Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008573.1 Hibiscus syriacus cultivar Beakdansim tig00111502_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: 313404
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:8458 original size:22 final size:22
Alignment explanation
Indices: 8433--8487 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
8423 AAGAGTAGTT
8433 GTTTCAAAACCTCCTCTTTGTG
1 GTTTCAAAACCTCCTCTTTGTG
8455 GTTTCAAAACCTCCTCTTTGTG
1 GTTTCAAAACCTCCTCTTTGTG
8477 GTTTCAAAACC
1 GTTTCAAAACC
8488 AGTAGGGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (22 bp):
GTTTCAAAACCTCCTCTTTGTG
Found at i:9746 original size:60 final size:60
Alignment explanation
Indices: 9682--9805 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
9672 TAAAGTAAAT
* ** * * *
9682 AAATGATCCTCTGA-ATATAGTGAGTTACTTTGTTGAGTCC-CCTGATTATAAAAAGTTATA
1 AAATGATCATCTGACA-ATAGAAAGTAACTTTGTTGAGTCCACCT-ACTATAAAAAGTTACA
* *
9742 AAATGATCATCTGACAGTAGAAAGTAACTTTGTTGAGTCCACCTACTATTAAAAGTTACA
1 AAATGATCATCTGACAATAGAAAGTAACTTTGTTGAGTCCACCTACTATAAAAAGTTACA
9802 AAAT
1 AAAT
9806 TACCACCTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 50 0.93
61 4 0.07
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (60 bp):
AAATGATCATCTGACAATAGAAAGTAACTTTGTTGAGTCCACCTACTATAAAAAGTTACA
Found at i:10231 original size:19 final size:19
Alignment explanation
Indices: 10207--10248 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
10197 AACGCACTGC
10207 AACACACCTAAGGATTAAG
1 AACACACCTAAGGATTAAG
10226 AACACACCTAAGGATTAAG
1 AACACACCTAAGGATTAAG
10245 AACA
1 AACA
10249 ACACAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (19 bp):
AACACACCTAAGGATTAAG
Found at i:13422 original size:131 final size:126
Alignment explanation
Indices: 13178--13540 Score: 415
Period size: 131 Copynumber: 2.8 Consensus size: 126
13168 ATAATTTTAA
** * * * *
13178 GAGTGAAAACAATAATATATAATTATTTCTAATCGAGAATAAATGACCTCTTACACCTTAAAGCA
1 GAGTGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* * * * *
13243 ATCATTTATTAC-TCTAATAGAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATCGAT
66 ATCATTTATTACTTC-AATCGAAATGAAGAGATATCATTATTCCATCTTAAAAATC-A-AT--AT
13307 T
126 T
* * *
13308 CGAGTGAAAATGATAATATCTAATGATTTCCAATCTAGAATAAATAACCTCTCATACCTTAAAGC
1 -GAGTGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGC
** *
13373 CTTCATTTATTGCTTCAATCGAAATGAAGAGATATCATTATTCCATCTTAAAAATCAATATT
65 AATCATTTATTACTTCAATCGAAATGAAGAGATATCATTATTCCATCTTAAAAATCAATATT
* * * * *
13435 -AGAGAGAATGATAATATCGAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAGAGCA
1 GAGTGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* * * * *
13499 GTCATTTATTACTCCAACCGAAATGAAAAGATATTATTATTC
66 ATCATTTATTACTTCAATCGAAATGAAGAGATATCATTATTC
13541 TCAACATCAA
Statistics
Matches: 199, Mismatches: 32, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
125 91 0.46
127 3 0.02
129 2 0.01
130 1 0.01
131 100 0.50
132 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (126 bp):
GAGTGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
ATCATTTATTACTTCAATCGAAATGAAGAGATATCATTATTCCATCTTAAAAATCAATATT
Found at i:13504 original size:125 final size:129
Alignment explanation
Indices: 13189--13540 Score: 417
Period size: 125 Copynumber: 2.7 Consensus size: 129
13179 AGTGAAAACA
* * * *
13189 ATAATATATAATTATTTCTAATCGAGAATAAATGACCTCTTACACCTTAAAGCAATCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTA
* * * * * *
13254 C-TCTAATAGAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATCGATTCGAGTGAAAA
66 CTTC-AATCGAAATGAAGAGATATCATTATTCCATCTTAAAAATCAATATC-ATTC-AGAGAAAA
13318 TG
128 TG
* * * ** *
13320 ATAATATCTAATGATTTCCAATCTAGAATAAATAACCTCTCATACCTTAAAGCCTTCATTTATTG
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTA
*
13385 CTTCAATCGAAATGAAGAGATATCATTATTCCATCTTAAAAATC-A-AT-ATT-AGAGAGAATG
66 CTTCAATCGAAATGAAGAGATATCATTATTCCATCTTAAAAATCAATATCATTCAGAGAAAATG
* * * *
13445 ATAATATCGAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAGAGCAGTCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTA
* * * *
13510 CTCCAACCGAAATGAAAAGATATTATTATTC
66 CTTCAATCGAAATGAAGAGATATCATTATTC
13541 TCAACATCAA
Statistics
Matches: 190, Mismatches: 30, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
125 91 0.48
127 3 0.02
129 2 0.01
130 1 0.01
131 91 0.48
132 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (129 bp):
ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTA
CTTCAATCGAAATGAAGAGATATCATTATTCCATCTTAAAAATCAATATCATTCAGAGAAAATG
Found at i:15492 original size:42 final size:41
Alignment explanation
Indices: 15426--15505 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 41
15416 AGTGAAATTC
15426 TAATTATTTAAATAAAAATCATTTATATAAAAATTCATCGA
1 TAATTATTTAAATAAAAATCATTTATATAAAAATTCATCGA
*
15467 TAATATATTTAAATAAAAATTATTTATATAAAAATTCAT
1 TAAT-TATTTAAATAAAAATCATTTATATAAAAATTCAT
15506 ATCATAGTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 4 0.11
42 33 0.89
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (41 bp):
TAATTATTTAAATAAAAATCATTTATATAAAAATTCATCGA
Found at i:15502 original size:15 final size:15
Alignment explanation
Indices: 15427--15502 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 15
15417 GTGAAATTCT
15427 AATTATTTAAATAAA
1 AATTATTTAAATAAA
* *
15442 AATCATTTATATAAA
1 AATTATTTAAATAAA
**
15457 AATTCA--TCGAT-AA
1 AATT-ATTTAAATAAA
*
15470 TA-TATTTAAATAAA
1 AATTATTTAAATAAA
*
15484 AATTATTTATATAAA
1 AATTATTTAAATAAA
15499 AATT
1 AATT
15503 CATATCATAG
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 6 0.13
14 6 0.13
15 31 0.67
16 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:19985 original size:62 final size:62
Alignment explanation
Indices: 19906--20030 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
19896 ACAATAGTTT
* * *
19906 CAGGGGAAAAAAGGTATTAGGAGTCTGTCAGACAGCTGCGCGACCATCCCGGGAAGACGAGG
1 CAGGGAAAAAAAAGTATTAGGAGTCTGTCAGACAGCTGCACGACCATCCCGGGAAGACGAGG
19968 CAGGGAAAAAAAAGTATTAGGAGTCTGTCAGACAGCTGCACGACCATCCCGGGAAGACGAGG
1 CAGGGAAAAAAAAGTATTAGGAGTCTGTCAGACAGCTGCACGACCATCCCGGGAAGACGAGG
20030 C
1 C
20031 TAACCGAGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.33, C:0.22, G:0.33, T:0.13
Consensus pattern (62 bp):
CAGGGAAAAAAAAGTATTAGGAGTCTGTCAGACAGCTGCACGACCATCCCGGGAAGACGAGG
Found at i:24800 original size:21 final size:20
Alignment explanation
Indices: 24775--24818 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
24765 TAAATATTTT
*
24775 TTAATTCAAAAAAGTTTATAA
1 TTAATTCAAAAAA-TATATAA
* *
24796 TTAATTTAAATAATATATAA
1 TTAATTCAAAAAATATATAA
24816 TTA
1 TTA
24819 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAATTCAAAAAATATATAA
Found at i:25066 original size:182 final size:183
Alignment explanation
Indices: 24754--25138 Score: 607
Period size: 182 Copynumber: 2.1 Consensus size: 183
24744 TTTTCTAATT
* * * *
24754 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAGTTTATAATTAATTTAAATAATATATAATT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAGTTTACAAATAATTTAAATAATATATAATT
*
24818 ATAAAATAAAAATTTTAGATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
66 ATAAAATAAAAAATTTAGATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
* * *
24883 GATTTTAAATTATTAATTGGGCTTTAAATGGTTTGGGCTT-AGCCCATATGCTA
131 GATCTTAAATTATTAATTGGGCTTTAAATGATTTGAG-TTGAGCCCATATGCTA
24936 TATATAATATATTTAATATTTTTTAATT-AAAAACAGTTTACAAATAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAA-AGTTTACAAATAATTTAAATAATATATAAT
*
25000 TATAAAATAAAAAATTTATATAA-TTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
65 TATAAAATAAAAAATTTAGATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* ** *
25064 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGAGTTGAGTTCATATGTTA
130 GGATCTTAAATTATTAATTGGGCTTTAAATGATTTGAGTTGAGCCCATATGCTA
25118 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
25139 AAAATTTAAT
Statistics
Matches: 187, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
181 2 0.01
182 118 0.63
183 67 0.36
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAGTTTACAAATAATTTAAATAATATATAATT
ATAAAATAAAAAATTTAGATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
GATCTTAAATTATTAATTGGGCTTTAAATGATTTGAGTTGAGCCCATATGCTA
Found at i:26321 original size:10 final size:11
Alignment explanation
Indices: 26303--26364 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 11
26293 ATATTTAAAA
26303 TTTATTTTTAT
1 TTTATTTTTAT
26314 TTTA-TTTTAT
1 TTTATTTTTAT
*
26324 TTTAGTATTTAAAGT
1 TTTA-T-TTT-TA-T
26339 TTTAGTTTTTAT
1 TTTA-TTTTTAT
26351 TTTATTATTTAT
1 TTTATT-TTTAT
26363 TT
1 TT
26365 AAGATTTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
10 10 0.23
11 6 0.14
12 12 0.28
13 4 0.09
14 4 0.09
15 7 0.16
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:26322 original size:35 final size:37
Alignment explanation
Indices: 26274--26356 Score: 93
Period size: 37 Copynumber: 2.4 Consensus size: 37
26264 TATATTTAAA
* *
26274 TTTTTAATTT-TTTAAAATTA-TATTTAAA-ATTTA-
1 TTTTTATTTTATTTTAAATTAGTATTTAAAGATTTAG
** *
26307 TTTTTATTTTATTTTATTTTAGTATTTAAAGTTTTAG
1 TTTTTATTTTATTTTAAATTAGTATTTAAAGATTTAG
26344 TTTTTATTTTATT
1 TTTTTATTTTATT
26357 ATTTATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 9 0.22
34 7 0.17
35 8 0.20
36 4 0.10
37 13 0.32
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (37 bp):
TTTTTATTTTATTTTAAATTAGTATTTAAAGATTTAG
Found at i:26359 original size:35 final size:34
Alignment explanation
