Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008316.1 Hibiscus syriacus cultivar Beakdansim tig00111013_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: 2380696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:282586 original size:23 final size:23
Alignment explanation
Indices: 282523--282586 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
282513 ATTTCGTCTC
282523 CTATATA-TATTTTTATTTATTTA
1 CTATATACTATTTTTA-TTATTTA
* *
282546 CTATATTC-CTTTTT-TTATTTA
1 CTATATACTATTTTTATTATTTA
282567 -TATTATACTATTTTTATTAT
1 CTA-TATACTATTTTTATTAT
282587 AAATATCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 2 0.06
21 11 0.33
22 5 0.15
23 15 0.45
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.66
Consensus pattern (23 bp):
CTATATACTATTTTTATTATTTA
Found at i:282610 original size:2 final size:2
Alignment explanation
Indices: 282603--282631 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
282593 CTTATATCAT
282603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
282632 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:282636 original size:2 final size:2
Alignment explanation
Indices: 282631--282657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
282621 TATATATATA
282631 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
282658 ATAGATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:282747 original size:19 final size:20
Alignment explanation
Indices: 282725--282777 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
282715 TTTTATACGT
*
282725 TTTTATATATTTTTTA-ATA
1 TTTTATATATTATTTATATA
* *
282744 TTTTATTTATTATTTATTTA
1 TTTTATATATTATTTATATA
282764 TTTATATATATTAT
1 TTT-TATATATTAT
282778 ATTTTTACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.50
20 5 0.18
21 9 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATATATTATTTATATA
Found at i:282754 original size:4 final size:4
Alignment explanation
Indices: 282745--282813 Score: 63
Period size: 4 Copynumber: 16.8 Consensus size: 4
282735 TTTTTAATAT
*
282745 TTTA TTTA -TTA TTTA TTTA TTTA TATA TATTA TATT- TTTA CTTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA T-TTA TTTA -TTTA -TTTA
282795 TTTA TTTA -TTA TTTTA TTT
1 TTTA TTTA TTTA -TTTA TTT
282814 TCTTAATATC
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
3 8 0.14
4 31 0.55
5 17 0.30
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:282762 original size:26 final size:25
Alignment explanation
Indices: 282727--282813 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 25
282717 TTATACGTTT
*
282727 TTATATATTT-TTTAATATTTTATTTA
1 TTATTTATTTATTT-ATA-TTTATTTA
*
282753 TTATTTATTTATTTATATATATTATA
1 TTATTTATTTATTTATATTTATT-TA
282779 TT-TTTACTTTATTT-TATTTATTTA
1 TTATTTA-TTTATTTATATTTATTTA
282803 TTATTTTATTT
1 TTA-TTTATTT
282814 TCTTAATATC
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
24 4 0.08
25 19 0.36
26 27 0.51
27 3 0.06
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (25 bp):
TTATTTATTTATTTATATTTATTTA
Found at i:282790 original size:13 final size:12
Alignment explanation
Indices: 282726--282813 Score: 51
Period size: 13 Copynumber: 7.2 Consensus size: 12
282716 TTTATACGTT
*
282726 TTTATATATTT-
1 TTTATATTTTTA
282737 TTTA-ATATTTTA
1 TTTATAT-TTTTA
*
282749 TTTAT-TATTTA
1 TTTATATTTTTA
*
282760 TTTAT-TTATATA
1 TTTATATT-TTTA
282772 TATTATATTTTTA
1 T-TTATATTTTTA
*
282785 CTTTATTTTATTTA
1 -TTTATATT-TTTA
282799 TTTAT-TATTTTA
1 TTTATAT-TTTTA
282811 TTT
1 TTT
282814 TCTTAATATC
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
10 2 0.03
11 17 0.27
12 17 0.27
13 19 0.31
14 7 0.11
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTATATTTTTA
Found at i:282959 original size:18 final size:17
Alignment explanation
Indices: 282914--282961 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
282904 TATGTACACA
282914 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
282931 TAATTTCTTTTACCTTTTT
1 TTATTT-TTTTACC-TTTT
282950 TTATTTTTTTAC
1 TTATTTTTTTAC
282962 TCCATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.27
18 10 0.38
19 9 0.35
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:283028 original size:19 final size:19
Alignment explanation
Indices: 283006--283048 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
282996 TTTTTTAACA
283006 TTTTATTCATT-TTGTTTAT
1 TTTTATT-ATTATTGTTTAT
*
283025 TTTTATTATTATTTTTTAT
1 TTTTATTATTATTGTTTAT
283044 TTTTA
1 TTTTA
283049 CGTGTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTATTATTATTGTTTAT
Found at i:283088 original size:26 final size:25
Alignment explanation
Indices: 283033--283081 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
283023 ATTTTTATTA
*
283033 TTATTTTTTATTTTTACGTGTTTTG
1 TTATTTTTCATTTTTACGTGTTTTG
* *
283058 TTATTTTTCATTTTTTCTTGTTTT
1 TTATTTTTCATTTTTACGTGTTTT
283082 ATTTATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.10, C:0.06, G:0.08, T:0.76
Consensus pattern (25 bp):
TTATTTTTCATTTTTACGTGTTTTG
Found at i:284662 original size:7 final size:7
Alignment explanation
Indices: 284648--284690 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
284638 AAATACTATA
284648 TGAATAG
1 TGAATAG
*
284655 TAAATAG
1 TGAATAG
284662 TGAATAG
1 TGAATAG
284669 TGAATAG
1 TGAATAG
284676 TGAATAG
1 TGAATAG
284683 TGAATAG
1 TGAATAG
284690 T
1 T
284691 ACGATGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (7 bp):
TGAATAG
Found at i:285589 original size:21 final size:21
Alignment explanation
Indices: 285540--285603 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
285530 CATATGAAAT
*
285540 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
285561 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
*
285583 TTGTCCCAAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
285604 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 19 0.50
22 19 0.50
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:285903 original size:14 final size:15
Alignment explanation
Indices: 285876--285904 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
285866 ATATCATATA
285876 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
285891 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
285905 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:288962 original size:69 final size:69
Alignment explanation
Indices: 288843--288980 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
288833 GATTTAAACT
*
288843 ATGAGATTGATCAAGCACAATCATTTCTGAATCAATGAATCATTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCAATGAATCATCTCACTCGAAGATCATAGAGCA
288908 TCAA
66 TCAA
* * * *
288912 ATGAGATTGATCAAGCACAATCATTTCTGAATTACTGCATCA-CTCTACTCGAAGATCATGGAGC
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCAATGAATCATCTC-ACTCGAAGATCATAGAGC
288976 ATCAA
65 ATCAA
288981 GAGAGAGACA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 2 0.03
69 61 0.97
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCTGAATCAATGAATCATCTCACTCGAAGATCATAGAGCA
TCAA
Found at i:289942 original size:31 final size:31
Alignment explanation
Indices: 289906--289999 Score: 143
Period size: 31 Copynumber: 3.0 Consensus size: 31
289896 GCATCTTTGA
289906 AGATTTAACATCAAATGTTGGGGCATTTTTT
1 AGATTTAACATCAAATGTTGGGGCATTTTTT
289937 AGATTTAACATCAAATGTTGGGGCATTTTTTT
1 AGATTTAACATCAAATGTTGGGGCA-TTTTTT
* * * *
289969 AGATTCAACATCGAATATTGGGGCATCTTTT
1 AGATTTAACATCAAATGTTGGGGCATTTTTT
290000 GGAATTCAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 30 0.52
32 28 0.48
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (31 bp):
AGATTTAACATCAAATGTTGGGGCATTTTTT
Found at i:289972 original size:32 final size:32
Alignment explanation
Indices: 289906--289999 Score: 145
Period size: 32 Copynumber: 3.0 Consensus size: 32
289896 GCATCTTTGA
289906 AGATTTAACATCAAATGTTGGGGCA-TTTTTT
1 AGATTTAACATCAAATGTTGGGGCATTTTTTT
289937 AGATTTAACATCAAATGTTGGGGCATTTTTTT
1 AGATTTAACATCAAATGTTGGGGCATTTTTTT
* * * *
289969 AGATTCAACATCGAATATTGGGGCATCTTTT
1 AGATTTAACATCAAATGTTGGGGCATTTTTT
290000 GGAATTCAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 25 0.43
32 33 0.57
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (32 bp):
AGATTTAACATCAAATGTTGGGGCATTTTTTT
Found at i:290007 original size:32 final size:33
Alignment explanation
Indices: 289894--290012 Score: 131
Period size: 32 Copynumber: 3.8 Consensus size: 33
289884 GGAACAATGA
* *
289894 GGGCATC-TTTGAAGATTTAACATCAAATGTTG
1 GGGCATCTTTTGGAGATTCAACATCAAATGTTG
* *
289926 GGGCAT-TTTT-TAGATTTAACATCAAATGTTG
1 GGGCATCTTTTGGAGATTCAACATCAAATGTTG
** * *
289957 GGGCAT-TTTTTTAGATTCAACATCGAATATTG
1 GGGCATCTTTTGGAGATTCAACATCAAATGTTG
289989 GGGCATCTTTTGGA-ATTCAACATC
1 GGGCATCTTTTGGAGATTCAACATC
290013 CCGATGCAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
31 30 0.38
32 43 0.55
33 5 0.06
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (33 bp):
GGGCATCTTTTGGAGATTCAACATCAAATGTTG
Found at i:290718 original size:106 final size:106
Alignment explanation
