Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 82 of 128
Found at i:26868715 original size:22 final size:19
Alignment explanation
Indices: 26868675--26868715 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 19
26868665 TTAATTAAGA
26868675 AATTAATTAAATTTATTTT
1 AATTAATTAAATTTATTTT
26868694 AATTAATATATAATATTATTTT
1 AATTAAT-TA-AAT-TTATTTT
26868716 TGGGAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 3 0.16
22 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTAATTAAATTTATTTT
Found at i:26871315 original size:25 final size:25
Alignment explanation
Indices: 26871287--26871338 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
26871277 AAGGATTCTA
26871287 ATGAGATAGTTTATTGCTATATCTT
1 ATGAGATAGTTTATTGCTATATCTT
26871312 ATGAGATAGTTTATTGCTATATCTT
1 ATGAGATAGTTTATTGCTATATCTT
26871337 AT
1 AT
26871339 CGAGTGTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (25 bp):
ATGAGATAGTTTATTGCTATATCTT
Found at i:26875226 original size:30 final size:32
Alignment explanation
Indices: 26875190--26875249 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
26875180 CCACAATATG
26875190 AATCTTTT-TT-GAAAGGTAAAATGACCAAGC
1 AATCTTTTATTCGAAAGGTAAAATGACCAAGC
*
26875220 AATCTTTTAATTCGAAAGGTACAATGACCA
1 AATCTTTT-ATTCGAAAGGTAAAATGACCA
26875250 TTTAACCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
32 2 0.08
33 16 0.62
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (32 bp):
AATCTTTTATTCGAAAGGTAAAATGACCAAGC
Found at i:26880991 original size:27 final size:28
Alignment explanation
Indices: 26880957--26881015 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
26880947 CTCTTTTATC
*
26880957 TTGT-CCAATGGACTTA-CCCGAGTTTA
1 TTGTCCCAACGGACTTATCCCGAGTTTA
* * *
26880983 TTGTCCCAACGGGCTTATCTCGTGTTTA
1 TTGTCCCAACGGACTTATCCCGAGTTTA
26881011 TTGTC
1 TTGTC
26881016 TTGATGGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 10 0.37
28 13 0.48
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (28 bp):
TTGTCCCAACGGACTTATCCCGAGTTTA
Found at i:26887287 original size:18 final size:18
Alignment explanation
Indices: 26887264--26887298 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26887254 TCAATTTTTA
26887264 AGTAAAGTATTATATTTG
1 AGTAAAGTATTATATTTG
* *
26887282 AGTAAATTATTCTATTT
1 AGTAAAGTATTATATTT
26887299 CTATTTACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (18 bp):
AGTAAAGTATTATATTTG
Found at i:26889937 original size:22 final size:22
Alignment explanation
Indices: 26889912--26889953 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
26889902 ATAAATATGA
26889912 TATTTAATTTC-TTATACTAATT
1 TATTT-ATTTCATTATACTAATT
*
26889934 TATTTATTTCATTTTACTAA
1 TATTTATTTCATTATACTAA
26889954 CACATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTATTTCATTATACTAATT
Found at i:26891374 original size:31 final size:31
Alignment explanation
Indices: 26891337--26891401 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
26891327 ATATTATGTA
26891337 TTATCATGACTAGTGTAGTATATAATTTCAT
1 TTATCATGACTAGTGTAGTATATAATTTCAT
26891368 TTATCATGACTAGTGTAGTATATAATTTCAT
1 TTATCATGACTAGTGTAGTATATAATTTCAT
26891399 TTA
1 TTA
26891402 AACTAACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.46
Consensus pattern (31 bp):
TTATCATGACTAGTGTAGTATATAATTTCAT
Found at i:26894491 original size:11 final size:11
Alignment explanation
Indices: 26894475--26894504 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
26894465 ATTTTAAACC
26894475 TTATTCTTGAT
1 TTATTCTTGAT
26894486 TTATTCTTGAT
1 TTATTCTTGAT
26894497 TTATTCTT
1 TTATTCTT
26894505 TATGCATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (11 bp):
TTATTCTTGAT
Found at i:26905618 original size:31 final size:31
Alignment explanation
Indices: 26905580--26905641 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
26905570 TATGAAAGAA
26905580 AGGATTAGTTCAAAAATTGTTACACGTTGTG
1 AGGATTAGTTCAAAAATTGTTACACGTTGTG
26905611 AGGATTAGTTCAAAAATTGTTACACGTTGTG
1 AGGATTAGTTCAAAAATTGTTACACGTTGTG
26905642 CGAGGAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (31 bp):
AGGATTAGTTCAAAAATTGTTACACGTTGTG
Found at i:26912232 original size:71 final size:72
Alignment explanation
Indices: 26912128--26912458 Score: 522
Period size: 72 Copynumber: 4.6 Consensus size: 72
26912118 ACAAAAAAAA
* * * * *
26912128 TATTATAAAAATAAAAATGTTATTTTATTATACATACCAAAAATAATAAATTGTTTTATTCACAA
1 TATTATAAAAATAAAATTATT-TTTTGTTATACATACCAAAAATACTAAATTGTTTTATT-AAAA
26912193 AAA-A-TAT
64 AAACATTAT
*
26912200 TATTATAAAAATAAAATTATTTTTTGTTATACATACCACAAATACTAAATTGTTTTATTAAAAAA
1 TATTATAAAAATAAAATTATTTTTTGTTATACATACCAAAAATACTAAATTGTTTTATTAAAAAA
26912265 ACATTAT
66 ACATTAT
*
26912272 TATTATAAAAATAAAATTATTTTTTGTTATACATACCACAAATACTAAATTGTTTTATTAAAAAA
1 TATTATAAAAATAAAATTATTTTTTGTTATACATACCAAAAATACTAAATTGTTTTATTAAAAAA
26912337 ACATTAT
66 ACATTAT
*
26912344 TATTATAAAAATAAAATTATTTTTTGTTATACATACCACAAATACTAAATTGTTTTATTAAAAAA
1 TATTATAAAAATAAAATTATTTTTTGTTATACATACCAAAAATACTAAATTGTTTTATTAAAAAA
26912409 ACATTAT
66 ACATTAT
** *
26912416 TATTATAAAAATAAAATTATTATTTTACTATACATACAAAAAA
1 TATTATAAAAATAAAATTATT-TTTTGTTATACATACCAAAAA
26912459 ATCAACATAC
Statistics
Matches: 246, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
70 6 0.02
71 36 0.15
72 187 0.76
73 17 0.07
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.40
Consensus pattern (72 bp):
TATTATAAAAATAAAATTATTTTTTGTTATACATACCAAAAATACTAAATTGTTTTATTAAAAAA
ACATTAT
Found at i:26912426 original size:20 final size:20
Alignment explanation
Indices: 26912402--26912439 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
26912392 ATTGTTTTAT
*
26912402 TAAAAA-AACATTATTATTA
1 TAAAAATAAAATTATTATTA
26912421 TAAAAATAAAATTATTATT
1 TAAAAATAAAATTATTATT
26912440 TTACTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAAATAAAATTATTATTA
Found at i:26913370 original size:21 final size:22
Alignment explanation
Indices: 26913326--26913384 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
26913316 TTTTATTTGA
*
26913326 AAATAA-AAAGTACATTTGAATT
1 AAATAATAAAGT-TATTTGAATT
26913348 AAATAATAAAGTTATTT-AATT
1 AAATAATAAAGTTATTTGAATT
*
26913369 AAA-AATTAAAGCTATT
1 AAATAA-TAAAGTTATT
26913385 CTGTATTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 10 0.30
23 5 0.15
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (22 bp):
AAATAATAAAGTTATTTGAATT
Found at i:26915942 original size:19 final size:18
Alignment explanation
Indices: 26915903--26915944 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
26915893 TGAATCACTG
*
26915903 AATTTTTAAAATATATCA
1 AATTTTTAAAATACATCA
26915921 AATTTTTGAAGAATACAT-A
1 AATTTTT-AA-AATACATCA
26915940 AATTT
1 AATTT
26915945 ATAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 8 0.38
20 6 0.29
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
AATTTTTAAAATACATCA
Found at i:26920451 original size:21 final size:21
Alignment explanation
Indices: 26920427--26920468 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
26920417 AGGTAAATTG
*
26920427 ATAAAAAAAGTAATACTAATA
1 ATAAAAAAAGTAATAATAATA
* *
26920448 ATAACAATAGTAATAATAATA
1 ATAAAAAAAGTAATAATAATA
26920469 GTATTAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (21 bp):
ATAAAAAAAGTAATAATAATA
Found at i:26921351 original size:18 final size:18
Alignment explanation
Indices: 26921324--26921358 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26921314 TTTGCTGCGT
*
26921324 CCTTTTTTGTTTCTTTGC
1 CCTTTGTTGTTTCTTTGC
*
26921342 CCTTTGTTGTTTGTTTG
1 CCTTTGTTGTTTCTTTG
26921359 TGTGCAGGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.66
Consensus pattern (18 bp):
CCTTTGTTGTTTCTTTGC
Found at i:26922185 original size:50 final size:50
Alignment explanation
Indices: 26922127--26922909 Score: 304
Period size: 50 Copynumber: 15.7 Consensus size: 50
26922117 TGCATCGCTT
* *
26922127 GGGG-AGTAAGATTTACTATTGTAGCTTTAATCTTTTGAATTGCAATATC
1 GGGGAAGTAAGATTCACTATTGTAGCTTTAATCTTTTGAACTGCAATATC
* * * * ** *
26922176 GGGGAAGTAAGATTCACCGA-TGTGGCTTTAATATGTTCCACTGC-ATCACC
1 GGGGAAGTAAGATTCA-CTATTGTAGCTTTAATCTTTTGAACTGCAAT-ATC
* * ** * *
26922226 TGGGAGGTAAGATTCGTTGTTGTAGCTTTAATCTTTTGAACTGCAATGTC
1 GGGGAAGTAAGATTCACTATTGTAGCTTTAATCTTTTGAACTGCAATATC
* * * * ** **
26922276 GGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGTTCCACTGC-ATCGCC
1 GGGGAAGTAAGATTCA-CTATTGTAGCTTTAATCTTTTGAACTGCAAT-ATC
** * * * * * *
26922326 TAGGAGGTAAAATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCAATGTA
1 GGGGAAGTAAGATTCACTATTGTAGCTTTAATCTTTTGAACTGCAATATC
* * * *** *
26922376 GGGGAAGCAAGATTCATCGA-TGTGGCTTTAAT-TTGTTCCGCTGC-ATCACC
1 GGGGAAGTAAGATTCA-CTATTGTAGCTTTAATCTT-TTGAACTGCAAT-ATC
* * * * * * *
26922426 TGGGAGGTAAGATTCGCTGTTATAGCTTTGATCTTTTGAACTGCAATGTC
1 GGGGAAGTAAGATTCACTATTGTAGCTTTAATCTTTTGAACTGCAATATC
* * * * ** * **
26922476 GGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTATTCCACTGCATTGCC
1 GGGGAAGTAAGATTCA-CTATTGTAGCTTTAATCTTTTGAACTGCAATATC
* * * * * *
26922526 TGGGAGGTAAGATTCGCTGTTATAGCTTTAATCTTTTGAACTGCAATGTC
1 GGGGAAGTAAGATTCACTATTGTAGCTTTAATCTTTTGAACTGCAATATC
* * * * ** * **
26922576 GGGGAAGCAAGATTCATCGA-TGTGGCTTTAATCTGTTCCACTGCATTGCC
1 GGGGAAGTAAGATTCA-CTATTGTAGCTTTAATCTTTTGAACTGCAATATC
** * * * * * *
26922626 TAGGAGGTAAAATTCATTGTTGTAGCTTTAATCTTTTGAACTGCAATGTT
1 GGGGAAGTAAGATTCACTATTGTAGCTTTAATCTTTTGAACTGCAATATC
* * * * *** **
26922676 GAGGAAGCAAGATTCATCGA-TGTGGCTTTAAT-TTGTTCCGCTGC-ATCGCC
1 GGGGAAGTAAGATTCA-CTATTGTAGCTTTAATCTT-TTGAACTGCAAT-ATC
* * * *
26922726 TGGGAGGTAAGATTCGA-TGTTGTAGCTTTAATCTTTTGAACTGCAATGTC
1 GGGGAAGTAAGATTC-ACTATTGTAGCTTTAATCTTTTGAACTGCAATATC
* * * * * ** **
26922776 GGGGAAGCAAGATTCACCGA-AGTGGCTTTAATCTGTTCCACTGC-ATCGCC
1 GGGGAAGTAAGATTCA-CTATTGTAGCTTTAATCTTTTGAACTGCAAT-ATC
*** * * * * * *
26922826 TATGAGGTAAGATTCGCTGTTATAACTTTAATCTTTTGAACTGCAATGTC
1 GGGGAAGTAAGATTCACTATTGTAGCTTTAATCTTTTGAACTGCAATATC
* * *
26922876 GGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCT
1 GGGGAAGTAAGATTCA-CTATTGTAGCTTTAATCT
26922910 GTTCCACTGC
Statistics
Matches: 508, Mismatches: 194, Indels: 63
0.66 0.25 0.08
Matches are distributed among these distances:
49 23 0.05
50 464 0.91
51 21 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (50 bp):
GGGGAAGTAAGATTCACTATTGTAGCTTTAATCTTTTGAACTGCAATATC
