AAAAAG AAAATG AAAAAG AAAATG ATAAA-- AAAA-G AAAA-G
1 AAAATG AAAATG AAAATG AAAATG AAAATG A-AAATG AAAATG AAAATG
* * *
12885811 AAAAGG AAAAT- AAAAAG AAAAGG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAA
12885838 GGGAAAGAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
4 3 0.05
5 14 0.25
6 35 0.64
7 3 0.05
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAATG
Found at i:12885783 original size:12 final size:12
Alignment explanation
Indices: 12885766--12885837 Score: 76
Period size: 12 Copynumber: 5.8 Consensus size: 12
12885756 AAAAATCAAA
12885766 AAAATGAAAAAG
1 AAAATGAAAAAG
12885778 AAAATGAAAAAG
1 AAAATGAAAAAG
12885790 AAAATGATAAAAAAAG
1 AAAATG----AAAAAG
*
12885806 AAAA-GAAAAGG
1 AAAATGAAAAAG
12885817 AAAAT-AAAAAG
1 AAAATGAAAAAG
*
12885828 AAAAGGAAAA
1 AAAATGAAAA
12885838 GGGAAAGAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
11 18 0.35
12 22 0.43
15 1 0.02
16 10 0.20
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (12 bp):
AAAATGAAAAAG
Found at i:12885793 original size:17 final size:17
Alignment explanation
Indices: 12885773--12885837 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
12885763 AAAAAAATGA
*
12885773 AAAAGAAAATGAAAAAG
1 AAAAGAAAAGGAAAAAG
*
12885790 AAAATGATAA--AAAAAG
1 AAAA-GAAAAGGAAAAAG
12885806 AAAAGAAAAGGAAAATA-
1 AAAAGAAAAGGAAAA-AG
12885823 AAAAGAAAAGGAAAA
1 AAAAGAAAAGGAAAA
12885838 GGGAAAGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.10
16 10 0.24
17 23 0.55
18 5 0.12
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (17 bp):
AAAAGAAAAGGAAAAAG
Found at i:12885821 original size:27 final size:26
Alignment explanation
Indices: 12885772--12885838 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 26
12885762 CAAAAAAATG
*
12885772 AAAAAGAAAATGAAAAAGAAAATGATAA
1 AAAAAGAAAA-GAAAAAGAAAAT-AAAA
*
12885800 AAAAAGAAAAGAAAAGGAAAATAAAA
1 AAAAAGAAAAGAAAAAGAAAATAAAA
12885826 AGAAAAGGAAAAG
1 A-AAAA-GAAAAG
12885839 GGAAAGAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 4 0.11
27 15 0.43
28 16 0.46
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (26 bp):
AAAAAGAAAAGAAAAAGAAAATAAAA
Found at i:12885839 original size:6 final size:5
Alignment explanation
Indices: 12885773--12885838 Score: 53
Period size: 5 Copynumber: 12.0 Consensus size: 5
12885763 AAAAAAATGA
*
12885773 AAAAG AAAATG AAAAAG AAAATG ATAAA- AAAAG AAAAG AAAAGG AAAATA
1 AAAAG AAAA-G -AAAAG AAAA-G A-AAAG AAAAG AAAAG AAAA-G AAAA-G
12885823 AAAAG AAAAGG AAAAG
1 AAAAG AAAA-G AAAAG
12885839 GGAAAGAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
4 3 0.06
5 23 0.45
6 18 0.35
7 7 0.14
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (5 bp):
AAAAG
Found at i:12885846 original size:17 final size:17
Alignment explanation
Indices: 12885766--12885838 Score: 71
Period size: 17 Copynumber: 4.3 Consensus size: 17
12885756 AAAAATCAAA
*
12885766 AAAATGAAAAAGAAAATGA
1 AAAA-GAAAAAGAAAA-GG
*
12885785 AAAAGAAAATGATAAA--
1 AAAAGAAAAAGA-AAAGG
12885801 AAAAG-AAAAGAAAAGG
1 AAAAGAAAAAGAAAAGG
*
12885817 AAAATAAAAAGAAAAGG
1 AAAAGAAAAAGAAAAGG
12885834 AAAAG
1 AAAAG
12885839 GGAAAGAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
14 3 0.07
15 5 0.11
16 9 0.20
17 15 0.33
18 7 0.15
19 7 0.15
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAGG
Found at i:12888109 original size:45 final size:45
Alignment explanation
Indices: 12888046--12890062 Score: 2314
Period size: 45 Copynumber: 45.1 Consensus size: 45
12888036 GGAGTAGGTT
* * * *
