Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007956.1 Hibiscus syriacus cultivar Beakdansim tig00110383_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: 3102597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 14
Found at i:681346 original size:63 final size:63
Alignment explanation
Indices: 681242--681380 Score: 156
Period size: 63 Copynumber: 2.2 Consensus size: 63
681232 TCTACCATTG
* ** * *
681242 TTCAGGATCCACATCCCATTGTTCAGGATTCACCTCTCATCGTTCCAGAGGCC-CCTCCCATCA
1 TTCAGGATCCACCTCCCATTGTTCAGGAGGCACCTCCCATCGTT-CAGAAGCCACCTCCCATCA
* * * * *
681305 TTCAGGATCCACCTCTCATTGTTCCA-GAGGCCCCTCCCATCGTTTAGAATCCACCTCCCATCG
1 TTCAGGATCCACCTCCCATTGTT-CAGGAGGCACCTCCCATCGTTCAGAAGCCACCTCCCATCA
681368 TTCAGGATCCACC
1 TTCAGGATCCACC
681381 CCGCATCATT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
62 5 0.08
63 57 0.89
64 2 0.03
ACGTcount: A:0.20, C:0.39, G:0.14, T:0.27
Consensus pattern (63 bp):
TTCAGGATCCACCTCCCATTGTTCAGGAGGCACCTCCCATCGTTCAGAAGCCACCTCCCATCA
Found at i:683432 original size:20 final size:20
Alignment explanation
Indices: 683369--683425 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
683359 CTATCTTTAA
683369 GAAAATCAAATTCGCAACTC
1 GAAAATCAAATTCGCAACTC
* **
683389 GAAAATCGAATTTACAACTC
1 GAAAATCAAATTCGCAACTC
*
683409 GAAAATAAAATTCGCAA
1 GAAAATCAAATTCGCAA
683426 TACGAAATCG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.21
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACTC
Found at i:683955 original size:12 final size:12
Alignment explanation
Indices: 683940--683973 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
683930 AGGTGAAGGC
*
683940 GATTGTGATTGA
1 GATTTTGATTGA
*
683952 GATTTTGATTGC
1 GATTTTGATTGA
683964 GATTTTGATT
1 GATTTTGATT
683974 TCCCTTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.50
Consensus pattern (12 bp):
GATTTTGATTGA
Found at i:686446 original size:12 final size:12
Alignment explanation
Indices: 686425--686458 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
686415 AGTTGTGGAT
*
686425 TTTGAGATTGTG
1 TTTGATATTGTG
686437 TTTGATATTGTG
1 TTTGATATTGTG
*
686449 TTTGGTATTG
1 TTTGATATTG
686459 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:687271 original size:20 final size:20
Alignment explanation
Indices: 687233--687418 Score: 99
Period size: 20 Copynumber: 9.3 Consensus size: 20
687223 TTTGTGTATT
687233 GAAATT-AAAATCTGTGTTGC
1 GAAATTAAAAATC-GTGTTGC
* *
687253 GAAATTAAAATTCGCGTTGC
1 GAAATTAAAAATCGTGTTGC
* **
687273 G-AATACAAAAATCAAGTTGC
1 GAAAT-TAAAAATCGTGTTGC
*** * * *
687293 GAAAACGAAATTCATATTGC
1 GAAATTAAAAATCGTGTTGC
* ** *
687313 GAAATTGAAAATCGCATTAC
1 GAAATTAAAAATCGTGTTGC
*
687333 G-AATTAGAAAATCTTGTTGC
1 GAAATTA-AAAATCGTGTTGC
** *
687353 GAAATGGAAACTCGTGTTGC
1 GAAATTAAAAATCGTGTTGC
* *
687373 GAATTTAAAAATCGAGTTGC
1 GAAATTAAAAATCGTGTTGC
*** *
687393 GAAAAGGAAATTCGTGTTGC
1 GAAATTAAAAATCGTGTTGC
687413 GAAATT
1 GAAATT
687419 GTCGAATTCG
Statistics
Matches: 122, Mismatches: 39, Indels: 10
0.71 0.23 0.06
Matches are distributed among these distances:
19 7 0.06
20 105 0.86
21 10 0.08
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.28
Consensus pattern (20 bp):
GAAATTAAAAATCGTGTTGC
Found at i:687376 original size:40 final size:40
Alignment explanation
Indices: 687309--687415 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 40
687299 GAAATTCATA
* ** * **
687309 TTGCGAAATTGAAAATCGCATTACGAA-TTAGAAAATCTTG
1 TTGCGAAATGGAAAATCGTGTTGCGAATTTA-AAAATCGAG
*
687349 TTGCGAAATGGAAACTCGTGTTGCGAATTTAAAAATCGAG
1 TTGCGAAATGGAAAATCGTGTTGCGAATTTAAAAATCGAG
* *
687389 TTGCGAAAAGGAAATTCGTGTTGCGAA
1 TTGCGAAATGGAAAATCGTGTTGCGAA
687416 ATTGTCGAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 54 0.95
41 3 0.05
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (40 bp):
TTGCGAAATGGAAAATCGTGTTGCGAATTTAAAAATCGAG
Found at i:687384 original size:60 final size:60
Alignment explanation
Indices: 687246--687386 Score: 149
Period size: 60 Copynumber: 2.4 Consensus size: 60
687236 ATTAAAATCT
* * * *
687246 GTGTTGCGAAATTAAAATTCGCGTTGCGAATACAAAAATCAAGTTGCGAAAACGAAATTC
1 GTGTTGCGAAATTAAAAATCGCATTACGAATACAAAAATCAAGTTGCGAAAACGAAACTC
* * * * ** **
687306 ATATTGCGAAATTGAAAATCGCATTACGAATTA-GAAAATCTTGTTGCGAAATGGAAACTC
1 GTGTTGCGAAATTAAAAATCGCATTACGAA-TACAAAAATCAAGTTGCGAAAACGAAACTC
*
687366 GTGTTGCGAATTTAAAAATCG
1 GTGTTGCGAAATTAAAAATCG
687387 AGTTGCGAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
60 62 0.97
61 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (60 bp):
GTGTTGCGAAATTAAAAATCGCATTACGAATACAAAAATCAAGTTGCGAAAACGAAACTC
Found at i:687439 original size:13 final size:13
Alignment explanation
Indices: 687421--687445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
687411 GCGAAATTGT
687421 CGAATTCGACTTG
1 CGAATTCGACTTG
687434 CGAATTCGACTT
1 CGAATTCGACTT
687446 CTGTGTTGCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (13 bp):
CGAATTCGACTTG
Found at i:687456 original size:20 final size:18
Alignment explanation
Indices: 687402--687522 Score: 71
Period size: 20 Copynumber: 6.1 Consensus size: 18
687392 CGAAAAGGAA
687402 ATTCGTGTTGCGAAATTGTCG
1 ATTCGTGTTGCG-AA-T-TCG
**
687423 AATTCGACTTGCGAATTCG
1 -ATTCGTGTTGCGAATTCG
*
687442 ACTTCTGTGTTGCGAATTCCAA
1 A-TTC-GTGTTGCGAATT-C-G
*
687464 ATTCGAGTTGCGAATTCTG
1 ATTCGTGTTGCGAATTC-G
** *
687483 AAACTGTGTTGCGAAATTAG
1 ATTC-GTGTTGCG-AATTCG
687503 AGTTCGTGTTGCGAATTCG
1 A-TTCGTGTTGCGAATTCG
687522 A
1 A
687523 AACCAAGTTG
Statistics
Matches: 77, Mismatches: 15, Indels: 17
0.71 0.14 0.16
Matches are distributed among these distances:
18 1 0.01
19 15 0.19
20 39 0.51
21 11 0.14
22 11 0.14
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (18 bp):
ATTCGTGTTGCGAATTCG
Found at i:687478 original size:40 final size:39
Alignment explanation
Indices: 687348--687525 Score: 135
Period size: 40 Copynumber: 4.4 Consensus size: 39
687338 AGAAAATCTT
* * * * *
687348 GTTGCGAAATGGAAACTCGTGTTGCGAATTTAAAAATCGA
1 GTTGCGAATTCGAAACT-GTGTTGCGAAATTAGAATTCGA
*** * *
687388 GTTGCGAAAAGGAAATTCGTGTTGCGAAATTGTCGAATTCGA
1 GTTGCGAATTCGAAACT-GTGTTGCGAAA-T-TAGAATTCGA
* **
687430 CTTGCGAATTCGACTTCTGTGTTGCG-AATTCCA-AATTCGA
1 GTTGCGAATTCGA-AACTGTGTTGCGAAATT--AGAATTCGA
* *
687470 GTTGCGAATTCTGAAACTGTGTTGCGAAATTAGAGTTCGT
1 GTTGCGAATTC-GAAACTGTGTTGCGAAATTAGAATTCGA
687510 GTTGCGAATTCGAAAC
1 GTTGCGAATTCGAAAC
687526 CAAGTTGCGA
Statistics
Matches: 111, Mismatches: 19, Indels: 17
0.76 0.13 0.12
Matches are distributed among these distances:
39 7 0.06
40 70 0.63
41 9 0.08
42 24 0.22
43 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (39 bp):
GTTGCGAATTCGAAACTGTGTTGCGAAATTAGAATTCGA
Found at i:687519 original size:60 final size:58
Alignment explanation
Indices: 687431--687544 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 58
687421 CGAATTCGAC
* * *
687431 TTGCGAATTCGACTTCTGTGTTGCGAATTCCAAATTCGAGTTGCGAATTCTGAAACTGTG
1 TTGCGAATTAGACTTCTGTGTTGCGAATTCCAAA-CCAAGTTGCGAATTC-GAAACTGTG
* *
687491 TTGCGAAATTAGAGTTC-GTGTTGCGAATTCGAAACCAAGTTGCGAATTCGAAAC
1 TTGCG-AATTAGACTTCTGTGTTGCGAATTCCAAACCAAGTTGCGAATTCGAAAC
687545 CAAGTTGCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 5 0.10
59 13 0.27
60 21 0.44
61 9 0.19
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (58 bp):
TTGCGAATTAGACTTCTGTGTTGCGAATTCCAAACCAAGTTGCGAATTCGAAACTGTG
Found at i:687532 original size:19 final size:19
Alignment explanation
Indices: 687510--687559 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
687500 TAGAGTTCGT
687510 GTTGCGAATTCGAAACCAA
1 GTTGCGAATTCGAAACCAA
687529 GTTGCGAATTCGAAACCAA
1 GTTGCGAATTCGAAACCAA
687548 GTTGCGAATTCG
1 GTTGCGAATTCG
687560 TTGATTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (19 bp):
GTTGCGAATTCGAAACCAA
Found at i:687769 original size:19 final size:16
Alignment explanation
Indices: 687735--687765 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
687725 TACAAAATCT
687735 AATAATTCATAATATA
1 AATAATTCATAATATA
*
687751 AATAATTCATTATAT
1 AATAATTCATAATAT
687766 TATATATATA
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:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:687773 original size:2 final size:2
Alignment explanation
Indices: 687761--687799 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
687751 AATAATTCAT
687761 TA TA T- TA 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 TA TA TA TA
687800 ACAAAAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:693859 original size:2 final size:2
Alignment explanation
Indices: 693852--693948 Score: 171
Period size: 2 Copynumber: 49.5 Consensus size: 2
693842 TCTTATACTC
*
693852 TA TA TA TA TA TA TA TA TA TA GA 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 TA TA TA TA TA
693894 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
693934 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
693949 CAAAAATTTT
Statistics
Matches: 91, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 89 0.98
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:694762 original size:2 final size:2
Alignment explanation
Indices: 694755--694786 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
694745 TCCCCTCTTT
694755 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
694787 ATGTGGGTTT
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:702504 original size:3 final size:3
Alignment explanation
Indices: 702491--702536 Score: 74
Period size: 3 Copynumber: 14.7 Consensus size: 3
702481 AAGTATTAAA
702491 AAT ATAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
702537 ATATTTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:702520 original size:19 final size:19
Alignment explanation
Indices: 702498--702539 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
702488 AAAAATATAT
702498 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
702517 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
702536 AATA
1 AATA
702540 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAATAATAATAATAATA
Found at i:703421 original size:124 final size:124
Alignment explanation
Indices: 703195--703474 Score: 411
Period size: 124 Copynumber: 2.3 Consensus size: 124
703185 CGATCCGTTG
* * *
703195 GGCACAATATCCTTCGTCGTGAAATTGAAATCGTGGATGGATCATTCGTCGTGAAGTTGAGCCTT
1 GGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGATCATTCGTCGTGAAGTTGAGCATT
* *
703260 GAATTGGATATCATTCGTTACGAAGTTAAAATCCAATCTAGAGATGGATGCTTCTTGT-
66 GAATTAGATATCATTCGTTACGAAGTTAAAATCCAATCTAGAGATGGATGCTACTTGTA
* * *
703318 GAGCACGATATCCTTTGTCGTGAAGTTGAAATCGTGGAT-GACTCCTTCGTTGTGAAGTTGAGCA
1 G-GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGA-TCATTCGTCGTGAAGTTGAGCA
* ** *
703382 TTGAATTAGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATGCTACTTGTA
64 TTGAATTAGATATCATTCGTTACGAAGTTAAAATCCAATCTAGAGATGGATGCTACTTGTA
*
703443 GGCACGATATCCTTCATCGTGAAGTTGAAATC
1 GGCACGATATCCTTCGTCGTGAAGTTGAAATC
703475 CAATCTTGAG
Statistics
Matches: 140, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
123 3 0.02
124 136 0.97
125 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (124 bp):
GGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGATCATTCGTCGTGAAGTTGAGCATT
GAATTAGATATCATTCGTTACGAAGTTAAAATCCAATCTAGAGATGGATGCTACTTGTA
Found at i:703783 original size:156 final size:153
Alignment explanation
Indices: 703502--703786 Score: 417
Period size: 156 Copynumber: 1.8 Consensus size: 153
703492 TACCAAATTG
*
703502 GCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCGCTTCGAGT
1 GCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCGCTTCGAGT
* * * *
703567 TCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTGGTTTGTTGACAG
66 CCAATAACCTTCGCTATGAAGTTGAAATTGACTCTAAATGAAACTAGAAAGTGATTTGTTGACAG
703632 ACGCTCCTTCACTGTGAAGTTGA
131 ACGCTCCTTCACTGTGAAGTTGA
* * * *
703655 GCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTGTAAGTTGTGTTGTTTCG
1 GCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAG-T-T-TCGCTTCG
* * * * *
703720 AGTCCAATAACCTTCGTTGTGAAGTTGAAATTGACTCTAAATGAAATTGGAAAGTTATTTGTTGA
63 AGTCCAATAACCTTCGCTATGAAGTTGAAATTGACTCTAAATGAAACTAGAAAGTGATTTGTTGA
703785 CA
128 CA
703787 CACAACTTTT
Statistics
Matches: 115, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
153 49 0.43
154 1 0.01
155 1 0.01
156 64 0.56
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (153 bp):
GCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCGCTTCGAGT
CCAATAACCTTCGCTATGAAGTTGAAATTGACTCTAAATGAAACTAGAAAGTGATTTGTTGACAG
ACGCTCCTTCACTGTGAAGTTGA
Found at i:705328 original size:13 final size:13
Alignment explanation
Indices: 705310--705339 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
705300 TTAATTGTGA
705310 AAAATTAAAAATT
1 AAAATTAAAAATT
*
705323 AAAATTAAAATTT
1 AAAATTAAAAATT
705336 AAAA
1 AAAA
705340 ACTCAATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:705487 original size:23 final size:23
Alignment explanation
Indices: 705436--705487 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
705426 AAATATGAAA
705436 TAAAAA-ATAAAAAAGAAAGTTT
1 TAAAAATATAAAAAAGAAAGTTT
** * *
705458 TTTAAATATATAAAATAAAGTTT
1 TAAAAATATAAAAAAGAAAGTTT
705481 TAAAAAT
1 TAAAAAT
705488 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.33
Consensus pattern (23 bp):
TAAAAATATAAAAAAGAAAGTTT
Found at i:706564 original size:20 final size:20
Alignment explanation
Indices: 706527--706564 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
706517 AAACACAACT
**
706527 ATTCGCAACTCAGTTTTCAA
1 ATTCGCAACTCAAATTTCAA
706547 ATTCGCAACTCAAATTTC
1 ATTCGCAACTCAAATTTC
706565 GCAACGCTAA
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:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (20 bp):
ATTCGCAACTCAAATTTCAA
Found at i:706595 original size:72 final size:72
Alignment explanation
Indices: 706500--706637 Score: 231
Period size: 72 Copynumber: 1.9 Consensus size: 72
706490 TTCGTAATGT
* * * *
706500 TAATTACCGATATAGGTAAACACAACTATTCGCAACTCAGTTTTCAAATTCGCAACTCAAATTTC
1 TAATTACCGATATAAGTAAACACAACTATTCACAACTCAGTTTTCAAATTAGCAACGCAAATTTC
706565 GCAACGC
66 GCAACGC
*
706572 TAATTACCGATATAAGTAAACACAACTATTCACAACTCAGTTTTCAAATTAGCAACGCGAATTTC
1 TAATTACCGATATAAGTAAACACAACTATTCACAACTCAGTTTTCAAATTAGCAACGCAAATTTC
706637 G
66 G
706638 TTTTCGCAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (72 bp):
TAATTACCGATATAAGTAAACACAACTATTCACAACTCAGTTTTCAAATTAGCAACGCAAATTTC
GCAACGC
Found at i:706900 original size:20 final size:20
Alignment explanation
Indices: 706875--706965 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
706865 TCGGTAATTA
706875 GCGTTGCGAATTTGAAAACC
1 GCGTTGCGAATTTGAAAACC
706895 GCGTTGCGAATTTGAAAACC
1 GCGTTGCGAATTTGAAAACC
* ** * *
706915 GCATTGCGCTTTTGGAGAATC
1 GCGTTGCGAATTT-GAAAACC
* * *
706936 GCGCTACGAATTTGAAAACT
1 GCGTTGCGAATTTGAAAACC
*
706956 GTGTTGCGAA
1 GCGTTGCGAA
706966 ATTAGTGTTC
Statistics
Matches: 54, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
20 41 0.76
21 13 0.24
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAACC
Found at i:709177 original size:27 final size:27
Alignment explanation
Indices: 709144--709213 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
709134 TAACCGGTTT
* *
709144 CGGTTTGTAAAAAACCGGTTTTTTATC
1 CGGTTTGAAAAAAACCGGTTTTTAATC
709171 CGGTTTGAAAAAAACCGGTTTTTAATC
1 CGGTTTGAAAAAAACCGGTTTTTAATC
709198 CGG--T-AAAAAAACCGGT
1 CGGTTTGAAAAAAACCGGT
709214 CGTTCAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
24 12 0.29
25 1 0.02
27 28 0.68
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (27 bp):
CGGTTTGAAAAAAACCGGTTTTTAATC
Found at i:711138 original size:12 final size:11
Alignment explanation
Indices: 711097--711138 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 11
711087 TGGTCACTGA
711097 AATTT-ATTTT
1 AATTTCATTTT
711107 AATTT-ATTTT
1 AATTTCATTTT
711117 AATTTGCATTTT
1 AATTT-CATTTT
711129 AAGTTTCATT
1 AA-TTTCATT
711139 CCGTTTCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 15 0.52
12 11 0.38
13 3 0.10
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (11 bp):
AATTTCATTTT
Found at i:716633 original size:29 final size:29
Alignment explanation
Indices: 716591--716649 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
716581 ATTTTCACCT
716591 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
716620 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
716649 A
1 A
716650 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:721162 original size:29 final size:29
Alignment explanation
Indices: 721120--721178 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
721110 ATTTTCACCT
721120 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
721149 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
721178 A
1 A
721179 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:722046 original size:15 final size:15
Alignment explanation
Indices: 722026--722056 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
722016 CAACAGATAA
722026 AATTTTTATTAAAAT
1 AATTTTTATTAAAAT
*
722041 AATTTTTATTTAAAT
1 AATTTTTATTAAAAT
722056 A
1 A
722057 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATTAAAAT
Found at i:722720 original size:18 final size:19
Alignment explanation
Indices: 722686--722722 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
722676 CACGGAATGT
722686 AAGATTACCAGTGGGAATAA
1 AAGATTACCA-TGGGAATAA
722706 AAGATTACC-TGGGAATA
1 AAGATTACCATGGGAATA
722723 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (19 bp):
AAGATTACCATGGGAATAA
Found at i:728389 original size:37 final size:37
Alignment explanation
Indices: 728339--728413 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
728329 CTAAATCTTG
728339 TATTCTGATCTGATGATGACGATGATATAAAAGAACA
1 TATTCTGATCTGATGATGACGATGATATAAAAGAACA
728376 TATTCTGATCTGATGATGACGATGATATAAAAGAACA
1 TATTCTGATCTGATGATGACGATGATATAAAAGAACA
728413 T
1 T
728414 GCACCGTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.31
Consensus pattern (37 bp):
TATTCTGATCTGATGATGACGATGATATAAAAGAACA
Found at i:733882 original size:55 final size:55
Alignment explanation
Indices: 733823--734093 Score: 347
Period size: 55 Copynumber: 5.0 Consensus size: 55
733813 AATCTTCTGA
* * *
733823 AATCGTGTCTGCTCTCTATTTCTTCAGAGCGTATAAGACTCGAACAATTTTCAAT
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAT
* *
733878 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAATAATCTTCAAT
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAT
* * *
733933 AATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATGACACTCGAACAATCTTCAAT
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAT
* *
733988 AATCGCGTCTGCTCCCTATTTCTTTTAGAGAGTATAAGACTCGAACAATCTTC-A-
1 AATCGTGTCTGCTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAAT
* * *
734042 AA-CGGGT-TCGCTCCCTAATTT-TTCAGAGAGTAT-AGAACACGAATAATCTTCA
1 AATCGTGTCT-GCTCCCT-ATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCA
734094 TCAAATGGGT
Statistics
Matches: 194, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
51 2 0.01
52 25 0.13
53 11 0.06
54 6 0.03
55 123 0.63
56 27 0.14
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (55 bp):
AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAT
Found at i:734158 original size:54 final size:54
Alignment explanation
Indices: 734036--734739 Score: 699
Period size: 54 Copynumber: 13.1 Consensus size: 54
734026 ACTCGAACAA
* * * * *
734036 TCTTCAAACGGGTTCGCTCCCTAATTT-TTCAGAGAGTATAGAACACGAATAATCT
1 TCTTCAAACGGGTTCGCTCCCT-CTTTCTTTAGGGAGTATGGAACTCGAAT-ATCT
* * * * * *
734091 TCATCAAATGGGTTCGCTCCCTCTTTCTCTAGGGTGTATGGAACTTGGATATCT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAATATCT
* * * *
734145 TCTTCAAACGGGTTCACTCCCTCTTTATTTAAGGAGTATGGAACTCGAAAATCT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAATATCT
** * * *
734199 TCTGAAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCG-A-A-CA
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAATATCT
* * * *
734250 TCTTCAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATGAAACTCGAACATCT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAATATCT
** * * * *
734304 TCTTCTTACGGGTTCGCTGCCTCTTTCTCTAGGGAGTATGAAACTCGAAAATCT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAATATCT
** * * * *
734358 TCTGAAAACGGGTTCTCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAAAATCT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAATATCT
** * * * * *
734412 TCTGAAAACGGGTTCGCT-TCTTTTTTTTTAAGGAGTATGGAACTCG-A-A-CA
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAATATCT
* * *
734462 TCTTCAAACGGGTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAATATCT
** * *
734516 TCTTCTTACGGGTTCGCTCCCTCTTTCTTTAGGAAGTATAGAACTCGAATAATCT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAT-ATCT
* * * *
734571 TCTGCTAACGGGTTCGCTCCCTCTTTCTTTCAGGAAGTATGGAACTCGAACATCT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTT-AGGGAGTATGGAACTCGAATATCT
** * * **
734626 TCTTCTTACGGGTTCGCTCCCTCTTTCTTTAGGAAGCATAAAACTCGAATAATCT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAT-ATCT
* * **
734681 T-TTGCTAACGGGTTCGCTCCCTCTTTCTTTCA-GAAGTATCAAACTCGAATATCT
1 TCTT-CAAACGGGTTCGCTCCCTCTTTCTTT-AGGGAGTATGGAACTCGAATATCT
734735 TCTTC
1 TCTTC
734740 TGCTTCACTA
Statistics
Matches: 552, Mismatches: 83, Indels: 29
0.83 0.12 0.04
Matches are distributed among these distances:
50 16 0.03
51 67 0.12
52 4 0.01
53 27 0.05
54 272 0.49
55 147 0.27
56 19 0.03
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (54 bp):
TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAATATCT
Found at i:734275 original size:159 final size:159
Alignment explanation
Indices: 733999--734736 Score: 715
Period size: 159 Copynumber: 4.6 Consensus size: 159
733989 ATCGCGTCTG
* * * **
733999 CTCCCTATTTCTTTTAGAGAGTAT-AAGACTCGAACAATCTTC---AAACGGGTTCGCTCCCTAA
1 CTCCCTCTTTCTCTAAG-GAGTATGAA-ACTCGAA-AATCTTCTGAAAACGGGTTCGCTCCCTCT
* * * *
734060 TT-TTTCAGAGAGTATAGAACACGAATAATCTTCATCAAATGGGTTCGCTCCCTCTTTCTCTAGG
63 TTCTTTAAG-GAGTATGGAACTCGAA-AATC-T--TCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * * *
734124 GTGTATGGAACTTGGATATCTTCTTCAAACGGGTTCA
123 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCA
* * * *
734161 CTCCCTCTTTATTTAAGGAGTATGGAACTCGAAAATCTTCTGAAAACGGGTTCGCTCCTTCTTTC
1 CTCCCTCTTTCTCTAAGGAGTATGAAACTCGAAAATCTTCTGAAAACGGGTTCGCTCCCTCTTTC
* * *
734226 TTTAAGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATGA
66 TTTAAGGAGTATGGAACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGG
** *
734291 AACTCGAACATCTTCTTCTTACGGGTTCG
131 AACTCGAACATCTTCTTCAAACGGGTTCA
* * * *
734320 CTGCCTCTTTCTCTAGGGAGTATGAAACTCGAAAATCTTCTGAAAACGGGTTCTCTCCTTCTTTC
1 CTCCCTCTTTCTCTAAGGAGTATGAAACTCGAAAATCTTCTGAAAACGGGTTCGCTCCCTCTTTC
* * * * *
734385 TTTAAGGAGTATGGAACTCGAAAATCTTCTGAAAACGGGTTCGCT-TCTTTTTTTTTAAGGAGTA
66 TTTAAGGAGTATGGAACTCGAAAATCTTC---AAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTA
734449 TGGAACTCGAACA---TCTTCAAACGGGTTCA
128 TGGAACTCGAACATCTTCTTCAAACGGGTTCA
* * * ****
734478 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTC
1 CTCCCTCTTTCTCTAAGGAGTATGAAACTCGAAAATCTTCTGAAAACGGGTTCGCTCCCTCTTTC
* * * *
734543 TTT-AGGAAGTATAGAACTCGAATAATCTTCTGCTAACGGGTTCGCTCCCTCTTTCTTTCAGGAA
66 TTTAAGG-AGTATGGAACTCGAA-AATC-T-T-CAAACGGGTTCGCTCCCTCTTTCTCT-AGGGA
** *
734607 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCG
125 GTATGGAACTCGAACATCTTCTTCAAACGGGTTCA
* * * * **
734642 CTCCCTCTTTCT-TTAGGAAGCATAAAACTCGAATAATCTTTTGCTAACGGGTTCGCTCCCTCTT
1 CTCCCTCTTTCTCTAAGG-AGTATGAAACTCGAA-AATCTTCTGAAAACGGGTTCGCTCCCTCTT
* * ** *
734706 TCTTTCAGAAGTATCAAACTCGAATATCTTC
64 TCTTTAAGGAGTATGGAACTCGAAAATCTTC
734737 TTCTGCTTCA
Statistics
Matches: 485, Mismatches: 70, Indels: 43
0.81 0.12 0.07
Matches are distributed among these distances:
157 3 0.01
158 86 0.18
159 160 0.33
160 16 0.03
161 60 0.12
162 33 0.07
163 36 0.07
164 45 0.09
165 44 0.09
166 2 0.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (159 bp):
CTCCCTCTTTCTCTAAGGAGTATGAAACTCGAAAATCTTCTGAAAACGGGTTCGCTCCCTCTTTC
TTTAAGGAGTATGGAACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGG
AACTCGAACATCTTCTTCAAACGGGTTCA
Found at i:734334 original size:213 final size:213
Alignment explanation
Indices: 734026--734740 Score: 873
Period size: 213 Copynumber: 3.3 Consensus size: 213
734016 AGAGTATAAG
* * * * *
734026 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTAATTTTTC-AGAGAGTAT-AGAACACGAATAAT
1 ACTCGAAC-ATCTTCAAACGGGTTCGCTCCCT-CTTTCTCTAGGGAGTATGA-AACTCGAA-CAT
* ** * * * * *
734089 CTTCATCAAATGGGTTCGCTCCCTCTTTCTCTAGGGTGTATGGAACTTGGATATCTTCTTCAAAC
62 CTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAATATCTTCTGCAAAC
*
734154 GGGTTCACTCCCTCTTTATTTAAGGAGTATGGAACTCGAAAATCTTCTGAAAACGGGTTCGCTCC
127 GGGTTCACTCCCTCTTTCTTTAAGGAGTATGGAACTCGAAAATCTTCTGAAAACGGGTTCGCTCC
734219 TTCTTTCTTTAAGGAGTATGGA
192 TTCTTTCTTTAAGGAGTATGGA
*
734241 ACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATGAAACTCGAACATCTTC
1 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATCTTC
* * * *
734306 TTCTTACGGGTTCGCTGCCTCTTTCTCTAGGGAGTATGAAACTCGAAAATCTTCTGAAAACGGGT
66 TTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAATATCTTCTGCAAACGGGT
* * *
734371 TCTCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAAAATCTTCTGAAAACGGGTTCGCTTCTT-T
131 TCACTCCCTCTTTCTTTAAGGAGTATGGAACTCGAAAATCTTCTGAAAACGGGTTCGCTCCTTCT
*
734435 TTTTTTAAGGAGTATGGA
196 TTCTTTAAGGAGTATGGA
* *
734453 ACTCGAACATCTTCAAACGGGTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTC
1 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATCTTC
* * * *
734518 TTCTTACGGGTTCGCTCCCTCTTTCTTTAGGAAGTATAGAACTCGAATAATCTTCTGCTAACGGG
66 TTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT-ATCTTCTGCAAACGGG
* * * **** *
734583 TTCGCTCCCTCTTTCTTTCAGGAAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCT
130 TTCACTCCCTCTTTCTTTAAGG-AGTATGGAACTCGAAAATCTTCTGAAAACGGGTTCGCTCCTT
* **
734648 CTTTCTTT-AGGAAGCATAAA
194 CTTTCTTTAAGG-AGTATGGA
* * * * * *
734668 ACTCGAATAATCTTTTGCTAACGGGTTCGCTCCCTCTTTCTTTCA-GAAGTATCAAACTCGAATA
1 ACTCGAA-CATC--TT-CAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGAAACTCGAACA
734732 TCTTCTTCT
61 TCTTCTTCT
734741 GCTTCACTAC
Statistics
Matches: 433, Mismatches: 56, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
212 122 0.28
213 156 0.36
214 75 0.17
215 27 0.06
216 3 0.01
218 2 0.00
219 47 0.11
220 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (213 bp):
ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATCTTC
TTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAATATCTTCTGCAAACGGGT
TCACTCCCTCTTTCTTTAAGGAGTATGGAACTCGAAAATCTTCTGAAAACGGGTTCGCTCCTTCT
TTCTTTAAGGAGTATGGA
Found at i:736046 original size:17 final size:16
Alignment explanation
Indices: 736033--736078 Score: 69
Period size: 14 Copynumber: 2.9 Consensus size: 16
736023 TCATTTTTCT
736033 TTCTTTTCTTTTTTTG
1 TTCTTTTCTTTTTTTG
736049 TTC--TTCTTTTTTTG
1 TTCTTTTCTTTTTTTG
736063 TTCTTCTTCTTTTTTT
1 TTCTT-TTCTTTTTTT
736079 ATCTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 14 0.52
16 3 0.11
17 10 0.37
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.80
Consensus pattern (16 bp):
TTCTTTTCTTTTTTTG
Found at i:736055 original size:14 final size:14
Alignment explanation
Indices: 736038--736088 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
736028 TTTCTTTCTT
736038 TTCTTTTTTTGTTC
1 TTCTTTTTTTGTTC
736052 TTCTTTTTTTGTTC
1 TTCTTTTTTTGTTC
736066 TTCTTCTTTTT-TT-
1 TTCTT-TTTTTGTTC
*
736079 ATCTTTTTTT
1 TTCTTTTTTT
736089 TATCTTCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
12 5 0.14
13 4 0.11
14 21 0.60
15 5 0.14
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (14 bp):
TTCTTTTTTTGTTC
Found at i:736089 original size:14 final size:15
Alignment explanation
Indices: 736026--736083 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
736016 TGAACCCTCA
736026 TTTTTCTTTCTT-TTC
1 TTTTT-TTTCTTCTTC
736041 TTTTTTTGTTCTTCTT-
1 -TTTTTT-TTCTTCTTC
*
736057 TTTTTGTTCTTCTTC
1 TTTTTTTTCTTCTTC
736072 TTTTTTTATCTT
1 TTTTTTT-TCTT
736084 TTTTTTATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 8 0.22
15 12 0.33
16 14 0.39
17 2 0.06
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTTTTCTTCTTC
Found at i:736089 original size:30 final size:30
Alignment explanation
Indices: 736033--736089 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
736023 TCATTTTTCT
*
736033 TTCTTTTCTTTTTTTGTTCTTCTTTTTTTG
1 TTCTTTTCTTTTTTTGATCTTCTTTTTTTG
736063 TTCTTCTTCTTTTTTT-ATCTT-TTTTTT
1 TTCTT-TTCTTTTTTTGATCTTCTTTTTT
736090 ATCTTCAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 9 0.36
31 10 0.40
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.81
Consensus pattern (30 bp):
TTCTTTTCTTTTTTTGATCTTCTTTTTTTG
Found at i:744377 original size:17 final size:16
Alignment explanation
Indices: 744355--744388 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
744345 TAAAAACAGT
744355 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
744372 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
744388 A
1 A
744389 TCCTCACGTG
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:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:754646 original size:17 final size:16
Alignment explanation
Indices: 754624--754657 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
754614 TAAAAACAGT
754624 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
754641 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
754657 A
1 A
754658 TCCTCACGTG
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:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:766620 original size:37 final size:37
Alignment explanation
Indices: 766570--766644 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
766560 TACACGGTGC
766570 ATGTTCTTTTATATCATCGTCATCATCAGATCAGAAT
1 ATGTTCTTTTATATCATCGTCATCATCAGATCAGAAT
*
766607 ATGTTCTTTTATATCATCGTCGTCATCAGATCAGAAT
1 ATGTTCTTTTATATCATCGTCATCATCAGATCAGAAT
766644 A
1 A
766645 AAAGATTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (37 bp):
