Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 2 of 132
Found at i:328149 original size:31 final size:30
Alignment explanation
Indices: 328104--328182 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
328094 TTCCACTCTC
* *
328104 AATCCTTGTCTTTTTCATATATTTA-AAATTT
1 AATCCTTCTATTTTTCA-AT-TTTAGAAATTT
* *
328135 AATCCTTTTATTTTTTAATTTTAGAAATTT
1 AATCCTTCTATTTTTCAATTTTAGAAATTT
*
328165 AATCCCTCTA-TTTTCAAT
1 AATCCTTCTATTTTTCAAT
328183 ATACACCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 11 0.27
30 16 0.39
31 14 0.34
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.54
Consensus pattern (30 bp):
AATCCTTCTATTTTTCAATTTTAGAAATTT
Found at i:335071 original size:3 final size:3
Alignment explanation
Indices: 335056--335087 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
335046 ATTAAGCTTA
*
335056 ATG ATG ATA ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
335088 AGCTGTGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:349025 original size:29 final size:30
Alignment explanation
Indices: 348978--349041 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
348968 TTTCATGCCA
**
348978 TTTTTTTT-AATTTTATGAATTTTTTATTT
1 TTTTTTTTGAATTTTATGAAAATTTTATTT
349007 TTATTTTTTGAA-TTT-TGAAAATTTTATTT
1 TT-TTTTTTGAATTTTATGAAAATTTTATTT
349036 TTTTTT
1 TTTTTT
349042 GAATACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 4 0.13
29 16 0.52
30 9 0.29
31 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (30 bp):
TTTTTTTTGAATTTTATGAAAATTTTATTT
Found at i:350732 original size:17 final size:18
Alignment explanation
Indices: 350710--350743 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
350700 GCTCTCTCTT
350710 TTTTTAGTTTT-ACTTTA
1 TTTTTAGTTTTAACTTTA
350727 TTTTTAGTTTTAACTTT
1 TTTTTAGTTTTAACTTT
350744 TCAAAGTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTTAGTTTTAACTTTA
Found at i:354427 original size:11 final size:11
Alignment explanation
Indices: 354411--354435 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
354401 AAAAAGAAAC
354411 TTCGTGAAATT
1 TTCGTGAAATT
354422 TTCGTGAAATT
1 TTCGTGAAATT
354433 TTC
1 TTC
354436 TATGTATATA
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:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (11 bp):
TTCGTGAAATT
Found at i:356874 original size:10 final size:9
Alignment explanation
Indices: 356848--356888 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
356838 TTAAATCCTT
*
356848 TAAAAATTA
1 TAAAAATAA
356857 TAAAAAT-A
1 TAAAAATAA
*
356865 T-AAACTAA
1 TAAAAATAA
356873 TAAAAATAA
1 TAAAAATAA
356882 TAAAAAT
1 TAAAAAT
356889 TATATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 4 0.14
8 4 0.14
9 20 0.71
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
TAAAAATAA
Found at i:401572 original size:29 final size:30
Alignment explanation
Indices: 401508--401574 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
401498 ATTTGGCCTT
*
401508 ATTTGATTCATTTTAATAGTACAGAGACAA
1 ATTTGATCCATTTTAATAGTACAGAGACAA
* * * *
401538 AATTGATCCA-TTTAATAGTAGAGGGACTA
1 ATTTGATCCATTTTAATAGTACAGAGACAA
401567 ATTTGATC
1 ATTTGATC
401575 AAGCACCTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (30 bp):
ATTTGATCCATTTTAATAGTACAGAGACAA
Found at i:412853 original size:22 final size:22
Alignment explanation
Indices: 412825--412874 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
412815 TACCAATTGT
412825 AAAAGTTGTCACTATATGACAA
1 AAAAGTTGTCACTATATGACAA
412847 AAAAGTTGTCACTATATGACAA
1 AAAAGTTGTCACTATATGACAA
412869 AAAAGT
1 AAAAGT
412875 CATTTGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (22 bp):
AAAAGTTGTCACTATATGACAA
Found at i:425661 original size:172 final size:170
Alignment explanation
Indices: 425368--425751 Score: 502
Period size: 172 Copynumber: 2.2 Consensus size: 170
425358 TTTAGAATTA
* * * *
425368 AGTGCAAATATGCAATGCAGTCAATGTGTTTGTAAAAAGTATTGACAGAAAGTGTTTCTATGCTT
1 AGTGCAAATATGCAATGTAGTCAATGTGTTTGTAAAAAGTATTAACAGAAAGTGGTTCTATGATT
* * * * * *
425433 TTTCGCATAAAATGTCATTTTCTCTAATACCCATTTTATGAAGTTTATCTCTTGAATGTATGTTA
66 TTACGCATAAAATCTCAATTTCTCTAATACCCATTTCATGAAGTTTATCTCTTGAATGTAAGTGA
*
425498 AGAAGCCC-TTAGT-TTCTTGTTTAGCTCGTTATTTTGAATG
131 AGAA-CCCGTTAGTCTT-TTGTTTAGCTAGTTATTTTGAATG
* *
425538 ATGTGCAAGATATGCAATGTAGTCAATGTGTTTGTAAAAAGTATTAACAGACAGTGGTTCTATTA
1 A-GTGCAA-ATATGCAATGTAGTCAATGTGTTTGTAAAAAGTATTAACAGAAAGTGGTTCTATGA
** * * * *
425603 TTTTACGTGTAAAATCTCAATTTCTGTGATGCCCATTTCATGAATTTTATCTCTTGAATGTAAGT
64 TTTTACGCATAAAATCTCAATTTCTCTAATACCCATTTCATGAAGTTTATCTCTTGAATGTAAGT
* *
425668 GAAGAACCCGTTAGTCTTTTGTTTAGGTAGTTATTTTGAATT
129 GAAGAACCCGTTAGTCTTTTGTTTAGCTAGTTATTTTGAATG
* *
425710 AGATACAAATATGGAATGTAGTCAATGTGTTTGTAAAAAGTA
1 AG-TGCAAATATGCAATGTAGTCAATGTGTTTGTAAAAAGTA
425752 CCAGCAGAAA
Statistics
Matches: 186, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
170 1 0.01
171 43 0.23
172 140 0.75
173 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (170 bp):
AGTGCAAATATGCAATGTAGTCAATGTGTTTGTAAAAAGTATTAACAGAAAGTGGTTCTATGATT
TTACGCATAAAATCTCAATTTCTCTAATACCCATTTCATGAAGTTTATCTCTTGAATGTAAGTGA
AGAACCCGTTAGTCTTTTGTTTAGCTAGTTATTTTGAATG
Found at i:426685 original size:21 final size:22
Alignment explanation
Indices: 426661--426702 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
426651 AGATGAAAGT
426661 GATTCTGAAAA-TGA-CGAAACA
1 GATTCT-AAAACTGATCGAAACA
426682 GATTCTAAAACTGATCGAAAC
1 GATTCTAAAACTGATCGAAAC
426703 CGTCTGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (22 bp):
GATTCTAAAACTGATCGAAACA
Found at i:427828 original size:23 final size:24
Alignment explanation
Indices: 427779--427828 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
427769 TTTTAGTTTT
*
427779 AAATTTTAAAAAATAAAAAAATTA
1 AAATTTTAAAAAATAAAAAAATAA
**
427803 AAATTTT-AAAAATAAAAGTATAA
1 AAATTTTAAAAAATAAAAAAATAA
427826 AAA
1 AAA
427829 GGAAATTCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATTTTAAAAAATAAAAAAATAA
Found at i:442769 original size:16 final size:18
Alignment explanation
Indices: 442748--442781 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
442738 TAAAAGATTT
442748 ATTTTAAT-TT-TTATAC
1 ATTTTAATATTATTATAC
442764 ATTTTAATATTATTATAC
1 ATTTTAATATTATTATAC
442782 GAATTGTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTAATATTATTATAC
Found at i:444591 original size:2 final size:2
Alignment explanation
Indices: 444584--444625 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
444574 GTGAGCCTCC
444584 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
444626 GTATGTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:446986 original size:14 final size:14
Alignment explanation
Indices: 446967--446994 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
446957 GGAAAAAAAA
446967 TTTAACTCGATTCG
1 TTTAACTCGATTCG
446981 TTTAACTCGATTCG
1 TTTAACTCGATTCG
446995 AATAATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
TTTAACTCGATTCG
Found at i:452557 original size:24 final size:24
Alignment explanation
Indices: 452529--452576 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
452519 GTACAATGGC
452529 TAAATCTTAAATTTTATAAAAAAA
1 TAAATCTTAAATTTTATAAAAAAA
452553 TAAATCTTAAATTTTATAAAAAAA
1 TAAATCTTAAATTTTATAAAAAAA
452577 ATATAAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAATCTTAAATTTTATAAAAAAA
Found at i:454306 original size:17 final size:18
Alignment explanation
Indices: 454271--454307 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
454261 ATATAATTAT
*
454271 TATATAAGATTTGTTAAA
1 TATATAAAATTTGTTAAA
454289 TATATAAAATTT-TTAAA
1 TATATAAAATTTGTTAAA
454306 TA
1 TA
454308 ACTCGTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATAAAATTTGTTAAA
Found at i:458323 original size:19 final size:19
Alignment explanation
Indices: 458310--458349 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
458300 TGAATTTCTT
458310 TTGCGTGTTAGAATGAATC
1 TTGCGTGTTAGAATGAATC
458329 TTGCGTGTTAGAATGAATC
1 TTGCGTGTTAGAATGAATC
458348 TT
1 TT
458350 TTTAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (19 bp):
TTGCGTGTTAGAATGAATC
Found at i:459697 original size:30 final size:31
Alignment explanation
Indices: 459649--459711 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
459639 AGTTTATATA
* *
459649 TTTATAATTTTTAAAAAGTTAAATTA-AATT
1 TTTATAATTTTTAAAAAGTCAAAGTATAATT
* **
459679 TTTATTATTTTTTGAAAGTCAAAGTATAATT
1 TTTATAATTTTTAAAAAGTCAAAGTATAATT
459710 TT
1 TT
459712 ACCCTAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (31 bp):
TTTATAATTTTTAAAAAGTCAAAGTATAATT
Found at i:460771 original size:31 final size:30
Alignment explanation
Indices: 460735--460807 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
460725 GATTAAATCA
*
460735 AAATTAAAGTTTCAAGTGTACATTTGAACC
1 AAATTAAAGTTTCAAGTGTACAATTGAACC
* * * *
460765 ACAATTAGAGTTTCACGTGTATAATTGCACC
1 A-AATTAAAGTTTCAAGTGTACAATTGAACC
460796 AAATTAAAGTTT
1 AAATTAAAGTTT
460808 ATGTACACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 11 0.31
31 25 0.69
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTGTACAATTGAACC
Found at i:461090 original size:61 final size:61
Alignment explanation
Indices: 460913--461082 Score: 182
Period size: 61 Copynumber: 2.8 Consensus size: 61
460903 TTAGTATAGT
* * * * *
460913 AACAAATTTAGCCATTAATGTTTACACATTCTATCAATTT-GATCCTAAATATAAAAAATTC
1 AACAAATTTAGCCATCAATATTTACAAAATCTGTCAATTTAG-TCCTAAATATAAAAAATTC
* * * * * * *
460974 AACAAATTTAGCCATTAATGTTTACAGAATTTGTCATTTTAGTTCTAATTATAAAAAATTC
1 AACAAATTTAGCCATCAATATTTACAAAATCTGTCAATTTAGTCCTAAATATAAAAAATTC
* *
461035 AATAAATTTGGCTC-TCAATATTTACAAAATCTGTCAATTTAGTCCTAA
1 AACAAATTTAGC-CATCAATATTTACAAAATCTGTCAATTTAGTCCTAA
461083 CTCTAAAATT
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
61 90 0.98
62 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (61 bp):
AACAAATTTAGCCATCAATATTTACAAAATCTGTCAATTTAGTCCTAAATATAAAAAATTC
Found at i:467570 original size:27 final size:27
