Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold601
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1259944
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 136746 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:953326 original size:22 final size:22
Alignment explanation
Indices: 953279--953327 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
953269 ATGTGTGACT
* *
953279 GAAAGATGACTGAAAGATGATT
1 GAAAAATGACTGAAAGATGATA
953301 GAAAAATGACTGAAAGATG-TCA
1 GAAAAATGACTGAAAGATGAT-A
953323 GAAAA
1 GAAAA
953328 GTAATAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.51, C:0.06, G:0.24, T:0.18
Consensus pattern (22 bp):
GAAAAATGACTGAAAGATGATA
Found at i:961362 original size:12 final size:12
Alignment explanation
Indices: 961345--961374 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
961335 TGTTATGCCA
961345 TTGTTTTTTTTT
1 TTGTTTTTTTTT
961357 TTGTTTTTTTTT
1 TTGTTTTTTTTT
*
961369 TGGTTT
1 TTGTTT
961375 ATTGAATTAA
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:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (12 bp):
TTGTTTTTTTTT
Found at i:963161 original size:21 final size:21
Alignment explanation
Indices: 963135--963449 Score: 391
Period size: 21 Copynumber: 15.0 Consensus size: 21
963125 TCTTCATAAT
*
963135 ATGATGATACTTCAACATTAC
1 ATGATGATACTTTAACATTAC
* *
963156 ATGATGGTACTTCAACATTAC
1 ATGATGATACTTTAACATTAC
963177 AT-ACTGATA-TTTCAACATTAC
1 ATGA-TGATACTTT-AACATTAC
*
963198 ATGATGGTACTTTAACATTAC
1 ATGATGATACTTTAACATTAC
* *
963219 ATGCTGATACTTCAACATTAC
1 ATGATGATACTTTAACATTAC
* *
963240 ATGATGGTGCTTTAACATTAC
1 ATGATGATACTTTAACATTAC
* *
963261 ATGCTGATACTTCAACATTAC
1 ATGATGATACTTTAACATTAC
* *
963282 GTGATGGTACTTTAACATTAC
1 ATGATGATACTTTAACATTAC
*
963303 ATGATGGTACTTTAACATTAC
1 ATGATGATACTTTAACATTAC
* *
963324 GTGCTGATACTTTAACATTAC
1 ATGATGATACTTTAACATTAC
*
963345 ATGCTGATACTTTAACATTAC
1 ATGATGATACTTTAACATTAC
*
963366 ATGCTGATACTTTAACATTAC
1 ATGATGATACTTTAACATTAC
* *
963387 ATGCTGATACTTCAACATTAC
1 ATGATGATACTTTAACATTAC
*
963408 ATGCTGATACTTTAACATTAC
1 ATGATGATACTTTAACATTAC
* *
963429 ATGATGGTACTATGAACATTA
1 ATGATGATACT-TTAACATTA
963450 TCTACATAAG
Statistics
Matches: 260, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
20 3 0.01
21 245 0.94
22 12 0.05
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (21 bp):
ATGATGATACTTTAACATTAC
Found at i:963185 original size:42 final size:42
Alignment explanation
Indices: 963139--963449 Score: 442
Period size: 42 Copynumber: 7.4 Consensus size: 42
963129 CATAATATGA
* *
963139 TGATACTTCAACATTACATGATGGTACTTCAACATTACATAC
1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC
*
963181 TGATATTTCAACATTACATGATGGTACTTTAACATTACATGC
1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC
*
963223 TGATACTTCAACATTACATGATGGTGCTTTAACATTACATGC
1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC
* *
963265 TGATACTTCAACATTACGTGATGGTACTTTAACATTACATGA
1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC
* * * * *
963307 TGGTACTTTAACATTACGTGCTGATACTTTAACATTACATGC
1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC
* * *
963349 TGATACTTTAACATTACATGCTGATACTTTAACATTACATGC
1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC
* * *
963391 TGATACTTCAACATTACATGCTGATACTTTAACATTACATGA
1 TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC
* *
963433 TGGTACTATGAACATTA
1 TGATACT-TCAACATTA
963450 TCTACATAAG
Statistics
Matches: 249, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
42 241 0.97
43 8 0.03
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (42 bp):
TGATACTTCAACATTACATGATGGTACTTTAACATTACATGC
Found at i:964243 original size:2 final size:2
Alignment explanation
Indices: 964236--964296 Score: 77
Period size: 2 Copynumber: 30.5 Consensus size: 2
964226 CCGTATGTGT
* * *
964236 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TT TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
964278 TC TC TC TT TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
964297 GAGTGTCTGC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (2 bp):
TC
Found at i:964556 original size:2 final size:2
Alignment explanation
Indices: 964551--964603 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
964541 GGGGGGGTTG
964551 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
964593 CT CT CT CT CT C
1 CT CT CT CT CT C
964604 CATGTTTTGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:964940 original size:2 final size:2
Alignment explanation
Indices: 964933--964980 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
964923 CTGTGCAAAA
964933 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
964975 CT CT CT
1 CT CT CT
964981 GTGTGTAAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:996176 original size:2 final size:2
Alignment explanation
Indices: 996169--996209 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
996159 NNNNNNNNNN
996169 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
996210 ACACACAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:999770 original size:2 final size:2
Alignment explanation
Indices: 999763--999810 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
999753 AACATAAACA
999763 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
999805 AG AG AG
1 AG AG AG
999811 TGTGTGTGGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:999815 original size:2 final size:2
Alignment explanation
Indices: 999810--999858 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
999800 GAGAGAGAGA
* *
999810 GT GT GT GT GG GT GT GG GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
999852 GT GT GT G
1 GT GT GT G
999859 ACACCCATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.55, T:0.45
Consensus pattern (2 bp):
GT
Found at i:1001262 original size:50 final size:50
Alignment explanation
Indices: 1001204--1001317 Score: 156
Period size: 50 Copynumber: 2.3 Consensus size: 50
1001194 TTGGAAAAAG
*
1001204 TTTTCAAAGTGCGTCAAATTTGGGACCAAATCAACGCACTTTGAAATTTT
1 TTTTCAAAGTGCGTCAAATTTGGGACCAAATCAACCCACTTTGAAATTTT
* * ** * *
1001254 TTTTCAAAGTTCGTTAAATTTTTGACCAAGTTAACCCACTTTGAAATTTT
1 TTTTCAAAGTGCGTCAAATTTGGGACCAAATCAACCCACTTTGAAATTTT
*
1001304 GTTTCAAAGTGCGT
1 TTTTCAAAGTGCGT
1001318 TTAGATGGTA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (50 bp):
TTTTCAAAGTGCGTCAAATTTGGGACCAAATCAACCCACTTTGAAATTTT
Found at i:1011338 original size:2 final size:2
Alignment explanation
Indices: 1011331--1011355 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1011321 NNNNNNNNNN
1011331 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1011356 TACGTTATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1012405 original size:2 final size:2
Alignment explanation
Indices: 1012398--1012482 Score: 143
Period size: 2 Copynumber: 42.5 Consensus size: 2
1012388 TGATAATAAT
1012398 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * *
1012440 AG GG GG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1012482 A
1 A
1012483 TCCAACTAAT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1017693 original size:17 final size:17
Alignment explanation
Indices: 1017671--1017705 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1017661 ATCACTTTGC
1017671 AACCACTATTGAAATAA
1 AACCACTATTGAAATAA
1017688 AACCACTATTGAAATAA
1 AACCACTATTGAAATAA
1017705 A
1 A
1017706 TTATTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (17 bp):
AACCACTATTGAAATAA
Found at i:1018158 original size:53 final size:53
Alignment explanation
Indices: 1018073--1018210 Score: 204
Period size: 53 Copynumber: 2.6 Consensus size: 53
1018063 GGGGTTACTT
* * * *
1018073 CACTGTTGAAATATAGTATTTCAATAGTGGTTAAGGATGCGATTCATTTCAAC
1 CACTATTGAAATAAAGTATTTCAATAGTGGTTAAGGATACCATTCATTTCAAC
** * *
1018126 CACTATTGAAATAATTTATTTCAATAGTGGTTAGGGATACCTTTCATTTCAAC
1 CACTATTGAAATAAAGTATTTCAATAGTGGTTAAGGATACCATTCATTTCAAC
1018179 CACTATTGAAATAAAGTATTTCAATAGTGGTT
1 CACTATTGAAATAAAGTATTTCAATAGTGGTT
1018211 GATTATGCAT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 75 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (53 bp):
CACTATTGAAATAAAGTATTTCAATAGTGGTTAAGGATACCATTCATTTCAAC
Found at i:1018506 original size:53 final size:53
Alignment explanation
Indices: 1018439--1018622 Score: 190
Period size: 53 Copynumber: 3.5 Consensus size: 53
1018429 ATAACATCCT
* * * *
1018439 ACCACTATTAAAATATTTTATTTCAATAATGGTTGTAATGAACCACAT-TCTGA
1 ACCACTATTGAAATAATTTATTTCAATAATGGTTGTAATGAAACACATACCT-A
* * * **
1018492 ACCACAATTGAAATAAATTATTTCAATAGTGGTTGTAATGAAATGCATACCTA
1 ACCACTATTGAAATAATTTATTTCAATAATGGTTGTAATGAAACACATACCTA
* * ** * * * *
1018545 ACCACTATTGAAATAATTTATTTCAATAGTGGATAAAATAAAACGCAGACCCA
1 ACCACTATTGAAATAATTTATTTCAATAATGGTTGTAATGAAACACATACCTA
*
1018598 ACCACTATTGAAATAATCTATTTCA
1 ACCACTATTGAAATAATTTATTTCA
1018623 TTCAATATTG
Statistics
Matches: 111, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
53 109 0.98
54 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (53 bp):
ACCACTATTGAAATAATTTATTTCAATAATGGTTGTAATGAAACACATACCTA
Found at i:1019430 original size:17 final size:17
Alignment explanation
Indices: 1019405--1019439 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1019395 ATTAAAATTA
*
1019405 TTTACTTCAATAGTGGT
1 TTTACTTCAAAAGTGGT
*
1019422 TTTATTTCAAAAGTGGT
1 TTTACTTCAAAAGTGGT
1019439 T
1 T
1019440 GCAGGGTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (17 bp):
TTTACTTCAAAAGTGGT
Found at i:1019438 original size:84 final size:83
Alignment explanation
Indices: 1019291--1019509 Score: 296
Period size: 84 Copynumber: 2.6 Consensus size: 83
1019281 AGTTCTTATC
* * * *
1019291 ATGAAATACATCCCCAACCTCTATTAAATCA-TTACTTCAATAGTGGTTGTATTTCAATAGTGGT
1 ATGAAATACATCCCCAACCACTATTAAATAATTTACTTCAATAGTGGTTTTATTTCAAAAGTGGT
1019355 TGCAAAGTCATTTTTCTA
66 TGCAAAGTCATTTTTCTA
* *
1019373 ATGAAATACGTCCCCAACCACTATTAAAATTATTTACTTCAATAGTGGTTTTATTTCAAAAGTGG
1 ATGAAATACATCCCCAACCACTATT-AAATAATTTACTTCAATAGTGGTTTTATTTCAAAAGTGG
** *
1019438 TTGCAGGGTGATTTTTCTA
65 TTGCAAAGTCATTTTTCTA
* * * *
1019457 ATGAAATGCATTCTCAACCACTATTGAAATAATTTATTTCAATAGTGGTTTTA
1 ATGAAATACATCCCCAACCACTATT-AAATAATTTACTTCAATAGTGGTTTTA
1019510 AGGTAAAGTC
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
82 23 0.19
83 5 0.04
84 92 0.77
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38
Consensus pattern (83 bp):
ATGAAATACATCCCCAACCACTATTAAATAATTTACTTCAATAGTGGTTTTATTTCAAAAGTGGT
TGCAAAGTCATTTTTCTA
Found at i:1029468 original size:25 final size:25
Alignment explanation
Indices: 1029435--1029483 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1029425 ATACTTTTAC
1029435 ACAATACTGACCAAAGGAAAAAAAT
1 ACAATACTGACCAAAGGAAAAAAAT
1029460 ACAATACTGACCAAAGGAAAAAAA
1 ACAATACTGACCAAAGGAAAAAAA
1029484 AAATATAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.61, C:0.16, G:0.12, T:0.10
Consensus pattern (25 bp):
ACAATACTGACCAAAGGAAAAAAAT
Found at i:1030242 original size:18 final size:16
Alignment explanation
Indices: 1030219--1030258 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
1030209 ACAAAATCGG
1030219 GAGAGAGAGAAAGAACAA
1 GAGAGAGAG-AA-AACAA
1030237 GAGAGAGAGAAAACAA
1 GAGAGAGAGAAAACAA
1030253 GAGAGA
1 GAGAGA
1030259 AAACAAGCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.50
17 2 0.09
18 9 0.41
ACGTcount: A:0.60, C:0.05, G:0.35, T:0.00
Consensus pattern (16 bp):
GAGAGAGAGAAAACAA
Found at i:1030270 original size:14 final size:12
Alignment explanation
Indices: 1030240--1030271 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1030230 AGAACAAGAG
1030240 AGAGAGAAAACA
1 AGAGAGAAAACA
1030252 AGAGAGAAAACA
1 AGAGAGAAAACA
*
1030264 AGCGAGAA
1 AGAGAGAA
1030272 GAATGTTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.62, C:0.09, G:0.28, T:0.00
Consensus pattern (12 bp):
AGAGAGAAAACA
Found at i:1040379 original size:3 final size:3
Alignment explanation
Indices: 1040371--1040431 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
1040361 AAATTAATTT
1040371 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1040419 ATG ATG ATG ATG A
1 ATG ATG ATG ATG A
1040432 AGTAAGCATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:1046777 original size:20 final size:20
Alignment explanation
Indices: 1046740--1046779 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1046730 TTTCATATTA
* **
1046740 AATAAGAGGTCTTTTGACCT
1 AATAACAGGTCTAATGACCT
1046760 AATAACAGGTCTAATGACCT
1 AATAACAGGTCTAATGACCT
1046780 GTAATAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
AATAACAGGTCTAATGACCT
Found at i:1048943 original size:2 final size:2
Alignment explanation
Indices: 1048936--1048982 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1048926 TTTGTACTTT
