Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015263.1 Kokia drynarioides strain JFW-HI SEQ_130308, 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: 1369056
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 871 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:17906 original size:19 final size:20
Alignment explanation
Indices: 17882--17919 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17872 TTCGATTCAA
17882 TCAG-TTTTGGGTCTCGGTC
1 TCAGTTTTTGGGTCTCGGTC
*
17901 TCAGTTTTTGGTTCTCGGT
1 TCAGTTTTTGGGTCTCGGT
17920 TCCAACTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.05, C:0.18, G:0.29, T:0.47
Consensus pattern (20 bp):
TCAGTTTTTGGGTCTCGGTC
Found at i:21382 original size:29 final size:29
Alignment explanation
Indices: 21325--21382 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
21315 ATTTTTAAAA
*
21325 TTTTAAAATTCAAAAATATTCAAACTATT
1 TTTTAAAATTCAAAAATATTAAAACTATT
*
21354 TTTTAAAATT-AAAAATCATTAAAATTATT
1 TTTTAAAATTCAAAAAT-ATTAAAACTATT
21383 ACAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (29 bp):
TTTTAAAATTCAAAAATATTAAAACTATT
Found at i:21405 original size:17 final size:17
Alignment explanation
Indices: 21372--21411 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
21362 TTAAAAATCA
21372 TTAAAATTATTACAATT
1 TTAAAATTATTACAATT
*
21389 TTAAATATTTTTA-AATT
1 TTAAA-ATTATTACAATT
21406 TTAAAA
1 TTAAAA
21412 AATAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 14 0.67
18 6 0.29
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAATTATTACAATT
Found at i:22745 original size:26 final size:26
Alignment explanation
Indices: 22682--22736 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
22672 CTGACACAAA
22682 TGGAGGGTTTTGAGTGACGGCACCCT
1 TGGAGGGTTTTGAGTGACGGCACCCT
*
22708 TGGAGGGTTTTGAAGTGGCGGCA-CCT
1 TGGAGGGTTTTG-AGTGACGGCACCCT
22734 TGG
1 TGG
22737 GGTTTTTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.15, C:0.16, G:0.42, T:0.27
Consensus pattern (26 bp):
TGGAGGGTTTTGAGTGACGGCACCCT
Found at i:22852 original size:29 final size:30
Alignment explanation
Indices: 22819--22880 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
22809 GTTTTGGTTT
**
22819 TTTACTAATTTAATACAAAAAAA-TATTTA
1 TTTACTAAAATAATACAAAAAAATTATTTA
* *
22848 TTTACTAAAATATTATAAAAAAATTATTTA
1 TTTACTAAAATAATACAAAAAAATTATTTA
22878 TTT
1 TTT
22881 TATTTGACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTACTAAAATAATACAAAAAAATTATTTA
Found at i:22883 original size:35 final size:35
Alignment explanation
Indices: 22844--22915 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
22834 CAAAAAAATA
*
22844 TTTATTT-ACTAAAATATTATAAAAAAATTATTTAT
1 TTTATTTGACTAAAATAATAT-AAAAAATTATTTAT
* *
22879 TTTATTTGACTAAAATAATATTAAAATTTATTTAT
1 TTTATTTGACTAAAATAATATAAAAAATTATTTAT
22914 TT
1 TT
22916 AATAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 21 0.64
36 12 0.36
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
TTTATTTGACTAAAATAATATAAAAAATTATTTAT
Found at i:23733 original size:24 final size:24
Alignment explanation
Indices: 23701--23747 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
23691 ATGTGGAACC
23701 AGTAGAAAATGAAGATCCAACTCT
1 AGTAGAAAATGAAGATCCAACTCT
*
23725 AGTAGAAAATGAAGATTCAACTC
1 AGTAGAAAATGAAGATCCAACTC
23748 CATGTATGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (24 bp):
AGTAGAAAATGAAGATCCAACTCT
Found at i:26129 original size:26 final size:26
Alignment explanation
Indices: 26089--26140 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
26079 ATGAATTTGA
*
26089 AATTAATTATGTTTAAT-TTTGTATTT
1 AATTAATAATGTTT-ATGTTTGTATTT
*
26115 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTATGTTTGTATTT
26141 TGGTTTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
AATTAATAATGTTTATGTTTGTATTT
Found at i:26170 original size:15 final size:16
Alignment explanation
Indices: 26159--26191 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
26149 GTGTTTAGTG
26159 TTTTAAATTTTAGGGT
1 TTTTAAATTTTAGGGT
26175 TTTTAAA-TTTAGGGT
1 TTTTAAATTTTAGGGT
26190 TT
1 TT
26192 ATGTTAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TTTTAAATTTTAGGGT
Found at i:26224 original size:21 final size:21
Alignment explanation
Indices: 26200--26239 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
26190 TTATGTTAAA
*
26200 GGTTTTGAATTTAAGGTTTAG
1 GGTTTTAAATTTAAGGTTTAG
26221 GGTTTTAAATTTAAGGTTT
1 GGTTTTAAATTTAAGGTTT
26240 CGAATAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (21 bp):
GGTTTTAAATTTAAGGTTTAG
Found at i:26332 original size:14 final size:15
Alignment explanation
Indices: 26312--26346 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
26302 TTGAGTTTAG
*
26312 GGTTTTAA-GTATAT
1 GGTTTTAAGGGATAT
26326 GGTTTTAAGGGATAT
1 GGTTTTAAGGGATAT
26341 GGTTTT
1 GGTTTT
26347 GAGTCAAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.49
Consensus pattern (15 bp):
GGTTTTAAGGGATAT
Found at i:28795 original size:5 final size:5
Alignment explanation
Indices: 28785--28814 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
28775 ACTTACTAAC
28785 AAAAT AAAAT AAAAT AAAAT AAAATT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAA
28815 ATAACTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:28912 original size:30 final size:32
Alignment explanation
Indices: 28877--28941 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
28867 AACATTAAAT
*
28877 AACAAATCAATTAAAA-ATTAAAT-TAAACAA
1 AACAAATCAATTAAAATAATAAATATAAACAA
* *
28907 AACAAATTACTTAAAATAATAAATACTAAACAA
1 AACAAATCAATTAAAATAATAAATA-TAAACAA
28940 AA
1 AA
28942 TATAACTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 14 0.48
31 6 0.21
33 9 0.31
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (32 bp):
AACAAATCAATTAAAATAATAAATATAAACAA
Found at i:29183 original size:12 final size:12
Alignment explanation
Indices: 29166--29207 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
29156 TCCTTCCTTA
* *
29166 TTTCTTTCTTTC
1 TTTCTTTTTTTT
29178 TTTCTTTTTTTT
1 TTTCTTTTTTTT
29190 TTTCTTTTTTTT
1 TTTCTTTTTTTT
29202 TTTCTT
1 TTTCTT
29208 CTCTAATGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:29195 original size:16 final size:17
Alignment explanation
Indices: 29170--29207 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
29160 TCCTTATTTC
29170 TTTCTTTCTTTCTTTTT
1 TTTCTTTCTTTCTTTTT
29187 TTT-TTTCTTT-TTTTT
1 TTTCTTTCTTTCTTTTT
29202 TTTCTT
1 TTTCTT
29208 CTCTAATGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 9 0.45
17 3 0.15
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTCTTTCTTTCTTTTT
Found at i:29393 original size:26 final size:27
Alignment explanation
Indices: 29364--29421 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
29354 TGGCAAAAAA
*
29364 CTCCAAA-GTGTCGCCACTTCAAAACC
1 CTCCAAAGGTGCCGCCACTTCAAAACC
*
29390 CTCCAAAGGTGCCGCCACTTCAAATCC
1 CTCCAAAGGTGCCGCCACTTCAAAACC
29417 CTCCA
1 CTCCA
29422 TCTGTGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.28, C:0.41, G:0.12, T:0.19
Consensus pattern (27 bp):
CTCCAAAGGTGCCGCCACTTCAAAACC
Found at i:30096 original size:140 final size:140
Alignment explanation
Indices: 29818--30087 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
29808 AATATAAACA
* *
29818 AATACTATCATATAATCATATCAGTATATTAAAAAAACTAATTTTTTATATATAACCTGTAATTT
1 AATACTATCATATAATCATACCAATATATTAAAAAAACTAATTTTTTATATATAACCTGTAATTT
29883 TTTTATATTTCATATGCACATAAATAAGTTAACTCTGTTTATTATATCTTTACAAATATATATAT
66 TTTTATATTTCATATGCACATAAATAAGTTAACTCTGTTTATTATATCTTTACAAATATATATAT
29948 ATATATATAT
131 ATATATATAT
*
29958 AATACTATCATATAATCATACCAATATATTAAAAAAACTAATTTTTTATATATAGCCTGTAATTT
1 AATACTATCATATAATCATACCAATATATTAAAAAAACTAATTTTTTATATATAACCTGTAATTT
30023 TTTTATATTTCATATGCACATAAATAAGTTAACTCTGTTTATTATATCTTTACAAATATATATAT
66 TTTTATATTTCATATGCACATAAATAAGTTAACTCTGTTTATTATATCTTTACAAATATATATAT
30088 TTGAATATAC
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (140 bp):
AATACTATCATATAATCATACCAATATATTAAAAAAACTAATTTTTTATATATAACCTGTAATTT
TTTTATATTTCATATGCACATAAATAAGTTAACTCTGTTTATTATATCTTTACAAATATATATAT
ATATATATAT
Found at i:31381 original size:21 final size:21
Alignment explanation
Indices: 31343--31382 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31333 GAGATGAATA
*
31343 GTGGCGGTGGAGGTGGAGGTG
1 GTGGCGGTGGAGGAGGAGGTG
* *
31364 GTGGCGTTGGGGGAGGAGG
1 GTGGCGGTGGAGGAGGAGG
31383 GGCTGGGAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.05, G:0.68, T:0.17
Consensus pattern (21 bp):
GTGGCGGTGGAGGAGGAGGTG
Found at i:39653 original size:194 final size:193
Alignment explanation
Indices: 39217--39662 Score: 529
Period size: 194 Copynumber: 2.3 Consensus size: 193
39207 ACCAGTACTT
* * * * * *
39217 GATGTTGCTCACACTAGCTATCGAGGACTTGCAACGTATGCGGTACCCCAGCCATCGGTACGGTG
1 GATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATA--GTG
* * * * *
39282 CCTGTCTGTACTATAAACTGTTCTCTAACGATGCTGCTCGCACGAGCTGTCAAGAGTATGCATAA
64 CATATCTGTACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCATAA
* *
