Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003267.1 Hibiscus syriacus cultivar Beakdansim tig00006866_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: 204893
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
File 1 of 2
Found at i:1901 original size:23 final size:22
Alignment explanation
Indices: 1863--1914 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
1853 CTGAAAAATC
1863 ATCAAATCGAGTATTGACCAAG
1 ATCAAATCGAGTATTGACCAAG
*
1885 ATCAAAGTCGGGTATTGACCAAG
1 ATCAAA-TCGAGTATTGACCAAG
1908 ATCAAAT
1 ATCAAAT
1915 TTCGAATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (22 bp):
ATCAAATCGAGTATTGACCAAG
Found at i:2779 original size:20 final size:19
Alignment explanation
Indices: 2758--2997 Score: 121
Period size: 20 Copynumber: 11.9 Consensus size: 19
2748 GCGATAGTCA
2758 GAATCTCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
2777 -AGAT-TCGTATTGCGATTTAC
1 GA-ATCTCG--TTGCGATTTAC
*
2797 GTAT-TCGTATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
* * *
2817 GGATACGCATTGCGATTTAC
1 GAAT-CTCGTTGCGATTTAC
*
2837 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
*
2857 -AGATACGCGTTGCGATTTAC
1 GA-AT-CTCGTTGCGATTTAC
*
2877 GTATCTTCGTTGCGATTTAC
1 GAATC-TCGTTGCGATTTAC
* * *
2897 GGATACGCGTTGCTATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* *
2918 GTATTGTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* * *
2938 GGATACGCGTTACGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* *
2959 GGATACTCGTTGCGATAGT-C
1 GAAT-CTCGTTGCGAT-TTAC
*
2979 AGAATCGCGTTGCGATTTA
1 -GAATCTCGTTGCGATTTA
2998 TATGTTCGCG
Statistics
Matches: 171, Mismatches: 31, Indels: 37
0.72 0.13 0.15
Matches are distributed among these distances:
18 5 0.03
19 6 0.04
20 121 0.71
21 37 0.22
22 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (19 bp):
GAATCTCGTTGCGATTTAC
Found at i:2810 original size:40 final size:41
Alignment explanation
Indices: 2763--3035 Score: 247
Period size: 40 Copynumber: 6.8 Consensus size: 41
2753 AGTCAGAATC
* *
2763 TCGTTGCGATTTACAGATTCGTATTGCGATTTACGTATTCG
1 TCGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCG
* *
2804 T-ATTGCGATTTACGGATACGCATTGCGATTTACGTATTC-
1 TCGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCG
* *
2843 TCGTTGCGATTTACAGATACGCGTTGCGATTTACGTA-TCT
1 TCGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCG
* * *
2883 TCGTTGCGATTTACGGATACGCGTTGCTATTTTACGTATT-G
1 TCGTTGCGATTTACAGATACGCATTGCGA-TTTACGTATTCG
* * * * *
2924 TCGTTGCGATTTACGGATACGCGTTACGATTTTACGGATAC-
1 TCGTTGCGATTTACAGATACGCATTGCGA-TTTACGTATTCG
* * ** *
2965 TCGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCG
1 TCGTTGCGAT-TTACAGATA-CGCATTGCGATTTACGTATTCG
* * * *
3006 -CGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGTTGCGATTTACAGATACGCATTGCGATT
3036 CTGGAAAATC
Statistics
Matches: 197, Mismatches: 25, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
39 4 0.02
40 124 0.63
41 67 0.34
42 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (41 bp):
TCGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCG
Found at i:2836 original size:60 final size:59
Alignment explanation
Indices: 2764--2955 Score: 185
Period size: 60 Copynumber: 3.2 Consensus size: 59
2754 GTCAGAATCT
* *
2764 CGTTGCGATTTACAGATTCGTATTGCGATTTACGTATTCGTATTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GATTCGTGTTGCGATTTACGTATTCGTGTTGCGATTTACGGATACG
* * * * *
2824 CATTGCGATTTACGTATTC-TCGTTGCGATTTACAG-ATACGCGTTGCGATTTACGTAT-CTT
1 CGTTGCGATTTACG-ATTCGT-GTTGCGATTTAC-GTATTCGTGTTGCGATTTACGGATAC-G
* * *
2884 CGTTGCGATTTACGGATACGCGTTGCTATTTTACGTATT-GTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GATTCGTGTTGCGA-TTTACGTATTCGT-GTTGCGATTTACGGATACG
*
2945 CGTTACGATTT
1 CGTTGCGATTT
2956 TACGGATACT
Statistics
Matches: 106, Mismatches: 16, Indels: 19
0.75 0.11 0.13
Matches are distributed among these distances:
59 3 0.03
60 68 0.64
61 34 0.32
62 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (59 bp):
CGTTGCGATTTACGATTCGTGTTGCGATTTACGTATTCGTGTTGCGATTTACGGATACG
Found at i:2878 original size:80 final size:80
Alignment explanation
Indices: 2761--2974 Score: 281
Period size: 80 Copynumber: 2.6 Consensus size: 80
2751 ATAGTCAGAA
* **
2761 TCTCGTTGCGATTTACAGATTCGTATTGCGATTTACGTA-TTCGTATTGCGATTTACGGATACGC
1 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTACTTCG--TTGCGATTTACGGATACGC
2825 ATTGCGA-TTTACGTAT
64 ATTGCGATTTTACGTAT
*
2841 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATCTTCGTTGCGATTTACGGATACGCG
1 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTA-CTTCGTTGCGATTTACGGATACGCA
*
2906 TTGCTATTTTACGTAT
65 TTGCGATTTTACGTAT
* * *
2922 TGTCGTTGCGATTTACGGATACGCGTTACGATTTTACGGATAC-TCGTTGCGAT
1 TCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTAC-G-TACTTCGTTGCGAT
2975 AGTCAGAATC
Statistics
Matches: 120, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
80 60 0.50
81 37 0.31
82 19 0.16
83 2 0.02
84 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (80 bp):
TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTACTTCGTTGCGATTTACGGATACGCAT
TGCGATTTTACGTAT
Found at i:3006 original size:20 final size:20
Alignment explanation
Indices: 2983--3035 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2973 ATAGTCAGAA
*
2983 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
3003 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
3023 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3036 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:3053 original size:21 final size:21
Alignment explanation
Indices: 3029--3080 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
3019 ATATTCGCGT
3029 TGCGATTCTGGAAAATCGCAA
1 TGCGATTCTGGAAAATCGCAA
* ** *
3050 TGCGAATT-TGTACTATCGCAT
1 TGCG-ATTCTGGAAAATCGCAA
3071 TGCGATTCTG
1 TGCGATTCTG
3081 AGAACTGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (21 bp):
TGCGATTCTGGAAAATCGCAA
Found at i:3435 original size:2 final size:2
Alignment explanation
Indices: 3430--3493 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
3420 TTTGCAACAG
3430 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3472 TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC
3494 GGCTCTATAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:7256 original size:13 final size:13
Alignment explanation
Indices: 7237--7312 Score: 62
Period size: 13 Copynumber: 5.3 Consensus size: 13
7227 ACCGTTTACC
7237 GACCCGACCCGTT
1 GACCCGACCCGTT
*
7250 TACCCGACCCGTT
1 GACCCGACCCGTT
7263 GACCCGACTCGACCCGTT
1 GA--C--C-CGACCCGTT
7281 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
7294 TACCGTTGACCCGTT
1 GACC--CGACCCGTT
7309 GACC
1 GACC
7313 GTTGACCACT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
13 25 0.49
14 1 0.02
15 12 0.24
16 1 0.02
17 1 0.02
18 11 0.22
ACGTcount: A:0.16, C:0.43, G:0.21, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:7266 original size:8 final size:8
Alignment explanation
Indices: 7255--7329 Score: 61
Period size: 8 Copynumber: 9.5 Consensus size: 8
7245 CCGTTTACCC
7255 GACCCGTT
1 GACCCGTT
*
7263 GACCCGACTC
1 GACCCG--TT
7273 GACCCGTT
1 GACCCGTT
7281 GACCC---
1 GACCCGTT
7286 GACCCGTT
1 GACCCGTT
*
7294 TA-CCGTT
1 GACCCGTT
7301 GACCCGTT
1 GACCCGTT
7309 GA-CCGTT
1 GACCCGTT
7316 GACCACTGTT
1 GACC-C-GTT
7326 GACC
1 GACC
7330 AAAACTTTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
5 5 0.09
7 13 0.24
8 21 0.39
9 1 0.02
10 14 0.26
ACGTcount: A:0.16, C:0.39, G:0.23, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:7275 original size:18 final size:18
Alignment explanation
Indices: 7254--7288 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
7244 CCCGTTTACC
7254 CGACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACT
7272 CGACCCGTTGACCCGAC
1 CGACCCGTTGACCCGAC
7289 CCGTTTACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (18 bp):
CGACCCGTTGACCCGACT
Found at i:7276 original size:31 final size:31
Alignment explanation
Indices: 7235--7293 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
7225 CGACCGTTTA
*
7235 CCGACCCGACCCGTTTACCCGACCCGTTGAC
1 CCGACCCGACCCGTTGACCCGACCCGTTGAC
*
7266 CCGACTCGACCCGTTGACCCGACCCGTT
1 CCGACCCGACCCGTTGACCCGACCCGTT
