Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 93 of 276
Found at i:29179449 original size:27 final size:27
Alignment explanation
Indices: 29179411--29179500 Score: 171
Period size: 27 Copynumber: 3.3 Consensus size: 27
29179401 GCCTAGCAGG
29179411 CTTCGTGCCGGTGATGTGTATTCGGGC
1 CTTCGTGCCGGTGATGTGTATTCGGGC
29179438 CTTCGTGCCGGTGATGTGTATTCGGGC
1 CTTCGTGCCGGTGATGTGTATTCGGGC
*
29179465 CTTCGTGCAGGTGATGTGTATTCGGGC
1 CTTCGTGCCGGTGATGTGTATTCGGGC
29179492 CTTCGTGCC
1 CTTCGTGCC
29179501 TACTAGGCTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.08, C:0.23, G:0.36, T:0.33
Consensus pattern (27 bp):
CTTCGTGCCGGTGATGTGTATTCGGGC
Found at i:29181271 original size:56 final size:56
Alignment explanation
Indices: 29181185--29181304 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
29181175 ACAAGGGATG
29181185 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
29181241 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
29181297 ATGGGCAA
1 ATGGGCAA
29181305 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:29182570 original size:79 final size:81
Alignment explanation
Indices: 29182434--29182616 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
29182424 TCGAATGATG
* *
29182434 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
29182498 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
29182513 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
29182575 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
29182593 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
29182617 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.65
80 30 0.34
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:29182632 original size:40 final size:40
Alignment explanation
Indices: 29182435--29182618 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
29182425 CGAATGATGT
* * * *
29182435 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
29182475 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
29182515 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29182553 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29182594 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
29182619 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:29182640 original size:79 final size:79
Alignment explanation
Indices: 29182487--29182651 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
29182477 GGACTAAGAT
* **
29182487 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
29182552 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
29182566 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
29182629 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
29182645 CCGAAGG
1 CCGAAGG
29182652 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:29189180 original size:56 final size:56
Alignment explanation
Indices: 29189094--29189213 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
29189084 ACAAGGGATG
29189094 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
29189150 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
29189206 ATGGGCAA
1 ATGGGCAA
29189214 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:29190478 original size:79 final size:81
Alignment explanation
Indices: 29190342--29190524 Score: 234
Period size: 79 Copynumber: 2.3 Consensus size: 81
29190332 TCAAATGATG
* *
29190342 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGAGTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGAGTAAGATCCGAAGGCATT
29190406 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * *
29190421 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGG-GTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGAG-TAAGAT-CCGAAGGC
29190482 ATTTGTGCGAGTTACTATA
63 ATTTGTGCGAGTTACTATA
* *
29190501 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
29190525 TGAACGAGTA
Statistics
Matches: 91, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
78 2 0.02
79 59 0.65
80 30 0.33
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGAGTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:29190540 original size:40 final size:40
Alignment explanation
Indices: 29190343--29190526 Score: 209
Period size: 40 Copynumber: 4.6 Consensus size: 40
29190333 CAAATGATGT
* * * *
29190343 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
*
29190383 CCGGAG-TAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGG-GCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
29190423 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29190461 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29190502 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
29190527 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
39 36 0.29
40 79 0.63
41 11 0.09
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:29190548 original size:79 final size:79
Alignment explanation
Indices: 29190395--29190559 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
29190385 GGAGTAAGAT
* **
29190395 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
29190460 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
29190474 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
29190537 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
29190553 CCGAAGG
1 CCGAAGG
29190560 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:29194993 original size:43 final size:43
Alignment explanation
Indices: 29194945--29195309 Score: 547
Period size: 43 Copynumber: 8.5 Consensus size: 43
29194935 ATTATAATTA
*
29194945 GGCCTTCGTGCCTAGCAGGCTTTGTGCAGGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
*
29194988 GGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
* * *
29195031 GGCCTTCGTGCCTAGCAGGCTTCT-TGCCAGTGATGTGAACTCG
1 GGCCTTCGTGCCTAGCAGGCTT-TGTGCCGGTGATGTGTATTCG
29195074 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
**
29195117 GGCCTTTATGCCTAGCAGGCTTCT-TGCCGGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTT-TGTGCCGGTGATGTGTATTCG
* *
29195160 GGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
* * *
29195203 AGCCTTCGTGCCTAGCAGGCTTCT-TACCGGTGATGTGTATTTG
1 GGCCTTCGTGCCTAGCAGGCTT-TGTGCCGGTGATGTGTATTCG
* * *
29195246 GGCCTTCGTGCCTAGAAGGCTTCGTGCCGGTGATGTGTACTCG
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
29195289 GGCCTTCGTGCCTAGCAGGCT
1 GGCCTTCGTGCCTAGCAGGCT
29195310 ATGATGCTGG
Statistics
Matches: 289, Mismatches: 27, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
42 1 0.00
43 287 0.99
44 1 0.00
ACGTcount: A:0.12, C:0.25, G:0.33, T:0.31
Consensus pattern (43 bp):
GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
Found at i:29195098 original size:129 final size:129
Alignment explanation
Indices: 29194945--29195309 Score: 606
Period size: 129 Copynumber: 2.8 Consensus size: 129
29194935 ATTATAATTA
*
29194945 GGCCTTCGTGCCTAGCAGGCTTTGTGCAGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTT
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTT
*
29195010 CGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCTTGCCAGTGATGTGAACTCG
66 CGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGAACTCG
**
29195074 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTTATGCCTAGCAGGCTT
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTT
* * *
29195139 CTTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGTATTCG
66 CGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGAACTCG
* * * *
29195203 AGCCTTCGTGCCTAGCAGGCTTCT-TACCGGTGATGTGTATTTGGGCCTTCGTGCCTAGAAGGCT
1 GGCCTTCGTGCCTAGCAGGCTT-TGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCT
*
29195267 TCGTGCCGGTGATGTGTACTCGGGCCTTCGTGCCTAGCAGGCT
65 TCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCT
29195310 ATGATGCTGG
Statistics
Matches: 220, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
129 219 1.00
130 1 0.00
ACGTcount: A:0.12, C:0.25, G:0.33, T:0.31
Consensus pattern (129 bp):
GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTT
CGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGAACTCG
Found at i:29195356 original size:45 final size:45
Alignment explanation
Indices: 29195286--29195387 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
29195276 TGATGTGTAC
* * * *
29195286 TCGGGCCTTCGTGCCTAGCAGGCTATGATGCTGGTG-GAATACTAT
1 TCGGGCCTTCGAGCCAAGCAGGCTATAATGCCGGTGAG-ATACTAT
* *
29195331 TCGGGCCTTTGAGCCAAGCATGCTATAATGCCGGTGAGATACTAT
1 TCGGGCCTTCGAGCCAAGCAGGCTATAATGCCGGTGAGATACTAT
*
29195376 TCGGGCTTTCGA
1 TCGGGCCTTCGA
29195388 TATCGGGCCT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 47 0.98
46 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (45 bp):
TCGGGCCTTCGAGCCAAGCAGGCTATAATGCCGGTGAGATACTAT
Found at i:29199501 original size:205 final size:205
Alignment explanation
Indices: 29199149--29199553 Score: 765
Period size: 205 Copynumber: 2.0 Consensus size: 205
29199139 AAATGCACTT
29199149 CATAAAAAAATATATTGTATATAATTGCTAATTGATACTAAAAATAAAAATAATAAAAAAAGTGA
1 CATAAAAAAATATATTGTATATAATTGCTAATTGATACTAAAAATAAAAATAATAAAAAAAGTGA
* *
29199214 CCAATCAAAAATTTGAAAAAAATTATAAATCAATTTAGTGTCTACAAGAATAAATTAGTCTTTCT
66 CCAATCAAAAATTTGAAAAAAATTATAAATCAAATTAGTGTCTACAAGAATAAATTAATCTTTCT
*
29199279 CTACTTTTTCTGTAAAACAAATTAATTATATAGAAATAAATTAATTTTTCTCTCATCGTTATGTA
131 CTACTTTTTCTGTAAAACAAATTAATTATATAAAAATAAATTAATTTTTCTCTCATCGTTATGTA
29199344 ACAACCAGTG
196 ACAACCAGTG
29199354 CATAAAAAAATATATTGTATATAATTGCTAATTGATACTAAAAATAAAAATAATAAAAAAAGTGA
1 CATAAAAAAATATATTGTATATAATTGCTAATTGATACTAAAAATAAAAATAATAAAAAAAGTGA
*
29199419 CCAATCAAAAATTTGAAAAAATTTATAAATCAAATTAGTGTCTACAAGAATAAATTAATCTTTCT
66 CCAATCAAAAATTTGAAAAAAATTATAAATCAAATTAGTGTCTACAAGAATAAATTAATCTTTCT
*
29199484 CTACTTTTTCTGTAAAACAAATTAATTATATAAAAATAAATTAATTTTTCTCTCCTCGTTATGTA
131 CTACTTTTTCTGTAAAACAAATTAATTATATAAAAATAAATTAATTTTTCTCTCATCGTTATGTA
29199549 ACAAC
196 ACAAC
29199554 TCATACCCGT
Statistics
Matches: 195, Mismatches: 5, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
205 195 1.00
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (205 bp):
CATAAAAAAATATATTGTATATAATTGCTAATTGATACTAAAAATAAAAATAATAAAAAAAGTGA
CCAATCAAAAATTTGAAAAAAATTATAAATCAAATTAGTGTCTACAAGAATAAATTAATCTTTCT
CTACTTTTTCTGTAAAACAAATTAATTATATAAAAATAAATTAATTTTTCTCTCATCGTTATGTA
ACAACCAGTG
Found at i:29200968 original size:50 final size:47
Alignment explanation
Indices: 29200893--29201077 Score: 176
Period size: 50 Copynumber: 3.9 Consensus size: 47
29200883 TGGGGTAAGA