Found at i:26922249 original size:100 final size:100
Alignment explanation
Indices: 26922065--26922943 Score: 1355
Period size: 100 Copynumber: 8.8 Consensus size: 100
26922055 TTTCTGTCTG
* * *
26922065 ACTGTAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCATCGCTTGGG
1 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGG
** *
26922130 -GAGTAAGATTTACTATTGTAGCTTTAATCTTTTGA
66 AG-GTAAGATTCGCTGTTGTAGCTTTAATCTTTTGA
* * * * *
26922165 ATTGCAATATCGGGGAAGTAAGATTCACCGATGTGGCTTTAATATGTTCCACTGCATCACCTGGG
1 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGG
*
26922230 AGGTAAGATTCGTTGTTGTAGCTTTAATCTTTTGA
66 AGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGA
*
26922265 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTAGG
1 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGG
*
26922330 AGGTAAAATTCGCTGTTGTAGCTTTAATCTTTTGA
66 AGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGA
* * * * *
26922365 ACTGCAATGTAGGGGAAGCAAGATTCATCGATGTGGCTTTAATTTGTTCCGCTGCATCACCTGGG
1 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGG
* *
26922430 AGGTAAGATTCGCTGTTATAGCTTTGATCTTTTGA
66 AGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGA
* *
26922465 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTATTCCACTGCATTGCCTGGG
1 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGG
*
26922530 AGGTAAGATTCGCTGTTATAGCTTTAATCTTTTGA
66 AGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGA
* * *
26922565 ACTGCAATGTCGGGGAAGCAAGATTCATCGATGTGGCTTTAATCTGTTCCACTGCATTGCCTAGG
1 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGG
* **
26922630 AGGTAAAATTCATTGTTGTAGCTTTAATCTTTTGA
66 AGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGA
* * * * *
26922665 ACTGCAATGTTGAGGAAGCAAGATTCATCGATGTGGCTTTAATTTGTTCCGCTGCATCGCCTGGG
1 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGG
*
26922730 AGGTAAGATTCGATGTTGTAGCTTTAATCTTTTGA
66 AGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGA
* **
26922765 ACTGCAATGTCGGGGAAGCAAGATTCACCGAAGTGGCTTTAATCTGTTCCACTGCATCGCCTATG
1 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGG
* *
26922830 AGGTAAGATTCGCTGTTATAACTTTAATCTTTTGA
66 AGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGA
**
26922865 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGATTGGG
1 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGG
26922930 AGGTAAGATTCGCT
66 AGGTAAGATTCGCT
26922944 ATCTTTACTA
Statistics
Matches: 709, Mismatches: 69, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
100 708 1.00
101 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (100 bp):
ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGG
AGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGA
Found at i:26924221 original size:17 final size:17
Alignment explanation
Indices: 26924181--26924227 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
26924171 TGGCTTCTCC
*
26924181 ATTTCCTTTTTCATTTTTT
1 ATTTTCTTTTTC--TTTTT
26924200 ATTTTCTATTTTCTTTTT
1 ATTTTCT-TTTTCTTTTT
26924218 -TTTTCTTTTT
1 ATTTTCTTTTT
26924228 ATTTGACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.15
17 6 0.23
18 5 0.19
19 6 0.23
20 5 0.19
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTCTTTTTCTTTTT
Found at i:26929918 original size:3 final size:3
Alignment explanation
Indices: 26929904--26929940 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
26929894 ATTGATAAAA
* *
26929904 AAT AAT ACT AAT AAT AAT AAT AGT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
26929941 TTAAACTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:26930982 original size:25 final size:27
Alignment explanation
Indices: 26930951--26931003 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
26930941 TGGGGAACAC
* *
26930951 TTTGGGCT-GTGTT-GGGTTTGGGTAT
1 TTTGGGCTAGAGTTCGGGTTTAGGTAT
26930976 TTTGGGCTAGAGTTCGGGTTTAGGTAT
1 TTTGGGCTAGAGTTCGGGTTTAGGTAT
26931003 T
1 T
26931004 GTATTAGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 4 0.17
27 12 0.50
ACGTcount: A:0.09, C:0.06, G:0.40, T:0.45
Consensus pattern (27 bp):
TTTGGGCTAGAGTTCGGGTTTAGGTAT
Found at i:26935886 original size:30 final size:30
Alignment explanation
Indices: 26935850--26935906 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
26935840 AAAAAAAGAC
26935850 AAAGCATTCAATTAAGAAATCTAACCAAAT
1 AAAGCATTCAATTAAGAAATCTAACCAAAT
26935880 AAAGCATTCAATTAAGAAATCTAACCA
1 AAAGCATTCAATTAAGAAATCTAACCA
26935907 GCAGTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.53, C:0.18, G:0.07, T:0.23
Consensus pattern (30 bp):
AAAGCATTCAATTAAGAAATCTAACCAAAT
Found at i:26941507 original size:31 final size:31
Alignment explanation
Indices: 26941472--26941531 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
26941462 AAAACTTCAA
* **
26941472 AATTTGAAAACTACAGTTACTAAAATTGACC
1 AATTTGAAAACTAAAGGGACTAAAATTGACC
*
26941503 AATTTGAAAAGTAAAGGGACTAAAATTGA
1 AATTTGAAAACTAAAGGGACTAAAATTGA
26941532 GCAAATTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (31 bp):
AATTTGAAAACTAAAGGGACTAAAATTGACC
Found at i:26947802 original size:22 final size:22
Alignment explanation
Indices: 26947762--26947803 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
26947752 AAGAAATATA
*
26947762 TAAAAATACATAAATATTTTTT
1 TAAAAATACATAAAAATTTTTT
26947784 TAAAAATA-ATAATAAATTTT
1 TAAAAATACATAA-AAATTTT
26947804 AAAAATATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAAATACATAAAAATTTTTT
Found at i:26947819 original size:19 final size:19
Alignment explanation
Indices: 26947781--26947819 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
26947771 ATAAATATTT
*
26947781 TTTTAAAAATAATAATAAA
1 TTTTAAAAATAATAACAAA
26947800 TTTTAAAAAT-ATACACAAA
1 TTTTAAAAATAATA-ACAAA
26947819 T
1 T
26947820 AACAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTTAAAAATAATAACAAA
Found at i:26948099 original size:12 final size:12
Alignment explanation
Indices: 26948084--26948111 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
26948074 TATATATTTT
26948084 TAAATATGAATA
1 TAAATATGAATA
26948096 TAAATATGAATA
1 TAAATATGAATA
26948108 TAAA
1 TAAA
26948112 ATTTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (12 bp):
TAAATATGAATA
Found at i:26948622 original size:48 final size:49
Alignment explanation
Indices: 26948570--26948668 Score: 146
Period size: 48 Copynumber: 2.0 Consensus size: 49
26948560 AAAATATTTT
*
26948570 TTTCAATTAAAATTATTCATTTGTTTTTGT-CAAAAACTAAAATACCCA
1 TTTCAATTAAAATTATTCATTTGTTTTTGTAAAAAAACTAAAATACCCA
** * *
26948618 TTTCAATTAAAATTATTTGTTTGTTTTTGTAAAAAAAGTAAATTACCCA
1 TTTCAATTAAAATTATTCATTTGTTTTTGTAAAAAAACTAAAATACCCA
26948667 TT
1 TT
26948669 ATTATTCATG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 28 0.62
49 17 0.38
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.44
Consensus pattern (49 bp):
TTTCAATTAAAATTATTCATTTGTTTTTGTAAAAAAACTAAAATACCCA
Found at i:26949358 original size:16 final size:16
Alignment explanation
Indices: 26949337--26949396 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
26949327 TTTTCTACTT
*
26949337 TATAATATATATTTTA
1 TATAATATATAATTTA
*
26949353 TATAATATGTAATTTA
1 TATAATATATAATTTA
* *
26949369 TATAAAAT-TAA-ATA
1 TATAATATATAATTTA
26949383 TATAATACTATAAT
1 TATAATA-TATAAT
26949397 GCAAACATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
14 8 0.22
15 4 0.11
16 24 0.67
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (16 bp):
TATAATATATAATTTA
Found at i:26951394 original size:39 final size:39
Alignment explanation
Indices: 26951259--26951394 Score: 184
Period size: 39 Copynumber: 3.5 Consensus size: 39
26951249 ATCCACTTTT
* *
26951259 AAGCATATATCACATTACACATATAATCACATAACA-TC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * * *
26951297 TAAGCATATATCACAATAATCATATAATTACATAACGTTT
1 -AAGCATATATCACAATACTCATATAATCACATAACATTC
26951337 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
26951376 AAGCATATGTCGCAATACT
1 AAGCATATATCACAATACT
26951395 AAAAAACATG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 83 0.99
40 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:26953316 original size:39 final size:39
Alignment explanation
Indices: 26953273--26953349 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
26953263 TTAACTACTA
* * *
26953273 ATTTTGCTAGTTTATTG-CATATAAATTGTTGAAATATTG
1 ATTTTGCTAATTCATTGTC-TATAAATTGCTGAAATATTG
* *
26953312 ATTTTGTTAATTCATTGTCTATAAATTGCTGAACTATT
1 ATTTTGCTAATTCATTGTCTATAAATTGCTGAAATATT
26953350 AACTCTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 31 0.97
40 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (39 bp):
ATTTTGCTAATTCATTGTCTATAAATTGCTGAAATATTG
Found at i:26957688 original size:22 final size:21
Alignment explanation
Indices: 26957663--26957703 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
26957653 TATCGAATAA
*
26957663 CAGATCATACTTTATCATATTT
1 CAGATCATAC-TGATCATATTT
26957685 CAGATCATACTGATCATAT
1 CAGATCATACTGATCATAT
26957704 AACATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (21 bp):
CAGATCATACTGATCATATTT
Found at i:26958626 original size:21 final size:22
Alignment explanation
Indices: 26958596--26958646 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
26958586 AATAAAATAA
*
26958596 AAATAAAAATAAA-AAATATTT
1 AAATATAAATAAACAAATATTT
*
26958617 AAATATAAATAAACACATATTT
1 AAATATAAATAAACAAATATTT
*
26958639 ATATATAA
1 AAATATAA
26958647 TGTAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATATAAATAAACAAATATTT
Found at i:26960935 original size:9 final size:9
Alignment explanation
Indices: 26960917--26960964 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
26960907 CATCCTTCTT
*
26960917 TCAACACTC
1 TCAACTCTC
*
26960926 TCAATTCTC
1 TCAACTCTC
*
26960935 TCAAACCCTC
1 TC-AACTCTC
*
26960945 TCAAGTCTC
1 TCAACTCTC
26960954 TCAACTCTC
1 TCAACTCTC
26960963 TC
1 TC
26960965 GTTTTTAATA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
9 24 0.77
10 7 0.23
ACGTcount: A:0.25, C:0.42, G:0.02, T:0.31
Consensus pattern (9 bp):
TCAACTCTC
Found at i:26969285 original size:49 final size:49
Alignment explanation
Indices: 26969196--26969292 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 49
26969186 TGTGGATATT
** *** *
26969196 GCGATACCATTGAAGGGTGGTCTCCAATCTTGGGTTTGTTGGAGGTATA
