Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 91 of 202
Found at i:27337566 original size:25 final size:25
Alignment explanation
Indices: 27337538--27337661 Score: 72
Period size: 25 Copynumber: 5.0 Consensus size: 25
27337528 CATACTAATT
* **
27337538 TACAACTCATTAGATTATACCGATC
1 TACAACTCATGAGAGCATACCGATC
* *
27337563 TACAGCTCGTGAGAGCATACCGATC
1 TACAACTCATGAGAGCATACCGATC
* * * * * *
27337588 TACAGCTCGTGTGAACATACTGATT
1 TACAACTCATGAGAGCATACCGATC
* * * *
27337613 TACAGCTCTTGAGATCATATCGATC
1 TACAACTCATGAGAGCATACCGATC
*
27337638 TAAAACTC--GAATGAGCATACCGAT
1 TACAACTCATG-A-GAGCATACCGAT
27337662 TCACAGCTCG
Statistics
Matches: 78, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
23 1 0.01
24 1 0.01
25 76 0.97
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (25 bp):
TACAACTCATGAGAGCATACCGATC
Found at i:27337617 original size:50 final size:50
Alignment explanation
Indices: 27337554--27337681 Score: 141
Period size: 50 Copynumber: 2.6 Consensus size: 50
27337544 TCATTAGATT
* * * **
27337554 ATACCGATCTACAGCTCGTGAGAGCATACCGATCTACAGCTCGTGTGAAC
1 ATACCGATTTACAGCTCGTGAGAGCATACCGATCTAAAACTCGAATGAAC
* * * * *
27337604 ATACTGATTTACAGCTCTTGAGATCATATCGATCTAAAACTCGAATGAGC
1 ATACCGATTTACAGCTCGTGAGAGCATACCGATCTAAAACTCGAATGAAC
*
27337654 ATACCGATTCACAGCTCGT-ATGAGCATA
1 ATACCGATTTACAGCTCGTGA-GAGCATA
27337682 TATGTACAGG
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
49 1 0.02
50 62 0.98
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (50 bp):
ATACCGATTTACAGCTCGTGAGAGCATACCGATCTAAAACTCGAATGAAC
Found at i:27337639 original size:75 final size:75
Alignment explanation
Indices: 27337516--27337681 Score: 203
Period size: 75 Copynumber: 2.2 Consensus size: 75
27337506 TTAGACCCAA
* * * *
27337516 AGCTCGTGTGAGCATACTAATTTACAACTCATTAGATTATACCGATCTACAGCTCGTGA-GAGCA
1 AGCTCGTGTGAGCATACTAATTTACAACTCATTAGATCATACCGATCTAAAACTCG-AATGAGCA
27337580 TACCGA-TCTAC
65 TACCGATTC-AC
* * * *
27337591 AGCTCGTGTGAACATACTGATTTACAGCTC-TTGAGATCATATCGATCTAAAACTCGAATGAGCA
1 AGCTCGTGTGAGCATACTAATTTACAACTCATT-AGATCATACCGATCTAAAACTCGAATGAGCA
27337655 TACCGATTCAC
65 TACCGATTCAC
*
27337666 AGCTCGTATGAGCATA
1 AGCTCGTGTGAGCATA
27337682 TATGTACAGG
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
74 3 0.04
75 73 0.94
76 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (75 bp):
AGCTCGTGTGAGCATACTAATTTACAACTCATTAGATCATACCGATCTAAAACTCGAATGAGCAT
ACCGATTCAC
Found at i:27338810 original size:20 final size:20
Alignment explanation
Indices: 27338777--27338815 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
27338767 GCCATATGGT
27338777 TTGGCTTGTGTTATGGTATC
1 TTGGCTTGTGTTATGGTATC
27338797 TTGG-TTGTGATTATGGTAT
1 TTGGCTTGTG-TTATGGTAT
27338816 TTTGAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.05, G:0.31, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATGGTATC
Found at i:27343630 original size:25 final size:25
Alignment explanation
Indices: 27343602--27343711 Score: 87
Period size: 25 Copynumber: 4.4 Consensus size: 25
27343592 TAGCTCGTAA
27343602 GAGCATACCGATCTACAACTCATGT
1 GAGCATACCGATCTACAACTCATGT
** * * *** *
27343627 GAGCATATTGATTTACAGCTTGCGA
1 GAGCATACCGATCTACAACTCATGT
* * *
27343652 GAGCATATCAATCTACAGCTCATGT
1 GAGCATACCGATCTACAACTCATGT
* *
27343677 GAGCATACCAATTTACAACTCGA-GT
1 GAGCATACCGATCTACAACTC-ATGT
27343702 GAGCATACCG
1 GAGCATACCG
27343712 GTTCACAGCT
Statistics
Matches: 65, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
25 64 0.98
26 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (25 bp):
GAGCATACCGATCTACAACTCATGT
Found at i:27343706 original size:50 final size:50
Alignment explanation
Indices: 27343566--27343710 Score: 166
Period size: 50 Copynumber: 2.9 Consensus size: 50
27343556 GTTCCGACCC
* * *
27343566 ACAGCTCGTGTGAGCATACTGATTTATAGCTCGTA-AGAGCATACCGATCT
1 ACAGCTCATGTGAGCATACTGATTTACAGCTCG-AGAGAGCATACCAATCT
* * * * *
27343616 ACAACTCATGTGAGCATATTGATTTACAGCTTGCGAGAGCATATCAATCT
1 ACAGCTCATGTGAGCATACTGATTTACAGCTCGAGAGAGCATACCAATCT
** * *
27343666 ACAGCTCATGTGAGCATACCAATTTACAACTCGAGTGAGCATACC
1 ACAGCTCATGTGAGCATACTGATTTACAGCTCGAGAGAGCATACC
27343711 GGTTCACAGC
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
50 77 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (50 bp):
ACAGCTCATGTGAGCATACTGATTTACAGCTCGAGAGAGCATACCAATCT
Found at i:27343723 original size:25 final size:26
Alignment explanation
Indices: 27343652--27343723 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 26
27343642 CAGCTTGCGA
*
27343652 GAGCATATCAA-TCTACAGCTC-ATGT
1 GAGCATACCAATTC-ACAGCTCGATGT
* *
27343677 GAGCATACCAATTTACAACTCGA-GT
1 GAGCATACCAATTCACAGCTCGATGT
**
27343702 GAGCATACCGGTTCACAGCTCG
1 GAGCATACCAATTCACAGCTCG
27343724 TATGATCATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (26 bp):
GAGCATACCAATTCACAGCTCGATGT
Found at i:27344862 original size:20 final size:20
Alignment explanation
Indices: 27344829--27344867 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
27344819 GCTATATGGT
27344829 TTGGCTTGTGTTATGGTATC
1 TTGGCTTGTGTTATGGTATC
27344849 TTGG-TTGTGATTATGGTAT
1 TTGGCTTGTG-TTATGGTAT
27344868 TTTGAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.05, G:0.31, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATGGTATC
Found at i:27346604 original size:34 final size:34
Alignment explanation
Indices: 27346561--27346628 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
27346551 AACTGAAGCG
27346561 TAGAAATGCGATCGAGCTAATCCATGATTTTCGC
1 TAGAAATGCGATCGAGCTAATCCATGATTTTCGC
*
27346595 TAGAAATGCGATTGAGCTAATCCATGATTTTCGC
1 TAGAAATGCGATCGAGCTAATCCATGATTTTCGC
27346629 CTTTCTTCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (34 bp):
TAGAAATGCGATCGAGCTAATCCATGATTTTCGC
Found at i:27348428 original size:15 final size:16
Alignment explanation
Indices: 27348398--27348434 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
27348388 GCTACAACTA
*
27348398 AAAATAAAATGAAATT
1 AAAATTAAATGAAATT
27348414 AAAATTAAA-GAAATT
1 AAAATTAAATGAAATT
27348429 AAAATT
1 AAAATT
27348435 TAAAAATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
AAAATTAAATGAAATT
Found at i:27356465 original size:50 final size:50
Alignment explanation
Indices: 27356337--27356573 Score: 228
Period size: 50 Copynumber: 4.8 Consensus size: 50
27356327 GATAATAACA
* * * * *
27356337 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGA-TGTTTCCTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACT-TCTCATCT-CGG
* * * * * * *
27356386 TACCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* * * **
27356436 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACTTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* * * *
27356486 TGCCAACGCCATGTCCCAAACATGGTATTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* *
27356536 TGCCAACGTCATGTCCCAGACATGATCTTACATGGGAC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAC
27356574 CTCTTTACCC
Statistics
Matches: 153, Mismatches: 32, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
49 37 0.24
50 116 0.76
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
Found at i:27358698 original size:40 final size:40
Alignment explanation
Indices: 27358640--27358801 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
27358630 AGTTTTAGTA
*
27358640 CAATGGCATGTCTT-ACATGCTTATGGTAATATAATCAATT
1 CAATGGCATG-CTTAACATGCTTATGGTAACATAATCAATT
*
27358680 CAATGGCATGCTTAACATGCTTAACATGCTTATGGTAACATATTCAATT
1 CAAT-G---G-----CATGCTTAACATGCTTATGGTAACATAATCAATT
*
27358729 CAATGGCATGCTTAACATGCTTATGGTAACATAATCATTT
1 CAATGGCATGCTTAACATGCTTATGGTAACATAATCAATT
*** * *
27358769 CAACATCATGTTTAACATGCTTACGGTAACATA
1 CAATGGCATGCTTAACATGCTTATGGTAACATA
27358802 TTCAGTACAT
Statistics
Matches: 103, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
40 64 0.62
41 1 0.01
44 1 0.01
45 1 0.01
48 4 0.04
49 32 0.31
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (40 bp):
CAATGGCATGCTTAACATGCTTATGGTAACATAATCAATT
Found at i:27358700 original size:9 final size:9
Alignment explanation
Indices: 27358686--27358711 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
27358676 AATTCAATGG
27358686 CATGCTTAA
1 CATGCTTAA
27358695 CATGCTTAA
1 CATGCTTAA
27358704 CATGCTTA
1 CATGCTTA
27358712 TGGTAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (9 bp):
CATGCTTAA
Found at i:27358727 original size:49 final size:49
Alignment explanation
Indices: 27358646--27358751 Score: 178
Period size: 49 Copynumber: 2.2 Consensus size: 49
27358636 AGTACAATGG
*
27358646 CATGTCTT-ACATGCTTATGGTAATATAATCAATTCAATGGCATGCTTAA
1 CATG-CTTAACATGCTTATGGTAACATAATCAATTCAATGGCATGCTTAA
*
27358695 CATGCTTAACATGCTTATGGTAACATATTCAATTCAATGGCATGCTTAA
1 CATGCTTAACATGCTTATGGTAACATAATCAATTCAATGGCATGCTTAA
27358744 CATGCTTA
1 CATGCTTA
27358752 TGGTAACATA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
48 3 0.06
49 51 0.94
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (49 bp):
CATGCTTAACATGCTTATGGTAACATAATCAATTCAATGGCATGCTTAA
Found at i:27365601 original size:18 final size:16
Alignment explanation
Indices: 27365578--27365617 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
27365568 TGAAAGAAAT
27365578 ATAAATGCCTAAAAATAA
1 ATAAATG-CTAAAAA-AA
*
27365596 ATAAATGCTAAGAAAA
1 ATAAATGCTAAAAAAA
27365612 ATAAAT
1 ATAAAT
27365618 TTCTCCCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 6 0.29
18 7 0.33
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.23
Consensus pattern (16 bp):
ATAAATGCTAAAAAAA
Found at i:27365613 original size:16 final size:17
Alignment explanation