Alignment explanation
Indices: 467526--467589 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
467516 AATTTTCAAA
* *
467526 AAATTAAATTAAATTTTTATTATTTTT
1 AAATTAAAATAAATTTTTATTATTATT
467553 AAATTAAAATATAA-TTTTATTATTATT
1 AAATTAAAATA-AATTTTTATTATTATT
*
467580 AATTTAAAAT
1 AAATTAAAAT
467590 TTTATAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
AAATTAAAATAAATTTTTATTATTATT
Found at i:476216 original size:445 final size:445
Alignment explanation
Indices: 475386--476697 Score: 2347
Period size: 445 Copynumber: 2.9 Consensus size: 445
475376 TATGGAGGCC
* ** * * * *
475386 TTTGTACCAGGATACGGATTGCATTTTGCTCCCTCTACTAAAAAAATGGGCAAAATAGTCCTTAT
1 TTTGTACTAGGAGCCGGATTGCATTCTGCTCCCTCTACTAAAAAAATGGGCAAATTAGTCCATGT
* * * * *
475451 GCATTAGATCAAAGAGTAAATTGATCATTCTATTAAAATTTTCATCTATTTCTACTGTTAAAAAC
66 ACATTAGATCAAAGAGTAAATTGGTCATTCTGTTAAAAATTTCATCTATTTCTATTGTTAAAAAC
* *
475516 TGTACAAGACCAGTTTGCTTTTTGATCTAATGTATAGGGACTTATTTTGTCCATTTTTTGAGTAG
131 TGTACAGGACCAGTTTGCTTTTTGATCTAATGTATAGGGACTTA-TTTGCCCATTTTTTGAGTAG
* * * * * **
475581 TGGGGGCAAAATGCAATCTCACACCTAGTACAGGGGCCTTCATGGTATTTATACCCGA-AAAAAA
195 AGGGGGAAAAATGCAATCTCACACCTAGTGCAGGGGCCTCCATGGTACTTATACCC-ACAAAGCA
* * *
475645 CCGTTTCTAGTATTCAGAATTTCACATTTCAAACTTTAGCAACAATGATTAACTATTTTTATCAT
259 CCTTTTCTAATATTCAGAATTTCACATTTCAAACTTTGGCAACAATGATTAACTATTTTTATCAT
*
475710 AGGACATGAGATCTCATTTATGAAGAAACAGTCTGACATAACAGCTATGCATTGTTTTGCCCTCG
324 AGGACATGAGATCTCATTTTTGAAGAAACAGTCTGACATAACAGCTATGCATTGTTTTGCCCTCG
475775 GAGATAAAAGGATCCACTTGAACATGTCAAAGAATTTGGAATATAAAATACTAGCAT
389 GAGATAAAAGGATCCACTTGAACATGTCAAAGAATTTGGAATATAAAATACTAGCAT
475832 TTTGTACTAGGAGCCGGATTGCATTCTGCTCCCTCTACTAAAAAAATGGGCAAATTAGTCCATGT
1 TTTGTACTAGGAGCCGGATTGCATTCTGCTCCCTCTACTAAAAAAATGGGCAAATTAGTCCATGT
475897 ACATTAGATCAAAGAGTAAATTGGTCATTCTGTTAAAAATTTCATCTATTTCTATTGTTAAAAAC
66 ACATTAGATCAAAGAGTAAATTGGTCATTCTGTTAAAAATTTCATCTATTTCTATTGTTAAAAAC
475962 TGTACAGGACCAGTTTGCTTTTTGATCTAATGTATAGGGACTTATTTGCCCATTTTTTGAGTAGA
131 TGTACAGGACCAGTTTGCTTTTTGATCTAATGTATAGGGACTTATTTGCCCATTTTTTGAGTAGA
476027 GGGGGAAAAATGCAATCTCACACCTAGTGCAGGGGCCTCCATGGTACTTATACCCACAAAGCACC
196 GGGGGAAAAATGCAATCTCACACCTAGTGCAGGGGCCTCCATGGTACTTATACCCACAAAGCACC
476092 TTTTCTAATATTCAGAATTTCACATTTCAAACTTTGGCAACAATGATTAACTATTTTTATCATAG
261 TTTTCTAATATTCAGAATTTCACATTTCAAACTTTGGCAACAATGATTAACTATTTTTATCATAG
476157 GACATGAGATCTCATTTTTGAAGAAACAGTCTGACATAACAGCTATGCATTGTTTTGCCCTCGGA
326 GACATGAGATCTCATTTTTGAAGAAACAGTCTGACATAACAGCTATGCATTGTTTTGCCCTCGGA
476222 GATAAAAGGATCCACTTGAACATGTCAAAGAATTTGGAATATAAAATACTAGCAT
391 GATAAAAGGATCCACTTGAACATGTCAAAGAATTTGGAATATAAAATACTAGCAT
*
476277 TTTGTACTAGGAGCCGGACTGCATTCTGCTCCCTCTACTAAAAAAATGGGCAAATTAGTCCATGT
1 TTTGTACTAGGAGCCGGATTGCATTCTGCTCCCTCTACTAAAAAAATGGGCAAATTAGTCCATGT
476342 ACATTAGATCAAAGAGTAAATTGGTCATTCTGTTAAAAATTTCATCTATTTCTATTGTTAAAAAC
66 ACATTAGATCAAAGAGTAAATTGGTCATTCTGTTAAAAATTTCATCTATTTCTATTGTTAAAAAC
476407 TGTACAGGACCAGTTTGCTTTTTGATCTAATGTATAGGGACTTATTTGCCCATTTTTTGAGTAGA
131 TGTACAGGACCAGTTTGCTTTTTGATCTAATGTATAGGGACTTATTTGCCCATTTTTTGAGTAGA
476472 GGGGGAAAAATGCAATCTCACACCTAGTGCAGGGGCCTCCATGGTACTTATACCCACAAAGCACC
196 GGGGGAAAAATGCAATCTCACACCTAGTGCAGGGGCCTCCATGGTACTTATACCCACAAAGCACC
476537 TTTTCTAATATTCAGAATTTCACATTTCAAACTTTGGCAACAATGATTAACTATTTTTATCATAG
261 TTTTCTAATATTCAGAATTTCACATTTCAAACTTTGGCAACAATGATTAACTATTTTTATCATAG
* *
476602 GACATGAGATCTCATTTTTGAAGAAACAGTCTGACATAACAGCTATGCATTGTTTTGTCCTCAGA
326 GACATGAGATCTCATTTTTGAAGAAACAGTCTGACATAACAGCTATGCATTGTTTTGCCCTCGGA
476667 GATAAAAGGATCCACTTGAACATGTCAAAGA
391 GATAAAAGGATCCACTTGAACATGTCAAAGA
476698 GAAATGCGAT
Statistics
Matches: 837, Mismatches: 28, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
444 1 0.00
445 675 0.81
446 161 0.19
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (445 bp):
TTTGTACTAGGAGCCGGATTGCATTCTGCTCCCTCTACTAAAAAAATGGGCAAATTAGTCCATGT
ACATTAGATCAAAGAGTAAATTGGTCATTCTGTTAAAAATTTCATCTATTTCTATTGTTAAAAAC
TGTACAGGACCAGTTTGCTTTTTGATCTAATGTATAGGGACTTATTTGCCCATTTTTTGAGTAGA
GGGGGAAAAATGCAATCTCACACCTAGTGCAGGGGCCTCCATGGTACTTATACCCACAAAGCACC
TTTTCTAATATTCAGAATTTCACATTTCAAACTTTGGCAACAATGATTAACTATTTTTATCATAG
GACATGAGATCTCATTTTTGAAGAAACAGTCTGACATAACAGCTATGCATTGTTTTGCCCTCGGA
GATAAAAGGATCCACTTGAACATGTCAAAGAATTTGGAATATAAAATACTAGCAT
Found at i:480507 original size:133 final size:136
Alignment explanation
Indices: 480279--480552 Score: 405
Period size: 142 Copynumber: 2.0 Consensus size: 136
480269 GTATTAAAAA
480279 AGTAAATTATACTGGTCAGCTTCCATTAATAAACATTTGTAGAATCATGAAATAGAAATATATAG
1 AGTAAATTATACTGGTCAGCTTCCATTAATAAACATTTGTAGAATC----AATAGAAATATATAG
* * * *
480344 AAATATAATATTACACGATAAAATACACCATTGAAAGTTTTATTTAACATATAGTTATTAAAATC
62 AAATATAATA-TACACGATAAAATAAACCATCGAAAGCTTCATTTAACATATAGTTA-TAAAATC
480409 AAAAGCAGAAAC
125 AAAAGCAGAAAC
*
480421 AGTAAATTATACTGGTCGGCTTCCATTAATAAACATTTGTAGAATC-AT-GAAA-ATATAGAAAT
1 AGTAAATTATACTGGTCAGCTTCCATTAATAAACATTTGTAGAATCAATAGAAATATATAGAAAT
480483 ATAA-A-ACTACGATAAAATAAACCATCGAAAGCTTCATTTAACATATAGTTATAAAATCAAAAG
66 ATAATATAC-ACGATAAAATAAACCATCGAAAGCTTCATTTAACATATAGTTATAAAATCAAAAG
480546 CAGAAAC
130 CAGAAAC
480553 TATAATCTGA
Statistics
Matches: 126, Mismatches: 5, Indels: 12
0.88 0.03 0.08
Matches are distributed among these distances:
132 21 0.17
133 39 0.31
134 1 0.01
135 14 0.11
136 4 0.03
137 2 0.02
142 45 0.36
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.29
Consensus pattern (136 bp):
AGTAAATTATACTGGTCAGCTTCCATTAATAAACATTTGTAGAATCAATAGAAATATATAGAAAT
ATAATATACACGATAAAATAAACCATCGAAAGCTTCATTTAACATATAGTTATAAAATCAAAAGC
AGAAAC
Found at i:481940 original size:21 final size:20
Alignment explanation
Indices: 481915--481953 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
481905 ATAATAATCT
*
481915 AAAAATTTTATATAAAATTTA
1 AAAAAATTTA-ATAAAATTTA
*
481936 AAAAAATTTAATTAAATT
1 AAAAAATTTAATAAAATT
481954 ATAATGCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAAATTTAATAAAATTTA
Found at i:487788 original size:28 final size:28
Alignment explanation
Indices: 487727--487790 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
487717 AACTATTCGA
* *
487727 AAGTTTTCATTTAAGTTATTGAATTGTT
1 AAGTTTTTATTTAAGTTACTGAATTGTT
** *
487755 CCGTTTTTATTTAAGTTACTGAGTTGTT
1 AAGTTTTTATTTAAGTTACTGAATTGTT
487783 AAGTTTTT
1 AAGTTTTT
487791 TTTCTTTTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.06, G:0.16, T:0.55
Consensus pattern (28 bp):
AAGTTTTTATTTAAGTTACTGAATTGTT
Found at i:490041 original size:24 final size:21
Alignment explanation
Indices: 490014--490064 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 21
490004 AAAAATATTT
490014 TTTTATTTTATAATTTTTTAATAA
1 TTTTATTTTA-AA-TTTTTAA-AA
490038 TTTTAATTTTAAATTTTTAAAA
1 TTTT-ATTTTAAATTTTTAAAA
490060 TTTTA
1 TTTTA
490065 AAAATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.04
22 6 0.23
23 7 0.27
24 6 0.23
25 6 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATTTTAAATTTTTAAAA
Found at i:490469 original size:11 final size:11
Alignment explanation
Indices: 490452--490511 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
490442 TTTATATAGT
490452 AATTTATATTA
1 AATTTATATTA
*
490463 TATTTATA-TA
1 AATTTATATTA
*
490473 AATTT-TAATA
1 AATTTATATTA
*
490483 AATTAATCATATA
1 AATTTAT-AT-TA
*
490496 TATTTATATTA
1 AATTTATATTA
490507 AATTT
1 AATTT
490512 CAAATTATAG
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
9 2 0.05
10 12 0.32
11 14 0.37
12 3 0.08
13 7 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTATATTA
Found at i:490481 original size:27 final size:28
Alignment explanation
Indices: 490451--490528 Score: 68
Period size: 33 Copynumber: 2.6 Consensus size: 28
490441 GTTTATATAG
490451 TAATTTATATTATATTTATA-TAAATTT
1 TAATTTATATTATATTTATATTAAATTT
490478 TAATAAATTAATCATATATATTTATATTAAATTT
1 TAAT---TT-AT-AT-TATATTTATATTAAATTT
* * *
490512 CAAATTATAGTATATTT
1 TAATTTATATTATATTT
490529 TTAATCATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
27 4 0.10
28 7 0.17
29 1 0.02
30 4 0.10
31 4 0.10
32 2 0.05
33 10 0.24
34 9 0.22
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (28 bp):
TAATTTATATTATATTTATATTAAATTT
Found at i:490699 original size:29 final size:30
Alignment explanation
Indices: 490657--490719 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
490647 ATTTCACTTC
* * * *
490657 CTTTTTTTTTTTCT-CAAAAAGTCATTTCA
1 CTTTTTCTTTTTCTAAAAAAAATAATTTCA
490686 CTTTTTCTTTTTCTAAAAAAAATAATTTCA
1 CTTTTTCTTTTTCTAAAAAAAATAATTTCA
490716 CTTT
1 CTTT
490720 CAAAACCCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.29, C:0.16, G:0.02, T:0.54
Consensus pattern (30 bp):
CTTTTTCTTTTTCTAAAAAAAATAATTTCA
Found at i:490767 original size:16 final size:16
Alignment explanation
Indices: 490746--490782 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
490736 AAGGAAAAAG
* *
490746 TAAATTATTTTTTCTT
1 TAAATTATTTGTTATT
490762 TAAATTATTTGTTATT
1 TAAATTATTTGTTATT
490778 TAAAT
1 TAAAT
490783 GAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
TAAATTATTTGTTATT
Found at i:493465 original size:4 final size:4
Alignment explanation
Indices: 493441--493490 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
493431 ACATGTTAAA
* * * * *
493441 ATAC ATGC ATAC ATGC ATAC ATAC AGAC ATAC ATTC ATAC ATAC GTAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
493489 AT
1 AT
493491 GTTAGTGATA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:496910 original size:8 final size:8
Alignment explanation
Indices: 496899--496927 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
496889 TATTTTTATT
496899 ATTTTAAA
1 ATTTTAAA
496907 ATTTTAAA
1 ATTTTAAA
496915 ATTTTAAA
1 ATTTTAAA
496923 ATTTT
1 ATTTT
496928 GAAGGGGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
ATTTTAAA
Found at i:501026 original size:11 final size:11
Alignment explanation
Indices: 501003--501065 Score: 90
Period size: 11 Copynumber: 5.5 Consensus size: 11
