Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008703.1 Hibiscus syriacus cultivar Beakdansim tig00111742_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: 1275178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:13542 original size:43 final size:43
Alignment explanation
Indices: 13492--13637 Score: 134
Period size: 46 Copynumber: 3.3 Consensus size: 43
13482 CCAGATCTCT
*
13492 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCC
1 TCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCC
* * * * ** * *
13535 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATC-TCT
1 TCATCACGTAAGAGCCGTGTCA--ACC-ATAGATAACCAG-CCGTCC
*
13581 TCATCATGTAAGAGCCGTGTCAA-CATTAGGATAACCAGCCGTCC
1 TCATCACGTAAGAGCCGTGTCAACCA-TA-GATAACCAGCCGTCC
13625 TCATCACGTAAGA
1 TCATCACGTAAGA
13638 ACCGAGTTAT
Statistics
Matches: 78, Mismatches: 18, Indels: 13
0.72 0.17 0.12
Matches are distributed among these distances:
43 23 0.29
44 22 0.28
45 3 0.04
46 29 0.37
47 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (43 bp):
TCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCC
Found at i:13597 original size:89 final size:90
Alignment explanation
Indices: 13482--13697 Score: 283
Period size: 90 Copynumber: 2.4 Consensus size: 90
13472 CATCCCCAGA
*
13482 CCAGATCTCTTCATCACGTATGAGCCGTGTCAACCA-TA-GATAACCAGCCGTCCTCATCACGTA
1 CCAGATCTCTTCATCACGTAAGAGCCGTGTCAA-CATTAGGATAACCAGCCGTCCTCATCACGTA
* *
13545 GGAACCGTGTTATCACCTTTAGATGG
65 AGAACCGAGTTATCACCTTTAGATGG
*
13571 CCAGATCTCTTCATCATGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAA
1 CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAA
* *
13636 GAACCGAGTTATCACCCTTCCTAAAAATGA
66 GAACCGAGTTATCA-CCTT--T--AGATGG
* * *
13666 CCAGATCTCCTCATCACGTAGGAGCCATGTCA
1 CCAGATCTCTTCATCACGTAAGAGCCGTGTCA
13698 CCCTTAGACG
Statistics
Matches: 110, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
88 2 0.02
89 33 0.30
90 38 0.35
91 4 0.04
93 1 0.01
95 32 0.29
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (90 bp):
CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAA
GAACCGAGTTATCACCTTTAGATGG
Found at i:13910 original size:3 final size:3
Alignment explanation
Indices: 13899--13959 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
13889 TTTTTTTCCG
*
13899 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCA TTA -TA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13944 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
13960 CAATTTTTGC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 6 0.12
3 43 0.83
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:14090 original size:26 final size:26
Alignment explanation
Indices: 14037--14158 Score: 230
Period size: 26 Copynumber: 4.8 Consensus size: 26
14027 ACCCACCAGA
14037 TTAGGGTTTCAAACCCT-AAATCAGT
1 TTAGGGTTTCAAACCCTAAAATCAGT
14062 TTAGGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCTAAAATCAGT
14088 TTAGGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCTAAAATCAGT
14114 TTAGGGTTTCAAACCCT-AAATCAGT
1 TTAGGGTTTCAAACCCTAAAATCAGT
14139 TTAGGGTTTCAAACCCTAAA
1 TTAGGGTTTCAAACCCTAAA
14159 TCCCCAACTG
Statistics
Matches: 95, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
25 42 0.44
26 53 0.56
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (26 bp):
TTAGGGTTTCAAACCCTAAAATCAGT
Found at i:14098 original size:51 final size:50
Alignment explanation
Indices: 14037--14160 Score: 230
Period size: 51 Copynumber: 2.4 Consensus size: 50
14027 ACCCACCAGA
14037 TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCT-AAATCAGT
14088 TTAGGGTTTCAAACCCTAAAATCAGTTTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGTTTAGGGTTTCAAACCCTAAATCAGT
14139 TTAGGGTTTCAAACCCTAAATC
1 TTAGGGTTTCAAACCCTAAATC
14161 CCCAACTGCA
Statistics
Matches: 72, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
50 5 0.07
51 42 0.58
52 25 0.35
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (50 bp):
TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAAATCAGT
Found at i:15623 original size:30 final size:31
Alignment explanation
Indices: 15583--15667 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
15573 TAGACTCATA
15583 AGTTTCTATTTTTACTATTTTAATCCC-TTT
1 AGTTTCTATTTTTACTATTTTAATCCCTTTT
* * *
15613 AGTTTTTA-TTTCATCTATTTTGATCCCTTTT
1 AGTTTCTATTTTTA-CTATTTTAATCCCTTTT
* *
15644 A-TTGCTATTTTTATTATTTTAATC
1 AGTTTCTATTTTTACTATTTTAATC
15668 ATGTATGTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 4 0.09
30 32 0.73
31 8 0.18
ACGTcount: A:0.20, C:0.14, G:0.05, T:0.61
Consensus pattern (31 bp):
AGTTTCTATTTTTACTATTTTAATCCCTTTT
Found at i:19453 original size:8 final size:8
Alignment explanation
Indices: 19435--19468 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
19425 TTCATTGTAC
19435 TTTTAATTT
1 TTTTAA-TT
19444 TTTTAATT
1 TTTTAATT
19452 TTTTAATT
1 TTTTAATT
19460 TTTTAATT
1 TTTTAATT
19468 T
1 T
19469 ACTTACTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.76
9 6 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTAATT
Found at i:20642 original size:83 final size:82
Alignment explanation
Indices: 20492--20667 Score: 264
Period size: 83 Copynumber: 2.1 Consensus size: 82
20482 ACTCTCCCTT
* * * *
20492 TTTTCC-TTCCTTTTGTTTATGATTTACATGGGTGGGAAAATTGCTAATGCCATGGGAAAACAGC
1 TTTTCCTTTTCTTTTGTTTATGATTTACATGGATGGGAAAATTGCTAATGCAATGGGAAAACAAC
20556 TAAGATCATGGTTTACC
66 TAAGATCATGGTTTACC
* *
20573 ATTTTCCTTTTCTTTTGTTTATGGTTTACATGGATGGGAAAATTGCTATTGCAATGGGAAAACAA
1 -TTTTCCTTTTCTTTTGTTTATGATTTACATGGATGGGAAAATTGCTAATGCAATGGGAAAACAA
*
20638 CTAAGATCATGGTTTGCC
65 CTAAGATCATGGTTTACC
*
20656 TCTTCCTTTTCT
1 TTTTCCTTTTCT
20668 GGGGTTTTCT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
82 17 0.20
83 68 0.80
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.40
Consensus pattern (82 bp):
TTTTCCTTTTCTTTTGTTTATGATTTACATGGATGGGAAAATTGCTAATGCAATGGGAAAACAAC
TAAGATCATGGTTTACC
Found at i:21007 original size:16 final size:16
Alignment explanation
Indices: 20986--21016 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20976 TTTATGTGAA
20986 GATGATGAAGGTTGAT
1 GATGATGAAGGTTGAT
*
21002 GATGATTAAGGTTGA
1 GATGATGAAGGTTGA
21017 GGTAGCATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (16 bp):
GATGATGAAGGTTGAT
Found at i:23684 original size:47 final size:47
Alignment explanation
Indices: 23500--23681 Score: 301
Period size: 47 Copynumber: 3.9 Consensus size: 47
23490 ATGAGCTAGC
* *
23500 TTACTAAAGGCACAAGGCCAATGTTTATTTCATTTAGGTTAATTCAT
1 TTACTAAAGGCACAAGGCCAGTGTTTATTTCACTTAGGTTAATTCAT
*
23547 TTACTAAAGGCACAAGGTCAGTGTTTATTTCACTTAGGTTAATTCAT
1 TTACTAAAGGCACAAGGCCAGTGTTTATTTCACTTAGGTTAATTCAT
* * *
23594 TTACTAAAGGCACAAGGTCAGTGTTTATTTCACTTGGGTTACTTCAT
1 TTACTAAAGGCACAAGGCCAGTGTTTATTTCACTTAGGTTAATTCAT
*
23641 TTACTAAAGGCACAAGGCCAGTGTTTATTTCACTTGGGTTA
1 TTACTAAAGGCACAAGGCCAGTGTTTATTTCACTTAGGTTA
23682 CTTTATTTCC
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 129 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (47 bp):
TTACTAAAGGCACAAGGCCAGTGTTTATTTCACTTAGGTTAATTCAT
Found at i:28322 original size:12 final size:12
Alignment explanation
Indices: 28297--28365 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
28287 ACGGAATTAT
* *
28297 CAGAAATCAAAA
1 CAGAATTCAGAA
28309 CAGAATTCAGAA
1 CAGAATTCAGAA
28321 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
28333 CAGAATCCATAT
1 CAGAATTCAGAA
*
28345 CAGAAATCAGAA
1 CAGAATTCAGAA
28357 CAGAATTCA
1 CAGAATTCA
28366 AGTCGGAAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.52, C:0.19, G:0.13, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:28329 original size:24 final size:24
Alignment explanation
Indices: 28297--28365 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
28287 ACGGAATTAT
*
28297 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * * *
28321 CAGATATCAGAACAGAATCCATAT
1 CAGAAATCAGAACAGAATTCAGAA
28345 CAGAAATCAGAACAGAATTCA
1 CAGAAATCAGAACAGAATTCA
28366 AGTCGGAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.52, C:0.19, G:0.13, T:0.16
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:28374 original size:24 final size:24
Alignment explanation
Indices: 28296--28379 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
28286 AACGGAATTA
*
28296 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * *
28319 AACAGATATCAGAACAGAATCCATA-
1 -TCAGAAATCAGAACAGAATTCA-AG
28344 TCAGAAATCAGAACAGAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
*
28368 TCGGAAATCAGA
1 TCAGAAATCAGA
28380 TAAAATATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
23 1 0.02
24 47 0.96
26 1 0.02
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.17
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:30110 original size:2 final size:2
Alignment explanation
Indices: 30103--30130 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30093 ATTAAAGTAA
30103 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
30131 TTTTTGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31924 original size:28 final size:28
Alignment explanation
Indices: 31882--31941 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
