Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007113.1 Hibiscus syriacus cultivar Beakdansim tig00018586_pilon, whole genome shotgun sequence
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: 836039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:263932 original size:18 final size:18
Alignment explanation
Indices: 263909--263943 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
263899 AGAAAAAGGC
*
263909 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
263927 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
263944 CAACTGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:264255 original size:140 final size:140
Alignment explanation
Indices: 264003--264272 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
263993 AAACGTTGTA
264003 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* * *
264068 TGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAATATGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACGAATTTGACTAT
264133 TATGTGTATT
131 TATGTGTATT
264143 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
264208 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACGAATTTGACTAT
264273 CGCAATGCGA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACGAATTTGACTAT
TATGTGTATT
Found at i:264268 original size:20 final size:20
Alignment explanation
Indices: 264243--264507 Score: 295
Period size: 20 Copynumber: 13.8 Consensus size: 20
264233 TTACACATTC
*
264243 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
264263 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
264283 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
264302 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
264317 ATATGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
264337 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
264357 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
264377 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
264397 ATTTGATTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
*
264417 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
264437 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
264451 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
264471 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
264491 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
264508 AGTAATCGTA
Statistics
Matches: 209, Mismatches: 22, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
14 21 0.10
15 3 0.01
16 1 0.00
18 1 0.00
19 4 0.02
20 178 0.85
21 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:264475 original size:74 final size:73
Alignment explanation
Indices: 264365--264546 Score: 283
Period size: 74 Copynumber: 2.5 Consensus size: 73
264355 GAATTTGTCT
264365 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
*
264430 AACGTGAAA
66 AACGAG-AA
*
264439 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
*
264504 AACGAGTA
66 AACGAGAA
* * * * *
264512 ATCGTAAAGCGTATTAGACTATTGCAACGCGAATT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATT
264547 GACTTTCGCG
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
73 31 0.31
74 69 0.69
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (73 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
AACGAGAA
Found at i:264574 original size:20 final size:20
Alignment explanation
Indices: 264545--264602 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
264535 GCAACGCGAA
264545 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* **
264565 TTGTCTTTCGTATTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
264585 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
264603 AAGTGTACCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:264761 original size:14 final size:14
Alignment explanation
Indices: 264701--264762 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
264691 CACAAATAAG
*
264701 AATTATTTACACATC
1 AATT-TTTACAAATC
**
264716 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
264731 AACTTTTACAAATC
1 AATTTTTACAAATC
*
264745 AATTTTTATAAATC
1 AATTTTTACAAATC
264759 AATT
1 AATT
264763 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:266272 original size:42 final size:42
Alignment explanation
Indices: 266165--266276 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
266155 TCTAGAATGT
* * * *
266165 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTAAACGA
* * ** *
266207 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTAAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTAAACGA
266249 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
266277 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTAAACGA
Found at i:266784 original size:18 final size:18
Alignment explanation
Indices: 266761--266827 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 18
266751 GAAACTTAAA
*
266761 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
266779 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG--AATGACT
* *
266799 ATCACAACGTGAATTTGACT
1 ATCGCAACGCGAA--TGACT
266819 ATCGCAACG
1 ATCGCAACG
266828 AAAGAATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 12 0.29
20 29 0.71
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:266797 original size:20 final size:20
Alignment explanation
Indices: 266772--266827 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
266762 TCGCAACACG
266772 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
* *
266792 AATGACTATCACAACGTGAA
1 AATGACTATCGCAACGCGAA
**
266812 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
266828 AAAGAATCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:266897 original size:20 final size:20
Alignment explanation
Indices: 266872--266917 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
266862 GATTCTTTCA
266872 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
**
266892 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCG
266912 TTGCGA
1 TTGCGA
266918 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:267088 original size:18 final size:18
Alignment explanation
Indices: 267065--267114 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
267055 TTTACTAAGC
267065 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
267083 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
267101 AACCTAAGTGAAAT
1 AATCTAAGTGAAAT
267115 TACGAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:268874 original size:20 final size:20
Alignment explanation
Indices: 268851--268904 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
268841 GAAACTTAAA
*
268851 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
268871 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
268891 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
268905 CTAAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:269550 original size:20 final size:20
Alignment explanation
Indices: 269518--269631 Score: 158
Period size: 20 Copynumber: 5.7 Consensus size: 20
269508 GCGCTTTGAA
*
269518 AATCGCATTGCGATAGTCA-
1 AATCGCGTTGCGATAGTCAG
* *
269537 ACACCGCGTTGCGACAGTCAG
1 A-ATCGCGTTGCGATAGTCAG
*
269558 AATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
269578 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
269598 AATCTCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
269618 AATCGCATTGCGAT
1 AATCGCGTTGCGAT
269632 TTACATATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
19 1 0.01
20 83 0.98
21 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:269680 original size:22 final size:22
Alignment explanation
Indices: 269652--269711 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
269642 GCATTGCGAT
269652 ATCGCAATGCGATAGTCGGAAA
1 ATCGCAATGCGATAGTCGGAAA
* * *
269674 ATCGCAACGCGAT-TTTGGAAA
1 ATCGCAATGCGATAGTCGGAAA
* *
269695 TTCGCAATGCGAAAGTC
1 ATCGCAATGCGATAGTC
269712 AGAATTGCGT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (22 bp):
ATCGCAATGCGATAGTCGGAAA
Found at i:269778 original size:19 final size:19
Alignment explanation
Indices: 269754--269803 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
269744 CGATACCGGA
*
269754 GATCGCGTTGCGAATTATC
1 GATCGCATTGCGAATTATC
269773 GATCGCATTGCGAATTATC
1 GATCGCATTGCGAATTATC
269792 GATCGCATTGCG
1 GATCGCATTGCG
269804 CTTTAGTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (19 bp):
GATCGCATTGCGAATTATC
Found at i:272425 original size:16 final size:16
Alignment explanation
Indices: 272404--272453 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
272394 TGCAAATCCA
272404 GGTACCCGGATTTTCG
1 GGTACCCGGATTTTCG
*
272420 GGTACCC-GATTTCCG
1 GGTACCCGGATTTTCG
*
272435 GGTA-CCGGAACTTTCG
1 GGTACCCGG-ATTTTCG
272451 GGT
1 GGT
272454 CGACGATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 12 0.41
16 15 0.52
ACGTcount: A:0.14, C:0.26, G:0.32, T:0.28
Consensus pattern (16 bp):
GGTACCCGGATTTTCG
Found at i:272436 original size:15 final size:16
Alignment explanation
Indices: 272404--272440 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
