Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold501
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: 850550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:500153 original size:13 final size:13
Alignment explanation
Indices: 500135--500160 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
500125 ATAGTAACCC
500135 ATGTATCGATACA
1 ATGTATCGATACA
500148 ATGTATCGATACA
1 ATGTATCGATACA
500161 TCTGGGTTTT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:506447 original size:19 final size:20
Alignment explanation
Indices: 506403--506453 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
506393 TTACCAGTTT
**
506403 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
506423 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
506442 CATGTATCGATA
1 CATGTATCGATA
506454 TACATCTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:507162 original size:20 final size:21
Alignment explanation
Indices: 507137--507187 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
507127 TTTAGGCATG
507137 TATCGATACATTCA-T-TTATA
1 TATCGATACATTCACTATT-TA
*
507157 TATCGATACATTTACTATTTA
1 TATCGATACATTCACTATTTA
507178 TATCGATACA
1 TATCGATACA
507188 AATTATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 13 0.46
21 13 0.46
22 2 0.07
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (21 bp):
TATCGATACATTCACTATTTA
Found at i:512099 original size:2 final size:2
Alignment explanation
Indices: 512092--512118 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
512082 AGCTTTGAAT
512092 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
512119 TTAAACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:513833 original size:17 final size:18
Alignment explanation
Indices: 513798--513835 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
513788 TCCAAATAGT
* *
513798 AAACTTTAATTTAACTTA
1 AAACTTAAATTCAACTTA
513816 AAACTTAAATTCAA-TTA
1 AAACTTAAATTCAACTTA
513833 AAA
1 AAA
513836 TTCAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
AAACTTAAATTCAACTTA
Found at i:514823 original size:17 final size:18
Alignment explanation
Indices: 514788--514827 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
514778 AGATAGTAAA
514788 TTTATATTCAATTAAAAT
1 TTTATATTCAATTAAAAT
*
514806 TTTATATTCAATT-GAAT
1 TTTATATTCAATTAAAAT
514823 TTTAT
1 TTTAT
514828 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTATATTCAATTAAAAT
Found at i:520530 original size:20 final size:19
Alignment explanation
Indices: 520507--520570 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
520497 CACATCCAAA
520507 TGTATCGATACATATTGCTT
1 TGTATCGATACATATT-CTT
520527 TGTATCGATAC--A---TT
1 TGTATCGATACATATTCTT
520541 T-TATCGATACATATTCTT
1 TGTATCGATACATATTCTT
*
520559 GGTATCGATACA
1 TGTATCGATACA
520571 CAGTGAATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 9 0.24
14 3 0.08
15 1 0.03
18 3 0.08
19 10 0.27
20 11 0.30
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATATTCTT
Found at i:520569 original size:32 final size:33
Alignment explanation
Indices: 520509--520570 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
520499 CATCCAAATG
*
520509 TATCGATACATATTGCTTTGTATCGATACATTT
1 TATCGATACATATTGCTTGGTATCGATACATTT
520542 TATCGATACATATT-CTTGGTATCGATACA
1 TATCGATACATATTGCTTGGTATCGATACA
520571 CAGTGAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (33 bp):
TATCGATACATATTGCTTGGTATCGATACATTT
Found at i:520656 original size:13 final size:13
Alignment explanation
Indices: 520619--520656 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
520609 AACTTACTTA
*
520619 GTATCGATACAGT
1 GTATCGATACATT
*
520632 GTATTGATACATT
1 GTATCGATACATT
520645 GTATCGATACAT
1 GTATCGATACAT
520657 GGTGAAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:523661 original size:13 final size:13
Alignment explanation
Indices: 523643--523668 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
523633 CATTAATGAA
523643 TGTATCGATACAT
1 TGTATCGATACAT
523656 TGTATCGATACAT
1 TGTATCGATACAT
523669 ATGGGATTTT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:532254 original size:35 final size:35
Alignment explanation
Indices: 532193--532287 Score: 158
Period size: 35 Copynumber: 2.8 Consensus size: 35
532183 AACAAAAATG
* *
532193 GGGAGAAATA-TTTTGAAAATATATTTGATAGAAA
1 GGGAGAAATATTTTTGAAAATAAATTTGATAAAAA
532227 GGGAGAAATATTTTTGAAAATAAATTTGATAAAAA
1 GGGAGAAATATTTTTGAAAATAAATTTGATAAAAA
532262 GGGAGAAATATTTTTG-AAATAAATTT
1 GGGAGAAATATTTTTGAAAATAAATTT
532288 ATTTTGTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
34 20 0.34
35 38 0.66
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (35 bp):
GGGAGAAATATTTTTGAAAATAAATTTGATAAAAA
Found at i:533151 original size:13 final size:13
Alignment explanation
Indices: 533118--533151 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
533108 TTACTTAGTA
*
533118 CGATACAGTGTAT
1 CGATACATTGTAT
*
533131 TGATACATTGTAT
1 CGATACATTGTAT
533144 CGATACAT
1 CGATACAT
533152 GGTGAAATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:537130 original size:8 final size:7
Alignment explanation
Indices: 537119--537147 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
537109 TATAAAATAT
537119 TTTTTAA
1 TTTTTAA
537126 TTTTTAA
1 TTTTTAA
537133 TTTTTAA
1 TTTTTAA
537140 TTTTTAA
1 TTTTTAA
537147 T
1 T
537148 AATAAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTTAA
Found at i:537741 original size:26 final size:26
Alignment explanation
Indices: 537704--537758 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
537694 TATATTTATA
*
537704 AAAAATATATTTATTCT-TTTAATTTTT
1 AAAAATATATTT-TT-TAATTAATTTTT
537731 AAAAA-ATATTTTTTAATTAATTTTT
1 AAAAATATATTTTTTAATTAATTTTT
537756 AAA
1 AAA
537759 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 1 0.04
25 14 0.54
26 6 0.23
27 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
AAAAATATATTTTTTAATTAATTTTT
Found at i:537786 original size:7 final size:7
Alignment explanation
Indices: 537776--537801 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
537766 TAAATATTTT
537776 TTATTAA
1 TTATTAA
537783 TTATTAA
1 TTATTAA
537790 TTATTAA
1 TTATTAA
537797 TTATT
1 TTATT
537802 TTCATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTATTAA
Found at i:538507 original size:18 final size:18
Alignment explanation
Indices: 538481--538528 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
538471 TAACTTGATA
*
538481 GTAAATAAAAATAATTTT
1 GTAATTAAAAATAATTTT
538499 GTAATTAAAAAT-ATTTT
1 GTAATTAAAAATAATTTT
*
538516 -TATTTAAAAATAA
1 GTAATTAAAAATAA
538529 AATAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 10 0.37
17 6 0.22
18 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
GTAATTAAAAATAATTTT
Found at i:538524 original size:16 final size:17
Alignment explanation
Indices: 538481--538527 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
538471 TAACTTGATA
*
538481 GTAAATAAAAATAATTTT
1 GTAATTAAAAAT-ATTTT
538499 GTAATTAAAAATATTTT
1 GTAATTAAAAATATTTT
*
538516 -TATTTAAAAATA
1 GTAATTAAAAATA
538528 AAATAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 11 0.41
17 5 0.19
18 11 0.41
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (17 bp):
GTAATTAAAAATATTTT
Found at i:538964 original size:171 final size:170
Alignment explanation
Indices: 538679--539020 Score: 614
Period size: 171 Copynumber: 2.0 Consensus size: 170
538669 GGGAGATAAG
* *
538679 TGAAATTATTTTTAAATCTAAATAATCATAATATTTTTTCAAAAAATAAAGTTATTTTATATTGT
1 TGAAATTATTTTTAAATCTAAAGAATCATAATACTTTTTCAAAAAATAAAGTTATTTTATATTGT
538744 ATTGGAGTCAAGTTTTGAGGCCTGCAAACAAACCCAACTCATATTCAAGTAATCCAATTTTTTTC
66 ATTGGAGTCAAGTTTTGAGGCCTGCAAACAAACCCAACTCATATTCAAGTAATCC-ATTTTTTTC
538809 AGTTTATATCTACATATGATATTTTCAATTATTAATTTCTA
130 AGTTTATATCTACATATGATATTTTCAATTATTAATTTCTA
538850 TGAAATTATTTTTAAATCTAAAGAGA-CATAATACTTTTTCAAAAAATAAAGTTATTTTATATTG
1 TGAAATTATTTTTAAATCTAAAGA-ATCATAATACTTTTTCAAAAAATAAAGTTATTTTATATTG
538914 TATTGGAGTCAAGTTTTGAGGCCTGCAAACAAACCCAACTCATATTCAAGTAATCCATTTTTTTC
65 TATTGGAGTCAAGTTTTGAGGCCTGCAAACAAACCCAACTCATATTCAAGTAATCCATTTTTTTC
* * *
538979 AGTTTATATTTATATATGATATTTTCAATTGTTAATTTCTA
130 AGTTTATATCTACATATGATATTTTCAATTATTAATTTCTA
539020 T
1 T
539021 TTATTTATTT
Statistics
Matches: 165, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
170 48 0.29
171 116 0.70
172 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (170 bp):
TGAAATTATTTTTAAATCTAAAGAATCATAATACTTTTTCAAAAAATAAAGTTATTTTATATTGT
ATTGGAGTCAAGTTTTGAGGCCTGCAAACAAACCCAACTCATATTCAAGTAATCCATTTTTTTCA
GTTTATATCTACATATGATATTTTCAATTATTAATTTCTA
Found at i:542731 original size:19 final size:21
Alignment explanation
Indices: 542685--542738 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
542675 TTTCAACAAT
542685 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
542706 ATGTATCGATACATA-AGT-A
1 TTGTATCGATACAAACAGTAA
542725 TTGTATCGATACAA
1 TTGTATCGATACAA
542739 TGTATCGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:549824 original size:11 final size:11
Alignment explanation
Indices: 549807--549840 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
549797 GAGTTCCTTT
549807 AAAAAAAAGAAC
1 AAAAAAAA-AAC
549819 AAAAAAAAAAC
1 AAAAAAAAAAC
549830 AAAACAAAAAA
1 AAAA-AAAAAA
549841 AACACACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:549826 original size:14 final size:14
Alignment explanation
Indices: 549807--549853 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
549797 GAGTTCCTTT
*
549807 AAAAAAAAGAACAA
1 AAAAAAAACAACAA
549821 AAAAAAAACAA-AA
1 AAAAAAAACAACAA
549834 CAAAAAAAACACACAA
1 -AAAAAAAACA-ACAA
549850 AAAA
1 AAAA
549854 GAGTGCAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.07
14 20 0.69
15 5 0.17
16 2 0.07
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAACAA
Found at i:549828 original size:16 final size:16
Alignment explanation
Indices: 549807--549842 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
549797 GAGTTCCTTT
*
549807 AAAAAAA-AGAACAAA
1 AAAAAAACAAAACAAA
549822 AAAAAAACAAAACAAA
1 AAAAAAACAAAACAAA
549838 AAAAA
1 AAAAA
549843 CACACAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAACAAA
Found at i:551151 original size:33 final size:33
Alignment explanation
Indices: 551051--551553 Score: 594
Period size: 33 Copynumber: 15.8 Consensus size: 33
551041 CTCTCTTTCT
*
551051 AAGTCCACGACTCAGTGGCA--TCTTTTCTTCA
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
551082 AAGTCCACGACTCAGTGGCATC-CTTTTCTTCC
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
* * * *
551114 AAGTCCATGACTCAATGGCATCTTTTTTCTTCA
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
** * *
551147 AAGTCCATAACTTAGTGGCA--TCTTTT-TTCT
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
* *
551177 AAGTCCATGACTCAGTAGCATC-CTTTTCTTCC
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
* *
551209 AAGTCCACAACTCAGTGGCATC-ATTTTCTTCC
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
* * * **
551241 AAGTCCACAACACAGTGGCATCTTTTTTCTTTA
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
551274 AAGTCCACGACTCAGTGGCATCTCTTTTC-T--
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
551304 AAGTCCACGACTCAGTGGCATC-CTTTTCTTCC
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
* *
551336 AAGTCCACAACTCAGTGGCATCTTTTTTCTTCC
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
* * * * **
551369 AAGTCCACAACACAATGGCATCTTTTTTCTTTA
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
*
551402 AAGTCCACGACTTAGTGGCATCTCTTTTC-T--
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
551432 AAGTCCACGACTCAGTGGCATC-CTTTTCTTCC
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
* **
551464 AAGTCCACGACTCAGTGGCATCTTTTTTCTTTA
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