39347 AGCATAGTCCTAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATATATTTCTCGAGTCAC
129 AGCATAATCCTAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATATATTTCTCGACTCAC
* * * * *
39412 AATGCTACTCACACGAGCTATCGAGGACTCGTAACATATGTGGTACCTCAGCCATTGATA-TG-A
1 GATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATAGTGCA
* * * *
39475 TATCTGTGC-ATATAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCATTAT
66 TATCTGTACTATA-AACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCATAAA
* * * * * * *
39539 GCATAAATCTTAGCCATCGTAGGGCCTGTAATCCATTCTTGGATTCTTTTCTCATTTCTCGACTC
130 GCAT-AATCCTAGCCATCGTAGGGCCTATAATCCATT-TAGGATCCATATAT-ATTTCTCGACTC
39604 AC
192 AC
* * *
39606 GATGCTGCTTACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACCATCG
1 GATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCGGTACCTCAGCCATCG
39663 TGTCAGTTTC
Statistics
Matches: 210, Mismatches: 37, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
190 3 0.01
191 56 0.27
192 31 0.15
193 9 0.04
194 62 0.30
195 49 0.23
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (193 bp):
GATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATAGTGCA
TATCTGTACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCATAAAG
CATAATCCTAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATATATTTCTCGACTCAC
Found at i:43414 original size:23 final size:23
Alignment explanation
Indices: 43388--43695 Score: 366
Period size: 23 Copynumber: 13.4 Consensus size: 23
43378 TTCTTATATC
43388 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATATGATT
* *
43411 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
* ** *
43434 TGTGCTTATGTATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
43457 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATATGATT
* * * *
43480 TGTGCTCAAATATCAATTTGATT
1 TATGCTTAAATATTAATATGATT
*
43503 TGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATATGATT
* *
43526 TGTGCTCAAATATTAATATGATT
1 TATGCTTAAATATTAATATGATT
*
43549 TATGCTTAAATATTAATTTGATT
1 TATGCTTAAATATTAATATGATT
* *
43572 TATGCTT-AATATTAAAATGGTT
1 TATGCTTAAATATTAATATGATT
* * *
43594 TGTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
* *
43617 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
* * *
43640 TGTGCTCAAATACTAATATGATT
1 TATGCTTAAATATTAATATGATT
* *
43663 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
*
43686 TGTGCTTAAA
1 TATGCTTAAA
43696 AAATTAAGAT
Statistics
Matches: 240, Mismatches: 44, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
22 17 0.07
23 223 0.93
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (23 bp):
TATGCTTAAATATTAATATGATT
Found at i:43855 original size:36 final size:36
Alignment explanation
Indices: 43765--43877 Score: 136
Period size: 36 Copynumber: 3.1 Consensus size: 36
43755 TGAAGATTGT
* * *
43765 TGTGAAAGTGAATATGTGAGTATGTTCTTCATGCCA
1 TGTGAAAGAGAATATGTGGGTATGTTCTTCATGCTA
* *
43801 TGTGACAGAAAATATGTGGGTATGTTCTTCATGCTA
1 TGTGAAAGAGAATATGTGGGTATGTTCTTCATGCTA
* * * * *
43837 TGTGATAGAGAATATGTGGTTACGTTTTTCATGCTG
1 TGTGAAAGAGAATATGTGGGTATGTTCTTCATGCTA
43873 TGTGA
1 TGTGA
43878 CTGATTATAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.26, C:0.10, G:0.27, T:0.38
Consensus pattern (36 bp):
TGTGAAAGAGAATATGTGGGTATGTTCTTCATGCTA
Found at i:48544 original size:35 final size:35
Alignment explanation
Indices: 48505--48578 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
48495 AGTTTATCTG
48505 ACTAGTGCTGGGCACACAA-ATCGACGGTGTATCCA
1 ACTAGTGCTGGGCACA-AACATCGACGGTGTATCCA
* ** *
48540 ACTAGTGCTGGGCGCAAACATCGTTGGTTTATCCA
1 ACTAGTGCTGGGCACAAACATCGACGGTGTATCCA
48575 ACTA
1 ACTA
48579 AAGTTGGGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (35 bp):
ACTAGTGCTGGGCACAAACATCGACGGTGTATCCA
Found at i:52069 original size:21 final size:21
Alignment explanation
Indices: 52019--52071 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
52009 GGATATAATA
* *
52019 TAAATGTTTGAT-TTAGATTT
1 TAAATGTTTCATATTAGATGT
* *
52039 TAAA-GCTTCATATTTGATGT
1 TAAATGTTTCATATTAGATGT
52059 TAAATGTTTCATA
1 TAAATGTTTCATA
52072 ATGCTTCGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 5 0.19
20 14 0.54
21 7 0.27
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (21 bp):
TAAATGTTTCATATTAGATGT
Found at i:57410 original size:94 final size:93
Alignment explanation
Indices: 57236--57461 Score: 312
Period size: 94 Copynumber: 2.4 Consensus size: 93
57226 TTTTTATATT
* * * * *
57236 CTCATCAGCTTAGTGTGAGCAGCATCGT-GA-GGGAACAATTATATGTACAAATACCGTATCGAT
1 CTCATCAGCTTAGTGTGAGCAGCATCGTATATGGTAACAGTTATATGTACAAATACCATATCAAT
*
57299 GACTGAGATACCGCATATGTTGCGAGTC
66 GACTGAGATACCACATATGTTGCGAGTC
* *
57327 CTCGTCAGCTTAGTGTGAGCAGCATCGTATATTGGTAACAGTTATATGTACAAATACCATATTAA
1 CTCATCAGCTTAGTGTGAGCAGCATCGTATA-TGGTAACAGTTATATGTACAAATACCATATCAA
* * *
57392 TGGCTGAGGTACCACATATGTTGTGAGTC
65 TGACTGAGATACCACATATGTTGCGAGTC
*
57421 CTCATCAGCTTAGTGTGAGCAGCATCATATACTGGTAACAG
1 CTCATCAGCTTAGTGTGAGCAGCATCGTATA-TGGTAACAG
57462 AAACAATTTT
Statistics
Matches: 118, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
91 27 0.23
92 1 0.01
94 90 0.76
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (93 bp):
CTCATCAGCTTAGTGTGAGCAGCATCGTATATGGTAACAGTTATATGTACAAATACCATATCAAT
GACTGAGATACCACATATGTTGCGAGTC
Found at i:60210 original size:6 final size:6
Alignment explanation
Indices: 60199--60230 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
60189 TGAGATCATT
60199 ATATAC ATATAC ATATAC ATATAC ATATAC AT
1 ATATAC ATATAC ATATAC ATATAC ATATAC AT
60231 GTTGATTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:63417 original size:12 final size:12
Alignment explanation
Indices: 63400--63424 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63390 ACTAAATAAT
63400 TAATAGCATTAA
1 TAATAGCATTAA
63412 TAATAGCATTAA
1 TAATAGCATTAA
63424 T
1 T
63425 CATAATAACA
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTAA
Found at i:68091 original size:13 final size:13
Alignment explanation
Indices: 68073--68097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68063 CACAAAATTA
68073 ACAAAAAAATTTT
1 ACAAAAAAATTTT
68086 ACAAAAAAATTT
1 ACAAAAAAATTT
68098 AATTAAGGCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
ACAAAAAAATTTT
Found at i:82415 original size:200 final size:200
Alignment explanation
Indices: 82088--82453 Score: 554
Period size: 200 Copynumber: 1.8 Consensus size: 200
82078 TCTTTTCTGT
* * * *** *
82088 AGAATCAAGTTGTCTCTGGTCATACCAGTTGGTTATACCAGACTAGACAACTCACGTTTTTTTGT
1 AGAATCAAGCTGTCTCTGGTCATACAAGTTGGTCATACCAGACTAGACAACTCACACATTTTTAT
* * *
82153 TCTTATCCGGAGAGCTGTCAGATGCAGCGACAATCCTAGACGCAATCTGAAATTACTTATGCAGT
66 TCTTATCCGGACAGCTGTCAGATGCAGCGACAATCCTAAACGCAATCTGAAATTACTTATGCAGC
* *
82218 GACATCAGTACCAAAACATGACAAAATTAAGGGTAAGTACAAGTTGTCCTTGTGCAGGTGTCCTT
131 GACATCAGTACCAAAACAGGACAAAATTAAGAGTAAGTACAAGTTGTCCTTGTGCAGGTGTCCTT
82283 TCATC
196 TCATC
* *
82288 AGAATCAAGCTGTCGT-TGGTCGTACAAGTTGGTCATACCAGACTGGACAACTCACACATTTTTA
1 AGAATCAAGCTGTC-TCTGGTCATACAAGTTGGTCATACCAGACTAGACAACTCACACATTTTTA
* * * *
82352 TTCTTATTCGGACAGCTGTTAGATGCGGTGACAATCCTAAACGCAATCTGAAATTACTTATGCAG
65 TTCTTATCCGGACAGCTGTCAGATGCAGCGACAATCCTAAACGCAATCTGAAATTACTTATGCAG
82417 CGACATCAGTACCAAAACAGGACAAAATTAAGAGTAA
130 CGACATCAGTACCAAAACAGGACAAAATTAAGAGTAA
82454 ATAGGCTAAG
Statistics
Matches: 147, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
200 146 0.99
201 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (200 bp):
AGAATCAAGCTGTCTCTGGTCATACAAGTTGGTCATACCAGACTAGACAACTCACACATTTTTAT
TCTTATCCGGACAGCTGTCAGATGCAGCGACAATCCTAAACGCAATCTGAAATTACTTATGCAGC
GACATCAGTACCAAAACAGGACAAAATTAAGAGTAAGTACAAGTTGTCCTTGTGCAGGTGTCCTT
TCATC
Found at i:86276 original size:23 final size:24
Alignment explanation
Indices: 86231--86277 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
86221 TCTTTTATAA
* *
86231 TTTTTTATTTTAGTTTGACTGGGAT
1 TTTTTTATTTTAG-TTAAATGGGAT
86256 TTTTTTATTTTAG-TAAATGGGA
1 TTTTTTATTTTAGTTAAATGGGA
86278 AAATTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
25 13 0.65
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.57
Consensus pattern (24 bp):
TTTTTTATTTTAGTTAAATGGGAT
Found at i:95179 original size:62 final size:63
Alignment explanation
Indices: 95054--95183 Score: 147
Period size: 62 Copynumber: 2.1 Consensus size: 63
95044 CGAGGTTGGT
* * * * * * *
95054 TTCAATTCGCATTTGTTAACTCACGATGACACCGAGTCATCGGACCTTTAATCCGTAATAGGA
1 TTCATTTCGCATTTGATAACTCACAATGACACAGAGTCATCGAACCTATAATCCGTAAAAGGA
* * *
95117 TTCATTTCTCATTTGAT-ACTCACAATGACACATAGTCATCGAACCTCATAATTCG-AAAAGGA
1 TTCATTTCGCATTTGATAACTCACAATGACACAGAGTCATCGAACCT-ATAATCCGTAAAAGGA
95179 TTCAT
1 TTCAT
95184 ATGCTCACGA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
62 36 0.64
63 20 0.36
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (63 bp):
TTCATTTCGCATTTGATAACTCACAATGACACAGAGTCATCGAACCTATAATCCGTAAAAGGA
Found at i:95215 original size:52 final size:52
Alignment explanation
Indices: 95132--95369 Score: 377
Period size: 52 Copynumber: 4.6 Consensus size: 52