12888046 GAAGATAGCATATTTTGTCTTCTTGTATTGGCAGC-ACAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA-AGTAGATC
* * * *
12888091 TAAGTTAGCAAATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
12888136 GCAGAGAGTAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
12888181 GAAGTTAGCATATATTGTCTTCCTATATTGGCAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
12888226 GAAGATAGCAAATTTTGTCTTCTTGTACTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12888271 GAAGATATCAGATCTTGTCTTCCTGTATTGGAAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12888316 GACGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * ** *
12888361 GAAGCTAGCAGATCTTATCTTTTTGTATTGGCAGCGAAGTAAATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12888406 GAAGATAGCTGATCTTATCTTCCTGTATTGGCAGCTAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12888451 AAAGATAGCAGATCTTGTCTTCCTGTATCGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* ** * *
12888496 GAAGATAGCAGATTTTGTCTTCCTGTATTGATAGTGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12888541 GAAGATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
12888586 GAAGATAGCAGATCTTGTCTTCCTGTATTGACAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
12888631 GAAGATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12888676 GAAGTTAGCAGATCTTGTCTTCCTGTATTGACAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * * * *
12888721 GAAGATAGCATATCTTGTATTACTGTAGTGGTAGCGACGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
** * * * * *
12888766 GAACTTAGCTGATCTTCTCTTCCTCTACTGGCAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12888811 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12888856 GAAGATAGTAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12888901 GAGGATAGCAGATCTTGTTTTCCTGTATTGGCAACGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
12888946 GAAGATAGCATAACTTGTCTTCCTGTATTGGCAGGGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12888991 GAAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12889036 GAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12889081 GAAGATAGCAGATCTTGTCTTCCTGTAGTGGCAGTGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * ** * *
12889126 GAAGTTAGTAGATCTTCTCTTTTTATATTGGCAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12889171 GAAGATAGCAGATCTTGTTTTCCTGTAGTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12889216 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12889261 GAAGATAGCAGATCTTGTCTTCTTGTATTGGCAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12889306 GAAGATAGCACATCTTGTCTTTCGGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12889351 GAAGATAGCAGATCTTGTCTTCCTGTATTGACAGCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAG----C-G-A--AGTA--G-A-----TC
* * *
12889412 GAAGATAGTAGATCTTGTCTTCCTATATTCGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12889457 GAACATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12889502 GAAGATAGCAGATCTTGTATTCCTGTATTGGCAACGAAATAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
12889547 GAAAATAGCAAATCTTGTCTTCCTGTGTTGGCAGCGAAATAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
12889592 GAAGATAGCAGCTATTGTCTTCCTGTACTGGCAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
** * * * *
12889637 GAAGATATTAGATCTTGTCTTCCTATACTAGCAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * * *
12889682 GAAGATTGCAGATCTTGTCATCCTGTACTAGTAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
12889727 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12889772 GAAGATAGCAGATCCTGTCTTCCTGTATTGGCAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