551497 AAGTCCACGACTCAGTGGCATCTCTTTTC-T--
1 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
*
551527 AAGTCCACGACTCAGTGGCATTTCTTT
1 AAGTCCACGACTCAGTGGCATCTCTTT
551554 AAGCCCACAA
Statistics
Matches: 415, Mismatches: 42, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.03
30 91 0.22
31 30 0.07
32 127 0.31
33 155 0.37
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.35
Consensus pattern (33 bp):
AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
Found at i:551215 original size:95 final size:96
Alignment explanation
Indices: 551051--551547 Score: 588
Period size: 95 Copynumber: 5.2 Consensus size: 96
551041 CTCTCTTTCT
* * *
551051 AAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCATC-CTTTTCTTCCA
1 AAGTCCACAACTCAGTGGCATCTTTT-TTCTAAGTCCACGACTCAGTGGCATCTCTTTTCTTCAA
* * * *
551115 AGTCCATGACTCAATGGCATCTTTTTTCTTCA
65 AGTCCACGACTCAGTGGCATCTCTTTTCTTCC
* * * * *
551147 AAGTCCATAACTTAGTGGCATCTTTTTTCTAAGTCCATGACTCAGTAGCATC-CTTTTCTTCCAA
1 AAGTCCACAACTCAGTGGCATCTTTTTTCTAAGTCCACGACTCAGTGGCATCTCTTTTCTTCAAA
* *
551211 GTCCACAACTCAGTGGCATC-ATTTTCTTCC
66 GTCCACGACTCAGTGGCATCTCTTTTCTTCC
*
551241 AAGTCCACAACACAGTGGCATCTTTTTTCTTTAAAGTCCACGACTCAGTGGCATCTCTTTTC-T-
1 AAGTCCACAACTCAGTGGCATCTTTTTTC--T-AAGTCCACGACTCAGTGGCATCTCTTTTCTTC
551304 -AAGTCCACGACTCAGTGGCATC-CTTTTCTTCC
63 AAAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
* * * * *
551336 AAGTCCACAACTCAGTGGCATCTTTTTTCTTCCAAGTCCACAACACAATGGCATCTTTTTTCTTT
1 AAGTCCACAACTCAGTGGCATCTTTTTTC-T--AAGTCCACGACTCAGTGGCATCTCTTTTCTTC
*
551401 AAAGTCCACGACTTAGTGGCATCTCTTTTC-T--
63 AAAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
* * * *
551432 AAGTCCACGACTCAGTGGCATCCTTTTCTTCCAAGTCCACGACTCAGTGGCATCTTTTTTCTTTA
1 AAGTCCACAACTCAGTGGCAT-CTTTT-TTCTAAGTCCACGACTCAGTGGCATCTCTTTTCTTCA
551497 AAGTCCACGACTCAGTGGCATCTCTTTTC-T--
64 AAGTCCACGACTCAGTGGCATCTCTTTTCTTCC
*
551527 AAGTCCACGACTCAGTGGCAT
1 AAGTCCACAACTCAGTGGCAT
551548 TTCTTTAAGC
Statistics
Matches: 359, Mismatches: 31, Indels: 23
0.87 0.08 0.06
Matches are distributed among these distances:
94 36 0.10
95 215 0.60
96 45 0.13
97 26 0.07
98 31 0.09
99 6 0.02
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (96 bp):
AAGTCCACAACTCAGTGGCATCTTTTTTCTAAGTCCACGACTCAGTGGCATCTCTTTTCTTCAAA
GTCCACGACTCAGTGGCATCTCTTTTCTTCC
Found at i:551424 original size:128 final size:128
Alignment explanation
Indices: 551039--551615 Score: 764
Period size: 128 Copynumber: 4.6 Consensus size: 128
551029 AATTCTTCAA
* *
551039 ATCTCTCTTTCTAAGTCCACGACTCAGTGGCAT-CTTTTCTTCAAAGTCCACGACTCAGTGGCAT
1 ATCTCT-TTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGGCAT
* ** * * ** *
551103 C-CTTTTCTTCCAAGTCCATGACTCAATGGCATCTTTTTTCTTCAAAGTCCATAACTTAGTGGC
65 CTTTTTTCTTCCAAGTCCACAACACAATGGCATCTTTTTTCTTTAAAGTCCACGACTCAGTGGC
* * *
551166 ATCTTTTTTCTAAGTCCATGACTCAGTAGCATCCTTTTCTTCCAAGTCCACAACTCAGTGGCATC
1 ATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGGCATC
* *
551231 -ATTTTCTTCCAAGTCCACAACACAGTGGCATCTTTTTTCTTTAAAGTCCACGACTCAGTGGC
66 TTTTTTCTTCCAAGTCCACAACACAATGGCATCTTTTTTCTTTAAAGTCCACGACTCAGTGGC
551293 ATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGGCATC
1 ATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGGCATC
*
551358 TTTTTTCTTCCAAGTCCACAACACAATGGCATCTTTTTTCTTTAAAGTCCACGACTTAGTGGC
66 TTTTTTCTTCCAAGTCCACAACACAATGGCATCTTTTTTCTTTAAAGTCCACGACTCAGTGGC
*
551421 ATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTTCCAAGTCCACGACTCAGTGGCATC
1 ATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGGCATC
** * * * *
551486 TTTTTTCTTTAAAGTCCACGACTCAGTGGCATCTCTTTTC--T-AAGTCCACGACTCAGTGGC
66 TTTTTTCTTCCAAGTCCACAACACAATGGCATCTTTTTTCTTTAAAGTCCACGACTCAGTGGC
* * * * * *
551546 AT-T-TCTT-TAAGCCCACAACTCTGTGGCAT--TTTTTTTCCTGTTAAGTCCACAACTCCGTGG
1 ATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTTCC----AAGTCCACAACTCAGTGG
551606 CAT-TTTTTTC
62 CATCTTTTTTC
551616 CTGTGCATCT
Statistics
Matches: 409, Mismatches: 35, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
120 8 0.02
122 19 0.05
123 10 0.02
124 20 0.05
125 20 0.05
126 25 0.06
127 150 0.37
128 157 0.38
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (128 bp):
ATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGGCATC
TTTTTTCTTCCAAGTCCACAACACAATGGCATCTTTTTTCTTTAAAGTCCACGACTCAGTGGC
Found at i:551596 original size:34 final size:33
Alignment explanation
Indices: 551552--551619 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
551542 TGGCATTTCT
*
551552 TTAAGCCCACAACTCTGTGGCATTTTTTTTCCTG
1 TTAAGCCCACAACTCCGTGGCA-TTTTTTTCCTG
*
551586 TTAAGTCCACAACTCCGTGGCATTTTTTTCCTG
1 TTAAGCCCACAACTCCGTGGCATTTTTTTCCTG
551619 T
1 T
551620 GCATCTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 12 0.38
34 20 0.62
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (33 bp):
TTAAGCCCACAACTCCGTGGCATTTTTTTCCTG
Found at i:551619 original size:33 final size:32
Alignment explanation
Indices: 551050--551615 Score: 535
Period size: 33 Copynumber: 17.9 Consensus size: 32
551040 TCTCTCTTTC
551050 TAAGTCCACGACTCAGTGGCATC--TTTTCTT
1 TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
* *
551080 CAAAGTCCACGACTCAGTGGCATC-CTTTTCTT
1 -TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
* * *
551112 CCAAGTCCATGACTCAATGGCATCTTTTTTCTT
1 -TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
* ** *
551145 CAAAGTCCATAACTTAGTGGCATCTTTTTTC--
1 -TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
* * *
551176 TAAGTCCATGACTCAGTAGCATC-CTTTTCTT
1 TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
* * *
551207 CCAAGTCCACAACTCAGTGGCATC-ATTTTCTT
1 -TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
* * *
551239 CCAAGTCCACAACACAGTGGCATCTTTTTTCTT
1 -TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
*
551272 TAAAGTCCACGACTCAGTGGCATCTCTTTTC--
1 T-AAGTCCACGACTCAGTGGCATCTTTTTTCTT
*
551303 TAAGTCCACGACTCAGTGGCATC-CTTTTCTT
1 TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
* *
551334 CCAAGTCCACAACTCAGTGGCATCTTTTTTCTT
1 -TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
* * * *
551367 CCAAGTCCACAACACAATGGCATCTTTTTTCTT
1 -TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
* *
551400 TAAAGTCCACGACTTAGTGGCATCTCTTTTC--
1 T-AAGTCCACGACTCAGTGGCATCTTTTTTCTT
*
551431 TAAGTCCACGACTCAGTGGCATC-CTTTTCTT
1 TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
*
551462 CCAAGTCCACGACTCAGTGGCATCTTTTTTCTT
1 -TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
*
551495 TAAAGTCCACGACTCAGTGGCATCTCTTTTC--
1 T-AAGTCCACGACTCAGTGGCATCTTTTTTCTT
551526 TAAGTCCACGACTCAGTGGCA-----TTTCTT
1 TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
* * * *
551553 TAAGCCCACAACTCTGTGGCATTTTTTTTCCTGT
1 TAAGTCCACGACTCAGTGGCATCTTTTTT-CT-T
* *
551587 TAAGTCCACAACTCCGTGGCAT-TTTTTTC
1 TAAGTCCACGACTCAGTGGCATCTTTTTTC
551616 CTGTGCATCT
Statistics
Matches: 463, Mismatches: 46, Indels: 51
0.83 0.08 0.09
Matches are distributed among these distances:
25 4 0.01
27 18 0.04
29 17 0.04
30 82 0.18
31 25 0.05
32 124 0.27
33 172 0.37
34 21 0.05
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (32 bp):
TAAGTCCACGACTCAGTGGCATCTTTTTTCTT
Found at i:551689 original size:36 final size:36
Alignment explanation
Indices: 551637--551736 Score: 182
Period size: 36 Copynumber: 2.8 Consensus size: 36
551627 TCTCCAAAAG
551637 CCCACACCTCCGTGGCATCCCTTTTTCCCTTTTAAT
1 CCCACACCTCCGTGGCATCCCTTTTTCCCTTTTAAT
*
551673 CCCACACCTCCATGGCATCCCTTTTTCCCTTTTAAT
1 CCCACACCTCCGTGGCATCCCTTTTTCCCTTTTAAT
*
551709 CCCACACCTCTGTGGCATCCCTTTTTCC
1 CCCACACCTCCGTGGCATCCCTTTTTCC
551737 TATAAGTCCA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.14, C:0.43, G:0.08, T:0.35
Consensus pattern (36 bp):
CCCACACCTCCGTGGCATCCCTTTTTCCCTTTTAAT
Found at i:551874 original size:49 final size:49
Alignment explanation
Indices: 551802--552803 Score: 691
Period size: 49 Copynumber: 21.2 Consensus size: 49
551792 GCATTGGCAC
* * *
551802 CTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACTTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* *
551851 CTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * *
551894 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTAAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTC--AT
* *
551946 CTTTAAGACCAATGTCGCTGGCCTTGAATTAGCACATTGGCA----C--
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * * *
551989 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATT-GT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * *
552037 CTTTAAGACCAATGTCTCTAGCCTTGAATCAGCACATTGG------CA-
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * *
552079 C---AAG-CCAGTATCGCTGGCCTTGAATTAGCATATTGGCACCTTT-AT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCAT
* * * * * **
552124 CTTTAATACCGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAACCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CT--TTCAT
* * *
552176 CTTTAAGTCCAATGTCGCTGGCCTTAAATCAGCACATTGG------CA-
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * *
552218 ---TAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACATTT-AT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC-TTTCAT
*
552264 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA-
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * * * *
552306 ---TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTT-GT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * *
552351 CTTTAAGACCAATGTCGCTGACCTTGAATTAGCACATTGGCA-----A-
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * * *
552394 ----AAGCCCAGTATCGCTAGCCTTGAATCAGCATATTGGCACCTTT-AT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCAT
* * * * **
552439 CTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAACCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CT--TTCAT
* * * *
552491 CTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCA-TGTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * * *
552539 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATCGACACCTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * *
552588 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGGCATATTGGCGCCTTCGTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCA-GCACATTGGC-ACTT--TCAT
** * * *
552641 CTTTAACTCCAATGTCGCTGGCCTAGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * * * *
552690 CTTTAAGTCCAAAATCGCTGGCCTTAAATCATCATATTGGCATCTTCGTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTT--TCAT
* * *
552742 CTTTAAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATTCTTTTCAT
1 CTTTAAGA-CCAATATCGCTGGCCTTGAATCAGCACATTGGCA--C-TTTCAT
*
552795 CTTCAAGAC
1 CTTTAAGAC
552804 TAATGTCGTT
Statistics
Matches: 746, Mismatches: 130, Indels: 151
0.73 0.13 0.15
Matches are distributed among these distances:
38 26 0.03
39 99 0.13
42 1 0.00
43 78 0.10
44 2 0.00
45 3 0.00
47 1 0.00
48 111 0.15
49 207 0.28
50 10 0.01
51 4 0.01
52 130 0.17
53 70 0.09
54 2 0.00
55 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (49 bp):
CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
Found at i:551995 original size:95 final size:91
Alignment explanation
Indices: 551759--552731 Score: 610
Period size: 87 Copynumber: 10.5 Consensus size: 91
551749 ACTCCGTGGC
551759 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAG--CATTGGCACCTTTAAGTCCAATATCGCTG
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTG
*
551822 GCCTTGAATTAGCATATTGGCACTTT
66 GCCTTGAATCAGCATATTGGCACTTT
*
551848 CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT
1 -ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT
*
551913 AGCCTTGAATCAGCATATTGGCACCTTTCT
65 GGCCTTGAATCAGCATATTGGCA-C-TT-T
*
