Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 51 of 290
Found at i:16799609 original size:83 final size:81
Alignment explanation
Indices: 16799458--16799682 Score: 298
Period size: 83 Copynumber: 2.8 Consensus size: 81
16799448 TATTCGGATG
* *
16799458 ATATCCGGGCTAAGTCCCGAAGGCATT-TGTGCTAG-TGACCATATCCGGGCTAAGTCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTGTGTGATAGTTGA-TATATCCGGGCTAAGTCCCGAAGG
*
16799521 CATTTGTGCTAGTGACT
65 CATTTGTGCCAGTGACT
* * *
16799538 ATATCTGGGCGAAGTCCCGAAGGCATTTGTGTGAGTAGTTGATATACCCGGGCTAAGTCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTGTGTGA-TAGTTGATATATCCGGGCTAAGTCCCGAAG
16799603 GCATTTGTGCCAGTGACT
64 GCATTTGTGCCAGTGACT
* * *
16799621 ATATCCGGGCTAAGACCCGAAGGCA-TGTGTGCA-AGTTGCTATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTGTGTG-ATAGTTGATATATCCGGGCTAAGTCCCGAAGG
16799683 TACTTGGGTT
Statistics
Matches: 128, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
79 15 0.12
80 34 0.27
81 8 0.06
82 5 0.04
83 63 0.49
84 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTGTGTGATAGTTGATATATCCGGGCTAAGTCCCGAAGGC
ATTTGTGCCAGTGACT
Found at i:16803119 original size:13 final size:13
Alignment explanation
Indices: 16803101--16803125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16803091 TGGTCATCAT
16803101 GGTGTGAACACAA
1 GGTGTGAACACAA
16803114 GGTGTGAACACA
1 GGTGTGAACACA
16803126 TGATCAATGC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:16805992 original size:30 final size:30
Alignment explanation
Indices: 16805936--16806020 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
16805926 TTCTTTTGTT
* *
16805936 TCAATTTCTTTTTCATCTTGTTTTTCACTC
1 TCAATTTCTTTTTCATCTTCTTTTTCAATC
**
16805966 TCAAATTTCTTTTTGTTC-TCTTTTTCAATC
1 TC-AATTTCTTTTTCATCTTCTTTTTCAATC
*
16805996 TCATTTTCTTTTTCAT-TTCCTTTTT
1 TCAATTTCTTTTTCATCTT-CTTTTT
16806021 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 12 0.27
30 20 0.44
31 13 0.29
ACGTcount: A:0.13, C:0.21, G:0.02, T:0.64
Consensus pattern (30 bp):
TCAATTTCTTTTTCATCTTCTTTTTCAATC
Found at i:16807697 original size:31 final size:31
Alignment explanation
Indices: 16807654--16807712 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
16807644 GAACCTCGGT
* *
16807654 ATAAGGGTGAACGAAACAGGGTTGACGCGGG
1 ATAAGGGGGAACGAAACAGGGATGACGCGGG
16807685 ATAAGGGGGAACGAAACAGGGATGACGC
1 ATAAGGGGGAACGAAACAGGGATGACGC
16807713 CACTACTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.41, T:0.10
Consensus pattern (31 bp):
ATAAGGGGGAACGAAACAGGGATGACGCGGG
Found at i:16808206 original size:13 final size:13
Alignment explanation
Indices: 16808188--16808212 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16808178 TGGTCATCAT
16808188 GGTGTGAACACAA
1 GGTGTGAACACAA
16808201 GGTGTGAACACA
1 GGTGTGAACACA
16808213 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:16812197 original size:4 final size:4
Alignment explanation
Indices: 16812190--16812220 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
16812180 AACATATATA
*
16812190 TATG TATG TATG TATG TTTG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
16812221 AAATTTCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (4 bp):
TATG
Found at i:16818057 original size:55 final size:55
Alignment explanation
Indices: 16817996--16818172 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
16817986 ATATTAAGTC
* * *
16817996 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
16818051 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
16818106 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
16818162 CGCACACTTAG
1 CGCACACTTAG
16818173 CGCCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:16818060 original size:28 final size:27
Alignment explanation
Indices: 16817996--16818147 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
16817986 ATATTAAGTC
* *
16817996 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
16818023 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
16818051 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
16818078 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
16818106 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
16818133 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16818148 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:16831179 original size:23 final size:22
Alignment explanation
Indices: 16831108--16831192 Score: 86
Period size: 21 Copynumber: 4.0 Consensus size: 22
16831098 ACCTAATCAA
*
16831108 AATACGACACATAA-GTGCCTG
1 AATACGACACACAAGGTGCCTG
*
16831129 AA-ACGACACACGAGGTGCCTG
1 AATACGACACACAAGGTGCCTG
* *
16831150 -CTGCGACACACAAGGTGCCTG
1 AATACGACACACAAGGTGCCTG
* *
16831171 AAATACGACACATAAAGTGCCT
1 -AATACGACACACAAGGTGCCT
16831193 AATCAATAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 9 0.18
21 26 0.51
23 16 0.31
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.15
Consensus pattern (22 bp):
AATACGACACACAAGGTGCCTG
Found at i:16831191 original size:44 final size:41
Alignment explanation
Indices: 16831112--16831192 Score: 99
Period size: 44 Copynumber: 1.9 Consensus size: 41
16831102 AATCAAAATA
* * *
16831112 CGACACATAAGTGCCTGAAACGACACACGAGGTGCCTGCTG
1 CGACACACAAGTGCCTGAAACGACACACAAAGTGCCTGCTG
*
16831153 CGACACACAAGGTGCCTGAAATACGACACATAAAGTGCCT
1 CGACACACAA-GTGCCTG-AA-ACGACACACAAAGTGCCT
16831193 AATCAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 9 0.27
42 7 0.21
43 2 0.06
44 15 0.45
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.15
Consensus pattern (41 bp):
CGACACACAAGTGCCTGAAACGACACACAAAGTGCCTGCTG
Found at i:16831431 original size:28 final size:28
Alignment explanation
Indices: 16831399--16831462 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
16831389 AACACACCAG
* *
16831399 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
16831427 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
16831455 TATAATCC
1 TATAATCC
16831463 ATCACCAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.44, C:0.31, G:0.03, T:0.22
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:16831454 original size:23 final size:23
Alignment explanation
Indices: 16831385--16831455 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 23
16831375 AAATGTCCAA
*
16831385 CCAAAACACACCAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
16831408 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
16831436 CCCAAACACACCAGAATAAT
1 CCAAAACACACCAGAATAAT
16831456 ATAATCCATC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 19 0.46
24 1 0.02
28 21 0.51
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:16832159 original size:16 final size:16
Alignment explanation
Indices: 16832138--16832171 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16832128 GAGTTACCGA
*
16832138 TTCATTTATCAGATAT
1 TTCATTAATCAGATAT
*
16832154 TTCATTAATCCGATAT
1 TTCATTAATCAGATAT
16832170 TT
1 TT
16832172 TTCTTTACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (16 bp):
TTCATTAATCAGATAT
Found at i:16843144 original size:62 final size:59
Alignment explanation
Indices: 16843070--16843188 Score: 166
Period size: 62 Copynumber: 2.0 Consensus size: 59
16843060 TATTTTATTA
* * * * *
16843070 ATTTAATATTAAATTTATTTTAATGTTTATCTTATAGATAAATATTCTATTATTTTAATAAG
1 ATTTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAGTTTAATAAG
16843132 ATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAGTTTAATA
1 ATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAGTTTAATA
16843189 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
59 22 0.42
60 1 0.02
61 1 0.02
62 28 0.54
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.52
Consensus pattern (59 bp):
ATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAGTTTAATAAG
Found at i:16888715 original size:53 final size:53
Alignment explanation
Indices: 16888539--16888745 Score: 171
Period size: 53 Copynumber: 3.8 Consensus size: 53
16888529 ATTAAGGTTT
* * * * * *
16888539 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAACTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAA-GTTCATAAGGC
* * * * ** * * * * *
16888593 AAGGAAATCATGTAAGACCATGTCAAGAAATATCATTGATAAACTACAATAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
16888648 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* * *
16888701 AAGGATACCATGTAAGACCATGTCAAGATATGACAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
16888746 TAATTAGGAA
Statistics
Matches: 115, Mismatches: 36, Indels: 5
0.74 0.23 0.03
Matches are distributed among these distances:
53 44 0.38
54 35 0.30
55 36 0.31
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:16891856 original size:39 final size:40
Alignment explanation
Indices: 16891739--16891922 Score: 195
Period size: 40 Copynumber: 4.7 Consensus size: 40
16891729 GCTCCTCGTT
*
16891739 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGT-ATCTCGCA
* *
16891779 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
*
16891819 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
* * *
16891858 CAAATGCCTTC-GAATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGT-ATC-TCGCA
16891899 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
16891923 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
38 1 0.01
39 50 0.40
40 63 0.51
41 10 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
Found at i:16891883 original size:79 final size:82
Alignment explanation
Indices: 16891739--16891922 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 82
16891729 GCTCCTCGTT
* * *
16891739 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGAACTTAACCCG
*
16891803 GAT-TTAGTAAC-TCGCA
66 GATATT-GTAACTTAGCA
**
16891819 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GAATCTTAGTC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAAT-TCGCACAAATGCCTTCGGAA-CTTAACC
*
16891880 CGGATATTGTCACTTAGCA
64 CGGATATTGTAACTTAGCA
16891899 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
16891923 CAGCATTCAA
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
78 13 0.14
79 56 0.62
80 22 0.24
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGAACTTAACCCG
GATATTGTAACTTAGCA
Found at i:16893009 original size:13 final size:13
Alignment explanation
Indices: 16892991--16893015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16892981 GGATGAGCAT
16892991 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
16893004 TTTTTTTTCTTT
1 TTTTTTTTCTTT
16893016 CTAGTTTCGG
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:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:16894792 original size:42 final size:43
Alignment explanation
Indices: 16894681--16894795 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
16894671 AAAGCTCGTA
* * *
16894681 CAATGCCAACGTCTCAGACGTGGTCTTACATGTAATCAAATAT
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAATAT
* * *
16894724 CAATGTCACTGTCCCAGACAGGGTCTTACATG-AAGTCAAATA-
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAA-TCAAATAT
* *
16894766 CGATGCCAATGTCCCAAACATGGTCTTACA
1 CAATGCCAATGTCCCAGACATGGTCTTACA
16894796 CATAAATCTC
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 27 0.45
43 33 0.55
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (43 bp):
CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAATAT
Found at i:16899283 original size:47 final size:47
Alignment explanation
Indices: 16899197--16899356 Score: 143
Period size: 47 Copynumber: 3.4 Consensus size: 47
16899187 CCACTTCAAC
* * * *
16899197 ACCATGTCTGGGACATGCATCAGCCAC-ATTACG-AGAGCCAGTGTAAG
