Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003251.1 Hibiscus syriacus cultivar Beakdansim tig00006834_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: 242961
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10410 original size:31 final size:31
Alignment explanation
Indices: 10372--10434 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
10362 GCTGACTGAG
10372 TTTGCAACTGTGTTTGTGACTCCATAGGGAC
1 TTTGCAACTGTGTTTGTGACTCCATAGGGAC
10403 TTTGCAACTGTGTTTGTGACTCCATAGGGAC
1 TTTGCAACTGTGTTTGTGACTCCATAGGGAC
10434 T
1 T
10435 ACCACCTCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (31 bp):
TTTGCAACTGTGTTTGTGACTCCATAGGGAC
Found at i:17486 original size:37 final size:37
Alignment explanation
Indices: 17412--17486 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
17402 TACTATAATT
* *
17412 AATTTATATATTTTATTTAAAAGTTTTAAATTCATAA
1 AATTTATATATTTTATTTAAAAGATTTAAAATCATAA
*
17449 AATTTATATAATTTTGTTTACAAA-ATTTAAAAT-ATAA
1 AATTTATAT-ATTTTATTTA-AAAGATTTAAAATCATAA
17486 A
1 A
17487 TAGGTATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 16 0.48
39 3 0.09
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (37 bp):
AATTTATATATTTTATTTAAAAGATTTAAAATCATAA
Found at i:24567 original size:18 final size:18
Alignment explanation
Indices: 24546--24602 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
24536 AAATATAATT
24546 ATATTTTATTAAATAAAA
1 ATATTTTATTAAATAAAA
* * *
24564 ATATTATAATTATAT-TAA
1 ATATT-TTATTAAATAAAA
24582 ATA-TTTATTAAAATAAAA
1 ATATTTTATT-AAATAAAA
24600 ATA
1 ATA
24603 ATGTATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 15 0.50
19 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTTTATTAAATAAAA
Found at i:24584 original size:24 final size:26
Alignment explanation
Indices: 24530--24584 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
24520 ATGCAAATGC
*
24530 AAATAAAAATATAATTATATTTTATT
1 AAATAAAAATATAATTATATTATATT
*
24556 AAATAAAAATATTA-TA-ATTATATT
1 AAATAAAAATATAATTATATTATATT
24580 AAATA
1 AAATA
24585 TTTATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 12 0.44
25 2 0.07
26 13 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AAATAAAAATATAATTATATTATATT
Found at i:24603 original size:42 final size:43
Alignment explanation
Indices: 24556--24644 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 43
24546 ATATTTTATT
* *
24556 AAATAAAAATATTA-TAATTATATTAAATATTTATTAAAATAA
1 AAATAAAAATATTATTAAGTATATTAAATACTTATTAAAATAA
** *
24598 AAAT-AATGTATTATTAAGTATATTAATTACTTATTAAAATAA
1 AAATAAAAATATTATTAAGTATATTAAATACTTATTAAAATAA
*
24640 TAATA
1 AAATA
24645 TTATTAAACT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
41 7 0.18
42 32 0.82
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (43 bp):
AAATAAAAATATTATTAAGTATATTAAATACTTATTAAAATAA
Found at i:41373 original size:2 final size:2
Alignment explanation
Indices: 41368--41393 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41358 ATATATATAT
41368 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
41394 TACTGAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42155 original size:60 final size:59
Alignment explanation
Indices: 42043--42155 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
42033 AATTATCCCG
* * * * * *
42043 ATTATAGGGTGTTGTTTTGTTGAGTTTCATATTATTGAAAGATACAAGATGATCATTCA
1 ATTATAGGGTATTGCTTTATTGAGTTCCATATTATTAAAAGATACAAAATGATCATTCA
*
42102 ATTATAGGGTATTGCTTTATTGAG-TCCATCGATTATTAAAAGTTACAAAATGAT
1 ATTATAGGGTATTGCTTTATTGAGTTCCAT--ATTATTAAAAGATACAAAATGAT
42156 AACCCGACTA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
58 4 0.09
59 21 0.47
60 20 0.44
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.41
Consensus pattern (59 bp):
ATTATAGGGTATTGCTTTATTGAGTTCCATATTATTAAAAGATACAAAATGATCATTCA
Found at i:53480 original size:20 final size:19
Alignment explanation
Indices: 53443--53603 Score: 71
Period size: 19 Copynumber: 8.3 Consensus size: 19
53433 TTAGGAACTA
*
53443 GATTTTTATGTT-GCAACCT
1 GATTTTTAT-TTAGAAACCT
*
53462 GATTTTTCATTTAGAAACCA
1 GATTTTT-ATTTAGAAACCT
* * *
53482 AATTTTT-TGTT-GTAACAT
1 GATTTTTAT-TTAGAAACCT
53500 GAGTTTTTATTTAGAAA-CT
1 GA-TTTTTATTTAGAAACCT
* *
53519 AGAGTTTTATGTT-GCAACCT
1 -GATTTTTAT-TTAGAAACCT
* *
53539 GATTTTTCATTTAGAAATCA
1 GATTTTT-ATTTAGAAACCT
** * *
53559 GATTTTTAGGTCGGAACCT
1 GATTTTTATTTAGAAACCT
* * *
53578 AATTTTTCATATAGAAACCA
1 GATTTTT-ATTTAGAAACCT
53598 GATTTT
1 GATTTT
53604 AGCCTAATTT
Statistics
Matches: 102, Mismatches: 28, Indels: 23
0.67 0.18 0.15
Matches are distributed among these distances:
18 6 0.06
19 48 0.47
20 48 0.47
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (19 bp):
GATTTTTATTTAGAAACCT
Found at i:53487 original size:39 final size:39
Alignment explanation
Indices: 53431--53603 Score: 206
Period size: 39 Copynumber: 4.5 Consensus size: 39
53421 CCCAAAATCA
* *
53431 ATTTAGGAACTAGATTTTTATGTTGCAACCTGATTTTTC
1 ATTTAGAAACCAGATTTTTATGTTGCAACCTGATTTTTC
* * *
53470 ATTTAGAAACCAAATTTTT-TGTTGTAACATGAGTTTTT-
1 ATTTAGAAACCAGATTTTTATGTTGCAACCTGA-TTTTTC
* *
53508 ATTTAGAAACTAGAGTTTTATGTTGCAACCTGATTTTTC
1 ATTTAGAAACCAGATTTTTATGTTGCAACCTGATTTTTC
* * * * *
53547 ATTTAGAAATCAGATTTTTAGGTCGGAACCTAATTTTTC
1 ATTTAGAAACCAGATTTTTATGTTGCAACCTGATTTTTC
*
53586 ATATAGAAACCAGATTTT
1 ATTTAGAAACCAGATTTT
53604 AGCCTAATTT
Statistics
Matches: 112, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
38 32 0.29
39 80 0.71
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (39 bp):
ATTTAGAAACCAGATTTTTATGTTGCAACCTGATTTTTC
Found at i:53584 original size:77 final size:77
Alignment explanation
Indices: 53431--53604 Score: 217
Period size: 77 Copynumber: 2.2 Consensus size: 77
53421 CCCAAAATCA
* * * *
53431 ATTTAGGAACTAGATTTTTATGTTGCAACCTGATTTTTCATTTAGAAACCAAATTTTTTGTTGTA
1 ATTTAGAAACTAGA-TTTTATGTTGCAACCTGATTTTTCATTTAGAAACCAAATTTTTGGTCGGA
*
53496 ACATGAGTTTTT-
65 ACATGAATTTTTC
* *
53508 ATTTAGAAACTAGAGTTTTATGTTGCAACCTGATTTTTCATTTAGAAATCAGATTTTTAGGTCGG
1 ATTTAGAAACTAGA-TTTTATGTTGCAACCTGATTTTTCATTTAGAAACCAAATTTTT-GGTCGG
*
53573 AACCT-AATTTTTC
64 AACATGAATTTTTC
* *
53586 ATATAGAAACCAGATTTTA
1 ATTTAGAAACTAGATTTTA
53605 GCCTAATTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
77 65 0.77
78 19 0.23
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (77 bp):
ATTTAGAAACTAGATTTTATGTTGCAACCTGATTTTTCATTTAGAAACCAAATTTTTGGTCGGAA
CATGAATTTTTC
Found at i:53613 original size:31 final size:31
Alignment explanation
Indices: 53575--53635 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
53565 TAGGTCGGAA
53575 CCTAATTTTTCATAT-AGAAACCAGATTTTAG
1 CCTAATTTTTCATATGA-AAACCAGATTTTAG
*
53606 CCTAATTTTTCATATGAAAACCTGATTTTA
1 CCTAATTTTTCATATGAAAACCAGATTTTA
