Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr9
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: 70906002
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 1642329 characters in sequence are not A, C, G, or T
File 177 of 221
Found at i:52220996 original size:69 final size:69
Alignment explanation
Indices: 52220885--52221014 Score: 251
Period size: 69 Copynumber: 1.9 Consensus size: 69
52220875 CTTCAGATAT
*
52220885 GCTTCATGCAAACTTTGGTTATAGCTTGGAATCATTATTCTACATGATCATAGCATAGTTTCTAT
1 GCTTCATGCAAACTTTGGTTATAGCTTGAAATCATTATTCTACATGATCATAGCATAGTTTCTAT
52220950 CTCG
66 CTCG
52220954 GCTTCATGCAAACTTTGGTTATAGCTTGAAATCATTATTCTACATGATCATAGCATAGTTT
1 GCTTCATGCAAACTTTGGTTATAGCTTGAAATCATTATTCTACATGATCATAGCATAGTTT
52221015 TAGCATCCCA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (69 bp):
GCTTCATGCAAACTTTGGTTATAGCTTGAAATCATTATTCTACATGATCATAGCATAGTTTCTAT
CTCG
Found at i:52222999 original size:4 final size:4
Alignment explanation
Indices: 52222990--52223016 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
52222980 GGAATGAAAA
52222990 AGGC AGGC AGGC AGGC AGGC AGGC AGG
1 AGGC AGGC AGGC AGGC AGGC AGGC AGG
52223017 GGGTGTGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.52, T:0.00
Consensus pattern (4 bp):
AGGC
Found at i:52224863 original size:16 final size:16
Alignment explanation
Indices: 52224844--52224874 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52224834 TTTACGTTAA
*
52224844 GTTTCTTTTCTTTTTT
1 GTTTATTTTCTTTTTT
52224860 GTTTATTTTCTTTTT
1 GTTTATTTTCTTTTT
52224875 ATTTTTAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.10, G:0.06, T:0.81
Consensus pattern (16 bp):
GTTTATTTTCTTTTTT
Found at i:52224923 original size:25 final size:25
Alignment explanation
Indices: 52224863--52224923 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
52224853 CTTTTTTGTT
*
52224863 TATTTTCTTTTTATTTTTAGATTAGG
1 TATTTTCTTTTTATTTTTAGAATA-G
**
52224889 T-TTTTCTTTTCCTTTTTAGAATA-
1 TATTTTCTTTTTATTTTTAGAATAG
52224912 TATTTTCTTTTT
1 TATTTTCTTTTT
52224924 GTTGTTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 9 0.30
25 19 0.63
26 1 0.03
ACGTcount: A:0.16, C:0.08, G:0.07, T:0.69
Consensus pattern (25 bp):
TATTTTCTTTTTATTTTTAGAATAG
Found at i:52235955 original size:13 final size:13
Alignment explanation
Indices: 52235937--52235964 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52235927 GACCAAAATC
52235937 TTAATTATAATAA
1 TTAATTATAATAA
52235950 TTAATTATAATAA
1 TTAATTATAATAA
52235963 TT
1 TT
52235965 CCGATAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATTATAATAA
Found at i:52246283 original size:3 final size:3
Alignment explanation
Indices: 52246275--52246309 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
52246265 TGCTTGCTTG
52246275 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -TT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
52246310 TTTGGATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:52251406 original size:12 final size:12
Alignment explanation
Indices: 52251389--52251436 Score: 87
Period size: 12 Copynumber: 4.0 Consensus size: 12
52251379 CGCAAAAGAG
52251389 GAGAAGAAGGAT
1 GAGAAGAAGGAT
52251401 GAGAAGAAGGAT
1 GAGAAGAAGGAT
*
52251413 GAGAAGAAAGAT
1 GAGAAGAAGGAT
52251425 GAGAAGAAGGAT
1 GAGAAGAAGGAT
52251437 AGCCGGAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.52, C:0.00, G:0.40, T:0.08
Consensus pattern (12 bp):
GAGAAGAAGGAT
Found at i:52259619 original size:29 final size:28
Alignment explanation
Indices: 52259568--52259637 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
52259558 AATAGTTTAT
* * *
52259568 ATTTTTATAATTTTGAAAAATTAAATTAA
1 ATTTTTAT-TTTTTAAAAAATTAAAATAA
52259597 ATTTTTATTTTTTAAAAAGATTAAAATAA
1 ATTTTTATTTTTTAAAAA-ATTAAAATAA
*
52259626 AATTTTATTTTT
1 ATTTTTATTTTT
52259638 ATTAATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 8 0.22
29 28 0.78
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
ATTTTTATTTTTTAAAAAATTAAAATAA
Found at i:52260470 original size:21 final size:22
Alignment explanation
Indices: 52260446--52260493 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
52260436 AACTACTAAT
*
52260446 AATATTATAA-AAATTAAATT-A
1 AATATTA-AAGAAAATAAATTCA
52260467 AATA-TAAAGAAAATAAATTCA
1 AATATTAAAGAAAATAAATTCA
52260488 AATATT
1 AATATT
52260494 CAAAACAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.09
20 11 0.48
21 9 0.39
22 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AATATTAAAGAAAATAAATTCA
Found at i:52277184 original size:46 final size:46
Alignment explanation
Indices: 52277131--52277222 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
52277121 AAGACCAGTA
52277131 ACAAAAGAAAAGACCATGAGAGAGAGGAAGTCGTAGAAAAACAATC
1 ACAAAAGAAAAGACCATGAGAGAGAGGAAGTCGTAGAAAAACAATC
52277177 ACAAAAGAAAAGACCATGAGAGAGAGGAAGTCGTAGAAAAACAATC
1 ACAAAAGAAAAGACCATGAGAGAGAGGAAGTCGTAGAAAAACAATC
52277223 TTTTCTGGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.54, C:0.13, G:0.24, T:0.09
Consensus pattern (46 bp):
ACAAAAGAAAAGACCATGAGAGAGAGGAAGTCGTAGAAAAACAATC
Found at i:52284265 original size:21 final size:21
Alignment explanation
Indices: 52284239--52284279 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52284229 ATCTGCTCAA
* *
52284239 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
52284260 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
52284280 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:52288500 original size:32 final size:34
Alignment explanation
Indices: 52288429--52288537 Score: 125
Period size: 34 Copynumber: 3.3 Consensus size: 34
52288419 ATATAATTAT
* * *
52288429 TTTTATATTAAATTATATTAAAATTTTTAAAATA
1 TTTTATTTTAAATTATATTAAAATATTTCAAATA
* **
52288463 CTTTATTTTAAATTATACTTTGAA-A-TT-AAATA
1 TTTTATTTTAAATTATA-TTAAAATATTTCAAATA
*
52288495 TTTTATATTAAATTATATTAAAATATTTCAAATA
1 TTTTATTTTAAATTATATTAAAATATTTCAAATA
52288529 TTTTATTTT
1 TTTTATTTT
52288538 TATATTTACT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
31 4 0.07
32 21 0.34
33 4 0.07
34 28 0.46
35 4 0.07
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (34 bp):
TTTTATTTTAAATTATATTAAAATATTTCAAATA
Found at i:52295473 original size:24 final size:24
Alignment explanation
Indices: 52295427--52295474 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
52295417 TAATGGTGAA
*
52295427 ATTATATTTCAATCAGATTTAATC
1 ATTATATTTCAATCAGATATAATC
* **
52295451 ATTATATTTTAATTTGATATAATC
1 ATTATATTTCAATCAGATATAATC
52295475 TATCATCTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (24 bp):
ATTATATTTCAATCAGATATAATC
Found at i:52299597 original size:19 final size:19
Alignment explanation
Indices: 52299573--52299636 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
52299563 AAATAAACAT
52299573 TAAAAAATTATTTTAAAAA
1 TAAAAAATTATTTTAAAAA
52299592 TAAAAAAAAATTATTTTAAAAA
1 T---AAAAAATTATTTTAAAAA
* **
52299614 TAAAAAATAAAATTAAAAA
1 TAAAAAATTATTTTAAAAA
52299633 TAAA
1 TAAA
52299637 TATTTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 20 0.51
22 19 0.49
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAAAATTATTTTAAAAA
Found at i:52299602 original size:22 final size:22
Alignment explanation
Indices: 52299574--52299620 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
52299564 AATAAACATT
52299574 AAAAAATTATTTTAAAAATAAA
1 AAAAAATTATTTTAAAAATAAA
52299596 AAAAAATTATTTTAAAAATAAA
1 AAAAAATTATTTTAAAAATAAA
52299618 AAA
1 AAA
52299621 TAAAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAAATTATTTTAAAAATAAA
Found at i:52311381 original size:8 final size:8
Alignment explanation
Indices: 52311368--52311399 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
52311358 GTTAAGTAAG
*
52311368 GGTAATTT
1 GGTAATTA
52311376 GGTAATTA
1 GGTAATTA
52311384 GGTAATTA
1 GGTAATTA
52311392 GGTAATTA
1 GGTAATTA
52311400 AAGATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (8 bp):
GGTAATTA
Found at i:52315556 original size:27 final size:27
Alignment explanation
Indices: 52315526--52315605 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
52315516 ATGGTATTAT
52315526 GAAATGGATATACAAAATGTTTATATG
1 GAAATGGATATACAAAATGTTTATATG
* ** *
52315553 GAAATAGATATATGAAATGGTTATAT-
1 GAAATGGATATACAAAATGTTTATATG
* ** *
52315579 GAAGTGCTTATACAAAATATTTATATG
1 GAAATGGATATACAAAATGTTTATATG
52315606 AATATAGATA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
26 18 0.45
27 22 0.55
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (27 bp):
GAAATGGATATACAAAATGTTTATATG
Found at i:52315572 original size:53 final size:53
Alignment explanation
Indices: 52315514--52315622 Score: 141
Period size: 53 Copynumber: 2.1 Consensus size: 53
52315504 GAGTAAACGA
* *
52315514 AAATGG-TATTATGAAATGGATATACAAAATGTTTATATGGAA-ATAGATATATG
1 AAATGGTTA-TATGAAATGCATATACAAAATATTTATAT-GAATATAGATATATG
* * *
52315567 AAATGGTTATATGAAGTGCTTATACAAAATATTTATATGAATATAGATATGTG
1 AAATGGTTATATGAAATGCATATACAAAATATTTATATGAATATAGATATATG
52315620 AAA
1 AAA
52315623 GGGACATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 3 0.06
53 44 0.90
54 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (53 bp):
AAATGGTTATATGAAATGCATATACAAAATATTTATATGAATATAGATATATG
Found at i:52317233 original size:37 final size:37
Alignment explanation
Indices: 52317168--52317276 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
52317158 TACGTATGAT
* *
52317168 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTATCTCTTGATCAGATAAGTGTAGC
*
