Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 140 of 213
Found at i:41872856 original size:18 final size:18
Alignment explanation
Indices: 41872812--41872856 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
41872802 ACTTAGGCTG
*
41872812 TGTCAACACTAATGCCTT
1 TGTCAACATTAATGCCTT
*
41872830 TGTCAACATTAATGTCTT
1 TGTCAACATTAATGCCTT
41872848 TGTCAACAT
1 TGTCAACAT
41872857 ATTTTTCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (18 bp):
TGTCAACATTAATGCCTT
Found at i:41879785 original size:33 final size:32
Alignment explanation
Indices: 41879717--41879793 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
41879707 CCCTTTCCAG
* *
41879717 ATCA-CCTTCACCATCAAATTCTACCCTTCATC
1 ATCACCCTTC-CCATCAAATTCTACCATTCAAC
* *
41879749 ATCACCCTTCCCATCAACTTCTACCTATTTAAC
1 ATCACCCTTCCCATCAAATTCTACC-ATTCAAC
41879782 ATCACCC-TCCCA
1 ATCACCCTTCCCA
41879794 AGCAGTCAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 23 0.59
33 16 0.41
ACGTcount: A:0.27, C:0.43, G:0.00, T:0.30
Consensus pattern (32 bp):
ATCACCCTTCCCATCAAATTCTACCATTCAAC
Found at i:41880521 original size:117 final size:116
Alignment explanation
Indices: 41880301--41880627 Score: 512
Period size: 117 Copynumber: 2.8 Consensus size: 116
41880291 GGTAACAATA
* * *
41880301 ATCAACAACATCAGGACCACTATCGTATCACAAATCGACAAAACAAA-CCTACATTGCGGCACTA
1 ATCAACAACATCGGGACCACTGTCGCATCACAAATCGACAAAACAAACCCTACATTGC-GCACTA
** * *
41880365 AAACAGCAATAATAAATCAAAAATAACCATATACAATTTTAACAATATCTTT
65 AAATTGCAATAATAAATCACAAATAACCATATACAATTTTAACAATAGCTTT
* * *
41880417 ATCAACAACATTGGGACCACTGTCGCATCACAAATCGACAAAACAAACCCTACATTGTCGCATTG
1 ATCAACAACATCGGGACCACTGTCGCATCACAAATCGACAAAACAAACCCTACATTG-CGCACTA
*
41880482 AAATTGCAATAATAAATCACAAATAACCATCTACAATTTTAACAATAGCTTT
65 AAATTGCAATAATAAATCACAAATAACCATATACAATTTTAACAATAGCTTT
*
41880534 ATCAACAACATCGAGACCACTGTCGCATCACAAATCGACAAAACAAACCCTACATTGCGACACTA
1 ATCAACAACATCGGGACCACTGTCGCATCACAAATCGACAAAACAAACCCTACATTGCG-CACTA
41880599 AAATTGCAATAATAAATCACAAATAACCA
65 AAATTGCAATAATAAATCACAAATAACCA
41880628 ACAAACCAAA
Statistics
Matches: 193, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
116 45 0.23
117 147 0.76
118 1 0.01
ACGTcount: A:0.45, C:0.25, G:0.08, T:0.22
Consensus pattern (116 bp):
ATCAACAACATCGGGACCACTGTCGCATCACAAATCGACAAAACAAACCCTACATTGCGCACTAA
AATTGCAATAATAAATCACAAATAACCATATACAATTTTAACAATAGCTTT
Found at i:41886021 original size:40 final size:40
Alignment explanation
Indices: 41885869--41886014 Score: 181
Period size: 40 Copynumber: 3.6 Consensus size: 40
41885859 TTGAATGATG
* * * *
41885869 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
41885909 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41885949 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
41885990 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41886015 AACGAGTAGC
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
39 1 0.01
40 82 0.88
41 10 0.11
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41886021 original size:80 final size:80
Alignment explanation
Indices: 41885869--41886047 Score: 195
Period size: 80 Copynumber: 2.2 Consensus size: 80
41885859 TTGAATGATG
* *
41885869 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
41885934 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * * *
41885949 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
*
41886012 TTGAACGAGTAGCTATA
64 TTGAACGAGTAGCTAAA
* *
41886029 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
41886048 TACGTGATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
79 17 0.20
80 60 0.71
81 7 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:41893860 original size:40 final size:40
Alignment explanation
Indices: 41893777--41893961 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
41893767 TTGAATGATG
* * * *
41893777 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
41893817 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
41893857 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41893897 TCCGGGTTAAGTCCCGAA-GCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
41893937 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41893962 AACGAGTAGC
Statistics
Matches: 129, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
39 35 0.27
40 86 0.67
41 8 0.06
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41893950 original size:79 final size:81
Alignment explanation
Indices: 41893777--41893961 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
41893767 TTGAATGATG
*
41893777 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
41893841 TGTGCGAGTTACTAAA
66 TGTGCGAGTTACTAAA
* * * * * **
41893857 TCCGGGTTAAGTCCCAAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAA-GCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
41893919 TTGTGCGAGTTACTATAA
65 TTGTGCGAGTTACTA-AA
*
41893937 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41893962 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
79 42 0.46
80 42 0.46
81 7 0.08
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTAAA
Found at i:41893968 original size:79 final size:78
Alignment explanation
Indices: 41893830--41893993 Score: 206
Period size: 79 Copynumber: 2.1 Consensus size: 78
41893820 GGACTAAGAT
* **
41893830 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTA-CT
1 CCGAA-GCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCAAAGGCATTTGAACGAG-TAGCT
*
41893894 AAATCCGGGTTAAGTC
64 AAATCC-GGTTAAATC
* *
41893910 CCGAAGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTA
1 CCGAAGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCAAAGGCATTTGAACGAGTAGCTA
* *
41893974 TATCCGGTTAAATT
65 AATCCGGTTAAATC
41893988 CCGAAG
1 CCGAAG
41893994 GTACGTGATT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 15 0.20
79 52 0.70
80 7 0.09
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (78 bp):
CCGAAGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCAAAGGCATTTGAACGAGTAGCTAA
ATCCGGTTAAATC
Found at i:41896166 original size:41 final size:41
Alignment explanation
Indices: 41896121--41896309 Score: 204
Period size: 41 Copynumber: 4.6 Consensus size: 41
41896111 CATTGAATGT
* *
41896121 AAGGGGTTTCTAAGTGTAGATTCCCTGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGTAGATTCCCCGAATCACTGATCAAA
* * *
41896162 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
1 AAGGGGTTGCTAAGTGTAGATTCCCCGAATCACTGATCAAA
*
41896203 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCACAA
1 AAGGGGTTGCTAAGTGTAGATTCCCCGAATCACTGATCA-AA
* * * * * *
41896245 AA-GGGTTGTTCAGTGCT-GATTCCCTGAATTATTGATTC-TA
1 AAGGGGTTGCTAAGTG-TAGATTCCCCGAATCACTGA-TCAAA
*
41896285 AAGGTGGTTGCTAAGTGTTGATTCC
1 AAGG-GGTTGCTAAGTGTAGATTCC
41896310 ACCGTATCCT
Statistics
Matches: 126, Mismatches: 16, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
40 3 0.02
41 101 0.80
42 22 0.17
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGTAGATTCCCCGAATCACTGATCAAA
Found at i:41896251 original size:82 final size:82
Alignment explanation
Indices: 41896121--41896301 Score: 240
Period size: 82 Copynumber: 2.2 Consensus size: 82
41896111 CATTGAATGT
* * *
41896121 AAGGGGTTTCTAAGTGTAGATTCCCTGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCC
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCC
41896186 CCGAATCATTGA-TCGAA
66 CCGAATCATTGATTC-AA
* * *
41896203 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCACAAAA-GGGTTGTTCAGTGCTGATTC
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCA-AAAAGGGGTTGCTAAGTGCAGATTC
* * *
41896267 CCTGAATTATTGATTCTA
65 CCCGAATCATTGATTCAA
41896285 AAGGTGGTTGCTAAGTG
1 AAGG-GGTTGCTAAGTG
41896302 TTGATTCCAC
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
82 69 0.79
83 18 0.21
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (82 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCC
CCGAATCATTGATTCAA
Found at i:41896387 original size:41 final size:43
Alignment explanation
Indices: 41896283--41896397 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 43
41896273 TTATTGATTC
** *
41896283 TAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATCCTTAATTT
1 TAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATCCAGAATTA
*
41896326 TGAAAGG-GGTTGCTATGTGTTGATTCC-CCGTATCACAGAA-TA
1 T-AAAGGTGGTTGCTAAGTGTTGATTCCACCGTATC-CAGAATTA
*
41896368 T-AAGGTGGTTGCTAAGTGTTGATTTCACCG
1 TAAAGGTGGTTGCTAAGTGTTGATTCCACCG
41896398 AGTAATGGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
40 4 0.06
41 18 0.29
42 12 0.19
43 23 0.37
44 5 0.08
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (43 bp):
TAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATCCAGAATTA
Found at i:41896391 original size:126 final size:122
Alignment explanation
Indices: 41896115--41896391 Score: 263
Period size: 126 Copynumber: 2.2 Consensus size: 122
41896105 GAGATTCATT
* * *
41896115 GAATGTAAGGGGTTTCTAAGTGTAGATTCCCTGAATCACTGATCAAAAAGGGGTTGCTAAGTGCA
1 GAATATAAGGGGTTGCTAAGTGTTGATTCCCTGAATCACTGATCAAAAAGGGGTTGCTAAGTGCA
* *
41896180 GATTCCCCGAATCATTGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACT
66 GATTCCCCGAATCATTAATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACA
* * * * * * * *
41896237 G-ATCACAAAAGGGTTGTTCAGTGCTGATTCCCTGAATTATTGATTC-TAAAGGTGGTTGCTAAG
1 GAAT-A-TAAGGGGTTGCTAAGTGTTGATTCCCTGAATCACTGA-TCAAAAAGG-GGTTGCTAAG
** * * * * ** *
41896300 TGTTGATTCCACCGTATCCTTAATTTTG-AAAGGGGTTGCTATGTGTTGATTCCCCGTATCACA
62 TGCAGATTCC-CCGAATCATTAA--TCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACA
41896363 GAATATAAGGTGGTTGCTAAGTGTTGATT
1 GAATATAAGG-GGTTGCTAAGTGTTGATT
41896392 TCACCGAGTA
Statistics
Matches: 119, Mismatches: 27, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
121 2 0.02
122 1 0.01
123 33 0.28
124 20 0.17
125 12 0.10
126 47 0.39
127 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (122 bp):
GAATATAAGGGGTTGCTAAGTGTTGATTCCCTGAATCACTGATCAAAAAGGGGTTGCTAAGTGCA
GATTCCCCGAATCATTAATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACA
Found at i:41901833 original size:11 final size:11
Alignment explanation
Indices: 41901819--41901845 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41901809 GTGTTTTTCA
41901819 AAAAAAATTCC
1 AAAAAAATTCC
41901830 AAAAAAATTCC
1 AAAAAAATTCC
41901841 AAAAA
1 AAAAA
41901846 TATTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCC
Found at i:41904069 original size:15 final size:16
Alignment explanation
Indices: 41904034--41904068 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
41904024 AAGAAAACCG
41904034 TTTTCGAATCAGATTT
1 TTTTCGAATCAGATTT
41904050 TTTTCGAATCAGATTT
1 TTTTCGAATCAGATTT
41904066 TTT
1 TTT
41904069 CCAACATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.54
Consensus pattern (16 bp):
TTTTCGAATCAGATTT
Found at i:41910248 original size:16 final size:16
Alignment explanation
Indices: 41910227--41910260 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41910217 GTATTCAACG
*
41910227 ATTTTATAGATTTATA
1 ATTTTATAGATTAATA
*
41910243 ATTTTATTGATTAATA
1 ATTTTATAGATTAATA
41910259 AT
1 AT
41910261 ATATTATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
ATTTTATAGATTAATA
Found at i:41911297 original size:3 final size:3
Alignment explanation
Indices: 41911289--41911345 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
