Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 45 of 310
Found at i:13332649 original size:28 final size:27
Alignment explanation
Indices: 13332583--13332651 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 27
13332573 TTTCTTAATT
*
13332583 TTTATTATTTATTATTTTATTTCATTT
1 TTTATTATTTATTATTTTATTTCATTA
* *
13332610 TATTAGTATTTATTATTTTATTTTATTA
1 T-TTATTATTTATTATTTTATTTCATTA
13332638 TTTATTACTTTATT
1 TTTATTA-TTTATT
13332652 TTTGGATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 6 0.17
28 30 0.83
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (27 bp):
TTTATTATTTATTATTTTATTTCATTA
Found at i:13332652 original size:12 final size:11
Alignment explanation
Indices: 13332583--13332643 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 11
13332573 TTTCTTAATT
13332583 TTTATTATTTA
1 TTTATTATTTA
*
13332594 TTATTTTATTTCA
1 TT-TATTATTT-A
*
13332607 TTTTATTA-GTA
1 -TTTATTATTTA
13332618 TTTATTATTTTA
1 TTTATTA-TTTA
13332630 TTTTATTATTTA
1 -TTTATTATTTA
13332642 TT
1 TT
13332644 ACTTTATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
10 7 0.17
11 5 0.12
12 14 0.35
13 12 0.30
14 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:13333833 original size:100 final size:100
Alignment explanation
Indices: 13333669--13333853 Score: 307
Period size: 100 Copynumber: 1.9 Consensus size: 100
13333659 AATAAATTTT
* * * *
13333669 TTAGGAGTATGTTGGGTTAAGTAACCGGGGTGGGGTGCTTGGCTGTCATCTCTCTTCGTGTCAAA
1 TTAGGAGTATGTTGAGCTAAGTAACCGGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAA
*
13333734 AGGTTCGATATGTTCTTAAGAAAAATATAAATAAA
66 AGGTTCGATATATTCTTAAGAAAAATATAAATAAA
*
13333769 TTAGGAGTATGTTGAGCTAAGTAACCGGGGTGGGGTACTTGGTTGTCATCTCTCTTCGCGTCAAA
1 TTAGGAGTATGTTGAGCTAAGTAACCGGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAA
*
13333834 AGGTTCGATGTATTCTTAAG
66 AGGTTCGATATATTCTTAAG
13333854 CAATAATAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 78 1.00
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.34
Consensus pattern (100 bp):
TTAGGAGTATGTTGAGCTAAGTAACCGGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAA
AGGTTCGATATATTCTTAAGAAAAATATAAATAAA
Found at i:13341418 original size:15 final size:15
Alignment explanation
Indices: 13341398--13341431 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
13341388 ACACACGGCC
13341398 GTGTAAAATGACCGT
1 GTGTAAAATGACCGT
*
13341413 GTGTAACATGACCGT
1 GTGTAAAATGACCGT
13341428 GTGT
1 GTGT
13341432 CGCACACGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (15 bp):
GTGTAAAATGACCGT
Found at i:13342510 original size:43 final size:43
Alignment explanation
Indices: 13342376--13342541 Score: 122
Period size: 43 Copynumber: 3.9 Consensus size: 43
13342366 ATAAGCACGT
* * * * *
13342376 ACAATGCC-ATATCCCAGATATGGTCTTATATGTTAT-CATATA
1 ACAATGCCAATGTCCTAGACATGGTCTTACATGTAATCCA-ATA
* * * * * * * * *
13342418 TCGATGTCACTGTCCTAGACAGGGTCTTACACGAAATCGATTA
1 ACAATGCCAATGTCCTAGACATGGTCTTACATGTAATCCAATA
13342461 ACAATGCCAATGTCCTAGACATGGTCTTACATGTAATCTCAAT-
1 ACAATGCCAATGTCCTAGACATGGTCTTACATGTAATC-CAATA
* * * **
13342504 ATAATGCCAATGTCCCAGACATTGTCTTTTATGTAATC
1 ACAATGCCAATGTCCTAGACATGGTCTTACATGTAATC
13342542 ACATCTCGAT
Statistics
Matches: 93, Mismatches: 28, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
42 5 0.05
43 85 0.91
44 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (43 bp):
ACAATGCCAATGTCCTAGACATGGTCTTACATGTAATCCAATA
Found at i:13344192 original size:17 final size:18
Alignment explanation
Indices: 13344156--13344192 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
13344146 ATAATAGTAA
13344156 TAATAAAATGCTAATAAG
1 TAATAAAATGCTAATAAG
13344174 TAAT-AAATG-TAATATAG
1 TAATAAAATGCTAATA-AG
13344191 TA
1 TA
13344193 CTAGAAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.54, C:0.03, G:0.11, T:0.32
Consensus pattern (18 bp):
TAATAAAATGCTAATAAG
Found at i:13344550 original size:25 final size:25
Alignment explanation
Indices: 13344505--13344566 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
13344495 TAATAACGAT
13344505 AATATAACAATAATAGTAATAA-AA
1 AATATAACAATAATAGTAATAATAA
13344529 AATAGTAACAATAATA-TAAATAATAA
1 AATA-TAACAATAATAGT-AATAATAA
*
13344555 AA-ATAAAAATAA
1 AATATAACAATAA
13344567 AAAGATAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 13 0.38
25 17 0.50
26 4 0.12
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (25 bp):
AATATAACAATAATAGTAATAATAA
Found at i:13344758 original size:3 final size:3
Alignment explanation
Indices: 13344478--13344747 Score: 123
Period size: 3 Copynumber: 92.0 Consensus size: 3
13344468 TTGCATTAAC
* * * * * *
13344478 AAT AAT AAT AGT AAG AAT AAT AAC GAT AAT -AT AAC AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
13344525 AA- AA- AAT AGT AAC AAT AAT -AT AAAT AAT AAA AAT AAA AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
13344567 AA- AGAT AACG AA- AAT AAT ACT GAC ACT GAC AAT AAT ACT AAT AAT
1 AAT A-AT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
13344612 AAC AAT -AT ATT AAT AAT ACT GAT -AT ATT CAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
13344658 AAT AAT AAT AAT AAT AAT AAT AAT AGT AGA- AAT AAC AAT CAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* ** *
13344702 AAGT AAT AAT AAT ACA- CAT AGG AAT AAT AAT AAT AAT AGT AAT AAT
1 AA-T AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13344748 TTGAATAATA
Statistics
Matches: 192, Mismatches: 59, Indels: 32
0.68 0.21 0.11
Matches are distributed among these distances:
2 21 0.11
3 162 0.84
4 9 0.05
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:13345349 original size:28 final size:29
Alignment explanation
Indices: 13345286--13345349 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
13345276 TTTTTCTCTT
* *
13345286 TTTATTTTATTTTATACTTGTTTAATATA
1 TTTATGTTATTTTATACTTATTTAATATA
* *
13345315 TGTATGTTATTTT-TACTTATATT-ATATG
1 TTTATGTTATTTTATACTTAT-TTAATATA
13345343 TTTATGT
1 TTTATGT
13345350 ATATAAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (29 bp):
TTTATGTTATTTTATACTTATTTAATATA
Found at i:13351334 original size:43 final size:42
Alignment explanation
Indices: 13351220--13351365 Score: 152
Period size: 43 Copynumber: 3.4 Consensus size: 42
13351210 TCCCAAATAT
* * * *
13351220 GGTCTTACATGTAATCAT-ATATCGATGCCATTGACCCAGACAG
1 GGTCTTACACGTAATCATCA-ATC-ATGCCAATGTCCCAGACAC
* *
13351263 GGTCTTACACGAAATCGATTAATCATGCCAATGTCCCAGACAC
1 GGTCTTACACGTAATC-ATCAATCATGCCAATGTCCCAGACAC
* *
13351306 GGTCTTACACGTAATC-TCAATACAATGCCAATGTCCTAGACAT
1 GGTCTTACACGTAATCATCAAT-C-ATGCCAATGTCCCAGACAC
*
13351349 GGTCTTACATGTAATCA
1 GGTCTTACACGTAATCA
13351366 CATCTCGATG
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
41 4 0.05
42 1 0.01
43 77 0.88
44 5 0.06
45 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (42 bp):
GGTCTTACACGTAATCATCAATCATGCCAATGTCCCAGACAC
Found at i:13354254 original size:27 final size:27
Alignment explanation
Indices: 13354232--13354340 Score: 152
Period size: 27 Copynumber: 4.1 Consensus size: 27
13354222 GTCACCAGAT
*
13354232 ACAGAT-ATTGTGGCAGAGCCACCA-G
1 ACAGATAATTGTGGCATAGCCACCAGG
* *
13354257 ATCAGATAATCGTGGCATTGCCACCAGG
1 A-CAGATAATTGTGGCATAGCCACCAGG
13354285 ACAGAT-ATATGTGGCATAGCCACCAGG
1 ACAGATAAT-TGTGGCATAGCCACCAGG
13354312 ACAGATAATTGTGGCATAGCCACCAGG
1 ACAGATAATTGTGGCATAGCCACCAGG
13354339 AC
1 AC
13354341 GCTTCCTCCA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
25 1 0.01
26 7 0.09
27 62 0.84
28 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (27 bp):
ACAGATAATTGTGGCATAGCCACCAGG
Found at i:13354742 original size:8 final size:8
Alignment explanation
Indices: 13354726--13354755 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
13354716 CTCAAAATAC
13354726 CGGCTTTT
1 CGGCTTTT
*
13354734 CGGCATTT
1 CGGCTTTT
13354742 CGGCTTTT
1 CGGCTTTT
13354750 CGGCTT
1 CGGCTT
13354756 GTGCCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:13355450 original size:22 final size:22
Alignment explanation
Indices: 13355422--13355467 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
13355412 AACTTGCATG
13355422 CATGTTATTTAAACATGTATAT
1 CATGTTATTTAAACATGTATAT
13355444 CATGTTATTTAAACATGTATAT
1 CATGTTATTTAAACATGTATAT
13355466 CA
1 CA
13355468 CCAATCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
CATGTTATTTAAACATGTATAT
Found at i:13357909 original size:40 final size:40
Alignment explanation
Indices: 13357854--13357961 Score: 189
Period size: 40 Copynumber: 2.7 Consensus size: 40
13357844 GAGCATTGGA
*
13357854 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
13357894 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
13357934 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
13357962 ATGTGTTTGC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
Found at i:13359760 original size:26 final size:26
Alignment explanation
Indices: 13359729--13359836 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
13359719 TGAAATGCCC
*
13359729 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
13359755 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
13359781 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
13359807 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
13359833 ATCA
1 ATCA
13359837 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:13367921 original size:6 final size:6
Alignment explanation
Indices: 13367871--13367918 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 6
13367861 GATGGATCAT
* *
13367871 GTGCCC GTGCCC GTGCCC GTGCCC GTGCCC ATGCCC GTGCCC ATGCCC