7294 TACCGTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.15, C:0.47, G:0.20, T:0.17
Consensus pattern (31 bp):
CCGACCCGACCCGTTGACCCGACCCGTTGAC
Found at i:7306 original size:15 final size:15
Alignment explanation
Indices: 7273--7329 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
7263 GACCCGACTC
*
7273 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
*
7286 GACCCGTTTACCGTT
1 GACCCGTTGACCGTT
7301 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
7316 GACCACTGTTGACC
1 GACC-C-GTTGACC
7330 AAAACTTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 11 0.30
15 18 0.49
16 1 0.03
17 7 0.19
ACGTcount: A:0.16, C:0.37, G:0.23, T:0.25
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:9776 original size:24 final size:25
Alignment explanation
Indices: 9749--9854 Score: 98
Period size: 24 Copynumber: 4.5 Consensus size: 25
9739 ATAAATTTTA
*
9749 TCTGATTTCCGACT-TGAATTCTGT
1 TCTGATTTCTGACTCTGAATTCTGT
***
9773 TCTGATAAATGAC-CTGAATTCTGT
1 TCTGATTTCTGACTCTGAATTCTGT
*
9797 TCTGA-TT-TGA-TCTGGATTCTGT
1 TCTGATTTCTGACTCTGAATTCTGT
* *
9819 TCTGATATCTG-TTCTGAATTCTGT
1 TCTGATTTCTGACTCTGAATTCTGT
*
9843 TTTGATTTCTGA
1 TCTGATTTCTGA
9855 TATCTTCGTT
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
22 18 0.28
23 1 0.02
24 46 0.71
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (25 bp):
TCTGATTTCTGACTCTGAATTCTGT
Found at i:9801 original size:12 final size:12
Alignment explanation
Indices: 9786--9853 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
9776 GATAAATGAC
9786 CTGAATTCTGTT
1 CTGAATTCTGTT
*
9798 CTG-ATT-TGAT
1 CTGAATTCTGTT
*
9808 CTGGATTCTGTT
1 CTGAATTCTGTT
9820 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
9832 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
9844 TTGATTTCTG
1 CTGAATTCTG
9854 ATATCTTCGT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
10 6 0.12
11 8 0.17
12 32 0.67
13 2 0.04
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:13133 original size:10 final size:10
Alignment explanation
Indices: 13115--13148 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
13105 GAAGACTGAA
13115 GAAGA-AAAG
1 GAAGAGAAAG
13124 GAAGAGAAAG
1 GAAGAGAAAG
13134 GAAGAGAAAG
1 GAAGAGAAAG
13144 GAAGA
1 GAAGA
13149 AGAACGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAGAAAG
Found at i:13159 original size:21 final size:19
Alignment explanation
Indices: 13116--13161 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
13106 AAGACTGAAG
*
13116 AAGAAAAGGAAGAGAAAGG
1 AAGAAAAGGAAGAGAAAGA
*
13135 AAGAGAAAGGAAGAAGAACGA
1 AAGA-AAAGGAAG-AGAAAGA
13156 AAGAAA
1 AAGAAA
13162 GGTAACGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 10 0.43
21 9 0.39
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (19 bp):
AAGAAAAGGAAGAGAAAGA
Found at i:14580 original size:13 final size:13
Alignment explanation
Indices: 14562--14587 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14552 TCTCTATTTT
14562 ATATAAAATATTA
1 ATATAAAATATTA
14575 ATATAAAATATTA
1 ATATAAAATATTA
14588 TATTTATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATAAAATATTA
Found at i:16580 original size:15 final size:15
Alignment explanation
Indices: 16560--16598 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
16550 TTCCTAAAGT
16560 CCTTGGCTCCACTAA
1 CCTTGGCTCCACTAA
16575 CCTTGGCTCCACTAA
1 CCTTGGCTCCACTAA
16590 CCTTGGCTC
1 CCTTGGCTC
16599 GAACCTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.15, C:0.41, G:0.15, T:0.28
Consensus pattern (15 bp):
CCTTGGCTCCACTAA
Found at i:16976 original size:30 final size:30
Alignment explanation
Indices: 16924--17073 Score: 238
Period size: 30 Copynumber: 5.2 Consensus size: 30
16914 AAGTTCGTCC
*
16924 CGACCTTCAAG-TTCGCTCCGACTGCATGG
1 CGACCTTCAAGCTTCGCCCCGACTGCATGG
*
16953 CGACCTTCAAGCTTCGCCTCGACTGCATGG
1 CGACCTTCAAGCTTCGCCCCGACTGCATGG
16983 CGACCTTCAAG-TT---CCCGACTGCATGG
1 CGACCTTCAAGCTTCGCCCCGACTGCATGG
*
17009 CGACCTTCAAGCTTCGCCCCGATTGCATGG
1 CGACCTTCAAGCTTCGCCCCGACTGCATGG
17039 CGACCTTCAAGCTTCGCCCCGACTGCATGG
1 CGACCTTCAAGCTTCGCCCCGACTGCATGG
17069 CGACC
1 CGACC
17074 AATCTCACCC
Statistics
Matches: 111, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.21
27 2 0.02
29 13 0.12
30 73 0.66
ACGTcount: A:0.17, C:0.37, G:0.23, T:0.22
Consensus pattern (30 bp):
CGACCTTCAAGCTTCGCCCCGACTGCATGG
Found at i:17013 original size:56 final size:57
Alignment explanation
Indices: 16924--17073 Score: 230
Period size: 56 Copynumber: 2.6 Consensus size: 57
16914 AAGTTCGTCC
*
16924 CGACCTTCAAGTTCGCTCCGACTGCATGGCGACCTTCAAGCTTCGCCTCGACTGCATGG
1 CGACCTTCAAGTTC-C-CCGACTGCATGGCGACCTTCAAGCTTCGCCCCGACTGCATGG
*
16983 CGACCTTCAAGTT-CCCGACTGCATGGCGACCTTCAAGCTTCGCCCCGATTGCATGG
1 CGACCTTCAAGTTCCCCGACTGCATGGCGACCTTCAAGCTTCGCCCCGACTGCATGG
17039 CGACCTTCAAGCTTCGCCCCGACTGCATGGCGACC
1 CGACCTTCAAG-TT--CCCCGACTGCATGGCGACC
17074 AATCTCACCC
Statistics
Matches: 85, Mismatches: 2, Indels: 7
0.90 0.02 0.07
Matches are distributed among these distances:
56 51 0.60
57 3 0.04
59 13 0.15
60 18 0.21
ACGTcount: A:0.17, C:0.37, G:0.23, T:0.22
Consensus pattern (57 bp):
CGACCTTCAAGTTCCCCGACTGCATGGCGACCTTCAAGCTTCGCCCCGACTGCATGG
Found at i:22750 original size:25 final size:25
Alignment explanation
Indices: 22673--22755 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
22663 TATTATAAAA
* * *
22673 TTAT-ATTTATAAATATAAATATATT
1 TTATAATTTAT-ATTATAATTAAATT
* *
22698 CTTATAATTGTA-ATATATTATTACATT
1 -TTATAATT-TATAT-TATAATTAAATT
22725 TTATAATTTATATTATAATTAAATT
1 TTATAATTTATATTATAATTAAATT
*
22750 TCATAA
1 TTATAA
22756 AGTATATTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
25 17 0.37
26 15 0.33
27 12 0.26
28 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (25 bp):
TTATAATTTATATTATAATTAAATT
Found at i:29390 original size:38 final size:37
Alignment explanation
Indices: 29294--29390 Score: 99
Period size: 37 Copynumber: 2.6 Consensus size: 37
29284 TTTTACCCTT
* *
29294 TTAT-TAAACTTTTTTATATTTTCAATTTTATAAAAAAA
1 TTATATAAA-TTTTTT-TAATTTAAATTTTATAAAAAAA
* * *
29332 TTATATAAATTTTATGAATTTAAATTTTTTAAAGAAAA
1 TTATATAAATTTTTTTAATTTAAATTTTATAAA-AAAA
29370 -TATATAAATATTTTTTAATTT
1 TTATATAAAT-TTTTTTAATTT
29391 GTTAAAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
37 23 0.47
38 22 0.45
39 4 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (37 bp):
TTATATAAATTTTTTTAATTTAAATTTTATAAAAAAA
Found at i:29538 original size:16 final size:17
Alignment explanation
Indices: 29517--29579 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
29507 ACATTCTCAG
*
29517 TAATCTTATTCC-CTGA
1 TAATCTTATCCCACTGA
29533 TAATCTTACATCCCACTGA
1 TAATCTT--ATCCCACTGA
*
29552 TAATCTTACATCCCTACTAA
1 TAATCTT--ATCCC-ACTGA
29572 TAATCTTA
1 TAATCTTA
29580 CATTCCGTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 7 0.17
18 5 0.12
19 18 0.44
20 11 0.27
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATCTTATCCCACTGA
Found at i:29553 original size:19 final size:20
Alignment explanation
Indices: 29529--29582 Score: 92
Period size: 19 Copynumber: 2.8 Consensus size: 20
29519 ATCTTATTCC
29529 CTGATAATCTTACATCCC-A
1 CTGATAATCTTACATCCCTA
29548 CTGATAATCTTACATCCCTA
1 CTGATAATCTTACATCCCTA
*
29568 CTAATAATCTTACAT
1 CTGATAATCTTACAT
29583 TCCGTGAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (20 bp):
CTGATAATCTTACATCCCTA
Found at i:37008 original size:28 final size:28
Alignment explanation
Indices: 36970--37051 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
36960 TCATTGTTCC
*
36970 CAAGCACTGACTTGACGAT-ATAATGTTT
1 CAAGCATTGACTTGACG-TCATAATGTTT
*
36998 CAAGCATTGACTTGGCGTCATAATGTTT
1 CAAGCATTGACTTGACGTCATAATGTTT
* * **
37026 CAAGTATTTACTTGACACCATAATGT
1 CAAGCATTGACTTGACGTCATAATGT
37052 AAACAAAGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.98
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (28 bp):
CAAGCATTGACTTGACGTCATAATGTTT
Found at i:41451 original size:22 final size:22
Alignment explanation
Indices: 41410--41476 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
41400 CTCGTATAAA
41410 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
41433 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
41455 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
41477 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:43195 original size:21 final size:21