1 GCGATACCATTGAAGGGTGGTCTCCAATCTCAGAACTGTTGGACGTATA
*
26969245 GCGATACCATTGAAGGGTGGTCTTCAATCTCAGAACTGTTGGACGTAT
1 GCGATACCATTGAAGGGTGGTCTCCAATCTCAGAACTGTTGGACGTAT
26969293 TGTGATTTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (49 bp):
GCGATACCATTGAAGGGTGGTCTCCAATCTCAGAACTGTTGGACGTATA
Found at i:26972895 original size:17 final size:18
Alignment explanation
Indices: 26972856--26972899 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
26972846 ACTTAAACCT
*
26972856 ACAAAATAACTAAAGAAA
1 ACAAAAGAACTAAAGAAA
* *
26972874 TCAAAAGAAC-AAGGAAA
1 ACAAAAGAACTAAAGAAA
26972891 ACAAAAGAA
1 ACAAAAGAA
26972900 AAAGTTAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.70, C:0.11, G:0.11, T:0.07
Consensus pattern (18 bp):
ACAAAAGAACTAAAGAAA
Found at i:26992374 original size:25 final size:25
Alignment explanation
Indices: 26992340--26992387 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
26992330 AGCAGGACCT
*
26992340 TGACTGATGCACAAATCAATTACCC
1 TGACCGATGCACAAATCAATTACCC
* *
26992365 TGACCGATGCACAACTTAATTAC
1 TGACCGATGCACAAATCAATTAC
26992388 AACTCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (25 bp):
TGACCGATGCACAAATCAATTACCC
Found at i:26993386 original size:28 final size:29
Alignment explanation
Indices: 26993327--26993387 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
26993317 GTAAGTTACG
*
26993327 ACATTCAGGGACCAAATCAAAAAAATTGAA
1 ACATTCAGGGA-CAAATCAAAAAAATTAAA
26993357 ACATTCAGGGA-AAAT-AAAAAAATTCAAA
1 ACATTCAGGGACAAATCAAAAAAATT-AAA
26993385 ACA
1 ACA
26993388 AGGGTCACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 9 0.31
28 9 0.31
30 11 0.38
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.16
Consensus pattern (29 bp):
ACATTCAGGGACAAATCAAAAAAATTAAA
Found at i:26994479 original size:39 final size:39
Alignment explanation
Indices: 26994394--26994606 Score: 225
Period size: 39 Copynumber: 5.5 Consensus size: 39
26994384 CTAGTGGATA
* * * *
26994394 ATGG-TCGTTTGAGCA-ACTCTCAGTAGAATCAGTGGGT
1 ATGGCTCGATTGAGCATACTTTTAGTAGAATCAGTAGGT
* * *
26994431 ATAGCTCGATTGAGCATACTTTTAGTAAAACCAGTAGGT
1 ATGGCTCGATTGAGCATACTTTTAGTAGAATCAGTAGGT
* *
26994470 ATGGATCGATTGA-CTATACTTTTATTAGAATCAGTAGGT
1 ATGGCTCGATTGAGC-ATACTTTTAGTAGAATCAGTAGGT
* * *
26994509 ATGGCTCGTTTGAGCATACTTTTAGTAGAATTAGTGGGT
1 ATGGCTCGATTGAGCATACTTTTAGTAGAATCAGTAGGT
* * * *
26994548 ATGGCTTGATTGAGCATACTTTCAGTGGAATCAATAGGT
1 ATGGCTCGATTGAGCATACTTTTAGTAGAATCAGTAGGT
* * *
26994587 ATAGCTTGATTGCGCATACT
1 ATGGCTCGATTGAGCATACT
26994607 ATCATACATT
Statistics
Matches: 146, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
37 3 0.02
38 11 0.08
39 131 0.90
40 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (39 bp):
ATGGCTCGATTGAGCATACTTTTAGTAGAATCAGTAGGT
Found at i:27003050 original size:184 final size:184
Alignment explanation
Indices: 27002741--27003109 Score: 578
Period size: 184 Copynumber: 2.0 Consensus size: 184
27002731 GAATGCGAAA
* *
27002741 ATGATTGTGCATTTATGATTTGGTATATTTATATTAATCTGTAGCTAACATCGACCTGGATTCCT
1 ATGATTGTGCATTTATGATTTGGTATATTTATATTAATCCGTAGCTAACATCGACATGGATTCCT
* * * *
27002806 CCAAATGGAAAGGAAAAGATATAGTCATCGACAAATAGCTCTGAGTTTATGGTTTGTATTTCTAT
66 CAAAATGGAAAGGAAAAGATAAAGTCATCGACAAATAGCTCGGAGTTTATGATTTGTATTTCTAT
*
27002871 AACCTGAACCTTTTAATTTGATGCATTACGAAA-TGTGTTGCATGGTAATAACAT
131 AACCTGAACCTTTTAATTTGATGCATTAC-AAATTGCGTTGCATGGTAATAACAT
** * * *
27002925 ATGATTGTGTTTTTATGATTTTGTATATTTATGTTAATCCGTAGCTAATATCGACATGGATTCCT
1 ATGATTGTGCATTTATGATTTGGTATATTTATATTAATCCGTAGCTAACATCGACATGGATTCCT
27002990 CAAAATGGAAAGGAAAAGATAAAGTCATCGACAAATAGCTCGGAGTTTATGATTTGTATTTCTAT
66 CAAAATGGAAAGGAAAAGATAAAGTCATCGACAAATAGCTCGGAGTTTATGATTTGTATTTCTAT
* * * *
27003055 AACTTGAACCTTTTCATTTGCTGCATTACAAATTGCGTTTCATGGTAATAACAT
131 AACCTGAACCTTTTAATTTGATGCATTACAAATTGCGTTGCATGGTAATAACAT
27003109 A
1 A
27003110 AGGTAAGCTG
Statistics
Matches: 168, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
183 3 0.02
184 165 0.98
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (184 bp):
ATGATTGTGCATTTATGATTTGGTATATTTATATTAATCCGTAGCTAACATCGACATGGATTCCT
CAAAATGGAAAGGAAAAGATAAAGTCATCGACAAATAGCTCGGAGTTTATGATTTGTATTTCTAT
AACCTGAACCTTTTAATTTGATGCATTACAAATTGCGTTGCATGGTAATAACAT
Found at i:27004039 original size:22 final size:25
Alignment explanation
Indices: 27004004--27004052 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
27003994 TAAGTGATAG
27004004 TGAATGTGATATTTA-ATGTT-TAA
1 TGAATGTGATATTTAGATGTTCTAA
*
27004027 TGAAT-TGGTATTTAGATGTTCTAA
1 TGAATGTGATATTTAGATGTTCTAA
27004051 TG
1 TG
27004053 GTTGTGCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 10 0.43
24 5 0.22
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (25 bp):
TGAATGTGATATTTAGATGTTCTAA
Found at i:27008301 original size:18 final size:18
Alignment explanation
Indices: 27008257--27008305 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
27008247 TTTGTGTGTG
27008257 TTATTTTTCTTGATTTTATGT
1 TTATTTTT-TTG--TTTATGT
27008278 TTATTTTTTTGTTTAT-T
1 TTATTTTTTTGTTTATGT
27008295 TTAATTTTTTT
1 TT-ATTTTTTT
27008306 CCTTTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.11
18 13 0.48
20 3 0.11
21 8 0.30
ACGTcount: A:0.14, C:0.02, G:0.06, T:0.78
Consensus pattern (18 bp):
TTATTTTTTTGTTTATGT
Found at i:27018632 original size:25 final size:25
Alignment explanation
Indices: 27018597--27018651 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
27018587 AAGTCAATGA
*
27018597 GTTACACGGCCTGACACACGGGCGT
1 GTTACACGGCCTGACACACGGGCAT
*
27018622 GTTACATGGCCTGACACACGGGCAT
1 GTTACACGGCCTGACACACGGGCAT
27018647 GTTAC
1 GTTAC
27018652 GTGACCGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.20
Consensus pattern (25 bp):
GTTACACGGCCTGACACACGGGCAT
Found at i:27020803 original size:30 final size:31
Alignment explanation
Indices: 27020767--27020826 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
27020757 AAACCTTTTA
*
27020767 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
27020797 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
27020827 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:27037150 original size:13 final size:13
Alignment explanation
Indices: 27037095--27037150 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
27037085 TAGATTTTTT
27037095 CTAAATATTATCA
1 CTAAATATTATCA
*
27037108 CTATATATTATCA
1 CTAAATATTATCA
27037121 CTAAATAATT-T--
1 CTAAAT-ATTATCA
27037132 -TAAATATTATCA
1 CTAAATATTATCA
27037144 CTAAATA
1 CTAAATA
27037151 ATTCAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
9 3 0.08
10 6 0.17
13 24 0.67
14 3 0.08
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:27038816 original size:13 final size:13
Alignment explanation
Indices: 27038798--27038823 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27038788 AAGTTGGTTG
27038798 ATATTTAAATGTT
1 ATATTTAAATGTT
27038811 ATATTTAAATGTT
1 ATATTTAAATGTT
27038824 TTTGGTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATATTTAAATGTT
Found at i:27040646 original size:23 final size:23
Alignment explanation
Indices: 27040613--27040726 Score: 129
Period size: 23 Copynumber: 5.0 Consensus size: 23
27040603 AACATGTCAG
*
27040613 ATAACATGAAGCACCGAAGTGCA
1 ATAACACGAAGCACCGAAGTGCA
**
27040636 ATAACACGAAGCACCGAAGTGTT
1 ATAACACGAAGCACCGAAGTGCA
* * **
27040659 GTAACACAAAGCACAAAAGTGCA
1 ATAACACGAAGCACCGAAGTGCA
* **
27040682 ATAACACGAAGCACCAAAGTGTT
1 ATAACACGAAGCACCGAAGTGCA
*
27040705 ATAACACGAAGCACTGAAGTGC
1 ATAACACGAAGCACCGAAGTGC
27040727 TAAATTCACG
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 74 1.00
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (23 bp):
ATAACACGAAGCACCGAAGTGCA
Found at i:27040725 original size:46 final size:46
Alignment explanation
Indices: 27040613--27040726 Score: 165
Period size: 46 Copynumber: 2.5 Consensus size: 46
27040603 AACATGTCAG
* * *
27040613 ATAACATGAAGCACCGAAGTGCAATAACACGAAGCACCGAAGTGTT
1 ATAACACGAAGCACAGAAGTGCAATAACACGAAGCACCAAAGTGTT
* * *
27040659 GTAACACAAAGCACAAAAGTGCAATAACACGAAGCACCAAAGTGTT
1 ATAACACGAAGCACAGAAGTGCAATAACACGAAGCACCAAAGTGTT
*
27040705 ATAACACGAAGCACTGAAGTGC
1 ATAACACGAAGCACAGAAGTGC
27040727 TAAATTCACG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (46 bp):
ATAACACGAAGCACAGAAGTGCAATAACACGAAGCACCAAAGTGTT
Found at i:27048674 original size:50 final size:50
Alignment explanation
Indices: 27048633--27048758 Score: 162
Period size: 50 Copynumber: 2.5 Consensus size: 50
27048623 ACATGAGAGT
* * **
27048633 TCTCATATAGGTGCCAACGCCGTGTCCCAGACATGGCCTTACGGGGGACA
1 TCTCATCTAGGTGCCAACGCCATGTCCCAGACATGGCCTTACATGGGACA
* * * * *
27048683 CCTCATCTTGGTGCCAACGCCATGTCCCAGACATTGTCTTACATGGGACC
1 TCTCATCTAGGTGCCAACGCCATGTCCCAGACATGGCCTTACATGGGACA
*
27048733 TCTCATCTCGGTGCCAACGCCATGTC
1 TCTCATCTAGGTGCCAACGCCATGTC
27048759 TGATAACTGA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.20, C:0.33, G:0.23, T:0.24
Consensus pattern (50 bp):
TCTCATCTAGGTGCCAACGCCATGTCCCAGACATGGCCTTACATGGGACA
Found at i:27049050 original size:50 final size:50
Alignment explanation
Indices: 27048957--27049348 Score: 498
Period size: 50 Copynumber: 7.8 Consensus size: 50
27048947 TTTCTTGTAC
* * * * * ** * *
27048957 TGCCAATGCCATATCCCATATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** ** * *
27049007 TGCCAATGCTGTGTCCCAGACATGGTCTTACGGGGGACATCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
27049057 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGAACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * *
27049107 TGCCAACGTCATGTCCCAAACATGTTCTTACATGGGACCTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
27049157 TGCCAACGCCATGTCCCAGGCATGATCTTATATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
27049207 TGCCAACGCCATGTCCCAGACATGATCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
27049257 TGCCAACGTCATGTCCCAGACATGGTCTTACATGGGACCTC-CTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-ATCTCGG
* *
27049307 TTCCAACGCCGTGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
27049349 TTACCCAAAT
Statistics
Matches: 300, Mismatches: 40, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
49 1 0.00
50 299 1.00
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:27049061 original size:363 final size:363
Alignment explanation
