Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008025.1 Hibiscus syriacus cultivar Beakdansim tig00110500_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: 2744542
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:459231 original size:60 final size:60
Alignment explanation
Indices: 459134--459248 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
459124 ACTGGTCTCT
* *
459134 CGACTATAAGACATTGCTTTATTGAATCCTCTAACTATTAAAAGTTACAAAATGACGCTC
1 CGACTATAAGACATTGCCTTATTGAAGCCTCTAACTATTAAAAGTTACAAAATGACGCTC
* * * *
459194 CGACTATAAGGCATTGCCTTGTTG-AGCCTCTCGACTATTAAGAGTTACAAAATGA
1 CGACTATAAGACATTGCCTTATTGAAGCCTCT-AACTATTAAAAGTTACAAAATGA
459249 TCACCCAACT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 6 0.12
60 42 0.88
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (60 bp):
CGACTATAAGACATTGCCTTATTGAAGCCTCTAACTATTAAAAGTTACAAAATGACGCTC
Found at i:461728 original size:35 final size:35
Alignment explanation
Indices: 461680--461748 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
461670 CAATTACAAA
*
461680 TATGGGACTGATTTATTTCTTAGATAGTAATTTAT
1 TATGGGACGGATTTATTTCTTAGATAGTAATTTAT
461715 TATGGGACGGATTTATTTCTTAGATAGTAATTTA
1 TATGGGACGGATTTATTTCTTAGATAGTAATTTA
461749 CCACGACACG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (35 bp):
TATGGGACGGATTTATTTCTTAGATAGTAATTTAT
Found at i:462035 original size:26 final size:24
Alignment explanation
Indices: 461990--462038 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
461980 TTTCCATATC
461990 TAAAATTTTATAATTCTGTACCCA
1 TAAAATTTTATAATTCTGTACCCA
462014 TAAAATATTTATTAAGTT-TGTACCC
1 TAAAAT-TTTA-TAA-TTCTGTACCC
462039 TCTTACATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 10 0.45
27 2 0.09
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (24 bp):
TAAAATTTTATAATTCTGTACCCA
Found at i:463838 original size:14 final size:16
Alignment explanation
Indices: 463805--463841 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
463795 AAATTCGCTT
463805 AAATAATTTAAATTTAC
1 AAATAATTTAAA-TTAC
463822 AAATAATTT-AA-TAC
1 AAATAATTTAAATTAC
463836 AAATAA
1 AAATAA
463842 ATACTAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
16 2 0.10
17 9 0.45
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAATTTAAATTAC
Found at i:469488 original size:31 final size:31
Alignment explanation
Indices: 469429--469489 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
469419 TATAGATAAG
*
469429 TTCAAATCATCCAAAAACAATATCAAACAAA
1 TTCAAATCATCCAAAAACAATATAAAACAAA
469460 TTCAAA-CATCCAAAAACCAA-AGTAAAACAA
1 TTCAAATCATCCAAAAA-CAATA-TAAAACAA
469490 TCCAAAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.59, C:0.23, G:0.02, T:0.16
Consensus pattern (31 bp):
TTCAAATCATCCAAAAACAATATAAAACAAA
Found at i:471422 original size:22 final size:23
Alignment explanation
Indices: 471375--471435 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
471365 GATTCCCTCC
*
471375 AGGGGGAATTGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
471398 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
471420 AGGGGGTATCGATTCC
1 AGGGGGAATCGGTTCC
471436 TCCTGCACCA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.25
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:484190 original size:15 final size:15
Alignment explanation
Indices: 484170--484199 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
484160 AATAAAAAAA
484170 ATCTAATTTCATGCT
1 ATCTAATTTCATGCT
484185 ATCTAATTTCATGCT
1 ATCTAATTTCATGCT
484200 TTATTCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (15 bp):
ATCTAATTTCATGCT
Found at i:486367 original size:2 final size:2
Alignment explanation
Indices: 486362--486399 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
486352 ATACACACAC
*
486362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
486400 GTCGGGTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:486751 original size:9 final size:9
Alignment explanation
Indices: 486732--486817 Score: 73
Period size: 9 Copynumber: 8.4 Consensus size: 9
486722 AAAAATTATG
486732 ATTTAAAATA
1 ATTT-AAATA
486742 ATTTAAATA
1 ATTTAAATA
486751 ATTTTTTAAATA
1 A---TTTAAATA
*
486763 ATTGAAATA
1 ATTTAAATA
486772 ATTTTTAAAATA
1 A--TTT-AAATA
486784 ATTTAAATA
1 ATTTAAATA
486793 ATTTTTAAAATA
1 A--TTT-AAATA
486805 ATTTAAATA
1 ATTTAAATA
486814 ATTT
1 ATTT
486818 TTAAAATAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 19
0.76 0.02 0.22
Matches are distributed among these distances:
9 29 0.45
10 10 0.15
11 5 0.08
12 21 0.32
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (9 bp):
ATTTAAATA
Found at i:486760 original size:12 final size:12
Alignment explanation
Indices: 486743--486827 Score: 71
Period size: 12 Copynumber: 7.8 Consensus size: 12
486733 TTTAAAATAA
486743 TTTAAATAATTT
1 TTTAAATAATTT
486755 TTTAAATAA---
1 TTTAAATAATTT
*
486764 TTGAAATAATTT
1 TTTAAATAATTT
*
486776 TTAAAATAA---
1 TTTAAATAATTT
486785 TTTAAATAATTT
1 TTTAAATAATTT
*
486797 TTAAAATAA---
1 TTTAAATAATTT
486806 TTTAAATAATTT
1 TTTAAATAATTT
*
486818 TTAAAATAAT
1 TTTAAATAAT
486828 ATATAAGACT
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
9 24 0.41
12 34 0.59
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (12 bp):
TTTAAATAATTT
Found at i:486763 original size:21 final size:21
Alignment explanation
Indices: 486733--486827 Score: 172
Period size: 21 Copynumber: 4.5 Consensus size: 21
486723 AAAATTATGA
486733 TTTAAAATAATTTAAATAATT
1 TTTAAAATAATTTAAATAATT
* *
486754 TTTTAAATAATTGAAATAATT
1 TTTAAAATAATTTAAATAATT
486775 TTTAAAATAATTTAAATAATT
1 TTTAAAATAATTTAAATAATT
486796 TTTAAAATAATTTAAATAATT
1 TTTAAAATAATTTAAATAATT
486817 TTTAAAATAAT
1 TTTAAAATAAT
486828 ATATAAGACT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (21 bp):
TTTAAAATAATTTAAATAATT
Found at i:487530 original size:287 final size:283
Alignment explanation
Indices: 487018--487576 Score: 947
Period size: 287 Copynumber: 2.0 Consensus size: 283
487008 TATTAATACT
* * *
487018 TTATCATTGTTTGCTATTATGTTGGGTTGATATCTTGGTAAGTCTGCTTATCCCCTTGGGTTGTT
1 TTATCATTGTTTGCTATTATGTTGGGTTGATATCTTGGTAAGTATGCTTAGCCCCTTGGGCTGTT
*
487083 TTATAAATATTGGGCCATTCTCATTAATGAAAATTGAGAACTTTTGATGTAAAATTGTTATTCTG
66 GTATAAATATTGGGCCATTCTCATTAATGAAAATTGAGAACTTTTGATGTAAAATTGTTATTCTG
*
487148 TTTTTGACTTTTGTCAAAATCCCTAAACCACTTTTCTATTCCCTTCATTTATCCTCTCTTCTTCA
131 TTTTTGACTTTTGTCAAAATCCCTAAACCACTTTTCTATTCCCTTCATTTATCCTCTCTACTTCA
* *
487213 TCACTAATATCTTCTCTGATTGCTTCTTTCATTGATGTTGCATTTCTAATTTAGTATCAGAGATA
196 TCACTAATATCTTCTCCGATTGCTTCTTTCATTGATGTTGCATTTCAAATTTAGTATCAGAGATA
487278 CAATGAATTGTGAATACTTTCTG
261 CAATGAATTGTGAATACTTTCTG
*
487301 TTATCATTGTTTGCTATTATGTTGGGTTGGTATCTTGGTAAGCAAGTATGCTTAGCCCCTTGGGC
1 TTATCATTGTTTGCTATTATGTTGGGTTGATATCTTGGT----AAGTATGCTTAGCCCCTTGGGC
* *
487366 TGTTGTATAAATATTGGGCCTTTCTCATTAATGAAAATTGAGAACTTTTGATGTAAAATTGTTCT
62 TGTTGTATAAATATTGGGCCATTCTCATTAATGAAAATTGAGAACTTTTGATGTAAAATTGTTAT
* *
487431 TCTGTTTTTGACTTTTGTCAAAATCCCTAAACCCCTTTTCTATTCGCTTCATTTATCCTCTCTAC
127 TCTGTTTTTGACTTTTGTCAAAATCCCTAAACCACTTTTCTATTCCCTTCATTTATCCTCTCTAC
*
487496 TTCATCGCTAATATCTTCTCCGATTGCTTCTTTCATTGATGTTGCATTTCAAATTTAGTATCAGA
192 TTCATCACTAATATCTTCTCCGATTGCTTCTTTCATTGATGTTGCATTTCAAATTTAGTATCAGA
* *
487561 GCTACAGTGAATTGTG
257 GATACAATGAATTGTG
487577 TTTGTTATCA
Statistics
Matches: 257, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
283 38 0.15
287 219 0.85
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (283 bp):
TTATCATTGTTTGCTATTATGTTGGGTTGATATCTTGGTAAGTATGCTTAGCCCCTTGGGCTGTT
GTATAAATATTGGGCCATTCTCATTAATGAAAATTGAGAACTTTTGATGTAAAATTGTTATTCTG
TTTTTGACTTTTGTCAAAATCCCTAAACCACTTTTCTATTCCCTTCATTTATCCTCTCTACTTCA
TCACTAATATCTTCTCCGATTGCTTCTTTCATTGATGTTGCATTTCAAATTTAGTATCAGAGATA
CAATGAATTGTGAATACTTTCTG
Found at i:492554 original size:34 final size:34
Alignment explanation
Indices: 492507--492583 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 34
492497 GGTGCTGATG
* *
492507 TTATGATTGCACTTGGAGTGTATTTTATGATTAA
1 TTATGATTGCACTTGGAGTGCATTTTATGATCAA
* *
492541 TTATGATTTCACTTGGAGTGCATTTTATGATCAG
1 TTATGATTGCACTTGGAGTGCATTTTATGATCAA
492575 TTATGATTG
1 TTATGATTG
492584 GAACAGTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.47
Consensus pattern (34 bp):
TTATGATTGCACTTGGAGTGCATTTTATGATCAA
Found at i:499019 original size:28 final size:28
Alignment explanation
Indices: 498979--499047 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 28
498969 GAATGATCAC
498979 TATGTCCCAAAGGACCACATAGAACACA
1 TATGTCCCAAAGGACCACATAGAACACA
*
499007 TATGTCCCAAAGGACCACATAGAACATA
1 TATGTCCCAAAGGACCACATAGAACACA
*
499035 TAGGTCCCGAAAG
1 TATGTCCC-AAAG
499048 ATCACGTAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 34 0.89
29 4 0.11
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (28 bp):
TATGTCCCAAAGGACCACATAGAACACA
Found at i:503306 original size:28 final size:28
Alignment explanation
Indices: 503232--503310 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
503222 GCAAGACCAC
* *
503232 TATGTCCCGAAGGACCACATAAAACACA
1 TATGTCCCGAAGGACCACGTAGAACACA
* * *
503260 TAAGTCCTGAAGAACCACGTAGAACACA
1 TATGTCCCGAAGGACCACGTAGAACACA
*
503288 TATGTCCCAAAGGACCACGTAGA
1 TATGTCCCGAAGGACCACGTAGA
503311 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.15
Consensus pattern (28 bp):
TATGTCCCGAAGGACCACGTAGAACACA
Found at i:524127 original size:8 final size:8
Alignment explanation
Indices: 524114--524143 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
524104 TAAGACCTTC
524114 AGAAAATG
1 AGAAAATG
524122 AGAAAATG
1 AGAAAATG
524130 AGAAAATG
1 AGAAAATG
524138 AGAAAA
1 AGAAAA
524144 GTAATTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (8 bp):
AGAAAATG
Found at i:524301 original size:42 final size:42
Alignment explanation
