Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007935.1 Hibiscus syriacus cultivar Beakdansim tig00110345_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: 1073174
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 6
Found at i:239839 original size:29 final size:29
Alignment explanation
Indices: 239800--239897 Score: 88
Period size: 25 Copynumber: 3.6 Consensus size: 29
239790 TGCTTGAAGA
*
239800 AAAAATGAAATAGAAAAAAAAGAGAAAAG
1 AAAAATAAAATAGAAAAAAAAGAGAAAAG
239829 AAAAATAAAAT-G---AAAAAGA-AAAAG
1 AAAAATAAAATAGAAAAAAAAGAGAAAAG
*
239853 -AAAA-AAAA-AGAAAAAAAAGAGAGAAAA
1 AAAAATAAAATAGAAAAAAAAGAGA-AAAG
*
239880 AAAGAAGAAAATA-AAAAA
1 AAA-AATAAAATAGAAAAA
239898 GGAGGGTCAA
Statistics
Matches: 57, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
22 5 0.09
23 4 0.07
24 5 0.09
25 14 0.25
26 1 0.02
27 3 0.05
28 3 0.05
29 12 0.21
30 9 0.16
31 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (29 bp):
AAAAATAAAATAGAAAAAAAAGAGAAAAG
Found at i:239842 original size:34 final size:34
Alignment explanation
Indices: 239801--239896 Score: 101
Period size: 34 Copynumber: 2.8 Consensus size: 34
239791 GCTTGAAGAA
* *
239801 AAAATGAAATAGAAAAA-AAAGAGAAAAGAAAAAT
1 AAAATGAAAAAGAAAAAGAAA-AAAAAAGAAAAAT
239835 AAAATGAAAAAGAAAAAGAAAAAAAAAGAAAAA-
1 AAAATGAAAAAGAAAAAGAAAAAAAAAGAAAAAT
239868 AAAGA-GAGAAAA-AAAGAAGAAAATAAAAA
1 AAA-ATGA-AAAAGAAA-AAGAAAA-AAAAA
239897 AGGAGGGTCA
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
33 8 0.15
34 39 0.71
35 8 0.15
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (34 bp):
AAAATGAAAAAGAAAAAGAAAAAAAAAGAAAAAT
Found at i:240276 original size:18 final size:18
Alignment explanation
Indices: 240223--240298 Score: 68
Period size: 18 Copynumber: 4.1 Consensus size: 18
240213 TATTTATTAA
240223 TAAATTCTAAGTTTATTTTCT
1 TAAATTC-AA-TTTATTTT-T
240244 CTAAATTC-A-TT-TTTTT
1 -TAAATTCAATTTATTTTT
*
240260 TAGATTCAATTTATTTTT
1 TAAATTCAATTTATTTTT
*
240278 GAAATTCAATTTATTCTTT
1 TAAATTCAATTTATT-TTT
240297 TA
1 TA
240299 TTTTGTAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
15 6 0.13
16 2 0.04
17 6 0.13
18 20 0.43
19 4 0.09
20 1 0.02
22 7 0.15
ACGTcount: A:0.29, C:0.09, G:0.04, T:0.58
Consensus pattern (18 bp):
TAAATTCAATTTATTTTT
Found at i:241564 original size:111 final size:115
Alignment explanation
Indices: 241407--241957 Score: 588
Period size: 122 Copynumber: 4.7 Consensus size: 115
241397 ATTACCATTG
*
241407 CCAGAGAAAGTTCATAATGAGAAGAATTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAG-AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* * ***
241472 ACTTGTTCAACCTTTTGCTCAAATTCAT-CACTTGATAGATCAGC-A-TTT
65 GCTTGTTCAACCTTTTGCTCAAATTCATAAAGGAGATAGATCAGCAATTTT
* * *
241520 CCAGAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
1 CCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAG
* * ** * *** *
241584 TTTGTTCAAACCTTTTGTTTGAATTCAT-CATTTGATGGA-C--CAACTTTT
66 CTTGTTC-AACCTTTTGCTCAAATTCATAAAGGAGATAGATCAGCAA-TTTT
* *
241632 CCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAG
1 CCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAG
* *
241697 CTTGTTCAACCTTTTGCATGACTATATT-ATAGAAGGAGATAGATCAACATCAACTTTT
66 CTTGTTCAACCTTTTGC-T--C-AAATTCATA-AAGGAGATAGAT---CAGCAA-TTTT
*
241755 CCAGAGAAAATTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAG-AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
*
241819 GCTTGTTCAACCTTTGCATGACTC-TA-TCATAAAAGGAGATAGATCAGCATCAATTTTT
65 GCTTGTTCAACCTTT---TG-CTCAAATTCAT-AAAGGAGATAGATCAG---CAA-TTTT
241877 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAG-AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
241941 GCTTGTTCAACCTTTTG
65 GCTTGTTCAACCTTTTG
241958 ATTGATTCTA
Statistics
Matches: 383, Mismatches: 28, Indels: 48
0.83 0.06 0.10
Matches are distributed among these distances:
109 1 0.00
110 1 0.00
111 62 0.16
112 43 0.11
113 69 0.18
115 2 0.01
116 3 0.01
117 6 0.02
119 4 0.01
121 2 0.01
122 101 0.26
123 56 0.15
124 29 0.08
126 3 0.01
127 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (115 bp):
CCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAG
CTTGTTCAACCTTTTGCTCAAATTCATAAAGGAGATAGATCAGCAATTTT
Found at i:242309 original size:3 final size:3
Alignment explanation
Indices: 242303--242384 Score: 84
Period size: 3 Copynumber: 27.7 Consensus size: 3
242293 ATAATAATAA
*
242303 TAT TAT T-T TAT TAT T-T TAT T-T TAT T-T TAC TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
242346 TAT TAT TATT TAT TAT TAT TAT TAAT TAAGT TAT TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT T-AT T-A-T TAT TAT TA
242385 CAGACCCAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 16
0.79 0.02 0.18
Matches are distributed among these distances:
2 10 0.14
3 48 0.70
4 9 0.13
5 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:242323 original size:13 final size:14
Alignment explanation
Indices: 242303--242365 Score: 76
Period size: 13 Copynumber: 4.5 Consensus size: 14
242293 ATAATAATAA
242303 TATTATTTTATTAT
1 TATTATTTTATTAT
242317 T-TTATTTTATT-T
1 TATTATTTTATTAT
* *
242329 TACTATTATATTAT
1 TATTATTTTATTAT
242343 TATTATTATTATTTAT
1 TATTATT-TTA-TTAT
242359 TATTATT
1 TATTATT
242366 ATTAATTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 2 0.05
13 18 0.44
14 8 0.20
15 2 0.05
16 11 0.27
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:242337 original size:16 final size:17
Alignment explanation
Indices: 242310--242384 Score: 84
Period size: 16 Copynumber: 4.5 Consensus size: 17
242300 TAATATTATT
242310 TTATTATT-TTATTTTA
1 TTATTATTATTATTTTA
* *
242326 TT-TTACTATTATATTA
1 TTATTATTATTATTTTA
242342 TTATTATTATTA-TTTA
1 TTATTATTATTATTTTA
* *
242358 TTATTATTATTAATTAA
1 TTATTATTATTATTTTA
242375 GTTATTATTA
1 -TTATTATTA
242385 CAGACCCAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
15 4 0.08
16 26 0.52
17 11 0.22
18 9 0.18
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (17 bp):
TTATTATTATTATTTTA
Found at i:242366 original size:13 final size:13
Alignment explanation
Indices: 242305--242383 Score: 69
Period size: 13 Copynumber: 6.1 Consensus size: 13
242295 AATAATAATA
242305 TTATT-TTATTATT
1 TTATTATTATTA-T
242318 TTATT-TTATT-T
1 TTATTATTATTAT
242329 TACTATTA-TATTA-
1 T--TATTATTATTAT
242342 TTATTATTATTAT
1 TTATTATTATTAT
242355 TTATTATTATTAT
1 TTATTATTATTAT
*
242368 TAATTAAGTTATTAT
1 TTATT-A-TTATTAT
242383 T
1 T
242384 ACAGACCCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
11 7 0.12
12 5 0.09
13 36 0.63
14 1 0.02
15 8 0.14
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:242380 original size:37 final size:37
Alignment explanation
Indices: 242303--242384 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 37
242293 ATAATAATAA
242303 TATTATT-TTATTATTTTATTTTATTTTACTATTATAT
1 TATTATTATTATTATTTTATTTTATTTTAC-ATTATAT
242340 TATTATTATTATTA-TTTATTATTATTATTA-ATTA-AGT
1 TATTATTATTATTATTTTATT-TTATT-TTACATTATA-T
242377 TATTATTA
1 TATTATTA
242385 CAGACCCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
36 1 0.02
37 26 0.63
38 11 0.27
39 3 0.07
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (37 bp):
TATTATTATTATTATTTTATTTTATTTTACATTATAT
Found at i:245225 original size:49 final size:49
Alignment explanation
Indices: 245094--245471 Score: 442
Period size: 49 Copynumber: 7.8 Consensus size: 49
245084 ACACTTTTTA
* * * *
245094 TGCC-AAAATGCACCATTATACGTTTAAC-AGTCATTAGTGGCACCTTTC
1 TGCCAAAAATGCACCTTTATGCATTTAACTTG-CATTAGTGGCACCTTTC
* * * *
245142 TGCC-AAAA--CACGCTGTTATGCATTTAACTCGCATTAATGGTACCTTTA
1 TGCCAAAAATGCAC-CT-TTATGCATTTAACTTGCATTAGTGGCACCTTTC
* * *
245190 TGCCAAAAATGCACCATTATGCATTTTACTTGCATTAGTAGCACCTTTC
1 TGCCAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGGCACCTTTC
** *
245239 TGCCAAAAATGCACCTTTATATATTTAACTTGCATTAGTGGCTCCTTTC
1 TGCCAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGGCACCTTTC
* * *
245288 TGCCAAAAATTCACCTGTATGCATTTAACTTGCATTAGTGACACCTTTC
1 TGCCAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGGCACCTTTC
* *
245337 TGCCAAAAATGCACCTTTATACATTAAACTTGCATTAGTGGCACCTTTC
1 TGCCAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGGCACCTTTC
* * * * *
245386 TGCGAAAAATGCACCTTTATGCATTTAACTTGCATTAATGACACATTTA
1 TGCCAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGGCACCTTTC
* * * *
245435 TACCAAAAATACACCTTTATTCATTTAACTTTCATTA
1 TGCCAAAAATGCACCTTTATGCATTTAACTTGCATTA
245472 TAGAGCAGTT
Statistics
Matches: 281, Mismatches: 43, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
46 3 0.01
47 1 0.00
48 37 0.13
49 236 0.84
50 1 0.00
51 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (49 bp):
TGCCAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGGCACCTTTC
Found at i:246561 original size:3 final size:3
Alignment explanation
Indices: 246555--246681 Score: 193
Period size: 3 Copynumber: 42.3 Consensus size: 3
246545 AGCACGGGAC
246555 AAG AAG ATAG AAG AAG AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
246600 AAG AAG AAG AAG AAG AAG AAG AAG AAT AAG AAG AAG AAT AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
246648 AAT AAA AAG AAG AAA AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
246682 CATATCTTTA
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
2 2 0.02
3 108 0.96
4 3 0.03
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:249632 original size:95 final size:95
Alignment explanation
Indices: 249507--249705 Score: 245
Period size: 95 Copynumber: 2.1 Consensus size: 95
249497 GACGAGGTAG
* * * * * *
249507 TATCAATACAATGGTAAGGGTATCGATACCAGGTAACATTGAACCTAATTTTGGTATCGATATCG
1 TATCGATACAATGGTAAGGGTATCGATACCAAGCAACATCGAACCTAATTTTGGTATCGATACCA
* * *
249572 GAAGGGGATATCGGTACCATAGTATAGTAA
66 CAAGGGGATATCGATACCATAGTAGAGTAA
* * * *
249602 TATCGATACCATGGTATGGGTATCGATACCAAGCCACATCGAATCTAATTTTGGTATCGATACCA
1 TATCGATACAATGGTAAGGGTATCGATACCAAGCAACATCGAACCTAATTTTGGTATCGATACCA
* * * *
249667 CAAGGGGGTGTCGATACCATAGTAGGGTAT
66 CAAGGGGATATCGATACCATAGTAGAGTAA
249697 TATCGATAC
1 TATCGATAC
249706 TGAAGAACCA
Statistics
Matches: 87, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
95 87 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (95 bp):
TATCGATACAATGGTAAGGGTATCGATACCAAGCAACATCGAACCTAATTTTGGTATCGATACCA
CAAGGGGATATCGATACCATAGTAGAGTAA