52317203 CACTTATCACTTTATTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTATCTCTTGATCAGATAAGTGTAGC
*
52317240 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTATCTCTTGATCAGATAAGTGTAGC
52317277 TAAAGCTATC
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 10 0.15
36 3 0.04
37 54 0.81
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTATCTCTTGATCAGATAAGTGTAGC
Found at i:52317293 original size:46 final size:46
Alignment explanation
Indices: 52317240--52317606 Score: 455
Period size: 46 Copynumber: 7.6 Consensus size: 46
52317230 TAAGTGTAGC
* **
52317240 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
52317286 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
52317332 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
52317384 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
52317430 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
52317482 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
52317528 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
52317580 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
52317607 AGTACTCAAA
Statistics
Matches: 287, Mismatches: 16, Indels: 36
0.85 0.05 0.11
Matches are distributed among these distances:
46 156 0.54
48 2 0.01
49 2 0.01
50 2 0.01
52 125 0.44
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:52317359 original size:52 final size:52
Alignment explanation
Indices: 52317283--52317600 Score: 417
Period size: 52 Copynumber: 6.3 Consensus size: 52
52317273 TAGCTAAAGC
* * *
52317283 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCAAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
52317336 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
52317388 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* *
52317434 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
52317486 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
52317532 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
52317584 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
52317601 ATCAGAAGTA
Statistics
Matches: 233, Mismatches: 19, Indels: 26
0.84 0.07 0.09
Matches are distributed among these distances:
46 86 0.37
49 1 0.00
52 128 0.55
53 18 0.08
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:52317405 original size:98 final size:98
Alignment explanation
Indices: 52317251--52317606 Score: 622
Period size: 98 Copynumber: 3.6 Consensus size: 98
52317241 ACTTATCACT
* * *
52317251 TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
* * *
52317316 GTATAGCCAAAGCTATCACTTATCACTTTTCAC
66 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
*
52317349 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
52317414 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
66 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
*
52317447 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
52317512 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
66 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
* *
52317545 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCAGA
52317607 AGTACTCAAA
Statistics
Matches: 248, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 248 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (98 bp):
TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
GTATAGCCGAAGCTATTACTTATCACTTTCCAC
Found at i:52330310 original size:45 final size:45
Alignment explanation
Indices: 52330260--52330353 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
52330250 AAATAGGTTA
52330260 TTGAGCTTTAATTTTTATTAGAATCTAAAGCCAGTAATCTTTTGT
1 TTGAGCTTTAATTTTTATTAGAATCTAAAGCCAGTAATCTTTTGT
* * *
52330305 TTGAGCTTTAATTTTTATTAGCATCTAAAGCTAGTAATGTTTTGT
1 TTGAGCTTTAATTTTTATTAGAATCTAAAGCCAGTAATCTTTTGT
52330350 TTGA
1 TTGA
52330354 AATAAAAACT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.48
Consensus pattern (45 bp):
TTGAGCTTTAATTTTTATTAGAATCTAAAGCCAGTAATCTTTTGT
Found at i:52334210 original size:64 final size:64
Alignment explanation
Indices: 52334109--52334239 Score: 253
Period size: 64 Copynumber: 2.0 Consensus size: 64
52334099 CTAGTGAACT
*
52334109 AGGATGCATAAAATGTTCAGTATCTTAATTCACTTCAAGTATCCACACAGCTGATAGTTTACTA
1 AGGATGCATAAAATATTCAGTATCTTAATTCACTTCAAGTATCCACACAGCTGATAGTTTACTA
52334173 AGGATGCATAAAATATTCAGTATCTTAATTCACTTCAAGTATCCACACAGCTGATAGTTTACTA
1 AGGATGCATAAAATATTCAGTATCTTAATTCACTTCAAGTATCCACACAGCTGATAGTTTACTA
52334237 AGG
1 AGG
52334240 GTTGAAAATT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (64 bp):
AGGATGCATAAAATATTCAGTATCTTAATTCACTTCAAGTATCCACACAGCTGATAGTTTACTA
Found at i:52338421 original size:7 final size:7
Alignment explanation
Indices: 52338411--52338437 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
52338401 TAGATTTGAC
52338411 CTATTTG
1 CTATTTG
52338418 CTATTTG
1 CTATTTG
52338425 CTATTTG
1 CTATTTG
52338432 CTATTT
1 CTATTT
52338438 ATTAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.59
Consensus pattern (7 bp):
CTATTTG
Found at i:52346054 original size:30 final size:31
Alignment explanation
Indices: 52346009--52346068 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
52345999 GGAGGTGGGA
*
52346009 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
52346040 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
52346069 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:52346300 original size:9 final size:9
Alignment explanation
Indices: 52346282--52346318 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
52346272 TATAGTTTGA
*
52346282 TATTCAAAT
1 TATTCGAAT
52346291 TATTCGAAT
1 TATTCGAAT
*
52346300 TATTCGAGT
1 TATTCGAAT
52346309 TATTCGAAT
1 TATTCGAAT
52346318 T
1 T
52346319 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:52353446 original size:64 final size:64
Alignment explanation
Indices: 52353364--52353484 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 64
52353354 TCATATATCG
* * * * * *
52353364 GGACGCTCATAAAGAGCTGCGGTATGTCCTCAATATATGCAGGATCCACACCGATCATATAATA
1 GGACACTCACAAAGAGCTGCGGTATGTCCGCAACACATGCAGGATCAACACCGATCATATAATA
* *
52353428 GGACACTCACAAAGAGCTGCGGTATGTTCGCAACACATGCAGGATCAATACCGATCA
1 GGACACTCACAAAGAGCTGCGGTATGTCCGCAACACATGCAGGATCAACACCGATCA
52353485 GGATGCTCGC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (64 bp):
GGACACTCACAAAGAGCTGCGGTATGTCCGCAACACATGCAGGATCAACACCGATCATATAATA
Found at i:52357825 original size:2 final size:2
Alignment explanation
Indices: 52357820--52357852 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
52357810 ACGAGCGAGC
52357820 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
52357853 TTTACACAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52358492 original size:2 final size:2
Alignment explanation
Indices: 52358487--52358517 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52358477 TTGTGTGAAC
52358487 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
52358518 TTTACACAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52359008 original size:665 final size:669
Alignment explanation
Indices: 52357728--52359069 Score: 2559
Period size: 665 Copynumber: 2.0 Consensus size: 669
52357718 GACAGCTCAC
52357728 TTTTTCTCCTCCTTTTGCAGATTACAGCAGCAACGCTACACACAGCAGAATTTAACATATTGGTA
1 TTTTTCTCCTCCTTTTGCAGATTACAGCAGCAACGCTACACACAGCAGAATTTAACATATTGGTA
52357793 GAGCTCACCTTGTGTGAACGAGCGAGCGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTTTAC
66 GAGCTCACCTTGTGT--A-GA--GAGC-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTTTAC
52357858 ACAGTTTTTGAGCTCAAACTACTTTTGAGTCTCCCAAAGAAATGTAACTGCAGGCATTAAAGCTG
125 ACAGTTTTTGAGCTCAAACTACTTTTGAGTCTCCCAAAGAAATGTAACTGCAGGCATTAAAGCTG
52357923 AAGGATTGATGCTTTTGCTTGTTTTATAGTCAGGGAAGAAGTCGGGGACCATCTTTCCCTGACGT
190 AAGGATTGATGCTTTTGCTTGTTTTATAGTCAGGGAAGAAGTCGGGGACCATCTTTCCCTGACGT
52357988 CTTATTCATTTCTTCTCAGCCAATTAGCTTTGCCTTTTTGAAGAACTAGCAGAGGCCTATGAATC
255 CTTATTCATTTCTTCTCAGCCAATTAGCTTTGCCTTTTTGAAGAACTAGCAGAGGCCTATGAATC
52358053 TATAGGTCTAATAGGTTTTGGCTGCTTAGTATATTAGTCTATTAGACCTATTCTTTTTCTTTTTC
320 TATAGGTCTAATAGGTTTTGGCTGCTTAGTATATTAGTCTATTAGACCTATTCTTTTTCTTTTTC
52358118 CCCAGAGAAGTAAGATAAAAAGTCATTGTTTTCCTCTAAAGCCTTATTAACATTTGTTGCTACTA
385 CCCAGAGAAGTAAGATAAAAAGTCATTGTTTTCCTCTAAAGCCTTATTAACATTTGTTGCTACTA
52358183 TGAACAAAGGTACATTTGCAGTTTGCCACATGCAGATGGAGGCTTTGTTACTTACTTTCCCTTCC
450 TGAACAAAGGTACATTTGCAGTTTGCCACATGCAGATGGAGGCTTTGTTACTTACTTTCCCTTCC
52358248 ATTTTTTATGCTTATTAAAGACAGGTTACTTCCATTATCTTTTTGGTTTTATTGTTAGTTAAAGT
515 ATTTTTTATGCTTATTAAAGACAGGTTACTTCCATTATCTTTTTGGTTTTATTGTTAGTTAAAGT
52358313 TAATCTATCCGAATCAGGTCTTCAGTTACTTACAAATGGCTCCTTAGTTTTT-TTTTATTTCTTT
580 TAATCTATCCGAATCAGGTCTTCAGTTACTTACAAATGGCTCCTTA-TTTTTATTTTATTTCTTT
52358377 GTCTTGTTTTCAGTAATACCATTCGT
644 GTCTTGTTTTCAGTAATACCATTCGT
52358403 TTTTTCTCCTCCTTTTGCAGATTACAGCAGCAACGCTACACACAGCAGAATTTAACATATTGGTA
1 TTTTTCTCCTCCTTTTGCAGATTACAGCAGCAACGCTACACACAGCAGAATTTAACATATTGGTA
52358468 GAGCTCACCTTGTGT-GA-A-C-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTTTACACAGTT
66 GAGCTCACCTTGTGTAGAGAGCAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTTTACACAGTT
52358529 TTTGAGCTCAAACTACTTTTGAGTCTCCCAAAGAAATGTAACTGCAGGCATTAAAGCTGAAGGAT
131 TTTGAGCTCAAACTACTTTTGAGTCTCCCAAAGAAATGTAACTGCAGGCATTAAAGCTGAAGGAT
52358594 TGATGCTTTTGCTTGTTTTATAGTCAGGGAAGAAGTCGGGGACCATCTTTCCCTGACGTCTTATT
196 TGATGCTTTTGCTTGTTTTATAGTCAGGGAAGAAGTCGGGGACCATCTTTCCCTGACGTCTTATT
52358659 CATTTCTTCTCAGCCAATTAGCTTTGCCTTTTTGAAGAACTAGCAGAGGCCTATGAATCTATAGG
