Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007725.1 Hibiscus syriacus cultivar Beakdansim tig00109972_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: 3026330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 14
Found at i:1532115 original size:17 final size:17
Alignment explanation
Indices: 1532093--1532148 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
1532083 GTTGAATAAA
1532093 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
1532110 TTCTTCTTCCTTCA-GATGAG
1 TTCTTC-TCATT-ATGA--AC
1532130 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
1532147 TT
1 TT
1532149 TCTCTGGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
17 9 0.30
18 7 0.23
19 7 0.23
20 7 0.23
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:1532311 original size:112 final size:110
Alignment explanation
Indices: 1532025--1532479 Score: 759
Period size: 104 Copynumber: 4.2 Consensus size: 110
1532015 AACTAAACAA
* *
1532025 CTCATTATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAAT
1 CTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAAC
1532090 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTT
66 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTT
1532135 CTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATG-ATTCAGGTAAAAGGTTGAAC
1 CTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAAC
1532199 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
66 AAATTCTTCTCATTATGAACTTCTTCTT-C--CTTCAGATGAGTTCTT
1532247 -TCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAAC
1 CTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAAC
*
1532311 AAATTCTTCTCATTATG-TCTTCTT-TTCCTTC--A-GAGTTCTT
66 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTT
*
1532351 CTCATTATGAACTTTCTCTGG-AAAGATGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAAC
1 CTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAAC
1532415 -AATTCTTCTCATTATGAACTTCTTCCTT-CTTCAGATGAGTTCTT
66 AAATTCTTCTCATTATGAACTTCTT-CTTCCTTCAGATGAGTTCTT
*
1532459 CTCATTATGAACTTTCCCTGG
1 CTCATTATGAACTTTCTCTGG
1532480 CAATGTTAAT
Statistics
Matches: 328, Mismatches: 6, Indels: 24
0.92 0.02 0.07
Matches are distributed among these distances:
103 16 0.05
104 56 0.17
105 25 0.08
106 2 0.01
107 5 0.02
108 28 0.09
109 48 0.15
110 46 0.14
111 49 0.15
112 53 0.16
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (110 bp):
CTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAAC
AAATTCTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTT
Found at i:1533436 original size:127 final size:130
Alignment explanation
Indices: 1533135--1533490 Score: 630
Period size: 127 Copynumber: 2.7 Consensus size: 130
1533125 GTAGTTCTTA
* *
1533135 CCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTCTGTCTAACCAGATCAGA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTC-GTCTAACCAGATCAGA
1533200 TAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCATGATTGGTTC
65 TAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATT-ATCTTCCAAATTCATGATTGGTTC
1533265 TG
129 TG
1533267 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT-TTC-TCTAACCAGATCAGAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCGTCTAACCAGATCAGAT
1533330 AACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAA-T-TCTTCCAAATTCAATGATTGGTTCT
66 AACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTATCTTCCAAATTC-ATGATTGGTTCT
1533393 G
130 G
1533394 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAACCAGATCAGA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTC-GTCTAACCAGATCAGA
1533459 TAACTCAAAGAACACTTCCAGAAGATGCTATT
65 TAACTCAAAGAACACTTCCAGAAGATGCTATT
1533491 CTGTCTAACC
Statistics
Matches: 218, Mismatches: 2, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
126 12 0.06
127 57 0.26
128 4 0.02
129 53 0.24
130 47 0.22
131 3 0.01
132 42 0.19
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (130 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCGTCTAACCAGATCAGAT
AACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTATCTTCCAAATTCATGATTGGTTCTG
Found at i:1533451 original size:50 final size:50
Alignment explanation
Indices: 1533397--1533686 Score: 498
Period size: 50 Copynumber: 5.9 Consensus size: 50
1533387 GGTTCTGCCA
1533397 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1533447 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1533497 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
*
1533547 AACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
* *
1533597 AACCAGATCAGATAACTCAAAGAACATTTCC--AAGATGCTTTTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
* *
1533645 AAACCAGATCAGATAACTCTAAG-A-ACTTCCAAAAGATGCTAT
1 -AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1533687 GAGTCTCTTT
Statistics
Matches: 230, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
47 5 0.02
48 17 0.07
49 30 0.13
50 178 0.77
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (50 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
Found at i:1534825 original size:9 final size:8
Alignment explanation
Indices: 1534812--1534882 Score: 56
Period size: 9 Copynumber: 8.4 Consensus size: 8
1534802 CTTGACCCCC
1534812 TTTCTTTT
1 TTTCTTTT
1534820 TCTTCTCTTT
1 T-TTCT-TTT
**
1534830 TTT-TTCA
1 TTTCTTTT
1534837 TTTCTATTT
1 TTTCT-TTT
1534846 TTTCTTTT
1 TTTCTTTT
1534854 CTTT-TTTCT
1 -TTTCTTT-T
1534863 TTTCTTTCT
1 TTTCTTT-T
1534872 TTTCTTTT
1 TTTCTTTT
1534880 TTT
1 TTT
1534883 TCTCTTCAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
7 4 0.08
8 16 0.31
9 28 0.54
10 4 0.08
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTCTTTT
Found at i:1534853 original size:5 final size:5
Alignment explanation
Indices: 1534812--1534885 Score: 66
Period size: 5 Copynumber: 15.0 Consensus size: 5
1534802 CTTGACCCCC
* * *
1534812 TTTCTT TTTCT TCTCT TTT-T TTTCA TTTCT ATT-T TTTCT TTTCTTT
1 TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC--T
1534858 TTTCT TTTC- TTTCT TTTCT TTT-T TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
1534886 CTTCAAGCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
4 15 0.27
5 32 0.57
6 4 0.07
7 5 0.09
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:1534861 original size:21 final size:21
Alignment explanation
Indices: 1534812--1534881 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 21
1534802 CTTGACCCCC
*
1534812 TTTCTTTTTCTTCTCTTTTTTTT
1 TTTC-TTTTCTT-TCTTTTCTTT
1534835 CATTTCTATTT-TTTCTTTTCTTT
1 --TTTCT-TTTCTTTCTTTTCTTT
1534858 TTTCTTTTCTTTCTTTTCTTT
1 TTTCTTTTCTTTCTTTTCTTT
1534879 TTT
1 TTT
1534882 TTCTCTTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 3 0.07
21 20 0.48
23 9 0.21
24 3 0.07
25 7 0.17
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTCTTTTCTTTCTTTTCTTT
Found at i:1534885 original size:14 final size:14
Alignment explanation
Indices: 1534811--1534883 Score: 80
Period size: 14 Copynumber: 5.4 Consensus size: 14
1534801 CCTTGACCCC
*
1534811 CTTTCTTTTTCTTCT
1 CTTT-TTTTTCTTTT
*
1534826 CTTTTTTTTCATTT
1 CTTTTTTTTCTTTT
*
1534840 CTATTTTTTCTTTT
1 CTTTTTTTTCTTTT
1534854 C--TTTTTTCTTTT
1 CTTTTTTTTCTTTT
*
1534866 CTTTCTTTTCTTTT
1 CTTTTTTTTCTTTT
1534880 -TTTT
1 CTTTT
1534884 CTCTTCAAGC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
12 12 0.24
13 3 0.06
14 31 0.62
15 4 0.08
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTTTTTCTTTT
Found at i:1545363 original size:17 final size:17
Alignment explanation
Indices: 1545323--1545374 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1545313 AAAATACTTG
*
1545323 TAAATAAACAT-ATAAA
1 TAAATAAAAATAATAAA
*
1545339 TATTATAAAAATAATAAA
1 TA-AATAAAAATAATAAA
*
1545357 TAAATAAAAATAAAAAA
1 TAAATAAAAATAATAAA
1545374 T
1 T
1545375 TTGAAAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 2 0.07
17 21 0.70
18 7 0.23
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATAAAAATAATAAA
Found at i:1546076 original size:13 final size:13
Alignment explanation
Indices: 1546052--1546086 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1546042 AATTTATTAT
1546052 ATATTT-ATAAAA
1 ATATTTAATAAAA
1546064 ATATTTAAT-AAA
1 ATATTTAATAAAA
1546076 ATATTTAATAA
1 ATATTTAATAA
1546087 TAAAAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTTAATAAAA
Found at i:1547006 original size:19 final size:19
Alignment explanation
Indices: 1546982--1547021 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1546972 TTTTTTTTTG
*
1546982 TTCTGTCTCTGTCCCTGGT
1 TTCTGTCTCTCTCCCTGGT
1547001 TTCTGTCTCTCTCCCTGGT
1 TTCTGTCTCTCTCCCTGGT
1547020 TT
1 TT
1547022 TTTGCTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.33, G:0.17, T:0.50
Consensus pattern (19 bp):
TTCTGTCTCTCTCCCTGGT
Found at i:1547515 original size:3 final size:3
Alignment explanation
Indices: 1547507--1547616 Score: 184
Period size: 3 Copynumber: 36.7 Consensus size: 3
1547497 TTAATATATT
*
1547507 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1547555 TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1547603 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
1547617 TGGATAAAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1552186 original size:2 final size:2
Alignment explanation
Indices: 1552179--1552236 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
