Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 97 of 182
Found at i:29318481 original size:26 final size:26
Alignment explanation
Indices: 29318417--29318482 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
29318407 TTCGACCTAT
* *
29318417 AGCTCGTGTGAGAAGGCCTATTTCAC
1 AGCTCGTGTGAGCAGGCCCATTTCAC
*
29318443 AGCTCGTGTGAGCAGGCCCATTTTAC
1 AGCTCGTGTGAGCAGGCCCATTTCAC
29318469 AGCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
29318483 ATGATGTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (26 bp):
AGCTCGTGTGAGCAGGCCCATTTCAC
Found at i:29319806 original size:96 final size:96
Alignment explanation
Indices: 29319642--29319830 Score: 378
Period size: 96 Copynumber: 2.0 Consensus size: 96
29319632 GCATATGGCT
29319642 TGGATACGGGCTAGGACACGAACGTATGTCCTTATTTCGATTGTTATATAGCCTGAGACATGGGT
1 TGGATACGGGCTAGGACACGAACGTATGTCCTTATTTCGATTGTTATATAGCCTGAGACATGGGT
29319707 GTGTGTCTTATCCATGTGAGTCACACGGGCA
66 GTGTGTCTTATCCATGTGAGTCACACGGGCA
29319738 TGGATACGGGCTAGGACACGAACGTATGTCCTTATTTCGATTGTTATATAGCCTGAGACATGGGT
1 TGGATACGGGCTAGGACACGAACGTATGTCCTTATTTCGATTGTTATATAGCCTGAGACATGGGT
29319803 GTGTGTCTTATCCATGTGAGTCACACGG
66 GTGTGTCTTATCCATGTGAGTCACACGG
29319831 CCTAGCCACA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (96 bp):
TGGATACGGGCTAGGACACGAACGTATGTCCTTATTTCGATTGTTATATAGCCTGAGACATGGGT
GTGTGTCTTATCCATGTGAGTCACACGGGCA
Found at i:29321812 original size:28 final size:28
Alignment explanation
Indices: 29321778--29321847 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
29321768 GTGAGCAGCC
** *
29321778 CAAATATCACAGGTTGTGTGAGCAAATT
1 CAAATATCACAACTTGTGTGAGCAAACT
29321806 CAAATATCACAACTTGTGTGAGCAAACT
1 CAAATATCACAACTTGTGTGAGCAAACT
*
29321834 CAAATATCATAACT
1 CAAATATCACAACT
29321848 CGTATGAGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (28 bp):
CAAATATCACAACTTGTGTGAGCAAACT
Found at i:29321855 original size:28 final size:28
Alignment explanation
Indices: 29321778--29321855 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
29321768 GTGAGCAGCC
** * * *
29321778 CAAATATCACAGGTTGTGTGAGCAAATT
1 CAAATATCACAACTCGTATGAGCAAACT
* *
29321806 CAAATATCACAACTTGTGTGAGCAAACT
1 CAAATATCACAACTCGTATGAGCAAACT
*
29321834 CAAATATCATAACTCGTATGAG
1 CAAATATCACAACTCGTATGAG
29321856 ACAATCGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (28 bp):
CAAATATCACAACTCGTATGAGCAAACT
Found at i:29323292 original size:16 final size:15
Alignment explanation
Indices: 29323271--29323300 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29323261 AATTAAATAC
29323271 AACAACATTCATTAAT
1 AACAACATT-ATTAAT
29323287 AACAACATTATTAA
1 AACAACATTATTAA
29323301 GTTGAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (15 bp):
AACAACATTATTAAT
Found at i:29324789 original size:29 final size:26
Alignment explanation
Indices: 29324754--29324807 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 26
29324744 AAAATCTCTT
*
29324754 CTGCTATTTCTGTTATTTATTTTCTTTTC
1 CTGCTATTT-TGTT-TTT-TTCTCTTTTC
29324783 CTGCTATTTTGTTTTTTTCTCTTTT
1 CTGCTATTTTGTTTTTTTCTCTTTT
29324808 TCTCTTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 8 0.33
27 3 0.12
28 4 0.17
29 9 0.38
ACGTcount: A:0.07, C:0.17, G:0.07, T:0.69
Consensus pattern (26 bp):
CTGCTATTTTGTTTTTTTCTCTTTTC
Found at i:29325752 original size:49 final size:49
Alignment explanation
Indices: 29325685--29325821 Score: 211
Period size: 49 Copynumber: 2.8 Consensus size: 49
29325675 TATTTTCTCA
* *
29325685 ATGCCATAGTCCAACTATGGTCTTACACGTAATCACATAACATATACCG
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATACCG
* *
29325734 ATGTCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATTCCG
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATACCG
* * *
29325783 ATGCCATATCCTAGCTATGGTCTTACACGGAATCACATA
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA
29325822 TCACTTATTT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 80 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (49 bp):
ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATACCG
Found at i:29327019 original size:23 final size:23
Alignment explanation
Indices: 29326993--29327091 Score: 135
Period size: 23 Copynumber: 4.3 Consensus size: 23
29326983 ATAAGTGCCA
29326993 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
29327016 CACTAATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
29327039 TATTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
29327062 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
29327085 CACTGAT
1 CACTGAT
29327092 CAATAACACT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:29330911 original size:20 final size:18
Alignment explanation
Indices: 29330888--29330921 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29330878 GCGCCGCGCT
29330888 CCTCC-CACGTGTGCCTG
1 CCTCCTCACGTGTGCCTG
29330905 CCTCCTCACGTGTGCCT
1 CCTCCTCACGTGTGCCT
29330922 CCGTACCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.06, C:0.47, G:0.21, T:0.26
Consensus pattern (18 bp):
CCTCCTCACGTGTGCCTG
Found at i:29335780 original size:376 final size:376
Alignment explanation
Indices: 29335087--29335838 Score: 1504
Period size: 376 Copynumber: 2.0 Consensus size: 376
29335077 TAGCCTCATT
29335087 GAAACAGCGTCGAAATGGTACAATCAGTTGAGCCGTACCGAGATTGGTTCATGGAGGGACCTAGC
1 GAAACAGCGTCGAAATGGTACAATCAGTTGAGCCGTACCGAGATTGGTTCATGGAGGGACCTAGC
29335152 ACAGGCATTCATGAAACAATACGGTCATGTAACGGATATGGTTCCCGATAGAATCACCTTGCAAA
66 ACAGGCATTCATGAAACAATACGGTCATGTAACGGATATGGTTCCCGATAGAATCACCTTGCAAA
29335217 ATTTGGAAAAGAAATCGAGCGAAAGTTTTAGGCAGTATGCACAAAGGTGGAGGGAGGTTGCAGTC
131 ATTTGGAAAAGAAATCGAGCGAAAGTTTTAGGCAGTATGCACAAAGGTGGAGGGAGGTTGCAGTC
29335282 CAGGTTCAGCCACCCCTCTTGGAGAAAGAGACGACAATGCTCTTCATCAATACACTGAAGGCCCC
196 CAGGTTCAGCCACCCCTCTTGGAGAAAGAGACGACAATGCTCTTCATCAATACACTGAAGGCCCC
29335347 GTTCATTACGCATATGTTAGAAAGCGCAACAAAAAGCTTTTCTGATATAGTTATGAATGGTTAAA
261 GTTCATTACGCATATGTTAGAAAGCGCAACAAAAAGCTTTTCTGATATAGTTATGAATGGTTAAA
29335412 TGATTGAGAATGCTATAAGAGCCGAAAAAATTGAGGCGGAAGAGAGTGATA
326 TGATTGAGAATGCTATAAGAGCCGAAAAAATTGAGGCGGAAGAGAGTGATA
29335463 GAAACAGCGTCGAAATGGTACAATCAGTTGAGCCGTACCGAGATTGGTTCATGGAGGGACCTAGC
1 GAAACAGCGTCGAAATGGTACAATCAGTTGAGCCGTACCGAGATTGGTTCATGGAGGGACCTAGC
29335528 ACAGGCATTCATGAAACAATACGGTCATGTAACGGATATGGTTCCCGATAGAATCACCTTGCAAA
66 ACAGGCATTCATGAAACAATACGGTCATGTAACGGATATGGTTCCCGATAGAATCACCTTGCAAA
29335593 ATTTGGAAAAGAAATCGAGCGAAAGTTTTAGGCAGTATGCACAAAGGTGGAGGGAGGTTGCAGTC
131 ATTTGGAAAAGAAATCGAGCGAAAGTTTTAGGCAGTATGCACAAAGGTGGAGGGAGGTTGCAGTC
29335658 CAGGTTCAGCCACCCCTCTTGGAGAAAGAGACGACAATGCTCTTCATCAATACACTGAAGGCCCC
196 CAGGTTCAGCCACCCCTCTTGGAGAAAGAGACGACAATGCTCTTCATCAATACACTGAAGGCCCC
29335723 GTTCATTACGCATATGTTAGAAAGCGCAACAAAAAGCTTTTCTGATATAGTTATGAATGGTTAAA
261 GTTCATTACGCATATGTTAGAAAGCGCAACAAAAAGCTTTTCTGATATAGTTATGAATGGTTAAA
29335788 TGATTGAGAATGCTATAAGAGCCGAAAAAATTGAGGCGGAAGAGAGTGATA
326 TGATTGAGAATGCTATAAGAGCCGAAAAAATTGAGGCGGAAGAGAGTGATA
29335839 AGAGGTCAAC
Statistics
Matches: 376, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
376 376 1.00
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.23
Consensus pattern (376 bp):
GAAACAGCGTCGAAATGGTACAATCAGTTGAGCCGTACCGAGATTGGTTCATGGAGGGACCTAGC
ACAGGCATTCATGAAACAATACGGTCATGTAACGGATATGGTTCCCGATAGAATCACCTTGCAAA
ATTTGGAAAAGAAATCGAGCGAAAGTTTTAGGCAGTATGCACAAAGGTGGAGGGAGGTTGCAGTC
CAGGTTCAGCCACCCCTCTTGGAGAAAGAGACGACAATGCTCTTCATCAATACACTGAAGGCCCC
GTTCATTACGCATATGTTAGAAAGCGCAACAAAAAGCTTTTCTGATATAGTTATGAATGGTTAAA
TGATTGAGAATGCTATAAGAGCCGAAAAAATTGAGGCGGAAGAGAGTGATA
Found at i:29337338 original size:27 final size:26
Alignment explanation
Indices: 29337301--29337351 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
29337291 AAAAAGGAGC
**
29337301 AAAAGAAAAAAATCAAAATCAAAACA
1 AAAAGAAAAAAAGAAAAATCAAAACA
29337327 AAAAGAAGAAAAAGAAAAATCAAAA
1 AAAAGAA-AAAAAGAAAAATCAAAA
29337352 ATCAAGGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.06
Consensus pattern (26 bp):
AAAAGAAAAAAAGAAAAATCAAAACA
Found at i:29337377 original size:13 final size:12
Alignment explanation
Indices: 29337361--29337409 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
29337351 AATCAAGGTC
*
29337361 AAAATGAAAATGA
1 AAAAAGAAAA-GA
*
29337374 AAAATAGAGAAGAA
1 AAAA-AGAAAAG-A
29337388 AAAAAGAAAAGA
1 AAAAAGAAAAGA
29337400 AAAAAGAAAA
1 AAAAAGAAAA
29337410 AGAGAAGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 11 0.35
13 11 0.35
14 9 0.29
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:29339762 original size:88 final size:87
Alignment explanation
Indices: 29339498--29340071 Score: 735
Period size: 88 Copynumber: 6.6 Consensus size: 87
29339488 CAGATCAGTG
* * *
29339498 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCATATCGAAAACA-AAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* * *
29339562 ATCGATTGCATTGGAGCTGGTTA
65 ATCGGTTGCAGTGGAGCAGGTTA
* * * * *
29339585 AAGACAACAGATCTTGTCTTCCTGCATTGACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
*
29339649 ATTGGTTGCAGTGGAGC-GGATTA
65 ATCGGTTGCAGTGGAGCAGG-TTA
** * *
29339672 AAGATATTAGATTTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
29339737 ATCGGTTGCAGTGGAGCAGGTTA
65 ATCGGTTGCAGTGGAGCAGGTTA
* * *
29339760 AAGATAGCAGATCTTGCCTTCCTACACT-ACAGCGAAGCAGATCGAAGATACCAACCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
*
29339824 CTCGGTTGCAGTGGAGCAGGTTA
65 ATCGGTTGCAGTGGAGCAGGTTA
*
29339847 AAGATAGCAGATCTTGCCCTCCTACGC-TGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCT--GCATGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTC
*
29339911 CCTCGGTTGCAGTGGAGCAGGTTA
64 CATCGGTTGCAGTGGAGCAGGTTA
* * *
29339935 AAGATAGCAGATCTTGCCCTCCTGCGCTGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGC-ATGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* * *
29340000 CTCGGTTGTAGTGGAGCAGGTTG
65 ATCGGTTGCAGTGGAGCAGGTTA
* * * * *
29340023 AAGATAGCAGATCTTACCTTTCTGCATCGACAGTGAAGTAGATCAAAGA
1 AAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGA
29340072 TTACAAGTCC
Statistics
Matches: 437, Mismatches: 39, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
86 5 0.01
87 198 0.45
88 230 0.53
89 4 0.01
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (87 bp):
AAGATAGCAGATCTTGCCTTCCTGCATGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCA
TCGGTTGCAGTGGAGCAGGTTA
Found at i:29339823 original size:175 final size:174
Alignment explanation
Indices: 29339498--29340071 Score: 744
Period size: 175 Copynumber: 3.3 Consensus size: 174
29339488 CAGATCAGTG
* * **
29339498 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCATATCGAA-AACAAAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCC
* * * * * * *
29339562 ATCGATTGCATTGGAGCTGGTTAAAGACAACAGATCTTGTCTTCCTGCATTGACAGCGAAGCAGA
65 ATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGA
* * *
29339627 TCGAA-AACAAAGCCTTGCCTCCATTGGTTGCAGTGGAGC-GGATTA
130 TCGAAGAACCAA-CCTTGCCTCCCTCGGTTGCAGTGGAGCAGG-TTA
** *
29339672 AAGATATTAGATTTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCC
*
29339737 ATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTACACT-ACAGCGAAGCAGA
65 ATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGA
29339801 TCGAAGATACCAACCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTA
130 TCGAAGA-ACCAACCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTA
* *
29339847 AAGATAGCAGATCTTGCCCTCCTACGC-TGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCT--GCATGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTC
* * * *
29339911 CCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCCTCCTGCGCTGACAACGAAGCAG
64 CATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAG
* * *
29339976 ATCGAAGACACCAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTG
129 ATCGAAGA-ACCAACCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTA
* * * * *
29340023 AAGATAGCAGATCTTACCTTTCTGCATCGACAGTGAAGTAGATCAAAGA
1 AAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGA
29340072 TTACAAGTCC
Statistics
Matches: 352, Mismatches: 38, Indels: 18
0.86 0.09 0.04
Matches are distributed among these distances:
173 1 0.00
174 61 0.17
175 189 0.54
176 99 0.28
177 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (174 bp):
AAGATAGCAGATCTTGCCTTCCTGCATGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCCA
TCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGAT
CGAAGAACCAACCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTA
Found at i:29340273 original size:44 final size:45
Alignment explanation
Indices: 29340205--29340415 Score: 137
Period size: 44 Copynumber: 4.6 Consensus size: 45
29340195 TGAAGCCAGT
*
29340205 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGA
* * * * * *
