Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002252.1 Hibiscus syriacus cultivar Beakdansim tig00004579_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: 91615
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:4656 original size:25 final size:25
Alignment explanation
Indices: 4626--4680 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
4616 TTGACAGCCC
4626 AACTCAAGTAATATGTAATGATTTT
1 AACTCAAGTAATATGTAATGATTTT
*
4651 AACTCAAGTAATGTGTAATGATTTT
1 AACTCAAGTAATATGTAATGATTTT
4676 AACTC
1 AACTC
4681 GTTAATGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (25 bp):
AACTCAAGTAATATGTAATGATTTT
Found at i:4998 original size:60 final size:60
Alignment explanation
Indices: 4897--5015 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
4887 CATTTGACAC
* * * * *
4897 GATGCCTTCAAGTTCCAAGGGGAGGCATTCAATTGCGAGCTTCTTCGACCTCAATGTCGA
1 GATGCCTTCAAGTTCCAAGGGGAGACATTCAACTACCAGCTTCTTCGACCTAAATGTCGA
* *
4957 GATGCCTTCAAGTT-CAAGGGGAATACATTCAACTACCAGCTTGTTCGACCTAAATGTCG
1 GATGCCTTCAAGTTCCAAGGGG-AGACATTCAACTACCAGCTTCTTCGACCTAAATGTCG
5016 GCATCGTGGA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 7 0.14
60 44 0.86
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (60 bp):
GATGCCTTCAAGTTCCAAGGGGAGACATTCAACTACCAGCTTCTTCGACCTAAATGTCGA
Found at i:6728 original size:39 final size:40
Alignment explanation
Indices: 6674--6769 Score: 149
Period size: 39 Copynumber: 2.4 Consensus size: 40
6664 GTCCATAACA
* *
6674 AAATAAAAACTTTACAATTGCTAGTAAAC-AAACAAAATT
1 AAATAAAAACTTTACAATTGATAGTAAACAAAAAAAAATT
*
6713 AAATAAAAACTTTACAATTGATGGTAAACAAAAAAAAATT
1 AAATAAAAACTTTACAATTGATAGTAAACAAAAAAAAATT
*
6753 AAATAAAAACATTACAA
1 AAATAAAAACTTTACAA
6770 ACTAAACAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 27 0.52
40 25 0.48
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.24
Consensus pattern (40 bp):
AAATAAAAACTTTACAATTGATAGTAAACAAAAAAAAATT
Found at i:7201 original size:21 final size:21
Alignment explanation
Indices: 7162--7217 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
7152 CCTTACGACG
** * *
7162 ATGGCATCTGACCTGGCTATA
1 ATGGCATCTGATATAGCTACA
*
7183 ATGGCATCTGATATAGCTACG
1 ATGGCATCTGATATAGCTACA
*
7204 ATGGAATCTGATAT
1 ATGGCATCTGATAT
7218 GGAAGTGGCG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (21 bp):
ATGGCATCTGATATAGCTACA
Found at i:12491 original size:2 final size:2
Alignment explanation
Indices: 12486--12514 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12476 TATGTGTATG
12486 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12515 TTATTACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19390 original size:25 final size:27
Alignment explanation
Indices: 19340--19390 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 27
19330 GACATCGCAT
19340 TTTTAATTAGTATTTTAATAATTTATA
1 TTTTAATTAGTATTTTAATAATTTATA
19367 TTTTAATTA-TATTTT-ATAATTTAT
1 TTTTAATTAGTATTTTAATAATTTAT
19391 TAAAGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 9 0.38
26 6 0.25
27 9 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTAATTAGTATTTTAATAATTTATA
Found at i:20300 original size:23 final size:23
Alignment explanation
Indices: 20270--20313 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
20260 AAAATTTCGG
20270 TGAGCTTAACGAGCAATGAGCAT
1 TGAGCTTAACGAGCAATGAGCAT
20293 TGAGCTTAACGAGCAATGAGC
1 TGAGCTTAACGAGCAATGAGC
20314 TTAACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.20
Consensus pattern (23 bp):
TGAGCTTAACGAGCAATGAGCAT
Found at i:20306 original size:16 final size:16
Alignment explanation
Indices: 20287--20318 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20277 AACGAGCAAT
*
20287 GAGCATTGAGCTTAAC
1 GAGCAATGAGCTTAAC
20303 GAGCAATGAGCTTAAC
1 GAGCAATGAGCTTAAC
20319 AAACAGCGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (16 bp):
GAGCAATGAGCTTAAC
Found at i:20794 original size:16 final size:17
Alignment explanation
Indices: 20763--20795 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20753 CTATAACTCA
*
20763 TTTATTGTTTTGGATAT
1 TTTATTATTTTGGATAT
