Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 155 of 311
Found at i:52733278 original size:27 final size:27
Alignment explanation
Indices: 52733248--52733309 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
52733238 ATTTACTAAA
52733248 ATACCCCTAAGTATG-AAAATTACCATT
1 ATACCCCTAAG-ATGCAAAATTACCATT
* *
52733275 ATACTCCT-AGGTGCAAAATTACCATT
1 ATACCCCTAAGATGCAAAATTACCATT
52733301 ATACCCCTA
1 ATACCCCTA
52733310 GGGTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.07
26 21 0.70
27 7 0.23
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (27 bp):
ATACCCCTAAGATGCAAAATTACCATT
Found at i:52733446 original size:27 final size:27
Alignment explanation
Indices: 52733415--52733527 Score: 149
Period size: 27 Copynumber: 4.2 Consensus size: 27
52733405 GAGGAAGCGT
*
52733415 TCTGGTGGGTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCAC-AATATCTGTA
*
52733442 TCTGGTGGCTCTGCCACAAATATCTGTT
1 TCTGGTGGCTCTGCCAC-AATATCTGTA
*
52733470 TCTAGTGGCTCTGCCACAATATCTGTA
1 TCTGGTGGCTCTGCCACAATATCTGTA
* *
52733497 TCTGGTGACTCTGTCACAATATCTGT-
1 TCTGGTGGCTCTGCCACAATATCTGTA
52733523 TCTGG
1 TCTGG
52733528 CAGCCATGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
26 5 0.06
27 57 0.73
28 16 0.21
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAATATCTGTA
Found at i:52733521 original size:54 final size:55
Alignment explanation
Indices: 52733414--52733523 Score: 161
Period size: 55 Copynumber: 2.0 Consensus size: 55
52733404 GGAGGAAGCG
* * *
52733414 TTCTGGTGGGTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTAGTGGCTCTGCCACAAATATCTGATCTGGTGACTCTGCCACAAATATCTGT
*
52733469 TTCTAGTGGCTCTGCCAC-AATATCTGTATCTGGTGACTCTGTCAC-AATATCTGT
1 TTCTAGTGGCTCTGCCACAAATATCTG-ATCTGGTGACTCTGCCACAAATATCTGT
52733523 T
1 T
52733524 CTGGCAGCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 18 0.36
55 32 0.64
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (55 bp):
TTCTAGTGGCTCTGCCACAAATATCTGATCTGGTGACTCTGCCACAAATATCTGT
Found at i:52740111 original size:13 final size:13
Alignment explanation
Indices: 52740093--52740123 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
52740083 TCGTGTCCTT
*
52740093 CACACGGTTGAGA
1 CACACGGTCGAGA
52740106 CACACGGTCGAGA
1 CACACGGTCGAGA
52740119 CACAC
1 CACAC
52740124 TGCCGTGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.26, T:0.10
Consensus pattern (13 bp):
CACACGGTCGAGA
Found at i:52741718 original size:42 final size:42
Alignment explanation
Indices: 52741603--52741726 Score: 142
Period size: 42 Copynumber: 2.9 Consensus size: 42
52741593 AGTACTGTAC
* * *
52741603 CAATGCCATATCCCAGACATGGTCTTACATGTAATCTCGTAT
1 CAATGACATATCCCAGATATGGTCTTACATGTAATCTCATAT
* * * *
52741645 CAATGCCAATAGCCTAGCTATGGTCTTACATG-AAGTCTCATAT
1 CAATGAC-ATATCCCAGATATGGTCTTACATGTAA-TCTCATAT
* *
52741688 CGATGACATATCCCAGATATGGTTTTACATGTAATCTCA
1 CAATGACATATCCCAGATATGGTCTTACATGTAATCTCA
52741727 GTAACCCCCA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 34 0.50
43 34 0.50
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (42 bp):
CAATGACATATCCCAGATATGGTCTTACATGTAATCTCATAT
Found at i:52758079 original size:39 final size:39
Alignment explanation
Indices: 52758036--52758117 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
52758026 AATTATGTTA
*
52758036 CCAGCACAAACCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACAAACCCTGCGGGACTTTAGCCCAGATACATTT
* * * * *
52758075 CCAGCACGAAGCTTGCGGGTCTTTAGCCCATATACATTT
1 CCAGCACAAACCCTGCGGGACTTTAGCCCAGATACATTT
52758114 CCAG
1 CCAG
52758118 TGTCTTGCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCAGCACAAACCCTGCGGGACTTTAGCCCAGATACATTT
Found at i:52769155 original size:49 final size:49
Alignment explanation
Indices: 52768978--52769209 Score: 275
Period size: 49 Copynumber: 4.7 Consensus size: 49
52768968 TCTATTGTGA
* * * * *
52768978 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTAT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-T
* * ** **
52769029 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* *
52769078 AGGTCACGTGTGTAGTACTAAGTACAGGCTACTACGTGTACTGGATAATT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* *
52769128 GGTCACGTGTATAGTACTAAGTTCAGGCTACTACGTGTACCGGATAATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* * *
52769177 GGTCGCATGTGTAGTACTATGTGCAGGCTACTA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
52769210 TGCGTACCAG
Statistics
Matches: 154, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
49 75 0.49
50 42 0.27
51 37 0.24
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:52769163 original size:99 final size:101
Alignment explanation
Indices: 52768977--52769217 Score: 290
Period size: 99 Copynumber: 2.4 Consensus size: 101
52768967 ATCTATTGTG
* * *
52768977 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTATGATCACGTGTGTA
1 AGGTCACATGTGTAGTACTAAGTACAGGCTACTACGCGTACCCGAAAACTATGATCACGTGTATA
52769042 GTACTAAGTGCAGGCTACTACGTGTATCAAATGGTT
66 GTACTAAGTGCAGGCTACTACGTGTATCAAATGGTT
* * ** * *
52769078 AGGTCACGTGTGTAGTACTAAGTACAGGCTACTACGTGTACTGGATAA-T-TGGTCACGTGTATA
1 AGGTCACATGTGTAGTACTAAGTACAGGCTACTACGCGTACCCGAAAACTATGATCACGTGTATA
* * ** **
52769141 GTACTAAGTTCAGGCTACTACGTGTACCGGATAATT
66 GTACTAAGTGCAGGCTACTACGTGTATCAAATGGTT
* * * *
52769177 -GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACC
1 AGGTCACATGTGTAGTACTAAGTACAGGCTACTACGCGTACC
52769218 AGATAGCCTT
Statistics
Matches: 118, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
98 34 0.29
99 42 0.36
100 1 0.01
101 41 0.35
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (101 bp):
AGGTCACATGTGTAGTACTAAGTACAGGCTACTACGCGTACCCGAAAACTATGATCACGTGTATA
GTACTAAGTGCAGGCTACTACGTGTATCAAATGGTT
Found at i:52772248 original size:15 final size:15
Alignment explanation
Indices: 52772228--52772292 Score: 64
Period size: 15 Copynumber: 4.4 Consensus size: 15
52772218 GTATCTTGGG
52772228 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
52772243 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
52772258 TTT-TTCTA-TCTTAGA
1 TTTCTT-TATTC-TGGA
*
52772273 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
52772287 TTTCTT
1 TTTCTT
52772293 GTTATCTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.27
15 26 0.63
16 4 0.10
ACGTcount: A:0.11, C:0.14, G:0.12, T:0.63
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:52772258 original size:30 final size:31
Alignment explanation
Indices: 52772224--52772292 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
52772214 TATCGTATCT
*
52772224 TGGGTTTCTT-TAT-TCTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCT-TAGATTTCTTTATTC
52772254 TGGGTTT-TTCTATCTTAGATTTCTTTATTC
1 TGGGTTTCTTCTATCTTAGATTTCTTTATTC
*
52772284 -GGTTTTCTT
1 TGGGTTTCTT
52772293 GTTATCTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 7 0.21
30 26 0.76
31 1 0.03
ACGTcount: A:0.10, C:0.13, G:0.16, T:0.61
Consensus pattern (31 bp):
TGGGTTTCTTCTATCTTAGATTTCTTTATTC
Found at i:52773616 original size:44 final size:43
Alignment explanation
Indices: 52773489--52773630 Score: 141
Period size: 44 Copynumber: 3.3 Consensus size: 43
52773479 AACGTATCTA
* *
52773489 ACGTGGTCTTACATGT-AATCAAATATCGAAGCC-ACTGTCCCAG
1 ACGTGGTCTTACATGTAAATCAAA-GTCGATGCCAAC-GTCCCAG
* * * *
52773532 ATAGT-GTATTACATG-AAATC-AAGTACGATGCTAATGTCCCAG
1 A-CGTGGTCTTACATGTAAATCAAAGT-CGATGCCAACGTCCCAG
*
52773574 ACGTGGTCTTACATGTAAATCATAAGTCGATGCCAACGTCCCAC
1 ACGTGGTCTTACATGTAAATCA-AAGTCGATGCCAACGTCCCAG
52773618 ACGTGGTCTTACA
1 ACGTGGTCTTACA
52773631 CGATAACACA
Statistics
Matches: 80, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
41 3 0.04
42 24 0.30
43 20 0.25
44 29 0.36
45 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (43 bp):
ACGTGGTCTTACATGTAAATCAAAGTCGATGCCAACGTCCCAG
Found at i:52776248 original size:26 final size:26
Alignment explanation
Indices: 52776178--52776248 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
52776168 CAACTCACCA
* * *
52776178 CAGCTCGTCAGAGCTTACCGATATAT
1 CAGCTCGTAAGAGCTTACTGACATAT
52776204 CAGCTCGTAAGAGCTTACTGACATAT
1 CAGCTCGTAAGAGCTTACTGACATAT
52776230 CAGCTCGTAAGAGCTTACT
1 CAGCTCGTAAGAGCTTACT
52776249 ATTTTAAGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (26 bp):
CAGCTCGTAAGAGCTTACTGACATAT
Found at i:52779552 original size:93 final size:91
Alignment explanation
Indices: 52779395--52779563 Score: 248
Period size: 93 Copynumber: 1.8 Consensus size: 91
52779385 CGCCCTAAGT
52779395 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCATCCATAAATGAACTCAGACTCAACTCAACG
1 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCATCCATAAATGAACTCAGACTCAACTCAACG
52779460 AGTTCGGATGCCTAGTTAAATCTCAC
66 AGTTCGGATGCCTAGTTAAATCTCAC
* * * * * * *
52779486 GAACTCGGACTCAACTTAACGAGTTCGGTCATTTGCATCCATAAGTGAACTCGGACTCAATTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGGC-GTT-CATCCATAAATGAACTCAGACTCAACTCAA
*
52779551 CGAGTTTGGATGC
64 CGAGTTCGGATGC
52779564 TCAACCATCC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
91 27 0.40
92 2 0.03
93 39 0.57
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCATCCATAAATGAACTCAGACTCAACTCAACG
AGTTCGGATGCCTAGTTAAATCTCAC
Found at i:52781970 original size:29 final size:30
Alignment explanation
Indices: 52781919--52782011 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 30
52781909 TTATGGAACA
*
52781919 AAGATAAA-A-AAACCGAATAAAGAAATCC
1 AAGATAAAGAGAACCCGAATAAAGAAATCC
*
52781947 AAGATAGAGA-AACCCGAATAAAGAAATCC
1 AAGATAAAGAGAACCCGAATAAAGAAATCC
* * * *
52781976 -AGAATAAAGAGATCCAGGATAAAGAAACCC
1 AAG-ATAAAGAGAACCCGAATAAAGAAATCC
52782006 AAGATA
1 AAGATA
52782012 CGATACTATG
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
28 9 0.17
29 25 0.46
30 18 0.33
31 2 0.04
ACGTcount: A:0.58, C:0.15, G:0.16, T:0.11
Consensus pattern (30 bp):
AAGATAAAGAGAACCCGAATAAAGAAATCC
Found at i:52781982 original size:15 final size:15
Alignment explanation
Indices: 52781933--52782002 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
