Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001174.1 Hibiscus syriacus cultivar Beakdansim tig00002338_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: 2182627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2113333 original size:24 final size:24
Alignment explanation
Indices: 2113306--2113355 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2113296 TTGATTTCAC
*
2113306 ATTAAATATCA-TATAATATTTTAT
1 ATTAAATAACATTA-AATATTTTAT
*
2113330 ATTACATAACATTAAATATTTTAT
1 ATTAAATAACATTAAATATTTTAT
2113354 AT
1 AT
2113356 ATAACTGCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTAAATAACATTAAATATTTTAT
Found at i:2115201 original size:2 final size:2
Alignment explanation
Indices: 2115194--2115228 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2115184 GTATTCACCC
2115194 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2115229 ACGTTAAATC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2116061 original size:2 final size:2
Alignment explanation
Indices: 2116054--2116094 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2116044 GTAAAGATTC
2116054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2116095 CATGGTGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2118448 original size:74 final size:74
Alignment explanation
Indices: 2118309--2118478 Score: 215
Period size: 74 Copynumber: 2.3 Consensus size: 74
2118299 GTAATTGTTC
* * *
2118309 CTAATAACAAGTATTAAAAAATATATAAATTTTAAGGGTAGCTCATAATAACAAGTATTAGAAAA
1 CTAATAACAAATATTAAAAAATATATAAATTTTAAGAGTAGCTCATAATAACAAATATTAGAAAA
2118374 AAT-GAGTCT
66 AATAGA-TCT
* *
2118383 CTAATAACAAATATTAAAGAAA-A-AGTAAATTTTAAGAGTATGTTTATAATAACAAATATTA-A
1 CTAATAACAAATATTAAA-AAATATA-TAAATTTTAAGAGTA-GCTCATAATAACAAATATTAGA
2118445 AAAAATAGATCT
63 AAAAATAGATCT
2118457 CTAATAA-AAAGTATTAAAAAAT
1 CTAATAACAAA-TATTAAAAAAT
2118479 TGGACTCCTA
Statistics
Matches: 85, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
73 7 0.08
74 56 0.66
75 22 0.26
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.30
Consensus pattern (74 bp):
CTAATAACAAATATTAAAAAATATATAAATTTTAAGAGTAGCTCATAATAACAAATATTAGAAAA
AATAGATCT
Found at i:2118489 original size:29 final size:29
Alignment explanation
Indices: 2118429--2118498 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
2118419 AGTATGTTTA
2118429 TAATAACAAATATTAAAAAAATAGATCTC
1 TAATAACAAATATTAAAAAAATAGATCTC
* *
2118458 TAATAA-AAAGTATTAAAAAATTGGA-CTCC
1 TAATAACAAA-TATTAAAAAAATAGATCT-C
2118487 TAATAACAAATA
1 TAATAACAAATA
2118499 AATATTAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 5 0.14
29 28 0.78
30 3 0.08
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (29 bp):
TAATAACAAATATTAAAAAAATAGATCTC
Found at i:2118545 original size:108 final size:110
Alignment explanation
Indices: 2118410--2118608 Score: 255
Period size: 108 Copynumber: 1.8 Consensus size: 110
2118400 AGAAAAAGTA
* * *
2118410 AATTTTAAGAGTATGTTTATAATAACAAATATTAAAAAAATAGAT-CTCTA-ATAAAAAGTATT-
1 AATTTTAAAAGTATGCTCATAATAACAAATATTAAAAAAAT-GATGC-CTAGATAAAAAGTATTA
2118472 AA-AAAATTGGACTCC-TAATAACAAATAAATATTAGAAAGGAAATTG
64 AAGAAAATTGGAC-CCTTAATAACAAATAAATATTAGAAAGGAAATTG
* * * * *
2118518 AATTTTAAAAGTATGCTCCTAATAACAAATTTTGAAAAAATTATGCCTATGATAATAAGTATTAA
1 AATTTTAAAAGTATGCTCATAATAACAAATATTAAAAAAATGATGCCTA-GATAAAAAGTATTAA
2118583 AGAAAATTGGACCCTTAATAACAAAT
65 AGAAAATTGGACCCTTAATAACAAAT
2118609 GTTAGAAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
107 5 0.06
108 36 0.47
109 11 0.14
110 4 0.05
111 21 0.27
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (110 bp):