Alignment explanation
Indices: 43171--43215 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43161 TCTTGTTCGT
* *
43171 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
43192 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
43213 TTG
1 TTG
43216 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:46331 original size:22 final size:22
Alignment explanation
Indices: 46290--46356 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
46280 CTCGTATAAA
46290 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
46313 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
46335 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
46357 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:48054 original size:21 final size:21
Alignment explanation
Indices: 48030--48074 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
48020 TCTTGTTCGT
* *
48030 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
48051 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
48072 TTG
1 TTG
48075 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:53905 original size:22 final size:23
Alignment explanation
Indices: 53879--53922 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
53869 AAATTTTAGT
*
53879 ATTTATTATATTTT-TTTAAATA
1 ATTTAATATATTTTATTTAAATA
53901 ATTTAATATATTTTATTTAAAT
1 ATTTAATATATTTTATTTAAAT
53923 TTAAAATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTAATATATTTTATTTAAATA
Found at i:53923 original size:20 final size:21
Alignment explanation
Indices: 53900--53940 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
53890 TTTTTTAAAT
*
53900 AATTTAATATA-TTTTATTTA
1 AATTTAAAATAGTTTTATTTA
53920 AATTTAAAATAGTTTTTATTT
1 AATTTAAAATAG-TTTTATTT
53941 TTTAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
AATTTAAAATAGTTTTATTTA
Found at i:58680 original size:29 final size:27
Alignment explanation
Indices: 58639--58694 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
58629 AAATCATCGG
*
58639 TGATCAATATATTTATCGATTTAACAC
1 TGATCAATATATTTATCGATCTAACAC
*
58666 TGATCAGATTATATTTTTCGATCTAACAC
1 TGATCA-A-TATATTTATCGATCTAACAC
58695 CCGTAGCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.24
28 1 0.04
29 18 0.72
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (27 bp):
TGATCAATATATTTATCGATCTAACAC
Found at i:59012 original size:10 final size:10
Alignment explanation
Indices: 58997--59036 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
58987 TTCATCACAC
58997 CAAATTCTCT
1 CAAATTCTCT
*
59007 CAAATTTTCT
1 CAAATTCTCT
*
59017 CAATTTCTCT
1 CAAATTCTCT
*
59027 CAAATACTCT
1 CAAATTCTCT
59037 ATCTGTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.42
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:59114 original size:17 final size:18
Alignment explanation
Indices: 59079--59119 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
59069 ATATTATGTA
*
59079 TTTAATTTATTAAAGTAT
1 TTTACTTTATTAAAGTAT
*
59097 TTTACTTTATTTAA-TAT
1 TTTACTTTATTAAAGTAT
59114 TTTACT
1 TTTACT
59120 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTAAAGTAT
Found at i:64166 original size:30 final size:29
Alignment explanation
Indices: 64104--64166 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
64094 TACTGCTACG
** *
64104 GGTGTTAGATCGGGAAATATAATTTGACC
1 GGTGTTAGATCGGGAAATATAAGATCACC
* *
64133 GGTGTTAGATCGGTAAATATACCGATCACC
1 GGTGTTAGATCGGGAAATATA-AGATCACC
64163 GGTG
1 GGTG
64167 ATTTTTCGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGGGAAATATAAGATCACC
Found at i:64989 original size:20 final size:21
Alignment explanation
Indices: 64964--65056 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
64954 TTTTCCCAAT
*
64964 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
64984 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
65005 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
65025 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
65046 TCGCAATGCGA
1 TCGCAATGCGA
65057 TACTTACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:65009 original size:41 final size:41
Alignment explanation
Indices: 64964--65056 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
64954 TTTTCCCAAT
*
64964 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
65005 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
65046 TCGCAATGCGA
1 TCGCAATGCGA
65057 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:65069 original size:41 final size:41
Alignment explanation
Indices: 64983--65117 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
64973 GAATAAGTAA
* ** *
64983 ATCGCAATGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
65024 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
65065 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
65106 TTCGCAACGCGA
1 ATCGCAACGCGA
65118 TACTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:65070 original size:20 final size:20
Alignment explanation
Indices: 65045--65138 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
65035 AATTGGGAAA
*
65045 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
65065 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
*
65086 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
65106 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
65126 TTCGCAACGCGAT
1 ATCGCAACGCGAT
65139 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:65688 original size:19 final size:19
Alignment explanation
Indices: 65650--65716 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
65640 TTCGAGAATG
65650 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
65670 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
65689 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
65708 AAAATCGCA
1 AAAATCGCA
65717 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:65758 original size:20 final size:19
Alignment explanation
Indices: 65712--65877 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
65702 GAAACCAAAA
*
65712 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
65731 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
65750 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
65770 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
65786 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
65803 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
65817 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
65836 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
65856 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
65876 TC
1 TC
65878 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.34
20 49 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:65793 original size:39 final size:39
Alignment explanation
Indices: 65717--65793 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
65707 CAAAATCGCA
* **
65717 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
65756 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
65794 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:65802 original size:33 final size:33
Alignment explanation
Indices: 65765--65852 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
65755 GTTGCGATTT
* *
65765 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
65798 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
65831 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
65853 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:67927 original size:42 final size:42
Alignment explanation
Indices: 67867--67989 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
67857 GCCCGACTCG
* * *
67867 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
67909 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
67951 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
67990 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:67947 original size:21 final size:21
Alignment explanation
Indices: 67923--67989 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
67913 TCATTCCTCG
67923 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
67944 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
67965 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
67986 AGAG
1 AGAG
