Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000697.1 Hibiscus syriacus cultivar Beakdansim tig00001357_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: 172836
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:3252 original size:30 final size:28
Alignment explanation
Indices: 3218--3310 Score: 141
Period size: 30 Copynumber: 3.2 Consensus size: 28
3208 GGATTTATTC
3218 GATTAAATGATACATGATGAGAATGACTTG
1 GATTAAATGATA-ATGATGAGAATGA-TTG
3248 GATTAAATGATAAATGATGAGAATGATTTG
1 GATTAAATGAT-AATGATGAGAATGA-TTG
*
3278 GATAAAATGATAATGATGAGAATGATTG
1 GATTAAATGATAATGATGAGAATGATTG
3306 GATTA
1 GATTA
3311 GTGGTTTAGA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
28 7 0.12
29 14 0.24
30 37 0.63
31 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (28 bp):
GATTAAATGATAATGATGAGAATGATTG
Found at i:4503 original size:54 final size:54
Alignment explanation
Indices: 4406--4633 Score: 307
Period size: 54 Copynumber: 4.2 Consensus size: 54
4396 CCAAATCAGT
* * *
4406 ACTACGTGTGCATTTCACGGAATTCATCCTATATGGATAAATAACCGTTTCGAC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
* * *
4460 ATTAAGTGTGCATTTCACGGAATTCATCCTATGTTGATGAATAATCGTTTC-AGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA-C
* ** * *
4514 ACTAATTGTATATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
* *
4568 ACTAAGTGTGCATTTCACGGAATTCAACCTATGTGGATGAATAATCGTTTCGAC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
4622 ACTATA-TGTGCA
1 ACTA-AGTGTGCA
4634 AAACACAGAA
Statistics
Matches: 150, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 148 0.99
55 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (54 bp):
ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
Found at i:4625 original size:108 final size:108
Alignment explanation
Indices: 4417--4618 Score: 341
Period size: 108 Copynumber: 1.9 Consensus size: 108
4407 CTACGTGTGC
* *
4417 ATTTCACGGAATTCATCCTATATGGATAAATAACCGTTTCGACATTAAGTGTGCATTTCACGGAA
1 ATTTCACGGAATTCATCCTATATGGATAAATAACCATTTCGACACTAAGTGTGCATTTCACGGAA
* *
4482 TTCATCCTATGTTGATGAATAATCGTTTCAGCACTAATTGTAT
66 TTCAACCTATGTGGATGAATAATCGTTTCAGCACTAATTGTAT
* * *
4525 ATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGGCACTAAGTGTGCATTTCACGGAA
1 ATTTCACGGAATTCATCCTATATGGATAAATAACCATTTCGACACTAAGTGTGCATTTCACGGAA
4590 TTCAACCTATGTGGATGAATAATCGTTTC
66 TTCAACCTATGTGGATGAATAATCGTTTC
4619 GACACTATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 87 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (108 bp):
ATTTCACGGAATTCATCCTATATGGATAAATAACCATTTCGACACTAAGTGTGCATTTCACGGAA
TTCAACCTATGTGGATGAATAATCGTTTCAGCACTAATTGTAT
Found at i:17936 original size:7 final size:7
Alignment explanation
Indices: 17924--17977 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
17914 GTTAGATTAC
17924 ACCCTAA
1 ACCCTAA
*
17931 ACCCTAT
1 ACCCTAA
*
17938 ACTCTAA
1 ACCCTAA
*
17945 ACCATAA
1 ACCCTAA
*
17952 ACCATAA
1 ACCCTAA
* *
17959 ATCTTAA
1 ACCCTAA
17966 ACCCTAA
1 ACCCTAA
17973 ACCCT
1 ACCCT
17978 TAATATGATT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (7 bp):
ACCCTAA
Found at i:20356 original size:33 final size:30
Alignment explanation
Indices: 20271--20361 Score: 155
Period size: 30 Copynumber: 2.9 Consensus size: 30
20261 GGAACTTAAT
20271 TTGACATGTTGCAATCTTTTGTAAGTAAAC
1 TTGACATGTTGCAATCTTTTGTAAGTAAAC
20301 TTGACATGTTGCAATCTTTTGTAAGTAAAC
1 TTGACATGTTGCAATCTTTTGTAAGTAAAC
20331 TTGACATGTTGCTACCATCTTTTGTAAGTAA
1 TTGACATGTTGC-A--ATCTTTTGTAAGTAA
20362 GCTTAACTGG
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
30 42 0.72
31 1 0.02
33 15 0.26
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (30 bp):
TTGACATGTTGCAATCTTTTGTAAGTAAAC
Found at i:20387 original size:33 final size:33
Alignment explanation
Indices: 20284--20389 Score: 112
Period size: 33 Copynumber: 3.3 Consensus size: 33
20274 ACATGTTGCA
* *
20284 ATCTTTTGTAAGTAAACTTGACATGTTG---CA