1048936 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1048978 AG AG A
1 AG AG A
1048983 TAACATAGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1050375 original size:173 final size:173
Alignment explanation
Indices: 1050111--1050591 Score: 479
Period size: 173 Copynumber: 2.8 Consensus size: 173
1050101 GGGCAACAAT
*
1050111 GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAATATCTTCTTCTCAGAAACTA
1 GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAATATCTTCTTCTCAGAAACAA
* * * *
1050176 ATTAGCCAGGAAAGCTGAAACTTGTGTGGTAA-CAT-TCTCAGGTAGTGTAGATTCAAAGATG-G
66 ATTAGCCAGGAAAACTGAAACTTGTGT-GAAAGCATCT-TCAGATAATGTAGATTCAAAGATGTG
*
1050238 AAAAATCATGATCCCCGGTTGTAGGGTGGGGCCACAATGGGGGGGG
129 -AAAATCATGACCCCCGGTTGTAGGGTGGGGCCACAATGGGGGGGG
**
1050284 GGGGGTCGATA-TTTTACATAGGAATATATAGAGTACTTCTTTAGAA-ATCTTCTTCTCAGAAAC
1 GGGGGTCGA-AGTTTTACATAGGAATATATAGAGTAAATCTTTA-AATATCTTCTTCTCAGAAAC
* * *
1050347 AAATCT-GCCAGTAAAACTGAACCTTGTGTGAAAGCATCTTCAGATAATGTAGATTCAAAGTTGT
64 AAAT-TAGCCAGGAAAACTGAAACTTGTGTGAAAGCATCTTCAGATAATGTAGATTCAAAGATGT
* ** * ** *
1050411 GAAAATCATGACCCCCAGAGGTAGGTTAAGGCCACAAT-------A
128 GAAAATCATGACCCCCGGTTGTAGGGTGGGGCCACAATGGGGGGGG
** * * * * * * **
1050450 GTTGATCGAAATTTTACATAGAAATA-AAAGAGTAAATCTTTAAAAATCTTCTTTTCAGAAAGTA
1 GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAATATCTTCTTCTCAGAAACAA
* * * * * * *
1050514 ATGAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTGA-AGTAGTGTAGATTCAAAGTTATGA
66 ATTAGCCAGGAAAACTGAAACTTGTGTGAAAGCATCTTCAGA-TAATGTAGATTCAAAGATGTGA
1050578 AAATCATGACCCCC
130 AAATCATGACCCCC
1050592 TGGGGTAGAG
Statistics
Matches: 262, Mismatches: 36, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
164 3 0.01
165 97 0.37
166 20 0.08
172 3 0.01
173 133 0.51
174 6 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (173 bp):
GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAATATCTTCTTCTCAGAAACAA
ATTAGCCAGGAAAACTGAAACTTGTGTGAAAGCATCTTCAGATAATGTAGATTCAAAGATGTGAA
AATCATGACCCCCGGTTGTAGGGTGGGGCCACAATGGGGGGGG
Found at i:1050549 original size:165 final size:163
Alignment explanation
Indices: 1050018--1050652 Score: 631
Period size: 165 Copynumber: 3.8 Consensus size: 163
1050008 ACCTTAAAAA
* * *
1050018 AGGAAAGCTGAAACTTGTGAT-ATAGCATTCTCAGGTAGTGAAGATTCAAAGTTGTGAAAATCAT
1 AGGAAAGCTGAAACTTGTG-TGAAAGCATTCTCAGATAGTGTAGATTCAAAGTTGTGAAAATCAT
* *
1050082 GACCCCCTAGGGTAAGGTGGGGCAACAATGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAA
65 GACCCCC-AGGGT-AGGTGGGGCCACAATGGGGGTCGAAATTTTACATAGGAATATATAGAGTAA
* *
1050147 ATCTTTAAATATCTTCTTCTCAGAAACTAATTAGCC
128 ATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCC
* * *
1050183 AGGAAAGCTGAAACTTGTGTGGTAA-CATTCTCAGGTAGTGTAGATTCAAAGATG-GAAAAATCA
1 AGGAAAGCTGAAACTTGTGT-GAAAGCATTCTCAGATAGTGTAGATTCAAAGTTGTG-AAAATCA
* *
1050246 TGATCCCC-GGTTGTAGGGTGGGGCCACAATGGGGGGGGGGGGGTCGATATTTTACATAGGAATA
64 TGACCCCCAGG--GTA-GGTGGGGCCACAAT--------GGGGGTCGAAATTTTACATAGGAATA
** * * *
1050310 TATAGAGTACTTCTTTAGAAATCTTCTTCTCAGAAACAAATCTGCC
118 TATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCC
* * * *
1050356 AGTAAAACTGAACCTTGTGTGAAAGCA-TCTTCAGATAATGTAGATTCAAAGTTGTGAAAATCAT
1 AGGAAAGCTGAAACTTGTGTGAAAGCATTC-TCAGATAGTGTAGATTCAAAGTTGTGAAAATCAT
** ** * * *
1050420 GACCCCCAGAGGTAGGTTAAGGCCACAATAGTTGATCGAAATTTTACATAGAAATA-AAAGAGTA
65 GACCCCCAG-GGTAGG-TGGGGCCACAAT-GGGGGTCGAAATTTTACATAGGAATATATAGAGTA
* * *
1050484 AATCTTTAAAAATCTTCTTTTCAGAAAGTAATGAGCC
127 AATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCC
* * *
1050521 AGGAAAGCTGAAACTTGTGTGAAAGCATCCTGA-AGTAGTGTAGATTCAAAGTTATGAAAATCAT
1 AGGAAAGCTGAAACTTGTGTGAAAGCATTCTCAGA-TAGTGTAGATTCAAAGTTGTGAAAATCAT
* * * ** *
1050585 GACCCCCTGGGGTAGAGT--AGCCACAATTGGGGGTCGAAGTTTTTTATAGGAATATATTGAGTA
65 GACCCCC-AGGGTAG-GTGGGGCCACAA-TGGGGGTCGAAATTTTACATAGGAATATATAGAGTA
1050648 AATCT
127 AATCT
1050653 ACCTCTGGTA
Statistics
Matches: 386, Mismatches: 58, Indels: 53
0.78 0.12 0.11
Matches are distributed among these distances:
163 28 0.07
164 16 0.04
165 177 0.46
166 25 0.06
172 7 0.02
173 130 0.34
174 2 0.01
175 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (163 bp):
AGGAAAGCTGAAACTTGTGTGAAAGCATTCTCAGATAGTGTAGATTCAAAGTTGTGAAAATCATG
ACCCCCAGGGTAGGTGGGGCCACAATGGGGGTCGAAATTTTACATAGGAATATATAGAGTAAATC
TTTAAAAATCTTCTTCTCAGAAACTAATCAGCC
Found at i:1051247 original size:16 final size:16
Alignment explanation
Indices: 1051223--1051266 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1051213 ATGGTAGACG
*
1051223 GACATCTCGGCCCAAC
1 GACACCTCGGCCCAAC
1051239 GACACCTCGGCCCAAC
1 GACACCTCGGCCCAAC
1051255 GACACCTCGGCC
1 GACACCTCGGCC
1051267 AAGGGCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.23, C:0.48, G:0.20, T:0.09
Consensus pattern (16 bp):
GACACCTCGGCCCAAC
Found at i:1052512 original size:16 final size:16
Alignment explanation
Indices: 1052491--1052544 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
1052481 GACCCGTCTT
* *
1052491 GGCCGAGGTGTCCTGG
1 GGCCGAGGTGTCGTTG
*
1052507 GGCCGAAGTGTCGTTG
1 GGCCGAGGTGTCGTTG
1052523 GGCCGAGGTGTCGTTG
1 GGCCGAGGTGTCGTTG
1052539 GGCCGA
1 GGCCGA
1052545 CATAGAGTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.09, C:0.22, G:0.48, T:0.20
Consensus pattern (16 bp):
GGCCGAGGTGTCGTTG
Found at i:1055641 original size:2 final size:2
Alignment explanation
Indices: 1055636--1055704 Score: 113
Period size: 2 Copynumber: 35.0 Consensus size: 2
1055626 TATATATATA
*
1055636 TG TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG T- TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1055677 TG TG TA TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1055705 CATTTGATAT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.01, C:0.01, G:0.48, T:0.49
Consensus pattern (2 bp):
TG
Found at i:1059395 original size:20 final size:19
Alignment explanation
Indices: 1059372--1059419 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
1059362 CAAATAAACA
1059372 ATGTTAAGACTTTATTTTAG
1 ATGTTAAGA-TTTATTTTAG
1059392 ATGTTTAGAAGATTTATTTTAG
1 ATG-TT--AAGATTTATTTTAG
1059414 AT-TTAA
1 ATGTTAA
1059420 ACCTAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 2 0.08
20 5 0.20
21 2 0.08
22 12 0.48
23 4 0.16
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (19 bp):
ATGTTAAGATTTATTTTAG
Found at i:1065481 original size:19 final size:19
Alignment explanation
Indices: 1065457--1065509 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
1065447 ATGCAAGACT
1065457 CCAAAGTTCGATGGTTACG
1 CCAAAGTTCGATGGTTACG
1065476 CCAAAG-TCTGATGGTTACG
1 CCAAAGTTC-GATGGTTACG
*
1065495 CCAAAGTCCGATGGT
1 CCAAAGTTCGATGGT
1065510 ATGTTGCCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 2 0.06
19 28 0.90
20 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (19 bp):
CCAAAGTTCGATGGTTACG
Found at i:1066061 original size:5 final size:5
Alignment explanation
Indices: 1066053--1066085 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
1066043 CAATGTCATG
1066053 TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA TGT
1 TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA TGT
1066086 CATGCCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (5 bp):
TGTAA
Found at i:1077093 original size:2 final size:2
Alignment explanation
Indices: 1077088--1077126 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1077078 ATATTTCAAC
1077088 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1077127 ATATTTAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1081590 original size:20 final size:20
Alignment explanation
Indices: 1081565--1081647 Score: 166
Period size: 20 Copynumber: 4.2 Consensus size: 20
1081555 AACAAAACTG
1081565 CAACTGGTTACAATCCATAT
1 CAACTGGTTACAATCCATAT
1081585 CAACTGGTTACAATCCATAT
1 CAACTGGTTACAATCCATAT
1081605 CAACTGGTTACAATCCATAT
1 CAACTGGTTACAATCCATAT
1081625 CAACTGGTTACAATCCATAT
1 CAACTGGTTACAATCCATAT
1081645 CAA
1 CAA
1081648 TTTGTTTTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (20 bp):
CAACTGGTTACAATCCATAT
Found at i:1082986 original size:1 final size:1
Alignment explanation
Indices: 1082930--1082967 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
1082920 ACTTTACTGA
1082930 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1082968 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1091191 original size:44 final size:44
Alignment explanation
Indices: 1091126--1091211 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
1091116 TCAGCAAAAG
*
1091126 TAGAATTAAGATGTTTTGTTTATCGGAATATTCCATTTTATTCA
1 TAGAATTAAGATGTTTCGTTTATCGGAATATTCCATTTTATTCA
* *
1091170 TAGAATTAAGATGTTTCGTTTATCGGAGTATTTCATTTTATT
1 TAGAATTAAGATGTTTCGTTTATCGGAATATTCCATTTTATT
1091212 TAACCAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (44 bp):
TAGAATTAAGATGTTTCGTTTATCGGAATATTCCATTTTATTCA
Found at i:1100072 original size:21 final size:21
Alignment explanation
Indices: 1100045--1100165 Score: 111
Period size: 21 Copynumber: 5.8 Consensus size: 21
1100035 GTCGACAGAC
*
1100045 CTGACAAGTTATCATAAAGAT
1 CTGACAAGTTGTCATAAAGAT
* *
1100066 TTGACAAGTTGTCATGAAGAT
1 CTGACAAGTTGTCATAAAGAT
*
1100087 CTGTCAAGTTGTCA-AAATGAT
1 CTGACAAGTTGTCATAAA-GAT
* * *
1100108 TTCACAAGTTGTCATAAAGGT
1 CTGACAAGTTGTCATAAAGAT
* *
1100129 CTGACAAGTTGATGAGAAA-AT
1 CTGACAAGTTG-TCATAAAGAT
* *
1100150 CTAACAAGTTGACATA
1 CTGACAAGTTGTCATA
1100166 GTTATCGATC
Statistics
Matches: 78, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
20 4 0.05
21 66 0.85
22 8 0.10
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (21 bp):
CTGACAAGTTGTCATAAAGAT
Found at i:1100109 original size:42 final size:42
Alignment explanation
Indices: 1100045--1100139 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
1100035 GTCGACAGAC
* * *
1100045 CTGACAAGTTATCATAAAGATTTGACAAGTTGTCATGAAGAT
1 CTGACAAGTTGTCATAAAGATTTCACAAGTTGTCATAAAGAT
* *
1100087 CTGTCAAGTTGTCA-AAATGATTTCACAAGTTGTCATAAAGGT
1 CTGACAAGTTGTCATAAA-GATTTCACAAGTTGTCATAAAGAT
1100129 CTGACAAGTTG
1 CTGACAAGTTG
1100140 ATGAGAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 3 0.07
42 43 0.93
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (42 bp):
CTGACAAGTTGTCATAAAGATTTCACAAGTTGTCATAAAGAT
Found at i:1101030 original size:11 final size:11
Alignment explanation
Indices: 1101008--1101113 Score: 131
Period size: 11 Copynumber: 9.6 Consensus size: 11
1100998 AAGCTTGATT
*
1101008 TAAACACAGAG
1 TAAACCCAGAG
*
1101019 TGAACCCAGAG
1 TAAACCCAGAG
*
1101030 TAAACCCAAAG
1 TAAACCCAGAG
*
1101041 TGAACCCAGAG
1 TAAACCCAGAG
*
1101052 TAAACCCAAAG
1 TAAACCCAGAG
*
1101063 TGAACCCAGAG
1 TAAACCCAGAG
*
1101074 TAAACCCAAAG
1 TAAACCCAGAG
1101085 TAAACCCAGAG
1 TAAACCCAGAG
*
1101096 TAAACCCAAAG
1 TAAACCCAGAG
*
1101107 TGAACCC
1 TAAACCC
1101114 CAACTGGACA
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 80 1.00
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.09
Consensus pattern (11 bp):
TAAACCCAGAG
Found at i:1101042 original size:22 final size:22
Alignment explanation
Indices: 1101017--1101113 Score: 185
Period size: 22 Copynumber: 4.4 Consensus size: 22
1101007 TTAAACACAG
1101017 AGTGAACCCAGAGTAAACCCAA
1 AGTGAACCCAGAGTAAACCCAA
1101039 AGTGAACCCAGAGTAAACCCAA
1 AGTGAACCCAGAGTAAACCCAA
1101061 AGTGAACCCAGAGTAAACCCAA
1 AGTGAACCCAGAGTAAACCCAA
*
1101083 AGTAAACCCAGAGTAAACCCAA
1 AGTGAACCCAGAGTAAACCCAA
1101105 AGTGAACCC
1 AGTGAACCC
1101114 CAACTGGACA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 73 1.00
ACGTcount: A:0.45, C:0.28, G:0.18, T:0.09
Consensus pattern (22 bp):
AGTGAACCCAGAGTAAACCCAA
Found at i:1102333 original size:173 final size:173
Alignment explanation
Indices: 1102136--1102512 Score: 453
Period size: 173 Copynumber: 2.2 Consensus size: 173
1102126 TGGGTCCTAA
1102136 ATTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTGTTT-GTTGCAGGTGCCCT
1 ATTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGT-TTTCGTTGCAGGTGCCCT
* * *
1102200 TTGATAGAAATT-TC-TAAGTAACTGCTGGTCCTACCAACTTCACCAAACTTGCATGGATTAG-T
65 CTGAT-GAAATTATCTTAA-TAACTACTGGT-CT--CAACTTCACCAAACTTGCATGG-TGAGTT
* * *
1102262 CT-T-ATACTGATGAACCAGA-CAGCTTGAATGCTAAATCTGAGCTATAG
124 CTATGATAATGATGAACCAGAGAAGCTTGAATGCTAAATCTGAGCCATAG
* *
1102309 GTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTCGTTGCAGGTGTCCTC
1 ATTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTCGTTGCAGGTGCCCTC
** * * * *
1102374 TGATGATTTTATCTTAATTACTACTGGTCTTAACTTCACCAAACTTGCATGGTGCGTTTTATGAT
66 TGATGAAATTATCTTAATAACTACTGGTCTCAACTTCACCAAACTTGCATGGTGAGTTCTATGAT
**
1102439 AATGATGCTCCAGAGAAGCTTGAATGCTAAATCTGAGCCATAG
131 AATGATGAACCAGAGAAGCTTGAATGCTAAATCTGAGCCATAG
** * * *
1102482 ATTTTGGATGCTGGATGAGGTTTAGTTTTTT