500993 TCAAATTTAT
501003 TTTAATCTTAAA
1 TTTAAT-TTAAA
*
501015 TTTATTTTAAA
1 TTTAATTTAAA
*
501026 TTCAATTTAAA
1 TTTAATTTAAA
501037 TTTAAATTTAAA
1 TTT-AATTTAAA
501049 TTTAATTTAAA
1 TTTAATTTAAA
501060 TTTAAT
1 TTTAAT
501066 GTTATTATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
11 30 0.65
12 16 0.35
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:501062 original size:17 final size:17
Alignment explanation
Indices: 500995--501082 Score: 85
Period size: 17 Copynumber: 5.2 Consensus size: 17
500985 TTTGAAAATC
*
500995 AAATTT-ATTTTAATCTT
1 AAATTTAATTTAAAT-TT
*
501012 AAATTTATTTTAAA-TT
1 AAATTTAATTTAAATTT
*
501028 CAATTTAAATTTAAATTT
1 AAATTT-AATTTAAATTT
501046 AAATTTAATTTAAATTT
1 AAATTTAATTTAAATTT
501063 -AATGTT-ATTATAAATTT
1 AAAT-TTAATT-TAAATTT
501080 AAA
1 AAA
501083 AAAAAAGTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
16 13 0.22
17 33 0.55
18 14 0.23
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (17 bp):
AAATTTAATTTAAATTT
Found at i:501082 original size:6 final size:6
Alignment explanation
Indices: 501010--501064 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
501000 TATTTTAATC
* *
501010 TTAAAT TT-ATT TTAAA- TTCAAT TTAAAT TTAAAT TTAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
501055 TTAAAT TTAA
1 TTAAAT TTAA
501065 TGTTATTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
5 13 0.31
6 29 0.69
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:501278 original size:15 final size:15
Alignment explanation
Indices: 501258--501288 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
501248 GCCTATGCTG
501258 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
501273 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
501288 C
1 C
501289 CATCCACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:501774 original size:3 final size:3
Alignment explanation
Indices: 501759--501791 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
501749 TGAAAGACAT
*
501759 TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
501792 ACCGAAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:502889 original size:30 final size:30
Alignment explanation
Indices: 502855--503079 Score: 360
Period size: 30 Copynumber: 7.5 Consensus size: 30
502845 TAGAAATTTC
502855 ATTTTGACCCCAAAACTTTTCCAAAATTAT
1 ATTTTGACCCCAAAACTTTTCCAAAATTAT
* **
502885 ATTTTGGCCCCAAAACTTTTTTAAAATTAT
1 ATTTTGACCCCAAAACTTTTCCAAAATTAT
*
502915 ATTTTGACCCCAAAACTTTTTCAAAATTAT
1 ATTTTGACCCCAAAACTTTTCCAAAATTAT
* *
502945 ATTTTGACCCCAAAACTTTTCTAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAT
* *
502975 ATTTTGACCCCTAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAT
503005 ATTTTGACCCCAAAACTTTTCCAAAATTAT
1 ATTTTGACCCCAAAACTTTTCCAAAATTAT
* *
503035 ATTTTGACCCTAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAT
503065 ATTTTGACCCCAAAA
1 ATTTTGACCCCAAAA
503080 AATCTCCTAA
Statistics
Matches: 180, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 180 1.00
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (30 bp):
ATTTTGACCCCAAAACTTTTCCAAAATTAT
Found at i:503188 original size:30 final size:30
Alignment explanation
Indices: 503094--503188 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
503084 TCCTAAATCT
* *
503094 CATTTTTAACCACGATTTCACTAAAATTTAC
1 CATTTTTAACCCCGATATCACTAAAA-TTAC
* * **
503125 CA-TTTT-ACCCTCGAAACCTTTAAAATT-C
1 CATTTTTAACCC-CGATATCACTAAAATTAC
*
503153 CATTTTTAACCCCGATATCACCAAAATTAC
1 CATTTTTAACCCCGATATCACTAAAATTAC
503183 CATTTT
1 CATTTT
503189 GCCCTCGGGT
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
28 3 0.06
29 20 0.41
30 24 0.49
31 2 0.04
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (30 bp):
CATTTTTAACCCCGATATCACTAAAATTAC
Found at i:504228 original size:11 final size:11
Alignment explanation
Indices: 504208--504240 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
504198 TAGACCGACG
504208 TTTT-AACGTT
1 TTTTAAACGTT
504218 TTTTAAACG-T
1 TTTTAAACGTT
504228 TTTTAAACGTT
1 TTTTAAACGTT
504239 TT
1 TT
504241 GTGGTGATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (11 bp):
TTTTAAACGTT
Found at i:504659 original size:19 final size:19
Alignment explanation
Indices: 504635--504684 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
504625 TTAAAAAACT
504635 AAATTATAT-AAACTTATTA
1 AAATTATATAAAACTTA-TA
504654 AAATTAT-TAAAACTTATA
1 AAATTATATAAAACTTATA
504672 AATATTATA-AAAA
1 AA-ATTATATAAAA
504685 TATAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTATATAAAACTTATA
Found at i:504770 original size:22 final size:22
Alignment explanation
Indices: 504740--504786 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
504730 CTTATTTAAG
504740 ATATTTAAAATT-TTAAAAAA-A
1 ATATTT-AAATTCTTAAAAAATA
504761 ATATATTAAATTCTTAAAAAATA
1 ATAT-TTAAATTCTTAAAAAATA
504784 ATA
1 ATA
504787 AAAATTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.39
22 10 0.43
23 4 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATATTTAAATTCTTAAAAAATA
Found at i:504791 original size:20 final size:19
Alignment explanation
Indices: 504745--504798 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
504735 TTAAGATATT
504745 TAAAATTTTAAAAAAAATA
1 TAAAATTTTAAAAAAAATA
504764 TATTAAATTCTTAAAAAATAATA
1 TA--AAATT-TTAAAAAA-AATA
*
504787 -AAAATTGTAAAA
1 TAAAATTTTAAAA
504799 TTTATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 7 0.23
20 5 0.17
21 5 0.17
22 9 0.30
23 4 0.13
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAATTTTAAAAAAAATA
Found at i:504825 original size:17 final size:18
Alignment explanation
Indices: 504777--504825 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
504767 TAAATTCTTA
* *
504777 AAAAATAATAAAAATTGT
1 AAAATTAATAAAAAATGT
* *
504795 AAAATTTATTAAAAAT-T
1 AAAATTAATAAAAAATGT
504812 AAAATTAATAAAAA
1 AAAATTAATAAAAA
504826 CTTATAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAATTAATAAAAAATGT
Found at i:510550 original size:15 final size:15
Alignment explanation
Indices: 510532--510561 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
510522 TTGAATTTGG
*
510532 TTTTTTAATATTTTA
1 TTTTTTAAAATTTTA
510547 TTTTTTAAAATTTTA
1 TTTTTTAAAATTTTA
510562 ATAATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTTAAAATTTTA
Found at i:510577 original size:23 final size:23
Alignment explanation
Indices: 510534--510578 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
510524 GAATTTGGTT
**
510534 TTTTAATATTTTATTTTTTAAAA
1 TTTTAATATTTTATTAATTAAAA
510557 TTTTAATAATTTT-TTAATTAAA
1 TTTTAAT-ATTTTATTAATTAAA
510579 TTAGGGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAATATTTTATTAATTAAAA
Found at i:520272 original size:21 final size:22
Alignment explanation
Indices: 520248--520289 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
520238 TGAATTTTTT
520248 AAAGTTATTTAGTAA-AATTTC
1 AAAGTTATTTAGTAATAATTTC
* *
520269 AAAGTTTTTTATTAATAATTT
1 AAAGTTATTTAGTAATAATTT
520290 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (22 bp):
AAAGTTATTTAGTAATAATTTC
Found at i:520447 original size:29 final size:27
Alignment explanation
Indices: 520399--520454 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
520389 TTCTTTACAT
*
520399 ATAAAAAGTTAAAATTAATTATAAATTAA
1 ATAAAAAATTAAAATTAATT-T-AATTAA
520428 ATAAAAAATT-AAATTCAATTTAATTAA
1 ATAAAAAATTAAAATT-AATTTAATTAA
520455 TCGTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
28 6 0.24
29 13 0.52
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
ATAAAAAATTAAAATTAATTTAATTAA
Found at i:524790 original size:15 final size:17
Alignment explanation
Indices: 524769--524809 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
524759 TAAATTTTTA
524769 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
524785 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
524801 AAAATTATA
1 AAAATTATA
524810 TTTTTACGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:524802 original size:24 final size:25
Alignment explanation
Indices: 524759--524809 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
524749 AAAATTAATT
* *
524759 TAAATTTTTAAAAATTATAAAAATA
1 TAAATTATTAAAAATGATAAAAATA
*
524784 TAAATTATT-AAAATGATAAAATTA
1 TAAATTATTAAAAATGATAAAAATA
524808 TA
1 TA
524810 TTTTTACGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
TAAATTATTAAAAATGATAAAAATA
Found at i:525359 original size:11 final size:12
Alignment explanation
Indices: 525343--525375 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
525333 AAAAACATAT
525343 TTATTTTCTCA-
1 TTATTTTCTCAG
525354 TTATTTTCTCAG
1 TTATTTTCTCAG
*
525366 TTCTTTTCTC
1 TTATTTTCTC
525376 TCCCTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.12, C:0.21, G:0.03, T:0.64
Consensus pattern (12 bp):
TTATTTTCTCAG
Found at i:525663 original size:17 final size:17
Alignment explanation
Indices: 525641--525675 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
525631 AAATAACATA
*
525641 ATTTAATAATATAAATT
1 ATTTAAAAATATAAATT
*
525658 ATTTAAAAATATATATT
1 ATTTAAAAATATAAATT
525675 A
1 A
525676 AAGTCATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTAAAAATATAAATT
Found at i:525972 original size:29 final size:28
Alignment explanation
Indices: 525934--525993 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
525924 TATTATAATA
**
525934 AAATAAATGGGGAAAATATTAAAAAAAT
1 AAATAAATGGAAAAAATATTAAAAAAAT
* *
525962 AAATAACATGGAAAAAATTTTAAAAAATT
1 AAATAA-ATGGAAAAAATATTAAAAAAAT
525991 AAA
1 AAA
525994 AATATCAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.23
Consensus pattern (28 bp):
AAATAAATGGAAAAAATATTAAAAAAAT
Found at i:526577 original size:18 final size:19
Alignment explanation
Indices: 526537--526579 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
526527 AAGATTATTG
526537 AATTGGGATGCCCATGAAA
1 AATTGGGATGCCCATGAAA
526556 AATTGGGATGCCCATG-AA
1 AATTGGGATGCCCATGAAA
526574 AATTGG
1 AATTGG
526580 CATTGAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (19 bp):
