Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 37 of 168
Found at i:9979085 original size:5 final size:5
Alignment explanation
Indices: 9979020--9979072 Score: 99
Period size: 5 Copynumber: 10.8 Consensus size: 5
9979010 AATTATTAAG
9979020 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
9979069 TATA
1 TATA
9979073 AGTAAATATA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.08
5 44 0.92
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:9979102 original size:10 final size:11
Alignment explanation
Indices: 9979089--9979118 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
9979079 TATAATAAAT
9979089 AAAGAAACA-A
1 AAAGAAACAGA
9979099 AAAGAAACAGA
1 AAAGAAACAGA
9979110 AAAGAAACA
1 AAAGAAACA
9979119 TGATAGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAACAGA
Found at i:9980438 original size:37 final size:40
Alignment explanation
Indices: 9980347--9980439 Score: 102
Period size: 41 Copynumber: 2.4 Consensus size: 40
9980337 CGACTTCGAG
* *
9980347 TCGATGAGACATTGGGTGTCAATTTACTACTTCAGATTAAT
1 TCGATGAGACACTGGGTGCCAATTTACTA-TTCAGATTAAT
* * *
9980388 TCGATGAGGCACTGGGTGCCAATTTACT-TT-GGTTTAA-
1 TCGATGAGACACTGGGTGCCAATTTACTATTCAGATTAAT
*
9980425 TCGATGAAACACTGG
1 TCGATGAGACACTGG
9980440 ATGTCAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
37 13 0.29
38 5 0.11
39 2 0.04
41 25 0.56
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGCCAATTTACTATTCAGATTAAT
Found at i:9993755 original size:24 final size:24
Alignment explanation
Indices: 9993728--9993871 Score: 71
Period size: 24 Copynumber: 5.8 Consensus size: 24
9993718 AAGCTCATAC
*
9993728 GAGCCAATAAC-AGGTAGCTCCGAA
1 GAGCCAATAACGA-GAAGCTCCGAA
*
9993752 GAGCCATTAACGAGAAGCTCCGAA
1 GAGCCAATAACGAGAAGCTCCGAA
* * *
9993776 TAGCCATATATCGAGAAG-TTC-AA
1 GAGCCA-ATAACGAGAAGCTCCGAA
* * **
9993799 GCGAGCC-ATATCGGGAAGCTCATAAA
1 --GAGCCAATAACGAGAAGCTC-CGAA
** *
9993825 GAGCCTTTAATCGGGAAGCTCACGAA
1 GAGCCAATAA-CGAGAAGCTC-CGAA
*
9993851 GAGCCATATAACGAGACGCTC
1 GAGCCA-ATAACGAGAAGCTC
9993872 ATAAGAGTTA
Statistics
Matches: 92, Mismatches: 18, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
23 12 0.13
24 33 0.36
25 16 0.17
26 28 0.30
27 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (24 bp):
GAGCCAATAACGAGAAGCTCCGAA
Found at i:9993871 original size:26 final size:26
Alignment explanation
Indices: 9993743--9993872 Score: 103
Period size: 26 Copynumber: 5.2 Consensus size: 26
9993733 AATAACAGGT
9993743 AGCTC-CGAAGAGCCAT-TAACGAGA
1 AGCTCACGAAGAGCCATATAACGAGA
* *
9993767 AGCTC-CGAATAGCCATATATCGAGA
1 AGCTCACGAAGAGCCATATAACGAGA
* * * *
9993792 AGTTCAAG-CGAGCCATAT--CGGGA
1 AGCTCACGAAGAGCCATATAACGAGA
** * *
9993815 AGCTCATAAAGAGCC-TTTAATCGGGA
1 AGCTCACGAAGAGCCATATAA-CGAGA
9993841 AGCTCACGAAGAGCCATATAACGAGA
1 AGCTCACGAAGAGCCATATAACGAGA
*
9993867 CGCTCA
1 AGCTCA
9993873 TAAGAGTTAA
Statistics
Matches: 82, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
23 11 0.13
24 20 0.24
25 19 0.23
26 28 0.34
27 4 0.05
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (26 bp):
AGCTCACGAAGAGCCATATAACGAGA
Found at i:9993956 original size:23 final size:23
Alignment explanation
Indices: 9993930--9993994 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
9993920 GAATGCTTTG
*
9993930 AAGAGCTATAACGTGAAGCTCAC
1 AAGAGCTATAACGGGAAGCTCAC
* *
9993953 AAGAACCATATAACGGGAAGCTCAT
1 AAG-AGC-TATAACGGGAAGCTCAC
*
9993978 AAGAGTTAATAACGGGA
1 AAGAGCT-ATAACGGGA
9993995 TACTCTTTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 4 0.12
24 12 0.35
25 18 0.53
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (23 bp):
AAGAGCTATAACGGGAAGCTCAC
Found at i:9997226 original size:49 final size:49
Alignment explanation
Indices: 9997171--9997316 Score: 211
Period size: 49 Copynumber: 3.0 Consensus size: 49
9997161 TTCATTTTCT
* * *
9997171 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
* * *
9997220 CGATGCCATAGCCCAGTTATGGTCTTACACGGAATCACATATCACTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
* *
9997269 CGATGCCATAGCCCAGCTATTGTCTTATACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACA-AATCACAT
9997317 GTTCACATGT
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 79 0.93
50 6 0.07
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (49 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
Found at i:9998194 original size:33 final size:34
Alignment explanation
Indices: 9998147--9998280 Score: 137
Period size: 33 Copynumber: 3.8 Consensus size: 34
9998137 GTTATCCGTT
*
9998147 ATCGGTGGATTCAGCACTTAGCAACCACCAATGA
1 ATCGGTGGAATCAGCACTTAGCAACCACCAATGA
* *
9998181 ATCGG-GGAATCAGCACTTAGCAACCCCTTTCACATTTAA
1 ATCGGTGGAATCAGCACTTAGCAACCAC---CA-A--TGA
*
9998220 GATACGGTGGGATCAGCACTTAGCAACCACCAATGA
1 -AT-CGGTGGAATCAGCACTTAGCAACCACCAATGA
*
9998256 TTCGG-GGAATCAGCACTTAGCAACC
1 ATCGGTGGAATCAGCACTTAGCAACC
9998281 CCTTTCACAT
Statistics
Matches: 83, Mismatches: 8, Indels: 19
0.75 0.07 0.17
Matches are distributed among these distances:
33 39 0.47
34 8 0.10
35 1 0.01
36 4 0.05
37 1 0.01
38 1 0.01
39 4 0.05
40 2 0.02
41 3 0.04
42 20 0.24
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (34 bp):
ATCGGTGGAATCAGCACTTAGCAACCACCAATGA
Found at i:9998272 original size:75 final size:75
Alignment explanation
Indices: 9998149--9998325 Score: 302
Period size: 75 Copynumber: 2.4 Consensus size: 75
9998139 TATCCGTTAT
9998149 CGGT-GGATTCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCA
1 CGGTGGGA-TCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCA
*
9998213 CATTTAAGATA
65 CATTTAAAATA
*
9998224 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGGATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
9998289 ATTTAAAATA
66 ATTTAAAATA
* *
9998299 TGGTGGGATCAGCACGTAGCAACCACC
1 CGGTGGGATCAGCACTTAGCAACCACC
9998326 TTTATAGTCA
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
75 94 0.97
76 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (75 bp):
CGGTGGGATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTTAAAATA
Found at i:9998411 original size:51 final size:49
Alignment explanation
Indices: 9998344--9998838 Score: 465
Period size: 51 Copynumber: 9.8 Consensus size: 49
9998334 CAATGGTAAC
* * * * * *
9998344 CGGTTCACATAGTAGCCTGCACGTAGTACTACACATGTGACCATTTCCAT
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTT-TAT
* * * ***
9998394 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAGCTATT
1 -CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCATTTTA-T
* * * * * * * *
9998446 TGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCCATCATT-C
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCAT-TTTAT
* * *
9998496 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAATTTTA-
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGA-C-CATTTTAT
* * *
9998546 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA-
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCA-TTTTAT
*
9998596 CGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATCATTTAT
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAT--TTTAT
* *
9998647 CGGTACACATAGTAGCCTTCACACAGTACTACACACGTGACCATCATTTAT
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAT--TTTAT
* * ** *
9998698 AGGTACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACC--ATTTTAT
* * *
9998749 CGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTAT
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-T-TTTAT
*
9998800 CGGTACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTG
9998839 TTCATCGATA
Statistics
Matches: 376, Mismatches: 55, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.00
49 5 0.01
50 125 0.33
51 240 0.64
52 4 0.01
53 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (49 bp):
CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTTTAT
Found at i:9998652 original size:28 final size:28
Alignment explanation
Indices: 9998621--9998703 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 28
9998611 CCTTCACATA
9998621 GTACTACACACGTGACCATCATTTATCG
1 GTACTACACACGTGACCATCATTTATCG
* * * *
9998649 GTAC-ACATA-GT-AGCCTTCA--CA-CA
1 GTACTACACACGTGA-CCATCATTTATCG
*
9998672 GTACTACACACGTGACCATCATTTATAG
1 GTACTACACACGTGACCATCATTTATCG
9998700 GTAC
1 GTAC
9998704 ACGTAGTAGC
Statistics
Matches: 39, Mismatches: 9, Indels: 14
0.63 0.15 0.23
Matches are distributed among these distances:
23 5 0.13
24 5 0.13
25 8 0.21
26 8 0.21
27 5 0.13
28 8 0.21
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (28 bp):
GTACTACACACGTGACCATCATTTATCG
Found at i:9998733 original size:102 final size:100
Alignment explanation
Indices: 9998344--9998838 Score: 552
Period size: 102 Copynumber: 4.9 Consensus size: 100
9998334 CAATGGTAAC
* * * * *
9998344 CGGTTCACATAGTAGCCTGCACGTAGTACTACACATGTGACCAT-TTCCATCCGATACACGTAGT
1 CGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCATATT-TAT-CGGTACACGTAGT
* * **
9998408 AGCCTGCACATAGTACTACACACGTGATCAAAGCTATT
64 AGCCTTCACATAGTACTACACACGTGACCAAATTTA-T
* * * * * *
9998446 TGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCCATCA-TT-CCGATACACGTAGT
1 CGGTACACATAGTAGCCTTCACATAGTACTACACATGTGA-CCAT-ATTTATCGGTACACGTAGT
* *
9998509 AGCCTGCACATAGTACTACACACGTGATCAAATTT-T
64 AGCCTTCACATAGTACTACACACGTGACCAAATTTAT
* * * * * *
9998545 ACGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCA-AGTTT-TACGGTTCACGTAG
1 -CGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCATA-TTTAT-CGGTACACGTAG
*
9998608 TAGCCTTCACATAGTACTACACACGTGACCATCATTTAT
63 TAGCCTTCACATAGTACTACACACGTGACCA-AATTTAT
* * *
9998647 CGGTACACATAGTAGCCTTCACACAGTACTACACACGTGACCATCATTTATAGGTACACGTAGTA
1 CGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCAT-ATTTATCGGTACACGTAGTA
* * *
9998712 GCCTTCACACAGTACTACACACGTGACCAAAGCTTCT
65 GCCTTCACATAGTACTACACACGTGACCAAA-TTTAT
*
9998749 CGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTATCGGTACACGTAGTA
1 CGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCA-TATTTATCGGTACACGTAGTA
*
9998814 GCCTTCACACAGTACTACACACGTG
65 GCCTTCACATAGTACTACACACGTG
9998839 TTCATCGATA
Statistics
Matches: 340, Mismatches: 39, Indels: 28
0.84 0.10 0.07
Matches are distributed among these distances:
97 1 0.00
99 5 0.01
100 71 0.21
101 89 0.26
102 166 0.49
103 7 0.02
104 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (100 bp):
CGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCATATTTATCGGTACACGTAGTAG
CCTTCACATAGTACTACACACGTGACCAAATTTAT
Found at i:10001630 original size:11 final size:13
Alignment explanation
Indices: 10001610--10001641 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
10001600 AATAAATTAA
10001610 TAAAATATCAT-T
1 TAAAATATCATAT
10001622 TAAAA-ATCATAT
1 TAAAATATCATAT
10001634 TAAAATAT
1 TAAAATAT
10001642 TAATAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:10007329 original size:30 final size:30
Alignment explanation
Indices: 10007295--10007352 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
10007285 CCTTGACTCT
*
10007295 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
10007325 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
10007353 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:10008923 original size:24 final size:24
Alignment explanation
Indices: 10008832--10008930 Score: 78
Period size: 23 Copynumber: 4.1 Consensus size: 24
10008822 AGGAGTGCTT
* *
10008832 ATAAAAGCACATAAACAGGAAGCTC
1 ATAAGAGC-CATAATCAGGAAGCTC
* *
10008857 ATATGAGCCATGTAA-C-GGAAAGCTT
1 ATAAGAGCCA--TAATCAGG-AAGCTC
** *
10008882 ATTCGAGCTATAAT-AGGAAGCTC
1 ATAAGAGCCATAATCAGGAAGCTC
10008905 ATAAGAGCCATAATCAGGAAGCTC
1 ATAAGAGCCATAATCAGGAAGCTC
10008929 AT
1 AT
10008931 GCAAGCTAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
23 19 0.33
24 17 0.29
25 19 0.33
26 3 0.05
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (24 bp):
ATAAGAGCCATAATCAGGAAGCTC
Found at i:10009060 original size:26 final size:27
Alignment explanation
Indices: 10009013--10009077 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 27
10009003 AGCGAGCCAT
* * * *
10009013 ATCGAGAAACTCACAAATAGCC-TTTA
1 ATCGGGAAGCTCACAAAGAGCCATATA
*
10009039 ATCGGGAAGCTCACGAAGAGCCATATA
1 ATCGGGAAGCTCACAAAGAGCCATATA
*
10009066 A-CGGGACGCTCA
1 ATCGGGAAGCTCA
10009078 TAAGAGTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (27 bp):
ATCGGGAAGCTCACAAAGAGCCATATA
Found at i:10013112 original size:55 final size:55
Alignment explanation
Indices: 10013042--10013161 Score: 177
Period size: 55 Copynumber: 2.2 Consensus size: 55
10013032 TGTTATATGG
* * * *
10013042 AGCCTTAGTGATCGACTCTATGAATGTGCTTTCGTGGCGAAATATGTTAAGTGAA
1 AGCCTTTGTGATCGACTCTATGAATGCGCTTTCATGGCAAAATATGTTAAGTGAA
* **
10013097 AGCCTTTGTGGTCGACTCTATGAATGCGCTTTCATGGCAAAATATGTTAAGTGGG
1 AGCCTTTGTGATCGACTCTATGAATGCGCTTTCATGGCAAAATATGTTAAGTGAA
10013152 AGCCTTTGTG
1 AGCCTTTGTG
10013162 TTGATTCTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (55 bp):
AGCCTTTGTGATCGACTCTATGAATGCGCTTTCATGGCAAAATATGTTAAGTGAA
Found at i:10013178 original size:55 final size:55
Alignment explanation
Indices: 10013042--10013189 Score: 163
Period size: 55 Copynumber: 2.7 Consensus size: 55
10013032 TGTTATATGG
* * * * *
10013042 AGCCTTAGTGATCGACTCTATGAATGTGCTTTCGTGGCGAAATATGTTAAGTGAA
1 AGCCTTTGTGGTCGACTCTATAAATGCGCTTTCGTGGCAAAATATGTTAAGTGAA
* * **
10013097 AGCCTTTGTGGTCGACTCTATGAATGCGCTTTCATGGCAAAATATGTTAAGTGGG
1 AGCCTTTGTGGTCGACTCTATAAATGCGCTTTCGTGGCAAAATATGTTAAGTGAA
* * * *
10013152 AGCCTTTGT-GTTGATTCTGTTAAATGCGCCTTCGTGGC
1 AGCCTTTGTGGTCGACTCT-ATAAATGCGCTTTCGTGGC
10013190 GAAGTCTGTT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 7 0.09
55 72 0.91
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (55 bp):
AGCCTTTGTGGTCGACTCTATAAATGCGCTTTCGTGGCAAAATATGTTAAGTGAA
Found at i:10017200 original size:22 final size:23
Alignment explanation
Indices: 10017156--10017200 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
10017146 CATGTCCATA
* *
10017156 TATATATATATTATAAAATGTATG
1 TATATATAAATTAT-AAAGGTATG
10017180 TATATATAAATTAT-AAGGTAT
1 TATATATAAATTATAAAGGTAT
10017201 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
24 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (23 bp):
TATATATAAATTATAAAGGTATG
Found at i:10020274 original size:85 final size:84
Alignment explanation
Indices: 10020184--10020638 Score: 271
Period size: 85 Copynumber: 5.3 Consensus size: 84
10020174 GCTTCAGTCT
*
10020184 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTACTCTACTGCAACTTCAGAGAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTACTCCACTGCAACTTCAGAGAGAT
10020249 AAGATTTCTGGTTTTAATCC
66 AAGATTTCTGGTTTT-ATCC
* * * * * * * *
10020269 ACTCCATTGCAACTTTAGGGAGATAGGATTGGTTCCTTTTG-TCTACTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGC----GATCTACTCCACTGCAACTTCAGAG
*** *
10020333 AGATAAGA---CTGGATGCGATCT
62 AGATAAGATTTCTGG-TTTTATCC
* * ** * *** ** * *
10020354 GCTCTACTGTAACTTCAAAGAGATAAGATCTATGGTTTTAATCCGCTCCATTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATGCGATCTACTCCACTGCAACTTCAGAGA
* ** * *
10020419 GATAGGATTGGT-TTCTTTTGTCT
63 GATAAGATT--TCTGGTTTTATCC
* ** *
10020442 GCTCCATTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGGTCTACTGCAACTTCAGAGAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTACTCCACTGCAACTTCAGAGAGAT
* *
10020507 AAGATCTATGGTTTTTATCC
66 AAGATTTCTGG-TTTTATCC
* * * * * *
10020527 GCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCGTTTGCTGCTCCACTGCAACTTCA-AGGA
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCG-AT-CTACTCCACTGCAACTTCAGA-GA
* * * *
10020591 GATAAG---CCTGGATGTGATCT
63 GATAAGATTTCTGG-TTTTATCC
* *
10020611 GCTCTACTGCAACTTCAGAGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
10020639 TCTGTGGTTT
Statistics
Matches: 279, Mismatches: 72, Indels: 39
0.72 0.18 0.10
Matches are distributed among these distances:
83 1 0.00
84 34 0.12
85 152 0.54
86 3 0.01
87 26 0.09
88 61 0.22
89 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (84 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTACTCCACTGCAACTTCAGAGAGAT
AAGATTTCTGGTTTTATCC
Found at i:10020332 original size:129 final size:129
Alignment explanation
Indices: 10020131--10020685 Score: 860
Period size: 129 Copynumber: 4.3 Consensus size: 129
10020121 AGATTCATCA
* * ** **
10020131 TTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTAGTAGCTTCAGTCTGCTCCACTGCAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCAA
* * *
10020196 CTTCAGGGAGATAAGACTGGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATTTCTGG
66 CTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
* * * * *
10020260 TTTTAATCCACTCCATTGCAACTTTAGGGAGATAGGATTGGTTCCTTTTGTCTACTCCACTGCAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCAA
* *
10020325 CTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGTAACTTCAAAGAGATAAGATCTATGG
66 CTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
* *
10020389 TTTTAATCCGCTCCATTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCATTGCAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCAA
*
10020454 CTTCAGGGAGATAAGACTGGATGCGATCTGGTCTACTGCAACTTCAGAGAGATAAGATCTATGG
66 CTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
* *
10020518 TTTTTATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCGTTTG-CTGCTCCACTGCAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCAA
* * * *
10020582 CTTCAAGGAGATAAGCCTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
66 CTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
* *
10020646 TTTTAATCCGCTCCACTACAACTTCAGGGAGTTAGGATTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTG
10020686 TAGCTTTACT
Statistics
Matches: 391, Mismatches: 35, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
128 109 0.28
129 282 0.72
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (129 bp):
TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCAA
CTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
Found at i:10020421 original size:44 final size:42
Alignment explanation
Indices: 10020131--10020676 Score: 345
Period size: 44 Copynumber: 12.7 Consensus size: 42
10020121 AGATTCATCA
* * *
10020131 TTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TTAGTAG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-G--G
* * *
10020175 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC-TGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGG
* *** * * * *
10020216 ATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATTTCTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGG
** * * *
10020260 TTTTAATCCACTCCATTGCAACTTTAGGGAGATAGGA-TTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGG
** *
10020301 TTCCTTTTGTCTACTCCACTGCAACTTCAGGGAGATAAGAC-TGG
1 -T--TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGG
* *** * * **
10020345 ATGCGATCTGCTCTACTGTAACTTCAAAGAGATAAGATCTATGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGG
* * *
10020389 TTTTAATCCGCTCCATTGCAACTTCAGGGAGATAGGA-TTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGG
** *
10020430 TTTCTTTTGTCTGCTCCATTGCAACTTCAGGGAGATAAGAC-TGG
1 --T-TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGG
* *** * * *
10020474 ATGCGATCTGGTCTACTGCAACTTCAGAGAGATAAGATCTATGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGG
* * *
10020518 TTTTTATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGG
* * *
10020559 TTTCGT-TTGCTGCTCCACTGCAACTTCAAGGAGATAAG-CCTGG
1 TTT--TAAT-CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGG
* * * * *
10020602 ATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGG
* *
10020646 TTTTAATCCGCTCCACTACAACTTCAGGGAG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAG
10020677 TTAGGATTGT
Statistics
Matches: 384, Mismatches: 92, Indels: 52
0.73 0.17 0.10
Matches are distributed among these distances:
41 125 0.33
42 8 0.02
43 34 0.09
44 217 0.57
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (42 bp):
TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGG
Found at i:10020998 original size:24 final size:24
Alignment explanation
Indices: 10020953--10020998 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
10020943 CGGATTGCCC
*
10020953 CCACTATAATCTTCAAATTTCAAT
1 CCACTATAATCTTCAAAGTTCAAT
* *
10020977 CCACTGTAATCTTCAAGGTTCA
1 CCACTATAATCTTCAAAGTTCA
10020999 GTCAATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.35
Consensus pattern (24 bp):
CCACTATAATCTTCAAAGTTCAAT
Found at i:10022434 original size:1 final size:1
Alignment explanation
Indices: 10022423--10022522 Score: 65
Period size: 1 Copynumber: 100.0 Consensus size: 1
10022413 CCCGGTAGAG
* * * * * * * * * *