Indices: 524254--524333 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 42
524244 TATTAGTAAG
* * *
524254 TCCTTCAGGCCATCAGTAAGTCTTTCGTGCATGATGATTAAA
1 TCCTTCAGGCCATCAGCAAGTCTTTCGAGCAAGATGATTAAA
* * * *
524296 TCCTTCTGGTCATCTGCCAGTCTTTCGAGCAAGATGAT
1 TCCTTCAGGCCATCAGCAAGTCTTTCGAGCAAGATGAT
524334 AAGTCATTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 31 1.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (42 bp):
TCCTTCAGGCCATCAGCAAGTCTTTCGAGCAAGATGATTAAA
Found at i:524320 original size:249 final size:247
Alignment explanation
Indices: 523884--524362 Score: 694
Period size: 249 Copynumber: 1.9 Consensus size: 247
523874 AGTTGTTTTG
* *
523884 GAAAATGAGAAAACAACTTCAAAAGTTTCTCATTTAAATCTTTTCAGAAAATGAAATTTTTGAAA
1 GAAAATGAGAAAACAACTTCAAAAGATTCTCATTTAAATATTTTCAGAAAATGAAATTTTTGAAA
**
523949 AGTAAGAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAACTAGTAAGTCCTTTGGG
66 AGTAAGAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAACTAGTAAGTCCTTCAGG
* * *
524014 CCATTAGTAACTATTTCGCACATGATGATTAAATCCTTTCGGTCATCTGTCAGTCTTTTGAGCAA
131 CCATCAGTAACTATTTCGCACATGATGATTAAATCCTTTCGGTCATCTGCCAGTCTTTCGAGCAA
* *
524079 TATGATAAGTCATTCAAGTCATCTATAAGACCTTCAGAAAATGAGAAAATGA
196 GATGATAAGTCATTCAAGCCATCTATAAGACCTTCAGAAAATGAGAAAATGA
* *
524131 GAAAATGAGAAAAGTAATTTTC-AAAGATTCTCATTT-AATATTTTCAGAAAATGAAATTTTTGA
1 GAAAATGAGAAAA-CAA-CTTCAAAAGATTCTCATTTAAATATTTTCAGAAAATGAAATTTTTGA
* * * *
524194 AAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCCATATTAGTAAGTCCTT
64 AAAGTAAG--AGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAACTAGTAAGTCCTT
* * **
524259 CAGGCCATCAGTAAGTCTTTCGTGCATGATGATTAAATCC-TTCTGGTCATCTGCCAGTCTTTCG
127 CAGGCCATCAGTAACTATTTCGCACATGATGATTAAATCCTTTC-GGTCATCTGCCAGTCTTTCG
***
524323 AGCAAGATGATAAGTCATTTGGGCCATCTATAAGACCTTC
191 AGCAAGATGATAAGTCATTCAAGCCATCTATAAGACCTTC
524363 GGGCAGGATG
Statistics
Matches: 205, Mismatches: 22, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
247 47 0.23
248 18 0.09
249 140 0.68
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (247 bp):
GAAAATGAGAAAACAACTTCAAAAGATTCTCATTTAAATATTTTCAGAAAATGAAATTTTTGAAA
AGTAAGAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAACTAGTAAGTCCTTCAGG
CCATCAGTAACTATTTCGCACATGATGATTAAATCCTTTCGGTCATCTGCCAGTCTTTCGAGCAA
GATGATAAGTCATTCAAGCCATCTATAAGACCTTCAGAAAATGAGAAAATGA
Found at i:524451 original size:235 final size:238
Alignment explanation
Indices: 524170--525043 Score: 956
Period size: 235 Copynumber: 3.5 Consensus size: 238
524160 CTCATTTAAT
*
524170 ATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAAC
1 ATTTTCAAAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAAC
* * * * *
524235 TATTTCCCATATTAGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGTGCATGATGATTAAATCCT
66 TATTTCCAAAATTAATAAGTCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCT
** *
524300 TCTGGTCATCTGCCAGTCTTTCGAGCAAGATGATAAGTCATTTGGGCCATCTATAAGACCTTCGG
131 TCTGGTCATCTGTTAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGG
*
524365 GCAGGATGTTTTCACATGATTTTCAAAAAATGAGAAA-AGT-A
196 GCATGATGTTTTCACATGATTTTCAAAAAATGAGAAATAGTAA
524406 ATTTTCAAAAAAT-AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAAC
1 ATTTTCAAAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAAC
* * *
524470 TATTTCCTAAATTATTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCT
66 TATTTCCAAAATTAATAAGTCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCT
* * * **
524535 TCTGGTCATCTGTTAGTCTTTAGAGCAAGATGATAAGTCCTTTGGGCCATCTAT--TA-CATCAA
131 TCTGGTCATCTGTTAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGG
*
524597 GCATGATGTTTTCAC-TGATTTTCAAACAATGAGAAAGCGATATTCAAAGTTTCTCAATTAA
196 GCATGATGTTTTCACATGATTTTCAAAAAATGAG--A---A-A-T---AG---------TAA
* * *
524658 TATTTTCAGAAAATGAAATATTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAA
1 -ATTTTCAAAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAA
* *
524723 CTATTTCCAAAATTAATAAGTCATTCAGACCATCAATAAGTCTTTCGAGCATGATGATTAAATCC
65 CTATTTCCAAAATTAATAAGTCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCC
* * *
524788 TT-TGGGTCATCTGTTAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGACATCTATAAGACCTTT
130 TTCT-GGTCATCTGTTAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCTATAAGACCTTC
* * *
524852 GGGCATGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCGATTTCCAA
194 GGGCATGATGTTTTCACATGATTTTCAAAAAATGAGAAA--TA-GT--AA
* *
524902 ATTTTATCATTTAATATATTCAGAAAATGAAATTTTTAAAAAGTAAGAAAGCGATTTCCAAAGTT
1 A-TTT-TC-------A-A---A-AAA-TGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTT
* ** * * * *
524967 TCTTACCTAGAAAACTATTTCCAAAATTGGTAAATCCTTC-GAACCATTATTAAGTCTTTCGAGC
51 TCTTACCTAGTAAACTATTTCCAAAATTAATAAGTCCTTCAG-GCCATCAATAAGTCTTTCGAGC
525031 ATGATGATTAAAT
115 ATGATGATTAAAT
525044 AAGTCGGGTT
Statistics
Matches: 542, Mismatches: 48, Indels: 74
0.82 0.07 0.11
Matches are distributed among these distances:
231 17 0.03
232 17 0.03
233 2 0.00
235 160 0.30
236 13 0.02
237 1 0.00
242 3 0.01
243 1 0.00
244 5 0.01
245 2 0.00
250 1 0.00
251 1 0.00
252 3 0.01
253 14 0.03
254 158 0.29
256 3 0.01
257 21 0.04
258 120 0.22
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (238 bp):
ATTTTCAAAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAAC
TATTTCCAAAATTAATAAGTCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCT
TCTGGTCATCTGTTAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGG
GCATGATGTTTTCACATGATTTTCAAAAAATGAGAAATAGTAA
Found at i:524808 original size:42 final size:41
Alignment explanation
Indices: 524761--524840 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
524751 ACCATCAATA
* * *
524761 AGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTGTT
1 AGTCTTTCGAGCAAGATGA-TAAATCCTTCGGGACATCTGTT
*
524803 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGACATCT
1 AGTCTTTCGAGCAAGATGATAAATCCTTCGGGACATCT
524841 ATAAGACCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 16 0.47
42 18 0.53
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (41 bp):
AGTCTTTCGAGCAAGATGATAAATCCTTCGGGACATCTGTT
Found at i:524984 original size:258 final size:253
Alignment explanation
Indices: 524409--525043 Score: 918
Period size: 254 Copynumber: 2.5 Consensus size: 253
524399 AAAAGTAATT
* *
524409 TTCAAAAAAT-AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTAT
1 TTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
* * *
524473 TTCCTAAATTATTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCT
66 TTCCAAAATTAATAAGTCCTTC-GACCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCT
* * *
524538 GGTCATCTGTTAGTCTTTAGAGCAAGATGATAAGTCCTTTGGGCCATCTATTACATCAAGCATGA
130 GGTCATCTGTTAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGACATCTATGACATCAAGCATGA
* *
524603 TGTTTTCACTGATTTTCAAACAATGAGAAAGCGATATTCAAAGTTTCTCAATTAATATT
195 TGTTTTCACTGATTTTCAAACAATGAGAAAGCGATATTCAAAGTTTATCAATTAATATA
*
524662 TTCAGAAAATGAAATATTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
1 TTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
*
524727 TTCCAAAATTAATAAGTCATTCAGACCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTT-T
66 TTCCAAAATTAATAAGTCCTTC-GACCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCT
* * ***
524791 GGGTCATCTGTTAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGACATCTATAAGACCTTTGGGC
130 -GGTCATCTGTTAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGACATCTAT--GA-CATCAAGC
* *
524856 ATGATGTTTTCACATGATTTTCGAAA-AATGAGAAAGCGAT-TTCCAAATTTTATCATTTAATAT
191 ATGATGTTTTCAC-TGATTTTC-AAACAATGAGAAAGCGATATT-CAAAGTTTATCAATTAATAT
524919 A
253 A
* *
524920 TTCAGAAAATGAAATTTTTAAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGAAAACTAT
1 TTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
** * * *
524985 TTCCAAAATTGGTAAATCCTTCGAACCATTATTAAGTCTTTCGAGCATGATGATTAAAT
66 TTCCAAAATTAATAAGTCCTTCG-ACCATCAATAAGTCTTTCGAGCATGATGATTAAAT
525044 AAGTCGGGTT
Statistics
Matches: 344, Mismatches: 29, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
253 10 0.03
254 158 0.46
256 1 0.00
257 20 0.06
258 152 0.44
259 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (253 bp):
TTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
TTCCAAAATTAATAAGTCCTTCGACCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCTG
GTCATCTGTTAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGACATCTATGACATCAAGCATGAT
GTTTTCACTGATTTTCAAACAATGAGAAAGCGATATTCAAAGTTTATCAATTAATATA
Found at i:525193 original size:3 final size:3
Alignment explanation
Indices: 525185--525272 Score: 90
Period size: 3 Copynumber: 28.7 Consensus size: 3
525175 TTTGTCCGAG
* * **
525185 TTA TTA TTA TTA ATA TTA TTA TTA TTA ATA TTTA ACA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
525231 TTA TTA TTA TTAA GTT- TTA -TA TTA TTTA TTA TTA TTA TTA TT
1 TTA TTA TTA TT-A -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT
525273 TATGTTTTTA
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.06
3 59 0.83
4 6 0.08
5 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:525225 original size:31 final size:30
Alignment explanation
Indices: 525190--525272 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 30
525180 CCGAGTTATT
*
525190 ATTATTAATATTATTATTATTAA-TATTTAAC
1 ATTATTATTATTATTATTATTAAGT-TTT-AC
*
525221 ATTATTATTATTATTATTATTAAGTTTTAT
1 ATTATTATTATTATTATTATTAAGTTTTAC
525251 ATTATTTATTATTATTATTATT
1 ATTA-TTATTATTATTATTATT
525273 TATGTTTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
30 5 0.10
31 42 0.88
32 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (30 bp):
ATTATTATTATTATTATTATTAAGTTTTAC
Found at i:525383 original size:25 final size:25
Alignment explanation
Indices: 525349--525398 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
525339 AAAACCAATG
