Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 80 of 210
Found at i:27932091 original size:42 final size:42
Alignment explanation
Indices: 27932005--27932101 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
27931995 AGTTAACTCA
* * ** *
27932005 TATGAGTTTCTGTTTAACCCTATTGGTTTTCAGTTAAGCTCT
1 TATGAGCTTCTGTTCAACCCTACAGGTTTTCAGTTAAGCACT
* *
27932047 TATGAGCTTCTGTTCAACCCTTACAGG-TTTCCGTTTAGCACT
1 TATGAGCTTCTGTTCAACCC-TACAGGTTTTCAGTTAAGCACT
*
27932089 TATGTGCTTCTGT
1 TATGAGCTTCTGT
27932102 GTAGCCTTCG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 42 0.91
43 4 0.09
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
TATGAGCTTCTGTTCAACCCTACAGGTTTTCAGTTAAGCACT
Found at i:27934937 original size:105 final size:106
Alignment explanation
Indices: 27934798--27935014 Score: 409
Period size: 105 Copynumber: 2.1 Consensus size: 106
27934788 CGATTTAGTG
27934798 GTTAGTTAGAAAAAGAAATTATTGAAGAAATTGGATAAAAACAAAGTATCGAGACCTCGATCTCG
1 GTTAGTTAGAAAAAGAAATTATTGAAGAAATTGGATAAAAACAAAGTATCGAGACCTCGATCTCG
*
27934863 TAAATTCAAGTCAAAAATATTTTTATAAATATTTATGAAGT
66 TAAATTCAAGTCAAAAATATTTTTATAAATATTTATGAAAT
27934904 GTTAGTTAG-AAAAGAAATTATTGAAGAAATTGGATAAAAACAAAGTATCGAGACCTCGATCTCG
1 GTTAGTTAGAAAAAGAAATTATTGAAGAAATTGGATAAAAACAAAGTATCGAGACCTCGATCTCG
*
27934968 TAAATTCAAGTCAAAAATATTTTTATTAATATTTATGAAAT
66 TAAATTCAAGTCAAAAATATTTTTATAAATATTTATGAAAT
27935009 GTTAGT
1 GTTAGT
27935015 GATGTGGTAT
Statistics
Matches: 109, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
105 100 0.92
106 9 0.08
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.32
Consensus pattern (106 bp):
GTTAGTTAGAAAAAGAAATTATTGAAGAAATTGGATAAAAACAAAGTATCGAGACCTCGATCTCG
TAAATTCAAGTCAAAAATATTTTTATAAATATTTATGAAAT
Found at i:27939994 original size:41 final size:41
Alignment explanation
Indices: 27939825--27939987 Score: 272
Period size: 41 Copynumber: 4.0 Consensus size: 41
27939815 NNNNNNNNNN
*
27939825 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
* *
27939866 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
*
27939907 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
* *
27939948 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTTATTCA
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCA
27939988 ATTCACCAAT
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 113 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
ATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
Found at i:27939994 original size:82 final size:82
Alignment explanation
Indices: 27939825--27939987 Score: 317
Period size: 82 Copynumber: 2.0 Consensus size: 82
27939815 NNNNNNNNNN
27939825 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
27939890 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
27939907 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
*
27939972 TTTATAACCTTATTCA
66 TTTATAACCTGATTCA
27939988 ATTCACCAAT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (82 bp):
ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
TTTATAACCTGATTCAT
Found at i:27940235 original size:17 final size:17
Alignment explanation
Indices: 27940210--27940242 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27940200 TTGTTCGATC
*
27940210 CACATATATATATATTA
1 CACACATATATATATTA
27940227 CACACATATATATATT
1 CACACATATATATATT
27940243 CGTACATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (17 bp):
CACACATATATATATTA
Found at i:27940253 original size:17 final size:18
Alignment explanation
Indices: 27940210--27940255 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
27940200 TTGTTCGATC
27940210 CACATATATATATATTACA
1 CACAT-TATATATATTACA
*
27940229 CACA-TATATATATT-CG
1 CACATTATATATATTACA
*
27940245 TACATTATATA
1 CACATTATATA
27940256 ATCACAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
19 4 0.17
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.39
Consensus pattern (18 bp):
CACATTATATATATTACA
Found at i:27945771 original size:30 final size:30
Alignment explanation
Indices: 27945737--27945822 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 30
27945727 AATTTGGATT
27945737 AAATCAAAATTTCATGTATAAATTTACACA-
1 AAATCAAAATTT-ATGTATAAATTTACACAC
* *
27945767 AAATCAAAGTTTATGTATAAAATTACACATC
1 AAATCAAAATTTATGTATAAATTTACACA-C
* * *
27945798 AAACCAGAATTTATGTATAATTTTA
1 AAATCAAAATTTATGTATAAATTTA
27945823 AGATATATCC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 16 0.34
30 11 0.23
31 20 0.43
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.35
Consensus pattern (30 bp):
AAATCAAAATTTATGTATAAATTTACACAC
Found at i:27945792 original size:29 final size:29
Alignment explanation
Indices: 27945737--27945817 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
27945727 AATTTGGATT
*
27945737 AAATCAAAATTTCATGTATAAATTTACACA-
1 AAATC-AAATTT-ATGTATAAAATTACACAC
27945767 AAATCAAAGTTTATGTATAAAATTACACATC
1 AAATCAAA-TTTATGTATAAAATTACACA-C
*
27945798 AAACCAGAATTTATGTATAA
1 AAATCA-AATTTATGTATAA
27945818 TTTTAAGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 19 0.42
30 8 0.18
31 16 0.36
32 2 0.04
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.32
Consensus pattern (29 bp):
AAATCAAATTTATGTATAAAATTACACAC
Found at i:27947952 original size:12 final size:13
Alignment explanation
Indices: 27947937--27947967 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
27947927 TTTAAGATTC
27947937 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
27947950 TTTTTCTTTT-TT
1 TTTTTCTTTTCTT
27947962 TTTTTC
1 TTTTTC
27947968 AACTTCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:27951794 original size:3 final size:3
Alignment explanation
Indices: 27951786--27951817 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
27951776 AAAATGCACA
27951786 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27951818 AAGGAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27954958 original size:27 final size:27
Alignment explanation
Indices: 27954901--27954964 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
27954891 GGTCTGCCAT
* * ** *
27954901 AGGCGGCACCAAAGGTGCCAGTGGCAG
1 AGGCGACACCAAAGGTGCCACTACCAC
27954928 AGGCGACACCAAAGGTGCCACTACCAC
1 AGGCGACACCAAAGGTGCCACTACCAC
27954955 AGGCGACACC
1 AGGCGACACC
27954965 TGTGCCATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.30, C:0.33, G:0.31, T:0.06
Consensus pattern (27 bp):
AGGCGACACCAAAGGTGCCACTACCAC
Found at i:27955139 original size:23 final size:23
Alignment explanation
Indices: 27955113--27955166 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
27955103 AAAAAAGAAA
*
27955113 AGAAAAAGAG-AGAAAGAGAATAG
1 AGAAAAAGAGAAGAAA-AAAATAG
27955136 AGAAAGGAAGAGAAGAAAAAAATAG
1 AGAAA--AAGAGAAGAAAAAAATAG
27955161 A-AAAAA
1 AGAAAAA
27955167 TAAGGTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 2 0.07
23 5 0.19
24 3 0.11
25 12 0.44
26 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (23 bp):
AGAAAAAGAGAAGAAAAAAATAG
Found at i:27955547 original size:76 final size:77
Alignment explanation
Indices: 27955342--27955565 Score: 249
Period size: 76 Copynumber: 2.9 Consensus size: 77
27955332 GTTTAGTTAT
* *
27955342 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-T-T-GTTAGTTAT
**
27955407 TAGGATTAGTAAAAACCC
60 TATTATTAGTAAAAACCC
* *** * *
27955425 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACACTA-TATTATTGTTAGTTATTATTT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAG-TAAAAAACTATTATTATTGTTAGTTATTATTA
27955488 TTAGT-AAAACCC
65 TTAGTAAAAACCC
* *
27955500 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTATTATTATTA-TTATTATTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGTTAGTTATTATTAT
27955564 TA
66 TA
27955566 TTATTATTAT
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
75 35 0.29
76 44 0.37
77 1 0.01
78 1 0.01
79 5 0.04
80 2 0.02
82 18 0.15
83 14 0.12
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (77 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGTTAGTTATTATTAT
TAGTAAAAACCC
Found at i:27955548 original size:3 final size:3
Alignment explanation
Indices: 27955540--27955589 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