272394 TGCAAATCCA
*
272404 GGTACCCGGATTTTCG
1 GGTACCCGGATTTCCG
272420 GGTACCC-GATTTCCG
1 GGTACCCGGATTTCCG
272435 GGTACC
1 GGTACC
272441 GGAACTTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.27
Consensus pattern (16 bp):
GGTACCCGGATTTCCG
Found at i:272512 original size:15 final size:15
Alignment explanation
Indices: 272492--272547 Score: 76
Period size: 15 Copynumber: 3.6 Consensus size: 15
272482 CGGATGTTAT
272492 GGGTACCCGGTAATC
1 GGGTACCCGGTAATC
**
272507 GGGTACCCGGATTTTGC
1 GGGTACCCGG-TAAT-C
272524 GGGTACCCGGTAATC
1 GGGTACCCGGTAATC
272539 GGGTACCCG
1 GGGTACCCG
272548 ATACCCGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 20 0.57
16 4 0.11
17 11 0.31
ACGTcount: A:0.16, C:0.27, G:0.36, T:0.21
Consensus pattern (15 bp):
GGGTACCCGGTAATC
Found at i:272515 original size:32 final size:32
Alignment explanation
Indices: 272479--272547 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
272469 CCGTGTCCCG
*
272479 ACCCGGATGTTATGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
* *
272511 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
272543 ACCCG
1 ACCCG
272548 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.23
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGGTAATCGGGT
Found at i:274309 original size:37 final size:38
Alignment explanation
Indices: 274259--274332 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
274249 TGTTCAGGTT
*
274259 GGGTCTGGTTTTTT-AAGTGTGATATTCGGGTCGAGTC
1 GGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGAGTC
274296 GGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGAGT
1 GGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGAGT
274333 TTTTTTAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 13 0.37
38 22 0.63
ACGTcount: A:0.15, C:0.09, G:0.36, T:0.39
Consensus pattern (38 bp):
GGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGAGTC
Found at i:274334 original size:28 final size:28
Alignment explanation
Indices: 274294--274355 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
274284 TCGGGTCGAG
*
274294 TCGGGTCGGGTTTTTTAAAGTGTGATAT
1 TCGGGTCGAGTTTTTTAAAGTGTGATAT
*
274322 TCGGGTCGAGTTTTTTTAAGTGTGATAT
1 TCGGGTCGAGTTTTTTAAAGTGTGATAT
274350 TCGGGT
1 TCGGGT
274356 TGGGTCGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (28 bp):
TCGGGTCGAGTTTTTTAAAGTGTGATAT
Found at i:274935 original size:44 final size:44
Alignment explanation
Indices: 274871--274954 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
274861 ATCTGACATG
* * * * *
274871 TCTGCGAATCAAACATAATATGGAATTGGATTCTAATTCCATTT
1 TCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCCATTT
274915 TCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCC
1 TCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCC
274955 TGACAGATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (44 bp):
TCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCCATTT
Found at i:275005 original size:18 final size:18
Alignment explanation
Indices: 274943--275007 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
274933 TATGAAATTG
*
274943 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
274960 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
* *
274978 TATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
274996 GATTCTAATTCC
1 GATTCCAATTCC
275008 CTCATAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
17 12 0.29
18 29 0.71
ACGTcount: A:0.28, C:0.29, G:0.06, T:0.37
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:284338 original size:18 final size:18
Alignment explanation
Indices: 284310--284351 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
284300 TCTCAGTTTC
284310 CCTTT-CCCTTTGACCCT
1 CCTTTCCCCTTTGACCCT
284327 CCTTTCCCCTTTGACCCT
1 CCTTTCCCCTTTGACCCT
284345 CCTTTCC
1 CCTTTCC
284352 ACTCCGATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.05, C:0.50, G:0.05, T:0.40
Consensus pattern (18 bp):
CCTTTCCCCTTTGACCCT
Found at i:285719 original size:23 final size:23
Alignment explanation
Indices: 285684--285752 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
285674 CCCTCTTGGG
* *
285684 GGGTATCGGTACCCTCCGAGCAA
1 GGGTACCGATACCCTCCGAGCAA
285707 GGGTACCGATACCCTCCGAGCAA
1 GGGTACCGATACCCTCCGAGCAA
285730 GGGTACCGATACCCTCCGAGCAA
1 GGGTACCGATACCCTCCGAGCAA
285753 TCTGTTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.14
Consensus pattern (23 bp):
GGGTACCGATACCCTCCGAGCAA
Found at i:287067 original size:30 final size:30
Alignment explanation
Indices: 287031--287272 Score: 461
Period size: 30 Copynumber: 8.1 Consensus size: 30
287021 GAAGGACCTA
287031 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
287061 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
287091 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
287121 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
287151 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
287181 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
287211 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
287241 TCC--AGGTCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
287269 TCCA
1 TCCA
287273 TATGTTCCTT
Statistics
Matches: 210, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
28 27 0.13
30 183 0.87
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:287594 original size:20 final size:20
Alignment explanation
Indices: 287569--287631 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
287559 TTCATATTCT
287569 TTCTTATGTCCTTTTCATAC
1 TTCTTATGTCCTTTTCATAC
* * *
287589 TTCTTATTTCATATTC-T--
1 TTCTTATGTCCTTTTCATAC
287606 TTCTTATGTCCTTTTCATAC
1 TTCTTATGTCCTTTTCATAC
287626 TTCTTA
1 TTCTTA
287632 CTTCATATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 13 0.38
18 1 0.03
19 1 0.03
20 19 0.56
ACGTcount: A:0.16, C:0.22, G:0.03, T:0.59
Consensus pattern (20 bp):
TTCTTATGTCCTTTTCATAC
Found at i:287598 original size:37 final size:37
Alignment explanation
Indices: 287556--287643 Score: 167
Period size: 37 Copynumber: 2.4 Consensus size: 37
287546 ATATTCTGTA
287556 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
1 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
287593 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
1 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
*
287630 TACTTCATATTCTT
1 TATTTCATATTCTT
287644 ATGAAATCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.17, C:0.22, G:0.02, T:0.59
Consensus pattern (37 bp):
TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
Found at i:287644 original size:13 final size:13
Alignment explanation
Indices: 287582--287644 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
287572 TTATGTCCTT
*
287582 TTCATACTTCTTAT
1 TTCATA-TTCTTAC
*
287596 TTCATATTCTTTC
1 TTCATATTCTTAC
* *
287609 TT-ATGTCCTT--
1 TTCATATTCTTAC
287619 TTCATACTTCTTAC
1 TTCATA-TTCTTAC
287633 TTCATATTCTTA
1 TTCATATTCTTA
287645 TGAAATCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
10 2 0.05
11 2 0.05
12 10 0.26
13 13 0.33
14 12 0.31
ACGTcount: A:0.19, C:0.22, G:0.02, T:0.57
Consensus pattern (13 bp):
TTCATATTCTTAC
Found at i:288832 original size:2 final size:2
Alignment explanation
Indices: 288825--288854 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
288815 ATCCCTATCC
288825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
288855 CATTTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:290484 original size:11 final size:11
Alignment explanation
Indices: 290468--290492 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
290458 AAAATCAATA
290468 TATATATATAT
1 TATATATATAT
290479 TATATATATAT
1 TATATATATAT
290490 TAT
1 TAT
290493 GAAAACATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATATAT
Found at i:290985 original size:23 final size:23
Alignment explanation
Indices: 290940--291001 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
290930 GTACCCTCCT
*
290940 GGGGGGTATCGGTACCTACTCAAA
1 GGGGGGTATCGGTACCCACTC-AA
* *
290964 GGGGGG-ATCTGTACCCATTCAA
1 GGGGGGTATCGGTACCCACTCAA
* *
290986 GGGGAGTATCGATACC
1 GGGGGGTATCGGTACC
291002 TCCTGCACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 7 0.23
23 18 0.58
24 6 0.19
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (23 bp):
GGGGGGTATCGGTACCCACTCAA
Found at i:293085 original size:301 final size:305
Alignment explanation
Indices: 292542--293150 Score: 1163
Period size: 301 Copynumber: 2.0 Consensus size: 305
292532 CCTAGTTACG
292542 GGAGCGTATGTTTCATCATAATCTATGCCCTCTTCTTGAGTATACTCTTGAGCAACAAGTCTAGT
1 GGAGCGTATGTTTCATCATAATCTATGCCCTCTTCTTGAGTATACTCTTGAGCAACAAGTCTAGT
292607 CTTGTTTCTCACTATAATTACCACTTTCATCAAGCTTATTTCTAAATACTCATCTAGTACCTACA
66 CTTGTTTCTCACTATAATTACCACTTTCATCAAGCTTATTTCTAAATACTCATCTAGTACCTACA
*
292672 ATAGATTTATTACTAGGCCTTTCAACTAATGTTCATACTCTACTTCTCTCAAATTGATTTAACTC
131 ATAGATTTATTACTAGGCCTTTCAACTAATGTTCATACTCTACTTCTCTCAAATTGATTTAACAC
292737 TTCTTGCATAGCCATAATCCAATGTTCATCATTTAATGTTTCTTTAATATTTTTAGGATTTATGC
196 TTCTTGCATAGCCATAATCCAATGTTCATCATTTAATGTTTCTTTAATATTTTTAGGATTTATGC