10022423 TTTTTTGTTTTTTTTATTTTTTATTTTCTTGTTTTTTTGTTTTTTTTTATTTTTTATTTTCTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
10022488 TTTTTCTTGTTTTTTTTATTCTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10022523 CCTCCACTGT
Statistics
Matches: 69, Mismatches: 30, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.05, C:0.04, G:0.06, T:0.85
Consensus pattern (1 bp):
T
Found at i:10022436 original size:8 final size:8
Alignment explanation
Indices: 10022423--10022520 Score: 83
Period size: 8 Copynumber: 11.8 Consensus size: 8
10022413 CCCGGTAGAG
10022423 TTTTTTGT
1 TTTTTTGT
10022431 TTTTTT-T
1 TTTTTTGT
*
10022438 ATTTTTTAT
1 -TTTTTTGT
*
10022447 TTTCTTGT
1 TTTTTTGT
10022455 TTTTTTGT
1 TTTTTTGT
*
10022463 TTTTTTTT
1 TTTTTTGT
*
10022471 ATTTTTTAT
1 -TTTTTTGT
*
10022480 TTTCTTGTT
1 TTTTTTG-T
10022489 TTTTCTTGT
1 TTTT-TTGT
10022498 TTTTTT-T
1 TTTTTTGT
10022505 ATTCTTTTGT
1 -TT-TTTTGT
10022515 TTTTTT
1 TTTTTT
10022521 TTCCTCCACT
Statistics
Matches: 74, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
7 2 0.03
8 45 0.61
9 23 0.31
10 4 0.05
ACGTcount: A:0.05, C:0.04, G:0.06, T:0.85
Consensus pattern (8 bp):
TTTTTTGT
Found at i:10022467 original size:33 final size:33
Alignment explanation
Indices: 10022423--10022517 Score: 140
Period size: 33 Copynumber: 2.8 Consensus size: 33
10022413 CCCGGTAGAG
10022423 TTTTTTG-TTTTTTTTATTTTTTATTTTCTTGT
1 TTTTTTGTTTTTTTTTATTTTTTATTTTCTTGT
10022455 TTTTTTGTTTTTTTTTATTTTTTATTTTCTTGT
1 TTTTTTGTTTTTTTTTATTTTTTATTTTCTTGT
*
10022488 TTTTTCT-TGTTTTTTTTATTCTTTTGTTTT
1 TTTTT-TGT-TTTTTTTTATT-TTTTATTTT
10022518 TTTTTCCTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
32 7 0.12
33 31 0.53
34 12 0.21
35 8 0.14
ACGTcount: A:0.05, C:0.04, G:0.06, T:0.84
Consensus pattern (33 bp):
TTTTTTGTTTTTTTTTATTTTTTATTTTCTTGT
Found at i:10022519 original size:43 final size:40
Alignment explanation
Indices: 10022423--10022521 Score: 121
Period size: 43 Copynumber: 2.4 Consensus size: 40
10022413 CCCGGTAGAG
10022423 TTTTTTGTTTTTTTTATTTTTTATTTTCTTGTTTTTTTGT
1 TTTTTTGTTTTTTTTATTTTTTATTTTCTTGTTTTTTTGT
*
10022463 TTTTTT-TTATTTTTTATTTTCTTGTTTTTTCTTGTTTTTTT-T
1 TTTTTTGTT-TTTTTTA-TTT-TT-TATTTTCTTGTTTTTTTGT
10022505 ATTCTTTTGTTTTTTTT
1 -TT-TTTTGTTTTTTTT
10022522 TCCTCCACTG
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
39 2 0.04
40 13 0.25
41 3 0.06
42 3 0.06
43 18 0.35
44 10 0.20
45 2 0.04
ACGTcount: A:0.05, C:0.04, G:0.06, T:0.85
Consensus pattern (40 bp):
TTTTTTGTTTTTTTTATTTTTTATTTTCTTGTTTTTTTGT
Found at i:10032449 original size:24 final size:23
Alignment explanation
Indices: 10032413--10032458 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
10032403 AACACCTTTT
* *
10032413 ATTCAAATTTTTTATTTTTTATTG
1 ATTCAAATATTTT-TTTTATATTG
*
10032437 ATTCCAATATTTTTTTTATATT
1 ATTCAAATATTTTTTTTATATT
10032459 TTTCAATCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (23 bp):
ATTCAAATATTTTTTTTATATTG
Found at i:10038754 original size:21 final size:22
Alignment explanation
Indices: 10038723--10038786 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
10038713 AAAATATTTT
10038723 TATTT-AAATTTAT-TATAA-AA
1 TATTTAAAATTTATAT-TAATAA
10038743 TATTTAAAATTTATATTAATAA
1 TATTTAAAATTTATATTAATAA
**
10038765 TA-TTAAAACATATAATTAATAA
1 TATTTAAAATTTAT-ATTAATAA
10038787 ACATTATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.13
21 20 0.53
22 13 0.34
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTTAAAATTTATATTAATAA
Found at i:10043931 original size:16 final size:17
Alignment explanation
Indices: 10043910--10043959 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
10043900 CCACATGCAT
*
10043910 ATAAAAAAACAAG-CAA
1 ATAAAAAAAAAAGTCAA
10043926 ATAAAAATAAAAAGTCAA
1 ATAAAAA-AAAAAGTCAA
*
10043944 ATAAATAAAAATAGTC
1 ATAAA-AAAAAAAGTC
10043960 CAAAAACAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 7 0.24
17 5 0.17
18 15 0.52
19 2 0.07
ACGTcount: A:0.70, C:0.08, G:0.06, T:0.16
Consensus pattern (17 bp):
ATAAAAAAAAAAGTCAA
Found at i:10043938 original size:22 final size:22
Alignment explanation
Indices: 10043910--10043956 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
10043900 CCACATGCAT
*
10043910 ATAAAAAAACAAGCAAATAAAA
1 ATAAAAAAACAAACAAATAAAA
** *
10043932 ATAAAAAGTCAAATAAATAAAA
1 ATAAAAAAACAAACAAATAAAA
10043954 ATA
1 ATA
10043957 GTCCAAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.15
Consensus pattern (22 bp):
ATAAAAAAACAAACAAATAAAA
Found at i:10044040 original size:39 final size:39
Alignment explanation
Indices: 10043995--10044071 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
10043985 AATTCTAACC
10043995 CGAATTACCCAATACACCCCAACCCAATAACCAAAAACT
1 CGAATTACCCAATACACCCCAACCCAATAACCAAAAACT
*
10044034 CGAATTACCCAATACACCCCAGCCCAATAACCAAAAAC
1 CGAATTACCCAATACACCCCAACCCAATAACCAAAAAC
10044072 CCTAAGCCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.45, C:0.39, G:0.04, T:0.12
Consensus pattern (39 bp):
CGAATTACCCAATACACCCCAACCCAATAACCAAAAACT
Found at i:10049631 original size:12 final size:12
Alignment explanation
Indices: 10049608--10049697 Score: 58
Period size: 12 Copynumber: 7.5 Consensus size: 12
10049598 AAAATTTAAA
10049608 AAAAATCAAAAAT
1 AAAAATC-AAAAT
*
10049621 CAAAATCAAAAT
1 AAAAATCAAAAT
*
10049633 AAAAA--AAAAG
1 AAAAATCAAAAT
** *
10049643 AAAAAAGAAGAAA
1 AAAAATCAA-AAT
10049656 AAAAATCAAAAT
1 AAAAATCAAAAT
* *
10049668 CAAGATCAAAAT
1 AAAAATCAAAAT
* *
10049680 GAAAATGAAAAT
1 AAAAATCAAAAT
*
10049692 GAAAAT
1 AAAAAT
10049698 GAGAAAAAGA
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
10 9 0.15
12 38 0.61
13 15 0.24
ACGTcount: A:0.73, C:0.07, G:0.08, T:0.12
Consensus pattern (12 bp):
AAAAATCAAAAT
Found at i:10049698 original size:6 final size:6
Alignment explanation
Indices: 10049675--10049699 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
10049665 AATCAAGATC
10049675 AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG A
10049700 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:10050648 original size:8 final size:7
Alignment explanation
Indices: 10050617--10050645 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
10050607 GATGAAGAAG
10050617 AATG-AA
1 AATGAAA
10050623 AATGAAA
1 AATGAAA
10050630 AATGAAA
1 AATGAAA
10050637 AATGAAA
1 AATGAAA
10050644 AA
1 AA
10050646 ATGGAGAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AATGAAA
Found at i:10051964 original size:42 final size:43
Alignment explanation
Indices: 10051854--10052338 Score: 645
Period size: 43 Copynumber: 11.3 Consensus size: 43
10051844 AGTGAAGATT
*
10051854 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACGGATCTAAGCG
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
* *
10051897 GCGGATCTTATCTTCTCCAGAAGTAGGGAAACAGATCTAAGC-
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
* *
10051939 ACGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGC-
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
* * *
10051981 ACGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAACG
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
* *
10052024 GCGGATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAACG
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
* *
10052067 GCGGATCTTATCTTCCCCAAGAGTAGGGAAACGGATCTAAGCG
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
* **
10052110 GCGGATCTTATCTTCCCCAAGAGTAGGGAGGCAGATCTAAGCG
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
* * * **
10052153 GCGAATCTTATCTTTCTCAGGAGTAGGGAGGCAGATCTAAGC-
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
* *
10052195 ACGGATATTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
* * **
10052238 GCGGATCTTATCTTTCCCAAGAGTAGGGAGGCAGATCTAAGC-
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
* * * * *
10052280 ACGAATCTTATCTTTCCCAAGAGTAGGGAAACAGATCGAAGACG
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAG-CG
*
10052324 GCGAATCTTATCTTC
1 GCGGATCTTATCTTC
10052339 AAGTGTAAGG
Statistics
Matches: 398, Mismatches: 40, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
42 150 0.38
43 235 0.59
44 13 0.03
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22
Consensus pattern (43 bp):
GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCG
Found at i:10052032 original size:85 final size:85
Alignment explanation
Indices: 10051855--10052338 Score: 655
Period size: 85 Copynumber: 5.7 Consensus size: 85
10051845 GTGAAGATTG
* * * * *
10051855 CGGATCTTATCTTCCCCAGGAGTAGGGAAACGGATCTAAGCGGCGGATCTTATCTTCTCCAGAAG
1 CGGATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGAATCTTATCTTCCCCAGGAG
10051920 TAGGGAAACAGATCTAAGCA
66 TAGGGAAACAGATCTAAGCA
* * *
10051940 CGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGC-ACGAATCTTATCTTCCCCAGGAG
1 CGGATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGAATCTTATCTTCCCCAGGAG
* *
10052004 TAGGGAAACAGATCTAAACGG
66 TAGGGAAACAGATCTAAGC-A
* * *
10052025 CGGATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAACGGCGGATCTTATCTTCCCCAAGAG
1 CGGATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGAATCTTATCTTCCCCAGGAG
* *
10052090 TAGGGAAACGGATCTAAGCGG
66 TAGGGAAACAGATCTAAGC-A
** * *
10052111 CGGATCTTATCTTCCCCAAGAGTAGGGAGGCAGATCTAAGCGGCGAATCTTATCTTTCTCAGGAG
1 CGGATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGAATCTTATCTTCCCCAGGAG
**
10052176 TAGGGAGGCAGATCTAAGCA
66 TAGGGAAACAGATCTAAGCA
* * * * *
10052196 CGGATATTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGCGGATCTTATCTTTCCCAAGAG
1 CGGATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGAATCTTATCTTCCCCAGGAG
**
10052261 TAGGGAGGCAGATCTAAGCA
66 TAGGGAAACAGATCTAAGCA
* * *
10052281 CGAATCTTATCTTTCCCAAGAGTAGGGAAACAGATCGAAGACGGCGAATCTTATCTTC
1 CGGATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAG-CGGCGAATCTTATCTTC
10052339 AAGTGTAAGG
Statistics
Matches: 355, Mismatches: 41, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
84 37 0.10
85 190 0.54
86 128 0.36
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (85 bp):
CGGATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGAATCTTATCTTCCCCAGGAG
TAGGGAAACAGATCTAAGCA
Found at i:10052570 original size:44 final size:43
Alignment explanation
Indices: 10052410--10053008 Score: 288
Period size: 44 Copynumber: 13.7 Consensus size: 43
10052400 TCACATCAGG
* * * * * *
