Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 21 of 322
Found at i:5984133 original size:58 final size:58
Alignment explanation
Indices: 5984005--5984125 Score: 215
Period size: 58 Copynumber: 2.1 Consensus size: 58
5983995 AAGTGAAGAC
*
5984005 TTATTAAGAAATAAAAATCAATGCAATAAGGGTCCAAACTGACTCGTGAAATAATTTA
1 TTATTAAGAAATAAAAATCAATGCAATAAGGGTCCAAAATGACTCGTGAAATAATTTA
* *
5984063 TTATTAAGAAATAAAAATCAATGTAATACGGGTCCAAAATGACTCGTGAAATAATTTA
1 TTATTAAGAAATAAAAATCAATGCAATAAGGGTCCAAAATGACTCGTGAAATAATTTA
5984121 TTATT
1 TTATT
5984126 TTGAAATATT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (58 bp):
TTATTAAGAAATAAAAATCAATGCAATAAGGGTCCAAAATGACTCGTGAAATAATTTA
Found at i:5984942 original size:24 final size:25
Alignment explanation
Indices: 5984908--5984954 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5984898 AAAAATCAAA
5984908 ATATTTAT-AAAAATTTCAAAAATT
1 ATATTTATAAAAAATTTCAAAAATT
* *
5984932 ATATTTTTAAAAAATTTTAAAAA
1 ATATTTATAAAAAATTTCAAAAA
5984955 ATTCTAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATTTATAAAAAATTTCAAAAATT
Found at i:5985452 original size:32 final size:32
Alignment explanation
Indices: 5985411--5985475 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
5985401 TTTGACAAAG
* *
5985411 TTATACATTTTGATATCTAAAGATAACAATAT
1 TTATACATTTTGACACCTAAAGATAACAATAT
* *
5985443 TTATACATTTTGGCACCTGAAGATAACAATAT
1 TTATACATTTTGACACCTAAAGATAACAATAT
5985475 T
1 T
5985476 AACTTTTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (32 bp):
TTATACATTTTGACACCTAAAGATAACAATAT
Found at i:5991063 original size:16 final size:16
Alignment explanation
Indices: 5991039--5991070 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5991029 ATCCGCAAGA
*
5991039 CTTATGTGCATGAATT
1 CTTACGTGCATGAATT
5991055 CTTACGTGCATGAATT
1 CTTACGTGCATGAATT
5991071 TCTCTTTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (16 bp):
CTTACGTGCATGAATT
Found at i:5997406 original size:19 final size:19
Alignment explanation
Indices: 5997384--5997420 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5997374 AATTTCTATA
*
5997384 TTATTATTATTATTGTTAC
1 TTATTATTATTACTGTTAC
5997403 TTATTATTATTACTGTTA
1 TTATTATTATTACTGTTA
5997421 TGTACATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TTATTATTATTACTGTTAC
Found at i:5997408 original size:13 final size:13
Alignment explanation
Indices: 5997382--5997416 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
5997372 TGAATTTCTA
5997382 TATTATTA-TTAT
1 TATTATTACTTAT
*
5997394 TATTGTTACTTAT
1 TATTATTACTTAT
5997407 TATTATTACT
1 TATTATTACT
5997417 GTTATGTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (13 bp):
TATTATTACTTAT
Found at i:5997794 original size:26 final size:26
Alignment explanation
Indices: 5997765--5997820 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
5997755 TGATACAAAT
5997765 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5997791 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5997817 TGAT
1 TGAT
5997821 GGGAATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5999335 original size:26 final size:26
Alignment explanation
Indices: 5999306--5999358 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
5999296 TTTACAGTTT
5999306 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
5999332 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
5999358 T
1 T
5999359 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:6003845 original size:25 final size:27
Alignment explanation
Indices: 6003808--6003860 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
6003798 TCAAACATGC
6003808 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
6003834 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
6003860 A
1 A
6003861 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:6005377 original size:26 final size:26
Alignment explanation
Indices: 6005347--6005398 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
6005337 TGAAATGCCC
*
6005347 ATCATGGAGCATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
6005373 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
6005399 GTCAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:6012704 original size:34 final size:34
Alignment explanation
Indices: 6012661--6012729 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
6012651 GAGGGAGAAG
6012661 AAGATATTGTAGCATCTATTTCTACCGATACACC
1 AAGATATTGTAGCATCTATTTCTACCGATACACC
*
6012695 AAGATATTGTAGCATCTATTTCTACCGATGCACC
1 AAGATATTGTAGCATCTATTTCTACCGATACACC
6012729 A
1 A
6012730 TACATTGAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (34 bp):
AAGATATTGTAGCATCTATTTCTACCGATACACC
Found at i:6017080 original size:43 final size:44
Alignment explanation
Indices: 6017019--6017102 Score: 161
Period size: 43 Copynumber: 1.9 Consensus size: 44
6017009 TATGCCTAAA
6017019 AAAAATGGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATAAT
1 AAAAATGGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATAAT
6017063 AAAAA-GGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGAT
1 AAAAATGGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGAT
6017103 TAACACAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 35 0.88
44 5 0.12
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.17
Consensus pattern (44 bp):
AAAAATGGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATAAT
Found at i:6017135 original size:43 final size:43
Alignment explanation
Indices: 6017019--6017137 Score: 145
Period size: 43 Copynumber: 2.7 Consensus size: 43
6017009 TATGCCTAAA
* *
6017019 AAAAATGGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATAAT
1 AAAAA-GGATCAAGATGAAAACCCGAAAAGGGCGTCTTGATAAC
*
6017063 AAAAAGGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATTAAC
1 AAAAAGGATCAAGATGAAAACCCGAAAAGGGCGTCTTGA-TAAC
*
6017107 ACAAAA-GAT-TAGAATGAAAACCCG-AAAGGGC
1 A-AAAAGGATCAAG-ATGAAAACCCGAAAAGGGC
6017138 ATTCTAATGA
Statistics
Matches: 69, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
43 43 0.62
44 22 0.32
45 4 0.06
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.15
Consensus pattern (43 bp):
AAAAAGGATCAAGATGAAAACCCGAAAAGGGCGTCTTGATAAC
Found at i:6017998 original size:18 final size:18
Alignment explanation
Indices: 6017975--6018009 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6017965 GCTGAGGTAA
6017975 TTTCAATTTCTGTTTTTT
1 TTTCAATTTCTGTTTTTT
6017993 TTTCAATTTCTGTTTTT
1 TTTCAATTTCTGTTTTT
6018010 CAAATTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTCAATTTCTGTTTTTT
Found at i:6018025 original size:14 final size:15
Alignment explanation
Indices: 6017991--6018023 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6017981 TTTCTGTTTT
*
6017991 TTTTTC-AATTTCTG
1 TTTTTCAAATTTATG
6018005 TTTTTCAAATTTATG
1 TTTTTCAAATTTATG
6018020 TTTT
1 TTTT
6018024 CAGAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTTCAAATTTATG
Found at i:6018186 original size:18 final size:18
Alignment explanation
Indices: 6018150--6018185 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
6018140 TATGCTGAGG
*
6018150 TATTTTCAATTTCTATTT
1 TATTTTCAATTTATATTT
6018168 TATTTT-AATTTATATTT
1 TATTTTCAATTTATATTT
6018185 T
1 T
6018186 TCAAAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTTCAATTTATATTT
Found at i:6018261 original size:14 final size:14
Alignment explanation
Indices: 6018242--6018277 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
6018232 CGCTGAGGTA
* *
6018242 TTTTCAATTTCTGC
1 TTTTCAAATTCAGC
6018256 TTTTCAAATTCAGC
1 TTTTCAAATTCAGC
6018270 TTTTCAAA
1 TTTTCAAA
6018278 AAAAATCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (14 bp):
TTTTCAAATTCAGC
Found at i:6018296 original size:90 final size:88
Alignment explanation
Indices: 6018079--6018614 Score: 515
Period size: 90 Copynumber: 6.0 Consensus size: 88
6018069 CGTTGAGGTA
6018079 TTTTC-AATTTATG--TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCA
1 TTTTCAAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TC-
* *
6018140 TATGCTGAGGTATTTTCAATTTCTATT
64 -ACGCTGAGGTATTTTCAATTTCT-GT
** ** * *
6018167 TTATTTTAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCGCAAGTCA
1 TT-TTCAAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
*
6018232 CGCTGAGGTATTTTCAATTTCTGC
65 CGCTGAGGTATTTTCAATTTCTGT
* * * * *
6018256 TTTTCAAATTCA-GCTTTTCAAAAAAAATCAACTCATATTGCAAGAGCTGAGTTGAGCCTCAAGA
1 TTTTCAAATTTATGCTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
*
6018320 CACGCTGAGGTATTTTCAATTTCCGT
63 CACGCTGAGGTATTTTCAATTTCTGT
* * * *
6018346 TTTTC-AAGTTATGCTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCAT
1 TTTTCAAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAC
*
6018410 GCTGAGGTATTTTCAATTTCTTTT
66 GCTGAGGTATTTTCAATTTC-TGT
** *
6018434 TTTTC-AATTTATATTTTTCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTC-GGATCA
1 TTTTCAAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCA
** *
6018497 CATG-TCGAGGTATTTTCAAAATCTGC
65 C--GCT-GAGGTATTTTCAATTTCTGT
* ** *
6018523 TTTTCAAA-TTAAG--TTTCAAAGAA-CTAACTCATATTGCGAGAAATGAGTTGAGCCT-TGGCT
1 TTTTCAAATTTATGCTTTTCAAA-AATC-AACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-T
* * *
6018583 CACGTGCTAAGCTATTTTCAATTTCTAT
63 CAC--GCTGAGGTATTTTCAATTTCTGT
6018611 TTTT
1 TTTT
6018615 AATGTCTGTT
Statistics
Matches: 379, Mismatches: 50, Indels: 38
0.81 0.11 0.08
Matches are distributed among these distances:
87 76 0.20
88 119 0.31
89 19 0.05
90 121 0.32