Found at i:250103 original size:59 final size:59
Alignment explanation
Indices: 250038--250435 Score: 625
Period size: 59 Copynumber: 6.7 Consensus size: 59
250028 TGGCACTAAA
* * *
250038 TGTGCTAAAATGATAATAAATTCATACTAACTGTATGAATTTCCATATAGGGCACTTCG
1 TGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
* *
250097 TGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGCATAGGGCATTTCG
1 TGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
*
250156 TGTCCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
1 TGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
* * *
250215 TGTGCTAAAATGATAAGAAATTCATACTATGTGTATGAATTTCTGTATAGGGTACTTCG
1 TGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
* *
250274 TGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGACACTTCA
1 TGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
* * * *
250333 TGTGCTAAAATGTTAAGAAATTCATACTATGTGTGTGAATTTCTGTATAGGGCACTTCG
1 TGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
* * * *
250392 TGCGCTAAAATGATAAGAAATTCGTACGAAGTGTATAAATTTCC
1 TGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCC
250436 ATATGGGAAA
Statistics
Matches: 308, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 308 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
Found at i:256670 original size:20 final size:22
Alignment explanation
Indices: 256630--256676 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
256620 GGGGTATTGG
256630 TACCATAGTATAGTAGTATCGA
1 TACCATAGTATAGTAGTATCGA
*
256652 TACCATGGTA-AGT-GTATCGA
1 TACCATAGTATAGTAGTATCGA
256672 TACCA
1 TACCA
256677 GGCCACATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.50
21 3 0.12
22 9 0.38
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (22 bp):
TACCATAGTATAGTAGTATCGA
Found at i:256677 original size:95 final size:93
Alignment explanation
Indices: 256547--256767 Score: 307
Period size: 95 Copynumber: 2.4 Consensus size: 93
256537 TACTGACGAG
* * ** *
256547 GTAGTATCCATACCATGGTAAGGGTATCGATACCAGTTAACATCGAACCTAATTTTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGAGTATCGATACCAGGCAACATCGAAACTAATTTTGGTATCGAT
* * * *
256612 ACCAGAAGGGGGTATTGGTACCATAGTATA
66 ACC-GAA-AGGGTATCGATACCATAGTAGA
* *
256642 GTAGTATCGATACCATGGTAAGTGTATCGATACCAGGCCACATCGAAACTAATTTTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGAGTATCGATACCAGGCAACATCGAAACTAATTTTGGTATCGAT
*
256707 ACCGAAAGGGTATCGATACCATAGTAGG
66 ACCGAAAGGGTATCGATACCATAGTAGA
*
256735 GTAGTATCGATACCATGGTAGGAGTATCGATAC
1 GTAGTATCGATACCATGGTAAGAGTATCGATAC
256768 TGAAGAACCA
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
93 48 0.42
94 3 0.03
95 62 0.55
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (93 bp):
GTAGTATCGATACCATGGTAAGAGTATCGATACCAGGCAACATCGAAACTAATTTTGGTATCGAT
ACCGAAAGGGTATCGATACCATAGTAGA
Found at i:256762 original size:20 final size:22
Alignment explanation
Indices: 256716--256767 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
256706 TACCGAAAGG
256716 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
*
256738 GTATCGATACCATGGTA-GG-A
1 GTATCGATACCATAGTAGGGTA
256758 GTATCGATAC
1 GTATCGATAC
256768 TGAAGAACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 16 0.55
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGTA
Found at i:257233 original size:57 final size:58
Alignment explanation
Indices: 257099--257433 Score: 476
Period size: 59 Copynumber: 5.8 Consensus size: 58
257089 ATGGCACTAA
*
257099 GTGTGCTTAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAA-TTTCGTATAGGGCACTTC
* * *
257158 GTGTGCTAAAATGATAAGAAATTCATACGAAGTGTATGAATTTC-TATAGGGTACTTG
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCGTATAGGGCACTTC
* * *
257215 GTGTGCTAAAATGATAAGAATTTCATACTAAGTGTATAAATTTC-CATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCGTATAGGGCACTTC
* * * *
257272 ATGTGCTAAAATGATAAGAAATTCATTCTAAGTGTATGAATTTCCTTATAGGGCACTTT
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTT-CGTATAGGGCACTTC
* * *
257331 ATGTACTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAA-TTTCGTATAGGGCACTTC
* * *
257390 GTTTTCTAAAATGATAAGAAATTCATACTAAGTCTATGAATTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTC
257434 CCTATGACAA
Statistics
Matches: 247, Mismatches: 26, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
57 101 0.41
58 9 0.04
59 134 0.54
60 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (58 bp):
GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCGTATAGGGCACTTC
Found at i:261622 original size:97 final size:97
Alignment explanation
Indices: 261503--261892 Score: 443
Period size: 97 Copynumber: 4.0 Consensus size: 97
261493 TTACACCATA
* * * * *
261503 AGTGGCACCTTTTATGC-CAAAATGTACCATTATACATTTAA-ATGTAATTAGTGGCACCTTTAT
1 AGTGGCACC-TTTATGCAAAAAATGCACCATTATGCATTTAACTTG-CATTAGTGGCACCTTTAT
* *
261566 GCTAAAATACA-CTGTTATGCATTTAACTCGCATT
64 GCAAAAATACACCT-TTATGCATTTAACTTGCATT
*
261600 AGTGGCACCTTTATGCAAAAAATGCACAATTATGCATTTAACTTGCATTAGTGGCACCTTTATGC
1 AGTGGCACCTTTATGCAAAAAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTATG-
*
261665 CAAAAATGA-A-CTTTATGCATTTAACTTGCATC
65 CAAAAAT-ACACCTTTATGCATTTAACTTGCATT
* * * * * * * *
261697 ATTGGCATCTTTCTGCCAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGACACCTTTCTTC
1 AGTGGCACCTTTATGCAAAAAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTT-ATG
* *
261762 CAAATATGCACCTTTATGCATTTAACTTGCATT
65 CAAAAATACACCTTTATGCATTTAACTTGCATT
* * *
261795 AGT-GCACCTTTCTGCCAAAAAA-GCACCTTTATGCATTTAACTTGCATTAGTGGCACCTTTCTG
1 AGTGGCACCTTTATG-CAAAAAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTATG
* *
261858 CGAAAAATGCACCTATATGCATTTAACTTGCATT
65 C-AAAAATACACCTTTATGCATTTAACTTGCATT
261892 A
1 A
261893 TAGAGCAGTT
Statistics
Matches: 255, Mismatches: 29, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
96 9 0.04
97 204 0.80
98 41 0.16
99 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35
Consensus pattern (97 bp):
AGTGGCACCTTTATGCAAAAAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTATGC
AAAAATACACCTTTATGCATTTAACTTGCATT
Found at i:261641 original size:49 final size:49
Alignment explanation
Indices: 261503--261892 Score: 486
Period size: 49 Copynumber: 8.0 Consensus size: 49
261493 TTACACCATA
* * * * *
261503 AGTGGCACCTTTTATGCC-AAAATGTACCATTATACATTTAA-ATGTAATT
1 AGTGGCACC-TTTATGCCAAAAATGCACCTTTATGCATTTAACTTG-CATT
* * *
261552 AGTGGCACCTTTATG-CTAAAATACA-CTGTTATGCATTTAACTCGCATT
1 AGTGGCACCTTTATGCCAAAAATGCACCT-TTATGCATTTAACTTGCATT
* **
261600 AGTGGCACCTTTATGCAAAAAATGCACAATTATGCATTTAACTTGCATT
1 AGTGGCACCTTTATGCCAAAAATGCACCTTTATGCATTTAACTTGCATT
* *
261649 AGTGGCACCTTTATGCCAAAAATG-AACTTTATGCATTTAACTTGCATC
1 AGTGGCACCTTTATGCCAAAAATGCACCTTTATGCATTTAACTTGCATT
* * *
261697 ATTGGCATCTTTCTGCCAAAAATGCACCTTTATGCATTTAACTTGCATT
1 AGTGGCACCTTTATGCCAAAAATGCACCTTTATGCATTTAACTTGCATT
* * * *
261746 AGTGACACCTTTCTTCCAAATATGCACCTTTATGCATTTAACTTGCATT
1 AGTGGCACCTTTATGCCAAAAATGCACCTTTATGCATTTAACTTGCATT
* *
261795 AGT-GCACCTTTCTGCCAAAAAAGCACCTTTATGCATTTAACTTGCATT
1 AGTGGCACCTTTATGCCAAAAATGCACCTTTATGCATTTAACTTGCATT
* * *
261843 AGTGGCACCTTTCTGCGAAAAATGCACCTATATGCATTTAACTTGCATT
1 AGTGGCACCTTTATGCCAAAAATGCACCTTTATGCATTTAACTTGCATT
261892 A
1 A
261893 TAGAGCAGTT
Statistics
Matches: 299, Mismatches: 35, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
47 2 0.01
48 126 0.42
49 171 0.57
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35
Consensus pattern (49 bp):
AGTGGCACCTTTATGCCAAAAATGCACCTTTATGCATTTAACTTGCATT
Found at i:261771 original size:146 final size:146
Alignment explanation
Indices: 261552--261892 Score: 472
Period size: 146 Copynumber: 2.3 Consensus size: 146
261542 AAATGTAATT
* * * * *
261552 AGTGGCACCTTTATG-CTAAAATACA-CTGTTATGCATTTAACTCGCATTAGTGGCACCTTTATG
1 AGTGGCACCTTTCTGCCAAAAATGCACCT-TTATGCATTTAACTTGCATTAGTGACACCTTTATG
*
261615 CAAAAAATGCACAATTATGCATTTAACTTGCATTAGTGGCACCTTTATGCCAAAAATG-AACTTT
65 CAAAAAATGCACAATTATGCATTTAACTTGCATTAGT-GCACCTTTATGCCAAAAAAGCAACTTT
261679 ATGCATTTAACTTGCATC
129 ATGCATTTAACTTGCATC
* * * *
261697 ATTGGCATCTTTCTGCCAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGACACCTTTCTTC
1 AGTGGCACCTTTCTGCCAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGACACCTTTATGC
* * ** * *
261762 CAAATATGCACCTTTATGCATTTAACTTGCATTAGTGCACCTTTCTGCCAAAAAAGCACCTTTAT
66 AAAAAATGCACAATTATGCATTTAACTTGCATTAGTGCACCTTTATGCCAAAAAAGCAACTTTAT
*
261827 GCATTTAACTTGCATT
131 GCATTTAACTTGCATC
* *
261843 AGTGGCACCTTTCTGCGAAAAATGCACCTATATGCATTTAACTTGCATTA
1 AGTGGCACCTTTCTGCCAAAAATGCACCTTTATGCATTTAACTTGCATTA
261893 TAGAGCAGTT
Statistics
Matches: 172, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
145 30 0.17
146 140 0.81
147 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (146 bp):
AGTGGCACCTTTCTGCCAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGACACCTTTATGC
AAAAAATGCACAATTATGCATTTAACTTGCATTAGTGCACCTTTATGCCAAAAAAGCAACTTTAT
GCATTTAACTTGCATC
Found at i:262421 original size:18 final size:19
Alignment explanation
Indices: 262398--262446 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
262388 CCTTTTTCCT
262398 AGTATCGATAC-CTACATC
1 AGTATCGATACACTACATC
*
262416 AGTATCGATACTAATTACATC
1 AGTATCGATAC--ACTACATC
262437 AGTATCGATA
1 AGTATCGATA
262447 TTGTTCATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.41
21 16 0.59
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (19 bp):
AGTATCGATACACTACATC
Found at i:275929 original size:35 final size:33
Alignment explanation
Indices: 275903--275970 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
275893 TATAATTTAG
275903 AGATACGAATGCACATATGCAAATGTAAAATGCAA
1 AGATACGAATGCA-A-ATGCAAATGTAAAATGCAA
275938 AGATACGAATGCAAATGCAAAATG-AAAATGCAA
1 AGATACGAATGCAAATGC-AAATGTAAAATGCAA
275971 CAAATGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 13 0.41
34 6 0.19
35 13 0.41
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.18
Consensus pattern (33 bp):
AGATACGAATGCAAATGCAAATGTAAAATGCAA
Found at i:279586 original size:12 final size:12
Alignment explanation
Indices: 279548--279613 Score: 61
Period size: 12 Copynumber: 5.7 Consensus size: 12
279538 CAAATGTTAT
279548 TATATTATATAA
1 TATATTATATAA
279560 TATA-TAT-T--
1 TATATTATATAA
279568 TATATTATA-AA
1 TATATTATATAA
279579 TCATATTATATAA
1 T-ATATTATATAA