27955530 AGTAAAAAAC
27955540 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27955588 TA
1 TA
27955590 CGCATATTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:27958364 original size:8 final size:8
Alignment explanation
Indices: 27958336--27958377 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
27958326 GAGCTTATGC
*
27958336 TGTAAAGT
1 TGTAATGT
*
27958344 TGTTATG-
1 TGTAATGT
27958351 TGTAATGT
1 TGTAATGT
27958359 TGTAATGT
1 TGTAATGT
27958367 TGTAATGT
1 TGTAATGT
27958375 TGT
1 TGT
27958378 TGTAACACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (8 bp):
TGTAATGT
Found at i:27960974 original size:17 final size:16
Alignment explanation
Indices: 27960950--27960985 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
27960940 TTTCAATGTA
*
27960950 TTTTTTATTTTCGGAT
1 TTTTTTATTTTCGAAT
27960966 TTTTCTTATTTTCGAAT
1 TTTT-TTATTTTCGAAT
27960983 TTT
1 TTT
27960986 ATTGCTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.69
Consensus pattern (16 bp):
TTTTTTATTTTCGAAT
Found at i:27961517 original size:156 final size:157
Alignment explanation
Indices: 27960959--27961650 Score: 1158
Period size: 157 Copynumber: 4.4 Consensus size: 157
27960949 ATTTTTTATT
* * *
27960959 TTCGGATTTTTCTTATTTTCGAATTTTATTGCTTTCAAAAAATATATTATTTTTGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTTGTATTTTATTA
27961024 TTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTATATAAATTTA
66 TTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTATATAAATTTA
27961089 GTAAAAAACCCTTATTTTGACCATTTG
131 GTAAAAAACCCTTATTTTGACCATTTG
*
27961116 TTCGTATTTTTCTTATTTTCGGATTTTACTACTTTCAAAAAATATATTATTTTTGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTTGTATTTTATTA
27961181 TTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTATATAAATTTA
66 TTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTATATAAATTTA
27961246 GTAAAAAACCCTTATTTTGACCATTTG
131 GTAAAAAACCCTTATTTTGACCATTTG
*
27961273 TTCGTATTTTTCTTATTTTCGGATTTTACTACTTTCAAAAAATATATTATTTTTGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTTGTATTTTATTA
* *
27961338 TTTTATATTATTTTAGTACATAATA-TTTGAAATGTATTATTTTAGTGCGTGTTTTATATAAATT
66 TTTTATATTATTTTAGTACATAA-AGTTTGAAATGTATTAATTTAGTGTGT-TTTTATATAAATT
* *
27961402 TAGT-AAAAACCC-TATTTTGGCCCTTTG
129 TAGTAAAAAACCCTTATTTTGACCATTTG
* * * *
27961429 TTCGTATTTTTCTTATTTTCAGATTTTATTACTTTTAAAAAATATACTATTTTCGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTTGTATTTTATTA
* * *
27961494 TTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTATGTTTTTTATATAAATTT
66 TTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTG-TTTTTATATAAATTT
27961559 AGTAAAAAACCCTTATTTT-AGCCATTTG
130 AGTAAAAAACCCTTATTTTGA-CCATTTG
* *
27961587 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTTGTTTTTTATT
1 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTTGTATTTTATT
27961651 TCTTTTTGTA
Statistics
Matches: 506, Mismatches: 22, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
156 135 0.27
157 281 0.56
158 90 0.18
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (157 bp):
TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTTGTATTTTATTA
TTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTATATAAATTTA
GTAAAAAACCCTTATTTTGACCATTTG
Found at i:27961658 original size:17 final size:17
Alignment explanation
Indices: 27961636--27961668 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27961626 AAATATACTA
*
27961636 TTTTTGTTTTTTATTTC
1 TTTTTGTATTTTATTTC
27961653 TTTTTGTATTTTATTT
1 TTTTTGTATTTTATTT
27961669 TTTAATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTGTATTTTATTTC
Found at i:27961845 original size:30 final size:30
Alignment explanation
Indices: 27961809--27961943 Score: 148
Period size: 30 Copynumber: 4.4 Consensus size: 30
27961799 AAATAAAATA
27961809 AAATAATAAAACATAGAATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
** *
27961839 AAATAATAAAACATA-AATAACAACATAAATAAT
1 AAATAATAAAACATAGAAT--GTACAT-AA-CAT
* * *
27961872 AAAATAATAAGACATGGTATGTACATAACAT
1 -AAATAATAAAACATAGAATGTACATAACAT
27961903 AAATAATAAAACATAGAATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
27961933 AAA-AATTAAAA
1 AAATAA-TAAAA
27961944 TTAAATTATG
Statistics
Matches: 86, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
29 5 0.06
30 50 0.58
31 6 0.07
32 4 0.05
33 6 0.07
34 13 0.15
35 2 0.02
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.23
Consensus pattern (30 bp):
AAATAATAAAACATAGAATGTACATAACAT
Found at i:27962185 original size:17 final size:17
Alignment explanation
Indices: 27962157--27962201 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
27962147 TTTTTTCCTT
27962157 TCTTTTTCCTTC-CCTCCC
1 TCTTTTT-CTTCTCCT-CC
*
27962175 TCTTTTTCTTCTCCTTC
1 TCTTTTTCTTCTCCTCC
27962192 TCTTTTTCTT
1 TCTTTTTCTT
27962202 TTTCCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
TCTTTTTCTTCTCCTCC
Found at i:27962242 original size:3 final size:3
Alignment explanation
Indices: 27962234--27962298 Score: 61
Period size: 3 Copynumber: 23.0 Consensus size: 3
27962224 CCTCCTTCCC
*
27962234 CTT CTT CTT CTT C-T CTT C-T CTT CTT C-T CTT C-T CTT TTT C-T CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
27962277 -TT CTT CTT CTCT CATT CTT CTT
1 CTT CTT CTT CT-T C-TT CTT CTT
27962299 TCCTGCAGCT
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
2 12 0.23
3 35 0.67
4 4 0.08
5 1 0.02
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:27962252 original size:5 final size:5
Alignment explanation
Indices: 27962236--27962283 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
27962226 TCCTTCCCCT
*
27962236 TCTTC TTCTTC TCTTC TC-T- TCTTC TCTTC TCTT- T-TTC TCTTT TCTTC
1 TCTTC -TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC
27962283 T
1 T
27962284 TCTCTCATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
3 4 0.11
4 4 0.11
5 23 0.64
6 5 0.14
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (5 bp):
TCTTC
Found at i:27962252 original size:8 final size:8
Alignment explanation
Indices: 27962236--27962297 Score: 55
Period size: 8 Copynumber: 8.1 Consensus size: 8
27962226 TCCTTCCCCT
27962236 TCTTCTTC
1 TCTTCTTC
27962244 T-TCTCTTC
1 TCT-TCTTC
27962252 TCTTCTTC
1 TCTTCTTC
27962260 TCTTC-TC
1 TCTTCTTC
27962267 T-TT-TTC
1 TCTTCTTC
27962273 TCTT-TTC
1 TCTTCTTC
27962280 TTCTTC-TC
1 -TCTTCTTC
27962288 TCATTCTTC
1 TC-TTCTTC
27962297 T
1 T
27962298 TTCCTGCAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
6 5 0.11
7 11 0.24
8 26 0.57
9 4 0.09
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.65
Consensus pattern (8 bp):
TCTTCTTC
Found at i:27962257 original size:13 final size:13
Alignment explanation
Indices: 27962234--27962288 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
27962224 CCTCCTTCCC
27962234 CTTCTTCTTCTTCT
1 CTTC-TCTTCTTCT
27962248 CTTCTCTTCTTCT
1 CTTCTCTTCTTCT
*
27962261 CTTCTCTTTTTCT
1 CTTCTCTTCTTCT
*
27962274 CTTTTCTTCTTCT
1 CTTCTCTTCTTCT
27962287 CT
1 CT
27962289 CATTCTTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
13 34 0.89
14 4 0.11
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
CTTCTCTTCTTCT
Found at i:27963078 original size:3 final size:3
Alignment explanation
Indices: 27963060--27963100 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
27963050 AGCTGCAGGA
27963060 AAG AAG AATG AGAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AA-G A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG
27963101 GGGAAAGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 31 0.86
4 4 0.11
5 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:27963435 original size:30 final size:30
Alignment explanation
Indices: 27963399--27963461 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
27963389 AATTTTAATT
*
27963399 TTTATGTTATGTACATTCTATGGT-TTATTA
1 TTTATGTTATGTACATACTAT-GTCTTATTA
*
27963429 TTTATGTTTTGTACATACTATGTCTTATTA
1 TTTATGTTATGTACATACTATGTCTTATTA
27963459 TTT
1 TTT
27963462 TATTATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.59
Consensus pattern (30 bp):
TTTATGTTATGTACATACTATGTCTTATTA
Found at i:27964029 original size:16 final size:17
