Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009633.1 Hibiscus syriacus cultivar Beakdansim tig00117032_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2608659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1389357 original size:36 final size:36
Alignment explanation
Indices: 1389308--1389417 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 36
1389298 AAATATTGAA
*
1389308 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
*
1389344 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--A
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * * * *
1389378 CTTCCAAAAGAAACTGTCTCAAGGGAGACGAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
1389414 GTTT
1 GTTT
1389418 AACGTAAAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
34 27 0.44
36 34 0.56
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:1389390 original size:34 final size:35
Alignment explanation
Indices: 1389317--1389406 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 35
1389307 AGTTTCAAGG
** * *
1389317 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TACTTCCAAAA
1389353 GAAACTGTCTCAAGAGAGACAAAA-ACTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
*
1389387 GAAACTGTCTCAAGGGAGAC
1 GAAACTGTCTCAAGAGAGAC
1389407 GAGATTTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 25 0.51
36 24 0.49
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
Found at i:1389522 original size:36 final size:36
Alignment explanation
Indices: 1389475--1389653 Score: 117
Period size: 36 Copynumber: 5.1 Consensus size: 36
1389465 AAGTTTATGC
1389475 TTCAAGAGAAACTGTCTCAATGGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAATGGAGACAAAATTTGT
* * * **
1389511 TTCAAGGGAAACTATCTC-ATGAGTGACAAAATTCAT
1 TTCAAGAGAAACTGTCTCAATG-GAGACAAAATTTGT
* * * *
1389547 TTCAAGGGGAA-TGTTTTCAAT---G-----TTTATGT
1 TTCAAGAGAAACTG-TCTCAATGGAGACAAAATT-TGT
1389576 TTCAAGAGAAACTGTCTCAATGGAGACAAAATTTTGT
1 TTCAAGAGAAACTGTCTCAATGGAGACAAAA-TTTGT
* * * ** *
1389613 TTCAAAAGAAAATGTCTCAAGGGAGATGAAATTAGT
1 TTCAAGAGAAACTGTCTCAATGGAGACAAAATTTGT
1389649 TTCAA
1 TTCAA
1389654 TGAAAACATA
Statistics
Matches: 108, Mismatches: 21, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
28 2 0.02
29 16 0.15
30 2 0.02
32 1 0.01
33 1 0.01
35 4 0.04
36 49 0.45
37 31 0.29
38 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (36 bp):
TTCAAGAGAAACTGTCTCAATGGAGACAAAATTTGT
Found at i:1389645 original size:37 final size:36
Alignment explanation
Indices: 1389573--1389653 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 36
1389563 TCAATGTTTA
* * *
1389573 TGTTTCAAGAGAAACTGTCTCAATGGAGACAAAATTT
1 TGTTTCAAAAGAAAATGTCTCAAGGGAGACAAAA-TT
**
1389610 TGTTTCAAAAGAAAATGTCTCAAGGGAGATGAAATT
1 TGTTTCAAAAGAAAATGTCTCAAGGGAGACAAAATT
*
1389646 AGTTTCAA
1 TGTTTCAA
1389654 TGAAAACATA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
36 9 0.24
37 29 0.76
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.30
Consensus pattern (36 bp):
TGTTTCAAAAGAAAATGTCTCAAGGGAGACAAAATT
Found at i:1389682 original size:102 final size:101
Alignment explanation
Indices: 1389459--1389690 Score: 245
Period size: 102 Copynumber: 2.3 Consensus size: 101
1389449 AAGGAAATTG
* ** *
1389459 TTTTCAA-AGTTTATGCTTCAAGAGAAACTGTCTCAATGGAGACAAAATTTGTTTCAAGGGAAAC
1 TTTTCAATA-TTTATGTTTCAAGAGAAACTGTCTCAATGGAGACAAAATTTGTTTCAAAAGAAAA
* * ** **
1389523 TATCTCATGAGTGACAAAATTCATTTCAAGGGGAATG
65 TATCTCAAGAGAGACAAAATTCATTTCAAGGAAAACA
*
1389560 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAATGGAGACAAAATTTTGTTTCAAAAGAAAA
1 TTTTCAATATTTATGTTTCAAGAGAAACTGTCTCAATGGAGACAAAA-TTTGTTTCAAAAGAAAA
* * ** *
1389625 TGTCTCAAGGGAGATGAAATT-AGTTTCAATGAAAACA
65 TATCTCAAGAGAGACAAAATTCA-TTTCAAGGAAAACA
* *
1389662 TATTTGAATATTT-TGTTTCAAGGGAAACT
1 T-TTTCAATATTTATGTTTCAAGAGAAACT
1389691 TGGAAACTGT
Statistics
Matches: 108, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
101 45 0.42
102 54 0.50
103 9 0.08
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (101 bp):
TTTTCAATATTTATGTTTCAAGAGAAACTGTCTCAATGGAGACAAAATTTGTTTCAAAAGAAAAT
ATCTCAAGAGAGACAAAATTCATTTCAAGGAAAACA
Found at i:1390030 original size:106 final size:106
Alignment explanation
Indices: 1389838--1390160 Score: 457
Period size: 106 Copynumber: 3.0 Consensus size: 106
1389828 TGTATTGTTC
* * * * * **
1389838 CGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* * * *** * *
1389903 GCCAGCCAGCCCTTTACTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
1389944 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1390009 ACCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
1390050 CGAGTCCAATATCCTTTGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* *
1390115 ACCAGTCATCCCTTCGTTGTGGAGTTGAACTTGTGTTGACT
66 ACCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1390156 CGAGT
1 CGAGT
1390161 GACACGATAT
Statistics
Matches: 194, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
106 194 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
ACCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:1390778 original size:32 final size:31
Alignment explanation
Indices: 1390737--1390823 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 31
1390727 TTTGCATCAG
* *
1390737 GATGTTGAATTCCCAAAGATGCCCCAATATTC
1 GATGTTGAA-TCTCAAAGATGCCCCAACATTC
* * *
1390769 GATGTTGAATCTAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAGATGCCCCAACATTC
*
1390800 GATGTAGAATCTTCAAAGATGCCC
1 GATGTTGAATC-TCAAAGATGCCC
1390824 TCATTGTTCC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 27 0.59
32 19 0.41
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (31 bp):
GATGTTGAATCTCAAAGATGCCCCAACATTC
Found at i:1391933 original size:13 final size:12
Alignment explanation
Indices: 1391912--1391964 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
1391902 TTTTCTTCAA
*
1391912 TTTTCCTCTATTT
1 TTTTTCTCT-TTT
1391925 TTTTTCTCTTTT
1 TTTTTCTCTTTT
* *
1391937 TATGTTCTCTTTGC
1 T-TTTTCTCTTT-T
1391951 TTTTTCTCTTTT
1 TTTTTCTCTTTT
1391963 TT
1 TT
1391965 CCCTTTTTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
12 6 0.18
13 26 0.79
14 1 0.03
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:1394632 original size:13 final size:13
Alignment explanation
Indices: 1394534--1394632 Score: 56
Period size: 13 Copynumber: 7.3 Consensus size: 13
1394524 TGATATTAAG
1394534 AAAAAAAAATAATA
1 AAAAAAAAAT-ATA
*
1394548 GAAAAAAATAAAATA
1 -AAAAAAA-AATATA
**
1394563 AAGTAAAAATATA
1 AAAAAAAAATATA
* * * *
1394576 ATATATATATATA
1 AAAAAAAAATATA
1394589 AATAAATAAAA-ATA
1 AA-AAA-AAAATATA
* * *
1394603 AAAATAGAATATT
1 AAAAAAAAATATA
1394616 AAAAAAAAATATA
1 AAAAAAAAATATA
1394629 AAAA
1 AAAA
1394633 CGTATAAAAT
Statistics
Matches: 62, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
12 3 0.05
13 33 0.53
14 12 0.19
15 12 0.19
16 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (13 bp):
AAAAAAAAATATA
Found at i:1394659 original size:18 final size:18
Alignment explanation
Indices: 1394526--1394663 Score: 64
Period size: 18 Copynumber: 8.0 Consensus size: 18
1394516 GTTATACATG
1394526 ATATTAAGAAAAAA-A-A
1 ATATTAAGAAAAAATATA
*
1394542 ATAAT-AGAAAAAA-ATA
1 ATATTAAGAAAAAATATA
* * *
1394558 AAATAAAGTAAAAATATA
1 ATATTAAGAAAAAATATA
* *
1394576 ATATATATA-TATAAATA-A
1 ATAT-TA-AGAAAAAATATA
* *
1394594 ATA--AAAATAAAAATAGA
1 ATATTAAGA-AAAAATATA
*
1394611 ATATTAAAAAAAAATATA
1 ATATTAAGAAAAAATATA
*
1394629 A-A--AACGTATAAAATATA
1 ATATTAA-G-AAAAAATATA
1394646 ATATTAAGAAAAAATATA
1 ATATTAAGAAAAAATATA
1394664 TACATAGTAA
Statistics
Matches: 93, Mismatches: 14, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
14 1 0.01
15 12 0.13
16 13 0.14
17 22 0.24
18 29 0.31
19 13 0.14
20 3 0.03
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (18 bp):
ATATTAAGAAAAAATATA
Found at i:1394788 original size:24 final size:23
Alignment explanation
Indices: 1394717--1394793 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
1394707 ATGATATAAG
* *
1394717 ATATATAT-AATAAAAATAATAT
1 ATATAAATAAATAAAAAAAATAT
1394739 AATATAAATAAA-AAAAAGAGGAATAT
1 -ATATAAATAAATAAAAA-A--AATAT
*
1394765 A-GTAAATAAATAAAAAAAATAT
1 ATATAAATAAATAAAAAAAATAT
*
1394787 ATTTAAA
1 ATATAAA
1394794 AATATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
22 6 0.14
23 16 0.36
24 11 0.25
25 6 0.14
26 5 0.11
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (23 bp):
ATATAAATAAATAAAAAAAATAT
Found at i:1395224 original size:17 final size:17
Alignment explanation
Indices: 1395204--1395246 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
1395194 CTATTAACAA
*
1395204 TAGAATCCTAATGCAAC
1 TAGACTCCTAATGCAAC
1395221 TAGACTCCTAATGCAAC
1 TAGACTCCTAATGCAAC
1395238 TAGACTCCT
1 TAGACTCCT
1395247 TGCTCGGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.26
Consensus pattern (17 bp):
TAGACTCCTAATGCAAC
Found at i:1397508 original size:18 final size:18
Alignment explanation
Indices: 1397485--1397543 Score: 109
Period size: 18 Copynumber: 3.3 Consensus size: 18
1397475 TTGGTGGTGG
1397485 AGGCTGGTTAAGCTCTAC
1 AGGCTGGTTAAGCTCTAC
1397503 AGGCTGGTTAAGCTCTAC
1 AGGCTGGTTAAGCTCTAC
*
1397521 AGTCTGGTTAAGCTCTAC
1 AGGCTGGTTAAGCTCTAC
1397539 AGGCT
1 AGGCT
1397544 TTCCTTTCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (18 bp):
AGGCTGGTTAAGCTCTAC
Found at i:1407372 original size:2 final size:2
Alignment explanation
Indices: 1407365--1407390 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1407355 TTGGTCTTAC
1407365 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1407391 ATTGTGTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1410038 original size:11 final size:11
Alignment explanation
