Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015302.1 Kokia drynarioides strain JFW-HI SEQ_130347, 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: 404437
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 205 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1095 original size:7 final size:7
Alignment explanation
Indices: 1066--1112 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
1056 CTCTTCCCCA
1066 TTTC-CC
1 TTTCTCC
*
1072 TTTCCCC
1 TTTCTCC
* *
1079 TTCCTTC
1 TTTCTCC
1086 TTTCTCC
1 TTTCTCC
1093 TTTCTCC
1 TTTCTCC
*
1100 TTTCCCC
1 TTTCTCC
1107 TTTCTC
1 TTTCTC
1113 GTTTTCAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
6 4 0.12
7 29 0.88
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (7 bp):
TTTCTCC
Found at i:1109 original size:14 final size:14
Alignment explanation
Indices: 1059--1112 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
1049 CGAAAGCCTC
1059 TTCCCCATTTC-CCT
1 TTCCCC-TTTCTCCT
* *
1073 TTCCCCTTCCTTCT
1 TTCCCCTTTCTCCT
*
1087 TTCTCCTTTCTCCT
1 TTCCCCTTTCTCCT
1101 TTCCCCTTTCTC
1 TTCCCCTTTCTC
1113 GTTTTCAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 3 0.09
14 30 0.91
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (14 bp):
TTCCCCTTTCTCCT
Found at i:1186 original size:14 final size:14
Alignment explanation
Indices: 1167--1205 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1157 GGGACGATCT
*
1167 TTTCTTCTTTCCAG
1 TTTCTTCTTTCCAC
*
1181 TTTCTTCTTTCCCC
1 TTTCTTCTTTCCAC
1195 TTTCTTCTTTC
1 TTTCTTCTTTC
1206 GGTAAGCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.03, C:0.33, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTCTTCTTTCCAC
Found at i:3711 original size:20 final size:20
Alignment explanation
Indices: 3675--3718 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3665 TCCAAACACC
*
3675 AAAAAATATTAATTTTTCTA
1 AAAAAATATTAATTTTTCCA
*
3695 AAAAAATAATTCA-TTTTCCA
1 AAAAAAT-ATTAATTTTTCCA
3715 AAAA
1 AAAA
3719 TTATTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATATTAATTTTTCCA
Found at i:3718 original size:21 final size:20
Alignment explanation
Indices: 3675--3718 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3665 TCCAAACACC
* *
3675 AAAAAATATTAATTTTTCTA
1 AAAAAATATTAATTTTCCAA
*
3695 AAAAAATAATTCATTTTCCAA
1 AAAAAAT-ATTAATTTTCCAA
3716 AAA
1 AAA
3719 TTATTTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATATTAATTTTCCAA
Found at i:6858 original size:33 final size:32
Alignment explanation
Indices: 6816--6914 Score: 92
Period size: 33 Copynumber: 3.0 Consensus size: 32
6806 ACTTTAGTGG
6816 ATAAATCAATGTATTTGGTTAAATGTAAGACT
1 ATAAATCAATGTATTTGGTTAAATGTAAGACT
* * * * * ***
6848 ATTAAATCAATTTTTTTTTGTTACACT-TTAGTGG
1 A-TAAATCAA-TGTATTTGGTTA-AATGTAAGACT
6882 ATAAATCAATGTATTTGGTTAAATGTAAGACT
1 ATAAATCAATGTATTTGGTTAAATGTAAGACT
6914 A
1 A
6915 CAAAACTATT
Statistics
Matches: 47, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
31 2 0.04
32 14 0.30
33 16 0.34
34 13 0.28
35 2 0.04
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (32 bp):
ATAAATCAATGTATTTGGTTAAATGTAAGACT
Found at i:6874 original size:66 final size:68
Alignment explanation
Indices: 6779--6914 Score: 258
Period size: 66 Copynumber: 2.0 Consensus size: 68
6769 TGATTAATCA
6779 TATTAAATCAATTTTCTTTCTTGTTACACTTTAGTGGATAAATCAATGTATTTGGTTAAATGTAA
1 TATTAAATCAATTTTCTTTCTTGTTACACTTTAGTGGATAAATCAATGTATTTGGTTAAATGTAA
6844 GAC
66 GAC
6847 TATTAAATCAATTTT-TTT-TTGTTACACTTTAGTGGATAAATCAATGTATTTGGTTAAATGTAA
1 TATTAAATCAATTTTCTTTCTTGTTACACTTTAGTGGATAAATCAATGTATTTGGTTAAATGTAA
6910 GAC
66 GAC
6913 TA
1 TA
6915 CAAAACTATT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
66 50 0.74
67 3 0.04
68 15 0.22
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (68 bp):
TATTAAATCAATTTTCTTTCTTGTTACACTTTAGTGGATAAATCAATGTATTTGGTTAAATGTAA
GAC
Found at i:31853 original size:27 final size:27
Alignment explanation
Indices: 31819--31873 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
31809 CAACTTGAAC
31819 ATACCCTCATTACAATATCCTTTTCCT
1 ATACCCTCATTACAATATCCTTTTCCT
31846 ATACCCTCATTACAATATCCTTTTCCT
1 ATACCCTCATTACAATATCCTTTTCCT
31873 A
1 A
31874 CATATATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (27 bp):
ATACCCTCATTACAATATCCTTTTCCT
Found at i:35665 original size:43 final size:43
Alignment explanation
Indices: 35539--35751 Score: 259
Period size: 43 Copynumber: 5.0 Consensus size: 43
35529 CGCTATTTTT
* * *
35539 AGAACATGATCTTTAGCGGCAC-TTTCCCAAAAATGCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAA
* *
35581 AGAACATGGTCTGTAGCGGCAC-TTTCCCAAAAACGCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAA
** * *
35623 AGAATGTGGTCTTTAGCGGCGCTTTTCCCACAAACGCAGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAA
* * * * *
35666 AGAACGTGGTCTTTGGCAGCGCTTTTCTCATAAACGCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAA
* * *
35709 AGAACATGGTCTTTAGCGGTGCTTTTCCCACAAACGCCACTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAA
35752 CATTAACAGA
Statistics
Matches: 148, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
42 57 0.39
43 91 0.61
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (43 bp):
AGAACATGGTCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAA
Found at i:36151 original size:66 final size:66
Alignment explanation
Indices: 36019--36152 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 66
36009 ATTTTGAAGC
* * * **
36019 TGTAGCTGCAGTTCGTCATAATTTTTTTGAGACTCTACTTCCCTCGTTGTTGCCTTGGCTTCAAG
1 TGTAGCTGAAGTTCATCATAATTTTTTTGAGACTCTACTTCCCTCGTTGCTGCCTCCGCTTCAAG
36084 T
66 T
* * * * *
36085 TGTAGCTGAAGTTCATCAT-ATTTTCTTTGAGCCTCTGCTTCTCTTGTTGCTGCCTCCGCTTTAA
1 TGTAGCTGAAGTTCATCATAATTTT-TTTGAGACTCTACTTCCCTCGTTGCTGCCTCCGCTTCAA
36149 GT
65 GT
36151 TG
1 TG
36153 AGCAATTTGC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 5 0.09
66 52 0.91
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.43
Consensus pattern (66 bp):
TGTAGCTGAAGTTCATCATAATTTTTTTGAGACTCTACTTCCCTCGTTGCTGCCTCCGCTTCAAG
T
Found at i:41857 original size:43 final size:41
Alignment explanation
Indices: 41779--41949 Score: 184
Period size: 43 Copynumber: 4.1 Consensus size: 41
41769 GTTTATTGGA
* ** *
41779 AAATGCCGCTATTACAATACCTTTAGCGGCGTTTTTCCCAT
1 AAATGCCGCTATTGCTTTACCTTTTGCGGCGTTTTTCCCAT
* * *
41820 AAATGCCGCTAATGCTTTGGACCTATTGCGGCGTTTTTCCTAT
1 AAATGCCGCTATTGCTTT--ACCTTTTGCGGCGTTTTTCCCAT
* * * *
41863 AAATGCCGCTATTGATTTACCTTTTGCGGCATTTATT--GAA
1 AAATGCCGCTATTGCTTTACCTTTTGCGGCGTTT-TTCCCAT
**
41903 AAACACCGCTATTGCTTTACCTTTTGCGGCGTTTTTCCCAT
1 AAATGCCGCTATTGCTTTACCTTTTGCGGCGTTTTTCCCAT
41944 AAATGC
1 AAATGC
41950 TATTATTGCT
Statistics
Matches: 104, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
39 2 0.02
40 31 0.30
41 33 0.32
42 2 0.02
43 36 0.35
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (41 bp):
AAATGCCGCTATTGCTTTACCTTTTGCGGCGTTTTTCCCAT
Found at i:41997 original size:29 final size:29
Alignment explanation
Indices: 41959--42018 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
41949 CTATTATTGC
41959 TTAACCTCAAAT-TTTTTTAAAAATTCTTA
1 TTAACCTCAAATATTTTTTAAAAATT-TTA
* *
41988 TTAATCTCAAATAATTTTTTAGAAATTTTA
1 TTAACCTCAAAT-ATTTTTTAAAAATTTTA
42018 T
1 T
42019 ATGAGCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 11 0.41
30 4 0.15
31 12 0.44
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (29 bp):
TTAACCTCAAATATTTTTTAAAAATTTTA
Found at i:46292 original size:71 final size:71
Alignment explanation
Indices: 46182--46328 Score: 161
Period size: 71 Copynumber: 2.1 Consensus size: 71
46172 CCTCCAAAGT
* * * * * *
46182 CAGTAGCCAAGGTCTTCTTTCCCCAGAACATCTACCGATAATTTGTTGAGTTATTTCGAAACAAC
1 CAGTAGCCAAGGTATCCTTTCCCCAGAACATCTACCGATAATCTATAGAGTTATTTCAAAACAAC
46247 TCAAGA
66 TCAAGA
* * * * * *
46253 CAGTAGCCAAGGTATCCTTTCCTCC-GTACTTCTATCGATACTCTATAGAGTTGTTTCAAAAGAA
1 CAGTAGCCAAGGTATCCTTTCC-CCAGAACATCTACCGATAATCTATAGAGTTATTTCAAAACAA
*
46317 CTCAAGT
65 CTCAAGA
46324 CAGTA
1 CAGTA
46329 TTGAAATGTA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
71 60 0.97
72 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (71 bp):
CAGTAGCCAAGGTATCCTTTCCCCAGAACATCTACCGATAATCTATAGAGTTATTTCAAAACAAC
TCAAGA
Found at i:46818 original size:24 final size:24
Alignment explanation
Indices: 46786--47152 Score: 313
Period size: 24 Copynumber: 15.3 Consensus size: 24
46776 ACAAATTCAT
* *
46786 TACGTTTACGCTTGCCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
*
46810 TACGTTTACGCTTGTCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
** **
46834 TACGTTTACGCTATTCAGCTTGCA
1 TACGTTTACGCTCGTCAGCTTATA
* *
46858 CACGTTTACGCTCGTTAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
* * * * *
46882 CACGTTTACACTTGTCATCTTACA
1 TACGTTTACGCTCGTCAGCTTATA
* *
46906 CACGTTTAAGCTCGTCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
* * **
46930 TACGTTTACGCTTGTTAGCTTGCA
1 TACGTTTACGCTCGTCAGCTTATA
* *
46954 CACGTTTACGCTCGTCAGCTTATT
1 TACGTTTACGCTCGTCAGCTTATA
*
46978 TACGTTTACTCTCGTCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
**
47002 TACGTTTACGCTCGTCAGCTTGCA
1 TACGTTTACGCTCGTCAGCTTATA
* * *
47026 CACGTTTACGCTCATTAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
* ** **
47050 TACATTTACGCTTTTCAGCTTGCA
1 TACGTTTACGCTCGTCAGCTTATA
* * * *
47074 CACATTTACGCTCATGAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
** * **
47098 TATTTTTACGCTCGTCTA-TTTGCA
1 TACGTTTACGCTCGTC-AGCTTATA
* * *
47122 CATGTTTACGCTCATCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
47146 TACGTTT
1 TACGTTT
47153 CCTTACTTTG
Statistics
Matches: 268, Mismatches: 73, Indels: 4
0.78 0.21 0.01
Matches are distributed among these distances:
23 1 0.00
24 266 0.99
25 1 0.00
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (24 bp):
TACGTTTACGCTCGTCAGCTTATA
Found at i:60199 original size:14 final size:15
Alignment explanation
Indices: 60170--60199 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