41911279 GAGCCCAAAA
41911289 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41911335 AAT AAT AAT AA
1 AAT AAT AAT AA
41911346 ACTAGTTGGT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:41918381 original size:46 final size:46
Alignment explanation
Indices: 41918314--41918405 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
41918304 AAAGCTAAAG
41918314 GAGGATGATTGCTCACATATAAATTAATAAGAAAATCATAAAACTA
1 GAGGATGATTGCTCACATATAAATTAATAAGAAAATCATAAAACTA
41918360 GAGGATGATTGCTCACATATAAATTAATAAGAAAATCATAAAACTA
1 GAGGATGATTGCTCACATATAAATTAATAAGAAAATCATAAAACTA
41918406 TCTACTCATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (46 bp):
GAGGATGATTGCTCACATATAAATTAATAAGAAAATCATAAAACTA
Found at i:41920316 original size:40 final size:38
Alignment explanation
Indices: 41920272--41920371 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 38
41920262 GGGAAATTAG
*
41920272 TAAAGTGCGTCCAGCTCAGCGCTTTTTTCCCTCTGACCAA
1 TAAAGTGCGTCCAGCTCAGCGC-CTTTT-CCTCTGACCAA
* * * * *
41920312 TAAAGTGCGTCTAACTCAGCACCTTTTCCTTTGACCAG
1 TAAAGTGCGTCCAGCTCAGCGCCTTTTCCTCTGACCAA
*
41920350 TAAAATGCGTCCAAG-TCAGCGC
1 TAAAGTGCGTCC-AGCTCAGCGC
41920372 ACTAGGAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
38 25 0.51
39 5 0.10
40 19 0.39
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (38 bp):
TAAAGTGCGTCCAGCTCAGCGCCTTTTCCTCTGACCAA
Found at i:41920476 original size:41 final size:40
Alignment explanation
Indices: 41920429--41920545 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 40
41920419 GTTTTAATTG
*
41920429 TTTAATTAGGATTTATAGTTTATTAAATTAAGGTTTA-GTGT
1 TTTAATTAGGGTTTAT-GTTTATTAAATTAAGGTTTATG-GT
* *
41920470 TTTAATTAGGGTTTAGGATTTAATAAATT-AGTGTTTATGGT
1 TTTAATTAGGGTTTATG-TTTATTAAATTAAG-GTTTATGGT
*
41920511 TTCAATTAGGGTTTAGTGTTTATT-AATTAAGGTTT
1 TTTAATTAGGGTTTA-TGTTTATTAAATTAAGGTTT
41920546 TAAGAAAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
40 11 0.17
41 52 0.80
42 2 0.03
ACGTcount: A:0.29, C:0.01, G:0.20, T:0.50
Consensus pattern (40 bp):
TTTAATTAGGGTTTATGTTTATTAAATTAAGGTTTATGGT
Found at i:41920482 original size:19 final size:20
Alignment explanation
Indices: 41920454--41920545 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 20
41920444 TAGTTTATTA
*
41920454 AATTAAGGTTTAGTG-TTTT
1 AATTAGGGTTTAGTGATTTT
41920473 AATTAGGGTTTAG-GATTTAAT
1 AATTAGGGTTTAGTGATTT--T
* * *
41920494 AAATTAGTGTTTA-TGGTTTC
1 -AATTAGGGTTTAGTGATTTT
*
41920514 AATTAGGGTTTAGTGTTTATT
1 AATTAGGGTTTAGTGATT-TT
*
41920535 AATTAAGGTTT
1 AATTAGGGTTT
41920546 TAAGAAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
18 1 0.02
19 26 0.45
20 4 0.07
21 12 0.21
22 15 0.26
ACGTcount: A:0.28, C:0.01, G:0.22, T:0.49
Consensus pattern (20 bp):
AATTAGGGTTTAGTGATTTT
Found at i:41920640 original size:29 final size:29
Alignment explanation
Indices: 41920607--41920680 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
41920597 TAGTGTTCAA
41920607 GGGTTCTGAAAAAATAATTTTGACAAGAT
1 GGGTTCTGAAAAAATAATTTTGACAAGAT
*
41920636 GGGTT-TCGAAAAAATAATTTTGACGAGAT
1 GGGTTCT-GAAAAAATAATTTTGACAAGAT
* *
41920665 GAGTTCTAAAAAAATA
1 GGGTTCTGAAAAAATA
41920681 TCTCGAGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 1 0.03
29 38 0.95
30 1 0.03
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (29 bp):
GGGTTCTGAAAAAATAATTTTGACAAGAT
Found at i:41923057 original size:14 final size:15
Alignment explanation
Indices: 41923023--41923071 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
41923013 GTTAAAATAT
41923023 ATATTATAATATTATA
1 ATATTA-AATATTATA
*
41923039 ATATTAAATCTTA-A
1 ATATTAAATATTATA
*
41923053 ATATTAAGTA-TAT-
1 ATATTAAATATTATA
41923066 ATATTA
1 ATATTA
41923072 TTTTATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 8 0.28
14 9 0.31
15 6 0.21
16 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
ATATTAAATATTATA
Found at i:41924083 original size:37 final size:40
Alignment explanation
Indices: 41923992--41924101 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 40
41923982 GACTTTGAGT
* **
41923992 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTTATT
1 CGATGAGACACTGGGTGTCAA-TTATTACTTCGGATATAGC
*
41924033 CGATGAGGCACTGGGTG-CGAA-T-TTACTTCGG-TATAGC
1 CGATGAGACACTGGGTGTC-AATTATTACTTCGGATATAGC
41924070 CGATGAGACACTGGGTGTCAAATTATTACTTC
1 CGATGAGACACTGGGTGTC-AATTATTACTTC
41924102 AAATTATCTG
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
37 19 0.32
38 12 0.20
39 2 0.03
40 8 0.14
41 18 0.31
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTATTACTTCGGATATAGC
Found at i:41924115 original size:40 final size:39
Alignment explanation
Indices: 41923993--41924131 Score: 106
Period size: 40 Copynumber: 3.5 Consensus size: 39
41923983 ACTTTGAGTC
* *
41923993 GATGAGACACTGGGTGTCAATTTATTACTTCGGATTTAT-T
1 GATGAGACACTGGGTGTCAAATTATTACTTC--AATTATCT
* * ** * *
41924033 CGATGAGGCACTGGGTG-CGAA-T-TTACTTCGGTATAGCC
1 -GATGAGACACTGGGTGTCAAATTATTACTTCAAT-TATCT
41924071 GATGAGACACTGGGTGTCAAATTATTACTTCAAATTATCT
1 GATGAGACACTGGGTGTCAAATTATTACTTC-AATTATCT
* * *
41924111 GATGAGGCATTGGGTGCCAAA
1 GATGAGACACTGGGTGTCAAA
41924132 CTGGTGTGTT
Statistics
Matches: 76, Mismatches: 16, Indels: 13
0.72 0.15 0.12
Matches are distributed among these distances:
36 1 0.01
37 17 0.22
38 10 0.13
39 2 0.03
40 30 0.39
41 16 0.21
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.32
Consensus pattern (39 bp):
GATGAGACACTGGGTGTCAAATTATTACTTCAATTATCT
Found at i:41930524 original size:4 final size:4
Alignment explanation
Indices: 41930515--41930619 Score: 83
Period size: 4 Copynumber: 25.0 Consensus size: 4
41930505 TAAGTAATAA
*
41930515 AAAG AAAG AAAG AAAG ATAG AAATG AAACAG AAAG -AAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAA-G -AA-AG AAAG AAAG AAAG AAAG AAAG
*
41930565 ATAG AAATG AAACAG AAAG -AAG AAAG AAAG AAA- AATA- AAAGGG AAAG
1 AAAG AAA-G -AA-AG AAAG AAAG AAAG AAAG AAAG AA-AG AAA--G AAAG
41930612 AAAG AAAG
1 AAAG AAAG
41930620 GAGAAAGACA
Statistics
Matches: 85, Mismatches: 4, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
3 9 0.11
4 59 0.69
5 6 0.07
6 9 0.11
7 2 0.02
ACGTcount: A:0.70, C:0.02, G:0.24, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:41930555 original size:34 final size:34
Alignment explanation
Indices: 41930516--41930597 Score: 164
Period size: 34 Copynumber: 2.4 Consensus size: 34
41930506 AAGTAATAAA
41930516 AAGAAAGAAAGAAAGATAGAAATGAAACAGAAAG
1 AAGAAAGAAAGAAAGATAGAAATGAAACAGAAAG
41930550 AAGAAAGAAAGAAAGATAGAAATGAAACAGAAAG
1 AAGAAAGAAAGAAAGATAGAAATGAAACAGAAAG
41930584 AAGAAAGAAAGAAA
1 AAGAAAGAAAGAAA
41930598 AATAAAAGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.70, C:0.02, G:0.23, T:0.05
Consensus pattern (34 bp):
AAGAAAGAAAGAAAGATAGAAATGAAACAGAAAG
Found at i:41930556 original size:30 final size:32
Alignment explanation
Indices: 41930514--41930619 Score: 134
Period size: 34 Copynumber: 3.4 Consensus size: 32
41930504 ATAAGTAATA
41930514 AAAAGAAAGAAAGAAAGATAGAAATGAAACAG
1 AAAAGAAAGAAAGAAAGATAGAAATGAAACAG
41930546 AAAGAAGAAAGAAAGAAAGATAGAAATGAAACAG
1 -AA-AAGAAAGAAAGAAAGATAGAAATGAAACAG
41930580 -AAAG-AAGAAAGAAAGA-A-AAAT-AAA-AGG
1 AAAAGAAAGAAAGAAAGATAGAAATGAAACA-G
*
41930607 GAAAGAAAGAAAG
1 AAAAGAAAGAAAG
41930620 GAGAAAGACA
Statistics
Matches: 69, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
26 1 0.01
27 4 0.06
28 8 0.12
29 8 0.12
30 12 0.17
31 3 0.04
32 1 0.01
33 2 0.03
34 30 0.43
ACGTcount: A:0.70, C:0.02, G:0.24, T:0.05
Consensus pattern (32 bp):
AAAAGAAAGAAAGAAAGATAGAAATGAAACAG
Found at i:41933859 original size:12 final size:12
Alignment explanation
Indices: 41933842--41933878 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
41933832 TATATACATT
41933842 AAAAATTATATA
1 AAAAATTATATA
*
41933854 AAAAATAATATA
1 AAAAATTATATA
41933866 AAAAATTAATATA
1 AAAAATT-ATATA
41933879 GGCGAGCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAAATTATATA
Found at i:41938683 original size:25 final size:25
Alignment explanation
Indices: 41938654--41938711 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
41938644 TTAATCAACA
*
41938654 TAAAATATTAA-TAATTTAAT-AAAT
1 TAAAAT-TTAATTAATTAAATAAAAT
41938678 TGAAAATTTAATTAATTAAATAAAAT
1 T-AAAATTTAATTAATTAAATAAAAT
41938704 TAAAATTT
1 TAAAATTT
41938712 TGGAGAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.17
25 20 0.67
26 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
TAAAATTTAATTAATTAAATAAAAT
Found at i:41947526 original size:15 final size:16
Alignment explanation
Indices: 41947508--41947537 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41947498 ATGATAAAAT
41947508 AATATTAA-ATAATTA
1 AATATTAATATAATTA
41947523 AATATTAATATAATT
1 AATATTAATATAATT
41947538 TTTTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATTAATATAATTA
Found at i:41947841 original size:17 final size:18
Alignment explanation
Indices: 41947804--41947844 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
41947794 CAATGCAAAG
*
41947804 TAAATAAATTATTAAAAA
1 TAAAAAAATTATTAAAAA
*
41947822 TAAAAAAATTA-TAAATA
1 TAAAAAAATTATTAAAAA
41947839 TAAAAA
1 TAAAAA
41947845 TTGGTTCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAAAATTATTAAAAA
Found at i:41948032 original size:19 final size:18
Alignment explanation
Indices: 41947996--41948053 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
41947986 AACATTAGAA
41947996 TTTAAAATTTTTTATATT
1 TTTAAAATTTTTTATATT
* *
41948014 TTTAGAATTATTTTTTA-T
1 TTTAAAATT-TTTTATATT
**
41948032 TTTAAAATTTTAAATATT
1 TTTAAAATTTTTTATATT
41948050 TTTA
1 TTTA
41948054 TTTTCATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
17 4 0.12
18 22 0.69
19 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTAAAATTTTTTATATT
Found at i:41948064 original size:24 final size:23
Alignment explanation
Indices: 41948025--41948077 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
41948015 TTAGAATTAT
41948025 TTTTTATTTTAAAATTTTAAATA
1 TTTTTATTTTAAAATTTTAAATA
* *
41948048 TTTTTATTTTCATAATTTTATATA
1 TTTTTATTTT-AAAATTTTAAATA
*
41948072 ATTTTA
1 TTTTTA
41948078 AAATATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTTATTTTAAAATTTTAAATA
Found at i:41949216 original size:6 final size:6
Alignment explanation
Indices: 41949205--41949229 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41949195 ACGTTAGCAA
41949205 ATAAAT ATAAAT ATAAAT ATAAAT A
1 ATAAAT ATAAAT ATAAAT ATAAAT A
41949230 ATTATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAAAT
Found at i:41949290 original size:14 final size:16
Alignment explanation
Indices: 41949256--41949291 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
41949246 AGACAACTTA
*
41949256 ATATAAGCAAATATTT
1 ATATAAACAAATATTT
41949272 ATATAAACAAATATTT
1 ATATAAACAAATATTT
41949288 ATAT
1 ATAT
41949292 TTAAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
ATATAAACAAATATTT
Found at i:41949821 original size:28 final size:28
Alignment explanation
Indices: 41949782--41949837 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
41949772 ACAACTTTTT
41949782 TTTTATTTACCAAAATATATAAAAAAAA
1 TTTTATTTACCAAAATATATAAAAAAAA
41949810 TTTTATTTACCAAAATATATAAAAAAAA
1 TTTTATTTACCAAAATATATAAAAAAAA
41949838 CTAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (28 bp):
