Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008292.1 Hibiscus syriacus cultivar Beakdansim tig00110956_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: 1591938
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 8
Found at i:255570 original size:25 final size:27
Alignment explanation
Indices: 255542--255605 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 27
255532 TCATTCCCCT
*
255542 AATTAATAAATAAT-CTACAAAT-TAA
1 AATTAATAAATAATACTAAAAATATAA
*
255567 AATT--TAAACTAATACTAAAAATATTA
1 AATTAATAAA-TAATACTAAAAATATAA
255593 AATTAATATAATA
1 AATTAATA-AATA
255606 TTCAAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
23 4 0.13
24 4 0.13
25 11 0.35
26 6 0.19
28 4 0.13
29 2 0.06
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (27 bp):
AATTAATAAATAATACTAAAAATATAA
Found at i:260042 original size:2 final size:2
Alignment explanation
Indices: 259997--260024 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
259987 TCTAATATGC
259997 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
260025 TAATTATCAA
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:262153 original size:37 final size:39
Alignment explanation
Indices: 262075--262154 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 39
262065 AACAAGTTCG
* *
262075 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
*
262114 AAAAT-TTATATATATTTT-TTTACAAAATTGAAAAT-AT
1 AAAATATT-TATATATTTTCTTTAAAAAATTGAAAATCAT
262151 AAAA
1 AAAA
262155 AGGTTTAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 6 0.16
38 16 0.43
39 15 0.41
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:264243 original size:177 final size:173
Alignment explanation
Indices: 263947--264274 Score: 478
Period size: 177 Copynumber: 1.9 Consensus size: 173
263937 TCGGGTCGAG
* *
263947 TTCGGGTTTAAGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGA
1 TTCGAGTTTAAGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGA
* * ** * * **
264012 ATAATTACAATAATACCACTTTATATATAATTTTTTCAATTAATTCATTGTTTTTATTAAATGAA
66 ATAATTACAATAATACCACTCTATATATAATTATCCCAATTAAGTCACTGTTTTTATTAAACAAA
264077 AATAAATTTTTTATTATTTCGGGTCAGATTTCTAATTCATATA
131 AATAAATTTTTTATTATTTCGGGTCAGATTTCTAATTCATATA
*
264120 TTCGAGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAAATATATAATTTTACCTTATATATTT
1 TTCGAGTTTAAGGTGAAAAATACCCGACCCG----AAAAAATATATAATTTTACCTTATATATTT
* *
264185 AGGAATAATTACAATAATACCCCTCTATATAT-ATATATCCCAATTAAGTCACTGTTTTTATTGA
62 AGGAATAATTACAATAATACCACTCTATATATAAT-TATCCCAATTAAGTCACTGTTTTTATTAA
*
264249 ACAAAAATAATTTTTTTATTATTTCG
126 ACAAAAATAAATTTTTTATTATTTCG
264275 AGCCGGGTCG
Statistics
Matches: 136, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
173 29 0.21
176 2 0.01
177 105 0.77
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (173 bp):
TTCGAGTTTAAGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGA
ATAATTACAATAATACCACTCTATATATAATTATCCCAATTAAGTCACTGTTTTTATTAAACAAA
AATAAATTTTTTATTATTTCGGGTCAGATTTCTAATTCATATA
Found at i:264678 original size:17 final size:18
Alignment explanation
Indices: 264653--264699 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
264643 TATGGAATTG
*
264653 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
264670 GATTACAATTCCTTCACA
1 GATTCCAATTCCTTCACA
264688 GATTCCAATTCC
1 GATTCCAATTCC
264700 CTAAGAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:265242 original size:19 final size:19
Alignment explanation
Indices: 265218--265254 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
265208 ATGAATTAGA
265218 AAATAAGGAAAGGTGGCTT
1 AAATAAGGAAAGGTGGCTT
265237 AAATAAGGAAAGGTGGCT
1 AAATAAGGAAAGGTGGCT
265255 ATCGTGCAAA
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:0.43, C:0.05, G:0.32, T:0.19
Consensus pattern (19 bp):
AAATAAGGAAAGGTGGCTT
Found at i:275057 original size:2 final size:2
Alignment explanation
Indices: 275050--275079 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
275040 GGATTTAAGC
*
275050 CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
275080 TGCAGAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:282187 original size:20 final size:21
Alignment explanation
Indices: 282164--282211 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
282154 TTTTATATTT
*
282164 AATTAAA-TGTTAAGATTAA-A
1 AATTAAATTCTTAA-ATTAAGA
282184 AATTAAATTCTTAAATTAAGA
1 AATTAAATTCTTAAATTAAGA
282205 AATTAAA
1 AATTAAA
282212 ATAATTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (21 bp):
AATTAAATTCTTAAATTAAGA
Found at i:285566 original size:2 final size:2
Alignment explanation
Indices: 285559--285621 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
285549 AAAATACTCG
285559 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
285601 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
285622 TCCTTCACTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:296641 original size:15 final size:15
Alignment explanation
Indices: 296621--296660 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
296611 ACCAAAAGCT
*
296621 GAGAAGAAGCCCGCC
1 GAGAAGAAGCCAGCC
296636 GAGAAGAAGCCAGCC
1 GAGAAGAAGCCAGCC
*
296651 GAGAAAAAGC
1 GAGAAGAAGC
296661 TTAGAGCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.25, G:0.33, T:0.00
Consensus pattern (15 bp):
GAGAAGAAGCCAGCC
Found at i:300194 original size:126 final size:126
Alignment explanation
Indices: 299969--300210 Score: 457
Period size: 126 Copynumber: 1.9 Consensus size: 126
299959 TAACTAAGGC
299969 TGTGTAGAAATCACGCATCAAGCGTTACTGTCCTCTGCCCACTTCAGATATGGCATAAACTCATG
1 TGTGTAGAAATCACGCATCAAGCGTTACTGTCCTCTGCCCACTTCAGATATGGCATAAACTCATG
* * *
300034 CAATGTAACACTCTAATTTAAGGGTTAAATTTAAGAAATTATAAAGTGGTGGATTATTATT
66 CAATGTAACACCCCAATTTAAGGGCTAAATTTAAGAAATTATAAAGTGGTGGATTATTATT
300095 TGTGTAGAAATCACGCATCAAGCGTTACTGTCCTCTGCCCACTTCAGATATGGCATAAACTCATG
1 TGTGTAGAAATCACGCATCAAGCGTTACTGTCCTCTGCCCACTTCAGATATGGCATAAACTCATG
300160 CAATGTAACACCCCAATTTAAGGGCTAAATTTAAGAAATTATAAAGTGGTG
66 CAATGTAACACCCCAATTTAAGGGCTAAATTTAAGAAATTATAAAGTGGTG
300211 AATTTAATTG
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 113 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (126 bp):
TGTGTAGAAATCACGCATCAAGCGTTACTGTCCTCTGCCCACTTCAGATATGGCATAAACTCATG
CAATGTAACACCCCAATTTAAGGGCTAAATTTAAGAAATTATAAAGTGGTGGATTATTATT
Found at i:303421 original size:12 final size:11
Alignment explanation
Indices: 303396--303462 Score: 53
Period size: 12 Copynumber: 5.7 Consensus size: 11
303386 CGTTACCTGA
*
303396 ATTCTGTTCTG
1 ATTCTGATCTG
303407 ATTCTGATCTAG
1 ATTCTGATCT-G
*
303419 ATTCTGTTCTG
1 ATTCTGATCTG
*
303430 ATATCTGATATG
1 AT-TCTGATCTG
* *
303442 AATTCTGCTTTG
1 -ATTCTGATCTG
303454 ATTTCTGAT
1 A-TTCTGAT
303463 ATCTCCGTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
11 13 0.29
12 30 0.67
13 2 0.04
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.49
Consensus pattern (11 bp):
ATTCTGATCTG
Found at i:303446 original size:24 final size:23
Alignment explanation
Indices: 303393--303464 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 23
303383 GTACGTTACC
*
303393 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATTCTGATA
303416 T-AGATTCTGTTCTGATATCTGATA
1 TGA-ATTCTGTTCTGAT-TCTGATA
303440 TGAATTCTGCTT-TGATTTCTGATA
1 TGAATTCTG-TTCTGA-TTCTGATA
303464 T
1 T
303465 CTCCGTTTAC
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
22 1 0.02
23 14 0.33
24 24 0.56
25 4 0.09
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.49
Consensus pattern (23 bp):
TGAATTCTGTTCTGATTCTGATA
Found at i:316296 original size:21 final size:20
Alignment explanation
Indices: 316272--316336 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
316262 ATATATTTTG
316272 ATACAGGAACCAATAAAACCA
1 ATACA-GAACCAATAAAACCA
* * *
316293 ATACTACAACAAATCAAACCA
1 ATAC-AGAACCAATAAAACCA
316314 ATACAAGAACCAATAAAACCA
1 ATAC-AGAACCAATAAAACCA
316335 AT
1 AT
316337 TACTAAACCT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.58, C:0.25, G:0.05, T:0.12
Consensus pattern (20 bp):
ATACAGAACCAATAAAACCA
Found at i:316345 original size:21 final size:21
Alignment explanation
Indices: 316279--316345 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
316269 TTGATACAGG
316279 AACCAATAAAACCAATACTAC
1 AACCAATAAAACCAATACTAC
* * * *
316300 AACAAATCAAACCAATACAAG
1 AACCAATAAAACCAATACTAC
316321 AACCAATAAAACCAATTACTA-
1 AACCAATAAAACCAA-TACTAC
316342 AACC
1 AACC
316346 TCCATCTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 34 0.89
22 4 0.11
ACGTcount: A:0.58, C:0.27, G:0.01, T:0.13
Consensus pattern (21 bp):
AACCAATAAAACCAATACTAC
Found at i:317440 original size:20 final size:20
Alignment explanation
Indices: 317415--317452 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
317405 CAGGCTTCAG
317415 AAATCTAAATATTGTAGTAA
