Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008128.1 Hibiscus syriacus cultivar Beakdansim tig00110683_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: 4987688
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 20
Found at i:14805 original size:20 final size:20
Alignment explanation
Indices: 14780--14842 Score: 126
Period size: 20 Copynumber: 3.1 Consensus size: 20
14770 ATCAATCAAG
14780 CTCGAAAATGAATCTACAAC
1 CTCGAAAATGAATCTACAAC
14800 CTCGAAAATGAATCTACAAC
1 CTCGAAAATGAATCTACAAC
14820 CTCGAAAATGAATCTACAAC
1 CTCGAAAATGAATCTACAAC
14840 CTC
1 CTC
14843 AATAACCTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.21
Consensus pattern (20 bp):
CTCGAAAATGAATCTACAAC
Found at i:19754 original size:22 final size:21
Alignment explanation
Indices: 19711--19756 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
19701 TAAAATCATT
19711 TTCATAAACTTTATGAAAATAC
1 TTCATAAACTTTA-GAAAATAC
19733 TTCATAATACTTTA-AAACATAC
1 TTCATAA-ACTTTAGAAA-ATAC
19755 TT
1 TT
19757 AGTAAAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.14
22 13 0.59
23 6 0.27
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.39
Consensus pattern (21 bp):
TTCATAAACTTTAGAAAATAC
Found at i:26458 original size:14 final size:14
Alignment explanation
Indices: 26422--26460 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
26412 TTTTTTATCT
*
26422 AAATAAATAAAATT
1 AAATAAATAAAATA
* *
26436 CAATTAATAAAATA
1 AAATAAATAAAATA
26450 AAATAAATAAA
1 AAATAAATAAA
26461 CTACCAAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAATAAAATA
Found at i:29069 original size:22 final size:21
Alignment explanation
Indices: 29019--29091 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
29009 TTGATTCATG
* * *
29019 GGGTATTGATACCTGTATGAA
1 GGGTATCGATACCTATGTGAA
**
29040 AAGTATCGATACCATATG-GAA
1 GGGTATCGATACC-TATGTGAA
*
29061 GGGGTATCGATACCTATGTGGA
1 -GGGTATCGATACCTATGTGAA
29083 GGGTATCGA
1 GGGTATCGA
29092 CACCCAGGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
21 26 0.63
22 15 0.37
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.27
Consensus pattern (21 bp):
GGGTATCGATACCTATGTGAA
Found at i:29086 original size:21 final size:22
Alignment explanation
Indices: 29042--29091 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
29032 TGTATGAAAA
29042 GTATCGATACCATATGGAAGGG
1 GTATCGATACCATATGGAAGGG
*
29064 GTATCGATACC-TATGTGGA-GG
1 GTATCGATACCATATG-GAAGGG
29085 GTATCGA
1 GTATCGA
29092 CACCCAGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (22 bp):
GTATCGATACCATATGGAAGGG
Found at i:29658 original size:20 final size:20
Alignment explanation
Indices: 29629--29666 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29619 AAATGTGATA
*
29629 ATGAGCTATGTGGAAGAACC
1 ATGAGATATGTGGAAGAACC
*
29649 ATGAGATATGTTGAAGAA
1 ATGAGATATGTGGAAGAA
29667 TCGGGCAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.08, G:0.29, T:0.24
Consensus pattern (20 bp):
ATGAGATATGTGGAAGAACC
Found at i:31081 original size:2 final size:2
Alignment explanation
Indices: 31062--31119 Score: 66
Period size: 2 Copynumber: 29.5 Consensus size: 2
31052 TATACAATAC
* * *
31062 TA TA TA -A TA TA -A TGA TA TA TG TG TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
31103 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
31120 TACATGAATG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:33441 original size:21 final size:22
Alignment explanation
Indices: 33415--33455 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
33405 AAAATGGAAG
*
33415 TTTTGAAAATTTG-AAGTTTGA
1 TTTTGAAAATTAGAAAGTTTGA
33436 TTTTGAAAATTAGAAAGTTT
1 TTTTGAAAATTAGAAAGTTT
33456 AGGGACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (22 bp):
TTTTGAAAATTAGAAAGTTTGA
Found at i:34197 original size:21 final size:21
Alignment explanation
Indices: 34122--34198 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
34112 TTGATTTATG
**
34122 GGGTATCGATACCTATATAAA
1 GGGTATCGATACCTATATGGA
**
34143 TAGTATCGATACC-ATATGGAA
1 GGGTATCGATACCTATATGG-A
**
34164 GGAGTATTAATACCTATATGGA
1 GG-GTATCGATACCTATATGGA
34186 GGGTATCGATACC
1 GGGTATCGATACC
34199 CAGGGAACTT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
20 4 0.09
21 21 0.49
22 12 0.28
23 6 0.14
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACCTATATGGA
Found at i:37573 original size:18 final size:18
Alignment explanation
Indices: 37550--37602 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
37540 AAACTTGGTT
37550 CAACTATCTTATAAGGTC
1 CAACTATCTTATAAGGTC
37568 CAACTATCTTATAAGGTC
1 CAACTATCTTATAAGGTC
37586 CAACTATCTTATAAGGT
1 CAACTATCTTATAAGGT
37603 TCAATTGGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (18 bp):
CAACTATCTTATAAGGTC
Found at i:38552 original size:20 final size:20
Alignment explanation
Indices: 38527--38578 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
38517 AGGTAAGAAA
38527 AGTATTGATACTCTCTAGGT
1 AGTATTGATACTCTCTAGGT
38547 AGTATTGATACTCTCTAGGT
1 AGTATTGATACTCTCTAGGT
*
38567 AGTATCGATACT
1 AGTATTGATACT
38579 ACTAGTTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (20 bp):
AGTATTGATACTCTCTAGGT
Found at i:39790 original size:29 final size:29
Alignment explanation
Indices: 39735--39790 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
39725 GTTTATGTCC
* * * * *
39735 CTTAGAATTTTATAAGTTCCAGTTCGTCA
1 CTTAAAATTTAATAAATTCAAGCTCGTCA
39764 CTTAAAATTTAATAAATTCAAGCTCGT
1 CTTAAAATTTAATAAATTCAAGCTCGT
39791 ACTCTAACAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (29 bp):
CTTAAAATTTAATAAATTCAAGCTCGTCA
Found at i:48417 original size:55 final size:55
Alignment explanation
Indices: 48269--48701 Score: 602
Period size: 55 Copynumber: 7.9 Consensus size: 55
48259 TGGATATTTC
* * ** *
48269 AACTCATTATAAATTTCATGGTTTTGCACACATAGTGCCGATACG-AAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * * *
48323 AACTAATTATGAA-TT-GTAGCGTTGCACACATAGTGCCAATACAAAAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * * *
48376 AACTCATTATTAATTTTGTGGGGTTGCACACATAGTACCAATACGGAAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
*
48431 AACTCATTATAAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* *
48486 AGCTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATGCGAAAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * *
48541 AGCTCGTTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACTAAAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * * *
48596 AATTCATTATGAATTTCGTGAGGTTGCACACATAATGCCAATACGGAAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * * *
48651 AACTCATTATGAATTTTGTGGGGTTGCACGCATAGTGTCAATACGGAAATT
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATT
48702 GCAACATATA
Statistics
Matches: 338, Mismatches: 38, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
52 22 0.07
53 22 0.07
54 13 0.04
55 281 0.83
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (55 bp):
AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
Found at i:49291 original size:11 final size:11
Alignment explanation
Indices: 49275--49300 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
49265 TATTTTACAT
49275 ATTTCACTTCG
1 ATTTCACTTCG
49286 ATTTCACTTCG
1 ATTTCACTTCG
49297 ATTT
1 ATTT
49301 TTACCACTTT
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:0.19, C:0.23, G:0.08, T:0.50
Consensus pattern (11 bp):
ATTTCACTTCG
Found at i:55647 original size:55 final size:55
Alignment explanation
Indices: 55242--55649 Score: 604
Period size: 55 Copynumber: 7.4 Consensus size: 55
55232 TGTTTTGGAT
* * * *
55242 ACATAGTGCCAATACAGAAATTCATAAACTAATTATGAATTTTGCT-AGGTTGCAC
1 ACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCG-TGGGGTTGCAC
* *
55297 ACATAGTGGCCAATACGAAAATTCATATAA-TCATTATGAATTTCGAGGGGTTGCAC
1 ACATAGT-GCCAATACGGAAATTCATA-AACTCATTATGAATTTCGTGGGGTTGCAC
*
55353 ACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCAC
1 ACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCAC
* * * * *
55408 ACATAGTGCTAATACAGAAATTCATAAACTCGTTATGAATTTTGTGGAGTTGCAC
1 ACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCAC
* *
55463 AGATAGTGCCAATACGGAAATTCATAAGCTCATTATGAATTTCGTGGGGTTGCAC
1 ACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCAC
* * *
55518 ACATAGTGCCAATACTGAAATTTATAAACTCATTATGAATTTCGTGGGGTTGTAC
1 ACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCAC
55573 ACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCAC
1 ACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCAC
* *
55628 ACATAGTACCAATATGGAAATT
1 ACATAGTGCCAATACGGAAATT
55650 GTAACATATA
Statistics
Matches: 319, Mismatches: 30, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
54 2 0.01
55 270 0.85
56 45 0.14
57 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (55 bp):
ACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCAC
Found at i:55807 original size:13 final size:13
Alignment explanation
Indices: 55789--55823 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
55779 CCTTTTTGTT
55789 TGCTTGATTCAGG
1 TGCTTGATTCAGG
55802 TGCTTGATTCAGG
1 TGCTTGATTCAGG
*
55815 AGCTTGATT
1 TGCTTGATT
55824 ACGATCTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (13 bp):
TGCTTGATTCAGG
Found at i:57294 original size:7 final size:7
Alignment explanation
Indices: 57282--57307 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
57272 GAGAGACAAT
57282 GGGAGGA
1 GGGAGGA
57289 GGGAGGA
1 GGGAGGA
57296 GGGAGGA
1 GGGAGGA
57303 GGGAG
1 GGGAG
57308 AAAAAGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (7 bp):
GGGAGGA
Found at i:60999 original size:7 final size:7
Alignment explanation
Indices: 60981--61096 Score: 71
Period size: 7 Copynumber: 16.9 Consensus size: 7
60971 AGATTACACC
60981 CTAAAC-
1 CTAAACT
60987 CTAAACT
1 CTAAACT
60994 CTAAACT
1 CTAAACT
* *
61001 ATAAATT
1 CTAAACT
* *
61008 ATAAACC
1 CTAAACT
61015 CTAAACT
1 CTAAACT
*
61022 ATAAA-T
1 CTAAACT
61028 CTTAAACT
1 C-TAAACT
*
61036 CTAAACC
1 CTAAACT
61043 CTAAA-T
1 CTAAACT
* *
61049 CCAAACC
1 CTAAACT
61056 CTAACAC-
1 CTAA-ACT
*
61063 ATAAA-T
1 CTAAACT
61069 CTTAAACT
1 C-TAAACT
* *
61077 CTAAGCC
1 CTAAACT
61084 CTAAACT
1 CTAAACT
61091 CTAAAC
1 CTAAAC
61097 CCTTAATCTG
Statistics
Matches: 83, Mismatches: 19, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
6 12 0.14
7 65 0.78
8 6 0.07
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.25
Consensus pattern (7 bp):
CTAAACT
Found at i:61012 original size:21 final size:21
Alignment explanation
Indices: 60988--61080 Score: 102
Period size: 21 Copynumber: 4.5 Consensus size: 21
60978 ACCCTAAACC
60988 TAAACTCTAAACTATAAAT-T
1 TAAACTCTAAACTATAAATCT
*
61008 ATAAACCCTAAACTATAAATCT
1 -TAAACTCTAAACTATAAATCT
**
61030 TAAACTCTAAACCCTAAATC-
1 TAAACTCTAAACTATAAATCT
* *
61050 CAAACCCTAACAC-ATAAATCT
1 TAAACTCTAA-ACTATAAATCT
