Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007418.1 Hibiscus syriacus cultivar Beakdansim tig00020063_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: 1198774
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:203218 original size:49 final size:49
Alignment explanation
Indices: 203134--203531 Score: 447
Period size: 49 Copynumber: 8.1 Consensus size: 49
203124 TATGCATTTT
* * *
203134 CATTAGTGGCACCTTTTATGTCGAAAATGCACCATTATGCATTTAACTTG
1 CATTAGTGGCACC-TTTCTGCCAAAAATGCACCATTATGCATTTAACTTG
* * *
203184 CATTAGTGGCACATTTTTGCCAAAAATGTACCATTATGCATTTAACTTG
1 CATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTG
* * * ** *
203233 CATTTA-TGGAACCTTTCTGCCAAAAAGGAACTTTTAAGCATTTAACTTG
1 CA-TTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTG
* *
203282 CATTAGTGGCACCTTTCTGCCAAAAATGCATCATAATGCATTTAACTTG
1 CATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTG
* * * *
203331 CTTTAGTGGTACATTTCTGCCAAAAATGCACCATTATGCATTTAGCTTG
1 CATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTG
* * * * * **
203380 CACTAGTGTCACATTTCTACAAAAAACACACCATTATGCATTTAACTTG
1 CATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTG
* * * ** * *
203429 CTTTAGTGGGACCTTTCTACCAAAAATGCACTTTTAAGCATTTAAATTG
1 CATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTG
* * * *
203478 CATTAGTGGCACCTTTCTACGAAAAATGCACCATTATGCATTTCACTTT
1 CATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTG
203527 CATTA
1 CATTA
203532 TAGAGCAGTT
Statistics
Matches: 289, Mismatches: 57, Indels: 5
0.82 0.16 0.01
Matches are distributed among these distances:
48 3 0.01
49 271 0.94
50 15 0.05
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (49 bp):
CATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTG
Found at i:205539 original size:30 final size:30
Alignment explanation
Indices: 205505--205574 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 30
205495 AACTATTACG
*
205505 AAAATAGCACCCTTTTTCAAAAAAATTCCC
1 AAAATATCACCCTTTTTCAAAAAAATTCCC
*
205535 AAAATATCA-CCTTTTTCAAAATAATTCCC
1 AAAATATCACCCTTTTTCAAAAAAATTCCC
205564 AAAATATCACC
1 AAAATATCACC
205575 GGGTCGGGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 28 0.76
30 9 0.24
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.29
Consensus pattern (30 bp):
AAAATATCACCCTTTTTCAAAAAAATTCCC
Found at i:212823 original size:29 final size:29
Alignment explanation
Indices: 212777--212932 Score: 285
Period size: 29 Copynumber: 5.3 Consensus size: 29
212767 AACTATTACG
*
212777 AAAATAGCACCCTTTTTCAAAATAATTCCC
1 AAAATATCA-CCTTTTTCAAAATAATTCCC
212807 AAAATATCACCTTTTTCAAAATAATTCCC
1 AAAATATCACCTTTTTCAAAATAATTCCC
212836 AAAATATCACCTTTTTCAAAATAATTCCC
1 AAAATATCACCTTTTTCAAAATAATTCCC
*
212865 AAAATATCACCTTTTTCAAAATAATTCTC
1 AAAATATCACCTTTTTCAAAATAATTCCC
212894 AAAATATCACCTTTTTCAAAATAATTCCC
1 AAAATATCACCTTTTTCAAAATAATTCCC
212923 AAAATATCAC
1 AAAATATCAC
212933 TAGGTCGGGT
Statistics
Matches: 123, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
29 115 0.93
30 8 0.07
ACGTcount: A:0.42, C:0.24, G:0.01, T:0.33
Consensus pattern (29 bp):
AAAATATCACCTTTTTCAAAATAATTCCC
Found at i:217252 original size:45 final size:45
Alignment explanation
Indices: 217201--217382 Score: 220
Period size: 45 Copynumber: 4.0 Consensus size: 45
217191 ATCAATAAAA
** * * *
217201 TTTCATTAGTCTCTCCTTTTATGCCTATAATGCACCGTTACGCAT
1 TTTCATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCAT
* * *
217246 TTTCATTACTGACACCTTTTATGCCGATAATGCACCGTTATACAT
1 TTTCATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCAT
* ** * **
217291 TTTTATTAGTGGCATATTTTAGGCCGATAATGCACAATTATGCAT
1 TTTCATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCAT
* *
217336 ATTCATTAGTGGCACCTTTTATGCCGATAATGCACTGTTATGCAT
1 TTTCATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCAT
217381 TT
1 TT
217383 AACTTGCATT
Statistics
Matches: 113, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 113 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (45 bp):
TTTCATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCAT
Found at i:217435 original size:49 final size:48
Alignment explanation
Indices: 217339--217729 Score: 364
Period size: 49 Copynumber: 8.0 Consensus size: 48
217329 TATGCATATT
* *
217339 CATTAGTGGCACCTTTTATGCCGATAATGCAC-TGTTATGCATTTAACTTG
1 CATTAGTGGCACC-TTT-TGCCAAAAATGCACAT-TTATGCATTTAACTTG
* * * *
217389 CATTAGTGTCACCTTTTAACAAAAAATGCACATTTAAGCATTTAACTTG
1 CATTAGTGGCACCTTTT-GCCAAAAATGCACATTTATGCATTTAACTTG
* *
217438 TATTAGTGGCACCTCTCTGCCAAAAATGCACCA-TTATGCATTTAACTTG
1 CATTAGTGGCACCT-TTTGCCAAAAATGCA-CATTTATGCATTTAACTTG
* * * *
217487 CATTATTGGCACCCTTCTT-CTAAAAATGCACTTTTAAGCATTTAACTTG
1 CATTAGTGGCA-CCTT-TTGCCAAAAATGCACATTTATGCATTTAACTTG
* * * *
217536 CATTAGTGGCATCTTTTTGCCAAAAATGAACCA-TTATGTATTTAACTGG
1 CATTAGTGGCA-CCTTTTGCCAAAAATGCA-CATTTATGCATTTAACTTG
*
217585 CATTAGTGGCACCTTTCTGCC-AAAATGTACCA-TTATGCATTTAACTTG
1 CATTAGTGGCACCTTT-TGCCAAAAATGCA-CATTTATGCATTTAACTTG
* ** *
217633 CATTAGTGGCACCTTTCTACCAAAAATGCATTTTTAGGCATTTAACTTG
1 CATTAGTGGCACCTTT-TGCCAAAAATGCACATTTATGCATTTAACTTG
* * * * *
217682 CATTAATGACACCTTTCTTCCAAAAATGCACCA-TTCTGAATTTAACTT
1 CATTAGTGGCACCTTT-TGCCAAAAATGCA-CATTTATGCATTTAACTT
217730 TCACTATAGA
Statistics
Matches: 284, Mismatches: 44, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
48 52 0.18
49 210 0.74
50 22 0.08
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (48 bp):
CATTAGTGGCACCTTTTGCCAAAAATGCACATTTATGCATTTAACTTG
Found at i:217680 original size:146 final size:146
Alignment explanation
Indices: 217339--217728 Score: 480
Period size: 146 Copynumber: 2.7 Consensus size: 146
217329 TATGCATATT
* * * * *
217339 CATTAGTGGCACCTTT-TATGCCGATAATGCACTGTTATGCATTTAACTTGCATTAGTGTCACCT
1 CATTAGTGGCACCTTTCTA--CCAAAAATGCACTTTTAAGCATTTAACTTGCATTAGTGACACCT
* * * * * *
217403 TTTAACAAAAAATGCA-CATTTAAGCATTTAACTTGTATTAGTGGCACCTCTCTGCCAAAAATGC
64 TTT-TCCAAAAATGCACCA-TTATGAATTTAACTGGCATTAGTGGCACCTCTCTGCCAAAAATGC
217467 ACCATTATGCATTTAACTTG
127 ACCATTATGCATTTAACTTG
* * * * * *
217487 CATTATTGGCACCCTTCTTCTAAAAATGCACTTTTAAGCATTTAACTTGCATTAGTGGCATCTTT
1 CATTAGTGGCACCTTTCTACCAAAAATGCACTTTTAAGCATTTAACTTGCATTAGTGACACCTTT
* * * *
217552 TTGCCAAAAATGAACCATTATGTATTTAACTGGCATTAGTGGCACCTTTCTGCC-AAAATGTACC
66 TT-CCAAAAATGCACCATTATGAATTTAACTGGCATTAGTGGCACCTCTCTGCCAAAAATGCACC
217616 ATTATGCATTTAACTTG
130 ATTATGCATTTAACTTG
* * *
217633 CATTAGTGGCACCTTTCTACCAAAAATGCATTTTTAGGCATTTAACTTGCATTAATGACACCTTT
1 CATTAGTGGCACCTTTCTACCAAAAATGCACTTTTAAGCATTTAACTTGCATTAGTGACACCTTT
*
217698 CTTCCAAAAATGCACCATTCTGAATTTAACT
66 -TTCCAAAAATGCACCATTATGAATTTAACT
217729 TTCACTATAG
Statistics
Matches: 207, Mismatches: 31, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
146 107 0.52
147 83 0.40
148 16 0.08
149 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (146 bp):
CATTAGTGGCACCTTTCTACCAAAAATGCACTTTTAAGCATTTAACTTGCATTAGTGACACCTTT
TTCCAAAAATGCACCATTATGAATTTAACTGGCATTAGTGGCACCTCTCTGCCAAAAATGCACCA
TTATGCATTTAACTTG
Found at i:218660 original size:38 final size:37
Alignment explanation
Indices: 218605--218680 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 37
218595 TTCTCCAAAA
218605 AAATTTGACACTAGTTTTTATTGTCTTGGTTTTGAGT
1 AAATTTGACACTAGTTTTTATTGTCTTGGTTTTGAGT
218642 AAATTTGGACACTAGTTTTTATTGTCTTGGTTTTGAGT
1 AAATTT-GACACTAGTTTTTATTGTCTTGGTTTTGAGT
218680 A
1 A
218681 TGATTCTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 6 0.16
38 32 0.84
ACGTcount: A:0.22, C:0.08, G:0.20, T:0.50
Consensus pattern (37 bp):
AAATTTGACACTAGTTTTTATTGTCTTGGTTTTGAGT
Found at i:221378 original size:21 final size:21
Alignment explanation
Indices: 221353--221392 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
221343 AGGTTTTTTT
221353 TATTTTAATAAT-GTAAAAATA
1 TATTTT-ATAATAGTAAAAATA
*
221374 TATTTTTTAATAGTAAAAA
1 TATTTTATAATAGTAAAAA
221393 ATGTACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
TATTTTATAATAGTAAAAATA
Found at i:221436 original size:42 final size:43
Alignment explanation
Indices: 221368--221463 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 43
221358 TAATAATGTA
* *
221368 AAAATATATT-TTTTAATAGTAAAAAATGT-ACAAATTATTAT
1 AAAATATATTATTTTAATAGTAAAAAATATAACAAATGATTAT
* ** *
221409 AAAATATATTATTTTAATCGTTTAAAATATAATAAATGATTAT
1 AAAATATATTATTTTAATAGTAAAAAATATAACAAATGATTAT
*
221452 -AGATATATTATT
1 AAAATATATTATT
221464 ATTTTTAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 10 0.22
42 26 0.57
43 10 0.22
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (43 bp):
AAAATATATTATTTTAATAGTAAAAAATATAACAAATGATTAT
Found at i:221476 original size:24 final size:24