1 AAATCTAAATATTGTAGTAA
317435 AAATCTAAATATTGTAGT
1 AAATCTAAATATTGTAGT
317453 GGATTGTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (20 bp):
AAATCTAAATATTGTAGTAA
Found at i:323594 original size:14 final size:14
Alignment explanation
Indices: 323551--323646 Score: 96
Period size: 14 Copynumber: 7.3 Consensus size: 14
323541 ACAGAGGGCT
323551 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
* * *
323565 CGTTCGGT-A-ATA
1 TGTTCGTTCATTTA
323577 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
323591 TGTTCG----TTTA
1 TGTTCGTTCATTTA
323601 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
**
323615 TGTTCGTTTGTTTA
1 TGTTCGTTCATTTA
*
323629 TGTTCGTTCGTTTA
1 TGTTCGTTCATTTA
323643 TGTT
1 TGTT
323647 TGTTTATGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
10 10 0.15
12 8 0.12
13 2 0.03
14 47 0.70
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.56
Consensus pattern (14 bp):
TGTTCGTTCATTTA
Found at i:323607 original size:24 final size:25
Alignment explanation
Indices: 323551--323670 Score: 138
Period size: 24 Copynumber: 4.7 Consensus size: 25
323541 ACAGAGGGCT
* * *
323551 TGTTCGTTCATTTACGTTCGGTAATA
1 TGTTCGTTCATTTATGTTCTGT-TTA
323577 TGTTCGTTCATTTATGTTC-GTTTA
1 TGTTCGTTCATTTATGTTCTGTTTA
323601 TGTTCGTTCATTTATGTTCGTTTGTTTA
1 TGTTCGTTCATTTATGTTC---TGTTTA
*
323629 TGTTCGTTCGTTTATGTT-TGTTTA
1 TGTTCGTTCATTTATGTTCTGTTTA
323653 TGTGT-GTTCATTTATGTT
1 TGT-TCGTTCATTTATGTT
323671 TATCTCATAT
Statistics
Matches: 85, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
24 42 0.49
25 3 0.04
26 18 0.21
28 22 0.26
ACGTcount: A:0.12, C:0.11, G:0.19, T:0.57
Consensus pattern (25 bp):
TGTTCGTTCATTTATGTTCTGTTTA
Found at i:323946 original size:24 final size:24
Alignment explanation
Indices: 323849--323952 Score: 93
Period size: 24 Copynumber: 4.4 Consensus size: 24
323839 TCGTTTTACA
* *
323849 TTCGTTTATGTTCATTTA-TTGTG
1 TTCGTTTATGTTCGTTCATTTGTG
* * *
323872 TTCATTTACGTTCGTTCGTTTGTG
1 TTCGTTTATGTTCGTTCATTTGTG
* * ** **
323896 TTCGTTTATGTTTGTTTACATCCG
1 TTCGTTTATGTTCGTTCATTTGTG
*
323920 TTCGTTTATGTTTGTTCATTTGTG
1 TTCGTTTATGTTCGTTCATTTGTG
323944 TTCGTTTAT
1 TTCGTTTAT
323953 CACTTAAATG
Statistics
Matches: 61, Mismatches: 19, Indels: 1
0.75 0.23 0.01
Matches are distributed among these distances:
23 13 0.21
24 48 0.79
ACGTcount: A:0.11, C:0.12, G:0.18, T:0.59
Consensus pattern (24 bp):
TTCGTTTATGTTCGTTCATTTGTG
Found at i:325953 original size:21 final size:21
Alignment explanation
Indices: 325928--325970 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
325918 TGTCAAGATA
325928 GCAGAACCTAGCAAGAAAACT
1 GCAGAACCTAGCAAGAAAACT
325949 GCAGAACCTAGCAAGAAAACT
1 GCAGAACCTAGCAAGAAAACT
325970 G
1 G
325971 AGGATGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (21 bp):
GCAGAACCTAGCAAGAAAACT
Found at i:326035 original size:18 final size:18
Alignment explanation
Indices: 325968--326037 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 18
325958 AGCAAGAAAA
*
325968 CTGAGGATGATGATGATT
1 CTGAGGATGAAGATGATT
*
325986 CAGAGGATGAA-AGTGATT
1 CTGAGGATGAAGA-TGATT
* *
326004 CTGATGACT-CAGATGATT
1 CTGAGGA-TGAAGATGATT
326022 CTGAGGATGAAGATGA
1 CTGAGGATGAAGATGA
326038 GCCTGATGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
17 2 0.05
18 37 0.90
19 2 0.05
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.27
Consensus pattern (18 bp):
CTGAGGATGAAGATGATT
Found at i:329455 original size:78 final size:78
Alignment explanation
Indices: 329316--329510 Score: 275
Period size: 78 Copynumber: 2.5 Consensus size: 78
329306 AAAAGAACGG
* * * * * *
329316 TGTTTTTCAGTTTCTGTGACCCCAAGAGAGACTACTTTCCCAACAAGATCAGAGATAAAAGAAGT
1 TGTTGTTCGGTTTCTGTGAACCCAAAAGAGCCTACTTTCCCAACAAGAACAGAGATAAAAGAAGT
329381 TTT-TTGTGATCAA
66 TTTGTT-TGATCAA
* * *
329394 TGTTGTTCGGTTTCTATGATCCCAAAAGAGCCTACTTTCCCAACAAGAACAGAGATGAAAGAAGT
1 TGTTGTTCGGTTTCTGTGAACCCAAAAGAGCCTACTTTCCCAACAAGAACAGAGATAAAAGAAGT
329459 TTTGTTTGATCAA
66 TTTGTTTGATCAA
* *
329472 TGTTGTCCGGTTTCCGTGAACCCAAAAGAGCCTACTTTC
1 TGTTGTTCGGTTTCTGTGAACCCAAAAGAGCCTACTTTC
329511 AGAAGAAAAG
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 102 0.98
79 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (78 bp):
TGTTGTTCGGTTTCTGTGAACCCAAAAGAGCCTACTTTCCCAACAAGAACAGAGATAAAAGAAGT
TTTGTTTGATCAA
Found at i:330295 original size:39 final size:39
Alignment explanation
Indices: 330252--330326 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
330242 CCAACCACCC
* *
330252 CAAAGCAAG-CAAGGGAAAGGAAACCAAAGTTTGCAACTG
1 CAAAGCAAGCCAA-GGAAAAGAAACCAAAGCTTGCAACTG
* *
330291 CAAAGCCAGCCAAGGAAAAGAAACCGAAGCTTGCAA
1 CAAAGCAAGCCAAGGAAAAGAAACCAAAGCTTGCAA
330327 AGCAAGGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 28 0.90
40 3 0.10
ACGTcount: A:0.47, C:0.21, G:0.24, T:0.08
Consensus pattern (39 bp):
CAAAGCAAGCCAAGGAAAAGAAACCAAAGCTTGCAACTG
Found at i:337098 original size:35 final size:35
Alignment explanation
Indices: 337052--337131 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
337042 AACACATTCA
*
337052 TCAATTACATTCTAAACCCCAAAATCCAAAATATT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATAGT
* ** *
337087 TCAATTACATTCTAAACCTCAACTTTCAAAATAGT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATAGT
337122 TCAATTACAT
1 TCAATTACAT
337132 GCCCAACCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.42, C:0.24, G:0.01, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAATAGT
Found at i:337899 original size:138 final size:137
Alignment explanation
Indices: 337620--337891 Score: 418
Period size: 138 Copynumber: 1.9 Consensus size: 137
337610 AAACTATTTA
* * * *
337620 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAATAGAAACTCGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* *
337685 AATTCAATTCGACTTGATTTAAATTTATAAACTCAAATAAAAAATCGATTAAACTATTTTATAAA
66 AATTCAATTCAACTTGATTTAAATTTATAAACTCAAATAAAAAATCGAGTAAACTATTTTAT-AA
337750 TTAAACTG
130 TTAAACTG
337758 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* *
337823 AATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTTGAGTCAACTATTTT
66 AATTCAATTCAACTTGATTTAAA-TTTATAAACTCAAAT--AAAAAA--TCGAGTAAACTATTTT
337888 ATAA
126 ATAA
337892 ACTGAATTGA
Statistics
Matches: 121, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
138 83 0.69
139 15 0.12
141 6 0.05
142 2 0.02
143 15 0.12
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (137 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAACTTGATTTAAATTTATAAACTCAAATAAAAAATCGAGTAAACTATTTTATAAT
TAAACTG
Found at i:338138 original size:35 final size:36
Alignment explanation
Indices: 338069--338149 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 36
338059 AGGGTTGGGC
*
338069 ATGTAATTGAAGTATTTTTATAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTTAGAATTTGAGGTTTAGA
*
338105 ATGTAATTGAATTA-TTTTAGAATTT-AGGATTTAGA
1 ATGTAATTGAAGTATTTTTAGAATTTGAGG-TTTAGA
338140 ATGTAATTGA
1 ATGTAATTGA
338150 TGATTGTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
34 3 0.07
35 26 0.62
36 13 0.31
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.46
Consensus pattern (36 bp):
ATGTAATTGAAGTATTTTTAGAATTTGAGGTTTAGA
Found at i:344074 original size:2 final size:2
Alignment explanation
Indices: 344067--344092 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
344057 CACCATATTC
344067 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
344093 GCTTATGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:344684 original size:26 final size:26
Alignment explanation
Indices: 344648--344698 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
344638 ATTAAATTAA
*
344648 TGATGCTCATCATTAGTGGTACTCAG
1 TGATGCTCATCATTAATGGTACTCAG
*
344674 TGATGCTCATCATTAATGGTGCTCA
1 TGATGCTCATCATTAATGGTACTCA
344699 TCATATCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (26 bp):
TGATGCTCATCATTAATGGTACTCAG
Found at i:349153 original size:31 final size:30
Alignment explanation
Indices: 349107--349186 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
349097 TTCGATAATA
*
349107 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAA-TATTTTATAATCATTTA-ATAAATT
* *
349138 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATCATTTAATAAATT
349169 TAATAAGTATTTTATAAT
1 TAATAA-TATTTTATAAT
349187 TTTTTTAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 36 0.86
32 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATCATTTAATAAATT
Found at i:349164 original size:19 final size:20
Alignment explanation
Indices: 349140--349189 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
349130 GATAAATTTA
*
349140 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
349159 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
349180 TT-ATAATTTT
1 TTAATAATTTT