Indices: 27048396--27049121 Score: 1335
Period size: 363 Copynumber: 2.0 Consensus size: 363
27048386 NNNNNNNNNN
27048396 TGATAACTGAGATACTCTTAATCTTATTAACTCACCTGAACTTGTCTATTAGGCTTTTACCTGAA
1 TGATAACTGAGATACTCTTAATCTTATTAACTCACCTGAACTTGTCTATTAGGCTTTTACCTGAA
*
27048461 CTTTCATGTAACATCGTCAATTTATTAGCCCGTTGAATCACTTGGAATACTAAGGATACTCGGGT
66 CTTTCATGTAACATCGTCAATTTATTAGCCCGTTGAATCACTTGGAATACTAAGGATACTCGAGT
*
27048526 CTCCTGTCTGAATATAACATGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTG
131 CTCCTGTCTGAATATAACATGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGATGTTTCTTG
* *
27048591 TACTGCCAATGCCATATCCTAGATATTGTCTTACATGAGAGTTCTCATATAGGTGCCAACGCCGT
196 TACTGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCAACGCCGT
*
27048656 GTCCCAGACATGGCCTTACGGGGGACACCTCATCTTGGTGCCAACGCCATGTCCCAGACATTGTC
261 GTCCCAGACATGGCCTTACGGGGGACACCTCATCTTGGTGCCAACGCCATGTCCCAGACATGGTC
*
27048721 TTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
326 TTACATGGAACCTCTCATCTCGGTGCCAACGCCATGTC
27048759 TGATAACTGAGATACTCTTAATCTTATTAACTCACCTGAACTTGTCTATTAGGCTTTTACCTGAA
1 TGATAACTGAGATACTCTTAATCTTATTAACTCACCTGAACTTGTCTATTAGGCTTTTACCTGAA
*
27048824 CTTTCATGTAACATCGTCTATTTATTAGCCCGTTGAATCACTTGGAATACTAAGGATACTCGAGT
66 CTTTCATGTAACATCGTCAATTTATTAGCCCGTTGAATCACTTGGAATACTAAGGATACTCGAGT
27048889 CTCCTGTCTGAATATAACATGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGATGTTTCTTG
131 CTCCTGTCTGAATATAACATGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGATGTTTCTTG
* * *
27048954 TACTGCCAATGCCATATCCCATATATGGTCTTACATGAGAGTTCTCATATAGGTGCCAATGCTGT
196 TACTGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCAACGCCGT
* *
27049019 GTCCCAGACATGGTCTTACGGGGGACATCTCATCTTGGTGCCAACGCCATGTCCCAGACATGGTC
261 GTCCCAGACATGGCCTTACGGGGGACACCTCATCTTGGTGCCAACGCCATGTCCCAGACATGGTC
*
27049084 TTACATGGAACCTCTCATCTCGGTGCCAACGTCATGTC
326 TTACATGGAACCTCTCATCTCGGTGCCAACGCCATGTC
27049122 CCAAACATGT
Statistics
Matches: 350, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
363 350 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (363 bp):
TGATAACTGAGATACTCTTAATCTTATTAACTCACCTGAACTTGTCTATTAGGCTTTTACCTGAA
CTTTCATGTAACATCGTCAATTTATTAGCCCGTTGAATCACTTGGAATACTAAGGATACTCGAGT
CTCCTGTCTGAATATAACATGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGATGTTTCTTG
TACTGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCAACGCCGT
GTCCCAGACATGGCCTTACGGGGGACACCTCATCTTGGTGCCAACGCCATGTCCCAGACATGGTC
TTACATGGAACCTCTCATCTCGGTGCCAACGCCATGTC
Found at i:27049345 original size:150 final size:150
Alignment explanation
Indices: 27048978--27049348 Score: 548
Period size: 150 Copynumber: 2.5 Consensus size: 150
27048968 TATCCCATAT
* ** * * * **
27048978 ATGGTCTTACATGAGAGTTCTCATATAGGTGCCAATGCTGTGTCCCAGACATGGTCTTACGGGGG
1 ATGGTCTTACATGGGACCTCTCATATTGGTGCCAACGCCGTGTCCCAGACATGGTCTTACATGGG
* *
27049043 ACATCTCATCTTGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGAACCTCTCATCTCGGT
66 ACCTCTCATCTTGGTGCCAACGCCATGTCCCAGACATGATCTTACATGGAACCTCTCATCTCGGT
27049108 GCCAACGTCATGTCCCAAAC
131 GCCAACGTCATGTCCCAAAC
* * * * *
27049128 ATGTTCTTACATGGGACCTCTCATATTGGTGCCAACGCCATGTCCCAGGCATGATCTTATATGGG
1 ATGGTCTTACATGGGACCTCTCATATTGGTGCCAACGCCGTGTCCCAGACATGGTCTTACATGGG
*
27049193 ACCTCTCATCTTGGTGCCAACGCCATGTCCCAGACATGATCTTACATGGGACCTCTCATCTCGGT
66 ACCTCTCATCTTGGTGCCAACGCCATGTCCCAGACATGATCTTACATGGAACCTCTCATCTCGGT
*
27049258 GCCAACGTCATGTCCCAGAC
131 GCCAACGTCATGTCCCAAAC
*
27049278 ATGGTCTTACATGGGACCTC-C-TATCTCGGTTCCAACGCCGTGTCCCAGACATGGTCTTACATG
1 ATGGTCTTACATGGGACCTCTCATAT-T-GGTGCCAACGCCGTGTCCCAGACATGGTCTTACATG
27049341 GGACCTCT
64 GGACCTCT
27049349 TTACCCAAAT
Statistics
Matches: 196, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
148 3 0.02
149 2 0.01
150 191 0.97
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (150 bp):
ATGGTCTTACATGGGACCTCTCATATTGGTGCCAACGCCGTGTCCCAGACATGGTCTTACATGGG
ACCTCTCATCTTGGTGCCAACGCCATGTCCCAGACATGATCTTACATGGAACCTCTCATCTCGGT
GCCAACGTCATGTCCCAAAC
Found at i:27052623 original size:18 final size:18
Alignment explanation
Indices: 27052600--27052638 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
27052590 AAGGGACATT
27052600 GATAAAGCTGGTGGTATG
1 GATAAAGCTGGTGGTATG
27052618 GATAAAGCTGGTGGTATG
1 GATAAAGCTGGTGGTATG
27052636 GAT
1 GAT
27052639 TTTGTTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.28
Consensus pattern (18 bp):
GATAAAGCTGGTGGTATG
Found at i:27052999 original size:3 final size:3
Alignment explanation
Indices: 27052991--27053022 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
27052981 AAGATTTAAG
*
27052991 AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
27053023 TCCTATATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:27054114 original size:79 final size:80
Alignment explanation
Indices: 27053981--27054140 Score: 227
Period size: 79 Copynumber: 2.0 Consensus size: 80
27053971 ATTATATGTA
* * *
27053981 TTATGAGAGGGTTTTGGGCCTCTTTTGTATTGAATCCAATTATATGTGTTTCCTGGACTTTTAAG
1 TTATGAGAGGATTTTGGGCCTCTCTTGTATTGAATCCAATTATATGTGTTTCCTGAACTTTTAA-
* *
27054046 CCAACACTTTATAATT
65 CAAACACTTTAAAATT
*
27054062 TTATGAG-GGATTTT-GGCCTCTCTTGTATT-AGGTCCAATTATATGTGTTTCCTGAACTTTTAA
1 TTATGAGAGGATTTTGGGCCTCTCTTGTATTGA-ATCCAATTATATGTGTTTCCTGAACTTTTAA
27054124 CAAACACTTTAAAATT
65 CAAACACTTTAAAATT
27054140 T
1 T
27054141 AGTCCAACCC
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
78 16 0.22
79 43 0.60
80 6 0.08
81 7 0.10
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (80 bp):
TTATGAGAGGATTTTGGGCCTCTCTTGTATTGAATCCAATTATATGTGTTTCCTGAACTTTTAAC
AAACACTTTAAAATT
Found at i:27062570 original size:41 final size:41
Alignment explanation
Indices: 27062505--27062615 Score: 159
Period size: 41 Copynumber: 2.7 Consensus size: 41
27062495 ACTAATTATA
* * *
27062505 CCCTGAATTGCACATACATCCCCCTTTTTGTACTTCGGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
** *
27062546 CTTTGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
*
27062587 CCCTGAATAGCACATACGTGCCCCTGTTT
1 CCCTGAATTGCACATACGTGCCCCTGTTT
27062616 ACACTCCGAT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (41 bp):
CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
Found at i:27073885 original size:25 final size:25
Alignment explanation
Indices: 27073851--27073900 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27073841 AGCCTAAAAG
27073851 TGGACGACCGAGAGGTGGTGTGACC
1 TGGACGACCGAGAGGTGGTGTGACC
27073876 TGGACGACCGAGAGGTGGTGTGACC
1 TGGACGACCGAGAGGTGGTGTGACC
27073901 AACTCCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.44, T:0.16
Consensus pattern (25 bp):
TGGACGACCGAGAGGTGGTGTGACC
Found at i:27090658 original size:418 final size:421
Alignment explanation
Indices: 27089821--27090661 Score: 1456
Period size: 418 Copynumber: 2.0 Consensus size: 421
27089811 GCATAACTTT
* * * *
27089821 TGATTCTTAGCTTCGGATTAAAATTTGATTTCAAATACTCTCATTAGGGACCTTATACTTTCTAT
1 TGATTCTTAACTTCGGATTAAAAATTGATTTCAAATACTCTCATTAGGGACCTTATAATTTATAT
*
27089886 TTCTAGCATAATTTCATGAAAAATTTTACATTTATTCAATTTGGTCCCTAATGTTACAAAACAAA
66 TTCTAGCATAATTTCATGAAAAATTTTACATTTATTCAATTGGGTCCCTAATGTTACAAAACAAA
27089951 CAAACAAGCTTAACTAACTTTACAATTTAGTCATTTTCACAATCTAAACTCAATATCTATCAATT
131 CAAACAAGCTTAACTAACTTTACAATTTAGTCATTTTCACAATCTAAACTCAATATCTATCAATT
* *
27090016 TCAAGATTAATTAATCAATTAATCAACATGGAAACTTGCTAAAATTTTAACAATTGATCAAATTG
196 TCAAG----AGT-ATCAATTAATCAACATGAAAACTTGCTAAAATTTTAACAATTGATCAAATTG
*
27090081 GTACATGGGCTAGCTAAATCAAGCTCCCATAATCCAAAATCTATAAAAATTACATGAAAAAGGGT
256 GTACATGGGCTAGCTAAATCAAGCTCCCATAATCCAAAATCTATAAAAATTACATGAAAAAGGGG
*
27090146 TTGTTTACCTTGAATTTTGCTTGTTCGAATGTTATGAAAGCTTTGAAGTTTTCTTTGGTTTTCAA
321 TTGTTTACCTTGAATTTTGCTTGTTCAAATGTTATGAAAGCTTTGAAGTTTTCTTTGGTTTTCAA
*
27090211 CTATGGTGGATGTTTAAAAGATAGAGAAGAAGAAGA
386 CTATGGTGGATGGTTAAAAGATAGAGAAGAAGAAGA
27090247 TGATTCTTAACTTCGGATTAAAAATTGATTTCAAATACTCTCATTAGGGACCTTATAATTTATAT
1 TGATTCTTAACTTCGGATTAAAAATTGATTTCAAATACTCTCATTAGGGACCTTATAATTTATAT
* * **
27090312 TTCTAGCATAATTTCATGACAAATTTTATATTTATTCAATTGGGTCCCTAATGTTACAAAATTAA
66 TTCTAGCATAATTTCATGAAAAATTTTACATTTATTCAATTGGGTCCCTAATGTTACAAAACAAA
27090377 CAAACAAGCTTAACTAACTTTACAATTTAGTTC-TTTTCACAATCTAAACTCAATATCTATCAAT
131 CAAACAAGCTTAACTAACTTTACAATTTAG-TCATTTTCACAATCTAAACTCAATATCTATCAAT
27090441 TTCAAG-GT-T-AATTAATCAACATGAAAACTTGCTAAAATTTTAACAATTGATCAAATTGGTAC
195 TTCAAGAGTATCAATTAATCAACATGAAAACTTGCTAAAATTTTAACAATTGATCAAATTGGTAC
*
27090503 ATGGGCTAGCTAAATCAAGCTCCCATAATCCAAAATCTATAAAAATTCCATGAAAAAGGGGTTGT
260 ATGGGCTAGCTAAATCAAGCTCCCATAATCCAAAATCTATAAAAATTACATGAAAAAGGGGTTGT
27090568 TTACCTTGAATTTTGCTTGTTCAAATGTTATGAAAGCTTTGAAGTTTTCTTTGGTTTTCAACTAT
325 TTACCTTGAATTTTGCTTGTTCAAATGTTATGAAAGCTTTGAAGTTTTCTTTGGTTTTCAACTAT
*
27090633 GGTGGATGGTTAAAAGATGGAGAAGAAGA
390 GGTGGATGGTTAAAAGATAGAGAAGAAGA
27090662 TGATAAATTA
Statistics
Matches: 398, Mismatches: 16, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
418 206 0.52
419 1 0.00
421 1 0.00
426 188 0.47
427 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (421 bp):
TGATTCTTAACTTCGGATTAAAAATTGATTTCAAATACTCTCATTAGGGACCTTATAATTTATAT
TTCTAGCATAATTTCATGAAAAATTTTACATTTATTCAATTGGGTCCCTAATGTTACAAAACAAA
CAAACAAGCTTAACTAACTTTACAATTTAGTCATTTTCACAATCTAAACTCAATATCTATCAATT
TCAAGAGTATCAATTAATCAACATGAAAACTTGCTAAAATTTTAACAATTGATCAAATTGGTACA
TGGGCTAGCTAAATCAAGCTCCCATAATCCAAAATCTATAAAAATTACATGAAAAAGGGGTTGTT
TACCTTGAATTTTGCTTGTTCAAATGTTATGAAAGCTTTGAAGTTTTCTTTGGTTTTCAACTATG
GTGGATGGTTAAAAGATAGAGAAGAAGAAGA
Found at i:27099509 original size:22 final size:23
Alignment explanation
Indices: 27099475--27099536 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
27099465 AATATTAGTA
27099475 TATTTAGTATTATTAATCTT-ATG
1 TATTTAGTATTATTAAT-TTCATG
27099498 TATTTA-TATTATTAATTTCATG
1 TATTTAGTATTATTAATTTCATG
* *
27099520 T-GTTATTATTATTAATT
1 TATTTAGTATTATTAATT
27099537 AGTTTCAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 5 0.14
22 25 0.69
23 6 0.17
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (23 bp):
TATTTAGTATTATTAATTTCATG
Found at i:27102821 original size:41 final size:41
Alignment explanation
Indices: 27102753--27102876 Score: 128
Period size: 41 Copynumber: 3.0 Consensus size: 41
27102743 ATTGTGTCAA
* *
27102753 GCCTTGAGCCTAGCAGGTTTCATGCCGGTGCACTGAATTAG
