Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000422.1 Hibiscus syriacus cultivar Beakdansim tig00000773_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: 2457469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:234652 original size:2 final size:2
Alignment explanation
Indices: 234641--234705 Score: 95
Period size: 2 Copynumber: 35.0 Consensus size: 2
234631 TAATATTAAC
234641 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
234681 TA T- TA -A 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
234706 ATTTGAATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
1 5 0.09
2 53 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:236846 original size:30 final size:31
Alignment explanation
Indices: 236791--236850 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
236781 AATTTAAGGT
236791 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAATGGTTTTTGGACTTGAATTGAATTTAC
236822 AAAATGGTTTTTGGACTT-AATTGAATTTA
1 AAAATGGTTTTTGGACTTGAATTGAATTTA
236851 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (31 bp):
AAAATGGTTTTTGGACTTGAATTGAATTTAC
Found at i:236958 original size:22 final size:22
Alignment explanation
Indices: 236930--236987 Score: 100
Period size: 21 Copynumber: 2.7 Consensus size: 22
236920 AGTGTGCCAA
236930 AGTGCATCCATGCACCCCCTGC
1 AGTGCATCCATGCACCCCCTGC
*
236952 AGTGCATCCATGCA-CCCCTGT
1 AGTGCATCCATGCACCCCCTGC
236973 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
236988 TGCATGTGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (22 bp):
AGTGCATCCATGCACCCCCTGC
Found at i:238434 original size:21 final size:21
Alignment explanation
Indices: 238376--238442 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
238366 TTTGAAAGTC
238376 AAAA-TGAAA-TTTTG-AAAA
1 AAAATTGAAAGTTTTGAAAAA
* * * * *
238394 AAGATTTAGAGCTTTCAAAAA
1 AAAATTGAAAGTTTTGAAAAA
238415 AAAATTGAAAGTTTTGAAAAA
1 AAAATTGAAAGTTTTGAAAAA
238436 GAAAATT
1 -AAAATT
238443 TTGATTTAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
18 3 0.09
19 3 0.09
20 3 0.09
21 20 0.57
22 6 0.17
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.28
Consensus pattern (21 bp):
AAAATTGAAAGTTTTGAAAAA
Found at i:239606 original size:31 final size:30
Alignment explanation
Indices: 239568--239628 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 30
239558 CAATTTAAGG
239568 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTT-AATTGAATTTA
*
239599 CAAAATGGTTTTTGGACTTAATTTAATTTA
1 CAAAATGGTTTTTGGACTTAATTGAATTTA
239629 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (30 bp):
CAAAATGGTTTTTGGACTTAATTGAATTTA
Found at i:239739 original size:20 final size:19
Alignment explanation
Indices: 239708--239825 Score: 112
Period size: 20 Copynumber: 5.7 Consensus size: 19
239698 AGTGTGTCAA
239708 AGTGCATCATGCACCCTGC
1 AGTGCATCATGCACCCTGC
239727 AGTGCATTCATGCACCCTGC
1 AGTGCA-TCATGCACCCTGC
*
239747 AGTGCATCTATGCACCCCTGT
1 AGTGCATC-ATGCA-CCCTGC
239768 AGTGCATCCATGCA-CCTGCCAC
1 AGTGCAT-CATGCACCCTG---C
* *
239790 TAGTGCATCGATGCACCATGT
1 -AGTGCATC-ATGCACCCTGC
239811 AGTGCATCCATGCAC
1 AGTGCAT-CATGCAC
239826 TCCATTTCGA
Statistics
Matches: 84, Mismatches: 4, Indels: 21
0.77 0.04 0.19
Matches are distributed among these distances:
19 12 0.14
20 37 0.44
21 18 0.21
22 2 0.02
23 12 0.14
24 3 0.04
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (19 bp):
AGTGCATCATGCACCCTGC
Found at i:239870 original size:20 final size:20
Alignment explanation
Indices: 239845--239906 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
239835 AATGCAATTA
* *
239845 GTGCATCGATGCATCTTGCT
1 GTGCATCGACGCATCCTGCT
*
239865 GTGCATCGACGCACCCTGCT
1 GTGCATCGACGCATCCTGCT
*
239885 GTGTATCGACGCATCCTGCT
1 GTGCATCGACGCATCCTGCT
239905 GT
1 GT
239907 ACATTCATGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.15, C:0.31, G:0.26, T:0.29
Consensus pattern (20 bp):
GTGCATCGACGCATCCTGCT
Found at i:240297 original size:34 final size:32
Alignment explanation
Indices: 240258--240327 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
240248 TTTTGTAAAG
* *
240258 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
240292 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
240324 GGGA
1 GGGA
240328 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:244996 original size:2 final size:2
Alignment explanation
Indices: 244991--245017 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
244981 ATTTGAAATG
244991 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 A
245018 AATGGGACTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:251737 original size:15 final size:15
Alignment explanation
Indices: 251719--251757 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
251709 GCGACCATAT
251719 CCACGACCTCCACGG
1 CCACGACCTCCACGG
251734 CCACGACCTCCACGG
1 CCACGACCTCCACGG
251749 CCACGACCT
1 CCACGACCT
251758 TTACCTCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.21, C:0.54, G:0.18, T:0.08
Consensus pattern (15 bp):
CCACGACCTCCACGG
Found at i:256020 original size:21 final size:22
Alignment explanation
Indices: 255996--256045 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
255986 TTATTGTGCC
255996 AGTTACAGAGTTAATTACA-AG
1 AGTTACAGAGTTAATTACATAG
*
256017 AGTTACAGAGTTAATTACATGG
1 AGTTACAGAGTTAATTACATAG
256039 AGTTACA
1 AGTTACA
256046 AAAGACTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (22 bp):
AGTTACAGAGTTAATTACATAG
Found at i:267890 original size:19 final size:19
Alignment explanation
Indices: 267830--267890 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
267820 TTTGTGCAGA
* *
267830 GGGAATCGATACCCTCATG
1 GGGAATCGATACCCCCCTG
* *
267849 AGGGAACCGAT-TCCCCCTAG
1 -GGGAATCGATACCCCCCT-G
267869 GGGAATCGATACCCCCCTG
1 GGGAATCGATACCCCCCTG
267888 GGG
1 GGG
267891 TTCTGGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.23, C:0.31, G:0.30, T:0.16
Consensus pattern (19 bp):
GGGAATCGATACCCCCCTG
Found at i:272634 original size:43 final size:43
Alignment explanation
Indices: 272573--272658 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
272563 CATTCATCTT
272573 ATGTGACAGAAATAAGTGTTATTCTAAAAAAATAAAAGGTAAA
1 ATGTGACAGAAATAAGTGTTATTCTAAAAAAATAAAAGGTAAA
*
272616 ATGTGATAGAAATAAGTGTTATTCTAAAAAAATAAAAGGTAAA
1 ATGTGACAGAAATAAGTGTTATTCTAAAAAAATAAAAGGTAAA
272659 CTATTCATTT
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:0.53, C:0.03, G:0.16, T:0.27
Consensus pattern (43 bp):
ATGTGACAGAAATAAGTGTTATTCTAAAAAAATAAAAGGTAAA
Found at i:273046 original size:27 final size:29
Alignment explanation
Indices: 273016--273069 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
273006 ATATAAAAAT
273016 ATTAAATTA-AATTTA-AATAATTTATCA
1 ATTAAATTATAATTTATAATAATTTATCA
* *
273043 ATTAAATTATTATTTATAATTATTTAT
1 ATTAAATTATAATTTATAATAATTTAT
273070 TTAATTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 5 0.22
29 9 0.39
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
ATTAAATTATAATTTATAATAATTTATCA
Found at i:274563 original size:43 final size:44
Alignment explanation
Indices: 274453--274553 Score: 177
Period size: 43 Copynumber: 2.3 Consensus size: 44
274443 GATAGACTTA
*
274453 TTTTTATTTATTTTGTTTCTTAATATTTTTATTTAATTATGGAT
1 TTTTTATTTATTTTGTTTCTTAATATTTTTATTTAATTATGGAC
*
274497 TTTTTATTTATTTTGTTTCTTAATA-TTTTATTTAATTATTGAC
1 TTTTTATTTATTTTGTTTCTTAATATTTTTATTTAATTATGGAC
274540 TTTTTATTTATTTT
1 TTTTTATTTATTTT
274554 ATTATTTAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
43 30 0.55
44 25 0.45
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (44 bp):
TTTTTATTTATTTTGTTTCTTAATATTTTTATTTAATTATGGAC
Found at i:275354 original size:11 final size:12
Alignment explanation
Indices: 275340--275401 Score: 78
Period size: 11 Copynumber: 5.5 Consensus size: 12
275330 TCGTTAAGAA
275340 CTCGAG-TCGAG
1 CTCGAGATCGAG
275351 CTCGAGATCGAG
1 CTCGAGATCGAG
*
275363 -TCGAGCTCGAG
1 CTCGAGATCGAG
*
275374 ATCGAG-TCGAG
1 CTCGAGATCGAG
275385 CTCGAGATCGAG
1 CTCGAGATCGAG
275397 -TCGAG
1 CTCGAG
275402 TCCATTCGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
11 31 0.67
12 15 0.33
ACGTcount: A:0.23, C:0.24, G:0.35, T:0.18
Consensus pattern (12 bp):
CTCGAGATCGAG
Found at i:275363 original size:17 final size:17
Alignment explanation
Indices: 275341--275401 Score: 122
Period size: 17 Copynumber: 3.6 Consensus size: 17
275331 CGTTAAGAAC
275341 TCGAGTCGAGCTCGAGA
1 TCGAGTCGAGCTCGAGA
275358 TCGAGTCGAGCTCGAGA
1 TCGAGTCGAGCTCGAGA
275375 TCGAGTCGAGCTCGAGA
1 TCGAGTCGAGCTCGAGA
275392 TCGAGTCGAG
1 TCGAGTCGAG
275402 TCCATTCGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.23, C:0.23, G:0.36, T:0.18
Consensus pattern (17 bp):
TCGAGTCGAGCTCGAGA
Found at i:277791 original size:12 final size:12
Alignment explanation
Indices: 277774--277799 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
277764 AATTTGATGG
277774 TTATATTCGTGA
1 TTATATTCGTGA
277786 TTATATTCGTGA
1 TTATATTCGTGA
277798 TT
1 TT
277800 GATAAGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (12 bp):
TTATATTCGTGA
Found at i:278488 original size:17 final size:17