349190 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:349185 original size:11 final size:10
Alignment explanation
Indices: 349109--349201 Score: 52
Period size: 11 Copynumber: 9.2 Consensus size: 10
349099 CGATAATATA
349109 ATAATTATTTT
1 ATAA-TATTTT
* *
349120 ATAGTATTTAG
1 ATAATATTT-T
349131 ATAA-A-TTT
1 ATAATATTTT
349139 ATTAATAATTTT
1 A-TAAT-ATTTT
*
349151 ATAATCTTTT
1 ATAATATTTT
*
349161 AATAA-ATTTA
1 -ATAATATTTT
349171 ATAAGTATTTT
1 ATAA-TATTTT
349182 ATAAT-TTTT
1 ATAATATTTT
*
349191 TTAA-ATTTT
1 ATAATATTTT
349200 AT
1 AT
349202 TGACGAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 20
0.68 0.11 0.22
Matches are distributed among these distances:
8 1 0.02
9 21 0.33
10 14 0.22
11 23 0.37
12 4 0.06
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (10 bp):
ATAATATTTT
Found at i:349265 original size:19 final size:19
Alignment explanation
Indices: 349241--349305 Score: 78
Period size: 19 Copynumber: 3.3 Consensus size: 19
349231 AACGATATCT
349241 AATATACTTTATTTGAAAA
1 AATATACTTTATTTGAAAA
* *
349260 AATATA-TTAAACTTAGTAAAA
1 AATATACTT-TA-TTTG-AAAA
349281 AATATACTTTATTTGAAAA
1 AATATACTTTATTTGAAAA
349300 AATATA
1 AATATA
349306 TTTTTTTCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.05
19 17 0.45
20 6 0.16
21 11 0.29
22 2 0.05
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (19 bp):
AATATACTTTATTTGAAAA
Found at i:349768 original size:31 final size:30
Alignment explanation
Indices: 349733--349819 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
349723 TCAATAAAGT
*
349733 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAACTATAAAATA-TTATTAAATTTA
* *
349764 TTAAAAGACTATAAAATTATTAATAAATTTA
1 TTAAAAAACTATAAAA-TATTATTAAATTTA
*
349795 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAACTATAAAAT-ATTATTA
349820 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (30 bp):
TTAAAAAACTATAAAATATTATTAAATTTA
Found at i:351196 original size:2 final size:2
Alignment explanation
Indices: 351189--351216 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
351179 AACATTAGTT
351189 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
351217 ATGAAAGTAT
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):
TA
Found at i:351697 original size:25 final size:26
Alignment explanation
Indices: 351651--351706 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
351641 ATTTGTTTAT
* * *
351651 AAATTTCTAAATAAATATTACATTAAA
1 AAATTTC-AAATAAAAAATACATAAAA
351678 AAATTTC-AATAAAAAATACATAAAA
1 AAATTTCAAATAAAAAATACATAAAA
351703 AAAT
1 AAAT
351707 CTAAAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 19 0.73
27 7 0.27
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (26 bp):
AAATTTCAAATAAAAAATACATAAAA
Found at i:352675 original size:23 final size:23
Alignment explanation
Indices: 352631--352675 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
352621 ACCGTGCCTC
* *
352631 ATACAAACAATTTTGATTTCTTT
1 ATACAAACAATATTGATATCTTT
352654 ATACAAAGCAATATTG-TATCTT
1 ATACAAA-CAATATTGATATCTT
352676 ACCCAATACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (23 bp):
ATACAAACAATATTGATATCTTT
Found at i:360304 original size:13 final size:13
Alignment explanation
Indices: 360286--360311 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
360276 AGTCATCAGA
360286 ATCTCGTGAAAGC
1 ATCTCGTGAAAGC
360299 ATCTCGTGAAAGC
1 ATCTCGTGAAAGC
360312 GCGTCCCCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
ATCTCGTGAAAGC
Found at i:365943 original size:20 final size:20
Alignment explanation
Indices: 365887--365945 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
365877 GTTATAGATA
*
365887 TTAATTTTAATATTAATTTT
1 TTAATATTAATATTAATTTT
365907 TTAAATAAATTAAATATTAA-TTT
1 TT-AAT--ATT-AATATTAATTTT
365930 TTAATATTATATATTA
1 TTAATATTA-ATATTA
365946 TAGATATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
19 1 0.03
20 11 0.33
21 3 0.09
22 3 0.09
23 7 0.21
24 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATATTAATATTAATTTT
Found at i:365962 original size:16 final size:14
Alignment explanation
Indices: 365856--365963 Score: 61
Period size: 14 Copynumber: 7.9 Consensus size: 14
365846 ACGCATGTAT
*
365856 TATTAGTTTTATAA
1 TATTAATTTTATAA
* *
365870 GT-TTTATGTTATAGA
1 -TATTAATTTTATA-A
365885 TATTAA-TTT-TAA
1 TATTAATTTTATAA
*
365897 TATTAATTTTTTAA
1 TATTAATTTTATAA
*
365911 -A-TAA-ATTA-AA
1 TATTAATTTTATAA
365921 TATTAATTTT-TAA
1 TATTAATTTTATAA
*
365934 TATTATATATTATAGA
1 TATTA-ATTTTATA-A
365950 TATTTAATTTTATA
1 TA-TTAATTTTATA
365964 TCATATAAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 23
0.68 0.10 0.22
Matches are distributed among these distances:
10 2 0.03
11 3 0.04
12 13 0.18
13 15 0.21
14 18 0.25
15 7 0.10
16 10 0.14
17 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
TATTAATTTTATAA
Found at i:368708 original size:22 final size:23
Alignment explanation
Indices: 368683--368750 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 23
368673 AAATAATTTT
368683 TTTAATTTTTATTTAA-A-AATTA
1 TTTAATTTTTATTTAATATAA-TA
368705 TTTAATGATATTTATTTAATATAATA
1 TTTAAT--T-TTTATTTAATATAATA
* *
368731 ATTAA-TTTTATTTATTATAA
1 TTTAATTTTTATTTAATATAA
368751 AAAATTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 19 0.49
23 1 0.03
24 1 0.03
25 9 0.23
26 7 0.18
27 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (23 bp):
TTTAATTTTTATTTAATATAATA
Found at i:368760 original size:23 final size:22
Alignment explanation
Indices: 368715--368760 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
368705 TTTAATGATA
*
368715 TTTATTTAATATAATAATTAAT
1 TTTATTTAATATAAAAATTAAT
*
368737 TTTATTTATTATAAAAAATTAAT
1 TTTATTTAATAT-AAAAATTAAT
368760 T
1 T
368761 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTATTTAATATAAAAATTAAT
Found at i:368772 original size:21 final size:21
Alignment explanation
Indices: 368738--368778 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
368728 ATAATTAATT
*
368738 TTATTTATTATAAAAAATTAA
1 TTATTAATTATAAAAAATTAA
* *
368759 TTATTAATTTTAAAATATTA
1 TTATTAATTATAAAAAATTA
368779 TAATAATTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATTAATTATAAAAAATTAA
Found at i:369973 original size:21 final size:21
Alignment explanation
Indices: 369944--369984 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
369934 AGAATTATTA
*
369944 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
369965 TAATTTTTTATAATAAATAA
1 TAATATTTTAAAATAAATAA
369985 AAATAATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:370017 original size:14 final size:13
Alignment explanation
Indices: 369995--370079 Score: 60
Period size: 13 Copynumber: 7.0 Consensus size: 13
369985 AAATAATTAT
369995 TATATTAAATAAA
1 TATATTAAATAAA
370008 TATCATTAAAT-AA
1 TAT-ATTAAATAAA
*
370021 T-TTTTAAATAAA
1 TATATTAAATAAA
* *
370033 -A-A-T-AATTAT
1 TATATTAAATAAA
370042 TATATTAAATAAA
1 TATATTAAATAAA
370055 TATCATTAAAT-AA
1 TAT-ATTAAATAAA
*
370068 T-TTTTAAATAAA
1 TATATTAAATAAA
370080 AATTTTTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
9 4 0.07
10 2 0.04
11 13 0.23
12 7 0.12
13 16 0.29
14 14 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (13 bp):
TATATTAAATAAA
Found at i:370031 original size:25 final size:25
Alignment explanation
Indices: 369999--370079 Score: 105
Period size: 25 Copynumber: 3.4 Consensus size: 25
369989 AATTATTATA
369999 TTAAATAAATATCATTAAATAATTT
1 TTAAATAAATATCATTAAATAATTT
* * * *
370024 TTAAATAAAAATAATT--ATTA-TA
1 TTAAATAAATATCATTAAATAATTT
370046 TTAAATAAATATCATTAAATAATTT
1 TTAAATAAATATCATTAAATAATTT
370071 TTAAATAAA
1 TTAAATAAA
370080 AATTTTTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 15 0.33
23 3 0.07
24 3 0.07
25 24 0.53
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
TTAAATAAATATCATTAAATAATTT
Found at i:370034 original size:47 final size:47
Alignment explanation
Indices: 369978--370082 Score: 210
Period size: 47 Copynumber: 2.2 Consensus size: 47
369968 TTTTTTATAA
369978 TAAATAAAAATAATTATTATATTAAATAAATATCATTAAATAATTTT
1 TAAATAAAAATAATTATTATATTAAATAAATATCATTAAATAATTTT
370025 TAAATAAAAATAATTATTATATTAAATAAATATCATTAAATAATTTT
1 TAAATAAAAATAATTATTATATTAAATAAATATCATTAAATAATTTT
370072 TAAATAAAAAT
1 TAAATAAAAAT
370083 TTTTTAAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (47 bp):
TAAATAAAAATAATTATTATATTAAATAAATATCATTAAATAATTTT
Found at i:370062 original size:22 final size:22
Alignment explanation
Indices: 369972--370054 Score: 94
Period size: 22 Copynumber: 3.6 Consensus size: 22
369962 AATTAATTTT
*
369972 TTATAATAAATAAAAATAATTA
1 TTATATTAAATAAAAATAATTA
* *
369994 TTATATTAAATAAATATCATTAAA
1 TTATATTAAATAAAAATAATT--A
* *
370018 TAATTTTTAAATAAAAATAATTA
1 TTA-TATTAAATAAAAATAATTA
370041 TTATATTAAATAAA
1 TTATATTAAATAAA
370055 TATCATTAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