1 ATTTCAGATGCTGGAGGAGGTTAAGGTTTTT
1102513 TGGAACAGGT
Statistics
Matches: 175, Mismatches: 22, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
169 2 0.01
170 23 0.13
171 1 0.01
172 22 0.13
173 124 0.71
174 3 0.02
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (173 bp):
ATTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTCGTTGCAGGTGCCCTC
TGATGAAATTATCTTAATAACTACTGGTCTCAACTTCACCAAACTTGCATGGTGAGTTCTATGAT
AATGATGAACCAGAGAAGCTTGAATGCTAAATCTGAGCCATAG
Found at i:1104834 original size:23 final size:23
Alignment explanation
Indices: 1104807--1104851 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1104797 AAACAATTAC
1104807 AAAACAAATAAAT-AGAATAAATT
1 AAAACAAATAAATAAG-ATAAATT
1104830 AAAACAAATAAATAAGATAAAT
1 AAAACAAATAAATAAGATAAAT
1104852 ACTGATGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAACAAATAAATAAGATAAATT
Found at i:1107897 original size:63 final size:63
Alignment explanation
Indices: 1107819--1108386 Score: 1100
Period size: 63 Copynumber: 9.0 Consensus size: 63
1107809 TTGTCTCAAT
*
1107819 AATAATGGTGCCCTTAGGATGCAACATGAACCTCATGTACATCAGAATACTACGGAAGATGAC
1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
*
1107882 AATAATGGTGCCCTTAGGATGCAACATGAACCTCGGGTACATCAGAATACTACGGAAGATGAC
1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1107945 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1108008 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1108071 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1108134 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1108197 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1108260 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
* *
1108323 AATAATGGTGCCCTTAGGATGCAACATGAACCTCGGGTACATCAGAATACTACGGTAGATGAC
1 AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
1108386 A
1 A
1108387 TTCCATTCCA
Statistics
Matches: 500, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 500 1.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (63 bp):
AATAATGGTGCCCTTAGGATGCAACATGAACCTCAGGTACATCAGAATACTACGGAAGATGAC
Found at i:1108753 original size:38 final size:38
Alignment explanation
Indices: 1108702--1109516 Score: 1477
Period size: 38 Copynumber: 21.4 Consensus size: 38
1108692 GGGGAAGACC
*
1108702 CAGACCAATACCACAGTCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
*
1108740 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1108778 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
*
1108816 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1108854 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
*
1108892 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1108930 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1108968 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
*
1109006 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
*
1109044 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1109082 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1109120 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
* *
1109158 CAGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAT
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
* *
1109196 CAGACCTATACCACAGCCCTAACTGTCGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1109234 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1109272 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1109310 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1109348 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1109386 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
** * *
1109424 CAGACCAATACCACAGCCCTAACTGTCTGTAAGGGTAT
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
* *
1109462 CAAACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
*
1109500 CAGACCGATACCACAGC
1 CAGACCAATACCACAGC
1109517 GTTAAGGTAG
Statistics
Matches: 752, Mismatches: 25, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 752 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.19
Consensus pattern (38 bp):
CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
Found at i:1109934 original size:24 final size:24
Alignment explanation
Indices: 1109886--1109934 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
1109876 AAGATGGGAT
*
1109886 AAATTTGTTAAAATTTAGAATTGA
1 AAATTTGTTAAAATTTAGAAATGA
1109910 AAATTT-TTAAAAATTTA-AAGATGA
1 AAATTTGTT-AAAATTTAGAA-ATGA
1109934 A
1 A
1109935 TCTTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (24 bp):
AAATTTGTTAAAATTTAGAAATGA
Found at i:1111584 original size:15 final size:16
Alignment explanation
Indices: 1111564--1111596 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1111554 TCACAGGGAA
1111564 TGAAA-GTCAATTCAT
1 TGAAACGTCAATTCAT
1111579 TGAAAGCGTCAATTCAT
1 TGAAA-CGTCAATTCAT
1111596 T
1 T
1111597 ATAAGCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (16 bp):
TGAAACGTCAATTCAT
Found at i:1112317 original size:35 final size:35
Alignment explanation
Indices: 1112278--1112411 Score: 162
Period size: 35 Copynumber: 3.8 Consensus size: 35
1112268 GGCTGGGGAC
1112278 AACCCCTGGGTAAGTGACTGGTTTGTGTGATAGGG
1 AACCCCTGGGTAAGTGACTGGTTTGTGTGATAGGG
**
1112313 AACCCCTGGGTTTGTGACTGGTTTGTGTGATAGGG
1 AACCCCTGGGTAAGTGACTGGTTTGTGTGATAGGG
* * **
1112348 AACCCCTGGGTATGGGACTGGTTTGTGTGGGA-GG
1 AACCCCTGGGTAAGTGACTGGTTTGTGTGATAGGG
* * * *
1112382 AGACCTCTTGGTAAGTGACCGATTTGTGTG
1 A-ACCCCTGGGTAAGTGACTGGTTTGTGTG
1112412 TGTGTGTGGG
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
34 3 0.03
35 83 0.97
ACGTcount: A:0.17, C:0.15, G:0.37, T:0.31
Consensus pattern (35 bp):
AACCCCTGGGTAAGTGACTGGTTTGTGTGATAGGG
Found at i:1112946 original size:35 final size:36
Alignment explanation
Indices: 1112902--1112969 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 36
1112892 AAGTTGGCCT
1112902 CTGGATAAGTGACC-GATTTGTGTG-GTAGGGGACCC
1 CTGGATAAGTGACCTG-TTTGTGTGTGTAGGGGACCC
* * *
1112937 CTGGGTAAGTGGCCTGTTTGTGTGTGTGGGGGA
1 CTGGATAAGTGACCTGTTTGTGTGTGTAGGGGA
1112970 GGGGGGCACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 20 0.71
36 8 0.29
ACGTcount: A:0.15, C:0.13, G:0.43, T:0.29
Consensus pattern (36 bp):
CTGGATAAGTGACCTGTTTGTGTGTGTAGGGGACCC
Found at i:1113096 original size:94 final size:93
Alignment explanation
Indices: 1112935--1113104 Score: 220
Period size: 93 Copynumber: 1.8 Consensus size: 93
1112925 GGTAGGGGAC
* * * * *
1112935 CCCTGGGTAAGTGGCCTGTTTGTGTGTGTGGGGGAGGGGGGCACTCTGGGTAAAGGACTGGTTTG
1 CCCTGCGTAAGTGACCTGTTTGTGTATGTGGGGGAGGGGGGAACTCTGGATAAAGGACTGGTTTG
*
1113000 TGTGTGTGTGTTTTTGTCTAGGGGGGTG
66 TGTGTATGTGTTTTTGTCTAGGGGGGTG
*
1113028 CCCTGCGTAAGTGACC-GTTATGTGTATG-GGGGGGGGGGGAGAACTCCTGGAT-AAGTGACTGG
1 CCCTGCGTAAGTGACCTGTT-TGTGTATGTGGGGGAGGGGG-GAACT-CTGGATAAAG-GACTGG
1113090 TTTGTGTGTATGTGT
62 TTTGTGTGTATGTGT
1113105 GTTGGGGGGG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
92 13 0.20
93 28 0.42
94 25 0.38
ACGTcount: A:0.13, C:0.12, G:0.44, T:0.32
Consensus pattern (93 bp):
CCCTGCGTAAGTGACCTGTTTGTGTATGTGGGGGAGGGGGGAACTCTGGATAAAGGACTGGTTTG
TGTGTATGTGTTTTTGTCTAGGGGGGTG
Found at i:1116666 original size:22 final size:22
Alignment explanation
Indices: 1116626--1116672 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1116616 GAGTAAACCT
* *
1116626 AAAGTAAACAGCGAGTGGACCC
1 AAAGTAAACACCGAATGGACCC
* *
1116648 AAAGTAAACCCCGAATGGACGC
1 AAAGTAAACACCGAATGGACCC
1116670 AAA
1 AAA
1116673 TTTTCAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (22 bp):
AAAGTAAACACCGAATGGACCC
Found at i:1117238 original size:18 final size:18
Alignment explanation
Indices: 1117215--1117252 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1117205 TATGCACACT
*
1117215 TGTACATGTATCTTCTCA
1 TGTACATGTAACTTCTCA
1117233 TGTACATGTAACTTCTCA
1 TGTACATGTAACTTCTCA
1117251 TG
1 TG
1117253 GCATAGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (18 bp):
TGTACATGTAACTTCTCA
Found at i:1120078 original size:79 final size:80
Alignment explanation
Indices: 1119940--1120091 Score: 243
Period size: 79 Copynumber: 1.9 Consensus size: 80
1119930 TTGTTATGTG
* * *
1119940 TGTTGTTATATTGTAGCTGTGGATAATTGTCAAACTTGTTTGGTCAATTTGTATTGTTATTTATT
1 TGTTGTTATATTGTAGCTATGGATAATTGTCAAACTTGTTTGGTCAATTTGCATAGTTATTTATT
1120005 TCTGATATTAGTCGA
66 TCTGATATTAGTCGA
* * *
1120020 TGTTGTTATATT-TAGCTATGGTTAATTGTCAAATTTGTTTGGTCAGTTTGCATAGTTATTTATT
1 TGTTGTTATATTGTAGCTATGGATAATTGTCAAACTTGTTTGGTCAATTTGCATAGTTATTTATT
1120084 TCTGATAT
66 TCTGATAT
1120092 CTGCCTATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
79 54 0.82
80 12 0.18
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.51
Consensus pattern (80 bp):
TGTTGTTATATTGTAGCTATGGATAATTGTCAAACTTGTTTGGTCAATTTGCATAGTTATTTATT
TCTGATATTAGTCGA
Found at i:1123490 original size:2 final size:2
Alignment explanation
Indices: 1123483--1123521 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1123473 CATTCGACAA
*
1123483 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1123522 GTTTTGAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:1123842 original size:2 final size:2
Alignment explanation
Indices: 1123835--1123876 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1123825 TGCGTAAAAC
1123835 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1123877 TATATATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1127224 original size:20 final size:20
Alignment explanation
Indices: 1127174--1127224 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
1127164 ACAAATAAAA
*
1127174 CCTTACAAATCGAAACAAAT
1 CCTTACAAATCGAAACAAAC
* *
1127194 CCTAACAAAAT-GAAACGAAC
1 CCTTAC-AAATCGAAACAAAC
1127214 CCTTACGAAAT
1 CCTTAC-AAAT
1127225 AAAATGATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.49, C:0.25, G:0.08, T:0.18
Consensus pattern (20 bp):
CCTTACAAATCGAAACAAAC
Found at i:1129750 original size:30 final size:30
Alignment explanation
Indices: 1129714--1129770 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
1129704 ACAGCCGACN
*
1129714 CCGGTCAATAGACTTCGATCTATTGGATCG
1 CCGGTCAATAGACTGCGATCTATTGGATCG
1129744 CCGGTCAATAGACTGCGATCTATTGGA
1 CCGGTCAATAGACTGCGATCTATTGGA
1129771 CCGGCAACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (30 bp):
CCGGTCAATAGACTGCGATCTATTGGATCG
Found at i:1138432 original size:15 final size:16
Alignment explanation
Indices: 1138395--1138434 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
1138385 CCGTGAGTTC
1138395 ACTTCGAGAGATCAAGA
1 ACTTCGAGAGATC-AGA
1138412 ACTTCGAGAGATC-GA
1 ACTTCGAGAGATCAGA
*
1138427 AGTTCGAG
1 ACTTCGAG
1138435 CCATCAAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (16 bp):
ACTTCGAGAGATCAGA
Found at i:1150553 original size:21 final size:21
Alignment explanation
Indices: 1150519--1150595 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
1150509 AATTTAATGC
* *
1150519 TATGCTATGGTATGCGATTT-
1 TATGATATGCTATGCGATTTG
1150539 TAATGATATGCTATGCGATTTG
1 T-ATGATATGCTATGCGATTTG
* * *
1150561 TATGCTATGCTATGAGATCTG
1 TATGATATGCTATGCGATTTG
* *
1150582 TATGCTATGATATG
1 TATGATATGCTATG
1150596 AGAAATTGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
20 1 0.02
21 47 0.96
22 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (21 bp):
TATGATATGCTATGCGATTTG
Found at i:1150596 original size:21 final size:21
Alignment explanation
Indices: 1150545--1150598 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1150535 ATTTTAATGA
* *
1150545 TATGCTATGCGATTTGTATGC
1 TATGCTATGAGATCTGTATGC
1150566 TATGCTATGAGATCTGTATGC
1 TATGCTATGAGATCTGTATGC
*
1150587 TATGATATGAGA
1 TATGCTATGAGA
1150599 AATTGAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (21 bp):
TATGCTATGAGATCTGTATGC
Found at i:1150642 original size:15 final size:15
Alignment explanation
Indices: 1150622--1150650 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1150612 TGCTTAATGA
1150622 TATGGTATGCTATGC
1 TATGGTATGCTATGC
1150637 TATGGTATGCTATG
1 TATGGTATGCTATG
1150651 AGATTTGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41
Consensus pattern (15 bp):
TATGGTATGCTATGC
Found at i:1150840 original size:21 final size:21
Alignment explanation
Indices: 1150814--1150890 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
1150804 ATGCTATGGT
* *
1150814 ATGCTATGGTATGAGATTCCA
1 ATGCTATGCTATGAGATTTCA
1150835 ATGCTATGCTATGAGATTTCA
1 ATGCTATGCTATGAGATTTCA
*
1150856 ATGCTATGCTATGAGATTTTA
1 ATGCTATGCTATGAGATTTCA
1150877 ATGCTATGCTATGA
1 ATGCTATGCTATGA
1150891 TATGGCGTAC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.38
Consensus pattern (21 bp):
ATGCTATGCTATGAGATTTCA
Found at i:1158346 original size:2 final size:2
Alignment explanation
Indices: 1158339--1158388 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1158329 TTGACCACAT