Indices: 290590--290806 Score: 308
Period size: 106 Copynumber: 2.0 Consensus size: 106
290580 ATATCGTGCC
* *
290590 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGCTCAACTCCACAACGAAGGGACGACTGATTGTCAACAAACAATTTCCC
*
290655 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTCCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
* * * * * **
290696 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGATTGTCAACAAACAATTTCTT
1 ACTCGAGACAACACAAGCTCAACTCCACAACGAAGGGACGACTGATTGTCAACAAACAATTTCCC
* * * *
290761 AGTTCCAGAGCCAATTTTAACTTCACGGTGTAGGATATTGG
66 AATTCCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
290802 ACTCG
1 ACTCG
290807 GAACAATACA
Statistics
Matches: 97, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
106 97 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGCTCAACTCCACAACGAAGGGACGACTGATTGTCAACAAACAATTTCCC
AATTCCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
Found at i:291063 original size:67 final size:68
Alignment explanation
Indices: 290954--291102 Score: 180
Period size: 68 Copynumber: 2.2 Consensus size: 68
290944 ACAGTTTCCA
* ** * *
290954 AGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCTCCTAAAA-CAAATTTTGTCTCCCTTGA
1 AGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCTCCTAAAATAAAATTTTATCTCCCTTGA
291016 GAC
66 GAC
*
291019 AGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTC-CCTTAAAATAAAATTTTATTTCCCTTG
1 AGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCTCC-TAAAATAAAATTTTATCTCCCTTG
291083 AGAC
65 AGAC
* * *
291087 CGTTTTTCATGAAACA
1 AGTTTCTCTTGAAACA
291103 ACATATATCT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
65 10 0.14
66 4 0.06
67 25 0.35
68 32 0.45
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (68 bp):
AGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCTCCTAAAATAAAATTTTATCTCCCTTGA
GAC
Found at i:292777 original size:149 final size:149
Alignment explanation
Indices: 292527--292839 Score: 574
Period size: 149 Copynumber: 2.1 Consensus size: 149
292517 TATAATTGCA
* *
292527 CCGAAGTG-CCGCGTAGAATTGCATCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
292591 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
292656 CCACAGAATATATATATATC
130 CCACAGAATATATATATATC
*
292676 CCGAAGGAGCGCGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
292741 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
292806 CACATAATATATATATATC
131 CACAGAATATATATATATC
292825 CCGAAGGACCGCGTA
1 CCGAAGGACCGCGTA
292840 GACCCTCGAC
Statistics
Matches: 158, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (149 bp):
CCGAAGGACCGCGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CACAGAATATATATATATC
Found at i:294337 original size:64 final size:63
Alignment explanation
Indices: 294239--294399 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
294229 TAATGAAGGT
* *
294239 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
294302 GG
62 GC
*
294304 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
294368 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
294400 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:295705 original size:110 final size:110
Alignment explanation
Indices: 295503--295755 Score: 302
Period size: 110 Copynumber: 2.3 Consensus size: 110
295493 GCTTCCCAGT
* * *
295503 TTCAGAGCCAATTTCAACTTCACAGCGAGCGATATTGGACTCAAGACAACACAAGCTCAAATTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAACGATATTGAACTCAAGACAACACAAGCTCAAATTCA
* * *
295568 TAACGAAGGGGCGACTGATTGTTAACAAATAACTTTTCAGTTTCA
66 CAACGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCA
* * * *
295613 TTCAGAGTCAATTTCAACTTCACAACGAATGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAACGATATTGAACTCAAGACAACACAAGCTCAAATTCA
* * * *
295678 CAACGAAGGGGCGGCTGGCTGTCAACAAACAA-TTTCCCAG-TTC-
66 CAACGAAGGGGCGACTGACTGTCAACAAATAACTTT-TCAGTTTCA
* *
295721 CT-A-AGCCAATTTCAACTTCACGACGGAA-GATATTG
1 TTCAGAGCCAATTTCAACTTCACAAC-GAACGATATTG
295756 GACTTGGAAC
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
106 26 0.21
107 4 0.03
108 1 0.01
109 6 0.05
110 87 0.70
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACGAACGATATTGAACTCAAGACAACACAAGCTCAAATTCA
CAACGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCA
Found at i:295870 original size:378 final size:378
Alignment explanation
Indices: 295170--295870 Score: 1233
Period size: 378 Copynumber: 1.9 Consensus size: 378
295160 TTGGGATGTT
* *
295170 ACAACACAACCTCAAATTCATAACGAAGGGTCGACTGATTGTTAACAAATAATTTTTCAGTTTCA
1 ACAACACAACCTCAAATTCATAACGAAGGGGCGACTGATTGTTAACAAATAACTTTTCAGTTTCA
*
295235 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGATCAACTTCA
66 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCGAGACAACACAAGATCAACTTCA
* * *
295300 CAATGAATGGGCGGCTGGCTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTCATG
131 CAACGAAGGGGCGGCTGGCTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTCACG
* * *
295365 ACGAAAGATATTGGATTTGGAACAATAGTACCTACTTGGATTTCAACTTCACGATGAAGGATATC
196 ACGAAAGATATTGGACTTGGAACAATACTACATACTTGGATTTCAACTTCACGATGAAGGATATC
* *
295430 CAATTACCATGCTCAACTTCACGACGAAGGTGCCACCCGCAGTTTCAACTTCACGGCGAAGGGGC
261 CAATTACCAGGCTCAACTTCACGACGAAGGTGCCACCCGCAGTTTCAACTTCACGACGAAGGGGC
295495 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGCGATATTGGACTCAAG
326 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGCGATATTGGACTCAAG
*
295548 ACAACACAAGCTCAAATTCATAACGAAGGGGCGACTGATTGTTAACAAATAACTTTTCAGTTTCA
1 ACAACACAACCTCAAATTCATAACGAAGGGGCGACTGATTGTTAACAAATAACTTTTCAGTTTCA
* *
295613 TTCAGAGTCAATTTCAACTTCACAACGAATGATATTGAACTCGAGACAACACAAGCTCAACTTCA
66 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCGAGACAACACAAGATCAACTTCA
295678 CAACGAAGGGGCGGCTGGCTGTCAACAAACAATTTCCCAGTTCCTA-AGCCAATTTCAACTTCAC
131 CAACGAAGGGGCGGCTGGCTGTCAACAAACAATTTCCCAGTTCC-AGAGCCAATTTCAACTTCAC
*
295742 GACGGAAGATATTGGACTTGGAACAATACTACATACTTGGATTTCAACTTCACGATGAAGGATAT
195 GACGAAAGATATTGGACTTGGAACAATACTACATACTTGGATTTCAACTTCACGATGAAGGATAT
* *
295807 CCAATTACCAGGCTCAACTTCACGACGAATGTGCCACCCGCGGTTTCAACTTCACGACGAAGGG
260 CCAATTACCAGGCTCAACTTCACGACGAAGGTGCCACCCGCAGTTTCAACTTCACGACGAAGGG
295871 AATCGTGCAC
Statistics
Matches: 305, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
378 304 1.00
379 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (378 bp):
ACAACACAACCTCAAATTCATAACGAAGGGGCGACTGATTGTTAACAAATAACTTTTCAGTTTCA
TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCGAGACAACACAAGATCAACTTCA
CAACGAAGGGGCGGCTGGCTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTCACG
ACGAAAGATATTGGACTTGGAACAATACTACATACTTGGATTTCAACTTCACGATGAAGGATATC
CAATTACCAGGCTCAACTTCACGACGAAGGTGCCACCCGCAGTTTCAACTTCACGACGAAGGGGC
TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGCGATATTGGACTCAAG
Found at i:297222 original size:24 final size:25
Alignment explanation
Indices: 297190--297236 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
297180 TAATTATATA
297190 TTTTTTATTTATTTAATA-TATTCT
1 TTTTTTATTTATTTAATACTATTCT
*
297214 TTTTTTATTTATTTTATACTATT
1 TTTTTTATTTATTTAATACTATT
297237 TTTATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTTTATTTATTTAATACTATTCT
Found at i:297255 original size:25 final size:23
Alignment explanation
Indices: 297170--297275 Score: 81
Period size: 25 Copynumber: 4.4 Consensus size: 23
297160 TATATATATA
297170 TATATATATTTAATTATATATTTTT
1 TATATATATTTAA-TATAT-TTTTT
297195 TAT-T-TATTTAATATATTCTTTT
1 TATATATATTTAATATATT-TTTT
* * *
297217 TTTATTTATTTTATACTATTTTTAT
1 TATATATATTTAATA-TATTTTT-T
* * *
297242 TATATATATTTTATATCATTATATA
1 TATATATATTTAATAT-ATT-TTTT
297267 TATATATAT
1 TATATATAT
297276 ATAAATGTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
21 1 0.01
22 11 0.16
23 8 0.12
24 13 0.19
25 33 0.49
26 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (23 bp):
TATATATATTTAATATATTTTTT
Found at i:297374 original size:17 final size:17
Alignment explanation
Indices: 297317--297375 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
297307 GGATATACAT
297317 TTTTTCTTAATATTCTA
1 TTTTTCTTAATATTCTA
* *
297334 TTTTATACATTTATA-TATA
1 TTTT-T-C-TTAATATTCTA
297353 TTTTTTCTTAATATTCTA
1 -TTTTTCTTAATATTCTA
297371 TTTTT
1 TTTTT
297376 ATTTTTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 14 0.42
18 5 0.15
19 5 0.15
20 9 0.27
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTCTTAATATTCTA
Found at i:297374 original size:18 final size:18
Alignment explanation
Indices: 297315--297375 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
297305 ATGGATATAC
297315 ATTTTTTCTTAATATTCT
1 ATTTTTTCTTAATATTCT
* * *
297333 ATTTTATACATTTATA-TAT
1 ATTTT-TTC-TTAATATTCT
297352 ATTTTTTCTTAATATTCT
1 ATTTTTTCTTAATATTCT
297370 ATTTTT
1 ATTTTT
297376 ATTTTTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 5 0.15
18 15 0.44
19 9 0.26
20 5 0.15
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTTCTTAATATTCT
Found at i:297408 original size:54 final size:55