52781923 TAAAAAAACC
52781933 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
* *
52781948 -AGATAGAGAAA-CCC
1 GA-ATAAAGAAATCCA
52781962 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
52781977 GAATAAAGAGATCCA
1 GAATAAAGAAATCCA
*
52781992 GGATAAAGAAA
1 GAATAAAGAAA
52782003 CCCAAGATAC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
14 11 0.24
15 34 0.76
ACGTcount: A:0.57, C:0.13, G:0.19, T:0.11
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:52782011 original size:15 final size:15
Alignment explanation
Indices: 52781935--52782011 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
52781925 AAAAAACCGA
52781935 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
52781950 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
52781964 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
52781978 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
52781994 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
52782009 ATA
1 ATA
52782012 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:52785098 original size:93 final size:93
Alignment explanation
Indices: 52784939--52785109 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
52784929 CGCCCTAAGT
*
52784939 GAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCAGAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAGCATTCGCATCCAGAAATGAACTCGGACTCAACTCAA
52785004 CGAGTTCGGATGCCTAGTTAAATCTCAC
66 CGAGTTCGGATGCCTAGTTAAATCTCAC
* * * * *
52785032 GAACTCGGACTCAACTCAACTAGTTCG-GACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGAG-CATTCGCATCCAGAAATGAACTCGGACTCAACTCA
52785096 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
52785110 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 70 0.99
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAGCATTCGCATCCAGAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTAAATCTCAC
Found at i:52785103 original size:46 final size:47
Alignment explanation
Indices: 52784934--52785106 Score: 185
Period size: 46 Copynumber: 3.7 Consensus size: 47
52784924 TAACCCGCCC
* * *
52784934 TAAGTGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
* * * **
52784980 GAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTAAAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-ATTTGCATCCA
* * *
52785028 TCA-CGAACTCGGACTCAACTCAACTAGTTCGGA-CATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
52785073 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52785107 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
45 2 0.02
46 56 0.55
47 30 0.29
48 2 0.02
49 2 0.02
50 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
Found at i:52795907 original size:28 final size:29
Alignment explanation
Indices: 52795791--52795895 Score: 137
Period size: 28 Copynumber: 3.7 Consensus size: 29
52795781 ACATACATGC
52795791 ATATGGCCCA-CTAGGCCCAATCTCATTT
1 ATATGGCCCATCTAGGCCCAATCTCATTT
* *
52795819 ATATGGCCCATC-AGGCCCAATTCGCATTC
1 ATATGGCCCATCTAGGCCCAA-TCTCATTT
* *
52795848 ATATGGCCCGT-TAGGCCCAGTCTCATTT
1 ATATGGCCCATCTAGGCCCAATCTCATTT
52795876 ATATGGCCCATCT-GGCCCAA
1 ATATGGCCCATCTAGGCCCAA
52795896 ATCACATTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
28 40 0.62
29 25 0.38
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (29 bp):
ATATGGCCCATCTAGGCCCAATCTCATTT
Found at i:52796150 original size:16 final size:15
Alignment explanation
Indices: 52796118--52796160 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
52796108 GTAGCCAAAC
*
52796118 TTTCGTCTTTTGGCA
1 TTTCGGCTTTTGGCA
*
52796133 TTTTGGCTTTTCGGCA
1 TTTCGGCTTTT-GGCA
52796149 TTTCGGCTTTTG
1 TTTCGGCTTTTG
52796161 TCGATCTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.05, C:0.19, G:0.23, T:0.53
Consensus pattern (15 bp):
TTTCGGCTTTTGGCA
Found at i:52797957 original size:46 final size:46
Alignment explanation
Indices: 52797888--52798055 Score: 175
Period size: 46 Copynumber: 3.6 Consensus size: 46
52797878 GTAACCCGCC
*
52797888 CCTAAGTGAACTCGGACTCAACTCAACGAGCTCAG-GTGTTCGCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCAGAGTGTTCGCAT
* *
52797933 CCATAAGTGAACTCGGACTCAACTCAACGAGTTTAGATGCCTAGTT-ACAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCAGA-G--T-GTTCGCAT
* * ***
52797983 -CTCA-CGAACTCGGACTCAACTCAACGAGTTC-GAACATTCGCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCAGAGTGTTCGCAT
52798026 CCGTAAGTGAACTCGGACTCAACTCAACGA
1 CC-TAAGTGAACTCGGACTCAACTCAACGA
52798056 CTTCGGATGC
Statistics
Matches: 101, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 4 0.04
46 55 0.54
47 25 0.25
48 3 0.03
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
CCTAAGTGAACTCGGACTCAACTCAACGAGTTCAGAGTGTTCGCAT
Found at i:52798065 original size:93 final size:93
Alignment explanation
Indices: 52797895--52798065 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 93
52797885 GCCCCTAAGT
***
52797895 GAACTCGGACTCAACTCAACGAGCTCAGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
52797960 CGAGTTTAGATGCCTAGTTACATCTCAC
66 CGACTTCAGATGCCTAGTTACATCTCAC
* *
52797988 GAACTCGGACTCAACTCAACGAGTTC-GAACATTCGCATCCGTAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCAG-ACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
52798052 ACGACTTCGGATGC
65 ACGACTTCAGATGC
52798066 TCAACCATCC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
92 1 0.01
93 68 0.99
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGACTTCAGATGCCTAGTTACATCTCAC
Found at i:52799729 original size:16 final size:16
Alignment explanation
Indices: 52799710--52799741 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52799700 AATTTTAAGT
52799710 TTTCAGGATTTTTGGG
1 TTTCAGGATTTTTGGG
52799726 TTTCAGGATTTTTGGG
1 TTTCAGGATTTTTGGG
52799742 GTGTTACACA
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:0.12, C:0.06, G:0.31, T:0.50
Consensus pattern (16 bp):
TTTCAGGATTTTTGGG
Found at i:52811647 original size:55 final size:55
Alignment explanation
Indices: 52811562--52811671 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
52811552 ACCTCGGACT
* *
52811562 CAGCTTGCCTTTTCTGCCAAATCAAGTTACTTTCTTCCACGGTGAGAGTTTCAAA
1 CAGCTTGCATTTTCTGCCAAATCAAATTACTTTCTTCCACGGTGAGAGTTTCAAA
52811617 CAGCTTGCATTTTCTGCCAAATCAAATTACTTTCTTCCACGGTGAGAGTTTCAAA
1 CAGCTTGCATTTTCTGCCAAATCAAATTACTTTCTTCCACGGTGAGAGTTTCAAA
52811672 AACACTTTGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (55 bp):
CAGCTTGCATTTTCTGCCAAATCAAATTACTTTCTTCCACGGTGAGAGTTTCAAA
Found at i:52819183 original size:50 final size:50
Alignment explanation
Indices: 52819053--52819241 Score: 238
Period size: 50 Copynumber: 3.8 Consensus size: 50
52819043 AGCCGAAGCT
* * * *
52819053 ATCTGATACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACA
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* * * *
52819102 ATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCACC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* * *
52819152 ATCTGATACACGTAGTAGCTTGCACTTAGTACTACACATGCGACTTAA-C
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* *
52819201 AGTATGGTACACGTAGTAGCCTGCACTTAGTACTACACACG
1 A-TCTGATACACGTAGTAGCCTGCACTTAGTACTACACACG
52819242 TGTATTCACA
Statistics
Matches: 119, Mismatches: 19, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
49 41 0.34
50 78 0.66
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
Found at i:52826136 original size:40 final size:39
Alignment explanation
Indices: 52826089--52826194 Score: 149
Period size: 40 Copynumber: 2.7 Consensus size: 39
52826079 CTACTCGCTC
* * *
52826089 AAATGCCTTCGGGACATAGCCCGGTTAGAGTAACTCGTAC
1 AAATGCCTTCGGGACTTAGCCCGGTT-GAGTAACTCGCAA
* *
52826129 AATTGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAA
1 AAATGCCTTCGGGACTTAGCCCGG-TTGAGTAACTCGCAA
52826169 AAATGCCTTCGGGACTTAGCCCGGTT
1 AAATGCCTTCGGGACTTAGCCCGGTT
52826195 TTCATCCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 2 0.03
40 55 0.93
41 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (39 bp):
AAATGCCTTCGGGACTTAGCCCGGTTGAGTAACTCGCAA
Found at i:52834235 original size:39 final size:39
Alignment explanation
Indices: 52834148--52834290 Score: 189
Period size: 39 Copynumber: 3.6 Consensus size: 39
52834138 ACTACTCGCT
* *
52834148 CAAATGCCTTCGGGACATAGCCCGG-TTAGAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATT--AGTAACTAGTA
* * *
52834188 CAATTGCCTTCGGGACTTAGCCCGGATTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTAGTA
* *
52834227 CAAATGCCTTCGGGACTTAGCCCGGATTAGTCACTAGTG
1 CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTAGTA
*
52834266 CAGATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
52834291 TTTTCATCCA
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
39 67 0.73
40 23 0.25
41 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTAGTA
Found at i:52836611 original size:27 final size:26
Alignment explanation
Indices: 52836544--52836614 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
52836534 TCAAATTGAC
*
52836544 AAAATGATTGTTTTGTCCTTACGTGGT
1 AAAATGATCGTTTTG-CCTTACGTGGT
* *
52836571 AAAATGA-CTATTTTGCCTTTATGTGGT
1 AAAATGATC-GTTTTGCC-TTACGTGGT
*
52836598 AAGATGATCGTTTTGCC
1 AAAATGATCGTTTTGCC
52836615 CCTATGTGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
26 2 0.06
27 33 0.92
28 1 0.03
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (26 bp):
AAAATGATCGTTTTGCCTTACGTGGT
Found at i:52844493 original size:50 final size:50
Alignment explanation
Indices: 52844368--52844556 Score: 229
Period size: 50 Copynumber: 3.8 Consensus size: 50
52844358 AGCCGAAGCT
* * * *
52844368 ATCTGATACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACA
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* * * * *
52844417 ATCCGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTCACC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* * *
52844467 ATCTGATACACGTAGTAGCTTGCACTTAGTACTACACATGCGACTTAA-C
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* *