279592 TATATTCATATATA
1 TATATT-ATATA-A
*
279606 TTTATTAT
1 TATATTAT
279614 TATTATTATT
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
8 4 0.09
9 3 0.07
10 1 0.02
11 4 0.09
12 17 0.38
13 10 0.22
14 6 0.13
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TATATTATATAA
Found at i:279618 original size:32 final size:29
Alignment explanation
Indices: 279544--279619 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 29
279534 CCTTCAAATG
*
279544 TTATTA-TATTATATAATATATATTTATA
1 TTATTATTATTATATAATATATATATATA
*
279572 TTATAAATCATATTATATAATATATTCATATATA
1 TTAT-TAT--TATTATATAATATA-T-ATATATA
279606 TTTATTATTATTAT
1 -TTATTATTATTAT
279620 TATTATTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
28 4 0.11
29 1 0.03
32 20 0.53
33 1 0.03
34 8 0.21
35 4 0.11
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
TTATTATTATTATATAATATATATATATA
Found at i:280677 original size:13 final size:12
Alignment explanation
Indices: 280661--280739 Score: 58
Period size: 13 Copynumber: 6.7 Consensus size: 12
280651 TTTTGTATTA
280661 TTATTTTTTTACT
1 TTATTTTTTTA-T
*
280674 TTATTATTTTA-
1 TTATTTTTTTAT
280685 -TATTTTTTTAT
1 TTATTTTTTTAT
*
280696 TTGATTATTTTATT
1 TT-ATTTTTTTA-T
* *
280710 TTATTTTGTTCT
1 TTATTTTTTTAT
*
280722 TT-GTTTTTTA-
1 TTATTTTTTTAT
280732 TTATTTTT
1 TTATTTTT
280740 CTTTTTACTA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
10 11 0.22
11 9 0.18
12 4 0.08
13 24 0.47
14 3 0.06
ACGTcount: A:0.16, C:0.03, G:0.04, T:0.77
Consensus pattern (12 bp):
TTATTTTTTTAT
Found at i:280692 original size:23 final size:23
Alignment explanation
Indices: 280662--280739 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
280652 TTTGTATTAT
280662 TATTTTTTTACTTTATTATTTTA
1 TATTTTTTTACTTTATTATTTTA
280685 TATTTTTTTA-TTTGATTATTTTA
1 TATTTTTTTACTTT-ATTATTTTA
* * *
280708 TTTTATTTTGTTCTTTGTT-TTTTA
1 TATT-TTTT-TACTTTATTATTTTA
280732 TTATTTTT
1 -TATTTTT
280740 CTTTTTACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
22 3 0.07
23 22 0.48
24 12 0.26
25 6 0.13
26 3 0.07
ACGTcount: A:0.17, C:0.03, G:0.04, T:0.77
Consensus pattern (23 bp):
TATTTTTTTACTTTATTATTTTA
Found at i:286512 original size:248 final size:247
Alignment explanation
Indices: 285958--286574 Score: 914
Period size: 248 Copynumber: 2.5 Consensus size: 247
285948 TTTAAGACAA
** * * * *
285958 CATTTGCAATATAGCTCAAGACAAGAAGGGCTATTTTCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
286023 GCTCAGCTCCAAGGAACATCATTTGCAGCATAGCTTAAGTCGAGAACGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * *
286088 CCCGAGTTCGATTACACTCAGCTTCGAGGGTATATAATTTACAGATAACTCAAGGCTAGAAGGGT
131 CCCGAGTTCGATTACACTCAGCTTCGAGGGCATATAATTTACACATAACTCAAGGCTAGAAAGGT
*
286153 TATCTGTCACCAAAGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCATAT
196 TATCTGTCACCAAAGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCACAT
* * * * * * * * *
286205 CATTTACAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTAT
1 CATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
286270 GCTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
66 GCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* *
286334 CCCCGAGTTCGCTTACACTCAGCTTCGAGGGCATATCATTTACAACATAACTCAAGGCTAGAAAG
130 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATAATTTAC-ACATAACTCAAGGCTAGAAAG
* *
286399 GTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACAT
194 GTTATCTGTCACCAAAGACCTTCGAATTCGACTACGCTCAGCTCCAA-GGCACAT
*
286453 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * *
286518 GCTCAGTTCCAAGGCATATCATTTGCAGCATAACCTAAGTCGAGAAGGGTTATCTGC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
286575 TAACCAAAGA
Statistics
Matches: 327, Mismatches: 39, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
246 3 0.01
247 151 0.46
248 170 0.52
249 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (247 bp):
CATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CCCGAGTTCGATTACACTCAGCTTCGAGGGCATATAATTTACACATAACTCAAGGCTAGAAAGGT
TATCTGTCACCAAAGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCACAT
Found at i:286701 original size:84 final size:84
Alignment explanation
Indices: 285958--286678 Score: 698
Period size: 84 Copynumber: 8.7 Consensus size: 84
285948 TTTAAGACAA
** * * * * *
285958 CATTTGCAATATAGCTCAAGACAAGAAGGGCTATTTTCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
286023 GCTCAGCTCCAAGGAACAT
66 GCTCAGCTCCAAGGCACAT
* ** *
286042 CATTTGCAGCATAGCTTAAGTCGAGAACGGCTATCTG----CCAAAGACCCCCGAGTTCGATTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * *
286103 ACTCAGCTTCGAGGGTATAT
66 GCTCAGC-TCCAAGGCACAT
* * * * * * * * *
286123 AATTTACAG-ATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAATTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
286186 GCTCAGCTCCAAGGCATAT
66 GCTCAGCTCCAAGGCACAT
* * * * * * * * *
286205 CATTTACAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTAT
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
286270 GCTCAGCT-CAACGGCACAT
66 GCTCAGCTCCAA-GGCACAT
**
286289 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCG-CTTA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGAC-TA
* * * *
286349 CACTCAGCTTCGAGGGCATAT
65 CGCTCAGC-TCCAAGGCACAT
* * * * * * * * * *
286370 CATTTACAACATAACTCAAGGCTAGAAAGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
286434 GCTCAGCT-CAACGGCACAT
66 GCTCAGCTCCAA-GGCACAT
286453 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
286518 GCTCAGTTCCAAGGCATAT
66 GCTCAGCTCCAAGGCACAT
* * * * * *
286537 CATTTGCAGCATAACCTAAGTCGAGAAGGGTTATCTGCTAACCAAAGACCTTCAAGTTCGACCAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
286602 GCTCAGCTCCAAGGCACAT
66 GCTCAGCTCCAAGGCACAT
* * * * *
286621 CATCTGCAGCATAGCTTAAGTCGAGAAGAGCTAT-TAGCCAACCGAGGACCTTTGAGTT
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT-GCCAACCAAAGACCTTCGAGTT
286679 TGATTACATT
Statistics
Matches: 516, Mismatches: 103, Indels: 36
0.79 0.16 0.05
Matches are distributed among these distances:
79 1 0.00
80 71 0.14
81 51 0.10
82 19 0.04
83 91 0.18
84 279 0.54
85 4 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (84 bp):
CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACAT
Found at i:287339 original size:20 final size:20
Alignment explanation
Indices: 287314--287396 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
287304 TCAAATGTTA
287314 TTATATTATATAATATATAT
1 TTATATTATATAATATATAT
287334 TTATATTATA-AATCATAT-T
1 TTATATTATATAAT-ATATAT
* * * *
287353 ATATAATATATTCATCTATAT
1 TTATATTATA-TAATATATAT
* *
287374 TTATTATTAT-TATTATTTAT
1 TTA-TATTATATAATATATAT
287394 TTA
1 TTA
287397 CATTTTTTCC
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
19 12 0.25
20 26 0.54
21 5 0.10
22 5 0.10
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATATTATATAATATATAT
Found at i:287353 original size:12 final size:12
Alignment explanation
Indices: 287315--287364 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
287305 CAAATGTTAT
287315 TATATTATATAA
1 TATATTATATAA
287327 TATA-TAT-T--
1 TATATTATATAA
287335 TATATTATA-AA
1 TATATTATATAA
287346 TCATATTATATAA
1 T-ATATTATATAA
287359 TATATT
1 TATATT
287365 CATCTATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
8 4 0.12
9 3 0.09
10 1 0.03
11 4 0.12
12 17 0.53
13 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATTATATAA
Found at i:287385 original size:32 final size:29
Alignment explanation
Indices: 287311--287386 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 29
287301 CCTTCAAATG
*
287311 TTATTA-TATTATATAATATATATTTATA
1 TTATTATTATTATATAATATATATCTATA
*
287339 TTATAAATCATATTATATAATATATTCATCTATA
1 TTAT-TAT--TATTATATAATATA-T-ATCTATA
287373 TTTATTATTATTAT
1 -TTATTATTATTAT
287387 TATTTATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
28 4 0.11
29 1 0.03
32 20 0.53
33 1 0.03
34 8 0.21
35 4 0.11
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (29 bp):
TTATTATTATTATATAATATATATCTATA
Found at i:288322 original size:4 final size:4
Alignment explanation
Indices: 288306--288350 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
288296 ATGTTCTTGC
288306 TTAT TTCAT TTAT TTAT TTAT TTA- TTAT TGT-T TTA- TTAT TTAT TT
1 TTAT TT-AT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TT
288351 TTCTTCCTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
3 7 0.19
4 24 0.67
5 5 0.14
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:288388 original size:24 final size:23
Alignment explanation
Indices: 288341--288388 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
288331 TATTGTTTTA
288341 TTATTTATTTTTCTTCCTCACTTT
1 TTATTTATTTTTCTTCCT-ACTTT
288365 TTATTTCATTTTTCTTTCCT-CTTT
1 TTATTT-ATTTTTC-TTCCTACTTT
288389 AACGTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 10 0.45
25 7 0.32
26 5 0.23
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (23 bp):
TTATTTATTTTTCTTCCTACTTT
Found at i:288541 original size:22 final size:22
Alignment explanation
Indices: 288513--288560 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
288503 TACTTATCTA
288513 TTTTC-TTTAATTTTGTTTATTT
1 TTTTCTTTTAATTTTG-TTATTT
**
288535 TTTTCTTTTCCTTTTGTTATTT
1 TTTTCTTTTAATTTTGTTATTT
288557 TTTT
1 TTTT
288561 TTATTTCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTTCTTTTAATTTTGTTATTT
Found at i:289673 original size:69 final size:67
Alignment explanation
Indices: 289571--289737 Score: 196
Period size: 69 Copynumber: 2.4 Consensus size: 67
289561 TGTAAATTAA
* * *
289571 AATA-TAT-TATTTAATTTGAATATTAGTAGGATAATTAT-TCTTTTGAATATGTCAAATTAAAA
1 AATATTATCTATTTAATTTGAATATTA-AAAGATAATTATAACTTTTGAATATGTCAAATTAAAA
*
289633 AGGT
65 A-AT
* * *
289637 ATTTATTATCTATTTAACTTTGAATATTAAAAGATAATTATACACTTTTGACTATTTCAAATTAA
1 A-ATATTATCTATTTAA-TTTGAATATTAAAAGATAATTATA-ACTTTTGAATATGTCAAATTAA
289702 AAAAT
63 AAAAT
289707 AATATTATCTATTTAAATTTGAATATTAAAA
1 AATATTATCTATTT-AATTTGAATATTAAAA
289738 TATATTTGGT
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
66 1 0.01
67 2 0.02
68 3 0.03
69 43 0.50
70 15 0.17
71 22 0.26
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.44
Consensus pattern (67 bp):
AATATTATCTATTTAATTTGAATATTAAAAGATAATTATAACTTTTGAATATGTCAAATTAAAAA
AT
Found at i:290859 original size:31 final size:31
Alignment explanation