Indices: 1410022--1410097 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
1410012 ATATTTTAAT
1410022 AATAATAATAA
1 AATAATAATAA
*
1410033 AATAATCATGAA
1 AATAATAAT-AA
*
1410045 GATAATAATTTAA
1 AATAATAA--TAA
1410058 ACAT-AT-ATCAA
1 A-ATAATAAT-AA
1410069 AAGTAATAATAA
1 AA-TAATAATAA
1410081 AATAA-AATAA
1 AATAATAATAA
1410091 TAATAAT
1 -AATAAT
1410098 TAAAATGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
10 7 0.14
11 20 0.39
12 15 0.29
13 6 0.12
14 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:1410093 original size:16 final size:17
Alignment explanation
Indices: 1410067--1410126 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 17
1410057 AACATATATC
1410067 AAAAGTAATAATAAAAT
1 AAAAGTAATAATAAAAT
*
1410084 AAAA-TAATAAT-AATT
1 AAAAGTAATAATAAAAT
* *
1410099 AAAA-TGA-AAGAAAAT
1 AAAAGTAATAATAAAAT
1410114 AAAAGTAATAATA
1 AAAAGTAATAATA
1410127 TTAAAACTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 2 0.06
15 16 0.47
16 9 0.26
17 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
AAAAGTAATAATAAAAT
Found at i:1410114 original size:19 final size:19
Alignment explanation
Indices: 1410072--1410115 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1410062 ATATCAAAAG
*
1410072 TAATAATAAAATAAAATAA
1 TAATAATAAAATAAAAGAA
*
1410091 TAATAATTAAAATGAAAGAA
1 TAATAA-TAAAATAAAAGAA
1410111 -AATAA
1 TAATAA
1410116 AAGTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
TAATAATAAAATAAAAGAA
Found at i:1410373 original size:18 final size:18
Alignment explanation
Indices: 1410350--1410391 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1410340 TTATTAGGGA
1410350 CTAAATGTGATATTTATC
1 CTAAATGTGATATTTATC
1410368 CTAAATGTGATATTTATC
1 CTAAATGTGATATTTATC
1410386 CTAAAT
1 CTAAAT
1410392 ATATTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (18 bp):
CTAAATGTGATATTTATC
Found at i:1411526 original size:3 final size:3
Alignment explanation
Indices: 1411507--1411571 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
1411497 TTGTAATATT
* *
1411507 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAG TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
1411554 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1411572 ACTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1411528 original size:24 final size:23
Alignment explanation
Indices: 1411500--1411571 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 23
1411490 ATGGGCTTTG
1411500 TAAT-ATTTAATAAATAATATATAA
1 TAATAATTTAAT-AATAATA-ATAA
1411524 TAATAATTATAATAATAATAATAA
1 TAATAATT-TAATAATAATAATAA
*
1411548 TAGTAATTTTAATAATAATAATAA
1 TAATAA-TTTAATAATAATAATAA
1411572 ACTTAAATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
24 28 0.64
25 12 0.27
26 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (23 bp):
TAATAATTTAATAATAATAATAA
Found at i:1411796 original size:76 final size:76
Alignment explanation
Indices: 1411699--1411885 Score: 304
Period size: 76 Copynumber: 2.5 Consensus size: 76
1411689 GATGGAAATG
* **
1411699 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCC-GAAGGCTTTTTAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTG-AGGCTTTGAAAACATCAAAAAGC
1411763 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
1411775 TTTGGAAACATCATGCACTGAAGGACCTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCT
1411840 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
1411851 TTTGGAAACATCATGCACTGAAGGGCTTATAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1411886 TGGGAAATAG
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
76 102 0.99
77 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:1412458 original size:24 final size:23
Alignment explanation
Indices: 1412423--1412467 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1412413 TGAACAAATT
*
1412423 CTTCTCATTATGAATTTCTTCTTC
1 CTTCTCATTATG-AGTTCTTCTTC
1412447 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGAGTTCTTCT
1412468 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.24, G:0.07, T:0.53
Consensus pattern (23 bp):
CTTCTCATTATGAGTTCTTCTTC
Found at i:1412548 original size:113 final size:111
Alignment explanation
Indices: 1412295--1412777 Score: 623
Period size: 113 Copynumber: 4.3 Consensus size: 111
1412285 GAATTATGCA
*
1412295 AAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
1412360 ATGAACT-TCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGAGC
66 ATGAACTCT-TCTGGAAAAGCTGATCCATCAAGTGATGAATTTAAGC
* *
1412406 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
1412471 TATGAACTCGATCTGGTAATGCTGAAT-CATCGAA-TGATGAATTTAAAC
65 TATGAACTC-TTCTGGAAAAGCTG-ATCCATC-AAGTGATGAATTTAAGC
1412519 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * *
1412584 TATGAACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGC
65 TATGAACTCTT-CTGGAAAAGCTGATCCATCAAGTGATGAATTTAAGC
* * *
1412632 GAAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGGGTTCTTCTCAT
1 -AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
1412697 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAA-TGATGAATTCAAGC
65 TATGAACTCT-TCTGGAAAAGCTGATCCATC-AAGTGATGAATTTAAGC
*
1412745 GAAAAGTTGAACAAGTTCTTCTCATTATGAACT
1 -AAAAGTTGAACAAATTCTTCTCATTATGAACT
1412778 CGATCTGGTA
Statistics
Matches: 331, Mismatches: 30, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
111 4 0.01
112 70 0.21
113 247 0.75
114 10 0.03
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (111 bp):
AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTAAGC
Found at i:1412692 original size:226 final size:224
Alignment explanation
Indices: 1412295--1412777 Score: 718
Period size: 226 Copynumber: 2.1 Consensus size: 224
1412285 GAATTATGCA
*
1412295 AAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1412360 ATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCT
66 ATGAACTTCTCTGGAAAAGCTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATTCT
* * *
1412425 TCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTCGATCTGGTAA
131 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGATCTGGAAA
* *
1412490 TGCTGAAT-CATCGAATGATGAATTTAAAC
196 AGCTG-ATCCATCGAATGATGAATTCAAAC
1412519 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
1412584 TATGAACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGCGAAAA-TTTGAACAAGT
65 TATGAACTTCT-CTGGAAAAGCTGATCCATCAAGAGATGGATTTGAGC-AAAAGGTTGAACAAAT
* ***
1412648 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGGGTTCTTCTCATTATGAACTTTCTCTGG
128 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGATCTGG
* *
1412713 AAAAGTTGATCCATCGAATGATGAATTCAAGC
193 AAAAGCTGATCCATCGAATGATGAATTCAAAC
*
1412745 GAAAAGTTGAACAAGTTCTTCTCATTATGAACT
1 -AAAAGTTGAACAAATTCTTCTCATTATGAACT
1412778 CGATCTGGTA
Statistics
Matches: 233, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
224 4 0.02
225 71 0.30
226 150 0.64
227 8 0.03
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (224 bp):
AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTCTCTGGAAAAGCTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGATCTGGAAA
AGCTGATCCATCGAATGATGAATTCAAAC
Found at i:1412773 original size:73 final size:73
Alignment explanation
Indices: 1412686--1412851 Score: 219
Period size: 73 Copynumber: 2.3 Consensus size: 73
1412676 CTTCAGATGG
** * *
1412686 GTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTG-ATCCATCGAATGATGAATTCAAGCGAAAA
1 GTTCTTCTCATTATGAACTTGATCTGGAAAAGCTGAAT-CATCGAATGATGAATTCAAAC-AAAA
1412750 -GTTGAACAA
64 GGTTGAACAA
* * * *
1412759 GTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAGG
1 GTTCTTCTCATTATGAACTTGATCTGGAAAAGCTGAATCATCGAATGATGAATTCAAACAAAAGG
1412824 TTGAACAA
66 TTGAACAA
*
1412832 ATTCTTCTCATTATGAACTT
1 GTTCTTCTCATTATGAACTT
1412852 CTTCTTCCTT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
72 4 0.05
73 75 0.93
74 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (73 bp):
GTTCTTCTCATTATGAACTTGATCTGGAAAAGCTGAATCATCGAATGATGAATTCAAACAAAAGG
TTGAACAA
Found at i:1412804 original size:299 final size:299
Alignment explanation
Indices: 1412459--1413076 Score: 1107
Period size: 299 Copynumber: 2.1 Consensus size: 299
1412449 TCTTCATATG
1412459 AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
1 AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
1412524 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
1412589 ACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGCGAAAA-TTTGAACAAGTTCTTC
131 ACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGC-AAAAGGTTGAACAAATTCTTC
* ****
1412653 TCATTATGAACTTCTTCTTCCTTCTTCAGATGGGTTCTTCTCATTATGAACTTTCTCTGGAAA-A
195 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAATA
*
1412717 GTTG-ATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
260 -CTGAAT-CATCGAATGATGAATTCAAGCGAAAAGTTGAACA
1412758 AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
1 AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
1412823 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1412888 ACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
131 ACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
*
1412953 CATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAATAC
196 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAATAC
1413018 TGAATCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
261 TGAATCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
1413057 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
1413077 TCTTCTTTTT
Statistics
Matches: 307, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
298 4 0.01
299 300 0.98
300 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (299 bp):
AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAATAC
TGAATCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
Found at i:1412875 original size:113 final size:113
Alignment explanation
Indices: 1412758--1413151 Score: 569
Period size: 113 Copynumber: 3.5 Consensus size: 113
1412748 AAGTTGAACA
* *
1412758 AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
1 AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATTTAAGCAAAAG
1412823 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*** * * * * *
1412871 AGTTCTTCTCATTATGAACTTTTACTGGCAATGTTG-ATCCATC-AAGAGATGGATTTGAGCAAA
1 AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAAT-CATCGAA-TGATGAATTTAAGCAAA
*
1412934 AGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
64 AGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * *
1412984 AGTTCTTCTCATTATGAACTCGAACTGGAAATACTGAATCATCGAATGATGAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATTTAAGC-AAAA
* **
1413049 -GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATG
65 GGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
**
1413097 AGTTCTTCTCATTATGAACTTTAACTGGTAATGCTGAATCATCGAATGATGAATT
1 AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATT
1413152 CATATCTTTG
Statistics
Matches: 247, Mismatches: 29, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
112 4 0.02
113 235 0.95
114 8 0.03
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATTTAAGCAAAAG
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:1413580 original size:22 final size:22
Alignment explanation
Indices: 1413555--1413609 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1413545 CATAAAGTTT
*
1413555 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
1413577 TCATCTTT-ATAAAGAGAATCTA
1 TCATCTTTGA-AAAGAGAATCTA
1413599 TCATCTTTGAA
1 TCATCTTTGAA
1413610 GAGCGTAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1414034 original size:54 final size:54
Alignment explanation
Indices: 1413946--1414114 Score: 227
Period size: 54 Copynumber: 3.2 Consensus size: 54
1413936 TAACAGGTTT
* *** * *
1413946 GTAAAACATTTAACAGTGCATTCATCCTTGCCTGTGGCTTCTGCTCAGATGTTC
1 GTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAGATGTTC
* *
1414000 GTAAAACATTTGACAACACATTCATCTTTTCCTGTGGTTTCTGTTCAGATGTTC
1 GTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAGATGTTC
*
1414054 GTAAAACATTTGACAACACATTCAT-TTTT-TTGTGGCTTCTGCTCAGATGTTC
1 GTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAGATGTTC
*
1414106 -TCAAACATT
1 GTAAAACATT
1414115 GAACCTCTTT
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
51 8 0.08
52 20 0.19
53 4 0.04
54 71 0.69
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAGATGTTC
Found at i:1422048 original size:14 final size:14
Alignment explanation
Indices: 1422014--1422067 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
1422004 TTGTGCAATA
* *
1422014 CAAATGCAAAGATG
1 CAAATGTAAATATG
1422028 CCAAATGTAAATATG
1 -CAAATGTAAATATG
1422043 CAAATGTAAA-ATTG
1 CAAATGTAAATA-TG
*
1422057 TAAATGTAAAT
1 CAAATGTAAAT
1422068 TTTTTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 1 0.03
14 21 0.62
15 12 0.35
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:1424589 original size:11 final size:11
Alignment explanation
Indices: 1424573--1424648 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
1424563 ATATTTTAAT
1424573 AATAATAATAA
1 AATAATAATAA
*
1424584 AATAATCATGAA
1 AATAATAAT-AA
*
1424596 GATAATAATTTAA
1 AATAATAA--TAA
1424609 ACAT-AT-ATCAA
1 A-ATAATAAT-AA
1424620 AAGTAATAATAA
1 AA-TAATAATAA
1424632 AATAA-AATAA
1 AATAATAATAA
1424642 TAATAAT
1 -AATAAT
1424649 TAAAATGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
10 7 0.14
11 20 0.39
12 15 0.29
13 6 0.12
14 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:1424644 original size:16 final size:17
Alignment explanation
Indices: 1424618--1424677 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 17
1424608 AACATATATC
1424618 AAAAGTAATAATAAAAT
1 AAAAGTAATAATAAAAT
*
1424635 AAAA-TAATAAT-AATT
1 AAAAGTAATAATAAAAT
* *
1424650 AAAA-TGA-AAGAAAAT
1 AAAAGTAATAATAAAAT
1424665 AAAAGTAATAATA
1 AAAAGTAATAATA
1424678 TTAAAACTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 2 0.06
15 16 0.47
16 9 0.26
17 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
AAAAGTAATAATAAAAT
Found at i:1424665 original size:19 final size:19
Alignment explanation
Indices: 1424623--1424666 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1424613 ATATCAAAAG
*
1424623 TAATAATAAAATAAAATAA
1 TAATAATAAAATAAAAGAA
*
1424642 TAATAATTAAAATGAAAGAA
1 TAATAA-TAAAATAAAAGAA
1424662 -AATAA
1 TAATAA
1424667 AAGTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
TAATAATAAAATAAAAGAA
Found at i:1426061 original size:3 final size:3
Alignment explanation
Indices: 1426042--1426106 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
1426032 TTGTAATATT
* *
1426042 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAG TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
1426089 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1426107 ACTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1426063 original size:24 final size:23
Alignment explanation
Indices: 1426035--1426106 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 23
1426025 ATGGGCTTTG
1426035 TAAT-ATTTAATAAATAATATATAA
1 TAATAATTTAAT-AATAATA-ATAA
1426059 TAATAATTATAATAATAATAATAA
1 TAATAATT-TAATAATAATAATAA
*
1426083 TAGTAATTTTAATAATAATAATAA
1 TAATAA-TTTAATAATAATAATAA
1426107 ACTTAAATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
24 28 0.64
25 12 0.27
26 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (23 bp):
TAATAATTTAATAATAATAATAA
Found at i:1426356 original size:23 final size:21
Alignment explanation
Indices: 1426318--1426360 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1426308 ATAATTATTT
1426318 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
1426339 AAAAATATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
1426360 A
1 A
1426361 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:1435485 original size:20 final size:20
Alignment explanation
Indices: 1435450--1435537 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
1435440 TTTTCCTAAT
*
1435450 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* *
1435470 TCGTAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
*
1435490 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
1435510 TCGCAATGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
1435530 TCGCAACG
1 TCGCAACG
1435538 AGATTCTGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 1 0.02
20 59 0.98
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:1435496 original size:40 final size:40
Alignment explanation
Indices: 1435450--1435535 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 40
1435440 TTTTCCTAAT
* *
1435450 TCGCAATGCGAATACGTAAATCGTAACGCGATTAC-GTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAAT-CTGTAAA
*
1435490 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGTAAA
1435530 TCGCAA
1 TCGCAA
1435536 CGAGATTCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
39 1 0.02
40 41 0.98
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGTAAA
Found at i:1435553 original size:60 final size:61
Alignment explanation
Indices: 1435409--1435556 Score: 160
Period size: 60 Copynumber: 2.4 Consensus size: 61
1435399 GTTTCCAGAT
* * * * *
1435409 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTCCTAATTCGCAATGCGAATACGTAAA
1 TCGCAACGCGATTCTGATTATCGCAATGCGATATACCTAAATCGCAATGCGAATACGTAAA
* * *
1435470 TCGTAACGCGATTAC-G-TAAATCGCAATGCGA-ATACGTAAATCGCAATGCGAAT-CTGTAAA
1 TCGCAACGCGATT-CTGAT-TATCGCAATGCGATATACCTAAATCGCAATGCGAATAC-GTAAA
*
1435530 TCGCAACGAGATTCTGATTATCGCAAT
1 TCGCAACGCGATTCTGATTATCGCAAT
1435557 ACTGAATTTC
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
59 2 0.03
60 43 0.61
61 25 0.35
62 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (61 bp):
TCGCAACGCGATTCTGATTATCGCAATGCGATATACCTAAATCGCAATGCGAATACGTAAA
Found at i:1436448 original size:24 final size:24
Alignment explanation
Indices: 1436397--1436450 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1436387 GTATTCAAAA
*
1436397 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGAAC
* *
1436421 TTTGATCTTGGTCAATACTCGAAT
1 TTTGATCTTGGTCAATACCCGAAC
1436445 TTTGAT
1 TTTGAT
1436451 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGAAC
Found at i:1438816 original size:20 final size:20
Alignment explanation
Indices: 1438791--1438884 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
1438781 GACATTCATT
1438791 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
1438811 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* * * *
1438831 TAACTATTGCAACGCAGAAT
1 TGACTATCGCAACGCGGAAA
1438851 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
1438871 TGACTATCGCAACG
1 TGACTATCGCAACG
1438885 AGAGAATCGC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 60 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:1438855 original size:40 final size:40
Alignment explanation
Indices: 1438793--1438884 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 40
1438783 CATTCATTTG
1438793 ACTATCGCAACGCGAATATGACTATCGCAACACGGAAATA
1 ACTATCGCAACGCGAATATGACTATCGCAACACGGAAATA
* * *
1438833 ACTATTGCAACGCAGAAT-TGACTATCGCAACGCGGAAATG
1 ACTATCGCAACGC-GAATATGACTATCGCAACACGGAAATA
1438873 ACTATCGCAACG
1 ACTATCGCAACG
1438885 AGAGAATCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
40 43 0.91
41 4 0.09
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (40 bp):
ACTATCGCAACGCGAATATGACTATCGCAACACGGAAATA
Found at i:1438913 original size:19 final size:19
Alignment explanation