Indices: 27365571--27365617 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
27365561 CTAACTCTGA
*
27365571 AAGAAATATAAATGCCT
1 AAGAAAAATAAATGCCT
*
27365588 AAAAATAAATAAATG-CT
1 AAGAA-AAATAAATGCCT
27365605 AAGAAAAATAAAT
1 AAGAAAAATAAAT
27365618 TTCTCCCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 8 0.31
17 10 0.38
18 8 0.31
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (17 bp):
AAGAAAAATAAATGCCT
Found at i:27366177 original size:16 final size:16
Alignment explanation
Indices: 27366158--27366210 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
27366148 ATAACAGTCC
27366158 TTAAATTTTAAAGTAA
1 TTAAATTTTAAAGTAA
*
27366174 TTAAATAATTAAA-TAA
1 TTAAAT-TTTAAAGTAA
27366190 TT-AATTTTAAAGTAA
1 TTAAATTTTAAAGTAA
27366205 TTAAAT
1 TTAAAT
27366211 AATTATTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 14 0.44
17 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (16 bp):
TTAAATTTTAAAGTAA
Found at i:27366184 original size:8 final size:8
Alignment explanation
Indices: 27366165--27366215 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
27366155 TCCTTAAATT
27366165 TTAAAGTAA
1 TTAAA-TAA
27366174 TTAAATAA
1 TTAAATAA
27366182 TTAAATAA
1 TTAAATAA
*
27366190 TT-AAT-T
1 TTAAATAA
27366196 TTAAAGTAA
1 TTAAA-TAA
27366205 TTAAATAA
1 TTAAATAA
27366213 TTA
1 TTA
27366216 TTAGTGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
6 2 0.05
7 5 0.14
8 20 0.54
9 10 0.27
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (8 bp):
TTAAATAA
Found at i:27366306 original size:17 final size:15
Alignment explanation
Indices: 27366274--27366318 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 15
27366264 TTATTGGGAG
*
27366274 TTAATTTGAGTTAAAT
1 TTAATTT-AATTAAAT
27366290 TTAAATATTAATTAAAT
1 TT-AAT-TTAATTAAAT
27366307 TTAATTTAATTA
1 TTAATTTAATTA
27366319 TAAAATAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 7 0.27
16 5 0.19
17 12 0.46
18 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
TTAATTTAATTAAAT
Found at i:27366322 original size:17 final size:17
Alignment explanation
Indices: 27366284--27366318 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
27366274 TTAATTTGAG
27366284 TTAAATTTAAATATTAA
1 TTAAATTTAAATATTAA
27366301 TTAAATTT-AAT-TTAA
1 TTAAATTTAAATATTAA
27366316 TTA
1 TTA
27366319 TAAAATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 3 0.17
17 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAATTTAAATATTAA
Found at i:27368403 original size:18 final size:18
Alignment explanation
Indices: 27368382--27368418 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27368372 GACTTAGTTT
27368382 AATTTTGGTTGTAATTCG
1 AATTTTGGTTGTAATTCG
27368400 AATTTTGGTTGTAATTCG
1 AATTTTGGTTGTAATTCG
27368418 A
1 A
27368419 CTTGGACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (18 bp):
AATTTTGGTTGTAATTCG
Found at i:27369299 original size:30 final size:31
Alignment explanation
Indices: 27369260--27369319 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
27369250 GGAGGTGGGA
*
27369260 TGGGAAGGGAATAAAATTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
27369291 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
27369320 TAAATGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:27369780 original size:15 final size:15
Alignment explanation
Indices: 27369760--27369788 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27369750 GTATTGTTGT
27369760 TTGATAACACGGTGA
1 TTGATAACACGGTGA
27369775 TTGATAACACGGTG
1 TTGATAACACGGTG
27369789 TGTAAGGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:27371919 original size:17 final size:17
Alignment explanation
Indices: 27371897--27371930 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27371887 GTCACAAATG
27371897 GTCCCACTTAAGTTTCA
1 GTCCCACTTAAGTTTCA
27371914 GTCCCACTTAAGTTTCA
1 GTCCCACTTAAGTTTCA
27371931 ATCTCCTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (17 bp):
GTCCCACTTAAGTTTCA
Found at i:27377895 original size:3 final size:3
Alignment explanation
Indices: 27377887--27377925 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
27377877 AAACAAACCT
27377887 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27377926 AGTTAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:27378744 original size:22 final size:23
Alignment explanation
Indices: 27378719--27378761 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
27378709 CCCTTCTCCT
27378719 CTCTGTTCTTT-TTTTCTTTTTG
1 CTCTGTTCTTTGTTTTCTTTTTG
* *
27378741 CTCTTTTTTTTGTTTTCTTTT
1 CTCTGTTCTTTGTTTTCTTTT
27378762 CGTTGCTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (23 bp):
CTCTGTTCTTTGTTTTCTTTTTG
Found at i:27379141 original size:6 final size:6
Alignment explanation
Indices: 27379130--27379172 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
27379120 ATATTGGGCC
* *
27379130 ATTACA ATTACA ATTATA ATTATA ATTATA ATTA-A ATT-TA ATT
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATT
27379173 TATAGTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
5 8 0.23
6 27 0.77
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTATA
Found at i:27388322 original size:17 final size:17
Alignment explanation
Indices: 27388300--27388336 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
27388290 CAGCATTGCC
*
27388300 TGGCGGATAGTATTACT
1 TGGCGGATACTATTACT
*
27388317 TGGCGGATACTATTGCT
1 TGGCGGATACTATTACT
27388334 TGG
1 TGG
27388337 TGGACATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.14, G:0.32, T:0.35
Consensus pattern (17 bp):
TGGCGGATACTATTACT
Found at i:27389204 original size:35 final size:35
Alignment explanation
Indices: 27389149--27389279 Score: 131
Period size: 35 Copynumber: 3.7 Consensus size: 35
27389139 TTGAGGACAA
*
27389149 ATCCCACCACAACACCAATACTTC-TTTCATAACAC
1 ATCCCACCACAACACTAATACTTCATTT-ATAACAC
* * * *
27389184 ATGCCACCACAACATTAATACTTCATTTATCATAC
1 ATCCCACCACAACACTAATACTTCATTTATAACAC
* * *
27389219 ATCCCACCACAACACTGATACTTCACTTATCACAC
1 ATCCCACCACAACACTAATACTTCATTTATAACAC
***
27389254 ATCTTGCCACAACA-TCAATACTTCAT
1 ATCCCACCACAACACT-AATACTTCAT
27389280 CCATCACACT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
34 1 0.01
35 75 0.95
36 3 0.04
ACGTcount: A:0.36, C:0.35, G:0.02, T:0.27
Consensus pattern (35 bp):
ATCCCACCACAACACTAATACTTCATTTATAACAC
Found at i:27392321 original size:16 final size:16
Alignment explanation
Indices: 27392300--27392356 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
27392290 TTTGGTTCGC
*
27392300 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
27392316 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
27392332 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
27392348 TGTAATGGA
1 TGTAATGGA
27392357 AAAACTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:27392623 original size:18 final size:17
Alignment explanation
Indices: 27392602--27392635 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27392592 TTATTATTAA
*
27392602 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
27392620 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
27392636 CTCTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:27400975 original size:31 final size:31
Alignment explanation
Indices: 27400914--27400975 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
27400904 ATTTGTCTTC
* *
27400914 TTTAATTTTATTTATTTTAGGCTATTTTTTA
1 TTTAATTTTATTTATTTTAGACTATATTTTA
27400945 TTTAATTTTATTT-TTTT-GCACTATAATTTTA
1 TTTAATTTTATTTATTTTAG-ACTAT-ATTTTA
27400976 GATTATTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 1 0.04
30 8 0.30
31 18 0.67
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (31 bp):
TTTAATTTTATTTATTTTAGACTATATTTTA
Found at i:27420688 original size:16 final size:18
Alignment explanation
Indices: 27420667--27420699 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
27420657 ACATCAAACT
27420667 CATCAAA-CGGT-AAAAG
1 CATCAAATCGGTCAAAAG
27420683 CATCAAATCGGTCAAAA
1 CATCAAATCGGTCAAAA
27420700 AACTGTAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.15
Consensus pattern (18 bp):
CATCAAATCGGTCAAAAG
Found at i:27435460 original size:79 final size:79
Alignment explanation
Indices: 27435329--27435482 Score: 299
Period size: 79 Copynumber: 1.9 Consensus size: 79
27435319 TGTTTTACCT
27435329 TTAATTCTTTATTTTCTGTTGCGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
1 TTAATTCTTTATTTTCTGTTGCGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
27435394 TAGATTCTATCCAC
66 TAGATTCTATCCAC
*
27435408 TTAATTCTTTATTTTCTGTTGTGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
1 TTAATTCTTTATTTTCTGTTGCGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
27435473 TAGATTCTAT
66 TAGATTCTAT
27435483 TCACCAACCC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (79 bp):
TTAATTCTTTATTTTCTGTTGCGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
TAGATTCTATCCAC
Found at i:27438548 original size:100 final size:100
Alignment explanation
Indices: 27438369--27438568 Score: 294
Period size: 100 Copynumber: 2.0 Consensus size: 100
27438359 CCTAAGGTCA
* * *
27438369 AAGGCAGGAAACCTATATTGCCTTTCCTACTTCCTTACCCCAAGTTCCACTTTCTCCTCCCTATC
1 AAGGCAAGAAACCTATATTGCCTCTCCTACTTCCTTACCCCAAGTTCCACTTGCTCCTCCCTATC
*
27438434 TTCTACTTCAACCACCCTAGTAGATGGCTCTTCGC
66 TTCTACTTCAACCACCCTAGTAGACGGCTCTTCGC
* * * *
27438469 AAGGCAAGCAACCTCTATTTCCTCTCCTACTTCCTTACTCCAAGTTCCACTTGCTCCTCCCTATC
1 AAGGCAAGAAACCTATATTGCCTCTCCTACTTCCTTACCCCAAGTTCCACTTGCTCCTCCCTATC
* *
27438534 TTCT-GTTCCGACCACCCTAGTAGACGGCTCTTCGC
66 TTCTACTT-CAACCACCCTAGTAGACGGCTCTTCGC