53636 TATGTATGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.41
Consensus pattern (31 bp):
CCTAATTTTTCATATGAAAACCAGATTTTAG
Found at i:55431 original size:2 final size:2
Alignment explanation
Indices: 55424--55457 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55414 ATTTATGATA
55424 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
55458 TATGTAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56355 original size:22 final size:21
Alignment explanation
Indices: 56330--56370 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
56320 TATAAAAAAT
56330 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
56352 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
56371 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:57082 original size:10 final size:10
Alignment explanation
Indices: 57067--57092 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
57057 ACTCTAAGTT
57067 TTGAAAAATA
1 TTGAAAAATA
57077 TTGAAAAATA
1 TTGAAAAATA
57087 TTGAAA
1 TTGAAA
57093 GTTTAGGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.31
Consensus pattern (10 bp):
TTGAAAAATA
Found at i:58066 original size:31 final size:31
Alignment explanation
Indices: 58025--58084 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
58015 ATACTTATTT
* *
58025 GATTTAAAACAAATAAAAAGCAAAAGAAATG
1 GATTGAAAACAAAGAAAAAGCAAAAGAAATG
* *
58056 GATTGAAAACAAAGCAAAAGTAAAAGAAA
1 GATTGAAAACAAAGAAAAAGCAAAAGAAA
58085 GGTGTTGGAA
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:0.65, C:0.07, G:0.15, T:0.13
Consensus pattern (31 bp):
GATTGAAAACAAAGAAAAAGCAAAAGAAATG
Found at i:61218 original size:8 final size:7
Alignment explanation
Indices: 61183--61263 Score: 53
Period size: 8 Copynumber: 11.4 Consensus size: 7
61173 ACTCAAGTAT
61183 ATATTTA
1 ATATTTA
*
61190 ATA-ATA
1 ATATTTA
61196 ATTATTTA
1 A-TATTTA
61204 A-ATTTA
1 ATATTTA
61210 ATGATTTA
1 AT-ATTTA
61218 A-ATTTA
1 ATATTTA
61224 ATAATTTA
1 AT-ATTTA
*
61232 ATAATTA
1 ATATTTA
*
61239 TTATTTTA
1 ATA-TTTA
*
61247 A-CTTTA
1 ATATTTA
61253 ATGATTTA
1 AT-ATTTA
61261 ATA
1 ATA
61264 ATTATTTAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
6 20 0.35
7 12 0.21
8 25 0.44
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (7 bp):
ATATTTA
Found at i:61225 original size:28 final size:28
Alignment explanation
Indices: 61194--61580 Score: 222
Period size: 28 Copynumber: 13.9 Consensus size: 28
61184 TATTTAATAA
* *
61194 TAATTATTTAAATTTAATGATTTAAATT
1 TAATGATTTAAATTTAATGATTTAACTT
* * *
61222 TAATAATTTAATAATT-ATTATTTTAACTT
1 TAATGATTTAA-ATTTAATGA-TTTAACTT
*
61251 TAATGATTT-AA--TAATTATTTAACTT
1 TAATGATTTAAATTTAATGATTTAACTT
* *** *
61276 TAATAATTTAAAGCAAATGATTTAA-TAA
1 TAATGATTTAAATTTAATGATTTAACT-T
* * * *
61304 TAATTACTTAACTTTAATGATTTTACTT
1 TAATGATTTAAATTTAATGATTTAACTT
*
61332 TAATGATTT-AATAATAATG-TCTTAACTT
1 TAATGATTTAAAT-TTAATGAT-TTAACTT
* * * * *
61360 TAACGATTT-AATAATAATTACTTAACTA
1 TAATGATTTAAAT-TTAATGATTTAACTT
*
61388 TAATGATTTAAATTTAATGATTTAAATT
1 TAATGATTTAAATTTAATGATTTAACTT
* *
61416 TAATGATTT-AATAATAATTATTTAACTT
1 TAATGATTTAAAT-TTAATGATTTAACTT
* * *
61444 TAATGATTTAAATTAAATAATTTAA-TAA
1 TAATGATTTAAATTTAATGATTTAACT-T
* * * *
61472 TAATTACTTAACTTTAATGATTTAATTT
1 TAATGATTTAAATTTAATGATTTAACTT
* * * * *
61500 TAATTATTT-AATAATAATTACTTGACTT
1 TAATGATTTAAAT-TTAATGATTTAACTT
* * * *
61528 TAATAATTTAATAATT-ATTATTTAATTT
1 TAATGATTTAA-ATTTAATGATTTAACTT
* *
61556 TAATGATTTAACTTTAATAATTTAA
1 TAATGATTTAAATTTAATGATTTAA
61581 TAATAGTAAA
Statistics
Matches: 277, Mismatches: 62, Indels: 40
0.73 0.16 0.11
Matches are distributed among these distances:
25 17 0.06
26 6 0.02
27 13 0.05
28 212 0.77
29 28 0.10
30 1 0.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (28 bp):
TAATGATTTAAATTTAATGATTTAACTT
Found at i:61412 original size:8 final size:8
Alignment explanation
Indices: 61388--61427 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
61378 TACTTAACTA
61388 TAATGATT
1 TAATGATT
61396 TAA--ATT
1 TAATGATT
61402 TAATGATT
1 TAATGATT
61410 TAA--ATT
1 TAATGATT
61416 TAATGATT
1 TAATGATT
61424 TAAT
1 TAAT
61428 AATAATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 12 0.43
8 16 0.57
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (8 bp):
TAATGATT
Found at i:61539 original size:42 final size:42
Alignment explanation
Indices: 61243--61581 Score: 321
Period size: 42 Copynumber: 8.1 Consensus size: 42
61233 TAATTATTAT
* * *
61243 TTTAACTTTAATGA-TT--TAATAATTATTTAACTTTAATAA
1 TTTAATTTTAATGATTTAATAATAATTACTTAACTTTAATGA
****
61282 TTTAAAGCAAATGATTTAATAATAATTACTTAACTTTAATGA
1 TTTAATTTTAATGATTTAATAATAATTACTTAACTTTAATGA
* * *
61324 TTTTACTTTAATGATTTAATAATAATGT-CTTAACTTTAACGA
1 TTTAATTTTAATGATTTAATAATAAT-TACTTAACTTTAATGA
** * * * * *
61366 TTTAATAATAATTACTTAACT-ATAATGATTTAAATTTAATGA
1 TTTAATTTTAATGATTTAA-TAATAATTACTTAACTTTAATGA
* *
61408 TTTAAATTTAATGATTTAATAATAATTATTTAACTTTAATGA
1 TTTAATTTTAATGATTTAATAATAATTACTTAACTTTAATGA
* * *
61450 TTTAAATTAAATAATTTAATAATAATTACTTAACTTTAATGA
1 TTTAATTTTAATGATTTAATAATAATTACTTAACTTTAATGA
* * *
61492 TTTAATTTTAATTATTTAATAATAATTACTTGACTTTAATAA
1 TTTAATTTTAATGATTTAATAATAATTACTTAACTTTAATGA
* * ** * * *
61534 TTTAATAATT-ATTATTTAATTTTAATGATTTAACTTTAATAA
1 TTTAAT-TTTAATGATTTAATAATAATTACTTAACTTTAATGA
61576 TTTAAT
1 TTTAAT
61582 AATAGTAAAG
Statistics
Matches: 249, Mismatches: 43, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
39 10 0.04
40 2 0.01
41 1 0.00
42 232 0.93
43 4 0.02
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (42 bp):
TTTAATTTTAATGATTTAATAATAATTACTTAACTTTAATGA
Found at i:61564 original size:14 final size:14
Alignment explanation
Indices: 61194--61581 Score: 185
Period size: 14 Copynumber: 27.9 Consensus size: 14
61184 TATTTAATAA
* *
61194 TAATTATTTAAATT
1 TAATGATTTAATTT
*
61208 TAATGATTTAAATT
1 TAATGATTTAATTT
* *
61222 TAATAATTTAATAAT
1 TAATGATTTAAT-TT
* *
61237 T-ATTATTTTAACTT
1 TAATGA-TTTAATTT
61251 TAATGATTTAA---
1 TAATGATTTAATTT
* *
61262 TAATTATTTAACTT
1 TAATGATTTAATTT
* ***
61276 TAATAATTTAAAGC
1 TAATGATTTAATTT
* **
61290 AAATGATTTAATAA
1 TAATGATTTAATTT
* * *
61304 TAATTACTTAACTT
1 TAATGATTTAATTT
* *
61318 TAATGATTTTACTT
1 TAATGATTTAATTT
**
61332 TAATGATTTAATAA
1 TAATGATTTAATTT
*
61346 TAATG-TCTTAACTT
1 TAATGAT-TTAATTT
* **
61360 TAACGATTTAATAA
1 TAATGATTTAATTT
* * * *
61374 TAATTACTTAACTA
1 TAATGATTTAATTT
*
61388 TAATGATTTAAATT
1 TAATGATTTAATTT
*
61402 TAATGATTTAAATT
1 TAATGATTTAATTT
**
61416 TAATGATTTAATAA
1 TAATGATTTAATTT
* *
61430 TAATTATTTAACTT
1 TAATGATTTAATTT
*
61444 TAATGATTTAAATT
1 TAATGATTTAATTT
* * **
61458 AAATAATTTAATAA
1 TAATGATTTAATTT
* * *
61472 TAATTACTTAACTT
1 TAATGATTTAATTT