10052410 TCTTATCTCCCTAAAGTTACAGTAGAGCAGACT-AAGTAAGCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAA-TA-A
* * **
10052454 TCTTATC-CCGACTGAAGTTGCAGTGGGGCAGATCGAAGATGACCAA
1 TCTTATCTCC--CTGAAGTTGCAGTGGAGCAGATTGAAG-T-AATAA
* *
10052500 TCTTATCTCCCTGAGGTTGCAATGGAGCAGATTGAAGTCAATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGT-AATAA
* * * *
10052544 TCCTATCTCCCTGAAGTTGTAGTGGAG-AGGATTAAAGTAATGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATTGAAGTAAT-AA
* * ** * * * **
10052588 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCA-TCA-GG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATAA
* * * * * * * *
10052629 TCTTGTCTCCCTGAGGTTGCAGCGGACCAGACTG-AGAAACGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAA-TAA
** * * * *
10052672 TCTTATCTCCCTGAAGTCACAATGGGGCAGACTGAAG-AAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAA--TAA
* * * * *
10052716 TCTTATCTCCCTGAGGTTTCAGTGGAGTAGATTGAATTCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGT-AATAA
* ** * * *
10052760 TCCTATCTCCCTGAAGTTATAGTGGATCGGATTAAAGTAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATA-A
* * * * ** * *
10052804 GCTTATCTCTCTGAAGCTGCAGT--AG-AG-TGGATCTCATCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAAT-A-A
* * *
10052845 TCTTATCTCACTGAAGTTGCAGTGGAGCAGACTGAAG-AAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAA--TAA
* * *
10052889 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAATTCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGT-AATAA
* * * *
10052933 TCCTATCTCCTTGAAGTTGTAGTGGAGC-GAATTAAAGTAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTGAAGTAATA-A
* *
10052977 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
10053009 CACATCAAGT
Statistics
Matches: 410, Mismatches: 116, Indels: 58
0.70 0.20 0.10
Matches are distributed among these distances:
40 6 0.01
41 49 0.12
42 1 0.00
43 46 0.11
44 246 0.60
45 44 0.11
46 12 0.03
47 5 0.01
48 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATAA
Found at i:10052785 original size:216 final size:217
Alignment explanation
Indices: 10052369--10052902 Score: 707
Period size: 216 Copynumber: 2.5 Consensus size: 217
10052359 AAGCCACGAG
* * *
10052369 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCACATCAGGTCTTATCTCCCTAAAGTTACAGTA
1 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCACATCAGGTCTTATCTCCCTGAAGTTGCAGTG
* * ** * *
10052434 GAGCAGACTAAGTAA-GCAGGTCTTATC-CCGACTGAAGTTGCAGTGGGGCAGATCGAAGATGAC
66 GAGCAGACTGAGAAACG-A-GTCTTATCTCC--CTGAAGTCACAATGGGGCAGATCGAAGAAGAC
*
10052497 CAATCTTATCTCCCTGAGGTTGCAATGGAGCAGATTGAAGTCAATAATCCTATCTCCCTGAAGTT
127 AAATCTTATCTCCCTGAGGTTGCAATGGAGCAGATTGAAGTCAATAATCCTATCTCCCTGAAGTT
* *
10052562 GTAGTGGAGAGGATTAAAGTAATGGA
192 ATAGTGGAGAGGATTAAAGTAATAGA
* * * *
10052588 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTGTCTCCCTGAGGTTGCAGCG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCACATCAGGTCTTATCTCCCTGAAGTTGCAGTG
*
10052653 GACCAGACTGAGAAACGAGTCTTATCTCCCTGAAGTCACAATGGGGCAGA-CTGAAGAAG-CAAA
66 GAGCAGACTGAGAAACGAGTCTTATCTCCCTGAAGTCACAATGGGGCAGATC-GAAGAAGACAAA
* * * * *
10052716 TCTTATCTCCCTGAGGTTTCAGTGGAGTAGATTGAATTCGATAATCCTATCTCCCTGAAGTTATA
130 TCTTATCTCCCTGAGGTTGCAATGGAGCAGATTGAAGTCAATAATCCTATCTCCCTGAAGTTATA
**
10052781 GTGGATCGGATTAAAGTAATAGA
195 GTGGAGAGGATTAAAGTAATAGA
* * * *
10052804 GCTTATCTCTCTGAAGCTGCAGTAGAGTGGATCTCATCAGGTCTTATCTCACTGAAGTTGCAGTG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCACATCAGGTCTTATCTCCCTGAAGTTGCAGTG
* * *
10052869 GAGCAGACTGAAGAAGCAAATCTTATCTCCCTGA
66 GAGCAGACTG-AGAAACGAGTCTTATCTCCCTGA
10052903 GGTTGCAGTG
Statistics
Matches: 276, Mismatches: 35, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
216 150 0.54
217 44 0.16
218 8 0.03
219 73 0.26
220 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (217 bp):
TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCACATCAGGTCTTATCTCCCTGAAGTTGCAGTG
GAGCAGACTGAGAAACGAGTCTTATCTCCCTGAAGTCACAATGGGGCAGATCGAAGAAGACAAAT
CTTATCTCCCTGAGGTTGCAATGGAGCAGATTGAAGTCAATAATCCTATCTCCCTGAAGTTATAG
TGGAGAGGATTAAAGTAATAGA
Found at i:10052879 original size:173 final size:173
Alignment explanation
Indices: 10052670--10053022 Score: 553
Period size: 173 Copynumber: 2.0 Consensus size: 173
10052660 CTGAGAAACG
* * *
10052670 AGTCTTATCTCCCTGAAGTCACAATGGGGCAGACTGAAGAAGCAAATCTTATCTCCCTGAGGTTT
1 AGTCTTATCTCACTGAAGTCACAATGGAGCAGACTGAAGAAGCAAATCTTATCTCCCTGAGGTTG
* * *
10052735 CAGTGGAGTAGATTGAATTCGATAATCCTATCTCCCTGAAGTTATAGTGGATCGGATTAAAGTAA
66 CAGTGGAGCAGATTGAATTCGATAATCCTATCTCCCTGAAGTTATAGTGGAGCGAATTAAAGTAA
** *
10052800 TAGAGCTTATCTCTCTGAAGCTGCAGTAGAGTGGATCTCATCA
131 TAGAGCTTATCTCTCTGAAGCTGCAGTAGAGCAGATCACATCA
* ** *
10052843 GGTCTTATCTCACTGAAGTTGCAGTGGAGCAGACTGAAGAAGCAAATCTTATCTCCCTGAGGTTG
1 AGTCTTATCTCACTGAAGTCACAATGGAGCAGACTGAAGAAGCAAATCTTATCTCCCTGAGGTTG
* *
10052908 CAGTGGAGCAGATTGAATTCGATAATCCTATCTCCTTGAAGTTGTAGTGGAGCGAATTAAAGTAA
66 CAGTGGAGCAGATTGAATTCGATAATCCTATCTCCCTGAAGTTATAGTGGAGCGAATTAAAGTAA
* *
10052973 TAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCA
131 TAGAGCTTATCTCTCTGAAGCTGCAGTAGAGCAGATCACATCA
10053016 AGTCTTA
1 AGTCTTA
10053023 CCGACTAAAT
Statistics
Matches: 162, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
173 162 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (173 bp):
AGTCTTATCTCACTGAAGTCACAATGGAGCAGACTGAAGAAGCAAATCTTATCTCCCTGAGGTTG
CAGTGGAGCAGATTGAATTCGATAATCCTATCTCCCTGAAGTTATAGTGGAGCGAATTAAAGTAA
TAGAGCTTATCTCTCTGAAGCTGCAGTAGAGCAGATCACATCA
Found at i:10053425 original size:39 final size:39
Alignment explanation
Indices: 10053379--10053455 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
10053369 AAAGTCTAAC
10053379 CCGAATTACCCAATACACCCCAACCCAATAACCAAAAAA
1 CCGAATTACCCAATACACCCCAACCCAATAACCAAAAAA
*
10053418 CCGAATTACCCAATACACCCCAGCCCAATAACCAAAAA
1 CCGAATTACCCAATACACCCCAACCCAATAACCAAAAA
10053456 CCCTAAGCCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.47, C:0.39, G:0.04, T:0.10
Consensus pattern (39 bp):
CCGAATTACCCAATACACCCCAACCCAATAACCAAAAAA
Found at i:10064002 original size:20 final size:21
Alignment explanation
Indices: 10063979--10064017 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
10063969 AAATTTATTT
10063979 TAATAATTTTAA-ATTTTAAA
1 TAATAATTTTAATATTTTAAA
*
10063999 TAATATTTTTAATATTTTA
1 TAATAATTTTAATATTTTA
10064018 TTGAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATAATTTTAATATTTTAAA
Found at i:10071146 original size:94 final size:94
Alignment explanation
Indices: 10071017--10071195 Score: 234
Period size: 94 Copynumber: 1.9 Consensus size: 94
10071007 ATGGGGTTAC
* * *
10071017 ATGTGTAAGACATTAGCTCGGCTATGGCGACATAGGTAATCCATTAGG-ACAATAAACACGGGGT
1 ATGTGTAAGACATTAACTCGACTATGGCGACATAGGTAATCCA-CAGGAACAATAAACACGGGGT
* *
10071081 AGTCCGTCAGGACATTAAACAAGGGATTAT
65 AGTCCGCCAGGACAGTAAACAAGGGATTAT
* * * * * *
10071111 ATGTGTAAGACCTTAACTCGATTATGGCGACATAGGTAGTCCACCGGAACAGTAAACATGGGGTA
1 ATGTGTAAGACATTAACTCGACTATGGCGACATAGGTAATCCACAGGAACAATAAACACGGGGTA
*
10071176 GTCTGCCAGGACAGTAAACA
66 GTCCGCCAGGACAGTAAACA
10071196 CAAGGTTGCG
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
93 2 0.03
94 70 0.97
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (94 bp):
ATGTGTAAGACATTAACTCGACTATGGCGACATAGGTAATCCACAGGAACAATAAACACGGGGTA
GTCCGCCAGGACAGTAAACAAGGGATTAT
Found at i:10071215 original size:94 final size:94
Alignment explanation
Indices: 10071039--10071230 Score: 208
Period size: 94 Copynumber: 2.0 Consensus size: 94
10071029 TTAGCTCGGC
* * * *
10071039 TATGGCGACATAGGTAATCCATTAGGACAATAAACACGGGGTAGTCCGTCAGGACATTAAACAAG
1 TATGGCGACATAGGTAATCCATCAGGACAATAAACACGGGGTAGTCCGCCAGGACAGTAAACAAA
* * * *
10071104 GGATTATATGTGTAAGACCTTAACTCGAT
66 GGATTACATGTGGAAGACCATAACTCAAT
* * * * *
10071133 TATGGCGACATAGGTAGTCCA-CCGGAACAGTAAACATGGGGTAGTCTGCCAGGACAGTAAACAC
1 TATGGCGACATAGGTAATCCATCAGG-ACAATAAACACGGGGTAGTCCGCCAGGACAGTAAACA-
* * *
10071197 AAGG-TTGCGTGTGGAAGACCATAGCTCAAT
64 AAGGATTACATGTGGAAGACCATAACTCAAT
10071227 TATG
1 TATG
10071231 ACATCATGTG
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
93 2 0.03
94 75 0.94
95 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.22
Consensus pattern (94 bp):
TATGGCGACATAGGTAATCCATCAGGACAATAAACACGGGGTAGTCCGCCAGGACAGTAAACAAA
GGATTACATGTGGAAGACCATAACTCAAT
Found at i:10076595 original size:21 final size:21
Alignment explanation
Indices: 10076572--10076618 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
10076562 AAAAGAAGAT
10076572 AAATAAAAAAAATACATTAATA
1 AAATAAAAAAAATA-ATTAATA
* * *
10076594 AAATTAAATAAATAATTAAAA
1 AAATAAAAAAAATAATTAATA
10076615 AAAT
1 AAAT
10076619 CACTCCCCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATAAAAAAAATAATTAATA
Found at i:10080302 original size:39 final size:39
Alignment explanation
Indices: 10080254--10080345 Score: 121
Period size: 39 Copynumber: 2.4 Consensus size: 39
10080244 TTTTAAGCAT
* **
10080254 ATATATCATATTACACATATAATCATGTAACATTCAAGC
1 ATATATCATAATACACATATAATCACATAACATTCAAGC
* * *
10080293 ATATATCATAATACTCATATAATTACATAACATTTAAGC
1 ATATATCATAATACACATATAATCACATAACATTCAAGC
*
10080332 ATATATCACAATAC
1 ATATATCATAATAC
10080346 TTAAAATCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (39 bp):
ATATATCATAATACACATATAATCACATAACATTCAAGC
Found at i:10082637 original size:46 final size:46
Alignment explanation
Indices: 10082575--10082668 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
10082565 TATTTTTGAA
10082575 GTTTTATGGTAGAAAATGAAAGGTTATTGTTAGATAAACAAATTTT
1 GTTTTATGGTAGAAAATGAAAGGTTATTGTTAGATAAACAAATTTT
*
10082621 GTTTTATGGTAGAAAATGAAAGGTTATTGTTAGATAAACAACTTTT
1 GTTTTATGGTAGAAAATGAAAGGTTATTGTTAGATAAACAAATTTT
10082667 GT
1 GT
10082669 AAAGAGAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.39
Consensus pattern (46 bp):
GTTTTATGGTAGAAAATGAAAGGTTATTGTTAGATAAACAAATTTT
Found at i:10083308 original size:25 final size:25
Alignment explanation
Indices: 10083249--10083314 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
10083239 ACACACCACA
*
10083249 GCTCTTATGAGCATCCCAATATTTG
1 GCTCTTATGAGCTTCCCAATATTTG
* *
10083274 GCT-TGCATGAGCTTCCCAATTTTTG
1 GCTCT-TATGAGCTTCCCAATATTTG
*
10083299 GCTCTTATGAGATTCC
1 GCTCTTATGAGCTTCC
10083315 TGATATACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.03
25 32 0.94