551943 AATCTTTAAGACCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCTTTAAGTCCAATATCGCT
1 -ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT
*
552008 GGCCTTGAATCAGCATATTGGCACATT
65 GGCCTTGAATCAGCATATTGGCACTTT
* * * *
552035 GTCTTTAAGACCAATGTCTCTAGCCTTGAATCAGCACATTGGCA-C---AAG-CCAGTATCGCTG
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTG
*
552095 GCCTTGAATTAGCATATTGGCACCTTT
66 GCCTTGAATCAGCATATTGGCA-CTTT
* * * *
552122 ATCTTTAATACCGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAACCATCTTTAAGTCCA
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG-----C-A-C--CTTTAAGTCCA
* * *
552187 ATGTCGCTGGCCTTAAATCAGCACATTGG--C---
57 ATATCGCTGGCCTTGAATCAGCATATTGGCACTTT
* * * * * *
552217 A----TAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACATTTATCTTTAAGACCAATG
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC------CTTTAAGTCCAATA
*
552278 TCGCTGGCCTTGAATCAGCACATTGG--C---
60 TCGCTGGCCTTGAATCAGCATATTGGCACTTT
* * * * * *
552305 A----TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGT
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C----CTTTAAGTCCAATAT
* * *
552366 CGCTGACCTTGAATTAGCACATTGGCA----
61 CGCTGGCCTTGAATCAGCATATTGGCACTTT
* * * * * * * *
552393 A-----AAGCCCAGTATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCGATG
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATA
* * * **
552453 TCGTTGGCCTTGAATCAGCACATCGGCACCTCAACC
60 TCGCTGGCCTTGAATCAGCATATTGGCA-CT---TT
* * * *
552489 ATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATGTCATCTTTAAGTCCAATAT
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA---C--CTTTAAGTCCAATAT
* * * *
552554 CGCTGGCCTTGAATCAGCACATCGACACCTTC
61 CGCTGGCCTTGAATCAGCATATTGGCA-CTTT
* * * * *
552586 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGGCATATTGGCGCCTTCGTCATCTTTAACTCC
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCA-GCACATT---G-----G-CACCTTTAAGTCC
* * * *
552651 AATGTCGCTGGCCTAGAATCAGCACATTGGCACCTTC
56 AATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTT
* ** * * *
552688 ATCTTTAAGTCCAAAATCGCTGGCCTTAAATCATCATATTGGCA
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
552732 TCTTCGTCAT
Statistics
Matches: 762, Mismatches: 68, Indels: 104
0.82 0.07 0.11
Matches are distributed among these distances:
84 1 0.00
85 1 0.00
86 33 0.04
87 121 0.16
88 120 0.16
89 1 0.00
90 34 0.04
91 69 0.09
92 53 0.07
93 4 0.01
94 3 0.00
95 86 0.11
96 1 0.00
97 33 0.04
98 9 0.01
100 45 0.06
101 71 0.09
102 73 0.10
103 1 0.00
106 1 0.00
107 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (91 bp):
ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTG
GCCTTGAATCAGCATATTGGCACTTT
Found at i:552217 original size:187 final size:185
Alignment explanation
Indices: 551759--552168 Score: 606
Period size: 187 Copynumber: 2.3 Consensus size: 185
551749 ACTCCGTGGC
*
551759 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAG--CATTGGCACCTTTAAGTCCAATATCGCTG
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATCGGCACCTTTAAGTCCAATATCGCTG
* * *
551822 GCCTTGAATTAGCATATTGGCACTTTCATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACA
66 GCCTTGAATCAGCATATTGGCACATTCATCTTTAAGACCAATGTCGTTAGCCTTGAATCAGCACA
551887 TTGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTA
131 TTGGCACC--TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTA
* *
551944 ATCTTTAAGACCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCTTTAAGTCCAATATCGCTG
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATCGGCACCTTTAAGTCCAATATCGCTG
*
552009 GCCTTGAATCAGCATATTGGCACATT-GTCTTTAAGACCAATGTC-TCTAGCCTTGAATCAGCAC
66 GCCTTGAATCAGCATATTGGCACATTCATCTTTAAGACCAATGTCGT-TAGCCTTGAATCAGCAC
* * *
552072 ATTGGCA-C-AAG-CCAGTATCGCTGGCCTTGAATTAGCATATTGGCACC-TT-T-
130 ATTGGCACCTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTA
* * *
552122 ATCTTTAATACCGATGTCGTTGGCCTTGAATCAGCACATCGGCACCT
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATCGGCACCT
552169 CAACCATCTT
Statistics
Matches: 209, Mismatches: 13, Indels: 13
0.89 0.06 0.06
Matches are distributed among these distances:
178 42 0.20
179 1 0.00
180 2 0.01
181 33 0.16
182 3 0.01
185 35 0.17
186 40 0.19
187 53 0.25
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (185 bp):
ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATCGGCACCTTTAAGTCCAATATCGCTG
GCCTTGAATCAGCATATTGGCACATTCATCTTTAAGACCAATGTCGTTAGCCTTGAATCAGCACA
TTGGCACCTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTA
Found at i:552238 original size:39 final size:39
Alignment explanation
Indices: 552179--552431 Score: 182
Period size: 39 Copynumber: 6.0 Consensus size: 39
552169 CAACCATCTT
* * *
552179 TAAGTCCAATGTCGCTGGCCTTAAATCAGCACATTGGCA
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* *
552218 TAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACATTTA
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGG--C----A
* *
552263 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 ----TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* *
552306 TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCA
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * * *
552345 CCTTGTCTTTAAGACCAATGTCGCTGACCTTGAATTAGCACATTGGCA
1 ---------TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * * *
552393 AAAGCCCAGTATCGCTAGCCTTGAATCAGCATATTGGCA
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
552432 CCTTTATCTT
Statistics
Matches: 168, Mismatches: 27, Indels: 38
0.72 0.12 0.16
Matches are distributed among these distances:
39 98 0.58
41 1 0.01
43 1 0.01
45 1 0.01
47 1 0.01
48 33 0.20
49 33 0.20
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (39 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
Found at i:552241 original size:178 final size:175
Alignment explanation
Indices: 551759--552258 Score: 480
Period size: 187 Copynumber: 2.7 Consensus size: 175
551749 ACTCCGTGGC
*
551759 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAG--CATTGGCACCTTTAAGTCCAATATCGCTG
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATCGGCACCTTTAAGTCCAATATCGCTG
* * * *
551822 GCCTTGAATTAGCATATTGGCACTTTCATCTTTAAGACCAATGTCGT-TGGCCTTGAATCAGCAC
66 GCCTTAAATCAGCACATTGG-A----CA---TTAAGACCAATATC-TCTGGCCTTGAATCAGCAC
551886 ATTGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTA
122 ATTGGCA-C---AAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTA
* *
551944 ATCTTTAAGACCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCTTTAAGTCCAATATCGCTG
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATCGGCACCTTTAAGTCCAATATCGCTG
* * * *
552009 GCCTTGAATCAGCATATTGGCACATTGTCTTTAAGACCAATGTCTCTAGCCTTGAATCAGCACAT
66 GCCTTAAATCAGCACATTGG-ACA------TTAAGACCAATATCTCTGGCCTTGAATCAGCACAT
* * *
552074 TGGCACAAG-CCAGTATCGCTGGCCTTGAATTAGCATATTGGCACC-TT-T-
124 TGGCACAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTA
* * *
552122 ATCTTTAATACCGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAACCATCTTTAAGTCCA
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATCGG-----C-A-C--CTTTAAGTCCA
* *
552187 ATGTCGCTGGCCTTAAATCAGCACATTGG-CA-TAAGCCCAATAT-TGCTGGCCTTGAATCAGCA
57 ATATCGCTGGCCTTAAATCAGCACATTGGACATTAAGACCAATATCT-CTGGCCTTGAATCAGCA
*
552249 TATTGGCACA
121 CATTGGCACA
552259 TTTATCTTTA
Statistics
Matches: 281, Mismatches: 18, Indels: 39
0.83 0.05 0.12
Matches are distributed among these distances:
177 1 0.00
178 72 0.26
179 1 0.00
180 2 0.01
181 33 0.12
182 3 0.01
183 3 0.01
184 1 0.00
185 38 0.14
186 40 0.14
187 87 0.31
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (175 bp):
ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATCGGCACCTTTAAGTCCAATATCGCTG
GCCTTAAATCAGCACATTGGACATTAAGACCAATATCTCTGGCCTTGAATCAGCACATTGGCACA
AGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTA
Found at i:552279 original size:140 final size:139
Alignment explanation
Indices: 551954--552305 Score: 418
Period size: 140 Copynumber: 2.6 Consensus size: 139
551944 ATCTTTAAGA
* * * * *
551954 CCAATGTCGCTGGCCTTGAATTAGCACATTGGCAC------CTTTAAGTCCAATATCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCCT
* * *** * *
552013 TGAATCAGCATATTGGCA---C-ATTGTCTTTAAGACCAATGTCTCTAGCCTTGAATCAGCACAT
66 TGAATCAGCACATCGGCACCTCAACCATCTTTAAGACCAATGTCGCTAGCCTTAAATCAGCACAT
552074 TGGCACAAG
131 TGGCACAAG
* * * * * *
552083 CCAGTATCGCTGGCCTTGAATTAGCATATTGGCACCTTTATCTTTAATACCGATGTCGTTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCCT
* *
552148 TGAATCAGCACATCGGCACCTCAACCATCTTTAAGTCCAATGTCGCTGGCCTTAAATCAGCACAT
66 TGAATCAGCACATCGGCACCTCAACCATCTTTAAGACCAATGTCGCTAGCCTTAAATCAGCACAT
*
552213 TGGCATAAG
131 TGGCACAAG
*
552222 CCCAATATTGCTGGCCTTGAATCAGCATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCC
1 -CCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCC
*
552287 TTGAATCAGCACATTGGCA
65 TTGAATCAGCACATCGGCA
552306 TAAGCCCAAT
Statistics
Matches: 186, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
129 32 0.17
135 35 0.19
138 1 0.01
139 43 0.23
140 75 0.40
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (139 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCCT
TGAATCAGCACATCGGCACCTCAACCATCTTTAAGACCAATGTCGCTAGCCTTAAATCAGCACAT
TGGCACAAG
Found at i:552389 original size:175 final size:176
Alignment explanation
Indices: 552144--552785 Score: 575
Period size: 175 Copynumber: 3.4 Consensus size: 176
552134 GATGTCGTTG
* * *
552144 GCCTTGAATCAGCACATCGGCACCTCAACCATCTTTAAGTCCAATGTCGCTGGCCTTAAATCAGC
1 GCCTTGAATCAGCATATTGGCACCT----CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
* *
552209 ACATTGGCATAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACATTTATCTTTAAGACC
62 ACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
552274 AATGTCGCTGGCCTTGAATCAGCACATTGGCA-TAAGCCCAATATCGCTA
127 AATGTCGCTGGCCTTGAATCAGCACATTGGCATTAAGCCCAATATCGCTA
** * * *
552323 GCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGACCTTGAATTAGCACAT
1 GCCTTGAATCAGCATATTGGCACCTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* * * *
552388 TGGCAAAAGCCCAGTATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCGATG
66 TGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATG
* *
552453 TCGTTGGCCTTGAATCAGCACATCGGCACCTCAACCATCTTTAAGCCCAATATCGCTA
131 TCGCTGGCCTTGAATCAGCACATTGG---------CA---TTAAGCCCAATATCGCTA
** *
552511 GCCTTGAATCAGCATATTGGCATGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACAT
1 GCCTTGAATCAGCATATTGGCACCTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* * * *
552576 CGACACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGGCATATTGGCGCCTTCGTCAT
66 TG------GCA----TAAGCCCAATATCGCTGGCCTTGAATCA-GCATATTGGCACCTT--T-AT
** * * *
552641 CTTTAACTCCAATGTCGCTGGCCTAGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAAATC
117 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA---TTAAGCCCAATATC
*
552706 GCTG
173 GCTA
* * ** *
552710 GCCTTAAATCATCATATTGGCATCTTCGTCATCTTTAAAACCCAATGTCGTTGGCCTTGAATCAG
1 GCCTTGAATCAGCATATTGGCA-C--C-TCATCTTT-AAGTCCAATGTCGCTGGCCTTGAATCAG
552775 CACATTGGCAT
61 CACATTGGCAT
552786 TCTTTTCATC
Statistics
Matches: 377, Mismatches: 54, Indels: 49
0.79 0.11 0.10
Matches are distributed among these distances:
175 117 0.31
179 23 0.06
184 2 0.01
188 75 0.20
194 3 0.01
198 26 0.07
199 56 0.15
201 1 0.00
202 36 0.10
203 8 0.02
204 30 0.08
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (176 bp):
GCCTTGAATCAGCATATTGGCACCTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
TGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATG
TCGCTGGCCTTGAATCAGCACATTGGCATTAAGCCCAATATCGCTA
Found at i:552406 original size:87 final size:87
Alignment explanation
Indices: 552174--552480 Score: 479
Period size: 88 Copynumber: 3.5 Consensus size: 87
552164 CACCTCAACC