61486 TAATGATTTAATTT
1 TAATGATTTAATTT
* **
61500 TAATTATTTAATAA
1 TAATGATTTAATTT
* * * *
61514 TAATTACTTGACTT
1 TAATGATTTAATTT
* *
61528 TAATAATTTAATAAT
1 TAATGATTTAAT-TT
*
61543 T-ATTATTTAATTT
1 TAATGATTTAATTT
*
61556 TAATGATTTAACTT
1 TAATGATTTAATTT
*
61570 TAATAATTTAAT
1 TAATGATTTAAT
61582 AATAGTAAAG
Statistics
Matches: 275, Mismatches: 89, Indels: 20
0.72 0.23 0.05
Matches are distributed among these distances:
11 10 0.04
13 3 0.01
14 249 0.91
15 13 0.05
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (14 bp):
TAATGATTTAATTT
Found at i:63974 original size:173 final size:173
Alignment explanation
Indices: 63685--64026 Score: 666
Period size: 173 Copynumber: 2.0 Consensus size: 173
63675 ATAAAATGAT
63685 CCCTAATTACTATTTGGTTCTCAACATTTTCAAACTTTGTAATTTAATCCCTAAATTTATAAATT
1 CCCTAATTACTATTTGGTTCTCAACATTTTCAAACTTTGTAATTTAATCCCTAAATTTATAAATT
* *
63750 CTTGCAAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATACCAACTTTTTATA
66 CTTGAAAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATACCAACTTTTAATA
63815 ATTTACTCTTATTCCTTAAATTCCTCAAATTTTACAAAACAAA
131 ATTTACTCTTATTCCTTAAATTCCTCAAATTTTACAAAACAAA
63858 CCCTAATTACTATTTGGTTCTCAACATTTTCAAACTTTGTAATTTAATCCCTAAATTTATAAATT
1 CCCTAATTACTATTTGGTTCTCAACATTTTCAAACTTTGTAATTTAATCCCTAAATTTATAAATT
63923 CTTGAAAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATACCAACTTTTAATA
66 CTTGAAAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATACCAACTTTTAATA
63988 ATTTACTCTTATTCCTTAAATTCCTCAAATTTTACAAAA
131 ATTTACTCTTATTCCTTAAATTCCTCAAATTTTACAAAA
64027 TGGTCCCTAA
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 167 1.00
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.39
Consensus pattern (173 bp):
CCCTAATTACTATTTGGTTCTCAACATTTTCAAACTTTGTAATTTAATCCCTAAATTTATAAATT
CTTGAAAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATACCAACTTTTAATA
ATTTACTCTTATTCCTTAAATTCCTCAAATTTTACAAAACAAA
Found at i:64783 original size:30 final size:30
Alignment explanation
Indices: 64747--64807 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
64737 AAATTGTGTT
64747 AAAGACGCCGAGAGATCCAACCTTCCATGC
1 AAAGACGCCGAGAGATCCAACCTTCCATGC
* * * *
64777 AAAGACGTCGAGAGCTCCAAGCTTCCGTGC
1 AAAGACGCCGAGAGATCCAACCTTCCATGC
64807 A
1 A
64808 CATCTGCTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (30 bp):
AAAGACGCCGAGAGATCCAACCTTCCATGC
Found at i:66697 original size:118 final size:119
Alignment explanation
Indices: 66568--66794 Score: 305
Period size: 118 Copynumber: 1.9 Consensus size: 119
66558 AAAAACATGA
* * * *
66568 TTAAATTTAATTAAAAATTGAATGAATAAATAAGAGAAATGGGAAAGGAGGGTCAAAA-CTAAAC
1 TTAAATTTAATTAAAAATT-AATGAATAAATAAGAGAAATGGAAAAAGAGGATCAAAAGCTAAAA
* * * *
66632 ATTTTATGAAATTATAAAAATTAG-GGTCTTAATTATAAATATAAAAAAAATTAG
65 ACTTTATAAAATTATAAAAATTAGAGATCTTAATTACAAATATAAAAAAAATTAG
* * * **
66686 TTAAATTTAATTCAAAATTAATGAATTAATAGGAGAAATGGAAAAAGATTATCAAAAGCTAAAAA
1 TTAAATTTAATTAAAAATTAATGAATAAATAAGAGAAATGGAAAAAGAGGATCAAAAGCTAAAAA
*
66751 CTTTATAAAATTATAAAAATTAGAGATCTTAATTACAAGTATAA
66 CTTTATAAAATTATAAAAATTAGAGATCTTAATTACAAATATAA
66795 TAAAGTAGGA
Statistics
Matches: 93, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
117 31 0.33
118 45 0.48
119 17 0.18
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.30
Consensus pattern (119 bp):
TTAAATTTAATTAAAAATTAATGAATAAATAAGAGAAATGGAAAAAGAGGATCAAAAGCTAAAAA
CTTTATAAAATTATAAAAATTAGAGATCTTAATTACAAATATAAAAAAAATTAG
Found at i:71387 original size:21 final size:21
Alignment explanation
Indices: 71346--71387 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
71336 TCATGTAATA
**
71346 TTTTATAGATATTTAATTTAT
1 TTTTATAGATATAAAATTTAT
71367 TTTTATAGAT-TAAAATATTAT
1 TTTTATAGATATAAAAT-TTAT
71388 ATATTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTTATAGATATAAAATTTAT
Found at i:84040 original size:6 final size:6
Alignment explanation
Indices: 84032--84065 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
84022 AGAGGAGGGG
*
84032 GAGAAG GAGAAT GAGAAT GAGAAT GAGAAT GAGA
1 GAGAAT GAGAAT GAGAAT GAGAAT GAGAAT GAGA
84066 GAGGGAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.38, T:0.12
Consensus pattern (6 bp):
GAGAAT
Found at i:87215 original size:2 final size:2
Alignment explanation
Indices: 87208--87283 Score: 134
Period size: 2 Copynumber: 38.0 Consensus size: 2
87198 GTTGCAGGAA
87208 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
**
87250 AT AT AT AT AT AT GC 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
87284 GCATGTGGAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:89006 original size:15 final size:13
Alignment explanation
Indices: 88986--89023 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
88976 CTTTCTTAGC
88986 ATTATCATATATATT
1 ATTATCAT-TAT-TT
89001 ATTATCATTATTT
1 ATTATCATTATTT
89014 A-TATCATTAT
1 ATTATCATTAT
89024 CATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 3 0.13
15 8 0.35
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATCATTATTT
Found at i:89088 original size:29 final size:29
Alignment explanation
Indices: 89055--89121 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
89045 ATCTTGTATT
89055 TATCATTTCTGCATATCATATAAAACATA
1 TATCATTTCTGCATATCATATAAAACATA
89084 TATCATTTCTGCATATCATATAAAACATA
1 TATCATTTCTGCATATCATATAAAACATA
89113 TATCATTTC
1 TATCATTTC
89122 ACCTAGAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.40
Consensus pattern (29 bp):
TATCATTTCTGCATATCATATAAAACATA
Found at i:89188 original size:2 final size:2
Alignment explanation
Indices: 89181--89218 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
89171 AATCAAAAAC
89181 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
89219 TTGTTATTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89355 original size:23 final size:23
Alignment explanation
Indices: 89321--89378 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
89311 CTCGTATAAA
* *
89321 TGCACCGAAGTGCCGCATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
89344 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
89367 TGCATCGTAGTG
1 TGCACCGTAGTG
89379 TCATATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:100891 original size:31 final size:31
Alignment explanation
Indices: 100837--100898 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
100827 TACAGTCTCC
* * *
100837 CAATATTTAGTTTGTTTGTAATATGGTCCCT
1 CAATATTTAGTCTATTTGCAATATGGTCCCT
100868 CAATATTTAGTCTATTTGCAATATGGTCCCT
1 CAATATTTAGTCTATTTGCAATATGGTCCCT
100899 GACCGTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (31 bp):
CAATATTTAGTCTATTTGCAATATGGTCCCT
Found at i:104099 original size:17 final size:17
Alignment explanation