AATTTTAAAAGTATGCTCATAATAACAAATATTAAAAAAATGATGCCTAGATAAAAAGTATTAAA
GAAAATTGGACCCTTAATAACAAATAAATATTAGAAAGGAAATTG
Found at i:2118752 original size:32 final size:32
Alignment explanation
Indices: 2118684--2118753 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
2118674 AGCAAGTCCC
** *
2118684 TAATAATAAATATTAGAAAACAATTGTACCTG
1 TAATAATAAATATTAGAAAACAATTAAACATG
*
2118716 TAATAATAAATATTAGAGAAA-AATTAAACATT
1 TAATAATAAATATTAGA-AAACAATTAAACATG
2118748 TAATAA
1 TAATAA
2118754 CTAGTATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 30 0.91
33 3 0.09
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (32 bp):
TAATAATAAATATTAGAAAACAATTAAACATG
Found at i:2127030 original size:20 final size:19
Alignment explanation
Indices: 2127005--2127058 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
2126995 ATGTGCAAAG
*
2127005 AACCGACTATGAACCGGTAA
1 AACCGA-TATGAACCGGCAA
*
2127025 AACCGATGTGAACCGGCAA
1 AACCGATATGAACCGGCAA
* *
2127044 AACCGGTGTGAACCG
1 AACCGATATGAACCG
2127059 ACGGTTCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 25 0.81
20 6 0.19
ACGTcount: A:0.35, C:0.26, G:0.26, T:0.13
Consensus pattern (19 bp):
AACCGATATGAACCGGCAA
Found at i:2127038 original size:19 final size:19
Alignment explanation
Indices: 2127014--2127058 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2127004 GAACCGACTA
*
2127014 TGAACCGGTAAAACCGATG
1 TGAACCGGCAAAACCGATG
*
2127033 TGAACCGGCAAAACCGGTG
1 TGAACCGGCAAAACCGATG
2127052 TGAACCG
1 TGAACCG
2127059 ACGGTTCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.29, T:0.13
Consensus pattern (19 bp):
TGAACCGGCAAAACCGATG
Found at i:2136615 original size:16 final size:17
Alignment explanation
Indices: 2136582--2136615 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2136572 CATTCTATTT
*
2136582 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
2136599 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
2136615 T
1 T
2136616 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:2136933 original size:22 final size:22
Alignment explanation
Indices: 2136908--2136950 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2136898 TAAAGTGATT
2136908 ATATTATATTATATAAATATAA
1 ATATTATATTATATAAATATAA
*
2136930 ATATTATATTTTATAAATATA
1 ATATTATATTATATAAATATA
2136951 TTTATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTATATTATATAAATATAA
Found at i:2136935 original size:17 final size:17
Alignment explanation
Indices: 2136913--2136964 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2136903 TGATTATATT
2136913 ATATTATATAAATATAA
1 ATATTATATAAATATAA
**
2136930 ATATTATAT-TTTATAA
1 ATATTATATAAATATAA
*
2136946 ATATATTTATAAAT-TAA
1 ATAT-TATATAAATATAA
2136963 AT
1 AT
2136965 GTGAGTGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 9 0.32
17 18 0.64
18 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTATATAAATATAA
Found at i:2137490 original size:3 final size:3
Alignment explanation
Indices: 2137476--2137590 Score: 95
Period size: 3 Copynumber: 38.3 Consensus size: 3
2137466 AAATTTTGCA
* * *
2137476 TAT TAA TAT TAT TAT TAT TAA TAT TAT TAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * * * * *
2137524 TAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2137572 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
2137591 TTAATTTACA
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 104 1.00
ACGTcount: A:0.34, C:0.10, G:0.01, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:2138342 original size:18 final size:18
Alignment explanation
Indices: 2138319--2138354 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2138309 CGAGACTCGA