12889817 GAAGATAGCAAATTTTGTCGTCCTGTACT-G--GC-----AG--C
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12889852 GAAGATAGCAAATCTTGTCTTCCTGTACTGGCAGC---G-A-AT-
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12889891 ----ATAGCAAATCTTGTCTTCCTGTATTGACAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12889932 GAAGATAGCCGATCTTGTTTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
12889977 GAAGATAGCAAATCTTGTGTTTCTATACTGGCAGCG-A--AGAT-
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
12890018 --AG-TA--A-ATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
12890057 GAAGAT
1 GAAGAT
12890063 TGTAAATCTT
Statistics
Matches: 1683, Mismatches: 249, Indels: 83
0.84 0.12 0.04
Matches are distributed among these distances:
35 78 0.05
36 3 0.00
37 2 0.00
38 9 0.01
39 4 0.00
40 2 0.00
41 2 0.00
42 6 0.00
44 2 0.00
45 1528 0.91
46 1 0.00
49 1 0.00
50 2 0.00
51 2 0.00
53 4 0.00
55 2 0.00
56 2 0.00
57 1 0.00
61 32 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
Found at i:12889390 original size:16 final size:16
Alignment explanation
Indices: 12889369--12889401 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12889359 CAGATCTTGT
12889369 CTTCCTGTATTGACAG
1 CTTCCTGTATTGACAG
*
12889385 CTTCCTGTATTGGCAG
1 CTTCCTGTATTGACAG
12889401 C
1 C
12889402 GAAGTAGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.36
Consensus pattern (16 bp):
CTTCCTGTATTGACAG
Found at i:12889469 original size:106 final size:106
Alignment explanation
Indices: 12889279--12889483 Score: 329
Period size: 106 Copynumber: 1.9 Consensus size: 106
12889269 CAGATCTTGT
* * * *
12889279 CTTCTTGTATTGGCAGCAAAGTAGATCGAAGATAGCACATCTTGTCTTTCGGTATTGGCAGCGAA
1 CTTCCTGTATTGGCAGCAAAGTAGATCGAAGATAGCACATCTTGTCTTCCGATATTCGCAGCGAA
*
12889344 GTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGACAG
66 GTAGATCGAACATAGCAGATCTTGTCTTCCTGTATTGACAG
* * * *
12889385 CTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGTAGATCTTGTCTTCCTATATTCGCAGCGAA
1 CTTCCTGTATTGGCAGCAAAGTAGATCGAAGATAGCACATCTTGTCTTCCGATATTCGCAGCGAA
12889450 GTAGATCGAACATAGCAGATCTTGTCTTCCTGTA
66 GTAGATCGAACATAGCAGATCTTGTCTTCCTGTA
12889484 CTGGCAGCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 90 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (106 bp):
CTTCCTGTATTGGCAGCAAAGTAGATCGAAGATAGCACATCTTGTCTTCCGATATTCGCAGCGAA
GTAGATCGAACATAGCAGATCTTGTCTTCCTGTATTGACAG
Found at i:12889862 original size:35 final size:35
Alignment explanation
Indices: 12889816--12890050 Score: 173
Period size: 35 Copynumber: 6.1 Consensus size: 35
12889806 TGAAGTAGAT
* *
12889816 CGAAGATAGCAAATTTTGTCGTCCTGTACTGGCAG
1 CGAAGATAGCAAATCTTGTCTTCCTGTACTGGCAG
12889851 CGAAGATAGCAAATCTTGTCTTCCTGTACTGGCAG
1 CGAAGATAGCAAATCTTGTCTTCCTGTACTGGCAG
* *
12889886 CGAATATAGCAAATCTTGTCTTCCTGTATTGACAGCAAAGTAG
1 CGAAGATAGCAAATCTTGTCTTCCTGTACTG---GC-----AG
** * *
12889929 ATCGAAGATAGCCGATCTTGTTTTCCTGTATTGGCAGCGAAGTAG
1 --CGAAGATAGCAAATCTTGTCTTCCTGTACT-G--GC-----AG
* * *
12889974 ATCGAAGATAGCAAATCTTGTGTTTCTATACTGGCAG
1 --CGAAGATAGCAAATCTTGTCTTCCTGTACTGGCAG
* *
12890011 CGAAGATAGTAAATCTTGTCTTCCTGTATTGGCAG
1 CGAAGATAGCAAATCTTGTCTTCCTGTACTGGCAG
12890046 CGAAG
1 CGAAG
12890051 CAGATCGAAG
Statistics
Matches: 169, Mismatches: 20, Indels: 22
0.80 0.09 0.10
Matches are distributed among these distances:
35 97 0.57
37 2 0.01
38 2 0.01
42 2 0.01
43 2 0.01
44 1 0.01
45 62 0.37
46 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (35 bp):