22 28 0.57
23 3 0.06
24 3 0.06
25 15 0.31
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
TTATATTAAATAAAAATAATTA
Found at i:370511 original size:11 final size:11
Alignment explanation
Indices: 370482--370517 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
370472 TATTTAAACA
370482 GGTATTGGGCC
1 GGTATTGGGCC
*
370493 GAGTATTGGGTC
1 G-GTATTGGGCC
370505 GGTATTGGGCC
1 GGTATTGGGCC
370516 GG
1 GG
370518 GAATCGGGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.11, C:0.14, G:0.47, T:0.28
Consensus pattern (11 bp):
GGTATTGGGCC
Found at i:370537 original size:2 final size:2
Alignment explanation
Indices: 370530--370614 Score: 65
Period size: 2 Copynumber: 45.5 Consensus size: 2
370520 ATCGGGCCAG
* * *
370530 AT AT AT AT AT AT AT AT TT AA AT -T AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
370571 AT TT A- AA AT -T AA AT TT AT -T A- AT AT -T 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
370608 AT AT AT A
1 AT AT AT A
370615 AATAATTATT
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
1 6 0.09
2 58 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:373789 original size:20 final size:20
Alignment explanation
Indices: 373746--373903 Score: 138
Period size: 20 Copynumber: 7.8 Consensus size: 20
373736 AAAAGTCGAA
*
373746 TTCGCAACTCGAATTTGACATT
1 TTCGCAACACGAATTT--CATT
*
373768 TTCGCAATACGAATTTCATT
1 TTCGCAACACGAATTTCATT
* * *
373788 TTCGCAACATGAGTTTCGTT
1 TTCGCAACACGAATTTCATT
* * **
373808 TTCGCAACTCGATTTTCAAA
1 TTCGCAACACGAATTTCATT
* *
373828 TTCGCAACACGAGTTTCAAT
1 TTCGCAACACGAATTTCATT
*
373848 TTCGCAACACGAATTTCGTT
1 TTCGCAACACGAATTTCATT
* * *
373868 TTCGCAACTCGATTTTCGA-A
1 TTCGCAACACGAATTTC-ATT
*
373888 TTCGCAACGCGAATTT
1 TTCGCAACACGAATTT
373904 AAATTTCGTA
Statistics
Matches: 111, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
20 97 0.87
22 14 0.13
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (20 bp):
TTCGCAACACGAATTTCATT
Found at i:373845 original size:60 final size:60
Alignment explanation
Indices: 373768--373911 Score: 216
Period size: 60 Copynumber: 2.4 Consensus size: 60
373758 ATTTGACATT
* * * *
373768 TTCGCAATACGAATTTCATTTTCGCAACATGAGTTTCGTTTTCGCAACTCGATTTTCAAA
1 TTCGCAACACGAATTTCAATTTCGCAACACGAATTTCGTTTTCGCAACTCGATTTTCAAA
* *
373828 TTCGCAACACGAGTTTCAATTTCGCAACACGAATTTCGTTTTCGCAACTCGATTTTCGAA
1 TTCGCAACACGAATTTCAATTTCGCAACACGAATTTCGTTTTCGCAACTCGATTTTCAAA
* *
373888 TTCGCAACGCGAATTTAAATTTCG
1 TTCGCAACACGAATTTCAATTTCG
373912 TAACTCAACT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (60 bp):
TTCGCAACACGAATTTCAATTTCGCAACACGAATTTCGTTTTCGCAACTCGATTTTCAAA
Found at i:373892 original size:40 final size:41
Alignment explanation
Indices: 373746--373917 Score: 156
Period size: 40 Copynumber: 4.2 Consensus size: 41
373736 AAAAGTCGAA
* *
373746 TTCGCAACTCGAATTT-GACATTTTCGCAATACGAATTTCATT
1 TTCGCAACTCGAGTTTCGA-A-TTTCGCAACACGAATTTCATT
* * * **
373788 TTCGCAACAT-GAGTTTCG-TTTTCGCAACTCGATTTTCAAA
1 TTCGCAAC-TCGAGTTTCGAATTTCGCAACACGAATTTCATT
* *
373828 TTCGCAACACGAGTTTC-AATTTCGCAACACGAATTTCGTT
1 TTCGCAACTCGAGTTTCGAATTTCGCAACACGAATTTCATT
* * * *
373868 TTCGCAACTCGATTTTCGAA-TTCGCAACGCGAATTTAAAT
1 TTCGCAACTCGAGTTTCGAATTTCGCAACACGAATTTCATT
*
373908 TTCGTAACTC
1 TTCGCAACTC
373918 AACTTTTAAT
Statistics
Matches: 104, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
40 87 0.84
41 2 0.02
42 13 0.12
43 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (41 bp):
TTCGCAACTCGAGTTTCGAATTTCGCAACACGAATTTCATT
Found at i:374547 original size:19 final size:19
Alignment explanation
Indices: 374507--374547 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
374497 AAAAGATTAA
**
374507 ATTGAAATGTTGGAATGTT
1 ATTGAAATGTTGGAATCAT
*
374526 ATTGAAATGTTGTAATCAT
1 ATTGAAATGTTGGAATCAT
374545 ATT
1 ATT
374548 TGACACACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (19 bp):
ATTGAAATGTTGGAATCAT
Found at i:375104 original size:59 final size:59
Alignment explanation
Indices: 375041--375221 Score: 172
Period size: 59 Copynumber: 3.2 Consensus size: 59
375031 GGTGAATTAG
375041 TATGAATGAGTTGTGATGGTTAATAAGTATAACTTTTACGTGTATTTGTTGTATACATA
1 TATGAATGAGTTGTGATGGTTAATAAGTATAACTTTTACGTGTATTTGTTGTATACATA
* * * ** * * *
375100 TATGAATGAG-T-T-AT--TTAGGT-A-TATTA-TGTTA--TGTAAGTG-GGCGA-A-TTA
1 TATGAATGAGTTGTGATGGTTA-ATAAGTATAACTTTTACGTGTATTTGTTG-TATACATA
375148 GTATGAATGAGTTGTGATGGTTAATAAGTATAACTTTTACGTGTATTTGTTGTATACATA
1 -TATGAATGAGTTGTGATGGTTAATAAGTATAACTTTTACGTGTATTTGTTGTATACATA
375208 TATGAATGAGTTGT
1 TATGAATGAGTTGT
375222 TTAGGCTACC
Statistics
Matches: 90, Mismatches: 16, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
48 2 0.02
49 12 0.13
50 8 0.09
51 1 0.01
52 6 0.07
53 5 0.06
54 8 0.09
55 5 0.06
56 6 0.07
57 1 0.01
58 8 0.09
59 26 0.29
60 2 0.02
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.43
Consensus pattern (59 bp):
TATGAATGAGTTGTGATGGTTAATAAGTATAACTTTTACGTGTATTTGTTGTATACATA
Found at i:375151 original size:108 final size:108
Alignment explanation
Indices: 375029--375226 Score: 378
Period size: 108 Copynumber: 1.8 Consensus size: 108
375019 TTATAGTTTT
*
375029 TGGGTGAATTAGTATGAATGAGTTGTGATGGTTAATAAGTATAACTTTTACGTGTATTTGTTGTA
1 TGGGCGAATTAGTATGAATGAGTTGTGATGGTTAATAAGTATAACTTTTACGTGTATTTGTTGTA
375094 TACATATATGAATGAGTTATTTAGGTATATTATGTTATGTAAG
66 TACATATATGAATGAGTTATTTAGGTATATTATGTTATGTAAG
375137 TGGGCGAATTAGTATGAATGAGTTGTGATGGTTAATAAGTATAACTTTTACGTGTATTTGTTGTA
1 TGGGCGAATTAGTATGAATGAGTTGTGATGGTTAATAAGTATAACTTTTACGTGTATTTGTTGTA
*
375202 TACATATATGAATGAGTTGTTTAGG
66 TACATATATGAATGAGTTATTTAGG
375227 CTACCTGGCC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 88 1.00
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.42
Consensus pattern (108 bp):
TGGGCGAATTAGTATGAATGAGTTGTGATGGTTAATAAGTATAACTTTTACGTGTATTTGTTGTA
TACATATATGAATGAGTTATTTAGGTATATTATGTTATGTAAG
Found at i:375864 original size:20 final size:20
Alignment explanation
Indices: 375839--375946 Score: 103
Period size: 20 Copynumber: 5.4 Consensus size: 20
375829 TTAAATTCAC
375839 GTTGCGAATTAGAAAATCGA
1 GTTGCGAATTAGAAAATCGA
375859 GTTGCGAATTAGAAAATCGA
1 GTTGCGAATTAGAAAATCGA
* * * *
375879 ATTGCGAA-AACAAAACTCGT
1 GTTGCGAATTAGAAAA-TCGA
*
375899 GTTGCGAATTTA-AAAATCTA
1 GTTGCGAA-TTAGAAAATCGA
** * *
375919 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAATTAGAAAATCGA
375939 GTTGCGAA
1 GTTGCGAA
375947 AATGTAAAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
19 6 0.08
20 60 0.85
21 4 0.06
22 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (20 bp):
GTTGCGAATTAGAAAATCGA
Found at i:375964 original size:22 final size:20
Alignment explanation
Indices: 375839--375968 Score: 68
Period size: 20 Copynumber: 6.4 Consensus size: 20
375829 TTAAATTCAC
** *
375839 GTTGCGAATTAGAAAATCGA
1 GTTGCGAAAAAGAAATTCGA
** *
375859 GTTGCGAATTAGAAAATCGA
1 GTTGCGAAAAAGAAATTCGA
* * *
375879 ATTGCGAAAACA-AAACTCGT
1 GTTGCGAAAA-AGAAATTCGA
* *
375899 GTTGCGAATTTAA-AAA-TCTA
1 GTTGCGAA--AAAGAAATTCGA
*
375919 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAATTCGA
* *
375939 GTTGCGAAAATGTAAAATTTGA
1 GTTGCGAAAAAG--AAATTCGA
375961 GTTGCGAA
1 GTTGCGAA
375969 TTCGACTTCT
Statistics
Matches: 88, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 63 0.72
21 5 0.06
22 15 0.17
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (20 bp):
GTTGCGAAAAAGAAATTCGA
Found at i:375968 original size:42 final size:40
Alignment explanation
Indices: 375851--375968 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 40
375841 TGCGAATTAG
* * *
375851 AAAA-TCGAGTTGCGAAT-TAGAAAATCGAATTGCGAAAAC
1 AAAACTCGTGTTGCGAATGTA-AAAATCTAGTTGCGAAAAC
*
375890 AAAACTCGTGTTGCGAATTTAAAAATCTAGTTGCGAAAA-
1 AAAACTCGTGTTGCGAATGTAAAAATCTAGTTGCGAAAAC
* *
375929 AGAAATTCGTGTTGCGAAAATGT-AAAATTTGAGTTGCGAA
1 A-AAACTCGTGTTGCG--AATGTAAAAATCT-AGTTGCGAA
375969 TTCGACTTCT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
39 5 0.07
40 41 0.61
41 8 0.12
42 13 0.19
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (40 bp):
AAAACTCGTGTTGCGAATGTAAAAATCTAGTTGCGAAAAC
Found at i:376008 original size:40 final size:40
Alignment explanation
Indices: 375953--376028 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
375943 CGAAAATGTA
* ***
375953 AAATTTGAGTTGCGAATTCGACTTCTGTGTTGTGAATTCC
1 AAATTCGAGTTGCGAATTCGAAAACTGTGTTGTGAATTCC
375993 AAATTCGAGTTGCGAATTCGAAAACTGTGTTGTGAA
1 AAATTCGAGTTGCGAATTCGAAAACTGTGTTGTGAA
376029 ATTTGCTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.36
Consensus pattern (40 bp):
AAATTCGAGTTGCGAATTCGAAAACTGTGTTGTGAATTCC
Found at i:376299 original size:18 final size:18
Alignment explanation
Indices: 376276--376310 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
376266 TACCCGACCC