TTTTATTTACCAAAATATATAAAAAAAA
Found at i:41949895 original size:27 final size:27
Alignment explanation
Indices: 41949857--41949933 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
41949847 AACCTGACAC
*
41949857 TTGGCGGCACCAAAGGTGCCAAA-TAA
1 TTGGCGGCACCAATGGTGCCAAAGTAA
* * *
41949883 GTTGGTGGCACCATTGGTGCCAAAGTCA
1 -TTGGCGGCACCAATGGTGCCAAAGTAA
41949911 TTGGCGGCACC-ATGGTGCCAAAG
1 TTGGCGGCACCAATGGTGCCAAAG
41949934 GAAAAAAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
26 11 0.26
27 30 0.70
28 2 0.05
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.19
Consensus pattern (27 bp):
TTGGCGGCACCAATGGTGCCAAAGTAA
Found at i:41950034 original size:19 final size:19
Alignment explanation
Indices: 41950007--41950076 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
41949997 AACTCATTTT
*
41950007 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
41950026 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
41950044 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
41950063 TTTTAATTTAATAA
1 TTTTAATTTAATAA
41950077 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:41950062 original size:37 final size:37
Alignment explanation
Indices: 41950012--41950082 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
41950002 ATTTTTTTTT
41950012 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
41950049 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
41950083 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:41950426 original size:20 final size:19
Alignment explanation
Indices: 41950390--41950432 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
41950380 ATTACTTAAT
*
41950390 AGTTTATTAAATTAAAATAG
1 AGTTTATTAAATAAAAAT-G
41950410 AGTTT-TTAAATAAAAAATG
1 AGTTTATTAAAT-AAAAATG
41950429 AGTT
1 AGTT
41950433 GAAGGGGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (19 bp):
AGTTTATTAAATAAAAATG
Found at i:41950689 original size:37 final size:37
Alignment explanation
Indices: 41950642--41950712 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
41950632 AGTATTACTT
41950642 AATAGTTTATTAAATTAAAATAGAGTTACTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTACTAAATGAG
* *
41950679 AATATTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTACTAAAT
41950713 AAAAAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTACTAAATGAG
Found at i:41950700 original size:18 final size:18
Alignment explanation
Indices: 41950642--41950716 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
41950632 AGTATTACTT
*
41950642 AATAGTTTATTAAATTAA
1 AATAATTTATTAAATTAA
* * * *
41950660 AATAGAGTTACTAAATGAG
1 AATA-ATTTATTAAATTAA
*
41950679 AATATTTTATTAAATTAA
1 AATAATTTATTAAATTAA
*
41950697 AATAGAGTTATTAAA-TAA
1 AATA-ATTTATTAAATTAA
41950715 AA
1 AA
41950717 AAATGAGTTG
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
18 22 0.51
19 21 0.49
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.37
Consensus pattern (18 bp):
AATAATTTATTAAATTAA
Found at i:41950717 original size:19 final size:19
Alignment explanation
Indices: 41950648--41950716 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
41950638 ACTTAATAGT
41950648 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * * **
41950667 TTACTAAATGAGAATA-TT
1 TTATTAAATTAAAATAGAG
41950685 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
41950704 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
41950717 AAATGAGTTG
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
18 18 0.46
19 21 0.54
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:41950724 original size:20 final size:19
Alignment explanation
Indices: 41950685--41950725 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
41950675 TGAGAATATT
* *
41950685 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
41950704 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
41950724 TT
1 TT
41950726 GAAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:41950869 original size:27 final size:26
Alignment explanation
Indices: 41950792--41950877 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 26
41950782 TTTTTTTTCC
*
41950792 TTTGGCACCATGGTGCCGCCAA-TGA
1 TTTGGCACCATGGTGCCGCCAATTTA
*
41950817 CTTTGGCACCAATGGTGCCACCAATTTA
1 -TTTGGCACC-ATGGTGCCGCCAATTTA
*
41950845 TTTGGCACCTTTGGTGCCGCCAATTTA
1 TTTGGCACC-ATGGTGCCGCCAATTTA
*
41950872 ATTGGC
1 TTTGGC
41950878 TGGTGTTAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 9 0.17
27 41 0.79
28 2 0.04
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (26 bp):
TTTGGCACCATGGTGCCGCCAATTTA
Found at i:41950978 original size:29 final size:28
Alignment explanation
Indices: 41950918--41951016 Score: 173
Period size: 28 Copynumber: 3.5 Consensus size: 28
41950908 TTTTTTTGAT
41950918 ATATTTTGGTAAATAAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
41950945 TATATTTTGGTAAATAAAAAAAAAGTTGTA
1 -ATATTTTGGTAAAT-AAAAAAAAGTTGTA
41950975 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
41951003 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
41951017 TTTTATTTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
28 42 0.61
29 25 0.36
30 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.38
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:41951034 original size:57 final size:57
Alignment explanation
Indices: 41950908--41951044 Score: 143
Period size: 57 Copynumber: 2.4 Consensus size: 57
41950898 TGTTTTTTGG
41950908 TTTTTTTGAT-ATATTTTGGTAAATAAAAAAAAGTTTATATATTTTGGTAAATAAAAA
1 TTTTTTT-ATAATATTTTGGTAAATAAAAAAAAGTTTATATATTTTGGTAAATAAAAA
***** * ****
41950965 AAAAGTTGTAATATTTTGGTAAATAAAAAAAAGTTGTA-ATATTTTGGTAAATTTTTA
1 TTTTTTTATAATATTTTGGTAAATAAAAAAAAGTT-TATATATTTTGGTAAATAAAAA
*
41951022 TTTTTTTATAATATTTTTGTAAA
1 TTTTTTTATAATATTTTGGTAAA
41951045 AAACCCCTTT
Statistics
Matches: 61, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
56 1 0.02
57 58 0.95
58 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (57 bp):
TTTTTTTATAATATTTTGGTAAATAAAAAAAAGTTTATATATTTTGGTAAATAAAAA
Found at i:41959283 original size:28 final size:26
Alignment explanation
Indices: 41959255--41959308 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
41959245 TTAAAAAATA
41959255 TTTATATTATTTAATAATTTTATATATAT
1 TTTAT-TTA-TTAA-AATTTTATATATAT
41959284 TTTATTTATTAAAATTTTATATATA
1 TTTATTTATTAAAATTTTATATATA
41959309 AACAACTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 13 0.52
27 4 0.16
28 3 0.12
29 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTATTTATTAAAATTTTATATATAT
Found at i:41959288 original size:24 final size:25
Alignment explanation
Indices: 41959252--41959308 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
41959242 ATTTTAAAAA
* *
41959252 ATATTTATATTATTTA-ATAATTTT
1 ATATATATATTATTTATAAAATTTT
*
41959276 ATATATATTTTATTTATTAAAATTTT
1 ATATATATATTATTTA-TAAAATTTT
41959302 ATATATA
1 ATATATA
41959309 AACAACTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 14 0.50
26 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATATATATATTATTTATAAAATTTT
Found at i:41960053 original size:24 final size:24
Alignment explanation
Indices: 41960032--41960080 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
41960022 AGTTAAAATG
*
41960032 TATATATAATTAAATATCAAAATAT
1 TATATA-AATTAAATAACAAAATAT
*
41960057 TTTATAAATTAAATAACAAAATAT
1 TATATAAATTAAATAACAAAATAT
41960081 AATTATGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
TATATAAATTAAATAACAAAATAT
Found at i:41960164 original size:35 final size:35
Alignment explanation
Indices: 41960115--41960181 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
41960105 ATTATAAAAA
* *
41960115 ATTATTTATATTATATTATATAATAATATATTAGG
1 ATTATTTATATTATATTAAATAAAAATATATTAGG
41960150 ATTATGTTAT-TTATATTAAATAAAAATATATT
1 ATTAT-TTATATTATATTAAATAAAAATATATT
41960182 TATATTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 25 0.86
36 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (35 bp):
ATTATTTATATTATATTAAATAAAAATATATTAGG
Found at i:41963419 original size:132 final size:132
Alignment explanation
Indices: 41963174--41963447 Score: 323
Period size: 132 Copynumber: 2.1 Consensus size: 132
41963164 TTCGTAGATC
*** * * * *
41963174 CATCATATCGAGTTTAAATGTGGCTTGTTAGGTATGCTGCGAGCTGTTAGAACATGACGTCTTCC
1 CATCATATCGAGTTTAAATGCAACTTGTTAGGTACGCTGCGAGCTATTAGAACATAACGTCTACC
* * * * *
41963239 TTGTCACTTGTATGGGTGGATCGTGCTCGCATGAATCTGGCCGCTGAGACTCTTTGGTTATTGGA
66 TTGCCACATGTATGGGTAGATCGTGCTCGCATGAATCTGACCGCTGAGACTCTTTCGTTATTGGA
41963304 AT
131 AT
* * * * *
41963306 CATCATGTCGAGTTTAAATGCAACTTGTTGGGTACGTTGCGAGTTATTAGAACCTAACGTCTACC
1 CATCATATCGAGTTTAAATGCAACTTGTTAGGTACGCTGCGAGCTATTAGAACATAACGTCTACC
* * * * * *
41963371 TTGCCACATGTATGGGTAGATCGTGCTTGCATGGATCTGATCGTTGAGATTTTTTCGTTATTGGA
66 TTGCCACATGTATGGGTAGATCGTGCTCGCATGAATCTGACCGCTGAGACTCTTTCGTTATTGGA
41963436 AT
131 AT
**
41963438 TGTCATATCG
1 CATCATATCG
41963448 CAAAAAAAAA
Statistics
Matches: 116, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
132 116 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (132 bp):
CATCATATCGAGTTTAAATGCAACTTGTTAGGTACGCTGCGAGCTATTAGAACATAACGTCTACC
TTGCCACATGTATGGGTAGATCGTGCTCGCATGAATCTGACCGCTGAGACTCTTTCGTTATTGGA
AT
Found at i:41965784 original size:27 final size:27
Alignment explanation
Indices: 41965754--41965834 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
41965744 GACAGCTTGA
41965754 CCCCTCCTGTCGAGAATGACAATGTGG
1 CCCCTCCTGTCGAGAATGACAATGTGG
* ** *
41965781 CCCCTCCTATTAAGAATGATAATGTGG
1 CCCCTCCTGTCGAGAATGACAATGTGG
* *
41965808 CCCTTCCTG-CTGAGAATGACAAAGTGG
1 CCCCTCCTGTC-GAGAATGACAATGTGG
41965835 GCCAAGATGC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (27 bp):
CCCCTCCTGTCGAGAATGACAATGTGG
Found at i:41966432 original size:144 final size:142
Alignment explanation
Indices: 41966218--41967057 Score: 553
Period size: 144 Copynumber: 5.9 Consensus size: 142
41966208 TTTAAAGCTA
* * * * * *
41966218 CGAGCCTTAATGATGACA-TCT-GAGAGCTTTTAACTCTCGTTAATTGTTTGGAGGGTTGCGGTA
1 CGAGCCTTAATGATGATAGT-TAG-GAGCTTTTAACTCTCGCTAACT-ATTGGAGGGCTGCGGTT
* ** * * *
41966281 TTGAACCTGCAAGCCTTAATAATAACAGCTGAGAGCTTTTAACTCTCGCTAACTATTTAGAGAGC
63 TTAAACCTGTGAGCTTTAATAATGACAGCTGAGAGCTTTTAACTCTCACTAACTATTT-GAGAGC
41966346 TGCGATTTTAATCCTG
127 TGCGATTTTAATCCTG
* * * ** *
41966362 TGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTGCTTGGAGGGCTGCAGCCTA
1 CGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACT-ATTGGAGGGCTGCGGTTTT
* * * * * * *
41966427 AAACCTATGAGCTTTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGAGGGGGTA
65 AAACCTGTGAGCTTTAATAATGACAGCTGAGAGCTTTTAACTCTCACTAACTATTTGA-GAGCTG
**
41966492 C-ATTTTTAATCAAG
129 CGA-TTTTAATCCTG
* * * * * * * **
41966506 TGAGCCTTAATAATGACAATTGGGAGTTTTTAACTCTCGTTAACTATTTAAGGGGCTGCGGTTTT
1 CGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTATTGGA-GGGCTGCGGTTTT
* * * * * * * * *
41966571 AGACCTGTGAGATTTAATGATGATAG-TTAGGAGCTTTTAACTCCCGCTAACTATTTGGGAGGTT
65 AAACCTGTGAGCTTTAATAATGACAGCTGA-GAGCTTTTAACTCTCACTAACTATTTGAGA-GCT
* *
41966635 GTGATATTGAA-CCTG
128 GCGAT-TTTAATCCTG
* * * * * * * *
41966650 CGAGCTTTAATAATAATTGTTGGGAGCTTTTAACTCTCGCTAACTATTTGAGGGACTACGATTTT
1 CGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTATTGGAGGG-CTGCGGTTTT
* * ** * * * * *