CGAAGATAGCAAATCTTGTCTTCCTGTACTGGCAG
Found at i:12889874 original size:80 final size:80
Alignment explanation
Indices: 12889771--12890072 Score: 275
Period size: 80 Copynumber: 3.8 Consensus size: 80
12889761 CGAAGTAGAT
* * * * *
12889771 CGAAGATAGCAGATCCTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAGATAGCAAATTTTGTC
1 CGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGATAGCAAATCTTGTC
12889836 GTCCTGTACTGGCAG
66 GTCCTGTACTGGCAG
*
12889851 CGAAGATAGCAAATCTTGTCTTCCTGTACTGGCAGC---G-A-AT-----ATAGCAAATCTTGTC
1 CGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGATAGCAAATCTTGTC
* *
12889906 TTCCTGTATTGACAGCAAAGTAG
66 GTCCTGTACTG---GC-----AG
** * *
12889929 ATCGAAGATAGCCGATCTTGTTTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTG
1 --CGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGATAGCAAATCTTG
* *
12889994 T-GTTTCTATACTGGCAG
64 TCG-TCCTGTACTGGCAG
* * *
12890011 CGAAGATAGTAAATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGATTGTAAATCTT
1 CGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGATAGCAAATCTT
12890073 ATCTTCCCAA
Statistics
Matches: 179, Mismatches: 22, Indels: 42
0.74 0.09 0.17
Matches are distributed among these distances:
70 23 0.13
73 2 0.01
75 2 0.01
76 1 0.01
77 1 0.01
78 2 0.01
80 119 0.66
82 2 0.01
83 1 0.01
84 1 0.01
85 2 0.01
87 2 0.01
90 21 0.12
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (80 bp):
CGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGATAGCAAATCTTGTC
GTCCTGTACTGGCAG
Found at i:12890008 original size:160 final size:160
Alignment explanation
Indices: 12889731--12890049 Score: 505
Period size: 160 Copynumber: 2.0 Consensus size: 160
12889721 TAGATTGAAG
* * *
12889731 ATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCT
1 ATAGCAAATCTTGTCTTCCTGTACTGACAGCAAAGTAGATCGAAGATAGCAGATCCTGTCTTCCT
* * *
12889796 GTATTGGCAGTGAAGTAGATCGAAGATAGCAAATTTTGTCGTCCTGTACTGGCAGCGAAGATAGC
66 GTATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTGTCGTCCTATACTGGCAGCGAAGATAGC
12889861 AAATCTTGTCTTCCTGTACTGGCAGCGAAT
131 AAATCTTGTCTTCCTGTACTGGCAGCGAAT
* * * *
12889891 ATAGCAAATCTTGTCTTCCTGTATTGACAGCAAAGTAGATCGAAGATAGCCGATCTTGTTTTCCT
1 ATAGCAAATCTTGTCTTCCTGTACTGACAGCAAAGTAGATCGAAGATAGCAGATCCTGTCTTCCT
*
12889956 GTATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTGT-GTTTCTATACTGGCAGCGAAGATAG
66 GTATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTGTCG-TCCTATACTGGCAGCGAAGATAG
* *
12890020 TAAATCTTGTCTTCCTGTATTGGCAGCGAA
130 CAAATCTTGTCTTCCTGTACTGGCAGCGAA
12890050 GCAGATCGAA
Statistics
Matches: 145, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
159 1 0.01
160 144 0.99
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (160 bp):
ATAGCAAATCTTGTCTTCCTGTACTGACAGCAAAGTAGATCGAAGATAGCAGATCCTGTCTTCCT
GTATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTGTCGTCCTATACTGGCAGCGAAGATAGC
AAATCTTGTCTTCCTGTACTGGCAGCGAAT
Found at i:12890214 original size:44 final size:44
Alignment explanation
Indices: 12890162--12890342 Score: 123
Period size: 44 Copynumber: 4.1 Consensus size: 44
12890152 GTAGATCTTG
*
12890162 TCTCCCTAAGCAGTAGTGGAGTAGATCGAAGGCAGCAAATCCTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAGCAAATCCTA
* * ** * * **
12890206 TCTTCCTAAGGTAGTAG-GGAAGCAGATTTAAGCCA-CTAATCCCC
1 TCTCCCTAA-GCAGTAGTGG-AGCAGATCGAAGGCAGCAAATCCTA
* * * * *** * * *
12890250 TCTCCCTTAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCCTG
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAGCAAATCCTA
* * * *