1 ACCATGTCTGGGACATGCATCAACCTCGA-AATGTA-AGCCAGTGTAAG
16899244 ACCATGTCTGGGACATGCATCAACCTCGAAATGTAAGCCAGTGTAAG
1 ACCATGTCTGGGACATGCATCAACCTCGAAATGTAAGCCAGTGTAAG
* ** * * *
16899291 A-CATGTCTGGTACATGCATTGA-CTACG-AGT-TGAGCTAGTGTAAG
1 ACCATGTCTGGGACATGCATCAACCT-CGAAATGTAAGCCAGTGTAAG
*
16899335 ACCATGTCCGGGACATGGCATC
1 ACCATGTCTGGGACAT-GCATC
16899357 GACATCCTAT
Statistics
Matches: 95, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
44 13 0.14
45 16 0.17
46 24 0.25
47 40 0.42
48 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (47 bp):
ACCATGTCTGGGACATGCATCAACCTCGAAATGTAAGCCAGTGTAAG
Found at i:16900544 original size:21 final size:22
Alignment explanation
Indices: 16900505--16900545 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16900495 TCGAATTGGT
16900505 CACACGGGCGTGTTGCCCCTCC
1 CACACGGGCGTGTTGCCCCTCC
*
16900527 CACACGGGTGTG-TGCCCCT
1 CACACGGGCGTGTTGCCCCT
16900546 GTGGCTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.10, C:0.41, G:0.29, T:0.20
Consensus pattern (22 bp):
CACACGGGCGTGTTGCCCCTCC
Found at i:16926659 original size:42 final size:43
Alignment explanation
Indices: 16926568--16926731 Score: 165
Period size: 43 Copynumber: 3.8 Consensus size: 43
16926558 AATACCAACA
*** *
16926568 TCCTAGATGTGGTCTTACATGTAATCAAATATCGATGCCACTG
1 TCCTAGATGTGGTCTTACACAAAATCAAATATCGATGCCAATG
*
16926611 TCCTAGATAG-GGTCTTACACAAAATCATATA-CGATGCCAATG
1 TCCTAGAT-GTGGTCTTACACAAAATCAAATATCGATGCCAATG
** *
16926653 TCCTAGACATGGTCTTACACGTAAATCACAA-ATCGATGCCAATG
1 TCCTAGATGTGGTCTTACAC-AAAATCA-AATATCGATGCCAATG
* * *
16926697 TCCCAGATGTCGTCTTACACAATAA-CACATATCGA
1 TCCTAGATGTGGTCTTACACAA-AATCAAATATCGA
16926732 AATCCTATGT
Statistics
Matches: 99, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
42 28 0.28
43 40 0.40
44 31 0.31
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (43 bp):
TCCTAGATGTGGTCTTACACAAAATCAAATATCGATGCCAATG
Found at i:16926712 original size:44 final size:43
Alignment explanation
Indices: 16926568--16926716 Score: 162
Period size: 42 Copynumber: 3.5 Consensus size: 43
16926558 AATACCAACA
* *
16926568 TCCTAGATGTGGTCTTACATGT-AATCAAATATCGATGCCACTG
1 TCCTAGATGTGGTCTTACACGTAAATCAAA-ATCGATGCCAATG
* *
16926611 TCCTAGATAG-GGTCTTACAC-AAAATC-ATATACGATGCCAATG
1 TCCTAGAT-GTGGTCTTACACGTAAATCAAAAT-CGATGCCAATG
**
16926653 TCCTAGACATGGTCTTACACGTAAATCACAAATCGATGCCAATG
1 TCCTAGATGTGGTCTTACACGTAAATCA-AAATCGATGCCAATG
* *
16926697 TCCCAGATGTCGTCTTACAC
1 TCCTAGATGTGGTCTTACAC
16926717 AATAACACAT
Statistics
Matches: 87, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
41 2 0.02
42 28 0.32
43 26 0.30
44 28 0.32
45 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
TCCTAGATGTGGTCTTACACGTAAATCAAAATCGATGCCAATG
Found at i:16926939 original size:16 final size:16
Alignment explanation
Indices: 16926920--16926954 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
16926910 TTAACAACAT
16926920 TTATTTACTTATGAAC
1 TTATTTACTTATGAAC
16926936 TTATTTACTTATGAAC
1 TTATTTACTTATGAAC
16926952 TTA
1 TTA
16926955 CCTCGTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (16 bp):
TTATTTACTTATGAAC
Found at i:16935231 original size:42 final size:42
Alignment explanation
Indices: 16935150--16935231 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
16935140 GGTGCAGGTT
* * *
16935150 ACACACGACCAAGACACGCGCCCGTGTTCTAGGCTGTGTATC
1 ACACACGACCAAGACACACGCCCGTGTTCTAGCCCGTGTATC
**
16935192 ACACACGACTGAGACACACGCCCGTGTCTCTA-CCCGTGTA
1 ACACACGACCAAGACACACGCCCGTGT-TCTAGCCCGTGTA
16935232 CCCAATTCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.88
43 4 0.12
ACGTcount: A:0.24, C:0.35, G:0.22, T:0.18
Consensus pattern (42 bp):
ACACACGACCAAGACACACGCCCGTGTTCTAGCCCGTGTATC
Found at i:16935448 original size:20 final size:22
Alignment explanation
Indices: 16935425--16935474 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
16935415 CCAATACTTG
*
16935425 CAAACATAT-A-CCAGCCAATT
1 CAAACATATAAGCAAGCCAATT
16935445 CAAACATTATAAGCAAGCCAATT
1 CAAACA-TATAAGCAAGCCAATT
*
16935468 CTAACAT
1 CAAACAT
16935475 CTAACATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.24
21 3 0.12
22 2 0.08
23 14 0.56
ACGTcount: A:0.46, C:0.26, G:0.06, T:0.22
Consensus pattern (22 bp):
CAAACATATAAGCAAGCCAATT
Found at i:16949232 original size:42 final size:40
Alignment explanation
Indices: 16949185--16949375 Score: 274
Period size: 42 Copynumber: 4.7 Consensus size: 40
16949175 GAGCATTGGA
16949185 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
16949225 ATATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 --ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
** * *
16949267 ATATATATCCGGGCTAATTCCCGAAGGCAATTGTGCAAGTTG
1 --ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
*
16949309 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* * *
16949349 CTATACCCGGGTTAAGACCCGAAGGCA
1 ATATATCCGGGCTAAGACCCGAAGGCA
16949376 ATTGAGCTTG
Statistics
Matches: 137, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 59 0.43
42 78 0.57
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
Found at i:16949332 original size:82 final size:81
Alignment explanation
Indices: 16949185--16949379 Score: 284
Period size: 82 Copynumber: 2.4 Consensus size: 81
16949175 GAGCATTGGA
* *
16949185 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATATCCGGGCTAAGACCCGAA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGA-ATATATCCGGGCTAAGACCCGAA
*
16949250 GGCATTTGTGCGAGTTG
65 GGCATTCGTGCGAGTTG
**
16949267 ATATATATCCGGGCTAATTCCCGAAGGCAATTGTGCAAGTTG-ATATATCCGGGCTAAGACCCGA
1 --ATATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGAATATATCCGGGCTAAGACCCGA
16949331 AGGCATTCGTGCGAGTTG
64 AGGCATTCGTGCGAGTTG
* * *
16949349 CTATACCCGGGTTAAGACCCGAAGGCAATTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTG
16949380 AGCTTGTGGT
Statistics
Matches: 101, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
80 26 0.26
82 39 0.39
84 36 0.36
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (81 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGAATATATCCGGGCTAAGACCCGAAG
GCATTCGTGCGAGTTG
Found at i:16952846 original size:39 final size:40
Alignment explanation
Indices: 16952770--16952850 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
16952760 CCTTTTATAG
16952770 TGGGGGACAAGCGTAGCTACGTGTGTCTTAAGGTCACTAAC
1 TGGGGGACAAGCGTAGCTACG-GTGTCTTAAGGTCACTAAC
*
16952811 TGGGGGATAAGCGTAGCTAC-GTGTCTTAAGGTCACTAAC
1 TGGGGGACAAGCGTAGCTACGGTGTCTTAAGGTCACTAAC
16952850 T
1 T
16952851 CAAAAGTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 20 0.51
41 19 0.49
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (40 bp):
TGGGGGACAAGCGTAGCTACGGTGTCTTAAGGTCACTAAC
Found at i:16955801 original size:3 final size:3
Alignment explanation
Indices: 16955793--16955823 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
16955783 GAGAGAGATG
16955793 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16955824 GAGAGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16956803 original size:10 final size:10
Alignment explanation
Indices: 16956788--16956821 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
16956778 CATATATTTG
16956788 AAAAATTATT
1 AAAAATTATT
16956798 AAAAATTATT
1 AAAAATTATT
16956808 AAAAA-TA-T
1 AAAAATTATT
16956816 AAAAAT
1 AAAAAT
16956822 AATACATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
10 15 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAATTATT
Found at i:16957754 original size:14 final size:13
Alignment explanation
Indices: 16957734--16957778 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
16957724 TTACTTGTAT
*
16957734 GTTATGGCTTAGG
1 GTTATGGTTTAGG
16957747 GTTTATGGGTTTAGG
1 G-TTAT-GGTTTAGG
*
16957762 GTTATGGTTTAGA
1 GTTATGGTTTAGG
16957775 GTTA
1 GTTA
16957779 ATGTTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 12 0.43
14 8 0.29
15 8 0.29
ACGTcount: A:0.18, C:0.02, G:0.36, T:0.44
Consensus pattern (13 bp):
GTTATGGTTTAGG
Found at i:16957828 original size:28 final size:29
Alignment explanation
Indices: 16957783--16957843 Score: 106
Period size: 28 Copynumber: 2.1 Consensus size: 29
16957773 GAGTTAATGT
16957783 TTTTGAAAAAAAAAAATTAGGGTTTAGGG
1 TTTTGAAAAAAAAAAATTAGGGTTTAGGG
*
16957812 TTTT-AAAAAAATAAATTAGGGTTTAGGG
1 TTTTGAAAAAAAAAAATTAGGGTTTAGGG
16957840 TTTT
1 TTTT
16957844 TTAAATTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (29 bp):
TTTTGAAAAAAAAAAATTAGGGTTTAGGG
Found at i:16958049 original size:14 final size:14
Alignment explanation
Indices: 16958014--16958055 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
16958004 CATACAGTTG
*
16958014 ATTCTGAAAAAATT
1 ATTCTGAAAAAATA
*
16958028 ATTTTGAAAAGAA-A
1 ATTCTGAAAA-AATA
16958042 ATTCTGAAAAAATA
1 ATTCTGAAAAAATA
16958056 TCTCAGGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.31
Consensus pattern (14 bp):
ATTCTGAAAAAATA
Found at i:16971624 original size:23 final size:23
Alignment explanation
Indices: 16971601--16971729 Score: 100
Period size: 23 Copynumber: 5.3 Consensus size: 23
16971591 TAAGCTCCTC
16971601 TTGAGCTGATAAACAGTAAGCTCTA
1 TTGAGCTGA-AAACAGTAAGCTC-A
16971626 TTGAGCTG-AAACAGTAAGCTCA
1 TTGAGCTGAAAACAGTAAGCTCA
* *
16971648 TATGAGCTG-AATCGGTAAGCTCCA
1 T-TGAGCTGAAAACAGTAAGCT-CA
* * * *
16971672 ATAAGCTGAAAACAATAAGCTCT
1 TTGAGCTGAAAACAGTAAGCTCA
* *
16971695 TATGAGCTGATACACCGGTAAGCTCA
1 T-TGAGCTGA-A-AACAGTAAGCTCA
16971721 TATGAGCTG
1 T-TGAGCTG
16971730 TGGTGAGTCC
Statistics
Matches: 84, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
22 2 0.02
23 37 0.44
24 18 0.21
25 9 0.11
26 18 0.21
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (23 bp):
TTGAGCTGAAAACAGTAAGCTCA
Found at i:16971694 original size:70 final size:75
Alignment explanation
Indices: 16971586--16971729 Score: 192
Period size: 70 Copynumber: 2.0 Consensus size: 75
16971576 TTGAGCCATG
** * *
16971586 ATCGGTAAGCTCCTCTTGAGCTGATAAACAGTAAGCTC-TATTGAGCTGA-A-A-CAGTAAGCTC
1 ATCGGTAAGCTCCTAATAAGCTGATAAACAATAAGCTCTTA-TGAGCTGATACACCAGTAAGCTC
16971647 ATATGAGCTGA
65 ATATGAGCTGA
*
16971658 ATCGGTAAGCTCC-AATAAGCTGA-AAACAATAAGCTCTTATGAGCTGATACACCGGTAAGCTCA
1 ATCGGTAAGCTCCTAATAAGCTGATAAACAATAAGCTCTTATGAGCTGATACACCAGTAAGCTCA
16971721 TATGAGCTG
66 TATGAGCTG
16971730 TGGTGAGTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
70 20 0.32
71 10 0.16
72 14 0.22
73 19 0.30
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (75 bp):
ATCGGTAAGCTCCTAATAAGCTGATAAACAATAAGCTCTTATGAGCTGATACACCAGTAAGCTCA
TATGAGCTGA
Found at i:16972030 original size:20 final size:20
Alignment explanation
Indices: 16972002--16972043 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
16971992 GTATTTCACT
* *
16972002 TTTACTCATGTAAACAGTAA
1 TTTAATCATATAAACAGTAA
*
16972022 TTTAATCATATAATCAGTAA
1 TTTAATCATATAAACAGTAA
16972042 TT
1 TT
16972044 CAAATTTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (20 bp):
TTTAATCATATAAACAGTAA
Found at i:16977183 original size:17 final size:17
Alignment explanation
Indices: 16977163--16977200 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
16977153 CAACAAAGAA
16977163 AGAAAGTAAGCAAAAAG
1 AGAAAGTAAGCAAAAAG
*
16977180 AGAAAGTAAGCAAAGAG
1 AGAAAGTAAGCAAAAAG
16977197 AGAA
1 AGAA
16977201 GCTCGAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.63, C:0.05, G:0.26, T:0.05
Consensus pattern (17 bp):
AGAAAGTAAGCAAAAAG
Found at i:16986762 original size:23 final size:23
Alignment explanation
Indices: 16986719--16986763 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16986709 AATAATAAAT