60160 ATTATTGTTG
60170 TAACTCCCTTGTCTA
1 TAACTCCCTTGTCTA
60185 TAACTCCCTTG-CTA
1 TAACTCCCTTGTCTA
60199 T
1 T
60200 GAGGAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (15 bp):
TAACTCCCTTGTCTA
Found at i:66564 original size:34 final size:34
Alignment explanation
Indices: 66521--66587 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
66511 CAATGGAGTC
66521 AGCTCATCATCTGTGAGATATTTTTTATTTAGTT
1 AGCTCATCATCTGTGAGATATTTTTTATTTAGTT
66555 AGCTCATCATCTGTGAGATATTTTTTATTTAGT
1 AGCTCATCATCTGTGAGATATTTTTTATTTAGT
66588 AAGTCCCACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (34 bp):
AGCTCATCATCTGTGAGATATTTTTTATTTAGTT
Found at i:69537 original size:13 final size:13
Alignment explanation
Indices: 69504--69537 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
69494 GGGACTGTGC
*
69504 TATAAAAAGTATT
1 TATAAAATGTATT
69517 TATAAAATGTATT
1 TATAAAATGTATT
*
69530 TATGAAAT
1 TATAAAAT
69538 ATTTAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (13 bp):
TATAAAATGTATT
Found at i:80839 original size:24 final size:24
Alignment explanation
Indices: 80800--80846 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
80790 TGGTTCGATG
** *
80800 GATAAAAAGAGGAAGAGGCACAAA
1 GATAAAAAGAAAAAGAAGCACAAA
80824 GATAAAAAGAAAAAGAAGCACAA
1 GATAAAAAGAAAAAGAAGCACAA
80847 GCAAGAGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.64, C:0.09, G:0.23, T:0.04
Consensus pattern (24 bp):
GATAAAAAGAAAAAGAAGCACAAA
Found at i:96786 original size:24 final size:24
Alignment explanation
Indices: 96745--96791 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
96735 GTTTAGAGTA
* *
96745 AAAATTGTCAGTGCAAATGTAATAT
1 AAAATTGTCAGAGAAAAT-TAATAT
96770 AAAA-TGTCAGAGAAAATTAATA
1 AAAATTGTCAGAGAAAATTAATA
96792 AAAGATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAATTGTCAGAGAAAATTAATAT
Found at i:98226 original size:15 final size:15
Alignment explanation
Indices: 98187--98236 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
98177 ACTTTTTATT
*
98187 TTTATTTTATTTTTCG
1 TTTA-TTTATTTTTGG
*
98203 TAT-TTTATTTCTT-G
1 TTTATTTATTT-TTGG
98217 TTTATTTATTTTTGG
1 TTTATTTATTTTTGG
98232 TTTAT
1 TTTAT
98237 GACTCAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 12 0.41
15 15 0.52
16 2 0.07
ACGTcount: A:0.14, C:0.04, G:0.08, T:0.74
Consensus pattern (15 bp):
TTTATTTATTTTTGG
Found at i:105987 original size:50 final size:50
Alignment explanation
Indices: 105928--106027 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
105918 AGTGACAAAA
105928 AAGAATTTACCTATAGAGTCTATTGTTTATATTGTTAAAGTCACTAACCC
1 AAGAATTTACCTATAGAGTCTATTGTTTATATTGTTAAAGTCACTAACCC
105978 AAGAATTTACCTATAGAGTCTATTGTTTATATTGTTAAAGTCACTAACCC
1 AAGAATTTACCTATAGAGTCTATTGTTTATATTGTTAAAGTCACTAACCC
106028 TTTAGGTCAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (50 bp):
AAGAATTTACCTATAGAGTCTATTGTTTATATTGTTAAAGTCACTAACCC
Found at i:107195 original size:68 final size:68
Alignment explanation
Indices: 107086--107221 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
107076 AAAAGTATGA
*
107086 ATTATAAAAGAGATTTTAATTGAAAAAAAGGGAAGGACCAATGGGGCAAATTCCCCTTTGGAATT
1 ATTATAAAAGAGATTTTAATTGAAAAAAAGGGAAGGACCAATGAGGCAAATTCCCCTTTGGAATT
107151 CAT
66 CAT
107154 ATTATAAAAGAGATTTTAATTGAAAAAAAGGGAAGGACCAATGAGGCAAATTCCCCTTTGGAATT
1 ATTATAAAAGAGATTTTAATTGAAAAAAAGGGAAGGACCAATGAGGCAAATTCCCCTTTGGAATT
107219 CAT
66 CAT
107222 TAGAGTCGTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (68 bp):
ATTATAAAAGAGATTTTAATTGAAAAAAAGGGAAGGACCAATGAGGCAAATTCCCCTTTGGAATT
CAT
Found at i:108717 original size:2 final size:2
Alignment explanation
Indices: 108712--108740 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
108702 TATATATATA
108712 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
108741 TGATGAAATG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:111461 original size:22 final size:22
Alignment explanation
Indices: 111431--111486 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
111421 TTAACTCACC
111431 ATTTCTGTAAC-CTACATAACATT
1 ATTT-TGTAACTCT-CATAACATT
* * *
111454 ATTTTGTAACTCTCCTCACTTT
1 ATTTTGTAACTCTCATAACATT
111476 ATTTTGTAACT
1 ATTTTGTAACT
111487 TTAATGATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.46
Consensus pattern (22 bp):
ATTTTGTAACTCTCATAACATT
Found at i:111877 original size:20 final size:20
Alignment explanation
Indices: 111848--111952 Score: 66
Period size: 20 Copynumber: 5.4 Consensus size: 20
111838 GCTACATCAG
*
111848 AAAATGATTTTAAAATTATT
1 AAAATTATTTTAAAATTATT
111868 AAAATTATTTTTTAAAA-TA-T
1 AAAATTA--TTTTAAAATTATT
*
111888 AAAATTA--TTAAATTTATTTT
1 AAAATTATTTTAAAATTA--TT
*
111908 AAAATTAATTT-AAA-TA-T
1 AAAATTATTTTAAAATTATT
111925 AAAA-T-TTTTAAAATTATTTT
1 AAAATTATTTTAAAATTA--TT
111945 AAAATTAT
1 AAAATTAT
111953 AATCATCATC
Statistics
Matches: 66, Mismatches: 4, Indels: 28
0.67 0.04 0.29
Matches are distributed among these distances:
15 3 0.05
16 9 0.14
17 9 0.14
20 29 0.44
21 5 0.08
22 11 0.17
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
AAAATTATTTTAAAATTATT
Found at i:111901 original size:37 final size:37
Alignment explanation
Indices: 111857--111953 Score: 117
Period size: 37 Copynumber: 2.6 Consensus size: 37
111847 GAAAATGATT
*
111857 TTAAAATTA-TTAAAATTATTTTTTAAAATATAAAATTA
1 TTAAAATTATTTAAAATTA-TATTT-AAATATAAAATTA
* *
111895 TTAAATTTATTTTAAAATTA-ATTTAAATATAAAATTT
1 TTAAAATTA-TTTAAAATTATATTTAAATATAAAATTA
111932 TTAAAATTATTTTAAAATTATA
1 TTAAAATTA-TTTAAAATTATA
111954 ATCATCATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
37 31 0.60
38 12 0.23
40 9 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
TTAAAATTATTTAAAATTATATTTAAATATAAAATTA
Found at i:111952 original size:11 final size:11
Alignment explanation
Indices: 111848--111952 Score: 64
Period size: 11 Copynumber: 9.7 Consensus size: 11
111838 GCTACATCAG
*
111848 AAAATGATTTT
1 AAAATTATTTT
111859 AAAATTA--TT
1 AAAATTATTTT
111868 AAAATTATTTTTT
1 AAAATTA--TTTT
111881 AAAA-TA---T
1 AAAATTATTTT
111888 AAAATTA--TT
1 AAAATTATTTT
*
111897 AAATTTATTTT
1 AAAATTATTTT
*
111908 AAAATTAATTT
1 AAAATTATTTT
*
111919 AAATATAAAATTTTT
1 AAA-AT--TA-TTTT
111934 AAAATTATTTT
1 AAAATTATTTT
111945 AAAATTAT
1 AAAATTAT
111953 AATCATCATC
Statistics
Matches: 75, Mismatches: 7, Indels: 24
0.71 0.07 0.23
Matches are distributed among these distances:
7 5 0.07
8 2 0.03
9 16 0.21
11 32 0.43
12 5 0.07
13 6 0.08
14 3 0.04
15 6 0.08
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:112697 original size:31 final size:30
Alignment explanation
Indices: 112662--112766 Score: 113
Period size: 32 Copynumber: 3.4 Consensus size: 30
112652 TTTTAAATTA
* *
112662 TTTAATAATTTTATTATGTCAAAAATATAAT
1 TTTAATAATTTTATTATTTTAAAAA-ATAAT
*
112693 TTTAATAGTTTTA-TATTTTAAAAAATAAT
1 TTTAATAATTTTATTATTTTAAAAAATAAT
* ** *
112722 TTAAATTTTTTTTTATATTTTTAAAAAATAAT
1 TTTAATAATTTTAT-TA-TTTTAAAAAATAAT
112754 TTTAATAATTTTA
1 TTTAATAATTTTA
112767 AAATCATTTG
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
29 14 0.23
30 9 0.15
31 14 0.23
32 23 0.38
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTAATAATTTTATTATTTTAAAAAATAAT
Found at i:116790 original size:30 final size:31
Alignment explanation
Indices: 116716--116793 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 31
116706 TATAAAATTA
* *
116716 GTACTCGAACTTTTTTATTTCTCTCAGATTG
1 GTACCCGAACTTTTTTTTTTCTCTCAGATTG
* *
116747 GTA-CCTAAATTTTTTTTTATC-CT-AGATTG
1 GTACCCGAACTTTTTTTTT-TCTCTCAGATTG
116776 GTACCCGAACTTTTTTTT
1 GTACCCGAACTTTTTTTT
116794 CCGTCCACTG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 9 0.23
30 25 0.64
31 5 0.13
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.50
Consensus pattern (31 bp):
GTACCCGAACTTTTTTTTTTCTCTCAGATTG
Found at i:117080 original size:20 final size:21
Alignment explanation
Indices: 117045--117102 Score: 91
Period size: 20 Copynumber: 2.8 Consensus size: 21
117035 TGTTTCGTTT
*
117045 TCACCATTGTTTTCCCTCACC
1 TCACCATCGTTTTCCCTCACC
117066 TCACCATCG-TTTCCCTCACC
1 TCACCATCGTTTTCCCTCACC
*
117086 TCACGATCGTTTTCCCT
1 TCACCATCGTTTTCCCT
117103 TTTTTCTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.14, C:0.43, G:0.07, T:0.36
Consensus pattern (21 bp):
TCACCATCGTTTTCCCTCACC
Found at i:117464 original size:16 final size:17
Alignment explanation
Indices: 117438--117470 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
117428 ATGTTTGTGA
117438 TTTTAAGGTTTAATGTT
1 TTTTAAGGTTTAATGTT
*
117455 TTTTAA-GTTTATTGTT
1 TTTTAAGGTTTAATGTT
117471 GTATATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (17 bp):
TTTTAAGGTTTAATGTT
Found at i:118757 original size:24 final size:24
Alignment explanation
Indices: 118696--118795 Score: 85
Period size: 24 Copynumber: 4.1 Consensus size: 24
118686 CTTCCAGATT
* * * *
118696 TTAGCTCATACGAGCACAGACAACA
1 TTAGCTCTTACGAGCCCAGA-ATCG
* * *
118721 TTATCTCTCACGAGCCCA-AGATGG
1 TTAGCTCTTACGAGCCCAGA-ATCG
*
118745 TTAGCTCTTACGAGCTCAGAATCG
1 TTAGCTCTTACGAGCCCAGAATCG
* *
118769 TTAGCTCTTACGAGCCTAGAATAG
1 TTAGCTCTTACGAGCCCAGAATCG
118793 TTA
1 TTA
118796 ACCAATATAC
Statistics
Matches: 59, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
24 44 0.75
25 15 0.25
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATCG
Found at i:138409 original size:17 final size:17
Alignment explanation
Indices: 138380--138413 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
138370 AACATCTTTG
138380 GTAAGCTTCATAGTTTA
1 GTAAGCTTCATAGTTTA
138397 GTAAG-TTCGATAGTTTA
1 GTAAGCTTC-ATAGTTTA
138414 AGGAGTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (17 bp):
GTAAGCTTCATAGTTTA
Found at i:140726 original size:38 final size:39
Alignment explanation
Indices: 140667--140761 Score: 138
Period size: 38 Copynumber: 2.4 Consensus size: 39
140657 TTTGTTTTTA
*
140667 AAAAGGAAGACTTATAACTCGGTAGAGC-AAGAGTGATT
1 AAAAGGAAGACTTATGACTCGGTAGAGCAAAGAGTGATT
* * *
140705 TAAAGGAAGATTTATGTCTCGGTAGAGCATAAGAGTGATT