Indices: 26294--26360 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
26284 TTTAAAATTA
26294 TATTTAAAATTTATTTTTATTTTATTTTATTTTAG
1 TATTTAAAATTTATTTTTATTTTA-TTTATTTTAG
*
26329 TATTTAAAGTTTTAGTTTTTATTTTA-TTATTT
1 TATTTAAA-ATTTA-TTTTTATTTTATTTATTT
26361 ATTTAAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
35 14 0.48
36 4 0.14
37 11 0.38
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (34 bp):
TATTTAAAATTTATTTTTATTTTATTTATTTTAG
Found at i:26383 original size:37 final size:37
Alignment explanation
Indices: 26294--26383 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 37
26284 TTTAAAATTA
* *
26294 TATTTAAAATTT-A-TTTTTATTTTATTTTATTTTAG
1 TATTTAAAGTTTGAGTTTTTATTTTATTTTATTTAAG
*
26329 TATTTAAAGTTTTAGTTTTTATTTTATTATTTATTTAAG
1 TATTTAAAGTTTGAGTTTTTATTTTA-T-TTTATTTAAG
*
26368 -ATTTAATG-TTGAGTTT
1 TATTTAAAGTTTGAGTTT
26384 AAAAAATTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
35 11 0.23
36 1 0.02
37 18 0.38
38 8 0.17
39 9 0.19
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (37 bp):
TATTTAAAGTTTGAGTTTTTATTTTATTTTATTTAAG
Found at i:27358 original size:33 final size:33
Alignment explanation
Indices: 27311--27377 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
27301 TTTGACCTTG
*
27311 GTATGTAACCATTGTTAAAGATATACACGAGAC
1 GTATATAACCATTGTTAAAGATATACACGAGAC
27344 GTATATAACCATTGTTAAAGATATACACGAGAC
1 GTATATAACCATTGTTAAAGATATACACGAGAC
27377 G
1 G
27378 GATTAAATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (33 bp):
GTATATAACCATTGTTAAAGATATACACGAGAC
Found at i:27482 original size:28 final size:29
Alignment explanation
Indices: 27451--27557 Score: 107
Period size: 29 Copynumber: 3.7 Consensus size: 29
27441 TTTTTTCATT
27451 TAAGTACTTCAAA-TA-TTTTTTATCAAAA
1 TAAGTACTT-AAAGTATTTTTTTATCAAAA
27479 TAAGTACTTAAAGTATTTTTTTATCAAAA
1 TAAGTACTTAAAGTATTTTTTTATCAAAA
*
27508 TAAATA-TCT-AAGTTATTTTCTTTTATCAAAA
1 TAAGTACT-TAAAG-TA-TTT-TTTTATCAAAA
*
27539 TAGGTA-TCTAAAGTATTTT
1 TAAGTACT-TAAAGTATTTT
27558 ATGTCAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
27 3 0.04
28 15 0.22
29 22 0.32
30 6 0.09
31 20 0.29
32 3 0.04
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (29 bp):
TAAGTACTTAAAGTATTTTTTTATCAAAA
Found at i:27498 original size:29 final size:29
Alignment explanation
Indices: 27466--27578 Score: 117
Period size: 29 Copynumber: 3.9 Consensus size: 29
27456 ACTTCAAATA
27466 TTTTTTATCAAAATAAGTA-CTTAAAGTAT
1 TTTTTTATCAAAATAAGTATC-TAAAGTAT
*
27495 TTTTTTATCAAAATAAATATCT-AAGTTATT
1 TTTTTTATCAAAATAAGTATCTAAAG-TA-T
*
27525 TTCTTTTATCAAAATAGGTATCTAAAGTA-
1 TT-TTTTATCAAAATAAGTATCTAAAGTAT
* *
27554 TTTTATGTCAAAAT-AGATATCTAAA
1 TTTTTTATCAAAATAAG-TATCTAAA
27579 CTACTCAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
27 1 0.01
28 21 0.29
29 23 0.32
30 4 0.06
31 20 0.28
32 3 0.04
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (29 bp):
TTTTTTATCAAAATAAGTATCTAAAGTAT
Found at i:27535 original size:31 final size:30
Alignment explanation
Indices: 27466--27557 Score: 118
Period size: 31 Copynumber: 3.1 Consensus size: 30
27456 ACTTCAAATA
27466 TTTTTTATCAAAATAAGTA-CTTAAAGTA-T
1 TTTTTTATCAAAATAAGTATC-TAAAGTATT
*
27495 TTTTTTATCAAAATAAATATCT-AAGTTATT
1 TTTTTTATCAAAATAAGTATCTAAAG-TATT
*
27525 TTCTTTTATCAAAATAGGTATCTAAAGTATT
1 TT-TTTTATCAAAATAAGTATCTAAAGTATT
27556 TT
1 TT
27558 ATGTCAAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
28 3 0.05
29 21 0.38
30 4 0.07
31 24 0.44
32 3 0.05
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.48
Consensus pattern (30 bp):
TTTTTTATCAAAATAAGTATCTAAAGTATT
Found at i:27754 original size:30 final size:29
Alignment explanation
Indices: 27675--27756 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 29
27665 ATATTTCAGG
*
27675 TATTTATTTTGTCTAAAAAA-ATACTTTAAA
1 TATTTATTTTG-ATAAAAAATA-ACTTTAAA
** * *
27705 TACATACTTTAATTAAAAAATAACTTTAAA
1 TATTTATTTTGA-TAAAAAATAACTTTAAA
27735 TATTTATTTTGATAGAAAAATA
1 TATTTATTTTGATA-AAAAATA
27757 TTTTAGGTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
29 2 0.05
30 37 0.93
31 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (29 bp):
TATTTATTTTGATAAAAAATAACTTTAAA
Found at i:46084 original size:2 final size:2
Alignment explanation
Indices: 46077--46112 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
46067 TCTTTTACAT
46077 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46113 GATGTACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46099 original size:17 final size:17
Alignment explanation
Indices: 46077--46109 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
46067 TCTTTTACAT
46077 TATATATATATATATAA
1 TATATATATATATATAA
46094 TATATATATATATATA
1 TATATATATATATATA
46110 TATGATGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATATATATATAA
Found at i:46324 original size:2 final size:2
Alignment explanation
Indices: 46317--46346 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46307 AGTGAATCGC
46317 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46347 CTTAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49018 original size:22 final size:21
Alignment explanation
Indices: 48965--49018 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
48955 CCGATATATC
* * *
48965 AAATATTATATTTATTATATA
1 AAATAATATATCTATTACATA
48986 AAATCAATATATCTATTACATTA
1 AAAT-AATATATCTATTACA-TA
*
49009 AAATAGTATA
1 AAATAATATA
49019 CTTATATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 17 0.63
23 6 0.22
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATAATATATCTATTACATA
Found at i:49445 original size:33 final size:31
Alignment explanation
Indices: 49376--49445 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 31
49366 CAAAGATCTG
*
49376 ATTATTATTTTATAAATAAATTTTGTTAAAT
1 ATTATTATTTTATAAATAAATTTTGTTAAAA
*
49407 A-TATTATTTTATATAA-AATATTTTATTTAAAA
1 ATTATTATTTTATA-AATAA-ATTTT-GTTAAAA
49439 ATTATTA
1 ATTATTA
49446 AAAATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 14 0.42
31 8 0.24
32 6 0.18
33 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
ATTATTATTTTATAAATAAATTTTGTTAAAA
Found at i:57592 original size:16 final size:16
Alignment explanation
Indices: 57571--57603 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
57561 TGAAATAGTG
57571 GGAGCTATCCGTAATA
1 GGAGCTATCCGTAATA
57587 GGAGCTATCCGTAATA
1 GGAGCTATCCGTAATA
57603 G
1 G
57604 AAGATATGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (16 bp):
GGAGCTATCCGTAATA
Found at i:75911 original size:5 final size:5
Alignment explanation
Indices: 75901--75926 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
75891 AGTCATATAT
75901 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
75927 GAAACATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:90037 original size:255 final size:255
Alignment explanation
Indices: 89363--90132 Score: 1188
Period size: 255 Copynumber: 3.0 Consensus size: 255
89353 CTTTTGTGTT
* *
89363 ATGATGTTCCTCGATGGTCTTCTGTAATGACGTTCTTGTTAATG-C-CTCATCCGACATGCAACA
1 ATGATGTTCCTCGATGCTCTTCTGTAATGACCTTCTTGTTAATGTCTCTCATCCGACATGCAACA
* * * *
89426 CGGAAAACAGTTCATTTTTGGTCTTCCTTGCAAAGCAAGACATCCCAAATTCTTGAAGAAAATGT
66 CGAAAAACAGTTCA-TTTTGGTCTTCCTTGCAAAGGAAGACATCCCAAATTCATGAACAAAATGT
* * * * * *
89491 TTGATATGTATGCTCAAGAATTAATGAAAACCAACAGCTGATCAATGGGAAACAAGAAACCTACC
130 CTGATATATATGCTCAAGAATGAAGGAAAATCAACAGCTGATCAATGGGAAACAGGAAACCTACC
89556 TCCTCCCGGAGGCAACCGAATCGTATTCGGTCCCTCAGGAGGGCACAAGGAACAATGTCTC
195 TCCTCCCGGAGGCAACCGAATCGTATTCGGTCCCTCAGGAGGGCACAAGGAACAATGTCTC
* * *
89617 ATGATGTTTCTTGATGCTCTTCTGTAATGACCTTCTTGTT-A-GTGTCTCATCCGACATGCAACA
1 ATGATGTTCCTCGATGCTCTTCTGTAATGACCTTCTTGTTAATGTCTCTCATCCGACATGCAACA
* *
89680 CGAAAAACAGTTCATTTTGGTTTTCCTTGCAAAGGAAGACATCCCAAATTCATGAACAAAATGAC
66 CGAAAAACAGTTCATTTTGGTCTTCCTTGCAAAGGAAGACATCCCAAATTCATGAACAAAATGTC
* * * *
89745 TGATATATATGCTCAAGAATGAAGGAAAATCAACAGCTGACCTATGGGAAACAGGACACCTACAT
131 TGATATATATGCTCAAGAATGAAGGAAAATCAACAGCTGATCAATGGGAAACAGGAAACCTACCT
*
89810 CCTCCCGGAGGCAACCGAATCATATTCGGTCCCTCAGGAGGGCACAAGGAACAATGTCTC
196 CCTCCCGGAGGCAACCGAATCGTATTCGGTCCCTCAGGAGGGCACAAGGAACAATGTCTC
* *
89870 ATGATGTTCCTCGATGCTCTTTTGTAATGACCTTCTTGTTAATGTCTCTCATCCGACATACAACA
1 ATGATGTTCCTCGATGCTCTTCTGTAATGACCTTCTTGTTAATGTCTCTCATCCGACATGCAACA
* * *
89935 CGAAAAACAATTCATTTCGGTCTTCCTTGAAAAGGAAGACATCCCAAATTCATGAACAAAATGTC
66 CGAAAAACAGTTCATTTTGGTCTTCCTTGCAAAGGAAGACATCCCAAATTCATGAACAAAATGTC
* *
90000 TGATATATATCCTCAAGAATGAAGGAAAATCAACAGCTGATCAATGGGAAACGGGAAACCTACCT
131 TGATATATATGCTCAAGAATGAAGGAAAATCAACAGCTGATCAATGGGAAACAGGAAACCTACCT
* * * * *
90065 CCTCCCGGAGGCAACCGAATCGTATTCAGCCCCTTAGGAGGGTACAAGGAACAATGTTTC
196 CCTCCCGGAGGCAACCGAATCGTATTCGGTCCCTCAGGAGGGCACAAGGAACAATGTCTC
*
90125 ATTATGTT
1 ATGATGTT
90133 TTTTTTTTCT
Statistics
Matches: 467, Mismatches: 45, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
252 1 0.00
253 198 0.42
254 68 0.15
255 200 0.43
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (255 bp):
ATGATGTTCCTCGATGCTCTTCTGTAATGACCTTCTTGTTAATGTCTCTCATCCGACATGCAACA
CGAAAAACAGTTCATTTTGGTCTTCCTTGCAAAGGAAGACATCCCAAATTCATGAACAAAATGTC
TGATATATATGCTCAAGAATGAAGGAAAATCAACAGCTGATCAATGGGAAACAGGAAACCTACCT
CCTCCCGGAGGCAACCGAATCGTATTCGGTCCCTCAGGAGGGCACAAGGAACAATGTCTC
Found at i:100009 original size:13 final size:13
Alignment explanation
Indices: 99991--100016 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
99981 ACCAACGCAT
99991 AATCAAATCAATA
1 AATCAAATCAATA