* * * *
552174 ATCTTTAAGTCCAATGTCGCTGGCCTTAAATCAGCACATTGGCATAAGCCCAATATTGCTGGCCT
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTAGCCT
*
552239 TGAATCAGCATATTGGCACATTT
66 TGAATCAGCATATTGGCAC-CTT
552262 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTAGCCT
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTAGCCT
552327 TGAATCAGCATATTGGCACCTT
66 TGAATCAGCATATTGGCACCTT
* * * * *
552349 GTCTTTAAGACCAATGTCGCTGACCTTGAATTAGCACATTGGCAAAAGCCCAGTATCGCTAGCCT
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTAGCCT
552414 TGAATCAGCATATTGGCACCTTT
66 TGAATCAGCATATTGGCACC-TT
* * *
552437 ATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATCGGCA
1 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
552481 CCTCAACCAT
Statistics
Matches: 202, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
87 82 0.41
88 120 0.59
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (87 bp):
ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTAGCCT
TGAATCAGCATATTGGCACCTT
Found at i:552474 original size:315 final size:316
Alignment explanation
Indices: 551848--552629 Score: 1102
Period size: 315 Copynumber: 2.4 Consensus size: 316
551838 TTGGCACTTT
*
551848 CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT
1 CATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA---TTAAGTCCAATATCGCT
* * *
551913 AGCCTTGAATCAGCATATTGGCACCTTTCTAATCTTTAAGACCAATGTCGCTGGCCTTGAATTAG
63 GGCCTTGAATCAGCATATTGGCA-CATT-T-ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAG
* *
551978 CACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTGTCTTTAA
125 CACATTGGCA-C--TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACATTGTCTTTAA
* * * *
552043 GACCAATGTCTCTAGCCTTGAATCAGCACATTGGCACAAGCCAGTATCGCTGGCCTTGAATTAGC
187 GACCAATGTCGCTAGCCTTGAATCAGCACATTGGCAAAAGCCAGTATCGCTAGCCTTGAATCAGC
*
552108 ATATTGGCACCTTTATCTTTAATACCGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAAC
252 ATATTGGCACCTTTATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAAC
* * * *
552173 CATCTTTAAGTCCAATGTCGCTGGCCTTAAATCAGCACATTGGCA-TAAGCCCAATATTGCTGGC
1 CATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTAAGTCCAATATCGCTGGC
552237 CTTGAATCAGCATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT
66 CTTGAATCAGCATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT
*
552302 GGCA-TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGT
131 GGCACTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACATTGTCTTTAAGACCAATGT
*
552366 CGCT-GACCTTGAATTAGCACATTGGCAAAAGCCCAGTATCGCTAGCCTTGAATCAGCATATTGG
196 CGCTAG-CCTTGAATCAGCACATTGGCAAAAG-CCAGTATCGCTAGCCTTGAATCAGCATATTGG
552430 CACCTTTATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAAC
259 CACCTTTATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAAC
* * * *
552488 CATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATGTCATCTTTAAGTCCAATA
1 CATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT-G---G-CA---TTAAGTCCAATA
* * * * * * *
552553 TCGCTGGCCTTGAATCAGCACATCGACACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATC
58 TCGCTGGCCTTGAATCAGCATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCCTTGAATC
*
552618 AGGCATATTGGC
123 A-GCACATTGGC
552630 GCCTTCGTCA
Statistics
Matches: 413, Mismatches: 32, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
313 1 0.00
314 83 0.20
315 123 0.30
316 1 0.00
318 43 0.10
319 2 0.00
320 5 0.01
321 36 0.09
324 68 0.16
325 51 0.12
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (316 bp):
CATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTAAGTCCAATATCGCTGGC
CTTGAATCAGCATATTGGCACATTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT
GGCACTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACATTGTCTTTAAGACCAATGT
CGCTAGCCTTGAATCAGCACATTGGCAAAAGCCAGTATCGCTAGCCTTGAATCAGCATATTGGCA
CCTTTATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAAC
Found at i:552671 original size:102 final size:100
Alignment explanation
Indices: 552402--552784 Score: 472
Period size: 102 Copynumber: 3.8 Consensus size: 100
552392 AAAAGCCCAG
** * *
552402 TATCGCTAGCCTTGAATCAGCATATTGGCACCTT-T-ATCTTTAAGACCGATGTCGTTGGCCTTG
1 TATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCATCTTTAACTCCAATGTCGCTGGCCTTG
* *
552465 AATCAGCACATCGGCACCTCAACCATCTTTAAGCCCAA
66 AATCAGCACATCGGCACCT---TCATCTTTAAGTCCAA
* *
552503 TATCGCTAGCCTTGAATCAGCATATTGGCA---TGTCATCTTTAAGTCCAATATCGCTGGCCTTG
1 TATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCATCTTTAACTCCAATGTCGCTGGCCTTG
*
552565 AATCAGCACATCGACACCTTCATCTTTAAGTCCAA
66 AATCAGCACATCGGCACCTTCATCTTTAAGTCCAA
* *
552600 TATCGCTGGCCTTGAATCAGGCATATTGGCGCCTTCGTCATCTTTAACTCCAATGTCGCTGGCCT
1 TATCGCTAGCCTTGAATCA-GCATATTGGCACCTT-GTCATCTTTAACTCCAATGTCGCTGGCCT
* *
552665 AGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
64 TGAATCAGCACATCGGCACCTTCATCTTTAAGTCCAA
* * * * * *
552702 AATCGCTGGCCTTAAATCATCATATTGGCATCTTCGTCATCTTTAAAAC-CCAATGTCGTTGGCC
1 TATCGCTAGCCTTGAATCAGCATATTGGCACCTT-GTCATCTTT--AACTCCAATGTCGCTGGCC
*
552766 TTGAATCAGCACATTGGCA
63 TTGAATCAGCACATCGGCA
552785 TTCTTTTCAT
Statistics
Matches: 252, Mismatches: 21, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
97 32 0.13
98 11 0.04
99 1 0.00
100 42 0.17
101 53 0.21
102 110 0.44
103 3 0.01
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.30
Consensus pattern (100 bp):
TATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCATCTTTAACTCCAATGTCGCTGGCCTTG
AATCAGCACATCGGCACCTTCATCTTTAAGTCCAA
Found at i:553558 original size:19 final size:21
Alignment explanation
Indices: 553512--553562 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
553502 TTTCAACAAT
553512 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
553533 ATGTATCGATACATA-AGT-A
1 TTGTATCGATACAAACAGTAA
553552 TTGTATCGATA
1 TTGTATCGATA
553563 TAATGTATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 11 0.41
20 3 0.11
21 13 0.48
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:556857 original size:16 final size:19
Alignment explanation
Indices: 556822--556863 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 19
556812 TCAAAGAGAT
556822 AATAGAAAATGCTATAAAG
1 AATAGAAAATGCTATAAAG
556841 AATA-AAAA-GCT-TAAAG
1 AATAGAAAATGCTATAAAG
556857 -ATAGAAA
1 AATAGAAA
556864 GACTTTCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 8 0.36
17 3 0.14
18 4 0.18
19 4 0.18
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.19
Consensus pattern (19 bp):
AATAGAAAATGCTATAAAG
Found at i:558167 original size:20 final size:19
Alignment explanation
Indices: 558142--558185 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
558132 CAATGTATCA
*
558142 ATACATTTTGGGATGCATCG
1 ATACATATTGGG-TGCATCG
* *
558162 ATACATATTGTGTGTATCG
1 ATACATATTGGGTGCATCG
558181 ATACA
1 ATACA
558186 AATTTGGCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (19 bp):
ATACATATTGGGTGCATCG
Found at i:558182 original size:19 final size:20
Alignment explanation
Indices: 558134--558185 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
558124 TTACAAGCCA
* *
558134 ATGTATCAATACATTTTGGG
1 ATGTATCGATACATATTGGG
* *
558154 ATGCATCGATACATATTGTG
1 ATGTATCGATACATATTGGG
558174 -TGTATCGATACA
1 ATGTATCGATACA
558186 AATTTGGCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATATTGGG
Found at i:558255 original size:20 final size:21
Alignment explanation
Indices: 558208--558260 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
558198 GCCAATGACC
**
558208 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
558229 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
558249 TGTATCGATACA
1 TGTATCGATACA
558261 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:558266 original size:13 final size:13
Alignment explanation
Indices: 558248--558272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
558238 ACATTTGGTC
558248 ATGTATCGATACA
1 ATGTATCGATACA
558261 ATGTATCGATAC
1 ATGTATCGATAC
558273 TATGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:560727 original size:13 final size:13
Alignment explanation
Indices: 560709--560749 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
560699 ATAAACCTTT
*
560709 TGTATCGATACAC
1 TGTATCGATACAA
560722 TGTATCGATACAA
1 TGTATCGATACAA
560735 TGTATCGATACAA
1 TGTATCGATACAA
560748 TG
1 TG
560750 AGTTTTCTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:566903 original size:19 final size:20
Alignment explanation
Indices: 566858--566906 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
566848 TTACAAGCCA
*
566858 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATATTGGG
*
566878 ATGTATCGATACATATTGTG
1 ATGTATCGATACATATTGGG
566898 -TGTATCGAT
1 ATGTATCGAT
566907 CCATGCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATATTGGG
Found at i:566916 original size:93 final size:93
Alignment explanation
Indices: 566784--567002 Score: 404
Period size: 93 Copynumber: 2.3 Consensus size: 93
566774 TCCCGTGTAA
566784 ATGTATCGATACA-ATTTGTGATGTATCGATACATGCATTTGAAAAATATAGCCGTTACTAGCCA
1 ATGTATCGATACATA-TTGTG-TGTATCGATACATGCATTTGAAAAATATAGCCGTTACTAGCCA
566848 TTACAAGCCAATGTATCGATACATTTTGGG
64 TTACAAGCCAATGTATCGATACATTTTGGG
*
566878 ATGTATCGATACATATTGTGTGTATCGATCCATGCATTTGAAAAATATAGCCGTTACTAGCCATT
1 ATGTATCGATACATATTGTGTGTATCGATACATGCATTTGAAAAATATAGCCGTTACTAGCCATT
566943 ACAAGCCAATGTATCGATACATTTTGGG
66 ACAAGCCAATGTATCGATACATTTTGGG
566971 ATGTATCGATACATATTGTGTGTATCGATACA
1 ATGTATCGATACATATTGTGTGTATCGATACA
567003 AATTTGGCTA
Statistics
Matches: 122, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
93 103 0.84
94 18 0.15
95 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (93 bp):
ATGTATCGATACATATTGTGTGTATCGATACATGCATTTGAAAAATATAGCCGTTACTAGCCATT
ACAAGCCAATGTATCGATACATTTTGGG
Found at i:566996 original size:19 final size:20
Alignment explanation
Indices: 566951--567002 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
566941 TTACAAGCCA
*
566951 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATATTGGG
*
566971 ATGTATCGATACATATTGTG
1 ATGTATCGATACATATTGGG
566991 -TGTATCGATACA
1 ATGTATCGATACA
567003 AATTTGGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATATTGGG
Found at i:567083 original size:20 final size:21
Alignment explanation
Indices: 567036--567088 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
567026 ACCAATGACC
**
567036 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
567057 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
567077 TGTATCGATACA
1 TGTATCGATACA
567089 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:567094 original size:13 final size:13
Alignment explanation
Indices: 567076--567100 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
567066 ACATTTGGTC
567076 ATGTATCGATACA
1 ATGTATCGATACA
567089 ATGTATCGATAC
1 ATGTATCGATAC
567101 TATGAAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:567115 original size:20 final size:21
Alignment explanation
Indices: 567090--567141 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
567080 ATCGATACAA
567090 TGTATCGATACTA-TGAAATC
1 TGTATCGATACTATTGAAATC
* *
567110 TGTATCGATAC-ATTTAAATG
1 TGTATCGATACTATTGAAATC
567130 TGTATCGATACT
1 TGTATCGATACT
567142 TTTTAGGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACTATTGAAATC
Found at i:567630 original size:15 final size:15
Alignment explanation
Indices: 567599--567637 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
567589 AAAAGTATGT
567599 AAATATATTTTTAAGA
1 AAATAT-TTTTTAAGA
*
567615 AAATATTTTTTTAGA
1 AAATATTTTTTAAGA
567630 AAAT-TTTT
1 AAATATTTT
567638 GGCCTCACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 12 0.55
16 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
AAATATTTTTTAAGA
Found at i:576380 original size:17 final size:17