1 GTGCCC GTGCCC GTGCCC GTGCCC GTGCCC GTGCCC GTGCCC GTGCCC
13367919 ATGTCCCCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.04, C:0.50, G:0.29, T:0.17
Consensus pattern (6 bp):
GTGCCC
Found at i:13378118 original size:20 final size:20
Alignment explanation
Indices: 13378093--13378132 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
13378083 AAAATATTTA
*
13378093 TTCTCTAAACCTTAACTCAT
1 TTCTCTAAACCTTAAATCAT
*
13378113 TTCTCTAATCCTTAAATCAT
1 TTCTCTAAACCTTAAATCAT
13378133 AAATTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCTCTAAACCTTAAATCAT
Found at i:13386569 original size:20 final size:20
Alignment explanation
Indices: 13386544--13386581 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13386534 ATGATATACC
*
13386544 ACATTTAACCATCACATGAA
1 ACATTTAACCATAACATGAA
*
13386564 ACATTTAAGCATAACATG
1 ACATTTAACCATAACATG
13386582 CACAATTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (20 bp):
ACATTTAACCATAACATGAA
Found at i:13397639 original size:53 final size:51
Alignment explanation
Indices: 13397570--13397673 Score: 120
Period size: 53 Copynumber: 2.0 Consensus size: 51
13397560 ACAAAGAAAG
* * *
13397570 GGAAAGAGAAAATTGAC-AGGGATTAATCCGAAAAATTTACGGTTTGTATTTCT
1 GGAAAGAGAAAATTGACGA-AGAGTAATCCG-AAAA-TTACGGTTTATATTTCT
** *
13397623 GGAAAGAGAAGGTTGACGAAGAGTAATCCGATAATTACGGTTTATATTTCT
1 GGAAAGAGAAAATTGACGAAGAGTAATCCGAAAATTACGGTTTATATTTCT
13397674 ATAAACTGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
51 16 0.36
52 3 0.07
53 24 0.55
54 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.30
Consensus pattern (51 bp):
GGAAAGAGAAAATTGACGAAGAGTAATCCGAAAATTACGGTTTATATTTCT
Found at i:13399267 original size:25 final size:26
Alignment explanation
Indices: 13399206--13399255 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
13399196 TATTTGTCTT
*
13399206 TATATTTG-TTT-TTATGTTTTTAAA
1 TATATTTGATTTATTATATTTTTAAA
13399230 TATATTTGATTTATTATATTTTTAAA
1 TATATTTGATTTATTATATTTTTAAA
13399256 ATTTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.35
25 3 0.13
26 12 0.52
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (26 bp):
TATATTTGATTTATTATATTTTTAAA
Found at i:13401485 original size:17 final size:17
Alignment explanation
Indices: 13401463--13401496 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13401453 TTAGAATTGG
13401463 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTATTTA
*
13401480 ATTGAGAAATTTATTTA
1 ATTGAGAAAATTATTTA
13401497 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (17 bp):
ATTGAGAAAATTATTTA
Found at i:13405258 original size:31 final size:31
Alignment explanation
Indices: 13405223--13405345 Score: 201
Period size: 31 Copynumber: 4.0 Consensus size: 31
13405213 CTTGTCACTT
*
13405223 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
13405254 GTAGCCGAAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
13405285 GCAACCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
13405316 GTAGCCGAAGCTACCACTTTTCACTTATCA
1 GTAGCCGAAGCTACCACTTTTCACTGATCA
13405346 TTTGTCCTTG
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 84 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:13405425 original size:50 final size:51
Alignment explanation
Indices: 13405316--13405426 Score: 179
Period size: 50 Copynumber: 2.2 Consensus size: 51
13405306 CACTGATCAG
* *
13405316 GTAGCCGAAGCTACCACTTTTCACTTATCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTACCACTTATCACTTATCACTTGTCCTTGATCAGATAAGT
* *
13405367 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTTCTTGATCAGATAAGT
1 GTAGCCGAAGCTACCACTTATCACTTATCACTTGTCCTTGATCAGATAAGT
13405417 GTAGCCGAAG
1 GTAGCCGAAG
13405427 ACATCCTAGG
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
50 32 0.57
51 24 0.43
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (51 bp):
GTAGCCGAAGCTACCACTTATCACTTATCACTTGTCCTTGATCAGATAAGT
Found at i:13408604 original size:43 final size:43
Alignment explanation
Indices: 13408519--13408605 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
13408509 CACCGTTGTG
* * * *
13408519 TCCAACCCCCACTACCATCGTCTTTCCTCTCAGTCCTTACTAT
1 TCCAACCCCCACCACCATCCTCTTTCCTCTCAGACCTCACTAT
13408562 TCCAACCCCCACCACC-TCTCTCTTTCCTCTC-GCACCTCACTAT
1 TCCAACCCCCACCACCATC-CTCTTTCCTCTCAG-ACCTCACTAT
13408605 T
1 T
13408606 GTAAAAAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 3 0.08
43 35 0.92
ACGTcount: A:0.17, C:0.48, G:0.03, T:0.31
Consensus pattern (43 bp):
TCCAACCCCCACCACCATCCTCTTTCCTCTCAGACCTCACTAT
Found at i:13410850 original size:18 final size:18
Alignment explanation
Indices: 13410813--13410851 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
13410803 CAAACACTAT
**
13410813 AAAATTATATAAAATGTA
1 AAAATTATATAAAAAATA
13410831 AAAATTATATAAAAAATA
1 AAAATTATATAAAAAATA
13410849 AAA
1 AAA
13410852 TATTTAGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAATTATATAAAAAATA
Found at i:13415578 original size:6 final size:6
Alignment explanation
Indices: 13415569--13415601 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
13415559 TTTATTCTAT
*
13415569 TTTTTA TTTTTA TTTCT- TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
13415602 ATTATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:13415590 original size:17 final size:17
Alignment explanation
Indices: 13415568--13415600 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13415558 ATTTATTCTA
13415568 TTTTTTATTTTTATTTC
1 TTTTTTATTTTTATTTC
13415585 TTTTTTATTTTTATTT
1 TTTTTTATTTTTATTT
13415601 TATTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTATTTTTATTTC
Found at i:13415896 original size:3 final size:3
Alignment explanation
Indices: 13415888--13415936 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
13415878 ATATTACTAC
13415888 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
13415934 ATT
1 ATT
13415937 GTCACATTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:13419580 original size:15 final size:15
Alignment explanation
Indices: 13419544--13419593 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
13419534 CGATGTCCTT
13419544 TTTGCAT-TCATGCA
1 TTTGCATCTCATGCA
13419558 TTTGCATCTCATAGCA
1 TTTGCATCTCAT-GCA
**
13419574 TTT-CATCGGAT-CA
1 TTTGCATCTCATGCA
13419587 TTTGCAT
1 TTTGCAT
13419594 TCAAAGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 10 0.32
16 6 0.19
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (15 bp):
TTTGCATCTCATGCA
Found at i:13427940 original size:88 final size:88
Alignment explanation
Indices: 13427827--13428138 Score: 248
Period size: 88 Copynumber: 3.6 Consensus size: 88
13427817 CAAATCGAAG
* * * * *
13427827 ACATAGCAGATTTGACTTTCGGATGTTCTCACACCGAAACAGATCCAAGATAACAGATCTGGCAT
1 ACATAGCAGATCTAACCTTCAGATGTTCTCACACCGAAGCAGATCCAAGATAACAGATCTGGCAT
13427892 CTCCATTTCGACGGAGAGCATAT
66 CTCCATTTCGACGGAGAGCATAT
* * * *
13427915 ACATAGCAGATCTAACCTTCAGATGTT-T-ATACTGAAGCAGACCCAAGAT----GATTTGGCAT
1 ACATAGCAGATCTAACCTTCAGATGTTCTCACACCGAAGCAGATCCAAGATAACAGATCTGGCA-
*** * * * * *
13427974 TCTTGTGTTTACAACGAACA-AATCGAAG
65 TC-TCCATTT-CGACGGAGAGCAT---AT
* * * * *
13428002 ACATAGCAGATTTGACTTTCGGATGTTCTCACGCCGAAGCAGATCCAAGATAACAGATCTGGCAT
1 ACATAGCAGATCTAACCTTCAGATGTTCTCACACCGAAGCAGATCCAAGATAACAGATCTGGCAT
* *
13428067 CTCCATTTCGAAGGAGAGCAGAT
66 CTCCATTTCGACGGAGAGCATAT
* * *
13428090 ACATAGCAAATCTAACCTTCAGATGATT-T--TACTGAAGCAGATCCAAGAT
1 ACATAGCAGATCTAACCTTCAGATG-TTCTCACACCGAAGCAGATCCAAGAT
13428139 GATTTGGCAT
Statistics
Matches: 166, Mismatches: 44, Indels: 30
0.69 0.18 0.12
Matches are distributed among these distances:
82 8 0.05
83 2 0.01
84 6 0.04
85 6 0.04
86 34 0.20
87 25 0.15
88 46 0.28
89 19 0.11
90 5 0.03
91 5 0.03
92 2 0.01
93 8 0.05
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (88 bp):
ACATAGCAGATCTAACCTTCAGATGTTCTCACACCGAAGCAGATCCAAGATAACAGATCTGGCAT
CTCCATTTCGACGGAGAGCATAT
Found at i:13427944 original size:175 final size:175
Alignment explanation
Indices: 13427735--13428189 Score: 750
Period size: 175 Copynumber: 2.6 Consensus size: 175
13427725 AGGAGCAAAT
* * *
13427735 CAGACACATAGCAGATCTAACTTTCATATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATT
1 CAGATACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATT
*
13427800 CTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCGAA
66 CTTGTGTTTACAACGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCGAA
*
13427865 ACAGATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAG
131 ACAGATCCAAGATAACAGATCTGGCATCTCCATTTCGAAGGAGAG
* *
13427910 CATATACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGACCCAAGATGATTTGGCATT
1 CAGATACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATT
*
13427975 CTTGTGTTTACAACGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACGCCGAA
66 CTTGTGTTTACAACGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCGAA
*
13428040 GCAGATCCAAGATAACAGATCTGGCATCTCCATTTCGAAGGAGAG
131 ACAGATCCAAGATAACAGATCTGGCATCTCCATTTCGAAGGAGAG
*
13428085 CAGATACATAGCAAATCTAACCTTCAGATGATTT-TACTGAAGCAGATCCAAGATGATTTGGCAT
1 CAGATACATAGCAGATCTAACCTTCAGATG-TTTATACTGAAGCAGATCCAAGATGATTTGGCAT
* * * * * *
13428149 CCTTGTGTTCACAATGAGCAAATCGAAGACACAGCTGATTT
65 TCTTGTGTTTACAACGAACAAATCGAAGACATAGCAGATTT
13428190 AGCTTTCACG
Statistics
Matches: 261, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
175 258 0.99
176 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (175 bp):
CAGATACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATT
CTTGTGTTTACAACGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCGAA
ACAGATCCAAGATAACAGATCTGGCATCTCCATTTCGAAGGAGAG
Found at i:13429975 original size:12 final size:12