27438569 CCTATCTTAC
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 2 0.02
100 87 0.98
ACGTcount: A:0.20, C:0.38, G:0.12, T:0.32
Consensus pattern (100 bp):
AAGGCAAGAAACCTATATTGCCTCTCCTACTTCCTTACCCCAAGTTCCACTTGCTCCTCCCTATC
TTCTACTTCAACCACCCTAGTAGACGGCTCTTCGC
Found at i:27442392 original size:50 final size:50
Alignment explanation
Indices: 27442327--27442426 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
27442317 AAACTATTAC
* *
27442327 AATACAAACAAATTAATATCTAATACAATCTAAACTAAAATCAACAAACT
1 AATACAAACAAATTAATACCTAATACAATCTAAACTAAAACCAACAAACT
* * *
27442377 AATATAAACATATTAATACCTAATACAATCTATACTAAAACCAACAAACT
1 AATACAAACAAATTAATACCTAATACAATCTAAACTAAAACCAACAAACT
27442427 GAGACGAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (50 bp):
AATACAAACAAATTAATACCTAATACAATCTAAACTAAAACCAACAAACT
Found at i:27455746 original size:15 final size:15
Alignment explanation
Indices: 27455714--27455751 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
27455704 AGATTAATTC
*
27455714 TTAATTAAGATTTTA
1 TTAATTAAGATTTAA
27455729 TTAACTTAAG-TTTAA
1 TTAA-TTAAGATTTAA
27455744 TTAATTAA
1 TTAATTAA
27455752 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 12 0.57
16 5 0.24
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (15 bp):
TTAATTAAGATTTAA
Found at i:27463417 original size:101 final size:102
Alignment explanation
Indices: 27463298--27463482 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
27463288 AAAGTGATGG
*
27463298 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-C-CAAAATGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGCAAAATGAT-GGTCACATGTGTAGT
27463361 ACTATGTGCAGGCTACTATGCGTACCAGATAGCTTTGA
65 ACTATGTGCAGGCTACTATGCGTACCAGATAGCTTTGA
* * * *
27463399 TCACGTGTGTAGTACTATGTGCAGGCTACTACTTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGCAAAATGATGGTCACATGTGTAGTA
27463464 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
27463483 TGAACCGGTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 36 0.47
102 35 0.45
103 6 0.08
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGCAAAATGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCAGATAGCTTTGA
Found at i:27463428 original size:51 final size:50
Alignment explanation
Indices: 27463295--27463484 Score: 222
Period size: 51 Copynumber: 3.8 Consensus size: 50
27463285 GTGAAAGTGA
* * * *
27463295 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCA-AAATGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATA-GTT
* * *
27463345 AGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGCTT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATAG-TT
* * * * *
27463396 TGATCACGTGTGTAGTACTATGTGCAGGCTACTACT-TGTATCGGATAGTGA
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTA-TGTGTACCAGATAGT-T
27463447 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
27463485 AACCGGTATC
Statistics
Matches: 118, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
50 41 0.35
51 76 0.64
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (50 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATAGTT
Found at i:27463483 original size:26 final size:26
Alignment explanation
Indices: 27463404--27463484 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
27463394 TTTGATCACG
27463404 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
*
27463430 CT-TGTA-T-CGGATAGTG-ATGG-TCAC-A
1 -TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
27463455 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
27463481 TGTG
1 TGTG
27463485 AACCGGTATC
Statistics
Matches: 42, Mismatches: 2, Indels: 21
0.65 0.03 0.32
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 21 0.50
27 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:27463559 original size:46 final size:44
Alignment explanation
Indices: 27463486--27463574 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 44
27463476 TACTATGTGA
*
27463486 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCT-AATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCCC
* *
27463529 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
27463575 ATCGTGTATC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 5 0.13
44 11 0.28
45 2 0.05
46 16 0.41
47 5 0.13
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (44 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCCC
Found at i:27463729 original size:16 final size:16
Alignment explanation
Indices: 27463708--27463739 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27463698 TGATTGAAAG
*
27463708 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
27463724 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
27463740 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:27470890 original size:25 final size:25
Alignment explanation
Indices: 27470853--27470910 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
27470843 TAGGCATTAC
* * * *
27470853 GCCACATAGGCTTTACAAGTAACTA
1 GCCACAAAAGCTTTACAAATAAATA
* *
27470878 GCCACAAAAGCTTTCCAAATAAATC
1 GCCACAAAAGCTTTACAAATAAATA
27470903 GCCACAAA
1 GCCACAAA
27470911 GGTTTCCCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (25 bp):
GCCACAAAAGCTTTACAAATAAATA
Found at i:27470957 original size:49 final size:49
Alignment explanation
Indices: 27470878--27470989 Score: 143
Period size: 49 Copynumber: 2.3 Consensus size: 49
27470868 CAAGTAACTA
* **
27470878 GCCACAAAAGCTTTCCAAATAAATCGCCACAAAGGTTTCCCAAACAATTC
1 GCCACAAAAGC-TTCCAAATAAATCACCACAAAGACTTCCCAAACAATTC
* * * *
27470928 GCCACAAAGGCTTCCAAGTAAATCACCACAAAGACTTCCCAAATAGTTC
1 GCCACAAAAGCTTCCAAATAAATCACCACAAAGACTTCCCAAACAATTC
*
27470977 ACCACAAAAGCTT
1 GCCACAAAAGCTT
27470990 GGTTTGGTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 43 0.81
50 10 0.19
ACGTcount: A:0.40, C:0.30, G:0.11, T:0.19
Consensus pattern (49 bp):
GCCACAAAAGCTTCCAAATAAATCACCACAAAGACTTCCCAAACAATTC
Found at i:27470978 original size:25 final size:25
Alignment explanation
Indices: 27470879--27470989 Score: 107
Period size: 25 Copynumber: 4.5 Consensus size: 25
27470869 AAGTAACTAG
* * * *
27470879 CCACAAAAGCTTTCCAAATAAATCG
1 CCACAAAGGCTTCCCAAATAATTCA
* * *
27470904 CCACAAAGGTTTCCCAAACAATTCG
1 CCACAAAGGCTTCCCAAATAATTCA
* *
27470929 CCACAAAGGCTT-CCAAGTAAATCA
1 CCACAAAGGCTTCCCAAATAATTCA
* *
27470953 CCACAAAGACTTCCCAAATAGTTCA
1 CCACAAAGGCTTCCCAAATAATTCA
*
27470978 CCACAAAAGCTT
1 CCACAAAGGCTT
27470990 GGTTTGGTTT
Statistics
Matches: 69, Mismatches: 16, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
24 19 0.28
25 50 0.72
ACGTcount: A:0.41, C:0.31, G:0.10, T:0.19
Consensus pattern (25 bp):
CCACAAAGGCTTCCCAAATAATTCA
Found at i:27475161 original size:40 final size:41
Alignment explanation
Indices: 27475050--27475178 Score: 233
Period size: 41 Copynumber: 3.2 Consensus size: 41
27475040 GGCACTTCAA
27475050 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
27475091 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
* *
27475132 CTGCTAGGCTTAT-GCCTGATTCAGATCACCGACACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
27475172 CTGCTAG
1 CTGCTAG
27475179 ACGTAAAGTC
Statistics
Matches: 86, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
40 32 0.37
41 54 0.63
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (41 bp):
CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
Found at i:27475201 original size:81 final size:82
Alignment explanation
Indices: 27475027--27475204 Score: 218
Period size: 81 Copynumber: 2.2 Consensus size: 82
27475017 CACTTAATTT
* * * *
27475027 AAACAGATTCACTGGCACTTCA-ACTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 AAACAG-TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGACACTTAGC
* * *
27475091 CTGCTAGGCTTATAGCCTG
64 CTGCTAGACGTAAAGCCTG
**
27475110 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTAT-GCCTGATTCAGATCACCGACACTTAGCCT
1 AAACAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGACACTTAGCCT
27475174 GCTAGACGTAAAGTCC-G
66 GCTAGACGTAAAG-CCTG
*
27475191 AAACATTTCACCGG
1 AAACAGTTCACCGG
27475205 TAATTAATCT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
81 50 0.62
82 27 0.33
83 4 0.05
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (82 bp):
AAACAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGACACTTAGCCT
GCTAGACGTAAAGCCTG
Found at i:27475630 original size:2 final size:2
Alignment explanation
Indices: 27475618--27475651 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
27475608 GATCATTCAA
27475618 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27475652 ATTACCAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27475889 original size:2 final size:2
Alignment explanation
Indices: 27475836--27475871 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
27475826 TAAATTCAAA
* *
27475836 AT AT AT AT AT AT AT AT AT AC AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27475872 TCGATCATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27476945 original size:28 final size:31
Alignment explanation
Indices: 27476913--27476971 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
27476903 TGTTTTGTTT
27476913 TTATTATAATAA-CATTAT-AAT-ATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
* *
27476941 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
27476972 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 3 0.12
31 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATAATAACCATTATAAATAATATAAA
Found at i:27479911 original size:25 final size:25
Alignment explanation
Indices: 27479881--27479940 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