*
1158339 GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1158381 GA GA GA GA
1 GA GA GA GA
1158389 AGTTGAATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1158921 original size:11 final size:11
Alignment explanation
Indices: 1158905--1158944 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1158895 TAAGCAAGTC
1158905 CTTAAAGGTGG
1 CTTAAAGGTGG
*
1158916 CTTAAAGGTGA
1 CTTAAAGGTGG
*
1158927 CTTAAAGG-AG
1 CTTAAAGGTGG
1158937 CTTAAAGG
1 CTTAAAGG
1158945 CTATACAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:1159031 original size:11 final size:11
Alignment explanation
Indices: 1159015--1159064 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
1159005 GTCCAAACTT
1159015 CTTTAAGCCAC
1 CTTTAAGCCAC
1159026 CTTTAAGCCAC
1 CTTTAAGCCAC
* *
1159037 ATTTTAGCCAC
1 CTTTAAGCCAC
*
1159048 CTTTAAG-CAT
1 CTTTAAGCCAC
1159058 CTTTAAG
1 CTTTAAG
1159065 TGGCATTTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.26
11 25 0.74
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1159082 original size:22 final size:22
Alignment explanation
Indices: 1159057--1159117 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
1159047 CCTTTAAGCA
* *
1159057 TCTTTAAGTGGCATTTACGCTC
1 TCTTTAAGTGGCCTTTACACTC
* *
1159079 TCTTTACACT-GCCTTTACACTG
1 TCTTTA-AGTGGCCTTTACACTC
1159101 TCTTTAAGTGGCCTTTA
1 TCTTTAAGTGGCCTTTA
1159118 AGTCAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43
Consensus pattern (22 bp):
TCTTTAAGTGGCCTTTACACTC
Found at i:1159453 original size:2 final size:2
Alignment explanation
Indices: 1159448--1159501 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1159438 GTGAAAAAAA
1159448 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1159490 TC TC TC TC TC TC
1 TC TC TC TC TC TC
1159502 AGTTCATCCG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1159912 original size:112 final size:112
Alignment explanation
Indices: 1159715--1159937 Score: 428
Period size: 112 Copynumber: 2.0 Consensus size: 112
1159705 AGTTTTGTTC
*
1159715 GTTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
*
1159780 GAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCAT
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
1159827 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1159892 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
1159938 CGTCAGGGTT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (112 bp):
GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
Found at i:1160968 original size:11 final size:11
Alignment explanation
Indices: 1160952--1161005 Score: 90
Period size: 11 Copynumber: 4.9 Consensus size: 11
1160942 AACTTTTTTA
1160952 TGGCTTAAAGG
1 TGGCTTAAAGG
1160963 TGGCTTAAAGG
1 TGGCTTAAAGG
* *
1160974 TAGCTAAAAGG
1 TGGCTTAAAGG
1160985 TGGCTTAAAGG
1 TGGCTTAAAGG
1160996 TGGCTTAAAG
1 TGGCTTAAAG
1161006 AAGTTTGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.31, C:0.09, G:0.33, T:0.26
Consensus pattern (11 bp):
TGGCTTAAAGG
Found at i:1161053 original size:11 final size:11
Alignment explanation
Indices: 1161037--1161065 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1161027 ATAAGTTGTC
1161037 CTTAAAGGTGG
1 CTTAAAGGTGG
1161048 CTTAAAGGTGG
1 CTTAAAGGTGG
1161059 CTTAAAG
1 CTTAAAG
1161066 ATAGTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:1161147 original size:11 final size:11
Alignment explanation
Indices: 1161131--1161162 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1161121 GCAATACATA
1161131 TAGCTTAAAGG
1 TAGCTTAAAGG
1161142 TAGCTTAAAGG
1 TAGCTTAAAGG
*
1161153 TGGCTTAAAG
1 TAGCTTAAAG
1161163 ATCGTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCTTAAAGG
Found at i:1161184 original size:11 final size:11
Alignment explanation
Indices: 1161168--1161206 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1161158 TAAAGATCGT
1161168 CTTTAAGCTAC
1 CTTTAAGCTAC
*
1161179 CTTTAAAC-AC
1 CTTTAAGCTAC
*
1161189 CTTTAAGCTAT
1 CTTTAAGCTAC
1161200 CTTTAAG
1 CTTTAAG
1161207 GAGGACTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:1161311 original size:20 final size:21
Alignment explanation
Indices: 1161272--1161312 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1161262 AGTAATTTAG
*
1161272 AAATACATTTTTAAAAAGAGGA
1 AAATACAGTTTT-AAAAGAGGA
1161294 AAATACAGTTTT-AAAGAGG
1 AAATACAGTTTTAAAAGAGG
1161313 CACACTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (21 bp):
AAATACAGTTTTAAAAGAGGA
Found at i:1165801 original size:25 final size:25
Alignment explanation
Indices: 1165763--1165814 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1165753 CACAATTCAG
* *
1165763 GAAAACACTTCTTGCCTACAGGGAT
1 GAAAACACTACTTGCCTACAGCGAT
1165788 GAAAACACTACTTGCCTACAGCGAT
1 GAAAACACTACTTGCCTACAGCGAT
1165813 GA
1 GA
1165815 TATCCCGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (25 bp):
GAAAACACTACTTGCCTACAGCGAT
Found at i:1182292 original size:162 final size:157
Alignment explanation
Indices: 1181965--1182340 Score: 366
Period size: 157 Copynumber: 2.3 Consensus size: 157
1181955 ACCAGGTTCA
* * * * * * *
1181965 AATTTAATTTTTTCTAAACCTTATTGTACATCGATAGGACAGTCCCTATCATATCCCAAGAGATG
1 AATTTAAATTTTT-AAAACCTTATTGTACATC-TTAAGACAGCCCCTATCATATCCCAAAAGATA
* * * * *
1182030 ATGTGTCTATTCATTAAATCATAAGAGTTCTGGGATCTAGGTTTTTTAAGGAGGGGTAAAGTCAA
64 ATGTATATATTCATTAAATCATAAGAGTTCTGGGATCTAAGTTTTTTAAGGAAGGATAAAGTCAA
* * * *
1182095 TTTTCTCTACTATTTTTCTTCCTGGATGT
129 TTTCCTCTACTATTTTTCTGCATGGATGC
* * *
1182124 AATTTAAA-TTTTAAAACCTTATTGCACATCTTTAAGACAGCCCCTATCATATTCCAAAATATAA
1 AATTTAAATTTTTAAAACCTTATTGTACATC-TTAAGACAGCCCCTATCATATCCCAAAAGATAA
* * * *
1182188 TGTATATATATTCATTATATCATAAGAGGAATTCTGGGATC-AAGTTTTTTTATGAATGATAAAC
65 TG--TATATATTCATTAAATCATAAGA-G--TTCTGGGATCTAAGTTTTTTAAGGAAGGATAAA-
1182252 GTCAATTTCCGT-TACT-TTTTTACTGCATGGATGC
124 GTCAATTTCC-TCTACTATTTTT-CTGCATGGATGC
** *
1182286 AATTTAAATTTTTTAAAA-CTTACCGTACATCTAAAGGACAGCCCCTATCATATCC
1 AATTTAAA-TTTTTAAAACCTTATTGTACATCTTAA-GACAGCCCCTATCATATCC
1182341 TAAGCGATGG
Statistics
Matches: 177, Mismatches: 29, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
157 44 0.25
158 4 0.02
159 27 0.15
160 1 0.01
161 21 0.12
162 43 0.24
163 29 0.16
164 8 0.05
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (157 bp):
AATTTAAATTTTTAAAACCTTATTGTACATCTTAAGACAGCCCCTATCATATCCCAAAAGATAAT
GTATATATTCATTAAATCATAAGAGTTCTGGGATCTAAGTTTTTTAAGGAAGGATAAAGTCAATT
TCCTCTACTATTTTTCTGCATGGATGC
Found at i:1184817 original size:38 final size:38
Alignment explanation
Indices: 1184764--1185144 Score: 593
Period size: 38 Copynumber: 10.1 Consensus size: 38
1184754 GGGGACGACC
*
1184764 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
* * *
1184802 CCGACCAATACCACAGCCCTAACTGTCGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
** *
1184840 CAGACCAATACCACAGCCCTATTTGTAGGTAAGTGTAG
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
*
1184878 CAGACCAATACCACAGCCCTAACTGTAGTTAAGTGTAT
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
*
1184916 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTTT
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
1184954 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
* *
1184992 CACACCAATACCACAGCCCTAACTGTAGGTAAGTGGAT
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
* *
1185030 CACACCAATACCACAGCCCTAACTGTCGGTAAGTGTAT
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
* *
1185068 CAGACCAATACCACAGCCCTAACTGTCGGT-AGTGTAA
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
* * *
1185105 CAAACCCATACCATAGCCCTAACTGTAGGTAAGTGTAT
1 CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
1185143 CA
1 CA
1185145 AACAAAAGGT
Statistics
Matches: 318, Mismatches: 24, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
37 32 0.10
38 286 0.90
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (38 bp):
CAGACCAATACCACAGCCCTAACTGTAGGTAAGTGTAT
Found at i:1185749 original size:166 final size:167
Alignment explanation
Indices: 1185468--1185801 Score: 445
Period size: 166 Copynumber: 2.0 Consensus size: 167
1185458 GGTGCGTGTC
* * * * ** * *
1185468 TTTAAAAATCTTCTTTTCAAGGACCACTGCACTAGAAATGCAAATTTTTACACAAAAGCTTGTAT
1 TTTAAAAATCTTCCTCTCAAGAACCACTGCACCAGAAATGCAAATAATAACACAAAAGCATGTAT
* * * * ** * *
1185533 ATATTGTGAAAATTCTAAATTGTAAAAATCTTGACCCTCGGATTAAAATTGGGGCCCCAGGTGGG
66 ATATAGTGAAAATTCTAAATTGTAAAAATCGTAACCCTCAGACCAAAATTGAGGCCCCAGGCGGG
* * *
1185598 GTTCAAAGTTCAACATAGAAATATATAGG-AAAATGT
131 GTTCAAAATTAAACATAGAAATACATAGGAAAAATGT
* * *
1185634 TTTAAAAATCTTCCTCTCAAGAATCACTGCACCAGAAATGCCAATAATAACACAAAGGCATGTAT
1 TTTAAAAATCTTCCTCTCAAGAACCACTGCACCAGAAATGCAAATAATAACACAAAAGCATGTAT
*
1185699 ATATAGTGAAGATTCTAAATTGTAAAAATCGTAACCCTCAGACCAAAATTGAGGCCCCAGGCGGG
66 ATATAGTGAAAATTCTAAATTGTAAAAATCGTAACCCTCAGACCAAAATTGAGGCCCCAGGCGGG
*
1185764 GTTCAAAATTAAATATAGAAATACATAGGAAAAATGT
131 GTTCAAAATTAAACATAGAAATACATAGGAAAAATGT
1185801 T
1 T
1185802 AACATGAGTT
Statistics
Matches: 143, Mismatches: 24, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
166 135 0.94
167 8 0.06
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (167 bp):
TTTAAAAATCTTCCTCTCAAGAACCACTGCACCAGAAATGCAAATAATAACACAAAAGCATGTAT
ATATAGTGAAAATTCTAAATTGTAAAAATCGTAACCCTCAGACCAAAATTGAGGCCCCAGGCGGG
GTTCAAAATTAAACATAGAAATACATAGGAAAAATGT
Found at i:1187690 original size:11 final size:11
Alignment explanation
Indices: 1187648--1187690 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1187638 CTAAACCCTA
1187648 GGTTTACTTTCTG
1 GGTTTAC-TT-TG
**
1187661 GGTTTACGCTG
1 GGTTTACTTTG
1187672 GGTTTACTTTG
1 GGTTTACTTTG
1187683 GGTTTACT
1 GGTTTACT
1187691 GAGTGGACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 19 0.73
13 7 0.27
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (11 bp):
GGTTTACTTTG
Found at i:1187933 original size:11 final size:11
Alignment explanation
Indices: 1187891--1187934 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
1187881 CTGCAATTTA
1187891 AAAGTAAACCC
1 AAAGTAAACCC
* *
1187902 AAACTAAACAC
1 AAAGTAAACCC
*
1187913 AGAGTAAACCC
1 AAAGTAAACCC
1187924 AAAGTAAACCC
1 AAAGTAAACCC
1187935 CGAGTGGACC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.55, C:0.27, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAGTAAACCC
Found at i:1188548 original size:42 final size:42
Alignment explanation
Indices: 1188489--1188571 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1188479 TAATGTAGTG
*
1188489 GAACCAAGACTTATCTTTCTTGATGTTGTTCTGTACAGTCTA
1 GAACCAAAACTTATCTTTCTTGATGTTGTTCTGTACAGTCTA
*
1188531 GAACCAAAAGTTATCTTTCTTGATGTTGTTCTGTACAGTCT
1 GAACCAAAACTTATCTTTCTTGATGTTGTTCTGTACAGTCT
1188572 GAGAGTTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (42 bp):
GAACCAAAACTTATCTTTCTTGATGTTGTTCTGTACAGTCTA
Found at i:1189179 original size:42 final size:42
Alignment explanation
Indices: 1189133--1189246 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
1189123 CATGAAACAA
*
1189133 ACCTTCTACCCCAGGGGAACTTAACTCTACCCCAGGAGTACG
1 ACCTTCTACCCCAGGGGAACTTAACTCGACCCCAGGAGTACG
* ** *
1189175 ACCTTCCACCCCAGGGGAACTTTTCTCGACCCCAGGAGTACT
1 ACCTTCTACCCCAGGGGAACTTAACTCGACCCCAGGAGTACG
* * *
1189217 ACCTTCTACCACAGGGGGACTTATCTCGAC
1 ACCTTCTACCCCAGGGGAACTTAACTCGAC
1189247 TCCATCAGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (42 bp):
ACCTTCTACCCCAGGGGAACTTAACTCGACCCCAGGAGTACG
Found at i:1194356 original size:8 final size:8
Alignment explanation
Indices: 1194335--1194400 Score: 80
Period size: 8 Copynumber: 8.4 Consensus size: 8
1194325 GATCACTTTT
1194335 TGTCCGTC
1 TGTCCGTC
1194343 -GTCCGTC
1 TGTCCGTC
1194350 TGTCCGTC
1 TGTCCGTC
*
1194358 CGTCCGTC
1 TGTCCGTC
1194366 TGTCCGTC
1 TGTCCGTC
* *
1194374 CGTCTGTC
1 TGTCCGTC
* *
1194382 CGTCTGTC
1 TGTCCGTC
1194390 TGTCCGTC
1 TGTCCGTC
1194398 TGT
1 TGT
1194401 AAACTTTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
7 7 0.14
8 44 0.86
ACGTcount: A:0.00, C:0.38, G:0.26, T:0.36
Consensus pattern (8 bp):
TGTCCGTC
Found at i:1194358 original size:4 final size:4
Alignment explanation
Indices: 1194336--1194397 Score: 72
Period size: 4 Copynumber: 15.8 Consensus size: 4
1194326 ATCACTTTTT
* * *
1194336 GTCC GT-C GTCC GTCT GTCC GTCC GTCC GTCT GTCC GTCC GTCT GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
* *
1194383 GTCT GTCT GTCC GTC
1 GTCC GTCC GTCC GTC
1194398 TGTAAACTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 3 0.06
4 46 0.94
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34
Consensus pattern (4 bp):
GTCC
Found at i:1194359 original size:12 final size:12
Alignment explanation
Indices: 1194336--1194397 Score: 90
Period size: 12 Copynumber: 5.2 Consensus size: 12
1194326 ATCACTTTTT