29200893 TGCCGATGCCATGTCCTAGACATGGTCTTACATAGGCTCTAGCATATCTG
1 TGCCGATG-CATGTCCTAGACATGGTCTTACATAGGCTCTA-CA-ATCTG
*
29200943 TGCCGATGCCATGTCCTAGACATGGTCTTAC--A--CT-GACACATCTCG
1 TGCCGATG-CATGTCCTAGACATGGTCTTACATAGGCTCTACA-ATCT-G
*
29200988 TAGCCGATGCATGTCCCT-GACATGGTCTTACACT-GGCTCTCACAATGTG
1 T-GCCGATGCATGT-CCTAGACATGGTCTTACA-TAGGCTCT-ACAATCTG
29201037 -GCCGATGCATGTCCTAGACAT-GTCTTACACTA-GCTC-ACAAT
1 TGCCGATGCATGTCCTAGACATGGTCTTACA-TAGGCTCTACAAT
29201078 AACCCATATG
Statistics
Matches: 119, Mismatches: 4, Indels: 30
0.78 0.03 0.20
Matches are distributed among these distances:
44 11 0.09
45 21 0.18
46 29 0.24
47 17 0.14
48 1 0.01
49 3 0.03
50 34 0.29
51 3 0.03
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (47 bp):
TGCCGATGCATGTCCTAGACATGGTCTTACATAGGCTCTACAATCTG
Found at i:29202398 original size:28 final size:29
Alignment explanation
Indices: 29202367--29202424 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
29202357 CTCACATATG
29202367 TTAGAA-TTTTTTCTAAATAAGTAATCAA
1 TTAGAATTTTTTTCTAAATAAGTAATCAA
29202395 TTAGAATTTTTTTCTAAATAAGTAATCAA
1 TTAGAATTTTTTTCTAAATAAGTAATCAA
29202424 T
1 T
29202425 CTTTCAACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (29 bp):
TTAGAATTTTTTTCTAAATAAGTAATCAA
Found at i:29203076 original size:22 final size:21
Alignment explanation
Indices: 29203040--29203095 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
29203030 AATTTTTAAG
* *
29203040 AAAAATATTATAATTGTT-TTA
1 AAAAATATAAAAATT-TTATTA
*
29203061 TAAAATATAGAAAATTTTATTA
1 AAAAATATA-AAAATTTTATTA
29203083 AAAAATATAAAAA
1 AAAAATATAAAAA
29203096 GTAGAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
AAAAATATAAAAATTTTATTA
Found at i:29203094 original size:20 final size:19
Alignment explanation
Indices: 29203056--29203094 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
29203046 ATTATAATTG
*
29203056 TTTTATAAAATATAGAAAA
1 TTTTATAAAAAATAGAAAA
*
29203075 TTTTATTAAAAAATATAAAA
1 TTTTA-TAAAAAATAGAAAA
29203095 AGTAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTTATAAAAAATAGAAAA
Found at i:29203198 original size:21 final size:20
Alignment explanation
Indices: 29203141--29203200 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
29203131 TAATATATAT
* *
29203141 AATTTTTAAAAATTTTCAAAA
1 AATTTATAAAAA-TTTAAAAA
*
29203162 AATATATAAAAA-TTAAAGAA
1 AATTTATAAAAATTTAAA-AA
29203182 AATTTATAAAAATTTAAAA
1 AATTTATAAAAATTTAAAA
29203201 TTATGACACA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 4 0.12
20 14 0.42
21 15 0.45
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
AATTTATAAAAATTTAAAAA
Found at i:29205474 original size:40 final size:40
Alignment explanation
Indices: 29205419--29205634 Score: 405
Period size: 40 Copynumber: 5.4 Consensus size: 40
29205409 CAATTGAGGA
29205419 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
29205459 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
29205499 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
29205539 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
29205579 TTATATCCGGGTTAAGTCTCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
29205619 TTATTTCCGGGTTAAG
1 TTATATCCGGGTTAAG
29205635 NNNNNNNNNN
Statistics
Matches: 172, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 172 1.00
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (40 bp):
TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
Found at i:29210140 original size:50 final size:50
Alignment explanation
Indices: 29210076--29210175 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
29210066 ATCTCAGGAC
29210076 ACTCCCGAATGAAATGATCCAATGCACCACATCGAAAACAACCAGTCTCA
1 ACTCCCGAATGAAATGATCCAATGCACCACATCGAAAACAACCAGTCTCA
29210126 ACTCCCGAATGAAATGATCCAATGCACCACATCGAAAACAACCAGTCTCA
1 ACTCCCGAATGAAATGATCCAATGCACCACATCGAAAACAACCAGTCTCA
29210176 GTTGGTCAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.40, C:0.32, G:0.12, T:0.16
Consensus pattern (50 bp):
ACTCCCGAATGAAATGATCCAATGCACCACATCGAAAACAACCAGTCTCA
Found at i:29210400 original size:27 final size:27
Alignment explanation
Indices: 29210362--29210417 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
29210352 GGCCTCTTAG
29210362 ATGTAGACTGACATGACTTGCTCATCT
1 ATGTAGACTGACATGACTTGCTCATCT
29210389 ATGTAGACTGACATGACTTGCTCATCT
1 ATGTAGACTGACATGACTTGCTCATCT
29210416 AT
1 AT
29210418 CTTTTATTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (27 bp):
ATGTAGACTGACATGACTTGCTCATCT
Found at i:29213230 original size:30 final size:30
Alignment explanation
Indices: 29213196--29213253 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29213186 CCTTAACTCT
29213196 AACTTTGGAAAAATTACAATTTTGCCCCTA
1 AACTTTGGAAAAATTACAATTTTGCCCCTA
* * * *
29213226 AACTTTTGCATATTTACAATTTTGCCCC
1 AACTTTGGAAAAATTACAATTTTGCCCC
29213254 AAGGCTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (30 bp):
AACTTTGGAAAAATTACAATTTTGCCCCTA
Found at i:29220183 original size:47 final size:47
Alignment explanation
Indices: 29220120--29220466 Score: 462
Period size: 47 Copynumber: 7.4 Consensus size: 47
29220110 CCCTTCGGGA
* *
29220120 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
29220167 CTTATCACATATATACACCTTT-ACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACA-CTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
29220214 CTTATCTCATATATACACCTTCAGATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
29220261 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
29220308 CTTATCACCTATATTCACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
29220355 CTTATCTCATATATACACCTTCAGATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
29220402 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
29220449 CTTATCACATATACACAC
1 CTTATCACATATATACAC
29220467 CTTGTACATC
Statistics
Matches: 257, Mismatches: 41, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
46 3 0.01
47 250 0.97
48 4 0.02
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:29220374 original size:141 final size:141
Alignment explanation
Indices: 29220120--29220476 Score: 617
Period size: 141 Copynumber: 2.5 Consensus size: 141
29220110 CCCTTCGGGA
* *
29220120 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
29220185 CTTTACATCCATCACATCGGCCATTAGGTCTTATCTCATATATACACCTTCAGATTCATCACGTT
66 CTTTACATCCATCACATCGGCCATTAGGTCTTATCTCATATATACACCTTCAGATTCATCACGTT
29220250 GGCCACTCGGC
131 GGCCACTCGGC
* *
29220261 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACCTATATTCA-
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
*
29220325 CTTTCACATTCATCACATCGGCCATTAGGTCTTATCTCATATATACACCTTCAGATTCATCACGT
66 CTTT-ACATCCATCACATCGGCCATTAGGTCTTATCTCATATATACACCTTCAGATTCATCACGT
29220390 TGGCCACTCGGC
130 TGGCCACTCGGC
* * *
29220402 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
29220467 CTTGTACATC
66 CTT-TACATC
29220477 AATTTCATCA
Statistics
Matches: 202, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
140 4 0.02
141 190 0.94
142 7 0.03
143 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
CTTTACATCCATCACATCGGCCATTAGGTCTTATCTCATATATACACCTTCAGATTCATCACGTT
GGCCACTCGGC
Found at i:29223847 original size:47 final size:47
Alignment explanation
Indices: 29223773--29223985 Score: 327
Period size: 47 Copynumber: 4.5 Consensus size: 47
29223763 TTCAGCACAA
*
29223773 AGGCCTTATCACATATATACACCTTCACATCCATCACATCGGCCATT
1 AGGCCTTATCACATATATACACCTTCACATTCATCACATCGGCCATT
* * * *
29223820 AGGTCTTATCTCATATATACACTTTCACATTCATCACATTGGCCATT
1 AGGCCTTATCACATATATACACCTTCACATTCATCACATCGGCCATT
* *
29223867 CGGCCTTATCACATATATACACCTTCACATTCATCACATTGGCCATT
1 AGGCCTTATCACATATATACACCTTCACATTCATCACATCGGCCATT
* * *
29223914 CGGCCTTATCACATATATACACTTTCACATTCATCACATCGACCATT
1 AGGCCTTATCACATATATACACCTTCACATTCATCACATCGGCCATT
*
29223961 AGGCCTTATCACATATACACACCTT
1 AGGCCTTATCACATATATACACCTT
29223986 GTACATCAAT
Statistics
Matches: 151, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 151 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
AGGCCTTATCACATATATACACCTTCACATTCATCACATCGGCCATT
Found at i:29223880 original size:22 final size:22
Alignment explanation
Indices: 29223852--29223927 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
29223842 TTTCACATTC
29223852 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
29223874 ATCACATATATACACCTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
29223898 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
29223921 ATCACAT
1 ATCACAT
29223928 ATATACACTT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:29227427 original size:39 final size:39
Alignment explanation
Indices: 29227373--29227516 Score: 166
Period size: 39 Copynumber: 3.7 Consensus size: 39
29227363 TTCAGTGATG
29227373 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
29227412 TATATCCGGACTTAAGGTCTGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* ** * * *
29227451 TATAAT-TGGACTTAAGGAACGCAGGCTACGTGCTAGAAA
1 TAT-ATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * *
29227490 TATGTCCGGGC-TAAAGTCCCGCAGGCT
1 TATATCCGGACTTAAGGT-CCGCAGGCT
29227517 TCGAGCTGGT
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
38 5 0.06
39 81 0.92
40 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:29227525 original size:78 final size:78
Alignment explanation
Indices: 29227380--29227532 Score: 175
Period size: 78 Copynumber: 2.0 Consensus size: 78
29227370 ATGTATATCC
** * * * * * *
29227380 GGACTTAAGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCTGCAGGCTATGTGC
1 GGACTTAAGGAACGCAGGCTACGTGCTAGAAATATATCCGGACTTAAAGTCCGCAGGCTATGAGC
29227445 TGGAATTATAATT
66 TGGAATTATAATT
* *
29227458 GGACTTAAGGAACGCAGGCTACGTGCTAGAAATATGTCCGGGC-TAAAGTCCCGCAGGCT-TCGA
1 GGACTTAAGGAACGCAGGCTACGTGCTAGAAATATATCCGGACTTAAAGT-CCGCAGGCTAT-GA
*
29227521 GCTGGTATTATA
64 GCTGGAATTATA
29227533 CCGGGTTTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
77 6 0.10
78 56 0.90
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (78 bp):
GGACTTAAGGAACGCAGGCTACGTGCTAGAAATATATCCGGACTTAAAGTCCGCAGGCTATGAGC
TGGAATTATAATT
Found at i:29228455 original size:57 final size:57
Alignment explanation
Indices: 29228367--29228481 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 57
29228357 CATATAACTT
* * * *
29228367 AAATATCAGTATTTATTTTATCTCGATCTTTGTTTATGTGTATAGACAATGTGAATG
1 AAATATCAGTATGTATTTCAGCTCGATCTTTGTTTATGTGTATAGAAAATGTGAATG
* *
29228424 AAATATCAGTATGTATTTCGGCTCGATCTTTGTTTATGTGTATTGAAAATGTGAATG
1 AAATATCAGTATGTATTTCAGCTCGATCTTTGTTTATGTGTATAGAAAATGTGAATG