1 ATCTTTTGTAAGTAAACTTAACATGTTGATACC
* *
20314 ATCTTTTGTAAGTAAACTTGACATGTTGCTACC
1 ATCTTTTGTAAGTAAACTTAACATGTTGATACC
* *
20347 ATCTTTTGTAAGTAAGCTTAAC-TGGTTGATATC
1 ATCTTTTGTAAGTAAACTTAACAT-GTTGATACC
*
20380 ATTTTTTGTA
1 ATCTTTTGTA
20390 TTATTTTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
30 28 0.42
32 1 0.02
33 37 0.56
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.43
Consensus pattern (33 bp):
ATCTTTTGTAAGTAAACTTAACATGTTGATACC
Found at i:20505 original size:37 final size:36
Alignment explanation
Indices: 20450--20523 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
20440 AGAAAAATAG
*
20450 TGTCATCTTGTATAAATTTGGATATGTTGTCATATT
1 TGTCATCTTGTATAAATTTAGATATGTTGTCATATT
* *
20486 TGTCATCTTTTTATAAATTTAGATGTGTTGTCATATT
1 TGTCATC-TTGTATAAATTTAGATATGTTGTCATATT
20523 T
1 T
20524 TGTAAACTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 7 0.21
37 27 0.79
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (36 bp):
TGTCATCTTGTATAAATTTAGATATGTTGTCATATT
Found at i:20757 original size:17 final size:17
Alignment explanation
Indices: 20735--20768 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20725 CGAGTTTGAA
20735 TTCGAGCTTGAACCGAG
1 TTCGAGCTTGAACCGAG
*
20752 TTCGAGCTTGAATCGAG
1 TTCGAGCTTGAACCGAG
20769 CTTGAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (17 bp):
TTCGAGCTTGAACCGAG
Found at i:25523 original size:3 final size:3
Alignment explanation
Indices: 25517--25590 Score: 98
Period size: 3 Copynumber: 25.0 Consensus size: 3
25507 ATAAATTTTT
* *
25517 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TTA TAA -AA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
25563 TAA TAAA TAA CAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA
25591 CAAATGGATG
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.06
3 55 0.89
4 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:26294 original size:111 final size:111
Alignment explanation
Indices: 25942--26373 Score: 491
Period size: 112 Copynumber: 3.8 Consensus size: 111
25932 GAATTAAGGC
* * *
25942 AAGGTTGAACAAGTTCTTCTCATTATGAACTTGTTC-TCCTTCTTCAGATGAATTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * ** *
26006 TGAACACTTCTGGAAATGTTGATCTATCTCCTTCTGTGATAGAATCATGCAA
66 TGAACTCTACTGGAAATATTGATCCA--T-C--GAGTGAT-GAATCAAGCAA
* * *
26058 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT-TTCAGATAAGTACTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
26122 TGAGCTTTCT-CTGTAAA-AGTTGATCCATCGAGTGATGAAATCAAGCGAA
66 TGAAC--TCTACTGGAAATA-TTGATCCATCGAGTGATG-AATCAAGC-AA
* * *
26171 AA-GTTAAACAAATTCTTCTCATTATGAATTTCCTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
26234 TGAACTCTACTGGAAATATTGATCCATCGAAG-GATGAATTCAAGCAA
66 TGAACTCTACTGGAAATATTGATCCATCG-AGTGATGAA-TCAAGCAA
* * *
26281 AAGGTTGAACAAATTCTTCTCATTATAAATTTCTTCTTCCTTCTTCAGATGACTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
26346 TGAACTCTACCTAGAAATATTGATCCAT
66 TGAACTCTA-CTGGAAATATTGATCCAT
26374 TGAATGTATG
Statistics
Matches: 277, Mismatches: 25, Indels: 31
0.83 0.08 0.09
Matches are distributed among these distances:
110 9 0.03
111 63 0.23
112 104 0.38
113 21 0.08
114 1 0.00
115 1 0.00
116 58 0.21
117 18 0.06
118 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (111 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTACTGGAAATATTGATCCATCGAGTGATGAATCAAGCAA
Found at i:27722 original size:18 final size:17
Alignment explanation
Indices: 27699--27771 Score: 92
Period size: 18 Copynumber: 4.1 Consensus size: 17
27689 CATTTGCAAG
27699 AATAAATTGAATTTCAGA
1 AATAAATTGAATTTC-GA
* *
27717 AATAAATTGGACTTTGGA
1 AATAAATT-GAATTTCGA
*
27735 AATATATTGAATTTCGAA
1 AATAAATTGAATTTCG-A
27753 AATAAATTGAATTTCGA
1 AATAAATTGAATTTCGA
27770 AA
1 AA
27772 AGATAAACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
17 9 0.19
18 33 0.70
19 5 0.11
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (17 bp):
AATAAATTGAATTTCGA