Alignment explanation
Indices: 221449--221508 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
221439 AATAAATGAT
*
221449 TATAGATATATT-ATTATTTTTAAA
1 TATA-ATATATTAATTATTTTAAAA
* *
221473 TATATTATTTTAATTATTTTAAAA
1 TATAATATATTAATTATTTTAAAA
221497 TACTAATATATT
1 TA-TAATATATT
221509 GTATATAGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 5 0.17
24 17 0.59
25 7 0.24
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TATAATATATTAATTATTTTAAAA
Found at i:222850 original size:31 final size:31
Alignment explanation
Indices: 222812--222912 Score: 139
Period size: 31 Copynumber: 3.3 Consensus size: 31
222802 TGGGGCCTAT
* *
222812 GGGCCTACCCAAGAAAGTTCTCAAGGCCACA
1 GGGCCTACCCAAGAAAGATCTCAGGGCCACA
*
222843 GGGCCTACCCAAGAAAGATCTCAGGGCCGCA
1 GGGCCTACCCAAGAAAGATCTCAGGGCCACA
* * *
222874 GGGCTTACCCAAGAATGATCTCAGGGCCATA
1 GGGCCTACCCAAGAAAGATCTCAGGGCCACA
*
222905 GAGCCTAC
1 GGGCCTAC
222913 ATAAGAGTCA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.30, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCCAAGAAAGATCTCAGGGCCACA
Found at i:225571 original size:17 final size:17
Alignment explanation
Indices: 225549--225596 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
225539 TTTGGTCAAA
**
225549 GTCAACGGTCAATGCCG
1 GTCAACGGTCAATGAAG
*
225566 GTCAACGGTCAGTGAAG
1 GTCAACGGTCAATGAAG
*
225583 GTTAACGGTCAATG
1 GTCAACGGTCAATG
225597 GCTCAGTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (17 bp):
GTCAACGGTCAATGAAG
Found at i:230616 original size:2 final size:2
Alignment explanation
Indices: 230611--230635 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
230601 TAAAACACAC
230611 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
230636 CCCTAATCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:230887 original size:24 final size:24
Alignment explanation
Indices: 230852--230963 Score: 154
Period size: 24 Copynumber: 4.7 Consensus size: 24
230842 CATAATTCAC
* *
230852 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAT
* *
230876 GTTAAGTATCATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
230900 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
*
230924 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
*
230948 GTCAAGTATCAGATCA
1 GTCAAGTATCATATCA
230964 TAAATCAAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:230983 original size:48 final size:48
Alignment explanation
Indices: 230852--230983 Score: 108
Period size: 48 Copynumber: 2.8 Consensus size: 48
230842 CATAATTCAC
* ** * * *
230852 GTCAAGTATCATATCAAAATCCAGGTTA-AGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAAATCAGA-AATCAGATCAGAATCCAA
* * ** * *
230900 GTCAAGTATCATATCAGAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAAATCAGAAATCAGATCAGAATCCAA
230948 GTCAAGTATCAGATCATAAAT-CAAATC-GAAAATCAG
1 GTCAAGTATCAGATCA-AAATCCAAATCAG-AAATCAG
230984 GTAAAATATT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
47 1 0.01
48 66 0.93
49 4 0.06
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCAGATCAAAATCCAAATCAGAAATCAGATCAGAATCCAA
Found at i:235579 original size:24 final size:24
Alignment explanation
Indices: 235547--235664 Score: 166
Period size: 24 Copynumber: 4.9 Consensus size: 24
235537 CATAATTCAC
* *
235547 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAT
* *
235571 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAT
235595 GTCAAGTATCAGATCAAAATCCAT
1 GTCAAGTATCAGATCAAAATCCAT
*
235619 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAT
235643 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
235665 AAATCGAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
23 2 0.02
24 76 0.90
25 6 0.07
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAT
Found at i:235615 original size:48 final size:48
Alignment explanation
Indices: 235547--235664 Score: 184
Period size: 48 Copynumber: 2.4 Consensus size: 48
235537 CATAATTCAC
*
235547 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAGGTCAGA-TATCAGATCAGAATCCAA
* *
235595 GTCAAGTATCAGATCAAAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAGGTCAGATATCAGATCAGAATCCAA
235643 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
235665 AAATCGAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
48 59 0.91
49 6 0.09
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAGATCAAAATCCAGGTCAGATATCAGATCAGAATCCAA
Found at i:235678 original size:48 final size:48
Alignment explanation
Indices: 235547--235678 Score: 144
Period size: 48 Copynumber: 2.8 Consensus size: 48
235537 CATAATTCAC
* ** *
235547 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAAATCAGA-AATCAGATCAGAATCCAA
** * *
235595 GTCAAGTATCAGATCAAAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAAATCAGAAATCAGATCAGAATCCAA
235643 GTCAAGTATCAGATCAGAAAT-CAAATC-GAAAATCAG
1 GTCAAGTATCAGATCA-AAATCCAAATCAG-AAATCAG
235679 GTAAAATATT
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
47 1 0.01
48 69 0.92
49 5 0.07
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (48 bp):
GTCAAGTATCAGATCAAAATCCAAATCAGAAATCAGATCAGAATCCAA
Found at i:238162 original size:30 final size:28
Alignment explanation
Indices: 238121--238469 Score: 239
Period size: 28 Copynumber: 12.4 Consensus size: 28
238111 ACAATCAACT
238121 ATTACGAAAATAAT-ACCTTTTTATAAAATA
1 ATTACGAAAAT-ATCA-CTTTTT-TAAAATA
* *
238151 ATTATGAAAATATCACTTTTTTGAAATA
1 ATTACGAAAATATCACTTTTTTAAAATA
* *
238179 ATTACCAAAATATCA-TTTTTTCGAAATA
1 ATTACGAAAATATCACTTTTTT-AAAATA
* **
238207 ATTACCAAAATATCACTTTTTCGAAATA
1 ATTACGAAAATATCACTTTTTTAAAATA
* * *
238235 ATTACCAAAATATCATTTTTTTTGAAATA
1 ATTACGAAAATATCA-CTTTTTTAAAATA
* * * *
238264 ATTACCAAAATATTATTTTTTTGAAATA
1 ATTACGAAAATATCACTTTTTTAAAATA
* **
238292 ATTACCAAAATATCACTTTTTCGAAATA
1 ATTACGAAAATATCACTTTTTTAAAATA
* *
238320 ATTACCAAAATATCACTTTTTTCGAAATA
1 ATTACGAAAATATCACTTTTTT-AAAATA
* * * * * *
238349 TTTACGAAACTAACACCTTCTTAACAGTA
1 ATTACGAAAATATCACTTTTTTAA-AATA
* *
238378 TTTACGAAACTAT---TTTTTTAAAAATA
1 ATTACGAAAATATCACTTTTTT-AAAATA
* *
238404 TTTACGAAACTAT---TTTTTTAAAAATA
1 ATTACGAAAATATCACTTTTTT-AAAATA
* * *
238430 TTTACGAAATTAACA-TTTTTTAACAATA
1 ATTACGAAAATATCACTTTTTTAA-AATA
* *
238458 TTTACAAAAATA
1 ATTACGAAAATA
238470 CCACCATAAC
Statistics
Matches: 281, Mismatches: 28, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
26 44 0.16
27 10 0.04
28 141 0.50
29 75 0.27
30 11 0.04
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (28 bp):
ATTACGAAAATATCACTTTTTTAAAATA
Found at i:238179 original size:28 final size:28
Alignment explanation
Indices: 238137--238353 Score: 310
Period size: 28 Copynumber: 7.6 Consensus size: 28
238127 AAAATAATAC
* **
238137 CTTTTTATAAAATAATTATGAAAATATCA
1 CTTTTT-TGAAATAATTACCAAAATATCA
238166 CTTTTTTGAAATAATTACCAAAATATCA
1 CTTTTTTGAAATAATTACCAAAATATCA
238194 -TTTTTTCGAAATAATTACCAAAATATCA
1 CTTTTTT-GAAATAATTACCAAAATATCA
*
238222 CTTTTTCGAAATAATTACCAAAATATCA
1 CTTTTTTGAAATAATTACCAAAATATCA
* *
238250 TTTTTTTTGAAATAATTACCAAAATATTA
1 -CTTTTTTGAAATAATTACCAAAATATCA
*
238279 TTTTTTTGAAATAATTACCAAAATATCA
1 CTTTTTTGAAATAATTACCAAAATATCA
*
238307 CTTTTTCGAAATAATTACCAAAATATCA
1 CTTTTTTGAAATAATTACCAAAATATCA
*
238335 CTTTTTTCGAAATATTTAC
1 CTTTTTT-GAAATAATTAC
238354 GAAACTAACA
Statistics
Matches: 172, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
27 6 0.03
28 120 0.70
29 46 0.27
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.41
Consensus pattern (28 bp):
CTTTTTTGAAATAATTACCAAAATATCA
Found at i:238269 original size:85 final size:84
Alignment explanation
Indices: 238146--238353 Score: 335
Period size: 85 Copynumber: 2.5 Consensus size: 84
238136 CCTTTTTATA
** *
238146 AAATAATTATGAAAATATCACTTTTTTGAAATAATTACCAAAATATCATTTTTTCGAAATAATTA
1 AAATAATTACCAAAATATCATTTTTTTGAAATAATTACCAAAATATCATTTTTTCGAAATAATTA
238211 CCAAAATATCACTTTTTCG
66 CCAAAATATCACTTTTTCG
* *
238230 AAATAATTACCAAAATATCATTTTTTTTGAAATAATTACCAAAATATTATTTTTTTGAAATAATT
1 AAATAATTACCAAAATATCA-TTTTTTTGAAATAATTACCAAAATATCATTTTTTCGAAATAATT
238295 ACCAAAATATCACTTTTTCG
65 ACCAAAATATCACTTTTTCG
* *
238315 AAATAATTACCAAAATATCACTTTTTTCGAAATATTTAC
1 AAATAATTACCAAAATATCA-TTTTTTTGAAATAATTAC
238354 GAAACTAACA
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 18 0.16
85 97 0.84
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (84 bp):
AAATAATTACCAAAATATCATTTTTTTGAAATAATTACCAAAATATCATTTTTTCGAAATAATTA
CCAAAATATCACTTTTTCG
Found at i:238448 original size:29 final size:26
Alignment explanation
Indices: 238376--238462 Score: 129
Period size: 26 Copynumber: 3.3 Consensus size: 26
238366 TTCTTAACAG
238376 TATTTACGAAACTATTTTTTTAAAAA
1 TATTTACGAAACTATTTTTTTAAAAA