92 43 0.11
93 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (88 bp):
TTTTCAAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAC
GCTGAGGTATTTTCAATTTCTGT
Found at i:6018509 original size:177 final size:175
Alignment explanation
Indices: 6018079--6018577 Score: 548
Period size: 177 Copynumber: 2.8 Consensus size: 175
6018069 CGTTGAGGTA
* * *
6018079 TTTTCAA-TT-TATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCATA
1 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACA
* * * *
6018142 TGCTGAGGTATTTTCAATTTCTATTTTATTTTAATTTATATTTTTCAAAAATCAACTCATATTGC
66 TGCTGAGGTATTTTCAATTTC--TGTT-TTTCAAATTAT-GTTTTCAAAAATCAACTCATATTGC
* *
6018207 GAGAGGTGAGTTGAGCCGCAAGTCACGCTGAGGTATTTTCAATTTCTGC
127 GAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTGC
* ** * * *
6018256 TTTTCAAATTCA-GCTTTTCAAAAAAAATCAACTCATATTGCAAGAGCTGAGTTGAGCCTCAAGA
1 TTTTC-AATTTATATTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGA
* *
6018320 -CAC--GCTGAGGTATTTTCAATTTCCGTTTTTCAAGTTATGCTTTTCAAAAATCAACTCATATT
61 TCACATGCTGAGGTATTTTCAATTTCTGTTTTTCAAATTATG-TTTTCAAAAATCAACTCATATT
* * * **
6018382 GCAAGAGGTGAGTTGAGCCTCAGGGCATGCTGAGGTATTTTCAATTTCTTTT
125 GCGAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTC-TGC
*
6018434 TTTTCAATTTATATTTTTCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACA
1 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACA
** * *
6018499 TG-TCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAG-TTTCAAAGAA-CTAACTCATATTGCG
66 TGCT-GAGGTATTTTCAATTTCTGTTTTTCAAATTATGTTTTCAAA-AATC-AACTCATATTGCG
**
6018561 AGAAATGAGTTGAGCCT
128 AGAGGTGAGTTGAGCCT
6018578 TGGCTCACGT
Statistics
Matches: 269, Mismatches: 37, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
174 2 0.01
175 46 0.17
176 30 0.11
177 112 0.42
178 15 0.06
179 5 0.02
180 20 0.07
182 38 0.14
183 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (175 bp):
TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACA
TGCTGAGGTATTTTCAATTTCTGTTTTTCAAATTATGTTTTCAAAAATCAACTCATATTGCGAGA
GGTGAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTGC
Found at i:6018724 original size:21 final size:21
Alignment explanation
Indices: 6018698--6018752 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
6018688 GAATAAAGAT
6018698 TGGAGCTAATCGAAGTTACAG
1 TGGAGCTAATCGAAGTTACAG
*
6018719 TGGAGCTAATCGAAGTTGCAG
1 TGGAGCTAATCGAAGTTACAG
*
6018740 TGGAACTAATCGA
1 TGGAGCTAATCGA
6018753 GGATATCAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.24
Consensus pattern (21 bp):
TGGAGCTAATCGAAGTTACAG
Found at i:6020329 original size:24 final size:24
Alignment explanation
Indices: 6020293--6020340 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
6020283 TATTATATTA
*
6020293 GTGTATATTATATTTACATACGTAT
1 GTGTATATTATATCTACATA-GTAT
6020318 GTGTAT-TTATATCTACATAGTAT
1 GTGTATATTATATCTACATAGTAT
6020341 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.18
24 12 0.55
25 6 0.27
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (24 bp):
GTGTATATTATATCTACATAGTAT
Found at i:6020428 original size:13 final size:13
Alignment explanation
Indices: 6020402--6020436 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
6020392 TGAATTTCTA
6020402 TATTATTA-TTAT
1 TATTATTACTTAT
*
6020414 TATTGTTACTTAT
1 TATTATTACTTAT
6020427 TATTATTACT
1 TATTATTACT
6020437 GTTATGTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (13 bp):
TATTATTACTTAT
Found at i:6020428 original size:19 final size:19
Alignment explanation
Indices: 6020404--6020440 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6020394 AATTTCTATA
*
6020404 TTATTATTATTATTGTTAC
1 TTATTATTATTACTGTTAC
6020423 TTATTATTATTACTGTTA
1 TTATTATTATTACTGTTA
6020441 TGTACATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TTATTATTATTACTGTTAC
Found at i:6020814 original size:26 final size:26
Alignment explanation
Indices: 6020785--6020866 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
6020775 TGATACAAAT
6020785 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
6020811 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
6020837 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
6020863 TGAT
1 TGAT
6020867 GGGAATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:6022381 original size:26 final size:26
Alignment explanation
Indices: 6022352--6022404 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
6022342 TTTACAGTTT
6022352 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
6022378 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
6022404 T
1 T
6022405 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:6023685 original size:15 final size:16
Alignment explanation
Indices: 6023665--6023694 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6023655 CATTGCCATG
6023665 TTATA-TTTTTATGTA
1 TTATATTTTTTATGTA
6023680 TTATATTTTTTATGT
1 TTATATTTTTTATGT
6023695 TATGTACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (16 bp):
TTATATTTTTTATGTA
Found at i:6029172 original size:20 final size:20
Alignment explanation
Indices: 6029147--6029187 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
6029137 TTTATCACAA
6029147 CTTAAGCACGACATATCTAG
1 CTTAAGCACGACATATCTAG
6029167 CTTAAGCACGACATATCTAG
1 CTTAAGCACGACATATCTAG
6029187 C
1 C
6029188 GTGATTGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (20 bp):
CTTAAGCACGACATATCTAG
Found at i:6032709 original size:22 final size:21
Alignment explanation
Indices: 6032681--6032726 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
6032671 AATAAGAAAT
6032681 AAAAGGA-ACAATTTAAATATAA
1 AAAAGGACA-AATTTAAA-ATAA
6032703 AAAAGGACTAAATTTAAAATAA
1 AAAAGGAC-AAATTTAAAATAA
6032725 AA
1 AA
6032727 TATCTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 13 0.59
23 8 0.36
24 1 0.05
ACGTcount: A:0.65, C:0.04, G:0.09, T:0.22
Consensus pattern (21 bp):
AAAAGGACAAATTTAAAATAA
Found at i:6035463 original size:31 final size:31
Alignment explanation
Indices: 6035428--6035491 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
6035418 ATAATACTGG
6035428 CAATGCTTGATATTCTCTCGACCTTCTGCAA
1 CAATGCTTGATATTCTCTCGACCTTCTGCAA
6035459 CAATGCTTGATATTCTCTCGACCTTCTGCAA
1 CAATGCTTGATATTCTCTCGACCTTCTGCAA
6035490 CA
1 CA
6035492 TTGATCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.34
Consensus pattern (31 bp):
CAATGCTTGATATTCTCTCGACCTTCTGCAA
Found at i:6038380 original size:131 final size:131
Alignment explanation
Indices: 6038093--6038469 Score: 395
Period size: 131 Copynumber: 2.9 Consensus size: 131
6038083 AGAAAAATAC
* *
6038093 GAGTGAAATTCCGAAGAGACATTCGATTATTTTGAACAAATGGGAAATTGCAACCCAACACGATA
1 GAGTGAAATTCCGAAG-GACTTTCGATTATTTTGAACAAATGAGAAATTGCAACCCAACACGATA
* * * * *** *
6038158 GGGCACT-ATTCCCCGAATCGCCAAACATAGAGTATTTTTTTCGTTTTAAAGGGTTTTTAGAAAA
65 GGGCA-TGATTCCACGAATTGTCAAACATCGAGTATTGCCTTCGTTTTAAAGGATTTTTAGAAAA
6038222 TGT
129 TGT
* * ** *
6038225 GAGTGAAATTCCGAA-GAATATTCGATTGTTTTGAACAAATGAGAAATCACAACCCAGCACGATA
1 GAGTGAAATTCCGAAGGACT-TTCGATTATTTTGAACAAATGAGAAATTGCAACCCAACACGATA
* * *
6038289 GGGCATGATT-CGCGAATTGTCAAACACCGAGTATTGCCTTCGTTTTAAAGGATTTTTGGAAGAC
65 GGGCATGATTCCACGAATTGTCAAACATCGAGTATTGCCTTCGTTTTAAAGGATTTTTAGAA-A-
6038353 ATG-
128 ATGT
** * * * *
6038356 G-GTGAAATTTTGAAGGGACTTTCGATTACTTTGAGCAAACGAGAAATTGCAACCCAACACGTTA
1 GAGTGAAATTCCGAA-GGACTTTCGATTATTTTGAACAAATGAGAAATTGCAACCCAACACGATA
* * * * * *
6038420 GGGCACGATTCCACGACTTGTCAAATATCGAATATCGCCTTTGTTTTAAA
65 GGGCATGATTCCACGAATTGTCAAACATCGAGTATTGCCTTCGTTTTAAA
6038470 TAATGGTGAA
Statistics
Matches: 202, Mismatches: 36, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
130 55 0.27
131 94 0.47
132 53 0.26
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (131 bp):
GAGTGAAATTCCGAAGGACTTTCGATTATTTTGAACAAATGAGAAATTGCAACCCAACACGATAG
GGCATGATTCCACGAATTGTCAAACATCGAGTATTGCCTTCGTTTTAAAGGATTTTTAGAAAATG
T
Found at i:6040007 original size:4 final size:4
Alignment explanation
Indices: 6039998--6040025 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
6039988 TATTGTATGC
6039998 GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT
6040026 TCATATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:6046779 original size:121 final size:121
Alignment explanation
Indices: 6046565--6046807 Score: 486
Period size: 121 Copynumber: 2.0 Consensus size: 121
6046555 TTGATGCATT
6046565 CGTTTTGATTATTTCAGGAAACCAAATTAATATTTTCCTTTAATTAATTTAGAAAATTCAATTAA
1 CGTTTTGATTATTTCAGGAAACCAAATTAATATTTTCCTTTAATTAATTTAGAAAATTCAATTAA
6046630 TTAAATTTATTTAATTAAAAAATTAATTAATTTACTTGGCTGGACATCCACGTTAG
66 TTAAATTTATTTAATTAAAAAATTAATTAATTTACTTGGCTGGACATCCACGTTAG
6046686 CGTTTTGATTATTTCAGGAAACCAAATTAATATTTTCCTTTAATTAATTTAGAAAATTCAATTAA
1 CGTTTTGATTATTTCAGGAAACCAAATTAATATTTTCCTTTAATTAATTTAGAAAATTCAATTAA
6046751 TTAAATTTATTTAATTAAAAAATTAATTAATTTACTTGGCTGGACATCCACGTTAG
66 TTAAATTTATTTAATTAAAAAATTAATTAATTTACTTGGCTGGACATCCACGTTAG
6046807 C
1 C
6046808 ATTTAAAACT
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (121 bp):
CGTTTTGATTATTTCAGGAAACCAAATTAATATTTTCCTTTAATTAATTTAGAAAATTCAATTAA
TTAAATTTATTTAATTAAAAAATTAATTAATTTACTTGGCTGGACATCCACGTTAG
Found at i:6057217 original size:32 final size:30
Alignment explanation
Indices: 6057176--6057234 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
6057166 ACCATTTTCC
* *
6057176 TTTAATTAATTTAGAAAATTCAGTTAATTAAA
1 TTTAATTAA-TTA-AAAAATCAATTAATTAAA
*
6057208 TTTATTTAATTAAAAAATCAATTAATT
1 TTTAATTAATTAAAAAATCAATTAATT