525349 GCCCAAGCTGCTAGGGTTTGAAGAA
1 GCCCAAGCTGCTAGGGTTTGAAGAA
525374 GCCCAAGCTGCTAGGGTTTGAAGAA
1 GCCCAAGCTGCTAGGGTTTGAAGAA
525399 ACCCTAGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (25 bp):
GCCCAAGCTGCTAGGGTTTGAAGAA
Found at i:530600 original size:23 final size:23
Alignment explanation
Indices: 530574--530642 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
530564 CACCACAGCT
* *
530574 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
*
530597 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCA
*
530620 CGTAGAATTGAACCGTAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
530643 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGTAGTGCCA
Found at i:536111 original size:23 final size:23
Alignment explanation
Indices: 536085--536153 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
536075 CACCACAGCT
* * *
536085 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
* *
536108 CGTAGAGTTGCACCGTAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCA
*
536131 CATAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
536154 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGTAGTGCCA
Found at i:539404 original size:261 final size:260
Alignment explanation
Indices: 538632--539391 Score: 986
Period size: 261 Copynumber: 2.9 Consensus size: 260
538622 ATTGATAAAA
* * * *
538632 AGATTTTCAAAGTTTCTAACCCAATAGACTATTTCCAAAATTGGTAAGTCCTTCGGGTCATCAAT
1 AGATTTCCAAAGTTTCTTACCCAATAGACTATTTCCAAAATTGGTAAGTCCTTTGGGTCATCAGT
* * *
538697 AAGTCTTTCGAGCATGATGATTAAACCCTTT-GTGTCATTTGTCAGTCTTTCAAGCAAGAAGATA
66 AAGTCTTTCGAGCATGATGATTAAA-TCTTTCGTGTCATTTGTCAGTCTTTCGAGCAAGATGATA
* * * * *
538761 AGTCTTTCAAGCCATCTATAAGACCTTTGGGAAAGATGCTTTCATATGATATTTTTGGAAAATGA
130 AGTCATTCGAG-CATCTATAAGACCTTTGGGCAAGATGCTTTCATATGATGTTTTTGAAAAATGA
* * *
538826 GAAAAGCAATTTTCAAAGTTTCTCATTTAATGTTGTCAAAAAATGAAATTTTTGAAAAGTAAGAA
194 GAAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTTAGAAAATGAAATTTTTGAAAAGTAAGAA
*
538891 TG
259 AG
* * * *
538893 AGATTTCCAAAGTTTATTACCCAATAGACTGTTTCCAAAATTAGTAAGT-CTTTCGGGTCATAAG
1 AGATTTCCAAAGTTTCTTACCCAATAGACTATTTCCAAAATTGGTAAGTCCTTT-GGGTCATCAG
* * *
538957 TAAGTCTTTCGAGCATGATGATTAAATCCTTCATGTCATCTGTCAGTCTTTCGAGCAAGATGATA
65 TAAGTCTTTCGAGCATGATGATTAAATCTTTCGTGTCATTTGTCAGTCTTTCGAGCAAGATGATA
* * * * * * * *
539022 AGTCCTTTGGGTCGTCTATAAGACATTTGGGCAAGATGATTTCATAAGATGTTTGTGAAAAATGA
130 AGTCATTCGAG-CATCTATAAGACCTTTGGGCAAGATGCTTTCATATGATGTTTTTGAAAAATGA
* * * * * *
539087 G-AAAGCGATTTTTAAAGTTTCTTATTTAGTATTTTTCAGAAAATGAAACTTTTGAAAAGTAAGA
194 GAAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTT-AGAAAATGAAATTTTTGAAAAGTAAGA
539151 AAG
258 AAG
** * * * *
539154 TTATTTCCAAAGTTTCTTACCTAGTAGACTATTTCTAAAATTGGTAAATCCTTTGGGTCATCAGT
1 AGATTTCCAAAGTTTCTTACCCAATAGACTATTTCCAAAATTGGTAAGTCCTTTGGGTCATCAGT
* * * *
539219 AAGTCTTTTGAGCATGATGATTAAATCTTTCGGGTCGTTTGTTAGTCTTTCGAGCAAGATGATAA
66 AAGTCTTTCGAGCATGATGATTAAATCTTTCGTGTCATTTGTCAGTCTTTCGAGCAAGATGATAA
* * * *
539284 GTCATTCGAGCAATTTATAAGACCTTTTGGCAAGATTCTTCCATATGATGTTTTTGAAAAATGAG
131 GTCATTCGAGC-ATCTATAAGACCTTTGGGCAAGATGCTTTCATATGATGTTTTTGAAAAATGAG
539349 AAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTTAGAAAAT
195 AAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTTAGAAAAT
539392 ATTTTTTTTG
Statistics
Matches: 422, Mismatches: 71, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
260 35 0.08
261 353 0.84
262 34 0.08
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (260 bp):
AGATTTCCAAAGTTTCTTACCCAATAGACTATTTCCAAAATTGGTAAGTCCTTTGGGTCATCAGT
AAGTCTTTCGAGCATGATGATTAAATCTTTCGTGTCATTTGTCAGTCTTTCGAGCAAGATGATAA
GTCATTCGAGCATCTATAAGACCTTTGGGCAAGATGCTTTCATATGATGTTTTTGAAAAATGAGA
AAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTTAGAAAATGAAATTTTTGAAAAGTAAGAAAG
Found at i:540466 original size:22 final size:22
Alignment explanation
Indices: 540441--540501 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
540431 CTGTACCATC
* *
540441 AGCAACACCAAGTTCGCCTCTA
1 AGCAACACCAAATCCGCCTCTA
*
540463 AGCAACACCAAATCCGCCTCCA
1 AGCAACACCAAATCCGCCTCTA
* *
540485 ATCAACGCCAAATCCGC
1 AGCAACACCAAATCCGC
540502 TCCTCAACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.34, C:0.41, G:0.11, T:0.13
Consensus pattern (22 bp):
AGCAACACCAAATCCGCCTCTA
Found at i:540515 original size:19 final size:21
Alignment explanation
Indices: 540465--540515 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
540455 CGCCTCTAAG
*
540465 CAACACCAAATCCGCCTCCAAT
1 CAACAGCAAATCCGCCTCC-AT
540487 CAAC-GCCAAATCCG-CTCC-T
1 CAACAG-CAAATCCGCCTCCAT
540506 CAACAGCAAA
1 CAACAGCAAA
540516 GGAAAACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 9 0.35
20 1 0.04
21 4 0.15
22 12 0.46
ACGTcount: A:0.37, C:0.43, G:0.08, T:0.12
Consensus pattern (21 bp):
CAACAGCAAATCCGCCTCCAT
Found at i:541971 original size:2 final size:2
Alignment explanation
Indices: 541964--542045 Score: 155
Period size: 2 Copynumber: 41.0 Consensus size: 2
541954 TCATAACATG
541964 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
*
542006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
542046 GCTCGCTTGC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:542130 original size:8 final size:8
Alignment explanation
Indices: 542111--542157 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
542101 TTTCATACTT
542111 TATATATG
1 TATATATG
542119 --TATATG
1 TATATATG
542125 TATATATG
1 TATATATG
*
542133 TATATGTG
1 TATATATG
* *
542141 TGTATATA
1 TATATATG
542149 TATATATG
1 TATATATG
542157 T
1 T
542158 GTACATATCC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
6 6 0.19
8 25 0.81
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (8 bp):
TATATATG
Found at i:542130 original size:14 final size:14
Alignment explanation
Indices: 542111--542139 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
542101 TTTCATACTT
542111 TATATATGTATATG
1 TATATATGTATATG
542125 TATATATGTATATG
1 TATATATGTATATG
542139 T
1 T
542140 GTGTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TATATATGTATATG
Found at i:542146 original size:18 final size:18
Alignment explanation
Indices: 542123--542159 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
542113 TATATGTATA
*
542123 TGTATATATGTATATGTG
1 TGTATATATATATATGTG
542141 TGTATATATATATATGTG
1 TGTATATATATATATGTG
542159 T
1 T
542160 ACATATCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (18 bp):
TGTATATATATATATGTG
Found at i:542165 original size:18 final size:18
Alignment explanation
Indices: 542126--542165 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
542116 ATGTATATGT
* **
542126 ATATATGTATATGTGTGT
1 ATATATATATATGTGTAC
542144 ATATATATATATGTGTAC
1 ATATATATATATGTGTAC
542162 ATAT
1 ATAT
542166 CCTATATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (18 bp):
ATATATATATATGTGTAC
Found at i:552198 original size:28 final size:28
Alignment explanation
Indices: 552155--552218 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
552145 GGATAATTTT
* * *
552155 TTATAAAGTTATAAAAGTTAGGGATCGTAA
1 TTATAAAG-TATAAAAATTA-GGACCCTAA
552185 TTATAAA-TATAAAAATTAGGACCCTAA
1 TTATAAAGTATAAAAATTAGGACCCTAA
552212 TTATAAA
1 TTATAAA
552219 CATTAAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 14 0.45
28 10 0.32
30 7 0.23
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (28 bp):
TTATAAAGTATAAAAATTAGGACCCTAA
Found at i:557852 original size:2 final size:2
Alignment explanation
Indices: 557847--557872 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
557837 AACCCCCCAA
557847 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
557873 GAAACAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:562637 original size:19 final size:19
Alignment explanation
Indices: 562601--562637 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
562591 TGAAAATGAT
*
562601 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
562620 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
562638 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:565786 original size:37 final size:36
Alignment explanation
Indices: 565752--565820 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
565742 TACAAATTGT
565752 AAAATATTTATAT-ATTTTCTATAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TATAAAAAATTAAATTC
* * *
565788 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTATAAAAAATTAAA
565821 AATATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 24 0.83
37 5 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTATAAAAAATTAAATTC
Found at i:578400 original size:53 final size:54
Alignment explanation
Indices: 578265--578519 Score: 413
Period size: 54 Copynumber: 4.7 Consensus size: 54
578255 GGTCAATCAC
* * * *
578265 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGAAAATTCAT
1 AAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCAT
578319 AAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCAT
1 AAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCAT
*
578373 -AACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGAAATTCAT
1 AAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCAT
*
578426 AAACTTATTATGAATTTCTTAGGTTGCACACATACTGCCAATACGAAAAATTCAT
1 AAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACG-AAAATTCAT
* **
578481 AAACTCATTATGAATTTCTTAGGTTATACACATAGTGCC
1 AAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCC
578520 CATTTGGGGA
Statistics
Matches: 188, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
53 52 0.28
54 93 0.49
55 43 0.23
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.33
Consensus pattern (54 bp):
AAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCAT
Found at i:578404 original size:107 final size:109
Alignment explanation
Indices: 578265--578519 Score: 424