Alignment explanation
Indices: 576360--576462 Score: 77
Period size: 17 Copynumber: 6.0 Consensus size: 17
576350 AAAAATAATT
*
576360 AAAATAGTATAATATAAA
1 AAAATAATATAATAT-AA
576378 AAAATAAATATAATAT-A
1 AAAAT-AATATAATATAA
576395 AAAATAATATGAATAT--
1 AAAATAATAT-AATATAA
* * * *
576411 AAAGTAACATGATTTAA
1 AAAATAATATAATATAA
*
576428 AATATAATATAATATAA
1 AAAATAATATAATATAA
* *
576445 CAAATAAAATAAATATAA
1 AAAATAATAT-AATATAA
576463 TATAAAAATA
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
15 3 0.04
16 13 0.19
17 30 0.45
18 12 0.18
19 9 0.13
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (17 bp):
AAAATAATATAATATAA
Found at i:576392 original size:5 final size:5
Alignment explanation
Indices: 576354--576467 Score: 58
Period size: 5 Copynumber: 22.8 Consensus size: 5
576344 AATTTTAAAA
* * * * *
576354 ATAAT -TAAA ATAGT ATAAT ATAAA AAAAT A-AAT ATAAT ATAAAA ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT
* * * *
576403 ATGAAT ATAA- AGTAAC ATGATTT AAAAT ATAAT ATAAT ATAAC A-AAT
1 AT-AAT ATAAT A-TAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT
*
576450 AAAAT A-AAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAA
576468 AAATAACATT
Statistics
Matches: 83, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
4 15 0.18
5 55 0.66
6 12 0.14
7 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (5 bp):
ATAAT
Found at i:576412 original size:11 final size:11
Alignment explanation
Indices: 576367--576473 Score: 69
Period size: 11 Copynumber: 9.5 Consensus size: 11
576357 ATTAAAATAG
576367 TATAATATAAA
1 TATAATATAAA
576378 -A-AA-ATAAA
1 TATAATATAAA
576386 TATAATATAAA
1 TATAATATAAA
* *
576397 AATAATATGAA
1 TATAATATAAA
576408 TATAA-AGTAACA
1 TATAATA-TAA-A
*
576420 TGATTTAAAATATAA
1 T-A--TAATATA-AA
576435 TATAATATAACA
1 TATAATATAA-A
* *
576447 AATAAAATAAA
1 TATAATATAAA
576458 TATAATATAAA
1 TATAATATAAA
*
576469 AATAA
1 TATAA
576474 CATTATCGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
8 5 0.07
9 3 0.04
10 4 0.05
11 35 0.47
12 17 0.23
13 1 0.01
14 1 0.01
15 7 0.09
16 2 0.03
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (11 bp):
TATAATATAAA
Found at i:576620 original size:77 final size:77
Alignment explanation
Indices: 576539--576698 Score: 173
Period size: 77 Copynumber: 2.1 Consensus size: 77
576529 AATATGGTCA
** *
576539 AAAATAAAAAATGATACCAAAAAATAAAACGAACATGACACAAAAA-ATAACA-AGAATATA-AA
1 AAAATAAAAAACAATACCAAAAAATAAAACGAACATGACA-AAAAATAAAACACA-AATATACAA
*
576601 AAAATAACACGATCT
64 AAAATAACAC-AACT
** * ** * *
576616 AAAATACGATACAATATGAAAAAATTAAACGAACATGATAAAAAATAAAACACAAATATACAAAA
1 AAAATAAAAAACAATACCAAAAAATAAAACGAACATGACAAAAAATAAAACACAAATATACAAAA
576681 AATAACACAACT
66 AATAACACAACT
576693 AAAATA
1 AAAATA
576699 CTACATGACC
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
76 5 0.07
77 51 0.74
78 13 0.19
ACGTcount: A:0.66, C:0.12, G:0.06, T:0.16
Consensus pattern (77 bp):
AAAATAAAAAACAATACCAAAAAATAAAACGAACATGACAAAAAATAAAACACAAATATACAAAA
AATAACACAACT
Found at i:576699 original size:77 final size:77
Alignment explanation
Indices: 576557--576699 Score: 202
Period size: 77 Copynumber: 1.9 Consensus size: 77
576547 AAATGATACC
* *
576557 AAAAAATAAAACGAACATGACACAAAAAATAACAAGAATATAAAAAAATAACACGATCTAAAATA
1 AAAAAATAAAACGAACATGACACAAAAAAAAACAAGAATATAAAAAAATAACACGAACTAAAATA
576622 CGATACAATATG
66 CGATACAATATG
* *
576634 AAAAAATTAAACGAACATGATA-AAAAATAAAACACA-AATATACAAAAAATAACAC-AACTAAA
1 AAAAAATAAAACGAACATGACACAAAAA-AAAACA-AGAATATA-AAAAAATAACACGAACTAAA
576696 ATAC
63 ATAC
576700 TACATGACCT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
76 5 0.08
77 41 0.69
78 13 0.22
ACGTcount: A:0.66, C:0.13, G:0.06, T:0.15
Consensus pattern (77 bp):
AAAAAATAAAACGAACATGACACAAAAAAAAACAAGAATATAAAAAAATAACACGAACTAAAATA
CGATACAATATG
Found at i:576903 original size:59 final size:60
Alignment explanation
Indices: 576770--576914 Score: 166
Period size: 59 Copynumber: 2.4 Consensus size: 60
576760 ATAGAGTAGC
* * * * *
576770 ATTTTAGATCGTATTATTTTTTCGTGTAATGTTCATTTTATTTTTTTTCTTATCTTATCAT
1 ATTTTAGATCGTGTTA-TTTTTCATGTAATGTTCAATTTATTTTTTTTCATATCATATCAT
* ** *
576831 ATTTTAGGTCGTGTTATTTTTCATGTCCTGTTCAATTTA-TTTTTTTCATATCATATTAT
1 ATTTTAGATCGTGTTATTTTTCATGTAATGTTCAATTTATTTTTTTTCATATCATATCAT
* *
576890 CTTTTACATCGTGTTCATTTTTCAT
1 ATTTTAGATCGTGTT-ATTTTTCAT
576915 ATATTCGTAT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 29 0.41
60 28 0.39
61 14 0.20
ACGTcount: A:0.19, C:0.12, G:0.09, T:0.59
Consensus pattern (60 bp):
ATTTTAGATCGTGTTATTTTTCATGTAATGTTCAATTTATTTTTTTTCATATCATATCAT
Found at i:577053 original size:35 final size:34
Alignment explanation
Indices: 576997--577129 Score: 106
Period size: 35 Copynumber: 3.8 Consensus size: 34
576987 TATATTTATT
* * *
576997 TTATTTTTTCATACCATTTGTATTTTCGATTGTG
1 TTATTTTTTTATATCATTTGTATTTTAGATTGTG
* *
577031 TTATTTTTTTATATCGTGTTGTATTTTAGATTGTT
1 TTATTTTTTTATATCAT-TTGTATTTTAGATTGTG
* * * **
577066 TTATTCTTTATATATTCATAT-TATATTTATATCATG
1 TTATT-TTTTTATA-TCATTTGTAT-TTTAGATTGTG
*
577102 TTAATTTTTTTGTATCATGTTGTATTTT
1 TT-ATTTTTTTATATCAT-TTGTATTTT
577130 TGATCATATT
Statistics
Matches: 77, Mismatches: 15, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
34 14 0.18
35 27 0.35
36 27 0.35
37 9 0.12
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (34 bp):
TTATTTTTTTATATCATTTGTATTTTAGATTGTG
Found at i:577734 original size:29 final size:28
Alignment explanation
Indices: 577673--577743 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 28
577663 GAAAAACGAT
* *
577673 AATATTTTAATAATATATTTAAAAATATC
1 AATA-TTTAATCATATATTTAAAAATATA
*
577702 AATATTTCAATCATTTATTTAAAAA-ATAA
1 AATATTT-AATCATATATTTAAAAATAT-A
577731 AATAGTTTAATCA
1 AATA-TTTAATCA
577744 ATGTGCCTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 5 0.14
29 28 0.78
30 3 0.08
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (28 bp):
AATATTTAATCATATATTTAAAAATATA
Found at i:579008 original size:22 final size:22
Alignment explanation
Indices: 578975--579030 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
578965 TTTTATTAAA
*
578975 AATTTTATAT-TTTATAAT-AT
1 AATTATATATATTTATAATAAT
578995 AATTATATATATTTATAATAAT
1 AATTATATATATTTATAATAAT
579017 AATTATA-AT-TTTAT
1 AATTATATATATTTAT
579031 TTTACTAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 14 0.42
21 10 0.30
22 9 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTATATATATTTATAATAAT
Found at i:579022 original size:12 final size:11
Alignment explanation
Indices: 578986--579025 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
578976 ATTTTATATT
578986 TTATAATATAA
1 TTATAATATAA
*
578997 TTAT-ATATAT
1 TTATAATATAA
579007 TTATAATAATAA
1 TTATAAT-ATAA
579019 TTATAAT
1 TTATAAT
579026 TTTATTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTATAATATAA
Found at i:579106 original size:19 final size:20
Alignment explanation
Indices: 579079--579118 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
579069 TTAAAAGAAT
579079 ATTAATAAAAA-TATATTTA
1 ATTAATAAAAATTATATTTA
*
579098 ATTATTAAAAATTATATTTA
1 ATTAATAAAAATTATATTTA
579118 A
1 A
579119 AAAAACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAATAAAAATTATATTTA
Found at i:579159 original size:20 final size:20
Alignment explanation
Indices: 579134--579173 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
579124 CATATTTTAA
* *
579134 AGGCGCCCACAGCGCACACT
1 AGGCGCACACAGCCCACACT
*
579154 AGGCGCACTCAGCCCACACT
1 AGGCGCACACAGCCCACACT
579174 CACCACACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.45, G:0.23, T:0.07
Consensus pattern (20 bp):
AGGCGCACACAGCCCACACT
Found at i:581482 original size:64 final size:64
Alignment explanation
Indices: 581376--581581 Score: 245
Period size: 63 Copynumber: 3.2 Consensus size: 64
581366 TTCATAATTA
* * * * *
581376 AATTATATCGATACATTGAGCCCAACGGTTATAATTTTAAATGCATTGTTTTCGACACATGGTG
1 AATTGTATCGATACATTGAGCCCAACGGCTATAATTTCAAATGCATTGTTATCGACACATGATG
* * * *
581440 AATTGTATCGAAACATTGAGCCCAACGGCTATAATTTCAAATGTATTG-TATCGATATATGATG
1 AATTGTATCGATACATTGAGCCCAACGGCTATAATTTCAAATGCATTGTTATCGACACATGATG
* * * * * * *
581503 AATTGTATTGATACACTAAGCCCAACGACTAGAATTTCAAATGCATTG-TATCGATACATTATG
1 AATTGTATCGATACATTGAGCCCAACGGCTATAATTTCAAATGCATTGTTATCGACACATGATG
*
581566 GATTGTATCGATACAT
1 AATTGTATCGATACAT
581582 AGGATTGTGT
Statistics
Matches: 121, Mismatches: 21, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
63 78 0.64
64 43 0.36
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (64 bp):
AATTGTATCGATACATTGAGCCCAACGGCTATAATTTCAAATGCATTGTTATCGACACATGATG
Found at i:581593 original size:20 final size:20
Alignment explanation
Indices: 581547--581589 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
581537 TTTCAAATGC
581547 ATTGTATCGATACATTATGG
1 ATTGTATCGATACATTATGG
581567 ATTGTATCGATACA-TA-GG
1 ATTGTATCGATACATTATGG
581585 ATTGT
1 ATTGT
581590 GTATGCGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.30
19 2 0.09
20 14 0.61
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTGTATCGATACATTATGG
Found at i:587828 original size:16 final size:16
Alignment explanation
Indices: 587809--587839 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
587799 AACTTTTACG
587809 AAATAATATCTTATTT
1 AAATAATATCTTATTT
587825 AAATAATATCTTATT
1 AAATAATATCTTATT
587840 GAAAGATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATAATATCTTATTT
Found at i:589279 original size:16 final size:17
Alignment explanation
Indices: 589255--589289 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
589245 TTAACGTAAA
*
589255 ATTATTTTTATATTTTT
1 ATTATTTTTATATTATT
589272 ATTA-TTTTATATTATT
1 ATTATTTTTATATTATT
589288 AT
1 AT
589290 AAAATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTATTTTTATATTATT
Found at i:589548 original size:39 final size:35
Alignment explanation
Indices: 589490--589573 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 35
589480 ATTTCATCTC
*
589490 TAAAATTCTCTTTACTTTATAATGTATATATTTTATTTCT
1 TAAAATT-TCTTTACTTTAT-AT-TATATA-TGT-TTTCT
*
589530 ATAAAATTTC-TTATTTTATATTATATATGTTTTCT
1 -TAAAATTTCTTTACTTTATATTATATATGTTTTCT
589565 TAAAATTTC
1 TAAAATTTC
589574 AATTAACTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
34 9 0.22
35 5 0.12
36 2 0.05
37 6 0.15
38 2 0.05
39 8 0.20
40 2 0.05
41 7 0.17
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.57
Consensus pattern (35 bp):
TAAAATTTCTTTACTTTATATTATATATGTTTTCT
Found at i:590163 original size:39 final size:38
Alignment explanation
Indices: 590114--590222 Score: 95
Period size: 38 Copynumber: 2.9 Consensus size: 38
590104 TATTTATTAA
**
590114 AAAAAT-ATATAATTAATATATTAATTTTTTAATTCAAT
1 AAAAATAATATAATTAATATATTAATTTTTT-ATAAAAT
* *
590152 AAAAATAATAT-ATCAA-ATATAAAATTTTTTATAAAAT
1 AAAAATAATATAATTAATATAT-TAATTTTTTATAAAAT
**
590189 AATAAATAA-ATAATTTTTA-ATTAA-TTTTTATAAA
1 AA-AAATAATATAATTAATATATTAATTTTTTATAAA
590223 TATTCATTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
36 10 0.17
37 15 0.26
38 28 0.48
39 5 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (38 bp):
AAAAATAATATAATTAATATATTAATTTTTTATAAAAT
Found at i:593341 original size:21 final size:21
Alignment explanation
Indices: 593317--593356 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
593307 AATTTTGGAT
* *
593317 ATTTGACTTTTATTAATTATA
1 ATTTAACTTTTAATAATTATA
*
593338 ATTTAATTTTTAATAATTA
1 ATTTAACTTTTAATAATTA
593357 ATTTTTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
ATTTAACTTTTAATAATTATA
Found at i:593357 original size:14 final size:15
Alignment explanation
Indices: 593335--593365 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
593325 TTTATTAATT
593335 ATAATTTAATTTTTA
1 ATAATTTAATTTTTA
593350 ATAA-TTAATTTTTA