41966715 -AATCTCGTGAGGTTTAATAATGACATTTGAGAGCTTTTAAATCTCACTAATTGTTTGGGGGCTG
65 AAACCT-GTGAGCTTTAATAATGACAGCTGAGAGCTTTTAACTCTCACTAACTATTTGAGAGCTG
* *
41966779 CAATTTTAAACCTG
129 CGATTTTAATCCTG
* * * *
41966793 CAAGCCTTAATGATGATAGCTAGGAGCTTTTAACTCTCGCTAACTATTTGG-GGGTTGTGGTTTT
1 CGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTA-TTGGAGGGCTGCGGTTTT
* * ** * * * * *
41966857 AAACCTGCGAGCCTTAATAATGACAATTGAGAGCTTTTAACTCTCACTAATTGTTTGGGTGGTTG
65 AAACCTGTGAGCTTTAATAATGACAGCTGAGAGCTTTTAACTCTCACTAACTATTTGAG-AGCTG
* * * * *
41966922 TGGTTTTAAACTTA
129 CGATTTTAATCCTG
* * * * * * * ** * * *
41966936 CGAGTCTGAATGAAGACAGCTAGGAGTTTTTAACTCTCGCTAAATATTTAAGGGGTTGTGGTATT
1 CGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTATTGGA-GGGCTGCGGTTTT
* * * ** *
41967001 GAACCTGCGAGCCTTAATAATGGTAGCTG-GAAGCTTTTAACTCTCACTAACTGTTTG
65 AAACCTGTGAGCTTTAATAATGACAGCTGAG-AGCTTTTAACTCTCACTAACTATTTG
41967058 GGTTTTTTAT
Statistics
Matches: 554, Mismatches: 123, Indels: 38
0.77 0.17 0.05
Matches are distributed among these distances:
142 60 0.11
143 122 0.22
144 363 0.66
145 9 0.02
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (142 bp):
CGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTATTGGAGGGCTGCGGTTTTA
AACCTGTGAGCTTTAATAATGACAGCTGAGAGCTTTTAACTCTCACTAACTATTTGAGAGCTGCG
ATTTTAATCCTG
Found at i:41966580 original size:216 final size:213
Alignment explanation
Indices: 41966292--41966903 Score: 638
Period size: 216 Copynumber: 2.8 Consensus size: 213
41966282 TGAACCTGCA
* ** *
41966292 AGCCTTAATAATAACAGCTGAGAGCTTTTAACTCTCGCTAACTATTTAGAGAGCTGCGATTTTAA
1 AGCCTTAATAATGACAATTGAGAGCTTTTAACTCTCGCTAACTATTTAG-GGGCTGCGATTTTAA
*
41966357 TCCTGTGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTGCTT-GGAGG-GCTG
65 -CCTGTGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTACTTGGGAGGTG-TG
* *
41966420 CAGCCTAAAACCTATGAGCTTTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGA
128 -A-CATAAAACCTACGAGCTTTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGA
**
41966485 GGGGGTAC-ATTTTTAATCAAGTG
191 GGGACTACGA-TTTTAATCAAGTG
* * * *
41966508 AGCCTTAATAATGACAATTGGGAGTTTTTAACTCTCGTTAACTATTTAAGGGGCTGCGGTTTTAG
1 AGCCTTAATAATGACAATTGAGAGCTTTTAACTCTCGCTAACTATTT-AGGGGCTGCGATTTTA-
** * *
41966573 ACCTGTGAGATTTAATGATGATAGTTAGGAGCTTTTAACTCCCGCTAACTATTTGGGAGGTTGTG
64 ACCTGTGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTACTTGGGAGG-TGTG
* ** * ** * * *
41966638 ATATTGAACCTGCGAGCTTTAATAATAATTGTTGGGAGCTTTTAACTCTCGCTAACTATTTGAGG
128 ACATAAAACCTACGAGCTTTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGAGG
**
41966703 GACTACGATTTTAATCTCGTG
193 GACTACGATTTTAATCAAGTG
** * * * * * * *
41966724 AGGTTTAATAATGACATTTGAGAGCTTTTAAATCTCACTAATTGTTTGGGGGCTGCAATTTTAAA
1 AGCCTTAATAATGACAATTGAGAGCTTTTAACTCTCGCTAACTATTTAGGGGCTGCGATTTT-AA
** * * *
41966789 CCTGCAAGCCTTAATGATGATAGCTAGGAGCTTTTAACTCTCGCTAACTATTTGGG-GGTTGTGG
65 CCTGTGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTACTTGGGAGG-TGTGA
** * * * * ** *
41966853 TTTTAAACCTGCGAGCCTTAATAATGACAATTGAGAGCTTTTAACTCTCAC
129 CATAAAACCTACGAGCTTTAATAATAACAGCTGGGAGCTTTTAACTCTCAC
41966904 TAATTGTTTG
Statistics
Matches: 332, Mismatches: 57, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
214 49 0.15
215 63 0.19
216 207 0.62
217 10 0.03
218 2 0.01
219 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (213 bp):
AGCCTTAATAATGACAATTGAGAGCTTTTAACTCTCGCTAACTATTTAGGGGCTGCGATTTTAAC
CTGTGAGCCTTAATGATGATAGTTAGGAGCTTTTAACTCTCGCTAACTACTTGGGAGGTGTGACA
TAAAACCTACGAGCTTTAATAATAACAGCTGGGAGCTTTTAACTCTCACCAACTATTTGAGGGAC
TACGATTTTAATCAAGTG
Found at i:41966820 original size:71 final size:71
Alignment explanation
Indices: 41966173--41967059 Score: 465
Period size: 72 Copynumber: 12.4 Consensus size: 71
41966163 ATCTGAGAGT
** * *** * * * *
41966173 TTTTAACTCTTGCTGACTGTTTGGGGGGTTACAGTTTTAAAGCTACGAGCCTTAATGATGACATC
1 TTTTAACTCTCACTAACTGTTT-GGGGGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACAGC
41966238 T-GAGAGC
65 TAG-GAGC
** * * * * * *
41966245 TTTTAACTCTCGTTAATTGTTTGGAGGGTTGCGGTATTGAACCTGCAAGCCTTAATAATAACAGC
1 TTTTAACTCTCACTAACTGTTTGG-GGGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACAGC
41966310 T-GAGAGC
65 TAG-GAGC
* * * * * * * * * * * *
41966317 TTTTAACTCTCGCTAACTATTTAGAGAGCTGCGATTTTAATCCTGTGAGCCTTAATGATGATAGT
1 TTTTAACTCTCACTAACTGTTT-GGGGGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACAGC
41966382 TAGGAGC
65 TAGGAGC
* * * ** ** * ** * *
41966389 TTTTAACTCTCGCTAACTGCTTGGAGGGCTGCAGCCTAAAACCTATGAGCTTTAATAATAACAGC
1 TTTTAACTCTCACTAACTGTTTGG-GGGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACAGC
*
41966454 TGGGAGC
65 TAGGAGC
* * * **** * ** * **
41966461 TTTTAACTCTCACCAACTATTTGAGGGGGTACATTTTTAATCAAGTGAGCCTTAATAATGACAAT
1 TTTTAACTCTCACTAACTGTTTG-GGGGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACAGC
* *
41966526 TGGGAGT
65 TAGGAGC
** * * * * * * ** * * *
41966533 TTTTAACTCTCGTTAACTATTTAAGGGGCTGCGGTTTTAGACCTGTGAGATTTAATGATGATAGT
1 TTTTAACTCTCACTAACTGTTT-GGGGGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACAGC
41966598 TAGGAGC
65 TAGGAGC
* * * * * * * * ** *
41966605 TTTTAACTCCCGCTAACTATTTGGGAGGTTGTGATATTGAACCTGCGAGCTTTAATAATAATTGT
1 TTTTAACTCTCACTAACTGTTTGGG-GGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACAGC
*
41966670 TGGGAGC
65 TAGGAGC
* * ** ** * * * **
41966677 TTTTAACTCTCGCTAACTATTTGAGGGACTACGATTTT-AATCTCGTGAGGTTTAATAATGACA-
1 TTTTAACTCTCACTAACTGTTTG-GGGGTTGTGGTTTTAAACCT-GCGAGCCTTAATAATGACAG
* *
41966740 TTTGAGAGC
64 CTAG-GAGC
* * * *** * * *
41966749 TTTTAAATCTCACTAATTGTTTGGGGGCTGCAATTTTAAACCTGCAAGCCTTAATGATGATAGCT
1 TTTTAACTCTCACTAACTGTTTGGGGGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACAGCT
41966814 AGGAGC
66 AGGAGC
* * *
41966820 TTTTAACTCTCGCTAACTATTTGGGGGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACA-AT
1 TTTTAACTCTCACTAACTGTTTGGGGGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACAGCT
*
41966884 TGAGAGC
66 AG-GAGC
* * * * *
41966891 TTTTAACTCTCACTAATTGTTTGGGTGGTTGTGGTTTTAAACTTACGAGTCTGAATGAA-GACAG
1 TTTTAACTCTCACTAACTGTTTGGG-GGTTGTGGTTTTAAACCTGCGAGCCTTAAT-AATGACAG
*
41966955 CTAGGAGT
64 CTAGGAGC
* * * * * * **
41966963 TTTTAACTCTCGCTAAATATTTAAGGGGTTGTGGTATTGAACCTGCGAGCCTTAATAATGGTAGC
1 TTTTAACTCTCACTAACTGTTT-GGGGGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACAGC
41967028 T-GGAAGC
65 TAGG-AGC
41967035 TTTTAACTCTCACTAACTGTTTGGG
1 TTTTAACTCTCACTAACTGTTTGGG
41967060 TTTTTTATGA
Statistics
Matches: 627, Mismatches: 169, Indels: 39
0.75 0.20 0.05
Matches are distributed among these distances:
70 2 0.00
71 123 0.20
72 491 0.78
73 11 0.02
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (71 bp):
TTTTAACTCTCACTAACTGTTTGGGGGTTGTGGTTTTAAACCTGCGAGCCTTAATAATGACAGCT
AGGAGC
Found at i:41967388 original size:13 final size:13
Alignment explanation
Indices: 41967370--41967397 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41967360 TAAGCAGGTG
41967370 TTGTATTTTTGAC
1 TTGTATTTTTGAC
41967383 TTGTATTTTTGAC
1 TTGTATTTTTGAC
41967396 TT
1 TT
41967398 TAGCTATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (13 bp):
TTGTATTTTTGAC
Found at i:41974498 original size:5 final size:5
Alignment explanation
Indices: 41974488--41974516 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
41974478 TTAAAATTAG
41974488 TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATA
41974517 ACTCAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:41975086 original size:22 final size:22
Alignment explanation
Indices: 41975060--41975106 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
41975050 TTTATATTAA
41975060 ATTATTTTATGATGATTGATTT
1 ATTATTTTATGATGATTGATTT
41975082 ATTATTTTATGATGATTGATTT
1 ATTATTTTATGATGATTGATTT
41975104 ATT
1 ATT
41975107 GCGCTCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.60
Consensus pattern (22 bp):
ATTATTTTATGATGATTGATTT
Found at i:41975970 original size:10 final size:9
Alignment explanation
Indices: 41975935--41975972 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
41975925 TTTAGATTAA
41975935 AAATTAATT
1 AAATTAATT
41975944 -AATTAAGTT
1 AAATTAA-TT
41975953 AAATTAATT
1 AAATTAATT
41975962 AAGATTAATT
1 AA-ATTAATT
41975972 A
1 A
41975973 GTTTAATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 6 0.23
9 6 0.23
10 14 0.54
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (9 bp):
AAATTAATT
Found at i:41975971 original size:14 final size:14
Alignment explanation
Indices: 41975937--41975972 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
41975927 TAGATTAAAA
41975937 ATTAATTAATTAAG
1 ATTAATTAATTAAG
41975951 -TTAAATTAATTAAG
1 ATT-AATTAATTAAG
41975965 ATTAATTA
1 ATTAATTA
41975973 GTTTAATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.10
14 16 0.80
15 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (14 bp):
ATTAATTAATTAAG
Found at i:41979846 original size:11 final size:13
Alignment explanation
Indices: 41979822--41979853 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
41979812 TAGTTTATTA
41979822 ATATTTTAATATG
1 ATATTTTAATATG
41979835 AT-TTTTAA-ATG
1 ATATTTTAATATG
41979846 ATATTTTA
1 ATATTTTA
41979854 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:41982537 original size:20 final size:20
Alignment explanation
Indices: 41982514--41982560 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
41982504 TGATTAAATG
41982514 ATTTAAAATATGTTTAATTC
1 ATTTAAAATATGTTTAATTC
41982534 ATTTAAAATATGTTTAATTC
1 ATTTAAAATATGTTTAATTC
41982554 ATTTAAA
1 ATTTAAA
41982561 TATTAAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (20 bp):
ATTTAAAATATGTTTAATTC
Found at i:41986412 original size:5 final size:5
Alignment explanation
Indices: 41986402--41986439 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
41986392 AAAACTCATA
*
41986402 AAAAT AAAAT AAAAT AAAAT ACAAT AAAAT AAATAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AA
41986440 CTAGTCAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:41988021 original size:42 final size:42
Alignment explanation
Indices: 41987932--41988072 Score: 212
Period size: 42 Copynumber: 3.4 Consensus size: 42
41987922 GATCTCGGTA
* * *
41987932 TCGCACATTTAGTGCCCGTTATTC-ACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
* *
41987973 TCGCACACTTAATGCCTGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
*
41988015 TTGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
*
41988057 TCCCACACTTAGTGCC
1 TCGCACACTTAGTGCC
41988073 ATTCATATAG
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 21 0.24
42 68 0.76
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
Found at i:41995216 original size:42 final size:41
Alignment explanation
Indices: 41995130--41995268 Score: 183
Period size: 42 Copynumber: 3.3 Consensus size: 41
41995120 GATCTCGGTA
* * *
41995130 TCGCACATTTAGTGCCTGTTA-TTCACATCGTCATTTTAGA-T
1 TCGCACACTTAGTGCC-GTTATTTAACATCATCATTTTA-ATT
*
41995171 TCGCACACTTAGTGTCCGTTATTTAACATCATCATTATAATT
1 TCGCACACTTAGTG-CCGTTATTTAACATCATCATTTTAATT
*
41995213 TCGCACACTTAGTGCTCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGC-CGTTATTTAACATCATCATTTTAATT
41995255 TCGCACACTTAGTG
1 TCGCACACTTAGTG
41995269 TCATTCATAT
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
41 19 0.22
42 69 0.78