26 1 0.03
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCCAATATTTG
Found at i:10083361 original size:25 final size:25
Alignment explanation
Indices: 10083333--10083397 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
10083323 AGCTTGATTA
*
10083333 AGCTTCCCGTTATACAGCTCACATG
1 AGCTTCCCGTTATACAGCTCACAAG
** **
10083358 AGCTTCCCGTTATATGGCTCGGAAG
1 AGCTTCCCGTTATACAGCTCACAAG
10083383 AGCTTCCCGTT-TACA
1 AGCTTCCCGTTATACA
10083398 TGTTTGTATA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 2 0.06
25 31 0.94
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (25 bp):
AGCTTCCCGTTATACAGCTCACAAG
Found at i:10086416 original size:14 final size:14
Alignment explanation
Indices: 10086397--10086436 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
10086387 ATGTATTGAT
10086397 TTCATACATGTGGA
1 TTCATACATGTGGA
* **
10086411 TTCATATATACGGA
1 TTCATACATGTGGA
10086425 TTCATACATGTG
1 TTCATACATGTG
10086437 AATTTATAGA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (14 bp):
TTCATACATGTGGA
Found at i:10086433 original size:28 final size:28
Alignment explanation
Indices: 10086397--10086462 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
10086387 ATGTATTGAT
* * *
10086397 TTCATACATGTGGATTCATATATACGGA
1 TTCATACATGTGAATTCATAGATACAGA
*
10086425 TTCATACATGTGAATTTATAGATACAGA
1 TTCATACATGTGAATTCATAGATACAGA
10086453 TTCATACATG
1 TTCATACATG
10086463 CAAATTTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (28 bp):
TTCATACATGTGAATTCATAGATACAGA
Found at i:10086610 original size:28 final size:28
Alignment explanation
Indices: 10086568--10086660 Score: 132
Period size: 28 Copynumber: 3.3 Consensus size: 28
10086558 ATTCTTCAAT
* *
10086568 TAGTTCATGCGGACTCTTGCTTGAGAGA
1 TAGTCCATGCAGACTCTTGCTTGAGAGA
*
10086596 TAGTCCATGCAGACTCTTGCTTAAGAGA
1 TAGTCCATGCAGACTCTTGCTTGAGAGA
* *
10086624 TAGTCTATGCAGACTCTTGCTTGAAAGA
1 TAGTCCATGCAGACTCTTGCTTGAGAGA
*
10086652 TAGCCCATG
1 TAGTCCATG
10086661 TGGACTATTG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (28 bp):
TAGTCCATGCAGACTCTTGCTTGAGAGA
Found at i:10088539 original size:21 final size:24
Alignment explanation
Indices: 10088497--10088545 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 24
10088487 TGTTGAGCCG
* *
10088497 ATTTTTATAAATTTTTAGTAA-TT
1 ATTTTTATAAATTTTAAATAATTT
10088520 ATTTTT-T-AATTTTAAATAATTT
1 ATTTTTATAAATTTTAAATAATTT
10088542 ATTT
1 ATTT
10088546 CTTTTGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 10 0.43
22 7 0.30
23 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTTTTATAAATTTTAAATAATTT
Found at i:10104754 original size:213 final size:213
Alignment explanation
Indices: 10104387--10104814 Score: 804
Period size: 213 Copynumber: 2.0 Consensus size: 213
10104377 TGTCCGTGTC
*
10104387 CATGTAACTCACTAACTTGGGTCACATGGCCATGCCACGCGTTTGTGGTCCAGGCTGTGTACCCT
1 CATGTAACTCACTAACTTGGGTCACATGGCAATGCCACGCGTTTGTGGTCCAGGCTGTGTACCCT
*
10104452 TCAAAATAACTCCACACGCCTGTGTGCAGGTCGTGTGCTAGGCCGTACAACTACCTCACTTACAA
66 TCAAAATAACTCCACACGCCTGTGTGCAGGTCGTGTGCTAGGCCGTACAACTACCTAACTTACAA
10104517 CCCTTCGAAAGCTACATGGGATCACACACGGCTGAGACACACGCCCGTGTCTCTGCTTGTGTGGA
131 CCCTTCGAAAGCTACATGGGATCACACACGGCTGAGACACACGCCCGTGTCTCTGCTTGTGTGGA
10104582 CGAAAGTAGGTCATTTTA
196 CGAAAGTAGGTCATTTTA
*
10104600 CATGTAACTCACTGACTTGGGTCACATGGCAATGCCACGCGTTTGT-GTGCCAGGCTGTGTACCC
1 CATGTAACTCACTAACTTGGGTCACATGGCAATGCCACGCGTTTGTGGT-CCAGGCTGTGTACCC
*
10104664 TTCGAAATAACTCCACACGCCTGTGTGCAGGTCGTGTGCTAGGCCGTACAACTACCTAACTTACA
65 TTCAAAATAACTCCACACGCCTGTGTGCAGGTCGTGTGCTAGGCCGTACAACTACCTAACTTACA
10104729 ACCCTTCGAAAGCTACATGGGATCACACACGGCTGAGACACACGCCCGTGTCTCTGCTTGTGTGG
130 ACCCTTCGAAAGCTACATGGGATCACACACGGCTGAGACACACGCCCGTGTCTCTGCTTGTGTGG
10104794 ACGAAAGTAGGTCATTTTA
195 ACGAAAGTAGGTCATTTTA
10104813 CA
1 CA
10104815 AGTTATTTTT
Statistics
Matches: 210, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
212 2 0.01
213 208 0.99
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (213 bp):
CATGTAACTCACTAACTTGGGTCACATGGCAATGCCACGCGTTTGTGGTCCAGGCTGTGTACCCT
TCAAAATAACTCCACACGCCTGTGTGCAGGTCGTGTGCTAGGCCGTACAACTACCTAACTTACAA
CCCTTCGAAAGCTACATGGGATCACACACGGCTGAGACACACGCCCGTGTCTCTGCTTGTGTGGA
CGAAAGTAGGTCATTTTA
Found at i:10105839 original size:31 final size:30
Alignment explanation
Indices: 10105801--10105880 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
10105791 AGCCAAAGCT
*
10105801 ATCCCTTTTTTATAATTTGATGGTCACCACC
1 ATCCC-TTTTCATAATTTGATGGTCACCACC
* * ***
10105832 ATCCCTTTTCATAGTTCGATGGTTGTCACC
1 ATCCCTTTTCATAATTTGATGGTCACCACC
10105862 ATCCCTTTTCATAATTTGA
1 ATCCCTTTTCATAATTTGA
10105881 GAGCCGAAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 36 0.88
31 5 0.12
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.42
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATGGTCACCACC
Found at i:10105973 original size:30 final size:29
Alignment explanation
Indices: 10105860--10106038 Score: 137
Period size: 30 Copynumber: 6.0 Consensus size: 29
10105850 ATGGTTGTCA
* *
10105860 CCATCCCTTTTCATAATTTGAGAGCCGAAG
1 CCATCCCTTTTCAT-ATTCGATAGCCGAAG
* * * * * *
10105890 CTATCCTTTTTTAGAGATT-GATAGCCAAAA
1 CCATCC-CTTTT-CATATTCGATAGCCGAAG
* *
10105920 CCATCCCCTTTCATATATTGATAGCCGAAG
1 CCATCCCTTTTCATAT-TCGATAGCCGAAG
* *
10105950 CCATCCCTTTTCATAGTTCGATAGTCGTCA-
1 CCATCCCTTTTCATA-TTCGATAGCCG-AAG
* *
10105980 TCATCCCTTTTCATAATCGATAGCCGAAG
1 CCATCCCTTTTCATATTCGATAGCCGAAG
** *
10106009 TTATCCCTTTCCATATTCGATAGCCGAAG
1 CCATCCCTTTTCATATTCGATAGCCGAAG
10106038 C
1 C
10106039 TATTCATTTT
Statistics
Matches: 116, Mismatches: 26, Indels: 15
0.74 0.17 0.10
Matches are distributed among these distances:
28 4 0.03
29 39 0.34
30 63 0.54
31 9 0.08
32 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (29 bp):
CCATCCCTTTTCATATTCGATAGCCGAAG
Found at i:10105973 original size:60 final size:59
Alignment explanation
Indices: 10105830--10106034 Score: 207
Period size: 60 Copynumber: 3.5 Consensus size: 59
10105820 ATGGTCACCA
* ** *
10105830 CCATCCCTTTTCATAGTTCGATGGTTGTCACCATCCCTTTTCATAATTTGAGAGCCGAAG
1 CCATCCCTTTTCATAGTTCGATAGCCGTCACCATCCCTTTTCATAA-TTGATAGCCGAAG
* * * * *** *
10105890 CTATCCTTTTTTAGAGATT-GATAGCCAAAACCATCCCCTTTCATATATTGATAGCCGAAG
1 CCATCCCTTTTCATAG-TTCGATAGCCGTCACCATCCCTTTTCATA-ATTGATAGCCGAAG
* * *
10105950 CCATCCCTTTTCATAGTTCGATAGTCGTCATCATCCCTTTTCATAATCGATAGCCGAAG
1 CCATCCCTTTTCATAGTTCGATAGCCGTCACCATCCCTTTTCATAATTGATAGCCGAAG
** *
10106009 TTATCCCTTTCCATA-TTCGATAGCCG
1 CCATCCCTTTTCATAGTTCGATAGCCG
10106035 AAGCTATTCA
Statistics
Matches: 115, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
58 10 0.09
59 27 0.23
60 75 0.65
61 3 0.03
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (59 bp):
CCATCCCTTTTCATAGTTCGATAGCCGTCACCATCCCTTTTCATAATTGATAGCCGAAG
Found at i:10107280 original size:29 final size:29
Alignment explanation
Indices: 10107247--10107305 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
10107237 CTATGTACCA
10107247 GGTCATGTGACAGACCATGTGAGCCACAC
1 GGTCATGTGACAGACCATGTGAGCCACAC
* * * *
10107276 GGTCATGTGATAGGCCGTGTGGGCCACAC
1 GGTCATGTGACAGACCATGTGAGCCACAC
10107305 G
1 G
10107306 AGTTGGGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.19
Consensus pattern (29 bp):
GGTCATGTGACAGACCATGTGAGCCACAC
Found at i:10111048 original size:25 final size:25
Alignment explanation
Indices: 10111014--10111117 Score: 84
Period size: 25 Copynumber: 4.2 Consensus size: 25
10111004 TGAGCATACT
* *
10111014 GATATTTGGCTCTCACGAGCTTCCA
1 GATAATTGGCTCTCATGAGCTTCCA
* *
10111039 GATTAA-TGGCTCTCTTGAGCTTCCC
1 GA-TAATTGGCTCTCATGAGCTTCCA
* ***
10111064 GATAATTGGCTCGCATGAGCTTTTT
1 GATAATTGGCTCTCATGAGCTTCCA
** * *
10111089 GATTTTTGGCTCTTATGAGCTTCCT
1 GATAATTGGCTCTCATGAGCTTCCA
10111114 GATA
1 GATA
10111118 TACAGCTCGA
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
24 3 0.05
25 56 0.92
26 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.38
Consensus pattern (25 bp):
GATAATTGGCTCTCATGAGCTTCCA
Found at i:10116546 original size:17 final size:17
Alignment explanation
Indices: 10116526--10116558 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10116516 TATAATTTAT
*
10116526 GAGTATTTTATATTTGA
1 GAGTATTTAATATTTGA
10116543 GAGTATTTAATATTTG
1 GAGTATTTAATATTTG
10116559 TAAATATTTT
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:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (17 bp):
GAGTATTTAATATTTGA
Found at i:10117109 original size:22 final size:21
Alignment explanation
Indices: 10117084--10117128 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
10117074 ATAAAGTAAT
*
10117084 ATTTAATTCTTAAATTTAATCA
1 ATTTAATCCTTAAATTTAA-CA
10117106 ATTTAATCCTTAAATTTAACA
1 ATTTAATCCTTAAATTTAACA
10117127 AT
1 AT
10117129 GTTTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTAATCCTTAAATTTAACA
Found at i:10124806 original size:14 final size:14
Alignment explanation
Indices: 10124783--10124830 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
10124773 CCAAAAATAA
*
10124783 AAATACCATAAAAT
1 AAATAACATAAAAT
10124797 AAATAACATAAATAAT
1 AAATAACAT-AA-AAT
10124813 ATATATAACATAAAAT
1 A-A-ATAACATAAAAT
10124829 AA
1 AA
10124831 TAATAAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 8 0.28
15 3 0.10
16 8 0.28
17 3 0.10
18 7 0.24
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATAACATAAAAT
Found at i:10124836 original size:16 final size:16
Alignment explanation
Indices: 10124776--10124836 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
10124766 TTTTTTTCCA
* *
10124776 AAAATAAAAATACCAT
1 AAAATAATAATAACAT
10124792 AAAAT-A-AATAACAT
1 AAAATAATAATAACAT
10124806 -AAATAATATATATAACAT
1 AAAAT-A-ATA-ATAACAT
10124824 AAAATAATAATAA
1 AAAATAATAATAA
10124837 AAACAAAACT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 4 0.11
14 7 0.18
15 1 0.03
16 10 0.26
17 4 0.11
18 8 0.21
19 4 0.11
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATAATAATAACAT
Found at i:10129507 original size:34 final size:34
Alignment explanation
Indices: 10129469--10129554 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 34
10129459 ACACTGTTAA
* *
10129469 CCATCCAACACACCACATGCTCGTACAAGCTAAT
1 CCATCCAGCACACCAAATGCTCGTACAAGCTAAT
**
10129503 CCATCCAGCACACCAAATGCTCGTATGAGCTAAT
1 CCATCCAGCACACCAAATGCTCGTACAAGCTAAT
*
10129537 CCATCCAGCACATCAAAT