61071 TAAACTCTAA
1 TAAACTCTAA
61081 GCCCTAAACT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
20 14 0.23
21 45 0.75
22 1 0.02
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAACTCTAAACTATAAATCT
Found at i:61019 original size:14 final size:14
Alignment explanation
Indices: 60982--61099 Score: 80
Period size: 14 Copynumber: 8.6 Consensus size: 14
60972 GATTACACCC
*
60982 TAAA-CCTAAACTC
1 TAAACCCTAAACTA
** *
60995 TAAACTATAAATTA
1 TAAACCCTAAACTA
61009 TAAACCCTAAACTA
1 TAAACCCTAAACTA
* * *
61023 TAAATCTTAAACTC
1 TAAACCCTAAACTA
*
61037 TAAACCCTAAA-TC
1 TAAACCCTAAACTA
*
61050 CAAACCCTAACAC-A
1 TAAACCCTAA-ACTA
* * *
61064 TAAATCTTAAACTC
1 TAAACCCTAAACTA
* *
61078 TAAGCCCTAAACTC
1 TAAACCCTAAACTA
61092 TAAACCCT
1 TAAACCCT
61100 TAATCTGATT
Statistics
Matches: 79, Mismatches: 22, Indels: 7
0.73 0.20 0.06
Matches are distributed among these distances:
13 17 0.22
14 62 0.78
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:61067 original size:41 final size:42
Alignment explanation
Indices: 61010--61099 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
61000 TATAAATTAT
61010 AAACCCTAAACTATAAATCTTAAACTCTAAACCCTAAA-TCC
1 AAACCCTAAACTATAAATCTTAAACTCTAAACCCTAAACTCC
* *
61051 AAACCCTAACAC-ATAAATCTTAAACTCTAAGCCCTAAACTCT
1 AAACCCTAA-ACTATAAATCTTAAACTCTAAACCCTAAACTCC
61093 AAACCCT
1 AAACCCT
61100 TAATCTGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 34 0.76
42 11 0.24
ACGTcount: A:0.44, C:0.31, G:0.01, T:0.23
Consensus pattern (42 bp):
AAACCCTAAACTATAAATCTTAAACTCTAAACCCTAAACTCC
Found at i:61259 original size:7 final size:7
Alignment explanation
Indices: 61170--61269 Score: 51
Period size: 7 Copynumber: 14.6 Consensus size: 7
61160 GTTAGATTAT
61170 ACCCTAA
1 ACCCTAA
*
61177 ACTCTAA
1 ACCCTAA
**
61184 ACTATAA
1 ACCCTAA
*
61191 ACCATAA
1 ACCCTAA
*
61198 ACCTTAA
1 ACCCTAA
*
61205 GCCCTAA
1 ACCCTAA
***
61212 ATTATAA
1 ACCCTAA
*
61219 ACTCT-A
1 ACCCTAA
61225 ACCCT-A
1 ACCCTAA
61231 ACCCTAA
1 ACCCTAA
*
61238 GCCCTAA
1 ACCCTAA
* *
61245 GCCTTAA
1 ACCCTAA
61252 ACCCTAA
1 ACCCTAA
* *
61259 ATCCTTA
1 ACCCTAA
61266 ACCC
1 ACCC
61270 AATTATGTGA
Statistics
Matches: 72, Mismatches: 20, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
6 11 0.15
7 61 0.85
ACGTcount: A:0.40, C:0.34, G:0.03, T:0.23
Consensus pattern (7 bp):
ACCCTAA
Found at i:62244 original size:11 final size:12
Alignment explanation
Indices: 62228--62347 Score: 135
Period size: 11 Copynumber: 10.5 Consensus size: 12
62218 GTGAGCAGTT
62228 GAGCTTG-AATC
1 GAGCTTGAAATC
62239 GAGCTTGAAATC
1 GAGCTTGAAATC
* *
62251 GATCTT-CAATC
1 GAGCTTGAAATC
62262 GAGCTTGAAATC
1 GAGCTTGAAATC
* *
62274 GATCTT-CAATC
1 GAGCTTGAAATC
62285 GAGCTTGAAAT-
1 GAGCTTGAAATC
*
62296 GAGCTT-CAATC
1 GAGCTTGAAATC
62307 GAGCTTGAAATC
1 GAGCTTGAAATC
*
62319 GAGCTT-CAATC
1 GAGCTTGAAATC
*
62330 AAGCTTGAAATC
1 GAGCTTGAAATC
62342 GAGCTT
1 GAGCTT
62348 CAATTGAGTT
Statistics
Matches: 89, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
10 3 0.03
11 46 0.52
12 40 0.45
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (12 bp):
GAGCTTGAAATC
Found at i:62265 original size:23 final size:23
Alignment explanation
Indices: 62228--62360 Score: 205
Period size: 23 Copynumber: 5.8 Consensus size: 23
62218 GTGAGCAGTT
*
62228 GAGCTTGAATCGAGCTTGAAATC
1 GAGCTTCAATCGAGCTTGAAATC
*
62251 GATCTTCAATCGAGCTTGAAATC
1 GAGCTTCAATCGAGCTTGAAATC
*
62274 GATCTTCAATCGAGCTTGAAAT-
1 GAGCTTCAATCGAGCTTGAAATC
62296 GAGCTTCAATCGAGCTTGAAATC
1 GAGCTTCAATCGAGCTTGAAATC
*
62319 GAGCTTCAATCAAGCTTGAAATC
1 GAGCTTCAATCGAGCTTGAAATC
* *
62342 GAGCTTCAATTGAGTTTGA
1 GAGCTTCAATCGAGCTTGA
62361 GTCTCGAGCT
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
22 21 0.21
23 81 0.79
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (23 bp):
GAGCTTCAATCGAGCTTGAAATC
Found at i:62313 original size:45 final size:46
Alignment explanation
Indices: 62228--62360 Score: 205
Period size: 45 Copynumber: 2.9 Consensus size: 46
62218 GTGAGCAGTT
* *
62228 GAGCTTGAATCGAGCTTGAAATCGATCTTCAATCGAGCTTGAAATC
1 GAGCTTCAATCGAGCTTGAAATCGAGCTTCAATCGAGCTTGAAATC
*
62274 GATCTTCAATCGAGCTTGAAAT-GAGCTTCAATCGAGCTTGAAATC
1 GAGCTTCAATCGAGCTTGAAATCGAGCTTCAATCGAGCTTGAAATC
* * *
62319 GAGCTTCAATCAAGCTTGAAATCGAGCTTCAATTGAGTTTGA
1 GAGCTTCAATCGAGCTTGAAATCGAGCTTCAATCGAGCTTGA
62361 GTCTCGAGCT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 42 0.53
46 37 0.47
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (46 bp):
GAGCTTCAATCGAGCTTGAAATCGAGCTTCAATCGAGCTTGAAATC
Found at i:62336 original size:68 final size:68
Alignment explanation
Indices: 62227--62360 Score: 214
Period size: 68 Copynumber: 2.0 Consensus size: 68
62217 AGTGAGCAGT
* * * *
62227 TGAGCTTGAATCGAGCTTGAAATCGATCTTCAATCGAGCTTGAAATCGATCTTCAATCGAGCTTG
1 TGAGCTTCAATCGAGCTTGAAATCGAGCTTCAATCAAGCTTGAAATCGAGCTTCAATCGAGCTTG
62292 AAA
66 AAA
* *
62295 TGAGCTTCAATCGAGCTTGAAATCGAGCTTCAATCAAGCTTGAAATCGAGCTTCAATTGAGTTTG
1 TGAGCTTCAATCGAGCTTGAAATCGAGCTTCAATCAAGCTTGAAATCGAGCTTCAATCGAGCTTG
62360 A
66 A
62361 GTCTCGAGCT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (68 bp):
TGAGCTTCAATCGAGCTTGAAATCGAGCTTCAATCAAGCTTGAAATCGAGCTTCAATCGAGCTTG
AAA
Found at i:63195 original size:20 final size:20
Alignment explanation
Indices: 63170--63210 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
63160 TAGTGTTAAA
* *
63170 TATAATTTTAAAAATATATT
1 TATAATTTCAAAAATAAATT
63190 TATAATTTCAAAAATAAATT
1 TATAATTTCAAAAATAAATT
63210 T
1 T
63211 TGAAAATCCA
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:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TATAATTTCAAAAATAAATT
Found at i:65274 original size:18 final size:18
Alignment explanation
Indices: 65253--65287 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
65243 AGAATTACAT
65253 ATAATAATATATATAATA
1 ATAATAATATATATAATA
65271 ATAATAATATATATAAT
1 ATAATAATATATATAAT
65288 TAAAAAAAGG
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATAATATATATAATA
Found at i:65286 original size:12 final size:14
Alignment explanation
Indices: 65211--65287 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 14
65201 TAATATTATT
65211 TAATAATATTAATAA
1 TAATAATA-TAATAA
*
65226 TAAT-ATATAACAA
1 TAATAATATAATAA
* *
65239 TAGTAGAATTACATATAA
1 TA--ATAA-TATA-ATAA
65257 TAATATATATAATAA
1 TAATA-ATATAATAA
65272 TAATAATATATATAA
1 TAATAATATA-ATAA
65287 T
1 T
65288 TAAAAAAAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
13 7 0.14
14 8 0.16
15 19 0.39
16 6 0.12
17 4 0.08
18 5 0.10
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:65549 original size:20 final size:19
Alignment explanation
Indices: 65524--65568 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
65514 ATTTTAAATG
65524 ATAATTAATATTATTTTATT
1 ATAATTAATATTATTTTA-T
*
65544 ATAATTTATTATTATTTTAT
1 ATAA-TTAATATTATTTTAT
65564 ATAAT
1 ATAAT
65569 ATCTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 9 0.39
21 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATAATTAATATTATTTTAT
Found at i:66146 original size:60 final size:57
Alignment explanation
Indices: 66041--66209 Score: 155
Period size: 60 Copynumber: 2.8 Consensus size: 57
66031 ATATACATAT
* **
66041 AATTTAGGAT-AAAATTGAAATATTCAAAAAGTTTG-GGGGCTAATTTAGAATGAAGATCAC
1 AATTTAGGATGAAAA-TGAAATGTTC-AAAAGTTTGAGGATC-AATTTA-AATGAA-ATCAC
* *
66101 AATTTAGGGATGAAAATGAAATGTTCAAAAGTTTGAGGATCAATTTAAATTGGTAATCAT
1 AATTTA-GGATGAAAATGAAATGTTCAAAAGTTTGAGGATCAATTTAAA-T-GAAATCAC
* * *
66161 AGTTTAAGGATGAAATTGAAATGTTTAAAAGTTT-AGGGATCAATTTAAA
1 AATTT-AGGATGAAAATGAAATGTTCAAAAGTTTGA-GGATCAATTTAAA
66210 ATGAGGGTTA
Statistics
Matches: 94, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
59 3 0.03
60 68 0.72
61 19 0.20
62 4 0.04
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.33
Consensus pattern (57 bp):
AATTTAGGATGAAAATGAAATGTTCAAAAGTTTGAGGATCAATTTAAATGAAATCAC
Found at i:66200 original size:29 final size:29
Alignment explanation
Indices: 66103--66200 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 29
66093 AAGATCACAA
* *
66103 TTTAGGGATGAAAATGAAATGTTCAAAAG
1 TTTAGGGATGAAATTGAAATGTTTAAAAG
* * *
66132 TTT-GAGGAT-CAATTTAAAT-TGGTAATCATAG
1 TTTAG-GGATGAAATTGAAATGT-TTAA--A-AG
*
66163 TTTAAGGATGAAATTGAAATGTTTAAAAG
1 TTTAGGGATGAAATTGAAATGTTTAAAAG
66192 TTTAGGGAT
1 TTTAGGGAT
66201 CAATTTAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
27 1 0.02
28 10 0.20
29 17 0.33
30 2 0.04
31 9 0.18
32 11 0.22
33 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (29 bp):
TTTAGGGATGAAATTGAAATGTTTAAAAG
Found at i:66211 original size:29 final size:29
Alignment explanation
Indices: 66119--66212 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
66109 GATGAAAATG
*
66119 AAATGTTCAAAAGTTT-GAGGATCAATTTA
1 AAATGTTTAAAAGTTTAG-GGATCAATTTA
* * * * * *
66148 AATTG-GTAATCATAGTTTAAGGATGAAATTG
1 AAATGTTTAA--A-AGTTTAGGGATCAATTTA
66179 AAATGTTTAAAAGTTTAGGGATCAATTTA
1 AAATGTTTAAAAGTTTAGGGATCAATTTA
66208 AAATG
1 AAATG
66213 AGGGTTACAA
Statistics
Matches: 47, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
28 2 0.04
29 23 0.49
30 2 0.04
31 17 0.36
32 3 0.06
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.35
Consensus pattern (29 bp):
AAATGTTTAAAAGTTTAGGGATCAATTTA
Found at i:73112 original size:20 final size:20
Alignment explanation
Indices: 73087--73131 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
73077 CAAATAGCAG
73087 CGAACCCTGTTTTCCATGAA
1 CGAACCCTGTTTTCCATGAA
73107 CGAACCCTGTTTTCCATGAA
1 CGAACCCTGTTTTCCATGAA
73127 CGAAC
1 CGAAC
73132 AAAGCATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (20 bp):
CGAACCCTGTTTTCCATGAA
Found at i:74881 original size:19 final size:19
Alignment explanation
Indices: 74854--74891 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
74844 TACACTGTTT
* *
74854 TTATTATAGTGTGTTCAAC
1 TTATAATAGAGTGTTCAAC
74873 TTATAATAGAGTGTTCAAC
1 TTATAATAGAGTGTTCAAC
74892 CAATGAAGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (19 bp):
TTATAATAGAGTGTTCAAC
Found at i:79996 original size:29 final size:33
Alignment explanation
Indices: 79921--79998 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 33
79911 TTTTAAAAAG
*
79921 TACACTTTTAGTCCCTAAACTTTTACAAAAGCTA
1 TACA-TTTTAGTCACTAAACTTTTACAAAAGCTA
* *
79955 TAC--TTTGGCCACTAAAC-TTT-CAAAA-CT-
1 TACATTTTAGTCACTAAACTTTTACAAAAGCTA
79982 TACATTTTAGTCACTAA
1 TACATTTTAGTCACTAA
79999 CCAAAATTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
27 3 0.08
28 2 0.05
29 15 0.41
30 3 0.08
31 11 0.30
34 3 0.08
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (33 bp):
TACATTTTAGTCACTAAACTTTTACAAAAGCTA
Found at i:86022 original size:20 final size:20
Alignment explanation
Indices: 85999--86063 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
85989 TTTTGTATTA
*
85999 ATACTGAAGTGTTGGTATCG