Indices: 104077--104109 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
104067 AACCCTCACT
*
104077 GATTTTAGTAGTGTTAG
1 GATTTTAGAAGTGTTAG
104094 GATTTTAGAAGTGTTA
1 GATTTTAGAAGTGTTA
104110 TCCGGATGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (17 bp):
GATTTTAGAAGTGTTAG
Found at i:108255 original size:64 final size:64
Alignment explanation
Indices: 108154--108283 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
108144 CAAATCCTAT
108154 CACTAGACCTCCTCGATCTCAAATAAATTCAAGTATCACGGCCCATTTTGCCAAAAGAAAAATA
1 CACTAGACCTCCTCGATCTCAAATAAATTCAAGTATCACGGCCCATTTTGCCAAAAGAAAAATA
108218 CACTAGACCTCCTCGATCTCAAATAAATTCAAGTATCACGGCCCATTTTGCCAAAAGAAAAATA
1 CACTAGACCTCCTCGATCTCAAATAAATTCAAGTATCACGGCCCATTTTGCCAAAAGAAAAATA
108282 CA
1 CA
108284 TATATTACAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (64 bp):
CACTAGACCTCCTCGATCTCAAATAAATTCAAGTATCACGGCCCATTTTGCCAAAAGAAAAATA
Found at i:110011 original size:19 final size:20
Alignment explanation
Indices: 109979--110025 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
109969 AATAAGTGTC
*
109979 TAAACTATAATATTTT-TTT
1 TAAACGATAATATTTTCTTT
*
109998 TAAACGATACTATTTTCTTT
1 TAAACGATAATATTTTCTTT
*
110018 TGAACGAT
1 TAAACGAT
110026 TCAGGTTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (20 bp):
TAAACGATAATATTTTCTTT
Found at i:111080 original size:36 final size:36
Alignment explanation
Indices: 111033--111107 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
111023 ACAGAGGTAC
111033 TTACTGAAAATATTTAACTTTGGTCAGTAAAGTTAT
1 TTACTGAAAATATTTAACTTTGGTCAGTAAAGTTAT
111069 TTACTGAAAATATTTAACTTTGGTCAGTAAAGTTAT
1 TTACTGAAAATATTTAACTTTGGTCAGTAAAGTTAT
111105 TTA
1 TTA
111108 TCTTTGTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (36 bp):
TTACTGAAAATATTTAACTTTGGTCAGTAAAGTTAT
Found at i:118743 original size:18 final size:18
Alignment explanation
Indices: 118720--118755 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
118710 TGTATCACAA
118720 CTGGCTGCAGATAAAAGG
1 CTGGCTGCAGATAAAAGG
118738 CTGGCTGCAGATAAAAGG
1 CTGGCTGCAGATAAAAGG
118756 ATAACATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (18 bp):
CTGGCTGCAGATAAAAGG
Found at i:122512 original size:17 final size:19
Alignment explanation
Indices: 122478--122515 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
122468 TAAATTGTTG
122478 TTAAATTTTATCAAATAAT
1 TTAAATTTTATCAAATAAT
122497 TTAAATTTT-T-AAATAAT
1 TTAAATTTTATCAAATAAT
122514 TT
1 TT
122516 TGAGTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAATTTTATCAAATAAT
Found at i:124191 original size:158 final size:158
Alignment explanation
Indices: 123976--124292 Score: 589
Period size: 158 Copynumber: 2.0 Consensus size: 158
123966 ATAAAGTTTG
*
123976 TTACCTACTTCAATTTGCTTCTTGGTCATATGCATAAGAAATAAACCTATAAGCGTGCCACTTTT
1 TTACCTACTTCAATTTGCTTATTGGTCATATGCATAAGAAATAAACCTATAAGCGTGCCACTTTT
* *
124041 TTCAAGTAGCATCAATAGAGTTATTTGGACACACAAAGTGCTCAATTCCTGTAACACCATAAATC
66 TTCAAGTAGCATCAATAGAGTTATTTGGACACAAAAAGTGCTCAATTCCTGTAACACCATAAACC
124106 AGTACGACACACAGTCAATCGAACAGAA
131 AGTACGACACACAGTCAATCGAACAGAA
124134 TTACCTACTTCAATTTGCTTATTGGTCATATGCATAAGAAATAAACCTATAAGCGTGCCACTTTT
1 TTACCTACTTCAATTTGCTTATTGGTCATATGCATAAGAAATAAACCTATAAGCGTGCCACTTTT
*
124199 TTCAAGTAGGATCAATAGAGTTATTTGGACACAAAAAGTGCTCAATTCCTGTAACACCATAAACC
66 TTCAAGTAGCATCAATAGAGTTATTTGGACACAAAAAGTGCTCAATTCCTGTAACACCATAAACC
*
124264 AGTACGACACACAGTCAATCGATCAGAA
131 AGTACGACACACAGTCAATCGAACAGAA
124292 T
1 T
124293 GCCACACGGA
Statistics
Matches: 154, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 154 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (158 bp):
TTACCTACTTCAATTTGCTTATTGGTCATATGCATAAGAAATAAACCTATAAGCGTGCCACTTTT
TTCAAGTAGCATCAATAGAGTTATTTGGACACAAAAAGTGCTCAATTCCTGTAACACCATAAACC
AGTACGACACACAGTCAATCGAACAGAA
Found at i:125759 original size:25 final size:25
Alignment explanation
Indices: 125729--125779 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
125719 GCTTTCTCCT
125729 ATTTCCTTCACTAAACAAAATGAGA
1 ATTTCCTTCACTAAACAAAATGAGA
125754 ATTTCCTTCACTAAACAAAATGAGA
1 ATTTCCTTCACTAAACAAAATGAGA
125779 A
1 A
125780 AATGGATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (25 bp):
ATTTCCTTCACTAAACAAAATGAGA
Found at i:127100 original size:26 final size:28
Alignment explanation
Indices: 127040--127101 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
127030 GAGTATTGCT
*
127040 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
127071 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
127097 GAGCT
1 GAGCT
127102 TAAAAGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:129205 original size:18 final size:19
Alignment explanation
Indices: 129160--129206 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
129150 ATATATGTTC
*
129160 ATAGTACAAACTCAAGCTA
1 ATAGTACAAACACAAGCTA
*
129179 AGCAGTACAAACACAAGC-A
1 A-TAGTACAAACACAAGCTA
129198 ATAGTACAA
1 ATAGTACAA
129207 TGTCTAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.29
19 3 0.12
20 14 0.58
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (19 bp):
ATAGTACAAACACAAGCTA
Found at i:137113 original size:18 final size:18
Alignment explanation
Indices: 137090--137134 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
137080 TCTCGACCCT
137090 AGGATAATGTTGATCTAG
1 AGGATAATGTTGATCTAG
*
137108 AGGATAATCTTGATCTAG
1 AGGATAATGTTGATCTAG
137126 AGGATAATG
1 AGGATAATG
137135 CTGTTAGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.31
Consensus pattern (18 bp):
AGGATAATGTTGATCTAG
Found at i:138561 original size:11 final size:12
Alignment explanation
Indices: 138531--138564 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
138521 ATTATTTAAA
138531 CGGGTATTGGGT
1 CGGGTATTGGGT
138543 CGGGTATTGGGT
1 CGGGTATTGGGT
138555 C-GGTATTGGG
1 CGGGTATTGGG
138565 CTGGGAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.09, C:0.09, G:0.50, T:0.32
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:138686 original size:13 final size:13
Alignment explanation
Indices: 138670--138702 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
138660 TTTAATATTT
138670 ATCGGGTCGGGTA
1 ATCGGGTCGGGTA
*
138683 ATCGGGGCGGGTA
1 ATCGGGTCGGGTA
138696 ATCGGGT
1 ATCGGGT
138703 AATCGGGGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.48, T:0.21
Consensus pattern (13 bp):
ATCGGGTCGGGTA
Found at i:142218 original size:2 final size:2
Alignment explanation
Indices: 142211--142249 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
142201 ATTTTTGTTT
142211 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
142250 TATGACAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:144115 original size:27 final size:27
Alignment explanation