1552169 CGTCAGCACT
*
1552179 TA TA TA TA TA -A TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1552220 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1552237 TAGTGCAGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1557795 original size:31 final size:31
Alignment explanation
Indices: 1557727--1557785 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1557717 AACAAGTTAC
*
1557727 TATTATAAAATGATCATTAAACTTATCAAAT
1 TATTATAAAAGGATCATTAAACTTATCAAAT
1557758 TATTATAAAAGGATCATTAAACTTATCA
1 TATTATAAAAGGATCATTAAACTTATCA
1557786 GTATTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.37
Consensus pattern (31 bp):
TATTATAAAAGGATCATTAAACTTATCAAAT
Found at i:1561714 original size:21 final size:20
Alignment explanation
Indices: 1561690--1561732 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1561680 GATGTAAGCT
*
1561690 TTAGGGTTTAAGATTTTGAGA
1 TTAGAGTTTAAGA-TTTGAGA
*
1561711 TTAGAGTTTATGATTTGAGA
1 TTAGAGTTTAAGATTTGAGA
1561731 TT
1 TT
1561733 GGGGGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (20 bp):
TTAGAGTTTAAGATTTGAGA
Found at i:1564225 original size:26 final size:26
Alignment explanation
Indices: 1564196--1564248 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1564186 ATTTATTTTT
*
1564196 ATCACCT-CTAAGAATTTTATAAGTTC
1 ATCACCTCCTAA-AATTTTAAAAGTTC
*
1564222 ATCATCTCCTAAAATTTTAAAAGTTC
1 ATCACCTCCTAAAATTTTAAAAGTTC
1564248 A
1 A
1564249 ACTCCCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCACCTCCTAAAATTTTAAAAGTTC
Found at i:1571512 original size:16 final size:17
Alignment explanation
Indices: 1571478--1571512 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1571468 TTAAAGCCCC
1571478 ATCAATTTACTTGATCT
1 ATCAATTTACTTGATCT
*
1571495 ATCAATTTA-TTTATCT
1 ATCAATTTACTTGATCT
1571511 AT
1 AT
1571513 ATGCATACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.51
Consensus pattern (17 bp):
ATCAATTTACTTGATCT
Found at i:1576234 original size:15 final size:16
Alignment explanation
Indices: 1576214--1576243 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1576204 AATTTTGATT
1576214 TTTAAAAA-TATATAA
1 TTTAAAAATTATATAA
1576229 TTTAAAAATTATATA
1 TTTAAAAATTATATA
1576244 TATATTCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTAAAAATTATATAA
Found at i:1577923 original size:16 final size:16
Alignment explanation
Indices: 1577902--1577932 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1577892 GATATACGAC
1577902 ATTTTCTACAGTATTT
1 ATTTTCTACAGTATTT
1577918 ATTTTCTACAGTATT
1 ATTTTCTACAGTATT
1577933 CATGGAACTC
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:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (16 bp):
ATTTTCTACAGTATTT
Found at i:1580822 original size:29 final size:29
Alignment explanation
Indices: 1580789--1580844 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1580779 GAATAGTGTA
1580789 ATTTACCTAAATTTAAAT-TGAATTAATGT
1 ATTTACCTAAATTTAAATAT-AATTAATGT
* *
1580818 ATTTACTTAAATTTTAATATAATTAAT
1 ATTTACCTAAATTTAAATATAATTAAT
1580845 TATATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (29 bp):
ATTTACCTAAATTTAAATATAATTAATGT
Found at i:1585057 original size:29 final size:29
Alignment explanation
Indices: 1585015--1585073 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1585005 TTCGGGTTTG
1585015 GACCTCGATCTTGCTTTGAAATGAGCTTC
1 GACCTCGATCTTGCTTTGAAATGAGCTTC
1585044 GACCTCGATCTTGCTTTGAAATGAGCTTC
1 GACCTCGATCTTGCTTTGAAATGAGCTTC
1585073 G
1 G
1585074 CAATAACCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (29 bp):
GACCTCGATCTTGCTTTGAAATGAGCTTC
Found at i:1599944 original size:12 final size:12
Alignment explanation
Indices: 1599927--1599954 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1599917 GCTGTCAATA
1599927 TATACGTATATG
1 TATACGTATATG
1599939 TATACGTATATG
1 TATACGTATATG
1599951 TATA
1 TATA
1599955 GTTTGGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (12 bp):
TATACGTATATG
Found at i:1601030 original size:3 final size:3
Alignment explanation
Indices: 1601022--1601061 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
1601012 AACAAGCTGT
* * *
1601022 AGA AGA AGA AGA AGA TGA AGA TGT AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1601062 AAAAGGCAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.60, C:0.00, G:0.33, T:0.07
Consensus pattern (3 bp):
AGA
Found at i:1603103 original size:14 final size:15
Alignment explanation
Indices: 1603078--1603106 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1603068 CGATGCGATA
1603078 ATAATATTAAATTAT
1 ATAATATTAAATTAT
1603093 ATAAT-TTAAATTAT
1 ATAATATTAAATTAT
1603107 TCTAAGTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATATTAAATTAT
Found at i:1603437 original size:25 final size:25
Alignment explanation
Indices: 1603404--1603483 Score: 133
Period size: 25 Copynumber: 3.2 Consensus size: 25
1603394 TCATGTTGGG
*
1603404 AGTAGTAGAAGATTGTCCTCACTTT
1 AGTACTAGAAGATTGTCCTCACTTT
*
1603429 AGTACTAGAAAATTGTCCTCACTTT
1 AGTACTAGAAGATTGTCCTCACTTT
1603454 AGTACTAGAAGATTGTCCTCACTTT
1 AGTACTAGAAGATTGTCCTCACTTT
*
1603479 CGTAC
1 AGTAC
1603484 AGATTTTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (25 bp):
AGTACTAGAAGATTGTCCTCACTTT
Found at i:1622613 original size:21 final size:21
Alignment explanation
Indices: 1622589--1622668 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
1622579 TAAGTTAAGA
*
1622589 TTTAGGGTTTAAGATTTATAG
1 TTTAGGGTTTAGGATTTATAG
*
1622610 TTTA-GATGTTATGGATTTATAG
1 TTTAGGGT-TTA-GGATTTATAG
* * *
1622632 TTTAAGGTTTAGGGTTTATAA
1 TTTAGGGTTTAGGATTTATAG
*
1622653 TTTAGGGTTTACGATT
1 TTTAGGGTTTAGGATT
1622669 AGGGTATAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.04
21 28 0.58
22 16 0.33
23 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTTAGGATTTATAG
Found at i:1627654 original size:20 final size:19
Alignment explanation
Indices: 1627629--1627680 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
1627619 TTGTGTGTGT
*
1627629 AAATCAATGATTTTATGATA
1 AAATCAATGA-TTTATAATA
1627649 AAATCAAT-A--TATAATA
1 AAATCAATGATTTATAATA
1627665 AAATCAATGATATTAT
1 AAATCAATGAT-TTAT
1627681 TCTCTTGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 14 0.52
17 1 0.04
19 1 0.04
20 11 0.41
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37
Consensus pattern (19 bp):
AAATCAATGATTTATAATA
Found at i:1627667 original size:16 final size:17
Alignment explanation
Indices: 1627646--1627677 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1627636 TGATTTTATG
1627646 ATAAAATCAAT-ATATA
1 ATAAAATCAATGATATA
1627662 ATAAAATCAATGATAT
1 ATAAAATCAATGATAT
1627678 TATTCTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAAATCAATGATATA
Found at i:1628524 original size:20 final size:20
Alignment explanation
Indices: 1628476--1628537 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1628466 AACTTAAATC
*
1628476 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1628496 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1628514 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1628533 AAAAT
1 AAAAT
1628538 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:1628612 original size:27 final size:27
Alignment explanation
Indices: 1628533--1628619 Score: 110
Period size: 23 Copynumber: 3.3 Consensus size: 27
1628523 TATATGATAT
1628533 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATATCTATAATATAATATT-A
* *
1628562 AAAATTAATAT-T-TCAT-TTAT-TTA
1 AAAATTAATATCTATAATATAATATTA
1628585 AAAATTAATATCTATAATATAATATTA
1 AAAATTAATATCTATAATATAATATTA
1628612 AAAATTAA
1 AAAATTAA
1628620 CATTTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 12 0.24
24 3 0.06
25 6 0.12
26 6 0.12
27 12 0.24
28 5 0.10
29 6 0.12
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAATTAATATCTATAATATAATATTA
Found at i:1628636 original size:50 final size:52
Alignment explanation
Indices: 1628533--1628646 Score: 187
Period size: 51 Copynumber: 2.2 Consensus size: 52
1628523 TATATGATAT
* *
1628533 AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTCATTTATTT-A
1 AAAATT-AATATCTATAATATAATATTAAAAAATTAACATTTAATTTATTTAA
1628585 AAAATTAATATCTATAATATAATATT-AAAAATTAACATTTAATTTATTTAA
1 AAAATTAATATCTATAATATAATATTAAAAAATTAACATTTAATTTATTTAA
1628636 AAAATTAATAT
1 AAAATTAATAT
1628647 TAAAATTAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
50 21 0.36
51 32 0.54
52 6 0.10
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (52 bp):
AAAATTAATATCTATAATATAATATTAAAAAATTAACATTTAATTTATTTAA
Found at i:1628649 original size:23 final size:23
Alignment explanation
Indices: 1628556--1628647 Score: 103
Period size: 23 Copynumber: 3.8 Consensus size: 23
1628546 TATAATATAA
* *
1628556 TATTAAAAAATTAATATTTCATT
1 TATTTAAAAATTAATATTTAATT
1628579 TATTTAAAAATTAATATCTATAATAT
1 TATTTAAAAATTAATAT-T-TAAT-T
* *
1628605 AATATTAAAAATTAACATTTAATT
1 TAT-TTAAAAATTAATATTTAATT
1628629 TATTTAAAAAATTAATATT
1 TATTT-AAAAATTAATATT
1628648 AAAATTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
23 18 0.31
24 16 0.28
25 7 0.12
26 4 0.07
27 13 0.22
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (23 bp):
TATTTAAAAATTAATATTTAATT
Found at i:1629919 original size:30 final size:30
Alignment explanation