20780 TTTATTATTTT-GATAT
1 TTTATTATTTTGGATAT
20796 ACACTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (17 bp):
TTTATTATTTTGGATAT
Found at i:21884 original size:158 final size:151
Alignment explanation
Indices: 21715--22018 Score: 346
Period size: 151 Copynumber: 2.0 Consensus size: 151
21705 AGTGAAATGC
* * * *
21715 AAAGTTAAGGGACTAAATAAAAAAGAGAGTATATTTTAGTAAAAAATAAGAATT-GAAGTTACAT
1 AAAGTTAAGGGACTAAAT-AAAAA-A-A--A-ATGTTA-TAAAAAAGAAGAATTAAAAG-CACAT
*
21779 AAGTATTCTATAG-TGGTATAGGAGCATGTGATTCAAATTT-GATAAAAAAAAGACTTAAAATGA
58 AAGTATTCTA-AGATGGTATAGGAGCATGTGATTCAAATTTAG-TAAAAAAAACACTTAAAATGA
21842 AGGATGAATTG-AAGAAATAAAGAAATCATAA
121 AGGATGAATTGAAAG-AATAAAGAAATCATAA
* ** *
21873 AAAGTTGAGGGACTAAATTGAAAAAAATGTTATAAAAAAGAGGAATTAAAAGCACATAAGTATTC
1 AAAGTTAAGGGACTAAATAAAAAAAAATGTTATAAAAAAGAAGAATTAAAAGCACATAAGTATTC
* * * * *
21938 TACGATGGTTTAGGAGCATGTGGTTCAAATTTAGTAAACAATACACTTAAAATGAAGGATGAATT
66 TAAGATGGTATAGGAGCATGTGATTCAAATTTAGTAAAAAAAACACTTAAAATGAAGGATGAATT
*
22003 GAAAGAATAAGGAAAT
131 GAAAGAATAAAGAAAT
22019 TAGGGACTAA
Statistics
Matches: 127, Mismatches: 15, Indels: 15
0.81 0.10 0.10
Matches are distributed among these distances:
150 1 0.01
151 91 0.72
152 12 0.09
153 1 0.01
155 1 0.01
156 1 0.01
157 3 0.02
158 17 0.13
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (151 bp):
AAAGTTAAGGGACTAAATAAAAAAAAATGTTATAAAAAAGAAGAATTAAAAGCACATAAGTATTC
TAAGATGGTATAGGAGCATGTGATTCAAATTTAGTAAAAAAAACACTTAAAATGAAGGATGAATT
GAAAGAATAAAGAAATCATAA
Found at i:25592 original size:9 final size:9
Alignment explanation
Indices: 25535--25594 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
25525 GGTCGGACCG
*
25535 GGTCAGACC
1 GGTCAAACC
25544 GGTCAAACC
1 GGTCAAACC
**
25553 GGTGTGAACC
1 GGT-CAAACC
25563 GGTCGAAACC
1 GGTC-AAACC
*
25573 AGTCAAAACC
1 GGTC-AAACC
25583 GGTCAAACC
1 GGTCAAACC
25592 GGT
1 GGT
25595 TTTTAGCCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
9 19 0.46
10 22 0.54
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.13
Consensus pattern (9 bp):
GGTCAAACC
Found at i:32770 original size:7 final size:7
Alignment explanation
Indices: 32758--32802 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
32748 GTCAAAGGAA
32758 GTCAACG
1 GTCAACG
32765 GTCAACG
1 GTCAACG
32772 GTCAACG
1 GTCAACG
*
32779 GTCAACA
1 GTCAACG
32786 GTCAACG
1 GTCAACG
*
32793 GTCAATG
1 GTCAACG
32800 GTC
1 GTC
32803 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:32816 original size:14 final size:14
Alignment explanation
Indices: 32799--32826 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
32789 AACGGTCAAT
32799 GGTCGGGTCGGGTC
1 GGTCGGGTCGGGTC
32813 GGTCGGGTCGGGTC
1 GGTCGGGTCGGGTC
32827 AGACCGGTCA
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:0.00, C:0.21, G:0.57, T:0.21
Consensus pattern (14 bp):
GGTCGGGTCGGGTC
Found at i:40015 original size:20 final size:20
Alignment explanation
Indices: 39963--40026 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
39953 AAACTTAAAT
* *
39963 TCGCAACATAAAAATGAAAA
1 TCGCAACGTGAAAATGAAAA
* *
39983 TCGCAATGCGAAAATGAAAA
1 TCGCAACGTGAAAATGAAAA
*
40003 TCGCAACGTGAAACT-AAAA
1 TCGCAACGTGAAAATGAAAA
40022 TCGCA
1 TCGCA
40027 TTGCGATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 9 0.24
20 28 0.76
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (20 bp):
TCGCAACGTGAAAATGAAAA
Found at i:40075 original size:20 final size:20
Alignment explanation
Indices: 40052--40090 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40042 TCGCGTTGCG
*
40052 ATTTTTGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
40072 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
40091 AAGTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:40097 original size:20 final size:20
Alignment explanation
Indices: 40058--40097 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40048 TGCGATTTTT
* *
40058 GTGTTGCGAATTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
40078 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
40098 AAAAACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.47