Alignment explanation
Indices: 13429958--13429989 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
13429948 AAAACTTTTC
13429958 TTTTATTATATA
1 TTTTATTATATA
13429970 TTTTATTATATA
1 TTTTATTATATA
13429982 TATTTATT
1 T-TTTATT
13429990 CTGTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTATTATATA
Found at i:13430005 original size:6 final size:6
Alignment explanation
Indices: 13429994--13430026 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
13429984 TTTATTCTGT
*
13429994 TTTTTA TTTTTA TTTCT- TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
13430027 ATTATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:13430007 original size:22 final size:22
Alignment explanation
Indices: 13429982--13430034 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
13429972 TTATTATATA
13429982 TATTTATTCTGT-TTTTTATTTT
1 TATTTATTCTGTATTTTTA-TTT
* * *
13430004 TATTTCTTTTTTATTTTTATTT
1 TATTTATTCTGTATTTTTATTT
13430026 TATTATATT
1 TATT-TATT
13430035 TTATATGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (22 bp):
TATTTATTCTGTATTTTTATTT
Found at i:13430015 original size:17 final size:17
Alignment explanation
Indices: 13429993--13430025 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13429983 ATTTATTCTG
13429993 TTTTTTATTTTTATTTC
1 TTTTTTATTTTTATTTC
13430010 TTTTTTATTTTTATTT
1 TTTTTTATTTTTATTT
13430026 TATTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTATTTTTATTTC
Found at i:13436545 original size:11 final size:11
Alignment explanation
Indices: 13436529--13436553 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13436519 CACCACTGTC
13436529 AAAAAATAAAA
1 AAAAAATAAAA
13436540 AAAAAATAAAA
1 AAAAAATAAAA
13436551 AAA
1 AAA
13436554 GCTGAAACAT
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:13437830 original size:21 final size:20
Alignment explanation
Indices: 13437806--13437844 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13437796 AAATTCAAAA
*
13437806 ATATGTATATAATTTTTAATT
1 ATATGTAT-TAAGTTTTAATT
*
13437827 ATATTTATTAAGTTTTAA
1 ATATGTATTAAGTTTTAA
13437845 GTGGTGGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATGTATTAAGTTTTAATT
Found at i:13444061 original size:16 final size:16
Alignment explanation
Indices: 13444024--13444077 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
13444014 TAGAGTGGAA
13444024 AGAAAATTGAAAGGAT
1 AGAAAATTGAAAGGAT
*
13444040 -GAAAAATTGAAAGGGT
1 AG-AAAATTGAAAGGAT
13444056 AGAAAATT-AGAAGGAT
1 AGAAAATTGA-AAGGAT
*
13444072 GGAAAA
1 AGAAAA
13444078 CATACTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 2 0.06
16 29 0.91
17 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.17
Consensus pattern (16 bp):
AGAAAATTGAAAGGAT
Found at i:13447687 original size:16 final size:16
Alignment explanation
Indices: 13447666--13447697 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
13447656 CTTTGGTAAA
13447666 GGCTTATGACAACAAC
1 GGCTTATGACAACAAC
13447682 GGCTTATGACAACAAC
1 GGCTTATGACAACAAC
13447698 TGACAAATAA
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:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (16 bp):
GGCTTATGACAACAAC
Found at i:13452135 original size:23 final size:23
Alignment explanation
Indices: 13452109--13452187 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
13452099 ATATAAATGT
13452109 AATAAATAATTTAAAATGGGTTC
1 AATAAATAATTTAAAATGGGTTC
** **
13452132 AATAAACCA-TTAAAATGAAAAATTC
1 AATAAATAATTTAAAATG---GGTTC
*
13452157 AGGCTAAATAATTTAAAATGGGTTC
1 A--ATAAATAATTTAAAATGGGTTC
13452182 AATAAA
1 AATAAA
13452188 CCATTAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
22 8 0.20
23 11 0.28
25 8 0.20
27 5 0.12
28 8 0.20
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (23 bp):
AATAAATAATTTAAAATGGGTTC
Found at i:13452146 original size:22 final size:22
Alignment explanation
Indices: 13452119--13452198 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 22
13452109 AATAAATAAT
13452119 TTAAAATGGGTTCAATAAACCA
1 TTAAAATGGGTTCAATAAACCA
** * **
13452141 TTAAAATGAAAAATTCAGGCTAAATAA
1 TTAAAATG---GGTTCA--ATAAACCA
13452168 TTTAAAATGGGTTCAATAAACCA
1 -TTAAAATGGGTTCAATAAACCA
13452191 TTAAAATG
1 TTAAAATG
13452199 AAAAATTCAG
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
22 16 0.38
23 5 0.12
25 8 0.19
27 5 0.12
28 8 0.19
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (22 bp):
TTAAAATGGGTTCAATAAACCA
Found at i:13452166 original size:50 final size:50
Alignment explanation
Indices: 13452111--13452220 Score: 211
Period size: 50 Copynumber: 2.2 Consensus size: 50
13452101 ATAAATGTAA
13452111 TAAATAATTTAAAATGGGTTCAATAAACCATTAAAATGAAAAATTCAGGC
1 TAAATAATTTAAAATGGGTTCAATAAACCATTAAAATGAAAAATTCAGGC
13452161 TAAATAATTTAAAATGGGTTCAATAAACCATTAAAATGAAAAATTCAGGC
1 TAAATAATTTAAAATGGGTTCAATAAACCATTAAAATGAAAAATTCAGGC
*
13452211 TAATTAATTT
1 TAAATAATTT
13452221 TTAAAATTAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (50 bp):
TAAATAATTTAAAATGGGTTCAATAAACCATTAAAATGAAAAATTCAGGC
Found at i:13460095 original size:132 final size:132
Alignment explanation
Indices: 13459939--13460189 Score: 362
Period size: 132 Copynumber: 1.9 Consensus size: 132
13459929 CTTTACTTGC
* * * *
13459939 TTGGTTTCTGGAGCACTAGCCTGCTCTGA-AGCCTGTATATTCTCCCTAGGAGGCTTCAT-GGCA
1 TTGGTTTCTGAAGCACTAGCCTGCT-TCACAGCCAGTATATTCTCCCTAGGAGGCTTCATAAG-A
*
13460002 TTCATAGGTAACTTGGCATCATCCTTATCAAAGAAGTCATCAGGAAGAGATCCTTTAACGTGCTT
64 TTCATAGGTAACTTGGCATCATCCCTATCAAAGAAGTCATCAGGAAGAGATCCTTTAACGTGCTT
13460067 TGTT
129 TGTT
* * *
13460071 TTGGTTTCTGAAGCACTAGCCTGCTTCACTGCCAGTTTATTCTCCCTTGGAGGCTTCATAAGATT
1 TTGGTTTCTGAAGCACTAGCCTGCTTCACAGCCAGTATATTCTCCCTAGGAGGCTTCATAAGATT
* ** *
13460136 CGTAGGTAACTTGGTTTCATCCCTATCAAAGAAGTTATCAGGAAGAGATCCTTT
66 CATAGGTAACTTGGCATCATCCCTATCAAAGAAGTCATCAGGAAGAGATCCTTT
13460190 CACTTTCTTG
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
131 2 0.02
132 102 0.97
133 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (132 bp):
TTGGTTTCTGAAGCACTAGCCTGCTTCACAGCCAGTATATTCTCCCTAGGAGGCTTCATAAGATT
CATAGGTAACTTGGCATCATCCCTATCAAAGAAGTCATCAGGAAGAGATCCTTTAACGTGCTTTG
TT
Found at i:13462647 original size:4 final size:4
Alignment explanation
Indices: 13462508--13462627 Score: 141
Period size: 4 Copynumber: 29.8 Consensus size: 4
13462498 AGTATTTATA
* * * * *
13462508 TCTG TCTA TCTG TCTA TCTG TCTA TCTG TCTA TCTG TCTTA TCTG TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TC-TG TCTG TCTG
* * *
13462557 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTC TCTG TCTC TCTG TCTC
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
* *
13462605 TCTG TCTA TCTG TCTA TCTG TCT
1 TCTG TCTG TCTG TCTG TCTG TCT
13462628 ATCTATCTAT
Statistics
Matches: 95, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
4 92 0.97
5 3 0.03
ACGTcount: A:0.06, C:0.28, G:0.16, T:0.51
Consensus pattern (4 bp):
TCTG
Found at i:13462649 original size:8 final size:8
Alignment explanation
Indices: 13462506--13462647 Score: 194
Period size: 8 Copynumber: 17.6 Consensus size: 8
13462496 AAAGTATTTA
13462506 TATCTGTC
1 TATCTGTC
13462514 TATCTGTC
1 TATCTGTC
13462522 TATCTGTC
1 TATCTGTC
13462530 TATCTGTC
1 TATCTGTC
13462538 TATCTGTC
1 TATCTGTC
13462546 TTATCTGTC
1 -TATCTGTC
*
13462555 TGTCTGTC
1 TATCTGTC
*
13462563 TGTCTGTC
1 TATCTGTC
*
13462571 TGTCTGTC
1 TATCTGTC
*
13462579 TGTCTGTC
1 TATCTGTC
*
13462587 TCTCTGTC
1 TATCTGTC
*
13462595 TCTCTGTC
1 TATCTGTC
*
13462603 TCTCTGTC
1 TATCTGTC
13462611 TATCTGTC
1 TATCTGTC
13462619 TATCTGTC
1 TATCTGTC
*
13462627 TATCTATC
1 TATCTGTC
*
13462635 TATCTATC
1 TATCTGTC
13462643 TATCT
1 TATCT
13462648 ATATATATAT
Statistics
Matches: 129, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
8 121 0.94
9 8 0.06
ACGTcount: A:0.09, C:0.27, G:0.13, T:0.51
Consensus pattern (8 bp):
TATCTGTC
Found at i:13465691 original size:30 final size:30
Alignment explanation
Indices: 13465657--13465753 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
13465647 ATATTTTATT
13465657 AATTTAATTTTAAATATAATAAATTTAATA
1 AATTTAATTTTAAATATAATAAATTTAATA
* * * **
13465687 AATTTAATTTTTAATATTCATAAAATTCGTA
1 AATTTAATTTTAAATA-TAATAAATTTAATA
* * * *
13465718 ATTTTAA-TTTAAATTCTACTAAATTCAATA
1 AATTTAATTTTAAA-TATAATAAATTTAATA
13465748 AATTTA
1 AATTTA
13465754 GCTCTCAATA
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
30 33 0.66
31 17 0.34
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (30 bp):
AATTTAATTTTAAATATAATAAATTTAATA
Found at i:13465939 original size:12 final size:12
Alignment explanation
Indices: 13465919--13465956 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
13465909 TTTCAAACTC
*
13465919 CAGCTCCAGCAG
1 CAGCCCCAGCAG
13465931 CAGCCCCAGCAG
1 CAGCCCCAGCAG
13465943 CAGCCCCAGCAG
1 CAGCCCCAGCAG
13465955 CA
1 CA
13465957 TCTCCGGCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.26, C:0.47, G:0.24, T:0.03
Consensus pattern (12 bp):
CAGCCCCAGCAG
Found at i:13471156 original size:21 final size:21
Alignment explanation
Indices: 13471110--13471156 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
13471100 TTGTGACGTG
**
13471110 ATTTTTTCTTGCTTCTTTTTC
1 ATTTTTTCTTGCTTCTAGTTC
*
13471131 CTTTTTTCTTGCTTCCTAGTT-
1 ATTTTTTCTTGCTT-CTAGTTC
13471152 ATTTT
1 ATTTT
13471157 GATCTTCACA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.06, C:0.19, G:0.06, T:0.68
Consensus pattern (21 bp):
ATTTTTTCTTGCTTCTAGTTC
Found at i:13478537 original size:19 final size:20
Alignment explanation
Indices: 13478515--13478554 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
13478505 ACAATAAGTG