29340249 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGA
1 AATCTTATCTCCCTGAGA-TTACAGT-G-G-AG--CGGATTAAAAT-AA---AGA
* * ** *
29340303 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT--AGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAAAGA
*
29340347 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA-A
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGA
* *
29340391 GATCTTATCTCTCTGA-AGTTACAGT
1 AATCTTATCTCCCTGAGA-TTACAGT
29340416 AGAGTAGATC
Statistics
Matches: 125, Mismatches: 26, Indels: 32
0.68 0.14 0.17
Matches are distributed among these distances:
43 5 0.04
44 74 0.59
45 2 0.02
46 1 0.01
47 2 0.02
49 10 0.08
50 4 0.03
51 2 0.02
52 1 0.01
53 3 0.02
54 20 0.16
55 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (45 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGA
Found at i:29340369 original size:98 final size:97
Alignment explanation
Indices: 29340191--29340371 Score: 231
Period size: 98 Copynumber: 1.8 Consensus size: 97
29340181 GTAATGAAGT
* * * * *
29340191 AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTA
1 AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAT-AAGAATCCTA
*
29340256 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATC
65 TCTCCCTGAAGTTACAGTAGAGTAGATCGCATC
* **
29340289 AGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAATCCT
1 AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAATAAG-AATCCT
29340353 ATCTCCCTG-AGATTACAGT
64 ATCTCCCTGAAG-TTACAGT
29340372 GGAGCGGATT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
97 4 0.06
98 64 0.90
99 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (97 bp):
AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAGAATCCTAT
CTCCCTGAAGTTACAGTAGAGTAGATCGCATC
Found at i:29340447 original size:142 final size:142
Alignment explanation
Indices: 29340191--29340457 Score: 507
Period size: 142 Copynumber: 1.9 Consensus size: 142
29340181 GTAATGAAGT
*
29340191 AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTA
1 AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
*
29340256 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGA
66 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAAATTGAAGCCAGAAATCTTATCTCCCTGAGA
29340321 TTACAGCGGAGC
131 TTACAGCGGAGC
*
29340333 AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
1 AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
29340398 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAAATTGAAGCCAGAAATCTTATCTCCC
66 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAAATTGAAGCCAGAAATCTTATCTCCC
29340458 AAGCGATGCA
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 122 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (142 bp):
AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAAATTGAAGCCAGAAATCTTATCTCCCTGAGA
TTACAGCGGAGC
Found at i:29340533 original size:50 final size:50
Alignment explanation
Indices: 29340464--29340750 Score: 340
Period size: 50 Copynumber: 5.7 Consensus size: 50
29340454 TCCCAAGCGA
*
29340464 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
* ** * * * * * **
29340514 TGCGGTTCAAAAGATTAAAGCTACAACAGCGAATCTTACCTCCCAGGCGG
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
* * * *
29340564 TGCAGTAGAGCAGATTAAAGCCACAACAGTGAATCTTGCCTCCCTGACAT
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
* * * *
29340614 TGCAGTGGAGCATATTAAAGCCACAACAGTGAATCTTGCCTCCCTGACAT
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
* *
29340664 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCATGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
** * **
29340714 TGCAGTTAAAAAGATTAAAGCCACAATGGCGAATCTT
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTT
29340751 ACTTTCCAAA
Statistics
Matches: 200, Mismatches: 37, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 200 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (50 bp):
TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
Found at i:29340631 original size:100 final size:100
Alignment explanation
Indices: 29340445--29340752 Score: 384
Period size: 100 Copynumber: 3.1 Consensus size: 100
29340435 TGAAGCCAGA
* *
29340445 AATCTTATCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCG
1 AATCTTACCTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCG
* * *
29340510 ACATTGCGGTTCAAAAGATTAAAGCTACAACAGCG
66 ACATTGCAGTGCAAAAGATTAAAGCCACAACAGCG
* * * * * *
29340545 AATCTTACCTCCCAGGCGGTGCAGTAGAGCAGATTAAAGCCACAACAGTGAATCTTGCCTCCCTG
1 AATCTTACCTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCG
* ** * *
29340610 ACATTGCAGTGGAGCATATTAAAGCCACAACAGTG
66 ACATTGCAGTGCAAAAGATTAAAGCCACAACAGCG
* * * *
29340645 AATCTTGCCTCCCTGAC-ATTGCAGTGGAACAGATTAAAGCCACAACAGCGAATCATGCTTCCCC
1 AATCTTACCTCCCAGGCGA-TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCC
** **
29340709 GACATTGCAGTTAAAAAGATTAAAGCCACAATGGCG
65 GACATTGCAGTGCAAAAGATTAAAGCCACAACAGCG
29340745 AATCTTAC
1 AATCTTAC
29340753 TTTCCAAAAG
Statistics
Matches: 172, Mismatches: 35, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
100 172 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (100 bp):
AATCTTACCTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCG
ACATTGCAGTGCAAAAGATTAAAGCCACAACAGCG
Found at i:29342176 original size:23 final size:23
Alignment explanation
Indices: 29342150--29342194 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29342140 CACGCATTTT
*
29342150 TTTATATAGTATAGACATATTCC
1 TTTATATAATATAGACATATTCC
* *
29342173 TTTATATAATATATATATATTC
1 TTTATATAATATAGACATATTC
29342195 TTAAACTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTATATAATATAGACATATTCC
Found at i:29346524 original size:36 final size:36
Alignment explanation
Indices: 29346484--29346563 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
29346474 GACAAGAAGG
* * *
29346484 AAGGAAAAATAAAAGAAAGAAATGAAAAAGAAAA-AT
1 AAGGAAAAACAAAA-AAACAAATGAAAAAGAAAAGAA
* **
29346520 AAGGAAGAACAAAAAAACAAATGATTAAGAAAAGAA
1 AAGGAAAAACAAAAAAACAAATGAAAAAGAAAAGAA
29346556 AAGGAAAA
1 AAGGAAAA
29346564 CGTTAATTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 16 0.44
36 20 0.56
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.07
Consensus pattern (36 bp):
AAGGAAAAACAAAAAAACAAATGAAAAAGAAAAGAA
Found at i:29355738 original size:54 final size:54
Alignment explanation
Indices: 29355656--29355780 Score: 232
Period size: 54 Copynumber: 2.3 Consensus size: 54
29355646 ATCACGGTCT
29355656 CGGGTGCGGGTGCTTCAACCGGTGGGTCGGCCTTCTCTTCTTCCCTGACTTCAA
1 CGGGTGCGGGTGCTTCAACCGGTGGGTCGGCCTTCTCTTCTTCCCTGACTTCAA
* *
29355710 CGGGTGCGGGTGCTTCAATCGGTGGGTCGGCCTTCTCTTCTTCCTTGACTTCAA
1 CGGGTGCGGGTGCTTCAACCGGTGGGTCGGCCTTCTCTTCTTCCCTGACTTCAA
29355764 CGGGTGCGGGTGCTTCA
1 CGGGTGCGGGTGCTTCA
29355781 GTTTCGACTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.09, C:0.29, G:0.32, T:0.30
Consensus pattern (54 bp):
CGGGTGCGGGTGCTTCAACCGGTGGGTCGGCCTTCTCTTCTTCCCTGACTTCAA
Found at i:29367732 original size:27 final size:27
Alignment explanation
Indices: 29367499--29367721 Score: 259
Period size: 27 Copynumber: 8.3 Consensus size: 27
29367489 AGAGGTCGAT
* *
29367499 AAATGATCGAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
29367526 AACTGACCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
** *
29367553 AAATGACCGAAATACCCCTGTAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
29367580 AAATGACCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
29367607 GAATGACCGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* **
29367634 AAATTG-TCGAAATACCTTCATAGGGTA
1 AAA-TGACCGAAATACCCCCATAGGGTA
** * *
29367661 AAATGACTAAAATACTCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
**
29367688 AAATGACTAAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
29367715 AAATGAC
1 AAATGAC
29367722 TATTATACCC
Statistics
Matches: 168, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 2 0.01
27 164 0.98
28 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:29367746 original size:81 final size:78
Alignment explanation
Indices: 29367508--29367749 Score: 236
Period size: 81 Copynumber: 3.0 Consensus size: 78
29367498 TAAATGATCG
* *
29367508 AAATACCCCCATAGGATAAACTGACCGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCT-
1 AAATA-CCCCATAGGATAAAATGACCGAAATACCCCCATAGGGTAAAATGA-CGAAATACCCCTA
* **
29367572 GTAAGGTAAAATGACCG
64 G-GA-GTAAAATGACTA
* * * * *
29367589 AAATACCCCTATAGGGTAGAATGACCGAAATACCCCCATAAGGTAAAATTGTCGAAATACCTTCA
1 AAATACCCC-ATAGGATAAAATGACCGAAATACCCCCATAGGGTAAAA-TGACGAAATACC--CC
29367654 TAGG-GTAAAATGACTA
62 TAGGAGTAAAATGACTA
** * *
29367670 AAATACTCCCATAGGATAAAATGACTAAAATACCCCCATAGGGTAAAATGACTATTATACCCCTA
1 AAATAC-CCCATAGGATAAAATGACCGAAATACCCCCATAGGGTAAAATGACGA-AATACCCCTA
*
29367735 GGAGATGAAATGACT
64 GGAG-TAAAATGACT
29367750 GTTATGGCTT
Statistics
Matches: 132, Mismatches: 20, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
79 5 0.04
80 9 0.07
81 110 0.83
82 5 0.04
83 2 0.02
84 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (78 bp):
AAATACCCCATAGGATAAAATGACCGAAATACCCCCATAGGGTAAAATGACGAAATACCCCTAGG
AGTAAAATGACTA
Found at i:29372914 original size:35 final size:35
Alignment explanation
Indices: 29372868--29372939 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
29372858 TTCAGAAATA
*
29372868 TCTCGCCTGCTTAGATAAAGAGTCGAAAGATATGG
1 TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
29372903 TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
1 TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
29372938 TC
1 TC
29372940 ATGCTGTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (35 bp):
TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
Found at i:29384425 original size:50 final size:53
Alignment explanation
Indices: 29384340--29384447 Score: 143
Period size: 50 Copynumber: 2.1 Consensus size: 53
29384330 TGATTCAAGA
*
29384340 ATGTTTATGAAGGAGGATGTGTAGCCTTCAGGCTTGACACAT-AGTGCCTAGGC
1 ATGTTTATGAAGGAGGATGTGTAGCCTTCAAGCTTGACAC-TCAGTGCCTAGGC
* **
29384393 ATGTTTCTGAA-G-GGATGT-TAGCCTTCAAGCTTGGTACTCAGTGCCTAGGC
1 ATGTTTATGAAGGAGGATGTGTAGCCTTCAAGCTTGACACTCAGTGCCTAGGC
29384443 ATGTT
1 ATGTT
29384448 CTTGGTTGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
49 1 0.02
50 32 0.64
51 6 0.12
52 1 0.02
53 10 0.20
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (53 bp):
ATGTTTATGAAGGAGGATGTGTAGCCTTCAAGCTTGACACTCAGTGCCTAGGC
Found at i:29388171 original size:11 final size:11
Alignment explanation
Indices: 29388157--29388232 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
29388147 GATAATCACT
29388157 TTAATATTAAA
1 TTAATATTAAA
29388168 TTAATA--AAA
1 TTAATATTAAA
*
29388177 -TATTATTAAA
1 TTAATATTAAA
*
29388187 ATAAGTATTAAA
1 TTAA-TATTAAA
29388199 TTAA-ATTTAATA
1 TTAATA-TTAA-A
29388211 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
29388224 ATAATATTA
1 TTAATATTA
29388233 TTTTTTTGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:29393984 original size:13 final size:13
Alignment explanation
Indices: 29393966--29393992 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29393956 TTCAACACTA
29393966 ACAGATTATCATG
1 ACAGATTATCATG
29393979 ACAGATTATCATG
1 ACAGATTATCATG
29393992 A
1 A
29393993 TACTATCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ACAGATTATCATG
Found at i:29405596 original size:516 final size:511
Alignment explanation
Indices: 29403274--29405761 Score: 4379
Period size: 511 Copynumber: 4.9 Consensus size: 511
29403264 TTGGGACGAA
* * **
29403274 AGTCGTCTACAAGCAAAGAAAAGGGAAAAGCGAAG-TTTGTTTAAAGCTTTCAACAAACCGGTGA
1 AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTT-TTTAAAGCTTTCAATAAACTAGTGA
* *
29403338 GTG-TTTGGGGTTCGCTGCTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTTTA
65 GTGTTTTGGGGTT-GCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTA
* * * **
29403402 AAACACCTAATCTAATTCCCGAGTGTAAGTTTCTTACTTTAACTTTTGTATTTTGTGATAAATGT
129 AAACACCTAATCTAAGTCCTGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAAT-T
* * * * * * *
29403467 -TTGTGTTATATTATAAGAAGTTCACACATGCGAACCATAGTTCGCATATGTAGTTTAGTCGAGT
193 CTTGTGTTATGTTATAAGGAGTTCATACACGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGT
* * * *
29403531 ATAGGATCGCAGACATCATGCTGCAAAGTATGTGACTGTGATATGTGTTAAATATGAAAATTAAT
258 ATAGGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAAT
29403596 ATCTGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCAT
323 ATCTGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCAT
29403661 AGGATTGTGAGTACTAACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAA
388 AGGATTGTGAGTACTAACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAA
29403726 AATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