100004 AATCAAATCAATA
1 AATCAAATCAATA
100017 TTCCATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
AATCAAATCAATA
Found at i:100472 original size:29 final size:29
Alignment explanation
Indices: 100430--100486 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
100420 TTGCTTTATG
100430 TTGATAAACAGCTTAGTGCTGCAGATACT
1 TTGATAAACAGCTTAGTGCTGCAGATACT
*
100459 TTGATAAACAGCTTAGTGCTGCTGATAC
1 TTGATAAACAGCTTAGTGCTGCAGATAC
100487 ATTATTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (29 bp):
TTGATAAACAGCTTAGTGCTGCAGATACT
Found at i:101248 original size:28 final size:26
Alignment explanation
Indices: 101209--101262 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
101199 TATCTTGAGA
101209 ATATTCTAAAATAAT-ATAAAAATAAT
1 ATATTCTAAAATAATCAT-AAAATAAT
*
101235 ATATATCTAAAAATATTCATAAAATAAT
1 ATAT-TCT-AAAATAATCATAAAATAAT
101263 CTAGATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 3 0.12
28 15 0.62
29 2 0.08
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
ATATTCTAAAATAATCATAAAATAAT
Found at i:108536 original size:31 final size:31
Alignment explanation
Indices: 108508--108566 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
108498 TATATGTGTT
*
108508 ACATCATATATTTTGACACATGACATGTGCA
1 ACATCATATATTTTAACACATGACATGTGCA
* * *
108539 ACATCATCTTTTTTAACACGTGACATGT
1 ACATCATATATTTTAACACATGACATGT
108567 TACAAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (31 bp):
ACATCATATATTTTAACACATGACATGTGCA
Found at i:118654 original size:15 final size:15
Alignment explanation
Indices: 118636--118665 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
118626 CTACAGTGCT
*
118636 ATTAGAACTTGTCAC
1 ATTAGAACTCGTCAC
118651 ATTAGAACTCGTCAC
1 ATTAGAACTCGTCAC
118666 GCCGATGTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (15 bp):
ATTAGAACTCGTCAC
Found at i:123740 original size:24 final size:25
Alignment explanation
Indices: 123691--123740 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
123681 TAAACAATAA
123691 TAATAAACATAATCTAATAATGCAACT
1 TAATAAACATAATC--ATAATGCAACT
123718 TAATAAACATAATC-TAATGCAAC
1 TAATAAACATAATCATAATGCAAC
123741 CTAGAGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.39
27 14 0.61
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.28
Consensus pattern (25 bp):
TAATAAACATAATCATAATGCAACT
Found at i:123952 original size:12 final size:12
Alignment explanation
Indices: 123935--123967 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
123925 ACAACAGTAA
123935 CAGTGCCCGAGC
1 CAGTGCCCGAGC
123947 CAGTGCCCGAGC
1 CAGTGCCCGAGC
123959 CAGTGCCCG
1 CAGTGCCCG
123968 TTTGCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.42, G:0.33, T:0.09
Consensus pattern (12 bp):
CAGTGCCCGAGC
Found at i:128264 original size:2 final size:2
Alignment explanation
Indices: 128254--128297 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
128244 AAAAAAGGAT
*
128254 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
128297 T
1 T
128298 CAAATATCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:131343 original size:75 final size:72
Alignment explanation
Indices: 131251--131402 Score: 241
Period size: 75 Copynumber: 2.1 Consensus size: 72
131241 AGTGAAAGTT
*
131251 CTTCAATTTCACCTGAATTTTCTTTCCTATGAGCAGTTTGTACTTCCTCATAGATCTGGTCTTCA
1 CTTCAATTTCACCTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATAGATCTGG---TCA
131316 CCTACATGAG
63 CCTACATGAG
* *
131326 CTTCAATTTCACTTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATTGATCTGGTCACCT
1 CTTCAATTTCACCTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATAGATCTGGTCACCT
*
131391 TCATGAG
66 ACATGAG
131398 CTTCA
1 CTTCA
131403 TCATGATTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
72 17 0.23
75 56 0.77
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (72 bp):
CTTCAATTTCACCTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATAGATCTGGTCACCT
ACATGAG
Found at i:135168 original size:21 final size:21
Alignment explanation
Indices: 135142--135181 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
135132 AAAAAAAGTC
135142 AGAAGGAAGATAAACTTTACT
1 AGAAGGAAGATAAACTTTACT
135163 AGAAGGAAGATAAACTTTA
1 AGAAGGAAGATAAACTTTA
135182 TTATAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (21 bp):
AGAAGGAAGATAAACTTTACT
Found at i:150716 original size:9 final size:9
Alignment explanation
Indices: 150704--150737 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
150694 GAATTCGGTT
150704 AATTAACCG
1 AATTAACCG
150713 AATTAACCG
1 AATTAACCG
150722 AATTAACCG
1 AATTAACCG
150731 AAATTAA
1 -AATTAA
150738 ATATTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:151270 original size:15 final size:15
Alignment explanation
Indices: 151250--151278 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
151240 AAAAAAAGTT
151250 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
151265 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
151279 CGGTCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:152915 original size:150 final size:153
Alignment explanation
Indices: 152641--152918 Score: 411
Period size: 150 Copynumber: 1.8 Consensus size: 153
152631 CCTGATCCTG
* * *
152641 CTGAAGCCGAAGCTAAGGATTTGTGTACCGGATCACTCGTCGCAGAGGAAGAAAACACCACCCTG
1 CTGAAGCCGAAGCTAAGGATTTGAGTACCGGACCACTCGTCGAAGAGGAAGAAAACACCACCCTG
* * * *
152706 GATGGAGGAGTAACACAAGCACATGAAGCTCCTTCTTCCGTTCAAACAGAGGAATCTAAGCAACA
66 GATGGAGGAGTAACACAAACAAAGGAAGCTCCGTCTTCCGTTCAAACAGAGGAATCTAAGCAACA
152771 ACTAATAAAAGAACCCGATCATC
131 ACTAATAAAAGAACCCGATCATC
* * * *
152794 CTGAAGCCTAAGCTAAGGATTTGAGTACCGGACCGCTTGTC-AAGGAGGAAG-AAA-A-CACCTT
1 CTGAAGCCGAAGCTAAGGATTTGAGTACCGGACCACTCGTCGAA-GAGGAAGAAAACACCACCCT
*
152855 GGATGGAGGAGTAACACAAACAAAGGAAGCTCCGTCTTCTGTTCAAACAGAGGAATCTAAGCAA
65 GGATGGAGGAGTAACACAAACAAAGGAAGCTCCGTCTTCCGTTCAAACAGAGGAATCTAAGCAA
152919 TAGCTTACAA
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
150 64 0.57
151 1 0.01
152 4 0.04
153 43 0.38
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (153 bp):
CTGAAGCCGAAGCTAAGGATTTGAGTACCGGACCACTCGTCGAAGAGGAAGAAAACACCACCCTG
GATGGAGGAGTAACACAAACAAAGGAAGCTCCGTCTTCCGTTCAAACAGAGGAATCTAAGCAACA
ACTAATAAAAGAACCCGATCATC
Found at i:153197 original size:221 final size:221
Alignment explanation
Indices: 152814--153255 Score: 884
Period size: 221 Copynumber: 2.0 Consensus size: 221
152804 AGCTAAGGAT
152814 TTGAGTACCGGACCGCTTGTCAAGGAGGAAGAAAACACCTTGGATGGAGGAGTAACACAAACAAA
1 TTGAGTACCGGACCGCTTGTCAAGGAGGAAGAAAACACCTTGGATGGAGGAGTAACACAAACAAA
152879 GGAAGCTCCGTCTTCTGTTCAAACAGAGGAATCTAAGCAATAGCTTACAAGTTGTTGACGAGGGA
66 GGAAGCTCCGTCTTCTGTTCAAACAGAGGAATCTAAGCAATAGCTTACAAGTTGTTGACGAGGGA
152944 CATAAACACACACTCACACATATGTTTCTGTGTGCATGTGACAGAAAATAATGATCATTTCCTCA
131 CATAAACACACACTCACACATATGTTTCTGTGTGCATGTGACAGAAAATAATGATCATTTCCTCA
153009 ATTCGAAGAATCGATAAACCAGAGCC
196 ATTCGAAGAATCGATAAACCAGAGCC
153035 TTGAGTACCGGACCGCTTGTCAAGGAGGAAGAAAACACCTTGGATGGAGGAGTAACACAAACAAA
1 TTGAGTACCGGACCGCTTGTCAAGGAGGAAGAAAACACCTTGGATGGAGGAGTAACACAAACAAA
153100 GGAAGCTCCGTCTTCTGTTCAAACAGAGGAATCTAAGCAATAGCTTACAAGTTGTTGACGAGGGA
66 GGAAGCTCCGTCTTCTGTTCAAACAGAGGAATCTAAGCAATAGCTTACAAGTTGTTGACGAGGGA
153165 CATAAACACACACTCACACATATGTTTCTGTGTGCATGTGACAGAAAATAATGATCATTTCCTCA
131 CATAAACACACACTCACACATATGTTTCTGTGTGCATGTGACAGAAAATAATGATCATTTCCTCA
153230 ATTCGAAGAATCGATAAACCAGAGCC
196 ATTCGAAGAATCGATAAACCAGAGCC
153256 AGAGGTTGGC
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
221 221 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (221 bp):
TTGAGTACCGGACCGCTTGTCAAGGAGGAAGAAAACACCTTGGATGGAGGAGTAACACAAACAAA
GGAAGCTCCGTCTTCTGTTCAAACAGAGGAATCTAAGCAATAGCTTACAAGTTGTTGACGAGGGA
CATAAACACACACTCACACATATGTTTCTGTGTGCATGTGACAGAAAATAATGATCATTTCCTCA
ATTCGAAGAATCGATAAACCAGAGCC
Found at i:154234 original size:39 final size:39
Alignment explanation
Indices: 154180--154259 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
154170 AGTAGATGTC
154180 TGATTCACGCAGCTATTGATGTTAGTGTTCTCTGTCACT
1 TGATTCACGCAGCTATTGATGTTAGTGTTCTCTGTCACT
*
154219 TGATTCACGGAGCTATTGATGTTAGTGTTCTCTGTCACT
1 TGATTCACGCAGCTATTGATGTTAGTGTTCTCTGTCACT
154258 TG
1 TG
154260 TGAGTTGATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (39 bp):
TGATTCACGCAGCTATTGATGTTAGTGTTCTCTGTCACT
Found at i:157202 original size:13 final size:13
Alignment explanation
Indices: 157172--157239 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 13
157162 TTTGAAAATA
157172 TTTAAAATATAA-
1 TTTAAAATATAAT
157184 -TTAAAATATAAT
1 TTTAAAATATAAT
157196 TTTAAAATA-AAT
1 TTTAAAATATAAT
* * *
157208 TAT-ATATTTAAT
1 TTTAAAATATAAT
*
157220 ATTTAAATTATCAAT
1 -TTTAAAATAT-AAT
157235 TTTAA
1 TTTAA
157240 TTTATTTTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
11 14 0.33
12 8 0.19
13 10 0.23
14 8 0.19
15 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTAAAATATAAT
Found at i:157211 original size:18 final size:20
Alignment explanation
Indices: 157185--157240 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 20
157175 AAAATATAAT
*
157185 TAAAATATAATTTTAA-A-A
1 TAAATTATAATTTTAATATA
*
157203 TAAATTAT-ATATTTAATATT
1 TAAATTATAAT-TTTAATATA
157223 TAAATTATCAATTTTAAT
1 TAAATTAT-AATTTTAAT
157241 TTATTTTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 2 0.06
18 12 0.39
19 1 0.03
20 8 0.26
21 6 0.19
22 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAATTATAATTTTAATATA
Found at i:157219 original size:24 final size:25
Alignment explanation