Indices: 1438889--1438976 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
1438879 GCAACGAGAG
1438889 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1438908 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1438927 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
1438941 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1438961 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
1438977 TAACCAAACA
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
14 8 0.13
16 4 0.07
17 3 0.05
18 3 0.05
19 32 0.53
20 10 0.17
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1438935 original size:52 final size:53
Alignment explanation
Indices: 1438856--1438976 Score: 190
Period size: 53 Copynumber: 2.3 Consensus size: 53
1438846 AGAATTGACT
**
1438856 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGC-GAAATGAAA
1 ATCGCAACGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAA
* *
1438909 ATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAA
1438962 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
1438977 TAACCAAACA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAA
Found at i:1439088 original size:14 final size:14
Alignment explanation
Indices: 1439069--1439105 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1439059 CATCAATTAA
1439069 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1439083 ACAAATCATCTTTT
1 ACAAATCAACATTT
1439097 ACAAATCAA
1 ACAAATCAA
1439106 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1440527 original size:21 final size:18
Alignment explanation
Indices: 1440503--1440547 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
1440493 GAACGGTGAG
1440503 AGGGGACTCTTGAGGAATGAT
1 AGGGGACTCTT---GAATGAT
*
1440524 AGGGGCCTCTTGAATGAT
1 AGGGGACTCTTGAATGAT
1440542 AGGGGA
1 AGGGGA
1440548 GGCCTATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 12 0.55
21 10 0.45
ACGTcount: A:0.27, C:0.11, G:0.40, T:0.22
Consensus pattern (18 bp):
AGGGGACTCTTGAATGAT
Found at i:1441109 original size:20 final size:20
Alignment explanation
Indices: 1441048--1441100 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1441038 GAAACTTAAA
*
1441048 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
1441068 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
1441088 ATCGCAATGCGAA
1 ATCGCAATGCGAA
1441101 TTTGACTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:1441115 original size:20 final size:20
Alignment explanation
Indices: 1441056--1441116 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
1441046 AAATCGCAAC
*
1441056 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCACAAT
*
1441076 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCACAAT
** *
1441096 GCGAATTTGACTATTACAAT
1 GCGAAAATGACTATCACAAT
1441116 G
1 G
1441117 AGAGAATCGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (20 bp):
GCGAAAATGACTATCACAAT
Found at i:1441173 original size:19 final size:19
Alignment explanation
Indices: 1441149--1441227 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
1441139 AAATCGCAAC
1441149 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* * *
1441168 GTGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* * *
1441187 GCGATTTTCA-TTTCTCATT
1 GCGATTAT-AGTTTCGCGTT
*
1441206 GCGATT-CA-TTTCGCGTT
1 GCGATTATAGTTTCGCGTT
1441223 GCGAT
1 GCGAT
1441228 AGTCATTTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
17 13 0.27
19 36 0.73
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.46
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:1441235 original size:19 final size:17
Alignment explanation
Indices: 1441178--1441227 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
1441168 GTGATTTTGG
1441178 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGA--TTCA
* *
1441197 TTTCTCATTGCGATTCA
1 TTTCGCGTTGCGATTCA
1441214 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1441228 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 16 0.59
19 11 0.41
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (17 bp):
TTTCGCGTTGCGATTCA
Found at i:1441457 original size:94 final size:94
Alignment explanation
Indices: 1441331--1441690 Score: 596
Period size: 94 Copynumber: 3.8 Consensus size: 94
1441321 CAAAAAAAAG
* *
1441331 AACAAAGACAAATACTAACTTCAAAGTATTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
1 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
1441396 GAACAAATTTACTTTCAACCAAAAGACAA
66 GAACAAATTTACTTTCAACCAAAAGACAA
1441425 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
1 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
* * *
1441490 GAACAAATTTACTTTTAATCGAAAGACAA
66 GAACAAATTTACTTTCAACCAAAAGACAA
* *
1441519 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAACAGAATTGACAGCAACC
1 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
*
1441584 GAATAAATTTAC-TTCAACCAAAAGACAA
66 GAACAAATTTACTTTCAACCAAAAGACAA
* * *
1441612 AACAAAAGACAATTACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAAC
1 AAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAC
*
1441677 CGAATAAATTTACT
65 CGAACAAATTTACT
1441691 AAGCAATCTA
Statistics
Matches: 248, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
93 16 0.06
94 232 0.94
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
GAACAAATTTACTTTCAACCAAAAGACAA
Found at i:1441562 original size:17 final size:17
Alignment explanation
Indices: 1441540--1441572 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1441530 ATACTAACTT
1441540 CACAGTGTTAA-AGAATA
1 CACAGT-TTAACAGAATA
1441557 CACAGTTTAACAGAAT
1 CACAGTTTAACAGAAT
1441573 TGACAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CACAGTTTAACAGAATA
Found at i:1443393 original size:20 final size:20
Alignment explanation
Indices: 1443370--1443425 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
1443360 TGAAATGAAA
1443370 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
1443390 ATCGCAATGCG-GA-AATGACT
1 ATCGCAA--CGAGAGAATGACT
1443410 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
1443426 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 24 0.75
21 2 0.06
22 2 0.06
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:1443447 original size:19 final size:19
Alignment explanation
Indices: 1443361--1443492 Score: 121
Period size: 19 Copynumber: 7.1 Consensus size: 19
1443351 TCTTTTGGTT
*
1443361 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
** *
1443380 GAGAATGACTATCGCAATGC
1 GA-AATGAAAATCGCAACGC
**
1443400 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1443418 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1443434 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1443453 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1443472 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1443491 GA
1 GA
1443493 TTTTGGTTTC
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 1 0.01
18 2 0.02
19 50 0.53
20 27 0.29
21 2 0.02
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1443474 original size:38 final size:37
Alignment explanation
Indices: 1443361--1443487 Score: 136
Period size: 38 Copynumber: 3.4 Consensus size: 37
1443351 TCTTTTGGTT
** *
1443361 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAATGC
1 GAAATGAAAATCGCAACGAGA-AAT-AAAATCGCAACGC
** *
1443400 GGAAATGACTATCGCAACGAG----AGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAAATAAAATCGCAACGC
1443434 GAAATGAAAATCGCAACGAGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAAA-TAAAATCGCAACGC
1443472 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1443488 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
33 18 0.24
34 10 0.14
38 28 0.38
40 18 0.24
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGAGAAATAAAATCGCAACGC
Found at i:1443536 original size:33 final size:33
Alignment explanation
Indices: 1443490--1443568 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
1443480 AATCGCAATG
**
1443490 CGATTTTGGTTTCGCGTTGCGATTATCTCGTTA
1 CGATTTTCATTTCGCGTTGCGATTATCTCGTTA
* *
1443523 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTATCTCGTTA
1443556 CGATTTTCATTTC
1 CGATTTTCATTTC
1443569 TCTCGTTGCG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTATCTCGTTA
Found at i:1443571 original size:21 final size:20
Alignment explanation
Indices: 1443552--1443623 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
1443542 CGATTCTCTC
1443552 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
1443572 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
1443593 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
1443613 GTTGCGATTTT
1 GTTGCGATTTT
1443624 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:1444209 original size:20 final size:20
Alignment explanation
Indices: 1444184--1444397 Score: 162
Period size: 20 Copynumber: 10.6 Consensus size: 20
1444174 CTTTAAAAAT
*
1444184 CGCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1444204 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* * *
1444224 TGTCGTTGTGATTTACGAATA
1 CG-CGTTGCGATTTACGGATA
* * * *
1444245 TGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
1444265 CTCGTTGCGATTTATAGATA
1 CGCGTTGCGATTTACGGATA
* * *
1444285 CGCGTTGTGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
1444305 CTCGTTATGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1444325 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1444345 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
1444366 CACGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
* *
1444387 CTCGTTACGAT
1 CGCGTTGCGAT
1444398 AGTCAGAATC
Statistics
Matches: 151, Mismatches: 36, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
20 100 0.66
21 51 0.34