453 AATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
29403785 AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
1 AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
29403850 TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
66 TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
29403915 ACACCTAATCTAAGTCCTGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
131 ACACCTAATCTAAGTCCTGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
29403980 GTGTTATGTTATAAGGAGTTCATACACGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATA
196 GTGTTATGTTATAAGGAGTTCATACACGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATA
* *
29404045 GGATCGCAGACATTATATTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAACTAATATC
261 GGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATC
* *
29404110 AGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAACTGGATATTGTTGGCATGCCATAGG
326 TGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGG
*
29404175 ATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
391 ATTGTGAGTACTAACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
29404240 AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
456 AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
*
29404296 AGTCATCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
1 AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
29404361 TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
66 TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
29404426 ACACCTAATCTAAGTCCTGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
131 ACACCTAATCTAAGTCCTGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
29404491 GTGTTATGTTATAAGGAGTTCATACACGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATA
196 GTGTTATGTTATAAGGAGTTCATACACGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATA
*
29404556 GGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATC
261 GGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATC
29404621 TGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGG
326 TGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGG
29404686 ATTGTGAGTACTAACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
391 ATTGTGAGTACTAACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
29404751 AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
456 AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
* *
29404807 AGTCGTTTACATGTAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
1 AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
*
29404872 TGTTTTGGGGTTGCTACTAGTACGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
66 TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
29404937 ACACCTAATCTAAGTCCTGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
131 ACACCTAATCTAAGTCCTGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
* *
29405002 GTGTTATGTTATAAGGAGTTCATACACGTGAACCATAGTTTGCATATATAGTGTAGCCGAGTATA
196 GTGTTATGTTATAAGGAGTTCATACACGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATA
*
29405067 GGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAACTAATATC
261 GGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATC
* * * *
29405132 AGTAATTGTGGCTATTTTGGTACTACGATATTTGAAACAACTGGACATTGTTGGCATGCCATAGG
326 TGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGG
*
29405197 ATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
391 ATTGTGAGTACTAACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
* * *
29405262 ATTATGTTTCGTCTATTAGTAACTTGATTATATTTGTGAAGTTGTGAACCTAATAG
456 AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
* *
29405318 AGTCGTCTACATGCAAAAAAAGAGAGAGGGAAAAACGAAGCTTTTTTAAAGCTTTCAATAAACTA
1 AGTCGTCTACATGC----AAAGA-AAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTA
* * ** *
29405383 GTGAGTGTTTTGGGGTTACTGCTAGTATGAGCAAACCATTGTGTTAAACAAGAGCTTAGGTTGGT
61 GTGAGTGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGT
*
29405448 CTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAA
126 CTAAAACACCTAATCTAAGTCCTGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAA
* *
29405513 TTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGA
191 TTCTTGTGTTATGTTATAAGGAGTTCATACACGTGAACCATAGTTTGCATATGTAGTTTAGCCGA
*
29405578 GTATAGGATCGCAGACATTATACTGCGAAGTATGAGATTGTGATATGTGTTAAATATGAAAATTA
256 GTATAGGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTA
29405643 ATATCTGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCC
321 ATATCTGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCC
* *
29405708 ATAGGATTGTGAGTACTTACCTTTGTGTTTTATGATTTGGGCGAAAGGCCCTAG
386 ATAGGATTGTGAGTACTAACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAG
29405762 TGTCACGGGA
Statistics
Matches: 1896, Mismatches: 73, Indels: 11
0.96 0.04 0.01
Matches are distributed among these distances:
510 1 0.00
511 1479 0.78
512 12 0.01
515 5 0.00
516 399 0.21
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (511 bp):
AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
ACACCTAATCTAAGTCCTGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
GTGTTATGTTATAAGGAGTTCATACACGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATA
GGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATC
TGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGG
ATTGTGAGTACTAACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
Found at i:29407117 original size:513 final size:513
Alignment explanation
Indices: 29406398--29409493 Score: 5378
Period size: 513 Copynumber: 6.0 Consensus size: 513
29406388 CCCCGTGACA
* *
29406398 CTAGGACAGGTTAGGAGAAATAATATGTTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
*
29406463 TGAACCTAACAGAGTCGTCTACAGGC-AAAAAAAAGGGAAAAACGAAGCTTTTTTAAAGCTTTCA
66 TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
* *
29406527 ATAAACTAGTGAGTGGTTTGAGGTTGCTGCTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTT
131 ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCTT
*
29406592 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGATGTAAGTTTCTTACTTTAACTTTCATATTTT
196 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
*
29406657 GTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATATGTAGT
261 GTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGT
29406722 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
326 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
* *
29406787 GAAAATTAATATCTGTAATTGTGGTTATTTTGGTACTATGATCTTTCAAACAATTGGATATTGTT
391 GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGTT
29406852 GGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
456 GGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
* *
29406910 CTAGGACAGGTTAGCAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
*
29406975 TGAACCTAGCAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
66 TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
* *
29407040 ATAAACTAGTGAGTGTTTTGGGGTTGCTGCTAGTATGAGCAAACCATTGTGTTAAACGAGAGCTT
131 ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCTT
* *
29407105 AAGTTGGTCTAAAACACCTAATCTAAGTCCCAGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
196 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
*
29407170 GTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATTTGAACCATAGTTTGCATATGTAGT
261 GTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGT
*
29407235 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGAGATTGTGATATGTGTTAAATAT
326 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
* * * * *
29407300 GACAATTAATATTTGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAATAATTGGAAATTTGT
391 GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATA-TTGT
* *
29407365 AGGCATGCCGTAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
455 TGGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
29407424 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
*
29407489 TGAACCTAACAGAGTCGTCTACAAGCAAAAAAAAAAGGG---AGCGAAGCTTTTTTAAAGCTTTC
66 TGAACCTAACAGAGTCGTCTACAGGC-AAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTC
* *
29407551 AATAAACTAGTGAGTGGTTTAGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACAAGAGCT
130 AATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCT
29407616 TAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTT
195 TAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTT
*
29407681 TGTGGTAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAG
260 TGTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAG
* *
29407746 TTTAGCCGAGTATAGGATCGCAGACATTATGTTGCGAAGAATGTGATTGTGATATGTGTTAAATA
325 TTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATA
**
29407811 TGAAAATTAATATCTGTAATTGTGTTTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGT
390 TGAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGT
29407876 TGGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
455 TGGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
*
29407935 CTAGGATAGGTTAGCAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
29408000 TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
66 TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
* *
29408065 ATAAACTAGTGAGTGTTTTGGGGTTGCTGCTAGTATGAGCAAACCATTGTGTTAAACGAGAGCTT
131 ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCTT
*
29408130 AAGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
196 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
*
29408195 GTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATATGTAGT
261 GTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGT
* *
29408260 TTAGCCGAGTATAGGATCGCAGACATTATGTTGCGAAGAATGTGATTGTGATATGTGTTAAATAT
326 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
29408325 GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGTT
391 GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGTT
*
29408390 GGCATGCCATAGAATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
456 GGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
*
29408448 CTAGGATAGGTTAGCAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
29408513 TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
66 TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
*
29408578 ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAATGAGAGCTT
131 ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCTT
29408643 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
196 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
* *
29408708 GTGATAAATTCTTGTGTTATGTTATAAGGAGTTCATACATCTGAACCATAGTTTGCATATGTAGT
261 GTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGT
*
29408773 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTTTGTGATTGTGATATGTGTTAAATAT
326 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
* *
29408838 GAAAATTAATATCTGTAATGGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTT
391 GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGTT
*
29408903 GGCATGCCATAGGATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCGAAAGGCC
456 GGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
* *
29408961 CTTGGACAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
* *
29409026 TGAACCTAACGGAGTCGTCTACAGGCAAAAAGAAAAAAAAGGGAAAAGTGAAGCTTTTTTAAAGC
66 TGAACCTAACAGAGTCGTCTACAGGC----A-AAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGC
*
29409091 TTTCAATAAACTAGTGAGTGTTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAG
126 TTTCAATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAG
*
29409156 AGCTTAGGTTGGTCTAAAACACCTAATCTAAGTCCCAGGTGTAAGTTTCTTACTTTAACTTTCAT
191 AGCTTAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCAT
*
29409221 ATTTTGTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATAT
256 ATTTTGTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATAT
* *
29409286 GTAGTTTAGCCGAGTGTAGGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTA
321 GTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTA
* ** *
29409351 AATATG-TAATTAATATGAGTAATTGTGGCTATTTTGGT-GT-TGCAATCTTTGAAA-AAGTTGG
386 AATATGAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATG--ATCTTTGAAACAA-TTGG
* * *
29409412 ATATTGTTGGCATG---T--CA-TG-GAGTACTCACCTTTGTGGTTTT-TGATTTGGGCGAGAGG
448 ATATTGTTGGCATGCCATAGGATTGTGAGTACTCACGTTTGT-GTTTTATGATTTGGGCGAAAGG
29409469 CC
512 CC
* *
29409471 ATGGGATAGGTTAGGAGAAATAA
1 CTAGGATAGGTTAGGAGAAATAA
29409494 GGGAATGATG
Statistics
Matches: 2471, Mismatches: 98, Indels: 32
0.95 0.04 0.01
Matches are distributed among these distances:
510 65 0.03
511 157 0.06
512 415 0.17
513 1323 0.54
514 149 0.06
515 13 0.01
516 3 0.00
517 57 0.02
518 289 0.12
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (513 bp):
CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCTT
AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
GTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGT
TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGTT
GGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
Found at i:29413771 original size:14 final size:14
Alignment explanation
Indices: 29413740--29413789 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
29413730 CCCCGAATCT
29413740 TTAAACCCTC-AA-C
1 TTAAA-CCTCAAACC
**
29413753 TTAAACCTTGAACC
1 TTAAACCTCAAACC
29413767 TTAAACCTCAAACC
1 TTAAACCTCAAACC
*
29413781 CTAAACCTC
1 TTAAACCTC
29413790 GAGGTTCAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 3 0.10
13 7 0.23
14 21 0.68
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (14 bp):
TTAAACCTCAAACC
Found at i:29414356 original size:26 final size:27
Alignment explanation
Indices: 29414304--29414366 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 27
29414294 TAAAAAAATA
29414304 ACCAAAATATTATAATTTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTTATTT
29414331 ACCAAAATATTATAA-TTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTTATTT
29414357 ACCAAAATAT
1 ACCAAAATAT
29414367 ACAAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 21 0.58
27 15 0.42
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
ACCAAAATATTATAATTTTTTTTATTT
Found at i:29414394 original size:19 final size:19
Alignment explanation
Indices: 29414359--29414396 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
29414349 TTTTATTTAC
*
29414359 CAAAATATACAAAAAAAAA
1 CAAAAAATACAAAAAAAAA
29414378 CAAAAAATA-AAAGAAAAAA
1 CAAAAAATACAAA-AAAAAA
29414397 AAACCTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.82, C:0.08, G:0.03, T:0.08
Consensus pattern (19 bp):
CAAAAAATACAAAAAAAAA
Found at i:29414813 original size:19 final size:19
Alignment explanation
Indices: 29414789--29414854 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
29414779 ATTAAAATAG
29414789 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
29414808 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
29414826 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
29414845 TTTAATTTAA
1 TTTAATTTAA
29414855 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:29415033 original size:82 final size:82
Alignment explanation
Indices: 29414944--29415100 Score: 296
Period size: 82 Copynumber: 1.9 Consensus size: 82
29414934 AAAAATAACA
* *
29414944 GAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAACATAAACA
1 GAAACATAAACTATTTTATCTATTTATAAACTTAATATATTCTTAATAGACTTATAACATAAAAA
29415009 TGTTAGACTAAATAATG
66 TGTTAGACTAAATAATG
29415026 GAAACATAAACTATTTTATCTATTTATAAACTTAATATATTCTTAATAGACTTATAACATAAAAA
1 GAAACATAAACTATTTTATCTATTTATAAACTTAATATATTCTTAATAGACTTATAACATAAAAA
29415091 TGTTAGACTA
66 TGTTAGACTA
29415101 TTTTAATTAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (82 bp):
GAAACATAAACTATTTTATCTATTTATAAACTTAATATATTCTTAATAGACTTATAACATAAAAA
TGTTAGACTAAATAATG
Found at i:29415208 original size:18 final size:19
Alignment explanation
Indices: 29415169--29415264 Score: 124
Period size: 19 Copynumber: 5.2 Consensus size: 19
29415159 ATTTTATATT
29415169 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
29415188 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
29415206 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
29415225 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
29415243 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
29415262 TTA
1 TTA
29415265 CTTAATTAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 30 0.47
19 34 0.53
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:29415210 original size:37 final size:37
Alignment explanation
Indices: 29415169--29415264 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
29415159 ATTTTATATT
*
29415169 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
29415206 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
29415243 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
29415265 CTTAATTAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:29415951 original size:30 final size:28
Alignment explanation
Indices: 29415903--29415964 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
29415893 TTTTTGGAGT
*
29415903 ATATTTTAATAAAT--AAAAAAATTATA
1 ATATTTTGATAAATAAAAAAAAATTATA
29415929 ATATTTTGATAAATAAAAAAAAATTATA
1 ATATTTTGATAAATAAAAAAAAATTATA
29415957 ATATTTTG
1 ATATTTTG
29415965 GTTATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 13 0.39
28 20 0.61
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
ATATTTTGATAAATAAAAAAAAATTATA
Found at i:29418468 original size:28 final size:28
Alignment explanation
Indices: 29418437--29418502 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
29418427 TCTGGGTCGA
29418437 GCCCGACCCAATTTTTTTACTTGG-CTCG
1 GCCCGACCCAATTTTTTTACTTGGCCT-G
*
29418465 GCCCAACCCAATTTTTTTACTTGGCCTG
1 GCCCGACCCAATTTTTTTACTTGGCCTG
29418493 GCCCGACCCA
1 GCCCGACCCA
29418503 TGGACAACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.17, C:0.36, G:0.17, T:0.30
Consensus pattern (28 bp):
GCCCGACCCAATTTTTTTACTTGGCCTG
Found at i:29426093 original size:39 final size:40
Alignment explanation
Indices: 29426005--29426093 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 40
29425995 GCTTTTTAAA
* **
29426005 CGTTTTTTTTTTGTTTTCTTCTTTTTCTTCTTTCCATTTT
1 CGTTTTTTTTTTGTTTTCTTCGTTTTCCCCTTTCCATTTT
29426045 C-TTTATTTTTTCT-TTTTCTT-GTTTTCCCCTTT-CATTTT
1 CGTTT-TTTTTT-TGTTTTCTTCGTTTTCCCCTTTCCATTTT
29426083 CAGTTTTTTTT
1 C-GTTTTTTTT
29426094 ACATAGTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
38 7 0.17
39 17 0.40
40 17 0.40
41 1 0.02
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.73
Consensus pattern (40 bp):
CGTTTTTTTTTTGTTTTCTTCGTTTTCCCCTTTCCATTTT
Found at i:29428223 original size:41 final size:41
Alignment explanation
Indices: 29428111--29428230 Score: 145
Period size: 41 Copynumber: 2.9 Consensus size: 41
29428101 ACCGGCTTTT
* *
29428111 AGCCTGCTAGACTTATAGT-TCGAA-ACATATCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCT-GAATA-ATTTCACCGGCATCA
* *
29428152 AGCCTGCTAGACGTATATTCTGAATAATTTCACCGGCATCA
1 AGCCTGCTAGACTTATAGTCTGAATAATTTCACCGGCATCA
* * *
29428193 AGCCTGCTAGACTTAAAGTCTGAATTATTTCACTGGCA
1 AGCCTGCTAGACTTATAGTCTGAATAATTTCACCGGCA
29428231 ATAAATCCGA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 66 0.97
42 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAATAATTTCACCGGCATCA
Found at i:29433767 original size:15 final size:15
Alignment explanation
Indices: 29433683--29433774 Score: 51
Period size: 15 Copynumber: 5.7 Consensus size: 15
29433673 TCTTTTTTAA
*
29433683 TTTTC-TTTTCTTCG
1 TTTTCTTTTTCTTCT
*
29433697 TTTTCTTTTTCTCACTT
1 TTTTCTTTTTCT-TC-T
* *
29433714 TTTTGATTTCTTTTTCT
1 TTTT-CTTT-TTCTTCT
* *
29433731 TTTTCTTCTTCACTTTCC
1 TTTTCTT-TT-TC-TTCT
29433749 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTCT
29433764 TTTTCATTTTT
1 TTTTC-TTTTT
29433775 ATTACAATGT
Statistics
Matches: 58, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
14 5 0.09
15 14 0.24
16 10 0.17
17 12 0.21
18 14 0.24
19 3 0.05
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:29435575 original size:175 final size:175
Alignment explanation
Indices: 29435284--29435633 Score: 691
Period size: 175 Copynumber: 2.0 Consensus size: 175
29435274 ATGAAGAAAA
*
29435284 CAACTATTTATAGACAGCCCCTAAGCTAGCCGAATAGTCACATACATTCTTAAGAACTAAGCAAA
1 CAACTATTTATAGACAGCACCTAAGCTAGCCGAATAGTCACATACATTCTTAAGAACTAAGCAAA
29435349 TGAACCCAATTAATTGAGCTAGCAAGGTTCGGCTGAATCTGAGCTCCAATGGTCAACTTCTAGAA
66 TGAACCCAATTAATTGAGCTAGCAAGGTTCGGCTGAATCTGAGCTCCAATGGTCAACTTCTAGAA
29435414 TGAGCAATGGACTTGGAAGCTTGAGGAAGGTGCATGGCAGCAGCT
131 TGAGCAATGGACTTGGAAGCTTGAGGAAGGTGCATGGCAGCAGCT
29435459 CAACTATTTATAGACAGCACCTAAGCTAGCCGAATAGTCACATACATTCTTAAGAACTAAGCAAA
1 CAACTATTTATAGACAGCACCTAAGCTAGCCGAATAGTCACATACATTCTTAAGAACTAAGCAAA
29435524 TGAACCCAATTAATTGAGCTAGCAAGGTTCGGCTGAATCTGAGCTCCAATGGTCAACTTCTAGAA
66 TGAACCCAATTAATTGAGCTAGCAAGGTTCGGCTGAATCTGAGCTCCAATGGTCAACTTCTAGAA
29435589 TGAGCAATGGACTTGGAAGCTTGAGGAAGGTGCATGGCAGCAGCT
131 TGAGCAATGGACTTGGAAGCTTGAGGAAGGTGCATGGCAGCAGCT
29435634 ATATTTGATT
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 174 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.23
Consensus pattern (175 bp):
CAACTATTTATAGACAGCACCTAAGCTAGCCGAATAGTCACATACATTCTTAAGAACTAAGCAAA
TGAACCCAATTAATTGAGCTAGCAAGGTTCGGCTGAATCTGAGCTCCAATGGTCAACTTCTAGAA
TGAGCAATGGACTTGGAAGCTTGAGGAAGGTGCATGGCAGCAGCT
Found at i:29436542 original size:24 final size:24
Alignment explanation
Indices: 29436515--29436589 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
29436505 ATTTGATATG
*
29436515 TTCTGTATGTGAAACTGAAATTGC
1 TTCTGTATATGAAACTGAAATTGC
* * *
29436539 TTCTGCATATGTAACTG-ATTTG-
1 TTCTGTATATGAAACTGAAATTGC
*
29436561 TTCTGTATCT-AAACT-AATATTGC
1 TTCTGTATATGAAACTGAA-ATTGC
29436584 TTCTGT
1 TTCTGT
29436590 TAGCTAACCG
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
21 5 0.12
22 11 0.28
23 10 0.25
24 14 0.35
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (24 bp):
TTCTGTATATGAAACTGAAATTGC
Found at i:29438763 original size:87 final size:88
Alignment explanation
Indices: 29438625--29438820 Score: 274
Period size: 87 Copynumber: 2.3 Consensus size: 88
29438615 CCCTCAAATT
* * *
29438625 AAAAAA-AAATTAAGCCCCT-CTTTTTTTTGCACTCAATTGAGTAGTTTAACTTTCAAAATGCAT
1 AAAAAAGAAATTAAGCCCCTGCTTTTTTTTGCACTCAACTGAGTACTTGAACTTTCAAAATGCAT
*
29438688 AAAAAAAACCCTCAAACTTCTTC
66 AAAAAAAACCCTCAAAATTCTTC
*
29438711 AAAAAAAGAAATTAAG-CCCTGCTTTTTTTT-CACTCAACTGGGTACTTGAACTTTCAAAATGCA
1 -AAAAAAGAAATTAAGCCCCTGCTTTTTTTTGCACTCAACTGAGTACTTGAACTTTCAAAATGCA
* *
29438774 TAAAAAAGACCCTCAAAATTTTTC
65 TAAAAAAAACCCTCAAAATTCTTC
* *
29438798 AAAACAGCAATTAAGCCCCTGCT
1 AAAAAAGAAATTAAGCCCCTGCT
29438821 CTTATTAAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
86 13 0.13
87 67 0.69
88 17 0.18
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (88 bp):
AAAAAAGAAATTAAGCCCCTGCTTTTTTTTGCACTCAACTGAGTACTTGAACTTTCAAAATGCAT
AAAAAAAACCCTCAAAATTCTTC
Found at i:29438845 original size:7 final size:7
Alignment explanation
Indices: 29438823--29438876 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
29438813 CCCCTGCTCT
29438823 TATTAAA
1 TATTAAA
*
29438830 AATTTAAA
1 TA-TTAAA
29438838 TATTAAA
1 TATTAAA
29438845 TATTAAA
1 TATTAAA
29438852 TATTATAA
1 TATTA-AA
29438860 -A--AAA
1 TATTAAA
29438864 TATTAAA
1 TATTAAA
*
29438871 TTTTAA
1 TATTAA
29438877 TAGAAATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 27 0.69
8 8 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TATTAAA
Found at i:29438907 original size:27 final size:28
Alignment explanation
Indices: 29438855--29438910 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
29438845 TATTAAATAT
*
29438855 TATAAAAAATATTAAATTTTAATAGAAA
1 TATAAAAAATATTAAAATTTAATAGAAA
* *
29438883 TATAACAAAT-TTAAAATTTATTAGAAA
1 TATAAAAAATATTAAAATTTAATAGAAA
29438910 T
1 T
29438911 TAGAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (28 bp):
TATAAAAAATATTAAAATTTAATAGAAA
Found at i:29439229 original size:20 final size:19
Alignment explanation
Indices: 29439179--29439230 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
29439169 ATTTTATGAA
29439179 TTTATAAAATTTTATATAT
1 TTTATAAAATTTTATATAT
* * *
29439198 TTTTTTATATTTCTATATAT
1 TTTATAAAATTT-TATATAT
29439218 TTTATAAAATTTT
1 TTTATAAAATTTT
29439231 TACGATTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATAAAATTTTATATAT
Found at i:29439230 original size:30 final size:30
Alignment explanation
Indices: 29439141--29439231 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 30
29439131 TTTTACGAAA
* * * * *
29439141 TTTATATTTCTTTACATTTTGTATAATTAT
1 TTTATATTTCTATAAATTTTATAAAATTTT
* *
29439171 TTTATGAATT-TATAAAATTTTAT-ATATTTT
1 TTTAT-ATTTCTAT-AAATTTTATAAAATTTT
*
29439201 TTTATATTTCTATATATTTTATAAAATTTT
1 TTTATATTTCTATAAATTTTATAAAATTTT
29439231 T
1 T
29439232 ACGATTTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
29 11 0.23
30 26 0.55
31 10 0.21
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTATATTTCTATAAATTTTATAAAATTTT
Found at i:29439239 original size:39 final size:38
Alignment explanation
Indices: 29439179--29439282 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 38
29439169 ATTTTATGAA
* * * *
29439179 TTTATAAAATTTTATA-TATTTTTTTATATTTCTATATAT
1 TTTATAAAATTTT-TACGATTTTTATAAATTTCTACA-AT
*
29439218 TTTATAAAATTTTTACGATTTTTATAAATTTGTACAAT
1 TTTATAAAATTTTTACGATTTTTATAAATTTCTACAAT
*
29439256 TTTATATATATTATTTTACGATTTTTA
1 TTTATA-A-AAT-TTTTACGATTTTTA
