Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 130 of 210
Found at i:43318287 original size:21 final size:21
Alignment explanation
Indices: 43318235--43318293 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
43318225 ATATGCCAAT
*
43318235 AGAAGCTCA-AA-AGCAGAAC
1 AGAAGCTCATAAGAGCTGAAC
*
43318254 AGAAGCTCATAAGATCTGAAC
1 AGAAGCTCATAAGAGCTGAAC
**
43318275 AGAAGCTTGTAAGAGCTGA
1 AGAAGCTCATAAGAGCTGA
43318294 TCCACTCGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 9 0.27
20 2 0.06
21 22 0.67
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTGAAC
Found at i:43318494 original size:39 final size:39
Alignment explanation
Indices: 43318440--43318517 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
43318430 CTTTCAATTT
*
43318440 AAACCGAATATCCAATTTAATATTATAATTCCAACAATA
1 AAACCGAATATCCAATTCAATATTATAATTCCAACAATA
43318479 AAACCGAATATCCAATTCAATATTATAATTCCAACAATA
1 AAACCGAATATCCAATTCAATATTATAATTCCAACAATA
43318518 GAATAAATAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.49, C:0.19, G:0.03, T:0.29
Consensus pattern (39 bp):
AAACCGAATATCCAATTCAATATTATAATTCCAACAATA
Found at i:43322202 original size:44 final size:44
Alignment explanation
Indices: 43322139--43322255 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 44
43322129 GATGTCATAG
* *
43322139 TATCTTTCAACCATGGTATTTCCTTTTCGAATATAATGCCTTGA
1 TATCTTTCAATCATGGTATTTCCTTTTCGAATATAATGCCATGA
* ** * *
43322183 TATCTTTGAATCATGGTATTTCCTTTTTTAGTATAATGTCATGA
1 TATCTTTCAATCATGGTATTTCCTTTTCGAATATAATGCCATGA
*
43322227 TATCTTTCAATCATGGTCTTTCCCTTTTC
1 TATCTTTCAATCATGGTATTT-CCTTTTC
43322256 TCAAATCAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
44 56 0.90
45 6 0.10
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (44 bp):
TATCTTTCAATCATGGTATTTCCTTTTCGAATATAATGCCATGA
Found at i:43324307 original size:43 final size:43
Alignment explanation
Indices: 43324240--43324369 Score: 115
Period size: 43 Copynumber: 3.0 Consensus size: 43
43324230 CATAGGATTT
* * *
43324240 TCGATATGTGTTTTCGCGTAAGACCACGTCTGGGACTTTGGCA
1 TCGATCTGTGTTTACGTGTAAGACCACGTCTGGGACTTTGGCA
* **
43324283 TCGA-CTTGTGTTTACGTGTAAGACC-CTATCTGGGACAGTGAG-A
1 TCGATC-TGTGTTTACGTGTAAGACCAC-GTCTGGGACTTTG-GCA
* * *
43324326 TCGATCTGTGATTGCATGTAAGACCACGTCTGGGA-TGTTGGCA
1 TCGATCTGTGTTTACGTGTAAGACCACGTCTGGGACT-TTGGCA
43324369 T
1 T
43324370 TGTACAAGCC
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
42 2 0.03
43 63 0.93
44 3 0.04
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (43 bp):
TCGATCTGTGTTTACGTGTAAGACCACGTCTGGGACTTTGGCA
Found at i:43328350 original size:29 final size:29
Alignment explanation
Indices: 43328286--43328351 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
43328276 TTGGGCACAC
* * * **
43328286 GCCCGTGTGCTTTACATGCTCGTGTGGTT
1 GCCCGTGTGCTTCACACGATCGTGTGGCA
*
43328315 GCTCGTGTGCTTCACACGATCGTGTGGCA
1 GCCCGTGTGCTTCACACGATCGTGTGGCA
43328344 GCCCGTGT
1 GCCCGTGT
43328352 CCCAAGCTGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.09, C:0.27, G:0.32, T:0.32
Consensus pattern (29 bp):
GCCCGTGTGCTTCACACGATCGTGTGGCA
Found at i:43344938 original size:17 final size:17
Alignment explanation
Indices: 43344912--43344944 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43344902 ATAGAAAGTC
43344912 AAAGACATGGGTATCAG
1 AAAGACATGGGTATCAG
*
43344929 AAAGATATGGGTATCA
1 AAAGACATGGGTATCA
43344945 AAATCTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.27, T:0.21
Consensus pattern (17 bp):
AAAGACATGGGTATCAG
Found at i:43364732 original size:24 final size:24
Alignment explanation
Indices: 43364699--43364786 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
43364689 TGTAGCATTT
*
43364699 TGTTTGGCCTTTGTGGCGTACTTC
1 TGTTTGGCCTTTGTGGCGCACTTC
* * * *
43364723 TATTTGGCCTTTTTGACACACTTC
1 TGTTTGGCCTTTGTGGCGCACTTC
* * *
43364747 TGTTCGGCCTTTGTAGCGCA-TTT
1 TGTTTGGCCTTTGTGGCGCACTTC
43364770 TGTTTGGCCTTTGTGGC
1 TGTTTGGCCTTTGTGGC
43364787 ATTCTGTTAG
Statistics
Matches: 50, Mismatches: 14, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
23 17 0.34
24 33 0.66
ACGTcount: A:0.08, C:0.22, G:0.25, T:0.45
Consensus pattern (24 bp):
TGTTTGGCCTTTGTGGCGCACTTC
Found at i:43364801 original size:20 final size:23
Alignment explanation
Indices: 43364684--43364804 Score: 65
Period size: 24 Copynumber: 5.4 Consensus size: 23
43364674 TTCATGGGGT
* *
43364684 GCCTTTGTA--GCATTTTGTTTG
1 GCCTTTGTAGCGCATTCTGTTTA
* * * *
43364705 GCCTTTGTGGCGTACTTCTATTTG
1 GCCTTTGTAGCGCA-TTCTGTTTA
* * **
43364729 GCCTTT-TTGACACACTTCTGTTCG
1 GCCTTTGTAG-CGCA-TTCTGTTTA
* *
43364753 GCCTTTGTAGCGCATTTTGTTTG
1 GCCTTTGTAGCGCATTCTGTTTA
43364776 GCCTTTGT-G-GCATTCTG-TTA
1 GCCTTTGTAGCGCATTCTGTTTA
43364796 GCCTTTGTA
1 GCCTTTGTA
43364805 ATGTATTTTG
Statistics
Matches: 79, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
20 10 0.13
21 15 0.19
22 1 0.01
23 19 0.24
24 32 0.41
25 2 0.03
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (23 bp):
GCCTTTGTAGCGCATTCTGTTTA
Found at i:43373836 original size:19 final size:20
Alignment explanation
Indices: 43373799--43373839 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
43373789 TACAACACAA
*
43373799 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
43373819 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
43373838 TT
1 TT
43373840 GCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:43374276 original size:26 final size:28
Alignment explanation
Indices: 43374246--43374311 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
43374236 CCGTGGGTTC
*
43374246 TTCTTTCTTTCTC-TTTTTCTTTT-TCT
1 TTCTTTCTTTCTCGTTTTGCTTTTGTCT
43374272 TTCTTTCTATT-TCGTTTTGCTTTTGTCT
1 TTCTTTCT-TTCTCGTTTTGCTTTTGTCT
*
43374300 TTCTTTATTTCT
1 TTCTTTCTTTCT
43374312 TTTATTACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 10 0.29
27 13 0.38
28 11 0.32
ACGTcount: A:0.03, C:0.20, G:0.05, T:0.73
Consensus pattern (28 bp):
TTCTTTCTTTCTCGTTTTGCTTTTGTCT
Found at i:43374408 original size:43 final size:40
Alignment explanation
Indices: 43374321--43374408 Score: 97
Period size: 43 Copynumber: 2.1 Consensus size: 40
43374311 TTTTATTACT
* *
43374321 ATAATATATGTATTTACTTAATTATTAAGTAAAACATATT
1 ATAATATATATATTTACTTAATTATTAAGTAAAACATATA
* *
43374361 ATAATATATATATTTTAACTTTAATTTATTAA-TAATATATATA
1 ATAATATATATA-TTT-AC-TTAA-TTATTAAGTAAAACATATA
43374404 ATAAT
1 ATAAT
43374409 TTTACACTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 11 0.28
41 3 0.08
42 2 0.05
43 17 0.43
44 7 0.17
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (40 bp):
ATAATATATATATTTACTTAATTATTAAGTAAAACATATA
Found at i:43376567 original size:3 final size:3
Alignment explanation
Indices: 43376559--43376627 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
43376549 CTAGACTTTG
43376559 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43376607 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
43376628 TCTTTGAATT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:43381703 original size:5 final size:5
Alignment explanation
Indices: 43381695--43381725 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
43381685 GAGATGGAAT
43381695 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
43381726 ATATTTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:43382357 original size:30 final size:30
Alignment explanation
Indices: 43382335--43382395 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
43382325 GGGAGGGGAG
*
43382335 GGGAGAGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGA-AGGAGTAAAAATTTTGGGGGGAAAGT
* *
43382366 GGGAAGGAGTAAAAATTTTGAGGGAAAAGT
1 GGGAAGGAGTAAAAATTTTGGGGGGAAAGT
43382396 AAAAAAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.20
Consensus pattern (30 bp):
GGGAAGGAGTAAAAATTTTGGGGGGAAAGT
Found at i:43385934 original size:39 final size:39
Alignment explanation
Indices: 43385874--43385953 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
43385864 CATATGCATC
*
43385874 TGGTGATAAGATCGTGAGTGAAGATCTTATGGCTAAGTT
1 TGGTGATAAGATCATGAGTGAAGATCTTATGGCTAAGTT
* *
43385913 TGGTGATAAGATCATGGGTGAAGATGTTATGGCTAAGTT
1 TGGTGATAAGATCATGAGTGAAGATCTTATGGCTAAGTT
43385952 TG
1 TG
43385954 AGGCTTTGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.06, G:0.33, T:0.34
Consensus pattern (39 bp):
TGGTGATAAGATCATGAGTGAAGATCTTATGGCTAAGTT
Found at i:43386130 original size:180 final size:177
Alignment explanation
Indices: 43385913--43386238 Score: 483
Period size: 180 Copynumber: 1.8 Consensus size: 177
43385903 TGGCTAAGTT
* * *
43385913 TGGTGATAAGATCATGGGTGAAGATGTTATGGCTAAGTTTGAGGCTTTGACAGAGAAGGCT-TCC
1 TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAGGCTTTGACAGAGAAGG-TGTCC
* * * * *
43385977 CATATTATAGCTGATGGTGTAGCTAGGATCCTTAAAGGTAAGGCTGCAGAATCAATCTCGCGTGG
65 CATATTATAGCTAATGATGTAGCTAGGATCATTAAAGATAAGGCTGCAGAATCAATCTCGCATGG
43386042 AAGAAATGAAGTTTCCCATGTCTATAATGAAGTAGAAGAAACATATGCATC
130 -AG--ATGAAGTTTCCCATGTCTATAATGAAGTAGAAGAAACATATGCATC
* *
43386093 TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAGGCTTTGACAGAGACGGTGTGCC
1 TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAGGCTTTGACAGAGAAGGTGTCCC
* * *
43386158 ATGTTATAGCTAATGATGTAGCTAGGATTATTAAAGATAAGGCTGCAGAATTAATCTCGCATGGA
66 ATATTATAGCTAATGATGTAGCTAGGATCATTAAAGATAAGGCTGCAGAATCAATCTCGCATGGA
*
43386223 GATGAAGTTTCGCATG
131 GATGAAGTTTCCCATG
43386239 CCACATATGC
Statistics
Matches: 131, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
177 14 0.11
179 3 0.02
180 114 0.87
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (177 bp):
TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAGGCTTTGACAGAGAAGGTGTCCC
ATATTATAGCTAATGATGTAGCTAGGATCATTAAAGATAAGGCTGCAGAATCAATCTCGCATGGA