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1444253 original size:41 final size:41
Alignment explanation
Indices: 1444186--1444392 Score: 274
Period size: 41 Copynumber: 5.1 Consensus size: 41
1444176 TTAAAAATCG
*
1444186 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
1444227 CGTTGTGATTTACGAATATGCATTGCGA-TTTACGTATTCT
1 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* ** *
1444267 CGTTGCGATTTATAGATACGCGTTGTGA-TTTACGTATTCT
1 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1444307 CGTTATGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * *
1444348 CGTTGCGATTTACGGATACACGTTGCGATTTTACGGATACT
1 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATTCT
1444389 CGTT
1 CGTT
1444393 ACGATAGTCA
Statistics
Matches: 142, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
40 67 0.47
41 75 0.53
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.41
Consensus pattern (41 bp):
CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:1444340 original size:81 final size:82
Alignment explanation
Indices: 1444186--1444438 Score: 291
Period size: 81 Copynumber: 3.1 Consensus size: 82
1444176 TTAAAAATCG
* * * * * *
1444186 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGTGATTTACGAATATGCATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTATGATTTACGGATACGCGTT
1444251 GCGA-TTTACGTATTCT
66 GCGATTTTACGTATTCT
** *
1444267 CGTTGCGATTTATAGATACGCGTTGTGA-TTTACGTATTCTCGTTATGATTTACGGATACGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTATGATTTACGGATACGCGTT
*
1444331 GCGATTTTACGTATTGT
66 GCGATTTTACGTATTCT
* * * * * *
1444348 CGTTGCGATTTACGGATACACGTTGCGATTTTACGGATACTCGTTACGATAGT-CAGA-ATCGCG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTATGAT-TTACGGATA-CGCG
* *
1444411 TTGCGATTTT-CATATTCG
64 TTGCGATTTTACGTATTCT
1444429 CGTTGCGATT
1 CGTTGCGATT
1444439 CTTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
80 35 0.24
81 75 0.51
82 35 0.24
83 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.40
Consensus pattern (82 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTATGATTTACGGATACGCGTT
GCGATTTTACGTATTCT
Found at i:1444417 original size:20 final size:20
Alignment explanation
Indices: 1444389--1444437 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
1444379 TACGGATACT
*
1444389 CGTTACGATAGTCAGAATCG
1 CGTTGCGATAGTCAGAATCG
** * *
1444409 CGTTGCGATTTTCATATTCG
1 CGTTGCGATAGTCAGAATCG
1444429 CGTTGCGAT
1 CGTTGCGAT
1444438 TCTTGAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAGAATCG
Found at i:1444499 original size:42 final size:42
Alignment explanation
Indices: 1444404--1444499 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 42
1444394 CGATAGTCAG
* * *
1444404 AATCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTTGAA
1 AATCGCGTTGCGAATTTTCATATTCGCATTACGATTCTTCAA
** *
1444445 AATCGCAATGCGAATTTGT-ACTA-TCGCATTACGATTCTTCAT
1 AATCGCGTTGCGAATTT-TCA-TATTCGCATTACGATTCTTCAA
1444487 AATCGCGTTGCGA
1 AATCGCGTTGCGA
1444500 TTCTGGGAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
41 10 0.23
42 31 0.70
43 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
AATCGCGTTGCGAATTTTCATATTCGCATTACGATTCTTCAA
Found at i:1447109 original size:16 final size:16
Alignment explanation
Indices: 1447088--1447121 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1447078 ATCTACCGTC
1447088 CATTCTTCCACCATTT
1 CATTCTTCCACCATTT
*
1447104 CATTCTTCCACCTTTT
1 CATTCTTCCACCATTT
1447120 CA
1 CA
1447122 CGAATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.38, G:0.00, T:0.44
Consensus pattern (16 bp):
CATTCTTCCACCATTT
Found at i:1447837 original size:21 final size:21
Alignment explanation
Indices: 1447813--1447852 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1447803 TTTTCAAAGG
1447813 CATGCACCGATACATCAATAC
1 CATGCACCGATACATCAATAC
* *
1447834 CATGCATCGATGCATCAAT
1 CATGCACCGATACATCAAT
1447853 GAATAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (21 bp):
CATGCACCGATACATCAATAC
Found at i:1447943 original size:64 final size:65
Alignment explanation
Indices: 1447834--1447958 Score: 171
Period size: 64 Copynumber: 1.9 Consensus size: 65
1447824 ACATCAATAC
*
1447834 CATGCATCGATGCATCAATGAATAAATTGAAACATCGAATACATTTCATGCACCGATGCACTCTT
1 CATGCATCGATGCATCAATGAATAAATTAAAACATCGAATACATTTCATGCACCGATGCACTCTT
* * * * * * *
1447899 CATGCATCTATGCA-CACTGATTTAATTAAAACATCGAATGCATTTGATGCATCGATGCAC
1 CATGCATCGATGCATCAATGAATAAATTAAAACATCGAATACATTTCATGCACCGATGCAC
1447959 CAGGCTATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
64 39 0.75
65 13 0.25
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.29
Consensus pattern (65 bp):
CATGCATCGATGCATCAATGAATAAATTAAAACATCGAATACATTTCATGCACCGATGCACTCTT
Found at i:1455658 original size:21 final size:21
Alignment explanation
Indices: 1455634--1455673 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1455624 TTTTCAAAGG
1455634 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
1455655 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
1455674 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:1455791 original size:64 final size:64
Alignment explanation
Indices: 1455634--1455798 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 64
1455624 TTTTCAAAGG
*
1455634 CATGCACCGATGCATCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCAT
1 CATGCACCGATGCA-CAA-ACCATGCATCGATGCA-CAATGAATAAATTAAAACATCGAATGCAT
1455699 TT
63 TT
**** * * *
1455701 CATGCACCGATGCACTCTTCATGCATCGATGCACACTGATTTAATTAAAACATCGAATGCATTT
1 CATGCACCGATGCACAAACCATGCATCGATGCACAATGAATAAATTAAAACATCGAATGCATTT
* * * *
1455765 GATGCATCGATGCACAAGCCAAGCATCGATGCAC
1 CATGCACCGATGCACAAACCATGCATCGATGCAC
1455799 CAGGCTATTT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 54 0.65
65 14 0.17
66 1 0.01
67 14 0.17
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (64 bp):
CATGCACCGATGCACAAACCATGCATCGATGCACAATGAATAAATTAAAACATCGAATGCATTT
Found at i:1455816 original size:64 final size:63
Alignment explanation
Indices: 1455634--1455843 Score: 172
Period size: 64 Copynumber: 3.2 Consensus size: 63
1455624 TTTTCAAAGG
* * * * ** *
1455634 CATGCACCGATGCATCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCAT
1 CATGCATCGATGCA-CAA-GCCAAGCATCGATGCA-CACTG-ATTTATTAAAACATCGAATGCAT
1455699 TT
62 TT
* **** *
1455701 CATGCACCGATGCACTCTTCATGCATCGATGCACACTGATTTAATTAAAACATCGAATGCATTT
1 CATGCATCGATGCACAAGCCAAGCATCGATGCACACTGATTT-ATTAAAACATCGAATGCATTT
* * * *
1455765 GATGCATCGATGCACAAGCCAAGCATCGATGCACCAGGCT-ATTT-TTCAAACATCGAATGTACT
1 CATGCATCGATGCACAAGCCAAGCATCGATGCA-CA--CTGATTTATTAAAACATCGAATGCATT
1455828 T
63 T
*
1455829 CATGCATCAATGCAC
1 CATGCATCGATGCAC
1455844 TCTGTAACAC
Statistics
Matches: 119, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
63 2 0.02
64 80 0.67
65 16 0.13
66 5 0.04
67 16 0.13
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (63 bp):
CATGCATCGATGCACAAGCCAAGCATCGATGCACACTGATTTATTAAAACATCGAATGCATTT
Found at i:1456787 original size:23 final size:23
Alignment explanation
Indices: 1456761--1456824 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1456751 CAGCTCATAT
1456761 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1456784 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1456807 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1456825 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1457011 original size:103 final size:103
Alignment explanation
Indices: 1456840--1457057 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
1456830 TAATGTCCAT
* * *
1456840 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
1456905 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1456943 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
1457008 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1457046 AAGGACCACATA
1 AAGGACCACATA
1457058 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1457904 original size:64 final size:64
Alignment explanation
Indices: 1457796--1458016 Score: 245
Period size: 64 Copynumber: 3.5 Consensus size: 64
1457786 TAATGAAGGT
* * * * *
1457796 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAATGG
1457859 G
64 G
* *
1457860 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
* * **
1457924 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATTAATGGG
**
1457987 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
1458017 ACACCTTCAA
Statistics
Matches: 136, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
63 4 0.03
64 126 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:1462778 original size:23 final size:23
Alignment explanation
Indices: 1462752--1462815 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1462742 CAGCTCATAT
1462752 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1462775 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1462798 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1462816 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1463002 original size:103 final size:103
Alignment explanation
Indices: 1462831--1463048 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1462821 TAATGTCCAT
* *
1462831 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1462896 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1462934 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1462999 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1463037 AAGGACCACATA
1 AAGGACCACATA
1463049 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1463893 original size:64 final size:64
Alignment explanation
Indices: 1463785--1464005 Score: 245
Period size: 64 Copynumber: 3.5 Consensus size: 64
1463775 TAATGAAGGT
* * * * *