27479871 TACCAAAAAA
27479881 GCTTCCCAAATAAATCGT-CATAAAG
1 GCTTCCCAAATAAATC-TCCATAAAG
*
27479906 GCTTCCCAACTAAATCTCCATAAAG
1 GCTTCCCAAATAAATCTCCATAAAG
27479931 GCTTCCCAAA
1 GCTTCCCAAA
27479941 CAATTTGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 1 0.03
25 31 0.97
ACGTcount: A:0.37, C:0.30, G:0.10, T:0.23
Consensus pattern (25 bp):
GCTTCCCAAATAAATCTCCATAAAG
Found at i:27505030 original size:22 final size:21
Alignment explanation
Indices: 27505005--27505058 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
27504995 ATTTATTTAA
**
27505005 TTATTTTTTGGTCTTTAGGAAT
1 TTATTTTTTGGTAATTAGG-AT
*
27505027 TTATTTCTTTTGTAATTAGGAT
1 TTATTT-TTTGGTAATTAGGAT
*
27505049 TTAATTTTTG
1 TTATTTTTTG
27505059 CAGAATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 3 0.12
22 13 0.50
23 10 0.38
ACGTcount: A:0.20, C:0.04, G:0.15, T:0.61
Consensus pattern (21 bp):
TTATTTTTTGGTAATTAGGAT
Found at i:27510402 original size:27 final size:26
Alignment explanation
Indices: 27510356--27510467 Score: 152
Period size: 27 Copynumber: 4.2 Consensus size: 26
27510346 ACACTCCAGA
* *
27510356 AAAAGGAAGCCTTTGAGGCGATCTATG
1 AAAAGGAAG-TTTTGTGGCGATCTATG
27510383 AAAAGGAAGTTGTTGTGGCGATCTATG
1 AAAAGGAAGTT-TTGTGGCGATCTATG
*
27510410 AAAAGGAAGTCTTTGTGGCGATCTATT
1 AAAAGGAAGT-TTTGTGGCGATCTATG
*
27510437 AAAAGGAAGCATTTGTGGCGATCTATG
1 AAAAGGAAG-TTTTGTGGCGATCTATG
27510464 AAAA
1 AAAA
27510468 AATAAAGAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
26 1 0.01
27 75 0.97
28 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.27
Consensus pattern (26 bp):
AAAAGGAAGTTTTGTGGCGATCTATG
Found at i:27510441 original size:54 final size:54
Alignment explanation
Indices: 27510356--27510534 Score: 173
Period size: 54 Copynumber: 3.3 Consensus size: 54
27510346 ACACTCCAGA
*
27510356 AAAAGGAAGCCTTTGAGGCGATCTATGAAAAGGAAG-TTGTTGTGGCGATCTATG
1 AAAAGGAAGCCTTTGAGGCGATCTATGAAAAGGAAGCAT-TTGTGGCGATCTATG
* * *
27510410 AAAAGGAAGTCTTTGTGGCGATCTATTAAAAGGAAGCATTTGTGGCGATCTATG
1 AAAAGGAAGCCTTTGAGGCGATCTATGAAAAGGAAGCATTTGTGGCGATCTATG
** ** * ** * * *
27510464 AAAAAATAAAGAATTT-ATGGCGATCTATTAAAAATAAACCTTTGTGGCGGTCTATG
1 --AAAAGGAAGCCTTTGA-GGCGATCTATGAAAAGGAAGCATTTGTGGCGATCTATG
*
27510520 AAAATGAAGCCTTTG
1 AAAAGGAAGCCTTTG
27510535 TGGAAAACCC
Statistics
Matches: 103, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
54 59 0.57
55 1 0.01
56 43 0.42
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (54 bp):
AAAAGGAAGCCTTTGAGGCGATCTATGAAAAGGAAGCATTTGTGGCGATCTATG
Found at i:27510508 original size:56 final size:56
Alignment explanation
Indices: 27510395--27510523 Score: 154
Period size: 56 Copynumber: 2.3 Consensus size: 56
27510385 AAGGAAGTTG
* ** * * *
27510395 TTGTGGCGATCTATG--AAAAGGAAGTCTTTGTGGCGATCTATTAAAAGGAAGCAT
1 TTGTGGCGATCTATGAAAAAAGAAAGAATTTATGGCGATCTATTAAAAAGAAACAT
* * *
27510449 TTGTGGCGATCTATGAAAAAATAAAGAATTTATGGCGATCTATTAAAAATAAACCT
1 TTGTGGCGATCTATGAAAAAAGAAAGAATTTATGGCGATCTATTAAAAAGAAACAT
*
27510505 TTGTGGCGGTCTATGAAAA
1 TTGTGGCGATCTATGAAAA
27510524 TGAAGCCTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 15 0.24
56 48 0.76
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (56 bp):
TTGTGGCGATCTATGAAAAAAGAAAGAATTTATGGCGATCTATTAAAAAGAAACAT
Found at i:27510511 original size:27 final size:27
Alignment explanation
Indices: 27510362--27510537 Score: 131
Period size: 27 Copynumber: 6.4 Consensus size: 27
27510352 CAGAAAAAGG
* * **
27510362 AAGCCTTTGAGGCGATCTATGAAAAGG
1 AAGCCTTTGTGGCGATCTATTAAAAAT
* * **
27510389 AAG-TTGTTGTGGCGATCTATGAAAAGG
1 AAGCCT-TTGTGGCGATCTATTAAAAAT
* **
27510416 AAGTCTTTGTGGCGATCTATTAAAAGG
1 AAGCCTTTGTGGCGATCTATTAAAAAT
* *
27510443 AAGCATTTGTGGCGATCTATGAAAAAAT
1 AAGCCTTTGTGGCGATCTAT-TAAAAAT
** *
27510471 AAAGAATTTATGGCGATCTATTAAAAAT
1 -AAGCCTTTGTGGCGATCTATTAAAAAT
* * *
27510499 AAACCTTTGTGGCGGTCTA-TGAAAAT
1 AAGCCTTTGTGGCGATCTATTAAAAAT
27510525 GAAGCCTTTGTGG
1 -AAGCCTTTGTGG
27510538 AAAACCCCGT
Statistics
Matches: 125, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
26 7 0.06
27 89 0.71
28 11 0.09
29 18 0.14
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (27 bp):
AAGCCTTTGTGGCGATCTATTAAAAAT
Found at i:27522038 original size:22 final size:23
Alignment explanation
Indices: 27522010--27522054 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
27522000 CTTTCGAGCT
*
27522010 ATAAAAATAATAA-AATATTTTA
1 ATAAAAATAATAATAAAATTTTA
*
27522032 ATAAAAATACTAATAAAATTTTA
1 ATAAAAATAATAATAAAATTTTA
27522055 GTTTTAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
ATAAAAATAATAATAAAATTTTA
Found at i:27524173 original size:68 final size:69
Alignment explanation
Indices: 27524094--27524228 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 69
27524084 TTTTAATAGT
* *
27524094 TTAATATTAAATTAAATTTAATACTTATATTAAT-AATATTTTATTAATTTAAAATTAAAGTGAT
1 TTAATATTAAATTAAATCTAATACTTATATTAATAAATATTATATTAATTTAAAATTAAAGTGAT
27524158 TATC
66 TATC
* * * * **
27524162 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTATTATTAAAGTGAT
1 TTAATATTAAATTAAATCTAATACTTATATTAATAAATATTATATTAATTTAAAATTAAAGTGAT
27524227 TA
66 TA
27524229 AGTTTAATTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 29 0.50
69 29 0.50
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (69 bp):
TTAATATTAAATTAAATCTAATACTTATATTAATAAATATTATATTAATTTAAAATTAAAGTGAT
TATC
Found at i:27524776 original size:24 final size:24
Alignment explanation
Indices: 27524727--27524781 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
27524717 TAAAGTAGGT
* *
27524727 TATA-TATTATTTTTATAATATTA
1 TATATTATAATTTTTATAATATCA
27524750 TATATTATAATTTTTATTAAT-TCA
1 TATATTATAATTTTTA-TAATATCA
*
27524774 TATTTTAT
1 TATATTAT
27524782 TAATAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 19 0.70
25 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TATATTATAATTTTTATAATATCA
Found at i:27524827 original size:15 final size:15
Alignment explanation
Indices: 27524802--27524855 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
27524792 ATTAAGAATG
* *
27524802 TTATTAAATTATATA
1 TTATTTAATTAAATA
* *
27524817 TTATTTTATTAAATT
1 TTATTTAATTAAATA
27524832 TTATTTAATTAAAT-
1 TTATTTAATTAAATA
27524846 TATATTTAAT
1 T-TATTTAAT
27524856 AATAATTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
14 1 0.03
15 32 0.97
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTTAATTAAATA
Found at i:27524869 original size:15 final size:15
Alignment explanation
Indices: 27524817--27524867 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
27524807 AAATTATATA
* *
27524817 TTATTTTATTAAATT
1 TTATTTAATAAAATT
*
27524832 TTATTTAATTAAATT
1 TTATTTAATAAAATT
*
27524847 ATATTTAATAATAATT
1 TTATTTAATAA-AATT
27524863 TTATT
1 TTATT
27524868 AAAATTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 23 0.74
16 8 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTTAATAAAATT
Found at i:27526536 original size:24 final size:23
Alignment explanation
Indices: 27526509--27526558 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
27526499 TAATACCAGC
*
27526509 ATGCAGAAAATTCTGCCAGTAAAA
1 ATGCAGAAAA-GCTGCCAGTAAAA
*
27526533 ATGCAGACAAGCTGCCAGTAAAA
1 ATGCAGAAAAGCTGCCAGTAAAA
27526556 ATG
1 ATG
27526559 TGATAAATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (23 bp):
ATGCAGAAAAGCTGCCAGTAAAA
Found at i:27529997 original size:13 final size:13
Alignment explanation
Indices: 27529970--27530000 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
27529960 TTGGCTTTTC
*
27529970 AAAAGCACTTTTG
1 AAAAGCACTTATG
27529983 AAAAGCACTTATG
1 AAAAGCACTTATG
27529996 AAAAG
1 AAAAG
27530001 GAGAAGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (13 bp):
AAAAGCACTTATG
Found at i:27530513 original size:13 final size:13
Alignment explanation
Indices: 27530495--27530557 Score: 90
Period size: 13 Copynumber: 4.8 Consensus size: 13
27530485 AAAACAAACA
27530495 TTTCAAAAGCACT
1 TTTCAAAAGCACT
27530508 TTTCAAAAGCACT
1 TTTCAAAAGCACT
* * * *
27530521 TTTCCACATCACC
1 TTTCAAAAGCACT
27530534 TTTCAAAAGCACT
1 TTTCAAAAGCACT
27530547 TTTCAAAAGCA
1 TTTCAAAAGCA
27530558 TTCCTAAACT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (13 bp):
TTTCAAAAGCACT
Found at i:27533260 original size:16 final size:16
Alignment explanation
Indices: 27533239--27533269 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27533229 TTCACTATTA
*
27533239 TGTCTTTTGTATTTTT
1 TGTCTTTTATATTTTT
27533255 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
27533270 ACATACATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:27536499 original size:18 final size:18
Alignment explanation
Indices: 27536459--27536501 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
27536449 TGTGTTTTCT
27536459 TAAAAACAGTTAATTTTA
1 TAAAAACAGTTAATTTTA
* *
27536477 GAAAAACAGTT-GTTTTAA
1 TAAAAACAGTTAATTTT-A
27536495 TAAAAAC
1 TAAAAAC
27536502 CGTTTTTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (18 bp):
TAAAAACAGTTAATTTTA
Found at i:27539108 original size:28 final size:30
Alignment explanation
Indices: 27539057--27539118 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
27539047 CATAATTTAA
*
27539057 CATAAAAATTCCTAAATGAAAAT-AAAGTC
1 CATAAAAATTCCTAAATCAAAATAAAAGTC
27539086 CATAAAAA-TCC-AAATCATAAATAAAAGTC
1 CATAAAAATTCCTAAATCA-AAATAAAAGTC
27539115 CATA
1 CATA
27539119 TATATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 5 0.17
28 7 0.23
29 18 0.60
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.23
Consensus pattern (30 bp):
CATAAAAATTCCTAAATCAAAATAAAAGTC