29228481 A
1 A
29228482 GATAATTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (57 bp):
AAATATCAGTATGTATTTCAGCTCGATCTTTGTTTATGTGTATAGAAAATGTGAATG
Found at i:29234337 original size:39 final size:39
Alignment explanation
Indices: 29234283--29234405 Score: 212
Period size: 39 Copynumber: 3.1 Consensus size: 39
29234273 TTCAGTGATG
29234283 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
29234322 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
29234361 TATATCCGAACTT-AGGCTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGG-TCCGCAGGCTATGTGCTGGAAT
29234400 ATATAT
1 -TATAT
29234406 ATATATAAAT
Statistics
Matches: 81, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
38 3 0.04
39 73 0.90
40 5 0.06
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:29234971 original size:26 final size:26
Alignment explanation
Indices: 29234942--29235021 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 26
29234932 TCGATATGGC
29234942 ATGTATAGGTTAGGCTGATGATAACG
1 ATGTATAGGTTAGGCTGATGATAACG
** * **
29234968 ATGT-TTTG-AAGGACTCGAT-ATGGC-
1 ATGTATAGGTTAGG-CT-GATGATAACG
29234992 ATGTATAGGTTAGGCTGATGATAACG
1 ATGTATAGGTTAGGCTGATGATAACG
29235018 ATGT
1 ATGT
29235022 TTTGAAATTG
Statistics
Matches: 38, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
24 10 0.26
25 14 0.37
26 14 0.37
ACGTcount: A:0.29, C:0.09, G:0.30, T:0.33
Consensus pattern (26 bp):
ATGTATAGGTTAGGCTGATGATAACG
Found at i:29234996 original size:50 final size:50
Alignment explanation
Indices: 29234928--29235027 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
29234918 GTTATATTTT
29234928 GGACTCGATATGGCATGTATAGGTTAGGCTGATGATAACGATGTTTTGAA
1 GGACTCGATATGGCATGTATAGGTTAGGCTGATGATAACGATGTTTTGAA
29234978 GGACTCGATATGGCATGTATAGGTTAGGCTGATGATAACGATGTTTTGAA
1 GGACTCGATATGGCATGTATAGGTTAGGCTGATGATAACGATGTTTTGAA
29235028 ATTGTAAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.32
Consensus pattern (50 bp):
GGACTCGATATGGCATGTATAGGTTAGGCTGATGATAACGATGTTTTGAA
Found at i:29240142 original size:11 final size:11
Alignment explanation
Indices: 29240126--29240162 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
29240116 TAGTACGTAA
29240126 TTGATAATGTC
1 TTGATAATGTC
*
29240137 TTGAT-ATG-A
1 TTGATAATGTC
29240146 TTGATAATGTC
1 TTGATAATGTC
29240157 TTGATA
1 TTGATA
29240163 TGTGTATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 5 0.23
10 6 0.27
11 11 0.50
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (11 bp):
TTGATAATGTC
Found at i:29240150 original size:20 final size:20
Alignment explanation
Indices: 29240125--29240164 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
29240115 TTAGTACGTA
29240125 ATTGATAATGTCTTGATATG
1 ATTGATAATGTCTTGATATG
29240145 ATTGATAATGTCTTGATATG
1 ATTGATAATGTCTTGATATG
29240165 TGTATGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (20 bp):
ATTGATAATGTCTTGATATG
Found at i:29240523 original size:38 final size:39
Alignment explanation
Indices: 29240437--29240561 Score: 198
Period size: 39 Copynumber: 3.2 Consensus size: 39
29240427 TTCAGTGATG
*
29240437 TATATCCGGACTTAAGGTTCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
29240476 TATATCCGGACTTAAGGTCCGCAGGCTATG-GCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * *
29240514 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
29240553 TATGTCCGG
1 TATATCCGG
29240562 GCTAGAGTCC
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
38 36 0.46
39 43 0.54
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:29240599 original size:77 final size:76
Alignment explanation
Indices: 29240437--29240599 Score: 188
Period size: 77 Copynumber: 2.1 Consensus size: 76
29240427 TTCAGTGATG
* * * *
29240437 TATATCCGGACTTAAGGTTCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGGC
1 TATA-CCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAGGTCCACAGGC
29240502 TATGGCTGGAAT
65 TATGGCTGGAAT
* *
29240514 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCCGGGC-T-AGAGTCCCACAG
1 TAT-ACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAG-GT-CCACAG
*
29240577 GCT-TCGAGCTGGTAT
63 GCTAT-G-GCTGGAAT
29240592 TATACCGG
1 TATACCGG
29240600 GTTTAAATTC
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
75 2 0.03
76 4 0.05
77 57 0.77
78 11 0.15
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (76 bp):
TATACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAGGTCCACAGGCT
ATGGCTGGAAT
Found at i:29241543 original size:51 final size:51
Alignment explanation
Indices: 29241467--29241569 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
29241457 GTGTATTGAC
29241467 AATGTGAATGAGATAATTAAATGTTTAGTTCGGTAATACCTCTTAGCCTTA
1 AATGTGAATGAGATAATTAAATGTTTAGTTCGGTAATACCTCTTAGCCTTA
29241518 AATGTGAATGAGATAATTAAATGTTTAGTTCGGTAATACCTCTTAGCCTTA
1 AATGTGAATGAGATAATTAAATGTTTAGTTCGGTAATACCTCTTAGCCTTA
29241569 A
1 A
29241570 TCCGACGATC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (51 bp):
AATGTGAATGAGATAATTAAATGTTTAGTTCGGTAATACCTCTTAGCCTTA
Found at i:29244981 original size:11 final size:10
Alignment explanation
Indices: 29244956--29245016 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
29244946 ACCAATAAAA
29244956 TAAA-TGAGC
1 TAAATTGAGC
*
29244965 TGAATTGTAGC
1 TAAATTG-AGC
29244976 TAAATTGAGC
1 TAAATTGAGC
**
29244986 TCGATTGAGC
1 TAAATTGAGC
29244996 TGAAA-TGAGC
1 T-AAATTGAGC
*
29245006 TCAATTGAGC
1 TAAATTGAGC
29245016 T
1 T
29245017 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:29245017 original size:20 final size:20
Alignment explanation
Indices: 29244957--29245017 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
29244947 CCAATAAAAT
*
29244957 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
29244977 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
29244998 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
29245018 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:29251729 original size:29 final size:29
Alignment explanation
Indices: 29251659--29251749 Score: 130
Period size: 29 Copynumber: 3.2 Consensus size: 29
29251649 AAGTCTACAT
*
29251659 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
*
29251687 TCATTCATATGGCCCACTAGGCCCAAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
* * *
29251716 ACATTCATACGGCCCATTTGGCCCAAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
29251745 ACATT
1 ACATT
29251750 TGTATACATG
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
28 22 0.39
29 34 0.61
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.23
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAAATC
Found at i:29255864 original size:40 final size:39
Alignment explanation
Indices: 29255820--29255923 Score: 156
Period size: 39 Copynumber: 2.6 Consensus size: 39
29255810 AGCCCGGTTA
29255820 TAGTAACTCGCACAAATGCCTTCGGGACTCAACCC-GAATT
1 TAGTAACTCGCACAAATGCCTTCGGG-CTCAACCCGGAA-T
* * *
29255860 TAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGCTCAACCCGGAAT
29255899 TAGTAACTCGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGG
29255924 ATCTTAGTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
39 31 0.53
40 28 0.47
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (39 bp):
TAGTAACTCGCACAAATGCCTTCGGGCTCAACCCGGAAT
Found at i:29255930 original size:40 final size:40
Alignment explanation
Indices: 29255792--29255976 Score: 202
Period size: 40 Copynumber: 4.7 Consensus size: 40
29255782 GCTACTCGTT
* * *
29255792 CAAAGGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
29255832 CAAATGCCTTCGGGACTCAACCC-GAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAA-TTAGTAACTCGCA
*
29255872 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
29255911 CAAATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
29255952 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29255977 CATCATTCGA
Statistics
Matches: 123, Mismatches: 13, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 77 0.63
41 12 0.10
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:29255960 original size:79 final size:81
Alignment explanation
Indices: 29255792--29255976 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
29255782 GCTACTCGTT
* *
29255792 CAAAGGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTCAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTCAACCCG
* *
29255856 AATTTAGTAACTCGCAC
65 AATATAGTAACTAGCAC
* * **
29255873 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTCAACCCG
* *
29255935 GATATAGTCACTTAGCA-
65 AATATAGTAAC-TAGCAC
29255952 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
29255977 CATCATTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 25 0.28
81 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (81 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTCAACCCGA
ATATAGTAACTAGCAC
Found at i:29267502 original size:27 final size:27
Alignment explanation
Indices: 29267454--29267506 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
29267444 CATTCTACCA
29267454 TACAAGGGTATTACGGTCATTTTACAC
1 TACAAGGGTATTACGGTCATTTTACAC
** *
29267481 TACAAGGGTATTTTGGTGATTTTACA
1 TACAAGGGTATTACGGTCATTTTACA
29267507 AACTAATGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (27 bp):
TACAAGGGTATTACGGTCATTTTACAC
Found at i:29278828 original size:180 final size:180
Alignment explanation
Indices: 29278571--29278947 Score: 754
Period size: 180 Copynumber: 2.1 Consensus size: 180
29278561 TGATTTATCT
29278571 TGAAAATAGACTCATTAGGGATTTTAAAAAAATAATTTTAAGCCTCTAATTATTTTTATCCAAAA
1 TGAAAATAGACTCATTAGGGATTTTAAAAAAATAATTTTAAGCCTCTAATTATTTTTATCCAAAA
29278636 TTTTGTGATTTTCAAAAGTCAGAACAGGGGATCACGTAATCATTCTGAACCAGTCTCACAAAAAC
66 TTTTGTGATTTTCAAAAGTCAGAACAGGGGATCACGTAATCATTCTGAACCAGTCTCACAAAAAC
29278701 ATAAATATCTCAAAATATAGAACTCCTTTTCTTGCTCTGTTTCTTTTATA
131 ATAAATATCTCAAAATATAGAACTCCTTTTCTTGCTCTGTTTCTTTTATA
29278751 TGAAAATAGACTCATTAGGGATTTTAAAAAAATAATTTTAAGCCTCTAATTATTTTTATCCAAAA
1 TGAAAATAGACTCATTAGGGATTTTAAAAAAATAATTTTAAGCCTCTAATTATTTTTATCCAAAA
29278816 TTTTGTGATTTTCAAAAGTCAGAACAGGGGATCACGTAATCATTCTGAACCAGTCTCACAAAAAC
66 TTTTGTGATTTTCAAAAGTCAGAACAGGGGATCACGTAATCATTCTGAACCAGTCTCACAAAAAC
29278881 ATAAATATCTCAAAATATAGAACTCCTTTTCTTGCTCTGTTTCTTTTATA
131 ATAAATATCTCAAAATATAGAACTCCTTTTCTTGCTCTGTTTCTTTTATA
29278931 TGAAAATAGACTCATTA
1 TGAAAATAGACTCATTA
29278948 AGCTTTAATT
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 197 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (180 bp):