AATTGGGATGCCCATGAAA
Found at i:527595 original size:378 final size:378
Alignment explanation
Indices: 526900--527627 Score: 1027
Period size: 378 Copynumber: 1.9 Consensus size: 378
526890 GGTTTGTATG
* * * *
526900 GATGATGGTGATTTCAGGAATGAGGAGGAGACGAGTCGTGGGTTGAAAGTTTCAAATTGTGATGA
1 GATGATGGTGATTTCAGGAATGAGGAGGAAACGAGTCATAGGTTGAAAGTTTCAAATAGTGATGA
* * * * *
526965 GAAGGAAGATCAAGCCTTGGCCCGAGGGAAGGGGAGTGAAGTTGAGGTTTTCAATGGATGGAGTG
66 GAAGGAAGATCAAACCTTAGCCCAAGGGAAGGGGAGTGAAGTCGAGGTTTTCAATGGATGGAATG
** *
527030 GAGTAAATGGTGATCGAGTTCTGGAATCTGAGAAACGATGTGAAGTTGAAAGACAAAGTGTTGAA
131 GAGTAAACAGTGATCAAG-TCTGGAATCTGAGAAACGATGTGAAGTTGAAAGACAAAGTGTTGAA
* *
527095 GCGAATGGCTGGAATAGAGCTTGTGATGAAAGAACGGAAGGGTTTGAAGAACAAATGGAAGGCAG
195 GCGAATGGCAGGAATAGAGCTTGTGATGAAAGAACGGAAGGGCTTGAAGAACAAATGGAAGGCAG
* *
527160 AAGGGAATCCATTAATGAGGTTCGAGAAGAAAGTCAACACTTTAATGAACAAATTGAACCGAGTC
260 AAGGGAATCCATTAATGAGGTTCGAGAAGAAAGTCAACACTTTAACGAACAAATTGAAACGAGTC
* *
527225 GTCATTTGGAGAAGCTTTGT-AAGAATGGAGAGATCTTATGTGTTAATAACGAA
325 ATCATTTGAAGAAGCTTTGTGAAGAATGGAGAGATCTTATGTGTTAATAACGAA
* * *
527278 GATGATGGTGATTTGCA-GAATGAGGAGGAAATGAGTCATAGGTTGAACGTTTCAAATAGTGTTG
1 GATGATGGTGATTT-CAGGAATGAGGAGGAAACGAGTCATAGGTTGAAAGTTTCAAATAGTGATG
* * * * * *
527342 AGAAGGAAGATCAAACTTTAGTCCAAGGGAAGTGGAGTGAAGTCGAGGCTTTT-GATGGCTGTAA
65 AGAAGGAAGATCAAACCTTAGCCCAAGGGAAGGGGAGTGAAGTCGAGG-TTTTCAATGGATGGAA
* * *
527406 TGGGGTAAACAGTGGTCAAG-CTGCAGAATCTGA-AACTCGATGTGAAGTTGAAAGACAAAGTGT
129 TGGAGTAAACAGTGATCAAGTCTG--GAATCTGAGAA-ACGATGTGAAGTTGAAAGACAAAGTGT
* * *
527469 TGAAGCGAATGGCCAGG-ATAGAGCTTGTGATGGAAGAATGGAAGGGCTTGAAGAGCAAATGGAA
191 TGAAGCGAATGG-CAGGAATAGAGCTTGTGATGAAAGAACGGAAGGGCTTGAAGAACAAATGGAA
* *
527533 GGCAGAAGGGAATCGATTAATGAGGTTCGAGAAGAAAGTCAACACTTTAACGGACAAATTGAAAC
255 GGCAGAAGGGAATCCATTAATGAGGTTCGAGAAGAAAGTCAACACTTTAACGAACAAATTGAAAC
*
527598 GATTCATCATTTGAAGAAGCTTTGTGAAGA
320 GAGTCATCATTTGAAGAAGCTTTGTGAAGA
527628 TGATGGTGAT
Statistics
Matches: 307, Mismatches: 36, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
376 3 0.01
377 2 0.01
378 289 0.94
379 13 0.04
ACGTcount: A:0.35, C:0.10, G:0.32, T:0.23
Consensus pattern (378 bp):
GATGATGGTGATTTCAGGAATGAGGAGGAAACGAGTCATAGGTTGAAAGTTTCAAATAGTGATGA
GAAGGAAGATCAAACCTTAGCCCAAGGGAAGGGGAGTGAAGTCGAGGTTTTCAATGGATGGAATG
GAGTAAACAGTGATCAAGTCTGGAATCTGAGAAACGATGTGAAGTTGAAAGACAAAGTGTTGAAG
CGAATGGCAGGAATAGAGCTTGTGATGAAAGAACGGAAGGGCTTGAAGAACAAATGGAAGGCAGA
AGGGAATCCATTAATGAGGTTCGAGAAGAAAGTCAACACTTTAACGAACAAATTGAAACGAGTCA
TCATTTGAAGAAGCTTTGTGAAGAATGGAGAGATCTTATGTGTTAATAACGAA
Found at i:531859 original size:16 final size:15
Alignment explanation
Indices: 531832--531898 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 15
531822 ATTAAATTTT
*
531832 TTATATTGTAATATA
1 TTATATTTTAATATA
*
531847 TTATTATTTTAATA-C
1 TTA-TATTTTAATATA
*
531862 TTATA-TTAAAGTAATA
1 TTATATTTTAA-T-ATA
531878 TTATATATTTAATATA
1 TTATAT-TTTAATATA
531894 TTATA
1 TTATA
531899 AATTATATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
13 4 0.10
14 3 0.07
15 7 0.17
16 22 0.54
17 1 0.02
18 4 0.10
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (15 bp):
TTATATTTTAATATA
Found at i:531948 original size:16 final size:17
Alignment explanation
Indices: 531898--531950 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
531888 AATATATTAT
*
531898 AAATTATATAATATACA
1 AAATTATATAATATAAA
531915 AAATTAATATAATATAAA
1 AAATT-ATATAATATAAA
*
531933 AAATTATA-AATTTAAA
1 AAATTATATAATATAAA
531949 AA
1 AA
531951 TAAATCAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 9 0.27
17 8 0.24
18 16 0.48
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTATATAATATAAA
Found at i:533383 original size:14 final size:13
Alignment explanation
Indices: 533364--533394 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
533354 CGACATCCCC
*
533364 TTTTTTGTCAAAA
1 TTTTTTTTCAAAA
533377 TTTTTTTTCAAAA
1 TTTTTTTTCAAAA
533390 TTTTT
1 TTTTT
533395 GGGTGTTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (13 bp):
TTTTTTTTCAAAA
Found at i:533451 original size:56 final size:56
Alignment explanation
Indices: 533387--533640 Score: 247
Period size: 56 Copynumber: 4.4 Consensus size: 56
533377 TTTTTTTTCA
*
533387 AAATTTTTGGGTGTTAGCCATCAAATGGCCGACACCCCCTATTTCAAAAAAAAATT
1 AAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCAAAAAAAAATT
* * * ***
533443 ACATTTTTGTGTGTTGGCTATTGCATGGCCGACACCCCCTATTTCAAAAAAAAATT
1 AAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCAAAAAAAAATT
* * ** * *
533499 ATATTTTTAGGTGTTGGCCATCAAATGGCCGACACTTCCTATTTCTCGAGAAAAAATTT
1 AAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTA-TT-TC-AAAAAAAAATT
* * * * *
533558 CAAATTTTTTTGGTTTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAGAAAAAAATT
1 -AAA-TTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTATT-TC-AAAAAAAAATT
* *
533618 CAATTTTTTTTGGTGTTGGCCAT
1 -AA-ATTTTTGGGTGTTGGCCAT
533641 TGCATGGCCT
Statistics
Matches: 164, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
56 81 0.49
57 2 0.01
58 2 0.01
59 9 0.05
60 38 0.23
61 32 0.20
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (56 bp):
AAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCAAAAAAAAATT
Found at i:533695 original size:47 final size:46
Alignment explanation
Indices: 533603--533696 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 46
533593 ACCCTCTTTT
* ***
533603 CTCGAGAAAAAAATTCAATTTTTTTTGGTGTTGGCCATTGCATGGC
1 CTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGC
533649 CTCGAGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGC
1 CTCGAGAAAAAAA-TTCAAATTTTTTTGGTGTTGGCCATCAAATGGC
533696 C
1 C
533697 GACACCCCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 13 0.30
47 30 0.70
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (46 bp):
CTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGC
Found at i:533868 original size:61 final size:58
Alignment explanation
Indices: 533653--533879 Score: 180
Period size: 59 Copynumber: 3.8 Consensus size: 58
533643 CATGGCCTCG
* *
533653 AGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCATGTTCTC-
1 AGAAAAAAAATTCAAATTTTTTT--TGTTGGTCATCAAATGGCCGACA-CCCC-TGTTCTCA
* * ** * *
533714 -G----AGATTTTGAATTTTTTTTGGTATTGGCCATCAAATGGCCGACACTTCCTGTTCTCA
1 AGAAAAAAAATTCAAATTTTTTTT-G--TTGGTCATCAAATGGCCGACAC-CCCTGTTCTCA
* * *
533771 AGAAAAAAAATTCAACTTTTTTTTGTTGGTCATCAAATGGTCGACACCCCTTTTCTCGA
1 AGAAAAAAAATTCAAATTTTTTTTGTTGGTCATCAAATGGCCGACACCCCTGTTCTC-A
* *
533830 A-TAAAAAAATTCTAAATTTTTTTAATGTTGGTCATCAAATGACCGACACC
1 AGAAAAAAAATTC-AAATTTTTTT--TGTTGGTCATCAAATGGCCGACACC
533880 AACTTCTCCT
Statistics
Matches: 135, Mismatches: 17, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
54 1 0.01
55 1 0.01
56 22 0.16
57 23 0.17
58 19 0.14
59 31 0.23
60 1 0.01
61 24 0.18
62 13 0.10
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (58 bp):
AGAAAAAAAATTCAAATTTTTTTTGTTGGTCATCAAATGGCCGACACCCCTGTTCTCA
Found at i:537330 original size:61 final size:60
Alignment explanation
Indices: 537255--537453 Score: 218
Period size: 61 Copynumber: 3.1 Consensus size: 60
537245 TTATTGAGAA
* *
537255 AAAAGGGGGGTGTCGGCCATCTGATGGCCAACACTAAAAAAATTTGAATTTTTTTCTCGAG
1 AAAA-GGGGGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAATTTTTTTCTCGAG
** *
537316 AAAAGGGGGATGTCGATCATTTGATCGCCAACACCAAAAAAATTTGAAATTTGAAATTTTTTTTC
1 AAAAGGGGG-TGTCGGCCATTTGATGGCCAACA-C--AAAAA----AAATTTG-AA-TTTTTTTC
537381 TCGAG
56 TCGAG
* * *
537386 AAAAGAGGGTGTCGGCCATTTGATGGCCAATACCAAAAAAATTTGAATTTTTTTCTCGAG
1 AAAAGGGGGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAATTTTTTTCTCGAG
537446 AAATAGGG
1 AAA-AGGG
537454 CCAACACCCA
Statistics
Matches: 115, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
60 21 0.18
61 28 0.24
62 8 0.07
64 4 0.03
66 4 0.03
68 8 0.07
69 21 0.18
70 21 0.18
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (60 bp):
AAAAGGGGGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAATTTTTTTCTCGAG
Found at i:537426 original size:70 final size:68
Alignment explanation
Indices: 537294--537432 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 68
537284 AACACTAAAA
* *
537294 AAATTTGAATTTTTTTCTCGAGAAAAGGGGGATGTCGATCATTTGATCGCCAACACCAAAAAAAT
1 AAATTTGAATTTTTTTCTCGAGAAAAGAGGGATGTCGACCATTTGATCGCCAACACCAAAAAAAT
537359 TTG
66 TTG
* * *
537362 AAATTTGAAATTTTTTTTCTCGAGAAAAGAGGG-TGTCGGCCATTTGATGGCCAATACCAAAAAA
1 AAATTTG-AA-TTTTTTTCTCGAGAAAAGAGGGATGTCGACCATTTGATCGCCAACACCAAAAAA
537426 ATTTG
64 ATTTG
537431 AA
1 AA
537433 TTTTTTTCTC
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
68 7 0.11
69 36 0.56
70 21 0.33
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (68 bp):
AAATTTGAATTTTTTTCTCGAGAAAAGAGGGATGTCGACCATTTGATCGCCAACACCAAAAAAAT
TTG
Found at i:537590 original size:55 final size:55
Alignment explanation
Indices: 537452--537578 Score: 173
Period size: 55 Copynumber: 2.3 Consensus size: 55
537442 CGAGAAATAG
*
537452 GGCCAACACCCAAAAATATAATTTTTTTTGAAATAGGGGGTGTCGGCCATCAAAT
1 GGCCAACACCCAAAAATATAATTTTTTTTGAAATAGGGGGTGTCGACCATCAAAT
* * * ** ***
537507 AGTCGACACCCAAAAATGCAATTTTTTTTGAAATAGGGGGTGTCGACCATTTGAT
1 GGCCAACACCCAAAAATATAATTTTTTTTGAAATAGGGGGTGTCGACCATCAAAT
537562 GGCCAACACCCAAAAAT
1 GGCCAACACCCAAAAAT
537579 TTTAAATTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (55 bp):
GGCCAACACCCAAAAATATAATTTTTTTTGAAATAGGGGGTGTCGACCATCAAAT
Found at i:540495 original size:13 final size:13
Alignment explanation
Indices: 540477--540502 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
540467 ACTTTAACTT
540477 TCACCATTTATAC
1 TCACCATTTATAC
540490 TCACCATTTATAC
1 TCACCATTTATAC
540503 ATTACGTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
TCACCATTTATAC
Found at i:549528 original size:29 final size:30
Alignment explanation
Indices: 549493--549552 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
549483 TGAAAGAAAC
*