95122 TTCTCATTTG
* * *
95132 ATACTCACAATGACACATAGTCATCGAACCTCATAATTCGAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* *
95184 ATGCTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* * *
95236 ATACTCACGATGACACATAGTTATCAAACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* *
95288 ATACTCACGATGACACATAGTCATTGAACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
95340 ATACTCACGATGACACATAGTCATCAGAAC
1 ATACTCACGATGACACATAGTCATC-GAAC
95370 TTTTGCATTT
Statistics
Matches: 171, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
52 167 0.98
53 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
Found at i:95936 original size:18 final size:16
Alignment explanation
Indices: 95905--95940 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
95895 CCTCAATACC
95905 ATTTCATTTCAATTTA
1 ATTTCATTTCAATTTA
95921 ATTTCATTCCTCAATTTA
1 ATTTCATT--TCAATTTA
95939 AT
1 AT
95941 ATTTACTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTCATTTCAATTTA
Found at i:96376 original size:16 final size:16
Alignment explanation
Indices: 96352--96384 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
96342 TCCTTACAAA
*
96352 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
96368 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
96384 T
1 T
96385 AAAATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:98703 original size:21 final size:21
Alignment explanation
Indices: 98678--98717 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
98668 TATGGGTATT
98678 GAGGAAGAGAAA-GAAGAAGAG
1 GAGGAAGA-AAAGGAAGAAGAG
*
98699 GAGGAGGAAAAGGAAGAAG
1 GAGGAAGAAAAGGAAGAAG
98718 GAAAAGAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (21 bp):
GAGGAAGAAAAGGAAGAAGAG
Found at i:107105 original size:14 final size:14
Alignment explanation
Indices: 107086--107119 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
107076 GCATCATAAG
107086 ATTATATCATGTTT
1 ATTATATCATGTTT
107100 ATTATATCATGTTT
1 ATTATATCATGTTT
107114 ATTATA
1 ATTATA
107120 ATTGAAGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (14 bp):
ATTATATCATGTTT
Found at i:109883 original size:36 final size:36
Alignment explanation
Indices: 109817--109893 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
109807 ATAATCACAA
*
109817 TCACATGACATGAAAAACATACCCACATATTTACTG
1 TCACATGACATGAAAAACATACCCACATATTCACTG
* * ** *
109853 TCACATGACATTAATAACATACCCTTATATTCACTT
1 TCACATGACATGAAAAACATACCCACATATTCACTG
109889 TCACA
1 TCACA
109894 ACAGTCACCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30
Consensus pattern (36 bp):
TCACATGACATGAAAAACATACCCACATATTCACTG
Found at i:110805 original size:28 final size:28
Alignment explanation
Indices: 110738--110793 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
110728 GCTTTGATGC
*
110738 TAATATAGAAAAACTCACGTTTTAGAGA
1 TAATATGGAAAAACTCACGTTTTAGAGA
* *
110766 TAATTTGGAAAAACTCACGTTTTGGAGA
1 TAATATGGAAAAACTCACGTTTTAGAGA
110794 AGATGATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (28 bp):
TAATATGGAAAAACTCACGTTTTAGAGA
Found at i:115601 original size:19 final size:19
Alignment explanation
Indices: 115577--115616 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
115567 TGTTCTTGAA
115577 TGCAAAGCATTACCAGCAC
1 TGCAAAGCATTACCAGCAC
115596 TGCAAAGCATTACCAGCAC
1 TGCAAAGCATTACCAGCAC
115615 TG
1 TG
115617 GGAAGTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.17
Consensus pattern (19 bp):
TGCAAAGCATTACCAGCAC
Found at i:117158 original size:16 final size:16
Alignment explanation
Indices: 117137--117169 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
117127 GGATCCTAAG
117137 AGCTTCACAATACCTT
1 AGCTTCACAATACCTT
117153 AGCTTCACAATACCTT
1 AGCTTCACAATACCTT
117169 A
1 A
117170 TTCCATTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (16 bp):
AGCTTCACAATACCTT
Found at i:122511 original size:37 final size:37
Alignment explanation
Indices: 122461--122554 Score: 188
Period size: 37 Copynumber: 2.5 Consensus size: 37
122451 AGTGGGACCA
122461 ATTCTTTGCAAAGAGGTATGGTTTTGAGCCGTTAATG
1 ATTCTTTGCAAAGAGGTATGGTTTTGAGCCGTTAATG
122498 ATTCTTTGCAAAGAGGTATGGTTTTGAGCCGTTAATG
1 ATTCTTTGCAAAGAGGTATGGTTTTGAGCCGTTAATG
122535 ATTCTTTGCAAAGAGGTATG
1 ATTCTTTGCAAAGAGGTATG
122555 CCACAGTACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.37
Consensus pattern (37 bp):
ATTCTTTGCAAAGAGGTATGGTTTTGAGCCGTTAATG
Found at i:132080 original size:23 final size:24
Alignment explanation
Indices: 132054--132099 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
132044 TATAGTATAG
*
132054 TTAATTAA-GCTAATGAAAAAAGA
1 TTAACTAAGGCTAATGAAAAAAGA
* *
132077 TTAACTAAGGTTAATGATAAAAG
1 TTAACTAAGGCTAATGAAAAAAG
132100 TTGTAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.28
Consensus pattern (24 bp):
TTAACTAAGGCTAATGAAAAAAGA
Found at i:158017 original size:20 final size:21
Alignment explanation
Indices: 157980--158036 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
157970 ATCATTAAGC
*
157980 CTTAATT-AATCATTTTTA-A
1 CTTAATTAAATCATATTTACA
157999 TCTTAATTAAATC-TATTTACA
1 -CTTAATTAAATCATATTTACA
*
158020 CTTAATATAAACCATAT
1 CTTAAT-TAAATCATAT
158037 CAATCCACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 18 0.58
21 10 0.32
22 3 0.10
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (21 bp):
CTTAATTAAATCATATTTACA
Found at i:160072 original size:17 final size:18
Alignment explanation
Indices: 160033--160076 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
160023 TTGCATTTTA
* *
160033 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCATT
160051 TTTATTTGTCACTGCA-T
1 TTTATTTGTCACTGCATT
160068 TTTATTTGT
1 TTTATTTGT
160077 TAGTACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (18 bp):
TTTATTTGTCACTGCATT
Found at i:160673 original size:11 final size:11
Alignment explanation
Indices: 160657--160682 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
160647 TCAGTCACTT
160657 AAAAAAAAAGA
1 AAAAAAAAAGA
160668 AAAAAAAAAGA
1 AAAAAAAAAGA
160679 AAAA
1 AAAA
160683 GGAAAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:170602 original size:21 final size:21
Alignment explanation
Indices: 170574--170619 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
170564 GTGATTTCGG
170574 ATGT-TAATGAAAGGCTTAGA
1 ATGTCTAATGAAAGGCTTAGA
*
170594 ATGTCTAATGAAAGGCTTAGG
1 ATGTCTAATGAAAGGCTTAGA
170615 ATGTC
1 ATGTC
170620 ATAAATGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (21 bp):
ATGTCTAATGAAAGGCTTAGA
Found at i:178346 original size:20 final size:21
Alignment explanation
Indices: 178308--178346 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
178298 TAAATAGAGC
*
178308 ATCACTGAGTTAGAAAATGCA
1 ATCACTAAGTTAGAAAATGCA
178329 ATCACTAAGTTA-AAAATG
1 ATCACTAAGTTAGAAAATG
178347 TCAAAAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (21 bp):
ATCACTAAGTTAGAAAATGCA
Found at i:179674 original size:15 final size:16
Alignment explanation
Indices: 179645--179678 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
179635 AATATCTCAT
*
179645 ACATGTTCACCATTTC
1 ACATGTTCACAATTTC
179661 ACAT-TTCACAATTTC
1 ACATGTTCACAATTTC
179676 ACA
1 ACA
179679 AGCAAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.35
Consensus pattern (16 bp):
ACATGTTCACAATTTC
Found at i:189647 original size:26 final size:26
Alignment explanation
Indices: 189611--189667 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
189601 TTTTGCGCGT
189611 AATTCTGGACACGTTCATGCAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
*
189637 AATTCTGGACATGTTCATGCAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
189663 -ATTCT
1 AATTCT
189668 TGGGTGCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (26 bp):
AATTCTGGACACGTTCATGCAGCGAC
Found at i:189694 original size:37 final size:38
Alignment explanation
Indices: 189653--189732 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
189643 GGACATGTTC
* *
189653 ATGCAGCGACA-TTCTTGGGTGCAA-TTGAAGCATATTT
1 ATGCAGCGACAGTTCTT-GATGCAATTTGAAGAATATTT
* *
189690 ATGCAGTGATAGTTCTTGATGCAATTTGAAGAATATTT
1 ATGCAGCGACAGTTCTTGATGCAATTTGAAGAATATTT
189728 ATGCA
1 ATGCA
189733 ACAATAATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 15 0.41
38 22 0.59
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (38 bp):
ATGCAGCGACAGTTCTTGATGCAATTTGAAGAATATTT
Found at i:189839 original size:37 final size:36
Alignment explanation
Indices: 189769--189842 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
189759 ATATTCCTGG
**
189769 GGCGACAGTTTTGATGCAATCTAGATGTACTCATGC
1 GGCGACAGTTTTGATGCAATCTAGAAATACTCATGC
* * *
189805 GGCGACAGTTTTGGGTGTAATCTAGAAATGCTCATGC
1 GGCGACAGTTTT-GATGCAATCTAGAAATACTCATGC
189842 G
1 G
189843 ATGACATGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 12 0.38
37 20 0.62
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (36 bp):
GGCGACAGTTTTGATGCAATCTAGAAATACTCATGC
Found at i:191023 original size:17 final size:17
Alignment explanation
Indices: 190984--191032 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