Indices: 1629883--1629950 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
1629873 CGTTTTTGCT
* *
1629883 ATGGATTCAATCTCTGGGTTTAGAAATTTA
1 ATGGATTCAATCTCTGGGTTTACAAATTCA
* *
1629913 ATGGATTTAATCTTTGGGTTTACAAATTCA
1 ATGGATTCAATCTCTGGGTTTACAAATTCA
1629943 ATGGATTC
1 ATGGATTC
1629951 TGAAATCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.41
Consensus pattern (30 bp):
ATGGATTCAATCTCTGGGTTTACAAATTCA
Found at i:1631854 original size:30 final size:30
Alignment explanation
Indices: 1631818--1631884 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1631808 ATGAAATCCA
*
1631818 CATTCCCTCATTTGGTTAGCACGAGAATCT
1 CATTCCCCCATTTGGTTAGCACGAGAATCT
* * *
1631848 CATTCCCCCGTTTGGTTAGCAGGGGAATCT
1 CATTCCCCCATTTGGTTAGCACGAGAATCT
1631878 CATTCCC
1 CATTCCC
1631885 GGTAATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.31
Consensus pattern (30 bp):
CATTCCCCCATTTGGTTAGCACGAGAATCT
Found at i:1635700 original size:2 final size:2
Alignment explanation
Indices: 1635693--1635744 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1635683 CACTATACAC
1635693 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
1635735 AT AT AT AT AT
1 AT AT AT AT AT
1635745 CGCAAGCCAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1638379 original size:85 final size:87
Alignment explanation
Indices: 1638244--1638414 Score: 256
Period size: 85 Copynumber: 2.0 Consensus size: 87
1638234 TCAAATTCCA
* * *
1638244 TACATAAAATGTTACAAACTGTTTATATACCCCTAACATCACAAATTACTTTAGTTCTAAAAACA
1 TACATAAAATGTTACAAACTGTTTACATACCCCTAACATCACAAAATACTTTAGTTCCAAAAACA
*
1638309 ACATATTGTAGTTCCACAAAGT
66 ACATATTGTAGTTCAACAAAGT
** * *
1638331 TACATAAAA-GTTACAATTTTTTTACATA-CCCTTACATCACAAAATACTTTAGTTCCAAAAACA
1 TACATAAAATGTTACAAACTGTTTACATACCCCTAACATCACAAAATACTTTAGTTCCAAAAACA
1638394 ACATATTGTAGTTCAACAAAG
66 ACATATTGTAGTTCAACAAAG
1638415 GTGCACAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
85 52 0.68
86 15 0.20
87 9 0.12
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (87 bp):
TACATAAAATGTTACAAACTGTTTACATACCCCTAACATCACAAAATACTTTAGTTCCAAAAACA
ACATATTGTAGTTCAACAAAGT
Found at i:1638631 original size:21 final size:21
Alignment explanation
Indices: 1638605--1638666 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1638595 GGATATGTTT
*
1638605 GTGTTGTAGTCTAAGATGAAG
1 GTGTTGTAGGCTAAGATGAAG
**
1638626 GTGTTGTAGGCTGCGATGAAG
1 GTGTTGTAGGCTAAGATGAAG
* * *
1638647 GTGCTGTAGGATGAGATGAA
1 GTGTTGTAGGCTAAGATGAA
1638667 TTTGTTACAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.26, C:0.06, G:0.39, T:0.29
Consensus pattern (21 bp):
GTGTTGTAGGCTAAGATGAAG
Found at i:1642792 original size:21 final size:20
Alignment explanation
Indices: 1642748--1642843 Score: 103
Period size: 21 Copynumber: 4.9 Consensus size: 20
1642738 CGAGGGTTAC
*
1642748 AGTGGTCCTACGGGAC-AT-
1 AGTGGTCCTTCGGGACAATA
1642766 AGTGGTCCTTCGGGACAATAA
1 AGTGGTCCTTCGGGACAAT-A
1642787 AGTGGTCCTTCGGGACAATA
1 AGTGGTCCTTCGGGACAATA
*
1642807 TAGTGGTCCTAT-GAGAC-AT-
1 -AGTGGTCCT-TCGGGACAATA
*
1642826 AGTGGTCCTTTGGGACAA
1 AGTGGTCCTTCGGGACAA
1642844 ATTTCAATGC
Statistics
Matches: 68, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.01
18 28 0.41
19 3 0.04
20 3 0.04
21 32 0.47
22 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAATA
Found at i:1642842 original size:18 final size:18
Alignment explanation
Indices: 1642748--1642842 Score: 93
Period size: 18 Copynumber: 4.9 Consensus size: 18
1642738 CGAGGGTTAC
*
1642748 AGTGGTCCTACGGGACAT
1 AGTGGTCCTTCGGGACAT
1642766 AGTGGTCCTTCGGGACAAT
1 AGTGGTCCTTCGGGAC-AT
1642785 AAAGTGGTCCTTCGGGACAATAT
1 --AGTGGTCCTTCGGGAC---AT
*
1642808 AGTGGTCCTAT-GAGACAT
1 AGTGGTCCT-TCGGGACAT
*
1642826 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
1642843 AATTTCAATG
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
17 1 0.02
18 31 0.47
19 2 0.03
21 29 0.44
22 1 0.02
23 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1643654 original size:21 final size:19
Alignment explanation
Indices: 1643620--1643663 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
1643610 TGTTCATTAT
1643620 TGTTTATACGGTATTGTTCAC
1 TGTTTATACGGTATT-TT-AC
**
1643641 TGTTTATATTGTATTTTAC
1 TGTTTATACGGTATTTTAC
1643660 TGTT
1 TGTT
1643664 CATAAAACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 13 0.62
ACGTcount: A:0.18, C:0.09, G:0.16, T:0.57
Consensus pattern (19 bp):
TGTTTATACGGTATTTTAC
Found at i:1647166 original size:157 final size:154
Alignment explanation
Indices: 1646932--1647469 Score: 566
Period size: 157 Copynumber: 3.4 Consensus size: 154
1646922 TGTGGTATAT
* * * * * *
1646932 GAGCATGTGGTTTAAATTTGGTGAAAAA-CGAACTTAAAATAAATGATAAATTGAAGGAATAAGG
1 GAGCATGTGGCTCAAATTTGAT-AAAAATAG-ACTTAAAATAAATGACAAATTGAAGAAATAAGG
1646996 AAATTATGAAAAATTGAAAGATTAAATTGAAAAAATAAAAATTAGTTATCAAAAAGAGGAATTGA
64 AAATTATGAAAAATTGAAAGATTAAATTGAAAAAATAAAAATT-GTTATCAAAAAGA-GAATTGA
* *
1647061 AAGTACTCATGTATTCTATTATGGTTAG
127 AAGTACACATGTATTCTACTATGGTTAG
* * * *
1647089 GAGCATGTGGCTCAAGTTTGATAAAAAATAGAGTTAAAATAAATGACGAATTGAATAAATAAGGA
1 GAGCATGTGGCTCAAATTTGAT-AAAAATAGACTTAAAATAAATGACAAATTGAAGAAATAAGGA
* * * *
1647154 TATTATGAAAAATT-AAAGGACTAAATTGAAAAATAAAAAAATTGTTAT-AAAAATATGAATTGA
65 AATTATGAAAAATTGAAA-GATTAAATTGAAAAA-ATAAAAATTGTTATCAAAAAGA-GAATTGA
* *
1647217 AAGTACACATGTACTCTGCTATGGTTTAG
127 AAGTACACATGTATTCTACTATGG-TTAG
* * ** *
1647246 TAGCATGTGACTCAAATTT-AGTGAAAAACGGACTTAAAATAAATGACAAAGTGAAGAAATAAGG
1 GAGCATGTGGCTCAAATTTGA-T-AAAAATAGACTTAAAATAAATGACAAATTGAAGAAATAAGG
* *
1647310 AGATTATGAAAAATTGAAGGACTT-AATTG-AAAAATAAAAATTTGTTATCAAAAAGCAGAATTG
64 AAATTATGAAAAATTGAAAGA-TTAAATTGAAAAAATAAAAA-TTGTTATCAAAAAG-AGAATTG
* * *
1647373 AAAGTAAACATGTATTCTACTATGATTTAA
126 AAAGTACACATGTATTCTACTATG-GTTAG
* * * * * * ** *
1647403 GAGCATGTTGTTCAAATTTGGTGAAAATAGACTTAAAATGAAGGAGGAATTGAAGAAATAATGAA
1 GAGCATGTGGCTCAAATTTGATAAAAATAGACTTAAAATAAATGACAAATTGAAGAAATAAGGAA
1647468 AT
66 AT
1647470 CATGGACTAA
Statistics
Matches: 314, Mismatches: 55, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
155 6 0.02
156 83 0.26
157 212 0.68
158 13 0.04
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (154 bp):
GAGCATGTGGCTCAAATTTGATAAAAATAGACTTAAAATAAATGACAAATTGAAGAAATAAGGAA
ATTATGAAAAATTGAAAGATTAAATTGAAAAAATAAAAATTGTTATCAAAAAGAGAATTGAAAGT
ACACATGTATTCTACTATGGTTAG
Found at i:1647694 original size:22 final size:22
Alignment explanation
Indices: 1647642--1647686 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1647632 TTTTGCTCAC
1647642 CACTACCTTCCGGTTCAAAAGG
1 CACTACCTTCCGGTTCAAAAGG
1647664 CACTACCTTCCGGTTCAAAAGG
1 CACTACCTTCCGGTTCAAAAGG
1647686 C
1 C
1647687 TCTGCCTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (22 bp):
CACTACCTTCCGGTTCAAAAGG
Found at i:1654500 original size:17 final size:17
Alignment explanation
Indices: 1654478--1654511 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1654468 TACTCATTTT
* *
1654478 TCCGAATCGTCGGTAAA
1 TCCGAAGCGCCGGTAAA
1654495 TCCGAAGCGCCGGTAAA
1 TCCGAAGCGCCGGTAAA
1654512 AATGAGAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (17 bp):
TCCGAAGCGCCGGTAAA
Found at i:1659726 original size:29 final size:30
Alignment explanation
Indices: 1659645--1659732 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 30
1659635 TAGACCTCTA
* ****
1659645 ATAATAAATATTAGAAAAAATTGAACCCACA
1 ATAATAAATATTAGAAAAAATTCAA-CTTTT
*
1659676 ATAATAAATATTAGAGAAAATT-AACTTTT
1 ATAATAAATATTAGAAAAAATTCAACTTTT
*
1659705 ATAATAAGTATTA-AAAATAATTCAACTT
1 ATAATAAATATTAGAAAA-AATTCAACTT
1659733 ATAACTTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.06
29 17 0.35
30 7 0.15
31 21 0.44
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.32
Consensus pattern (30 bp):
ATAATAAATATTAGAAAAAATTCAACTTTT
Found at i:1669614 original size:21 final size:21
Alignment explanation
Indices: 1669561--1669615 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1669551 TGTTATCAAC
1669561 CATGAACTACCACGTCAACAT
1 CATGAACTACCACGTCAACAT
* * * *
1669582 TATGTACAACCACGTCAATAT
1 CATGAACTACCACGTCAACAT
1669603 CATGAACTACCAC
1 CATGAACTACCAC
1669616 ATCATCACAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.31, G:0.09, T:0.22
Consensus pattern (21 bp):
CATGAACTACCACGTCAACAT
Found at i:1673177 original size:162 final size:159
Alignment explanation
Indices: 1672871--1673191 Score: 606
Period size: 162 Copynumber: 2.0 Consensus size: 159
1672861 CTAAAATTAG
1672871 GATAAAATACGCGAGTGACCATTCAACTATTGTTCCATTTCACTTTGATTCTTCATTAGGCCACC
1 GATAAAATACGCGAGTGACCATTCAACTATTGTTCCATTTCACTTTGATTCTTCATTAGGCCACC
1672936 AACTATTTAAATACTTCAACCAAGCTACTTACGTTAAAATTTAATAGAAAAAGCAATGCGCCAAT
66 AACTATTTAAATACTTCAACCAAGCTACTTACGTTAAAATTTAATAGAAAAAGCAATGCGCCAAT
1673001 TTATAATTTTGGTATAATTACACTATTTC
131 TTATAATTTTGGTATAATTACACTATTTC
*
1673030 GATAAACTACGCGAGTGACCATTCAACTATTGTTCCATTTCACTTTGATTTCTTCATTAGGCCAC
1 GATAAAATACGCGAGTGACCATTCAACTATTGTTCCATTTCACTTTGA-TTCTTCATTAGGCCA-
1673095 CCAACTATTTAAATACTTCAACCAAGCTACTTACCGTTAAAATTTAATAGAAAAAGCAATGCGCC
64 CCAACTATTTAAATACTTCAACCAAGCTACTTA-CGTTAAAATTTAATAGAAAAAGCAATGCGCC
1673160 AATTTATAATTTTGGTATAATTACACTATTTC
128 AATTTATAATTTTGGTATAATTACACTATTTC
1673192 TCCCTGTTAC
Statistics
Matches: 158, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