ATGTTCTTTTATATCATCGTCATCATCAGATCAGAAT
Found at i:769780 original size:17 final size:17
Alignment explanation
Indices: 769738--769781 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
769728 AACATTTAAT
**
769738 TTATTTTTTTTCAATAA
1 TTATTTTTTTAAAATAA
* *
769755 TAATATTTTTAAAATAA
1 TTATTTTTTTAAAATAA
769772 TTATTTTTTT
1 TTATTTTTTT
769782 GAATGATTAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTTTTTTAAAATAA
Found at i:770608 original size:17 final size:18
Alignment explanation
Indices: 770575--770608 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
770565 CCGCTACTAG
770575 TGAACCGATCAGAATCGC
1 TGAACCGATCAGAATCGC
*
770593 TGAACCGTTC-GAATCG
1 TGAACCGATCAGAATCG
770609 GACTGGATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (18 bp):
TGAACCGATCAGAATCGC
Found at i:774828 original size:37 final size:37
Alignment explanation
Indices: 774778--774851 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
774768 TAAATCTTGA
774778 ATTCTGATCTGATGATGACGATAATATAAAAGAACAT
1 ATTCTGATCTGATGATGACGATAATATAAAAGAACAT
*
774815 ATTCTGATCTGATGATGACGATGATATAAAAGAACAT
1 ATTCTGATCTGATGATGACGATAATATAAAAGAACAT
774852 GCACCGTGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.30
Consensus pattern (37 bp):
ATTCTGATCTGATGATGACGATAATATAAAAGAACAT
Found at i:786243 original size:2 final size:2
Alignment explanation
Indices: 786236--786278 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
786226 TCCTCAACAT
786236 TA TA TA TA TA 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 TA TA TA TA TA
786278 T
1 T
786279 TTAACCAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:787223 original size:11 final size:11
Alignment explanation
Indices: 787206--787264 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
787196 GCAACAAATC
787206 ATAACAAACTA
1 ATAACAAACTA
*
787217 CTAACAAACTA
1 ATAACAAACTA
787228 ATAACAAACTA
1 ATAACAAACTA
* *
787239 AGT-CCTAACTA
1 A-TAACAAACTA
787250 ATAACAAA-TA
1 ATAACAAACTA
787260 ATAAC
1 ATAAC
787265 GAATCTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 8 0.20
11 31 0.77
12 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.02, T:0.20
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:787233 original size:22 final size:21
Alignment explanation
Indices: 787198--787238 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
787188 CCAAGTAAGC
*
787198 AACAAATCATAACAAACTACT
1 AACAAATAATAACAAACTACT
787219 AACAAACTAATAACAAACTA
1 AACAAA-TAATAACAAACTA
787239 AGTCCTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.61, C:0.22, G:0.00, T:0.17
Consensus pattern (21 bp):
AACAAATAATAACAAACTACT
Found at i:787637 original size:36 final size:35
Alignment explanation
Indices: 787586--787834 Score: 311
Period size: 36 Copynumber: 7.0 Consensus size: 35
787576 AAAAGATGAA
*
787586 CACTTGAATCGAAAGTGTCGATGCTTCCTTCCATTT
1 CACTTGAATCGAAAGTGTCGATGCTTCCTTCC-GTT
* * *
787622 GACTTGAATCAAAAGTGTCGATGTTTCCTTCCGTTT
1 CACTTGAATCGAAAGTGTCGATGCTTCCTTCCG-TT
* * * *
787658 GACTTGAATCAAAAGTGCCGATGCTTCATTCCGTT
1 CACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
787693 CGACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
1 C-ACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
* *
787729 CACTTAAATCGAAAGTGCCGATGCTTCCTTCCGTT
1 CACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
* * ** *
787764 CACTTAAATCGAAATTACCAGATGCTTCCTTTCGTT
1 CACTTGAATCGAAAGTGTC-GATGCTTCCTTCCGTT
*
787800 CACTTGAATCGAAAGTGTCGATGC-TCCTTTCGTT
1 CACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
787834 C
1 C
787835 TTCTTATTCA
Statistics
Matches: 190, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
34 11 0.06
35 56 0.29
36 123 0.65
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (35 bp):
CACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
Found at i:787709 original size:72 final size:71
Alignment explanation
Indices: 787586--787834 Score: 322
Period size: 71 Copynumber: 3.5 Consensus size: 71
787576 AAAAGATGAA
* * * * *
787586 CACTTGAATCGAAAGTGTCGATGCTTCCTTCCATTTGACTTGAATCAAAAGTGTCGATGTTTCCT
1 CACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCT
787651 TCCGTTT
66 TCCG-TT
* * *
787658 GACTTGAATCAAAAGTGCCGATGCTTCATTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCT
1 CACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCT
787723 TCCGTT
66 TCCGTT
* * * **
787729 CACTTAAATCGAAAGTGCCGATGCTTCCTTCCGTTC-ACTTAAATCGAAATTACCAGATGCTTCC
1 CACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCGACTTGAATCGAAAGTGTC-GATGCTTCC
*
787793 TTTCGTT
65 TTCCGTT
* *
787800 CACTTGAATCGAAAGTGTCGATGC-TCCTTTCGTTC
1 CACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
787835 TTCTTATTCA
Statistics
Matches: 156, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
70 24 0.15
71 71 0.46
72 61 0.39
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (71 bp):
CACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCT
TCCGTT
Found at i:791904 original size:18 final size:18
Alignment explanation
Indices: 791878--791919 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
791868 AAAGAATATT
* *
791878 AAAAGATTTTAATGCATA
1 AAAAAATTTTAACGCATA
*
791896 AAAAAATTTTCACGCATA
1 AAAAAATTTTAACGCATA
791914 AAAAAA
1 AAAAAA
791920 ATAAATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (18 bp):
AAAAAATTTTAACGCATA
Found at i:793995 original size:34 final size:34
Alignment explanation
Indices: 793952--794016 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
793942 CCAATTATTT
793952 GTTGTAGGCCGCTCCATTCCTAATTCTTTACCGG
1 GTTGTAGGCCGCTCCATTCCTAATTCTTTACCGG
*
793986 GTTGTAGGCCGGTCCATTCCTAATTCTTTAC
1 GTTGTAGGCCGCTCCATTCCTAATTCTTTAC
794017 GGGATGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.15, C:0.28, G:0.20, T:0.37
Consensus pattern (34 bp):
GTTGTAGGCCGCTCCATTCCTAATTCTTTACCGG
Found at i:794411 original size:18 final size:17
Alignment explanation
Indices: 794381--794414 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
794371 TTATTTATTT
*
794381 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
794398 ATATGAAAAAATAATAT
1 ATAT-AAAAAATAATAT
794415 TACGATATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:801647 original size:15 final size:15
Alignment explanation
Indices: 801629--801674 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
801619 TCCTTTTTTA
801629 ATTTTTATTAACTTT
1 ATTTTTATTAACTTT
*
801644 ATTTTTA-TAAC-AT
1 ATTTTTATTAACTTT
*
801657 ATTTTTTTCTAACTTT
1 ATTTTTAT-TAACTTT
801673 AT
1 AT
801675 GTCACCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 7 0.28
14 4 0.16
15 11 0.44
16 3 0.12
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTTATTAACTTT
Found at i:803155 original size:72 final size:72
Alignment explanation
Indices: 803038--803188 Score: 275
Period size: 72 Copynumber: 2.1 Consensus size: 72
803028 AAACCCGCAA
* *
803038 ACCATTTTATCCTTTCATTTTTCTCTTGTTGTATGTCCAGTTGCTTGATTATGACCTTTGGGGTC
1 ACCATTTTATCCTTTCATTTTTCTCATGTTGTATATCCAGTTGCTTGATTATGACCTTTGGGGTC
803103 TGGAATG
66 TGGAATG
803110 ACCATTTTATCCTTTCATTTTTCTCATGTTGTATATCCAGTTGCTTGATTATGACCTTTGGGGTC
1 ACCATTTTATCCTTTCATTTTTCTCATGTTGTATATCCAGTTGCTTGATTATGACCTTTGGGGTC
803175 TGGAATG
66 TGGAATG
*
803182 AGCATTT
1 ACCATTT
803189 GTGGACAGTA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.17, C:0.18, G:0.19, T:0.46
Consensus pattern (72 bp):
ACCATTTTATCCTTTCATTTTTCTCATGTTGTATATCCAGTTGCTTGATTATGACCTTTGGGGTC
TGGAATG
Found at i:805014 original size:105 final size:105
Alignment explanation
Indices: 804806--805015 Score: 258
Period size: 105 Copynumber: 2.0 Consensus size: 105
804796 GACCACATAT
* * * *
804806 AAATTCCTTAATAACCATATACATATACCAAGGATCAAGTAAGTGTCTCAAAAGACCTCATACAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
*
804871 GCTCCAAAGAATACATATACGTCCCGAAGGACCACGTAGA
66 GCTCCAAAGAATACATATACGTCCCGAAAGACCACGTAGA
* * * * * *
804911 AAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATACGTGTCGCAAAGGACCTCATAGAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
* * * * * * *
804976 GTTCCATAGGATACCTATATGTCCTGAAAGACCGCGTAGA
66 GCTCCAAAGAATACATATACGTCCCGAAAGACCACGTAGA
805016 CCTTCGACTC
Statistics
Matches: 87, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
105 87 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (105 bp):
AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
GCTCCAAAGAATACATATACGTCCCGAAAGACCACGTAGA
Found at i:806510 original size:22 final size:22
Alignment explanation
Indices: 806485--806565 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
806475 TCGGTTGAGG
*
806485 GGGTATCGATTCCCCTTTGAAT
1 GGGTACCGATTCCCCTTTGAAT
806507 GGGTACCGATTCTCCC-TTGAAT
1 GGGTACCGATTC-CCCTTTGAAT
*** *
806529 GGGTATTAATT-CCCATTGAAT
1 GGGTACCGATTCCCCTTTGAAT
806550 GGGTACCGATTCCCCT
1 GGGTACCGATTCCCCT
806566 AGCCCAGAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.06
21 14 0.29
22 28 0.58
23 3 0.06
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (22 bp):
GGGTACCGATTCCCCTTTGAAT
Found at i:807336 original size:17 final size:17
Alignment explanation
Indices: 807314--807353 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
807304 TGTATACTAG
807314 AAATGAAATAAACCCAA
1 AAATGAAATAAACCCAA
807331 AAATGAAATAAACCCAA
1 AAATGAAATAAACCCAA
*
807348 ATATGA
1 AAATGA
807354 GCAGAATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.62, C:0.15, G:0.07, T:0.15
Consensus pattern (17 bp):
AAATGAAATAAACCCAA
Found at i:808892 original size:3 final size:3
Alignment explanation
Indices: 808869--808934 Score: 62
Period size: 3 Copynumber: 21.3 Consensus size: 3
808859 AAAAAACCAG
* * *
808869 TAA TAA CAA TAA TAG TAAA TAA TAA TAA TAA TAA TAAA TAT TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
808916 TAA T-A TAAA TAA CAA TAA T
1 TAA TAA T-AA TAA TAA TAA T
808935 CCAGACAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.04
3 42 0.82
4 7 0.14
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:808893 original size:19 final size:18
Alignment explanation