1 ATACCGAAGTGTTGGTATCG
* *
86019 ATACCAAAGTGGTGGTATCG
1 ATACCGAAGTGTTGGTATCG
*
86039 ATACCGAAGTGTTGGTATCC
1 ATACCGAAGTGTTGGTATCG
86059 ATACC
1 ATACC
86064 AGATGAATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (20 bp):
ATACCGAAGTGTTGGTATCG
Found at i:86112 original size:21 final size:21
Alignment explanation
Indices: 86074--86124 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
86064 AGATGAATTG
*
86074 GTATCCATACGGGATAAACT-
1 GTATCCATACGCGATAAACTA
86094 GATATCCATAC-CGACTAAACTA
1 G-TATCCATACGCGA-TAAACTA
86116 GTATCCATA
1 GTATCCATA
86125 TCGAAGACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 23 0.85
22 1 0.04
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (21 bp):
GTATCCATACGCGATAAACTA
Found at i:87086 original size:20 final size:21
Alignment explanation
Indices: 87042--87089 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
87032 TACTAGGGGT
*
87042 AGTATCACTACCCTCCCATAGG
1 AGTATCACTA-CCTCCAATAGG
*
87064 AGTATCACTA-CTCCAATATG
1 AGTATCACTACCTCCAATAGG
87084 AGTATC
1 AGTATC
87090 GATACATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.58
22 10 0.42
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.27
Consensus pattern (21 bp):
AGTATCACTACCTCCAATAGG
Found at i:93329 original size:55 final size:55
Alignment explanation
Indices: 93194--93606 Score: 558
Period size: 55 Copynumber: 7.5 Consensus size: 55
93184 ATCCATGGAT
* * * * * * *
93194 TTGCACACGTAGTGTCGATACGGTAATTCACAAACTCATTATGAA-TTAGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
* * *
93248 TTGCACACATAGTACCAATACAGAAATTCATAAATTCATTATGAATTTCGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
* * *
93303 TTCCACACATAGTGCCAATATGGAAATTCATAAACTTATTATGAATTTCGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
*
93358 TTGCACACATAGTGCCAATATGGAAATTCATAAACTCATTATGAATTTCGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
* ** * *
93413 TTGTACACATAGTGCCAATACAAAAATTAATAAACTCATTATGAATTTTGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
* * * * *
93468 TTGCATACATAGTGCCAATAAGAAAATTCTTAAACTCATTATGAATTTCGTGAGA
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
* ** * *
93523 TTGCACACATAATGCCAATATAGAAATTCATAAACTCATTATGAATTTCATAAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
93578 TTGCACACATAGTGCCAATACGGAAATTC
1 TTGCACACATAGTGCCAATACGGAAATTC
93607 CAACATATAC
Statistics
Matches: 314, Mismatches: 44, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
54 37 0.12
55 277 0.88
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (55 bp):
TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
Found at i:97802 original size:12 final size:12
Alignment explanation
Indices: 97776--97809 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
97766 TATTGGTTAC
97776 GAAAATGAGATGT
1 GAAAATGA-ATGT
97789 GAAAATGAATGT
1 GAAAATGAATGT
*
97801 GAAAGTGAA
1 GAAAATGAA
97810 AGATGAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (12 bp):
GAAAATGAATGT
Found at i:98656 original size:17 final size:18
Alignment explanation
Indices: 98634--98671 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
98624 AGTTTCATAT
*
98634 TAAATA-ATTGCATATTA
1 TAAATAGATTACATATTA
98651 TAAATAGTATTACATATTA
1 TAAATAG-ATTACATATTA
98670 TA
1 TA
98672 TTAAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (18 bp):
TAAATAGATTACATATTA
Found at i:107117 original size:16 final size:15
Alignment explanation
Indices: 107096--107138 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
107086 GGCAATCATT
107096 TTTCTTGCATTTTACA
1 TTTCTT-CATTTTACA
*
107112 TTTCTTCAATTTTGCA
1 TTTCTTC-ATTTTACA
107128 TTTCTTTCATT
1 TTTC-TTCATT
107139 CATTTCACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 1 0.04
16 20 0.83
17 3 0.12
ACGTcount: A:0.16, C:0.19, G:0.05, T:0.60
Consensus pattern (15 bp):
TTTCTTCATTTTACA
Found at i:110617 original size:6 final size:5
Alignment explanation
Indices: 110603--110641 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
110593 ATGCTTGAAG
110603 AAGAA AAGAAA AAGAAA AAGAA AAGAA AAGAA AAGAA AA
1 AAGAA AAG-AA AAG-AA AAGAA AAGAA AAGAA AAGAA AA
110642 TAAATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 22 0.67
6 11 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:111339 original size:16 final size:16
Alignment explanation
Indices: 111314--111381 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
111304 GTTTCTAATG
*
111314 AAAAAA-GAAAGAAAA
1 AAAAAAGGAAAAAAAA
*
111329 ATAAAAGGAAAAAAAA
1 AAAAAAGGAAAAAAAA
*
111345 AAAAAAGAAAAAGATAAGA
1 AAAAAAGGAAAA-A-AA-A
*
111364 AAAAAAGCAATAAAAAA
1 AAAAAAGGAA-AAAAAA
111381 A
1 A
111382 TCAGGAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
15 5 0.12
16 18 0.42
17 3 0.07
18 4 0.09
19 11 0.26
20 2 0.05
ACGTcount: A:0.82, C:0.01, G:0.12, T:0.04
Consensus pattern (16 bp):
AAAAAAGGAAAAAAAA
Found at i:111340 original size:21 final size:20
Alignment explanation
Indices: 111316--111369 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
111306 TTCTAATGAA
* *
111316 AAAAGAAAGAAAAATAAAAGG
1 AAAAGAAA-AAAAAGAAAAAG
*
111337 AAAAAAAAAAAAAAGAAAAAG
1 -AAAAGAAAAAAAAGAAAAAG
*
111358 ATAAGAAAAAAA
1 AAAAGAAAAAAA
111370 GCAATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 10 0.37
21 10 0.37
22 7 0.26
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (20 bp):
AAAAGAAAAAAAAGAAAAAG
Found at i:111343 original size:15 final size:15
Alignment explanation
Indices: 111314--111356 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
111304 GTTTCTAATG
111314 AAAAAAGAAAGAAAAA
1 AAAAAAGAAA-AAAAA
* *
111330 TAAAAGGAAAAAAAA
1 AAAAAAGAAAAAAAA
111345 AAAAAAGAAAAA
1 AAAAAAGAAAAA
111357 GATAAGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (15 bp):
AAAAAAGAAAAAAAA
Found at i:111351 original size:27 final size:26
Alignment explanation
Indices: 111314--111369 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
111304 GTTTCTAATG
* *
111314 AAAAAAGAAAGAAAAATAAAAGGAAAA
1 AAAAAAAAAAGAAAAAGAAAA-GAAAA
*
111341 AAAAAAAAAAGAAAAAGATAAGAAAA
1 AAAAAAAAAAGAAAAAGAAAAGAAAA
111367 AAA
1 AAA
111370 GCAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (26 bp):
AAAAAAAAAAGAAAAAGAAAAGAAAA
Found at i:111355 original size:11 final size:11
Alignment explanation
Indices: 111313--111381 Score: 59
Period size: 13 Copynumber: 5.9 Consensus size: 11
111303 TGTTTCTAAT
*
111313 GAAAAAAGAAA
1 GAAAAAAAAAA
*
111324 GAAAAATAAAAG
1 GAAAAA-AAAAA
111336 GAAAAAAAAAA
1 GAAAAAAAAAA
*
111347 -AAAAGAAAAA
1 GAAAAAAAAAA
111357 GATAAGAAAAAAA
1 GA-AA-AAAAAAA
111370 GCAATAAAAAAA
1 G-AA-AAAAAAA
111382 TCAGGAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
10 9 0.19
11 11 0.23
12 11 0.23
13 14 0.30
14 2 0.04
ACGTcount: A:0.81, C:0.01, G:0.13, T:0.04
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:112212 original size:43 final size:43
Alignment explanation
Indices: 112160--112249 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 43
112150 ATCCTTCATT
* * *
112160 GAAGGAGTTGGAT-AGGTGACAACCTTTCACTTGAT-CTTTCACA
1 GAAGAAGTTGGATCA-GTGAAAACATTTCACTTGATGC-TTCACA
* *
112203 GAAGAAGTTGGATCAGTGAAAATATTTCGCTTGATGCTTCACA
1 GAAGAAGTTGGATCAGTGAAAACATTTCACTTGATGCTTCACA
112246 GAAG
1 GAAG
112250 GGGTTGAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 38 0.95
44 2 0.05
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (43 bp):
GAAGAAGTTGGATCAGTGAAAACATTTCACTTGATGCTTCACA
Found at i:115790 original size:64 final size:64
Alignment explanation
Indices: 115650--115771 Score: 199
Period size: 64 Copynumber: 1.9 Consensus size: 64
115640 ATTGTTCAAG
* *
115650 GTGTATCGATGCACATGAAGTATATCGATGCACTCCTTTAAAATAAAAACATTGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTATATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
* * *
115714 GTGTATCGATGCACAAGTAGTATATCGATGCATTCCTTTAAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTATATCGATGCACTCCTTTAAAATAAAAACATCGAATG
115772 GGATTTATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTATATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
Found at i:116482 original size:23 final size:23
Alignment explanation
Indices: 116452--116500 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
116442 ACATCTTATA
*
116452 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
*
116475 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCAATTATACG
116498 TGG
1 TGG
116501 TGTGGTGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:122020 original size:4 final size:4
Alignment explanation
Indices: 122011--122037 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
122001 GAAGTTCAAC
122011 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
122038 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:122194 original size:12 final size:12
Alignment explanation
Indices: 122177--122201 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
122167 TAGGGTTTTG
122177 TTGTTGTTGTTT
1 TTGTTGTTGTTT
122189 TTGTTGTTGTTT
1 TTGTTGTTGTTT
122201 T
1 T
122202 ACCCCAGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (12 bp):
TTGTTGTTGTTT
Found at i:124622 original size:23 final size:23
Alignment explanation
Indices: 124596--124639 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
124586 ATCTAATATG
124596 GCACTACGGTGCAATTCTACGCT
1 GCACTACGGTGCAATTCTACGCT
*
124619 GCACTTCGGTGCAATTCTACG
1 GCACTACGGTGCAATTCTACG
124640 AGTTGTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGCT
Found at i:128366 original size:27 final size:27
Alignment explanation
Indices: 128326--128385 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
128316 ACCATGAACA
128326 ACACCTTAGCGAGCTAGCTCATCTCGG
1 ACACCTTAGCGAGCTAGCTCATCTCGG
*
128353 ACACCTTAGTGAGCTAGCTCATCTCGG
1 ACACCTTAGCGAGCTAGCTCATCTCGG
*
128380 AAACCT
1 ACACCT
128386 ATCACACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (27 bp):
ACACCTTAGCGAGCTAGCTCATCTCGG
Found at i:129255 original size:3 final size:3
Alignment explanation
Indices: 129247--129292 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
129237 TAAATACATA
*
129247 TAT TAT TAT TAT TAT TGT TAT TAT TAT TA- TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
129293 CATTGCTAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:155070 original size:17 final size:17
Alignment explanation
Indices: 155048--155081 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
155038 CATTAATTGA
* *
155048 TGACAATGAGTTGTCAT
1 TGACAAAGAGATGTCAT
155065 TGACAAAGAGATGTCAT
1 TGACAAAGAGATGTCAT
155082 AATTGATACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (17 bp):
TGACAAAGAGATGTCAT
Found at i:163448 original size:18 final size:18
Alignment explanation
Indices: 163427--163465 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
163417 TACAATGTAT
163427 TCAACCTCTGTCATAGAA