1463785 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAATGG
1463848 G
64 G
* *
1463849 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
* * **
1463913 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATTAATGGG
**
1463976 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
1464006 ACACCTTCAA
Statistics
Matches: 136, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
63 4 0.03
64 126 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:1478763 original size:59 final size:59
Alignment explanation
Indices: 1478700--1479208 Score: 468
Period size: 59 Copynumber: 8.6 Consensus size: 59
1478690 TTACCAAATG
1478700 GCACTATGGGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
1 GCACTATGGGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
*
1478759 GCACTGA-GTGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
1 GCACT-ATGGGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
* *
1478818 GCACTGA-GTGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTTCATATGGA
1 GCACT-ATGGGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
* * * * * *
1478877 GCA-T-TGAGTGTGCTAAAATGATAAGGAAATCCTATTGAATATATGAATTTCCATATAGG-
1 GCACTATG-G-GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATAT-GGA
* ** * *
1478936 GCATTATATGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGA
1 GCACTATGGGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
* * * * * * *
1478995 GCA--ATGAGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGAATTTTCAGATAGG-
1 GCACTATG-G-GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATAT-GGA
* ** * * * ***
1479054 GCATTATATGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGAAAAA
1 GCACTATGGGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
* * * * * *
1479113 GCACTAAGGGTGCTACAA-GGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGG-
1 GCACTATGGGTGCTAAAATGG-TAAGGGAATCATACTGAGT-GTATGAATTTCCATAT-GGA
*
1479172 GCACTTCAT--GTGCTAAAAATGGTAAAGGAATCATACT
1 GCAC-T-ATGGGTGCT-AAAATGGTAAGGGAATCATACT
1479209 AATGGTATGG
Statistics
Matches: 378, Mismatches: 51, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
57 3 0.01
58 7 0.02
59 339 0.90
60 23 0.06
61 6 0.02
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (59 bp):
GCACTATGGGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGA
Found at i:1478799 original size:31 final size:31
Alignment explanation
Indices: 1478761--1478859 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 31
1478751 CATATGGAGC
1478761 ACTGAGTGTGCTAAAATGGTAAGGGAATCAT
1 ACTGAGTGTGCTAAAATGGTAAGGGAATCAT
* * * *** * *
1478792 ACTGAGTGT-ATGAATTTCCATATGG-AGC--
1 ACTGAGTGTGCTAAAATGGTA-AGGGAATCAT
1478820 ACTGAGTGTGCTAAAATGGTAAGGGAATCAT
1 ACTGAGTGTGCTAAAATGGTAAGGGAATCAT
1478851 ACTGAGTGT
1 ACTGAGTGT
1478860 ATGAATTTTC
Statistics
Matches: 47, Mismatches: 16, Indels: 10
0.64 0.22 0.14
Matches are distributed among these distances:
28 12 0.26
29 7 0.15
30 7 0.15
31 21 0.45
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.28
Consensus pattern (31 bp):
ACTGAGTGTGCTAAAATGGTAAGGGAATCAT
Found at i:1478828 original size:28 final size:28
Alignment explanation
Indices: 1478733--1478828 Score: 77
Period size: 28 Copynumber: 3.3 Consensus size: 28
1478723 AGGGAATCAT
1478733 ACTGAGTGTATGAATTTCCATATGGAGC
1 ACTGAGTGTATGAATTTCCATATGGAGC
* * * *** * *
1478761 ACTGAGTGTGCTAAAATGGTA-AGGGAATC
1 ACTGAGTGT-ATGAATTTCCATATGG-AGC
1478790 ATACTGAGTGTATGAATTTCCATATGGAGC
1 --ACTGAGTGTATGAATTTCCATATGGAGC
1478820 ACTGAGTGT
1 ACTGAGTGT
1478829 GCTAAAATGG
Statistics
Matches: 47, Mismatches: 16, Indels: 10
0.64 0.22 0.14
Matches are distributed among these distances:
28 21 0.45
29 7 0.15
30 7 0.15
31 12 0.26
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (28 bp):
ACTGAGTGTATGAATTTCCATATGGAGC
Found at i:1478846 original size:118 final size:118
Alignment explanation
Indices: 1478709--1479296 Score: 649
Period size: 118 Copynumber: 5.0 Consensus size: 118
1478699 GGCACTATGG
1478709 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGCTA
1 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGCTA
* * * * *
1478774 AAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATAT-GGAGCACTGAGT
66 AAATGGTAAGGAAATCATATTGAATATATGAATTTCCATATAGG-GCACTGAAT
* *
1478827 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTTCATATGGAGCATTGAGTGTGCTA
1 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGCTA
* * *
1478892 AAATGATAAGGAAATCCTATTGAATATATGAATTTCCATATAGGGCA-TTATAT
66 AAATGGTAAGGAAATCATATTGAATATATGAATTTCCATATAGGGCACTGA-AT
* * *
1478945 GTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCAATGAGTGTGCTA
1 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGCTA
* * * *
1479010 AAATGATAAGGAAATCATATTGAATATATGAATTTTCAGATAGGGCA-TTATAT
66 AAATGGTAAGGAAATCATATTGAATATATGAATTTCCATATAGGGCACTGA-AT
* * * *** * *
1479063 GTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGAAAAAGCACTAAGGGTGCTA
1 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGCTA
* * * * **
1479128 CAA-GGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGGGCACTTCAT
66 AAATGG-TAAGGAAATCATATTGAATA-TATGAATTTCCATATAGGGCACTGAAT
* * * **
1479181 GTGCTAAAAATGGTAAAGGAATCATACT-AATGGTATGGATTCTCGCATA-GG-GCACTTCGTGT
1 GTGCT-AAAATGGTAAGGGAATCATACTGAGT-GTATGAATT-TC-CATATGGAGCACTGAGTGT
* *
1479243 GCTAAAAT-GAAGAGGAAATCATATT-AAGTATATG-ATATTCCATATAGAGCACTG
62 GCTAAAATGGTA-AGGAAATCATATTGAA-TATATGAAT-TTCCATATAGGGCACTG
1479297 GGAGTGCTAA
Statistics
Matches: 410, Mismatches: 47, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
117 7 0.02
118 316 0.77
119 80 0.20
120 4 0.01
121 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (118 bp):
GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGCTA
AAATGGTAAGGAAATCATATTGAATATATGAATTTCCATATAGGGCACTGAAT
Found at i:1479186 original size:177 final size:176
Alignment explanation
Indices: 1478709--1479295 Score: 592
Period size: 177 Copynumber: 3.3 Consensus size: 176
1478699 GGCACTATGG
* * *
1478709 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGCTA
1 GTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGAATTTCCATATAGAGCACTAAGTGTGCTA
*
1478774 AAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGCTAAAATGG
66 AAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGCTAAAATGG
* * * *
1478839 TAAGGGAATCATACTGAGTGTATGAATTTTCATATGGAGCATTGAGT
131 TAA-GGAATCATACTGAATATATGAATTTTCAGATGGAGCATTGAAT
* * * * * * *
1478886 GTGCTAAAATGATAAGGAAATCCTATTGAATATATGAATTTCCATATAGGGCATTATA-TGTGCT
1 GTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGAATTTCCATATAGAGCACTA-AGTGTGCT
* *
1478950 AAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCAATGAGTGTGCTAAAATG
65 AAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGCTAAAATG
* *
1479015 ATAAGGAAATCATATTGAATATATGAATTTTCAGATAGG-GCATT-ATAT
130 GTAAGG-AATCATACTGAATATATGAATTTTCAGAT-GGAGCATTGA-AT
* * * * *
1479063 GTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGAAAAAGCACTAAGGGTGCTA
1 GTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGAATTTCCATATAGAGCACTAAGTGTGCTA
* * * * *
1479128 CAA-GGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGG-GCACTTCA-TGTGCTAAA
66 AAATGG-TAAGGAAATCATACTGAGT-GTATGAATTTCCATAT-GGAGCAC-TGAGTGTGCT-AA
* * *
1479189 AATGGTAAAGGAATCATACT-AATGGTATGGATTCTC-GCATAGG-GCACTTCG--T
126 AATGGT-AAGGAATCATACTGAAT-ATATGAATTTTCAG-AT-GGAGCA-TT-GAAT
* *
1479241 GTGCTAAAAT-G-AAGAGGAAATCATATTAAGTATATG-ATATTCCATATAGAGCACT
1 GTGCTAAAATGGTAAG-GG-AATCATATTGAGTGTATGAAT-TTCCATATAGAGCACT
1479296 GGGAGTGCTA
Statistics
Matches: 343, Mismatches: 48, Indels: 37
0.80 0.11 0.09
Matches are distributed among these distances:
176 11 0.03
177 247 0.72
178 79 0.23
179 6 0.02
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (176 bp):
GTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGAATTTCCATATAGAGCACTAAGTGTGCTA
AAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGCTAAAATGG
TAAGGAATCATACTGAATATATGAATTTTCAGATGGAGCATTGAAT
Found at i:1479304 original size:59 final size:59
Alignment explanation
Indices: 1478709--1479306 Score: 447
Period size: 59 Copynumber: 10.1 Consensus size: 59
1478699 GGCACTATGG
* * *
1478709 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGT
1 GTGCTAAAATGGTAAAGGAATCATACTAAGTGTATGAATTTCCATATAGAGCACTGAGT
* * *
1478768 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGT
1 GTGCTAAAATGGTAAAGGAATCATACTAAGTGTATGAATTTCCATATAGAGCACTGAGT
* * * * *
1478827 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTTCATATGGAGCATTGAGT
1 GTGCTAAAATGGTAAAGGAATCATACTAAGTGTATGAATTTCCATATAGAGCACTGAGT
* * * * * * *
1478886 GTGCTAAAATGAT-AAGGAAATCCTATTGAA-TATATGAATTTCCATATAGGGCA-TTATAT
1 GTGCTAAAATGGTAAAGG-AATCATACT-AAGTGTATGAATTTCCATATAGAGCACTGA-GT
* * * *
1478945 GTGCTAAAATGGT-AAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCAATGAGT
1 GTGCTAAAATGGTAAAGG-AATCATACTAAGTGTATGAATTTCCATATAGAGCACTGAGT
* * * * * * * *
1479004 GTGCTAAAATGAT-AAGGAAATCATATTGAA-TATATGAATTTTCAGATAGGGCA-TTATAT
1 GTGCTAAAATGGTAAAGG-AATCATACT-AAGTGTATGAATTTCCATATAGAGCACTGA-GT
* * * * * * * * *
1479063 GTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGAAAAAGCACTAAGG
1 GTGCTAAAATGGTAAAGGAATCATACTAAGTGTATGAATTTCCATATAGAGCACTGAGT
* * * * *
1479122 GTGCTACAA-GG-ATAAGGAAATCATACTAA-TAGTATGGATTTTCATATAGGGCACTTCA-T
1 GTGCTAAAATGGTA-AAGG-AATCATACTAAGT-GTATGAATTTCCATATAGAGCAC-TGAGT
* * **
1479181 GTGCTAAAAATGGTAAAGGAATCATACTAA-TGGTATGGATTCTCGC--ATAGGGCACTTCGT
1 GTGCT-AAAATGGTAAAGGAATCATACTAAGT-GTATGAATT-TC-CATATAGAGCACTGAGT
* * * *
1479241 GTGCTAAAAT-G-AAGAGGAAATCATATTAAGTATATG-ATATTCCATATAGAGCACTGGGA
1 GTGCTAAAATGGTAA-AGG-AATCATACTAAGTGTATGAAT-TTCCATATAGAGCACTGAGT
1479300 GTGCTAA