159 47 0.30
160 15 0.09
161 33 0.21
162 63 0.40
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (159 bp):
GATAAAATACGCGAGTGACCATTCAACTATTGTTCCATTTCACTTTGATTCTTCATTAGGCCACC
AACTATTTAAATACTTCAACCAAGCTACTTACGTTAAAATTTAATAGAAAAAGCAATGCGCCAAT
TTATAATTTTGGTATAATTACACTATTTC
Found at i:1673883 original size:39 final size:36
Alignment explanation
Indices: 1673837--1673927 Score: 114
Period size: 36 Copynumber: 2.4 Consensus size: 36
1673827 TTTTTGGGCC
1673837 ACCCGACCCGACCCGA-GAAA-GAAGGGTTTTTCACCCGTG
1 ACCCGACCCGACCCGACGAAATGAA-GG--TTTCACCC--G
*
1673876 ACCCGACCCGACCCGACGAAATTAAGGTTTCACCCG
1 ACCCGACCCGACCCGACGAAATGAAGGTTTCACCCG
1673912 ACCCGACCCGACCCGA
1 ACCCGACCCGACCCGA
1673928 ATATATGACT
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
36 17 0.35
38 8 0.16
39 16 0.33
40 6 0.12
41 2 0.04
ACGTcount: A:0.26, C:0.40, G:0.22, T:0.12
Consensus pattern (36 bp):
ACCCGACCCGACCCGACGAAATGAAGGTTTCACCCG
Found at i:1678610 original size:23 final size:21
Alignment explanation
Indices: 1678578--1678634 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1678568 AAAAAGTTTA
*
1678578 TATGAGACGTTTTCATTCATCTT
1 TATGACACGTTTTCA-T-ATCTT
* *
1678601 TATGACACGTTTTTATATTTT
1 TATGACACGTTTTCATATCTT
*
1678622 TTTGACACGTTTT
1 TATGACACGTTTT
1678635 TCGATCGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 16 0.53
22 1 0.03
23 13 0.43
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.53
Consensus pattern (21 bp):
TATGACACGTTTTCATATCTT
Found at i:1688337 original size:4 final size:4
Alignment explanation
Indices: 1688328--1688360 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1688318 AGCAAACACT
1688328 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1688361 AATAGCAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:1688930 original size:14 final size:14
Alignment explanation
Indices: 1688911--1688940 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1688901 TAGGGATAGG
1688911 TATGTACCATTACC
1 TATGTACCATTACC
1688925 TATGTACCATTACC
1 TATGTACCATTACC
1688939 TA
1 TA
1688941 GGGATGCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (14 bp):
TATGTACCATTACC
Found at i:1689479 original size:23 final size:23
Alignment explanation
Indices: 1689419--1689479 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1689409 AAATTTCAGT
*
1689419 GAATTTAACGAGCAACGAACATC
1 GAATTTAACGAGCAACAAACATC
* *
1689442 GAGTTTAA-TAGGCAACAAACATC
1 GAATTTAACGA-GCAACAAACATC
1689465 -AATCTTAACGAGCAA
1 GAAT-TTAACGAGCAA
1689480 AGAGTCAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
22 3 0.10
23 26 0.87
24 1 0.03
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (23 bp):
GAATTTAACGAGCAACAAACATC
Found at i:1690557 original size:2 final size:2
Alignment explanation
Indices: 1690550--1690582 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1690540 AAACGAGTGA
1690550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1690583 AATAAAGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1693617 original size:14 final size:14
Alignment explanation
Indices: 1693598--1693624 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1693588 CTCAATTAAT
1693598 TTTATGTTCGTTTG
1 TTTATGTTCGTTTG
1693612 TTTATGTTCGTTT
1 TTTATGTTCGTTT
1693625 ATCATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.19, T:0.67
Consensus pattern (14 bp):
TTTATGTTCGTTTG
Found at i:1704267 original size:2 final size:2
Alignment explanation
Indices: 1704260--1704284 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1704250 ATTGACATTG
1704260 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1704285 CACTATAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1704670 original size:20 final size:21
Alignment explanation
Indices: 1704645--1704685 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1704635 TTAATATATC
1704645 AAATATAATC-TAAAATTATA
1 AAATATAATCGTAAAATTATA
* *
1704665 AAATATATTCGTAATATTATA
1 AAATATAATCGTAAAATTATA
1704686 TTTTTCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATATAATCGTAAAATTATA
Found at i:1707180 original size:756 final size:759
Alignment explanation
Indices: 1705727--1707238 Score: 2978
Period size: 756 Copynumber: 2.0 Consensus size: 759
1705717 GGGAATACAA
1705727 ATAAACAGGGATAAAGTACATAAATGGTCCTCTGACTATAGGGTATCTTTATTGAGTCCATTGAC
1 ATAAACAGGGATAAAGTACATAAATGGTCCTCTGACTATAGGGTATCTTTATTGAGTCCATTGAC
1705792 TATTACAAGTTACAAAATGGTTCCTTGAAGACGTTACTTTGTTGAGTCTCTTGACTATTAAAAGA
66 TATTACAAGTTACAAAATGGTTCCTTGAAGACGTTACTTTGTTGAGTCTCTTGACTATTAAAAGA
1705857 TATAAAATGATCACTCAACTATTCATAAGTTACAAACTTATCATTTTTTGTTAAAAGTTTAATGG
131 TATAAAATGATCACTCAACTATTCATAAGTTACAAACTTATCATTTTTTGTTAAAAGTTTAATGG
1705922 TAATCTGAGGTGGACGTTAACCTGTTGATTAGGATATAATAAAATCTAATCTCAAAATCTCAAAT
196 TAATCTGAGGTGGACGTTAACCTGTTGATTAGGATATAATAAAATCTAATCTCAAAATCTCAAAT
1705987 AACTATCATATCCGGTCAACATGTTAACGTTCAACTCAAACAATTATCATTTTTTAACAAGAAAT
261 AACTATCATATCCGGTCAACATGTTAACGTTCAACTCAAACAATTATCATTTTTTAACAAGAAAT
1706052 ATTGAATTTGGAACATATTAATAGTCGGGTGACCATTTTATAACTTTTAATAGTTGAATGTCTCA
326 ATTGAATTTGGAACATATTAATAGTCGGGTGACCATTTTATAACTTTTAATAGTTGAATGTCTCA
1706117 ACGGAGCAGTGTCTTATAGTCGGGGATCATTTTGTATGTTTTAATAGTGAGAGACTCAACAAAGT
391 ACGGAGCAGTGTCTTATAGTCGGGGATCATTTTGTATGTTTTAATAGTGAGAGACTCAACAAAGT
1706182 AGACCCTATAATTGGAAGACAATTTATGTACTTCACCCAATAAACAAATACATTGAGTCTTGCAT
456 AGACCCTATAATTGGAAGACAATTTATGTACTTCACCCAATAAACAAATACATTGAGTCTTGCAT
1706247 TATATTAAAACACACACCATACAAAGTACAAACAATTTAATACCCCATACACCCTGTTCCAGGAG
521 TATATTAAAACACACACCATACAAAGTACAAACAATTTAATACCCCATACACCCTGTTCCAGGAG
1706312 GATCAAAGAGCGCAAGAATCTCTATTTATTCCAGCTATACATTTTCGATGTAGGTTCATCTTTAA
586 GATCAAAGAGCGCAAGAATCTCTATTTATTCCAGCTATACATTTTCGATGTAGGTTCATCTTTAA
1706377 GGATCACAATTAGCTTGACTATAAGAACTGGTCCAGTTGCAATCTTCACTCGACACTTCTTCCGA
651 GGATCACAATTAGCTTGACTATAAGAACTGGTCCAGTTGCAATCTTCACTCGACACTTCTTCCGA
1706442 TGACTGTGAGGTCGGAGGCGGAGGCGAATACT-CCATGACTTCC
716 TGACTGTGAGGTCGGAGGCGGAGGCGAATACTCCCATGACTTCC
1706485 ATAAACAGGGATAAAGTACATAAATGGTCCTCTGACTATAGGGTATCTTTATTGAGTCCATTGAC
1 ATAAACAGGGATAAAGTACATAAATGGTCCTCTGACTATAGGGTATCTTTATTGAGTCCATTGAC
1706550 TATTACAAGTTACAAAATGGTTCCTTGAAGACGTTACTTTGTTGAGTCTCTTGACTATTAAAAGA
66 TATTACAAGTTACAAAATGGTTCCTTGAAGACGTTACTTTGTTGAGTCTCTTGACTATTAAAAGA
1706615 TATAAAATGATCACTCAACTATTCATAAGTTACAAACTTATCATTTTTTGTTAAAAGTTTAATGG
131 TATAAAATGATCACTCAACTATTCATAAGTTACAAACTTATCATTTTTTGTTAAAAGTTTAATGG
1706680 TAATCTGAGGTGGACGTTAACCTGTTGATTAGGATATAATAAAATCTAATCTCAAAATCTCAAAT
196 TAATCTGAGGTGGACGTTAACCTGTTGATTAGGATATAATAAAATCTAATCTCAAAATCTCAAAT
1706745 AACTATCATAT-C-GTCAACATGTTAACGTTC-ACTCAAACAATTATCATTTTTTAACAAGAAAT
261 AACTATCATATCCGGTCAACATGTTAACGTTCAACTCAAACAATTATCATTTTTTAACAAGAAAT
1706807 ATTGAATTTGGAACATATTAATAGTCGGGTGACCATTTTATAACTTTTAATAGTTGAATGTCTCA
326 ATTGAATTTGGAACATATTAATAGTCGGGTGACCATTTTATAACTTTTAATAGTTGAATGTCTCA
1706872 ACGGAGCAGTGTCTTATAGTCGGGGATCATTTTGTATGTTTTAATAGTTGAGAGACTCAACAAAG
391 ACGGAGCAGTGTCTTATAGTCGGGGATCATTTTGTATGTTTTAATAG-TGAGAGACTCAACAAAG
1706937 TAGACCCTATAATTGGAAGACAATTTATGTACTTCACCCAATAAACAAATACATTGAGTCTTGCA
455 TAGACCCTATAATTGGAAGACAATTTATGTACTTCACCCAATAAACAAATACATTGAGTCTTGCA
*
1707002 TTATATTAAAACACACACCATACAAAGTACCAACAATTTAATACCCCATACACCCTGTTCCAGGA
520 TTATATTAAAACACACACCATACAAAGTACAAACAATTTAATACCCCATACACCCTGTTCCAGGA
1707067 GGATCAAAGAGCGCAAGAATCTCTATTTATTCCAGCTATACATTTTCGATGTAGGTTCATCTTTA
585 GGATCAAAGAGCGCAAGAATCTCTATTTATTCCAGCTATACATTTTCGATGTAGGTTCATCTTTA
1707132 AGGATCACAATTAGCTTGACTATAAGAACTGGTCCAGTTGCAATCTTCACTCGACACTTCTTCCG
650 AGGATCACAATTAGCTTGACTATAAGAACTGGTCCAGTTGCAATCTTCACTCGACACTTCTTCCG
1707197 ATGACTGTGAGGTCGGAGGCGGAGGCGAATACTCCCATGACT
715 ATGACTGTGAGGTCGGAGGCGGAGGCGAATACTCCCATGACT
1707239 CTCCGGTCGG
Statistics
Matches: 751, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
755 144 0.19
756 327 0.44
757 9 0.01
758 271 0.36
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (759 bp):
ATAAACAGGGATAAAGTACATAAATGGTCCTCTGACTATAGGGTATCTTTATTGAGTCCATTGAC
TATTACAAGTTACAAAATGGTTCCTTGAAGACGTTACTTTGTTGAGTCTCTTGACTATTAAAAGA
TATAAAATGATCACTCAACTATTCATAAGTTACAAACTTATCATTTTTTGTTAAAAGTTTAATGG
TAATCTGAGGTGGACGTTAACCTGTTGATTAGGATATAATAAAATCTAATCTCAAAATCTCAAAT
AACTATCATATCCGGTCAACATGTTAACGTTCAACTCAAACAATTATCATTTTTTAACAAGAAAT
ATTGAATTTGGAACATATTAATAGTCGGGTGACCATTTTATAACTTTTAATAGTTGAATGTCTCA
ACGGAGCAGTGTCTTATAGTCGGGGATCATTTTGTATGTTTTAATAGTGAGAGACTCAACAAAGT
AGACCCTATAATTGGAAGACAATTTATGTACTTCACCCAATAAACAAATACATTGAGTCTTGCAT
TATATTAAAACACACACCATACAAAGTACAAACAATTTAATACCCCATACACCCTGTTCCAGGAG
GATCAAAGAGCGCAAGAATCTCTATTTATTCCAGCTATACATTTTCGATGTAGGTTCATCTTTAA
GGATCACAATTAGCTTGACTATAAGAACTGGTCCAGTTGCAATCTTCACTCGACACTTCTTCCGA
TGACTGTGAGGTCGGAGGCGGAGGCGAATACTCCCATGACTTCC
Found at i:1708152 original size:14 final size:14
Alignment explanation
Indices: 1708133--1708159 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1708123 CTTCATTGGA
1708133 TTAAAATTTAAAGT
1 TTAAAATTTAAAGT
1708147 TTAAAATTTAAAG
1 TTAAAATTTAAAG
1708160 ATTCTTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
TTAAAATTTAAAGT
Found at i:1710364 original size:21 final size:21
Alignment explanation
Indices: 1710340--1710383 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1710330 TTGACGGCGG