*
2138319 CCACCATTGCTTCATCAG
1 CCACCATTACTTCATCAG
*
2138337 CCACCATTACTTTATCAG
1 CCACCATTACTTCATCAG
2138355 AGTAATAATC
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:0.25, C:0.36, G:0.08, T:0.31
Consensus pattern (18 bp):
CCACCATTACTTCATCAG
Found at i:2139196 original size:2 final size:2
Alignment explanation
Indices: 2139189--2139221 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2139179 GTCCTTTATG
2139189 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 T
2139222 TTGTACATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2139331 original size:22 final size:22
Alignment explanation
Indices: 2139306--2139357 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
2139296 TTTGCAATAG
2139306 ATATTTCATTCTTTATATCTAT
1 ATATTTCATTCTTTATATCTAT
2139328 ATATTTCATTCTTTATATCTAT
1 ATATTTCATTCTTTATATCTAT
2139350 ATATTTCA
1 ATATTTCA
2139358 ATTCGTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTCATTCTTTATATCTAT
Found at i:2139559 original size:5 final size:5
Alignment explanation
Indices: 2139549--2139607 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
2139539 ATAATAATAT
** * * *
2139549 TTTTA TTTTA TTTTA TTTTTA TAATA TTTCA TTTTCA TTTTG TTTTA TTTAA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA
2139601 TTTTA TT
1 TTTTA TT
2139608 ATTGACGATG
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
5 32 0.76
6 10 0.24
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:2139567 original size:16 final size:16
Alignment explanation
Indices: 2139546--2139607 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
2139536 ATTATAATAA
2139546 TATTTTTATTTTATTT
1 TATTTTTATTTTATTT
**
2139562 TATTTTTATAATATTT
1 TATTTTTATTTTATTT
* * *
2139578 CATTTTCATTTTGTTT
1 TATTTTTATTTTATTT
*
2139594 TA-TTTAATTTTATT
1 TATTTTTATTTTATT
2139608 ATTGACGATG
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
15 10 0.28
16 26 0.72
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.73
Consensus pattern (16 bp):
TATTTTTATTTTATTT
Found at i:2139588 original size:27 final size:27
Alignment explanation
Indices: 2139542--2139594 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2139532 TAAAATTATA
*
2139542 ATAATATTTTTATTTTATTTTATTTTT
1 ATAATATTTTCATTTTATTTTATTTTT
*
2139569 ATAATA-TTTCATTTTCATTTTGTTTT
1 ATAATATTTTCATTTT-ATTTTATTTT
2139595 ATTTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (27 bp):
ATAATATTTTCATTTTATTTTATTTTT
Found at i:2142140 original size:15 final size:15
Alignment explanation
Indices: 2142102--2142157 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
2142092 CACATTTTCA
*
2142102 ATAGTCACATAGAT-
1 ATAGTCACATAGCTC
2142116 -TA-TCACATAGCTC
1 ATAGTCACATAGCTC
*
2142129 ATAGTTACATAGCTC
1 ATAGTCACATAGCTC
2142144 ATAGTCACATAGCT
1 ATAGTCACATAGCT
2142158 TATATCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
12 9 0.25
13 2 0.06
14 2 0.06
15 23 0.64
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (15 bp):
ATAGTCACATAGCTC
Found at i:2143722 original size:15 final size:15
Alignment explanation
Indices: 2143702--2143754 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
2143692 GTGACATTAA
2143702 CTATGTGATAATAAG
1 CTATGTGATAATAAG
*
2143717 CTATGTGATTAA-ATG
1 CTATGTGA-TAATAAG
2143732 CTTATGTGAT-ATAAG
1 C-TATGTGATAATAAG
*
2143747 TTATGTGA
1 CTATGTGA
2143755 ATTATTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 8 0.25
15 14 0.44
16 10 0.31
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.40
Consensus pattern (15 bp):
CTATGTGATAATAAG
Found at i:2143879 original size:23 final size:23