6057235 TATTTAGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.54
31 3 0.12
32 8 0.33
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (30 bp):
TTTAATTAATTAAAAAATCAATTAATTAAA
Found at i:6059308 original size:27 final size:28
Alignment explanation
Indices: 6059278--6059339 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
6059268 ATATTGCGTG
** * *
6059278 TATATATATATTTTAATATTATAT-TTT
1 TATATATATACCTTAATACTATATCATT
*
6059305 TATACATATACCTTAATACTATATCATT
1 TATATATATACCTTAATACTATATCATT
6059333 TATATAT
1 TATATAT
6059340 TTTCATTTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (28 bp):
TATATATATACCTTAATACTATATCATT
Found at i:6072006 original size:43 final size:42
Alignment explanation
Indices: 6071950--6072052 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 42
6071940 TATTATTGCT
* *
6071950 CTAAGCAATAGGGTAACAAGCCAAATTTTCAAACCTTAAACCC
1 CTAAGCAGTAGGGTAACAAGCCAAATTTACAAACC-TAAACCC
* *** * *
6071993 CTAAGCAGTAGGGTAACAGGTTGAATTTACAGATCTAAACCC
1 CTAAGCAGTAGGGTAACAAGCCAAATTTACAAACCTAAACCC
*
6072035 CTAAGCAGTAGGGAAACA
1 CTAAGCAGTAGGGTAACA
6072053 GATCAATGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
42 24 0.47
43 27 0.53
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.20
Consensus pattern (42 bp):
CTAAGCAGTAGGGTAACAAGCCAAATTTACAAACCTAAACCC
Found at i:6072199 original size:42 final size:42
Alignment explanation
Indices: 6072152--6072267 Score: 162
Period size: 41 Copynumber: 2.8 Consensus size: 42
6072142 TAAAACCCAT
*
6072152 AGCAGATCTCCTTGAAGTTTTAGTGGAATTGATCAAAGCTAC
1 AGCAGATCTCCTTGAAGTTTCAGTGGAATTGATCAAAGCTAC
* * *
6072194 AGCAGATCTCCCTGAAGTTTCAGTGG-ATTAATCGAAGCTAC
1 AGCAGATCTCCTTGAAGTTTCAGTGGAATTGATCAAAGCTAC
* * *
6072235 AACAGATCTTCTTAAAGTTTCAGTGGAATTGAT
1 AGCAGATCTCCTTGAAGTTTCAGTGGAATTGAT
6072268 TGAAGTCACG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 35 0.55
42 29 0.45
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (42 bp):
AGCAGATCTCCTTGAAGTTTCAGTGGAATTGATCAAAGCTAC
Found at i:6079888 original size:19 final size:16
Alignment explanation
Indices: 6079841--6079880 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
6079831 GAAAGCACCT
6079841 TCCTGCTGCTCCTCCA
1 TCCTGCTGCTCCTCCA
6079857 TCCTGCTGCTCCTCCA
1 TCCTGCTGCTCCTCCA
6079873 TCCTGCTG
1 TCCTGCTG
6079881 GCTCTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.47, G:0.15, T:0.33
Consensus pattern (16 bp):
TCCTGCTGCTCCTCCA
Found at i:6097486 original size:67 final size:67
Alignment explanation
Indices: 6097413--6097582 Score: 340
Period size: 67 Copynumber: 2.5 Consensus size: 67
6097403 CCTAGGGATT
6097413 AAAGTTTAGGAATATTAAGCAAAAATTAAAAGTATCTCTACCTGCTATTGGCATCAATTTAAGCT
1 AAAGTTTAGGAATATTAAGCAAAAATTAAAAGTATCTCTACCTGCTATTGGCATCAATTTAAGCT
6097478 TC
66 TC
6097480 AAAGTTTAGGAATATTAAGCAAAAATTAAAAGTATCTCTACCTGCTATTGGCATCAATTTAAGCT
1 AAAGTTTAGGAATATTAAGCAAAAATTAAAAGTATCTCTACCTGCTATTGGCATCAATTTAAGCT
6097545 TC
66 TC
6097547 AAAGTTTAGGAATATTAAGCAAAAATTAAAAGTATC
1 AAAGTTTAGGAATATTAAGCAAAAATTAAAAGTATC
6097583 GATACCCTTA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 103 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.32
Consensus pattern (67 bp):
AAAGTTTAGGAATATTAAGCAAAAATTAAAAGTATCTCTACCTGCTATTGGCATCAATTTAAGCT
TC
Found at i:6099939 original size:21 final size:20
Alignment explanation
Indices: 6099915--6099953 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
6099905 GAGTATTTTT
6099915 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
6099936 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
6099954 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:6102034 original size:18 final size:18
Alignment explanation
Indices: 6102007--6102044 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6101997 GTATGTATTT
6102007 TGTATATTAGACTTATAA
1 TGTATATTAGACTTATAA
*
6102025 TGTATCTTAGACTTATAA
1 TGTATATTAGACTTATAA
6102043 TG
1 TG
6102045 CTTAGGCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (18 bp):
TGTATATTAGACTTATAA
Found at i:6105736 original size:62 final size:62
Alignment explanation
Indices: 6105658--6105845 Score: 367
Period size: 62 Copynumber: 3.0 Consensus size: 62
6105648 TGAACTTAGG
*
6105658 TGAATTTGGTTAATTGAAAAAAGATATGGGAATTGAAAAAAAACAAGTCTTTGTTGTGTTGA
1 TGAATTTGGTTCATTGAAAAAAGATATGGGAATTGAAAAAAAACAAGTCTTTGTTGTGTTGA
6105720 TGAATTTGGTTCATTGAAAAAAGATATGGGAATTGAAAAAAAACAAGTCTTTGTTGTGTTGA
1 TGAATTTGGTTCATTGAAAAAAGATATGGGAATTGAAAAAAAACAAGTCTTTGTTGTGTTGA
6105782 TGAATTTGGTTCATTGAAAAAAGATATGGGAATTGAAAAAAAACAAGTCTTTGTTGTGTTGA
1 TGAATTTGGTTCATTGAAAAAAGATATGGGAATTGAAAAAAAACAAGTCTTTGTTGTGTTGA
6105844 TG
1 TG
6105846 GGACTGAATT
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 125 1.00
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (62 bp):
TGAATTTGGTTCATTGAAAAAAGATATGGGAATTGAAAAAAAACAAGTCTTTGTTGTGTTGA
Found at i:6106783 original size:168 final size:164
Alignment explanation
Indices: 6106485--6106789 Score: 353
Period size: 168 Copynumber: 1.8 Consensus size: 164
6106475 GCTGTTCTGT
* * **
6106485 CTTTGCACTTATGGTGATAATCAAGTATGCTATTGATTATATATGAGGTAATCTTAGCTTGATTG
1 CTTTGCACATATGGTGATAATAAAGTATGCTATTGATTATATATGAGGTAATCTTAGCCCGATTG
* ** *
6106550 GCATCGAGATGGTCCGTAGAAGGCTTGCATAGAATTGTTTTCATTATCGAACTGTATGAGGAAGA
66 GCATCGAGATGGTCCGTAGAAGGCTTGCATAGAAATGTTTTCATTATCGAAAAGTAAGAGGAAGA
*
6106615 ATGAATTACGGTATACGTTTTATTGCTCTCCTCA
131 ATAAATTACGGTATACGTTTTATTGCTCTCCTCA
* * * *
6106649 CTTTGCACATATTGTGATGATAAAAGTATGCTATTGATTATATATAATGAGTTAATCTTGGCCCG
1 CTTTGCACATATGGTGATAAT-AAAGTATGCTATTGA-T-TATAT-ATGAGGTAATCTTAGCCCG
* * * * * ** *
6106714 ATTGGCATCTAGCTGGTCCGTGGAGGGCTTGCCTAGAAATGTTTTTGTTGT-GAAAAAGTACAG-
62 ATTGGCATCGAGATGGTCCGTAGAAGGCTTGCATAGAAATGTTTTCATTATCG-AAAAGTA-AGA
6106777 GGAAGAATAAATT
125 GGAAGAATAAATT
6106790 GGGGGTCAGT
Statistics
Matches: 114, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
164 18 0.16
165 14 0.12
166 1 0.01
167 6 0.05
168 74 0.65
169 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (164 bp):
CTTTGCACATATGGTGATAATAAAGTATGCTATTGATTATATATGAGGTAATCTTAGCCCGATTG
GCATCGAGATGGTCCGTAGAAGGCTTGCATAGAAATGTTTTCATTATCGAAAAGTAAGAGGAAGA
ATAAATTACGGTATACGTTTTATTGCTCTCCTCA
Found at i:6110281 original size:21 final size:21
Alignment explanation
Indices: 6110244--6110292 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6110234 TTCACCGTGC
*
6110244 AATATTTTTTTAGATTTTATA
1 AATATTTTTTGAGATTTTATA
*
6110265 AATATTTTTCTGA-ATTTTTTA
1 AATATTTTT-TGAGATTTTATA
*
6110286 CATATTT
1 AATATTT
6110293 ATTTCTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (21 bp):
AATATTTTTTGAGATTTTATA
Found at i:6119200 original size:21 final size:21
Alignment explanation
Indices: 6119174--6119214 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6119164 AGACAAGCGA
* *
6119174 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
6119195 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
6119215 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:6119464 original size:38 final size:38
Alignment explanation
Indices: 6119411--6119487 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
6119401 TTGTTGATGA
6119411 TGATATTCCTATCACTTATTAAGAAGCAATGCAAAGCT
1 TGATATTCCTATCACTTATTAAGAAGCAATGCAAAGCT
*
6119449 TGATATTCCTGTCACTTATTAAGAAGCAATGCAAAGCT
1 TGATATTCCTATCACTTATTAAGAAGCAATGCAAAGCT
6119487 T
1 T
6119488 AGAAAGTGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (38 bp):
TGATATTCCTATCACTTATTAAGAAGCAATGCAAAGCT
Found at i:6123015 original size:3 final size:3
Alignment explanation
Indices: 6123007--6123103 Score: 56
Period size: 3 Copynumber: 31.3 Consensus size: 3
6122997 NNNNNNNNNN
* * * *
6123007 TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TAC TGT TAT GTACA TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TA-T TAT
* * *
6123055 TAT T-T ATAC TA- TACT TAA TAT TAT TAT TAT TA- TATT TAC TAT TAT
1 TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
6123100 TAT T
1 TAT T
6123104 TATAAATATT
Statistics
Matches: 72, Mismatches: 13, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
2 5 0.07
3 56 0.78
4 11 0.15
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:6123033 original size:13 final size:13
Alignment explanation
Indices: 6123007--6123103 Score: 62
Period size: 12 Copynumber: 7.5 Consensus size: 13
6122997 NNNNNNNNNN
6123007 TATTATTA-TTAT
1 TATTATTACTTAT
*
6123019 TATTGTTACTTAT
1 TATTATTACTTAT
6123032 TATTATTACTGTTAT
1 TATTATTAC--TTAT
* *
6123047 GTACATATTATTTA-
1 -TA-TTATTACTTAT
* *
6123061 TACTA-TACTTAA
1 TATTATTACTTAT
6123073 TATTATTA-TTAT
1 TATTATTACTTAT
6123085 TA-TATTTAC-TAT
1 TATTA-TTACTTAT
6123097 TATTATT
1 TATTATT
6123104 TATAAATATT
Statistics
Matches: 67, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
11 7 0.10
12 28 0.42
13 18 0.27
15 7 0.10
16 2 0.03
17 5 0.07
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (13 bp):
TATTATTACTTAT
Found at i:6123033 original size:19 final size:19
Alignment explanation
Indices: 6123009--6123045 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6122999 NNNNNNNNTA
*
6123009 TTATTATTATTATTGTTAC
1 TTATTATTATTACTGTTAC
6123028 TTATTATTATTACTGTTA
1 TTATTATTATTACTGTTA
6123046 TGTACATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TTATTATTATTACTGTTAC
Found at i:6130904 original size:21 final size:21
Alignment explanation
Indices: 6130878--6130918 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6130868 AGACGAGCGA