Found at i:28142 original size:24 final size:22
Alignment explanation
Indices: 28115--28166 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
28105 TTTCTATATA
*
28115 TTTTTTCATCATTTTTTTCTTTTT
1 TTTTTT-ATCA-TTTTTTCTTTTC
*
28139 TTTTCTTTTCATTTTTTCTTTTC
1 TTTT-TTATCATTTTTTCTTTTC
28162 TTTTT
1 TTTTT
28167 CTTCTTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.04
23 15 0.60
24 7 0.28
25 2 0.08
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTTATCATTTTTTCTTTTC
Found at i:28155 original size:14 final size:13
Alignment explanation
Indices: 28136--28172 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
28126 TTTTTTTCTT
28136 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
*
28149 ATTTTTTCTTTTC
1 TTTTTTTCTTTTC
28162 TTTTTCTTCTT
1 TTTTT-TTCTT
28173 CAAGCATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:28167 original size:24 final size:24
Alignment explanation
Indices: 28127--28174 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
28117 TTTTCATCAT
28127 TTTTTTCTTTTTTTTTCTT-TTCA
1 TTTTTTCTTTTTTTTTCTTCTTCA
28150 TTTTTTCTTTTCTTTTTCTTCTTCA
1 TTTTTTCTTTT-TTTTTCTTCTTCA
28175 AGCATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 11 0.48
24 8 0.35
25 4 0.17
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTTTCTTTTTTTTTCTTCTTCA
Found at i:35531 original size:15 final size:15
Alignment explanation
Indices: 35511--35542 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
35501 TGCAATGAAT
35511 AATGAATGTATGCAA
1 AATGAATGTATGCAA
35526 AATGAATGTATGCAA
1 AATGAATGTATGCAA
35541 AA
1 AA
35543 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:41170 original size:3 final size:3
Alignment explanation
Indices: 41164--41234 Score: 92
Period size: 3 Copynumber: 24.0 Consensus size: 3
41154 AATTGTTTAT
* *
41164 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TTA TAA -AA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
41210 TAA TAAA TAA CAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA
41235 AAACAAATGG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
2 4 0.07
3 52 0.88
4 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:41206 original size:25 final size:23
Alignment explanation
Indices: 41169--41234 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 23
41159 TTTATTAATA
41169 ATAATAATAATAATAATAATAAAATT
1 ATAA-AATAATAATAATAAT-AAA-T
*
41195 ATAAAATAATAATATTAATAAAT
1 ATAAAATAATAATAATAATAAAT
*
41218 A-ACAATAATAATAATAA
1 ATAAAATAATAATAATAA
41235 AAACAAATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 14 0.38
23 2 0.05
24 3 0.08
25 14 0.38
26 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
ATAAAATAATAATAATAATAAAT
Found at i:46338 original size:64 final size:62
Alignment explanation
Indices: 46268--46446 Score: 182
Period size: 64 Copynumber: 2.8 Consensus size: 62
46258 TGGGACACTT
* *
46268 AGTGCATCGGTGCACTAAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGGCTG
1 AGTGCATCGATGCA-T-AGGATGCATCGATGCATAAAATGCATTCGATGTTTG-AAAATAGGCCG
* * * **
46333 A-TGCATCGATGCATTGCTTG-TGCATTGATGCATCAAATGCATTCGATGTTTGAAAATATTCCG
1 AGTGCATCGATGCATAG---GATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGGCCG
* * *
46396 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAG-GA-TGCATCGATGCATAAAATGCATTCGATGTT
46447 CAATTAAATC
Statistics
Matches: 96, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
62 2 0.02
63 10 0.10
64 82 0.85
65 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (62 bp):
AGTGCATCGATGCATAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGGCCG
Found at i:54947 original size:64 final size:62
Alignment explanation
Indices: 54878--55056 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 62
54868 TGGGACACTT
*
54878 AGTGCATCGGTGCACTAAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAA-ATAGCCT
1 AGTGCATCGATGCA-T-AGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAT-GCC-
54942 G