Indices: 808869--808934 Score: 87
Period size: 19 Copynumber: 3.6 Consensus size: 18
808859 AAAAAACCAG
*
808869 TAATAACAATAATAGTAAA
1 TAATAATAATAATA-TAAA
808888 TAATAATAATAATAATAAA
1 TAATAATAATAAT-ATAAA
*
808907 TATTAATAATAATATAAA
1 TAATAATAATAATATAAA
*
808925 TAACAATAAT
1 TAATAATAAT
808935 CCAGACAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 13 0.31
19 28 0.67
20 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATATAAA
Found at i:815266 original size:32 final size:32
Alignment explanation
Indices: 815225--815288 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
815215 CAAAAGGAAG
815225 AAAGAGTATAAAGTGAATTTCAAGATAAGCAA
1 AAAGAGTATAAAGTGAATTTCAAGATAAGCAA
815257 AAAGAGTATAAAGTGAATTTCAAGATAAGCAA
1 AAAGAGTATAAAGTGAATTTCAAGATAAGCAA
815289 CTAAAGATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.22
Consensus pattern (32 bp):
AAAGAGTATAAAGTGAATTTCAAGATAAGCAA
Found at i:816286 original size:64 final size:64
Alignment explanation
Indices: 816210--816434 Score: 229
Period size: 64 Copynumber: 3.5 Consensus size: 64
816200 TTGTTTGAAT
* ** **
816210 GTGCACCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAAGTAATGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATT
816273 C
64 C
* * *
816274 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTG
1 GTGCATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTC
* * * * ** * * *
816338 GTGCATCGATGCATAAGGAGTGCATTGATGCATCCCAGTAATAATACTACATCGAATACATTTT
1 GTGCATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTC
* * * *
816402 ATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGTAATGCATCGATGCAT
816435 ACCTTCATTA
Statistics
Matches: 137, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
64 131 0.96
65 6 0.04
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (64 bp):
GTGCATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTC
Found at i:816736 original size:2 final size:2
Alignment explanation
Indices: 816729--816771 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
816719 CATGCATAAG
816729 AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
816770 AT
1 AT
816772 GTTCATGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:817059 original size:31 final size:31
Alignment explanation
Indices: 817021--817273 Score: 452
Period size: 31 Copynumber: 8.2 Consensus size: 31
817011 AGAGTCGAGG
817021 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
817052 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
817083 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
817114 GTCTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
817145 GTTTATATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
817176 GTCTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
817207 ATTTATATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
817238 GTCTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
817269 GTTTA
1 GTTTA
817274 TATTGTGACC
Statistics
Matches: 210, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 210 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:818016 original size:15 final size:15
Alignment explanation
Indices: 817996--818025 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
817986 AATTCAAAGA
817996 AAATAGAATAAGTAC
1 AAATAGAATAAGTAC
818011 AAATAGAATAAGTAC
1 AAATAGAATAAGTAC
818026 CCAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (15 bp):
AAATAGAATAAGTAC
Found at i:818103 original size:16 final size:15
Alignment explanation
Indices: 818028--818101 Score: 67
Period size: 16 Copynumber: 4.7 Consensus size: 15
818018 ATAAGTACCC
818028 AATAAAATAAATATAA
1 AATAAAATAAATA-AA
*
818044 ACTAAAATAAATTAAA
1 AATAAAATAAA-TAAA
* * **
818060 AATTAAATTACGAAA
1 AATAAAATAAATAAA
*
818075 AATTAAATGAAATAAA
1 AATAAAAT-AAATAAA
818091 AATAAAATAAA
1 AATAAAATAAA
818102 ATGTGTTACC
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
15 14 0.30
16 30 0.65
17 2 0.04
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAAAATAAATAAA
Found at i:819280 original size:21 final size:21
Alignment explanation
Indices: 819255--819306 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
819245 TTTGGAAGGA
819255 AAAGATGGTGGAGTTTCAGAG
1 AAAGATGGTGGAGTTTCAGAG
819276 AAAGATGGTGGAGTTTCAGAG
1 AAAGATGGTGGAGTTTCAGAG
*
819297 AGAGATGGTG
1 AAAGATGGTG
819307 TCGGATCGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.40, T:0.23
Consensus pattern (21 bp):
AAAGATGGTGGAGTTTCAGAG
Found at i:821657 original size:30 final size:30
Alignment explanation
Indices: 821617--821719 Score: 179
Period size: 30 Copynumber: 3.4 Consensus size: 30
821607 GGTTCTTCGG
* * *
821617 GACCTATGGATAATTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
821647 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
821677 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
821707 GACCTCTGGATAG
1 GACCTCTGGATAG
821720 GTCCTTCGGG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:824219 original size:15 final size:15
Alignment explanation
Indices: 824199--824233 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
824189 AGAGATATTC
824199 TCTTCATCATCTTCT
1 TCTTCATCATCTTCT
824214 TCTTCATCATCTTCT
1 TCTTCATCATCTTCT
824229 TCTTC
1 TCTTC
824234 TTCTTCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.34, G:0.00, T:0.54
Consensus pattern (15 bp):
TCTTCATCATCTTCT
Found at i:824220 original size:12 final size:12
Alignment explanation
Indices: 824199--824239 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
824189 AGAGATATTC
*
824199 TCTTCATCATCT
1 TCTTCTTCATCT
*
824211 TCTTCTTCATCA
1 TCTTCTTCATCT
*
824223 TCTTCTTCTTCT
1 TCTTCTTCATCT
824235 TCTTC
1 TCTTC
824240 ATGTACGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.10, C:0.34, G:0.00, T:0.56
Consensus pattern (12 bp):
TCTTCTTCATCT
Found at i:826002 original size:30 final size:30
Alignment explanation
Indices: 825937--826065 Score: 170
Period size: 30 Copynumber: 4.2 Consensus size: 30
825927 AAGGAATATA
* * * * *
825937 TGGATAGTTTACCTAGGTTCTTCAGGACCTA
1 TGGATAG-TTACCGAGGATCTTTATGACCTC
825968 TGGATAGTT-CTCGAGGATCTTTATGACCTC
1 TGGATAGTTAC-CGAGGATCTTTATGACCTC
825998 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
826028 TGGATAGTTACAGAGGATCTTTTATGACCTC
1 TGGATAGTTACCGAGGATC-TTTATGACCTC
826059 TGGATAG
1 TGGATAG
826066 GTCCTTTGGG
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.01
30 62 0.70
31 26 0.29
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:830378 original size:30 final size:29
Alignment explanation
Indices: 830342--830407 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 29
830332 TCGGGGCCTA
*
830342 TGGATAGTTATCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGA-CTC
830372 TGGATAGTTACCGAGGATCTTTATGACTC
1 TGGATAGTTACCGAGGATCTTTATGACTC
830401 TGGATAG
1 TGGATAG
830408 GTCCTTCGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 10 0.29
30 25 0.71
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (29 bp):
TGGATAGTTACCGAGGATCTTTATGACTC
Found at i:837991 original size:21 final size:21
Alignment explanation
Indices: 837967--838009 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
837957 TAAATTTTAC
*
837967 TAAAAATTCAATGAAATAAAA
1 TAAAAATTAAATGAAATAAAA
*
837988 TAAAATTTAAATGAAATAAAA
1 TAAAAATTAAATGAAATAAAA
838009 T
1 T
838010 TGACTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAAAATTAAATGAAATAAAA
Found at i:837999 original size:16 final size:16
Alignment explanation
Indices: 837980--838010 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
837970 AAATTCAATG
837980 AAATAAAATAAAATTT
1 AAATAAAATAAAATTT
*
837996 AAATGAAATAAAATT
1 AAATAAAATAAAATT
838011 GACTAAAAAT
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:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATAAAATAAAATTT
Found at i:841517 original size:21 final size:21
Alignment explanation
Indices: 841491--841561 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
841481 TAATGAAAAA
841491 ATAATTCCTAAAAAACAAGAG
1 ATAATTCCTAAAAAACAAGAG
* *
841512 ATAATTCTTGAAAATATTCAA-A-
1 ATAATTCCT-AAAA-A-ACAAGAG
* *
841534 CTAAAATCCTAAAAAACAAGAG
1 AT-AATTCCTAAAAAACAAGAG
841556 ATAATT
1 ATAATT
841562 TCGAATTCTA
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
20 3 0.08
21 13 0.36
22 10 0.28
23 7 0.19
24 3 0.08
ACGTcount: A:0.55, C:0.13, G:0.07, T:0.25
Consensus pattern (21 bp):
ATAATTCCTAAAAAACAAGAG
Found at i:855465 original size:60 final size:60
Alignment explanation
Indices: 855318--855492 Score: 174
Period size: 60 Copynumber: 2.9 Consensus size: 60
855308 AGGTGATACA
* * * * * *
855318 AAGACGCATCCCTGAGACACG-TTTTACATGAGTTTTAGCTGACTATGATGTCACGCGGGT
1 AAGACGCATCCC-CAGAGACGATTTTACCTGGGTTTTAGCTGACTAGGATGCCACGCGGGT
* *** *
855378 AAGGCGCATCCCCAGAGACGCGCTTACCTGGGTTTTAGTTGACTAGGATGCCACGCGGGT
1 AAGACGCATCCCCAGAGACGATTTTACCTGGGTTTTAGCTGACTAGGATGCCACGCGGGT
* * * * * *
855438 AAGACGCATCCCCGGGGATGATTTTACCTTGGTTTT-GCTGAATCGGATGCCACGC
1 AAGACGCATCCCCAGAGACGATTTTACCTGGGTTTTAGCTGACTAGGATGCCACGC
855493 TGATTTTTTT
Statistics
Matches: 93, Mismatches: 21, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
59 22 0.24
60 71 0.76
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.26
Consensus pattern (60 bp):
AAGACGCATCCCCAGAGACGATTTTACCTGGGTTTTAGCTGACTAGGATGCCACGCGGGT
Found at i:856120 original size:22 final size:22
Alignment explanation
Indices: 856095--856138 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
856085 ATGAATTTTT
856095 TTATAATAAATAA-TATTAATTA
1 TTATAATAAATAATTA-TAATTA
* *
856117 TTATATTCAATAATTATAATTA
1 TTATAATAAATAATTATAATTA
856139 ATCATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TTATAATAAATAATTATAATTA
Found at i:856219 original size:14 final size:13
Alignment explanation
Indices: 856195--856231 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
856185 CCAAATATCA
856195 TAAA-ATAATTTT
1 TAAATATAATTTT
856207 TAAATACTAA-TTT
1 TAAATA-TAATTTT
856220 TAAATATAATTT
1 TAAATATAATTT
856232 ATTTAGGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.32