261 CATTTCTTCTCAGCCAATTAGCTTTGCCTTTTTGAAGAACTAGCAGAGGCCTATGAATCTATAGG
52358724 TCTAATAGGTTTTGGCTGCTTAGTATATTAGTCTATTAGACCTATTCTTTTTCTTTTTCCCCAGA
326 TCTAATAGGTTTTGGCTGCTTAGTATATTAGTCTATTAGACCTATTCTTTTTCTTTTTCCCCAGA
52358789 GAAGTAAGATAAAAAGTCATTGTTTTCCTCTAAAGCCTTATTAACATTTGTTGCTACTATGAACA
391 GAAGTAAGATAAAAAGTCATTGTTTTCCTCTAAAGCCTTATTAACATTTGTTGCTACTATGAACA
* * *
52358854 AAGGTACATTTGCAGTTTTCCACATTCAGATGGATGCTTTGTTACTTACTTTCCCTTCCATTTTT
456 AAGGTACATTTGCAGTTTGCCACATGCAGATGGAGGCTTTGTTACTTACTTTCCCTTCCATTTTT
52358919 TATGCTTATTAAAGACAGGTTACTTCCATTATCTTTTTGGTTTTATTGTTAGTTAAAGTTAATCT
521 TATGCTTATTAAAGACAGGTTACTTCCATTATCTTTTTGGTTTTATTGTTAGTTAAAGTTAATCT
52358984 ATCCGAATCAGGTCTTCAGTTACTTACAAATGGCTCCTTATTTTTATTTTATTTCTTTGTCTTGT
586 ATCCGAATCAGGTCTTCAGTTACTTACAAATGGCTCCTTATTTTTATTTTATTTCTTTGTCTTGT
52359049 TTTCAGTAATACCATTCGT
651 TTTCAGTAATACCATTCGT
52359068 TT
1 TT
52359070 ACTTCATTCC
Statistics
Matches: 663, Mismatches: 3, Indels: 12
0.98 0.00 0.02
Matches are distributed among these distances:
664 5 0.01
665 574 0.87
667 1 0.00
668 1 0.00
671 2 0.00
675 80 0.12
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (669 bp):
TTTTTCTCCTCCTTTTGCAGATTACAGCAGCAACGCTACACACAGCAGAATTTAACATATTGGTA
GAGCTCACCTTGTGTAGAGAGCAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTTTACACAGTT
TTTGAGCTCAAACTACTTTTGAGTCTCCCAAAGAAATGTAACTGCAGGCATTAAAGCTGAAGGAT
TGATGCTTTTGCTTGTTTTATAGTCAGGGAAGAAGTCGGGGACCATCTTTCCCTGACGTCTTATT
CATTTCTTCTCAGCCAATTAGCTTTGCCTTTTTGAAGAACTAGCAGAGGCCTATGAATCTATAGG
TCTAATAGGTTTTGGCTGCTTAGTATATTAGTCTATTAGACCTATTCTTTTTCTTTTTCCCCAGA
GAAGTAAGATAAAAAGTCATTGTTTTCCTCTAAAGCCTTATTAACATTTGTTGCTACTATGAACA
AAGGTACATTTGCAGTTTGCCACATGCAGATGGAGGCTTTGTTACTTACTTTCCCTTCCATTTTT
TATGCTTATTAAAGACAGGTTACTTCCATTATCTTTTTGGTTTTATTGTTAGTTAAAGTTAATCT
ATCCGAATCAGGTCTTCAGTTACTTACAAATGGCTCCTTATTTTTATTTTATTTCTTTGTCTTGT
TTTCAGTAATACCATTCGT
Found at i:52366512 original size:21 final size:20
Alignment explanation
Indices: 52366487--52366525 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
52366477 GAATTTTTAT
52366487 TTTTAAATGTTTTATATAACA
1 TTTTAAATGTTTTA-ATAACA
* *
52366508 TTTTATATTTTTTAATAA
1 TTTTAAATGTTTTAATAA
52366526 TTTAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTAAATGTTTTAATAACA
Found at i:52389086 original size:42 final size:42
Alignment explanation
Indices: 52389037--52389133 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 42
52389027 CTTGGTATCG
* *
52389037 CACACTTAGTGCCCGTTATTCAACATCATCATTTTAATTTCA
1 CACACTTAGTGCCCATTATCCAACATCATCATTTTAATTTCA
* *
52389079 CACACTTAGTGCCCATTATCCAACATCATTATTTTAATTTCG
1 CACACTTAGTGCCCATTATCCAACATCATCATTTTAATTTCA
52389121 CACACTTAGTGCC
1 CACACTTAGTGCC
52389134 GTTCATATAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (42 bp):
CACACTTAGTGCCCATTATCCAACATCATCATTTTAATTTCA
Found at i:52390036 original size:16 final size:17
Alignment explanation
Indices: 52390003--52390036 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
52389993 TATAAATTTA
*
52390003 ATATTTACCTTATTACT
1 ATATTAACCTTATTACT
52390020 ATATTAACCTT-TTACT
1 ATATTAACCTTATTACT
52390036 A
1 A
52390037 ATAATTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAACCTTATTACT
Found at i:52390911 original size:57 final size:60
Alignment explanation
Indices: 52390836--52390958 Score: 173
Period size: 57 Copynumber: 2.1 Consensus size: 60
52390826 CTCGTTCCCA
*
52390836 TTTTCCACATATTTTTCGGGAGGGATATATC-A-A-GATCACCCGTCCGGGCTAGAT-CT
1 TTTTCCACATATTCTTCGGGAGGGATATATCGATAGGATCACCCGTCCGGGCTAGATCCT
*
52390892 TTTTCACACATATTCTTCGGGAGGGCTATATCAGGATAGGATCACCCGTCCGGGCTAGATCCT
1 TTTTC-CACATATTCTTCGGGAGGGATATATC--GATAGGATCACCCGTCCGGGCTAGATCCT
52390955 TTTT
1 TTTT
52390959 ACTGTCAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
56 5 0.09
57 24 0.41
60 1 0.02
61 1 0.02
62 21 0.36
63 6 0.10
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (60 bp):
TTTTCCACATATTCTTCGGGAGGGATATATCGATAGGATCACCCGTCCGGGCTAGATCCT
Found at i:52396700 original size:20 final size:20
Alignment explanation
Indices: 52396666--52396707 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
52396656 AACTATTTAC
** *
52396666 ATAATATTATTTGAATATTT
1 ATAATATTAAATGAATAATT
52396686 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
52396706 AT
1 AT
52396708 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:52397214 original size:24 final size:24
Alignment explanation
Indices: 52397187--52397238 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52397177 TTAGTAAGTC
*
52397187 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
52397211 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
52397235 AAAT
1 AAAT
52397239 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:52399184 original size:24 final size:24
Alignment explanation
Indices: 52399157--52399208 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52399147 TTAGTAAGTC
*
52399157 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
52399181 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
52399205 AAAT
1 AAAT
52399209 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:52401845 original size:18 final size:18
Alignment explanation
Indices: 52401812--52401846 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52401802 ATAACTTTTA
*
52401812 AAAGTAAAAACTAAAAAT
1 AAAGTAAAAACGAAAAAT
*
52401830 AAAGTAAAACCGAAAAA
1 AAAGTAAAAACGAAAAA
52401847 AGAAAGAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.11
Consensus pattern (18 bp):
AAAGTAAAAACGAAAAAT
Found at i:52410354 original size:29 final size:27
Alignment explanation
Indices: 52410294--52410363 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 27
52410284 GGGGGGGTTT
*
52410294 TTTACACAAATAGGGTAAGAAAAAAAA
1 TTTACTCAAATAGGGTAAGAAAAAAAA
* *
52410321 ATTACTCAAATAGAGTGTAAGAAAAAATA
1 TTTACTCAAATAG-G-GTAAGAAAAAAAA
*
52410350 TTTACTAAAATAGG
1 TTTACTCAAATAGG
52410364 TTATTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 11 0.31
28 2 0.06
29 23 0.64
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.24
Consensus pattern (27 bp):
TTTACTCAAATAGGGTAAGAAAAAAAA
Found at i:52410801 original size:12 final size:12
Alignment explanation
Indices: 52410784--52410809 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52410774 TTTGTGAATT
52410784 TTTTAGAAGATA
1 TTTTAGAAGATA
52410796 TTTTAGAAGATA
1 TTTTAGAAGATA
52410808 TT
1 TT
52410810 GTGAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTTAGAAGATA
Found at i:52410905 original size:22 final size:22
Alignment explanation
Indices: 52410878--52410945 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
52410868 TGGATTAGAA
*
52410878 TTTTGTATGAATATTCTAATTT
1 TTTTGTATGAATATTGTAATTT
* *
52410900 TTTTGTATTAACATTGTAA-TT
1 TTTTGTATGAATATTGTAATTT
*
52410921 TTTT-TATGAATATTGTAATTA
1 TTTTGTATGAATATTGTAATTT
52410942 TTTT
1 TTTT
52410946 ATAATTAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 12 0.31
21 11 0.28
22 16 0.41
ACGTcount: A:0.28, C:0.03, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTTGTATGAATATTGTAATTT
Found at i:52411027 original size:19 final size:19
Alignment explanation
Indices: 52410980--52411143 Score: 111
Period size: 19 Copynumber: 8.1 Consensus size: 19
52410970 TTGGATTAGT
* *
52410980 ATTTTGTATAAATATTGCA
1 ATTTTGTATGAATATTGTA
52410999 ATTTTTTTGTATGAATATTGTA
1 A---TTTTGTATGAATATTGTA
52411021 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
*
52411040 ATTATTTTAT-AATTAAATTTGT-
1 ATT-TTGTATGAA-T--A-TTGTA
* * *
52411062 ATTTATAGTTTTGGAT-TAGT-
1 ATTT-T-G-TATGAATATTGTA
52411082 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
*
52411101 ATTTTTTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
52411120 ATTTTTTTGTATGAATATTGTA
1 A---TTTTGTATGAATATTGTA
52411142 AT
1 AT
52411144 ATTATAATTT
Statistics
Matches: 116, Mismatches: 12, Indels: 34
0.72 0.07 0.21
Matches are distributed among these distances:
17 5 0.04
18 4 0.03
19 45 0.39
20 13 0.11
21 1 0.01
22 40 0.34
23 4 0.03
24 3 0.03
25 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (19 bp):
ATTTTGTATGAATATTGTA
Found at i:52411046 original size:22 final size:22
Alignment explanation
Indices: 52410979--52411047 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 22
52410969 TTTGGATTAG
* *
52410979 TATTTTGTATAAATATTGCAAT
1 TATTTTGTATGAATATTGTAAT
*
52411001 TTTTTTGTATGAATATTGT-A-
1 TATTTTGTATGAATATTGTAAT
52411021 -ATTTTGTATGAATATTGTAAT
1 TATTTTGTATGAATATTGTAAT
52411042 TATTTT
1 TATTTT
52411048 ATAATTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 17 0.43
20 1 0.03
21 1 0.03
22 21 0.52
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (22 bp):
TATTTTGTATGAATATTGTAAT
Found at i:52411050 original size:102 final size:103
Alignment explanation
Indices: 52410859--52411143 Score: 447
Period size: 102 Copynumber: 2.8 Consensus size: 103
52410849 ATATTTAGTG
* * *
52410859 TTTATAG-TTTGGATTAGAATTTTGTATGAATATT-CTAATTTTTTTGTATTAACATTGTAATTT
1 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGC-AATTTTTTTGTATGAATATTGTAATTT
*
52410922 TTTTATGAATATTGTAATTATTTTATAATTAAATTTGTA
65 TTGTATGAATATTGTAATTATTTTATAATTAAATTTGTA
*
52410961 TTTATAGTTTTGGATTAGTATTTTGTATAAATATTGCAATTTTTTTGTATGAATATTGTAA-TTT
1 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTT
52411025 TGTATGAATATTGTAATTATTTTATAATTAAATTTGTA
66 TGTATGAATATTGTAATTATTTTATAATTAAATTTGTA
*
52411063 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAA--TTTTT-TATGAATATTGTAATTTT