Alignment explanation
Indices: 2143853--2143930 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 23
2143843 TTCAGGATAA
2143853 TTCTACGTGGTCATTAGGGACAT
1 TTCTACGTGGTCATTAGGGACAT
** * *
2143876 TTCTACGCAGTCCTTTGGGGA-A-
1 TTCTACGTGGT-CATTAGGGACAT
* * * *
2143898 ATCTATGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCATTAGGGACAT
2143921 TTCTACGTGG
1 TTCTACGTGG
2143931 CACTTCGGTG
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
21 7 0.17
22 8 0.20
23 18 0.45
24 7 0.17
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.35
Consensus pattern (23 bp):
TTCTACGTGGTCATTAGGGACAT
Found at i:2151356 original size:12 final size:12
Alignment explanation
Indices: 2151339--2151368 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2151329 CTAGTTAACA
2151339 TGAATTATTTAT
1 TGAATTATTTAT
2151351 TGAATTATTTAT
1 TGAATTATTTAT
*
2151363 TTAATT
1 TGAATT
2151369 TAATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (12 bp):
TGAATTATTTAT
Found at i:2155093 original size:18 final size:18
Alignment explanation
Indices: 2155072--2155154 Score: 68
Period size: 18 Copynumber: 4.8 Consensus size: 18
2155062 TAAAACAAGT
* *
2155072 GAAAATGTATAAAATAAA
1 GAAAATGAAGAAAATAAA
2155090 GAAAATGAAGAAAATAAA
1 GAAAATGAAGAAAATAAA
* *
2155108 -ATAA--AACAAAATAAA
1 GAAAATGAAGAAAATAAA
2155123 -AAAAT-AAGATAAATAAA
1 GAAAATGAAGA-AAATAAA
*
2155140 GTAAAATAAAGAAAA
1 G-AAAATGAAGAAAA
2155155 GGAAAAAAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
15 13 0.24
16 3 0.06
17 10 0.19
18 16 0.30
19 8 0.15
20 4 0.07
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (18 bp):
GAAAATGAAGAAAATAAA
Found at i:2155094 original size:9 final size:9
Alignment explanation
Indices: 2155082--2155154 Score: 66
Period size: 9 Copynumber: 8.4 Consensus size: 9
2155072 GAAAATGTAT
2155082 AAAATAAAG
1 AAAATAAAG
*
2155091 AAAATGAAG
1 AAAATAAAG
2155100 AAAAT-AA-
1 AAAATAAAG
* *
2155107 AATA-AAAC
1 AAAATAAAG
2155115 AAAATAAA-
1 AAAATAAAG
2155123 AAAAT-AAG
1 AAAATAAAG
2155131 ATAAATAAAG
1 A-AAATAAAG
2155141 TAAAATAAAG
1 -AAAATAAAG
2155151 AAAA
1 AAAA
2155155 GGAAAAAAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
7 7 0.13
8 11 0.20
9 24 0.44
10 11 0.20
11 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.08, T:0.14
Consensus pattern (9 bp):
AAAATAAAG
Found at i:2155108 original size:5 final size:5
Alignment explanation
Indices: 2155100--2155149 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
2155090 GAAAATGAAG
* * *
2155100 AAAAT AAAAT AAAAC AAAAT -AAA- AAAAT AAGAT -AAAT AAAGT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
2155147 AAA
1 AAA
2155150 GAAAAGGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
4 9 0.25
5 27 0.75
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:2155110 original size:23 final size:22
Alignment explanation
Indices: 2155080--2155154 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
2155070 GTGAAAATGT
* *
2155080 ATAAAATAAAGAAAATGAAGAAA
1 ATAAAATAAACAAAAT-AAAAAA
2155103 ATAAAATAAAACAAAATAAAAAA
1 ATAAAAT-AAACAAAATAAAAAA
* * *
2155126 ATAAGATAAATAAAGTAAAATAA
1 ATAAAATAAACAAAATAAAA-AA
*
2155149 AGAAAA
1 ATAAAA
2155155 GGAAAAAAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 11 0.26
23 24 0.56
24 8 0.19
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.15
Consensus pattern (22 bp):
ATAAAATAAACAAAATAAAAAA
Found at i:2155349 original size:15 final size:15
Alignment explanation
Indices: 2155312--2155349 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2155302 AAAGAAAAGA
2155312 AAAAAAATAAAAGTG
1 AAAAAAATAAAAGTG
*