13478515 TTATCATAAT-CAATTAAAT
1 TTATCATAATACAATTAAAT
* *
13478534 TTATCATGATACAATTTAAT
1 TTATCATAATACAATTAAAT
13478554 T
1 T
13478555 CATTTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (20 bp):
TTATCATAATACAATTAAAT
Found at i:13479772 original size:19 final size:19
Alignment explanation
Indices: 13479727--13479773 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
13479717 TAAATATTAA
*
13479727 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
13479746 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
13479765 AATAAAAAT
1 AATAAAAAT
13479774 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:13479826 original size:18 final size:18
Alignment explanation
Indices: 13479803--13479849 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
13479793 TAAATAAAAT
*
13479803 ACAGCAAGTCTTTTACTA
1 ACAGCAAGTCCTTTACTA
13479821 ACAGCAAGTCCTTTACTA
1 ACAGCAAGTCCTTTACTA
13479839 ACAGCAAGTCC
1 ACAGCAAGTCC
13479850 AAATACAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.26
Consensus pattern (18 bp):
ACAGCAAGTCCTTTACTA
Found at i:13480248 original size:23 final size:23
Alignment explanation
Indices: 13480222--13480357 Score: 125
Period size: 23 Copynumber: 5.9 Consensus size: 23
13480212 TCCAGCAACT
13480222 AAACACTTCAATTTGCAGCGA-TA
1 AAACACTTCAATTTGCAGC-ATTA
* *
13480245 AAACA-TCTCAATTTCCAGCAACT-
1 AAACACT-TCAATTTGCAGC-ATTA
*
13480268 AAACACTTCAATTTGCAGTACTTA
1 AAACACTTCAATTTGCAGCA-TTA
* * * *
13480292 AAACACTTTAATTTACAACATTT
1 AAACACTTCAATTTGCAGCATTA
* * *
13480315 AAGCACTTCAATTTACAGCATTT
1 AAACACTTCAATTTGCAGCATTA
13480338 AAACACTTCAATTTGCAGCA
1 AAACACTTCAATTTGCAGCA
13480358 CTTTAACATC
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
22 2 0.02
23 73 0.78
24 18 0.19
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.31
Consensus pattern (23 bp):
AAACACTTCAATTTGCAGCATTA
Found at i:13480372 original size:46 final size:46
Alignment explanation
Indices: 13480225--13480492 Score: 170
Period size: 46 Copynumber: 6.0 Consensus size: 46
13480215 AGCAACTAAA
* * * ** *
13480225 CACTTCAATTTGCAGCGA-TAAAACA-TCTCAATTTCCAGCAACTAAA
1 CACTTCAATTTACAGC-ATTTAAACACT-TCAATTTACAGCATTTAAG
* * * * *
13480271 CACTTCAATTTGCAGTACTTAAAACACTTTAATTTACAACATTTAAG
1 CACTTCAATTTACAGCA-TTTAAACACTTCAATTTACAGCATTTAAG
*
13480318 CACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAA-
1 CACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCA-TTTAAG
* * * *
13480364 CA-TCTCAATTAACAACATTTATACAAC-TCAA-TTACAGCGA-TAAAG
1 CACT-TCAATTTACAGCATTTAAAC-ACTTCAATTTACAGC-ATTTAAG
* *
13480409 CA-TCTCAATTT-C--C----AGACACTTCAATTTACAACATTTAAG
1 CACT-TCAATTTACAGCATTTAAACACTTCAATTTACAGCATTTAAG
* * *
13480448 CACTTCAACTTACAGCATTTAAACACTTCAATTTGCAGCACTTAA
1 CACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCATTTAA
13480493 AAAACAGTAG
Statistics
Matches: 176, Mismatches: 27, Indels: 38
0.73 0.11 0.16
Matches are distributed among these distances:
37 2 0.01
38 8 0.05
39 18 0.10
40 2 0.01
42 2 0.01
44 4 0.02
45 18 0.10
46 79 0.45
47 42 0.24
48 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (46 bp):
CACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCATTTAAG
Found at i:13480486 original size:23 final size:23
Alignment explanation
Indices: 13480424--13480493 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
13480414 CAATTTCCAG
*
13480424 ACACTTCAATTTACAACATTTAA
1 ACACTTCAATTTACAGCATTTAA
* *
13480447 GCACTTCAACTTACAGCATTTAA
1 ACACTTCAATTTACAGCATTTAA
* *
13480470 ACACTTCAATTTGCAGCACTTAA
1 ACACTTCAATTTACAGCATTTAA
13480493 A
1 A
13480494 AAACAGTAGC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (23 bp):
ACACTTCAATTTACAGCATTTAA
Found at i:13484604 original size:7 final size:7
Alignment explanation
Indices: 13484588--13484629 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
13484578 AAACACTTAA
13484588 CCCTAGAC
1 CCCTA-AC
13484596 CCCTAAC
1 CCCTAAC
*
13484603 CCTTAAC
1 CCCTAAC
13484610 CCCTAAC
1 CCCTAAC
*
13484617 CTCTAAC
1 CCCTAAC
13484624 CCCTAA
1 CCCTAA
13484630 ACCTTAATCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 25 0.83
8 5 0.17
ACGTcount: A:0.29, C:0.50, G:0.02, T:0.19
Consensus pattern (7 bp):
CCCTAAC
Found at i:13484607 original size:21 final size:20
Alignment explanation
Indices: 13484583--13484664 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 20
13484573 AACATAAACA
13484583 CTTAACCCTAGACCCCTAACC
1 CTTAACCCTA-ACCCCTAACC
*
13484604 CTTAACCCCTAACCTCTAACCC
1 CTTAA-CCCTAACCCCTAA-CC
* *
13484626 CTAAACCTTAATCCCC-AACC
1 CTTAACCCTAA-CCCCTAACC
* *
13484646 CTTAAACCATAATCCCTAA
1 CTT-AACCCTAACCCCTAA
13484665 ACCCATAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
20 7 0.14
21 28 0.57
22 14 0.29
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.22
Consensus pattern (20 bp):
CTTAACCCTAACCCCTAACC
Found at i:13484616 original size:28 final size:28
Alignment explanation
Indices: 13484585--13484647 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
13484575 CATAAACACT
*
13484585 TAACCCTAGACCCCTAACCCTTAA-CCCC
1 TAACCCTA-ACCCCTAAACCTTAATCCCC
13484613 TAACCTCTAACCCCTAAACCTTAATCCCC
1 TAACC-CTAACCCCTAAACCTTAATCCCC
13484642 -AACCCT
1 TAACCCT
13484648 TAAACCATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 2 0.06
28 23 0.72
29 7 0.22
ACGTcount: A:0.30, C:0.48, G:0.02, T:0.21
Consensus pattern (28 bp):
TAACCCTAACCCCTAAACCTTAATCCCC
Found at i:13484648 original size:14 final size:14
Alignment explanation
Indices: 13484585--13484650 Score: 75
Period size: 14 Copynumber: 4.7 Consensus size: 14
13484575 CATAAACACT
13484585 TAACCC-TAGACCCC
1 TAACCCTTA-ACCCC
13484599 TAACCCTTAACCCC
1 TAACCCTTAACCCC
13484613 TAA-CCTCTAACCCC
1 TAACCCT-TAACCCC
*
13484627 TAAACCTTAATCCCC
1 TAACCCTTAA-CCCC
13484642 -AACCCTTAA
1 TAACCCTTAA
13484651 ACCATAATCC
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
13 3 0.06
14 35 0.74
15 9 0.19
ACGTcount: A:0.32, C:0.45, G:0.02, T:0.21
Consensus pattern (14 bp):
TAACCCTTAACCCC
Found at i:13484670 original size:15 final size:15
Alignment explanation
Indices: 13484648--13484682 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
13484638 CCCCAACCCT
*
13484648 TAAA-CCATAATCCC
1 TAAACCCATAATCCA
13484662 TAAACCCATAATCCA
1 TAAACCCATAATCCA
13484677 TAAACC
1 TAAACC
13484683 TTAAAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACCCATAATCCA
Found at i:13484677 original size:22 final size:21
Alignment explanation
Indices: 13484621--13484679 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
13484611 CCTAACCTCT
* * *
13484621 AACCCCTAAACCTTAATCCCC
1 AACCCATAAACCATAATCCCA
*
13484642 AACCCTTAAACCATAATCCCTA
1 AACCCATAAACCATAATCCC-A
*
13484664 AACCCATAATCCATAA
1 AACCCATAAACCATAA
13484680 ACCTTAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCCATAAACCATAATCCCA
Found at i:13484687 original size:22 final size:21
Alignment explanation
Indices: 13484650--13484721 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
13484640 CCAACCCTTA
* *
13484650 AACCATAATCCCTAAACCCAT
1 AACCATAAACCTTAAACCCAT
**
13484671 AATCCATAAACCTTAAA-ATAGT
1 AA-CCATAAACCTTAAACCCA-T
*
13484693 AACTCATAAACCTTAAACCCTT
1 AAC-CATAAACCTTAAACCCAT
13484715 AACCATA
1 AACCATA
13484722 TGCCCTAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
21 8 0.20
22 32 0.80
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (21 bp):
AACCATAAACCTTAAACCCAT
Found at i:13485140 original size:39 final size:39
Alignment explanation
Indices: 13485097--13485205 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 39
13485087 TGCAAAATTT
* * * *
13485097 TTAGCGGCATTTTCT-CAAAGCGCTGCTAAAGATCGAGCG
1 TTAGCGGCATTTT-TAAAAAGCGCCGCTAAAGATAGAGCA
**
13485136 TTAGCGGTGTTTGTTAAAAAGCGCCGCTAAAGATAGAGCA
1 TTAGCGGCATTT-TTAAAAAGCGCCGCTAAAGATAGAGCA
* *
13485176 TTAGCGCCATTTTTTAAAAAGTGCCGCTAA
1 TTAGCGGCA-TTTTTAAAAAGCGCCGCTAA
13485206 TGTCACTGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
39 11 0.19
40 43 0.75
41 3 0.05
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (39 bp):
TTAGCGGCATTTTTAAAAAGCGCCGCTAAAGATAGAGCA
Found at i:13485193 original size:40 final size:40
Alignment explanation
Indices: 13485113--13485205 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
13485103 GCATTTTCTC
* * * ***
13485113 AAAGCGCTGCTAAAGATCGAGCGTTAGCGGTGTTTGTTAA
1 AAAGCGCCGCTAAAGATAGAGCATTAGCGCCATTTGTTAA
*
13485153 AAAGCGCCGCTAAAGATAGAGCATTAGCGCCATTTTTTAA
1 AAAGCGCCGCTAAAGATAGAGCATTAGCGCCATTTGTTAA
*
13485193 AAAGTGCCGCTAA
1 AAAGCGCCGCTAA
13485206 TGTCACTGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (40 bp):
AAAGCGCCGCTAAAGATAGAGCATTAGCGCCATTTGTTAA
Found at i:13487537 original size:35 final size:36
Alignment explanation
Indices: 13487483--13487595 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 36
13487473 CCACCAAAAT
* *
13487483 ACACCAGATGCTCACAAGAGTTAGTCAATCCGAAAC
1 ACACCAGATGCTCACAAGAGCTAATCAATCCGAAAC
* * * *
13487519 ACACCA-ATGCTTATAAGAGCTAATCCATCTGAAAC
1 ACACCAGATGCTCACAAGAGCTAATCAATCCGAAAC
* *
13487554 ACACTAG-TGGCTC-CGAAGAGCTAATCCAA-CTGAAAC
1 ACACCAGAT-GCTCAC-AAGAGCTAAT-CAATCCGAAAC
13487590 ACACCA
1 ACACCA
13487596 AAACAGAAAG
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
35 29 0.47
36 31 0.50
37 2 0.03
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.18
Consensus pattern (36 bp):
ACACCAGATGCTCACAAGAGCTAATCAATCCGAAAC
Found at i:13488982 original size:30 final size:30
Alignment explanation
Indices: 13488948--13489008 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
13488938 ACTTAACAAG
13488948 CAAATG-CTTCTAAAATAATAAAAAAATTAA