1 AAAAGGAAGACTTATGACTCGGTAGAGCA-AAGAGTGATT
140745 AAAAGGAAGACTTATGA
1 AAAAGGAAGACTTATGA
140762 ACCTATGAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 24 0.50
40 24 0.50
ACGTcount: A:0.41, C:0.08, G:0.26, T:0.24
Consensus pattern (39 bp):
AAAAGGAAGACTTATGACTCGGTAGAGCAAAGAGTGATT
Found at i:142366 original size:60 final size:60
Alignment explanation
Indices: 142300--142414 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 60
142290 ATAAACAGTC
* *
142300 ATACAAACATAACAGTAAACATAACATACATAATTATGTATACATAACATACATACAAAT
1 ATACAAACATAACAGTAAACATAACATACATAATCATATATACATAACATACATACAAAT
*
142360 ATACAAACATAACAGTAAGCATAACATACATAATCATATATACATAACATACATA
1 ATACAAACATAACAGTAAACATAACATACATAATCATATATACATAACATACATA
142415 ACAGTATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.24
Consensus pattern (60 bp):
ATACAAACATAACAGTAAACATAACATACATAATCATATATACATAACATACATACAAAT
Found at i:142407 original size:23 final size:23
Alignment explanation
Indices: 142379--142447 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
142369 TAACAGTAAG
142379 CATAACATACATAATCATATATA
1 CATAACATACATAATCATATATA
*
142402 CATAACATACATAA-CA-GTAT-
1 CATAACATACATAATCATATATA
* *
142422 -ATAACATACATAATTATACATA
1 CATAACATACATAATCATATATA
142444 CATA
1 CATA
142448 TAGTAAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 13 0.34
20 1 0.03
21 5 0.13
22 2 0.05
23 17 0.45
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.29
Consensus pattern (23 bp):
CATAACATACATAATCATATATA
Found at i:142427 original size:10 final size:9
Alignment explanation
Indices: 142339--142447 Score: 72
Period size: 9 Copynumber: 12.3 Consensus size: 9
142329 ATAATTATGT
142339 ATACATAAC
1 ATACATAAC
142348 ATACAT-AC
1 ATACATAAC
142356 A-A-ATATAC
1 ATACATA-AC
*
142364 AAACATAAC
1 ATACATAAC
142373 AGTAAGCATAAC
1 A-T-A-CATAAC
142385 ATACAT-A-
1 ATACATAAC
*
142392 AT-CAT-AT
1 ATACATAAC
142399 ATACATAAC
1 ATACATAAC
142408 ATACATAAC
1 ATACATAAC
*
142417 AGTATATAAC
1 A-TACATAAC
*
142427 ATACATAATT
1 ATACATAA-C
142437 ATACAT-AC
1 ATACATAAC
142445 ATA
1 ATA
142448 TAGTAAAGAA
Statistics
Matches: 82, Mismatches: 6, Indels: 25
0.73 0.05 0.22
Matches are distributed among these distances:
6 6 0.07
7 5 0.06
8 13 0.16
9 31 0.38
10 18 0.22
11 2 0.02
12 7 0.09
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.26
Consensus pattern (9 bp):
ATACATAAC
Found at i:142427 original size:42 final size:45
Alignment explanation
Indices: 142339--142449 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 45
142329 ATAATTATGT
142339 ATACATAA-CATACATACAAATATACAAACATAACAGTAAGCATAAC
1 ATACATAATCATACATAC--ATATACAAACATAACAGTAAGCATAAC
* * *
142385 ATACATAATCATATATACATA-ACATACATAACAGT-A-TATAAC
1 ATACATAATCATACATACATATACAAACATAACAGTAAGCATAAC
*
142427 ATACATAATTATACATACATATA
1 ATACATAATCATACATACATATA
142450 GTAAAGAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
42 24 0.41
43 2 0.03
44 13 0.22
45 3 0.05
46 8 0.14
47 8 0.14
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.26
Consensus pattern (45 bp):
ATACATAATCATACATACATATACAAACATAACAGTAAGCATAAC
Found at i:142579 original size:30 final size:30
Alignment explanation
Indices: 142543--142606 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
142533 ACAAAAACAA
*
142543 AAAAAATAAAAGTTAGATATAATACGAATT
1 AAAAAATAAAAGTTAGATATAATACGAAAT
*
142573 AAAAAATAAAAGTTATATATAATACGAAAT
1 AAAAAATAAAAGTTAGATATAATACGAAAT
142603 AAAA
1 AAAA
142607 CAATCAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.25
Consensus pattern (30 bp):
AAAAAATAAAAGTTAGATATAATACGAAAT
Found at i:144759 original size:51 final size:51
Alignment explanation
Indices: 144704--144877 Score: 258
Period size: 51 Copynumber: 3.4 Consensus size: 51
144694 GAATTCATAT
* * * *** *
144704 TCACGATGACACTAAGTTATCGGACCTTTAATCCACCATGGATTCATTTAC
1 TCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATTTAC
*
144755 TCACGATGACACTTAGTCATCAGACTTTTAATCCGTAAAGGATTCATTTAC
1 TCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATTTAC
* *
144806 TGACGATGACACTTAGTCATCGAACTTTTAATCCGTAAAGGATTCATTTAC
1 TCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATTTAC
144857 TCACGATGACACTTAGTCATC
1 TCACGATGACACTTAGTCATC
144878 AAACCCTTTC
Statistics
Matches: 111, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 111 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
TCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATTTAC
Found at i:148863 original size:41 final size:41
Alignment explanation
Indices: 148808--148961 Score: 263
Period size: 41 Copynumber: 3.8 Consensus size: 41
148798 TACCTTTAAC
* * *
148808 CATATTCTCATTCTCATCTCGAGACATGAGTCTTCATTAAT
1 CATAATCTCATTCTCATTTCGAGACATGAGTCTTCATTATT
* *
148849 CAGAATCTCATTCTCATTTCGAGACATGAGTCTTCCTTATT
1 CATAATCTCATTCTCATTTCGAGACATGAGTCTTCATTATT
148890 CATAATCTCATTCTCATTTCGAGACATGAGTCTTCATTATT
1 CATAATCTCATTCTCATTTCGAGACATGAGTCTTCATTATT
148931 CATAATCTCATTCTCATTTCGAGACATGAGT
1 CATAATCTCATTCTCATTTCGAGACATGAGT
148962 ATTCCATTTA
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 106 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (41 bp):
CATAATCTCATTCTCATTTCGAGACATGAGTCTTCATTATT
Found at i:149378 original size:22 final size:21
Alignment explanation
Indices: 149331--149378 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
149321 AACTTTCATA
*
149331 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* * *
149352 TTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
149374 ATTAA
1 ATTAA
149379 TCAATATTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:151226 original size:38 final size:38
Alignment explanation
Indices: 151175--151250 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
151165 GATAAACGAG
151175 CATTTATGGCTCTCAATGCAAACAATAATTTTCGGCTT
1 CATTTATGGCTCTCAATGCAAACAATAATTTTCGGCTT
151213 CATTTATGGCTCTCAATGCAAACAATAATTTTCGGCTT
1 CATTTATGGCTCTCAATGCAAACAATAATTTTCGGCTT
151251 AGGGCATCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (38 bp):
CATTTATGGCTCTCAATGCAAACAATAATTTTCGGCTT
Found at i:155554 original size:41 final size:41
Alignment explanation
Indices: 155397--155554 Score: 246
Period size: 41 Copynumber: 3.9 Consensus size: 41
155387 CTCCTTTAAC
* * *
155397 CATATTCTCATTCTCATCTCGAGACATGAGTCTT-TCTTAAT
1 CATAATCTCATTCTCATTTCGAGACATGAGTCTTCT-TTATT
* *
155438 CAAAATCTCATTCTCATTTCGAGACATGAGTCTTCCTTATT
1 CATAATCTCATTCTCATTTCGAGACATGAGTCTTCTTTATT
155479 CATAATCTCATTCTCATTTCGAGACATGAGTCTTCTTTATT
1 CATAATCTCATTCTCATTTCGAGACATGAGTCTTCTTTATT
*
155520 CATAATCTCATTCTCATTTCAAGACATGAGTCTTC
1 CATAATCTCATTCTCATTTCGAGACATGAGTCTTC
155555 CATTTATAGA
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
41 108 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (41 bp):
CATAATCTCATTCTCATTTCGAGACATGAGTCTTCTTTATT
Found at i:155974 original size:22 final size:21
Alignment explanation
Indices: 155927--155974 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
155917 GACTTTCATA
*
155927 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* * *
155948 GTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
155970 ATTAA
1 ATTAA
155975 TCAATATTCT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:162754 original size:16 final size:16
Alignment explanation
Indices: 162733--162765 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
162723 AAAGAAAAGG
162733 AAGAAATAATCTCGCT
1 AAGAAATAATCTCGCT
162749 AAGAAATAATCTCGCT
1 AAGAAATAATCTCGCT
162765 A
1 A
162766 TTCAGGCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.24
Consensus pattern (16 bp):
AAGAAATAATCTCGCT
Found at i:174592 original size:20 final size:18
Alignment explanation
Indices: 174543--174593 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 18
174533 ATTCAAGTAA
*
174543 TTTACCTTTTATCAACAT
1 TTTACCTTTTATCAAAAT
174561 TTTACACTTTTACTCTAAAAT
1 TTTAC-CTTTTA-TC-AAAAT
174582 TTTACCTTTTAT
1 TTTACCTTTTAT
174594 TCAATTTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.17
19 7 0.24
20 8 0.28
21 9 0.31
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTACCTTTTATCAAAAT
Found at i:175131 original size:15 final size:15
Alignment explanation
Indices: 175095--175133 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
175085 TACTTATATT
*
175095 AAAATTTAATTAACC
1 AAAATTTAATTAAAC
**
175110 ATTATTTAATTAAAC
1 AAAATTTAATTAAAC
175125 AAAATTTAA
1 AAAATTTAA
175134 AAAAAGTGGA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTTAATTAAAC
Found at i:179846 original size:2 final size:2
Alignment explanation
Indices: 179839--179864 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
179829 ATTTATTGCA
179839 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
179865 TTGCTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:180532 original size:18 final size:18
Alignment explanation
Indices: 180498--180539 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
180488 ATGTACTAAA
*
180498 AAAT-AAAATGCAGTGAC
1 AAATAAAAATGCAATGAC
*
180515 AAATAAAAATTCAATGAC
1 AAATAAAAATGCAATGAC
*
180533 AACTAAA
1 AAATAAA
180540 TGAGATGCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.19
Consensus pattern (18 bp):
AAATAAAAATGCAATGAC
Found at i:189108 original size:13 final size:13
Alignment explanation
Indices: 189090--189115 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
189080 CCACATTTCC
189090 CATTTCAAATGTT
1 CATTTCAAATGTT
189103 CATTTCAAATGTT
1 CATTTCAAATGTT
189116 TCTTCTTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
CATTTCAAATGTT
Found at i:191762 original size:19 final size:20
Alignment explanation
Indices: 191736--191786 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
191726 ATTCAAGTAA
*
191736 TTTA-ACTTTTATC-AACAT
1 TTTACACTTTTATCTAAAAT
191754 TTTACACTTTTACTCTAAAAT
1 TTTACACTTTTA-TCTAAAAT
191775 TTTAC-CTTTTAT
1 TTTACACTTTTAT
191787 TCAATTTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.14
19 8 0.28
20 8 0.28
21 9 0.31