2155327 AAACAAATAATAAGT-
1 AAAAAAATAA-AAGTG
2155342 AAAAAAAT
1 AAAAAAAT
2155350 GACAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.16
Consensus pattern (15 bp):
AAAAAAATAAAAGTG
Found at i:2155397 original size:2 final size:2
Alignment explanation
Indices: 2155390--2155414 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2155380 TAATAATAAG
2155390 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 A
2155415 ATAAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2155568 original size:15 final size:15
Alignment explanation
Indices: 2155535--2155583 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2155525 AATGCTAAGG
*
2155535 AAAAGAAAAG-GAAA
1 AAAATAAAAGTGAAA
2155549 AAAATAAAAGTGAAA
1 AAAATAAAAGTGAAA
*
2155564 CAAATAATAAGT-AAA
1 AAAATAA-AAGTGAAA
2155579 AAAAT
1 AAAAT
2155584 GACAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 9 0.30
15 17 0.57
16 4 0.13
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAATAAAAGTGAAA
Found at i:2155597 original size:234 final size:229
Alignment explanation
Indices: 2155186--2155653 Score: 823
Period size: 234 Copynumber: 2.0 Consensus size: 229
2155176 ATAGTAAATA
2155186 AATAAAGAAGTAAGACCATAATGACAACATTCGTGTATAAATAATGCAAGATAAAAATAAATAAA
1 AATAAAGAAGTAAGACCATAATGACAACATTCGTGTATAAATAATGCAAGATAAAAATAAATAAA
*
2155251 AAAGAAATAAAAAAACGAGTATAAAATGAATGTGCATAAAAATGCTAAGGAAAAGAAAAGAAAAA
66 AAAGAAAAAAAAAAACGAGTATAAAATGAATGTGCATAAAAATGCTAAGGAAAAGAAAAGAAAAA
2155316 AAATAAAAGTGAAACAAATAATAAGTAAAAAAATGACAAAAATAAAAACACAAAATAATAATAAT
131 AAATAAAAGTGAAACAAATAATAAGTAAAAAAATGACAAAAATAAAAACACAAAATAATAATAAT
2155381 AATAATAAG-ACACACACACACACACACACACAC
196 AATAATAAGAACACACACACACACACACACACAC
2155414 AATAAAGAAAGTAAGACCATAATGACAACATTCGTGTATAAAATAATGCAAGAT-AAAATAAATA
1 AATAAAG-AAGTAAGACCATAATGACAACATTCGTGTAT-AAATAATGCAAGATAAAAATAAAT-
*
2155478 AAAAAATAAGAAAAGAAAAACGAGTAAATAAAATGAATGTGCATAAAAATGCTAAGGAAAAGAAA
63 AAAAAAGAA-AAAA-AAAAACGAGT--ATAAAATGAATGTGCATAAAAATGCTAAGGAAAAGAAA
*
2155543 AGGAAAAAAATAAAAGTGAAACAAATAATAAGTAAAAAAATGACAAAAATAAAAACACAAAATAA
124 AGAAAAAAAATAAAAGTGAAACAAATAATAAGTAAAAAAATGACAAAAATAAAAACACAAAATAA
2155608 TAATAATAATAATAAGATACACACACACACACACACACACAC
189 TAATAATAATAATAAGA-ACACACACACACACACACACACAC
2155650 AATA
1 AATA
2155654 CTCCAATATA
Statistics
Matches: 228, Mismatches: 3, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
228 7 0.03
229 40 0.18
230 22 0.10
231 3 0.01
232 10 0.04
234 118 0.52
236 28 0.12
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.16
Consensus pattern (229 bp):
AATAAAGAAGTAAGACCATAATGACAACATTCGTGTATAAATAATGCAAGATAAAAATAAATAAA
AAAGAAAAAAAAAAACGAGTATAAAATGAATGTGCATAAAAATGCTAAGGAAAAGAAAAGAAAAA
AAATAAAAGTGAAACAAATAATAAGTAAAAAAATGACAAAAATAAAAACACAAAATAATAATAAT
AATAATAAGAACACACACACACACACACACACAC
Found at i:2155633 original size:2 final size:2
Alignment explanation
Indices: 2155626--2155650 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2155616 ATAATAAGAT
2155626 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 A
2155651 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2157070 original size:13 final size:13
Alignment explanation
Indices: 2157052--2157084 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2157042 ATTTTTTTTC
2157052 TTATTTTACTTAT
1 TTATTTTACTTAT
*
2157065 TTATTTTATTTAT
1 TTATTTTACTTAT
2157078 TTATTTT
1 TTATTTT
2157085 TCCCTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTACTTAT
Found at i:2161242 original size:183 final size:183
Alignment explanation
Indices: 2160934--2161470 Score: 941
Period size: 183 Copynumber: 2.9 Consensus size: 183