Alignment explanation
Indices: 27964008--27964041 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27963998 CAGTATATTT
*
27964008 TTTGAAAGTAA-AAAAA
1 TTTGAAAATAAGAAAAA
27964024 TTTGAAAATAAGAAAAA
1 TTTGAAAATAAGAAAAA
27964041 T
1 T
27964042 ACGAACAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (17 bp):
TTTGAAAATAAGAAAAA
Found at i:27964177 original size:159 final size:158
Alignment explanation
Indices: 27963665--27964202 Score: 851
Period size: 158 Copynumber: 3.4 Consensus size: 158
27963655 TACGAAAAGA
* * ** *
27963665 AATAAAAAATGAAAATAGTATATTTACTGAAAGTAATAAAATCCGAAAAAAAAAGAAAAATACGA
1 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCG--AAAATAAGAAAAATACGA
27963730 ACAAATAGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAAATAATACATTT
64 ACAAATAGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAAATAATACATTT
27963795 CAAACATTATGTACTAAAATAATATAAAAT
129 CAAACATTATGTACTAAAATAATATAAAAT
* *
27963825 AATAAATTATGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAAC
1 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAAC
* * *
27963890 AAACAGCCAAAATAAGGGCTTTTTACTAAATTTATATAAAAAATACACTAAAATAATACATTTCA
66 AAATAGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAAATAATACATTTCA
27963955 AACATTATGTACTAAAATAATATAAAAT
131 AACATTATGTACTAAAATAATATAAAAT
* * * **
27963983 AATAAAATACAAAAACAGTATATTTTTTGAAAGTAAAAAAATTTGAAAATAAGAAAAATACGAAC
1 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAAC
* *
27964048 AAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAACACACACTAAATTAATACATTTC
66 AAATAGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAA-ACACACTAAAATAATACATTTC
* * *
27964113 AAACTTTCTATACTAAAATAATATAAAAT
130 AAACATTATGTACTAAAATAATATAAAAT
* *
27964142 AATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAAATCCTAAAATAAGAAAAATAC
1 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATAC
27964203 ATTGAAATTA
Statistics
Matches: 347, Mismatches: 30, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
158 206 0.59
159 100 0.29
160 41 0.12
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.28
Consensus pattern (158 bp):
AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAAC
AAATAGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAAATAATACATTTCA
AACATTATGTACTAAAATAATATAAAAT
Found at i:27969484 original size:41 final size:40
Alignment explanation
Indices: 27969386--27969484 Score: 92
Period size: 41 Copynumber: 2.4 Consensus size: 40
27969376 TAGTGTAAAA
* * *
27969386 ACTAACAATCATACTAACTAAAATAATAATTAGGGTTTTT
1 ACTAACAATAATACTAACCAAAATAATAATTAGAGTTTTT
*** * *
27969426 ACTAATTTTAATAACTAACCATAATAATATTATTA-ATTTTTT
1 ACTAACAATAAT-ACTAACCAAAATAATA--ATTAGAGTTTTT
27969468 ACTAACAATAATACTAA
1 ACTAACAATAATACTAA
27969485 GTAACAATAA
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
40 8 0.18
41 19 0.42
42 14 0.31
43 4 0.09
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.38
Consensus pattern (40 bp):
ACTAACAATAATACTAACCAAAATAATAATTAGAGTTTTT
Found at i:27969688 original size:13 final size:13
Alignment explanation
Indices: 27969674--27969714 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
27969664 CTATTTTTTT
*
27969674 TCTTCTCTTTCTT
1 TCTTCTCTTTCTC
27969687 TC-TC-CTTTCTC
1 TCTTCTCTTTCTC
*
27969698 TATTCTCTTTCTC
1 TCTTCTCTTTCTC
27969711 TCTT
1 TCTT
27969715 TTTCTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 7 0.30
12 4 0.17
13 12 0.52
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTTCTCTTTCTC
Found at i:27969757 original size:3 final size:3
Alignment explanation
Indices: 27969739--27969773 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
27969729 CCGGCACAGC
* *
27969739 CTT CTC CTT TTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
27969774 CTTTCTCCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:27969779 original size:9 final size:9
Alignment explanation
Indices: 27969748--27969807 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
27969738 CCTTCTCCTT
27969748 TTTCTTCT-
1 TTTCTTCTC
27969756 TCTTCTTCT-
1 T-TTCTTCTC
27969765 TCTTCTTCTC
1 T-TTCTTCTC
*
27969775 TTTCTCCTCC
1 TTTCTTCT-C
*
27969785 TTTCCTTTTC
1 TTT-CTTCTC
27969795 TTTCTTCTC
1 TTTCTTCTC
27969804 TTTC
1 TTTC
27969808 GTGCAGCTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
8 1 0.02
9 31 0.70
10 9 0.20
11 3 0.07
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTCTTCTC
Found at i:27969912 original size:27 final size:27
Alignment explanation
Indices: 27969877--27969943 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
27969867 ACATGACACA
* * *
27969877 GGTGTCGCCTGTGACAGTGACACCTTT
1 GGTGCCGCCTGTGACACTAACACCTTT
* * *
27969904 GGTGCCGCCTCTGCCACTAATACCTTT
1 GGTGCCGCCTGTGACACTAACACCTTT
*
27969931 GGTGCCACCTGTG
1 GGTGCCGCCTGTG
27969944 GCAGACTCTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.13, C:0.31, G:0.27, T:0.28
Consensus pattern (27 bp):
GGTGCCGCCTGTGACACTAACACCTTT
Found at i:27973429 original size:32 final size:32
Alignment explanation
Indices: 27973393--27973458 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
27973383 TCATTTTATG
27973393 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
1 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
27973425 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
1 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
27973457 TT
1 TT
27973459 CGTTTCATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (32 bp):
TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
Found at i:27977419 original size:18 final size:18
Alignment explanation
Indices: 27977392--27977436 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
27977382 GTGAGGTAAG
*
27977392 TATTAATATTAGTATTAA
1 TATTATTATTAGTATTAA
*
27977410 TATTATTATTAGTATTAT
1 TATTATTATTAGTATTAA
27977428 TATTATTAT
1 TATTATTAT
27977437 GAGTGGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
TATTATTATTAGTATTAA
Found at i:27977433 original size:6 final size:6
Alignment explanation
Indices: 27977392--27977436 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
27977382 GTGAGGTAAG
* * * *
27977392 TATTAA TATTAG TATTAA TATTAT TATTAG TATTAT TATTAT TAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TAT
27977437 GAGTGGGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (6 bp):
TATTAT
Found at i:27981116 original size:20 final size:20
Alignment explanation
Indices: 27981091--27981138 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
27981081 TAAATCGAGC
*
27981091 CTTTGATGCCCTAAAAATAG
1 CTTTGAGGCCCTAAAAATAG
*
27981111 CTTTGAGGCCTTAAAAATAG
1 CTTTGAGGCCCTAAAAATAG
*
27981131 TTTTGAGG
1 CTTTGAGG
27981139 TAATTCAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (20 bp):
CTTTGAGGCCCTAAAAATAG
Found at i:27983974 original size:11 final size:11
Alignment explanation
Indices: 27983960--27983985 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27983950 TTAGATTAAA
27983960 ATATTATTATT
1 ATATTATTATT
27983971 ATATTATTATT
1 ATATTATTATT
27983982 ATAT
1 ATAT
27983986 ATATAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATATTATTATT
Found at i:27984018 original size:16 final size:17
Alignment explanation
Indices: 27983997--27984028 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
27983987 TATAAAACAA
27983997 AAGAAAGAAA-AGAAAT
1 AAGAAAGAAACAGAAAT
27984013 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
27984029 GCTTAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:27984980 original size:25 final size:25
Alignment explanation
Indices: 27984929--27984984 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
27984919 ACTTTAGCGC
* ****
27984929 GCTCTCTGATTATTAGCACTTTGGT
1 GCTCTCTGATTACTAGCACGACAGT
27984954 GCTCTCTGATTACTAGCACGACAGT
1 GCTCTCTGATTACTAGCACGACAGT
27984979 GCTCTC
1 GCTCTC
27984985 CGTTTAGCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.36
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGACAGT
Found at i:28011510 original size:25 final size:25
Alignment explanation
Indices: 28011476--28011526 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
28011466 TATGACTGAG