GATGAAGTTTCCCATGTCTATAATGAAGTAGAAGAAACATATGCATC
Found at i:43390166 original size:27 final size:28
Alignment explanation
Indices: 43390110--43390172 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 28
43390100 AAAAAATAAT
*
43390110 CAAAATATTATAACTTTTTTTTATTAAC
1 CAAAATATTATAACTTTTTTCTATTAAC
*
43390138 CAAAATATTATAA-TTTTTTCTATTTAC
1 CAAAATATTATAACTTTTTTCTATTAAC
43390165 CAAAATAT
1 CAAAATAT
43390173 ACCAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 20 0.61
28 13 0.39
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
CAAAATATTATAACTTTTTTCTATTAAC
Found at i:43390272 original size:27 final size:27
Alignment explanation
Indices: 43390242--43390312 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
43390232 TCGTGCTAAG
* *
43390242 GTGATTGGCGGCACCAAATGTGCCATA
1 GTGATTGGCGGCACCAAAGGTGCCAAA
43390269 GTGATTGGCGGCACCAAAGGTGCCAAA
1 GTGATTGGCGGCACCAAAGGTGCCAAA
**
43390296 GACATTGGCGGCACCAA
1 GTGATTGGCGGCACCAA
43390313 TGTTATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.31, T:0.17
Consensus pattern (27 bp):
GTGATTGGCGGCACCAAAGGTGCCAAA
Found at i:43390465 original size:27 final size:28
Alignment explanation
Indices: 43390409--43390471 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 28
43390399 AAAAAATAAT
*
43390409 CAAAATATTATAACTTTTTTTTATTAAC
1 CAAAATATTATAACTTTTTTCTATTAAC
*
43390437 CAAAATATTATAA-TTTTTTCTATTTAC
1 CAAAATATTATAACTTTTTTCTATTAAC
43390464 CAAAATAT
1 CAAAATAT
43390472 ACCAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 20 0.61
28 13 0.39
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
CAAAATATTATAACTTTTTTCTATTAAC
Found at i:43390571 original size:27 final size:27
Alignment explanation
Indices: 43390541--43390611 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
43390531 TCGTGCTAAG
* *
43390541 GTGATTGGCGGCACCAAATGTGCCATA
1 GTGATTGGCGGCACCAAAGGTGCCAAA
43390568 GTGATTGGCGGCACCAAAGGTGCCAAA
1 GTGATTGGCGGCACCAAAGGTGCCAAA
**
43390595 GACATTGGCGGCACCAA
1 GTGATTGGCGGCACCAA
43390612 TGTTATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.31, T:0.17
Consensus pattern (27 bp):
GTGATTGGCGGCACCAAAGGTGCCAAA
Found at i:43390626 original size:299 final size:300
Alignment explanation
Indices: 43390078--43390676 Score: 1191
Period size: 299 Copynumber: 2.0 Consensus size: 300
43390068 GGGGTTTTTT
43390078 ACTAAATTATTATAAAAAAATAAAAAAATAATCAAAATATTATAACTTTTTTTTATTAACCAAAA
1 ACTAAATTATTATAAAAAAATAAAAAAATAATCAAAATATTATAACTTTTTTTTATTAACCAAAA
43390143 TATTATAATTTTTTCTATTTACCAAAATATACCAAAAAAAACAAAAAATAGAAAGAAAAAAAACC
66 TATTATAATTTTTTCTATTTACCAAAATATACCAAAAAAAACAAAAAATAGAAAGAAAAAAAACC
43390208 TACACCGATTTGACAACACTCTGGTCGTGCTAAGGTGATTGGCGGCACCAAATGTGCCATAGTGA
131 TACACCGATTTGACAACACTCTGGTCGTGCTAAGGTGATTGGCGGCACCAAATGTGCCATAGTGA
43390273 TTGGCGGCACCAAAGGTGCCAAAGACATTGGCGGCACCAATGTTATAATAGAGCCGGTCGGTTGT
196 TTGGCGGCACCAAAGGTGCCAAAGACATTGGCGGCACCAATGTTATAATAGAGCCGGTCGGTTGT
43390338 TGGGGGGGGAGAAGGAGAGGGAAAGAAAGAAAGAAAGAAA
261 TGGGGGGGGAGAAGGAGAGGGAAAGAAAGAAAGAAAGAAA
43390378 ACTAAATTA-TATAAAAAAATAAAAAAATAATCAAAATATTATAACTTTTTTTTATTAACCAAAA
1 ACTAAATTATTATAAAAAAATAAAAAAATAATCAAAATATTATAACTTTTTTTTATTAACCAAAA
43390442 TATTATAATTTTTTCTATTTACCAAAATATACCAAAAAAAACAAAAAATAGAAAGAAAAAAAACC
66 TATTATAATTTTTTCTATTTACCAAAATATACCAAAAAAAACAAAAAATAGAAAGAAAAAAAACC
43390507 TACACCGATTTGACAACACTCTGGTCGTGCTAAGGTGATTGGCGGCACCAAATGTGCCATAGTGA
131 TACACCGATTTGACAACACTCTGGTCGTGCTAAGGTGATTGGCGGCACCAAATGTGCCATAGTGA
43390572 TTGGCGGCACCAAAGGTGCCAAAGACATTGGCGGCACCAATGTTATAATAGAGCCGGTCGGTTGT
196 TTGGCGGCACCAAAGGTGCCAAAGACATTGGCGGCACCAATGTTATAATAGAGCCGGTCGGTTGT
43390637 TGGGGGGGGAGAAGGAGAGGGAAAGAAAGAAAGAAAGAAA
261 TGGGGGGGGAGAAGGAGAGGGAAAGAAAGAAAGAAAGAAA
43390677 GAAAGGAAGG
Statistics
Matches: 299, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
299 290 0.97
300 9 0.03
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (300 bp):
ACTAAATTATTATAAAAAAATAAAAAAATAATCAAAATATTATAACTTTTTTTTATTAACCAAAA
TATTATAATTTTTTCTATTTACCAAAATATACCAAAAAAAACAAAAAATAGAAAGAAAAAAAACC
TACACCGATTTGACAACACTCTGGTCGTGCTAAGGTGATTGGCGGCACCAAATGTGCCATAGTGA
TTGGCGGCACCAAAGGTGCCAAAGACATTGGCGGCACCAATGTTATAATAGAGCCGGTCGGTTGT
TGGGGGGGGAGAAGGAGAGGGAAAGAAAGAAAGAAAGAAA
Found at i:43390664 original size:4 final size:4
Alignment explanation
Indices: 43390657--43390716 Score: 61
Period size: 4 Copynumber: 15.0 Consensus size: 4
43390647 GAAGGAGAGG
* *
43390657 GAAA GAAA GAAA GAAA GAAA GAAA GGAAG GAGAG GAAA GAAA G-AA -AAA
1 GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA GAAA GAAA
*
43390705 GAAG GAAA GAAA
1 GAAA GAAA GAAA
43390717 AGGAAAGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
3 4 0.08
4 37 0.77
5 7 0.15
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:43390707 original size:10 final size:10
Alignment explanation
Indices: 43390692--43390839 Score: 54
Period size: 10 Copynumber: 14.6 Consensus size: 10
43390682 GAAGGAGAGG
43390692 AAAGAAAGAA
1 AAAGAAAGAA
*
43390702 AAAGAAGGAA
1 AAAGAAAGAA
* *
43390712 AGA-AAAGGA
1 AAAGAAAGAA
*
43390721 AAGGAAAGGAGA
1 AAAGAAA-GA-A
** *
43390733 ATGGAAAAAA
1 AAAGAAAGAA
*
43390743 AAAG-TAGAA
1 AAAGAAAGAA
*
43390752 GAAG-AAGAA
1 AAAGAAAGAA
* *
43390761 GAAGAAGAGGA
1 AAAGAA-AGAA
*
43390772 AAGGAGAAGAAA
1 AAAGA-AAG-AA
43390784 AAAGAAAGAA
1 AAAGAAAGAA
*
43390794 AAAGAAGGAA
1 AAAGAAAGAA
* *
43390804 AGA-AAAGGA
1 AAAGAAAGAA
43390813 AAAGAGAAGAGA
1 AAAGA-AAGA-A
43390825 AAA-AAAGAA
1 AAAGAAAGAA
*
43390834 GAAGAA
1 AAAGAA
43390840 GAGGGAAGGA
Statistics
Matches: 100, Mismatches: 27, Indels: 22
0.67 0.18 0.15
Matches are distributed among these distances:
9 28 0.28
10 38 0.38
11 17 0.17
12 17 0.17
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:43390723 original size:5 final size:5
Alignment explanation
Indices: 43390656--43390730 Score: 58
Period size: 4 Copynumber: 16.6 Consensus size: 5
43390646 AGAAGGAGAG
*
43390656 GGAAA -GAAA -GAAA -GAAA -GAAA -GAAA GG-AA GGAGA GGAAA -GAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
* * *
43390699 GAAAA AG-AA GGAAA GAAAA GGAAA GGAAA GGA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGA
43390731 GAATGGAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
4 31 0.53
5 27 0.47
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:43390723 original size:18 final size:17
Alignment explanation
Indices: 43390656--43390723 Score: 75
Period size: 18 Copynumber: 3.9 Consensus size: 17
43390646 AGAAGGAGAG
43390656 GGAAAGAAA-GAAAGAA
1 GGAAAGAAAGGAAAGAA
* *
43390672 AGAAAGAAAGGAAGGAGA
1 GGAAAGAAAGGAAAGA-A
*
43390690 GGAAAGAAAGAAAAAGAA
1 GGAAAGAAAG-GAAAGAA
43390708 GGAAAGAAAAGGAAAG
1 GGAAAG-AAAGGAAAG
43390724 GAAAGGAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 8 0.19
17 5 0.12
18 21 0.50
19 8 0.19
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GGAAAGAAAGGAAAGAA
Found at i:43390754 original size:3 final size:3
Alignment explanation
Indices: 43390748--43390841 Score: 60
Period size: 3 Copynumber: 33.0 Consensus size: 3
43390738 AAAAAAAAGT
* *
43390748 AGA AGA AGA AGA AGA AGA AGA GGAA AGG AGA AGA A-A A-A AGAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AG-A AGA
* * *
43390793 AAA AGA AGG A-A AGA A-A AGGA A-A AG- AGA AG- AGA A-A AAA AGA
1 AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA
43390833 AGA AGA AGA
1 AGA AGA AGA
43390842 GGGAAGGAAG
Statistics
Matches: 72, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
2 15 0.21
3 50 0.69
4 7 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:43390811 original size:36 final size:36
Alignment explanation
Indices: 43390656--43390866 Score: 153
Period size: 36 Copynumber: 5.6 Consensus size: 36
43390646 AGAAGGAGAG
*
43390656 GGAAAGAAAGAAAGAAAGAAAGAAAGGAAGGAGAGGAAA
1 GGAAAGAAA-AAAGAAAGAAAG-AA-GAAGGAAAGGAAA
*
43390695 -GAAAG-AAAAAGAAGGAAAGAA-AAGGAAAGGAAA
1 GGAAAGAAAAAAGAAAGAAAGAAGAAGGAAAGGAAA
*
43390728 GGAGAATGGAAAAAAAAAGTAGAAGAAGAAGAAGAAGAAGAGGAAA
1 GGA-AA--GAAAAAAGAA--AG-A-AAGAAGAAG--GAA-AGGAAA
*
43390774 GGAGAAGAAAAAAGAAAGAAA-AAGAAGGAAAGAAAA
1 GGA-AAGAAAAAAGAAAGAAAGAAGAAGGAAAGGAAA
* * * *
43390810 GGAAAAGAGAAGAGAAAAAAAGAAGAA-GAAGAGGGAA
1 GG-AAAGAAAAAAGAAAGAAAGAAGAAGGAA-AGGAAA
* *
43390847 GGAAGGAAAAAAAAAAGAAA
1 GGAAAGAAAAAAGAAAGAAA
43390867 AAAATTGTAA
Statistics
Matches: 140, Mismatches: 16, Indels: 35
0.73 0.08 0.18
Matches are distributed among these distances:
33 11 0.08
34 2 0.01
35 4 0.03
36 48 0.34
37 18 0.13
38 12 0.09
39 6 0.04
40 3 0.02
41 2 0.01
42 7 0.05
43 3 0.02
44 9 0.06
45 3 0.02
46 12 0.09
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (36 bp):
GGAAAGAAAAAAGAAAGAAAGAAGAAGGAAAGGAAA
Found at i:43390811 original size:82 final size:79
Alignment explanation
Indices: 43390660--43390841 Score: 194
Period size: 82 Copynumber: 2.3 Consensus size: 79
43390650 GGAGAGGGAA
* * * *
43390660 AGAAAGAAAGAAAGAAAGAA-AGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAG
1 AGAAAAAAAG-AAG-AAGAAGAAGAAGAAGAGGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAAG
* *
43390724 GAAAGGAGAATG-GAA-
64 AAAAGGA-AAAGAGAAG
43390739 A-AAAAAAGTAGAAGAAGAAGAAGAAGAAGAGGAAAGGAGAAGAAAAAAGAAAGAAA-AAGAAGG
1 AGAAAAAA--AGAAGAAGAAGAAGAAGAAGAGGAAA-GA-AAG-AAAAAGAAAGAAAGAA-AAGG
43390802 AAAGAAAAGGAAAAGAGAAG
60 AAAGAAAAGGAAAAGAGAAG
43390822 AGAAAAAAAGAAGAAGAAGA
1 AGAAAAAAAGAAGAAGAAGA
43390842 GGGAAGGAAG
Statistics
Matches: 87, Mismatches: 6, Indels: 17
0.79 0.05 0.15
Matches are distributed among these distances:
78 10 0.11
79 17 0.20
80 4 0.05
81 8 0.09
82 41 0.47
83 1 0.01
84 6 0.07
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (79 bp):
AGAAAAAAAGAAGAAGAAGAAGAAGAAGAGGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAAGAA
AAGGAAAAGAGAAG
Found at i:43390825 original size:26 final size:25
Alignment explanation
Indices: 43390748--43390860 Score: 68
Period size: 26 Copynumber: 4.2 Consensus size: 25
43390738 AAAAAAAAGT
43390748 AGAAGAAGAAGAAGAAGAAGAGGAAAGGAGA
1 AGAA-AAGAA-AAG-AGAAGA-G-AAGGA-A
* *
43390779 AGAAAAAAGAAAGA-AAAAGAAGGAA
1 AGAAAAGA-AAAGAGAAGAGAAGGAA
**
43390804 AGAAAAGGAAAAGAGAAGAGAAAAAA
1 AGAAAA-GAAAAGAGAAGAGAAGGAA
* *
43390830 AGAAGAAGAAGAGGGAAG-GAAGGAA
1 AGAA-AAGAAAAGAGAAGAGAAGGAA
*
43390855 AAAAAA
1 AGAAAA
43390861 AAGAAAAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
24 2 0.03
25 20 0.30
26 27 0.40
27 3 0.04
28 3 0.04
29 1 0.01
30 6 0.09
31 5 0.07
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (25 bp):
AGAAAAGAAAAGAGAAGAGAAGGAA
Found at i:43390839 original size:32 final size:29
Alignment explanation
Indices: 43390792--43390870 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
43390782 AAAAAGAAAG
43390792 AAAAAGAAGGAAAGAAAAGGAAAAGAGAAGAGAA
1 AAAAAGAA-G-AAGAAAAGG-AAAG-GAAG-GAA
* *
43390826 AAAAAGAAGAAGAAGAGGGAAGGAAGGAA
1 AAAAAGAAGAAGAAAAGGAAAGGAAGGAA
* *
43390855 AAAAAAAAGAAAAAAA
1 AAAAAGAAGAAGAAAA
43390871 TTGTAATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 16 0.40
30 4 0.10
31 3 0.08
32 8 0.20
33 1 0.03
34 8 0.20
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (29 bp):
AAAAAGAAGAAGAAAAGGAAAGGAAGGAA
Found at i:43391422 original size:16 final size:15
Alignment explanation
Indices: 43391396--43391425 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
43391386 GTACTGAAAT
43391396 AATATAAAATAATAA
1 AATATAAAATAATAA
43391411 AATATGAAAATAATA
1 AATAT-AAAATAATA
43391426 TATTTTTATT
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:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:43395303 original size:13 final size:13
Alignment explanation
Indices: 43395285--43395332 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
43395275 CTCAAATTTT
43395285 TCAAAAGCACTTC
1 TCAAAAGCACTTC
43395298 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
43395311 TCAAAAGCATTTT
1 TCAAAAGCACTTC
43395324 TCAAAAGCA
1 TCAAAAGCA
43395333 ATGAAGAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:43397949 original size:11 final size:11
Alignment explanation
Indices: 43397933--43397959 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
43397923 TTTATAACTT
43397933 AATTTGGATAC
1 AATTTGGATAC
43397944 AATTTGGATAC
1 AATTTGGATAC
43397955 AATTT
1 AATTT
43397960 AAGCATAAGC
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:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (11 bp):
AATTTGGATAC
Found at i:43401340 original size:27 final size:27
Alignment explanation
Indices: 43401268--43401343 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
43401258 AACACGAGTA
* *
43401268 GTGCCGCCAATCA-GTATAGCACCATTG
1 GTGCCGCCAATCACCT-TGGCACCATTG
** * *
43401295 GTGCCGCCAATGTCTTTGGCACCTTTG
1 GTGCCGCCAATCACCTTGGCACCATTG
43401322 GTGCCGCCAATCACCTTGGCAC
1 GTGCCGCCAATCACCTTGGCAC
43401344 AACCAGGGTG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.18, C:0.33, G:0.24, T:0.25
Consensus pattern (27 bp):
GTGCCGCCAATCACCTTGGCACCATTG
Found at i:43401432 original size:26 final size:25
Alignment explanation
Indices: 43401403--43401461 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
43401393 TTTTTAGTAT
43401403 ATTTTGGTAAATAAAAAAATTATAAC
1 ATTTTGGTAAA-AAAAAAATTATAAC
* * *
43401429 ATTTTGATAAAAAAAAAGTTATAAT
1 ATTTTGGTAAAAAAAAAATTATAAC
43401454 ATTTTGGT
1 ATTTTGGT
43401462 TATTTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (25 bp):
ATTTTGGTAAAAAAAAAATTATAAC
Found at i:43402496 original size:27 final size:27
Alignment explanation
Indices: 43402424--43402499 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
43402414 AACACGAGTA
* *
43402424 GTGCCGCCAATCA-GTATAGCACCATTG
1 GTGCCGCCAATCACCT-TGGCACCATTG
** * *
43402451 GTGCCGCCAATGTCTTTGGCACCTTTG
1 GTGCCGCCAATCACCTTGGCACCATTG
43402478 GTGCCGCCAATCACCTTGGCAC
1 GTGCCGCCAATCACCTTGGCAC
43402500 AACCAGGGTG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.18, C:0.33, G:0.24, T:0.25
Consensus pattern (27 bp):
GTGCCGCCAATCACCTTGGCACCATTG
Found at i:43402588 original size:26 final size:25
Alignment explanation
Indices: 43402559--43402617 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
43402549 TTTTTAGTAT
43402559 ATTTTGGTAAATAAAAAAATTATAAC
1 ATTTTGGTAAA-AAAAAAATTATAAC
* * *
43402585 ATTTTGATAAAAAAAAAGTTATAAT
1 ATTTTGGTAAAAAAAAAATTATAAC
43402610 ATTTTGGT
1 ATTTTGGT
43402618 TATTTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (25 bp):
ATTTTGGTAAAAAAAAAATTATAAC
Found at i:43409175 original size:12 final size:13
Alignment explanation
Indices: 43409158--43409187 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
43409148 CAATAATTTC
43409158 AAAAAACAAAA-A
1 AAAAAACAAAAGA
43409170 AAAAAACAAAAGA
1 AAAAAACAAAAGA
43409183 AAAAA
1 AAAAA
43409188 GAACGAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAGA
Found at i:43411107 original size:209 final size:209
Alignment explanation
Indices: 43410747--43411373 Score: 1011
Period size: 209 Copynumber: 3.0 Consensus size: 209
43410737 CTTTAGCCAG
* * * **
43410747 CTAATGTTTGGTAGTGACTAGATAATAAGTATAACAATCGTTCCCTTTTGATTCAAAATCTAGTT
1 CTAATGTTTGGTAGTGACTAGTTAATAAGTATAACAATCGTTCCCCTTTGATTCGAAGGCTAGTT
* * * * *
43410812 ATAAAATAACCAAACGAGGACCTAAAATTATGGGTTAGAAGCGATGGAGATGAAATAATTTAAAA
66 ATAAAGTAGCCAAACGAGGACCTAAAATTATGGGTTAGAAGCGTTGGAGATGAGATAATCTAAAA
43410877 AGTAAAATATATTGGCCATTTTAGCTTCGACCTCTAGAGGGGTGTTCTTATGGCTTTGCTTGGTA
131 AGTAAAATATATTGGCCATTTTAGCTTCGACCTCTAGAGGGGTGTTCTTATGGCTTTGCTTGGTA
*
43410942 TCATCAATTAGATT
196 TCATCAGTTAGATT
*
43410956 CTAATGTCTGGTAGTGACTAGTTAATAAGTATAACAATCGTTCCCCTTTGATTCGAAGGCTAGTT
1 CTAATGTTTGGTAGTGACTAGTTAATAAGTATAACAATCGTTCCCCTTTGATTCGAAGGCTAGTT
* *
43411021 ATAAAGTAGCCAAATGAGGACCTAGAATTATGGGTTAGAAGCGTTGGAGATGAGATAATCTAAAA
66 ATAAAGTAGCCAAACGAGGACCTAAAATTATGGGTTAGAAGCGTTGGAGATGAGATAATCTAAAA
* **
43411086 AGTAAAATATATTGGCCATTTTAGCTTCAACCTCTAGAGAAGTGTTCTTATGGCTTTGCTTGGTA
131 AGTAAAATATATTGGCCATTTTAGCTTCGACCTCTAGAGGGGTGTTCTTATGGCTTTGCTTGGTA
43411151 TCATCAGTTAGATT
196 TCATCAGTTAGATT
* * *
43411165 CTAATGTTTGATAGTGACTAATTAATAAGTATAACAATCGTTCCCCTTTGATTCGGAGGCTAGTT
1 CTAATGTTTGGTAGTGACTAGTTAATAAGTATAACAATCGTTCCCCTTTGATTCGAAGGCTAGTT
* *
43411230 ATAAAGTAGCCAAACGAGTACCTAAAATTATGGGTTAGAAACGTTGGAGATGAGATAATCTAAAA
66 ATAAAGTAGCCAAACGAGGACCTAAAATTATGGGTTAGAAGCGTTGGAGATGAGATAATCTAAAA
* * * * *
43411295 AGTAAAATTTATTGGCTATTTTAGCTTCGACCTCTAAAGGGGTGTCCTTATAGCTTTGCTTGGTA
131 AGTAAAATATATTGGCCATTTTAGCTTCGACCTCTAGAGGGGTGTTCTTATGGCTTTGCTTGGTA
43411360 TCATCAGTTAGATT
196 TCATCAGTTAGATT
43411374 GACACAATGG
Statistics
Matches: 385, Mismatches: 33, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
209 385 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (209 bp):
CTAATGTTTGGTAGTGACTAGTTAATAAGTATAACAATCGTTCCCCTTTGATTCGAAGGCTAGTT
ATAAAGTAGCCAAACGAGGACCTAAAATTATGGGTTAGAAGCGTTGGAGATGAGATAATCTAAAA
AGTAAAATATATTGGCCATTTTAGCTTCGACCTCTAGAGGGGTGTTCTTATGGCTTTGCTTGGTA
TCATCAGTTAGATT
Found at i:43420571 original size:24 final size:24
Alignment explanation
Indices: 43420513--43420578 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
43420503 GCTTCAAAGA
* *
43420513 GCTATTAACGAGAAGCTCGAGAGG
1 GCTAATAACGGGAAGCTCGAGAGG
43420537 GCTAATAACGGGAAGCTCGAGAGG
1 GCTAATAACGGGAAGCTCGAGAGG
*
43420561 GCTAATAACGGGACGCTC
1 GCTAATAACGGGAAGCTC
43420579 TTTCGAGCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.32, C:0.20, G:0.33, T:0.15
Consensus pattern (24 bp):
GCTAATAACGGGAAGCTCGAGAGG
Found at i:43422556 original size:36 final size:36
Alignment explanation
Indices: 43422509--43422578 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
43422499 TTTGTTTGAA
43422509 GTATTAGAGGTTATTTATAAGACTTCTTCCAGAACT
1 GTATTAGAGGTTATTTATAAGACTTCTTCCAGAACT
43422545 GTATTAGAGGTTATTTATAAGACTTCTTCCAGAA
1 GTATTAGAGGTTATTTATAAGACTTCTTCCAGAA
43422579 TTCACTAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (36 bp):
GTATTAGAGGTTATTTATAAGACTTCTTCCAGAACT
Found at i:43424280 original size:34 final size:34
Alignment explanation
Indices: 43424237--43424306 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
43424227 AAAATACATA
*
43424237 TTGGTGCCGCCAACAAAAATGGTGACACCGATTT
1 TTGGTGCCGCCAACAAAAATGGCGACACCGATTT
43424271 TTGGTGCCGCCAACAAAAATGGCGACACCGATTT
1 TTGGTGCCGCCAACAAAAATGGCGACACCGATTT
43424305 TT
1 TT
43424307 TTTTAAATGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (34 bp):
TTGGTGCCGCCAACAAAAATGGCGACACCGATTT
Found at i:43426431 original size:16 final size:18
Alignment explanation
Indices: 43426405--43426443 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
43426395 ACTTCAAGTG
43426405 TCATATTAAATA-AAAAA
1 TCATATTAAATACAAAAA
*
43426422 TCAT-TTAAATACCAAAA
1 TCATATTAAATACAAAAA
43426439 TCATA
1 TCATA
43426444 ATTAGTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (18 bp):
TCATATTAAATACAAAAA
Found at i:43426906 original size:12 final size:12
Alignment explanation
Indices: 43426875--43426900 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43426865 TTCAACTAAT
43426875 AAAGCAAACAAA
1 AAAGCAAACAAA
43426887 AAAGCAAACAAA
1 AAAGCAAACAAA
43426899 AA
1 AA
43426901 CTCAAATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAGCAAACAAA
Found at i:43427561 original size:49 final size:50
Alignment explanation
Indices: 43427481--43427597 Score: 159
Period size: 50 Copynumber: 2.4 Consensus size: 50
43427471 TCAAACATTG
* **
43427481 ATGGGCGGCACC-AGTGTATTTAAAAAAAAAATT-GGTGTTGGCCATGT-A