52844516 AGTATGGTACACGTAGTAGCCTGCACTTAGTACTACACACG
1 A-TCTGATACACGTAGTAGCCTGCACTTAGTACTACACACG
52844557 TGTATTCACA
Statistics
Matches: 117, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
49 40 0.34
50 77 0.66
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
Found at i:52855387 original size:25 final size:25
Alignment explanation
Indices: 52855358--52855405 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
52855348 TTAAAATATG
* * *
52855358 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
52855383 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
52855406 GTTTAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:52855489 original size:11 final size:11
Alignment explanation
Indices: 52855453--52855508 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
52855443 CATGGTATGT
52855453 ATGATATGCAC
1 ATGATATGCAC
* *
52855464 ATGACATG--T
1 ATGATATGCAC
52855473 ATGATATGCAC
1 ATGATATGCAC
*
52855484 ATGATATG--T
1 ATGATATGCAC
52855493 ATGATATGCAC
1 ATGATATGCAC
52855504 ATGAT
1 ATGAT
52855509 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:52855508 original size:20 final size:20
Alignment explanation
Indices: 52855442--52855508 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
52855432 ATTTTGATAA
*
52855442 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
52855462 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
52855482 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
52855502 ACATGAT
1 ACATGAT
52855509 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:52855587 original size:25 final size:25
Alignment explanation
Indices: 52855559--52855678 Score: 208
Period size: 25 Copynumber: 4.9 Consensus size: 25
52855549 AGGAAGTGTA
52855559 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
52855584 AAAGGGCTTATGCCCTAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
52855609 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
52855634 AAAGGGCTTATGCCCCAGTTATTA-
1 AAAGGGCTTATGCCCCAGTTATGAT
52855658 AAAGGGCTT-TGCCCCAGTTAT
1 AAAGGGCTTATGCCCCAGTTAT
52855679 TAAAAGAGGC
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
23 12 0.13
24 9 0.10
25 71 0.77
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (25 bp):
AAAGGGCTTATGCCCCAGTTATGAT
Found at i:52855712 original size:75 final size:75
Alignment explanation
Indices: 52855559--52855702 Score: 206
Period size: 75 Copynumber: 1.9 Consensus size: 75
52855549 AGGAAGTGTA
* *
52855559 AAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCTAGTTATGATAAAGGGCTTATGCCC
1 AAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTAGGCCC
52855624 CAGTTATGAT
66 CAGTTATGAT
* *
52855634 AAAGGGCTTATGCCCCAGTTATTA-AAAGGGCTT-TGCCCCAGTTATTA-AAAGAGGC-TAGGCC
1 AAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTATGATAAAG-GGCTTAGGCC
52855695 TCCAGTTA
65 -CCAGTTA
52855703 AATGGTAAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
72 9 0.14
73 22 0.35
74 9 0.14
75 23 0.37
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (75 bp):
AAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTAGGCCC
CAGTTATGAT
Found at i:52863044 original size:17 final size:18
Alignment explanation
Indices: 52863022--52863059 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
52863012 TATAATAAGG
52863022 TTATTAAGGTAAAT-TTA
1 TTATTAAGGTAAATATTA
* *
52863039 TTATTAATGTTAATATTA
1 TTATTAAGGTAAATATTA
52863057 TTA
1 TTA
52863060 AAAGAAAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
TTATTAAGGTAAATATTA
Found at i:52863999 original size:22 final size:22
Alignment explanation
Indices: 52863974--52864022 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
52863964 CACGTATGAA
52863974 CTTACTATTCAGCTCGATAAAG
1 CTTACTATTCAGCTCGATAAAG
* * * *
52863996 CTTATTGTTCAGCTTGATAGAG
1 CTTACTATTCAGCTCGATAAAG
52864018 CTTAC
1 CTTAC
52864023 CCTTTCATCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (22 bp):
CTTACTATTCAGCTCGATAAAG
Found at i:52872193 original size:14 final size:14
Alignment explanation
Indices: 52872174--52872200 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52872164 TTGGTAACCT
52872174 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
52872188 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
52872201 AGGTATTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GTAAAAGCTTTTCC
Found at i:52874976 original size:20 final size:20
Alignment explanation
Indices: 52874928--52874993 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
52874918 CATCCAAACA
*
52874928 CCAGAAAAGCAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
*
52874948 -CAAAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
52874967 CCAGAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
52874987 CCAGAAA
1 CCAGAAA
52874994 TAATTTTCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
19 17 0.40
20 25 0.60
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (20 bp):
CCAGAAAAGTAAATCATTTT
Found at i:52876260 original size:27 final size:28
Alignment explanation
Indices: 52876230--52876391 Score: 120
Period size: 27 Copynumber: 6.0 Consensus size: 28
52876220 CTGCAATGGC
52876230 ATTTCGA-TAATTTTACAAATTGGGGGT
1 ATTTCGAGTAATTTTACAAATTGGGGGT
* *
52876257 ATTTC-AGTTATTTTACAAGTTGGGGGT
1 ATTTCGAGTAATTTTACAAATTGGGGGT
* * * ** * *
52876284 CTTTAGA-TAATTTCATGAATCGAGGGT
1 ATTTCGAGTAATTTTACAAATTGGGGGT
* **
52876311 ATTTCG-GTAATTTCACAAATCAGGGGT
1 ATTTCGAGTAATTTTACAAATTGGGGGT
* **
52876338 A-TTCCAGTAATTTTACAACCTGGGGGT
1 ATTTCGAGTAATTTTACAAATTGGGGGT
* * *
52876365 ATTT-TAGTAATTTTACAGATTGAGGGT
1 ATTTCGAGTAATTTTACAAATTGGGGGT
52876392 CTTAACGACC
Statistics
Matches: 102, Mismatches: 28, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
26 4 0.04
27 95 0.93
28 3 0.03
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (28 bp):
ATTTCGAGTAATTTTACAAATTGGGGGT
Found at i:52876293 original size:54 final size:55
Alignment explanation
Indices: 52876235--52876394 Score: 137
Period size: 54 Copynumber: 2.9 Consensus size: 55
52876225 ATGGCATTTC
* *
52876235 GATAATTTTACAAATTGGGGGTATTTCAGTTATTTTACAAGTTGGGGGTCTT-TA
1 GATAATTTTACAAATTGGGGGTATTTCAGTAATTTTACAAGTTGGGGGTCTTCCA
* ** * * * * * ** *
52876289 GATAATTTCATGAATCGAGGGTATTTCGGTAATTTCACAAATCAGGGGTATTCCA
1 GATAATTTTACAAATTGGGGGTATTTCAGTAATTTTACAAGTTGGGGGTCTTCCA
** * *
52876344 G-TAATTTTACAACCTGGGGGTATTTTAGTAATTTTAC-AGATTGAGGGTCTT
1 GATAATTTTACAAATTGGGGGTATTTCAGTAATTTTACAAG-TTGGGGGTCTT
52876395 AACGACCCAA
Statistics
Matches: 76, Mismatches: 28, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
53 1 0.01
54 73 0.96
55 2 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (55 bp):
GATAATTTTACAAATTGGGGGTATTTCAGTAATTTTACAAGTTGGGGGTCTTCCA
Found at i:52877453 original size:53 final size:53
Alignment explanation
Indices: 52877373--52877479 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
52877363 TAACACCCTT
52877373 ACATAGCACCCGATTCCAAAATGGTACTGACTGCCTACCTTGAATAGCAATCG
1 ACATAGCACCCGATTCCAAAATGGTACTGACTGCCTACCTTGAATAGCAATCG
52877426 ACATAGCACCCGATTCCAAAATGGTACTGACTGCCTACCTTGAATAGCAATCG
1 ACATAGCACCCGATTCCAAAATGGTACTGACTGCCTACCTTGAATAGCAATCG
52877479 A
1 A
52877480 TTCCTCTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (53 bp):
ACATAGCACCCGATTCCAAAATGGTACTGACTGCCTACCTTGAATAGCAATCG
Found at i:52881614 original size:29 final size:29
Alignment explanation
Indices: 52881542--52881621 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 29
52881532 CATACATGCT
*
52881542 TATGGCCCACTAGGCCC-AATCTCATTCA
1 TATGGCCCACTAGGCCCAAATCACATTCA
*
52881570 TATGGCCCA-TCGGGCCCAAATCACA-TCTA
1 TATGGCCCACT-AGGCCCAAATCACATTC-A
*
52881599 TATGGCCAACTAGG-CCAAATCAC
1 TATGGCCCACTAGGCCCAAATCAC
52881622 TTTTACAGTC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 1 0.02
28 25 0.57
29 17 0.39
30 1 0.02
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (29 bp):
TATGGCCCACTAGGCCCAAATCACATTCA
Found at i:52881883 original size:16 final size:16
Alignment explanation
Indices: 52881845--52881892 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
52881835 CCAAACTTTC
52881845 AGCTTTTCGGCATTTA
1 AGCTTTTCGGCATTTA
* * *
52881861 AGATTTTTGGCATTTT
1 AGCTTTTCGGCATTTA
*
52881877 AGCTTTTCGGGATTTA
1 AGCTTTTCGGCATTTA
52881893 CCGATCTACT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (16 bp):
AGCTTTTCGGCATTTA
Found at i:52884072 original size:93 final size:93
Alignment explanation
Indices: 52883944--52884114 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
52883934 GCCCATAAGC
* * *
52883944 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52884009 CGAGTTCGGATGCCTAGTTACATCTCAT
66 CGAGTTCGGATGCCTAGTTACATCTCAT
*
52884037 GAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52884102 CGAGTTCGGATGC
66 CGAGTTCGGATGC
52884115 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAT
Found at i:52884111 original size:46 final size:46
Alignment explanation
Indices: 52883936--52884111 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
52883926 TGTAACCCGC
* * * *
52883936 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
52883982 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
52884032 -C-TCA-TGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
52884075 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52884112 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:52892837 original size:64 final size:64
Alignment explanation
Indices: 52892753--52892879 Score: 236
Period size: 64 Copynumber: 2.0 Consensus size: 64
52892743 GTATGCGACC
* *
52892753 TATCCCGTAGCTCTCTTGTCTACATGGTGTACACATATTATCACCCATGCAACCTAGCTACATA
1 TATCCCGTAGCTCTCATGTCTACATAGTGTACACATATTATCACCCATGCAACCTAGCTACATA
52892817 TATCCCGTAGCTCTCATGTCTACATAGTGTACACATATTATCACCCATGCAACCTAGCTACAT
1 TATCCCGTAGCTCTCATGTCTACATAGTGTACACATATTATCACCCATGCAACCTAGCTACAT
52892880 CATAATGTCT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.31
Consensus pattern (64 bp):