* *
16986719 TTATATTATTTTTTAAAAGTAAC
1 TTATATTATATTTAAAAAGTAAC
16986742 TTATA-TATATTTAAAATAGTAA
1 TTATATTATATTTAAAA-AGTAA
16986764 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TTATATTATATTTAAAAAGTAAC
Found at i:16987827 original size:61 final size:63
Alignment explanation
Indices: 16987727--16987851 Score: 182
Period size: 61 Copynumber: 2.0 Consensus size: 63
16987717 TCAATTTGTA
* * *
16987727 TTAGATATTGTAATTATTTAAGTTTTTTTTTATCTAATTAATGTT-TAGATACTA-TTTATAT
1 TTAGATATTGTAATTATTTAACTTTATTTTTATCAAATTAATGTTGTAGATACTACTTTATAT
* * *
16987788 TTAGATGTTGTAATTATTTAACTTTATTTTTATCAAATTAATTTTGTAGATACTACTTTGTAT
1 TTAGATATTGTAATTATTTAACTTTATTTTTATCAAATTAATGTTGTAGATACTACTTTATAT
16987851 T
1 T
16987852 AGTTTACCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 40 0.71
62 9 0.16
63 7 0.12
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (63 bp):
TTAGATATTGTAATTATTTAACTTTATTTTTATCAAATTAATGTTGTAGATACTACTTTATAT
Found at i:16988354 original size:3 final size:3
Alignment explanation
Indices: 16988346--16988384 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
16988336 ATTTGAATAA
16988346 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
16988385 ATCATCAGTT
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:16995300 original size:16 final size:16
Alignment explanation
Indices: 16995281--16995319 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
16995271 TACAAAAGAA
16995281 AATAA-ATAAATAAATG
1 AATAATATAAA-AAATG
*
16995297 AATAATATAAAAAGTG
1 AATAATATAAAAAATG
16995313 AATAATA
1 AATAATA
16995320 ATTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (16 bp):
AATAATATAAAAAATG
Found at i:16996711 original size:44 final size:43
Alignment explanation
Indices: 16996571--16996893 Score: 163
Period size: 44 Copynumber: 7.3 Consensus size: 43
16996561 CTATATCTTC
* * * * *
16996571 AGGGAAATAAGATTCACTATCTTTAGTCTGCTCCACTACAACTT
1 AGGGAGATAAGATTC-GTATCTTCAATCTGCTCCACTACTACTT
* ** * * *
16996615 CAGGGAGATAAGATTTGTGGCTTAAATCTGCTCCATTGCTGCTACAT
1 -AGGGAGATAAGATTCGTATCTTCAATCTGCTCCA---CTACTACTT
*
16996662 A--GAGATAAGATTCGTCATCTTCGATCTGCTCCACTACTACTT
1 AGGGAGATAAGATTCGT-ATCTTCAATCTGCTCCACTACTACTT
* * * * *
16996704 AGGGAGATAA-AATCTGCAATTTTCAATCTGCTCCACTGCAACTT
1 AGGGAGATAAGATTC-G-TATCTTCAATCTGCTCCACTACTACTT
* * *
16996748 CAGGGAGATAAGACTT-GTATC-ACGAACCTGCTCCACT-GTAACTT
1 -AGGGAGATAAGA-TTCGTATCTTC-AATCTGCTCCACTACT-ACTT
* ** * ** * * * **
16996792 CAAGGAGATAAGGCTGGTGGCTTAAATCTGCTCAATTACCGCTAT
1 -AGGGAGATAAGATTCGTATCTTCAATCTGCTCCACTACTACT-T
* * *
16996837 ATGGAGATAAGATTCGCAGTCTTCAATCTGCTCCACTACTGCTT
1 AGGGAGATAAGATTCGTA-TCTTCAATCTGCTCCACTACTACTT
16996881 AGGGAGATAAGAT
1 AGGGAGATAAGAT
16996894 CTGTAATCTT
Statistics
Matches: 205, Mismatches: 55, Indels: 37
0.69 0.19 0.12
Matches are distributed among these distances:
42 8 0.04
43 5 0.02
44 126 0.61
45 57 0.28
46 2 0.01
47 7 0.03
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (43 bp):
AGGGAGATAAGATTCGTATCTTCAATCTGCTCCACTACTACTT
Found at i:16996918 original size:177 final size:176
Alignment explanation
Indices: 16996598--16996935 Score: 446
Period size: 177 Copynumber: 1.9 Consensus size: 176
16996588 TATCTTTAGT
* * * * * *
16996598 CTGCTCCACTACAACTTCAGGGAGATAAGATTTGTGGCTTAAATCTGCTCCATTGCTGCTACATA
1 CTGCTCCACTACAACTTCAAGGAGATAAGACTGGTGGCTTAAATCTGCTCAATTACCGCTACATA
*
16996663 GAGATAAGATTCGTCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAAATCTGCAATTTTC
66 GAGATAAGATTCGTCATCTTCAATCTGCTCCACTACTACTTAGGGAGATAAAATCTGCAATTTTC
* *
16996728 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCACGAAC
131 AACCTACTCCACTGCAAC-TCAGGGAGATAAGACTTGTATCACGAAC
** * * *
16996775 CTGCTCCACTGTAACTTCAAGGAGATAAGGCTGGTGGCTTAAATCTGCTCAATTACCGCTATATG
1 CTGCTCCACTACAACTTCAAGGAGATAAGACTGGTGGCTTAAATCTGCTCAATTACCGCTACATA
* * *
16996840 GAGATAAGATTCG-CAGTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
66 GAGATAAGATTCGTCA-TCTTCAATCTGCTCCACTACTACTTAGGGAGATAAAATCTGCAAT-TT
* * **
16996904 T-AGCCTATTCCACTGCTGCTCAGGGAGATAAG
129 TCAACCTACTCCACTGCAACTCAGGGAGATAAG
16996936 GCTAATGGCC
Statistics
Matches: 138, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
176 15 0.11
177 120 0.87
178 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (176 bp):
CTGCTCCACTACAACTTCAAGGAGATAAGACTGGTGGCTTAAATCTGCTCAATTACCGCTACATA
GAGATAAGATTCGTCATCTTCAATCTGCTCCACTACTACTTAGGGAGATAAAATCTGCAATTTTC
AACCTACTCCACTGCAACTCAGGGAGATAAGACTTGTATCACGAAC
Found at i:17001723 original size:21 final size:21
Alignment explanation
Indices: 17001680--17001723 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
17001670 AAAATGCAAG
* * *
17001680 AAAATAATATTTGCTTAGGAT
1 AAAAGAATATTTGCTCAGAAT
17001701 AAAAGAATATTTGCTCAGAAT
1 AAAAGAATATTTGCTCAGAAT
17001722 AA
1 AA
17001724 GACATAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.32
Consensus pattern (21 bp):
AAAAGAATATTTGCTCAGAAT
Found at i:17009663 original size:16 final size:16
Alignment explanation
Indices: 17009644--17009682 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
17009634 TACAAAAGAA
17009644 AATAA-ATAAATAAATG
1 AATAATATAAA-AAATG
*
17009660 AATAATATAAAAAGTG
1 AATAATATAAAAAATG
17009676 AATAATA
1 AATAATA
17009683 ATTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (16 bp):
AATAATATAAAAAATG
Found at i:17017148 original size:19 final size:19
Alignment explanation
Indices: 17017126--17017180 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
17017116 GTTAATTTTT
17017126 TTATATAATTTTAAGTTAA
1 TTATATAATTTTAAGTTAA
**
17017145 TTAT-T-ATTTTATTTTTTAA
1 TTATATAATTTTA--AGTTAA
17017164 TTATATAATTATTAAGT
1 TTATATAATT-TTAAGT
17017181 AAGTTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
17 6 0.22
18 1 0.04
19 12 0.44
20 2 0.07
21 3 0.11
22 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
TTATATAATTTTAAGTTAA
Found at i:17018961 original size:23 final size:23
Alignment explanation
Indices: 17018926--17018969 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
17018916 AACTAAATTC
17018926 ACTTACTTTTCTAACTCAATTTAT
1 ACTTACTTTTCT-ACTCAATTTAT
*
17018950 ACTT-CTTTTCTACTTAATTT
1 ACTTACTTTTCTACTCAATTT
17018970 CTTGCTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 7 0.37
24 4 0.21
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (23 bp):
ACTTACTTTTCTACTCAATTTAT
Found at i:17020550 original size:18 final size:18
Alignment explanation
Indices: 17020527--17020589 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
17020517 AAATAACATA
17020527 ATTTTTTATATAAAAATT
1 ATTTTTTATATAAAAATT
* * * *
17020545 ATTTTTTAAATCATACATA
1 ATTTTTTATAT-AAAAATT
17020564 ATTTTTTATATAAAAATT
1 ATTTTTTATATAAAAATT
17020582 ATTTTTTA
1 ATTTTTTA
17020590 AATCATATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 22 0.61
19 14 0.39
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTTATATAAAAATT
Found at i:17020566 original size:37 final size:37
Alignment explanation
Indices: 17020522--17020596 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
17020512 AATGAAAATA
17020522 ACATAATTTTTTATATAAAAATTATTTTTTAAATCAT
1 ACATAATTTTTTATATAAAAATTATTTTTTAAATCAT
17020559 ACATAATTTTTTATATAAAAATTATTTTTTAAATCAT
1 ACATAATTTTTTATATAAAAATTATTTTTTAAATCAT
17020596 A
1 A
17020597 TAAAAGTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (37 bp):
ACATAATTTTTTATATAAAAATTATTTTTTAAATCAT
Found at i:17021462 original size:18 final size:18
Alignment explanation
Indices: 17021439--17021476 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17021429 AATATATATT
*
17021439 AACCCAAGTACCTAACCC
1 AACCCAAGTACCCAACCC
*
17021457 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
17021475 AA
1 AA
17021477 TAATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.45, G:0.03, T:0.11
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:17021469 original size:13 final size:13
Alignment explanation
Indices: 17021453--17021477 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17021443 CAAGTACCTA
17021453 ACCCAACCCAATT
1 ACCCAACCCAATT
17021466 ACCCAACCCAAT
1 ACCCAACCCAAT
17021478 AATAAAAATT
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:17021515 original size:5 final size:6
Alignment explanation
Indices: 17021502--17021542 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
17021492 ATAATTTAAT
*
17021502 AAATAA AAATAA AATTCTAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AA--ATAA AAATAA AAATAA AAATAA AAA
17021543 AAATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:17021543 original size:20 final size:20
Alignment explanation
Indices: 17021502--17021544 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17021492 ATAATTTAAT
* **
17021502 AAATAAAAATAAAATTCTAA
1 AAATAAAAATAAAAATAAAA
17021522 AAATAAAAATAAAAATAAAA
1 AAATAAAAATAAAAATAAAA
17021542 AAA
1 AAA
17021545 ATATAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (20 bp):
AAATAAAAATAAAAATAAAA
Found at i:17021586 original size:9 final size:9
Alignment explanation
Indices: 17021562--17021602 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
17021552 TTTATACAAA
*
17021562 TAATTCAGT
1 TAATTCGGT
17021571 TAATTCGGT
1 TAATTCGGT
*
17021580 TAATTCGGG
1 TAATTCGGT
*
17021589 TAATTAGGT
1 TAATTCGGT
17021598 TAATT
1 TAATT
17021603 TTATACTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:17023290 original size:56 final size:56
Alignment explanation
Indices: 17023197--17023402 Score: 220
Period size: 56 Copynumber: 3.6 Consensus size: 56
17023187 TATCATATTA
* * **
17023197 TAGGATTACTAGTCCAGGCTAAATCCTGTCTCCAACATATGCTCACAAGAGCTTAAT
1 TAGGATTACCAGTCCAGGCTAAATCCTATCTGTAACATATGCTC-CAAGAGCTTAAT
* * *
17023254 TAGGATTACCAAT-CAGGCTAAATCCTTTCTGTAACATATGCTCTGAAGAGCTTAAT
1 TAGGATTACCAGTCCAGGCTAAATCCTATCTGTAACATATGCTC-CAAGAGCTTAAT
* * * *
17023310 TAAGACTACCAGTCCAGGCTAAACCCTAAT-TGTAACATATGCT-CGAGAGCAATTATAT
1 TAGGATTACCAGTCCAGGCTAAATCCT-ATCTGTAACATATGCTCCAAGAGC--TTA-AT
* *
17023368 CAGGATTACCAGTCCGGGCTAAATCCTATCTGTAA
1 TAGGATTACCAGTCCAGGCTAAATCCTATCTGTAA
17023403 TGAGGTCAAT
Statistics
Matches: 124, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
55 5 0.04
56 48 0.39
57 41 0.33
58 30 0.24
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (56 bp):
TAGGATTACCAGTCCAGGCTAAATCCTATCTGTAACATATGCTCCAAGAGCTTAAT
Found at i:17033270 original size:29 final size:29
Alignment explanation
Indices: 17033227--17033377 Score: 212
Period size: 29 Copynumber: 5.2 Consensus size: 29
17033217 GAGTGCTAAA
17033227 CGATGGTCGAAACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* ** * *
17033256 TGATGGTCGTCACCATCTCTTTCCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
*
17033285 CGATGGTCGAAACCATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * *
17033314 CGATGGTTGAAACCATCCTTTTTTATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
*
17033343 CGATGGTCGTAACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
17033372 CGATGG
1 CGATGG
17033378 GCGTCGATAT
Statistics
Matches: 103, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 103 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:17037835 original size:94 final size:94
Alignment explanation
Indices: 17037707--17040899 Score: 3112
Period size: 94 Copynumber: 34.0 Consensus size: 94
17037697 TCACAGTTTC
* * * * * * * * *
17037707 ATCTTACTCCATTGCAACTTCAAGGAGATAAGATTTGCTGTTGTAGCTTCATTCCAACCTACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * *
17037772 AACTTCAGGGGTACAAGATTTGTAGCTTC
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * * * ** *