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (41 bp):
TCGCACACTTAGTGCCGTTATTTAACATCATCATTTTAATT
Found at i:42007603 original size:11 final size:10
Alignment explanation
Indices: 42007582--42007606 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42007572 CTAAATAACC
42007582 AAAAGAAAAA
1 AAAAGAAAAA
42007592 AAAAGAAAAA
1 AAAAGAAAAA
42007602 AAAAG
1 AAAAG
42007607 GTGAAAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:42022992 original size:26 final size:26
Alignment explanation
Indices: 42022956--42023007 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
42022946 AATCGATTGC
42022956 AATACACTCTTAATAAAAAATTCATT
1 AATACACTCTTAATAAAAAATTCATT
42022982 AATACACTCTTAATAAAAAATTCATT
1 AATACACTCTTAATAAAAAATTCATT
42023008 CTCTCCTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (26 bp):
AATACACTCTTAATAAAAAATTCATT
Found at i:42025593 original size:34 final size:34
Alignment explanation
Indices: 42025480--42025603 Score: 124
Period size: 34 Copynumber: 3.6 Consensus size: 34
42025470 ACATATACGA
* * * *
42025480 ATATCATATCAGAATATCACATTACCAAAAACAT
1 ATATCATATCAGAATGTCATATTTCCATAAACAT
* *
42025514 ATATCAAACCAGAATGTCATATTTCCATAAACAT
1 ATATCATATCAGAATGTCATATTTCCATAAACAT
* * * * *
42025548 A-AACTAGATCAGAGTGTCATATTTTCATAAATAT
1 ATATC-ATATCAGAATGTCATATTTCCATAAACAT
*
42025582 ATATCATATCAGAATGTTATAT
1 ATATCATATCAGAATGTCATAT
42025604 CAGATCAAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
33 2 0.03
34 68 0.94
35 2 0.03
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.32
Consensus pattern (34 bp):
ATATCATATCAGAATGTCATATTTCCATAAACAT
Found at i:42029896 original size:22 final size:23
Alignment explanation
Indices: 42029868--42029914 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
42029858 TAACGGTGTT
*
42029868 AATAACTAGA-TCCAAAAAATAA
1 AATAACTAAATTCCAAAAAATAA
*
42029890 AATAACTAAATTCCTAAAAATAA
1 AATAACTAAATTCCAAAAAATAA
42029913 AA
1 AA
42029915 ATATAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.21
Consensus pattern (23 bp):
AATAACTAAATTCCAAAAAATAA
Found at i:42029917 original size:29 final size:28
Alignment explanation
Indices: 42029882--42029940 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
42029872 ACTAGATCCA
42029882 AAAAATAAAATAACTAAATTCCTAAAAAT
1 AAAAATAAAATAACTAAATTCC-AAAAAT
* * * *
42029911 AAAAATATAATCATTAAATTCCAAATAT
1 AAAAATAAAATAACTAAATTCCAAAAAT
42029939 AA
1 AA
42029941 GAATTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (28 bp):
AAAAATAAAATAACTAAATTCCAAAAAT
Found at i:42036296 original size:39 final size:39
Alignment explanation
Indices: 42036246--42036333 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
42036236 GTGTTACAAT
* * *
42036246 TTATATTAAAAAATTAC-CATAAATGTAATAAATA-TTTTA
1 TTATATTAAAAAA-CACAAATAAATATAATAAA-AGTTTTA
42036285 TTATATTAAAAAACACAAATAAATATAATAAAAGTTTTA
1 TTATATTAAAAAACACAAATAAATATAATAAAAGTTTTA
*
42036324 TTGTATTAAA
1 TTATATTAAA
42036334 TATAATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 3 0.07
39 40 0.93
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (39 bp):
TTATATTAAAAAACACAAATAAATATAATAAAAGTTTTA
Found at i:42040941 original size:21 final size:21
Alignment explanation
Indices: 42040911--42040950 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42040901 TTAATGTTAA
42040911 TATTAATATAAAATTTAAATT
1 TATTAATATAAAATTTAAATT
* *
42040932 TATTACTATAAATTTTAAA
1 TATTAATATAAAATTTAAA
42040951 AATTTTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTAATATAAAATTTAAATT
Found at i:42041020 original size:21 final size:20
Alignment explanation
Indices: 42040964--42041012 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
42040954 TTTATGTATT
**
42040964 TTTATATATTTTTAAATTTA
1 TTTATATATTTTTAAAAATA
*
42040984 TTAATATATTTTTTAAAAATA
1 TTTATATA-TTTTTAAAAATA
42041005 TTTATATA
1 TTTATATA
42041013 CTTATTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATATATTTTTAAAAATA
Found at i:42041026 original size:50 final size:50
Alignment explanation
Indices: 42040924--42041027 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 50
42040914 TAATATAAAA
* * *
42040924 TTTAAATTTATTACTATAAATTTTAAAAATTTTATGTATTTTTATATATT
1 TTTAAATTTATTAATATAAATTTTAAAAATTTTATATATTATTATATATT
** *
42040974 TTTAAATTTATTAATATATTTTTTAAAAATATTTATATACTTATTA-ATTTT
1 TTTAAATTTATTAATATAAATTTTAAAAAT-TTTATATA-TTATTATATATT
42041025 TTT
1 TTT
42041028 TAGAATTGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 27 0.59
51 14 0.30
52 5 0.11
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (50 bp):
TTTAAATTTATTAATATAAATTTTAAAAATTTTATATATTATTATATATT
Found at i:42042187 original size:98 final size:98
Alignment explanation
Indices: 42042013--42042209 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
42042003 GTACAATAAA
*
42042013 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
42042078 CCTCTAGAATCCCAAACTCGGAATATTTCTTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
* *
42042111 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACTCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
42042176 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
42042209 A
1 A
42042210 TTATTTTTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:42042909 original size:24 final size:26
Alignment explanation
Indices: 42042880--42042928 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
42042870 ATATAAATAT
42042880 GAAAATATTC-ATT-AAAAAATATAA
1 GAAAATATTCGATTAAAAAAATATAA
*
42042904 GAAAATATTCGTTTAAAAAAATATA
1 GAAAATATTCGATTAAAAAAATATA
42042929 TACATGTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 2 0.09
26 10 0.45
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (26 bp):
GAAAATATTCGATTAAAAAAATATAA
Found at i:42043356 original size:13 final size:13
Alignment explanation
Indices: 42043338--42043363 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42043328 AATAAAAGGG
42043338 TAAAAAATAAAAA
1 TAAAAAATAAAAA
42043351 TAAAAAATAAAAA
1 TAAAAAATAAAAA
42043364 AACTTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:42043749 original size:19 final size:19
Alignment explanation
Indices: 42043697--42043845 Score: 239
Period size: 19 Copynumber: 7.8 Consensus size: 19
42043687 AATCATATAT
*
42043697 TCTAATATTGCATATCATA
1 TCTAAGATTGCATATCATA
42043716 TCTAAGATT--ATATCATA
1 TCTAAGATTGCATATCATA
42043733 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
42043752 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
42043771 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
42043792 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
42043811 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
42043830 TATAAGATTGCATATC
1 TCTAAGATTGCATATC
42043846 CTCAAAAATT
Statistics
Matches: 122, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
17 17 0.14
19 86 0.70
21 19 0.16
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:42043792 original size:59 final size:59
Alignment explanation
Indices: 42043690--42043844 Score: 241
Period size: 59 Copynumber: 2.7 Consensus size: 59
42043680 ATTACAAAAT
*
42043690 CATAT-AT-TCTAATATTGCATATCATATCTAAGA-T---TATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTGCATATATCATATCTAAGATTG
42043743 CATATCATATCTAAGATTGCATATCATATCTAAGATTGCATATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTGCATATATCATATCTAAGATTG
* *
42043802 CATATCATATCTAGGATTGCATATCATATATAAGATTGCATAT
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTGCATAT
42043845 CCTCAAAAAT
Statistics
Matches: 93, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
53 5 0.05
54 2 0.02
55 25 0.27
56 1 0.01
59 60 0.65
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (59 bp):
CATATCATATCTAAGATTGCATATCATATCTAAGATTGCATATATCATATCTAAGATTG
Found at i:42044168 original size:44 final size:43
Alignment explanation
Indices: 42044074--42044615 Score: 328
Period size: 44 Copynumber: 12.6 Consensus size: 43
42044064 TAGTCTACTT
* ***
42044074 CACTGCAACTTCAGGGAGATAAGA-CTA-GATGCGATCTGCT-
1 CACTGCAACTTCAGGGAGATAAGATCTAGGTTTTAATCTGCTC
* * * *
42044114 CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCCC
1 CACTGCAACTTCAGGGAGATAAGATCT-AGGTTTTAATCTGCTC
* * *
42044158 CACTGCAACTTCAAGGAGATAGGAT-TATCGGCTTTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATCTA--GGTTTTAATCTGCTC
* * * * *
42044202 CACTGCAACTTCAGGGAGATAAGA-CTTGCCATCTTCAGTCTGCCC
1 CACTGCAACTTCAGGGAGATAAGATCTAG--GT-TTTAATCTGCTC
* * *
42044247 CACTGCAACTTCA-GGAGGATAAGA-CTTGCTTACTTAGTCTGCTC
1 CACTGCAACTTCAGGGA-GATAAGATCTAGGTT--TTAATCTGCTC
* ***
42044291 CACTGCAACTTCAGGGAGATAAGA-CTA-GATGCGATCTGCT-
1 CACTGCAACTTCAGGGAGATAAGATCTAGGTTTTAATCTGCTC
* * * *
42044331 CTCTGCAAATTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTC
1 CACTGCAACTTCAGGGAGATAAGATCT-AGGTTTTAATCTGCTC
* * *
42044375 CAATGCAACTTCAGGGAGATAGGAT-TATCGGCTTTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATCTA--GGTTTTAATCTGCTC
* ** * *
42044419 CACTGCAACTTCAGGGAGATAAGA-CTTGCGATCTCCAGTCTGCCC
1 CACTGCAACTTCAGGGAGATAAGATCTAG-G-T-TTTAATCTGCTC
* * *
42044464 CACTGCAACTTCA-GGAGGATAAGA-CTTGCTTATTTAGTCTGCTC
1 CACTGCAACTTCAGGGA-GATAAGATCTAG-GT-TTTAATCTGCTC
* * *** *
42044508 CACTGCAACTTCAGGGAGATAAGA-ATA-GATGCGATCTACT-
1 CACTGCAACTTCAGGGAGATAAGATCTAGGTTTTAATCTGCTC
* *** * *
42044548 CTCTGCAACTTCAAAAAGATAAGATTTGAGGTTTTAAT-TCACTC
1 CACTGCAACTTCAGGGAGATAAGATCT-AGGTTTTAATCT-GCTC
42044592 CACTGCAACTTCAGGGAGATAAGA
1 CACTGCAACTTCAGGGAGATAAGA
42044616 CTTGCCATCT
Statistics
Matches: 388, Mismatches: 83, Indels: 58
0.73 0.16 0.11
Matches are distributed among these distances:
40 63 0.16
41 17 0.04
42 9 0.02
43 27 0.07
44 200 0.52
45 72 0.19
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (43 bp):
CACTGCAACTTCAGGGAGATAAGATCTAGGTTTTAATCTGCTC
Found at i:42044292 original size:89 final size:88
Alignment explanation
Indices: 42044021--42044531 Score: 307
Period size: 89 Copynumber: 5.9 Consensus size: 88
42044011 TGCCATCTTC
* * * **
42044021 AGTCTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTTCTTATTT-AGTCTACTTCACTGCAAC
1 AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGC-CATTTCAGTCTGCCCCACTGCAAC
* * * *
42044083 TTCAGGGAGATAAGACTAG-ATGC-G
63 TTCAGGGAGATAAGACTTGCTTACTT
* * * * * * *
42044107 A-TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAG--GTTTTAATCCGCCCCACTGCAACT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCCATTTCAGTCTGCCCCACTGCAACT
* * *
42044168 TCAAGGAGATAGGATTATCGGC-T--TT
64 TCAGGGAGATAAGACT-T--GCTTACTT
*
42044193 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCAT-TTCAGTCTGCCCCACTGCAACTT
42044258 CA-GGAGGATAAGACTTGCTTACTT
65 CAGGGA-GATAAGACTTGCTTACTT
* * * * *
42044282 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG--A-TGC-GATCTG-CTCTCTGCAAATT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATTTCAG-TCTGCCCCACTGCAACTT
* * *
42044342 CAGAGAGATAAGATCTGAGGTT--TT
65 CAGGGAGATAAGA-CT-TGCTTACTT
* * * * * * * *
42044366 AATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGGC-TTT-AATCTGCTCCACTGCAACT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT-T-GCCATTTCAGTCTGCCCCACTGCAACT
* *
42044429 TCAGGGAGATAAGACTTGC-GATCTCC
64 TCAGGGAGATAAGACTTGCTTA-CT-T
* * *
42044455 AGTCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTATTT-AGTCTGCTCCACTGCAACT