TATCCCGTAGCTCTCATGTCTACATAGTGTACACATATTATCACCCATGCAACCTAGCTACATA
Found at i:52893648 original size:30 final size:30
Alignment explanation
Indices: 52893614--52893674 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
52893604 TCCTTAACTC
*
52893614 AAACTTTTGCAAAATTATAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
52893644 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
52893674 A
1 A
52893675 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:52895884 original size:47 final size:47
Alignment explanation
Indices: 52895821--52896350 Score: 817
Period size: 47 Copynumber: 11.3 Consensus size: 47
52895811 CCCTTCGGGA
* * * *
52895821 CTTATCACATTTATACACTTTAACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * * * *
52895868 CTTATCACATATATACACCTCCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
52895915 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
52895962 CTTATCACAGATATACACTTTCACATTCATTACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
52896009 CTTGTCACATATATACACTTTCACATTAATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
52896056 TTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
52896103 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
52896150 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
52896197 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
52896244 TTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
52896291 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
52896338 CTTATCACATATA
1 CTTATCACATATA
52896351 CATATCTTGT
Statistics
Matches: 439, Mismatches: 44, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 439 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:52899469 original size:21 final size:21
Alignment explanation
Indices: 52899444--52899484 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
52899434 AAGAAAGTAC
52899444 TCCGGTTCAGTAGAAAAAGCG
1 TCCGGTTCAGTAGAAAAAGCG
52899465 TCCGGTTCAGTAGAAAAAGC
1 TCCGGTTCAGTAGAAAAAGC
52899485 AAATTGAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.20
Consensus pattern (21 bp):
TCCGGTTCAGTAGAAAAAGCG
Found at i:52901178 original size:44 final size:44
Alignment explanation
Indices: 52901107--52901257 Score: 159
Period size: 43 Copynumber: 3.5 Consensus size: 44
52901097 TATGTGTTAT
* * *
52901107 CGTGTAAGACCACGTCTAGGACGTTGGCATCGACT-TATGATTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGA-TATTTGATTTA
*
52901151 CGTGTAAGACCATGTCTGGGACATTGGCATC-ATATTTGATTT-
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTTA
* * * *
52901193 TGTGTAAGACC-CTATCTGGGACAGTGGCATTGATATTTGA-TTA
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCGATATTTGATTTA
* *
52901236 CATGTAAGACCACGTCTCGGAC
1 CGTGTAAGACCACGTCTGGGAC
52901258 GTTGCCATTG
Statistics
Matches: 89, Mismatches: 13, Indels: 11
0.79 0.12 0.10
Matches are distributed among these distances:
42 28 0.31
43 32 0.36
44 29 0.33
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (44 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTTA
Found at i:52901243 original size:43 final size:42
Alignment explanation
Indices: 52901148--52901247 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
52901138 GACTTATGAT
* *
52901148 TTACGTGTAAGACCATGTCTGGGACATTGGCATCATATTTGA
1 TTACGTGTAAGACCATATCTGGGACAGTGGCATCATATTTGA
** * *
52901190 TTTTGTGTAAGACCCTATCTGGGACAGTGGCATTGATATTTGA
1 TTACGTGTAAGACCATATCTGGGACAGTGGCA-TCATATTTGA
*
52901233 TTACATGTAAGACCA
1 TTACGTGTAAGACCA
52901248 CGTCTCGGAC
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 27 0.57
43 20 0.43
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (42 bp):
TTACGTGTAAGACCATATCTGGGACAGTGGCATCATATTTGA
Found at i:52904928 original size:47 final size:47
Alignment explanation
Indices: 52904869--52905153 Score: 403
Period size: 47 Copynumber: 6.1 Consensus size: 47
52904859 GAAATGATAG
*
52904869 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
52904916 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
52904963 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
52905010 TAAGGCCTAAT-GACCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAG-CCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
52905057 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * ** * * *
52905103 CAGGGCCGAGTGGCCAACATGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
52905150 TAAG
1 TAAG
52905154 TCTCGAAGGG
Statistics
Matches: 219, Mismatches: 16, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
46 40 0.18
47 178 0.81
48 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:52905328 original size:37 final size:37
Alignment explanation
Indices: 52905272--52905350 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
52905262 CCGAGCTCTA
* * * *
52905272 AAGACTCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
52905309 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
52905346 AAGAC
1 AAGAC
52905351 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:52916766 original size:43 final size:43
Alignment explanation
Indices: 52916700--52916814 Score: 178
Period size: 43 Copynumber: 2.7 Consensus size: 43
52916690 AATAAACTCG
* *
52916700 CACACTTAGTGCTAATTAGTTAACCGAAGCTATAATTGTATCC
1 CACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATCC
*
52916743 CACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATCG
1 CACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATCC
52916786 CACACTTAGTGCCAA-TAGATTAAACCGAA
1 CACACTTAGTGCCAATTA-ATT-AACCGAA
52916815 CTTATATCGG
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
42 2 0.03
43 58 0.87
44 7 0.10
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (43 bp):
CACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATCC
Found at i:52922135 original size:29 final size:29
Alignment explanation
Indices: 52922103--52922159 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
52922093 ATTTACTCAT
52922103 ACATGATCAACATCTCATAATTTAACCCC
1 ACATGATCAACATCTCATAATTTAACCCC
** * *
52922132 ACATTTTCATCATTTCATAATTTAACCC
1 ACATGATCAACATCTCATAATTTAACCC
52922160 TTAAATGGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (29 bp):
ACATGATCAACATCTCATAATTTAACCCC
Found at i:52925419 original size:46 final size:46
Alignment explanation
Indices: 52925352--52925526 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 46
52925342 AACCCGCCCC
* *
52925352 TAAGTGAACTCGGGCTCAACTCAACGAGCTCAGG-TGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGATGTTCGCATCCA
* * * *
52925398 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG-TTCGCATCCA
* * **
52925444 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCA
52925491 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
52925527 CTCAACCATC
Statistics
Matches: 105, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
45 4 0.04
46 65 0.62
47 34 0.32
48 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCA
Found at i:52925470 original size:93 final size:93
Alignment explanation
Indices: 52925357--52925527 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
52925347 GCCCCTAAGT
* **
52925357 GAACTCGGGCTCAACTCAACGAGCTCAGG-TGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
52925421 ACGAGTTCGGATGCCTAGTTACATTTCAC
65 ACGAGTTCGGATGCCTAGTTACATTTCAC
*
52925450 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52925515 CGAGTTCGGATGC
66 CGAGTTCGGATGC
52925528 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:52925979 original size:30 final size:30
Alignment explanation
Indices: 52925945--52926005 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
52925935 CATTTAATAC
52925945 AAACTTTGGAAAAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
* * *
52925975 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
52926005 A
1 A
52926006 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCCCT
Found at i:52928758 original size:43 final size:43
Alignment explanation
Indices: 52928638--52928800 Score: 132
Period size: 43 Copynumber: 3.8 Consensus size: 43
52928628 AGCTTGTACA
** * **
52928638 ATGCCAACATCCCAGACGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCAAATAT-G
** * * * *
52928681 ATGCCTCTGCCCCAAACAGGGTCTTACAC-GAAATCAAATATG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCAAATATG
* * ** *
52928723 ATGCGAATGTCCCAGACATGGTCTTACACATAAATCATAGGTC
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCAAATATG
*
52928766 ATTGCCAACGTCCCAGACATGGTCTTACACGATAA
1 A-TGCCAATGTCCCAGACATGGTCTTACAC-ATAA
52928801 CACATATCGA
Statistics
Matches: 93, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
42 24 0.26
43 39 0.42
44 26 0.28
45 4 0.04
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACATAAATCAAATATG
Found at i:52953049 original size:42 final size:42
Alignment explanation
Indices: 52952943--52953082 Score: 111
Period size: 42 Copynumber: 3.3 Consensus size: 42
52952933 TATGTGACTT
*** * * *
52952943 CGTGTAAGACCACATCTGGGACATTGGCATCAATTTGAGATTTA
1 CGTGTAAGACCATGGCTGGGACAGTGGCATCGATAT--GATTTA
** * *
52952987 CGTGTAAGACCATGTTTGGGATATTGGCATCGTATATGATTT-
1 CGTGTAAGACCATGGCTGGGACAGTGGCATCG-ATATGATTTA
* * *
52953029 CGTGTAAGACCCTGGCTGGGACAGTGGCATCGATATCTAATTA
1 CGTGTAAGACCATGGCTGGGACAGTGGCATCGATAT-GATTTA
*
52953072 CATGTAAGACC
1 CGTGTAAGACC
52953083 TCGTCTGGGA
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
41 4 0.05
42 30 0.38
43 15 0.19
44 27 0.34
45 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (42 bp):
CGTGTAAGACCATGGCTGGGACAGTGGCATCGATATGATTTA
Found at i:52953091 original size:43 final size:43
Alignment explanation
Indices: 52952943--52953101 Score: 119
Period size: 43 Copynumber: 3.7 Consensus size: 43
52952933 TATGTGACTT
* * * * * * *
52952943 CGTGTAAGACCACATCTGGGACATTGGCATCAATTTGAGATTTA
1 CGTGTAAGACCTCGTCTGGGACAGTGGCATCGATAT-ATAATTA
* * * * *
52952987 CGTGTAAGACCAT-GTTTGGGATATTGGCATCG-TATATGATTT
1 CGTGTAAGACC-TCGTCTGGGACAGTGGCATCGATATATAATTA
* *
52953029 CGTGTAAGACC-CTGGCTGGGACAGTGGCATCGATATCTAATTA