1 CAAATGCCTT-TAAAATAATAAAAAAATTAA
*
13488978 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAATTAA
13489008 C
1 C
13489009 GATAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.26
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAAAAAATTAA
Found at i:13494658 original size:28 final size:28
Alignment explanation
Indices: 13494607--13494669 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
13494597 ATCCCAAAAA
* *
13494607 TTCAACGTCCATATTGCAATGGTCAAAT
1 TTCAACGTCCATAATGCAACGGTCAAAT
* *
13494635 TTCAACGTCCATAATGTAACGGTCAGAT
1 TTCAACGTCCATAATGCAACGGTCAAAT
*
13494663 TCCAACG
1 TTCAACG
13494670 ATCATATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (28 bp):
TTCAACGTCCATAATGCAACGGTCAAAT
Found at i:13494675 original size:28 final size:28
Alignment explanation
Indices: 13494609--13494691 Score: 69
Period size: 28 Copynumber: 3.0 Consensus size: 28
13494599 CCCAAAAATT
* ** * * *
13494609 CAACGTCCATATTGCAATGGTCAAATTT
1 CAACGTCCATAATATAACGGTCAGATTC
*
13494637 CAACGTCCATAATGTAACGGTCAGATTC
1 CAACGTCCATAATATAACGGTCAGATTC
* *
13494665 CAACGAT-CATATTATAACGGTTAGATT
1 CAACG-TCCATAATATAACGGTCAGATT
13494692 TTTGCATTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 45 0.98
29 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (28 bp):
CAACGTCCATAATATAACGGTCAGATTC
Found at i:13511269 original size:172 final size:172
Alignment explanation
Indices: 13510978--13511316 Score: 563
Period size: 172 Copynumber: 2.0 Consensus size: 172
13510968 AAAGATGGGT
* *
13510978 ATACATTTTCTGTTTGGTTGGGCTAGGCTGGGTAATTTATTTTTTAATTGTTTTTCTTGGTTTTA
1 ATACATTTTCTGTTTGGTTGGGCTAGGCTGGGCAATTTATTTTTTAATTGTTTGTCTTGGTTTTA
* * *
13511043 TGTTTCATTGGTGGTTTTTGGGCTCATTGGGGTTGGCCAGAACTTTTGTTTTGTTTTTTCTTTTA
66 TGTTTCATTGCTGGTTTTCGGGCTCATTGGGGTTGGCCAAAACTTTTGTTTTGTTTTTTCTTTTA
* *
13511108 ATACAACCTGGTCTTTTATTCAAAGAAAATAAAAGAACTAAG
131 ATACAACCTGGTCTTTTATTCAAAAAAAAAAAAAGAACTAAG
* *
13511150 ATACTTTTTCTGTTTGGTTGGGCTAGGCTGGGCAATTTATTTTTTAGTTG-TTGTCTTGGTTTTA
1 ATACATTTTCTGTTTGGTTGGGCTAGGCTGGGCAATTTATTTTTTAATTGTTTGTCTTGGTTTTA
*
13511214 TGTTTCATTGCTGGTTTTCGGGCTTATTGGGGTTGGGCCAAAACTTTTGTTTTGTTTTTTCTTTT
66 TGTTTCATTGCTGGTTTTCGGGCTCATTGGGGTT-GGCCAAAACTTTTGTTTTGTTTTTTCTTTT
*
13511279 AATACAACTTGGTCTTTTATTCAAAAAAAAAAAAAGAA
130 AATACAACCTGGTCTTTTATTCAAAAAAAAAAAAAGAA
13511317 AGAAAGAAAA
Statistics
Matches: 155, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
171 44 0.28
172 111 0.72
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (172 bp):
ATACATTTTCTGTTTGGTTGGGCTAGGCTGGGCAATTTATTTTTTAATTGTTTGTCTTGGTTTTA
TGTTTCATTGCTGGTTTTCGGGCTCATTGGGGTTGGCCAAAACTTTTGTTTTGTTTTTTCTTTTA
ATACAACCTGGTCTTTTATTCAAAAAAAAAAAAAGAACTAAG
Found at i:13514811 original size:3 final size:3
Alignment explanation
Indices: 13514670--13514791 Score: 81
Period size: 3 Copynumber: 40.7 Consensus size: 3
13514660 CTTAATAATG
* * * * * *
13514670 TAT TAT TAT TAC TAT TAT TTT TAT TTT TAT TTT TAT TAC TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
13514718 TAC TAT CT-T TGT TAT TAT TAT TAT TAT TAT TAT TA- TAT T-T TCTT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
* *
13514762 TACT TAT ACAT TAT TGT TAT TAT TA- TAT TA
1 TA-T TAT -TAT TAT TAT TAT TAT TAT TAT TA
13514792 ACCAATTTAA
Statistics
Matches: 91, Mismatches: 20, Indels: 16
0.72 0.16 0.13
Matches are distributed among these distances:
2 7 0.08
3 76 0.84
4 8 0.09
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:13515093 original size:3 final size:3
Alignment explanation
Indices: 13515087--13515138 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
13515077 TTAGATTTTT
* * * * *
13515087 TTA TTA -TA TTA TTA ATA TCA TTA TCA TTA TTT TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13515134 TTA TT
1 TTA TT
13515139 TATTTATTAG
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:13515126 original size:21 final size:21
Alignment explanation
Indices: 13515093--13515139 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
13515083 TTTTTTATTA
*
13515093 TATTATTAATATCATTATCAT
1 TATTTTTAATATCATTATCAT
* *
13515114 TATTTTTATTATCATTATTAT
1 TATTTTTAATATCATTATCAT
13515135 TATTT
1 TATTT
13515140 ATTTATTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTAATATCATTATCAT
Found at i:13519221 original size:21 final size:22
Alignment explanation
Indices: 13519197--13519240 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
13519187 TTTTAGTGAT
* *
13519197 GCTTTGAATGTTTAAA-TGCAA
1 GCTTGGAATGATTAAATTGCAA
13519218 GCTTGGAATGATTAAATTGCAA
1 GCTTGGAATGATTAAATTGCAA
13519240 G
1 G
13519241 TTTTTATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (22 bp):
GCTTGGAATGATTAAATTGCAA
Found at i:13529513 original size:9 final size:9
Alignment explanation
Indices: 13529499--13529523 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
13529489 AATTAAATTA
13529499 CATGAAAAT
1 CATGAAAAT
13529508 CATGAAAAT
1 CATGAAAAT
13529517 CATGAAA
1 CATGAAA
13529524 TGGAACCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (9 bp):
CATGAAAAT
Found at i:13536678 original size:21 final size:22
Alignment explanation
Indices: 13536641--13536693 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
13536631 TTTATTTTAT
13536641 TTTTAAAA-ATTCTTAACAATAA
1 TTTTAAAATATTCTTAACAA-AA
13536663 TTTTAAAATA-TC-TAACAAAA
1 TTTTAAAATATTCTTAACAAAA
13536683 TATTTAAAATA
1 T-TTTAAAATA
13536694 AATATAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.10
21 15 0.52
22 10 0.34
23 1 0.03
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATATTCTTAACAAAA
Found at i:13536952 original size:15 final size:15
Alignment explanation
Indices: 13536932--13536964 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
13536922 TGATTGAAGC
13536932 AAAAAATAAAAATAA
1 AAAAAATAAAAATAA
13536947 AAAAAATAAAAATAA
1 AAAAAATAAAAATAA
13536962 AAA
1 AAA
13536965 TATTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAATAAAAATAA
Found at i:13540804 original size:22 final size:22
Alignment explanation
Indices: 13540741--13540804 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 22
13540731 TAATATAAAA
13540741 TAAT-TATAATATAT-AAT-AT
1 TAATGTATAATATATAAATAAT
* * *
13540760 GAAAGTAT-ATATGTAAA-AA-
1 TAATGTATAATATATAAATAAT
13540779 TAATGTATAATATATAAATAAT
1 TAATGTATAATATATAAATAAT
13540801 TAAT
1 TAAT
13540805 AAAGATATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
19 13 0.39
20 14 0.42
21 2 0.06
22 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (22 bp):
TAATGTATAATATATAAATAAT
Found at i:13540814 original size:19 final size:18
Alignment explanation
Indices: 13540790--13540838 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
13540780 AATGTATAAT
13540790 ATATAAATAATTAATAAAG
1 ATATAAATAATTAA-AAAG
* * *
13540809 ATATAATACAAGTAAAAAT
1 ATATAA-ATAATTAAAAAG
13540828 ATATAAATAAT
1 ATATAAATAAT
13540839 AATGTAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 3 0.12
19 15 0.62
20 6 0.25
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (18 bp):
ATATAAATAATTAAAAAG
Found at i:13540834 original size:38 final size:36
Alignment explanation
Indices: 13540787--13540886 Score: 105
Period size: 38 Copynumber: 2.6 Consensus size: 36
13540777 AATAATGTAT
13540787 AATATATAAATAATTAATAAAGAT-ATAATACAAGTAAA
1 AATATATAAATAA-TAATAAA-ATAATAATA-AAGTAAA
**
13540825 AATATATAAATAATAATGTAAAATAATAATAATTTAAA
1 AATATATAAATAATAA--TAAAATAATAATAAAGTAAA
13540863 AATATAT-AATAAATAATAATAATA
1 AATATATAAAT-AATAATAA-AATA
13540887 TGAAATAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
36 3 0.05
37 10 0.18
38 32 0.58
39 10 0.18
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (36 bp):
AATATATAAATAATAATAAAATAATAATAAAGTAAA
Found at i:13540854 original size:16 final size:17
Alignment explanation
Indices: 13540833--13540874 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
13540823 AAAATATATA
13540833 AATAATAATGT-AAAAT
1 AATAATAATGTAAAAAT
*
13540849 AATAATAATTTAAAAAT
1 AATAATAATGTAAAAAT
13540866 ATATAATAA
1 A-ATAATAA
13540875 ATAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.43
17 6 0.26
18 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AATAATAATGTAAAAAT
Found at i:13540870 original size:57 final size:57
Alignment explanation
Indices: 13540768--13540896 Score: 149
Period size: 57 Copynumber: 2.2 Consensus size: 57
13540758 ATGAAAGTAT
* *
13540768 ATATGTAAA-AATAATGTATAATATATAAATAATTAATAAAGATATAATACAAGTAAAA
1 ATATATAAATAATAATGTAAAATATATAAATAATTAATAAAGATATAATA-AA-TAAAA
* *
13540826 ATATATAAATAATAATGTAAAATA-AT-AATAATTTAA-AAATATATAATAAATAATA
1 ATATATAAATAATAATGTAAAATATATAAATAA-TTAATAAAGATATAATAAATAAAA
13540881 ATAATATGAAATAATA
1 AT-ATAT-AAATAATA
13540897 TATGGTTAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
55 6 0.10
56 6 0.10
57 24 0.38
58 14 0.22
59 13 0.21
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.33
Consensus pattern (57 bp):
ATATATAAATAATAATGTAAAATATATAAATAATTAATAAAGATATAATAAATAAAA
Found at i:13540894 original size:16 final size:15
Alignment explanation
Indices: 13540828--13540896 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 15
13540818 AAGTAAAAAT
13540828 ATATAAATAATAAT-
1 ATATAAATAATAATA
*
13540842 GTA-AAATAATAATA
1 ATATAAATAATAATA
*
13540856 ATTTAAA-AAT-AT-
1 ATATAAATAATAATA
13540868 ATAATAAATAATAATA
1 AT-ATAAATAATAATA
13540884 ATATGAAATAATA
1 ATAT-AAATAATA
13540897 TATGGTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 2 0.05
13 16 0.36
14 9 0.20
15 7 0.16
16 10 0.23
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
ATATAAATAATAATA
Found at i:13541032 original size:20 final size:19