1 TCAACCTCTGTCATAGAA
*
163445 TCAACCTCTGTCGTAGAA
1 TCAACCTCTGTCATAGAA
163463 TCA
1 TCA
163466 GCTACTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (18 bp):
TCAACCTCTGTCATAGAA
Found at i:166009 original size:41 final size:41
Alignment explanation
Indices: 165908--166019 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 41
165898 GGGTTTTCTT
* * *
165908 ATGAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATG
1 ATGA-TAAGTCCTTCGGGTCATCAATAAGTCTTTCGAGAAAG
* * ** *
165950 ATGCTTAAATCCTTCGGGTCATGTATAAGTCTTTTGAGAAAG
1 ATG-ATAAGTCCTTCGGGTCATCAATAAGTCTTTCGAGAAAG
*
165992 ATGATAAGTCCTTCGGGTCATCCATAAG
1 ATGATAAGTCCTTCGGGTCATCAATAAG
166020 ACCTTCGAAC
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
41 21 0.37
42 36 0.63
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (41 bp):
ATGATAAGTCCTTCGGGTCATCAATAAGTCTTTCGAGAAAG
Found at i:166256 original size:277 final size:277
Alignment explanation
Indices: 165755--166284 Score: 841
Period size: 277 Copynumber: 1.9 Consensus size: 277
165745 GGGGTTTCTT
* *
165755 GATGTTTTCAAATGCGTTTTTATAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGATTATCTCC
1 GATGTTTTCAAATGAGTTTTTATAAACTAAGTCTGATTTTCAAGGGTTTCTTGATGATTATCTCC
*
165820 AAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTTAGGGGCTCCTTAATGACAACTAAGAAACTAA
66 AAAGAATTTTTAAACGAAGCTAAGCCTAATTTTTAGGGGCTCCTTAATGACAACTAAGAAACTAA
* *
165885 GCTTGATTTTCAAGGGTTTTCTTATGAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATG
131 GCTTGATTTTCAAGGGTTTTCTTATGAGTAAGTCCTTCAGGCCAACAATAAGTCTTTCGAGCATG
* * *
165950 ATGCTTAAATCCTTCGGGTCATGTATAAGTCTTTTGAGAAAGATGATAAGTCCTTCGGGTCATCC
196 ATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTTAAGAAAGATGAAAAGTCCTTCGGGTCATCC
166015 ATAAGACCTTCGAACAG
261 ATAAGACCTTCGAACAG
*
166032 GATGTTTTCAAATGAGTTTTTATAAACTAAG-CATGATTTTCAAGGGTTTTTTGATGATTATCTC
1 GATGTTTTCAAATGAGTTTTTATAAACTAAGTC-TGATTTTCAAGGGTTTCTTGATGATTATCTC
* * *
166096 CAAAGAATTTTTAAACGAAGCTAGGCCTAATTTTTAGGGGTTCCTTGATGACAACTCAA-AAACT
65 CAAAGAATTTTTAAACGAAGCTAAGCCTAATTTTTAGGGGCTCCTTAATGACAACT-AAGAAACT
* * * * *
166160 AAGTTTTATTTTCTAGGG-TTTCTTGATGAGTAAGTCCTTTAGGCCAACAGTAAGTCTTTCGAGC
129 AAGCTTGATTTTCAAGGGTTTTCTT-ATGAGTAAGTCCTTCAGGCCAACAATAAGTCTTTCGAGC
* *
166224 ATGATGCTTAAATCCTTCGGGTTATCTATAAGTCTTTTAAGCAAGATGAAAAGTCCTTCGG
193 ATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTTAAGAAAGATGAAAAGTCCTTCGG
166285 ACAGGATCTT
Statistics
Matches: 231, Mismatches: 19, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
276 7 0.03
277 222 0.96
278 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (277 bp):
GATGTTTTCAAATGAGTTTTTATAAACTAAGTCTGATTTTCAAGGGTTTCTTGATGATTATCTCC
AAAGAATTTTTAAACGAAGCTAAGCCTAATTTTTAGGGGCTCCTTAATGACAACTAAGAAACTAA
GCTTGATTTTCAAGGGTTTTCTTATGAGTAAGTCCTTCAGGCCAACAATAAGTCTTTCGAGCATG
ATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTTAAGAAAGATGAAAAGTCCTTCGGGTCATCC
ATAAGACCTTCGAACAG
Found at i:166484 original size:258 final size:256
Alignment explanation
Indices: 166021--166518 Score: 701
Period size: 258 Copynumber: 1.9 Consensus size: 256
166011 ATCCATAAGA
* * * * * *
166021 CCTTCGAACAGGATGTTTTCAAATGAGTTTTTATAAACTAAGCATGATTTTCAAGGGTTTTTTGA
1 CCTTCGAACAGGATCTTCTCAAATGAGGTTTTAGAAACTAAGCATGATTTTCAAGGGTTTCTTCA
* * *
166086 TGATTATCTCCAAAGAATTTTTAAACGAAGCTAGGCCTAATTTTTAGGGGTTCCTTGATGACAAC
66 TGATTATCTCCAAAGAATTTTTAAAAGAAGCTAAGCCTAATTCTTAGGGGTTCCTTGATGACAAC
* * * * *
166151 TCAAAAACTAAGTTTTATTTTCTAGGGTTTCTTGATGAGTAAGTCCTTTAGGCCAACAGTAAGTC
131 TCAAAAACCAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCAGGCCAACAGTAAGTC
* *
166216 TTTCGAGCATGATGCTTAAATCCTTCGGGTTATCTATAAGTCTTTTAAGCAAGATGAAAAGT
196 TTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTATAAGT-TTTTAAGCAAGATGAAAAGT
* ** *
166278 CCTTCGGACAGGATCTTCTCAAATGAGGTTTTAGAAACTAAGGTTGATTTTCAGGGGTTTCTTCA
1 CCTTCGAACAGGATCTTCTCAAATGAGGTTTTAGAAACTAAGCATGATTTTCAAGGGTTTCTTCA
* * * *
166343 TGATTATCTCCAGATAGTTTTTAAAAGAAAGCTAAGCCTAATTCTTAGGGGTTCCTTGGTGACAA
66 TGATTATCTCCAAAGAATTTTTAAAAG-AAGCTAAGCCTAATTCTTAGGGGTTCCTTGATGACAA
* * * *
166408 -TTAAGAAACCAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGTCATCAGTAAG
130 CTCAA-AAACCAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCAGGCCAACAGTAAG
*
166472 TCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATTTATAAGTTTTT
194 TCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTATAAGTTTTT
166519 CGCGTAAAAT
Statistics
Matches: 210, Mismatches: 29, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
257 85 0.40
258 125 0.60
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (256 bp):
CCTTCGAACAGGATCTTCTCAAATGAGGTTTTAGAAACTAAGCATGATTTTCAAGGGTTTCTTCA
TGATTATCTCCAAAGAATTTTTAAAAGAAGCTAAGCCTAATTCTTAGGGGTTCCTTGATGACAAC
TCAAAAACCAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCAGGCCAACAGTAAGTC
TTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTATAAGTTTTTAAGCAAGATGAAAAGT
Found at i:168380 original size:23 final size:23
Alignment explanation
Indices: 168354--168401 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
168344 TTTGTTTTGT
* * *
168354 TTTTACTATTTTTATTATTTTTA
1 TTTTACTATTCTAATTATGTTTA
*
168377 TTTTATTATTCTAATTATGTTTA
1 TTTTACTATTCTAATTATGTTTA
168400 TT
1 TT
168402 AATTGTTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTTACTATTCTAATTATGTTTA
Found at i:183037 original size:31 final size:31
Alignment explanation
Indices: 182984--183081 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 31
182974 AAATTCATGG
*
182984 GTTAAACTGATA-TTTATCTAAAATTTAAGA
1 GTTAAACTAATATTTTATCTAAAATTTAAGA
* *
183014 GTTAAACTAATATTTTATTTAAAATTTAGGA
1 GTTAAACTAATATTTTATCTAAAATTTAAGA
*
183045 GTTAAATTAATATTTTATCTAAAATTTAATGA
1 GTTAAACTAATATTTTATCTAAAATTTAA-GA
183077 -TTAAA
1 GTTAAA
183082 TTAAAAAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
30 11 0.18
31 47 0.78
32 2 0.03
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (31 bp):
GTTAAACTAATATTTTATCTAAAATTTAAGA
Found at i:192212 original size:18 final size:17
Alignment explanation
Indices: 192184--192217 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
192174 CGGAAAAAAG
192184 TATTAATTATTATTATA
1 TATTAATTATTATTATA
192201 TATTATATTATTATTAT
1 TATTA-ATTATTATTAT
192218 TACATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTAATTATTATTATA
Found at i:192215 original size:21 final size:22
Alignment explanation
Indices: 192184--192226 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
192174 CGGAAAAAAG
*
192184 TATTAATTATTATTATATATTA
1 TATTAATTATTATTACATATTA
192206 TATT-ATTATTATTACATATTA
1 TATTAATTATTATTACATATTA
192227 ATACATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTAATTATTATTACATATTA
Found at i:193408 original size:18 final size:19
Alignment explanation
Indices: 193371--193419 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
193361 TAATTTAGGC
*
193371 ATATTATTATATATTTTAAT
1 ATATTATTAT-TATTATAAT
193391 ATATTATTATTA-TATAAT
1 ATATTATTATTATTATAAT
193409 ATATTATTATT
1 ATATTATTATT
193420 GTAATCATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 16 0.57
19 2 0.07
20 10 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTATTATTATTATAAT
Found at i:193415 original size:15 final size:14
Alignment explanation
Indices: 193372--193418 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
193362 AATTTAGGCA
193372 TATTAT-TATATAT
1 TATTATATATATAT
193385 T-TTA-ATATATTAT
1 TATTATATATA-TAT
193398 TATTATATAATATAT
1 TATTATAT-ATATAT
193413 TATTAT
1 TATTAT
193419 TGTAATCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 7 0.24
13 5 0.17
14 3 0.10
15 11 0.38
16 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATATATATAT
Found at i:196572 original size:32 final size:32
Alignment explanation
Indices: 196535--196596 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
196525 TTTCACCAGT
*
196535 ACTAAC-TAATTTCTTTTCTTTTGTTTGTGTAC
1 ACTAACAT-ATTTCTTTTCTTTTGATTGTGTAC
196567 ACTAACATATTTCTTTTCTTTTGATTGTGT
1 ACTAACATATTTCTTTTCTTTTGATTGTGT
196597 CATTTTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.19, C:0.15, G:0.10, T:0.56
Consensus pattern (32 bp):
ACTAACATATTTCTTTTCTTTTGATTGTGTAC
Found at i:197211 original size:210 final size:210
Alignment explanation
Indices: 196817--197251 Score: 534
Period size: 210 Copynumber: 2.1 Consensus size: 210
196807 GGTAATCCAC
* * * *
196817 TGATTCGAGGAGTAATCCAACACTGGAGTATTTTCTACAATCATGTCATCACTAGTCATCCAAGA
1 TGATTCGAGGAGTAATCCAACACTGAAGTATTTTCTACAATCATGTCAGCACTAGTCATCAAAAA
* * * * ** * *
196882 GCGACATAGTGACATCAGTATCGCTGAGGCATTAACGGAGTTGGTTTACAGAGTATTGAGGGGCA
66 GCGACACACTGACATCAGCACCGCTGAGGCATTAACAAAGTTCGTTTACAGAGCATTGAGGGGCA
* * * *
196947 TCAGTTTCAAATATGAAGATCCAATATGAAACTATGAGCTCGACGATCGTGCAGTATTCGAGACT
131 TCAGTTCCAAATATGAAGATCCAAGATCAAACCATGAGCTCGACGATCGTGCAGTATTCGAGACT
197012 AAAATGATGATACAG
196 AAAATGATGATACAG
*
197027 TGATTCGAGGAGTAATCCAGA-ACTGAAGT-TTTCTCTACAATCATGTTAGCACTAGTCATCAAA
1 TGATTCGAGGAGTAATCCA-ACACTGAAGTATTT-TCTACAATCATGTCAGCACTAGTCATCAAA
** * *
197090 AAGCGATGCACTGACTTCAGCACCGTTGAGGCATTAACAAAGTTCGTTTACAGAGCATTGAGGGG
64 AAGCGACACACTGACATCAGCACCGCTGAGGCATTAACAAAGTTCGTTTACAGAGCATTGAGGGG
* * * *
197155 TATCAGTTCCAAATATGAAGATCCGAGA-CAAACCAGTGAGCTTGACGATTGTGCAGTATTCGAG
129 CATCAGTTCCAAATATGAAGATCCAAGATCAAACCA-TGAGCTCGACGATCGTGCAGTATTCGAG
* * * * *
197219 ATTGAAATTATGATTCAT
193 ACTAAAATGATGATACAG
* *
197237 TCATCCGAGGAGTAA
1 TGATTCGAGGAGTAA
197252 CTCAACAGTA
Statistics
Matches: 190, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
209 8 0.04
210 181 0.95
211 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (210 bp):
TGATTCGAGGAGTAATCCAACACTGAAGTATTTTCTACAATCATGTCAGCACTAGTCATCAAAAA
GCGACACACTGACATCAGCACCGCTGAGGCATTAACAAAGTTCGTTTACAGAGCATTGAGGGGCA
TCAGTTCCAAATATGAAGATCCAAGATCAAACCATGAGCTCGACGATCGTGCAGTATTCGAGACT
AAAATGATGATACAG
Found at i:198987 original size:13 final size:13
Alignment explanation
Indices: 198946--198988 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
198936 GGATCAATAT
198946 TTTTGCATCTGCA
1 TTTTGCATCTGCA
*
198959 TTTT-CATATTTGCA
1 TTTTGC--ATCTGCA
198973 TTTTGCATCTGCA
1 TTTTGCATCTGCA
198986 TTT
1 TTT
198989 CATTTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 1 0.04
13 13 0.52
14 10 0.40
15 1 0.04
ACGTcount: A:0.16, C:0.19, G:0.12, T:0.53
Consensus pattern (13 bp):
TTTTGCATCTGCA
Found at i:203086 original size:15 final size:14
Alignment explanation
Indices: 203055--203103 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
203045 ATTGCACTTG
*
203055 AAGAAGAAAAAATAA
1 AAGAA-AAAAAAAAA
203070 AAGAAAAAAGAAAAA
1 AAGAAAAAA-AAAAA
203085 AAGAAAAGAAAAGAAA
1 AAGAAAA-AAAA-AAA
203101 AAG
1 AAG
203104 GGACGAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.13
15 18 0.60
16 8 0.27