1 ATAATTTAATTTTTA
593364 AT
1 AT
593366 TAAAACGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAATTTAATTTTTA
Found at i:594328 original size:16 final size:16
Alignment explanation
Indices: 594304--594335 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
594294 TAAATTTTAT
*
594304 AAACGTTTATATACCA
1 AAACATTTATATACCA
594320 AAACATTTATATACCA
1 AAACATTTATATACCA
594336 TTTTGATGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (16 bp):
AAACATTTATATACCA
Found at i:595340 original size:21 final size:21
Alignment explanation
Indices: 595314--595367 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
595304 TATAATTTTA
*
595314 TATCGATACAAACAGT-AAATG
1 TATCGATACAAAC-CTAAAATG
**
595335 TATCGATACATGCCTAAAATG
1 TATCGATACAAACCTAAAATG
595356 TATCGATACAAA
1 TATCGATACAAA
595368 GCCACCCTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (21 bp):
TATCGATACAAACCTAAAATG
Found at i:597968 original size:77 final size:77
Alignment explanation
Indices: 597877--598147 Score: 278
Period size: 77 Copynumber: 3.5 Consensus size: 77
597867 CTTCTATAAC
597877 ATTAAATTTTTCATCTTAGGGATACTCCAACCCCGTTATTTCTGAAGGGATACTCCAA-CCCATT
1 ATTAAATTTTTCATCTT-GGGATACTCCAACCCCGTTATTT-TGAAGGGATACTCCAACCCCATT
**
597941 TTTATTTTTGAAAT
64 TTTATTTTCAAAAT
* * * *
597955 ATT-ATTTTTTCATCTCGGAGATACTCCAACCCCATTATTTTTAAGGGATACTCCAACCCCATTT
1 ATTAAATTTTTCATCTTGG-GATACTCCAACCCCGTTATTTTGAAGGGATACTCCAACCCCATTT
598019 TTATTTTCAAAAT
65 TTATTTTCAAAAT
* * * * ** ****
598032 ATTAAAATTTTCATCTTGGGAATAC-CTCAACCTCGTTATTTTTTAGGGGATACTTTAACCGTGC
1 ATTAAATTTTTCATCTTGGG-ATACTC-CAACCCCGTTA-TTTTGAAGGGATACTCCAACCCCAT
598096 TTTTATTTTCAAAAT
63 TTTTATTTTCAAAAT
* * *
598111 ATTAAAATTTTCATCATCGGGGGTACTCCAACCCCGT
1 ATTAAATTTTTCATC-T-TGGGATACTCCAACCCCGT
598148 ATTCAAAAGA
Statistics
Matches: 163, Mismatches: 21, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
76 17 0.10
77 54 0.33
78 28 0.17
79 48 0.29
80 12 0.07
81 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.39
Consensus pattern (77 bp):
ATTAAATTTTTCATCTTGGGATACTCCAACCCCGTTATTTTGAAGGGATACTCCAACCCCATTTT
TATTTTCAAAAT
Found at i:598827 original size:315 final size:315
Alignment explanation
Indices: 598147--599408 Score: 2366
Period size: 315 Copynumber: 4.0 Consensus size: 315
598137 TCCAACCCCG
*
598147 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAATTTTTCTC
1 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTC
*
598212 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTATAAAAAAAAAAATCTTCATAGA
66 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTT-TAAAAAAAAAAATCTTCACAGA
598277 ATCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACA
130 ATCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACA
* *
598342 CACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCGTTATTTTGTATAAATATGTTCATTA
195 CACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCGTTA
*
598407 TTTTTTTTCTGTTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
260 TTTTTTTTCCGTTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
598463 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTC
1 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTC
598528 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTT-AAAAAAAAAATCTTCACAGAA
66 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTTAAAAAAAAAAATCTTCACAGAA
598592 TCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACAC
131 TCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACAC
* *
598657 ACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCGTTATTTGGTATAAATATGTTCGTTAT
196 ACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCGTTA-
598722 TTTTTTTTCCGTTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
260 TTTTTTTTCCGTTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
*
598778 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTAAATTTCTTTTAAATTTTAAACTTTTCTC
1 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTC
598843 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTT-AAAAAAAAAATCTTCACAGAA
66 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTTAAAAAAAAAAATCTTCACAGAA
598907 TCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACAC
131 TCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACAC
*
598972 GCTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCGTTAT
196 ACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCGTTA-
*
599037 TTTTTTTTCCATTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
260 TTTTTTTTCCGTTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
599093 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTC
1 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTC
599158 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTTAAAAAAAAAAATCTTCACAGAA
66 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTTAAAAAAAAAAATCTTCACAGAA
* *
599223 TCCGATCAAGTCTTAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACAT
131 TCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACAC
599288 ACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCGTTAT
196 ACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCGTTAT
*
599353 TTTTTTTCCGTTTTACTAACATGTTTTCTTTTATAGGGACCTTATGCATTCATCC
261 TTTTTTTCCGTTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
599408 T
1 T
599409 TTAAAAACTA
Statistics
Matches: 928, Mismatches: 16, Indels: 5
0.98 0.02 0.01
Matches are distributed among these distances:
314 147 0.16
315 528 0.57
316 253 0.27
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (315 bp):
TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTC
TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTTAAAAAAAAAAATCTTCACAGAA
TCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACAC
ACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCGTTAT
TTTTTTTCCGTTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
Found at i:599266 original size:631 final size:630
Alignment explanation
Indices: 598147--599408 Score: 2366
Period size: 631 Copynumber: 2.0 Consensus size: 630
598137 TCCAACCCCG
* *
598147 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAATTTTTCTC
1 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTAAATTTCTTTTAAATTTTAAACTTTTCTC
*
598212 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTATAAAAAAAAAAATCTTCATAGA
66 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTATAAAAAAAAAAATCTTCACAGA
598277 ATCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACA
131 ATCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACA
*
598342 CACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCGTTATTTTGTATAAATATGTTCATTA
196 CACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCATTA
**
598407 TTTTTTTTCTGTTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCCTATTCAAAA
261 TTTTTTTTCCATTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCCTATTCAAAA
598472 GAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTCTAGGGTACC
326 GAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTCTAGGGTACC
598537 CTTAGATCATTAATCCTAACCTCCCATTTTTTTTAAAAAAAAAATCTTCACAGAATCCGATCAAG
391 CTTAGATCATTAATCCTAACCTCCCATTTTTTTTAAAAAAAAAATCTTCACAGAATCCGATCAAG
598602 TCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACACACTTCGACCA
456 TCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACACACTTCGACCA
*
598667 TCCATCCTCTTTATGTATTTTTGTGTGCGTTATTTGGTATAAATATGTTCGTTATTTTTTTTTCC
521 TCCATCCTCTTTATGTATTTTTGTGTGCATTATTTGGTATAAATATGTTCGTTA-TTTTTTTTCC
598732 GTTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
585 GTTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
598778 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTAAATTTCTTTTAAATTTTAAACTTTTCTC
1 TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTAAATTTCTTTTAAATTTTAAACTTTTCTC
598843 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTT-T-AAAAAAAAAATCTTCACAGA
66 TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTATAAAAAAAAAAATCTTCACAGA
598906 ATCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACA
131 ATCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACA
* *
598971 CGCTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCGTTA
196 CACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCATTA
599036 TTTTTTTTTCCATTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCCTATTCAAA
261 -TTTTTTTTCCATTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCCTATTCAAA
599101 AGAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTCTAGGGTAC
325 AGAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTCTAGGGTAC
599166 CCTTAGATCATTAATCCTAACCTCCCATTTTTTTTAAAAAAAAAAATCTTCACAGAATCCGATCA
390 CCTTAGATCATTAATCCTAACCTCCCATTTTTTTT-AAAAAAAAAATCTTCACAGAATCCGATCA
* *
599231 AGTCTTAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACATACTTCGAC
454 AGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACACACTTCGAC
*
599296 CATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCGTTATTTTTTTTC
519 CATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTGGTATAAATATGTTCGTTATTTTTTTTC
*
599361 CGTTTTACTAACATGTTTTCTTTTATAGGGACCTTATGCATTCATCC
584 CGTTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
599408 T
1 T
599409 TTAAAAACTA
Statistics
Matches: 616, Mismatches: 13, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
629 146 0.24
630 219 0.36
631 251 0.41
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (630 bp):
TATTCAAAAGAGACACTCCAACCCTGTTTCTTTTTTAAATTTCTTTTAAATTTTAAACTTTTCTC
TAGGGTACCCTTAGATCATTAATCCTAACCTCCCATTTTTTTATAAAAAAAAAAATCTTCACAGA
ATCCGATCAAGTCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACA
CACTTCGACCATCCATCCTCTTTATGTATTTTTGTGTGCATTATTTTGTATAAATATGTTCATTA
TTTTTTTTCCATTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCCTATTCAAAA
GAGACACTCCAACCCTGTTTCTTTTTTGAATTTCTTTTAAATTTTAAACTTTTCTCTAGGGTACC
CTTAGATCATTAATCCTAACCTCCCATTTTTTTTAAAAAAAAAATCTTCACAGAATCCGATCAAG
TCTCAACATTGTTATCATGATTATTCATCAATAACCAAAGACAATCACGAGACACACTTCGACCA
TCCATCCTCTTTATGTATTTTTGTGTGCATTATTTGGTATAAATATGTTCGTTATTTTTTTTCCG
TTTTACTAACATGTTTCCTTTTATAGGGACCTTATGCATTCATCC
Found at i:612657 original size:20 final size:20
Alignment explanation
Indices: 612632--612684 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
612622 ATGTATCAAA
* *
612632 TGTATCGATTCATTGAAGAT
1 TGTATCGATACATTGAAAAT
612652 TGTATCGATACATTGAAAAT
1 TGTATCGATACATTGAAAAT
*
612672 TTTATCGATACAT
1 TGTATCGATACAT
612685 CTAGGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTGAAAAT
Found at i:614216 original size:24 final size:24
Alignment explanation
Indices: 614189--614236 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
614179 ATTTAAAAAG
614189 TATCTATCTAACAGTTATACCCTT
1 TATCTATCTAACAGTTATACCCTT
*
614213 TATCTATCTAACAGTTGTACCCTT
1 TATCTATCTAACAGTTATACCCTT
614237 CTCCCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (24 bp):
TATCTATCTAACAGTTATACCCTT
Found at i:619631 original size:13 final size:14
Alignment explanation
Indices: 619606--619634 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
619596 TATGTTTAGG
619606 TTTATTCATTTTAT
1 TTTATTCATTTTAT
619620 TTTATT-ATTTTAT
1 TTTATTCATTTTAT
619633 TT
1 TT
619635 ACCTTCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTCATTTTAT
Found at i:620217 original size:71 final size:72
Alignment explanation
Indices: 620131--620288 Score: 212
Period size: 71 Copynumber: 2.2 Consensus size: 72
620121 AAAGGCAAAC
* * * *
620131 TTTTAAGGGATTTTTCATAGCTTGGCCAAATTTAGAAGAGCATTTTGGT-CATTTTCCAAGTCAA
1 TTTTAAGGGATTTTTCATAGCTTAGCCAAACTTAGAAGAGCATTTTAGTAAATTTTCCAAGTCAA
620195 GCATGCA
66 GCATGCA
* * *
620202 TTTTAAGGGCA-TTTTCCTAGCTTAGCCTAACTTAGAAGGGCATTTTAGTAAATTTTCCAAGTCA
1 TTTTAAGGG-ATTTTTCATAGCTTAGCCAAACTTAGAAGAGCATTTTAGTAAATTTTCCAAGTCA