1 AGTCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGC-CATTTCAGTCTGCCCCACTGCAACT
42044518 TCAGGGAGATAAGA
64 TCAGGGAGATAAGA
42044532 ATAGATGCGA
Statistics
Matches: 329, Mismatches: 59, Indels: 71
0.72 0.13 0.15
Matches are distributed among these distances:
83 3 0.01
84 98 0.30
85 19 0.06
86 10 0.03
87 19 0.06
88 54 0.16
89 126 0.38
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (88 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATTTCAGTCTGCCCCACTGCAACTTC
AGGGAGATAAGACTTGCTTACTT
Found at i:42044652 original size:44 final size:44
Alignment explanation
Indices: 42044589--42044795 Score: 111
Period size: 44 Copynumber: 4.7 Consensus size: 44
42044579 TTTTAATTCA
**
42044589 CTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAACCTT
1 CTCCACTGCTGCTT-AGGGAGATAAGACTTGCCATCTTCAACCTT
* * * *** *
42044634 CTCCGCTGCTGCTTAGGGAGACAAGGCTTAG-TGGCTTAAATCTGCTT
1 CTCCACTGCTGCTTAGGGAGATAAGACTT-GCCATCTTCAA-C--CTT
* * * * *
42044681 C-CCACT-AT-CTT-GGAAAGATAAGA-TTCGCCATCTTCGATCTG
1 CTCCACTGCTGCTTAGG-GAGATAAGACTT-GCCATCTTCAACCTT
* * * *
42044722 CTCCACTACTGCTTAGGGAGATAAGATTTACAATCTTCAACCTT
1 CTCCACTGCTGCTTAGGGAGATAAGACTTGCCATCTTCAACCTT
* * * *
42044766 CTCCGCTGCTGCTCAGGGAGACAAGGCTTG
1 CTCCACTGCTGCTTAGGGAGATAAGACTTG
42044796 GTGGCTTAAA
Statistics
Matches: 115, Mismatches: 36, Indels: 23
0.66 0.21 0.13
Matches are distributed among these distances:
41 3 0.03
42 5 0.04
43 6 0.05
44 75 0.65
45 18 0.16
46 4 0.03
47 4 0.03
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (44 bp):
CTCCACTGCTGCTTAGGGAGATAAGACTTGCCATCTTCAACCTT
Found at i:42044654 original size:217 final size:217
Alignment explanation
Indices: 42044011--42044612 Score: 1033
Period size: 217 Copynumber: 2.8 Consensus size: 217
42044001 TAGGAATTAG
* * * *
42044011 TGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTTCTTATTTAGTCTACTTCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTGCTCCA
42044076 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
* * *
42044141 AAGGTTTTAATCCGCCCCACTGCAACTTCAAGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
131 GAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
42044206 GCAACTTCAGGGAGATAAGACT
196 GCAACTTCAGGGAGATAAGACT
*
42044228 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTGCTCCA
*
42044293 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAAATTCAGAGAGATAAGATCT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
*
42044358 GAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
131 GAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
42044423 GCAACTTCAGGGAGATAAGACT
196 GCAACTTCAGGGAGATAAGACT
* *
42044445 TGCGATCTCCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTGCTCCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTGCTCCA
* * * * *
42044510 CTGCAACTTCAGGGAGATAAGAATAGATGCGATCTACTCTCTGCAACTTCAAAAAGATAAGATTT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
* *
42044575 GAGGTTTTAATTCACTCCACTGCAACTTCAGGGAGATA
131 GAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
42044613 AGACTTGCCA
Statistics
Matches: 363, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 363 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTGCTCCA
CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
GAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
GCAACTTCAGGGAGATAAGACT
Found at i:42044742 original size:132 final size:132
Alignment explanation
Indices: 42044604--42045256 Score: 1085
Period size: 132 Copynumber: 4.9 Consensus size: 132
42044594 CTGCAACTTC
* * * *
42044604 AGGGAGATAAGACTTGCCATCTTCAACCTTCTCCGCTGCTGCTTAGGGAGACAAGGCTTAGTGGC
1 AGGGAGATAAGACTTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
*
42044669 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
42044734 TT
131 TT
*
42044736 AGGGAGATAAGATTTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGACTTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
*
42044801 TTAAATCTGCTTTCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
42044866 TT
131 TT
* * * *
42044868 AGGGAGATAAGA-TCTATAATCTTCAACCTTCTCTGCTGCTGCTGAGAGAGACAAGGCTTGGTGG
1 AGGGAGATAAGACT-TACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGG
* *
42044932 CTTAAATCTGCTTCCTACTATCTTGGAAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTG
65 CTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTG
*
42044997 TTT
130 CTT
* * * *
42045000 AGGGAGATAAGA-TCTACAATCTTTAACCTTCTCCGCTACTGCTCAGAGAGACAATGCTTGGTGG
1 AGGGAGATAAGACT-TACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGG
**
42045064 CTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCATCGTCTTCGATCTGCTCCACTACTG
65 CTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTG
42045129 CTT
130 CTT
*
42045132 AGGGAGATAAGATTTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGACTTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
42045197 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
42045257 GTCAATGCAG
Statistics
Matches: 487, Mismatches: 32, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 485 1.00
133 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (132 bp):
AGGGAGATAAGACTTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
TT
Found at i:42045140 original size:44 final size:44
Alignment explanation
Indices: 42044696--42045256 Score: 162
Period size: 44 Copynumber: 12.8 Consensus size: 44
42044686 TATCTTGGAA
* * *
42044696 AGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
42044740 AGATAAGATT--TACAATCTTCAACCTTCTCCGCTGCTGCTCAGGG
1 AGATAAGATTCGT-C-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
42044784 AGACAAGGCTTGGT-GGCTTAAATCTGCTTTCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGTCGTCTTCAATCTGC--TCCACTACTGCTTAGG-G
* *
42044828 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * ** * * *
42044872 AGATAAGA-TCTATAATCTTCAACCTTCTCTGCTGCTGCTGAGAG
1 AGATAAGATTC-GTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
42044916 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCTACTA-T-CTT-GGAA
1 AGATAA-GATTCGTCGTCTTCAATCTGC-TCC-ACTACTGCTTAGG-G
* *
42044960 AGATAAGATTCG-CTGTCTTCGATCTGCTCCACTACTGTTTAGGG
1 AGATAAGATTCGTC-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
42045004 AGATAAGA-TC-TACAATCTTTAACCTTCTCCGCTACTGCTCAGAG
1 AGATAAGATTCGT-C-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
42045048 AGACAATGCTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
42045092 AGATAAGATTCATCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
42045136 AGATAAGATT--TACAATCTTCAACCTTCTCCGCTGCTGCTCAGGG
1 AGATAAGATTCGT-C-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
42045180 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
42045224 AGATAAGATTCGCCGTCTTCGATCTGCTCCACT
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACT
42045257 GTCAATGCAG
Statistics
Matches: 357, Mismatches: 116, Indels: 90
0.63 0.21 0.16
Matches are distributed among these distances:
42 23 0.06
43 36 0.10
44 254 0.71
45 23 0.06
46 18 0.05
47 3 0.01
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (44 bp):
AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:42046542 original size:11 final size:10
Alignment explanation
Indices: 42046522--42046546 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42046512 TTCACTTTCA
42046522 TTTTTGTTTT
1 TTTTTGTTTT
42046532 TTTTTGTTTT
1 TTTTTGTTTT
42046542 TTTTT
1 TTTTT
42046547 AATCTGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:42047274 original size:180 final size:180
Alignment explanation
Indices: 42046972--42047324 Score: 652
Period size: 180 Copynumber: 2.0 Consensus size: 180
42046962 TGCACGTTCC
*
42046972 CTTCAGGCCACAATCTCCATTATCCCCTTATGAAGTAAGATTTCATTCCTGTTCTACCATCCTCA
1 CTTCAGGCCACAATCTCCATTATCCCCTCATGAAGTAAGATTTCATTCCTGTTCTACCATCCTCA
*
42047037 ACAAGTCTGAAAATAGGCTACAATCTATGTCATCTTTAAAGTCATGAGATCCCTCTAAACACAGA
66 ACAAGTCTGAAAATAGGCTACAATCTATGTCATCTTTAAAGCCATGAGATCCCTCTAAACACAGA
* *
42047102 TCTCACTCAAAAGGAACTTCTGAGTTCGTAACAACATCACTCAAAAGGAA
131 TCCCACTCAAAAGGAACTTCTGAGTCCGTAACAACATCACTCAAAAGGAA
*
42047152 CTTCAGGCCACAATCTCCATTGTCCCCTCATGAAGTAAGATTTCATTCCTGTTCTACCATCCTCA
1 CTTCAGGCCACAATCTCCATTATCCCCTCATGAAGTAAGATTTCATTCCTGTTCTACCATCCTCA
42047217 ACAAGTCTGAAAATAGGCTACAATCTATGTCATCTTTAAAGCCATGAGATCCCTCTAAACACAGA
66 ACAAGTCTGAAAATAGGCTACAATCTATGTCATCTTTAAAGCCATGAGATCCCTCTAAACACAGA
*
42047282 TCCCACTCAAAAGGAACTTCTGAGTCCGTAACAGCATCACTCA
131 TCCCACTCAAAAGGAACTTCTGAGTCCGTAACAACATCACTCA
42047325 TGTCATTGAT
Statistics
Matches: 167, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
180 167 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (180 bp):
CTTCAGGCCACAATCTCCATTATCCCCTCATGAAGTAAGATTTCATTCCTGTTCTACCATCCTCA
ACAAGTCTGAAAATAGGCTACAATCTATGTCATCTTTAAAGCCATGAGATCCCTCTAAACACAGA
TCCCACTCAAAAGGAACTTCTGAGTCCGTAACAACATCACTCAAAAGGAA
Found at i:42051394 original size:98 final size:98
Alignment explanation
Indices: 42051220--42051416 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
42051210 GTACAATAAA
* * *
42051220 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACATCCAATTCGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
42051285 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
*
42051318 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
42051383 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
42051416 A
1 A
42051417 TTATTTTTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:42052115 original size:25 final size:25
Alignment explanation
Indices: 42052078--42052133 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
42052068 ATATACATAT
42052078 AAATAT-GAAAATATTC-ATTAAAA
1 AAATATAGAAAATATTCGATTAAAA
*
42052101 AAATATAGAAAAATATTCGTTTAAAA
1 AAATATAG-AAAATATTCGATTAAAA
42052127 AAATATA
1 AAATATA
42052134 TACATGTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 6 0.21
24 1 0.03
25 9 0.31
26 13 0.45
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (25 bp):
AAATATAGAAAATATTCGATTAAAA
Found at i:42052561 original size:13 final size:13
Alignment explanation
Indices: 42052543--42052568 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42052533 AATAAAAGGG
42052543 TAAAAAATAAAAA
1 TAAAAAATAAAAA
42052556 TAAAAAATAAAAA
1 TAAAAAATAAAAA
42052569 AACTTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:42052932 original size:19 final size:19
Alignment explanation
Indices: 42052899--42053009 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
42052889 AATCATATAT
*
42052899 TCTAATATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
42052918 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
42052937 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
42052956 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
42052975 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
42052994 TATAAGATTGCATATC
1 TCTAAGATTGCATATC
42053010 CTCAAAAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 84 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:42052947 original size:38 final size:38
Alignment explanation
Indices: 42052876--42053009 Score: 169
Period size: 38 Copynumber: 3.4 Consensus size: 38
42052866 AAATTAAATC
* *
42052876 TCTAAGATTACAAAATCATATATTCTAATATTGCATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCTAAGATTGCATATCATA
*