31872 GTTGGGCCTG
* **
31882 TAATATAAATAAAATTATTTATTAATAA
1 TAATATAAATAAAATCAAATATTAATAA
31910 TAATAATAAAT-AAATCAAATATTAATAA
1 TAAT-ATAAATAAAATCAAATATTAATAA
31938 TAAT
1 TAAT
31942 TTTAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
TAATATAAATAAAATCAAATATTAATAA
Found at i:36429 original size:24 final size:24
Alignment explanation
Indices: 36363--36448 Score: 75
Period size: 24 Copynumber: 3.6 Consensus size: 24
36353 TGAATTCTGT
* *
36363 TATGATACTTGACCTGGATTATGA
1 TATGATACTTGACCTAGATTATAA
* * *
36387 TCTGATAC-TGACATAGATTCTAA
1 TATGATACTTGACCTAGATTATAA
* * * *
36410 TATGATACATGACCTTGATTTTTA
1 TATGATACTTGACCTAGATTATAA
*
36434 TCTGATACTTGACCT
1 TATGATACTTGACCT
36449 GAATTATGTT
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
23 18 0.37
24 31 0.63
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (24 bp):
TATGATACTTGACCTAGATTATAA
Found at i:37086 original size:20 final size:21
Alignment explanation
Indices: 37046--37086 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
37036 TGAAAATCTG
*
37046 TTTTATTTTGAATACTGATAAC
1 TTTTATTTTG-ATACTCATAAC
37068 TTTTATTTTG-TACTCATAA
1 TTTTATTTTGATACTCATAA
37087 ATGATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTATTTTGATACTCATAAC
Found at i:39591 original size:26 final size:26
Alignment explanation
Indices: 39561--39632 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 26
39551 AGAATATCAC
*
39561 CAAGCCAAGGAATGAATGGACATCCT
1 CAAGCCAAGAAATGAATGGACATCCT
*** *
39587 CAAGCTTTGAAATGAATGTACATCCT
1 CAAGCCAAGAAATGAATGGACATCCT
***
39613 CAAGCTTTGAAATGAATGGA
1 CAAGCCAAGAAATGAATGGA
39633 AAAACATTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (26 bp):
CAAGCCAAGAAATGAATGGACATCCT
Found at i:39626 original size:22 final size:24
Alignment explanation
Indices: 39574--39632 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 24
39564 GCCAAGGAAT
39574 GAATGGACATCCTCAAGCTTTGAAA
1 GAATGGACATCCTCAAGCTTTG-AA
*
39599 TGAATGTACATCCTCAAGCTTTGAAA
1 -GAATGGACATCCTCAAGCTTTG-AA
39625 TGAATGGA
1 -GAATGGA
39633 AAAACATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (24 bp):
GAATGGACATCCTCAAGCTTTGAA
Found at i:40605 original size:23 final size:23
Alignment explanation
Indices: 40572--40651 Score: 115
Period size: 23 Copynumber: 3.4 Consensus size: 23
40562 TGTTATGCTA
40572 ACTTACCTGGATTCTGATCTGAT
1 ACTTACCTGGATTCTGATCTGAT
*
40595 ACTTACATGGATTCTGATCTGAT
1 ACTTACCTGGATTCTGATCTGAT
* *
40618 ACATGACCTGGATTCTGATCTAAT
1 AC-TTACCTGGATTCTGATCTGAT
40642 ACTTGACCTG
1 ACTT-ACCTG
40652 AATTATGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
23 25 0.50
24 25 0.50
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36
Consensus pattern (23 bp):
ACTTACCTGGATTCTGATCTGAT
Found at i:40634 original size:24 final size:23
Alignment explanation
Indices: 40576--40651 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 23
40566 ATGCTAACTT
*
40576 ACCTGGATTCTGATCTGATACTT
1 ACCTGGATTCTGATCTGATACTG
*
40599 ACATGGATTCTGATCTGATACATG
1 ACCTGGATTCTGATCTGATAC-TG
*
40623 ACCTGGATTCTGATCTAATACTTG
1 ACCTGGATTCTGATCTGATAC-TG
40647 ACCTG
1 ACCTG
40652 AATTATGTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 20 0.43
24 27 0.57
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (23 bp):
ACCTGGATTCTGATCTGATACTG
Found at i:41481 original size:16 final size:14
Alignment explanation
Indices: 41452--41485 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
41442 AATCTACCCA
41452 TTGACTGTTGACCG
1 TTGACTGTTGACCG
41466 TTGACTGGTCTGACCG
1 TTGACT-GT-TGACCG
41482 TTGA
1 TTGA
41486 GTTCTACCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 2 0.11
16 10 0.56
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (14 bp):
TTGACTGTTGACCG
Found at i:55813 original size:107 final size:107
Alignment explanation
Indices: 55624--55823 Score: 321
Period size: 107 Copynumber: 1.9 Consensus size: 107
55614 CTTTTTTAAG
* *
55624 CATACTTTAAGGGGAGTCATCTCATCACACAACCATCCCATACTCTAAGTGAAAGGGAGCAAACC
1 CATACTTTAAGGGGAGTCAGCTCATCACACAACCATCCCACACTCTAAGTGAAAGGGAGCAAACC
* * *
55689 TTCCACCCTCGATCTAGTCATGTAGAGTTTTTTTTCTTAAAA
66 TTCCACCCTCAAGCTAGTCAGGTAGAGTTTTTTTTCTTAAAA
* *
55731 CATACTTTAAGGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAGGGAGCATACC
1 CATACTTTAAGGGGAGTCAGCTCATCACACAACCATCCCACACTCTAAGTGAAAGGGAGCAAACC
55796 TTCCACCC-CTAAGCTAGTCAGGTAGAGT
66 TTCCACCCTC-AAGCTAGTCAGGTAGAGT
55824 CATCCCATGA
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
106 1 0.01
107 84 0.99
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (107 bp):
CATACTTTAAGGGGAGTCAGCTCATCACACAACCATCCCACACTCTAAGTGAAAGGGAGCAAACC
TTCCACCCTCAAGCTAGTCAGGTAGAGTTTTTTTTCTTAAAA
Found at i:57135 original size:16 final size:16
Alignment explanation
Indices: 57111--57142 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57101 GCACATCTTC
57111 ATGCACACCTTTCTGT
1 ATGCACACCTTTCTGT
*
57127 ATGCTCACCTTTCTGT
1 ATGCACACCTTTCTGT
57143 CGAAAGGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.31, G:0.12, T:0.41
Consensus pattern (16 bp):
ATGCACACCTTTCTGT
Found at i:61010 original size:134 final size:128
Alignment explanation
Indices: 60686--61064 Score: 352
Period size: 134 Copynumber: 2.9 Consensus size: 128
60676 CATTTTCCCA
* * * *
60686 AGATTTGGTATACCTTAAGAGCAGTGAAGCAAATCAAGTTCAGTTAAATCTTCCCTAAAGAGAAA
1 AGATTTGATATTCCTGAAGAGCAGTGAAGCAAATCAAGTTCA-TTTAATCTTCCCTAAAGAGAAA
*
60751 CGAAGTGAATCAAAATTTTCAAGATCTGATTACCCGAAAAAGTGGAACAAATTCTTCTTATTTC
65 CGAAGTGAATCAAAATTTTCAAGATCTGATTACCCGAAAAAGTGGAACAAATCCTTCTTATTTC
* * *** * * * *
60815 AGATTTGATCTTCCTGAGGAGCAACAAAGCAAATCAAATCTGATTTAATCTTCCCTAAAGAGTAG
1 AGATTTGATATTCCTGAAGAGCAGTGAAGCAAATCAAGT-TCATTTAATCTTCCCTAAAGAGAAA
* ** * * *
60880 CGAAGTGGATCAAAATTTTCCCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAAATCC-TCTTT
65 CGAAGTGAATCAAAATTTTCAAGA-TCTGAT-TACCCGAAA-A--AGTGGAACAAATCCTTC-TT
* *
60944 CTTTT
124 ATTTC
* * * * **
60949 AGATTTTG-TATTCTTGAAGAGTAGTGAAGCAAATCAAGTTCATTTCAACCTTCCCTGAAGAGCG
1 AGA-TTTGATATTCCTGAAGAGCAGTGAAGCAAATCAAGTTCATTT-AATCTTCCCTAAAGAGAA
* * * *
61013 ACGAATTAAATCAAATTTTTC-AGATCTGATTACCCG-AAAAGTGGATCAAATC
64 ACGAAGTGAATCAAAATTTTCAAGATCTGATTACCCGAAAAAGTGGAACAAATC
61065 TTGACCTACC
Statistics
Matches: 197, Mismatches: 44, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
127 12 0.06
129 71 0.36
130 10 0.05
131 11 0.06
132 7 0.04
133 9 0.05
134 73 0.37
135 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (128 bp):
AGATTTGATATTCCTGAAGAGCAGTGAAGCAAATCAAGTTCATTTAATCTTCCCTAAAGAGAAAC
GAAGTGAATCAAAATTTTCAAGATCTGATTACCCGAAAAAGTGGAACAAATCCTTCTTATTTC
Found at i:64194 original size:20 final size:21
Alignment explanation
Indices: 64163--64208 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
64153 ACAATGCATT
64163 CAAATCAAAATGAACAAAATA
1 CAAATCAAAATGAACAAAATA
* **
64184 TAAAT-AAAATGGTCAAAATA
1 CAAATCAAAATGAACAAAATA
64204 CAAAT
1 CAAAT
64209 GTAGAAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.63, C:0.11, G:0.07, T:0.20
Consensus pattern (21 bp):
CAAATCAAAATGAACAAAATA
Found at i:65118 original size:20 final size:20
Alignment explanation
Indices: 65095--65135 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
65085 GGTTACCTGA
65095 AGAAAATGAATACCTTGATG
1 AGAAAATGAATACCTTGATG
65115 AGAAAATGAATACCTTGATG
1 AGAAAATGAATACCTTGATG
65135 A
1 A
65136 TAAGAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (20 bp):
AGAAAATGAATACCTTGATG
Found at i:65141 original size:23 final size:21
Alignment explanation
Indices: 65092--65144 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
65082 AATGGTTACC
65092 TGAAGAAAATGAATACCTTGA
1 TGAAGAAAATGAATACCTTGA
65113 TG-AGAAAATGAATACCTTGA
1 TGAAGAAAATGAATACCTTGA
65133 TGATAAGAAAAT
1 TG--AAGAAAAT
65145 TTTCTTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 20 0.69
21 2 0.07
23 7 0.24
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.25
Consensus pattern (21 bp):
TGAAGAAAATGAATACCTTGA
Found at i:65708 original size:40 final size:40
Alignment explanation
Indices: 65671--65864 Score: 192
Period size: 40 Copynumber: 4.8 Consensus size: 40
65661 AATGTGATAA
*
65671 TGATCCAACTCCTTATGTGATGGATGAGCCAAGGTGATGC
1 TGATCCAACTCCTTATGTGATGGATGAGCCAAAGTGATGC
* * * * * *
65711 TTATCCATCTTCTTATGTGATGGACGAGCAAAAATGATGC
1 TGATCCAACTCCTTATGTGATGGATGAGCCAAAGTGATGC
* * **
65751 TAAT-AAACCTCCTTATGTGATGGATGAGTGAAAGTGATGC
1 TGATCCAA-CTCCTTATGTGATGGATGAGCCAAAGTGATGC
** *
65791 TGATCCAACTCCTTATGTGATGGACAAGCAAAATGATGATGC
1 TGATCCAACTCCTTATGTGATGGATGAGCCAAA-G-TGATGC
* * **
65833 TGATTCAACTTCTTATGTGATAAATGAGCCAA
1 TGATCCAACTCCTTATGTGATGGATGAGCCAA
65865 GGTCGGTGCT
Statistics
Matches: 122, Mismatches: 28, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
39 1 0.01
40 87 0.71
41 3 0.02
42 31 0.25
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (40 bp):
TGATCCAACTCCTTATGTGATGGATGAGCCAAAGTGATGC
Found at i:65788 original size:80 final size:79
Alignment explanation
Indices: 65679--65828 Score: 228
Period size: 80 Copynumber: 1.9 Consensus size: 79
65669 AATGATCCAA
* * * * *
65679 CTCCTTATGTGATGGATGAGCCAAGGTGATGCTTATCCATCTTCTTATGTGATGGACGAGCAAAA