1 CCATCCAGCACACCAAAT
10129555 AACACTGTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.35, C:0.36, G:0.10, T:0.19
Consensus pattern (34 bp):
CCATCCAGCACACCAAATGCTCGTACAAGCTAAT
Found at i:10138824 original size:9 final size:9
Alignment explanation
Indices: 10138806--10138834 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
10138796 ATATTTAATG
10138806 ATTTTA-TA
1 ATTTTATTA
10138814 ATTTTATTA
1 ATTTTATTA
10138823 ATTTTATTA
1 ATTTTATTA
10138832 ATT
1 ATT
10138835 AATAATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTTATTA
Found at i:10139651 original size:43 final size:43
Alignment explanation
Indices: 10139546--10139633 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
10139536 TAATTGTAAC
* ** **
10139546 TTAAATTCTAATTATTTTAAATGTGTAATTATCTCAACTTCTA
1 TTAAATTATAATTATTTTAAATGTACAATTATCAAAACTTCTA
10139589 TTAAATTATAATTATTTTAAATGTACAATTATCAAAACTTCTA
1 TTAAATTATAATTATTTTAAATGTACAATTATCAAAACTTCTA
10139632 TT
1 TT
10139634 TTATTTCAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (43 bp):
TTAAATTATAATTATTTTAAATGTACAATTATCAAAACTTCTA
Found at i:10140036 original size:17 final size:17
Alignment explanation
Indices: 10140016--10140056 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
10140006 ATTTGTATTT
10140016 AAATAATAATATTTAAA
1 AAATAATAATATTTAAA
** *
10140033 AAATAATTGTTTTTAAA
1 AAATAATAATATTTAAA
10140050 AAATAAT
1 AAATAAT
10140057 TTACAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATAATAATATTTAAA
Found at i:10140543 original size:20 final size:20
Alignment explanation
Indices: 10140520--10140562 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
10140510 AACGTAGTAC
10140520 AATAGAACAAAACAAAACAA
1 AATAGAACAAAACAAAACAA
* *
10140540 AATAGAGCAGAACAAAACAA
1 AATAGAACAAAACAAAACAA
10140560 AAT
1 AAT
10140563 GGTATAGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.70, C:0.14, G:0.09, T:0.07
Consensus pattern (20 bp):
AATAGAACAAAACAAAACAA
Found at i:10140596 original size:25 final size:25
Alignment explanation
Indices: 10140568--10140618 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
10140558 AAAATGGTAT
10140568 AGAGCAGAGCAGAACTGAA-CAGAGC
1 AGAGCAGAGCAGAA-TGAACCAGAGC
* *
10140593 AGAGTAGAGTAGAATGAACCAGAGC
1 AGAGCAGAGCAGAATGAACCAGAGC
10140618 A
1 A
10140619 TGTATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.45, C:0.16, G:0.31, T:0.08
Consensus pattern (25 bp):
AGAGCAGAGCAGAATGAACCAGAGC
Found at i:10141671 original size:13 final size:13
Alignment explanation
Indices: 10141655--10141679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10141645 GGCCTGGACA
10141655 CACACCTGTGTGT
1 CACACCTGTGTGT
10141668 CACACCTGTGTG
1 CACACCTGTGTG
10141680 ATTCCTGCAT
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:0.16, C:0.32, G:0.24, T:0.28
Consensus pattern (13 bp):
CACACCTGTGTGT
Found at i:10147595 original size:17 final size:17
Alignment explanation
Indices: 10147573--10147607 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
10147563 ATGTCGAATC
10147573 ATGATTTCTTGTGACTT
1 ATGATTTCTTGTGACTT
10147590 ATGATTTCTTGTGACTT
1 ATGATTTCTTGTGACTT
10147607 A
1 A
10147608 GGTAGCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.51
Consensus pattern (17 bp):
ATGATTTCTTGTGACTT
Found at i:10148936 original size:22 final size:23
Alignment explanation
Indices: 10148893--10148936 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
10148883 ACCAAAAGGT
10148893 AAAAGTTTAATTGATTTCTTCAG
1 AAAAGTTTAATTGATTTCTTCAG
* *
10148916 AAAAGTTTGA-TGATTTTTTCA
1 AAAAGTTTAATTGATTTCTTCA
10148937 AACCCTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (23 bp):
AAAAGTTTAATTGATTTCTTCAG
Found at i:10156362 original size:64 final size:65
Alignment explanation
Indices: 10156250--10156392 Score: 243
Period size: 64 Copynumber: 2.2 Consensus size: 65
10156240 AGTACAAGCC
*
10156250 ATAGCATGTCTGATCAAGAATCACAATCAGTTCTTGCCAGAGATGTAGAAATCGAATGATGTA-G
1 ATAGGATGTC-GATCAAGAATCACAATCAGTTCTTGCCAGAGATGTAGAAATCGAATGATGTAGG
10156314 A
65 A
*
10156315 ATAGGATGTCGATCAAGAATCACAATCAGTTCTTGCCAGAGATGTAGAAATCGAATGGTGTAGGA
1 ATAGGATGTCGATCAAGAATCACAATCAGTTCTTGCCAGAGATGTAGAAATCGAATGATGTAGGA
*
10156380 CTAGGATGTCGAT
1 ATAGGATGTCGAT
10156393 ATTTGTCCAT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
64 51 0.69
65 23 0.31
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (65 bp):
ATAGGATGTCGATCAAGAATCACAATCAGTTCTTGCCAGAGATGTAGAAATCGAATGATGTAGGA
Found at i:10156830 original size:24 final size:25
Alignment explanation
Indices: 10156789--10156839 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
10156779 TAAAATAAGC
**
10156789 ATAACAAATATATTTTAA-TTT-AT
1 ATAACAAATATAAGTTAACTTTGAT
10156812 ATAACAAAATATAAGTTAACTTTGAT
1 ATAAC-AAATATAAGTTAACTTTGAT
10156838 AT
1 AT
10156840 GCAGTTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.22
24 11 0.48
25 3 0.13
26 4 0.17
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (25 bp):
ATAACAAATATAAGTTAACTTTGAT
Found at i:10161873 original size:3 final size:3
Alignment explanation
Indices: 10161865--10161897 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
10161855 TCTAATCACT
*
10161865 ATG ATG ATG GTG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
10161898 GGTTCAAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:10162744 original size:4 final size:4
Alignment explanation
Indices: 10162735--10162761 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10162725 TTTTTTCTCG
10162735 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
10162762 CGAAATACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:10167206 original size:6 final size:6
Alignment explanation
Indices: 10167190--10167249 Score: 63
Period size: 6 Copynumber: 9.8 Consensus size: 6
10167180 ATGAGTTCAG
10167190 ACAAAA A-AAAA AC-AAA ACAAAA ACAAAA ATCAAAAA ACAAAA ATCAAAA
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA A-C-AAAA ACAAAA A-CAAAA
10167239 A-AAAA ATCAAA
1 ACAAAA A-CAAA
10167250 GTCAAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
5 15 0.32
6 16 0.34
7 11 0.23
8 5 0.11
ACGTcount: A:0.82, C:0.13, G:0.00, T:0.05
Consensus pattern (6 bp):
ACAAAA
Found at i:10167225 original size:14 final size:14
Alignment explanation
Indices: 10167196--10167249 Score: 73
Period size: 14 Copynumber: 4.2 Consensus size: 14
10167186 TCAGACAAAA
10167196 AAAAAAC-AAAA-C
1 AAAAAACAAAAATC
10167208 -AAAAACAAAAATC
1 AAAAAACAAAAATC
10167221 AAAAAACAAAAATC
1 AAAAAACAAAAATC
10167235 -AAAAA-AAAAATC
1 AAAAAACAAAAATC
10167247 AAA
1 AAA
10167250 GTCAAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 6 0.16
12 11 0.29
13 8 0.21
14 13 0.34
ACGTcount: A:0.81, C:0.13, G:0.00, T:0.06
Consensus pattern (14 bp):
AAAAAACAAAAATC
Found at i:10167238 original size:32 final size:30
Alignment explanation
Indices: 10167192--10167257 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 30
10167182 GAGTTCAGAC
*
10167192 AAAAAAAAAACAAAACAAAAA-CAAAAATCA
1 AAAAAAAAAACAAAAAAAAAATC-AAAATCA
*
10167222 AAAAACAAAAATCAAAAAAAAAATCAAAGTCA
1 AAAAA-AAAAA-CAAAAAAAAAATCAAAATCA
10167254 AAAA
1 AAAA
10167258 TAGGAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 5 0.16
31 5 0.16
32 20 0.65
33 1 0.03
ACGTcount: A:0.80, C:0.12, G:0.02, T:0.06
Consensus pattern (30 bp):
AAAAAAAAAACAAAAAAAAAATCAAAATCA
Found at i:10167257 original size:26 final size:26
Alignment explanation
Indices: 10167196--10167249 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
10167186 TCAGACAAAA
10167196 AAAAAAC-AAAACAAAAACAAAAATC
1 AAAAAACAAAAACAAAAACAAAAATC
10167221 AAAAAACAAAAATCAAAAA-AAAAATC
1 AAAAAACAAAAA-CAAAAACAAAAATC
10167247 AAA
1 AAA
10167250 GTCAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 7 0.26
26 14 0.52
27 6 0.22
ACGTcount: A:0.81, C:0.13, G:0.00, T:0.06
Consensus pattern (26 bp):
AAAAAACAAAAACAAAAACAAAAATC
Found at i:10168089 original size:7 final size:7
Alignment explanation
Indices: 10168077--10168123 Score: 71
Period size: 7 Copynumber: 7.0 Consensus size: 7
10168067 CTCGGAGTAA
10168077 AAAAATG
1 AAAAATG
10168084 AAAAATG
1 AAAAATG
*
10168091 -AGAATG
1 AAAAATG
10168097 AAAAATG
1 AAAAATG
10168104 AAAAATG
1 AAAAATG
10168111 -AAAATG
1 AAAAATG
10168117 AAAAATG
1 AAAAATG
10168124 GAGAGGCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 11 0.31
7 25 0.69
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:10168098 original size:13 final size:14
Alignment explanation
Indices: 10168077--10168123 Score: 71
Period size: 13 Copynumber: 3.5 Consensus size: 14
10168067 CTCGGAGTAA
10168077 AAAAATGAAAAATG
1 AAAAATGAAAAATG
*
10168091 -AGAATGAAAAATG
1 AAAAATGAAAAATG
10168104 AAAAATG-AAAATG
1 AAAAATGAAAAATG
10168117 AAAAATG
1 AAAAATG
10168124 GAGAGGCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 25 0.83
14 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (14 bp):
AAAAATGAAAAATG
Found at i:10168102 original size:20 final size:20
Alignment explanation
Indices: 10168077--10168123 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
10168067 CTCGGAGTAA
*
10168077 AAAAATGAAAAATGAGAATG
1 AAAAATGAAAAATGAAAATG
10168097 AAAAATGAAAAATGAAAATG
1 AAAAATGAAAAATGAAAATG
10168117 AAAAATG
1 AAAAATG
10168124 GAGAGGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAAATGAAAAATGAAAATG
Found at i:10169535 original size:46 final size:46
Alignment explanation
Indices: 10169339--10169527 Score: 270
Period size: 46 Copynumber: 4.1 Consensus size: 46
10169329 GTTATAGCGA
* *
10169339 ATCTTATCTTCCTGTATTTGGCAGCGAATGAGATCGAAGATAGCAG
1 ATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAGCAG
* * *
10169385 ATATTATCTTCCTATATTTGGCAGCGGAAGAGATCGAAGATAGCAG
1 ATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAGCAG
* * *
10169431 TTCTTATATTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAG
1 ATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAGCAG
* * * *
10169477 ATCTTGTCTTCCTGTATTTGGCAGCAGAGGATATCGAAGATAACAG
1 ATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAGCAG
10169523 ATCTT
1 ATCTT
10169528 GTTTTCCTNN
Statistics
Matches: 126, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 126 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (46 bp):
ATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAGCAG
Found at i:10169891 original size:132 final size:132