Found at i:27544757 original size:22 final size:22
Alignment explanation
Indices: 27544716--27544757 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
27544706 CAGATAAAAC
*
27544716 AATTAAAATAAATAACTAAGAT
1 AATTAAAATAAATAAATAAGAT
27544738 AATTAAAATAGAA-AAATAAG
1 AATTAAAATA-AATAAATAAG
27544758 GAAGAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (22 bp):
AATTAAAATAAATAAATAAGAT
Found at i:27546783 original size:17 final size:17
Alignment explanation
Indices: 27546761--27546794 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27546751 CCCATTAATG
*
27546761 AAATAAACCAAATAAAA
1 AAATAAACAAAATAAAA
*
27546778 AAATAAATAAAATAAAA
1 AAATAAACAAAATAAAA
27546795 CCAAATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (17 bp):
AAATAAACAAAATAAAA
Found at i:27546798 original size:27 final size:26
Alignment explanation
Indices: 27546761--27546811 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
27546751 CCCATTAATG
27546761 AAATAAACCAAATAAAAAAATAAATA
1 AAATAAACCAAATAAAAAAATAAATA
* *
27546787 AAATAAAACCAAATTAAAAATTAAA
1 AAAT-AAACCAAATAAAAAAATAAA
27546812 GGTCCACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.18
Consensus pattern (26 bp):
AAATAAACCAAATAAAAAAATAAATA
Found at i:27560162 original size:147 final size:147
Alignment explanation
Indices: 27559895--27560188 Score: 588
Period size: 147 Copynumber: 2.0 Consensus size: 147
27559885 AAGAAAAGAT
27559895 GCACTTGGGATTAGATGTGGATGTTCAAAAGTTAGAGACTGAGAAATTAAGAAAAGGTGAGAACA
1 GCACTTGGGATTAGATGTGGATGTTCAAAAGTTAGAGACTGAGAAATTAAGAAAAGGTGAGAACA
27559960 AGGCCGATGAGGACCTGGACAGTTTGAAGACGGACTATAAGAAGTTGAGGTTGTCAATAAGAACT
66 AGGCCGATGAGGACCTGGACAGTTTGAAGACGGACTATAAGAAGTTGAGGTTGTCAATAAGAACT
27560025 GCTGGGTTAGGGAAAAC
131 GCTGGGTTAGGGAAAAC
27560042 GCACTTGGGATTAGATGTGGATGTTCAAAAGTTAGAGACTGAGAAATTAAGAAAAGGTGAGAACA
1 GCACTTGGGATTAGATGTGGATGTTCAAAAGTTAGAGACTGAGAAATTAAGAAAAGGTGAGAACA
27560107 AGGCCGATGAGGACCTGGACAGTTTGAAGACGGACTATAAGAAGTTGAGGTTGTCAATAAGAACT
66 AGGCCGATGAGGACCTGGACAGTTTGAAGACGGACTATAAGAAGTTGAGGTTGTCAATAAGAACT
27560172 GCTGGGTTAGGGAAAAC
131 GCTGGGTTAGGGAAAAC
27560189 TTCAGAACAA
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.36, C:0.11, G:0.31, T:0.22
Consensus pattern (147 bp):
GCACTTGGGATTAGATGTGGATGTTCAAAAGTTAGAGACTGAGAAATTAAGAAAAGGTGAGAACA
AGGCCGATGAGGACCTGGACAGTTTGAAGACGGACTATAAGAAGTTGAGGTTGTCAATAAGAACT
GCTGGGTTAGGGAAAAC
Found at i:27569424 original size:55 final size:57
Alignment explanation
Indices: 27569293--27569431 Score: 212
Period size: 57 Copynumber: 2.5 Consensus size: 57
27569283 TGATGGAAGG
* * *
27569293 GGACCAAAGTGAAAACCCGCAAAGGACGCTTTGCTTCTTAAAAAAAATATTTGGAGG
1 GGACCAAAGTGAAAACCCGCAAAGGGCACTTTGCTTCTTAAAAAAAATATTTGGAGA
27569350 GGACCAAAGTGAAAACCCGCAAAGGGCACTTTGCTTCCTT-AAAAAAA-ATTTGGAGA
1 GGACCAAAGTGAAAACCCGCAAAGGGCACTTTGCTT-CTTAAAAAAAATATTTGGAGA
*
27569406 GG-CCAAGGTGAAAACCCGCAAAGGGC
1 GGACCAAAGTGAAAACCCGCAAAGGGC
27569432 GCCTTAAGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
55 23 0.30
56 10 0.13
57 41 0.53
58 3 0.04
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.17
Consensus pattern (57 bp):
GGACCAAAGTGAAAACCCGCAAAGGGCACTTTGCTTCTTAAAAAAAATATTTGGAGA
Found at i:27570725 original size:45 final size:43
Alignment explanation
Indices: 27570631--27570750 Score: 116
Period size: 45 Copynumber: 2.7 Consensus size: 43
27570621 TTGCATCAGG
* * *
27570631 TCTTATCTCCCTGTAGTTACAGCGGAGCAGACTAAGTAAGCAGA
1 TCTTATCTCCCTG-AGTTGCAGTGGAGCAGACTAAGTAAGCAAA
* * *
27570675 TCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCTAAG-ATGGCAAA
1 TCTTATCTCCCTG-AGTTGCAGTGGAGCAGA-CTAAGTA-AGCAAA
* *
27570720 TCTTATTTCCCTGAGATTGCAGTGGAACAGA
1 TCTTATCTCCCTGAG-TTGCAGTGGAGCAGA
27570751 TTGAAGCCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
44 29 0.47
45 33 0.53
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
Found at i:27570815 original size:44 final size:44
Alignment explanation
Indices: 27570549--27570824 Score: 161
Period size: 44 Copynumber: 6.3 Consensus size: 44
27570539 CAACTAATCC
* ** *
27570549 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAGTAACAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACATCAGATCT
** * * ** * *
27570593 TATCTAACTGAAGTTGCAGTAGAGTGGATT---GCATCAGGTCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACATCAGATCT
* * * * *
27570634 TATCTCCCTGTAGTTACAGCGGAGCAGACTAAGTA-AGCAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAA-AACATCAGATCT
* * * * *** *
27570678 TATCCCCCTGAAGTTGCAGTGGGGCAGATCTAAGATGGCAAATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGAT-TAAAACATCAGATCT
* * * ** *
27570723 TATTTCCCTG-AGATTGCAGTGGAACAGATTGAAGCCGAT-A-ATCC
1 TATCTCCCTGAAG-TTACAGTGGAGCAGATT-AAAAC-ATCAGATCT
*
27570767 TATCTCCCTGAAGTTACAGTGGAACAGATTAAAACATCAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACATCAGATCT
*
27570811 TATCTCTCTGAAGT
1 TATCTCCCTGAAGT
27570825 AGAGCAGATC
Statistics
Matches: 176, Mismatches: 44, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
41 29 0.16
42 2 0.01
43 4 0.02
44 103 0.59
45 38 0.22
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACATCAGATCT
Found at i:27571328 original size:17 final size:18
Alignment explanation
Indices: 27571306--27571343 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
27571296 CCCATTAGTG
*
27571306 AAATAAACCAAAT-AAAC
1 AAATAAACAAAATAAAAC
*
27571323 AAATAAATAAAATAAAAC
1 AAATAAACAAAATAAAAC
27571341 AAA
1 AAA
27571344 ATTAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (18 bp):
AAATAAACAAAATAAAAC
Found at i:27580876 original size:174 final size:174
Alignment explanation
Indices: 27580548--27580903 Score: 624
Period size: 174 Copynumber: 2.0 Consensus size: 174
27580538 CTCAATCTAA
* *
27580548 AAAAGAACATATGAAATATCACGAATTAGAAGTAGACAACAAGAACAACTTACGCAGAACCCCTT
1 AAAAGAACAGATGAAATATCACGAATTAGAAGTAGACAACAAAAACAACTTACGCAGAACCCCTT
*
27580613 CAATTGAACAATGAACAATGCTAACCTTCAATTTAATTCAATAGTAAAATCACGGGGACAAGTAA
66 CAATTGAACAATGAACAACGCTAACCTTCAATTTAATTCAATAGTAAAATCACGGGGACAAGTAA
*
27580678 AAAGAAAACCAAAAGTGAAAAAAAAAATAGTAACCAGAACCTAG
131 AAAGAAAACCAAAAGCGAAAAAAAAAATAGTAACCAGAACCTAG
* *
27580722 AAAAGAACAGATGAAATCTCACGAATTAGAAGTAGACAACAAAAACAACTTACGCAGAACCTCTT
1 AAAAGAACAGATGAAATATCACGAATTAGAAGTAGACAACAAAAACAACTTACGCAGAACCCCTT
* *
27580787 CAATTGAATAATGAACAACGCTGAACCTTCAATTTAATTCAATAGTATAATCACGGGGACAAGTA
66 CAATTGAACAATGAACAACGCT-AACCTTCAATTTAATTCAATAGTAAAATCACGGGGACAAGTA
27580852 AAAAGAAAACCAAAAGCG-AAAAAAAAATAGTAACCAGAACCTAG
130 AAAAGAAAACCAAAAGCGAAAAAAAAAATAGTAACCAGAACCTAG
27580896 AAAAGAAC
1 AAAAGAAC
27580904 GTAGAAGAAA
Statistics
Matches: 173, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
174 115 0.66
175 58 0.34
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (174 bp):
AAAAGAACAGATGAAATATCACGAATTAGAAGTAGACAACAAAAACAACTTACGCAGAACCCCTT
CAATTGAACAATGAACAACGCTAACCTTCAATTTAATTCAATAGTAAAATCACGGGGACAAGTAA
AAAGAAAACCAAAAGCGAAAAAAAAAATAGTAACCAGAACCTAG
Found at i:27588849 original size:27 final size:27
Alignment explanation
Indices: 27588772--27588837 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
27588762 AAACTTTTCT
*
27588772 AAAAG-AAACTCAAGAGAAATTCTTGA
1 AAAAGAAAACTCAAGAGAAATTATTGA
*
27588798 AAAAAAAAACTCAAGAGAAATTATTG-
1 AAAAGAAAACTCAAGAGAAATTATTGA
27588824 AAAAGAAAACTCAA
1 AAAAGAAAACTCAA
27588838 AAAGAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 17 0.47
27 19 0.53
ACGTcount: A:0.61, C:0.11, G:0.12, T:0.17
Consensus pattern (27 bp):
AAAAGAAAACTCAAGAGAAATTATTGA
Found at i:27591546 original size:22 final size:22
Alignment explanation
Indices: 27591518--27591560 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
27591508 TTTATTGTTC
27591518 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
27591540 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
27591561 TAGCCAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:27592974 original size:2 final size:2
Alignment explanation
Indices: 27592963--27592996 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
27592953 CATGCCAATC
27592963 TA TA -A TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27592997 AAAGCACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27592988 original size:17 final size:17
Alignment explanation
Indices: 27592963--27592996 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27592953 CATGCCAATC
27592963 TATAATATATATATATA
1 TATAATATATATATATA
*
27592980 TATATTATATATATATA
1 TATAATATATATATATA
27592997 AAAGCACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAATATATATATATA
Found at i:27593295 original size:13 final size:13
Alignment explanation
Indices: 27593279--27593304 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27593269 AATTTAAGTT
27593279 TTTTAATTAAATA
1 TTTTAATTAAATA
27593292 TTTTAATTAAATA
1 TTTTAATTAAATA
27593305 AATATAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTAATTAAATA
Found at i:27593520 original size:24 final size:26
Alignment explanation
Indices: 27593492--27593539 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
27593482 AATTGAAAAT
27593492 AAATATATTT-TAT-AAT-TTAATTAA
1 AAATAT-TTTATATAAATATTAATTAA
27593516 AAATATTTTATATAAATATTAATT
1 AAATATTTTATATAAATATTAATT
27593540 GCATCTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 9 0.43
25 3 0.14
26 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AAATATTTTATATAAATATTAATTAA
Found at i:27598163 original size:16 final size:16
Alignment explanation
Indices: 27598142--27598174 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
27598132 AATGTAAATC