1 GTGCTAA
1479307 TATTATAAGA
Statistics
Matches: 449, Mismatches: 64, Indels: 52
0.79 0.11 0.09
Matches are distributed among these distances:
57 4 0.01
58 23 0.05
59 362 0.81
60 51 0.11
61 7 0.02
62 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.30
Consensus pattern (59 bp):
GTGCTAAAATGGTAAAGGAATCATACTAAGTGTATGAATTTCCATATAGAGCACTGAGT
Found at i:1479525 original size:44 final size:44
Alignment explanation
Indices: 1479355--1479543 Score: 308
Period size: 44 Copynumber: 4.3 Consensus size: 44
1479345 TGAAATTATA
* * *
1479355 GTAAGTAGATTGATAAAATAAGCTTACGAGCTTATGGAATAAAT-
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG-ATTAATG
*
1479399 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATTAATG
1479443 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATTAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATTAATG
1479487 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATTAAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATT-AATG
*
1479532 GTATGTATATTG
1 GTAAGTATATTG
1479544 ATAAGAAATC
Statistics
Matches: 137, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
43 4 0.03
44 118 0.86
45 15 0.11
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.33
Consensus pattern (44 bp):
GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATTAATG
Found at i:1479960 original size:30 final size:30
Alignment explanation
Indices: 1479921--1479980 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1479911 TAGCAGATAC
1479921 TGTAACAGTTACTGTAGCGTATCGATGCAT
1 TGTAACAGTTACTGTAGCGTATCGATGCAT
*
1479951 TGTAGCAGTTACTGTAGCGTATCGATGCAT
1 TGTAACAGTTACTGTAGCGTATCGATGCAT
1479981 AATATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (30 bp):
TGTAACAGTTACTGTAGCGTATCGATGCAT
Found at i:1488358 original size:24 final size:23
Alignment explanation
Indices: 1488313--1488359 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1488303 ATCTTCTTTC
* *
1488313 TTTTCTCATCTTAATTGTTTATA
1 TTTTCTCATCTTAATAGATTATA
*
1488336 TTTTCTTCATTTTAATAGATTATA
1 TTTTC-TCATCTTAATAGATTATA
1488360 GATTGTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTCTCATCTTAATAGATTATA
Found at i:1490726 original size:29 final size:29
Alignment explanation
Indices: 1490670--1490734 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
1490660 TTATTTCAAG
*
1490670 CTAACTACTAACTTTTATTTTATCGCATAT
1 CTAACCACTAACTTTTATTTTATCGCAT-T
* *
1490700 -TAACCACTAACTTTTATTTTCTTGCATT
1 CTAACCACTAACTTTTATTTTATCGCATT
1490728 CTAACCA
1 CTAACCA
1490735 TTGGTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.45
Consensus pattern (29 bp):
CTAACCACTAACTTTTATTTTATCGCATT
Found at i:1490928 original size:40 final size:39
Alignment explanation
Indices: 1490861--1490963 Score: 102
Period size: 40 Copynumber: 2.6 Consensus size: 39
1490851 TAACATTTTG
*
1490861 TTTT-TTTT-TTGTTCTTACTAACTTACTAACATTCTAAC
1 TTTTATTTTATTGTT-TTACTAACATACTAACATTCTAAC
* * * *
1490899 TTTTATTTTATTGTTTATACTAACATACTAACTTTTTTAT
1 TTTTATTTTATTGTTT-TACTAACATACTAACATTCTAAC
1490939 TTTTATTTTTTATTGTTTTTACTAA
1 TTTTA--TTTTATTG-TTTTACTAA
1490964 TTTATTAACA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
38 4 0.07
39 5 0.09
40 28 0.52
42 14 0.26
43 3 0.06
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.61
Consensus pattern (39 bp):
TTTTATTTTATTGTTTTACTAACATACTAACATTCTAAC
Found at i:1491747 original size:24 final size:24
Alignment explanation
Indices: 1491720--1491819 Score: 74
Period size: 24 Copynumber: 4.2 Consensus size: 24
1491710 AAACGGAGAT
*
1491720 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
1491744 ATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
1491768 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
1491792 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1491816 ATCA
1 ATCA
1491820 AAAGTCAGAT
Statistics
Matches: 55, Mismatches: 21, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1492991 original size:18 final size:18
Alignment explanation
Indices: 1492964--1492999 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1492954 CGATCTTATT
1492964 ATTTAATTCAGTCATTTC
1 ATTTAATTCAGTCATTTC
* *
1492982 ATTTACTTCAGTCCTTTC
1 ATTTAATTCAGTCATTTC
1493000 GAACGTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTAATTCAGTCATTTC
Found at i:1494315 original size:7 final size:7
Alignment explanation
Indices: 1494303--1494334 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1494293 TGGTCAACTT
1494303 CGGTCAA
1 CGGTCAA
1494310 CGGTCAA
1 CGGTCAA
1494317 CGGGTCAA
1 C-GGTCAA
1494325 CGGTCAA
1 CGGTCAA
1494332 CGG
1 CGG
1494335 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1494324 original size:15 final size:15
Alignment explanation
Indices: 1494304--1494350 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1494294 GGTCAACTTC
1494304 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1494319 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1494334 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1494347 GGTC
1 GGTC
1494351 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1494355 original size:18 final size:18
Alignment explanation
Indices: 1494332--1494408 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
1494322 CAACGGTCAA
1494332 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1494350 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
*
1494363 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
1494381 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1494399 CGGGTCGGGT
1 CGGGTCGGGT
1494409 TGTGACCGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.12, C:0.21, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1494364 original size:31 final size:31
Alignment explanation
Indices: 1494326--1494404 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
1494316 ACGGGTCAAC
1494326 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
1494357 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1494388 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1494405 GGGTTGTGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:1494368 original size:8 final size:8
Alignment explanation
Indices: 1494304--1494350 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1494294 GGTCAACTTC
1494304 GGTCAAC-
1 GGTCAACG
1494311 GGTCAACG
1 GGTCAACG
1494319 GGTCAAC-
1 GGTCAACG
1494326 GGTCAACG
1 GGTCAACG
1494334 GGT---CG
1 GGTCAACG
1494339 GGTCAACG
1 GGTCAACG
1494347 GGTC
1 GGTC
1494351 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1494404 original size:13 final size:13
Alignment explanation
Indices: 1494311--1494386 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
1494301 TTCGGTCAAC
*
1494311 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1494326 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1494339 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
1494357 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1494370 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1494383 GGTC
1 GGTC
1494387 GGGTCAACGG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.53
15 12 0.23
18 13 0.25
ACGTcount: A:0.17, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1496563 original size:24 final size:24
Alignment explanation
Indices: 1496536--1496638 Score: 80
Period size: 24 Copynumber: 4.3 Consensus size: 24
1496526 AAACGGAGAT
*
1496536 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
1496560 ATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
1496584 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
1496608 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1496632 ATCAGAA
1 ATCAGAA
1496639 GTCAGATAAA
Statistics
Matches: 57, Mismatches: 22, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1497807 original size:18 final size:18
Alignment explanation
Indices: 1497780--1497815 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1497770 CGATCTTATT
1497780 ATTTAATTCAGTCATTTC
1 ATTTAATTCAGTCATTTC
* *
1497798 ATTTACTTCAGTCCTTTC
1 ATTTAATTCAGTCATTTC
1497816 GAACAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTAATTCAGTCATTTC
Found at i:1499131 original size:7 final size:7
Alignment explanation
Indices: 1499119--1499150 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1499109 TGGTCAACTT
1499119 CGGTCAA
1 CGGTCAA
1499126 CGGTCAA
1 CGGTCAA
1499133 CGGGTCAA
1 C-GGTCAA
1499141 CGGTCAA
1 CGGTCAA
1499148 CGG
1 CGG
1499151 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1499140 original size:15 final size:15
Alignment explanation
Indices: 1499120--1499166 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1499110 GGTCAACTTC
1499120 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1499135 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1499150 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1499163 GGTC
1 GGTC
1499167 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1499171 original size:18 final size:18
Alignment explanation
Indices: 1499148--1499224 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
1499138 CAACGGTCAA
1499148 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1499166 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
*
1499179 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
1499197 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1499215 CGGGTCGGGT
1 CGGGTCGGGT
1499225 TGTGACCGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.12, C:0.21, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1499180 original size:31 final size:31
Alignment explanation
Indices: 1499142--1499220 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
1499132 ACGGGTCAAC