Alignment explanation
Indices: 278450--278494 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
278440 ATTTAATTAA
278450 AATATATTTAATAAGCT
1 AATATATTTAATAAGCT
*
278467 AATAT-TTT-TTAAGCT
1 AATATATTTAATAAGCT
*
278482 AATATATATAATA
1 AATATATTTAATA
278495 TTACGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 11 0.48
16 5 0.22
17 7 0.30
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (17 bp):
AATATATTTAATAAGCT
Found at i:278544 original size:3 final size:3
Alignment explanation
Indices: 278536--278614 Score: 83
Period size: 3 Copynumber: 26.7 Consensus size: 3
278526 CATCCATTTG
* *
278536 TTA TTA TTA TTA TT- TTA TTTA TTA CTA TTA TTA TT- TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
278580 -TA TTA TAA TTA TTTA TTA ATA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
278615 TACAGACCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
2 6 0.10
3 51 0.81
4 6 0.10
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:280046 original size:3 final size:3
Alignment explanation
Indices: 280038--280074 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
280028 CATATATTTA
280038 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
280075 AGTCATGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:280934 original size:27 final size:25
Alignment explanation
Indices: 280904--280959 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
280894 ATTATAATTC
280904 TTTTT-AAAAAATTATATATACTTAT
1 TTTTTCAAAAAATTATATATA-TTAT
* * *
280929 TATTTTCATATATTTATATATATTAT
1 T-TTTTCAAAAAATTATATATATTAT
280955 TTTTT
1 TTTTT
280960 ATCAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 5 0.19
26 9 0.35
27 12 0.46
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTTTCAAAAAATTATATATATTAT
Found at i:292169 original size:23 final size:23
Alignment explanation
Indices: 292141--292197 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
292131 GTGACATATT
*
292141 TCTCTGCCTTTATGACATGTTTA
1 TCTCTGCCTTTATGACACGTTTA
* * *
292164 TCTCTGTCC-TTGTGTCACGTTTT
1 TCTCTG-CCTTTATGACACGTTTA
292187 TCTCTGCCTTT
1 TCTCTGCCTTT
292198 TGGTAACTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 24 0.86
24 2 0.07
ACGTcount: A:0.09, C:0.26, G:0.14, T:0.51
Consensus pattern (23 bp):
TCTCTGCCTTTATGACACGTTTA
Found at i:293149 original size:29 final size:27
Alignment explanation
Indices: 293103--293178 Score: 75
Period size: 29 Copynumber: 2.8 Consensus size: 27
293093 TACTTTTGTT
* *
293103 TTAATAATATGTAATAATTATTAATAAAA
1 TTAATATTATTTAATAA-T-TTAATAAAA
* *
293132 TTAATATTATTTATTAATTTCATAAAA
1 TTAATATTATTTAATAATTTAATAAAA
*
293159 -TAATATTATTGAAT-ATTTAA
1 TTAATATTATTTAATAATTTAA
293179 AATATACTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 5 0.12
26 12 0.30
27 8 0.20
28 1 0.03
29 14 0.35
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (27 bp):
TTAATATTATTTAATAATTTAATAAAA
Found at i:293227 original size:8 final size:8
Alignment explanation
Indices: 293211--293260 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
293201 ATAATATTCT
293211 TATTTTAA
1 TATTTTAA
*
293219 TATTATAA
1 TATTTTAA
293227 T-TTTTAA
1 TATTTTAA
293234 TATTTTAA
1 TATTTTAA
* *
293242 TTATATTAT
1 -TATTTTAA
293251 TATTTTAA
1 TATTTTAA
293259 TA
1 TA
293261 AATAATTAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 6 0.18
8 22 0.65
9 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTTAA
Found at i:293233 original size:15 final size:15
Alignment explanation
Indices: 293213--293243 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
293203 AATATTCTTA
293213 TTTTAATATTATAAT
1 TTTTAATATTATAAT
*
293228 TTTTAATATTTTAAT
1 TTTTAATATTATAAT
293243 T
1 T
293244 ATATTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTAATATTATAAT
Found at i:293546 original size:13 final size:14
Alignment explanation
Indices: 293521--293549 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
293511 TAAATACCGT
293521 AAAATAAATTTTAA
1 AAAATAAATTTTAA
293535 AAAATAAA-TTTAA
1 AAAATAAATTTTAA
293548 AA
1 AA
293550 TTAAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATAAATTTTAA
Found at i:293580 original size:15 final size:14
Alignment explanation
Indices: 293556--293594 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
293546 AAAATTAAAT
*
293556 AATTTATTTTACGA
1 AATTTATTTTTCGA
*
293570 AATTTATTTTTCGG
1 AATTTATTTTTCGA
*
293584 AATCTATTTTT
1 AATTTATTTTT
293595 TAAAAACTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (14 bp):
AATTTATTTTTCGA
Found at i:300877 original size:160 final size:161
Alignment explanation
Indices: 300696--301014 Score: 505
Period size: 162 Copynumber: 2.0 Consensus size: 161
300686 TACTTATAAT
* * *
300696 AAAGTATCGACATTTTCAACATATTCGGTACCTCTTTACCGGTTTTGTCATTTCG-ACCGATTTT
1 AAAGTATCGACATTATCAACATATTCGATACCTCTTTACCGGTTTTATCATTTCGAACCGATTTT
* *
300760 GTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTTTATT
66 GTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATAGACACTTTATT
300825 AGCACTATAACTTATTCTCTTTTAAATTCAA
131 AGCACTATAACTTATTCTCTTTTAAATTCAA
* *
300856 AAAGTATCGACATTATCAACATATTCGATAGCTCTTTACTGGTTTTATCATTTCGAAACCGATTT
1 AAAGTATCGACATTATCAACATATTCGATACCTCTTTACCGGTTTTATCATTTCG-AACCGATTT
* * *
300921 TGTCATATTTTTACCTGTTATATTGTTATGGATTGATACATTTTTATAAAGTATATACACTTTAT
65 TGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATAGACACTTTAT
* * *
300986 TAGCGCTATAACTTCTTTTCTTTTAAATT
130 TAGCACTATAACTTATTCTCTTTTAAATT
301015 TTAAAAGTGT
Statistics
Matches: 144, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
160 50 0.35
162 94 0.65
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.45
Consensus pattern (161 bp):
AAAGTATCGACATTATCAACATATTCGATACCTCTTTACCGGTTTTATCATTTCGAACCGATTTT
GTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATAGACACTTTATT
AGCACTATAACTTATTCTCTTTTAAATTCAA
Found at i:301122 original size:20 final size:20
Alignment explanation
Indices: 301071--301123 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
301061 TCCGATAACG
301071 TTTTACCTGTTTTGTCATTT
1 TTTTACCTGTTTTGTCATTT
* ** *
301091 ATAGACCGGTTTTGTCATTT
1 TTTTACCTGTTTTGTCATTT
*
301111 TTTTACATGTTTT
1 TTTTACCTGTTTT
301124 ATTGTTATAG
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.58
Consensus pattern (20 bp):
TTTTACCTGTTTTGTCATTT
Found at i:301387 original size:111 final size:112
Alignment explanation
Indices: 301036--301497 Score: 687
Period size: 112 Copynumber: 4.1 Consensus size: 112
301026 GATACTTATA
* * *
301036 ATAAAGTATCGACACTATCAACAAATCCGATAACGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
301101 TTTGTCATTTTTTT-ACATGTTTTATTGTTATAGATCGATATATTTTT
66 TTTGTCATTTTTTTAAC-TGTTATATTGTTATAGATCAATACATTTTT
*
301148 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
301213 TTTGTCATTTTTTTAACTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTAACTGTTATATTGTTATAGATCAATACATTTTT
* * * *
301260 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACC-GT
1 ATAAAGTATCGACACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
301324 TTTGTCATTTTTTTACCTATTATATTGTTAT-GAATTAATACATTTTT
66 TTTGTCATTTTTTTAACTGTTATATTGTTATAG-ATCAATACATTTTT
* * *
301371 ATAAAGTATCGACACTTTCAATATATCCGGTAACGCTTTACCTGTTTTGTCATTTATATACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
301436 TTTGTCATTTTTTTAACTGTTATATTATTATAGATTAATATATTTTT
66 TTTGTCATTTTTTTAACTGTTATATTGTTATAGATCAATACATTTTT
301483 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
301498 AAACCGACAA
Statistics
Matches: 325, Mismatches: 21, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
110 1 0.00
111 102 0.31
112 219 0.67
113 3 0.01
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTAACTGTTATATTGTTATAGATCAATACATTTTT
Found at i:301412 original size:223 final size:224
Alignment explanation
Indices: 301036--301497 Score: 703
Period size: 223 Copynumber: 2.1 Consensus size: 224
301026 GATACTTATA
*
301036 ATAAAGTATCGACACTATCAACAAATCCGATAACGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACAAATCCGATAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
301101 TTTGTCATTTTTTTACATGTTTTATTGTTATAGATCGATATATTTTTATAAAGTATCGACACTAT
66 TTTGTCATTTTTTTACATATTATATTGTTATAGATCAATACATTTTTATAAAGTATCGACACTAT
*
301166 CAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTAACT
131 CAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTAACT
* * *
301231 GTTATATTGTTATGGATCGATACATTTTT
196 GTTATATTATTATAGATCAATACATTTTT
* * * * * *
301260 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACC-GT
1 ATAAAGTATCGACACTATCAACAAATCCGATAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
301324 TTTGTCATTTTTTTACCTATTATATTGTTAT-GAATTAATACATTTTTATAAAGTATCGACACTT
66 TTTGTCATTTTTTTACATATTATATTGTTATAG-ATCAATACATTTTTATAAAGTATCGACACTA
* *
301388 TCAATATATCCGGTAACGCTTTACCTGTTTTGTCATTTATATACCGGTTTTGTCATTTTTTTAAC
130 TCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTAAC
* *
301453 TGTTATATTATTATAGATTAATATATTTTT
195 TGTTATATTATTATAGATCAATACATTTTT
301483 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
301498 AAACCGACAA
Statistics