28011476 TGAATCTAGGTTATCTCTATAAAAC
1 TGAATCTAGGTTATCTCTATAAAAC
28011501 TGAATCTAGGTTATCTCTATAAAAC
1 TGAATCTAGGTTATCTCTATAAAAC
28011526 T
1 T
28011527 AAGGTATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (25 bp):
TGAATCTAGGTTATCTCTATAAAAC
Found at i:28025825 original size:15 final size:15
Alignment explanation
Indices: 28025805--28025835 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28025795 ATTACATAAT
28025805 ATATAAAATAATATA
1 ATATAAAATAATATA
*
28025820 ATATAAAATATTATA
1 ATATAAAATAATATA
28025835 A
1 A
28025836 ACTTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAAAATAATATA
Found at i:28028486 original size:3 final size:3
Alignment explanation
Indices: 28028478--28028514 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
28028468 TAGAAACAAT
28028478 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28028515 GAACAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28030003 original size:16 final size:16
Alignment explanation
Indices: 28029982--28030017 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
28029972 TTTGGTTCGC
28029982 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28029998 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28030014 TGTA
1 TGTA
28030018 ATAGCAGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:28041759 original size:22 final size:22
Alignment explanation
Indices: 28041733--28041778 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
28041723 ATATGTTTCG
28041733 ATATATGCTAT-ATTAGATTGAA
1 ATATATGC-ATGATTAGATTGAA
*
28041755 ATATATGCATGATTATATTGAA
1 ATATATGCATGATTAGATTGAA
28041777 AT
1 AT
28041779 TTTAGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (22 bp):
ATATATGCATGATTAGATTGAA
Found at i:28044208 original size:17 final size:17
Alignment explanation
Indices: 28044186--28044222 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
28044176 ATCGTAACGC
28044186 TTAGTCTCTTAATTGGG
1 TTAGTCTCTTAATTGGG
28044203 TTAGTCTCTTAATTGGG
1 TTAGTCTCTTAATTGGG
28044220 TTA
1 TTA
28044223 TAAAATGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.11, G:0.22, T:0.49
Consensus pattern (17 bp):
TTAGTCTCTTAATTGGG
Found at i:28045098 original size:21 final size:21
Alignment explanation
Indices: 28045072--28045127 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
28045062 AACAGCGGTG
*
28045072 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
28045093 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
28045114 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
28045128 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:28050507 original size:24 final size:24
Alignment explanation
Indices: 28050456--28050508 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
28050446 ATCCCCATAT
* *
28050456 TTTTTTCGTTTTAAGTAATTTAAT
1 TTTTTTCCTTTTAAGTAATTTAAA
* **
28050480 TTTTTTCCTTTTATGTTCTTTAAA
1 TTTTTTCCTTTTAAGTAATTTAAA
28050504 TTTTT
1 TTTTT
28050509 CTCTTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.68
Consensus pattern (24 bp):
TTTTTTCCTTTTAAGTAATTTAAA
Found at i:28056552 original size:95 final size:95
Alignment explanation
Indices: 28056389--28056579 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
28056379 AATCTCCTTA
28056389 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
28056454 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
*
28056484 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTGCATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
28056549 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
28056579 G
1 G
28056580 CTATTCCTTT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (95 bp):
GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
TCTCATGATGGCTTGCACCCCAATTGTTTT
Found at i:28072388 original size:31 final size:29
Alignment explanation
Indices: 28072318--28072391 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
28072308 GGCTCAGGTT
* *
28072318 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
28072347 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
28072378 ACATTTTAGTCACT
1 ACATTTTAGTCACT
28072392 GATCCATTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:28072615 original size:89 final size:91
Alignment explanation
Indices: 28072464--28072638 Score: 336
Period size: 89 Copynumber: 1.9 Consensus size: 91
28072454 CAAACAAAAA
28072464 TCTTTCTTTTCCATTCTCTTATGCTTCTCCCTTTGTTTTCCTCCCTTCTCCACTTCTTTCAACGT
1 TCTTTCTTTTCCATTCTCTTATGCTTCTCCCTTTGTTTTCCTCCCTTCTCCACTTCTTTCAACGT
28072529 AGTTTTTC-ATGTTTT-TTTTAACTT
66 AGTTTTTCTATGTTTTATTTTAACTT
28072553 TCTTTCTTTTCCATTCTCTTATGCTTCTCCCTTTGTTTTCCTCCCTTCTCCACTTCTTTCAACGT
1 TCTTTCTTTTCCATTCTCTTATGCTTCTCCCTTTGTTTTCCTCCCTTCTCCACTTCTTTCAACGT
28072618 AGTTTTTCTATGTTTTATTTT
66 AGTTTTTCTATGTTTTATTTT
28072639 TTTGAACAAT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
89 73 0.87
90 7 0.08
91 4 0.05
ACGTcount: A:0.10, C:0.28, G:0.06, T:0.57
Consensus pattern (91 bp):
TCTTTCTTTTCCATTCTCTTATGCTTCTCCCTTTGTTTTCCTCCCTTCTCCACTTCTTTCAACGT
AGTTTTTCTATGTTTTATTTTAACTT
Found at i:28073021 original size:31 final size:29
Alignment explanation
Indices: 28072957--28073025 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
28072947 ACGATAATGT
* *
28072957 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATGTCAAACAA
* *
28072986 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT--GTCAAACAA
28073017 AAGTGACTA
1 AAGTGACTA
28073026 TTTTGGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGTCAAACAA
Found at i:28074788 original size:12 final size:13
Alignment explanation
Indices: 28074759--28074791 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28074749 TTTTTAACTA
*
28074759 ATAATTGTAAATT
1 ATAATTATAAATT
28074772 ATAATTATAAA-T
1 ATAATTATAAATT
28074784 ATAATTAT
1 ATAATTAT
28074792 CACAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
ATAATTATAAATT
Found at i:28075163 original size:19 final size:22
Alignment explanation
Indices: 28075135--28075180 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 22
28075125 AGATCATACC
28075135 TTTT-AAATAAT-TTT-TAAT-
1 TTTTAAAATAATCTTTATAATA
28075153 TTTTAAAATAATCTTTATAATA
1 TTTTAAAATAATCTTTATAATA
28075175 TTTTAA
1 TTTTAA
28075181 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 3 0.12
21 4 0.17
22 6 0.25
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAATAATCTTTATAATA
Found at i:28085476 original size:19 final size:21
Alignment explanation
Indices: 28085441--28085495 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
28085431 TTATTTTTAT
28085441 ATTTTTATACTTTTT-AAATA
1 ATTTTTATACTTTTTAAAATA
28085461 ATTTTTA-A-TTTCTTAAAATA
1 ATTTTTATACTTT-TTAAAATA
*
28085481 ATTTTTATAATTTTT
1 ATTTTTATACTTTTT
28085496 TTTGGAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 3 0.10
19 3 0.10
20 19 0.61
21 3 0.10
22 3 0.10
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTATACTTTTTAAAATA
Found at i:28086186 original size:7 final size:7
Alignment explanation
Indices: 28086174--28086204 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
28086164 TATAATAATA
28086174 AAAATTT
1 AAAATTT
28086181 AAAATTT
1 AAAATTT
28086188 AAAATTT
1 AAAATTT
28086195 AAAATTT
1 AAAATTT
28086202 AAA
1 AAA
28086205 GATATCTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:28089579 original size:3 final size:3
Alignment explanation
Indices: 28089571--28089602 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28089561 GGTTGGGGAT
28089571 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
28089603 GATGATAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:28094416 original size:29 final size:29
Alignment explanation
Indices: 28094361--28094417 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
28094351 ATGTTTACAG
** *
28094361 TTCAAAATAGGTTATTTACATACATAATT
1 TTCAAAATAAATTATTTACATAAATAATT
* *
28094390 TTCAAAATAAATTATTTTCGTAAATAAT
1 TTCAAAATAAATTATTTACATAAATAAT
28094418 AAAATTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (29 bp):
TTCAAAATAAATTATTTACATAAATAATT
Found at i:28097105 original size:10 final size:10
Alignment explanation