29439283 ATAATTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
38 10 0.18
39 29 0.53
40 2 0.04
41 14 0.25
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (38 bp):
TTTATAAAATTTTTACGATTTTTATAAATTTCTACAAT
Found at i:29439240 original size:20 final size:20
Alignment explanation
Indices: 29439217--29439291 Score: 73
Period size: 19 Copynumber: 3.8 Consensus size: 20
29439207 TTTCTATATA
29439217 TTTTATAAAATTTTTACGAT
1 TTTTATAAAATTTTTACGAT
* *
29439237 TTTTAT-AAATTTGTACAAT
1 TTTTATAAAATTTTTACGAT
* *
29439256 TTTATATATATTATTTTACGAT
1 TTT-TATAAAAT-TTTTACGAT
*
29439278 TTTTA-ATAATTTTT
1 TTTTATAAAATTTTT
29439292 TAATATCTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 18 0.40
20 13 0.29
21 4 0.09
22 10 0.22
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTATAAAATTTTTACGAT
Found at i:29439458 original size:85 final size:84
Alignment explanation
Indices: 29439369--29439560 Score: 235
Period size: 86 Copynumber: 2.3 Consensus size: 84
29439359 ATAAAAGCAA
29439369 GGGCTTAATTGGTTTTTTTTTA-GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCC
1 GGGCTTAATTGGTTTTTTTTTAGGTTTGAGGG-CTTTTT-ATGCATTTTGAAAGTTCAAGTACCC
* **
29439433 AATTGAGTGCAAAAAAAGTAG
64 AAATGAGTGCAAAAAAAACAG
* ** * * *
29439454 GGGCTTAATTGCTTTTTTTGAAAAGGTTTGAGGGCTTTTTATGCATTTTTAAAGTTTAAGTACCG
1 GGGCTTAATTGGTTTTTTT--TTAGGTTTGAGGGCTTTTTATGCATTTTGAAAGTTCAAGTACCC
*
29439519 AAATGAGTGTAAAAAAAACAG
64 AAATGAGTGCAAAAAAAACAG
*
29439540 AGGCTTAATT-GTTTTTTTTTA
1 GGGCTTAATTGGTTTTTTTTTA
29439561 AAAAGAATTT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
83 1 0.01
85 25 0.28
86 48 0.53
87 7 0.08
88 9 0.10
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (84 bp):
GGGCTTAATTGGTTTTTTTTTAGGTTTGAGGGCTTTTTATGCATTTTGAAAGTTCAAGTACCCAA
ATGAGTGCAAAAAAAACAG
Found at i:29439515 original size:86 final size:88
Alignment explanation
Indices: 29439391--29439563 Score: 242
Period size: 86 Copynumber: 2.0 Consensus size: 88
29439381 TTTTTTTTTA
* ** *
29439391 GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAGTAGGG
1 GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAAAACAGAG
29439456 GCTTAATTGCTTTTTTTGAAAAG
66 GCTTAATTGCTTTTTTTGAAAAG
* * * *
29439479 GTTTGAGGG-CTTTTT-ATGCATTTTTAAAGTTTAAGTACCGAAATGAGTGTAAAAAAAACAGAG
1 GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAAAACAGAG
* *
29439542 GCTTAATTGTTTTTTTTTAAAA
66 GCTTAATTGCTTTTTTTGAAAA
29439564 AGAATTTGAG
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
86 60 0.80
87 6 0.08
88 9 0.12
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (88 bp):
GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAAAACAGAG
GCTTAATTGCTTTTTTTGAAAAG
Found at i:29443240 original size:20 final size:21
Alignment explanation
Indices: 29443207--29443264 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
29443197 TACAAATCAA
*
29443207 TAAAAGTT-ATAAAAATTA-T
1 TAAAATTTAATAAAAATTATT
* *
29443226 TAAACTTTAATAAAAAATATT
1 TAAAATTTAATAAAAATTATT
*
29443247 TAAAATTTACTAAAAATT
1 TAAAATTTAATAAAAATT
29443265 GAAAAAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 6 0.19
20 9 0.29
21 16 0.52
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAATTTAATAAAAATTATT
Found at i:29443643 original size:22 final size:22
Alignment explanation
Indices: 29443613--29443656 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
29443603 TAATAAAAAA
**
29443613 TAAATATTTCTTATATTTTTTAT
1 TAAATATTTAATA-ATTTTTTAT
29443636 TAAA-ATTTAATAATTTTTTAT
1 TAAATATTTAATAATTTTTTAT
29443657 AACTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 6 0.32
23 4 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TAAATATTTAATAATTTTTTAT
Found at i:29443657 original size:30 final size:30
Alignment explanation
Indices: 29443582--29443668 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
29443572 AAAAATTTTT
* * *
29443582 ATAATATTTTTTTCTAATTTTTAATAAAAA
1 ATAATAATTTTTTATAATTTTTATTAAAAA
* * *
29443612 ATAA-ATATTTCTTATATTTTTTATTAAAAT
1 ATAATA-ATTTTTTATAATTTTTATTAAAAA
*
29443642 TTAATAATTTTTTATAACTTTTTATTA
1 ATAATAATTTTTTATAA-TTTTTATTA
29443669 TTTTTTGCCA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
29 1 0.02
30 34 0.76
31 10 0.22
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
ATAATAATTTTTTATAATTTTTATTAAAAA
Found at i:29447755 original size:25 final size:26
Alignment explanation
Indices: 29447695--29447779 Score: 95
Period size: 26 Copynumber: 3.3 Consensus size: 26
29447685 AATTTTCTCG
* *
29447695 AAATTTTA-CAGGAGGCAAAATCGCCA
1 AAATTTTACCAGGA-GTAAAATAGCCA
29447721 AAATTTTACCAGGAGTAAAATAGCC-
1 AAATTTTACCAGGAGTAAAATAGCCA
* *
29447746 AAATTTTACCAAGG-GTAAAATTGTCA
1 AAATTTTACC-AGGAGTAAAATAGCCA
29447772 AAATTTTA
1 AAATTTTA
29447780 TTGGGGTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
25 19 0.37
26 28 0.54
27 5 0.10
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (26 bp):
AAATTTTACCAGGAGTAAAATAGCCA
Found at i:29450719 original size:16 final size:15
Alignment explanation
Indices: 29450677--29450719 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
29450667 GGACGAATAC
*
29450677 ATTTCTCG-ATGTCG
1 ATTTCTCGAATGTTG
29450691 ATTTCTC-AATGTTG
1 ATTTCTCGAATGTTG
29450705 ATTTTCTCGAATGTT
1 A-TTTCTCGAATGTT
29450720 TACAGGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 13 0.52
15 6 0.24
16 6 0.24
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (15 bp):
ATTTCTCGAATGTTG
Found at i:29454555 original size:18 final size:18
Alignment explanation
Indices: 29454514--29454555 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29454504 TTCATGATTC
29454514 ATAA-TTTTTAATTTTTA
1 ATAATTTTTTAATTTTTA
*
29454531 ATTATTTTTTCAATTTTT-
1 ATAATTTTTT-AATTTTTA
29454549 ATAATTT
1 ATAATTT
29454556 ATATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 11 0.52
19 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
ATAATTTTTTAATTTTTA
Found at i:29454623 original size:29 final size:30
Alignment explanation
Indices: 29454555--29454623 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 30
29454545 TTTTATAATT
*
29454555 TATA-TTTTTTTCATTTTGTAATAATTTTA
1 TATATTTTTTTTCATCTTGTAATAATTTTA
29454584 -ATAATTCTTTTTTCA-CTT-TAATAAGTTTTA
1 TAT-ATT-TTTTTTCATCTTGTAATAA-TTTTA
29454614 TATATTTTTT
1 TATATTTTTT
29454624 ATGATTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
28 2 0.06
29 11 0.32
30 11 0.32
31 10 0.29
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (30 bp):
TATATTTTTTTTCATCTTGTAATAATTTTA
Found at i:29456339 original size:26 final size:26
Alignment explanation
Indices: 29456258--29456339 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
29456248 GATAGGTCGC
29456258 ATGTGTAGTACTATGTGCAGGCTACT
1 ATGTGTAGTACTATGTGCAGGCTACT
* * *
29456284 ACGTGTA-T-CGAATG-GTAATGG-TCAC-
1 ATGTGTAGTAC-TATGTG-CA-GGCT-ACT
29456309 ATGTGTAGTACTATGTGCAGGCTACT
1 ATGTGTAGTACTATGTGCAGGCTACT
29456335 ATGTG
1 ATGTG
29456340 AACCGAACAT
Statistics
Matches: 41, Mismatches: 6, Indels: 18
0.63 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.39
26 21 0.51
27 2 0.05
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
ATGTGTAGTACTATGTGCAGGCTACT
Found at i:29456396 original size:44 final size:45
Alignment explanation
Indices: 29456341--29456434 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
29456331 TACTATGTGA
* *
29456341 ACCGAACATCATTGATTAGTAA-GTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
29456385 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
29456430 ACCGA
1 ACCGA
29456435 GTATCTGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 20 0.44
45 25 0.56
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:29458012 original size:30 final size:28
Alignment explanation
Indices: 29457953--29458027 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 28
29457943 TTTTAAAATT
29457953 TTATAAAA-ATTCAAAAATAAATAAAAA
1 TTATAAAATATTCAAAAATAAATAAAAA
29457980 TTATAAAATATTCCAAATATATAAAT-AAAA
1 TTATAAAATATT-CAAA-A-ATAAATAAAAA
*
29458010 TTATAAAATATTAAAAAA
1 TTATAAAATATTCAAAAA
29458028 ATATTACTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
27 9 0.21
28 4 0.09
29 7 0.16
30 17 0.40
31 6 0.14
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (28 bp):
TTATAAAATATTCAAAAATAAATAAAAA
Found at i:29458033 original size:21 final size:21
Alignment explanation
Indices: 29457994--29458033 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29457984 AAAATATTCC
*
29457994 AAATATATAAATAAAATTATA
1 AAATATATAAAAAAAATTATA
29458015 AAATAT-TAAAAAAATATTA
1 AAATATATAAAAAAA-ATTA
29458034 CTAATCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATATAAAAAAAATTATA
Found at i:29468500 original size:12 final size:12
Alignment explanation
Indices: 29468466--29468520 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
29468456 TATCTAGAAA
*
29468466 TAATA-TTATTT
1 TAATATTTAATT
29468477 TAATAGTTTAATAT
1 TAATA-TTTAAT-T
29468491 TAA-ATTTAATT
1 TAATATTTAATT
29468502 TAATATTT-ATCT
1 TAATATTTAAT-T
29468514 TAATATT
1 TAATATT
29468521 ATTTTATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
11 11 0.29
12 18 0.47
13 5 0.13
14 4 0.11
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (12 bp):
TAATATTTAATT
Found at i:29468505 original size:17 final size:17
Alignment explanation
Indices: 29468483--29468576 Score: 54
Period size: 17 Copynumber: 5.4 Consensus size: 17
29468473 ATTTTAATAG
29468483 TTTAATATTAAATTTAA
1 TTTAATATTAAATTTAA
*
29468500 TTTAATATT-TATCTTAA
1 TTTAATATTAAAT-TTAA
*
29468517 TATT-ATTTTATTAATTTAA
1 T-TTAATATTA--AATTTAA
29468536 --TAATATTAAAGTGATT-A
1 TTTAATATTAAA-T--TTAA
*
29468553 TCTTAATATTTAATTTAA
1 T-TTAATATTAAATTTAA
29468571 TTTAAT
1 TTTAAT
29468577 GATAAGGTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 26
0.66 0.06 0.29
Matches are distributed among these distances:
15 2 0.03
16 4 0.07
17 31 0.53
18 6 0.10
19 5 0.08
20 11 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTAATATTAAATTTAA
Found at i:29479095 original size:17 final size:17
Alignment explanation
Indices: 29479073--29479110 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
29479063 TATTATTTAT
29479073 TTAATTAATTGAATTAA
1 TTAATTAATTGAATTAA
* *
29479090 TTAATTAATTTACTTAA
1 TTAATTAATTGAATTAA
29479107 TTAA
1 TTAA
29479111 ATTATTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TTAATTAATTGAATTAA
Found at i:29488361 original size:43 final size:43
Alignment explanation
Indices: 29488247--29488366 Score: 154
Period size: 42 Copynumber: 2.8 Consensus size: 43
29488237 CATAGGATTC
* *
29488247 CGATATGTGATTACGTGTAAGACCATGCCTGGGACATCGGCGT
1 CGATATATGATTACGTGTAAGACCATGTCTGGGACATCGGCGT
* *
29488290 CG-TATATGATTTCGTGTAAGACCCTGTCTGGGACAGT-GGCGT
1 CGATATATGATTACGTGTAAGACCATGTCTGGGACA-TCGGCGT
* * *
29488332 CGATATTTGATTACATGTAAGATCATGTCTGGGAC
1 CGATATATGATTACGTGTAAGACCATGTCTGGGAC
29488367 GTTGGCATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 36 0.55
43 30 0.45
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
CGATATATGATTACGTGTAAGACCATGTCTGGGACATCGGCGT
Found at i:29491918 original size:33 final size:33
Alignment explanation
Indices: 29491876--29492008 Score: 130
Period size: 31 Copynumber: 4.1 Consensus size: 33
29491866 AAAAATTAGA
*
29491876 TTATATATCATTAAATTAAATTATTTAAATATT
1 TTATTTATCATTAAATTAAATTATTTAAATATT
* * *
29491909 TTATGTATCATTATATTGAATTATTTAAATA--
1 TTATTTATCATTAAATTAAATTATTTAAATATT
* *
29491940 TAATTTATCATTATATTAAATTATTT-AA-ATT
1 TTATTTATCATTAAATTAAATTATTTAAATATT
* * ** *
29491971 TTATTTATTATTATATTTACTTTTTTTAAATATT
1 TTATTTATCATTA-AATTAAATTATTTAAATATT
29492005 TTAT
1 TTAT
29492009 ATGTCATAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
29 1 0.01
30 2 0.02
31 34 0.41
32 8 0.10
33 30 0.37
34 7 0.09
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (33 bp):
TTATTTATCATTAAATTAAATTATTTAAATATT
Found at i:29491952 original size:31 final size:31
Alignment explanation
Indices: 29491875--29491987 Score: 145
Period size: 31 Copynumber: 3.6 Consensus size: 31
29491865 AAAAAATTAG
* *
29491875 ATTATATATCATTAAATTAAATTATTTAAAT
1 ATTATTTATCATTATATTAAATTATTTAAAT
* *
29491906 ATTTTATGTATCATTATATTGAATTATTTAAAT
1 A--TTATTTATCATTATATTAAATTATTTAAAT
*
29491939 ATAATTTATCATTATATTAAATTATTTAAAT
1 ATTATTTATCATTATATTAAATTATTTAAAT
* *
29491970 TTTATTTATTATTATATT
1 ATTATTTATCATTATATT
29491988 TACTTTTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
31 43 0.61
33 28 0.39
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (31 bp):
ATTATTTATCATTATATTAAATTATTTAAAT
Found at i:29493380 original size:39 final size:38
Alignment explanation
Indices: 29493294--29493380 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 38
29493284 TATTTAATAC
*
29493294 AATAAAATATTTATTATATTTATCAGTGTTTTTTAATAT