Matches: 215, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
222 1 0.00
223 159 0.74
224 55 0.26
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (224 bp):
ATAAAGTATCGACACTATCAACAAATCCGATAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACATATTATATTGTTATAGATCAATACATTTTTATAAAGTATCGACACTAT
CAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTAACT
GTTATATTATTATAGATCAATACATTTTT
Found at i:302151 original size:20 final size:20
Alignment explanation
Indices: 302126--302219 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
302116 AATTGGAAAA
302126 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
302146 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
302166 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
302187 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
302207 TTCGCAACGCGAT
1 ATCGCAATGCGAT
302220 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:302840 original size:33 final size:33
Alignment explanation
Indices: 302794--302876 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
302784 GAAACCAAAA
*
302794 TCGCATTGCGATTCTCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTCTCTCGTCGCGATAGTCATT
* *
302827 TCGCGTTGTGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCTCGTCGCGATAGTCATT
*
302860 TCCGCGTTACGATTCTC
1 T-CGCGTTGCGATTCTC
302877 ATTATCTCGT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 31 0.70
34 13 0.30
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.39
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTCGCGATAGTCATT
Found at i:302878 original size:20 final size:20
Alignment explanation
Indices: 302855--302901 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
302845 GTTGCGATAG
302855 TCATTTCCGCGTTACGATTC
1 TCATTTCCGCGTTACGATTC
* * *
302875 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTACGATTC
302895 TCATTTC
1 TCATTTC
302902 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTACGATTC
Found at i:305071 original size:21 final size:21
Alignment explanation
Indices: 305047--305113 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
305037 TCATTCCTCG
305047 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
305068 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
305089 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
305110 AGAG
1 AGAG
305114 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:305071 original size:42 final size:42
Alignment explanation
Indices: 304995--305113 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
304985 GACTCGCCTG
* * * * * * *
304995 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
305037 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
305079 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
305114 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:306482 original size:14 final size:14
Alignment explanation
Indices: 306463--306498 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
306453 ATTGTTTAAT
306463 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
306477 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
306491 TGATTTGT
1 TGATTTGT
306499 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:306661 original size:19 final size:19
Alignment explanation
Indices: 306613--306668 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
306603 CTATCACAAT
306613 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
*
306631 -CG--A-GAGAATCGCAAC
1 GCGAAATGAAAATCGCAAC
306646 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
306665 GCGA
1 GCGA
306669 TTCCCTCGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 10 0.32
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 15 0.48
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.09
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:306726 original size:19 final size:19
Alignment explanation
Indices: 306704--306768 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
306694 CATTATGAAA
*
306704 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
306723 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
306738 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
306756 TTCGCATTGCGAT
1 TTCGCATTGCGAT
306769 AGTAATTTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:309068 original size:12 final size:12
Alignment explanation
Indices: 309051--309075 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
309041 TCTTCGGGGA
309051 CTTTTTCTTCTT
1 CTTTTTCTTCTT
309063 CTTTTTCTTCTT
1 CTTTTTCTTCTT
309075 C
1 C
309076 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:310118 original size:20 final size:20
Alignment explanation
Indices: 310039--310126 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
310029 TATTATCTCT
* *
310039 TTGCGAAAGTCAGAATCGCA
1 TTGCGATAGTCAGTATCGCA
*
310059 TTGCGAAAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
* * *
310079 TTGCAATTTTGT-ATTATCGCA
1 TTGCGA--TAGTCAGTATCGCA
310100 TTGCGATAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
310120 TTGCGAT
1 TTGCGAT
310127 TTTCCCAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
19 3 0.05
20 39 0.68
21 13 0.23
22 2 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGTATCGCA
Found at i:310145 original size:41 final size:41
Alignment explanation
Indices: 310053--310147 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
310043 GAAAGTCAGA
* ** *
310053 ATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTGTATT
1 ATCGCATTGCGATAGTCAGTATCGCATTGCAATTTTCCAAT
*
310094 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCATTGCGATAGTCAGTATCGCATTGCAATTTT-CCAAT
*
310136 -TCGCGTTGCGAT
1 ATCGCATTGCGAT
310148 TTACTTATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATAGTCAGTATCGCATTGCAATTTTCCAAT
Found at i:310576 original size:13 final size:13
Alignment explanation
Indices: 310560--310611 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
310550 TGTTTTTTAA
310560 TTTTTATTAAATT
1 TTTTTATTAAATT
310573 TTTTTATTAAGATCT
1 TTTTTATTAA-AT-T
** *
310588 TCATTATTAAAGT
1 TTTTTATTAAATT
310601 TTTTTATTAAA
1 TTTTTATTAAA
310612 ATATTTTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 20 0.62
14 3 0.09
15 9 0.28
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (13 bp):
TTTTTATTAAATT
Found at i:310618 original size:13 final size:13
Alignment explanation
Indices: 310560--310619 Score: 57
Period size: 13 Copynumber: 4.4 Consensus size: 13
310550 TGTTTTTTAA
*
310560 TTTTTATTAAATT
1 TTTTTATTAAAAT
*
310573 TTTTTATTAAGAT
1 TTTTTATTAAAAT
* *
310586 CTTCATTATTAAAGT
1 -TT-TTTATTAAAAT
310601 TTTTTATTAAAAT
1 TTTTTATTAAAAT
310614 ATTTTT
1 -TTTTT
310620 CATTTATTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
13 20 0.54
14 9 0.24
15 8 0.22
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (13 bp):
TTTTTATTAAAAT
Found at i:312855 original size:20 final size:20
Alignment explanation
Indices: 312827--312880 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
312817 AATTAAGTAT
*
312827 GGTATCGATACCCCCTACAG
1 GGTACCGATACCCCCTACAG
*
312847 GGTACCGATACCCCCTATAG
1 GGTACCGATACCCCCTACAG
312867 GGTACCGATACCCC
1 GGTACCGATACCCC
312881 TGTGAACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.24, C:0.37, G:0.20, T:0.19
Consensus pattern (20 bp):
GGTACCGATACCCCCTACAG
Found at i:312966 original size:22 final size:21
Alignment explanation
Indices: 312916--312995 Score: 103
Period size: 20 Copynumber: 3.9 Consensus size: 21
312906 ACCGAATGCT
312916 TGAATGGTATCGATA-CCCTCA
1 TGAATGGTATCGATACCCCT-A
*
312937 -CAATGGTATCGATACCCCTA
1 TGAATGGTATCGATACCCCTA
312957 TGTAATGGTATCGATACCCCTA
1 TG-AATGGTATCGATACCCCTA
*
312979 TG-ATGGTACCGATACCC
1 TGAATGGTATCGATACCC
312996 TAAGGCATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
20 28 0.53
21 4 0.08
22 21 0.40
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
TGAATGGTATCGATACCCCTA
Found at i:315948 original size:33 final size:33
Alignment explanation
Indices: 315899--315967 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
315889 TTTACTAAAC
* *
315899 TTACTATTAAATAATCATTTCCTCCACTACACA
1 TTACCATTAAACAATCATTTCCTCCACTACACA
* *
315932 TTACCATTAAACAATCATTTTCTCCACTACCCA
1 TTACCATTAAACAATCATTTCCTCCACTACACA
315965 TTA
1 TTA
315968 AATAAATTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.36
Consensus pattern (33 bp):
TTACCATTAAACAATCATTTCCTCCACTACACA
Found at i:319327 original size:19 final size:19
Alignment explanation
Indices: 319303--319340 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
319293 ATTAACAGAC
*
319303 TATTCTGCATAATAAAGTA
1 TATTCTACATAATAAAGTA
319322 TATTCTACATAATAAAGTA
1 TATTCTACATAATAAAGTA
319341 AAGGCCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (19 bp):
TATTCTACATAATAAAGTA
Found at i:319379 original size:25 final size:21
Alignment explanation
Indices: 319334--319375 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
319324 TTCTACATAA
319334 TAAAGTAAAGGCCATGTATAT
1 TAAAGTAAAGGCCATGTATAT
319355 TAAAGTAAAGGCCATGTATAT
1 TAAAGTAAAGGCCATGTATAT
319376 ATATGGATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