17037801 ATCTTGCTTCACTACAACTTCATGGAGATAAGATTCACCATTGTAATTTCATTCTAACCCACTGC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * * *
17037866 AAATTTAGGGATATAGGATTTCTAG-TTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * *
17037894 CATCTTGCTCCACTGCAATTTCAGGGAGTTAAGATTCGCTATTGTAGCTTCAACCCGATCCACTA
1 -ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTA
17037959 CAACTTCAGGGGTATAGGATTTGTAGCTTT
65 CAACTTCAGGGGTATAGGATTTGTAGCTTT
** ** * * *
17037989 ATCTTG-TACCACTGCAACTTCAGGGAGATAAGATTCATTATTGTAGTTTCAATCTGACCCATTG
1 ATCTTGCT-CCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTA
*
17038053 CAACTTTAGGGGTATAGGATTTGTAGCTTT
65 CAACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * *
17038083 ATCTTGCTCCATTGCAATTTCAGAGAGATAAGATTCACTATAGTAACTTTAATCCGACCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
17038148 AACTTCAGGGGTATAGGATTTGTAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * * * *
17038177 ATCTTGCTCCATTACAACTTCAGGGAGATAATATTTGCTATTGTAGCTTCAGTTCGACCCATTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * *
17038242 AACTTCAGAGGTATAAGAATTGTAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* ** * * * * *
17038271 ATCTTACTCCACTGCAACTTCAGAAAGATAAGACTT-GCTACTATAATTTCAATCCTACCCACTG
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCTATTGTAACTTCAATCCGACCCACTA
17038335 CAACTTCAGGGGTATAGGATTTGTAGCTTT
65 CAACTTCAGGGGTATAGGATTTGTAGCTTT
* ** * ** *** *
17038365 ATCTTGCTCCACTGCAATTTCAAAGAGATAAGATTCGCTATTGTAGCTTCAATTTGATGTACTAT
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
*
17038430 AACTTCAGGGGTATAAGATTTGTAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * * * * *
17038459 TTCTTACTCTACTGTAACTTCAGGGAGATAAGATTTGCTATGGTAACTTCAATCCAACCCATTGC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * * *
17038524 AACTTCAGGGGTACAGGATTTGTAACATC
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * * *
17038553 ATCTTACTTCACTGCAACTTCAGAGAGATAAGATTTGCTATGGTAACTTGAATCCGACCCACTGC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * * *
17038618 AACTTTAGGGGTATAAGATTTATAGCTTC
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * **
17038647 ATCTTACTCCATTGGAACTTCAGGGAGATAAGATTCTCTATTGTAGCTTCAATTTGACCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * ** *
17038712 AACTTTAGGGTTATAAAATTTATAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * ** * **
17038741 ATCTTGTTCCACTGCAACTTTAGATAGATAAGATTCGCTATTGTAGCTTCAATTTGACCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * ** *
17038806 AACTTTAGGGTTATAAAATTTATAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * ** * **
17038835 ATCTTGTTCCACTGCAACTTTAGATAGATAAGATTCGCTATTGTAGCTTCAATTTGACCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * ** *
17038900 AACTTTAGGGTTATAAAATTTATAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * ** * *
17038929 ATCTTGTTCCACTGCAACTTTAGATAGATAAGATTCGCTATTGTAGCTTCAATCCGACCTACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
17038994 AACTTCCA-GGGTATAGGATTTGTAGCTTT
66 AACTT-CAGGGGTATAGGATTTGTAGCTTT
* * ** * *
17039023 ATCTTGCTCCATTGCAACTTTAAAGAGATAAGATTCGCTATTGTAGCTTCAATCTGACCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
*
17039088 AACTTTAGGGGTATAGGATTTGTAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * ** * *
17039117 ATCTTGCTCCATTGCAACTTTAAAGAGATAAGATTCGCTATTGTAGCTTCAATCTGACCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
*
17039182 AACTTTAGGGGTATAGGATTTGTAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * ** * *
17039211 ATCTTGCTCCATTGCAACTTTAAAGAGATAAGATTCGCTATTGTAGCTTCAATCTGACCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
*
17039276 AACTTTAGGGGTATAGGATTTGTAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * * ** * * * * *
17039305 ATCTTGCTTCACTACAACTTTTA-TGATATAAGATTCACTATAATAACTTTAATCCAACCTATTG
1 ATCTTGCTCCACTGCAAC-TTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTA
* * * * *
17039369 TAAGTTTA-GGGTATAAGATTTGTAGCTTC
65 CAACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * *
17039398 ATCTTGTTCCACTACAACTTTAGGGAGATAGGATTCGCTATCGTAACTTTAATCCGACCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* *
17039463 AACTTTAGGGGTATAGGATTTGTAGCTTC
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* ** * * *
17039492 ATCTTGCTCCACTGCAACTTTAAAGTGATAAGATTCGCTATTGTAGCTTCAATCCGACCTACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
*
17039557 AACTTCCA-GGGTATAAGATTTGTAGCTTT
66 AACTT-CAGGGGTATAGGATTTGTAGCTTT
* * * * * * * *
17039586 ATCTTGCTCCATTGCAACTTCAAGGAGATAAGACTCGTTACTGTAATTTCAATCCTACCTACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
*
17039651 AACTTCAGGGGTATAGGATTTCTAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * * * *
17039680 ATATTGCTCCACTGCAACTTTAGAGAGATGAGATTCGCTATTGTAGCTTCAATTCGACGCACTGC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* *
17039745 AACTTCAAGGGTATAGGATTTGTACCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
** * * * * ** *
17039774 ATCTTGCTCCACTATAACTTTAAGAAGATAAGATTCACTATAATAACTTCAATCCAACCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * *
17039839 AACTTTAGAGGTATAGGATTTGTAGCTTC
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
** * * * * *
17039868 ATCTTATTCCACTACAACTTC-GGGAGATAAGATTCACTATGGTAACTTTAATCAGACCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
17039932 AACTTCAGGGGTATAGGATTTGTAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
** * * * * * * *
17039961 ATCTTGCTCCACTATAATTTTAGAGAGATAAGATTAGCTATGGTAACTTCAATCTGACCCACTTG
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCAC-TA
*
17040026 C-ACTTCAGGGGTATAGGATTTGTAGCTTC
65 CAACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * ** * ** *
17040055 ATTTTGCTCCATTGCAACTTTAGGGAGATAAAATTTACTATGGTAACTTCAATCAAACTCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* *
17040120 AACTTCAGGGGTATGGGATTTGTAGCTTC
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * * *
17040149 ATCTTACTCTACTACAACTTTAGGGAGATAAGATTCACTATGGTAACTTCAAT-CGAACCTACTA
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCG-ACCCACTA
* * *
17040213 CAACTTCAGGGGAATAAGATTTGTAGATTT
65 CAACTTCAGGGGTATAGGATTTGTAGCTTT
* ** * * * ** *
17040243 ATCTTACTCTGCTGCAACTTTAGGGAGATAAGATTCGCTATGGTAACATCAATCTAACCCACTGC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * * *
17040308 AACTTCAGTGGTATATGATTTATAGCTTC
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * *
17040337 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTATGGTAACTTCAATCTGACCCATTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * * *
17040402 AACTTTAGGGGTATAGGTTTTATAGCTTC
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * * * *
17040431 GTCTTGTTCCACTGTAACTTCAAGGAGATAAGATTCACTATGGTAACTTTAATCCGACCCACTGC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * *
17040496 AACTTTAGGGGTATAGGTTTTGTAGCTTC
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
*** * * * * * * * * *
17040525 ATCTTGCTCCACCATAATTTCTGGGAGGTAAGTTTTGCTATGGTAACTTCAATTCGACCTACTGC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
*
17040590 AATTTCAGGGGTATAGGATTTGTAGCTTT
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* ** * ** * * * *
17040619 ATCTTACTCCACTATAACTTTAGGGAGATAAGATTTTCTATGGTAACTTCAATCTGACCCATTGC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* *
17040684 AACTTCAGGAGTATAGGATTTGTAGCTTA
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * * * * * *
17040713 ATCTTACTCCACTGCAACTTTAGGGAGATAAAATTCGTTATGGTGACTTTAATTCGACCTACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
* * *
17040778 AACTTTAGAGGTATAGGATTTGTAGCTTC
66 AACTTCAGGGGTATAGGATTTGTAGCTTT
* * * * ** * * ** *
17040807 ATCTTGCTCCAGTGCACCTTCAGGGAGATAAGATTCACCATTGTAGTTTCATTCCAACTAACTGC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
** *
17040872 AACTTCAGATGTATAGGACTTGTAGCTT
66 AACTTCAGGGGTATAGGATTTGTAGCTT
17040900 CAATCTGACC
Statistics
Matches: 2630, Mismatches: 451, Indels: 36
0.84 0.14 0.01
Matches are distributed among these distances:
92 4 0.00
93 160 0.06
94 2452 0.93
95 14 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (94 bp):
ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATTGTAACTTCAATCCGACCCACTAC
AACTTCAGGGGTATAGGATTTGTAGCTTT
Found at i:17038213 original size:44 final size:44
Alignment explanation
Indices: 17037767--17039324 Score: 175
Period size: 44 Copynumber: 33.2 Consensus size: 44
17037757 ATTCCAACCT
* * *
17037767 ACTACAACTTCAGGGGTACAAGATTTGTAGCTTCATCTTGCTTC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* * **
17037811 ACTACAACTTCATGGAG-ATAAGATTCACCATTGTA-ATTTCATTCTAAC-CC
1 ACTACAACTTCA-GGGGTATAAGA-T-----TTGTAGCTTT-A-TCTTGCTCC
* * * * * *
17037861 ACTGCAAATTTAGGGATATAGGATTTCTAG-TTTCATCTTGCTCC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTT-ATCTTGCTCC
* * * * ** *
17037905 ACTGCAATTTCAGGGAGT-TAAGATTCGCTATTGTAGCTTCAACCCGATCC
1 ACTACAACTTCAGGG-GTATAAGA-----T-TTGTAGCTTTATCTTGCTCC
*
17037955 ACTACAACTTCAGGGGTATAGGATTTGTAGCTTTATCTTG-TACC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCT-CC
*
17037999 ACTGCAACTTCAGGGAG-ATAAGATTCATTATTGTAG-TTTCAATC-TGAC-CC
1 ACTACAACTTCAGGG-GTATAAG----A-T-TTGTAGCTTT--ATCTTG-CTCC
* * * *
17038049 ATTGCAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* * * * * *
17038093 ATTGCAATTTCAGAGAG-ATAAGATTCACTATAGTAACTTTAATC-CGAC-CC
1 ACTACAACTTCAG-GGGTATAAGA-T---T-T-GTAGCTTT-ATCTTG-CTCC
*
17038143 ACTACAACTTCAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* * * * *
17038187 ATTACAACTTCAGGGAGATAATATTTGCTATTGTAGCTTCAGT-TCGAC-CC
1 ACTACAACTTCAGGG-G-T-ATA--AGAT-TTGTAGCTTTA-TCTTG-CTCC
* * * *
17038237 ATTACAACTTCAGAGGTATAAGAATTGTAGCTTTATCTTACTCC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* ** * * * *
17038281 ACTGCAACTTCAGAAAG-ATAAGACTTGCTA-CTATAATTTCAATCCTACCC
1 ACTACAACTTCAG-GGGTATAAGATTTG-TAGCT-T--TATC-TTGCT--CC
* *
17038331 ACTGCAACTTCAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* * * * * * **
17038375 ACTGCAATTTCAAAGAG-ATAAGATTCGCTATTGTAGCTTCAAT-TTGATGT
1 ACTACAACTTC-AGGGGTATAAGA-----T-TTGTAGCTT-TATCTTGCTCC
* * * *
17038425 ACTATAACTTCAGGGGTATAAGATTTGTAGCTTTTTCTTACTCT
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
** * ***
17038469 ACTGTAACTTCAGGGAG-ATAAGATTTGCTATGGTAACTTCAATCCAAC-CC
1 ACTACAACTTCAGGG-GTATAAGATTTG-TA--G---CTT-TATCTTGCTCC
* * * * * * * * *
17038519 ATTGCAACTTCAGGGGTACAGGATTTGTAACATCATCTTACTTC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* * * *
17038563 ACTGCAACTTCAGAGAG-ATAAGATTTGCTATGGTAACTTGAATC-CGAC-CC
1 ACTACAACTTCAG-GGGTATAAGATTTG-TA--G---CTT-TATCTTG-CTCC
* * * * *
17038613 ACTGCAACTTTAGGGGTATAAGATTTATAGCTTCATCTTACTCC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* ** *
17038657 ATTGGAACTTCAGGGAG-ATAAGATTCTCTATTGTAGCTTCAAT-TTGAC-CC
1 ACTACAACTTCAGGG-GTATAAGA-----T-TTGTAGCTT-TATCTTG-CTCC
* * * * *
17038707 ACTACAACTTTAGGGTTATAAAATTTATAGCTTTATCTTGTTCC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* * ** *
17038751 ACTGCAACTTTAGATAG-ATAAGATTCGCTATTGTAGCTTCAAT-TTGAC-CC
1 ACTACAACTTCAG-GGGTATAAGA-----T-TTGTAGCTT-TATCTTG-CTCC
* * * * *
17038801 ACTACAACTTTAGGGTTATAAAATTTATAGCTTTATCTTGTTCC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* * ** *
17038845 ACTGCAACTTTAGATAG-ATAAGATTCGCTATTGTAGCTTCAAT-TTGAC-CC
1 ACTACAACTTCAG-GGGTATAAGA-----T-TTGTAGCTT-TATCTTG-CTCC
* * * * *
17038895 ACTACAACTTTAGGGTTATAAAATTTATAGCTTTATCTTGTTCC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* * ** * * *
17038939 ACTGCAACTTTAGATAG-ATAAGATTCGCTATTGTAGCTTCAATC-CGAC-CT