67990 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:69369 original size:13 final size:14
Alignment explanation
Indices: 69338--69373 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
69328 TTATGTTTAA
69338 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
69352 GTGATTTGT-AAAG
1 TTGATTTGTAAAAG
69365 TTGATTTGT
1 TTGATTTGT
69374 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:71846 original size:23 final size:23
Alignment explanation
Indices: 71819--71864 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
71809 CCTCCTCATT
71819 ATCATCAACAACATATTCCTCGG
1 ATCATCAACAACATATTCCTCGG
*
71842 ATCATCAACAACATCTTCCTCGG
1 ATCATCAACAACATATTCCTCGG
71865 CAAAAATTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.26
Consensus pattern (23 bp):
ATCATCAACAACATATTCCTCGG
Found at i:73054 original size:19 final size:19
Alignment explanation
Indices: 73030--73075 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
73020 ATTCATTTGA
*
73030 CTATCGCAA-GTGAAAATGG
1 CTATCGCAACGCGAAAA-GG
73049 CTATCGCAACGCGAAAAGG
1 CTATCGCAACGCGAAAAGG
*
73068 TTATCGCA
1 CTATCGCA
73076 CGAGAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (19 bp):
CTATCGCAACGCGAAAAGG
Found at i:73127 original size:14 final size:15
Alignment explanation
Indices: 73107--73201 Score: 68
Period size: 14 Copynumber: 5.8 Consensus size: 15
73097 TGAAAATCGC
73107 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
73122 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
73139 CATTGCGATTTTTTTTCG
1 -ATTGCGA--TTTTCTCG
73157 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
*
73173 -TTGCGATTTCATTTCG
1 ATTGCGATTT--TCTCG
73189 CATTGCGATTTTC
1 -ATTGCGATTTTC
73202 ATTTCGCATT
Statistics
Matches: 65, Mismatches: 4, Indels: 21
0.72 0.04 0.23
Matches are distributed among these distances:
14 20 0.31
16 12 0.18
17 3 0.05
18 20 0.31
19 6 0.09
21 4 0.06
ACGTcount: A:0.13, C:0.20, G:0.18, T:0.49
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:73163 original size:51 final size:52
Alignment explanation
Indices: 73103--73252 Score: 216
Period size: 51 Copynumber: 2.9 Consensus size: 52
73093 GAAATGAAAA
*
73103 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTT-TTT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
73154 TCGCATTGCGATTTTCTCGTTGCGA-TTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
* *
73205 TCGCATTGCGA-TTTCATTCGCATTGCGATTTCCATTTCGCGTTGCGAT
1 TCGCATTGCGATTTTC--TCG--TTGCGATTTTCATTTCGCATTGCGAT
73253 AGTGTGTTTG
Statistics
Matches: 90, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
50 26 0.29
51 38 0.42
52 3 0.03
54 6 0.07
55 17 0.19
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:73188 original size:32 final size:34
Alignment explanation
Indices: 73122--73235 Score: 135
Period size: 32 Copynumber: 3.3 Consensus size: 34
73112 GATTTTCTCG
**
73122 TTGCGATTTTCATTTCGCATTGCGATTTTTTTTCGCA
1 TTGCGATTTTC--TTCG-ATTGCGATTTCATTTCGCA
73159 TTGCGATTTTC-TCG-TTGCGATTTCATTTCGCA
1 TTGCGATTTTCTTCGATTGCGATTTCATTTCGCA
73191 TTGCGATTTTCATTTCGCATTGCGATTTCA-TTCGCA
1 TTGCGATTTTC--TTCG-ATTGCGATTTCATTTCGCA
73227 TTGCGATTT
1 TTGCGATTT
73236 CCATTTCGCG
Statistics
Matches: 70, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
32 27 0.39
34 3 0.04
35 3 0.04
36 15 0.21
37 22 0.31
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (34 bp):
TTGCGATTTTCTTCGATTGCGATTTCATTTCGCA
Found at i:73240 original size:18 final size:19
Alignment explanation
Indices: 73103--73252 Score: 175
Period size: 19 Copynumber: 8.6 Consensus size: 19
73093 GAAATGAAAA
73103 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
73119 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
73136 TCGCATTGCGATTTT-TTT
1 TCGCATTGCGATTTTCATT
73154 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
73170 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
73186 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
73205 TCGCATTGCGA-TTTCA-T
1 TCGCATTGCGATTTTCATT
*
73222 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
73241 TCGCGTTGCGAT
1 TCGCATTGCGAT
73253 AGTGTGTTTG
Statistics
Matches: 117, Mismatches: 3, Indels: 25
0.81 0.02 0.17
Matches are distributed among these distances:
13 4 0.03
14 17 0.15
16 9 0.08
17 15 0.13
18 32 0.27
19 40 0.34
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:75255 original size:20 final size:19
Alignment explanation
Indices: 75220--75286 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
75210 CGAACTTAAA
*
75220 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGAAT
**
75239 ATCGCAACGCGGAAATGGTT
1 ATCGCAACGC-GAAATGAAT
* *
75259 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAT
75278 ATCGCAACG
1 ATCGCAACG
75287 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAT
Found at i:75320 original size:19 final size:19
Alignment explanation
Indices: 75293--75426 Score: 83
Period size: 19 Copynumber: 7.6 Consensus size: 19
75283 AACGACAAAA
*
75293 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
75312 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
75328 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
* *
75344 TCACGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
75360 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
75377 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
75396 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
75416 TCGTGTTGCGA
1 TCGCGTTGCGA
75427 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
14 19 0.20
15 3 0.03
16 6 0.06
17 2 0.02
18 14 0.15
19 32 0.34
20 17 0.18
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:75334 original size:14 final size:14
Alignment explanation
Indices: 75315--75372 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
75305 TTTCATTTCG
75315 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
75329 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
75345 CACGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
75361 CGTTGCGATTTT
1 CGTTGCGATTTT
75373 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:75345 original size:32 final size:33
Alignment explanation
Indices: 75298--75388 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
75288 CAAAATCGCA
75298 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
75331 TTGCGA-TTTCATTTCACGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
75363 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
75389 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:75407 original size:20 final size:19
Alignment explanation
Indices: 75373--75426 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
75363 TTGCGATTTT
*
75373 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
75392 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
75412 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
75427 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:75917 original size:18 final size:18
Alignment explanation
Indices: 75891--75935 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
75881 GTCGATCAGA
* *
75891 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
75909 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
75927 TGATGGCTC
1 TGATGGCTC
75936 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:77487 original size:22 final size:22
Alignment explanation
Indices: 77462--77505 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
77452 GATTTAGATA
77462 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
77484 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
77506 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:77775 original size:20 final size:20
Alignment explanation
Indices: 77672--77783 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
77662 CGCTTTGAAA
77672 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
77692 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
77712 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* *
77732 ATCG--TTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
77751 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
*
77771 ATCGCATTACGAT
1 ATCGCATTGCGAT
77784 TTCCCAATTC
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.12
19 10 0.13
20 50 0.67
21 6 0.08