TAAAGTAAAGGCCATGTATAT
Found at i:325755 original size:23 final size:22
Alignment explanation
Indices: 325725--325806 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
325715 GCATGACCCA
325725 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * **
325747 CGTGCATCGGTGCATAAGCAA-G
1 -GTGCATCGATGCACATTCAAGG
* *
325769 ATGAATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
325792 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
325807 TGTTAAGTGA
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
21 12 0.27
22 3 0.07
23 17 0.39
24 12 0.27
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:325818 original size:44 final size:42
Alignment explanation
Indices: 325706--325825 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 42
325696 ACCCGACTGA
* * *
325706 TGCATCGATGCATGACCCAGTGCATCGATGCACATTCAAGGCG
1 TGCATCGATGCAT-AGCAAGTGAATCGATGCACATTCAAGGCG
*
325749 TGCATCGGTGCATAAGCAAGATGAATCGATGCACATTCAAAGG-G
1 TGCATCGATGCAT-AGCAAG-TGAATCGATGCACATTC-AAGGCG
*
325793 ATGCATCGATGCACT-GTTAAGTGAATCGATGCA
1 -TGCATCGATGCA-TAG-CAAGTGAATCGATGCA
325826 TTAAGCACAA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
43 16 0.25
44 30 0.46
45 18 0.28
46 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.23
Consensus pattern (42 bp):
TGCATCGATGCATAGCAAGTGAATCGATGCACATTCAAGGCG
Found at i:329669 original size:22 final size:21
Alignment explanation
Indices: 329627--329666 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
329617 GAGTTTATTT
*
329627 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
329648 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
329667 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:331672 original size:20 final size:20
Alignment explanation
Indices: 331647--331726 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
331637 AAAAGCCTGA
331647 GTGCATCGATGCATGGTCTT
1 GTGCATCGATGCATGGTCTT
** *
331667 GTGCATCGATGCATCAAATGCACTAA
1 GTGCATCGATG---C--ATGGTCT-T
*
331693 ATGCATCGATGCATGGTCTT
1 GTGCATCGATGCATGGTCTT
331713 GTGCATCGATGCAT
1 GTGCATCGATGCAT
331727 CAAATGCACT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
20 24 0.52
21 5 0.11
23 2 0.04
25 5 0.11
26 10 0.22
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATGGTCTT
Found at i:331701 original size:46 final size:46
Alignment explanation
Indices: 331648--331779 Score: 221
Period size: 46 Copynumber: 2.9 Consensus size: 46
331638 AAAGCCTGAG
331648 TGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTAAA
1 TGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTAAA
*
331694 TGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTAAG
1 TGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTAAA
* * *
331740 TGCATCGATGCATGAT-ATGTGCATCGATGCATAAAATGCA
1 TGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
331780 TTCGATGTTC
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 22 0.27
46 60 0.73
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (46 bp):
TGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTAAA
Found at i:332192 original size:31 final size:31
Alignment explanation
Indices: 332156--332227 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
332146 TGAAGAAATA
* *
332156 AATGAAAAATACTTTATTAAAAAACTTTAAT
1 AATGAAAAATACCTTAATAAAAAACTTTAAT
* *
332187 AATGAAAAAGACCTTAATAGAAAACTTTAAT
1 AATGAAAAATACCTTAATAAAAAACTTTAAT
*
332218 AA-AAAAAATA
1 AATGAAAAATA
332228 AAAAGACATC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 6 0.17
31 29 0.83
ACGTcount: A:0.60, C:0.07, G:0.06, T:0.28
Consensus pattern (31 bp):
AATGAAAAATACCTTAATAAAAAACTTTAAT
Found at i:332461 original size:13 final size:13
Alignment explanation
Indices: 332439--332502 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 13
332429 GAAATAAATG
332439 AAAAATACTTTAAT
1 AAAAA-ACTTTAAT
332453 AAAAAACTTTAATAAT
1 AAAAAAC-TT--TAAT
*
332469 AAAAAAGACCTTAAT
1 -AAAAA-ACTTTAAT
*
332484 AGAAAACTTTAAT
1 AAAAAACTTTAAT
332497 AAAAAA
1 AAAAAA
332503 TAAAAAGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
13 14 0.34
14 11 0.27
15 4 0.10
16 4 0.10
17 6 0.15
18 2 0.05
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (13 bp):
AAAAAACTTTAAT
Found at i:332483 original size:31 final size:30
Alignment explanation
Indices: 332439--332502 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
332429 GAAATAAATG
* *
332439 AAAAATACTTTAATAAAAAACTTTAATAATA
1 AAAAAGACCTTAATAAAAAACTTTAATAA-A
*
332470 AAAAAGACCTTAATAGAAAACTTTAATAAA
1 AAAAAGACCTTAATAAAAAACTTTAATAAA
332500 AAA
1 AAA
332503 TAAAAAGACA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (30 bp):
AAAAAGACCTTAATAAAAAACTTTAATAAA
Found at i:332650 original size:77 final size:78
Alignment explanation
Indices: 332522--332673 Score: 238
Period size: 77 Copynumber: 2.0 Consensus size: 78
332512 ATCATTATTT
332522 CATAATGATACAAAACTTTAATAAAAAATAGAAAAAATAGAATGATAAAAAAATGGTAGCTTTAA
1 CATAATGATACAAAACTTTAATAAAAAATAGAAAAAATAGAATGATAAAAAAATGGTAGCTTTAA
332587 TAAAAGATTTGGA
66 TAAAAGATTTGGA
* *
332600 CATAATGATA-AAAATCTTTAA-AAAAAAT-GAAAAAAATATAATGATAAAAAAATGGTAGGTTT
1 CATAATGATACAAAA-CTTTAATAAAAAATAG-AAAAAATAGAATGATAAAAAAATGGTAGCTTT
*
332662 AGTAAAAGATTT
64 AATAAAAGATTT
332674 TGTATATTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
76 1 0.01
77 52 0.75
78 16 0.23
ACGTcount: A:0.57, C:0.04, G:0.12, T:0.27
Consensus pattern (78 bp):
CATAATGATACAAAACTTTAATAAAAAATAGAAAAAATAGAATGATAAAAAAATGGTAGCTTTAA
TAAAAGATTTGGA
Found at i:333649 original size:3 final size:3
Alignment explanation
Indices: 333641--333684 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
333631 CTAATTATAT
*
333641 TTA TTA TTA ATA -TA TATA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
333685 CAAATAATAC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:333660 original size:15 final size:14
Alignment explanation
Indices: 333636--333678 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
333626 CGATACTAAT
333636 TATATTTATTATTAA
1 TATA-TTATTATTAA
*
333651 TATATATATTATTAT
1 TATAT-TATTATTAA
333666 TATATTATTATTA
1 TATATTATTATTA
333679 TTATTACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATATTATTATTAA
Found at i:333670 original size:17 final size:17
Alignment explanation
Indices: 333636--333684 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
333626 CGATACTAAT
333636 TATAT-TTATTATTAATA
1 TATATATTATTATT-ATA
333653 TATATATTATTATTATA
1 TATATATTATTATTATA
333670 T-TATTATTATTATTA
1 TATA-TATTATTATTA
333685 CAAATAATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.07
17 20 0.67
18 8 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATATTATTATTATA
Found at i:340525 original size:8 final size:8
Alignment explanation
Indices: 340512--340579 Score: 54
Period size: 8 Copynumber: 8.9 Consensus size: 8
340502 CTCATCCATC
*
340512 AAAAAAAT
1 AAAAAAAG
*
340520 AAAAAAAT
1 AAAAAAAG
*
340528 AAGAAAAG
1 AAAAAAAG
340536 AAAGAAAA-
1 AAA-AAAAG
*
340544 AGAAAAAG
1 AAAAAAAG
340552 AAAAAAAG
1 AAAAAAAG
340560 ---AAAAG
1 AAAAAAAG
*
340565 AAAAGAAG
1 AAAAAAAG
340573 AAAAAAA
1 AAAAAAA
340580 ATTGAATCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
5 5 0.10
7 4 0.08
8 35 0.73
9 4 0.08
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:340558 original size:24 final size:23
Alignment explanation
Indices: 340522--340578 Score: 53
Period size: 25 Copynumber: 2.3 Consensus size: 23
340512 AAAAAAATAA
*
340522 AAAAATAAGAAAAG-AAAGAAAA
1 AAAAAAAAGAAAAGAAAAGAAAA
*
340544 AGAAAAAGAAAAAAAGAAAAGAAAA
1 A-AAAAA-AAGAAAAGAAAAGAAAA
340569 GAAGAAAAAA
1 -AA-AAAAAA
340579 AATTGAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 1 0.04
23 4 0.14
24 7 0.25
25 11 0.39
26 5 0.18
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAAAAAAGAAAAGAAAAGAAAA
Found at i:340560 original size:29 final size:31
Alignment explanation
Indices: 340512--340580 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
340502 CTCATCCATC
*
340512 AAAAAAATAAAAAAATAAGAAAAG-AAAGAA-
1 AAAAAAA-AGAAAAATAAGAAAAGAAAAGAAG
340542 AAAGAAAAAGAAAAA-AAGAAAAGAAAAGAAG
1 AAA-AAAAAGAAAAATAAGAAAAGAAAAGAAG
340573 AAAAAAAA
1 AAAAAAAA
340581 TTGAATCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 8 0.23
30 20 0.57
31 7 0.20
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (31 bp):
AAAAAAAAGAAAAATAAGAAAAGAAAAGAAG
Found at i:340579 original size:24 final size:24
Alignment explanation
Indices: 340522--340580 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
340512 AAAAAAATAA
* *
340522 AAAAATAAGAAAAGAAAGAAAAAG
1 AAAAAGAAAAAAAGAAAGAAAAAG
340546 AAAAAGAAAAAAAGAAA-AGAAAAG
1 AAAAAGAAAAAAAGAAAGA-AAAAG
*
340570 AAGAA-AAAAAA
1 AAAAAGAAAAAA
340581 TTGAATCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.23
24 24 0.77
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAAAGAAAAAAAGAAAGAAAAAG
Found at i:343797 original size:42 final size:42
Alignment explanation
Indices: 343738--343819 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
343728 CAAAAATTTG
* *