Alignment explanation
Indices: 13541004--13541045 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
13540994 AGGAAGATAT
13541004 TAAGTAAT-ATAATAAAATA
1 TAAGTAATAAT-ATAAAATA
13541023 TAAGTAAATAATATAAAATA
1 TAAGT-AATAATATAAAATA
13541043 TAA
1 TAA
13541046 TACATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 14 0.67
21 2 0.10
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
TAAGTAATAATATAAAATA
Found at i:13543086 original size:204 final size:204
Alignment explanation
Indices: 13542681--13543233 Score: 822
Period size: 204 Copynumber: 2.7 Consensus size: 204
13542671 AAATCTGCTT
* * * *
13542681 CTTCGATTTGTTTTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAGCATAAGCAC
1 CTTCGATTTGTTCTCTGACAATA-AGAGATACCAAATCATCTTAGATTTGCTTCAGCATAAACAC
** *
13542746 GCAAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACTATCTT
65 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAAC-ATCTT
* ** * *
13542811 GGATCTTGCTTCAGTGAAATTATCTGAAGGTGAGATCTGCTATATATCTGCTCTTCATCAAAGTG
129 GGATCTTGCTTCAGTGAAATCATCTGAAGGTGAGATCTGCTATATATCTGCTCCCCACCAAAGTA
13542876 GAGATGCCAGA
194 GAGATGCCAGA
* *
13542887 CTTCCATTTGTTCTCTGACAAT-AGAGATACCAAATCATTTTAGATTTGCTTCAGCATAAACACG
1 CTTCGATTTGTTCTCTGACAATAAGAGATACCAAATCATCTTAGATTTGCTTCAGCATAAACACG
* * *
13542951 TGAAAGCCAAATCAGCTACGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTG
66 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAA-CATCTTG
* * * *
13543016 GATCTTGCTTCAGTGAAATCATCTGAAGGTGAGATCTTCTATGTATCTTCTCCCCGCCAAAGTAG
130 GATCTTGCTTCAGTGAAATCATCTGAAGGTGAGATCTGCTATATATCTGCTCCCCACCAAAGTAG
13543081 AGATGCCAGA
195 AGATGCCAGA
* * *
13543091 CTTCGATTTGGTCTCTGACAATACAGAGATACCAAATCATCTTAGATTTGTTTCAGCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATA-AGAGATACCAAATCATCTTAGATTTGCTTCAGCATAAACAC
*
13543156 GTGAAAGCCAAAT-AGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATTCCAAACCATCTT
65 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAA-CATCTT
13543220 GGATCTTGCTTCAG
129 GGATCTTGCTTCAG
13543234 GCCAGATCTG
Statistics
Matches: 314, Mismatches: 30, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
204 181 0.58
205 62 0.20
206 71 0.23
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (204 bp):
CTTCGATTTGTTCTCTGACAATAAGAGATACCAAATCATCTTAGATTTGCTTCAGCATAAACACG
TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACATCTTGG
ATCTTGCTTCAGTGAAATCATCTGAAGGTGAGATCTGCTATATATCTGCTCCCCACCAAAGTAGA
GATGCCAGA
Found at i:13545623 original size:26 final size:26
Alignment explanation
Indices: 13545584--13545639 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
13545574 TGATACAAAT
13545584 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
13545610 TGATAAT-GGTTTAGGTAAATGTTCCA
1 TGATAATAGG-TTAGGTAAATGTTCCA
13545636 TGAT
1 TGAT
13545640 GGGAATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:13552154 original size:30 final size:30
Alignment explanation
Indices: 13552118--13552177 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
13552108 ACTGTCGAAT
13552118 TTTACAACCCCCATCGTGATAAGCCTCTCC
1 TTTACAACCCCCATCGTGATAAGCCTCTCC
*
13552148 TTTACAACCCCCATCGTGGTAAGCCTCTCC
1 TTTACAACCCCCATCGTGATAAGCCTCTCC
13552178 ACGGCCTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.40, G:0.12, T:0.27
Consensus pattern (30 bp):
TTTACAACCCCCATCGTGATAAGCCTCTCC
Found at i:13553728 original size:14 final size:16
Alignment explanation
Indices: 13553693--13553729 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
13553683 CAAACGATGC
13553693 GATG-AAATGCTATGA
1 GATGCAAATGCTATGA
13553708 GATGCAAATGC-ATGA
1 GATGCAAATGCTATGA
13553723 -ATGCAAA
1 GATGCAAA
13553730 AAGCCATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
GATGCAAATGCTATGA
Found at i:13560417 original size:22 final size:22
Alignment explanation
Indices: 13560354--13560417 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 22
13560344 TAATATAAAA
13560354 TAAT-TATAATATAT-AAT-AT
1 TAATGTATAATATATAAATAAT
* * *
13560373 GAAAGTAT-ATATGTAAA-AA-
1 TAATGTATAATATATAAATAAT
13560392 TAATGTATAATATATAAATAAT
1 TAATGTATAATATATAAATAAT
13560414 TAAT
1 TAAT
13560418 AAAGATATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
19 13 0.39
20 14 0.42
21 2 0.06
22 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (22 bp):
TAATGTATAATATATAAATAAT
Found at i:13560427 original size:19 final size:18
Alignment explanation
Indices: 13560403--13560451 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
13560393 AATGTATAAT
13560403 ATATAAATAATTAATAAAG
1 ATATAAATAATTAA-AAAG
* * *
13560422 ATATAACACAAGTAAAAAT
1 ATATAA-ATAATTAAAAAG
13560441 ATATAAATAAT
1 ATATAAATAAT
13560452 AATGTAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 3 0.12
19 15 0.62
20 6 0.25
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (18 bp):
ATATAAATAATTAAAAAG
Found at i:13560467 original size:16 final size:17
Alignment explanation
Indices: 13560446--13560487 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
13560436 AAAATATATA
13560446 AATAATAATGT-AAAAT
1 AATAATAATGTAAAAAT
* *
13560462 AATAATTATTTAAAAAT
1 AATAATAATGTAAAAAT
13560479 ATATAATAA
1 A-ATAATAA
13560488 ATAATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
17 6 0.29
18 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AATAATAATGTAAAAAT
Found at i:13560645 original size:20 final size:19
Alignment explanation
Indices: 13560617--13560658 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
13560607 AGGAAGATAT
13560617 TAAGTAAT-ATAATAAAATA
1 TAAGTAATAAT-ATAAAATA
13560636 TAAGTAAATAATATAAAATA
1 TAAGT-AATAATATAAAATA
13560656 TAA
1 TAA
13560659 TACATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 14 0.67
21 2 0.10
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
TAAGTAATAATATAAAATA
Found at i:13563485 original size:112 final size:112
Alignment explanation
Indices: 13563281--13563499 Score: 368
Period size: 112 Copynumber: 2.0 Consensus size: 112
13563271 CCTCTGAAAG
* * *
13563281 AATGAGTTGAAGCTTTCAAAGCCTGCTCTATTGAGGTAGAAGTTCTGTTCATCTTCTGCTCATGG
1 AATGAGTTGAAACTTTCAAAGCCTGCTCTATTGAGGTAGAAGTTCTGTTAATATTCTGCTCATGG
* *
13563346 ACCAACAAGGAGCTCTGAAGTTTATCAAGAGTGAGTTCATCAAGAGT
66 ACCAAAAAGGAGCTCTGAAGTTTATCAAGAGTGAGTGCATCAAGAGT
13563393 AATGAGTTGAAACTTTCAAAGCCTGCTCTATTGAGGTAGAAGTTCTGTTAATATTCTGCTCATGG
1 AATGAGTTGAAACTTTCAAAGCCTGCTCTATTGAGGTAGAAGTTCTGTTAATATTCTGCTCATGG
*
13563458 ACCAAAAATGAGCTCTGAA-TTTCATCAAGAGTGAGTGCATCA
66 ACCAAAAAGGAGCTCTGAAGTTT-ATCAAGAGTGAGTGCATCA
13563500 GTATCCTTAG
Statistics
Matches: 100, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
111 3 0.03
112 97 0.97
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (112 bp):
AATGAGTTGAAACTTTCAAAGCCTGCTCTATTGAGGTAGAAGTTCTGTTAATATTCTGCTCATGG
ACCAAAAAGGAGCTCTGAAGTTTATCAAGAGTGAGTGCATCAAGAGT
Found at i:13567443 original size:43 final size:42
Alignment explanation
Indices: 13567328--13567464 Score: 177
Period size: 43 Copynumber: 3.2 Consensus size: 42
13567318 AGAAAATAGA
*
13567328 CTTTTAGCGGCGTTTGTTGGGAAA-GCACAACTAAAAGTCATGG
1 CTTTTAGCGGCGTTTGTTGGGAAATGC-C-GCTAAAAGTCATGG
13567371 CTTTTAGCGGCGTTTGTTGGGAAAGTGCCGCTAAAAGTCATGG
1 CTTTTAGCGGCGTTTGTTGGGAAA-TGCCGCTAAAAGTCATGG
* * * **
13567414 CTTTTAGCGGCGGTTTTTTGGCAAATGCCGCTAAAAGCCATTA
1 CTTTTAGCGGC-GTTTGTTGGGAAATGCCGCTAAAAGTCATGG
13567457 CTTTTAGC
1 CTTTTAGC
13567465 TGCGCTTTTC
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
43 71 0.84
44 12 0.14
45 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.31
Consensus pattern (42 bp):
CTTTTAGCGGCGTTTGTTGGGAAATGCCGCTAAAAGTCATGG
Found at i:13567609 original size:31 final size:31
Alignment explanation
Indices: 13567543--13567609 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
13567533 CTTCCTGCAT
* *
13567543 TAAAATCCAACCAAATACAACAAATATAGTA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
* * * *
13567574 TAAAATGCAGCCAAAAACAACAAATTTAGCG
1 TAAAATCCAACCAAAAACAACAAATATAGCA
13567605 TAAAA
1 TAAAA
13567610 AATACAACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.57, C:0.18, G:0.07, T:0.18
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAGCA
Found at i:13567870 original size:21 final size:21
Alignment explanation
Indices: 13567857--13567932 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
13567847 TCTGCTGCCA
13567857 TCGCTGCTGCCTCTGCCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
*
13567878 TCG-TTCGTGCCTCTGCCTCCC
1 TCGCTGC-TGCCTCTGCCTCCC
* *
13567899 TCGCTGCTGCCGCTGCCTTCC
1 TCGCTGCTGCCTCTGCCTCCC
* *
13567920 TCTCTGTTGCCTC
1 TCGCTGCTGCCTC
13567933 CATTCTAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.00, C:0.47, G:0.20, T:0.33
Consensus pattern (21 bp):
TCGCTGCTGCCTCTGCCTCCC
Found at i:13568372 original size:13 final size:14
Alignment explanation
Indices: 13568347--13568375 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13568337 TGATGAATTG
13568347 AATTAAACAATTAT
1 AATTAAACAATTAT
13568361 AATTAAAC-ATTAT
1 AATTAAACAATTAT
13568374 AA
1 AA
13568376 ATATTTAGAA
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:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:13570633 original size:77 final size:77
Alignment explanation
Indices: 13570506--13570662 Score: 278
Period size: 77 Copynumber: 2.0 Consensus size: 77
13570496 ATCTTTGAGA
13570506 CTCACACATCGAGATATATTTGACGCATACGCATCTGGGACCTTTATATCCTTCAACACCATGCA
1 CTCACACATCGAGATATATTTGACGCATACGCATCTGGGACCTTTATATCCTTCAACACCATGCA
*
13570571 GAATACTTCTTT
66 GAACACTTCTTT
* * *
13570583 CTCACACATCGAGATATATTTGACGCATATGCATCTGGGACCTTTATATCCTTCAAGACTATGCA