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:41652 original size:42 final size:42
Alignment explanation
Indices: 41583--41681 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
41573 CCCCCCACTT
* * * *
41583 CGAGAGCCATCACCTGATCGAGTCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
* *
41625 TGAGAGCCATCACCTGATTGAGCCGATTATACACCTCCACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
41667 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
41682 ATTTAATCAC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.27, C:0.34, G:0.19, T:0.19
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
Found at i:42283 original size:21 final size:21
Alignment explanation
Indices: 42257--42348 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
42247 CCTGTCATCA
*
42257 TTCAAGAGGCTCCTCCTATCG
1 TTCAAGAGGCCCCTCCTATCG
* *
42278 TTCAAGAGTCCCCTCCTATTG
1 TTCAAGAGGCCCCTCCTATCG
42299 TTCAAGAGGCCCCT-CTCATCG
1 TTCAAGAGGCCCCTCCT-ATCG
* *
42320 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTCCTATCG
42341 TTCAAGAG
1 TTCAAGAG
42349 CCCGATTCAC
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
20 2 0.03
21 59 0.95
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCTATCG
Found at i:43857 original size:20 final size:20
Alignment explanation
Indices: 43832--43893 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
43822 AAGATACACT
43832 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
**
43852 TTCGCATTGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
43872 TTCGCAACACGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
43892 TT
1 TT
43894 TGCGTTGCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:44165 original size:18 final size:18
Alignment explanation
Indices: 44142--44177 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
44132 AAGCCGGTTG
44142 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
* *
44160 TGATTGCGATTTTTATTT
1 TGATTGAGATTTTGATTT
44178 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.19, T:0.58
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:46985 original size:24 final size:24
Alignment explanation
Indices: 46958--47003 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
46948 ATCATCAAAA
*
46958 TCCGAGTATTGACCAAGATCAATG
1 TCCGAGTATTAACCAAGATCAATG
*
46982 TCCGGGTATTAACCAAGATCAA
1 TCCGAGTATTAACCAAGATCAA
47004 ATTTCGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (24 bp):
TCCGAGTATTAACCAAGATCAATG
Found at i:47151 original size:12 final size:12
Alignment explanation
Indices: 47130--47163 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
47120 GGTTGTGGGT
*
47130 TTTGAGATTGTG
1 TTTGATATTGTG
47142 TTTGATATTGTG
1 TTTGATATTGTG
*
47154 TTTGGTATTG
1 TTTGATATTG
47164 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:47794 original size:14 final size:15
Alignment explanation
Indices: 47758--47795 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
47748 GAAATCATTG
47758 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
47773 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
47788 AAAAATTA
1 AAAAATTA
47796 GAGATTGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:48015 original size:40 final size:39
Alignment explanation
Indices: 47964--48080 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 39
47954 TTGTGAAATT
47964 AAAATTTGTGTTGCGAATTCAAAAATCGAGTTGCGAAAA
1 AAAATTTGTGTTGCGAATTCAAAAATCGAGTTGCGAAAA
* **** * * *
48003 CAAAATTCGTGTTGCGAAAAGGAAACTTGTGTTGCGAAAA
1 -AAAATTTGTGTTGCGAATTCAAAAATCGAGTTGCGAAAA
* *
48043 ATAAATTTGCGTTGCGAATTCAGAAATCGAGTTGCGAA
1 A-AAATTTGTGTTGCGAATTCAAAAATCGAGTTGCGAA
48081 TTTGAAAATC
Statistics
Matches: 58, Mismatches: 18, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
39 1 0.02
40 57 0.98
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (39 bp):
AAAATTTGTGTTGCGAATTCAAAAATCGAGTTGCGAAAA
Found at i:48021 original size:20 final size:20
Alignment explanation
Indices: 47964--48060 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
47954 TTGTGAAATT