1710340 GCTTCTTGCACTTGGCGCATC
1 GCTTCTTGCACTTGGCGCATC
1710361 GCTTCTTGCACTTGGCGCATC
1 GCTTCTTGCACTTGGCGCATC
1710382 GC
1 GC
1710384 ATCCTGTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.34, G:0.25, T:0.32
Consensus pattern (21 bp):
GCTTCTTGCACTTGGCGCATC
Found at i:1710394 original size:21 final size:21
Alignment explanation
Indices: 1710346--1710394 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1710336 GCGGGCTTCT
* *
1710346 TGCACTTGGCGCATCGCTTCT
1 TGCACTTGGCGCATCGCATCC
1710367 TGCACTTGGCGCATCGCATCC
1 TGCACTTGGCGCATCGCATCC
*
1710388 TGTACTT
1 TGCACTT
1710395 CGCGATTAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.12, C:0.33, G:0.22, T:0.33
Consensus pattern (21 bp):
TGCACTTGGCGCATCGCATCC
Found at i:1712434 original size:30 final size:30
Alignment explanation
Indices: 1712398--1712523 Score: 157
Period size: 30 Copynumber: 4.2 Consensus size: 30
1712388 CGGCTGAATC
*
1712398 GGATTAATTCTCCATTCTGACATCTACATA
1 GGATTAATTCTCCATTCTGACATCTACATG
1712428 GGATTAATTC-CCTATTCTGACAATC-ACATG
1 GGATTAATTCTCC-ATTCTGAC-ATCTACATG
* * * *
1712458 GAACTAATTCCCCATTCTGACATCTGCATG
1 GGATTAATTCTCCATTCTGACATCTACATG
* *
1712488 GGATTAATTCTCGATTCTGACATCTGCATG
1 GGATTAATTCTCCATTCTGACATCTACATG
1712518 GGATTA
1 GGATTA
1712524 TATCCCCGTT
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.06
30 74 0.88
31 5 0.06
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (30 bp):
GGATTAATTCTCCATTCTGACATCTACATG
Found at i:1712739 original size:10 final size:10
Alignment explanation
Indices: 1712724--1712760 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
1712714 TAATATGTTC
1712724 GTTCATTTAT
1 GTTCATTTAT
1712734 GTTCATTTAT
1 GTTCATTTAT
*
1712744 GTTCGTTTAT
1 GTTCATTTAT
1712754 GTTCATT
1 GTTCATT
1712761 CGTTTATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:1712747 original size:24 final size:24
Alignment explanation
Indices: 1712717--1712784 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
1712707 CATTCGGTAA
1712717 TATGTTCGTTCATTTATGTTCATT
1 TATGTTCGTTCATTTATGTTCATT
* *
1712741 TATGTTCGTTTATGTTCA--TTCGTT
1 TATGTTCGTTCAT-TT-ATGTTCATT
1712765 TATGTGT-GTTCATTTATGTT
1 TATGT-TCGTTCATTTATGTT
1712785 TAACACAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
22 1 0.03
23 2 0.06
24 29 0.81
25 3 0.08
26 1 0.03
ACGTcount: A:0.15, C:0.10, G:0.16, T:0.59
Consensus pattern (24 bp):
TATGTTCGTTCATTTATGTTCATT
Found at i:1714052 original size:60 final size:60
Alignment explanation
Indices: 1713947--1714059 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
1713937 ATAGTCGGGT
* * * * *
1713947 GATCATTTTTTAACTTTTGATAGTCGAGGGACTTAATAAACCAATATTCTATAATTAGAG
1 GATCATTTTGTAACTTTTAATAGTCAAAGGACTTAATAAACCAATACTCTATAATTAGAG
* * *
1714007 GATCGTTTTGTAACTTTTAATAGTCAAATGACTTAATAAAGCAATACTCTATA
1 GATCATTTTGTAACTTTTAATAGTCAAAGGACTTAATAAACCAATACTCTATA
1714060 GTAAGGGGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTCAAAGGACTTAATAAACCAATACTCTATAATTAGAG
Found at i:1714083 original size:60 final size:61
Alignment explanation
Indices: 1713950--1714084 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 61
1713940 GTCGGGTGAT
* * * * * *
1713950 CATTTTT-TAACTTTTGATAGTCGAGGGACTTAATAAACCAATATTCTATAATTAGAGGAT
1 CATTTTTGTAACTTTTAATAGTCAAAGGACTTAATAAACCAATACTCTATAATAAGAGGAC
* * * * *
1714010 C-GTTTTGTAACTTTTAATAGTCAAATGACTTAATAAAGCAATACTCTATAGTAAGGGGAC
1 CATTTTTGTAACTTTTAATAGTCAAAGGACTTAATAAACCAATACTCTATAATAAGAGGAC
1714070 CATTTTTGT-ACTTTT
1 CATTTTTGTAACTTTT
1714085 CCTAAAATAT
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
59 4 0.07
60 51 0.84
61 6 0.10
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (61 bp):
CATTTTTGTAACTTTTAATAGTCAAAGGACTTAATAAACCAATACTCTATAATAAGAGGAC
Found at i:1719030 original size:72 final size:72
Alignment explanation
Indices: 1718949--1719103 Score: 251
Period size: 72 Copynumber: 2.2 Consensus size: 72
1718939 ATATTTCTTG
*
1718949 AAAATTTTAATTTCTTATATGACTTAAGTA-ATTTTTTGTATTTTCTATTGAATA-TTTAATTTC
1 AAAATTTTAATTTCTTATATGACTTAAGCATATTTTTTGTATTTTCTATTG--TAGTTTAATTTC
1719012 ACATCTTCT
64 ACATCTTCT
* *
1719021 AAAATTTTAATTTCTTATATGACTTAAGCATTTTTTTTGTATTTTCTATTGTAGTTTAATTTTAC
1 AAAATTTTAATTTCTTATATGACTTAAGCATATTTTTTGTATTTTCTATTGTAGTTTAATTTCAC
1719086 ATCTTCT
66 ATCTTCT
1719093 AAAATTTTAAT
1 AAAATTTTAAT
1719104 ATGAATTTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
71 2 0.03
72 57 0.73
73 19 0.24
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (72 bp):
AAAATTTTAATTTCTTATATGACTTAAGCATATTTTTTGTATTTTCTATTGTAGTTTAATTTCAC
ATCTTCT
Found at i:1719957 original size:87 final size:87
Alignment explanation
Indices: 1719810--1719985 Score: 318
Period size: 87 Copynumber: 2.0 Consensus size: 87
1719800 CGTTCCGGTA
1719810 TTCGAAGCCTGAGGTGGATTGTGGCCTGCCTGAGATGGTGCTGTATTTGAATGATGTCCCCATAA
1 TTCGAAGCCTGAGGTGGATTGTGGCCTGCCTGAGATGGTGCTGTATTTGAATGATGTCCCCATAA
1719875 TCCCGCTTTACTCTGTCCGTTG
66 TCCCGCTTTACTCTGTCCGTTG
1719897 TTCGAAGCCTGAGGTGGATTGTGGCCTGCCTGAGATGGTGCTGTATTTGAATGACT-TCCCCATA
1 TTCGAAGCCTGAGGTGGATTGTGGCCTGCCTGAGATGGTGCTGTATTTGAATGA-TGTCCCCATA
* *
1719961 CTCTCGCTTTACTCTGTCCGTTG
65 ATCCCGCTTTACTCTGTCCGTTG
1719984 TT
1 TT
1719986 ATCTTCTGCG
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
87 85 0.99
88 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (87 bp):
TTCGAAGCCTGAGGTGGATTGTGGCCTGCCTGAGATGGTGCTGTATTTGAATGATGTCCCCATAA
TCCCGCTTTACTCTGTCCGTTG
Found at i:1722199 original size:21 final size:20
Alignment explanation
Indices: 1722173--1722244 Score: 90
Period size: 21 Copynumber: 3.5 Consensus size: 20
1722163 TTTGCAGAAG
1722173 ATCGCAACGAGATAAATGAAA
1 ATCGCAACGAGA-AAATGAAA
* **
1722194 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAAAATGAAA
*
1722214 GTCGCAACGAGAGAAATGAAA
1 ATCGCAACGAGA-AAATGAAA
1722235 ATCGCAACGA
1 ATCGCAACGA
1722245 TTCATTTCGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.38
21 26 0.62
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (20 bp):
ATCGCAACGAGAAAATGAAA
Found at i:1722269 original size:18 final size:19
Alignment explanation
Indices: 1722246--1722281 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1722236 TCGCAACGAT
1722246 TCATTTCGCG-TGCGATTG
1 TCATTTCGCGTTGCGATTG
1722264 TCATTTCGCGTTGCGATT
1 TCATTTCGCGTTGCGATT
1722282 CTCTCGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.11, C:0.22, G:0.25, T:0.42
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATTG
Found at i:1724294 original size:184 final size:186
Alignment explanation
Indices: 1723984--1724447 Score: 877
Period size: 184 Copynumber: 2.5 Consensus size: 186
1723974 TAGATTGCTT
*
1723984 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1724049 TTTGTCTTTG-TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1724113 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1724169 AGTAAATTTGTTCGGTTGCTG-CAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1724232 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1724297 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1724353 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1724418 -TTGTCTTTGTTTTGTC-TTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
1724448 TGCAATCCAT
Statistics
Matches: 275, Mismatches: 1, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
183 35 0.13
184 162 0.59
185 59 0.21
186 19 0.07
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1724372 original size:93 final size:93
Alignment explanation
Indices: 1723984--1724447 Score: 877
Period size: 93 Copynumber: 5.1 Consensus size: 93
1723974 TAGATTGCTT
*
1723984 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1724049 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1724076 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1724141 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1724169 AGTAAATTTGTTCGGTTGCTG-CAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1724232 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1724260 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1724325 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1724353 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1724418 -TTGTCTTTGTTTTGTC-TTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1724443 AGTAA
1 AGTAA
1724448 TGCAATCCAT
Statistics
Matches: 368, Mismatches: 1, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
90 6 0.02
91 76 0.21
92 136 0.37
93 150 0.41
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1724535 original size:19 final size:19
Alignment explanation
Indices: 1724495--1724623 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1724485 TAGTTTACTT
* *
1724495 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1724515 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1724534 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1724553 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1724567 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1724586 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1724600 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1724619 TCGCA
1 TCGCA
1724624 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1724574 original size:33 final size:32
Alignment explanation