Indices: 28097090--28097119 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28097080 GTAAGACATA
28097090 TTATAAATAT
1 TTATAAATAT
28097100 TTATAAATA-
1 TTATAAATAT
28097109 TTATAAATAT
1 TTATAAATAT
28097119 T
1 T
28097120 AAGCAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTATAAATAT
Found at i:28097112 original size:9 final size:9
Alignment explanation
Indices: 28097087--28097120 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
28097077 TTGGTAAGAC
28097087 ATATTATAA
1 ATATTATAA
28097096 ATATTTATAA
1 ATA-TTATAA
28097106 ATATTATAA
1 ATATTATAA
28097115 ATATTA
1 ATATTA
28097121 AGCAATGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATTATAA
Found at i:28104080 original size:29 final size:30
Alignment explanation
Indices: 28104013--28104083 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
28104003 ATTTGATCTT
* *
28104013 ATTTAATTCTTTTTAATAATACAATGACTA
1 ATTTAATTCTATTTAATAATACAAGGACTA
* * *
28104043 AATTGATTC-ATTTAATAATA-GAGGAACTA
1 ATTTAATTCTATTTAATAATACAAGG-ACTA
28104072 ATTTAATTCTAT
1 ATTTAATTCTAT
28104084 CCCTATAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
28 2 0.06
29 21 0.66
30 9 0.28
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (30 bp):
ATTTAATTCTATTTAATAATACAAGGACTA
Found at i:28106187 original size:19 final size:16
Alignment explanation
Indices: 28106147--28106191 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
28106137 TTGAAAATTC
28106147 AAAA-TTAAAAATAAA
1 AAAATTTAAAAATAAA
28106162 AAAATTTAACAAATAAA
1 AAAATTTAA-AAATAAA
28106179 AAATTATTTAAAA
1 AAA--ATTTAAAA
28106192 GTTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.15
16 4 0.15
17 10 0.38
18 2 0.08
19 6 0.23
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATTTAAAAATAAA
Found at i:28106731 original size:20 final size:20
Alignment explanation
Indices: 28106706--28106754 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
28106696 TTTTCTTTAA
28106706 ATTATTTTATTTATA-AGACT
1 ATTATTTTATTTATAGA-ACT
*
28106726 ATTATTTTATTTATAGAATT
1 ATTATTTTATTTATAGAACT
28106746 ATTATTTTA
1 ATTATTTTA
28106755 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (20 bp):
ATTATTTTATTTATAGAACT
Found at i:28106831 original size:22 final size:24
Alignment explanation
Indices: 28106787--28106841 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
28106777 AATGAGAAAA
* *
28106787 ATATTTATTTATAATTTTATAT-G
1 ATATTTATTTATAAATCTATATGG
28106810 -TATTTATTTATAAAATCT-TATGG
1 ATATTTATTTAT-AAATCTATATGG
28106833 ATATTTATT
1 ATATTTATT
28106842 GAAAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 14 0.52
23 5 0.19
24 8 0.30
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (24 bp):
ATATTTATTTATAAATCTATATGG
Found at i:28110334 original size:1 final size:1
Alignment explanation
Indices: 28110328--28110352 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
28110318 ATTCATGAGG
28110328 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
28110353 GGTTTGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:28113246 original size:37 final size:38
Alignment explanation
Indices: 28113191--28113279 Score: 130
Period size: 37 Copynumber: 2.4 Consensus size: 38
28113181 ATGCAATTTT
*
28113191 AAAAATATATTAAAAAAATACGAACTGATAAATTTTGA
1 AAAAATATATTAAAAAAATACGAACTGATAAATTTTCA
* *
28113229 AAAAATAT-TTAAGAAAATACGATCTGATAAATTTTCA
1 AAAAATATATTAAAAAAATACGAACTGATAAATTTTCA
28113266 AAAAA-A-ATTAAAAA
1 AAAAATATATTAAAAA
28113280 TAAAATGCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
36 7 0.15
37 31 0.67
38 8 0.17
ACGTcount: A:0.60, C:0.06, G:0.07, T:0.28
Consensus pattern (38 bp):
AAAAATATATTAAAAAAATACGAACTGATAAATTTTCA
Found at i:28114306 original size:37 final size:37
Alignment explanation
Indices: 28114265--28114341 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
28114255 ATTCCAAAAA
*
28114265 TAATA-TTATTTTAATA-TATTTAATATTAAATTTAAT-T
1 TAATACTTAGTTTAATAGTATTT--TATTAAA-TTAATAT
28114302 TAATACTTAGTTTAATAGTATTTTATTAAATTAATAT
1 TAATACTTAGTTTAATAGTATTTTATTAAATTAATAT
28114339 TAA
1 TAA
28114342 AGTGATTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
36 5 0.14
37 16 0.44
38 10 0.28
39 5 0.14
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (37 bp):
TAATACTTAGTTTAATAGTATTTTATTAAATTAATAT
Found at i:28114420 original size:21 final size:22
Alignment explanation
Indices: 28114395--28114457 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 22
28114385 ATATAAATAT
28114395 TATATTAATTTAATAAGATTTA
1 TATATTAATTTAATAAGATTTA
*
28114417 -ATATTAAATTTAATCTAATATTTA
1 TATATT-AATTTAA--TAAGATTTA
28114441 TCTATATTAATTTAATA
1 --TATATTAATTTAATA
28114458 TTAAAGTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
21 5 0.15
22 7 0.21
24 10 0.29
26 7 0.21
27 5 0.15
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATTAATTTAATAAGATTTA
Found at i:28116513 original size:27 final size:27
Alignment explanation
Indices: 28116475--28116541 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
28116465 TCATGCCCCA
* *
28116475 TGTTTAATGTCCTAGCG-AATTTCCTCG
1 TGTTTACTGTCCTAACGTAATTTCC-CG
* *
28116502 TGTTTACTGTCCCAACGTACTTTCCCG
1 TGTTTACTGTCCTAACGTAATTTCCCG
*
28116529 CGTTTACTGTCCT
1 TGTTTACTGTCCT
28116542 GACGGACTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 27 0.82
28 6 0.18
ACGTcount: A:0.15, C:0.28, G:0.16, T:0.40
Consensus pattern (27 bp):
TGTTTACTGTCCTAACGTAATTTCCCG
Found at i:28126542 original size:22 final size:22
Alignment explanation
Indices: 28126516--28126557 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28126506 ATAAATACTG
*
28126516 TAACATG-GTAATTTTTTTATAA
1 TAACATGAG-AATTGTTTTATAA
28126538 TAACATGAGAATTGTTTTAT
1 TAACATGAGAATTGTTTTAT
28126558 GTAAATGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (22 bp):
TAACATGAGAATTGTTTTATAA
Found at i:28128273 original size:13 final size:13
Alignment explanation
Indices: 28128257--28128290 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28128247 AGAGTTGTAG
28128257 AAAATAAACAAAA
1 AAAATAAACAAAA
*
28128270 AAAATAAATAAAA
1 AAAATAAACAAAA
*
28128283 TAAATAAA
1 AAAATAAA
28128291 ATAGAAGAAA
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:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAACAAAA
Found at i:28128282 original size:9 final size:9
Alignment explanation
Indices: 28128258--28128310 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
28128248 GAGTTGTAGA
28128258 AAATAAACA-
1 AAATAAA-AT
28128267 AAA-AAAAT
1 AAATAAAAT
28128275 AAATAAAAT
1 AAATAAAAT
28128284 AAATAAAAT
1 AAATAAAAT
* *
28128293 AGAAGAAAGT
1 A-AATAAAAT
28128303 AAATAAAA
1 AAATAAAA
28128311 AACGCAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 1 0.03
8 6 0.16
9 23 0.62
10 7 0.19
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (9 bp):
AAATAAAAT
Found at i:28129266 original size:46 final size:44
Alignment explanation
Indices: 28129109--28129274 Score: 190
Period size: 44 Copynumber: 3.7 Consensus size: 44
28129099 AGATCCTTTA
* * *
28129109 ATCTGCTCCACTGTAATCTCAAGGAGATAGGAT-TACTATCTTTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTA-TATCTTCG
* * * ** *
28129153 ATCTGCTTCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTATATCTTCG
*
28129197 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGATATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT-ATA-TCTTCG
* *
28129243 GTCTACTCCACTGTAATCTCAGGGAGATAAGA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA
28129275 CCTGTATAAT
Statistics
Matches: 100, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
44 65 0.65
45 2 0.02
46 33 0.33
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTATATCTTCG
Found at i:28140497 original size:44 final size:43
Alignment explanation
Indices: 28140456--28140542 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 43
28140446 ATATATAAGT
* *
28140456 AAGCATATACATATA-TACGTATATAACTATCATAAAATATAA
1 AAGCATATACATATAGTACATATATAACAATCATAAAATATAA
* * **
28140498 AAGTATATATATATAGGTACATATATAGGAATCATAAAATATAA
1 AAGCATATACATATA-GTACATATATAACAATCATAAAATATAA
28140542 A
1 A
28140543 GAATATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
42 13 0.35
44 24 0.65