* **
47964 AAAATTTGTGTTGCGAATTC
1 AAAATTCGTGTTGCGAAAAC
* *
47984 AAAAATCGAGTTGCGAAAAC
1 AAAATTCGTGTTGCGAAAAC
*
48004 AAAATTCGTGTTGCGAAAAGG
1 AAAATTCGTGTTGCGAAAA-C
*
48025 AAACTT-GTGTTGCGAAAA-
1 AAAATTCGTGTTGCGAAAAC
* *
48043 ATAAATTTGCGTTGCGAA
1 A-AAATTCGTGTTGCGAA
48061 TTCAGAAATC
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
18 1 0.02
19 4 0.06
20 53 0.84
21 5 0.08
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (20 bp):
AAAATTCGTGTTGCGAAAAC
Found at i:48076 original size:20 final size:20
Alignment explanation
Indices: 48053--48122 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
48043 ATAAATTTGC
48053 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATTCAGAAATCGA
* *
48073 GTTGCGAATT-TGAAAATCGC
1 GTTGCGAATTCAG-AAATCGA
48093 GTTGCG-ATTGCAGAAA-CTGA
1 GTTGCGAATT-CAGAAATC-GA
*
48113 GTTACGAATT
1 GTTGCGAATT
48123 TGGAAACTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 5 0.12
20 31 0.77
21 4 0.10
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (20 bp):
GTTGCGAATTCAGAAATCGA
Found at i:48130 original size:20 final size:20
Alignment explanation
Indices: 48105--48146 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
48095 TGCGATTGCA
*
48105 GAAACTGAGTTACGAATTTG
1 GAAACTGAGTTACGAAATTG
*
48125 GAAACTGTGTTACGAAATTG
1 GAAACTGAGTTACGAAATTG
48145 GA
1 GA
48147 GTTCGCATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (20 bp):
GAAACTGAGTTACGAAATTG
Found at i:49181 original size:22 final size:23
Alignment explanation
Indices: 49155--49226 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
49145 ATAAATTTAC
49155 CTTTATGACACGTTTT-TTATGT
1 CTTTATGACACGTTTTCTTATGT
*
49177 CTTTATGACAAGTTTTCTTATGT
1 CTTTATGACACGTTTTCTTATGT
* * *
49200 ATTTATGACACATTTTCTTCTGT
1 CTTTATGACACGTTTTCTTATGT
49223 CTTT
1 CTTT
49227 TGTCATGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 15 0.35
23 28 0.65
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.54
Consensus pattern (23 bp):
CTTTATGACACGTTTTCTTATGT
Found at i:51694 original size:13 final size:13
Alignment explanation
Indices: 51676--51700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51666 AAAATACTGG
51676 ATTCGGATATCAA
1 ATTCGGATATCAA
51689 ATTCGGATATCA
1 ATTCGGATATCA
51701 GACACTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATTCGGATATCAA
Found at i:55273 original size:14 final size:15
Alignment explanation
Indices: 55244--55285 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
55234 TTGTCGCTCA
*
55244 TATCCCTAACAACCT
1 TATCCCCAACAACCT
55259 TATCCCCAA-AACCT
1 TATCCCCAACAACCT
*
55273 TCAACCCCAACAA
1 T-ATCCCCAACAA
55286 TTTTATCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 6 0.26
15 15 0.65
16 2 0.09
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19
Consensus pattern (15 bp):
TATCCCCAACAACCT
Found at i:56243 original size:22 final size:21
Alignment explanation
Indices: 56218--56264 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
56208 ATTTTTTTTA
56218 ATTTACTCTTCT-ACATTTATTT
1 ATTTA-TCTTCTAACA-TTATTT
*
56240 ATTTATTTTCTAACATTATTT
1 ATTTATCTTCTAACATTATTT
56261 ATTT
1 ATTT
56265 TTACTCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTATCTTCTAACATTATTT
Found at i:58522 original size:2 final size:2
Alignment explanation
Indices: 58515--58549 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58505 AATGAATAGT
58515 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58550 GCACCATGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60334 original size:20 final size:22
Alignment explanation
Indices: 60309--60348 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
60299 AGTTGTATAT
60309 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
60329 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
60349 TCTGCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:60668 original size:30 final size:30
Alignment explanation
Indices: 60621--60680 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
60611 AAACTTTGAA
*
60621 TAAATTTAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