238402 TATTTACGAAACTATTTTTTTAAAAA
1 TATTTACGAAACTATTTTTTTAAAAA
* * *
238428 TATTTACGAAATTAACATTTTTTAACAA
1 TATTTACGAAACT-A-TTTTTTTAAAAA
238456 TATTTAC
1 TATTTAC
238463 AAAAATACCA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
26 38 0.68
27 1 0.02
28 17 0.30
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.46
Consensus pattern (26 bp):
TATTTACGAAACTATTTTTTTAAAAA
Found at i:242075 original size:28 final size:28
Alignment explanation
Indices: 242043--242222 Score: 272
Period size: 28 Copynumber: 6.4 Consensus size: 28
242033 ACCTTTTTTA
*
242043 AAATAATTACGAAAATATCACTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTCG
* *
242071 AAATAATTACTAAAATATCATTTTTTTCG
1 AAATAATTACCAAAATATCA-CTTTTTCG
242100 AAATAATTACCAAAATATCACTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTCG
* *
242128 AAATAATTACCAAAATATCATTTTTTTG
1 AAATAATTACCAAAATATCACTTTTTCG
242156 AAATAATTACCAAAATATCACTTTTTTCG
1 AAATAATTACCAAAATATCAC-TTTTTCG
242185 AAATAATTACC-AAATATCACTTTTTTCG
1 AAATAATTACCAAAATATCAC-TTTTTCG
*
242213 AAATATTTAC
1 AAATAATTAC
242223 GAAACTAACA
Statistics
Matches: 141, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
28 98 0.70
29 43 0.30
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.39
Consensus pattern (28 bp):
AAATAATTACCAAAATATCACTTTTTCG
Found at i:242107 original size:57 final size:56
Alignment explanation
Indices: 242043--242222 Score: 290
Period size: 57 Copynumber: 3.2 Consensus size: 56
242033 ACCTTTTTTA
*
242043 AAATAATTACGAAAATATCACTTTTTCGAAATAATTACTAAAATATCATTTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTCGAAATAATTAC-AAAATATCATTTTTTTCG
242100 AAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAAATATCATTTTTTT-G
1 AAATAATTACCAAAATATCACTTTTTCGAAATAATTA-CAAAATATCATTTTTTTCG
* *
242156 AAATAATTACCAAAATATCACTTTTTTCGAAATAATTACCAAATATCACTTTTTTCG
1 AAATAATTACCAAAATATCAC-TTTTTCGAAATAATTACAAAATATCATTTTTTTCG
*
242213 AAATATTTAC
1 AAATAATTAC
242223 GAAACTAACA
Statistics
Matches: 116, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
56 37 0.32
57 78 0.67
58 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.39
Consensus pattern (56 bp):
AAATAATTACCAAAATATCACTTTTTCGAAATAATTACAAAATATCATTTTTTTCG
Found at i:242163 original size:85 final size:85
Alignment explanation
Indices: 242035--242222 Score: 290
Period size: 85 Copynumber: 2.2 Consensus size: 85
242025 AAAATAATAC
* * * *
242035 CTTTTTT-AAAATAATTACGAAAATATCACTTTTTCGAAATAATTACTAAAATATCATTTTTTTC
1 CTTTTTTCGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAAATATCACTTTTTTC
242099 GAAATAATTACCAAAATATCA
66 GAAATAATTACC-AAATATCA
* *
242120 C-TTTTTCGAAATAATTACCAAAATATCATTTTTTTGAAATAATTACCAAAATATCACTTTTTTC
1 CTTTTTTCGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAAATATCACTTTTTTC
242184 GAAATAATTACCAAATATCA
66 GAAATAATTACCAAATATCA
*
242204 CTTTTTTCGAAATATTTAC
1 CTTTTTTCGAAATAATTAC
242223 GAAACTAACA
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
84 14 0.15
85 80 0.85
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (85 bp):
CTTTTTTCGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAAATATCACTTTTTTC
GAAATAATTACCAAATATCA
Found at i:242291 original size:26 final size:26
Alignment explanation
Indices: 242214--242291 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
242204 CTTTTTTCGA
242214 AATATTTACGAAACTAACACCTTCTTAAC
1 AATATTTACGAAACTAACA--TT-TTAAC
* *** *
242243 AGTATTTACGAAACTATTTTTTTAAT
1 AATATTTACGAAACTAACATTTTAAC
*
242269 AATATTTATGAAACTAACATTTT
1 AATATTTACGAAACTAACATTTT
242292 TTTAACAATA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
26 22 0.56
27 2 0.05
29 15 0.38
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (26 bp):
AATATTTACGAAACTAACATTTTAAC
Found at i:242301 original size:29 final size:29
Alignment explanation
Indices: 242214--242301 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
242204 CTTTTTTCGA
** *
242214 AATATTTACGAAACTAACACCTTCTTAAC
1 AATATTTACGAAACTAACATTTTTTTAAC
* *
242243 AGTATTTACGAAACT---ATTTTTTTAAT
1 AATATTTACGAAACTAACATTTTTTTAAC
*
242269 AATATTTATGAAACTAACATTTTTTTAAC
1 AATATTTACGAAACTAACATTTTTTTAAC
242298 AATA
1 AATA
242302 GTTATAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
26 20 0.42
29 28 0.58
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (29 bp):
AATATTTACGAAACTAACATTTTTTTAAC
Found at i:247221 original size:44 final size:44
Alignment explanation
Indices: 247170--247254 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
247160 TAAAACAGAA
*
247170 ACTGAAACAGAAACACA-TTTGATGCAACATTTTCAATATAACAG
1 ACTGAAACAGAAACA-AGTTTGATGCAACATTTGCAATATAACAG
*
247214 ACTGAAACAGAAACAAGTTTGATGCTACATTTGCAATATAA
1 ACTGAAACAGAAACAAGTTTGATGCAACATTTGCAATATAA
247255 AAAGTAACTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 1 0.03
44 37 0.97
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (44 bp):
ACTGAAACAGAAACAAGTTTGATGCAACATTTGCAATATAACAG
Found at i:249654 original size:2 final size:2
Alignment explanation
Indices: 249647--249673 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
249637 GTTTGAAGTG
249647 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
249674 TACGATCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:251232 original size:30 final size:30
Alignment explanation
Indices: 251184--251253 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
251174 TAAGAGTTAG
* * *
251184 ATTACTATTTTATGTAAATTTTA-AGGTCCA
1 ATTAATATTTTATCTAAA-TTTAGAGGTCAA
*
251214 ATTAATATTTTGTCTAAATTTAGAGGTCAA
1 ATTAATATTTTATCTAAATTTAGAGGTCAA
*
251244 ATTAAAATTT
1 ATTAATATTT
251254 AACCATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (30 bp):
ATTAATATTTTATCTAAATTTAGAGGTCAA
Found at i:256492 original size:13 final size:14
Alignment explanation
Indices: 256469--256503 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
256459 GCATATGGGA
*
256469 ATTTTATTATTATT
1 ATTTTAATATTATT
256483 -TTTTAATATTATT
1 ATTTTAATATTATT
256496 ATTTTAAT
1 ATTTTAAT
256504 TAGATTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTAATATTATT
Found at i:260402 original size:32 final size:31
Alignment explanation
Indices: 260330--260406 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
260320 CTAATGTGAC
* *
260330 TCTTAGGTAGGCTCTGCGACCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
* *
260361 TCTTGGGTAGGCCCTGC-AGCCCTAAGATATAT
1 TCTTAGGTAGGCCCTGCGA-CCCTAAGAT-CAT
260393 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
260407 CGTGGCCCCG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 23 0.59
32 15 0.38
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
Found at i:266710 original size:13 final size:13
Alignment explanation
Indices: 266692--266727 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
266682 TCATAACCCG
266692 ACCCGACCCGTTT
1 ACCCGACCCGTTT
266705 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
266718 ACCCAACCCG
1 ACCCGACCCG
266728 ACCTGTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.50, G:0.14, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:266739 original size:18 final size:18
Alignment explanation
Indices: 266705--266739 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
266695 CGACCCGTTT
*
266705 ACCCGACCCGTTTACCCA
1 ACCCGACCCGTTGACCCA
*
266723 ACCCGACCTGTTGACCC
1 ACCCGACCCGTTGACCC
266740 GACCAGTTGA
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:0.20, C:0.49, G:0.14, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCA
Found at i:269324 original size:12 final size:12
Alignment explanation
Indices: 269309--269367 Score: 66
Period size: 12 Copynumber: 4.9 Consensus size: 12
269299 GATACATTAC
269309 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
269321 CTGATTTCTGAT
1 CTGAATTCTGTT
*
269333 CTGGATTCTGTT
1 CTGAATTCTGTT
*
269345 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
269357 CTGAATTCTGT
1 CTGAATTCTGT
269368 CTTGATTTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:269327 original size:48 final size:47
Alignment explanation
Indices: 269272--269380 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 47
269262 AAATATTTTA
*
269272 TCTGATTTCTGA-CTTGAATTCTGTTCTGATA-CATTACCTGAATTCTG
1 TCTGATTTCTGATC-TGAATTCTGTTCTGATATC-TGACCTGAATTCTG
* *
269319 TTCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATCTGAATTCTG
1 -TCTGATTTCTGATCTGAATTCTGTTCTGATATCTGACCTGAATTCTG
269367 TCTTGATTTCTGAT
1 TC-TGATTTCTGAT
269381 ATCTCCGTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
47 2 0.04
48 51 0.93
49 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (47 bp):
TCTGATTTCTGATCTGAATTCTGTTCTGATATCTGACCTGAATTCTG