292802 ATGAAATAAATGCAAC-A-TA-ATACATTTCTAAGAGAAGATCGA
261 ATGAAATAAATGCAACAATTACATACATTTCTAAGAGAAGATCGA
292844 GGAGCGTATGTTTCATCATAATCTATGCCCTCTTCTTGAGTATACTCTTGAGCAACAAGTCTAGT
1 GGAGCGTATGTTTCATCATAATCTATGCCCTCTTCTTGAGTATACTCTTGAGCAACAAGTCTAGT
292909 CTTGTTTCTCACTAT-ATTACCACTTTCATCAAGCTTATTTCTAAATACTCATCTAGTACCTACA
66 CTTGTTTCTCACTATAATTACCACTTTCATCAAGCTTATTTCTAAATACTCATCTAGTACCTACA
292973 ATAGATTTATTACTAGGCCTTTCAACTAATGTTCATACTCTACTTCTCTCAAATTGATTTAACAC
131 ATAGATTTATTACTAGGCCTTTCAACTAATGTTCATACTCTACTTCTCTCAAATTGATTTAACAC
293038 TTCTTGCATAGCCATAATCCAATGTTCATCATTTAATGTTTCTTTAATATTTTTAGGATTTATGC
196 TTCTTGCATAGCCATAATCCAATGTTCATCATTTAATGTTTCTTTAATATTTTTAGGATTTATGC
293103 ATGAAATAAATGCAACATAATTACATACATTTCTAAGAGAAGATCGA
261 ATGAAATAAATGCAAC--AATTACATACATTTCTAAGAGAAGATCGA
293150 G
1 G
293151 TTGTTGCCCC
Statistics
Matches: 301, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
301 194 0.64
302 80 0.27
304 1 0.00
305 2 0.01
306 24 0.08
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.39
Consensus pattern (305 bp):
GGAGCGTATGTTTCATCATAATCTATGCCCTCTTCTTGAGTATACTCTTGAGCAACAAGTCTAGT
CTTGTTTCTCACTATAATTACCACTTTCATCAAGCTTATTTCTAAATACTCATCTAGTACCTACA
ATAGATTTATTACTAGGCCTTTCAACTAATGTTCATACTCTACTTCTCTCAAATTGATTTAACAC
TTCTTGCATAGCCATAATCCAATGTTCATCATTTAATGTTTCTTTAATATTTTTAGGATTTATGC
ATGAAATAAATGCAACAATTACATACATTTCTAAGAGAAGATCGA
Found at i:295142 original size:21 final size:21
Alignment explanation
Indices: 295118--295157 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
295108 AAGACTATTT
295118 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTTGAAACA
295139 TCATTTTTATATTTTGAAA
1 TCATTTTTATATTTTGAAA
295158 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTATATTTTGAAACA
Found at i:298655 original size:24 final size:24
Alignment explanation
Indices: 298628--298674 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
298618 TTCCGATTTA
*
298628 AATTATGTTATGCTTTCTGATCTT
1 AATTATGTTATGATTTCTGATCTT
* *
298652 AATTCTGTTCTGATTTCTGATCT
1 AATTATGTTATGATTTCTGATCT
298675 GATATCTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.13, T:0.53
Consensus pattern (24 bp):
AATTATGTTATGATTTCTGATCTT
Found at i:298669 original size:12 final size:12
Alignment explanation
Indices: 298662--298710 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
298652 AATTCTGTTC
*
298662 TGATTTCTGATC
1 TGATTTCTGATA
*
298674 TGATATCTGATA
1 TGATTTCTGATA
*
298686 TGATTTCTGTTA
1 TGATTTCTGATA
*
298698 TGATTTCTTATA
1 TGATTTCTGATA
298710 T
1 T
298711 CTCCATTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.53
Consensus pattern (12 bp):
TGATTTCTGATA
Found at i:298682 original size:24 final size:24
Alignment explanation
Indices: 298636--298694 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
298626 TAAATTATGT
* * *
298636 TATGCTTTCTGATCTTAATTCTGT
1 TATGATTTCTGATCTGAATTCTGA
*
298660 TCTGATTTCTGATCTG-ATATCTGA
1 TATGATTTCTGATCTGAAT-TCTGA
298684 TATGATTTCTG
1 TATGATTTCTG
298695 TTATGATTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (24 bp):
TATGATTTCTGATCTGAATTCTGA
Found at i:299034 original size:152 final size:153
Alignment explanation
Indices: 298732--299036 Score: 352
Period size: 152 Copynumber: 2.0 Consensus size: 153
298722 TGACAGAAAA
* * * *
298732 AAATGTTTTATTTGGAGGAATATTATTGGAGGAAGTATATATACAGGCTCCTCGGTTTTGTGTTC
1 AAATATTTTATTTGGAGGAATATTATTGGAGGAAGTATATAGACAGGCTCATCGGCTTTGTGTTC
* * * * * * **
298797 AGGGTCTTATTGTTGTGCTGGGTTGTATGGTTTTGGGGAACCTACACATTATGATGTATTCGGTT
66 AGGGCCTTACTGTTGTGCGGGGGTGTATGGTTATAGGGAACCTACACATTATGATGTA-TCAATT
* * *
298862 GGGGGATTTACTATGGTTTTTGAT
130 GAGGGAATTACTATGATTTTTGAT
* *
298886 AAATATTTTATTTGG-GG-GTATTGTTGGAGGAAGTATAT-GA-AGGCTCATCGGCTTTGTGCTT
1 AAATATTTTATTTGGAGGAATATTATTGGAGGAAGTATATAGACAGGCTCATCGGCTTTGTG-TT
*
298947 -AGGGCCTTACTGTTGTGCAGGGGGTGTATGGTTATAGGGAGCCTACACATTATGAACATGTA-C
65 CAGGGCCTTACTGTTGTGC-GGGGGTGTATGGTTATAGGGAACCTACACATTATG---ATGTATC
299010 AATTGAGGGAATTACTATGATTTTTGA
126 AATTGAGGGAATTACTATGATTTTTGA
299037 ATTTTAAAAA
Statistics
Matches: 128, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
150 32 0.25
151 33 0.26
152 42 0.33
153 2 0.02
154 19 0.15
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.38
Consensus pattern (153 bp):
AAATATTTTATTTGGAGGAATATTATTGGAGGAAGTATATAGACAGGCTCATCGGCTTTGTGTTC
AGGGCCTTACTGTTGTGCGGGGGTGTATGGTTATAGGGAACCTACACATTATGATGTATCAATTG
AGGGAATTACTATGATTTTTGAT
Found at i:302260 original size:2 final size:2
Alignment explanation
Indices: 302253--302299 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
302243 TACCTGAACA
302253 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
302295 AC AC A
1 AC AC A
302300 TATATATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:302304 original size:2 final size:2
Alignment explanation
Indices: 302299--302334 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
302289 ACACACACAC
*
302299 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
302335 CACTTGAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:303114 original size:24 final size:24
Alignment explanation
Indices: 303087--303180 Score: 116
Period size: 24 Copynumber: 3.9 Consensus size: 24
303077 TTCAGATTTT
* *
303087 ATTCTGTTCTGATTTATGATATGA
1 ATTCTGTTATGATTTCTGATATGA
* * *
303111 ATTCTTTTCTGATTTCTGATCTGA
1 ATTCTGTTATGATTTCTGATATGA
*
303135 ATTCTGTTATGATATCTGATATGA
1 ATTCTGTTATGATTTCTGATATGA
* *
303159 TTTCTGTTATGATTTCTTATAT
1 ATTCTGTTATGATTTCTGATAT
303181 CTCTATTTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.53
Consensus pattern (24 bp):
ATTCTGTTATGATTTCTGATATGA
Found at i:303133 original size:12 final size:12
Alignment explanation
Indices: 303088--303175 Score: 77
Period size: 12 Copynumber: 7.3 Consensus size: 12
303078 TCAGATTTTA
*
303088 TTCTGTTCTGAT
1 TTCTGTTATGAT
* * *
303100 TTATGATATGAA
1 TTCTGTTATGAT
* *
303112 TTCTTTTCTGAT
1 TTCTGTTATGAT
* * *
303124 TTCTGATCTGAA
1 TTCTGTTATGAT
303136 TTCTGTTATGAT
1 TTCTGTTATGAT
* *
303148 ATCTGATATGAT
1 TTCTGTTATGAT
303160 TTCTGTTATGAT
1 TTCTGTTATGAT
303172 TTCT
1 TTCT
303176 TATATCTCTA
Statistics
Matches: 57, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 57 1.00
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.53
Consensus pattern (12 bp):
TTCTGTTATGAT
Found at i:303465 original size:152 final size:156
Alignment explanation
Indices: 303201--303507 Score: 419
Period size: 152 Copynumber: 2.0 Consensus size: 156
303191 ATGATGGAAA
* *
303201 AAATGTTTTATTTGGGGGAATATTATTGGAGGAATTATATATGCAGGCTCATCGGCTTTGTGCTC
1 AAATGTTTTATTTGGGGGAATATTATTGGAGGAATTATATATGAAGGCTCATCGGCTATGTGCTC
* * * *
303266 AGGGCCTTACTGTTGTGCCAGGGTTGTATGGTTCTGAGGAACTTACACATTAT-GATGTGT-TCG
66 AGGGCCTTACTGTTGTGCCAGGGGTGTATGGTTATGAGGAACCTACACATTATGGACGTGTGT-G
* * *
303329 GTTGGGGGATTTACTATGGTTTTTGAT
130 GTTGAGGGAATTACTATGATTTTTGAT
* * * *
303356 AAATGTTTTATTT-GGGGAGTATTGTTGGAGGAA-T-TATATGAAGGCTCCTCGGCTATGTGCTT
1 AAATGTTTTATTTGGGGGAATATTATTGGAGGAATTATATATGAAGGCTCATCGGCTATGTGCTC
* *
303418 AGGGCCTTACTGTTGTG-CAGGGGGTGTATGGTTATGGGGAGCCTACACATTATGGACGTGTGTG
66 AGGGCCTTACTGTTGTGCCA-GGGGTGTATGGTTATGAGGAACCTACACATTATGGACGTGTGTG
303482 GTTGAGGGAATTACTATGATTTTTGA
130 GTTGAGGGAATTACTATGATTTTTGA
303508 ATTTTAAAAA
Statistics
Matches: 134, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
151 2 0.01
152 69 0.51
153 31 0.23
154 19 0.14
155 13 0.10
ACGTcount: A:0.21, C:0.11, G:0.31, T:0.37
Consensus pattern (156 bp):
AAATGTTTTATTTGGGGGAATATTATTGGAGGAATTATATATGAAGGCTCATCGGCTATGTGCTC
AGGGCCTTACTGTTGTGCCAGGGGTGTATGGTTATGAGGAACCTACACATTATGGACGTGTGTGG
TTGAGGGAATTACTATGATTTTTGAT
Found at i:305470 original size:21 final size:20
Alignment explanation
Indices: 305406--305470 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
305396 GCGATGACTG
*
305406 TTGACC-GCGTTTACCGACA
1 TTGACCAGCGTTGACCGACA
* * *
305425 TTGACCACCGTTGACCAAAA
1 TTGACCAGCGTTGACCGACA
305445 TTTGACCAGCGTTGACCGACCA
1 -TTGACCAGCGTTGACCGA-CA
305467 TTGA
1 TTGA
305471 ACGACCTTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
19 6 0.17
20 9 0.25
21 20 0.56
22 1 0.03
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (20 bp):
TTGACCAGCGTTGACCGACA
Found at i:307630 original size:12 final size:12
Alignment explanation
Indices: 307609--307737 Score: 125
Period size: 12 Copynumber: 10.8 Consensus size: 12
307599 TCCGATTTTA
*
307609 TTCTGTTATGAT
1 TTCTGATATGAT
*
307621 TTCTGATATGAA
1 TTCTGATATGAT
* *
307633 TTCTGTTCTGAT
1 TTCTGATATGAT
*
307645 TTCTGATATGAA
1 TTCTGATATGAT
* *
307657 TTCTGTTTTGAT
1 TTCTGATATGAT
*
307669 TTCTGATTTGAT
1 TTCTGATATGAT
* *
307681 TTCTGATTTGAA
1 TTCTGATATGAT
*
307693 TTCT-ATTCTGAT
1 TTCTGA-TATGAT
*
307705 ATCTGATATGAT
1 TTCTGATATGAT
*
307717 TTCTGTTATGAT
1 TTCTGATATGAT
307729 TTCTGATAT
1 TTCTGATAT
307738 CTCCATTTAA
Statistics
Matches: 95, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
11 1 0.01
12 93 0.98
13 1 0.01
ACGTcount: A:0.21, C:0.10, G:0.16, T:0.53
Consensus pattern (12 bp):