* *
6130878 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
6130899 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
6130919 TTGAGCAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:6140650 original size:48 final size:48
Alignment explanation
Indices: 6140598--6140692 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
6140588 AGTAGTATTT
* *
6140598 AATTGTGCTATTAAATTACTATAGAAGGTATATTCTGTCTAAGGAAAA
1 AATTGTGCTATTAAATTACTATAGAAGGGATATTCTGACTAAGGAAAA
6140646 AATTGTGCTATTAAATTACTATAGAAGGGATATTCTGACTAAGGAAA
1 AATTGTGCTATTAAATTACTATAGAAGGGATATTCTGACTAAGGAAA
6140693 GACTTGGTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (48 bp):
AATTGTGCTATTAAATTACTATAGAAGGGATATTCTGACTAAGGAAAA
Found at i:6143104 original size:21 final size:21
Alignment explanation
Indices: 6143078--6143118 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6143068 AGACGAGCAA
* *
6143078 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
6143099 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
6143119 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:6148396 original size:69 final size:69
Alignment explanation
Indices: 6148239--6148398 Score: 176
Period size: 69 Copynumber: 2.3 Consensus size: 69
6148229 AGTTTGCAAA
* * *
6148239 TCCAAAATAGCTCGCGAACCTACGTTCCCAGTTGATATTATAAAAACTCGCCGGTTTAAGATCGC
1 TCCAAAATAGCTCGCGGACCTAAGTTCCCAGCTGATATTATAAAAACTCGCCGGTTTAAGATCGC
6148304 AACC
66 AACC
* * * * ** * * *
6148308 TCCAAGACAACTCGCGGACCTAAGTTCCTAGCTGATATTATAAAGGCTCTCCGGTTTAATATTGC
1 TCCAAAATAGCTCGCGGACCTAAGTTCCCAGCTGATATTATAAAAACTCGCCGGTTTAAGATCGC
**
6148373 AGGC
66 AACC
**
6148377 TCCAAAATAGCTCATGGACCTA
1 TCCAAAATAGCTCGCGGACCTA
6148399 CGTTTCCTGC
Statistics
Matches: 72, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (69 bp):
TCCAAAATAGCTCGCGGACCTAAGTTCCCAGCTGATATTATAAAAACTCGCCGGTTTAAGATCGC
AACC
Found at i:6148557 original size:69 final size:68
Alignment explanation
Indices: 6148446--6148877 Score: 341
Period size: 69 Copynumber: 6.3 Consensus size: 68
6148436 NACGTTTCCT
* * * ** * *
6148446 GCTGATATTATAAAGGCTCGCTAGTTTAAGA-CTGTAGCCTCCAAAACAGCTCGCGAACCTACGC
1 GCTGATATTATAAAGGCTCAC-CGATTAAGATC-ACAGCCTCCAAAACAGCTCGCGAACCTATGT
*
6148510 TCCTA
64 TCCCA
* * * *** *
6148515 GCTGATATTATAAAGGCTCACCGATCTAAGATCGCATCCTCCAAAACAACTCAAAAACCTATATT
1 GCTGATATTATAAAGGCTCACCGAT-TAAGATCACAGCCTCCAAAACAGCTCGCGAACCTATGTT
6148580 CCCA
65 CCCA
* * * * * * *
6148584 ACTGATATTATAAAGGTTCGA-AGATTTAAGATCACAGCCTCCAAAATAGCTCGTGGACCTACGT
1 GCTGATATTATAAAGGCTC-ACCGA-TTAAGATCACAGCCTCCAAAACAGCTCGCGAACCTATGT
6148648 TCCCA
64 TCCCA
* * * * * * * * * * *
6148653 GCTAATATTGTAAAGGCTCGCTAGTTTAAAATCACAGCCTCCAAAGCAGCTTGTGGACCTATGCT
1 GCTGATATTATAAAGGCTCAC-CGATTAAGATCACAGCCTCCAAAACAGCTCGCGAACCTATGTT
*
6148718 CTCA
65 CCCA
* ** * *
6148722 GCTGATATTGTAAAGGCTCACCGAATTAAGATCGTAGCCTTCAAAACAACT-GACGAACCTATGT
1 GCTGATATTATAAAGGCTCACCG-ATTAAGATCACAGCCTCCAAAACAGCTCG-CGAACCTATGT
*
6148786 TCCTA
64 TCCCA
* * ** *
6148791 GCTAATATTGTAAAGGCTTGCCAGATTAAGATCACAGTCTCCAAAACAGCTCGC-AGACCTATGT
1 GCTGATATTATAAAGGCTCACC-GATTAAGATCACAGCCTCCAAAACAGCTCGCGA-ACCTATGT
6148855 TCCCA
64 TCCCA
6148860 GCTGATATTATAAAGGCT
1 GCTGATATTATAAAGGCT
6148878 AGACGGTTTA
Statistics
Matches: 287, Mismatches: 65, Indels: 22
0.77 0.17 0.06
Matches are distributed among these distances:
68 5 0.02
69 275 0.96
70 7 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (68 bp):
GCTGATATTATAAAGGCTCACCGATTAAGATCACAGCCTCCAAAACAGCTCGCGAACCTATGTTC
CCA
Found at i:6148695 original size:138 final size:137
Alignment explanation
Indices: 6148446--6148907 Score: 437
Period size: 138 Copynumber: 3.4 Consensus size: 137
6148436 NACGTTTCCT
*
6148446 GCTGATATTATAAAGGCTCGCTAG-TTTAAGA-CTGTAGCCTCCAAAACAGCTCGCGAACCTACG
1 GCTGATATTATAAAGGCTCG-AAGATTTAAGATC-GTAGCCTCCAAAACAGCTCGCGAACCTACG
* * * * * * * * * * *
6148509 CTCCTAGCTGATATTATAAAGGCTCACCGATCTAAGATCGCATCCTCCAAAACAACTCAAAAACC
64 TTCCTAGCTAATATTGTAAAGGCTCGCAG-TTTAAGATCACAGCCTCCAAAACAGCTCGAAGACC
*
6148574 TATATTCCCA
128 TATGTTCCCA
* * ** * * *
6148584 ACTGATATTATAAAGGTTCGAAGATTTAAGATCACAGCCTCCAAAATAGCTCGTGGACCTACGTT
1 GCTGATATTATAAAGGCTCGAAGATTTAAGATCGTAGCCTCCAAAACAGCTCGCGAACCTACGTT
* * * * **
6148649 CCCAGCTAATATTGTAAAGGCTCGCTAGTTTAAAATCACAGCCTCCAAAGCAGCTTGTGGACCTA
66 CCTAGCTAATATTGTAAAGGCTCGC-AGTTTAAGATCACAGCCTCCAAAACAGCTCGAAGACCTA
* *
6148714 TGCTCTCA
130 TGTTCCCA
* * * * * *
6148722 GCTGATATTGTAAAGGCTC-ACCGAATTAAGATCGTAGCCTTCAAAACAACT-GACGAACCTATG
1 GCTGATATTATAAAGGCTCGA-AGATTTAAGATCGTAGCCTCCAAAACAGCTCG-CGAACCTACG
* * * *
6148785 TTCCTAGCTAATATTGTAAAGGCTTGCCAGATTAAGATCACAGTCTCCAAAACAGCTCGCAGACC
64 TTCCTAGCTAATATTGTAAAGGCTCG-CAGTTTAAGATCACAGCCTCCAAAACAGCTCGAAGACC
6148850 TATGTTCCCA
128 TATGTTCCCA
* * * * * *
6148860 GCTGATATTATAAAGGCTAGACGGTTTAATACCGTAACCTCCAAAACA
1 GCTGATATTATAAAGGCTCGAAGATTTAAGATCGTAGCCTCCAAAACA
6148908 AGTCACGGGC
Statistics
Matches: 257, Mismatches: 60, Indels: 14
0.78 0.18 0.04
Matches are distributed among these distances:
137 4 0.02
138 249 0.97
139 4 0.02
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (137 bp):
GCTGATATTATAAAGGCTCGAAGATTTAAGATCGTAGCCTCCAAAACAGCTCGCGAACCTACGTT
CCTAGCTAATATTGTAAAGGCTCGCAGTTTAAGATCACAGCCTCCAAAACAGCTCGAAGACCTAT
GTTCCCA
Found at i:6148902 original size:69 final size:69
Alignment explanation
Indices: 6148446--6148979 Score: 310
Period size: 69 Copynumber: 7.8 Consensus size: 69
6148436 NACGTTTCCT
* ** * *
6148446 GCTGATATTATAAAGGCTCGCTAGTTTAAGA-CTGTAGCCTCCAAAACAGCTCGC-GAACCTACG
1 GCTGATATTATAAAGGCTAGCCGGTTTAAGATC-GCAGCCTCCAAAACAGCTCGCAG-ACCTATG
* *
6148509 CTCCTA
64 TTCCCA
* * * * ** * *
6148515 GCTGATATTATAAAGGCTCA-CCGATCTAAGATCGCATCCTCCAAAACAACTCAAAAACCTATAT
1 GCTGATATTATAAAGGCT-AGCCGGTTTAAGATCGCAGCCTCCAAAACAGCTCGCAGACCTATGT
6148579 TCCCA
65 TCCCA
* * * ** * * * ** *
6148584 ACTGATATTATAAAGGTTCGAAGATTTAAGATCACAGCCTCCAAAATAGCTCGTGGACCTACGTT
1 GCTGATATTATAAAGGCTAGCCGGTTTAAGATCGCAGCCTCCAAAACAGCTCGCAGACCTATGTT
6148649 CCCA
66 CCCA
* * * ** * * * * ** *
6148653 GCTAATATTGTAAAGGCTCGCTAGTTTAAAATCACAGCCTCCAAAGCAGCTTGTGGACCTATGCT
1 GCTGATATTATAAAGGCTAGCCGGTTTAAGATCGCAGCCTCCAAAACAGCTCGCAGACCTATGTT
*
6148718 CTCA
66 CCCA
* ** * * *
6148722 GCTGATATTGTAAAGGCTCA-CCGAATTAAGATCGTAGCCTTCAAAACAACT-G-ACGAACCTAT
1 GCTGATATTATAAAGGCT-AGCCGGTTTAAGATCGCAGCCTCCAAAACAGCTCGCA-G-ACCTAT
*
6148784 GTTCCTA
63 GTTCCCA
* * * * * * *
6148791 GCTAATATTGTAAAGGCTTGCCAGATTAAGATCACAGTCTCCAAAACAGCTCGCAGACCTATGTT
1 GCTGATATTATAAAGGCTAGCCGGTTTAAGATCGCAGCCTCCAAAACAGCTCGCAGACCTATGTT
6148856 CCCA
66 CCCA
* * * * * * * * *
6148860 GCTGATATTATAAAGGCTAGACGGTTTAATACCGTAACCTCCAAAACAAG-TCACGGGCCTACGT
1 GCTGATATTATAAAGGCTAGCCGGTTTAAGATCGCAGCCTCCAAAAC-AGCTCGCAGACCTATGT
*
6148924 TCTCA
65 TCCCA
* * ** * * * *
6148929 ACTGATATTATAAAGGTTAGTTGATTTAGGATCGTAGCCTCC-GAACAGCTC
1 GCTGATATTATAAAGGCTAGCCGGTTTAAGATCGCAGCCTCCAAAACAGCTC
6148980 ATTGATTTAA
Statistics
Matches: 354, Mismatches: 99, Indels: 25
0.74 0.21 0.05
Matches are distributed among these distances:
67 2 0.01
68 7 0.02
69 339 0.96
70 5 0.01
71 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (69 bp):
GCTGATATTATAAAGGCTAGCCGGTTTAAGATCGCAGCCTCCAAAACAGCTCGCAGACCTATGTT
CCCA
Found at i:6148903 original size:207 final size:207
Alignment explanation
Indices: 6148437--6148907 Score: 538
Period size: 207 Copynumber: 2.3 Consensus size: 207
6148427 NNNNNNNNNN
* * * *
6148437 ACGTTTCCTGCTGATATTATAAAGGCTCGCTAGTTTAAGACTGTAGCCTCCAAAACAGCTCGCGA
1 ACGTTCCCAGCTGATATTATAAAGGCTCGCTAGTTTAAAACCGTAGCCTCCAAAACAGCTCGCGA
*
6148502 ACCTACGCTCCTAGCTGATATTATAAAGGCTCACCGATCTAAGATCGCATCCTCCAAAACAACTC
66 ACCTACGCTCCTAGCTGATATTATAAAGGCTCACCGATCTAAGATCGCAGCCTCCAAAACAACTC
* *
6148567 AAAAACCTATATTCCCAACTGATATTATAAAGGTTCGAAGATTTAAGATCACAGCCTCCAAAATA
131 AAAAACCTATATTCCCAACTAATATTATAAAGGTTCGAAGATTTAAGATCACAGCCTCCAAAACA
**
6148632 GCTCGTGGACCT
196 GCTCGCAGACCT
* * * ** * * * *
6148644 ACGTTCCCAGCTAATATTGTAAAGGCTCGCTAGTTTAAAATCACAGCCTCCAAAGCAGCTTGTGG
1 ACGTTCCCAGCTGATATTATAAAGGCTCGCTAGTTTAAAACCGTAGCCTCCAAAACAGCTCGCGA
* * * *
6148709 ACCTATGCT-CTCAGCTGATATTGTAAAGGCTCACCGAAT-TAAGATCGTAGCCTTCAAAACAAC
66 ACCTACGCTCCT-AGCTGATATTATAAAGGCTCACCG-ATCTAAGATCGCAGCCTCCAAAACAAC
* ** * * * * * *
6148772 TGACGAACCTATGTTCCTAGCTAATATTGTAAAGGCTT-GCCAGA-TTAAGATCACAGTCTCCAA
129 TCAAAAACCTATATTCCCAACTAATATTATAAAGG-TTCG-AAGATTTAAGATCACAGCCTCCAA
6148835 AACAGCTCGCAGACCT
192 AACAGCTCGCAGACCT
* * * * *
6148851 ATGTTCCCAGCTGATATTATAAAGGCTAGAC-GGTTTAATACCGTAACCTCCAAAACA
1 ACGTTCCCAGCTGATATTATAAAGGCTCG-CTAGTTTAAAACCGTAGCCTCCAAAACA
6148908 AGTCACGGGC
Statistics
Matches: 217, Mismatches: 42, Indels: 10
0.81 0.16 0.04
Matches are distributed among these distances:
206 2 0.01
207 207 0.95
208 8 0.04
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (207 bp):
ACGTTCCCAGCTGATATTATAAAGGCTCGCTAGTTTAAAACCGTAGCCTCCAAAACAGCTCGCGA
ACCTACGCTCCTAGCTGATATTATAAAGGCTCACCGATCTAAGATCGCAGCCTCCAAAACAACTC
AAAAACCTATATTCCCAACTAATATTATAAAGGTTCGAAGATTTAAGATCACAGCCTCCAAAACA
GCTCGCAGACCT
Found at i:6149757 original size:18 final size:18
Alignment explanation
Indices: 6149718--6149791 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
6149708 GAAAGATTAT
* * *
6149718 TTATTCAGTAACAGTTAG
1 TTATTCAGTAACAATCAA
*
6149736 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAA
* * *
6149754 TTATTCAATAATAATCAG
1 TTATTCAGTAACAATCAA