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:88762 original size:6 final size:6
Alignment explanation
Indices: 88751--88777 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
88741 CTATCAAATC
88751 AATTAA AATTAA AATTAA AATTAA AAT
1 AATTAA AATTAA AATTAA AATTAA AAT
88778 AATTATTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTAA
Found at i:89611 original size:21 final size:21
Alignment explanation
Indices: 89582--89638 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
89572 AATGAGTTCT
89582 AAACTCTAAATCATAAACAATA
1 AAAC-CTAAATCATAAACAATA
**
89604 AAACCTAAATCATAAATTATA
1 AAACCTAAATCATAAACAATA
*
89625 AACCCTAAATCATA
1 AAACCTAAATCATA
89639 CTTACCTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (21 bp):
AAACCTAAATCATAAACAATA
Found at i:89703 original size:7 final size:7
Alignment explanation
Indices: 89679--89731 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
89669 AATTAATATC
*
89679 TAAACCT
1 TAAACCA
89686 TAAACTC-
1 TAAAC-CA
*
89693 TAAATCA
1 TAAACCA
*
89700 TAAACCT
1 TAAACCA
89707 TAAACCA
1 TAAACCA
89714 TAAACCA
1 TAAACCA
*
89721 TAAACCC
1 TAAACCA
89728 TAAA
1 TAAA
89732 TCCGATTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 1 0.03
7 37 0.95
8 1 0.03
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCA
Found at i:89703 original size:21 final size:21
Alignment explanation
Indices: 89679--89731 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
89669 AATTAATATC
*
89679 TAAACCTTAAACTC-TAAATCA
1 TAAACCTTAAAC-CATAAACCA
89700 TAAACCTTAAACCATAAACCA
1 TAAACCTTAAACCATAAACCA
*
89721 TAAACCCTAAA
1 TAAACCTTAAA
89732 TCCGATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCTTAAACCATAAACCA
Found at i:90022 original size:14 final size:14
Alignment explanation
Indices: 90003--90030 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
89993 ATAAGAAACA
90003 CATGTATACTTCTT
1 CATGTATACTTCTT
90017 CATGTATACTTCTT
1 CATGTATACTTCTT
90031 AGTTCAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
CATGTATACTTCTT
Found at i:94033 original size:32 final size:33
Alignment explanation
Indices: 93967--94041 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
93957 ATATTTTAAG
* **
93967 TATAAAATTGAAAATTATTTTTGTTTAATAATT
1 TATAAAATTGAAAATTATTTCTGTCCAATAATT
* *
94000 TATAAAATT-AAAATTATTTCTGTCCCATCATT
1 TATAAAATTGAAAATTATTTCTGTCCAATAATT
94032 TATATAAATT
1 TATA-AAATT
94042 CTAATACTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 22 0.61
33 14 0.39
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (33 bp):
TATAAAATTGAAAATTATTTCTGTCCAATAATT
Found at i:100257 original size:12 final size:11
Alignment explanation
Indices: 100240--100303 Score: 55
Period size: 10 Copynumber: 6.0 Consensus size: 11
100230 TTAACACACA
100240 CATATATCATAT
1 CATATAT-ATAT
100252 CATATA-AT-T
1 CATATATATAT
* * *
100261 CATATCACAAAA
1 CATAT-ATATAT
100273 CATATATATAT
1 CATATATATAT
100284 -ATATATATAT
1 CATATATATAT
100294 -ATATATATAT
1 CATATATATAT
100304 ATCACATACA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 6 0.14
10 23 0.52
11 4 0.09
12 11 0.25
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (11 bp):
CATATATATAT
Found at i:100281 original size:2 final size:2
Alignment explanation
Indices: 100274--100305 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
100264 ATCACAAAAC
100274 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
100306 CACATACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104369 original size:31 final size:31
Alignment explanation
Indices: 104331--104517 Score: 304
Period size: 31 Copynumber: 6.0 Consensus size: 31
104321 CCCGAAGGAC
* *
104331 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
104362 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
104393 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
104424 CAGTCCATATGTCCCGAATAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
104455 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
104486 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
104517 C
1 C
104518 CCTCGACCCT
Statistics
Matches: 148, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
31 147 0.99
32 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:105279 original size:63 final size:63
Alignment explanation
Indices: 105172--105390 Score: 253
Period size: 63 Copynumber: 3.5 Consensus size: 63
105162 TAATGAAGGT
* * * * **
105172 ATGCATCGATGCACTACTGATGCATCGATGCATAAAATGTATTCGATGTTGT-ATTATTGCTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTT-TCACTATTAATGG
* ***
105235 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCACTATTAATGG
* * **
105298 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTTA-TTTTAAAAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTCACTATTAATGG
**
105361 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
105391 ACACCTTCAA
Statistics
Matches: 133, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
62 1 0.01
63 103 0.77
64 29 0.22
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCACTATTAATGG
Found at i:108567 original size:31 final size:31
Alignment explanation
Indices: 108529--108684 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
108519 CCCGAAGGAC
* *
108529 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
108560 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
108591 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
108622 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
108653 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
108684 C
1 C
108685 CCTCGACCCT
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:109449 original size:64 final size:63
Alignment explanation
Indices: 109341--109561 Score: 196
Period size: 64 Copynumber: 3.5 Consensus size: 63
109331 TAATGAAGGT
* * * * * * **
109341 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-AGATTGCATTCGATGTT-TCACTATTAATGGG
* *
109405 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-AGATTGCATTCGATGTTTCACTATTAATGGG
* * * * * **
109469 ATGCATCGATGTACTACTTATGCATCGATACATGAATTGCATTCGATGTATTTA-TTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCAAG-ATTGCATTCGATGT-TTCACTATTAATGGG
**
109532 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
109562 ACACCTTCAA
Statistics
Matches: 131, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
63 4 0.03
64 124 0.95
65 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCAAGATTGCATTCGATGTTTCACTATTAATGGG
Found at i:110385 original size:20 final size:20
Alignment explanation
Indices: 110357--110432 Score: 104
Period size: 20 Copynumber: 3.9 Consensus size: 20
110347 CACTGAATAT
110357 TTGTCCCGAAGGACCACTAG
1 TTGTCCCGAAGGACCACTAG
* *
110377 TTGTTCCGAAGAACCACTA-
1 TTGTCCCGAAGGACCACTAG
110396 -TGTCCCGAAGGACCACT-G
1 TTGTCCCGAAGGACCACTAG
110414 TTTGTCCCGAAGGACCACT
1 -TTGTCCCGAAGGACCACT
110433 GATAATCCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
18 15 0.31
20 34 0.69
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.22
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTAG
Found at i:110409 original size:38 final size:38
Alignment explanation
Indices: 110358--110432 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
110348 ACTGAATATT
*
110358 TGTCCCGAAGGACCACTAG-TTGTTCCGAAGAACCACTA
1 TGTCCCGAAGGACCACT-GTTTGTCCCGAAGAACCACTA
*
110396 TGTCCCGAAGGACCACTGTTTGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACTGTTTGTCCCGAAGAACCACT
110433 GATAATCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (38 bp):
TGTCCCGAAGGACCACTGTTTGTCCCGAAGAACCACTA
Found at i:111704 original size:20 final size:20
Alignment explanation
Indices: 111679--111734 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
111669 TTCCCCTTGA
*
111679 AGTGCATCGATGCATTATAT
1 AGTGCATCGATGCATTATAC
*
111699 AGTGCATCGATGTATTATAC
1 AGTGCATCGATGCATTATAC
111719 AGTGCATCGATGCATT
1 AGTGCATCGATGCATT
111735 CTTTAACATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTATAC
Found at i:114126 original size:32 final size:36
Alignment explanation
Indices: 114085--114167 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 36
114075 TTATATATCT
* *
114085 TATAACATATACA-ATAA-TCAT-TAAC-ACACATA
1 TATATCATATACATATAATTCATATAACAAAACATA
*
114117 TATATCATAT-CATATAATTCATATCACAAAACATA