1 CTCACACATCGAGATATATTTGACGCATACGCATCTGGGACCTTTATATCCTTCAACACCATGCA
13570648 GAACACTTCTTT
66 GAACACTTCTTT
13570660 CTC
1 CTC
13570663 TTTCTTTGAC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (77 bp):
CTCACACATCGAGATATATTTGACGCATACGCATCTGGGACCTTTATATCCTTCAACACCATGCA
GAACACTTCTTT
Found at i:13570968 original size:12 final size:12
Alignment explanation
Indices: 13570951--13570975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13570941 TCATCCTCTC
13570951 CATCAGATTCAT
1 CATCAGATTCAT
13570963 CATCAGATTCAT
1 CATCAGATTCAT
13570975 C
1 C
13570976 CCTCGATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (12 bp):
CATCAGATTCAT
Found at i:13572927 original size:64 final size:64
Alignment explanation
Indices: 13572766--13572919 Score: 290
Period size: 64 Copynumber: 2.4 Consensus size: 64
13572756 CATTTTCAAG
* *
13572766 TATAGATTTATGTATTATGTAAGTTAAGTAAGTTTCGTAAGCTAGTTATGTAAGATATGAATGA
1 TATATATTTAAGTATTATGTAAGTTAAGTAAGTTTCGTAAGCTAGTTATGTAAGATATGAATGA
13572830 TATATATTTAAGTATTATGTAAGTTAAGTAAGTTTCGTAAGCTAGTTATGTAAGATATGAATGA
1 TATATATTTAAGTATTATGTAAGTTAAGTAAGTTTCGTAAGCTAGTTATGTAAGATATGAATGA
13572894 TATATATTTAAGTATTATGTAAGTTA
1 TATATATTTAAGTATTATGTAAGTTA
13572920 TTTAAGTTAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 88 1.00
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (64 bp):
TATATATTTAAGTATTATGTAAGTTAAGTAAGTTTCGTAAGCTAGTTATGTAAGATATGAATGA
Found at i:13572972 original size:95 final size:96
Alignment explanation
Indices: 13572873--13573133 Score: 311
Period size: 95 Copynumber: 2.7 Consensus size: 96
13572863 TTCGTAAGCT
* * *
13572873 AGTTATGTAAGATATG-AATGATATATATTTAAGTATTATGTAAGTTATTTAAGTTATGATATGA
1 AGTTATATAAGTTATGTAATGATATATATTTAAGTATTATGTAAGTTATATAAGTTATGATATGA
*
13572937 TATATATTTATGTAAATTATATATTTATCTA
66 TATATATTTATGTAAATTATATATATATCTA
* * *
13572968 AGTTATATAAGTTATGTAA-GTTATATAAGTT-A-TATATATGTAAGTTATGTAAGTTATGATAT
1 AGTTATATAAGTTATGTAATGATATAT-ATTTAAGTAT-TATGTAAGTTATATAAGTTATGATAT
* *
13573030 GATATATATTTATGTAAGTTATATATATATGTA
64 GATATATATTTATGTAAATTATATATATATCTA
* * *
13573063 AGTTATATAAGTTATGTAAGTTATATAATTATCTAAG--TTATATAAGTTATATAAGTTATG-TA
1 AGTTATATAAGTTATGTAA-TGATAT-A-TATTTAAGTATTATGTAAGTTATATAAGTTATGATA
*
13573125 TGTTATATA
63 TGATATATA
13573134 AGCCATGTAA
Statistics
Matches: 142, Mismatches: 15, Indels: 17
0.82 0.09 0.10
Matches are distributed among these distances:
94 3 0.02
95 95 0.67
96 15 0.11
97 23 0.16
98 4 0.03
99 2 0.01
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (96 bp):
AGTTATATAAGTTATGTAATGATATATATTTAAGTATTATGTAAGTTATATAAGTTATGATATGA
TATATATTTATGTAAATTATATATATATCTA
Found at i:13572973 original size:9 final size:9
Alignment explanation
Indices: 13572908--13573201 Score: 223
Period size: 9 Copynumber: 33.4 Consensus size: 9
13572898 TATTTAAGTA
*
13572908 TTATGTAAG
1 TTATATAAG
*
13572917 TTATTTAAG
1 TTATATAAG
*
13572926 TTATGATATG
1 TTAT-ATAAG
* *
13572936 ATATAT-AT
1 TTATATAAG
* *
13572944 TTATGTAAA
1 TTATATAAG
*
13572953 TTATAT-AT
1 TTATATAAG
*
13572961 TTATCTAAG
1 TTATATAAG
13572970 TTATATAAG
1 TTATATAAG
*
13572979 TTATGTAAG
1 TTATATAAG
13572988 TTATATAAG
1 TTATATAAG
13572997 TTATAT-A-
1 TTATATAAG
*
13573004 -TATGTAAG
1 TTATATAAG
*
13573012 TTATGTAAG
1 TTATATAAG
*
13573021 TTATGATATG
1 TTAT-ATAAG
* *
13573031 ATATAT-AT
1 TTATATAAG
*
13573039 TTATGTAAG
1 TTATATAAG
13573048 TTATAT-A-
1 TTATATAAG
*
13573055 TATATGTAAG
1 T-TATATAAG
13573065 TTATATAAG
1 TTATATAAG
*
13573074 TTATGTAAG
1 TTATATAAG
13573083 TTATATAA-
1 TTATATAAG
*
13573091 TTATCTAAG
1 TTATATAAG
13573100 TTATATAAG
1 TTATATAAG
13573109 TTATATAAG
1 TTATATAAG
* *
13573118 TTATGTATG
1 TTATATAAG
13573127 TTATATAAG
1 TTATATAAG
** *
13573136 CCATGTAAG
1 TTATATAAG
13573145 TTATATAAG
1 TTATATAAG
*
13573154 TTATAT-AT
1 TTATATAAG
*
13573162 TTATCTAAG
1 TTATATAAG
13573171 TTATATAAG
1 TTATATAAG
* *
13573180 TTATGTACG
1 TTATATAAG
13573189 TT-TATTAAG
1 TTATA-TAAG
13573198 TTAT
1 TTAT
13573202 GTAAATTATG
Statistics
Matches: 220, Mismatches: 50, Indels: 29
0.74 0.17 0.10
Matches are distributed among these distances:
6 4 0.02
7 2 0.01
8 34 0.15
9 166 0.75
10 14 0.06
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (9 bp):
TTATATAAG
Found at i:13572990 original size:71 final size:72
Alignment explanation
Indices: 13572908--13573210 Score: 235
Period size: 71 Copynumber: 4.2 Consensus size: 72
13572898 TATTTAAGTA
* * * * *
13572908 TTATGTAAGTTATTTAAGTTATGATATGATATATATTTATGTAAATTATAT-ATTTATCTAAGTT
1 TTATGTAAGTTATATAAGTTATGATAAGATATATATTTATCTAAATTATATAAGTTATGTAAGTT
13572972 ATATAAG
66 ATATAAG
* * * * * *
13572979 TTATGTAAGTTATATAAGTTAT-ATATATGTAAGTTATGTAAGTTAT-GATATGATATATATTTA
1 TTATGTAAGTTATATAAGTTATGATA-A-G--A--TATAT-ATTTATCTAAATTATATA-AGTTA
13573042 TGTAAGTTATAT-A-
58 TGTAAGTTATATAAG
* * * *
13573055 TATATGTAAGTTATATAAGTTATG-TAAGTTATATAATTATCTAAGTTATATAAGTTATATAAGT
1 T-TATGTAAGTTATATAAGTTATGATAAGATATATATTTATCTAAATTATATAAGTTATGTAAGT
* *
13573119 TATGTATG
65 TATATAAG
* ** * * * *
13573127 TTATATAAGCCATGTAAGTTAT-ATAAGTTATATATTTATCTAAGTTATATAAGTTATGTACGTT
1 TTATGTAAGTTATATAAGTTATGATAAGATATATATTTATCTAAATTATATAAGTTATGTAAGTT
13573191 -TATTAAG
66 ATA-TAAG
*
13573198 TTATGTAAATTAT
1 TTATGTAAGTTAT
13573211 GATATCAAAT
Statistics
Matches: 184, Mismatches: 32, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
70 23 0.12
71 99 0.54
72 2 0.01
74 1 0.01
75 1 0.01
76 13 0.07
77 29 0.16
78 16 0.09
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (72 bp):
TTATGTAAGTTATATAAGTTATGATAAGATATATATTTATCTAAATTATATAAGTTATGTAAGTT
ATATAAG
Found at i:13573134 original size:62 final size:62
Alignment explanation
Indices: 13572908--13573210 Score: 267
Period size: 62 Copynumber: 4.8 Consensus size: 62
13572898 TATTTAAGTA
* * * * * * *
13572908 TTATGTAAGTTATTTAAGTTATGATATGATATAT-ATTTATGTAAATTATATATTTATCTAAG
1 TTATATAAGTTATATAAGTTATG-TATGTTATATAAGTTATGTAAGTTATATAATTATATAAG
* * * *
13572970 TTATATAAGTTATGTAAGTTATATAAGTTATATATATGTAAGTTATGTAAGTTATGAT-ATGATA
1 TTATATAAGTTATATAAG-T-TAT--G-TATGT-TATATAAGTTATGTAAGTTAT-ATAATTATA
*
13573034 TATAT
59 TA-AG
* * *
13573039 TTATGTAAGTTATAT-A-TATATGTAAGTTATATAAGTTATGTAAGTTATATAATTATCTAAG
1 TTATATAAGTTATATAAGT-TATGTATGTTATATAAGTTATGTAAGTTATATAATTATATAAG
** *
13573100 TTATATAAGTTATATAAGTTATGTATGTTATATAAGCCATGTAAGTTATATAAGTTATAT-AT
1 TTATATAAGTTATATAAGTTATGTATGTTATATAAGTTATGTAAGTTATATAA-TTATATAAG
* * *
13573162 TTATCTAAGTTATATAAGTTATGTACGTT-TATTAAGTTATGTAAATTAT
1 TTATATAAGTTATATAAGTTATGTATGTTATA-TAAGTTATGTAAGTTAT
13573211 GATATCAAAT
Statistics
Matches: 197, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
61 19 0.10
62 116 0.59
63 10 0.05
64 4 0.02
66 9 0.05
67 4 0.02
68 19 0.10
69 16 0.08
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (62 bp):
TTATATAAGTTATATAAGTTATGTATGTTATATAAGTTATGTAAGTTATATAATTATATAAG
Found at i:13573151 original size:95 final size:95
Alignment explanation
Indices: 13572906--13573201 Score: 339
Period size: 95 Copynumber: 3.0 Consensus size: 95
13572896 TATATTTAAG
* *
13572906 TATTATGTAAGTTATTTAAGTTATGATATGATATATATTTATGTAAATTATATATTTATCTAAGT
1 TATTATGTAAGTTATATAAGTTATGATATGATATATATTTATGTAAGTTATATA-TTATCTAAGT
13572971 TATATAAGTTATGTAAGTTATATAAGTTATA
65 TATATAAGTTATGTAAGTTATATAAGTTATA
* *
13573002 TA-TATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATATATATATGTAAGT
1 TATTATGTAAGTTATATAAGTTATGATATGATATATATTTATGTAAGTTATATAT-TATCTAAGT
*
13573066 TATATAAGTTATGTAAGTTATATAA-TTATC
65 TATATAAGTTATGTAAGTTATATAAGTTATA
* * *
13573096 TAAGTTATATAAGTTATATAAGTTATG-TATGTTATATAAGCCATGTAAGTTATATAAGTTATAT
1 T-A-TTATGTAAGTTATATAAGTTATGATATG--ATAT-----A--T-ATTTATGTAAGTTATAT
*
13573160 ATTTATCTAAGTTATATAAGTTATGTACGTT-TATTAAGTTAT
54 A-TTATCTAAGTTATATAAGTTATGTAAGTTATA-TAAGTTAT
13573202 GTAAATTATG
Statistics
Matches: 173, Mismatches: 10, Indels: 23
0.84 0.05 0.11
Matches are distributed among these distances:
94 6 0.03
95 83 0.48
96 6 0.03
97 20 0.12
98 4 0.02
103 1 0.01
105 3 0.02
106 45 0.26
107 5 0.03
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (95 bp):
TATTATGTAAGTTATATAAGTTATGATATGATATATATTTATGTAAGTTATATATTATCTAAGTT
ATATAAGTTATGTAAGTTATATAAGTTATA
Found at i:13573373 original size:14 final size:14
Alignment explanation
Indices: 13573323--13573376 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
13573313 AAGTTGCGGG
*
13573323 ATTAAATAATATATA
1 ATTAAATAAT-TTTA
*
13573338 ATTAAATAATTTTT
1 ATTAAATAATTTTA
* *
13573352 ATAAAAATTATTTTA
1 AT-TAAATAATTTTA
13573367 ATTAAATAAT
1 ATTAAATAAT
13573377 ATACATGTCG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 10 0.32
15 21 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTAAATAATTTTA
Found at i:13573579 original size:24 final size:24
Alignment explanation
Indices: 13573552--13573622 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
13573542 TTAACTTAAA
*
13573552 TGATAAAACGAACGATAATATTTG
1 TGATAAAACGGACGATAATATTTG
*
13573576 TGATAAAACGGACAATAATATTTG
1 TGATAAAACGGACGATAATATTTG
* *
13573600 TTATAAAACGGACGAGAATATTT
1 TGATAAAACGGACGATAATATTT
13573623 CAATAATAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (24 bp):
TGATAAAACGGACGATAATATTTG
Found at i:13573860 original size:64 final size:64
Alignment explanation
Indices: 13573670--13573862 Score: 343
Period size: 64 Copynumber: 3.0 Consensus size: 64
13573660 ATATTTTATT
* * *
13573670 AAATATTTGTATATTAGAT-GGACATATTATATTAATAAATAAATATATTAAAAATCGTGATAA
1 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
*
13573733 AAATATTTGTATATTAGATGAGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