620266 AGCATGCA
65 AGCATGCA
*
620274 TTTTAGAGGTATTTT
1 TTTTA-AGGGATTTT
620289 CTTACCTTAG
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
71 41 0.55
72 28 0.37
73 6 0.08
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (72 bp):
TTTTAAGGGATTTTTCATAGCTTAGCCAAACTTAGAAGAGCATTTTAGTAAATTTTCCAAGTCAA
GCATGCA
Found at i:622661 original size:21 final size:19
Alignment explanation
Indices: 622637--622684 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
622627 CAATGATATC
622637 GATACAATTGCATATTGTATG
1 GATACAATTGCA-ATTGT-TG
* * *
622658 GATATAATTGTAATTGTTT
1 GATACAATTGCAATTGTTG
622677 GATACAAT
1 GATACAAT
622685 ATCACATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 8 0.35
20 5 0.22
21 10 0.43
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (19 bp):
GATACAATTGCAATTGTTG
Found at i:623364 original size:12 final size:13
Alignment explanation
Indices: 623349--623400 Score: 61
Period size: 12 Copynumber: 3.9 Consensus size: 13
623339 AAAGAAAACC
623349 AAAAAAAAAAG-G
1 AAAAAAAAAAGAG
623361 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
*
623374 AAAAGAAAAAAAAAG
1 -AAA-AAAAAAAGAG
*
623389 AAAAAGAAAAGA
1 AAAAAAAAAAGA
623401 AAAGAAATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 11 0.32
13 8 0.24
14 6 0.18
15 9 0.26
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:623399 original size:21 final size:20
Alignment explanation
Indices: 623349--623403 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
623339 AAAGAAAACC
*
623349 AAAAAA-AAAAG-GAAAAAA
1 AAAAAAGAAAAGAAAAAAAA
*
623367 AAAAGAGAAAAGAAAAAAAA
1 AAAAAAGAAAAGAAAAAAAA
623387 AGAAAAAGAAAAGAAAA
1 A-AAAAAGAAAAGAAAA
623404 GAAATGGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.16
19 5 0.16
20 7 0.23
21 14 0.45
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAGAAAAAAAA
Found at i:623404 original size:5 final size:5
Alignment explanation
Indices: 623350--623407 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
623340 AAGAAAACCA
* * *
623350 AAAAA AAAAGG AAAA- AAAA- AAGAG AAAAG AAAAA AAAAG AAAAAG AAAAG
1 AAAAG AAAA-G AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG
623400 AAAAG AAA
1 AAAAG AAA
623408 TGGTTTCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
4 7 0.16
5 29 0.64
6 9 0.20
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:624117 original size:58 final size:58
Alignment explanation
Indices: 624047--624311 Score: 225
Period size: 58 Copynumber: 4.6 Consensus size: 58
624037 TTAAATAGTA
* * *
624047 TTATGTCATTTCATACATTTTAAGGTCATTTTAGCT-ATTTATT-ATAATTTAGGGA-CCT
1 TTATGCCATTTCATGCATTTTAAGGTCATTTTAG-TAATTT-TTCATAATTTA-GGATCAT
* * ** * *
624105 TTATGCCATTTCATGCATTTT-AGGTTCATTTTACTCATTTGCCATGATTTAGGATTAT
1 TTATGCCATTTCATGCATTTTAAGG-TCATTTTAGTAATTTTTCATAATTTAGGATCAT
** * * * * * *
624163 TTATGTAATTTCATGTATTTTAAGATCATTTTAGTAATTTTTCATAATTAACGACCTT
1 TTATGCCATTTCATGCATTTTAAGGTCATTTTAGTAATTTTTCATAATTTAGGATCAT
* * * *
624221 TTA-GGCATTTTCATGCATTGTAAGCTCATTCTAGTAATTTTTCATAATTTAGGATCAT
1 TTATGCCA-TTTCATGCATTTTAAGGTCATTTTAGTAATTTTTCATAATTTAGGATCAT
* * * *
624279 TTATGCAATTTCATACATTTTATGGTCACTTTA
1 TTATGCCATTTCATGCATTTTAAGGTCATTTTA
624312 ATCATTTTCC
Statistics
Matches: 160, Mismatches: 40, Indels: 14
0.75 0.19 0.07
Matches are distributed among these distances:
57 9 0.06
58 147 0.92
59 4 0.03
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (58 bp):
TTATGCCATTTCATGCATTTTAAGGTCATTTTAGTAATTTTTCATAATTTAGGATCAT
Found at i:624271 original size:116 final size:116
Alignment explanation
Indices: 624047--624300 Score: 282
Period size: 116 Copynumber: 2.2 Consensus size: 116
624037 TTAAATAGTA
* * **
624047 TTATGTCATTTCATACATTTTAAGGTCATTTTAGCTATTTATTATAATTTAGGGACCTTTATGCC
1 TTATGTAATTTCATACATTTTAAGATCATTTTAGCTATTTATTATAATTTAACGACCTTTATGCC
* * * * * * *
624112 ATTTCATGCATTTTAGGTTCATTTTACTCATTTGCCATGATTTAGGATTAT
66 ATTTCATGCATTGTAAGCTCATTCTACTAATTTGCCATAATTTAGGATCAT
**
624163 TTATGTAATTTCATGTATTTTAAGATCATTTTAG-TAATTT-TTCATAA-TTAACGACCTTT-TA
1 TTATGTAATTTCATACATTTTAAGATCATTTTAGCT-ATTTATT-ATAATTTAACGACCTTTAT-
* * **
624224 GGCATTTTCATGCATTGTAAGCTCATTCTAGTAATTTTTCATAATTTAGGATCAT
63 GCCA-TTTCATGCATTGTAAGCTCATTCTACTAATTTGCCATAATTTAGGATCAT
*
624279 TTATGCAATTTCATACATTTTA
1 TTATGTAATTTCATACATTTTA
624301 TGGTCACTTT
Statistics
Matches: 114, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
114 1 0.01
115 16 0.14
116 97 0.85
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (116 bp):
TTATGTAATTTCATACATTTTAAGATCATTTTAGCTATTTATTATAATTTAACGACCTTTATGCC
ATTTCATGCATTGTAAGCTCATTCTACTAATTTGCCATAATTTAGGATCAT
Found at i:639077 original size:1 final size:1
Alignment explanation
Indices: 639071--639105 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
639061 CAATCAAGTG
* *
639071 AAAAAAAAAAAAAAAAAAAAAAAAACAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
639106 GCCTCGCACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:641099 original size:26 final size:26
Alignment explanation
Indices: 641070--641121 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
641060 TAAGTTAGAG
*
641070 AAAATTTTTTGTGATCGTTTTGTGTC
1 AAAATTTTTTATGATCGTTTTGTGTC
*
641096 AAAATTTTTTATGTTCGTTTTGTGTC
1 AAAATTTTTTATGATCGTTTTGTGTC
641122 TTCCTCTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.08, G:0.17, T:0.56
Consensus pattern (26 bp):
AAAATTTTTTATGATCGTTTTGTGTC
Found at i:645773 original size:16 final size:15
Alignment explanation
Indices: 645754--645783 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
645744 TATTAATTAT
645754 AAATTTAAATCAAATC
1 AAATTTAAA-CAAATC
645770 AAATTTAAACAAAT
1 AAATTTAAACAAAT
645784 TATTTGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTTAAACAAATC
Found at i:646454 original size:18 final size:19
Alignment explanation
Indices: 646413--646456 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
646403 TTATGTTATA
* *
646413 AATATTTTTTTAGTAACTT
1 AATATTTTTTTAGAAAATT
646432 AATATTTTTTTAGAAAATT
1 AATATTTTTTTAGAAAATT
646451 -ATATTT
1 AATATTT
646457 AATTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
AATATTTTTTTAGAAAATT
Found at i:646811 original size:20 final size:20
Alignment explanation
Indices: 646786--646825 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
646776 ATGTTATCCA
646786 TAACCTCTAAACAAATATTT
1 TAACCTCTAAACAAATATTT
646806 TAACCTCTAAACAAATATTT
1 TAACCTCTAAACAAATATTT
646826 GTCCATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (20 bp):
TAACCTCTAAACAAATATTT
Found at i:647607 original size:18 final size:19
Alignment explanation
Indices: 647572--647607 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
647562 TGAATGAAAG
*
647572 AATGTATTTTTTAGATAAA
1 AATGTAGTTTTTAGATAAA
647591 AATGTAGTTTTTA-ATAA
1 AATGTAGTTTTTAGATAA
647608 TTAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (19 bp):
AATGTAGTTTTTAGATAAA
Found at i:648430 original size:23 final size:24
Alignment explanation
Indices: 648404--648455 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
648394 TAAACATCAA
648404 ATAAATAA-ATATACAAATA-TTTT
1 ATAAATAATATATA-AAATATTTTT
*
648427 ATAAA-AATATATAATATATTTTT
1 ATAAATAATATATAAAATATTTTT
648450 ATAAAT
1 ATAAAT
648456 TAAGTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
ATAAATAATATATAAAATATTTTT
Found at i:648455 original size:21 final size:21
Alignment explanation
Indices: 648408--648455 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
648398 CATCAAATAA
648408 ATAAATATACAAATATTTTAT
1 ATAAATATACAAATATTTTAT
* *
648429 AAAAATATATAATATATTTT-T
1 ATAAATATACAA-ATATTTTAT
648450 ATAAAT
1 ATAAAT
648456 TAAGTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAATATACAAATATTTTAT
Found at i:651202 original size:13 final size:13
Alignment explanation
Indices: 651184--651208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
651174 CATAAAGTGT
651184 TGTATCGATACAA
1 TGTATCGATACAA
651197 TGTATCGATACA
1 TGTATCGATACA
651209 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:651206 original size:33 final size:33
Alignment explanation
Indices: 651164--651230 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
651154 TTCAACGATT
651164 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
651197 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
651230 T
1 T
651231 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:651289 original size:13 final size:13
Alignment explanation
Indices: 651271--651295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
651261 ATTACTCAAA
651271 TGTATCGATACAT
1 TGTATCGATACAT
651284 TGTATCGATACA
1 TGTATCGATACA
651296 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:651360 original size:52 final size:52
Alignment explanation
Indices: 651304--651432 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
651294 CACTGATCTT
* *
651304 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATATATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
651356 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
651408 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
651433 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:657155 original size:16 final size:16
Alignment explanation
Indices: 657136--657210 Score: 80
Period size: 16 Copynumber: 4.7 Consensus size: 16
657126 AAAATGACTT
657136 GAACCCGAAATGATCC
1 GAACCCGAAATGATCC
* *
657152 GAACTCAAAATGATCC
1 GAACCCGAAATGATCC
* *
657168 AAACCCAAAATGA-CTC
1 GAACCCGAAATGATC-C
*
657184 GAATCCGAAATGATCC
1 GAACCCGAAATGATCC
*
657200 GAACCTGAAAT
1 GAACCCGAAAT
657211 AGCTAGAACA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
15 1 0.02
16 46 0.96
17 1 0.02
ACGTcount: A:0.43, C:0.27, G:0.15, T:0.16
Consensus pattern (16 bp):
GAACCCGAAATGATCC
Found at i:659578 original size:21 final size:21
Alignment explanation
Indices: 659553--659604 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
659543 AAATTGGTTA
659553 AAAAATATTTTTATAAGA-TAAT
1 AAAAA-ATTTTTATAA-ATTAAT
*
659575 AAAAAATATTTATAAATTAAT
1 AAAAAATTTTTATAAATTAAT
659596 AAAAAATTT
1 AAAAAATTT
659605 AAATTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 21 0.78
22 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAAATTTTTATAAATTAAT
Found at i:663877 original size:1 final size:1
Alignment explanation
Indices: 663873--663897 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
663863 AAAATGCGGT
663873 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
663898 CTGGGGCCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:670978 original size:18 final size:17
Alignment explanation
Indices: 670941--670980 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
670931 CTATTTGTAG
* *
670941 AAAAATAATAATTGATT
1 AAAAATAATAATTAACT
670958 AAAAATACATAATTAACT
1 AAAAATA-ATAATTAACT
670976 AAAAA
1 AAAAA
670981 GTGACACGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAAATAATAATTAACT
Found at i:671782 original size:3 final size:3
Alignment explanation
Indices: 671774--671809 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
671764 GGGTTTGGAT
*
671774 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGA TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
671810 AGGAGGAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.00, G:0.64, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:672462 original size:13 final size:12
Alignment explanation
Indices: 672434--672496 Score: 56
Period size: 13 Copynumber: 5.2 Consensus size: 12
672424 TATAACTTTT
672434 ATATTTAAAATA
1 ATATTTAAAATA
*
672446 ATATTTAAAAATG
1 ATATTT-AAAATA
*
672459 ATATTTCAAGATA
1 ATATTT-AAAATA
* *
672472 ATA-TTGATATA
1 ATATTTAAAATA
*
672483 ATATTTTAAATA
1 ATATTTAAAATA
672495 AT
1 AT
672497 TTAGTACATA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 7 0.17