Alignment explanation
Indices: 297327--297471 Score: 136
Period size: 57 Copynumber: 2.6 Consensus size: 55
297317 TTTTTCTTAA
* *
297327 TATTCTATTT-TATACATTTATATATATTTTTTCTTA-ATATTCTATTTTTATT-TT
1 TATT-TATTTATATATATATATATATATTTTTT-TTACATATTCTATTTTTATTATT
* *
297381 TATTTATTTATATATATATATATATATTATATTTTTACTTTATTTTATTTTTATTATT
1 TATTTATTTATATATATATATATATATT-T-TTTTTAC-ATATTCTATTTTTATTATT
* * * *
297439 T-TTTCTTAATATCATATATATCTTTATTTTTTT
1 TATTTATTTATAT-ATATATATATATATTTTTTT
297472 ATTTGTTTTA
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
53 5 0.07
54 20 0.26
55 4 0.05
56 7 0.09
57 24 0.32
58 16 0.21
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (55 bp):
TATTTATTTATATATATATATATATATTTTTTTTACATATTCTATTTTTATTATT
Found at i:297467 original size:37 final size:38
Alignment explanation
Indices: 297424--297517 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 38
297414 TTTACTTTAT
297424 TTTATTTTTATTA-TT-TTTT-CTTAATATCATATATATC
1 TTTATTTTTATTATTTGTTTTACTTAATAT--TATATATC
*
297461 TTTATTTTT-TTATTTGTTTTACTTAGTATTATATA--
1 TTTATTTTTATTATTTGTTTTACTTAATATTATATATC
297496 TTTATTATTT-TTATTTGTTTTA
1 TTTATT-TTTATTATTTGTTTTA
297518 GTAAATACTA
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
35 6 0.12
36 18 0.35
37 17 0.33
38 4 0.08
39 7 0.13
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.69
Consensus pattern (38 bp):
TTTATTTTTATTATTTGTTTTACTTAATATTATATATC
Found at i:297481 original size:54 final size:57
Alignment explanation
Indices: 297345--297481 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 57
297335 TTTATACATT
* * *
297345 TATA-TATATTTTTTCTTAATATTCTATTTTTATTTTTATTTATTTATATATATATATA
1 TATATTATATTTTTACTT--TATTTTATTTTTATTTTTATTTACTTATATATATATATA
297403 TATATTATATTTTTACTTTATTTTATTTTTATTATTT-TTT-CTTA-ATATCATATATA
1 TATATTATATTTTTACTTTATTTTATTTTTATT-TTTATTTACTTATATAT-ATATATA
* * *
297459 TCT-TTATTTTTTTA-TTTGTTTTA
1 TATATTATATTTTTACTTTATTTTA
297482 CTTAGTATTA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
54 8 0.11
55 14 0.20
56 12 0.17
57 17 0.24
58 7 0.10
59 12 0.17
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (57 bp):
TATATTATATTTTTACTTTATTTTATTTTTATTTTTATTTACTTATATATATATATA
Found at i:297495 original size:39 final size:35
Alignment explanation
Indices: 297416--297528 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 35
297406 ATTATATTTT
*
297416 TACTTTAT-TTTATTTTTATTA-TT-TTTT-CTTAA
1 TACTATATATTTATTTTT-TTATTTGTTTTACTTAA
*
297448 TATCATATATATCTTTATTTTTTTATTTGTTTTACTTAG
1 TA-C-TATATA--TTTATTTTTTTATTTGTTTTACTTAA
* * *
297487 TATTATATATTTATTATTTTTATTTGTTTTAGTAAA
1 TACTATATATTTATT-TTTTTATTTGTTTTACTTAA
297523 TACTAT
1 TACTAT
297529 TTTATATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
32 2 0.03
33 1 0.02
34 4 0.06
35 6 0.09
36 25 0.38
37 17 0.26
38 4 0.06
39 6 0.09
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (35 bp):
TACTATATATTTATTTTTTTATTTGTTTTACTTAA
Found at i:297585 original size:18 final size:19
Alignment explanation
Indices: 297553--297588 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
297543 TTTTTATTCC
297553 TTTTTAATTTCTTTTACTT
1 TTTTTAATTTCTTTTACTT
*
297572 TTTTTTATTT-TTTTACT
1 TTTTTAATTTCTTTTACT
297589 CCATTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTAATTTCTTTTACTT
Found at i:297671 original size:9 final size:9
Alignment explanation
Indices: 297631--297706 Score: 66
Period size: 9 Copynumber: 8.1 Consensus size: 9
297621 TTTTTTAACA
297631 TTTTATTCAT
1 TTTTATT-AT
297641 TTTGT-TTAT
1 TTT-TATTAT
297650 TTTTATTAT
1 TTTTATTAT
297659 TTTTATTAT
1 TTTTATTAT
* *
297668 TTTTACGT-G
1 TTTTA-TTAT
297677 TTTTATTAT
1 TTTTATTAT
*
297686 TTTTCATTTT
1 TTTT-ATTAT
297696 TATTTATTAT
1 T-TTTATTAT
297706 T
1 T
297707 CTCACGTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
8 2 0.04
9 32 0.59
10 16 0.30
11 4 0.07
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (9 bp):
TTTTATTAT
Found at i:303871 original size:10 final size:10
Alignment explanation
Indices: 303856--303897 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
303846 TTTATCACAC
303856 CAAATTCTCT
1 CAAATTCTCT
303866 CAAATTCTCT
1 CAAATTCTCT
*
303876 -AAATTTCTTT
1 CAAA-TTCTCT
*
303886 CAAATACTCT
1 CAAATTCTCT
303896 CA
1 CA
303898 TTTTAAGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:304160 original size:111 final size:111
Alignment explanation
Indices: 304020--304241 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
304010 TGGAAATCAT
*
304020 ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
304085 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATGTAATGCATGATTATTAGATTAAGAATTAA
304131 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
304196 TAATTAGTTGATTCATGTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATGTAATGCATGATTATTAGATTAAGAATTAA
304242 TTTTTGTAAT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATGTAATGCATGATTATTAGATTAAGAATTAA
Found at i:308527 original size:21 final size:21
Alignment explanation
Indices: 308498--308550 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
308488 ATTCTGACTA
308498 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
308519 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
308540 TCGCAATGCGA
1 TCGCATTGCGA
308551 ATACGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:308571 original size:41 final size:42
Alignment explanation
Indices: 308525--308667 Score: 179
Period size: 41 Copynumber: 3.5 Consensus size: 42
308515 AAATTCGCGT
* * * * *
308525 TGCGATTTTCCTAATTCGCAATGCGAA-TACGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAATACGAATTAGGAAAATCGCAA
*
308566 CGCGA-TTACGTAAATCGCAATACGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAATACGAATTAGGAAAATCGCAA
*
308607 TGCG-TTTACGTAAATCGTAATACGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAATACGAATTAGGAAAATCGCAA
*
308648 TGCGA-ATACGT-AATCGCAAT
1 TGCGATTTACGTAAATCGCAAT
308668 GCGATTTACG
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
40 25 0.28
41 64 0.72
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (42 bp):
TGCGATTTACGTAAATCGCAATACGAATTAGGAAAATCGCAA
Found at i:308622 original size:61 final size:60
Alignment explanation
Indices: 308540--308680 Score: 149
Period size: 61 Copynumber: 2.3 Consensus size: 60
308530 TTTTCCTAAT
** * * * *
308540 TCGCAATGCGAATACGAAAATCGCAACGCG-ATTACGTAAATCGCAATACGAATTAGGAAAA
1 TCGCAATGCGTTTACGTAAATCGCAACACGAATTACGAAAATCGCAATACGAA-TACG-AAA
* * * * *
308601 TCGCAATGCGTTTACGTAAATCGTAATACGAATTAGGAAAATCGCAATGCGAATACGTAA
1 TCGCAATGCGTTTACGTAAATCGCAACACGAATTACGAAAATCGCAATACGAATACGAAA
308661 TCGCAATGCGATTTACGTAA
1 TCGCAATGCG-TTTACGTAA
308681 CCGAATTGCG
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
60 12 0.18
61 36 0.54
62 19 0.28
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (60 bp):
TCGCAATGCGTTTACGTAAATCGCAACACGAATTACGAAAATCGCAATACGAATACGAAA
Found at i:308679 original size:20 final size:20
Alignment explanation
Indices: 308525--308788 Score: 164
Period size: 20 Copynumber: 13.0 Consensus size: 20
308515 AAATTCGCGT
* *
308525 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTACGTAA-TCGCAA
* *
308546 TGCGA-ATACGAAAATCGCAA
1 TGCGATTTACG-TAATCGCAA
*
308566 CGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGT-AATCGCAA
* * * *
308586 TACGAATTAGGAAAATCGCAA
1 TGCGATTTACG-TAATCGCAA
*
308607 TGCG-TTTACGTAAATCGTAA
1 TGCGATTTACGT-AATCGCAA
* * * *
308627 TACGAATTAGGAAAATCGCAA
1 TGCGATTTACG-TAATCGCAA
*
308648 TGCGA-ATACGTAATCGCAA
1 TGCGATTTACGTAATCGCAA
*
308667 TGCGATTTACGTAACCG-AA
1 TGCGATTTACGTAATCGCAA
* *
308686 TTGCGATTTACGTAATCACAT
1 -TGCGATTTACGTAATCGCAA
*
308707 TGCGATTTTAC-TAATTCGCAT
1 TGCGA-TTTACGTAA-TCGCAA
* * *
308728 TGCGATTTTCCTAATTCGCAC
1 TGCGATTTACGTAA-TCGCAA
* *
308749 TTCGATTTACGTAATCGCAT
1 TGCGATTTACGTAATCGCAA
308769 TGCGATTTA-GTAAATCGCAA
1 TGCGATTTACGT-AATCGCAA
308789 CGAGATTCTG
Statistics
Matches: 190, Mismatches: 39, Indels: 29
0.74 0.15 0.11
Matches are distributed among these distances:
19 17 0.09
20 100 0.53
21 73 0.38
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (20 bp):
TGCGATTTACGTAATCGCAA
Found at i:308730 original size:41 final size:40
Alignment explanation
Indices: 308640--308787 Score: 151
Period size: 41 Copynumber: 3.7 Consensus size: 40
308630 GAATTAGGAA
* * *
308640 AATCGCAATGCGA-ATACGTAATCGCAATGCGATTTACGT
1 AATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
* * *
308679 AACCGAATTGCGATTTACGTAATCACATTGCGATTTTAC-T
1 AATCGCATTGCGATTTACGTAATCGCATTGCGA-TTTACGT
* *
308719 AATTCGCATTGCGATTTTCCTAATTCGCACTT-CGATTTACGT
1 AA-TCGCATTGCGATTTACGTAA-TCGCA-TTGCGATTTACGT
308761 AATCGCATTGCGATTTA-GTAAATCGCA
1 AATCGCATTGCGATTTACGT-AATCGCA
308788 ACGAGATTCT
Statistics
Matches: 89, Mismatches: 13, Indels: 13
0.77 0.11 0.11
Matches are distributed among these distances:
39 10 0.11
40 25 0.28
41 42 0.47
42 10 0.11
43 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (40 bp):
AATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
Found at i:309357 original size:178 final size:179
Alignment explanation
Indices: 309057--309414 Score: 709
Period size: 178 Copynumber: 2.0 Consensus size: 179
309047 TTAATTTAAA
309057 ATAATGAAATCATCGAATGTTGATCGTGTTTGGATAGATTTGTGTTTTGTAGGGTCATGGGAGAA
1 ATAATGAAATCATCGAATGTTGATCGTGTTTGGATAGATTTGTGTTTTGTAGGGTCATGGGAGAA
309122 TGTTCATGGTGTTTTACAATATATGCCTTTACCCATGAATCTTCAACTAAAACTGTCATTAAAAA
66 TGTTCATGGTGTTTTACAATATATGCCTTTACCCATGAATCTTCAACTAAAACTGTCATTAAAAA
309187 AGTTAACTTATGAAACTCTAATGTTACGTGTTGCAAATAAATTGAATTT
131 AGTTAACTTATGAAACTCTAATGTTACGTGTTGCAAATAAATTGAATTT
309236 ATAATGAAATCATCGAATGTTGATCGTGTTTGGATAGATTTGTG-TTTGTAGGGTCATGGGAGAA
1 ATAATGAAATCATCGAATGTTGATCGTGTTTGGATAGATTTGTGTTTTGTAGGGTCATGGGAGAA
309300 TGTTCATGGTGTTTTACAATATATGCCTTTACCCATGAATCTTCAACTAAAACTGTCATTAAAAA
66 TGTTCATGGTGTTTTACAATATATGCCTTTACCCATGAATCTTCAACTAAAACTGTCATTAAAAA
309365 AGTTAACTTATGAAACTCTAATGTTACGTGTTGCAAATAAATTGAATTT
131 AGTTAACTTATGAAACTCTAATGTTACGTGTTGCAAATAAATTGAATTT
309414 A
1 A
309415 GAGCCCCTAA
Statistics
Matches: 179, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
178 135 0.75
179 44 0.25
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (179 bp):
ATAATGAAATCATCGAATGTTGATCGTGTTTGGATAGATTTGTGTTTTGTAGGGTCATGGGAGAA
TGTTCATGGTGTTTTACAATATATGCCTTTACCCATGAATCTTCAACTAAAACTGTCATTAAAAA
AGTTAACTTATGAAACTCTAATGTTACGTGTTGCAAATAAATTGAATTT
Found at i:312224 original size:20 final size:19
Alignment explanation
Indices: 312196--312250 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
312186 CAATCATCTT
*
312196 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
312216 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
312235 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
312251 AGAGAATCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:312238 original size:19 final size:20
Alignment explanation
Indices: 312157--312250 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
312147 GGCATTCATT
*
312157 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* **
312177 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-C-GCGGAAA
*
312198 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
312218 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
**
312237 TGAAAATCGCAACG
1 TGACTATCGCAACG
312251 AGAGAATCAC
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 16 0.28
20 27 0.47
21 13 0.23
22 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:312269 original size:33 final size:33
Alignment explanation
Indices: 312227--312316 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
312217 ATGACTATCG
312227 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
* *
312260 CAATGCGAAATGAAAATCGCAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
*
312293 CAAAGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
312317 CAAATTTAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCA
Found at i:312312 original size:19 final size:19
Alignment explanation
Indices: 312203--312314 Score: 64
Period size: 19 Copynumber: 6.4 Consensus size: 19
312193 CTTAATGTCT
* **
312203 ATCGCAACGCGGAAATGACT
1 ATCGCAAAGC-GAAATGAAA
*
312223 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
312242 ATCGC-AA-CG--A-GAGA
1 ATCGCAAAGCGAAATGAAA
* *
312256 ATCACAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
**
312275 ATCGC-AA-CG--A-GGGA
1 ATCGCAAAGCGAAATGAAA
312289 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
312308 ATCGCAA
1 ATCGCAA
312315 CGCAAATTTA
Statistics
Matches: 68, Mismatches: 14, Indels: 21
0.66 0.14 0.20
Matches are distributed among these distances:
14 14 0.21
15 5 0.07
16 4 0.06
17 4 0.06
18 4 0.06
19 28 0.41
20 9 0.13
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:312348 original size:19 final size:19
Alignment explanation
Indices: 312326--312391 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
312316 GCAAATTTAG
312326 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
312345 TTTCACGTTACGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
312361 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
312378 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
312392 AGTCATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
14 9 0.25
16 3 0.08
17 3 0.08
19 21 0.58
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:312517 original size:14 final size:14
Alignment explanation
Indices: 312498--312534 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
312488 CATCAATTAA
312498 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
312512 ACAAATCATCTTTT
1 ACAAATCAACTTTT
312526 ACAAATCAA
1 ACAAATCAA
312535 TTAAAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:313972 original size:42 final size:42
Alignment explanation
Indices: 313926--314009 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
313916 CGATGACAAT
* * *
313926 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
313968 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
314010 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:314438 original size:19 final size:19
Alignment explanation
Indices: 314399--314450 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
314389 AATGGAACTT
*
314399 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAAC--GCAAAATG
**
314420 ACTATCGCAACGCAAAATG
1 AAAATCGCAACGCAAAATG
314439 AAAATCGCAACG
1 AAAATCGCAACG
314451 AGAATCGCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 17 0.65
21 9 0.35
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCAAAATG
Found at i:314458 original size:31 final size:32
Alignment explanation
Indices: 314423--314482 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
314413 AAAAATGACT
**
314423 ATCGCAACGC-AAAATGAAAATCGCAACGAGA
1 ATCGCAACGCGAAAACAAAAATCGCAACGAGA
*
314454 ATCGCAACGCGAAACCAAAAATCGCAACG
1 ATCGCAACGCGAAAACAAAAATCGCAACG
314483 CGATTATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (32 bp):
ATCGCAACGCGAAAACAAAAATCGCAACGAGA
Found at i:314553 original size:20 final size:20
Alignment explanation
Indices: 314510--314565 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
314500 TGCGATTTTG
314510 TCGTTGCGATTTTCA-TCTC
1 TCGTTGCGATTTTCATTCTC
*
314529 GCGTTGCGATTTTCATTCTC
1 TCGTTGCGATTTTCATTCTC
314549 TCGTTGCGATTTTCATT
1 TCGTTGCGATTTTCATT
314566 TCAACCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (20 bp):
TCGTTGCGATTTTCATTCTC
Found at i:314803 original size:85 final size:87
Alignment explanation
Indices: 314656--314948 Score: 387
Period size: 94 Copynumber: 3.3 Consensus size: 87
314646 ATGGATTGCA
* *
314656 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
314720 TTAGCAGCA-AA-TGAACAAAT
66 TTAGCAGCACAACCGAACAAAT
314740 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
314805 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGC---A---GCA-CAACCGAACAAAT
*
314834 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCATAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
314899 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGC---A---GCA-CAACCGAACAAAT
314928 TTAC-TTCAACCAAAAGACAAA
1 TTACTTTCAACCAAAAGACAAA
314949 TACTAACTTC
Statistics
Matches: 194, Mismatches: 5, Indels: 11
0.92 0.02 0.05
Matches are distributed among these distances:
84 4 0.02
85 63 0.32
88 1 0.01
91 3 0.02
93 19 0.10
94 104 0.54
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (87 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGCACAACCGAACAAAT
Found at i:314830 original size:94 final size:94
Alignment explanation
Indices: 314723--314948 Score: 409
Period size: 94 Copynumber: 2.4 Consensus size: 94
314713 ACACAGTTTA
**
314723 GCAGCAAATGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGT
1 GCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGT
314788 GTTAAAGAATACACAGTTTAGCAGAATTG
66 GTTAAAGAATACACAGTTTAGCAGAATTG
*
314817 GCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCATAGT
1 GCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGT
314882 GTTAAAGAATACACAGTTTAGCAGAATTG
66 GTTAAAGAATACACAGTTTAGCAGAATTG
*
314911 GCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAA
1 GCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAA
314949 TACTAACTTC
Statistics
Matches: 128, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
93 17 0.13
94 111 0.87
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.20
Consensus pattern (94 bp):
GCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGT
GTTAAAGAATACACAGTTTAGCAGAATTG
Found at i:315005 original size:78 final size:79
Alignment explanation
Indices: 314858--315010 Score: 236
Period size: 78 Copynumber: 1.9 Consensus size: 79
314848 AAGACAAAAC
* * *
314858 AAAGACAAATACTAACTTCATAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGCTTAGCAGAATTGGCAGCAACCGAA
314923 TAAATTTACTTCAACCA
63 TAAATTTACTTCAACCA
*
314940 AAAGACAAATACTAACTTCACAGTGTT-AATAAACAGCTTAGCAGTATTGGCAGCAACCGAATAA