343738 TAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCATGATGTC
1 TAAATCATTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGTC
* *
343780 TAAATCATTCGGGTCATCTGTTAGTCTTTCGAGCAAGATG
1 TAAATCATTCGGGTCATCTGTAAGTCTTTAGAGCAAGATG
343820 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (42 bp):
TAAATCATTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGTC
Found at i:344070 original size:248 final size:249
Alignment explanation
Indices: 343657--344585 Score: 1384
Period size: 249 Copynumber: 3.7 Consensus size: 249
343647 TTTTCCAAAG
* *
343657 TTTCTCATTTAATCTTTTCT-AAAAATGAAATTTTTG-AAAGTAAGAAGCTTCTTACCCAGTAAA
1 TTTCTCATTTAA--TGTTCTAAAAAATGAAATTTTTGAAAAGTAAGAAGTTTCTTACCCAGTAAA
343720 TTATTTCCCAAAAATTTGTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCATGATGTCTAAAT
64 TTATTTCCCAAAAATTTGTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCATGATGTCTAAAT
* * *
343785 CATTCGGGTCATCTGTTAGTCTTTCGAGCAAGATGATAAGTCCTTAGGG-CATCCGTCAAACCTT
129 CCTTCGGGTCATCTATTAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTT
* *
343849 TGGGTAGGATGTTTACATATGATTTTCGCATGAAAATGAGAAAGCGATTTTTTAAG
194 TGGGTAGGATGTTTACATATGATTTTCGCATGAAAATGAGAAAGCGATTTTTAAAA
343905 TTTCTCATTTAATGTTCTAAAAAATGAAATTTTTGAAAAGTAAGAAGTTTCTTACCCAGTAAATT
1 TTTCTCATTTAATGTTCTAAAAAATGAAATTTTTGAAAAGTAAGAAGTTTCTTACCCAGTAAATT
* *
343970 ATTTCCCACAAATTTGTAAATTCTTCGGGTCATCTGTAAGTCTTTAGAGCATGATGTCTAAATCC
66 ATTTCCCAAAAATTTGTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCATGATGTCTAAATCC
* * *
344035 TTCGAGTCATCTGTTAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATACGTCAAACCTTTG
131 TTCGGGTCATCTATTAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTG
* * *
344100 GGTAGGATGTTTACATGTGATTTTCACATGAAAATGAGAAAGCGATTTTTGAAA
196 GGTAGGATGTTTACATATGATTTTCGCATGAAAATGAGAAAGCGATTTTTAAAA
* * *
344154 TTTCTCATTTAATGTTCTATAAAATGCAATTTTTGAAAAGTAAGAAGTTTCTTACCTAGTAAATT
1 TTTCTCATTTAATGTTCTAAAAAATGAAATTTTTGAAAAGTAAGAAGTTTCTTACCCAGTAAATT
* * * *
344219 ATCTCCAAAAAATTTGTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATG-CTTAAATC
66 ATTTCCCAAAAATTTGTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCATGATGTC-TAAATC
* * * * * *
344283 CTTCGGGTCATCTATAAGCCTTTCGAGCCAGATGACAAGTCCTTAGGGTCATCCGTCAAACCTTT
130 CTTCGGGTCATCTATTAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTT
* *
344348 GGGTAGGATGTTTACATATGATTTTCGCATGAAAATGAGAAAGCAATTTTCAAAA
195 GGGTAGGATGTTTACATATGATTTTCGCATGAAAATGAGAAAGCGATTTTTAAAA
* * * *
344403 TTTCTCATTTAATGTTTTAGAAAATGAAATTTTTGAAAAGTAAAAAGTTTCTTACCTAGTAAATT
1 TTTCTCATTTAATGTTCTAAAAAATGAAATTTTTGAAAAGTAAGAAGTTTCTTACCCAGTAAATT
* * * * *
344468 ATTTCCCACAAATTTGTAAATCCTTCGGGTCATTTGTCAA-TCTTTCGAGCCA-AATGTTTAAAT
66 ATTTCCCAAAAATTTGTAAATCCTTCGGGTCATCTGT-AAGTCTTTAGAG-CATGATGTCTAAAT
* * *
344531 CCTTAGGGTCATTTATTAGTCTTTCAAGCAAAATGAATAAGTCCTTAGGGCCATC
129 CCTTCGGGTCATCTATTAGTCTTTCAAGCAAGATG-ATAAGTCCTTAGGGCCATC
344586 TGTAAGACCT
Statistics
Matches: 618, Mismatches: 55, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
246 5 0.01
247 16 0.03
248 148 0.24
249 429 0.69
250 20 0.03
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (249 bp):
TTTCTCATTTAATGTTCTAAAAAATGAAATTTTTGAAAAGTAAGAAGTTTCTTACCCAGTAAATT
ATTTCCCAAAAATTTGTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCATGATGTCTAAATCC
TTCGGGTCATCTATTAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTG
GGTAGGATGTTTACATATGATTTTCGCATGAAAATGAGAAAGCGATTTTTAAAA
Found at i:344540 original size:42 final size:42
Alignment explanation
Indices: 344476--344580 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 42
344466 TTATTTCCCA
* * *
344476 CAAAT-TTGTAAATCCTTCGGGTCATTTGTCAATCTTTCGAGC
1 CAAATGTT-TAAATCCTTAGGGTCATTTATCAATCTTTCAAGC
* *
344518 CAAATGTTTAAATCCTTAGGGTCATTTATTAGTCTTTCAAGC
1 CAAATGTTTAAATCCTTAGGGTCATTTATCAATCTTTCAAGC
* ** *
344560 AAAATGAATAAGTCCTTAGGG
1 CAAATGTTTAAATCCTTAGGG
344581 CCATCTGTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 51 0.96
43 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (42 bp):
CAAATGTTTAAATCCTTAGGGTCATTTATCAATCTTTCAAGC
Found at i:344762 original size:3 final size:3
Alignment explanation
Indices: 344754--344794 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
344744 CTAATTATAT
* *
344754 TTA TTA TTA ATA CTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
344795 CAAATAAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:344905 original size:17 final size:17
Alignment explanation
Indices: 344883--344917 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
344873 TACAAGATCA
*
344883 ACCTGGTCTAGGCCCAG
1 ACCTGGTCTAAGCCCAG
*
344900 ACCTGGTTTAAGCCCAG
1 ACCTGGTCTAAGCCCAG
344917 A
1 A
344918 TGGCCCAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (17 bp):
ACCTGGTCTAAGCCCAG
Found at i:346182 original size:62 final size:62
Alignment explanation
Indices: 346116--346275 Score: 257
Period size: 62 Copynumber: 2.6 Consensus size: 62
346106 AAATAATGAC
* * * *
346116 TAATTAAAATAATAATAAAAACCCATAGTGCTATTATTATTAATGAAAAGGTAGAAGCATTA
1 TAATTAAAATAATAATAAAAACCCATAGTGCTATCATTATTAATAAAAAGATAGAAGCATCA
**
346178 TAATTAAAATAATAATAAAAACTAATAGTGCTATCATTATTAATAAAAAGATAGAAGCATCA
1 TAATTAAAATAATAATAAAAACCCATAGTGCTATCATTATTAATAAAAAGATAGAAGCATCA
*
346240 TAATTAAAATAATAATAAAAACCCATAGTACTATCA
1 TAATTAAAATAATAATAAAAACCCATAGTGCTATCA
346276 CATATGTATA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 89 1.00
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.29
Consensus pattern (62 bp):
TAATTAAAATAATAATAAAAACCCATAGTGCTATCATTATTAATAAAAAGATAGAAGCATCA
Found at i:346444 original size:9 final size:9
Alignment explanation
Indices: 346430--346462 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
346420 TATCTTATGC
346430 TAATTAATT
1 TAATTAATT
346439 TAATTAATT
1 TAATTAATT
*
346448 TTA-TAATT
1 TAATTAATT
346456 TAATTAA
1 TAATTAA
346463 AGAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:347477 original size:18 final size:18
Alignment explanation
Indices: 347439--347472 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
347429 AAGTTTATCT
347439 TTTTAATTAAAATTAATA
1 TTTTAATTAAAATTAATA
347457 TTTT-ATTAAAA-TAATA
1 TTTTAATTAAAATTAATA
347473 AATTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 7 0.44
18 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTAATTAAAATTAATA
Found at i:357190 original size:42 final size:42
Alignment explanation
Indices: 357131--357213 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
357121 GGCGGAATGA
357131 CAACGTGGCATGGGTCTGGGCAAGGTTGGAGTCTCTGCATGT
1 CAACGTGGCATGGGTCTGGGCAAGGTTGGAGTCTCTGCATGT
*
357173 CAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCTGCATG
1 CAACGTGGCATGGGTCTGGGCAAGGTTGGAGTCTCTGCATG
357214 GCTGTGCATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.16, C:0.19, G:0.40, T:0.25
Consensus pattern (42 bp):
CAACGTGGCATGGGTCTGGGCAAGGTTGGAGTCTCTGCATGT
Found at i:358506 original size:29 final size:29
Alignment explanation
Indices: 358408--358541 Score: 124
Period size: 29 Copynumber: 4.5 Consensus size: 29
358398 GACGCCGGCA
* *
358408 TGCATGGCGACCTATAAGGTCGCTGGGCG
1 TGCATGGCGACCTACAAGGTCGCTGGGAG
* * * *
358437 TACATGGCGACCTACCATCTTGGTCGCCGGGAT
1 TGCATGGCGACCTA-CA---AGGTCGCTGGGAG
*
358470 TGCTTGGCGACCTACAAGGTCGCTGGGAG
1 TGCATGGCGACCTACAAGGTCGCTGGGAG
*** *
358499 TGCATGGCGACCTTGTAGGTCGCTTGGAG
1 TGCATGGCGACCTACAAGGTCGCTGGGAG
*
358528 TGCTTGGCGACCTA
1 TGCATGGCGACCTA
358542 TGGTTGGGTT
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
29 59 0.71
30 1 0.01
32 2 0.02
33 21 0.25
ACGTcount: A:0.16, C:0.25, G:0.34, T:0.24
Consensus pattern (29 bp):
TGCATGGCGACCTACAAGGTCGCTGGGAG
Found at i:358509 original size:62 final size:61
Alignment explanation
Indices: 358395--358511 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 61
358385 TGGCCCAACG
* *
358395 TTGGACGCCGGCATGCATGGCGACCTATAAGGTCGCTGGGCGTACATGGCGACCTACCATC
1 TTGGACGCCGGCATGCATGGCGACCTACAAGGTCGCTGGGAGTACATGGCGACCTACCATC
* * * *
358456 TTGGTCGCCGGGATTGCTTGGCGACCTACAAGGTCGCTGGGAGTGCATGGCGACCT
1 TTGGACGCCGGCA-TGCATGGCGACCTACAAGGTCGCTGGGAGTACATGGCGACCT
358512 TGTAGGTCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
61 11 0.22
62 38 0.78
ACGTcount: A:0.17, C:0.27, G:0.34, T:0.21
Consensus pattern (61 bp):
TTGGACGCCGGCATGCATGGCGACCTACAAGGTCGCTGGGAGTACATGGCGACCTACCATC
Found at i:359472 original size:60 final size:59
Alignment explanation
Indices: 359345--359532 Score: 175
Period size: 60 Copynumber: 3.1 Consensus size: 59
359335 TCACACTACT
* * * * * * * *
359345 CAAATTATGATCTCCATTTTAAATAAGTTCTT-AAACTTTTAATTATTTCAATTTTATCTT
1 CAAACTATGATCTTCATTCTAAATTA-CTCTTCAAACTTTTAA-AATTTCAATTTCATCTC
* * * *
359405 TAGACTATGA-CTTTCTTTCTAAATTACTCTTCAAACTTTTGAACATTTCAATTTCATCTC
1 CAAACTATGATC-TTCATTCTAAATTACTCTTCAAACTTTT-AAAATTTCAATTTCATCTC
**
359465 CAAACTATGATCTTCATTCTAAATTACTCCCCAAACTTTTTTAAAATTTCAATTTCATC-C
1 CAAACTATGATCTTCATTCTAAATTACTCTTCAAAC--TTTTAAAATTTCAATTTCATCTC
359525 CAAACTAT
1 CAAACTAT
359533 ACGTATATAC
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
59 5 0.05