Period size: 107 Copynumber: 2.4 Consensus size: 109
578255 GGTCAATCAC
* * *
578265 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTAT
1 AAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTAT
*
578330 GAATTTCTTAGGTTGCACACATAGTGCCAATACG-AAAATTCAT
66 GAATTTCTTAGGTTGCACACATACTGCCAATACGAAAAATTCAT
* *
578373 -AACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTAT
1 AAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTAT
578437 GAATTTCTTAGGTTGCACACATACTGCCAATACGAAAAATTCAT
66 GAATTTCTTAGGTTGCACACATACTGCCAATACGAAAAATTCAT
**
578481 AAACTCATTATGAATTTCTTAGGTTATACACATAGTGCC
1 AAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCC
578520 CATTTGGGGA
Statistics
Matches: 136, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
107 92 0.68
108 9 0.07
109 35 0.26
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.33
Consensus pattern (109 bp):
AAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTAT
GAATTTCTTAGGTTGCACACATACTGCCAATACGAAAAATTCAT
Found at i:581310 original size:21 final size:21
Alignment explanation
Indices: 581267--581322 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
581257 AAATAAGTTT
**
581267 GGGATCGATCCTTTAAGCCAA
1 GGGATCGATCCTTTAAGAAAA
**
581288 GGGATCGATCCTTTTTGAAAA
1 GGGATCGATCCTTTAAGAAAA
* *
581309 GGGGTAGATCCTTT
1 GGGATCGATCCTTT
581323 CCCCTAAGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (21 bp):
GGGATCGATCCTTTAAGAAAA
Found at i:589181 original size:21 final size:20
Alignment explanation
Indices: 589139--589189 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
589129 AAAATAAAGA
*
589139 GATCGATCCTTTTTTAGAGG
1 GATCGATCCTTTTTTACAGG
589159 GATCGAT-CTTTTTTCACATGG
1 GATCGATCCTTTTTT-ACA-GG
*
589180 GATCAATCCT
1 GATCGATCCT
589190 ATGGTGGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 7 0.27
20 9 0.35
21 8 0.31
22 2 0.08
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
GATCGATCCTTTTTTACAGG
Found at i:593433 original size:23 final size:24
Alignment explanation
Indices: 593390--593438 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
593380 ATGAATTTTA
**
593390 TTATGAAATATTTTTATAAT-ATT
1 TTATGAAATATTTACATAATAATT
593413 TTATGAAATGATTTACA-AATAATT
1 TTATGAAAT-ATTTACATAATAATT
593437 TT
1 TT
593439 GGATATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (24 bp):
TTATGAAATATTTACATAATAATT
Found at i:597647 original size:48 final size:48
Alignment explanation
Indices: 597576--597667 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
597566 CATAGTACTG
*
597576 ATACGAAAATGCAACGTAGGCATTAAACAAAATCGATCTATAACCTTT
1 ATACGAAAATGCAACGTAGGCATTAAACAAAATCGATCGATAACCTTT
* *
597624 ATACGAAAATGCAACTTATGCATTAAACAAAATCGATCGATAAC
1 ATACGAAAATGCAACGTAGGCATTAAACAAAATCGATCGATAAC
597668 ATCATACACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (48 bp):
ATACGAAAATGCAACGTAGGCATTAAACAAAATCGATCGATAACCTTT
Found at i:601081 original size:23 final size:23
Alignment explanation
Indices: 601055--601110 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
601045 TGTCATGAAT
601055 GACCACATAGGATTATCCCAAAG
1 GACCACATAGGATTATCCCAAAG
* * *
601078 GACCACATAGGTTTGTCCCGAAG
1 GACCACATAGGATTATCCCAAAG
601101 GACCACATAG
1 GACCACATAG
601111 AACCCTCGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (23 bp):
GACCACATAGGATTATCCCAAAG
Found at i:601093 original size:46 final size:46
Alignment explanation
Indices: 601022--601110 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
601012 GCCATATATC
* * * * * *
601022 TATCCCGAAGGACTATATAGTTTTGTCATGAATGACCACATAGGAT
1 TATCCCAAAGGACCACATAGGTTTGTCACGAAGGACCACATAGGAT
*
601068 TATCCCAAAGGACCACATAGGTTTGTCCCGAAGGACCACATAG
1 TATCCCAAAGGACCACATAGGTTTGTCACGAAGGACCACATAG
601111 AACCCTCGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (46 bp):
TATCCCAAAGGACCACATAGGTTTGTCACGAAGGACCACATAGGAT
Found at i:601696 original size:22 final size:20
Alignment explanation
Indices: 601648--601698 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
601638 GGTACATTAC
*
601648 TATCGATACTCCTCCTATTG
1 TATCGATACTCCTCCTATGG
* *
601668 TACCGATACGTCCCTTCTATGG
1 TATCGATAC-T-CCTCCTATGG
601690 TATCGATAC
1 TATCGATAC
601699 CCACTTCGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 8 0.32
21 1 0.04
22 16 0.64
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.35
Consensus pattern (20 bp):
TATCGATACTCCTCCTATGG
Found at i:601785 original size:63 final size:63
Alignment explanation
Indices: 601686--601825 Score: 226
Period size: 63 Copynumber: 2.2 Consensus size: 63
601676 CGTCCCTTCT
* * *
601686 ATGGTATCGATACCCACTTCGGAATCGTTACCAGTTTAGCATTCTAGAATTTCATACTTGATA
1 ATGGTATCGATACCCACTTCCGAACCGATACCAGTTTAGCATTCTAGAATTTCATACTTGATA
* *
601749 ATGGTATCGATACCCACTTCCGTACCGATACCAGTTTAGCATTCTAGAATTTTATACTTGATA
1 ATGGTATCGATACCCACTTCCGAACCGATACCAGTTTAGCATTCTAGAATTTCATACTTGATA
*
601812 ATTGTATCGATACC
1 ATGGTATCGATACC
601826 TTACCCTTAG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (63 bp):
ATGGTATCGATACCCACTTCCGAACCGATACCAGTTTAGCATTCTAGAATTTCATACTTGATA
Found at i:603036 original size:32 final size:33
Alignment explanation
Indices: 602995--603063 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
602985 GGATCCCCAA
602995 AAGATTAAGATAATGTCAGAGTGAGAACCGCCT
1 AAGATTAAGATAATGTCAGAGTGAGAACCGCCT
*
603028 AAGA-TAAGATAATGTTAGAGTGAGAACCGCCT
1 AAGATTAAGATAATGTCAGAGTGAGAACCGCCT
603060 AAGA
1 AAGA
603064 ATGTCATCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 31 0.89
33 4 0.11
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (33 bp):
AAGATTAAGATAATGTCAGAGTGAGAACCGCCT
Found at i:616267 original size:15 final size:15
Alignment explanation
Indices: 616231--616268 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
616221 TTTTAAAAAT
* *
616231 AGAAATATGGTAATT
1 AGAAAAATGGTAATA
616246 A-AAAAATGGTAATA
1 AGAAAAATGGTAATA
616260 AGAAAAATG
1 AGAAAAATG
616269 ATATTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (15 bp):
AGAAAAATGGTAATA
Found at i:619544 original size:17 final size:17
Alignment explanation
Indices: 619522--619558 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
619512 TAAAACACAA
619522 TACATACATGGTTAATC
1 TACATACATGGTTAATC
619539 TACATACATGGTTAATC
1 TACATACATGGTTAATC
619556 TAC
1 TAC
619559 GAGAATGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (17 bp):
TACATACATGGTTAATC
Found at i:620489 original size:194 final size:199
Alignment explanation
Indices: 620059--620520 Score: 501
Period size: 194 Copynumber: 2.3 Consensus size: 199
620049 TAATGTCATG
* * * * * * * *
620059 TATGTGTCGATATTAGCTTTAATTGAAAGATAAGTTGCAATAGTACGCATTTAAGCTTAAAAATT
1 TATGTGTCGATATTAGCATAAACTGAAAGATAAGTTGCAATACTACGCCTCTAATCTTATAAATT
* * * * * * *
620124 ACAAAACAAAATCAGTTAACTTCACGGTAGTACCTCTCGAACATGTCTATGAAGCGATTTTAACT
66 ACAAAACAAAATCAGTTAA--TCACAGAAATACCTCCCAAACATGTCTATCAAGCCATTTTAACT
* * *
620189 TGTTATTCATGAACAAAACCAAGCTTTGAATCTATTTTCAACGTGATTTTTACCTCTCTTAAAAT
129 TGTTATTCATGAACAAAACCAAGCTTTGAAACCATTTTCAACGTGAATTTTACCTCTCTTAAAAT
**
620254 GTCTTG
194 GTCTCA
* * * *
620260 TATATG-CTGATATTACCCTCAACTGAAAGATAAGTTGCAATACTACGCCTCTAATCTTATAAAT
1 TATGTGTC-GATATTAGCATAAACTGAAAGATAAGTTGCAATACTACGCCTCTAATCTTATAAAT
*
620324 TACAAAA-AAAATC-GATT-A-CA-AGAAATA-CTCCCCAAACATGTCTATCAAGCCATTTTAGC
65 TACAAAACAAAATCAG-TTAATCACAGAAATACCT-CCCAAACATGTCTATCAAGCCATTTTAAC
* * * * *
620383 TTGTTCTTCATGCACAAAACCAAGCTTTGAAACCATTTTCCACGT-AATTTTACCATGT-TTACA
128 TTGTTATTCATGAACAAAACCAAGCTTTGAAACCATTTTCAACGTGAATTTTACC-TCTCTTAAA
*
620446 ATTTCTCA
192 ATGTCTCA
* **
620454 TATGTGTCGATATTAGCATAAACTGAAAGATAAGTTTCAATACTATACCTCTAATCTTATAAATT
1 TATGTGTCGATATTAGCATAAACTGAAAGATAAGTTGCAATACTACGCCTCTAATCTTATAAATT
620519 AC
66 AC
620521 GATAATTTTT
Statistics
Matches: 220, Mismatches: 36, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
194 77 0.35
195 71 0.32
196 2 0.01
199 2 0.01
200 9 0.04
201 59 0.27
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (199 bp):
TATGTGTCGATATTAGCATAAACTGAAAGATAAGTTGCAATACTACGCCTCTAATCTTATAAATT
ACAAAACAAAATCAGTTAATCACAGAAATACCTCCCAAACATGTCTATCAAGCCATTTTAACTTG
TTATTCATGAACAAAACCAAGCTTTGAAACCATTTTCAACGTGAATTTTACCTCTCTTAAAATGT
CTCA
Found at i:621184 original size:13 final size:13
Alignment explanation
Indices: 621166--621208 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
621156 TTACATAATT
621166 TTAAAATAAAAAA
1 TTAAAATAAAAAA
621179 TTAAAAATTAAAAAA
1 TT-AAAA-TAAAAAA
*
621194 TTAAATTAAATAAA
1 TTAAAATAAA-AAA
621208 T
1 T
621209 ACAAATGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.23
14 11 0.42
15 9 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TTAAAATAAAAAA
Found at i:621190 original size:15 final size:14
Alignment explanation
Indices: 621168--621198 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
621158 ACATAATTTT
621168 AAAATAAAAAATTA
1 AAAATAAAAAATTA
621182 AAAATTAAAAAATTA
1 AAAA-TAAAAAATTA
621197 AA
1 AA
621199 TTAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATAAAAAATTA
Found at i:621336 original size:23 final size:23
Alignment explanation
Indices: 621310--621365 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
621300 GAATGTTAGG
*
621310 ATAAAATAAT-TTTAAAATTAGAA
1 ATAAAATAATATTTAAAA-TAAAA
*
621333 ATAAAACAATATTTAAAATAAAA
1 ATAAAATAATATTTAAAATAAAA
621356 ATAAATATAA
1 ATAAA-ATAA
621366 AATAGAGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
ATAAAATAATATTTAAAATAAAA
Found at i:632661 original size:20 final size:20
Alignment explanation
Indices: 632621--632675 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
632611 TGCATATCAT
*
632621 ATAGTTGCATA-T-TAAATA
1 ATAGTTGCATATTGTAAAAA
*
632639 ATAGTGGCATATTGTAAAAA
1 ATAGTTGCATATTGTAAAAA
*
632659 ATAATTGCAT-TTGTAAA
1 ATAGTTGCATATTGTAAA
632676 TTACATAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 10 0.32
19 8 0.26