60650 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
60681 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:60820 original size:20 final size:19
Alignment explanation
Indices: 60793--60850 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
60783 TGTTTAATGA
60793 AAAAGATACCAATTGTTAC
1 AAAAGATACCAATTGTTAC
*
60812 AAAAGGATACTAATTGTTA-
1 AAAA-GATACCAATTGTTAC
*
60831 AAAAGATAACCAAATGTTAC
1 AAAAGAT-ACCAATTGTTAC
60851 CAATTGTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 3 0.09
19 17 0.52
20 13 0.39
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (19 bp):
AAAAGATACCAATTGTTAC
Found at i:63866 original size:21 final size:21
Alignment explanation
Indices: 63836--63875 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
63826 ACGATAAGGG
* *
63836 GTATCGGTACCCCTTCATACA
1 GTATCAGTACCACTTCATACA
*
63857 GTATCAGTACTACTTCATA
1 GTATCAGTACCACTTCATA
63876 AAATTCAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (21 bp):
GTATCAGTACCACTTCATACA
Found at i:64122 original size:30 final size:30
Alignment explanation
Indices: 64075--64133 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
64065 AAACTTTGAA
64075 TAAATTCAATTAAGTCCA-AAAACATTTTG
1 TAAATTCAATTAAGTCCACAAAACATTTTG
*
64104 TAAATTCAATTCAAGTCCACAAACCATTTT
1 TAAATTCAATT-AAGTCCACAAAACATTTT
64134 ACCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 7 0.26
31 9 0.33
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCACAAAACATTTTG
Found at i:64530 original size:24 final size:25
Alignment explanation
Indices: 64503--64553 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
64493 ATGGGTTATT
*
64503 TTATGTAAG-AAATAT-TGTTTATGC
1 TTAT-TAAGTAAATATATATTTATGC
*
64527 TTATTAAGTTAATATATATTTATGC
1 TTATTAAGTAAATATATATTTATGC
64552 TT
1 TT
64554 GTTGTACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 9 0.39
25 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (25 bp):
TTATTAAGTAAATATATATTTATGC
Found at i:72281 original size:11 final size:10
Alignment explanation
Indices: 72265--72323 Score: 63
Period size: 11 Copynumber: 6.0 Consensus size: 10
72255 AGAAGAAAGG
72265 GAAAAAAGAGA
1 GAAAAAAGA-A
72276 GAAAAAAG--
1 GAAAAAAGAA
72284 GAAAAGAA-AA
1 GAAAA-AAGAA
72294 -AAAAAAGAA
1 GAAAAAAGAA
72303 GAAAAAAGAAA
1 GAAAAAAG-AA
72314 GAAAAAAGAA
1 GAAAAAAGAA
72324 AGAATAAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
8 7 0.17
9 8 0.19
10 9 0.21
11 18 0.43
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
GAAAAAAGAA
Found at i:72287 original size:25 final size:23
Alignment explanation
Indices: 72257--72327 Score: 63
Period size: 26 Copynumber: 2.9 Consensus size: 23
72247 ACACTCAAAG
72257 AAGAAAGGGAAAAAAGAGAGAAAA
1 AAGAAA-GGAAAAAAGAGAGAAAA
* *
72281 AAGGAAAAGAAAAAAAAAAGAAGAAAA
1 AA-G-AAAG-GAAAAAAGAG-AGAAAA
*
72308 AAGAAA-GAAAAAAGAAAGAA
1 AAGAAAGGAAAAAAGAGAGAA
72328 TAAGTAACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
22 4 0.11
23 7 0.18
24 2 0.05
25 5 0.13
26 12 0.32
27 8 0.21
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (23 bp):
AAGAAAGGAAAAAAGAGAGAAAA
Found at i:72289 original size:26 final size:27
Alignment explanation
Indices: 72266--72327 Score: 92
Period size: 25 Copynumber: 2.3 Consensus size: 27
72256 GAAGAAAGGG
72266 AAAAAAGAGAGAAAAAAGGAAAAGAAAA
1 AAAAAAGA-AGAAAAAAGGAAAAGAAAA
72294 AAAAAAGAAGAAAAAA-G-AAAGAAAA
1 AAAAAAGAAGAAAAAAGGAAAAGAAAA
*
72319 AAGAAAGAA
1 AAAAAAGAA
72328 TAAGTAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 16 0.48
26 1 0.03
27 8 0.24
28 8 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (27 bp):
AAAAAAGAAGAAAAAAGGAAAAGAAAA
Found at i:72296 original size:14 final size:13
Alignment explanation
Indices: 72266--72324 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
72256 GAAGAAAGGG
*
72266 AAAAAAG-AGAGA
1 AAAAAAGAAAAGA
*
72278 AAAAAGGAAAAGA
1 AAAAAAGAAAAGA
*
72291 AAAAAAAAAGAAG-
1 AAAAAAGAA-AAGA
72304 AAAAAAG-AAAG-
1 AAAAAAGAAAAGA
72315 AAAAAAGAAA
1 AAAAAAGAAA
72325 GAATAAGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 10 0.26