Indices: 290821--290889 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
290811 TGATCACATT
290821 TTAATTAAATAAAAACAAAAGTAACT-ATATC
1 TTAATTAAATAAAAACAAAAGTAA-TAATATC
**
290852 TTAATTAAATAAAAATGAAAGTAATAATATC
1 TTAATTAAATAAAAACAAAAGTAATAATATC
290883 TTGAATT
1 TT-AATT
290890 TCTAGCCACA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 1 0.03
31 29 0.85
32 4 0.12
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (31 bp):
TTAATTAAATAAAAACAAAAGTAATAATATC
Found at i:293444 original size:42 final size:42
Alignment explanation
Indices: 293398--293480 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
293388 TTTATTGGTG
*
293398 TTTTTCCAACAAACGCCGTTAAAGGTCAGATCTATAGTGGCA
1 TTTTTCCAACAAACGCCGCTAAAGGTCAGATCTATAGTGGCA
* *
293440 TTTTTTCAACAAACGTCGCTAAAGGTCAGATCTATAGTGGC
1 TTTTTCCAACAAACGCCGCTAAAGGTCAGATCTATAGTGGC
293481 GTTTACAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (42 bp):
TTTTTCCAACAAACGCCGCTAAAGGTCAGATCTATAGTGGCA
Found at i:293844 original size:42 final size:42
Alignment explanation
Indices: 293782--293868 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
293772 TTTAATGCCA
293782 CAATAGAGTTGGAATATAGTGGCGTTTGGTTTACAAACGCCG
1 CAATAGAGTTGGAATATAGTGGCGTTTGGTTTACAAACGCCG
* * *
293824 CAATAGAGTTTGCATGTAGTGGCGTTTGGTTTACAAACGCCG
1 CAATAGAGTTGGAATATAGTGGCGTTTGGTTTACAAACGCCG
293866 CAA
1 CAA
293869 AGTAACTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (42 bp):
CAATAGAGTTGGAATATAGTGGCGTTTGGTTTACAAACGCCG
Found at i:302063 original size:21 final size:21
Alignment explanation
Indices: 302039--302100 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
302029 ATAAAGCAAG
*
302039 GGAAGTAGAGAGAGTAGCAGC
1 GGAAGTAGAGAGAGAAGCAGC
* * *
302060 GGAAGCAGCGAGAGCAGCAGC
1 GGAAGTAGAGAGAGAAGCAGC
* *
302081 AGAAGTAAAGAGAGAAGCAG
1 GGAAGTAGAGAGAGAAGCAG
302101 TGACAACACA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.42, C:0.13, G:0.40, T:0.05
Consensus pattern (21 bp):
GGAAGTAGAGAGAGAAGCAGC
Found at i:302632 original size:43 final size:43
Alignment explanation
Indices: 302584--302750 Score: 185
Period size: 41 Copynumber: 3.9 Consensus size: 43
302574 GCGTTTGTGG
* * *
302584 AAAAAACGCCGCTAAATATCAATACCTATTGCGGCATTTTTCT
1 AAAAAACGCCGCTAAATCTCAACACCTATTGCGGCATTTTTAT
* * * *
302627 CAAAAACGCCGCTAAATTTCAACACCTATTGCGG--TGTTTGT
1 AAAAAACGCCGCTAAATCTCAACACCTATTGCGGCATTTTTAT
* * * *
302668 GAAAAACACCGCTAAATCTCAACACCTATTGCGGCATTTGTAAG
1 AAAAAACGCCGCTAAATCTCAACACCTATTGCGGCATTT-TTAT
* * *
302712 AAAAAATGCCTCTAAATCTCAAAACCTATTGCGGCATTT
1 AAAAAACGCCGCTAAATCTCAACACCTATTGCGGCATTT
302751 GTAAGATGCT
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
41 36 0.35
43 33 0.32
44 35 0.34
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (43 bp):
AAAAAACGCCGCTAAATCTCAACACCTATTGCGGCATTTTTAT
Found at i:302716 original size:84 final size:87
Alignment explanation
Indices: 302576--302745 Score: 220
Period size: 84 Copynumber: 2.0 Consensus size: 87
302566 ATTTTACGGC
* * * **
302576 GTTTGTGGAAAAAACGCCGCTAAATATCAATACCTATTGCGGCATTTTTCTC-AAAAACGCCGCT
1 GTTTGTGGAAAAAACACCGCTAAATATCAACACCTATTGCGGCATTTGTAACAAAAAACGCCGCT
* *
302640 AAATTTCAACACCTATTGCGGT
66 AAATCTCAAAACCTATTGCGGT
* * * *
302662 GTTTGT-G-AAAAACACCGCTAAATCTCAACACCTATTGCGGCATTTGTAAGAAAAAATGCCTCT
1 GTTTGTGGAAAAAACACCGCTAAATATCAACACCTATTGCGGCATTTGTAACAAAAAACGCCGCT
302725 AAATCTCAAAACCTATTGCGG
66 AAATCTCAAAACCTATTGCGG
302746 CATTTGTAAG
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
84 36 0.50
85 30 0.42
86 6 0.08
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.28
Consensus pattern (87 bp):
GTTTGTGGAAAAAACACCGCTAAATATCAACACCTATTGCGGCATTTGTAACAAAAAACGCCGCT
AAATCTCAAAACCTATTGCGGT
Found at i:302732 original size:44 final size:44
Alignment explanation
Indices: 302583--302756 Score: 203
Period size: 44 Copynumber: 4.0 Consensus size: 44
302573 GGCGTTTGTG
* * **
302583 GAAAAAACGCCGCTAAATATCAATACCTATTGCGGCATTT-TTC
1 GAAAAAACGCCGCTAAATCTCAACACCTATTGCGGCATTTGTAA
** * **
302626 TCAAAAACGCCGCTAAATTTCAACACCTATTGCGGTGTTTGT--
1 GAAAAAACGCCGCTAAATCTCAACACCTATTGCGGCATTTGTAA
*
302668 G-AAAAACACCGCTAAATCTCAACACCTATTGCGGCATTTGTAA
1 GAAAAAACGCCGCTAAATCTCAACACCTATTGCGGCATTTGTAA
* * *
302711 GAAAAAATGCCTCTAAATCTCAAAACCTATTGCGGCATTTGTAA
1 GAAAAAACGCCGCTAAATCTCAACACCTATTGCGGCATTTGTAA
302755 GA
1 GA
302757 TGCTAATTAT
Statistics
Matches: 112, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
41 36 0.32
43 35 0.31
44 41 0.37
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (44 bp):
GAAAAAACGCCGCTAAATCTCAACACCTATTGCGGCATTTGTAA
Found at i:303784 original size:16 final size:16
Alignment explanation
Indices: 303763--303797 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
303753 TCCCAAGGTC
* *
303763 TAAATTATTCGTGGTT
1 TAAATTATCCATGGTT
303779 TAAATTATCCATGGTT
1 TAAATTATCCATGGTT
303795 TAA
1 TAA
303798 TATGAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (16 bp):
TAAATTATCCATGGTT
Found at i:304577 original size:45 final size:44
Alignment explanation
Indices: 304494--304730 Score: 221
Period size: 44 Copynumber: 5.4 Consensus size: 44
304484 GTGATGAGAG
** *
304494 ACAAACGCCGCAAAA-G-CTCGAGATATATAATGGTGTTTTTTGGAT
1 ACAAACGCCGCAAAATGTCT-G-G-TATATAGCGGCGTTTTTTGGAT
* ** * * * *
304539 ACAAACGCCACAAAATGTCTACATCTATAGAGTCGTTTTTCGGAT
1 ACAAACGCCGCAAAATGTCT-GGTATATAGCGGCGTTTTTTGGAT
* * *
304584 ACAAACGCCGCAACAA-GTCTGGTAAATAGTGGCATTTTTTGGAT
1 ACAAACGCCGCAA-AATGTCTGGTATATAGCGGCGTTTTTTGGAT
* * * *
304628 ACAAACGCTGCAAAATGTTTGGTATATAGCGACATTTTTTGGAT
1 ACAAACGCCGCAAAATGTCTGGTATATAGCGGCGTTTTTTGGAT
** *
304672 ACAAACGCTACAAAAGGTCTGGTATATAGCGGCGTTTTTT-GAT
1 ACAAACGCCGCAAAATGTCTGGTATATAGCGGCGTTTTTTGGAT
304715 ACAAACGCCGCAAAAT
1 ACAAACGCCGCAAAAT
304731 ATCTAAACTT
Statistics
Matches: 156, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
43 18 0.12
44 87 0.56
45 46 0.29
46 3 0.02
47 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (44 bp):
ACAAACGCCGCAAAATGTCTGGTATATAGCGGCGTTTTTTGGAT
Found at i:310458 original size:42 final size:42
Alignment explanation
Indices: 310367--310472 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 42
310357 GGATTGCACA
* * *
310367 ATTGCGGCTTTTATAATAAAAACACCACTAAAGAACATAAAT
1 ATTGCGGCGTTTATTACAAAAACACCACTAAAGAACATAAAT
* **** * *
310409 ATGGCGGCGTTTATTACAAAAACACCACTATCTTACATGATT
1 ATTGCGGCGTTTATTACAAAAACACCACTAAAGAACATAAAT
310451 ATTGCGGCGTTTATTAACAAAA
1 ATTGCGGCGTTTATT-ACAAAA
310473 TGCCACTAAA
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 46 0.88
43 6 0.12
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (42 bp):
ATTGCGGCGTTTATTACAAAAACACCACTAAAGAACATAAAT
Found at i:311040 original size:82 final size:82
Alignment explanation
Indices: 310888--311040 Score: 191
Period size: 82 Copynumber: 1.9 Consensus size: 82
310878 TGTAACAACG
* * * * * * * * *
310888 CCACTATATATGAATCATATTGTGGCGTTTGTATGAAAACGTCGTTAAATTACTGTATTTTTCGT
1 CCACTATATATGAACCATATTGTGGCGTTTCTATAAAAACGCCGCTAAATTAATGCATTTTGCGG
310953 CTTTTGTTGAGAAAACA
66 CTTTTGTTGAGAAAACA
* *
310970 CCACTATATATGAACCCTATTGTGGCGTTTCTATAAAAACGCCGCTAATTTAAT-CATTTTGCGG
1 CCACTATATATGAACCATATTGTGGCGTTTCTATAAAAACGCCGCTAAATTAATGCATTTTGCGG
311034 CGTTTTG
66 C-TTTTG
311041 AATTAAAACG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
81 8 0.14
82 51 0.86
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (82 bp):
CCACTATATATGAACCATATTGTGGCGTTTCTATAAAAACGCCGCTAAATTAATGCATTTTGCGG
CTTTTGTTGAGAAAACA
Found at i:318327 original size:19 final size:20
Alignment explanation
Indices: 318305--318354 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
318295 TTGTTATTTG
318305 ATTAGTTAG-GCTGTTGATA
1 ATTAGTTAGTGCTGTTGATA
*
318324 ATTAGTTAGATTGCTGTTGTTA
1 ATTAGTTAG--TGCTGTTGATA
318346 ATTAGTTAG
1 ATTAGTTAG
318355 ATTGTTAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 9 0.33
22 18 0.67
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (20 bp):
ATTAGTTAGTGCTGTTGATA
Found at i:318342 original size:22 final size:22
Alignment explanation
Indices: 318314--318358 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
318304 GATTAGTTAG
318314 GCTGTTGATAATTAGTTAGATT
1 GCTGTTGATAATTAGTTAGATT
*
318336 GCTGTTGTTAATTAGTTAGATT
1 GCTGTTGATAATTAGTTAGATT
318358 G
1 G
318359 TTAGTTAGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.47
Consensus pattern (22 bp):
GCTGTTGATAATTAGTTAGATT
Found at i:328245 original size:16 final size:17
Alignment explanation
Indices: 328224--328256 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
328214 AATAGTTATC
*
328224 TTAAAAA-ATTATTTTA
1 TTAAAAATATTAATTTA
328240 TTAAAAATATTAATTTA
1 TTAAAAATATTAATTTA
328257 CTAATAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAAAATATTAATTTA
Found at i:339286 original size:20 final size:20
Alignment explanation
Indices: 339258--339295 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
339248 TTTCTAGGTT
*
339258 ATAGCATCAATATTGGATTA
1 ATAGCATCAATACTGGATTA
*
339278 ATAGTATCAATACTGGAT
1 ATAGCATCAATACTGGAT
339296 GAACTGGATG
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:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (20 bp):
ATAGCATCAATACTGGATTA
Found at i:345639 original size:53 final size:53
Alignment explanation
Indices: 345491--345641 Score: 257
Period size: 53 Copynumber: 2.8 Consensus size: 53
345481 CTTTCGACAC
* *
345491 TGTGTGCACCCATGGTATTCATAATAAGTTTGTGAATTACCAGTTCAGCACTA
1 TGTGTGCACCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCAGCACTA
* *
345544 TGTGTGCACCCATGGTGTTCATAATGAGTTTGTGAATTACCATTTCGGCACTA
1 TGTGTGCACCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCAGCACTA
*
345597 TGTGTGCACCCATAGTATTCATAATGAGTTTGTGAATTACCATTT
1 TGTGTGCACCCATGGTATTCATAATGAGTTTGTGAATTACCATTT
345642 AATTACCTTA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 92 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (53 bp):
TGTGTGCACCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCAGCACTA
Found at i:348057 original size:20 final size:21
Alignment explanation
Indices: 348008--348063 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
347998 TACCAGAAGG
* *
348008 GGGTATCGGTACCATAGTATA
1 GGGTATCGATACCATAGTAAA
*
348029 GTAGTATCGATACCATAG-AAA
1 G-GGTATCGATACCATAGTAAA
348050 GGGTATCGATACCA
1 GGGTATCGATACCA