20 13 0.42
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (20 bp):
ATAGTTGCATATTGTAAAAA
Found at i:633102 original size:2 final size:2
Alignment explanation
Indices: 633095--633129 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
633085 CATTATGCGT
633095 TA TA TA TA TA TA TA TA TA TA TA T- 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
633130 ATGAACCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:633174 original size:10 final size:10
Alignment explanation
Indices: 633159--633189 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
633149 GGCCTACCCC
633159 TTTCATTTTT
1 TTTCATTTTT
633169 TTTCATTTTT
1 TTTCATTTTT
633179 TTTCATTTTT
1 TTTCATTTTT
633189 T
1 T
633190 ATCCACCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCATTTTT
Found at i:633427 original size:16 final size:16
Alignment explanation
Indices: 633406--633442 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
633396 ACCTTTTGAA
633406 GACTCGGAAAAACAGC
1 GACTCGGAAAAACAGC
633422 GACTCGGAAAAACAGC
1 GACTCGGAAAAACAGC
633438 GACTC
1 GACTC
633443 CTCAGCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.27, G:0.24, T:0.08
Consensus pattern (16 bp):
GACTCGGAAAAACAGC
Found at i:634077 original size:13 final size:13
Alignment explanation
Indices: 634059--634085 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
634049 ATGTAAAATA
634059 AATAATTAATAAT
1 AATAATTAATAAT
634072 AATAATTAATAAT
1 AATAATTAATAAT
634085 A
1 A
634086 TTTTATAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATAATTAATAAT
Found at i:635549 original size:11 final size:10
Alignment explanation
Indices: 635528--635625 Score: 53
Period size: 10 Copynumber: 9.8 Consensus size: 10
635518 GAGGAACGAA
*
635528 AAGAGAAAAG
1 AAGAAAAAAG
635538 ATAGAAAAAAG
1 A-AGAAAAAAG
*
635549 AAGAAGGAAAAA
1 AAGAA--AAAAG
*
635561 AAGAAAAGAG
1 AAGAAAAAAG
* *
635571 AA-AATATAG
1 AAGAAAAAAG
*
635580 AA-AAATAAG
1 AAGAAAAAAG
635589 AAGAAAAAAGG
1 AAGAAAAAA-G
635600 AA-AAAGAAA-
1 AAGAAA-AAAG
635609 AAG-AAAAAG
1 AAGAAAAAAG
*
635618 AGGAAAAA
1 AAGAAAAA
635626 GGGAAAAACA
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
8 3 0.04
9 19 0.28
10 22 0.32
11 15 0.22
12 9 0.13
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:635558 original size:14 final size:14
Alignment explanation
Indices: 635525--635616 Score: 57
Period size: 14 Copynumber: 6.4 Consensus size: 14
635515 ATAGAGGAAC
*
635525 GAAAAGAGAAAAGATA
1 GAAAAAAGAAAAG--A
635541 GAAAAAAGAAGAAG-
1 GAAAAAAGAA-AAGA
635555 GAAAAAAAGAAAAGA
1 G-AAAAAAGAAAAGA
635570 GAAAATATAGAAAA-A
1 GAAAA-A-AGAAAAGA
* * *
635585 -TAAGAAGAAAAAA
1 GAAAAAAGAAAAGA
*
635598 GGAAAAAGAAAA-A
1 GAAAAAAGAAAAGA
635611 GAAAAA
1 GAAAAA
635617 GAGGAAAAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
12 6 0.10
13 8 0.13
14 19 0.30
15 12 0.19
16 15 0.24
17 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (14 bp):
GAAAAAAGAAAAGA
Found at i:635562 original size:15 final size:15
Alignment explanation
Indices: 635526--635574 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
635516 TAGAGGAACG
* *
635526 AAAAGAGAAAAGATA
1 AAAAAAGAAAAGAGA
635541 GAAAAAAGAAGAAG-GA
1 -AAAAAAGAA-AAGAGA
635557 AAAAAAGAAAAGAGA
1 AAAAAAGAAAAGAGA
635572 AAA
1 AAA
635575 TATAGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 3 0.10
15 14 0.48
16 9 0.31
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAAAAAGAAAAGAGA
Found at i:635597 original size:37 final size:37
Alignment explanation
Indices: 635525--635609 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 37
635515 ATAGAGGAAC
635525 GAAAAGAGAAAAGATAGAAAAAAGAAGAAGGAAAAAAA
1 GAAAAGAGAAAAGATAGAAAAAAGAAGAA-GAAAAAAA
* * *
635563 GAAAAGAGAAAATATAG-AAAAATAAGAAGAAAAAAG
1 GAAAAGAGAAAAGATAGAAAAAAGAAGAAGAAAAAAA
635599 GAAAA-AGAAAA
1 GAAAAGAGAAAA
635610 AGAAAAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 6 0.14
36 12 0.27
37 10 0.23
38 16 0.36
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (37 bp):
GAAAAGAGAAAAGATAGAAAAAAGAAGAAGAAAAAAA
Found at i:635602 original size:20 final size:21
Alignment explanation
Indices: 635558--635626 Score: 79
Period size: 20 Copynumber: 3.3 Consensus size: 21
635548 GAAGAAGGAA
*
635558 AAAAAGAAAAGAGAAAATATA-G
1 AAAAAGAAAA-AGAAAA-AGAGG
* *
635580 AAAAATAAGAAGAAAAA-AGG
1 AAAAAGAAAAAGAAAAAGAGG
635600 AAAAAGAAAAAGAAAAAGAGG
1 AAAAAGAAAAAGAAAAAGAGG
635621 AAAAAG
1 AAAAAG
635627 GGAAAAACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.02
20 17 0.41
21 15 0.37
22 8 0.20
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.04
Consensus pattern (21 bp):
AAAAAGAAAAAGAAAAAGAGG
Found at i:635609 original size:12 final size:12
Alignment explanation
Indices: 635558--635618 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 12
635548 GAAGAAGGAA
635558 AAAAAGAAAAGAG
1 AAAAAGAAAA-AG
*
635571 AAAATATAGAAAAAT
1 -AAA-A-AGAAAAAG
*
635586 AAGAAGAAAAAAGG
1 AAAAAG-AAAAA-G
635600 AAAAAGAAAAAG
1 AAAAAGAAAAAG
635612 AAAAAGA
1 AAAAAGA
635619 GGAAAAAGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
12 10 0.26
13 11 0.28
14 10 0.26
15 2 0.05
16 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:635615 original size:5 final size:6
Alignment explanation
Indices: 635558--635618 Score: 50
Period size: 6 Copynumber: 9.2 Consensus size: 6
635548 GAAGAAGGAA
* *
635558 AAAAAG AAAAGAG AAAATATAG AAAAAT AAGAAG AAAAAAGG AAAAAG
1 AAAAAG AAAA-AG -AAA-A-AG AAAAAG AAAAAG -AAAAA-G AAAAAG
635606 AAAAAG AAAAAG A
1 AAAAAG AAAAAG A
635619 GGAAAAAGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
6 23 0.51
7 12 0.27
8 7 0.16
9 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:635616 original size:21 final size:21
Alignment explanation
Indices: 635558--635626 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
635548 GAAGAAGGAA
*
635558 AAAAAGAAAAGAGAAAATATA-G
1 AAAAAGAAAA-AGAAAA-AAAGG
* *
635580 AAAAATAAGAAG-AAAAAAGG
1 AAAAAGAAAAAGAAAAAAAGG
*
635600 AAAAAGAAAAAGAAAAAGAGG
1 AAAAAGAAAAAGAAAAAAAGG
635621 AAAAAG
1 AAAAAG
635627 GGAAAAACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.05
20 14 0.36
21 15 0.38
22 8 0.21
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.04
Consensus pattern (21 bp):
AAAAAGAAAAAGAAAAAAAGG
Found at i:635618 original size:29 final size:29
Alignment explanation
Indices: 635526--635633 Score: 80
Period size: 29 Copynumber: 3.7 Consensus size: 29
635516 TAGAGGAACG
* *
635526 AAAAG-AGAAAAGATAGAAAAAAGAAGAAGGA
1 AAAAGAAGAAAA-A-AGGAAAAAGAA-AAAGA
* * *
635557 AAAA-AAGAAAAGA-GAAAATATAGAAA-A
1 AAAAGAAGAAAAAAGGAAAA-AGAAAAAGA
*
635584 ATAAGAAGAAAAAAGGAAAAAGAAAAAGA
1 AAAAGAAGAAAAAAGGAAAAAGAAAAAGA
* *
635613 AAAAGAGGAAAAAGGGAAAAA
1 AAAAGAAGAAAAAAGGAAAAA
635634 CAAATCAAGT
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
27 4 0.07
28 19 0.32
29 27 0.45
31 10 0.17
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (29 bp):
AAAAGAAGAAAAAAGGAAAAAGAAAAAGA
Found at i:635760 original size:14 final size:14
Alignment explanation
Indices: 635741--635767 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
635731 GAGAGATGTT
635741 AAAGAAAAAAAATA
1 AAAGAAAAAAAATA
635755 AAAGAAAAAAAAT
1 AAAGAAAAAAAAT
635768 GACAAGTAGC
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:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAGAAAAAAAATA
Found at i:638734 original size:42 final size:41
Alignment explanation
Indices: 638687--638768 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
638677 CATCAGTGAG
* * * *
638687 TCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAA
1 TCTTTCGAGCAAGATG-ATAAATCCTTCGGGCCATCCATAAA
*
638729 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
1 TCTTTCGAGCAAGATGATAAATCCTTCGGGCCATCCATAA
638769 GACCTTCGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 20 0.57
42 15 0.43
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (41 bp):
TCTTTCGAGCAAGATGATAAATCCTTCGGGCCATCCATAAA
Found at i:639900 original size:134 final size:133
Alignment explanation
Indices: 639289--639848 Score: 627
Period size: 134 Copynumber: 4.2 Consensus size: 133
639279 AAGCAAATCG
* * ** * * * * *
639289 GCCTCGATACAATATTCCCTGAGCAACATTGGAATGAATCAACGTCCCTAGATCTGATTTTCCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGCAATGAATCAACGTCCCCAAATCTAATTTTCCCT
* * * ** *
639354 CAAGAAAAAGCGGAACATATCTATATTTCTCTTTCAATATTTGATATTCCCTAAGTAACAGTGGA
66 TAAGAAAAAG-TGAACAGATC----CCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGA
639419 ACAAGTTT
126 ACAAGTTT
* * *
639427 GCCTCGATTCAATCTTCCTTGAGTGACAGTGCAATGAATCAATGTCCCCAAATC-AGATTTTCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGCAATGAATCAACGTCCCCAAATCTA-ATTTTCCC
* * * * *
639491 TTAAGAAAAAACTAAACAGATCCCTCTCTTTTAAGGTTTGATATTCCCTGAGTAACAGTGGAACA
65 TTAAG-AAAAAGTGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACA
639556 AGTTT
129 AGTTT
* ** * * *
639561 GTCTTTATTTAATCTTCCCTGAGTGACAGTGCAATGAATCAACGTCCCTATATCTAATTTTCCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGCAATGAATCAACGTCCCCAAATCTAATTTTCCCT
* * * * *
639626 TAAGAAGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAATGGAACAA
66 TAAGAAAAAGTG-AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAA
*
639691 GTCT
130 GTTT
* * * * **
639695 ACCTCGAATCAATCCTCCCTGAGTGACAGTGGAAAAAATCAACGTCCCCAAATCTAATTTTCCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGCAATGAATCAACGTCCCCAAATCTAATTTTCCCT
* *
639760 CAAGAAAAAGTGAACTAGATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAATAGTGGAACAA
66 TAAGAAAAAGTGAAC-AGATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAA
*
639825 ATTT
130 GTTT
*
639829 CCCTCGATTCAATCTTCCCT
1 GCCTCGATTCAATCTTCCCT
639849 TAATAACAAT
Statistics
Matches: 354, Mismatches: 63, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
133 7 0.02
134 279 0.79
135 1 0.00