376276 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
* *
376294 AAAATATTATTTTTATT
1 AAAATAATATATTTATT
376311 TTTATATAAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:392884 original size:24 final size:25
Alignment explanation
Indices: 392847--392893 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
392837 CAAACATGAT
392847 TTAAATAAATATAATTAA-ATTAATA
1 TTAAATAAATATAA-TAATATTAATA
*
392872 TTAAA-AATTATAATAATATTAA
1 TTAAATAAATATAATAATATTAA
392894 GGGTTAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 12 0.60
25 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAAATAAATATAATAATATTAATA
Found at i:393883 original size:33 final size:33
Alignment explanation
Indices: 393845--393909 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
393835 TATACTGCAC
*
393845 CACTCAAACAATCATCTTGATGATCGCTCAAAG
1 CACTCAAACAATCATCTTGACGATCGCTCAAAG
*
393878 CACTCAAACGATCATCTTGACGATCGCTCAAA
1 CACTCAAACAATCATCTTGACGATCGCTCAAA
393910 CTATTGTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.23
Consensus pattern (33 bp):
CACTCAAACAATCATCTTGACGATCGCTCAAAG
Found at i:400451 original size:24 final size:27
Alignment explanation
Indices: 400396--400456 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 27
400386 GCATTTGTAA
*
400396 TTTATTTTGATTTCTTTCTCCTTTTCACT
1 TTTATTTTGATTTCATTCTCCTTTT--CT
400425 TTTATTTT-ATTTCATT-TCCTTTT-T
1 TTTATTTTGATTTCATTCTCCTTTTCT
400449 TTTATTTT
1 TTTATTTT
400457 TTTACTAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 9 0.29
27 7 0.23
28 7 0.23
29 8 0.26
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTATTTTGATTTCATTCTCCTTTTCT
Found at i:402305 original size:26 final size:25
Alignment explanation
Indices: 402274--402330 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
402264 AGACATGTTG
*
402274 TGCATTTTG-TTACTTTTCTTTACAT
1 TGCATTATGATTACTTTT-TTTACAT
* *
402299 TCGCATTATGATTCCTTTTTTTTCAT
1 T-GCATTATGATTACTTTTTTTACAT
402325 TGCATT
1 TGCATT
402331 CACATGTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 6 0.22
26 14 0.52
27 7 0.26
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.58
Consensus pattern (25 bp):
TGCATTATGATTACTTTTTTTACAT
Found at i:404768 original size:106 final size:106
Alignment explanation
Indices: 404200--405075 Score: 1436
Period size: 105 Copynumber: 8.3 Consensus size: 106
404190 CTCGAGAGTA
*
404200 AATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
404265 GACCGCTGCTTGTCAA-AAACAACTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
404305 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
404370 GACCACTGGTTGTCAATAAAC-ATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
*
404410 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
404475 GACCGCTGGTTGTCAATAAAC-ATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
404515 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
404580 GACCGCTGGTTGTCAATAAA-TATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
* * *
404620 AATTTCGACTTCACAGCGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
404685 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
* * * * *
404726 AATTTCAAATTCCCAGCGAATGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
404791 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
*
404832 AATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
404897 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
404938 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * *
405003 GACCGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
* ** *
405044 AATTACAACTTCACGGCGGAGGATATTGGACT
1 AATTTCAACTTCACAACGAAGGATATTGGACT
405076 TAGAACAATA
Statistics
Matches: 729, Mismatches: 39, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
105 382 0.52
106 347 0.48
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
Found at i:405517 original size:84 final size:82
Alignment explanation
Indices: 405266--405518 Score: 269
Period size: 84 Copynumber: 3.0 Consensus size: 82
405256 AGAAGGAGTG
* *
405266 TCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAATGGCACATCATTTGCAGCATAG
1 TCTGC-AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTGCAGCATAG
*
405331 CTTAAGTCGAGAAGGGCTA
64 CTTAAGTCAAGAAGGGCTA
** * * * * * *
405350 TCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGTATATCATTTGCAGCATAA
1 TCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TC-AAGGCACATCATTTGCAGCATAG
* *
405412 CTTAAGTCTAGAAGGGTTA
64 CTTAAGTCAAGAAGGGCTA
* * *
405431 TCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTCTAAGGCACAACATTTGCAACATAG
1 TCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC-AAGGCACATCATTTGCAGCATAG
* *
405496 CTCAAGGCAAGAAGGGCTA
64 CTTAAGTCAAGAAGGGCTA
405515 TCTG
1 TCTG
405519 TCAATAATAT
Statistics
Matches: 135, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
80 25 0.19
81 41 0.30
82 1 0.01
84 42 0.31
85 26 0.19
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (82 bp):
TCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTGCAGCATAGCT
TAAGTCAAGAAGGGCTA
Found at i:407466 original size:24 final size:27
Alignment explanation
Indices: 407411--407471 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 27
407401 GCATTTGTAA
*
407411 TTTATTTTGATTTCTTTCTCCTTTTCACT
1 TTTATTTTGATTTCATTCTCCTTTT--CT
407440 TTTATTTT-ATTTCATT-TCCTTTT-T
1 TTTATTTTGATTTCATTCTCCTTTTCT
407464 TTTATTTT
1 TTTATTTT
407472 TTTACTAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 9 0.29
27 7 0.23
28 7 0.23
29 8 0.26
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTATTTTGATTTCATTCTCCTTTTCT
Found at i:413400 original size:23 final size:23
Alignment explanation
Indices: 413370--413416 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
413360 CAATTATATA
413370 TCTAATCCTATTCAGATTCAATG
1 TCTAATCCTATTCAGATTCAATG
413393 TCTAATCCTATTCAGATTCAATG
1 TCTAATCCTATTCAGATTCAATG
413416 T
1 T
413417 TTTTCAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (23 bp):
TCTAATCCTATTCAGATTCAATG
Found at i:419191 original size:21 final size:21
Alignment explanation
Indices: 419166--419210 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
419156 AACATGTCAC
* *
419166 ATTAAAAATTATTAATTTTTA
1 ATTAAAAATGATTAATTTATA
419187 ATTAAAAATGATTAATTTATA
1 ATTAAAAATGATTAATTTATA
419208 ATT
1 ATT
419211 TGATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTAAAAATGATTAATTTATA
Found at i:425974 original size:18 final size:18
Alignment explanation
Indices: 425951--425995 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
425941 TCACGGAATG
*
425951 TAAGATTACCAATGGGAA
1 TAAGATTACCAACGGGAA
* **
425969 TAAGATTATCGGCGGGAA
1 TAAGATTACCAACGGGAA
425987 TAAGATTAC
1 TAAGATTAC
425996 TAGGAATGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.24
Consensus pattern (18 bp):
TAAGATTACCAACGGGAA
Found at i:427041 original size:51 final size:51
Alignment explanation
Indices: 426965--427068 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
426955 GAGCATCGCC
* *
426965 TTCATCCACTACGTACAATGTTCACCATGAAAGAGCTTTGAGTGGTAAGTA
1 TTCATCCACAACGTACAATGCTCACCATGAAAGAGCTTTGAGTGGTAAGTA
427016 TTCATCCACAACGTACAATGCTCACCATGAAAGAGCTTTGAGTGGTAAGTA
1 TTCATCCACAACGTACAATGCTCACCATGAAAGAGCTTTGAGTGGTAAGTA
427067 TT
1 TT
427069 TCTGGTAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (51 bp):
TTCATCCACAACGTACAATGCTCACCATGAAAGAGCTTTGAGTGGTAAGTA
Found at i:428365 original size:11 final size:12
Alignment explanation
Indices: 428341--428383 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
428331 GTCGAATACC
428341 TAAAATATATTT
1 TAAAATATATTT
428353 TAAAATA-ATTT
1 TAAAATATATTT
428364 TAAGAAATATAATTT
1 T-A-AAATAT-ATTT
428379 TAAAA
1 TAAAA
428384 GATAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 5 0.19
12 8 0.30
13 8 0.30
14 1 0.04
15 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
TAAAATATATTT
Found at i:433611 original size:16 final size:16
Alignment explanation
Indices: 433588--433632 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
433578 GGTGTGCAAA
433588 TCTGGGTACCCGGATT
1 TCTGGGTACCCGGATT
*
433604 TTTGGGTACCC-GATT
1 TCTGGGTACCCGGATT
*
433619 TCCGGGTACCCGGA
1 TCTGGGTACCCGGA
433633 ACTTCCGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.13, C:0.27, G:0.31, T:0.29
Consensus pattern (16 bp):
TCTGGGTACCCGGATT
Found at i:433690 original size:17 final size:16
Alignment explanation
Indices: 433668--433732 Score: 62
Period size: 15 Copynumber: 4.1 Consensus size: 16
433658 CCGTGTCCCG
*
433668 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
433685 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
*
433700 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
*
433717 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
433732 A
1 A