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (14 bp):
AAGAAAAAAAAAAA
Found at i:203102 original size:19 final size:19
Alignment explanation
Indices: 203055--203102 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
203045 ATTGCACTTG
*
203055 AAGAAGAAAAAATAAAAGAA
1 AAGAA-AAAAAAGAAAAGAA
*
203075 AAAAGAAAAAAAGAAAAGAA
1 AAGA-AAAAAAAGAAAAGAA
203095 AAGAAAAA
1 AAGAAAAA
203103 GGGACGAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 19 0.79
21 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (19 bp):
AAGAAAAAAAAGAAAAGAA
Found at i:204732 original size:126 final size:126
Alignment explanation
Indices: 204482--204765 Score: 297
Period size: 126 Copynumber: 2.3 Consensus size: 126
204472 ACTTATCATA
* * * * *
204482 GTATGAGCAGTGTTATCATCC-TTAGATGGACAAGACACATGAACAGAAGAGCAGTGTCATCCCT
1 GTATGAACAGTGTTATCA-CCTTTAGATGGCCAAGACACATGAACAGAAGAGCAGTATCATCACA
* ** *
204546 TGACCAGATCTCCTCATTATATAGGAGTTGTGTCAACCTAGATAACCAGCCGTCCCCATCA-
65 CGACCAGATCTCCTCATTATATAGGAACTATGTCAACCTAGATAACCAGCCGTCCCCATCAC
* *
204607 G-AGTGAAACAGTGTTATCACCTTTAGATGGCCAAGACTCATGAACAGATGAGCAGTATCATCAC
1 GTA-TG-AACAGTGTTATCACCTTTAGATGGCCAAGACACATGAACAGAAGAGCAGTATCATCAC
* * * * * ** **
204671 ACGATCATATCTCCTTATTATGTAGGAACTATGTCAA-CTCGGATAACCAGTTGTCTTCATCAC
64 ACGACCAGATCTCCTCATTATATAGGAACTATGTCAACCT-AGATAACCAGCCGTCCCCATCAC
* * *
204734 GTATGAGCTGTGTTATTACCTTTAGATGGCCA
1 GTATGAACAGTGTTATCACCTTTAGATGGCCA
204766 GAACTCTTCA
Statistics
Matches: 130, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
124 1 0.01
125 7 0.05
126 118 0.91
127 3 0.02
128 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (126 bp):
GTATGAACAGTGTTATCACCTTTAGATGGCCAAGACACATGAACAGAAGAGCAGTATCATCACAC
GACCAGATCTCCTCATTATATAGGAACTATGTCAACCTAGATAACCAGCCGTCCCCATCAC
Found at i:204861 original size:43 final size:43
Alignment explanation
Indices: 204813--204909 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 43
204803 CCTGATCTCC
* *
204813 TCATCATGTAGGAG-CTATGTCAATCCTTGATA-ACCAAAACTCT
1 TCATCACGTAGGAGTC-ATGTCAACCCTT-ATACACCAAAACTCT
* * *
204856 TCATCACGTATGAGTCGTGTCAACCCTTATACGACCAGAACTCT
1 TCATCACGTAGGAGTCATGTCAACCCTTATAC-ACCAAAACTCT
204900 TCATCACGTA
1 TCATCACGTA
204910 TGAGAAGTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
42 3 0.07
43 22 0.48
44 21 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (43 bp):
TCATCACGTAGGAGTCATGTCAACCCTTATACACCAAAACTCT
Found at i:205082 original size:3 final size:3
Alignment explanation
Indices: 205076--205116 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
205066 AAAAAAATAT
205076 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
205117 CATTTTTGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:211333 original size:20 final size:21
Alignment explanation
Indices: 211303--211342 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
211293 AGCCGCTGGG
211303 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
211324 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
211343 CTATATAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:213485 original size:17 final size:16
Alignment explanation
Indices: 213463--213500 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
213453 CTCGGTAAGC
213463 TTCTCTTCTTTCTTTTT
1 TTCTCTTCTTT-TTTTT
*
213480 TTCTC-TGTTTTTTTT
1 TTCTCTTCTTTTTTTT
213495 TTCTCT
1 TTCTCT
213501 GTTTCTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 10 0.53
16 4 0.21
17 5 0.26
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (16 bp):
TTCTCTTCTTTTTTTT
Found at i:213495 original size:15 final size:15
Alignment explanation
Indices: 213475--213504 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
213465 CTCTTCTTTC
213475 TTTTTTTCTCTGTTT
1 TTTTTTTCTCTGTTT
213490 TTTTTTTCTCTGTTT
1 TTTTTTTCTCTGTTT
213505 CTTTGCTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTTTTTCTCTGTTT
Found at i:213979 original size:3 final size:3
Alignment explanation
Indices: 213971--214031 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
213961 GGCCTGGTTG
* *
213971 TAA TAA TAA TAT TAA TAA TAA TAA AAA TATA TAA TAAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
*
214017 TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA
214032 AACCGGGACA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:214512 original size:113 final size:113
Alignment explanation
Indices: 214377--215022 Score: 803
Period size: 113 Copynumber: 5.7 Consensus size: 113
214367 ATAGAGTCCT
* ** * *
214377 GCAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
214442 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
* *
214490 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
214555 ATTATGAAC-TTCTCTTGAAAAACTGATCCATCAAATGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
** * * * * * * *
214602 ATAAAAAGTTGAAGAAGTTCTTCTCATTATGAACTTATTCTTCTTTCATCAGATGAGTTCTTCCC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * * ** *
214667 ATTATGAACTCGAC-CTGGCAATGTTGATCCATC-TCTGATGAATTCAA
66 ATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
* * * *
214714 TCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
214779 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
* * * *
214827 GCAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAATTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
214892 ATTATGAACTTTCCCTGGCAAAGCTAATCCATCAATTGATGAATTTAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
**
214940 ATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTT
215005 CTCATTATGAACCTTTCT
63 CTCATTATGAA-CTTTCT
215023 GGCAATGTTA
Statistics
Matches: 451, Mismatches: 74, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
112 190 0.42
113 233 0.52
114 1 0.00
115 1 0.00
116 21 0.05
117 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
Found at i:214801 original size:337 final size:339
Alignment explanation
Indices: 214378--215039 Score: 1033
Period size: 337 Copynumber: 2.0 Consensus size: 339
214368 TAGAGTCCTG
* *
214378 CAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
214443 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAAT
* * *
214508 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAAC-TTCTCTTG
131 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAATTCTTCTCATTATGAACTTTCCCTGG
* * *
214572 AAAAACTGATCCATCAAATGATGAATTCAAATAAAAAGTTGAAGAAGTTCTTCTCATTATGAACT
196 AAAAACTAATCCATCAAATGATGAATTCAAATAAAAAGTTGAACAAATTCTTCTCATTATGAACT
* *
214637 TATTCTTCTTTCATC-A-GATGAGTTCTTCCCATTATGAACTCGACCTGGCAATGTTGATCCATC
261 TATTCTTCCTTCATCAATGATGAGTTCTTCCCATTATGAAC-CGACCTGGCAATGTTAATCCATC
214700 TCTGATGAATTCAAT
325 TCTGATGAATTCAAT
* *
214715 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
214780 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAAT
* *
214845 TCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAATTCTTCTCATTATGAACTTTCCCTGG
131 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAATTCTTCTCATTATGAACTTTCCCTGG
* * * * *
214910 CAAAGCTAATCCATCAATTGATGAATTTAAATAAAAGGTTGAACAAATTCTTCTCATTATGAACT
196 AAAAACTAATCCATCAAATGATGAATTCAAATAAAAAGTTGAACAAATTCTTCTCATTATGAACT
* * * ***
214975 TCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACCTTTCTGGCAATGTTAATCCATC
261 TATTCTTCCTTCATCA-ATGATGAGTTCTTCCCATTATGAACCGACCTGGCAATGTTAATCCATC
215040 AATTGATGGA
Statistics
Matches: 293, Mismatches: 28, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
337 176 0.60
338 75 0.26
340 20 0.07
341 22 0.08
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (339 bp):
CAAAAAGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAAT
TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAATTCTTCTCATTATGAACTTTCCCTGG
AAAAACTAATCCATCAAATGATGAATTCAAATAAAAAGTTGAACAAATTCTTCTCATTATGAACT
TATTCTTCCTTCATCAATGATGAGTTCTTCCCATTATGAACCGACCTGGCAATGTTAATCCATCT
CTGATGAATTCAAT
Found at i:216162 original size:87 final size:83
Alignment explanation
Indices: 215773--216243 Score: 788
Period size: 83 Copynumber: 5.6 Consensus size: 83
215763 GGTTTTATAT
* *
215773 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
215838 TTCAATGATTGA-TTTAC
66 TTCAATGATTGATTTTAC
*
215855 CAAACCAGATCAGATAA-TCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTATTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
*
215919 TTCAATGATTTATTTTAC
66 TTCAATGATTGATTTTAC
*
215937 CAAACCAGATCAGATAACTCAAAGACATTCACTTCCAG-A-ATGCCATGAGCACATTATTCTTCC
1 CAAACCAGATCAGATAACTCAAAGA-A--CACTTCCAGAAGATGCTATGAGCACATTATTCTTCC
216000 AAATTCAATGATTGATTTTAC
63 AAATTCAATGATTGATTTTAC
216021 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
216086 TTCAATGATTGATTTTAC
66 TTCAATGATTGATTTTAC
*
216104 CAAACCAGATCAGATAACTCAAAGAACATTTACTTCCAGAAGATGCCATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAGAAC----ACTTCCAGAAGATGCTATGAGCACATTATTCTTC
216169 CAAATTCAATGATTGATTTTAC
62 CAAATTCAATGATTGATTTTAC
*
216191 CAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGAGCACAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
216244 GGCATTTGTT
Statistics
Matches: 367, Mismatches: 11, Indels: 21
0.92 0.03 0.05
Matches are distributed among these distances:
81 66 0.18
82 38 0.10
83 103 0.28
84 68 0.19
85 1 0.00
86 9 0.02
87 82 0.22
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
TTCAATGATTGATTTTAC
Found at i:216234 original size:170 final size:169
Alignment explanation
Indices: 215773--216243 Score: 814
Period size: 170 Copynumber: 2.8 Consensus size: 169
215763 GGTTTTATAT
* * *
215773 CAAACCAAATCAGAGAACTCAAAGAAC---ACTTCCAGAAGATGCTATGAGCACATTATTCTTCC
1 CAAACCAGATCAGATAACTCAAAGAACATTACTTCCAGAAGATGCCATGAGCACATTATTCTTCC
215835 AAATTCAATGATTGA-TTTACCAAACCAGATCAGATAA-TCAAAGAACACTTCCAGAAGATGCTA
66 AAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
*
215898 TGAGCACATTATTATTCCAAATTCAATGATTTATTTTAC
131 TGAGCACATTATTATTCCAAATTCAATGATTGATTTTAC
215937 CAAACCAGATCAGATAACTCAAAG-ACATTCACTTCCAG-A-ATGCCATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAGAACATT-ACTTCCAGAAGATGCCATGAGCACATTATTCTTC
215999 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
65 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
*
216064 ATGAGCACATTATTCTTCCAAATTCAATGATTGATTTTAC
130 ATGAGCACATTATTATTCCAAATTCAATGATTGATTTTAC
216104 CAAACCAGATCAGATAACTCAAAGAACATTTACTTCCAGAAGATGCCATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAGAACA-TTACTTCCAGAAGATGCCATGAGCACATTATTCTTC
*
216169 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCT
65 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
216234 ATGAGCACAT
130 ATGAGCACAT
216244 GGCATTTGTT
Statistics
Matches: 291, Mismatches: 6, Indels: 14
0.94 0.02 0.05
Matches are distributed among these distances:
163 2 0.01
164 22 0.08
165 38 0.13
166 23 0.08
167 95 0.33
168 11 0.04
169 3 0.01
170 97 0.33