Indices: 1724531--1724623 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1724521 CGCGAAACCA
**
1724531 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1724563 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1724596 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1724624 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1724621 original size:52 final size:52
Alignment explanation
Indices: 1724495--1724623 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1724485 TAGTTTACTT
**
1724495 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1724547 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1724600 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1724624 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1724660 original size:14 final size:14
Alignment explanation
Indices: 1724641--1724697 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1724631 TTTCATTTCG
1724641 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1724655 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1724672 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1724688 CGTTGCGATT
1 CGTTGCGATT
1724698 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1724666 original size:33 final size:33
Alignment explanation
Indices: 1724624--1724716 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1724614 CAAAATCGCA
*
1724624 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1724657 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1724690 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1724717 TTGGTTTCGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1724724 original size:19 final size:19
Alignment explanation
Indices: 1724619--1724733 Score: 106
Period size: 19 Copynumber: 6.6 Consensus size: 19
1724609 GAAACCAAAA
*
1724619 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1724638 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1724654 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1724671 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1724687 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1724704 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1724723 TCGTGTTGCGA
1 TCGCGTTGCGA
1724734 AAGTAAACTA
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
14 15 0.19
16 11 0.14
17 11 0.14
19 41 0.53
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1726672 original size:14 final size:14
Alignment explanation
Indices: 1726653--1726688 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1726643 GATTGTTAAT
1726653 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1726667 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
1726681 TGATTTGT
1 TGATTTGT
1726689 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1726812 original size:19 final size:19
Alignment explanation
Indices: 1726796--1726911 Score: 172
Period size: 19 Copynumber: 6.4 Consensus size: 19
1726786 AAAAATGACT
1726796 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1726815 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1726834 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1726853 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1726867 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1726886 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
1726905 ATCGCAA
1 ATCGCAA
1726912 CGAGAGAATC
Statistics
Matches: 89, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 67 0.75
20 6 0.07
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1726943 original size:52 final size:53
Alignment explanation
Indices: 1726814--1726929 Score: 218
Period size: 52 Copynumber: 2.2 Consensus size: 53
1726804 GCGAAATGAA
1726814 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1726866 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1726918 AATCGCAATGCG
1 AATCGCAATGCG
1726930 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 57 0.90
53 6 0.10
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
Found at i:1726963 original size:14 final size:16
Alignment explanation
Indices: 1726943--1727132 Score: 89
Period size: 14 Copynumber: 11.6 Consensus size: 16
1726933 ATAATTTCGC
1726943 ATTGCGATTCTC-TCG
1 ATTGCGATTCTCATCG
*
1726958 -TTGCGATTTTCATTCG
1 ATTGCGATTCTCA-TCG
*
1726974 CATTGCGATTTTCATTCG
1 -ATTGCGATTCTCA-TCG
1726992 CATTGCGATTCTC-TCG
1 -ATTGCGATTCTCATCG
*
1727008 -TTGCGATTTTCATTTCG
1 ATTGCGATTCTCA--TCG
*
1727025 CATTGCGATTTTCATTTCG
1 -ATTGCGATTCTCA--TCG
1727044 CATTGCGATTCTC-TCG
1 -ATTGCGATTCTCATCG
*
1727060 -TTGCGATTTTCATTTCCG
1 ATTGCGATTCTCA--T-CG
1727078 CATTGCGATT-TCAT-G
1 -ATTGCGATTCTCATCG
*
1727093 -TTG-GATTTTCATTTCG
1 ATTGCGATTCTCA--TCG
1727109 CATTGCGATTCTC-TCG
1 -ATTGCGATTCTCATCG
1727125 -TTGCGATT
1 ATTGCGATT
1727133 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 6, Indels: 45
0.74 0.03 0.23
Matches are distributed among these distances:
12 4 0.03
13 6 0.04
14 38 0.26
15 2 0.01
16 13 0.09
17 5 0.03
18 33 0.22
19 38 0.26
20 8 0.05
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (16 bp):
ATTGCGATTCTCATCG
Found at i:1726977 original size:32 final size:33
Alignment explanation
Indices: 1726936--1727132 Score: 210
Period size: 32 Copynumber: 5.9 Consensus size: 33
1726926 TGCGTTTATA
1726936 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
1726969 A-TTCGCATTGCGATTTTCATTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGATTCTC--TCG--TTGCGATT-T-TC
* * * * *
1727007 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1727038 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1727071 ATTTCCGCATTGCGATT-TCAT-GTTG-GATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
1727103 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1727133 GTAATTTCCG
Statistics
Matches: 137, Mismatches: 11, Indels: 32
0.76 0.06 0.18
Matches are distributed among these distances:
31 22 0.16
32 38 0.28
33 37 0.27
34 16 0.12
35 1 0.01
36 8 0.06
37 3 0.02
38 6 0.04
39 6 0.04
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:1727032 original size:19 final size:19
Alignment explanation
Indices: 1726958--1727118 Score: 162
Period size: 19 Copynumber: 9.4 Consensus size: 19
1726948 GATTCTCTCG
1726958 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
1726976 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
*
1726994 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1727008 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1727027 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1727046 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1727060 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1727080 TTGCGA-TTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
1727093 TTG-GATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1727111 TTGCGATT
1 TTGCGATT
1727119 CTCTCGTTGC
Statistics
Matches: 120, Mismatches: 4, Indels: 37
0.75 0.02 0.23
Matches are distributed among these distances:
12 2 0.02
13 8 0.07
14 12 0.10
15 2 0.02
16 17 0.14
17 10 0.08
18 29 0.24
19 34 0.28
20 6 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1727091 original size:52 final size:52
Alignment explanation
Indices: 1726936--1727088 Score: 283
Period size: 52 Copynumber: 3.0 Consensus size: 52
1726926 TGCGTTTATA
1726936 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA-TTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1726987 A-TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1727038 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTT
1727089 CATGTTGGAT
Statistics
Matches: 99, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
50 32 0.32
51 19 0.19
52 35 0.35
53 13 0.13
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1729419 original size:12 final size:12
Alignment explanation
Indices: 1729402--1729426 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1729392 TCTTCGGGGA
1729402 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1729414 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1729426 C
1 C
1729427 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1730356 original size:20 final size:20
Alignment explanation
Indices: 1730328--1730557 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
1730318 AAATTTCAGT
* * *
1730328 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1730348 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1730368 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1730388 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1730408 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1730428 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1730448 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1730468 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1730488 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1730508 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1730528 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1730548 GTTGCGATTT
1 GTTGCGATTT
1730558 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1730574 original size:21 final size:21
Alignment explanation
Indices: 1730544--1730626 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
1730534 ATTTTCATAT
*