Indices: 144085--144162 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
144075 CTCAAATTGA
144085 TGCTGGCTAGGCCGGTGTTCGAATGGC
1 TGCTGGCTAGGCCGGTGTTCGAATGGC
144112 TGCTGGCTAGGCCGGTGTTCGAATGGC
1 TGCTGGCTAGGCCGGTGTTCGAATGGC
* * *
144139 TGCTGGGTGGGCCGGTGATCGAAT
1 TGCTGGCTAGGCCGGTGTTCGAAT
144163 TGCGGGTGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.12, C:0.21, G:0.42, T:0.26
Consensus pattern (27 bp):
TGCTGGCTAGGCCGGTGTTCGAATGGC
Found at i:144178 original size:27 final size:27
Alignment explanation
Indices: 144093--144289 Score: 243
Period size: 27 Copynumber: 7.3 Consensus size: 27
144083 GATGCTGGCT
* * * * **
144093 AGGCCGGTGTTCGAATGGCTGCTGGCT
1 AGGCCGGTGATCGAATTGCGGGTGGGG
* * * *
144120 AGGCCGGTGTTCGAATGGCTGCTGGGTG
1 AGGCCGGTGATCGAATTGCGGGTGGG-G
*
144148 -GGCCGGTGATCGAATTGCGGGTGAGG
1 AGGCCGGTGATCGAATTGCGGGTGGGG
144174 AGGCCGGTGATCGAATTGCGGGTGGGG
1 AGGCCGGTGATCGAATTGCGGGTGGGG
*
144201 AGGCCGGTGATCAAATTGCGGGTGGGG
1 AGGCCGGTGATCGAATTGCGGGTGGGG
*
144228 AGGCCGGTGATCAAATTGCGGGTGGGG
1 AGGCCGGTGATCGAATTGCGGGTGGGG
* *
144255 AGGCCGGTAATCGAATTGCTGGTGGGG
1 AGGCCGGTGATCGAATTGCGGGTGGGG
144282 AGGCCGGT
1 AGGCCGGT
144290 TGTTATAATG
Statistics
Matches: 156, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
26 1 0.01
27 155 0.99
ACGTcount: A:0.15, C:0.17, G:0.47, T:0.21
Consensus pattern (27 bp):
AGGCCGGTGATCGAATTGCGGGTGGGG
Found at i:144778 original size:2 final size:2
Alignment explanation
Indices: 144771--144802 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
144761 TCTTCTAATT
144771 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
144803 GGATGTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:150716 original size:37 final size:37
Alignment explanation
Indices: 150666--150739 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
150656 AAGTTTATCC
* *
150666 GTTTTATATTATTATAAGTTTGTTTCCAACATAAAAT
1 GTTTTATACTATTATAAGTTCGTTTCCAACATAAAAT
150703 GTTTTATACTATTATAAGTTCGTTTCCAACATAAAAT
1 GTTTTATACTATTATAAGTTCGTTTCCAACATAAAAT
150740 CCTCCATATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (37 bp):
GTTTTATACTATTATAAGTTCGTTTCCAACATAAAAT
Found at i:155358 original size:2 final size:2
Alignment explanation
Indices: 155351--155377 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
155341 GACATAGAAC
155351 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
155378 CCAGTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:156405 original size:31 final size:31
Alignment explanation
Indices: 156347--156438 Score: 84
Period size: 31 Copynumber: 3.0 Consensus size: 31
156337 ATTTGAATCC
** *
156347 TAAATTTTAAATAAAATAT-ACATTTAATTTT
1 TAAATTTTTGATAAAATATCA-AATTAATTTT
*
156378 TAAATTTTTGATAAAATATCAAATTAA-TTC
1 TAAATTTTTGATAAAATATCAAATTAATTTT
*
156408 TAAATTTTTAGACTAAAAAATC-AA-TAATTTT
1 TAAATTTTT-GA-TAAAATATCAAATTAATTTT
156439 AATTGAATTC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
30 14 0.27
31 28 0.55
32 9 0.18
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (31 bp):
TAAATTTTTGATAAAATATCAAATTAATTTT
Found at i:158151 original size:31 final size:31
Alignment explanation
Indices: 158116--158183 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
158106 TTTATTTTGA
*
158116 AATTAGATCACTCATAT-GTACTCTTATTAAT
1 AATTAGATCACTCAT-TCGTACTCTTACTAAT
* * *
158147 AATTAGGTGACTCATTCGTAGTCTTACTAAT
1 AATTAGATCACTCATTCGTACTCTTACTAAT
*
158178 AGTTAG
1 AATTAG
158184 TTCATTTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (31 bp):
AATTAGATCACTCATTCGTACTCTTACTAAT
Found at i:158571 original size:21 final size:21
Alignment explanation
Indices: 158542--158582 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
158532 GTGAATCACA
*
158542 TTGCAATTTTCTAAATTCGCG
1 TTGCAATTTTCCAAATTCGCG
*
158563 TTGCGATTTTCCAAATTCGC
1 TTGCAATTTTCCAAATTCGC
158583 AACGCGAATT
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:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (21 bp):
TTGCAATTTTCCAAATTCGCG
Found at i:158589 original size:21 final size:21
Alignment explanation
Indices: 158547--158589 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
158537 TCACATTGCA
* ***
158547 ATTTTCTAAATTCGCGTTGCG
1 ATTTTCCAAATTCGCAACGCG
158568 ATTTTCCAAATTCGCAACGCG
1 ATTTTCCAAATTCGCAACGCG
158589 A
1 A
158590 ATTTATAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (21 bp):
ATTTTCCAAATTCGCAACGCG
Found at i:158622 original size:20 final size:20
Alignment explanation
Indices: 158599--158637 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
158589 AATTTATAAA
158599 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
158619 TCGCAATACAGAAGTCAAA
1 TCGCAACACAGAAGTCAAA
158638 GCGCATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:158797 original size:26 final size:26
Alignment explanation
Indices: 158768--158827 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
158758 ACATCCGTCC
*
158768 CCATCTCTGACGAAATTCGTCTATCT
1 CCATCTCTGACGAAATCCGTCTATCT
158794 CCATCTCTGACGAAATCCGTCTATCT
1 CCATCTCTGACGAAATCCGTCTATCT
158820 CCATCTCT
1 CCATCTCT
158828 CATAGCAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.22, C:0.35, G:0.10, T:0.33
Consensus pattern (26 bp):
CCATCTCTGACGAAATCCGTCTATCT
Found at i:159237 original size:20 final size:19
Alignment explanation
Indices: 159184--159237 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
159174 AAATCGCAAC
*
159184 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCATT
* *
159203 GCGATTTTCATTTTCGCATT
1 GCGAATTT-AGTTTCGCATT
159223 GCGAATTTAAGTTTC
1 GCGAATTT-AGTTTC
159238 AGAAGCTACT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCATT
Found at i:161027 original size:63 final size:63
Alignment explanation
Indices: 160928--161047 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 63
160918 AGGTTGGTAC
* *
160928 TTTACGTGAAGACAGTGGTGCGCTACGTGACAAGGTA-CGATCTTTACATGGTGAGGTGGATAT
1 TTTACGCGAAGACAATGGTGCGCTACGTGACAAGGTATCGA-CTTTACATGGTGAGGTGGATAT
* *** * *
160991 TTTACGCGATGACAATGGTGCGCTACGTGGTGAGGTATCTACTTTACGTGGTGAGGT
1 TTTACGCGAAGACAATGGTGCGCTACGTGACAAGGTATCGACTTTACATGGTGAGGT
161048 AGCCGCTCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 46 0.96
64 2 0.04
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.30
Consensus pattern (63 bp):
TTTACGCGAAGACAATGGTGCGCTACGTGACAAGGTATCGACTTTACATGGTGAGGTGGATAT
Found at i:161059 original size:21 final size:21
Alignment explanation
Indices: 161013--161061 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
161003 CAATGGTGCG
* *
161013 CTACGTGGTGAGGTATCTACT
1 CTACGTGGTGAGGTAGCCACT
* *
161034 TTACGTGGTGAGGTAGCCGCT
1 CTACGTGGTGAGGTAGCCACT
161055 CTACGTG
1 CTACGTG