1 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAA--TT
52411125 TTTGTATGAATATTGTAAT
64 TTTGTATGAATATTGTAAT
52411144 ATTATAATTT
Statistics
Matches: 171, Mismatches: 7, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
99 14 0.08
100 5 0.03
102 104 0.61
103 47 0.27
104 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.56
Consensus pattern (103 bp):
TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTT
TGTATGAATATTGTAATTATTTTATAATTAAATTTGTA
Found at i:52411162 original size:27 final size:26
Alignment explanation
Indices: 52411092--52411221 Score: 123
Period size: 27 Copynumber: 5.2 Consensus size: 26
52411082 ATTTTGTATG
*
52411092 AATATTGTAATTTTTTATGAATATTGT
1 AATATT-TAATTTTATATGAATATTGT
*
52411119 -A-ATTT--TTTTGTATGAATATTGT
1 AATATTTAATTTTATATGAATATTGT
* *
52411141 AATATTATAATTTTATGTGAATATTGC
1 AATATT-TAATTTTATATGAATATTGT
52411168 AAT-TTT--TTTGTA-ATGAATATTGT
1 AATATTTAATTT-TATATGAATATTGT
*
52411191 AATATTGTAATTTTGTATGAATATTGT
1 AATATT-TAATTTTATATGAATATTGT
52411218 AATA
1 AATA
52411222 CTGTTGAGGA
Statistics
Matches: 85, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
22 16 0.19
23 16 0.19
24 8 0.09
25 6 0.07
26 4 0.05
27 35 0.41
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (26 bp):
AATATTTAATTTTATATGAATATTGT
Found at i:52411196 original size:50 final size:49
Alignment explanation
Indices: 52411092--52411216 Score: 196
Period size: 49 Copynumber: 2.5 Consensus size: 49
52411082 ATTTTGTATG
* *
52411092 AATATTGTAATTTTTTATGAATATTGTAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTATATGAATATTGCAATTTTTTTGTATGAATATTGT
* *
52411141 AATATTATAATTTTATGTGAATATTGCAATTTTTTTGTAATGAATATTGT
1 AATATTGTAATTTTATATGAATATTGCAATTTTTTTGT-ATGAATATTGT
*
52411191 AATATTGTAATTTTGTATGAATATTG
1 AATATTGTAATTTTATATGAATATTG
52411217 TAATACTGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
49 34 0.50
50 34 0.50
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.54
Consensus pattern (49 bp):
AATATTGTAATTTTATATGAATATTGCAATTTTTTTGTATGAATATTGT
Found at i:52411357 original size:60 final size:60
Alignment explanation
Indices: 52411279--52411397 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
52411269 CGAGCTCCAC
* ** * * *
52411279 TAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTACTAGTAATTTAGGATTAAGCTATAAATTGTTGTGTTTG
*
52411339 TAATTA-TTTAAAATTTAATTTACTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGTTT
1 TAATTATTTTAAAA-TTAATTTACTAGTAATTTAGGATTAAGCTATAAATTGTTGTGTTT
52411398 AGTTTAGTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 6 0.12
60 45 0.88
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTACTAGTAATTTAGGATTAAGCTATAAATTGTTGTGTTTG
Found at i:52411483 original size:37 final size:38
Alignment explanation
Indices: 52411431--52411511 Score: 155
Period size: 37 Copynumber: 2.2 Consensus size: 38
52411421 AATATAAAGT
52411431 TTATAAAAAAGTTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAGTTAAAAATCATTTTATTAAAAGTTTAA
52411469 TTATAAAAAA-TTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAGTTAAAAATCATTTTATTAAAAGTTTAA
52411506 TTATAA
1 TTATAA
52411512 CTAACTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 33 0.77
38 10 0.23
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (38 bp):
TTATAAAAAAGTTAAAAATCATTTTATTAAAAGTTTAA
Found at i:52411976 original size:38 final size:38
Alignment explanation
Indices: 52411933--52412014 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
52411923 AAAAAGTCAG
*
52411933 TTATAATTAAACTTTTAATAAAATGATTTTTAACTTTT
1 TTATAATTAAACTTTTAATAAAATAATTTTTAACTTTT
*
52411971 TTATAATTAAACTTTTAATAAAATAATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATAATTTTTAACTTTT
52412009 TTATAA
1 TTATAA
52412015 ACTTTATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATAATTTTTAACTTTT
Found at i:52412124 original size:60 final size:60
Alignment explanation
Indices: 52412047--52412166 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
52412037 AATACTAAAC
* * * * *
52412047 TAAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTA
1 TAAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTA
*
52412107 TAAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTA
1 TAAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTA
52412167 CAATATTCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 4 0.08
60 49 0.92
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.33
Consensus pattern (60 bp):
TAAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTA
Found at i:52412267 original size:31 final size:27
Alignment explanation
Indices: 52412210--52412337 Score: 141
Period size: 27 Copynumber: 5.1 Consensus size: 27
52412200 TATCCCGACG
52412210 TTACAATATTCATACAAAATTACAATA
1 TTACAATATTCATACAAAATTACAATA
52412237 TTACAATATTCATTAC-AAA--A-AA-A
1 TTACAATATTCA-TACAAAATTACAATA
* * *
52412260 TTGCAATATTCATATAAAATTATAATA
1 TTACAATATTCATACAAAATTACAATA
52412287 TTACAATATTCATAC-AAA--A-AA-A
1 TTACAATATTCATACAAAATTACAATA
*
52412309 TTACAATATTTATACAAAATTACAATA
1 TTACAATATTCATACAAAATTACAATA
52412336 TT
1 TT
52412338 CATACAAAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
22 17 0.20
23 20 0.24
24 3 0.04
25 3 0.04
26 7 0.08
27 32 0.38
28 3 0.04
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (27 bp):
TTACAATATTCATACAAAATTACAATA
Found at i:52412287 original size:50 final size:49
Alignment explanation
Indices: 52412157--52412337 Score: 226
Period size: 50 Copynumber: 3.7 Consensus size: 49
52412147 AATTAATTAT
*
52412157 AAAATAATTACAATATTCATACAAAAATTACAATATTACAATA-T-AT-C
1 AAAAAAATTACAATATTCATAC-AAAATTACAATATTACAATATTCATAC
*** **
52412204 -CCGACGTTACAATATTCATACAAAATTACAATATTACAATATTCATTAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCA-TAC
* * *
52412253 AAAAAAATTGCAATATTCATATAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
*
52412302 AAAAAAATTACAATATTTATACAAAATTACAATATT
1 AAAAAAATTACAATATTCATACAAAATTACAATATT
52412338 CATACAAAAT
Statistics
Matches: 111, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
45 20 0.18
46 16 0.14
47 1 0.01
48 1 0.01
49 36 0.32
50 37 0.33
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (49 bp):
AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
Found at i:52412334 original size:41 final size:41
Alignment explanation
Indices: 52412286--52412450 Score: 132
Period size: 41 Copynumber: 4.1 Consensus size: 41
52412276 AAATTATAAT
*
52412286 ATTACAATATTCATACAAAAAAATTACAATATTTATACAAA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
* * *
52412327 ATTACAATATTCATACAAAATACTAA-TCCAAAACTGTAAATAC-AA
1 ATTACAATATTCATACAAAA-A--AATTACAATA-T-T-CATACAAA
* *
52412372 ATT--TA-ATT-AT--AAAATAATTACAATATTCATA-AATA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAA-A
* *
52412407 ATTACAATATTCAGACAAAAAAATTAGAATATTCATACAAA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
52412448 ATT
1 ATT
52412451 CTAATCCAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 32
0.69 0.09 0.23
Matches are distributed among these distances:
34 4 0.04
35 5 0.05
36 3 0.03
37 6 0.06
38 3 0.03
39 5 0.05
41 45 0.47
42 6 0.06
43 6 0.06
44 3 0.03
45 6 0.06
46 4 0.04
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.32
Consensus pattern (41 bp):
ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
Found at i:52412405 original size:19 final size:19
Alignment explanation
Indices: 52412383--52412419 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
52412373 TTTAATTATA
52412383 AAATAATTACAATATTCAT
1 AAATAATTACAATATTCAT
52412402 AAATAATTACAATATTCA
1 AAATAATTACAATATTCA
52412420 GACAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATAATTACAATATTCAT
Found at i:52412437 original size:22 final size:22
Alignment explanation
Indices: 52412382--52412448 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
52412372 ATTTAATTAT
*
52412382 AAAATAATTACAATATTC--A-
1 AAAAAAATTACAATATTCAGAC
* *
52412401 TAAATAATTACAATATTCAGAC
1 AAAAAAATTACAATATTCAGAC
* *
52412423 AAAAAAATTAGAATATTCATAC
1 AAAAAAATTACAATATTCAGAC
52412445 AAAA
1 AAAA
52412449 TTCTAATCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
19 17 0.43
21 1 0.03
22 22 0.55
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.28
Consensus pattern (22 bp):
AAAAAAATTACAATATTCAGAC
Found at i:52412450 original size:19 final size:19
Alignment explanation
Indices: 52412210--52412347 Score: 90
Period size: 19 Copynumber: 8.1 Consensus size: 19
52412200 TATCCCGACG
52412210 TTACAATATTCATACAAAA
1 TTACAATATTCATACAAAA
*
52412229 TTACAATA-T--TACAATA
1 TTACAATATTCATACAAAA
* *
52412245 TT-C-AT-TACA-AAAAAA
1 TTACAATATTCATACAAAA
* *
52412260 TTGCAATATTCATATAAAA
1 TTACAATATTCATACAAAA
* *
52412279 TTATAATA-T--TACAATA
1 TTACAATATTCATACAAAA
*
52412295 TT-C-ATA--CA-AAAAAA
1 TTACAATATTCATACAAAA
*
52412309 TTACAATATTTATACAAAA
1 TTACAATATTCATACAAAA
52412328 TTACAATATTCATACAAAA
1 TTACAATATTCATACAAAA
52412347 T
1 T
52412348 ACTAATCCAA
Statistics
Matches: 89, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
14 11 0.12
15 8 0.09
16 19 0.21
17 2 0.02
18 6 0.07
19 43 0.48
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (19 bp):
TTACAATATTCATACAAAA
Found at i:52412619 original size:14 final size:13
Alignment explanation
Indices: 52412606--52412645 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
52412596 TTTTCTTTCT
52412606 TTCTTTCTTCTTC
1 TTCTTTCTTCTTC
52412619 TTCTTCTCTTCTTC
1 TTCTT-TCTTCTTC
*