TTCTGATATGAT
Found at i:307632 original size:48 final size:48
Alignment explanation
Indices: 307592--307685 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
307582 GAATATTTTA
**
307592 TCTGATTTCCGAT-TTTATTCTGTTATGATTTCTGATATGAATTCTGT
1 TCTGATTTCCGATATGAATTCTGTTATGATTTCTGATATGAATTCTGT
* * * *
307639 TCTGATTTCTGATATGAATTCTGTTTTGATTTCTGATTTGATTTCTG
1 TCTGATTTCCGATATGAATTCTGTTATGATTTCTGATATGAATTCTG
307686 ATTTGAATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 12 0.30
48 28 0.70
ACGTcount: A:0.18, C:0.12, G:0.16, T:0.54
Consensus pattern (48 bp):
TCTGATTTCCGATATGAATTCTGTTATGATTTCTGATATGAATTCTGT
Found at i:326246 original size:106 final size:104
Alignment explanation
Indices: 326023--326238 Score: 319
Period size: 111 Copynumber: 2.0 Consensus size: 104
326013 CAAAATGTTG
*
326023 GAGCAATTCAATTCTATCAAATTCTTCATCTAAGAAGTGCTTCAAACCCAGAAAAGCAAAACATT
1 GAGCAATTCAATTCTATCAAATTCTTCATCTAAGAAGTGCTTCAAACCCAGAAAAGCAAAACACT
* *
326088 TGTGGCTGGAAACGTAAAGGATTTCAAGGGCATCCCGGATT
66 TGTGGCTGGAAACGT-AA-GATTTCAAGGGCAGCCCAGATT
*
326129 GAGCAATTCAATTCTATCAAATTCTTCATCTAAGAAGTCAAGTGCTTCTAACCCAGAAAAGCAAA
1 GAGCAATTCAATTCTATCAAATTCTTCATCT---AAG--AAGTGCTTCAAACCCAGAAAAGCAAA
326194 ACACTTGTGGCTGGAAACGT-A-ATTTCAAGGGCAGCCCAGATT
61 ACACTTGTGGCTGGAAACGTAAGATTTCAAGGGCAGCCCAGATT
326236 GAG
1 GAG
326239 AGATCAATGA
Statistics
Matches: 101, Mismatches: 4, Indels: 9
0.89 0.04 0.08
Matches are distributed among these distances:
106 31 0.31
107 22 0.22
109 4 0.04
111 44 0.44
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (104 bp):
GAGCAATTCAATTCTATCAAATTCTTCATCTAAGAAGTGCTTCAAACCCAGAAAAGCAAAACACT
TGTGGCTGGAAACGTAAGATTTCAAGGGCAGCCCAGATT
Found at i:335861 original size:42 final size:41
Alignment explanation
Indices: 335809--335910 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
335799 TCCAAAATTA
* * * *
335809 ATAATTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATG
* * *
335850 ATTGAATCCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATG
1 A-TAAATCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATG
*
335892 ATAAATCATTCGGGTCATC
1 ATAAATCCTTCGGGTCATC
335911 TATAAGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 17 0.33
42 34 0.67
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
ATAAATCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATG
Found at i:335877 original size:256 final size:255
Alignment explanation
Indices: 335414--336121 Score: 1029
Period size: 256 Copynumber: 2.7 Consensus size: 255
335404 TCAGGCCATC
* * *
335414 GCATGATGTTTCACATGATTTGAAAAATGAGAAAGTGATTTTCAAAGTTTCACATTTAGTATTTT
1 GCATGATGTTTCACATTATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTT
* * * * *
335479 CAGAAAATGAAATTTTTTAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACTTGGTAAACTATTT
66 CAAAAAATGAAATTTTTAAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTT
* *
335544 CCAAAATTAGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAACCCTTCGGG
131 CCAAAATTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
* * *
335609 TTATATGTCAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTCCAG
196 TCATATGTCAGTCTTTCAAGCAAGATGATAAATCATTCGGGCCATCTATAAGACCTCCAG
*
335669 GCATGATGTTTTCACATTATTTGAAAAATGAGAAAGCGATTTTCAAAGTTACTCATTTAGTATTT
1 GCATGATG-TTTCACATTATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTT
*
335734 TCAAAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATT
65 TCAAAAAATGAAATTTTTAAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATT
* * *
335799 TCCAAAATTAATAATTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTGAATCCTTCGG
130 TCCAAAATTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* * ***
335864 GTCATCTGTCAGTCTTTCAAGCAAGATGATAAATCATTCGGGTCATCTATAAGACCTTTGG
195 GTCATATGTCAGTCTTTCAAGCAAGATGATAAATCATTCGGGCCATCTATAAGACCTCCAG
* * * * * *
335925 GCAAGATGCTTTCATATGATAAATTGAAAAATTAGAAAGCGATTTTCAAGGTTTCTCATTTAGAA
1 GCATGATG-TTTCACAT--T-ATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTA
**
335990 TTTTTCAAAAAATGATTTTTTTTAAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAA
62 -TTTTCAAAAAATGA-AATTTTTAAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAA
* * * * *
336055 CTATTTCCAAACTTGGTAAGTCCTTCAGGCCATCATTAAGTCTTTCGAGCATGACGATTAAATCC
125 CTATTTCCAAAATTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCC
336120 TT
190 TT
336122 TAGGTCATTT
Statistics
Matches: 406, Mismatches: 41, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
255 8 0.02
256 239 0.59
258 1 0.00
259 39 0.10
260 14 0.03
261 105 0.26
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (255 bp):
GCATGATGTTTCACATTATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTT
CAAAAAATGAAATTTTTAAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTT
CCAAAATTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
TCATATGTCAGTCTTTCAAGCAAGATGATAAATCATTCGGGCCATCTATAAGACCTCCAG
Found at i:336272 original size:3 final size:3
Alignment explanation
Indices: 336264--336319 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
336254 TGTATGAGTT
* * * * * *
336264 TTA TTA TTA TTA TTA ATA TTA TTA TTG TTG TTG TTG TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
336312 TTA TTA TT
1 TTA TTA TT
336320 TATTTTTTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:339865 original size:20 final size:20
Alignment explanation
Indices: 339818--339868 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
339808 TTTCATCGAG
* *
339818 GGATCAATCCTTTTGGTTAA
1 GGATCGATCCTTTTGGTGAA
339838 GAGATCGATCCTTTT-GTGAA
1 G-GATCGATCCTTTTGGTGAA
339858 TGGATCGATCC
1 -GGATCGATCC
339869 CAAACTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
GGATCGATCCTTTTGGTGAA
Found at i:342259 original size:21 final size:20
Alignment explanation
Indices: 342233--342271 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
342223 GTTGTCATGC
342233 AATAATAGTTGCATAATGCAT
1 AATAATAGTT-CATAATGCAT
*
342254 AATAATGGTTCATAATGC
1 AATAATAGTTCATAATGC
342272 CTTGTAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
AATAATAGTTCATAATGCAT
Found at i:346924 original size:20 final size:21
Alignment explanation
Indices: 346887--346928 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
346877 GTCATGCAAC
*
346887 TAATAATTGTTGCATAATGCA
1 TAATAATGGTTGCATAATGCA
346908 TAATAATGGTT-CATAATGCA
1 TAATAATGGTTGCATAATGCA
346928 T
1 T
346929 TGTAAGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
TAATAATGGTTGCATAATGCA
Found at i:349513 original size:20 final size:21
Alignment explanation
Indices: 349476--349517 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
349466 GTCATGCAAC
349476 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
*
349497 TAATAATGGTT-CATAATGCA
1 TAATAATAGTTGCATAATGCA
349517 T
1 T
349518 TGTAAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Found at i:351460 original size:133 final size:133
Alignment explanation
Indices: 351222--351465 Score: 400
Period size: 133 Copynumber: 1.8 Consensus size: 133
351212 GATTATATAC
*
351222 CGGTATAATAATAATATAAACGGTCAAATATTTACAACCTAACCAATTAAAACAATTTATGCGCA
1 CGGTATAATAATAATATAAACGGTCAAATATTGACAACCTAACCAATTAAAACAATTTATGCGCA
* *
351287 ACCTATTACTTTAAGCTTGCTGCCGGTTTATTTATAGGGTTAATAAAACTTATATTGACAACCTA
66 ACCTATTACTTTAAACTTGCTACCGGTTTATTTATAGGGTTAATAAAACTTATATTGACAACCTA
351352 TTA
131 TTA
* * * * *
351355 CGGTATAATAATAATGTAAATGGTCAAATATTGACAACCTAACCGGA-TAAAACATTTTATGTGC
1 CGGTATAATAATAATATAAACGGTCAAATATTGACAACCTAACC-AATTAAAACAATTTATGCGC
351419 AACCTATTACTTTAAACTTGCTACCGGTTTATTTATAGGGTTAATAA
65 AACCTATTACTTTAAACTTGCTACCGGTTTATTTATAGGGTTAATAA
351466 TAATGTAAAC
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
133 101 0.99
134 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (133 bp):
CGGTATAATAATAATATAAACGGTCAAATATTGACAACCTAACCAATTAAAACAATTTATGCGCA
ACCTATTACTTTAAACTTGCTACCGGTTTATTTATAGGGTTAATAAAACTTATATTGACAACCTA
TTA
Found at i:351991 original size:19 final size:20
Alignment explanation
Indices: 351951--351994 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
351941 TAATGGATTT
*
351951 AATATTGATACTTTTTTCCC
1 AATATCGATACTTTTTTCCC
351971 AATATCGATACTTTTTT-CC
1 AATATCGATACTTTTTTCCC
351990 AATAT
1 AATAT
351995 GCTCTCACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.48
Consensus pattern (20 bp):
AATATCGATACTTTTTTCCC
Found at i:352871 original size:43 final size:43
Alignment explanation
Indices: 352810--352891 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
352800 TTTTATCTGG
** **
352810 TTAGGTTGTCAATATTTTACCTTTTACATTATTATTATACCGA
1 TTAGGTTGAAAATATTTTACAGTTTACATTATTATTATACCGA
* *
352853 TTAGGTTGAAAATATTTTACAGTTTATATTATTCTTATA
1 TTAGGTTGAAAATATTTTACAGTTTACATTATTATTATA
352892 TTGGTAGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (43 bp):
TTAGGTTGAAAATATTTTACAGTTTACATTATTATTATACCGA
Found at i:353367 original size:145 final size:144
Alignment explanation
Indices: 353096--353957 Score: 1113
Period size: 145 Copynumber: 6.0 Consensus size: 144
353086 TATAGATACT
* * *