549493 TTAACAGCTT-AGTGGCTTAA-AAAAACTTT
1 TTAACAG-TTCAGTGACTTAACAAAAACTTT
549522 TTAACAGTTCAGTGACTTAACTAAAAACTTT
1 TTAACAGTTCAGTGACTTAAC-AAAAACTTT
549553 CGAATAGTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 2 0.07
29 16 0.59
31 9 0.33
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (30 bp):
TTAACAGTTCAGTGACTTAACAAAAACTTT
Found at i:560452 original size:14 final size:14
Alignment explanation
Indices: 560421--560454 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
560411 TTGACAGGGT
*
560421 TTTTTTTTTTAATA
1 TTTTATTTTTAATA
560435 -TTTATTTTTAATA
1 TTTTATTTTTAATA
560448 TTTTATT
1 TTTTATT
560455 ACTCTTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTAATA
Found at i:563991 original size:12 final size:12
Alignment explanation
Indices: 563976--564000 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
563966 TAGGTTTTGC
563976 TATTTGTTTAAG
1 TATTTGTTTAAG
563988 TATTTGTTTAAG
1 TATTTGTTTAAG
564000 T
1 T
564001 TTGAAGACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TATTTGTTTAAG
Found at i:564522 original size:17 final size:17
Alignment explanation
Indices: 564502--564561 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
564492 TTTAAAATGG
*
564502 ATTTAAATTTATTTTAA
1 ATTTAAATTTAATTTAA
** *
564519 ATTTAAATTTGCTCTAA
1 ATTTAAATTTAATTTAA
* *
564536 ATTTAAGTTTAATTGAA
1 ATTTAAATTTAATTTAA
564553 ATTTAAATT
1 ATTTAAATT
564562 GATATTAACC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTAATTTAA
Found at i:565428 original size:12 final size:12
Alignment explanation
Indices: 565407--565437 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
565397 AATATAATAT
*
565407 TAATATTTTTAA
1 TAATAATTTTAA
565419 TAATAATTTTAA
1 TAATAATTTTAA
565431 TAATAAT
1 TAATAAT
565438 AAAAAAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATTTTAA
Found at i:565434 original size:15 final size:15
Alignment explanation
Indices: 565378--565439 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
565368 AATAACAGTT
*
565378 ATAAGTTTTAATAGTA
1 ATAA-TTTTAATAATA
* * *
565394 ATAAATATAATATTA
1 ATAATTTTAATAATA
565409 AT-ATTTT--TAATA
1 ATAATTTTAATAATA
565421 ATAATTTTAATAATA
1 ATAATTTTAATAATA
565436 ATAA
1 ATAA
565440 AAAAGAGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
12 6 0.16
13 5 0.14
14 3 0.08
15 19 0.51
16 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATAATTTTAATAATA
Found at i:566426 original size:29 final size:28
Alignment explanation
Indices: 566390--566500 Score: 125
Period size: 29 Copynumber: 3.8 Consensus size: 28
566380 CCTTAAACTA
566390 TTCAAAAATTATATTTTGACCCCAAAAC
1 TTCAAAAATTATATTTTGACCCCAAAAC
* *
566418 TTCTAAAAATTATATTTTGACCTCGAAAC
1 TTC-AAAAATTATATTTTGACCCCAAAAC
* *
566447 TACCAAAAATTACTATTTTGACCCAAAAAC
1 T-TCAAAAATTA-TATTTTGACCCCAAAAC
*
566477 TTCCAAAATTCCAT-TTTTGACCCC
1 TTCAAAAATT--ATATTTTGACCCC
566501 GATTTTACCA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
28 3 0.04
29 48 0.70
30 17 0.25
31 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (28 bp):
TTCAAAAATTATATTTTGACCCCAAAAC
Found at i:566495 original size:59 final size:59
Alignment explanation
Indices: 566392--566762 Score: 275
Period size: 59 Copynumber: 6.4 Consensus size: 59
566382 TTAAACTATT
* * * **
566392 CAAAAATTA-TATTTTGACCCCAAAAC-TTCTAAAAATT--ATATTTTGACCTCGAAACTAC
1 CAAAAATTACTATTTT-ACCCCAAAACTTTC-CAAAATTCCAT-TTTTAACCCCGAATTTAC
* * *
566450 CAAAAATTACTATTTTGACCCAAAAAC-TTCCAAAATTCCATTTTTGACCCCGATTTTAC
1 CAAAAATTACTATTTT-ACCCCAAAACTTTCCAAAATTCCATTTTTAACCCCGAATTTAC
* * * *
566509 CAAAAATAACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCG-ATTTCAC
1 CAAAAATTACTATTTTACCCCAAAACTTTCCAAAATTCCATTTTTAACCCCGAATTT-AC
* * * *
566568 CAAAAAATACTACTTTACCCCCAAACTTTCCAAAA-TCCTATTTTTAACCTCG-ATTTCAC
1 CAAAAATTACTATTTTACCCCAAAACTTTCCAAAATTCC-ATTTTTAACCCCGAATTT-AC
* * * *
566627 TAAAAATTACCATTTTACCCC-GAACTTTCCAAAA-TCTCATTTTTTAACCTC-AATTTCAC
1 CAAAAATTACTATTTTACCCCAAAACTTTCCAAAATTC-CA-TTTTTAACCCCGAATTT-AC
* * * ** * * * *
566686 CAAAAATTACCA-TTT--CCCTAAACTTTTCAAAATTTAAATTTTGACCTCGATTTTAC
1 CAAAAATTACTATTTTACCCCAAAACTTTCCAAAATTCCATTTTTAACCCCGAATTTAC
* *
566742 CAAAAATTACCATTTTGCCCC
1 CAAAAATTACTATTTTACCCC
566763 CAGACGTCCA
Statistics
Matches: 266, Mismatches: 32, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
56 26 0.10
57 19 0.07
58 48 0.18
59 171 0.64
60 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (59 bp):
CAAAAATTACTATTTTACCCCAAAACTTTCCAAAATTCCATTTTTAACCCCGAATTTAC
Found at i:566511 original size:29 final size:28
Alignment explanation
Indices: 566479--566572 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 28
566469 CCAAAAACTT
566479 CCAAAATTCCATTTTTGACCCCGATTTTA
1 CCAAAATTCCATTTTT-ACCCCGATTTTA
* * *
566508 CCAAAAATAACCA-TTTTACCCCCAAACTTT-
1 CC-AAAAT-TCCATTTTTA-CCCC-GATTTTA
* *
566538 CTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAATTCCATTTTT-ACCCCGATTTTA
566567 CCAAAA
1 CCAAAA
566573 AATACTACTT
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
28 6 0.12
29 21 0.43
30 15 0.31
31 7 0.14
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (28 bp):
CCAAAATTCCATTTTTACCCCGATTTTA
Found at i:566542 original size:118 final size:116
Alignment explanation
Indices: 566392--566764 Score: 370
Period size: 118 Copynumber: 3.2 Consensus size: 116
566382 TTAAACTATT
* * * **
566392 CAAAAATTA-TATTTTGACCCCAAAAC-TTCTAAAAATT-ATATTTTGACCTCGAAACT-ACCAA
1 CAAAAATTACCATTTT-ACCCCCAAACTTTCT-AAAATTCAT-TTTTAACCTCGAATTTCACCAA
*
566453 AAATTACTATTTTGACCCAAAAAC-TTCCAAAATTCCATTTTTGACCCCGATTTTAC
63 AAATTACTA-TTT-ACCC-AAAACTTTCCAAAATTCCATTTTTGACCTCGATTTTAC
* *
566509 CAAAAATAACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCG-ATTTCACCAAAA
1 CAAAAATTACCATTTTACCCCCAAACTTTCTAAAATT-CATTTTTAACCTCGAATTTCACCAAAA
* * * *
566573 AATACTACTTTACCCCCAAACTTTCCAAAA-TCCTATTTTTAACCTCGATTTCAC
65 ATTACTA-TTTA-CCCAAAACTTTCCAAAATTCC-ATTTTTGACCTCGATTTTAC
* * *
566627 TAAAAATTACCATTTTA-CCCCGAACTTTCCAAAATCTCATTTTTTAACCTC-AATTTCACCAAA
1 CAAAAATTACCATTTTACCCCCAAACTTTCTAAAAT-TCA-TTTTTAACCTCGAATTTCACCAAA
* * * ** *
566690 AATTACCATTT-CCCTAAACTTTTCAAAATTTAAATTTTGACCTCGATTTTAC
64 AATTACTATTTACCCAAAACTTTCCAAAATTCCATTTTTGACCTCGATTTTAC
*
566742 CAAAAATTACCATTTTGCCCCCA
1 CAAAAATTACCATTTTACCCCCA
566765 GACGTCCAGA
Statistics
Matches: 213, Mismatches: 30, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
115 47 0.22
116 5 0.02
117 54 0.25
118 105 0.49
119 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (116 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCATTTTTAACCTCGAATTTCACCAAAAA
TTACTATTTACCCAAAACTTTCCAAAATTCCATTTTTGACCTCGATTTTAC
Found at i:566660 original size:58 final size:58
Alignment explanation
Indices: 566448--566762 Score: 311
Period size: 59 Copynumber: 5.4 Consensus size: 58
566438 CCTCGAAACT
* * * * *
566448 ACCAAAAATTACTATTTTGACCCAAAAAC-TTCCAAAATTCC-ATTTTTGACCCCGATTTT
1 ACCAAAAATTACCATTTT-ACCC-CAAACTTTCCAAAA-TCCTATTTTTAACCTCGATTTC
* * *
566507 ACCAAAAATAACCATTTTACCCCCAAACTTTCTAAAATTCC-ATTTTTAACCCCGATTTC
1 ACCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAA-TCCTATTTTTAACCTCGATTTC
* * *
566566 ACCAAAAAATACTACTTTACCCCCAAACTTTCCAAAATCCTATTTTTAACCTCGATTTC
1 ACCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATCCTATTTTTAACCTCGATTTC
* * *
566625 ACTAAAAATTACCATTTTACCCCGAACTTTCCAAAAT-CTCATTTTTTAACCTCAATTTC
1 ACCAAAAATTACCATTTTACCCCAAACTTTCCAAAATCCT-A-TTTTTAACCTCGATTTC
* * * * * *
566684 ACCAAAAATTACCA-TTT-CCCTAAACTTTTCAAAAT-TTAAATTTTGACCTCGATTTT
1 ACCAAAAATTACCATTTTACCCCAAACTTTCCAAAATCCT-ATTTTTAACCTCGATTTC
*
566740 ACCAAAAATTACCATTTTGCCCC
1 ACCAAAAATTACCATTTTACCCC
566763 CAGACGTCCA
Statistics
Matches: 220, Mismatches: 29, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
56 27 0.12
57 22 0.10
58 32 0.15
59 139 0.63
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
ACCAAAAATTACCATTTTACCCCAAACTTTCCAAAATCCTATTTTTAACCTCGATTTC
Found at i:579247 original size:200 final size:200
Alignment explanation
Indices: 578904--579700 Score: 1159
Period size: 200 Copynumber: 4.0 Consensus size: 200
578894 AACAATCAGT
* * *
578904 GAGGCGGTAATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAA-AGCAAGCAAA
1 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACA-CGAGCAAA
* * * * *
578968 TCTTCGAACCCAACTTCCTGATAAGACACTGAGAAGTAGGTCGAAACAATAAAATGGTTAGCTTC
65 TCTTCAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
* *
579033 CTGATGAGATACAGAGAAGTGGACCAAATTTGTCTCCCTGAGGAGATCCAGAGAAGCAAATTAAA
130 CTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAA
579098 ACAACA
195 ACAACA
* * * *
579104 GAGGCGGTCATCTTCCTGATGAGATCCAGAGAAGAATACTAACTCAACGCTCAACACGAGCCAAT
1 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCAAAT
** * * *
579169 CTTCGTACCCAGCTTCCTGACGAGACACTGAGAAGCAGGTTGAAGTAATAAAATGGTTAGCTTCC
66 CTTCAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* * *
579234 TGATGAGATACAGAAAAGTGGACCAAATTTGTCTTCCTGAGGAGATTCAGAGAAGCAAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
579299 CAACA
196 CAACA
* *
579304 GAGGTGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
1 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCAAAT
*
579369 CTTCATACCC-GACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
66 CTTCAAACCCAG-CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
* * *
579433 CTGATGAGACACAGAGAAGTGGACCAAATTCATCTTCCTGAGGAGATCCAGAGAAGCGAATTAAA
130 CTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAA
579498 ACAAGC-
195 ACAA-CA
* * * * **
579504 GAGGTGACCATCTTCTTGATGAGACACAGAGAAGAATACCAACTCAACGCTCAATGCGAGCAAAT
1 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCAAAT
* * * *
579569 CTTCAAACCCAGCTTCCTGATGAGACATTGAGAAGTAGGTCGAAGAAATAAAAAGGTTAGCTTCC
66 CTTCAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* * * * *
579634 TGATGAGATAAAAAGAAGTGGACCGAATTCGTCTTCTTGAGGAGATCCAGAGAAGCGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
579699 CA
196 CA
579701 GATAATTATG