12890294 TATCCCTAAGTAGTAGTGGAGCAGATCGAAGGCAGCGAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAGCAAATCCTA
12890338 TCTCC
1 TCTCC
12890343 TTGGCGTTAC
Statistics
Matches: 93, Mismatches: 40, Indels: 8
0.66 0.28 0.06
Matches are distributed among these distances:
43 13 0.14
44 63 0.68
45 17 0.18
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAGCAAATCCTA
Found at i:12890289 original size:132 final size:132
Alignment explanation
Indices: 12890066--12890340 Score: 415
Period size: 132 Copynumber: 2.1 Consensus size: 132
12890056 CGAAGATTGT
* * *
12890066 AAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTACGCCACCAGTCCTATCTCCCTGAGCAG
1 AAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCCATCTCCCTGAGCAG
* * * * *
12890131 CGGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTCCCTAAGCAGTAGTGGAGTAGATCGAAGGCA
66 CAGTGGAGTAGGTCGAAGATTGTAGATCCTGTATCCCTAAGCAGTAGTGGAGCAGATCGAAGGCA
12890196 GC
131 GC
* * * * *
12890198 AAATCCTATCTTCCTAAGGTAGTAGGGAAGCAGATTTAAGCCACTAATCCCCTCTCCCTTAGCAG
1 AAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCCATCTCCCTGAGCAG
*
12890263 CAGTGGAGTAGGTCGAAGATTGTAGATCCTGTATCCCTAAGTAGTAGTGGAGCAGATCGAAGGCA
66 CAGTGGAGTAGGTCGAAGATTGTAGATCCTGTATCCCTAAGCAGTAGTGGAGCAGATCGAAGGCA
12890328 GC
131 GC
*
12890330 GAATCTTATCT
1 AAATCTTATCT
12890341 CCTTGGCGTT
Statistics
Matches: 127, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
132 127 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (132 bp):
AAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCCATCTCCCTGAGCAG
CAGTGGAGTAGGTCGAAGATTGTAGATCCTGTATCCCTAAGCAGTAGTGGAGCAGATCGAAGGCA
GC
Found at i:12890487 original size:44 final size:45
Alignment explanation
Indices: 12890422--12890515 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 45
12890412 AGATCAAGAC
*
12890422 TGAAGATAACCAACCTTATCTTCCTGAAGTTACAGTGGAGCCGGT
1 TGAAGATAACCAACCTTATCTTCCTGAAGTTACAGTGGAGCAGGT
* * * *
12890467 TGAAGAT-ATCAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGGT
1 TGAAGATAACCAACCTTATCTTCCTGAAGTTACAGTGGAGCAGGT
12890511 TGAAG
1 TGAAG
12890516 GAAGTAAGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 37 0.84
45 7 0.16
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (45 bp):
TGAAGATAACCAACCTTATCTTCCTGAAGTTACAGTGGAGCAGGT
Found at i:12890816 original size:19 final size:19
Alignment explanation
Indices: 12890792--12890845 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
12890782 CTTGAAAAAG
*
12890792 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAA
12890811 GATATGCAATCTTAGATAA
1 GATATGCAATCTTAGATAA
12890830 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
12890846 AGATAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:12890871 original size:22 final size:22
Alignment explanation
Indices: 12890792--12890868 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 22
12890782 CTTGAAAAAG
*
12890792 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAA
12890811 GATATGCAATCTT---AGATAA
1 GATATGCAATCTTAGAAGATAA
12890830 GATATGCAATCTTAGAAGATAA
1 GATATGCAATCTTAGAAGATAA
* *
12890852 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
12890869 GATTTAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 31 0.61
22 8 0.16
23 12 0.24
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAA
Found at i:12891736 original size:24 final size:24
Alignment explanation
Indices: 12891707--12891821 Score: 96
Period size: 23 Copynumber: 4.9 Consensus size: 24
12891697 GTATTGTATA
*
12891707 TTATTATTTTAGATTTATCATGTT