1 ATGGCCGGCACCAAGTACATTTAAAAAAAAAATTGGGTGTTGGCCA-GTAA
* *
43427529 ATGGTCGGCACCAAGTACATTTAATAAAAAAATTGGGTGTTGGCCAGTAA
1 ATGGCCGGCACCAAGTACATTTAAAAAAAAAATTGGGTGTTGGCCAGTAA
43427579 ATGGCCGGCACCAAGTACA
1 ATGGCCGGCACCAAGTACA
43427598 ATTTTCGGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
48 11 0.18
49 20 0.33
50 30 0.49
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (50 bp):
ATGGCCGGCACCAAGTACATTTAAAAAAAAAATTGGGTGTTGGCCAGTAA
Found at i:43427784 original size:116 final size:114
Alignment explanation
Indices: 43427554--43427788 Score: 290
Period size: 116 Copynumber: 2.0 Consensus size: 114
43427544 TACATTTAAT
* * *
43427554 AAAAAAATTGGGTGTTGGCCAGTAAATGGCCGGCACCAAGTACAATTTTCGGTTCTCAAGGCAAT
1 AAAAAAATTGGGTGTTGGCCAATAAATGGCCGGCACCAAGTACAATTTTCGGCTCCCAAGGCAAT
* * *
43427619 TTGTTTTTACTTTGAGACATTGATGATCGGCACCAGTGTATTTAAAAAAA
66 TTGTTTTTACTTTGAGACACTGATGACCAGCACCAGTGTATTT-AAAAAA
* * * *
43427669 GAAAAAAATTGGGTGTTGGCCAATAGATGGCTGGCACCAAGTACAATTTTTGGCTCCCAATGCAT
1 -AAAAAAATTGGGTGTTGGCCAATAAATGGCCGGCACCAAGTACAATTTTCGGCTCCCAAGGCA-
* * * * * *
43427734 TTTTTTTTTTATTTTGGGACACTGATGGCCAGTACCAGTGTCATTTAAAAAA
64 ATTTGTTTTTACTTTGAGACACTGATGACCAGCACCAGTGT-ATTTAAAAAA
43427786 AAA
1 AAA
43427789 TTGTCTTCCA
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
116 59 0.58
117 38 0.38
118 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (114 bp):
AAAAAAATTGGGTGTTGGCCAATAAATGGCCGGCACCAAGTACAATTTTCGGCTCCCAAGGCAAT
TTGTTTTTACTTTGAGACACTGATGACCAGCACCAGTGTATTTAAAAAA
Found at i:43430900 original size:21 final size:21
Alignment explanation
Indices: 43430860--43430915 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
43430850 TTAATATGAA
* *
43430860 AAAAAAATTAAAATGGAAAGA-
1 AAAATAATT-AAATGAAAAGAG
*
43430881 AAGATAACTTAAATGAAAAGAG
1 AAAATAA-TTAAATGAAAAGAG
43430903 AAAATAATTAAAT
1 AAAATAATTAAAT
43430916 TTAAATGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.20
Consensus pattern (21 bp):
AAAATAATTAAATGAAAAGAG
Found at i:43430905 original size:27 final size:26
Alignment explanation
Indices: 43430875--43431022 Score: 68
Period size: 27 Copynumber: 5.9 Consensus size: 26
43430865 AATTAAAATG
43430875 GAAAGAAAGATAACTTAAATGAAAAGA
1 GAAAGAAA-ATAACTTAAATGAAAAGA
* * *
43430902 GAAA-ATAATTAAATTTAAATG-AAA-T
1 GAAAGA-AAAT-AACTTAAATGAAAAGA
*
43430927 G--AGAAAA-AA-TTAAATTAAAATG-
1 GAAAGAAAATAACTTAAATGAAAA-GA
*
43430949 GAAAGAAAGATAACTTAAATGAAATGA
1 GAAAGAAA-ATAACTTAAATGAAAAGA
* *
43430976 GAAA-AAAATTAAATTTAAATGGAAA-A
1 GAAAGAAAA-T-AACTTAAATGAAAAGA
* *
43431002 -AAAG-AGATAATTTAAATGAAA
1 GAAAGAAAATAACTTAAATGAAA
43431023 TGGAAATGGA
Statistics
Matches: 94, Mismatches: 12, Indels: 34
0.67 0.09 0.24
Matches are distributed among these distances:
20 6 0.06
21 5 0.05
22 1 0.01
23 15 0.16
24 7 0.07
25 8 0.09
26 13 0.14
27 39 0.41
ACGTcount: A:0.62, C:0.01, G:0.14, T:0.22
Consensus pattern (26 bp):
GAAAGAAAATAACTTAAATGAAAAGA
Found at i:43430936 original size:21 final size:21
Alignment explanation
Indices: 43430916--43431003 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 21
43430906 ATAATTAAAT
43430916 TTAAA-TGAAATGAGAAAAAA
1 TTAAATTGAAATGAGAAAAAA
*
43430936 TTAAATTAAAATGGAAAGAAAGATAA
1 TTAAATTGAAAT-G--AGAAA-A-AA
43430962 CTTAAA-TGAAATGAGAAAAAAA
1 -TTAAATTGAAATGAG-AAAAAA
*
43430984 TTAAATTTAAATG-GAAAAAA
1 TTAAATTGAAATGAGAAAAAA
43431004 AGAGATAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
20 11 0.20
21 11 0.20
22 9 0.16
23 3 0.05
24 8 0.14
25 2 0.04
26 7 0.12
27 5 0.09
ACGTcount: A:0.62, C:0.01, G:0.14, T:0.23
Consensus pattern (21 bp):
TTAAATTGAAATGAGAAAAAA
Found at i:43430951 original size:74 final size:72
Alignment explanation
Indices: 43430857--43430996 Score: 244
Period size: 74 Copynumber: 1.9 Consensus size: 72
43430847 AATTTAATAT
*
43430857 GAAAAAAAAATTAAAATGGAAAGAAAGATAACTTAAATGAAAAGAGAAAATAATTAAATTTAAAT
1 GAAAAAAAAATTAAAATGGAAAGAAAGATAACTTAAATGAAAAGAGAAAAAAATTAAATTTAAAT
43430922 GAAATGA
66 GAAATGA
*
43430929 GAAAAAATTAAATTAAAATGGAAAGAAAGATAACTTAAATGAAATGAGAAAAAAATTAAATTTAA
1 GAAAAAA--AAATTAAAATGGAAAGAAAGATAACTTAAATGAAAAGAGAAAAAAATTAAATTTAA
43430994 ATG
64 ATG
43430997 GAAAAAAAGA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
72 7 0.11
74 57 0.89
ACGTcount: A:0.63, C:0.01, G:0.14, T:0.22
Consensus pattern (72 bp):
GAAAAAAAAATTAAAATGGAAAGAAAGATAACTTAAATGAAAAGAGAAAAAAATTAAATTTAAAT
GAAATGA
Found at i:43430999 original size:48 final size:50
Alignment explanation
Indices: 43430916--43431028 Score: 171
Period size: 48 Copynumber: 2.3 Consensus size: 50
43430906 ATAATTAAAT
*
43430916 TTAAATGAAATGAG-AAAAAATTAAATTAAAATGG-AAAGAA-AGATAAC
1 TTAAATGAAATGAGAAAAAAATTAAATTAAAATGGAAAAAAAGAGATAAC
* *
43430963 TTAAATGAAATGAGAAAAAAATTAAATTTAAATGGAAAAAAAGAGATAAT
1 TTAAATGAAATGAGAAAAAAATTAAATTAAAATGGAAAAAAAGAGATAAC
43431013 TTAAATGAAATG-GAAA
1 TTAAATGAAATGAGAAA
43431029 TGGAAATGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
47 14 0.23
48 19 0.32
49 9 0.15
50 18 0.30
ACGTcount: A:0.61, C:0.01, G:0.15, T:0.23
Consensus pattern (50 bp):
TTAAATGAAATGAGAAAAAAATTAAATTAAAATGGAAAAAAAGAGATAAC
Found at i:43431004 original size:21 final size:22
Alignment explanation
Indices: 43430900--43431004 Score: 79
Period size: 26 Copynumber: 4.5 Consensus size: 22
43430890 TAAATGAAAA
*
43430900 GAGAAAATAATTAAATTTAAAT
1 GAGAAAAAAATTAAATTTAAAT
*
43430922 GAAATGAGAAAAAATTAAATTAAAAT
1 G--A-GA-AAAAAATTAAATTTAAAT
* *
43430948 GGAAAGAAAGATAACTTAAA-TGAAAT
1 -G--AGAAA-A-AAATTAAATTTAAAT
43430974 GAGAAAAAAATTAAATTTAAAT
1 GAGAAAAAAATTAAATTTAAAT
43430996 G-GAAAAAAA
1 GAGAAAAAAA
43431005 GAGATAATTT
Statistics
Matches: 69, Mismatches: 6, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
21 15 0.22
22 8 0.12
23 5 0.07
24 1 0.01
25 5 0.07
26 24 0.35
27 11 0.16
ACGTcount: A:0.63, C:0.01, G:0.13, T:0.23
Consensus pattern (22 bp):
GAGAAAAAAATTAAATTTAAAT
Found at i:43431039 original size:5 final size:5
Alignment explanation
Indices: 43431015--43431076 Score: 70
Period size: 5 Copynumber: 11.6 Consensus size: 5
43431005 GAGATAATTT
* *
43431015 AAATG AAATGG AAATGG AAATG AAATG AAATG GAATG GAATAG AAATAG
1 AAATG AAAT-G AAAT-G AAATG AAATG AAATG AAATG AAAT-G AAAT-G
43431064 AAATG AAATG AAA
1 AAATG AAATG AAA
43431077 AAAAAATGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
5 32 0.60
6 21 0.40
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:43431051 original size:27 final size:27
Alignment explanation
Indices: 43431016--43431076 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
43431006 AGATAATTTA
*
43431016 AATGAAATGGAAATGGAAAT-GAAATGA
1 AATGAAATGG-AATAGAAATAGAAATGA
*
43431043 AATGGAATGGAATAGAAATAGAAATGA
1 AATGAAATGGAATAGAAATAGAAATGA
43431070 AATGAAA
1 AATGAAA
43431077 AAAAAATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.18
Consensus pattern (27 bp):
AATGAAATGGAATAGAAATAGAAATGA
Found at i:43431511 original size:19 final size:19
Alignment explanation
Indices: 43431484--43431522 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
43431474 GAAATGTTAA
43431484 ATGAATATGAAATGAAATG
1 ATGAATATGAAATGAAATG
* *
43431503 ATGATTATGAAATGGAATG
1 ATGAATATGAAATGAAATG
43431522 A
1 A
43431523 AAGTTTAAAT
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:0.49, C:0.00, G:0.23, T:0.28
Consensus pattern (19 bp):
ATGAATATGAAATGAAATG
Found at i:43431593 original size:20 final size:18
Alignment explanation
Indices: 43431546--43431643 Score: 90
Period size: 18 Copynumber: 5.1 Consensus size: 18
43431536 AATAAATTAT
*
43431546 AAATTTAAATGAAAACAA
1 AAATTTAAATGAAAATAA
* *
43431564 AAAGTGAAATGAAAATAA
1 AAATTTAAATGAAAATAA
43431582 AAATTATGAAATGAGAAATAA
1 AAATT-T-AAATGA-AAATAA
43431603 TTAAATTTAAATGGAAAA-AA
1 --AAATTTAAAT-GAAAATAA
43431623 ATAATTTAAATGAAAAGTAA
1 A-AATTTAAATGAAAA-TAA
43431643 A
1 A
43431644 TGTAAATGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
18 25 0.38
19 9 0.14
20 11 0.17
21 13 0.20
22 3 0.05
23 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.11, T:0.24
Consensus pattern (18 bp):
AAATTTAAATGAAAATAA
Found at i:43431657 original size:5 final size:5
Alignment explanation
Indices: 43431630--43431710 Score: 92
Period size: 5 Copynumber: 15.6 Consensus size: 5
43431620 AAAATAATTT
* *
43431630 AAATG AAAAG TAAATG TAAATG AAATG AAATG AAATGG AAATAC AAATG
1 AAATG AAATG -AAATG -AAATG AAATG AAATG AAAT-G AAAT-G AAATG
*
43431679 AAATG AAAAG -AATG AAATG AAATG AAATG AAA
1 AAATG AAATG AAATG AAATG AAATG AAATG AAA
43431711 AAAAGAAAGA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
4 3 0.05
5 44 0.67
6 19 0.29
ACGTcount: A:0.62, C:0.01, G:0.19, T:0.19
Consensus pattern (5 bp):
AAATG
Found at i:43431662 original size:27 final size:25
Alignment explanation
Indices: 43431630--43431710 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 25
43431620 AAAATAATTT
*
43431630 AAATGAAAAGTAAATGTAAATGAAATG
1 AAATGAAATG-AAATG-AAATGAAATG
*
43431657 AAATGAAATGGAAATACAAATGAAATG
1 AAATGAAAT-GAAAT-GAAATGAAATG
*
43431684 AAAAG-AATGAAATGAAATGAAATG
1 AAATGAAATGAAATGAAATGAAATG
43431708 AAA
1 AAA
43431711 AAAAGAAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
24 13 0.27
25 5 0.10
26 3 0.06
27 26 0.54
28 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.19, T:0.19
Consensus pattern (25 bp):
AAATGAAATGAAATGAAATGAAATG
Found at i:43431729 original size:24 final size:24
Alignment explanation
Indices: 43431636--43431722 Score: 88
Period size: 27 Copynumber: 3.5 Consensus size: 24
43431626 ATTTAAATGA
*
43431636 AAAGTAAATGTAAATGAAATGAAATG
1 AAAG-AAATG-AAATGAAATGAAAAG
*
43431662 AAATGGAAATACAAATGAAATGAAAAG
1 AAA--GAAAT-GAAATGAAATGAAAAG
*
43431689 AATGAAATGAAATGAAATGAAAA-
1 AAAGAAATGAAATGAAATGAAAAG