348064 AGACACATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 12 0.40
21 4 0.13
22 14 0.47
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (21 bp):
GGGTATCGATACCATAGTAAA
Found at i:348072 original size:95 final size:94
Alignment explanation
Indices: 347938--348156 Score: 264
Period size: 95 Copynumber: 2.3 Consensus size: 94
347928 GACGAGGTAA
* *
347938 TATCGATAACATGGTAAGGGTATCGATACCAGATAACATCGAACCTAA-TTTTGATATCGATACC
1 TATCGATACCAT-GAAAGGGTATCGATACCAGATAACATCGAACCTAATTTTTG-TATCGATACC
* * *
348002 AG-AAGGGGGTATCGGTACCATAGTATAGTAG
64 -GTAAGGGGGTATCGATACCATAATAGAGTAG
* *
348033 TATCGATACCATAGAAAGGGTATCGATACCAAGA-CACATCGAATCTAATTTTTGTATCGATACC
1 TATCGATACCAT-GAAAGGGTATCGATACC-AGATAACATCGAACCTAATTTTTGTATCGATACC
* *
348097 GTAAGGGGGTATTGATACCATAATAGGGTAG
64 GTAAGGGGGTATCGATACCATAATAGAGTAG
* *
348128 TATCGATACCATTATAGGAGTATCGATAC
1 TATCGATACCATGAAAGG-GTATCGATAC
348157 TGTGTTAAGT
Statistics
Matches: 108, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
94 5 0.05
95 95 0.88
96 8 0.07
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (94 bp):
TATCGATACCATGAAAGGGTATCGATACCAGATAACATCGAACCTAATTTTTGTATCGATACCGT
AAGGGGGTATCGATACCATAATAGAGTAG
Found at i:348135 original size:22 final size:20
Alignment explanation
Indices: 348086--348156 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 20
348076 TCTAATTTTT
* * *
348086 GTATCGATACCGTAA-GGGG
1 GTATCGATACCATAATAGGA
*
348105 GTATTGATACCATAATAGGGTA
1 GTATCGATACCATAATA-GG-A
*
348127 GTATCGATACCATTATAGGA
1 GTATCGATACCATAATAGGA
348147 GTATCGATAC
1 GTATCGATAC
348157 TGTGTTAAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 13 0.30
20 11 0.26
21 4 0.09
22 15 0.35
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28
Consensus pattern (20 bp):
GTATCGATACCATAATAGGA
Found at i:348532 original size:59 final size:59
Alignment explanation
Indices: 348477--348870 Score: 641
Period size: 59 Copynumber: 6.7 Consensus size: 59
348467 ATGGCACTAA
*
348477 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGCATAGGGCACTT-
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
348535 GTGTGAC-AAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTG-CTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * **
348594 GTGTGCTAAAATGATATGAAATTCGTACTAAGTGTATGAATTTCTATATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
*
348653 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTG
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* *
348712 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCTTATAAGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * *
348771 GTGTGATAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACCTT-
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCA-CTTC
*
348830 GTGTGCTAAAATGATAAGAAGTTCATACTAAGTGTATGAAT
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAAT
348871 AGTTGATAAA
Statistics
Matches: 311, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
58 56 0.18
59 252 0.81
60 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
Found at i:349624 original size:182 final size:183
Alignment explanation
Indices: 349317--349685 Score: 686
Period size: 182 Copynumber: 2.0 Consensus size: 183
349307 TTTCAAATGG
* *
349317 AAAACTGGTTTAAAAGTGATATGACATTTGTATCTCTATACATAACGGTATGCATGAGATGTGTG
1 AAAACTGGTTTAAAAGTGATATGACATTTGTATCTCTATACATAACGGTATACATGAGATGAGTG
*
349382 TTACATTTATTAGTATCAGAGCTATAGGTTTAGCCGATTCTCAGCCGAATCAAGTGTAAA-TTTT
66 TTACATTTATTAGTATCAGAGCTATAAGTTTAGCCGATTCTCAGCCGAATCAAGTGTAAATTTTT
349446 AATGTAAAAAGAGGTTACATGCCACTAAGATGTCAAGGTTACTGATAGGGTAT
131 AATGTAAAAAGAGGTTACATGCCACTAAGATGTCAAGGTTACTGATAGGGTAT
*
349499 AAAACTGGTTTAAAAGTGATGTGACATTTGTATCTCTATACATAACGGTATACATGAGATGAGTG
1 AAAACTGGTTTAAAAGTGATATGACATTTGTATCTCTATACATAACGGTATACATGAGATGAGTG
*
349564 TTACATTTATTAGTATCAGAGCTATAAGTTTAGCCGATTCTCGGCCGAATCAAGTGTAAATTTTT
66 TTACATTTATTAGTATCAGAGCTATAAGTTTAGCCGATTCTCAGCCGAATCAAGTGTAAATTTTT
349629 AATGTAAAAAGAGGTTACATGCCACTAAGATGTCAAGGTTACTGATAGGGTAT
131 AATGTAAAAAGAGGTTACATGCCACTAAGATGTCAAGGTTACTGATAGGGTAT
349682 AAAA
1 AAAA
349686 TGAATCTGAA
Statistics
Matches: 181, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
182 120 0.66
183 61 0.34
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (183 bp):
AAAACTGGTTTAAAAGTGATATGACATTTGTATCTCTATACATAACGGTATACATGAGATGAGTG
TTACATTTATTAGTATCAGAGCTATAAGTTTAGCCGATTCTCAGCCGAATCAAGTGTAAATTTTT
AATGTAAAAAGAGGTTACATGCCACTAAGATGTCAAGGTTACTGATAGGGTAT
Found at i:355121 original size:20 final size:20
Alignment explanation
Indices: 355096--355147 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
355086 TGATATAATC
* *
355096 AGTATCGATTCCGATGAGGT
1 AGTATCGATACCGACGAGGT
*
355116 AGTATCGATACTGACGAGGT
1 AGTATCGATACCGACGAGGT
355136 AGTATCGATACC
1 AGTATCGATACC
355148 ATGGTAAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (20 bp):
AGTATCGATACCGACGAGGT
Found at i:355303 original size:94 final size:95
Alignment explanation
Indices: 355134--355338 Score: 236
Period size: 94 Copynumber: 2.2 Consensus size: 95
355124 TACTGACGAG
** * *
355134 GTAGTATCGATACCATGGTAAGGGTATGGATACCAGATAATATCGAACCTAATTTTGGTGTCAAT
1 GTAGTATCGATACCATGGTAAGGGTATCAATACCAGATAACATCGAACCTAATTTTGGTATCAAT
355199 ACCAGAA-GGGGTATCGGTAGCATAGTATA
66 ACCAGAAGGGGGTATCGGTAGCATAGTATA
* * * *
355228 GTAGTATCTATACCATGGTAAGGGTATCAATACCAAGA-CACATCGAATCTAATTTTGGTATCGA
1 GTAGTATCGATACCATGGTAAGGGTATCAATACC-AGATAACATCGAACCTAATTTTGGTATCAA
* * * * **
355292 TACC-GTTAGGGGGTATCGATACCATAATAGG
65 TACCAG-AAGGGGGTATCGGTAGCATAGTATA
*
355323 GTGGTATCGATACCAT
1 GTAGTATCGATACCAT
355339 TATAGAAGTA
Statistics
Matches: 92, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
93 1 0.01
94 57 0.62
95 34 0.37
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGGGTATCAATACCAGATAACATCGAACCTAATTTTGGTATCAAT
ACCAGAAGGGGGTATCGGTAGCATAGTATA
Found at i:355331 original size:22 final size:21
Alignment explanation
Indices: 355283--355343 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
355273 AATCTAATTT
*
355283 TGGTATCGATACCGT-TAGGG
1 TGGTATCGATACCATATAGGG
355303 -GGTATCGATACCATAATAGGG
1 TGGTATCGATACCAT-ATAGGG
355324 TGGTATCGATACCATTATAG
1 TGGTATCGATACCA-TATAG
355344 AAGTATCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 13 0.36
21 5 0.14
22 17 0.47
23 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
TGGTATCGATACCATATAGGG
Found at i:355723 original size:59 final size:57
Alignment explanation
Indices: 355686--356020 Score: 422
Period size: 59 Copynumber: 5.7 Consensus size: 57
355676 ATGGCACTAA
*
355686 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTT-C-TATAGGGCACTTC
* *
355745 GTGTGCTAAAATGATAAGAAATTCATTCTAAGTGTAT-AATTTCAGTGTAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTC--TATAGGGCACTTC
* *
355803 GTGTTCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTG
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAA-TTTC-TATAGGGCACTTC
* *
355862 GTGTTCTAAATTGATAAGAAATTCATACTAAGTGTATGAATTTCCTTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTT-C-TATAGGGCACTTC
* * * *
355921 GTGTGCTAAAATGTTAATAAATTCATACTAAGTGTATGAATTTCTTTATTGTGCACCTT-
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTC--TATAGGGCA-CTTC
* * * *
355980 ATGTTCTAAAATGATAAGAAGTTCATACTATGTGTATGAAT
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAAT
356021 GGTTGATAAA
Statistics
Matches: 248, Mismatches: 22, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
57 1 0.00
58 56 0.23
59 184 0.74
60 7 0.03
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (57 bp):
GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTATAGGGCACTTC
Found at i:355962 original size:118 final size:117
Alignment explanation
Indices: 355686--356020 Score: 476
Period size: 118 Copynumber: 2.8 Consensus size: 117
355676 ATGGCACTAA
* *
355686 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTT-GTGTTC
* *
355751 TAAAATGATAAGAAATTCATTCTAAGTGTAT-AATTTCAGTGTAGGGCACTTC
65 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCAGTATAGGGCACTTC
* *
355803 GTGTTCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTGGTGTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTT-GTGTTC
* **
355868 TAAATTGATAAGAAATTCATACTAAGTGTATGAATTTCCTTATAGGGCACTTC
65 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCAGTATAGGGCACTTC
* * * * *
355921 GTGTGCTAAAATGTTAATAAATTCATACTAAGTGTATGAA-TTTCTTTATTGTGCACCTTATGTT
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTC-GTATTGGGCA-CTTGTGTT
* *
355985 CTAAAATGATAAGAAGTTCATACTATGTGTATGAAT
64 CTAAAATGATAAGAAATTCATACTAAGTGTATGAAT
356021 GGTTGATAAA
Statistics
Matches: 195, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
117 93 0.48
118 99 0.51
119 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (117 bp):
GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTGTGTTCT
AAAATGATAAGAAATTCATACTAAGTGTATGAATTTCAGTATAGGGCACTTC
Found at i:356769 original size:21 final size:22
Alignment explanation
Indices: 356743--356783 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
356733 CCAAGATAGG
356743 GAGTATCGGTACT-CCTTTAAT
1 GAGTATCGGTACTACCTTTAAT
*
356764 GAGTATTGGTACTACCTTTA
1 GAGTATCGGTACTACCTTTA
356784 TAATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (22 bp):
GAGTATCGGTACTACCTTTAAT
Found at i:364828 original size:17 final size:17
Alignment explanation
Indices: 364808--364849 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
364798 TCCTTTACAT
* *
364808 TACTATTTCTTTTATTG
1 TACTATTTATCTTATTG
*
364825 TACTATTTATCTTGTTG
1 TACTATTTATCTTATTG
364842 TACTATTT
1 TACTATTT
364850 TTTATTGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.62
Consensus pattern (17 bp):
TACTATTTATCTTATTG
Found at i:364906 original size:17 final size:18
Alignment explanation
Indices: 364874--364918 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
364864 TAATGTTCTA
* *
364874 TATCTTTTATTGTATTG-
1 TATCTTTTACTATATTGT
364891 TATCTTTTACTATATTGT
1 TATCTTTTACTATATTGT
364909 TAT-TTTTACT
1 TATCTTTTACT
364919 GTGCTATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 22 0.88
18 3 0.12
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (18 bp):
TATCTTTTACTATATTGT
Found at i:365455 original size:17 final size:18
Alignment explanation
Indices: 365423--365490 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 18