161062 AGATTGTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.20, G:0.33, T:0.31
Consensus pattern (21 bp):
CTACGTGGTGAGGTAGCCACT
Found at i:161398 original size:21 final size:21
Alignment explanation
Indices: 161374--161441 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
161364 CCTATCATTA
161374 AAGAGGCCCCTCTCATCGTTC
1 AAGAGGCCCCTCTCATCGTTC
* *
161395 AAGAGGCCCTCTCCCA-CAATTC
1 AAGAGGCCC-CTCTCATC-GTTC
*
161417 AAGAGGCCCCTGTCATCGTTC
1 AAGAGGCCCCTCTCATCGTTC
161438 AAGA
1 AAGA
161442 TGTCTCTCCC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGAGGCCCCTCTCATCGTTC
Found at i:161462 original size:42 final size:43
Alignment explanation
Indices: 161344--161463 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 43
161334 GATGCACATG
* * * *
161344 TCATCGCTCAAGAGG-CATCTCCTATC-ATTAAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCTCTCCCA-CAATTCAAGAGGCCCCTC
*
161386 TCATCGTTCAAGAGGCCCTCTCCCACAATTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCTCTCCCACAATTCAAGAGGCCCCTC
* * **
161429 TCATCGTTCAAGATG-TCTCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCTCTCCCACAATTCAAGAG
161464 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 32 0.48
43 35 0.52
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (43 bp):
TCATCGTTCAAGAGGCCCTCTCCCACAATTCAAGAGGCCCCTC
Found at i:162909 original size:37 final size:36
Alignment explanation
Indices: 162853--162973 Score: 109
Period size: 37 Copynumber: 3.6 Consensus size: 36
162843 AAAAGTTGAT
*
162853 TTGTTTAATTGATGAGTAAATAAGAATTATTTTTTGC
1 TTGTTTAATTGATGTGTAAATAAG-ATTATTTTTTGC
* *
162890 TTGTTTAATTGATTTGT-AA-AAG-----TTTAT--
1 TTGTTTAATTGATGTGTAAATAAGATTATTTTTTGC
162917 TTGTTTAATTGATGTGTAAATAAGACTTATTTTTTGC
1 TTGTTTAATTGATGTGTAAATAAGA-TTATTTTTTGC
*
162954 TAT-TTTAATTGATTTGTAAA
1 T-TGTTTAATTGATGTGTAAA
162974 AGTTGATTTG
Statistics
Matches: 67, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
27 16 0.24
28 2 0.03
29 7 0.10
35 7 0.10
36 2 0.03
37 32 0.48
38 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (36 bp):
TTGTTTAATTGATGTGTAAATAAGATTATTTTTTGC
Found at i:162936 original size:64 final size:64
Alignment explanation
Indices: 162826--162985 Score: 259
Period size: 64 Copynumber: 2.5 Consensus size: 64
162816 GTTTAATTGA
*
162826 ATTTTACATTGATTTTTAAAAGTTGATTTGTTTAATTGATGAGTAAATAAGAATTATTTTTTGCT
1 ATTTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGTAAATAAGAATTATTTTTTGCT
* * *
162891 -TGTTTAATTGATTTGTAAAAGTTTATTTGTTTAATTGATGTGTAAATAAGACTTATTTTTTGCT
1 AT-TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGTAAATAAGAATTATTTTTTGCT
162955 ATTTTAATTGATTTGTAAAAGTTGATTTGTT
1 ATTTTAATTGATTTGTAAAAGTTGATTTGTT
162986 GTTTATTCAA
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
64 83 0.94
65 5 0.06
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.53
Consensus pattern (64 bp):
ATTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGTAAATAAGAATTATTTTTTGCT
Found at i:165788 original size:24 final size:24
Alignment explanation
Indices: 165754--165807 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
165744 CTGAAACATC
165754 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * * *
165778 ATCAAAGTCCGGGTATTGACTAAT
1 ATCAAAATCCGAGTATTGACCAAG
165802 ATCAAA
1 ATCAAA
165808 TTTCAAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:166779 original size:40 final size:41
Alignment explanation
Indices: 166735--166833 Score: 130
Period size: 40 Copynumber: 2.4 Consensus size: 41
166725 TTGTTAAATT
166735 AAATTCGTGTTGCGAATTCGAAAATC-GAGTTGCGAATTTG
1 AAATTCGTGTTGCGAATTCGAAAATCAGAGTTGCGAATTTG
* * * *
166775 AAATTC-AGTTGCGAATTTGAAATTCAGTGTTGCGAATTTG
1 AAATTCGTGTTGCGAATTCGAAAATCAGAGTTGCGAATTTG
*
166815 AAATTCAGTGTTGCAAATT
1 AAATTC-GTGTTGCGAATT
166834 TGACTTCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
39 16 0.32
40 25 0.50
42 9 0.18
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.35
Consensus pattern (41 bp):
AAATTCGTGTTGCGAATTCGAAAATCAGAGTTGCGAATTTG
Found at i:166784 original size:19 final size:19
Alignment explanation
Indices: 166743--166823 Score: 117
Period size: 19 Copynumber: 4.1 Consensus size: 19
166733 TTAAATTCGT
* *
166743 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTC-A
166763 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
166782 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
166801 GTGTTGCGAATTTGAAATTCA
1 --GTTGCGAATTTGAAATTCA
166822 GT
1 GT
166824 GTTGCAAATT
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
19 22 0.39
20 16 0.28
21 19 0.33
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:166808 original size:21 final size:21
Alignment explanation
Indices: 166735--166836 Score: 140
Period size: 21 Copynumber: 5.0 Consensus size: 21
166725 TTGTTAAATT
*
166735 AAATTC-GTGTTGCGAATTCG
1 AAATTCAGTGTTGCGAATTTG
* *
166755 AAAATC-GAGTTGCGAATTTG
1 AAATTCAGTGTTGCGAATTTG
166775 AAATTCA--GTTGCGAATTTG
1 AAATTCAGTGTTGCGAATTTG
166794 AAATTCAGTGTTGCGAATTTG
1 AAATTCAGTGTTGCGAATTTG
*
166815 AAATTCAGTGTTGCAAATTTG
1 AAATTCAGTGTTGCGAATTTG
166836 A
1 A
166837 CTTCTTTGTT
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
19 19 0.26
20 22 0.30
21 33 0.45
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (21 bp):
AAATTCAGTGTTGCGAATTTG
Found at i:166882 original size:20 final size:21
Alignment explanation
Indices: 166845--166894 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
166835 GACTTCTTTG
*
166845 TTGCGATTTTCTAAATTCACA
1 TTGCGATTTACTAAATTCACA
* *
166866 TTGCGATTTAC-AAATTCGCG
1 TTGCGATTTACTAAATTCACA
166886 TTGCGATTT
1 TTGCGATTT
166895 GACTTATGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (21 bp):
TTGCGATTTACTAAATTCACA
Found at i:166929 original size:19 final size:19
Alignment explanation
Indices: 166866--166921 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
166856 TAAATTCACA
166866 TTGCGATTTACAAATTCGCG
1 TTGCGATTTACAAATT-GCG
** *
166886 TTGCGATTTGACTTA-TGTG
1 TTGCGATTT-ACAAATTGCG
166905 TTGCGATTTACAAATTG
1 TTGCGATTTACAAATTG
166922 GATTGCGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.10
19 13 0.45
20 10 0.34
21 3 0.10
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.41
Consensus pattern (19 bp):
TTGCGATTTACAAATTGCG
Found at i:167184 original size:12 final size:12
Alignment explanation
Indices: 167158--167203 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
167148 AAAATTGAAA
*
167158 ATATATCAA-AT
1 ATATATTAATAT
167169 ATATATTAATAT
1 ATATATTAATAT
167181 ATATATTAATAT
1 ATATATTAATAT
167193 -TA-ATT-ATAT
1 ATATATTAATAT
167202 AT
1 AT
167204 TTTATTCACA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
9 4 0.12
10 4 0.12
11 10 0.31
12 14 0.44