1194336 GTCCGTC-GTCC
1 GTCCGTCTGTCC
* *
1194347 GTCTGTCCGTCC
1 GTCCGTCTGTCC
1194359 GTCCGTCTGTCC
1 GTCCGTCTGTCC
1194371 GTCCGTCTGTCC
1 GTCCGTCTGTCC
*
1194383 GTCTGTCTGTCC
1 GTCCGTCTGTCC
1194395 GTC
1 GTC
1194398 TGTAAACTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
11 6 0.13
12 40 0.87
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:1195991 original size:186 final size:186
Alignment explanation
Indices: 1195734--1196106 Score: 746
Period size: 186 Copynumber: 2.0 Consensus size: 186
1195724 AAGTAAAAAA
1195734 AATTGTCAAAATTTATTAAGAAAATTTTCAAAGTCTGTTCTTCCAGAAACAAACTTTAACAACTT
1 AATTGTCAAAATTTATTAAGAAAATTTTCAAAGTCTGTTCTTCCAGAAACAAACTTTAACAACTT
1195799 ATTGTATTGTAAACTTAACCTTTTTTAGCTCACCTGAGCCAAAGGCTCAAGTGAGCTTTTCTGAT
66 ATTGTATTGTAAACTTAACCTTTTTTAGCTCACCTGAGCCAAAGGCTCAAGTGAGCTTTTCTGAT
1195864 CACAATTTCTCCGTTGTCTGTCGTCGTCGTTGTTGTCGTTGTTGTAAACTTTTCAC
131 CACAATTTCTCCGTTGTCTGTCGTCGTCGTTGTTGTCGTTGTTGTAAACTTTTCAC
1195920 AATTGTCAAAATTTATTAAGAAAATTTTCAAAGTCTGTTCTTCCAGAAACAAACTTTAACAACTT
1 AATTGTCAAAATTTATTAAGAAAATTTTCAAAGTCTGTTCTTCCAGAAACAAACTTTAACAACTT
1195985 ATTGTATTGTAAACTTAACCTTTTTTAGCTCACCTGAGCCAAAGGCTCAAGTGAGCTTTTCTGAT
66 ATTGTATTGTAAACTTAACCTTTTTTAGCTCACCTGAGCCAAAGGCTCAAGTGAGCTTTTCTGAT
1196050 CACAATTTCTCCGTTGTCTGTCGTCGTCGTTGTTGTCGTTGTTGTAAACTTTTCAC
131 CACAATTTCTCCGTTGTCTGTCGTCGTCGTTGTTGTCGTTGTTGTAAACTTTTCAC
1196106 A
1 A
1196107 TTTTCATCTT
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
186 187 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (186 bp):
AATTGTCAAAATTTATTAAGAAAATTTTCAAAGTCTGTTCTTCCAGAAACAAACTTTAACAACTT
ATTGTATTGTAAACTTAACCTTTTTTAGCTCACCTGAGCCAAAGGCTCAAGTGAGCTTTTCTGAT
CACAATTTCTCCGTTGTCTGTCGTCGTCGTTGTTGTCGTTGTTGTAAACTTTTCAC
Found at i:1196532 original size:165 final size:165
Alignment explanation
Indices: 1196261--1197082 Score: 786
Period size: 166 Copynumber: 5.0 Consensus size: 165
1196251 GTTGGTATTT
* * * * * * * *
1196261 TTTAAAAATCTTCTTCTCAAAAACTATTCGGCC-TGAAAGCTTAAACTTGTGTGGAGGCATCATT
1 TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTC
* *
1196325 AGGTAGTGTAGATTCAAGTTTGATCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATAGGG
66 AGATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAAT-GGG
*
1196390 GG-T-CATGTTTTACATAGGAATATATAGAGAAAATC
130 GGATAAAT-TTTTACATAGGAATATATAGAGAAAATC
1196425 TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTC
1 TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTC
*
1196490 AGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGG
66 AGATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAA-TGGG
* ** * * *
1196555 GGATCAGGTTTTATATCGGAATATATAGAGGAAATC
130 GGATAAATTTTTACATAGGAATATATAGAGAAAATC
* * * * * *
1196591 TTTTAAAAATCTTCTTCTC-AAAATTATTTGGCCAAGAAAGCTCAAATTGGCA-TGTAACCATCC
1 -TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTG-AGTGGAAGCATCC
* * * * *
1196654 TTAGGA-AGTGTAGATTCAAGTTTGTTCAAATCATTGTCCCTGGGGGTAGGGCGGGGTCACAATG
64 TCA-GATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATG
1196718 GGGGATAAATTTTT--ATA-G-----ATAGAGAAAATC
128 GGGGATAAATTTTTACATAGGAATATATAGAGAAAATC
* * *
1196748 TTTAAAAGTCTTCTTCTCAAAAA-TATTAGGCCAGGAAAGCCCAAATTTGAGTGGAAGCATCCCC
1 TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTC
* * * * * * * *
1196812 AGATCA-TATAGATTCAAATTTGTTTAAATAATAGT--CCAGTGGTATGGTGAGGCCACAATGGG
66 AGAT-AGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATGGG
* *
1196874 GGATGAATTTTTACTTAGGAATATATAGAGAAAATC
130 GGATAAATTTTTACATAGGAATATATAGAGAAAATC
* * * * * * * * * *
1196910 TTTAAAAATCTTCTTTTTAAAGACTATTTGGCCAGAAAAGGTTTAAAATTGTA-TAGAGGCATCC
1 TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAA-GCTCAAATTTG-AGTGGAAGCATCC
* * * * ** * * * ***
1196974 TCCGGTAGTGTAAATTCAAGTTTG--CAAAATCACAGTCCCTAGTGGTAGGGCGGGACCGTGATG
64 TCAGATAGTGTAGATTCAAGTTTGTTC-AAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATG
** * *
1197037 GCGGTTTGAATTTTTACATAGGAATATAAAGAGAAAATC
128 G-GGGATAAATTTTTACATAGGAATATATAGAGAAAATC
1197076 TTTAAAA
1 TTTAAAA
1197083 GTATTCTTGG
Statistics
Matches: 542, Mismatches: 89, Indels: 52
0.79 0.13 0.08
Matches are distributed among these distances:
154 31 0.06
155 3 0.01
156 75 0.14
157 17 0.03
162 32 0.06
163 24 0.04
164 64 0.12
165 118 0.22
166 157 0.29
167 21 0.04
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (165 bp):
TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTC
AGATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATGGGG
GATAAATTTTTACATAGGAATATATAGAGAAAATC
Found at i:1196703 original size:331 final size:318
Alignment explanation
Indices: 1196260--1196947 Score: 832
Period size: 331 Copynumber: 2.1 Consensus size: 318
1196250 TGTTGGTATT
* * * **
1196260 TTTTAAAAATCTTCTTCTCAAAAACTATTCGGCCTGAAAGCTTAAACTTGTGTGGAGGCATCATT
1 TTTTAAAAATCTTCTTCTC-AAAACTATTTGGCCAGAAAGCTCAAACTTGTGTGGAACCATCATT
* *
1196325 AGGTAGTGTAGATTCAAGTTTGATCAAATCATAGTCCCCGGGGGTAGGGTGGGGCCACAATAGGG
65 AGGAAGTGTAGATTCAAGTTTGATCAAATCATAGTCCCCGGGGGTAGGGCGGGGCCACAAT-GGG
*
1196390 GG-T-CATGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATT
129 GGATAAAT-TTTT--ATA-G-----ATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAA-TATT
* * * *
1196453 AGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGAT-AGTGTAGATTCAAGTTTGTTCAA
184 AGGCCAGGAAAGCCCAAATTTGAGTGGAAGCATCCCCAGATCA-TATAGATTCAAATTTGTTCAA
* * * * * *
1196517 ATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAGGTTTTA-TATCGGAATATAT
248 ATAATAGT--CCAGGGGTAGGGTGAGGCCACAA-TGGGGGATCAAGTTTTACT-TAGGAATATAT
*
1196581 AGAGGAAATC
309 AGAGAAAATC
* * *
1196591 TTTTAAAAATCTTCTTCTCAAAATTATTTGGCCAAGAAAGCTCAAA-TTG-GCATGTAACCATCC
1 TTTTAAAAATCTTCTTCTCAAAACTATTTGGCC-AGAAAGCTCAAACTTGTG--TGGAACCATCA
* * * *
1196654 TTAGGAAGTGTAGATTCAAGTTTGTTCAAATCATTGTCCCTGGGGGTAGGGCGGGGTCACAATGG
63 TTAGGAAGTGTAGATTCAAGTTTGATCAAATCATAGTCCCCGGGGGTAGGGCGGGGCCACAATGG
*
1196719 GGGATAAATTTTTATAGATAGAGAAAATCTTTAAAAGTCTTCTTCTCAAAAATATTAGGCCAGGA
128 GGGATAAATTTTTATAGATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAATATTAGGCCAGGA
*
1196784 AAGCCCAAATTTGAGTGGAAGCATCCCCAGATCATATAGATTCAAATTTGTTTAAATAATAGTCC
193 AAGCCCAAATTTGAGTGGAAGCATCCCCAGATCATATAGATTCAAATTTGTTCAAATAATAGTCC
* * * *
1196849 AGTGGTATGGTGAGGCCACAATGGGGGATGAATTTTTACTTAGGAATATATAGAGAAAATC
258 AGGGGTAGGGTGAGGCCACAATGGGGGATCAAGTTTTACTTAGGAATATATAGAGAAAATC
* *
1196910 -TTTAAAAATCTTCTTTTTAAAGACTATTTGGCCAGAAA
1 TTTTAAAAATCTTCTTCTCAAA-ACTATTTGGCCAGAAA
1196948 AGGTTTAAAA
Statistics
Matches: 314, Mismatches: 35, Indels: 29
0.83 0.09 0.08
Matches are distributed among these distances:
318 24 0.08
319 43 0.14
320 20 0.06
322 67 0.21
323 35 0.11
328 1 0.00
329 4 0.01
330 20 0.06
331 98 0.31
332 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (318 bp):
TTTTAAAAATCTTCTTCTCAAAACTATTTGGCCAGAAAGCTCAAACTTGTGTGGAACCATCATTA
GGAAGTGTAGATTCAAGTTTGATCAAATCATAGTCCCCGGGGGTAGGGCGGGGCCACAATGGGGG
ATAAATTTTTATAGATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAATATTAGGCCAGGAAAG
CCCAAATTTGAGTGGAAGCATCCCCAGATCATATAGATTCAAATTTGTTCAAATAATAGTCCAGG
GGTAGGGTGAGGCCACAATGGGGGATCAAGTTTTACTTAGGAATATATAGAGAAAATC
Found at i:1197862 original size:2 final size:2
Alignment explanation
Indices: 1197855--1197897 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1197845 TCCATAACAC
1197855 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1197897 T
1 T
1197898 AAATTGCACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1198004 original size:163 final size:165
Alignment explanation
Indices: 1197710--1198014 Score: 515
Period size: 163 Copynumber: 1.8 Consensus size: 165
1197700 GGGTGGGTGG
1197710 GTGTGTGTGTGTGTGTGACAAAATTGCACAATCTCTGTCTGGAAGGAAAAATTAGAACAGAGTAC
1 GTGTGTGTGTGTGTGTGACAAAATTGCACAATCTCTGTCTGGAAGGAAAAATTAGAACAGAG-A-
* *
1197775 TAGTTTGGTATTTTAAAATCTGAATCGGTTAACTAAATTTATAACTGTCGCATTAGCATTCTGAT
64 TA-TCTGGTATTTTAAAATCTAAATCGGTTAACTAAATTTATAACTGTCGCATTAGCATTCTGAT
1197840 TGGCTTCCATAACACTGTGTGTGTGTGTGTGTGTGTGT
128 TGGCTTCCATAACACTGTGTGTGTGTGTGTGTGTGTGT
***
1197878 GTGTGTGTGTGTGTGTGTGTAAATTGCACAATCTCTGTCTGGAAGGAAAAATTAGAACAGAG-T-
1 GTGTGTGTGTGTGTGTGACAAAATTGCACAATCTCTGTCTGGAAGGAAAAATTAGAACAGAGATA
*
1197941 TCTGGTATTTTAAAATCTAAATCGGTTAACTAAATTTATAACTTTCGCATTAGCATTCTGATTGG
66 TCTGGTATTTTAAAATCTAAATCGGTTAACTAAATTTATAACTGTCGCATTAGCATTCTGATTGG
1198006 CTTCCATAA
131 CTTCCATAA
1198015 TACATTTATA
Statistics
Matches: 131, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
163 71 0.54
165 1 0.01
168 59 0.45
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (165 bp):
GTGTGTGTGTGTGTGTGACAAAATTGCACAATCTCTGTCTGGAAGGAAAAATTAGAACAGAGATA
TCTGGTATTTTAAAATCTAAATCGGTTAACTAAATTTATAACTGTCGCATTAGCATTCTGATTGG
CTTCCATAACACTGTGTGTGTGTGTGTGTGTGTGT
Found at i:1198399 original size:16 final size:16
Alignment explanation
Indices: 1198371--1199007 Score: 506
Period size: 16 Copynumber: 37.6 Consensus size: 16
1198361 AAGAATTTTT
*
1198371 ATGCTACATTACAATG
1 ATGCTGCATTACAATG
* *
1198387 ATGTTGTATTACAATG
1 ATGCTGCATTACAATG
*
1198403 ATGCTGCATTGCAATG
1 ATGCTGCATTACAATG
* *
1198419 ATGCTACATTTCAATG
1 ATGCTGCATTACAATG
1198435 ATGCTGCATTA-ATATG
1 ATGCTGCATTACA-ATG
*
1198451 ATGCTGTATTACAATG
1 ATGCTGCATTACAATG
* * *
1198467 ATGCTGTAGTAGAATG
1 ATGCTGCATTACAATG
** *
1198483 ATTATACATTACAATG
1 ATGCTGCATTACAATG
1198499 ATGCTGCATTACAATG
1 ATGCTGCATTACAATG
* *
1198515 AAGCTACATTACAATG
1 ATGCTGCATTACAATG
* *
1198531 ATGCTGTATTACAATA
1 ATGCTGCATTACAATG
* * *
1198547 ATACTGCATGACAATT
1 ATGCTGCATTACAATG
1198563 ATGCTGCATTACATAACAATG
1 ATGCTGCA-T---T-ACAATG
*
1198584 ATGCTACATTACAATG
1 ATGCTGCATTACAATG
* * * *
1198600 ACGCTACATTGCAAAG
1 ATGCTGCATTACAATG
1198616 ATGCTGCATTACAATG
1 ATGCTGCATTACAATG
* *
1198632 ATTCGGCATTACAATG
1 ATGCTGCATTACAATG
*
1198648 ATGCCGCATTACAATG
1 ATGCTGCATTACAATG
1198664 ATGCTGCATTACATTACAATG
1 ATGCTG-----CATTACAATG
1198685 ATGCTAG-ATTGA-AATG
1 ATGCT-GCATT-ACAATG
* *
1198701 TTGCTGCATTACAATT
1 ATGCTGCATTACAATG
* *
1198717 ATTCTGCAGTACAATG
1 ATGCTGCATTACAATG
* *
1198733 ATGCTACATTACAGTG
1 ATGCTGCATTACAATG
*
1198749 ATGCTGTATTACAATG
1 ATGCTGCATTACAATG
1198765 ATGCTGCATTACAATG
1 ATGCTGCATTACAATG
*
1198781 GTGCTGCATTACAATG
1 ATGCTGCATTACAATG
*
1198797 ATGCTGCATTACATTACAACG
1 ATGCTG-----CATTACAATG
*
1198818 ATGCTGCATTACATTACAACG
1 ATGCTG-----CATTACAATG
1198839 ATGCTGTATTACATTACAATG
1 ATGCTG-----CATTACAATG
1198860 ATGCTGCATTGCATTACAATG
1 A---TGC--TGCATTACAATG
*
1198881 ATGCTACATTACAATG
1 ATGCTGCATTACAATG
1198897 ATGCTGCATTACAATG
1 ATGCTGCATTACAATG
1198913 ATGCTGCATTACAATG
1 ATGCTGCATTACAATG
1198929 ATGCTGTATTACATTACAATG
1 ATGCTG-----CATTACAATG
* *
1198950 ATGCTACCTTACAATG
1 ATGCTGCATTACAATG
* * *
1198966 TTGCTACATTGCAATG
1 ATGCTGCATTACAATG
*
1198982 ATGCTGCATTACAATC
1 ATGCTGCATTACAATG
1198998 ATGCTGCATT
1 ATGCTGCATT
1199008 GCAAGCTCTC
Statistics
Matches: 512, Mismatches: 78, Indels: 62
0.79 0.12 0.10
Matches are distributed among these distances:
15 3 0.01
16 392 0.77
17 4 0.01
18 3 0.01
20 1 0.00
21 103 0.20
22 1 0.00
24 3 0.01
26 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (16 bp):
ATGCTGCATTACAATG
Found at i:1198581 original size:21 final size:21
Alignment explanation
Indices: 1198557--1198596 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1198547 ATACTGCATG
* *
1198557 ACAATTATGCTGCATTACATA
1 ACAATGATGCTACATTACATA
1198578 ACAATGATGCTACATTACA
1 ACAATGATGCTACATTACA
1198597 ATGACGCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (21 bp):
ACAATGATGCTACATTACATA
Found at i:1198623 original size:69 final size:69
Alignment explanation
Indices: 1198509--1198644 Score: 166
Period size: 69 Copynumber: 2.0 Consensus size: 69
1198499 ATGCTGCATT
* ** * *
1198509 ACAATGAAGCTACATTACAATGATGCTGTATTACAATAATACTGCATGACAATTATGCTGCATTA
1 ACAATGAAGCTACATTACAATGACGCTACATTACAATAATACTGCATGACAATGATGCGGCATTA
1198574 CATA
66 CATA
* * * * *
1198578 ACAATGATGCTACATTACAATGACGCTACATTGCAA-AGATGCTGCATTACAATGATTCGGCATT
1 ACAATGAAGCTACATTACAATGACGCTACATTACAATA-ATACTGCATGACAATGATGCGGCATT
1198642 ACA
65 ACA
1198645 ATGATGCCGC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 1 0.02
69 55 0.98
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (69 bp):
ACAATGAAGCTACATTACAATGACGCTACATTACAATAATACTGCATGACAATGATGCGGCATTA
CATA
Found at i:1198962 original size:21 final size:21
Alignment explanation
Indices: 1198787--1198954 Score: 186
Period size: 21 Copynumber: 8.7 Consensus size: 21
1198777 AATGGTGCTG
1198787 CATTACAATGATGCTGCATTA
1 CATTACAATGATGCTGCATTA
*
1198808 CATTACAACGATGCTGCATTA
1 CATTACAATGATGCTGCATTA
* *
1198829 CATTACAACGATGCTGTATTA
1 CATTACAATGATGCTGCATTA
*
1198850 CATTACAATGATGCTGCATTG
1 CATTACAATGATGCTGCATTA