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (43 bp):
AAGCATATACATATAGTACATATATAACAATCATAAAATATAA
Found at i:28144593 original size:15 final size:17
Alignment explanation
Indices: 28144558--28144595 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
28144548 GAATGAAAAG
*
28144558 AAAATTGAAAGAGTAGA
1 AAAATAGAAAGAGTAGA
28144575 AAAATAGAAAGA-T-GA
1 AAAATAGAAAGAGTAGA
28144590 AAAATA
1 AAAATA
28144596 TAATTGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 1 0.05
17 11 0.55
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (17 bp):
AAAATAGAAAGAGTAGA
Found at i:28150574 original size:31 final size:31
Alignment explanation
Indices: 28150509--28150612 Score: 135
Period size: 30 Copynumber: 3.4 Consensus size: 31
28150499 TTATTTTTTA
*
28150509 TTTTTTTAATTTTAAAATACTTTTTT-TAA-A-
1 TTTTTTTAATTTTAAAAT--TTTTTTAAAATAC
*
28150539 TTTTTTAAATTTTAAAATTTTTTTAAAATAC
1 TTTTTTTAATTTTAAAATTTTTTTAAAATAC
*
28150570 -TTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTAAAATTTTTTTAAAATAC
28150600 TTTTTTTAATTTT
1 TTTTTTTAATTTT
28150613 TGTTTTAATT
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
28 6 0.09
29 2 0.03
30 46 0.70
31 12 0.18
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTTTTAATTTTAAAATTTTTTTAAAATAC
Found at i:28150592 original size:11 final size:11
Alignment explanation
Indices: 28150548--28150604 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
28150538 ATTTTTTAAA
*
28150548 TTTTAAAATTT
1 TTTTAAAATAT
28150559 TTTTAAAATACT
1 TTTTAAAATA-T
*
28150571 TTTT----TAA
1 TTTTAAAATAT
28150578 TTTTAAAATAT
1 TTTTAAAATAT
28150589 TTTTAAAATACT
1 TTTTAAAATA-T
28150601 TTTT
1 TTTT
28150605 TTAATTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
7 4 0.11
8 2 0.05
11 21 0.57
12 10 0.27
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:28150593 original size:41 final size:41
Alignment explanation
Indices: 28150518--28150597 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
28150508 ATTTTTTTAA
**
28150518 TTTTAAAATACTTTTTTTAAATTTTTTAAATTTTAAAATTT
1 TTTTAAAATACTTTTTTTAAATTTTAAAAATTTTAAAATTT
28150559 TTTTAAAATAC-TTTTTT-AATTTTAAAATATTTTTAAAAT
1 TTTTAAAATACTTTTTTTAAATTTTAAAA-A-TTTTAAAAT
28150598 ACTTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 8 0.23
40 7 0.20
41 20 0.57
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (41 bp):
TTTTAAAATACTTTTTTTAAATTTTAAAAATTTTAAAATTT
Found at i:28153544 original size:19 final size:19
Alignment explanation
Indices: 28153520--28153558 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28153510 ATTTATCGTT
28153520 TTATAGCAAAGTCATCACA
1 TTATAGCAAAGTCATCACA
28153539 TTATAGCAAAGTCATCACA
1 TTATAGCAAAGTCATCACA
28153558 T
1 T
28153559 AGCTTATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (19 bp):
TTATAGCAAAGTCATCACA
Found at i:28154363 original size:43 final size:42
Alignment explanation
Indices: 28154316--28154455 Score: 138
Period size: 42 Copynumber: 3.3 Consensus size: 42
28154306 TCCCAGACCT
* * *
28154316 GGTCTTACATGTAATCAAATAACGATGCCACTATCTCATACAA
1 GGTCTTACACGTAATCAAAT-ACGATGCCAATATCTCAGACAA
* * * *
28154359 GGTCTTACACGAAATCATATACGATGCCAATGTCTCAGACAT
1 GGTCTTACACGTAATCAAATACGATGCCAATATCTCAGACAA
* * **
28154401 GGTCTTACACGTAAATCTCAAAT-CGATGCCAACATCCCAGACGT
1 GGTCTTACACGT-AA--TCAAATACGATGCCAATATCTCAGACAA
28154445 GGTCTTACACG
1 GGTCTTACACG
28154456 ATATCACATA
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
42 29 0.36
43 19 0.23
44 28 0.35
45 5 0.06
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (42 bp):
GGTCTTACACGTAATCAAATACGATGCCAATATCTCAGACAA
Found at i:28155463 original size:13 final size:13
Alignment explanation
Indices: 28155445--28155471 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28155435 CACAAACGAT
28155445 AAAATTTTCACAC
1 AAAATTTTCACAC
28155458 AAAATTTTCACAC
1 AAAATTTTCACAC
28155471 A
1 A
28155472 TATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:28165804 original size:16 final size:17
Alignment explanation
Indices: 28165783--28165820 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
28165773 TAAAATTTAA
28165783 TTTTATTGCTATA-TTT
1 TTTTATTGCTATACTTT
**
28165799 TTTTATTTTTATACTTT
1 TTTTATTGCTATACTTT
28165816 TTTTA
1 TTTTA
28165821 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTATTGCTATACTTT
Found at i:28169243 original size:16 final size:17
Alignment explanation
Indices: 28169216--28169253 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
28169206 AATAAAAAAC
28169216 ATATAT-TTTAT-ATTA
1 ATATATGTTTATAATTA
28169231 ATATATGTTTATAATTA
1 ATATATGTTTATAATTA
28169248 A-ATATG
1 ATATATG
28169254 AATATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 10 0.48
17 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
ATATATGTTTATAATTA
Found at i:28170992 original size:4 final size:4
Alignment explanation
Indices: 28170983--28171042 Score: 120
Period size: 4 Copynumber: 15.0 Consensus size: 4
28170973 TATATATCAT
28170983 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
28171031 TACA TACA TACA
1 TACA TACA TACA
28171043 ATAATGTACT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:28171365 original size:30 final size:30
Alignment explanation
Indices: 28171331--28171388 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
28171321 GTCTACGCCA
28171331 CCATCGGCATCTCCTTCTCCTTCCTCTCCG
1 CCATCGGCATCTCCTTCTCCTTCCTCTCCG
*
28171361 CCATCTGCATCTCCTTCTCCTTCCTCTC
1 CCATCGGCATCTCCTTCTCCTTCCTCTC
28171389 TGGCTGCGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.07, C:0.50, G:0.07, T:0.36
Consensus pattern (30 bp):
CCATCGGCATCTCCTTCTCCTTCCTCTCCG
Found at i:28172973 original size:19 final size:19
Alignment explanation
Indices: 28172951--28172988 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28172941 CCATTGTCAC
*
28172951 CCACCGTAATAAAATTTGT
1 CCACAGTAATAAAATTTGT
*
28172970 CCACAGTAATTAAATTTGT
1 CCACAGTAATAAAATTTGT
28172989 TATTAACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
CCACAGTAATAAAATTTGT
Found at i:28174520 original size:16 final size:16
Alignment explanation
Indices: 28174496--28174544 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
28174486 ATGTACGTGT
* *
28174496 ATAAACAAATATATAA
1 ATAAACAAACAAATAA
*
28174512 ATAAGCAAACAAATAA
1 ATAAACAAACAAATAA
**
28174528 ATAAATGAACAAATAA
1 ATAAACAAACAAATAA
28174544 A
1 A
28174545 GGATTAAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.18
Consensus pattern (16 bp):
ATAAACAAACAAATAA
Found at i:28178493 original size:13 final size:13
Alignment explanation
Indices: 28178477--28178509 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28178467 GGGTTTGTAA
28178477 AAAATAAATAAAT
1 AAAATAAATAAAT
*
28178490 AAAATAAGTAAAT
1 AAAATAAATAAAT
28178503 -AAATAAA
1 AAAATAAA
28178510 AACAGGAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:28179334 original size:30 final size:31
Alignment explanation
Indices: 28179278--28179336 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
28179268 GGAGGTGGGA
* *
28179278 TGGGAGGGGTGTAAAAGTTTTAGGGGAAAAG
1 TGGGAGGGGAGTAAAAATTTTAGGGGAAAAG
*
28179309 TGGGA-GGGAGTAAAAATTTTCGGGGAAA
1 TGGGAGGGGAGTAAAAATTTTAGGGGAAA
28179337 GTAAATGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.34, C:0.02, G:0.42, T:0.22
Consensus pattern (31 bp):
TGGGAGGGGAGTAAAAATTTTAGGGGAAAAG
Found at i:28179546 original size:9 final size:9
Alignment explanation
Indices: 28179532--28179565 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
28179522 TATAGTTTGA
*
28179532 TATTCGGGT
1 TATTCGAGT
*
28179541 TATTCGAAT
1 TATTCGAGT
28179550 TATTCGAGT
1 TATTCGAGT
28179559 TATTCGA
1 TATTCGA
28179566 ATTCAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.44
Consensus pattern (9 bp):
TATTCGAGT
Found at i:28179555 original size:18 final size:18
Alignment explanation
Indices: 28179532--28179568 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
28179522 TATAGTTTGA
*
28179532 TATTCGGGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
28179550 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
28179568 T
1 T
28179569 CAAAACTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (18 bp):
TATTCGAGTTATTCGAAT