1 ACTACAACTTCAG-GGGTATAAGA-----T-TTGTAGCTT-TATCTTG-CTCC
*
17038989 ACTACAACTTCCA-GGGTATAGGATTTGTAGCTTTATCTTGCTCC
1 ACTACAACTT-CAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* * * * * *
17039033 ATTGCAACTTTAAAGAG-ATAAGATTCGCTATTGTAGCTTCAATC-TGAC-CC
1 ACTACAAC-TTCAGGGGTATAAGA-----T-TTGTAGCTT-TATCTTG-CTCC
* *
17039083 ACTACAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* * * * * *
17039127 ATTGCAACTTTAAAGAG-ATAAGATTCGCTATTGTAGCTTCAATC-TGAC-CC
1 ACTACAAC-TTCAGGGGTATAAGA-----T-TTGTAGCTT-TATCTTG-CTCC
* *
17039177 ACTACAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
* * * * * *
17039221 ATTGCAACTTTAAAGAG-ATAAGATTCGCTATTGTAGCTTCAATC-TGAC-CC
1 ACTACAAC-TTCAGGGGTATAAGA-----T-TTGTAGCTT-TATCTTG-CTCC
* * *
17039271 ACTACAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTTC
1 ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
17039315 ACTACAACTT
1 ACTACAACTT
17039325 TTATGATATA
Statistics
Matches: 1093, Mismatches: 234, Indels: 374
0.64 0.14 0.22
Matches are distributed among these distances:
43 47 0.04
44 445 0.41
45 55 0.05
46 6 0.01
47 14 0.01
48 6 0.01
49 58 0.05
50 414 0.38
51 48 0.04
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (44 bp):
ACTACAACTTCAGGGGTATAAGATTTGTAGCTTTATCTTGCTCC
Found at i:17039325 original size:44 final size:44
Alignment explanation
Indices: 17038989--17039513 Score: 177
Period size: 44 Copynumber: 11.3 Consensus size: 44
17038979 AATCCGACCT
*
17038989 ACTACAACTTCCA-GGGTATAGGATTTGTAGCTTTATCTTGCTCC
1 ACTACAACTT-TAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
* * * * * *
17039033 ATTGCAACTTTAAAGAG-ATAAGATTCGCTATTGTAGCTTCAATC-TGAC-CC
1 ACTACAACTTT-AGGGGTAT-AG----GAT-TTGTAGCTT-TATCTTG-CTCC
17039083 ACTACAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
1 ACTACAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
* * * * * *
17039127 ATTGCAACTTTAAAGAG-ATAAGATTCGCTATTGTAGCTTCAATC-TGAC-CC
1 ACTACAACTTT-AGGGGTAT-AG----GAT-TTGTAGCTT-TATCTTG-CTCC
17039177 ACTACAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
1 ACTACAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
* * * * * *
17039221 ATTGCAACTTTAAAGAG-ATAAGATTCGCTATTGTAGCTTCAATC-TGAC-CC
1 ACTACAACTTT-AGGGGTAT-AG----GAT-TTGTAGCTT-TATCTTG-CTCC
*
17039271 ACTACAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTTC
1 ACTACAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
* * * * * **
17039315 ACTACAACTTTTA-TGATATAAGA-TT-CA-CTATAATAACTTTAATCC
1 ACTACAAC-TTTAGGGGTATAGGATTTGTAGCT-T--TATC-TTGCTCC
* * * * *
17039360 AACCTATTGTAAGTTTA-GGGTATAAGATTTGTAGCTTCATCTTGTTCC
1 -A-CTA---CAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
* *
17039408 ACTACAACTTTAGGGAG-ATAGGATTCGCTATCGTAACTTTAATC-CGAC-CC
1 ACTACAACTTTAGGG-GTATAGGA-T---T-T-GTAGCTTT-ATCTTG-CTCC
*
17039458 ACTACAACTTTAGGGGTATAGGATTTGTAGCTTCATCTTGCTCC
1 ACTACAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
*
17039502 ACTGCAACTTTA
1 ACTACAACTTTA
17039514 AAGTGATAAG
Statistics
Matches: 353, Mismatches: 65, Indels: 126
0.65 0.12 0.23
Matches are distributed among these distances:
41 2 0.01
42 2 0.01
43 24 0.07
44 116 0.33
45 31 0.09
46 5 0.01
47 4 0.01
48 6 0.02
49 38 0.11
50 106 0.30
51 17 0.05
52 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (44 bp):
ACTACAACTTTAGGGGTATAGGATTTGTAGCTTTATCTTGCTCC
Found at i:17046457 original size:11 final size:11
Alignment explanation
Indices: 17046443--17046468 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17046433 AAATAATATT
17046443 ATAATAAAAGA
1 ATAATAAAAGA
17046454 ATAATAAAAGA
1 ATAATAAAAGA
17046465 ATAA
1 ATAA
17046469 AATTATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (11 bp):
ATAATAAAAGA
Found at i:17046652 original size:8 final size:8
Alignment explanation
Indices: 17046639--17046667 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
17046629 AAAGTGCCAG
17046639 AAATAAAA
1 AAATAAAA
17046647 AAAT-AAA
1 AAATAAAA
17046654 AAATAAAA
1 AAATAAAA
17046662 AAATAA
1 AAATAA
17046668 GTAGGTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATAAAA
Found at i:17046657 original size:15 final size:15
Alignment explanation
Indices: 17046639--17046667 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17046629 AAAGTGCCAG
17046639 AAATAAAAAAATAAA
1 AAATAAAAAAATAAA
17046654 AAATAAAAAAATAA
1 AAATAAAAAAATAA
17046668 GTAGGTAAAG
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
AAATAAAAAAATAAA
Found at i:17047560 original size:21 final size:21
Alignment explanation
Indices: 17047534--17047585 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
17047524 AATGAACTAC
*
17047534 TTTTTTTTGAACTTCG-TTGTT
1 TTTTTTTTGAA-TTCGATTCTT
*
17047555 TTTTTTTTGTATTCGATTTCTT
1 TTTTTTTTGAATTCGA-TTCTT
17047577 TTTTTTTTG
1 TTTTTTTTG
17047586 TTACAATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 4 0.15
21 10 0.37
22 13 0.48
ACGTcount: A:0.08, C:0.08, G:0.12, T:0.73
Consensus pattern (21 bp):
TTTTTTTTGAATTCGATTCTT
Found at i:17059968 original size:26 final size:27
Alignment explanation
Indices: 17059918--17059972 Score: 103
Period size: 26 Copynumber: 2.1 Consensus size: 27
17059908 ATCACTAACT
17059918 AATACTAATCTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
17059945 AATACTAATCTAA-ACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
17059971 AA
1 AA
17059973 AAATAGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.55, C:0.11, G:0.07, T:0.27
Consensus pattern (27 bp):
AATACTAATCTAATACTAATAGAATAG
Found at i:17059995 original size:13 final size:13
Alignment explanation
Indices: 17059961--17059987 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17059951 AATCTAAACT
17059961 AATAGAATAGAAA
1 AATAGAATAGAAA
17059974 AATAGAATAGAAA
1 AATAGAATAGAAA
17059987 A
1 A
17059988 TACTAATATA
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:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AATAGAATAGAAA
Found at i:17060492 original size:10 final size:10
Alignment explanation
Indices: 17060477--17060501 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17060467 GATGGAAGGG
17060477 AAAAAAATAA
1 AAAAAAATAA
17060487 AAAAAAATAA
1 AAAAAAATAA
17060497 AAAAA
1 AAAAA
17060502 GAGGGGAAAA
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:17062669 original size:27 final size:28
Alignment explanation
Indices: 17062613--17062674 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
17062603 TGTCAAATGA
17062613 TTTTAACTTTACTTATAAAAGTTGGTTT
1 TTTTAACTTTACTTATAAAAGTTGGTTT
17062641 TTTTAACTTTACTTATAAAAGTTGGTTT
1 TTTTAACTTTACTTATAAAAGTTGGTTT
*
17062669 TCTTAA
1 TTTTAA
17062675 TAACTTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (28 bp):
TTTTAACTTTACTTATAAAAGTTGGTTT
Found at i:17062680 original size:26 final size:27
Alignment explanation
Indices: 17062623--17062680 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
17062613 TTTTAACTTT
* *
17062623 ACTTATAAAAGTTGGTTTTTTTAACTTT
1 ACTTATAAAAGTTGGTTTTCTTAAC-TA
17062651 ACTTATAAAAGTTGGTTTTCTTAA-TA
1 ACTTATAAAAGTTGGTTTTCTTAACTA
17062677 ACTT
1 ACTT
17062681 TAATGTAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.18
28 23 0.82
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (27 bp):
ACTTATAAAAGTTGGTTTTCTTAACTA
Found at i:17068250 original size:40 final size:39
Alignment explanation
Indices: 17068194--17068328 Score: 209
Period size: 40 Copynumber: 3.4 Consensus size: 39
17068184 ATGATAACCG
17068194 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
17068233 GAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 G-GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* *
17068273 GGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATATCC
1 -GGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
*
17068313 GGCTAAATCCCGAAGG
1 GGCTAAGTCCCGAAGG
17068329 TACTTGGTTT
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
39 18 0.20
40 71 0.79
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:17076207 original size:39 final size:40
Alignment explanation
Indices: 17076110--17076207 Score: 162
Period size: 40 Copynumber: 2.5 Consensus size: 40
17076100 CGGATAATAA
* *
17076110 CCGGGCTAAGTTCCGAAGGCATTTGAGCGAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTAGCTATAT
17076150 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTAGCTATAT
*
17076190 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
17076208 TACTTGGTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 15 0.27
40 40 0.73
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTAGCTATAT
Found at i:17083864 original size:242 final size:245
Alignment explanation
Indices: 17083569--17084334 Score: 791
Period size: 242 Copynumber: 3.1 Consensus size: 245
17083559 TAATAAACAA
* * * * * **
17083569 TAATATCTAATGTACTCCTATTATATATAACTATTATTGTAATATAAATTATAATAAAAGGTATA
1 TAATATATAATGTACTACTATTATATATAACTATCATTATATTATAAATTATAATAAAAAATATA
* *
17083634 GTATTATATGATATTATAATGTTTAATCGTAGATGCATATATACAAACTATTA-ATAT-T-TGAT
66 GTATTATATGATATTATAATGTTTAATCATTGATGCATATATACAAACTATTATATATATATGAT
*
17083696 ATGATATAACATTATATGATATAGTAGGAGGCTAATTTTCAAATGAACGAAAAGTATAGGGGCTT
131 ATGATATAACATTATATAATATAGTAGGAGGCTAATTTTCAAATGAACGAAAAGTATAGGGGCTT
17083761 AGAGCATATTTCAACTAGTATAATAATAAACAATAATATATAATAATATG
196 AGAGCATATTTCAACTAGTATAATAATAAACAATAATATATAATAATATG
* *
17083811 TAGTATATAATGTACTACTATTATATATAACTATCATTATATTATAGATTATAATAAAAAATATA
1 TAATATATAATGTACTACTATTATATATAACTATCATTATATTATAAATTATAATAAAAAATATA
* * * *
17083876 ATATTATATGATATTATAATGTTTAATCATTTATGCATATGTATAAACTATTAATATTTTATATA
66 GTATTATATGATATTATAATGTTTAATCATTGATGCATATATACAAACTA-T--TA---TATATA
* * * * * *
17083941 CTATACTATATGATATACCATTATATAATATAATAGGAGAGATAACTTTCAAATGTACGAAAAGT
125 -TAT--GATATGATATAACATTATATAATATAGTAGGAG-GCTAATTTTCAAATGAACGAAAAGT
* * *
17084006 ATAGGGACTTA-AGGCATATTTCATCCAG--T-ATAAT----AAT-A-A-ATAATAATATG
186 ATAGGGGCTTAGA-GCATATTTCAACTAGTATAATAATAAACAATAATATATAATAATATG
* * * * *
17084056 TAATATATAATGTACTACCATTATGTGTAACTATCATTATATTATATATTATAATAAAATATATA
1 TAATATATAATGTACTACTATTATATATAACTATCATTATATTATAAATTATAATAAAAAATATA
* * * *
17084121 GTATTACATGATATTAT-ATCGCTTAATAATTGATGCACATATATAAACTATTAATATATTATAT
66 GTATTATATGATATTATAAT-GTTTAATCATTGATG--CATATAT--AC-A--AA-CTATTATAT
* *
17084185 ACTATATGATATGATATAATATTATATAATATAGTA--AGACTAATTTTCAAAT-ATACGAAAAG
122 A-TATATGATATGATATAACATTATATAATATAGTAGGAGGCTAATTTTCAAATGA-ACGAAAAG
* * *
17084247 TATAAGGGCATAGAGCATA-TTCAACTGGTATAATAATAAACAATAATATAGT-ATAATAAT-
185 TATAGGGGCTTAGAGCATATTTCAACTAGTATAATAATAAACAATAATATA-TAATAAT-ATG
*
17084307 TAATATATATGATGAACTACTATTATAT
1 TAATATATA--ATGTACTACTATTATAT
17084335 TATAGAATAA
Statistics
Matches: 428, Mismatches: 56, Indels: 69
0.77 0.10 0.12
Matches are distributed among these distances:
241 6 0.01
242 133 0.31
243 5 0.01
244 7 0.02
245 124 0.29
246 1 0.00
247 14 0.03
248 8 0.02
249 6 0.01
250 4 0.01
251 16 0.04
252 12 0.03
253 17 0.04
254 30 0.07
255 45 0.11
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (245 bp):
TAATATATAATGTACTACTATTATATATAACTATCATTATATTATAAATTATAATAAAAAATATA
GTATTATATGATATTATAATGTTTAATCATTGATGCATATATACAAACTATTATATATATATGAT
ATGATATAACATTATATAATATAGTAGGAGGCTAATTTTCAAATGAACGAAAAGTATAGGGGCTT
AGAGCATATTTCAACTAGTATAATAATAAACAATAATATATAATAATATG
Found at i:17083934 original size:27 final size:24
Alignment explanation
Indices: 17083874--17083934 Score: 59
Period size: 27 Copynumber: 2.3 Consensus size: 24
17083864 ATAAAAAATA
**
17083874 TAATATTATATGATATTATAATGTT
1 TAATATT-TATGATATTATAAACTT
17083899 TAATCATTTATGCATATGTATAAACTAT