353096 TTATAAAGATCGATACTTTATATATGTGTATCGATACATTTTCATGCAAATTGTTTGAGAAAGCA
1 TTATAAACATCGATACTTTATATATGTGTATCGATACCTTTTCATGCAAATTGTTTGAGAGAGCA
*
353161 TATTGGAAACAAAGTATCGATACTGTCACAACAAGTATCGATATTTTGACATTGAAAATATTGCA
66 TACTGGAAACAAAGTATCGATACTGTCACAACAAGTATCGATA-TTTGACATTGAAAATATTGCA
*
353226 TATTTTATTTCAAAA
130 TATTTTGTTTCAAAA
* *
353241 TTATAAACATCGATACTTTATATATGTGTATCGATACCTTTTCATGCAAATTATTTTAGAGAGCA
1 TTATAAACATCGATACTTTATATATGTGTATCGATACCTTTTCATGCAAATTGTTTGAGAGAGCA
* * * ** * *
353306 TACTGG-AACAAAAGTATCGATATTGTCATAACAAGTATCAATATGTTGACATTTCATATATTAC
66 TACTGGAAAC-AAAGTATCGATACTGTCACAACAAGTATCGATAT-TTGACATTGAAAATATTGC
**
353370 ATATTTTGTTTTGAAA
129 ATATTTTGTTTCAAAA
* * *
353386 TTATAAAGATCGATTACTTTATATATGTGTATCGATACGTTTTCGTGCAAATTGTTTGAGAGAGC
1 TTATAAACATCGA-TACTTTATATATGTGTATCGATACCTTTTCATGCAAATTGTTTGAGAGAGC
*
353451 ATACTGGAAACAAAGTATCGATGCTGTCACAACAAGTATCGATACTTTGACATTGAAAATATTGC
65 ATACTGGAAACAAAGTATCGATACTGTCACAACAAGTATCGATA-TTTGACATTGAAAATATTGC
353516 ATATTTTGTTTCAAAA
129 ATATTTTGTTTCAAAA
* * *
353532 TTATAAACATTGATACTTTATATATGGGTATCGATATCTTTTCATGCAAATTGTTTGAGAGAGCA
1 TTATAAACATCGATACTTTATATATGTGTATCGATACCTTTTCATGCAAATTGTTTGAGAGAGCA
353597 TACTGGAAACAAAGTATCGATACTGT--C-ACAAGTATCGATACTTTGACATTGAAAATATTGCA
66 TACTGGAAACAAAGTATCGATACTGTCACAACAAGTATCGATA-TTTGACATTGAAAATATTGCA
353659 TATTTTGTTTCAAAA
130 TATTTTGTTTCAAAA
* *
353674 TTATAAACATCAATATTTTATATATGTGTATCGATACCTTTTCATGCAAATTGTTTGAGAGAGCA
1 TTATAAACATCGATACTTTATATATGTGTATCGATACCTTTTCATGCAAATTGTTTGAGAGAGCA
* * * * * * ** * **
353739 CACAGG-AACAAAAGTATCGATACTATCATAACAAGTATCGATACGTTAACATTTCATATATTAT
66 TACTGGAAAC-AAAGTATCGATACTGTCACAACAAGTATCGATA-TTTGACATTGAAAATATTGC
*
353803 ATATTTTGTTTCGAAA
129 ATATTTTGTTTCAAAA
* * * * *
353819 TTATAAATAACGATATTTTATATATGTGTATCGATACGTGTTCATGCAAATTGTTTGAGAGAGCA
1 TTATAAACATCGATACTTTATATATGTGTATCGATACCTTTTCATGCAAATTGTTTGAGAGAGCA
* * * *** ** * ** *
353884 TACTCGAAAAAAAAGTATTGATACCACCGTAATAAGTATCGATACCGTGACATTGAAGATATTGC
66 TACT-GGAAACAAAGTATCGATACTGTCACAACAAGTATCGATA-TTTGACATTGAAAATATTGC
353949 ATATTTTGT
129 ATATTTTGT
353958 ATATTGAAAC
Statistics
Matches: 629, Mismatches: 77, Indels: 21
0.87 0.11 0.03
Matches are distributed among these distances:
141 3 0.00
142 129 0.21
143 1 0.00
144 4 0.01
145 312 0.50
146 174 0.28
147 6 0.01
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (144 bp):
TTATAAACATCGATACTTTATATATGTGTATCGATACCTTTTCATGCAAATTGTTTGAGAGAGCA
TACTGGAAACAAAGTATCGATACTGTCACAACAAGTATCGATATTTGACATTGAAAATATTGCAT
ATTTTGTTTCAAAA
Found at i:353621 original size:20 final size:18
Alignment explanation
Indices: 353596--353638 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
353586 TTGAGAGAGC
353596 ATACTGGAAACAAAGTATCG
1 ATACT-GAAAC-AAGTATCG
**
353616 ATACTGTCACAAGTATCG
1 ATACTGAAACAAGTATCG
353634 ATACT
1 ATACT
353639 TTGACATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.62
19 3 0.14
20 5 0.24
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (18 bp):
ATACTGAAACAAGTATCG
Found at i:353923 original size:433 final size:435
Alignment explanation
Indices: 353096--353957 Score: 1327
Period size: 433 Copynumber: 2.0 Consensus size: 435
353086 TATAGATACT
* *
353096 TTATAAAGATCGATACTTTATATATGTGTATCGATACATTTTCATGCAAATTGTTTGAGAAAGCA
1 TTATAAACATCGATACTTTATATATGGGTATCGATACATTTTCATGCAAATTGTTTGAGAAAGCA
* *
353161 TATTGGAAACAAAGTATCGATACTGTCACAACAAGTATCGATATTTTGACATTGAAAATATTGCA
66 TACTGGAAACAAAGTATCGATACTGT-ACAACAAGTATCGATACTTTGACATTGAAAATATTGCA
*
353226 TATTTTATTTCAAAATTATAAACATCGATACTTTATATATGTGTATCGATACCTTTTCATGCAAA
130 TATTTTATTTCAAAATTATAAACATCAATACTTTATATATGTGTATCGATACCTTTTCATGCAAA
* * * * * * *
353291 TTATTTTAGAGAGCATACTGGAACAAAAGTATCGATATTGTCATAACAAGTATCAATATGTTGAC
195 TTATTTGAGAGAGCACACAGGAACAAAAGTATCGATACTATCATAACAAGTATCAATACGTTAAC
* *
353356 ATTTCATATATTACATATTTTGTTTTGAAATTATAAAGATCGATTACTTTATATATGTGTATCGA
260 ATTTCATATATTACATATTTTGTTTCGAAATTATAAAGAACGATTACTTTATATATGTGTATCGA
* * * * * ***
353421 TACGTTTTCGTGCAAATTGTTTGAGAGAGCATACTGGAAACAAAGTATCGATGCTGTCACAACAA
325 TACGTGTTCATGCAAATTGTTTGAGAGAGCATACTGAAAAAAAAGTATCGATACCACCACAACAA
**
353486 GTATCGATACTTTGACATTGAAAATATTGCATATTTTGTTTCAAAA
390 GTATCGATACCGTGACATTGAAAATATTGCATATTTTGTTTCAAAA
* *
353532 TTATAAACATTGATACTTTATATATGGGTATCGATATC-TTTTCATGCAAATTGTTTGAGAGAGC
1 TTATAAACATCGATACTTTATATATGGGTATCGATA-CATTTTCATGCAAATTGTTTGAGAAAGC
353596 ATACTGGAAACAAAGTATCGATACTGT-C-ACAAGTATCGATACTTTGACATTGAAAATATTGCA
65 ATACTGGAAACAAAGTATCGATACTGTACAACAAGTATCGATACTTTGACATTGAAAATATTGCA
* *
353659 TATTTTGTTTCAAAATTATAAACATCAATATTTTATATATGTGTATCGATACCTTTTCATGCAAA
130 TATTTTATTTCAAAATTATAAACATCAATACTTTATATATGTGTATCGATACCTTTTCATGCAAA
* *
353724 TTGTTTGAGAGAGCACACAGGAACAAAAGTATCGATACTATCATAACAAGTATCGATACGTTAAC
195 TTATTTGAGAGAGCACACAGGAACAAAAGTATCGATACTATCATAACAAGTATCAATACGTTAAC
* * *
353789 ATTTCATATATTATATATTTTGTTTCGAAATTATAAATAACGA-TATTTTATATATGTGTATCGA
260 ATTTCATATATTACATATTTTGTTTCGAAATTATAAAGAACGATTACTTTATATATGTGTATCGA
* ** *
353853 TACGTGTTCATGCAAATTGTTTGAGAGAGCATACTCGAAAAAAAAGTATTGATACCACCGTAATA
325 TACGTGTTCATGCAAATTGTTTGAGAGAGCATACT-GAAAAAAAAGTATCGATACCACCACAACA
*
353918 AGTATCGATACCGTGACATTGAAGATATTGCATATTTTGT
389 AGTATCGATACCGTGACATTGAAAATATTGCATATTTTGT
353958 ATATTGAAAC
Statistics
Matches: 386, Mismatches: 38, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
432 53 0.14
433 247 0.64
434 1 0.00
436 84 0.22
437 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (435 bp):
TTATAAACATCGATACTTTATATATGGGTATCGATACATTTTCATGCAAATTGTTTGAGAAAGCA
TACTGGAAACAAAGTATCGATACTGTACAACAAGTATCGATACTTTGACATTGAAAATATTGCAT
ATTTTATTTCAAAATTATAAACATCAATACTTTATATATGTGTATCGATACCTTTTCATGCAAAT
TATTTGAGAGAGCACACAGGAACAAAAGTATCGATACTATCATAACAAGTATCAATACGTTAACA
TTTCATATATTACATATTTTGTTTCGAAATTATAAAGAACGATTACTTTATATATGTGTATCGAT
ACGTGTTCATGCAAATTGTTTGAGAGAGCATACTGAAAAAAAAGTATCGATACCACCACAACAAG
TATCGATACCGTGACATTGAAAATATTGCATATTTTGTTTCAAAA
Found at i:354382 original size:21 final size:21
Alignment explanation
Indices: 354334--354383 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
354324 AATAAGCAAG
*
354334 ATCGATACTTCCATAAAAAGT
1 ATCGATACTTACATAAAAAGT
* * * *
354355 TTAGATACTTATATTAAAAGT
1 ATCGATACTTACATAAAAAGT
354376 ATCGATAC
1 ATCGATAC
354384 CGTCATTAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (21 bp):
ATCGATACTTACATAAAAAGT
Found at i:359068 original size:12 final size:12
Alignment explanation
Indices: 359020--359068 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
359010 AATTCCCCAA
*
359020 TCTACCTTCTTT
1 TCTACCTTCTCT
*
359032 TCTACCTTCTAT
1 TCTACCTTCTCT
* *
359044 TCTTCATTCTCT
1 TCTACCTTCTCT
*
359056 TCTACCTTATCT
1 TCTACCTTCTCT
359068 T
1 T
359069 TTTTCTCCTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (12 bp):
TCTACCTTCTCT
Found at i:367200 original size:22 final size:21
Alignment explanation
Indices: 367166--367207 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
367156 GAGTTTGAGC
367166 ATTGACTGAGCGACGATGTGG
1 ATTGACTGAGCGACGATGTGG
* *
367187 ATTGAGTGAAGCGATGATGTG
1 ATTGACTG-AGCGACGATGTG
367208 CGGCGGTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.26, C:0.10, G:0.38, T:0.26
Consensus pattern (21 bp):
ATTGACTGAGCGACGATGTGG
Found at i:373932 original size:20 final size:20
Alignment explanation
Indices: 373909--373951 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
373899 TCAAATTCGT
373909 AACCGGTTTTATCAAATTTC
1 AACCGGTTTTATCAAATTTC
*
373929 AACCGGTTTTGTCAAATTTC
1 AACCGGTTTTATCAAATTTC
373949 AAC
1 AAC
373952 TTGTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (20 bp):
AACCGGTTTTATCAAATTTC
Found at i:375231 original size:17 final size:17
Alignment explanation
Indices: 375206--375244 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
375196 CTTTATCTCA
*
375206 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
375223 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
375240 -TTTAT
1 ATTTAT
375245 CTCATTATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:378005 original size:3 final size:3
Alignment explanation
Indices: 377997--378050 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
377987 TAATCTCCAT
*
377997 TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTC TT- TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
378042 TTA TTA TTA
1 TTA TTA TTA
378051 ATTCAATATA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
2 6 0.13
3 41 0.87
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:378015 original size:14 final size:14
Alignment explanation
Indices: 377996--378049 Score: 78
Period size: 14 Copynumber: 4.1 Consensus size: 14
377986 GTAATCTCCA
377996 TTTATTATTATTAT
1 TTTATTATTATTAT
378010 TTTATTATTATTA-
1 TTTATTATTATTAT
*
378023 -TTATTCTT-TTAT
1 TTTATTATTATTAT
378035 TTTATTATTATTAT
1 TTTATTATTATTAT
378049 T
1 T
378050 AATTCAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 7 0.20
13 7 0.20
14 18 0.51
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:378038 original size:25 final size:26