1 CTCCTTATGTGATGGATGAGCCAAAGTGATGCTGATCCAACTCCTTATGTGATGGACAAGC-AAA
65744 ATGATGCTAATAAAC
65 ATGATGCTAATAAAC
**
65759 CTCCTTATGTGATGGATGAGTGAAAGTGATGCTGATCCAACTCCTTATGTGATGGACAAGCAAAA
1 CTCCTTATGTGATGGATGAGCCAAAGTGATGCTGATCCAACTCCTTATGTGATGGACAAGCAAAA
65824 TGATG
66 TGATG
65829 ATGCTGATTC
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 9 0.14
80 54 0.86
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (79 bp):
CTCCTTATGTGATGGATGAGCCAAAGTGATGCTGATCCAACTCCTTATGTGATGGACAAGCAAAA
TGATGCTAATAAAC
Found at i:66042 original size:117 final size:116
Alignment explanation
Indices: 65889--66137 Score: 295
Period size: 117 Copynumber: 2.1 Consensus size: 116
65879 CAATTCTTTA
* * * *
65889 TATGATTGAATCGAGCTAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTATCCCTCATCAGA
1 TATGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCAGA
* * * *
65954 TGGGTTCTTCTCATTATGAACTCTCCACTGA-AAATGTTGA-TCCACCTCCTTC
66 TGAGTT-TTCTAATTACGAACTCTCCA-TGAGAAATGTTGATTCC-CCTCATTC
* * * ** *
66006 TGTGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAGCTTCTTCTCTTTCATCGGA
1 TATGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCAGA
* *
66071 TGAGTTTTCTAATTACGAACTCTTCATTAGAAATGTTGATTCCCCTCATTC
66 TGAGTTTTCTAATTACGAACTCTCCATGAGAAATGTTGATTCCCCTCATTC
**
66122 TACAATGGAATCGAAC
1 TATGATGGAATCGAAC
66138 AAAGTGATAA
Statistics
Matches: 111, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
115 2 0.02
116 46 0.41
117 63 0.57
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (116 bp):
TATGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCAGA
TGAGTTTTCTAATTACGAACTCTCCATGAGAAATGTTGATTCCCCTCATTC
Found at i:87614 original size:60 final size:60
Alignment explanation
Indices: 87487--87623 Score: 134
Period size: 60 Copynumber: 2.3 Consensus size: 60
87477 ACAATCGAAT
* * **
87487 GATCATTTTATAACTTTTAATAGTCGTGAGACTCAACAAAACACCACCCTATTGTTGAAG
1 GATCATTTTATAACTTTTAATAGTCGTGAGACTAAACAAAACAACACCCTATAATTGAAG
* * ** * ** *
87547 GACCATTTTATAACTTTTGATA-TTTTAGGGACTAAACAAAGTAACACCCTATAATTGAGG
1 GATCATTTTATAACTTTTAATAGTCGT-GAGACTAAACAAAACAACACCCTATAATTGAAG
87607 GATCATTTGTAT-ACTTT
1 GATCATTT-TATAACTTT
87624 ATTAAAAAAG
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
59 2 0.03
60 57 0.92
61 3 0.05
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAGTCGTGAGACTAAACAAAACAACACCCTATAATTGAAG
Found at i:90073 original size:2 final size:2
Alignment explanation
Indices: 90061--90091 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
90051 GTTTTTGAAG
90061 AT AT A- 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
90092 TTAAAAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90125 original size:60 final size:58
Alignment explanation
Indices: 90014--90125 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 58
90004 ATATATGAAA
* * *
90014 ATATATAATATATAGATATGTCAAAAAATAATATATTGTTTTTGAAGATATAATATAT
1 ATATATAATATATAGATATGTAAAAAAATAATATATAGTTTTTGAAAATATAATATAT
* *
90072 ATATATATATATATATATATTTAAAAAACAT-ATACTATAGTTTTTGAAAATATA
1 ATATATA-ATATATAGATATGTAAAAAA-ATAATA-TATAGTTTTTGAAAATATA
90126 TAACATAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 7 0.15
59 20 0.43
60 19 0.41
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (58 bp):
ATATATAATATATAGATATGTAAAAAAATAATATATAGTTTTTGAAAATATAATATAT
Found at i:90142 original size:43 final size:43
Alignment explanation
Indices: 90078--90177 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
90068 ATATATATAT
*
90078 ATATATATATATATTTAAAAAACATATACTATAG-TTTTTGAAA
1 ATATATA-ACATATTTAAAAAACATATACTATAGTTTTTTGAAA
* *
90121 ATATATAACATAGTTTTAAAAACATATAGTATAGTTTTTTGAAA
1 ATATATAACATA-TTTAAAAAACATATACTATAGTTTTTTGAAA
*
90165 ATATATAATATAT
1 ATATATAACATAT
90178 ATAGTTTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
42 4 0.08
43 27 0.53
44 20 0.39
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (43 bp):
ATATATAACATATTTAAAAAACATATACTATAGTTTTTTGAAA
Found at i:90168 original size:21 final size:19
Alignment explanation
Indices: 90101--90171 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 19
90091 TTTAAAAAAC
90101 ATATACTATAGTTTTTGAAA
1 ATATA-TATAGTTTTTGAAA
**
90121 ATATATAACATAGTTTTAAAAA
1 ATATAT---ATAGTTTTTGAAA
90143 CATATAGTATAGTTTTTTGAAA
1 -ATATA-TATAG-TTTTTGAAA
90165 ATATATA
1 ATATATA
90172 ATATATATAG
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 1 0.02
20 7 0.17
21 9 0.22
22 18 0.44
23 5 0.12
24 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (19 bp):
ATATATATAGTTTTTGAAA
Found at i:90183 original size:27 final size:28
Alignment explanation
Indices: 90144--90209 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
90134 TTTTAAAAAC
90144 ATATAGTATAGTTTTTTG-AAA-ATATATA
1 ATATA-TATAG-TTTTTGAAAACATATATA
*
90172 ATATATATAGTTTTTGAAAACCATATGTA
1 ATATATATAGTTTTTGAAAA-CATATATA
90201 ATATATATA
1 ATATATATA
90210 TATATATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.18
27 8 0.24
28 5 0.15
29 15 0.44
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (28 bp):
ATATATATAGTTTTTGAAAACATATATA
Found at i:90208 original size:2 final size:2
Alignment explanation
Indices: 90201--90269 Score: 56
Period size: 2 Copynumber: 36.0 Consensus size: 2
90191 ACCATATGTA
* *
90201 AT AT AT AT AT AT AT AT AT AT AT TT GAA AT -T AT A- AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
* * *
90241 AT AT AT TT TT A- AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90270 TAAGCTTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
1 4 0.07
2 51 0.93
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:91761 original size:13 final size:13
Alignment explanation
Indices: 91743--91772 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
91733 CTGACAGTAA
91743 TCGAGTCCCGAAT
1 TCGAGTCCCGAAT
91756 TCGAGTCCCGAAT
1 TCGAGTCCCGAAT
91769 TCGA
1 TCGA
91773 TTCAATTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (13 bp):
TCGAGTCCCGAAT
Found at i:92601 original size:15 final size:15
Alignment explanation
Indices: 92581--92618 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
92571 AATTTTATTT
92581 TTATTATCATTTCGA
1 TTATTATCATTTCGA
*
92596 TTATTATCATTTTGA
1 TTATTATCATTTCGA
92611 TTATTATC
1 TTATTATC
92619 TTTATTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (15 bp):
TTATTATCATTTCGA
Found at i:95822 original size:20 final size:20
Alignment explanation
Indices: 95797--95837 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
95787 AATAAATAAA
*
95797 AAAGGAACCACTTTGTACAT
1 AAAGGAACCACTTCGTACAT
*
95817 AAAGGAACCTCTTCGTACAT
1 AAAGGAACCACTTCGTACAT
95837 A
1 A
95838 CACTGAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (20 bp):
AAAGGAACCACTTCGTACAT
Found at i:99171 original size:20 final size:21
Alignment explanation
Indices: 99129--99172 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
99119 TTACCGGTAT
*
99129 GAATTTGGAAAAATGGACTTC
1 GAATTTGGAAAAATGGACGTC
* *
99150 GAATTTGGACACA-GGACGTC
1 GAATTTGGAAAAATGGACGTC
99170 GAA
1 GAA
99173 AAACATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (21 bp):
GAATTTGGAAAAATGGACGTC
Found at i:104666 original size:31 final size:30
Alignment explanation
Indices: 104607--104666 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
104597 TTGAATCCTT
**
104607 TTAATTCAATTTTTTTTTATTTTTTATTTC
1 TTAATTCAATTTTTTTTTATTTAATATTTC
*
104637 TTAATTTAATTTTGTTTTTATTTAATATTT
1 TTAATTCAATTTT-TTTTTATTTAATATTT
104667 AAAACAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (30 bp):
TTAATTCAATTTTTTTTTATTTAATATTTC
Found at i:118720 original size:21 final size:19
Alignment explanation
Indices: 118682--118727 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
118672 AATTAATCAT
118682 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
118702 ACTAATATTAAAGAGCTAAGA
1 ACTAATATT-AA-AGCTAAGA
118723 A-TAAT
1 ACTAAT
118728 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:132174 original size:30 final size:31
Alignment explanation
Indices: 132125--132194 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
132115 GGCCTTACAG
*
132125 AAATTTAGG-GACCATTTTG-TAATATTAGA
1 AAATTTAGGAGACCAATTTGTTAATATTAGA
*
132154 AAATTTAGGAGACCAATTTGTTAATTTTAGA
1 AAATTTAGGAGACCAATTTGTTAATATTAGA
*
132185 AAAGTTAGGA
1 AAATTTAGGA
132195 ATGGTTGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 9 0.25
30 9 0.25
31 18 0.50
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.36
Consensus pattern (31 bp):
AAATTTAGGAGACCAATTTGTTAATATTAGA
Found at i:133098 original size:40 final size:39
Alignment explanation
Indices: 133053--133178 Score: 144
Period size: 40 Copynumber: 3.2 Consensus size: 39
133043 TACACGATAG
* * *
133053 TGTGTAAGGACACTAAGTGCATATGGTGGACACGACCTTA
1 TGTGTAA-TACACTCAGTGTATATGGTGGACACGACCTTA
* ** *
133093 TGTGTAATACACTTCGGTGTATATGGTGGGTACCACCTTA
1 TGTGTAATACAC-TCAGTGTATATGGTGGACACGACCTTA
* *
133133 TTTGTAATACATTTCAGTGTATATGGTGGACACGACCTTA
1 TGTGTAATACA-CTCAGTGTATATGGTGGACACGACCTTA
133173 TGTGTA
1 TGTGTA
133179 GCACTACAGT
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
39 4 0.06
40 66 0.94
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (39 bp):