1 TATATCATATACATATAATTCATATAACAAAACATA
*
114152 TATAT-ATATATATATA
1 TATATCATATACATATA
114168 TCACATACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 2 0.05
32 13 0.31
33 4 0.10
34 7 0.17
35 16 0.38
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (36 bp):
TATATCATATACATATAATTCATATAACAAAACATA
Found at i:115118 original size:24 final size:20
Alignment explanation
Indices: 115062--115119 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
115052 TTTCCCTTGA
*
115062 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
115082 AGTGCATCAATGCATTCCTTAAC
1 AGTGCATCGATGCATT-C-T-AC
115105 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
115120 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:116872 original size:14 final size:15
Alignment explanation
Indices: 116847--116879 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
116837 TCTTTTTATC
116847 CAAAAGTAAAATATT
1 CAAAAGTAAAATATT
116862 CAAAA-TAAAATATT
1 CAAAAGTAAAATATT
116876 -AAAA
1 CAAAA
116880 AAATCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (15 bp):
CAAAAGTAAAATATT
Found at i:116913 original size:23 final size:22
Alignment explanation
Indices: 116874--116920 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
116864 AAATAAAATA
116874 TTAAAAAAATCAAAATATCTTT
1 TTAAAAAAATCAAAATATCTTT
* * *
116896 TTAAACAAAATTATAATATTTTT
1 TTAAA-AAAATCAAAATATCTTT
116919 TT
1 TT
116921 TTAACATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAAAAAATCAAAATATCTTT
Found at i:120505 original size:3 final size:3
Alignment explanation
Indices: 120497--120535 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
120487 AATATTAATT
*
120497 TTA TTA TTA TTA TTA TTA CTT- TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
120536 CATTTACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.88
4 2 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:120519 original size:21 final size:21
Alignment explanation
Indices: 120487--120541 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
120477 TTTTTTGTTA
*
120487 AATATTAATTTTATTATTATT
1 AATATTACTTTTATTATTATT
*
120508 ATTATTACTTTTATTATTATT
1 AATATTACTTTTATTATTATT
*
120529 AATATTACATTTA
1 AATATTACTTTTA
120542 CATTTTTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
AATATTACTTTTATTATTATT
Found at i:124910 original size:8 final size:8
Alignment explanation
Indices: 124897--125015 Score: 84
Period size: 8 Copynumber: 14.2 Consensus size: 8
124887 AAACAAAGAG
*
124897 AAAGAAAC
1 AAAGAAAA
124905 AAAGAAAAA
1 AAAG-AAAA
124914 AAAGAAAAACA
1 AAAG--AAA-A
124925 AAAGAAAA
1 AAAGAAAA
124933 AAA-AAAA
1 AAAGAAAA
124940 AAA-AAAA
1 AAAGAAAA
124947 AAAGAAAA
1 AAAGAAAA
124955 AAAGAGAGAA
1 AAAGA-A-AA
*
124965 AAA-AAGA
1 AAAGAAAA
124972 AAAGAAAA
1 AAAGAAAA
* *
124980 CAACAAAGA
1 AAAGAAA-A
*
124989 AAA-AAGA
1 AAAGAAAA
124996 AAAGAAAA
1 AAAGAAAA
125004 AGAAGACAAA
1 A-AAGA-AAA
125014 AA
1 AA
125016 CACAAAGACA
Statistics
Matches: 92, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
7 22 0.24
8 32 0.35
9 20 0.22
10 13 0.14
11 5 0.05
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:124927 original size:12 final size:11
Alignment explanation
Indices: 124909--125004 Score: 111
Period size: 11 Copynumber: 8.3 Consensus size: 11
124899 AGAAACAAAG
124909 AAAAAAAAGAA
1 AAAAAAAAGAA
*
124920 AAACAAAAGAA
1 AAAAAAAAGAA
*
124931 AAAAAAAAAAA
1 AAAAAAAAGAA
124942 AAAAAAAAGAA
1 AAAAAAAAGAA
*
124953 AAAAAGAGAGAAA
1 AAAAA-AAAG-AA
124966 AAAAGAAAAGAA
1 AAAA-AAAAGAA
*
124978 AACAACAAAGAA
1 AA-AAAAAAGAA
124990 AAAAGAAAAGAA
1 AAAA-AAAAGAA
125002 AAA
1 AAA
125005 GAAGACAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
11 36 0.50
12 24 0.33
13 11 0.15
14 1 0.01
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:124930 original size:20 final size:20
Alignment explanation
Indices: 124901--124979 Score: 81
Period size: 20 Copynumber: 3.9 Consensus size: 20
124891 AAAGAGAAAG
124901 AAAC-AAAGAAAAAAAAGAA
1 AAACAAAAGAAAAAAAAGAA
*
124920 AAACAAAAGAAAAAAAAAAAAA
1 AAACAAAAG--AAAAAAAAGAA
* *
124942 AAAAAAAAGAAAAAAAGAGAG
1 AAACAAAAGAAAAAAA-AGAA
124963 AAA-AAAAGAAAAGAAAA
1 AAACAAAAGAAAA-AAAA
124980 CAACAAAGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.08
20 21 0.41
21 8 0.16
22 18 0.35
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (20 bp):
AAACAAAAGAAAAAAAAGAA
Found at i:124947 original size:34 final size:34
Alignment explanation
Indices: 124886--125004 Score: 109
Period size: 33 Copynumber: 3.4 Consensus size: 34
124876 AGATCCAATC
* * * *
124886 AAAAC-AAAGAGAAAGAAACAAAGAAAAAAAAGA
1 AAAACAAAAGAAAAAAAAAAAAAAAAAAAAAAGA
124919 AAAACAAAAG-AAAAAAAAAAAAAAAAAAAAAGA
1 AAAACAAAAGAAAAAAAAAAAAAAAAAAAAAAGA
* *
124952 AAAA-AAGAGAGAAAAAAAGAAAAGAAAACAACAAAGAA
1 AAAACAA-A-AGAAAAAAA-AAAA-AAAAAAAAAAAG-A
*
124990 AAAAGAAAAGAAAAA
1 AAAACAAAAGAAAAA
125005 GAAGACAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
32 2 0.03
33 29 0.40
34 6 0.08
35 6 0.08
36 4 0.06
37 17 0.24
38 6 0.08
39 2 0.03
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (34 bp):
AAAACAAAAGAAAAAAAAAAAAAAAAAAAAAAGA
Found at i:125015 original size:1 final size:1
Alignment explanation
Indices: 124909--125004 Score: 66
Period size: 1 Copynumber: 96.0 Consensus size: 1
124899 AGAAACAAAG
* * * * * * * *
124909 AAAAAAAAGAAAAACAAAAGAAAAAAAAAAAAAAAAAAAAAGAAAAAAAGAGAGAAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
124974 AGAAAACAACAAAGAAAAAAGAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
125005 GAAGACAAAA
Statistics
Matches: 67, Mismatches: 28, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:125015 original size:12 final size:10
Alignment explanation
Indices: 124895--125007 Score: 95
Period size: 11 Copynumber: 10.4 Consensus size: 10
124885 CAAAACAAAG
124895 AGAAAGAAACAA
1 AGAAA-AAA-AA
124907 AG-AAAAAAA
1 AGAAAAAAAA
124916 AGAAAAACAAA
1 AGAAAAA-AAA
124927 AGAAAAAAAA
1 AGAAAAAAAA
124937 A-AAAAAAAA
1 AGAAAAAAAA
*
124946 AAAAGAAAAAA
1 AGAA-AAAAAA
124957 AGAGAGAAAAAA
1 AGA-A-AAAAAA
124969 AGAAAAGAAAACA
1 AG-AAA-AAAA-A
*
124982 ACAAAGAAAAA
1 AGAAA-AAAAA
124993 AGAAAAGAAAA
1 AGAAAA-AAAA
125004 AGAA
1 AGAA
125008 GACAAAAACA
Statistics
Matches: 89, Mismatches: 3, Indels: 19
0.80 0.03 0.17
Matches are distributed among these distances:
9 13 0.15
10 14 0.16
11 34 0.38
12 25 0.28
13 3 0.03
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:125029 original size:58 final size:57
Alignment explanation
Indices: 124886--125029 Score: 134
Period size: 58 Copynumber: 2.5 Consensus size: 57
124876 AGATCCAATC
* *
124886 AAAACAAAGAGAAAGAA-ACAAAGAAAA-AAAAGAAAAACAAAAGAAAAAAAAAAAAA
1 AAAAAAAAGA-AAAAAACACAAAGAAAAGAAAAGAAAAACAAAAGAAAAAAAAAAAAA
* * * * *
124942 AAAAAAAAGAAAAAAAGAGAGAAAAAAAGAAAAG-AAAACAACAA-AGAAAAAAGAAAAG
1 AAAAAAAAGAAAAAAACACA-AAGAAAAGAAAAGAAAAACAA-AAGA-AAAAAAAAAAAA
* *
125000 AAAAAGAAGACAAAAACACAAAGACAAAGA
1 AAAAAAAAGAAAAAAACACAAAGA-AAAGA
125030 GTCCCTTGAC
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
55 5 0.07
56 11 0.15
57 17 0.24
58 38 0.54
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (57 bp):
AAAAAAAAGAAAAAAACACAAAGAAAAGAAAAGAAAAACAAAAGAAAAAAAAAAAAA
Found at i:125919 original size:24 final size:23
Alignment explanation
Indices: 125866--125922 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
125856 CGAAAGGTGC
125866 AATATTTTCAAAATCTTTGATTA
1 AATATTTTCAAAATCTTTGATTA
* *
125889 AACATTTTTAAAACTCTTTTGA-TA
1 AATATTTTCAAAA-TC-TTTGATTA
*
125913 GATATTTTCA
1 AATATTTTCA
125923 GACTTTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 11 0.41
24 11 0.41
25 5 0.19
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (23 bp):
AATATTTTCAAAATCTTTGATTA
Found at i:126232 original size:18 final size:19
Alignment explanation
Indices: 126209--126244 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
126199 ATACATCAAT
126209 ACATACAAACA-TATATAC
1 ACATACAAACATTATATAC
*
126227 ACATACATACATTATATA
1 ACATACAAACATTATATA
126245 TAAAAGTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (19 bp):
ACATACAAACATTATATAC
Found at i:126900 original size:101 final size:101
Alignment explanation
Indices: 126695--126918 Score: 230
Period size: 101 Copynumber: 2.2 Consensus size: 101
126685 AACAAACTTC