1198871 CATTACAATGA---TGC--TA
1 CATTACAATGATGCTGCATTA
1198887 CATTACAATGATGCTG-----
1 CATTACAATGATGCTGCATTA
1198903 CATTACAATGATGCTGCA---
1 CATTACAATGATGCTGCATTA
*
1198921 --TTACAATGATGCTGTATTA
1 CATTACAATGATGCTGCATTA
1198940 CATTACAATGATGCT
1 CATTACAATGATGCT
1198955 ACCTTACAAT
Statistics
Matches: 130, Mismatches: 7, Indels: 20
0.83 0.04 0.13
Matches are distributed among these distances:
16 43 0.33
18 3 0.02
19 2 0.02
21 82 0.63
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (21 bp):
CATTACAATGATGCTGCATTA
Found at i:1203368 original size:20 final size:20
Alignment explanation
Indices: 1203343--1203447 Score: 101
Period size: 20 Copynumber: 5.3 Consensus size: 20
1203333 GTACTGTAAA
1203343 ATATACCATGTACATCATAG
1 ATATACCATGTACATCATAG
* *
1203363 ATATACCATTTACA-CAGTGAA
1 ATATACCATGTACATCA-T-AG
1203384 ATATACCATGTACATCATAG
1 ATATACCATGTACATCATAG
* * * *
1203404 ATATACCATTTACACCGTAAA
1 ATATACCATGTACATCAT-AG
1203425 ATATACCATGT--AT-ATAG
1 ATATACCATGTACATCATAG
1203442 ATATAC
1 ATATAC
1203448 TATTTACACT
Statistics
Matches: 69, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
17 7 0.10
18 1 0.01
19 3 0.04
20 30 0.43
21 26 0.38
22 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (20 bp):
ATATACCATGTACATCATAG
Found at i:1203398 original size:41 final size:41
Alignment explanation
Indices: 1203335--1203685 Score: 366
Period size: 41 Copynumber: 8.5 Consensus size: 41
1203325 GTGGGAGTGT
1203335 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC
1 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC
* *
1203376 ACAGTGAAATATACCATGTACATCATAGATATACCATTTAC
1 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC
* *
1203417 ACCGTAAAATATACCATGT--AT-ATAGATATACTATTTAC
1 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC
*
1203455 ACTGTAAAATATACCATGT--AT-ATAGATATACTATTTAC
1 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC
*
1203493 ACTGTAAAATATACCATGTACA-C---CATATACCATTTAC
1 ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC
* * *
1203530 ACTGTGAAAA-ATACTATGTACACCATAGATATACAATTTAC
1 ACTGT-AAAATATACCATGTACATCATAGATATACCATTTAC
* * *
1203571 ACTGTGAAATATACCATGTACACTGTAAAATATACCATGATATACCGTTTAC
1 ACTGTAAAATATACCATGTACA---T----CAT---A-GATATACCATTTAC
* *
1203623 ACTGTAAAATATACCATGTACACCATAGATATTA-TATTTAC
1 ACTGTAAAATATACCATGTACATCATAGATA-TACCATTTAC
*
1203664 ACTGTAAAATATACCACGTACA
1 ACTGTAAAATATACCATGTACA
1203686 CTGTAAAATA
Statistics
Matches: 266, Mismatches: 23, Indels: 42
0.80 0.07 0.13
Matches are distributed among these distances:
37 28 0.11
38 77 0.29
39 2 0.01
40 4 0.02
41 114 0.43
42 3 0.01
45 2 0.01
48 2 0.01
51 1 0.00
52 33 0.12
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.31
Consensus pattern (41 bp):
ACTGTAAAATATACCATGTACATCATAGATATACCATTTAC
Found at i:1203447 original size:17 final size:17
Alignment explanation
Indices: 1203425--1203485 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
1203415 ACACCGTAAA
1203425 ATATACCATGTATATAG
1 ATATACCATGTATATAG
* * * *
1203442 ATATACTATTTACACTGTAAA
1 ATATACCATGT--A-TAT-AG
1203463 ATATACCATGTATATAG
1 ATATACCATGTATATAG
1203480 ATATAC
1 ATATAC
1203486 TATTTACACT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
17 16 0.50
18 2 0.06
19 2 0.06
20 2 0.06
21 10 0.31
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (17 bp):
ATATACCATGTATATAG
Found at i:1203522 original size:16 final size:16
Alignment explanation
Indices: 1203501--1203531 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1203491 ACACTGTAAA
1203501 ATATACCATGTACACC
1 ATATACCATGTACACC
*
1203517 ATATACCATTTACAC
1 ATATACCATGTACAC
1203532 TGTGAAAAAT
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:0.39, C:0.29, G:0.03, T:0.29
Consensus pattern (16 bp):
ATATACCATGTACACC
Found at i:1203609 original size:21 final size:21
Alignment explanation
Indices: 1203480--1203609 Score: 103
Period size: 21 Copynumber: 6.5 Consensus size: 21
1203470 ATGTATATAG
* *
1203480 ATATACTATTTACACTGTAAA
1 ATATACCATGTACACTGTAAA
*
1203501 ATATACCATGTACAC-----C
1 ATATACCATGTACACTGTAAA
*
1203517 ATATACCATTTACACTGTGAAA
1 ATATACCATGTACACTGT-AAA
* ** *
1203539 A-ATACTATGTACACCAT-AG
1 ATATACCATGTACACTGTAAA
* * *
1203558 ATATACAATTTACACTGTGAA
1 ATATACCATGTACACTGTAAA
1203579 ATATACCATGTACACTGTAAA
1 ATATACCATGTACACTGTAAA
1203600 ATATACCATG
1 ATATACCATG
1203610 ATATACCGTT
Statistics
Matches: 83, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
16 14 0.17
19 2 0.02
20 12 0.14
21 54 0.65
22 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (21 bp):
ATATACCATGTACACTGTAAA
Found at i:1203614 original size:31 final size:31
Alignment explanation
Indices: 1203579--1203648 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
1203569 ACACTGTGAA
1203579 ATATACCATGTACACTGTAAAATATACCATG
1 ATATACCATGTACACTGTAAAATATACCATG
* *
1203610 ATATACCGTTTACACTGTAAAATATACCATG
1 ATATACCATGTACACTGTAAAATATACCATG
*
1203641 -TACACCAT
1 ATATACCAT
1203649 AGATATTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 6 0.17
31 29 0.83
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (31 bp):
ATATACCATGTACACTGTAAAATATACCATG
Found at i:1203636 original size:21 final size:21
Alignment explanation
Indices: 1203610--1203758 Score: 95
Period size: 21 Copynumber: 6.8 Consensus size: 21
1203600 ATATACCATG
* *
1203610 ATATACCGTTTACACTGTAAA
1 ATATACCATGTACACTGTAAA
** *
1203631 ATATACCATGTACACCAT-AG
1 ATATACCATGTACACTGTAAA
* *
1203651 ATATTA-TATTTACACTGTAAA
1 ATA-TACCATGTACACTGTAAA
*
1203672 ATATACCACGTACACTGTAAAATATAAA
1 ATATACCATGTACACTG-------TAAA
*
1203700 ATATACCATGTACACTGTAGA
1 ATATACCATGTACACTGTAAA
* *
1203721 ATATACAATGTACACTGCAAAA
1 ATATACCATGTACACTG-TAAA
*
1203743 ATATACCATATACACT
1 ATATACCATGTACACT
1203759 CTATTGGACT
Statistics
Matches: 97, Mismatches: 20, Indels: 21
0.70 0.14 0.15
Matches are distributed among these distances:
20 14 0.14
21 47 0.48
22 16 0.16
28 20 0.21
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.30
Consensus pattern (21 bp):
ATATACCATGTACACTGTAAA
Found at i:1203647 original size:93 final size:93
Alignment explanation
Indices: 1203480--1203735 Score: 306
Period size: 93 Copynumber: 2.7 Consensus size: 93
1203470 ATGTATATAG
* *
1203480 ATATACTATTTACACTGTAAAATATACCATGTACACCATATACCATTTACACTGTGAAAA-ATAC
1 ATATACCATGTACACTGTAAAATATACCATG------ATATACCATTTACACTGT-AAAATATAC
* *
1203544 TATGTACACCATAGATA-TACAATTTACACTGTGAA
59 AATGTACACCATAGATATTA-AATTTACACTGTAAA
* *
1203579 ATATACCATGTACACTGTAAAATATACCATGATATACCGTTTACACTGTAAAATATACCATGTAC
1 ATATACCATGTACACTGTAAAATATACCATGATATACCATTTACACTGTAAAATATACAATGTAC
*
1203644 ACCATAGATATTATATTTACACTGTAAA
66 ACCATAGATATTAAATTTACACTGTAAA
* * * *
1203672 ATATACCACGTACACTGTAAAATATA--A-AATATACCATGTACACTGTAGAATATACAATGTAC
1 ATATACCATGTACACTGTAAAATATACCATGATATACCATTTACACTGTAAAATATACAATGTAC
1203734 AC
66 AC
1203736 TGCAAAAATA
Statistics
Matches: 143, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
90 32 0.22
91 1 0.01
92 4 0.03
93 75 0.52
94 2 0.01
99 29 0.20
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (93 bp):
ATATACCATGTACACTGTAAAATATACCATGATATACCATTTACACTGTAAAATATACAATGTAC
ACCATAGATATTAAATTTACACTGTAAA
Found at i:1203712 original size:28 final size:28
Alignment explanation
Indices: 1203668--1203725 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1203658 ATTTACACTG
1203668 TAAAATATACCACGTACACTGTAAAATA
1 TAAAATATACCACGTACACTGTAAAATA
* *
1203696 TAAAATATACCATGTACACTGTAGAATA
1 TAAAATATACCACGTACACTGTAAAATA
1203724 TA
1 TA
1203726 CAATGTACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.28
Consensus pattern (28 bp):
TAAAATATACCACGTACACTGTAAAATA
Found at i:1204880 original size:4 final size:4
Alignment explanation
Indices: 1204873--1204953 Score: 63
Period size: 4 Copynumber: 20.2 Consensus size: 4
1204863 ATTTCTTCAT
* * * * *
1204873 TCAA TCAA TCAC TCAC TCAA TCAA TCAA TCAA TCGA TCGA CCAA TCAA
1 TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA
* ** * * *
1204921 TCGA TTGA TCAA TCAA TCGA TCGA CCAA TCAA T
1 TCAA TCAA TCAA TCAA TCAA TCAA TCAA TCAA T
1204954 TGATCAATTA
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 63 1.00
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (4 bp):
TCAA
Found at i:1204917 original size:16 final size:16
Alignment explanation
Indices: 1204898--1204958 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
1204888 CTCAATCAAT
1204898 CAATCAATCGATCGAC
1 CAATCAATCGATCGAC
* *
1204914 CAATCAATCGATTGAT
1 CAATCAATCGATCGAC
1204930 CAATCAATCGATCGAC
1 CAATCAATCGATCGAC
*
1204946 CAATCAATTGATC
1 CAATCAATCGATC
1204959 AATTAACCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (16 bp):
CAATCAATCGATCGAC
Found at i:1209517 original size:21 final size:21
Alignment explanation
Indices: 1209493--1209579 Score: 111
Period size: 21 Copynumber: 4.1 Consensus size: 21
1209483 GACCGTGGTG
1209493 GTTGTTGCTGGAATAGTTGTT
1 GTTGTTGCTGGAATAGTTGTT
*
1209514 GTTGTTGCTGGGATAGTTGTT
1 GTTGTTGCTGGAATAGTTGTT
* * * * *
1209535 GTTGTTGTTTGAATTGTGGTG
1 GTTGTTGCTGGAATAGTTGTT
*
1209556 GTTGTTGTTGGAATAGTTGTT
1 GTTGTTGCTGGAATAGTTGTT
1209577 GTT
1 GTT
1209580 AGTTCAGCAG
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.11, C:0.02, G:0.36, T:0.51
Consensus pattern (21 bp):
GTTGTTGCTGGAATAGTTGTT
Found at i:1209610 original size:18 final size:18
Alignment explanation
Indices: 1209571--1210274 Score: 261
Period size: 18 Copynumber: 37.8 Consensus size: 18
1209561 TGTTGGAATA
* **
1209571 GTTGTTGTTAGTTCAGCA
1 GTTGTTGTTTGTTCAGTG
*
1209589 GTTGTTGTTTGTTGAGTGG
1 GTTGTTGTTTGTTCAGT-G
*
1209608 TTGTTGTTGTTATTGGCTCAGTG
1 --GTTGTTG-T-TT-GTTCAGTG
*
1209631 GTTGTTGTTTGTTCTGTTG
1 GTTGTTGTTTGTTCAG-TG
* *
1209650 TTGTTGTTGTAATTGGCTCAGTT
1 --GTTGTTGT--TT-GTTCAGTG
*
1209673 GTTGTTGTTTGTTCAGTA
1 GTTGTTGTTTGTTCAGTG
1209691 GTTGTTGTAATTGGTTCAGTG
1 GTTGTTGT--TT-GTTCAGTG
* *
1209712 GATGTTGTTTGTTCTGTAGTT
1 GTTGTTGTTTGTTC---AGTG
*
1209733 GTTGTTATTTGTTCAGTG
1 GTTGTTGTTTGTTCAGTG
**** *
1209751 GTTGTTGTCAACTCAATG
1 GTTGTTGTTTGTTCAGTG
*
1209769 GTGGTTGTTTGTTCAGTG
1 GTTGTTGTTTGTTCAGTG
* *
1209787 GTTGTTGTTTGTTCTGTT
1 GTTGTTGTTTGTTCAGTG
1209805 GTTGTTGTTATTGGTTCAGTG
1 GTTGTTG-T-TT-GTTCAGTG
* *
1209826 GATGTTGTTTGTTCTA-TT
1 GTTGTTGTTTGTTC-AGTG
1209844 GTTGTTGTGATTGGTTCAGTG
1 GTTGTTGT--TT-GTTCAGTG
**
1209865 GTTG-TAATTGATTCAGTG
1 GTTGTTGTTTG-TTCAGTG
* *
1209883 GTTGTTGTTTGTTCTGTT
1 GTTGTTGTTTGTTCAGTG
* *
1209901 GTTGTTGATTGTTCAGTA
1 GTTGTTGTTTGTTCAGTG
* * *
1209919 GTCGATGTTTGTTCA-TCA
1 GTTGTTGTTTGTTCAGT-G
*
1209937 GTTGTTGTTGGTT--GCTG
1 GTTGTTGTTTGTTCAG-TG
*
1209954 AGTTGTTGTTTGTTC-CTCG
1 -GTTGTTGTTTGTTCAGT-G
* * **
1209973 GTGGTTGTTTGTTCTGCA
1 GTTGTTGTTTGTTCAGTG
* * *
1209991 GTTGTTGTTTGCTC-CTCA
1 GTTGTTGTTTGTTCAGT-G
* **
1210009 GTTGTTGTTTGTTCTGCA
1 GTTGTTGTTTGTTCAGTG
*
1210027 GTTGTTGTTTG--CATTTCG
1 GTTGTTGTTTGTTCA-GT-G
**
1210045 GTTGTTGTTTGTTCAGCA
1 GTTGTTGTTTGTTCAGTG
* *
1210063 GTTGTTGTTTGTTC-CTCA
1 GTTGTTGTTTGTTCAGT-G
* * * *
1210081 GTAGTTGTTTGCTC-CTCA
1 GTTGTTGTTTGTTCAGT-G
* **
1210099 GTTGTTGTTTGTTCTGCA
1 GTTGTTGTTTGTTCAGTG
* *
1210117 GTTGTTGTTTGCTC-TTCG
1 GTTGTTGTTTGTTCAGT-G
* **
1210135 GTTGTTGTTTGTTGAGCA
1 GTTGTTGTTTGTTCAGTG
* *
1210153 GTTGTTGTTTGTTC-CTCA
1 GTTGTTGTTTGTTCAGT-G
* *
1210171 GTTGTTGTTTGTTC-TTCA
1 GTTGTTGTTTGTTCAGT-G
* * *
1210189 GTTGTTGTTTGCTC-CTCA
1 GTTGTTGTTTGTTCAGT-G
* **
1210207 GTTGTTGTTTGTTCTGCA
1 GTTGTTGTTTGTTCAGTG
* *
1210225 GTTGTTGTTTGCTC-TTCG
1 GTTGTTGTTTGTTCAGT-G
* **
1210243 GTTGTTGTTTGTTCTGCA
1 GTTGTTGTTTGTTCAGTG
1210261 GTTGTTGTTTGTTC
1 GTTGTTGTTTGTTC
1210275 CTCAGTTGTT
Statistics
Matches: 527, Mismatches: 110, Indels: 98
0.72 0.15 0.13
Matches are distributed among these distances:
16 1 0.00
17 2 0.00
18 399 0.76
19 17 0.03
20 12 0.02
21 80 0.15
22 1 0.00
23 6 0.01
24 9 0.02
ACGTcount: A:0.08, C:0.10, G:0.29, T:0.53
Consensus pattern (18 bp):
GTTGTTGTTTGTTCAGTG
Found at i:1209630 original size:24 final size:24
Alignment explanation
Indices: 1209603--1209681 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
1209593 TTGTTTGTTG
1209603 AGTGGTTGTTGTTGTTATTGGCTC
1 AGTGGTTGTTGTTGTTATTGGCTC
*
1209627 AGTGGTTGTTG-T-TTGTT--CT-
1 AGTGGTTGTTGTTGTTATTGGCTC
* *
1209646 -GTTGTTGTTGTTGTAATTGGCTC
1 AGTGGTTGTTGTTGTTATTGGCTC
*
1209669 AGTTGTTGTTGTT
1 AGTGGTTGTTGTT
1209682 TGTTCAGTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
18 9 0.20
19 1 0.02
20 5 0.11
22 6 0.13
23 1 0.02
24 23 0.51
ACGTcount: A:0.08, C:0.06, G:0.32, T:0.54
Consensus pattern (24 bp):
AGTGGTTGTTGTTGTTATTGGCTC
Found at i:1209699 original size:39 final size:39
Alignment explanation
Indices: 1209610--1209920 Score: 278
Period size: 39 Copynumber: 8.1 Consensus size: 39