12 9 0.23
13 17 0.44
14 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAGA
Found at i:72324 original size:11 final size:11
Alignment explanation
Indices: 72285--72327 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
72275 AGAAAAAAGG
*
72285 AAAAGAAAAAA
1 AAAAGAAAGAA
72296 AAAAG-AAGAA
1 AAAAGAAAGAA
72306 AAAAGAAAGAA
1 AAAAGAAAGAA
72317 AAAAGAAAGAA
1 AAAAGAAAGAA
72328 TAAGTAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:73571 original size:52 final size:51
Alignment explanation
Indices: 73495--73690 Score: 236
Period size: 52 Copynumber: 3.8 Consensus size: 51
73485 GGTCCATATT
* *
73495 ATCCATGT-GGGTATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTA
73545 ATCCATGTGGGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTA
1 ATCCATGT-GGGGCATCTTGAAGGCTCACATCAGCATG-AAAAGACAGAAGTA
* * * *
73598 ATCCATGTGGGGCATCTTGAAAAG-TCACATCAACATGAAGAGACAAAAGTA
1 ATCCATGTGGGGCATCTTG-AAGGCTCACATCAGCATGAAAAGACAGAAGTA
* * * * *
73649 ATTCATG-GTGGGCATTTTAAAGTCTCACACCAGCATGAAAAG
1 ATCCATGTG-GGGCATCTTGAAGGCTCACATCAGCATGAAAAG
73691 GTTGGGATAT
Statistics
Matches: 126, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
50 11 0.09
51 41 0.33
52 50 0.40
53 24 0.19
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (51 bp):
ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTA
Found at i:73677 original size:51 final size:50
Alignment explanation
Indices: 73516--73690 Score: 183
Period size: 51 Copynumber: 3.4 Consensus size: 50
73506 TATCTTGAAG
* * * *
73516 GCTCACATCAGCATGAAAAGATAGAAGTAATCCATGTGGGGGCATCTTGAAG
1 GCTCACATCAGCATGAAAAGACAGAAGTAATCCATG-GTGGGCAT-TTTAAA
*
73568 GCTCACATCAGCATGAAAAAGACAGAAGTAATCCAT-GTGGGGCATCTTGAAAA
1 GCTCACATCAGCATG-AAAAGACAGAAGTAATCCATGGT-GGGCAT-TT-TAAA
* * * *
73621 G-TCACATCAACATGAAGAGACAAAAGTAATTCATGGTGGGCATTTTAAA
1 GCTCACATCAGCATGAAAAGACAGAAGTAATCCATGGTGGGCATTTTAAA
*
73670 GTCTCACACCAGCATGAAAAG
1 G-CTCACATCAGCATGAAAAG
73691 GTTGGGATAT
Statistics
Matches: 105, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
49 4 0.04
50 2 0.02
51 39 0.37
52 38 0.36
53 22 0.21
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (50 bp):
GCTCACATCAGCATGAAAAGACAGAAGTAATCCATGGTGGGCATTTTAAA
Found at i:74217 original size:54 final size:49
Alignment explanation
Indices: 74124--74223 Score: 146
Period size: 54 Copynumber: 1.9 Consensus size: 49
74114 CACTGACAAG
74124 AAATCTGGGCAGAAGCCACAGGATGAATGTGTGGTCAAATGTTTTACGA
1 AAATCTGGGCAGAAGCCACAGGATGAATGTGTGGTCAAATGTTTTACGA
*
74173 AAATCTGGGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTA
1 AAATCTGGGCAGAAGCCAC-----AGGATGAATGTGTGGTCAAATGTTTTA
74224 TGAACCACTG
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
49 19 0.42
54 26 0.58
ACGTcount: A:0.34, C:0.13, G:0.27, T:0.26
Consensus pattern (49 bp):
AAATCTGGGCAGAAGCCACAGGATGAATGTGTGGTCAAATGTTTTACGA
Found at i:75272 original size:22 final size:22
Alignment explanation
Indices: 75247--75316 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
75237 GGTTCCTTGA
75247 TGATAAGCTTGAGGGACCATCG
1 TGATAAGCTTGAGGGACCATCG
* * * *
75269 TGATATG-TAG-GGGTTCC-TTG
1 TGATAAGCTTGAGGG-ACCATCG
75289 ATGATAAGCTTGAGGGACCATCG
1 -TGATAAGCTTGAGGGACCATCG
75312 TGATA
1 TGATA
75317 TGTAGGGGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
20 5 0.14
21 10 0.29
22 15 0.43
23 5 0.14
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (22 bp):
TGATAAGCTTGAGGGACCATCG
Found at i:75272 original size:25 final size:25
Alignment explanation
Indices: 75244--75315 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
75234 AGGGGTTCCT
75244 TGATGATAAGCTTGAGGGACCATCG
1 TGATGATAAGCTTGAGGGACCATCG
* *
75269 TGAT-AT--G-TAG-GGGTTCC-T--
1 TGATGATAAGCTTGAGGG-ACCATCG
75287 TGATGATAAGCTTGAGGGACCATCG
1 TGATGATAAGCTTGAGGGACCATCG
75312 TGAT
1 TGAT
75316 ATGTAGGGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 18
0.61 0.07 0.32
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 4 0.12
21 5 0.15
22 5 0.15
23 4 0.12
24 2 0.06
25 8 0.24
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.29