190974 ATATATATGG
* **
190984 AAATGCAATGACAATGT
1 AAATGCAGTGACAATAA
*
191001 AGATGCAGTGACAATAA
1 AAATGCAGTGACAATAA
*
191018 AAATGCAGGGACAAT
1 AAATGCAGTGACAAT
191033 TATACTACAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.18
Consensus pattern (17 bp):
AAATGCAGTGACAATAA
Found at i:191728 original size:12 final size:12
Alignment explanation
Indices: 191711--191735 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
191701 TTTGTCTCGA
191711 CATCTTTTTCTT
1 CATCTTTTTCTT
191723 CATCTTTTTCTT
1 CATCTTTTTCTT
191735 C
1 C
191736 CTCCACACGA
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:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (12 bp):
CATCTTTTTCTT
Found at i:194356 original size:37 final size:38
Alignment explanation
Indices: 194314--194395 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
194304 GGACATGCTC
*
194314 ATGCAGCAACA-TTCCTGGGA-GCAA-TTGAAGAATATTT
1 ATGCAGCAACAGTT-CT-GGATGCAATTTCAAGAATATTT
* *
194351 ATGCAGCGATAGTTCTGGATGCAATTTCAAGAATATTT
1 ATGCAGCAACAGTTCTGGATGCAATTTCAAGAATATTT
194389 ATGCAGC
1 ATGCAGC
194396 GACAATCTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
36 3 0.08
37 15 0.38
38 21 0.54
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (38 bp):
ATGCAGCAACAGTTCTGGATGCAATTTCAAGAATATTT
Found at i:194522 original size:36 final size:37
Alignment explanation
Indices: 194453--194522 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
194443 ATGCAATTTG
*
194453 GAAGTGCTCATGCGATGATAGTTTTGGGCGCAATCTA
1 GAAGTGCTCATGCGATGACAGTTTTGGGCGCAATCTA
*
194490 GAAGTGCTCGTGCG-TGACA-TGTTTGGGCGCAAT
1 GAAGTGCTCATGCGATGACAGT-TTTGGGCGCAAT
194523 TTTGGATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 1 0.03
36 16 0.53
37 13 0.43
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (37 bp):
GAAGTGCTCATGCGATGACAGTTTTGGGCGCAATCTA
Found at i:198011 original size:54 final size:54
Alignment explanation
Indices: 197953--198061 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
197943 CCAGTGTCAA
*
197953 AGACCGTGTAACTCACTGACTTGAGATACACGACCGTGTCCCAGCCCGTGACTT
1 AGACCATGTAACTCACTGACTTGAGATACACGACCGTGTCCCAGCCCGTGACTT
* * * ** * *
198007 AGACCATGTAACTCACTGACTTGGGATGCATGGTCGTGTCCCAGCCTGTGTCTT
1 AGACCATGTAACTCACTGACTTGAGATACACGACCGTGTCCCAGCCCGTGACTT
198061 A
1 A
198062 AACTATGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (54 bp):
AGACCATGTAACTCACTGACTTGAGATACACGACCGTGTCCCAGCCCGTGACTT
Found at i:201411 original size:21 final size:21
Alignment explanation
Indices: 201331--201411 Score: 74
Period size: 24 Copynumber: 3.7 Consensus size: 21
201321 TATATTATTG
* *
201331 TTTTGGTG-CTTTTTTTAGTA
1 TTTTGGTGTTTTTTTTTACTA
* * *
201351 TTTTGGTTGCTATTTTTTGCTA
1 TTTTGG-TGTTTTTTTTTACTA
201373 TTTTGGTGTTGTTGTTTTTTACTA
1 TTTTGGTG-T-TT-TTTTTTACTA
201397 TTTTGGTGTTTTTTT
1 TTTTGGTGTTTTTTT
201412 ACTGTTTTAG
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 6 0.12
21 8 0.16
22 16 0.33
23 2 0.04
24 17 0.35
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.68
Consensus pattern (21 bp):
TTTTGGTGTTTTTTTTTACTA
Found at i:201418 original size:29 final size:28
Alignment explanation
Indices: 201385--201448 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
201375 TTGGTGTTGT
201385 TGTTTT-TTACTATTTTGGTGTTTTTTTAC
1 TGTTTTATTACTATTTT-G-GTTTTTTTAC
* *
201414 TGTTTTAGTTATTGTTTTGGTTTTTTTAC
1 TGTTTTA-TTACTATTTTGGTTTTTTTAC
201443 TGTTTT
1 TGTTTT
201449 GATGTTGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 22 0.71
30 1 0.03
31 8 0.26
ACGTcount: A:0.09, C:0.05, G:0.16, T:0.70
Consensus pattern (28 bp):
TGTTTTATTACTATTTTGGTTTTTTTAC
Found at i:201470 original size:26 final size:26
Alignment explanation
Indices: 201434--201516 Score: 118
Period size: 26 Copynumber: 3.3 Consensus size: 26
201424 ATTGTTTTGG
201434 TTTTT-TTACTGTTTTGATGTTGTTA
1 TTTTTGTTACTGTTTTGATGTTGTTA
201459 TTTTTGTTACTGTTTTGATGTTGTTA
1 TTTTTGTTACTGTTTTGATGTTGTTA
* * *
201485 TTTTTGTTGCTGTTTT--TATTGCTA
1 TTTTTGTTACTGTTTTGATGTTGTTA
201509 TTTTTGTT
1 TTTTTGTT
201517 GTTTTGTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
24 14 0.26
25 5 0.09
26 35 0.65
ACGTcount: A:0.10, C:0.05, G:0.17, T:0.69
Consensus pattern (26 bp):
TTTTTGTTACTGTTTTGATGTTGTTA
Found at i:201474 original size:12 final size:12
Alignment explanation
Indices: 201451--201517 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
201441 ACTGTTTTGA
*
201451 TGTTGTTATTTT
1 TGTTGCTATTTT
* *
201463 TGTTACTGTTTT
1 TGTTGCTATTTT
*
201475 GATGTTGTTATTTT
1 --TGTTGCTATTTT
*
201489 TGTTGCTGTTTT
1 TGTTGCTATTTT
*
201501 TATTGCTATTTT
1 TGTTGCTATTTT
201513 TGTTG
1 TGTTG
201518 TTTTGTTGTT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
12 33 0.79
14 9 0.21
ACGTcount: A:0.09, C:0.04, G:0.19, T:0.67
Consensus pattern (12 bp):
TGTTGCTATTTT
Found at i:201525 original size:44 final size:44
Alignment explanation
Indices: 201477--201586 Score: 143
Period size: 44 Copynumber: 2.5 Consensus size: 44
201467 ACTGTTTTGA
** * *
201477 TGTTGTTATTTTTGTTGCTGTTTTTATTGCTATTTTTGTTGTTT
1 TGTTGTTATTTTTACTGCTGTTTTGATTGCTATTTTGGTTGTTT
*
201521 TGTTGTTATTTTTACTGCTGTTTTGATTGTTATTTTGGTTGTTT
1 TGTTGTTATTTTTACTGCTGTTTTGATTGCTATTTTGGTTGTTT
* *
201565 AGATGTTATTTTTA-TGC-GTTTT
1 TGTTGTTATTTTTACTGCTGTTTT
201587 TACTATTGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 5 0.08
43 3 0.05
44 51 0.86
ACGTcount: A:0.10, C:0.05, G:0.19, T:0.66
Consensus pattern (44 bp):
TGTTGTTATTTTTACTGCTGTTTTGATTGCTATTTTGGTTGTTT
Found at i:201551 original size:32 final size:32
Alignment explanation
Indices: 201486--201551 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
201476 ATGTTGTTAT
* * *
201486 TTTTGTTGCTGTTTTTATTGCTATTTTTGTTG
1 TTTTGTTGCTATTTTTACTGCTAGTTTTGTTG
*
201518 TTTTGTTGTTATTTTTACTGCT-GTTTTGATTG
1 TTTTGTTGCTATTTTTACTGCTAGTTTTG-TTG
201550 TT
1 TT
201552 ATTTTGGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 5 0.17
32 24 0.83
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.68
Consensus pattern (32 bp):
TTTTGTTGCTATTTTTACTGCTAGTTTTGTTG
Found at i:201585 original size:21 final size:22
Alignment explanation
Indices: 201523--201585 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 22
201513 TGTTGTTTTG
*
201523 TTGTTATTTTTACTGCTGTTTTGA
1 TTGTTATTTTTA-TGC-GTTTAGA
** *
201547 TTGTTATTTTGGT-TGTTTAGA
1 TTGTTATTTTTATGCGTTTAGA
201568 -TGTTATTTTTATGCGTTT
1 TTGTTATTTTTATGCGTTT
201586 TTACTATTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
20 10 0.32
21 10 0.32
23 1 0.03
24 10 0.32
ACGTcount: A:0.13, C:0.05, G:0.19, T:0.63
Consensus pattern (22 bp):
TTGTTATTTTTATGCGTTTAGA
Found at i:203411 original size:12 final size:12
Alignment explanation
Indices: 203394--203418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
203384 GAAAAAGAAA
203394 AAGAATTTTTTG
1 AAGAATTTTTTG
203406 AAGAATTTTTTG
1 AAGAATTTTTTG
203418 A
1 A
203419 TCGAACCGTG
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (12 bp):
AAGAATTTTTTG
Found at i:208972 original size:27 final size:26
Alignment explanation
Indices: 208928--208988 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
208918 ATAAAGCACA
*
208928 AATGAAAAAAAACTAAAAACACAAAAG
1 AATG-AAAAAAACAAAAAACACAAAAG
*
208955 AATGAAAAAAACAAAAAACACGAAAG
1 AATGAAAAAAACAAAAAACACAAAAG
208981 AATGAAAA
1 AATGAAAA
208989 GCTGAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.74, C:0.10, G:0.10, T:0.07
Consensus pattern (26 bp):
AATGAAAAAAACAAAAAACACAAAAG
Found at i:214142 original size:32 final size:33
Alignment explanation
Indices: 214069--214144 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
214059 TCCAATTTGA
* * * * *
214069 TACTCAAACTTGATACTTTTTTTTTTAATTTGG
1 TACTTAAACTTGACACTTTTTCTTATAAGTTGG
*
214102 TACATAAACTTGACAC-TTTTCTTATAAGTTGG
1 TACTTAAACTTGACACTTTTTCTTATAAGTTGG
214134 TACTTAAACTT
1 TACTTAAACTT
214145 TTTGCGGTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 23 0.64
33 13 0.36
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.47
Consensus pattern (33 bp):
TACTTAAACTTGACACTTTTTCTTATAAGTTGG
Found at i:214172 original size:93 final size:87
Alignment explanation
Indices: 214017--214191 Score: 197
Period size: 91 Copynumber: 1.9 Consensus size: 87
214007 ATTTCGTATC
* ** *
214017 TAAACTTGACACTTTTTTTAATTTAGTACTAAATTTTTATTGTCCAATTTGATACTCAAACTTGA
1 TAAACTTGACACTTTTTTTAAGTTAGTACTAAATTTTTACGGTCCAATTTAATACTCAAACTTG-
* *
214082 TACTTTTTTTTTTAATTTGGTACA
65 -ACTCTTTTTTCTAATTTGGTACA
* * * **
214106 TAAACTTGACACTTTTCTTATAAGTTGGTACTTAAACTTTTTGCGGTCTAATTTAATACTTGAAC
1 TAAACTTGACACTTTT-TT-TAAGTTAGTAC-TAAA-TTTTTACGGTCCAATTTAATACTCAAAC
214171 TTGACTCTTTTTTCTAATTTG
62 TTGACTCTTTTTTCTAATTTG
214192 ATACCTAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
89 16 0.23
90 2 0.03
91 25 0.35
92 4 0.06
93 24 0.34
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (87 bp):
TAAACTTGACACTTTTTTTAAGTTAGTACTAAATTTTTACGGTCCAATTTAATACTCAAACTTGA
CTCTTTTTTCTAATTTGGTACA
Found at i:214471 original size:13 final size:13
Alignment explanation