TGTGTAATACACTCAGTGTATATGGTGGACACGACCTTA
Found at i:133475 original size:20 final size:20
Alignment explanation
Indices: 133424--133480 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
133414 AACAGTACCA
133424 ATATTGTATGAATAGTATCG
1 ATATTGTATGAATAGTATCG
* * *
133444 ACACTGTATGAATAGTATTG
1 ATATTGTATGAATAGTATCG
* *
133464 ATATTGTGTGAACAGTA
1 ATATTGTATGAATAGTA
133481 ATAAATAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (20 bp):
ATATTGTATGAATAGTATCG
Found at i:134928 original size:15 final size:15
Alignment explanation
Indices: 134908--134937 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
134898 TTTAGCTGAT
*
134908 TGAGTCTAGTAGAGC
1 TGAGTCGAGTAGAGC
134923 TGAGTCGAGTAGAGC
1 TGAGTCGAGTAGAGC
134938 CTCTTGGATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.13, G:0.37, T:0.23
Consensus pattern (15 bp):
TGAGTCGAGTAGAGC
Found at i:135572 original size:18 final size:18
Alignment explanation
Indices: 135531--135588 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
135521 AAAAATAATG
*
135531 TTAAATAATATAATAAA-A
1 TTAAATAAAATAA-AAATA
*
135549 TAAAATAAAATAAAAATA
1 TTAAATAAAATAAAAATA
* *
135567 TTAAATTAAA-AGAAATA
1 TTAAATAAAATAAAAATA
135584 TTAAA
1 TTAAA
135589 GAATGATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 14 0.41
18 20 0.59
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
TTAAATAAAATAAAAATA
Found at i:135857 original size:46 final size:46
Alignment explanation
Indices: 135807--135898 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
135797 ATTTAATATT
135807 TTGGTATTTACACCTAATTACGTCCTATAAATACCCTCTAAAACCC
1 TTGGTATTTACACCTAATTACGTCCTATAAATACCCTCTAAAACCC
*
135853 TTGGTATTTACACCTAATTATGTCCTATAAATACCCTCTAAAACCC
1 TTGGTATTTACACCTAATTACGTCCTATAAATACCCTCTAAAACCC
135899 AAAAATCATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.34
Consensus pattern (46 bp):
TTGGTATTTACACCTAATTACGTCCTATAAATACCCTCTAAAACCC
Found at i:136953 original size:37 final size:34
Alignment explanation
Indices: 136905--137053 Score: 99
Period size: 31 Copynumber: 4.6 Consensus size: 34
136895 TATAAAAATA
* *
136905 ATATATATAATAATCCTATAATGTAGTATAATGT-AT
1 ATATATATAATAAT-ATATAA--TACTATAATGTAAT
*
136941 ATAATATATAATAATATATAATACTATAAT-TTA-
1 AT-ATATATAATAATATATAATACTATAATGTAAT
*
136974 ATATATAT-AT-A-ATAT-ATACTATTATG--AT
1 ATATATATAATAATATATAATACTATAATGTAAT
137002 ATATATTATAA-AATA-ATAATACTATAA-G-AAT
1 ATATA-TATAATAATATATAATACTATAATGTAAT
*
137033 ACAATATATATATAATATATA
1 A-TATATATA-ATAATATATA
137054 CTACGTAATA
Statistics
Matches: 94, Mismatches: 5, Indels: 30
0.73 0.04 0.23
Matches are distributed among these distances:
27 1 0.01
28 14 0.15
29 7 0.07
30 6 0.06
31 18 0.19
32 10 0.11
33 7 0.07
34 12 0.13
36 7 0.07
37 12 0.13
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (34 bp):
ATATATATAATAATATATAATACTATAATGTAAT
Found at i:136975 original size:20 final size:17
Alignment explanation
Indices: 136887--137053 Score: 100
Period size: 16 Copynumber: 9.7 Consensus size: 17
136877 ATATACTTTA
*
136887 ATATAATATATAAAAAT
1 ATATAATATATAATAAT
136904 A-AT-ATATATAATAAT
1 ATATAATATATAATAAT
* *
136919 CCTATAATGTAGTATAAT-GT
1 -ATATAA--TA-TATAATAAT
136939 ATATAATATATAATAAT
1 ATATAATATATAATAAT
*
136956 ATATAATA-CT-ATAAT
1 ATATAATATATAATAAT
136971 -T-TAATATATATATAAT
1 ATATAATATATA-ATAAT
* *
136987 ATATACTATTATGATATAT
1 ATATAATA-TATAATA-AT
137006 ATTATAA-A-ATAATAAT
1 A-TATAATATATAATAAT
* *
137022 ACTATAAGAATACAATATAT
1 A-TATAA-TATATAATA-AT
137042 ATATAATATATA
1 ATATAATATATA
137054 CTACGTAATA
Statistics
Matches: 116, Mismatches: 15, Indels: 37
0.69 0.09 0.22
Matches are distributed among these distances:
13 5 0.04
14 2 0.02
15 16 0.14
16 22 0.19
17 20 0.17
18 13 0.11
19 22 0.19
20 10 0.09
21 6 0.05
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (17 bp):
ATATAATATATAATAAT
Found at i:137019 original size:43 final size:40
Alignment explanation
Indices: 136889--137053 Score: 109
Period size: 43 Copynumber: 3.9 Consensus size: 40
136879 ATACTTTAAT
* * **
136889 ATAATATATAA-AAATAATATATATAATAATCCTATAATGTA
1 ATAATATATAATATATAATA-ATAT-ATAATACTATAAAATA
**
136930 GTATAATGTATATAATATATAATAATATATAATACTATAATTTA
1 --ATAA--TATATAATATATAATAATATATAATACTATAAAATA
* * *
136974 ATATATATATAATATATACTATTATGATATATATTATAAAATA
1 ATA-ATATATAATATATAATAATAT-ATA-ATACTATAAAATA
* *
137017 ATAATACTATAAGAATACAATATATATATAATA-TATA
1 ATAATA-TATAA-TATATAATA-ATATATAATACTATA
137054 CTACGTAATA
Statistics
Matches: 101, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
41 18 0.18
42 13 0.13
43 26 0.26
44 23 0.23
45 14 0.14
46 7 0.07
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (40 bp):
ATAATATATAATATATAATAATATATAATACTATAAAATA
Found at i:137055 original size:31 final size:32
Alignment explanation
Indices: 136939--137057 Score: 122
Period size: 31 Copynumber: 3.8 Consensus size: 32
136929 AGTATAATGT
* *
136939 ATATAATATATA-ATAATATATAATACT-ATA
1 ATATAATATATATATAATATATACTACTAAGA
* * *
136969 ATTTAATATATATATAATATATACTATTATGA
1 ATATAATATATATATAATATATACTACTAAGA
* *
137001 TATATATTATA-AAATAATA-ATACTA-TAAGA
1 -ATATAATATATATATAATATATACTACTAAGA
*
137031 ATACAATATATATATAATATATACTAC
1 ATATAATATATATATAATATATACTAC
137058 GTAATATATG
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
29 8 0.11
30 22 0.31
31 25 0.35
32 8 0.11
33 8 0.11
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (32 bp):
ATATAATATATATATAATATATACTACTAAGA
Found at i:141133 original size:21 final size:21
Alignment explanation
Indices: 141107--141147 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
141097 CTTGGGGCAC
141107 ATATATGTCCCGAAGGACCAT
1 ATATATGTCCCGAAGGACCAT
141128 ATATATGTCCCGAAGGACCA
1 ATATATGTCCCGAAGGACCA
141148 CTCCTTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
ATATATGTCCCGAAGGACCAT
Found at i:145836 original size:33 final size:34
Alignment explanation
Indices: 145799--145863 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
145789 AACCTAAAAT
*
145799 ATGCATCTATACGCTACAGT-ACTGCAACAGTGC
1 ATGCATCGATACGCTACAGTAACTGCAACAGTGC
* *
145832 ATGCATCGATACGCTATAGTAACTGCTACAGT
1 ATGCATCGATACGCTACAGTAACTGCAACAGT
145864 AATTTTTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (34 bp):
ATGCATCGATACGCTACAGTAACTGCAACAGTGC
Found at i:146609 original size:24 final size:24
Alignment explanation
Indices: 146577--146624 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
146567 AGTCTTCCAT
*
146577 ATGATGTATAAAATATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
146601 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
146625 TATGTCATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:148972 original size:20 final size:20
Alignment explanation
Indices: 148943--148981 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
148933 AGAGCTCATA
*
148943 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
148963 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
148982 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:160765 original size:30 final size:29
Alignment explanation
Indices: 160721--160791 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
160711 GATCAACCAT
* *
160721 TTTACAGAATTATCACCAATTTAAGAAATA
1 TTTACAAAAATATCACCAATTTAA-AAATA
*
160751 TTTACAAAAATATCACCATTTTAAAAATA
1 TTTACAAAAATATCACCAATTTAAAAATA
*
160780 ATTACCAAAAAT
1 TTTA-CAAAAAT
160792 TACTTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 8 0.22
30 28 0.78
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (29 bp):
TTTACAAAAATATCACCAATTTAAAAATA
Found at i:160784 original size:29 final size:29
Alignment explanation
Indices: 160722--160913 Score: 145
Period size: 29 Copynumber: 6.5 Consensus size: 29
160712 ATCAACCATT
* * * *
160722 TTACAGAATTATCACCAATTTAAGAAATAT
1 TTACAAAAATATCACCATTTTAA-AAATAA
160752 TTACAAAAATATCACCATTTTAAAAATAA
1 TTACAAAAATATCACCATTTTAAAAATAA
****
160781 TTACCAAAAATTACTTTTTATTTTTAAAAA-AA
1 TTA-CAAAAA-TA-TCACCA-TTTTAAAAATAA
** * *
160813 TTATGAAAATAGCACCATTTTCAAAATAA
1 TTACAAAAATATCACCATTTTAAAAATAA
* * * * *
160842 TTACCAAAATATGACAATTTTTAAAACAA
1 TTACAAAAATATCACCATTTTAAAAATAA
* *
160871 TTACTAAAATATCACCATTTT-CAAATAA
1 TTACAAAAATATCACCATTTTAAAAATAA
*
160899 TTACTAAAATATCAC
1 TTACAAAAATATCAC
160914 TCGGTCAACA
Statistics
Matches: 129, Mismatches: 28, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
28 28 0.22
29 51 0.40
30 28 0.22
31 6 0.05
32 7 0.05
33 9 0.07
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (29 bp):
TTACAAAAATATCACCATTTTAAAAATAA
Found at i:160887 original size:58 final size:59
Alignment explanation
Indices: 160752--160910 Score: 191
Period size: 61 Copynumber: 2.7 Consensus size: 59
160742 TAAGAAATAT
* * * *
160752 TTACAAAAATATCACCATTTTAAAAATAATTACCAAAA-ATTACTTTTTATTTTTAAAAAAA
1 TTACTAAAATATCACCATTTTCAAAATAATTACCAAAATATGAC---TAATTTTTAAAAAAA
* *
160813 TTA-TGAAAATAGCACCATTTTCAAAATAATTACCAAAATATGAC-AATTTTTAAAACAA
1 TTACT-AAAATATCACCATTTTCAAAATAATTACCAAAATATGACTAATTTTTAAAAAAA
*
160871 TTACTAAAATATCACCATTTTC-AAATAATTACTAAAATAT
1 TTACTAAAATATCACCATTTTCAAAATAATTACCAAAATAT
160911 CACTCGGTCA
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