Consensus pattern (25 bp):
TGATGATAAGCTTGAGGGACCATCG
Found at i:75275 original size:43 final size:43
Alignment explanation
Indices: 75212--75545 Score: 434
Period size: 43 Copynumber: 8.0 Consensus size: 43
75202 GAAACTAAGA
* * *
75212 TTGAGGGACCATCGTTATATGTAGGGGTTCCTTGATGATAAGC
1 TTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAGC
* *
75255 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGATAAGC
1 TTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAGC
*
75298 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGC
1 TTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAGC
* *
75341 TTGAGGGACCAAAGTGATATGTAGGGGTTCCTTAATGACAAGC
1 TTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAGC
* * * * * * *
75384 TTAAGGAACCATCGTGATATATAGGGGTTCTTTTATGACAAGT
1 TTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAGC
*
75427 TTGAGGGACCAACATGATATGTAGGGGTTCCTTGATGACAAGC
1 TTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAGC
75470 TTGAGGGACCAACGTG--A--T---GGTTCCTTGATGA-ACA-C
1 TTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACA-AGC
* *
75505 TTGAGGGACCAACGTGATATATAGGGGTTCCTTGGTGACAA
1 TTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAA
75546 CTAAGAAATT
Statistics
Matches: 259, Mismatches: 23, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
35 18 0.07
36 14 0.05
37 1 0.00
39 2 0.01
41 1 0.00
42 13 0.05
43 210 0.81
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (43 bp):
TTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAGC
Found at i:75515 original size:35 final size:36
Alignment explanation
Indices: 75452--75522 Score: 119
Period size: 35 Copynumber: 2.0 Consensus size: 36
75442 GATATGTAGG
75452 GGTTCCTTGATGACAAGCTTGAGGGACCAACGTGAT
1 GGTTCCTTGATGACAAGCTTGAGGGACCAACGTGAT
75488 GGTTCCTTGATGA-ACA-CTTGAGGGACCAACGTGAT
1 GGTTCCTTGATGACA-AGCTTGAGGGACCAACGTGAT
75523 ATATAGGGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 20 0.59
36 14 0.41
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (36 bp):
GGTTCCTTGATGACAAGCTTGAGGGACCAACGTGAT
Found at i:75638 original size:42 final size:41
Alignment explanation
Indices: 75579--75728 Score: 167
Period size: 42 Copynumber: 3.6 Consensus size: 41
75569 AGGAGTTTCT
* *
75579 TGATGAGTAAGTCCTTCGGGCCATCAGTGAGTCTTTCGAGCA
1 TGATG-GTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
* *
75621 TGATGTGTAAATCCTTCGGGTCATCAGCAAGTCTTTCGAGCA
1 TGATG-GTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
* *
75663 TGATGCGGAAATCCTTCGGGTCATCTA-TAAGTCTTTCGAGCA
1 TGATG-GTAAATCCTTCGGGCCATC-AGTAAGTCTTTCGAGCA
* * * *
75705 AGATGATAAGTCCTTTGGGCCATC
1 TGATGGTAAATCCTTCGGGCCATC
75729 CATAAGACCT
Statistics
Matches: 93, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
41 14 0.15
42 78 0.84
43 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (41 bp):
TGATGGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
Found at i:75867 original size:90 final size:90
Alignment explanation
Indices: 75711--76168 Score: 661
Period size: 90 Copynumber: 5.1 Consensus size: 90
75701 AGCAAGATGA
* * * *
75711 TAAGTCCTTTGGGCCATCCATAAGACCTTCAGTGTAGGATGTTTTCAAATAAGATTTAAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTAAGAAACT
75776 AAGCCTTCGGGGGTTTCTTGATTTT
66 AAGCCTTCGGGGGTTTCTTGATTTT
* *
75801 TATGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTTAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTAAGAAACT
*
75866 AAGCCTTCGGGGGTTTCTTGATTTG
66 AAGCCTTCGGGGGTTTCTTGATTTT
* * * *
75891 TAAGTGCTACGGGCCATCTATAAGA-CTTCAGTACATG-ATGTTTTCAAATGAGATTTAAGAAAC
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA-GAATGTTTTCAAATGAGATTTAAGAAAC
* *
75954 TAAGCCTTCGGGCGTTTCTTGATTTG
65 TAAGCCTTCGGGGGTTTCTTGATTTT
* * * **
75980 TAAGTCCTTCAGGCAATGCATAAGAAATTCAGTGCAGAATGTTTTCAAATGAGATTTAAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTAAGAAACT
76045 AAGCCTTCGGGGGTTTCTTGATTTT
66 AAGCCTTCGGGGGTTTCTTGATTTT
* * *
76070 TAAGTCATTCGAGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAA-AAAC
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGA-TTTAAGAAAC