Indices: 214448--214498 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
214438 TTAGAAAAAA
214448 AAAAGTATCAAATT
1 AAAA-TATCAAATT
214462 AAAATATCAAATT
1 AAAATATCAAATT
**
214475 AAAA-AAAAAATT
1 AAAATATCAAATT
*
214487 TAAATATCAAAT
1 AAAATATCAAAT
214499 GAAGAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 9 0.29
13 18 0.58
14 4 0.13
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (13 bp):
AAAATATCAAATT
Found at i:214491 original size:25 final size:26
Alignment explanation
Indices: 214457--214510 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
214447 AAAAAGTATC
*
214457 AAATTAAAATATCAAATTAA-AAAAA
1 AAATTAAAATATCAAATGAAGAAAAA
*
214482 AAATTTAAATATCAAATGAAGAAAAA
1 AAATTAAAATATCAAATGAAGAAAAA
214508 AAA
1 AAA
214511 AATCAAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (26 bp):
AAATTAAAATATCAAATGAAGAAAAA
Found at i:216759 original size:13 final size:13
Alignment explanation
Indices: 216741--216771 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
216731 TGAATATTTA
*
216741 ATATTCAGTACTT
1 ATATTCAATACTT
216754 ATATTCAATACTT
1 ATATTCAATACTT
216767 ATATT
1 ATATT
216772 TACCAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.48
Consensus pattern (13 bp):
ATATTCAATACTT
Found at i:225940 original size:2 final size:2
Alignment explanation
Indices: 225933--225964 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
225923 TGACTTTTAA
*
225933 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
225965 TTGTAGAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:225969 original size:12 final size:12
Alignment explanation
Indices: 225933--225969 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
225923 TGACTTTTAA
*
225933 ATATATATATAT
1 ATATATATATGT
225945 ATATATATATGT
1 ATATATATATGT
*
225957 ATATATATTTGT
1 ATATATATATGT
225969 A
1 A
225970 GAATGTAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (12 bp):
ATATATATATGT
Found at i:227920 original size:22 final size:21
Alignment explanation
Indices: 227892--227933 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
227882 TGAATGGGGA
*
227892 AGTGGAAGGATGGAAAGAGTAG
1 AGTGGAAAGATGGAAA-AGTAG
227914 AGTGGAAAGATGGAAAAGTA
1 AGTGGAAAGATGGAAAAGTA
227934 ATGAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.45, C:0.00, G:0.40, T:0.14
Consensus pattern (21 bp):
AGTGGAAAGATGGAAAAGTAG
Found at i:236936 original size:22 final size:22
Alignment explanation
Indices: 236908--236952 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
236898 CGACCATTCT
236908 CCAAAACAAACTACCCAACAAA
1 CCAAAACAAACTACCCAACAAA
*
236930 CCAAAACAAACTACCTAACAAA
1 CCAAAACAAACTACCCAACAAA
236952 C
1 C
236953 TTAAAGATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.36, G:0.00, T:0.07
Consensus pattern (22 bp):
CCAAAACAAACTACCCAACAAA
Found at i:238807 original size:22 final size:21
Alignment explanation
Indices: 238766--238814 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
238756 CTGCTTAGTA
238766 TATTTTTTTTTAATATTTATT
1 TATTTTTTTTTAATATTTATT
*
238787 TATTTATTTTT-ATCATATTATT
1 TATTTTTTTTTAAT-AT-TTATT
238809 TATTTT
1 TATTTT
238815 CATTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 12 0.50
22 10 0.42
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (21 bp):
TATTTTTTTTTAATATTTATT
Found at i:238809 original size:18 final size:16
Alignment explanation
Indices: 238786--238995 Score: 116
Period size: 15 Copynumber: 12.9 Consensus size: 16
238776 TAATATTTAT
238786 TTATTTATTTTTATCATA
1 TTATTTATTTTTAT--TA
*
238804 TTATTTATTTTCATTA
1 TTATTTATTTTTATTA
238820 TT-TTTATTTTTATTTA
1 TTATTTATTTTTA-TTA
* *
238836 CT-TTTATTATGTTGTT-
1 TTATTTATT-T-TTATTA
*
238852 TTATTTATTATTATTA
1 TTATTTATTTTTATTA
*
238868 TTA-TTATTATTATTA
1 TTATTTATTTTTATTA
*
238883 TTA-TTATTATTCA--A
1 TTATTTATT-TTTATTA
*
238897 TGT-TTTATTTTCTCATCA
1 T-TATTTATTTT-T-ATTA
*
238915 TTATTTCTATTATTATTA
1 TTA-TT-TATTTTTATTA
*
238933 TTTATTTAATTTTATT-
1 -TTATTTATTTTTATTA
*
238949 TTCATTTATTTTTATTT
1 TT-ATTTATTTTTATTA
**
238966 TTATTTATAGTTATTA
1 TTATTTATTTTTATTA
*
238982 TT-TTTATTATTATT
1 TTATTTATTTTTATT
238996 GTAGGACCTT
Statistics
Matches: 154, Mismatches: 20, Indels: 39
0.72 0.09 0.18
Matches are distributed among these distances:
14 4 0.03
15 51 0.33
16 46 0.30
17 20 0.13
18 22 0.14
19 6 0.04
20 5 0.03
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (16 bp):
TTATTTATTTTTATTA
Found at i:238828 original size:6 final size:6
Alignment explanation
Indices: 238817--238995 Score: 68
Period size: 6 Copynumber: 29.8 Consensus size: 6
238807 TTTATTTTCA
* * *
238817 TTATTT TTATTT TTA--T TTACTT TTATTAT GTT-GTT TTATTT ATTATTA
1 TTATTT TTATTT TTATTT TTATTT TTATT-T -TTATTT TTATTT -TTATTT
* * * * ** **
238865 TTATTA TTATTA TTATTA TTATTA TTA-TT CAATGTT TTATTT TCTCATCA
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTAT-TT TTATTT T-T-ATTT
* * * *
238915 TTATTT CTATTA TTATTAT TTA--T TTAATT TTATTT TCA--T TTATTT
1 TTATTT TTATTT TTATT-T TTATTT TTATTT TTATTT TTATTT TTATTT
* * *
238960 TTATTT TTATTT ATAGTTA TTATTT TTATTA TTATT
1 TTATTT TTATTT TTA-TTT TTATTT TTATTT TTATT
238996 GTAGGACCTT
Statistics
Matches: 132, Mismatches: 25, Indels: 32
0.70 0.13 0.17
Matches are distributed among these distances:
4 11 0.08
5 4 0.03
6 92 0.70
7 20 0.15
8 5 0.04
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (6 bp):
TTATTT
Found at i:238862 original size:3 final size:3
Alignment explanation
Indices: 238856--238995 Score: 87
Period size: 3 Copynumber: 46.7 Consensus size: 3
238846 GTTGTTTTAT
* *
238856 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTCA ATG TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
* * * *
238901 TTA TT- TTC TCA TCA TTA TT- TCTA TTA TTA TTA TTTA TT- TAA TT-
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA -TTA TTA TTA TTA
* * *
238944 TTA TT- TTCA TTTA TTT TTA TTT TTA TT- TATA GTTA TTA TTT TTA TTA
1 TTA TTA TT-A -TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA
238991 TTA TT
1 TTA TT
238996 GTAGGACCTT
Statistics
Matches: 109, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
2 11 0.10
3 86 0.79
4 9 0.08
5 3 0.03
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:241213 original size:9 final size:9
Alignment explanation
Indices: 241199--241241 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
241189 ATTTTATTCT
241199 AAAAAAA-G
1 AAAAAAAGG
*
241207 CAAAAAAGG
1 AAAAAAAGG
241216 AAAAAAAGG
1 AAAAAAAGG
*
241225 AAAAAATATG
1 AAAAAA-AGG
241235 AAAAAAA
1 AAAAAAA
241242 ATAAGAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 6 0.20
9 16 0.53
10 8 0.27
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:241264 original size:9 final size:9
Alignment explanation
Indices: 241199--241264 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
241189 ATTTTATTCT
*
241199 AAAAAAAGC
1 AAAAAAAGA
*
241208 AAAAAAGGA
1 AAAAAAAGA
*
241217 AAAAAAGGA
1 AAAAAAAGA
*
241226 AAAAATATGAAA
1 AAAAA-A--AGA
241238 AAAAATAAGA
1 AAAAA-AAGA
241248 AAAGAAAAGA
1 AAA-AAAAGA
241258 AAAAAAA
1 AAAAAAA
241265 TGTGTTTGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
9 25 0.52
10 13 0.27
11 2 0.04
12 8 0.17
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:241600 original size:40 final size:40
Alignment explanation
Indices: 241555--241675 Score: 98
Period size: 40 Copynumber: 3.2 Consensus size: 40
241545 TGTTCGACTA
241555 TTGAGTGCATAGTACTTGAACCTTAAACATTTTGAGTGCT
1 TTGAGTGCATAGTACTTGAACCTTAAACATTTTGAGTGCT
* * * * * *
241595 TTGAGTGAATCATTA-GTGAGA-ATGT-CA-ATTCT---TG--
1 TTGAGTGCAT-AGTACTTGA-ACCT-TAAACATTTTGAGTGCT
241629 TTGAGTGCATAGTACTTGAACCTTAAACATTTTGAGTGCT
1 TTGAGTGCATAGTACTTGAACCTTAAACATTTTGAGTGCT
241669 TTGAGTG
1 TTGAGTG
241676 AATCATTAGT
Statistics
Matches: 57, Mismatches: 12, Indels: 24
0.61 0.13 0.26
Matches are distributed among these distances:
33 5 0.09
34 14 0.25
35 4 0.07
36 2 0.04
38 2 0.04
39 4 0.07
40 21 0.37
41 5 0.09
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (40 bp):
TTGAGTGCATAGTACTTGAACCTTAAACATTTTGAGTGCT
Found at i:241644 original size:74 final size:74
Alignment explanation
Indices: 241555--241706 Score: 304
Period size: 74 Copynumber: 2.1 Consensus size: 74
241545 TGTTCGACTA
241555 TTGAGTGCATAGTACTTGAACCTTAAACATTTTGAGTGCTTTGAGTGAATCATTAGTGAGAATGT
1 TTGAGTGCATAGTACTTGAACCTTAAACATTTTGAGTGCTTTGAGTGAATCATTAGTGAGAATGT
241620 CAATTCTTG
66 CAATTCTTG
241629 TTGAGTGCATAGTACTTGAACCTTAAACATTTTGAGTGCTTTGAGTGAATCATTAGTGAGAATGT
1 TTGAGTGCATAGTACTTGAACCTTAAACATTTTGAGTGCTTTGAGTGAATCATTAGTGAGAATGT
241694 CAATTCTTG
66 CAATTCTTG
241703 TTGA
1 TTGA
241707 TTTTGAATTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (74 bp):
TTGAGTGCATAGTACTTGAACCTTAAACATTTTGAGTGCTTTGAGTGAATCATTAGTGAGAATGT
CAATTCTTG
Found at i:243850 original size:26 final size:26
Alignment explanation
Indices: 243827--243880 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
243817 ATAAGAGCGT
*
243827 AACTCTGTCTGGGCTCGAATGAGCTA
1 AACTCTGTCTGGGCTCAAATGAGCTA
* * *
243853 AATTCTGTTTGGGCTTAAATGAGCTA
1 AACTCTGTCTGGGCTCAAATGAGCTA