1 TTATTATTTTAAATTTATCATGTT
* *
12891731 TTATTATTTGT-AATTTATCA-ATA
1 TTATTATTT-TAAATTTATCATGTT
*
12891754 TTATTATTTTAAATTCAT--TGTT
1 TTATTATTTTAAATTTATCATGTT
**
12891776 AACATTATTTTAAATTTATCATG-T
1 -TTATTATTTTAAATTTATCATGTT
* *
12891800 ATATCTATTTCAAATTTATCAT
1 TTAT-TATTTTAAATTTATCAT
12891822 TAATATTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
22 2 0.03
23 34 0.47
24 34 0.47
25 3 0.04
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (24 bp):
TTATTATTTTAAATTTATCATGTT
Found at i:12891785 original size:70 final size:69
Alignment explanation
Indices: 12891703--12891905 Score: 184
Period size: 69 Copynumber: 2.9 Consensus size: 69
12891693 AAGTGTATTG
* * ** *
12891703 TATATTATTATTTTAGATTTATCATGTTTTAT-TATTTGTAATTTATCAATATTATTATTTTAAA
1 TATACTATTATTTTAGATTTATCATG-TATATCTATTTCAAATTTATCAATAATA-T-TTTTAAA
*
12891767 TTCATTG
63 TTCATTA
* *
12891774 T-TAAC-ATTATTTTAAATTTATCATGTATATCTATTTCAAATTTATCATTAATATTTTTAAATT
1 TAT-ACTATTATTTTAGATTTATCATGTATATCTATTTCAAATTTATCAATAATATTTTTAAATT
*
12891837 TATTA
65 CATTA
* * * *
12891842 TATACTATTATTTTGGATTTATCACGTATGAT-TATTCCAGAA-TTATC-ATCAAAATTTTTAAA
1 TATACTATTATTTTAGATTTATCATGTAT-ATCTATTTCA-AATTTATCAAT-AATATTTTTAAA
12891904 TT
63 TT
12891906 TTATATGTAT
Statistics
Matches: 110, Mismatches: 15, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
68 16 0.15
69 50 0.45
70 42 0.38
71 2 0.02
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (69 bp):
TATACTATTATTTTAGATTTATCATGTATATCTATTTCAAATTTATCAATAATATTTTTAAATTC
ATTA
Found at i:12891827 original size:24 final size:23
Alignment explanation
Indices: 12891661--12891865 Score: 123
Period size: 24 Copynumber: 8.8 Consensus size: 23
12891651 TGTTTATACT
*
12891661 TATTATTATTAAATTAATCATTAA
1 TATTATT-TTAAATTTATCATTAA
* * * ** *
12891685 TATTA-TCTAAGTGTATTGTATAT
1 TATTATTTTAAATTTATCAT-TAA
* **
12891708 TATTATTTTAGATTTATCATGTTT
1 TATTATTTTAAATTTATCAT-TAA
* *
12891732 TATTATTTGT-AATTTATCAATAT
1 TATTATTT-TAAATTTATCATTAA
* **
12891755 TATTATTTTAAATTCATTGTTAA
1 TATTATTTTAAATTTATCATTAA
*
12891778 CATTATTTTAAATTTATCATGT-A
1 TATTATTTTAAATTTATCAT-TAA
*
12891801 TATCTATTTCAAATTTATCATTAA
1 TAT-TATTTTAAATTTATCATTAA
* *
12891825 TA-T-TTTTAAATTTATTATATAC
1 TATTATTTTAAATTTATCAT-TAA
**
12891847 TATTATTTTGGATTTATCA
1 TATTATTTTAAATTTATCA
12891866 CGTATGATTA
Statistics
Matches: 136, Mismatches: 35, Indels: 20
0.71 0.18 0.10
Matches are distributed among these distances:
21 13 0.10
22 13 0.10
23 47 0.35
24 62 0.46
25 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (23 bp):
TATTATTTTAAATTTATCATTAA
Found at i:12891888 original size:69 final size:69
Alignment explanation
Indices: 12891779--12891932 Score: 179
Period size: 69 Copynumber: 2.2 Consensus size: 69
12891769 CATTGTTAAC
* * * *
12891779 ATTATTTTAAATTTATCATGTATATCTATTTCAAATTTATCATTAATATTTTTAAA-TTTATTAT
1 ATTATTTTAAATTTATCACGTATATCTATTCCAAATTTATCATCAAAATTTTTAAATTTTA-TAT
12891843 ATACT
65 ATACT
**
12891848 ATTATTTTGGATTTATCACGTATGAT-TATTCCAGAA-TTATCATCAAAATTTTTAAATTTTATA
1 ATTATTTTAAATTTATCACGTAT-ATCTATTCCA-AATTTATCATCAAAATTTTTAAATTTTATA
* *
12891911 TGTATT
64 TATACT
*
12891917 ATTATTTCAAATTTAT
1 ATTATTTTAAATTTAT
12891933 TATATATTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
69 63 0.89
70 8 0.11
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.53
Consensus pattern (69 bp):
ATTATTTTAAATTTATCACGTATATCTATTCCAAATTTATCATCAAAATTTTTAAATTTTATATA
TACT
Found at i:12891956 original size:24 final size:23
Alignment explanation