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (169 bp):
CAAACCAGATCAGATAACTCAAAGAACATTACTTCCAGAAGATGCCATGAGCACATTATTCTTCC
AAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
TGAGCACATTATTATTCCAAATTCAATGATTGATTTTAC
Found at i:217586 original size:1 final size:1
Alignment explanation
Indices: 217582--217645 Score: 65
Period size: 1 Copynumber: 64.0 Consensus size: 1
217572 CTTTTTCTTC
* * * * * * *
217582 TTTTTTCTTCTTTTTTTTTTTTTTTTTTTCTTTTTTTTCTTTTTCTTTTTTTTCTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
217646 CTCTTCAAGC
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:217586 original size:9 final size:9
Alignment explanation
Indices: 217572--217647 Score: 67
Period size: 7 Copynumber: 8.9 Consensus size: 9
217562 CTTGACCCCC
217572 CTTTTTCTT
1 CTTTTTCTT
217581 CTTTTTTCTT
1 C-TTTTTCTT
217591 CTTTTT-TT
1 CTTTTTCTT
217599 -TTTTT-TT
1 CTTTTTCTT
217606 -TTTTTC-T
1 CTTTTTCTT
217613 -TTTTT-TT
1 CTTTTTCTT
217620 CTTTTTCTT
1 CTTTTTCTT
*
217629 TTTTTTCTTTT
1 CTTTTTC--TT
217640 CTTTTTCT
1 CTTTTTCT
217648 CTTCAAGCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
7 19 0.33
8 7 0.12
9 15 0.26
10 9 0.16
11 8 0.14
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
CTTTTTCTT
Found at i:217586 original size:10 final size:10
Alignment explanation
Indices: 217573--217647 Score: 84
Period size: 10 Copynumber: 7.7 Consensus size: 10
217563 TTGACCCCCC
217573 TTTTTCTTCT
1 TTTTTCTTCT
217583 TTTTTCTTCT
1 TTTTTCTTCT
* *
217593 TTTTTTTTTT
1 TTTTTCTTCT
*
217603 TTTTTTTTCT
1 TTTTTCTTCT
217613 TTTTT-TTC-
1 TTTTTCTTCT
217621 TTTTTCTT-T
1 TTTTTCTTCT
*
217630 TTTTTCTTTT
1 TTTTTCTTCT
217640 CTTTTTCT
1 -TTTTTCT
217648 CTTCAAGCAT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
8 5 0.09
9 13 0.22
10 33 0.57
11 7 0.12
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:217602 original size:15 final size:14
Alignment explanation
Indices: 217573--217645 Score: 92
Period size: 14 Copynumber: 5.0 Consensus size: 14
217563 TTGACCCCCC
*
217573 TTTTTCTTCTTTTT
1 TTTTTTTTCTTTTT
*
217587 TCTTCTTTTTTTTTTT
1 T-TT-TTTTTCTTTTT
217603 TTTTTTTTCTTTTT
1 TTTTTTTTCTTTTT
217617 TTTCTTTTTCTTTTT
1 TTT-TTTTTCTTTTT
*
217632 TTTCTTTTCTTTTT
1 TTTTTTTTCTTTTT
217646 CTCTTCAAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
14 24 0.46
15 18 0.35
16 10 0.19
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTCTTTTT
Found at i:217605 original size:29 final size:30
Alignment explanation
Indices: 217574--217651 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
217564 TGACCCCCCT
* *
217574 TTTTCTTCTTTTTTCTTCTTTTTTTTTTTT
1 TTTTTTTCTTTTTTCTTCTTTTTTCTTTTT
217604 TTTTTTTCTTTTTT-TTC-TTTTTCTTTTT
1 TTTTTTTCTTTTTTCTTCTTTTTTCTTTTT
217632 TTTCTTTTCTTTTTCTCTTC
1 TTT-TTTTCTTTTT-TCTTC
217652 AAGCATAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 13 0.30
29 13 0.30
30 14 0.33
31 3 0.07
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (30 bp):
TTTTTTTCTTTTTTCTTCTTTTTTCTTTTT
Found at i:223663 original size:15 final size:15
Alignment explanation
Indices: 223640--223671 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
223630 TGAAATGAAT
223640 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
223655 AATGCATGTATGCAA
1 AATGAATGTATGCAA
223670 AA
1 AA
223672 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:228597 original size:14 final size:14
Alignment explanation
Indices: 228578--228606 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
228568 CTCTTCTTTC
228578 TTTTTTTCTCTGTT
1 TTTTTTTCTCTGTT
228592 TTTTTTTCTCTGTT
1 TTTTTTTCTCTGTT
228606 T
1 T
228607 CTTTGCTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTTTCTCTGTT
Found at i:229098 original size:3 final size:3
Alignment explanation
Indices: 229090--229151 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
229080 GGCCTGGTTG
* *
229090 TAA TAA TAA TAT TAA TAA TAA TAA AAA TATA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
*
229137 TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA
229152 AACCGGGACA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:229631 original size:113 final size:113
Alignment explanation
Indices: 229496--230171 Score: 777
Period size: 113 Copynumber: 6.0 Consensus size: 113
229486 ATAGAGTCCT
* ** * *
229496 GCAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
229561 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
* *
229609 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
229674 ATTATGAAC-TTCTCTTGAAAAACTGATCCATCAAATGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
** * * * * * * *
229721 ATAAAA-ATTGAACAAGTTCTTCTCATTATGAACTTATTCTTCTTTCATCAGATTAGTTCTTCCC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * * ** *
229785 ATTATGAACTCGAC-CTGGCAATGTTGATCCATC-TCTGATGAATTCAA
66 ATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
* * * *
229832 TCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
229897 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
* * * * * *
229945 GCAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATAAATTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
230010 ATTATGAACTTTCCCTGGCAAAGCTAATCCATCAATTGATGAATTTAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
**
230058 ATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTT
* * * * * *
230123 CTCATTATGAACTCTT-TCTGGCAATGTTAATCCATCAATTGATGGATTT
63 CTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGAATTT
230172 GAATCTTTGC
Statistics
Matches: 472, Mismatches: 82, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
111 74 0.16
112 127 0.27
113 218 0.46
115 1 0.00
116 50 0.11
117 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
Found at i:231138 original size:87 final size:83
Alignment explanation
Indices: 230898--231373 Score: 808
Period size: 83 Copynumber: 5.6 Consensus size: 83
230888 GGTTTTATAT
* *
230898 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
230963 TTCAATGATTGATTTTAC
66 TTCAATGATTGATTTTAC
*
230981 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTATTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
*
231046 TTCAATGATTTATTTTAC
66 TTCAATGATTGATTTTAC
*
231064 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAG-A-A--CACTTCCAGAAGATGCTATGAGCACATTATTCTTC
231129 CAAATTCAATGATTGATTTTAC
62 CAAATTCAATGATTGATTTTAC
231151 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
231216 TTCAATGATTGATTTTAC
66 TTCAATGATTGATTTTAC
* *
231234 CAAACCAGATCAGATAACTCAAAGAACATTTACTTCCAGAAGATGCCATAAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAGAAC----ACTTCCAGAAGATGCTATGAGCACATTATTCTTC
231299 CAAATTCAATGATTGATTTTAC
62 CAAATTCAATGATTGATTTTAC
*
231321 CAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGAGCACAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
231374 GGCATTTGTT
Statistics
Matches: 372, Mismatches: 13, Indels: 16
0.93 0.03 0.04
Matches are distributed among these distances:
83 209 0.56
84 1 0.00
85 2 0.01
86 1 0.00
87 159 0.43
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
TTCAATGATTGATTTTAC
Found at i:231176 original size:170 final size:170
Alignment explanation
Indices: 230898--231373 Score: 852
Period size: 170 Copynumber: 2.8 Consensus size: 170
230888 GGTTTTATAT
* * *
230898 CAAACCAAATCAGAGAACTCAAAG-A-A--CACTTCCAGAAGATGCTATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
230959 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
66 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
*
231024 ATGAGCACATTATTATTCCAAATTCAATGATTTATTTTAC
131 ATGAGCACATTATTATTCCAAATTCAATGATTGATTTTAC
231064 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
231129 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
66 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
*
231194 ATGAGCACATTATTCTTCCAAATTCAATGATTGATTTTAC
131 ATGAGCACATTATTATTCCAAATTCAATGATTGATTTTAC
* *
231234 CAAACCAGATCAGATAACTCAAAGAACATTTACTTCCAGAAGATGCCATAAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
*
231299 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCT
66 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
231364 ATGAGCACAT
131 ATGAGCACAT
231374 GGCATTTGTT
Statistics
Matches: 298, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
166 22 0.07
167 1 0.00
168 1 0.00
170 274 0.92
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (170 bp):
CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
ATGAGCACATTATTATTCCAAATTCAATGATTGATTTTAC
Found at i:232753 original size:18 final size:18
Alignment explanation
Indices: 232723--232766 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
232713 TTTTTTCTTC
232723 TTTTTTCTCTCTTTTTTT
1 TTTTTTCTCTCTTTTTTT
232741 TTCTTTT-TCTCTTTTTTT
1 TT-TTTTCTCTCTTTTTTT
232759 TTTTTTCT
1 TTTTTTCT
232767 TTTTCTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.17
18 16 0.67
19 4 0.17
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTCTCTCTTTTTTT
Found at i:232775 original size:22 final size:22
Alignment explanation
Indices: 232712--232775 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
232702 CTTGACCCCC
* *
232712 CTTTTTTCTTCTTTTT-TCTCT
1 CTTTTTTTTTCTTTTTCTCTTT
232733 CTTTTTTTTTCTTTTTCTCTTT
1 CTTTTTTTTTCTTTTTCTCTTT
*
232755 TTTTTTTTTTCTTTTTCTCTT
1 CTTTTTTTTTCTTTTTCTCTT
232776 CAAGCATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 15 0.38
22 24 0.62
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
CTTTTTTTTTCTTTTTCTCTTT
Found at i:243732 original size:14 final size:14
Alignment explanation
Indices: 243713--243739 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
243703 CTTCTTTCTA
243713 TTTTTCTCTGTTTT
1 TTTTTCTCTGTTTT
243727 TTTTTCTCTGTTT
1 TTTTTCTCTGTTT
243740 CTTTGCTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (14 bp):
TTTTTCTCTGTTTT
Found at i:244217 original size:3 final size:3
Alignment explanation
Indices: 244209--244269 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
244199 GGCCTGGTTG
* *
244209 TAA TAA TAA TAT TAA TAA TAA TAA AAA TATA TAA TAAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
244255 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
244270 AACCGGGACA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:249535 original size:29 final size:28
Alignment explanation
Indices: 249495--249608 Score: 111
Period size: 29 Copynumber: 3.9 Consensus size: 28
249485 TTAATTTATT
249495 AAATATATTTTATTCTTATCTTAACTAA
1 AAATATATTTTATTCTTATCTTAACTAA
* *
249523 AAACTATATTTTAATCTTATCTTAACTTAT
1 AAA-TATATTTTATTCTTATCTTAAC-TAA
* * * * *
249553 ATATATATATTATTCCTACCTTAAGTTAAA
1 AAATATATTTTATTCTTATCTTAA-CT-AA
* *
249583 AAATATATTTTATTATCATCTTAACT
1 AAATATATTTTATTCTTATCTTAACT
249609 TTTAAAAATA
Statistics
Matches: 66, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
28 3 0.05
29 40 0.61
30 23 0.35