Indices: 157168--157235 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 25
157158 TTATTTTGAA
157168 AATATTTAAAATATAATTAAAATAT
1 AATATTTAAAATATAATTAAAATAT
* *
157193 AAT-TTTAAAATA-AATTATATATTT
1 AATATTTAAAATATAATTA-AAATAT
*
157217 AATATTTAAATTATCAATT
1 AATATTTAAAATAT-AATT
157236 TTAATTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 5 0.14
24 16 0.44
25 11 0.31
27 4 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (25 bp):
AATATTTAAAATATAATTAAAATAT
Found at i:159511 original size:20 final size:20
Alignment explanation
Indices: 159488--159539 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
159478 AACGCGATCC
159488 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
159508 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
159528 CCAAAATCGCAA
1 CCAGAATCGCAA
159540 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:159556 original size:21 final size:20
Alignment explanation
Indices: 159529--159627 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
159519 AATCAGTTTC
159529 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
159550 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
159571 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
159591 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
159612 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
159628 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:159656 original size:20 final size:20
Alignment explanation
Indices: 159594--159787 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
159584 CGATTTTCCA
* ** *
159594 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
159614 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
159634 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
159654 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
159674 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
159694 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
159714 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
159734 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
159754 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
159775 AAATCGCAACGCG
1 AAATCGCAACGCG
159788 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:159678 original size:60 final size:60
Alignment explanation
Indices: 159594--159787 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
159584 CGATTTTCCA
* ** * *
159594 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
159654 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
159714 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
159775 AAATCGCAACGCG
1 AAATCGCAACGCG
159788 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:160207 original size:33 final size:33
Alignment explanation
Indices: 160168--160238 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
160158 TTCACTTAGA
*
160168 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
160201 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
160234 TTTCA
1 TTTCA
160239 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:160370 original size:22 final size:20
Alignment explanation
Indices: 160316--160371 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
160306 TTTGCAGAAG
*
160316 AGTCGCAACGAGATAAATGA
1 AGTCGCAACGAGAGAAATGA
*
160336 AATCGCAACGAGAG-AATGA
1 AGTCGCAACGAGAGAAATGA
*
160355 CTGTCGCAACGAGAGAA
1 -AGTCGCAACGAGAGAA
160372 TCGCAACGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 5 0.17
20 24 0.80
21 1 0.03
ACGTcount: A:0.43, C:0.18, G:0.27, T:0.12
Consensus pattern (20 bp):
AGTCGCAACGAGAGAAATGA
Found at i:160377 original size:14 final size:14
Alignment explanation
Indices: 160358--160412 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
160348 AGAATGACTG
160358 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
160372 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
160391 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
160405 TCGCAACG
1 TCGCAACG
160413 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:160425 original size:33 final size:33
Alignment explanation
Indices: 160358--160428 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
160348 AGAATGACTG
***
160358 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
160391 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
160424 TCGCA
1 TCGCA
160429 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:160446 original size:19 final size:19
Alignment explanation
Indices: 160424--160521 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
160414 GAAACCAAAA
*
160424 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
160443 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
160457 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
160476 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
160490 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
160509 TCGCGTTGCGATT
1 TCGCGTTGCGATT
160522 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:160465 original size:14 final size:14
Alignment explanation
Indices: 160446--160535 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
160436 TTTCATTTCG
160446 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
160460 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
160479 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
160493 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
160510 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
160526 CGTTGCGATT
1 CGTTGCGATT
160536 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:160471 original size:33 final size:33
Alignment explanation
Indices: 160429--160543 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
160419 CAAAATCGCA
160429 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
160462 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
160495 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
160528 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
160544 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:162555 original size:93 final size:93
Alignment explanation
Indices: 162242--162620 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
162232 TAGATTGCTT
*
162242 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
162307 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
162334 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
162398 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
162426 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
162491 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
162519 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
162584 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
162612 AGTAAATTT
1 AGTAAATTT
162621 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
91 12 0.04
92 140 0.49
93 132 0.46
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:162578 original size:185 final size:185
Alignment explanation
Indices: 162242--162622 Score: 737
Period size: 185 Copynumber: 2.1 Consensus size: 185
162232 TAGATTGCTT
162242 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
162307 TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
162372 TGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
162426 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
162491 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTG-TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
162556 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
162612 AGTAAATTTAT
1 AGTAAATTTAT
162623 CCATTCAAGT
Statistics
Matches: 193, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 74 0.38
185 79 0.41
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:162704 original size:19 final size:19
Alignment explanation
Indices: 162664--162792 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
162654 TAGTTTACTT
* *
162664 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
162684 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
162703 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
162722 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
162736 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
162755 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
162769 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
162788 TCGCA
1 TCGCA
162793 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:162743 original size:33 final size:32
Alignment explanation
Indices: 162700--162792 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
162690 CGCGAAACCA
**
162700 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
162732 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
162765 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
162793 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:162790 original size:52 final size:52
Alignment explanation
Indices: 162664--162792 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
162654 TAGTTTACTT
**
162664 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
162716 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
162769 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
162793 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:162810 original size:19 final size:19
Alignment explanation
Indices: 162788--162922 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
162778 GAAACCAAAA
*