1730544 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1730565 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
1730586 TTGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1730607 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1730627 CTGATTTGCG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1730617 original size:42 final size:43
Alignment explanation
Indices: 1730524--1730622 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1730514 ATTTATGTGT
* *
1730524 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1730565 TCGCAATGCGAATTTGT-ACTATT-GCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1730607 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1730623 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 32 0.68
43 5 0.11
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1736586 original size:18 final size:16
Alignment explanation
Indices: 1736548--1736588 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
1736538 ATTTATAGGC
*
1736548 AATTATTACAAAAATA
1 AATTATTACAAAAACA
1736564 AATTATTACAAAAAACA
1 AATTATTAC-AAAAACA
1736581 ATATTATT
1 A-ATTATT
1736589 CAAGTTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.41
17 7 0.32
18 6 0.27
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (16 bp):
AATTATTACAAAAACA
Found at i:1739870 original size:15 final size:16
Alignment explanation
Indices: 1739850--1739884 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1739840 CGTAATATAT
1739850 GGTACCCGCAAG-TCG
1 GGTACCCGCAAGTTCG
*
1739865 GGTACCCGCTAGTTCG
1 GGTACCCGCAAGTTCG
1739881 GGTA
1 GGTA
1739885 ATATGGTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.17, C:0.29, G:0.34, T:0.20
Consensus pattern (16 bp):
GGTACCCGCAAGTTCG
Found at i:1741740 original size:2 final size:2
Alignment explanation
Indices: 1741733--1741762 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1741723 TTTAAATTAT
*
1741733 TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1741763 CTTTATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1743016 original size:10 final size:10
Alignment explanation
Indices: 1743001--1743097 Score: 52
Period size: 10 Copynumber: 9.0 Consensus size: 10
1742991 AACACAAATG
1743001 AACGAACATA
1 AACGAACATA
*
1743011 AACGAACACAAA
1 AACG-A-ACATA
1743023 CGAACGAACATA
1 --AACGAACATA
*
1743035 AACAAACATAATA
1 AACGAAC---ATA
*
1743048 AATGAACATA
1 AACGAACATA
*
1743058 AACGAACGTAA
1 AACGAACAT-A
*
1743069 AACGAATATA
1 AACGAACATA
*
1743079 AATGAACA-A
1 AACGAACATA
*
1743088 AACAAACATA
1 AACGAACATA
1743098 TAAAATTAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 18
0.68 0.14 0.19
Matches are distributed among these distances:
9 7 0.11
10 28 0.43
11 9 0.14
12 8 0.12
13 9 0.14
14 4 0.06
ACGTcount: A:0.62, C:0.18, G:0.09, T:0.11
Consensus pattern (10 bp):
AACGAACATA
Found at i:1743018 original size:24 final size:24
Alignment explanation
Indices: 1742984--1743064 Score: 103
Period size: 24 Copynumber: 3.4 Consensus size: 24
1742974 CATTTAAATG
*
1742984 ATAAACAAACACAAATGAACGAAC
1 ATAAACGAACACAAATGAACGAAC
*
1743008 ATAAACGAACACAAACGAACGAAC
1 ATAAACGAACACAAATGAACGAAC
* *
1743032 ATAAAC-AA-ACATAATAAATGAAC
1 ATAAACGAACACA-AATGAACGAAC
1743055 ATAAACGAAC
1 ATAAACGAAC
1743065 GTAAAACGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.06
23 16 0.33
24 30 0.61
ACGTcount: A:0.62, C:0.20, G:0.09, T:0.10
Consensus pattern (24 bp):
ATAAACGAACACAAATGAACGAAC
Found at i:1743233 original size:24 final size:24
Alignment explanation
Indices: 1743199--1743256 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1743189 AACATAAACG
* *
1743199 AACGAATATAAACAAATGAAAGTA
1 AACGAACATAAACAAACGAAAGTA
* *
1743223 AACGAACATAAACGAACGAACGTA
1 AACGAACATAAACAAACGAAAGTA
*
1743247 AATGAACATA
1 AACGAACATA
1743257 TTATTGAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (24 bp):
AACGAACATAAACAAACGAAAGTA
Found at i:1754671 original size:23 final size:24
Alignment explanation
Indices: 1754616--1754671 Score: 60
Period size: 28 Copynumber: 2.2 Consensus size: 24
1754606 AAATTATTGA
*
1754616 ATATATTTTATTCTTATCTTAACT
1 ATATATTTTAATCTTATCTTAACT
1754640 AAAAATATATTTTAATCTTATCTTAACT
1 ----ATATATTTTAATCTTATCTTAACT
1754668 -TATA
1 ATATA
1754672 AATTATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.15
28 23 0.85
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATATTTTAATCTTATCTTAACT
Found at i:1754683 original size:37 final size:35
Alignment explanation
Indices: 1754642--1754739 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 35
1754632 TCTTAACTAA
1754642 AAATATATTTTAATCTTATCTTAACTTATAAATTATT
1 AAATATATTTTAATCTTAT-TTAACTTA-AAATTATT
*
1754679 AAATATATTCTAA---T-TTTAAC-TAAAATTATT
1 AAATATATTTTAATCTTATTTAACTTAAAATTATT
*
1754709 AAATAT-TATTTATTCTTATATTAACTTAAAA
1 AAATATAT-TTTAATCTTAT-TTAACTTAAAA
1754740 ATATATATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
29 1 0.02
30 17 0.33
31 2 0.04
32 5 0.10
33 2 0.04
34 2 0.04
35 5 0.10
36 5 0.10
37 12 0.24
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (35 bp):
AAATATATTTTAATCTTATTTAACTTAAAATTATT
Found at i:1754741 original size:37 final size:36
Alignment explanation
Indices: 1754642--1754741 Score: 95
Period size: 35 Copynumber: 2.9 Consensus size: 36
1754632 TCTTAACTAA
* * *
1754642 AAATATATTTTAATCTTATCTTAACTTATAAATTATT
1 AAATATA-TTTATTCTTATATTAACTTAAAAATTATT
* *
1754679 -AA-ATA--TATTCTAATTTTAAC-T-AAAATTATT
1 AAATATATTTATTCTTATATTAACTTAAAAATTATT
1754709 AAATATTATTTATTCTTATATTAACTTAAAAAT
1 AAATA-TATTTATTCTTATATTAACTTAAAAAT
1754742 ATATATTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
30 8 0.16
31 3 0.06
32 13 0.26
33 2 0.04
35 16 0.32
36 3 0.06
37 5 0.10
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (36 bp):
AAATATATTTATTCTTATATTAACTTAAAAATTATT
Found at i:1754785 original size:31 final size:29
Alignment explanation
Indices: 1754715--1754817 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 29
1754705 TATTAAATAT
* *
1754715 TATTTATTCTTATATTAACTTAAAAA-TA
1 TATTTATTCTTATTTTAATTTAAAAATTA
1754743 TA--TATT-TTATTTTAATTTAAAAATGTA
1 TATTTATTCTTATTTTAATTTAAAAAT-TA
1754770 TATTTTATTCTTATTTTAATTTAATAAA-TA
1 TA-TTTATTCTTATTTTAATTTAA-AAATTA
* *
1754800 TATTTATTTTTATCTTAA
1 TATTTATTCTTATTTTAA
1754818 CTATAATTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
25 15 0.23
26 4 0.06
27 4 0.06
28 2 0.03
29 14 0.22
30 8 0.12
31 14 0.22
32 3 0.05
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (29 bp):
TATTTATTCTTATTTTAATTTAAAAATTA
Found at i:1754804 original size:30 final size:30
Alignment explanation
Indices: 1754587--1754817 Score: 121
Period size: 29 Copynumber: 7.7 Consensus size: 30
1754577 AACATTAAAT
* * *
1754587 ATATATTTTATT-TT-TTCTTAAATTATTGA
1 ATATATTTTATTCTTATT-TTAATTTAATAA
* *
1754616 ATATATTTTATTCTTATCTTAA-CTAA-AA
1 ATATATTTTATTCTTATTTTAATTTAATAA
* * *
1754644 ATATATTTTAATCTTATCTTAACTT-ATAA
1 ATATATTTTATTCTTATTTTAATTTAATAA
* *
1754673 AT-TATTAAATATATTCTAATTTTAACTAAAATTATTAA
1 ATATATT---T-TATTCTTATTTTAA-T----TTAATAA
* *
1754711 ATAT-TATTTATTCTTATATTAACTTAA-AA
1 ATATAT-TTTATTCTTATTTTAATTTAATAA
1754740 ATATA---TATT-TTATTTTAATTTAA-AA
1 ATATATTTTATTCTTATTTTAATTTAATAA
1754765 ATGTATATTTTATTCTTATTTTAATTTAATAA
1 A--TATATTTTATTCTTATTTTAATTTAATAA
* *
1754797 ATATA-TTTATTTTTATCTTAA
1 ATATATTTTATTCTTATTTTAA
1754818 CTATAATTTT
Statistics
Matches: 159, Mismatches: 19, Indels: 48
0.70 0.08 0.21
Matches are distributed among these distances:
25 15 0.09
26 4 0.03
27 4 0.03
28 27 0.17
29 39 0.25
30 17 0.11
31 16 0.10
32 14 0.09
35 12 0.08
36 1 0.01
37 2 0.01
38 6 0.04
39 2 0.01
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.55
Consensus pattern (30 bp):
ATATATTTTATTCTTATTTTAATTTAATAA
Found at i:1754939 original size:29 final size:29
Alignment explanation
Indices: 1754907--1754963 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
1754897 AAGTTTAAAA
* * * *
1754907 AAGACTAAAATATTTTTTTTATTTTATTT
1 AAGAATAAAATATATATTTAATTTTATTT
*
1754936 AAGAATAAACTATATATTTAATTTTATT
1 AAGAATAAAATATATATTTAATTTTATT
1754964 AGATGTGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (29 bp):
AAGAATAAAATATATATTTAATTTTATTT
Found at i:1757429 original size:2 final size:2
Alignment explanation
Indices: 1757422--1757465 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1757412 TAAATTCACA
*
1757422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1757464 AT
1 AT
1757466 TAGCTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1757526 original size:27 final size:24
Alignment explanation
Indices: 1757470--1757540 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 24
1757460 ATATATTAGC
1757470 TTAAAAATACTTTTTATTTTAACTTA
1 TTAAAAATA--TTTTATTTTAACTTA
*
1757496 TTAAATATATTTTATTATTAACTTAA
1 TTAAAAATATTTTATT-TTAACTT-A
1757522 TTTAAAAATATTTTATTTT
1 -TTAAAAATATTTTATTTT
1757541 TATTTTCATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.17
25 7 0.17
26 11 0.28
27 15 0.38
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAAAAATATTTTATTTTAACTTA
Found at i:1757754 original size:30 final size:31
Alignment explanation
Indices: 1757699--1757765 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
1757689 TGATGATCAC
1757699 ATCTTAATTAAATAAAAACAGAAGTGACCAT