27598142 AAGAGTTGCAAAATTA
1 AAGAGTTGCAAAATTA
27598158 AAGAGTTGCAAAATTA
1 AAGAGTTGCAAAATTA
27598174 A
1 A
27598175 CACTTATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (16 bp):
AAGAGTTGCAAAATTA
Found at i:27599304 original size:12 final size:12
Alignment explanation
Indices: 27599287--27599317 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27599277 GCCAAACAGG
27599287 CGTGTGCCCAGC
1 CGTGTGCCCAGC
27599299 CGTGTGCCCAGC
1 CGTGTGCCCAGC
*
27599311 CATGTGC
1 CGTGTGC
27599318 GACACACAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.39, G:0.32, T:0.19
Consensus pattern (12 bp):
CGTGTGCCCAGC
Found at i:27602734 original size:17 final size:17
Alignment explanation
Indices: 27602712--27602745 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27602702 CAAATATGGG
*
27602712 ATTTTTATTCTTTTTCT
1 ATTTTTATTATTTTTCT
27602729 ATTTTTATTATTTTTCT
1 ATTTTTATTATTTTTCT
27602746 TTACTTTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTATTATTTTTCT
Found at i:27607389 original size:7 final size:7
Alignment explanation
Indices: 27607379--27607431 Score: 70
Period size: 7 Copynumber: 7.0 Consensus size: 7
27607369 TGATATATTT
27607379 TTATGTA
1 TTATGTA
27607386 TTATGTAA
1 TTATGT-A
27607394 GTTATGTAA
1 -TTATGT-A
27607403 GTTATGTA
1 -TTATGTA
27607411 TTATGTA
1 TTATGTA
27607418 TTATGTA
1 TTATGTA
27607425 TTATGTA
1 TTATGTA
27607432 AGTACTGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
7 27 0.61
8 2 0.05
9 15 0.34
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (7 bp):
TTATGTA
Found at i:27607400 original size:9 final size:9
Alignment explanation
Indices: 27607386--27608003 Score: 523
Period size: 9 Copynumber: 71.4 Consensus size: 9
27607376 TTTTTATGTA
27607386 TTATGTAAG
1 TTATGTAAG
27607395 TTATGTAAG
1 TTATGTAAG
27607404 TTATGT-A-
1 TTATGTAAG
27607411 TTATGT-A-
1 TTATGTAAG
27607418 TTATGT-A-
1 TTATGTAAG
27607425 TTATGTAAG
1 TTATGTAAG
27607434 -TACTGTAAG
1 TTA-TGTAAG
*
27607443 TAATGTAAG
1 TTATGTAAG
27607452 TTATGTAAG
1 TTATGTAAG
*
27607461 TAATGT-A-
1 TTATGTAAG
27607468 TTATGTAAG
1 TTATGTAAG
*
27607477 TTGTGTATA-
1 TTATGTA-AG
*
27607486 ATAT-TAA-
1 TTATGTAAG
27607493 TTATGTAAG
1 TTATGTAAG
**
27607502 TTGGGT-A-
1 TTATGTAAG
*
27607509 TAATGTAAG
1 TTATGTAAG
*
27607518 TTAAG-AAGG
1 TTATGTAA-G
27607527 TTATGT-A-
1 TTATGTAAG
27607534 TTATGTAAG
1 TTATGTAAG
*
27607543 TTATTTAAG
1 TTATGTAAG
27607552 TTATGTAAG
1 TTATGTAAG
27607561 TTATGTAAG
1 TTATGTAAG
*
27607570 TTATTTAAG
1 TTATGTAAG
27607579 TTATGTAAG
1 TTATGTAAG
*
27607588 TTATCTAAG
1 TTATGTAAG
*
27607597 TTACGTAAG
1 TTATGTAAG
* *
27607606 TTATTTAAT
1 TTATGTAAG
27607615 TTATGTAAG
1 TTATGTAAG
27607624 TTATGTAAG
1 TTATGTAAG
* *
27607633 TTATTTAAT
1 TTATGTAAG
27607642 TTATGTAAG
1 TTATGTAAG
27607651 TTATGTAAG
1 TTATGTAAG
*
27607660 TTATGTAAA
1 TTATGTAAG
* *
27607669 TTAAGTTA-
1 TTATGTAAG
27607677 TCTATGTAAG
1 T-TATGTAAG
27607687 TTATGTAAG
1 TTATGTAAG
27607696 TTATCTATGTAAG
1 ---T-TATGTAAG
*
27607709 TTATGTAGG
1 TTATGTAAG
** *
27607718 CAACGT-A-
1 TTATGTAAG
*
27607725 TTATGTAAA
1 TTATGTAAG
*
27607734 TGATGTAAG
1 TTATGTAAG
*
27607743 TTA-GAAAGG
1 TTATGTAA-G
27607752 TTATGT-A-
1 TTATGTAAG
27607759 TTATGTAAG
1 TTATGTAAG
*
27607768 TTATTTAAG
1 TTATGTAAG
27607777 TTATGTAAG
1 TTATGTAAG
27607786 TTATGTAAG
1 TTATGTAAG
*
27607795 TTATCTAAG
1 TTATGTAAG
27607804 TTATGTAAG
1 TTATGTAAG
* *
27607813 TTATTTAAT
1 TTATGTAAG
*
27607822 TTGTGTAAG
1 TTATGTAAG
27607831 TTA--TAA-
1 TTATGTAAG
27607837 --ATGTAAG
1 TTATGTAAG
*
27607844 TTATGTAGG
1 TTATGTAAG
**
27607853 CAATGT-A-
1 TTATGTAAG
*
27607860 TTATGTAAA
1 TTATGTAAG
*
27607869 TAATGTAAG
1 TTATGTAAG
*
27607878 TTA-GAAAGG
1 TTATGTAA-G
27607887 TTATGT-A-
1 TTATGTAAG
27607894 TTATGTAAG
1 TTATGTAAG
*
27607903 TTATTTAAG
1 TTATGTAAG
27607912 TTATGTAAG
1 TTATGTAAG
27607921 TTATGTAAG
1 TTATGTAAG
27607930 TTATGTAAG
1 TTATGTAAG
27607939 TTATGTAAG
1 TTATGTAAG
* *
27607948 TTATTTAAT
1 TTATGTAAG
27607957 TTATGTAAG
1 TTATGTAAG
27607966 TTATGTAAG
1 TTATGTAAG
*
27607975 TTATGTAGG
1 TTATGTAAG
27607984 TTATGT-A-
1 TTATGTAAG
*
27607991 TTATGTTAG
1 TTATGTAAG
27608000 TTAT
1 TTAT
27608004 TATGTTATTA
Statistics
Matches: 490, Mismatches: 79, Indels: 80
0.76 0.12 0.12
Matches are distributed among these distances:
4 1 0.00
6 3 0.01
7 66 0.13
8 28 0.06
9 377 0.77
10 6 0.01
12 1 0.00
13 8 0.02
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:27607688 original size:13 final size:13
Alignment explanation
Indices: 27607652--27607712 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
27607642 TTATGTAAGT
*
27607652 TATGTAAGTTATG
1 TATGTAAGTTATC
27607665 TAAAT-TAAGTTATC
1 T--ATGTAAGTTATC
27607679 TATGTAAG---T-
1 TATGTAAGTTATC
27607688 TATGTAAGTTATC
1 TATGTAAGTTATC
27607701 TATGTAAGTTAT
1 TATGTAAGTTAT
27607713 GTAGGCAACG
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
9 8 0.20
10 1 0.03
12 3 0.08
13 17 0.43
14 9 0.22
15 2 0.05
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.46
Consensus pattern (13 bp):
TATGTAAGTTATC
Found at i:27607698 original size:22 final size:22
Alignment explanation
Indices: 27607670--27607715 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
27607660 TTATGTAAAT
27607670 TAAGTTATCTATGTAAGTTATG
1 TAAGTTATCTATGTAAGTTATG
27607692 TAAGTTATCTATGTAAGTTATG
1 TAAGTTATCTATGTAAGTTATG
27607714 TA
1 TA
27607716 GGCAACGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (22 bp):
TAAGTTATCTATGTAAGTTATG
Found at i:27608021 original size:20 final size:19
Alignment explanation
Indices: 27607984--27608023 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
27607974 GTTATGTAGG
* *
27607984 TTATGTATTATGTTAGTTA
1 TTATGTATTATATAAGTTA
27608003 TTATGTTATTATATAAGTTA
1 TTATG-TATTATATAAGTTA
27608023 T
1 T
27608024 GCAAGTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (19 bp):
TTATGTATTATATAAGTTA
Found at i:27608139 original size:17 final size:18
Alignment explanation
Indices: 27608107--27608140 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27608097 TGATTGAAAA
27608107 ATTTTGAAAAAAATATAG
1 ATTTTGAAAAAAATATAG
*
27608125 ATTTT-AAAAATATATA
1 ATTTTGAAAAAAATATA
27608141 CATTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATTTTGAAAAAAATATAG
Found at i:27610301 original size:337 final size:336
Alignment explanation
Indices: 27609572--27610308 Score: 765
Period size: 337 Copynumber: 2.2 Consensus size: 336
27609562 TGTTCAAACC
* * * * * *
27609572 GAAACGGCGCCGTTTAATTAAGCTTTAATGCACAATTTTGGCGTTTTCTGTAAAAACGCCAGTAA
1 GAAACGGCGCCGTTTTATTAAGCTTCAATGCACAATTCT-GCGTTTTCTTTTAAAACGCCACTAA
* * *
27609637 AAATTAATTTGCTTAAGCTAAACGAAGCTGTTTCAGCAATATTTTATGTCACTTTTGCGGCGTTT
65 AAATTAATTTGCTTAAGCTAAACGAAGCTGTTTCAGCAATATTTCAAGTCACTTTTGCGACGTTT
** * *
27609702 GGTGTAAAAACGCCACAAAAAATTAACAAAAACGGCGCCGTTGGATTAATATAGAGAAAATGCTA
130 CCTGTAAAAACGCCACAAAAAATTAACAAAAACGGCGCCATTGAATTAATATAGAGAAAATGCTA
* * * *
27609767 AGTATAAAAGCGTGTACAGAGACGACGTCATTTAGCAAAAATTTTAAGACACTTTGGCGGCGTTT
195 AGTATAAAAGCGTGGACAGAAACGACGTCATTCAACAAAAATTTTAAGACACTTTGGCGGCGTTT
* * *
27609832 ATTGAACAAACGCCGCTATAGCTTGTGCATTTACGGCATTTCTAGAGAAGCGCCACAAAGAATGA
260 ATTGAACAAACGCCGCTATAGCTTATGCATTTACGGCATTTCTAGAAAAACGCCACAAAGAATGA
*
27609897 AGGTTCTAATCT
325 AAGTTCTAATCT
* * * *
27609909 GAAACGGCGCCGTTTTGTTAAGATTTC-ATGCACATTTCTGTCGTTTTCCTTTAAAACGCCACTA
1 GAAACGGCGCCGTTTTATTAAG-CTTCAATGCACAATTCTG-CGTTTTCTTTTAAAACGCCACTA
* * * **
27609973 GAAATTAATTTGCTTAAGTTAGACGTCGAC-GTTT-AGCCAATATTTCAAGTCACTTTTGCGACG
64 AAAATTAATTTGCTTAAGCTAAACGAAG-CTGTTTCAG-CAATATTTCAAGTCACTTTTGCGACG
* * * * *
27610036 TTTCCTG-AACAAACGCCACTAAAAATTAACATAAACGGTGTCATTTAATTAATATAGAGAAAAT
127 TTTCCTGTAA-AAACGCCACAAAAAATTAACAAAAACGGCGCCATTGAATTAATATAGAGAAAAT
* * * * * * *
27610100 GCTAAGT-TAAAAATCGTGGATAGAAACGGCGTCGTTCAACCAAAATTTTAAGTCACTTTTGCGG
191 GCTAAGTAT-AAAAGCGTGGACAGAAACGACGTCATTCAACAAAAATTTTAAGACACTTTGGCGG
* * * * * * *
27610164 CGTTTCTTGTACAAACGCCGCTAGT-GCTTAAT-CA-TTAGTGGCGTTTTTATTAAAAACGCCGC
255 CGTTTATTGAACAAACGCCGCTA-TAGCTT-ATGCATTTA-CGGCATTTCTA-GAAAAACGCCAC
* *** *
27610226 TAATTGTTAAAGTTCTAATC-
316 AAAGAATGAAAGTTCTAATCT
* * *
27610246 GAAAACTGCGCCGTTTTATTAAGCTTCAATGTACAGTTCTAGCGTTTT-TTTTAAAAACGCCAC
1 G-AAACGGCGCCGTTTTATTAAGCTTCAATGCACAATTCT-GCGTTTTCTTTT-AAAACGCCAC
27610309 AAAGTAATTA
Statistics
Matches: 326, Mismatches: 60, Indels: 27
0.79 0.15 0.07
Matches are distributed among these distances:
336 9 0.03
337 244 0.75
338 72 0.22
339 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (336 bp):
GAAACGGCGCCGTTTTATTAAGCTTCAATGCACAATTCTGCGTTTTCTTTTAAAACGCCACTAAA
AATTAATTTGCTTAAGCTAAACGAAGCTGTTTCAGCAATATTTCAAGTCACTTTTGCGACGTTTC
CTGTAAAAACGCCACAAAAAATTAACAAAAACGGCGCCATTGAATTAATATAGAGAAAATGCTAA
GTATAAAAGCGTGGACAGAAACGACGTCATTCAACAAAAATTTTAAGACACTTTGGCGGCGTTTA
TTGAACAAACGCCGCTATAGCTTATGCATTTACGGCATTTCTAGAAAAACGCCACAAAGAATGAA
AGTTCTAATCT
Found at i:27610467 original size:2 final size:2
Alignment explanation
Indices: 27610460--27610485 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27610450 TAATTTGGTC
27610460 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
27610486 CCAAAATAAT
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27611967 original size:113 final size:113
Alignment explanation
Indices: 27611718--27612140 Score: 591
Period size: 113 Copynumber: 3.7 Consensus size: 113
27611708 ACCCATAAAC
*
27611718 GCCACTAAATCCCCCGAAAGCTCAGAAAACGGCGTCGTTAGGCTTAGG-ATTTTTGCGCCGCCTT
1 GCCACTAAAT-CCCCGAAAGCTCAGAAAACGGCGTCGTTAGGCTTAGGTATTTTTGCGGCG-CTT
* * *
27611782 CTCAAAATCGCCGCTAAAGCCTTGGGCATTAGCGGCGTTTACTTAAAAAC