57 17 0.20
58 31 0.36
59 1 0.01
61 34 0.39
62 4 0.05
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (59 bp):
TTACTAAAATATCACCATTTTCAAAATAATTACCAAAATATGACTAATTTTTAAAAAAA
Found at i:168118 original size:29 final size:29
Alignment explanation
Indices: 168051--168265 Score: 199
Period size: 29 Copynumber: 7.6 Consensus size: 29
168041 ATCAATTATT
* * * * *
168051 TTACACAATTATCACCCTTCTAAGAAATAT
1 TTACAAAAATATCACCCTTTTCA-AAATAA
168081 TTACAAAAATATCACCCTTTTCAAAATAA
1 TTACAAAAATATCACCCTTTTCAAAATAA
* * * *
168110 TTACCAAAATATCA-CTTTTTTAAAAAAA
1 TTACAAAAATATCACCCTTTTCAAAATAA
*
168138 TT-CAAAAATATCA-TC-TTT-AAAA-AA
1 TTACAAAAATATCACCCTTTTCAAAATAA
** * * *
168162 TTAGGAAAGTAGCACCATTTTCAAAATAA
1 TTACAAAAATATCACCCTTTTCAAAATAA
* *
168191 TTACCAAAATATCACCATTTTCAAAATAA
1 TTACAAAAATATCACCCTTTTCAAAATAA
* *
168220 TTACTAAAATATCACCATTTTCAAAATAA
1 TTACAAAAATATCACCCTTTTCAAAATAA
*
168249 TTACTAAAATATCACCC
1 TTACAAAAATATCACCC
168266 GGTCAACAGT
Statistics
Matches: 156, Mismatches: 24, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
24 4 0.03
25 11 0.07
26 3 0.02
27 13 0.08
28 17 0.11
29 89 0.57
30 19 0.12
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (29 bp):
TTACAAAAATATCACCCTTTTCAAAATAA
Found at i:168349 original size:19 final size:19
Alignment explanation
Indices: 168327--168363 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
168317 AACCGATTCG
*
168327 AACCGGTCAACCCGGTTTA
1 AACCGGTCAAACCGGTTTA
168346 AACCGGTCAAACCGGTTT
1 AACCGGTCAAACCGGTTT
168364 CAAGCACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (19 bp):
AACCGGTCAAACCGGTTTA
Found at i:178038 original size:42 final size:43
Alignment explanation
Indices: 177946--178051 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 43
177936 TTTATAATGT
* *
177946 TAAAATATATTA-TTTAATGGTAAAACATATAGTAAATTATTA
1 TAAAATATATTATTTTAATGGTAAAACATATAATAAATAATTA
* *
177988 TAAAATATATTATTTTAATCGTTTAAA-ATATAATAAATAATTA
1 TAAAATATATTATTTTAAT-GGTAAAACATATAATAAATAATTA
*
178031 TAGATATAATATTATTATTAA
1 TA-AAAT-ATATTATT-TTAA
178052 ATATATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
42 12 0.22
43 22 0.41
44 8 0.15
45 8 0.15
46 4 0.07
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (43 bp):
TAAAATATATTATTTTAATGGTAAAACATATAATAAATAATTA
Found at i:179896 original size:3 final size:3
Alignment explanation
Indices: 179888--180015 Score: 229
Period size: 3 Copynumber: 42.7 Consensus size: 3
179878 GAACATAGGA
* * *
179888 ATT ATT ATT ATT ATT ACT ATT ACT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
179936 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
179984 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
180016 CATCATCTGT
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 119 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:192186 original size:94 final size:94
Alignment explanation
Indices: 192079--192274 Score: 338
Period size: 94 Copynumber: 2.1 Consensus size: 94
192069 CCATCTTCAC
* * * *
192079 AATGGTATTCACAAAATCTATCTGATTTTTCAGCTACGTCCTTCTATATGGAACTCAACAGTCCT
1 AATGGCATTCACAAAATCTATCTGATTTTGCAGCTACATCCTTCTATATGGAACTCAACAGCCCT
*
192144 TTCTTCTTCATTTTCCCATATACCCACCT
66 TTCTTCTTCATTTGCCCATATACCCACCT
192173 AATGGCATTCACAAAATCTATCTGATTTTGCAGCTACATCCTTCTATATGGAACTCAACAGCCCT
1 AATGGCATTCACAAAATCTATCTGATTTTGCAGCTACATCCTTCTATATGGAACTCAACAGCCCT
*
192238 TTCTTCTTCATTTGCTCATATACCCACCT
66 TTCTTCTTCATTTGCCCATATACCCACCT
192267 AATGGCAT
1 AATGGCAT
192275 CTTTTCTTCT
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.36
Consensus pattern (94 bp):
AATGGCATTCACAAAATCTATCTGATTTTGCAGCTACATCCTTCTATATGGAACTCAACAGCCCT
TTCTTCTTCATTTGCCCATATACCCACCT
Found at i:196821 original size:4 final size:4
Alignment explanation
Indices: 196812--196846 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
196802 ACACATTCGA
196812 AAAT AAAT AAAT AAAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AA
196847 GGTTAGAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:196829 original size:13 final size:13
Alignment explanation
Indices: 196811--196846 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
196801 TACACATTCG
196811 AAAATAAATAAAT
1 AAAATAAATAAAT
196824 AAAATAAATAAAT
1 AAAATAAATAAAT
196837 -AAATAAATAA
1 AAAATAAATAA
196847 GGTTAGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:199966 original size:3 final size:3
Alignment explanation
Indices: 199958--200132 Score: 79
Period size: 3 Copynumber: 55.7 Consensus size: 3
199948 TAGTATTTTA
** * * * *
199958 AAT AAT AAT AAT AAT AAAT ACG ACT AAC AATT AAT AAC AAT AAGG AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA-T AAT AAT AAT AA-T AAT
* * * * *
200006 AAT AAC AAT ATT ATT ACT AAT AAT AAT AAAT ACAT -AT AAC AATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT AAT AA-T AAT
* * *
200053 AAA AAT AA- AA- AAT AATT AAT ATTT ATT AAT AAT -AT CAAT AAT GAAT
1 AAT AAT AAT AAT AAT AA-T AAT A-AT AAT AAT AAT AAT -AAT AAT -AAT
*
200099 AAT AAT AAT AACT AAT AAT AACC AAT AAT AAT AA
1 AAT AAT AAT AA-T AAT AAT AA-T AAT AAT AAT AA
200133 AACATTTCGG
Statistics
Matches: 134, Mismatches: 23, Indels: 30
0.72 0.12 0.16
Matches are distributed among these distances:
2 8 0.06
3 97 0.72
4 29 0.22
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:199977 original size:16 final size:16
Alignment explanation
Indices: 199956--200132 Score: 71
Period size: 16 Copynumber: 11.0 Consensus size: 16
199946 ATTAGTATTT
199956 TAAATAATAATAATAA
1 TAAATAATAATAATAA
** * *
199972 TAAATACGACTAACAA
1 TAAATAATAATAATAA
* * *
199988 TTAATAACAATAAGGAA
1 TAAATAATAATAA-TAA
* *
200005 T-AATAACAAT-ATTA
1 TAAATAATAATAATAA
* *
200019 TTACTAATAATAATAAA
1 TAAATAATAATAAT-AA
* *
200036 TACAT-ATAACAATTAA
1 TAAATAATAATAA-TAA
200052 TAAA-AATAA-AA-AA
1 TAAATAATAATAATAA
* * *
200065 TAATTAATATTTATTAA
1 TAAATAATA-ATAATAA
200082 TAATATCAATAATGAATAA
1 TAA-AT-AATAAT-AATAA
200101 T-AATAATAACTAATAA
1 TAAATAATAA-TAATAA
**
200117 TAACCAATAATAATAA
1 TAAATAATAATAATAA
200133 AACATTTCGG
Statistics
Matches: 119, Mismatches: 27, Indels: 30
0.68 0.15 0.17
Matches are distributed among these distances:
13 5 0.04
14 6 0.05
15 10 0.08
16 65 0.55
17 21 0.18
18 3 0.03
19 9 0.08
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (16 bp):
TAAATAATAATAATAA
Found at i:200102 original size:10 final size:9
Alignment explanation
Indices: 199958--200132 Score: 79
Period size: 10 Copynumber: 18.6 Consensus size: 9
199948 TAGTATTTTA
199958 AATAATAAT
1 AATAATAAT
199967 AATAATAAAT
1 AATAAT-AAT
** * *
199977 ACGACTAAC
1 AATAATAAT
*
199986 AATTAATAAC
1 AA-TAATAAT
*
199996 AATAAGGAAT
1 AATAA-TAAT
*
200006 AATAACAAT
1 AATAATAAT
* * *
200015 ATTATTACT
1 AATAATAAT
200024 AATAATAAT
1 AATAATAAT
200033 AAATACAT-AT
1 -AATA-ATAAT
*
200043 AACAATTAAT
1 AATAA-TAAT
*
200053 AAAAATAA-
1 AATAATAAT
200061 AA-AATAATT
1 AATAATAA-T
* *
200070 AATATTTATT
1 AATA-ATAAT
200080 AATAAT-AT
1 AATAATAAT
200088 CAATAATGAAT
1 -AATAAT-AAT
200099 AATAATAAT
1 AATAATAAT
200108 AACTAATAAT
1 AA-TAATAAT
*
200118 AACCAATAAT
1 AA-TAATAAT
200128 AATAA
1 AATAA
200133 AACATTTCGG
Statistics
Matches: 126, Mismatches: 25, Indels: 30
0.70 0.14 0.17
Matches are distributed among these distances:
7 5 0.04
8 4 0.03
9 49 0.39
10 62 0.49
11 6 0.05
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (9 bp):
AATAATAAT
Found at i:200105 original size:13 final size:12
Alignment explanation
Indices: 199958--200132 Score: 79
Period size: 13 Copynumber: 13.9 Consensus size: 12
199948 TAGTATTTTA
199958 AATAATAATAAT
1 AATAATAATAAT
** *
199970 AATAAATACGACT
1 AAT-AATAATAAT
* *
199983 AACAATTAATAAC
1 AATAA-TAATAAT
*
199996 AATAAGGAATAAT
1 AATAA-TAATAAT
* * *
200009 AACAATATTATT
1 AATAATAATAAT
*
200021 ACTAATAATAAT
1 AATAATAATAAT
*
200033 AAATACAT-ATAAC
1 -AATA-ATAATAAT
*
200046 AATTAATAAAAAT
1 AA-TAATAATAAT
200059 AA-AA-AATAATT
1 AATAATAATAA-T
* *
200070 AATATTTATTAAT
1 AATA-ATAATAAT
200083 AAT-ATCAATAAT
1 AATAAT-AATAAT
200095 GAATAATAATAAT
1 -AATAATAATAAT
*
200108 AACTAATAATAACC
1 AA-TAATAATAA-T
200122 AATAATAATAA
1 AATAATAATAA
200133 AACATTTCGG
Statistics
Matches: 118, Mismatches: 30, Indels: 29
0.67 0.17 0.16
Matches are distributed among these distances:
10 4 0.03
11 6 0.05
12 29 0.25
13 69 0.58
14 10 0.08
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:204260 original size:56 final size:56
Alignment explanation
Indices: 204194--204300 Score: 151
Period size: 56 Copynumber: 1.9 Consensus size: 56
204184 GTATCCCACT
*
204194 TAAAACAGAAACAGAAACAAAAACACGTTTGATGCAACATTTCCAATATAACAGAC
1 TAAAACAGAAACAGAAACAAAAACAAGTTTGATGCAACATTTCCAATATAACAGAC
* * * * * *
204250 TAAAATAGAAACTGAAACAGAAATAAGTTTGATGCTACATTTGCAATATAA
1 TAAAACAGAAACAGAAACAAAAACAAGTTTGATGCAACATTTCCAATATAA
204301 AAAGGAACTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 44 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.22
Consensus pattern (56 bp):
TAAAACAGAAACAGAAACAAAAACAAGTTTGATGCAACATTTCCAATATAACAGAC
Found at i:207237 original size:30 final size:30
Alignment explanation
Indices: 207196--207265 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