52412633 TCCTTTCTCTCTT
1 TTCTTTCT-TCTT
52412646 TTTTTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
TTCTTTCTTCTTC
Found at i:52412800 original size:27 final size:27
Alignment explanation
Indices: 52412770--52412832 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
52412760 AGAAGGCCAC
52412770 CATTGGCGCCTCTCTATGAGGCACCTT
1 CATTGGCGCCTCTCTATGAGGCACCTT
52412797 CATTGGCGCCTCTCTATGAGGCACCTT
1 CATTGGCGCCTCTCTATGAGGCACCTT
*
52412824 CAATGGCGC
1 CATTGGCGC
52412833 TTACCTGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.16, C:0.33, G:0.24, T:0.27
Consensus pattern (27 bp):
CATTGGCGCCTCTCTATGAGGCACCTT
Found at i:52414333 original size:13 final size:14
Alignment explanation
Indices: 52414312--52414348 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
52414302 TCCAAGTCAG
52414312 ATAAAATAATTAAA
1 ATAAAATAATTAAA
*
52414326 AT-AAATAACTAAA
1 ATAAAATAATTAAA
52414339 ATAAAATAAT
1 ATAAAATAAT
52414349 AAATCAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAATAATTAAA
Found at i:52416231 original size:13 final size:14
Alignment explanation
Indices: 52416210--52416246 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
52416200 TCCAAGTCAG
52416210 ATAAAATAATTAAA
1 ATAAAATAATTAAA
*
52416224 AT-AAATAACTAAA
1 ATAAAATAATTAAA
52416237 ATAAAATAAT
1 ATAAAATAAT
52416247 AAATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAATAATTAAA
Found at i:52420780 original size:18 final size:17
Alignment explanation
Indices: 52420754--52420793 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
52420744 TCATCAATCT
* *
52420754 AATTAAAAAATTATTACA
1 AATTTAAAAATT-TTAAA
52420772 AATTTAAAAATTTTAAA
1 AATTTAAAAATTTTAAA
52420789 AATTT
1 AATTT
52420794 CAGTTCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTAAAAATTTTAAA
Found at i:52429178 original size:15 final size:15
Alignment explanation
Indices: 52429158--52429188 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52429148 CCTCGTCTGT
52429158 TGAATGGATTCGAGG
1 TGAATGGATTCGAGG
52429173 TGAATGGATTCGAGG
1 TGAATGGATTCGAGG
52429188 T
1 T
52429189 TCACTAGCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.39, T:0.29
Consensus pattern (15 bp):
TGAATGGATTCGAGG
Found at i:52435600 original size:41 final size:41
Alignment explanation
Indices: 52435574--52435714 Score: 228
Period size: 41 Copynumber: 3.4 Consensus size: 41
52435564 AATTAGCCTA
* * * *
52435574 CTAGACTTAAAGTCCGAATTATTTCACCGGCCTTAAACCTG
1 CTAGACTTTAAGTCTGAATTATATCACCGGCATTAAACCTG
* *
52435615 CTAGACTTTAAGTCTGAATTATATCACCGGCCTTAAGCCTG
1 CTAGACTTTAAGTCTGAATTATATCACCGGCATTAAACCTG
52435656 CTAGACTTTAAGTCTGAATTATATCACCGGCATTAAACCTG
1 CTAGACTTTAAGTCTGAATTATATCACCGGCATTAAACCTG
52435697 CTAGACTTTAAGTCTGAA
1 CTAGACTTTAAGTCTGAA
52435715 AATTTCAATT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (41 bp):
CTAGACTTTAAGTCTGAATTATATCACCGGCATTAAACCTG
Found at i:52438387 original size:205 final size:205
Alignment explanation
Indices: 52438035--52438444 Score: 820
Period size: 205 Copynumber: 2.0 Consensus size: 205
52438025 CCAAGCCCAG
52438035 CCCGACCCAAAATATAGGTTTAAAATTTTATATAAATTTGTCTATATTTGTAAAAGACTAACCCA
1 CCCGACCCAAAATATAGGTTTAAAATTTTATATAAATTTGTCTATATTTGTAAAAGACTAACCCA
52438100 ATGTAATGGCCTAAATTCAAGGTTATCAGAATAGTGGTTTCGTAACCACAAATCCGAATTAAAGA
66 ATGTAATGGCCTAAATTCAAGGTTATCAGAATAGTGGTTTCGTAACCACAAATCCGAATTAAAGA
52438165 GAAATTTATTGTAATATTTTTGCATGAATATTGATATGATAGGAAAATCATATGAAAATATCGAT
131 GAAATTTATTGTAATATTTTTGCATGAATATTGATATGATAGGAAAATCATATGAAAATATCGAT
52438230 AGAAAAAAAA
196 AGAAAAAAAA
52438240 CCCGACCCAAAATATAGGTTTAAAATTTTATATAAATTTGTCTATATTTGTAAAAGACTAACCCA
1 CCCGACCCAAAATATAGGTTTAAAATTTTATATAAATTTGTCTATATTTGTAAAAGACTAACCCA
52438305 ATGTAATGGCCTAAATTCAAGGTTATCAGAATAGTGGTTTCGTAACCACAAATCCGAATTAAAGA
66 ATGTAATGGCCTAAATTCAAGGTTATCAGAATAGTGGTTTCGTAACCACAAATCCGAATTAAAGA
52438370 GAAATTTATTGTAATATTTTTGCATGAATATTGATATGATAGGAAAATCATATGAAAATATCGAT
131 GAAATTTATTGTAATATTTTTGCATGAATATTGATATGATAGGAAAATCATATGAAAATATCGAT
52438435 AGAAAAAAAA
196 AGAAAAAAAA
52438445 TTACCGATTT
Statistics
Matches: 205, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 205 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (205 bp):
CCCGACCCAAAATATAGGTTTAAAATTTTATATAAATTTGTCTATATTTGTAAAAGACTAACCCA
ATGTAATGGCCTAAATTCAAGGTTATCAGAATAGTGGTTTCGTAACCACAAATCCGAATTAAAGA
GAAATTTATTGTAATATTTTTGCATGAATATTGATATGATAGGAAAATCATATGAAAATATCGAT
AGAAAAAAAA
Found at i:52440308 original size:60 final size:60
Alignment explanation
Indices: 52440236--52440375 Score: 280
Period size: 60 Copynumber: 2.3 Consensus size: 60
52440226 TAGGGTCTAA
52440236 ATTTAGCCTGGACTGGTAATTTAGATCCAAGCTCATTAGAGTAAATTGTCGTTGGAGGGG
1 ATTTAGCCTGGACTGGTAATTTAGATCCAAGCTCATTAGAGTAAATTGTCGTTGGAGGGG
52440296 ATTTAGCCTGGACTGGTAATTTAGATCCAAGCTCATTAGAGTAAATTGTCGTTGGAGGGG
1 ATTTAGCCTGGACTGGTAATTTAGATCCAAGCTCATTAGAGTAAATTGTCGTTGGAGGGG
52440356 ATTTAGCCTGGACTGGTAAT
1 ATTTAGCCTGGACTGGTAAT
52440376 CCCGTTGTAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 80 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (60 bp):
ATTTAGCCTGGACTGGTAATTTAGATCCAAGCTCATTAGAGTAAATTGTCGTTGGAGGGG
Found at i:52447577 original size:46 final size:46
Alignment explanation
Indices: 52447510--52447867 Score: 662
Period size: 46 Copynumber: 7.8 Consensus size: 46
52447500 TTTGAGTACT
*
52447510 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
52447556 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
52447602 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
52447648 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
52447694 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
52447740 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
52447786 TCTGATCAAGTGACAAAATGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
52447832 TCTGATCAAGTGACAAAGTGATCAGTGGTAGCCTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
52447868 AAAGTAAATG
Statistics
Matches: 304, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 304 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:52466325 original size:10 final size:10
Alignment explanation
Indices: 52466310--52466337 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
52466300 ATGGTAATGT
52466310 AGACTGGTGC
1 AGACTGGTGC
52466320 AGACTGGTGC
1 AGACTGGTGC
52466330 AGACTGGT
1 AGACTGGT
52466338 CATCAACAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.21
Consensus pattern (10 bp):
AGACTGGTGC
Found at i:52475958 original size:31 final size:33
Alignment explanation
Indices: 52475923--52475996 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 33
52475913 GCCTATTGCT
* * *
52475923 TTTTGTTGCTT-TTTTACTATT-T-TTGTTACTG
1 TTTTGTTG-TTGTTTCACTATTATATTGCTACTA
*
52475954 TTTTGGTGTTGTTTCACTATTATATTGCTACTA
1 TTTTGTTGTTGTTTCACTATTATATTGCTACTA
52475987 TTTTGTTGTT
1 TTTTGTTGTT
52475997 ATTATTAGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 2 0.06
31 16 0.46
32 1 0.03
33 16 0.46
ACGTcount: A:0.12, C:0.09, G:0.15, T:0.64
Consensus pattern (33 bp):
TTTTGTTGTTGTTTCACTATTATATTGCTACTA
Found at i:52481955 original size:46 final size:45
Alignment explanation
Indices: 52481887--52482013 Score: 157
Period size: 46 Copynumber: 2.8 Consensus size: 45
52481877 TGGAATGCAG
* * *
52481887 GTATGGTAATTCAGTAAAGAAAATCATACTGAGTTGT-AGAACGTAA
1 GTATGGTATTTCAGT-AAGAAAACCATACTGAGTTGTGA-AAAGTAA
* *
52481933 GTATGGTATTTCAGTAACGAAAACCATACTAAGTTGTGAAAAGTAG
1 GTATGGTATTTCAGTAA-GAAAACCATACTGAGTTGTGAAAAGTAA
*
52481979 GTATGGTATTTTAGTGAAGAAAACCATACTGAGTT
1 GTATGGTATTTCAGT-AAGAAAACCATACTGAGTT
52482014 ATAGCATTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
45 2 0.03
46 66 0.93
47 3 0.04
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (45 bp):
GTATGGTATTTCAGTAAGAAAACCATACTGAGTTGTGAAAAGTAA
Found at i:52482969 original size:4 final size:4
Alignment explanation
Indices: 52482960--52482985 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
52482950 AGGACCGGGT
52482960 GTGG GTGG GTGG GTGG GTGG GTGG GT
1 GTGG GTGG GTGG GTGG GTGG GTGG GT
52482986 CTTATCTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.73, T:0.27
Consensus pattern (4 bp):
GTGG
Found at i:52484182 original size:24 final size:24
Alignment explanation
Indices: 52484147--52484193 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
52484137 TCATGTAAAA
* *
52484147 ATATATAGTTATCATAATTATAAT
1 ATATATAATTATCATAATAATAAT
*
52484171 ATATATAATTATCGTAATAATAA
1 ATATATAATTATCATAATAATAA
52484194 CATTTGCTAA
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:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
ATATATAATTATCATAATAATAAT
Found at i:52484468 original size:18 final size:19
Alignment explanation
Indices: 52484431--52484468 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
52484421 CACATTTTTG
* *
52484431 TCAAATTTACTTAAATAAT
1 TCAAATTTACATAAAGAAT
52484450 TCAAATTT-CATAAAGAAT
1 TCAAATTTACATAAAGAAT
52484468 T
1 T
52484469 TGAGAAGTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (19 bp):
TCAAATTTACATAAAGAAT
Found at i:52491402 original size:19 final size:19
Alignment explanation
Indices: 52491374--52491417 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
52491364 TAATTATTAT
52491374 ATTTAAATATT-TAAATATA
1 ATTTAAATATTCTAAATA-A
* *
52491393 ATTTATATATTCTAATTAA
1 ATTTAAATATTCTAAATAA
52491412 ATTTAA
1 ATTTAA
52491418 TAAATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTAAATATTCTAAATAA
Found at i:52491478 original size:26 final size:30