13573797 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
13573861 AA
1 AA
13573863 GTTACAAAAA
Statistics
Matches: 124, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
63 19 0.15
64 105 0.85
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (64 bp):
AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
Found at i:13576999 original size:17 final size:17
Alignment explanation
Indices: 13576973--13577006 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13576963 TATATAATTG
*
13576973 AAATATGTTATAATATA
1 AAATAAGTTATAATATA
13576990 AAATAAGTTATAATATA
1 AAATAAGTTATAATATA
13577007 TTAAGTGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAATAAGTTATAATATA
Found at i:13578220 original size:24 final size:24
Alignment explanation
Indices: 13578180--13578313 Score: 141
Period size: 24 Copynumber: 5.7 Consensus size: 24
13578170 GAAATGATTT
13578180 TGGCACTA--TGTGCGAATTTGAA
1 TGGCACTATGTGTGCGAATTTGAA
*
13578202 TGGCACTATGTGTGCGAATTTGTA
1 TGGCACTATGTGTGCGAATTTGAA
* *
13578226 TGGCACTATGTGTGCGGATTTGTA
1 TGGCACTATGTGTGCGAATTTGAA
* *
13578250 TGGCACTATGTGTGCGGATTGGAA
1 TGGCACTATGTGTGCGAATTTGAA
* * * *
13578274 TGTCAATATGTATGTGAATTACT-AA
1 TGGCACTATGTGTGCGAATT--TGAA
13578299 -GGCACTATGTGTGCG
1 TGGCACTATGTGTGCG
13578314 GGTTAACATG
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
22 8 0.09
24 84 0.89
25 2 0.02
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (24 bp):
TGGCACTATGTGTGCGAATTTGAA
Found at i:13584566 original size:17 final size:17
Alignment explanation
Indices: 13584541--13584573 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13584531 ATATAATTGT
*
13584541 AATATGTTATAATATAA
1 AATAAGTTATAATATAA
13584558 AATAAGTTATAATATA
1 AATAAGTTATAATATA
13584574 TTAAGTGGGG
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:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
AATAAGTTATAATATAA
Found at i:13585754 original size:24 final size:24
Alignment explanation
Indices: 13585727--13585862 Score: 159
Period size: 24 Copynumber: 5.7 Consensus size: 24
13585717 GAAATGATTT
13585727 TGGCACTATGTGTGCGAATTTGAA
1 TGGCACTATGTGTGCGAATTTGAA
*
13585751 TGGCACTATGTGTGCGAATTTGTA
1 TGGCACTATGTGTGCGAATTTGAA
* *
13585775 TGGCACTATGTGTGCGGATTTGTA
1 TGGCACTATGTGTGCGAATTTGAA
* *
13585799 TGGCACTATGTGTGCGGATTGGAA
1 TGGCACTATGTGTGCGAATTTGAA
* * * *
13585823 TGTCAATATGTATGTGAATTACT-AA
1 TGGCACTATGTGTGCGAATT--TGAA
13585848 -GGCACTATGTGTGCG
1 TGGCACTATGTGTGCG
13585863 GGTTAACATG
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
24 94 0.98
25 2 0.02
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (24 bp):
TGGCACTATGTGTGCGAATTTGAA
Found at i:13585852 original size:72 final size:72
Alignment explanation
Indices: 13585727--13585863 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 72
13585717 GAAATGATTT
* * * ** *
13585727 TGGCACTATGTGTGCGAATTTGAATGGCACTATGTGTGCGAATTTGTATGGCACTATGTGTGCGG
1 TGGCACTATGTGTGCGAATTGGAATGGCAATATGTATGCGAATTACTAAGGCACTATGTGTGCGG
13585792 ATTTGTA
66 ATTTGTA
* * *
13585799 TGGCACTATGTGTGCGGATTGGAATGTCAATATGTATGTGAATTACTAAGGCACTATGTGTGCGG
1 TGGCACTATGTGTGCGAATTGGAATGGCAATATGTATGCGAATTACTAAGGCACTATGTGTGCGG
13585864 GTTAACATGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.34
Consensus pattern (72 bp):
TGGCACTATGTGTGCGAATTGGAATGGCAATATGTATGCGAATTACTAAGGCACTATGTGTGCGG
ATTTGTA
Found at i:13585879 original size:72 final size:72
Alignment explanation
Indices: 13585727--13585880 Score: 182
Period size: 72 Copynumber: 2.1 Consensus size: 72
13585717 GAAATGATTT
* * * ** *
13585727 TGGCACTATGTGTGCGAATTTGAATGGCACTATGTGTGCGAATTTGTATGGCACTATGTGTGCGG
1 TGGCACTATGTGTGCGAATTGGAATGGCAATATGTATGCGAATTACTAAGGCACTATGTGTGCGG
***
13585792 ATTTGTA
66 ATTAACA
* * *
13585799 TGGCACTATGTGTGCGGATTGGAATGTCAATATGTATGTGAATTACTAAGGCACTATGTGTGCGG
1 TGGCACTATGTGTGCGAATTGGAATGGCAATATGTATGCGAATTACTAAGGCACTATGTGTGCGG
*
13585864 GTTAACA
66 ATTAACA
*
13585871 TGGTACTATG
1 TGGCACTATG
13585881 GATATGAATT
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.34
Consensus pattern (72 bp):
TGGCACTATGTGTGCGAATTGGAATGGCAATATGTATGCGAATTACTAAGGCACTATGTGTGCGG
ATTAACA
Found at i:13587802 original size:18 final size:18
Alignment explanation
Indices: 13587768--13587802 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
13587758 TTGATTTATT
*
13587768 TAATATATAATTTAAAAA
1 TAATATATAATTAAAAAA
13587786 TAATATA-AATTAAAAAA
1 TAATATATAATTAAAAAA
13587803 CAATCAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAATATATAATTAAAAAA
Found at i:13587981 original size:26 final size:26
Alignment explanation
Indices: 13587916--13587983 Score: 111
Period size: 26 Copynumber: 2.6 Consensus size: 26
13587906 AAGAATTAGA
*
13587916 TAAAATTTGAAATATTGAAAATTATT
1 TAAAATTTGAAATCTTGAAAATTATT
13587942 TAAAATTTGAAATCTTGAAAATTATT
1 TAAAATTTGAAATCTTGAAAATTATT
13587968 CT-AAATTTGAAATCTT
1 -TAAAATTTGAAATCTT
13587984 TAAATTTTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 39 0.98
27 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (26 bp):
TAAAATTTGAAATCTTGAAAATTATT
Found at i:13588261 original size:15 final size:14
Alignment explanation
Indices: 13588229--13588359 Score: 66
Period size: 14 Copynumber: 8.9 Consensus size: 14
13588219 TTTAAACCCC
* *
13588229 AAACTATAAACCCCT
1 AAACCATAAA-CCTT
13588244 AAACCATGAAACCTT
1 AAACCAT-AAACCTT
13588259 AAACCATGATTAACCATT
1 AAACCAT-A--AACC-TT
* *
13588277 AACCCCTAAACCTT
1 AAACCATAAACCTT
** *
13588291 AAACCCCAACCCTT
1 AAACCATAAACCTT
*
13588305 AAACCATAAACC-A
1 AAACCATAAACCTT
*
13588318 AAATCCCTAAACCTT
1 AAA-CCATAAACCTT
* * **
13588333 AAAACATTAACTCAA
1 AAACCATAAAC-CTT
13588348 AAACCATAAACC
1 AAACCATAAACC
13588360 CCTCTCCCAT
Statistics
Matches: 89, Mismatches: 20, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
13 3 0.03
14 36 0.40
15 35 0.39
16 3 0.03
17 5 0.06
18 7 0.08
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.19
Consensus pattern (14 bp):
AAACCATAAACCTT
Found at i:13588301 original size:21 final size:21
Alignment explanation
Indices: 13588277--13588335 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
13588267 ATTAACCATT
**
13588277 AACCCCTAAACCTTAAACCCC
1 AACCCCTAAACCTTAAACCAA
* *
13588298 AACCCTTAAACCATAAACCAA
1 AACCCCTAAACCTTAAACCAA
*
13588319 AATCCCTAAACCTTAAA
1 AACCCCTAAACCTTAAA
13588336 ACATTAACTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (21 bp):
AACCCCTAAACCTTAAACCAA
Found at i:13588337 original size:29 final size:28
Alignment explanation
Indices: 13588301--13588359 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
13588291 AAACCCCAAC
* *
13588301 CCTTAAACCATAAAC-CAAAATCCCTAAA
1 CCTTAAA-CATAAACTCAAAAACCATAAA
*
13588329 CCTTAAAACATTAACTCAAAAACCATAAA
1 CCTT-AAACATAAACTCAAAAACCATAAA
13588358 CC
1 CC
13588360 CCTCTCCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.19
Consensus pattern (28 bp):
CCTTAAACATAAACTCAAAAACCATAAA
Found at i:13588859 original size:28 final size:29
Alignment explanation
Indices: 13588819--13588873 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
13588809 AATAAATTGT
*
13588819 ATTTTAATCAATATAA-ATATAAATAAACC
1 ATTTAAATCAATA-AATATATAAATAAACC
*
13588848 ATTTAAAT-AATAAATATATAGATAAA
1 ATTTAAATCAATAAATATATAAATAAA
13588874 ATACTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 14 0.61
29 7 0.30
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (29 bp):
ATTTAAATCAATAAATATATAAATAAACC
Found at i:13589055 original size:40 final size:39
Alignment explanation
Indices: 13588998--13589103 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 39
13588988 GATATTTTTT
* * **
13588998 GCGGCATTTTT-AGAAACGCCGCTAATGGTCAACCTATA
1 GCGGCGTTTTTAAAAAACGCCGCTAATACTCAACCTATA
*
13589036 GCGGCGTTTGTTAAAAAACGCCGCTAATACTCAACCTTTA
1 GCGGCGTTT-TTAAAAAACGCCGCTAATACTCAACCTATA
* * * *
13589076 GTGGCGTTTTTTAGAAACACCGCTAATA
1 GCGGCGTTTTTAAAAAACGCCGCTAATA
13589104 AAACTAAGGG
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
38 8 0.14
39 18 0.32
40 31 0.54
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (39 bp):
GCGGCGTTTTTAAAAAACGCCGCTAATACTCAACCTATA
Found at i:13589236 original size:116 final size:115
Alignment explanation
Indices: 13589034--13589410 Score: 560
Period size: 116 Copynumber: 3.3 Consensus size: 115
13589024 GGTCAACCTA
* * *
13589034 TAGCGGCGTTTGTT-AAAAAACGCCGCTAATACTCAACCTTTAGTGGCGTTTTTTAGAAACACCG
1 TAGCGGCGTTTTTTGTAAAAACGCCGCTAATACTCAACCTTTAGTGGCGTTTTTTAGAAACGCCG
13589098 CTAATAAAACTAAGGGCCGAAACGAAACGACTGCGTCTTGCTGAAATTAT
66 CTAATAAAACTAAGGGCCGAAACGAAACGACTGCGTCTTGCTGAAATTAT
* * *
13589148 TAGCGGCGTTTTTTGTAAAATCGCCACTAATACTCAACCTTTAGTGGCGTTTTTTTAGAAATGCC
1 TAGCGGCGTTTTTTGTAAAAACGCCGCTAATACTCAACCTTTAGTGGCG-TTTTTTAGAAACGCC
*
13589213 GCTAATAAAACTAAGGGCCGAAACGAAACGACTACGTCTTGCTGAAATTAT
65 GCTAATAAAACTAAGGGCCGAAACGAAACGACTGCGTCTTGCTGAAATTAT
** *
13589264 TAATGGCGTTTTTTTTGTAAAAGCGCCGCTAATACTCAACCTTTAGTGGCGTTTTTTAGAAACGC
1 TAGCGGCG--TTTTTTGTAAAAACGCCGCTAATACTCAACCTTTAGTGGCGTTTTTTAGAAACGC
* * *
13589329 CGCTAATGAAACTAAGGGTCGAAACGAAACGACTGCGTCTTGCAGAAATTAT
64 CGCTAATAAAACTAAGGGCCGAAACGAAACGACTGCGTCTTGCTGAAATTAT
* * **
13589381 TAGCGG-TTTTTTTGCAAAAGTGCCGCTAAT
1 TAGCGGCGTTTTTTGTAAAAACGCCGCTAAT
13589411 GCTTGATCTA
Statistics
Matches: 238, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
114 34 0.14
115 31 0.13
116 69 0.29
117 65 0.27
118 39 0.16
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (115 bp):
TAGCGGCGTTTTTTGTAAAAACGCCGCTAATACTCAACCTTTAGTGGCGTTTTTTAGAAACGCCG
CTAATAAAACTAAGGGCCGAAACGAAACGACTGCGTCTTGCTGAAATTAT
Done.