* *
6149772 TTACTCAGTATCAATCAA
1 TTATTCAGTAACAATCAA
6149790 TT
1 TT
6149792 TATCGGTTAT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:6150098 original size:6 final size:6
Alignment explanation
Indices: 6150089--6150121 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
6150079 TGTCGAATCG
*
6150089 GTAACG GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTA
6150122 GTCGGCACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:6152833 original size:21 final size:21
Alignment explanation
Indices: 6152788--6152859 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 21
6152778 CAATGCATTA
6152788 TAATTTTATTATTTTAAGTCAAATT
1 TAATTTTATTA-TTT-A-T-AAATT
6152813 TAATTTTGA-TATTTATAAATT
1 TAATTTT-ATTATTTATAAATT
* *
6152834 TAAATTTATTTTTTATACAATT
1 TAATTTTATTATTTATA-AATT
6152856 TAAT
1 TAAT
6152860 AATCATCCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.02
21 18 0.44
22 8 0.20
23 1 0.02
24 3 0.07
25 9 0.22
26 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TAATTTTATTATTTATAAATT
Found at i:6153957 original size:20 final size:20
Alignment explanation
Indices: 6153932--6153977 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
6153922 CAAAAAAAAA
* *
6153932 TCAAAATAATTT-TCAAATTT
1 TCAAAAT-ATTTATAAAAATT
6153952 TCAAAATATTTATAAAAATT
1 TCAAAATATTTATAAAAATT
6153972 TCAAAA
1 TCAAAA
6153978 AATATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (20 bp):
TCAAAATATTTATAAAAATT
Found at i:6157172 original size:20 final size:20
Alignment explanation
Indices: 6157109--6157172 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
6157099 ATAGAATTAT
6157109 TATTAAATATAATTTAATAA
1 TATTAAATATAATTTAATAA
* * * * *
6157129 TA-AATAATTTAATATATTAT
1 TATTA-AATATAATTTAATAA
*
6157149 TATTAAATATAATTTACTAA
1 TATTAAATATAATTTAATAA
6157169 TATT
1 TATT
6157173 CTTAATATGA
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTAAATATAATTTAATAA
Found at i:6158179 original size:70 final size:70
Alignment explanation
Indices: 6158105--6158313 Score: 418
Period size: 70 Copynumber: 3.0 Consensus size: 70
6158095 TATATATATG
6158105 TATATATATATTTGTTATTAATTATATATTATTCATATAAAAGGAAAGGTCCTTTGGACTTTCCT
1 TATATATATATTTGTTATTAATTATATATTATTCATATAAAAGGAAAGGTCCTTTGGACTTTCCT
6158170 TCGTA
66 TCGTA
6158175 TATATATATATTTGTTATTAATTATATATTATTCATATAAAAGGAAAGGTCCTTTGGACTTTCCT
1 TATATATATATTTGTTATTAATTATATATTATTCATATAAAAGGAAAGGTCCTTTGGACTTTCCT
6158240 TCGTA
66 TCGTA
6158245 TATATATATATTTGTTATTAATTATATATTATTCATATAAAAGGAAAGGTCCTTTGGACTTTCCT
1 TATATATATATTTGTTATTAATTATATATTATTCATATAAAAGGAAAGGTCCTTTGGACTTTCCT
6158310 TCGT
66 TCGT
6158314 TCACACGTGA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 139 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (70 bp):
TATATATATATTTGTTATTAATTATATATTATTCATATAAAAGGAAAGGTCCTTTGGACTTTCCT
TCGTA
Found at i:6158453 original size:30 final size:30
Alignment explanation
Indices: 6158419--6158479 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
6158409 AGATTTGAAA
** *
6158419 TTTTAAAATTTAAAAATAGAGAAATTAAAT
1 TTTTAAAAAATAAAAATAGAAAAATTAAAT
* *
6158449 TTTTAAAAAATAAAAGTATAAAAATTAAAT
1 TTTTAAAAAATAAAAATAGAAAAATTAAAT
6158479 T
1 T
6158480 GTATATATAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (30 bp):
TTTTAAAAAATAAAAATAGAAAAATTAAAT
Found at i:6159253 original size:17 final size:14
Alignment explanation
Indices: 6159210--6159255 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 14
6159200 TTTTTTTAGA
6159210 TTAAAATATTATTT
1 TTAAAATATTATTT
6159224 TTAAAAT-TTATTT
1 TTAAAATATTATTT
6159237 TTATTGAAATATTATTT
1 TTA---AAATATTATTT
6159254 TT
1 TT
6159256 CATAAGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.32
14 7 0.25
16 4 0.14
17 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
TTAAAATATTATTT
Found at i:6166727 original size:18 final size:18
Alignment explanation
Indices: 6166704--6166792 Score: 99
Period size: 18 Copynumber: 4.9 Consensus size: 18
6166694 TCATCAATAT
6166704 TAATCAGTTATTCAGTAA
1 TAATCAGTTATTCAGTAA
*
6166722 TAATCATTTATTCAGTAA
1 TAATCAGTTATTCAGTAA
* *
6166740 CAGTC-GTTTATTCAGTAA
1 TAATCAG-TTATTCAGTAA
* * *
6166758 CAGTCAATTATTCAGTAA
1 TAATCAGTTATTCAGTAA
*
6166776 TAATCATTTATTCAGTA
1 TAATCAGTTATTCAGTA
6166793 CCTTTATTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (18 bp):
TAATCAGTTATTCAGTAA
Found at i:6166753 original size:36 final size:36
Alignment explanation
Indices: 6166705--6166792 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
6166695 CATCAATATT
* * *
6166705 AATCAGTTATTCAGTAATAATCATTTATTCAGTAAC
1 AATCATTTATTCAGTAACAATCAATTATTCAGTAAC
* * * *
6166741 AGTCGTTTATTCAGTAACAGTCAATTATTCAGTAAT
1 AATCATTTATTCAGTAACAATCAATTATTCAGTAAC
6166777 AATCATTTATTCAGTA
1 AATCATTTATTCAGTA
6166793 CCTTTATTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (36 bp):
AATCATTTATTCAGTAACAATCAATTATTCAGTAAC
Found at i:6173172 original size:2 final size:2
Alignment explanation
Indices: 6173165--6173197 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6173155 CTCTTTATTT
6173165 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6173198 TAAATAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6173859 original size:45 final size:45
Alignment explanation
Indices: 6173770--6173870 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 45
6173760 GTAACAGTAG
* *
6173770 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCAAATTGATAA
1 CAGTAACAGTAACAATATTCGACACACAAAGTGCCAAATAGATAA
* * * **
6173815 TAGTAATAGTAACAATATTCGACACATAAAGTGCTGAATAGATAA
1 CAGTAACAGTAACAATATTCGACACACAAAGTGCCAAATAGATAA
6173860 CAGTAACAGTA
1 CAGTAACAGTA
6173871 GCAGTAACAG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.23
Consensus pattern (45 bp):
CAGTAACAGTAACAATATTCGACACACAAAGTGCCAAATAGATAA
Found at i:6174549 original size:15 final size:15
Alignment explanation
Indices: 6174523--6174561 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6174513 CCCATTTTCG
6174523 TTTCTGTTCCTTTATT
1 TTTCT-TTCCTTTATT
* *
6174539 TTTGTTTCCTTTCTT
1 TTTCTTTCCTTTATT
6174554 TTTCTTTC
1 TTTCTTTC
6174562 TTTCTTTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.03, C:0.21, G:0.05, T:0.72
Consensus pattern (15 bp):
TTTCTTTCCTTTATT
Found at i:6176586 original size:20 final size:20
Alignment explanation
Indices: 6176546--6176597 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
6176536 AAATACAAAT
* *
6176546 ATAATCATAATATATATTCAA
1 ATAATTATAA-ATATAATCAA
6176567 ATAATTATAAATATAATCAA
1 ATAATTATAAATATAATCAA
6176587 ATCAA-TATAAA
1 AT-AATTATAAA
6176598 ATACTATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAATTATAAATATAATCAA
Found at i:6185621 original size:30 final size:30
Alignment explanation
Indices: 6185587--6185648 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
6185577 ACTTATTTTA
6185587 TTGTTAATTTTGTTATTATTTCAAAGGCAT
1 TTGTTAATTTTGTTATTATTTCAAAGGCAT
* *
6185617 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTCAAAGGCAT
6185647 TT
1 TT
6185649 ACTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTCAAAGGCAT
Found at i:6187611 original size:15 final size:15
Alignment explanation
Indices: 6187559--6187675 Score: 58
Period size: 14 Copynumber: 8.1 Consensus size: 15
6187549 TTTATACTAC
*
6187559 AAAATATTT-TTATC
1 AAAATATTTATTATT
*
6187573 AATATATTTATTAATGT
1 AAAATATTTATT-AT-T
6187590 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
*
6187607 AAAATA-TTAATATT
1 AAAATATTTATTATT
*
6187621 -AAATA-TT-TTGTT
1 AAAATATTTATTATT
6187633 AAGAATA-TTA-T-TT
1 AA-AATATTTATTATT
6187646 AAAAT-TATTATT-TT
1 AAAATAT-TTATTATT
*
6187660 TAAA-ATTTATTATT
1 AAAATATTTATTATT
6187674 AA
1 AA
6187676 TATAATAATA
Statistics
Matches: 82, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
12 6 0.07
13 20 0.24
14 32 0.39
15 7 0.09
16 3 0.04
17 1 0.01
18 3 0.04
19 10 0.12
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:6187669 original size:16 final size:16
Alignment explanation
Indices: 6187638--6187674 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
6187628 TTGTTAAGAA
6187638 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
6187654 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
6187670 TATTA
1 TATTA
6187675 ATATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:6187675 original size:13 final size:14
Alignment explanation
Indices: 6187593--6187689 Score: 78
Period size: 13 Copynumber: 7.1 Consensus size: 14
6187583 TTAATGTAAT
6187593 AAATATTTATTATTA
1 AAATA-TTATTATTA
*
6187608 AAATATTAATATT-
1 AAATATTATTATTA
*
6187621 AAATATT-TTGTTA
1 AAATATTATTATTA
6187634 AGAATATTA-T-TTA
1 A-AATATTATTATTA
*
6187647 AAATTATTATTTTTA
1 AAA-TATTATTATTA
6187662 AAAT-TTATTATTA
1 AAATATTATTATTA
* * *
6187675 ATATAATAATATTA
1 AAATATTATTATTA
6187689 A
1 A
6187690 GTTTGATTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
12 5 0.07
13 28 0.41
14 24 0.35
15 11 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
AAATATTATTATTA
Found at i:6189415 original size:72 final size:73
Alignment explanation
Indices: 6189339--6189475 Score: 222
Period size: 73 Copynumber: 1.9 Consensus size: 73
6189329 TTTAAATTCA
6189339 TGTTTTCTTTGCATTTTCCGA-TTTTTCCTGGGTTTTTTACAACTGCGATAGCTGGTAAATGTTA
1 TGTTTTCTTTGCATTTTCCGATTTTTTCCTGGGTTTTTTACAACTGCGATAGCTGGTAAATGTTA
6189403 TTTTTCTC
66 TTTTTCTC
* * * * *
6189411 TGTTTTCTTTGCATTTTTCGATTTTTTCCTGGTTTTTTTACAACTTCGTTATCTGGTAAATGTTA
1 TGTTTTCTTTGCATTTTCCGATTTTTTCCTGGGTTTTTTACAACTGCGATAGCTGGTAAATGTTA