1 GCCTTGAGCCTAGCAGGCTTCATGCCGGTGAACTGAATTAG
*
27102794 GCCTTGAGCCTAGC-GAGCTTCGA-GCCGGTGAATTGAATTAG
1 GCCTTGAGCCTAGCAG-GCTTC-ATGCCGGTGAACTGAATTAG
* ** * *
27102835 GTCTTGAGCCTATAAGGCTTCGTGCCGATGAACT-ATATTAG
1 GCCTTGAGCCTAGCAGGCTTCATGCCGGTGAACTGA-ATTAG
27102876 G
1 G
27102877 TAACTTGTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
40 2 0.03
41 65 0.94
42 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (41 bp):
GCCTTGAGCCTAGCAGGCTTCATGCCGGTGAACTGAATTAG
Found at i:27112164 original size:78 final size:79
Alignment explanation
Indices: 27112035--27112201 Score: 318
Period size: 78 Copynumber: 2.1 Consensus size: 79
27112025 ATATGAGTCT
*
27112035 CTTTTATATTGGGTTCAATTATAAGTGCTCTATGGACATTTAACCCAACACTTTATAATTCAATT
1 CTTTTCTATTGGGTTCAATTATAAGTGCTCTATGGACATTTAACCCAACACTTTATAATTCAATT
27112100 CAACCCAAC-CATG
66 CAACCCAACACATG
27112113 CTTTTCTATTGGGTTCAATTATAAGTGCTCTATGGACATTTAACCCAACACTTTATAATTCAATT
1 CTTTTCTATTGGGTTCAATTATAAGTGCTCTATGGACATTTAACCCAACACTTTATAATTCAATT
27112178 CAACCCAACACATG
66 CAACCCAACACATG
27112192 CTTTTCTATT
1 CTTTTCTATT
27112202 TTCTAAAATA
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
78 73 0.84
79 14 0.16
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.38
Consensus pattern (79 bp):
CTTTTCTATTGGGTTCAATTATAAGTGCTCTATGGACATTTAACCCAACACTTTATAATTCAATT
CAACCCAACACATG
Found at i:27116174 original size:41 final size:41
Alignment explanation
Indices: 27116088--27116187 Score: 130
Period size: 41 Copynumber: 2.5 Consensus size: 41
27116078 CTATCTGATT
* * * *
27116088 AGCACAAAGTGTGCG-AACTAAATGATGAGGTTGAATATCG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
*
27116128 AGCACTAAGTGTGCGAAACTAAATAATGATGTTAAATAACG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
* *
27116169 GGCACTAAGTGTGAGAAAC
1 AGCACTAAGTGTGCGAAAC
27116188 CGAGATCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 14 0.27
41 38 0.73
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (41 bp):
AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
Found at i:27117405 original size:2 final size:2
Alignment explanation
Indices: 27117398--27117430 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27117388 ATCTTGGATA
*
27117398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27117431 CTTTAAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27124100 original size:18 final size:19
Alignment explanation
Indices: 27124077--27124113 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
27124067 TGAAATTATT
*
27124077 TTTATTTTTGT-TGGAAGA
1 TTTATTTTTATATGGAAGA
27124095 TTTATTTTTATATGGAAGA
1 TTTATTTTTATATGGAAGA
27124114 AGGAAGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (19 bp):
TTTATTTTTATATGGAAGA
Found at i:27124534 original size:17 final size:17
Alignment explanation
Indices: 27124512--27124562 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
27124502 ATTATTTTTT
27124512 ATATAAAAATTTAAAAA
1 ATATAAAAATTTAAAAA
* *
27124529 ATATAATACTTT-AAAA
1 ATATAAAAATTTAAAAA
*
27124545 TTACTAAAAATATTAAAA
1 ATA-TAAAAAT-TTAAAA
27124563 TAAATATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 6 0.23
17 15 0.58
18 2 0.08
19 3 0.12
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAATTTAAAAA
Found at i:27130017 original size:28 final size:27
Alignment explanation
Indices: 27129965--27130021 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
27129955 ATGTTTTTTT
* * *
27129965 AACCCTGAACCCTAAATCTAAAATCTCA
1 AACCCTAAACCCAAAATATAAAATC-CA
*
27129993 AACCCTAAACCCAAAATATAGAATCCA
1 AACCCTAAACCCAAAATATAAAATCCA
27130020 AA
1 AA
27130022 ATCTGAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.49, C:0.30, G:0.04, T:0.18
Consensus pattern (27 bp):
AACCCTAAACCCAAAATATAAAATCCA
Found at i:27130130 original size:15 final size:14
Alignment explanation
Indices: 27130091--27130130 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
27130081 TCGAACCTTT
27130091 AAACCTTAAAC-TC
1 AAACCTTAAACATC
*
27130104 AAACCCTAAACATC
1 AAACCTTAAACATC
27130118 AAATCCTTAAACA
1 AAA-CCTTAAACA
27130131 CTGAACTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 10 0.43
14 5 0.22
15 8 0.35
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCTTAAACATC
Found at i:27130417 original size:9 final size:9
Alignment explanation
Indices: 27130392--27130426 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
27130382 GTGTTTGTTT
27130392 ATAATTTAA
1 ATAATTTAA
*
27130401 A-AAATTAA
1 ATAATTTAA
27130409 ATAATTTAA
1 ATAATTTAA
27130418 ATAATTTAA
1 ATAATTTAA
27130427 TTAAAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATAATTTAA
Found at i:27131517 original size:14 final size:14
Alignment explanation
Indices: 27131498--27131524 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27131488 ATAAATTATC
27131498 TTATAATATAATAT
1 TTATAATATAATAT
27131512 TTATAATATAATA
1 TTATAATATAATA
27131525 AATCTTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATAATATAATAT
Found at i:27135871 original size:7 final size:7
Alignment explanation
Indices: 27135859--27135887 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
27135849 AAGTAGTTTT
27135859 TTTTATA
1 TTTTATA
27135866 TTTTATA
1 TTTTATA
27135873 TTTTATA
1 TTTTATA
27135880 TTTTATA
1 TTTTATA
27135887 T
1 T
27135888 GTTAGCTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTATA
Found at i:27140428 original size:53 final size:51
Alignment explanation
Indices: 27140378--27140557 Score: 168
Period size: 51 Copynumber: 3.5 Consensus size: 51
27140368 AGATTAAAAG
*
27140378 AAAAATTGGGTGTTGGGACACTGAT-GCCGACACCCTAGTACCTGGTTTAAA
1 AAAAATTGGGTGCTGGGACACTGATGGCCGACACCCTAGTACC-GGTTTAAA
* * * * * *
27140429 AAAAATT-AGTGCTAGGACATTGATGGCCGACACTCTTGTACCAGATTTAAA
1 AAAAATTGGGTGCTGGGACACTGATGGCCGACACCCTAGTACC-GGTTTAAA
* * * * * *
27140480 AACAAATTGGATGCTGGGACACTGATGGCTGGCACCCCAGTACCAGATT-AA
1 AA-AAATTGGGTGCTGGGACACTGATGGCCGACACCCTAGTACCGGTTTAAA
* * *
27140531 AAAAATTGGGTGTTGGAACACTAATGG
1 AAAAATTGGGTGCTGGGACACTGATGG
27140558 TCGGTACCTT
Statistics
Matches: 102, Mismatches: 24, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
50 34 0.33
51 35 0.34
52 7 0.07
53 26 0.25
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (51 bp):
AAAAATTGGGTGCTGGGACACTGATGGCCGACACCCTAGTACCGGTTTAAA
Found at i:27140461 original size:51 final size:53
Alignment explanation
Indices: 27140393--27140534 Score: 164
Period size: 53 Copynumber: 2.7 Consensus size: 53
27140383 TTGGGTGTTG
* *
27140393 GGACACTGAT-GCCGACACCCTAGTACCTGGTTTAAAAA-AAATTAG-TGCTA
1 GGACACTGATGGCCGACACCCTAGTACCAGATTTAAAAACAAATTAGATGCTA
* * * * *
27140443 GGACATTGATGGCCGACACTCTTGTACCAGATTTAAAAACAAATTGGATGCTG
1 GGACACTGATGGCCGACACCCTAGTACCAGATTTAAAAACAAATTAGATGCTA
* * * *
27140496 GGACACTGATGGCTGGCACCCCAGTACCAGATTAAAAAA
1 GGACACTGATGGCCGACACCCTAGTACCAGATTTAAAAA
27140535 ATTGGGTGTT
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
50 9 0.12
51 24 0.32
52 6 0.08
53 36 0.48
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (53 bp):
GGACACTGATGGCCGACACCCTAGTACCAGATTTAAAAACAAATTAGATGCTA
Found at i:27140531 original size:103 final size:103
Alignment explanation
Indices: 27140338--27140535 Score: 249
Period size: 103 Copynumber: 1.9 Consensus size: 103
27140328 TTTTGGGTGT
* * *
27140338 TAGGACATTGATGGTCTGCACCCTTATACCAGATTAAAAGAAAAATTGGGTGTTGGGACACTGAT
1 TAGGACATTGATGGTCCGCACCCTTATACCAGATTAAAAGAAAAATTGGATGCTGGGACACTGAT
* * *
27140403 GCCGACACCCTAGTACCTGGTTTAAAAAAAATTAGTGC
66 GCCGACACCCCAGTACCTAGATTAAAAAAAATTAGTGC
* * *
27140441 TAGGACATTGATGG-CCGACACTCTTGTACCAGATTTAAAA-ACAAATTGGATGCTGGGACACTG
1 TAGGACATTGATGGTCCG-CACCCTTATACCAGA-TTAAAAGAAAAATTGGATGCTGGGACACTG
* *
27140504 ATGGCTGGCACCCCAGTACC-AGATTAAAAAAA
64 AT-GCCGACACCCCAGTACCTAGATTAAAAAAA
27140536 TTGGGTGTTG
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
102 2 0.02
103 59 0.73
104 20 0.25
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (103 bp):
TAGGACATTGATGGTCCGCACCCTTATACCAGATTAAAAGAAAAATTGGATGCTGGGACACTGAT
GCCGACACCCCAGTACCTAGATTAAAAAAAATTAGTGC
Found at i:27144115 original size:14 final size:17
Alignment explanation
Indices: 27144080--27144120 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
27144070 TTAATATATA
27144080 AATTATATTATTAAATT
1 AATTATATTATTAAATT
27144097 AATTATATTA-TAAA-T
1 AATTATATTATTAAATT
27144112 -ATTATATTA
1 AATTATATTA
27144121 AGAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.38
15 1 0.04
16 4 0.17
17 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTATATTATTAAATT
Found at i:27144357 original size:15 final size:17
Alignment explanation
Indices: 27144339--27144370 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27144329 CAGAATAGAA
27144339 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
27144354 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
27144371 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:27147089 original size:123 final size:123
Alignment explanation
Indices: 27146870--27147106 Score: 474
Period size: 123 Copynumber: 1.9 Consensus size: 123
27146860 ACTGAGTATG
27146870 AAATACTCAGCGTACGGTTGTTTCCGTGCGCAGGTCGATAGAAGTCAAAGGTCCCGGTTCAACAT
1 AAATACTCAGCGTACGGTTGTTTCCGTGCGCAGGTCGATAGAAGTCAAAGGTCCCGGTTCAACAT
27146935 CCAGATCAATCCCGACTTCAGCATAACTTTGGTGATGTATATTTTCTTTTGGTAATGT
66 CCAGATCAATCCCGACTTCAGCATAACTTTGGTGATGTATATTTTCTTTTGGTAATGT
27146993 AAATACTCAGCGTACGGTTGTTTCCGTGCGCAGGTCGATAGAAGTCAAAGGTCCCGGTTCAACAT
1 AAATACTCAGCGTACGGTTGTTTCCGTGCGCAGGTCGATAGAAGTCAAAGGTCCCGGTTCAACAT
27147058 CCAGATCAATCCCGACTTCAGCATAACTTTGGTGATGTATATTTTCTTT
66 CCAGATCAATCCCGACTTCAGCATAACTTTGGTGATGTATATTTTCTTT
27147107 AGTAAATGTG
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 114 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (123 bp):
AAATACTCAGCGTACGGTTGTTTCCGTGCGCAGGTCGATAGAAGTCAAAGGTCCCGGTTCAACAT
CCAGATCAATCCCGACTTCAGCATAACTTTGGTGATGTATATTTTCTTTTGGTAATGT
Found at i:27148688 original size:45 final size:45
Alignment explanation
Indices: 27148624--27148717 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
27148614 AACAGATACT
* *
27148624 CGGTGGATTCAACACATAGCAACCACCTCATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTCACTAATCAATGATGTC
* *
27148669 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAACACATAGCAACCACCTCACTAATCAATGATGTC