64 CTCAAAAACGCCGCTAAAGCCTTGGGCATTAGCGGCGCTTACTTAAAAAT
27611832 GCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTAGGCTTAGGTATTTTTGCGGCGCATTC
1 GCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTAGGCTTAGGTATTTTTGCGGCGC-TTC
* *
27611897 CCAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTGAC-TAAAAAT
65 TCAAAAACGCCGCTAAAGCCTTGGGCATTAGCGGCGCTT-ACTTAAAAAT
* * * * * * *
27611946 GCCGCTAAAT-CCCAAAAGCTCAAAAAATGGCGTCGTTGGGCTTAAGTATTTTTGCAGCGCTGTC
1 GCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTAGGCTTAGGTATTTTTGCGGCGCT-TC
* *
27612010 TCAAAAATGCCGCTAAAGCCCTGGGCATTAGCGGCGCTTACTTAAAAAT
65 TCAAAAACGCCGCTAAAGCCTTGGGCATTAGCGGCGCTTACTTAAAAAT
* * *
27612059 GTCACTAAATCCCCGAAAGCTCAGCAAACGGTGTCGTTAGGCTTAGGTATTTTTGCGGCGCTTAC
1 GCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTAGGCTTAGGTATTTTTGCGGCGCTT-C
* *
27612124 TTAAAAACGCCGTTAAA
65 TCAAAAACGCCGCTAAA
27612141 TCGCCAAAAG
Statistics
Matches: 272, Mismatches: 30, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
112 3 0.01
113 135 0.50
114 132 0.49
115 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (113 bp):
GCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTAGGCTTAGGTATTTTTGCGGCGCTTCT
CAAAAACGCCGCTAAAGCCTTGGGCATTAGCGGCGCTTACTTAAAAAT
Found at i:27612168 original size:73 final size:73
Alignment explanation
Indices: 27612040--27612189 Score: 192
Period size: 73 Copynumber: 2.1 Consensus size: 73
27612030 CTGGGCATTA
* * * ** ** *
27612040 GCGGCGCTTACTTAAAAATGTCACTAAATCCCCGAAAGCTCAGCAAACGGTGTCGTTAGGCTTAG
1 GCGGCGCTTACTTAAAAACGCCACTAAATCCCCAAAAGCTCAAAAAAAAGCGTCGTTAGGCTTAG
*
27612105 GTATTTTT
66 GTATTTTC
** *
27612113 GCGGCGCTTACTTAAAAACGCCGTTAAATCGCCAAAAGCTCAAAAAAAAGCGTCGTTAGGCTTAG
1 GCGGCGCTTACTTAAAAACGCCACTAAATCCCCAAAAGCTCAAAAAAAAGCGTCGTTAGGCTTAG
27612178 GTATTTTC
66 GTATTTTC
27612186 GCGG
1 GCGG
27612190 TGCATTCACA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (73 bp):
GCGGCGCTTACTTAAAAACGCCACTAAATCCCCAAAAGCTCAAAAAAAAGCGTCGTTAGGCTTAG
GTATTTTC
Found at i:27612327 original size:116 final size:114
Alignment explanation
Indices: 27612171--27612502 Score: 303
Period size: 116 Copynumber: 2.9 Consensus size: 114
27612161 AGCGTCGTTA
*
27612171 GGCTTAGG-TATTTTCGCGGTGCATTCACAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCACT
1 GGCTTAGGTTTTTTTCGCGGTGCATTCACAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCACT
* * * * *
27612235 TGAC-TAAAAACGCCGCCAGATCCCTGAAAAGCTCAGAAAATGGCATCGCTG
66 T-ACTTAAAAACGCCACCAAATCCCCG-AAAGCTCAG-AAACGACATCGCTG
* * * * *
27612286 GGCTTAGGTTTTTTTTGCGGTGC-TTTACCATAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC
1 GGCTTAGGTTTTTTTCGCGGTGCATTCA-CAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCAC
* * *
27612350 TTACTTAAAAACGCCACTAAATCCCCGAAAGCTTAGAAACGACATCGTTG
65 TTACTTAAAAACGCCACCAAATCCCCGAAAGCTCAGAAACGACATCGCTG
* * ** * * ** * * * * *
27612400 GGCTTACGTTTTTCT-ATGGCGCTTTTTCAAAAACACCGCTAAAGCCTTGAGCTTTCGCAGCGCT
1 GGCTTAGGTTTTTTTCGCGGTGCATTCACAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCACT
* * * * *
27612464 TTCTTAAAAAACGCCGCTAAATCCCCGAAAACTCGGAAA
66 TACTT-AAAAACGCCACCAAATCCCCGAAAGCTCAGAAA
27612503 ACGGCGTCGT
Statistics
Matches: 181, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
113 39 0.22
114 56 0.31
115 21 0.12
116 65 0.36
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (114 bp):
GGCTTAGGTTTTTTTCGCGGTGCATTCACAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCACT
TACTTAAAAACGCCACCAAATCCCCGAAAGCTCAGAAACGACATCGCTG
Found at i:27612531 original size:416 final size:412
Alignment explanation
Indices: 27611734--27612537 Score: 970
Period size: 416 Copynumber: 1.9 Consensus size: 412
27611724 AAATCCCCCG
* ** * * * *
27611734 AAAGCTCAGAAAACGGCGTCGTTAGGCTTAGGATTTTTGCGCCGCCTTCTCAAAATCGCCGCTAA
1 AAAGCTCAAAAAAAAGCGTCGTTAGGCTTAGGATTTTCGCGCCGCATTCACAAAAACGCCGCTAA
* * * * * *
27611799 AGCCTTGGGCATTAGCGGCGTTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGC
66 AGCCCTGAGCATTAGCAGCCTTGACTTAAAAACGCCACCAAATCCCCGAAAGCTCAGAAAACGGC
* * * *
27611864 GTCGTTAGGCTTAGGTATTTTTGCGGCGCATTCCCAAAAACGCCGCTAAAGCCTTGAGCATTAGC
131 ATCGCTAGGCTTAGGTATTTTTGCGGCGCATTACCAAAAACGCCGCTAAAGCCCTGAGCATTAGC
* * * * *
27611929 GGCGCTTGACTAAAAATGCCGCTAAATCCCAAAAGCTCAAAAAATGGCGTCGTTGGGCTTAAGTA
196 GGCGCTTGACTAAAAACGCCACTAAATCCCAAAAGCTCAAAAAACGACATCGTTGGGCTTAAGTA
** * * *
27611994 TTTTTGCAGCGCTGTCTCAAAAATGCCGCTAAAGCCCTGGGCATTAGCGGCGCTTACTTAAAAAT
261 TTTTTG-AGCGCTGTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCAGCGCTTACTTAAAAAC
* * * * *
27612059 GTCACTAAATCCCCGAAAGCTCAGCAAACGGTGTCGTTAGGCTTAGGTATTTTTGCGGCGCTTAC
325 GCCACTAAATCCCCGAAAACTCAGAAAACGGCGTCGTTAGGATTAGGTATTTTTGCGGCGCTTAC
27612124 TTAAAAACGCCGTTAAATCGCCA
390 TTAAAAACGCCGTTAAATCGCCA
**
27612147 AAAGCTCAAAAAAAAGCGTCGTTAGGCTTAGGTATTTTCGCGGTGCATTCACAAAAACGCCGCTA
1 AAAGCTCAAAAAAAAGCGTCGTTAGGCTTAGG-ATTTTCGCGCCGCATTCACAAAAACGCCGCTA
* * * *
27612212 AAGCCCTGAGCATTAGCAGCACTTGAC-TAAAAACGCCGCCAGATCCCTGAAAAGCTCAGAAAAT
65 AAGCCCTGAGCATTAGCAGC-CTTGACTTAAAAACGCCACCAAATCCCCG-AAAGCTCAGAAAAC
* * * * *
27612276 GGCATCGCTGGGCTTAGGTTTTTTTTGCGGTGCTTTACCATAAACGCCGCTAAAGCCCTGAGCAT
128 GGCATCGCTAGGCTTAGG-TATTTTTGCGGCGCATTACCAAAAACGCCGCTAAAGCCCTGAGCAT
* * *
27612341 TAGCGGCGCTT-ACTTAAAAACGCCACTAAATCCCCGAAAGCT-TAGAAACGACATCGTTGGGCT
192 TAGCGGCGCTTGAC-TAAAAACGCCACTAAAT-CCCAAAAGCTCAAAAAACGACATCGTTGGGCT
* * * * * * * *
27612404 TACGTTTTTCTATG-GCGCTTTTTCAAAAACACCGCTAAAGCCTTGAGCTTTCGCAGCGCTTTCT
255 TAAGTATTT-T-TGAGCGCTGTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCAGCGCTTACT
* * *
27612468 TAAAAAACGCCGCTAAATCCCCGAAAACTCGGAAAACGGCGTCGTTGGGATTAGGTA-TTTTGCG
318 T-AAAAACGCCACTAAATCCCCGAAAACTCAGAAAACGGCGTCGTTAGGATTAGGTATTTTTGCG
27612532 GCGCTT
382 GCGCTT
27612538 TATGGAAAAA
Statistics
Matches: 325, Mismatches: 57, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
413 29 0.09
414 61 0.19
415 34 0.10
416 143 0.44
417 56 0.17
418 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (412 bp):
AAAGCTCAAAAAAAAGCGTCGTTAGGCTTAGGATTTTCGCGCCGCATTCACAAAAACGCCGCTAA
AGCCCTGAGCATTAGCAGCCTTGACTTAAAAACGCCACCAAATCCCCGAAAGCTCAGAAAACGGC
ATCGCTAGGCTTAGGTATTTTTGCGGCGCATTACCAAAAACGCCGCTAAAGCCCTGAGCATTAGC
GGCGCTTGACTAAAAACGCCACTAAATCCCAAAAGCTCAAAAAACGACATCGTTGGGCTTAAGTA
TTTTTGAGCGCTGTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCAGCGCTTACTTAAAAACG
CCACTAAATCCCCGAAAACTCAGAAAACGGCGTCGTTAGGATTAGGTATTTTTGCGGCGCTTACT
TAAAAACGCCGTTAAATCGCCA
Found at i:27612555 original size:114 final size:113
Alignment explanation
Indices: 27612116--27612539 Score: 417
Period size: 114 Copynumber: 3.7 Consensus size: 113
27612106 TATTTTTGCG
* * * ** * *
27612116 GCGCTTACTTAAAAACGCCGTTAAATCGCC-AAAAGCTCAAAAAAAAGCGTCGTTAGGCTTAGGT
1 GCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGT
* *
27612180 ATTTTCGCGGTGCATTCACAAAAACGCCGCTAAAGCCCTGAGCATTAGCA
66 ATTTT-GCGGCGC-TTTACAAAAACGCCGCTAAAGCCCTGAGCATTAGCA
* * * * * *
27612230 GCACTTGAC-TAAAAACGCCGCCAGATCCCTGAAAAGCTCAGAAAATGGCATCGCTGGGCTTAGG
1 GCGCTT-ACTTAAAAACGCCGCTAAATCCCCGAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGG
* * * *
27612294 TTTTTTTTGCGGTGCTTTACCATAAACGCCGCTAAAGCCCTGAGCATTAGCG
65 --TATTTTGCGGCGCTTTA-CAAAAACGCCGCTAAAGCCCTGAGCATTAGCA
* * * *
27612346 GCGCTTACTTAAAAACGCCACTAAATCCCCG-AAAGCTTAG-AAACGACATCGTTGGGCTTACGT
1 GCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGT
* ** * * * * *
27612409 TTTTCTATGGCGCTTTTTCAAAAACACCGCTAAAGCCTTGAGCTTTCGCA
66 ATTT-TGCGGCGC-TTTACAAAAACGCCGCTAAAGCCCTGAGCATTAGCA
* * * *
27612459 GCGCTTTCTTAAAAAACGCCGCTAAATCCCCGAAAA-CTCGGAAAACGGCGTCGTTGGGATTAGG
1 GCGCTTACTT-AAAAACGCCGCTAAATCCCCGAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGG
27612523 TATTTTGCGGCGCTTTA
65 TATTTTGCGGCGCTTTA
27612540 TGGAAAAAGC
Statistics
Matches: 251, Mismatches: 48, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
112 5 0.02
113 43 0.17
114 71 0.28
115 67 0.27
116 60 0.24
117 5 0.02
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (113 bp):
GCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGT
ATTTTGCGGCGCTTTACAAAAACGCCGCTAAAGCCCTGAGCATTAGCA
Found at i:27612782 original size:26 final size:27
Alignment explanation
Indices: 27612727--27612797 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 27
27612717 TATATCTATG
* *
27612727 TATACATACATACATTTTGATAATACA
1 TATATATACATATATTTTGATAATACA
* **
27612754 TATATGTACATATATTTT-ATAATTTA
1 TATATATACATATATTTTGATAATACA
*
27612780 TATATATACATATGTTTT
1 TATATATACATATATTTT
27612798 TGTTATATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 22 0.59
27 15 0.41
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.48
Consensus pattern (27 bp):
TATATATACATATATTTTGATAATACA
Found at i:27615320 original size:41 final size:41
Alignment explanation
Indices: 27615268--27615374 Score: 142
Period size: 41 Copynumber: 2.6 Consensus size: 41
27615258 ACACGGCACC
* ** * *
27615268 AAGCCTACTAGGCATAAAGCCTGATAGGGTACACTGGCATG
1 AAGCCTGCTAGGCATAAAGCCTGATACAGTACACCGGCATA
* * *
27615309 AAGCCTGCTAGGCATAAAGCTTGATACATTTCACCGGCATA
1 AAGCCTGCTAGGCATAAAGCCTGATACAGTACACCGGCATA
27615350 AAGCCTGCTAGGCATAAAGCCTGAT
1 AAGCCTGCTAGGCATAAAGCCTGAT
27615375 GCATTAATAT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (41 bp):
AAGCCTGCTAGGCATAAAGCCTGATACAGTACACCGGCATA
Found at i:27619933 original size:24 final size:24
Alignment explanation
Indices: 27619899--27619960 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
27619889 CGTTGTAATT
*
27619899 GTATCACGAATACAATGGTGAAGC
1 GTATCATGAATACAATGGTGAAGC