TGAAAATAGACTCATTAGGGATTTTAAAAAAATAATTTTAAGCCTCTAATTATTTTTATCCAAAA
TTTTGTGATTTTCAAAAGTCAGAACAGGGGATCACGTAATCATTCTGAACCAGTCTCACAAAAAC
ATAAATATCTCAAAATATAGAACTCCTTTTCTTGCTCTGTTTCTTTTATA
Found at i:29284774 original size:30 final size:30
Alignment explanation
Indices: 29284740--29284800 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29284730 TCATTAACTC
29284740 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
29284770 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
29284800 A
1 A
29284801 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:29286030 original size:13 final size:13
Alignment explanation
Indices: 29286012--29286036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29286002 TAATGGTATA
29286012 TTGAATCCATGAT
1 TTGAATCCATGAT
29286025 TTGAATCCATGA
1 TTGAATCCATGA
29286037 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:29287605 original size:47 final size:47
Alignment explanation
Indices: 29287551--29288094 Score: 1016
Period size: 47 Copynumber: 11.6 Consensus size: 47
29287541 TATTTGAATA
29287551 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
29287598 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
29287645 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
29287692 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
29287739 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
29287786 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
29287833 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
29287880 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
29287927 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
29287974 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
29288021 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
29288068 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
29288095 TCCCGAAGGG
Statistics
Matches: 487, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 487 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:29289161 original size:48 final size:48
Alignment explanation
Indices: 29289090--29289685 Score: 1111
Period size: 48 Copynumber: 12.4 Consensus size: 48
29289080 GGGGTGTTAC
*
29289090 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
29289138 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
29289186 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
29289234 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
29289282 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
29289330 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
29289378 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
29289426 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
29289474 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
29289522 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* * *
29289570 GTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCTAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
29289618 ATGTGAAATATACATGAGCTATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* * *
29289666 GTGTGAAATATGTAGGAGAT
1 ATGTGAAATATATATGAGAT
29289686 GTGTGTATAT
Statistics
Matches: 534, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 534 1.00
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (48 bp):
ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
Found at i:29298219 original size:68 final size:66
Alignment explanation
Indices: 29298147--29298294 Score: 174
Period size: 67 Copynumber: 2.2 Consensus size: 66
29298137 GATCATGTGT
* * * *
29298147 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC-AG-CA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
29298210 TGTAG
62 TGTAG
* * *
29298215 ACAAGAGAGCTACAGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
29298280 AG
65 AG
29298282 ACAAGAGAGCTAC
1 ACAAGAGAGCTAC
29298295 GAGATAAATT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
64 24 0.34
65 3 0.04
66 3 0.04
67 27 0.39
68 13 0.19
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:29300052 original size:38 final size:40
Alignment explanation
Indices: 29299996--29300123 Score: 161
Period size: 38 Copynumber: 3.1 Consensus size: 40
29299986 TGAATCAATA
29299996 TATGTAACCGTGGCATATCCACTTAGCACCACGTTACATG
1 TATGTAACCGTGGCATATCCACTTAGCACCACGTTACATG
* *
29300036 T-T-TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATA
1 TATGTAACCGTGGCATATCCACTTAGCACCACG-T--T--A-C-ATG
29300081 TATGTAACCGTGGCATATCCACTTAGCACCACGTTACATG
1 TATGTAACCGTGGCATATCCACTTAGCACCACGTTACATG
29300121 TAT
1 TAT
29300124 CAATATGTGT
Statistics
Matches: 75, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
38 28 0.37
39 2 0.03
40 6 0.08
41 2 0.03
42 1 0.01
43 1 0.01
44 2 0.03
45 3 0.04
46 2 0.03
47 28 0.37
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (40 bp):
TATGTAACCGTGGCATATCCACTTAGCACCACGTTACATG
Found at i:29300076 original size:85 final size:85
Alignment explanation
Indices: 29299965--29300121 Score: 305
Period size: 85 Copynumber: 1.8 Consensus size: 85
29299955 GTTACAGTAC
*
29299965 ATCCACTTAGCACCATGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGT
1 ATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGT
29300030 TACATGTTTAACCGTGGTAT
66 TACATGTTTAACCGTGGTAT
29300050 ATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGT
1 ATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGT
29300115 TACATGT
66 TACATGT
29300122 ATCAATATGT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (85 bp):
ATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGT
TACATGTTTAACCGTGGTAT
Found at i:29300107 original size:47 final size:48
Alignment explanation
Indices: 29300038--29300160 Score: 194
Period size: 48 Copynumber: 2.6 Consensus size: 48
29300028 GTTACATGTT
29300038 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* * *
29300085 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* *
29300133 TAATCGTTGTATATCCACTTAGCACCAC
1 TAACCGTGGTATATCCACTTAGCACCAC
29300161 ATTTTTTCAT
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 31 0.45
48 38 0.55
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
Found at i:29301971 original size:40 final size:41
Alignment explanation
Indices: 29301833--29302017 Score: 213
Period size: 40 Copynumber: 4.6 Consensus size: 41
29301823 GCTACTCGTT
* *
29301833 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCA
* * *
29301873 CAAATGCCTTCGGGACTCAACCC-GAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCA
*
29301913 CCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCA
* * * *
29301952 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAATATAGTAAC-TCGCA
29301993 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29302018 CATCATTCGA
Statistics
Matches: 123, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 79 0.64
41 11 0.09
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCA
Found at i:29302001 original size:79 final size:81
Alignment explanation
Indices: 29301833--29302017 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
29301823 GCTACTCGTT
* *
29301833 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTCAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTCAACCCG
* *
29301897 AATTTAGTAACTCGCAC
65 AATATAGTAACTAGCAC
* * **
29301914 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTCAACCCG
* * *
29301976 GATATGGTCACTTAGCA-
65 AATATAGTAAC-TAGCAC
29301993 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
29302018 CATCATTCGA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 57 0.65
80 25 0.28
81 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (81 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTCAACCCGA
ATATAGTAACTAGCAC
Found at i:29303212 original size:56 final size:56
Alignment explanation
Indices: 29303145--29303264 Score: 224
Period size: 56 Copynumber: 2.1 Consensus size: 56
29303135 TATTAGTTTA
29303145 TTGCCCATGCTTCTTATTTT-ATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTAATT-TTCCATTAACACAACATGTTTCATGACATGTT
29303201 TTGCCCATGCTTCTTATTTTAATTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTAATTTTCCATTAACACAACATGTTTCATGACATGTT
29303257 TTGCCCAT
1 TTGCCCAT
29303265 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
56 60 0.95
57 3 0.05
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.44
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTAATTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:29306142 original size:15 final size:15
Alignment explanation
Indices: 29306122--29306153 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29306112 ACCAGATTTA
29306122 GGAATTCTTTCCTAC
1 GGAATTCTTTCCTAC
29306137 GGAATTCTTTCCTAC
1 GGAATTCTTTCCTAC
29306152 GG
1 GG
29306154 GCGTCCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (15 bp):
GGAATTCTTTCCTAC
Found at i:29306945 original size:19 final size:20
Alignment explanation
Indices: 29306921--29306976 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
29306911 CAGGAGTCCA
29306921 GATTTTTTTTTT-AAAAACC
1 GATTTTTTTTTTAAAAAACC
29306940 GATTTTTTTTTTAAAAAACC
1 GATTTTTTTTTTAAAAAACC
*
29306960 AATTTTTTTTTTGAAAA
1 GATTTTTTTTTT-AAAA
29306977 TCTTCATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 12 0.35
20 18 0.53
21 4 0.12
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (20 bp):
GATTTTTTTTTTAAAAAACC
Found at i:29308021 original size:55 final size:56
Alignment explanation
Indices: 29307956--29308070 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
29307946 AGCATGGCTG
* *
29307956 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
29308012 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
29308067 CCAG
1 CCAG
29308071 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.56
56 22 0.42
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:29308033 original size:27 final size:27
Alignment explanation
Indices: 29307981--29308070 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
29307971 GTGACAGAGT
29307981 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* *
29308010 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
29308037 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
29308065 CACCAG
1 CACCAG
29308071 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:29308223 original size:28 final size:28
Alignment explanation
Indices: 29308176--29308240 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
29308166 AAATTAACCC
*
29308176 TAGGGGTATAGAGGTTATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
29308204 TAGGGGTATA-ATGGTAATTTTGCATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
29308232 TAGGGGTAT
1 TAGGGGTAT
29308241 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:29317629 original size:39 final size:39
Alignment explanation
Indices: 29317573--29317731 Score: 239
Period size: 39 Copynumber: 4.1 Consensus size: 39
29317563 CATGGTATTT
*
29317573 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATGTGCTG
* *
29317612 GGAATATATCCGGACATGAGGTCCGCAGGCTATGTGCTA
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATGTGCTG
* *
29317651 GAAATATATCCGGACTTGAAGTCCGCAGGCTATGTGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATGTGCTG
* *
29317690 GAAATATATCCGGACTTGAAGG-CCGCAGGCTACGTGCTG
1 GAAATATATCCGGACATG-AGGTCCGCAGGCTATGTGCTG
29317729 GAA
1 GAA
29317732 TCGTACCCGG
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 108 0.98
40 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (39 bp):
GAAATATATCCGGACATGAGGTCCGCAGGCTATGTGCTG
Found at i:29326099 original size:47 final size:47
Alignment explanation
Indices: 29326047--29326542 Score: 823
Period size: 47 Copynumber: 10.6 Consensus size: 47
29326037 GATAATTGTG
* * * *
29326047 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
29326094 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
29326141 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
29326188 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
29326235 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
29326282 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
29326329 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* * *
29326376 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* * *
29326423 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* * * *
29326470 ATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAG-GCCGAATGGCCAATGTGATGA
** *
29326517 ATGTGAAAGCATATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
29326543 TCCCGAAGGG
Statistics
Matches: 428, Mismatches: 19, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
46 2 0.00
47 424 0.99
48 2 0.00
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
Found at i:29327059 original size:18 final size:18
Alignment explanation
Indices: 29327036--29327077 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
29327026 TTGCTTAAAA
29327036 CTTACTAAGCATTAAATG
1 CTTACTAAGCATTAAATG
29327054 CTTACTAAGCATTAAATG
1 CTTACTAAGCATTAAATG
29327072 CTTACT
1 CTTACT
29327078 CCGTTCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (18 bp):
CTTACTAAGCATTAAATG
Found at i:29328673 original size:38 final size:38
Alignment explanation
Indices: 29328609--29328683 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
29328599 AATCCGAGTT
*
29328609 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
29328647 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
29328684 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:29329056 original size:40 final size:40
Alignment explanation
Indices: 29328737--29329044 Score: 438
Period size: 40 Copynumber: 7.7 Consensus size: 40
29328727 AGGTCTCGAC
* *
29328737 GATG-ATCCGGGCTAATTCCAGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
29328776 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
29328816 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
29328856 GATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
29328896 GATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * * *
29328936 GTTGTATCCGGACTAAGTTCCAAAGAGCATTTGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * *
29328976 GATATATCCGTGCTAAGTTCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * *
29329016 GTTATATCCGGGCTAGGTCCCGAAGAGCA
1 GATGTATCCGGGCTAAGTCCCGAAGAGCA
29329045 ATCATGCTGG
Statistics
Matches: 240, Mismatches: 28, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
39 4 0.02
40 236 0.98
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:29345428 original size:48 final size:48
Alignment explanation
Indices: 29345373--29345472 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 48
29345363 AGAGAAGTTT
* * **
29345373 TTAAATTGTTTGAAATTTTTATGGGTCGGTTTTGTATAGTTGGTTGAG
1 TTAAATTGTTCGAAATTTTGATGGCCCGGTTTTGTATAGTTGGTTGAG
29345421 TTAAATTGTTCGAAATTTTGATGGCCCGGTTTTGTATAGTTGGTTGAG
1 TTAAATTGTTCGAAATTTTGATGGCCCGGTTTTGTATAGTTGGTTGAG
29345469 TTAA
1 TTAA
29345473 GTCAGGTAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.05, G:0.26, T:0.47
Consensus pattern (48 bp):
TTAAATTGTTCGAAATTTTGATGGCCCGGTTTTGTATAGTTGGTTGAG
Found at i:29345859 original size:23 final size:23
Alignment explanation
Indices: 29345828--29345940 Score: 110
Period size: 23 Copynumber: 5.0 Consensus size: 23
29345818 CGAGCTAATG
* *
29345828 AACAATAAGCTCTATTGAGCTGA
1 AACAGTAAGCTCTATAGAGCTGA
*
29345851 AACAGTAAGTTCTATCA-AGCTG-
1 AACAGTAAGCTCTAT-AGAGCTGA
*
29345873 AACAGTAAGCTC-ATAGAGCTAA
1 AACAGTAAGCTCTATAGAGCTGA
*
29345895 AACAGTAAGCTCCA-ATGAGCTGA
1 AACAGTAAGCTCTATA-GAGCTGA
*
29345918 TAACAGCAAGCTCT-TAGAGCTGA
1 -AACAGTAAGCTCTATAGAGCTGA
29345941 TATATCGGTA
Statistics
Matches: 75, Mismatches: 8, Indels: 14
0.77 0.08 0.14
Matches are distributed among these distances:
20 1 0.01
21 6 0.08
22 24 0.32
23 32 0.43
24 12 0.16
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (23 bp):
AACAGTAAGCTCTATAGAGCTGA
Found at i:29345879 original size:22 final size:22
Alignment explanation
Indices: 29345826--29345906 Score: 76
Period size: 22 Copynumber: 3.6 Consensus size: 22
29345816 CCCGAGCTAA
* **
29345826 TGAACAATAAGCTCTATTGAGC
1 TGAACAGTAAGCTCTATCAAGC
*
29345848 TGAAACAGTAAGTTCTATCAAGC
1 TG-AACAGTAAGCTCTATCAAGC
29345871 TGAACAGTAAGCTC-AT-AGAGC
1 TGAACAGTAAGCTCTATCA-AGC
*
29345892 TAAAACAGTAAGCTC
1 T-GAACAGTAAGCTC
29345907 CAATGAGCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.02
21 6 0.12
22 25 0.50
23 18 0.36
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (22 bp):
TGAACAGTAAGCTCTATCAAGC
Found at i:29345916 original size:44 final size:44
Alignment explanation
Indices: 29345826--29345938 Score: 111
Period size: 44 Copynumber: 2.5 Consensus size: 44
29345816 CCCGAGCTAA
* * * * *
29345826 TGAACAATAAGCTCTATTGAGCTGAAACAGTAAGTTCTATCAAGC
1 TGAACAGTAAGCTC-ATAGAGCTAAAACAGTAAGTCCAATCAAGC
*
29345871 TGAACAGTAAGCTCATAGAGCTAAAACAGTAAGCTCCAAT-GAGC
1 TGAACAGTAAGCTCATAGAGCTAAAACAGTAAG-TCCAATCAAGC
* *
29345915 TGATAACAGCAAGCTCTTAGAGCT
1 TG--AACAGTAAGCTCATAGAGCT
29345939 GATATATCGG
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
44 22 0.39
45 17 0.30
46 18 0.32
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (44 bp):
TGAACAGTAAGCTCATAGAGCTAAAACAGTAAGTCCAATCAAGC
Found at i:29345941 original size:23 final size:23
Alignment explanation
Indices: 29345819--29345965 Score: 99
Period size: 23 Copynumber: 6.3 Consensus size: 23
29345809 AGCTCCACCC
* * *
29345819 GAGCTAATGAACAATAAGCTCTATT
1 GAGCTGAT-AACAGTAAGCTC-ATA
*
29345844 GAGCTGA-AACAGTAAGTTCTATCA
1 GAGCTGATAACAGTAAGCTC-AT-A
29345868 -AGCTG--AACAGTAAGCTCATA
1 GAGCTGATAACAGTAAGCTCATA
*
29345888 GAGCT-AAAACAGTAAGCTCCA-A
1 GAGCTGATAACAGTAAGCT-CATA
* *
29345910 TGAGCTGATAACAGCAAGCTCTTA
1 -GAGCTGATAACAGTAAGCTCATA
*
29345934 GAGCTGATATATCGGTAAGCTCATA
1 GAGCTGATA-A-CAGTAAGCTCATA
29345959 CGAGCTG
1 -GAGCTG
29345966 TGATGAGTCC
Statistics
Matches: 100, Mismatches: 11, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.01
21 6 0.06
22 23 0.23
23 35 0.35
24 13 0.13
25 16 0.16
26 6 0.06
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (23 bp):
GAGCTGATAACAGTAAGCTCATA
Found at i:29347427 original size:54 final size:54
Alignment explanation
Indices: 29347304--29347505 Score: 199
Period size: 54 Copynumber: 3.7 Consensus size: 54
29347294 ATCCCATATT
* * * * * * *
29347304 TCATGCGAACCTATGTTGTTATGCGAACTTATGCTATTATACGAACCTATGATA
1 TCATGCAAACCTATGTTGTTATGCAAACCTATGTTATTATATGAACATATGTTA
* * * * * *
29347358 TTATGCGAACCTATGTTGTTATGCAAACCTATGTTATCATGTGAGCTTATGTTA
1 TCATGCAAACCTATGTTGTTATGCAAACCTATGTTATTATATGAACATATGTTA
* * *
29347412 TCATGCAAACTTATGTTATTATG-AGAACCTATGTTGTTATATGAACATATGTTA
1 TCATGCAAACCTATGTTGTTATGCA-AACCTATGTTATTATATGAACATATGTTA
* * ** *
29347466 TCATACAAACCTATGTTTTTATGTGAACATATGTTATTAT
1 TCATGCAAACCTATGTTGTTATGCAAACCTATGTTATTAT
29347506 GTGTGTCTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
53 1 0.01
54 120 0.99
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (54 bp):
TCATGCAAACCTATGTTGTTATGCAAACCTATGTTATTATATGAACATATGTTA
Found at i:29347508 original size:18 final size:18
Alignment explanation
Indices: 29347306--29347506 Score: 177
Period size: 18 Copynumber: 11.2 Consensus size: 18
29347296 CCCATATTTC
*
29347306 ATGCGAACCTATGTTGTT
1 ATGCGAACCTATGTTATT
* *
29347324 ATGCGAACTTATGCTATT
1 ATGCGAACCTATGTTATT
* *
29347342 ATACGAACCTATGATATT
1 ATGCGAACCTATGTTATT
*
29347360 ATGCGAACCTATGTTGTT
1 ATGCGAACCTATGTTATT
* *
29347378 ATGCAAACCTATGTTATC
1 ATGCGAACCTATGTTATT
* * * *
29347396 ATGTGAGCTTATGTTATC
1 ATGCGAACCTATGTTATT
* *
29347414 ATGCAAACTTATGTTATT
1 ATGCGAACCTATGTTATT
* *
29347432 ATGAGAACCTATGTTGTT
1 ATGCGAACCTATGTTATT
** * *
29347450 ATATGAACATATGTTATC
1 ATGCGAACCTATGTTATT
* * *
29347468 ATACAAACCTATGTTTTT
1 ATGCGAACCTATGTTATT
* *
29347486 ATGTGAACATATGTTATT
1 ATGCGAACCTATGTTATT
29347504 ATG
1 ATG
29347507 TGTGTCTTAA
Statistics
Matches: 144, Mismatches: 39, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 144 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (18 bp):
ATGCGAACCTATGTTATT
Found at i:29354039 original size:29 final size:29
Alignment explanation
Indices: 29353972--29354039 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
29353962 CAAGTCTACA
* *
29353972 TACATGCATATGGCCCACTAGGCCCAATC
1 TACATTCATATGGACCACTAGGCCCAATC
*
29354001 TA-ATTCATATGGACCATTAGGCCCAAATC
1 TACATTCATATGGACCACTAGGCCC-AATC
29354030 -ACATTCATAT
1 TACATTCATAT
29354040 ACATGCTCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 20 0.59
29 14 0.41
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (29 bp):
TACATTCATATGGACCACTAGGCCCAATC
Found at i:29354295 original size:11 final size:11
Alignment explanation
Indices: 29354279--29354304 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29354269 CCGATATATT
29354279 GTGTGTGTGCA
1 GTGTGTGTGCA
29354290 GTGTGTGTGCA
1 GTGTGTGTGCA
29354301 GTGT
1 GTGT
29354305 ATTAACACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.46, T:0.38