*
126695 GTCTCGCTTGAGACATTTTT-TTATGAAATAAAAATTTAAATTTGTTGTACTTGAAACAAAATTA
1 GTCTCGCTTGAGACATTTTTCTTATGAAATAAAAATTTAAATTTATTGTACTTGAAACAAAATTA
* * *
126759 TCTCACTTGAGATTGTTATTTCTTTCAAAACAATTCT
66 TCTCACTTGAGATCGTTATTTC-TTCAAAAAAAATCT
* *
126796 GTCTCGTTTGAGACATTTTTCCTT-TGAGAATACAAATTTCAAATTTATT-TCACATT-AAACAA
1 GTCTCGCTTGAGACATTTTT-CTTATGA-AATAAAAATTT-AAATTTATTGT-AC-TTGAAACAA
* *
126858 AGTTGATCTCTCTTGAGATCG-T-TTTC-TCAAAAAAAAAT-T
61 AATT-ATCTCACTTGAGATCGTTATTTCTTC-AAAAAAAATCT
* *
126897 GTCTCACTTGAGACAGTTTTCT
1 GTCTCGCTTGAGACATTTTTCT
126919 AAAAACAAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
100 2 0.02
101 39 0.38
102 10 0.10
103 17 0.16
104 20 0.19
105 16 0.15
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (101 bp):
GTCTCGCTTGAGACATTTTTCTTATGAAATAAAAATTTAAATTTATTGTACTTGAAACAAAATTA
TCTCACTTGAGATCGTTATTTCTTCAAAAAAAATCT
Found at i:126916 original size:34 final size:33
Alignment explanation
Indices: 126864--126929 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
126854 ACAAAGTTGA
*
126864 TCTCTCTTGAGATCGTTTTCTCAAAAAAAAATTG
1 TCTCACTTGAGATCGTTTTCT-AAAAAAAAATTG
*
126898 TCTCACTTGAGA-CAGTTTTCTAAAAACAAATT
1 TCTCACTTGAGATC-GTTTTCTAAAAAAAAATT
126930 TTGTCTCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (33 bp):
TCTCACTTGAGATCGTTTTCTAAAAAAAAATTG
Found at i:126984 original size:36 final size:35
Alignment explanation
Indices: 126879--126985 Score: 103
Period size: 36 Copynumber: 3.1 Consensus size: 35
126869 CTTGAGATCG
* * *
126879 TTTTCTCAAAAA-AAA-ATTGTCTCACTTGAGACAG
1 TTTTCT-AAAAACAAATGTTGTCTCAGTTGAGACAA
* * *
126913 TTTTCTAAAAACAAATTTTGTCTC-GTTTAAAACAA
1 TTTTCTAAAAACAAATGTTGTCTCAG-TTGAGACAA
*
126948 TTTCTCTTAAAACAAATGTTGTCTCAGTTGAGACAA
1 TTT-TCTAAAAACAAATGTTGTCTCAGTTGAGACAA
126984 TT
1 TT
126986 CTCCAAATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
33 5 0.08
34 9 0.15
35 16 0.27
36 28 0.47
37 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (35 bp):
TTTTCTAAAAACAAATGTTGTCTCAGTTGAGACAA
Found at i:127163 original size:30 final size:29
Alignment explanation
Indices: 127089--127172 Score: 69
Period size: 30 Copynumber: 2.8 Consensus size: 29
127079 GTGAAAAAAT
* * * * *
127089 CTTTGAGTCCTTTCTTTTCAAACACCTAT
1 CTTTGAGTCATTTCTATTAAAACACCCAC
* * *
127118 CTTTGAGTTAATTTCTCTTGAAACACCCAC
1 CTTTGAG-TCATTTCTATTAAAACACCCAC
*
127148 CTTTGAGATCGTTTCTATTAAAACA
1 CTTTGAG-TCATTTCTATTAAAACA
127173 AATATTATTT
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 7 0.16
30 36 0.84
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (29 bp):
CTTTGAGTCATTTCTATTAAAACACCCAC
Found at i:127519 original size:29 final size:28
Alignment explanation
Indices: 127479--127564 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 28
127469 TGAAAAATCA
127479 TTGA-ATAGGTTTCTTTGGGAAACAAAATT
1 TTGAGATA-GTTTCTTT-GGAAACAAAATT
*
127508 TTGAGATAGTTTCTTT-TAAGA-AAAATCT
1 TTGAGATAGTTTCTTTGGAA-ACAAAAT-T
* *
127536 TTGAGTTTGTTTCTTTGGAAACAAAATT
1 TTGAGATAGTTTCTTTGGAAACAAAATT
127564 T
1 T
127565 ACCATCTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
27 7 0.15
28 19 0.40
29 19 0.40
30 3 0.06
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (28 bp):
TTGAGATAGTTTCTTTGGAAACAAAATT
Found at i:127764 original size:29 final size:29
Alignment explanation
Indices: 127727--127787 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
127717 TGCTTTTGAA
127727 AAACATCATCCTTGAGTCT-GTTTCTTTTG
1 AAACATCATCCTTGAGT-TGGTTTCTTTTG
* *
127756 AAACATCATCTTTTAGTTGGTTTCTTTTG
1 AAACATCATCCTTGAGTTGGTTTCTTTTG
127785 AAA
1 AAA
127788 TCAATATCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (29 bp):
AAACATCATCCTTGAGTTGGTTTCTTTTG
Found at i:128128 original size:40 final size:39
Alignment explanation
Indices: 128072--128151 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 39
128062 TTCCTAAAGA
* * *
128072 TGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC
1 TGACCAGAACTATTCATCACATATGAGCCCTGTCA-CCCC
*
128112 TGACCAGATCTATTCATCACATATGAGCCCTGTCACCCC
1 TGACCAGAACTATTCATCACATATGAGCCCTGTCACCCC
128151 T
1 T
128152 AGATAACCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 5 0.14
40 31 0.86
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (39 bp):
TGACCAGAACTATTCATCACATATGAGCCCTGTCACCCC
Found at i:128262 original size:40 final size:39
Alignment explanation
Indices: 128207--128284 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
128197 TCCTAAAGAT
*
128207 GACCAGAACTCTTCATCACGTATGAGCTGTGTCATCCCCC
1 GACCAGAACTCTTCATCACGTATGAGCCGTGTCA-CCCCC
*
128247 GACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCC
1 GACCAGAACTCTTCATCACGTATGAGCCGTGTCACCCC
128285 TAGATAACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (39 bp):
GACCAGAACTCTTCATCACGTATGAGCCGTGTCACCCCC
Found at i:128420 original size:134 final size:134
Alignment explanation
Indices: 127796--128413 Score: 948
Period size: 134 Copynumber: 4.6 Consensus size: 134
127786 AATCAATATC
* * * * *
127796 CCTAAAGATGGCCAGAACTCTTCATCATGTATGAGCCGTGTCATCCACCGACTAGATCTCTTTAT
1 CCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCTTCAT
* * * * * *
127861 CACGTAGGAGCCGTGTCAACCATAGATAACTAGCCGTCCTCATCACGTAGGAACCGAGTTATCAC
66 CACGTATGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCAT
*
127926 CCTT
131 TCTT
* * **
127930 CCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCATGTTATTTCCCGACCAGATCTCTTCAT
1 CCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCTTCAT
127995 CACGTATGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCAT
66 CACGTATGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCAT
128060 TCTT
131 TCTT
* *
128064 CCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTATTCAT
1 CCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCTTCAT
* * **
128129 CACATATGAGCCCTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAATTGAGTTATCAT
66 CACGTATGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCAT
128194 TCTT
131 TCTT
*
128198 CCTAAAGATGACCAGAACTCTTCATCACGTATGAGCTGTGTCATCCCCCGACCAGATCTCTTCAT
1 CCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCTTCAT
* *
128263 CACGTATGAGCCGTGTCACCCCTAGATAACCAACTGTCCTCATCGCGTAGGAACCGAGTTATCAT
66 CACGTATGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCAT
128328 TCTT
131 TCTT
* * * * * *
128332 CCTAAAGATGACCAAAACTCTTCATCGCGTATGAGGCGTGTCATACCCTGACCAGACCTCTTCAT
1 CCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCTTCAT
*
128397 CACGTATGAGCAGTGTC
66 CACGTATGAGCCGTGTC
128414 GTCCCTAACA
Statistics
Matches: 441, Mismatches: 43, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
134 441 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (134 bp):
CCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCTTCAT
CACGTATGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCAT
TCTT
Found at i:128606 original size:3 final size:3
Alignment explanation
Indices: 128589--128635 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
128579 TTTTTTTTTT
* *
128589 TTA TTT TTA TT- TTA TTA TTA TTA TTA CTT- TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
128633 TTA
1 TTA
128636 CATTTACATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 31 0.84
4 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:128619 original size:18 final size:17
Alignment explanation
Indices: 128574--128634 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
128564 TTTTGTTAAA
* *
128574 TATTATT-TTTTTTTTT
1 TATTATTATTTTATTAT
*
128590 TATTTTTATTTTATTAT
1 TATTATTATTTTATTAT
128607 TATTATTACTTTTATTAT
1 TATTATTA-TTTTATTAT
*
128625 TATTAATATT
1 TATTATTATT
128635 ACATTTACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
16 6 0.16
17 16 0.42
18 16 0.42
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTATTATTTTATTAT
Found at i:128626 original size:21 final size:21
Alignment explanation
Indices: 128600--128641 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
128590 TATTTTTATT
* *
128600 TTATTATTATTATTACTTTTA
1 TTATTATTAATATTACATTTA
128621 TTATTATTAATATTACATTTA
1 TTATTATTAATATTACATTTA
128642 CATTTTTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTATTAATATTACATTTA
Found at i:131772 original size:20 final size:20
Alignment explanation
Indices: 131736--131773 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