Found at i:269340 original size:24 final size:24
Alignment explanation
Indices: 269272--269380 Score: 125
Period size: 24 Copynumber: 4.5 Consensus size: 24
269262 AAATATTTTA
269272 TCTGATTTCTGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* * *
269296 TCTGA-TACATTACCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
*
269320 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
269344 TCTGATATCTGATCTGAATTCTG-
1 TCTGATTTCTGATCTGAATTCTGT
269367 TCTTGATTTCTGAT
1 TC-TGATTTCTGAT
269381 ATCTCCGTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
23 4 0.06
24 65 0.90
25 3 0.04
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:269377 original size:12 final size:13
Alignment explanation
Indices: 269322--269380 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 13
269312 AATTCTGTTC
269322 TGATTTCTGATCT
1 TGATTTCTGATCT
* *
269335 GGA-TTCTGTTC-
1 TGATTTCTGATCT
*
269346 TGATATCTGATC-
1 TGATTTCTGATCT
*
269358 TGAATTCTG-TCT
1 TGATTTCTGATCT
269370 TGATTTCTGAT
1 TGATTTCTGAT
269381 ATCTCCGTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
11 4 0.11
12 28 0.80
13 3 0.09
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.49
Consensus pattern (13 bp):
TGATTTCTGATCT
Found at i:271517 original size:13 final size:13
Alignment explanation
Indices: 271498--271573 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
271488 GTCATAACCC
271498 GACCCGACCCGTT
1 GACCCGACCCGTT
*
271511 TACCCGACCCGTT
1 GACCCGACCCGTT
271524 GACCCGACCCGACTTGTT
1 GACCCGA-CC--C--GTT
**
271542 GACCTAACCCGTT
1 GACCCGACCCGTT
*
271555 GACCCGACCTGTT
1 GACCCGACCCGTT
271568 GACCCG
1 GACCCG
271574 TTGACCAGCG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 37 0.73
14 2 0.04
15 1 0.02
16 1 0.02
17 2 0.04
18 8 0.16
ACGTcount: A:0.17, C:0.42, G:0.21, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:271532 original size:31 final size:31
Alignment explanation
Indices: 271494--271563 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
271484 ACCGGTCATA
* *
271494 ACCCGACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCAACCCGTTG
** *
271525 ACCCGACCCGACTTGTTGACCTAACCCGTTG
1 ACCCGACCCGACCCGTTGACCCAACCCGTTG
271556 ACCCGACC
1 ACCCGACC
271564 TGTTGACCCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.19, C:0.46, G:0.19, T:0.17
Consensus pattern (31 bp):
ACCCGACCCGACCCGTTGACCCAACCCGTTG
Found at i:274151 original size:12 final size:12
Alignment explanation
Indices: 274136--274196 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
274126 GATACATTAC
*
274136 CTGAATTCTGTT
1 CTGAATTCTGAT
*
274148 CTGATTTCTGAT
1 CTGAATTCTGAT
* *
274160 CTGGATTCTGTT
1 CTGAATTCTGAT
274172 CTG-ATATCTGAT
1 CTGAAT-TCTGAT
274184 CTGAATTCT-AT
1 CTGAATTCTGAT
274195 CT
1 CT
274197 TGATTTCTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
11 6 0.15
12 33 0.80
13 2 0.05
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (12 bp):
CTGAATTCTGAT
Found at i:274188 original size:48 final size:48
Alignment explanation
Indices: 274099--274192 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
274089 AAATATTTTA
*
274099 TCTGATTACTGACTTGAATTCTGTTCTGATACATTACCTGAATTCTGT
1 TCTGATTACTGACTTGAATTCTGTTCTGATACATGACCTGAATTCTGT
* * *
274147 TCTGATTTCTGA-TCTGGATTCTGTTCTGATATC-TGATCTGAATTCT
1 TCTGATTACTGACT-TGAATTCTGTTCTGATA-CATGACCTGAATTCT
274193 ATCTTGATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 1 0.03
48 38 0.95
49 1 0.03
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (48 bp):
TCTGATTACTGACTTGAATTCTGTTCTGATACATGACCTGAATTCTGT
Found at i:274200 original size:24 final size:24
Alignment explanation
Indices: 274113--274192 Score: 108
Period size: 24 Copynumber: 3.3 Consensus size: 24
274103 ATTACTGACT
* *
274113 TGAATTCTGTTCTGATA-CATTACC
1 TGAATTCTGTTCTGATATC-TGATC
*
274137 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
*
274161 TGGATTCTGTTCTGATATCTGATC
1 TGAATTCTGTTCTGATATCTGATC
274185 TGAATTCT
1 TGAATTCT
274193 ATCTTGATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
24 48 0.98
25 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.46
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:276992 original size:13 final size:15
Alignment explanation
Indices: 276962--276994 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
276952 CATATATTTC
276962 TAAAAAATATCAAGA
1 TAAAAAATATCAAGA
276977 TAAAAAATAT-AA-A
1 TAAAAAATATCAAGA
276990 TAAAA
1 TAAAA
276995 TATTCATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 2 0.11
15 10 0.56
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (15 bp):
TAAAAAATATCAAGA
Found at i:277100 original size:5 final size:5
Alignment explanation
Indices: 277090--277137 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
277080 TCTATCTTGC
* * * * *
277090 AATTT AATTT ACTTT AATCT AATTT AATCT ACTTT AATCT AATTT AAT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AAT
277138 CATTAAAAAA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (5 bp):
AATTT
Found at i:277107 original size:10 final size:10
Alignment explanation
Indices: 277090--277138 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
277080 TCTATCTTGC
*
277090 AATTTAATTT
1 AATTTAATCT
*
277100 ACTTTAATCT
1 AATTTAATCT
277110 AATTTAATCT
1 AATTTAATCT
*
277120 ACTTTAATCT
1 AATTTAATCT
277130 AATTTAATC
1 AATTTAATC
277139 ATTAAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (10 bp):
AATTTAATCT
Found at i:277115 original size:20 final size:20
Alignment explanation
Indices: 277090--277138 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
277080 TCTATCTTGC
*
277090 AATTTAATTTACTTTAATCT
1 AATTTAATCTACTTTAATCT
277110 AATTTAATCTACTTTAATCT
1 AATTTAATCTACTTTAATCT
277130 AATTTAATC
1 AATTTAATC
277139 ATTAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTAATCTACTTTAATCT
Found at i:277338 original size:28 final size:30
Alignment explanation
Indices: 277298--277355 Score: 102
Period size: 28 Copynumber: 2.0 Consensus size: 30
277288 AAATTATAGT
277298 GTTGCTACAGTACCACGCTAG-A-TGTAGC
1 GTTGCTACAGTACCACGCTAGTACTGTAGC
277326 GTTGCTACAGTACCACGCTAGTACTGTAGC
1 GTTGCTACAGTACCACGCTAGTACTGTAGC
277356 TATCTTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 21 0.75
29 1 0.04
30 6 0.21
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (30 bp):
GTTGCTACAGTACCACGCTAGTACTGTAGC
Found at i:278040 original size:184 final size:184
Alignment explanation
Indices: 277731--278099 Score: 738
Period size: 184 Copynumber: 2.0 Consensus size: 184
277721 AATAACCCTC
277731 TTGATTACTTCAAATCTGCCTTAACGTTTAGACAAGGCTTAACAAATCCAGGTGAGTATATATGT
1 TTGATTACTTCAAATCTGCCTTAACGTTTAGACAAGGCTTAACAAATCCAGGTGAGTATATATGT
277796 TTCCTTTGTACTTGCTTTTATATCTTCTGTTATTGAGTTCATGTATAAGATGGTTGAAAAGTTGG
66 TTCCTTTGTACTTGCTTTTATATCTTCTGTTATTGAGTTCATGTATAAGATGGTTGAAAAGTTGG
277861 AATGATGTAATTTCCATGGGTTTCATTATTATATTATTATTAGTATTATTATAT
131 AATGATGTAATTTCCATGGGTTTCATTATTATATTATTATTAGTATTATTATAT
277915 TTGATTACTTCAAATCTGCCTTAACGTTTAGACAAGGCTTAACAAATCCAGGTGAGTATATATGT
1 TTGATTACTTCAAATCTGCCTTAACGTTTAGACAAGGCTTAACAAATCCAGGTGAGTATATATGT
277980 TTCCTTTGTACTTGCTTTTATATCTTCTGTTATTGAGTTCATGTATAAGATGGTTGAAAAGTTGG
66 TTCCTTTGTACTTGCTTTTATATCTTCTGTTATTGAGTTCATGTATAAGATGGTTGAAAAGTTGG
278045 AATGATGTAATTTCCATGGGTTTCATTATTATATTATTATTAGTATTATTATAT
131 AATGATGTAATTTCCATGGGTTTCATTATTATATTATTATTAGTATTATTATAT
278099 T
1 T
278100 ATACAACAAG
Statistics
Matches: 185, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 185 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.44
Consensus pattern (184 bp):
TTGATTACTTCAAATCTGCCTTAACGTTTAGACAAGGCTTAACAAATCCAGGTGAGTATATATGT
TTCCTTTGTACTTGCTTTTATATCTTCTGTTATTGAGTTCATGTATAAGATGGTTGAAAAGTTGG
AATGATGTAATTTCCATGGGTTTCATTATTATATTATTATTAGTATTATTATAT
Found at i:278563 original size:15 final size:16
Alignment explanation
Indices: 278533--278565 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
278523 AAAAAGTGTT
*
278533 TAAATTATATAAATAA
1 TAAATAATATAAATAA
278549 TAAATAATA-AAATAA
1 TAAATAATATAAATAA
278564 TA
1 TA
278566 TATCGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATAATATAAATAA
Found at i:279029 original size:17 final size:16
Alignment explanation
Indices: 279002--279036 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
278992 AAAAAACTTC
279002 AATGATAGAAACTGAG
1 AATGATAGAAACTGAG
*
279018 AATGAGTAGAAATTGAG
1 AATGA-TAGAAACTGAG
279035 AA
1 AA
279037 ATTAATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.20
Consensus pattern (16 bp):
AATGATAGAAACTGAG
Found at i:279462 original size:17 final size:17
Alignment explanation
Indices: 279440--279489 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
279430 AAATTCTTCT