1 AATAAAATATTCATTATATTTATCAGTGTTTTTT-ATAT
*
29493333 AATAAAATATTCATTATATTTATGGTAGTGTTTTTT-T-T
1 AATAAAATATTCATTATATTTAT--CAGTGTTTTTTATAT
29493371 AATATAAATA
1 AATA-AAATA
29493381 CTTTTTAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
38 5 0.12
39 28 0.65
41 10 0.23
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (38 bp):
AATAAAATATTCATTATATTTATCAGTGTTTTTTATAT
Found at i:29502876 original size:20 final size:20
Alignment explanation
Indices: 29502833--29502874 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
29502823 TAAAGAAAGT
29502833 AAATGCAATGGAAAGTAATG
1 AAATGCAATGGAAAGTAATG
29502853 AAATGCAAAT-GAAAGTAA-G
1 AAATGC-AATGGAAAGTAATG
29502872 AAA
1 AAA
29502875 ATTTGGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 14 0.67
21 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.17
Consensus pattern (20 bp):
AAATGCAATGGAAAGTAATG
Found at i:29503353 original size:15 final size:16
Alignment explanation
Indices: 29503333--29503362 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29503323 TGGTGCCTTA
29503333 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
29503348 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
29503363 AGCATGCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:29509535 original size:49 final size:49
Alignment explanation
Indices: 29509482--29509641 Score: 146
Period size: 49 Copynumber: 3.3 Consensus size: 49
29509472 ATGCATGGTT
* * *
29509482 TAATTAAAATGCAAACTAAATAAACAAATGAGCTACATAATGCATGACA
1 TAATTAAAATGCAAACTTAATAAACATATGAGATACATAATGCATGACA
* * * * * *
29509531 TAATTTAATATGC-AACTTAATTAACATAGGAGTTACTTAATACATGACA
1 TAA-TTAAAATGCAAACTTAATAAACATATGAGATACATAATGCATGACA
** * * *
29509580 TAATTAAAACACAAACTTTATGAACATATGAGATGCATTAATGCATGA-A
1 TAATTAAAATGCAAACTTAATAAACATATGAGATACA-TAATGCATGACA
29509629 TTAATT-AAATGCA
1 -TAATTAAAATGCA
29509642 GAAAACATAA
Statistics
Matches: 87, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
48 6 0.07
49 59 0.68
50 22 0.25
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.29
Consensus pattern (49 bp):
TAATTAAAATGCAAACTTAATAAACATATGAGATACATAATGCATGACA
Found at i:29509685 original size:32 final size:31
Alignment explanation
Indices: 29509630--29509709 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 31
29509620 ATGCATGAAT
* *
29509630 TAATT-AAATGCAGAAAACATAATGTAAATCA
1 TAATTAAAATGCA-AACACATAATGCAAATCA
*
29509661 TAATTAAAGATGCAAACACATAATGCAAGTCA
1 TAATTAAA-ATGCAAACACATAATGCAAATCA
29509693 TAATTAAATATGCAAAC
1 TAATTAAA-ATGCAAAC
29509710 TTATTAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
31 5 0.12
32 33 0.77
33 5 0.12
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (31 bp):
TAATTAAAATGCAAACACATAATGCAAATCA
Found at i:29514108 original size:217 final size:217
Alignment explanation
Indices: 29513758--29514320 Score: 892
Period size: 217 Copynumber: 2.6 Consensus size: 217
29513748 ACTGGTATGT
* * * * * * *
29513758 TTAGTCTGCCCCACTGCAATTTCAGGGGGATAAGGCTAGATGCGATCTACTCTCTGCAACTTTAG
1 TTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
* * * *
29513823 AGAGATAAGATCCAAGGTTTTAATCTGCTCCACTGCAACCTCAGGGAGATAGGATTATCGGTTTT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
* *
29513888 AATCTGCCCCACTGCAACTTCTGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
131 AATCTGCCCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
*
29513953 TAGGAGGATAAGACTTGCTTAC
196 CAGGAGGATAAGACTTGCTTAC
29513975 TTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
* * * *
29514040 GGACATAAGATCTAAGGTTTTAATCCGCTCTATTGCAACTTCAGGGAGATAGGATTATCGGCTTT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
* * *
29514105 AATCTGCTCCGCTACAACTTCAGGGAGATAAGATTTGCCATCTTTAGTCTGCCTCACTGCAACTT
131 AATCTGCCCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
29514170 CAGGAGGATAAGACTTGCTTAC
196 CAGGAGGATAAGACTTGCTTAC
*
29514192 TTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTAGATGCGATCTGCTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
** *
29514257 AGAGATAAGATCTGTGATTTTAATCCGCTCCACTGCAACTTCCAGGGAGATAGGATTATCGGCT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTT-CAGGGAGATAGGATTATCGGCT
29514321 ACGAATTTGT
Statistics
Matches: 316, Mismatches: 29, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
217 294 0.93
218 22 0.07
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (217 bp):
TTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
AATCTGCCCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
CAGGAGGATAAGACTTGCTTAC
Found at i:29514291 original size:84 final size:85
Alignment explanation
Indices: 29514152--29514314 Score: 208
Period size: 84 Copynumber: 1.9 Consensus size: 85
29514142 CCATCTTTAG
* * * *
29514152 TCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGTAACTT-CA
1 TCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGATTA-TTAATCCGCTCCACTGCAACTTCCA
29514216 GGGAGATAAGATTAGATGCGA
65 GGGAGATAAGATTAGATGCGA
*
29514237 TCTG-CTCTCTGCAACTTCA-GAGAGATAAGATCTGTGATT-TTAATCCGCTCCACTGCAACTTC
1 TCTGCCTCACTGCAACTTCAGGAG-GATAAGA-CT-TGATTATTAATCCGCTCCACTGCAACTTC
*
29514299 CAGGGAGATAGGATTA
63 CAGGGAGATAAGATTA
29514315 TCGGCTACGA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
83 3 0.04
84 40 0.59
85 21 0.31
86 4 0.06
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (85 bp):
TCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGATTATTAATCCGCTCCACTGCAACTTCCAG
GGAGATAAGATTAGATGCGA
Found at i:29514298 original size:44 final size:43
Alignment explanation
Indices: 29513811--29514308 Score: 299
Period size: 44 Copynumber: 11.4 Consensus size: 43
29513801 GATCTACTCT
* * ** *
29513811 CTGCAACTTTAGAGAGATAAGATCCAAGGTTTTAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGAT-CTTGATTTTAATCTGCTCCA
* * * *
29513855 CTGCAACCTCAGGGAGATAGGAT-TATCGGTTTTAATCTGCCCCA
1 CTGCAACTTCAGGGAGATAAGATCT-T-GATTTTAATCTGCTCCA
* * *
29513899 CTGCAACTTCTGGGAGATAAGAT-TTGCCATCTTCAGTCTGC-CTCA
1 CTGCAACTTCAGGGAGATAAGATCTTG--AT-TTTAATCTGCTC-CA
* * *
29513944 CTGCAACTTTA-GGAGGATAAGA-CTTGCTTACTTAGTCTGCTCCA
1 CTGCAACTTCAGGGA-GATAAGATCTTGATT--TTAATCTGCTCCA
* * *** *
29513988 CTGTAACTTCAGGGAGATAAGA-CTAGA-TGCGATCTGCT-CT
1 CTGCAACTTCAGGGAGATAAGATCTTGATTTTAATCTGCTCCA
* * * * *
29514028 CTGCAACTTCAGGGACATAAGATCTAAGGTTTTAATCCGCTCTA
1 CTGCAACTTCAGGGAGATAAGATCT-TGATTTTAATCTGCTCCA
* * ** *
29514072 TTGCAACTTCAGGGAGATAGGAT-TATCGGCTTTAATCTGCTCCG
1 CTGCAACTTCAGGGAGATAAGATCT-T-GATTTTAATCTGCTCCA
* *
29514116 CTACAACTTCAGGGAGATAAGAT-TTGCCATCTTTAGTCTGC-CTCA
1 CTGCAACTTCAGGGAGATAAGATCTTG--AT-TTTAATCTGCTC-CA
* *
29514161 CTGCAACTTCA-GGAGGATAAGA-CTTGCTTACTTAGTCTGCTCCA
1 CTGCAACTTCAGGGA-GATAAGATCTTGATT--TTAATCTGCTCCA
* * *** *
29514205 CTGTAACTTCAGGGAGATAAGAT-TAGA-TGCGATCTGCT-CT
1 CTGCAACTTCAGGGAGATAAGATCTTGATTTTAATCTGCTCCA
* *
29514245 CTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCT-TGATTTTAATCTGCTCCA
29514289 CTGCAACTTCCAGGGAGATA
1 CTGCAACTT-CAGGGAGATA
29514309 GGATTATCGG
Statistics
Matches: 352, Mismatches: 69, Indels: 65
0.72 0.14 0.13
Matches are distributed among these distances:
40 43 0.12
41 15 0.04
42 8 0.02
43 22 0.06
44 188 0.53
45 76 0.22
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (43 bp):
CTGCAACTTCAGGGAGATAAGATCTTGATTTTAATCTGCTCCA
Found at i:29527657 original size:31 final size:31
Alignment explanation
Indices: 29527621--29527694 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 31
29527611 GTTATATACC
*
29527621 TATATACATACATGCGTTTTTATA-A-TGTATA
1 TATATACATACA--CATTTTTATACACTGTATA
*
29527652 TATATACACGTACACATTTTTATACACTGTCTA
1 TATATACA--TACACATTTTTATACACTGTATA
29527685 TATATACATA
1 TATATACATA
29527695 TATATACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
31 19 0.51
32 1 0.03
33 17 0.46
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (31 bp):
TATATACATACACATTTTTATACACTGTATA
Found at i:29527745 original size:21 final size:21
Alignment explanation
Indices: 29527721--29527763 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
29527711 CTTTATATTT
29527721 TATAACTTATATGCATA-TCTA
1 TATAAC-TATATGCATATTCTA
* *
29527742 TATATCTATGTGCATATTCTA
1 TATAACTATATGCATATTCTA
29527763 T
1 T
29527764 TTTCATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.47
Consensus pattern (21 bp):
TATAACTATATGCATATTCTA
Found at i:29529741 original size:55 final size:55
Alignment explanation
Indices: 29529644--29529751 Score: 139
Period size: 55 Copynumber: 2.0 Consensus size: 55
29529634 AGCTATAACT
* * * *
29529644 AAGTTTTCGTATTTCTACATAAAGCTAATATTTCTCACTATCATATAATTAAACA
1 AAGTTGTCGTATTTCTACATAAAGCTAATATCTCTAACTATCAAATAATTAAACA
*
29529699 AAGTTGTCGTATTTCTACAATAAAG-T-ATGATCTCTAATTATCAAATAATTAAA
1 AAGTTGTCGTATTTCTAC-ATAAAGCTAAT-ATCTCTAACTATCAAATAATTAAA
29529752 ATAAGAGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
54 2 0.04
55 38 0.83
56 6 0.13
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (55 bp):
AAGTTGTCGTATTTCTACATAAAGCTAATATCTCTAACTATCAAATAATTAAACA
Found at i:29536336 original size:21 final size:21
Alignment explanation
Indices: 29536297--29536345 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
29536287 AACAATTTTC
*
29536297 TTTT-TCCTTTTTTTCCCTCCT
1 TTTTCTCCTTTCTTTCCCT-CT
29536318 TTTTCTCCTTTCTTT-CCTCT
1 TTTTCTCCTTTCTTTCCCTCT
29536338 TTCTTCTC
1 TT-TTCTC
29536346 TAACCCCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 4 0.16
21 12 0.48
22 9 0.36
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTCTCCTTTCTTTCCCTCT
Found at i:29543582 original size:31 final size:30
Alignment explanation
Indices: 29543537--29543624 Score: 83
Period size: 31 Copynumber: 3.0 Consensus size: 30
29543527 TTAATGATGC
*
29543537 ATAAAATATTTTAAA-AACTTAAATATAATA
1 ATAAATTATTTTAAACAA-TTAAATATAATA
* *
29543567 ATAAATTATATTTAAACAATTTAATATAATG
1 ATAAATTAT-TTTAAACAATTAAATATAATA
* * *
29543598 ATAAA-T-GTTTAAATAATTTAATATAAT
1 ATAAATTATTTTAAACAATTAAATATAAT
29543625 GTTACATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 19 0.37
30 9 0.18
31 21 0.41
32 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (30 bp):
ATAAATTATTTTAAACAATTAAATATAATA
Found at i:29544393 original size:33 final size:33
Alignment explanation
Indices: 29544336--29544429 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
29544326 ACTCAAACTT
* * * *
29544336 TTACCTAGACCTTATGCATACAACAATCAATTC
1 TTACCTAGGCCATATACATGCAACAATCAATTC
*
29544369 TTACCTTA-GCCATATACATGCAACAATCGATTC
1 TTACC-TAGGCCATATACATGCAACAATCAATTC
*
29544402 TTACCTAGGTCATATACATGCAACAATC
1 TTACCTAGGCCATATACATGCAACAATC
29544430 TATTTCATAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
32 2 0.04
33 49 0.92
34 2 0.04
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.30
Consensus pattern (33 bp):
TTACCTAGGCCATATACATGCAACAATCAATTC
Found at i:29544738 original size:2 final size:2
Alignment explanation
Indices: 29544731--29544756 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29544721 TTACGAAGCG
29544731 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
29544757 TATATATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:29545547 original size:74 final size:71
Alignment explanation
Indices: 29545369--29545547 Score: 198
Period size: 71 Copynumber: 2.5 Consensus size: 71
29545359 AACTTTATTT
* * ** * * * * **
29545369 GATGTTGCTCACTCAAGCTGTCAAGAATCTGCAACACGTGCTAGATCTTAGTCATTGACAAAGTA
1 GATGCTGCTCACTCAAGTTGTTGAGAATCCGCAACACATACTAGATCTCAACCATTGACAAAGTA
29545434 TAATGC
66 TAATGC
* *
29545440 GATGCTACTCACTCAAGTTGCTGAGAATCCGCAACACATACTAGATCTCAACCATTG-CTAAAGT
1 GATGCTGCTCACTCAAGTTGTTGAGAATCCGCAACACATACTAGATCTCAACCATTGAC-AAAGT
29545504 ATAATGATC
65 ATAATG--C
*
29545513 TTATGCTGCTCACTCAAGTTGTTGAGAATCCGCAA
1 -GATGCTGCTCACTCAAGTTGTTGAGAATCCGCAA
29545548 TTTATGTTGG
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
70 1 0.01
71 56 0.63
73 1 0.01
74 31 0.35
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (71 bp):
GATGCTGCTCACTCAAGTTGTTGAGAATCCGCAACACATACTAGATCTCAACCATTGACAAAGTA
TAATGC
Found at i:29547988 original size:21 final size:22
Alignment explanation
Indices: 29547956--29547996 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
29547946 AGAATTTTGA
29547956 AAAATAAATAAATAAA-AATTAT
1 AAAATAAATAAA-AAATAATTAT
29547978 AAAAT-AATAAAAAATAATT
1 AAAATAAATAAAAAATAATT
29547997 TTATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 10 0.56
22 5 0.28
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAATAAATAAAAAATAATTAT
Found at i:29557009 original size:44 final size:42
Alignment explanation
Indices: 29556945--29557413 Score: 468
Period size: 42 Copynumber: 11.1 Consensus size: 42
29556935 TAACTGATAC
**
29556945 ACGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTCATAATC-AAGGAT
* * * * *