162788 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
162807 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
162823 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
162840 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
162856 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
162873 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
162892 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
162912 TCGTGTTGCGA
1 TCGCGTTGCGA
162923 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:162829 original size:14 final size:14
Alignment explanation
Indices: 162810--162866 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
162800 TTTCATTTCG
162810 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
162824 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
162841 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
162857 CGTTGCGATT
1 CGTTGCGATT
162867 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:162835 original size:33 final size:33
Alignment explanation
Indices: 162793--162885 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
162783 CAAAATCGCA
*
162793 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
162826 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
162859 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
162886 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:164780 original size:38 final size:38
Alignment explanation
Indices: 164737--164809 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
164727 AATTGATTGT
*
164737 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
164775 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
164810 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:164796 original size:19 final size:19
Alignment explanation
Indices: 164732--164796 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
164722 AGTTTAATTG
*
164732 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
164751 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
164769 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
164789 ATTGATTT
1 ATTGATTT
164797 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:164810 original size:14 final size:14
Alignment explanation
Indices: 164791--164826 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
164781 ATTGTTTAAT
164791 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
164805 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
164819 TGATTTGT
1 TGATTTGT
164827 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:164949 original size:19 final size:19
Alignment explanation
Indices: 164933--165034 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
164923 AAAAATGACT
164933 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
164952 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
164971 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
164985 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
165004 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
165024 ATCGCAATGCG
1 ATCGCAATGCG
165035 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:165083 original size:33 final size:33
Alignment explanation
Indices: 165041--165369 Score: 235
Period size: 33 Copynumber: 9.5 Consensus size: 33
165031 TGCGTTTATA
165041 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
165074 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
165110 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
165145 ATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
165183 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
165216 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
165256 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
165287 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
165320 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
165354 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
165370 GTATTTTCCG
Statistics
Matches: 252, Mismatches: 21, Indels: 46
0.79 0.07 0.14
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 101 0.40
34 29 0.12
35 19 0.08
36 19 0.08
37 2 0.01
38 56 0.22
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:165087 original size:19 final size:19
Alignment explanation
Indices: 165063--165369 Score: 367
Period size: 19 Copynumber: 17.4 Consensus size: 19
165053 GATTATCTCG
165063 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
165082 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
165101 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
165115 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
165134 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
165153 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
165172 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
165191 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
165205 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
165224 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
165243 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
165257 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
165276 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
165295 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
165309 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
165329 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
165343 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
165362 TTGCGATT
1 TTGCGATT
165370 GTATTTTCCG
Statistics
Matches: 250, Mismatches: 12, Indels: 52
0.80 0.04 0.17
Matches are distributed among these distances:
14 35 0.14
16 31 0.12
17 28 0.11
18 3 0.01
19 141 0.56
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:165103 original size:52 final size:52
Alignment explanation
Indices: 165041--165341 Score: 267
Period size: 52 Copynumber: 5.6 Consensus size: 52
165031 TGCGTTTATA
165041 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
1 ATTTCG-ATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
*
165093 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
1 ATTTCG-ATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
*
165145 ATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCG-ATTGCGA--TT--TCTCG--TTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * * * *
165204 GTTGCGATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * * * *
165256 GTTGCGATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * *
165308 GTTGCGATTTTC-ATTTC-CGCATTGCGATTTTCAT
1 ATTTCGA-TTGCGATTTCTCG--TTGCGATTTTCAT
165342 GTTGGGATTT
Statistics
Matches: 228, Mismatches: 11, Indels: 19
0.88 0.04 0.07
Matches are distributed among these distances:
51 1 0.00
52 164 0.72
53 13 0.06
54 4 0.02
55 5 0.02
56 2 0.01
57 27 0.12
58 3 0.01
59 9 0.04
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGATTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
Found at i:165138 original size:71 final size:71
Alignment explanation
Indices: 165063--165302 Score: 364
Period size: 71 Copynumber: 3.4 Consensus size: 71
165053 GATTATCTCG
165063 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
165128 TTCGCA
66 TTCGCA
* *
165134 TTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATT
*
165197 TTC-TCTCG--
61 TTCATTTCGCA
*
165205 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
165270 TTCGCA
66 TTCGCA
165276 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
165303 CTCTCGTTGC
Statistics
Matches: 152, Mismatches: 7, Indels: 20
0.85 0.04 0.11
Matches are distributed among these distances:
66 6 0.04
68 7 0.05
69 7 0.05
71 111 0.73
73 7 0.05
74 8 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:167689 original size:12 final size:12
Alignment explanation
Indices: 167672--167696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
167662 TCTTCGGGGA
167672 CTTTTTCTTCTT
1 CTTTTTCTTCTT
167684 CTTTTTCTTCTT
1 CTTTTTCTTCTT
167696 C
1 C
167697 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:167904 original size:24 final size:24
Alignment explanation
Indices: 167870--167916 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
167860 CTGAAACATC
167870 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
167894 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
167917 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:168616 original size:20 final size:20
Alignment explanation
Indices: 168588--168956 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
168578 AAATTTCAGT
* * * *
168588 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
168608 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
168628 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
168648 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
168668 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
168688 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
168708 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
168728 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
168748 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
168768 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
168788 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
168808 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
168828 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
168848 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
168868 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