42052918 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
42052956 TCTAAGATTGCATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
42052994 TATAAGATTGCATATC
1 TCTAAGATTACATATC
42053010 CTCAAAAATT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
38 68 0.80
39 3 0.04
41 4 0.05
42 10 0.12
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:42053610 original size:80 final size:82
Alignment explanation
Indices: 42053496--42053663 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 82
42053486 GTTATGTATT
* * * *
42053496 TATATTAAAAATAGGACCCCACTTAATTATATTTAAAATTTAACAAAAAAATGATACTC-ACTTT
1 TATATTAAAAATAGGACCCCACTTAATCATATTTAAAACTTAACAAAAAAATAAGA-TCAACTTT
*
42053560 GAATATAATTAAAA-ATA
65 AAATATAATTAAAATATA
* ** ***
42053577 TATATTACAAATAGGA-TTCACTTAATCATATTTAAAACTTAATTTAAAAATAAGATCAACTTTA
1 TATATTAAAAATAGGACCCCACTTAATCATATTTAAAACTTAACAAAAAAATAAGATCAACTTTA
42053641 AATATAATTAAAATATA
66 AATATAATTAAAATATA
42053658 TATATT
1 TATATT
42053664 TTGGAACTCA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
79 2 0.03
80 48 0.65
81 24 0.32
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.36
Consensus pattern (82 bp):
TATATTAAAAATAGGACCCCACTTAATCATATTTAAAACTTAACAAAAAAATAAGATCAACTTTA
AATATAATTAAAATATA
Found at i:42072460 original size:21 final size:20
Alignment explanation
Indices: 42072436--42072480 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
42072426 TAACTTAAGG
42072436 GAAACAATCTTAAAATCGAGT
1 GAAACAAT-TTAAAATCGAGT
* * *
42072457 GAAACAGTTTTAAATCGATT
1 GAAACAATTTAAAATCGAGT
42072477 GAAA
1 GAAA
42072481 ATTTTTAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (20 bp):
GAAACAATTTAAAATCGAGT
Found at i:42073972 original size:24 final size:25
Alignment explanation
Indices: 42073930--42073978 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
42073920 AATTTTTTAA
42073930 TTATTTTTTAAAA-AGTTTTAAATT
1 TTATTTTTTAAAATAGTTTTAAATT
**
42073954 TTATTTTTTAAAATTTTTTTAAATT
1 TTATTTTTTAAAATAGTTTTAAATT
42073979 GTAAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TTATTTTTTAAAATAGTTTTAAATT
Found at i:42075767 original size:18 final size:18
Alignment explanation
Indices: 42075744--42075787 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
42075734 ATGCTAGATG
* *
42075744 TGTATCCTAGCCCTTTTA
1 TGTATCCTAACCCTTATA
42075762 TGTATCCTAACCCTTATA
1 TGTATCCTAACCCTTATA
*
42075780 TGTTTCCT
1 TGTATCCT
42075788 TTTTCTAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:42077294 original size:97 final size:96
Alignment explanation
Indices: 42077145--42077425 Score: 361
Period size: 97 Copynumber: 2.9 Consensus size: 96
42077135 AGTAACCCTA
* * *
42077145 AACCCCAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTT-ACTTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAAT
*
42077210 TTTTTAAAAATTTATAATTAATTTACTCAAGT
65 TTTTAAAAAATTTATAATTAATTTACTCAAGT
* * * *
42077242 AACCCTAAACCCTAATTTATTTAATTTTTTTCATAAAAACCCTTAACTCTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTT-ACTTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAAT
* *
42077307 TTTTAAAAAAATT-TAATTAAATTACTCAAGT
65 TTTTAAAAAATTTATAATTAATTTACTCAAGT
* * ** * *
42077338 AACCCTAAACCCTAATTTAATTGCTTTTTTCTTAAAAAACAATAAACACGAAA-CCTAATCCAA-
1 AACCCTAAACCCTAATTTATTTACTTTTTTCTT-AAAAACCCTAAACACTAAACCCTAATCTAAT
*
42077401 TTTTGAAAAATTTATAATTAATTTA
65 TTTTAAAAAATTTATAATTAATTTA
42077426 ATTGACAAAC
Statistics
Matches: 159, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
94 11 0.07
95 27 0.17
96 52 0.33
97 69 0.43
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (96 bp):
AACCCTAAACCCTAATTTATTTACTTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATT
TTTAAAAAATTTATAATTAATTTACTCAAGT
Found at i:42079684 original size:20 final size:19
Alignment explanation
Indices: 42079647--42079685 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
42079637 TTTTTGGGTG
*
42079647 ATTTAATAGAGAAGTAAAA
1 ATTTAATAGAGAACTAAAA
*
42079666 ATTTAAATAGAGGACTAAAA
1 ATTT-AATAGAGAACTAAAA
42079686 TGATTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (19 bp):
ATTTAATAGAGAACTAAAA
Found at i:42080745 original size:23 final size:24
Alignment explanation
Indices: 42080690--42080745 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
42080680 TTGATTTGTA
* *
42080690 ATATATCATTATTTCAAATTTATC
1 ATATATTATTATTTCAAACTTATC
*
42080714 ATGTATTATTATTT-AAACTTATC
1 ATATATTATTATTTCAAACTTATC
*
42080737 ATATTTTAT
1 ATATATTAT
42080746 GTAAATTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.54
Consensus pattern (24 bp):
ATATATTATTATTTCAAACTTATC
Found at i:42104654 original size:17 final size:17
Alignment explanation
Indices: 42104632--42104667 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
42104622 TTTATTTACG
42104632 TTTCATTATTGA-TATTA
1 TTTCATTATT-ATTATTA
42104649 TTTCATTATTATTATTA
1 TTTCATTATTATTATTA
42104666 TT
1 TT
42104668 GTTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.06
17 17 0.94
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTCATTATTATTATTA
Found at i:42117040 original size:50 final size:50
Alignment explanation
Indices: 42116915--42117352 Score: 325
Period size: 50 Copynumber: 8.9 Consensus size: 50
42116905 AAACCATAGT
* * * * * *
42116915 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT--TTGGCA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACA
* ** * * * *
42116963 ATGCAGCGGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCGACA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACA
* * * * **
42117013 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT--CTGGTA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACA
* *** * * * * *
42117061 ATGCAACGGAACATATTGAAGCTACAACAGCGAATCTCACTTCCCCGACA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACA
* * * * **
42117111 TTGCAATTTAAAAGATCGAAGCCACAAC-GACGAATCTTACTT--TTGGGGA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAG-CGAATCTTACTTCCCT-GACA
** * * *
42117160 -TGCAGCGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACA
* * * *
42117209 TTGCAGTTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACA
** * * *
42117259 TTGCAGCGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACA
* * * * *
42117309 TTGCAGTTTAAAGGATCGAAGCCACAACGGCGAATCTTATTTCC
1 TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCC
42117353 TCGGCAAGAC
Statistics
Matches: 289, Mismatches: 91, Indels: 18
0.73 0.23 0.05
Matches are distributed among these distances:
48 98 0.34
49 6 0.02
50 185 0.64
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (50 bp):
TTGCAGTTGAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACA
Found at i:42117084 original size:98 final size:98
Alignment explanation
Indices: 42116915--42117347 Score: 659
Period size: 98 Copynumber: 4.4 Consensus size: 98
42116905 AAACCATAGT
*
42116915 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTTGGCAATGCAGCGGAACAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCAATGCAGCGGAACAGATT
42116980 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * *
42117013 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGTAATGCAACGGAACATATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCAATGCAGCGGAACAGATT
42117078 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * **
42117111 TTGCAATTTAAAAGATCGAAGCCACAACGACGAATCTTACTTTTGGGGATGCAGCGGAACAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCAATGCAGCGGAACAGATT
* * *
42117176 GAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * * * *
42117209 TTGCAGTTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCATTGCAGCGGAACAGA
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT--CTGGCAATGCAGCGGAACAGA
* * *
42117274 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
64 TTGAAGCTACAACAGCGAATCTCACTTCCCCGACA
* *
42117309 TTGCAGTTTAAAGGATCGAAGCCACAACGGCGAATCTTA
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTA
42117348 TTTCCTCGGC
Statistics
Matches: 308, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
98 221 0.72
100 87 0.28
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (98 bp):
TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCAATGCAGCGGAACAGATT
GAAGCTACAACAGCGAATCTCACTTCCCCGACA
Found at i:42118927 original size:17 final size:17
Alignment explanation
Indices: 42118895--42118939 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
42118885 TTTATTTACG
42118895 TTTCATTATTGA-TATTA
1 TTTCATTATT-ATTATTA
*
42118912 TTTCATTATTATTATTG
1 TTTCATTATTATTATTA
42118929 TTT--TTATTATT
1 TTTCATTATTATT
42118940 TATTCTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 8 0.31
16 1 0.04
17 17 0.65
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (17 bp):
TTTCATTATTATTATTA
Found at i:42124708 original size:27 final size:26
Alignment explanation
Indices: 42124667--42124780 Score: 84
Period size: 27 Copynumber: 4.2 Consensus size: 26
42124657 AAAAGGCAAC
* *
42124667 AAAGAATATTCTTTGTGGTGAACTCTG
1 AAAGAATA-ACTTTGTGGTGAACTCTA
* * *
42124694 AAAGAATAACTTTTGCGGTAAATTCTA
1 AAAGAATAAC-TTTGTGGTGAACTCTA
* * *
42124721 AAAGAATAAACTCTATGGCGAACTCTA
1 AAAGAAT-AACTTTGTGGTGAACTCTA
* ***
42124748 AAAGAATAGCCTTTGTCACGAACTCTA
1 AAAGAATA-ACTTTGTGGTGAACTCTA
42124775 AAAGAA
1 AAAGAA
42124781 CTCTAAAAGA
Statistics
Matches: 68, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
26 2 0.03
27 63 0.93
28 3 0.04
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (26 bp):
AAAGAATAACTTTGTGGTGAACTCTA
Found at i:42124798 original size:14 final size:11
Alignment explanation
Indices: 42124767--42124791 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42124757 CCTTTGTCAC
42124767 GAACTCTAAAA
1 GAACTCTAAAA
42124778 GAACTCTAAAA
1 GAACTCTAAAA
42124789 GAA
1 GAA
42124792 TAACTCTTGT
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:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (11 bp):
GAACTCTAAAA
Found at i:42128676 original size:18 final size:19
Alignment explanation
Indices: 42128653--42128693 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
42128643 CAATTTCACA
*
42128653 AAATAAATATTACTT-ATT
1 AAATAAATATTAATTAATT
*
42128671 AAATAAATTTTAATTAATT
1 AAATAAATATTAATTAATT
42128690 AAAT
1 AAAT
42128694 TTTCAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATAAATATTAATTAATT
Found at i:42128703 original size:16 final size:16
Alignment explanation
Indices: 42128668--42128712 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
42128658 AATATTACTT
42128668 ATTAAATAAATTTT-A
1 ATTAAATAAATTTTCA
*
42128683 ATTAATTAAATTTTCA
1 ATTAAATAAATTTTCA
42128699 ATTAAAT-AATTTTC
1 ATTAAATAAATTTTC
42128713 TCAATCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAATAAATTTTCA
Found at i:42142068 original size:24 final size:24
Alignment explanation
Indices: 42142019--42142065 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
42142009 TATCAATTTA
*
42142019 TTTATTACATAAATTATTATTAAT
1 TTTATTAAATAAATTATTATTAAT
42142043 TTTATTTAAATAAA-TATTGATTA
1 TTTA-TTAAATAAATTATT-ATTA
42142066 TTTAATTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTATTAAATAAATTATTATTAAT
Found at i:42143586 original size:22 final size:22
Alignment explanation
Indices: 42143543--42143613 Score: 83
Period size: 22 Copynumber: 3.1 Consensus size: 22
42143533 TTCACAAACT
42143543 AATTCTCTCTCAAATTTTCTCTCA