13 12 0.55
14 3 0.14
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (13 bp):
TAAATATAATTTT
Found at i:859565 original size:138 final size:137
Alignment explanation
Indices: 859317--859955 Score: 857
Period size: 138 Copynumber: 4.6 Consensus size: 137
859307 TACTATTCAC
* * * * * * * *
859317 GTGAAAGCATGTTCTCGGGGCCACGCATTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAAGCGTGTTCCCGGGGGCGCGCCTTCCATTGTTATGTCAAAGAATATGTTATCATTGCCCT
* * * *
859382 ATTATGTCACTCATATCCCCCAGGGAACTATTTATGTTAGTACCTATTATGTTTGAAGGGACTTG
66 ATTATGTCACTCATATCCCCC-GGGAACTATTCATGTCAGTACCTATTATTTTTGAGGGGACTTG
859447 GCAAAGTG
130 GCAAAGTG
* * * *
859455 GTGAATGCGTGTTCCCGGGGGCGCGCTTTCCATTATTTTGTCAAAGAATATGTTATCATTGCCCT
1 GTGAAAGCGTGTTCCCGGGGGCGCGCCTTCCATTGTTATGTCAAAGAATATGTTATCATTGCCCT
* * *
859520 ATTATGTCACTCATGTCCCCCTGGGAACTATTTATGTCAGTACCTATTATATTTGAGGGGACTTG
66 ATTATGTCACTCATATCCCCC-GGGAACTATTCATGTCAGTACCTATTATTTTTGAGGGGACTTG
*
859585 GCAAAGAG
130 GCAAAGTG
* * * ** *
859593 GCGAAAGCGTGTTTCCGGGGGCACGCCTTTGATTGTTATGTCAAAGAATATGTTATCATTGTCCT
1 GTGAAAGCGTGTTCCCGGGGGCGCGCCTTCCATTGTTATGTCAAAGAATATGTTATCATTGCCCT
* *
859658 ATTATATCACTCATATCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTTTTAGGGGACTTG
66 ATTATGTCACTCATATCCCCC-GGGAACTATTCATGTCAGTACCTATTATTTTTGAGGGGACTTG
859723 GCAAAGTG
130 GCAAAGTG
* * * *
859731 GTAAAAGCGCGTTTCCGGGGG-GCGCCTTCAATTGTTATGTCAAAGAATATGTTATCATTGCCCT
1 GTGAAAGCGTGTTCCCGGGGGCGCGCCTTCCATTGTTATGTCAAAGAATATGTTATCATTGCCCT
* *
859795 ATTATGTCACTCATGTCCCCCGGGTAACTATTCATGTCAGTACCTATTATTTTTTAGGGGACTTG
66 ATTATGTCACTCATATCCCCCGGG-AACTATTCATGTCAGTACCTATTATTTTTGAGGGGACTTG
* *
859860 GGAAACTG
130 GCAAAGTG
** * * *
859868 GTGAAAGCGCATTCCCGGGGGCGCGCCTTCGATTGTTATGTTAGAGAATATGTTATCATTGCCCT
1 GTGAAAGCGTGTTCCCGGGGGCGCGCCTTCCATTGTTATGTCAAAGAATATGTTATCATTGCCCT
*
859933 ATTATGTCGCTCATATCCCCCGG
66 ATTATGTCACTCATATCCCCCGG
859956 AGACGTAGAG
Statistics
Matches: 450, Mismatches: 49, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
136 3 0.01
137 122 0.27
138 325 0.72
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (137 bp):
GTGAAAGCGTGTTCCCGGGGGCGCGCCTTCCATTGTTATGTCAAAGAATATGTTATCATTGCCCT
ATTATGTCACTCATATCCCCCGGGAACTATTCATGTCAGTACCTATTATTTTTGAGGGGACTTGG
CAAAGTG
Found at i:859876 original size:275 final size:276
Alignment explanation
Indices: 859332--859955 Score: 901
Period size: 275 Copynumber: 2.3 Consensus size: 276
859322 AGCATGTTCT
* * * * *
859332 CGGGGCCACGCATTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATA
1 CGGGGGCACGCCTTCGATTGTTATGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATA
* * * * *
859397 TCCCCCAGGGAACTATTTATGTTAGTACCTATTATGTTTGAAGGGACTTGGCAAAGTGGTGAATG
66 TCCCCCGGGGAACTATTCATGTCAGTACCTATTATGTTTGAAGGGACTTGGCAAAGTGGTAAAAG
* * * *
859462 CGTGTTCCCGGGGGCGCGCTTTCCATTATTTTGTCAAAGAATATGTTATCATTGCCCTATTATGT
131 CGCGTTCCCGGGGGCGCGCCTTCAATTATTATGTCAAAGAATATGTTATCATTGCCCTATTATGT
* *
859527 CACTCATGTCCCCCTGGGAACTATTTATGTCAGTACCTATTATATTTGAGGGGACTTGGCAAAGA
196 CACTCATGTCCCCCTGGGAACTATTCATGTCAGTACCTATTATATTTGAGGGGACTTGGCAAACA
** *
859592 GGCGAAAGCGTGTTTC
261 GGCGAAAGCGCATTCC
* * * *
859608 CGGGGGCACGCCTTTGATTGTTATGTCAAAGAATATGTTATCATTGTCCTATTATATCACTCATA
1 CGGGGGCACGCCTTCGATTGTTATGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATA
* * *
859673 TCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTTTTAGGGGACTTGGCAAAGTGGTAAAAG
66 TCCCCCGGGGAACTATTCATGTCAGTACCTATTATGTTTGAAGGGACTTGGCAAAGTGGTAAAAG
* *
859738 CGCGTTTCCGGGGG-GCGCCTTCAATTGTTATGTCAAAGAATATGTTATCATTGCCCTATTATGT
131 CGCGTTCCCGGGGGCGCGCCTTCAATTATTATGTCAAAGAATATGTTATCATTGCCCTATTATGT
* * *
859802 CACTCATGTCCCCC-GGGTAACTATTCATGTCAGTACCTATTATTTTTTAGGGGACTTGGGAAAC
196 CACTCATGTCCCCCTGGG-AACTATTCATGTCAGTACCTATTATATTTGAGGGGACTTGGCAAAC
* *
859866 TGGTGAAAGCGCATTCC
260 AGGCGAAAGCGCATTCC
* * *
859883 CGGGGGCGCGCCTTCGATTGTTATGTTAGAGAATATGTTATCATTGCCCTATTATGTCGCTCATA
1 CGGGGGCACGCCTTCGATTGTTATGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATA
859948 TCCCCCGG
66 TCCCCCGG
859956 AGACGTAGAG
Statistics
Matches: 307, Mismatches: 40, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
274 3 0.01
275 179 0.58
276 125 0.41
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (276 bp):
CGGGGGCACGCCTTCGATTGTTATGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATA
TCCCCCGGGGAACTATTCATGTCAGTACCTATTATGTTTGAAGGGACTTGGCAAAGTGGTAAAAG
CGCGTTCCCGGGGGCGCGCCTTCAATTATTATGTCAAAGAATATGTTATCATTGCCCTATTATGT
CACTCATGTCCCCCTGGGAACTATTCATGTCAGTACCTATTATATTTGAGGGGACTTGGCAAACA
GGCGAAAGCGCATTCC
Found at i:860270 original size:14 final size:14
Alignment explanation
Indices: 860247--860277 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
860237 TAACACGTGG
*
860247 GTTTTGATGTATAT
1 GTTTTAATGTATAT
860261 GTTTTAATGTATAT
1 GTTTTAATGTATAT
860275 GTT
1 GTT
860278 AAGGATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:860443 original size:34 final size:34
Alignment explanation
Indices: 860398--860470 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
860388 TTAAGTTGAA
860398 TTTAATGTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACTATAATTTGTAT
* *
860432 TTTAATTTTAAATTTTGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACTATAATTTGTAT
860466 TTTAA
1 TTTAA
860471 AAACATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATACTATAATTTGTAT
Found at i:861012 original size:21 final size:21
Alignment explanation
Indices: 860988--861054 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
860978 GGTGTCATAA
*
860988 AACCTTGCGGGCTAGGCATGT
1 AACCTTGCGGGCTAGGAATGT
*
861009 AACCTGGCGGGCTAGGAATGT
1 AACCTTGCGGGCTAGGAATGT
* *
861030 AACCCTGTGGGCTAGGAATGT
1 AACCTTGCGGGCTAGGAATGT
861051 AACC
1 AACC
861055 CTGTGGAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21
Consensus pattern (21 bp):
AACCTTGCGGGCTAGGAATGT
Found at i:861082 original size:42 final size:42
Alignment explanation
Indices: 861036--861140 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
861026 ATGTAACCCT
* * *
861036 GTGGGCTAGGAATGTAACCCTGTGGAGATGGCATATGAACTG
1 GTGGGCTAGGCATGTACCCCTGAGGAGATGGCATATGAACTG
* * *
861078 GTGGGCTTGGCATATACCCCTGAGGAGATGGCATCTGAACTG
1 GTGGGCTAGGCATGTACCCCTGAGGAGATGGCATATGAACTG
* *
861120 GAGGGCTGGGCATGTACCCCT
1 GTGGGCTAGGCATGTACCCCT
861141 ATGGCATCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.23
Consensus pattern (42 bp):
GTGGGCTAGGCATGTACCCCTGAGGAGATGGCATATGAACTG
Found at i:866237 original size:2 final size:2
Alignment explanation
Indices: 866193--866220 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
866183 AATTAACATA
866193 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
866221 TATTTTTTTA
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:867178 original size:37 final size:37
Alignment explanation
Indices: 867088--867184 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
867078 CCTTTTCGTA
*
867088 CTACTAGGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
867125 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** *
867162 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
867185 GATAAGATCC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:868299 original size:33 final size:31
Alignment explanation
Indices: 868240--868306 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
868230 TCTTTTCGTC
* * *
868240 ATTTAATTTATTATTTATATTTTACTTTTTT
1 ATTTAATTTATAATTTATATTGTACTTTGTT
*
868271 ATTTATTTTATAATATTATATTCGTACTTTGTT
1 ATTTAATTTATAAT-TTATATT-GTACTTTGTT
868304 ATT
1 ATT
868307 ATTATTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 12 0.40
32 7 0.23
33 11 0.37
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (31 bp):
ATTTAATTTATAATTTATATTGTACTTTGTT
Found at i:872794 original size:16 final size:16
Alignment explanation
Indices: 872773--872812 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
872763 AAAAGAAGCA
872773 AAAAAGAACAAAAAT-
1 AAAAAGAACAAAAATC
872788 AAGAAAGAACAAAAATC
1 AA-AAAGAACAAAAATC
872805 AAAAAGAA
1 AAAAAGAA
872813 AAATGGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.78, C:0.07, G:0.10, T:0.05
Consensus pattern (16 bp):
AAAAAGAACAAAAATC
Found at i:873447 original size:22 final size:22
Alignment explanation
Indices: 873419--873473 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
873409 GCTACCCCAT
873419 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
873441 CAAACCTTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGC
*
873463 AAAACCTTTGA
1 CAAACCTTTGA
873474 CCAAACATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:874511 original size:106 final size:106
Alignment explanation
Indices: 874294--875449 Score: 1538
Period size: 106 Copynumber: 11.0 Consensus size: 106
874284 ATATCTTGCC
* * * * * * *
874294 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAATAATTTTCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
874358 AATTTCAGAGCCAATTTTAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
874399 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
874464 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
874505 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
874570 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
874611 ACTCCAGAAAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
874676 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGTTATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
874717 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG----T---CAA--TCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
874773 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
874814 ACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCT
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
874879 AATTTCAGAGCCAATTTCAACTTCTCAACGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
874920 ACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
874985 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
875026 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCTC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