6189476 ATTACTTGTA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
72 20 0.34
73 39 0.66
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (73 bp):
TGTTTTCTTTGCATTTTCCGATTTTTTCCTGGGTTTTTTACAACTGCGATAGCTGGTAAATGTTA
TTTTTCTC
Found at i:6190887 original size:28 final size:28
Alignment explanation
Indices: 6190855--6190911 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
6190845 AATCTTTGCA
*
6190855 ACGCCTGAAAGAGAATATTCATACAGTC
1 ACGCCTGAAAGAGAATATTAATACAGTC
*
6190883 ACGCCTGAAAGAGCATATTAATACAGTC
1 ACGCCTGAAAGAGAATATTAATACAGTC
6190911 A
1 A
6190912 TCTAAACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (28 bp):
ACGCCTGAAAGAGAATATTAATACAGTC
Found at i:6193591 original size:18 final size:18
Alignment explanation
Indices: 6193568--6193605 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6193558 TATTGTTTTC
6193568 AAAATTTATTATTAAAAT
1 AAAATTTATTATTAAAAT
*
6193586 AAAATTTATTATTAATAT
1 AAAATTTATTATTAAAAT
6193604 AA
1 AA
6193606 TTATATTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATTTATTATTAAAAT
Found at i:6206689 original size:15 final size:15
Alignment explanation
Indices: 6206671--6206700 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6206661 AAATTTTAAT
*
6206671 TTTTTATAGTTTATA
1 TTTTTATAATTTATA
6206686 TTTTTATAATTTATA
1 TTTTTATAATTTATA
6206701 AAGGATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTATAATTTATA
Found at i:6212735 original size:19 final size:20
Alignment explanation
Indices: 6212695--6212738 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
6212685 GTCTCTTTAG
* *
6212695 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
6212714 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
6212733 GCATTA
1 GCATTA
6212739 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:6221338 original size:18 final size:18
Alignment explanation
Indices: 6221318--6221352 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
6221308 TTTTTTAAAA
6221318 AAAAATAAAAAAT-AATT
1 AAAAATAAAAAATCAATT
6221335 AAAAATAAAAAATCAATT
1 AAAAATAAAAAATCAATT
6221353 TTACCAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATAAAAAATCAATT
Found at i:6236774 original size:70 final size:70
Alignment explanation
Indices: 6236661--6236800 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
6236651 CGAAAAGCGA
6236661 GAGGATTTTGAAGAAGAAGACCCAGCACCAGATGCACCATCACCTACAGATTTGGCATCAATGGT
1 GAGGATTTTGAAGAAGAAGACCCAGCACCAGATGCACCATCACCTACAGATTTGGCATCAATGGT
6236726 ATGTG
66 ATGTG
*
6236731 GAGGATTTTGAAGAAGAAGACCCAGCACCAGATGCACCATCACCTACATATTTGGCATCAATGGT
1 GAGGATTTTGAAGAAGAAGACCCAGCACCAGATGCACCATCACCTACAGATTTGGCATCAATGGT
6236796 ATGTG
66 ATGTG
6236801 TAACGCCACA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (70 bp):
GAGGATTTTGAAGAAGAAGACCCAGCACCAGATGCACCATCACCTACAGATTTGGCATCAATGGT
ATGTG
Found at i:6237646 original size:61 final size:61
Alignment explanation
Indices: 6237547--6238077 Score: 652
Period size: 61 Copynumber: 8.7 Consensus size: 61
6237537 ACATGGTTGG
* *
6237547 ATTTGGCTCTCAGTAGCATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAACTGA
1 ATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGA
* * * *
6237608 ATTTGGCTCTCAGTAGCACAACAGTGAGCCAATCCAGCTCCTTTCATAGTTAGATAGCTGA
1 ATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGA
* * *
6237669 ATTTGGCTCTCAGTAGCACAACAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGA
1 ATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGA
* * * *
6237730 ATTTCGCTATCAGTAGAATATCAGTGAGCCAATTCAGTTCCTTTCATAGTTACATAGCTGA
1 ATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGA
* * * *
6237791 ATTCGGCTCTCAGTAGAATATCAGTGAGTCAATTAAGTTCCTTTCATAGTTAGATAGCTGA
1 ATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGA
* * * * * *
6237852 ATTTGGCTCTAAGTAGAATATCAGTGAGTCGATTCAGCTCCTTCCATAGATACATAGCTGA
1 ATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGA
* * * *
6237913 ATTTGGCTCTCAGTAGAACATCAGTGAGTCTATTCAGCCCCTTTCATAGTTAGATAGCTGA
1 ATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGA
* * * * * * * * * *
6237974 ATTGGGCTCT-TGTATAAAATCAATGAGCCAATTAAGTTCCTTCCAAAGTTACATAGCTGA
1 ATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGA
* * * * *
6238034 TTTTGGCTCTAAGTA-ATATATCAGTCAACCAATTCCAGTTCCTT
1 ATTTGGCTCTCAGTAGA-ATATCAGTGAGCCAATT-CAGCTCCTT
6238078 CCANNNNNNN
Statistics
Matches: 413, Mismatches: 54, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
60 47 0.11
61 358 0.87
62 8 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (61 bp):
ATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGA
Found at i:6252562 original size:18 final size:19
Alignment explanation
Indices: 6252536--6252571 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6252526 TAAACTAAAT
*
6252536 TTAACTCCCT-AATTTCAC
1 TTAAATCCCTAAATTTCAC
6252554 TTAAATCCCTAAATTTCA
1 TTAAATCCCTAAATTTCA
6252572 AAATTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATCCCTAAATTTCAC
Found at i:6253016 original size:17 final size:17
Alignment explanation
Indices: 6252984--6253016 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6252974 ACTTAAACAT
6252984 TAATATTATAATATATA
1 TAATATTATAATATATA
6253001 TAATACTTATAA-ATAT
1 TAATA-TTATAATATAT
6253017 CTATCTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATTATAATATATA
Found at i:6253585 original size:14 final size:15
Alignment explanation
Indices: 6253566--6253594 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6253556 TTGTTATAAA
6253566 AATATATAA-ATATT
1 AATATATAATATATT
6253580 AATATATAATATATT
1 AATATATAATATATT
6253595 TTTAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATATAATATATT
Found at i:6254023 original size:30 final size:30
Alignment explanation
Indices: 6253989--6254051 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
6253979 ACTTATTTTA
6253989 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
* *
6254019 TTGTTAATTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
6254049 TTG
1 TTG
6254052 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:6265114 original size:25 final size:24
Alignment explanation
Indices: 6265086--6265133 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
6265076 ATCATGGGAA
6265086 AAATGTG-AAGACATTGAAATGTATT
1 AAATGTGAAAGA-ATTGAAA-GTATT
6265111 AAATGTGAAAGAATTGAAAGTAT
1 AAATGTGAAAGAATTGAAAGTAT
6265134 AATATATGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 14 0.64
26 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.21, T:0.29
Consensus pattern (24 bp):
AAATGTGAAAGAATTGAAAGTATT
Found at i:6279429 original size:15 final size:15
Alignment explanation
Indices: 6279409--6279439 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6279399 ATCTTGGAAC
6279409 TAAGAAATGTTGTGT
1 TAAGAAATGTTGTGT
6279424 TAAGAAATGTTGTGT
1 TAAGAAATGTTGTGT
6279439 T
1 T
6279440 TCTTTATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (15 bp):
TAAGAAATGTTGTGT
Found at i:6281589 original size:54 final size:54
Alignment explanation
Indices: 6281526--6281633 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
6281516 TTTAATAGTC
*
6281526 ACTTATTTTTGGATGATTTCTTAAACTTTTAATTTCTTTCCAGGAATCGGAAGA
1 ACTTATTTTTGGATGATTTCTTAAACTTTTAATTGCTTTCCAGGAATCGGAAGA
*
6281580 ACTTATTTTTGGATGATTTCTTAAACTTTTAATTGCTTTCCAGGGATCGGAAGA
1 ACTTATTTTTGGATGATTTCTTAAACTTTTAATTGCTTTCCAGGAATCGGAAGA
6281634 GCCCCATCAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.44
Consensus pattern (54 bp):
ACTTATTTTTGGATGATTTCTTAAACTTTTAATTGCTTTCCAGGAATCGGAAGA
Found at i:6289430 original size:31 final size:30
Alignment explanation
Indices: 6289376--6289435 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
6289366 ATCTCTATCT
* *
6289376 TTTTTAAAGAATTAAATTAAATTTTTATCAA
1 TTTTAAAAGAATTAAAGTAAA-TTTTATCAA
6289407 TTTTAAAAG-ATTAAAGTATAATTTTATCA
1 TTTTAAAAGAATTAAAGTA-AATTTTATCA
6289436 TTATTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (30 bp):
TTTTAAAAGAATTAAAGTAAATTTTATCAA
Found at i:6289460 original size:16 final size:17
Alignment explanation
Indices: 6289436--6289468 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6289426 AATTTTATCA
*
6289436 TTATTAATT-TAAAATT
1 TTATAAATTATAAAATT
6289452 TTATAAATTATAAAATT
1 TTATAAATTATAAAATT
6289469 AAGCAGGGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATAAATTATAAAATT
Found at i:6289470 original size:23 final size:22
Alignment explanation
Indices: 6289426--6289470 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
6289416 ATTAAAGTAT
* * *
6289426 AATTTTATCATTATTAATTTAA
1 AATTTTATAATTATAAAATTAA
6289448 AATTTTATAAATTATAAAATTAA
1 AATTTTAT-AATTATAAAATTAA
6289471 GCAGGGCCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTTATAATTATAAAATTAA
Found at i:6302182 original size:18 final size:18
Alignment explanation
Indices: 6302149--6302183 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6302139 GTATTTGATG
**
6302149 TATTTTATTTTTAAAATT
1 TATTTTATTTAAAAAATT
6302167 TATTTTATTTAAAAAAT
1 TATTTTATTTAAAAAAT
6302184 ATAAAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTTATTTAAAAAATT
Found at i:6318356 original size:138 final size:140
Alignment explanation
Indices: 6318078--6318497 Score: 619
Period size: 141 Copynumber: 3.0 Consensus size: 140
6318068 CCAACTCCAC
* *
6318078 ATGCTACCATTTGGTCATAGCTTGAAAAGACTCTCTCTAATTCTACTACTAATCTTACGAGATAA
1 ATGCTACCATTAGGTCATAGCTTGAAAAGAC-CTCTCTAATCCTACTACTAATCTTACGAGATAA