365413 TTCCTTTCAC
*
365423 TATACTATTT-TCTTTACA
1 TATACTATTTCT-TTTACT
365441 T-TACTATTTCTTTTA-T
1 TATACTATTTCTTTTACT
* *
365457 TATACTATTTCTCTT-GT
1 TATACTATTTCTTTTACT
*
365474 TGTACTATTTCTTTTAC
1 TATACTATTTCTTTTAC
365491 GGCTTCCTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 1 0.02
17 38 0.93
18 2 0.05
ACGTcount: A:0.21, C:0.16, G:0.03, T:0.60
Consensus pattern (18 bp):
TATACTATTTCTTTTACT
Found at i:367386 original size:26 final size:26
Alignment explanation
Indices: 367334--367387 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
367324 CATTTCCATG
* *
367334 AAATTCTCATAATTTCATTATATGAT
1 AAATTCTCATAATTTCATGATAAGAT
*
367360 AAATT-TCATAATTATCATGCTAAGAT
1 AAATTCTCATAATT-TCATGATAAGAT
367386 AA
1 AA
367388 TAGAGTTGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.41
Consensus pattern (26 bp):
AAATTCTCATAATTTCATGATAAGAT
Found at i:373446 original size:23 final size:23
Alignment explanation
Indices: 373406--373451 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
373396 CCGATACTTC
* *
373406 TCCTTGGGTATCGGTACTCCCCT
1 TCCTAGGGTATCGATACTCCCCT
* *
373429 TCCTAGGGTATTGATACTTCCCT
1 TCCTAGGGTATCGATACTCCCCT
373452 GAGTATTGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.13, C:0.30, G:0.20, T:0.37
Consensus pattern (23 bp):
TCCTAGGGTATCGATACTCCCCT
Found at i:374618 original size:20 final size:20
Alignment explanation
Indices: 374591--374646 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
374581 CAAACATGCA
*
374591 TAGG-GGTTTTGAAACCCCT
1 TAGGTGGTTTCGAAACCCCT
374610 TAGGTGGTTTCGAAACCCCT
1 TAGGTGGTTTCGAAACCCCT
374630 TAGGTGGTTTCGAAACC
1 TAGGTGGTTTCGAAACC
374647 TCACTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (20 bp):
TAGGTGGTTTCGAAACCCCT
Found at i:380562 original size:14 final size:14
Alignment explanation
Indices: 380545--380684 Score: 70
Period size: 16 Copynumber: 9.3 Consensus size: 14
380535 ATAAACGTAC
380545 TATAATATATATTA
1 TATAATATATATTA
*
380559 TATAAT-T-T-TTT
1 TATAATATATATTA
* *
380570 TGAAAACTATATATATTT
1 T-ATAA-TATA--TATTA
*
380588 TATACTATAATATATA
1 TATAATAT-ATAT-TA
380604 TATATATATATATATA
1 TATA-ATATATAT-TA
380620 TATAACTATATATATA
1 TATAA-TATATAT-TA
380636 TATATATATATATATA
1 TATA-ATATATAT-TA
* *
380652 TTATAATAAATACTA
1 -TATAATATATATTA
* *
380667 TATACTACATATTA
1 TATAATATATATTA
380681 TATA
1 TATA
380685 TATGTTTTCA
Statistics
Matches: 102, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
11 3 0.03
12 4 0.04
13 2 0.02
14 22 0.22
15 6 0.06
16 49 0.48
17 12 0.12
18 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (14 bp):
TATAATATATATTA
Found at i:380705 original size:19 final size:18
Alignment explanation
Indices: 380680--380726 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
380670 ACTACATATT
*
380680 ATATATATGTTTTCAAAA
1 ATATATATATTTTCAAAA
* *
380698 ACTATATATATTTTTAAAT
1 A-TATATATATTTTCAAAA
380717 ATATATATAT
1 ATATATATAT
380727 ATATATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (18 bp):
ATATATATATTTTCAAAA
Found at i:380706 original size:37 final size:37
Alignment explanation
Indices: 380588--380731 Score: 125
Period size: 37 Copynumber: 3.8 Consensus size: 37
380578 ATATATATTT
380588 TATACTATA-ATATATATATATATATATATATATATAACTA
1 TATA-TATACATATATATATATATAT-TATA-ATA-AACTA
*
380628 TATATATATATATATATATATATATTATAATAAA-TA
1 TATATATACATATATATATATATATTATAATAAACTA
* *
380664 CTATATACTACATAT-TATATATATGTTTTCAA-AAACTA
1 -TATATA-TACATATATATATATATATTAT-AATAAACTA
*** *
380702 TATATATTTTTAAATATATATATATATATA
1 TATATATACATATATATATATATAT-TATA
380732 TATTATAAGA
Statistics
Matches: 88, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
36 5 0.06
37 40 0.45
38 15 0.17
39 8 0.09
40 20 0.23
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.47
Consensus pattern (37 bp):
TATATATACATATATATATATATATTATAATAAACTA
Found at i:380752 original size:2 final size:2
Alignment explanation
Indices: 380577--380738 Score: 124
Period size: 2 Copynumber: 82.0 Consensus size: 2
380567 TTTTGAAAAC
*
380577 TA TA TA TA T- TT TA TA CTA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
380618 TA TA TA -A CTA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
380658 TA AA TA CTA TA TA CTA CA TA T- TA TA TA TA TG T- TT TCA AA AA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* * *
380699 CTA TA TA TA TT TT TA AA TA TA TA TA TA TA TA TA TA T- TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
380739 AGAACCATAT
Statistics
Matches: 133, Mismatches: 13, Indels: 28
0.76 0.07 0.16
Matches are distributed among these distances:
1 8 0.06
2 117 0.88
3 8 0.06
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:380804 original size:10 final size:9
Alignment explanation
Indices: 380791--380823 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
380781 TTTTTTCAAA
380791 AATATACTAT
1 AATATA-TAT
380801 AATATATAT
1 AATATATAT
380810 -ATATATAT
1 AATATATAT
380818 AATATA
1 AATATA
380824 GATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 8 0.36
10 6 0.27
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (9 bp):
AATATATAT
Found at i:382090 original size:42 final size:42
Alignment explanation
Indices: 381934--382116 Score: 135
Period size: 42 Copynumber: 4.4 Consensus size: 42
381924 TATGAGTTTG
*
381934 AGTCAAGTGGGATATTCTTTAGGTGATTCCCCTTC-CTAGGAA
1 AGTCAAGTGAGATATTCTTTAGGTGATTCCCCTTCAC-AGGAA
* * * ** * *
381976 AGCCATA-TAAGATACTCTCCAGATGATTCCCCTTCATAGGAA
1 AGTCA-AGTGAGATATTCTTTAGGTGATTCCCCTTCACAGGAA
* * *
382018 AGT-ATA-TGAGATATTATTT-GGATGAATCCCCTTCACGGGAA
1 AGTCA-AGTGAGATATTCTTTAGG-TGATTCCCCTTCACAGGAA
* * ***
382059 AGTCAGGTGAGATATTCTTTAGGTGACTCCCCTTCGTGGGAA
1 AGTCAAGTGAGATATTCTTTAGGTGATTCCCCTTCACAGGAA
382101 AGAT-AAGTGAGATATT
1 AG-TCAAGTGAGATATT
382117 TTTTCAGCCG
Statistics
Matches: 110, Mismatches: 24, Indels: 14
0.74 0.16 0.09
Matches are distributed among these distances:
40 1 0.01
41 30 0.27
42 75 0.68
43 4 0.04
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (42 bp):
AGTCAAGTGAGATATTCTTTAGGTGATTCCCCTTCACAGGAA
Found at i:387077 original size:34 final size:34
Alignment explanation
Indices: 387029--387120 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
387019 TTGTTTGCAT
* ** * *
387029 AATAAGCACTCCATGTGTTATTATCGGAAACAGA
1 AATATGCACTCCATGTGCAATCATCAGAAACAGA
*
387063 AATATGCACTCCATGTGCAATCATCAGATACAGA
1 AATATGCACTCCATGTGCAATCATCAGAAACAGA
* *
387097 AATATGCACTCTAGGTGCAATCAT
1 AATATGCACTCCATGTGCAATCAT
387121 ATAATGTACA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (34 bp):
AATATGCACTCCATGTGCAATCATCAGAAACAGA
Found at i:388948 original size:21 final size:21
Alignment explanation
Indices: 388888--388948 Score: 97
Period size: 21 Copynumber: 2.9 Consensus size: 21
388878 AGCTTAACCC
*
388888 AAAAATCAATCGAATAATCCT
1 AAAAATCAATTGAATAATCCT
388909 AAAAATCAATTGAATAATCCT
1 AAAAATCAATTGAATAATCCT
388930 AAAAATCAAATTGAA-AATC
1 AAAAATC-AATTGAATAATC
388949 TTACCTCTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 31 0.82
22 7 0.18
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAAATCAATTGAATAATCCT
Found at i:391341 original size:2 final size:2
Alignment explanation
Indices: 391334--391385 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
391324 TACAAGTTGA
391334 AT AT AT AT AT AT 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 AT AT AT AT AT AT
391376 AT AT AT AT AT
1 AT AT AT AT AT
391386 GCACCGTAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:401434 original size:15 final size:15
Alignment explanation
Indices: 401392--401449 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
401382 TTTCAAAAAC
401392 TATATATATATAT-A
1 TATATATATATATAA
*
401406 TAT-TTTATATTATAA
1 TATATATATA-TATAA
401421 TATA-ATACTATATAA
1 TATATATA-TATATAA
401436 TATATATATATATA
1 TATATATATATATA
401450 CTTTTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 5 0.14
14 6 0.16
15 21 0.57
16 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:401469 original size:2 final size:2
Alignment explanation
Indices: 401392--401449 Score: 63
Period size: 2 Copynumber: 31.0 Consensus size: 2
401382 TTTCAAAAAC
*
401392 TA TA TA TA TA TA TA TA T- TT TA TA T- TA TA -A TA TA -A TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
401431 TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
401450 CTTTTAAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
1 5 0.10
2 42 0.86
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:401506 original size:22 final size:20
Alignment explanation
Indices: 401439--401529 Score: 80
Period size: 19 Copynumber: 4.5 Consensus size: 20
401429 TATATAATAT
401439 ATATATATATACTTTTAAAAA
1 ATATATATATA-TTTTAAAAA
*
401460 CTATATATAT-TTTTAAAAA
1 ATATATATATATTTTAAAAA
*
401479 ATAATATATATATATTCT-AAGA
1 AT-ATATATATAT-TT-TAAAAA
* *
401501 ACA-ATATATATTTTCAAAA
1 ATATATATATATTTTAAAAA
401520 ATATACTATA
1 ATATA-TATA
401530 ATATATATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
18 1 0.02
19 17 0.30
20 17 0.30
21 15 0.26
22 6 0.11
23 1 0.02
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.42
Consensus pattern (20 bp):
ATATATATATATTTTAAAAA
Found at i:401520 original size:41 final size:43
Alignment explanation
Indices: 401434--401538 Score: 133
Period size: 42 Copynumber: 2.4 Consensus size: 43
401424 AATACTATAT
* *
401434 AATATATATATATATACTTTTAAAAACTATATATATTTTTAAAA
1 AATATATATATATATA-TTCTAAAAACAATATATATTTTTAAAA
* *
401478 AATA-ATATATATATATTCTAAGAACAATATATA-TTTTCAAA
1 AATATATATATATATATTCTAAAAACAATATATATTTTTAAAA
401519 AATATACTATAATATATATT
1 AATATA-TAT-ATATATATT
401539 TATGTATTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
41 11 0.20
42 16 0.30
43 14 0.26
44 13 0.24
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (43 bp):
AATATATATATATATATTCTAAAAACAATATATATTTTTAAAA
Found at i:406219 original size:18 final size:18
Alignment explanation
Indices: 406193--406227 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
406183 TCGAAAGGAC
*
406193 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
406211 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
406228 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:411340 original size:18 final size:18
Alignment explanation