138 62 0.18
139 5 0.01
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (133 bp):
GCCTCGATTCAATCTTCCCTGAGTGACAGTGCAATGAATCAACGTCCCCAAATCTAATTTTCCCT
TAAGAAAAAGTGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAG
TTT
Found at i:641082 original size:27 final size:24
Alignment explanation
Indices: 641026--641080 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
641016 GGCGACGACG
*
641026 CGACGACTGGCGAGGGTAAGGGAT
1 CGACGACTAGCGAGGGTAAGGGAT
641050 CGACGACTAGCGAGGGTAAGGGAT
1 CGACGACTAGCGAGGGTAAGGGAT
641074 CGACGAC
1 CGACGAC
641081 GACCAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.42, T:0.11
Consensus pattern (24 bp):
CGACGACTAGCGAGGGTAAGGGAT
Found at i:646152 original size:19 final size:20
Alignment explanation
Indices: 646115--646152 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
646105 TCTAATTAAC
*
646115 CATATTTTCGCTTTTTTCCT
1 CATATTTTCGCTTTATTCCT
646135 CATATTTTC-CTTTATTCC
1 CATATTTTCGCTTTATTCC
646153 CTTTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.13, C:0.26, G:0.03, T:0.58
Consensus pattern (20 bp):
CATATTTTCGCTTTATTCCT
Found at i:650190 original size:21 final size:20
Alignment explanation
Indices: 650164--650202 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
650154 ATGAATGTAA
650164 AAACATGGAAAATAGAAATAT
1 AAACATGGAAAATA-AAATAT
650185 AAACATGGAAAATAAAAT
1 AAACATGGAAAATAAAAT
650203 GCAAAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (20 bp):
AAACATGGAAAATAAAATAT
Found at i:652479 original size:3 final size:3
Alignment explanation
Indices: 652471--652514 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
652461 AAGTTAGTAA
* *
652471 AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT ATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
652515 CGATGAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:653746 original size:5 final size:5
Alignment explanation
Indices: 653732--653881 Score: 84
Period size: 5 Copynumber: 31.0 Consensus size: 5
653722 TAACATAAGG
* *
653732 TAAAG TAAAA T-AAA -AAAA CAAAA T-AAA TAAAA T-AAA T-AAA T-AAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
* * * * * * *
653776 TAAAA CAAAG TAAAA TAAAA TAGAAA TAAAG TAAGA CAAAA TTAAA GAAAA
1 TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TAAAA
* * * *
653827 TTAAA TAAAA -AACA -AAAA CAAGAA -AACA TAAAA TGAAAA TAAAA TAAATA
1 TAAAA TAAAA TAAAA TAAAA TAA-AA TAAAA TAAAA T-AAAA TAAAA TAAA-A
653877 TAAAA
1 TAAAA
653882 ACAAAACTAC
Statistics
Matches: 113, Mismatches: 22, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
4 29 0.26
5 67 0.59
6 17 0.15
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:653761 original size:17 final size:17
Alignment explanation
Indices: 653739--653794 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
653729 AGGTAAAGTA
653739 AAATAAAA-AAACAAAAT
1 AAATAAAACAAA-AAAAT
* *
653756 AAATAAAATAAATAAAT
1 AAATAAAACAAAAAAAT
653773 AAATAAAACAAAGTAAAAT
1 AAATAAAACAAA--AAAAT
653792 AAA
1 AAA
653795 ATAGAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 23 0.70
18 3 0.09
19 7 0.21
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.16
Consensus pattern (17 bp):
AAATAAAACAAAAAAAT
Found at i:653816 original size:21 final size:20
Alignment explanation
Indices: 653746--653817 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
653736 GTAAAATAAA
653746 AAAACAAAATAAATA-AAA-T
1 AAAACAAAATAAA-ACAAAGT
*
653765 AAATAAATAAATAAAACAAAGT
1 AAA-ACA-AAATAAAACAAAGT
* *
653787 AAAATAAAATAGAAATAAAGT
1 AAAACAAAATA-AAACAAAGT
*
653808 AAGACAAAAT
1 AAAACAAAAT
653818 TAAAGAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 3 0.07
20 8 0.19
21 28 0.65
22 4 0.09
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.17
Consensus pattern (20 bp):
AAAACAAAATAAAACAAAGT
Found at i:653847 original size:64 final size:62
Alignment explanation
Indices: 653749--653869 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 62
653739 AAATAAAAAA
* * *
653749 ACAAAATAAATAAAATAAATAAATAAATAAAACAAAGTAAA-ATAAAAT-AGAAATAAAGTAAG
1 ACAAAATAAAGAAAATAAATAAATAAAAAAAAC-AAGAAAACATAAAATGA-AAATAAAGTAAG
653811 ACAAAATTAAAGAAAATTAAATAAA-AAACAAAAACAAGAAAACATAAAATGAAAATAAA
1 ACAAAA-TAAAGAAAA-TAAATAAATAAA-AAAAACAAGAAAACATAAAATGAAAATAAA
653870 ATAAATATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
62 6 0.12
63 17 0.33
64 27 0.53
65 1 0.02
ACGTcount: A:0.74, C:0.05, G:0.06, T:0.16
Consensus pattern (62 bp):
ACAAAATAAAGAAAATAAATAAATAAAAAAAACAAGAAAACATAAAATGAAAATAAAGTAAG
Found at i:653947 original size:16 final size:15
Alignment explanation
Indices: 653901--653948 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
653891 CCTTATATAT
653901 ATAATAGAAAAAATAA
1 ATAATAGAAAAAAT-A
* *
653917 ATAAAATAAATAAATA
1 ATAATAGAAA-AAATA
653933 ATAATAGAAACAAATA
1 ATAATAGAAA-AAATA
653949 TATATATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (15 bp):
ATAATAGAAAAAATA
Found at i:654037 original size:3 final size:3
Alignment explanation
Indices: 654010--654053 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
654000 GAAAAAGAAA
*
654010 AAT AAGT AAA AAT ATAT ACAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AA
654054 GAACAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
3 27 0.75
4 9 0.25
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:654082 original size:17 final size:17
Alignment explanation
Indices: 654060--654095 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
654050 ATAAGAACAA
654060 AAAAAAGAAAAAATAAT
1 AAAAAAGAAAAAATAAT
*
654077 AAAAAAGAAAAGATAAT
1 AAAAAAGAAAAAATAAT
654094 AA
1 AA
654096 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (17 bp):
AAAAAAGAAAAAATAAT
Found at i:654087 original size:22 final size:22
Alignment explanation
Indices: 654058--654104 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
654048 TAATAAGAAC
654058 AAAA-AAAAGA-AAAAATAATAA
1 AAAAGAAAAGATAAAAAT-ATAA
*
654079 AAAAGAAAAGATAATAATATAA
1 AAAAGAAAAGATAAAAATATAA
654101 AAAA
1 AAAA
654105 TATATGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 14 0.61
23 5 0.22
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (22 bp):
AAAAGAAAAGATAAAAATATAA
Found at i:656940 original size:31 final size:31
Alignment explanation
Indices: 656904--656970 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
656894 ATTTGTTTTT
**
656904 AATTTAATCTCTAAACTTTAAATATGATATC
1 AATTTAATCTCTAAACTTTAAATAAAATATC
* *
656935 AATTTAATCTCTAAATTTTAGATAAAATATC
1 AATTTAATCTCTAAACTTTAAATAAAATATC
656966 AATTT
1 AATTT
656971 GATTCTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (31 bp):
AATTTAATCTCTAAACTTTAAATAAAATATC
Found at i:665559 original size:23 final size:25
Alignment explanation
Indices: 665533--665587 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
665523 AAATCCAGCA
665533 AAGAAAATCAAAGCACTC-AAAA-G
1 AAGAAAATCAAAGCACTCAAAAATG
* *
665556 AAGAAATTGAAAGCACTCAAAAATG
1 AAGAAAATCAAAGCACTCAAAAATG
665581 AAGAAAA
1 AAGAAAA
665588 ATAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 16 0.59
24 4 0.15
25 7 0.26
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.11
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAAATG
Found at i:665593 original size:16 final size:16
Alignment explanation
Indices: 665581--665612 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
665571 CTCAAAAATG
665581 AAGAAAAATAAAAGAA
1 AAGAAAAATAAAAGAA
665597 AAGAAAAAT-AAAGAA
1 AAGAAAAATAAAAGAA
665612 A
1 A
665613 GTTGAAGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (16 bp):
AAGAAAAATAAAAGAA
Found at i:668904 original size:19 final size:21
Alignment explanation
Indices: 668869--668914 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
668859 TAATTAACCA
*
668869 TATTTTCGCTTT-TTTCCTTT
1 TATTTTCGCTTTATTCCCTTT
668889 TATTTTC-CTTTATTCCCTTT
1 TATTTTCGCTTTATTCCCTTT
*
668909 TCTTTT
1 TATTTT
668915 ATTATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.07, C:0.22, G:0.02, T:0.70
Consensus pattern (21 bp):
TATTTTCGCTTTATTCCCTTT
Found at i:673600 original size:21 final size:20
Alignment explanation
Indices: 673574--673612 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
673564 ATAAATGTAA
673574 AAACATGGAAAATAGAAATAT
1 AAACATGGAAAATA-AAATAT
673595 AAACATGGAAAATAAAAT
1 AAACATGGAAAATAAAAT
673613 GCAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (20 bp):
AAACATGGAAAATAAAATAT
Found at i:675891 original size:3 final size:3
Alignment explanation
Indices: 675883--675911 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
675873 AAGTTAGTAA
675883 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
675912 CGATGAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:677143 original size:9 final size:9
Alignment explanation
Indices: 677085--677316 Score: 74
Period size: 9 Copynumber: 24.7 Consensus size: 9
677075 AGAATAGCTA
677085 AAAAT-AAT
1 AAAATAAAT
*
677093 AAAATAACT
1 AAAATAAAT
* *
677102 AACATAAGGT
1 AAAATAA-AT
*
677112 AAAGTGAAAT
1 AAAAT-AAAT
* *
677122 AAAAAAAAC
1 AAAATAAAT
677131 AAAATAAAT
1 AAAATAAAT
677140 AAAATAAAT
1 AAAATAAAT
677149 -AAATAAA-
1 AAAATAAAT
677156 ACAAAGTAAAAT
1 A-AAA-T-AAAT
677168 AAAATAGAAAT
1 AAAAT--AAAT
* *
677179 AAAGTAAGAC
1 AAAATAA-AT
677189 AAAATTAAAT
1 AAAA-TAAAT
677199 AAAATTAAAT
1 AAAA-TAAAT
677209 AAAA-AACA-
1 AAAATAA-AT
*
677217 AAAACAAGA-
1 AAAATAA-AT
677226 AAACATAAA-
1 AAA-ATAAAT
*
677235 AATGA-AAAT
1 AA-AATAAAT
677244 AAAATAAAT
1 AAAATAAAT
677253 ATAAA-AACA-
1 A-AAATAA-AT
*
677262 AAAATAACTT
1 AAAATAA-AT
*
677272 ATATATATAAT
1 A-AAATA-AAT
677283 AGAAA-AAAT
1 A-AAATAAAT
677292 -AAATAAAAT
1 AAAAT-AAAT
677301 AAAATAAAT
1 AAAATAAAT
677310 AATAATA
1 AA-AATA
677317 GGAACAAATA
Statistics
Matches: 172, Mismatches: 25, Indels: 52
0.69 0.10 0.21
Matches are distributed among these distances:
7 3 0.02