1499142 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
1499173 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1499204 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1499221 GGGTTGTGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:1499184 original size:8 final size:8
Alignment explanation
Indices: 1499120--1499166 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1499110 GGTCAACTTC
1499120 GGTCAAC-
1 GGTCAACG
1499127 GGTCAACG
1 GGTCAACG
1499135 GGTCAAC-
1 GGTCAACG
1499142 GGTCAACG
1 GGTCAACG
1499150 GGT---CG
1 GGTCAACG
1499155 GGTCAACG
1 GGTCAACG
1499163 GGTC
1 GGTC
1499167 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1499220 original size:13 final size:13
Alignment explanation
Indices: 1499127--1499202 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
1499117 TTCGGTCAAC
*
1499127 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1499142 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1499155 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
1499173 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1499186 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1499199 GGTC
1 GGTC
1499203 GGGTCAACGG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.53
15 12 0.23
18 13 0.25
ACGTcount: A:0.17, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1500065 original size:15 final size:15
Alignment explanation
Indices: 1500045--1500082 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1500035 GCAATTTATT
1500045 TTTGATTTTATTTTA
1 TTTGATTTTATTTTA
*
1500060 TTTGATTTGATTTTA
1 TTTGATTTTATTTTA
1500075 TTT-ATTTT
1 TTTGATTTT
1500083 GCAGCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (15 bp):
TTTGATTTTATTTTA
Found at i:1500083 original size:20 final size:20
Alignment explanation
Indices: 1500045--1500081 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1500035 GCAATTTATT
1500045 TTTGATTTTATTTTATTTGA
1 TTTGATTTTATTTTATTTGA
1500065 TTTGATTTTA-TTTATTT
1 TTTGATTTTATTTTATTT
1500082 TGCAGCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (20 bp):
TTTGATTTTATTTTATTTGA
Found at i:1500942 original size:13 final size:13
Alignment explanation
Indices: 1500923--1500990 Score: 79
Period size: 13 Copynumber: 5.5 Consensus size: 13
1500913 GTCACAACCC
1500923 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1500936 TACCCGACCCGTT
1 GACCCGACCCGTT
1500949 GACCCGA-CC--T
1 GACCCGACCCGTT
**
1500959 GACCCGACATGTT
1 GACCCGACCCGTT
*
1500972 GACTCGACCCGTT
1 GACCCGACCCGTT
1500985 GACCCG
1 GACCCG
1500991 TTGACCGTCG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
10 8 0.18
12 2 0.05
13 34 0.77
ACGTcount: A:0.18, C:0.43, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1500963 original size:23 final size:23
Alignment explanation
Indices: 1500937--1500980 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1500927 CGACCCGTTT
*
1500937 ACCCGACCCGTTGACCCGACCTG
1 ACCCGACACGTTGACCCGACCTG
* *
1500960 ACCCGACATGTTGACTCGACC
1 ACCCGACACGTTGACCCGACC
1500981 CGTTGACCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.16
Consensus pattern (23 bp):
ACCCGACACGTTGACCCGACCTG
Found at i:1502311 original size:18 final size:18
Alignment explanation
Indices: 1502285--1502319 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1502275 TCGAAAGGAC
*
1502285 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1502303 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1502320 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1508780 original size:17 final size:17
Alignment explanation
Indices: 1508758--1508791 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1508748 TGCATCAATT
1508758 ATGAGACTGATAAGCAA
1 ATGAGACTGATAAGCAA
1508775 ATGAGACTGATAAGCAA
1 ATGAGACTGATAAGCAA
1508792 TATATGTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (17 bp):
ATGAGACTGATAAGCAA
Found at i:1519998 original size:22 final size:23
Alignment explanation
Indices: 1519973--1520035 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 23
1519963 TATAAATGTT
*
1519973 AAAAAATATAATTATAATTATGA
1 AAAAAATATAATTATAATTACGA
*
1519996 AAAATAATATTTATTATAATTACGA
1 AAAA-AATA-TAATTATAATTACGA
*
1520021 AAAATA-ATAATTATA
1 AAAAAATATAATTATA
1520036 TTTAATAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.21
23 5 0.15
24 5 0.15
25 17 0.50
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.37
Consensus pattern (23 bp):
AAAAAATATAATTATAATTACGA
Found at i:1520016 original size:25 final size:25
Alignment explanation
Indices: 1519983--1520034 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1519973 AAAAAATATA
* *
1519983 ATTATAATTATGAAAAATAATATTT
1 ATTATAATTACGAAAAATAATAATT
1520008 ATTATAATTACGAAAAATAATAATT
1 ATTATAATTACGAAAAATAATAATT
1520033 AT
1 AT
1520035 ATTTAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTATAATTACGAAAAATAATAATT
Found at i:1520429 original size:30 final size:31
Alignment explanation
Indices: 1520370--1520436 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 31
1520360 AAAAATGTTA
1520370 AAAAAAATATTGTTAATATATATACATTTTT
1 AAAAAAATATTGTTAATATATATACATTTTT
*
1520401 ATAAAAAATATTGTTAATATAT-T-TATTTTT
1 A-AAAAAATATTGTTAATATATATACATTTTT
1520431 AAAAAA
1 AAAAAA
1520437 CTTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.15
30 7 0.21
31 2 0.06
32 20 0.59
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (31 bp):
AAAAAAATATTGTTAATATATATACATTTTT
Found at i:1520471 original size:24 final size:23
Alignment explanation
Indices: 1520439--1520484 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1520429 TTAAAAAACT
1520439 TTAATAATATTTATTA-TAATTAAA
1 TTAATAATA--TATTAGTAATTAAA
1520463 TTAATAATATATTAGTAATTAA
1 TTAATAATATATTAGTAATTAA
1520485 TTTATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 7 0.33
24 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATAATATATTAGTAATTAAA
Found at i:1520652 original size:18 final size:18
Alignment explanation
Indices: 1520616--1520654 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1520606 GAATGTTAAA
** *
1520616 AATAATAATTTTAATTTT
1 AATAATAATAATAACTTT
1520634 AATAATAATAATAACTTT
1 AATAATAATAATAACTTT
1520652 AAT
1 AAT
1520655 CTAATATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAATAATAATAACTTT
Found at i:1521771 original size:27 final size:27
Alignment explanation
Indices: 1521693--1521765 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
1521683 TGTTGATGTT
* *
1521693 ATATTTTAATGAATGCGATTAATATCA
1 ATATTTGAATGAATGTGATTAATATCA
* *
1521720 ATATTTGAATTAATGTAATTAATATCA
1 ATATTTGAATGAATGTGATTAATATCA
1521747 ATATTTGAATGAATGTGAT
1 ATATTTGAATGAATGTGAT
1521766 GGATATTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.42
Consensus pattern (27 bp):
ATATTTGAATGAATGTGATTAATATCA
Found at i:1522726 original size:19 final size:19
Alignment explanation
Indices: 1522698--1522735 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1522688 TATAAAACAA
* *
1522698 AATTATATAATTATTAAAT
1 AATTAAATAATTATAAAAT
1522717 AATTAAATAATTATAAAAT
1 AATTAAATAATTATAAAAT
1522736 TCAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTAAATAATTATAAAAT
Found at i:1522766 original size:25 final size:25
Alignment explanation
Indices: 1522712--1522782 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
1522702 ATATAATTAT
* *
1522712 TAAATAATTAAATAAT-TATAAAAT
1 TAAATAAATAAATAATATATAAAAC
1522736 TCAAATAAATAAATAATAT-TAGAAAC
1 T-AAATAAATAAATAATATATA-AAAC
*
1522762 TAAATAAATAAATTATATATA
1 TAAATAAATAAATAATATATA
1522783 TACATCAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.03
25 32 0.80
26 7 0.17
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (25 bp):
TAAATAAATAAATAATATATAAAAC
Found at i:1523908 original size:21 final size:20
Alignment explanation
Indices: 1523869--1523909 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1523859 CCATGAATAG
*
1523869 TGCTACAGTATATGATGCAC
1 TGCTACAGTATACGATGCAC
*
1523889 TGCTACAGTGTACCGATGCAC
1 TGCTACAGTATA-CGATGCAC
1523910 ACAAACATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (20 bp):
TGCTACAGTATACGATGCAC
Found at i:1523955 original size:21 final size:21
Alignment explanation
Indices: 1523930--1523973 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1523920 AATATAAATT
*
1523930 GTGTATCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
1523951 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
1523972 GT
1 GT
1523974 AACTTCAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTACA
Found at i:1524090 original size:23 final size:23
Alignment explanation
Indices: 1524060--1524114 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
1524050 GTTTAAAACA
1524060 TTACAAAACTTGATTATATGATT
1 TTACAAAACTTGATTATATGATT
1524083 TTACAAAACTTGATTATATGATT
1 TTACAAAACTTGATTATATGATT
1524106 TTACAAAAC
1 TTACAAAAC
1524115 CGATTAGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (23 bp):
TTACAAAACTTGATTATATGATT
Found at i:1524402 original size:18 final size:18
Alignment explanation
Indices: 1524376--1524410 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1524366 GCATATATAC
*
1524376 CATCCTTATCAACATCAA
1 CATCATTATCAACATCAA
*
1524394 CATCATTATCAATATCA
1 CATCATTATCAACATCA
1524411 TGTAATACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (18 bp):
CATCATTATCAACATCAA
Found at i:1524773 original size:25 final size:25
Alignment explanation
Indices: 1524739--1524788 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1524729 AAAATATGGT
* *
1524739 ATGAACAGTAACTTGCTACAGTACC
1 ATGAACAGTAACCTGCTACAATACC
1524764 ATGAACAGTAACCTGCTACAATACC
1 ATGAACAGTAACCTGCTACAATACC
1524789 CAAAAATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (25 bp):
ATGAACAGTAACCTGCTACAATACC
Done.