131726 TTTTTTAAAA
**
131736 AAAAATAAAATTTAAATATT
1 AAAAATAAAATAAAAATATT
131756 AAAAATAAAATAAAAATA
1 AAAAATAAAATAAAAATA
131774 ATAATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATAAAATAAAAATATT
Found at i:131782 original size:25 final size:23
Alignment explanation
Indices: 131729--131783 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
131719 ATGCATGTTT
* *
131729 TTTAAAAAAAAATAAAATTTAAA
1 TTTAAAAAAAAATAAAAATAAAA
131752 TATTAAAAATAAAATAAAAATAATAA
1 T-TTAAAAA-AAAATAAAAATAA-AA
131778 TTTAAA
1 TTTAAA
131784 TACTAAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 7 0.26
25 16 0.59
26 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
TTTAAAAAAAAATAAAAATAAAA
Found at i:140258 original size:18 final size:18
Alignment explanation
Indices: 140232--140266 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
140222 AAGATAATGA
140232 TGATAATAACGATGATGC
1 TGATAATAACGATGATGC
* *
140250 TGATGATAAGGATGATG
1 TGATAATAACGATGATG
140267 AAGTTGATGA
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:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (18 bp):
TGATAATAACGATGATGC
Found at i:143513 original size:19 final size:19
Alignment explanation
Indices: 143489--143525 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
143479 TTTACAAATG
143489 CTTAAATACAATCGTCTTT
1 CTTAAATACAATCGTCTTT
* *
143508 CTTAAATCCATTCGTCTT
1 CTTAAATACAATCGTCTT
143526 AACAGAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.43
Consensus pattern (19 bp):
CTTAAATACAATCGTCTTT
Found at i:148556 original size:30 final size:29
Alignment explanation
Indices: 148495--148557 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
148485 ATCAATCTTG
*
148495 CCACCAAACTATTTTTTGTCTCAATTCGA
1 CCACCAAACTATTTTTTGTCTCAATTAGA
148524 CCACCAAACT-TTTTAATTG-CTTCAATTAGA
1 CCACCAAACTATTTT--TTGTC-TCAATTAGA
148554 CCAC
1 CCAC
148558 TCTACGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.13
29 11 0.37
30 15 0.50
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.35
Consensus pattern (29 bp):
CCACCAAACTATTTTTTGTCTCAATTAGA
Found at i:149543 original size:28 final size:28
Alignment explanation
Indices: 149470--149550 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 28
149460 TTGTCAATTG
* *
149470 TCACCACAAAACCTAACAATATCAGCTA
1 TCACCATAAAACCTAACAATATCAACTA
* ***
149498 TCCCTCATATGTCCTAACAATATCAACTA
1 TCAC-CATAAAACCTAACAATATCAACTA
149527 TCACCATAAAACCTAACAATATCA
1 TCACCATAAAACCTAACAATATCA
149551 GCTGATCAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
28 20 0.48
29 22 0.52
ACGTcount: A:0.43, C:0.31, G:0.02, T:0.23
Consensus pattern (28 bp):
TCACCATAAAACCTAACAATATCAACTA
Found at i:151104 original size:16 final size:15
Alignment explanation
Indices: 151058--151104 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
151048 AATAAGCTCC
151058 AATCAATCTAAAACA
1 AATCAATCTAAAACA
*
151073 AATGCAAGCTAAAACA
1 AAT-CAATCTAAAACA
*
151089 AAGTCAATCTATAACA
1 AA-TCAATCTAAAACA
151105 TACTGGTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 3 0.11
16 23 0.85
17 1 0.04
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (15 bp):
AATCAATCTAAAACA
Found at i:151718 original size:13 final size:13
Alignment explanation
Indices: 151700--151768 Score: 63
Period size: 13 Copynumber: 5.3 Consensus size: 13
151690 CCAACAACTG
151700 TATGCATGAACAA
1 TATGCATGAACAA
*
151713 TATGCAAT-AACAT
1 TATGC-ATGAACAA
151726 TATGCA-GTAACAA
1 TATGCATG-AACAA
*
151739 TATGTAAT-AACAA
1 TATG-CATGAACAA
*
151752 TATGCATGAAGAA
1 TATGCATGAACAA
151765 TATG
1 TATG
151769 TATTACCAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
12 3 0.07
13 39 0.87
14 3 0.07
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (13 bp):
TATGCATGAACAA
Found at i:151769 original size:26 final size:26
Alignment explanation
Indices: 151700--151770 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 26
151690 CCAACAACTG
* *
151700 TATGCATGAACAATATGCAATAACAT
1 TATGCATGAACAATATGTAATAACAA
151726 TATGCA-GTAACAATATGTAATAACAA
1 TATGCATG-AACAATATGTAATAACAA
*
151752 TATGCATGAAGAATATGTA
1 TATGCATGAACAATATGTA
151771 TTACCAAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
25 1 0.03
26 38 0.95
27 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.28
Consensus pattern (26 bp):
TATGCATGAACAATATGTAATAACAA
Found at i:153718 original size:15 final size:15
Alignment explanation
Indices: 153698--153731 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
153688 TGGCTCAGCT
*
153698 GGTTCATTAATTTCG
1 GGTTCAGTAATTTCG
*
153713 GGTTCAGTAATTTCT
1 GGTTCAGTAATTTCG
153728 GGTT
1 GGTT
153732 GAACTGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (15 bp):
GGTTCAGTAATTTCG
Found at i:153719 original size:24 final size:24
Alignment explanation
Indices: 153674--153719 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
153664 ATCAATTTCA
**
153674 GGTTCATTAATTTTTGGCTCAGCT
1 GGTTCATTAATTTCGGGCTCAGCT
*
153698 GGTTCATTAATTTCGGGTTCAG
1 GGTTCATTAATTTCGGGCTCAG
153720 TAATTTCTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.43
Consensus pattern (24 bp):
GGTTCATTAATTTCGGGCTCAGCT
Found at i:153739 original size:39 final size:39
Alignment explanation
Indices: 153657--153740 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 39
153647 TCAGCAGGTT
* * *
153657 CTGGTTCATCAATTTCAGGTTCATTAATTTTTGGCTCAG
1 CTGGTTCATCAATTTCAGGTTCAGTAATTTCTGGCTCAA
* * * *
153696 CTGGTTCATTAATTTCGGGTTCAGTAATTTCTGGTTGAA
1 CTGGTTCATCAATTTCAGGTTCAGTAATTTCTGGCTCAA
153735 CTGGTT
1 CTGGTT
153741 TTGCTTCATC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.44
Consensus pattern (39 bp):
CTGGTTCATCAATTTCAGGTTCAGTAATTTCTGGCTCAA
Found at i:154408 original size:15 final size:15
Alignment explanation
Indices: 154390--154419 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
154380 ATTCATATAC
154390 AACATATACATGCAG
1 AACATATACATGCAG
154405 AACATATACATGCAG
1 AACATATACATGCAG
154420 TACTCACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
AACATATACATGCAG
Found at i:155149 original size:64 final size:68
Alignment explanation
Indices: 155070--155226 Score: 205
Period size: 74 Copynumber: 2.3 Consensus size: 68
155060 TTTTCTGCGA
155070 TGAAGGCGAATGGGTTTTC-A-G-A-CGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGA
1 TGAAGGCGAATGGGTTTTCAACGAATCGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGA
155131 GGT
66 GGT
155134 TGAAGGCGAATGGGTTTTCAGACGAAATCTCTCGAAATCTCTCTAAAGTGCGAAGGATTTTCAGA
1 TGAAGGCGAATGGGTTTTCA-ACG-AA----TCGAAATCTCTCTAAAGTGCGAAGGATTTTCAGA
*
155199 TGAGGAGGT
60 CGAGGAGGT
**
155208 TGAAGGAAAATGGGTTTTC
1 TGAAGGCGAATGGGTTTTC
155227 TGCGATGAAG
Statistics
Matches: 80, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
64 19 0.24
66 1 0.01
67 1 0.01
69 1 0.01
74 58 0.73
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (68 bp):
TGAAGGCGAATGGGTTTTCAACGAATCGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGA
GGT
Found at i:155810 original size:16 final size:16
Alignment explanation
Indices: 155785--155817 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
155775 AAAAACAATT
155785 GCAAGGGTGATTGAGC
1 GCAAGGGTGATTGAGC
*
155801 GCAAGTGTGATTGAGC
1 GCAAGGGTGATTGAGC
155817 G
1 G
155818 TCCATTGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.42, T:0.21
Consensus pattern (16 bp):
GCAAGGGTGATTGAGC
Found at i:155944 original size:19 final size:20
Alignment explanation
Indices: 155904--155951 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
155894 TAAAAAAATA
155904 AAAGTTTAGGAACTAAAATTG
1 AAAGTTTAGGAACT-AAATTG
* *
155925 ATAGTTTAGGTACT-AATTG
1 AAAGTTTAGGAACTAAATTG
155944 AAAGTTTA
1 AAAGTTTA
155952 CCCAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 12 0.50
21 12 0.50
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (20 bp):
AAAGTTTAGGAACTAAATTG
Found at i:159650 original size:17 final size:18
Alignment explanation
Indices: 159630--159678 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
159620 AATAAATCCA
*
159630 AAATATAAATAATAT-GG
1 AAATATAAATAATATAAG
*
159647 AAATGA-AAATAATATAAT
1 AAAT-ATAAATAATATAAG
159665 AAATATAAATAATA
1 AAATATAAATAATA
159679 CCATATACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AAATATAAATAATATAAG
Done.