279440 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
279457 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
279471 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
279488 AA
1 AA
279490 ACATGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:283699 original size:3 final size:3
Alignment explanation
Indices: 283691--283729 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
283681 ACATAGGAAC
283691 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
283730 CATCTATACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:285036 original size:11 final size:11
Alignment explanation
Indices: 285020--285044 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
285010 GAGTCCCATA
285020 CTTGAATTGTG
1 CTTGAATTGTG
285031 CTTGAATTGTG
1 CTTGAATTGTG
285042 CTT
1 CTT
285045 CAGAGAGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.12, G:0.24, T:0.48
Consensus pattern (11 bp):
CTTGAATTGTG
Found at i:302608 original size:10 final size:10
Alignment explanation
Indices: 302575--302630 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
302565 GCTGCTGGAA
*
302575 ACCGGTTTTCA
1 ACCGG-TTTCG
* *
302586 ACCAGTTTTG
1 ACCGGTTTCG
302596 ACCGGTTTCG
1 ACCGGTTTCG
302606 ACCGG-TTCG
1 ACCGGTTTCG
302615 AACCGGTTT-G
1 -ACCGGTTTCG
302625 ACCGGT
1 ACCGGT
302631 CTGAACCGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 10 0.26
10 22 0.58
11 6 0.16
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (10 bp):
ACCGGTTTCG
Found at i:302629 original size:19 final size:20
Alignment explanation
Indices: 302596--302640 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
302586 ACCAGTTTTG
302596 ACCGGTTTCGACCGGT-TCGA
1 ACCGGTTTCGACCGGTCT-GA
302616 ACCGGTTT-GACCGGTCTGA
1 ACCGGTTTCGACCGGTCTGA
302635 ACCGGT
1 ACCGGT
302641 CTGATCTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.16, C:0.29, G:0.31, T:0.24
Consensus pattern (20 bp):
ACCGGTTTCGACCGGTCTGA
Found at i:302673 original size:22 final size:22
Alignment explanation
Indices: 302647--302695 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
302637 CGGTCTGATC
*
302647 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCAACCGT
302669 TGACCCGACCCGACCCAACCGT
1 TGACCCGACCCGACCCAACCGT
302691 TGACC
1 TGACC
302696 GTTGACTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.10
Consensus pattern (22 bp):
TGACCCGACCCGACCCAACCGT
Found at i:309852 original size:10 final size:9
Alignment explanation
Indices: 309827--309861 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
309817 GGCTGCTGGA
309827 AACCGGTTT
1 AACCGGTTT
309836 AACCGGTTCT
1 AACCGGTT-T
*
309846 GACCGGTTT
1 AACCGGTTT
309855 AACCGGT
1 AACCGGT
309862 CTGCACCGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:309852 original size:19 final size:19
Alignment explanation
Indices: 309828--309870 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
309818 GCTGCTGGAA
309828 ACCGGTTTAACCGGTTCTG-
1 ACCGGTTTAACCGG-TCTGC
309847 ACCGGTTTAACCGGTCTGC
1 ACCGGTTTAACCGGTCTGC
309866 ACCGG
1 ACCGG
309871 CATGACCCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (19 bp):
ACCGGTTTAACCGGTCTGC
Found at i:309888 original size:19 final size:19
Alignment explanation
Indices: 309866--309920 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
309856 ACCGGTCTGC
309866 ACCGGCATGACCCGACCCG
1 ACCGGCATGACCCGACCCG
* *
309885 ACCGACCTGACCCGACCCG
1 ACCGGCATGACCCGACCCG
*
309904 ACCCG-ACTGACCCGACC
1 ACCGGCA-TGACCCGACC
309921 GTTGACCCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.51, G:0.22, T:0.05
Consensus pattern (19 bp):
ACCGGCATGACCCGACCCG
Found at i:309896 original size:14 final size:15
Alignment explanation
Indices: 309874--309920 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
309864 GCACCGGCAT
309874 GACCCGACCCGA-CC
1 GACCCGACCCGACCC
*
309888 GACCTGACCCGACCC
1 GACCCGACCCGACCC
*
309903 GACCCGA-CTGACCC
1 GACCCGACCCGACCC
309917 GACC
1 GACC
309921 GTTGACCCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 21 0.72
15 8 0.28
ACGTcount: A:0.21, C:0.53, G:0.21, T:0.04
Consensus pattern (15 bp):
GACCCGACCCGACCC
Found at i:309906 original size:24 final size:24
Alignment explanation
Indices: 309874--309920 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
309864 GCACCGGCAT
*
309874 GACCCGACCCGACCGACCTGACCC
1 GACCCGACCCGACCGACCCGACCC
*
309898 GACCCGACCCGACTGACCCGACC
1 GACCCGACCCGACCGACCCGACC
309921 GTTGACCCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.53, G:0.21, T:0.04
Consensus pattern (24 bp):
GACCCGACCCGACCGACCCGACCC
Found at i:309933 original size:5 final size:5
Alignment explanation
Indices: 309874--309920 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
309864 GCACCGGCAT
* *
309874 GACCC GACCC GA-CC GACCT GACCC GACCC GACCC GA-CT GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
309921 GTTGACCCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 7 0.19
5 29 0.81
ACGTcount: A:0.21, C:0.53, G:0.21, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:317137 original size:9 final size:9
Alignment explanation
Indices: 317123--317197 Score: 51
Period size: 10 Copynumber: 7.8 Consensus size: 9
317113 GGCTGCTAGA
317123 AACCGGTTT
1 AACCGGTTT
317132 AACCGGTTTT
1 AACCGG-TTT
317142 CAACCGGTTCT
1 -AACCGGTT-T
*
317153 GACCGGTTT
1 AACCGGTTT
* * *
317162 GACTGGTTCG
1 AACCGGTT-T
317172 AACCGGTTT
1 AACCGGTTT
* *
317181 GACCGGTCTG
1 AACCGGT-TT
317191 AACCGGT
1 AACCGGT
317198 CTGACCCGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
9 20 0.38
10 25 0.48
11 7 0.13
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:317148 original size:20 final size:21
Alignment explanation
Indices: 317123--317161 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
317113 GGCTGCTAGA
317123 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
317143 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
317162 GACTGGTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:317159 original size:10 final size:10
Alignment explanation
Indices: 317144--317203 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
317134 CCGGTTTTCA
317144 ACCGGTTCTG
1 ACCGGTTCTG
317154 ACCGGTT-TG
1 ACCGGTTCTG
*
317163 ACTGGTTC-G
1 ACCGGTTCTG
317172 AACCGGTT-TG
1 -ACCGGTTCTG
317182 ACCGG-TCTG
1 ACCGGTTCTG
317191 AACCGG-TCTG
1 -ACCGGTTCTG
317201 ACC
1 ACC
317204 CGACCCGACC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
8 1 0.02
9 19 0.44
10 23 0.53
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.27
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:317176 original size:19 final size:19
Alignment explanation
Indices: 317144--317203 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
317134 CCGGTTTTCA
317144 ACCGGTTCTG-ACCGGTTTG
1 ACCGG-TCTGAACCGGTTTG
*
317163 ACTGGT-TCGAACCGGTTTG
1 ACCGGTCT-GAACCGGTTTG
*
317182 ACCGGTCTGAACCGGTCTG
1 ACCGGTCTGAACCGGTTTG
317201 ACC
1 ACC
317204 CGACCCGACC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 1 0.03
18 2 0.06
19 31 0.89
20 1 0.03
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.27
Consensus pattern (19 bp):
ACCGGTCTGAACCGGTTTG
Found at i:317210 original size:5 final size:5
Alignment explanation
Indices: 317200--317254 Score: 69
Period size: 5 Copynumber: 11.0 Consensus size: 5
317190 GAACCGGTCT
*
317200 GACCC GACCC GA-CC GACCC GA-CC GACCC GACCGTT GACCC GACCC GACCC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACCC
317250 GACCC
1 GACCC
317255 AACCGTTGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 8 0.18
5 32 0.73
7 4 0.09
ACGTcount: A:0.20, C:0.55, G:0.22, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:317217 original size:9 final size:9
Alignment explanation
Indices: 317203--317253 Score: 66
Period size: 9 Copynumber: 5.2 Consensus size: 9
317193 CCGGTCTGAC
317203 CCGACCCGA
1 CCGACCCGA
317212 CCGACCCGA
1 CCGACCCGA
317221 CCGACCCGA
1 CCGACCCGA
317230 CCGTTGACCCGA
1 CC---GACCCGA
317242 CCCGACCCGA
1 -CCGACCCGA
317252 CC
1 CC
317254 CAACCGTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
9 22 0.58
10 7 0.18
12 7 0.18
13 2 0.05
ACGTcount: A:0.20, C:0.55, G:0.22, T:0.04
Consensus pattern (9 bp):
CCGACCCGA
Found at i:317259 original size:27 final size:26
Alignment explanation
Indices: 317212--317265 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
317202 CCCGACCCGA
*
317212 CCGACCCGACCGACCCGACCGTTGAC
1 CCGACCCGACCGACCCAACCGTTGAC
317238 CCGACCCGACCCGACCCAACCGTTGAC
1 CCGACCCGA-CCGACCCAACCGTTGAC
317265 C
1 C
317266 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.20, C:0.52, G:0.20, T:0.07
Consensus pattern (26 bp):
CCGACCCGACCGACCCAACCGTTGAC