1 CGTGTAAGACCTC-GTCTGGGACAGTGGCATCGATATATAATTA
*
52953072 CATGTAAGACCTCGTCTGGGAC-GTTGGCAT
1 CGTGTAAGACCTCGTCTGGGACAG-TGGCAT
52953102 TGTATAAGCT
Statistics
Matches: 90, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
42 30 0.33
43 33 0.37
44 27 0.30
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCTCGTCTGGGACAGTGGCATCGATATATAATTA
Found at i:52955667 original size:32 final size:33
Alignment explanation
Indices: 52955621--52955684 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
52955611 AACGGTGGGT
52955621 ACTGGGCCGAAG-CCCTTTTCAGA-ATACAGTAA
1 ACTGGGCCGAAGCCCCTTTTCAGATA-ACAGTAA
**
52955653 ACTGGGCCTTAGCCCCTTTTCAGATAACAGTA
1 ACTGGGCCGAAGCCCCTTTTCAGATAACAGTA
52955685 TGGCCCATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.36
33 17 0.61
34 1 0.04
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (33 bp):
ACTGGGCCGAAGCCCCTTTTCAGATAACAGTAA
Found at i:52956054 original size:27 final size:26
Alignment explanation
Indices: 52955998--52956054 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
52955988 CAACCTTAAC
* * *
52955998 CCTAGGGGTATATCAGTAATTTTGCT
1 CCTAGGGGTAAATCAGTAATTTTCCA
52956024 CCTAGGGGTAAATCTA-TAAATTTTCCA
1 CCTAGGGGTAAATC-AGT-AATTTTCCA
52956051 CCTA
1 CCTA
52956055 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTTTCCA
Found at i:52958295 original size:3 final size:3
Alignment explanation
Indices: 52958287--52958314 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
52958277 TTTTCCTATC
52958287 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
52958315 TTTATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:52958332 original size:24 final size:23
Alignment explanation
Indices: 52958305--52958363 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
52958295 ATAATAATAA
*
52958305 TAATAATAATTTTATAAATATATC
1 TAATAATAAATTTA-AAATATATC
* * *
52958329 TAATAAAAAAATTTAAAATATCTG
1 TAAT-AATAAATTTAAAATATATC
52958353 TAATAATAAAT
1 TAATAATAAAT
52958364 ACAGTAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 6 0.21
24 15 0.52
25 8 0.28
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATAATAAATTTAAAATATATC
Found at i:52962475 original size:27 final size:27
Alignment explanation
Indices: 52962445--52962523 Score: 115
Period size: 27 Copynumber: 3.0 Consensus size: 27
52962435 AATCTCATAT
* *
52962445 CTGTAGGCTAGCATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
52962472 CTGTAGGGTAGAATTACTGAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
52962499 CTGTAGGGTAGAATTAC-CAAATACC
1 CTGTAGGGTAGAATTACTGAAATACC
52962524 TTTGGTTTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 6 0.13
27 41 0.87
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTGAAATACCC
Found at i:52962539 original size:26 final size:27
Alignment explanation
Indices: 52962510--52962632 Score: 124
Period size: 27 Copynumber: 4.6 Consensus size: 27
52962500 TGTAGGGTAG
** *
52962510 AATTACC-AAATACCTTTGGTTTACAA
1 AATTACCAAAATACCCCTAGTTTACAA
**
52962536 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTACAA
**
52962563 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTACAA
* ***
52962590 AATAACCAAAATACCCCT-GATTTGTGA
1 AATTACCAAAATACCCCTAG-TTTACAA
52962617 AATTACCAAAATACCC
1 AATTACCAAAATACCC
52962633 TCGACCTGTA
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
26 8 0.09
27 79 0.91
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTACAA
Found at i:52962754 original size:81 final size:80
Alignment explanation
Indices: 52962535--52962767 Score: 233
Period size: 81 Copynumber: 2.9 Consensus size: 80
52962525 TTGGTTTACA
* * * * * *
52962535 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATAACCAA
1 AAATTACCAAAATACCCCTAACTTTG-AAAATTACCGAAATACCCTTAATTTGTAAAATTA-CGA
52962599 AATACCCCTGATTTGTG
64 AATACCCCTGATTTGTG
* * * * *
52962616 AAATTACCAAAATACCCTCGACCTGT-AAAATTACCGAAATA-CCTTCGACTTGTAAAATTATCG
1 AAATTACCAAAATACCC-CTAACTTTGAAAATTACCGAAATACCCTT-AATTTGTAAAATTA-CG
52962679 AAATACCCGC-GATTTGT-
63 AAATACCC-CTGATTTGTG
* * *
52962696 AAAGTTACCAAAATACCCCTAATTTTGAAAAGTACCGAAATACCCTTAATTTGGAAAATTACAGA
1 AAA-TTACCAAAATACCCCTAACTTTGAAAATTACCGAAATACCCTTAATTTGTAAAATTAC-GA
52962761 AATACCC
64 AATACCC
52962768 TTGACTTTCA
Statistics
Matches: 124, Mismatches: 20, Indels: 16
0.77 0.12 0.10
Matches are distributed among these distances:
80 11 0.09
81 105 0.85
82 6 0.05
83 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (80 bp):
AAATTACCAAAATACCCCTAACTTTGAAAATTACCGAAATACCCTTAATTTGTAAAATTACGAAA
TACCCCTGATTTGTG
Found at i:52962769 original size:27 final size:27
Alignment explanation
Indices: 52962534--52962767 Score: 208
Period size: 27 Copynumber: 8.7 Consensus size: 27
52962524 TTTGGTTTAC
*
52962534 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAATTTGT
*
52962561 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAATTTGT
* *
52962588 AAAATAACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCCTAATTTGT
* * **
52962615 GAAATTACCAAAATA-CCCTCGACCTGT
1 AAAATTACCAAAATACCCCT-AATTTGT
* * * *
52962642 AAAATTACCGAAATA-CCTTCGACTTGT
1 AAAATTACCAAAATACCCCT-AATTTGT
* * *
52962669 AAAATTATCGAAATACCCGC-GATTTGT
1 AAAATTACCAAAATACCC-CTAATTTGT
*
52962696 AAAGTTACCAAAATACCCCTAATTT-T
1 AAAATTACCAAAATACCCCTAATTTGT
* * * *
52962722 GAAAAGTACCGAAATACCCTTAATTTGG
1 -AAAATTACCAAAATACCCCTAATTTGT
52962750 AAAATTA-CAGAAATACCC
1 AAAATTACCA-AAATACCC
52962768 TTGACTTTCA
Statistics
Matches: 175, Mismatches: 25, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
26 7 0.04
27 166 0.95
28 2 0.01
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAATTTGT
Found at i:52962839 original size:27 final size:27
Alignment explanation
Indices: 52962789--52962844 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
52962779 AAATTATATT
* *
52962789 AATACCATTGGTTTGCATAATTACTAA
1 AATACCATTGGTTTGCAGAATTACCAA
* * *
52962816 AATACCTTTGGTTTGTAGATTTACCAA
1 AATACCATTGGTTTGCAGAATTACCAA
52962843 AA
1 AA
52962845 CATCCTTGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (27 bp):
AATACCATTGGTTTGCAGAATTACCAA
Found at i:52962925 original size:27 final size:26
Alignment explanation
Indices: 52962895--52962968 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
52962885 TAAAAAAACT
52962895 GTAATGCCCCTGTAGGGTGAAATGACC
1 GTAATGCCCCTGTAGGGT-AAATGACC
* *
52962922 GTAAAGCCCCTGTAGAGTAAATTGACC
1 GTAATGCCCCTGTAGGGTAAA-TGACC
* *
52962949 -TAATACCCCTGTATGGTAAA
1 GTAATGCCCCTGTAGGGTAAA
52962969 ATGATGATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 19 0.47
27 21 0.52
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (26 bp):
GTAATGCCCCTGTAGGGTAAATGACC
Found at i:52963191 original size:27 final size:27
Alignment explanation
Indices: 52963114--52963192 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
52963104 GGAAGTTCTG
* * *
52963114 TACTGGTGACTATGCCACATTCACTGT
1 TACTGGTGGCTATGCCACATTTACTGA
* *
52963141 TAGTGGTGGCTATGCCACAATTACTGA
1 TACTGGTGGCTATGCCACATTTACTGA
*
52963168 TACTGGTGGCTTTGCCACATTTACT
1 TACTGGTGGCTATGCCACATTTACT
52963193 ATTTCTGGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (27 bp):
TACTGGTGGCTATGCCACATTTACTGA
Found at i:52964520 original size:31 final size:31
Alignment explanation
Indices: 52964485--52964546 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
52964475 CTAGGAAATA
*
52964485 TGGAATGTTGAAAATGATTTAGGCAACTATT
1 TGGAATGTTGAAAATGAATTAGGCAACTATT
52964516 TGGAATGTTGAAAATGAATTAGGCAACTATT
1 TGGAATGTTGAAAATGAATTAGGCAACTATT
52964547 GTTTGGATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (31 bp):
TGGAATGTTGAAAATGAATTAGGCAACTATT
Found at i:52965519 original size:10 final size:10
Alignment explanation
Indices: 52965482--52965518 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
52965472 GAACATGTTG
52965482 AATTTTAATT
1 AATTTTAATT
52965492 AATTTATAATT
1 AATTT-TAATT
*
52965503 AATTTTGATT
1 AATTTTAATT
52965513 AATTTT
1 AATTTT
52965519 GGTTATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (10 bp):
AATTTTAATT
Found at i:52971252 original size:29 final size:27
Alignment explanation
Indices: 52971234--52971303 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
52971224 ATATTAAGTC
52971234 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
52971261 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
52971289 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
52971304 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:52971297 original size:28 final size:28
Alignment explanation
Indices: 52971234--52971330 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
52971224 ATATTAAGTC
*
52971234 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
52971261 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
52971289 CGCACACTTAGTGCTGTACAATTTAAAC-
1 CGCACACTTAGTGCTATATAA-TCAAACT
52971317 CGCACACTTAGTGC
1 CGCACACTTAGTGC
52971331 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
27 22 0.34
28 37 0.58
29 5 0.08
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:52979330 original size:27 final size:26
Alignment explanation
Indices: 52979316--52979382 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
52979306 TTAAGTCCGT
52979316 ACACTCAGTGCTATATAATCAACTCGC
1 ACACTCAGTGCTATAT-ATCAACTCGC
*
52979343 ACACTTAGTGCTATATAATCAAACTCGC
1 ACACTCAGTGCTATAT-ATC-AACTCGC
*
52979371 ACACTTAGTGCT
1 ACACTCAGTGCT
52979383 GTACAATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 19 0.50
28 19 0.50
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (26 bp):
ACACTCAGTGCTATATATCAACTCGC
Found at i:52979376 original size:28 final size:28
Alignment explanation
Indices: 52979316--52979410 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
52979306 TTAAGTCCGT
*
52979316 ACACTCAGTGCTATATAATC-AACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
52979343 ACACTTAGTGCTATATAATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
* * * *
52979371 ACACTTAGTGCTGTACAATTTAAACCCGC