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATATTAATAT
Found at i:172284 original size:43 final size:42
Alignment explanation
Indices: 172221--172481 Score: 146
Period size: 42 Copynumber: 6.1 Consensus size: 42
172211 CCCTTTAATT
** *
172221 TTTTTTAATTTTAGTTTTTATCTTTATAATTGAGATCCCTAA
1 TTTTTTAATCCTACTTTTTATCTTTATAATTGAGATCCCTAA
* **
172263 TTTTTGTAATCCTACCTTTTATCTTTATAA-TGAGGGCCCTTAA
1 TTTTT-TAATCCTACTTTTTATCTTTATAATTGAGATCCC-TAA
* *
172306 TTTTTTTAAATCCCA-TTTTTTTACATTTATAATTGATGAT-CCTAA
1 -TTTTTT-AATCCTACTTTTTAT-C-TTTATAATTGA-GATCCCTAA
* * * * * * * **
172351 GTTTTTCAATCCCAAC-TTATACCTTTATAATTAAGCT-CTTTC
1 -TTTTTTAAT-CCTACTTTTTATCTTTATAATTGAGATCCCTAA
* *
172393 TTTTTTCAAT-CTCACTTTTTACCTTTATAATT--GATGCCCTAT
1 TTTTTT-AATCCT-ACTTTTTATCTTTATAATTGAGAT-CCCTAA
* *
172435 TTTTTTAAT-ATATCTTTTTATCTTTATAATTG-GGTCCCTAA
1 TTTTTTAATCCTA-CTTTTTATCTTTATAATTGAGATCCCTAA
172476 TTTTTT
1 TTTTTT
172482 TTCAATCATA
Statistics
Matches: 169, Mismatches: 33, Indels: 35
0.71 0.14 0.15
Matches are distributed among these distances:
40 4 0.02
41 39 0.23
42 44 0.26
43 39 0.23
44 16 0.09
45 21 0.12
46 5 0.03
47 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.53
Consensus pattern (42 bp):
TTTTTTAATCCTACTTTTTATCTTTATAATTGAGATCCCTAA
Found at i:172439 original size:42 final size:44
Alignment explanation
Indices: 172216--172506 Score: 162
Period size: 43 Copynumber: 6.8 Consensus size: 44
172206 TTTAACCCTT
* * * * *
172216 TAATTTTTTTTAATTTTAGTTTTTATCTTTATAATTGA-GATCCC
1 TAATTTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGA-CCC
* * * *
172260 TAATTTTTGT-AATC-CTACCTTTTATCTTTATAA-TGAGGGCCC
1 TAATTTTTTTCAATCTC-ACTTTTTACCTTTATAATTGAGGACCC
* * * * * *
172302 TTAATTTTTTTAAATCCCATTTTTTTACATTTATAATTGATGATCC
1 -TAATTTTTTTCAATCTCA-CTTTTTACCTTTATAATTGAGGACCC
* * * * *
172348 TAA-GTTTTTCAATCCCAAC-TTATACCTTTATAATT-AAG-CTC
1 TAATTTTTTTCAATCTC-ACTTTTTACCTTTATAATTGAGGACCC
* *
172389 T-TTCTTTTTTCAATCTCACTTTTTACCTTTATAATTGATG-CCC
1 TAAT-TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGACCC
* * *
172432 T-ATTTTTTT-AATAT-ATCTTTTTATCTTTATAATTG-GGTCCC
1 TAATTTTTTTCAATCTCA-CTTTTTACCTTTATAATTGAGGACCC
*
172473 TAATTTTTTTTCAATCAT-ACTTTTTACTTTTATA
1 TAA-TTTTTTTCAATC-TCACTTTTTACCTTTATA
172507 GTTTAAGCCC
Statistics
Matches: 194, Mismatches: 35, Indels: 36
0.73 0.13 0.14
Matches are distributed among these distances:
40 2 0.01
41 30 0.15
42 41 0.21
43 55 0.28
44 41 0.21
45 19 0.10
46 6 0.03
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (44 bp):
TAATTTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGACCC
Found at i:172452 original size:41 final size:44
Alignment explanation
Indices: 172393--172506 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 44
172383 AAGCTCTTTC
*
172393 TTTTTTCAATC-TCACTTTTTACCTTTATAATT-GATGCCCT-A-T
1 TTTTTTCAATCAT-ACTTTTTACCTTTATAATTGGGT-CCCTAATT
*
172435 TTTTTT-AAT-ATATCTTTTTATCTTTATAATTGGGTCCCTAATT
1 TTTTTTCAATCATA-CTTTTTACCTTTATAATTGGGTCCCTAATT
*
172478 TTTTTTCAATCATACTTTTTACTTTTATA
1 TTTTTTCAATCATACTTTTTACCTTTATA
172507 GTTTAAGCCC
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
40 1 0.02
41 25 0.41
42 9 0.15
43 7 0.11
44 16 0.26
45 3 0.05
ACGTcount: A:0.23, C:0.16, G:0.04, T:0.57
Consensus pattern (44 bp):
TTTTTTCAATCATACTTTTTACCTTTATAATTGGGTCCCTAATT
Found at i:175586 original size:26 final size:26
Alignment explanation
Indices: 175550--175603 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
175540 GTATTTCTTA
175550 ATGGAGAATTGGTTGAAGATGTGTTC
1 ATGGAGAATTGGTTGAAGATGTGTTC
175576 ATGGAGAATTGGTTGAAGATGTGTTC
1 ATGGAGAATTGGTTGAAGATGTGTTC
175602 AT
1 AT
175604 TACTAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.35
Consensus pattern (26 bp):
ATGGAGAATTGGTTGAAGATGTGTTC
Found at i:177644 original size:16 final size:16
Alignment explanation
Indices: 177615--177648 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
177605 CTCGTGTTCA
*
177615 TTAAGTTCGCTACTCG
1 TTAAGCTCGCTACTCG
*
177631 TTAAGCTCGTTACTCG
1 TTAAGCTCGCTACTCG
177647 TT
1 TT
177649 TCATTGCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (16 bp):
TTAAGCTCGCTACTCG
Found at i:183906 original size:2 final size:2
Alignment explanation
Indices: 183869--183893 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
183859 GTTTTTAAGA
183869 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
183894 CTAGCCTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:185838 original size:31 final size:31
Alignment explanation
Indices: 185796--185873 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
185786 TTCAACGTCC
* *
185796 AAGTGATCAAAACTTAATAAAATAATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
* *
185827 ATGTGACCAAAACTTAATAAAACAATAACTT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
185858 AAGTGACCAAAACTTA
1 AAGTGACCAAAACTTA
185874 TGTTTTTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:186075 original size:31 final size:31
Alignment explanation
Indices: 186033--186138 Score: 142
Period size: 31 Copynumber: 3.4 Consensus size: 31
186023 TAACCTTCAA
* * *
186033 TGACCACATCTTAATTAAAACAAAACAAAAG
1 TGACCAAATCTTAACTAAAACGAAACAAAAG
* *
186064 TGACCAAATCTTAACTAAAATGAAACGAAAG
1 TGACCAAATCTTAACTAAAACGAAACAAAAG
*
186095 TGACCAAATATTAACTAAAACGAAACGAAAA-
1 TGACCAAATCTTAACTAAAACGAAAC-AAAAG
186126 TGACCAAATCTTA
1 TGACCAAATCTTA
186139 TATTTTTCTG
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
31 62 0.95
32 3 0.05
ACGTcount: A:0.53, C:0.18, G:0.09, T:0.20
Consensus pattern (31 bp):
TGACCAAATCTTAACTAAAACGAAACAAAAG
Found at i:190315 original size:30 final size:30
Alignment explanation
Indices: 190279--190345 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
190269 GTAAATTACG
* *
190279 TAAATTGGTCACTATC-GTTATCGTTTGTTA
1 TAAATTGGTCACTAACAG-TATCATTTGTTA
*
190309 TAAATTGGTCATTAACAGTATCATTTGTTA
1 TAAATTGGTCACTAACAGTATCATTTGTTA
*
190339 CAAATTG
1 TAAATTG
190346 AATTGGGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (30 bp):
TAAATTGGTCACTAACAGTATCATTTGTTA
Found at i:191762 original size:19 final size:19
Alignment explanation
Indices: 191738--191787 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
191728 TCCCTATCGG
191738 TGCATCGATGCACTACCTA
1 TGCATCGATGCACTACCTA
191757 TGCATCGATGCACTACCTA
1 TGCATCGATGCACTACCTA
*
191776 TGCATCGGTGCA
1 TGCATCGATGCA
191788 TAAATGGCAT
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:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCACTACCTA
Found at i:193705 original size:2 final size:2
Alignment explanation
Indices: 193700--193727 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
193690 ATTAGAAAAA
193700 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