Found at i:319997 original size:2 final size:2
Alignment explanation
Indices: 319990--320018 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
319980 CAAACATTTC
319990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
320019 CATTGTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:325876 original size:328 final size:328
Alignment explanation
Indices: 325279--325941 Score: 1299
Period size: 328 Copynumber: 2.0 Consensus size: 328
325269 AGAGGAGAGA
325279 ATTTTCGGCTTATACACCATTAATCTTGACCATAGTTCGCTGGTGGTTGTCACAGCCATCACCAT
1 ATTTTCGGCTTATACACCATTAATCTTGACCATAGTTCGCTGGTGGTTGTCACAGCCATCACCAT
325344 CTGGCACGTCAGGCTGTCGTGAGCAAACCCGTACCAACTATCATTGTTGAATCGTCGCGTCAATC
66 CTGGCACGTCAGGCTGTCGTGAGCAAACCCGTACCAACTATCATTGTTGAATCGTCGCGTCAATC
325409 GTGGAGGACCGATCGAATATCCACCCGAGAAAACCCAACGATTTGCTATTTTTCCCTGATCCAAG
131 GTGGAGGACCGATCGAATATCCACCCGAGAAAACCCAACGATTTGCTATTTTTCCCTGATCCAAG
325474 CCACAACGGATTTCCAAAAGCCTCACCGCCCTTATAATTGTAATGTTCAACTGATTCCAACCAAA
196 CCACAACGGATTTCCAAAAGCCTCACCGCCCTTATAATTGTAATGTTCAACTGATTCCAACCAAA
325539 ACCCAATGGGTATGTCTCCTTGCCGTAGATCTTTCATAGTCATCGTTTGATAAGAATTTCGACCA
261 ACCCAATGGGTATGTCTCCTTGCCGTAGATCTTTCATAGTCATCGTTTGATAAGAATTTCGACCA
325604 TTT
326 TTT
325607 ATTTTCGGCTTATACACCATTAATCTTGACCATAGTTCGCTGGTGGTTGTCACAGCCATCACCAT
1 ATTTTCGGCTTATACACCATTAATCTTGACCATAGTTCGCTGGTGGTTGTCACAGCCATCACCAT
**
325672 CTGGCACGTCAGGCTGTCGTGAGTTAACCCGTACCAACTATCATTGTTGAATCGTCGCGTCAATC
66 CTGGCACGTCAGGCTGTCGTGAGCAAACCCGTACCAACTATCATTGTTGAATCGTCGCGTCAATC
325737 GTGGAGGACCGATCGAATATCCACCCGAGAAAACCCAACGATTTGCTATTTTTCCCTGATCCAAG
131 GTGGAGGACCGATCGAATATCCACCCGAGAAAACCCAACGATTTGCTATTTTTCCCTGATCCAAG
325802 CCACAACGGATTTCCAAAAGCCTCACCGCCCTTATAATTGTAATGTTCAACTGATTCCAACCAAA
196 CCACAACGGATTTCCAAAAGCCTCACCGCCCTTATAATTGTAATGTTCAACTGATTCCAACCAAA
*
325867 ACCCAATGGGTATGTCTCCTTGCCGTAGATCTTTCATAGTCATCGTTTGATAAGACTTTCGACCA
261 ACCCAATGGGTATGTCTCCTTGCCGTAGATCTTTCATAGTCATCGTTTGATAAGAATTTCGACCA
325932 TTT
326 TTT
325935 ATTTTCG
1 ATTTTCG
325942 TTGTTTCACC
Statistics
Matches: 332, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
328 332 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (328 bp):
ATTTTCGGCTTATACACCATTAATCTTGACCATAGTTCGCTGGTGGTTGTCACAGCCATCACCAT
CTGGCACGTCAGGCTGTCGTGAGCAAACCCGTACCAACTATCATTGTTGAATCGTCGCGTCAATC
GTGGAGGACCGATCGAATATCCACCCGAGAAAACCCAACGATTTGCTATTTTTCCCTGATCCAAG
CCACAACGGATTTCCAAAAGCCTCACCGCCCTTATAATTGTAATGTTCAACTGATTCCAACCAAA
ACCCAATGGGTATGTCTCCTTGCCGTAGATCTTTCATAGTCATCGTTTGATAAGAATTTCGACCA
TTT
Found at i:326866 original size:17 final size:17
Alignment explanation
Indices: 326839--326872 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
326829 GAGATGTAAA
326839 ATGACATGGA-TTGACC
1 ATGACATGGATTTGACC
326855 ATGACAATGGATTTGACC
1 ATGAC-ATGGATTTGACC
326873 TGAGCATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (17 bp):
ATGACATGGATTTGACC
Found at i:327173 original size:27 final size:27
Alignment explanation
Indices: 327116--327177 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
327106 GAAAGGTCTG
* * ***
327116 AAATACCCTTGAACTCTAAAATGATTG
1 AAATACCCTTAAACTCTAAAATAACCA
327143 AAATACCCTTAAACTCTAAAATAACCA
1 AAATACCCTTAAACTCTAAAATAACCA
327170 AAATACCC
1 AAATACCC
327178 GGACCTCTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (27 bp):
AAATACCCTTAAACTCTAAAATAACCA
Found at i:327906 original size:39 final size:39
Alignment explanation
Indices: 327860--327952 Score: 141
Period size: 39 Copynumber: 2.4 Consensus size: 39
327850 ACGCTACGGC
*
327860 TAGGGTAAGTTCTTACCGCAGACTCCTTTGATTTATGCA
1 TAGGGTAAGTTCTTACCACAGACTCCTTTGATTTATGCA
* * * *
327899 TAGGGTAAGTCCTTACCACAGACTCCTTTGCTTTGTGCG
1 TAGGGTAAGTTCTTACCACAGACTCCTTTGATTTATGCA
327938 TAGGGTAAGTTCTTA
1 TAGGGTAAGTTCTTA
327953 TCATAAGCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (39 bp):
TAGGGTAAGTTCTTACCACAGACTCCTTTGATTTATGCA
Found at i:327968 original size:39 final size:39
Alignment explanation
Indices: 327860--327981 Score: 111
Period size: 39 Copynumber: 3.1 Consensus size: 39
327850 ACGCTACGGC
* ** * * **
327860 TAGGGTAAGTTCTTACCGCAGACTCCTTTGATTTATGCA
1 TAGGGTAAGTCCTTACCAAAGACTCATTTGCTTCGTGCA
* * * *
327899 TAGGGTAAGTCCTTACCACAGACTCCTTTGCTTTGTGCG
1 TAGGGTAAGTCCTTACCAAAGACTCATTTGCTTCGTGCA
* *
327938 TAGGGTAAGTTCTTATCATAAG-CTCATTTGCTTCGTGCA
1 TAGGGTAAGTCCTTACCA-AAGACTCATTTGCTTCGTGCA
327977 TAGGG
1 TAGGG
327982 GAAAACCTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 69 0.97
40 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (39 bp):
TAGGGTAAGTCCTTACCAAAGACTCATTTGCTTCGTGCA
Found at i:330897 original size:12 final size:12
Alignment explanation
Indices: 330880--330957 Score: 59
Period size: 12 Copynumber: 6.5 Consensus size: 12
330870 GCTTTATCTA
330880 ATTTCTGTTCTG
1 ATTTCTGTTCTG
**
330892 ATTTCTAATCTG
1 ATTTCTGTTCTG
** *
330904 AACTCTGTTATG
1 ATTTCTGTTCTG
* *
330916 ATTTCTGATATGG
1 ATTTCTGTTCT-G
330929 A-TTCTGTTCTG
1 ATTTCTGTTCTG
**
330940 ATTTCTACTCTG
1 ATTTCTGTTCTG
330952 ATTTCT
1 ATTTCT
330958 TATATGGATT
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
11 2 0.04
12 46 0.92
13 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.14, T:0.51
Consensus pattern (12 bp):
ATTTCTGTTCTG
Found at i:330910 original size:24 final size:24
Alignment explanation
Indices: 330883--330952 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
330873 TTATCTAATT
330883 TCTGTTCTGATTTCTAATCTGAAC
1 TCTGTTCTGATTTCTAATCTGAAC
* * * * *
330907 TCTGTTATGATTTCTGATATGGAT
1 TCTGTTCTGATTTCTAATCTGAAC
*
330931 TCTGTTCTGATTTCTACTCTGA
1 TCTGTTCTGATTTCTAATCTGA
330953 TTTCTTATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.49
Consensus pattern (24 bp):
TCTGTTCTGATTTCTAATCTGAAC
Found at i:330940 original size:36 final size:36
Alignment explanation
Indices: 330900--330973 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 36
330890 TGATTTCTAA
**
330900 TCTGAACTCTGTTATGATTTCTGATATGGATTCTGT
1 TCTGAACTCTACTATGATTTCTGATATGGATTCTGT
** * * *
330936 TCTGATTTCTACTCTGATTTCTTATATGGATTTTGT
1 TCTGAACTCTACTATGATTTCTGATATGGATTCTGT
330972 TC
1 TC
330974 GGATATCTGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.51
Consensus pattern (36 bp):
TCTGAACTCTACTATGATTTCTGATATGGATTCTGT
Found at i:330957 original size:24 final size:23
Alignment explanation
Indices: 330874--330957 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 23
330864 ATGAATGCTT
*
330874 TATCTAATTTCTGTTCTGATTTC
1 TATCTGATTTCTGTTCTGATTTC
** *
330897 TAATCTGAACTCTGTTATGATTTC
1 T-ATCTGATTTCTGTTCTGATTTC
*
330921 TGATATGGA-TTCTGTTCTGATTTC
1 T-ATCT-GATTTCTGTTCTGATTTC
330945 TACTCTGATTTCT
1 TA-TCTGATTTCT
330958 TATATGGATT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
23 4 0.08
24 42 0.88
25 2 0.04
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51
Consensus pattern (23 bp):
TATCTGATTTCTGTTCTGATTTC
Found at i:340062 original size:19 final size:19
Alignment explanation
Indices: 340036--340079 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
340026 ACTGTTAATA
*
340036 TTTA-TTATTATTTTCCCT
1 TTTATTTATTATTTTCCAT
* *
340054 TTTATTTATTTTTTTCTAT
1 TTTATTTATTATTTTCCAT
340073 TTTATTT
1 TTTATTT
340080 TATCAAATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTATTATTTTCCAT
Found at i:343571 original size:10 final size:11
Alignment explanation
Indices: 343555--343579 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
343545 ACTGAATTAA
343555 AAAAAAACTTC
1 AAAAAAACTTC
343566 AAAAAAACTTC
1 AAAAAAACTTC
343577 AAA
1 AAA
343580 TGATTAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAACTTC
Found at i:349331 original size:20 final size:20
Alignment explanation
Indices: 349291--349329 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
349281 CATTGCAGAA
*
349291 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
349311 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
349330 GAACTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:366907 original size:39 final size:40
Alignment explanation
Indices: 366816--366908 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 40
366806 ACAATGAAAG
* *
366816 GAGCAAACGGTAAAGTTTTCCCCTATGCATGATGCAAAAT
1 GAGCAAACGGTAAGGTTTTCCCCTATGCATGAAGCAAAAT
* * * *
366856 GGGCAAATGGTAAGGTTTTCCCCTATGTATGAAG-TAAAT
1 GAGCAAACGGTAAGGTTTTCCCCTATGCATGAAGCAAAAT
**
366895 GAGCTTACGGTAAG
1 GAGCAAACGGTAAG
366909 ATCTTACCTT
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
39 14 0.33
40 29 0.67
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (40 bp):
GAGCAAACGGTAAGGTTTTCCCCTATGCATGAAGCAAAAT
Found at i:368090 original size:27 final size:26
Alignment explanation