43431712 AAAGAAA-GAAA
1 AAAGAAATGAAA
43431723 GATGAAAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
22 4 0.08
23 6 0.11
24 14 0.26
25 5 0.09
26 3 0.06
27 20 0.38
28 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.18, T:0.16
Consensus pattern (24 bp):
AAAGAAATGAAATGAAATGAAAAG
Found at i:43431936 original size:22 final size:20
Alignment explanation
Indices: 43431908--43431950 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
43431898 GGAATGATAT
43431908 TAAAATAGAGAAAAAATTTAAA
1 TAAAATA-AG-AAAAATTTAAA
*
43431930 TAAAATATGAAAAATTTAAA
1 TAAAATAAGAAAAATTTAAA
43431950 T
1 T
43431951 GACCCTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 1 0.05
22 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (20 bp):
TAAAATAAGAAAAATTTAAA
Found at i:43432108 original size:19 final size:18
Alignment explanation
Indices: 43432086--43432124 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
43432076 TATATTAGGG
43432086 AAAAAATAAATTTAAATGAA
1 AAAAAAT-AA-TTAAATGAA
43432106 AAAAAATAATTAAATGAA
1 AAAAAATAATTAAATGAA
43432124 A
1 A
43432125 TGTTAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAAAAATAATTAAATGAA
Found at i:43432137 original size:5 final size:5
Alignment explanation
Indices: 43432117--43432213 Score: 68
Period size: 5 Copynumber: 17.2 Consensus size: 5
43432107 AAAAATAATT
* * *
43432117 AAATG AAATG TTAAATG AAATATG AATATG GAATG AAATG TAATTTG TAATG
1 AAATG AAATG --AAATG -AA-ATG AA-ATG AAATG AAATG -AA-ATG AAATG
43432169 AATATG AAATG AAATG AAATG TTAAATG AATATG AAATG AAATG A
1 AA-ATG AAATG AAATG AAATG --AAATG AA-ATG AAATG AAATG A
43432214 TGATTATGAA
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
5 39 0.51
6 22 0.29
7 15 0.20
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.30
Consensus pattern (5 bp):
AAATG
Found at i:43432179 original size:28 final size:28
Alignment explanation
Indices: 43432138--43432213 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 28
43432128 TAAATGAAAT
* * *
43432138 ATGAATATGGAATGAAATGTAAT-TTGTA
1 ATGAATATGAAATGAAATGAAATGTT-AA
43432166 ATGAATATGAAATGAAATGAAATGTTAA
1 ATGAATATGAAATGAAATGAAATGTTAA
43432194 ATGAATATGAAATGAAATGA
1 ATGAATATGAAATGAAATGA
43432214 TGATTATGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 42 0.95
29 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (28 bp):
ATGAATATGAAATGAAATGAAATGTTAA
Found at i:43432231 original size:19 final size:19
Alignment explanation
Indices: 43432194--43432232 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
43432184 GAAATGTTAA
*
43432194 ATGAATATGAAATGAAATG
1 ATGAATATGAAACGAAATG
* *
43432213 ATGATTATGAAACGGAATG
1 ATGAATATGAAACGAAATG
43432232 A
1 A
43432233 AAGTTTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.23, T:0.26
Consensus pattern (19 bp):
ATGAATATGAAACGAAATG
Found at i:43432278 original size:19 final size:22
Alignment explanation
Indices: 43432236--43432334 Score: 75
Period size: 19 Copynumber: 4.5 Consensus size: 22
43432226 GGAATGAAAG
43432236 TTTAAATGAAAATAAATTATAAA
1 TTTAAATGAAAATAAA-TATAAA
43432259 TTTAAATGAAAAT-AA-A-AAA
1 TTTAAATGAAAATAAATATAAA
*
43432278 TTGAAATGAAAATGAGAAATAATTAAA
1 TTTAAATGAAAAT---AAAT-A-TAAA
* *
43432305 TTTAACTGGAAA-AAA-AT-AA
1 TTTAAATGAAAATAAATATAAA
43432324 TTTAAATGAAA
1 TTTAAATGAAA
43432335 TGGAAGTGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
19 26 0.42
20 2 0.03
21 1 0.02
22 2 0.03
23 18 0.29
25 1 0.02
27 12 0.19
ACGTcount: A:0.61, C:0.01, G:0.09, T:0.29
Consensus pattern (22 bp):
TTTAAATGAAAATAAATATAAA
Found at i:43432331 original size:46 final size:42
Alignment explanation
Indices: 43432236--43432334 Score: 110
Period size: 46 Copynumber: 2.3 Consensus size: 42
43432226 GGAATGAAAG
*
43432236 TTTAAATGAAAATAAATTATAAATTTAAATGAAAATAAAAAA
1 TTTAAATGAAAATAAATAATAAATTTAAATGAAAATAAAAAA
* * *
43432278 TTGAAATGAAAATGAGAAATAATTAAATTTAACTGGAAAA-AAATAA
1 TTTAAATGAAAAT---AAATAA-TAAATTTAAAT-GAAAATAAAAAA
43432324 TTTAAATGAAA
1 TTTAAATGAAA
43432335 TGGAAGTGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
42 12 0.26
45 5 0.11
46 25 0.53
47 5 0.11
ACGTcount: A:0.61, C:0.01, G:0.09, T:0.29
Consensus pattern (42 bp):
TTTAAATGAAAATAAATAATAAATTTAAATGAAAATAAAAAA
Found at i:43432338 original size:24 final size:24
Alignment explanation
Indices: 43432267--43432339 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
43432257 AATTTAAATG
* *
43432267 AAAATAA-AAAATTGAAATGAAAA
1 AAAATAATTAAATTGAAATGGAAA
* *
43432290 TGAGAAATAATTAAATTTAACTGGAAA
1 --A-AAATAATTAAATTGAAATGGAAA
43432317 AAAATAATTTAAA-TGAAATGGAA
1 AAAATAA-TTAAATTGAAATGGAA
43432340 GTGTAAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
24 14 0.36
25 7 0.18
26 6 0.15
27 12 0.31
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.25
Consensus pattern (24 bp):
AAAATAATTAAATTGAAATGGAAA
Found at i:43432352 original size:5 final size:5
Alignment explanation
Indices: 43432327--43432384 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
43432317 AAAATAATTT
* *
43432327 AAATG AAATGG AAGTG TAAATG AAATG AAATGG AAATGG AAATC AAATG
1 AAATG AAAT-G AAATG -AAATG AAATG AAAT-G AAAT-G AAATG AAATG
43432376 AAATG AAAT
1 AAATG AAAT
43432385 AATCTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
5 27 0.59
6 19 0.41
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.21
Consensus pattern (5 bp):
AAATG
Found at i:43432354 original size:22 final size:22
Alignment explanation
Indices: 43432327--43432384 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
43432317 AAAATAATTT
* * *
43432327 AAATGAAATGGAAGTGTAAATG
1 AAATGAAATGGAAATGGAAATC
43432349 AAATGAAATGGAAATGGAAATC
1 AAATGAAATGGAAATGGAAATC
43432371 AAATGAAAT-GAAAT
1 AAATGAAATGGAAAT
43432385 AATCTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.21
Consensus pattern (22 bp):
AAATGAAATGGAAATGGAAATC
Found at i:43432368 original size:17 final size:16
Alignment explanation
Indices: 43432327--43432384 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
43432317 AAAATAATTT
* *
43432327 AAATGAAATGGAAGTGT
1 AAATGAAAT-GAAATGG
43432344 AAATGAAATGAAATGG
1 AAATGAAATGAAATGG
*
43432360 AAATGGAAATCAAAT-G
1 AAAT-GAAATGAAATGG
43432376 AAATGAAAT
1 AAATGAAAT
43432385 AATCTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 5 0.14
16 14 0.38
17 18 0.49
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.21
Consensus pattern (16 bp):
AAATGAAATGAAATGG
Found at i:43432759 original size:49 final size:48
Alignment explanation
Indices: 43432681--43432773 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 48
43432671 AAGTTGTACA
* * *
43432681 TGGTGCCGGCCATCTACTGGCATGCACCAAAATTTTTTTTTAATATGTT
1 TGGTGCCAGCCATCTACTGGCATGAACC-AAATTTTTTTTAAATATGTT
43432730 TGGTGCCAGCCAT-TACGTGGCCA-GAACCAAATTTTTTTTAAATA
1 TGGTGCCAGCCATCTAC-TGG-CATGAACCAAATTTTTTTTAAATA
43432774 CTGGTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
48 18 0.46
49 19 0.49
50 2 0.05
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (48 bp):
TGGTGCCAGCCATCTACTGGCATGAACCAAATTTTTTTTAAATATGTT
Found at i:43433161 original size:29 final size:30
Alignment explanation
Indices: 43433100--43433163 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
43433090 AATAAAAGCC
*
43433100 TTTTTTTTAAAATTTACCGAAATGGGCTGA
1 TTTTTTTTAAAATTTACCGAAATGGGCTCA
** * *
43433130 TTTTTTTTATTATTTACCGGAATGGTC-CA
1 TTTTTTTTAAAATTTACCGAAATGGGCTCA
43433159 TTTTT
1 TTTTT
43433164 CGGGAAATTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (30 bp):
TTTTTTTTAAAATTTACCGAAATGGGCTCA
Found at i:43433469 original size:51 final size:51
Alignment explanation
Indices: 43433409--43433523 Score: 194
Period size: 51 Copynumber: 2.3 Consensus size: 51
43433399 TCCTCTCTAA
*
43433409 TCCTCTCAATTTCCTTCCAAATTTCTCTCAAACCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
* *
43433460 TCCTCTCAATTTACTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
*
43433511 TCCCCTCAATTTC
1 TCCTCTCAATTTC
43433524 ATTTTTTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (51 bp):
TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
Found at i:43433471 original size:22 final size:22
Alignment explanation
Indices: 43433446--43433527 Score: 56
Period size: 22 Copynumber: 3.4 Consensus size: 22
43433436 TCAAACCCAT
43433446 ATTTAATTTCAATTTCCTCTCA
1 ATTTAATTTCAATTTCCTCTCA
* * *
43433468 ATTTACTTCCAAAATTCTCTCAAATCCA
1 ATTTAATTTC-AATTTC-CTC---T-CA
*
43433496 TATTTAATTTCAATTTCCCCTCA
1 -ATTTAATTTCAATTTCCTCTCA
*
43433519 ATTTCATTT
1 ATTTAATTT
43433528 TTTAAAATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
22 16 0.36
23 7 0.16
24 4 0.09
27 3 0.07
28 7 0.16
29 8 0.18
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTAATTTCAATTTCCTCTCA
Found at i:43433559 original size:30 final size:32
Alignment explanation
Indices: 43433525--43433589 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 32
43433515 CTCAATTTCA
43433525 TTTTTT-AAAATAATTTTAAA-TTTTTTATAT
1 TTTTTTAAAAATAATTTTAAATTTTTTTATAT
43433555 TTTTTTAAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAAATAATTTTAAATTTTTTTATAT
43433587 TTT
1 TTT
43433590 CATCAATGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 6 0.18
31 14 0.42
32 13 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (32 bp):
TTTTTTAAAAATAATTTTAAATTTTTTTATAT
Found at i:43434069 original size:99 final size:99
Alignment explanation
Indices: 43433898--43434094 Score: 367
Period size: 99 Copynumber: 2.0 Consensus size: 99
43433888 TGCGTTGATC
* *
43433898 GAGAGGTGGAGACCCGAGACGCACACATTCCATCTTCCATGTGGAGAGTGCACTATCACTCTAGA
1 GAGAGATGGAGACCCGAGACGCACACATTCCATCTTCCATGTGGAGAGTGCACTATCACTCTAAA
43433963 AGATGTCCATCTGCAATTGGGATTGCCGGTGGAT