1 TAAT-ATTTATG-ATAT-TATAAACT-T
17083927 TAATATTT
1 TAATATTT
17083935 TATATACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 8 0.27
26 7 0.23
27 10 0.33
28 5 0.17
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (24 bp):
TAATATTTATGATATTATAAACTT
Found at i:17084111 original size:245 final size:244
Alignment explanation
Indices: 17083363--17084497 Score: 1003
Period size: 245 Copynumber: 4.7 Consensus size: 244
17083353 AATATACATA
* * * *
17083363 TAACTA-CTATTATAATATAGATTATAATAAAAGATATAGTATTACATAATATTATAATGTTTAA
1 TAACTATC-ATTATATTATAGATTATAATAAAAAATATAATATTACATGATATTATAATGTTTAA
** *** *
17083427 TCATCAACATATATATATACACACTATTAATA-TTT-TATACGATATGATAT-AT-T---ATTAT
65 TCATTTATGCATATATATA-A-ACTATTAATATTTTATATACTATATGATATGATATAACATTAT
* * * * * * * *
17083485 ATAATATAGCAGGAGGGCTAACTTTTAAATGTACGAAAATTATAGAGACTTAAAGAATATTTCAA
128 ATAATATAGTAGGAGAGATAACTTTCAAATGTACGAAAAGTATAG-GGCTTAGAGCATATTTCAA
* * * *
17083550 CTAGT-T--TAAT-AATAA-ACA-A--TAATATCTAATGTACTCCTATTATATA
192 CTAGTATAATAATAAATAATA-ATATGTAATATATAATGTACTACTATTATGTG
* * * * ** * *
17083596 TAACTATTATTGTAATATAAATTATAATAAAAGGTATAGTATTATATGATATTATAATGTTTAAT
1 TAACTATCATTATATTATAGATTATAATAAAAAATATAATATTACATGATATTATAATGTTTAAT
* ** * *
17083661 CGTAGATGCATATATACAAAC------TA--TTA-ATA-T-T-TGATATGATATAACATTATATG
66 CATTTATGCATATATATAAACTATTAATATTTTATATACTATATGATATGATATAACATTATATA
* * *
17083714 ATATAGTAGGAG-GCTAATTTTCAAATGAACGAAAAGTATAGGGGCTTAGAGCATATTTCAACTA
131 ATATAGTAGGAGAGATAACTTTCAAATGTACGAAAAGTATA-GGGCTTAGAGCATATTTCAACTA
* * *
17083778 GTATAATAATAAACAATAATATATAATAATATGTAGTATATAATGTACTACTATTATATA
195 G--T-ATAAT----AAT-A-A-ATAATAATATGTAATATATAATGTACTACTATTATGTG
*
17083838 TAACTATCATTATATTATAGATTATAATAAAAAATATAATATTATATGATATTATAATGTTTAAT
1 TAACTATCATTATATTATAGATTATAATAAAAAATATAATATTACATGATATTATAATGTTTAAT
* *
17083903 CATTTATGCATATGTATAAACTATTAATATTTTATATACTATACT-ATATGATATACCATTATAT
66 CATTTATGCATATATATAAACTATTAATATTTTATATACTATA-TGATATGATATAACATTATAT
* *
17083967 AATATAATAGGAGAGATAACTTTCAAATGTACGAAAAGTATAGGGACTTA-AGGCATATTTCATC
130 AATATAGTAGGAGAGATAACTTTCAAATGTACGAAAAGTATAGGG-CTTAGA-GCATATTTCAAC
* *
17084031 CAGTATAATAATAAATAATAATATGTAATATATAATGTACTACCATTATGTG
193 TAGTATAATAATAAATAATAATATGTAATATATAATGTACTACTATTATGTG
* * * *
17084083 TAACTATCATTATATTATATATTATAATAAAATATATAGTATTACATGATATTAT-ATCGCTTAA
1 TAACTATCATTATATTATAGATTATAATAAAAAATATAATATTACATGATATTATAAT-GTTTAA
* * * * *
17084147 TAATTGATGCACATATATAAACTATTAATATATTATATACTATATGATATGATATAATATTATAT
65 TCATTTATGCATATATATAAACTATTAATATTTTATATACTATATGATATGATATAACATTATAT
* * * *
17084212 AATATAGTA--AGA-CTAATTTTCAAATATACGAAAAGTATAAGGGCATAGAGCATA-TTCAACT
130 AATATAGTAGGAGAGATAACTTTCAAATGTACGAAAAGTAT-AGGGCTTAGAGCATATTTCAACT
* * *
17084273 GGTATAATAATAAACAATAATATAGT-ATA-ATAAT-TAATA-TA-TATGATG
194 AGTATAATAATAAATAATAATAT-GTAATATATAATGTACTACTATTATG-TG
* ** * **
17084321 -AACTA-CTATTATATTATAGAATA-ACATAAAAGGTATTATATTACATGATATTATAACATTTA
1 TAACTATC-ATTATATTATAGATTATA-ATAAAAAATATAATATTACATGATATTATAATGTTTA
17084383 ATCATTAATGCATATGCATATATATAAACTATTAATATATTT-TATACTATATGATATGATATAA
64 ATCA-T--T---TATGCATATATATAAACTATTAATAT-TTTATATACTATATGATATGATATAA
* *
17084447 CATTATATAATATAGTAGGAGAGCA-AACTTTCAAATGTAGGAAAAATATAG
122 CATTATATAATATAGTAGGAGAG-ATAACTTTCAAATGTACGAAAAGTATAG
17084498 AGATTTAGAG
Statistics
Matches: 748, Mismatches: 92, Indels: 112
0.79 0.10 0.12
Matches are distributed among these distances:
221 6 0.01
222 3 0.00
223 1 0.00
224 5 0.01
225 46 0.06
226 19 0.03
227 1 0.00
229 1 0.00
231 3 0.00
232 1 0.00
233 69 0.09
235 3 0.00
236 2 0.00
237 54 0.07
238 6 0.01
239 9 0.01
240 8 0.01
241 29 0.04
242 131 0.18
243 70 0.09
244 5 0.01
245 159 0.21
246 21 0.03
247 1 0.00
248 5 0.01
250 3 0.00
251 3 0.00
252 6 0.01
253 2 0.00
254 33 0.04
255 43 0.06
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.38
Consensus pattern (244 bp):
TAACTATCATTATATTATAGATTATAATAAAAAATATAATATTACATGATATTATAATGTTTAAT
CATTTATGCATATATATAAACTATTAATATTTTATATACTATATGATATGATATAACATTATATA
ATATAGTAGGAGAGATAACTTTCAAATGTACGAAAAGTATAGGGCTTAGAGCATATTTCAACTAG
TATAATAATAAATAATAATATGTAATATATAATGTACTACTATTATGTG
Found at i:17084878 original size:27 final size:27
Alignment explanation
Indices: 17084835--17084888 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
17084825 GGTATTAGAC
* *
17084835 TTGAGATTTGGGCATAATTAGTTTATT
1 TTGAGATTTGGGCATAATGAGTATATT
*
17084862 TTGAG-TTTGGGTGATAATGAGTATATT
1 TTGAGATTTGGG-CATAATGAGTATATT
17084889 GTTTGGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.46
Consensus pattern (27 bp):
TTGAGATTTGGGCATAATGAGTATATT
Found at i:17086026 original size:44 final size:44
Alignment explanation
Indices: 17085976--17086063 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
17085966 CCCTAAGGGA
17085976 AAACTCCAAAAACCGTAAGCTTTTAGCCATTAAATTTGTGAGTT
1 AAACTCCAAAAACCGTAAGCTTTTAGCCATTAAATTTGTGAGTT
17086020 AAACTCCAAAAACCGTAAGCTTTTAGCCATTAAATTTGTGAGTT
1 AAACTCCAAAAACCGTAAGCTTTTAGCCATTAAATTTGTGAGTT
17086064 CAATTAGGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (44 bp):
AAACTCCAAAAACCGTAAGCTTTTAGCCATTAAATTTGTGAGTT
Found at i:17086756 original size:21 final size:21
Alignment explanation
Indices: 17086732--17086787 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
17086722 AACAGCGGTG
* *
17086732 GCGGTAAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
17086753 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
17086774 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
17086788 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:17088929 original size:20 final size:20
Alignment explanation
Indices: 17088904--17088949 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
17088894 ATTGGGCCTT
17088904 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
17088924 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
17088943 GCCCATA
1 GCCCATA
17088950 ACAAAATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:17090752 original size:180 final size:180
Alignment explanation
Indices: 17090450--17090812 Score: 699
Period size: 180 Copynumber: 2.0 Consensus size: 180
17090440 GAAGGAAGAA
17090450 TTCGGTACTTAGGAGATCTAACTTTGCATTTTTCGGCTTTTTGAGATACTGAGAAGAGAATAGAA
1 TTCGGTACTTAGGAGATCTAACTTTGCATTTTTCGGCTTTTTGAGATACTGAGAAGAGAATAGAA
*
17090515 TGAAAGGGAAGGCTCTAGGTGGCTAACCCGAATTCGGTAAAACAAAAAGAAAATAAAGCTTGCCC
66 TGAAAGGGAAGGCTCTAGGGGGCTAACCCGAATTCGGTAAAACAAAAAGAAAATAAAGCTTGCCC
*
17090580 TAATGGCCATTCAAACCCACGGCCCAACCTTCTTAAAGCCCTAATCGAAT
131 TAATGGCCATTCAAACCCACGGCCCAACCTTCCTAAAGCCCTAATCGAAT
17090630 TTCGGTACTTAGGAGATCTAACTTTGCATTTTTCGGCTTTTTGAGATACTGAGAAGAGAATAGAA
1 TTCGGTACTTAGGAGATCTAACTTTGCATTTTTCGGCTTTTTGAGATACTGAGAAGAGAATAGAA
*
17090695 TGAAAGGGAAGGCTCTAGGGGGCTAACCCTAATTCGGTAAAACAAAAAGAAAATAAAGCTTGCCC
66 TGAAAGGGAAGGCTCTAGGGGGCTAACCCGAATTCGGTAAAACAAAAAGAAAATAAAGCTTGCCC
17090760 TAATGGCCATTCAAACCCACGGCCCAACCTTCCTAAAGCCCTAATCGAAT
131 TAATGGCCATTCAAACCCACGGCCCAACCTTCCTAAAGCCCTAATCGAAT
17090810 TTC
1 TTC
17090813 TACTTAAGCT
Statistics
Matches: 180, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
180 180 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (180 bp):
TTCGGTACTTAGGAGATCTAACTTTGCATTTTTCGGCTTTTTGAGATACTGAGAAGAGAATAGAA
TGAAAGGGAAGGCTCTAGGGGGCTAACCCGAATTCGGTAAAACAAAAAGAAAATAAAGCTTGCCC
TAATGGCCATTCAAACCCACGGCCCAACCTTCCTAAAGCCCTAATCGAAT
Found at i:17095180 original size:32 final size:32
Alignment explanation
Indices: 17095112--17095240 Score: 222
Period size: 32 Copynumber: 4.0 Consensus size: 32
17095102 CATAAAAAAT
17095112 ATCATACATTAGTTTTACATATAAAAAAAGTAG
1 ATCATACATTAGTTTTACATAT-AAAAAAGTAG
* *
17095145 ATCATACATTAGGTTTACATATAAAAAAGTTG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
*
17095177 ATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
17095209 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
17095241 TATAGTTATA
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 69 0.77
33 21 0.23
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (32 bp):
ATCATACATTAGTTTTACATATAAAAAAGTAG
Found at i:17095973 original size:7 final size:7
Alignment explanation
Indices: 17095961--17095994 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
17095951 CCTACAAAAC
17095961 ATGTTAA
1 ATGTTAA
17095968 ATGTTAA
1 ATGTTAA
17095975 ATGTTAA
1 ATGTTAA
17095982 ATGTTAA
1 ATGTTAA
17095989 ATGTTA
1 ATGTTA
17095995 TACTCAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (7 bp):
ATGTTAA
Found at i:17097539 original size:24 final size:22
Alignment explanation
Indices: 17097494--17097542 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 22
17097484 TTTAGATCGA
*
17097494 TTTAATTTTTTGTTTTTATTAT
1 TTTAATTTTTTGTCTTTATTAT
17097516 TTTAATTTGTTTAGTCTTTATTAT
1 TTTAATTT-TTT-GTCTTTATTAT
17097540 TTT
1 TTT
17097543 TACCAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.33
23 3 0.12
24 13 0.54
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.73
Consensus pattern (22 bp):
TTTAATTTTTTGTCTTTATTAT
Found at i:17100615 original size:41 final size:39
Alignment explanation
Indices: 17100570--17100702 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 39
17100560 CAGTTCAGCC
*
17100570 GATGATGCATTACGTGCCAGTATAATTGCTTTGGTATATTT
1 GATGATGCATTACATGCCAGTAT-ATTG-TTTGGTATATTT
* * * * * *
17100611 GATGATGCAATTACATGTCAGTATTTTTTTTAGTACATCT
1 GATGATGC-ATTACATGCCAGTATATTGTTTGGTATATTT
* *
17100651 GATGATGCACTTTGCATGCCAGTATGATTGTTTCGGTTTATTT
1 GATGATGCA--TTACATGCCAGTAT-ATTGTTT-GGTATATTT
17100694 GATGATGCA
1 GATGATGCA
17100703 CTATGTGTGC
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
39 1 0.01
40 17 0.24
41 22 0.31
42 18 0.25
43 14 0.19
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (39 bp):
GATGATGCATTACATGCCAGTATATTGTTTGGTATATTT
Found at i:17100751 original size:43 final size:43
Alignment explanation
Indices: 17100647--17100753 Score: 151
Period size: 43 Copynumber: 2.5 Consensus size: 43
17100637 TTTTTAGTAC
* ** * *
17100647 ATCTGATGATGCACTTTGCATGCCAGTATGATTGTTTCGGTTT
1 ATCTGATGATGCACTATGTGTGCCAATATGATTGGTTCGGTTT
*
17100690 ATTTGATGATGCACTATGTGTGCCAATATGATTGGTTCGGTTT
1 ATCTGATGATGCACTATGTGTGCCAATATGATTGGTTCGGTTT
*
17100733 GTCTGATGATGCACTATGTGT
1 ATCTGATGATGCACTATGTGT
17100754 TCCAGTATAC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (43 bp):
ATCTGATGATGCACTATGTGTGCCAATATGATTGGTTCGGTTT
Found at i:17100823 original size:43 final size:43
Alignment explanation
Indices: 17100737--17100834 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
17100727 CGGTTTGTCT
17100737 GATGATGCACTATGTGTTCCAGTATACATTTTTTGGTACATCC
1 GATGATGCACTATGTGTTCCAGTATACATTTTTTGGTACATCC
* * * **
17100780 GGTGATGCACTATGTGTGT-CAGTATA-TTTTCTTTTGTTTATCC
1 GATGATGCACTATGTGT-TCCAGTATACATTT-TTTGGTACATCC
17100823 GATGATGCACTA
1 GATGATGCACTA
17100835 CAGTGCAAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 3 0.06
43 43 0.91
44 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.42
Consensus pattern (43 bp):
GATGATGCACTATGTGTTCCAGTATACATTTTTTGGTACATCC
Found at i:17111052 original size:20 final size:18
Alignment explanation
Indices: 17111029--17111078 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
17111019 ACAGAGAGTT
17111029 ACACGGGCGTGTCCAGAGCC
1 ACACGGGCGTGT-CAGA-CC
* *
17111049 ACACGGGTGTGTGAGACC
1 ACACGGGCGTGTCAGACC
*
17111067 ATACGGGCGTGT
1 ACACGGGCGTGT
17111079 GACTCTCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 12 0.46
19 3 0.12
20 11 0.42
ACGTcount: A:0.20, C:0.26, G:0.38, T:0.16