875091 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
875132 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCT
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
875197 AATTTCAGAGCCAATTTCAACTTCTCAACGAAGGATCTT-G
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *** * * *
875237 ACCCAAGACAACACAAGCAACTCAACTTCACGACGAAGGGGTGGCTGATTGTC---ACACAAATT
1 ACTCAAGACAACGCAAG---TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTT
* *
875299 -TC-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
63 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * * * * *
875340 ACTCGGGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
** * * * *
875405 GGTTCCAGAGCCAATTTCATCTGCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
875446 ACTC
1 ACTC
875450 GGAACAATGC
Statistics
Matches: 940, Mismatches: 90, Indels: 41
0.88 0.08 0.04
Matches are distributed among these distances:
97 87 0.09
99 3 0.00
100 28 0.03
101 1 0.00
102 32 0.03
103 22 0.02
104 4 0.00
105 73 0.08
106 662 0.70
108 28 0.03
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:875132 original size:415 final size:415
Alignment explanation
Indices: 874294--875449 Score: 1579
Period size: 415 Copynumber: 2.8 Consensus size: 415
874284 ATATCTTGCC
* * * *
874294 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAATAATTTTCCA
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT---C---AA--TCCCA
*
874359 ATTTCAGAGCCAATTTTAACTTCACAGCGTAGGATATTGGACTCAAGACAACACAAGTTCAACTT
58 ATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACACAAGTTCAACTT
* * *
874424 CACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
123 CACGACGAAGGGACCGCTGGTTGTCAATAAACAAATTCCTAATTTCAGAGCCAATTTCAACTTCA
*
874489 CAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
188 CAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
*
874554 CAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
253 CAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
874619 AAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCAG
318 AAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCAG
*
874684 AGCCAATTTCAACTTCACAACGAAGGTTATTGG
383 AGCCAATTTCAACTTCACAACGAAGGATATTGG
*
874717 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATCCCAATTTCAGA
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATCCCAATTTCAGA
**
874782 GCCAATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAATGCAAGTTCAACTTCACGACGA
66 GCCAATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGA
* * *
874847 AGGGACCGCTGGTTGTCAATAAACAACTTCCTAATTTCAGAGCCAATTTCAACTTCTCAACGAAG
131 AGGGACCGCTGGTTGTCAATAAACAAATTCCTAATTTCAGAGCCAATTTCAACTTCACAGCGAAG
* * *
874912 GATCTTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAAC
196 GATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* * *
874977 AACTTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
261 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACGCAA
* * * *
875042 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCTCAATTTCAGAGCCAATT
326 GTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT
* *
875107 TCAACTTCACAGCGTAGGATATTGG
391 TCAACTTCACAACGAAGGATATTGG
875132 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCT
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT------C--CC-
* * * * * *
875197 AATTTCAGAGCCAATTTCAACTTCTCAACGAAGGATCTT-GACCCAAGACAACACAAGCAACTCA
57 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACACAAG---TTCA
*** * * * *
875261 ACTTCACGACGAAGGGGTGGCTGATTGTC---ACACAAATT--TCA-TTCAGAGTCAATTTCAAC
119 ACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAATTCCTAATTTCAGAGCCAATTTCAAC
** * * *
875320 TTCACAGCGAAGGATATTGGACTCGGGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGG
184 TTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* * ** * * * * *
875385 TTGTCAACAAATAATTTCCCGGTTCCAGAGCCAATTTCATCTGCACGACGGAGGATATTGGACTC
249 TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
875450 GGAACAATGC
Statistics
Matches: 656, Mismatches: 65, Indels: 27
0.88 0.09 0.04
Matches are distributed among these distances:
415 391 0.60
417 2 0.00
420 128 0.20
421 3 0.00
423 69 0.11
424 35 0.05
426 28 0.04
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (415 bp):
ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATCCCAATTTCAGA
GCCAATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGA
AGGGACCGCTGGTTGTCAATAAACAAATTCCTAATTTCAGAGCCAATTTCAACTTCACAGCGAAG
GATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACGCAA
GTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT
TCAACTTCACAACGAAGGATATTGG
Found at i:876235 original size:37 final size:37
Alignment explanation
Indices: 876178--876282 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
876168 CATTTTCGTC
* *
876178 CTACTAGGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
876215 TTGCTAAGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
876252 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
876283 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:876719 original size:2 final size:2
Alignment explanation
Indices: 876712--876759 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
876702 CTTAATTATT
876712 TA TA TA TA TA 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 TA TA TA TA TA
876754 TA TA TA
1 TA TA TA
876760 CATACTTGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:876913 original size:21 final size:22
Alignment explanation
Indices: 876881--876923 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
876871 TCCTTTTACT
876881 TATTTATATTATTATATTTTTA
1 TATTTATATTATTATATTTTTA
876903 TATTT-TATTATTATATTTTTA
1 TATTTATATTATTATATTTTTA
876924 CTTTCCCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTATATTATTATATTTTTA
Found at i:876973 original size:17 final size:16
Alignment explanation
Indices: 876953--876988 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
876943 ATTCTTGTAT
*
876953 TATTATTTATATTTTTA
1 TATTATTTAT-TTGTTA
876970 TATTATTTATTTGTTA
1 TATTATTTATTTGTTA
876986 TAT
1 TAT
876989 ATATATATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
TATTATTTATTTGTTA
Found at i:877570 original size:28 final size:27
Alignment explanation
Indices: 877506--877570 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
877496 ATTTATTTTC
877506 TTTT-TCTTT-TTCTTTTTTATATATA
1 TTTTATCTTTGTTCTTTTTTATATATA
* *
877531 TTTTATTATTTGTTTTTTTTTACT-TACTA
1 TTTTA-TCTTTGTTCTTTTTTA-TATA-TA
877560 TTTTATCTTTG
1 TTTTATCTTTG
877571 CTTTCTTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 4 0.12
27 4 0.12
28 16 0.50
29 8 0.25
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (27 bp):
TTTTATCTTTGTTCTTTTTTATATATA
Found at i:878344 original size:36 final size:36
Alignment explanation
Indices: 878297--878369 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
878287 TTTTAGGTCC
* *
878297 ATAAGGAATTACCAGATTGATTGGAGTTGAACCTGT
1 ATAAGGAATTACCAGATTGATCGGAGCTGAACCTGT
* *
878333 ATAAGGAATTACCAGCTTGATCGGAGCTGAGCCTGT
1 ATAAGGAATTACCAGATTGATCGGAGCTGAACCTGT
878369 A
1 A
878370 GTGACTTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (36 bp):
ATAAGGAATTACCAGATTGATCGGAGCTGAACCTGT
Found at i:885666 original size:19 final size:19
Alignment explanation
Indices: 885642--885687 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
885632 TGTAAGCTTA
885642 GTGCAGGTTTAGCACTACG
1 GTGCAGGTTTAGCACTACG
885661 GTGCAGGTTTAGCACTACG
1 GTGCAGGTTTAGCACTACG
885680 GTGCAGGT
1 GTGCAGGT
885688 ATTTTACTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.26
Consensus pattern (19 bp):
GTGCAGGTTTAGCACTACG
Found at i:885842 original size:45 final size:45
Alignment explanation
Indices: 885778--886007 Score: 397
Period size: 45 Copynumber: 5.1 Consensus size: 45
885768 GTAAGCATGC
* *
885778 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTGTATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
885823 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
885868 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTTGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
885913 AAATAAGCTTACGAGCTTATGAAATAAATGGTAAGTATATTTGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
885958 AAATAAGCTTACGAGCTTATGAAATAAATGGTAAGTGTATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
886003 AAATA
1 AAATA
886008 TTGGACATGC
Statistics
Matches: 179, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 179 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:885917 original size:24 final size:24
Alignment explanation
Indices: 885890--885963 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 24
885880 GAGCTTATGG
885890 AATAAATGGTAAGTATATTTGTAA
1 AATAAATGGTAAGTATATTTGTAA
* * **
885914 AAT-AA-GCTTACG-AGCTTATG-A-
1 AATAAATG-GTAAGTATATT-TGTAA
885935 AATAAATGGTAAGTATATTTGTAA
1 AATAAATGGTAAGTATATTTGTAA
885959 AATAA
1 AATAA
885964 GCTTACGAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
21 3 0.09
22 12 0.34
23 12 0.34
24 8 0.23
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.34
Consensus pattern (24 bp):
AATAAATGGTAAGTATATTTGTAA
Found at i:894177 original size:21 final size:23
Alignment explanation
Indices: 894136--894180 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
894126 TACATATTAA
*
894136 TTATATAAATAATTATATTTATT
1 TTATATAAATAAATATATTTATT
894159 TTATATAAA-AAATAT-TTTATT
1 TTATATAAATAAATATATTTATT
894180 T
1 T
894181 ATTCCTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 5 0.24
23 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATATAAATAAATATATTTATT
Found at i:899297 original size:30 final size:30
Alignment explanation
Indices: 899262--899341 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
899252 TCATTTTTTG
*
899262 AATATTTTCGGTTATTTTTTAGCACCTAAT
1 AATATTTTCGGTCATTTTTTAGCACCTAAT
*
899292 AATATTTTCGGTCATTTTTTAGCGCCTAAT
1 AATATTTTCGGTCATTTTTTAGCACCTAAT
* * *
899322 AATGTTTCCAGTCATTTTTT
1 AATATTTTCGGTCATTTTTT
899342 TTTTAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.50