1 ATCTTAATTAAATAAAAACAGAAGTGACCAT
* *
1757730 ATCTTAATT-AATAATAAC-GAAAGTGACTAT
1 ATCTTAATTAAATAAAAACAG-AAGTGACCAT
1757760 ATCTTA
1 ATCTTA
1757766 TATTTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 1 0.03
30 23 0.70
31 9 0.27
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAGAAGTGACCAT
Found at i:1763507 original size:15 final size:15
Alignment explanation
Indices: 1763470--1763510 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1763460 GCACATACAT
1763470 CACATGCTCCACCAG
1 CACATGCTCCACCAG
* *
1763485 CGCATGCTCCACCTG
1 CACATGCTCCACCAG
*
1763500 CACCTGCTCCA
1 CACATGCTCCA
1763511 TTAAATGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.20, C:0.49, G:0.15, T:0.17
Consensus pattern (15 bp):
CACATGCTCCACCAG
Found at i:1764045 original size:96 final size:96
Alignment explanation
Indices: 1763871--1764051 Score: 317
Period size: 96 Copynumber: 1.9 Consensus size: 96
1763861 GGACAACCCA
* * *
1763871 TGTGTTGCTCCATTTCAGCGTGTTTCTTCAACGCATGGTGACGAAACTCATGGGACCACATCAAT
1 TGTGCTGCTCCATTTCAACGTGTTTCTTCAACGCATGGTGACGAAACTCATGGGACCACATCAAC
*
1763936 TAGTGCGCAAGTGGAAGCTGGAACCTGCCCT
66 TAATGCGCAAGTGGAAGCTGGAACCTGCCCT
*
1763967 TGTGCTGCTTCATTTCAACGTGTTTCTTCAACGCATGGTGACGAAACTCATGGGACCACATCAAC
1 TGTGCTGCTCCATTTCAACGTGTTTCTTCAACGCATGGTGACGAAACTCATGGGACCACATCAAC
1764032 TAATGCGCAAGTGGAAGCTG
66 TAATGCGCAAGTGGAAGCTG
1764052 TTTCAGCGCA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 80 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (96 bp):
TGTGCTGCTCCATTTCAACGTGTTTCTTCAACGCATGGTGACGAAACTCATGGGACCACATCAAC
TAATGCGCAAGTGGAAGCTGGAACCTGCCCT
Found at i:1770096 original size:11 final size:11
Alignment explanation
Indices: 1770080--1770139 Score: 66
Period size: 11 Copynumber: 5.3 Consensus size: 11
1770070 TATATTTCGT
1770080 TTTTTATTAAA
1 TTTTTATTAAA
1770091 TTTTTATTAAA
1 TTTTTATTAAA
*
1770102 TTTTTATTATA
1 TTTTTATTAAA
*
1770113 TTTATATTTAAA
1 TTTTTA-TTAAA
* *
1770125 TAATTTAATAAA
1 T-TTTTATTAAA
1770137 TTT
1 TTT
1770140 ATTTGTTATA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 27 0.68
12 10 0.25
13 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTTATTAAA
Found at i:1773841 original size:37 final size:36
Alignment explanation
Indices: 1773769--1773842 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
1773759 GTTGAAAAAT
*
1773769 ATTTATATATTCTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTCTCTTTAAAAAATTAAAATCATAAA
* * *
1773805 ATTTATATAATTTTTTTTACAAAATTTAAAAT-ATAAA
1 ATTTATAT-ATTCTCTTTA-AAAAATTAAAATCATAAA
1773842 A
1 A
1773843 AGATTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 8 0.25
37 14 0.44
38 10 0.31
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (36 bp):
ATTTATATATTCTCTTTAAAAAATTAAAATCATAAA
Found at i:1782311 original size:32 final size:32
Alignment explanation
Indices: 1782271--1782371 Score: 125
Period size: 32 Copynumber: 3.2 Consensus size: 32
1782261 ATAATGATTG
*
1782271 TAAA-TTTATCGAACTGTTATAAAACGATCAT
1 TAAATTTTATCGAACTGTTATAAAATGATCAT
* * * * *
1782302 TGAATTTTATCAAACTATTATAAAATAATCAC
1 TAAATTTTATCGAACTGTTATAAAATGATCAT
*
1782334 CAAATTTTATCGAACTGTTA-AAAATGATCAT
1 TAAATTTTATCGAACTGTTATAAAATGATCAT
1782365 TAAATTT
1 TAAATTT
1782372 ATTTAAACTT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
31 18 0.32
32 38 0.68
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.38
Consensus pattern (32 bp):
TAAATTTTATCGAACTGTTATAAAATGATCAT
Found at i:1785427 original size:2 final size:2
Alignment explanation
Indices: 1785420--1785457 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1785410 TTCTTGTATG
1785420 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
1785458 CAGGTCACTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1790192 original size:20 final size:20
Alignment explanation
Indices: 1790167--1790209 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1790157 AATGTTAGGG
*
1790167 ATGTGAGCATTCAATGTCAA
1 ATGTGAGCATTAAATGTCAA
1790187 ATGTGAGCATTAAATGTCAA
1 ATGTGAGCATTAAATGTCAA
1790207 ATG
1 ATG
1790210 GTTGAGAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (20 bp):
ATGTGAGCATTAAATGTCAA
Found at i:1792225 original size:23 final size:23
Alignment explanation
Indices: 1792198--1792305 Score: 110
Period size: 23 Copynumber: 4.7 Consensus size: 23
1792188 TAGCATTTGC
* *
1792198 AAACATGTTTATTTAGCGTTCGT
1 AAACATGTTCATTTAACGTTCGT
* ** * *
1792221 GAACATGTTTGTTTAACTTTCAT
1 AAACATGTTCATTTAACGTTCGT
* *
1792244 AAACATGTTCGTTTAACATTCGT
1 AAACATGTTCATTTAACGTTCGT
* *
1792267 CAACATATTCATTT-ACGTTCGT
1 AAACATGTTCATTTAACGTTCGT
1792289 AAACATGTTCATTTAAC
1 AAACATGTTCATTTAAC
1792306 ATTAATTCAA
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
22 19 0.28
23 50 0.72
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (23 bp):
AAACATGTTCATTTAACGTTCGT
Found at i:1792266 original size:46 final size:45
Alignment explanation
Indices: 1792198--1792308 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 45
1792188 TAGCATTTGC
* * * * * ** *
1792198 AAACATGTTTATTTAGCGTTCGTGAACATGTTTGTTTAACTTTCAT
1 AAACATGTTCATTTAACATTCGTCAACATATTCATTT-ACGTTCAT
* *
1792244 AAACATGTTCGTTTAACATTCGTCAACATATTCATTTACGTTCGT
1 AAACATGTTCATTTAACATTCGTCAACATATTCATTTACGTTCAT
1792289 AAACATGTTCATTTAACATT
1 AAACATGTTCATTTAACATT
1792309 AATTCAATGT
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
45 25 0.46
46 29 0.54
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (45 bp):
AAACATGTTCATTTAACATTCGTCAACATATTCATTTACGTTCAT
Found at i:1797740 original size:2 final size:2
Alignment explanation
Indices: 1797733--1797758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1797723 CTCCCAGAAC
1797733 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
1797759 TGATTTGCAC
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):
AT
Found at i:1799188 original size:22 final size:21
Alignment explanation
Indices: 1799138--1799189 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
1799128 ATTCTTTTTC
*
1799138 TTTTTGAAAAAAATGTATCCT
1 TTTTTTAAAAAAATGTATCCT
**
1799159 TTAATTAAAAAAATCGT-TCTCT
1 TTTTTTAAAAAAAT-GTATC-CT
1799181 TTTTTTAAA
1 TTTTTTAAA
1799190 CACGTAGAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (21 bp):
TTTTTTAAAAAAATGTATCCT
Found at i:1812940 original size:14 final size:14
Alignment explanation
Indices: 1812921--1812964 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
1812911 TAATTACTCC
1812921 TTTAATCATTTAGA
1 TTTAATCATTTAGA
1812935 TTTAATCATTTAGA
1 TTTAATCATTTAGA
*
1812949 ATTAATCATTTAGA
1 TTTAATCATTTAGA
1812963 TT
1 TT
1812965 GTTTGATTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTAATCATTTAGA
Found at i:1815202 original size:29 final size:29
Alignment explanation
Indices: 1815169--1815240 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
1815159 ATTGACAAGG
*
1815169 GAAAGAATATATTTATTTTTGAAAAGTAT
1 GAAAGAATATATTTAATTTTGAAAAGTAT
1815198 GAAAGAATATATTTAATTTTGAAAAGTAT
1 GAAAGAATATATTTAATTTTGAAAAGTAT
1815227 GAAAGAATATATTT
1 GAAAGAATATATTT
1815241 TGATAGGAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (29 bp):
GAAAGAATATATTTAATTTTGAAAAGTAT
Found at i:1828603 original size:3 final size:3
Alignment explanation
Indices: 1828595--1828634 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1828585 ATCTCACCCA
1828595 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1828635 CCTTTCATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1830277 original size:15 final size:15
Alignment explanation
Indices: 1830257--1830286 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1830247 CAGAACATAC
*
1830257 CAGTAGACTAGATAG
1 CAGTAGACCAGATAG
1830272 CAGTAGACCAGATAG
1 CAGTAGACCAGATAG
1830287 TAGCATACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.27, T:0.17
Consensus pattern (15 bp):
CAGTAGACCAGATAG
Found at i:1831068 original size:69 final size:69
Alignment explanation
Indices: 1830957--1831096 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
1830947 CACTTGGTAG
1830957 AAATCCAGTAGTCATTTAAGGATTCAAACTTTAATTTTTAACTACTCCTTGATTTAATCCTTTAA
1 AAATCCAGTAGTCATTTAAGGATTCAAACTTTAATTTTTAACTACTCCTTGATTTAATCCTTTAA
1831022 TAAA
66 TAAA
1831026 AAATCCAGTAGTCATTTAAGGATTCAAACTTTAATTTTTAACTACTCCTTGATTTAATCCTTTAA
1 AAATCCAGTAGTCATTTAAGGATTCAAACTTTAATTTTTAACTACTCCTTGATTTAATCCTTTAA
1831091 TAAA
66 TAAA
1831095 AA
1 AA
1831097 TATTAATTTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (69 bp):
AAATCCAGTAGTCATTTAAGGATTCAAACTTTAATTTTTAACTACTCCTTGATTTAATCCTTTAA
TAAA
Found at i:1837953 original size:19 final size:19
Alignment explanation
Indices: 1837929--1837965 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1837919 GTAACTCGAA
*
1837929 TTCAATTCGAGTCGAGTTT
1 TTCAATTCGAATCGAGTTT
1837948 TTCAATTCGAATCGAGTT
1 TTCAATTCGAATCGAGTT
1837966 GAAATAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (19 bp):
TTCAATTCGAATCGAGTTT
Found at i:1838880 original size:2 final size:2
Alignment explanation
Indices: 1838869--1838930 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
1838859 GTATACTAAC
1838869 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1838910 TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
1838931 ATTTGAATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.