Alignment explanation
Indices: 10169640--10170046 Score: 679
Period size: 132 Copynumber: 3.1 Consensus size: 132
10169630 NNNNNNGGCT
* *
10169640 AATCTTATCTTCCTAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCTTAAGCAGT
1 AATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGT
* * * *
10169705 AGTGGAGTAGGTTGAAGATTACAAATTCTGTCACCCTAATCAGTTGTGGAGCAGATCGAAGATGG
66 AGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAATCAGTAGTGGAGCAGATCAAAGATGG
10169770 TG
131 TG
* *
10169772 AATCATATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGTAGT
1 AATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGT
* *
10169837 AGTTGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAATCAGTAGTGGCGCAGATCAAAGATGG
66 AGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAATCAGTAGTGGAGCAGATCAAAGATGG
*
10169902 TT
131 TG
* *
10169904 AATCTTATCTTCCGAATATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGT
1 AATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGT
* *
10169969 AGTGGAATAGGTTGAAGATTGTAGATTCTGTCACCCTAATCAGTAGTGGAGCAGATCAAAGATGG
66 AGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAATCAGTAGTGGAGCAGATCAAAGATGG
10170034 TG
131 TG
10170036 AATCTTATCTT
1 AATCTTATCTT
10170047 TCNNNNNNNN
Statistics
Matches: 255, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 255 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (132 bp):
AATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGT
AGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAATCAGTAGTGGAGCAGATCAAAGATGG
TG
Found at i:10171085 original size:11 final size:11
Alignment explanation
Indices: 10171071--10171095 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10171061 TTTGTCTCGT
10171071 TTTTTTATTTA
1 TTTTTTATTTA
10171082 TTTTTTATTTA
1 TTTTTTATTTA
10171093 TTT
1 TTT
10171096 CGAAATACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:10181203 original size:22 final size:22
Alignment explanation
Indices: 10181178--10181221 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
10181168 ATCACAACTA
10181178 CATGTAAAAATAATCCTAAGTT
1 CATGTAAAAATAATCCTAAGTT
10181200 CATGTAAAAATAATCCTAAGTT
1 CATGTAAAAATAATCCTAAGTT
10181222 TTGGCATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CATGTAAAAATAATCCTAAGTT
Found at i:10184860 original size:19 final size:19
Alignment explanation
Indices: 10184836--10184892 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
10184826 AGAGAGTTAT
10184836 CATTCAGTCAAATTCAAAC
1 CATTCAGTCAAATTCAAAC
*
10184855 CATTCA-T--AATT---AT
1 CATTCAGTCAAATTCAAAC
10184868 CATTCAGTCAAATTCAAAC
1 CATTCAGTCAAATTCAAAC
10184887 CATTCA
1 CATTCA
10184893 TATAATGCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
13 7 0.23
14 1 0.03
16 8 0.27
18 1 0.03
19 13 0.43
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.32
Consensus pattern (19 bp):
CATTCAGTCAAATTCAAAC
Found at i:10184868 original size:32 final size:32
Alignment explanation
Indices: 10184832--10184894 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
10184822 TGTTAGAGAG
10184832 TTATCATTCAGTCAAATTCAAACCATTCATAA
1 TTATCATTCAGTCAAATTCAAACCATTCATAA
10184864 TTATCATTCAGTCAAATTCAAACCATTCATA
1 TTATCATTCAGTCAAATTCAAACCATTCATA
10184895 TAATGCGGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (32 bp):
TTATCATTCAGTCAAATTCAAACCATTCATAA
Found at i:10185018 original size:42 final size:42
Alignment explanation
Indices: 10184971--10185051 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
10184961 TATATACGCC
10184971 ACACGGCCTAGACACACGCCCATGTCCTTGCCCGTGTGGCTT
1 ACACGGCCTAGACACACGCCCATGTCCTTGCCCGTGTGGCTT
* * *
10185013 ACACGGCCTGGGCACACGCCCATGTCCTTGTCCGTGTGG
1 ACACGGCCTAGACACACGCCCATGTCCTTGCCCGTGTGG
10185052 TTTTAAAGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.15, C:0.37, G:0.27, T:0.21
Consensus pattern (42 bp):
ACACGGCCTAGACACACGCCCATGTCCTTGCCCGTGTGGCTT
Found at i:10192121 original size:20 final size:21
Alignment explanation
Indices: 10192098--10192136 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10192088 TCAAAGAAGT
*
10192098 AAAAT-AAAAGGAAGAAAAGA
1 AAAATAAAAAGAAAGAAAAGA
10192118 AAAATAAAAAGAAAGAAAA
1 AAAATAAAAAGAAAGAAAA
10192137 AGAAGCAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (21 bp):
AAAATAAAAAGAAAGAAAAGA
Found at i:10192555 original size:16 final size:16
Alignment explanation
Indices: 10192534--10192580 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
10192524 TCTCTACTTT
*
10192534 ATTTATACTTCTTGTC
1 ATTTATACTTCTTATC
* *
10192550 ATTTATAATTCTTATT
1 ATTTATACTTCTTATC
10192566 ATTTATACTTCTTAT
1 ATTTATACTTCTTAT
10192581 GCCTATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.26, C:0.13, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTATACTTCTTATC
Found at i:10192677 original size:23 final size:21
Alignment explanation
Indices: 10192642--10192685 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
10192632 TAAAATACGC
10192642 TTTCTTTTCTCTCCTATTCTTTT
1 TTTCTTTTCTCT-CTA-TCTTTT
10192665 TTTCTTTAT-TCTCTATCTTTT
1 TTTCTTT-TCTCTCTATCTTTT
10192686 ATTTTATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.30
22 3 0.15
23 10 0.50
24 1 0.05
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTTTTCTCTCTATCTTTT
Found at i:10197652 original size:14 final size:14
Alignment explanation
Indices: 10197633--10197660 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10197623 TTTTTTTGAA
10197633 TGTAAAATATTTTC
1 TGTAAAATATTTTC
10197647 TGTAAAATATTTTC
1 TGTAAAATATTTTC
10197661 ATTGTTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
TGTAAAATATTTTC
Found at i:10198915 original size:66 final size:66
Alignment explanation
Indices: 10198809--10198940 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
10198799 TTCTTTTTGT
* *
10198809 TTTTAATAAACTTAAGCTTCAAGTTGTTAGTAGAAACTTTTTAATACAACATTTATTACATTAAT
1 TTTTAATAAACTTAAGCTTCAAGTTCTTAGTACAAACTTTTTAATACAACATTTATTACATTAAT
10198874 C
66 C
*
10198875 TTTTAATAAACTTAAGCTTTAAGTTCTTAGTACAAACTTTTTAATACAACATTTATTACATTAAT
1 TTTTAATAAACTTAAGCTTCAAGTTCTTAGTACAAACTTTTTAATACAACATTTATTACATTAAT
10198940 C
66 C
10198941 AATGTACTGT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (66 bp):
TTTTAATAAACTTAAGCTTCAAGTTCTTAGTACAAACTTTTTAATACAACATTTATTACATTAAT
C
Found at i:10199367 original size:2 final size:2
Alignment explanation
Indices: 10199360--10199387 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10199350 ATTGTTGTTA
10199360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10199388 TAATTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10199447 original size:26 final size:25
Alignment explanation
Indices: 10199418--10199466 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
10199408 ATATATTATG
*
10199418 TTTTAATTCTAAACTAAAAAATAATT
1 TTTTAATTC-AAAATAAAAAATAATT
**
10199444 TTTTTCTTCAAAATAAAAAATAA
1 TTTTAATTCAAAATAAAAAATAA
10199467 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (25 bp):
TTTTAATTCAAAATAAAAAATAATT
Found at i:10201612 original size:18 final size:17
Alignment explanation
Indices: 10201588--10201636 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
10201578 TTATTAGTTA
10201588 AAATAAAATAAAAAAAT
1 AAATAAAATAAAAAAAT
* **
10201605 AAAGTAAAGTAAGTAAAT
1 AAA-TAAAATAAAAAAAT
*
10201623 AAATAAAAGAAAAA
1 AAATAAAATAAAAA
10201637 GAAACAAAAG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (17 bp):
AAATAAAATAAAAAAAT
Found at i:10202439 original size:40 final size:39
Alignment explanation
Indices: 10202395--10202479 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 39
10202385 TTGAGACTGA
10202395 TACTGAACTGAATTATGGAA-TACTGAATATTGTTTTTGAG
1 TACTGAACTGAATTAT-GAAGTACTGAATATTG-TTTTGAG
* * *
10202435 TACTGAATTGAATTGTGAAGTTACTGAATATTGTTTTGTG
1 TACTGAACTGAATTATGAAG-TACTGAATATTGTTTTGAG
10202475 TACTG
1 TACTG
10202480 CATTGAACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
39 3 0.08
40 25 0.62
41 12 0.30
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.42
Consensus pattern (39 bp):
TACTGAACTGAATTATGAAGTACTGAATATTGTTTTGAG
Found at i:10202473 original size:23 final size:21
Alignment explanation
Indices: 10202415--10202474 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
10202405 AATTATGGAA
10202415 TACTGAATATTGTTTT-TGAG
1 TACTGAATATTGTTTTGTGAG
**
10202435 TACTG-A-ATTGAATTGTGAAG
1 TACTGAATATTGTTTTGTG-AG
10202455 TTACTGAATATTGTTTTGTG
1 -TACTGAATATTGTTTTGTG
10202475 TACTGCATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 6 0.19
19 3 0.10
20 7 0.23
21 5 0.16
22 1 0.03
23 9 0.29
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.47
Consensus pattern (21 bp):
TACTGAATATTGTTTTGTGAG
Found at i:10202485 original size:40 final size:41
Alignment explanation
Indices: 10202415--10202502 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 41
10202405 AATTATGGAA
*
10202415 TACTGAATATTGTTTTTGAGTACTGAATTGAA-TTGTGAAGT
1 TACTGAATATTGTTTTTGAGTACTGAATTGAACTT-TGAAAT
* *
10202456 TACTGAATATTG-TTTTGTGTACTGCATTGAACTTTGAAAT
1 TACTGAATATTGTTTTTGAGTACTGAATTGAACTTTGAAAT
10202496 TACTGAA
1 TACTGAA
10202503 GTAATGAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 29 0.67
41 14 0.33
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (41 bp):
TACTGAATATTGTTTTTGAGTACTGAATTGAACTTTGAAAT
Found at i:10202774 original size:45 final size:44
Alignment explanation
Indices: 10202721--10202805 Score: 134
Period size: 45 Copynumber: 1.9 Consensus size: 44
10202711 TGTTACCAAT
*
10202721 TTGACACTTTGTGTGTTGAATACTATTACAGTTACTGCTATAGA
1 TTGACACTTTGCGTGTTGAATACTATTACAGTTACTGCTATAGA
* *
10202765 TTGAGCACTTTGCGTGTTGAATACTGTTACTGTTACTGCTA
1 TTGA-CACTTTGCGTGTTGAATACTATTACAGTTACTGCTA
10202806 CCGTTACTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 4 0.11
45 33 0.89
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (44 bp):
TTGACACTTTGCGTGTTGAATACTATTACAGTTACTGCTATAGA
Found at i:10206469 original size:11 final size:11
Alignment explanation
Indices: 10206455--10206495 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
10206445 TGTTTTCTCC
10206455 CTATTTTGCTA
1 CTATTTTGCTA
*
10206466 CTATTTTACTA
1 CTATTTTGCTA
* *
10206477 TTATGTTGCTA
1 CTATTTTGCTA
10206488 CTATTTTG
1 CTATTTTG
10206496 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:10208774 original size:37 final size:37
Alignment explanation