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTACACTTTTATCTAAAAT
Found at i:193292 original size:29 final size:30
Alignment explanation
Indices: 193260--193480 Score: 140
Period size: 30 Copynumber: 7.4 Consensus size: 30
193250 ATTTTGGTGC
*
193260 CAAAATATAATTTTT-GGAAGTTCAGGGGT
1 CAAAATCTAATTTTTAGGAAGTTCAGGGGT
*
193289 C-AAATCTAAATTTTTAGGAAGTTCAGAGGT
1 CAAAATCT-AATTTTTAGGAAGTTCAGGGGT
* * * *
193319 CAAATTCGAATTTTTGGGAAGTTC-GGCAGT
1 CAAAATCTAATTTTTAGGAAGTTCAGG-GGT
* * *
193349 -TAAATCTAAATTTTTAGAAAGTTTAGGGGT
1 CAAAATCT-AATTTTTAGGAAGTTCAGGGGT
193379 CAAAA-CTTAA--TTTACGGAAAGTT-AGGGGGT
1 CAAAATC-TAATTTTTA-GG-AAGTTCA-GGGGT
* * *
193409 CAAAA-CTTAATTTTTAGAAATTTTAGGGGT
1 CAAAATC-TAATTTTTAGGAAGTTCAGGGGT
* *
193439 CAAAATATAA-TTTT-GGAAAGTTTAGGGGT
1 CAAAATCTAATTTTTAGG-AAGTTCAGGGGT
* *
193468 TAAAATGTAATTT
1 CAAAATCTAATTT
193481 CTAAACAAAA
Statistics
Matches: 152, Mismatches: 23, Indels: 33
0.73 0.11 0.16
Matches are distributed among these distances:
28 10 0.07
29 38 0.25
30 88 0.58
31 12 0.08
32 4 0.03
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (30 bp):
CAAAATCTAATTTTTAGGAAGTTCAGGGGT
Found at i:193464 original size:60 final size:60
Alignment explanation
Indices: 193260--193466 Score: 215
Period size: 60 Copynumber: 3.5 Consensus size: 60
193250 ATTTTGGTGC
* * *
193260 CAAAATATAATTTTTGG-AAGTTCA-GGGGTCAAATCTAAATTTTTAGGAAGTTCAGAGGT
1 CAAAATATAATTTTTGGAAAGTT-AGGGGGTCAAATCTAAATTTTTAGAAAGTTTAGGGGT
* ** * * ** *
193319 CAAATTCGAATTTTTGGGAAGTTCGGCAGTTAAATCTAAATTTTTAGAAAGTTTAGGGGT
1 CAAAATATAATTTTTGGAAAGTTAGGGGGTCAAATCTAAATTTTTAGAAAGTTTAGGGGT
** * * *
193379 CAAAACT-TAATTTACGGAAAGTTAGGGGGTCAAAACTTAATTTTTAGAAATTTTAGGGGT
1 CAAAA-TATAATTTTTGGAAAGTTAGGGGGTCAAATCTAAATTTTTAGAAAGTTTAGGGGT
193439 CAAAATATAA-TTTTGGAAAGTTTAGGGG
1 CAAAATATAATTTTTGGAAAG-TTAGGGG
193467 TTAAAATGTA
Statistics
Matches: 119, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
59 23 0.19
60 95 0.80
61 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.34
Consensus pattern (60 bp):
CAAAATATAATTTTTGGAAAGTTAGGGGGTCAAATCTAAATTTTTAGAAAGTTTAGGGGT
Found at i:195240 original size:39 final size:39
Alignment explanation
Indices: 195192--195268 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
195182 GGATGAATGT
* *
195192 TTCAATCTGCCCCATGGTCGGGGTATGAGATTGGATGGC
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGC
* * *
195231 TTCACTCTGCCTCATGATCGGGGTAAGAGATTGTATGG
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGG
195269 TGTCCTCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.30
Consensus pattern (39 bp):
TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGC
Found at i:195794 original size:119 final size:122
Alignment explanation
Indices: 195418--196621 Score: 553
Period size: 123 Copynumber: 9.9 Consensus size: 122
195408 TTGTTACTTA
* * *
195418 TTTGACCCACTTCTCCGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCGCTTTGAGCTTC
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGG-TTGAAGTTTCACTCGCATTGAGCTTC
* * *
195483 ACTTCATTATTTTGGTCTACTTCTCTGTATCTCATTAGAAAGATGACCA-TTTCATTGT
65 GCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTT-ATTGT
* * * *
195541 TTTGACTCACTTCTCTATATCTTATCAAGAAGATGGGGTTTGAAGTTT-ATTTCGCATTGAGCTT
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGG-TTGAAGTTTCA-CTCGCATTGAGCTT
* * * * *
195605 CGCTTCACTGTTTTAGTCTACTTCTCTGTATCTCATCAGGAAGATGATCACTTCATTGT
64 CGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGT
* *
195664 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGG-T-AAGTTTCACTCACATTGAG-TTTG
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTGAAGTTTCACTCGCATTGAGCTTCG
** * * * * * * *
195726 CTTTGTTAATTTGGTCCACTTTTTTATATCTCATCAGGAAGATAACCACTTTATTAT
66 CTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGT
* * **** * * * * * * **
195783 TTTAACCCACTTCTCTGTATCTCATCAGGAAGATAACCACTTTATTATTTTAACCCACTTCTTTG
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGAT--GGGGTTGA--AGTTTCACTCGCAT-TGAG
* * ** * ** * * * * *
195848 -TATCTCATCAGGAAGATAGGGTTCGAAGTT-TC---AT-TCA-CATTG-AGCT--CCACTTCAT
61 CT-TCGCTTCA-TTA-TTTTGG-TC-TACTTCTCTGTATCTCATCA-GGAAGATGACCACTTTAT
*
195903 TGA
120 TGT
** * * * *** * * * ***
195906 TTTGGTCTACTTCTTTGTATCTTATCAAGAAGATGACCACTTTATTGTTTTGAC-C-CATTTTTC
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATG--GGGTTGA-AG-TTTCACTCGCATTGAGC
** * **** * ** * * * * * *
195969 TATATC-TCATCA-GGAAG-ATA-TGGTTTGAAGTTTCACTC--GCA-TTGAGCTTCACTTCATT
62 T-TCGCTTCATTATTTTGGTCTACTTCTCTGTA-TCTCA-TCAGGAAGATGA-C--CACTTTATT
196027 GT
121 GT
** * * * * * * *
196029 TTTGGTCTACTTCTCTATATCTCATCAGGAAGATGAGGTTTAAAGTTTCATTCGCATTGAGTTTC
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATG-GGGTTGAAGTTTCACTCGCATTGAGCTTC
* * *
196094 GCTTCATTGTTTTGGTCTACTTCTCTGTATTTCATCAGGAAGATGACCACTTCATTGT
65 GCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGT
* * * **
196152 TTTGACCCACTTTTGTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCATATTGAGCTTC
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGG-TTGAAGTTTCACTCGCATTGAGCTTC
* * * * * * * * *
196217 ACTTCATTGTTTTGGTCTACTTCTTTGTATCTAATTAAGAAGATGACCTCTTCATCGT
65 GCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGT
* * * *
196275 TTTAATCCACTTCTCTGTATCTCATCAGGAAGATAGGGGTTAGAAGTTTCACTCACATTGAGCTT
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGAT-GGGGTT-GAAGTTTCACTCGCATTGAGCTT
* * * * * * * *
196340 CGCTTCA-TAGATGTGGTCCACTTCTTTGTATGTCAACAAGAAGGTGA-C-C---A--G-
64 CGCTTCATTA-TTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGT
* * * * *
196391 -TT---CCACTCCTCTATATCTCCTCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTGC
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGG-TTGAAGTTTCACTCGCATTGAGCTTC
* * * * * *
196452 GCTTCGTTAATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACCGCTTCATTGT
65 GCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGT
* * * * * *
196510 TTTGATCCACTTCTCTATATCTGATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCC
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGG-TTGAAGTTTCACTCGCATTGAGCTTC
* *
196575 AG-TTCGTTGA-TTTGGT-TCACTTCTCTGTATCTAATCAGGAAGATGAC
65 -GCTTCATT-ATTTTGGTCT-ACTTCTCTGTATCTCATCAGGAAGATGAC
196622 TGCTTCATTT
Statistics
Matches: 840, Mismatches: 177, Indels: 128
0.73 0.15 0.11
Matches are distributed among these distances:
111 62 0.07
112 29 0.03
113 2 0.00
114 2 0.00
115 2 0.00
116 1 0.00
117 3 0.00
118 4 0.00
119 84 0.10
120 27 0.03
121 15 0.02
122 19 0.02
123 469 0.56
124 72 0.09
125 23 0.03
126 10 0.01
127 5 0.01
128 1 0.00
129 4 0.00
130 3 0.00
131 3 0.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (122 bp):
TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTGAAGTTTCACTCGCATTGAGCTTCG
CTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGT
Found at i:195812 original size:48 final size:48
Alignment explanation
Indices: 195752--195865 Score: 219
Period size: 48 Copynumber: 2.4 Consensus size: 48
195742 CACTTTTTTA
195752 TATCTCATCAGGAAGATAACCACTTTATTATTTTAACCCACTTCTCTG
1 TATCTCATCAGGAAGATAACCACTTTATTATTTTAACCCACTTCTCTG
*
195800 TATCTCATCAGGAAGATAACCACTTTATTATTTTAACCCACTTCTTTG
1 TATCTCATCAGGAAGATAACCACTTTATTATTTTAACCCACTTCTCTG
195848 TATCTCATCAGGAAGATA
1 TATCTCATCAGGAAGATA
195866 GGGTTCGAAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.37
Consensus pattern (48 bp):
TATCTCATCAGGAAGATAACCACTTTATTATTTTAACCCACTTCTCTG
Found at i:195983 original size:171 final size:167
Alignment explanation
Indices: 195624--195988 Score: 451
Period size: 171 Copynumber: 2.2 Consensus size: 167
195614 GTTTTAGTCT
* * * * *
195624 ACTTCTCTGTATCTCATCAGGAAGATGATCACTTCATTGTTTTGACCCACTTCTCTGTATCTCAT
1 ACTTCTCTATATCTCATCAGGAAGATAACCACTTCATTATTTTAACCCACTTCTCTGTATCTCAT
*** ** *
195689 CAAGAAGATGGGGTAAGTTTCACTCACATTGAGTTTGCTTTGTTAATTTGGTCCACTTTTTTATA
66 CAAGAAGATGGGGTAAGTTTCACTCACATTGAGTCCACTTCATTAATTTGGTCCACTTCTTTATA
*
195754 TCTCATCAGGAAGATAACCACTTTATTATTTTAACCC
131 TCTCATCAAGAAGATAACCACTTTATTATTTTAACCC
* * *
195791 ACTTCTCTGTATCTCATCAGGAAGATAACCACTTTATTATTTTAACCCACTTCTTTGTATCTCAT
1 ACTTCTCTATATCTCATCAGGAAGATAACCACTTCATTATTTTAACCCACTTCTCTGTATCTCAT
* * * * *
195856 CAGGAAGATAGGGTTCGAAGTTTCATTCACATTGAGCTCCACTTCATTGATTTGGTCTACTTCTT
66 CAAGAAGAT-GGGGT--AAGTTTCACTCACATTGAG-TCCACTTCATTAATTTGGTCCACTTCTT
* * * * *
195921 TGTATCTTATCAAGAAGATGACCACTTTATTGTTTTGACCC
127 TATATCTCATCAAGAAGATAACCACTTTATTATTTTAACCC
* *
195962 ATTTTTCTATATCTCATCAGGAAGATA
1 ACTTCTCTATATCTCATCAGGAAGATA
195989 TGGTTTGAAG
Statistics
Matches: 168, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
167 67 0.40
168 4 0.02
170 18 0.11
171 79 0.47
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (167 bp):
ACTTCTCTATATCTCATCAGGAAGATAACCACTTCATTATTTTAACCCACTTCTCTGTATCTCAT
CAAGAAGATGGGGTAAGTTTCACTCACATTGAGTCCACTTCATTAATTTGGTCCACTTCTTTATA
TCTCATCAAGAAGATAACCACTTTATTATTTTAACCC
Found at i:196069 original size:75 final size:76
Alignment explanation
Indices: 195967--196139 Score: 278
Period size: 75 Copynumber: 2.3 Consensus size: 76
195957 GACCCATTTT
*
195967 TCTATATCTCATCAGGAAGAT-ATGGTTTGAAGTTTCACTCGCATTGAGCTTCACTTCATTGTTT
1 TCTATATCTCATCAGGAAGATGATGGTTTAAAGTTTCACTCGCATTGAGCTTCACTTCATTGTTT
196031 TGGTCTACTTC
66 TGGTCTACTTC
* * *
196042 TCTATATCTCATCAGGAAGATGA-GGTTTAAAGTTTCATTCGCATTGAGTTTCGCTTCATTGTTT
1 TCTATATCTCATCAGGAAGATGATGGTTTAAAGTTTCACTCGCATTGAGCTTCACTTCATTGTTT
196106 TGGTCTACTTC
66 TGGTCTACTTC
* *
196117 TCTGTATTTCATCAGGAAGATGA
1 TCTATATCTCATCAGGAAGATGA
196140 CCACTTCATT
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
75 90 0.99
76 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (76 bp):
TCTATATCTCATCAGGAAGATGATGGTTTAAAGTTTCACTCGCATTGAGCTTCACTTCATTGTTT
TGGTCTACTTC
Found at i:196150 original size:48 final size:48
Alignment explanation
Indices: 196095--196186 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
196085 TTGAGTTTCG