Alignment explanation
Indices: 377997--378050 Score: 92
Period size: 25 Copynumber: 2.1 Consensus size: 26
377987 TAATCTCCAT
377997 TTATTATTATTATTTTATTATTATTA
1 TTATTATTATTATTTTATTATTATTA
*
378023 TTATTCTT-TTATTTTATTATTATTA
1 TTATTATTATTATTTTATTATTATTA
378048 TTA
1 TTA
378051 ATTCAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (26 bp):
TTATTATTATTATTTTATTATTATTA
Found at i:379483 original size:22 final size:23
Alignment explanation
Indices: 379455--379502 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
379445 TTTATGATAT
*
379455 TTATTTAATATAATAATTAA-TA
1 TTATTTAATATAAAAATTAATTA
*
379477 TTATTTATTATAAAAATTAATTA
1 TTATTTAATATAAAAATTAATTA
379500 TTA
1 TTA
379503 ATTTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATTTAATATAAAAATTAATTA
Found at i:379497 original size:26 final size:25
Alignment explanation
Indices: 379431--379499 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
379421 TAAAAATTTG
* *
379431 TATTTAAAAATTATTTTATGATATT
1 TATTTAAAAATTAATTAATGATATT
379456 TATTTAATATAA-TAATTAAT-ATTATT
1 TATTTAA-A-AATTAATTAATGA-TATT
379482 TATTATAAAAATTAATTA
1 TATT-TAAAAATTAATTA
379500 TTAATTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
25 10 0.27
26 22 0.59
27 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (25 bp):
TATTTAAAAATTAATTAATGATATT
Found at i:381230 original size:26 final size:26
Alignment explanation
Indices: 381200--381257 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
381190 TGCCGTTTGT
* *
381200 GAGGGGTTGGCGACCGCATGTTTGGA
1 GAGGGGTCGACGACCGCATGTTTGGA
381226 GAGGGGTCGACGACCGCATGTTTGGA
1 GAGGGGTCGACGACCGCATGTTTGGA
381252 GAGGGG
1 GAGGGG
381258 GAGGGTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.17, C:0.16, G:0.48, T:0.19
Consensus pattern (26 bp):
GAGGGGTCGACGACCGCATGTTTGGA
Found at i:381670 original size:29 final size:29
Alignment explanation
Indices: 381615--381670 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
381605 TCACTTTTAC
* * *
381615 GTTTTATTTTATTTTATTTTTGACATCTT
1 GTTTCATTTTATTTTAATTTAGACATCTT
*
381644 GTTTCATTTTATTTTAATTTAGTCATC
1 GTTTCATTTTATTTTAATTTAGACATC
381671 ATTTTTCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (29 bp):
GTTTCATTTTATTTTAATTTAGACATCTT
Found at i:381677 original size:29 final size:28
Alignment explanation
Indices: 381616--381677 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
381606 CACTTTTACG
* *
381616 TTTT-ATTTTATTTTATTTTTGACATCT
1 TTTTCATTTTATTTTAATTTAGACATCT
*
381643 TGTTTCATTTTATTTTAATTTAGTCATCAT
1 T-TTTCATTTTATTTTAATTTAGACATC-T
381673 TTTTC
1 TTTTC
381678 TATGGTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 1 0.03
28 3 0.10
29 23 0.79
30 2 0.07
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.66
Consensus pattern (28 bp):
TTTTCATTTTATTTTAATTTAGACATCT
Found at i:382812 original size:136 final size:136
Alignment explanation
Indices: 382512--382886 Score: 355
Period size: 136 Copynumber: 2.7 Consensus size: 136
382502 GATTTAGGAG
* *
382512 AATTTTTAATTTGGTCATCTCTTTTGCTCGAGGTTTTGA-TTTAATTATTCGATATTCCATAATT
1 AATTTTTTATTTGGTCAT-TCTTTTGCTCGAGG-TTTCATTTTAATTATTCGA-ATT--ATAATT
* * * * * * **
382576 GATTAAAATTAATTAGGATTATTATTAGAGCTTTCACTTTAGGTTTAATTTCAAATTAAGTCCTT
61 GATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAAGCTAAATTGAAAATTAAGTCCTT
* *
382641 AAATTTAGGCG
126 AAATTAAGGCA
* ** * *
382652 AA-TTCTTAGTTTAATCCTCACTTTTGCTCGAGGTTTCATTTTAATTATTCGAATTA-AATTGAT
1 AATTTTTTA-TTTGGTCAT-TCTTTTGCTCGAGGTTTCATTTTAATTATTCGAATTATAATTGAT
*
382715 TAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAAGCTAAATTGAAAACTT-AGTCCTTTA
64 TAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAAGCTAAATTGAAAA-TTAAGTCCTTAA
382779 ATTAAGGCA
128 ATTAAGGCA
* * * * * *
382788 AATTTTTTATTTGGTCATTGCTTTTACTCGAGGCTCCATTTTAATTGTTCAAATCAAATAATTGA
1 AATTTTTTATTTGGTCATT-CTTTTGCTCGAGGTTTCATTTTAATTATTCGAAT--TATAATTGA
* * * *
382853 TTAAAATTGACTAAG-TTAATAATTAGAACCTCCA
63 TTAAAATTAATTAGGATTAAT-ATTAGAGCCTCCA
382887 TTTTCAGGTT
Statistics
Matches: 193, Mismatches: 33, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
136 103 0.53
137 8 0.04
138 6 0.03
139 41 0.21
140 35 0.18
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (136 bp):
AATTTTTTATTTGGTCATTCTTTTGCTCGAGGTTTCATTTTAATTATTCGAATTATAATTGATTA
AAATTAATTAGGATTAATATTAGAGCCTCCACTTTAAGCTAAATTGAAAATTAAGTCCTTAAATT
AAGGCA
Found at i:407915 original size:20 final size:20
Alignment explanation
Indices: 407887--407926 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
407877 TGATATTAAT
*
407887 TTTTTTTTAGACAAGTAAAA
1 TTTTATTTAGACAAGTAAAA
**
407907 TTTTATTTATCCAAGTAAAA
1 TTTTATTTAGACAAGTAAAA
407927 GTCAATACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (20 bp):
TTTTATTTAGACAAGTAAAA
Found at i:412787 original size:46 final size:46
Alignment explanation
Indices: 412734--412837 Score: 208
Period size: 46 Copynumber: 2.3 Consensus size: 46
412724 ATCTGTTCGA
412734 ATGTCTTCTATCCTTTCTTTCTTTGAAAATCTCTTTTCCGAAATAT
1 ATGTCTTCTATCCTTTCTTTCTTTGAAAATCTCTTTTCCGAAATAT
412780 ATGTCTTCTATCCTTTCTTTCTTTGAAAATCTCTTTTCCGAAATAT
1 ATGTCTTCTATCCTTTCTTTCTTTGAAAATCTCTTTTCCGAAATAT
412826 ATGTCTTCTATC
1 ATGTCTTCTATC
412838 ATGACATCTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.21, C:0.22, G:0.07, T:0.50
Consensus pattern (46 bp):
ATGTCTTCTATCCTTTCTTTCTTTGAAAATCTCTTTTCCGAAATAT
Found at i:413621 original size:24 final size:25
Alignment explanation
Indices: 413571--413628 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
413561 AGCGATATGG
*
413571 TAATATTT-TTTTTATAATTAATGT
1 TAATATTTATTGTTATAATTAATGT
**
413595 TAATATTTATTGTTATGTTTAAT-T
1 TAATATTTATTGTTATAATTAATGT
413619 TAA-ATTTATT
1 TAATATTTATT
413629 ATGAATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.23
24 12 0.40
25 11 0.37
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (25 bp):
TAATATTTATTGTTATAATTAATGT
Found at i:415214 original size:21 final size:21
Alignment explanation
Indices: 415184--415231 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
415174 GCAGGGGTAC
* *
415184 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
415205 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
415226 ATGCCA
1 ATGCCA
415232 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:415261 original size:21 final size:21
Alignment explanation
Indices: 415235--415328 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
415225 TATGCCATCT
415235 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
415256 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
415277 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* * *
415298 CCGCCA-GGTCACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
415319 CCGCAGGGTT
1 CCGCAGGGTT
415329 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.28, T:0.19
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:415900 original size:34 final size:34
Alignment explanation
Indices: 415850--415947 Score: 133
Period size: 34 Copynumber: 2.9 Consensus size: 34
415840 AAATGTTTTT
*
415850 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * * *
415884 AAAATAAAAATAATATTATTCAAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
415918 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
415948 CATTAAATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:417009 original size:128 final size:128
Alignment explanation
Indices: 416781--417143 Score: 690
Period size: 128 Copynumber: 2.8 Consensus size: 128
416771 TTACCTGATT
416781 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
416846 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
*
416909 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGTAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
416974 TGACAAAATAATGGAAGACGCGCCCCCGGGAACGCGCCTTCAAGTCCCTTGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
*
417037 TACTAATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
417102 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCA
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCA
417144 TGTGAATAGT
Statistics
Matches: 229, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 229 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
Found at i:417237 original size:8 final size:8
Alignment explanation
Indices: 417224--417264 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
417214 TCACAAGCTT
417224 TCAAATTC
1 TCAAATTC
417232 TCAAATTC
1 TCAAATTC
* *
417240 CCAAACTC
1 TCAAATTC
417248 T-AAATTC
1 TCAAATTC
417255 TCAAATTC
1 TCAAATTC
417263 TC
1 TC
417265 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:422156 original size:3 final size:3
Alignment explanation
Indices: 422148--422178 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
422138 ACATTTTAAT
422148 TAA TAA TAA TAA TAA TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
422179 CGATTTCGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:422797 original size:2 final size:2
Alignment explanation