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (28 bp):
AAATATATTTTATTCTTATCTTAACTAA
Found at i:249590 original size:59 final size:58
Alignment explanation
Indices: 249497--249609 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 58
249487 AATTTATTAA
* * * * * *
249497 ATATATTTTATTCTTATCTTAACTAAAAACTATATTTTAATCTTATCTTAACTTATAT
1 ATATATATTATTCCTACCTTAACTAAAAAATATATTTTAATATCATCTTAACTTATAT
* *
249555 ATATATATTATTCCTACCTTAAGTTAAAAAATATATTTTATTATCATCTTAACTT
1 ATATATATTATTCCTACCTTAA-CTAAAAAATATATTTTAATATCATCTTAACTT
249610 TTAAAAATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
58 19 0.41
59 27 0.59
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (58 bp):
ATATATATTATTCCTACCTTAACTAAAAAATATATTTTAATATCATCTTAACTTATAT
Found at i:249780 original size:25 final size:24
Alignment explanation
Indices: 249738--249801 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 24
249728 ATTAAAAATT
*
249738 TATTTATTCTTATCTTAAGTTGAAAA
1 TATTTATT-TTATTTTAA-TTGAAAA
*
249764 TATTTATTTTATTTTAATTTAAAA
1 TATTTATTTTATTTTAATTGAAAA
249788 -ATTCATATTTTATT
1 TATT--TATTTTATT
249802 CTTACTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 3 0.09
24 6 0.18
25 17 0.50
26 8 0.24
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (24 bp):
TATTTATTTTATTTTAATTGAAAA
Found at i:249800 original size:30 final size:29
Alignment explanation
Indices: 249759--249841 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 29
249749 ATCTTAAGTT
249759 GAAA-ATA-TTTATTTTATTTTAATTTAA
1 GAAATATATTTTATTTTATTTTAATTTAA
*
249786 -AAATTCATATTTTATTCTTACTTTAATTTAA
1 GAAA-T-ATATTTTATT-TTATTTTAATTTAA
249817 GAAATATATTTTATTTTTATTTTAA
1 GAAATATATTTTA-TTTTATTTTAA
249842 CTATAAATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
26 3 0.06
29 3 0.06
30 22 0.47
31 16 0.34
32 3 0.06
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (29 bp):
GAAATATATTTTATTTTATTTTAATTTAA
Found at i:259743 original size:2 final size:2
Alignment explanation
Indices: 259736--259765 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
259726 TATTTATCAA
259736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
259766 TTATGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:265328 original size:22 final size:22
Alignment explanation
Indices: 265260--265337 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
265250 TTCATGAAAT
* * *
265260 TGCCCTAGCACTGGTACTAAAA
1 TGCCTTAGCACTGATACTAAAG
* *
265282 TGCCTTGGCACTGATACGT-AGG
1 TGCCTTAGCACTGATAC-TAAAG
* *
265304 TGCATTCGCACTGATACTAAAG
1 TGCCTTAGCACTGATACTAAAG
265326 TGCCTTAGCACT
1 TGCCTTAGCACT
265338 ACGGGTATAT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 1 0.02
22 42 0.95
23 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (22 bp):
TGCCTTAGCACTGATACTAAAG
Found at i:267792 original size:45 final size:45
Alignment explanation
Indices: 267720--267865 Score: 141
Period size: 45 Copynumber: 3.2 Consensus size: 45
267710 AAAATGAATA
** * * *
267720 CATAAATGAAAT-ACATAACGGTGCATTATTGGCATGAAAGGATGC
1 CATAAATGAAATGA-ATAATAGTACATTATCGGCATGAAAAGATGC
*
267765 CATACATGAAATGAATAATAGTACATTATCGGCATGAAAAGATGC
1 CATAAATGAAATGAATAATAGTACATTATCGGCATGAAAAGATGC
* * * * ** * *
267810 CATAAATGAAATGCATAATGGTGCTTTATCGATATGAAAGGATGA
1 CATAAATGAAATGAATAATAGTACATTATCGGCATGAAAAGATGC
*
267855 TATAAATGAAA
1 CATAAATGAAA
267866 ATAAAAAATA
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
45 83 0.99
46 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (45 bp):
CATAAATGAAATGAATAATAGTACATTATCGGCATGAAAAGATGC
Found at i:273914 original size:43 final size:44
Alignment explanation
Indices: 273774--273917 Score: 166
Period size: 45 Copynumber: 3.2 Consensus size: 44
273764 AAAATGAATA
** *
273774 CATAAATGAAATGCATAATGGTGCATTATCATAATGAAAGGATTC
1 CATAAATGAAATGCATAA-GGTGCATTATCAGCATGAAAGGATGC
* * *
273819 CATAAATGAAATGCATAACGGTGCATTATCGGCATGAAATGATGT
1 CATAAATGAAATGCATAA-GGTGCATTATCAGCATGAAAGGATGC
* * *
273864 CAAAAATGAATATGCAT-A-GTGCATTATAAGCATGAACGGATGC
1 CATAAATGAA-ATGCATAAGGTGCATTATCAGCATGAAAGGATGC
273907 CATAAATGAAA
1 CATAAATGAAA
273918 ATAAAGAATA
Statistics
Matches: 84, Mismatches: 14, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
42 1 0.01
43 29 0.35
45 48 0.57
46 6 0.07
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (44 bp):
CATAAATGAAATGCATAAGGTGCATTATCAGCATGAAAGGATGC
Found at i:275342 original size:20 final size:20
Alignment explanation
Indices: 275296--275342 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
275286 GTGGTCATCA
* *
275296 AAGTAAAAGGTTTTCATGATG
1 AAGT-AAAGGGTTTCATGATC
*
275317 GA-TAAAGGGTTTCATGATC
1 AAGTAAAGGGTTTCATGATC
275336 AAGTAAA
1 AAGTAAA
275343 TTATAACACC
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 15 0.71
20 5 0.24
21 1 0.05
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.30
Consensus pattern (20 bp):
AAGTAAAGGGTTTCATGATC
Found at i:277270 original size:14 final size:14
Alignment explanation
Indices: 277251--277281 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
277241 AAGTATTATC
277251 AGACTAATACATCA
1 AGACTAATACATCA
277265 AGACTAATACATCA
1 AGACTAATACATCA
277279 AGA
1 AGA
277282 ATGATAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (14 bp):
AGACTAATACATCA
Found at i:281167 original size:231 final size:231
Alignment explanation
Indices: 280719--284820 Score: 4716
Period size: 231 Copynumber: 17.9 Consensus size: 231
280709 TTTATAAGTT
* ** *
280719 AAAAATGAGAAAAACTTCTCATTTAAATA-TGAAAATGGAAATTGTTGAAAAGTAAGAAAAG--T
1 AAAAATGAGGAAAGTTTCTCATTTAAA-ACTG-AAATTGAAATTGTTGAAAAGTAAGAAAAGTTT
* * * * *
280781 -TTA---A-TAAACTATTTCAAAAGTTGGTAAGTGATTCGGGCCATCAATAAATCTTTTGAGCAT
64 CTTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCAT
* ** * * *
280841 GATGCTTAAATCATTCAGGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGACATC
129 GATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC
* *
280906 CATAAGACCTTCGGACATGATGTATTCACATGATTTCA
194 CATAAGACCTTCGGACAGGATGTTTTCACATGATTTCA
* *
280944 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAATAGAAATTGTTGAAAAGTAAGAAAAGTTTTT
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAATTGAAATTGTTGAAAAGTAAGAAAAGTTTCT
* * * * *
281009 TACCTAGTAAACTATTTCCAAAGTTGGTAACTCCTTCGTGTCATCAATAAGTCTTTCGAGCATGA
66 TACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGA
** * ** * *
281074 TGCTTAAATCCTTCAGGTCATTTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTAAGGACATCAA
131 TGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCA
* **
281139 TAAGACCTTCGGATAGGATGTTTTCACATGATTTTT
196 TAAGACCTTCGGACAGGATGTTTTCACATGATTTCA
* *
281175 AAAAATGAGAAAAGTTTCTCATTTAAAACT-AAAATGAAAATTGTTGAAAAGTAAGAAAAGTTTC
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAATTG-AAATTGTTGAAAAGTAAGAAAAGTTTC
* * *
281239 TTACCTAGTAAACTATTTCCAAACTTGGTAAGTCATTCGGGTCATCAGTAAGTCTTTCGGGCATG
65 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * * * * * *
281304 ATGTTTAAATACTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTTCTTTGTGCCATCT
130 ATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
* * * *
281369 ATAAGACTTTTGGGCAGGATGTTTTCATATGATTTCGA
195 ATAAGACCTTCGGACAGGATGTTTTCACATGATTTC-A
* * * * *
281407 AAAAAAGAGGAAAGTTTCTCATTTAAAACTAAAATTTGAAATTTTTGAAAAGTAAGACAGGTTTC
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAA-TTGAAATTGTTGAAAAGTAAGAAAAGTTTC
* * * *
281472 TTACCTAGTGAACTATTTCCAAAATTGGTAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCATG
65 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * * * * *
281537 ATGTTTAAATCCTTTTGGTCATCTATAAGCCTTTCAAGAAAGATGATAAGTCC-T-------T-C
130 ATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
* **
281593 ----G------GG-CAGGATGTTTTCACGTGATTTTG
195 ATAAGACCTTCGGACAGGATGTTTTCACATGATTTCA
* * * * *
281619 AAAAATAAGAAAAGTTTCTCATTTAAATCTGAAAATGGAAATTGTTGAAAAATAAGAAAAGTTTC
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTG-AAATTGAAATTGTTGAAAAGTAAGAAAAGTTTC
* * * * *
281684 TTACCTAGTAAATTATTTCCAAAGTTGGTAAGACCTTCGGGCCATCAGTAAGTCTTTCGAACATA
65 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATG
* *
281749 ATTCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTTGGG-CATTC
130 ATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCA-TC
* * * *
281813 CATAAGACCTTGGGGCAGGATATTTTCACATGATTTCG
194 CATAAGACCTTCGGACAGGATGTTTTCACATGATTTCA
* * **
281851 AAAAATGAGGATAGTTTCTCATTTAAAACTTAAAGAGAAATTTGTT-AAAAGTAA-AAAATGTTT
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAATTGAAA-TTGTTGAAAAGTAAGAAAA-GTTT
* *
281914 CTTACCTAGTAAACTATTTCCAAAGTTAGTAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCAT
64 CTTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * * * * *
281979 CATGCTTAAATCCTTTGGGTTATCTATAAGTCTTTTGAGCAATATGATAAGTTCTTCGGGCCATC
129 GATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC
* *
282044 CATAAGACCTTCGTG-CAAGATGTTTTCACATGA-TTCG
194 CATAAGACCTTCG-GACAGGATGTTTTCACATGATTTCA
* * * *
282081 AAAAATGAGGAAAGTTTCTCATTTGAAACTAAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTC
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAA-TTGAAATTGTTGAAAAGTAAGAAAAGTTTC
* * * * *
282146 TTACCTAGTAAACTATTTTCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCGTG
65 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * *
282211 ATG-TTAAAATCCATTGGGTCATCTGTAAGCCTTTC-ATGCATGATGATAAGTCCTTCGGGCCAT
130 ATGCTT-AAATCCTTTGGGTCATCTGTAAGTCTTTCGA-GCAAGATGATAAGTCCTTCGGGCCAT
* **
282274 CCATAAAACCTTCAGG-CAGGATGTTTTCACATGATTTTG
193 CCATAAGACCTTC-GGACAGGATGTTTTCACATGATTTCA
* * *
282313 AAAAATGAGGAAAGTTTATCATTTAAAACTGAAATGGAAATAGTTGAAAAGTAAGAAAAGTTTCT
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAATTGAAATTGTTGAAAAGTAAGAAAAGTTTCT
* *
282378 TACCTAGGAAACTATTTCCAAAGTTGGTAAGTCATTCGAGCCATCAGTAAGTCTTTCGAGCATGA
66 TACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * * * * * **
282443 TGCTTAAATCATTCGGGCCATTTGTAAGTCTTTCAAGCAAGATGATAAGTCTTTCATGCCATCCA
131 TGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCA
** * * *
282508 TAAGACCTTCGGGTAGGATGTATTCACATGATTACG
196 TAAGACCTTCGGACAGGATGTTTTCACATGATTTCA
* * * *
282544 AAAAATAAGGAAAGTTTCTCATTTAAAACTGAAATGGAAATTGGTT-AAAAGTAAAAAAAGCTTC
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAATTGAAATT-GTTGAAAAGTAAGAAAAGTTTC
* * * *
282608 TAACTTAGTAAAATATTTCCAAAGTTGGTAAGTCCTTC-GG---T-AGTAAGTCTTTCGAGCATT
65 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCA-T
* * * * *
282668 G-TGCTTAAATCCTATGGGTCATTTGTAAGTCTTTCGAGAAATATGATAAGTCTTTCGGGCCATC
129 GATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC
* *
282732 TATAAGACCTTCGTG-CAAGATGTTTTCACATGATTTCGA
194 CATAAGACCTTCG-GACAGGATGTTTTCACATGATTTC-A
* *
282771 AAAAA-GAGGAAAGTTTCTCATTTGAAACTGAAATTTGAAATTTTTGAAAAGTAAG-AAAGTTTT
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAA-TTGAAATTGTTGAAAAGTAAGAAAAG-TTT