66 AGATGTCCATCTGCAATTGGGATTGCCGGTGGAT
*
43433997 GAGAGATGGAGACCCGAGACGCACACATTCCATCTTCCATGTGGAGAGTGCACTGTCACTCTAAA
1 GAGAGATGGAGACCCGAGACGCACACATTCCATCTTCCATGTGGAGAGTGCACTATCACTCTAAA
43434062 AGATGTCCATCTGCAATTGGGATTGCCGGTGGA
66 AGATGTCCATCTGCAATTGGGATTGCCGGTGGA
43434095 CGGGCACCAG
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (99 bp):
GAGAGATGGAGACCCGAGACGCACACATTCCATCTTCCATGTGGAGAGTGCACTATCACTCTAAA
AGATGTCCATCTGCAATTGGGATTGCCGGTGGAT
Found at i:43434780 original size:7 final size:7
Alignment explanation
Indices: 43434768--43434792 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43434758 AGTCGATTGA
43434768 TATTTAG
1 TATTTAG
43434775 TATTTAG
1 TATTTAG
43434782 TATTTAG
1 TATTTAG
43434789 TATT
1 TATT
43434793 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:43437165 original size:28 final size:27
Alignment explanation
Indices: 43437104--43437165 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 27
43437094 TGCCGTATTT
43437104 AAATTTATTATTTGATGTAATAAAATAG
1 AAATTT-TTATTTGATGTAATAAAATAG
**
43437132 -AA-TTTTATTTGATGTAATACGCATAG
1 AAATTTTTATTTGATGTAATA-AAATAG
43437158 AAATTTTT
1 AAATTTTT
43437166 TCGAGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
25 15 0.52
26 6 0.21
27 4 0.14
28 4 0.14
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.45
Consensus pattern (27 bp):
AAATTTTTATTTGATGTAATAAAATAG
Found at i:43437968 original size:55 final size:55
Alignment explanation
Indices: 43437884--43438066 Score: 339
Period size: 55 Copynumber: 3.3 Consensus size: 55
43437874 NNNNNNNNNN
43437884 TTAATAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGAC
1 TTAATAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGAC
* *
43437939 TTAATAATTTTACATAATTCGATAATTTTACTAACCATTAACACAATTTTTGGAA
1 TTAATAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGAC
*
43437994 TTAATAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTGGAC
1 TTAATAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGAC
43438049 TTAATAATTTTACATAAT
1 TTAATAATTTTACATAAT
43438067 GTTAGATTTG
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 123 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.44
Consensus pattern (55 bp):
TTAATAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGAC
Found at i:43441373 original size:123 final size:123
Alignment explanation
Indices: 43441154--43441493 Score: 551
Period size: 123 Copynumber: 2.8 Consensus size: 123
43441144 CTTGCTACTG
*
43441154 TAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAAAAG
1 TAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAG
*
43441219 CGATTTTATACTATTTGCTCAGAAACGTC-AAAAAATATATTTCTTACATGACCAACTA
66 CGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAT-TACTTCTTACATGACCAACTA
* *
43441277 TAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGTATCCTGGTAGAAG
1 TAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAG
* * * * * *
43441342 CAATTTTATAATATTTGCTTAGAAACGTCAAAAAAATTACTTCTTACATGACCTATTG
66 CGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTACTTCTTACATGACCAACTA
*
43441400 TAGC--AATCGCGTCCAAGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAG
1 TAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAG
43441463 CGATTTTATACTATTTGCTCAGAAACGTCAA
66 CGATTTTATACTATTTGCTCAGAAACGTCAA
43441494 CTCGAAATAA
Statistics
Matches: 200, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
121 84 0.42
123 109 0.55
124 7 0.04
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (123 bp):
TAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAG
CGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTACTTCTTACATGACCAACTA
Found at i:43445550 original size:120 final size:122
Alignment explanation
Indices: 43445327--43445569 Score: 463
Period size: 120 Copynumber: 2.0 Consensus size: 122
43445317 CAAAAAGATA
43445327 AAGTCAATGATACTTTTATGCATTTAATGTAATTCATCTTTTCTTTTCCAAAAAAAAAAAAAAAA
1 AAGTCAATGATACTTTTATGCATTTAATGTAATTCATCTTTTCTTTTCCAAAAAAAAAAAAAAAA
43445392 ATAAGAACATGAGGAAATTGTAATTAAATCTTTTGTTAACATCAAAGATAATTTGGC
66 ATAAGAACATGAGGAAATTGTAATTAAATCTTTTGTTAACATCAAAGATAATTTGGC
43445449 AAGTCAATGA-ACTTTTATGCATTTAATGTAATTCATCTTTTCTTTTCC-AAAAAAAAAAAAAAA
1 AAGTCAATGATACTTTTATGCATTTAATGTAATTCATCTTTTCTTTTCCAAAAAAAAAAAAAAAA
*
43445512 CTAAGAACATGAGGAAATTGTAATTAAATCTTTTGTTAACATCAAAGATAATTTGGC
66 ATAAGAACATGAGGAAATTGTAATTAAATCTTTTGTTAACATCAAAGATAATTTGGC
43445569 A
1 A
43445570 TGTGTAAAAT
Statistics
Matches: 120, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
120 72 0.60
121 38 0.32
122 10 0.08
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (122 bp):
AAGTCAATGATACTTTTATGCATTTAATGTAATTCATCTTTTCTTTTCCAAAAAAAAAAAAAAAA
ATAAGAACATGAGGAAATTGTAATTAAATCTTTTGTTAACATCAAAGATAATTTGGC
Found at i:43448251 original size:85 final size:85
Alignment explanation
Indices: 43448108--43448278 Score: 324
Period size: 85 Copynumber: 2.0 Consensus size: 85
43448098 GAAATTTGCA
*
43448108 ATATGATCCATTAATTTTTAATCCATGGAAGATTAGATTAATAGAGCAATCATCGTTTCATTTAG
1 ATATGATCCATTAATTTTTAATCCATGGAAGATTAGATTAATAGAGCAATCATCGTTTCATATAG
43448173 CTGTTTTATACATGACCATT
66 CTGTTTTATACATGACCATT
*
43448193 ATATGATCCATTAATTTTTAATCCATGGAAGATTAGATTATTAGAGCAATCATCGTTTCATATAG
1 ATATGATCCATTAATTTTTAATCCATGGAAGATTAGATTAATAGAGCAATCATCGTTTCATATAG
43448258 CTGTTTTATACATGACCATT
66 CTGTTTTATACATGACCATT
43448278 A
1 A
43448279 ATCAGATTCT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (85 bp):
ATATGATCCATTAATTTTTAATCCATGGAAGATTAGATTAATAGAGCAATCATCGTTTCATATAG
CTGTTTTATACATGACCATT
Found at i:43448564 original size:133 final size:134
Alignment explanation
Indices: 43448325--43448597 Score: 530
Period size: 133 Copynumber: 2.0 Consensus size: 134
43448315 TTTAATAAAT
43448325 ATTTAAAATCTTGACTCAAGTTTCGTTGGATATTATTAATGAATTTTTAAAAAAAAAAATGTTAT
1 ATTTAAAATCTTGACTCAAGTTTCGTTGGATATTATTAATGAATTTTTAAAAAAAAAAATGTTAT
*
43448390 TAGATATTATTAATATATAGATAAAAGTATTAATTTTCTGATAAAATTTTATTCGAATTTAATTT
66 TAGATATTATTAATATATAGATAAAAATATTAATTTTCTGATAAAATTTTATTCGAATTTAATTT
43448455 GAAC
131 GAAC
43448459 ATTTAAAATC-TGACTCAAGTTTCGTTGGATATTATTAATGAATTTTTAAAAAAAAAAATGTTAT
1 ATTTAAAATCTTGACTCAAGTTTCGTTGGATATTATTAATGAATTTTTAAAAAAAAAAATGTTAT
43448523 TAGATATTATTAATATATAGATAAAAATATTAATTTTCTGATAAAATTTTATTCGAATTTAATTT
66 TAGATATTATTAATATATAGATAAAAATATTAATTTTCTGATAAAATTTTATTCGAATTTAATTT
43448588 GAAC
131 GAAC
43448592 ATTTAA
1 ATTTAA
43448598 GAGTCGATTT
Statistics
Matches: 138, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
133 128 0.93
134 10 0.07
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.43
Consensus pattern (134 bp):
ATTTAAAATCTTGACTCAAGTTTCGTTGGATATTATTAATGAATTTTTAAAAAAAAAAATGTTAT
TAGATATTATTAATATATAGATAAAAATATTAATTTTCTGATAAAATTTTATTCGAATTTAATTT
GAAC
Found at i:43455168 original size:54 final size:54
Alignment explanation
Indices: 43455004--43455139 Score: 227
Period size: 54 Copynumber: 2.5 Consensus size: 54
43454994 GTTGGCCCAT
43455004 ACGGGCACAGTGAGTTACATGGACTGGCAACACGATCGTGTGACCCTAAGTTAC
1 ACGGGCACAGTGAGTTACATGGACTGGCAACACGATCGTGTGACCCTAAGTTAC
* * *
43455058 ATGGGCACAGTGAGTTACATGGACTGACGACACGATCGTGTGACCCTAAGTTAC
1 ACGGGCACAGTGAGTTACATGGACTGGCAACACGATCGTGTGACCCTAAGTTAC
* *
43455112 ACGGTCACAGTGAGTTACATGGTCTGGC
1 ACGGGCACAGTGAGTTACATGGACTGGC
43455140 CATACGACCG
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (54 bp):
ACGGGCACAGTGAGTTACATGGACTGGCAACACGATCGTGTGACCCTAAGTTAC
Found at i:43455714 original size:17 final size:17
Alignment explanation
Indices: 43455692--43455728 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
43455682 CTAATATACA
43455692 ATGTCAGTTTAGACACG
1 ATGTCAGTTTAGACACG
43455709 ATGTCAGTTTAGACACG
1 ATGTCAGTTTAGACACG
43455726 ATG
1 ATG
43455729 ACTTTGTAGT
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:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (17 bp):
ATGTCAGTTTAGACACG
Found at i:43456845 original size:27 final size:27
Alignment explanation
Indices: 43456807--43456858 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
43456797 AACTAATGCC
43456807 GCCTACAAGATTGGCACCACTGGTGCT
1 GCCTACAAGATTGGCACCACTGGTGCT
* *
43456834 GCCTACAAGATTGGTACCATTGGTG
1 GCCTACAAGATTGGCACCACTGGTG
43456859 TCGCCTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (27 bp):
GCCTACAAGATTGGCACCACTGGTGCT
Found at i:43456864 original size:27 final size:26
Alignment explanation
Indices: 43456806--43456879 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 26
43456796 GAACTAATGC
43456806 CGCCTACAAGATTGGCACCACTGGTG
1 CGCCTACAAGATTGGCACCACTGGTG
* *
43456832 CTGCCTACAAGATTGGTACCATTGGTG
1 C-GCCTACAAGATTGGCACCACTGGTG
* * *
43456859 TCGCCTATAACATTAGCACCA
1 -CGCCTACAAGATTGGCACCA
43456880 GTTTTGGTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.03
27 38 0.95
28 1 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (26 bp):
CGCCTACAAGATTGGCACCACTGGTG
Found at i:43464459 original size:7 final size:8
Alignment explanation
Indices: 43464443--43464469 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
43464433 AATTATTTTT
43464443 AAAATAAA
1 AAAATAAA
43464451 AAAATAAA
1 AAAATAAA
43464459 AAAATAAA
1 AAAATAAA
43464467 AAA
1 AAA
43464470 GTATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:43465914 original size:22 final size:23
Alignment explanation
Indices: 43465871--43465919 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
43465861 AGCCTGGGTT
* *
43465871 ATTAAAATTATATTTTTATTAAA
1 ATTAAAACTATATTGTTATTAAA
43465894 ATTAAAACTA-ATTGTTATTAAA
1 ATTAAAACTATATTGTTATTAAA
43465916 ATTA
1 ATTA
43465920 TATCAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTAAAACTATATTGTTATTAAA
Found at i:43465928 original size:22 final size:21