** * *
196095 CTTCATTGTTTTGGTCTACTTCTCTGTATTTCATCAGGAAGATGACCA
1 CTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGACCA
* *
196143 CTTCATTGTTTTGACCCACTTTTGTGTATCTCATCAGGAAGATG
1 CTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAGGAAGATG
196187 GGGTTTGAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (48 bp):
CTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGACCA
Found at i:196261 original size:198 final size:199
Alignment explanation
Indices: 195839--196262 Score: 620
Period size: 198 Copynumber: 2.1 Consensus size: 199
195829 ATTTTAACCC
*
195839 ACTTCTTTGTATCTCATCAGGAAGAT-AGGGTTCGAAGTTTCATTCACATTGAGCTCCACTTCAT
1 ACTTCTTTGTATCTCATCAGGAAGATGAGGGTTCAAAGTTTCATTCACATTGAGCTCCACTTCAT
* * *
195903 TGATTTGGTCTACTTCTTTGTATCTTATCAAGAAGATGACCACTTTATTGTTTTGACCCATTTTT
66 TGATTTGGTCTACTTCTCTGTATCTTATCAAGAAGATGACCACTTCATTGTTTTGACCCACTTTT
* *
195968 CTATATCTCATCAGGAAGATATGGTTTGAAGTTTCACTCGCATTGAGCTTCACTTCATTGTTTTG
131 CTATATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGTTTTG
196033 GTCT
196 GTCT
* * * * * * *
196037 ACTTCTCTATATCTCATCAGGAAGATGA-GGTTTAAAGTTTCATTCGCATTGAGTTTCGCTTCAT
1 ACTTCTTTGTATCTCATCAGGAAGATGAGGGTTCAAAGTTTCATTCACATTGAGCTCCACTTCAT
* *
196101 TGTTTTGGTCTACTTCTCTGTAT-TTCATCAGGAAGATGACCACTTCATTGTTTTGACCCACTTT
66 TGATTTGGTCTACTTCTCTGTATCTT-ATCAAGAAGATGACCACTTCATTGTTTTGACCCACTTT
* * * *
196165 TGTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCATATTGAGCTTCACTTCATTGTTTT
130 TCTATATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGTTTT
196230 GGTCT
195 GGTCT
* * *
196235 ACTTCTTTGTATCTAATTAAGAAGATGA
1 ACTTCTTTGTATCTCATCAGGAAGATGA
196263 CCTCTTCATC
Statistics
Matches: 200, Mismatches: 24, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
197 2 0.01
198 197 0.99
199 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.41
Consensus pattern (199 bp):
ACTTCTTTGTATCTCATCAGGAAGATGAGGGTTCAAAGTTTCATTCACATTGAGCTCCACTTCAT
TGATTTGGTCTACTTCTCTGTATCTTATCAAGAAGATGACCACTTCATTGTTTTGACCCACTTTT
CTATATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGTTTTG
GTCT
Found at i:196926 original size:49 final size:49
Alignment explanation
Indices: 196873--197175 Score: 234
Period size: 49 Copynumber: 6.2 Consensus size: 49
196863 CATCTTCAGT
* * * *
196873 GTATAAGATTCACCGTTACGGCCTAAATCTTTCCCTTCACATCTCTAGG
1 GTATAAGATTCGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCTAAG
* * * * *
196922 GTATAAGGTTTGCCGTTGCGGCCTCAACCTTTCTCTTCACATCTTTAAG
1 GTATAAGATTCGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCTAAG
* ** ** * ** *
196971 GT-TCAAGATTCGTCGTTGCGGTTTCAATC-TGGCTTTCTTATTTCTAAG
1 GTAT-AAGATTCGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCTAAG
* * * * * *
197019 GTATAAGATTTGTCGTTGCGGCCTCAACCTTTTCCTTCTCATCTCTAGG
1 GTATAAGATTCGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCTAAG
* * * * * *
197068 GTACAAGATTCGTCATTACGGCCTTAATCTTTCCCTACACATAC-CTAAG
1 GTATAAGATTCGCCGTTGCGGCCTCAATCTTTCCCTTCACAT-CTCTAAG
** * * * *
197117 GTACGAGATTCGCCATTGCGGCCTCTATCTTTCCCTTCACATCTTTAAA
1 GTATAAGATTCGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCTAAG
*
197166 GTATATGATT
1 GTATAAGATT
197176 TGACATTTCC
Statistics
Matches: 195, Mismatches: 54, Indels: 10
0.75 0.21 0.04
Matches are distributed among these distances:
48 36 0.18
49 158 0.81
50 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.37
Consensus pattern (49 bp):
GTATAAGATTCGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCTAAG
Found at i:197097 original size:97 final size:97
Alignment explanation
Indices: 196916--197097 Score: 242
Period size: 97 Copynumber: 1.9 Consensus size: 97
196906 CCTTCACATC
* * * *
196916 TCTAGGGTATAAGGTTTGCCGTTGCGGCCTCAACCTTTCTCTTCACATCTTTAAGGTTCAAGATT
1 TCTAAGGTATAAGATTTGCCGTTGCGGCCTCAACCTTTCTCTTCACATCTCTAAGGTACAAGATT
* * *
196981 CGTCGTTGCGGTTTCAATCTGGCTTTCTTATT
66 CGTCATTACGGCTTCAATCTGGCTTTCTTATT
* * *
197013 TCTAAGGTATAAGATTTGTCGTTGCGGCCTCAACCTTT-TCCTTCTCATCTCTAGGGTACAAGAT
1 TCTAAGGTATAAGATTTGCCGTTGCGGCCTCAACCTTTCT-CTTCACATCTCTAAGGTACAAGAT
197077 TCGTCATTACGGCCTT-AATCT
65 TCGTCATTACGG-CTTCAATCT
197098 TTCCCTACAC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
96 1 0.01
97 70 0.96
98 2 0.03
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (97 bp):
TCTAAGGTATAAGATTTGCCGTTGCGGCCTCAACCTTTCTCTTCACATCTCTAAGGTACAAGATT
CGTCATTACGGCTTCAATCTGGCTTTCTTATT
Found at i:198024 original size:18 final size:17
Alignment explanation
Indices: 198003--198087 Score: 66
Period size: 18 Copynumber: 4.8 Consensus size: 17
197993 TGACCTCTCC
198003 TTTTTTCTTTTTTCCTCTT
1 TTTTTTCTTTTTT-C-CTT
* *
198022 TTTTTTGTTCTTTTTCTT
1 TTTTTTCTT-TTTTCCTT
*
198040 TTCTTTTCCTTTTTCCTT
1 TT-TTTTCTTTTTTCCTT
198058 CTTTTTTC-TTTTT-CTT
1 -TTTTTTCTTTTTTCCTT
*
198074 TTTCTCTCTTTTTT
1 TTT-TTTCTTTTTT
198088 TTTCTCTCTC
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
15 3 0.05
16 6 0.11
17 10 0.18
18 17 0.31
19 15 0.27
20 4 0.07
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTTTTTCCTT
Found at i:198027 original size:12 final size:12
Alignment explanation
Indices: 198010--198114 Score: 56
Period size: 12 Copynumber: 8.3 Consensus size: 12
198000 TCCTTTTTTC
198010 TTTTTTCCTCTT
1 TTTTTTCCTCTT
**
198022 TTTTTTGTTCTT
1 TTTTTTCCTCTT
*
198034 TTTCTTTTCT-TT
1 TTT-TTTCCTCTT
*
198046 TCCTTTTTCCT-TC
1 T--TTTTTCCTCTT
*
198059 TTTTTT-CTTTT
1 TTTTTTCCTCTT
198070 TCTTTTTCTCTCTTTT
1 T-TTTTTC-CTC--TT
198086 TTTTTCTCTCTCTT
1 TTTTT-TC-CTCTT
198100 TTTTTTCC-CTT
1 TTTTTTCCTCTT
198111 TTTT
1 TTTT
198115 GGGTAAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
10 2 0.03
11 14 0.19
12 22 0.29
13 13 0.17
14 11 0.15
15 4 0.05
16 9 0.12
ACGTcount: A:0.00, C:0.22, G:0.01, T:0.77
Consensus pattern (12 bp):
TTTTTTCCTCTT
Found at i:198035 original size:11 final size:11
Alignment explanation
Indices: 198005--198102 Score: 60
Period size: 10 Copynumber: 8.9 Consensus size: 11
197995 ACCTCTCCTT
198005 TTTTCTTTTT-
1 TTTTCTTTTTC
** *
198015 TCCTCTTTTTT
1 TTTTCTTTTTC
198026 TTGTTCTTTTTC
1 TT-TTCTTTTTC
*
198038 TTTTCTTTTCC
1 TTTTCTTTTTC
*
198049 TTTTTCCTTCTT-
1 -TTTT-CTTTTTC
198061 TTTTCTTTTTC
1 TTTTCTTTTTC
* *
198072 TTTT-TCTCTC
1 TTTTCTTTTTC
198082 TTTT-TTTTTC
1 TTTTCTTTTTC
*
198092 TCTCTCTTTTT
1 T-TTTCTTTTT
198103 TTTCCCTTTT
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
10 26 0.39
11 19 0.28
12 18 0.27
13 4 0.06
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:198052 original size:39 final size:37
Alignment explanation
Indices: 198005--198105 Score: 123
Period size: 39 Copynumber: 2.6 Consensus size: 37
197995 ACCTCTCCTT
*
198005 TTTTCTTTTTTCCTCTTTTTTTTGTTCTTTTTCTTTTC
1 TTTTCTTTTTTCCTCTTTTTTTTGTTCTTTTTC-TCTC
* *
198043 TTTTCCTTTTTCCTTCTTTTTTCTTTTTCTTTTTCTCTC
1 TTTTCTTTTTTCC-TCTTTTTT-TTGTTCTTTTTCTCTC
198082 TTTT-TTTTTCTCTCTCTTTTTTTT
1 TTTTCTTTTT-TC-CTCTTTTTTTT
198106 CCCTTTTTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
38 18 0.33
39 25 0.45
40 12 0.22
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (37 bp):
TTTTCTTTTTTCCTCTTTTTTTTGTTCTTTTTCTCTC
Found at i:198064 original size:23 final size:23
Alignment explanation
Indices: 198038--198087 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
198028 GTTCTTTTTC
198038 TTTTCTTTTCCTTTTTC-CTTCTT
1 TTTTCTTTTCCTTTTTCTC-TCTT
*
198061 TTTTCTTTTTCTTTTTCTCTCTT
1 TTTTCTTTTCCTTTTTCTCTCTT
198084 TTTT
1 TTTT
198088 TTTCTCTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTCTTTTCCTTTTTCTCTCTT
Found at i:198101 original size:49 final size:49
Alignment explanation
Indices: 198007--198103 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 49
197997 CTCTCCTTTT
* *
198007 TTCTTTTTTCCTCTTTTTTTTGTTCTTTTTCTTTTCTTTTCCTTTTTCC
1 TTCTTTTTTCCTCTTTTTTTTCTTCTTTTTCTTTTCTTCTCCTTTTTCC
* *
198056 TTCTTTTTT-CTTTTTCTTTTTCTCTCTTTTT-TTTTCTCTCTCTTTTTT
1 TTCTTTTTTCCTCTTT-TTTTTCT-TCTTTTTCTTTTCT-TCTCCTTTTT
198104 TTCCCTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
48 5 0.12
49 21 0.51
50 15 0.37
ACGTcount: A:0.00, C:0.22, G:0.01, T:0.77
Consensus pattern (49 bp):
TTCTTTTTTCCTCTTTTTTTTCTTCTTTTTCTTTTCTTCTCCTTTTTCC
Found at i:198103 original size:16 final size:15
Alignment explanation
Indices: 198005--198105 Score: 70
Period size: 16 Copynumber: 6.5 Consensus size: 15
197995 ACCTCTCCTT
198005 TTTTCTTTTTTC-CTC
1 TTTT-TTTTTTCTCTC
198020 TTTTTTTTGTTCT-T-
1 TTTTTTTT-TTCTCTC
198034 TTTCTTTTCTTT-TC-C
1 TTT-TTTT-TTTCTCTC
*
198049 TTTTTCCTTCTTT-TTTC
1 TTTTT--TT-TTTCTCTC
198066 TTTTTCTTTTTCTCTC
1 TTTTT-TTTTTCTCTC
198082 TTTTTTTTTCTCTCTC
1 TTTTTTTTT-TCTCTC
198098 TTTTTTTT
1 TTTTTTTT
198106 CCCTTTTTTG
Statistics
Matches: 73, Mismatches: 2, Indels: 21
0.76 0.02 0.22
Matches are distributed among these distances:
14 10 0.14
15 24 0.33
16 33 0.45
17 6 0.08
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (15 bp):
TTTTTTTTTTCTCTC
Found at i:199056 original size:17 final size:16
Alignment explanation
Indices: 199036--199100 Score: 51
Period size: 18 Copynumber: 3.7 Consensus size: 16
199026 CATCTCAACC
199036 CTTTTATTTTTCTTTTT
1 CTTTT-TTTTTCTTTTT
199053 CTTTTCTTTCTT-TCTTTT
1 CTTTT-TTT-TTCT-TTTT
*
199071 CTTTCTTTCTTTCTTTTCC
1 CTTT-TTT-TTTCTTTT-T
199090 CTTTTTTTTTC
1 CTTTTTTTTTC
199101 GACCTCTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
17 13 0.32
18 20 0.50
19 7 0.17
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (16 bp):
CTTTTTTTTTCTTTTT
Found at i:199064 original size:4 final size:4
Alignment explanation
Indices: 199050--199086 Score: 56
Period size: 4 Copynumber: 8.8 Consensus size: 4
199040 TATTTTTCTT
199050 TTTC TTTTC TTTC TTTC TTTTC TTTC TTTC TTTC TTT
1 TTTC -TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTT
199087 TCCCTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 23 0.74
5 8 0.26
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:199064 original size:9 final size:9
Alignment explanation
Indices: 199044--199088 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