Alignment explanation
Indices: 52491423--52491482 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 30
52491413 TTTAATAAAT
*
52491423 AATTAATATTAATTACTTAGAAATATTTAA
1 AATTAATATTAATTACTTAGAAACATTTAA
*
52491453 AATTAATATT-ATTA-TTA-AAACATTAAA
1 AATTAATATTAATTACTTAGAAACATTTAA
52491480 AAT
1 AAT
52491483 AAGTTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 11 0.39
28 3 0.11
29 4 0.14
30 10 0.36
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATTACTTAGAAACATTTAA
Found at i:52491670 original size:13 final size:13
Alignment explanation
Indices: 52491646--52491696 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
52491636 ACACTCAAAT
52491646 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
52491659 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
52491672 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
52491685 TTTTCAAAAGCA
1 TTTTCAAAAGCA
52491697 ATGAAGAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:52491850 original size:31 final size:31
Alignment explanation
Indices: 52491789--52491851 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
52491779 TTATTATTAT
* *
52491789 ATATAAGTTGAAGATGATTTAAACAAAAAAA
1 ATATAAGTTGAAGATGATTAAAAAAAAAAAA
52491820 ATATAAGTTGAAGA-G-TTAAAATAAATAAAAA
1 ATATAAGTTGAAGATGATTAAAA-AAA-AAAAA
52491851 A
1 A
52491852 ATGAATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 5 0.18
30 3 0.11
31 20 0.71
ACGTcount: A:0.60, C:0.02, G:0.13, T:0.25
Consensus pattern (31 bp):
ATATAAGTTGAAGATGATTAAAAAAAAAAAA
Found at i:52495995 original size:41 final size:43
Alignment explanation
Indices: 52495944--52496093 Score: 166
Period size: 43 Copynumber: 3.5 Consensus size: 43
52495934 TCAATTCCAC
* * *
52495944 TGTCCTAGACAGGGTCTTACACG-AATCA-AA-TATGATGCCAA
1 TGTCCCAGACAGGGTCTTACACGTAAACACAAGT-CGATGCCAA
*
52495985 TGTCCCAGACATGGTCTTACACGTAAACACAAGTCGATGCCAA
1 TGTCCCAGACAGGGTCTTACACGTAAACACAAGTCGATGCCAA
* *
52496028 CGTCCCAGAC-GTGGTCTTACATGTAAACACAAGTCGATGCCAA
1 TGTCCCAGACAG-GGTCTTACACGTAAACACAAGTCGATGCCAA
**
52496071 CATCCCAGAC-GAGGTCTTACACG
1 TGTCCCAGACAG-GGTCTTACACG
52496094 AAATCATATC
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
41 21 0.22
42 4 0.04
43 69 0.73
44 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (43 bp):
TGTCCCAGACAGGGTCTTACACGTAAACACAAGTCGATGCCAA
Found at i:52496036 original size:43 final size:43
Alignment explanation
Indices: 52495977--52496093 Score: 182
Period size: 43 Copynumber: 2.7 Consensus size: 43
52495967 AATCAAATAT
*
52495977 GATGCCAATGTCCCAGACATGGTCTTACACGTAAACACAAGTC
1 GATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAGTC
* *
52496020 GATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACAAGTC
1 GATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAGTC
*
52496063 GATGCCAACATCCCAGACGA-GGTCTTACACG
1 GATGCCAACGTCCCAGAC-ATGGTCTTACACG
52496094 AAATCATATC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.20
Consensus pattern (43 bp):
GATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAGTC
Found at i:52498983 original size:18 final size:18
Alignment explanation
Indices: 52498960--52499020 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
52498950 CAAGGTCACG
*
52498960 ATCAATAGAGTCACTATC
1 ATCAATAGCGTCACTATC
*
52498978 ATCAATAGCGTCACTAGC
1 ATCAATAGCGTCACTATC
*
52498996 ATCAATATCGTCACTATC
1 ATCAATAGCGTCACTATC
52499014 ATCAATA
1 ATCAATA
52499021 TCGATATCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (18 bp):
ATCAATAGCGTCACTATC
Found at i:52499021 original size:18 final size:18
Alignment explanation
Indices: 52498969--52499035 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
52498959 GATCAATAGA
*
52498969 GTCACTATCATCAATAGC
1 GTCACTATCATCAATATC
*
52498987 GTCACTAGCATCAATATC
1 GTCACTATCATCAATATC
52499005 GTCACTATCATCAATATC
1 GTCACTATCATCAATATC
52499023 G--A-TATCATCAATA
1 GTCACTATCATCAATA
52499036 AGAAAACCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
15 11 0.24
16 1 0.02
18 34 0.74
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (18 bp):
GTCACTATCATCAATATC
Found at i:52502660 original size:3 final size:3
Alignment explanation
Indices: 52502652--52502716 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
52502642 TTAATTTTCA
* *
52502652 TAT TAT TAT TAT TAT TAT TAT TATT TAT TTT TAC TAT T-T TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* *
52502696 TAT TTT TAT TTT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
52502717 TTTGCAGGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.12
3 41 0.82
4 3 0.06
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (3 bp):
TAT
Found at i:52502679 original size:22 final size:22
Alignment explanation
Indices: 52502654--52502717 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 22
52502644 AATTTTCATA
*
52502654 TTATTATTATTATTATTATTAT
1 TTATTTTTATTATTATTATTAT
*
52502676 TTATTTTTACTATT-TTA-T-T
1 TTATTTTTATTATTATTATTAT
*
52502695 TTATTTTTATTTTTATT-TTAT
1 TTATTTTTATTATTATTATTAT
52502716 TT
1 TT
52502718 TTGCAGGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 13 0.37
20 4 0.11
21 6 0.17
22 12 0.34
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (22 bp):
TTATTTTTATTATTATTATTAT
Found at i:52502689 original size:13 final size:12
Alignment explanation
Indices: 52502663--52502719 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
52502653 ATTATTATTA
*
52502663 TTATTATTATTAT
1 TTATTTTTA-TAT
52502676 TTATTTTTACTAT
1 TTATTTTTA-TAT
*
52502689 TT-TATTTTATTT
1 TTAT-TTTTATAT
52502701 TTATTTTTAT-T
1 TTATTTTTATAT
52502712 TTATTTTT
1 TTATTTTT
52502720 GCAGGGAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
11 9 0.23
12 11 0.28
13 19 0.49
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTTTATAT
Found at i:52502719 original size:6 final size:6
Alignment explanation
Indices: 52502633--52502719 Score: 70
Period size: 6 Copynumber: 14.0 Consensus size: 6
52502623 TAAAAAGAAC
* * * * *
52502633 ATTTTA ATTTTA ATTTTCAT ATTATT ATTATT ATTATT ATTATTT ATTTTT
1 ATTTTT ATTTTT ATTTT--T ATTTTT ATTTTT ATTTTT ATT-TTT ATTTTT
52502684 ACTATTTT A-TTTT ATTTTT ATTTTT A-TTTT ATTTTT
1 A-T-TTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
52502720 GCAGGGAAAC
Statistics
Matches: 71, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
5 10 0.14
6 46 0.65
7 6 0.08
8 9 0.13
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.72
Consensus pattern (6 bp):
ATTTTT
Found at i:52502719 original size:12 final size:12
Alignment explanation
Indices: 52502633--52502719 Score: 54
Period size: 14 Copynumber: 6.9 Consensus size: 12
52502623 TAAAAAGAAC
* *
52502633 ATTTTAATTTTA
1 ATTTTATTTTTT
*
52502645 ATTTTCATATTATT
1 ATTTT-AT-TTTTT
52502659 ATTATTATTATTATT
1 ATT-TTATT-TT-TT
52502674 A-TTTATTTTTACT
1 ATTTTATTTTT--T
*
52502687 ATTTTATTTTAT
1 ATTTTATTTTTT
52502699 -TTTTA-TTTTT
1 ATTTTATTTTTT
52502709 ATTTTATTTTT
1 ATTTTATTTTT
52502720 GCAGGGAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
10 4 0.07
11 11 0.19
12 12 0.20
13 9 0.15
14 18 0.31
15 5 0.08
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTATTTTTT
Found at i:52507517 original size:20 final size:20
Alignment explanation
Indices: 52507479--52507518 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52507469 CAAAAAATGA
**
52507479 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
52507499 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
52507519 GGAAAATATT
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:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:52508878 original size:35 final size:36
Alignment explanation
Indices: 52508831--52508907 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 36
52508821 ATTATCATTG
*
52508831 TCAATAATTTCAATATCCAACAAGCTTAAAACATAA
1 TCAATAAATTCAATATCCAACAAGCTTAAAACATAA
* *
52508867 T-AATAAATTCAATATCCAATAAGGTTAAAACATAA
1 TCAATAAATTCAATATCCAACAAGCTTAAAACATAA
52508902 TCAATA
1 TCAATA
52508908 TCTAACAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 32 0.86
36 5 0.14
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.29
Consensus pattern (36 bp):
TCAATAAATTCAATATCCAACAAGCTTAAAACATAA
Found at i:52510560 original size:37 final size:37
Alignment explanation
Indices: 52510510--52510581 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
52510500 CTTATTTTTT
52510510 CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
1 CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
*
52510547 CCATTAGATTAGAATTCACTACCTATTTAATTAAT
1 CCATTAGATTAGAATTCACTAACTATTTAATTAAT
52510582 TATGACCAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (37 bp):
CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
Found at i:52513078 original size:11 final size:11
Alignment explanation
Indices: 52513062--52513092 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
52513052 TAGGTGGAGG
52513062 ACCGGAGGTAT
1 ACCGGAGGTAT
52513073 ACCGGAGGTAT
1 ACCGGAGGTAT
52513084 ACCGGAGGT
1 ACCGGAGGT
52513093 GGACCGGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.39, T:0.16
Consensus pattern (11 bp):
ACCGGAGGTAT
Found at i:52513098 original size:11 final size:11
Alignment explanation
Indices: 52513061--52513099 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
52513051 CTAGGTGGAG
52513061 GACCGGAGGTA
1 GACCGGAGGTA
*
52513072 TACCGGAGGTA
1 GACCGGAGGTA
* *
52513083 TACCGGAGGTG
1 GACCGGAGGTA
52513094 GACCGG
1 GACCGG