433733 TCCGATACCC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
15 17 0.43
16 6 0.15
17 17 0.43
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:433700 original size:15 final size:15
Alignment explanation
Indices: 433680--433732 Score: 70
Period size: 15 Copynumber: 3.4 Consensus size: 15
433670 CCGGATGTTA
433680 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
**
433695 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
433711 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
433727 CGGGTA
1 CGGGTA
433733 TCCGATACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 17 0.53
16 4 0.12
17 11 0.34
ACGTcount: A:0.17, C:0.25, G:0.36, T:0.23
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:433704 original size:32 final size:32
Alignment explanation
Indices: 433668--433732 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
433658 CCGTGTCCCG
433668 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
* *
433700 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
433732 A
1 A
433733 TCCGATACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGGTAATCGGGT
Found at i:439429 original size:103 final size:103
Alignment explanation
Indices: 439204--439421 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
439194 GTAGAGGGTC
439204 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
439269 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
439307 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
439372 TTGATTCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
439410 TATGTGGACCTT
1 TATGTGGTCCTT
439422 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:439471 original size:23 final size:23
Alignment explanation
Indices: 439445--439488 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
439435 TATGGCACTA
439445 CGGTGCAATTCTACGCGGCACGC
1 CGGTGCAATTCTACGCGGCACGC
*
439468 CGGTGCAATTCTACGTGGCAC
1 CGGTGCAATTCTACGCGGCAC
439489 TTAGGTGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.20
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACGC
Found at i:439495 original size:23 final size:22
Alignment explanation
Indices: 439437--439500 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
439427 CATTATTATA
439437 TGGCACTACGGTGCAATTCTACG
1 TGGCACTA-GGTGCAATTCTACG
* **
439460 CGGCACGCCGGTGCAATTCTACG
1 TGGCAC-TAGGTGCAATTCTACG
439483 TGGCACTTAGGTGCAATT
1 TGGCAC-TAGGTGCAATT
439501 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
TGGCACTAGGTGCAATTCTACG
Found at i:445573 original size:21 final size:21
Alignment explanation
Indices: 445531--445573 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
445521 TTTATGGGCT
* *
445531 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
445552 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
445573 A
1 A
445574 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:446269 original size:103 final size:103
Alignment explanation
Indices: 446090--446304 Score: 394
Period size: 103 Copynumber: 2.1 Consensus size: 103
446080 GTAGAGGGTC
* *
446090 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGATCTGGTGAGACACATAC
1 TATGTGGTCATTCGAGACATATATGTATTCTTTGGAACATGTGTGAGATCTGGTGAGACACATAC
446155 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
446193 TATGTGGTCATTCGAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGAGACATATATGTATTCTTTGGAACATGTGTGAGATCTGGTGAGACACATAC
*
446258 TTGATTCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
446296 TATGTGGTC
1 TATGTGGTC
446305 CTTATGGACA
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCATTCGAGACATATATGTATTCTTTGGAACATGTGTGAGATCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:446357 original size:23 final size:23
Alignment explanation
Indices: 446324--446386 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
446314 ATTATTATAT
446324 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
446347 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
446370 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
446387 ATATGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:456660 original size:21 final size:21
Alignment explanation
Indices: 456634--456674 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
456624 TCTTTTTTGA
456634 GTATTTGTCGGAAATTAATGG
1 GTATTTGTCGGAAATTAATGG
456655 GTATTTGTCGGAAATTAATG
1 GTATTTGTCGGAAATTAATG
456675 TGATCGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.27, T:0.39
Consensus pattern (21 bp):
GTATTTGTCGGAAATTAATGG
Found at i:457061 original size:42 final size:42
Alignment explanation
Indices: 457001--457081 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
456991 ACTTTAGATG
** * *
457001 TCTAAAATTTTTTTACTCAAAATA-AGTGTTGATATTTTCGTA
1 TCTAAAAACTTTTCACTCAAAATAGA-TGTTAATATTTTCGTA
457043 TCTAAAAACTTTTCACTCAAAATAGATGTTAATATTTTC
1 TCTAAAAACTTTTCACTCAAAATAGATGTTAATATTTTC
457082 TTCGTTACAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.44
Consensus pattern (42 bp):
TCTAAAAACTTTTCACTCAAAATAGATGTTAATATTTTCGTA
Found at i:461380 original size:2 final size:2
Alignment explanation
Indices: 461375--461434 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
461365 TATATATATA
461375 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
461417 TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG
461435 GAGAAGAGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:462700 original size:2 final size:2
Alignment explanation
Indices: 462693--462718 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
462683 TTTGTTATTA
462693 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
462719 TAAATAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:465483 original size:45 final size:45
Alignment explanation
Indices: 465414--465503 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
465404 GTAATTTGTC
465414 AGTAGATACGTATATTTATACATTCAAGTT-TCAACTTGGTTTGAT
1 AGTAGATACGTATATTTATACATTCAAGTTCT-AACTTGGTTTGAT
*
465459 AGTATATACGTATATTTATACATTCAAGTTCTAACTTGGTTTGAT
1 AGTAGATACGTATATTTATACATTCAAGTTCTAACTTGGTTTGAT
465504 GCTACATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (45 bp):
AGTAGATACGTATATTTATACATTCAAGTTCTAACTTGGTTTGAT
Found at i:470608 original size:23 final size:23
Alignment explanation
Indices: 470582--470642 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
470572 CTCGAATAAA
470582 TGCACCGAAGTGCCACGTAAAAT
1 TGCACCGAAGTGCCACGTAAAAT
* *
470605 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAAAAT
* *
470628 TGCACTGTAGTGCCA
1 TGCACCGAAGTGCCA
470643 TATAAGATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAAAAT
Found at i:475798 original size:29 final size:29
Alignment explanation
Indices: 475741--475798 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
475731 GTGTTGGCCA
* *
475741 TAGGTCACCATGCCTTCCGGGCGACCTAC
1 TAGGTCACCATGCCTTCCCGACGACCTAC
* * *
475770 TAGGTCGCCATGTCTTCCCGACGAGCTAC
1 TAGGTCACCATGCCTTCCCGACGACCTAC
475799 GAGAGATTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.17, C:0.36, G:0.24, T:0.22
Consensus pattern (29 bp):
TAGGTCACCATGCCTTCCCGACGACCTAC
Found at i:475893 original size:14 final size:14
Alignment explanation
Indices: 475874--475906 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
475864 GCGAGAGCAT
475874 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
475888 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
475902 GCGAG
1 CCGAG
475907 CTATGCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.39, G:0.33, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:481781 original size:31 final size:31
Alignment explanation
Indices: 481738--481812 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
481728 TAATTAAAAG
* **
481738 TTTAAGTACTAAAATGGACTAAAACTGATAGA
1 TTTAGGTACTAAAATGGAAGAAAACTGATA-A
*
481770 -TTAGGTACTAAAATTGAAGAAAACTGATAA
1 TTTAGGTACTAAAATGGAAGAAAACTGATAA
481800 TTTAGGTACTAAA
1 TTTAGGTACTAAA
481813 TGTGTTTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (31 bp):
TTTAGGTACTAAAATGGAAGAAAACTGATAA
Found at i:483806 original size:2 final size:2
Alignment explanation
Indices: 483734--483796 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
483724 CGTGTGTGTG
483734 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
483776 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
483797 TAATTATATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:503143 original size:12 final size:12
Alignment explanation
Indices: 503126--503151 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
503116 GCTCTCGAGT
503126 CTTCTGGGACAA
1 CTTCTGGGACAA
503138 CTTCTGGGACAA
1 CTTCTGGGACAA
503150 CT
1 CT
503152 GACTATAGTC
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:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (12 bp):