27619923 GTATCATGAATACAATGGTGAAGC
1 GTATCATGAATACAATGGTGAAGC
27619947 -TCATCATGAA-ACAA
1 GT-ATCATGAATACAA
27619961 AAGGTATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 5 0.14
24 31 0.86
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (24 bp):
GTATCATGAATACAATGGTGAAGC
Found at i:27621518 original size:25 final size:26
Alignment explanation
Indices: 27621466--27621518 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
27621456 TTTTCTCCAA
* **
27621466 AATTTTATCATGGGTAAAATAGTTAT
1 AATTTTACCATGGGTAAAATAGGGAT
*
27621492 AATTTTACCA-GGGTAAAATTGGGAT
1 AATTTTACCATGGGTAAAATAGGGAT
27621517 AA
1 AA
27621519 AAAAATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.36
Consensus pattern (26 bp):
AATTTTACCATGGGTAAAATAGGGAT
Found at i:27623915 original size:14 final size:16
Alignment explanation
Indices: 27623885--27623917 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
27623875 AACAATGTAT
27623885 AAATCATATATCAAGA
1 AAATCATATATCAAGA
27623901 AAATCATA-A-CAAGA
1 AAATCATATATCAAGA
27623915 AAA
1 AAA
27623918 GAGATTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (16 bp):
AAATCATATATCAAGA
Found at i:27624290 original size:65 final size:65
Alignment explanation
Indices: 27624165--27624290 Score: 198
Period size: 65 Copynumber: 1.9 Consensus size: 65
27624155 TTTATTCCCT
* **
27624165 TAAAATATTAAAGTAACGGTTATTTGTAGGTAAAATTTTGACGCATATTCAAATGGCAAAAGTAA
1 TAAAATATTAAAGTAACAGTTATTTGTAGGTAAAATTTTGACGCATATTCAAATAACAAAAGTAA
* * *
27624230 TAAAATATTAAAGTAACAGTTATTTGTAGGTGAAATTTTGACTCGTATTCAAATAACAAAA
1 TAAAATATTAAAGTAACAGTTATTTGTAGGTAAAATTTTGACGCATATTCAAATAACAAAA
27624291 TTATTTTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (65 bp):
TAAAATATTAAAGTAACAGTTATTTGTAGGTAAAATTTTGACGCATATTCAAATAACAAAAGTAA
Found at i:27627163 original size:17 final size:18
Alignment explanation
Indices: 27627143--27627176 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27627133 ATTTATTGGT
*
27627143 ATTAT-TAATTTTTTTAA
1 ATTATATAATTATTTTAA
27627160 ATTATATAATTATTTTA
1 ATTATATAATTATTTTA
27627177 GGTTTTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTATATAATTATTTTAA
Found at i:27631746 original size:19 final size:18
Alignment explanation
Indices: 27631706--27631746 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
27631696 AATACTTTGT
* *
27631706 ATTATGTTATTTATATAC
1 ATTATGTAATTTATACAC
27631724 ATTATGTAATTTATAACAC
1 ATTATGTAATTTAT-ACAC
27631743 ATTA
1 ATTA
27631747 AAAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTATGTAATTTATACAC
Found at i:27632627 original size:27 final size:27
Alignment explanation
Indices: 27632592--27632653 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
27632582 TACATATCTT
*
27632592 TAATAAGTTACTTACATTTTAACAAGG
1 TAATCAGTTACTTACATTTTAACAAGG
27632619 TAATCAGTTACTTACATTTTAACAAGG
1 TAATCAGTTACTTACATTTTAACAAGG
27632646 TAATCAGT
1 TAATCAGT
27632654 ATCGTGTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (27 bp):
TAATCAGTTACTTACATTTTAACAAGG
Found at i:27633192 original size:19 final size:18
Alignment explanation
Indices: 27633156--27633198 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
27633146 ATATCGCATC
27633156 ATTTT-AAATTTATTGAT
1 ATTTTAAAATTTATTGAT
*
27633173 ATTTTAAAATGTTTTTGAT
1 ATTTTAAAAT-TTATTGAT
27633192 ATATTTA
1 AT-TTTA
27633199 TAGTATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 9 0.41
20 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (18 bp):
ATTTTAAAATTTATTGAT
Found at i:27637989 original size:29 final size:28
Alignment explanation
Indices: 27637958--27638014 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
27637948 TTCTCATCAA
27637958 TTTGAATTAATATGTTAATAATAAAAATAT
1 TTTGAATTAA-AT-TTAATAATAAAAATAT
* * *
27637988 TTTTATTTAAATTTAATTATAAAAATA
1 TTTGAATTAAATTTAATAATAAAAATA
27638015 ACAACATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.58
29 2 0.08
30 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (28 bp):
TTTGAATTAAATTTAATAATAAAAATAT
Found at i:27638865 original size:2 final size:2
Alignment explanation
Indices: 27638858--27638883 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27638848 CAAAACAGTA
27638858 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
27638884 TCTTTCAAAT
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27645012 original size:34 final size:35
Alignment explanation
Indices: 27644968--27645034 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
27644958 CAGTAAAATG
*
27644968 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
27645002 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
27645035 CTGCTGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:27647736 original size:14 final size:14
Alignment explanation
Indices: 27647697--27647737 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
27647687 ATTATTATTT
27647697 AATTAAATAATTGA
1 AATTAAATAATTGA
27647711 AATTCAAA-AATTG-
1 AATT-AAATAATTGA
27647724 AATTAAATTAATTG
1 AATTAAA-TAATTG
27647738 GTCGTTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.12
13 4 0.17
14 14 0.58
15 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (14 bp):
AATTAAATAATTGA
Found at i:27650642 original size:17 final size:17
Alignment explanation
Indices: 27650620--27650653 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
27650610 ACACGGCCCA
27650620 TACACGC-CTGTGTGGCC
1 TACACGCTC-GTGTGGCC
27650637 TACACGCTCGTGTGGCC
1 TACACGCTCGTGTGGCC
27650654 CACATGACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (17 bp):
TACACGCTCGTGTGGCC
Found at i:27651848 original size:45 final size:45
Alignment explanation
Indices: 27651784--27651884 Score: 175
Period size: 45 Copynumber: 2.2 Consensus size: 45
27651774 TAACAGAATA
27651784 GATTTCCTCCTCAACACATTAACGTGTTGATCTAGAATCTGAACC
1 GATTTCCTCCTCAACACATTAACGTGTTGATCTAGAATCTGAACC
*
27651829 GATTTCCTCCTCAACACATTAATGTGTTGATCTAGAATCTGAACC
1 GATTTCCTCCTCAACACATTAACGTGTTGATCTAGAATCTGAACC
27651874 GACTCTTCCTC
1 GA-T-TTCCTC
27651885 AAATTTCAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
45 46 0.87
46 1 0.02
47 6 0.11
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.33
Consensus pattern (45 bp):
GATTTCCTCCTCAACACATTAACGTGTTGATCTAGAATCTGAACC
Found at i:27657771 original size:70 final size:70
Alignment explanation
Indices: 27657680--27657814 Score: 209
Period size: 70 Copynumber: 1.9 Consensus size: 70
27657670 ATGGCCTAGC
*
27657680 ACACGGCCGTGTGGCATCGATAGGCCCCAATTTTGGCTTTTGTCATTCGTTGTTTTTCGAGTTTC
1 ACACGGCCGTGTGGCATCGATAGGCCCCAATTTTGGCTTTTGTCATTCGTTGTTTTTCAAGTTTC
27657745 TCGTT
66 TCGTT
* * **
27657750 ACACGGTCC-TGTGGCGTCGATAGGCCCTAATTTTGGCTTTTGTTGTTCGTTGTTTTTCAAGTTT
1 ACACGG-CCGTGTGGCATCGATAGGCCCCAATTTTGGCTTTTGTCATTCGTTGTTTTTCAAGTTT
27657814 C
65 C
27657815 CTGTTATACA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 57 0.97
71 2 0.03
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.41
Consensus pattern (70 bp):
ACACGGCCGTGTGGCATCGATAGGCCCCAATTTTGGCTTTTGTCATTCGTTGTTTTTCAAGTTTC
TCGTT
Found at i:27658458 original size:3 final size:3
Alignment explanation
Indices: 27658452--27658496 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
27658442 ACTACTTGAT
* *
27658452 TTA TTA TAA GTA T-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
27658497 CAAAAAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:27658860 original size:17 final size:17
Alignment explanation
Indices: 27658840--27658874 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
27658830 CAAGAAAGCT
27658840 TATAAAAATTGGCAAAA
1 TATAAAAATTGGCAAAA
27658857 TATAAAAATTGGCAAAA
1 TATAAAAATTGGCAAAA
27658874 T
1 T
27658875 TAGCTAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (17 bp):
TATAAAAATTGGCAAAA
Found at i:27667352 original size:27 final size:27
Alignment explanation
Indices: 27667290--27667352 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
27667280 TGTCAAAAAA
27667290 TATAA-TATAATTATAAAATAATTAAAT
1 TATAATTA-AATTATAAAATAATTAAAT
*
27667317 TATACTTAAATTATTAAAAT-ATTAAAT
1 TATAATTAAATTA-TAAAATAATTAAAT
*
27667344 TTTAATTAA
1 TATAATTAA
27667353 TTTTATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
TATAATTAAATTATAAAATAATTAAAT
Found at i:27670999 original size:25 final size:25
Alignment explanation
Indices: 27670971--27671052 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 25
27670961 GTATACTCAT
*
27670971 ACGAGCTATGAATCGGTATGCTCTC
1 ACGAGCTATGAATCGGTAAGCTCTC
* *
27670996 ACGAGCTGTAAATCGGTAAGCTCAT-
1 ACGAGCTATGAATCGGTAAGCTC-TC
* *
27671021 ACGAGATGA-GAATTGGTAAGCTCTC
1 ACGAGCT-ATGAATCGGTAAGCTCTC
*
27671046 ATGAGCT
1 ACGAGCT
27671053 GCAAATTGGT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
24 1 0.02
25 43 0.96
26 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (25 bp):
ACGAGCTATGAATCGGTAAGCTCTC
Found at i:27671044 original size:50 final size:50
Alignment explanation
Indices: 27670966--27671075 Score: 150
Period size: 50 Copynumber: 2.2 Consensus size: 50
27670956 TACATGTATA
* * *
27670966 CTCATACGAGCTATGAATCGGTATGCTCTCACGAGCTGTAAATCGGTAAG
1 CTCATACGAGATATGAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAAG
* * *
27671016 CTCATACGAGATGA-GAATTGGTAAGCTCTCATGAGCTGCAAATTGGTAAG
1 CTCATACGAGAT-ATGAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAAG
27671066 CTCATACGAG
1 CTCATACGAG
27671076 CTGTGGTGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 52 0.98
51 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (50 bp):
CTCATACGAGATATGAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAAG
Done.