8 25 0.15
9 69 0.40
10 46 0.27
11 27 0.16
12 2 0.01
ACGTcount: A:0.72, C:0.04, G:0.05, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:677144 original size:5 final size:5
Alignment explanation
Indices: 677118--677308 Score: 94
Period size: 5 Copynumber: 38.4 Consensus size: 5
677108 AGGTAAAGTG
* * *
677118 AAATA AAA-A AAACA AAAT- AAATA AAAT- AAAT- AAATA AAACA AAGTA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * * * *
677164 AAATA AAATA GAAATA AAGTA AGACA AAATT AAATA AAATT AAATA AAA-A
1 AAATA AAATA -AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * * *
677214 ACA-A AAACA AGAA-A ACATAA AAATGA AAATA AAATA AATATAA AAACAA
1 AAATA AAATA A-AATA AAAT-A AAAT-A AAATA AAATA AA-AT-A AAA-TA
** * * *
677263 AAATA ACTTA TATATA TAATA GAA-A AAAT- AAATA AAATA AAATA AA
1 AAATA AAATA -AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
677309 TAATAATAGG
Statistics
Matches: 142, Mismatches: 30, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
4 30 0.21
5 83 0.58
6 26 0.18
7 3 0.02
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:677306 original size:23 final size:22
Alignment explanation
Indices: 677118--677308 Score: 93
Period size: 23 Copynumber: 8.0 Consensus size: 22
677108 AGGTAAAGTG
* *
677118 AAATAAAAAAAACAAAATAAATA
1 AAATAAATAAAATAAAATAAA-A
*
677141 AAATAAAT-AAATAAAACAAAGTA
1 AAATAAATAAAATAAAATAAA--A
*
677164 AAATAAAATAGAAATAAAGTAAGACA
1 AAAT-AAATA-AAATAAAATAA-A-A
*
677190 AAATTAAATAAAATTAAATAAAA
1 AAA-TAAATAAAATAAAATAAAA
* * * *
677213 AACA-AAA-ACAAGAAAACATAA
1 AA-ATAAATAAAATAAAATAAAA
677234 AAATGAAAATAAAATAAATATAAAA
1 AAAT--AAATAAAATAAA-ATAAAA
677259 ACAA-AAATAACTTATATATATAATAGAAA
1 A-AATAAATAA---A-ATA-A-AATA-AAA
677288 AAATAAATAAAATAAAATAAA
1 AAATAAATAAAATAAAATAAA
677309 TAATAATAGG
Statistics
Matches: 130, Mismatches: 17, Indels: 43
0.68 0.09 0.23
Matches are distributed among these distances:
20 1 0.01
21 11 0.08
22 15 0.12
23 29 0.22
24 13 0.10
25 17 0.13
26 22 0.17
27 5 0.04
28 6 0.05
29 11 0.08
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (22 bp):
AAATAAATAAAATAAAATAAAA
Found at i:677451 original size:18 final size:18
Alignment explanation
Indices: 677428--677465 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
677418 AATAAGAACA
677428 AAAAAAAGAAAAAATAAT
1 AAAAAAAGAAAAAATAAT
*
677446 AAAAAAAGAAAAGATAAT
1 AAAAAAAGAAAAAATAAT
677464 AA
1 AA
677466 TATAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.11
Consensus pattern (18 bp):
AAAAAAAGAAAAAATAAT
Found at i:679238 original size:29 final size:31
Alignment explanation
Indices: 679196--679267 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
679186 GTGATAGGCA
*
679196 TCTTCTTGAAAGAC-C-ATGTTGTTTGGTCG
1 TCTTCTTGAAAGACTCTATGTCGTTTGGTCG
679225 TCTTCTTGAAAGACTCTATGTCGTTTGGTCG
1 TCTTCTTGAAAGACTCTATGTCGTTTGGTCG
679256 T-TTGCTTGAAAG
1 TCTT-CTTGAAAG
679268 GTGTCATGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 14 0.36
30 3 0.08
31 22 0.56
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (31 bp):
TCTTCTTGAAAGACTCTATGTCGTTTGGTCG
Found at i:682225 original size:29 final size:31
Alignment explanation
Indices: 682183--682254 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
682173 ATGATAGTCA
682183 TCTTCTTGAAAGAC-C-ATGTTGTTTGGTCG
1 TCTTCTTGAAAGACTCAATGTTGTTTGGTCG
* *
682212 TCTTCTTGAAAGACTCAATGTTTTTTGGTTG
1 TCTTCTTGAAAGACTCAATGTTGTTTGGTCG
*
682243 TATTCTTGAAAG
1 TCTTCTTGAAAG
682255 GTGTCATGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 14 0.37
30 1 0.03
31 23 0.61
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (31 bp):
TCTTCTTGAAAGACTCAATGTTGTTTGGTCG
Found at i:683607 original size:31 final size:31
Alignment explanation
Indices: 683540--683599 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
683530 CAATTTAAGG
*
683540 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
683571 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
683600 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:683691 original size:19 final size:19
Alignment explanation
Indices: 683664--683730 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
683654 AATGTTTTTA
*
683664 TGAATAGTAATTTCCTATT
1 TGAACAGTAATTTCCTATT
* *
683683 TGAACAGTAAATTACTATT
1 TGAACAGTAATTTCCTATT
* * *
683702 TGAATAGT-ATATCACTGTT
1 TGAACAGTAATTTC-CTATT
683721 TGAACAGTAA
1 TGAACAGTAA
683731 CTCGAGGCTC
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
18 2 0.05
19 34 0.92
20 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (19 bp):
TGAACAGTAATTTCCTATT
Found at i:683862 original size:21 final size:21
Alignment explanation
Indices: 683836--683877 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
683826 ATTTGAATAT
*
683836 TATGAAGAGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
*
683857 TATGAAGGGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
683878 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:683939 original size:21 final size:21
Alignment explanation
Indices: 683906--683945 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
683896 TTTTTGCATA
*
683906 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
683928 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
683946 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:684200 original size:34 final size:32
Alignment explanation
Indices: 684161--684230 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
684151 TTTTGTAAAG
*
684161 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
684195 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
684227 GGGA
1 GGGA
684231 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:687091 original size:31 final size:31
Alignment explanation
Indices: 687024--687083 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
687014 CAATTTAAGG
*
687024 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
687055 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
687084 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:687175 original size:19 final size:19
Alignment explanation
Indices: 687148--687213 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
687138 AATGTTTTTA
* *
687148 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
687167 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* * *
687186 TGAATAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
687205 TGAACAGTA
1 TGAACAGTA
687214 CCCCGAGGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:687321 original size:21 final size:21
Alignment explanation
Indices: 687288--687327 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
687278 TTTTTGCATA
*
687288 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
687310 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
687328 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:687587 original size:34 final size:32
Alignment explanation
Indices: 687544--687613 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
687534 TTTTATAAAG
*
687544 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
687578 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
687610 GGGA
1 GGGA
687614 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:690570 original size:38 final size:43
Alignment explanation
Indices: 690499--690586 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 43
690489 AAAAATATTA
*
690499 AATTAAATTAAATAATTTATCATTTTAATTAAAAATTAA-AAAT
1 AATTAAATTAAATAATTTATCATGTTAATT-AAAATTAATAAAT
690542 AATTAAA-TAAAT-ATTTAT-ATGTT-A-TAAAATTAATAAAT
1 AATTAAATTAAATAATTTATCATGTTAATTAAAATTAATAAAT
*
690580 TATTAAA
1 AATTAAA
690587 AATTAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
37 8 0.19
38 11 0.26
39 1 0.02
40 4 0.10
41 6 0.14
42 5 0.12
43 7 0.17
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (43 bp):
AATTAAATTAAATAATTTATCATGTTAATTAAAATTAATAAAT
Found at i:690641 original size:17 final size:17
Alignment explanation
Indices: 690621--690664 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
690611 AATAGAATAC
*
690621 AAATTAAATTATTTTAA
1 AAATTAAATTATATTAA
*
690638 AAA-TAAATAAATATTAA
1 AAATTAAAT-TATATTAA
690655 AAATTAAATT
1 AAATTAAATT
690665 CTATCATAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 5 0.23
17 12 0.55
18 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTAAATTATATTAA
Found at i:692589 original size:32 final size:33
Alignment explanation
Indices: 692529--692654 Score: 91
Period size: 32 Copynumber: 3.9 Consensus size: 33
692519 ATATTCTTGA
* *
692529 TGTGCATTATTTGAATGA-AAAACT-AACTCTGT
1 TGTGCATTATATGAAT-ACAATACTGAACTCTGT
* **
692561 TGTGCATTATTTGAATACAATA-TGAACTCTAA
1 TGTGCATTATATGAATACAATACTGAACTCTGT
* * * * * *
692593 TATGCATTACATGCATGCAGTATTG-ACTCTGT
1 TGTGCATTATATGAATACAATACTGAACTCTGT
**
692625 TGTGCATTATATGAACGCAATACTG-ACTCT
1 TGTGCATTATATGAATACAATACTGAACTCT
692655 ACTGAGTATT
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
31 2 0.03
32 70 0.95
33 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (33 bp):
TGTGCATTATATGAATACAATACTGAACTCTGT
Found at i:696154 original size:46 final size:45
Alignment explanation
Indices: 695975--696196 Score: 324
Period size: 44 Copynumber: 4.9 Consensus size: 45
695965 GTAAGCATGC
**
695975 AAATAAGCTTACGAGCTTATGGAAT-AATGACAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
696019 AATTAAGCTTACGAGCTTATGGAAT-AATGGCAAATATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
696063 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
696108 AAATAAGTTTACGAGCTTATGGGATTAAATAGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
696154 AAATAAGCTTACGAGCTTATGTG-ATAAAATGGTAAGTATATTG
1 AAATAAGCTTACGAGCTTATG-GAAT-AAATGGTAAGTATATTG
696197 ATAGGAAATT
Statistics
Matches: 162, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
44 65 0.40
45 38 0.23