29556988 CCCGGTGAAATTAGCACTTAGCAACCACCTTATAATCAATGAT
1 -ACGGTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGAT
* * *
29557031 ACGG-GGAATCATCACATAGCAACC-CCTTTCACAATCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACC--TCATAATCAAGGAT
**
29557073 ACGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTCATAATC-AAGGAT
* * * * *
29557116 CCCGGTGAAATTAGCACTTAGCAACCACCTTATAATCAATGAT
1 -ACGGTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGAT
* * *
29557159 ACGG-GGAATCATCACATAGCAACC-CCTTTCACAATCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACC--TCATAATCAAGGAT
* *
29557201 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGAT
* * *
29557243 ACGG-GGAATCATCACATAGCAACC-CCTTTCACAATCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACC--TCATAATCAAGGAT
* *
29557285 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGAT
* * *
29557327 ACGG-GGAATCAACACATAGCAACC-CCTTTCACAATCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACC--TCATAATCAAGGAT
* * * *
29557369 GCGGTGGAATCAGCACTTGGCAACCACCTTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGAT
29557411 ACG
1 ACG
29557414 AGTTCACATA
Statistics
Matches: 344, Mismatches: 63, Indels: 38
0.77 0.14 0.09
Matches are distributed among these distances:
40 8 0.02
41 68 0.20
42 113 0.33
43 87 0.25
44 68 0.20
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (42 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGAT
Found at i:29557099 original size:84 final size:83
Alignment explanation
Indices: 29556945--29557413 Score: 559
Period size: 84 Copynumber: 5.5 Consensus size: 83
29556935 TAACTGATAC
* ** * * * * *
29556945 ACGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCCCGGTGAAATTAGCACTTAGC
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATC-AATGAT-ACGG-GGAATCAGCACATAGC
* *
29557010 AACCACCTT-ATAATCAATGAT
63 AACC-CCTTCACAATCAAGGAT
* * * * *
29557031 ACGG-GGAATCATCACATAGCAACC-CCTTTCACAATCAAGGATACGGTGGAATCAGCACTTAGC
1 ACGGTGGAATCAGCACTTAGCAACCACC-TT-ATAATCAATGATACGG-GGAATCAGCACATAGC
***
29557094 AACCACC-TCATGTTCAAAGGAT
63 AACC-CCTTCACAATC-AAGGAT
* * * *
29557116 CCCGGTGAAATTAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCATCACATAGCAA
1 -ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAA
29557181 CCCCTTTCACAATCAAGGAT
65 CCCC-TTCACAATCAAGGAT
*
29557201 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCATCACATAGCAAC
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAAC
29557266 CCCTTTCACAATCAAGGAT
66 CCC-TTCACAATCAAGGAT
*
29557285 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAAC
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAAC
29557350 CCCTTTCACAATCAAGGAT
66 CCC-TTCACAATCAAGGAT
* *
29557369 GCGGTGGAATCAGCACTTGGCAACCACCTTATAATCAATGATACG
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACG
29557414 AGTTCACATA
Statistics
Matches: 344, Mismatches: 30, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
83 1 0.00
84 240 0.70
85 54 0.16
86 29 0.08
87 18 0.05
88 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (83 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAAC
CCCTTCACAATCAAGGAT
Found at i:29557173 original size:128 final size:126
Alignment explanation
Indices: 29556945--29557413 Score: 590
Period size: 128 Copynumber: 3.7 Consensus size: 126
29556935 TAACTGATAC
** *
29556945 ACGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCCCGGTGAAATTAGCACTTAGC
1 ACGGTGGAATCAGCACTTAGCAACCACCTCATAATC-AAGGAT-CCGGTGAAATCAGCACTTAGC
29557010 AACCACCTTATAATCAATGATACGGGGAATCATCACATAGCAACCCCTTTCACAATCAAGGAT
64 AACCACCTTATAATCAATGATACGGGGAATCATCACATAGCAACCCCTTTCACAATCAAGGAT
** *
29557073 ACGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCCCGGTGAAATTAGCACTTAGC
1 ACGGTGGAATCAGCACTTAGCAACCACCTCATAATC-AAGGAT-CCGGTGAAATCAGCACTTAGC
29557138 AACCACCTTATAATCAATGATACGGGGAATCATCACATAGCAACCCCTTTCACAATCAAGGAT
64 AACCACCTTATAATCAATGATACGGGGAATCATCACATAGCAACCCCTTTCACAATCAAGGAT
* * * * * *
29557201 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGG-GGAATCATCACATAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGATCCGGTGAAATCAGCACTTAGCAA
* * * * * *
29557265 CC-CCTTTCACAATCAAGGATACGGTGGAATCAGCACTTAGCAACCACC-TT-ATAATCAATGAT
66 CCACC-TT-ATAATCAATGATACGG-GGAATCATCACATAGCAACC-CCTTTCACAATCAAGGAT
* * * * * *
29557327 ACGG-GGAATCAACACATAGCAACC-CCTTTCACAATCAAGGATGCGGTGGAATCAGCACTTGGC
1 ACGGTGGAATCAGCACTTAGCAACCACC--TCATAATCAAGGATCCGGTGAAATCAGCACTTAGC
29557390 AACCACCTTATAATCAATGATACG
64 AACCACCTTATAATCAATGATACG
29557414 AGTTCACATA
Statistics
Matches: 307, Mismatches: 26, Indels: 18
0.87 0.07 0.05
Matches are distributed among these distances:
124 4 0.01
125 36 0.12
126 58 0.19
127 44 0.14
128 165 0.54
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (126 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGATCCGGTGAAATCAGCACTTAGCAA
CCACCTTATAATCAATGATACGGGGAATCATCACATAGCAACCCCTTTCACAATCAAGGAT
Found at i:29557448 original size:26 final size:26
Alignment explanation
Indices: 29557418--29557498 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
29557408 GATACGAGTT
29557418 CACATAGTAGCCTGCACATAATACTA
1 CACATAGTAGCCTGCACATAATACTA
*
29557444 CACAT-GT-GACCAT-CAC-T-ATCCGATA
1 CACATAGTAG-CC-TGCACATAATAC--TA
* *
29557469 CACGTAGTAGCCTGCACATAGTACTA
1 CACATAGTAGCCTGCACATAATACTA
29557495 CACA
1 CACA
29557499 CGTGATCATC
Statistics
Matches: 41, Mismatches: 5, Indels: 18
0.64 0.08 0.28
Matches are distributed among these distances:
23 3 0.07
24 2 0.05
25 14 0.34
26 18 0.44
27 2 0.05
28 2 0.05
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (26 bp):
CACATAGTAGCCTGCACATAATACTA
Found at i:29561310 original size:10 final size:10
Alignment explanation
Indices: 29561295--29561380 Score: 51
Period size: 10 Copynumber: 9.0 Consensus size: 10
29561285 TTTGAAATAT
29561295 TTTAATATAA
1 TTTAATATAA
29561305 TTTAATATAA
1 TTTAATATAA
** *
29561315 AAT-ATTTAA
1 TTTAATATAA
29561324 TTTCAAAATATAA
1 TTT---AATATAA
*
29561337 TTTAAAATAA
1 TTTAATATAA
29561347 ---AATAT--
1 TTTAATATAA
*
29561352 TTTAA-ATAT
1 TTTAATATAA
29561361 TTTAATATAA
1 TTTAATATAA
29561371 TTTAATATAA
1 TTTAATATAA
29561381 AAATAATTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 20
0.66 0.10 0.23
Matches are distributed among these distances:
7 6 0.11
8 2 0.04
9 11 0.19
10 30 0.53
13 8 0.14
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTAATATAA
Found at i:29561320 original size:34 final size:33
Alignment explanation
Indices: 29561277--29561382 Score: 144
Period size: 34 Copynumber: 3.2 Consensus size: 33
29561267 AAATATAAAA
29561277 ATAAAATATTTGAAATATTTTAATATAATTTAAT
1 ATAAAATATTT-AAATATTTTAATATAATTTAAT
** *
29561311 ATAAAATATTT-AAT-TTCAAAATATAATTTAAA
1 ATAAAATATTTAAATATT-TTAATATAATTTAAT
29561343 ATAAAATATTTTAAATATTTTAATATAATTTAAT
1 ATAAAATA-TTTAAATATTTTAATATAATTTAAT
29561377 ATAAAA
1 ATAAAA
29561383 ATAATTATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
31 2 0.03
32 23 0.37
33 3 0.05
34 32 0.52
35 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (33 bp):
ATAAAATATTTAAATATTTTAATATAATTTAAT
Found at i:29561398 original size:66 final size:64
Alignment explanation
Indices: 29561266--29561460 Score: 203
Period size: 66 Copynumber: 3.1 Consensus size: 64
29561256 TTGAACCTAG
* *
29561266 AAAATAT-A-AAAATAAAATATTTGAAATATTTTAATATAATTTAATAT-AAAATATTTA-ATTT
1 AAAATATAATAAAATAAAATATTTTAAATATTTTAATATAATTTAATATAAAAATAATTATA-TT
29561327 CAAAATATAATTTAAAATAAAATATTTTAAATATTTTAATATAATTTAATATAAAAATAATTATA
1 -AAAATATAA--TAAAATAAAATATTTTAAATATTTTAATATAATTTAATATAAAAATAATTATA
29561392 TT
63 TT
* * * * *
29561394 AAAATATTAAT-AAATTATATATTTT---TATTTT-AT-TAAATTATATTTAATAATAATTATAT
1 AAAATA-TAATAAAATAAAATATTTTAAATATTTTAATATAATTTA-ATATAAAAATAATTATAT
29561453 T
64 T
29561454 AAAATAT
1 AAAATAT
29561461 GATTAGATTA
Statistics
Matches: 118, Mismatches: 7, Indels: 19
0.82 0.05 0.13
Matches are distributed among these distances:
59 7 0.06
60 25 0.21
61 6 0.05
62 7 0.06
63 1 0.01
64 12 0.10
65 1 0.01
66 44 0.37
67 14 0.12
68 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (64 bp):
AAAATATAATAAAATAAAATATTTTAAATATTTTAATATAATTTAATATAAAAATAATTATATT
Found at i:29561400 original size:32 final size:31
Alignment explanation
Indices: 29561298--29561400 Score: 109
Period size: 32 Copynumber: 3.2 Consensus size: 31
29561288 GAAATATTTT
29561298 AATATAATTTAATATAAAATATTTA-ATTTCAA
1 AATATAATTTAATATAAAATATTTATA-TT-AA
* **
29561330 AATATAATTTAAAATAAAATATTTTAAATATTTT
1 AATATAATTTAATATAAAATA-TTT--ATATTAA
*
29561364 AATATAATTTAATATAAAAATAATTATATTAA
1 AATATAATTTAATAT-AAAATATTTATATTAA
29561396 AATAT
1 AATAT
29561401 TAATAAATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
32 30 0.51
33 3 0.05
34 16 0.27
35 9 0.15
36 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (31 bp):
AATATAATTTAATATAAAATATTTATATTAA
Found at i:29561453 original size:26 final size:28
Alignment explanation
Indices: 29561424--29561543 Score: 70
Period size: 26 Copynumber: 4.2 Consensus size: 28
29561414 ATTTTTATTT
29561424 TATTAAATTATATTTA-ATA-ATAATTA
1 TATTAAATTATATTTAGATATATAATTA
* * * *
29561450 TATTAAAATATGA-TTAGATTATTTATTTTT
1 TATTAAATTAT-ATTTAGA-TATATA-ATTA
* * * * *
29561480 TCATTAAATTATTTTTATATATTTTTATTTT
1 T-ATTAAATTATATTTAGATA--TATAATTA
29561511 TATTAAATTATATTTA-ATA-ATAATTA
1 TATTAAATTATATTTAGATATATAATTA
29561537 TATTAAA
1 TATTAAA
29561544 ATATGATTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
26 24 0.32
27 2 0.03
28 2 0.03
29 5 0.07
30 19 0.26
31 18 0.24
32 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.56
Consensus pattern (28 bp):
TATTAAATTATATTTAGATATATAATTA
Found at i:29561487 original size:31 final size:29
Alignment explanation
Indices: 29561450--29561574 Score: 80
Period size: 31 Copynumber: 4.2 Consensus size: 29
29561440 ATAATAATTA
29561450 TATTAAAATATGATTAGATTATTTATTTTTT
1 TATTAAAATATGATTA-A-TATTTATTTTTT
* * **
29561481 CATTAAATTATTTTTATATATTT-TTATTTT
1 TATTAAAATATGATTA-ATATTTATT-TTTT
* ** *
29561511 TATTAAATTAT-ATTTAATA---ATAATTA
1 TATTAAAATATGA-TTAATATTTATTTTTT
29561537 TATTAAAATATGATTAAATTATTTATTTTTT
1 TATTAAAATATGATT-AA-TATTTATTTTTT
29561568 TATTAAA
1 TATTAAA
29561575 TTATTTTTAA
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
26 14 0.20
27 4 0.06
28 2 0.03
29 5 0.07
30 22 0.31
31 24 0.34
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (29 bp):
TATTAAAATATGATTAATATTTATTTTTT
Found at i:29561527 original size:87 final size:86
Alignment explanation
Indices: 29561408--29561583 Score: 325
Period size: 87 Copynumber: 2.0 Consensus size: 86
29561398 TATTAATAAA
*
29561408 TTATATATTTTTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAGATTATT
1 TTATATATTTTTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATT
29561473 TATTTTTTCATTAAATTATTT
66 TATTTTTTCATTAAATTATTT
29561494 TTATATATTTTTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTAT
1 TTATATATTTTTA-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTAT
*
29561559 TTATTTTTTTATTAAATTATTT
65 TTATTTTTTCATTAAATTATTT
29561581 TTA
1 TTA
29561584 ATAATAATCG
Statistics
Matches: 87, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 13 0.15
87 74 0.85
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.59
Consensus pattern (86 bp):
TTATATATTTTTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATT
TATTTTTTCATTAAATTATTT
Found at i:29561784 original size:16 final size:15
Alignment explanation
Indices: 29561763--29561830 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 15
29561753 TAAATTATTG
*
29561763 ATTACATCTTTATTCC
1 ATTACAT-TCTATTCC
29561779 ATTACAGTTCTATTCC
1 ATTACA-TTCTATTCC
*
29561795 ATTACAACTCTATTCC
1 ATTAC-ATTCTATTCC
*
29561811 ATAATA-ATTTTATTCC
1 AT--TACATTCTATTCC
29561827 ATTA
1 ATTA
29561831 TAGCGAACCA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 2 0.05
16 38 0.86
17 2 0.05
18 2 0.05
ACGTcount: A:0.31, C:0.22, G:0.01, T:0.46
Consensus pattern (15 bp):
ATTACATTCTATTCC
Found at i:29561800 original size:32 final size:32
Alignment explanation
Indices: 29561763--29561830 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
29561753 TAAATTATTG
* * * *
29561763 ATTACATCTTTATTCCATTACAGTTCTATTCC
1 ATTACAACTCTATTCCATAACAATTCTATTCC
* *
29561795 ATTACAACTCTATTCCATAATAATTTTATTCC
1 ATTACAACTCTATTCCATAACAATTCTATTCC
29561827 ATTA
1 ATTA
29561831 TAGCGAACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.01, T:0.46
Consensus pattern (32 bp):
ATTACAACTCTATTCCATAACAATTCTATTCC
Found at i:29562313 original size:15 final size:15
Alignment explanation
Indices: 29562293--29562344 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
29562283 GCTACAAAAC
29562293 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