60 77 0.73
61 19 0.18
62 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.44
Consensus pattern (59 bp):
CAAACTATGATCTTCATTCTAAATTACTCTTCAAACTTTTAAAATTTCAATTTCATCTC
Found at i:362301 original size:19 final size:18
Alignment explanation
Indices: 362273--362308 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
362263 TTTCACTAAT
*
362273 AGAGGAAATATTACAAAG
1 AGAGGAAATAATACAAAG
362291 AGAGAGAAATAATACAAA
1 AGAG-GAAATAATACAAA
362309 TAACCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.61, C:0.06, G:0.19, T:0.14
Consensus pattern (18 bp):
AGAGGAAATAATACAAAG
Found at i:378092 original size:20 final size:21
Alignment explanation
Indices: 378067--378107 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
378057 TTTTACCCCA
378067 GTTCAT-ACAATATCGATATT
1 GTTCATCACAATATCGATATT
*
378087 GTTCATCCCAATATCGATATT
1 GTTCATCACAATATCGATATT
378108 TTGGTTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (21 bp):
GTTCATCACAATATCGATATT
Found at i:382514 original size:18 final size:18
Alignment explanation
Indices: 382491--382538 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
382481 CTAAAATTGA
* *
382491 TATCGATACTAGGGTCAG
1 TATCGATACTAAGGCCAG
382509 TATCGATACCCTAAGGCCAG
1 TATCGATA--CTAAGGCCAG
382529 TATCGATACT
1 TATCGATACT
382539 TACAAGCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 10 0.38
20 16 0.62
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (18 bp):
TATCGATACTAAGGCCAG
Found at i:385113 original size:2 final size:2
Alignment explanation
Indices: 385106--385141 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
385096 CCATCTATTC
385106 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
385142 TAAAAGCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:386411 original size:26 final size:26
Alignment explanation
Indices: 386375--386427 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
386365 CCTGCCACTT
386375 CCAGTTTTGATCCGCTTTGAGAGGTC
1 CCAGTTTTGATCCGCTTTGAGAGGTC
386401 CCAGTTTTGATCCGCTTTGAGAGGTC
1 CCAGTTTTGATCCGCTTTGAGAGGTC
386427 C
1 C
386428 AAATCAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.25, G:0.26, T:0.34
Consensus pattern (26 bp):
CCAGTTTTGATCCGCTTTGAGAGGTC
Found at i:390306 original size:29 final size:29
Alignment explanation
Indices: 390243--390322 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
390233 CTCATCTAAC
390243 TAAATTGATGTAAGCAAT---ATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
390270 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
390299 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
390323 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.27
27 4 0.08
29 31 0.65
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:395019 original size:158 final size:153
Alignment explanation
Indices: 394703--395019 Score: 564
Period size: 158 Copynumber: 2.0 Consensus size: 153
394693 CACTTAGAGC
394703 TCTTAATTTTAATTGATGCTTAAAACTAAATGGGAATGAGTATACTACTCAAGAACAATCCTACA
1 TCTTAATTTTAATTGATGCTTAAAACTAAATGGGAATGAGTATACTACTCAAGAACAATCCTACA
394768 CCACACAAATAAAAACTAATTTAAACCATTAAAGTCACAAATACCTAAATCTCATCTAACTAAAT
66 CCACACAAATAAAAACTAATTTAAACCATTAAAGTCACAAATACCTAAATCTCATCTAACTAAAT
394833 TGATGTAAGCAATGACATCATTA
131 TGATGTAAGCAATGACATCATTA
394856 TCTTAATTTTAATTGATGCTTAAAACTAAAATGGGAATGAGTATTTATACTACTCAAGAACAATC
1 TCTTAATTTTAATTGATGCTTAAAACT-AAATGGGAATGAG----TATACTACTCAAGAACAATC
*
394921 CTACACCACACAAATAAAAACTAATTTAAACCATTAAAGTCTACAAATACCTAACTCTCATCTAA
61 CTACACCACACAAATAAAAACTAATTTAAACCATTAAAGTC-ACAAATACCTAAATCTCATCTAA
394986 CTAAATTGATGTAAGCAATGACATCATTA
125 CTAAATTGATGTAAGCAATGACATCATTA
395015 -CTTAA
1 TCTTAA
395020 ATGATGTAAG
Statistics
Matches: 157, Mismatches: 1, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
153 27 0.17
154 13 0.08
158 66 0.42
159 51 0.32
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (153 bp):
TCTTAATTTTAATTGATGCTTAAAACTAAATGGGAATGAGTATACTACTCAAGAACAATCCTACA
CCACACAAATAAAAACTAATTTAAACCATTAAAGTCACAAATACCTAAATCTCATCTAACTAAAT
TGATGTAAGCAATGACATCATTA
Found at i:395025 original size:29 final size:29
Alignment explanation
Indices: 394987--395066 Score: 142
Period size: 29 Copynumber: 2.7 Consensus size: 29
394977 CTCATCTAAC
394987 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
395017 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
395046 TAAATGATGTAAGCAATGACA
1 TAAATGATGTAAGCAATGACA
395067 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:398667 original size:82 final size:81
Alignment explanation
Indices: 398517--398685 Score: 304
Period size: 82 Copynumber: 2.1 Consensus size: 81
398507 CTTTCATACT
398517 TTTGTTCATGATTGGTGGTCTCCACTCTCCAAAGTTCTAGTTGATCCTATTATTTCAGTAAAATT
1 TTTGTTCATGATTGGTGGTCTCCACTCTCCAAAGTTCTAGTTGATCCTATTATTTCAGTAAAATT
398582 TTATTATGAGCCCCTA
66 TTATTATGAGCCCCTA
398598 TTTGTTCATTGATTGGTGGTCTCCACTCTCCAAAGTTCTAGTTGATCCTATTTATTTCAGTAAAA
1 TTTGTTCA-TGATTGGTGGTCTCCACTCTCCAAAGTTCTAGTTGATCCTA-TTATTTCAGTAAAA
398663 -TTTATTATGAGCCCCTA
64 TTTTATTATGAGCCCCTA
398680 TATTGT
1 T-TTGT
398686 ATGTGAATGT
Statistics
Matches: 85, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
81 8 0.09
82 59 0.69
83 18 0.21
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (81 bp):
TTTGTTCATGATTGGTGGTCTCCACTCTCCAAAGTTCTAGTTGATCCTATTATTTCAGTAAAATT
TTATTATGAGCCCCTA
Found at i:401842 original size:19 final size:19
Alignment explanation
Indices: 401814--401851 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
401804 AAATAATATT
*
401814 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
*
401833 CTAAAACCTATTTAAAATA
1 CTAAAACCTAATTAAAATA
401852 AAATACCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:401863 original size:75 final size:76
Alignment explanation
Indices: 401740--401955 Score: 301
Period size: 76 Copynumber: 2.9 Consensus size: 76
401730 CTAAACATCT
* ** * * *
401740 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATATTTAAAACAAAAATAATAT-TT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
* *
401803 AAAATAATATTC
65 AAAACAATATCC
*
401815 TAAATCCTAATTAAAATACTAAAACCTATTTAAAATAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
401880 AAACAATATCC
66 AAACAATATCC
* * *
401891 TAAAACTTAATTAAAATATTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
401956 TGTTTAAAAT
Statistics
Matches: 126, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
74 5 0.04
75 49 0.39
76 72 0.57
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.29
Consensus pattern (76 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAACAATATCC
Found at i:402897 original size:34 final size:36
Alignment explanation
Indices: 402859--402932 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 36
402849 CTTTTTTTCC
*
402859 GAACAAG-GGTGTTTTTTTTG-TTGTTCGAAACAGT
1 GAACAAGTGGTGTTTTTTCTGATTGTTCGAAACAGT
* * *
402893 GAACAAGTTGTTGTTTTTTCTGATTTTTTGAAACAGT
1 GAACAAG-TGGTGTTTTTTCTGATTGTTCGAAACAGT
402930 GAA
1 GAA
402933 TTTTTTTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 7 0.21
36 11 0.33
37 15 0.45
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (36 bp):
GAACAAGTGGTGTTTTTTCTGATTGTTCGAAACAGT
Found at i:403898 original size:5 final size:5
Alignment explanation
Indices: 403888--403937 Score: 50
Period size: 5 Copynumber: 10.4 Consensus size: 5
403878 AGATTTGTTC
* * * *
403888 AAATA AAATA AAATA AAAT- AACTC AAATA AAAT- AAATA GAATG AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
403936 AA
1 AA
403938 GTTCGCTGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
4 7 0.19
5 29 0.81
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:403934 original size:19 final size:19
Alignment explanation
Indices: 403888--403937 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
403878 AGATTTGTTC
*
403888 AAATAAAATAAAATAAAAT
1 AAATCAAATAAAATAAAAT
*
403907 AACTCAAATAAAAT-AAAT
1 AAATCAAATAAAATAAAAT
*
403925 AGAATGAAATAAA
1 A-AATCAAATAAA
403938 GTTCGCTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (19 bp):
AAATCAAATAAAATAAAAT
Found at i:410348 original size:75 final size:75
Alignment explanation
Indices: 410244--410452 Score: 289
Period size: 75 Copynumber: 2.8 Consensus size: 75
410234 ATCTTAAATT
* * *
410244 CTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACTTAAAACAATA-ATAATATTTAAAATA
1 CTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACTTAAAACAA-AGATAAAATATAAAATA
* **
410307 ATATTCTAACTC
64 ATATCCTAAAAC
*
410319 CTAATTAAAATACTAAAACCTACTTAAACTAAAATA-TCTAAAACAAAGATAAAATATAAAATAA
1 CTAATTAAAATACTAAAACCTATTTAAACTAAAATACT-TAAAACAAAGATAAAATATAAAATAA
410383 TATCCTAAAAC
65 TATCCTAAAAC
* *
410394 TTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 CTAATTAAAATACTAAAACCTATTTAAACTAAAATACTTAAAACAAAGATAAAATATAA
410453 TGTTTAAAAT
Statistics
Matches: 120, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
74 7 0.06
75 113 0.94
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (75 bp):
CTAATTAAAATACTAAAACCTATTTAAACTAAAATACTTAAAACAAAGATAAAATATAAAATAAT
ATCCTAAAAC
Found at i:420326 original size:21 final size:21