207186 TAAGAGTTAG
* * *
207196 ATTAGTATTTTGTGTAAATTTC-AAGGTCAA
1 ATTAATATTTTGTCTAAA-TTCAAAGATCAA
*
207226 ATTAATATTTTGTCTATATTCAAAGATCAA
1 ATTAATATTTTGTCTAAATTCAAAGATCAA
*
207256 ATTAAAATTT
1 ATTAATATTT
207266 AACCATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 3 0.09
30 31 0.91
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (30 bp):
ATTAATATTTTGTCTAAATTCAAAGATCAA
Found at i:207813 original size:43 final size:43
Alignment explanation
Indices: 207727--207822 Score: 99
Period size: 43 Copynumber: 2.3 Consensus size: 43
207717 TTTATAATGT
* *
207727 TAAAATATATT-CTTTAATAGTAAAAAATGTAACAAATTATTA
1 TAAAATATATTACTTTAATAGTAAAAAATATAACAAATGATTA
** * *
207769 TAAAATATATTACTTTAATTA-TTTAAAATATAATAAATGGTTA
1 TAAAATATATTACTTTAA-TAGTAAAAAATATAACAAATGATTA
*
207812 T-AGATATATTA
1 TAAAATATATTA
207823 TTATTAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
42 20 0.44
43 23 0.51
44 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (43 bp):
TAAAATATATTACTTTAATAGTAAAAAATATAACAAATGATTA
Found at i:208731 original size:12 final size:12
Alignment explanation
Indices: 208716--208781 Score: 89
Period size: 12 Copynumber: 5.6 Consensus size: 12
208706 GTTATTTAAA
208716 CGGGTATTGGGC
1 CGGGTATTGGGC
*
208728 CGGGTATTGGGT
1 CGGGTATTGGGC
*
208740 CGGGTATTGGGT
1 CGGGTATTGGGC
208752 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
208763 CGGGAATCGGGC
1 CGGGTATTGGGC
208775 CGGGTAT
1 CGGGTAT
208782 ATATATATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.21
12 38 0.79
ACGTcount: A:0.11, C:0.15, G:0.48, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:208743 original size:24 final size:24
Alignment explanation
Indices: 208716--208781 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 24
208706 GTTATTTAAA
*
208716 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGGGTATTGGGC
*
208740 CGGGTATTGGGTC-GGTATTGGGC
1 CGGGTATTGGGCCGGGTATTGGGC
* *
208763 CGGGAATCGGGCCGGGTAT
1 CGGGTATTGGGCCGGGTAT
208782 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.11, C:0.15, G:0.48, T:0.26
Consensus pattern (24 bp):
CGGGTATTGGGCCGGGTATTGGGC
Found at i:208839 original size:24 final size:25
Alignment explanation
Indices: 208779--208863 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 25
208769 TCGGGCCGGG
208779 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
208802 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
* * *
208826 T-T-TATTAATATTATATATATATATA
1 TATATATT-ATATTATTTAAAT-TAAA
208851 TATATATATATAT
1 TATATAT-TATAT
208864 ATAAATAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
22 4 0.08
23 8 0.16
24 24 0.49
25 4 0.08
26 1 0.02
27 7 0.14
28 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:208844 original size:2 final size:2
Alignment explanation
Indices: 208833--208866 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
208823 AAATTTATTA
208833 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
208867 AATAATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208917 original size:13 final size:12
Alignment explanation
Indices: 208886--208922 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
208876 TTTTAATATT
*
208886 TATCGGGTCGGG
1 TATCGGGGCGGG
208898 TATCGGGGCGGG
1 TATCGGGGCGGG
208910 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
208923 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:208984 original size:6 final size:6
Alignment explanation
Indices: 208973--209007 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
208963 AAATGGGTTT
* *
208973 TCCCCG TCCCCG TCCCCA TCCCCG TCCCCA TCCCC
1 TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG TCCCC
209008 ATTTATCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.06, C:0.69, G:0.09, T:0.17
Consensus pattern (6 bp):
TCCCCG
Found at i:208994 original size:12 final size:12
Alignment explanation
Indices: 208973--209007 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
208963 AAATGGGTTT
*
208973 TCCCCGTCCCCG
1 TCCCCATCCCCG
208985 TCCCCATCCCCG
1 TCCCCATCCCCG
208997 TCCCCATCCCC
1 TCCCCATCCCC
209008 ATTTATCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.69, G:0.09, T:0.17
Consensus pattern (12 bp):
TCCCCATCCCCG
Found at i:208996 original size:18 final size:18
Alignment explanation
Indices: 208973--209009 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
208963 AAATGGGTTT
*
208973 TCCCCGTCCCCGTCCCCA
1 TCCCCGTCCCCATCCCCA
208991 TCCCCGTCCCCATCCCCA
1 TCCCCGTCCCCATCCCCA
209009 T
1 T
209010 TTATCATCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.65, G:0.08, T:0.19
Consensus pattern (18 bp):
TCCCCGTCCCCATCCCCA
Found at i:219346 original size:31 final size:30
Alignment explanation
Indices: 219287--219392 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
219277 TGAATTTAGG
* * * *
219287 GGTC-AATTCATATTTTATATAGAGTTTAA
1 GGTCAAATTAATATTTTATGTAAATTTTAA
* * *
219316 GAGTTAGATTACTATTTTATGTAAATTTTAA
1 G-GTCAAATTAATATTTTATGTAAATTTTAA
* *
219347 GGTCAAATTAATATTTTGTGTAAA-TTAACA
1 GGTCAAATTAATATTTTATGTAAATTTTA-A
*
219377 GGTCAAATTAAAATTT
1 GGTCAAATTAATATTT
219393 AACCATTTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
29 4 0.07
30 37 0.61
31 20 0.33
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (30 bp):
GGTCAAATTAATATTTTATGTAAATTTTAA
Found at i:220671 original size:2 final size:2
Alignment explanation
Indices: 220664--220694 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
220654 TTCTTAACGG
220664 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 A
220695 AAATTAAAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:220758 original size:24 final size:24
Alignment explanation
Indices: 220711--220811 Score: 139
Period size: 24 Copynumber: 4.2 Consensus size: 24
220701 AAACATAATT
* * * *
220711 CAGGTCAAGTAGCAAATCAGAATC
1 CAGGTCAAGTATCATATAAAAATC
* *
220735 TATGTCAAGTATCATATAAAAATC
1 CAGGTCAAGTATCATATAAAAATC
220759 CAGGTCAAGTATCATATAAAAATC
1 CAGGTCAAGTATCATATAAAAATC
*
220783 CAGGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCATATAAAAATC
220807 CAGGT
1 CAGGT
220812 AAAAAATTAG
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCATATAAAAATC
Found at i:221583 original size:29 final size:29
Alignment explanation
Indices: 221526--221735 Score: 215
Period size: 29 Copynumber: 7.2 Consensus size: 29
221516 TTTACACAAT
* * *
221526 TATCACCCTTTTAAGAAATATTTAAGAAAA
1 TATCACCATTTTAA-AAATAATTACGAAAA
*
221556 TATCACCATTTTAAAAATAATTACGAAAC
1 TATCACCATTTTAAAAATAATTACGAAAA
** *
221585 TATCACTTTTTTAAAAATAATTACGAAAC
1 TATCACCATTTTAAAAATAATTACGAAAA
** *
221614 TATCACTTTTTTAAAAATAATTATGAAAA
1 TATCACCATTTTAAAAATAATTACGAAAA
* * * *
221643 TATAACCTTTTTTAAAAAAAATTA-AAAAA
1 TATCACC-ATTTTAAAAATAATTACGAAAA
* * *
221672 TAGCACCATTTTCAAAATAATTACCAAAA
1 TATCACCATTTTAAAAATAATTACGAAAA
* * *
221701 TAACACCATTTTGAAAATAATTACTAAAA
1 TATCACCATTTTAAAAATAATTACGAAAA
221730 TATCAC
1 TATCAC
221736 TCGGTCAACG
Statistics
Matches: 156, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
28 13 0.08
29 115 0.74
30 28 0.18
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (29 bp):
TATCACCATTTTAAAAATAATTACGAAAA
Found at i:227866 original size:2 final size:2
Alignment explanation
Indices: 227859--227917 Score: 82
Period size: 2 Copynumber: 29.5 Consensus size: 2
227849 GTATTGGACC
* * * *
227859 AT AT AT AT AT GT GT GT AT AT AT TT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
227901 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
227918 GACAATCATT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:230675 original size:42 final size:42
Alignment explanation
Indices: 230628--230734 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
230618 AAGAGAATGA
*
230628 ACTAATAAGTCTTTTGATTTATGTTTTATGAATGGATCATGG
1 ACTAATAAGTCTTTTGATTTATGTTTAATGAATGGATCATGG
230670 ACTAATAAGTCTTTTGATTTATGTTTAATGAATGGATCATGG
1 ACTAATAAGTCTTTTGATTTATGTTTAATGAATGGATCATGG
* *
230712 ACTAATATGTCCTTTGATTTATG
1 ACTAATAAGTCTTTTGATTTATG
230735 GGAAGGAAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (42 bp):
ACTAATAAGTCTTTTGATTTATGTTTAATGAATGGATCATGG
Found at i:243429 original size:17 final size:16
Alignment explanation
Indices: 243407--243438 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
243397 CTGTTATGCT
243407 TTCTGATTTGAATTCTA
1 TTCTGATTTG-ATTCTA
243424 TTCTGATTTGATTCT
1 TTCTGATTTGATTCT
243439 GTTATGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.56
Consensus pattern (16 bp):
TTCTGATTTGATTCTA
Found at i:244928 original size:2 final size:2
Alignment explanation
Indices: 244921--244961 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
244911 GGGTTTGAAG
244921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
244962 TAGGATACAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:251225 original size:21 final size:21
Alignment explanation
Indices: 251199--251243 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
251189 AGTTTGATAG
251199 CGATCGAATGGAGTAAATGGT
1 CGATCGAATGGAGTAAATGGT
251220 CGATCGAATGGAGTAAATGGT
1 CGATCGAATGGAGTAAATGGT
251241 CGA
1 CGA
251244 CCGATGTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (21 bp):