27148714 CGGT
1 CGGT
27148718 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTCACTAATCAATGATGTC
Found at i:27148788 original size:51 final size:51
Alignment explanation
Indices: 27148712--27148896 Score: 176
Period size: 51 Copynumber: 3.6 Consensus size: 51
27148702 ATCAATGATG
* * * * *
27148712 TTCGGTTCACATAGTAGCCTACACATAGTATTACACATGTGATCGTTACCA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGATCGATACCA
* * * * *
27148763 TTCGATACACGTAGTAGTCTGCACATAGTACTACACACGTGATCGAAACTA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGATCGATACCA
* * * * * * *
27148814 TCCGGTACGCATAGTGGCCTGCACATAGTACTACACATGCGA-C-CTATCA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGATCGATACCA
* *
27148863 TTCCGGTACAAGTAGTAGCCTTCACATAGTACTA
1 TT-CGGTACACGTAGTAGCCTGCACATAGTACTA
27148897 TACACATGAC
Statistics
Matches: 105, Mismatches: 28, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
49 3 0.03
50 27 0.26
51 75 0.71
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (51 bp):
TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGATCGATACCA
Found at i:27152622 original size:10 final size:11
Alignment explanation
Indices: 27152609--27152637 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
27152599 AAATTGAACT
27152609 AAAAAAAA-GA
1 AAAAAAAAGGA
27152619 AAAAAAAAGGA
1 AAAAAAAAGGA
27152630 AAAAAAAA
1 AAAAAAAA
27152638 CTAAATTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGGA
Found at i:27154692 original size:19 final size:19
Alignment explanation
Indices: 27154670--27154707 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
27154660 AATTTAATTT
*
27154670 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
27154689 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
27154708 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:27154858 original size:22 final size:22
Alignment explanation
Indices: 27154803--27154889 Score: 129
Period size: 22 Copynumber: 3.7 Consensus size: 22
27154793 ATATACCGAC
27154803 ATTACAATATTCATACAAAATTATAA
1 ATTACAATATTCATAC-AAA--A-AA
27154829 TATTACAATATTCATACAAAAAA
1 -ATTACAATATTCATACAAAAAA
27154852 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
27154874 ATTACAATATTCATAC
1 ATTACAATATTCATAC
27154890 TAAATATAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
22 38 0.63
23 2 0.03
24 1 0.02
26 3 0.05
27 16 0.27
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
ATTACAATATTCATACAAAAAA
Found at i:27154969 original size:27 final size:27
Alignment explanation
Indices: 27154937--27155008 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
27154927 AAAATATTGC
* * *
27154937 AATTTTATATGAATATTGTAATTTTGT
1 AATTTTGTATGAATATTGTAATATTAT
27154964 AATTTTGTATGAATATTGTAATATTAT
1 AATTTTGTATGAATATTGTAATATTAT
27154991 AATTTTGTATGAATATTG
1 AATTTTGTATGAATATTG
27155009 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (27 bp):
AATTTTGTATGAATATTGTAATATTAT
Found at i:27181604 original size:50 final size:50
Alignment explanation
Indices: 27181533--27181628 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
27181523 TTCTTTGAAT
* * * *
27181533 TTTTTAGAATTAGGATCAAATTGAAATCATTTGTAAATTTTGAGGGTTAA
1 TTTTTAAAATTAGGATCAAATTGAAATAATATGTAAAATTTGAGGGTTAA
* *
27181583 TTTTTAAAATTATGA-CTAAATTGATATAATATGTAAAATTTGAGGG
1 TTTTTAAAATTAGGATC-AAATTGAAATAATATGTAAAATTTGAGGG
27181629 CTAAATTTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.03
50 38 0.97
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.42
Consensus pattern (50 bp):
TTTTTAAAATTAGGATCAAATTGAAATAATATGTAAAATTTGAGGGTTAA
Found at i:27182519 original size:78 final size:80
Alignment explanation
Indices: 27182430--27182605 Score: 234
Period size: 82 Copynumber: 2.2 Consensus size: 80
27182420 TAGAATAACT
* *
27182430 AATTTTGTATGAACAAAAT-TT-TATATTCTTAGATA-CGGAGAATTAAAATC-GATCAACTCTC
1 AATTTTGTATGAACAAAATATTATATATTCTTAGATATC-AAGAATCAAAATCAG-TCAACTCTC
27182491 AATTTCACCACCATCTA
64 AATTTCACCACCATCTA
* *
27182508 AATTTTGTATGAACAAAATAAATTATATATTTTTAGATATCAAGAATCAAAATCAGTCAGCTCTC
1 AATTTTGTATGAACAAAAT--ATTATATATTCTTAGATATCAAGAATCAAAATCAGTCAACTCTC
*
27182573 AGTTTCACCACCATCTA
64 AATTTCACCACCATCTA
*
27182590 AATTTTCTATGAACAA
1 AATTTTGTATGAACAA
27182606 TTTTTTTTTC
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
78 19 0.22
81 2 0.02
82 63 0.73
83 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.35
Consensus pattern (80 bp):
AATTTTGTATGAACAAAATATTATATATTCTTAGATATCAAGAATCAAAATCAGTCAACTCTCAA
TTTCACCACCATCTA
Found at i:27182911 original size:20 final size:22
Alignment explanation
Indices: 27182888--27182927 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
27182878 TTATTAGTAT
27182888 AATTTTTT-ATTTG-TTTAATG
1 AATTTTTTAATTTGATTTAATG
27182908 AATTTTTTAATTTGATTTAA
1 AATTTTTTAATTTGATTTAA
27182928 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (22 bp):
AATTTTTTAATTTGATTTAATG
Found at i:27183394 original size:14 final size:14
Alignment explanation
Indices: 27183375--27183452 Score: 50
Period size: 14 Copynumber: 5.1 Consensus size: 14
27183365 TTGATTGCCA
27183375 GTAAAATATTTTCT
1 GTAAAATATTTTCT
27183389 GTAAAATGA-TTTCT
1 GTAAAAT-ATTTTCT
*
27183403 GGAAAATGTTTTACTTTTCT
1 GTAAAA-----TA-TTTTCT
*
27183423 GTAAAATTATTTACT
1 GTAAAA-TATTTTCT
*
27183438 GGAAAATATTTTCT
1 GTAAAATATTTTCT
27183452 G
1 G
27183453 GTGTTTGATT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
14 25 0.49
15 11 0.22
16 3 0.06
18 1 0.02
19 1 0.02
20 10 0.20
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (14 bp):
GTAAAATATTTTCT
Found at i:27183426 original size:34 final size:35
Alignment explanation
Indices: 27183383--27183449 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
27183373 CAGTAAAATA
*
27183383 TTTTCTGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
*
27183417 TTTTCTGTAAAATTATTTACTGGAAAATATTTT
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
27183450 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.49
Consensus pattern (35 bp):
TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:27189882 original size:18 final size:18
Alignment explanation
Indices: 27189859--27189901 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
27189849 ATTCAATATG
27189859 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
27189877 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
27189895 TAATTAA
1 TAATTAA
27189902 AAATCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:27192515 original size:89 final size:88
Alignment explanation
Indices: 27192394--27192562 Score: 241
Period size: 89 Copynumber: 1.9 Consensus size: 88
27192384 AATTAAACCT
* * * * **
27192394 TTTTTTTTGCACTTAATTGAGTACTTGAACTTTCAAAATGTATCAAAAAGACCCTCAAGCTTCTT
1 TTTTTTTTCCACTCAATTGAGTACTCGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTCTT
27192459 CAAAAAAAGCAATTAAACTCATGC
66 C-AAAAAAGCAATTAAACTCATGC
* *
27192483 TTTTTTTTCCACTCAATT-AGGTACTCGAACTTTCAAAATGCATCAAAAAGTCCCTCAAAATTTT
1 TTTTTTTTCCACTCAATTGA-GTACTCGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTCT
27192547 TCAAAAAAGCAATTAA
65 TCAAAAAAGCAATTAA
27192563 GCCCCTGCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
88 15 0.21
89 56 0.79
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.34
Consensus pattern (88 bp):
TTTTTTTTCCACTCAATTGAGTACTCGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTCTT
CAAAAAAGCAATTAAACTCATGC
Found at i:27192641 original size:9 final size:8
Alignment explanation
Indices: 27192619--27192695 Score: 73
Period size: 9 Copynumber: 8.8 Consensus size: 8
27192609 AAACAATAAA
27192619 ATTTTTAT
1 ATTTTTAT
*
27192627 ATTTTTGT
1 ATTTTTAT
27192635 ATATTTTAT
1 AT-TTTTAT
27192644 AATTTTTAT
1 -ATTTTTAT
27192653 GATTTTTAT
1 -ATTTTTAT
*
27192662 AAAATTTTAT
1 --ATTTTTAT
27192672 ATTTTGTAT
1 ATTTT-TAT
27192681 GATTTTTAT
1 -ATTTTTAT
27192690 ATTTTT
1 ATTTTT
27192696 TTTCTAATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
8 19 0.33
9 25 0.43
10 14 0.24
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (8 bp):
ATTTTTAT
Found at i:27192697 original size:28 final size:28
Alignment explanation
Indices: 27192618--27192690 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
27192608 TAAACAATAA
* *
27192618 AATTTTTAT-ATTTTTGT-ATATTTTAT
1 AATTTTTATGATTTTTATAAAATTTTAT
27192644 AATTTTTATGATTTTTATAAAATTTTAT
1 AATTTTTATGATTTTTATAAAATTTTAT
27192672 -ATTTTGTATGATTTTTATA
1 AATTTT-TATGATTTTTATA
27192691 TTTTTTTTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.21
27 12 0.29
28 21 0.50
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (28 bp):
AATTTTTATGATTTTTATAAAATTTTAT
Found at i:27192889 original size:94 final size:95
Alignment explanation
Indices: 27192712--27192894 Score: 210
Period size: 94 Copynumber: 1.9 Consensus size: 95
27192702 ATTTTTAATA
* ** * * *
27192712 AAAGTAGGGGTTTAATTACTTTTTTTGAAAAAGTTTGAGGGTCTTTTTAATGCATTTTGAAAGTT
1 AAAGTAGGGGCTTAATTACTTTTTTTGAAAAAGTTTGAGACTCTTTTTAATACATTTTAAAAATT
* * * *
27192777 CAAGTATCCAATTGAGTAAAAAAATAAAAG
66 CAAATACCCAAATAAGTAAAAAAATAAAAG
* *
27192807 AAAGTAGGGGCTTAATT-GTTTTTTTG-AAAAGATTTGAGAACT-TTTTTGATACATTTTAAAAA
1 AAAGTAGGGGCTTAATTACTTTTTTTGAAAAAG-TTTGAG-ACTCTTTTTAATACATTTTAAAAA
*
27192869 TTTAAATACCCAAATAAGTAAAAAAA
64 TTCAAATACCCAAATAAGTAAAAAAA
27192895 AAGTAGAGGC
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
93 5 0.07
94 51 0.70
95 17 0.23
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (95 bp):
AAAGTAGGGGCTTAATTACTTTTTTTGAAAAAGTTTGAGACTCTTTTTAATACATTTTAAAAATT
CAAATACCCAAATAAGTAAAAAAATAAAAG
Found at i:27195678 original size:22 final size:21
Alignment explanation
Indices: 27195650--27195691 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27195640 AAACGAAACA
27195650 GAAAGAAAAGAAAAGAA-AAAGG
1 GAAAG-AAAG-AAAGAAGAAAGG
27195672 GAAAGAAAGAAAGAAGAAAG
1 GAAAGAAAGAAAGAAGAAAG
27195692 ATAAGGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAGAAAGG
Found at i:27197902 original size:21 final size:21
Alignment explanation
Indices: 27197820--27197902 Score: 58
Period size: 21 Copynumber: 4.0 Consensus size: 21
27197810 AAGCTTGAAG
* * *
27197820 GCTGAACAGAAGCTCATGAGA
1 GCTGAACAGAAACCCATAAGA
* * *
27197841 GCTAAACAGAAACCTATAAGG
1 GCTGAACAGAAACCCATAAGA
* * * ***
27197862 GTTGAATAGAAGCTTGTAAGA