46 59 0.36
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:696815 original size:11 final size:11
Alignment explanation
Indices: 696799--696823 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
696789 CATTTTAAGA
696799 AAATCAATTTT
1 AAATCAATTTT
696810 AAATCAATTTT
1 AAATCAATTTT
696821 AAA
1 AAA
696824 ATAGAAATAG
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATCAATTTT
Found at i:700020 original size:17 final size:16
Alignment explanation
Indices: 699994--700028 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
699984 GTTGGGCACC
699994 TATGGTTAAGGATCCA
1 TATGGTTAAGGATCCA
700010 TATGTGTTAAGGATCCA
1 TATG-GTTAAGGATCCA
700027 TA
1 TA
700029 CCCATGACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (16 bp):
TATGGTTAAGGATCCA
Found at i:700521 original size:574 final size:574
Alignment explanation
Indices: 699433--700574 Score: 2167
Period size: 574 Copynumber: 2.0 Consensus size: 574
699423 CAATTTTTTA
699433 CCATATGTGTTAAAGATCCATACCCATGACACTTTCTTGAAAGTTTAAAGCACATTCCTTGTTGA
1 CCATATGTGTTAAAGATCCATACCCATGACACTTTCTTGAAAGTTTAAAGCACATTCCTTGTTGA
699498 TTTTAACCACCACGCTTGTATTCTAGATAATCCAAAACTCTACCAATACTTTTAAAATTATAAAA
66 TTTTAACCACCACGCTTGTATTCTAGATAATCCAAAACTCTACCAATACTTTTAAAATTATAAAA
*
699563 CCCTACTACTAACCTCTGGCATGTCTGAAGTGACTGAGCTAGCGTCACTCTTCTATGCTCACGTT
131 CCCTACTACTAACCTCTGACATGTCTGAAGTGACTGAGCTAGCGTCACTCTTCTATGCTCACGTT
*
699628 GACTATGGGTCCTCCTTGCCACTGATCGAGATATATCTACTAACACCAAGTCTTCATACTCGAGG
196 GACCATGGGTCCTCCTTGCCACTGATCGAGATATATCTACTAACACCAAGTCTTCATACTCGAGG
699693 TGCTGAATTATGCCACAAACCTATTCTCATGCTCTAATCTGAACCACTTTAAGAGGCTCTGCCCC
261 TGCTGAATTATGCCACAAACCTATTCTCATGCTCTAATCTGAACCACTTTAAGAGGCTCTGCCCC
*
699758 TAATTACACATTAATATCAAAATATAGCCCCTCAATAGACCTTCTTCACTTCAAGGGCTTGGTCA
326 TAATTACACATTAATATCAAAATATAGCCCCTCAATAGACCTTCTTCACTTCAAGGGCTCGGTCA
* * *
699823 CAATCGATTCTAAAGCCTAATAACTCAACCTAAGAATCTTTTTTTCTCAAGTTCATGCACCAAGT
391 CAACCAATTATAAAGCCTAATAACTCAACCTAAGAATCTTTTTTTCTCAAGTTCATGCACCAAGT
699888 GATCTCCCTAAACTAGCTAAGAGAATTGTATTCTCAAATCATCCATATACGCCTTACTAATATAC
456 GATCTCCCTAAACTAGCTAAGAGAATTGTATTCTCAAATCATCCATATACGCCTTACTAATATAC
* *
699953 TTGCTATGGATTCGCTTGGGAACATATTCCAGTTGGGCACCTATGGTTAAGGAT
521 TTGCTATAGATTCGCTTGGGAACATATTCCAGTTGGGAACCTATGGTTAAGGAT
*
700007 CCATATGTGTTAAGGATCCATACCCATGACACTTTCTTGAAAGTTTAAAGCACATTCCTTGTTGA
1 CCATATGTGTTAAAGATCCATACCCATGACACTTTCTTGAAAGTTTAAAGCACATTCCTTGTTGA
*
700072 TTTTAACCACCACGCTTGTATTCTAGATAATCCAAAACTCTACCAATGCTTTTAAAATTATAAAA
66 TTTTAACCACCACGCTTGTATTCTAGATAATCCAAAACTCTACCAATACTTTTAAAATTATAAAA
700137 CCCTACTACTAACCTCTGACATGTCTGAAGTGACTGAGCTAGCGTCACTCTTCTATGCTCACGTT
131 CCCTACTACTAACCTCTGACATGTCTGAAGTGACTGAGCTAGCGTCACTCTTCTATGCTCACGTT
*
700202 GACCATGGGTCCTCCTTGCCACTGATCGAGATATATCTACTGACACCAAGTCTTCATACTCGAGG
196 GACCATGGGTCCTCCTTGCCACTGATCGAGATATATCTACTAACACCAAGTCTTCATACTCGAGG
700267 TGCTGAATTATGCCACAAACCTATTCTCATGCTCTAATCTGAACCACTTTAAGAGGCTCTGCCCC
261 TGCTGAATTATGCCACAAACCTATTCTCATGCTCTAATCTGAACCACTTTAAGAGGCTCTGCCCC
*
700332 TAATTACACATTAATATCAAAATATAGCCCCTCAATGGACCTTCTTCACTTCAAGGGCTCGGTCA
326 TAATTACACATTAATATCAAAATATAGCCCCTCAATAGACCTTCTTCACTTCAAGGGCTCGGTCA
*
700397 CAACCAATTATAGAGCCTAATAACTCAACCTAAGAATCTTTTTTTCTCAAGTTCATGCACCAAGT
391 CAACCAATTATAAAGCCTAATAACTCAACCTAAGAATCTTTTTTTCTCAAGTTCATGCACCAAGT
700462 GATCTCCCTAAACTAGCTAAGAGAATTGTATTCTCAAATCATCCATATACGCCTTACTAATATAC
456 GATCTCCCTAAACTAGCTAAGAGAATTGTATTCTCAAATCATCCATATACGCCTTACTAATATAC
700527 TTGCTATAGATTCGCTTGGGAACATATTCCAGTTGGGAACCTATGGTT
521 TTGCTATAGATTCGCTTGGGAACATATTCCAGTTGGGAACCTATGGTT
700575 GTAAAGCCAT
Statistics
Matches: 555, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
574 555 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (574 bp):
CCATATGTGTTAAAGATCCATACCCATGACACTTTCTTGAAAGTTTAAAGCACATTCCTTGTTGA
TTTTAACCACCACGCTTGTATTCTAGATAATCCAAAACTCTACCAATACTTTTAAAATTATAAAA
CCCTACTACTAACCTCTGACATGTCTGAAGTGACTGAGCTAGCGTCACTCTTCTATGCTCACGTT
GACCATGGGTCCTCCTTGCCACTGATCGAGATATATCTACTAACACCAAGTCTTCATACTCGAGG
TGCTGAATTATGCCACAAACCTATTCTCATGCTCTAATCTGAACCACTTTAAGAGGCTCTGCCCC
TAATTACACATTAATATCAAAATATAGCCCCTCAATAGACCTTCTTCACTTCAAGGGCTCGGTCA
CAACCAATTATAAAGCCTAATAACTCAACCTAAGAATCTTTTTTTCTCAAGTTCATGCACCAAGT
GATCTCCCTAAACTAGCTAAGAGAATTGTATTCTCAAATCATCCATATACGCCTTACTAATATAC
TTGCTATAGATTCGCTTGGGAACATATTCCAGTTGGGAACCTATGGTTAAGGAT
Found at i:703121 original size:19 final size:19
Alignment explanation
Indices: 703093--703147 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
703083 TTTTGTTCAT
703093 AGTTTAGAAACTTTGTAAG
1 AGTTTAGAAACTTTGTAAG
*
703112 AGTTTTGAAACCTCTAT-TAAG
1 AGTTTAGAAA-CT-T-TGTAAG
*
703133 AGTTTCGAAACTTTG
1 AGTTTAGAAACTTTG
703148 CACCCAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 1 0.03
19 10 0.33
20 4 0.13
21 14 0.47
22 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (19 bp):
AGTTTAGAAACTTTGTAAG
Found at i:704073 original size:23 final size:23
Alignment explanation
Indices: 704046--704199 Score: 254
Period size: 23 Copynumber: 6.7 Consensus size: 23
704036 GAGACTCGAA
704046 CTCGATTCAAGCTCGATTTTAAG
1 CTCGATTCAAGCTCGATTTTAAG
704069 CTCGATTCAAGCTCGATTTTAAG
1 CTCGATTCAAGCTCGATTTTAAG
704092 CTCGATTCAAGCTCGATTTTAAG
1 CTCGATTCAAGCTCGATTTTAAG
*
704115 CTCGATTCAAACTCGATTTTAAG
1 CTCGATTCAAGCTCGATTTTAAG
*
704138 CTCGATTCAAGCTCGATTTTGAG
1 CTCGATTCAAGCTCGATTTTAAG
* *
704161 CTCGATTCAAGCTCAATTTTGAG
1 CTCGATTCAAGCTCGATTTTAAG
* *
704184 CACGATTTAAGCTCGA
1 CTCGATTCAAGCTCGA
704200 GGATGGGTTA
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 124 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (23 bp):
CTCGATTCAAGCTCGATTTTAAG
Found at i:705636 original size:7 final size:7
Alignment explanation
Indices: 705626--705698 Score: 58
Period size: 7 Copynumber: 10.4 Consensus size: 7
705616 TCATATCACA
*
705626 TAAACTC
1 TAAACCC
705633 TAAACCC
1 TAAACCC
705640 TAAACCC
1 TAAACCC
* *
705647 TAAATCT
1 TAAACCC
* *
705654 TAAATCA
1 TAAACCC
* *
705661 T-ATCACA
1 TAAAC-CC
*
705668 TAAACTC
1 TAAACCC
705675 TAAACCC
1 TAAACCC
705682 TAAACCC
1 TAAACCC
705689 TAAACCC
1 TAAACCC
705696 TAA
1 TAA
705699 GCATTATCAC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
6 1 0.02
7 51 0.94
8 2 0.04
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:705707 original size:84 final size:84
Alignment explanation
Indices: 705551--705712 Score: 263
Period size: 84 Copynumber: 1.9 Consensus size: 84
705541 ATGTTTAATG
* * * *
705551 AACCCTAAACCCTAAATCTTAAATCATATCACATAAATTCTAAACTCTAAACCCTAAATCTTAAA
1 AACCCTAAACCCTAAATCTTAAATCATATCACATAAACTCTAAACCCTAAACCCTAAACCCTAAA
*
705616 TCATATCACATAAACTCTA
66 GCATATCACATAAACTCTA
705635 AACCCTAAACCCTAAATCTTAAATCATATCACATAAACTCTAAACCCTAAACCCTAAACCCT-AA
1 AACCCTAAACCCTAAATCTTAAATCATATCACATAAACTCTAAACCCTAAACCCTAAACCCTAAA
705699 GCATTATCACATAA
66 GCA-TATCACATAA
705713 TTAGAAGGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
83 4 0.06
84 68 0.94
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.26
Consensus pattern (84 bp):
AACCCTAAACCCTAAATCTTAAATCATATCACATAAACTCTAAACCCTAAACCCTAAACCCTAAA
GCATATCACATAAACTCTA
Found at i:705712 original size:42 final size:42
Alignment explanation
Indices: 705551--705692 Score: 266
Period size: 42 Copynumber: 3.4 Consensus size: 42
705541 ATGTTTAATG
*
705551 AACCCTAAACCCTAAATCTTAAATCATATCACATAAATTCTA
1 AACCCTAAACCCTAAATCTTAAATCATATCACATAAACTCTA
*
705593 AACTCTAAACCCTAAATCTTAAATCATATCACATAAACTCTA
1 AACCCTAAACCCTAAATCTTAAATCATATCACATAAACTCTA
705635 AACCCTAAACCCTAAATCTTAAATCATATCACATAAACTCTA
1 AACCCTAAACCCTAAATCTTAAATCATATCACATAAACTCTA
705677 AACCCTAAACCCTAAA
1 AACCCTAAACCCTAAA
705693 CCCTAAGCAT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 97 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (42 bp):
AACCCTAAACCCTAAATCTTAAATCATATCACATAAACTCTA
Found at i:706021 original size:12 final size:11
Alignment explanation
Indices: 706004--706047 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
705994 ATTAAATAAA
*
706004 TAATTTTTTTAT
1 TAATTTATTT-T
706016 TAATTTATTTT
1 TAATTTATTTT
*
706027 TAATATATTTT
1 TAATTTATTTT
*
706038 TAATATATTT
1 TAATTTATTT
706048 ATTCATCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTATTTT
Found at i:706035 original size:11 final size:11
Alignment explanation
Indices: 706015--706083 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
706005 AATTTTTTTA
*
706015 TTAATTTATTT
1 TTAATATATTT
706026 TTAATATATTT
1 TTAATATATTT
706037 TTAATATATTT
1 TTAATATATTT
*
706048 ATTCATCA-A---
1 -TTAAT-ATATTT
*
706057 -TAATGTATTT
1 TTAATATATTT
706067 TTAATATATTT
1 TTAATATATTT
706078 TTAATA
1 TTAATA
706084 ATGTAATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
7 4 0.09
11 36 0.78
12 5 0.11
13 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (11 bp):
TTAATATATTT
Found at i:708877 original size:45 final size:45
Alignment explanation
Indices: 708826--709047 Score: 241
Period size: 45 Copynumber: 4.9 Consensus size: 45
708816 ATGAATAAAA
* *
708826 GAAAATGCATAACTTTGCATTATCGACATAAAAGGTGCCATTAAT
1 GAAAATGCATAACTGTGCATTATCGACATAAAAGGTGCCACTAAT
* *
708871 GAAAATGCATAA-TGGTGCATTATCAACATAAAAGGTGACACTAAT
1 GAAAATGCATAACT-GTGCATTATCGACATAAAAGGTGCCACTAAT
* * * * * *
708916 GAATATGCATAACGGTGCATTTTTGGCATAAAAGGTGCCAGTAAT
1 GAAAATGCATAACTGTGCATTATCGACATAAAAGGTGCCACTAAT
* * * * *
708961 GAAAATACATAATTGTGTATTATC-AGTATAAAAGGTGCTACTAAT
1 GAAAATGCATAACTGTGCATTATCGA-CATAAAAGGTGCCACTAAT
* * * *
709006 GAAAATGCATAACGGTGCATCATTGGCATAAAAGGTGCCACT
1 GAAAATGCATAACTGTGCATTATCGACATAAAAGGTGCCACT
709048 CATGGTATTC
Statistics
Matches: 141, Mismatches: 32, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
44 1 0.01
45 140 0.99
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (45 bp):
GAAAATGCATAACTGTGCATTATCGACATAAAAGGTGCCACTAAT
Done.