168888 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
168908 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
168928 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
168948 GTTGCGATT
1 GTTGCGATT
168957 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 34, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 5 0.02
20 297 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:169495 original size:20 final size:20
Alignment explanation
Indices: 169458--169495 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
169448 AAAAAGTTAT
* *
169458 TTAAAATATTATTTTTTTAC
1 TTAAAATATTACTATTTTAC
169478 TTAAAATATTACTATTTT
1 TTAAAATATTACTATTTT
169496 TTTAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAAAATATTACTATTTTAC
Found at i:169637 original size:21 final size:21
Alignment explanation
Indices: 169598--169637 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
169588 TAAAGCGCCC
*
169598 AATAATAATGTTTCCGGTAGA
1 AATAATAATGTTTCAGGTAGA
*
169619 AATAATAATGTTTTAGGTA
1 AATAATAATGTTTCAGGTA
169638 ATTTTTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (21 bp):
AATAATAATGTTTCAGGTAGA
Found at i:170077 original size:21 final size:20
Alignment explanation
Indices: 170020--170079 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
170010 ATATTAAATT
*
170020 ATAAAATTATAAAAT-TTTA
1 ATAAAAATATAAAATATTTA
*
170039 GTATAAAAT-T-AAATATTTA
1 ATA-AAAATATAAAATATTTA
170058 ATAAAAATATAAAAGTATTTA
1 ATAAAAATATAAAA-TATTTA
170079 A
1 A
170080 AATATATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 9 0.27
19 10 0.30
20 7 0.21
21 7 0.21
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
ATAAAAATATAAAATATTTA
Found at i:170095 original size:17 final size:17
Alignment explanation
Indices: 170059--170097 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
170049 AAATATTTAA
170059 TAAAAATATAAAAGTATT
1 TAAAAATATAAAAG-ATT
170077 TAAAATATATAAAAG-TT
1 TAAAA-ATATAAAAGATT
170094 TAAA
1 TAAA
170098 GCTTTTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
TAAAAATATAAAAGATT
Found at i:175982 original size:60 final size:60
Alignment explanation
Indices: 175850--175983 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
175840 ATTAGGCACT
* * * *
175850 GGATTTGTCACTGGTGTGCTCAATGGGACTCCTCCAGCCGGGGCAGGATACGTAGTTACA
1 GGATTCGTCACCGGTGTGCTCAACGGGACTCCTCCAGCCGGCGCAGGATACGTAGTTACA
* * * * * * *
175910 GGATTCGCCACCGGTGTGCTCACCGGGACTCCTCCAGTCGGCGCGGGGTACGTCGTTACC
1 GGATTCGTCACCGGTGTGCTCAACGGGACTCCTCCAGCCGGCGCAGGATACGTAGTTACA
*
175970 GGATTCTTCACCGG
1 GGATTCGTCACCGG
175984 CTGCTGCGCC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.16, C:0.29, G:0.32, T:0.23
Consensus pattern (60 bp):
GGATTCGTCACCGGTGTGCTCAACGGGACTCCTCCAGCCGGCGCAGGATACGTAGTTACA
Found at i:176631 original size:2 final size:2
Alignment explanation
Indices: 176624--176658 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
176614 ATCGTAGTGA
176624 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
176659 AAGAAAAGCT
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:177142 original size:2 final size:2
Alignment explanation
Indices: 177137--177212 Score: 81
Period size: 2 Copynumber: 40.5 Consensus size: 2
177127 TTTTATTTTT
* * *
177137 TA TA TA TT TA TA T- TT TA T- TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
177177 TA CA TA TA TA TA TA TA TA TA TA TA T- TA T- TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
177213 TTATTTTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
1 5 0.08
2 57 0.92
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:177150 original size:22 final size:22
Alignment explanation
Indices: 177125--177219 Score: 77
Period size: 22 Copynumber: 4.3 Consensus size: 22
177115 CGTTCGAAAT
* * *
177125 TATTTTATTTTTTATATATTTA
1 TATTTTATTATATATATATATA
177147 TATTTTATTATATATATATATA
1 TATTTTATTATATATATATATA
** *
177169 TATACATATACATATATATATATA
1 TAT-TTTAT-TATATATATATATA
* *
177193 TATATATATTAT-TAT-TATATT
1 TAT-TTTATTATATATATATATA
177214 TATTTT
1 TATTTT
177220 TTTTATTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.03
21 8 0.13
22 25 0.41
23 5 0.08
24 21 0.34
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTATTATATATATATATA
Found at i:178038 original size:29 final size:29
Alignment explanation
Indices: 178002--178086 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
177992 ACCCAACCCA
* *
178002 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCGGCGACCTAC
* * *
178031 TAGGTCGCCATGCACTCCGGGCGACCAAG
1 TAGGTCGCCATGCACTCCCGGCGACCTAC
* *
178060 GAGGTCGCCATGCACACCCGGCGACCT
1 TAGGTCGCCATGCACTCCCGGCGACCT
178087 TGTCTCCTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.14
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCGGCGACCTAC
Found at i:180243 original size:14 final size:14
Alignment explanation
Indices: 180224--180277 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
180214 CACAATTCAC
180224 AATCTTAAACCATA
1 AATCTTAAACCATA
180238 AATCTTAAACTCA-A
1 AATCTTAAAC-CATA
*
180252 AATTTTAAACC-TCA
1 AATCTTAAACCAT-A
*
180266 AATCATAAACCA
1 AATCTTAAACCA
180278 CACACACTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 1 0.03
14 30 0.91
15 2 0.06
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (14 bp):
AATCTTAAACCATA
Found at i:180816 original size:28 final size:26
Alignment explanation
Indices: 180772--180827 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
180762 TCTTAAAAAA
*
180772 TTTAATTTTTATATAATTATATTAATT
1 TTTAATTTTTATATAATGATA-TAATT
180799 TTTATATTTTCTAT-TAATGATATAATT
1 TTTA-ATTTT-TATATAATGATATAATT
180826 TT
1 TT
180828 ACATCTCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 11 0.42
28 12 0.46
29 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTAATTTTTATATAATGATATAATT
Found at i:182409 original size:17 final size:17
Alignment explanation
Indices: 182387--182431 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
182377 AAAAGAAAGT
182387 TAAATAATTATAATATC
1 TAAATAATTATAATATC
* *
182404 TAAATAATGAGTAGTATC
1 TAAATAATTA-TAATATC
182422 TAAAT-ATTAT
1 TAAATAATTAT
182432 TTTGGTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 12 0.50
18 11 0.46
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (17 bp):
TAAATAATTATAATATC
Found at i:182423 original size:18 final size:17
Alignment explanation
Indices: 182387--182427 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
182377 AAAAGAAAGT
*
182387 TAAATAATTATAATATC
1 TAAATAATGATAATATC
*
182404 TAAATAATGAGTAGTATC
1 TAAATAATGA-TAATATC
182422 TAAATA
1 TAAATA
182428 TTATTTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (17 bp):
TAAATAATGATAATATC
Found at i:182464 original size:62 final size:62
Alignment explanation
Indices: 182354--182508 Score: 206
Period size: 62 Copynumber: 2.5 Consensus size: 62
182344 ATTCAAAGGT
* * * *
182354 GTATCTAAATAATAATTTGGTAAAAAAGAAAGTTAAATAATTATAATATCTAAATAATG-AGTA
1 GTATCTAAATATTATTTTGGTAAAAAA-ATAGTTAAATAATTATAATATCTAAAT-ACGAAGTA
*
182417 GTATCTAAATATTATTTTGGTAAAAAAATAGTTAAGTAATTATAATATCTAAATACGAAGTA
1 GTATCTAAATATTATTTTGGTAAAAAAATAGTTAAATAATTATAATATCTAAATACGAAGTA
* *
182479 GTATCTAAATGTT-TATTTGGTAAAAGAATA
1 GTATCTAAATATTAT-TTTGGTAAAAAAATA
182509 AAGTGTAAGA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
61 3 0.04
62 55 0.66
63 25 0.30
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (62 bp):
GTATCTAAATATTATTTTGGTAAAAAAATAGTTAAATAATTATAATATCTAAATACGAAGTA
Found at i:184597 original size:14 final size:15
Alignment explanation
Indices: 184564--184601 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
184554 ATAACTTTTT
*
184564 TTTAAATTATTAATA
1 TTTAATTTATTAATA
*
184579 TTTAATTTATTCATA
1 TTTAATTTATTAATA
184594 -TTAATTTA
1 TTTAATTTA
184602 AATTAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATTTATTAATA
Found at i:189504 original size:12 final size:12
Alignment explanation
Indices: 189491--189701 Score: 323
Period size: 12 Copynumber: 17.6 Consensus size: 12
189481 AATCACCATA
*
189491 TACATATACATA
1 TACATATACATG
*
189503 TACATATACATA
1 TACATATACATG
*
189515 TACATATACATA
1 TACATATACATG
*
189527 TACATATACATA
1 TACATATACATG
189539 TACATATACATG
1 TACATATACATG
189551 TACATATACATG
1 TACATATACATG
189563 TACATATACATG
1 TACATATACATG
189575 TACATATACATG
1 TACATATACATG
189587 TACATATACATG
1 TACATATACATG
189599 TACATATACATG
1 TACATATACATG
189611 TACATATACATG
1 TACATATACATG
189623 TACATATACATG
1 TACATATACATG
189635 TACATATACATG
1 TACATATACATG
189647 TACATATACATG
1 TACATATACATG
***
189659 TACATATACGCA
1 TACATATACATG
* **
189671 TACACATACACA
1 TACATATACATG
*
189683 TACATATACATA
1 TACATATACATG
189695 TACATAT
1 TACATAT
189702 CTCCAACCAA
Statistics
Matches: 191, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 191 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (12 bp):
TACATATACATG
Found at i:190881 original size:21 final size:22
Alignment explanation
Indices: 190857--190904 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
190847 AACTGTAATT
190857 ATAATATAATATTTATTCAA-A
1 ATAATATAATATTTATTCAATA
** *
190878 ATAAT-TTTTATTTATTTAATA
1 ATAATATAATATTTATTCAATA
190899 ATAATA
1 ATAATA
190905 CTTAAAGACC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATATAATATTTATTCAATA
Found at i:191210 original size:2 final size:2
Alignment explanation
Indices: 191203--191237 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
191193 AGAACAATAG
191203 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