1209600 TTGAGTGGTT
* * *
1209610 GTTGTTGTTATTGGCTCAGTGGTTGTTGTTTGTTCTGTT
1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA
* *
1209649 GTTGTTGTTGTAATTGGCTCAGTTGTTGTTGTTTGTTCAGTA
1 GTTGTTG-T-T-ATTGGTTCAGTGGTTGTTGTTTGTTCAGTA
* * *
1209691 GTTGTTGTAATTGGTTCAGTGGATGTTGTTTGTTCTGTA
1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA
* **** * *
1209730 GTTGTTGTTATTTGTTCAGTGGTTGTTGTCAACTCAATG
1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA
* * *
1209769 GTGGTTG-T-TT-GTTCAGTGGTTGTTGTTTGTTCTGTT
1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA
* *
1209805 GTTGTTGTTATTGGTTCAGTGGATGTTGTTTGTTCTA-TT
1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTC-AGTA
* ** *
1209844 GTTGTTGTGATTGGTTCAGTGGTTG-TAATTGATTCAGTG
1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTG-TTCAGTA
* * *
1209883 GTTGTTG-T-TT-GTTCTGTTGTTGTTGATTGTTCAGTA
1 GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA
1209919 GT
1 GT
1209921 CGATGTTTGT
Statistics
Matches: 223, Mismatches: 39, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
36 43 0.19
37 10 0.04
38 8 0.04
39 125 0.56
40 1 0.00
41 2 0.01
42 34 0.15
ACGTcount: A:0.10, C:0.06, G:0.30, T:0.53
Consensus pattern (39 bp):
GTTGTTGTTATTGGTTCAGTGGTTGTTGTTTGTTCAGTA
Found at i:1209805 original size:15 final size:17
Alignment explanation
Indices: 1209673--1211601 Score: 408
Period size: 18 Copynumber: 105.5 Consensus size: 17
1209663 TGGCTCAGTT
*
1209673 GTTGTTGTTTGTTCAGTA
1 GTTGTTGTTTGTTCA-TG
1209691 GTTGTTGTAATTGGTTCAGTG
1 GTTGTTGT--TT-GTTCA-TG
*
1209712 GATGTTGTTTGTTC-TG
1 GTTGTTGTTTGTTCATG
1209728 TAGTTGTTGTTATTTGTTCAGTG
1 --GTTGTTG---TTTGTTCA-TG
****
1209751 GTTGTTGTCAACTCAATG
1 GTTGTTGTTTGTTC-ATG
*
1209769 GTGGTTGTTTGTTCAGTG
1 GTTGTTGTTTGTTCA-TG
1209787 GTTGTTGTTTGTTC-TG
1 GTTGTTGTTTGTTCATG
1209803 TTGTTGTTGTTATTGGTTCAGTG
1 --GTTGTTG-T-TT-GTTCA-TG
* *
1209826 GATGTTGTTTGTTCTATT
1 GTTGTTGTTTGTTC-ATG
1209844 GTTGTTGTGATTGGTTCAGTG
1 GTTGTTGT--TT-GTTCA-TG
**
1209865 GTTG-TAATTGATTCAGTG
1 GTTGTTGTTTG-TTCA-TG
1209883 GTTGTTGTTTGTTC-TG
1 GTTGTTGTTTGTTCATG
* *
1209899 TTGTTGTTGATTGTTCAGTA
1 --GTTGTTGTTTGTTCA-TG
* * *
1209919 GTCGATGTTTGTTCATCA
1 GTTGTTGTTTGTTCAT-G
*
1209937 GTTGTTGTTGGTTGC-TG
1 GTTGTTGTTTGTT-CATG
*
1209954 AGTTGTTGTTTGTTCCTCG
1 -GTTGTTGTTTGTTCAT-G
*
1209973 GTGGTTGTTTGTTC-TG
1 GTTGTTGTTTGTTCATG
* * *
1209989 CAGTTGTTGTTTGCTCCTCA
1 --GTTGTTGTTTGTTCAT-G
1210009 GTTGTTGTTTGTTC-TG
1 GTTGTTGTTTGTTCATG
1210025 CAGTTGTTGTTTG--CATTTCG
1 --GTTGTTGTTTGTTCA--T-G
1210045 GTTGTTGTTTGTTCA-G
1 GTTGTTGTTTGTTCATG
* *
1210061 CAGTTGTTGTTTGTTCCTCA
1 --GTTGTTGTTTGTTCAT-G
* * * *
1210081 GTAGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
1210099 GTTGTTGTTTGTTC-TG
1 GTTGTTGTTTGTTCATG
* *
1210115 CAGTTGTTGTTTGCTCTTCG
1 --GTTGTTGTTTGTTCAT-G
*
1210135 GTTGTTGTTTGTTGA-G
1 GTTGTTGTTTGTTCATG
* *
1210151 CAGTTGTTGTTTGTTCCTCA
1 --GTTGTTGTTTGTTCAT-G
* *
1210171 GTTGTTGTTTGTTCTTCA
1 GTTGTTGTTTGTTCAT-G
* * *
1210189 GTTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
1210207 GTTGTTGTTTGTTC-TG
1 GTTGTTGTTTGTTCATG
* *
1210223 CAGTTGTTGTTTGCTCTTCG
1 --GTTGTTGTTTGTTCAT-G
1210243 GTTGTTGTTTGTTC-TG
1 GTTGTTGTTTGTTCATG
*
1210259 CAGTTGTTGTTTGTTCCTCAGTT
1 --GTTGTTGTTTG-T--TCA-TG
*
1210282 GTTGTTGTTTCTTC-T-
1 GTTGTTGTTTGTTCATG
* *
1210297 GTCG-TGCTTTGTTCTTG
1 GTTGTTG-TTTGTTCATG
** *
1210314 AGTTGTTGTTACCTCCTCGGTTG
1 -GTTGTTGTT---TGTTC--ATG
* * * *
1210337 TTGTTGTTATTTGCTCCTCA
1 --GTTGTTGTTTGTTCAT-G
* * * *
1210357 GTAGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
* *
1210375 GTTGTTGTTTGTTCTTCT
1 GTTGTTGTTTGTTCAT-G
* * *
1210393 GTCGTGGTTTGTTCTTGG
1 GTTGTTGTTTGTTCAT-G
* *
1210411 GTTGTTGTTTGTTCTTCT
1 GTTGTTGTTTGTTCAT-G
* * *
1210429 GTCGTGGTTTGTTCTTGG
1 GTTGTTGTTTGTTCAT-G
*
1210447 GTTGTTGTTTGCTC-TG
1 GTTGTTGTTTGTTCATG
* * *
1210463 CAGTTGTTGTTTGCTCCTCA
1 --GTTGTTGTTTGTTCAT-G
*
1210483 GTTGTTGTTTGCTT-TTCG
1 GTTGTTGTTTG-TTCAT-G
* * *
1210501 GTTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
*
1210519 GTTGTTGTTTGTTCTTCG
1 GTTGTTGTTTGTTCAT-G
* * * *
1210537 GTCGTGGTTTGTTCCTCA
1 GTTGTTGTTTGTTCAT-G
* *
1210555 GTTGTTGTTTGTTCTTCT
1 GTTGTTGTTTGTTCAT-G
* *
1210573 GTCGTTGTTTGCTCATCG
1 GTTGTTGTTTGTTCAT-G
*
1210591 GTTGTTGTTTGTTCTTG
1 GTTGTTGTTTGTTCATG
* * *
1210608 CGTTGTTGTTTGCTCTTCC
1 -GTTGTTGTTTGTTCAT-G
* * *
1210627 GTTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
* *
1210645 GCTGTTGTTTGTTCTTCG
1 GTTGTTGTTTGTTCAT-G
* * * *
1210663 GTCGTGGTTTGTTCCTCA
1 GTTGTTGTTTGTTCAT-G
* *
1210681 GTTGTTGTTTGTTCTTCT
1 GTTGTTGTTTGTTCAT-G
* * *
1210699 GTCGTTGTTTGCTCCTCG
1 GTTGTTGTTTGTTCAT-G
*
1210717 GTTGTTGTTTGTTCTTG
1 GTTGTTGTTTGTTCATG
* * *
1210734 CGTTGTTGTTTGCTCTTCC
1 -GTTGTTGTTTGTTCAT-G
* * *
1210753 GTTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
* * *
1210771 GCTGTTGTTTGTTCTTCT
1 GTTGTTGTTTGTTCAT-G
* * * *
1210789 GTCGTGGTTTGTTCCTCA
1 GTTGTTGTTTGTTCAT-G
* *
1210807 GTTGTTGTTTGTTCTTCC
1 GTTGTTGTTTGTTCAT-G
* * *
1210825 GTTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
* * *
1210843 GCTGTTGTTTGTTCTTCT
1 GTTGTTGTTTGTTCAT-G
* * *
1210861 GTTGTGGTTTGTTCTTCT
1 GTTGTTGTTTGTTCAT-G
* *
1210879 GTTGTGGTTTGTTCCTCG
1 GTTGTTGTTTGTTCAT-G
* * * *
1210897 GTTGTGGTTTGTCCTTCT
1 GTTGTTGTTTGTTCAT-G
* * *
1210915 GTTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
*
1210933 GTTGTTGTTTGTTCTTCG
1 GTTGTTGTTTGTTCAT-G
* * *
1210951 GTCGTTGTTTGTTCCTCA
1 GTTGTTGTTTGTTCAT-G
*
1210969 GTTGTTGTTTGTTCTTCG
1 GTTGTTGTTTGTTCAT-G
1210987 GTTGTTGTTTGCTCCTCGGATG
1 GTTGTTGTTTG-T--TC--ATG
*
1211009 CTGTTGTTGTTTGTTCCTCG
1 --GTTGTTGTTTGTTCAT-G
* * * *
1211029 ATTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
*
1211047 GTTGTTGTTTGTTCTTG
1 GTTGTTGTTTGTTCATG
* * *
1211064 CGTTGTTGTTTGCTCTTCT
1 -GTTGTTGTTTGTTCAT-G
* * *
1211083 GTTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
*
1211101 GTTGTTGTTTGTTCTTCG
1 GTTGTTGTTTGTTCAT-G
* * * *
1211119 GTCGTGGTTTGTTCCTCA
1 GTTGTTGTTTGTTCAT-G
*
1211137 GTTGTTGTTTGTTCTTCG
1 GTTGTTGTTTGTTCAT-G
1211155 GTTGTTGTTTGCTCCTCGGATG
1 GTTGTTGTTTG-T--TC--ATG
* *
1211177 CTGTTGTTATTTGTTCCTCG
1 --GTTGTTGTTTGTTCAT-G
1211197 GTTGTTGTTTGCTCCTCAT-
1 GTTGTTGTTTG-T--TCATG
*
1211216 -TTGTTGTTTGTTCTTG
1 GTTGTTGTTTGTTCATG
* * *
1211232 CGTTGTTGTTTGCTCTTCT
1 -GTTGTTGTTTGTTCAT-G
* * *
1211251 GTTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
*
1211269 GTTGTTGTTTGTTCTTCG
1 GTTGTTGTTTGTTCAT-G
* * * *
1211287 GTCGTGGTTTGTTCCTCA
1 GTTGTTGTTTGTTCAT-G
* *
1211305 GTTGTTGTTTGTTCTTCT
1 GTTGTTGTTTGTTCAT-G
* *
1211323 GTTGTGGTTTGTTCTTGG
1 GTTGTTGTTTGTTCAT-G
** *
1211341 GTTGTTGTTTGCCCCTCG
1 GTTGTTGTTTGTTCAT-G
* * *
1211359 GTTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
*
1211377 GTTGTTGTTTGTTCCTCG
1 GTTGTTGTTTGTTCAT-G
* * *
1211395 GTTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCAT-G
* *
1211413 GTTGTTGTTTGTTCTTCT
1 GTTGTTGTTTGTTCAT-G
* * *
1211431 GTCGTGGTTTGTTCTTGG
1 GTTGTTGTTTGTTCAT-G
** *
1211449 GTTGTTGTTTGCCCCTCG
1 GTTGTTGTTTGTTCAT-G
* * *
1211467 GTTGTTGTTTGCTCTTCT
1 GTTGTTGTTTGTTCAT-G
* * *
1211485 GTTGTGGTTTGTTCTTCT
1 GTTGTTGTTTGTTCAT-G
* *
1211503 GTTGTGGTTTGTTCCTCG
1 GTTGTTGTTTGTTCAT-G
* * *
1211521 GTTGTGGTTTGTCCTTCG
1 GTTGTTGTTTGTTCAT-G
* *
1211539 GTTGTTGTTTGCTCTTCG
1 GTTGTTGTTTGTTCAT-G
* * *
1211557 GTTGTTGATTGCTCCTCG
1 GTTGTTGTTTGTTCAT-G
* *
1211575 GTTGTTGTTTGCTCCTCG
1 GTTGTTGTTTGTTCAT-G
1211593 GTTGTTGTT
1 GTTGTTGTT
1211602 GTTGTTGTTT
Statistics
Matches: 1522, Mismatches: 272, Indels: 234
0.75 0.13 0.12
Matches are distributed among these distances:
14 2 0.00
15 12 0.01
16 14 0.01
17 14 0.01
18 1314 0.86
19 28 0.02
20 18 0.01
21 77 0.05
22 2 0.00
23 12 0.01
24 29 0.02
ACGTcount: A:0.04, C:0.15, G:0.27, T:0.54
Consensus pattern (17 bp):
GTTGTTGTTTGTTCATG
Found at i:1209824 original size:114 final size:114
Alignment explanation
Indices: 1209667--1209920 Score: 355
Period size: 114 Copynumber: 2.2 Consensus size: 114
1209657 TGTAATTGGC
*
1209667 TCAGTTGTTGTTGTTTGTTCAGTAGTTGTTGTAATTGGTTCAGTGGATGTTGTTTGTTCTGTAGT
1 TCAGTTGTTGTTGTTTGTTCAGTAGTTGTTGTAATTGGTTCAGTGGATGTTGTTTGTTCTATAGT
* * **
1209732 TGTTGTTATTTGTTCAGTGGTTGTTGTCAACTCAATGGTGGTTGTTTGT
66 TGTTGTGATTGGTTCAGTGGTTGTAATCAACTCAATGGTGGTTGTTTGT
* * * * *
1209781 TCAGTGGTTGTTGTTTGTTCTGTTGTTGTTGTTATTGGTTCAGTGGATGTTGTTTGTTCTATTGT
1 TCAGTTGTTGTTGTTTGTTCAGTAGTTGTTGTAATTGGTTCAGTGGATGTTGTTTGTTCTATAGT
** * * *
1209846 TGTTGTGATTGGTTCAGTGGTTGTAATTGATTCAGTGGTTGTTGTTTGT
66 TGTTGTGATTGGTTCAGTGGTTGTAATCAACTCAATGGTGGTTGTTTGT
* *
1209895 TCTGTTGTTGTTGATTGTTCAGTAGT
1 TCAGTTGTTGTTGTTTGTTCAGTAGT
1209921 CGATGTTTGT
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
114 120 1.00
ACGTcount: A:0.11, C:0.06, G:0.30, T:0.53
Consensus pattern (114 bp):
TCAGTTGTTGTTGTTTGTTCAGTAGTTGTTGTAATTGGTTCAGTGGATGTTGTTTGTTCTATAGT
TGTTGTGATTGGTTCAGTGGTTGTAATCAACTCAATGGTGGTTGTTTGT
Found at i:1210280 original size:18 final size:18
Alignment explanation
Indices: 1209924--1211702 Score: 1359
Period size: 18 Copynumber: 98.3 Consensus size: 18
1209914 CAGTAGTCGA
*
1209924 TGTTTGTTCATCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1209942 TGTTGGTTGCTGAGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1209960 TGTTTGTTCCTCGGTGGT
1 TGTTTGTTCCTCAGTTGT
1209978 TGTTTGTT-CTGCAGTTGT
1 TGTTTGTTCCT-CAGTTGT
*
1209996 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
1210014 TGTTTGTT-CTGCAGTTGT
1 TGTTTGTTCCT-CAGTTGT
*
1210032 TGTTTGCATT--TCGGTTGT
1 TGTTTG--TTCCTCAGTTGT
**
1210050 TGTTTGTTCAGCAGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1210068 TGTTTGTTCCTCAGTAGT
1 TGTTTGTTCCTCAGTTGT
*
1210086 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
1210104 TGTTTGTT-CTGCAGTTGT
1 TGTTTGTTCCT-CAGTTGT
* * *
1210122 TGTTTGCTCTTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
***
1210140 TGTTTGTTGAGCAGTTGT
1 TGTTTGTTCCTCAGTTGT
1210158 TGTTTGTTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1210176 TGTTTGTTCTTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1210194 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
1210212 TGTTTGTT-CTGCAGTTGT
1 TGTTTGTTCCT-CAGTTGT
* * *
1210230 TGTTTGCTCTTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
1210248 TGTTTGTT-CTGCAGTTGT
1 TGTTTGTTCCT-CAGTTGT
1210266 TGTTTGTTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1210284 TG-TTGTTTCTTCTGTCG-
1 TGTTTG-TTCCTCAGTTGT
* *
1210301 TGCTTTGTTCTTGAGTTGT
1 TG-TTTGTTCCTCAGTTGT
*** *
1210320 TGTTACCTCCTCGGTTGTTGT
1 TGTTTGTTCCTC---AGTTGT
* *
1210341 TGTTATTTGCTCCTCAGTAGT
1 TG---TTTGTTCCTCAGTTGT
*
1210362 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1210380 TGTTTGTTCTTCTGTCGT
1 TGTTTGTTCCTCAGTTGT
* * **
1210398 GGTTTGTTCTTGGGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1210416 TGTTTGTTCTTCTGTCGT
1 TGTTTGTTCCTCAGTTGT
* * **
1210434 GGTTTGTTCTTGGGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1210452 TGTTTGCT-CTGCAGTTGT
1 TGTTTGTTCCT-CAGTTGT
*
1210470 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1210488 TGTTTGCTT-TTCGGTTGT
1 TGTTTG-TTCCTCAGTTGT
*
1210506 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1210524 TGTTTGTTCTTCGGTCGT
1 TGTTTGTTCCTCAGTTGT
*
1210542 GGTTTGTTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1210560 TGTTTGTTCTTCTGTCGT
1 TGTTTGTTCCTCAGTTGT
* * *
1210578 TGTTTGCTCATCGGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1210596 TGTTTGTTCTTGC-GTTGT
1 TGTTTGTTCCT-CAGTTGT
* * *
1210614 TGTTTGCTCTTCCGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1210632 TGTTTGCTCCTCAGCTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1210650 TGTTTGTTCTTCGGTCGT
1 TGTTTGTTCCTCAGTTGT
*
1210668 GGTTTGTTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1210686 TGTTTGTTCTTCTGTCGT
1 TGTTTGTTCCTCAGTTGT
* *
1210704 TGTTTGCTCCTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1210722 TGTTTGTTCTTGC-GTTGT
1 TGTTTGTTCCT-CAGTTGT
* * *
1210740 TGTTTGCTCTTCCGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1210758 TGTTTGCTCCTCAGCTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1210776 TGTTTGTTCTTCTGTCGT
1 TGTTTGTTCCTCAGTTGT
*
1210794 GGTTTGTTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1210812 TGTTTGTTCTTCCGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1210830 TGTTTGCTCCTCAGCTGT
1 TGTTTGTTCCTCAGTTGT
* *
1210848 TGTTTGTTCTTCTGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1210866 GGTTTGTTCTTCTGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1210884 GGTTTGTTCCTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1210902 GGTTTG-TCCTTCTGTTGT
1 TGTTTGTTCC-TCAGTTGT
*
1210920 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1210938 TGTTTGTTCTTCGGTCGT