Alignment explanation
Indices: 43465868--43465925 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
43465858 CCGAGCCTGG
43465868 GTTATTAAAATTATAT---TT
1 GTTATTAAAATTATATCAATT
* *
43465886 -TTATTAAAATTAAAACTAATT
1 GTTATTAAAATTATATC-AATT
43465907 GTTATTAAAATTATATCAA
1 GTTATTAAAATTATATCAA
43465926 ATTATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 13 0.42
21 4 0.13
22 14 0.45
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (21 bp):
GTTATTAAAATTATATCAATT
Found at i:43465998 original size:19 final size:19
Alignment explanation
Indices: 43465974--43466038 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
43465964 ATCTAACATT
43465974 TTGTTAGTAAAATTATTAA
1 TTGTTAGTAAAATTATTAA
*
43465993 TTGTTAGTAAAGTTATTAAA
1 TTGTTAGTAAAATTATT-AA
* *
43466013 TT-ATA-TCAAATTATTAA
1 TTGTTAGTAAAATTATTAA
43466030 TTGTTAGTA
1 TTGTTAGTA
43466039 CCAGTCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 4 0.11
18 10 0.27
19 19 0.51
20 4 0.11
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.48
Consensus pattern (19 bp):
TTGTTAGTAAAATTATTAA
Found at i:43466135 original size:12 final size:12
Alignment explanation
Indices: 43466118--43466149 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
43466108 TTATATCAGA
43466118 TTAGGGTTAAGG
1 TTAGGGTTAAGG
43466130 TTAGGGTTAAGG
1 TTAGGGTTAAGG
43466142 TTAGGGTT
1 TTAGGGTT
43466150 TTTGTTAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.38
Consensus pattern (12 bp):
TTAGGGTTAAGG
Found at i:43466203 original size:27 final size:27
Alignment explanation
Indices: 43466173--43466265 Score: 114
Period size: 27 Copynumber: 3.2 Consensus size: 27
43466163 AGGTTTTGGT
43466173 GTTTTTAAGTTAAGGGTTAGGGTTAGG
1 GTTTTTAAGTTAAGGGTTAGGGTTAGG
43466200 GTTTTTAAGTTAAGGGTTAGGGTTATGGTTAGG
1 GTTTTTAAGTTAAGGGTTA--G----GGTTAGG
* *
43466233 GTTTTTAAGCTAAGGGTTAGGGCTAGG
1 GTTTTTAAGTTAAGGGTTAGGGTTAGG
43466260 GTTTTT
1 GTTTTT
43466266 TAGGGTTTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
27 31 0.53
29 1 0.02
31 1 0.02
33 25 0.43
ACGTcount: A:0.20, C:0.02, G:0.35, T:0.42
Consensus pattern (27 bp):
GTTTTTAAGTTAAGGGTTAGGGTTAGG
Found at i:43466230 original size:33 final size:33
Alignment explanation
Indices: 43466185--43466578 Score: 269
Period size: 33 Copynumber: 11.6 Consensus size: 33
43466175 TTTTAAGTTA
*
43466185 AGGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTT
1 AGGGTTATGGTTAGGGTTTTTAAGTTAAGGGTT
*
43466218 AGGGTTATGGTTAGGGTTTTTAAGCTAAGGGTTAGGGCT
1 AGGGTTATGGTTAGGGTTTTTAAGTTAAGGG-T-----T
* *
43466257 AGGGTTTTTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTTTT
1 AGGG----TTATGG-TTAGG-GTTTTTAAGTTAAGGG---TT
* *
43466299 A-AGTTAAGGGTTAGGGTTAGGGTTT---TTAA--GTT
1 AGGGTT-ATGGTTAGGGTT----TTTAAGTTAAGGGTT
**
43466331 AAGGGTTAAAGTTAGGGTTTTTAAGTTAAGGGTT
1 -AGGGTTATGGTTAGGGTTTTTAAGTTAAGGGTT
* *
43466365 AGGGTTATGGTTATGGTTTTTAAGTTAATGGTT
1 AGGGTTATGGTTAGGGTTTTTAAGTTAAGGGTT
* * * *
43466398 AGGGTTAAGGCTAGGGTTTTT--GTTAAAGTTT
1 AGGGTTATGGTTAGGGTTTTTAAGTTAAGGGTT
* * * *
43466429 TGGTGTTTTTAAGTTAAGGGTTTTTAAGTAAAGGGTT
1 AGG-G-TTAT-GGTT-AGGGTTTTTAAGTTAAGGGTT
*
43466466 A--G---T-GTTAGGGTTTTTTAGTTAAGGGTT
1 AGGGTTATGGTTAGGGTTTTTAAGTTAAGGGTT
43466493 AGGGTTATGGTTAGGGTTTTTAAGTTAAGGGTT
1 AGGGTTATGGTTAGGGTTTTTAAGTTAAGGGTT
43466526 AGGGTTATGGTTAGGG-TTTTAAGTTAAGGGTT
1 AGGGTTATGGTTAGGGTTTTTAAGTTAAGGGTT
* *
43466558 AGGGTTAAGGCTAGGGTTTTT
1 AGGGTTATGGTTAGGGTTTTT
43466579 GTTAGGGTTT
Statistics
Matches: 289, Mismatches: 33, Indels: 78
0.72 0.08 0.19
Matches are distributed among these distances:
27 20 0.07
28 3 0.01
29 4 0.01
30 1 0.00
31 10 0.03
32 38 0.13
33 132 0.46
34 10 0.03
35 10 0.03
36 3 0.01
37 17 0.06
38 4 0.01
39 5 0.02
40 3 0.01
41 1 0.00
42 2 0.01
43 5 0.02
44 4 0.01
45 15 0.05
47 2 0.01
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.43
Consensus pattern (33 bp):
AGGGTTATGGTTAGGGTTTTTAAGTTAAGGGTT
Found at i:43466250 original size:60 final size:60
Alignment explanation
Indices: 43466173--43466564 Score: 286
Period size: 60 Copynumber: 6.4 Consensus size: 60
43466163 AGGTTTTGGT
43466173 GTTTTTAAGTTAAGGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTATGGTTAGG
1 GTTTTTAAGTTAAGGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTATGGTTAGG
* * * * *
43466233 GTTTTTAAGCTAAGGGTTAGGGCTAGGG-TTTT---TT-AGGGTTTTGGTGTTTTTAAGTTAAGG
1 GTTTTTAAGTTAAGGGTTAGGGTTAGGGTTTTTAAGTTAAGGG-TTAGG-G-TTAT-GGTT-AGG
*
43466293 GTTTTTAAGTTAAGGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTA-----A-AGTTAGG
1 GTTTTTAAGTTAAGGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTATGGTTAGG
* * *
43466347 GTTTTTAAGTTAAGGGTTAGGGTTATGGTTATGGTTTTTAAGTTAATGGTTAGGGTTAAGGCTAG
1 GTTTTTAAGTTAAGGGTTAGGGTTA--G----GGTTTTTAAGTTAAGGGTTAGGGTTATGGTTAG
43466412 G
60 G
*
43466413 GTTTTT--GTTAA-AGTT----TT-GGTGTTTTTAAGTTAAGGGTTTTTAAGTAAAGGGTTA-GT
1 GTTTTTAAGTTAAGGGTTAGGGTTAGG-GTTTTTAAGTTAAGGG----T---T--AGGGTTATG-
43466469 GTTAGG
55 GTTAGG
*
43466475 GTTTTTTAGTTAAGGGTTAGGGTTATGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTATGGTTAG
1 GTTTTTAAGTTAAGGGTTA--G----GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTATGGTTAG
43466540 G
60 G
43466541 G-TTTTAAGTTAAGGGTTAGGGTTA
1 GTTTTTAAGTTAAGGGTTAGGGTTA
43466565 AGGCTAGGGT
Statistics
Matches: 267, Mismatches: 17, Indels: 97
0.70 0.04 0.25
Matches are distributed among these distances:
52 1 0.00
53 15 0.06
54 28 0.10
55 8 0.03
56 8 0.03
57 2 0.01
58 3 0.01
59 14 0.05
60 75 0.28
61 5 0.02
62 18 0.07
63 4 0.01
64 14 0.05
65 24 0.09
66 25 0.09
67 1 0.00
68 1 0.00
71 1 0.00
75 18 0.07
76 2 0.01
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.44
Consensus pattern (60 bp):
GTTTTTAAGTTAAGGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTATGGTTAGG
Found at i:43466320 original size:27 final size:27
Alignment explanation
Indices: 43466290--43466404 Score: 149
Period size: 27 Copynumber: 4.0 Consensus size: 27
43466280 TTTTAAGTTA
43466290 AGGGTTTTTAAGTTAAGGGTTAGGGTT
1 AGGGTTTTTAAGTTAAGGGTTAGGGTT
**
43466317 AGGGTTTTTAAGTTAAGGGTTAAAGTT
1 AGGGTTTTTAAGTTAAGGGTTAGGGTT
43466344 AGGGTTTTTAAGTTAAGGGTTAGGGTT
1 AGGGTTTTTAAGTTAAGGGTTAGGGTT
*
43466371 ATGGTTATGGTTTTTAAGTTAATGGTTAGGGTT
1 A--G----GGTTTTTAAGTTAAGGGTTAGGGTT
43466404 A
1 A
43466405 AGGCTAGGGT
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
27 51 0.66
29 1 0.01
33 25 0.32
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (27 bp):
AGGGTTTTTAAGTTAAGGGTTAGGGTT
Found at i:43466452 original size:14 final size:15
Alignment explanation
Indices: 43466433--43466465 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
43466423 AAGTTTTGGT
*
43466433 GTTTTTAAGTTAAGG
1 GTTTTTAAGTAAAGG
43466448 GTTTTTAAGTAAAGG
1 GTTTTTAAGTAAAGG
43466463 GTT
1 GTT
43466466 AGTGTTAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (15 bp):
GTTTTTAAGTAAAGG
Found at i:43466634 original size:5 final size:6
Alignment explanation
Indices: 43466487--43466638 Score: 69
Period size: 6 Copynumber: 24.0 Consensus size: 6
43466477 TTTTTAGTTA
* * *
43466487 AGGGTT AGGGTT ATGGTT AGGGTTTTT A-AGTT AAGGGTT AGGGTT ATGGTT
1 AGGGTT AGGGTT AGGGTT AGGG---TT AGGGTT -AGGGTT AGGGTT AGGGTT
* * * ***
43466538 AGGGTTTT A-AGTT AAGGGTT AGGGTT AAGGCT AGGGTT TTTGTT AGGGTTT
1 AGGG--TT AGGGTT -AGGGTT AGGGTT AGGGTT AGGGTT AGGGTT AGGG-TT
* *
43466589 TGGTGTTTT A-AGTT AAGGGTT AGGGTT AGGGTT AGGGTT A-GGTT AGGGTT
1 AGG-G--TT AGGGTT -AGGGTT AGGGTT AGGGTT AGGGTT AGGGTT AGGGTT
43466639 TGTCAATTAA
Statistics
Matches: 109, Mismatches: 22, Indels: 30
0.68 0.14 0.19
Matches are distributed among these distances:
5 11 0.10
6 72 0.66
7 15 0.14
8 5 0.05
9 6 0.06
ACGTcount: A:0.19, C:0.01, G:0.39, T:0.41
Consensus pattern (6 bp):
AGGGTT
Found at i:43467204 original size:18 final size:18
Alignment explanation
Indices: 43467178--43467221 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
43467168 GACTGAGAAA
* * *
43467178 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
43467196 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
43467214 AGGATACA
1 AGGATACA
43467222 CACCTGGCAT
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:0.45, C:0.09, G:0.27, T:0.18
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:43469046 original size:11 final size:11
Alignment explanation
Indices: 43469032--43469118 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 11
43469022 GAGAAATTTA
43469032 AGAGGAAATTG
1 AGAGGAAATTG
*
43469043 AGAGCAAATTG
1 AGAGGAAATTG
**
43469054 AGATTAAA-T-
1 AGAGGAAATTG
* *
43469063 A-TGG-ATTTG
1 AGAGGAAATTG
43469072 AGA-GAAATTTG
1 AGAGGAAA-TTG
43469083 -GAAGGAAATTG
1 AG-AGGAAATTG
* *
43469094 AGAGCAATTTG
1 AGAGGAAATTG
43469105 AGAGGAAATTG
1 AGAGGAAATTG
43469116 AGA
1 AGA
43469119 AATGATTAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 3 0.05
11 42 0.76
12 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:43469076 original size:51 final size:51
Alignment explanation
Indices: 43469008--43469107 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
43468998 TAAAAATTAA
43469008 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * * *
43469059 AAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAATTTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
43469108 GGAAATTGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.27, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:43469094 original size:22 final size:22
Alignment explanation
Indices: 43469069--43469118 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
43469059 AAATATGGAT
43469069 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
*
43469091 TTGAGAGCAATTTGAGAGGAAA
1 TTGAGAGAAATTTGAGAGGAAA