* * * * *
282834 TTTACCTAGTAAACTATTTCCAAAATTGGTAAGTTATTCGGGCCATTAGTAAGTCTTTCAAGCAT
64 CTTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * *
282899 GATGCTTAAATCCTTTGGGTCATCTGTAAGCCTTTCGAACAAGATGATAAGTCCTTCGTGCCATC
129 GATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC
* **
282964 CATAAAACCTTCAGG-CAGGATGTTTTCACATGATTTTG
194 CATAAGACCTTC-GGACAGGATGTTTTCACATGATTTCA
* * * *
283002 AAAAATGAGGAAAGTTTATCATTTAAAACTGAAATGGAAATAGTTAAAAAGTAAGAAAAGTTTCT
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAATTGAAATTGTTGAAAAGTAAGAAAAGTTTCT
* *
283067 TACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGAGCTATCAGTAAGTCTTTCGAGCATGA
66 TACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * * * * ** *
283132 TGCTTAAATCATTCGGGCCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCTTTCATGCCATCTA
131 TGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCA
* * *
283197 TAAGACCTTCGGGA-AGGATGTCTTCACATGATTACG
196 TAAGACCTTC-GGACAGGATGTTTTCACATGATTTCA
* * * *
283233 AAAAATAAGGAAAATTTCTCATTTAAAACTGAAATGGAAATTGGTT-AAAAGTAAGAAAAGCTTC
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAATTGAAATT-GTTGAAAAGTAAGAAAAGTTTC
* * * *
283297 TAACCTAGTAAACTATTTCCAAAGTTGGTAATTCTTTCGGTCCATCAGTAAGTCTTTCGAGCATT
65 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCA-T
* * * *
283362 G-TGCTTAAATCCTTTGGGTCATTTGTAAGTCTTTTGAGAAAGATGATAAGTCTTTCGGGCCATC
129 GATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC
* * *
283426 TATAAGACCTTCGTG-CAAGATGTTTTCACATGATTTTGA
194 CATAAGACCTTCG-GACAGGATGTTTTCACATGA-TTTCA
* *
283465 AAAAA-GAGGAAAGTTTCTCATTTGAAACTGAAATTTGAAATTTTTGAAAAGTAAG-AAAGTTTT
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAA-TTGAAATTGTTGAAAAGTAAGAAAAG-TTT
* * * *
283528 CTTACCTAGTAAACTATTT-CAAAATTGGTAAGTCATTCGGGCCATCAGTATGTCTTTCAATCAT
64 CTTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCAT
* *
283592 GATGCTTAAATCCTTTGGGTCATCTGTAAATCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATC
129 GATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC
* * * * *
283657 TATAAAACCTTCGGGCATGATGTTTACACATGATTTCA
194 CATAAGACCTTCGGACAGGATGTTTTCACATGATTTCA
* * *
283695 AAAAATGAGGAAAGTTTCTCATTTAAAATTGAAATAGGAATTGGTT-AAAAGTAAGAAAAGTTTC
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAATTGAAATT-GTTGAAAAGTAAGAAAAGTTTC
* * * *
283759 GTACCTAGTAAACTATTTCCAAAGTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATG
65 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATG
* *
283824 ATGCTTAAATCCTTTGGGTCCTCTGTAAGTCTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCC
130 ATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
* * *
283889 ATAAGACCTTCGTG-CAAGATGTTTTTAGATGATTTCAA
195 ATAAGACCTTCG-GACAGGATGTTTTCACATGATTTC-A
* * * *
283927 AAAAATGAGGAAAGTTTCTCATTTTAAACTGAAATTTGAAATTTTTGAAAAGAAAGAAAGGTTTC
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAA-TTGAAATTGTTGAAAAGTAAGAAAAGTTTC
* * * *
283992 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCCATCAGTGAGTGTTTCGAGTATG
65 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * * * * * *
284057 ATGTTTAAATCCTTTGGGTCATCTGTACGCCTTTCAAGCAAGATGATAAATCCTTCAGGTCATCC
130 ATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
** **
284122 ATAAGACCTTCGGGTAGGATGTTTTCATGTGATTTCA
195 ATAAGACCTTCGGACAGGATGTTTTCACATGATTTCA
* * * * * *
284159 AAAGACGAAGAAAGTTTCTCATTTAAAACTGAAATTTGAAATTTTTGAAAAATAAGAAAGGTTTC
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAA-TTGAAATTGTTGAAAAGTAAGAAAAGTTTC
* * * *
284224 TTGCCTAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGTCATCAGTAAGTCTTTTGAGCATG
65 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * *
284289 ATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCC
130 ATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
* ** * *
284354 AGAAGACCTTCGGGTAGGAAGTTTTCACGTGATTTCA
195 ATAAGACCTTCGGACAGGATGTTTTCACATGATTTCA
* * * * * *
284391 AAAGATGAGGAAAGTTTCTTATTTAAAACTAAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTA
1 AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAA-TTGAAATTGTTGAAAAGTAAGAAAAGTTTC
* * * * * * * *
284456 TTACCTAATAAACTATTTCCAAAGTTAGTAAGTCCTTCGAGTCATTAGTAAGTCTTTTGAGCTTG
65 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * * * * * * * *
284521 ATGCTTAAATCATTCGGGTCATCTATAAGACTATCGAGCAAGATGATAAGTCTTTCGTGACATCT
130 ATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
* * * *
284586 ATGAGACCTTCGGGCAAGATGTTTTCAGATG-TCTCTC-
195 ATAAGACCTTCGGACAGGATGTTTTCACATGAT-T-TCA
* * * * *
284623 GAAAATTAGAAAAGTTTCTCATTTAAATA-TGAAAATT-AAATTTTTGAAAAATAAGAAAAGTTT
1 AAAAATGAGGAAAGTTTCTCATTTAAA-ACTG-AAATTGAAATTGTTGAAAAGTAAGAAAAGTTT
* * * * **
284686 CTTACCTAGTAAAC-AATTCTCAAATTTGGTAAGTCCTTCGGGCCATCAGTATGT-TTTTAAGCA
64 CTTACCTAGTAAACTATTTC-CAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCA
* * * * *
284749 TGATG-TTCAAATCCTTCGGGTCATCTATAA-ACTTCTCGAGCGAGATGATAAGTCCTTCGAGCC
128 TGATGCTT-AAATCCTTTGGGTCATCTGTAAGTCTT-TCGAGCAAGATGATAAGTCCTTCGGGCC
284812 ATCCATAAG
191 ATCCATAAG
284821 TCCCTCGTGC
Statistics
Matches: 3351, Mismatches: 436, Indels: 175
0.85 0.11 0.04
Matches are distributed among these distances:
212 155 0.05
213 23 0.01
214 2 0.00
220 2 0.00
221 1 0.00
224 29 0.01
225 28 0.01
226 134 0.04
227 61 0.02
228 2 0.00
229 5 0.00
230 171 0.05
231 1654 0.49
232 778 0.23
233 304 0.09
234 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (231 bp):
AAAAATGAGGAAAGTTTCTCATTTAAAACTGAAATTGAAATTGTTGAAAAGTAAGAAAAGTTTCT
TACCTAGTAAACTATTTCCAAAGTTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGA
TGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCA
TAAGACCTTCGGACAGGATGTTTTCACATGATTTCA
Found at i:281369 original size:41 final size:42
Alignment explanation
Indices: 281287--281378 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 42
281277 GGGTCATCAG
* * * *
281287 TAAGTCTTTCGGGCATGATGTTTAAATACTTTGGGTCATCTA
1 TAAGTCTTTCGAGCAAGATGTATAAATACTTTGGGCCATCTA
* * *
281329 TAAGTCTTTCGAGCAAGATG-ATAAGTTCTTTGTGCCATCTA
1 TAAGTCTTTCGAGCAAGATGTATAAATACTTTGGGCCATCTA
*
281370 TAAGACTTT
1 TAAGTCTTT
281379 TGGGCAGGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 24 0.57
42 18 0.43
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGTATAAATACTTTGGGCCATCTA
Found at i:287184 original size:2 final size:2
Alignment explanation
Indices: 287177--287338 Score: 184
Period size: 2 Copynumber: 82.0 Consensus size: 2
287167 CATGCATGCA
* * * * * *
287177 TG TG TG TG TA TG TA TG TG TA TA TG TA TG TG TG TG TG TA TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
287219 T- TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * *
287260 TG TG TG TA TG TG TA TA TG TA TG TG TA TA TG TA TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
287302 TG TC TG TG T- TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
287339 GGAATGACTT
Statistics
Matches: 136, Mismatches: 22, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
1 2 0.01
2 134 0.99
ACGTcount: A:0.08, C:0.01, G:0.41, T:0.51
Consensus pattern (2 bp):
TG
Found at i:307114 original size:11 final size:11
Alignment explanation
Indices: 307098--307145 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
307088 AAAAATAAAT
307098 GAAATTAAAAC
1 GAAATTAAAAC
307109 GAAATTAAAAC
1 GAAATTAAAAC
**
307120 -AAAAAAAAAC
1 GAAATTAAAAC
*
307130 GAAAATAAAAC
1 GAAATTAAAAC
307141 GAAAT
1 GAAAT
307146 GGGTTGCCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 8 0.25
11 24 0.75
ACGTcount: A:0.71, C:0.08, G:0.08, T:0.12
Consensus pattern (11 bp):
GAAATTAAAAC
Found at i:310316 original size:21 final size:21
Alignment explanation
Indices: 310286--310353 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
310276 ACTTTGGAAT
310286 TTTTCATGGGATGCAACCAGC
1 TTTTCATGGGATGCAACCAGC
* *
310307 TTTTCCTGGGATGCAACCAGT
1 TTTTCATGGGATGCAACCAGC
*
310328 TTTTCATGGGATGTAACCAGC
1 TTTTCATGGGATGCAACCAGC
310349 TTTTC
1 TTTTC
310354 TTGTGAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (21 bp):
TTTTCATGGGATGCAACCAGC
Found at i:311793 original size:12 final size:13
Alignment explanation
Indices: 311778--311820 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
311768 AGAATAAATT
311778 AATAAATAA-TAA
1 AATAAATAATTAA
311790 AATAAATAATTAA
1 AATAAATAATTAA
*
311803 ATATAAATCATTTAA
1 A-ATAAAT-AATTAA
311818 AAT
1 AAT
311821 GGAAGATAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 4 0.15
14 8 0.30
15 6 0.22
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAAATAATTAA
Found at i:317926 original size:15 final size:16
Alignment explanation
Indices: 317906--317941 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
317896 GCTTCAGGGC
317906 TTTAC-TTTGGGTCTT
1 TTTACTTTTGGGTCTT
*
317921 TTTACTTTTTGGTCTT
1 TTTACTTTTGGGTCTT
317937 TTTAC
1 TTTAC
317942 ACTTTAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.08, C:0.14, G:0.14, T:0.64
Consensus pattern (16 bp):
TTTACTTTTGGGTCTT
Found at i:320194 original size:18 final size:18
Alignment explanation
Indices: 320162--320210 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
320152 TCTTCATCTT
* *
320162 CTTTTTTTTACTTTAATTA
1 CTTTTATTTA-TTTAATCA
*
320181 CTTTTATTTATTTAATCG
1 CTTTTATTTATTTAATCA
320199 CTTTTA-TTATTT
1 CTTTTATTTATTT
320211 TAATATCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 6 0.22
18 12 0.44
19 9 0.33
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.67
Consensus pattern (18 bp):
CTTTTATTTATTTAATCA
Found at i:323105 original size:6 final size:6
Alignment explanation
Indices: 323094--323127 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
323084 ATTCCATTAC
*
323094 ATTTTT ATTTTT ATTATT ATTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT
323128 CGATCGAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:324072 original size:18 final size:18
Alignment explanation
Indices: 324020--324079 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 18
324010 ATGCTCCATT
*
324020 AAAAAAAATGTTGAATGCGA
1 AAAAAAAATGTTG--TTCGA
*
324040 AAAAAACAA--TAGTTCGA
1 AAAAAA-AATGTTGTTCGA
324057 AAAAAAAATGTTGTTC-A
1 AAAAAAAATGTTGTTCGA
324074 AAAAAA
1 AAAAAA
324080 GAGAAAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
16 2 0.06
17 17 0.50
18 5 0.15
19 2 0.06
20 6 0.18
21 2 0.06
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (18 bp):
AAAAAAAATGTTGTTCGA
Found at i:325828 original size:18 final size:18
Alignment explanation
Indices: 325782--325824 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
325772 TCTTCTTATT
*
325782 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATCGCTTTTA
325801 TTTATTTAATCGCTTTTA
1 TTTATTTAATCGCTTTTA
325819 -TTATTT
1 TTTATTT
325825 TAATATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCGCTTTTA
Done.