Indices: 12891898--12891956 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 23
12891888 CATCAAAATT
12891898 TTTAAATT-TTATATGTATTATTA
1 TTTAAATTATTATA-GTATTATTA
12891921 TTTCAAATTTATTATA-TATTATTTA
1 TTT-AAA-TTATTATAGTATTA-TTA
12891946 TTGTAAATTAT
1 TT-TAAATTAT
12891957 CCAATTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
23 3 0.10
24 12 0.39
25 10 0.32
26 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (23 bp):
TTTAAATTATTATAGTATTATTA
Found at i:12896450 original size:34 final size:34
Alignment explanation
Indices: 12896397--12896461 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
12896387 TTTTTTAGGA
* * *
12896397 TTAGGGTTTTGTTTATTTAAATTAGGGTTTAAGG
1 TTAGGGTTTTATTTATTTAAAGTAAGGTTTAAGG
* *
12896431 TTAGGTTTTTATTTGTTTAAAGTAAGGTTTA
1 TTAGGGTTTTATTTATTTAAAGTAAGGTTTA
12896462 GGGGGGTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (34 bp):
TTAGGGTTTTATTTATTTAAAGTAAGGTTTAAGG
Found at i:12897248 original size:7 final size:7
Alignment explanation
Indices: 12897238--12897351 Score: 60
Period size: 7 Copynumber: 16.6 Consensus size: 7
12897228 CGAACCTCGA
12897238 GGTTTAG
1 GGTTTAG
12897245 GGTTT-G
1 GGTTTAG
12897251 GGTTT-G
1 GGTTTAG
*
12897257 GGTTTGG
1 GGTTTAG
*
12897264 GGTTTAA
1 GGTTTAG
*
12897271 GATTTA-
1 GGTTTAG
*
12897277 GGTTTGG
1 GGTTTAG
*
12897284 GGTTTAAA
1 GGTTT-AG
*
12897292 GGTTTAA
1 GGTTTAG
12897299 GG-TTATG
1 GGTTTA-G
12897306 GGTTTAG
1 GGTTTAG
*
12897313 TGTTT-G
1 GGTTTAG
12897319 AGGTTT-G
1 -GGTTTAG
*
12897326 GGTTTAAA
1 GGTTT-AG
* *
12897334 AGTGTAG
1 GGTTTAG
12897341 GGTTTAG
1 GGTTTAG
12897348 GGTT
1 GGTT
12897352 ACAAGTTACA
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
6 25 0.30
7 47 0.57
8 11 0.13
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:12897266 original size:13 final size:13
Alignment explanation
Indices: 12897238--12897330 Score: 64
Period size: 13 Copynumber: 6.9 Consensus size: 13
12897228 CGAACCTCGA
12897238 GGTTTAGGGTTTG
1 GGTTTAGGGTTTG
12897251 GGTTT-GGGTTTGG
1 GGTTTAGGGTTT-G
* * *
12897264 GGTTTAAGATTTA
1 GGTTTAGGGTTTG
* *
12897277 GGTTTGGGGTTTAAA
1 GGTTTAGGGTTT--G
*
12897292 GGTTTAAGGTTATG
1 GGTTTAGGGTT-TG
*
12897306 GGTTTAGTGTTTG
1 GGTTTAGGGTTTG
12897319 AGGTTT-GGGTTT
1 -GGTTTAGGGTTT
12897331 AAAAGTGTAG
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
12 6 0.10
13 27 0.44
14 18 0.29
15 10 0.16
16 1 0.02
ACGTcount: A:0.14, C:0.00, G:0.40, T:0.46
Consensus pattern (13 bp):
GGTTTAGGGTTTG
Found at i:12897329 original size:20 final size:20
Alignment explanation
Indices: 12897236--12897331 Score: 83
Period size: 20 Copynumber: 4.8 Consensus size: 20
12897226 CTCGAACCTC
* *
12897236 GAGGTTTAGGGTTTGGGTTT
1 GAGGTTTGGGGTTTAGGTTT
*
12897256 G-GGTTTGGGGTTTAAGATTT
1 GAGGTTTGGGGTTT-AGGTTT
12897276 -AGGTTTGGGGTTTAAAGGTTT
1 GAGGTTTGGGGTTT--AGGTTT
*
12897297 AAGGTTAT-GGGTTTAGTGTTT
1 GAGGTT-TGGGGTTTAG-GTTT
12897318 GAGGTTT-GGGTTTA
1 GAGGTTTGGGGTTTA
12897332 AAAGTGTAGG
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
19 11 0.17
20 27 0.42
21 15 0.23
22 11 0.17
23 1 0.02
ACGTcount: A:0.16, C:0.00, G:0.40, T:0.45
Consensus pattern (20 bp):
GAGGTTTGGGGTTTAGGTTT
Found at i:12897739 original size:60 final size:60
Alignment explanation
Indices: 12897675--12897793 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 60
12897665 ATGTGGCAAA
**
12897675 ATTTTATTAG-TGCCTAAAAACCT-TAATTTTTAGGATC-ATTCTAATGTAAGTTATTCCCTT
1 ATTTTATT-GCTGCCTAAAAA-CTATAATTTTTAGGA-CGATTCTAATACAAGTTATTCCCTT
* * *
12897735 ATTTTGTTGCTGCCTAAAAACTATACTTTTTAGGACGATTCTAATACAATTTATTCCCT