Indices: 411314--411348 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
411304 TCGAAAGGAC
*
411314 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
411332 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
411349 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:417331 original size:16 final size:16
Alignment explanation
Indices: 417310--417342 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
417300 TAATAAATAA
417310 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
417326 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
417342 A
1 A
417343 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:417423 original size:10 final size:10
Alignment explanation
Indices: 417408--417482 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
417398 CATTTAATAA
417408 ATAAACGAAC
1 ATAAACGAAC
417418 ATAAACGAAC
1 ATAAACGAAC
417428 ----ACGAAC
1 ATAAACGAAC
417434 ATAAACGAAC
1 ATAAACGAAC
** *
417444 ACGAAC-ATAA
1 ATAAACGA-AC
417454 ATGAACACGAAC
1 AT-AA-ACGAAC
417466 ATAAACGAAC
1 ATAAACGAAC
417476 ATAAACG
1 ATAAACG
417483 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:417433 original size:16 final size:16
Alignment explanation
Indices: 417412--417476 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
417402 TAATAAATAA
417412 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
417428 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
417444 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
417460 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
417476 A
1 A
417477 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:418526 original size:24 final size:24
Alignment explanation
Indices: 418499--418549 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
418489 TATTGGGTTA
* *
418499 AACATAAATGAATGAACATAAACG
1 AACATAAACGAACGAACATAAACG
* *
418523 AACATAACCGAACGAACATAACCG
1 AACATAAACGAACGAACATAAACG
418547 AAC
1 AAC
418550 GTTCACGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.22, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:418536 original size:14 final size:14
Alignment explanation
Indices: 418519--418550 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
418509 AATGAACATA
418519 AACGAACATAACCG
1 AACGAACATAACCG
418533 AACGAACATAACCG
1 AACGAACATAACCG
418547 AACG
1 AACG
418551 TTCACGAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:421430 original size:17 final size:17
Alignment explanation
Indices: 421410--421457 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
421400 TGAAATATCT
421410 ATAAAATAATAATACAA
1 ATAAAATAATAATACAA
* *
421427 ATAAAATATTAGATTCAA
1 ATAAAATAATA-ATACAA
*
421445 TTAAAA-AATAATA
1 ATAAAATAATAATA
421458 ATTAAATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 2 0.08
17 13 0.52
18 10 0.40
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAAAATAATAATACAA
Found at i:421465 original size:19 final size:21
Alignment explanation
Indices: 421429--421472 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
421419 TAATACAAAT
* *
421429 AAAATATTAGATTCAATTA-A
1 AAAATAATAGATTAAATTATA
421449 AAAATAATA-ATTAAATTATA
1 AAAATAATAGATTAAATTATA
421469 AAAA
1 AAAA
421473 AACTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATAATAGATTAAATTATA
Found at i:421791 original size:14 final size:14
Alignment explanation
Indices: 421772--421802 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
421762 TTAAATGATA
421772 AACGAACACAAATG
1 AACGAACACAAATG
*
421786 AACGAACATAAATG
1 AACGAACACAAATG
421800 AAC
1 AAC
421803 AAATGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:422058 original size:14 final size:14
Alignment explanation
Indices: 422039--422072 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
422029 CACATAAACG
422039 AACATAAACGAACA
1 AACATAAACGAACA
* *
422053 AACATAAATGAACG
1 AACATAAACGAACA
422067 AACATA
1 AACATA
422073 TTACTGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.18, G:0.09, T:0.12
Consensus pattern (14 bp):
AACATAAACGAACA
Found at i:429925 original size:31 final size:28
Alignment explanation
Indices: 429882--429942 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
429872 AACACGTATA
429882 TTCAGTTCAAAATGACTGAGCACCTCTATGC
1 TTCAGTTCAAAAT--CTG-GCACCTCTATGC
*
429913 TTCAG-TCTAAAATCTGGCACCTCTGTGC
1 TTCAGTTC-AAAATCTGGCACCTCTATGC
429941 TT
1 TT
429943 TGTAATGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 13 0.46
29 3 0.11
30 2 0.07
31 10 0.36
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (28 bp):
TTCAGTTCAAAATCTGGCACCTCTATGC
Found at i:430042 original size:54 final size:53
Alignment explanation
Indices: 429911--430051 Score: 138
Period size: 54 Copynumber: 2.6 Consensus size: 53
429901 GCACCTCTAT
* * * *
429911 GCTTCAGTCTAAAATCTGGCACCTCTGTGCTTTGTAATGATTAAGAACCTCTGT
1 GCTTCAATCTAAAATCT-GCACCTATGTGCTTTGGAATGATTAAGAACCTCTGC
* * ** * ** *
429965 GCTTTAAACTAGGATCTGACACCTATGTGCTTTGGGATGATTGCGTACCTCTGC
1 GCTTCAATCTAAAATCTG-CACCTATGTGCTTTGGAATGATTAAGAACCTCTGC
*
430019 GCTTCAATCTAAAATCTAGCACCTTTGTGCTTT
1 GCTTCAATCTAAAATCT-GCACCTATGTGCTTT
430052 AAAATTTATT
Statistics
Matches: 68, Mismatches: 17, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
53 1 0.01
54 66 0.97
55 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (53 bp):
GCTTCAATCTAAAATCTGCACCTATGTGCTTTGGAATGATTAAGAACCTCTGC
Found at i:432093 original size:3 final size:3
Alignment explanation
Indices: 432085--432124 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
432075 AAGAAAGAAA
432085 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
432125 TAACATACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:432223 original size:13 final size:14
Alignment explanation
Indices: 432166--432233 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
432156 CAAATAAAAA
432166 AATATTATAATAAT
1 AATATTATAATAAT
432180 AATA--ATAAT--T
1 AATATTATAATAAT
* * *
432190 ATTATTATTATTAT
1 AATATTATAATAAT
432204 AAATATTATAA-AAT
1 -AATATTATAATAAT
432218 AATATTATAATAAT
1 AATATTATAATAAT
432232 AA
1 AA
432234 CAACATAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
10 4 0.09
12 9 0.21
13 10 0.23
14 12 0.28
15 8 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATTATAATAAT
Found at i:435756 original size:24 final size:24
Alignment explanation
Indices: 435729--435779 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
435719 AACGGATATA
* *
435729 TCAAAAATCAAAACATAATTCAGG
1 TCAAAAATCAAAACAGAATCCAGG
** *
435753 TCAAGTATCAAATCAGAATCCAGG
1 TCAAAAATCAAAACAGAATCCAGG
435777 TCA
1 TCA
435780 TGTATCAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.22
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAATCCAGG
Found at i:435784 original size:24 final size:23
Alignment explanation
Indices: 435735--435842 Score: 119
Period size: 24 Copynumber: 4.6 Consensus size: 23
435725 TATATCAAAA
* *
435735 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAATCATAATCCAGGTC-AGT
*
435759 ATCAAATCAGAATCCAGGTCATGT
1 ATCAAATCATAATCCAGGTCA-GT
* *
435783 ATCAAATCATAATCCATGTCAAT
1 ATCAAATCATAATCCAGGTCAGT
*
435806 ATCATATCATAATCCAGGTCAGGT
1 ATCAAATCATAATCCAGGTCA-GT
435830 ATCATAA-CATAAT
1 ATCA-AATCATAAT
435843 TCAAATCGGA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
23 21 0.30
24 49 0.69
25 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (23 bp):
ATCAAATCATAATCCAGGTCAGT
Found at i:435832 original size:47 final size:47
Alignment explanation
Indices: 435739--435842 Score: 138
Period size: 47 Copynumber: 2.2 Consensus size: 47
435729 TCAAAAATCA
* *
435739 AAACATAATTCAGGTCAAGTATCAAATCAGAATCCAGGTCATGTATC
1 AAACATAATCCAGGTCAAGTATCAAATCAGAATCCAGGTCAGGTATC
* * *
435786 AAATCATAATCCATGTCAA-TATCATATCATAATCCAGGTCAGGTATC
1 AAA-CATAATCCAGGTCAAGTATCAAATCAGAATCCAGGTCAGGTATC
435833 ATAACATAAT
1 A-AACATAAT
435843 TCAAATCGGA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
47 35 0.70
48 15 0.30
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (47 bp):
AAACATAATCCAGGTCAAGTATCAAATCAGAATCCAGGTCAGGTATC
Found at i:436925 original size:26 final size:27
Alignment explanation
Indices: 436895--436946 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
436885 GATATTCTTG
*
436895 GGTCA-TTTCCAT-TCCAGGTGTATTAT
1 GGTCATTTTACATATCCA-GTGTATTAT
436921 GGTCATTTTACATATCCAGTGTATTA
1 GGTCATTTTACATATCCAGTGTATTA
436947 CAATCATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 14 0.61
28 4 0.17
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (27 bp):
GGTCATTTTACATATCCAGTGTATTAT
Found at i:437960 original size:22 final size:22
Alignment explanation
Indices: 437932--437982 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
437922 CCCAGAAAAA
437932 GTCAACGGTCGTTCAATGGCCG
1 GTCAACGGTCGTTCAATGGCCG
437954 GTCAACGGTCGTTCAATGGCCG
1 GTCAACGGTCGTTCAATGGCCG
437976 GTCAACG
1 GTCAACG
437983 CCGATCAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (22 bp):
GTCAACGGTCGTTCAATGGCCG
Found at i:440171 original size:24 final size:24
Alignment explanation
Indices: 440158--440251 Score: 127
Period size: 24 Copynumber: 4.0 Consensus size: 24
440148 AAACATAATT
440158 CAGGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
440182 CAGGTCATGTATCAGATCATAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
440206 CATGTC-AGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* * *
440229 CAGGTCAGGTATCATAACAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
440252 TCAAATAGAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
23 20 0.33
24 40 0.67
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:440221 original size:47 final size:48
Alignment explanation
Indices: 440151--440242 Score: 150
Period size: 47 Copynumber: 1.9 Consensus size: 48
440141 AAAATCAAAA
* *
440151 CATAATTCAGGTCAAGTATCAGATCAGAATCCAGGTCATGTATCAGAT
1 CATAATCCAGGTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAT
*
440199 CATAATCCATGTC-AGTATCAGATCAGAATCCAGGTCAGGTATCA
1 CATAATCCAGGTCAAGTATCAGATCAGAATCCAGGTCAGGTATCA
440243 TAACAGAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 30 0.73
48 11 0.27
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (48 bp):
CATAATCCAGGTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAT
Found at i:442415 original size:17 final size:17
Alignment explanation