199034 CCCTTTTATT
199044 TTTCTTTTTC
1 TTTC-TTTTC
199054 TTT-TCTTTC
1 TTTCT-TTTC
199063 TTTCTTTTC
1 TTTCTTTTC
199072 TTTC-TTTC
1 TTTCTTTTC
199080 TTTCTTTTC
1 TTTCTTTTC
199089 CCTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 9 0.28
9 19 0.59
10 4 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:199088 original size:13 final size:13
Alignment explanation
Indices: 199050--199086 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
199040 TATTTTTCTT
199050 TTTCTTTTCTTTC
1 TTTCTTTTCTTTC
199063 TTTCTTTTCTTTC
1 TTTCTTTTCTTTC
199076 TTTC-TTTCTTT
1 TTTCTTTTCTTT
199087 TCCCTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTCTTTTCTTTC
Found at i:201912 original size:32 final size:32
Alignment explanation
Indices: 201845--201906 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
201835 ATCAAAAATA
* *
201845 AAATAAATAAATAAACGAGATTAAATTTAGAAG
1 AAATAAATAAATAAAC-AGATTAAATTAAAAAG
201878 AAATAAA-AAATAAA-AGATTAAATTAAAAA
1 AAATAAATAAATAAACAGATTAAATTAAAAA
201907 AAGAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 13 0.48
32 7 0.26
33 7 0.26
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (32 bp):
AAATAAATAAATAAACAGATTAAATTAAAAAG
Found at i:202041 original size:30 final size:29
Alignment explanation
Indices: 201987--202221 Score: 111
Period size: 30 Copynumber: 7.9 Consensus size: 29
201977 GCCAAAACAT
*
201987 AATTTTTA-GATGTTCAGGGGTCAAATCTA
1 AATTTTTAGGAAGTTC-GGGGTCAAATCTA
*
202016 AATTTTTAGGAAGTTCGGAGGTCAAATATA
1 AATTTTTAGGAAGTTCGG-GGTCAAATCTA
* * * *
202046 AAATTTTGGGAAGTTAGGGGGTTAAATCTA
1 AATTTTTAGGAAGTT-CGGGGTCAAATCTA
* * * *
202076 AAGTTTT-GGAAAGTTCGAGGGTTAAAACTT
1 AATTTTTAGG-AAGTTCG-GGGTCAAATCTA
* * * * *
202106 AATTTGTGGGAAGTTTAGGGGTCAAAACTT
1 AATTTTTAGGAAG-TTCGGGGTCAAATCTA
* ** * * *
202136 AATTTTT-GGAAATTTTAGGGTTAAAACTT
1 AATTTTTAGG-AAGTTCGGGGTCAAATCTA
** *
202165 AATTTTT-GGAAAACTCGAGGGTCAAATCCA
1 AATTTTTAGG-AAGTTCG-GGGTCAAATCTA
202195 AATTTTT-GGAAAGTTCGCGGGGTCAAA
1 AATTTTTAGG-AAGTT--CGGGGTCAAA
202222 ATGCAATTTC
Statistics
Matches: 165, Mismatches: 30, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
29 41 0.25
30 107 0.65
31 15 0.09
32 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.34
Consensus pattern (29 bp):
AATTTTTAGGAAGTTCGGGGTCAAATCTA
Found at i:202067 original size:60 final size:59
Alignment explanation
Indices: 202002--202222 Score: 164
Period size: 60 Copynumber: 3.7 Consensus size: 59
201992 TTAGATGTTC
202002 AGGGGTCAAATCTAAATTTTTAGGAAGTTCG-GAGGTCAAATA-TAAAATTT-TGGGAAG-TT
1 AGGGGTCAAATCTAAATTTTT-GGAAGTTCGAG-GGTCAAA-ACT-AAATTTGTGGGAAGTTT
* * * *
202061 AGGGGGTTAAATCTAAAGTTTTGGAAAGTTCGAGGGTTAAAACTTAATTTGTGGGAAGTTT
1 A-GGGGTCAAATCTAAATTTTTGG-AAGTTCGAGGGTCAAAACTAAATTTGTGGGAAGTTT
* * * ** * * * ***
202122 AGGGGTCAAAACTTAATTTTTGGAAATTTTAGGGTTAAAACTTAATTT-TTGGAAAACT
1 AGGGGTCAAATCTAAATTTTTGGAAGTTCGAGGGTCAAAACTAAATTTGTGGGAAGTTT
* * *
202180 CGAGGGTCAAATCCAAATTTTTGGAAAGTTCGCGGGGTCAAAA
1 AG-GGGTCAAATCTAAATTTTTGG-AAGTTCG-AGGGTCAAAA
202223 TGCAATTTCA
Statistics
Matches: 129, Mismatches: 24, Indels: 16
0.76 0.14 0.09
Matches are distributed among these distances:
58 7 0.05
59 49 0.38
60 61 0.47
61 12 0.09
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.33
Consensus pattern (59 bp):
AGGGGTCAAATCTAAATTTTTGGAAGTTCGAGGGTCAAAACTAAATTTGTGGGAAGTTT
Found at i:202161 original size:29 final size:29
Alignment explanation
Indices: 202064--202176 Score: 127
Period size: 30 Copynumber: 3.8 Consensus size: 29
202054 GGAAGTTAGG
* * * **
202064 GGGTTAAATCTAAAGTTTTGGAAAGTTCGA
1 GGGTTAAAACTTAATTTTTGGAAA-TTTTA
* * *
202094 GGGTTAAAACTTAATTTGTGGGAAGTTTA
1 GGGTTAAAACTTAATTTTTGGAAATTTTA
*
202123 GGGGTCAAAACTTAATTTTTGGAAATTTTA
1 -GGGTTAAAACTTAATTTTTGGAAATTTTA
202153 GGGTTAAAACTTAATTTTTGGAAA
1 GGGTTAAAACTTAATTTTTGGAAA
202177 ACTCGAGGGT
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 25 0.36
30 44 0.64
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (29 bp):
GGGTTAAAACTTAATTTTTGGAAATTTTA
Found at i:202187 original size:59 final size:60
Alignment explanation
Indices: 202079--202211 Score: 153
Period size: 59 Copynumber: 2.2 Consensus size: 60
202069 AAATCTAAAG
* * ** **
202079 TTTTGGAAAGTTCGAGGGTTAAAACTTAATTTGTGGGAAGTTTAGGGGTCAAAACTTAAT
1 TTTTGGAAAGTTCGAGGGTTAAAACTTAATTTGTGGAAACTCGAGGGGTCAAAACCAAAT
** * *
202139 TTTTGGAAA-TTTTAGGGTTAAAACTTAATTTTTGGAAAACTCGA-GGGTCAAATCCAAAT
1 TTTTGGAAAGTTCGAGGGTTAAAACTTAATTTGTGG-AAACTCGAGGGGTCAAAACCAAAT
202198 TTTTGGAAAGTTCG
1 TTTTGGAAAGTTCG
202212 CGGGGTCAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
59 44 0.75
60 15 0.25
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.36
Consensus pattern (60 bp):
TTTTGGAAAGTTCGAGGGTTAAAACTTAATTTGTGGAAACTCGAGGGGTCAAAACCAAAT
Found at i:202363 original size:16 final size:16
Alignment explanation
Indices: 202342--202393 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
202332 ATTATTGGGA
*
202342 AAAATTGAAATAAATT
1 AAAATTGAAACAAATT
*
202358 AAAATT-AGCACAAATT
1 AAAATTGA-AACAAATT
*
202374 -AAATTGAAACAAATA
1 AAAATTGAAACAAATT
202389 AAAAT
1 AAAAT
202394 GAGGAAGGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (16 bp):
AAAATTGAAACAAATT
Found at i:203051 original size:8 final size:8
Alignment explanation
Indices: 203038--203073 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
203028 AAAAGAACTG
203038 ATGTATAT
1 ATGTATAT
203046 ATGTATAT
1 ATGTATAT
203054 ATGTATAT
1 ATGTATAT
203062 ATGTTATAT
1 ATG-TATAT
203071 ATG
1 ATG
203074 GGTATGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (8 bp):
ATGTATAT
Found at i:205732 original size:54 final size:54
Alignment explanation
Indices: 205674--205787 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 54
205664 GGTCATGAAG
** * *
205674 AACTCTAAA-AGAACAGAATGTATGATGAACTCTGAAGAAACAATATGTATGGCA
1 AACTCTAAAGA-AACAGAATGTATGACAAACTATGAAGAAACAATAGGTATGGCA
* * * **
205728 AACTCTAAAGAAATAGTATGTATGACAAACTATGAAGGAACGGTAGGTATGGCA
1 AACTCTAAAGAAACAGAATGTATGACAAACTATGAAGAAACAATAGGTATGGCA
205782 AACTCT
1 AACTCT
205788 GAAGGAAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 49 0.98
55 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (54 bp):
AACTCTAAAGAAACAGAATGTATGACAAACTATGAAGAAACAATAGGTATGGCA
Found at i:205756 original size:27 final size:27
Alignment explanation
Indices: 205674--205787 Score: 95
Period size: 27 Copynumber: 4.2 Consensus size: 27
205664 GGTCATGAAG
* **
205674 AACTCTAAA-AGAACAGAATGTATGATG
1 AACTCTAAAGA-AACAGTATGTATGACA
* * *
205701 AACTCTGAAGAAACAATATGTATGGCA
1 AACTCTAAAGAAACAGTATGTATGACA
*
205728 AACTCTAAAGAAATAGTATGTATGACA
1 AACTCTAAAGAAACAGTATGTATGACA
* * * * * *
205755 AACTATGAAGGAACGGTAGGTATGGCA
1 AACTCTAAAGAAACAGTATGTATGACA
205782 AACTCT
1 AACTCT
205788 GAAGGAAAAT
Statistics
Matches: 68, Mismatches: 18, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
27 67 0.99
28 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (27 bp):
AACTCTAAAGAAACAGTATGTATGACA
Found at i:205794 original size:27 final size:27
Alignment explanation
Indices: 205701--205791 Score: 110
Period size: 27 Copynumber: 3.4 Consensus size: 27
205691 ATGTATGATG
*
205701 AACTCTGAAGAAACAATATGTATGGCA
1 AACTCTGAAGAAACAGTATGTATGGCA
* * *
205728 AACTCTAAAGAAATAGTATGTATGACA
1 AACTCTGAAGAAACAGTATGTATGGCA
* * * *
205755 AACTATGAAGGAACGGTAGGTATGGCA
1 AACTCTGAAGAAACAGTATGTATGGCA
205782 AACTCTGAAG
1 AACTCTGAAG
205792 GAAAATGCCT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (27 bp):
AACTCTGAAGAAACAGTATGTATGGCA
Found at i:208263 original size:21 final size:21
Alignment explanation
Indices: 208237--208287 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
208227 ACAACCTAAA
208237 GGCCAAATTAAAGATGTCCTT
1 GGCCAAATTAAAGATGTCCTT
*
208258 GGCCAAATTAAAGATGTTCTT
1 GGCCAAATTAAAGATGTCCTT
*
208279 GTCCAAATT
1 GGCCAAATT
208288 GATAAGCCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (21 bp):
GGCCAAATTAAAGATGTCCTT
Found at i:213843 original size:24 final size:24
Alignment explanation
Indices: 213798--213844 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
213788 TGGTTCAACG
**
213798 GATAAAAAAAGGAAGAGGCACAAA
1 GATAAAAAAAGGAAGAAACACAAA
213822 GATAAAAAGAA-GAAGAAACACAA
1 GATAAAAA-AAGGAAGAAACACAA
213845 CGAAGAGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.66, C:0.09, G:0.21, T:0.04
Consensus pattern (24 bp):
GATAAAAAAAGGAAGAAACACAAA
Found at i:214632 original size:13 final size:13
Alignment explanation
Indices: 214594--214633 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
214584 AATGAGGAAA
214594 AGAAAAGAAAAA-
1 AGAAAAGAAAAAG
*
214606 AAAAAGAGAAAAAG
1 AGAAA-AGAAAAAG
214620 AGAAAAGAAAAAG
1 AGAAAAGAAAAAG
214633 A
1 A
214634 AATATTGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 16 0.67
14 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAAAG
Found at i:214633 original size:6 final size:6
Alignment explanation
Indices: 214591--214635 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
214581 GTGAATGAGG
*
214591 AAAAG- AAAAGA AAAAAA AAAGAGA AAAAGA GAAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAA-AGA AAAAGA -AAAAGA AAAAGA AA
214636 TATTGCTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 5 0.14
6 19 0.54
7 11 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:225512 original size:7 final size:7
Alignment explanation
Indices: 225500--225524 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
225490 ATTTAAATAT
225500 TCAACAC
1 TCAACAC
225507 TCAACAC
1 TCAACAC
225514 TCAACAC
1 TCAACAC
225521 TCAA
1 TCAA
225525 AACATTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (7 bp):
TCAACAC
Found at i:236028 original size:354 final size:354
Alignment explanation
Indices: 235379--236098 Score: 1080
Period size: 354 Copynumber: 2.0 Consensus size: 354
235369 AAGAAATGAC
* ** *
235379 TTAAGATGTTCTCTTGCATCTTCATAAGGTAAGCCCGCATATTGCTTATTTGAGTTAAGCATTTG