Found at i:28183642 original size:82 final size:80
Alignment explanation
Indices: 28183543--28183706 Score: 292
Period size: 82 Copynumber: 2.0 Consensus size: 80
28183533 TTAGGATGTT
* *
28183543 TGCCAATTAACACCCACACAATAAAAACACTTTAGCTGGTAAAACACAACGAATTGCTCACAAGT
1 TGCCAATTAACACCCACACAATAAAAACACTTAAGCTAGTAAAACACAACGAATTGCTCACAAGT
28183608 GCTTGTAGGAAAAAGA
66 GCTTGTAGG-AAAAGA
28183624 TGCCAATTAAACACCCACACAATAAAAACACTTAAGCTAGTAAAACACAACGAATTGCTCACAAG
1 TGCCAATT-AACACCCACACAATAAAAACACTTAAGCTAGTAAAACACAACGAATTGCTCACAAG
28183689 TGCTTGTAGGAAAAGA
65 TGCTTGTAGGAAAAGA
28183705 TG
1 TG
28183707 AAGAATTGAA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
81 16 0.20
82 64 0.80
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.20
Consensus pattern (80 bp):
TGCCAATTAACACCCACACAATAAAAACACTTAAGCTAGTAAAACACAACGAATTGCTCACAAGT
GCTTGTAGGAAAAGA
Found at i:28184551 original size:17 final size:18
Alignment explanation
Indices: 28184519--28184553 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28184509 TGAAATTTAT
*
28184519 CAAGTTTTATTTCAAAAA
1 CAAGCTTTATTTCAAAAA
28184537 CAAGCTTTA-TTCAAAAA
1 CAAGCTTTATTTCAAAAA
28184554 TATTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (18 bp):
CAAGCTTTATTTCAAAAA
Found at i:28189302 original size:22 final size:23
Alignment explanation
Indices: 28189260--28189303 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28189250 CATAATGTAT
*
28189260 TTTTAAAAAAAGATATTTAAAAG
1 TTTTAAAAAAAGATATATAAAAG
*
28189283 TTTTAAAGAAA-ATATATAAAA
1 TTTTAAAAAAAGATATATAAAA
28189304 ATTNNNNNNN
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (23 bp):
TTTTAAAAAAAGATATATAAAAG
Found at i:28192818 original size:28 final size:28
Alignment explanation
Indices: 28192787--28192849 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
28192777 ATTCTCAATC
**
28192787 TTCAATCTCCCGTTTTTAA-TTTTATATT
1 TTCAATCTCCAATTTTTAATTTTTA-ATT
* *
28192815 TTCAATATTCAATTTTTAATTTTTAATT
1 TTCAATCTCCAATTTTTAATTTTTAATT
28192843 TTCAATC
1 TTCAATC
28192850 CTCAATTCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.27, C:0.14, G:0.02, T:0.57
Consensus pattern (28 bp):
TTCAATCTCCAATTTTTAATTTTTAATT
Found at i:28192830 original size:21 final size:21
Alignment explanation
Indices: 28192806--28192848 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28192796 CCGTTTTTAA
28192806 TTTTATATTTTCAATATTCAAT
1 TTTTA-ATTTTCAATATTCAAT
* *
28192828 TTTTAATTTTTAATTTTCAAT
1 TTTTAATTTTCAATATTCAAT
28192849 CCTCAATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAATTTTCAATATTCAAT
Found at i:28192854 original size:28 final size:28
Alignment explanation
Indices: 28192799--28192856 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
28192789 CAATCTCCCG
*
28192799 TTTTTAATTTTATATTTTCAATATTCAA
1 TTTTTAATTTTATATTTTCAATACTCAA
*
28192827 TTTTTAATTTT-TAATTTTCAATCCTCAA
1 TTTTTAATTTTAT-ATTTTCAATACTCAA
28192855 TT
1 TT
28192857 CTCAAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTAATTTTATATTTTCAATACTCAA
Found at i:28195278 original size:4 final size:4
Alignment explanation
Indices: 28195271--28195327 Score: 87
Period size: 4 Copynumber: 14.2 Consensus size: 4
28195261 TTTACTTTTC
* *
28195271 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
28195319 CATG TATG T
1 TATG TATG T
28195328 GTTGTGTATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:28198509 original size:8 final size:9
Alignment explanation
Indices: 28198482--28198507 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28198472 CACGTTCACC
28198482 GGGTAAAAA
1 GGGTAAAAA
28198491 GGGTAAAAA
1 GGGTAAAAA
28198500 GGGTAAAA
1 GGGTAAAA
28198508 GGAAGAGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.35, T:0.12
Consensus pattern (9 bp):
GGGTAAAAA
Found at i:28198842 original size:6 final size:6
Alignment explanation
Indices: 28198831--28198857 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28198821 TGCAAGATCC
28198831 CTGCTT CTGCTT CTGCTT CTGCTT CTG
1 CTGCTT CTGCTT CTGCTT CTGCTT CTG
28198858 ATACTAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.19, T:0.48
Consensus pattern (6 bp):
CTGCTT
Found at i:28198974 original size:15 final size:15
Alignment explanation
Indices: 28198965--28198999 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28198955 ACCAGCTCCT
28198965 CCTCCTCCAGCACCA
1 CCTCCTCCAGCACCA
* *
28198980 CCTCCTGCGGCACCA
1 CCTCCTCCAGCACCA
28198995 CCTCC
1 CCTCC
28199000 CAAAGCAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.60, G:0.11, T:0.14
Consensus pattern (15 bp):
CCTCCTCCAGCACCA
Found at i:28203108 original size:24 final size:23
Alignment explanation
Indices: 28203041--28203108 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
28203031 AATTTATTTG
28203041 ATATATTTTTC-TTTATA-TATA
1 ATATATTTTTCTTTTATAGTATA
* **
28203062 ATATTTATTTTTGTAGTATTAGTATA
1 ATA--TATTTTTCTTTTA-TAGTATA
28203088 ATATATTTTTCTTTCTATAGT
1 ATATATTTTTCTTT-TATAGT
28203109 TGCTACTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
21 3 0.09
23 7 0.20
24 14 0.40
25 4 0.11
26 7 0.20
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.60
Consensus pattern (23 bp):
ATATATTTTTCTTTTATAGTATA
Found at i:28203790 original size:35 final size:35
Alignment explanation
Indices: 28203751--28203819 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
28203741 TAATTTGAAT
* *
28203751 ATTTTATATTTATC-TCAAATAATATTAATGTTATA
1 ATTTTAGAATTATCTTCAAATAAT-TTAATGTTATA
* *
28203786 ATTTTAGAATTATCTTCAATTTATTTAATGTTAT
1 ATTTTAGAATTATCTTCAAATAATTTAATGTTAT
28203820 TGTTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 22 0.76
36 7 0.24
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (35 bp):
ATTTTAGAATTATCTTCAAATAATTTAATGTTATA
Found at i:28204568 original size:19 final size:19
Alignment explanation
Indices: 28204531--28204572 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
28204521 ATGTTATAAT
28204531 TATAGGAAATCTAAAATTA
1 TATAGGAAATCTAAAATTA
*
28204550 CTATAGTAAATCT-AAATTA
1 -TATAGGAAATCTAAAATTA
28204569 TATA
1 TATA
28204573 ATTTAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
20 11 0.52
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (19 bp):
TATAGGAAATCTAAAATTA
Found at i:28208231 original size:12 final size:12
Alignment explanation
Indices: 28208210--28208244 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28208200 AATAAGAACA
28208210 TACATAAAAATG
1 TACATAAAAATG
* *
28208222 TCCATCAAAATG
1 TACATAAAAATG
28208234 TACATAAAAAT
1 TACATAAAAAT
28208245 ACATATGGCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (12 bp):
TACATAAAAATG
Found at i:28208508 original size:17 final size:18
Alignment explanation
Indices: 28208475--28208508 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28208465 ATTTATTTTG
28208475 TAAATCAACAATTATAAA
1 TAAATCAACAATTATAAA
*
28208493 TAAATC-ACACTTATAA
1 TAAATCAACAATTATAA
28208509 TGTACATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAATCAACAATTATAAA
Found at i:28225050 original size:42 final size:42
Alignment explanation
Indices: 28225004--28225115 Score: 170
Period size: 42 Copynumber: 2.7 Consensus size: 42
28224994 AGCTGAACGG
* *
28225004 AAACCCATAAGGGTTAATCTGAAGCTCAGAAGAGCTAAACTA
1 AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTA
* *
28225046 AAACCCATTAGGGTTAAACTGAAGCTCAAAAGAGCTGAACTA
1 AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTA
* *
28225088 AAACCCATAAAGGTTAAACTGAAACTCA
1 AAACCCATAAGGGTTAAACTGAAGCTCA
28225116 TATGAGTTAC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.19
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTA
Found at i:28225107 original size:21 final size:21
Alignment explanation
Indices: 28225039--28225117 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
28225029 TCAGAAGAGC
* *
28225039 TAAACTAAAACCCATTAGGGT
1 TAAACTAAAACCCATAAAGGT
* * * *
28225060 TAAACTGAAGCTCA-AAAGAGC
1 TAAACTAAAACCCATAAAG-GT
*
28225081 TGAACTAAAACCCATAAAGGT
1 TAAACTAAAACCCATAAAGGT
* *
28225102 TAAACTGAAACTCATA
1 TAAACTAAAACCCATA
28225118 TGAGTTACTG
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 2 0.05
21 36 0.86
22 4 0.10