** * * *
6318143 ATCACTAGCTTAATGAGACCTACGTCAATCTCTTCGTCTATACAAGTCCCTCCTCTAAAAAGAGT
65 ATCACTAGCACAATGAGACCCACGTCAATCTCTTCATCTATACAAGTCCCTCCTCTAAAAAGAGA
6318208 CAAACTCTCTT
130 CAAACTCTCTT
* *
6318219 ATGCTACCATTAGGTCATAACTTGAAAAGA-CTCTCTAATCCTACTGCTAATCTTACGAGATAAA
1 ATGCTACCATTAGGTCATAGCTTGAAAAGACCTCTCTAATCCTACTACTAATCTTACGAGATAAA
*
6318283 TCACTAGCACAATGAGACCCAC-ACAATCTCTTCATCTATACAAGTCCCTCCTCTAAAAAGAGAC
66 TCACTAGCACAATGAGACCCACGTCAATCTCTTCATCTATACAAGTCCCTCCTCTAAAAAGAGAC
6318347 AAACTCTCTT
131 AAACTCTCTT
* * * * * * *
6318357 ATGCTATCATTAAGTCATAGCTTAAAAAGACTCTCTCTAATCTTACTACTAATTTTACAAAATAA
1 ATGCTACCATTAGGTCATAGCTTGAAAAGAC-CTCTCTAATCCTACTACTAATCTTACGAGATAA
* * * *
6318422 ATCGCTAGCACAATGAGACTCACGTCAATCTCTTCATCTATACAAGTGCGTCCTCTAAAAAGAGA
65 ATCACTAGCACAATGAGACCCACGTCAATCTCTTCATCTATACAAGTCCCTCCTCTAAAAAGAGA
6318487 CAAACTCTCTT
130 CAAACTCTCTT
6318498 CCTCCAAGAG
Statistics
Matches: 252, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
138 75 0.30
139 51 0.20
140 49 0.19
141 77 0.31
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.30
Consensus pattern (140 bp):
ATGCTACCATTAGGTCATAGCTTGAAAAGACCTCTCTAATCCTACTACTAATCTTACGAGATAAA
TCACTAGCACAATGAGACCCACGTCAATCTCTTCATCTATACAAGTCCCTCCTCTAAAAAGAGAC
AAACTCTCTT
Found at i:6320071 original size:40 final size:38
Alignment explanation
Indices: 6320027--6320157 Score: 145
Period size: 40 Copynumber: 3.3 Consensus size: 38
6320017 GATTATGCAT
* *
6320027 TAGCGGCGTTTGGAGCAAAAACGCCGCTAAAACTGAGTAA
1 TAGCGGCGTTTGG-TC-CAAACGCCGCTAAAACTGAGTAA
* * *
6320067 TAGCGGCGTTTTGGTCCAAATGCCGCTAAAAACTTAGAAA
1 TAGCGGCG-TTTGGTCCAAACGCCGCT-AAAACTGAGTAA
*
6320107 TAGCGGCATTTTTGGTCCAAACGCCGCTAAAACTGAGTAA
1 TAGCGGC--GTTTGGTCCAAACGCCGCTAAAACTGAGTAA
*
6320147 TAGAGGCGTTT
1 TAGCGGCGTTT
6320158 TTTTAAGAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
38 3 0.04
39 9 0.12
40 42 0.55
41 22 0.29
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (38 bp):
TAGCGGCGTTTGGTCCAAACGCCGCTAAAACTGAGTAA
Found at i:6320160 original size:41 final size:40
Alignment explanation
Indices: 6320045--6320159 Score: 169
Period size: 40 Copynumber: 2.9 Consensus size: 40
6320035 TTTGGAGCAA
6320045 AAACGCCGCTAAAACTGAGTAATAGCGGCG-TTTTGGTCC
1 AAACGCCGCTAAAACTGAGTAATAGCGGCGTTTTTGGTCC
* * * *
6320084 AAATGCCGCTAAAAACTTAGAAATAGCGGCATTTTTGGTCC
1 AAACGCCGCT-AAAACTGAGTAATAGCGGCGTTTTTGGTCC
*
6320125 AAACGCCGCTAAAACTGAGTAATAGAGGCGTTTTT
1 AAACGCCGCTAAAACTGAGTAATAGCGGCGTTTTT
6320160 TTAAGAAAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 9 0.14
40 38 0.58
41 18 0.28
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (40 bp):
AAACGCCGCTAAAACTGAGTAATAGCGGCGTTTTTGGTCC
Found at i:6321863 original size:58 final size:58
Alignment explanation
Indices: 6321793--6321908 Score: 207
Period size: 59 Copynumber: 2.0 Consensus size: 58
6321783 TCCAAAACAG
*
6321793 ATTTCCCCCAATTCCACA-ATTTCCTAATCCCTAAAATTTTCCCAAAATCCATAGCCA
1 ATTTCCCCCAATTCCACAGATTTCCTAATCCCTAAAATTTCCCCAAAATCCATAGCCA
6321850 NATTTCCCCCAATTCCACAGATTTCCTAATCCCTAAAATTTCCCCAAAATCCATAGCCA
1 -ATTTCCCCCAATTCCACAGATTTCCTAATCCCTAAAATTTCCCCAAAATCCATAGCCA
6321909 TCTGCTGCTG
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 18 0.32
59 38 0.68
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.28
Consensus pattern (58 bp):
ATTTCCCCCAATTCCACAGATTTCCTAATCCCTAAAATTTCCCCAAAATCCATAGCCA
Found at i:6322670 original size:47 final size:46
Alignment explanation
Indices: 6322600--6322693 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 46
6322590 GCCATTCCTT
*
6322600 TCCAGTTTACTTGCTAACAAAACTATTACCATTCATCTAGCAGGAA
1 TCCAGTTTACTAGCTAACAAAACTATTACCATTCATCTAGCAGGAA
*
6322646 TNCCAGTTTACTAGCTAACAAAACTGTTACCATTCATCTAGCAGGAA
1 T-CCAGTTTACTAGCTAACAAAACTATTACCATTCATCTAGCAGGAA
6322693 T
1 T
6322694 GACCACTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.02
47 44 0.98
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.30
Consensus pattern (46 bp):
TCCAGTTTACTAGCTAACAAAACTATTACCATTCATCTAGCAGGAA
Found at i:6326614 original size:17 final size:17
Alignment explanation
Indices: 6326569--6326605 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
6326559 TAGGAGTTTC
6326569 AACAATAATCATAACAA
1 AACAATAATCATAACAA
6326586 AACAATAATCATAACAA
1 AACAATAATCATAACAA
6326603 AAC
1 AAC
6326606 TTTAATCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.16
Consensus pattern (17 bp):
AACAATAATCATAACAA
Found at i:6328975 original size:3 final size:3
Alignment explanation
Indices: 6328967--6329071 Score: 51
Period size: 3 Copynumber: 36.3 Consensus size: 3
6328957 AAGGAATATT
* * * * *
6328967 ATA ATA ATA A-C ATA ATA ATA ATA TTA ATA ATC AT- ATT ATA GTTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * * *
6329011 GTA ATT CTA ATA CTA ATT A-A ATA ATA AT- ATA A-A A-A ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
*
6329053 ATA ATA ACA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
6329072 AGTAAAAATA
Statistics
Matches: 76, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
2 10 0.13
3 61 0.80
4 5 0.07
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6328975 original size:11 final size:11
Alignment explanation
Indices: 6328935--6329070 Score: 59
Period size: 11 Copynumber: 11.9 Consensus size: 11
6328925 ATGTGGGTAG
6328935 AATAATAA-AT
1 AATAATAATAT
6328945 AATAAGTAA-AT
1 AATAA-TAATAT
* *
6328956 AAAGGAATATTAT
1 -AA-TAATAATAT
*
6328969 AATAATAACAT
1 AATAATAATAT
6328980 AATAATAATATT
1 AATAATAATA-T
6328992 AATAATCATATTAT
1 AATAAT-A-A-TAT
* * *
6329006 AGTTAGTAATTCT
1 A-ATAATAA-TAT
*
6329019 AATACTAAT-T
1 AATAATAATAT
6329029 AAATAATAATAT
1 -AATAATAATAT
6329041 AA-AA-AATA-
1 AATAATAATAT
*
6329049 AATAATAATAAC
1 AATAATAAT-AT
6329061 AATAATAATA
1 AATAATAATA
6329071 AAGTAAAAAT
Statistics
Matches: 99, Mismatches: 12, Indels: 29
0.71 0.09 0.21
Matches are distributed among these distances:
8 2 0.02
9 6 0.06
10 11 0.11
11 33 0.33
12 28 0.28
13 10 0.10
14 4 0.04
15 5 0.05
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (11 bp):
AATAATAATAT
Found at i:6332419 original size:12 final size:12
Alignment explanation
Indices: 6332402--6332426 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6332392 ACCCAAAACC
6332402 CTTAGCCCAAAA
1 CTTAGCCCAAAA
6332414 CTTAGCCCAAAA
1 CTTAGCCCAAAA
6332426 C
1 C
6332427 ACTAACCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CTTAGCCCAAAA
Found at i:6342319 original size:24 final size:24
Alignment explanation
Indices: 6342292--6342359 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 24
6342282 AACATTTGGC
6342292 ATTT-GAACTTAATATTTTTTTTTA
1 ATTTGGAACTTAA-ATTTTTTTTTA
* *
6342316 ATTTGGTACTTCAATTTTTTTTATCCA
1 ATTTGGAACTTAAATTTTTTTT-T--A
*
6342343 ATTTGGTACTTAAATTT
1 ATTTGGAACTTAAATTT
6342360 GACACTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 13 0.35
25 7 0.19
27 17 0.46
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.57
Consensus pattern (24 bp):
ATTTGGAACTTAAATTTTTTTTTA
Found at i:6345818 original size:18 final size:18
Alignment explanation
Indices: 6345791--6345832 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
6345781 CTTTTTTAGG
6345791 AATG-TTTTTG-TCTCAAA
1 AATGCTTTTTGTTC-CAAA
*
6345808 AGTGCTTTTTGTTCCAAA
1 AATGCTTTTTGTTCCAAA
6345826 AATGCTT
1 AATGCTT
6345833 CTTAGAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 16 0.76
19 2 0.10
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (18 bp):
AATGCTTTTTGTTCCAAA
Found at i:6346242 original size:143 final size:138
Alignment explanation
Indices: 6345901--6346273 Score: 410
Period size: 139 Copynumber: 2.7 Consensus size: 138
6345891 TCCCATCTTT
* * * * * *
6345901 ACCAGGCATATATTCTGCCTCCTCCATATGTGGAATAAGCAACTCGACAACCCCATTTGATCATT
1 ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCATG
* * *
6345966 TTCAGTAAATCACTTCAGTTTCTTAAGCTTCTCTTCTCTTCAAGTCCCACTTTCAAGATCATGTA
66 TTCAGT-AATTACTTCAGTTTCTTCAGCTTCTCTCCTCTTCAAGTCCCACTTTCAAGATCATGTA
**
6346031 TCAATGTAA
130 TCAATCAAA
* * * *
6346040 ACCAGGCATTTACCCTGTTTCTTCCATATGTAGAACAAGCAACT-TAACAACCCCATTTGATCAT
1 ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCT-ACAACCCCATTTGATCAT
* * * *
6346104 GTTCAGTACCTTACTTCAGTTTCTTCAGCTTTTCTCCT-TTGAAGTCCTA-TCTTCAAGATCATG
65 GTTCAGTA-ATTACTTCAGTTTCTTCAGCTTCTCTCCTCTTCAAGTCCCACT-TTCAAGATCATG
6346167 TATCAAACAATCAAA
128 TAT----CAATCAAA
* * * *
6346182 ACCAGGCATGTATCCTAGCTTCTTCCATATTTAGAATATGCAACTCTATAACCCCATTTGATCAT
1 ACCAGGCATATATCCT-GCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCAT
* *
6346247 GTTCAATAATTCACTTCAGTTTTTTCA
65 GTTCAGTAATT-ACTTCAGTTTCTTCA
6346274 AATCCCATCT
Statistics
Matches: 195, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
137 1 0.01
138 25 0.13
139 84 0.43
142 22 0.11
143 62 0.32
144 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (138 bp):
ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCATG
TTCAGTAATTACTTCAGTTTCTTCAGCTTCTCTCCTCTTCAAGTCCCACTTTCAAGATCATGTAT
CAATCAAA
Found at i:6350075 original size:42 final size:42
Alignment explanation
Indices: 6350026--6350315 Score: 330
Period size: 42 Copynumber: 6.7 Consensus size: 42
6350016 AGCCCCACAA
* **
6350026 TTAATCCCAACTCAATTAGGATTTATCTTTTTAACATTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAATTTTTCAT
* *
6350068 TTAATCCCAACTCAATTAGGATTTATCTTTTTTAGCTTTTT-AT
1 TTAATCCCACCTCAATTAGGATTTATC-TTTTTA-ATTTTTCAT
* *
6350111 TTAATCCCAACTTAATTAGGATTTAAGCTTATCTTTTTAATTTTTCAT
1 TTAATCCCACCTCAATTAGGA--T----TTATCTTTTTAATTTTTCAT