Indices: 422790--422845 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
422780 TCACTAGTCA
422790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
422832 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
422846 TCTAGAAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:424262 original size:12 final size:12
Alignment explanation
Indices: 424245--424269 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
424235 CACATGTGAA
424245 AGAAGAGAGAGT
1 AGAAGAGAGAGT
424257 AGAAGAGAGAGT
1 AGAAGAGAGAGT
424269 A
1 A
424270 TCATAGTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.40, T:0.08
Consensus pattern (12 bp):
AGAAGAGAGAGT
Found at i:425188 original size:21 final size:21
Alignment explanation
Indices: 425162--425300 Score: 67
Period size: 21 Copynumber: 6.9 Consensus size: 21
425152 ACATAGAATT
425162 TGTCCCGAAGGACCACATATA
1 TGTCCCGAAGGACCACATATA
*
425183 TGTCCCGAAGGATCAC-----
1 TGTCCCGAAGGACCACATATA
** *
425199 --TCCTTAAGGATCACATATA
1 TGTCCCGAAGGACCACATATA
* * * * *
425218 TATTCCAAAGGACCAAATATG
1 TGTCCCGAAGGACCACATATA
* *
425239 TGTCCCGAAGAACCGCATATA
1 TGTCCCGAAGGACCACATATA
* * * *
425260 TGTTCCAAAGGATTACATATATA
1 TGTCCCGAAGGA--CCACATATA
*
425283 TATCCCGAAGGACCACAT
1 TGTCCCGAAGGACCACAT
425301 TGAACCCTCG
Statistics
Matches: 82, Mismatches: 27, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
14 12 0.15
21 55 0.67
23 15 0.18
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:430943 original size:5 final size:5
Alignment explanation
Indices: 430935--430964 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
430925 GCATACATCA
*
430935 CATAT CATAT CATAT CATAT CATAT AATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT
430965 TAAAGCATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (5 bp):
CATAT
Found at i:431458 original size:12 final size:12
Alignment explanation
Indices: 431441--431474 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
431431 ATGAATAGTG
431441 ATGAACAGTACC
1 ATGAACAGTACC
431453 ATGAACAGTACC
1 ATGAACAGTACC
*
431465 GTGAACAGTA
1 ATGAACAGTA
431475 TACCGATGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:441922 original size:18 final size:18
Alignment explanation
Indices: 441899--441949 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
441889 GTGTTCTCTG
441899 TGGTCCTTCGGGACATAA
1 TGGTCCTTCGGGACATAA
* *
441917 TGGTCCTTCGAGACATAG
1 TGGTCCTTCGGGACATAA
* *
441935 TGGTCATACGGGACA
1 TGGTCCTTCGGGACA
441950 AATTCTACGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAA
Found at i:448402 original size:16 final size:16
Alignment explanation
Indices: 448381--448451 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
448371 GGTATTACCC
448381 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
448397 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
*
448413 GACATGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
448429 GACCTATTTTTAACCT
1 GACCTGTTTTCAACCT
*
448445 AACCTGT
1 GACCTGT
448452 AAATGATCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:448742 original size:14 final size:14
Alignment explanation
Indices: 448720--448766 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
448710 TGCAAAAGAA
*
448720 AATTAATATAGTTT
1 AATTTATATAGTTT
448734 AATTTATATA----
1 AATTTATATAGTTT
448744 AA-TTATATAGTTT
1 AATTTATATAGTTT
448757 AATTTATATA
1 AATTTATATA
448767 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:448753 original size:23 final size:24
Alignment explanation
Indices: 448719--448768 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
448709 ATGCAAAAGA
448719 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
448743 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
448766 AAA
1 AAA
448769 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:449088 original size:9 final size:9
Alignment explanation
Indices: 449074--449107 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
449064 AGTAATTTAC
449074 TTTATATAG
1 TTTATATAG
449083 TTTATATA-
1 TTTATATAG
*
449091 TATATATAG
1 TTTATATAG
449100 TTTATATA
1 TTTATATA
449108 TACTATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (9 bp):
TTTATATAG
Found at i:449125 original size:20 final size:18
Alignment explanation
Indices: 449076--449114 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
449066 TAATTTACTT
449076 TATATAGTTTATATATA-
1 TATATAGTTTATATATAC
449093 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
449111 TATA
1 TATA
449115 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:449503 original size:14 final size:14
Alignment explanation
Indices: 449481--449559 Score: 74
Period size: 14 Copynumber: 5.6 Consensus size: 14
449471 TCCATTTATA
449481 TTAGGGTTTATGAT
1 TTAGGGTTTATGAT
*
449495 TTAGTGTTTAGTG-T
1 TTAGGGTTTA-TGAT
*
449509 TT-GTGGTTTA-AAGT
1 TTAG-GGTTTATGA-T
449523 TTAGGGTTTATGAT
1 TTAGGGTTTATGAT
* *
449537 TTATGATTTATGAT
1 TTAGGGTTTATGAT
449551 TTAGGGTTT
1 TTAGGGTTT
449560 CTATAAACTA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
13 1 0.02
14 46 0.90
15 4 0.08
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (14 bp):
TTAGGGTTTATGAT
Found at i:449510 original size:21 final size:21
Alignment explanation
Indices: 449481--449539 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
449471 TCCATTTATA
**
449481 TTAGGGTTTATGATTTAGTGT
1 TTAGGGTTTATGATTTAAAGT
* * *
449502 TTAGTGTTTGTGGTTTAAAGT
1 TTAGGGTTTATGATTTAAAGT
449523 TTAGGGTTTATGATTTA
1 TTAGGGTTTATGATTTA
449540 TGATTTATGA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (21 bp):
TTAGGGTTTATGATTTAAAGT
Found at i:449516 original size:28 final size:28
Alignment explanation
Indices: 449485--449559 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
449475 TTTATATTAG
* *
449485 GGTTTATGATTTAGTGTTTAGTG-TTTGT
1 GGTTTATGATTTAGGGTTTA-TGATTTAT
*
449513 GGTTTA-AAGTTTAGGGTTTATGATTTAT
1 GGTTTATGA-TTTAGGGTTTATGATTTAT
*
449541 GATTTATGATTTAGGGTTT
1 GGTTTATGATTTAGGGTTT
449560 CTATAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 3 0.08
28 35 0.90
29 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (28 bp):
GGTTTATGATTTAGGGTTTATGATTTAT
Found at i:449539 original size:7 final size:7
Alignment explanation
Indices: 449529--449553 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
449519 AAGTTTAGGG
449529 TTTATGA
1 TTTATGA
449536 TTTATGA
1 TTTATGA
449543 TTTATGA
1 TTTATGA
449550 TTTA
1 TTTA
449554 GGGTTTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TTTATGA
Found at i:449546 original size:21 final size:21
Alignment explanation
Indices: 449474--449546 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
449464 GTGCTAGTCC
449474 ATTTAT-A-TTAGGGTTTATG
1 ATTTATGATTTAGGGTTTATG
* *
449493 ATTTAGTG-TTTAGTGTTTGTG
1 ATTTA-TGATTTAGGGTTTATG
* *
449514 GTTTA-AAGTTTAGGGTTTATG
1 ATTTATGA-TTTAGGGTTTATG
449535 ATTTATGATTTA
1 ATTTATGATTTA
449547 TGATTTAGGG
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 5 0.12
20 1 0.03
21 33 0.82
22 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (21 bp):
ATTTATGATTTAGGGTTTATG
Found at i:449596 original size:49 final size:49
Alignment explanation
Indices: 449543--449650 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 49
449533 TGATTTATGA
* ** *
449543 TTTATGATTTAGGGTTTCTATAAACTATATATTTTA-TTACTTTATATAG
1 TTTATG-TATAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAG
* * *
449592 TTTATGTATAGTGTTTTTATAAACTATATAAGTAATTTATTTTATATAG
1 TTTATGTATAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAG
*
449641 TTTATATATA
1 TTTATGTATA
449651 TATATAGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
48 23 0.46
49 27 0.54
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (49 bp):
TTTATGTATAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAG
Found at i:449614 original size:48 final size:49
Alignment explanation
Indices: 449556--449650 Score: 129
Period size: 49 Copynumber: 2.0 Consensus size: 49
449546 ATGATTTAGG
** * *
449556 GTTTCTATAAACTATATATTTTA-TTACTTTATATAGTTTATGTATAGT
1 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATAGT
* *
449604 GTTTTTATAAACTATATAAGTAATTTATTTTATATAGTTTATATATA
1 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATA
449651 TATATAGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 19 0.47
49 21 0.52
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (49 bp):
GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATAGT
Found at i:449646 original size:9 final size:9
Alignment explanation
Indices: 449632--449665 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
449622 AGTAATTTAT
449632 TTTATATAG
1 TTTATATAG
449641 TTTATATA-
1 TTTATATAG
*
449649 TATATATAG
1 TTTATATAG
449658 TTTATATA
1 TTTATATA
449666 TACTATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (9 bp):
TTTATATAG
Found at i:449683 original size:20 final size:18
Alignment explanation
Indices: 449634--449672 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
449624 TAATTTATTT
449634 TATATAGTTTATATATA-
1 TATATAGTTTATATATAC
449651 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