Consensus pattern (11 bp):
GTGTGTGTGCA
Found at i:29358547 original size:29 final size:29
Alignment explanation
Indices: 29358489--29358596 Score: 157
Period size: 29 Copynumber: 3.8 Consensus size: 29
29358479 TATAGCCCAC
*
29358489 TAGGCCC-AATCTCATTCATATGGACCAT
1 TAGGCCCAAATCACATTCATATGGACCAT
* *
29358517 TAGGCCCAAATCATATTCATGTGG-CCGAT
1 TAGGCCCAAATCACATTCATATGGACC-AT
*
29358546 TAGGCCCAAATCACATTCATACGGACCAT
1 TAGGCCCAAATCACATTCATATGGACCAT
29358575 TAGGCCCAAATCACATTCATAT
1 TAGGCCCAAATCACATTCATAT
29358597 ACATGCTCTC
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
28 9 0.13
29 59 0.84
30 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (29 bp):
TAGGCCCAAATCACATTCATATGGACCAT
Found at i:29363112 original size:30 final size:29
Alignment explanation
Indices: 29363057--29363152 Score: 120
Period size: 29 Copynumber: 3.3 Consensus size: 29
29363047 GCCCAATCTA
* *
29363057 ATTCATATGGACCATTAGGCCCAAATCAT
1 ATTCATATGGCCCATTAGGCCCAAATCAC
* *
29363086 ATTCATGTGGCCCATTAGGCCCCAAATCGC
1 ATTCATATGGCCCATTAGG-CCCAAATCAC
***
29363116 ATTCATACAACCCATTAGGCCCAAATCAC
1 ATTCATATGGCCCATTAGGCCCAAATCAC
29363145 ATTCATAT
1 ATTCATAT
29363153 ACATGCTCTC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 33 0.59
30 23 0.41
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.26
Consensus pattern (29 bp):
ATTCATATGGCCCATTAGGCCCAAATCAC
Found at i:29365479 original size:14 final size:13
Alignment explanation
Indices: 29365451--29365487 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
29365441 ATCTTGGGAT
29365451 ATTAA-AACAATA
1 ATTAAGAACAATA
29365463 ATTAAGAACACATA
1 ATTAAGAACA-ATA
29365477 ATTAAGAACAA
1 ATTAAGAACAA
29365488 GTTAAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 13 0.57
ACGTcount: A:0.62, C:0.11, G:0.05, T:0.22
Consensus pattern (13 bp):
ATTAAGAACAATA
Found at i:29372628 original size:26 final size:26
Alignment explanation
Indices: 29372592--29372645 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
29372582 TAACGTCTAA
29372592 TCCCTAGATTGAATGATTGAGACTTT
1 TCCCTAGATTGAATGATTGAGACTTT
29372618 TCCCTAGATTGAATGATTGAGACTTT
1 TCCCTAGATTGAATGATTGAGACTTT
29372644 TC
1 TC
29372646 TCTAATTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (26 bp):
TCCCTAGATTGAATGATTGAGACTTT
Found at i:29375936 original size:30 final size:33
Alignment explanation
Indices: 29375900--29375961 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
29375890 CAGACTTTCT
29375900 TTTTGGGT-TTTTAAAT-T-ATAAGTAGTTTTA
1 TTTTGGGTATTTTAAATGTAATAAGTAGTTTTA
* *
29375930 TTTTGGGTATTTTTAATGTAATAAGTATTTTT
1 TTTTGGGTATTTTAAATGTAATAAGTAGTTTT
29375962 TAAAATTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 8 0.30
31 7 0.26
32 1 0.04
33 11 0.41
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (33 bp):
TTTTGGGTATTTTAAATGTAATAAGTAGTTTTA
Found at i:29381737 original size:40 final size:40
Alignment explanation
Indices: 29381657--29381800 Score: 148
Period size: 41 Copynumber: 3.5 Consensus size: 40
29381647 GAGCTTGGTC
* * *
29381657 TCGAAGGGCTTTTGAGCCAGTGCTAATAACTGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGATCATAACCG-ACTTAGTT
*
29381698 TCGAAGGGCTTTAGAGCCAGT-ATCATAACCAGACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGATCATAACC-GACTTAGTT
* * * * * *
29381738 CCGAAGGGCCTTCGAGCCAGTGGTC-TAATCCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGTGATCATAA-CCGA-CTTAGTT
29381779 TCGAAGGGCTTTTGAGCCAGTG
1 TCGAAGGGCTTTTGAGCCAGTG
29381801 CTAAGAATCG
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
40 37 0.43
41 49 0.57
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
TCGAAGGGCTTTTGAGCCAGTGATCATAACCGACTTAGTT
Found at i:29381816 original size:41 final size:41
Alignment explanation
Indices: 29381646--29381816 Score: 145
Period size: 41 Copynumber: 4.2 Consensus size: 41
29381636 GGTCTAAATC
29381646 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAA-
1 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAAT
* * * * * *
29381686 CTGAACTTAGTTTCGAAGGGCTTTAGAGCCAGT-ATCATAA-
1 C-GAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAAT
* * * * * *
29381726 CCAGACTTAGT-TCCGAAGGGCCTTCGAGCCAGTGGT-CTAAT
1 CGAG-CTTGGTCT-CGAAGGGCTTTTGAGCCAGTGCTAATAAT
*
29381767 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAAGAAT
1 -CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAAT
*
29381809 CGGGCTTG
1 CGAGCTTG
29381817 ATTCCGAAGG
Statistics
Matches: 103, Mismatches: 20, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
39 2 0.02
40 34 0.33
41 60 0.58
42 7 0.07
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.27
Consensus pattern (41 bp):
CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAAT
Found at i:29384608 original size:40 final size:40
Alignment explanation
Indices: 29384562--29384786 Score: 276
Period size: 40 Copynumber: 5.6 Consensus size: 40
29384552 CTTGCACAAG
* * *
29384562 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
29384602 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAC
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
29384642 GCCTTCGGGTTTTAGCCCGGATATAATCACTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
29384682 GCCTTCGGGTCTTAGCCCGGATATAG-CAACT--CACATGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACA--AAT
* * * *
29384722 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
29384763 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
29384787 CATTCGAATA
Statistics
Matches: 157, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
38 4 0.03
39 1 0.01
40 123 0.78
41 25 0.16
43 4 0.03
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:29384657 original size:80 final size:79
Alignment explanation
Indices: 29384526--29384786 Score: 285
Period size: 80 Copynumber: 3.3 Consensus size: 79
29384516 CTCAAGAAAT
* * * ** * * * *
29384526 CTTCGGGATTTAG-CCGGATATAACTACTTGCACAAGGCCTTCGGGTCTTAGCCCGGATGTGGTC
1 CTTCGGGACTTAGCCCGGATATAGCAACTCACAGAACGCCTTCGGGTCTTAGCCCGGATATAGTC
*
29384590 ACTAGCATAAATGC
66 ACTAGCACAAATGC
* *
29384604 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACA-AACGCCTTCGGGTTTTAGCCCGGATATA
1 CTTCGGGACTTAGCCCGGATATAG-CAACT--CACAGAACGCCTTCGGGTCTTAGCCCGGATATA
*
29384667 ATCACTAGCACAAATGC
63 GTCACTAGCACAAATGC
* * * * *
29384684 CTTCGGGTCTTAGCCCGGATATAGCAACTCACATGAATGCCTTCGGATCTTAGTCCGGTTATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTCACA-GAACGCCTTCGGGTCTTAGCCCGGATATAGT
*
29384749 CACCTAGCACAAAAGC
65 CA-CTAGCACAAATGC
29384765 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
29384787 CATTCGAATA
Statistics
Matches: 154, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
78 16 0.10
79 12 0.08
80 91 0.59
81 35 0.23
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTCACAGAACGCCTTCGGGTCTTAGCCCGGATATAGTC
ACTAGCACAAATGC
Found at i:29392099 original size:28 final size:28
Alignment explanation
Indices: 29392033--29392160 Score: 175
Period size: 28 Copynumber: 4.5 Consensus size: 28
29392023 CATGAGATTG
* * **
29392033 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
29392062 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
29392090 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
29392119 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
29392147 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
29392161 GACTTACTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 45 0.51
29 44 0.49
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:29392122 original size:57 final size:57
Alignment explanation
Indices: 29392033--29392160 Score: 186
Period size: 57 Copynumber: 2.2 Consensus size: 57
29392023 CATGAGATTG
*
29392033 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
* * * *
29392090 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATA
*
29392147 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
29392161 GACTTACTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
Found at i:29397150 original size:40 final size:40
Alignment explanation
Indices: 29397067--29397286 Score: 268
Period size: 40 Copynumber: 5.5 Consensus size: 40
29397057 ACCCAAGTAT
** * *
29397067 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
29397105 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
29397145 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
29397185 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
29397225 CTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
29397265 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
29397287 CATTCGAATA
Statistics
Matches: 156, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 16 0.10
40 127 0.81
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:29399686 original size:28 final size:29
Alignment explanation
Indices: 29399655--29399766 Score: 111
Period size: 29 Copynumber: 3.9 Consensus size: 29
29399645 ATACATGCAC
* *
29399655 ATGGCCCACTAGGCCTAA-TCTTATTCAA
1 ATGGCCCACTAGGCCCAATTCATATTCAA
**
29399683 ATGGCCCATCT-GGCCCAATTCATATTCTT
1 ATGGCCCA-CTAGGCCCAATTCATATTCAA
* *
29399712 ATGGCCCACTAGGCCCAATTCACATTCAT
1 ATGGCCCACTAGGCCCAATTCATATTCAA
* * * *
29399741 ATGGCCTATTAGGCCAAAATCATATT
1 ATGGCCCACTAGGCCCAATTCATATT
29399767 ATATTCATGC
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
28 16 0.23
29 54 0.77
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (29 bp):
ATGGCCCACTAGGCCCAATTCATATTCAA
Found at i:29399764 original size:58 final size:57
Alignment explanation
Indices: 29399655--29399766 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 57
29399645 ATACATGCAC
* ** * *
29399655 ATGGCCCACTAGGCCTAATCTTATTCAAATGGCCCATCTGGCCCAATTCATATTCTT
1 ATGGCCCACTAGGCCCAATCACATTCAAATGGCCCATCTGGCCAAAATCATATTCTT
* *
29399712 ATGGCCCACTAGGCCCAATTCACATTCATATGGCCTAT-TAGGCCAAAATCATATT
1 ATGGCCCACTAGGCCCAA-TCACATTCAAATGGCCCATCT-GGCCAAAATCATATT
29399767 ATATTCATGC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
57 18 0.39
58 28 0.61
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (57 bp):
ATGGCCCACTAGGCCCAATCACATTCAAATGGCCCATCTGGCCAAAATCATATTCTT
Found at i:29401248 original size:16 final size:16
Alignment explanation
Indices: 29401227--29401260 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29401217 GAAAAATTCA
29401227 AGATTTCAAGATTTTT
1 AGATTTCAAGATTTTT
**
29401243 AGATTTCGGGATTTTT
1 AGATTTCAAGATTTTT
29401259 AG
1 AG
29401261 GGCATTACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (16 bp):
AGATTTCAAGATTTTT