193728 TAACATGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:209949 original size:2 final size:2
Alignment explanation
Indices: 209942--209973 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
209932 ATGTCATACG
*
209942 TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
209974 ATATATATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:213033 original size:190 final size:192
Alignment explanation
Indices: 212672--213058 Score: 636
Period size: 190 Copynumber: 2.0 Consensus size: 192
212662 GAAATTTAAA
*
212672 TTTAATTTTAGTCTTACTTAAAGAGGAGAGTAAGGAAGACCCTAAGAAAAAGGAGAATATTTCTA
1 TTTAATTTTAGTCTTACTTAAAGAGGAGAGGAAGGAAGACCCTAAGAAAAAGGAGAATATTTCTA
* * *
212737 ATTGATCTAGACTTTATAACAAAAAAATATAAGGAAAAAAATAAACAGTTTGACAATGAACGTTC
66 ATAGATCTAGAATTTATAACAAAAAAATATAAGGAAAAAAATAAACAGTTTGACAATGAACGCTC
* *
212802 AATCACTCTACTATAATCACTGATATAAAAAACTTGTGACCTCTAAAAATAAAAATAATTCC
131 AATCACTCTACTATAATCACTGATATAAAAAACTCGTGACCTCTAAAAACAAAAATAATTCC
*
212864 TTTAATTTTAGTCTTACTTAAAGAGGAGGGGAAGGAAGACCCTAA-AAAAAGGAGAATATTTCTA
1 TTTAATTTTAGTCTTACTTAAAGAGGAGAGGAAGGAAGACCCTAAGAAAAAGGAGAATATTTCTA
212928 ATAGATCTAGAATTTATAACAAAAAAATATAAGG-AAAAAATAAACAGTTTGACAATGAACGCTC
66 ATAGATCTAGAATTTATAACAAAAAAATATAAGGAAAAAAATAAACAGTTTGACAATGAACGCTC
** * * *
212992 AATCA-TCATGTTATAGTCACTGATATTAAAAACTCGTGACCTCTAAGAACAAAAATAATTCC
131 AATCACTC-TACTATAATCACTGATATAAAAAACTCGTGACCTCTAAAAACAAAAATAATTCC
213054 TTTAA
1 TTTAA
213059 CCACGAAGTA
Statistics
Matches: 182, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
189 2 0.01
190 86 0.47
191 51 0.28
192 43 0.24
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (192 bp):
TTTAATTTTAGTCTTACTTAAAGAGGAGAGGAAGGAAGACCCTAAGAAAAAGGAGAATATTTCTA
ATAGATCTAGAATTTATAACAAAAAAATATAAGGAAAAAAATAAACAGTTTGACAATGAACGCTC
AATCACTCTACTATAATCACTGATATAAAAAACTCGTGACCTCTAAAAACAAAAATAATTCC
Found at i:214769 original size:16 final size:16
Alignment explanation
Indices: 214748--214797 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
214738 ATCTAGTGGG
214748 AATGAAAATTTACGAT
1 AATGAAAATTTACGAT
*
214764 AATGAAAATTTATGAT
1 AATGAAAATTTACGAT
214780 AATGAAAATTTACGAT
1 AATGAAAATTTACGAT
214796 AA
1 AA
214798 CAAATGACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (16 bp):
AATGAAAATTTACGAT
Found at i:225120 original size:32 final size:32
Alignment explanation
Indices: 225038--225125 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 32
225028 GTAAAATGTT
225038 CATATGTTCCT-TAGAACATAGGT-ATATTATC
1 CATATGTT-CTGTAGAACATAGGTAATATTATC
* * * *
225069 CATATGTCCCG-AAAGACATAGGTAAT-TCTGTC
1 CATATGTTCTGTAGA-ACATAGGTAATAT-TATC
225101 CATATGTTCTGTAGAACATAGGTAA
1 CATATGTTCTGTAGAACATAGGTAA
225126 ACCCTCGACT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
30 3 0.07
31 16 0.36
32 24 0.53
33 2 0.04
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (32 bp):
CATATGTTCTGTAGAACATAGGTAATATTATC
Found at i:238876 original size:30 final size:30
Alignment explanation
Indices: 238830--239023 Score: 180
Period size: 30 Copynumber: 6.5 Consensus size: 30
238820 TCATATGAGG
* * *
238830 ATCCCAAACAGA-GTCAGGATGGAGATA-TA
1 ATCCCATACAGATGTCAGAATGGGGA-ACTA
* *
238859 ATCTCATACAGATGTCAGAA-CGGGAACTA
1 ATCCCATACAGATGTCAGAATGGGGAACTA
* * * *
238888 ATCTCATATAGATGTTAGAATGGGGATCTA
1 ATCCCATACAGATGTCAGAATGGGGAACTA
*
238918 ATCCCATGCAGATGTCAGAATGGGGAACTA
1 ATCCCATACAGATGTCAGAATGGGGAACTA
* * * *
238948 ATCCCATACAGAGGTCAGAACGAGGAATTA
1 ATCCCATACAGATGTCAGAATGGGGAACTA
* *
238978 ATCCCATGA-AGATGTCAGAATGGGAAATTA
1 ATCCCAT-ACAGATGTCAGAATGGGGAACTA
* *
239008 ATCCCATGCATATGTC
1 ATCCCATACAGATGTC
239024 GAACGAGGAA
Statistics
Matches: 135, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
28 1 0.01
29 33 0.24
30 100 0.74
31 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (30 bp):
ATCCCATACAGATGTCAGAATGGGGAACTA
Found at i:238980 original size:60 final size:61
Alignment explanation
Indices: 238857--239033 Score: 200
Period size: 60 Copynumber: 3.0 Consensus size: 61
238847 GATGGAGATA
* * * * * * * *
238857 TAATCTCATACAGATGTCAGAA-CGGGAACTAATCTCATATAGATGTTAGAATG-GGGATC
1 TAATCCCATGCAGATGTCAGAATGGGGAACTAATCCCATACAGATGTCAGAACGAGGAATC
*
238916 TAATCCCATGCAGATGTCAGAATGGGGAACTAATCCCATACAGAGGTCAGAACGAGGAAT-
1 TAATCCCATGCAGATGTCAGAATGGGGAACTAATCCCATACAGATGTCAGAACGAGGAATC
* * * * *
238976 TAATCCCATGAAGATGTCAGAATGGGAAATTAATCCCATGCATATGTC-GAACGAGGAA
1 TAATCCCATGCAGATGTCAGAATGGGGAACTAATCCCATACAGATGTCAGAACGAGGAA
239034 CGAGGTCCAT
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
59 30 0.30
60 67 0.66
61 4 0.04
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (61 bp):
TAATCCCATGCAGATGTCAGAATGGGGAACTAATCCCATACAGATGTCAGAACGAGGAATC
Found at i:239013 original size:90 final size:89
Alignment explanation
Indices: 238857--239023 Score: 230
Period size: 90 Copynumber: 1.9 Consensus size: 89
238847 GATGGAGATA
* * * * *
238857 TAATCTCATACAGATGTCAGAACGGGAACTAATCTCATATAGATGTTAGAATGGGGATCTAATCC
1 TAATCCCATACAGAGGTCAGAACGGGAACTAATCCCATATAGATGTCAGAATGGGAATCTAATCC
238922 CATGCAGATGTCAGAATGGGGAAC
66 CATGCAGATGTCAGAATGGGGAAC
*
238946 TAATCCCATACAGAGGTCAGAACGAGGAATTAATCCCATGA-AGATGTCAGAATGGGAAAT-TAA
1 TAATCCCATACAGAGGTCAGAACG-GGAACTAATCCCAT-ATAGATGTCAGAATGGG-AATCTAA
*
239009 TCCCATGCATATGTC
63 TCCCATGCAGATGTC
239024 GAACGAGGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
89 22 0.32
90 43 0.63
91 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (89 bp):
TAATCCCATACAGAGGTCAGAACGGGAACTAATCCCATATAGATGTCAGAATGGGAATCTAATCC
CATGCAGATGTCAGAATGGGGAAC
Found at i:240466 original size:24 final size:23
Alignment explanation
Indices: 240439--240486 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
240429 TTTAACTCTC
240439 GTTA-ATTCTCATTCTTCTTCTCCA
1 GTTATATTCTC-TTCTTC-TCTCCA
*
240463 GTTATATTTTCTTCTTCTCTCCA
1 GTTATATTCTCTTCTTCTCTCCA
240486 G
1 G
240487 AGCATTTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 10 0.45
25 5 0.23
ACGTcount: A:0.15, C:0.27, G:0.06, T:0.52
Consensus pattern (23 bp):
GTTATATTCTCTTCTTCTCTCCA
Found at i:241225 original size:48 final size:48
Alignment explanation
Indices: 241154--241250 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
241144 AAATAGTCCT
* *
241154 GAATGTGTTGACTCTTCATTTTTCTGATCCCATTATTCTATTTTGCAG
1 GAATGTGTTGACTCTTCATTTTTCTCATCCCATTATTCTATTTTACAG
* * *
241202 GAATGTGTTTACTAC-TCATTTTTCTCATCCTATTATTCTCTTTTACAG
1 GAATGTGTTGACT-CTTCATTTTTCTCATCCCATTATTCTATTTTACAG
241250 G
1 G
241251 TTATGAAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 42 0.98
49 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (48 bp):
GAATGTGTTGACTCTTCATTTTTCTCATCCCATTATTCTATTTTACAG
Done.