1 AATTC-CTCTCAAA-TTTCTCTCA
*
42143567 ATTTCCTCTC-AATTTGCTCTCA
1 AATTCCTCTCAAATTT-CTCTCA
42143589 AATTCCT-TCCAAATTTCTCTCA
1 AATTCCTCT-CAAATTTCTCTCA
42143611 AAT
1 AAT
42143614 CCATATTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.10
22 24 0.57
23 10 0.24
24 4 0.10
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.44
Consensus pattern (22 bp):
AATTCCTCTCAAATTTCTCTCA
Found at i:42143612 original size:11 final size:11
Alignment explanation
Indices: 42143543--42143613 Score: 67
Period size: 11 Copynumber: 6.3 Consensus size: 11
42143533 TTCACAAACT
42143543 AATTCTCTCTCA
1 AATT-TCTCTCA
42143555 AATTTTCTCTC-
1 AA-TTTCTCTCA
42143566 AATTTCCTCTC-
1 AATTT-CTCTCA
42143577 AATTTGCTCTCA
1 AATTT-CTCTCA
*
42143589 AATTCCT-TCCA
1 AATTTCTCT-CA
42143600 AATTTCTCTCA
1 AATTTCTCTCA
42143611 AAT
1 AAT
42143614 CCATATTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
10 4 0.08
11 32 0.63
12 13 0.25
13 2 0.04
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.44
Consensus pattern (11 bp):
AATTTCTCTCA
Found at i:42143638 original size:51 final size:51
Alignment explanation
Indices: 42143573--42143672 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
42143563 CTCAATTTCC
42143573 TCTCAATTTGCTCTCAAATTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * * * * *
42143624 TCTCAATTTTCTCTCAAGTTCCTCTTAGATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTT
42143673 TTAAATATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.03, T:0.45
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:42145489 original size:18 final size:18
Alignment explanation
Indices: 42145462--42145501 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42145452 CAGGTGCGTT
* *
42145462 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
42145480 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
42145498 TCCT
1 TCCT
42145502 TTTCCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:42145782 original size:21 final size:21
Alignment explanation
Indices: 42145758--42145805 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
42145748 GATGCCCTAT
*
42145758 CGGAAGAACCAGAATCC-CCGC
1 CGGAAGAACCACAA-CCGCCGC
*
42145779 CGGAGGAACCACAACCGCCGC
1 CGGAAGAACCACAACCGCCGC
42145800 CGGAAG
1 CGGAAG
42145806 CTGAAGGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.31, C:0.38, G:0.29, T:0.02
Consensus pattern (21 bp):
CGGAAGAACCACAACCGCCGC
Found at i:42146083 original size:43 final size:42
Alignment explanation
Indices: 42146036--42146396 Score: 256
Period size: 43 Copynumber: 8.0 Consensus size: 42
42146026 TTTAATTGGC
* *
42146036 AAACCCCAACCCTTAACTTAAAAATCATAACACCTTAACCTAA
1 AAACCCCAACCCTTAACTTAAAAACCCTAAC-CCTTAACCTAA
42146079 AAACCCTAACCCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAA
1 AAA--C---CCC-AACCCTTAACTTAAAAACCCTAAC-CCTTAACCTAA
*
42146128 AAACCCCAACGCTAACCGTTAACTTAAAACCCCTAACCCATTAACCTAA
1 AAACCCCAA--C---CC-TTAACTTAAAAACCCTAACCC-TTAACCTAA
* * *
42146177 AAACCCTAACCCTAACCCTTAACTTAAAAACCCTAGCCCATTCACCTAC
1 AAA--C---CCC-AACCCTTAACTTAAAAACCCTAACCC-TTAACCTAA
* * * * *
42146226 AAATCCTAACCCTTAACTTTAAAACCATAACCCTTAACTTAA
1 AAACCCCAACCCTTAACTTAAAAACCCTAACCCTTAACCTAA
* * * * ** **
42146268 AAACCCTAAACTCTTTACTTTAAAACTGTAACCCTTAAATTAA
1 AAACCC-CAACCCTTAACTTAAAAACCCTAACCCTTAACCTAA
* * * *
42146311 AAACCCTAAACCCTTAACTTTAAAACCGTAACCCTTAA-ATAAA
1 AAACCC-CAACCCTTAACTTAAAAACCCTAACCCTTAACCT-AA
* * *
42146354 AAACCCTAACACTTAACTTAAAAACCCTAACCCTTAACTTAA
1 AAACCCCAACCCTTAACTTAAAAACCCTAACCCTTAACCTAA
42146396 A
1 A
42146397 TATAATTTGA
Statistics
Matches: 265, Mismatches: 31, Indels: 45
0.78 0.09 0.13
Matches are distributed among these distances:
42 42 0.16
43 102 0.38
44 5 0.02
45 2 0.01
47 1 0.00
48 7 0.03
49 97 0.37
50 2 0.01
51 1 0.00
53 1 0.00
54 3 0.01
55 2 0.01
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.23
Consensus pattern (42 bp):
AAACCCCAACCCTTAACTTAAAAACCCTAACCCTTAACCTAA
Found at i:42146098 original size:27 final size:27
Alignment explanation
Indices: 42146063--42146211 Score: 156
Period size: 27 Copynumber: 5.9 Consensus size: 27
42146053 TTAAAAATCA
42146063 TAACACCTTAACCTAAAAACCCTAACCC
1 TAAC-CCTTAACCTAAAAACCCTAACCC
*
42146091 TAACCCTTAACTTAAAAACCCTAA--C
1 TAACCCTTAACCTAAAAACCCTAACCC
* *
42146116 --A-CCTTAACCTAAAAACCCCAACGC
1 TAACCCTTAACCTAAAAACCCTAACCC
* * *
42146140 TAACCGTTAACTTAAAACCCCTAACCC
1 TAACCCTTAACCTAAAAACCCTAACCC
42146167 --A---TTAACCTAAAAACCCTAACCC
1 TAACCCTTAACCTAAAAACCCTAACCC
*
42146189 TAACCCTTAACTTAAAAACCCTA
1 TAACCCTTAACCTAAAAACCCTA
42146212 GCCCATTCAC
Statistics
Matches: 100, Mismatches: 11, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
22 37 0.37
23 1 0.01
24 2 0.02
25 2 0.02
26 1 0.01
27 53 0.53
28 4 0.04
ACGTcount: A:0.42, C:0.36, G:0.01, T:0.20
Consensus pattern (27 bp):
TAACCCTTAACCTAAAAACCCTAACCC
Found at i:42146111 original size:21 final size:21
Alignment explanation
Indices: 42146036--42146396 Score: 272
Period size: 21 Copynumber: 16.0 Consensus size: 21
42146026 TTTAATTGGC
*
42146036 AAACCCCAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
* * *
42146057 AAATCATAACACCTTAACCTAAAA
1 AAACCCTAAC-CCTTAA-CT-TAA
42146081 ACCCTAACCCTAACCCTTAACTTAA
1 A----AACCCTAACCCTTAACTTAA
*
42146106 AAACCCTAACACCTTAACCTAA
1 AAACCCTAAC-CCTTAACTTAA
*
42146128 AAACCCCAACGCTAACCGTTAACTTAA
1 AAA---C--C-CTAACCCTTAACTTAA
* *
42146155 AACCCCTAACCCATTAACCTAAAA
1 AAACCCTAACCC-TTAA-CT-TAA
42146179 ACCCTAACCCTAACCCTTAACTTAA
1 A----AACCCTAACCCTTAACTTAA
* * * *
42146204 AAACCCTAGCCCATTCACCTAC
1 AAACCCTAACCC-TTAACTTAA
* *
42146226 AAATCCTAACCCTTAACTTTA
1 AAACCCTAACCCTTAACTTAA
*
42146247 AAACCATAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
* * *
42146268 AAACCCTAAACTCTTTACTTTA
1 AAACCCT-AACCCTTAACTTAA
** *
42146290 AAACTGTAACCCTTAAATTAA
1 AAACCCTAACCCTTAACTTAA
*
42146311 AAACCCTAAACCCTTAACTTTA
1 AAACCCT-AACCCTTAACTTAA
* * *
42146333 AAACCGTAACCCTTAAATAAA
1 AAACCCTAACCCTTAACTTAA
*
42146354 AAACCCTAACACTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
42146375 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
42146396 A
1 A
42146397 TATAATTTGA
Statistics
Matches: 265, Mismatches: 51, Indels: 48
0.73 0.14 0.13
Matches are distributed among these distances:
21 125 0.47
22 74 0.28
23 4 0.02
24 7 0.03
25 7 0.03
26 4 0.02
27 22 0.08
28 22 0.08
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.23
Consensus pattern (21 bp):
AAACCCTAACCCTTAACTTAA
Found at i:42146116 original size:49 final size:48
Alignment explanation
Indices: 42146037--42146396 Score: 305
Period size: 49 Copynumber: 7.9 Consensus size: 48
42146027 TTAATTGGCA
* * *
42146037 AACCCCAACCCTTAACTTAAAAATCATAACACCTTAACCTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCTAAC-CCTTAACCTAAAAACCCT
*
42146086 AACCCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAAAAACCCC
1 AACCCTAACCCTTAACTTAAAAACCCTAAC-CCTTAACCTAAAAACCCT
* * *
42146135 AACGCTAACCGTTAACTTAAAACCCCTAACCCATTAACCTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCTAACCC-TTAACCTAAAAACCCT
* * *
42146184 AACCCTAACCCTTAACTTAAAAACCCTAGCCCATTCACCTACAAA---T
1 AACCCTAACCCTTAACTTAAAAACCCTAACCC-TTAACCTAAAAACCCT
* * *
42146230 ---CCTAACCCTTAACTTTAAAACCATAACCCTTAACTTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAAAACCCT
* * * ** **
42146275 -A----AACTCTTTACTTTAAAACTGTAACCCTTAAATTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAAAACCCT
* * *
42146318 -A----AACCCTTAACTTTAAAACCGTAACCCTTAA-AT-AAAA----
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAAAACCCT
* *
42146355 AACCCTAACACTTAACTTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAA
42146397 TATAATTTGA
Statistics
Matches: 266, Mismatches: 33, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
38 1 0.00
41 4 0.02
42 37 0.14
43 92 0.35
44 2 0.01
45 1 0.00
46 1 0.00
48 2 0.01
49 126 0.47
ACGTcount: A:0.43, C:0.33, G:0.01, T:0.23
Consensus pattern (48 bp):
AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAAAACCCT
Found at i:42146269 original size:64 final size:60
Alignment explanation
Indices: 42146089--42146396 Score: 211
Period size: 64 Copynumber: 4.7 Consensus size: 60
42146079 AAACCCTAAC
* * *
42146089 CCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAAAAACCCCAACGCTAACCGTTAACTTA
1 CCTAACCCTTAACTTAAAAACCCTAAC-CCTTAACTTAAAAA---C--C-CTAACCCTT-ACATA
42146154 AAA
58 AAA
* *
42146157 CCCCTAACCCATTAACCTAAAAACCCTAACCCTAACCCTTAACTTAAAAACCCTAGCCCATTCAC
1 --CCTAACCC-TTAA-CT-TAAA----AACCCTAACCCTTAACTTAAAAACCCTAACCC-TT-AC
*
42146222 CTACAAA
55 ATA-AAA
* * * *
42146229 TCCTAACCCTTAACTTTAAAACCATAACCCTTAACTTAAAAACCCTAAACTCTTTACTTTAAAA
1 -CCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCT-AAC-CCTTAC-ATAAAA
* * * * *
42146293 CTGTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTTAAAACCGTAACCCTTAAATAAAAAA
1 C-CTAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACCCTTACAT--AAAA
*
42146357 CCCTAACACTTAACTTAAAAACCCTAACCCTTAACTTAAA
1 -CCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
42146397 TATAATTTGA
Statistics
Matches: 195, Mismatches: 26, Indels: 41
0.74 0.10 0.16
Matches are distributed among these distances:
62 1 0.01
63 19 0.10
64 77 0.39
65 26 0.13
66 1 0.01
68 2 0.01
69 2 0.01
70 17 0.09
71 19 0.10
72 5 0.03
73 4 0.02
76 13 0.07
77 9 0.05
ACGTcount: A:0.42, C:0.32, G:0.02, T:0.24
Consensus pattern (60 bp):
CCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTACATAAAA
Found at i:42147220 original size:126 final size:126
Alignment explanation
Indices: 42146994--42147582 Score: 948
Period size: 126 Copynumber: 4.7 Consensus size: 126
42146984 ACTAGAAGCG
* * *
42146994 ATTTTATACTGTTTGCTCAGAAACGTCAAGTCAAAATTATTTTTCCAGGACCTACTGTAGCAAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
* *
42147059 GCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATATCATCCTGCTTGCAGCGTT
66 GCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTT
* * * *
42147120 GTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCCATTGTAGCAAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
* *
42147185 GCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTTAAATAGCATCCTGCTTGCAGCGTT
66 GCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTT
*
42147246 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCGAGGACCTACTGTAGCAAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
42147311 GCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTT
66 GCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTT
* * *
42147372 ATTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACAGTAGCAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCTACTGTAGCAAA
* * * *
42147437 AGCGCGTCCACGAGGGCGCAATTTCAAAAATTCTTCTCATAA-AGCATCCTGCTTGAAGCATT
65 AGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTGCTTGCAGCGTT
*
42147499 -TTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
* *
42147563 GCGCGTACACGTGGGCGCGA
66 GCGCGTCCACGAGGGCGCGA
42147583 CTTAAAAAAT
Statistics
Matches: 428, Mismatches: 33, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
125 38 0.09
126 314 0.73
127 74 0.17
128 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (126 bp):
ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAA
GCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTT
Done.