43469113 TTGAGA
1 TTGAGA
43469119 AATGATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.32, T:0.24
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:43470506 original size:16 final size:16
Alignment explanation
Indices: 43470485--43470516 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43470475 TTTCTTAGTT
43470485 TTTTTAACATTTTCAA
1 TTTTTAACATTTTCAA
43470501 TTTTTAACATTTTCAA
1 TTTTTAACATTTTCAA
43470517 ATTGACATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTTAACATTTTCAA
Found at i:43474017 original size:7 final size:7
Alignment explanation
Indices: 43474005--43474029 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43473995 AAAAATTAAG
43474005 TATTTTA
1 TATTTTA
43474012 TATTTTA
1 TATTTTA
43474019 TATTTTA
1 TATTTTA
43474026 TATT
1 TATT
43474030 AAAGCAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTTA
Found at i:43475261 original size:18 final size:18
Alignment explanation
Indices: 43475238--43475274 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
43475228 TTAAGTAAAC
43475238 AAAAATGTTACAAAGAAT
1 AAAAATGTTACAAAGAAT
*
43475256 AAAAATGTTGCAAAGAAT
1 AAAAATGTTACAAAGAAT
43475274 A
1 A
43475275 CTATACTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.22
Consensus pattern (18 bp):
AAAAATGTTACAAAGAAT
Found at i:43478320 original size:41 final size:41
Alignment explanation
Indices: 43478275--43478356 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
43478265 AATCTAATTG
*
43478275 GGAAAATAATTT-TCTTATCCTAATAAAATACTAAAAAATAA
1 GGAAAAT-ATTTCCCTTATCCTAATAAAATACTAAAAAATAA
* * * *
43478316 GGAAAATATTTCCCTTATTCTAATAAACTGCTAAAAGATAA
1 GGAAAATATTTCCCTTATCCTAATAAAATACTAAAAAATAA
43478357 AATAAAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 4 0.11
41 31 0.89
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (41 bp):
GGAAAATATTTCCCTTATCCTAATAAAATACTAAAAAATAA
Found at i:43478418 original size:19 final size:19
Alignment explanation
Indices: 43478394--43478434 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
43478384 TGATTTATTC
*
43478394 TAAGATTTATCTTCCTAAA
1 TAAGATTTATCTACCTAAA
43478413 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
43478432 TAA
1 TAA
43478435 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:43489837 original size:39 final size:39
Alignment explanation
Indices: 43489778--43489858 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
43489768 CCAGCGTTAG
* *
43489778 ACGGTTCGGAGCTGCAAGGGACTCGGAGAGGGCCACACA
1 ACGGTTCGGAACTACAAGGGACTCGGAGAGGGCCACACA
*
43489817 ACGGTTCGGAACTACGAGGGACTCGGAGAGGGCCACACA
1 ACGGTTCGGAACTACAAGGGACTCGGAGAGGGCCACACA
43489856 ACG
1 ACG
43489859 ACACTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.27, C:0.26, G:0.37, T:0.10
Consensus pattern (39 bp):
ACGGTTCGGAACTACAAGGGACTCGGAGAGGGCCACACA
Found at i:43494279 original size:27 final size:28
Alignment explanation
Indices: 43494232--43494293 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
43494222 CAACACTGTC
43494232 AATTTATCTTTTTTGTTTTTTGGGGATT
1 AATTTATCTTTTTTGTTTTTTGGGGATT
43494260 AATTTATCTTTTTTGTTTTTTGGGGATT
1 AATTTATCTTTTTTGTTTTTTGGGGATT
*
43494288 ATTTTA
1 AATTTA
43494294 CAACATGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.16, C:0.03, G:0.16, T:0.65
Consensus pattern (28 bp):
AATTTATCTTTTTTGTTTTTTGGGGATT
Found at i:43502845 original size:28 final size:28
Alignment explanation
Indices: 43502814--43502936 Score: 210
Period size: 28 Copynumber: 4.4 Consensus size: 28
43502804 AAAAGTTTGG
* * **
43502814 GTACCAATCTGGGACAAAAAATTCATAA
1 GTACCAATTTGAGACAAAAAAACCATAA
43502842 GTACCAATTTGAGACAAAAAAACCATAA
1 GTACCAATTTGAGACAAAAAAACCATAA
43502870 GTACCAATTTGAGACAAAAAAACCATAA
1 GTACCAATTTGAGACAAAAAAACCATAA
43502898 GTACCAATTTGAGACAAAAAAACCATAA
1 GTACCAATTTGAGACAAAAAAACCATAA
43502926 GTACCAATTTG
1 GTACCAATTTG
43502937 GGAAAAGTGG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 91 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.20
Consensus pattern (28 bp):
GTACCAATTTGAGACAAAAAAACCATAA
Found at i:43503855 original size:18 final size:19
Alignment explanation
Indices: 43503832--43503868 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
43503822 CGAACTTCAT
43503832 TTAATTCG-AAAAACATAA
1 TTAATTCGAAAAAACATAA
*
43503850 TTAATTTGAAAAAACATAA
1 TTAATTCGAAAAAACATAA
43503869 AATCATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (19 bp):
TTAATTCGAAAAAACATAA
Found at i:43503898 original size:7 final size:7
Alignment explanation
Indices: 43503886--43503914 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
43503876 TTTCAGGTTA
43503886 TTTTCAT
1 TTTTCAT
43503893 TTTTCAT
1 TTTTCAT
43503900 TTTTCA-
1 TTTTCAT
43503906 TTTTCAT
1 TTTTCAT
43503913 TT
1 TT
43503915 CCATTTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTCAT
Found at i:43503909 original size:13 final size:14
Alignment explanation
Indices: 43503886--43503914 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
43503876 TTTCAGGTTA
43503886 TTTTCATTTTTCAT
1 TTTTCATTTTTCAT
43503900 TTTTCA-TTTTCAT
1 TTTTCATTTTTCAT
43503913 TT
1 TT
43503915 CCATTTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCATTTTTCAT
Found at i:43503981 original size:57 final size:56
Alignment explanation
Indices: 43503894--43504023 Score: 158
Period size: 57 Copynumber: 2.3 Consensus size: 56
43503884 TATTTTCATT
* *
43503894 TTTCATTT-TTCATTTTCATTTCCATTTTGGAGAAAA-CA-ACATTCATTTCCAAATGG
1 TTTCATTTCTCCATTTTCATTTCCATCTTGGA-AAAAGCATA-ATT-ATTTCCAAATGG
* *
43503950 TTTCATTTCTCCATTTTCATTTTCATCTTGGAAAAAGTCATAATTATTTCCAAATGT
1 TTTCATTTCTCCATTTTCATTTCCATCTTGGAAAAAG-CATAATTATTTCCAAATGG
43504007 TTTCTATTTCTCCATTT
1 TTTC-ATTTCTCCATTT
43504024 CACCATTTCT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
56 12 0.18
57 35 0.54
58 17 0.26
59 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.48
Consensus pattern (56 bp):
TTTCATTTCTCCATTTTCATTTCCATCTTGGAAAAAGCATAATTATTTCCAAATGG
Found at i:43508015 original size:2 final size:2
Alignment explanation
Indices: 43508010--43508035 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43508000 ATATGCATCC
43508010 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
43508036 GATTAGGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43511565 original size:30 final size:30
Alignment explanation
Indices: 43511529--43511596 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
43511519 GTCACCACTA
* *
43511529 ACCATTTTCCGTTATAGACGTAACGAAGCT
1 ACCATTTTACGTTAGAGACGTAACGAAGCT
* * *
43511559 ACCATTTTACGTTAGATACTTAACGGAGCT
1 ACCATTTTACGTTAGAGACGTAACGAAGCT
*
43511589 GCCATTTT
1 ACCATTTT
43511597 TCATCCCCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (30 bp):
ACCATTTTACGTTAGAGACGTAACGAAGCT
Found at i:43517570 original size:50 final size:50
Alignment explanation
Indices: 43517452--43517690 Score: 289
Period size: 50 Copynumber: 4.6 Consensus size: 50
43517442 GATAATAACA
* * ** * *
43517452 TGCCAAAGCCATGTCCCAGACATGCTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * **
43517503 TACCCATGTCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
43517553 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
43517603 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
43517658 ATGCCAATGCCATGTCCCAGACATGGTCTTACA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACA
43517691 AAAAAAATCT
Statistics
Matches: 160, Mismatches: 22, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
50 92 0.57
51 30 0.19
53 4 0.03
55 2 0.01
56 32 0.20
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:43518352 original size:49 final size:49
Alignment explanation
Indices: 43518297--43518461 Score: 149
Period size: 49 Copynumber: 3.4 Consensus size: 49
43518287 CCTAGTTCAT
*
43518297 GGTGGTTATACGGTCACAGGTTCAAATATAACTAAGGCT-TTCAATTTAC
1 GGTGGTTATACGGTCACAGGTTCAAATATAACTAAGGCTCTT-AATTGAC
** *
43518346 GGTGGTTATATAGT-ACCAGGTTCAAATATAACTAAGGCTCTTAGTTGAC
1 GGTGGTTATACGGTCA-CAGGTTCAAATATAACTAAGGCTCTTAATTGAC
* * * * * * *
43518395 GGTGGTTATGCGATCACGGGTTTAAGTATAACT-CGAGCTC-CAAGTTGAC
1 GGTGGTTATACGGTCACAGGTTCAAATATAACTAAG-GCTCTTAA-TTGAC
* *
43518444 AGTGGTTATACGATCACA
1 GGTGGTTATACGGTCACA
43518462 AGTTTAAGTT
Statistics
Matches: 94, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
48 3 0.03
49 88 0.94
50 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (49 bp):
GGTGGTTATACGGTCACAGGTTCAAATATAACTAAGGCTCTTAATTGAC
Found at i:43522463 original size:28 final size:28
Alignment explanation
Indices: 43522405--43522515 Score: 125
Period size: 28 Copynumber: 4.0 Consensus size: 28
43522395 CACGAAATTG
* *
43522405 ATTTGCTCACAGAAGCTGTAATATTCT-A
1 ATTTGCTCACACAAGCTGTGATATT-TGA
* *
43522433 ATTTGCTCACACGAGCTGTGACATTTGA
1 ATTTGCTCACACAAGCTGTGATATTTGA
* * * *
43522461 ATTTTCTTAGACAAGCTATGATATTTGA
1 ATTTGCTCACACAAGCTGTGATATTTGA
*
43522489 ATTTGCTCACAAAAGCTGTGATATTTG
1 ATTTGCTCACACAAGCTGTGATATTTG
43522516 GGTTGCTTAC
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
27 1 0.01
28 66 0.99
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (28 bp):
ATTTGCTCACACAAGCTGTGATATTTGA
Found at i:43523110 original size:34 final size:34
Alignment explanation
Indices: 43523072--43523142 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
43523062 AGTTGATTCA
43523072 AATCCCGATTTAT-GATAATTCATTTCAATTCATC
1 AATCCCGATTTATAG-TAATTCATTTCAATTCATC
43523106 AATCCCGATTTATAGTAATTCATTTCAATTCATC
1 AATCCCGATTTATAGTAATTCATTTCAATTCATC
43523140 AAT
1 AAT
43523143 TCTAAACATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 35 0.97
35 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.41
Consensus pattern (34 bp):
AATCCCGATTTATAGTAATTCATTTCAATTCATC
Done.