1 TTAAGATGCTCTCTTGCATCTTCATAAGGTAAGCCCGCATATTGCCCATTCGAGTTAAGCATTTG
* * * * *
235444 AAACATCACAGGCTTCAATTCAAAATTTCCAGCTTGTATAACTGGTCTAATAACCCCTGGTTGTA
66 AAACATCACAGACTTCAATTCAAAATTTCCAACTTGTATAACTGGTCTAACAACCCATGGTAGTA
* * * * *
235509 AATCATCGAGTATAGGAACAATGAATTCTCTGATTGTCTTGTTTTGCACCTGTTCTTCTTGTGAA
131 AATCATCGAGTACAGGAACAATGAATTCTCTAATTGCCCTGTTTTACACCTGTTCTTCTTGTGAA
* * *
235574 GGCGGTGTTATATTATTAAAGAGTGGTGGCTGCACTAGAGGAACAACATTTTGTGACAGCAATGG
196 GGCGATGGTATATTATTAAAGAGTGATGGCTGCACTAGAGGAACAACATTTTGTGACAGCAATGG
* * *
235639 TGGAATATCATTGTTATTTCCAACCATTTTTCTTTGTGCTTGCTTTTTCCTTCGAAGTGTCCTTT
261 TGGAATATCATTATTATTTCCAACCATTTTTCTTTGTGCTTGCTTTTTCCTCCGAAGTATCCTTT
** *
235704 CGAGTTTTGGATCAAAAGTAACAATATTG
326 CGAGTAATGGATCAAAACTAACAATATTG
*
235733 TTAAGATGCTCTCTTGCATCTTCATAAGGTAAGCTCGCATATTGCCCATTCGAGTTAAGCATTTG
1 TTAAGATGCTCTCTTGCATCTTCATAAGGTAAGCCCGCATATTGCCCATTCGAGTTAAGCATTTG
* * * * *
235798 AAACATCACCGATTTTAATTCAAAATTTTCAACTTGTATAGCTGGTCTAACAACCCATGGTAGTA
66 AAACATCACAGACTTCAATTCAAAATTTCCAACTTGTATAACTGGTCTAACAACCCATGGTAGTA
* *
235863 AATCATTGAGTACAGGAACAATGAATTCTCTAATTGCCCTGTTTTACACCTGTTCTTCTTGTGGA
131 AATCATCGAGTACAGGAACAATGAATTCTCTAATTGCCCTGTTTTACACCTGTTCTTCTTGTGAA
* * * *
235928 GGCGATGGTATATTATTAACGAGTTATGGCTGCATTAGAGGAACAACATTTTGTGACAGTAATGG
196 GGCGATGGTATATTATTAAAGAGTGATGGCTGCACTAGAGGAACAACATTTTGTGACAGCAATGG
* * *
235993 TGGTATATCATTATTATTTCCAGCCATTTTTCTTTGTGTTTGCTTTTTCCTCCGAAGTATCCTTT
261 TGGAATATCATTATTATTTCCAACCATTTTTCTTTGTGCTTGCTTTTTCCTCCGAAGTATCCTTT
236058 CGAGTAATGGATCAAAACTAACAATATTG
326 CGAGTAATGGATCAAAACTAACAATATTG
*
236087 TTAGGATTGCTC
1 TTAAGA-TGCTC
236099 CTTATGGACA
Statistics
Matches: 326, Mismatches: 39, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
354 321 0.98
355 5 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (354 bp):
TTAAGATGCTCTCTTGCATCTTCATAAGGTAAGCCCGCATATTGCCCATTCGAGTTAAGCATTTG
AAACATCACAGACTTCAATTCAAAATTTCCAACTTGTATAACTGGTCTAACAACCCATGGTAGTA
AATCATCGAGTACAGGAACAATGAATTCTCTAATTGCCCTGTTTTACACCTGTTCTTCTTGTGAA
GGCGATGGTATATTATTAAAGAGTGATGGCTGCACTAGAGGAACAACATTTTGTGACAGCAATGG
TGGAATATCATTATTATTTCCAACCATTTTTCTTTGTGCTTGCTTTTTCCTCCGAAGTATCCTTT
CGAGTAATGGATCAAAACTAACAATATTG
Found at i:237811 original size:28 final size:28
Alignment explanation
Indices: 237780--237845 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
237770 TGGCAGGGCT
* * *
237780 GACCATATATTATTCAGGCGGCAGAGTC
1 GACCATATATCATTCAAGCGGCAGAATC
* *
237808 GACCATATATCATTCAAGTGGTAGAATC
1 GACCATATATCATTCAAGCGGCAGAATC
237836 GACCATATAT
1 GACCATATAT
237846 AGAAACTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (28 bp):
GACCATATATCATTCAAGCGGCAGAATC
Found at i:240601 original size:48 final size:47
Alignment explanation
Indices: 240489--240606 Score: 114
Period size: 50 Copynumber: 2.4 Consensus size: 47
240479 AATTTACATG
* * * * *
240489 TATATATATTCTGTCTTTCTATCTGTTTGTGTATATATATTTTCTTT
1 TATATATATTCTTTCTATCTATATGTGTGTGCATATATATTTTCTTT
*
240536 TCATATATTCTTCCTTTCTATCTATATGTGTGTGCATATACT-TTTT-TTT
1 T-ATATA-TATT-CTTTCTATCTATATGTGTGTGCATATA-TATTTTCTTT
240585 ATATATATAATTCTTTCTATCT
1 -TATATAT-ATTCTTTCTATCT
240607 TACATATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
47 1 0.02
48 16 0.28
49 13 0.22
50 27 0.47
51 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.58
Consensus pattern (47 bp):
TATATATATTCTTTCTATCTATATGTGTGTGCATATATATTTTCTTT
Found at i:241744 original size:253 final size:247
Alignment explanation
Indices: 241285--241782 Score: 762
Period size: 253 Copynumber: 2.0 Consensus size: 247
241275 ACTCACATTC
*** * * * *
241285 GCTATTTTTTTTTTAAAAAATGAGAGCACTCTATAGTTTTCACCCAATTTTAACACACTTCATTT
1 GCTATTTTTTTAGAAAAAAATCAGAGCACTCTACAGTTTTCACCCAATTTTAACACACATCACTT
* *
241350 CTTTAGTTGGAATAATATCAAATATGTGGCGGGTTCGAAAACAGATATTTCATACTTTTTTCATA
66 CTTCAGTTGGAATAATATCAAATATGTGACGGGTTCGAAAACAGATATTTCATACTTTTTTCATA
*
241415 AAAATTTTGATTTATATTTAACTAATACTTATAAATATATTATATGAAGTGGGTTGTAGAACGGA
131 AAAATTTTGATTTATATTTAACTAATACTTATAAATATATTATATGAAGTGGGTCGTAGAACGGA
**
241480 TATAAAGGAAATTAGATGGGTCTGGAGACCCACGTGGGTGGTGAGACGGGTT
196 TATAAAGGAAATTAGATGGGTCTGGAGACCCACGTAAGTGGTGAGACGGGTT
*
241532 GCTATTTTTTTAGAAAAAAATCAGAGCACTCTACAGTTTTTCACCCAATTTTAACACTCATCACT
1 GCTATTTTTTTAGAAAAAAATCAGAGCACTCTACAG-TTTTCACCCAATTTTAACACACATCACT
* * *
241597 TCTTCAGTTGGAATAATGTCACATATGTGACGGGGTTCGAAGACAGATATTTCATACTTTTTTCA
65 TCTTCAGTTGGAATAATATCAAATATGTGAC-GGGTTCGAAAACAGATATTTCATACTTTTTTCA
* *
241662 TAAAAATTTTGATTTATATTTATTTAACTGATACTTATAAATATATTATATGAAGTGGGTCGTAT
129 TAAAAATTTTGA-TT-TA--TATTTAACTAATACTTATAAATATATTATATGAAGTGGGTCGTAG
* *
241727 AATGGATATAAAGGAAATTAGATGGGTCTGGAGACCCATGTAAGTGGTGAGACGGG
190 AACGGATATAAAGGAAATTAGATGGGTCTGGAGACCCACGTAAGTGGTGAGACGGG
241783 AATGGTTTTA
Statistics
Matches: 225, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
247 31 0.14
248 52 0.23
249 44 0.20
250 2 0.01
251 2 0.01
253 94 0.42
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (247 bp):
GCTATTTTTTTAGAAAAAAATCAGAGCACTCTACAGTTTTCACCCAATTTTAACACACATCACTT
CTTCAGTTGGAATAATATCAAATATGTGACGGGTTCGAAAACAGATATTTCATACTTTTTTCATA
AAAATTTTGATTTATATTTAACTAATACTTATAAATATATTATATGAAGTGGGTCGTAGAACGGA
TATAAAGGAAATTAGATGGGTCTGGAGACCCACGTAAGTGGTGAGACGGGTT
Found at i:241976 original size:53 final size:53
Alignment explanation
Indices: 241896--242003 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
241886 GATGCGGAGA
**
241896 AAGCACCCCGCACCCTCTTGCCCAATTGAGATCCCTAGATGCAGTTGAAGAGT
1 AAGCACCCCGCACCCTCCCGCCCAATTGAGATCCCTAGATGCAGTTGAAGAGT
241949 AAGCACCCCGCACCCTCCCGCCCAATTGAGATCCCTAGATGCAGTTGAAGAGT
1 AAGCACCCCGCACCCTCCCGCCCAATTGAGATCCCTAGATGCAGTTGAAGAGT
242002 AA
1 AA
242004 AATTATTTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (53 bp):
AAGCACCCCGCACCCTCCCGCCCAATTGAGATCCCTAGATGCAGTTGAAGAGT
Found at i:242595 original size:6 final size:6
Alignment explanation
Indices: 242584--242609 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
242574 CAAAAGGGAA
242584 GAAGAT GAAGAT GAAGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GA
242610 GAGGCGTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GAAGAT
Found at i:265074 original size:41 final size:41
Alignment explanation
Indices: 265019--265099 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
265009 AAGAAGTTAG
265019 ATATAAAGTTCCTTCAGTCTGGTCCATTAGTTGCAAGGTAT
1 ATATAAAGTTCCTTCAGTCTGGTCCATTAGTTGCAAGGTAT
265060 ATATAAAGTTCCTTCAGTCTGGTCCATTAGTTGCAAGGTA
1 ATATAAAGTTCCTTCAGTCTGGTCCATTAGTTGCAAGGTA
265100 GCTCTGCCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (41 bp):
ATATAAAGTTCCTTCAGTCTGGTCCATTAGTTGCAAGGTAT
Found at i:266479 original size:21 final size:21
Alignment explanation
Indices: 266455--266508 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
266445 AAAGTGACAA
*
266455 TTCTACCGATACAAGTGTCT-C
1 TTCTACCGATACAAGTCT-TAC
*
266476 TTCTACCGAAACAAGTCTTAC
1 TTCTACCGATACAAGTCTTAC
*
266497 TTCTACAGATAC
1 TTCTACCGATAC
266509 TAAAAAATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (21 bp):
TTCTACCGATACAAGTCTTAC
Found at i:276525 original size:18 final size:19
Alignment explanation
Indices: 276492--276527 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
276482 TACCTCAAAC
*
276492 CCCCAAACATTTTTACTTT
1 CCCCAAACACTTTTACTTT
276511 CCCCAAA-ACTTTTACTT
1 CCCCAAACACTTTTACTT
276528 CCCTCCCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.39
Consensus pattern (19 bp):
CCCCAAACACTTTTACTTT
Found at i:276680 original size:30 final size:30
Alignment explanation
Indices: 276645--276705 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
276635 AAAATTTTTT
*
276645 ATTTTCCCCCAAAACTTTTACT-TCCTCCC
1 ATTTTTCCCCAAAACTTTTACTCTCCTCCC
* *
276674 ATTTTTCCCTAAAACTTTTACTCTCCTTCC
1 ATTTTTCCCCAAAACTTTTACTCTCCTCCC
276704 AT
1 AT
276706 CCCACCCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (30 bp):
ATTTTTCCCCAAAACTTTTACTCTCCTCCC
Found at i:283443 original size:28 final size:28
Alignment explanation
Indices: 283411--283471 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
283401 GGGTAATCAA
*
283411 TGTAATTGGTGAAGTCTATTGAATATGG
1 TGTAATTGGTGAAGTCTACTGAATATGG
* *
283439 TGTAATTGGTGAGGTCTACTGAATTTGG
1 TGTAATTGGTGAAGTCTACTGAATATGG
283467 TGTAA
1 TGTAA
283472 CTGGAGAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.05, G:0.30, T:0.39
Consensus pattern (28 bp):
TGTAATTGGTGAAGTCTACTGAATATGG
Found at i:284758 original size:20 final size:20
Alignment explanation
Indices: 284698--284758 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
284688 AAAAGGATAA
* * *
284698 AATCAAGTTTAAATGGTTTC
1 AATCAAGTTAAAATTGTTTT
**
284718 AATTGAGTTAAACA-T-TTTT
1 AATCAAGTTAAA-ATTGTTTT
284737 AATCAAGTTAAAATTGTTTT
1 AATCAAGTTAAAATTGTTTT
284757 AA
1 AA
284759 AACAAGTTAG
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
20 15 0.48
21 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (20 bp):
AATCAAGTTAAAATTGTTTT
Found at i:288424 original size:37 final size:39
Alignment explanation
Indices: 288383--288458 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 39
288373 GAGGGTTGAG
288383 TCTTAAG-GTTTGGGTAGAAA-CATTAAGGGAG-TTGTAA
1 TCTTAAGAGTTTGGGTAGAAATC-TTAAGGGAGATTGTAA
*
288420 TCTTAAGATTTTGGGTAGAAATCTTAAGGGAGATTGTAA
1 TCTTAAGAGTTTGGGTAGAAATCTTAAGGGAGATTGTAA
288459 GGTTAAACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
37 7 0.20
38 21 0.60
39 7 0.20
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (39 bp):
TCTTAAGAGTTTGGGTAGAAATCTTAAGGGAGATTGTAA
Found at i:293605 original size:167 final size:168
Alignment explanation
Indices: 293323--293664 Score: 677
Period size: 167 Copynumber: 2.0 Consensus size: 168
293313 ATTTGAGATG
293323 AAAGATCTTGAAAAAACAATATTTTGTCTTGGCCTGCAGATCAAGCATTTAAAAGATGGAATTCA
1 AAAGATCTTGAAAAAACAATATTTTGTCTTGGCCTGCAGATCAAGCATTTAAAAGATGGAATTCA
293388 TGTCCATCAGTCAACTTATACGGAAAAGATATTAAAGAAATTTTATATGGATAAAGCACATTCAT
66 TGTCCATCAGTCAACTTATACGGAAAAGATATTAAAGAAATTTTATATGGATAAAGCACATTCAT