CGATCGAATGGAGTAAATGGT
Found at i:252044 original size:41 final size:42
Alignment explanation
Indices: 251997--252091 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
251987 CTGCCCGAAT
* * * *
251997 CTTATAGATGGCCTAAAGGACTT-ATCATCTTGGTCGAAAGA
1 CTTATAGATGGCCCAAAGGACTTAAGCATCATGCTCGAAAGA
** *
252038 CTTATAGATAACCCAAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCAAAGGACTTAAGCATCATGCTCGAAAGA
*
252080 CTTATTGATGGC
1 CTTATAGATGGC
252092 TCGAGGGACT
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
41 19 0.44
42 24 0.56
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (42 bp):
CTTATAGATGGCCCAAAGGACTTAAGCATCATGCTCGAAAGA
Found at i:252279 original size:57 final size:56
Alignment explanation
Indices: 252202--252525 Score: 281
Period size: 57 Copynumber: 5.8 Consensus size: 56
252192 ATCTTTTTTA
252202 AAAAATTCTTTGGAAATAATCATCAAGAAACCCCCT-AAAATCAGGCTTAGCATCTTT
1 AAAAATTCTTTGGAAA-AATCATCAAGAAA-CCCCTGAAAATCAGGCTTAGCATCTTT
* * *
252259 AAAAATTCTTTGGAAATAATCATTAAGAAACCTCTGAAAATCAGGCTTAGCTTCTTT
1 AAAAATTCTTTGGAAA-AATCATCAAGAAACCCCTGAAAATCAGGCTTAGCATCTTT
* * *
252316 AAAAATTCTTTGGAAATGATCATCAAGAAACCCCTGAGAATCATGCTTAG--T-TTAT
1 AAAAATTCTTTGGAAA-AATCATCAAGAAACCCCTGAAAATCAGGCTTAGCATCTT-T
* * * * *
252371 AAATAAACTCATTTTG-AAAA-CATCAAGAAACCCCTAAAAATTAGGCTTAG-ATTCTAT
1 -AA-AAATTC-TTTGGAAAAATCATCAAGAAACCCCTGAAAATCAGGCTTAGCA-TCTTT
* * * * * *
252428 CAAAATTATTT-TAAAAA-CATCAAGAAACCCATGAAAATCAGGCTTAACTTCTTT
1 AAAAATTCTTTGGAAAAATCATCAAGAAACCCCTGAAAATCAGGCTTAGCATCTTT
* * **
252482 CAAAA-TCGTTGGAAAACATCATATCAAGAAACCTATGAAAATCA
1 AAAAATTCTTTGGAAAA-ATC--ATCAAGAAACCCCTGAAAATCA
252526 AACCTAGATT
Statistics
Matches: 222, Mismatches: 30, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
53 3 0.01
54 48 0.22
55 33 0.15
56 9 0.04
57 103 0.46
58 26 0.12
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (56 bp):
AAAAATTCTTTGGAAAAATCATCAAGAAACCCCTGAAAATCAGGCTTAGCATCTTT
Found at i:256921 original size:32 final size:32
Alignment explanation
Indices: 256880--256968 Score: 142
Period size: 32 Copynumber: 2.8 Consensus size: 32
256870 TATGACTACA
* *
256880 CTTGGGTAGGCTCTGAGGCCCCAAGGTATTTC
1 CTTGGGTAGGCTCTAAGGCCCCAAGGTATTCC
256912 CTTGGGTAGGCTCTAAGGCCCCAAGGTATTCC
1 CTTGGGTAGGCTCTAAGGCCCCAAGGTATTCC
* *
256944 CTTGGGTAGTCTCTTAGGCCCCAAG
1 CTTGGGTAGGCTCTAAGGCCCCAAG
256969 TTACACTCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
CTTGGGTAGGCTCTAAGGCCCCAAGGTATTCC
Found at i:258102 original size:98 final size:99
Alignment explanation
Indices: 257902--258091 Score: 301
Period size: 98 Copynumber: 1.9 Consensus size: 99
257892 TAATCATTTT
* * * *
257902 GTAATAAGTATACCAAAGTATCTTATATGTTATGATTCAATCTGTGCAAATAAGGGAATATTGTC
1 GTAATAAGTATACCAAAGTATCTTATATGTTATGACTCAACCTGCGCAAAAAAGGGAATATTGTC
* *
257967 ATTATTCGTCCCAATTTTGGAAGTTACAACAATA
66 AATATTCATCCCAATTTTGGAAGTTACAACAATA
*
258001 GTAA-AAGTATACCAAAGTATCTTATCTGTTATGACTCAACCTGCGCAAAAAAGGGAATATTGTC
1 GTAATAAGTATACCAAAGTATCTTATATGTTATGACTCAACCTGCGCAAAAAAGGGAATATTGTC
*
258065 AATATTCATTCCAATTTTGGAAGTTAC
66 AATATTCATCCCAATTTTGGAAGTTAC
258092 CCCATGAGTA
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
98 79 0.95
99 4 0.05
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (99 bp):
GTAATAAGTATACCAAAGTATCTTATATGTTATGACTCAACCTGCGCAAAAAAGGGAATATTGTC
AATATTCATCCCAATTTTGGAAGTTACAACAATA
Found at i:258664 original size:46 final size:46
Alignment explanation
Indices: 258609--258703 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
258599 TAAAACTCAT
258609 TTATTTTGTTAGGGATTTAAGAAAACAAGGAAAGTTAAAATTTTGG
1 TTATTTTGTTAGGGATTTAAGAAAACAAGGAAAGTTAAAATTTTGG
258655 TTATTTTGTTAGGGATTTAAGAAAACAAGGAAAGTTAAAATTTTGG
1 TTATTTTGTTAGGGATTTAAGAAAACAAGGAAAGTTAAAATTTTGG
258701 TTA
1 TTA
258704 AGTTACTTAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.38
Consensus pattern (46 bp):
TTATTTTGTTAGGGATTTAAGAAAACAAGGAAAGTTAAAATTTTGG
Found at i:259121 original size:45 final size:45
Alignment explanation
Indices: 259070--259361 Score: 401
Period size: 45 Copynumber: 6.5 Consensus size: 45
259060 TAATCCAAAG
* *
259070 GCATTAAAGGCATGAAAGGATGTCATAAATGAAATGCATAATGGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGT
* * * * **
259115 GCATTAAATGCATGAAGGGATTCCATAAATAAAATGCATAACATT
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGT
*
259160 GCATTAAAGGCATGAAATGATGCCATAAATGAAATGCATAACGGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGT
*
259205 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCA-AACTGAT
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAC-GGT
* * *
259250 ACATTAAAGGCATGAAAGGATGCCATAAATGGAATGCATAAC-AT
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGT
**
259294 -CACAATAAGGACATGAAAGGATGCCATAAATGAAATGCATAACGGT
1 GCATTA-AAGG-CATGAAAGGATGCCATAAATGAAATGCATAACGGT
259340 GCATTAAAGGCATGAAAGGATG
1 GCATTAAAGGCATGAAAGGATG
259362 TTGTTGAAAA
Statistics
Matches: 216, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
43 3 0.01
44 9 0.04
45 193 0.89
46 8 0.04
47 3 0.01
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.22
Consensus pattern (45 bp):
GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGT
Found at i:259317 original size:135 final size:135
Alignment explanation
Indices: 259070--259361 Score: 444
Period size: 135 Copynumber: 2.2 Consensus size: 135
259060 TAATCCAAAG
* * * * *
259070 GCATTAAAGGCATGAAAGGATGTCATAAATGAAATGCATAATGGTGCATTAAATGCATGAAGGGA
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAATGATACATTAAAGGCATGAAAGGA
* ** * *
259135 TTCCATAAATAAAATGCATAACATTGCATTAAAGGCATGAAATGATGCCATAAATGAAATGCATA
66 TGCCATAAATAAAATGCATAACATCACAATAAAGGCATGAAAGGATGCCATAAATGAAATGCATA
259200 ACGGT
131 ACGGT
259205 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCA-AACTGATACATTAAAGGCATGAAAGG
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAA-TGATACATTAAAGGCATGAAAGG
**
259269 ATGCCATAAATGGAATGCATAACATCACAAT-AAGGACATGAAAGGATGCCATAAATGAAATGCA
65 ATGCCATAAATAAAATGCATAACATCACAATAAAGG-CATGAAAGGATGCCATAAATGAAATGCA
259333 TAACGGT
129 TAACGGT
259340 GCATTAAAGGCATGAAAGGATG
1 GCATTAAAGGCATGAAAGGATG
259362 TTGTTGAAAA
Statistics
Matches: 143, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
134 6 0.04
135 137 0.96
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.22
Consensus pattern (135 bp):
GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAATGATACATTAAAGGCATGAAAGGA
TGCCATAAATAAAATGCATAACATCACAATAAAGGCATGAAAGGATGCCATAAATGAAATGCATA
ACGGT
Found at i:259692 original size:18 final size:18
Alignment explanation
Indices: 259669--259713 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
259659 AAATGGATAC
259669 CGATACCCTACCTAGTAT
1 CGATACCCTACCTAGTAT
259687 CGATACCCTACCTAGTAT
1 CGATACCCTACCTAGTAT
259705 CGATACCCT
1 CGATACCCT
259714 TACATATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.36, G:0.11, T:0.27
Consensus pattern (18 bp):
CGATACCCTACCTAGTAT
Found at i:259915 original size:44 final size:44
Alignment explanation
Indices: 259819--259916 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
259809 GCATGTTCGG
* *
259819 TATCGATACTACTTTACATAGTAGTATCGATACTCACTGGACGA
1 TATCGATACTACTTCACATAGTAGTATCGATACTCACTGGACAA
* *
259863 TTTTGATACTA-TTGCACATAGTAGTATCGATACTTC-CTGGACAA
1 TATCGATACTACTT-CACATAGTAGTATCGATAC-TCACTGGACAA
259907 TATCGATACT
1 TATCGATACT
259917 GTTGAGTTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 2 0.04
44 42 0.91
45 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (44 bp):
TATCGATACTACTTCACATAGTAGTATCGATACTCACTGGACAA
Found at i:265337 original size:42 final size:42
Alignment explanation
Indices: 265275--265370 Score: 156
Period size: 42 Copynumber: 2.3 Consensus size: 42
265265 TTGTGCACTT
* *
265275 GGTATCGATACTGGTCACCCAATACCGATACTACTCTTGCTA
1 GGTATCGATATTGGTCACCCAATACCAATACTACTCTTGCTA
* *
265317 GGTATCGATATTGGTTACCCAGTACCAATACTACTCTTGCTA
1 GGTATCGATATTGGTCACCCAATACCAATACTACTCTTGCTA
265359 GGTATCGATATT
1 GGTATCGATATT
265371 ACTATCATAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (42 bp):
GGTATCGATATTGGTCACCCAATACCAATACTACTCTTGCTA
Found at i:265388 original size:42 final size:42
Alignment explanation
Indices: 265297--265390 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
265287 GGTCACCCAA
* ** *
265297 TACCGATACTACTCTTGCTAGGTATCGATATTGGTTACCCAG
1 TACCAATACTACTCTTGCTAGGTATCGATATTACTTACACAG
*
265339 TACCAATACTACTCTTGCTAGGTATCGATATTAC-TATCATAG
1 TACCAATACTACTCTTGCTAGGTATCGATATTACTTA-CACAG
*
265381 TATCAATACT
1 TACCAATACT
265391 GATATCATTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 2 0.04
42 43 0.96
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (42 bp):
TACCAATACTACTCTTGCTAGGTATCGATATTACTTACACAG
Found at i:268996 original size:90 final size:90
Alignment explanation
Indices: 268850--269021 Score: 258
Period size: 90 Copynumber: 1.9 Consensus size: 90
268840 GAAATATATA
** * * *
268850 ATGGTGCATTAAAGGCATGATAGTATTCCATAAATGAAATGTATAATGGTGTATTAAA-GACATG
1 ATGGTGCATTAAAGGCATGATAGTAAGCCATAAATGAAATGCATAACGGTGCATTAAACG-CATG
268914 AAAGGATGTCATAAATGATATGCATG
65 AAAGGATGTCATAAATGATATGCATG