243879 AA
1 AA
243881 TTTTATTTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (26 bp):
AACTCTGTCTGGGCTCAAATGAGCTA
Found at i:243881 original size:26 final size:26
Alignment explanation
Indices: 243836--243958 Score: 133
Period size: 26 Copynumber: 4.7 Consensus size: 26
243826 TAACTCTGTC
* *
243836 TGGGCTCGAATGAGCTAAATTCTGTT
1 TGGGCTTGAATGAGCTAAATTCTATT
* *
243862 TGGGCTTAAATGAGCTAAATTTTATT
1 TGGGCTTGAATGAGCTAAATTCTATT
* *
243888 TGGGCTCGAATGAACTAAATTCTATT
1 TGGGCTTGAATGAGCTAAATTCTATT
* *
243914 TGGGCTCGTAA-AAGCTAAATTCTATCT
1 TGGGCTTG-AATGAGCTAAATTCTAT-T
*
243941 T-GGCTTGTATGAGCTAAA
1 TGGGCTTGAATGAGCTAAA
243959 ATTTCTGGAA
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.01
26 76 0.94
27 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (26 bp):
TGGGCTTGAATGAGCTAAATTCTATT
Found at i:243896 original size:52 final size:52
Alignment explanation
Indices: 243836--243958 Score: 153
Period size: 52 Copynumber: 2.4 Consensus size: 52
243826 TAACTCTGTC
* *
243836 TGGGCTCGAATGAGCTAAATTCTGTTTGGGCT-TAAATGAGCTAAATTTTAT-T
1 TGGGCTCGAATGAGCTAAATTCTATTTGGGCTCTAAA--AGCTAAATTCTATCT
*
243888 TGGGCTCGAATGAACTAAATTCTATTTGGGCTCGTAAAAGCTAAATTCTATCT
1 TGGGCTCGAATGAGCTAAATTCTATTTGGGCTC-TAAAAGCTAAATTCTATCT
* *
243941 T-GGCTTGTATGAGCTAAA
1 TGGGCTCGAATGAGCTAAA
243959 ATTTCTGGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
52 56 0.90
53 2 0.03
54 4 0.06
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (52 bp):
TGGGCTCGAATGAGCTAAATTCTATTTGGGCTCTAAAAGCTAAATTCTATCT
Found at i:249551 original size:37 final size:37
Alignment explanation
Indices: 249511--249585 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
249501 TATATTTGTT
* *
249511 AATAAAATAT-AATTATATTTTAT-ACTT-AATTTTA
1 AATAATATATCAATCATATTTTATAACTTAAATTTTA
*
249545 AATAATATATCAATCATATTTTATAACTTAAATTTTT
1 AATAATATATCAATCATATTTTATAACTTAAATTTTA
249582 AATA
1 AATA
249586 TTAATTTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 9 0.26
35 12 0.34
36 4 0.11
37 10 0.29
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (37 bp):
AATAATATATCAATCATATTTTATAACTTAAATTTTA
Found at i:249747 original size:15 final size:15
Alignment explanation
Indices: 249727--249796 Score: 66
Period size: 15 Copynumber: 5.2 Consensus size: 15
249717 CTAATACAAA
249727 AAAGTTATAATTTCT
1 AAAGTTATAATTTCT
*
249742 AAAGTTAAAATTT-T
1 AAAGTTATAATTTCT
249756 AAA---ATAA---CT
1 AAAGTTATAATTTCT
249765 AAAGTTATAATTTCT
1 AAAGTTATAATTTCT
*
249780 AAAGTTAAAATTT-T
1 AAAGTTATAATTTCT
249794 AAA
1 AAA
249797 ATAAATAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
9 4 0.09
11 3 0.07
12 4 0.09
14 8 0.18
15 26 0.58
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (15 bp):
AAAGTTATAATTTCT
Found at i:249753 original size:38 final size:38
Alignment explanation
Indices: 249711--249797 Score: 131
Period size: 38 Copynumber: 2.3 Consensus size: 38
249701 TAAAGATGAT
*
249711 AAATTTCTAATACAA-AAAAGTTATAATTTCTAAAGTTA
1 AAATTT-TAAAACAACAAAAGTTATAATTTCTAAAGTTA
* *
249749 AAATTTTAAAATAACTAAAGTTATAATTTCTAAAGTTA
1 AAATTTTAAAACAACAAAAGTTATAATTTCTAAAGTTA
249787 AAATTTTAAAA
1 AAATTTTAAAA
249798 TAAATAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 6 0.13
38 39 0.87
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.38
Consensus pattern (38 bp):
AAATTTTAAAACAACAAAAGTTATAATTTCTAAAGTTA
Found at i:249798 original size:38 final size:38
Alignment explanation
Indices: 249727--249805 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
249717 CTAATACAAA
*
249727 AAAGTTATAATTTCTAAAGTTAAAATTTTAAAATAACT
1 AAAGTTATAATTTCTAAAGTTAAAATTTTAAAATAAAT
249765 AAAGTTATAATTTCTAAAGTTAAAATTTTAAAATAAAT
1 AAAGTTATAATTTCTAAAGTTAAAATTTTAAAATAAAT
249803 AAA
1 AAA
249806 TTTGAAGTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (38 bp):
AAAGTTATAATTTCTAAAGTTAAAATTTTAAAATAAAT
Found at i:250491 original size:58 final size:59
Alignment explanation
Indices: 250375--250506 Score: 160
Period size: 58 Copynumber: 2.3 Consensus size: 59
250365 AACTTTAATG
* *** *
250375 TAAGAACAATTAT-AAAGTTTAGGGACTAATTTGGACAAAAGAAATTCAAGTTATAATA
1 TAAGAACAATTATCAAAGTTTAGGGACTAATTTGAACAAAAGAAATTCAAACCACAATA
* * *
250433 TGAGAACAATTATCAAAGTTTAGGGACTGATTTGAACAAAA-AAATTCAAACCCCAATA
1 TAAGAACAATTATCAAAGTTTAGGGACTAATTTGAACAAAAGAAATTCAAACCACAATA
* *
250491 TAAAAACAATTGTCAA
1 TAAGAACAATTATCAA
250507 TTTCATAAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
58 37 0.60
59 25 0.40
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (59 bp):
TAAGAACAATTATCAAAGTTTAGGGACTAATTTGAACAAAAGAAATTCAAACCACAATA
Found at i:251100 original size:9 final size:9
Alignment explanation
Indices: 251082--251112 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
251072 AGCTATTCAC
251082 AAAAAA-AA
1 AAAAAACAA
251090 AAAAAACAA
1 AAAAAACAA
251099 AAAAAACAA
1 AAAAAACAA
251108 AAAAA
1 AAAAA
251113 GTACAGCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:251100 original size:15 final size:16
Alignment explanation
Indices: 251080--251111 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
251070 ACAGCTATTC
251080 ACAAAAAAAA-AAAAA
1 ACAAAAAAAACAAAAA
251095 ACAAAAAAAACAAAAA
1 ACAAAAAAAACAAAAA
251111 A
1 A
251112 AGTACAGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (16 bp):
ACAAAAAAAACAAAAA
Found at i:262925 original size:40 final size:40
Alignment explanation
Indices: 262860--262972 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 40
262850 TCAAATTGTT
* * * *
262860 TGAACTGGCAGTGACACTGTGAACACTGTGATACTATAAC
1 TGAACAGGCAGTGACATTGTAAACACTGCGATACTATAAC
* * * * *
262900 TGAGCAGGCAGTGACATTGTAAACACTGCAATGCTATCAT
1 TGAACAGGCAGTGACATTGTAAACACTGCGATACTATAAC
* * *
262940 TGAACTGACAGTGATATTGTAAACACTGCGATA
1 TGAACAGGCAGTGACATTGTAAACACTGCGATA
262973 TTGCAATTGG
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (40 bp):
TGAACAGGCAGTGACATTGTAAACACTGCGATACTATAAC
Found at i:265552 original size:15 final size:16
Alignment explanation
Indices: 265525--265554 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
265515 TTAGTGTTTA
265525 TGTTTTGAGGGTTTTT
1 TGTTTTGAGGGTTTTT
265541 TGTTTTGA-GGTTTT
1 TGTTTTGAGGGTTTT
265555 CGAAGTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.07, C:0.00, G:0.30, T:0.63
Consensus pattern (16 bp):
TGTTTTGAGGGTTTTT
Found at i:267366 original size:24 final size:24
Alignment explanation
Indices: 267315--267369 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
267305 TCTTTTAGTT
* *
267315 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTAATTTGTTTCAATC
* * *
267339 AAACTTTGTTAATTTGTTTGAGTC
1 AAACTCTGTTAATTTGTTTCAATC
267363 AAACTCT
1 AAACTCT
267370 TATTAGTCTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTAATTTGTTTCAATC
Found at i:273016 original size:12 final size:11
Alignment explanation
Indices: 272979--273049 Score: 65
Period size: 12 Copynumber: 6.4 Consensus size: 11
272969 AAAACATAAA
*
272979 AAAATAACATC
1 AAAATAACAAC
272990 AAAATAAC-A-
1 AAAATAACAAC
272999 AAAATAACAAC
1 AAAATAACAAC
*
273010 TAAAATAACAGC
1 -AAAATAACAAC
*
273022 AAAAATAGCAAC
1 -AAAATAACAAC
*
273034 AAAAATAACAGC
1 -AAAATAACAAC
273046 AAAA
1 AAAA
273050 ACAATACCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 8 0.16
10 1 0.02
11 12 0.24
12 29 0.58
ACGTcount: A:0.69, C:0.15, G:0.04, T:0.11
Consensus pattern (11 bp):
AAAATAACAAC
Found at i:273033 original size:24 final size:24
Alignment explanation
Indices: 272978--273050 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
272968 TAAAACATAA
*
272978 AAAAATAACATC-AAAAT-A-A-C
1 AAAAATAACAACAAAAATAACAGC
*
272998 AAAAATAACAACTAAAATAACAGC
1 AAAAATAACAACAAAAATAACAGC
*
273022 AAAAATAGCAACAAAAATAACAGC
1 AAAAATAACAACAAAAATAACAGC
273046 AAAAA
1 AAAAA
273051 CAATACCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
20 11 0.24
21 5 0.11
22 1 0.02
23 1 0.02
24 28 0.61
ACGTcount: A:0.70, C:0.15, G:0.04, T:0.11
Consensus pattern (24 bp):
AAAAATAACAACAAAAATAACAGC
Found at i:273050 original size:12 final size:12
Alignment explanation
Indices: 272995--273050 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
272985 ACATCAAAAT
272995 AACAAAAATAAC
1 AACAAAAATAAC
*
273007 AACTAAAATAAC
1 AACAAAAATAAC
* *
273019 AGCAAAAATAGC
1 AACAAAAATAAC
273031 AACAAAAATAAC
1 AACAAAAATAAC
*
273043 AGCAAAAA
1 AACAAAAA
273051 CAATACCAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.70, C:0.16, G:0.05, T:0.09
Consensus pattern (12 bp):
AACAAAAATAAC
Found at i:273100 original size:21 final size:21
Alignment explanation
Indices: 273076--273150 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
273066 AAAAAATAGC
273076 ACCAAAACAATAAAAAAAAAA
1 ACCAAAACAATAAAAAAAAAA
** *
273097 ACCAAAAC-AGCAAAAAAACA
1 ACCAAAACAATAAAAAAAAAA
* * **
273117 ATCAAAACAGTAAAAAAAAGT
1 ACCAAAACAATAAAAAAAAAA
*
273138 TCCAAAACAATAA
1 ACCAAAACAATAA
273151 TATAATTTTT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.71, C:0.17, G:0.04, T:0.08
Consensus pattern (21 bp):
ACCAAAACAATAAAAAAAAAA
Found at i:273113 original size:17 final size:18