Found at i:29402895 original size:46 final size:46
Alignment explanation
Indices: 29402845--29403016 Score: 176
Period size: 46 Copynumber: 3.7 Consensus size: 46
29402835 TGGGCATCCA
29402845 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
* *
29402891 AACTCGTTGAGTTGAGCCCGAGTT---TGA-GAGATGT-AACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGTGAA-T--G--TCCG
* * * *
29402938 AGCTCGTTGAGTTGAGTCCGAGTTCACTTCTGGATGTGAACG-CCC
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
*
29402983 AAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGG
1 AA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29403017 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
42 3 0.03
43 8 0.08
45 4 0.04
46 52 0.50
47 26 0.25
48 1 0.01
50 6 0.06
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
Found at i:29406883 original size:29 final size:29
Alignment explanation
Indices: 29406809--29406927 Score: 127
Period size: 29 Copynumber: 4.2 Consensus size: 29
29406799 TACATACATG
*
29406809 CATATGGCCCACTAGGCCCAA-TCTTATT
1 CATATGGCCCACTAGGCCCAATTCATATT
* *
29406837 CAAATGGCCTATCT-GGCCCAATTCATATT
1 CATATGGCCCA-CTAGGCCCAATTCATATT
* * * *
29406866 CTTATGGTCCACTAGGCCCATTTCACATT
1 CATATGGCCCACTAGGCCCAATTCATATT
* *
29406895 CATATGGCCCATTAGGCCCAAATCATATT
1 CATATGGCCCACTAGGCCCAATTCATATT
29406924 -ATAT
1 CATAT
29406928 TCATGCTCAC
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
28 22 0.30
29 51 0.70
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (29 bp):
CATATGGCCCACTAGGCCCAATTCATATT
Found at i:29427021 original size:40 final size:40
Alignment explanation
Indices: 29426951--29427097 Score: 251
Period size: 40 Copynumber: 3.7 Consensus size: 40
29426941 CTACTTGCTT
29426951 AAATGCCTTCGGGAC-TAGCCCGGTTATAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
* *
29426990 AAATGCCTTCGGGACTTAGCCCGATTATAGTAACTTGCAC
1 AAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
*
29427030 AAATGCCTTCGGGAATTAGCCCGGTTATAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
*
29427070 AAATTCCTTCGGGACTTAGCCCGGTTAT
1 AAATGCCTTCGGGACTTAGCCCGGTTAT
29427098 CATCCGAATA
Statistics
Matches: 100, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 15 0.15
40 85 0.85
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
Found at i:29435045 original size:40 final size:40
Alignment explanation
Indices: 29435001--29435189 Score: 306
Period size: 40 Copynumber: 4.7 Consensus size: 40
29434991 GCTACTTGCT
* *
29435001 CAAATGCCTTCAGGACTTAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
29435041 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * *
29435081 CAAATTCCTTCGAGACTTAGCCCGGATATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
29435121 CAAATGCCTTCGGGACTTAGCCCGTTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
29435161 CAAATGCCTTCGGGACTTAGCCCGATTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
29435190 CATCCGAATA
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 137 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:29439286 original size:47 final size:46
Alignment explanation
Indices: 29439205--29439321 Score: 123
Period size: 47 Copynumber: 2.5 Consensus size: 46
29439195 GCGAATGCCG
* * *
29439205 TGTCCCAGACACGGTCTTACACTGGCACATATCTC-AAGTCGAAGCCA
1 TGTCCTAGACATGGTCTTACACT-GCACATATCTCGAAGCCGAAG-CA
* * *
29439252 TGTCTTAGACATGGTCTTACACTG-ACTATCATCTCGTAGCCGACGCA
1 TGTCCTAGACATGGTCTTACACTGCAC-AT-ATCTCGAAGCCGAAGCA
29439299 TGTCCTAGACAT-GTCTTACACTG
1 TGTCCTAGACATGGTCTTACACTG
29439322 GCTTACGCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
45 2 0.03
46 14 0.23
47 38 0.63
48 6 0.10
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (46 bp):
TGTCCTAGACATGGTCTTACACTGCACATATCTCGAAGCCGAAGCA
Found at i:29439380 original size:46 final size:46
Alignment explanation
Indices: 29439290--29439416 Score: 141
Period size: 46 Copynumber: 2.7 Consensus size: 46
29439280 TCATCTCGTA
* *
29439290 GCCGACGCATGTCCTAGACATGTCTTACACTGGCTTACGCCTCAAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGCCTCAAG
* *
29439336 GCCGATGCATGTCCCAGACATGTCTTACACTAGGAC-T-CGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACT-GG-CTTACGCCTCAAG
* * *
29439382 GCCAATACCATGTCCCAGACATGGTTTTACACTGG
1 GCCGAT-GCATGTCCCAGACAT-GTCTTACACTGG
29439417 TTGTCATAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
46 41 0.59
47 19 0.27
48 10 0.14
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGCCTCAAG
Found at i:29445090 original size:4 final size:4
Alignment explanation
Indices: 29445083--29445109 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
29445073 ATATATATAC
29445083 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
29445110 TACAAACCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:29449555 original size:33 final size:33
Alignment explanation
Indices: 29449511--29449591 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
29449501 GTGAATAACA
*
29449511 CAGTATCAGTACAGTTTGGGCCAAAGCACTATT
1 CAGTATCAGTACAGTCTGGGCCAAAGCACTATT
* *
29449544 CCGTATCAGTACAGTCTGGGCCAAAGCCCTATT
1 CAGTATCAGTACAGTCTGGGCCAAAGCACTATT
* *
29449577 CAGTAACAATACAGT
1 CAGTATCAGTACAGT
29449592 ACGATGTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (33 bp):
CAGTATCAGTACAGTCTGGGCCAAAGCACTATT
Found at i:29450052 original size:27 final size:27
Alignment explanation
Indices: 29449969--29450060 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 27
29449959 GGGCATAATC
* * *
29449969 GTCATTTTACCATATAGAGGTATTACG
1 GTCATTTTACCATACAGGGGCATTACG
* * * *
29449996 GTAACTTTACCTTACAGGGGCTTTACG
1 GTCATTTTACCATACAGGGGCATTACG
* *
29450023 GTCATTTTACCCTACAGGGGCATTAGG
1 GTCATTTTACCATACAGGGGCATTACG
*
29450050 GTCTTTTTACC
1 GTCATTTTACC
29450061 TATTAAGGGT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGCATTACG
Found at i:29451422 original size:27 final size:27
Alignment explanation
Indices: 29451375--29451437 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
29451365 TGTGGTAAAG
* * *
29451375 CCACCAGTATCAGTAATTGTGGCATAA
1 CCACCAGTAACAGGAATTGTGACATAA
*
29451402 CCACCAGTAACAGCGAA-TGTGACATAG
1 CCACCAGTAACAG-GAATTGTGACATAA
*
29451429 TCACCAGTA
1 CCACCAGTA
29451438 CAGAAGTTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 28 0.93
28 2 0.07
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (27 bp):
CCACCAGTAACAGGAATTGTGACATAA
Found at i:29451668 original size:27 final size:27
Alignment explanation
Indices: 29451579--29451660 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
29451569 GGCATAATCA
*
29451579 TCATTTTACCATACAGGGGTATTACGG
1 TCATTTTACCCTACAGGGGTATTACGG
* * * *
29451606 TCACTTTACCCGACACGGGCT-TTACAG
1 TCATTTTACCCTACA-GGGGTATTACGG
29451633 TCATTTTACCCTACAGGGGTATTACGG
1 TCATTTTACCCTACAGGGGTATTACGG
29451660 T
1 T
29451661 TTTTTTACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
26 4 0.09
27 36 0.82
28 4 0.09
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGTATTACGG
Found at i:29454511 original size:28 final size:28
Alignment explanation
Indices: 29454479--29454558 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 28
29454469 CATACATGTT
*
29454479 TATGGCCCACTAGGCCCAATCTCAT-TCA
1 TATGGCCCACTAGGCCCAATCACATCT-A
* *
29454507 TATGGCACATTAGGCCCAAATCACATCTA
1 TATGGCCCACTAGGCCC-AATCACATCTA
*
29454536 TGTGGCCCACTAGGCCCAATCAC
1 TATGGCCCACTAGGCCCAATCAC
29454559 TTTTATAGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 21 0.48
29 22 0.50
30 1 0.02
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.23
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATCTA
Found at i:29454549 original size:29 final size:28
Alignment explanation
Indices: 29454479--29454558 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 28
29454469 CATACATGTT
*
29454479 TATGGCCCACTAGGCCCAATCTCATTCA
1 TATGGCCCACTAGGCCCAATCACATTCA
* *
29454507 TATGGCACATTAGGCCCAAATCACA-TCTA
1 TATGGCCCACTAGGCCC-AATCACATTC-A
*
29454536 TGTGGCCCACTAGGCCCAATCAC
1 TATGGCCCACTAGGCCCAATCAC
29454559 TTTTATAGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 23 0.52
29 21 0.48
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.23
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATTCA
Found at i:29458036 original size:27 final size:26
Alignment explanation
Indices: 29457990--29458044 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
29457980 ATTCCACACA
* * *
29457990 TAGGGGTATTTTGGTTATTTTCTCCCT
1 TAGGGGCATTTCGGTAATTTT-TCCCT
29458017 TAGGGGCATTTCGGTAATTTTTCCCT
1 TAGGGGCATTTCGGTAATTTTTCCCT
29458043 TA
1 TA
29458045 TCACGAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (26 bp):
TAGGGGCATTTCGGTAATTTTTCCCT
Found at i:29458369 original size:28 final size:28
Alignment explanation
Indices: 29458324--29458401 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
29458314 CATACATGTT
*
29458324 TATGGCCCACTAGGCCCAATCTCAT-TCA
1 TATGGCCCACTAGGCCCAATCACATCT-A
* *
29458352 TATGGCCCATTAGACCCAAATCACATCTA
1 TATGGCCCACTAGGCCC-AATCACATCTA
*
29458381 TATAGCCCACTAGGCCCAATC
1 TATGGCCCACTAGGCCCAATC
29458402 GTTTTTATAG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 19 0.45
29 22 0.52
30 1 0.02
ACGTcount: A:0.29, C:0.35, G:0.13, T:0.23
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATCTA
Found at i:29459607 original size:40 final size:40
Alignment explanation
Indices: 29459575--29459884 Score: 390
Period size: 40 Copynumber: 7.8 Consensus size: 40
29459565 CCAGCATGAT
* * * *
29459575 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGTACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** *
29459615 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
29459655 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * * *
29459695 TTCTCTCCGAGACTTAGCCCGGATACATC-C-AGTACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** *
29459733 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
29459773 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
29459813 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
29459853 TGCTCTTCGGGACTTAGCCCGGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
29459885 CTCAATTCTC
Statistics
Matches: 231, Mismatches: 37, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
38 29 0.13
39 2 0.01
40 200 0.87
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:29459813 original size:118 final size:118
Alignment explanation
Indices: 29459605--29459884 Score: 479
Period size: 118 Copynumber: 2.4 Consensus size: 118
29459595 GGATATAACA