293453 TGAGTACCCTGATGGTTGTAAGATCGTTAGATGTGAAT
131 TGAGTACCCTGATGGTTGTAAGATCGTTAGATGTGAAT
293491 AAAGA-CTTGAAAAAACAATATTTTGTCTTGGCCTGCAGATCAAGCATTTAAAAGATGGAATTCA
1 AAAGATCTTGAAAAAACAATATTTTGTCTTGGCCTGCAGATCAAGCATTTAAAAGATGGAATTCA
293555 TGTCCATCAGTCAACTTATACGGAAAAGATATTAAAGAAATTTTATATGGATAAAGCACATTCAT
66 TGTCCATCAGTCAACTTATACGGAAAAGATATTAAAGAAATTTTATATGGATAAAGCACATTCAT
293620 TGAGTACCCTGATGGTTGTAAGATCGTTAGATGTGAAT
131 TGAGTACCCTGATGGTTGTAAGATCGTTAGATGTGAAT
293658 AAAGATC
1 AAAGATC
293665 AATTTCGTCC
Statistics
Matches: 173, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
167 167 0.97
168 6 0.03
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (168 bp):
AAAGATCTTGAAAAAACAATATTTTGTCTTGGCCTGCAGATCAAGCATTTAAAAGATGGAATTCA
TGTCCATCAGTCAACTTATACGGAAAAGATATTAAAGAAATTTTATATGGATAAAGCACATTCAT
TGAGTACCCTGATGGTTGTAAGATCGTTAGATGTGAAT
Found at i:295203 original size:11 final size:11
Alignment explanation
Indices: 295187--295214 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
295177 TTACATGGAA
295187 AATTACGATAT
1 AATTACGATAT
295198 AATTACGATAT
1 AATTACGATAT
295209 AATTAC
1 AATTAC
295215 ACTTTATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (11 bp):
AATTACGATAT
Found at i:295673 original size:25 final size:24
Alignment explanation
Indices: 295612--295675 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
295602 GGCACCTAGT
* *
295612 CCCAATGCCTGTTGCCGCTGCTGC
1 CCCAATGCATGCTGCCGCTGCTGC
* *
295636 CCCAAT-TACTGCTGCCGTGTGCTGC
1 CCCAATGCA-TGCTGCCG-CTGCTGC
295661 CCCAATGCATGCTGC
1 CCCAATGCATGCTGC
295676 TACTTGCATG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 13 0.41
25 18 0.56
26 1 0.03
ACGTcount: A:0.12, C:0.39, G:0.23, T:0.25
Consensus pattern (24 bp):
CCCAATGCATGCTGCCGCTGCTGC
Found at i:297417 original size:128 final size:128
Alignment explanation
Indices: 297182--297440 Score: 421
Period size: 128 Copynumber: 2.0 Consensus size: 128
297172 GAGGAAAAAA
* *
297182 ATGATATTTACTTGTGTTTTTAATAAAAATCAAGGGTTCATGCATACTAAATAATACTCATAGCA
1 ATGATATTTACTTATGTTTTTAATAAAAATCAAGGGCTCATGCATACTAAATAATACTCATAGCA
297247 TAATATCTTAAAAGATCAAATAAAATATCATGCAAAAAAAAGCAAACCTAAACCCTAAATCTC
66 TAATATCTTAAAAGATCAAATAAAATATCATGCAAAAAAAAGCAAACCTAAACCCTAAATCTC
**
297310 ATGATATTTACTTATGTTTTTAATAAAAATCGGGGGCTCATGCATACTAAATAATACTCATAGCA
1 ATGATATTTACTTATGTTTTTAATAAAAATCAAGGGCTCATGCATACTAAATAATACTCATAGCA
* * * * *
297375 TAATATCTTAAAAG-TACAAATAAAATGTCATGTAAAATAAAGCAAATCTAAATCCTAAATCTC
66 TAATATCTTAAAAGAT-CAAATAAAATATCATGCAAAAAAAAGCAAACCTAAACCCTAAATCTC
297438 ATG
1 ATG
297441 CCATAGTTCA
Statistics
Matches: 121, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
127 1 0.01
128 120 0.99
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.31
Consensus pattern (128 bp):
ATGATATTTACTTATGTTTTTAATAAAAATCAAGGGCTCATGCATACTAAATAATACTCATAGCA
TAATATCTTAAAAGATCAAATAAAATATCATGCAAAAAAAAGCAAACCTAAACCCTAAATCTC
Found at i:297819 original size:2 final size:2
Alignment explanation
Indices: 297812--297842 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
297802 ATACTTACAT
297812 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
297843 TATATTTACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:299051 original size:26 final size:26
Alignment explanation
Indices: 299020--299108 Score: 74
Period size: 25 Copynumber: 3.5 Consensus size: 26
299010 TTTAGCTCAA
* * *
299020 ACGAGCCCAGATAGAGTTTAGCTCTT
1 ACGAGCCCAAACAGAGTATAGCTCTT
* *
299046 ATGAGCCCAAACAGAGTATCGCTCTT
1 ACGAGCCCAAACAGAGTATAGCTCTT
* ** * *
299072 ACGAG-CCAGACAGAACATCGCTATT
1 ACGAGCCCAAACAGAGTATAGCTCTT
299097 ACGAG-CCAAACA
1 ACGAGCCCAAACA
299109 AAATATCACT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 27 0.52
26 25 0.48
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (26 bp):
ACGAGCCCAAACAGAGTATAGCTCTT
Found at i:299091 original size:25 final size:25
Alignment explanation
Indices: 299040--299108 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
299030 ATAGAGTTTA
* **
299040 GCTCTTATGAGCCCAAACAGAGTATC
1 GCTCTTACGAG-CCAAACAGAACATC
*
299066 GCTCTTACGAGCCAGACAGAACATC
1 GCTCTTACGAGCCAAACAGAACATC
*
299091 GCTATTACGAGCCAAACA
1 GCTCTTACGAGCCAAACA
299109 AAATATCACT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 27 0.73
26 10 0.27
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (25 bp):
GCTCTTACGAGCCAAACAGAACATC
Found at i:299123 original size:25 final size:25
Alignment explanation
Indices: 299052--299140 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
299042 TCTTATGAGC
* *
299052 CCAAACAGAGTATCGCTCTTACGAG
1 CCAAACAGAATATCGCTATTACGAG
* *
299077 CCAGACAGAACATCGCTATTACGAG
1 CCAAACAGAATATCGCTATTACGAG
* * *
299102 CCAAACAAAATATCACTTTTAC-ATG
1 CCAAACAGAATATCGCTATTACGA-G
*
299127 CCAAATAGAATATC
1 CCAAACAGAATATC
299141 TTCAGCGTCT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 1 0.02
25 51 0.98
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.21
Consensus pattern (25 bp):
CCAAACAGAATATCGCTATTACGAG
Found at i:304690 original size:22 final size:22
Alignment explanation
Indices: 304642--304690 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
304632 TTTATCATTA
* *
304642 AACTTAATTAATCATTTTCTTT
1 AACTTAATTAATCACTATCTTT
304664 AACTTAATTAATACACTAT-TTT
1 AACTTAATTAAT-CACTATCTTT
*
304686 CACTT
1 AACTT
304691 TAATATCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (22 bp):
AACTTAATTAATCACTATCTTT
Found at i:307795 original size:53 final size:53
Alignment explanation
Indices: 307715--307818 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
307705 CCTTAACTCT
307715 TTCAATTCAGTAGATGACATCCTATACGGTGGAATTGAAATCGGTACAGTTCC
1 TTCAATTCAGTAGATGACATCCTATACGGTGGAATTGAAATCGGTACAGTTCC
*
307768 TTCAATTCAGTAGATGACATCTTATACGGTGGAATTGAAATCGGTACAGTT
1 TTCAATTCAGTAGATGACATCCTATACGGTGGAATTGAAATCGGTACAGTT
307819 TCAAGTACTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (53 bp):
TTCAATTCAGTAGATGACATCCTATACGGTGGAATTGAAATCGGTACAGTTCC
Found at i:314285 original size:51 final size:51
Alignment explanation
Indices: 314094--314282 Score: 261
Period size: 51 Copynumber: 3.7 Consensus size: 51
314084 TCATATAGGA
* ** * * *
314094 ATTCATATACTCACAATGACACAAAGTCATCGGACCCTTAATCCATCATGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCCTTAATCCGTAAAGG
* * *
314145 ATTCATTTACTCACGATAACACTTAGTCATTGGACCCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCCTTAATCCGTAAAGG
* *
314196 ATTCATATACTCACGATGACACTTAGTCATCGCACCTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCCTTAATCCGTAAAGG
* *
314247 ATTCATTTACTCATGATGACACTTAGTCATCGGACC
1 ATTCATATACTCACGATGACACTTAGTCATCGGACC
314283 TTTTCCTTTA
Statistics
Matches: 121, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 121 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCCTTAATCCGTAAAGG
Found at i:318061 original size:15 final size:15
Alignment explanation
Indices: 318033--318076 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
318023 CTAACTTCGG
318033 TTAATTACACTTAAGGT
1 TTAATTA-A-TTAAGGT
*
318050 TTAATTAATTAAGTT
1 TTAATTAATTAAGGT
*
318065 TTTATTAATTAA
1 TTAATTAATTAA
318077 TTATGATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 17 0.68
16 1 0.04
17 7 0.28
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (15 bp):
TTAATTAATTAAGGT
Found at i:320683 original size:21 final size:22
Alignment explanation
Indices: 320637--320698 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
320627 CGATCTGAGG
*
320637 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
320658 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATAGAATT
*
320680 AAAAGA-AATAGAAAATAGA
1 AAAA-ATAAAAGAAAATAGA
320699 GGTGTCGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:323223 original size:41 final size:41
Alignment explanation
Indices: 323166--323253 Score: 176
Period size: 41 Copynumber: 2.1 Consensus size: 41
323156 TTTATTTTGA
323166 TACATAAATTTATTAAATAAGTCATCTATAAAATAAAAATT
1 TACATAAATTTATTAAATAAGTCATCTATAAAATAAAAATT
323207 TACATAAATTTATTAAATAAGTCATCTATAAAATAAAAATT
1 TACATAAATTTATTAAATAAGTCATCTATAAAATAAAAATT
323248 TACATA
1 TACATA
323254 TAAGAAAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.36
Consensus pattern (41 bp):
TACATAAATTTATTAAATAAGTCATCTATAAAATAAAAATT
Found at i:323917 original size:17 final size:18
Alignment explanation
Indices: 323895--323928 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
323885 GTAAGGATCA
323895 CAAAAA-AAAAAAAAAAG
1 CAAAAATAAAAAAAAAAG
323912 CAAAAATAAAAAAAAAA
1 CAAAAATAAAAAAAAAA
323929 AAGAATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.88, C:0.06, G:0.03, T:0.03
Consensus pattern (18 bp):
CAAAAATAAAAAAAAAAG
Found at i:324276 original size:3 final size:3
Alignment explanation
Indices: 324268--324303 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
324258 TCATTCACAC
324268 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
324304 ATTACTTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:325347 original size:7 final size:7
Alignment explanation
Indices: 325337--325385 Score: 80
Period size: 7 Copynumber: 7.0 Consensus size: 7
325327 CCCTTTCCTT
325337 CTTTCTC
1 CTTTCTC
325344 CTTTCTC
1 CTTTCTC
325351 CTTTCTC
1 CTTTCTC
*
325358 CTTTATC
1 CTTTCTC
325365 CTTTCTC
1 CTTTCTC
*
325372 CTTTATC
1 CTTTCTC
325379 CTTTCTC
1 CTTTCTC
325386 GTTTTCAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.04, C:0.39, G:0.00, T:0.57
Consensus pattern (7 bp):
CTTTCTC
Found at i:325356 original size:14 final size:14
Alignment explanation
Indices: 325337--325385 Score: 89
Period size: 14 Copynumber: 3.5 Consensus size: 14
325327 CCCTTTCCTT
*
325337 CTTTCTCCTTTCTC
1 CTTTCTCCTTTATC
325351 CTTTCTCCTTTATC
1 CTTTCTCCTTTATC
325365 CTTTCTCCTTTATC
1 CTTTCTCCTTTATC
325379 CTTTCTC
1 CTTTCTC
325386 GTTTTCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.04, C:0.39, G:0.00, T:0.57
Consensus pattern (14 bp):
CTTTCTCCTTTATC
Done.