191238 CAAACATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:199138 original size:24 final size:24
Alignment explanation
Indices: 199111--199158 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
199101 CGTACAATCA
199111 GATTCAACAAAATATTCACAATTC
1 GATTCAACAAAATATTCACAATTC
199135 GATTCAACAAAATATTCACAATTC
1 GATTCAACAAAATATTCACAATTC
199159 AACTAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.29
Consensus pattern (24 bp):
GATTCAACAAAATATTCACAATTC
Found at i:199160 original size:19 final size:21
Alignment explanation
Indices: 199112--199168 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 21
199102 GTACAATCAG
199112 ATTCAACAAAATATTCACAATT
1 ATTCAACAAAATATTCACAA-T
199134 CGATTCAACAAAATATTCAC-A-
1 --ATTCAACAAAATATTCACAAT
*
199155 ATTCAACTAAATAT
1 ATTCAACAAAATAT
199169 GCAATGAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 13 0.41
23 1 0.03
24 18 0.56
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (21 bp):
ATTCAACAAAATATTCACAAT
Found at i:205772 original size:35 final size:37
Alignment explanation
Indices: 205713--205786 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 37
205703 ATACCTAAAG
*
205713 TTTAGTTTTTGTTTTATTTTAGTACACCGTT-AAAAT
1 TTTAGTTTTTGTTTCATTTTAGTACACCGTTCAAAAT
*
205749 TTTAGTTTTT-TTTCATTTTAGTACCCCGTTCAAAAT
1 TTTAGTTTTTGTTTCATTTTAGTACACCGTTCAAAAT
205785 TT
1 TT
205787 AACGTTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 18 0.51
36 17 0.49
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.55
Consensus pattern (37 bp):
TTTAGTTTTTGTTTCATTTTAGTACACCGTTCAAAAT
Found at i:206336 original size:29 final size:27
Alignment explanation
Indices: 206286--206349 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
206276 TTTTGATCAG
*
206286 AACGTTTATTTTATGGTTAAAGTACTTTT
1 AACGTTTATTTTATGGTAAAAG-A-TTTT
206315 AACGTTTATTTTAT-GTAAAAAGATTTT
1 AACGTTTATTTTATGGT-AAAAGATTTT
*
206342 TACGTTTA
1 AACGTTTA
206350 ACTGAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 11 0.34
28 3 0.09
29 18 0.56
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (27 bp):
AACGTTTATTTTATGGTAAAAGATTTT
Found at i:208319 original size:12 final size:12
Alignment explanation
Indices: 208302--208326 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
208292 GGGGAAGTTC
208302 ATATTTGTATTT
1 ATATTTGTATTT
208314 ATATTTGTATTT
1 ATATTTGTATTT
208326 A
1 A
208327 AAAGTCCGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (12 bp):
ATATTTGTATTT
Found at i:212821 original size:60 final size:60
Alignment explanation
Indices: 212715--212829 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
212705 GTGTATATAT
*
212715 ATAGTTTGGGATGAAATTGGAAAGTTCAAAAAGTTTGGGGTCTAATTTAGAATGAAGGCA
1 ATAGTTTGGGATGAAATTGGAAAGTTCAAAAAGTTTGGGATCTAATTTAGAATGAAGGCA
*
212775 ATAGTTTGAGGATGAAATT-GAACTGTTC-AAAAGTTTGAGGAT-TAATTTAGAATGA
1 ATAGTTTG-GGATGAAATTGGAA-AGTTCAAAAAGTTTG-GGATCTAATTTAGAATGA
212830 TAATCATAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
60 33 0.66
61 17 0.34
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.32
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGGAAAGTTCAAAAAGTTTGGGATCTAATTTAGAATGAAGGCA
Found at i:212839 original size:60 final size:60
Alignment explanation
Indices: 212715--212846 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
212705 GTGTATATAT
* *
212715 ATAGTTTGGGATGAAATTGGAAAGTTCAAAAAGTTTGGGGTCTAATTTAGAATGAAGGCA
1 ATAGTTTGGGATGAAATTGGAAAGTTCAAAAAGTTTGGGATCTAATTTAGAATGAAAGCA
* *
212775 ATAGTTTGAGGATGAAATT-GAACTGTTC-AAAAGTTTGAGGAT-TAATTTAGAATGATAATC-
1 ATAGTTTG-GGATGAAATTGGAA-AGTTCAAAAAGTTTG-GGATCTAATTTAGAATGA-AAGCA
212835 ATAGTTTAGGGA
1 ATAGTTT-GGGA
212847 CATAGGACAC
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
60 43 0.68
61 20 0.32
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGGAAAGTTCAAAAAGTTTGGGATCTAATTTAGAATGAAAGCA
Found at i:212989 original size:6 final size:6
Alignment explanation
Indices: 212978--213011 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
212968 TTTCTTTTAT
212978 CATGTC CATGTC CATGTC CATGTC CATGTC CATG
1 CATGTC CATGTC CATGTC CATGTC CATGTC CATG
213012 ATTGATGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (6 bp):
CATGTC
Found at i:213287 original size:4 final size:4
Alignment explanation
Indices: 213278--214722 Score: 2744
Period size: 4 Copynumber: 365.2 Consensus size: 4
213268 CCCTTGCCAT
213278 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213326 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213374 TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA -GTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213420 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213468 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213516 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213564 TGTA TGTA TGTA TGTA TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213610 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213658 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
213706 TGTA TGTA TGTA GGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213754 TGTA TGTA TGTA TGTA TGTA TGTA TG-A TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213801 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213849 TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213895 TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213941 TGTA TGTA TGTA TGTA TGTA TGTA T-TA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
213988 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214036 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214084 TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214131 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214179 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214227 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214275 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214323 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214371 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGT- TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214417 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214463 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-TA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214510 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
214558 TGTA TGTA -GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA GTATA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -TGTA
214606 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214654 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
214702 TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA T
214723 ATGGGTTAAA
Statistics
Matches: 1419, Mismatches: 4, Indels: 36
0.97 0.00 0.02
Matches are distributed among these distances:
2 8 0.01
3 27 0.02
4 1381 0.97
5 3 0.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:216681 original size:47 final size:48
Alignment explanation
Indices: 216626--216727 Score: 188
Period size: 47 Copynumber: 2.1 Consensus size: 48
216616 ATAATATTAC
*
216626 TATAATTAATTTATATATTTTCTTTAAAAATTTTAAATTCATAATA-T
1 TATAATTAATTTATATATTTTCTTTAAAAATTTTAAATTCATAAAATT
216673 TATAATTAATTTATATATTTTCTTTAAAAATTTTAAATTCATAAAATT
1 TATAATTAATTTATATATTTTCTTTAAAAATTTTAAATTCATAAAATT
216721 TATAATT
1 TATAATT
216728 TTTTTTTACA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 45 0.85
48 8 0.15
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (48 bp):
TATAATTAATTTATATATTTTCTTTAAAAATTTTAAATTCATAAAATT
Found at i:218007 original size:24 final size:23
Alignment explanation
Indices: 217967--218039 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 23
217957 ACTTGTTTTT
* *
217967 TTTAT-ATATTTTTAAAAATTTA
1 TTTATAATATTATAAAAAATTTA
* * *
217989 TATTA-AATTATTCTAAAAAGTATA
1 T-TTATAA-TATTATAAAAAATTTA
218013 TTTATAATATTATAAAAATATTTA
1 TTTATAATATTATAAAAA-ATTTA
218037 TTT
1 TTT
218040 TATTTTTCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
22 1 0.03
23 17 0.44
24 21 0.54
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (23 bp):
TTTATAATATTATAAAAAATTTA
Found at i:218088 original size:22 final size:22
Alignment explanation
Indices: 218060--218110 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
218050 ATCATATTAT
218060 TTATTTATTTAAAATAATAATA
1 TTATTTATTTAAAATAATAATA
* *
218082 TTATTTATTTGAAATAATATTA
1 TTATTTATTTAAAATAATAATA
*
218104 TTTTTTA
1 TTATTTA
218111 AATTATCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATTTATTTAAAATAATAATA
Found at i:218097 original size:19 final size:18
Alignment explanation
Indices: 218075--218140 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 18
218065 TATTTAAAAT
218075 AATAATATTATTTATTTGA
1 AATAATATTATTTATTT-A
218094 AATAATATTATTT-TTTA
1 AATAATATTATTTATTTA
218111 AAT--TATCTATTTAGGTTTA
1 AATAATAT-TATTTA--TTTA
218130 AATAATATTAT
1 AATAATATTAT
218141 ACAGAACCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.07
16 5 0.12
17 4 0.10
18 3 0.07
19 20 0.49
20 3 0.07
21 3 0.07
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (18 bp):
AATAATATTATTTATTTA
Found at i:218316 original size:23 final size:24
Alignment explanation
Indices: 218264--218322 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
218254 ATTTTAAAAT
218264 TAAATA-AATTTTTTATAATATTA
1 TAAATATAATTTTTTATAATATTA
*
218287 TAAATATACTTTTTTATAATTATT-
1 TAAATATAATTTTTTATAA-TATTA
*
218311 T-CATATAATTTT
1 TAAATATAATTTT