Statistics
Matches: 546, Mismatches: 47, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
199 1 0.00
200 542 0.99
201 3 0.01
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (200 bp):
GAGGCGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCAAAT
CTTCAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
CAACA
Found at i:581038 original size:12 final size:12
Alignment explanation
Indices: 581017--581047 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
581007 AATATAATAT
*
581017 TAATATTTTTAA
1 TAATAATTTTAA
581029 TAATAATTTTAA
1 TAATAATTTTAA
581041 TAATAAT
1 TAATAAT
581048 AAAAAAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATTTTAA
Found at i:581044 original size:15 final size:15
Alignment explanation
Indices: 580988--581049 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
580978 AATAACAGTT
*
580988 ATAAGTTTTAATAGTA
1 ATAA-TTTTAATAATA
* * *
581004 ATAAATATAATATTA
1 ATAATTTTAATAATA
581019 AT-ATTTT--TAATA
1 ATAATTTTAATAATA
581031 ATAATTTTAATAATA
1 ATAATTTTAATAATA
581046 ATAA
1 ATAA
581050 AAAAGAGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
12 6 0.16
13 5 0.14
14 3 0.08
15 19 0.51
16 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATAATTTTAATAATA
Found at i:582115 original size:29 final size:29
Alignment explanation
Indices: 582005--582157 Score: 139
Period size: 30 Copynumber: 5.1 Consensus size: 29
581995 TAAACTATTC
** *
582005 AAAAATTATATTTTGACCTTAAAACTTTTT
1 AAAAATTATATTTTGACCCCAAAAC-TTCT
* * *
582035 AAAAATTACACTTTGACCCTC-GAACTCCTCT
1 AAAAATTATATTTTGACCC-CAAAACT--TCT
* *
582066 -GAAATTACATTTTTGACCCCAAAACTTCT
1 AAAAATTATA-TTTTGACCCCAAAACTTCT
* *
582095 AAAAATTATATTTTGACCCCAAAACTACC
1 AAAAATTATATTTTGACCCCAAAACTTCT
*
582124 AAAAATTACTATTTTGACCCCAAAACTTCC
1 AAAAATTA-TATTTTGACCCCAAAACTTCT
582154 AAAA
1 AAAA
582158 TTCCATTTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
29 29 0.28
30 59 0.58
31 14 0.14
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAAATTATATTTTGACCCCAAAACTTCT
Found at i:582156 original size:30 final size:30
Alignment explanation
Indices: 582067--582157 Score: 141
Period size: 30 Copynumber: 3.1 Consensus size: 30
582057 AACTCCTCTG
*
582067 AAATTAC-ATTTTTGACCCCAAAACTTCTAA
1 AAATTACTA-TTTTGACCCCAAAACTTCCAA
*
582097 AAATTA-TATTTTGACCCCAAAACTACCAA
1 AAATTACTATTTTGACCCCAAAACTTCCAA
582126 AAATTACTATTTTGACCCCAAAACTTCCAA
1 AAATTACTATTTTGACCCCAAAACTTCCAA
582156 AA
1 AA
582158 TTCCATTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
29 25 0.45
30 31 0.55
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.30
Consensus pattern (30 bp):
AAATTACTATTTTGACCCCAAAACTTCCAA
Found at i:582158 original size:29 final size:30
Alignment explanation
Indices: 582067--582172 Score: 132
Period size: 29 Copynumber: 3.6 Consensus size: 30
582057 AACTCCTCTG
*
582067 AAATTAC-ATTTTTGACCCCAAAACTTCTAA
1 AAATTACTATTTTTGACCCCAAAACTTC-CA
*
582097 AAATTA-TA-TTTTGACCCCAAAACTACCAA
1 AAATTACTATTTTTGACCCCAAAACTTCC-A
582126 AAATTACTA-TTTTGACCCCAAAACTTCCA
1 AAATTACTATTTTTGACCCCAAAACTTCCA
*
582155 AAATT-CCATTTTTGACCC
1 AAATTACTATTTTTGACCC
582173 TGATTTCACC
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.03
29 39 0.57
30 27 0.40
ACGTcount: A:0.39, C:0.25, G:0.04, T:0.32
Consensus pattern (30 bp):
AAATTACTATTTTTGACCCCAAAACTTCCA
Found at i:582168 original size:59 final size:59
Alignment explanation
Indices: 582067--582250 Score: 157
Period size: 59 Copynumber: 3.1 Consensus size: 59
582057 AACTCCTCTG
*
582067 AAATTACATTTTTGACCCCAAAACTTCTAAAAATT--ATATTTTGACCCCAAAACT-ACCAA
1 AAATTACA-TTTTGACCCCAAAACTTC-CAAAATTCCAT-TTTTGACCCCAAAACTCACCAA
** **
582126 AAATTACTATTTTGACCCCAAAACTTCCAAAATTCCATTTTTGA-CCCTGATTTCACCAA
1 AAATTAC-ATTTTGACCCCAAAACTTCCAAAATTCCATTTTTGACCCCAAAACTCACCAA
* * * * **
582185 AAATCACCATTTT-ACCGCC-GAACTTTCCAAAATTCCATTTTTAACCCC-GATTTCACCAA
1 AAATTA-CATTTTGACC-CCAAAAC-TTCCAAAATTCCATTTTTGACCCCAAAACTCACCAA
582244 AAATTAC
1 AAATTAC
582251 CACTTTACCT
Statistics
Matches: 108, Mismatches: 9, Indels: 17
0.81 0.07 0.13
Matches are distributed among these distances:
58 18 0.17
59 83 0.77
60 7 0.06
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (59 bp):
AAATTACATTTTGACCCCAAAACTTCCAAAATTCCATTTTTGACCCCAAAACTCACCAA
Found at i:582258 original size:59 final size:58
Alignment explanation
Indices: 582150--582275 Score: 198
Period size: 59 Copynumber: 2.2 Consensus size: 58
582140 ACCCCAAAAC
* * *
582150 TTCCAAAATTCCATTTTTGACCCTGATTTCACCAAAAATCACCATTTTACCGCCGAACT
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATCACCACTTTACC-CCGAACT
* *
582209 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCACTTTACCTCGAACT
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATCACCACTTTACCCCGAACT
582267 TTCCAAAAT
1 TTCCAAAAT
582276 CCCAAAAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
58 15 0.24
59 47 0.76
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (58 bp):
TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATCACCACTTTACCCCGAACT
Found at i:582272 original size:29 final size:29
Alignment explanation
Indices: 582122--582274 Score: 90
Period size: 29 Copynumber: 5.2 Consensus size: 29
582112 CCCAAAACTA
* *
582122 CCAAAAATTACTATTTTGACCCCAAAAC-TT
1 CCAAAAATTACCATTTT-ACCCC-GAACTTT
*
582152 CC-AAAATT-CCATTTTTGACCCTG-A-TTT
1 CCAAAAATTACCA-TTTT-ACCCCGAACTTT
*
582179 CACCAAAAATCACCATTTTACCGCCGAACTTT
1 --CCAAAAATTACCATTTTACC-CCGAACTTT
582211 CC-AAAATT-CCATTTTTAACCCCG-A-TTT
1 CCAAAAATTACCA-TTTT-ACCCCGAACTTT
* *
582238 CACCAAAAATTACCACTTTACCTCGAACTTT
1 --CCAAAAATTACCATTTTACCCCGAACTTT
582269 CCAAAA
1 CCAAAA
582275 TCCCAAAAAT
Statistics
Matches: 98, Mismatches: 8, Indels: 35
0.70 0.06 0.25
Matches are distributed among these distances:
27 6 0.06
28 6 0.06
29 45 0.46
30 28 0.29
31 10 0.10
32 3 0.03
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.31
Consensus pattern (29 bp):
CCAAAAATTACCATTTTACCCCGAACTTT
Found at i:582302 original size:37 final size:37
Alignment explanation
Indices: 582240--582313 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
582230 CCCGATTTCA
582240 CCAAAAATTACCACTTTACCTCGAACTTTCCAAAATC
1 CCAAAAATTACCACTTTACCTCGAACTTTCCAAAATC
*
582277 CCAAAAATTACCATTTTATCC-CGAACTTTCCAAAATC
1 CCAAAAATTACCACTTTA-CCTCGAACTTTCCAAAATC
582314 TCATTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 33 0.94
38 2 0.06
ACGTcount: A:0.38, C:0.31, G:0.03, T:0.28
Consensus pattern (37 bp):
CCAAAAATTACCACTTTACCTCGAACTTTCCAAAATC
Found at i:582341 original size:155 final size:156
Alignment explanation
Indices: 582113--582407 Score: 393
Period size: 155 Copynumber: 1.9 Consensus size: 156
582103 TATTTTGACC
* *
582113 CCAAAACTACCAAAAATTACTATTTTGACCCCAAAACTTCCAAAATTCCATTTTTGACCCTGATT
1 CCAAAACTACCAAAAATTACCATTTTGACCCCAAAACTTCCAAAATTCCATTTTTGAACCTGATT
* * *
582178 TCACCAAAAATCACCATTTTACCGC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
66 TCACCAAAAATCACCA-TTTACCCCTCAAACTTTCCAAAATTCAATTTTTAACCCCGATTTCACC
582242 AAAAATTACCACTTTACCTCGAACTTT
130 AAAAATTACCACTTTACCTCGAACTTT
* * * *
582269 CCAAAA-TCCCAAAAATTACCATTTT-ATCCC-GAACTTTCCAAAA-TCTCATTTTTTAACCTCG
1 CCAAAACTACCAAAAATTACCATTTTGACCCCAAAAC-TTCCAAAATTC-CATTTTTGAACCT-G
* * * * *
582330 ATTTCACCAAAAATTACCATTTCCCCCTCAAACTTTCCAAAATTCAATTTTTGACCTCGATTTTA
63 ATTTCACCAAAAATCACCATTTACCCCTCAAACTTTCCAAAATTCAATTTTTAACCCCGATTTCA
582395 CCAAAAATTACCA
128 CCAAAAATTACCA
582408 TTTTGCCCTC
Statistics
Matches: 121, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
153 5 0.04
154 29 0.24
155 81 0.67
156 6 0.05
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (156 bp):
CCAAAACTACCAAAAATTACCATTTTGACCCCAAAACTTCCAAAATTCCATTTTTGAACCTGATT
TCACCAAAAATCACCATTTACCCCTCAAACTTTCCAAAATTCAATTTTTAACCCCGATTTCACCA
AAAATTACCACTTTACCTCGAACTTT
Found at i:582345 original size:96 final size:96
Alignment explanation
Indices: 582181--582372 Score: 282
Period size: 96 Copynumber: 2.0 Consensus size: 96
582171 CCTGATTTCA
582181 CCAAAAATCACCATTTTACCGCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
1 CCAAAAATCACCATTTTACCGCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
*
582246 ATTACCACTTT-ACCTCGAACTTTCCAAAATC
66 ATTACCA-TTTCACCTCAAACTTTCCAAAATC
* * *
582277 CCAAAAATTACCATTTTATC-CCGAACTTTCCAAAA-TCTCATTTTTTAACCTCGATTTCACCAA
1 CCAAAAATCACCATTTTACCGCCGAACTTTCCAAAATTC-CA-TTTTTAACCCCGATTTCACCAA
*
582340 AAATTACCATTTCCCCCTCAAACTTTCCAAAAT
64 AAATTACCATTT-CACCTCAAACTTTCCAAAAT
582373 TCAATTTTTG
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
94 2 0.02
95 20 0.23
96 48 0.55
97 17 0.20
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (96 bp):
CCAAAAATCACCATTTTACCGCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
ATTACCATTTCACCTCAAACTTTCCAAAATC
Found at i:582412 original size:30 final size:30
Alignment explanation
Indices: 582319--582418 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 30
582309 AAATCTCATT
* *
582319 TTTTAACCTCGATTTCACCAAAAATTACCA
1 TTTTGACCTCGATTTTACCAAAAATTACCA
*** * * *
582349 TTTCCCCCTCAAACTTT-CC-AAAATT-CAA
1 TTTTGACCTC-GATTTTACCAAAAATTACCA
582377 TTTTTGACCTCGATTTTACCAAAAATTACCA
1 -TTTTGACCTCGATTTTACCAAAAATTACCA
*
582408 TTTTGCCCTCG
1 TTTTGACCTCG
582419 GGCGTCCAAA
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
28 6 0.12
29 15 0.29
30 25 0.49
31 5 0.10
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.36
Consensus pattern (30 bp):
TTTTGACCTCGATTTTACCAAAAATTACCA
Found at i:582417 original size:59 final size:60
Alignment explanation
Indices: 582277--582417 Score: 196
Period size: 59 Copynumber: 2.4 Consensus size: 60
582267 TTCCAAAATC
* * *
582277 CCAAAAATTACCATTTTATCC-CGAACTTTCCAAAATCTCATTTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATCTCAATTTTTAACCTCGATTTCA
** * *
582336 CCAAAAATTACCATTTCCCCCTCAAACTTTCCAAAAT-TCAATTTTTGACCTCGATTTTA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATCTCAATTTTTAACCTCGATTTCA
*
582395 CCAAAAATTACCATTTTGCCCTC