Indices: 368017--368093 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 26
368007 GGCATTTCGA
* * *
368017 TCATTTTAGAGCTCATGGTATTTTGG
1 TCATTTTAGAGTTCAAGGTATTTTAG
* *
368043 TTATTTTAGAGTTTAAGGGTATTTTAG
1 TCATTTTAGAGTTCAA-GGTATTTTAG
368070 TCATTTTAGAGTTCCAAGGTATTT
1 TCATTTTAGAGTT-CAAGGTATTT
368094 CATTCCTTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 12 0.29
27 28 0.67
28 2 0.05
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.48
Consensus pattern (26 bp):
TCATTTTAGAGTTCAAGGTATTTTAG
Found at i:368970 original size:25 final size:25
Alignment explanation
Indices: 368941--368997 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
368931 AAATAAATCC
368941 AATATTAGAACAAA-ATTGAGAAAAT
1 AATATTA-AACAAACATTGAGAAAAT
* **
368966 GATATTATCCAAACATTGAGAAAAT
1 AATATTAAACAAACATTGAGAAAAT
368991 AATATTA
1 AATATTA
368998 TCCAAACAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (25 bp):
AATATTAAACAAACATTGAGAAAAT
Found at i:368998 original size:25 final size:25
Alignment explanation
Indices: 368951--369005 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
368941 AATATTAGAA
*
368951 CAAA-ATTGAGAAAATGATATTATC
1 CAAACATTGAGAAAATAATATTATC
368975 CAAACATTGAGAAAATAATATTATC
1 CAAACATTGAGAAAATAATATTATC
369000 CAAACA
1 CAAACA
369006 GTGAAACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.25
Consensus pattern (25 bp):
CAAACATTGAGAAAATAATATTATC
Found at i:369016 original size:25 final size:25
Alignment explanation
Indices: 368957--369017 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
368947 AGAACAAAAT
* *
368957 TGAGAAAATGATATTATCCAAACAT
1 TGAGAAAATAATATTATCCAAACAG
368982 TGAGAAAATAATATTATCCAAACAG
1 TGAGAAAATAATATTATCCAAACAG
369007 TGA-AACAATAA
1 TGAGAA-AATAA
369018 CATATAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 2 0.06
25 31 0.94
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.25
Consensus pattern (25 bp):
TGAGAAAATAATATTATCCAAACAG
Found at i:370674 original size:22 final size:22
Alignment explanation
Indices: 370646--370699 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
370636 TAAGGGGGCC
370646 ATTTTCCTTTGACCGGGAAAAT
1 ATTTTCCTTTGACCGGGAAAAT
370668 ATTTTCCTTTGACCGGGAAAAT
1 ATTTTCCTTTGACCGGGAAAAT
370690 ATTTTCCTTT
1 ATTTTCCTTT
370700 TCCTTTGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.43
Consensus pattern (22 bp):
ATTTTCCTTTGACCGGGAAAAT
Found at i:373379 original size:35 final size:35
Alignment explanation
Indices: 373333--373402 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
373323 CCATCAACCC
*
373333 TTCAACTAGATTCTCTTCAAAGTAATTAGTAACAA
1 TTCAACTAGATTCTCTTCAAAGTAATTAATAACAA
373368 TTCAACTAGATTCTCTTCAAAGTAATTAATAACAA
1 TTCAACTAGATTCTCTTCAAAGTAATTAATAACAA
373403 ATCTTACAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (35 bp):
TTCAACTAGATTCTCTTCAAAGTAATTAATAACAA
Found at i:376465 original size:30 final size:30
Alignment explanation
Indices: 376426--376531 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
376416 AAGAAAGGTT
* ** *
376426 AAATTTTAATTTGACCTTTGAATTTAGATA
1 AAATATTAATTTGACCTTAAAATTTACATA
376456 AAATATTAATTTGACCTTAAAATTTACATA
1 AAATATTAATTTGACCTTAAAATTTACATA
* * * * * *
376486 AAATAGTAATGTAACACTTAAACTCTATATA
1 AAATATTAATTTGAC-CTTAAAATTTACATA
*
376517 AAATATGAA-TTGACC
1 AAATATTAATTTGACC
376532 CCTAAATTCA
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
29 1 0.02
30 41 0.67
31 19 0.31
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (30 bp):
AAATATTAATTTGACCTTAAAATTTACATA
Found at i:386378 original size:2 final size:2
Alignment explanation
Indices: 386371--386395 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
386361 TTCTATTTTA
386371 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
386396 ATTATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:386959 original size:17 final size:18
Alignment explanation
Indices: 386933--386970 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
386923 AACATCTTTT
386933 AAACAATTTTAAGA-AAA
1 AAACAATTTTAAGATAAA
*
386950 AAACATTTTTAAGATAAA
1 AAACAATTTTAAGATAAA
386968 AAA
1 AAA
386971 TTGATATGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
AAACAATTTTAAGATAAA
Found at i:389395 original size:24 final size:24
Alignment explanation
Indices: 389368--389416 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
389358 CATATCTCAT
*
389368 AACAGAATTCAAATCAGAAATCAG
1 AACAGAATTCAAATCAGAAACCAG
* *
389392 AACATATTTCAAATCAGAAACCAG
1 AACAGAATTCAAATCAGAAACCAG
389416 A
1 A
389417 TAAAATATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.53, C:0.18, G:0.10, T:0.18
Consensus pattern (24 bp):
AACAGAATTCAAATCAGAAACCAG
Found at i:390553 original size:17 final size:18
Alignment explanation
Indices: 390520--390553 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
390510 TCCATTCTGT
*
390520 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
390538 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
390554 GACCTTTCAA
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:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:391863 original size:15 final size:15
Alignment explanation
Indices: 391843--391875 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
391833 GTCAACGCCA
391843 GTCAACGGTCAACGG
1 GTCAACGGTCAACGG
*
391858 GTCAACGGTTAACGG
1 GTCAACGGTCAACGG
391873 GTC
1 GTC
391876 GATCAACGGG
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:0.24, C:0.24, G:0.33, T:0.18
Consensus pattern (15 bp):
GTCAACGGTCAACGG
Found at i:391901 original size:18 final size:18
Alignment explanation
Indices: 391855--391914 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
391845 CAACGGTCAA
*
391855 CGGGTCAACGGTTAACGGGT
1 CGGGTCAACGGGT--CGGGT
*
391875 C-GATCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
391892 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
391910 CGGGT
1 CGGGT
391915 TGTGACCGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 6 0.17
18 20 0.56
19 9 0.25
20 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:394572 original size:15 final size:16
Alignment explanation
Indices: 394542--394575 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
394532 GGTCAACAAT
394542 GGTCAACGCCGGTCAAC
1 GGTCAACG-CGGTCAAC
394559 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
394574 GG
1 GG
394576 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:396377 original size:31 final size:31
Alignment explanation
Indices: 396322--396380 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
396312 TTAGGTCCAT
* *
396322 AAGGAATTACCAATCGATGTTGAACCTGTCA
1 AAGGAATTACCAATCAATGCTGAACCTGTCA
396353 AAGGAATTACCAA-CAACTGCTGAACCTG
1 AAGGAATTACCAATCAA-TGCTGAACCTG
396381 CTAGTCTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAATCAATGCTGAACCTGTCA
Found at i:396554 original size:16 final size:16
Alignment explanation
Indices: 396533--396570 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
396523 TACATTTCAG
*
396533 TAAATCCATAATCAAC
1 TAAATCCAAAATCAAC
*
396549 TAAATCCAAAATCAGC
1 TAAATCCAAAATCAAC
396565 TAAATC
1 TAAATC
396571 ATACAGTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.24, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAATCCAAAATCAAC
Found at i:402859 original size:22 final size:22
Alignment explanation
Indices: 402827--402881 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
402817 AGAATTTGTT
402827 GATA-CTTTGCACCAATTAGCG
1 GATATCTTTGCACCAATTAGCG
402848 GATATCTTTGCACCAATTAGCG
1 GATATCTTTGCACCAATTAGCG
402870 GATATCTTTGCA
1 GATATCTTTGCA
402882 AAACCTTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (22 bp):
GATATCTTTGCACCAATTAGCG
Found at i:404894 original size:21 final size:21
Alignment explanation
Indices: 404852--404895 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
404842 ACTCTGGGAG
* *
404852 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
404873 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
404894 CT
1 CT
404896 CCTCCTCCGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:405495 original size:13 final size:13
Alignment explanation
Indices: 405477--405501 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
405467 ACCATGTCAC
405477 ATTGATTATGAAT
1 ATTGATTATGAAT
405490 ATTGATTATGAA
1 ATTGATTATGAA
405502 ACTAATGGCT
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGATTATGAAT
Found at i:406158 original size:46 final size:46
Alignment explanation
Indices: 406077--406210 Score: 198
Period size: 46 Copynumber: 2.9 Consensus size: 46
406067 GAACATCGAA
* * * *
406077 TGCATTTCATGCATCGATGCAC-ATACCATGAATCGATGCACTAAG
1 TGCATTTGATGCACCGATGCACAAGACCATGCATCGATGCACTAAG
* * *