12 16 0.39
13 18 0.44
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.43
Consensus pattern (12 bp):
ATATTTAAAATA
Found at i:677769 original size:2 final size:2
Alignment explanation
Indices: 677762--677805 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
677752 TAGATTTGTG
677762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
677804 AT
1 AT
677806 GAATTATTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:679636 original size:18 final size:18
Alignment explanation
Indices: 679610--679645 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
679600 TTATGAAATT
*
679610 CTTATATAGAAATCTACA
1 CTTACATAGAAATCTACA
679628 CTTACATAGAAATCTACA
1 CTTACATAGAAATCTACA
679646 TACTCTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (18 bp):
CTTACATAGAAATCTACA
Found at i:682595 original size:2 final size:2
Alignment explanation
Indices: 682588--682629 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
682578 AATATTAATA
**
682588 AT AT AT AT GC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
682630 TTATGTGTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:684655 original size:92 final size:92
Alignment explanation
Indices: 684521--684690 Score: 220
Period size: 92 Copynumber: 1.8 Consensus size: 92
684511 GATTTTAAAG
* * ** *
684521 ATTAGACTAATGCATAGATTATTTTTGAGAATTGGATTCCTTTAGCA-AAAAAG-AAAATAAAGT
1 ATTAGACTAATGCATAGATTATTTTTAAAAATCAGATTCCTTT-G-ATAAAAAGAAAAAAAAAGT
684584 -TAATTGATTATAAATTTTAGACAACAAAA
64 CT-ATTGATTATAAATTTTAGACAACAAAA
* * *
684613 ATTAGATTAATTCATAGATTATTTTTAAAAATCAGATTCCTTTGATAGAAAGAAAAAAAAAGTCT
1 ATTAGACTAATGCATAGATTATTTTTAAAAATCAGATTCCTTTGATAAAAAGAAAAAAAAAGTCT
684678 ATTGATTATAAAT
66 ATTGATTATAAAT
684691 ATCATACTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
90 1 0.01
91 6 0.09
92 59 0.88
93 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (92 bp):
ATTAGACTAATGCATAGATTATTTTTAAAAATCAGATTCCTTTGATAAAAAGAAAAAAAAAGTCT
ATTGATTATAAATTTTAGACAACAAAA
Found at i:686854 original size:11 final size:12
Alignment explanation
Indices: 686830--686859 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
686820 ATCTCTTTTG
686830 TTATTTTTACTT
1 TTATTTTTACTT
686842 TTATTTTTA-TT
1 TTATTTTTACTT
686853 TTATTTT
1 TTATTTT
686860 AATTAATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (12 bp):
TTATTTTTACTT
Found at i:688251 original size:51 final size:50
Alignment explanation
Indices: 688178--688307 Score: 165
Period size: 51 Copynumber: 2.6 Consensus size: 50
688168 GGAGTATCCC
*
688178 TTTGGAAAT--AACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGT
1 TTTGGAAATAAAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATGT
* * *
688226 TTTGGAAATAAAACTGGGGTTAGAGTATCTCCGATTGTGAAAAATTGATGT
1 TTTGGAAATAAAAC-GGGGTTAGAGTATCCCCGATGGTGAAAAATCGATGT
* * * *
688277 TTTAGAAATAAAACCGGGTTGGGGTATCCCC
1 TTTGGAAATAAAACGGGGTTAGAGTATCCCC
688308 TTAGAAGTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
48 9 0.13
50 16 0.23
51 45 0.64
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (50 bp):
TTTGGAAATAAAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATGT
Found at i:688286 original size:130 final size:130
Alignment explanation
Indices: 688111--688597 Score: 613
Period size: 130 Copynumber: 3.8 Consensus size: 130
688101 GAGATAACAT
* * * * * * *
688111 GGGGCTGGAGTATCCTCGATTATGAAAAATTGGTGGTCT-GAAAATAAAATCGGGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTAG-AAATAAAATCGGGGTTGAAGTAT
* * *
688175 CCCTTTGGAAATAACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGGAAATAAAAC
65 CCCCTTAGAAATAACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGAAAATAAAAC
*
688240 T
130 C
* * * **
688241 GGGGTTAGAGTATCTCCGATTGTGAAAAATTGATGTTTTAGAAATAAAA-CCGGGTTGGGGTATC
1 GGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGAAGTATC
* * * ** * * *
688305 CCCTTAGAAGTAACGAGGTTGGAGTATCCCCGATTATGAAAAAT-TAGTGTTTTTAAAATAAAAC
66 CCCTTAGAAATAACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGA-TGTTTTGAAAATAAAAC
688369 C
130 C
* * * *
688370 AGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTAAAAATAAAACCGGGGTTGAAGTATC
1 GGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGAAGTATC
* *
688435 CCCTTAGAAATAACGGGGTTAGAGTATCCCTGATGGTGGTAAATCGATGTTTTGAAAATAAAACC
66 CCCTTAGAAATAACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGAAAATAAAACC
* * *
688500 GGAGATGGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGAGGTTGAAGTAT-
1 GGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGAAGTATC
* *
688564 CCCTCAGAAATAACGGGGTTGGAGTATCCCCGAT
66 CCCTTAGAAATAACGGGGTTAGAGTATCCCCGAT
688598 TGTAAAAAAA
Statistics
Matches: 303, Mismatches: 50, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
128 1 0.00
129 139 0.46
130 161 0.53
131 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (130 bp):
GGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGAAGTATC
CCCTTAGAAATAACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGAAAATAAAACC
Found at i:688399 original size:51 final size:51
Alignment explanation
Indices: 688321--688437 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 51
688311 GAAGTAACGA
*
688321 GGTTGGAGTATCCCCGATTATGAAAAATT-AGTGTTTTTAAAATAAAACCAG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGA-TGTTTTAAAAATAAAACCAG
* * *
688372 GGTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTAAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAAAAATAAAACCAG
*
688423 GGTTGAAGTATCCCC
1 GGTTGGAGTATCCCC
688438 TTAGAAATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 59 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAAAAATAAAACCAG
Found at i:688464 original size:79 final size:79
Alignment explanation
Indices: 688371--688516 Score: 211
Period size: 79 Copynumber: 1.8 Consensus size: 79
688361 AATAAAACCA
* * * * *
688371 GGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTAAAAATAAAACCGGGGTTGAAGTATCC
1 GGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTAAAAATAAAACCGGAGATGAAGTATCC
688436 CCTTAGAAATAACG
66 CCTTAGAAATAACG
* * * *
688450 GGGTTAGAGTATCCCTGATGGTGGTAAATCGATGTTTTGAAAATAAAACCGGAGATGGAGTATCC
1 GGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTAAAAATAAAACCGGAGATGAAGTATCC
688515 CC
66 CC
688517 GATTGTGAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 58 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (79 bp):
GGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTAAAAATAAAACCGGAGATGAAGTATCC
CCTTAGAAATAACG
Found at i:688521 original size:259 final size:260
Alignment explanation
Indices: 688116--688617 Score: 729
Period size: 259 Copynumber: 1.9 Consensus size: 260
688106 AACATGGGGC
* * * * * *
688116 TGGAGTATCCTCGATTATGAAAAATTGGTGGTCTGAAAATAAAATCGGGGTTGGAGTATCCCTTT
1 TGGAGTATCCCCGATTATGAAAAATTGATGGTCTAAAAATAAAACCGGGGTTGAAGTATCCCCTT
* * * * *
688181 GGAAATAACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGGAAATAAAACTGGGGT
66 AGAAATAACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGAAAATAAAACCGGAGA
* ** *
688246 TAGAGTATCTCCGATTGTGAAAAATTGATGTTTTAGAAATAAAACCG-GGTTGGGGTATCCCCTT
131 TAGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGAAGTAT-CCCTC
* *
688310 AGAAGTAACGAGGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTTAAAATAAAACCAGGG
195 AGAAATAACGAGGTTGGAGTATCCCCGATTATAAAAAAATTAGTGTTTTTAAAATAAAACCAGGG
688374 T
260 T
* * * *
688375 TGGAGTATCCCCGATTGTGGAAAATTGATGTTTTAAAAATAAAACCGGGGTTGAAGTATCCCCTT
1 TGGAGTATCCCCGATTATGAAAAATTGATGGTCTAAAAATAAAACCGGGGTTGAAGTATCCCCTT
* *
688440 AGAAATAACGGGGTTAGAGTATCCCTGATGGTGGTAAATCGATGTTTTGAAAATAAAACCGGAGA
66 AGAAATAACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGAAAATAAAACCGGAGA
* *
688505 TGGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGAGGTTGAAGTATCCCTCA
131 TAGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGAAGTATCCCTCA
* * *
688570 GAAATAACGGGGTTGGAGTATCCCCGATTGTAAAAAAATTGGTGTTTT
196 GAAATAACGAGGTTGGAGTATCCCCGATTATAAAAAAATTAGTGTTTT
688618 GGAAGTAAAA
Statistics
Matches: 213, Mismatches: 28, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
259 190 0.89
260 23 0.11
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (260 bp):
TGGAGTATCCCCGATTATGAAAAATTGATGGTCTAAAAATAAAACCGGGGTTGAAGTATCCCCTT
AGAAATAACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGAAAATAAAACCGGAGA
TAGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGAAGTATCCCTCA
GAAATAACGAGGTTGGAGTATCCCCGATTATAAAAAAATTAGTGTTTTTAAAATAAAACCAGGGT
Found at i:691029 original size:49 final size:50
Alignment explanation
Indices: 690973--691102 Score: 201
Period size: 49 Copynumber: 2.6 Consensus size: 50
690963 AAAAATGCCT
* * *
690973 GAATGTATCGATACATTGCAA-AATGTATCGGTACATCTGGGT-AAACCTA
1 GAATGTATCGATACAATG-AACAATGTATCGATACATCTGGGTAAAACCCA
691022 GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCCA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCCA
*
691072 GAATGTATCGATACAATGAATAATGTATCGA
1 GAATGTATCGATACAATGAACAATGTATCGA
691103 CACAAATTGT
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
48 2 0.03
49 37 0.49
50 36 0.48
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (50 bp):
GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCCA
Found at i:691991 original size:31 final size:30
Alignment explanation
Indices: 691953--692057 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 30
691943 TAGTAACATA
691953 ATATAAATGATAAAAAAATACTATAAAAATG
1 ATATAAATGATAAAAAAATA-TATAAAAATG
* * *
691984 ATATAAATGACAAAAACATA-ATATAAATG
1 ATATAAATGATAAAAAAATATATAAAAATG
* * *
692013 ATATAAATAATAGAAATAGATATTGTAGAAAA-G
1 ATATAAATGATA-AAA-AAATA-TATA-AAAATG
692046 ATATAAATGATA
1 ATATAAATGATA
692058 GAAACATAAG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
29 18 0.30
30 3 0.05
31 22 0.37
33 14 0.23
34 3 0.05
ACGTcount: A:0.61, C:0.03, G:0.10, T:0.27
Consensus pattern (30 bp):
ATATAAATGATAAAAAAATATATAAAAATG
Found at i:692061 original size:18 final size:19
Alignment explanation
Indices: 692008--692061 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 19
691998 AACATAATAT
*
692008 AAAT-GATATAAATAATAG
1 AAATAGATATAAATGATAG
692026 AAATAGATAT---TG-TAG
1 AAATAGATATAAATGATAG
692041 AAA-AGATATAAATGATAG
1 AAATAGATATAAATGATAG
692059 AAA
1 AAA
692062 CATAAGCAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
14 6 0.20
15 6 0.20
16 1 0.03
17 2 0.07
18 10 0.33
19 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (19 bp):
AAATAGATATAAATGATAG
Found at i:692079 original size:62 final size:62
Alignment explanation
Indices: 691938--692103 Score: 160
Period size: 62 Copynumber: 2.7 Consensus size: 62
691928 TCTTATAATG
* *
691938 AACATTAGTAACATAATATAAATGATA-AAA-AAATACTATAAAAATGATATAAATGACAAA
1 AACATAAGTAACATAATATAAATAATAGAAATAAATACTATAAAAATGATATAAATGACAAA
* * * * * * *
691998 AACATAA-TATAAATGATATAAATAATAGAAATAGATATTGTAGAAAA-GATATAAATGATAGA
1 AACATAAGTA-ACATAATATAAATAATAGAAATAAATACTATA-AAAATGATATAAATGACAAA
* * * * *
692060 AACATAAGCAACATAATATAAGTTATAGAAATACATAATATAAA
1 AACATAAGTAACATAATATAAATAATAGAAATAAATACTATAAA
692104 GGAATTATTA
Statistics
Matches: 84, Mismatches: 17, Indels: 9
0.76 0.15 0.08
Matches are distributed among these distances:
59 2 0.02
60 20 0.24
61 5 0.06
62 52 0.62
63 5 0.06
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (62 bp):
AACATAAGTAACATAATATAAATAATAGAAATAAATACTATAAAAATGATATAAATGACAAA
Found at i:692198 original size:14 final size:14
Alignment explanation
Indices: 692179--692212 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
692169 ATTCATAACA
*
692179 TTAATAGACAAGAT
1 TTAATACACAAGAT
692193 TTAATACACAAGAT
1 TTAATACACAAGAT
692207 TTAATA
1 TTAATA
692213 TTCCTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (14 bp):
TTAATACACAAGAT
Done.