* * * * *
6350159 TTAATCTCACCTCAATTAAGATTTATGTTTTTAGTTTTTTAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAATTTTTCAT
* *
6350201 TTAATCACACCTCAATTAGGATTTATCTTTTTATTTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAATTTTTCAT
* * *
6350243 TTAATCTCACCTCAATTAGGATTCATTTTTTTAATTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAATTTTTCAT
* *
6350285 TTAATCTCACCTCAATTAGGATTTATGTTTT
1 TTAATCCCACCTCAATTAGGATTTATCTTTT
6350316 CAGGAGGATT
Statistics
Matches: 216, Mismatches: 23, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
42 148 0.69
43 28 0.13
44 3 0.01
45 1 0.00
46 1 0.00
47 5 0.02
48 25 0.12
49 5 0.02
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (42 bp):
TTAATCCCACCTCAATTAGGATTTATCTTTTTAATTTTTCAT
Found at i:6350203 original size:133 final size:126
Alignment explanation
Indices: 6350026--6350315 Score: 366
Period size: 133 Copynumber: 2.2 Consensus size: 126
6350016 AGCCCCACAA
* * * *
6350026 TTAATCCCAACTCAATTAGGATTTATCTTTTTAACATTTCATTTAATCCCAACTCAATTAGGATT
1 TTAATCTCACCTCAATTAGGATTTATGTTTTTAACATTTCATTTAATCACAACTCAATTAGGATT
*
6350091 TATCTTTTTTAGCTTTTT-ATTTAATCCCAACTTAATTAGGATTTAAGCTTATCTTTTTAATTTT
66 TATC-TTTTTA-CTTTTTCATTTAATCCCAACTCAATTAGGA-TT---C--ATCTTTTTAATTTT
6350155 TCAT
123 TCAT
* *** * *
6350159 TTAATCTCACCTCAATTAAGATTTATGTTTTTAGTTTTTTATTTAATCACACCTCAATTAGGATT
1 TTAATCTCACCTCAATTAGGATTTATGTTTTTAACATTTCATTTAATCACAACTCAATTAGGATT
* * * *
6350224 TATCTTTTTATTTTTTCATTTAATCTCACCTCAATTAGGATTCATTTTTTTAATTTTTCAT
66 TATCTTTTTACTTTTTCATTTAATCCCAACTCAATTAGGATTCATCTTTTTAATTTTTCAT
6350285 TTAATCTCACCTCAATTAGGATTTATGTTTT
1 TTAATCTCACCTCAATTAGGATTTATGTTTT
6350316 CAGGAGGATT
Statistics
Matches: 140, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
126 47 0.34
128 1 0.01
131 7 0.05
132 26 0.19
133 59 0.42
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (126 bp):
TTAATCTCACCTCAATTAGGATTTATGTTTTTAACATTTCATTTAATCACAACTCAATTAGGATT
TATCTTTTTACTTTTTCATTTAATCCCAACTCAATTAGGATTCATCTTTTTAATTTTTCAT
Found at i:6350260 original size:84 final size:84
Alignment explanation
Indices: 6350026--6350315 Score: 364
Period size: 84 Copynumber: 3.4 Consensus size: 84
6350016 AGCCCCACAA
** * *
6350026 TTAATCCCAACTCAATTAGGATTTATCTTTTTAACATTTCATTTAATCCCAACTCAATTAGGATT
1 TTAATCCCAACTCAATTAGGATTTATCTTTTTAATTTTTCATTTAATCTCACCTCAATTAGGATT
*
6350091 TATCTTTTTTAGCTTTTTAT
66 TAT-TTTTTTAGTTTTTTAT
*
6350111 TTAATCCCAACTTAATTAGGATTTAAGCTTATCTTTTTAATTTTTCATTTAATCTCACCTCAATT
1 TTAATCCCAACTCAATTAGGA--T----TTATCTTTTTAATTTTTCATTTAATCTCACCTCAATT
* *
6350176 AAGATTTATGTTTTTAGTTTTTTAT
60 AGGATTTATTTTTTTAGTTTTTTAT
* * *
6350201 TTAATCACACCTCAATTAGGATTTATCTTTTTATTTTTTCATTTAATCTCACCTCAATTAGGATT
1 TTAATCCCAACTCAATTAGGATTTATCTTTTTAATTTTTCATTTAATCTCACCTCAATTAGGATT
* * *
6350266 CATTTTTTTAATTTTTCAT
66 TATTTTTTTAGTTTTTTAT
* * *
6350285 TTAATCTCACCTCAATTAGGATTTATGTTTT
1 TTAATCCCAACTCAATTAGGATTTATCTTTT
6350316 CAGGAGGATT
Statistics
Matches: 180, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
84 85 0.47
85 20 0.11
87 1 0.01
88 1 0.01
90 32 0.18
91 41 0.23
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (84 bp):
TTAATCCCAACTCAATTAGGATTTATCTTTTTAATTTTTCATTTAATCTCACCTCAATTAGGATT
TATTTTTTTAGTTTTTTAT
Found at i:6355781 original size:19 final size:19
Alignment explanation
Indices: 6355757--6355795 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6355747 TATTATTAAT
*
6355757 ACATTTATAATTATAATAA
1 ACATTTATAATTAAAATAA
*
6355776 ACATTTATTATTAAAATAA
1 ACATTTATAATTAAAATAA
6355795 A
1 A
6355796 ATTAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
ACATTTATAATTAAAATAA
Found at i:6356041 original size:17 final size:18
Alignment explanation
Indices: 6356011--6356046 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
6356001 TAAATTTACC
6356011 AGGAACTCTTTTTTGAAG
1 AGGAACTCTTTTTTGAAG
6356029 AGGAACT-TTTTTTGAAG
1 AGGAACTCTTTTTTGAAG
6356046 A
1 A
6356047 ATAAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (18 bp):
AGGAACTCTTTTTTGAAG
Found at i:6357434 original size:21 final size:22
Alignment explanation
Indices: 6357397--6357440 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
6357387 TTCGTATTTT
6357397 ACAAATTAAATACAAAA-TAAA
1 ACAAATTAAATACAAAATTAAA
*
6357418 ACAAATTAAA-ATTAAAATTAAA
1 ACAAATTAAATA-CAAAATTAAA
6357440 A
1 A
6357441 TTATTCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 14 0.70
22 5 0.25
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (22 bp):
ACAAATTAAATACAAAATTAAA
Found at i:6364648 original size:6 final size:6
Alignment explanation
Indices: 6364637--6365573 Score: 1865
Period size: 6 Copynumber: 156.2 Consensus size: 6
6364627 TAAGCACTTG
6364637 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6364685 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6364733 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6364781 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6364829 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6364877 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6364925 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6364973 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6365021 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6365069 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6365117 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6365165 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6365213 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6365261 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6365309 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6365357 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6365405 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6365453 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
*
6365501 CATATA CATATA CATATA CATATA CATATA CATATA CATATG CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
6365549 CATATA CATATA CATATA CATATA C
1 CATATA CATATA CATATA CATATA C
6365574 TAAAAAAGAT
Statistics
Matches: 929, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 929 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
CATATA
Found at i:6366473 original size:27 final size:27
Alignment explanation
Indices: 6366443--6366510 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
6366433 GTGTAAGTCC
* *
6366443 CAGAGGTGGCACCGGTTGTGCCTCTGG
1 CAGAGGCGGCACCGGTCGTGCCTCTGG
*
6366470 CAGAGGCGGCACCGGTCGTGCCTCTAG
1 CAGAGGCGGCACCGGTCGTGCCTCTGG
* *
6366497 CATAGGCGACACCG
1 CAGAGGCGGCACCG
6366511 ATTTTGCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.16, C:0.31, G:0.37, T:0.16
Consensus pattern (27 bp):
CAGAGGCGGCACCGGTCGTGCCTCTGG
Found at i:6368686 original size:18 final size:19
Alignment explanation
Indices: 6368658--6368695 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
6368648 TACTAAGAAA
6368658 AATTCAAAATAAAAAAAAT
1 AATTCAAAATAAAAAAAAT
*
6368677 AATT-AAAATAAACAAAAT
1 AATTCAAAATAAAAAAAAT
6368695 A
1 A
6368696 TAAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AATTCAAAATAAAAAAAAT
Found at i:6373623 original size:6 final size:6
Alignment explanation
Indices: 6373612--6373660 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
6373602 TCTATTTATT
*
6373612 TATGTA TATGTA TATGCA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
6373660 T
1 T
6373661 CTATCCTGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (6 bp):
TATGTA
Found at i:6374710 original size:11 final size:11
Alignment explanation
Indices: 6374694--6374718 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6374684 AATAAAATAA
6374694 AATAATTATAT
1 AATAATTATAT
6374705 AATAATTATAT
1 AATAATTATAT
6374716 AAT
1 AAT
6374719 TAAAAATAAT
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:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATAATTATAT
Found at i:6377191 original size:12 final size:12
Alignment explanation
Indices: 6377174--6377198 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6377164 AAGTATATCA
6377174 GCTTTAGTTTTT
1 GCTTTAGTTTTT
6377186 GCTTTAGTTTTT
1 GCTTTAGTTTTT
6377198 G
1 G
6377199 AGGTATAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (12 bp):
GCTTTAGTTTTT
Found at i:6378209 original size:21 final size:21
Alignment explanation
Indices: 6378185--6378224 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
6378175 CGTGTCAATA
6378185 TTTA-ATTATAAATATTTAATT
1 TTTATATT-TAAATATTTAATT
6378206 TTTATATTTAAATATTTAA
1 TTTATATTTAAATATTTAA
6378225 ATATAGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATATTTAAATATTTAATT
Found at i:6378501 original size:13 final size:13
Alignment explanation
Indices: 6378483--6378520 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
6378473 ACACTCAAAT
6378483 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
6378496 TTCTCAAAAGTAC
1 TTCTCAAAAGCAC
6378509 TTCTCAAAAGCA
1 TTCTCAAAAGCA
6378521 ATGAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.26, G:0.08, T:0.26
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:6383265 original size:16 final size:17
Alignment explanation
Indices: 6383244--6383289 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
6383234 CGTAAATAGT
6383244 TAAAATAATTTAAAT-A
1 TAAAATAATTTAAATCA
* *
6383260 TAAAATAATTAAAATCT
1 TAAAATAATTTAAATCA
*
6383277 TAAAATGATTTAA
1 TAAAATAATTTAA
6383290 TTATGAATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAAATAATTTAAATCA
Done.