* *
76134 TAGGCCTTCAGGGGTTTCTTGATTTT
65 TAAGCCTTCGGGGGTTTCTTGATTTT
*
76160 TAAATCCTT
1 TAAGTCCTT
76169 TAGGTCATCA
Statistics
Matches: 328, Mismatches: 36, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
89 79 0.24
90 244 0.74
91 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (90 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTAAGAAACT
AAGCCTTCGGGGGTTTCTTGATTTT
Found at i:75947 original size:179 final size:180
Alignment explanation
Indices: 75721--76168 Score: 677
Period size: 179 Copynumber: 2.5 Consensus size: 180
75711 TAAGTCCTTT
* *
75721 GGGCCATCCATAAGACCTTCAGTGTAGGATGTTTTCAAATAAGATTTAAGAAACTAAGCCTTCGG
1 GGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCGG
* * * **
75786 GGGTTTCTTGATTTTTATGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAAT
66 GGGTTTCTTGATTTTTAAGTCCTTCAGGCAATCCATAAGAAATTCAGTGCAGAATGTTTTCAAAT
*
75851 GAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTGC-TAC
131 GAGATTTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGT-CATAC
* * *
75901 GGGCCATCTATAAGA-CTTCAGTACATGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCGG
1 GGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCGG
* * *
75965 GCGTTTCTTGATTTGTAAGTCCTTCAGGCAATGCATAAGAAATTCAGTGCAGAATGTTTTCAAAT
66 GGGTTTCTTGATTTTTAAGTCCTTCAGGCAATCCATAAGAAATTCAGTGCAGAATGTTTTCAAAT
* *
76030 GAGATTTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCATTC
131 GAGATTTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCATAC
* * *
76080 GAGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAA-AAACTAGGCCTTCA
1 GGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGA-TTTAAGAAACTAAGCCTTCG
*
76144 GGGGTTTCTTGATTTTTAAATCCTT
65 GGGGTTTCTTGATTTTTAAGTCCTT
76169 TAGGTCATCA
Statistics
Matches: 240, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
178 1 0.00
179 160 0.67
180 74 0.31
181 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (180 bp):
GGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCGG
GGGTTTCTTGATTTTTAAGTCCTTCAGGCAATCCATAAGAAATTCAGTGCAGAATGTTTTCAAAT
GAGATTTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCATAC
Found at i:76218 original size:42 final size:41
Alignment explanation
Indices: 76159--76266 Score: 137
Period size: 42 Copynumber: 2.6 Consensus size: 41
76149 TTCTTGATTT
** *
76159 TTAAATCCTTTAGGTCATC-AGTAAGTCTTTCGAGCATGATG
1 TTAAATCCTTCGGGTCATCTA-TAAGTCTTTCGAGCAAGATG
76200 CTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATG
1 -TTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATG
* * *
76242 ATAAGTCCTTCGGGCCATCTATAAG
1 TTAAATCCTTCGGGTCATCTATAAG
76267 ACCTTCGGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 22 0.37
42 36 0.61
43 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (41 bp):
TTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATG
Found at i:76262 original size:41 final size:42
Alignment explanation
Indices: 76180--76266 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 42
76170 AGGTCATCAG
* * *
76180 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTA
1 TAAGTCTTTCGAGCAAGATGCATAAATCCTTCGGGCCATCTA
*
76222 TAAGTCTTTCGAGCAAGATG-ATAAGTCCTTCGGGCCATCTA
1 TAAGTCTTTCGAGCAAGATGCATAAATCCTTCGGGCCATCTA
76263 TAAG
1 TAAG
76267 ACCTTCGGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 22 0.54
42 19 0.46
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGCATAAATCCTTCGGGCCATCTA
Found at i:90106 original size:3 final size:3
Alignment explanation
Indices: 90098--90172 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
90088 CATAGGTATA
90098 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
90146 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
90173 TATTATTATT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:90177 original size:3 final size:3
Alignment explanation
Indices: 90171--90207 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
90161 GATGATGATG
90171 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
90208 ATTTGTTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Done.