1 ACACTTAGTGCTATATAA-TCAAACTCGC
52979400 ACACTTAGTGC
1 ACACTTAGTGC
52979411 CAATCTCATG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 19 0.31
28 23 0.38
29 19 0.31
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (28 bp):
ACACTTAGTGCTATATAATCAAACTCGC
Found at i:52984627 original size:20 final size:20
Alignment explanation
Indices: 52984602--52984644 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
52984592 ATTTTGATAA
52984602 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
52984622 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
52984642 ACA
1 ACA
52984645 CGAGATGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:52984652 original size:20 final size:20
Alignment explanation
Indices: 52984609--52984652 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
52984599 TAAACATGAT
* *
52984609 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACACGAG
52984629 ATGTATGATATGCACACGAG
1 ATGTATGATATGCACACGAG
52984649 ATGT
1 ATGT
52984653 TCATAAATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACACGAG
Found at i:52984723 original size:24 final size:24
Alignment explanation
Indices: 52984696--52984839 Score: 188
Period size: 24 Copynumber: 6.0 Consensus size: 24
52984686 GGAGAAAGTG
52984696 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
52984720 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
52984744 CAAAAGGGCTTATGCCCTAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
52984768 -TAAAGGGCTTATGCCCCAGTTATT
1 CAAAAGGGCTTATGCCCCAGTTA-T
*
52984792 AAAAAGGGCTT-TGCCCCAGTTA-
1 CAAAAGGGCTTATGCCCCAGTTAT
*
52984814 CTAAAAGAGGC-TAGGCCTCCAGTTAT
1 C-AAAAG-GGCTTATGCC-CCAGTTAT
52984840 ATGATAAAGC
Statistics
Matches: 107, Mismatches: 6, Indels: 12
0.86 0.05 0.10
Matches are distributed among these distances:
23 26 0.24
24 65 0.61
25 16 0.15
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:52990989 original size:40 final size:40
Alignment explanation
Indices: 52990944--52991254 Score: 412
Period size: 40 Copynumber: 7.8 Consensus size: 40
52990934 GGATATAGCT
* * *
52990944 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
52990984 ACTCGCACAATTGCCTTCGAGG-CTTAGCTCGGATTTAGTA
1 ACTCGCACAAATGCCTTCG-GGACTTAGCCCGGATTTAGTA
*
52991024 ACTCGCACAAATGCCTTCGGGACTTAGCCTGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
52991064 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
52991104 ACTCACAGAATTGCCTTCGGGACTTAGCACGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
52991144 ACTCGCACAAATGCCTTCGGGACTTAGCCCGAATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
52991184 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* ** *
52991223 ACTAGTGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
52991255 TTTTTATCCA
Statistics
Matches: 241, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
39 33 0.14
40 204 0.85
41 4 0.02
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:52998363 original size:40 final size:40
Alignment explanation
Indices: 52998318--52998508 Score: 267
Period size: 40 Copynumber: 4.8 Consensus size: 40
52998308 GGATATAGCT
* * * *
52998318 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
52998358 ACTCGCACAATTGCCTTCGGGACTTAGCTCGGATTTAGTA
1 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
52998398 ACTCGCACAAATGCCTTCGGGACTTAGCCCGAATTTAGTA
1 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
*
52998438 ACTCGCACAATTGCCTTCAGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
52998478 ACTCATACAATTGCGTTCGGGACTTAGCCCG
1 ACTCGCACAATTGCCTTCGGGACTTAGCCCG
52998509 TTTTTCATCC
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 133 0.99
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:53002595 original size:9 final size:9
Alignment explanation
Indices: 53002583--53002639 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
53002573 TTTGATAAAC
53002583 ATGATATGT
1 ATGATATGT
*
53002592 ATGATATGCAC
1 ATGATATG--T
*
53002603 ATGACATGT
1 ATGATATGT
*
53002612 ATGATATGCAC
1 ATGATATG--T
53002623 ATGATATGT
1 ATGATATGT
53002632 ATGATATG
1 ATGATATG
53002640 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:53002606 original size:20 final size:20
Alignment explanation
Indices: 53002581--53002643 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
53002571 ATTTTGATAA
53002581 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
53002601 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
53002621 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
53002641 ACA
1 ACA
53002644 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53002801 original size:24 final size:24
Alignment explanation
Indices: 53002695--53002789 Score: 147
Period size: 24 Copynumber: 4.0 Consensus size: 24
53002685 GGAGGAAGTG
*
53002695 CAAAAGGGCTTATGCCTCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
53002719 CAAAAGGGTTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
53002743 CAAAAGGGCTTATGCCCCAGTTATT
1 CAAAAGGGCTTATGCCCCAGTTA-T
*
53002768 AAAAAGGGCTT-TGCCCCAGTTA
1 CAAAAGGGCTTATGCCCCAGTTA
53002790 CTAAAAGAGG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
24 55 0.83
25 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:53005442 original size:15 final size:15
Alignment explanation
Indices: 53005422--53005451 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53005412 ATTATGAAAC
53005422 ATATGTTTTGGATTA
1 ATATGTTTTGGATTA
*
53005437 ATATGTTTTGTATTA
1 ATATGTTTTGGATTA
53005452 GAATTTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (15 bp):
ATATGTTTTGGATTA
Found at i:53008916 original size:30 final size:30
Alignment explanation
Indices: 53008882--53008942 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53008872 TCCTTAACTC
53008882 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
53008912 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
53008942 A
1 A
53008943 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:53013361 original size:30 final size:30
Alignment explanation
Indices: 53013325--53013385 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53013315 TCCTTAACTC
53013325 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
53013355 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
53013385 A
1 A
53013386 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:53015369 original size:43 final size:42
Alignment explanation
Indices: 53015243--53015382 Score: 149
Period size: 43 Copynumber: 3.3 Consensus size: 42
53015233 TCTCAAATAG
*
53015243 GGTCTTACACAAAAATCTCAATCGAGGCCTGTGTCCCAAACAC
1 GGTCTTACAC-GAAATCTCAATCGAGGCCTGTGTCCCAAACAC
* ** *
53015286 GGTCTTACACGAAA--TCAGATACGATGCCCATGTCCCAAACAT
1 GGTCTTACACGAAATCTCA-AT-CGAGGCCTGTGTCCCAAACAC
* * *
53015328 GGTCTTATATGTAAATCTCAATCGAGGCCTGTGTCCTAAACAC
1 GGTCTTACACG-AAATCTCAATCGAGGCCTGTGTCCCAAACAC
*
53015371 AGTCTTACACGA
1 GGTCTTACACGA
53015383 TGTCTCAGAC
Statistics
Matches: 77, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
40 3 0.04
41 2 0.03
42 30 0.39
43 37 0.48
44 2 0.03
45 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (42 bp):
GGTCTTACACGAAATCTCAATCGAGGCCTGTGTCCCAAACAC
Found at i:53019416 original size:39 final size:39
Alignment explanation
Indices: 53019372--53019467 Score: 149
Period size: 39 Copynumber: 2.5 Consensus size: 39
53019362 CGGGACTTTA
*
53019372 AGCCCGAATATAATACCAGCACAAATGCCTTCGGGGCTT
1 AGCCCGAATATAACACCAGCACAAATGCCTTCGGGGCTT
* *
53019411 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
1 AGCCCGAATATAACACCAGCACAAATGCCTTCGGGGCTT
53019450 AGCCC-AGATATAACACCA
1 AGCCCGA-ATATAACACCA
53019468 AATCATATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (39 bp):
AGCCCGAATATAACACCAGCACAAATGCCTTCGGGGCTT
Found at i:53019845 original size:19 final size:19
Alignment explanation
Indices: 53019821--53019861 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
53019811 GTTATAATAT
*
53019821 TAATATTCTTTTAATATTA
1 TAATATTCATTTAATATTA
*
53019840 TAATATTCATTTCATATTA
1 TAATATTCATTTAATATTA
53019859 TAA
1 TAA
53019862 AACAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATATTCATTTAATATTA
Found at i:53020659 original size:15 final size:15
Alignment explanation
Indices: 53020611--53020693 Score: 91
Period size: 15 Copynumber: 5.7 Consensus size: 15
53020601 TAAAGATAAC
*
53020611 AAGAAAACC-GAATA
1 AAGAAACCCAGAATA
* *
53020625 AAGAAATCTA-AGATA
1 AAGAAACCCAGA-ATA
*
53020640 GAGAAACCCAGAATA
1 AAGAAACCCAGAATA
53020655 AAGAAACCCAGAATA
1 AAGAAACCCAGAATA
*
53020670 AAGAAATCCAGAATA
1 AAGAAACCCAGAATA
53020685 AAG-AACCCA
1 AAGAAACCCA
53020694 TGATACAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
14 13 0.22
15 44 0.76
16 1 0.02
ACGTcount: A:0.59, C:0.17, G:0.14, T:0.10
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:53021780 original size:14 final size:14
Alignment explanation
Indices: 53021761--53021798 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
53021751 TATATATATA
53021761 TCATAATTTTTTAT
1 TCATAATTTTTTAT
53021775 TCATAATTTTTTAT
1 TCATAATTTTTTAT
*
53021789 TCATACTTTT
1 TCATAATTTT
53021799 CTGAATCGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (14 bp):
TCATAATTTTTTAT
Found at i:53025274 original size:42 final size:43
Alignment explanation
Indices: 53025167--53025284 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 43
53025157 GTACCAATGT
* * * *
53025167 CATATCCCAGATATGGTCTTACA-TATAATCTCGTATTGATGC
1 CATATGCCAGATATGGTCTTACACGATAATCTCATATCGATGC
* * *
53025209 CA-ATAGCCCAGCTATGGTCTTACACGA-AGTCTCATATCGATTC
1 CATAT-G-CCAGATATGGTCTTACACGATAATCTCATATCGATGC
*
53025252 CATATGCCAGATATGGTCTTACACG-TAAACTCA
1 CATATGCCAGATATGGTCTTACACGATAATCTCA
53025285 ACAACCCTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
41 2 0.03
42 25 0.41
43 31 0.51
44 3 0.05
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (43 bp):
CATATGCCAGATATGGTCTTACACGATAATCTCATATCGATGC
Found at i:53027570 original size:50 final size:51
Alignment explanation