Alignment explanation
Indices: 273091--273134 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
273081 AACAATAAAA
273091 AAAAAAAC-CAAAACAGC
1 AAAAAAACACAAAACAGC
*
273108 AAAAAAACAATCAAAACAGT
1 AAAAAAAC-A-CAAAACAGC
273128 AAAAAAA
1 AAAAAAA
273135 AGTTCCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
20 15 0.65
ACGTcount: A:0.75, C:0.16, G:0.05, T:0.05
Consensus pattern (18 bp):
AAAAAAACACAAAACAGC
Found at i:277985 original size:28 final size:28
Alignment explanation
Indices: 277932--277986 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
277922 TTTTAAATAG
*
277932 ACTATTAAAATTATAAAATTGTAATTTT
1 ACTATTAAAAATATAAAATTGTAATTTT
*
277960 ACTATTGAAAAATATACAATTG-AATTT
1 ACTATT-AAAAATATAAAATTGTAATTT
277987 CAACCCCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (28 bp):
ACTATTAAAAATATAAAATTGTAATTTT
Found at i:281807 original size:59 final size:58
Alignment explanation
Indices: 281729--282026 Score: 307
Period size: 59 Copynumber: 5.1 Consensus size: 58
281719 TAATTTTGAG
* * *
281729 AGTTTCAGGATCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTAGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT-GAATTTTTGGA
* * **
281788 AGTTTTGGGGTCAAAAATGGGATATTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT-GAATTTTTGGA
* * * **
281847 AGTTTCGGGGACAAAAATGGGATTTTTGTAAGTTAGAAGGTAAAAATGGAATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT-GAATTTTTGGA
* * * *
281906 AGTTTCGAGGTAAAAAATGGGATTTCTGGAAGTTCGGGGGT-AAAATGGATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAATTTTTGGA
* * ** * *
281963 AG-TTCAGGGGT--AAAATGGTAATTTTTGGAGGTTTTGGGGTCAAAAATGAGTTTTTTAGA
1 AGTTTC-GGGGTCAAAAATGG-GATTTTTGGAAGTTCGGGGGT-AAAAATGA-ATTTTTGGA
282022 AGTTT
1 AGTTT
282027 GAGGGTAAAA
Statistics
Matches: 199, Mismatches: 34, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
55 7 0.04
56 19 0.10
57 16 0.08
58 11 0.06
59 144 0.72
60 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (58 bp):
AGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAATTTTTGGA
Found at i:281820 original size:30 final size:29
Alignment explanation
Indices: 281741--282036 Score: 269
Period size: 29 Copynumber: 10.1 Consensus size: 29
281731 TTTCAGGATC
**
281741 AAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGGATTTTTGGAAGTTTAGGGGT
* * * *
281770 AAAAATAGAATTTTTAGAAGTTTTGGGGT
1 AAAAATGGGATTTTTGGAAGTTTAGGGGT
*
281799 CAAAAATGGGATATTTGGAAGTTTAGGGGT
1 -AAAAATGGGATTTTTGGAAGTTTAGGGGT
* * *
281829 AAAAATGGAATTTTTGGAAGTTTCGGGGAC
1 AAAAATGGGATTTTTGGAAGTTTAGGGG-T
* *
281859 AAAAATGGGATTTTTGTAAG-TTAGAAGGT
1 AAAAATGGGATTTTTGGAAGTTTAG-GGGT
* * *
281888 AAAAATGGAATTTTTGGAAGTTTCGAGGT
1 AAAAATGGGATTTTTGGAAGTTTAGGGGT
* **
281917 AAAAAATGGGATTTCTGGAAGTTCGGGGGT
1 -AAAAATGGGATTTTTGGAAGTTTAGGGGT
*
281947 -AAAAT-GGATTTTTGGAAGTTCAGGGGT
1 AAAAATGGGATTTTTGGAAGTTTAGGGGT
* * *
281974 -AAAATGGTAATTTTTGGAGGTTTTGGGGT
1 AAAAATGG-GATTTTTGGAAGTTTAGGGGT
* * *
282003 CAAAAATGAGTTTTTTAGAAGTTT-GAGGGT
1 -AAAAATGGGATTTTTGGAAGTTTAG-GGGT
282033 AAAA
1 AAAA
282037 TGGTAATTGT
Statistics
Matches: 219, Mismatches: 38, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
27 25 0.11
28 6 0.03
29 96 0.44
30 86 0.39
31 6 0.03
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (29 bp):
AAAAATGGGATTTTTGGAAGTTTAGGGGT
Found at i:282049 original size:29 final size:29
Alignment explanation
Indices: 281708--282060 Score: 116
Period size: 29 Copynumber: 12.1 Consensus size: 29
281698 AGACATTCAG
* * *
281708 GGGTAAAAGGGTAATTTTGAG-AGTTTCA
1 GGGTAAAATGGTAATTTTTAGAAGTTTGA
* * * * *
281736 GGATCAAAAATGG-GATTTTTGGAAGTTCGG
1 GGGT--AAAATGGTAATTTTTAGAAGTTTGA
*
281766 GGGTAAAAATAG-AATTTTTAGAAGTTTTG-
1 GGGT-AAAATGGTAATTTTTAGAAG-TTTGA
* * *
281795 GGGTCAAAAATGG-GATATTTGGAAGTTT-A
1 GGGT--AAAATGGTAATTTTTAGAAGTTTGA
*
281824 GGGGTAAAAATGG-AATTTTTGGAAGTTTCG-
1 -GGGT-AAAATGGTAATTTTTAGAAGTTT-GA
* * *
281854 GGGACAAAAATGG-GATTTTT-GTAAGTTAGA
1 GGG--TAAAATGGTAATTTTTAG-AAGTTTGA
* *
281884 AGGTAAAAATGG-AATTTTTGGAAGTTTCGA
1 GGGT-AAAATGGTAATTTTTAGAAGTTT-GA
* * * * *
281914 -GGTAAAAAATGG-GATTTCTGGAAGTTCGG
1 GGGT--AAAATGGTAATTTTTAGAAGTTTGA
* *
281943 GGGTAAAATGG--ATTTTTGGAAG-TTCA
1 GGGTAAAATGGTAATTTTTAGAAGTTTGA
* *
281969 GGGGTAAAATGGTAATTTTTGGAGGTTTTG-
1 -GGGTAAAATGGTAATTTTTAGAAG-TTTGA
281999 GGGTCAAAAATGAGT--TTTTTAGAAGTTTGA
1 GGGT--AAAATG-GTAATTTTTAGAAGTTTGA
*
282029 GGGTAAAATGGTAATTGTTAGACAGTTT-A
1 GGGTAAAATGGTAATTTTTAGA-AGTTTGA
282058 GGG
1 GGG
282061 ACCTCCGGGG
Statistics
Matches: 256, Mismatches: 39, Indels: 59
0.72 0.11 0.17
Matches are distributed among these distances:
26 1 0.00
27 23 0.09
28 16 0.06
29 107 0.42
30 99 0.39
31 8 0.03
32 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.33
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTAGAAGTTTGA
Found at i:283238 original size:19 final size:19
Alignment explanation
Indices: 283202--283239 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
283192 GGTTTTTTTA
*
283202 TTTTAATTAATATTAATTT
1 TTTTAATTAATATAAATTT
283221 TTTTAA-TAATAATAAATTT
1 TTTTAATTAAT-ATAAATTT
283240 CATTTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTAATTAATATAAATTT
Found at i:284774 original size:205 final size:205
Alignment explanation
Indices: 284420--284788 Score: 623
Period size: 205 Copynumber: 1.8 Consensus size: 205
284410 GGTCTTCATT
*
284420 AGGAAGATGACTGCGTCGTTCGTTTCAATCCGCTTCTCTGTATCTCATCGGGAAGACGAATTTGG
1 AGGAAGATGACTGCATCGTTCGTTTCAATCCGCTTCTCTGTATCTCATCGGGAAGACGAATTTGG
*
284485 TCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATGGCTTCGACCTGCTTCTCAGCATCTC
66 TCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATGGCTTCGACCTGCTTCTCAACATCTC
*
284550 ATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGACTTGATCTTCTTCTCA
131 ATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGACTTGATCTTCTTCTCA
284615 GTATCTTATC
196 GTATCTTATC
* * **
284625 AGGAAGATGA-TCGCATCGTTTGTTTCAATCCGCTTCTCTTTATCTCATCGGGAAGATTAATTTG
1 AGGAAGATGACT-GCATCGTTCGTTTCAATCCGCTTCTCTGTATCTCATCGGGAAGACGAATTTG
* *
284689 GTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAATATCT
65 GTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATGGCTTCGACCTGCTTCTCAACATCT
* *
284754 CATCAGGAAGCTGAGGTTCGAATATTTGTTCACAT
130 CATCAGGAAGCTGAGGTTCGAAGATTTGCTCACAT
284789 ATTGGTTTTC
Statistics
Matches: 152, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
204 1 0.01
205 151 0.99
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (205 bp):
AGGAAGATGACTGCATCGTTCGTTTCAATCCGCTTCTCTGTATCTCATCGGGAAGACGAATTTGG
TCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATGGCTTCGACCTGCTTCTCAACATCTC
ATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGACTTGATCTTCTTCTCA
GTATCTTATC
Found at i:296595 original size:29 final size:30
Alignment explanation
Indices: 296552--296649 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
296542 TAAAAGGGTA
* *
296552 ATTTTGAGAGTTTCAGGATCTAAAATGGGAT
1 ATTTTGA-AGCTTCAGGATCAAAAATGGGAT
* * *
296583 TTTTTGAAG-TTCAGGGT-AAAAATGGAAT
1 ATTTTGAAGCTTCAGGATCAAAAATGGGAT
** *
296611 ATTTAAAAGCTTCGGGATCAAAAATGGGAT
1 ATTTTGAAGCTTCAGGATCAAAAATGGGAT
*
296641 ATTTGGAAG
1 ATTTTGAAG
296650 TTCGGGGGTA
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
28 15 0.28
29 13 0.25
30 19 0.36
31 6 0.11
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.33
Consensus pattern (30 bp):
ATTTTGAAGCTTCAGGATCAAAAATGGGAT
Found at i:296636 original size:30 final size:29
Alignment explanation
Indices: 296589--296674 Score: 86
Period size: 30 Copynumber: 3.0 Consensus size: 29
296579 GGATTTTTTG
*
296589 AAGTTCAGGG-TAAAAATGGAATATTTAA
1 AAGTTCGGGGATAAAAATGGAATATTTAA
* **
296617 AAGCTTC-GGGATCAAAAATGGGATATTTGG
1 AAG-TTCGGGGAT-AAAAATGGAATATTTAA
* *
296647 AAGTTCGGGGGTAAAAATGGAATTTTTA
1 AAGTTCGGGGATAAAAATGGAATATTTA
296675 GATGTTTTGG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 6 0.13
29 20 0.43
30 21 0.45
ACGTcount: A:0.38, C:0.06, G:0.27, T:0.29
Consensus pattern (29 bp):
AAGTTCGGGGATAAAAATGGAATATTTAA
Found at i:296691 original size:59 final size:58
Alignment explanation
Indices: 296534--296916 Score: 360
Period size: 58 Copynumber: 6.5 Consensus size: 58
296524 ATTTTAGACA
* * * * * *
296534 TTCGGGGGTAAAAGGGTAATTTTGAG-AGTTTCAGGATCTAAAATGGGATTTTTTGAAG
1 TTCGGGGGTAAAATGG-AATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * * * *
296592 TTC-AGGGTAAAAATGGAATATTTAAAAGCTTCGGGATCAAAAATGGGATATTTGGAAG
1 TTCGGGGGT-AAAATGGAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * **
296650 TTCGGGGGTAAAAATGGAATTTTTAGATGTTTTGGGGTCAAATTTGGGATTTTTGGAAG
1 TTCGGGGGT-AAAATGGAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * *
296709 TTC-GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAATAATGAGATTTTTGGAAG
1 TTCGGGGGT-AAAATGGAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * *
296767 TTCGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGT-TAAAATGAGATTTTTGGAAG
1 TTCGGGGGTAAAATGG-AATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * * * * * *
296825 TTCAGGGGTAAAATGATAATTTTTGGAGGTTTTGGGTTCAAAATTGGGATTTTTAGAAG
1 TTCGGGGGTAAAATG-GAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * *
296884 TTTGAGGGTAAAATGGTAATTTTCAGATAGTTT
1 TTCGGGGGTAAAATGG-AATTTTTAGA-AGTTT
296917 AGGGACTTTC
Statistics
Matches: 271, Mismatches: 45, Indels: 16
0.82 0.14 0.05
Matches are distributed among these distances:
57 10 0.04
58 148 0.55
59 109 0.40
60 4 0.01
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.36
Consensus pattern (58 bp):
TTCGGGGGTAAAATGGAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
Found at i:296763 original size:117 final size:115
Alignment explanation
Indices: 296534--296916 Score: 421
Period size: 117 Copynumber: 3.3 Consensus size: 115
296524 ATTTTAGACA
* * * * * *
296534 TTCGGGGGTAAAAGGGTAATTTTGAGA-GTTTCAGGATCTAAAATGGGATTTTTTGAAGTTCAGG
1 TTCGGGGGTAAAATGGTAATTTTTAGATGTTTCGGGGTC-AAAATGGGATTTTTGGAAGTTCGGG
* ** * * *
296598 GTAAAAATGGAATATTTAAAAGCTTCGGGATCAAAAATGGGATATTTGGAAG
65 GTAAAAATGGAATTTTTGGAAGTTTTGGGATC-AAAATGGGATTTTTGGAAG
* *
296650 TTCGGGGGTAAAAATGG-AATTTTTAGATGTTTTGGGGTCAAATTTGGGATTTTTGGAAGTTCGG
1 TTCGGGGGT-AAAATGGTAATTTTTAGATGTTTCGGGGTCAAA-ATGGGATTTTTGGAAGTTCGG
* *
296714 GGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAATAATGAGATTTTTGGAAG
64 GGTAAAAATGGAATTTTTGGAAGTTTTGGGATCAA-AATGGGATTTTTGGAAG
* * * *
296767 TTCGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTTAAAATGAGATTTTTGGAAGTTCAGGG
1 TTCGGGGGTAAAATGGTAATTTTTAGATGTTTCGGGGTCAAAATGGGATTTTTGGAAGTTC-GGG
* * * *
296832 GT-AAAATGATAATTTTTGGAGGTTTTGGGTTCAAAATTGGGATTTTTAGAAG
65 GTAAAAATG-GAATTTTTGGAAGTTTTGGGATCAAAA-TGGGATTTTTGGAAG
* * *
296884 TTTGAGGGTAAAATGGTAATTTTCAGATAGTTT
1 TTCGGGGGTAAAATGGTAATTTTTAGAT-GTTT
296917 AGGGACTTTC
Statistics
Matches: 226, Mismatches: 32, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
116 55 0.24
117 167 0.74
118 4 0.02
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.36
Consensus pattern (115 bp):
TTCGGGGGTAAAATGGTAATTTTTAGATGTTTCGGGGTCAAAATGGGATTTTTGGAAGTTCGGGG
TAAAAATGGAATTTTTGGAAGTTTTGGGATCAAAATGGGATTTTTGGAAG
Found at i:296905 original size:29 final size:28
Alignment explanation
Indices: 296573--296906 Score: 219
Period size: 29 Copynumber: 11.5 Consensus size: 28
296563 TTCAGGATCT
* * ** *
296573 AAAATGGGATTTTTTGAAGTTCAGGGTA
1 AAAATGGAATTTTTGGAAGTTTGGGGTC
* ** * *
296601 AAAATGGAATATTTAAAAGCTTCGGGATC
1 AAAATGGAATTTTTGGAAG-TTTGGGGTC
* * * *
296630 AAAAATGGGATATTTGGAAGTTCGGGGGTA
1 -AAAATGGAATTTTTGGAAGTT-TGGGGTC
* *
296660 AAAATGGAATTTTTAGATGTTTTGGGGTC
1 AAAATGGAATTTTTGGAAG-TTTGGGGTC
* * * *
296689 AAATTTGGGATTTTTGGAAGTTCGGGGTA
1 AAA-ATGGAATTTTTGGAAGTTTGGGGTC
296718 AAAATGGAATTTTTGGAAGTTTTGGGGTC
1 AAAATGGAATTTTTGGAAG-TTTGGGGTC
*
296747 AATAAT-GAGATTTTTGGAAGTTCGGGGGT-
1 AA-AATGGA-ATTTTTGGAAGTT-TGGGGTC
*
296776 AAAATGGTAATTTTTGGAAGTTTCGGGGTT
1 AAAATGG-AATTTTTGGAAGTTT-GGGGTC
*
296806 AAAAT-GAGATTTTTGGAAGTTCAGGGGT-
1 AAAATGGA-ATTTTTGGAAGTT-TGGGGTC
* * *
296834 AAAATGATAATTTTTGGAGGTTTTGGGTTC
1 AAAATG-GAATTTTTGGAAG-TTTGGGGTC
* *
296864 AAAATTGGGATTTTTAGAAGTTTGAGGGT-
1 AAAA-TGGAATTTTTGGAAGTTTG-GGGTC
296893 AAAATGGTAATTTT
1 AAAATGG-AATTTT
296907 CAGATAGTTT
Statistics
Matches: 242, Mismatches: 42, Indels: 43
0.74 0.13 0.13
Matches are distributed among these distances:
28 41 0.17
29 121 0.50
30 78 0.32
31 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTGGGGTC
Found at i:298763 original size:6 final size:6
Alignment explanation
Indices: 298754--298818 Score: 77
Period size: 6 Copynumber: 11.5 Consensus size: 6
298744 TTTTGAAATC
298754 AAATTT AAATTT AAA-TT AAATTT AAATTT AAA-TT -AATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
298799 GAAA--T AAATCT AAATTT AAA
1 -AAATTT AAATTT AAATTT AAA
298819 AAAAAAAAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
4 5 0.10
5 10 0.19
6 34 0.65
7 3 0.06
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
AAATTT
Found at i:298772 original size:11 final size:11
Alignment explanation
Indices: 298758--298814 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
298748 GAAATCAAAT
298758 TTAAATTTAAA
1 TTAAATTTAAA
298769 TTAAATTTAAA
1 TTAAATTTAAA
*
298780 TTTAAA-TTAAT
1 -TTAAATTTAAA
298791 TTAAATTTGAAA
1 TTAAATTT-AAA
*
298803 -TAAATCTAAA
1 TTAAATTTAAA
298813 TT
1 TT
298815 TAAAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 8 0.21
11 24 0.62
12 7 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:298774 original size:17 final size:17
Alignment explanation
Indices: 298739--298818 Score: 101
Period size: 17 Copynumber: 4.7 Consensus size: 17
298729 TTTGGACTTT
* *
298739 TTTAATTTTGAAATCAAA
1 TTTAAATTT-AAATTAAA
298757 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATTAAA
298774 TTTAAATTTAAATT-AA
1 TTTAAATTTAAATTAAA
298790 TTTAAATTTGAAA-TAAA
1 TTTAAATTT-AAATTAAA
*
298807 TCTAAATTTAAA
1 TTTAAATTTAAA
298819 AAAAAAAAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.26
17 34 0.60
18 8 0.14
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:298796 original size:33 final size:33
Alignment explanation
Indices: 298755--298818 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
298745 TTTGAAATCA
*
298755 AATTTAAATTT-AAATTAAATTTAAATTTAAATT
1 AATTTAAATTTGAAA-TAAATCTAAATTTAAATT
298788 AATTTAAATTTGAAATAAATCTAAATTTAAA
1 AATTTAAATTTGAAATAAATCTAAATTTAAA
298819 AAAAAAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (33 bp):
AATTTAAATTTGAAATAAATCTAAATTTAAATT
Found at i:300654 original size:84 final size:83
Alignment explanation
Indices: 300364--300673 Score: 280
Period size: 84 Copynumber: 3.8 Consensus size: 83
300354 TAATTATTAT
* * * * * * *
300364 AAAATCCAAATATAGAATATAATCTGTTAATC-GATGGGAATAAATCTCGAAACAGATTTAGTCA
1 AAAATCCAAATATAGAATAAAATATGTTAAACAG-CGGGAATAAATCTCGAAACAAATTTATTTA
300428 ACTTATTTTATTTGGAAAC
65 ACTTATTTTATTTGGAAAC
* * * * * * *
300447 AAAAT-CAAA-CTGGAATAAAATCTATTAAACAGCGGGAATAACTCCCTAAACAAATTTATTT-A
1 AAAATCCAAATATAGAATAAAATATGTTAAACAGCGGGAATAAATCTCGAAACAAATTTATTTAA
*
300509 CTTCATTATTATTTGGAACC
66 CTT-ATT-TTATTTGGAAAC
* * * *
300529 AAAATCCAAATATAGAATCAAATATGTTGAATAGC-AGAATAAATAC-CGAAACAAATTTATTTA
1 AAAATCCAAATATAGAATAAAATATGTTAAACAGCGGGAATAAAT-CTCGAAACAAATTTATTTA
*
300592 ACTTATTCTCGT-TTTGGAAAT
65 ACTTATT-T--TATTTGGAAAC
* *
300613 AAAAT-CAAA-ATAGAATAAAATATGTTAAACGGCGGGAAATAAATCTCAAAACAAA-TTATTT
1 AAAATCCAAATATAGAATAAAATATGTTAAACAGCGGG-AATAAATCTCGAAACAAATTTATTT
300674 TCTAATTTTA
Statistics
Matches: 183, Mismatches: 32, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
80 4 0.02
81 41 0.22
82 41 0.22
83 47 0.26
84 49 0.27
85 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.30
Consensus pattern (83 bp):
AAAATCCAAATATAGAATAAAATATGTTAAACAGCGGGAATAAATCTCGAAACAAATTTATTTAA
CTTATTTTATTTGGAAAC
Found at i:302740 original size:18 final size:18
Alignment explanation
Indices: 302705--302741 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
302695 TGAGTTTTCG
* *
302705 AATTCGAATAACTTGAAT
1 AATTCGAATAAATCGAAT
302723 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCGAAT
302741 A
1 A
302742 TCAAACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (18 bp):
AATTCGAATAAATCGAAT
Found at i:310005 original size:17 final size:17
Alignment explanation
Indices: 309983--310043 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
309973 CACATACTTC
309983 ATAAAAATTTAAAAAAA
1 ATAAAAATTTAAAAAAA
*
310000 ATAAAAATACTTAAAATTTAA
1 ATAAAAAT--TTAAAA--AAA
* *
310021 AT-AAACTTCAAAAAAA
1 ATAAAAATTTAAAAAAA
310037 ATAAAAA
1 ATAAAAA
310044 ATATATATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
16 4 0.12
17 11 0.32
18 5 0.15
19 6 0.18
20 4 0.12
21 4 0.12
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAAAAATTTAAAAAAA
Found at i:313867 original size:22 final size:23
Alignment explanation
Indices: 313833--313877 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
313823 TTTATTTTAG
* *
313833 TTATTTTGGT-AAAATTGATTTT
1 TTATTTTAGTAAAAATTAATTTT
*
313855 TTATTTTATTAAAAATTAATTTT
1 TTATTTTAGTAAAAATTAATTTT
313878 AAAAAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (23 bp):
TTATTTTAGTAAAAATTAATTTT
Found at i:313885 original size:15 final size:17
Alignment explanation
Indices: 313865--313902 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
313855 TTATTTTATT
313865 AAAAATTA-ATTT-TAA
1 AAAAATTATATTTATAA
313880 AAAAA-TATATTTATAA
1 AAAAATTATATTTATAA
313896 AAAAATT
1 AAAAATT
313903 GTAAATTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 9 0.45
16 8 0.40
17 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAATTATATTTATAA
Found at i:313896 original size:16 final size:15
Alignment explanation
Indices: 313859--313901 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
313849 GATTTTTTAT
* *
313859 TTTATTAAAAATTAA
1 TTTATAAAAAAATAA
313874 TTT-TAAAAAAATATA
1 TTTATAAAAAAATA-A
313889 TTTATAAAAAAAT
1 TTTATAAAAAAAT
313902 TGTAAATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.33
15 7 0.29
16 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTATAAAAAAATAA
Done.