1 AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGCTTAGCAGAATTGGCAGCAACCGAATAA
315004 ATTTACT
66 ATTTACT
315011 AAGTAATCTA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
78 41 0.61
82 26 0.39
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (79 bp):
AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGCTTAGCAGAATTGGCAGCAACCGAATAA
ATTTACTTCAACCA
Found at i:316698 original size:20 final size:20
Alignment explanation
Indices: 316673--316732 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
316663 CTTTTGGTTG
316673 AAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
* *
316693 AAATGAAAATCGCAACGCGG
1 AAATGAAAATCGCAACGAGA
**
316713 AAATGACTATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
316733 GAATCGCAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (20 bp):
AAATGAAAATCGCAACGAGA
Found at i:316761 original size:33 final size:33
Alignment explanation
Indices: 316672--316793 Score: 154
Period size: 33 Copynumber: 3.5 Consensus size: 33
316662 TCTTTTGGTT
316672 GAAATGAAAATCGCAACGAGAAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAG---A-G--AATCGCAACGC
**
316711 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
316745 GAAATGAAAATTGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
316778 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
316794 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
33 45 0.59
34 11 0.14
36 1 0.01
37 1 0.01
40 18 0.24
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:316877 original size:20 final size:20
Alignment explanation
Indices: 316824--316878 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
316814 GCGATTATCT
316824 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
**
316843 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
316863 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
316879 CTCGAAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:317423 original size:20 final size:20
Alignment explanation
Indices: 317400--317493 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
317390 CGATAGTCAG
317400 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
317420 ATTCACATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
317440 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
317461 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
317481 ATTCGCATTGCGA
1 ATTCGCATTGCGA
317494 ATTAGGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 45 0.73
21 17 0.27
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:317449 original size:41 final size:40
Alignment explanation
Indices: 317400--317493 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
317390 CGATAGTCAG
* *
317400 ATTCGCATTGCGATTTACGTATTCACATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCT
* * * *
317440 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCT
317481 ATTCGCATTGCGA
1 ATTCGCATTGCGA
317494 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCT
Found at i:317514 original size:21 final size:21
Alignment explanation
Indices: 317490--317535 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
317480 TATTCGCATT
317490 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
317511 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
317532 GCGA
1 GCGA
317536 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:328745 original size:15 final size:15
Alignment explanation
Indices: 328725--328778 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
328715 ACTTGATTAC
328725 AAAGTAAAACTAAAT
1 AAAGTAAAACTAAAT
* *
328740 AAAGTAAAAATCTATTAC
1 AAAGT-AAAA-CTA-AAT
*
328758 AAAGGAAAACTAAAT
1 AAAGTAAAACTAAAT
328773 AAAGTA
1 AAAGTA
328779 GAAATCTACT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 11 0.37
16 7 0.23
17 7 0.23
18 5 0.17
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.20
Consensus pattern (15 bp):
AAAGTAAAACTAAAT
Found at i:328767 original size:33 final size:33
Alignment explanation
Indices: 328720--328786 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
328710 TATATACTTG
*
328720 ATTACAAAGTAAAACTAAATAAAGTAAAAATCT
1 ATTACAAAGGAAAACTAAATAAAGTAAAAATCT
*
328753 ATTACAAAGGAAAACTAAATAAAGTAGAAATCT
1 ATTACAAAGGAAAACTAAATAAAGTAAAAATCT
328786 A
1 A
328787 CTCTAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.22
Consensus pattern (33 bp):
ATTACAAAGGAAAACTAAATAAAGTAAAAATCT
Found at i:333160 original size:38 final size:39
Alignment explanation
Indices: 333081--333161 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 39
333071 AACAAGTTGG
*
333081 AAAATATTTATATATTTTCTTTTAAAAAATTAAATTCAT
1 AAAATATTTATATATTTTCTTTTAAAAAATTAAAATCAT
*
333120 AAAAT-TTATATATATTTT-TTTTATAAAATTGAAAAT-AT
1 AAAATATT-TATATATTTTCTTTTAAAAAATT-AAAATCAT
333158 AAAA
1 AAAA
333162 AGGTTTAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
38 19 0.50
39 19 0.50
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTTAAAAAATTAAAATCAT
Found at i:334488 original size:29 final size:29
Alignment explanation
Indices: 334446--334504 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
334436 AGAAAGACTA
334446 GCTTTCATTTACCCCACTATTGTTTTGGT
1 GCTTTCATTTACCCCACTATTGTTTTGGT
334475 GCTTTCATTTACCCCACTATTGTTTTGGT
1 GCTTTCATTTACCCCACTATTGTTTTGGT
334504 G
1 G
334505 TTATATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.14, C:0.24, G:0.15, T:0.47
Consensus pattern (29 bp):
GCTTTCATTTACCCCACTATTGTTTTGGT
Found at i:341274 original size:14 final size:14
Alignment explanation
Indices: 341255--341282 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
341245 CCACTGCTCT
341255 GCGGTGGCAAAGTC
1 GCGGTGGCAAAGTC
341269 GCGGTGGCAAAGTC
1 GCGGTGGCAAAGTC
341283 ATACTGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.43, T:0.14
Consensus pattern (14 bp):
GCGGTGGCAAAGTC
Found at i:351022 original size:22 final size:23
Alignment explanation
Indices: 350990--351034 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
350980 TATTTTACTT
350990 ATTTACTCTTTTGTCCTTT-TTAA
1 ATTTACTCTTTT-TCCTTTATTAA
351013 ATTTA-TCTTTTTCCTTTATTAA
1 ATTTACTCTTTTTCCTTTATTAA
351035 TCACAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 10 0.48
23 5 0.24
ACGTcount: A:0.20, C:0.16, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTACTCTTTTTCCTTTATTAA
Found at i:352074 original size:2 final size:2
Alignment explanation
Indices: 352067--352100 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
352057 TTTCTATTCA
352067 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
352101 TTAAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:355574 original size:2 final size:2
Alignment explanation
Indices: 355567--355607 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
355557 GGTTAAACTA
355567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
355608 GTTTTGAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:369749 original size:21 final size:21
Alignment explanation
Indices: 369698--369750 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
369688 ATTATGACTA
*
369698 TCGCAATGCAATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
369719 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
369740 TCGCAATGCGA
1 TCGCAATGCGA
369751 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:369765 original size:20 final size:21
Alignment explanation
Indices: 369740--369791 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
369730 TTTTCCCAAT
*
369740 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* *
369760 TCGCAACGCGAATTAGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
369781 TCACAATGCGA
1 TCGCAATGCGA
369792 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:369804 original size:41 final size:41
Alignment explanation
Indices: 369759--369853 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
369749 GAATAAGTAA
* * *
369759 ATCGCAACGCGA-ATTAGGAAAATCACAATGCGATACTGACT
1 ATCGCAACGCGATAATA-CAAAATCACAACGCGATACTGACT
* *
369800 ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACAAAATCACAACGCGATACTGACT
*
369841 TTCGCAACGCGAT
1 ATCGCAACGCGAT
369854 TCTGACTTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 44 0.94
42 3 0.06
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGATAATACAAAATCACAACGCGATACTGACT
Found at i:369847 original size:20 final size:20
Alignment explanation
Indices: 369822--369909 Score: 176
Period size: 20 Copynumber: 4.4 Consensus size: 20
369812 TAATACAAAA
369822 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
369842 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
369862 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
369882 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
369902 TCGCAACG
1 TCGCAACG
369910 AGATAATACA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:370515 original size:20 final size:20
Alignment explanation
Indices: 370460--370508 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
370450 CAACGGGGAA