2160924 ATTAAATCCG
2160934 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* ** *
2160999 ATAGATTATGTTTAAACTCGGACACTGCTCGGACACTTGGCGATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
2161064 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
*
2161117 TAAAGCTGAGGTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
2161182 ATAGATTATGTTCAAACTATGACACTGCTCAGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
2161247 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
* *
2161300 TAAAGCTGAGCTATTCCACTAAGGCAATTGATTATAGAGGAAACTCGAAAACCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
2161365 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
2161429 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
2161471 TAAACCTGAT
Statistics
Matches: 337, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
182 1 0.00
183 336 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:2162871 original size:105 final size:104
Alignment explanation
Indices: 2162690--2163009 Score: 481
Period size: 105 Copynumber: 3.1 Consensus size: 104
2162680 ACAGTTTCTC
*
2162690 TTGAAAACATTTCCCTTGAAATTAATTTTTTTCTCTCC-TGAGATAGTTTCCCTCGAAACAGAAA
1 TTGAAAACATTTCCCTTGAAA-TGATTTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAA
*
2162754 ATTTTGTCTCCCTTAAGACAGTTTTCTCTGAAACAT-AACA
65 ATTTTGTCTCCCTTGAGACAG-TTTCTCTGAAACATAAACA
2162794 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
1 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTC-CTTGAGATAGTTTCCCTCGAAACAGAAA
2162859 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 ATTTTGTCTCCCTTGAGACAGTTTCTC-TGAAACATAAACA
* * * *
2162900 TTGAAAACATTTCCCTTGAAATGAATTTTATCTC-GCTTGAGATAGTTTCCCTTGAAAC-G--AA
1 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAA
* *
2162961 TTTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTTGTCTCCCTTGAGACAGTTTCTCT-GAAACATAAACA
2163001 TTGAAAACA
1 TTGAAAACA
2163010 ATTTAACGAA
Statistics
Matches: 203, Mismatches: 8, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
100 1 0.00
101 47 0.23
103 15 0.07
104 50 0.25
105 54 0.27
106 36 0.18
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAA
TTTTGTCTCCCTTGAGACAGTTTCTCTGAAACATAAACA
Found at i:2162956 original size:36 final size:36
Alignment explanation
Indices: 2162909--2162984 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
2162899 ATTGAAAACA
* * *
2162909 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
2162945 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
2162981 TTTC
1 TTTC
2162985 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:2163382 original size:105 final size:105
Alignment explanation
Indices: 2163184--2163814 Score: 914
Period size: 105 Copynumber: 6.0 Consensus size: 105
2163174 ATATCGTGAC
* * * * *
2163184 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGA-CGACTGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCC
2163248 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2163290 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
2163355 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2163395 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
2163460 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATACTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
2163500 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
2163565 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * ** *
2163605 ACTCCAGACAACGCAAGTTCAACTCCACGATGAAGGGATTGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
2163666 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