1 TGTTTGTTCCTCAGTTGT
1210956 TGTTTGTTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1210974 TGTTTGTTCTTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1210992 TGTTTGCTCCTCGGATGCTGTTGT
1 TGTTTGTTCCTC--A----GTTGT
1211016 TGTTTGTTCCTC-GATTGT
1 TGTTTGTTCCTCAG-TTGT
*
1211034 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1211052 TGTTTGTTCTTGC-GTTGT
1 TGTTTGTTCCT-CAGTTGT
* * *
1211070 TGTTTGCTCTTCTGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1211088 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1211106 TGTTTGTTCTTCGGTCGT
1 TGTTTGTTCCTCAGTTGT
*
1211124 GGTTTGTTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1211142 TGTTTGTTCTTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1211160 TGTTTGCTCCTCGGATGCTGTTGT
1 TGTTTGTTCCTC--A----GTTGT
* *
1211184 TATTTGTTCCTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1211202 TGTTTGCTCCTCATTTGT
1 TGTTTGTTCCTCAGTTGT
*
1211220 TGTTTGTTCTTGC-GTTGT
1 TGTTTGTTCCT-CAGTTGT
* * *
1211238 TGTTTGCTCTTCTGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1211256 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1211274 TGTTTGTTCTTCGGTCGT
1 TGTTTGTTCCTCAGTTGT
*
1211292 GGTTTGTTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1211310 TGTTTGTTCTTCTGTTGT
1 TGTTTGTTCCTCAGTTGT
* * **
1211328 GGTTTGTTCTTGGGTTGT
1 TGTTTGTTCCTCAGTTGT
** *
1211346 TGTTTGCCCCTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1211364 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1211382 TGTTTGTTCCTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1211400 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1211418 TGTTTGTTCTTCTGTCGT
1 TGTTTGTTCCTCAGTTGT
* * **
1211436 GGTTTGTTCTTGGGTTGT
1 TGTTTGTTCCTCAGTTGT
** *
1211454 TGTTTGCCCCTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1211472 TGTTTGCTCTTCTGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1211490 GGTTTGTTCTTCTGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1211508 GGTTTGTTCCTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1211526 GGTTTG-TCCTTCGGTTGT
1 TGTTTGTTCC-TCAGTTGT
* * *
1211544 TGTTTGCTCTTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1211562 TGATTGCTCCTCGGTTGT
1 TGTTTGTTCCTCAGTTGT
*
1211580 TGTTTGCTCCTC-G--GT
1 TGTTTGTTCCTCAGTTGT
1211595 TG-TTG-T--T--GTTGT
1 TGTTTGTTCCTCAGTTGT
* *
1211607 TGTTTG-CCCTTCGGTTGT
1 TGTTTGTTCC-TCAGTTGT
*
1211625 TGTTTGCTCCTCAGTTGT
1 TGTTTGTTCCTCAGTTGT
* * *
1211643 TGTTTGTTCTTCTGTCG-
1 TGTTTGTTCCTCAGTTGT
* *
1211660 TGCCTTGTTCCTCGGTTGT
1 TG-TTTGTTCCTCAGTTGT
1211679 TGTTTGTT-CTGCAGTTGT
1 TGTTTGTTCCT-CAGTTGT
1211697 TGTTTG
1 TGTTTG
1211703 CTCTTCTGTC
Statistics
Matches: 1429, Mismatches: 267, Indels: 130
0.78 0.15 0.07
Matches are distributed among these distances:
10 1 0.00
11 1 0.00
12 4 0.00
13 4 0.00
14 3 0.00
15 4 0.00
16 3 0.00
17 32 0.02
18 1294 0.91
19 29 0.02
20 2 0.00
21 13 0.01
24 39 0.03
ACGTcount: A:0.03, C:0.17, G:0.26, T:0.54
Consensus pattern (18 bp):
TGTTTGTTCCTCAGTTGT
Found at i:1211608 original size:45 final size:45
Alignment explanation
Indices: 1211557--1211646 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
1211547 TTGCTCTTCG
*
1211557 GTTGTTGATTGCTCC-TCGGTTGTTGTTTGCTCCTCGGTTGTTGTT
1 GTTGTTGATTGC-CCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGTT
*
1211602 GTTGTTGTTTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGTT
1 GTTGTTGATTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGTT
1211647 TGTTCTTCTG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 2 0.05
45 40 0.95
ACGTcount: A:0.02, C:0.18, G:0.28, T:0.52
Consensus pattern (45 bp):
GTTGTTGATTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGTT
Found at i:1211610 original size:27 final size:27
Alignment explanation
Indices: 1211575--1211628 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1211565 TTGCTCCTCG
1211575 GTTGTTGTTTGCTCC-TCGGTTGTTGTT
1 GTTGTTGTTTGC-CCTTCGGTTGTTGTT
1211602 GTTGTTGTTTGCCCTTCGGTTGTTGTT
1 GTTGTTGTTTGCCCTTCGGTTGTTGTT
1211629 TGCTCCTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.00, C:0.15, G:0.30, T:0.56
Consensus pattern (27 bp):
GTTGTTGTTTGCCCTTCGGTTGTTGTT
Found at i:1211672 original size:81 final size:81
Alignment explanation
Indices: 1211521--1211682 Score: 209
Period size: 81 Copynumber: 2.0 Consensus size: 81
1211511 TTGTTCCTCG
* * * * *
1211521 GTTGTGGTTTGTCCTTCGGTTGTTGTTTGCTCTTCGGTTGTTGATTGCTCCTCGGTTGTTGTTTG
1 GTTGTGGTTTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGATTGCTCCTCGGTCGTTGCTTG
1211586 CTCCTCGGTTGTTGTT
66 CTCCTCGGTTGTTGTT
* * * * *
1211602 GTTGTTGTTTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGTTTGTTCTTCTGTCG-TGCCTT
1 GTTGTGGTTTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGATTGCTCCTCGGTCGTTG-CTT
*
1211666 GTTCCTCGGTTGTTGTT
65 GCTCCTCGGTTGTTGTT
1211683 TGTTCTGCAG
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
80 2 0.03
81 67 0.97
ACGTcount: A:0.01, C:0.19, G:0.28, T:0.52
Consensus pattern (81 bp):
GTTGTGGTTTGCCCTTCGGTTGTTGTTTGCTCCTCAGTTGTTGATTGCTCCTCGGTCGTTGCTTG
CTCCTCGGTTGTTGTT
Found at i:1211696 original size:99 final size:99
Alignment explanation
Indices: 1211518--1211700 Score: 237
Period size: 99 Copynumber: 1.8 Consensus size: 99
1211508 GGTTTGTTCC
* *
1211518 TCGGTTGTGGTTTGTCCTTCGGTTGTTGTTTGCTCTTCGGTTGTTGATTGCTCCTCGGTTGTTGT
1 TCGGTTGTGGTTTGTCCTTCAGTTGTTGTTTGCTCTTCGGTCGTTGATTGCTCCTCGGTTGTTGT
*
1211583 TTGCTCCTCGGTTGTTGTTGTTGTTGTTTGCCCT
66 TTGCTCCTCAGTTGTTGTTGTTGTTGTTTGCCCT
* * * * *
1211617 TCGGTTGTTGTTTGCTCC-TCAGTTGTTGTTTGTTCTTCTGTCG-TGCCTTGTTCCTCGGTTGTT
1 TCGGTTGTGGTTTG-TCCTTCAGTTGTTGTTTGCTCTTCGGTCGTTG-ATTGCTCCTCGGTTGTT
*
1211680 GTTTG-TTCTGCAGTTGTTGTT
64 GTTTGCTCCT-CAGTTGTTGTT
1211701 TGCTCTTCTG
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
98 5 0.07
99 64 0.89
100 3 0.04
ACGTcount: A:0.02, C:0.18, G:0.28, T:0.52
Consensus pattern (99 bp):
TCGGTTGTGGTTTGTCCTTCAGTTGTTGTTTGCTCTTCGGTCGTTGATTGCTCCTCGGTTGTTGT
TTGCTCCTCAGTTGTTGTTGTTGTTGTTTGCCCT
Found at i:1211743 original size:18 final size:18
Alignment explanation
Indices: 1211720--1211754 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1211710 GTCGTCGTTA
1211720 CTTCGTCCGTTGTTGTTT
1 CTTCGTCCGTTGTTGTTT
*
1211738 CTTCGTCGGTTGTTGTT
1 CTTCGTCCGTTGTTGTT
1211755 GGTTCAGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.26, T:0.54
Consensus pattern (18 bp):
CTTCGTCCGTTGTTGTTT
Found at i:1212007 original size:18 final size:18
Alignment explanation
Indices: 1211986--1212572 Score: 274
Period size: 18 Copynumber: 32.8 Consensus size: 18
1211976 TGGTTCGGTG
* *
1211986 GTTGTTATTTGTTCATCA
1 GTTGTTGTTTGTTCTTCA
*
1212004 GTTGTTGTTTGTTCCTGC-
1 GTTGTTGTTTGTT-CTTCA
**
1212022 GTTGTTGTTTGTTCTTTT
1 GTTGTTGTTTGTTCTTCA
*
1212040 GTTGTTGTCTGTTCTTCA
1 GTTGTTGTTTGTTCTTCA
*
1212058 GTTGTTGTTAG---TTCA
1 GTTGTTGTTTGTTCTTCA
* *
1212073 GTTGTTGCTTGTTCTTCG
1 GTTGTTGTTTGTTCTTCA
* *
1212091 GTTGTTGTTTGTACATT-T
1 GTTGTTGTTTGTTC-TTCA
*
1212109 GTTGTTGTCTGTTCTTCA
1 GTTGTTGTTTGTTCTTCA
* * * *
1212127 GTAGTAGTCTGTTCTTCG
1 GTTGTTGTTTGTTCTTCA
* *
1212145 GTTGTTGTTTGTTCAGT-G
1 GTTGTTGTTTGTTC-TTCA
* *
1212163 GTTGTTGTTTGCTCCTCA
1 GTTGTTGTTTGTTCTTCA
* * * *
1212181 GTTGTAGTTGGTTCAAT-G
1 GTTGTTGTTTGTTC-TTCA
*
1212199 GTTGTTGTCTGTTCTTCA
1 GTTGTTGTTTGTTCTTCA
* *
1212217 GTTGTTGTTGGTTCAAT-A
1 GTTGTTGTTTGTTC-TTCA
* * *
1212235 ATTGTAGTCTGTTCTTCA
1 GTTGTTGTTTGTTCTTCA
** *
1212253 GTTGTTGTTAATTCAAT-A
1 GTTGTTGTTTGTTC-TTCA
* *
1212271 CTTGTTGTCTGTTCTTC-
1 GTTGTTGTTTGTTCTTCA
*
1212288 GATTGTTG-TTGATTCAAT-A
1 G-TTGTTGTTTG-TTC-TTCA
* *
1212307 GTTGTAGTCTGTTCTTCA
1 GTTGTTGTTTGTTCTTCA
* ***
1212325 GTTGTTGTTGGTTCCGAA
1 GTTGTTGTTTGTTCTTCA
* *
1212343 GTTGTTGTCTGTTCTTCG
1 GTTGTTGTTTGTTCTTCA
* *
1212361 GTTGTTG-TCGATTCAAT-A
1 GTTGTTGTTTG-TTC-TTCA
* *
1212379 GTTGTAGTCTGTTCTTCA
1 GTTGTTGTTTGTTCTTCA
** *
1212397 GTTGTTGTTAATTCAAT-A
1 GTTGTTGTTTGTTC-TTCA
* *
1212415 GTTGTAGTCTGTTCTTCA
1 GTTGTTGTTTGTTCTTCA
*
1212433 GTTGTTG-TTGATTCAAT-A
1 GTTGTTGTTTG-TTC-TTCA
* *
1212451 GTTGTAGTCTGTTCTTCA
1 GTTGTTGTTTGTTCTTCA
* ***
1212469 GTTGTTGTTGGTTCCGAA
1 GTTGTTGTTTGTTCTTCA
* *
1212487 GTTGTTGTCTGTTCTTCG
1 GTTGTTGTTTGTTCTTCA
* ***
1212505 GTTGTTGTTGGTTCCGAA
1 GTTGTTGTTTGTTCTTCA
* *
1212523 GTTGTTGTCTGTTCTTCG
1 GTTGTTGTTTGTTCTTCA
* * *
1212541 GTTGTTGTTTTTTCGGT-G
1 GTTGTTGTTTGTTC-TTCA
1212559 GTTGTTGTTTGTTC
1 GTTGTTGTTTGTTC
1212573 CCCAGTGGTT
Statistics
Matches: 409, Mismatches: 128, Indels: 64
0.68 0.21 0.11
Matches are distributed among these distances:
15 13 0.03
17 17 0.04
18 360 0.88
19 19 0.05
ACGTcount: A:0.10, C:0.12, G:0.25, T:0.53
Consensus pattern (18 bp):
GTTGTTGTTTGTTCTTCA
Found at i:1212062 original size:21 final size:19
Alignment explanation
Indices: 1211944--1212066 Score: 60
Period size: 21 Copynumber: 6.3 Consensus size: 19
1211934 TTGGGCCCCG
*
1211944 GTTGTTGTCTCTTCTTCGGTT
1 GTTGTTGT-TGTTCTTC-GTT
* * *
1211965 GTTGTTGTTATTGGTTCGGTG
1 GTTGTTGTTGTT-CTTC-GTT
* *
1211986 GTTGTTATTTGTTCATCAGTT
1 GTTGTT-GTTGTTCTTC-GTT
*
1212007 GTTG-T-TTGTTCCTGCGTT
1 GTTGTTGTTGTT-CTTCGTT
1212025 GTTG-T-TTGTTCTT--TT
1 GTTGTTGTTGTTCTTCGTT
1212040 GTTGTTGTCTGTTCTTCAGTT
1 GTTGTTGT-TGTTCTTC-GTT
1212061 GTTGTT
1 GTTGTT
1212067 AGTTCAGTTG
Statistics
Matches: 81, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
15 6 0.07
16 1 0.01
17 3 0.04
18 25 0.31
19 2 0.02
20 4 0.05
21 36 0.44
22 4 0.05
ACGTcount: A:0.04, C:0.11, G:0.26, T:0.59
Consensus pattern (19 bp):
GTTGTTGTTGTTCTTCGTT
Found at i:1212062 original size:33 final size:33
Alignment explanation
Indices: 1212025--1212128 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
1212015 TTCCTGCGTT
1212025 GTTGTTTGTTCTTTTGTTGTTGTCTGTTCTTCA
1 GTTGTTTGTTCTTTTGTTGTTGTCTGTTCTTCA
* ** *
1212058 GTTG-TTGTTAGTTCAGTTGTTG-CTTGTTCTTCGGTT
1 GTTGTTTGTT-CTTTTGTTGTTGTC-TGTTCTTC---A
* *
1212094 GTTGTTTGTACATTTGTTGTTGTCTGTTCTTCA
1 GTTGTTTGTTCTTTTGTTGTTGTCTGTTCTTCA
1212127 GT
1 GT
1212129 AGTAGTCTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
32 6 0.11
33 23 0.43
36 20 0.37
37 5 0.09
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.59
Consensus pattern (33 bp):
GTTGTTTGTTCTTTTGTTGTTGTCTGTTCTTCA
Found at i:1212167 original size:69 final size:68
Alignment explanation
Indices: 1212025--1212168 Score: 159
Period size: 69 Copynumber: 2.1 Consensus size: 68
1212015 TTCCTGCGTT
* * *
1212025 GTTGTTTGTTCTTTTGTTGTTGTCTGTTCTTCAGTTGTTGTTAGTTCAGTTGTTGCTTGTTCTTC
1 GTTGTTTGTACATTTGTTGTTGTCTGTTCTTCAGTTGTTGTTACTTCAGTTGTTGC-TGTTCTTC
* *
1212090 GGTT
65 AGTG
* *
1212094 GTTGTTTGTACATTTGTTGTTGTCTGTTCTTCAGTAGTAGTCTGTT-CTTCGGTTGTTG-T-TTG
1 GTTGTTTGTACATTTGTTGTTGTCTGTTCTTCAGT--T-GT-TGTTACTTCAGTTGTTGCTGTTC
1212156 TTCAGTG
62 TTCAGTG
1212163 GTTGTT
1 GTTGTT
1212169 GTTTGCTCCT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
69 46 0.72
70 1 0.02
71 1 0.02
72 12 0.19
73 4 0.06
ACGTcount: A:0.06, C:0.11, G:0.26, T:0.57
Consensus pattern (68 bp):
GTTGTTTGTACATTTGTTGTTGTCTGTTCTTCAGTTGTTGTTACTTCAGTTGTTGCTGTTCTTCA
GTG
Found at i:1212572 original size:72 final size:72
Alignment explanation
Indices: 1212133--1212549 Score: 536
Period size: 72 Copynumber: 5.8 Consensus size: 72
1212123 TTCAGTAGTA
* * * * * * *
1212133 GTCTGTTCTTCGGTTGTTGTTTG-TTCAGTGGTTGTTGTTTGCTCCTCAGTTGTAGTTGGTTCAA
1 GTCTGTTCTTCGGTTGTTG-TTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCAA
*
1212197 TGGTTGTT
65 TAGTTGTT
* * * **
1212205 GTCTGTTCTTCAGTTGTTGTTGGTTCAATAATTGTAGTCTGTTCTTCAGTTGTTGTTAATTCAAT
1 GTCTGTTCTTCGGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCAAT
*
1212270 ACTTGTT
66 AGTTGTT
* *
1212277 GTCTGTTCTTCGATTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCCGA
1 GTCTGTTCTTCGGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTT-CAA
1212342 -AGTTGTT
65 TAGTTGTT
* **
1212349 GTCTGTTCTTCGGTTGTTGTCGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTAATTCAAT
1 GTCTGTTCTTCGGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCAAT
*
1212414 AGTTGTA
66 AGTTGTT
* *
1212421 GTCTGTTCTTCAGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCCGA
1 GTCTGTTCTTCGGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTT-CAA
1212486 -AGTTGTT
65 TAGTTGTT
* * * *
1212493 GTCTGTTCTTCGGTTGTTGTTGGTTCCGA-AGTTGTTGTCTGTTCTTCGGTTGTTGTT
1 GTCTGTTCTTCGGTTGTTGTTGATT-CAATAGTTGTAGTCTGTTCTTCAGTTGTTGTT
1212550 TTTTCGGTGG
Statistics
Matches: 302, Mismatches: 38, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
71 5 0.02
72 291 0.96
73 6 0.02
ACGTcount: A:0.12, C:0.13, G:0.25, T:0.51
Consensus pattern (72 bp):
GTCTGTTCTTCGGTTGTTGTTGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCAAT
AGTTGTT
Done.