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (21 bp):
TAAACTAAAACCCATAAAGGT
Found at i:28226379 original size:26 final size:28
Alignment explanation
Indices: 28226324--28226381 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
28226314 AATTTTAAAA
* *
28226324 TATTTTTAAAATATATATTTTTATTTTT
1 TATTTTTAAAATATATATTTTTAGTGTT
*
28226352 TATTTTTAAAATA-A-ATTTTTGGTGTT
1 TATTTTTAAAATATATATTTTTAGTGTT
28226378 TATT
1 TATT
28226382 AAAAAAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 13 0.48
27 1 0.04
28 13 0.48
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (28 bp):
TATTTTTAAAATATATATTTTTAGTGTT
Found at i:28250205 original size:12 final size:12
Alignment explanation
Indices: 28250188--28250213 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28250178 CAAAACAGGC
28250188 TTTTAGTGGCGT
1 TTTTAGTGGCGT
28250200 TTTTAGTGGCGT
1 TTTTAGTGGCGT
28250212 TT
1 TT
28250214 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.31, T:0.54
Consensus pattern (12 bp):
TTTTAGTGGCGT
Found at i:28250262 original size:40 final size:40
Alignment explanation
Indices: 28250218--28250354 Score: 134
Period size: 40 Copynumber: 3.5 Consensus size: 40
28250208 GCGTTTGGAT
*
28250218 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGCTTTAG
1 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTTAG
** * *
28250258 AAAAAACATCGCTAAAGATCCAGTATTAGCGGCGTTTTTAG
1 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCG-TTTTAG
* * * * **
28250299 -GAAAACGCAGCTAAAAA-CTAGCATTAGCGGCGTTTTCC
1 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTTAG
* *
28250337 AAAAAGCGCCGCAAAAAA
1 AAAAAACGCCGCTAAAAA
28250355 CCTAAGCACA
Statistics
Matches: 77, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
38 4 0.05
39 26 0.34
40 42 0.55
41 5 0.06
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTTAG
Found at i:28250739 original size:41 final size:41
Alignment explanation
Indices: 28250393--28250732 Score: 526
Period size: 41 Copynumber: 8.3 Consensus size: 41
28250383 TTTCGGGGCG
28250393 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTC-
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
* *
28250433 TTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
*
28250474 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTAGTC-
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
28250514 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
* * * * *
28250555 TTAGAGGCGTTTTTTAGGAAGCGCCGCTAATGCTCCGGGCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
* *
28250596 TTAGCGGCGTTTTTGAAGAAACGCCACTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
28250637 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC-GAGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTG-GTCT
* *
28250678 TTAGCGGCGTTTTTTGAA-AAGCGCTGCTAATGCTCGGGTCT
1 TTAGCGGCG-TTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
28250719 TTAGCGGCGTTTTT
1 TTAGCGGCGTTTTT
28250733 AAAAAAGTGC
Statistics
Matches: 274, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
40 83 0.30
41 182 0.66
42 9 0.03
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
Found at i:28251533 original size:21 final size:22
Alignment explanation
Indices: 28251509--28251550 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28251499 GCCTTTTTTT
28251509 CCCTAA-ATTCCCCCCTAAAAC
1 CCCTAATATTCCCCCCTAAAAC
* *
28251530 CCCTAATTTTTCCCCCTAAAA
1 CCCTAATATTCCCCCCTAAAA
28251551 TTTGTATCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.31, C:0.43, G:0.00, T:0.26
Consensus pattern (22 bp):
CCCTAATATTCCCCCCTAAAAC
Found at i:28256280 original size:42 final size:43
Alignment explanation
Indices: 28256219--28256313 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
28256209 AGATATGTTT
* ** *
28256219 TAGCGGTGTTTGTGTGAAAAG-CGTCGCTAAAGGCCTATTCTA
1 TAGCGGCGTTTGTACGAAAAGTCGTCGCTAAAGACCTATTCTA
* * * *
28256261 TAGCGGCGTTTGTACGAAAAGTCGTTGCTAAATATCTGTTCTA
1 TAGCGGCGTTTGTACGAAAAGTCGTCGCTAAAGACCTATTCTA
28256304 TAGCGGCGTT
1 TAGCGGCGTT
28256314 CTTTAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 18 0.41
43 26 0.59
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (43 bp):
TAGCGGCGTTTGTACGAAAAGTCGTCGCTAAAGACCTATTCTA
Found at i:28262154 original size:16 final size:18
Alignment explanation
Indices: 28262115--28262148 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28262105 TAAGTTTATA
28262115 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
28262132 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
28262149 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:28264461 original size:3 final size:3
Alignment explanation
Indices: 28264453--28264484 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28264443 TAAAGTGAAG
28264453 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28264485 CCATTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28264755 original size:8 final size:9
Alignment explanation
Indices: 28264729--28264754 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28264719 AAATAGAAGA
28264729 AGAAGGGGG
1 AGAAGGGGG
28264738 AGAAGGGGG
1 AGAAGGGGG
28264747 AGAAGGGG
1 AGAAGGGG
28264755 ATGTTCAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (9 bp):
AGAAGGGGG
Found at i:28265994 original size:75 final size:75
Alignment explanation
Indices: 28265892--28266035 Score: 200
Period size: 75 Copynumber: 1.9 Consensus size: 75
28265882 TGGGCACACA
* * *
28265892 ATCGTCAGTTAATCCGACTAGCGCTGGGCGCAAACACCGTTGGTTCATCCAACTAGAGCTGGGCT
1 ATCGTCAGTTAACCCGACTAGCACTGGGCGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGCT
28265957 CACAACTATT
66 CACAACTATT
* * ** *
28265967 ATCGTCAG-TATACCCGACTAGCACTGGGTGCAAATAGTGTTAGTTTATCCAACTAGAGCTGGGC
1 ATCGTCAGTTA-ACCCGACTAGCACTGGGCGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGC
28266031 TCACA
65 TCACA
28266036 TTCAATACTG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 2 0.03
75 58 0.97
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (75 bp):
ATCGTCAGTTAACCCGACTAGCACTGGGCGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGCT
CACAACTATT
Found at i:28266060 original size:75 final size:75
Alignment explanation
Indices: 28265892--28266074 Score: 199
Period size: 75 Copynumber: 2.4 Consensus size: 75
28265882 TGGGCACACA
* * * *
28265892 ATCGTCAGTTAATCCGACTAGCGCTGGGCGCAAACACCGTTGGTTCATCCAACTAGAGCTGGGCT
1 ATCGTCAGTAAACCCGACTAGCGCTGGGTGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGCT
*
28265957 CACAACTATT
66 CACAACTAAT
* * * ** *
28265967 ATCGTCAGTATACCCGACTAGCACTGGGTGCAAATAGTGTTAGTTTATCCAACTAGAGCTGGGCT
1 ATCGTCAGTAAACCCGACTAGCGCTGGGTGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGCT
*
28266032 CAC-ATTCAAT
66 CACAACT-AAT
* **
28266042 A-CTGTCGGTAAATTCGACTAGCGCTGGGTGCAA
1 ATC-GTCAGTAAACCCGACTAGCGCTGGGTGCAA
28266075 TCTTCTTTGC
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
74 3 0.03
75 86 0.97
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (75 bp):
ATCGTCAGTAAACCCGACTAGCGCTGGGTGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGCT
CACAACTAAT
Found at i:28267185 original size:117 final size:118
Alignment explanation
Indices: 28266993--28267227 Score: 447
Period size: 117 Copynumber: 2.0 Consensus size: 118
28266983 GACTGTGAAC
28266993 CTACTGTAGGGACGGTAAGGATACCTAGACCCCTAATTGACTGAAATGATTGAAAGATTGTTGTA
1 CTACTGTAGGGACGGTAAGGATACCTAGACCCCTAATTGACTGAAATGATTGAAAGATTGTTGTA
28267058 TGCCTATATAAAATATGTAACAG-CCCGATTCTGGGCCTAGTCGGAATAGTGGT
66 TGCCTATATAAAATATGTAACAGCCCCG-TTCTGGGCCTAGTCGGAATAGTGGT
28267111 CTACTGTA-GGACGGTAAGGATACCTAGACCCCTAATTGACTGAAATGATTGAAAGATTGTTGTA
1 CTACTGTAGGGACGGTAAGGATACCTAGACCCCTAATTGACTGAAATGATTGAAAGATTGTTGTA
28267175 TGCCTATATAAAATATGTAACAGCCCCGTTCTGGGCCTAGTCGGAATAGTGGT
66 TGCCTATATAAAATATGTAACAGCCCCGTTCTGGGCCTAGTCGGAATAGTGGT
28267228 TTCGGGACCA
Statistics
Matches: 116, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
117 104 0.90
118 12 0.10
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (118 bp):
CTACTGTAGGGACGGTAAGGATACCTAGACCCCTAATTGACTGAAATGATTGAAAGATTGTTGTA
TGCCTATATAAAATATGTAACAGCCCCGTTCTGGGCCTAGTCGGAATAGTGGT
Done.