2163705 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * * *
2163770 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
2163811 ACTC
1 ACTC
2163815 GGAACAATGC
Statistics
Matches: 482, Mismatches: 36, Indels: 14
0.91 0.07 0.03
Matches are distributed among these distances:
100 80 0.17
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 305 0.63
106 82 0.17
107 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:2164409 original size:37 final size:37
Alignment explanation
Indices: 2164356--2164460 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
2164346 CATTTTCATC
2164356 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
2164393 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
2164430 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
2164461 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:2164855 original size:17 final size:16
Alignment explanation
Indices: 2164816--2164858 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
2164806 TATTATATGG
2164816 ATATT-TTATTCATTT
1 ATATTATTATTCATTT
*
2164831 ATTTTTATTATTCATGTT
1 A-TATTATTATTCAT-TT
2164849 ATATTATTAT
1 ATATTATTAT
2164859 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.04
16 3 0.13
17 16 0.70
18 3 0.13
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (16 bp):
ATATTATTATTCATTT
Found at i:2164917 original size:2 final size:2
Alignment explanation
Indices: 2164912--2164969 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
2164902 CTATTTTTAT
*
2164912 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2164954 T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
2164970 TTTTTAATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2165514 original size:25 final size:26
Alignment explanation
Indices: 2165477--2165525 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
2165467 TCTTATCTTA
* * *
2165477 CTTATTTATTTTTTTTTCCCTTGTAT
1 CTTATTTAGTTTTCTTTACCTTGTAT
2165503 CTTATTT-GTTTTCTTTACCTTGT
1 CTTATTTAGTTTTCTTTACCTTGT
2165526 TTATCTAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.10, C:0.16, G:0.06, T:0.67
Consensus pattern (26 bp):
CTTATTTAGTTTTCTTTACCTTGTAT
Found at i:2172135 original size:43 final size:42
Alignment explanation
Indices: 2172081--2172176 Score: 113
Period size: 43 Copynumber: 2.3 Consensus size: 42
2172071 TTTTTTTGCC
* * *
2172081 GAAGAGGAAAAATTGATTGTTTTTTTTAG-AATTTAGAAGAGA
1 GAAGAGGAAAAATTAATT-TATTTTTTAGCAATTTAGAAAAGA
* *
2172123 GAAGAGGGAAAAATTAATTTATTTTTTGGCAATTTAGAAAAGG
1 GAAGA-GGAAAAATTAATTTATTTTTTAGCAATTTAGAAAAGA
*
2172166 GAAGAAGAAAA
1 GAAGAGGAAAA
2172177 TTTTATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 18 0.39
43 28 0.61
ACGTcount: A:0.45, C:0.01, G:0.24, T:0.30
Consensus pattern (42 bp):
GAAGAGGAAAAATTAATTTATTTTTTAGCAATTTAGAAAAGA
Found at i:2172502 original size:12 final size:12
Alignment explanation
Indices: 2172464--2172807 Score: 103
Period size: 12 Copynumber: 27.6 Consensus size: 12
2172454 TCATTTATGT
2172464 TTATGATATATA-
1 TTAT-ATATATAC
* *
2172476 -TATATACACAC
1 TTATATATATAC
*
2172487 TTATGTATATAC
1 TTATATATATAC
*
2172499 TTATATACATAC
1 TTATATATATAC
2172511 ----ATATATAC
1 TTATATATATAC
*
2172519 TTATGTATATAC
1 TTATATATATAC
2172531 TTATATACATATAC
1 TTATAT--ATATAC
2172545 TTATATATCATAC
1 TTATATAT-ATAC
*
2172558 TTTATACTTATATATT
1 -TTATA--TATATA-C
*
2172574 TTATATACATAC
1 TTATATATATAC
*
2172586 CTATATATAGCTAC
1 TTATATATA--TAC
**
2172600 TTTTATATATATGTG
1 --TTATATATAT-AC
* * * *
2172615 TGTATGTGTGTGTAA
1 T-TA--TATATATAC
2172630 TTATATATATA-
1 TTATATATATAC
2172641 TATATATATATAC