370460 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
370480 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
370500 ATCGCAACG
1 ATCGCAACG
370509 AGCAAATCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:370561 original size:14 final size:14
Alignment explanation
Indices: 370542--370606 Score: 76
Period size: 14 Copynumber: 4.3 Consensus size: 14
370532 AATTGCATTA
370542 CGATTTTCTCGTTG
1 CGATTTTCTCGTTG
370556 CGATTTTCTCGTTG
1 CGATTTTCTCGTTG
370570 CGATTTTCATTTCGCATTG
1 CGATTTTC---TCG--TTG
*
370589 CGATTCTCTCGTTG
1 CGATTTTCTCGTTG
370603 CGAT
1 CGAT
370607 AGTCAGTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
14 29 0.64
16 3 0.07
17 3 0.07
19 10 0.22
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (14 bp):
CGATTTTCTCGTTG
Found at i:370794 original size:40 final size:41
Alignment explanation
Indices: 370719--370796 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
370709 AAGAATTATG
* * **
370719 TACACATCAATTAAACAAATCAACATTTACAAATAATTTTT
1 TACAAATCAATTAAACAAATCAAAAAATACAAATAATTTTT
370760 TACAAATCAATTAAAC-AATCAAAAAATA-ATAATAATT
1 TACAAATCAATTAAACAAATCAAAAAATACA-AATAATT
370797 CTTATTTCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.03
40 16 0.50
41 15 0.47
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (41 bp):
TACAAATCAATTAAACAAATCAAAAAATACAAATAATTTTT
Found at i:372224 original size:40 final size:42
Alignment explanation
Indices: 372180--372270 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
372170 CCTCTTCAAC
372180 GATGACAGTGG-CCTCTTGAACG-GTGG-GGGGACTCTTGAGG
1 GATGACAG-GGACCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
372220 GATGATAGGGACCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGACCTCTTGAACGAGTGGAGGGGACTCTTGAGG
372262 GATGACAGG
1 GATGACAGG
372271 TGAGTCGGAC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 2 0.04
40 18 0.40
41 3 0.07
42 22 0.49
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGACCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:372250 original size:21 final size:20
Alignment explanation
Indices: 372163--372259 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 20
372153 TGGAAAGGTG
*
372163 GGAGGGACCTCTTCAACGAT
1 GGAGGGACCTCTTGAACGAT
* *
372183 GACAGTGG-CCTCTTGAACGGT
1 G-GAG-GGACCTCTTGAACGAT
* **
372204 GGGGGGA-CTCTTGAGGGAT
1 GGAGGGACCTCTTGAACGAT
*
372223 GATAGGGACCTCTTGAACGATT
1 G-GAGGGACCTCTTGAACGA-T
372245 GGAGGGGA-CTCTTGA
1 GGA-GGGACCTCTTGA
372260 GGGATGACAG
Statistics
Matches: 57, Mismatches: 13, Indels: 13
0.69 0.16 0.16
Matches are distributed among these distances:
19 12 0.21
20 6 0.11
21 31 0.54
22 8 0.14
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.23
Consensus pattern (20 bp):
GGAGGGACCTCTTGAACGAT
Found at i:372631 original size:20 final size:20
Alignment explanation
Indices: 372606--372678 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
372596 GAATAATAGT
372606 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
372626 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
* *
372646 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAC
* *
372666 TGACTATCGCAAC
1 TTACTTTCGCAAC
372679 GCGGAAATGG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:372679 original size:20 final size:20
Alignment explanation
Indices: 372612--372704 Score: 96
Period size: 20 Copynumber: 4.7 Consensus size: 20
372602 TAGTTTACTT
* * * *
372612 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
* * * *
372632 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
372652 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
372672 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
372692 TCGCAACGCGAAA
1 TCGCAACGCGAAA
372705 TGAAATTCGC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:372714 original size:19 final size:18
Alignment explanation
Indices: 372651--372737 Score: 84
Period size: 19 Copynumber: 4.5 Consensus size: 18
372641 GAAACTTACT
*
372651 TTCGCAACGCGAAAATGAC
1 TTCGCAACGCG-AAATGAA
**
372670 TATCGCAACGCGGAAATGGC
1 T-TCGCAACGC-GAAATGAA
372690 TATCGCAACGCGAAATGAAA
1 T-TCGCAACGCGAAATG-AA
*
372710 TTCGCAATGCGAAATGAAA
1 TTCGCAACGCGAAATG-AA
372729 TTCGCAACG
1 TTCGCAACG
372738 ACAAAATCGC
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
19 32 0.53
20 27 0.45
21 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (18 bp):
TTCGCAACGCGAAATGAA
Found at i:372753 original size:33 final size:33
Alignment explanation
Indices: 372711--372789 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
372701 GAAATGAAAT
* *
372711 TCGCAATGCGAAATGAAATTCGCAACGACAAAA
1 TCGCAATGCGAAATGAAAATCACAACGACAAAA
372744 TCGCAATGCGAAATGAAAATCACAACGACAAAA
1 TCGCAATGCGAAATGAAAATCACAACGACAAAA
*
372777 TCGCAACGCGAAA
1 TCGCAATGCGAAA
372790 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCACAACGACAAAA
Found at i:372764 original size:19 final size:19
Alignment explanation
Indices: 372691--372764 Score: 77
Period size: 19 Copynumber: 4.2 Consensus size: 19
372681 GGAAATGGCT
*
372691 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
372710 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
372729 TTCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
372743 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
372762 ATC
1 ATC
372765 ACAACGACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 30 0.67
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:372845 original size:20 final size:19
Alignment explanation
Indices: 372811--372865 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
372801 TTACGATTTT
*
372811 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
372830 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
372850 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
372866 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:373569 original size:41 final size:42
Alignment explanation
Indices: 373524--373614 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 42
373514 CCTCTTCAAC
* *
373524 GATGACAGTGGCCTCTTGAACG-GTG-GGGGGAACTCTTGAGG
1 GATGACAGAGGCCTCTTGAACGAGTGTAGGGG-ACTCTTGAGG
* *
373565 GATGATAGAGGCCTCTTGAACGATTGTAGGGGACTCTTGAGG
1 GATGACAGAGGCCTCTTGAACGAGTGTAGGGGACTCTTGAGG
373607 GATGACAG
1 GATGACAG
373615 GTGAGTCGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 20 0.47
42 19 0.44
43 4 0.09
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.23
Consensus pattern (42 bp):
GATGACAGAGGCCTCTTGAACGAGTGTAGGGGACTCTTGAGG
Found at i:373582 original size:21 final size:21
Alignment explanation
Indices: 373555--373611 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
373545 GGTGGGGGGA
373555 ACTCTTGAGGGATGATAGAGG
1 ACTCTTGAGGGATGATAGAGG
* ** *
373576 CCTCTTGAACGATTG-TAGGGG
1 ACTCTTGAGGGA-TGATAGAGG
373597 ACTCTTGAGGGATGA
1 ACTCTTGAGGGATGA
373612 CAGGTGAGTC
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.26
Consensus pattern (21 bp):
ACTCTTGAGGGATGATAGAGG
Found at i:373978 original size:20 final size:20
Alignment explanation
Indices: 373953--373991 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
373943 TAAGAATAGT
373953 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
*
373973 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
373992 ATGGCTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:374002 original size:20 final size:20
Alignment explanation
Indices: 373979--374031 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
373969 AAACTTACTT
373979 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
*
373999 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
374019 TCGCAACGCGAAA
1 TCGCAACGCGAAA
374032 TGAAATTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.26, G:0.26, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGGCTA
Found at i:374063 original size:33 final size:33
Alignment explanation
Indices: 374018--374097 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
374008 GGAAATGGCT
* **
374018 ATCGCAACGCGAAATGAAATTTGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
*
374051 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
374084 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
374098 CACAAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCACAACGACAAA
Found at i:374141 original size:19 final size:19
Alignment explanation
Indices: 374104--374164 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
374094 GAAACACAAA
**
374104 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATAGTCATT
*
374123 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATAGTCATT
*
374142 TCCGCGTTGCGATAGTCATT
1 T-CGCATTGCGATAGTCATT
374162 TCG
1 TCG
374165 TGTTGCGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 19 0.53
20 17 0.47
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (19 bp):
TCGCATTGCGATAGTCATT
Found at i:374153 original size:20 final size:19
Alignment explanation
Indices: 374119--374172 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
374109 TTGCGATTTT