Indices: 10208733--10208808 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
10208723 TGAAAGCATA
10208733 ATTGAATTCCAACATCATTGACAAATGAAAAGTATGC
1 ATTGAATTCCAACATCATTGACAAATGAAAAGTATGC
10208770 ATTGAATTCCAACATCATTGACAAATGAAAAGTATGC
1 ATTGAATTCCAACATCATTGACAAATGAAAAGTATGC
10208807 AT
1 AT
10208809 GAAATACACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (37 bp):
ATTGAATTCCAACATCATTGACAAATGAAAAGTATGC
Found at i:10209792 original size:27 final size:27
Alignment explanation
Indices: 10209762--10209816 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
10209752 AATATAATAT
10209762 AATTA-TAAAATAATTAAATTGTAATTA
1 AATTATTAAAAT-ATTAAATTGTAATTA
* * *
10209789 AATTATTAACATATTGAATTTTAATTA
1 AATTATTAAAATATTAAATTGTAATTA
10209816 A
1 A
10209817 TTTTATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (27 bp):
AATTATTAAAATATTAAATTGTAATTA
Found at i:10217687 original size:5 final size:5
Alignment explanation
Indices: 10217679--10217710 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
10217669 GGATATTATT
10217679 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
10217711 TTACAACAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:10221035 original size:19 final size:20
Alignment explanation
Indices: 10221011--10221055 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
10221001 ATTGTATTCC
10221011 ATATTTCATT-TTTATTTTA
1 ATATTTCATTCTTTATTTTA
*
10221030 ATATTTGATTCTTTATTTTA
1 ATATTTCATTCTTTATTTTA
10221050 ATATTT
1 ATATTT
10221056 TATAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (20 bp):
ATATTTCATTCTTTATTTTA
Found at i:10221065 original size:20 final size:20
Alignment explanation
Indices: 10221022--10221068 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
10221012 TATTTCATTT
***
10221022 TTATTTTAATATTTGATTCT
1 TTATTTTAATATTTGATAAA
*
10221042 TTATTTTAATATTTTATAAA
1 TTATTTTAATATTTGATAAA
10221062 TTATTTT
1 TTATTTT
10221069 TCTAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATTTTAATATTTGATAAA
Found at i:10229274 original size:15 final size:16
Alignment explanation
Indices: 10229254--10229292 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
10229244 GTTGTGCAAC
10229254 TTCTTTTTTTTAT-TT
1 TTCTTTTTTTTATATT
*
10229269 TTCTTTCTTTTATATT
1 TTCTTTTTTTTATATT
*
10229285 TTGTTTTT
1 TTCTTTTT
10229293 AAATTGAGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (16 bp):
TTCTTTTTTTTATATT
Found at i:10230411 original size:9 final size:9
Alignment explanation
Indices: 10230373--10230419 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
10230363 ATATTTATAT
10230373 ATGTATAATA
1 ATGTATAA-A
*
10230383 AGTATATAAA
1 A-TGTATAAA
10230393 AT-TA-AAA
1 ATGTATAAA
10230400 ATGTATAAA
1 ATGTATAAA
10230409 ATGTATAAA
1 ATGTATAAA
10230418 AT
1 AT
10230420 TAAAATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
7 5 0.15
8 4 0.12
9 15 0.45
10 3 0.09
11 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (9 bp):
ATGTATAAA
Found at i:10230421 original size:25 final size:27
Alignment explanation
Indices: 10230373--10230424 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
10230363 ATATTTATAT
10230373 ATGTATAATAAGTATATAAAATTAAAA
1 ATGTATAATAAGTATATAAAATTAAAA
*
10230400 ATGTATAA-AA-TGTATAAAATTAAAA
1 ATGTATAATAAGTATATAAAATTAAAA
10230425 TTTAATGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 14 0.58
26 2 0.08
27 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.33
Consensus pattern (27 bp):
ATGTATAATAAGTATATAAAATTAAAA
Found at i:10232448 original size:27 final size:27
Alignment explanation
Indices: 10232406--10232604 Score: 231
Period size: 27 Copynumber: 7.3 Consensus size: 27
10232396 CAGAAAGGTT
* *
10232406 GTAAGATTACCGAAATACCCTCGACGG
1 GTAAAATTACCGAAATACCCTCGATGG
*
10232433 GTAAAATTACCAAAATACCCTCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
*
10232460 GTAAAATTACCGAAATA-CCTCCGAAGG
1 GTAAAATTACCGAAATACCCT-CGATGG
* *
10232487 GTAAAATTATCGAAATACCCTCAATGG
1 GTAAAATTACCGAAATACCCTCGATGG
* *
10232514 GTAAAATTACCAAAATAACCTCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
** *
10232541 GTAAAATTATTGAAATA-CCTCCTGAAGG
1 GTAAAATTACCGAAATACCCT-C-GATGG
**
10232569 GTAAAATTGTCGAAATACCCTCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
*
10232596 GTTAAATTA
1 GTAAAATTA
10232605 TTAAAATACC
Statistics
Matches: 146, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.04
27 114 0.78
28 23 0.16
29 3 0.02
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (27 bp):
GTAAAATTACCGAAATACCCTCGATGG
Found at i:10232556 original size:81 final size:82
Alignment explanation
Indices: 10232406--10232604 Score: 310
Period size: 81 Copynumber: 2.4 Consensus size: 82
10232396 CAGAAAGGTT
* * * *
10232406 GTAAGATTACCGAAATACCCTCGACGGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTACC
1 GTAAAATTATCGAAATACCCTCGATGGGTAAAATTACCAAAATAACCTCGATGGGTAAAATTACC
10232471 GAAATACCTCC-GAAGG
66 GAAATACCTCCTGAAGG
* **
10232487 GTAAAATTATCGAAATACCCTCAATGGGTAAAATTACCAAAATAACCTCGATGGGTAAAATTATT
1 GTAAAATTATCGAAATACCCTCGATGGGTAAAATTACCAAAATAACCTCGATGGGTAAAATTACC
10232552 GAAATACCTCCTGAAGG
66 GAAATACCTCCTGAAGG
* *
10232569 GTAAAATTGTCGAAATACCCTCGATGGGTTAAATTA
1 GTAAAATTATCGAAATACCCTCGATGGGTAAAATTA
10232605 TTAAAATACC
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 69 0.64
82 38 0.36
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (82 bp):
GTAAAATTATCGAAATACCCTCGATGGGTAAAATTACCAAAATAACCTCGATGGGTAAAATTACC
GAAATACCTCCTGAAGG
Found at i:10232628 original size:27 final size:28
Alignment explanation
Indices: 10232417--10232628 Score: 132
Period size: 27 Copynumber: 7.8 Consensus size: 28
10232407 TAAGATTACC
* * **
10232417 GAAATA-CCCTCGACGGGTAAAATTACC
1 GAAATACCCCCCGAAGGGTAAAATTATT
* * * **
10232444 AAAATA-CCCTCGATGGGTAAAATTACC
1 GAAATACCCCCCGAAGGGTAAAATTATT
* *
10232471 GAAATA-CCTCCGAAGGGTAAAATTATC
1 GAAATACCCCCCGAAGGGTAAAATTATT
* **
10232498 GAAATA-CCCTC-AATGGGTAAAATTACC
1 GAAATACCCCCCGAA-GGGTAAAATTATT
* * * *
10232525 AAAATA-ACCTCGATGGGTAAAATTATT
1 GAAATACCCCCCGAAGGGTAAAATTATT
* * * *
10232552 GAAATACCTCCTGAAGGGTAAAATTGTC
1 GAAATACCCCCCGAAGGGTAAAATTATT
* * *
10232580 GAAATA-CCCTCGATGGGTTAAATTATT
1 GAAATACCCCCCGAAGGGTAAAATTATT
*
10232607 AAAATACCCCCCGAAGGGTAAA
1 GAAATACCCCCCGAAGGGTAAA
10232629 CCAAAATGCC
Statistics
Matches: 147, Mismatches: 34, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
26 2 0.01
27 112 0.76
28 33 0.22
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (28 bp):
GAAATACCCCCCGAAGGGTAAAATTATT
Found at i:10238475 original size:6 final size:6
Alignment explanation
Indices: 10238466--10238513 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
10238456 TTTATTTCTA
* * * *
10238466 TTATTT TTATTGT TTATTT CTATTA TTATTT TTACTA TTATTT TTATT
1 TTATTT TTATT-T TTATTT TTATTT TTATTT TTATTT TTATTT TTATT
10238514 ATTCTTAGTA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (6 bp):
TTATTT
Found at i:10238556 original size:13 final size:12
Alignment explanation
Indices: 10238441--10238516 Score: 71
Period size: 12 Copynumber: 5.9 Consensus size: 12
10238431 TACCCTTTTC
*
10238441 TTTTTCTTATTA
1 TTTTTATTATTA
10238453 TTGTTTATTTCTATTA
1 TT-TTTA--T-TATTA
*
10238469 TTTTTATTGTTTA
1 TTTTTATT-ATTA
*
10238482 TTTCTATTATTA
1 TTTTTATTATTA
*
10238494 TTTTTACTATTA
1 TTTTTATTATTA
10238506 TTTTTATTATT
1 TTTTTATTATT
10238517 CTTAGTATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
12 26 0.50
13 14 0.27
15 5 0.10
16 7 0.13
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:10238563 original size:21 final size:20
Alignment explanation
Indices: 10238464--10238575 Score: 76
Period size: 20 Copynumber: 5.8 Consensus size: 20
10238454 TGTTTATTTC
*
10238464 TATTATTTTTATT-GTTTAT
1 TATTATTTTTATTATTTTAT
* *
10238483 T-TCTATTATTA-T-TTTTAC
1 TAT-TATTTTTATTATTTTAT
*
10238501 TATTATTTTTATTATTCTTAG
1 TATTATTTTTATTATT-TTAT
*
10238522 TATT-TTTTCT-TTCTTTT-T
1 TATTATTTT-TATTATTTTAT
10238540 TATTATTGTTTATTATTTTAT
1 TATTATT-TTTATTATTTTAT
* *
10238561 TATTCTTATTATTAT
1 TATTATTTTTATTAT
10238576 GATTAGTATC
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
18 18 0.25
19 15 0.21
20 25 0.34
21 15 0.21
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (20 bp):
TATTATTTTTATTATTTTAT
Found at i:10243083 original size:21 final size:21
Alignment explanation
Indices: 10243057--10243097 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10243047 AATTATTCTA
10243057 AAAATTGTAAAAAAAAACTTC
1 AAAATTGTAAAAAAAAACTTC
* *
10243078 AAAATTTTTAAAAAAAACTT
1 AAAATTGTAAAAAAAAACTT
10243098 GTTTTAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATTGTAAAAAAAAACTTC
Found at i:10245955 original size:40 final size:40
Alignment explanation
Indices: 10245900--10246028 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
10245890 GCGTTTGGAC
*
10245900 AAAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTT
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTT
** *
10245940 AAAAAACGCCGCTAAAGGTCTAGCATTAGCGGCGCTTTTT
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTT
** *
10245980 GGAAAACGCTGCTAAAAAT-AAGCATTAGCGGCG-TTTTT
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTT
*
10246018 CAAAAAGCGCC
1 -AAAAAACGCC
10246029 ACAAAAAACC
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
38 5 0.07
39 19 0.26
40 50 0.68
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTT
Found at i:10246151 original size:41 final size:41
Alignment explanation
Indices: 10246087--10246271 Score: 275
Period size: 41 Copynumber: 4.5 Consensus size: 41
10246077 TTTAACAGCG
* *
10246087 TTTTTGAAAAAGCGCCTCTAATGCTCGGGCCTTTAGCGGCA
1 TTTTTAAAAAAGCGCCGCTAATGCTCGGGCCTTTAGCGGCA
*
10246128 TTTTTAAAAAAGCGCCGCCAATGCTCGGGCCTTTAGCGG-A
1 TTTTTAAAAAAGCGCCGCTAATGCTCGGGCCTTTAGCGGCA
*
10246168 GTTTTTAAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGGCA
1 -TTTTTAAAAAAGCGCCGCTAATGCTCGGGCCTTTAGCGGCA
* * *
10246210 TTTTT-GAAAAGTGCCGCTAATGCTCGTGCCTTTAGCGGCA
1 TTTTTAAAAAAGCGCCGCTAATGCTCGGGCCTTTAGCGGCA
*
10246250 TTTTTTAAAAAGCGCCGCTAAT
1 TTTTTAAAAAAGCGCCGCTAAT
10246272 AATAATAAAA
Statistics
Matches: 130, Mismatches: 11, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
40 37 0.28
41 92 0.71
42 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (41 bp):
TTTTTAAAAAAGCGCCGCTAATGCTCGGGCCTTTAGCGGCA
Done.