406122 TGCGTTTGATGCACCGGTGCACAAGACCATGCATCGATGCACTTAG
1 TGCATTTGATGCACCGATGCACAAGACCATGCATCGATGCACTAAG
406168 TGCATTTGATGCACCGATGCACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCACCGATGCACAAGACCATGCATCGATGCACT
406211 CAGGGTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 18 0.23
46 61 0.77
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (46 bp):
TGCATTTGATGCACCGATGCACAAGACCATGCATCGATGCACTAAG
Found at i:407663 original size:59 final size:59
Alignment explanation
Indices: 407572--407700 Score: 206
Period size: 59 Copynumber: 2.2 Consensus size: 59
407562 ACTTTTACGC
*
407572 AAATATCACCCTAACAAAAATTAATTATGTATTAAGCACCCTTTTAAAAATATTTACAA
1 AAATAACACCCTAACAAAAATTAATTATGTATTAAGCACCCTTTTAAAAATATTTACAA
* *
407631 AAATAACACCTTAACAAAAATTAATT-TCGTATTAGGCACCCTTTTAAAAATATTTACAA
1 AAATAACACCCTAACAAAAATTAATTAT-GTATTAAGCACCCTTTTAAAAATATTTACAA
*
407690 AAATAGCACCC
1 AAATAACACCC
407701 GAGTTTTACA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 1 0.02
59 63 0.98
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.30
Consensus pattern (59 bp):
AAATAACACCCTAACAAAAATTAATTATGTATTAAGCACCCTTTTAAAAATATTTACAA
Found at i:407698 original size:29 final size:29
Alignment explanation
Indices: 407606--407700 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
407596 TTATGTATTA
407606 AGCACCCTTTTAAAAATATTTACAAAAAT
1 AGCACCCTTTTAAAAATATTTACAAAAAT
* ** ** *
407635 AACA-CCTTAACAAAAATTAATTT-C-GTATT
1 AGCACCCTT-TTAAAAA-T-ATTTACAAAAAT
407664 AGGCACCCTTTTAAAAATATTTACAAAAAT
1 A-GCACCCTTTTAAAAATATTTACAAAAAT
407694 AGCACCC
1 AGCACCC
407701 GAGTTTTACA
Statistics
Matches: 47, Mismatches: 12, Indels: 14
0.64 0.16 0.19
Matches are distributed among these distances:
28 8 0.17
29 19 0.40
30 12 0.26
31 8 0.17
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.29
Consensus pattern (29 bp):
AGCACCCTTTTAAAAATATTTACAAAAAT
Found at i:407740 original size:13 final size:13
Alignment explanation
Indices: 407722--407746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
407712 ATTTCACAAG
407722 TCGGGTCAACGGT
1 TCGGGTCAACGGT
407735 TCGGGTCAACGG
1 TCGGGTCAACGG
407747 GTCTAGTCGG
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:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
TCGGGTCAACGGT
Found at i:408635 original size:21 final size:20
Alignment explanation
Indices: 408611--408676 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 20
408601 TCTGCCACTA
408611 CATTATTATATT-TATAGTGCC
1 CATTATT-TATTCT-TAGTGCC
408632 CATTATTTCATTCTTAGTGCC
1 CATTATTT-ATTCTTAGTGCC
408653 CATTATTTTATTCTTAGTGCC
1 CATTA-TTTATTCTTAGTGCC
408674 CAT
1 CAT
408677 AAGATTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.02
21 37 0.88
22 4 0.10
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.48
Consensus pattern (20 bp):
CATTATTTATTCTTAGTGCC
Found at i:412388 original size:23 final size:23
Alignment explanation
Indices: 412362--412405 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
412352 TATTAAAATG
412362 TTATACAATTATAT-TTTTATTTC
1 TTAT-CAATTATATATTTTATTTC
* *
412385 TTATTATTTATATATTTTATT
1 TTATCAATTATATATTTTATT
412406 AGTTTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (23 bp):
TTATCAATTATATATTTTATTTC
Found at i:418110 original size:21 final size:21
Alignment explanation
Indices: 418086--418147 Score: 106
Period size: 21 Copynumber: 2.9 Consensus size: 21
418076 TGATTTTTGC
418086 ATATGATGTTATCATGAATAT
1 ATATGATGTTATCATGAATAT
418107 ATATGATGTTATCATGAATAT
1 ATATGATGTTATCATGAATAT
*
418128 ATATGATTTTTATCATGAAT
1 ATATGA-TGTTATCATGAAT
418148 GTTATTTTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
21 27 0.69
22 12 0.31
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (21 bp):
ATATGATGTTATCATGAATAT
Found at i:418501 original size:20 final size:20
Alignment explanation
Indices: 418476--418518 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
418466 TATATTGGGC
* *
418476 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
418496 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
418516 TAT
1 TAT
418519 GGAATAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:423048 original size:20 final size:20
Alignment explanation
Indices: 423023--423061 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
423013 GAGAAAGTTG
423023 GAAGTATAGTTGAGGAGGCC
1 GAAGTATAGTTGAGGAGGCC
423043 GAAGTATAGTTGAGGAGGC
1 GAAGTATAGTTGAGGAGGC
423062 AATGGGCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.41, T:0.21
Consensus pattern (20 bp):
GAAGTATAGTTGAGGAGGCC
Found at i:425296 original size:3 final size:3
Alignment explanation
Indices: 425284--425366 Score: 98
Period size: 3 Copynumber: 27.7 Consensus size: 3
425274 TTGTCCTTTC
* * * *
425284 TAT T-T TAT TAT TAT TAT TAT T-T TTT TAT TAC TAT TAT CAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
425330 TAT TAT TAT TAT TAT TAT TATT TATT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TA
425367 AATAATAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
2 4 0.06
3 59 0.84
4 7 0.10
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:426767 original size:2 final size:2
Alignment explanation
Indices: 426760--426814 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
426750 ATAAAAACAA
426760 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
426802 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
426815 GTTGCTTTAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:430609 original size:17 final size:16
Alignment explanation
Indices: 430587--430620 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
430577 TAAAAATAGT
430587 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
430604 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
430620 A
1 A
430621 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:445830 original size:30 final size:30
Alignment explanation
Indices: 445760--445832 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
445750 AATGGATTTA
* *
445760 TTTAGTGACCAAATTATAAATTTGGTAAAG
1 TTTAGTGACCAAAGTATAAATTTGGAAAAG
* *
445790 ATGAGTGACCAAAGTATAAACTTT-GAAAAG
1 TTTAGTGACCAAAGTATAAA-TTTGGAAAAG
*
445820 TTTAGGGACCAAA
1 TTTAGTGACCAAA
445833 ATGTAATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 32 0.91
31 3 0.09
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (30 bp):
TTTAGTGACCAAAGTATAAATTTGGAAAAG
Found at i:446566 original size:11 final size:11
Alignment explanation
Indices: 446550--446581 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
446540 ATTTGAGTGA
446550 GAAAAATTATG
1 GAAAAATTATG
446561 GAAAAATTATG
1 GAAAAATTATG
446572 GAAAAATTAT
1 GAAAAATTAT
446582 ATAAGGTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (11 bp):
GAAAAATTATG
Found at i:446646 original size:30 final size:30
Alignment explanation
Indices: 446611--446671 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
446601 TTGAAAGTAT
* *
446611 TCTATAAGCTTTAGAAAATTTGGG-GACCAA
1 TCTATAA-ATTTAGAAAAGTTGGGAGACCAA
*
446641 TCTATAAATTTTGAAAAGTTGGGAGACCAA
1 TCTATAAATTTAGAAAAGTTGGGAGACCAA
446671 T
1 T
446672 TTGTAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (30 bp):
TCTATAAATTTAGAAAAGTTGGGAGACCAA
Found at i:448682 original size:47 final size:45
Alignment explanation
Indices: 448607--448783 Score: 194
Period size: 51 Copynumber: 3.8 Consensus size: 45
448597 TATAAAATCC
* *
448607 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* **
448652 CTTACCATTTAAATTCCATAAGCTCATAAGCTTATATTTTTTTGCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGC-T-TA--TTTTACCAATATA
*
448703 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
448750 CTTGCCA-TTATTCTAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
448784 GTATGCTTAC
Statistics
Matches: 114, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
44 23 0.20
45 10 0.09
46 2 0.02
47 33 0.29
48 1 0.01
49 4 0.04
50 1 0.01
51 40 0.35
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:453953 original size:41 final size:41
Alignment explanation
Indices: 453863--453954 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
453853 TCGTAAGTCA
* * * *
453863 TTCGGGCCATCTGTAAGTCTTTCGAGCAAGATGTTTAAATC
1 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGTATAAACC
*
453904 TTCGGGTCATCTGTAAGCCTTTCGAGCAATATG-ATAAAGCC
1 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGTATAAA-CC
*
453945 TTCTGGTCAT
1 TTCGGGTCAT
453955 TCATAAGACC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
40 4 0.09
41 40 0.91
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34
Consensus pattern (41 bp):
TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGTATAAACC
Done.