1 T-TATATATATAC
2172654 TTATATTATATAC
1 TTATA-TATATAC
*
2172667 TTATA-AGTATAA
1 TTATATA-TATAC
2172679 TGTATAGTTATATA-
1 T-TATA--TATATAC
*
2172693 TATATATTATATAA
1 T-TATA-TATATAC
* *
2172707 GTATATACTTATAA
1 TTATATA--TATAC
**
2172721 TGTATGCATA-AC
1 T-TATATATATAC
2172733 ATTATATATATA-
1 -TTATATATATAC
2172745 -TATATATATA-
1 TTATATATATAC
2172755 -TATATATATA-
1 TTATATATATAC
2172765 TATATATATATA-
1 T-TATATATATAC
2172777 TATATATATATA-
1 T-TATATATATAC
2172789 TATATATATATA-
1 T-TATATATATAC
2172801 TTATATA
1 TTATATA
2172808 CATGCATATC
Statistics
Matches: 260, Mismatches: 35, Indels: 75
0.70 0.09 0.20
Matches are distributed among these distances:
8 7 0.03
10 25 0.10
11 11 0.04
12 107 0.41
13 42 0.16
14 35 0.13
15 17 0.07
16 16 0.06
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (12 bp):
TTATATATATAC
Found at i:2172515 original size:20 final size:20
Alignment explanation
Indices: 2172492--2172592 Score: 79
Period size: 20 Copynumber: 5.3 Consensus size: 20
2172482 CACACTTATG
2172492 TATATACTTATATACATACA
1 TATATACTTATATACATACA
* * *
2172512 TATATACTTATGTATATACT
1 TATATACTTATATACATACA
* *
2172532 TATATAC--ATATACTTATA
1 TATATACTTATATACATACA
*
2172550 TATCATACTT-TATAC-T-TA
1 TAT-ATACTTATATACATACA
* *
2172568 TATAT-TTTATATACATACC
1 TATATACTTATATACATACA
2172587 TATATA
1 TATATA
2172593 TAGCTACTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
16 2 0.03
17 7 0.11
18 15 0.24
19 10 0.16
20 29 0.46
ACGTcount: A:0.40, C:0.13, G:0.01, T:0.47
Consensus pattern (20 bp):
TATATACTTATATACATACA
Found at i:2172544 original size:26 final size:26
Alignment explanation
Indices: 2172513--2172569 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
2172503 ATACATACAT
*
2172513 ATATACTTATGTAT-ATACTTATATAC
1 ATATACTTATATATCATACTT-TATAC
2172539 ATATACTTATATATCATACTTTATAC
1 ATATACTTATATATCATACTTTATAC
*
2172565 TTATA
1 ATATA
2172570 TATTTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (26 bp):
ATATACTTATATATCATACTTTATAC
Found at i:2172636 original size:2 final size:2
Alignment explanation
Indices: 2172631--2172903 Score: 227
Period size: 2 Copynumber: 139.5 Consensus size: 2
2172621 TGTGTGTAAT
2172631 TA TA TA TA TA TA TA TA TA TA TA CT- TA TA T- TA TA TA CT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
*
2172672 -A GTA TA -A TG TA TA GT- TA TA TA TA TA TA T- TA TA TA -A GTA
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
2172710 TA TA CT- TA TA -A TG TA TG CA TA -A CA T- TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2172749 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2172791 TA TA TA TA TA T- TA TA TA CA TG CA TA TCA TA T- TA TCA TA -A CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA TA
* * * *
2172832 T- TCA TCG TA TG TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA T-A T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2172875 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
2172904 TAAAATTGAT
Statistics
Matches: 222, Mismatches: 24, Indels: 50
0.75 0.08 0.17
Matches are distributed among these distances:
1 16 0.07
2 193 0.87
3 13 0.06
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2173709 original size:26 final size:26
Alignment explanation
Indices: 2173649--2173700 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2173639 AACCATCAAA
*
2173649 TTGACCTGACATGACAGGTATCTGAT
1 TTGACATGACATGACAGGTATCTGAT
* *
2173675 TTGATATGACCTGACAGG-ATCTGAT
1 TTGACATGACATGACAGGTATCTGAT
2173700 T
1 T
2173701 GAAACATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (26 bp):
TTGACATGACATGACAGGTATCTGAT
Done.