*
374119 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
374138 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
374158 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
374173 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:374171 original size:19 final size:19
Alignment explanation
Indices: 374104--374172 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
374094 GAAACACAAA
* **
374104 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
* *
374123 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATAGTCATT
374142 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATAGTCATT
*
374162 TCGTGTTGCGA
1 TCGCGTTGCGA
374173 AAGTAAACTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 26 0.60
20 17 0.40
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:374863 original size:41 final size:42
Alignment explanation
Indices: 374818--374909 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
374808 CCTCTTCAAC
*
374818 GATGACAGTGGCCTCTTGAACG-GT-GAGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGA-GGGGACTCTTGAGG
* * *
374859 GATGATAGGGGTCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
374901 GATGACAGG
1 GATGACAGG
374910 TAAGTCGGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
41 19 0.43
42 23 0.52
43 2 0.05
ACGTcount: A:0.22, C:0.14, G:0.41, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:374874 original size:21 final size:21
Alignment explanation
Indices: 374841--374905 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
374831 TCTTGAACGG
374841 TGAG-GGGGACTCTTGAGGGA
1 TGAGAGGGGACTCTTGAGGGA
* * **
374861 TGATAGGGGTCTCTTGAACGA
1 TGAGAGGGGACTCTTGAGGGA
374882 TTG-GAGGGGACTCTTGAGGGA
1 -TGAGAGGGGACTCTTGAGGGA
374903 TGA
1 TGA
374906 CAGGTAAGTC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
20 5 0.15
21 27 0.79
22 2 0.06
ACGTcount: A:0.22, C:0.11, G:0.43, T:0.25
Consensus pattern (21 bp):
TGAGAGGGGACTCTTGAGGGA
Found at i:375271 original size:20 final size:20
Alignment explanation
Indices: 375246--375284 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
375236 GAAGAATAGT
375246 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
*
375266 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
375285 ATGACTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:375295 original size:20 final size:20
Alignment explanation
Indices: 375252--375324 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
375242 TAGTTTACTT
* * * *
375252 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
375272 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* * *
375292 TCGCAATGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
375312 TCGCAACGCGAAA
1 TCGCAACGCGAAA
375325 TGAAATTCGC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:375373 original size:33 final size:33
Alignment explanation
Indices: 375331--375409 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
375321 GAAATGAAAT
* *
375331 TCGCAATGCGAAATGAAATTCGCAACGACAAAA
1 TCGCAATGCGAAATGAAAATCACAACGACAAAA
375364 TCGCAATGCGAAATGAAAATCACAACGACAAAA
1 TCGCAATGCGAAATGAAAATCACAACGACAAAA
*
375397 TCGCAACGCGAAA
1 TCGCAATGCGAAA
375410 CATAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCACAACGACAAAA
Found at i:375384 original size:19 final size:19
Alignment explanation
Indices: 375272--375384 Score: 83
Period size: 19 Copynumber: 6.1 Consensus size: 19
375262 AAACTTACTT
* **
375272 TCGCAACGCGAAAATGACTA
1 TCGCAATGCG-AAATGAAAA
***
375292 TCGCAATGCGGAAATGGCTA
1 TCGCAATGC-GAAATGAAAA
* *
375312 TCGCAACGCGAAATGAAAT
1 TCGCAATGCGAAATGAAAA
*
375331 TCGCAATGCGAAATGAAAT
1 TCGCAATGCGAAATGAAAA
*
375350 TCGCAA--CG--A-CAAAA
1 TCGCAATGCGAAATGAAAA
375364 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
375383 TC
1 TC
375385 ACAACGACAA
Statistics
Matches: 76, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 36 0.47
20 24 0.32
21 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:375444 original size:20 final size:20
Alignment explanation
Indices: 375416--375466 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
375406 GAAACATAAA
*
375416 TCGCATTGCGATAGCCATTT
1 TCGCGTTGCGATAGCCATTT
*
375436 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATAGCCATTT
*
375456 TCGTGTTGCGA
1 TCGCGTTGCGA
375467 AAGTAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATAGCCATTT
Found at i:376151 original size:42 final size:41
Alignment explanation
Indices: 376095--376197 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 41
376085 GTGAATCGGG
* *
376095 CTCTGGAAAGGTGGGAGGGACATATTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGAC-TATTCAACGATGACAGTGGC
* * * ** *
376137 CTCTTGAACGGTGGGGGGGACTCTTGAGGGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGACTATTCAACGATGACAGTGGC
* *
376178 CTCTTGAACGATTGGAGGGA
1 CTCTTGAACGGTGGGAGGGA
376198 ACTCTTGAGG
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
41 32 0.64
42 18 0.36
ACGTcount: A:0.23, C:0.16, G:0.39, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTATTCAACGATGACAGTGGC
Found at i:376177 original size:41 final size:42
Alignment explanation
Indices: 376125--376215 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
376115 CATATTCAAC
* *
376125 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGTGGCCTCTTGAACGAGTGGAGGGAACTCTTGAGG
* *
376166 GATGATAGTGGCCTCTTGAACGATTGGAGGGAACTCTTGAGG
1 GATGACAGTGGCCTCTTGAACGAGTGGAGGGAACTCTTGAGG
376208 GATGACAG
1 GATGACAG
376216 GTGAGTCGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 21 0.48
42 23 0.52
ACGTcount: A:0.22, C:0.15, G:0.40, T:0.23
Consensus pattern (42 bp):
GATGACAGTGGCCTCTTGAACGAGTGGAGGGAACTCTTGAGG
Found at i:376531 original size:25 final size:25
Alignment explanation
Indices: 376501--376562 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
376491 AGTAAGCACT
376501 TATATAAACATTTAAAAGGACAACA
1 TATATAAACATTTAAAAGGACAACA
*
376526 TATATAAACATTTAAAATGACAACA
1 TATATAAACATTTAAAAGGACAACA
376551 TATATAAACATT
1 TATATAAACATT
376563 CTAGAAGAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (25 bp):
TATATAAACATTTAAAAGGACAACA
Found at i:376628 original size:20 final size:20
Alignment explanation
Indices: 376605--376657 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
376595 AAACTTACTT
*
376605 TCGCACCGCGAAAAAGACTA
1 TCGCAACGCGAAAAAGACTA
* * *
376625 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAAAGACTA
376645 TCGCAACGCGAAA
1 TCGCAACGCGAAA
376658 TTCGCAACGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.28, G:0.25, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAAAGACTA
Found at i:376693 original size:19 final size:19
Alignment explanation
Indices: 376669--376737 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 19
376659 TCGCAACGAC
*
376669 AAAATCGTAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
376688 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
* *
376702 AAAATCGTATTGCGAAATG
1 AAAATCGCAATGCGAAATG
*
376721 AAAATCGCAACGCGAAA
1 AAAATCGCAATGCGAAA
376738 CACAAATCGC
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
14 8 0.22
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.62
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.16
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:376699 original size:33 final size:33
Alignment explanation
Indices: 376654--376732 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
376644 ATCGCAACGC
*
376654 GAAATTCGCAACGACAAAATCGTAATGCGAAAT
1 GAAAATCGCAACGACAAAATCGTAATGCGAAAT
*
376687 GAAAATCGCAACGACAAAATCGTATTGCGAAAT
1 GAAAATCGCAACGACAAAATCGTAATGCGAAAT
376720 GAAAATCGCAACG
1 GAAAATCGCAACG
376733 CGAAACACAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (33 bp):
GAAAATCGCAACGACAAAATCGTAATGCGAAAT
Found at i:376754 original size:19 final size:19
Alignment explanation
Indices: 376701--376754 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
376691 ATCGCAACGA
*
376701 CAAAATCGTATTGCGAAAT
1 CAAAATCGCATTGCGAAAT
* **
376720 GAAAATCGCAACGCGAAA-
1 CAAAATCGCATTGCGAAAT
376738 CACAAATCGCATTGCGA
1 CA-AAATCGCATTGCGA
376755 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 1 0.04
19 26 0.96
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.17
Consensus pattern (19 bp):
CAAAATCGCATTGCGAAAT
Found at i:376766 original size:19 final size:19
Alignment explanation
Indices: 376744--376826 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
376734 GAAACACAAA
376744 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
376763 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
376782 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
376798 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
376815 TCGTATTGCGAT
1 TCGCATTGCGAT
376827 AGCAATTCCC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 6 0.11
15 3 0.05
16 4 0.07
17 4 0.07
18 3 0.05
19 35 0.64
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:376862 original size:20 final size:20