268940 ATGGTGCATTAAAGGCATGAATAG-AAGCCATAAATGAAATGCATAACGGTGCATTAAACGCATG
1 ATGGTGCATTAAAGGCATG-ATAGTAAGCCATAAATGAAATGCATAACGGTGCATTAAACGCATG
*
269004 AAAGGATGTTATAAATGA
65 AAAGGATGTCATAAATGA
269022 AAATAAATGA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
90 69 0.93
91 5 0.07
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (90 bp):
ATGGTGCATTAAAGGCATGATAGTAAGCCATAAATGAAATGCATAACGGTGCATTAAACGCATGA
AAGGATGTCATAAATGATATGCATG
Found at i:269005 original size:45 final size:45
Alignment explanation
Indices: 268827--269023 Score: 211
Period size: 45 Copynumber: 4.4 Consensus size: 45
268817 TTGACTCAAC
* **
268827 AGATGCCAAAAATGAAATATATAATGGTGCATTAAAGGCATG-AT
1 AGATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAT
* * * *
268871 AGTATTCCATAAATGAAATGTATAATGGTGTATTAAAGACATGAA-
1 AG-ATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAT
* * *
268916 AGGATGTCATAAATGATATGCATGATGGTGCATTAAAGGCATGAAT
1 A-GATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAT
* * *
268962 AGAAGCCATAAATGAAATGCATAACGGTGCATTAAACGCATGAA-
1 AGATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAT
**
269006 AGGATGTTATAAATGAAA
1 A-GATGCCATAAATGAAA
269024 ATAAATGATA
Statistics
Matches: 127, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
44 3 0.02
45 121 0.95
46 3 0.02
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (45 bp):
AGATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAT
Found at i:269433 original size:8 final size:8
Alignment explanation
Indices: 269416--269449 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
269406 ACTGCAAAGA
269416 TTAATATG
1 TTAATATG
*
269424 TTAATTTG
1 TTAATATG
269432 TTAATATG
1 TTAATATG
269440 TTAATATG
1 TTAATATG
269448 TT
1 TT
269450 TTTCAATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (8 bp):
TTAATATG
Found at i:271257 original size:12 final size:12
Alignment explanation
Indices: 271240--271311 Score: 65
Period size: 12 Copynumber: 6.0 Consensus size: 12
271230 AAATGGAGAT
*
271240 ATCAGAAATCAA
1 ATCAGAAATCAG
*
271252 ATCAGAATTCAG
1 ATCAGAAATCAG
* *
271264 ATCATATATCAG
1 ATCAGAAATCAG
271276 ATCAG-AATCCAG
1 ATCAGAAAT-CAG
*
271288 ATTAGAAATCAG
1 ATCAGAAATCAG
* *
271300 AACAGAATTCAG
1 ATCAGAAATCAG
271312 GTAATGTATC
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
11 2 0.04
12 42 0.89
13 3 0.06
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (12 bp):
ATCAGAAATCAG
Found at i:271274 original size:24 final size:24
Alignment explanation
Indices: 271240--271311 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
271230 AAATGGAGAT
271240 ATCAGAAATCAAATCAGAATTCAG
1 ATCAGAAATCAAATCAGAATTCAG
* * * *
271264 ATCATATATCAGATCAGAATCCAG
1 ATCAGAAATCAAATCAGAATTCAG
*
271288 ATTAGAAATCAGAA-CAGAATTCAG
1 ATCAGAAATCA-AATCAGAATTCAG
271312 GTAATGTATC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 37 0.97
25 1 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAATCAGAATTCAG
Found at i:275943 original size:18 final size:18
Alignment explanation
Indices: 275891--275943 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
275881 ACGATCAACT
* **
275891 GTCAACGAGTCGGGTTAG
1 GTCAACGGGTCGGGTCGG
* *
275909 GTTAACGGGTCGTGTCGG
1 GTCAACGGGTCGGGTCGG
275927 GTCAACGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
275944 AGTTGGAACC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.43, T:0.23
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCGG
Found at i:279602 original size:18 final size:18
Alignment explanation
Indices: 279579--279619 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
279569 CAACAATCAA
279579 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
279597 CGGGTCAATGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
279615 CGGGT
1 CGGGT
279620 TAGAACTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.20, G:0.51, T:0.20
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:281674 original size:24 final size:23
Alignment explanation
Indices: 281647--281718 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
281637 AAACATAGAT
*
281647 ATCAGAAATCAAAGCAGAATTCAG
1 ATCAAAAATCAAA-CAGAATTCAG
* * * *
281671 ATCATATATCATATCAGAATCCAG
1 ATCAAAAATCA-AACAGAATTCAG
*
281695 ATCAAAAATCAGAACATAATTCAG
1 ATCAAAAATCA-AACAGAATTCAG
281719 GTAATGTATC
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 36 0.97
25 1 0.03
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.22
Consensus pattern (23 bp):
ATCAAAAATCAAACAGAATTCAG
Found at i:283863 original size:23 final size:23
Alignment explanation
Indices: 283832--283885 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
283822 GTTCGAGTCA
*
283832 GGTCAGGTCAGGTCAACGGGTCG
1 GGTCGGGTCAGGTCAACGGGTCG
* * *
283855 TGTCGGGTCGGGTTAACGGGTCG
1 GGTCGGGTCAGGTCAACGGGTCG
283878 GGTCGGGT
1 GGTCGGGT
283886 TGGAACCGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.11, C:0.19, G:0.48, T:0.22
Consensus pattern (23 bp):
GGTCGGGTCAGGTCAACGGGTCG
Found at i:288264 original size:18 final size:18
Alignment explanation
Indices: 288243--288293 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
288233 GTCAACGGGT
288243 CGGGTCAGGTCGGGTCAA
1 CGGGTCAGGTCGGGTCAA
*
288261 CGGGTCAGGTCGAGTCAA
1 CGGGTCAGGTCGGGTCAA
* *
288279 CGGTTCGGGTCGGGT
1 CGGGTCAGGTCGGGT
288294 TGGAACTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.20
Consensus pattern (18 bp):
CGGGTCAGGTCGGGTCAA
Found at i:288287 original size:23 final size:22
Alignment explanation
Indices: 288233--288289 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 22
288223 CAGTCAACGG
*
288233 GTCAACGGGTCGGGTCAGGTCGG
1 GTCAAC-GGTCGGGTCAGGTCGA
288256 GTCAA----CGGGTCAGGTCGA
1 GTCAACGGTCGGGTCAGGTCGA
288274 GTCAACGGTTCGGGTC
1 GTCAACGG-TCGGGTC
288290 GGGTTGGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
18 17 0.61
23 11 0.39
ACGTcount: A:0.16, C:0.23, G:0.42, T:0.19
Consensus pattern (22 bp):
GTCAACGGTCGGGTCAGGTCGA
Found at i:290300 original size:12 final size:12
Alignment explanation
Indices: 290277--290337 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
290267 AAACGTAGAT
*
290277 ATCAGAAATCAG
1 ATCAGAATTCAG
*
290289 AGCAGAATTCAG
1 ATCAGAATTCAG
*
290301 ATCA-TATATCAG
1 ATCAGAAT-TCAG
*
290313 ATCAGAATCCAG
1 ATCAGAATTCAG
*
290325 ATCAGAAATCAG
1 ATCAGAATTCAG
290337 A
1 A
290338 ACATAAATCA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.20
Consensus pattern (12 bp):
ATCAGAATTCAG
Found at i:290304 original size:24 final size:24
Alignment explanation
Indices: 290277--290337 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
290267 AAACGTAGAT
*
290277 ATCAGAAATCAGAGCAGAATTCAG
1 ATCAGAAATCAGAGCAGAATCCAG
* * *
290301 ATCATATATCAGATCAGAATCCAG
1 ATCAGAAATCAGAGCAGAATCCAG
290325 ATCAGAAATCAGA
1 ATCAGAAATCAGA
290338 ACATAAATCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAGCAGAATCCAG
Found at i:290318 original size:36 final size:36
Alignment explanation
Indices: 290277--290348 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
290267 AAACGTAGAT
* * *
290277 ATCAGAAAT-CAGAGCAGAATTCAGATCATATATCAG
1 ATCAG-AATCCAGAGCAGAAATCAGAACATAAATCAG
*
290313 ATCAGAATCCAGATCAGAAATCAGAACATAAATCAG
1 ATCAGAATCCAGAGCAGAAATCAGAACATAAATCAG
290349 GTAATGTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 3 0.10
36 28 0.90
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.19
Consensus pattern (36 bp):
ATCAGAATCCAGAGCAGAAATCAGAACATAAATCAG
Found at i:290359 original size:48 final size:47
Alignment explanation
Indices: 290277--290385 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 47
290267 AAACGTAGAT
* * * * *
290277 ATCAGAAATCAGAGCAGAATTCAGATCATATATCAGATCAGAATCCA
1 ATCAGAAATCAGAACAGAAATCAGATAATATATCAAAACAGAATCCA
* * * *
290324 GATCAGAAATCAGAACATAAATCAGGTAATGTATCAAAACAGAATTCA
1 -ATCAGAAATCAGAACAGAAATCAGATAATATATCAAAACAGAATCCA
*
290372 AGTCAAAAATCAGA
1 A-TCAGAAATCAGA
290386 TAAAATATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.02
48 49 0.98
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.20
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAAATCAGATAATATATCAAAACAGAATCCA
Found at i:294782 original size:48 final size:49
Alignment explanation
Indices: 294703--294808 Score: 112
Period size: 48 Copynumber: 2.2 Consensus size: 49
294693 CGGAGATATC
* * *
294703 AGAAATCA-AAGCAGAATTCAGATCACATATC-ATATAAGAA-TCTAGATT
1 AGAAATCAGAAGCAGAATTCAGATAACATATCAAAAT-AGAATTCAAG-TT
* **
294751 AGAAATCAGAA-CAGAATTCAGGTAATGTATCAAAATAGAATTCAAGTT
1 AGAAATCAGAAGCAGAATTCAGATAACATATCAAAATAGAATTCAAGTT
294799 AGAAATCAGA
1 AGAAATCAGA
294809 TAAAATATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
48 40 0.82
49 9 0.18
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (49 bp):
AGAAATCAGAAGCAGAATTCAGATAACATATCAAAATAGAATTCAAGTT
Found at i:297141 original size:18 final size:18
Alignment explanation
Indices: 297118--297152 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
297108 AGTAAATGGG
297118 TCAGGTCAACGGGTCGGT
1 TCAGGTCAACGGGTCGGT
297136 TCAGGTCAACGGGTCGG
1 TCAGGTCAACGGGTCGG
297153 GTCTGGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.40, T:0.20
Consensus pattern (18 bp):
TCAGGTCAACGGGTCGGT
Done.