Indices: 53027446--53027634 Score: 191
Period size: 50 Copynumber: 3.7 Consensus size: 51
53027436 AACCATGTCT
* * * * *
53027446 TACACATAGTGGCCTGCACTTAGTACCACACATGTGATCGAAGCTATCGGG
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGG
* * *
53027497 TACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAA-CCATCTGG
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGG
* * * * ****
53027547 TACACATAATAGCTTGCACTTAGTACTACACACGTGACCTAAAACCATTTTA
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCT-AAGCCATCGGG
* * *
53027599 AACACATAGTATCCTGCACATAGTACTACACATGTG
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTG
53027635 TTCTCACAAT
Statistics
Matches: 114, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
50 41 0.36
51 38 0.33
52 35 0.31
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (51 bp):
TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGG
Found at i:53035370 original size:27 final size:27
Alignment explanation
Indices: 53035340--53035632 Score: 116
Period size: 27 Copynumber: 10.9 Consensus size: 27
53035330 TGTAGGATAG
*
53035340 AATTACTGAAATACCCTTAGTTTACAA
1 AATTACTGAAATACCCTTAGTTTATAA
** * * *
53035367 AATTACCAAAATACTCCTGA-TTTGTGA
1 AATTACTGAAATAC-CCTTAGTTTATAA
* * * *
53035394 AATTACCGAAATACCC-TCGACTTGTAA
1 AATTACTGAAATACCCTTAG-TTTATAA
**
53035421 AATTACTGAAATACCCTT-GACCTATAA
1 AATTACTGAAATACCCTTAG-TTTATAA
** * * ***
53035448 AATTACCAAAATACTCTCAACCTATAA
1 AATTACTGAAATACCCTTAGTTTATAA
*
53035475 AATTA-TCGAAATACCCTT-GATTTGTAA
1 AATTACT-GAAATACCCTTAG-TTTATAA
** * * **
53035502 AATTACCAAAATACCCCTAATTTGGAA
1 AATTACTGAAATACCCTTAGTTTATAA
** * **
53035529 AATTACCAAAATACCCTTAATTTGGAA
1 AATTACTGAAATACCCTTAGTTTATAA
* *
53035556 AATTA-TAGAAATACCCTTGACTTTAAAA
1 AATTACT-GAAATACCCTT-AGTTTATAA
* * * *
53035584 AATTA-TAAAATACCATTGGTTTACAA
1 AATTACTGAAATACCCTTAGTTTATAA
*
53035610 AATTA-TCGAAATACCCTTGGTTT
1 AATTACT-GAAATACCCTTAGTTT
53035633 GTAGATTTAC
Statistics
Matches: 209, Mismatches: 45, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
26 14 0.07
27 178 0.85
28 17 0.08
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACTGAAATACCCTTAGTTTATAA
Found at i:53035423 original size:54 final size:54
Alignment explanation
Indices: 53035365--53035560 Score: 207
Period size: 54 Copynumber: 3.6 Consensus size: 54
53035355 CTTAGTTTAC
* * *
53035365 AAAATTACCAAAATACTCC-TGATTTGTGAAATTACCGAAATACCCTCGACTTGT
1 AAAATTACCAAAATAC-CCTTGATTTGTAAAATTACCAAAATACCCTCAACTTGT
** ** * * * *
53035419 AAAATTACTGAAATACCCTTGACCTATAAAATTACCAAAATACTCTCAACCTAT
1 AAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAAATACCCTCAACTTGT
* * * *
53035473 AAAATTATCGAAATACCCTTGATTTGTAAAATTACCAAAATACCC-CTAATTTGG
1 AAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAAATACCCTC-AACTTGT
* *
53035527 AAAATTACCAAAATACCCTTAATTTGGAAAATTA
1 AAAATTACCAAAATACCCTTGATTTGTAAAATTA
53035561 TAGAAATACC
Statistics
Matches: 115, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
53 3 0.03
54 112 0.97
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (54 bp):
AAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAAATACCCTCAACTTGT
Found at i:53035450 original size:81 final size:80
Alignment explanation
Indices: 53035340--53035623 Score: 254
Period size: 81 Copynumber: 3.5 Consensus size: 80
53035330 TGTAGGATAG
* *
53035340 AATTACTGAAATACCCTTAGTTTACAAAATTACCAAAATACTCCTGATTTGTGAAATTACCGAAA
1 AATTACTGAAATACCCTTA-TTTACAAAATTACCAAAATACTCCTAATTTGTGAAATTATCGAAA
*
53035405 TACCCTCGACTTGTAA
65 TACCCTTGACTTGTAA
** * ** * *
53035421 AATTACTGAAATACCCTTGACCTATAAAATTACCAAAATACT-CTCAACCTATAAAATTATCGAA
1 AATTACTGAAATACCCTT-ATTTACAAAATTACCAAAATACTCCT-AATTTGTGAAATTATCGAA
*
53035485 ATACCCTTGATTTGTAA
64 ATACCCTTGACTTGTAA
** * ** *
53035502 AATTACCAAAATACCCCTAATTTGGAAAATTACCAAAATAC-CCTTAATTTG-GAAAATTATAGA
1 AATTACTGAAATA-CCCTTATTTACAAAATTACCAAAATACTCC-TAATTTGTG-AAATTATCGA
53035565 AATACCCTTGACTT-TAAAA
63 AATACCCTTGACTTGT--AA
* * * * *
53035584 AATTA-TAAAATACCATTGGTTTACAAAATTATCGAAATAC
1 AATTACTGAAATACCCTT-ATTTACAAAATTACCAAAATAC
53035624 CCTTGGTTTG
Statistics
Matches: 162, Mismatches: 32, Indels: 18
0.76 0.15 0.08
Matches are distributed among these distances:
80 6 0.04
81 143 0.88
82 13 0.08
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.31
Consensus pattern (80 bp):
AATTACTGAAATACCCTTATTTACAAAATTACCAAAATACTCCTAATTTGTGAAATTATCGAAAT
ACCCTTGACTTGTAA
Found at i:53035594 original size:54 final size:54
Alignment explanation
Indices: 53035473--53035628 Score: 145
Period size: 54 Copynumber: 2.9 Consensus size: 54
53035463 CTCAACCTAT
* * * * **
53035473 AAAATTATCGAAATACCCTTGATTTGTAAAATTACCA-AAATACCCCT-AATTTGG
1 AAAATTAT-AAAATACCCTTGATTTGCAAAATTA-TAGAAATACCCTTGAATTTAA
* * * *
53035527 AAAATTACCAAAATACCCTTAATTTGGAAAATTATAGAAATACCCTTGACTTTAA
1 AAAATTA-TAAAATACCCTTGATTTGCAAAATTATAGAAATACCCTTGAATTTAA
* * * *
53035582 AAAATTATAAAATACCATTGGTTTACAAAATTATCGAAATACCCTTG
1 AAAATTATAAAATACCCTTGATTTGCAAAATTATAGAAATACCCTTG
53035629 GTTTGTAGAT
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
53 1 0.01
54 71 0.86
55 11 0.13
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (54 bp):
AAAATTATAAAATACCCTTGATTTGCAAAATTATAGAAATACCCTTGAATTTAA
Found at i:53036159 original size:22 final size:22
Alignment explanation
Indices: 53036107--53036162 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
53036097 GCCAATTGTT
* *
53036107 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTCTGCACCAAC
* *
53036129 CT-ACATATGGCTCTGTACCAAC
1 CTGA-TTATGGCTCTGCACCAAC
53036151 CTGATTATGGCT
1 CTGATTATGGCT
53036163 GTGTGCGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (22 bp):
CTGATTATGGCTCTGCACCAAC
Found at i:53047752 original size:26 final size:26
Alignment explanation
Indices: 53047723--53047775 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
53047713 AATCACAAAG
53047723 ATCAATTCAAGCAGATCAATATATTC
1 ATCAATTCAAGCAGATCAATATATTC
53047749 ATCAATTCAAGCAGATCAATATATTC
1 ATCAATTCAAGCAGATCAATATATTC
53047775 A
1 A
53047776 CTAAGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (26 bp):
ATCAATTCAAGCAGATCAATATATTC
Found at i:53057218 original size:47 final size:48
Alignment explanation
Indices: 53057102--53057225 Score: 162
Period size: 47 Copynumber: 2.6 Consensus size: 48
53057092 GTTAGAGATT
* * * * *
53057102 GTGTAAGACCATGTTTGGGACATGGCGTCGGCCTTTATTTTGATAGTCA
1 GTGTAAGACCATGTTTGGGACATGGCATCGGACTTGA-TTAGATAGCCA
*
53057151 GTGTAAGACCATGTTTGGGACATAGCATC-GACTTGA-TAGATGAGCCA
1 GTGTAAGACCATGTTTGGGACATGGCATCGGACTTGATTAGAT-AGCCA
53057198 GTGTAAGACCATGTTTGGGACATGGCAT
1 GTGTAAGACCATGTTTGGGACATGGCAT
53057226 TGGAGTTATA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
46 4 0.06
47 31 0.46
48 5 0.07
49 27 0.40
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (48 bp):
GTGTAAGACCATGTTTGGGACATGGCATCGGACTTGATTAGATAGCCA
Found at i:53067022 original size:74 final size:77
Alignment explanation
Indices: 53066886--53067036 Score: 281
Period size: 74 Copynumber: 2.0 Consensus size: 77
53066876 GTTACCGGAC
53066886 AAACATACAAACATTAAACTAAAATACGGGCCATAAAATTTCATTCATATTTCAAAACGTTCATT
1 AAACATACAAACATTAAACTAAAATACGGGCCATAAAATTTCATTCATATTTCAAAACGTTCATT
53066951 CACTTACACATA
66 CACTTACACATA
53066963 AAACATAC-AACATT-AACTAAAATACGGGCCATAAAA-TTCATTCATATTTCAAAACGTTCATT
1 AAACATACAAACATTAAACTAAAATACGGGCCATAAAATTTCATTCATATTTCAAAACGTTCATT
53067025 CACTTACACATA
66 CACTTACACATA
53067037 GTCCTTATTT
Statistics
Matches: 74, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
74 38 0.51
75 22 0.30
76 6 0.08
77 8 0.11
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.28
Consensus pattern (77 bp):
AAACATACAAACATTAAACTAAAATACGGGCCATAAAATTTCATTCATATTTCAAAACGTTCATT
CACTTACACATA
Found at i:53067518 original size:26 final size:27
Alignment explanation
Indices: 53067493--53067543 Score: 79
Period size: 25 Copynumber: 1.9 Consensus size: 27
53067483 ATGCAAAATA
53067493 ACATTGAGACT-TCA-ATATATATAAT
1 ACATTGAGACTATCATATATATATAAT
53067518 ACATTGAGACTAGTCATATATATATA
1 ACATTGAGACTA-TCATATATATATA
53067544 CATGTCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.48
27 3 0.13
28 9 0.39
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (27 bp):
ACATTGAGACTATCATATATATATAAT
Found at i:53074495 original size:47 final size:44
Alignment explanation
Indices: 53074432--53074545 Score: 140
Period size: 47 Copynumber: 2.5 Consensus size: 44
53074422 TGTGTGCTAA
* *
53074432 TGTAAGACATGTCTGGGACATGCATCGGCCT-AGAGATGTAAGCCAG
1 TGTAAAACATGTCTGGGACATGCATC-GACTGAGAGATGT--GCCAG
*
53074478 TGTAAAACATTGTCTGGGACATGCATCGACTGCGAGATGTGCCAG
1 TGTAAAACA-TGTCTGGGACATGCATCGACTGAGAGATGTGCCAG
*
53074523 TGTAAGACCATGTCTGGGACATG
1 TGTAA-AACATGTCTGGGACATG
53074546 GCATGGGCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
45 23 0.38
46 14 0.23
47 24 0.39
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (44 bp):
TGTAAAACATGTCTGGGACATGCATCGACTGAGAGATGTGCCAG
Found at i:53074537 original size:45 final size:45
Alignment explanation
Indices: 53074432--53074545 Score: 151
Period size: 45 Copynumber: 2.5 Consensus size: 45
53074422 TGTGTGCTAA
*
53074432 TGTAAGACATGTCTGGGACATGCATCGGCCTAGAGATGTAAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCGGACTAGAGATGT-AGCCAG
* *
53074478 TGTAAAACATTGTCTGGGACATGCATC-GACTGCGAGATGT-GCCAG
1 TGTAAGACA-TGTCTGGGACATGCATCGGACT-AGAGATGTAGCCAG
53074523 TGTAAGACCATGTCTGGGACATG
1 TGTAAGA-CATGTCTGGGACATG
53074546 GCATGGGCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
45 24 0.39
46 13 0.21
47 24 0.39
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (45 bp):
TGTAAGACATGTCTGGGACATGCATCGGACTAGAGATGTAGCCAG
Found at i:53078303 original size:40 final size:40
Alignment explanation
Indices: 53078219--53078443 Score: 271
Period size: 40 Copynumber: 5.7 Consensus size: 40
53078209 TTGAATGATG
* * *
53078219 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
* *
53078259 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