CTTCTGGGACAA
Found at i:506830 original size:20 final size:20
Alignment explanation
Indices: 506805--506848 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
506795 TATGTATATA
*
506805 TATATAT-ATATTTAGGGGAT
1 TATATATCA-ATTTAAGGGAT
506825 TATATATCAATTTAAGGGAT
1 TATATATCAATTTAAGGGAT
506845 TATA
1 TATA
506849 AGATTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (20 bp):
TATATATCAATTTAAGGGAT
Found at i:507975 original size:19 final size:18
Alignment explanation
Indices: 507960--507994 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
507950 AAAAAAATAA
507960 ATAAAATAA-TTTAAAAT
1 ATAAAATAATTTTAAAAT
*
507977 ATATAATAATTTTAAAAT
1 ATAAAATAATTTTAAAAT
507995 TTCAAATGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAAATAATTTTAAAAT
Found at i:508022 original size:26 final size:26
Alignment explanation
Indices: 507992--508044 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
507982 ATAATTTTAA
507992 AATTTCAAATGACGTCTACCCGGCTT
1 AATTTCAAATGACGTCTACCCGGCTT
508018 AATTTCAAATGACGTCTACCCGGCTT
1 AATTTCAAATGACGTCTACCCGGCTT
508044 A
1 A
508045 GTACATCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (26 bp):
AATTTCAAATGACGTCTACCCGGCTT
Found at i:509599 original size:16 final size:15
Alignment explanation
Indices: 509552--509598 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
509542 TTTTAGCATG
509552 TAATAAAAATGAAAAA
1 TAATAAAAAT-AAAAA
*
509568 TAATCAAATATAAAAA
1 TAAT-AAAAATAAAAA
509584 TAA-AAATAATAAAAA
1 TAATAAA-AATAAAAA
509599 AATTAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.11
15 7 0.26
16 12 0.44
17 5 0.19
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (15 bp):
TAATAAAAATAAAAA
Found at i:510493 original size:22 final size:23
Alignment explanation
Indices: 510469--510512 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
510459 TATATTGTAA
*
510469 TTTATATATTAAAAACGTTTTAT
1 TTTAAATATTAAAAACGTTTTAT
* *
510492 TTTAAATTTTAAAAATGTTTT
1 TTTAAATATTAAAAACGTTTT
510513 GCTTTTTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTAAATATTAAAAACGTTTTAT
Found at i:511195 original size:48 final size:47
Alignment explanation
Indices: 511095--511195 Score: 112
Period size: 48 Copynumber: 2.1 Consensus size: 47
511085 TGAGGATGAT
* ** * * *
511095 TTTGAAATGTTTAAAATTTTAAGGACTAATTTAAAATGAGACTTATAG
1 TTTG-AATGTTCAAAAACTTAAGGACCAATTTAAAATGAGACTCATAA
**
511143 TTTGAATGTTCAAAAACTTAAGAGACCAATTTAAAATGAGGGTCATAA
1 TTTGAATGTTCAAAAACTTAAG-GACCAATTTAAAATGAGACTCATAA
511191 TTTGA
1 TTTGA
511196 GGATATGTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 15 0.34
48 29 0.66
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (47 bp):
TTTGAATGTTCAAAAACTTAAGGACCAATTTAAAATGAGACTCATAA
Found at i:521033 original size:20 final size:20
Alignment explanation
Indices: 521010--521049 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
521000 AGCATCCACA
521010 AAACTAAAAGTTATGTCAAG
1 AAACTAAAAGTTATGTCAAG
521030 AAACTAAAAGTTATGTCAAG
1 AAACTAAAAGTTATGTCAAG
521050 TTTTTCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (20 bp):
AAACTAAAAGTTATGTCAAG
Found at i:523986 original size:14 final size:14
Alignment explanation
Indices: 523967--523996 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
523957 TATAATTATC
*
523967 AATAATGTATTTTT
1 AATAATGTAATTTT
523981 AATAATGTAATTTT
1 AATAATGTAATTTT
523995 AA
1 AA
523997 AAAATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:526403 original size:2 final size:2
Alignment explanation
Indices: 526396--526421 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
526386 ATGACAACTA
526396 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
526422 TGGTTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:527490 original size:86 final size:87
Alignment explanation
Indices: 527320--527493 Score: 341
Period size: 86 Copynumber: 2.0 Consensus size: 87
527310 TCACTAATTA
527320 ACCCTAAACTCAATAAATCAAATATCGATTATTAAATGAAAAAAAAATAAATTAATGATGCAGAG
1 ACCCTAAACTCAATAAATCAAATATCGATTATTAAATGAAAAAAAAATAAATTAATGATGCAGAG
527385 ATTCAACTATATGACTATTCTC
66 ATTCAACTATATGACTATTCTC
527407 ACCCTAAACTCAATAAATCAAATATCGATTATTAAATG-AAAAAAAATAAATTAATGATGCAGAG
1 ACCCTAAACTCAATAAATCAAATATCGATTATTAAATGAAAAAAAAATAAATTAATGATGCAGAG
527471 ATTCAACTATATGACTATTCTC
66 ATTCAACTATATGACTATTCTC
527493 A
1 A
527494 AAGGTGAGGA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 49 0.56
87 38 0.44
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (87 bp):
ACCCTAAACTCAATAAATCAAATATCGATTATTAAATGAAAAAAAAATAAATTAATGATGCAGAG
ATTCAACTATATGACTATTCTC
Found at i:528943 original size:15 final size:15
Alignment explanation
Indices: 528917--528955 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
528907 TTTAGTCCTA
528917 ATTTAG-ATTGTTTT
1 ATTTAGTATTGTTTT
528931 ATTTAGTATTGTTTT
1 ATTTAGTATTGTTTT
*
528946 ATTTATTATT
1 ATTTAGTATT
528956 ATAATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (15 bp):
ATTTAGTATTGTTTT
Found at i:529114 original size:4 final size:4
Alignment explanation
Indices: 529105--529134 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
529095 CATATTATAC
529105 TATT TATT TATT TATT TATT TATTT TATT T
1 TATT TATT TATT TATT TATT TA-TT TATT T
529135 TCATTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:529213 original size:20 final size:20
Alignment explanation
Indices: 529184--529222 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
529174 CTAACCTTTT
529184 TTTATATATTATTATTTTAC
1 TTTATATATTATTATTTTAC
*
529204 TTTATTTATTATTATTTTA
1 TTTATATATTATTATTTTA
529223 TTATTTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATATATTATTATTTTAC
Found at i:533148 original size:106 final size:106
Alignment explanation
Indices: 532995--534045 Score: 1721
Period size: 106 Copynumber: 9.9 Consensus size: 106
532985 TTCAGTTTCA
* * *
532995 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * *
533060 CAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
*
533101 TTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
533166 CGACGAAGGGACCGCTGGTTGTAAAC-AACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
*
533206 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
533271 CGACGAAGGGGCCGCTGGTTGTCAAC-AACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
* *
533311 TTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
533376 CGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
* * * * * *
533417 TTCAGCGCCAATTTCAACTTCATAGCGAAGGATATTGGACTTCGGACAACTCAAGTTCAATTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
533482 CGACGAAGGGACCGCTGGTTGTCAAC-AATAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
* *
533522 TTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
533587 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
* *
533628 ATCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
533693 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
* *
533734 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
533799 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
*
533840 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
533905 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
* * * *
533946 TTCAGAGTCAATTTCAACTTCATAGCGAAGGATATTGGACTCAAGACAACGTAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
534011 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
534046 TCAACTTCAC
Statistics
Matches: 887, Mismatches: 56, Indels: 4
0.94 0.06 0.00
Matches are distributed among these distances:
105 295 0.33
106 592 0.67
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
Found at i:533819 original size:212 final size:212
Alignment explanation
Indices: 532995--534054 Score: 1723
Period size: 211 Copynumber: 5.0 Consensus size: 212
532985 TTCAGTTTCA
* * *
532995 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * * *
533060 CAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTCATAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
*
533125 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTAA
131 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
533190 AC-AACAACTTCCCAAT
196 ACAAACAACTTCTCAAT
*
533206 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
533271 CGACGAAGGGGCCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* * *
533335 ACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCA
131 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * *
533400 ATAAACAATTTCCCAAT
196 ACAAACAACTTCTCAAT
* * * * * *
533417 TTCAGCGCCAATTTCAACTTCATAGCGAAGGATATTGGACTTCGGACAACTCAAGTTCAATTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
533482 CGACGAAGGGACCGCTGGTTGTCAAC-AATAACTTCCCAATTTTAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
*
533546 GCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