1 GCTGAACAGAAACCCATAAGA
27197883 GCTGAACAGAAACCCATAAG
1 GCTGAACAGAAACCCATAAG
27197903 GGTTAAACAA
Statistics
Matches: 43, Mismatches: 19, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCTGAACAGAAACCCATAAGA
Found at i:27197926 original size:42 final size:42
Alignment explanation
Indices: 27197824--27197957 Score: 135
Period size: 42 Copynumber: 3.2 Consensus size: 42
27197814 TTGAAGGCTG
* * * *
27197824 AACAGAAGCTCATGAGAGCTAAACAGAAACCTATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
* **
27197866 AATAGAAGCTTGTAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
* * ** * *
27197908 AACAAAAGCTCA-ATAGAGCTGAACGGAAACTAATATGAGTTA
1 AACAGAAGCTCATA-AGAGCTGAACAGAAACCCATAAGGGTTA
27197950 AACAGAAG
1 AACAGAAG
27197958 TTCGTGAGAG
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
41 1 0.01
42 73 0.99
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
Found at i:27213084 original size:22 final size:21
Alignment explanation
Indices: 27213056--27213097 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27213046 AAACGAAACA
27213056 GAAAGAAAAGAAAAGAA-AAAGG
1 GAAAG-AAAG-AAAGAAGAAAGG
27213078 GAAAGAAAGAAAGAAGAAAG
1 GAAAGAAAGAAAGAAGAAAG
27213098 ATAAGGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAGAAAGG
Found at i:27215308 original size:21 final size:21
Alignment explanation
Indices: 27215226--27215308 Score: 58
Period size: 21 Copynumber: 4.0 Consensus size: 21
27215216 AAGCTTGAAG
* * *
27215226 GCTGAACAGAAGCTCATGAGA
1 GCTGAACAGAAACCCATAAGA
* * *
27215247 GCTAAACAGAAACCTATAAGG
1 GCTGAACAGAAACCCATAAGA
* * * ***
27215268 GTTGAATAGAAGCTTGTAAGA
1 GCTGAACAGAAACCCATAAGA
27215289 GCTGAACAGAAACCCATAAG
1 GCTGAACAGAAACCCATAAG
27215309 GGTTAAACAA
Statistics
Matches: 43, Mismatches: 19, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCTGAACAGAAACCCATAAGA
Found at i:27215332 original size:42 final size:42
Alignment explanation
Indices: 27215230--27215363 Score: 135
Period size: 42 Copynumber: 3.2 Consensus size: 42
27215220 TTGAAGGCTG
* * * *
27215230 AACAGAAGCTCATGAGAGCTAAACAGAAACCTATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
* **
27215272 AATAGAAGCTTGTAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
* * ** * *
27215314 AACAAAAGCTCA-ATAGAGCTGAACGGAAACTAATATGAGTTA
1 AACAGAAGCTCATA-AGAGCTGAACAGAAACCCATAAGGGTTA
27215356 AACAGAAG
1 AACAGAAG
27215364 TTCGTGAGAG
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
41 1 0.01
42 73 0.99
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
Found at i:27220824 original size:9 final size:9
Alignment explanation
Indices: 27220812--27220877 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
27220802 TTTATGATTT
27220812 TTTTTATAA
1 TTTTTATAA
27220821 TTTTTATAA
1 TTTTTATAA
*
27220830 GTTTATATTAA
1 -TTTTTA-TAA
* * *
27220841 TCTTAATATT
1 TTTTTATA-A
27220851 TTTTTATAA
1 TTTTTATAA
**
27220860 TTTTTATGG
1 TTTTTATAA
27220869 TTTTTATAA
1 TTTTTATAA
27220878 AATTTTAATA
Statistics
Matches: 42, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
9 25 0.60
10 14 0.33
11 3 0.07
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:27220861 original size:39 final size:39
Alignment explanation
Indices: 27220810--27220898 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
27220800 TTTTTATGAT
*
27220810 TTTTTTTATAATTTTTATAAGTTTATAT-TAATCTTAATA
1 TTTTTTTATAATTTTTAT-AGTTTATATAAAATCTTAATA
* * *
27220849 TTTTTTTATAATTTTTATGGTTTTTATAAAATTTTAATA
1 TTTTTTTATAATTTTTATAGTTTATATAAAATCTTAATA
*
27220888 GTTTTTTATAA
1 TTTTTTTATAA
27220899 AATTGTAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 7 0.16
39 37 0.84
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (39 bp):
TTTTTTTATAATTTTTATAGTTTATATAAAATCTTAATA
Found at i:27220950 original size:20 final size:20
Alignment explanation
Indices: 27220843--27220983 Score: 106
Period size: 20 Copynumber: 6.6 Consensus size: 20
27220833 TATATTAATC
*
27220843 TTAATATTTTTT-TATAATT
1 TTAATATTTTTTATAAAATT
* **
27220862 TTTATGGTTTTTATAAAATT
1 TTAATATTTTTTATAAAATT
27220882 TTAATAGTTTTTTATAAAATT
1 TTAATA-TTTTTTATAAAATT
*
27220903 GTAAATATTTTTTTATTTGATTAGAATT
1 -TTAATA-TTTTTTA--T-A--A-AATT
*
27220931 TTTATATTTTTTATAAAA-T
1 TTAATATTTTTTATAAAATT
27220950 TTAATAGTTTTTTATAAAATT
1 TTAATA-TTTTTTATAAAATT
*
27220971 GTAAATATTTTTT
1 -TTAATATTTTTT
27220984 TATTTGATTA
Statistics
Matches: 97, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
19 15 0.15
20 24 0.25
21 21 0.22
22 17 0.18
23 1 0.01
24 2 0.02
25 1 0.01
26 7 0.07
27 5 0.05
28 4 0.04
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
TTAATATTTTTTATAAAATT
Found at i:27220976 original size:68 final size:68
Alignment explanation
Indices: 27220858--27221020 Score: 281
Period size: 68 Copynumber: 2.4 Consensus size: 68
27220848 ATTTTTTTAT
**
27220858 AATTTTTATGGTTTTTATAAAATTTTAATAGTTTTTTATAAAATTGTAAATATTTTTTTATTTGA
1 AATTTTTATATTTTTTATAAAA-TTTAATAGTTTTTTATAAAATTGTAAATATTTTTTTATTTGA
27220923 TTAG
65 TTAG
27220927 AATTTTTATATTTTTTATAAAATTTAATAGTTTTTTATAAAATTGTAAATATTTTTTTATTTGAT
1 AATTTTTATATTTTTTATAAAATTTAATAGTTTTTTATAAAATTGTAAATATTTTTTTATTTGAT
27220992 TAG
66 TAG
* *
27220995 AATTTTTATATTTTTTACAATATTTA
1 AATTTTTATATTTTTTATAAAATTTA
27221021 TAAAATTTTA
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
68 70 0.78
69 20 0.22
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (68 bp):
AATTTTTATATTTTTTATAAAATTTAATAGTTTTTTATAAAATTGTAAATATTTTTTTATTTGAT
TAG
Found at i:27227938 original size:25 final size:24
Alignment explanation
Indices: 27227888--27227938 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
27227878 ATGGATTTAA
*
27227888 TTTTTATTTTTTAATTTGATGTTT
1 TTTTTATTTTTTAATTTGATGATT
27227912 TTTTTATATTTTTAATTTTGA-GATT
1 TTTTTAT-TTTTTAA-TTTGATGATT
27227937 TT
1 TT
27227939 AATTTTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 12 0.50
26 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.73
Consensus pattern (24 bp):
TTTTTATTTTTTAATTTGATGATT
Found at i:27228299 original size:6 final size:6
Alignment explanation
Indices: 27228288--27228314 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
27228278 GGAGATTGGA
27228288 AAAATG AAAATG AAAATG AAAATG AAA
1 AAAATG AAAATG AAAATG AAAATG AAA
27228315 CTTCAGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:27232088 original size:17 final size:18
Alignment explanation
Indices: 27232056--27232092 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
27232046 AAAACACTTA
*
27232056 ATATAATTTTTTAAATTT
1 ATATAATTTATTAAATTT
27232074 ATATAA-TTATTAAATTT
1 ATATAATTTATTAAATTT
27232091 AT
1 AT
27232093 TAAAAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATAATTTATTAAATTT
Found at i:27232154 original size:19 final size:19
Alignment explanation
Indices: 27232124--27232162 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
27232114 TTAAAAAACA
27232124 TTATTTTATAAAA-TAAAT
1 TTATTTTATAAAATTAAAT
27232142 TTATTTATATAAAATTAAAT
1 TTATTT-TATAAAATTAAAT
27232162 T
1 T
27232163 AATCTCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 7 0.37
20 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTTTATAAAATTAAAT
Found at i:27232590 original size:19 final size:19
Alignment explanation
Indices: 27232560--27232598 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
27232550 TTAAAAAACA
27232560 TTATTTTATAAAA-TAAAT
1 TTATTTTATAAAATTAAAT
27232578 TTATTTATATAAAATTAAAT
1 TTATTT-TATAAAATTAAAT
27232598 T
1 T
27232599 AATCTCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 7 0.37
20 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTTTATAAAATTAAAT
Found at i:27232922 original size:436 final size:437
Alignment explanation
Indices: 27232100--27232973 Score: 1741
Period size: 436 Copynumber: 2.0 Consensus size: 437
27232090 TATTAAAAAG
27232100 AACCCATAATTTTTTTAAAAAACATTATTTTATAAAATAAATTTATTTATATAAAATTAAATTAA
1 AACCCATAATTTTTTTAAAAAACATTATTTTATAAAATAAATTTATTTATATAAAATTAAATTAA
27232165 TCTCTTTCCATCCACTAAAACTCAAACCCGAAAATCTTTAATCTTTTTACTTTCAACATTCATTC
66 TCTCTTTCCATCCACTAAAACTCAAACCCGAAAATCTTTAATCTTTTTACTTTCAACATTCATTC
27232230 ACTTTTCTCTCAACTTTCTCTTATTCTCTCTCTCTCACACACACTATAAATTTTACAAAATATGT
131 ACTTTTCTCTCAACTTTCTCTTATTCTCTCTCTCTCACACACACTATAAATTTTACAAAATATGT
27232295 GATTAATAATTCACTAGTTCCAAGTGAATCTCTTTAATTTGGTTCAAGATTTATTGGTTAATCTC
196 GATTAATAATTCACTAGTTCCAAGTGAATCTCTTTAATTTGGTTCAAGATTTATTGGTTAATCTC
27232360 TATAAAATTAGAATTGGGACTTTTTTTGTGATAGATTATTAGTTTTATGCAATATTTAGATTTTA
261 TATAAAATTAGAATTGGGACTTTTTTTGTGATAGATTATTAGTTTTATGCAATATTTAGATTTTA
27232425 TTGATTGAATGATTTTGAGATATAGATTTTATATGAGATCCCTAACATCTTAATTAGATAATAAT
326 TTGATTGAATGATTTTGAGATATAGATTTTATATGAGATCCCTAACATCTTAATTAGATAATAAT
27232490 TTGTAGGTCCTTGAAGAAATTAGGATTGATTGTCTTTATAATCTTGA
391 TTGTAGGTCCTTGAAGAAATTAGGATTGATTGTCTTTATAATCTTGA
27232537 AACCCATAA-TTTTTTAAAAAACATTATTTTATAAAATAAATTTATTTATATAAAATTAAATTAA
1 AACCCATAATTTTTTTAAAAAACATTATTTTATAAAATAAATTTATTTATATAAAATTAAATTAA
27232601 TCTCTTTCCATCCACTAAAACTCAAACCCGAAAATCTTTAATCTTTTTACTTTCAACATTCATTC
66 TCTCTTTCCATCCACTAAAACTCAAACCCGAAAATCTTTAATCTTTTTACTTTCAACATTCATTC
27232666 ACTTTTCTCTCAACTTTCTCTTATTCTCTCTCTCTCACACACACTATAAATTTTACAAAATATGT
131 ACTTTTCTCTCAACTTTCTCTTATTCTCTCTCTCTCACACACACTATAAATTTTACAAAATATGT
27232731 GATTAATAATTCACTAGTTCCAAGTGAATCTCTTTAATTTGGTTCAAGATTTATTGGTTAATCTC
196 GATTAATAATTCACTAGTTCCAAGTGAATCTCTTTAATTTGGTTCAAGATTTATTGGTTAATCTC
27232796 TATAAAATTAGAATTGGGACTTTTTTTGTGATAGATTATTAGTTTTATGCAATATTTAGATTTTA
261 TATAAAATTAGAATTGGGACTTTTTTTGTGATAGATTATTAGTTTTATGCAATATTTAGATTTTA
27232861 TTGATTGAATGATTTTGAGATATAGATTTTATATGAGATCCCTAACATCTTAATTAGATAATAAT
326 TTGATTGAATGATTTTGAGATATAGATTTTATATGAGATCCCTAACATCTTAATTAGATAATAAT
27232926 TTGTAGGTCCTTGAAGAAATTAGGATTGATTGTCTTTATAATCTTGA
391 TTGTAGGTCCTTGAAGAAATTAGGATTGATTGTCTTTATAATCTTGA
27232973 A
1 A
27232974 TTTCTTGATT
Statistics
Matches: 437, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
436 428 0.98
437 9 0.02
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (437 bp):
AACCCATAATTTTTTTAAAAAACATTATTTTATAAAATAAATTTATTTATATAAAATTAAATTAA
TCTCTTTCCATCCACTAAAACTCAAACCCGAAAATCTTTAATCTTTTTACTTTCAACATTCATTC
ACTTTTCTCTCAACTTTCTCTTATTCTCTCTCTCTCACACACACTATAAATTTTACAAAATATGT
GATTAATAATTCACTAGTTCCAAGTGAATCTCTTTAATTTGGTTCAAGATTTATTGGTTAATCTC