Alignment explanation
Indices: 420297--420351 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
420287 TTTTGGCCGG
* * * *
420297 ACAGTTACCAATAGCGGTAGA
1 ACAGGTACCAAAAGCAGCAGA
420318 ACAGGTACCAAAAAGCAGCAGA
1 ACAGGTACC-AAAAGCAGCAGA
420340 ACAGGTACCAAA
1 ACAGGTACCAAA
420352 CAACGGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (21 bp):
ACAGGTACCAAAAGCAGCAGA
Found at i:420670 original size:23 final size:23
Alignment explanation
Indices: 420638--420696 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
420628 TACCATGAAG
*
420638 AAACAGAGTTTTTCGGCTCTGGT
1 AAACATAGTTTTTCGGCTCTGGT
* *
420661 AAACATAGTTTTCCGGTTCTGGT
1 AAACATAGTTTTTCGGCTCTGGT
*
420684 AAACATGGTTTTT
1 AAACATAGTTTTT
420697 ATTCTGAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (23 bp):
AAACATAGTTTTTCGGCTCTGGT
Found at i:425268 original size:4 final size:4
Alignment explanation
Indices: 425261--425293 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
425251 TTTATATATA
425261 TATG TATG TATG TATG TATG TA-- TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
425294 CACAGTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.07
4 25 0.93
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:427410 original size:54 final size:54
Alignment explanation
Indices: 427345--427779 Score: 371
Period size: 54 Copynumber: 8.1 Consensus size: 54
427335 CAACTACAAT
427345 AATAAATCAATCCATATTTTAAAATAAATAAATCAATACTAACAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATAAATCAATACTAACAAATTATTTAA
* *
427399 AATAAATCAATCCATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAAT-AAATCAATACTAACAAATTATTTAA
* *
427453 AATAAATCAATCCATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAAT-AAATCAATACTAACAAATTATTTAA
* *** * *
427507 AATAAATCAATTCATACAACTACAAT-AATAAATCAAT-C---CATA-T-TTTAA
1 AATAAATCAATCCATA-TTTTAAAATAAATAAATCAATACTAACAAATTATTTAA
** * ** * * *
427555 AATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-CAAAC-CA-TATTTTAA
1 AATAAATCAATCCATA-TTTTAAAATAAAT-AAATCAATACTAACAAATTA-TTTAA
* ** * *
427609 AATAATTCAATCCATACTAATAAATTATTTAAAATAAATCAAT-CTATAC-AACTA--CAA
1 AATAAATCAATCCATA-TTTTAAA--A--T-AAATAAATCAATACTA-ACAAATTATTTAA
* * *
427666 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 -AATAAATCAATCCATATTTTAAAATAAATAAATCAATACTAACAAATTATTTAA
* * *
427721 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATAAATCAATACTAACAAATTATTTAA
427775 AATAA
1 AATAA
427780 TTTATTTTAA
Statistics
Matches: 324, Mismatches: 35, Indels: 44
0.80 0.09 0.11
Matches are distributed among these distances:
48 26 0.08
49 2 0.01
50 10 0.03
52 13 0.04
53 14 0.04
54 208 0.64
55 12 0.04
57 7 0.02
58 25 0.08
59 5 0.02
60 2 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATAAATCAATACTAACAAATTATTTAA
Found at i:427431 original size:22 final size:23
Alignment explanation
Indices: 427265--427378 Score: 81
Period size: 22 Copynumber: 4.7 Consensus size: 23
427255 TAATAAATTA
427265 TTTAAAATAAATCAATCCAT-AT
1 TTTAAAATAAATCAATCCATAAT
* *
427287 TTTAAAATAATTC-ATACTAATAAATT
1 TTTAAAATAAATCAAT-C-CAT-AA-T
*
427313 ATTTAAAATAAATCAATCCATACAAC
1 -TTTAAAATAAATCAATCCAT--AAT
**
427339 TACAATAATAAATCAATCCAT-AT
1 TTTAA-AATAAATCAATCCATAAT
*
427362 TTTAAAATAAATAAATC
1 TTTAAAATAAATCAATC
427379 AATACTAACA
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
21 2 0.03
22 24 0.34
23 6 0.08
25 4 0.06
26 18 0.25
27 15 0.21
28 2 0.03
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (23 bp):
TTTAAAATAAATCAATCCATAAT
Found at i:427445 original size:22 final size:22
Alignment explanation
Indices: 427396--427444 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
427386 ACAAATTATT
**
427396 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
427418 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
427441 TAAA
1 TAAA
427445 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:427455 original size:32 final size:32
Alignment explanation
Indices: 427416--427523 Score: 146
Period size: 32 Copynumber: 3.7 Consensus size: 32
427406 CAATCCATAT
427416 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
427448 TTTAAAATAAATCAA-TC---C--AT--A-T-
1 TTTAAAATAAATCAATTCATACTAATAAATTA
427470 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
427502 TTTAAAATAAATCAATTCATAC
1 TTTAAAATAAATCAATTCATAC
427524 AACTACAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 20
0.77 0.00 0.23
Matches are distributed among these distances:
22 15 0.23
23 3 0.05
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 3 0.05
32 37 0.56
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (32 bp):
TTTAAAATAAATCAATTCATACTAATAAATTA
Found at i:427474 original size:22 final size:22
Alignment explanation
Indices: 427448--427490 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
427438 TAATAAATTA
427448 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
427470 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
427491 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:427499 original size:22 final size:22
Alignment explanation
Indices: 427450--427498 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
427440 ATAAATTATT
**
427450 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
427472 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
427495 TAAA
1 TAAA
427499 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:427525 original size:188 final size:187
Alignment explanation
Indices: 427255--427779 Score: 743
Period size: 188 Copynumber: 2.8 Consensus size: 187
427245 ACAACTACAA
427255 TAATAAATTATTTAAAATAAATCAATCCATATTTT---A-AAATAATTCATACTAATAAATTATT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAATTCATACTAATAAATTATT
* *
427316 TAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAATCAA
66 TAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCA
* * *
427381 TACTAACAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
131 TACTAATAAATTATTTAAAATAAATCAAACCATATTTTAAAATAAATCAATCCATAC
427438 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT-AATTCATACTAATAAATTAT
*
427503 TTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
65 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
*
427568 ATACTAATAAATTATTTAAAATAAATCAAACCATATTTTAAAATAATTCAATCCATAC
130 ATACTAATAAATTATTTAAAATAAATCAAACCATATTTTAAAATAAATCAATCCATAC
* ** **
427626 TAATAAATTATTTAAAATAAATCAAT-C-TA---TACAACTACAATAATAAAT-C-AATCCA-TA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTA-AAATA-AATAATTCATACTAATAAATTA
*
427683 TTTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATA
64 -TTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATA
427747 AATCAATCCATACTAATAAATTATTTAAAATAA
121 AATCAATCCATACTAATAAATTATTTAAAATAA
427780 TTTATTTTAA
Statistics
Matches: 313, Mismatches: 14, Indels: 25
0.89 0.04 0.07
Matches are distributed among these distances:
181 2 0.01
182 28 0.09
183 40 0.13
184 10 0.03
185 3 0.01
186 4 0.01
187 5 0.02
188 221 0.71
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (187 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAATTCATACTAATAAATTATT
TAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCA
TACTAATAAATTATTTAAAATAAATCAAACCATATTTTAAAATAAATCAATCCATAC
Found at i:427537 original size:134 final size:134
Alignment explanation
Indices: 427270--427779 Score: 742
Period size: 134 Copynumber: 3.8 Consensus size: 134
427260 AATTATTTAA
427270 AATAAATCAATCCATATTTTAAAAT-AAT---T-CATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* ** **
427330 CCATACAACTACAATAATAAATCAATCCATA-TTTTAAA--A--T-AAATAAATCAATACTA-AC
66 CCAT---ATTTTAA-AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-CTATAC
* *
427388 AAATTATTTAA-
126 -AACTA--CAAT
*
427399 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
427464 CCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT-TCATACAACT
66 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCT-ATACAACT
427528 ACAAT
130 ACAAT
*
427533 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
427598 CCATATTTTAAAATAATTCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTA
66 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTA
427663 CAAT
131 CAAT
427667 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
427732 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
66 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
427780 TTTATTTTAA
Statistics
Matches: 352, Mismatches: 14, Indels: 25
0.90 0.04 0.06
Matches are distributed among these distances:
129 25 0.07
130 18 0.05
131 9 0.03
133 4 0.01
134 275 0.78
135 7 0.02
136 14 0.04
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (134 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTA
CAAT
Found at i:427579 original size:22 final size:22
Alignment explanation
Indices: 427504--427578 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
427494 ATAAATTATT
* *
427504 TAAAATAAATCAATTCATACAA
1 TAAAATAAATCAATCCATATAA
**
427526 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
427552 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