131 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
533611 ACAAACAACTTCTCAAT
196 ACAAACAACTTCTCAAT
* *
533628 ATCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
533693 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* *
533758 ACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
131 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
533823 ACAAACAACTTCTCAAT
196 ACAAACAACTTCTCAAT
*
533840 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * *
533905 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCATA
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* *
533970 GCGAAGGATATTGGACTCAAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
131 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
534035 ATAAACAACTT-TCAAC
196 ACAAACAACTTCTCAAT
534051 TTCA
1 TTCA
534055 CGACGGAGGA
Statistics
Matches: 786, Mismatches: 61, Indels: 4
0.92 0.07 0.00
Matches are distributed among these distances:
210 97 0.12
211 382 0.49
212 307 0.39
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (212 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ACAAACAACTTCTCAAT
Found at i:535641 original size:15 final size:15
Alignment explanation
Indices: 535615--535653 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
535605 TTTAGTCCTA
535615 ATTTAG-ATTGTTTT
1 ATTTAGTATTGTTTT
535629 ATTTAGTATTGTTTT
1 ATTTAGTATTGTTTT
*
535644 ATTTATTATT
1 ATTTAGTATT
535654 ATAATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (15 bp):
ATTTAGTATTGTTTT
Found at i:535754 original size:2 final size:2
Alignment explanation
Indices: 535713--535746 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
535703 ACATCTCTTT
*
535713 TA TA TA TA TA TA TA AA 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
535747 GTTATATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:535923 original size:8 final size:8
Alignment explanation
Indices: 535896--535944 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
535886 TTAGCTAACC
*
535896 TTTTTTTA
1 TTTTATTA
*
535904 TATTATTA
1 TTTTATTA
535912 TTATTACTTTA
1 TT-TTA--TTA
535923 TTTTATTA
1 TTTTATTA
535931 TTTTATTA
1 TTTTATTA
535939 TTTTAT
1 TTTTAT
535945 ATTATCTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
8 24 0.69
9 3 0.09
10 3 0.09
11 5 0.14
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTATTA
Found at i:535926 original size:27 final size:26
Alignment explanation
Indices: 535896--535957 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
535886 TTAGCTAACC
535896 TTTTTTTATATTATTATTATTACT-TTA
1 TTTTTTTATATTATTATT-TTA-TATTA
* *
535923 TTTTATTATTTTATTATTTTATATTA
1 TTTTTTTATATTATTATTTTATATTA
535949 TCTTTTTTA
1 T-TTTTTTA
535958 CTAACTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.03
26 7 0.23
27 22 0.73
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTTTTATATTATTATTTTATATTA
Found at i:535944 original size:13 final size:14
Alignment explanation
Indices: 535901--535949 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
535891 TAACCTTTTT
535901 TTATATTATTATTA
1 TTATATTATTATTA
535915 TTACT-TTATT-TTA
1 TTA-TATTATTATTA
*
535928 TTATTTTATTATT-
1 TTATATTATTATTA
535941 TTATATTAT
1 TTATATTAT
535950 CTTTTTTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 1 0.03
13 19 0.61
14 10 0.32
15 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATATTATTATTA
Found at i:536019 original size:2 final size:2
Alignment explanation
Indices: 536012--536061 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
536002 ATATTTGTAG
536012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
536054 AT AT AT AT
1 AT AT AT AT
536062 TTCCCTTTGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:537466 original size:14 final size:14
Alignment explanation
Indices: 537447--537473 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
537437 TTTAATTAAA
537447 ATATTTAAAATTGT
1 ATATTTAAAATTGT
537461 ATATTTAAAATTG
1 ATATTTAAAATTG
537474 CATTGATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATATTTAAAATTGT
Found at i:538487 original size:18 final size:18
Alignment explanation
Indices: 538466--538517 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
538456 AATAATAAAT
538466 TAATTTAAATAAAATTGA
1 TAATTTAAATAAAATTGA
* * *
538484 TAATTT-ATTAAAAATGT
1 TAATTTAAATAAAATTGA
538501 TAGATTTATAATAAAAT
1 TA-ATTTA-AATAAAAT
538518 AATAGAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 10 0.38
18 10 0.38
20 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (18 bp):
TAATTTAAATAAAATTGA
Found at i:541903 original size:24 final size:25
Alignment explanation
Indices: 541855--541903 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
541845 TATCAAGAGC
* *
541855 TTTAATTCAGTTGATGTATTTTAAT
1 TTTAATTCAGTTGATCTATTATAAT
*
541880 TTTAATTCATTTG-TCTATTATAAT
1 TTTAATTCAGTTGATCTATTATAAT
541904 ATTTGATTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (25 bp):
TTTAATTCAGTTGATCTATTATAAT
Found at i:548378 original size:74 final size:74
Alignment explanation
Indices: 548046--548474 Score: 528
Period size: 74 Copynumber: 5.8 Consensus size: 74
548036 TTCAACATAT
* * ** *
548046 CCGGTAGGTAGTTTAATGTATTAGGTAGCG-C-ATAATTTTTTACCGTTTACATTATTAGCAACT
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACC
*
548109 TTCAAACAA
66 TTCAAAAAA
* *
548118 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTA--TTTTTTTACCGTTTACATTATTAACAATC
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACC
*
548181 TTAAAAAAAA
66 TT-CAAAAAA
* * * * * * **
548191 GCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTATTTTATCATTTACATTATCAACAATA
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACC
*
548256 TTTAAACAAA
66 TTCAAA-AAA
* *
548266 CCGATAGCTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACC
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACC
548331 TTCAAAAAA
66 TTCAAAAAA
** * * * * *
548340 CCGGTATATAATTTAATATAATAGGTAACACCTATTTTTTTTTACCGTTTACATCATTAGCAACC
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACC
548405 TTCAAAAAAAA
66 TTC--AAAAAA
*
548416 CCGGTAGGTACTTTAATGTAATAGGTAGCGCCTA--TTTTTTTACCGTTTACATTATTAGC
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGC
548475 CGTTTTTAAC
Statistics
Matches: 308, Mismatches: 41, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
72 55 0.18
73 39 0.13
74 91 0.30
75 89 0.29
76 34 0.11
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (74 bp):
CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACC
TTCAAAAAA
Found at i:548444 original size:150 final size:148
Alignment explanation
Indices: 548081--548474 Score: 522
Period size: 150 Copynumber: 2.7 Consensus size: 148
548071 TAGCGCATAA
* *
548081 TTTTTTACCGTTTACATTATTAGCAACTTTC-AAACAACCGGTAGGTATTTTAATGTAATAGGTA
1 TTTTTTACCGTTTACATTATTAGCAACATTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTA
* * * * * *
548145 GCGCCTATTTTTTTACCGTTTACATTATTAACAATCTTAAAAAAAAGCGGTAGGTATTTTAATGT
66 GCGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAAACCGGTAGATAATTTAATAT
* *
548210 AATAGGTAGCGCCTATTT
131 AATAGGTAACACCTATTT
* * * * * * * * * *
548228 TATTTTATCATTTACATTATCAACAATATTTAAACAAACCGATAGCTATTTTAATGTAATAGGTA
1 TTTTTTACCGTTTACATTATTAGCAACATTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTA
* *
548293 GCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACCTT-CAAAAAACCGGTATATAATTTAAT
66 GCGCCTA--TTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAAACCGGTAGATAATTTAAT
548357 ATAATAGGTAACACCTATTT
129 ATAATAGGTAACACCTATTT
* * *
548377 TTTTTTACCGTTTACATCATTAGCAACCTTCAAAAAAAACCGGTAGGTACTTTAATGTAATAGGT
1 TTTTTTACCGTTTACATTATTAGCAACATTC-AAAAAAACCGGTAGGTATTTTAATGTAATAGGT
548442 AGCGCCTATTTTTTTACCGTTTACATTATTAGC
65 AGCGCCTATTTTTTTACCGTTTACATTATTAGC
548475 CGTTTTTAAC
Statistics
Matches: 208, Mismatches: 35, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
147 23 0.11
148 61 0.29
149 58 0.28
150 66 0.32
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (148 bp):
TTTTTTACCGTTTACATTATTAGCAACATTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTA
GCGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAAACCGGTAGATAATTTAATAT
AATAGGTAACACCTATTT
Found at i:554195 original size:19 final size:19
Alignment explanation
Indices: 554167--554250 Score: 87
Period size: 19 Copynumber: 4.2 Consensus size: 19
554157 GCGATTTTGA
*
554167 AAAATATGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
554186 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
554206 GAAAAACGTGTTGCGATAGTT
1 --AAAATGTGTTGCGATAGTT
* *
554227 AAATAAGTGTTGCGATAGTG
1 AAA-ATGTGTTGCGATAGTT
554247 AAAA
1 AAAA
554251 ATCCAAAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
19 19 0.35
20 19 0.35
21 2 0.04
22 15 0.27
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Done.