52513100 TGGAGGTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.23, C:0.21, G:0.44, T:0.13
Consensus pattern (11 bp):
GACCGGAGGTA
Found at i:52517944 original size:21 final size:21
Alignment explanation
Indices: 52517918--52517976 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
52517908 TGTTCATGTT
52517918 GAATTAATTGATGAATTAGGG
1 GAATTAATTGATGAATTAGGG
52517939 GAATTAATTGATGAATTAGGG
1 GAATTAATTGATGAATTAGGG
52517960 G--TTAAATTGATTGAATT
1 GAATT-AATTGA-TGAATT
52517977 TCAAGTTACG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 28 0.78
ACGTcount: A:0.37, C:0.00, G:0.25, T:0.37
Consensus pattern (21 bp):
GAATTAATTGATGAATTAGGG
Found at i:52520584 original size:46 final size:46
Alignment explanation
Indices: 52520517--52520656 Score: 226
Period size: 46 Copynumber: 3.0 Consensus size: 46
52520507 CATGGCAAAG
* * *
52520517 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
*
52520563 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACCGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
*
52520609 TGTGAAAAGTAGGTATGCTATTTCGGTAAAGAAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAG-AAAACCATACTGAGT
52520656 T
1 T
52520657 ATAGCAATGT
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
46 72 0.83
47 15 0.17
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
Found at i:52521618 original size:25 final size:25
Alignment explanation
Indices: 52521590--52521683 Score: 170
Period size: 25 Copynumber: 3.8 Consensus size: 25
52521580 CTTTAGCGCA
52521590 CTCTCTGATTATTAGCACGTTGGTG
1 CTCTCTGATTATTAGCACGTTGGTG
52521615 CTCTCTGATTATTAGCACGTTGGTG
1 CTCTCTGATTATTAGCACGTTGGTG
*
52521640 CTCTCTGATTATTAGCACGTTGATG
1 CTCTCTGATTATTAGCACGTTGGTG
*
52521665 CTCTCTGATTACTAGCACG
1 CTCTCTGATTATTAGCACG
52521684 ACAATGCTCT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 67 1.00
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.38
Consensus pattern (25 bp):
CTCTCTGATTATTAGCACGTTGGTG
Found at i:52521692 original size:50 final size:50
Alignment explanation
Indices: 52521590--52521694 Score: 156
Period size: 50 Copynumber: 2.1 Consensus size: 50
52521580 CTTTAGCGCA
* * ****
52521590 CTCTCTGATTATTAGCACGTTGGTGCTCTCTGATTATTAGCACGTTGGTG
1 CTCTCTGATTATTAGCACGTTGATGCTCTCTGATTACTAGCACGACAATG
52521640 CTCTCTGATTATTAGCACGTTGATGCTCTCTGATTACTAGCACGACAATG
1 CTCTCTGATTATTAGCACGTTGATGCTCTCTGATTACTAGCACGACAATG
52521690 CTCTC
1 CTCTC
52521695 CGTTTAGCAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (50 bp):
CTCTCTGATTATTAGCACGTTGATGCTCTCTGATTACTAGCACGACAATG
Found at i:52533658 original size:3 final size:3
Alignment explanation
Indices: 52533650--52533676 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52533640 GCATAAAAGA
52533650 TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG
52533677 AATGCCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TAG
Found at i:52548627 original size:40 final size:40
Alignment explanation
Indices: 52548567--52548664 Score: 160
Period size: 40 Copynumber: 2.5 Consensus size: 40
52548557 ACCAGTTTGG
* *
52548567 CACCCAATGCCTCATTGAATAATTCGAGGCAATAAGTTGA
1 CACCCAGTGCCTCATCGAATAATTCGAGGCAATAAGTTGA
*
52548607 CACCCAGTGCCTCATCGAATAATTTGAGGCAATAAGTTGA
1 CACCCAGTGCCTCATCGAATAATTCGAGGCAATAAGTTGA
*
52548647 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
52548665 CTCGAAGTCG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATTCGAGGCAATAAGTTGA
Found at i:52551088 original size:5 final size:5
Alignment explanation
Indices: 52551078--52551108 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
52551068 AATTTGATGG
52551078 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
52551109 AACATAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATTAA
Found at i:52552131 original size:25 final size:25
Alignment explanation
Indices: 52552019--52552292 Score: 178
Period size: 25 Copynumber: 11.1 Consensus size: 25
52552009 CCATTATTTA
* * *
52552019 GCTCTTATGAGCATCCTG-TTATATG
1 GCTCTCATGAGCTTCCCGATTA-ATG
* * *
52552044 GCTCTCACGAGCTTCCCG-TTATTTA
1 GCTCTCATGAGCTTCCCGATTA-ATG
* * *
52552069 GCTCTTATGAACATCCCG-TTATATG
1 GCTCTCATGAGCTTCCCGATTA-ATG
52552094 GCTCTCATGAGCTTCCCGATTAATG
1 GCTCTCATGAGCTTCCCGATTAATG
* * *
52552119 GCTCTCTTAAGCTTCCC-ATTTATG
1 GCTCTCATGAGCTTCCCGATTAATG
52552143 GCTCGT-ATGAGC-TCCCGA-TAATTG
1 GCTC-TCATGAGCTTCCCGATTAA-TG
* * *
52552167 GCTTTCATGAGCTTTCTGATTAATG
1 GCTCTCATGAGCTTCCCGATTAATG
* *
52552192 GCTCTC-TGGAGCTTCTCGA-TATTG
1 GCTCTCAT-GAGCTTCCCGATTAATG
* *
52552216 GCT-TGCATGAGCTTCCTGATT-ACG
1 GCTCT-CATGAGCTTCCCGATTAATG
* *
52552240 ACTCTTATGAGCTTCCCG-TTACATG
1 GCTCTCATGAGCTTCCCGATTA-ATG
*
52552265 GCTCACATGAGCTTCCC-ATTATATG
1 GCTCTCATGAGCTTCCCGATTA-ATG
52552290 GCT
1 GCT
52552293 TGGAAGAGCT
Statistics
Matches: 193, Mismatches: 41, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
23 10 0.05
24 58 0.30
25 119 0.62
26 6 0.03
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATTAATG
Found at i:52552193 original size:49 final size:49
Alignment explanation
Indices: 52552091--52552280 Score: 133
Period size: 49 Copynumber: 3.9 Consensus size: 49
52552081 ATCCCGTTAT
* * * * *
52552091 ATGGCTCTCAT-GAGCTTCCCGATTAATGGCTCT-CTTAAGCTTCC-CATTT
1 ATGGCTCT-ATGGAGCTTCCCGA-TATTGGCT-TGCATGAGCTTCCTGATTA
* *
52552140 ATGGCTCGTAT-GAGC-TCCCGATAATTGGCTTTCATGAGCTTTCTGATTA
1 ATGGCTC-TATGGAGCTTCCCGAT-ATTGGCTTGCATGAGCTTCCTGATTA
* *
52552189 ATGGCTCTCTGGAGCTTCTCGATATTGGCTTGCATGAGCTTCCTGATT-
1 ATGGCTCTATGGAGCTTCCCGATATTGGCTTGCATGAGCTTCCTGATTA
* * * * **
52552237 ACGACTCTTAT-GAGCTTCCCGTTACATGGCTCACATGAGCTTCC
1 ATGGCTC-TATGGAGCTTCCCGATA-TTGGCTTGCATGAGCTTCC
52552281 CATTATATGG
Statistics
Matches: 115, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
47 2 0.02
48 38 0.33
49 68 0.59
50 7 0.06
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (49 bp):
ATGGCTCTATGGAGCTTCCCGATATTGGCTTGCATGAGCTTCCTGATTA
Found at i:52552218 original size:73 final size:73
Alignment explanation
Indices: 52552092--52552292 Score: 194
Period size: 73 Copynumber: 2.7 Consensus size: 73
52552082 TCCCGTTATA
* * *
52552092 TGGCTCTCATGAGCTTCCCGATTAATGGCTCTCTTAAGCTTCCCATTTATGGCTCGTATGAGCTC
1 TGGCTCTCATGAGCTTCCCGATTAATGGCTCTCTGAAGCTTCCCATATATGGCTCGCATGAGCTC
52552157 CCGATAAT
66 CCGATAAT
* * * * * *
52552165 TGGCTTTCATGAGCTTTCTGATTAATGGCTCTCTGGAGCTTCTCGATAT-TGGCTTGCATGAGCT
1 TGGCTCTCATGAGCTTCCCGATTAATGGCTCTCTGAAGCTTC-CCATATATGGCTCGCATGAGC-
* *
52552229 TCCTGATTA-
64 TCCCGATAAT
* * * *
52552238 CGACTCTTATGAGCTTCCCG-TTACATGGCTCACATG-AGCTTCCCATTATATGGCT
1 TGGCTCTCATGAGCTTCCCGATTA-ATGGCTCTC-TGAAGCTTCCCA-TATATGGCT
52552293 TGGAAGAGCT
Statistics
Matches: 103, Mismatches: 19, Indels: 11
0.77 0.14 0.08
Matches are distributed among these distances:
72 5 0.05
73 80 0.78
74 18 0.17
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (73 bp):
TGGCTCTCATGAGCTTCCCGATTAATGGCTCTCTGAAGCTTCCCATATATGGCTCGCATGAGCTC
CCGATAAT
Found at i:52556487 original size:44 final size:45
Alignment explanation
Indices: 52556434--52556536 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
52556424 TGTCTTTGAC
* * *
52556434 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
** * *
52556478 ATGGACTTACATGGCTCAATCTTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAAT
52556524 ATGGACTTACATG
1 ATGGACTTACATG
52556537 GCTCATTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 32 0.64
46 18 0.36
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:52556535 original size:46 final size:44
Alignment explanation
Indices: 52556456--52556541 Score: 136
Period size: 46 Copynumber: 1.9 Consensus size: 44
52556446 GAATTATTCC
*
52556456 TGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAATCT
1 TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCT
*
52556500 TGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 TGTCTCCAAAGCCATA--TATAATATGGACTTACATGGCTCA
52556542 TTTCTGTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 15 0.39
46 23 0.61
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (44 bp):
TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCT
Found at i:52564539 original size:16 final size:15
Alignment explanation
Indices: 52564500--52564548 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
52564490 TTGACTTGAT
*
52564500 TAATTTTTAAATTTA
1 TAATTTTTATATTTA
52564515 TAATATTTTATATTATA
1 TAAT-TTTTATATT-TA
*
52564532 TTATTTTTATATATTA
1 TAATTTTTATAT-TTA
52564548 T
1 T
52564549 GTAATTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
16 19 0.66
17 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TAATTTTTATATTTA
Found at i:52564660 original size:74 final size:72
Alignment explanation
Indices: 52564559--52564694 Score: 157
Period size: 74 Copynumber: 1.9 Consensus size: 72
52564549 GTAATTTATA
* * ** * *
52564559 ATATATAAAAATAAATATATACTAAATACAT-AATATTATTCTAATGTAAATATTAAAATAATAT
1 ATATAAAAAAATAAATAAATAAAAAATACATGAA-ATTATT-AAATATAAA-ATTAAAATAATAT
52564623 TAAGATGATT
63 TAAGATGATT
* * *
52564633 ATATAAAAAAATCAATAAATAAAAAATATATGAAATTATTAAATATCAAATTAAAATAATAT
1 ATATAAAAAAATAAATAAATAAAAAATACATGAAATTATTAAATATAAAATTAAAATAATAT
52564695 AAATATTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
72 13 0.25
73 6 0.12
74 31 0.60
75 2 0.04
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (72 bp):
ATATAAAAAAATAAATAAATAAAAAATACATGAAATTATTAAATATAAAATTAAAATAATATTAA
GATGATT
Found at i:52566335 original size:21 final size:21
Alignment explanation