53078299 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGATACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
53078338 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
53078378 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTA-AA
* *
53078419 -CCAGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53078444 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
39 35 0.21
40 117 0.71
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:53078461 original size:80 final size:80
Alignment explanation
Indices: 53078272--53078476 Score: 213
Period size: 80 Copynumber: 2.6 Consensus size: 80
53078262 GGACTAAGAT
** * *
53078272 CCGAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGATACT
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGATACT
* *
53078335 AAATCCGGGTTAAGTC
65 AAATCCAGGCTAAGTC
** * * *
53078351 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGATACTA
*
53078416 TAA-CCAGGCTATGTC
66 -AATCCAGGCTAAGTC
* * *
53078431 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
53078477 TACGTGATTT
Statistics
Matches: 109, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
78 1 0.01
79 49 0.45
80 57 0.52
81 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGATACTA
AATCCAGGCTAAGTC
Found at i:53078466 original size:119 final size:119
Alignment explanation
Indices: 53078219--53078449 Score: 279
Period size: 119 Copynumber: 1.9 Consensus size: 119
53078209 TTGAATGATG
* *
53078219 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* * **
53078284 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGATACTAAA
66 GTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTGGAACGAGATACTAAA
* * * **
53078338 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * *
53078401 TTGTGCGAGTTACT-ATAACCAGGCTATGTCCCGAAGGCATTTGAACGAG
64 TTGTGCGAGATACTAAT-ACCAGGCTAAG-CCCGAAGGCATTGGAACGAG
53078450 GAGCTATATC
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
118 3 0.03
119 67 0.71
120 24 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTGGAACGAGATACTAAA
Found at i:53086206 original size:40 final size:40
Alignment explanation
Indices: 53086122--53086346 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
53086112 TTGAATGATG
* * *
53086122 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
* *
53086162 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
53086202 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGATACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
53086241 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
53086281 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTA-AA
*
53086322 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53086347 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
39 35 0.21
40 118 0.71
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:53086369 original size:119 final size:119
Alignment explanation
Indices: 53086122--53086352 Score: 288
Period size: 119 Copynumber: 1.9 Consensus size: 119
53086112 TTGAATGATG
* *
53086122 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
53086187 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGATACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGATACTAAA
* * * **
53086241 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * *
53086304 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAG
53086353 GAGCTATATC
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
118 3 0.03
119 68 0.72
120 24 0.25
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGATACTAAA
Found at i:53094288 original size:34 final size:34
Alignment explanation
Indices: 53094240--53094311 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
53094230 CCCATACTCG
*
53094240 TAACCCACGGCAGAGCGAAATACGAGGCATTACC
1 TAACCCACGCCAGAGCGAAATACGAGGCATTACC
53094274 TAACCCACGCCAGAGCGAAATACGAGGCATTACC
1 TAACCCACGCCAGAGCGAAATACGAGGCATTACC
53094308 TAAC
1 TAAC
53094312 TCGATCTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.36, C:0.31, G:0.21, T:0.12
Consensus pattern (34 bp):
TAACCCACGCCAGAGCGAAATACGAGGCATTACC
Found at i:53096888 original size:29 final size:29
Alignment explanation
Indices: 53096822--53096938 Score: 110
Period size: 29 Copynumber: 4.0 Consensus size: 29
53096812 TGAATATAAG
* * * * * *
53096822 GTGATTTGGGCCTAACGGGCCATATAAAG
1 GTGAATTGGGCCTGATGGGCCATTTGAAT
* * * *
53096851 GTGATTTGGGCCTAATAGGTCATTTGAA-
1 GTGAATTGGGCCTGATGGGCCATTTGAAT
**
53096879 GATGAATTGGGCCTGATGGGCCACATGAAT
1 G-TGAATTGGGCCTGATGGGCCATTTGAAT
53096909 GTGAATTGGGCCTGATGGGCCATTTGAAT
1 GTGAATTGGGCCTGATGGGCCATTTGAAT
53096938 G
1 G
53096939 AAATGGGCCA
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
28 1 0.01
29 71 0.97
30 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (29 bp):
GTGAATTGGGCCTGATGGGCCATTTGAAT
Found at i:53096900 original size:58 final size:56
Alignment explanation
Indices: 53096827--53096960 Score: 144
Period size: 58 Copynumber: 2.4 Consensus size: 56
53096817 ATAAGGTGAT
* * *
53096827 TTGGGCCTAACGGGCCATATAAAGGTGATTTGGGCCTAATAGGTCATTTGAAGATGAA
1 TTGGGCCTAATGGGCCATATAAAGGTGAATTGGGCCTAATAGGCCATTTG-A-ATGAA
* * * * * *
53096885 TTGGGCCTGATGGGCCACATGAATGTGAATTGGGCCTGATGGGCCATTTGAATGAA
1 TTGGGCCTAATGGGCCATATAAAGGTGAATTGGGCCTAATAGGCCATTTGAATGAA
*
53096941 ATGGGCC-AAGTGGGCCATAT
1 TTGGGCCTAA-TGGGCCATAT
53096961 GCATGTATGT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
55 1 0.02
56 20 0.32
57 1 0.02
58 41 0.65
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (56 bp):
TTGGGCCTAATGGGCCATATAAAGGTGAATTGGGCCTAATAGGCCATTTGAATGAA
Found at i:53098421 original size:46 final size:46
Alignment explanation
Indices: 53098227--53098497 Score: 155
Period size: 46 Copynumber: 5.8 Consensus size: 46
53098217 TGGGGTAAAG
* * *
53098227 TGCCGATGCCATATCCCAGACATGGTCTTACAC-ATGCTCTAGCATATCTG-
1 TGCCGATG-CATGTCCCAGACAT-GTCTTACACTA-GCACT--CGTATC-GA
* * * *
53098277 TGCCGATGCTGTGTCCCAGACATAGTCTTACACT-G-ACACATCTCG-
1 TGCCGATGC-ATGTCCCAGACAT-GTCTTACACTAGCACTCGTATCGA
* * * *
53098322 TAGCCGATACATGTCCCAGACATGTCTTACACT-G-ATTTATGTCTCGA
1 T-GCCGATGCATGTCCCAGACATGTCTTACACTAGCA-CT-CGTATCGA
* *
53098369 GGCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTTTCGA
1 TGCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTATCGA
* ** * * * *
53098415 TCCCGATGCCATGTTTCAAACATGGTCTTACACTGGCTCTCATAAT-G-
1 TGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCGT-ATCGA
*
53098462 TGGCTGATGCATGTCCCAGACATGTCTTACACTAGC
1 T-GCCGATGCATGTCCCAGACATGTCTTACACTAGC
53098498 TCAAAATAAC
Statistics
Matches: 177, Mismatches: 32, Indels: 28
0.75 0.14 0.12
Matches are distributed among these distances:
44 12 0.07
45 14 0.08
46 71 0.40
47 25 0.14
48 24 0.14
49 3 0.02
50 28 0.16
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
TGCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTATCGA
Found at i:53102758 original size:43 final size:43
Alignment explanation
Indices: 53102694--53102817 Score: 139
Period size: 43 Copynumber: 3.0 Consensus size: 43
53102684 TACCATACCA
* * **
53102694 ATGCC-ATATCCTAGATATGGTCTTACATGGGATCTCAAATTG
1 ATGCCAATAGCCTAGATATGGTCTTACACGAAATCTCAAATTG
* * *
53102736 ATGCCAATAGCCTAGCTGTGGTCTTACACGAAATCTCATATTG
1 ATGCCAATAGCCTAGATATGGTCTTACACGAAATCTCAAATTG
*
53102779 ATGCC-ATATCC-AGATATGGTCTTACACGTAAA-CTCAAAT
1 ATGCCAATAGCCTAGATATGGTCTTACACG-AAATCTCAAAT
53102818 AACCCTAATG
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 21 0.30
42 13 0.19
43 35 0.51
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (43 bp):
ATGCCAATAGCCTAGATATGGTCTTACACGAAATCTCAAATTG
Found at i:53110810 original size:52 final size:52
Alignment explanation
Indices: 53110685--53110846 Score: 224
Period size: 52 Copynumber: 3.2 Consensus size: 52
53110675 GGGAAATTAC
*
53110685 TCACTTAGCACCA-TGCCATGGACTTATTTCACTTAGAT-TCCATGGAC--ATT
1 TCACTTAGCA-CATTGCCATGGACTTATTTCACTTAGATGT-CATGGTCTTATT
*
53110735 TCACTTAGCACATTGCCGTGGACTTATTTCACTTAGATGTCATGGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGTCATGGTCTTATT
* * * *
53110787 TCACTTAGCGCATTGCCATGGACTTATTTCACTGAGATGCCATTGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGTCATGGTCTTATT
53110839 TCACTTAG
1 TCACTTAG
53110847 ATGCCATGCT
Statistics
Matches: 101, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
49 2 0.02
50 40 0.40
51 1 0.01
52 58 0.57
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (52 bp):
TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGTCATGGTCTTATT
Found at i:53110868 original size:24 final size:24
Alignment explanation
Indices: 53110697--53110870 Score: 163
Period size: 24 Copynumber: 7.0 Consensus size: 24
53110687 ACTTAGCACC
*
53110697 ATGCCATGGACTTATTTCACTTAG
1 ATGCCATGGTCTTATTTCACTTAG
* *
53110721 ATTCCATGGAC--ATTTCACTTAG
1 ATGCCATGGTCTTATTTCACTTAG
* *
53110743 CACATTGCCGTGGACTTATTTCACTTAG
1 ---A-TGCCATGGTCTTATTTCACTTAG
*
53110771 ATGTCATGGTCTTATTTCACTTAGCG
1 ATGCCATGGTCTTATTTCACTTA--G
* *
53110797 CATTGCCATGGACTTATTTCACTGAG
1 -A-TGCCATGGTCTTATTTCACTTAG
*
53110823 ATGCCATTGTCTTATTTCACTTAG
1 ATGCCATGGTCTTATTTCACTTAG
* *
53110847 ATGCCATGCTTTTATTTCACTTAG
1 ATGCCATGGTCTTATTTCACTTAG
53110871 CACAATGTCA
Statistics
Matches: 125, Mismatches: 15, Indels: 20
0.78 0.09 0.12
Matches are distributed among these distances:
22 11 0.09
24 70 0.56
25 3 0.02
26 10 0.08
27 1 0.01
28 30 0.24
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (24 bp):
ATGCCATGGTCTTATTTCACTTAG
Found at i:53122419 original size:68 final size:67
Alignment explanation
Indices: 53122347--53122496 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
53122337 CATCATGTGT
* * * *
53122347 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
53122409 ATGTAG
62 ATGTAG
** * *
53122415 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
53122480 AG
66 AG
53122482 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
53122497 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Done.