218323 CATAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 15 0.48
24 12 0.39
25 4 0.13
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (24 bp):
TAAATATAATTTTTTATAATATTA
Found at i:225881 original size:3 final size:3
Alignment explanation
Indices: 225873--225933 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
225863 TAAACTGAGG
225873 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
225921 AGA AGA AGA AGA A
1 AGA AGA AGA AGA A
225934 CCACGTGTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:228267 original size:43 final size:41
Alignment explanation
Indices: 228206--228358 Score: 148
Period size: 43 Copynumber: 3.6 Consensus size: 41
228196 ATAATAATAA
* * *
228206 AAAAATTGGGATTGAAAAAAATTAGGGGCTAAATTATAAAGCT
1 AAAAA-TGAGATT-AAAAAAATTAGGAGCTCAATTATAAAGCT
* *
228249 AAAAATGAGATTAAAAAAATTAGAGACCTCAATTATAAAGAT
1 AAAAATGAGATTAAAAAAATTAG-GAGCTCAATTATAAAGCT
* * *
228291 AGAAAAGGATATTGTAAAAAAA-TATGAGCTCAATTATAAAGGC-
1 A-AAAATGAGA-T-TAAAAAAATTAGGAGCTCAATTATAAA-GCT
228334 AAAAAGTGAGATTAAAAAAATTAGG
1 AAAAA-TGAGATTAAAAAAATTAGG
228359 GTTATTAATT
Statistics
Matches: 90, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
41 19 0.21
42 29 0.32
43 30 0.33
44 4 0.04
45 8 0.09
ACGTcount: A:0.54, C:0.05, G:0.18, T:0.24
Consensus pattern (41 bp):
AAAAATGAGATTAAAAAAATTAGGAGCTCAATTATAAAGCT
Found at i:228283 original size:42 final size:41
Alignment explanation
Indices: 228206--228357 Score: 141
Period size: 42 Copynumber: 3.6 Consensus size: 41
228196 ATAATAATAA
* * * *
228206 AAAAATTGGGATTGAAAAAAATTAGGGGCTAAATTATAAAGCT
1 AAAAAGTGAGATT-AAAAAAATTA-GAGCTCAATTATAAAGCT
*
228249 AAAAA-TGAGATTAAAAAAATTAGAGACCTCAATTATAAAGAT
1 AAAAAGTGAGATTAAAAAAATTAGAG--CTCAATTATAAAGCT
*
228291 AGAAAAG-GATATTGTAAAAAAA-TATGAGCTCAATTATAAAGGC-
1 A-AAAAGTGAGA-T-TAAAAAAATTA-GAGCTCAATTATAAA-GCT
228334 AAAAAGTGAGATTAAAAAAATTAG
1 AAAAAGTGAGATTAAAAAAATTAG
228358 GGTTATTAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
40 2 0.02
41 19 0.21
42 28 0.30
43 28 0.30
44 4 0.04
45 11 0.12
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAAAGTGAGATTAAAAAAATTAGAGCTCAATTATAAAGCT
Found at i:229222 original size:44 final size:44
Alignment explanation
Indices: 229143--229238 Score: 140
Period size: 44 Copynumber: 2.2 Consensus size: 44
229133 TAATTTTTTT
* * *
229143 TAAATATTTATATTTTTATTATAGATAATTTTAGATATAATATTA
1 TAAATATTTAAATTTGTATTATAGATAATTCTAGATAT-ATATTA
229188 TAAATATTTAAATTTGTA-TATAGATAATTCTAGATATATATTA
1 TAAATATTTAAATTTGTATTATAGATAATTCTAGATATATATTA
*
229231 TTAATATT
1 TAAATATT
229239 ATTTTAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
43 13 0.28
44 18 0.38
45 16 0.34
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (44 bp):
TAAATATTTAAATTTGTATTATAGATAATTCTAGATATATATTA
Found at i:231439 original size:58 final size:58
Alignment explanation
Indices: 231359--231595 Score: 298
Period size: 58 Copynumber: 4.1 Consensus size: 58
231349 AACTTTATTA
*
231359 TTAGGGTTAGGGTTTTACTTCATTAGTCAACATGATTAAACCTTAATTTTATTATGTT
1 TTAGGGTTAGGGTTTTACTTCATTACTCAACATGATTAAACCTTAATTTTATTATGTT
* * * *
231417 TTAGGGTTTGGGTTTTATTTCATTACTCAACATGATTAAACTTTAACTTTATTATGTT
1 TTAGGGTTAGGGTTTTACTTCATTACTCAACATGATTAAACCTTAATTTTATTATGTT
* ** * * *
231475 TTAGGGTTAGAGTTTTACTTCATTACTCAATGTGATTAAATCTTAGTTTTATTATATT
1 TTAGGGTTAGGGTTTTACTTCATTACTCAACATGATTAAACCTTAATTTTATTATGTT
** * * *
231533 TTAAGATTTAGGGTTTTATTTCATTGCTCAACACTG-TTAAATCTT-ATTTTATTATGTT
1 TT-AGGGTTAGGGTTTTACTTCATTACTCAACA-TGATTAAACCTTAATTTTATTATGTT
231591 TTAGG
1 TTAGG
231596 AGGCATTATC
Statistics
Matches: 152, Mismatches: 25, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
57 2 0.01
58 116 0.76
59 32 0.21
60 2 0.01
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (58 bp):
TTAGGGTTAGGGTTTTACTTCATTACTCAACATGATTAAACCTTAATTTTATTATGTT
Found at i:231514 original size:116 final size:116
Alignment explanation
Indices: 231312--231595 Score: 327
Period size: 116 Copynumber: 2.5 Consensus size: 116
231302 AGAGTTCAAA
* ** * *
231312 ATTTAGGGTTTTATTTCATTTCTCAACA---TTAGGTACTAACTTTATTA----TTAGGGTTAGG
1 ATTTAGGGTTTTATTTCATTACTCAACACTGTTAAAT-CTTACTTTATTATGTTTTAGGGTTAGA
* * *
231370 GTTTTACTTCATTAGTCAACATGATTAAACCTTAATTTTATTATGTTTTAGG
65 GTTTTACTTCATTACTCAACATGATTAAACCTTAATTTTATTATATTTTAAG
*
231422 GTTT-GGGTTTTATTTCATTACTCAACA-TGATTAAA-CTTTAACTTTATTATGTTTTAGGGTTA
1 ATTTAGGGTTTTATTTCATTACTCAACACTG-TTAAATC-TT-ACTTTATTATGTTTTAGGGTTA
** * *
231484 GAGTTTTACTTCATTACTCAATGTGATTAAATCTTAGTTTTATTATATTTTAAG
63 GAGTTTTACTTCATTACTCAACATGATTAAACCTTAATTTTATTATATTTTAAG
* *
231538 ATTTAGGGTTTTATTTCATTGCTCAACACTGTTAAATCTTATTTTATTATGTTTTAGG
1 ATTTAGGGTTTTATTTCATTACTCAACACTGTTAAATCTTACTTTATTATGTTTTAGG
231596 AGGCATTATC
Statistics
Matches: 146, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
109 22 0.15
110 4 0.03
111 1 0.01
112 12 0.08
116 75 0.51
117 29 0.20
118 3 0.02
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (116 bp):
ATTTAGGGTTTTATTTCATTACTCAACACTGTTAAATCTTACTTTATTATGTTTTAGGGTTAGAG
TTTTACTTCATTACTCAACATGATTAAACCTTAATTTTATTATATTTTAAG
Found at i:232332 original size:66 final size:66
Alignment explanation
Indices: 232254--232387 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
232244 AAATGGCATG
*
232254 ACGGATGTCGATTTGTTCTTACAAGGACAGCTTGAGAACAACACCGGAGATCCTGTGTCCGTCCC
1 ACGGATGTCGATTTGTTCTTACAAGGACAGCTTGAGAACAACACCAGAGATCCTGTGTCCGTCCC
232319 T
66 T
*
232320 ACGGATGTCGATTTGTTCTTACAAGGACAGCTTGAGAACAACACCAGATATCCTGTGTCCGTCCC
1 ACGGATGTCGATTTGTTCTTACAAGGACAGCTTGAGAACAACACCAGAGATCCTGTGTCCGTCCC
232385 T
66 T
232386 AC
1 AC
232388 AAACATGGTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (66 bp):
ACGGATGTCGATTTGTTCTTACAAGGACAGCTTGAGAACAACACCAGAGATCCTGTGTCCGTCCC
T
Found at i:232429 original size:30 final size:30
Alignment explanation
Indices: 232395--232456 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
232385 TACAAACATG
* * *
232395 GTTGATTACAGTTTGTTGATGAACAATGCC
1 GTTGATAACAGTGTGTTGACGAACAATGCC
232425 GTTGATAACAGTGTGTTGACGAACAATGCC
1 GTTGATAACAGTGTGTTGACGAACAATGCC
232455 GT
1 GT
232457 CGGTGGTGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (30 bp):
GTTGATAACAGTGTGTTGACGAACAATGCC
Found at i:232430 original size:16 final size:16
Alignment explanation
Indices: 232409--232456 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
232399 ATTACAGTTT
232409 GTTGATGAACAATGCC
1 GTTGATGAACAATGCC
* *
232425 GTTGAT-AACAGTG-T
1 GTTGATGAACAATGCC
*
232439 GTTGACGAACAATGCC
1 GTTGATGAACAATGCC
232455 GT
1 GT
232457 CGGTGGTGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 5 0.20
15 12 0.48
16 8 0.32
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (16 bp):
GTTGATGAACAATGCC
Found at i:242202 original size:75 final size:72
Alignment explanation
Indices: 242055--242267 Score: 251
Period size: 75 Copynumber: 3.0 Consensus size: 72
242045 AATTTAAAAT
* * *
242055 AATATTTTAAATATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTA
1 AATATTATATATATTTTATTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTA
* *
242120 AGTTTTAG
65 GGATTTAG
* *
242128 GATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTAAT
1 AATATTA--TATATATTTTAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTAAT
242193 TAGGATTTAG
63 TAGGATTTAG
* *
242203 AATATTATAT-TATTTT-TTTTA----GGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTA
1 AATATTATATATATTTTATTTTATCTTTGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTA
242261 GGATTTA
65 GGATTTA
242268 AGATGTTTTA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
65 5 0.04
66 36 0.29
70 4 0.03
71 1 0.01
72 6 0.05
73 7 0.06
75 38 0.30
76 28 0.22
ACGTcount: A:0.30, C:0.01, G:0.11, T:0.58
Consensus pattern (72 bp):
AATATTATATATATTTTATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAG
GATTTAG
Found at i:242223 original size:76 final size:76
Alignment explanation
Indices: 242046--242210 Score: 244
Period size: 76 Copynumber: 2.2 Consensus size: 76
242036 TTAAACTCAA
* * * *
242046 ATTTAAAATAATATTTTAAATATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGAATATTATTTT-TATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
242110 ATTTTAATTAAG
65 ATTTTAATTAAG
* *
242122 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
1 ATTTAGAATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
*
242186 TTTTAATTAGG
66 TTTTAATTAAG
242197 ATTTAGAATATTAT
1 ATTTAGAATATTAT
242211 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 38 0.48
76 41 0.52
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.57
Consensus pattern (76 bp):
ATTTAGAATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
TTTTAATTAAG
Found at i:243170 original size:24 final size:24
Alignment explanation
Indices: 243138--243187 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
243128 TATCGATTGC
243138 TTTGCCTACCGTACCCAATTATAT
1 TTTGCCTACCGTACCCAATTATAT
243162 TTTGCCTACCGTACCCAATTATAT
1 TTTGCCTACCGTACCCAATTATAT
243186 TT
1 TT
243188 GGTCATAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (24 bp):
TTTGCCTACCGTACCCAATTATAT
Found at i:243637 original size:20 final size:19
Alignment explanation
Indices: 243600--243638 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
243590 CTTCACACTA
*
243600 TTTTTAAAAATAATATTAT
1 TTTTTAAAAATAACATTAT
*
243619 TTTTTAATAAATGACATTAT
1 TTTTTAA-AAATAACATTAT
243639 ATTTGATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
TTTTTAAAAATAACATTAT
Done.