29562308 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
*
29562327 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
29562342 ATT
1 ATT
29562345 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:29562330 original size:19 final size:19
Alignment explanation
Indices: 29562306--29562342 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29562296 TATTATTAAT
*
29562306 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
29562325 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
29562343 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:29562395 original size:13 final size:13
Alignment explanation
Indices: 29562377--29562401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29562367 TTGTGAAGAA
29562377 TATTATTAAAATT
1 TATTATTAAAATT
29562390 TATTATTAAAAT
1 TATTATTAAAAT
29562402 AAAATTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTATTAAAATT
Found at i:29581858 original size:18 final size:18
Alignment explanation
Indices: 29581818--29581860 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
29581808 AATTTAAAAG
* * *
29581818 ATTAAAAAATTATATATT
1 ATTAAAAAATTAAAAATC
*
29581836 TTTAAAAAATTAAAAATC
1 ATTAAAAAATTAAAAATC
29581854 ATTAAAA
1 ATTAAAA
29581861 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTAAAAAATTAAAAATC
Found at i:29587774 original size:8 final size:8
Alignment explanation
Indices: 29587761--29587789 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
29587751 GGTCTATGCG
29587761 TGTAGAAA
1 TGTAGAAA
29587769 TGTAGAAA
1 TGTAGAAA
29587777 TGTAGAAA
1 TGTAGAAA
29587785 TGTAG
1 TGTAG
29587790 TAAAACTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (8 bp):
TGTAGAAA
Found at i:29588431 original size:33 final size:33
Alignment explanation
Indices: 29588389--29588508 Score: 197
Period size: 33 Copynumber: 3.6 Consensus size: 33
29588379 TCAACATAAG
*
29588389 TGATTGGAACATCTATCAGGGCAGCTTCATCGA-
1 TGATTGGAACATCTATCGGGGCAGCTTCATC-AT
*
29588422 TGATTGGAACATCTATCGGGGCAGCTTCGTCAT
1 TGATTGGAACATCTATCGGGGCAGCTTCATCAT
*
29588455 TGATTGGAACATCTATTGGGGCAGCTTCATCAT
1 TGATTGGAACATCTATCGGGGCAGCTTCATCAT
29588488 TGATTGGAACATCTATCGGGG
1 TGATTGGAACATCTATCGGGG
29588509 GAGATTTAGC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
32 1 0.01
33 80 0.99
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (33 bp):
TGATTGGAACATCTATCGGGGCAGCTTCATCAT
Found at i:29599074 original size:35 final size:35
Alignment explanation
Indices: 29599035--29599104 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
29599025 GTATATTTGC
29599035 CAAGGTTTAGGTTATATCTTTGCTTAAACAATATG
1 CAAGGTTTAGGTTATATCTTTGCTTAAACAATATG
29599070 CAAGGTTTAGGTTATATCTTTGCTTAAACAATATG
1 CAAGGTTTAGGTTATATCTTTGCTTAAACAATATG
29599105 TCTTTTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (35 bp):
CAAGGTTTAGGTTATATCTTTGCTTAAACAATATG
Found at i:29600088 original size:29 final size:29
Alignment explanation
Indices: 29600054--29600113 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
29600044 TTGGCTATTA
* *
29600054 AAAATTTTCAAATAAGGAAGTTTTCTTTC
1 AAAATTTTCAAATAAGGAAATTTTCATTC
29600083 AAAATTTTCAAATAAGGAAATTTTCATTC
1 AAAATTTTCAAATAAGGAAATTTTCATTC
29600112 AA
1 AA
29600114 TTATGGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.38
Consensus pattern (29 bp):
AAAATTTTCAAATAAGGAAATTTTCATTC
Found at i:29600105 original size:16 final size:16
Alignment explanation
Indices: 29600055--29600108 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
29600045 TGGCTATTAA
29600055 AAATTTTCAAATAAGG
1 AAATTTTCAAATAAGG
* ** *
29600071 AAGTTTTC-TTTCA--
1 AAATTTTCAAATAAGG
29600084 AAATTTTCAAATAAGG
1 AAATTTTCAAATAAGG
29600100 AAATTTTCA
1 AAATTTTCA
29600109 TTCAATTATG
Statistics
Matches: 27, Mismatches: 8, Indels: 6
0.66 0.20 0.15
Matches are distributed among these distances:
13 7 0.26
14 2 0.07
15 2 0.07
16 16 0.59
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (16 bp):
AAATTTTCAAATAAGG
Found at i:29600174 original size:21 final size:21
Alignment explanation
Indices: 29600149--29600194 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
29600139 AGCCTTTTTT
29600149 TTAATAGGTATGTTTTTATCA
1 TTAATAGGTATGTTTTTATCA
*
29600170 TTAATAGGTATGTTTTTGTCA
1 TTAATAGGTATGTTTTTATCA
29600191 TTAA
1 TTAA
29600195 CCTGTTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (21 bp):
TTAATAGGTATGTTTTTATCA
Found at i:29610328 original size:50 final size:50
Alignment explanation
Indices: 29610252--29610482 Score: 259
Period size: 50 Copynumber: 4.6 Consensus size: 50
29610242 TTGGGTAAAT
* *
29610252 AGGTCCCGTGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
* * * *
29610302 AGGTCCCATATAAGACCACGTTTGGGACATGGCGTTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
** * *
29610352 AGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
** * * * * *
29610402 AACTCCCATGGAAGACCATATTTGGGACATGGCATTGGCA--GTACATGAA
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAG
** *
29610451 ACATCCCATGTAAAACCATGTCTGGGACATGG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGG
29610483 TTTTGGCATG
Statistics
Matches: 152, Mismatches: 28, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
48 1 0.01
49 31 0.20
50 120 0.79
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
Found at i:29618797 original size:24 final size:24
Alignment explanation
Indices: 29618770--29618948 Score: 151
Period size: 24 Copynumber: 7.3 Consensus size: 24
29618760 CAGCTCATAT
**
29618770 GAGCATACCAATTACAGCTTTTGA
1 GAGCATACCAATTACAGCTCGTGA
* * * *
29618794 GAGCATACTGATTTATAGCTCGTGT
1 GAGCATAC-CAATTACAGCTCGTGA
* * *
29618819 GTGCATATCAATTACAGCTTGTGA
1 GAGCATACCAATTACAGCTCGTGA
* *
29618843 GAGCATACCGATTTACAGCTCGTGT
1 GAGCATACC-AATTACAGCTCGTGA
* *
29618868 GTGCATATCAATTACAGCTCGTGA
1 GAGCATACCAATTACAGCTCGTGA
* * *
29618892 GAGCATATCGATTTACAGCTCGTGT
1 GAGCATA-CCAATTACAGCTCGTGA
* * * *
29618917 GAGCATATCGATTACAACTCGTGT
1 GAGCATACCAATTACAGCTCGTGA
29618941 GAGCATAC
1 GAGCATAC
29618949 ATGTATAGGA
Statistics
Matches: 119, Mismatches: 33, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
24 64 0.54
25 55 0.46
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (24 bp):
GAGCATACCAATTACAGCTCGTGA
Found at i:29618824 original size:25 final size:24
Alignment explanation
Indices: 29618794--29618947 Score: 157
Period size: 24 Copynumber: 6.3 Consensus size: 24
29618784 CAGCTTTTGA
*
29618794 GAGCATACTGATTTATAGCTCGTGT
1 GAGCATA-TGATTTACAGCTCGTGT
* * * * *
29618819 GTGCATATCAATTACAGCTTGTGA
1 GAGCATATGATTTACAGCTCGTGT
*
29618843 GAGCATACCGATTTACAGCTCGTGT
1 GAGCATA-TGATTTACAGCTCGTGT
* * * *
29618868 GTGCATATCAATTACAGCTCGTGA
1 GAGCATATGATTTACAGCTCGTGT
29618892 GAGCATATCGATTTACAGCTCGTGT
1 GAGCATAT-GATTTACAGCTCGTGT
*
29618917 GAGCATATCGA-TTACAACTCGTGT
1 GAGCATAT-GATTTACAGCTCGTGT
29618941 GAGCATA
1 GAGCATA
29618948 CATGTATAGG
Statistics
Matches: 105, Mismatches: 22, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
24 57 0.54
25 48 0.46
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (24 bp):
GAGCATATGATTTACAGCTCGTGT
Found at i:29618833 original size:49 final size:49
Alignment explanation
Indices: 29618772--29618948 Score: 248
Period size: 49 Copynumber: 3.6 Consensus size: 49
29618762 GCTCATATGA
* * *
29618772 GCATACCAATTACAGCTTTTGAGAGCATACTGATTTATAGCTCGTGTGT
1 GCATATCAATTACAGCTTGTGAGAGCATACTGATTTACAGCTCGTGTGT
*
29618821 GCATATCAATTACAGCTTGTGAGAGCATACCGATTTACAGCTCGTGTGT
1 GCATATCAATTACAGCTTGTGAGAGCATACTGATTTACAGCTCGTGTGT
* *
29618870 GCATATCAATTACAGCTCGTGAGAGCATA-TCGATTTACAGCTCGTGTGA
1 GCATATCAATTACAGCTTGTGAGAGCATACT-GATTTACAGCTCGTGTGT
* * * *
29618919 GCATATCGATTACAACTCGTGTGAGCATAC
1 GCATATCAATTACAGCTTGTGAGAGCATAC
29618949 ATGTATAGGA
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
49 116 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (49 bp):
GCATATCAATTACAGCTTGTGAGAGCATACTGATTTACAGCTCGTGTGT
Found at i:29621568 original size:5 final size:5
Alignment explanation
Indices: 29621560--29621603 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
29621550 TACTGTACTT
* *
29621560 ACCTC ACCTC ACCTC ACCTT ACCTT ACCTC ACCTC ACCTC ACCT
1 ACCTC ACCTC ACCTC ACCTC ACCTC ACCTC ACCTC ACCTC ACCT
29621604 TGTGGCTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.20, C:0.55, G:0.00, T:0.25
Consensus pattern (5 bp):
ACCTC
Found at i:29624842 original size:30 final size:29
Alignment explanation
Indices: 29624806--29624868 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
29624796 AGAAAAAGCC
29624806 TTTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTTCAAAATTTACCGAAATGGGCC-A
* ** * *
29624836 TTTTTTTGATTATTTACCGGAATGGTCCA
1 TTTTTTTCAAAATTTACCGAAATGGGCCA
29624865 TTTT
1 TTTT
29624869 CCAGGAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (29 bp):
TTTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:29628428 original size:10 final size:10
Alignment explanation
Indices: 29628413--29628437 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29628403 CAGATCTAAC
29628413 ATTATGTAAA
1 ATTATGTAAA
29628423 ATTATGTAAA
1 ATTATGTAAA
29628433 ATTAT
1 ATTAT
29628438 TAAGCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:29628562 original size:56 final size:57
Alignment explanation
Indices: 29628420--29628563 Score: 152
Period size: 56 Copynumber: 2.5 Consensus size: 57
29628410 AACATTATGT
* * *
29628420 AAAATTATGTAAAATTATTAAGCCAAAAAAATTTTCTTAATGGTTAGAAAAATTTATC
1 AAAA-TATGTAAAATTATTAAGCCAAAAAAATTGTCTTAATAGTTAGAAAAATGTATC
* * * ** *
29628478 -AAATAATCTCAAATTATTAAGTCC--AAAAATTGTGTTAATAGTTATTAAAGTGT-TC
1 AAAAT-ATGTAAAATTATTAAG-CCAAAAAAATTGTCTTAATAGTTAGAAAAATGTATC
29628533 AAAATATGTAAAATTATTAAGCCAAAAAAAT
1 AAAATATGTAAAATTATTAAGCCAAAAAAAT
29628564 ATGTAAAATT
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
54 2 0.03
55 16 0.23
56 33 0.47
57 17 0.24
58 2 0.03
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.35
Consensus pattern (57 bp):
AAAATATGTAAAATTATTAAGCCAAAAAAATTGTCTTAATAGTTAGAAAAATGTATC
Found at i:29628566 original size:26 final size:26
Alignment explanation
Indices: 29628533--29628587 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
29628523 TAAAGTGTTC
29628533 AAAATATGTAAAATTATTAAGCCAAA
1 AAAATATGTAAAATTATTAAGCCAAA
29628559 AAAATATGTAAAATTATTAAGCCAAA
1 AAAATATGTAAAATTATTAAGCCAAA
29628585 AAA
1 AAA
29628588 CTTTAGGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.25
Consensus pattern (26 bp):
AAAATATGTAAAATTATTAAGCCAAA
Found at i:29628638 original size:28 final size:28
Alignment explanation
Indices: 29628589--29629129 Score: 593
Period size: 28 Copynumber: 18.4 Consensus size: 28
29628579 GCCAAAAAAC
* * *
29628589 TTTAGGTTAGTTTTGGGTTTTTAATTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
* *
29628617 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
1 TTTAGGTTA-GATTAGGGTTTTTAGTTAA
*
29628646 TTTAGGTTATATTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
29628674 TTTAGGTTAGATTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
*
29628702 TTTAGGTTAGGGTTAGGTTAGGGTTTTTAATTAA
1 TTTAGGTTA--G--A--TTAGGGTTTTTAGTTAA
* *
29628736 TTTAGGTTAGATTA-GGTTTTAAATTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
*
29628763 TTTAGGTTAGATTAGGGTTTTTAGGTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
29628791 TTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
1 TTTAGGTTA--G--A--TTAGGGTTTTTAGTTAA
* * *
29628825 TTTAGGTTATATTA-GGTTTTAAATTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
*
29628852 TTTAGGTTAGATTAGGGTTTTTAGGTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
*
29628880 TTTAAGTTAGGGTTAGTTAGGGTTTTTAGTTAA
1 TTTAGGTTA--G--A-TTAGGGTTTTTAGTTAA
* * *
29628913 TTTAGGTTAGATTA-GGTTTTAAATTAC
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
29628940 TTTAGGTTAGATTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
*
29628968 TTTAGGTTAGATTATGGTTTTTAGTTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
29628996 TTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
1 TTTAGGTTA--G--A--TTAGGGTTTTTAGTTAA
*
29629030 TTTAGGTTAGATTATGGTTTTTAGTTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
29629058 TTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
1 TTTAGGTTA--G--A--TTAGGGTTTTTAGTTAA
* *
29629092 TTTAGGTTAGATTAGGTTTTTTAATTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
29629120 TTTAGGTTAG
1 TTTAGGTTAG
29629130 TGTTAGGTTA
Statistics
Matches: 447, Mismatches: 33, Indels: 66
0.82 0.06 0.12
Matches are distributed among these distances:
27 74 0.17
28 203 0.45
29 28 0.06
30 9 0.02
31 1 0.00
32 8 0.02
33 24 0.05
34 100 0.22
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (28 bp):
TTTAGGTTAGATTAGGGTTTTTAGTTAA
Done.