Consensus pattern (18 bp):
ACACGGGCGTGTCAGACC
Found at i:17116470 original size:10 final size:9
Alignment explanation
Indices: 17116455--17116505 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
17116445 TATCAAAATT
17116455 ATAATATAA
1 ATAATATAA
17116464 CATAATATAA
1 -ATAATATAA
*
17116474 ATATTATAA
1 ATAATATAA
*
17116483 AAAATTATAA
1 ATAA-TATAA
17116493 A-ACATATAA
1 ATA-ATATAA
17116502 ATAA
1 ATAA
17116506 GGAGTTGAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
9 18 0.51
10 17 0.49
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (9 bp):
ATAATATAA
Found at i:17119566 original size:13 final size:13
Alignment explanation
Indices: 17119550--17119608 Score: 66
Period size: 13 Copynumber: 4.4 Consensus size: 13
17119540 AAGTCTAGAG
17119550 AAAAAGAGAAAGA
1 AAAAAGAGAAAGA
*
17119563 AAAAAGAAAAAGA
1 AAAAAGAGAAAGA
17119576 AAAGAAGA-AAGAGA
1 AAA-AAGAGAA-AGA
*
17119590 AAAAAAAGAAAGA
1 AAAAAGAGAAAGA
17119603 ATAAAA
1 A-AAAA
17119609 TAAAATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
13 24 0.60
14 16 0.40
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAAAGAGAAAGA
Found at i:17119572 original size:6 final size:6
Alignment explanation
Indices: 17119548--17119600 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
17119538 TAAAGTCTAG
* *
17119548 AGAAAA AGAGAA AGAAAAA AGAAAA AG-AAA AGAAGAA AGAGAA A-AAAA
1 AGAAAA AGAAAA AG-AAAA AGAAAA AGAAAA AGAA-AA AGAAAA AGAAAA
17119596 AGAAA
1 AGAAA
17119601 GAATAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 9 0.23
6 20 0.51
7 10 0.26
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:17119579 original size:18 final size:18
Alignment explanation
Indices: 17119548--17119600 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
17119538 TAAAGTCTAG
17119548 AGAAAAAGAGAAAGAAAAA
1 AGAAAAAGA-AAAGAAAAA
*
17119567 AGAAAAAGAAAAGAAGAA
1 AGAAAAAGAAAAGAAAAA
17119585 AGAGAAAA-AAAAGAAA
1 AGA-AAAAGAAAAGAAA
17119601 GAATAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 18 0.58
19 13 0.42
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAAAAGAAAAA
Found at i:17119608 original size:14 final size:14
Alignment explanation
Indices: 17119556--17119608 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
17119546 AGAGAAAAAG
17119556 AGAAAGAAAAAAGAA
1 AGAAA-AAAAAAGAA
*
17119571 A-AAGAAAAGAAGAA
1 AGAA-AAAAAAAGAA
17119585 AGAGAAAAAAAAGAA
1 AGA-AAAAAAAAGAA
17119600 AGAATAAAA
1 AGAA-AAAA
17119609 TAAAATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 12 0.38
15 19 0.59
16 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AGAAAAAAAAAGAA
Found at i:17125890 original size:16 final size:16
Alignment explanation
Indices: 17125869--17125900 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17125859 TACAAAAACA
17125869 GGCTATAAAAGTTTTT
1 GGCTATAAAAGTTTTT
17125885 GGCTATAAAAGTTTTT
1 GGCTATAAAAGTTTTT
17125901 CCTTCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (16 bp):
GGCTATAAAAGTTTTT
Found at i:17135038 original size:17 final size:17
Alignment explanation
Indices: 17135016--17135048 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17135006 TTCTTATCAT
*
17135016 TTATTATTTATCGGGCA
1 TTATTATTGATCGGGCA
17135033 TTATTATTGATCGGGC
1 TTATTATTGATCGGGC
17135049 TTTGTCAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (17 bp):
TTATTATTGATCGGGCA
Found at i:17146969 original size:31 final size:31
Alignment explanation
Indices: 17146926--17146989 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
17146916 CCTTTTCATA
17146926 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
17146957 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
17146988 TT
1 TT
17146990 ACGGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:17147258 original size:23 final size:24
Alignment explanation
Indices: 17147182--17147325 Score: 204
Period size: 24 Copynumber: 6.0 Consensus size: 24
17147172 GCTTTTTCAT
*
17147182 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
17147207 ATAACTGGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
17147232 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
17147255 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
17147279 ATAACTAGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
17147303 ATAATTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
17147326 GCACTTCCTC
Statistics
Matches: 110, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
23 24 0.22
24 55 0.50
25 25 0.23
26 6 0.05
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:17147396 original size:9 final size:9
Alignment explanation
Indices: 17147382--17147458 Score: 55
Period size: 9 Copynumber: 7.9 Consensus size: 9
17147372 ATCTCGTGTG
17147382 CATATCATA
1 CATATCATA
*
17147391 CATATCATGTG
1 CATATCA--TA
17147402 CATATCATA
1 CATATCATA
* *
17147411 CATGTCATGTG
1 CATATCA--TA
17147422 CATATCATA
1 CATATCATA
*
17147431 CATATCATGTG
1 CATATCA--TA
*
17147442 CATATTATA
1 CATATCATA
17147451 CATATCAT
1 CATATCAT
17147459 GTTTATCAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
9 30 0.58
11 22 0.42
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (9 bp):
CATATCATA
Found at i:17147401 original size:20 final size:20
Alignment explanation
Indices: 17147378--17147460 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
17147368 GAACATCTCG
17147378 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
17147398 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
17147418 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
17147438 TGTGCATATTATACATATCA
1 TGTGCATATCATACATATCA
17147458 TGT
1 TGT
17147461 TTATCAAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:17147525 original size:25 final size:25
Alignment explanation
Indices: 17147497--17147544 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
17147487 ATATATAAAC
* * *
17147497 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
17147522 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
17147545 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:17155104 original size:31 final size:31
Alignment explanation
Indices: 17155061--17155124 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
17155051 CCTTTTCATA
17155061 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
17155092 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
17155123 TT
1 TT
17155125 ATGGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:17155410 original size:24 final size:24
Alignment explanation
Indices: 17155344--17156396 Score: 2074
Period size: 24 Copynumber: 43.9 Consensus size: 24
17155334 CTATTTTAGG
17155344 AACTGGGGCA-AAGCCCTTTTTTAAT
1 AACTGGGGCATAAGCCC--TTTTAAT
17155369 AACTGGGGCATAAG-CCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155392 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155416 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155440 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155464 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155488 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155512 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155536 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155560 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155584 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155608 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155632 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155656 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155680 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155704 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155728 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155752 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155776 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155800 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155824 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155848 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155872 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155896 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155920 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155944 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155968 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17155992 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156016 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156040 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156064 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156088 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156112 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156136 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156160 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156184 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156208 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156232 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156256 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156280 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156304 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156328 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156352 AACTGGGGCATAAGCCCTTTTAAT
1 AACTGGGGCATAAGCCCTTTTAAT
17156376 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
17156397 GCACTTCCTC
Statistics
Matches: 1026, Mismatches: 0, Indels: 5
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 0.02
24 990 0.96
25 12 0.01
26 3 0.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
AACTGGGGCATAAGCCCTTTTAAT
Found at i:17156472 original size:20 final size:20
Alignment explanation
Indices: 17156449--17156511 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
17156439 GAACATCTCG
*
17156449 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
*
17156469 TGTGGATATCATACATATCA
1 TGTGCATATCATACATATCA
17156489 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
17156509 TGT
1 TGT
17156512 TTATCAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:17159534 original size:22 final size:22
Alignment explanation
Indices: 17159499--17159541 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17159489 CTACGATATT
*
17159499 TACGGCCTTTAGCCGTCCTGTC
1 TACGGCCTTGAGCCGTCCTGTC
* *
17159521 TACGGCGTTGAGCCGTTCTGT
1 TACGGCCTTGAGCCGTCCTGT
17159542 TAACTTAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.30, G:0.28, T:0.33
Consensus pattern (22 bp):
TACGGCCTTGAGCCGTCCTGTC
Found at i:17168647 original size:41 final size:42
Alignment explanation
Indices: 17168578--17168696 Score: 127
Period size: 41 Copynumber: 2.8 Consensus size: 42
17168568 TGGCATCAAT
* * *
17168578 ATATGTGATTACGTATAATACCATGTCTGGGACATCGACATCG
1 ATATGTGATTACGTGTAAGACCCTGTCTGGGACAT-GACATCG
* * *
17168621 -TATTTGATT-CGTGTAAGACCCTGTCTGGGATAGTGGCATCG
1 ATATGTGATTACGTGTAAGACCCTGTCTGGGACA-TGACATCG
*
17168662 ATATGTGATTACATGTAAGACCAC-GTCTGGGACAT
1 ATATGTGATTACGTGTAAGACC-CTGTCTGGGACAT
17168697 TGGCATTGTA
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
41 25 0.40
42 18 0.29
43 19 0.30
44 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
ATATGTGATTACGTGTAAGACCCTGTCTGGGACATGACATCG
Found at i:17173321 original size:14 final size:13
Alignment explanation
Indices: 17173298--17173329 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
17173288 GAAATATCAA
17173298 AACAATAATTAAG
1 AACAATAATTAAG
17173311 AACACATAATTAAG
1 AACA-ATAATTAAG
17173325 AACAA
1 AACAA