29459605 CCAGTACGAATGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTT
1 CCAGTACGAATGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTT
*
29459670 AGTCCGGATACATCACTAGCACGAATTCTCTCCGAGACTTAGCCCGGATACAT
66 AGTCCGGATACATCACTAGCACGAATGCTCTCCGAGACTTAGCCCGGATACAT
29459723 CCAGTACGAATGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTT
1 CCAGTACGAATGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTT
*
29459788 AGTCCGGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATACAT
66 AGTCCGGATACATCACTAGCACGAATGCTCTCCGAGACTTAGCCCGGATACAT
* ** * *
29459841 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
1 C-C-AGTACGAATGCTCTTCGGGGTTTAGCACGGATATATCACT
29459885 CTCAATTCTC
Statistics
Matches: 153, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
118 117 0.76
119 1 0.01
120 35 0.23
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (118 bp):
CCAGTACGAATGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTT
AGTCCGGATACATCACTAGCACGAATGCTCTCCGAGACTTAGCCCGGATACAT
Found at i:29459867 original size:158 final size:158
Alignment explanation
Indices: 29459575--29459881 Score: 447
Period size: 158 Copynumber: 1.9 Consensus size: 158
29459565 CCAGCATGAT
* * ***
29459575 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGTACGAATGCTCTTCGGGGTTTAGCACGGATA
1 TGCTCTTCGGGACCTAGCACGGATATAACACCAGCACGAATGCTCTTCGGAACTTAGCACGGATA
* * *
29459640 TATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATTCTCTCCGA
66 CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTCCGA
29459705 GACTTAGCCCGGATACATCCAGTACGAA
131 GACTTAGCCCGGATACATCCAGTACGAA
*** * *
29459733 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTC-CGGAT
1 TGCTCTTCGGGACCTAGCACGGATATAACACCAGCACGAATGCTCTTCGGAACTTAG-CACGGAT
*
29459797 ACATCACTAGCACGAATGCTCTTC-GAGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTC
65 ACATCACTAGCACGAATGCTCTTCGGA-ACTTAGCCCGGATACATCACTAGCACGAATGCTCTCC
*
29459861 GGGACTTAGCCCGGATACATC
129 GAGACTTAGCCCGGATACATC
29459882 ACTCTCAATT
Statistics
Matches: 132, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
157 2 0.02
158 129 0.98
159 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (158 bp):
TGCTCTTCGGGACCTAGCACGGATATAACACCAGCACGAATGCTCTTCGGAACTTAGCACGGATA
CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTCCGA
GACTTAGCCCGGATACATCCAGTACGAA
Found at i:29461148 original size:37 final size:37
Alignment explanation
Indices: 29461098--29461176 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
29461088 TTATTACGAA
* * *
29461098 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
29461135 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
29461172 GTCTT
1 GTCTT
29461177 TAGAGCTCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:29461500 original size:45 final size:45
Alignment explanation
Indices: 29461306--29462547 Score: 2270
Period size: 45 Copynumber: 27.3 Consensus size: 45
29461296 TTATCACATT
* * * * *
29461306 TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCA-CATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGG-CCT-T-ATCATA
*
29461353 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTTTCACATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT--C--ATA
29461402 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT--CATA
29461449 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29461494 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29461539 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29461584 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
*
29461629 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTTTCACATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT--C--ATA
29461678 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29461723 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29461768 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29461813 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29461858 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29461903 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29461948 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29461993 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29462038 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29462083 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29462128 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29462173 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29462218 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29462263 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29462308 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29462353 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29462398 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
29462443 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
*
29462488 TATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT--CATA
29462535 TATACACTTTCAC
1 TATACACTTTCAC
29462548 GTATACACAC
Statistics
Matches: 1174, Mismatches: 10, Indels: 22
0.97 0.01 0.02
Matches are distributed among these distances:
45 988 0.84
46 3 0.00
47 94 0.08
49 89 0.08
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (45 bp):
TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
Found at i:29466567 original size:17 final size:17
Alignment explanation
Indices: 29466545--29466586 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
29466535 AACAAAAGGA
*
29466545 GATTTTGGGGTTTTA-AG
1 GATTTTGGAG-TTTAGAG
29466562 GATTTTAGGAGTTTAGAG
1 GATTTT-GGAGTTTAGAG
29466580 GATTTTG
1 GATTTTG
29466587 AAAAAGTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (17 bp):
GATTTTGGAGTTTAGAG
Found at i:29478018 original size:20 final size:20
Alignment explanation
Indices: 29477993--29478067 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
29477983 GATGCATAAT
29477993 AGAGGCACCGAAGTGCAAAC
1 AGAGGCACCGAAGTGCAAAC
* * *
29478013 AGAGGCA-TGAATGTGCGATC
1 AGAGGCACCGAA-GTGCAAAC
* * *
29478033 AAAGGCACTGAAGTGCAAAT
1 AGAGGCACCGAAGTGCAAAC
* *
29478053 AGAGGAACCAAAGTG
1 AGAGGCACCGAAGTG
29478068 TAATTCTCGT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 3 0.07
20 35 0.83
21 4 0.10
ACGTcount: A:0.40, C:0.17, G:0.31, T:0.12
Consensus pattern (20 bp):
AGAGGCACCGAAGTGCAAAC
Found at i:29482003 original size:45 final size:45
Alignment explanation
Indices: 29481939--29482068 Score: 190
Period size: 45 Copynumber: 2.9 Consensus size: 45
29481929 CGCACAGTAT
* *
29481939 TATTCGGGCCTTTGAGCCTAGCAAGTTATAATGCCAGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGATAC
*
29481984 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGATAC
* * *
29482029 TATTTGGG-CTTTCGAGCCTAGTAGGCTATAATGTCAGTGA
1 TATTCGGGCCTTT-GAGCCTAGCAGGCTATAATGCCAGTGA
29482069 AATGATATTA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 4 0.05
45 73 0.95
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGATAC
Found at i:29495351 original size:24 final size:23
Alignment explanation
Indices: 29495306--29495351 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
29495296 AGAACTTTTA
* *
29495306 ATCAGGAAGCTCACGAAGAGCCT
1 ATCAGGAAGCTCACAAAAAGCCT
29495329 ATCAGGAATGCTCACAAAAAGCC
1 ATCAGGAA-GCTCACAAAAAGCC
29495352 ATGTAATAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.13
Consensus pattern (23 bp):
ATCAGGAAGCTCACAAAAAGCCT
Found at i:29496748 original size:20 final size:20
Alignment explanation
Indices: 29496723--29496766 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
29496713 CTTTTCTTTC
*
29496723 GAAATCAGATTTGTGGTTCT
1 GAAATCAGATTTGTGGTCCT
29496743 GAAATCAGATTTGTGGTCCT
1 GAAATCAGATTTGTGGTCCT
29496763 GAAA
1 GAAA
29496767 CCACTATTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (20 bp):
GAAATCAGATTTGTGGTCCT
Found at i:29498114 original size:31 final size:31
Alignment explanation
Indices: 29498079--29498141 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
29498069 CCTTTTCATA
29498079 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
29498110 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
29498141 T
1 T
29498142 CACTTTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:29498421 original size:26 final size:25
Alignment explanation
Indices: 29498350--29498433 Score: 109
Period size: 26 Copynumber: 3.4 Consensus size: 25
29498340 CTGGAGGCCT
*
29498350 AGCCTCTTTTAAT-AACTGGGGC-AA
1 AGCC-CTTTTGATAAACTGGGGCAAA
29498374 AGCCCTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
* *
29498399 AGCCCTTTTCGGTAAATTGGGGCAAA
1 AGCCCTTTT-GATAAACTGGGGCAAA
29498425 AGCCCTTTT
1 AGCCCTTTT
29498434 TGCACTTCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
23 7 0.13
24 13 0.24
25 11 0.20
26 23 0.43
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCAAA
Found at i:29499858 original size:24 final size:24
Alignment explanation
Indices: 29499811--29499858 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
29499801 GAAATCCCCT
*
29499811 CTCTAATCCCCTCAAATCGGCTAA
1 CTCTAATCCCCTCAAATCGCCTAA
*
29499835 CTCTACTCCCTCTCAAATC-CCTAA
1 CTCTAATCCC-CTCAAATCGCCTAA
29499859 AATCTCTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.27, C:0.42, G:0.04, T:0.27
Consensus pattern (24 bp):
CTCTAATCCCCTCAAATCGCCTAA
Found at i:29518974 original size:37 final size:37
Alignment explanation
Indices: 29518915--29519024 Score: 175
Period size: 37 Copynumber: 3.0 Consensus size: 37
29518905 AGCTCCGATG
* *
29518915 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGAAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAAA
* *
29518952 AAATCTCCACACGTAGTCATCGGGTCTTACACGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAAA
*
29518989 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAA
29519025 TATATTTCCA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAAA
Found at i:29522666 original size:28 final size:27
Alignment explanation
Indices: 29522578--29522668 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 27
29522568 CTGACTGATT
*
29522578 TCGCACACATAGCGCTC-GATTAAAGAAC
1 TCGCACACATAGTGCTCAG-TT-AAGAAC
* * **
29522606 TCACACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTG-CTCAGTTAAGAA-C
29522635 TCGCACACATAGTGCTCAGTTGAAGAAC
1 TCGCACACATAGTGCTCAGTT-AAGAAC
29522663 TCGCAC
1 TCGCAC
29522669 TCTCAGTGCC
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
28 28 0.56
29 22 0.44
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (27 bp):
TCGCACACATAGTGCTCAGTTAAGAAC
Done.