Alignment explanation
Indices: 376800--376865 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
376790 CGATTTTGTC
**
376800 GTTGCGATTTTCA-TTTCGT
1 GTTGCGATAGTCATTTTCGT
* ** *
376819 ATTGCGATAG-CAATTCCCGC
1 GTTGCGATAGTC-ATTTTCGT
376839 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
376859 GTTGCGA
1 GTTGCGA
376866 AAGTAAACTA
Statistics
Matches: 34, Mismatches: 10, Indels: 5
0.69 0.20 0.10
Matches are distributed among these distances:
18 1 0.03
19 8 0.24
20 24 0.71
21 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:377422 original size:18 final size:18
Alignment explanation
Indices: 377399--377446 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
377389 CGGGTCGATC
377399 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
377417 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
377435 AGGTGATGGCTC
1 AGGTGATGGCTC
377447 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:378791 original size:20 final size:20
Alignment explanation
Indices: 378766--378803 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
378756 AATAGTTTCT
378766 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
378786 GAAAATGACAATCGCAAC
1 GAAAATGAAAATCGCAAC
378804 GAGAGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.21, G:0.16, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:379309 original size:21 final size:20
Alignment explanation
Indices: 379277--379390 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
379267 CGCTTTGAAA
* * *
379277 ATCGCATTGCGATTATGTATT
1 ATCGCGTTGCGA-TAAGTAGT
*
379298 ATCTCGTTGCGA-AAGTCAGT
1 ATCGCGTTGCGATAAGT-AGT
379318 ATCGCGTTGCGA-AAGTAGT
1 ATCGCGTTGCGATAAGTAGT
** *
379337 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGA-TAAGTAGT
379358 ATCGCGTTGCGATAA-TCAGT
1 ATCGCGTTGCGATAAGT-AGT
* *
379378 ATCACATTGCGAT
1 ATCGCGTTGCGAT
379391 TTTCCAATAT
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 19 0.25
20 31 0.41
21 26 0.34
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAAGTAGT
Found at i:379377 original size:60 final size:60
Alignment explanation
Indices: 379277--379389 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
379267 CGCTTTGAAA
* * *
379277 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCACATTGCGAAAGTAGT
* *
379337 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAA-TCAGTATCACATTGCGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGA-AAGTCAGTATCACATTGCGA
379390 TTTTCCAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 45 0.96
61 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (60 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCACATTGCGAAAGTAGT
Found at i:379390 original size:41 final size:41
Alignment explanation
Indices: 379317--379410 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 41
379307 CGAAAGTCAG
* * ** *
379317 TATCGCGTTGCGA-AAGTAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAAGTAGTATCACATTGCGATTTTCCAA
379357 TATCGCGTTGCGATAA-TCAGTATCACATTGCGATTTTCCAA
1 TATCGCGTTGCGATAAGT-AGTATCACATTGCGATTTTCCAA
379398 TAT-GCGTTGCGAT
1 TATCGCGTTGCGAT
379411 TTACTTATTC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 24 0.51
41 23 0.49
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAAGTAGTATCACATTGCGATTTTCCAA
Found at i:379800 original size:2 final size:2
Alignment explanation
Indices: 379793--379823 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
379783 CTGTAGGGTG
379793 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 T
379824 TATCAATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:390757 original size:21 final size:22
Alignment explanation
Indices: 390731--390783 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
390721 TCTGAGTTGA
*
390731 TTAATATTCTATTCGT-GTTCG
1 TTAATATTATATTCGTAGTTCG
* *
390752 TTAATATTATTTTTGTAGTTCG
1 TTAATATTATATTCGTAGTTCG
*
390774 TTAAAATTAT
1 TTAATATTAT
390784 TAAAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (22 bp):
TTAATATTATATTCGTAGTTCG
Found at i:396754 original size:257 final size:248
Alignment explanation
Indices: 396283--396853 Score: 806
Period size: 252 Copynumber: 2.2 Consensus size: 248
396273 CTTATTCATA
396283 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGAGTCGGGTTTCTAATTCATATATTCAGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGAGTCGGGTTTCTAATTCATATA-T----T
* *
396348 CGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGTCGGTTTTTTAAGTGTGATATTCGGGTCAAG
61 CGGGTCAGGTCGGGTGAAACTTTATTTTGGTCGGTCGATTTTTTAAGTGTGATATTCGGGTCAAG
* * *
396413 TCGAGTTCGGGTTTAGGGTGAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTT
126 TCGAGTTCGGGTTTAGGGTGAAAAAACCCGACCCAAAAAAATATATAATTTTACCTTATATATTT
* * *
396478 AGATATAATTACAATAATA-CATCTCTATATATA-TTTTTTCAATTAAGTCATTGTTTT
191 AGATATAATTACAATAATACCCT-TCTATATATATTTTTTTCAATTAAGTCAATATTTT
* *
396535 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGAGTCGGGTTTCTAATTCATATATTCGGGT
* **
396600 CAGGTCGGGTGAAACTTTATTTTGTTCGGGTCAGATTTTTTAAGTGTGATATTCGGGTCGGGTCG
66 CAGGTCGGGTGAAACTTTATTTTGGTC-GGTC-GATTTTTTAAGTGTGATATTCGGGTCAAGTCG
*
396665 GGTTCGGGTTTAGGGTGAAAAAAAACCCGGACCAACCCAAAAAAAATATATAATTTTACCTTATA
129 AGTTCGGGTTTAGGGTG--AAAAAACCC-G----ACCC-AAAAAAATATATAATTTTACCTTATA
396730 TATTTAGGA-ATAATTACAATAATACCCTTCTATATATATTTTTTTCAATTAAGTCAATATTTT
186 TATTTA-GATATAATTACAATAATACCCTTCTATATATATTTTTTTCAATTAAGTCAATATTTT
* * *
396793 TATTGAATAAAAATAATTTTTTTATTATTTTGTGTCGTGTCGGGTTTCTAATTCATATATT
1 TATTGAATAAAAAT-ATTTTTTTATTATTTCGGGTCGAGTCGGGTTTCTAATTCATATATT
396854 GAATAAAAAT
Statistics
Matches: 287, Mismatches: 18, Indels: 21
0.88 0.06 0.06
Matches are distributed among these distances:
247 31 0.11
248 4 0.01
249 45 0.16
251 9 0.03
252 57 0.20
256 4 0.01
257 55 0.19
258 40 0.14
259 42 0.15
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.42
Consensus pattern (248 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGAGTCGGGTTTCTAATTCATATATTCGGGT
CAGGTCGGGTGAAACTTTATTTTGGTCGGTCGATTTTTTAAGTGTGATATTCGGGTCAAGTCGAG
TTCGGGTTTAGGGTGAAAAAACCCGACCCAAAAAAATATATAATTTTACCTTATATATTTAGATA
TAATTACAATAATACCCTTCTATATATATTTTTTTCAATTAAGTCAATATTTT
Found at i:397255 original size:17 final size:18
Alignment explanation
Indices: 397233--397279 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
397223 TATGGAATTG
*
397233 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
397250 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
397268 GATTCTAATTCC
1 GATTCCAATTCC
397280 CTCATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:402113 original size:43 final size:43
Alignment explanation
Indices: 402050--402135 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
402040 GATTGGTGAA
402050 GCATGTAAGCACGTGCTAGTCACATGACTTACGGTCAAGCAAC
1 GCATGTAAGCACGTGCTAGTCACATGACTTACGGTCAAGCAAC
*
402093 GCATGTAAGCACGTGTTAGTCACATGACTTACGGTCAAGCAAC
1 GCATGTAAGCACGTGCTAGTCACATGACTTACGGTCAAGCAAC
402136 ACTCCAAAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (43 bp):
GCATGTAAGCACGTGCTAGTCACATGACTTACGGTCAAGCAAC
Found at i:405825 original size:37 final size:37
Alignment explanation
Indices: 405744--405830 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
405734 AAACATGTAT
* *
405744 ATATATGCATGAACTGAAGTTGCATATGAAGAAGTTC
1 ATATATACATGAACTGAAGTTACATATGAAGAAGTTC
*
405781 ATGTATACATGAACTGAAGTTACAGT-TGAAGAAGTT-
1 ATATATACATGAACTGAAGTTACA-TATGAAGAAGTTC
*
405817 ATTATATACCTGAA
1 A-TATATACATGAA
405831 AATTAGATTG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
36 1 0.02
37 41 0.95
38 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (37 bp):
ATATATACATGAACTGAAGTTACATATGAAGAAGTTC
Found at i:412472 original size:95 final size:95
Alignment explanation
Indices: 412364--412538 Score: 314
Period size: 95 Copynumber: 1.8 Consensus size: 95
412354 AGACAGAGTA
*
412364 AACAGAGATAGCCAGTACCTAAAGATCACAATCCATAAGCAAAAAAGAAAGCAAATTTCAGCAGA
1 AACAGAGATAGCCAGTACCTAAAGATCACAATCCATAAGCAAAAAAGAAAGCAAATTACAGCAGA
412429 TCTAGAGAGTAAAAAAGAAAACAAAAACCC
66 TCTAGAGAGTAAAAAAGAAAACAAAAACCC
* *
412459 AACAGAGATAGCCAGTACCTAAAGATCACAATCTATAAGCAAAAAAGAAAGCAAATTACCGCAGA
1 AACAGAGATAGCCAGTACCTAAAGATCACAATCCATAAGCAAAAAAGAAAGCAAATTACAGCAGA
*
412524 TCTAGAGATTAAAAA
66 TCTAGAGAGTAAAAA
412539 GATTAATAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 76 1.00
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.14
Consensus pattern (95 bp):
AACAGAGATAGCCAGTACCTAAAGATCACAATCCATAAGCAAAAAAGAAAGCAAATTACAGCAGA
TCTAGAGAGTAAAAAAGAAAACAAAAACCC
Found at i:412711 original size:40 final size:40
Alignment explanation
Indices: 412656--412735 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
412646 TGATTTGAGC
412656 TTCAAAAGCATTAAACTCAAAGCCACAGGCTTTTCTTCTT
1 TTCAAAAGCATTAAACTCAAAGCCACAGGCTTTTCTTCTT
412696 TTCAAAAGCATTAAACTCAAAGCCACAGGCTTTTCTTCTT
1 TTCAAAAGCATTAAACTCAAAGCCACAGGCTTTTCTTCTT
412736 ACTTTTCGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (40 bp):
TTCAAAAGCATTAAACTCAAAGCCACAGGCTTTTCTTCTT
Done.