Indices: 52566294--52566335 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
52566284 TCCTCCTCCT
*
52566294 CCTCCACCCCCGCCGCCACCA
1 CCTCCACCCCCGCCACCACCA
*
52566315 CCTCCACCTCCC-CCACGACCA
1 CCTCCACC-CCCGCCACCACCA
52566336 ACACCTCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.17, C:0.69, G:0.07, T:0.07
Consensus pattern (21 bp):
CCTCCACCCCCGCCACCACCA
Found at i:52573186 original size:22 final size:21
Alignment explanation
Indices: 52573161--52573203 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
52573151 TAGACGAAGT
*
52573161 ATAATATTATTTAATTACATAA
1 ATAATATAATTTAATTA-ATAA
*
52573183 ATAATATAATTTACTTAATAA
1 ATAATATAATTTAATTAATAA
52573204 CTACATGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATATAATTTAATTAATAA
Found at i:52575552 original size:25 final size:25
Alignment explanation
Indices: 52575513--52575606 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 25
52575503 AGCATCCCGT
**
52575513 ATGGCTCTCACGAGCTTCCCGATTA
1 ATGGCTCTCTTGAGCTTCCCGATTA
* * *
52575538 ATGACTCTCTTGAGCTTTCCG-TTT
1 ATGGCTCTCTTGAGCTTCCCGATTA
*
52575562 ATGGCTCAT-ATGAGCTTCCCGA-TA
1 ATGGCTC-TCTTGAGCTTCCCGATTA
*
52575586 ATTGGCTCTCTAGAGCTTCCC
1 A-TGGCTCTCTTGAGCTTCCC
52575607 AATATTGGCT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
24 21 0.39
25 33 0.61
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (25 bp):
ATGGCTCTCTTGAGCTTCCCGATTA
Found at i:52575625 original size:24 final size:25
Alignment explanation
Indices: 52575514--52575629 Score: 73
Period size: 24 Copynumber: 4.7 Consensus size: 25
52575504 GCATCCCGTA
* *
52575514 TGGCTCTCACGAGCTTCCCGATTAA-
1 TGGCTCTCATGAGCTTCCC-AATAAT
* * * ** *
52575539 TGACTCTCTTGAGCTTTCCGTTTA-
1 TGGCTCTCATGAGCTTCCCAATAAT
*
52575563 TGGCTCAT-ATGAGCTTCCCGATAAT
1 TGGCTC-TCATGAGCTTCCCAATAAT
52575588 TGGCTCTC-TAGAGCTTCCCAAT-AT
1 TGGCTCTCAT-GAGCTTCCCAATAAT
52575612 TGGCT-TGCATGAGCTTCC
1 TGGCTCT-CATGAGCTTCC
52575630 TGATTACGAC
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
23 1 0.01
24 38 0.52
25 34 0.47
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (25 bp):
TGGCTCTCATGAGCTTCCCAATAAT
Found at i:52577900 original size:44 final size:44
Alignment explanation
Indices: 52577795--52578008 Score: 232
Period size: 44 Copynumber: 4.6 Consensus size: 44
52577785 TACGTATGAT
*
52577795 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCT-GAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
*
52577838 CATTTATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CA-CT-T-A--T--CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
*
52577889 CACTTATCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
* *
52577933 CACTTATCACTTGCCACTTGTCATTGATCAGATAAGTGTAGCTGAAGCTAC
1 CAC-T-T-A--T--CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
* *
52577984 TACTTATCACTTGTCATTGATCAGA
1 CACTTATCACTTGTCACTGATCAGA
52578009 AGTACTCAAA
Statistics
Matches: 148, Mismatches: 8, Indels: 29
0.80 0.04 0.16
Matches are distributed among these distances:
43 2 0.01
44 58 0.39
45 2 0.01
46 4 0.03
47 1 0.01
48 3 0.02
49 3 0.02
50 31 0.21
51 44 0.30
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (44 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:52577963 original size:95 final size:94
Alignment explanation
Indices: 52577795--52578006 Score: 352
Period size: 95 Copynumber: 2.2 Consensus size: 94
52577785 TACGTATGAT
* * *
52577795 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAGCTACCATTTATCACTTGCCACTTGTC
1 CACTTATCACTTGTCACTGATCAAATAAGTGTAGCTAAGCTACCACTTATCACTTGCCACTTGTC
52577860 ACTGATCAGATAAGTGTAGCTAAAGCTAC
66 ACTGATCAGATAAGTGTAGCTAAAGCTAC
52577889 CACTTATCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTTGT
1 CACTTATCACTTGTCACTGATCAAATAAGTGTAGCT-AAGCTACCACTTATCACTTGCCACTTGT
* *
52577954 CATTGATCAGATAAGTGTAGCTGAAGCTAC
65 CACTGATCAGATAAGTGTAGCTAAAGCTAC
* *
52577984 TACTTATCACTTGTCATTGATCA
1 CACTTATCACTTGTCACTGATCA
52578007 GAAGTACTCA
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 35 0.32
95 75 0.68
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (94 bp):
CACTTATCACTTGTCACTGATCAAATAAGTGTAGCTAAGCTACCACTTATCACTTGCCACTTGTC
ACTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:52577996 original size:51 final size:51
Alignment explanation
Indices: 52577793--52577996 Score: 280
Period size: 51 Copynumber: 4.2 Consensus size: 51
52577783 CTTACGTATG
** * *
52577793 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCT-GAGCTACCATTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
52577843 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC-T
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
52577893 -T-A--T--CACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
52577938 ATCACTTGCCACTTGTCATTGATCAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
52577989 ATCACTTG
1 ATCACTTG
52577997 TCATTGATCA
Statistics
Matches: 137, Mismatches: 9, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
44 39 0.28
45 1 0.01
46 2 0.01
47 1 0.01
48 1 0.01
49 2 0.01
50 37 0.27
51 54 0.39
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (51 bp):
ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:52582408 original size:26 final size:26
Alignment explanation
Indices: 52582371--52582423 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
52582361 AAATGGAAAG
52582371 TAAACACAAAAGTTCGCAACAAATGT
1 TAAACACAAAAGTTCGCAACAAATGT
*
52582397 TAAACACGAAAGTTCGCAACAAATGT
1 TAAACACAAAAGTTCGCAACAAATGT
52582423 T
1 T
52582424 GAACCTCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (26 bp):
TAAACACAAAAGTTCGCAACAAATGT
Found at i:52585706 original size:47 final size:47
Alignment explanation
Indices: 52585573--52585779 Score: 184
Period size: 47 Copynumber: 4.3 Consensus size: 47
52585563 ATAGTAAAAT
** * *
52585573 TATGGTCTTGCACA-TAGTCACATATCACATACCGAGGCCATAGCCCAGC
1 TATGGTCTTATACAGTAG-CACATATCAC--ACCGATGCCATAGCCCAGA
* * * * *
52585622 CATGGTCTTATAC-GGATCACATATCACACTGATGCCATATCCCAGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* *
52585668 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATATCCCGGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* * * * *
52585715 TATGGTCTTATACGGAAGCACAAATCACATTTCTCCGAAGCCATAGCCCAGC
1 TATGGTCTTATACAGTAGCACATATCACA-----CCGATGCCATAGCCCAGA
52585767 TATGGTCTTATAC
1 TATGGTCTTATAC
52585780 GGAAATCACA
Statistics
Matches: 130, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
46 27 0.21
47 55 0.42
48 10 0.08
49 11 0.08
52 27 0.21
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (47 bp):
TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
Found at i:52588821 original size:24 final size:24
Alignment explanation
Indices: 52588780--52588826 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
52588770 TTTTTAAAGC
*
52588780 AATTGATTTTGGGTTTTTTTTTTA
1 AATTGATTTTGGGTTTTTGTTTTA
*
52588804 AATTTATTTT-GGTATTTTGTTTT
1 AATTGATTTTGGGT-TTTTGTTTT
52588827 GAAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (24 bp):
AATTGATTTTGGGTTTTTGTTTTA
Found at i:52603994 original size:17 final size:17
Alignment explanation
Indices: 52603972--52604010 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
52603962 TGTAATTAAT
52603972 TTTAAAAGTTTAATATA
1 TTTAAAAGTTTAATATA
* *
52603989 TTTAAAATTTTGATATA
1 TTTAAAAGTTTAATATA
*
52604006 CTTAA
1 TTTAA
52604011 TATATATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (17 bp):
TTTAAAAGTTTAATATA
Found at i:52604144 original size:22 final size:21
Alignment explanation
Indices: 52604119--52604179 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
52604109 TATAAACAAT
52604119 TTTAAATTTTTAATATATTCAA
1 TTTAAATTTTTAATATATT-AA
* * *
52604141 TTTATATTTTTAAAATA-TAT
1 TTTAAATTTTTAATATATTAA
*
52604161 TTTAAAATTTTAATATATT
1 TTTAAATTTTTAATATATT
52604180 TTTTAATAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 15 0.47
21 2 0.06
22 15 0.47
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAAATTTTTAATATATTAA
Found at i:52604171 original size:20 final size:20
Alignment explanation
Indices: 52604148--52604185 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52604138 CAATTTATAT
52604148 TTTTAAAATATATTTTAAAA
1 TTTTAAAATATATTTTAAAA
* *
52604168 TTTTAATATATTTTTTAA
1 TTTTAAAATATATTTTAA
52604186 TAGGTAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAAAATATATTTTAAAA
Found at i:52604230 original size:18 final size:18
Alignment explanation
Indices: 52604207--52604270 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
52604197 AAAAAAGATC
52604207 TTTTAATATATTTAAAAT
1 TTTTAATATATTTAAAAT
* * *
52604225 TTTTAAAAAAATTAAAAAT
1 TTTT-AATATATTTAAAAT
52604244 TTTTAA-ATATATTAAAAT
1 TTTTAATATAT-TTAAAAT
*
52604262 TTTAAATAT
1 TTTTAATAT
52604271 GTTAAAGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
17 3 0.08
18 17 0.46
19 17 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTTAATATATTTAAAAT
Found at i:52604266 original size:17 final size:18
Alignment explanation
Indices: 52604207--52604276 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
52604197 AAAAAAGATC
52604207 TTTT-AATATATTTAAAAT
1 TTTTAAATATA-TTAAAAT
* *
52604225 TTTTAAAAAAATTAAAAAT
1 TTTTAAATATATT-AAAAT
52604244 TTTTAAATATATTAAAA-
1 TTTTAAATATATTAAAAT
*
52604261 TTTTAAATATGTTAAA
1 TTTTAAATATATTAAA
52604277 GAAAAAGTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
17 15 0.33
18 10 0.22
19 20 0.44
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (18 bp):
TTTTAAATATATTAAAAT
Done.