TATAAAATTAGAATTGGGACTTTTTTTGTGATAGATTATTAGTTTTATGCAATATTTAGATTTTA
TTGATTGAATGATTTTGAGATATAGATTTTATATGAGATCCCTAACATCTTAATTAGATAATAAT
TTGTAGGTCCTTGAAGAAATTAGGATTGATTGTCTTTATAATCTTGA
Found at i:27240486 original size:132 final size:133
Alignment explanation
Indices: 27240334--27240598 Score: 507
Period size: 132 Copynumber: 2.0 Consensus size: 133
27240324 TTTGATAAAT
27240334 AAAATGTCTATTTTAGACATGTAGTTATAAAGTAACAAATATGCATCTAAATAATGTTCAACTTA
1 AAAATGTCTATTTTAGACATGTAGTTATAAAGTAACAAATATGCATCTAAATAATGTTCAACTTA
27240399 ATTAATATTTATGATATTTTAGTAA-GAATAAAAATAATTTATTATAATTTATTGTTTATATTTT
66 ATTAATATTTATGATATTTTAGTAAGGAA-AAAAATAATTTATTATAATTTATTGTTTATATTTT
27240463 AATA
130 AATA
27240467 AAAATGTCTA-TTTAGACATGTAGTTATAAAGTAACAAATATGCATCTAAATAATGTTCAACTTA
1 AAAATGTCTATTTTAGACATGTAGTTATAAAGTAACAAATATGCATCTAAATAATGTTCAACTTA
27240531 ATTAATATTTATGATATTTTAGTAAGGAAAAAAATAATTTATTATAATTTATTGTTTATATTTTA
66 ATTAATATTTATGATATTTTAGTAAGGAAAAAAATAATTTATTATAATTTATTGTTTATATTTTA
27240596 ATA
131 ATA
27240599 TATGAAATAT
Statistics
Matches: 131, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
132 118 0.90
133 13 0.10
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (133 bp):
AAAATGTCTATTTTAGACATGTAGTTATAAAGTAACAAATATGCATCTAAATAATGTTCAACTTA
ATTAATATTTATGATATTTTAGTAAGGAAAAAAATAATTTATTATAATTTATTGTTTATATTTTA
ATA
Found at i:27242102 original size:15 final size:15
Alignment explanation
Indices: 27242082--27242112 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27242072 CTTATAAGGA
27242082 ACCAAGCCTTTTTAC
1 ACCAAGCCTTTTTAC
27242097 ACCAAGCCTTTTTAC
1 ACCAAGCCTTTTTAC
27242112 A
1 A
27242113 GGATCTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.06, T:0.32
Consensus pattern (15 bp):
ACCAAGCCTTTTTAC
Found at i:27244820 original size:37 final size:37
Alignment explanation
Indices: 27244770--27244841 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
27244760 ACTAAAAAAC
**
27244770 AGAACAACATAAGAAGCTCATTTAAGATTCATCAAAT
1 AGAACAACATAAGAAGCTCAACTAAGATTCATCAAAT
27244807 AGAACAACATAAGAAGCTCAACTAAGATTCATCAA
1 AGAACAACATAAGAAGCTCAACTAAGATTCATCAA
27244842 TAAAAACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (37 bp):
AGAACAACATAAGAAGCTCAACTAAGATTCATCAAAT
Found at i:27245903 original size:338 final size:338
Alignment explanation
Indices: 27245287--27245963 Score: 1189
Period size: 338 Copynumber: 2.0 Consensus size: 338
27245277 TTAAGGATGT
27245287 AAATGGCAAGGACAAGCTTAGATTGTTTATCTTAGTGTGCTTCACAATCTTATTGAATATCAGCT
1 AAATGGCAAGGACAAGCTTAGATTGTTTATCTTAGTGTGCTTCACAATCTTATTGAATATCAGCT
27245352 ATCCCGTTTTCTTAGTTATCACATTTCTTTGGTTATTAGGAAACCAATTTCCAGTAGAAATTGCA
66 ATCCCGTTTTCTTAGTTATCACATTTCTTTGGTTATTAGGAAACCAATTTCCAGTAGAAATTGCA
*
27245417 TGTAGAGTAGCATAAGTTAGTGGTAGATATAAAGCCTTGAAATCTTGCCCATTTGTACATGTTGC
131 TGTAGAGTAGCATAAGTTAGTGATAGATATAAAGCCTTGAAATCTTGCCCATTTGTACATGTTGC
27245482 TGGAATTTCAGTAGTGAGCTACTTGGTAATCTCATCACAGGATTCACCAAACTCATCATTATCAA
196 TGGAATTTCAGTAGTGAGCTACTTGGTAATCTCATCACAGGATTCACCAAACTCATCATTATCAA
*
27245547 TGCACTAGTGATTCATGAAATCAATAATCTTTTCAAAACTAAATGTAAACTAGC-GTCTTCAAAC
261 TGCACTAGTGATTCATGAAATCAATAATCTTTCCAAAACTAAATGTAAACTA-CTGTCTTCAAAC
27245611 ATATGCTTGTTAGG
325 ATATGCTTGTTAGG
**
27245625 AAATGGCAAGGACAAGCTTAGATTGTTTATCTTAGTGTGCTTCACAATCTTATTGAATATCATTT
1 AAATGGCAAGGACAAGCTTAGATTGTTTATCTTAGTGTGCTTCACAATCTTATTGAATATCAGCT
* *
27245690 ATCCCGTTTTCTTGGTTATCACATTTCTTTGGTTATTAGGAAACCAATTTCCAGTAGCAATTGCA
66 ATCCCGTTTTCTTAGTTATCACATTTCTTTGGTTATTAGGAAACCAATTTCCAGTAGAAATTGCA
* **
27245755 TGT-GAAGTAGCATAAGTTAGTGATAGATTTAAAGTTTTGAAATCTTGCCCATTTGTACATGTTG
131 TGTAG-AGTAGCATAAGTTAGTGATAGATATAAAGCCTTGAAATCTTGCCCATTTGTACATGTTG
* *
27245819 CTTGAA-TTCTAGTAGTGAGCTACTTGGTAATCTCATCACTGGATTCACCAAACTCATCATTATC
195 CTGGAATTTC-AGTAGTGAGCTACTTGGTAATCTCATCACAGGATTCACCAAACTCATCATTATC
* *
27245883 AATGCACTAGTGATTCATGAAATCAATAATCTTTCCAAAATTGAATGTAAACTACTGTCTTCAAA
259 AATGCACTAGTGATTCATGAAATCAATAATCTTTCCAAAACTAAATGTAAACTACTGTCTTCAAA
27245948 CATATGCTTGTTAGG
324 CATATGCTTGTTAGG
27245963 A
1 A
27245964 TTTTGTGCCC
Statistics
Matches: 323, Mismatches: 13, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
337 5 0.02
338 318 0.98
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (338 bp):
AAATGGCAAGGACAAGCTTAGATTGTTTATCTTAGTGTGCTTCACAATCTTATTGAATATCAGCT
ATCCCGTTTTCTTAGTTATCACATTTCTTTGGTTATTAGGAAACCAATTTCCAGTAGAAATTGCA
TGTAGAGTAGCATAAGTTAGTGATAGATATAAAGCCTTGAAATCTTGCCCATTTGTACATGTTGC
TGGAATTTCAGTAGTGAGCTACTTGGTAATCTCATCACAGGATTCACCAAACTCATCATTATCAA
TGCACTAGTGATTCATGAAATCAATAATCTTTCCAAAACTAAATGTAAACTACTGTCTTCAAACA
TATGCTTGTTAGG
Found at i:27272489 original size:18 final size:18
Alignment explanation
Indices: 27272437--27272489 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 18
27272427 GAAACTCTTT
27272437 ATCCTTCAGGGATTTTAA
1 ATCCTTCAGGGATTTTAA
**
27272455 ATCCATTTTGGGATTTTAA
1 ATCC-TTCAGGGATTTTAA
*
27272474 ATCCTTCAGAGATTTT
1 ATCCTTCAGGGATTTT
27272490 CATATATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (18 bp):
ATCCTTCAGGGATTTTAA
Found at i:27293608 original size:25 final size:24
Alignment explanation
Indices: 27293577--27293623 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
27293567 AATAAATTTC
*
27293577 ATATTAATATTGAATAAATATAATG
1 ATATTAATATTAAATAAA-ATAATG
27293602 ATATTAATATTAAATAAAATAA
1 ATATTAATATTAAATAAAATAA
27293624 AATTCTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATTAATATTAAATAAAATAATG
Found at i:27295658 original size:116 final size:116
Alignment explanation
Indices: 27295525--27295751 Score: 454
Period size: 116 Copynumber: 2.0 Consensus size: 116
27295515 CCAAGGGACA
27295525 ATGGTGGGGGTGGTGGAGTGGGAGAAGGAGAGGGAGAGGGACGGGGTGGAAAGGATTTTTACTTT
1 ATGGTGGGGGTGGTGGAGTGGGAGAAGGAGAGGGAGAGGGACGGGGTGGAAAGGATTTTTACTTT
27295590 ATTTTATTTAATGTTAATATAATTATATTTATAAAATTAAAATTTAATAAT
66 ATTTTATTTAATGTTAATATAATTATATTTATAAAATTAAAATTTAATAAT
27295641 ATGGTGGGGGTGGTGGAGTGGGAGAAGGAGAGGGAGAGGGACGGGGTGGAAAGGATTTTTACTTT
1 ATGGTGGGGGTGGTGGAGTGGGAGAAGGAGAGGGAGAGGGACGGGGTGGAAAGGATTTTTACTTT
27295706 ATTTTATTTAATGTTAATATAATTATATTTATAAAATTAAAATTTA
66 ATTTTATTTAATGTTAATATAATTATATTTATAAAATTAAAATTTA
27295752 TTATATATAT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 111 1.00
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (116 bp):
ATGGTGGGGGTGGTGGAGTGGGAGAAGGAGAGGGAGAGGGACGGGGTGGAAAGGATTTTTACTTT
ATTTTATTTAATGTTAATATAATTATATTTATAAAATTAAAATTTAATAAT
Found at i:27302180 original size:3 final size:3
Alignment explanation
Indices: 27302172--27302198 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27302162 TTTTTAAATT
27302172 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
27302199 AAACCCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27305379 original size:17 final size:17
Alignment explanation
Indices: 27305357--27305391 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27305347 TATATTATTT
*
27305357 TATTATTTAATATAATA
1 TATTATATAATATAATA
*
27305374 TATTATATAATATTATA
1 TATTATATAATATAATA
27305391 T
1 T
27305392 TGTATTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTATATAATATAATA
Found at i:27305392 original size:5 final size:5
Alignment explanation
Indices: 27305339--27305412 Score: 55
Period size: 5 Copynumber: 15.2 Consensus size: 5
27305329 ATGTTTTAAA
* * * *
27305339 TATAT TA-A- TATAT TATTT TATTAT T-TAA TATAA TATAT TATAT AATAT
1 TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT
* * *
27305387 TATAT TGTAT TGTAT TATAT TGTAT T
1 TATAT TATAT TATAT TATAT TATAT T
27305413 TGAGGCGGCA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
3 2 0.04
4 5 0.09
5 46 0.82
6 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:27305477 original size:5 final size:5
Alignment explanation
Indices: 27305456--27305526 Score: 72
Period size: 5 Copynumber: 13.4 Consensus size: 5
27305446 TTTTTTGAAG
* *
27305456 TATAT TATTAT TTTAT TATATT GTAAAT TATAT TATAT TATAT TATAT
1 TATAT TA-TAT TATAT TATA-T -TATAT TATAT TATAT TATAT TATAT
27305504 TATAT TAT-T ATATTAT TATAT TA
1 TATAT TATAT -TA-TAT TATAT TA
27305527 GGTAAAATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
4 1 0.02
5 42 0.75
6 9 0.16
7 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:27305523 original size:8 final size:8
Alignment explanation
Indices: 27305456--27305526 Score: 67
Period size: 8 Copynumber: 8.9 Consensus size: 8
27305446 TTTTTTGAAG
27305456 TATATTAT
1 TATATTAT
*
27305464 TATTTTAT
1 TATATTAT
*
27305472 TATATT-G
1 TATATTAT
*
27305479 TAAATTA-
1 TATATTAT
27305486 TAT-TATAT
1 TATAT-TAT
27305494 TATATTATAT
1 TATA-T-TAT
27305504 TATATTAT
1 TATATTAT
27305512 TATATTAT
1 TATATTAT
27305520 TATATTA
1 TATATTA
27305527 GGTAAAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
6 1 0.02
7 9 0.17
8 33 0.62
9 1 0.02
10 9 0.17
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (8 bp):
TATATTAT
Found at i:27305759 original size:23 final size:23
Alignment explanation
Indices: 27305733--27305776 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
27305723 AAACGAATAG
*
27305733 AGAAAGGAAA-AAAGGAAAAAGAA
1 AGAAA-GAAAGAAAAGAAAAAGAA
27305756 AGAAAGAAAGAAAAGAAAAAG
1 AGAAAGAAAGAAAAGAAAAAG
27305777 GAAAAATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (23 bp):
AGAAAGAAAGAAAAGAAAAAGAA
Found at i:27315801 original size:66 final size:64
Alignment explanation
Indices: 27315707--27315888 Score: 163
Period size: 66 Copynumber: 2.8 Consensus size: 64
27315697 TTCGACTAAC
* ** * *
27315707 ATATATATAATTCATATAATTACATTCAACTTATGAATCTCAACACATATATTTGGCTAAATATA
1 ATATATATAATTCATACAATT-TTTTCAACTTATGAATCTCAACACATATATTTGGCT-AACACA
27315772 T
64 T
* * * * *
27315773 ATATATATAATTTATACAATTTGTTTCAATTTAT-AGAGCTCAAAACATACA-TTGGCTAACACA
1 ATATATATAATTCATACAATTT-TTTCAACTTATGA-ATCTCAACACATATATTTGGCTAACACA
27315836 T
64 T
* * * *
27315837 ATATATACAATTCATAC-ATTTTTTTAACTTATAGAATTTAAAACACATATAT
1 ATATATATAATTCATACAATTTTTTCAACTTAT-GAATCT-CAACACATATAT
27315889 ACATAATCGG
Statistics
Matches: 91, Mismatches: 19, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
62 9 0.10
63 6 0.07
64 29 0.32
65 7 0.08
66 40 0.44
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (64 bp):
ATATATATAATTCATACAATTTTTTCAACTTATGAATCTCAACACATATATTTGGCTAACACAT
Done.