1 CCAAAAATTACCATTTTACCCTC
582418 GGGCGTCCAA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 58 0.81
60 14 0.19
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (60 bp):
CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATCTCAATTTTTAACCTCGATTTCA
Found at i:584089 original size:58 final size:58
Alignment explanation
Indices: 584003--584112 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
583993 GGGCCTGAAC
* * *
584003 CTTTTTTTGTCCAAGTTAGACTCTAAACTTGACAATTGT-TCTCACATTGGGGTCCAAA
1 CTTTTTTTGTCCAAGTTAGACCCTAAACTTAACAATTGTACCT-ACATTGGGGTCCAAA
*
584061 CTTTTTTTGTCCTAA-TTAGGCCCTAAACTTAACAATTGTACCTACATTGGGG
1 CTTTTTTTGTCC-AAGTTAGACCCTAAACTTAACAATTGTACCTACATTGGGG
584113 CTTGAGTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
58 42 0.91
59 4 0.09
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (58 bp):
CTTTTTTTGTCCAAGTTAGACCCTAAACTTAACAATTGTACCTACATTGGGGTCCAAA
Found at i:584902 original size:15 final size:14
Alignment explanation
Indices: 584863--584904 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
584853 TATAATGTTA
*
584863 AATTTAGTTTT-TT
1 AATTTATTTTTATT
*
584876 AATTTTTTTTTATT
1 AATTTATTTTTATT
584890 AATTTGATTTTTATT
1 AATTT-ATTTTTATT
584905 TTGATTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 9 0.38
14 7 0.29
15 8 0.33
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (14 bp):
AATTTATTTTTATT
Found at i:593136 original size:48 final size:48
Alignment explanation
Indices: 593080--593176 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
593070 GCTAACAAAG
* **
593080 GAAAACACTTTCTTTTGTTTCTTTGCTCAATTTCCTTTAAAAAAAAAT
1 GAAAACACTTTCTTTTGTTTCTTCGCTCAATTTCCTAGAAAAAAAAAT
593128 GAAAACACTTTCTTTTGTTTCTTCGCTCAATTTCCTAGAAAAAAAAAT
1 GAAAACACTTTCTTTTGTTTCTTCGCTCAATTTCCTAGAAAAAAAAAT
593176 G
1 G
593177 TTTCCCCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (48 bp):
GAAAACACTTTCTTTTGTTTCTTCGCTCAATTTCCTAGAAAAAAAAAT
Found at i:595541 original size:27 final size:30
Alignment explanation
Indices: 595483--595541 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
595473 AAAATTATTC
*
595483 ATAAATTTTGATTTGATGTGTAATATTATAT
1 ATAAATTTTGATTT-ATGTATAATATTATAT
* *
595514 ATAAATTTTTATTT-TGTATAATTTTATA
1 ATAAATTTTGATTTATGTATAATATTATA
595542 CATTAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.48
31 13 0.52
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (30 bp):
ATAAATTTTGATTTATGTATAATATTATAT
Found at i:595714 original size:27 final size:29
Alignment explanation
Indices: 595657--595711 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
595647 AAGTTTAATT
*
595657 TATATATTTAAACTGCAATTAAAATTTTA
1 TATATATTTAAACTGCAATCAAAATTTTA
595686 TATATATTTAAA-T-CAAATCAAAATTT
1 TATATATTTAAACTGC-AATCAAAATTT
595712 ATACATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 1 0.04
28 11 0.46
29 12 0.50
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (29 bp):
TATATATTTAAACTGCAATCAAAATTTTA
Found at i:596409 original size:19 final size:19
Alignment explanation
Indices: 596381--596420 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
596371 TCAATTTGAT
*
596381 TTTTATTCAAAATTTAATG
1 TTTTAGTCAAAATTTAATG
* *
596400 TTTTAGTCAACATTTATTG
1 TTTTAGTCAAAATTTAATG
596419 TT
1 TT
596421 ATACCTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (19 bp):
TTTTAGTCAAAATTTAATG
Found at i:600908 original size:6 final size:6
Alignment explanation
Indices: 600897--600936 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
600887 ACACCTCTCT
*
600897 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCT TCTT
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTT
600937 TTTGATTCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (6 bp):
TCTTCA
Found at i:601679 original size:25 final size:25
Alignment explanation
Indices: 601650--601701 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
601640 TGTTTATGGT
601650 TTGAGTTTAAGGTTT-GAGATTTATA
1 TTGAGTTTAAGGTTTCGA-ATTTATA
**
601675 TTGAGTTTTGGGTTTCGAATTTATA
1 TTGAGTTTAAGGTTTCGAATTTATA
601700 TT
1 TT
601702 TAAATAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.52
Consensus pattern (25 bp):
TTGAGTTTAAGGTTTCGAATTTATA
Found at i:602160 original size:23 final size:23
Alignment explanation
Indices: 602134--602295 Score: 94
Period size: 23 Copynumber: 6.9 Consensus size: 23
602124 TTTTTTTTAC
*
602134 TGTTTTGGTTGCTGTTTTGGTGT
1 TGTTTTGGTTGTTGTTTTGGTGT
** ** *
602157 TGTTGTTTTTTACTATTTTGGTTGT
1 TGTT-TTGGTTGTTGTTTTGG-TGT
**
602182 TGTTTTGG-TGTTGTTTTTACTGT
1 TGTTTTGGTTGTTG-TTTTGGTGT
**
602205 TGTTTTGG-TGTTGTTTTTACTGT
1 TGTTTTGGTTGTTG-TTTTGGTGT
* * * *
602228 TATTTTTGTTGTTATTTTGCTGT
1 TGTTTTGGTTGTTGTTTTGGTGT
* * * *
602251 TATTTTTGCTGCTGTTTTGGTTGT
1 TGTTTTGGTTGTTGTTTTGG-TGT
*
602275 TGTTTTGGTTGTTATTTTGGT
1 TGTTTTGGTTGTTGTTTTGGT
602296 TGTTTGGATG
Statistics
Matches: 110, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
23 63 0.57
24 40 0.36
25 7 0.06
ACGTcount: A:0.05, C:0.04, G:0.25, T:0.65
Consensus pattern (23 bp):
TGTTTTGGTTGTTGTTTTGGTGT
Found at i:602176 original size:36 final size:36
Alignment explanation
Indices: 602126--602196 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
602116 TTTGATGCTT
*
602126 TTTTTTACTGTTTTGGTTGCTGTTTTGGTGTTGTTG
1 TTTTTTACTATTTTGGTTGCTGTTTTGGTGTTGTTG
*
602162 TTTTTTACTATTTTGGTTGTTGTTTTGGTGTTGTT
1 TTTTTTACTATTTTGGTTGCTGTTTTGGTGTTGTT
602197 TTTACTGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.04, C:0.04, G:0.25, T:0.66
Consensus pattern (36 bp):
TTTTTTACTATTTTGGTTGCTGTTTTGGTGTTGTTG
Found at i:602209 original size:59 final size:59
Alignment explanation
Indices: 602143--602299 Score: 185
Period size: 58 Copynumber: 2.7 Consensus size: 59
602133 CTGTTTTGGT
** * * *
602143 TGCTGTTTTGGTGTTGTTGTTTTTTACTATTTTGGTTGTTGTTTTGGTGTTGTTTTTAC
1 TGCTGTTTTGGTGTTGTTGTTTTTTGTTATTTTGGTTGTTATTTTGCTGTTATTTTTAC
* ** * *
602202 TGTTGTTTTGGTGTTGTT-TTTACTGTTATTTTTGTTGTTATTTTGCTGTTATTTTTGC
1 TGCTGTTTTGGTGTTGTTGTTTTTTGTTATTTTGGTTGTTATTTTGCTGTTATTTTTAC
602260 TGCTGTTTT-G-GTTGTTGTTTTGGTTGTTATTTTGGTTGTT
1 TGCTGTTTTGGTGTTGTTGTTTT--TTGTTATTTTGGTTGTT
602300 TGGATGTTAT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
56 6 0.07
57 4 0.05
58 39 0.48
59 32 0.40
ACGTcount: A:0.05, C:0.04, G:0.25, T:0.66
Consensus pattern (59 bp):
TGCTGTTTTGGTGTTGTTGTTTTTTGTTATTTTGGTTGTTATTTTGCTGTTATTTTTAC
Found at i:602246 original size:35 final size:35
Alignment explanation
Indices: 602172--602300 Score: 88
Period size: 35 Copynumber: 3.7 Consensus size: 35
602162 TTTTTTACTA
* * * **
602172 TTTTGGTTGTTGTTTTGGTGTTGTTTTTACTGTTG
1 TTTTTGTTGTTATTTTGCTGTTGTTTTTGTTGTTG
* *
602207 TTTTGGTGTTG-T-TTTTACTGTTATTTTTGTTGTT-
1 TTTT--TGTTGTTATTTTGCTGTTGTTTTTGTTGTTG
* * * *
602241 ATTTTGCTGTTATTTTTGCTGCTGTTTTGGTTGTTG
1 TTTTTGTTGTTA-TTTTGCTGTTGTTTTTGTTGTTG
*
602277 TTTTGGTTGTTATTTTG--GTTGTTT
1 TTTTTGTTGTTATTTTGCTGTTGTTT
602301 GGATGTTATT
Statistics
Matches: 72, Mismatches: 16, Indels: 14
0.71 0.16 0.14
Matches are distributed among these distances:
32 4 0.06
33 7 0.10
34 3 0.04
35 44 0.61
36 10 0.14
37 4 0.06
ACGTcount: A:0.05, C:0.04, G:0.25, T:0.67
Consensus pattern (35 bp):
TTTTTGTTGTTATTTTGCTGTTGTTTTTGTTGTTG
Found at i:602281 original size:12 final size:12
Alignment explanation
Indices: 602134--602299 Score: 108
Period size: 12 Copynumber: 14.1 Consensus size: 12
602124 TTTTTTTTAC
*
602134 TGTTTTGGTTGC
1 TGTTTTGGTTGT
602146 TGTTTTGGTGTTGT
1 TGTTTT-G-GTTGT
**
602160 TGTTTT--TTAC
1 TGTTTTGGTTGT
*
602170 TATTTTGGTTGT
1 TGTTTTGGTTGT
602182 TGTTTTGG-TGT
1 TGTTTTGGTTGT
***
602193 TGTTTTTACTGT
1 TGTTTTGGTTGT
602205 TGTTTTGG-TGT
1 TGTTTTGGTTGT
***
602216 TGTTTTTACTGT
1 TGTTTTGGTTGT
* *
602228 TATTTTTGTTGT
1 TGTTTTGGTTGT
* *
602240 TATTTT-GCTGT
1 TGTTTTGGTTGT
* * * *
602251 TATTTTTGCTGC
1 TGTTTTGGTTGT
602263 TGTTTTGGTTGT
1 TGTTTTGGTTGT
602275 TGTTTTGGTTGT
1 TGTTTTGGTTGT
*
602287 TATTTTGGTTGT
1 TGTTTTGGTTGT
602299 T
1 T
602300 TGGATGTTAT
Statistics
Matches: 124, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.06
11 28 0.23
12 78 0.63
13 1 0.01
14 10 0.08
ACGTcount: A:0.05, C:0.04, G:0.25, T:0.66
Consensus pattern (12 bp):
TGTTTTGGTTGT
Found at i:602313 original size:21 final size:21
Alignment explanation
Indices: 602273--602312 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
602263 TGTTTTGGTT
*
602273 GTTGTTTTGGTTGTTATTTTG
1 GTTGTTTTGGATGTTATTTTG
602294 GTTG-TTTGGATGTTATTTT
1 GTTGTTTTGGATGTTATTTT
602313 TATACGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.07, C:0.00, G:0.28, T:0.65
Consensus pattern (21 bp):
GTTGTTTTGGATGTTATTTTG
Found at i:606611 original size:2 final size:2
Alignment explanation
Indices: 606597--606632 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
606587 AACCGACAAA
*
606597 AC AC AC A- AA AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
606633 TATATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:606637 original size:2 final size:2
Alignment explanation
Indices: 606632--606662 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
606622 ACACACACAC
606632 AT 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 AT A
606663 CACATCCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:609372 original size:18 final size:18
Alignment explanation
Indices: 609349--609385 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
609339 CACAACTTTA
609349 TCTTTTACATTAAACTTC
1 TCTTTTACATTAAACTTC
609367 TCTTTTACATTAAACTTC
1 TCTTTTACATTAAACTTC
609385 T
1 T
609386 ATATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (18 bp):
TCTTTTACATTAAACTTC
Found at i:614053 original size:29 final size:30
Alignment explanation
Indices: 613988--614063 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
613978 ATCTCAAAAC
*
613988 TATACATGAATTATGATTTAATATGCAATTG
1 TATACATGAATTTTGATTT-ATATGCAATTG
* *
614019 TATACATGAATTTTGATTT-TGTGCAATTT
1 TATACATGAATTTTGATTTATATGCAATTG
*