Indices: 442393--442425 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
442383 GTCAACGGTG
442393 GTCAACGCCGGTCAACA
1 GTCAACGCCGGTCAACA
442410 GTCAACGCCGGTCAAC
1 GTCAACGCCGGTCAAC
442426 TGGTCAAAGA
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:0.27, C:0.36, G:0.24, T:0.12
Consensus pattern (17 bp):
GTCAACGCCGGTCAACA
Found at i:442474 original size:15 final size:15
Alignment explanation
Indices: 442440--442475 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
442430 CAAAGAGCCG
* *
442440 GGTCAGACTGGGTCG
1 GGTCGGACTGGGTCA
442455 GGTCGGACTGGGTCA
1 GGTCGGACTGGGTCA
442470 GGTCGG
1 GGTCGG
442476 GTCAAACCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.19, G:0.50, T:0.19
Consensus pattern (15 bp):
GGTCGGACTGGGTCA
Found at i:447610 original size:2 final size:2
Alignment explanation
Indices: 447605--447636 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
447595 GCTATATATA
447605 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
447637 CGTGGTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:461892 original size:45 final size:44
Alignment explanation
Indices: 461841--462041 Score: 314
Period size: 45 Copynumber: 4.5 Consensus size: 44
461831 TGAATAAATT
*
461841 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAG-ATGTCATAATTGA
461886 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGTCATAATTGA
461931 AATGCATATGGGTGCATTATTGGCATGAAAGTATGTCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAG-ATGTCATAATTGA
* *
461976 AATGCATATGGGTGCATTTTTGGCATGAAATGATGTTATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGTCATAATTGA
462021 ACATGCATAAT-GGTGCATTAT
1 A-ATGCAT-ATGGGTGCATTAT
462042 AAGTATGAAT
Statistics
Matches: 147, Mismatches: 4, Indels: 9
0.92 0.03 0.06
Matches are distributed among these distances:
44 1 0.01
45 127 0.86
46 17 0.12
47 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (44 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGATGTCATAATTGA
Found at i:468737 original size:45 final size:45
Alignment explanation
Indices: 468668--468868 Score: 296
Period size: 45 Copynumber: 4.4 Consensus size: 45
468658 TGAATAAATT
* *
468668 AATGTATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
468713 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
*
468758 AATTCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
* * * ** *
468803 AATGCATATGGGTGCATTTTTTGCATGAAATGATGTTATAACTGAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTG-A
468849 AATGCATAAT-GGTGCATTAT
1 AATGCAT-ATGGGTGCATTAT
468869 AAGTATGAAT
Statistics
Matches: 143, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
45 124 0.87
46 17 0.12
47 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
Found at i:470338 original size:14 final size:14
Alignment explanation
Indices: 470319--470347 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
470309 TTTTTTAATT
470319 TTGAGTTATTCGAG
1 TTGAGTTATTCGAG
470333 TTGAGTTATTCGAG
1 TTGAGTTATTCGAG
470347 T
1 T
470348 CAACTAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.45
Consensus pattern (14 bp):
TTGAGTTATTCGAG
Found at i:473350 original size:1 final size:1
Alignment explanation
Indices: 473344--473370 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
473334 AAATACTTCG
473344 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
473371 GCTGTTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:474186 original size:22 final size:22
Alignment explanation
Indices: 474143--474186 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
474133 AAAAGTTAAA
*
474143 ATAATTTTTGAATTAATTTTAT
1 ATAATTTTTGAATTAATATTAT
*
474165 ATAATTTTT-ACTTAATGATTAT
1 ATAATTTTTGAATTAAT-ATTAT
474187 CAAGTCATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (22 bp):
ATAATTTTTGAATTAATATTAT
Found at i:475454 original size:2 final size:2
Alignment explanation
Indices: 475442--475564 Score: 237
Period size: 2 Copynumber: 61.5 Consensus size: 2
475432 AGAAACAGAG
*
475442 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
475484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
475526 TA TA 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 TA TA T
475565 CCATTTTCAG
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 119 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:484214 original size:13 final size:13
Alignment explanation
Indices: 484187--484220 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
484177 ATATCAAAAG
*
484187 ATATATTACACATA
1 ATATA-TACAAATA
484201 ATATATACAAATA
1 ATATATACAAATA
484214 ATATATA
1 ATATATA
484221 GGTATATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATATACAAATA
Found at i:485267 original size:21 final size:22
Alignment explanation
Indices: 485241--485281 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
485231 CCAGGACAAG
485241 GAGTATCGATA-CTCCTTTAAT
1 GAGTATCGATACCTCCTTTAAT
*
485262 GAGTATCGGTACCTCCTTTA
1 GAGTATCGATACCTCCTTTA
485282 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (22 bp):
GAGTATCGATACCTCCTTTAAT
Found at i:489097 original size:484 final size:485
Alignment explanation
Indices: 488136--489099 Score: 1813
Period size: 486 Copynumber: 2.0 Consensus size: 485
488126 TTATTTTGTT
* *
488136 AATAAGTTTCGATACCTATCGTGGTATCGGTACATATTTTGTATTTTGTTATTTCTCGGAGTCAA
1 AATAAGTTTCGATACCTATCGTGGTATCAGTACACATTTTGTATTTTGTTATTTCTCGGAGTCAA
* * * *
488201 AATCAATTGAGGGGTAGCGGTACTTTTTGGCTAGGTATCGGTACCTCTATATAAAAGGGTATCGC
66 AACCAAATGAGGGGCAGCGGTACCTTTTGGCTAGGTATCGGTACCTCTATATAAAAGGGTATCGC
*
488266 TACCCTATGGGGTATCAGTACCTCTTTTGCATTCGATGTTTGAGGGTTATCGATACTCGTTAAAG
131 TACCCTATGGGGTATCAGTACCTATTTTGCATTCGATGTTTGAGGGTTATCGATACTCGTTAAAG
488331 AGGTATCGGTACCTTCCTATTAAAAACTCATTTTGACTCGATTGTAGTTTGAAATACTTTGTAAA
196 AGGTATCGGTACCTTCCTATTAAAAACTCATTTTGACTCGATTGTAGTTTG-AATACTTTGTAAA
488396 AAATACTTCAAAAATATTTTAAGAGTGAAACACAATTTTTCATTTAAATAAGGAGTAAAATTGAT
260 AAATACTTCAAAAATATTTTAAGAGTGAAACACAATTTTTCATTTAAATAAGGAGTAAAATTGAT
488461 ATTTGAAAAACTTGGAGTAATATTTGTGATATTCGATTAATTGAATCGAGTATTATATTTAAATC
325 ATTTGAAAAACTTGGAGTAATATTTGTGATATTCGATTAATTGAATCGAGTATTATATTTAAATC
*
488526 GAATATAAAATATTAAAATTCATTAACACTTTATTTGTTATATCGAAACATCAAAAATGTTTTTA
390 GAATATAAAATATTAAAATTCATTAACACTTTATTTGTTATATCGAAACATCAAAAATGTTTTCA
488591 ACAATCTCCCCCTTTTTGATATAACTATGTA
455 ACAATCTCCCCCTTTTTGATATAACTATGTA
*
488622 AATAAGTTTCGATACCTATCGTGGTCTCAGTACACATTTTGTATTTTGTTATTTCTCGGAGTCAA
1 AATAAGTTTCGATACCTATCGTGGTATCAGTACACATTTTGTATTTTGTTATTTCTCGGAGTCAA
488687 AACCAAATGAGGGGCAGCGGTACCTTTTGGCTAGGTATCGGTACCTCTATATAAAAGGGTATCGC
66 AACCAAATGAGGGGCAGCGGTACCTTTTGGCTAGGTATCGGTACCTCTATATAAAAGGGTATCGC
*
488752 TGCCCTATGGGGTATCAGTACCTATTTTGCATTCGATGTTTGAGGGTTATCGATACTCGTTAAAG
131 TACCCTATGGGGTATCAGTACCTATTTTGCATTCGATGTTTGAGGGTTATCGATACTCGTTAAAG
488817 AGGTATCGGTACCTTCCTATTAAAAACTCATTTTGACTCGATTGTAGTTTG-ATACTTTGTAAAA
196 AGGTATCGGTACCTTCCTATTAAAAACTCATTTTGACTCGATTGTAGTTTGAATACTTTGTAAAA
488881 AATACTTCAAAAATATTTTAAGAGTGAAACACAATTTTTCATTTAAATAAGGAGTAAAATTGATA
261 AATACTTCAAAAATATTTTAAGAGTGAAACACAATTTTTCATTTAAATAAGGAGTAAAATTGATA
488946 TTTGAAAAACTTGGAGTAATATTTGTGATATTCGATTAATTGAATCGAGTATTATATTTAAATCG
326 TTTGAAAAACTTGGAGTAATATTTGTGATATTCGATTAATTGAATCGAGTATTATATTTAAATCG
*
489011 AATATAAAATGTTAAAATTCATTAACACTTTATTTGTTATATCGAAACATCAAAAATGTTTTCAA
391 AATATAAAATATTAAAATTCATTAACACTTTATTTGTTATATCGAAACATCAAAAATGTTTTCAA
489076 CAATCTCCCCCTTTTTGATATAAC
456 CAATCTCCCCCTTTTTGATATAAC
489100 ATAATATTTT
Statistics
Matches: 467, Mismatches: 11, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
484 230 0.49
486 237 0.51
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (485 bp):
AATAAGTTTCGATACCTATCGTGGTATCAGTACACATTTTGTATTTTGTTATTTCTCGGAGTCAA
AACCAAATGAGGGGCAGCGGTACCTTTTGGCTAGGTATCGGTACCTCTATATAAAAGGGTATCGC
TACCCTATGGGGTATCAGTACCTATTTTGCATTCGATGTTTGAGGGTTATCGATACTCGTTAAAG
AGGTATCGGTACCTTCCTATTAAAAACTCATTTTGACTCGATTGTAGTTTGAATACTTTGTAAAA
AATACTTCAAAAATATTTTAAGAGTGAAACACAATTTTTCATTTAAATAAGGAGTAAAATTGATA
TTTGAAAAACTTGGAGTAATATTTGTGATATTCGATTAATTGAATCGAGTATTATATTTAAATCG
AATATAAAATATTAAAATTCATTAACACTTTATTTGTTATATCGAAACATCAAAAATGTTTTCAA
CAATCTCCCCCTTTTTGATATAACTATGTA
Found at i:489476 original size:21 final size:21
Alignment explanation
Indices: 489452--489497 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
489442 AACAAACAAA
*
489452 CAAACCAAACAACCAAATATT
1 CAAAACAAACAACCAAATATT
*
489473 CAAAACAAACATCCAAATATT
1 CAAAACAAACAACCAAATATT
489494 CAAA
1 CAAA
489498 TACATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (21 bp):
CAAAACAAACAACCAAATATT
Found at i:491921 original size:21 final size:21
Alignment explanation
Indices: 491895--491934 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
491885 AATAGGAAGA
* *
491895 TATCGATACCTCTTTAACAAG
1 TATCGATACCCCTTAAACAAG
491916 TATCGATACCCCTTAAACA
1 TATCGATACCCCTTAAACA
491935 TCGAATGCAA
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:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (21 bp):
TATCGATACCCCTTAAACAAG
Found at i:494363 original size:16 final size:18
Alignment explanation
Indices: 494342--494378 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
494332 TTTTTTATTC
494342 TTTGTTGAAAT-TCAA-T
1 TTTGTTGAAATGTCAAGT
*
494358 TTTGTTTAAATGTCAAGT
1 TTTGTTGAAATGTCAAGT
494376 TTT
1 TTT
494379 TAAAGCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 4 0.22
18 4 0.22
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (18 bp):
TTTGTTGAAATGTCAAGT
Found at i:495825 original size:34 final size:34
Alignment explanation
Indices: 495782--495849 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
495772 ACTACCTTAG
495782 ATCCTCACTAAGGATTTTCTAACAAATTAACTAA
1 ATCCTCACTAAGGATTTTCTAACAAATTAACTAA
*
495816 ATCCTCACTAAGGATTTTTTAACAAATTAACTAA
1 ATCCTCACTAAGGATTTTCTAACAAATTAACTAA
495850 TTTGTTCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (34 bp):
ATCCTCACTAAGGATTTTCTAACAAATTAACTAA
Found at i:496701 original size:20 final size:21
Alignment explanation
Indices: 496671--496710 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
496661 AGCCGTTGGG
*
496671 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCAATACTAT
496692 GCCT-ATGGTATCAATACTA
1 GCCTGATGGTATCAATACTA
496711 CTATATAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCAATACTAT
Done.