17173330 GTCAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:17186185 original size:40 final size:41
Alignment explanation
Indices: 17186009--17186221 Score: 200
Period size: 41 Copynumber: 5.2 Consensus size: 41
17185999 GTTAGTAATA
* * *
17186009 AAACGCCA-TAAAAAAATGAGTAATAGCGGCGTTTTTATT-C
1 AAACGCCACT-AAAAACTGAGAAATAGCGGCGTTTTTGTTCC
* *
17186049 AAATCGCCACTAAAAACTGAGCAATAGCGGCGTTTTTGGTCC
1 AAA-CGCCACTAAAAACTGAGAAATAGCGGCGTTTTTGTTCC
* * * *
17186091 AAACACCGCTAAAAATTGAGAAATAGTGGCGTTTTTG-TCC
1 AAACGCCACTAAAAACTGAGAAATAGCGGCGTTTTTGTTCC
* *
17186131 AAACGCCACTAAAAACTAAGAAATAGCGGCGTTTTTGTTAC
1 AAACGCCACTAAAAACTGAGAAATAGCGGCGTTTTTGTTCC
** * *** *
17186172 AAACGCTGC-AAAAAGTTGATCTATAGCGGCGTTTTTTTATCC
1 AAACGCCACTAAAAA-CTGAGAAATAGCGGCGTTTTTGT-TCC
17186214 AAACGCCA
1 AAACGCCA
17186222 TAAGAAGTTG
Statistics
Matches: 141, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
40 43 0.30
41 85 0.60
42 13 0.09
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (41 bp):
AAACGCCACTAAAAACTGAGAAATAGCGGCGTTTTTGTTCC
Found at i:17186203 original size:81 final size:81
Alignment explanation
Indices: 17186019--17186221 Score: 237
Period size: 81 Copynumber: 2.5 Consensus size: 81
17186009 AAACGCCATA
* * * * *
17186019 AAAAAATGAGTAATAGCGGCGTTTTTATTCAAATCGCCACTAAAAACTGAGCAATAGCGGCGTTT
1 AAAAATTGAGAAATAGCGGCGTTTTTATCCAAA-CGCCACTAAAAACTAAGAAATAGCGGCGTTT
*
17186084 TTGGTCCAAACACCGCT
65 TTGGTACAAACACCGCT
* *
17186101 AAAAATTGAGAAATAGTGGCGTTTTTGTCCAAACGCCACTAAAAACTAAGAAATAGCGGCGTTTT
1 AAAAATTGAGAAATAGCGGCGTTTTTATCCAAACGCCACTAAAAACTAAGAAATAGCGGCGTTTT
* * *
17186166 TGTTACAAACGCTGC-
66 TGGTACAAACACCGCT
***
17186181 AAAAAGTTGATCTATAGCGGCGTTTTTTTATCCAAACGCCA
1 AAAAA-TTGAGAAATAGCGGCG--TTTTTATCCAAACGCCA
17186222 TAAGAAGTTG
Statistics
Matches: 102, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
80 5 0.05
81 53 0.52
82 28 0.27
83 16 0.16
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (81 bp):
AAAAATTGAGAAATAGCGGCGTTTTTATCCAAACGCCACTAAAAACTAAGAAATAGCGGCGTTTT
TGGTACAAACACCGCT
Found at i:17186230 original size:42 final size:40
Alignment explanation
Indices: 17186153--17186232 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 40
17186143 AAACTAAGAA
17186153 ATAGCGGCGTTTTTGTTACAAACGCTGCAAAAAGTTGATCT
1 ATAGCGGCGTTTTTGTTACAAACGC-GCAAAAAGTTGATCT
17186194 ATAGCGGCGTTTTT-TTATCCAAACGC-CATAAGAAGTTGA
1 ATAGCGGCGTTTTTGTTA--CAAACGCGCA-AA-AAGTTGA
17186233 ACACCCATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
40 5 0.14
41 16 0.46
42 14 0.40
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (40 bp):
ATAGCGGCGTTTTTGTTACAAACGCGCAAAAAGTTGATCT
Found at i:17186992 original size:7 final size:7
Alignment explanation
Indices: 17186977--17187085 Score: 62
Period size: 7 Copynumber: 15.7 Consensus size: 7
17186967 GTTCATGGAA
*
17186977 TTAGTGT
1 TTAGGGT
17186984 TTAGGGT
1 TTAGGGT
***
17186991 TTAAAAT
1 TTAGGGT
17186998 TTA-GGT
1 TTAGGGT
* *
17187004 TTAAGTT
1 TTAGGGT
*
17187011 TTAAGGT
1 TTAGGGT
17187018 TTAGGGT
1 TTAGGGT
17187025 GTT-GGGT
1 -TTAGGGT
*
17187032 TTATGGT
1 TTAGGGT
*
17187039 TTA-GTT
1 TTAGGGT
17187045 TATAGGGT
1 T-TAGGGT
17187053 TTAGGGT
1 TTAGGGT
**
17187060 TTAGTCT
1 TTAGGGT
*
17187067 ATAGGGT
1 TTAGGGT
*
17187074 TTTGGGT
1 TTAGGGT
17187081 TTAGG
1 TTAGG
17187086 ATATTGGGTA
Statistics
Matches: 77, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
6 9 0.12
7 63 0.82
8 5 0.06
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (7 bp):
TTAGGGT
Found at i:17187052 original size:21 final size:21
Alignment explanation
Indices: 17187028--17187084 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
17187018 TTAGGGTGTT
*
17187028 GGGTTTATGGTTTAGTTTATA
1 GGGTTTATGGTTTAGTCTATA
*
17187049 GGGTTTAGGGTTTAGTCTATA
1 GGGTTTATGGTTTAGTCTATA
17187070 GGGTTT-TGGGTTTAG
1 GGGTTTAT-GGTTTAG
17187085 GATATTGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.16, C:0.02, G:0.35, T:0.47
Consensus pattern (21 bp):
GGGTTTATGGTTTAGTCTATA
Found at i:17187094 original size:21 final size:21
Alignment explanation
Indices: 17187028--17187104 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
17187018 TTAGGGTGTT
**
17187028 GGGTTTAT-GGTTTAGTTTATA
1 GGGTTT-TGGGTTTAGGATATA
* **
17187049 GGGTTTAGGGTTTAGTCTATA
1 GGGTTTTGGGTTTAGGATATA
*
17187070 GGGTTTTGGGTTTAGGATATT
1 GGGTTTTGGGTTTAGGATATA
*
17187091 GGGTATTGGGTTTA
1 GGGTTTTGGGTTTA
17187105 CAAATTAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.17, C:0.01, G:0.35, T:0.47
Consensus pattern (21 bp):
GGGTTTTGGGTTTAGGATATA
Found at i:17190755 original size:27 final size:27
Alignment explanation
Indices: 17190723--17190779 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
17190713 ACCTTAATGT
17190723 TAAATATATATCATA-CAATAACTTACA
1 TAAATATATATCATATC-ATAACTTACA
17190750 TAAATATATATCATATCATAACTTACA
1 TAAATATATATCATATCATAACTTACA
17190777 TAA
1 TAA
17190780 TACATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (27 bp):
TAAATATATATCATATCATAACTTACA
Found at i:17190787 original size:34 final size:34
Alignment explanation
Indices: 17190746--17190865 Score: 123
Period size: 43 Copynumber: 3.2 Consensus size: 34
17190736 TACAATAACT
17190746 TACATAAATATATATCATATCATAACTTACATAA
1 TACATAAATATATATCATATCATAACTTACATAA
*
17190780 TACATAAATATATATCATGTAATAACTTACATAACTTACGTAA
1 TACATAAATATATATC-----AT-A--T-CATAACTTACATAA
*
17190823 TACATAAATATATATCATATAATAACTTACATAA
1 TACATAAATATATATCATATCATAACTTACATAA
17190857 CTTACATAA
1 --TACATAA
17190866 TACATAAATA
Statistics
Matches: 72, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
34 28 0.39
35 1 0.01
36 7 0.10
37 1 0.01
38 2 0.03
39 2 0.03
40 1 0.01
42 1 0.01
43 29 0.40
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (34 bp):
TACATAAATATATATCATATCATAACTTACATAA
Found at i:17190792 original size:27 final size:27
Alignment explanation
Indices: 17190723--17190792 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
17190713 ACCTTAATGT
* *
17190723 TAAATATATATCATA-CAATAACTTACA
1 TAAACATAAATCATATC-ATAACTTACA
* *
17190750 TAAATATATATCATATCATAACTTACA
1 TAAACATAAATCATATCATAACTTACA
17190777 TAATACATAAAT-ATAT
1 TAA-ACATAAATCATAT
17190793 ATCATGTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 32 0.82
28 7 0.18
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAACATAAATCATATCATAACTTACA
Found at i:17190814 original size:43 final size:43
Alignment explanation
Indices: 17190766--17190950 Score: 271
Period size: 43 Copynumber: 4.3 Consensus size: 43
17190756 TATATCATAT
*
17190766 CATAACTTACATAATACATAAATATATATCATGTAATAACTTA
1 CATAACTTACATAATACATAAATATATATCATATAATAACTTA
*
17190809 CATAACTTACGTAATACATAAATATATATCATATAATAACTTA
1 CATAACTTACATAATACATAAATATATATCATATAATAACTTA
* * *
17190852 CATAACTTACATAATACATAAATATATTTCATATCATAATTTA
1 CATAACTTACATAATACATAAATATATATCATATAATAACTTA
* * **
17190895 CATAACTTACATACCTTACATAAATTTATATCATAGGATAACTTA
1 CATAACTTACATA--ATACATAAATATATATCATATAATAACTTA
17190940 CATAACTTACA
1 CATAACTTACA
17190951 AAACTTACTT
Statistics
Matches: 128, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
43 93 0.73
45 35 0.27
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (43 bp):
CATAACTTACATAATACATAAATATATATCATATAATAACTTA
Found at i:17190815 original size:9 final size:9
Alignment explanation
Indices: 17190801--17190967 Score: 80
Period size: 9 Copynumber: 19.0 Consensus size: 9
17190791 ATATCATGTA
17190801 ATAACTTAC
1 ATAACTTAC
17190810 ATAACTTAC
1 ATAACTTAC
*
17190819 GTAA--TAC
1 ATAACTTAC
* *
17190826 ATAA-ATAT
1 ATAACTTAC
*
17190834 ATATCATATA-
1 ATAAC-T-TAC
17190844 ATAACTTAC
1 ATAACTTAC
17190853 ATAACTTAC
1 ATAACTTAC
17190862 ATAA--TAC
1 ATAACTTAC
* *
17190869 ATAA-ATAT
1 ATAACTTAC
** *
17190877 ATTTCATATC
1 ATAACTTA-C
*
17190887 ATAATTTAC
1 ATAACTTAC
17190896 ATAACTTAC
1 ATAACTTAC
*
17190905 ATACCTTAC
1 ATAACTTAC
* *
17190914 ATAAATT-T
1 ATAACTTAC
* * *
17190922 ATATCATAGG
1 ATAACTTA-C
17190932 ATAACTTAC
1 ATAACTTAC
17190941 ATAACTTAC
1 ATAACTTAC
*
17190950 AAAACTTAC
1 ATAACTTAC
*
17190959 TTAACTTAC
1 ATAACTTAC
17190968 GTAATACATA
Statistics
Matches: 119, Mismatches: 29, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
7 13 0.11
8 15 0.13
9 75 0.63
10 14 0.12
11 2 0.02
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:17190978 original size:88 final size:86
Alignment explanation
Indices: 17190766--17190978 Score: 214
Period size: 86 Copynumber: 2.5 Consensus size: 86
17190756 TATATCATAT
* ** * * * *
17190766 CATAACTTACATAATACATAAATATATATCATGTAATAACTTACATAACTTACGTAATACATAAA
1 CATAACTTACAAAATACATAAATATACGTAATATCATAACTTACATAACTTACATAATACATAAA
*
17190831 TATATATCATATAATAACTTA
66 TATATATCATAGAATAACTTA
* ** * * *
17190852 CATAACTTACATAATACATAAATATATTTCATATCATAATTTACATAACTTACATACCTTACATA
1 CATAACTTACAAAATACATAAATATACGTAATATCATAACTTACATAACTTACATA--ATACATA
* *
17190917 AATTTATATCATAGGATAACTTA
64 AATATATATCATAGAATAACTTA
* *
17190940 CATAACTTACAAAACTTACTTAACT-TACGTAATA-CATAA
1 CATAACTTACAAAA--TACATAAATATACGTAATATCATAA
17190979 ATATACACTT
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
86 51 0.47
88 44 0.41
89 6 0.06
90 7 0.06
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.35
Consensus pattern (86 bp):
CATAACTTACAAAATACATAAATATACGTAATATCATAACTTACATAACTTACATAATACATAAA
TATATATCATAGAATAACTTA
Found at i:17196055 original size:13 final size:14
Alignment explanation
Indices: 17196039--17196067 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17196029 TTATAAATAT
17196039 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
17196052 TTATAATGGTTTAA
1 TTATAATGGTTTAA
17196066 TT
1 TT
17196068 CGCCATTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:17196844 original size:30 final size:31
Alignment explanation
Indices: 17196759--17196849 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 31
17196749 ATCATTTTAG
* * *
17196759 ATTTAATATTTTTGGTTGTATTTTTTATGCTAC
1 ATTTACTATTTTTGGTTGGA--TTTAATGCTAC
* * *
17196792 ATTTACTGTTTTTGGTTGGATTTCATGCTAT
1 ATTTACTATTTTTGGTTGGATTTAATGCTAC
*
17196823 ATTTGCTATTTTTGG-TGGATTTAATGC
1 ATTTACTATTTTTGGTTGGATTTAATGC
17196850 AGGAAGGGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 11 0.22
31 22 0.44
33 17 0.34
ACGTcount: A:0.19, C:0.08, G:0.18, T:0.56
Consensus pattern (31 bp):
ATTTACTATTTTTGGTTGGATTTAATGCTAC
Found at i:17196983 original size:43 final size:43
Alignment explanation
Indices: 17196936--17197061 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
17196926 AAAAAAGTCG
17196936 TGACTTTTAGAGGCACTTTTCCCACAAACGTCGCTAAAAGCCA
1 TGACTTTTAGAGGCACTTTTCCCACAAACGTCGCTAAAAGCCA
* * * * * *
17196979 TGACTTTTTGTGGCGCTTCT-CCAGAAACCTCCGCTAAAAGCCA
1 TGACTTTTAGAGGCACTTTTCCCACAAACGT-CGCTAAAAGCCA
* * * *
17197022 TGACTTTTAGCGGCACTTTCCCCACAAATGCCGCTAAAAG
1 TGACTTTTAGAGGCACTTTTCCCACAAACGTCGCTAAAAG
17197062 TCAAGATTTT
Statistics
Matches: 66, Mismatches: 15, Indels: 4
0.78 0.18 0.05
Matches are distributed among these distances:
42 8 0.12
43 52 0.79
44 6 0.09
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.26
Consensus pattern (43 bp):
TGACTTTTAGAGGCACTTTTCCCACAAACGTCGCTAAAAGCCA
Found at i:17205976 original size:18 final size:19
Alignment explanation
Indices: 17205942--17205979 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
17205932 GATGCAAATT
17205942 ATATATGATGTAAATGAAA
1 ATATATGATGTAAATGAAA
*
17205961 ATATATG-TGTATATGAAA
1 ATATATGATGTAAATGAAA
17205979 A
1 A
17205980 GTACGTTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (19 bp):
ATATATGATGTAAATGAAA
Done.