427575 TAAA
1 TAAA
427579 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:427589 original size:32 final size:31
Alignment explanation
Indices: 427550--427779 Score: 148
Period size: 32 Copynumber: 8.3 Consensus size: 31
427540 CAATCCATAT
427550 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
427582 TTTAAAATAAATC-A---A-AC-CAT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
427604 TTTAAAATAATTCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* *
427636 TTTAAAATAAATCAATCTATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
427666 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
427684 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
427716 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
427738 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
427770 TTTAAAATAA
1 TTTAAAATAA
427780 TTTATTTTAA
Statistics
Matches: 155, Mismatches: 7, Indels: 72
0.66 0.03 0.31
Matches are distributed among these distances:
20 1 0.01
22 42 0.27
23 5 0.03
24 4 0.03
25 1 0.01
26 20 0.13
27 4 0.03
28 7 0.05
30 3 0.02
31 6 0.04
32 62 0.40
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:427608 original size:22 final size:22
Alignment explanation
Indices: 427582--427624 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
427572 TAATAAATTA
427582 TTTAAAATAAATCAAACCATAT
1 TTTAAAATAAATCAAACCATAT
* *
427604 TTTAAAATAATTCAATCCATA
1 TTTAAAATAAATCAAACCATA
427625 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAAACCATAT
Found at i:427713 original size:22 final size:22
Alignment explanation
Indices: 427638--427712 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
427628 ATAAATTATT
* *
427638 TAAAATAAATCAATCTATACAA
1 TAAAATAAATCAATCCATATAA
**
427660 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
427686 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
427709 TAAA
1 TAAA
427713 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:427742 original size:22 final size:22
Alignment explanation
Indices: 427716--427816 Score: 91
Period size: 22 Copynumber: 4.5 Consensus size: 22
427706 TAATAAATTA
427716 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
427738 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** *
427761 AATAAATTATTTAAAAT-AAT--TTAT
1 TTTAAA--A--T-AAATCAATCCATAT
427785 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
427807 TTTATAATAA
1 TTTAAAATAA
427817 TTTATTTTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
19 4 0.06
20 4 0.06
22 34 0.54
23 5 0.08
24 5 0.08
25 3 0.05
27 4 0.06
28 4 0.06
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:427790 original size:15 final size:15
Alignment explanation
Indices: 427761--427923 Score: 166
Period size: 15 Copynumber: 10.5 Consensus size: 15
427751 AATCCATACT
427761 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
*
427775 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
427790 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
427812 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
427827 AATAAATTATTTTAT
1 AATAAATTATTTTAA
427842 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
427857 AATAAATTATTTTAT
1 AATAAATTATTTTAA
* *
427872 GATAAATTATTTTAT
1 AATAAATTATTTTAA
* *
427887 AATAAAATATTTTAT
1 AATAAATTATTTTAA
*
427902 AATAAAATATTTTAA
1 AATAAATTATTTTAA
427917 AATAAAT
1 AATAAAT
427924 AACCTTATTA
Statistics
Matches: 127, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
14 8 0.06
15 103 0.81
17 1 0.01
18 2 0.02
19 2 0.02
20 1 0.01
22 10 0.08
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:427803 original size:69 final size:67
Alignment explanation
Indices: 427707--427863 Score: 201
Period size: 69 Copynumber: 2.3 Consensus size: 67
427697 AATCCATACT
*
427707 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAAT-AATCAAT-CATA-AAATAAATTAT
427770 TTTAA
63 TTTAA
* * ** **
427775 AATAATTTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATCATAAAATAAATTATTTT
*
427840 AT
66 AA
427842 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
427864 TATTTTATGA
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
66 9 0.12
67 27 0.35
68 13 0.17
69 29 0.37
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATCATAAAATAAATTATTTT
AA
Found at i:427840 original size:30 final size:30
Alignment explanation
Indices: 427804--427923 Score: 195
Period size: 30 Copynumber: 4.0 Consensus size: 30
427794 AATCAATCCA
*
427804 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
427834 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
* * *
427864 TATTTTATGATAAATTATTTTATAATAAAA
1 TATTTTATAATAAATTATTTTAAAATAAAT
*
427894 TATTTTATAATAAAATATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
427924 AACCTTATTA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 82 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
TATTTTATAATAAATTATTTTAAAATAAAT
Found at i:427855 original size:45 final size:45
Alignment explanation
Indices: 427803--427923 Score: 188
Period size: 45 Copynumber: 2.7 Consensus size: 45
427793 AAATCAATCC
*
427803 ATATTTTATAATAATTTATTTTAAAATAAATTATTTTATAATAAA
1 ATATTTTATAATAAATTATTTTAAAATAAATTATTTTATAATAAA
* * **
427848 TTATTTTAAAATAAATTATTTTATGATAAATTATTTTATAATAAA
1 ATATTTTATAATAAATTATTTTAAAATAAATTATTTTATAATAAA
*
427893 ATATTTTATAATAAAATATTTTAAAATAAAT
1 ATATTTTATAATAAATTATTTTAAAATAAAT
427924 AACCTTATTA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (45 bp):
ATATTTTATAATAAATTATTTTAAAATAAATTATTTTATAATAAA
Found at i:430363 original size:3 final size:3
Alignment explanation
Indices: 430355--430381 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
430345 GCCTCTCTGT
430355 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
430382 GACCAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:434985 original size:23 final size:23
Alignment explanation
Indices: 434959--435004 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
434949 AAAAAATAGA
*
434959 GAAAACTTACCATAAAGATAAAG
1 GAAAACATACCATAAAGATAAAG
**
434982 GAAAACATGTCATAAAGATAAAG
1 GAAAACATACCATAAAGATAAAG
435005 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.17
Consensus pattern (23 bp):
GAAAACATACCATAAAGATAAAG
Found at i:435259 original size:14 final size:14
Alignment explanation
Indices: 435240--435266 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
435230 TATCAATCCA
435240 TGCTTGCTGCCATT
1 TGCTTGCTGCCATT
435254 TGCTTGCTGCCAT
1 TGCTTGCTGCCAT
435267 GTAAGTCAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.30, G:0.22, T:0.41
Consensus pattern (14 bp):
TGCTTGCTGCCATT
Found at i:439662 original size:21 final size:21
Alignment explanation
Indices: 439636--439705 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
439626 AATCCCTTGA
439636 TATCGATACTCTTACCTAGAG
1 TATCGATACTCTTACCTAGAG
* * *
439657 TATCGATACTCTAACATATGGG
1 TATCGATACTCTTACCTA-GAG
*
439679 TATCGATA--C-TACCTCGAG
1 TATCGATACTCTTACCTAGAG
439697 TATCGATAC
1 TATCGATAC
439706 CAAAAATGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
18 10 0.25
19 3 0.08
20 1 0.03
21 16 0.40
22 10 0.25
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (21 bp):
TATCGATACTCTTACCTAGAG
Found at i:439744 original size:105 final size:105
Alignment explanation
Indices: 439571--439772 Score: 243
Period size: 105 Copynumber: 1.9 Consensus size: 105
439561 TGACCTTAGA
* * **
439571 GGGTATGAGTACTACCCTGAGTACCTATACCAAAAATGACTTTGATGTTCTGAAAAATCCCTTGA
1 GGGTATGAGTACTACCCTGAGTACCGATACCAAAAATGACTTTGATGTTCTGAAAAATACCTCAA
*
439636 TATCGATACTCTTACCT-AGAGTATCGATACTCTAACATAT
66 TATCGATACTCTT-CATGAGAGTATCGATACTCTAACATAT
* * *
439676 GGGTATCGA-TACTA-CCTCGAGTATCGATACCAAAAATG-GTTTCGATGTT-TTAGAAAATACC
1 GGGTAT-GAGTACTACCCT-GAGTACCGATACCAAAAATGACTTT-GATGTTCTGA-AAAATACC
*
439737 TCAATATCGATACTCTTCATGGGAGTATCGATACTC
62 TCAATATCGATACTCTTCATGAGAGTATCGATACTC
439773 CATTCCTAGT
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
104 10 0.12
105 71 0.86
106 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (105 bp):
GGGTATGAGTACTACCCTGAGTACCGATACCAAAAATGACTTTGATGTTCTGAAAAATACCTCAA
TATCGATACTCTTCATGAGAGTATCGATACTCTAACATAT
Found at i:439913 original size:21 final size:19
Alignment explanation
Indices: 439862--439914 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
439852 ACCAAGCCTA
*
439862 GGGTATTGATACCCATAGC
1 GGGTATTGATACCCATAAC
* *
439881 GGAGCATCGATACCACATAAAC
1 GG-GTATTGATACC-CAT-AAC
439903 GGGTATTGATAC
1 GGGTATTGATAC
439915 TCCCTACTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 9 0.35
21 11 0.42
22 4 0.15
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (19 bp):
GGGTATTGATACCCATAAC
Found at i:441972 original size:35 final size:35
Alignment explanation
Indices: 441933--442007 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
441923 AAAATACTTT
441933 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
* * * *
441968 AATTTGGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
442003 AATTT
1 AATTT
442008 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
Done.