449669 TATA
1 TATA
449673 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:449706 original size:13 final size:13
Alignment explanation
Indices: 449696--449722 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
449686 TACATATTAT
449696 ATAAAATTATTTA
1 ATAAAATTATTTA
449709 ATAAAATTATTTA
1 ATAAAATTATTTA
449722 A
1 A
449723 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:449732 original size:15 final size:14
Alignment explanation
Indices: 449696--449738 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
449686 TACATATTAT
449696 ATAAAATTATTT-A
1 ATAAAATTATTTAA
449709 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
449723 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
449738 A
1 A
449739 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:450945 original size:21 final size:21
Alignment explanation
Indices: 450916--450974 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
450906 TTTATTTATA
* **
450916 TTAGGGTTTATGATTTAGTGT
1 TTAGGGTTTATGGTTTAAAGT
* *
450937 TTAGTGTTTGTGGTTTAAAGT
1 TTAGGGTTTATGGTTTAAAGT
450958 TTAGGGTTTATGGTTTA
1 TTAGGGTTTATGGTTTA
450975 TGGTTTAAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.53
Consensus pattern (21 bp):
TTAGGGTTTATGGTTTAAAGT
Found at i:450980 original size:21 final size:20
Alignment explanation
Indices: 450916--450981 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
450906 TTTATTTATA
*
450916 TTAGGGTTTATGATTTAGTGT
1 TTAGGGTTTATGGTTTAG-GT
* * *
450937 TTAGTGTTTGTGGTTTAAAGT
1 TTAGGGTTTATGGTTT-AGGT
450958 TTAGGGTTTATGGTTTATGGT
1 TTAGGGTTTATGGTTTA-GGT
450979 TTA
1 TTA
450982 AAGTTTCTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (20 bp):
TTAGGGTTTATGGTTTAGGT
Found at i:451023 original size:49 final size:49
Alignment explanation
Indices: 450970--451078 Score: 130
Period size: 49 Copynumber: 2.2 Consensus size: 49
450960 AGGGTTTATG
* ** *
450970 GTTTATGGTTTAAAGTTTCTATAAACTATATATTTTA-CTACTTTATATA
1 GTTTAT-GTATAAAGTTTCTATAAACTATATAAGTAATCTACTTTATATA
** *
451019 GTTTATGTATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATA
1 GTTTATGTATAAAGTTTCTATAAACTATATAAGTAATCTACTTTATATA
*
451068 GTTTATATATA
1 GTTTATGTATA
451079 TATATATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 24 0.47
49 27 0.53
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (49 bp):
GTTTATGTATAAAGTTTCTATAAACTATATAAGTAATCTACTTTATATA
Found at i:451038 original size:48 final size:49
Alignment explanation
Indices: 450984--451078 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
450974 ATGGTTTAAA
** * *
450984 GTTTCTATAAACTATATATTTTA-CTACTTTATATAGTTTATGTATAGT
1 GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATAGT
*
451032 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATA
1 GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATA
451079 TATATATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 20 0.49
49 21 0.51
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (49 bp):
GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATAGT
Found at i:451513 original size:21 final size:21
Alignment explanation
Indices: 451475--451528 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
451465 TTATATTAGG
**
451475 GTTTATGATTTAGTGTTTAAT
1 GTTTATGATTTAAAGTTTAAT
*
451496 GTTTGTGATTTAAAGTTT-AT
1 GTTTATGATTTAAAGTTTAAT
*
451516 GGTTTATGGTTTA
1 -GTTTATGATTTA
451529 TGATTTAGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (21 bp):
GTTTATGATTTAAAGTTTAAT
Found at i:451593 original size:48 final size:49
Alignment explanation
Indices: 451539--451632 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
451529 TGATTTAGGA
* ** * *
451539 TTTCTATAAATTATATATTTTA-TTACTTTATATAGTTTATGTATAGTG
1 TTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATAGTG
451587 TTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATA
1 TTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATA
451633 TATATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 18 0.45
49 22 0.55
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.53
Consensus pattern (49 bp):
TTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATAGTG
Found at i:451630 original size:2 final size:2
Alignment explanation
Indices: 451625--451666 Score: 57
Period size: 2 Copynumber: 20.0 Consensus size: 2
451615 TTATATAGTT
*
451625 TA TA TA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
451667 CATGGTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 33 0.92
3 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:451677 original size:29 final size:27
Alignment explanation
Indices: 451614--451669 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
451604 AGTAATTTAC
*
451614 TTTATATAGTTTATATATATATATATA
1 TTTATATAGTTTATATATATATACATA
451641 TATATATATAGTTTATATATACTATACAT
1 T-T-TATATAGTTTATATATA-TATACAT
451670 GGTTTATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 1 0.04
29 17 0.68
30 6 0.24
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (27 bp):
TTTATATAGTTTATATATATATACATA
Found at i:451844 original size:21 final size:20
Alignment explanation
Indices: 451818--451895 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 20
451808 TTCATTTATA
*
451818 TTAGTGTTTATGGTTTAGTGT
1 TTAGGGTTTATGGTTTA-TGT
* *
451839 TTAGTGTTTATGGTTTAAAG-
1 TTAGGGTTTATGGTTT-ATGT
*
451859 TTAGGGTGTATGGTTTATGAT
1 TTAGGGTTTATGGTTTATG-T
*
451880 TTAGGGTTTAGGGTTT
1 TTAGGGTTTATGGTTT
451896 CTATAAACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.04
20 14 0.29
21 31 0.65
22 1 0.02
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (20 bp):
TTAGGGTTTATGGTTTATGT
Found at i:452030 original size:38 final size:38
Alignment explanation
Indices: 451946--452030 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
451936 TATTGTTTCT
* *
451946 ATAAACTATATAAGTAATTTACTTTATATAATATATAT
1 ATAAACTATATAAGTAAATTACTTTATATAATATATAG
* *
451984 ATAAACTATATAAAGTAAATTAC-TTATATAGTTTATAG
1 ATAAACTATAT-AAGTAAATTACTTTATATAATATATAG
452022 A-AACACTAT
1 ATAA-ACTAT
452031 GCATATTACA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 2 0.05
38 29 0.71
39 10 0.24
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (38 bp):
ATAAACTATATAAGTAAATTACTTTATATAATATATAG
Found at i:452065 original size:23 final size:23
Alignment explanation
Indices: 452039--452117 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
452029 ATGCATATTA
452039 CATTAATATACATATCATACATG
1 CATTAATATACATATCATACATG
*
452062 CATTAATA-A-ATTATACATATATG
1 CATTAATATACA-TAT-CATACATG
* *
452085 CATACATATTATACATA-CATGCATG
1 CAT---TAATATACATATCATACATG
452110 CATTAATA
1 CATTAATA
452118 AATTATATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
21 1 0.02
22 8 0.18
23 18 0.41
25 9 0.20
26 4 0.09
27 3 0.07
28 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.35
Consensus pattern (23 bp):
CATTAATATACATATCATACATG
Found at i:453427 original size:21 final size:21
Alignment explanation
Indices: 453401--453441 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
453391 CGCGAATGCA
453401 TTGCGATTTCCCAAATTCGCG
1 TTGCGATTTCCCAAATTCGCG
* *
453422 TTGCGATTTTCCTAATTCGC
1 TTGCGATTTCCCAAATTCGC
453442 AATGCGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGCG
Found at i:453447 original size:21 final size:21
Alignment explanation
Indices: 453402--453448 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
453392 GCGAATGCAT
**
453402 TGCGATTTCCCAAATTCGCGT
1 TGCGATTTCCCAAATTCGCAA
* *
453423 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTCCCAAATTCGCAA
453444 TGCGA
1 TGCGA
453449 ATACGTAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TGCGATTTCCCAAATTCGCAA
Found at i:453469 original size:20 final size:20
Alignment explanation
Indices: 453438--453624 Score: 252
Period size: 20 Copynumber: 9.3 Consensus size: 20
453428 TTTTCCTAAT
453438 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** ** *
453458 CCGCAACACGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
453479 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
453499 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
453519 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
453539 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
453559 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
*
453579 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
453599 TCTCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
453619 TCGCAA
1 TCGCAA
453625 CGAGATTCTG
Statistics
Matches: 145, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 128 0.88
21 15 0.10
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:454513 original size:24 final size:24
Alignment explanation
Indices: 454486--454539 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
454476 GTATTCGAAA
*
454486 TTTGATCTTGGTCAATTCCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
454510 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
454534 TTTGAT
1 TTTGAT
454540 GATTTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Done.