1 ATTTTATTGCTGCCTAAAAACTATAATTTTTAGGACGATTCTAATACAAGTTATTCCCT
12897794 AATAAATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
59 4 0.08
60 47 0.92
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (60 bp):
ATTTTATTGCTGCCTAAAAACTATAATTTTTAGGACGATTCTAATACAAGTTATTCCCTT
Found at i:12904190 original size:2 final size:2
Alignment explanation
Indices: 12904178--12904208 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12904168 TGGGAGACAT
*
12904178 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
12904209 TTTAAAGACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12905666 original size:38 final size:38
Alignment explanation
Indices: 12905613--12905716 Score: 154
Period size: 38 Copynumber: 2.7 Consensus size: 38
12905603 TGGTAACCAA
* *
12905613 CCGATAACACGCCAGTTTGCTCATAAGAGCTATTTCAT
1 CCGATAACACACCAGTTTGCTCATAAGAGCTATTCCAT
* *
12905651 CTGATAACACACCAGTTTGCTCATAAGAGTTATTCCAT
1 CCGATAACACACCAGTTTGCTCATAAGAGCTATTCCAT
* *
12905689 CCAATAATACACCAGTTTGCTCATAAGA
1 CCGATAACACACCAGTTTGCTCATAAGA
12905717 TTTATAATTG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 59 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (38 bp):
CCGATAACACACCAGTTTGCTCATAAGAGCTATTCCAT
Found at i:12912982 original size:7 final size:7
Alignment explanation
Indices: 12912970--12913003 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
12912960 ACTTTGGCTA
12912970 AAACCCT
1 AAACCCT
12912977 AAACCCT
1 AAACCCT
*
12912984 AAACTCT
1 AAACCCT
12912991 AAAACCCT
1 -AAACCCT
12912999 AAACC
1 AAACC
12913004 TTTACAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCCT
Found at i:12926881 original size:13 final size:13
Alignment explanation
Indices: 12926863--12926894 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12926853 GAGCATATAT
12926863 AAAACATAACTTG
1 AAAACATAACTTG
*
12926876 AAAACATAAGTTG
1 AAAACATAACTTG
12926889 AAAACA
1 AAAACA
12926895 GAGTTCATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.19
Consensus pattern (13 bp):
AAAACATAACTTG
Found at i:12927519 original size:25 final size:25
Alignment explanation
Indices: 12927491--12927552 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
12927481 TTGCAATGAA
*
12927491 TTTGGTGAACCCCTTTATCGCATCT
1 TTTGGTGAACCACTTTATCGCATCT
* *
12927516 TTTGGTGTACACTACTTTATCGTATCT
1 TTTGGTG-A-ACCACTTTATCGCATCT
*
12927543 TTTGGCGAAC
1 TTTGGTGAAC
12927553 TCTTTACTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 9 0.29
26 2 0.06
27 20 0.65
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.42
Consensus pattern (25 bp):
TTTGGTGAACCACTTTATCGCATCT
Found at i:12938619 original size:18 final size:18
Alignment explanation
Indices: 12938598--12938634 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12938588 TTTTTAAACA
12938598 TTATTTCTATTTT-TATTG
1 TTATTTC-ATTTTATATTG
12938616 TTATTTCATTTTATATTG
1 TTATTTCATTTTATATTG
12938634 T
1 T
12938635 GTTTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.70
Consensus pattern (18 bp):
TTATTTCATTTTATATTG
Found at i:12944680 original size:7 final size:7
Alignment explanation
Indices: 12944651--12944693 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
12944641 ACTTTTACAT
12944651 TTAAAAA
1 TTAAAAA
*
12944658 TATGAAAA
1 T-TAAAAA
12944666 TTAAAAAAA
1 TT--AAAAA
12944675 TTAAAAA
1 TTAAAAA
12944682 TTAAAAA
1 TTAAAAA
12944689 TTAAA
1 TTAAA
12944694 TCTTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 19 0.61
8 6 0.19
9 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (7 bp):
TTAAAAA
Done.