Consensus pattern (30 bp):
AATATTTTCGGTCATTTTTTAGCACCTAAT
Found at i:899660 original size:15 final size:15
Alignment explanation
Indices: 899637--899669 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
899627 AAGTTTTAAA
899637 ACTTACATTACAATT
1 ACTTACATTACAATT
*
899652 ACTTGCATTACAATT
1 ACTTACATTACAATT
899667 ACT
1 ACT
899670 AAACTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (15 bp):
ACTTACATTACAATT
Found at i:908114 original size:42 final size:42
Alignment explanation
Indices: 908062--908235 Score: 305
Period size: 42 Copynumber: 4.2 Consensus size: 42
908052 TGATGTTGAT
* *
908062 TTTA-TTTAGACTTATTGAGACTTATTAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
908103 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
*
908145 TTTATTTTAGACTTATTGAGACTTAATGATGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
*
908187 TTTATTTTAGACTTATTTAGACTTAATGGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
908229 TTTATTT
1 TTTATTT
908236 ACTTGTTTAT
Statistics
Matches: 127, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 4 0.03
42 123 0.97
ACGTcount: A:0.24, C:0.05, G:0.19, T:0.52
Consensus pattern (42 bp):
TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
Found at i:909732 original size:18 final size:18
Alignment explanation
Indices: 909709--909747 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
909699 ATATACAGTA
909709 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
909727 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
909745 GTC
1 GTC
909748 TTTTAGGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.28
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:909756 original size:18 final size:18
Alignment explanation
Indices: 909709--909757 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
909699 ATATACAGTA
*
909709 GTCCTTCGGGACATAGTG
1 GTCCTTCAGGACATAGTG
*
909727 GTCCTTCGGGACATAGTG
1 GTCCTTCAGGACATAGTG
* *
909745 GTCTTTTAGGACA
1 GTCCTTCAGGACA
909758 AATATTCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (18 bp):
GTCCTTCAGGACATAGTG
Found at i:913890 original size:18 final size:18
Alignment explanation
Indices: 913867--913903 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
913857 AGGGATATAC
*
913867 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
913885 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
913903 A
1 A
913904 TATAGTGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:913934 original size:24 final size:22
Alignment explanation
Indices: 913883--913928 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
913873 CCTTCGGGAC
*
913883 ATAGTGGTCATTCGGGACATAT
1 ATAGTGGTCATTCGGGACAAAT
* *
913905 ATAGTGGTCTTTCGGGATAAAT
1 ATAGTGGTCATTCGGGACAAAT
913927 AT
1 AT
913929 TCAGTGCCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.35
Consensus pattern (22 bp):
ATAGTGGTCATTCGGGACAAAT
Found at i:914532 original size:21 final size:21
Alignment explanation
Indices: 914506--914546 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
914496 GATATTTTTG
914506 TGCATCGATACACTGTAGCAA
1 TGCATCGATACACTGTAGCAA
*
914527 TGCATCGATGCACTGTAGCA
1 TGCATCGATACACTGTAGCA
914547 CTGTTCACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACTGTAGCAA
Found at i:914616 original size:30 final size:30
Alignment explanation
Indices: 914538--914623 Score: 118
Period size: 30 Copynumber: 2.9 Consensus size: 30
914528 GCATCGATGC
**
914538 ACTGTAGCACTGTTCACGACACTGTTCATT
1 ACTGTAGCACTGTTCACGGTACTGTTCATT
* *
914568 ACTGTAGCACTGTTCACGGTAATGTTCTTT
1 ACTGTAGCACTGTTCACGGTACTGTTCATT
* *
914598 ATTGTAGTACTGTTCACGGTACTGTT
1 ACTGTAGCACTGTTCACGGTACTGTT
914624 TATAGCGTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (30 bp):
ACTGTAGCACTGTTCACGGTACTGTTCATT
Found at i:915134 original size:35 final size:35
Alignment explanation
Indices: 915071--915141 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
915061 AAGTTATGCA
*
915071 AAGGGTATCGATACCTAAAAGATAGTATCGATACC
1 AAGGGTATCGATACCTAAAAGACAGTATCGATACC
* *
915106 AAGGGTATCGATACC-ATAAGGCACGTATCGATACC
1 AAGGGTATCGATACCTAAAAGACA-GTATCGATACC
915141 A
1 A
915142 TTTTGAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 5 0.16
35 27 0.84
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (35 bp):
AAGGGTATCGATACCTAAAAGACAGTATCGATACC
Found at i:915932 original size:21 final size:21
Alignment explanation
Indices: 915872--915926 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
915862 TCGATGGTTC
* *
915872 TACGAGTTCCTTCGAGATATA
1 TACGAGGTCCTTCGAGACATA
915893 TACGAGGTCCTTCGAGACATA
1 TACGAGGTCCTTCGAGACATA
915914 TACGAGGTCCTTC
1 TACGAGGTCCTTC
915927 AGGACAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (21 bp):
TACGAGGTCCTTCGAGACATA
Found at i:919598 original size:28 final size:29
Alignment explanation
Indices: 919538--919599 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
919528 AAATATTATA
* **
919538 AATTGAATGAAATTAAAAATATTCCTATT
1 AATTAAATGAAATTAAAAATATTCCTACG
919567 AATTAAATGAAATT-AAAATA-TCCGTACG
1 AATTAAATGAAATTAAAAATATTCC-TACG
919595 AATTA
1 AATTA
919600 TCTGGTCCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 3 0.10
28 13 0.45
29 13 0.45
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (29 bp):
AATTAAATGAAATTAAAAATATTCCTACG
Found at i:930044 original size:17 final size:18
Alignment explanation
Indices: 930006--930053 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
929996 TGTTTTTGAG
930006 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
930024 GGAATTGGAATCTGT-AA
1 GGAATTGGAATCTGTGAA
*
930041 GGAATTGAAATCT
1 GGAATTGGAATCT
930054 AATTTCATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:930092 original size:44 final size:44
Alignment explanation
Indices: 930042--930162 Score: 197
Period size: 44 Copynumber: 2.8 Consensus size: 44
930032 AATCTGTAAG
*
930042 GAATTGAAATCTAATTTCATATTCTGTTTGGTTGACAAGAAATT
1 GAATTGAAATCTAATTCCATATTCTGTTTGGTTGACAAGAAATT
*
930086 GAATTGAAATCTAATTCCATATTATGTTTGGTTGACAAGAAATT
1 GAATTGAAATCTAATTCCATATTCTGTTTGGTTGACAAGAAATT
* * *
930130 GAATTGGAATCCAATTCCATATTCCGTTTGGTT
1 GAATTGAAATCTAATTCCATATTCTGTTTGGTT
930163 CGCAGACATG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (44 bp):
GAATTGAAATCTAATTCCATATTCTGTTTGGTTGACAAGAAATT
Found at i:930785 original size:254 final size:258
Alignment explanation
Indices: 930462--931089 Score: 837
Period size: 268 Copynumber: 2.4 Consensus size: 258
930452 TCCATCTGAG
*
930462 ACCCGACCCGACCAAAATAAAGTTTCACCCGACCTGACCCGACCCGAATATATGAATTAGAAGCC
1 ACCCGACCCGACCAAAATAAAGTTTCACCC-A----ACCCGACCCGAATATATGAATTAGAAACC
930527 CGACCCGACCCGAAATAA-AAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAA
61 CGACCCGACCCGAAATAATAAAAAA-TATTTTTATTCAATAAAAACAGTGACTTAATT-AAAAAA
* * *
930591 -AT-TATATAGAGGGGTATTGTTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT-T-TT
124 TATATATATAGAGGGGTATTATTATAATTATTCCTAAATATATAAAGTAAAATTATATATATATT
* *
930652 TTGGGTCAAGTCGGGTCGGGTATTTTTCAC-CTTAAACCCG-AACCCGACCCGAATATCACACTT
189 TTCGG----GTCGGGACGGGTATTTTTCACTC-TAAACCCGAAACCCGACCCGAATATCACACTT
930715 -AAAAAA-A-
249 AAAAAAACAC
* *
930722 A-CTGACCCGACCAAAATAAAGTTTCACCCAACCCGACCTGAATATATGAATTAGAAACCCGACC
1 ACCCGACCCGACCAAAATAAAGTTTCACCCAACCCGACCCGAATATATGAATTAGAAACCCGACC
*
930786 CGACCCGAAATAATAAAAAAAATATTTTATTCAATAAAAACAGTGACTTAATTAAAAAATATATA
66 CGACCCGAAATAATAAAAAATAT-TTTTATTCAATAAAAACAGTGACTTAATTAAAAAATATATA
930851 TATAGAGGGGTATTATTATAATTATTCCTAAATATATAAAGTAAAATTATATATATATTTTCGGG
130 TATAGAGGGGTATTATTATAATTATTCCTAAATATATAAAGTAAAATTATATATATATTTTCGGG
930916 TCGGGACGGGTATTTTTCACTCTAAACCCGAACTCAACCCGACCCGAATATCACACTTAAAAAAA
195 TCGGGACGGGTATTTTTCACTCTAAACCCG-A---AACCCGACCCGAATATCACACTTAAAAAAA
930981 CCGACCC
256 -C-A--C
** * * *
930988 GACCCGACCCGACCAAAATAAAGTTTCACCTGACCCAACCCAAATATATGAATTAGAAACTCGAC
1 -ACCCGACCCGACCAAAATAAAGTTTCACCCAACCCGACCCGAATATATGAATTAGAAACCCGAC
*
931053 CCGACCCAAAATAATAAAATAATATTTTTATTCAATA
65 CCGACCCGAAATAATAAAA-AATATTTTTATTCAATA
931090 TATAAATAAG
Statistics
Matches: 328, Mismatches: 18, Indels: 36
0.86 0.05 0.09
Matches are distributed among these distances:
254 81 0.25
255 38 0.12
256 53 0.16
257 1 0.00
258 7 0.02
259 50 0.15
260 7 0.02
263 1 0.00
267 1 0.00
268 85 0.26
269 4 0.01
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (258 bp):
ACCCGACCCGACCAAAATAAAGTTTCACCCAACCCGACCCGAATATATGAATTAGAAACCCGACC
CGACCCGAAATAATAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTAAAAAATATATAT
ATAGAGGGGTATTATTATAATTATTCCTAAATATATAAAGTAAAATTATATATATATTTTCGGGT
CGGGACGGGTATTTTTCACTCTAAACCCGAAACCCGACCCGAATATCACACTTAAAAAAACAC
Found at i:935535 original size:26 final size:26
Alignment explanation
Indices: 935505--935554 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
935495 TCTAAACTTG
935505 TGTGTTGTAACTTGTAACTTGTGTGT
1 TGTGTTGTAACTTGTAACTTGTGTGT
**
935531 TGTGTTGTGTCTTGTAACTTGTGT
1 TGTGTTGTAACTTGTAACTTGTGT
935555 CTAATTGTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.12, C:0.08, G:0.28, T:0.52
Consensus pattern (26 bp):
TGTGTTGTAACTTGTAACTTGTGTGT
Found at i:935701 original size:22 final size:22
Alignment explanation
Indices: 935654--935709 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
935644 AAAAGAATTC
* *
935654 TCTTTTTAATGAAAGGGCTTAA
1 TCTTTTTCATGAAAGGACTTAA
*
935676 -CTTTTTCATGAAAGGATTTAA
1 TCTTTTTCATGAAAGGACTTAA
935697 TCTTTTTCATGAA
1 TCTTTTTCATGAA
935710 GAGAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (22 bp):
TCTTTTTCATGAAAGGACTTAA
Found at i:935717 original size:23 final size:21
Alignment explanation
Indices: 935672--935717 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
935662 ATGAAAGGGC
*
935672 TTAACTTTTTCATGAAAGGAT
1 TTAACTTTTTCATGAAAGAAT
935693 TTAATCTTTTTCATGAAGAGAAT
1 TTAA-CTTTTTCATGAA-AGAAT
935716 TT
1 TT
935718 TTATAATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 12 0.55
23 6 0.27
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.46
Consensus pattern (21 bp):
TTAACTTTTTCATGAAAGAAT
Done.