614048 TATACATAAAATTTTG
1 TATACAT-GAATTTTG
614064 GTTTGATCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.38
30 7 0.17
31 18 0.45
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.46
Consensus pattern (30 bp):
TATACATGAATTTTGATTTATATGCAATTG
Found at i:614068 original size:29 final size:29
Alignment explanation
Indices: 614011--614068 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
614001 TGATTTAATA
* *
614011 TGCAATTGTATACATGAATTTTGATTTTG
1 TGCAATTGTATACATAAATTTTGAGTTTG
*
614040 TGCAATTTTATACATAAAATTTTG-GTTTG
1 TGCAATTGTATACAT-AAATTTTGAGTTTG
614069 ATCCAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (29 bp):
TGCAATTGTATACATAAATTTTGAGTTTG
Found at i:616847 original size:3 final size:3
Alignment explanation
Indices: 616839--616864 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
616829 ATAAAAAGAA
616839 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
616865 ATAAAAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:632510 original size:2 final size:2
Alignment explanation
Indices: 632503--632528 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
632493 CAGCTCAAGG
632503 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
632529 CATACAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:633295 original size:126 final size:124
Alignment explanation
Indices: 632889--633423 Score: 526
Period size: 126 Copynumber: 4.3 Consensus size: 124
632879 TTTTAAAGCT
* * * * *
632889 AATTCATGAATGAATTTA-AAAAAAAGGGTTTTCTTTTG-TTTTCT-CATATATTTGTTTTGAAA
1 AATTCATGAATAAAATTATTAAAAAAGGGTTTTCTCTTGTTTTTTTCCATATATTTG-TTTGAAA
* * * * * *
632951 TTCATGACTG--TTTTTTTAAAAAGGGTTTTCTCTCTCTTTTTTTTCTTCATATATTTGCTTTGA
65 TTCATGAATGAAATTATTTAAAAAAGG--TT-T-TCTCTTGTTTTT-TTCATATATTTGTTTTGA
* * *
633014 GATTCATGAATGAAATTATTTTTTTAAAAAAAGGGTTTTCTCTT-TTTTTTT-C---T-TGT-TT
1 AATTCATGAAT-AAA--A--TTATT-AAAAAAGGGTTTTCTCTTGTTTTTTTCCATATATTTGTT
** *
633072 TGAAATTCATGAATTTAATTA-TTAAAAAAGGTTTTCTCTTGTTTTTTTTCATATATTTGTTCTG
60 TGAAATTCATGAATGAAATTATTTAAAAAAGGTTTTCTCTTG-TTTTTTTCATATATTTGTTTTG
633136 A
124 A
* *
633137 AATTCATGAATAAAATTACTAAAAAGAAGGTTTTCTCTTGTTTTTTTCCATATATTTGCTTTGAA
1 AATTCATGAATAAAATTATTAAAAA-AGGGTTTTCTCTTGTTTTTTTCCATATATTTG-TTTGAA
* *
633202 ATTCATGAATGAAATTATTGTAGAAAAGTGTTTTCTCTTG-TTCTTTCATAT-TTT-TTTTGA
64 ATTCATGAATGAAATTATT-TAAAAAAG-GTTTTCTCTTGTTTTTTTCATATATTTGTTTTGA
* * *
633262 AATCCATGAATGAAATTATGTTAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTTTAGA
1 AATTCATGAATAAAATTA--TTAAAAAAGGGTTTTCTCTTGTTTTTTTCCATATATTTGTTT-GA
* *
633327 AATTCATGAATGAAATTATTAAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTTTAGA
63 AATTCATGAATGAAATTATTTAAAAAA-GGTTTTCTCTTG-TTTTTTTCATATATTTGTTTTGA
633391 AATTCATGAATAAAATTATTAAAAAAGGGTTTT
1 AATTCATGAATAAAATTATTAAAAAAGGGTTTT
633424 TTCCCATTTT
Statistics
Matches: 342, Mismatches: 37, Indels: 60
0.78 0.08 0.14
Matches are distributed among these distances:
117 5 0.01
118 15 0.04
119 7 0.02
120 2 0.01
122 3 0.01
123 33 0.10
124 8 0.02
125 52 0.15
126 94 0.27
127 51 0.15
128 14 0.04
129 33 0.10
130 2 0.01
132 23 0.07
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (124 bp):
AATTCATGAATAAAATTATTAAAAAAGGGTTTTCTCTTGTTTTTTTCCATATATTTGTTTGAAAT
TCATGAATGAAATTATTTAAAAAAGGTTTTCTCTTGTTTTTTTCATATATTTGTTTTGA
Found at i:633336 original size:190 final size:183
Alignment explanation
Indices: 632893--633423 Score: 593
Period size: 190 Copynumber: 2.9 Consensus size: 183
632883 AAAGCTAATT
* * * *
632893 CATGAATGAATTTA-AAAAAAAGGGTTTTCT-TT-TGTTTTCTCATATATTTGTTTTGAAATTCA
1 CATGAATGAAATTATTAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTG-TTTGAAATTCA
* *** * * *
632955 TGACTGTTTTTTTAAAAAG--GGTTTTCTCTCTCTTTTTTTTCTTCATATATTTGCTTTGAGATT
65 TGAATAAATTATTAAAAAGAAGGTTTTCTCT-T-GTTTTTTTC--CATATATTTGCTTTGAAATT
* *
633018 CATGAATGAAATTATTTTTTTAAAAAAAGGGTTTTCTCTTTTTTTTTCTTGTTTTGAAATT
126 CATGAATGAAATTA---TTGTAAAAAAAGGGTTTTCTCTTTTTTTTTCTTGTTTTGAAATC
**
633079 CATGAATTTAATTATTAAAAAA-GGTTTTCTCTTGTTTTTTTTCATATATTTGTTCTGAAATTCA
1 CATGAATGAAATTATTAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTT-TGAAATTCA
*
633143 TGAATAAAATTACTAAAAAGAAGGTTTTCTCTTGTTTTTTTCCATATATTTGCTTTGAAATTCAT
65 TGAAT-AAATTATTAAAAAGAAGGTTTTCTCTTGTTTTTTTCCATATATTTGCTTTGAAATTCAT
* * *
633208 GAATGAAATTATTGT-AGAAAAGTGTTTTCTCTTGTTCTTTCATAT-TTTTTTTGAAATC
129 GAATGAAATTATTGTAAAAAAAGGGTTTTCTCTT-TT-TTT--T-TCTTGTTTTGAAATC
633266 CATGAATGAAATTATGTTAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTTTAGAAATT
1 CATGAATGAAATTA--TTAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTTT-GAAATT
*
633331 CATGAATGAAATTATTAAAAA-AAGGGTTTTCTCTTGTTTTTTTTCATATATTTG-TTTAGAAAT
63 CATGAAT-AAATTATTAAAAAGAA-GGTTTTCTCTTGTTTTTTTCCATATATTTGCTTT-GAAAT
*
633394 TCATGAATAAAATTA-T-T-AAAAAAGGGTTTT
125 TCATGAATGAAATTATTGTAAAAAAAGGGTTTT
633424 TTCCCATTTT
Statistics
Matches: 300, Mismatches: 27, Indels: 34
0.83 0.07 0.09
Matches are distributed among these distances:
183 16 0.05
184 5 0.02
185 3 0.01
186 19 0.06
187 67 0.22
188 42 0.14
189 32 0.11
190 106 0.35
191 10 0.03
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (183 bp):
CATGAATGAAATTATTAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTTTGAAATTCAT
GAATAAATTATTAAAAAGAAGGTTTTCTCTTGTTTTTTTCCATATATTTGCTTTGAAATTCATGA
ATGAAATTATTGTAAAAAAAGGGTTTTCTCTTTTTTTTTCTTGTTTTGAAATC
Found at i:633437 original size:64 final size:62
Alignment explanation
Indices: 632889--633423 Score: 553
Period size: 64 Copynumber: 8.5 Consensus size: 62
632879 TTTTAAAGCT
* * * *
632889 AATTCATGAATGAATTTA-AAAAAAAGGGTTTTCT-TT-TGTTTTCTCATATATTTGTTTTGA
1 AATTCATGAATGAAATTATTAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTG-TTTGA
* * * * *
632949 AATTCATGACTG--TTTTTTTAAAAAGGGTTTTCTCTCTCTTTTTTTTCTTCATATATTTGCTTT
1 AATTCATGAATGAAATTATTAAAAAAGGG-TTT-TCTCT-TGTTTTTT-TTCATATATTTG-TTT
633012 GA
61 GA
* *
633014 GATTCATGAATGAAATTATTTTTTTAAAAAAAGGGTTTTCTC-T-TTTTTTTTC---T-TGT-TT
1 AATTCATGAATGAAATTA-----TT-AAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTT
633072 TGA
60 TGA
**
633075 AATTCATGAATTTAATTATTAAAAAA-GGTTTTCTCTTGTTTTTTTTCATATATTTGTTCTGA
1 AATTCATGAATGAAATTATTAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTT-TGA
* * * *
633137 AATTCATGAATAAAATTACTAAAAAGAAGGTTTTCTCTTGTTTTTTTCCATATATTTGCTTTGA
1 AATTCATGAATGAAATTATTAAAAA-AGGGTTTTCTCTTGTTTTTTTTCATATATTTG-TTTGA
* * * *
633201 AATTCATGAATGAAATTATTGTAGAAAAGTGTTTTCTCTTG--TTCTTTCATAT-TTTTTTTGA
1 AATTCATGAATGAAATTA-T-TAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTTTGA
*
633262 AATCCATGAATGAAATTATGTTAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTTTAGA
1 AATTCATGAATGAAATTA--TTAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTTT-GA
633327 AATTCATGAATGAAATTATTAAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTTTAGA
1 AATTCATGAATGAAATTATT-AAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTTT-GA
*
633391 AATTCATGAATAAAATTATTAAAAAAGGGTTTT
1 AATTCATGAATGAAATTATTAAAAAAGGGTTTT
633424 TTCCCATTTT
Statistics
Matches: 404, Mismatches: 37, Indels: 65
0.80 0.07 0.13
Matches are distributed among these distances:
54 9 0.02
55 7 0.02
56 11 0.03
58 3 0.01
59 9 0.02
60 16 0.04
61 65 0.16
62 30 0.07
63 38 0.09
64 123 0.30
65 59 0.15
66 5 0.01
67 5 0.01
68 6 0.01
69 1 0.00
71 4 0.01
72 5 0.01
73 8 0.02
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (62 bp):
AATTCATGAATGAAATTATTAAAAAAGGGTTTTCTCTTGTTTTTTTTCATATATTTGTTTGA
Found at i:637704 original size:20 final size:19
Alignment explanation
Indices: 637668--637718 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
637658 AATTAATTTT
*
637668 AAAAATTTTAAAAATTTAA
1 AAAAATTATAAAAATTTAA
637687 AAAAATTATAAAATATTTAA
1 AAAAATTATAAAA-ATTTAA
*
637707 AATAATTA-AAAA
1 AAAAATTATAAAA
637719 GTATGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTATAAAAATTTAA
Found at i:637718 original size:10 final size:9
Alignment explanation
Indices: 637666--637747 Score: 60
Period size: 9 Copynumber: 8.9 Consensus size: 9
637656 TTAATTAATT
*
637666 TTAAAAATT
1 TTAAAAATA
637675 TTAAAAAT-
1 TTAAAAATA
*
637683 TTAAAAAAA
1 TTAAAAATA
637692 TTATAAAATA
1 TTA-AAAATA
*
637702 TTTAAAATAA
1 TTAAAAAT-A
637712 TTAAAAAGTA
1 TTAAAAA-TA
*
637722 TGAAAAAGTA
1 TTAAAAA-TA
*
637732 -TAAAATTA
1 TTAAAAATA
*
637740 TAAAAAAT
1 TTAAAAAT
637748 GTATGTTTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
8 9 0.15
9 25 0.42
10 24 0.41
11 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (9 bp):
TTAAAAATA
Found at i:639695 original size:2 final size:2
Alignment explanation
Indices: 639688--639715 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
639678 GTATGGAACA
639688 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
639716 TGCATAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:645730 original size:13 final size:13
Alignment explanation
Indices: 645712--645737 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
645702 TTGAAGCTCT
645712 AAACCCTTTATCC
1 AAACCCTTTATCC
645725 AAACCCTTTATCC
1 AAACCCTTTATCC
645738 CAAGGCTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (13 bp):
AAACCCTTTATCC
Found at i:655194 original size:13 final size:13
Alignment explanation
Indices: 655176--655216 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
655166 TTTTTGGAAA
655176 AAAGTCAACAGTC
1 AAAGTCAACAGTC
655189 AAAGTCAACAGTC
1 AAAGTCAACAGTC
*
655202 AATAGTTAA-AGTC
1 AA-AGTCAACAGTC
655215 AA
1 AA
655217 CGATCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.20
Consensus pattern (13 bp):
AAAGTCAACAGTC
Found at i:655203 original size:20 final size:20
Alignment explanation
Indices: 655178--655217 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
655168 TTTGGAAAAA
655178 AGTCAACAGTCAAAGTCAAC
1 AGTCAACAGTCAAAGTCAAC
* *
655198 AGTCAATAGTTAAAGTCAAC
1 AGTCAACAGTCAAAGTCAAC
655218 GATCAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (20 bp):
AGTCAACAGTCAAAGTCAAC
Done.