62 G
* * *
54943 -GTGCATCGATGCATTGCTTG-TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCCG
1 AGTGCATCGATGCATAG---GATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCG
* * *
55006 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAG-GA-TGCATCGATGCATAAAATGCATTCGATGTT
55057 CAATTAAATC
Statistics
Matches: 99, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 92 0.93
65 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCG
Found at i:55075 original size:64 final size:61
Alignment explanation
Indices: 54899--55086 Score: 180
Period size: 64 Copynumber: 2.9 Consensus size: 61
54889 GCACTAAGGA
* * * ***
54899 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATTGCTTG
1 TGCATCGATGCATAAAATGCATTCGATG-TTCAAAAAT--CATGGTGCATCGATGCATGGAGAG
* * *
54963 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTC-CGAGTGCATCGATGCATGGAGAG
1 TGCATCGATGCATAAAATGCATTCGATG-TTCAAAA-A-TCATG-GTGCATCGATGCATGGAGAG
* *
55027 TGCATCGGTGCATGAAATGCATTCGATGTTCAATTAAATCATAGGTGCATCGATGCATGG
1 TGCATCGATGCATAAAATGCATTCGATGTTCAA--AAATCAT-GGTGCATCGATGCATGG
55087 TTTGATGCAT
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
63 7 0.07
64 95 0.89
65 4 0.04
66 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (61 bp):
TGCATCGATGCATAAAATGCATTCGATGTTCAAAAATCATGGTGCATCGATGCATGGAGAG
Found at i:63169 original size:19 final size:18
Alignment explanation
Indices: 63145--63184 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
63135 ATTATTTTTT
63145 ATATTAATATATTATGTAA
1 ATATTAATATATTAT-TAA
* *
63164 ATATTATTTTATTATTAA
1 ATATTAATATATTATTAA
63182 ATA
1 ATA
63185 ATATTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATATTAATATATTATTAA
Found at i:63184 original size:18 final size:19
Alignment explanation
Indices: 63154--63190 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
63144 TATATTAATA
*
63154 TATTATGTAAATATTATTT
1 TATTATGTAAATAATATTT
63173 TATTAT-TAAATAATATTT
1 TATTATGTAAATAATATTT
63191 ATATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TATTATGTAAATAATATTT
Found at i:64962 original size:21 final size:21
Alignment explanation
Indices: 64932--64979 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
64922 GTAGGGGTAC
* *
64932 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
64953 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
64974 ATGCCA
1 ATGCCA
64980 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:65009 original size:21 final size:21
Alignment explanation
Indices: 64983--65076 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
64973 TATGCCATCT
* *
64983 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
65004 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
65025 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
65046 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
65067 CCGCAGGGTT
1 CCGCAGGGTT
65077 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:65658 original size:33 final size:34
Alignment explanation
Indices: 65599--65695 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
65589 AAATGTTTTT
*
65599 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
65633 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
65666 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
65696 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:65702 original size:34 final size:33
Alignment explanation
Indices: 65597--65702 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
65587 ATAAATGTTT
*
65597 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
65631 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
65663 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
65698 TTAAA
1 TTAAA
65703 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:66307 original size:126 final size:126
Alignment explanation
Indices: 66082--66811 Score: 1408
Period size: 126 Copynumber: 5.8 Consensus size: 126
66072 TTTAAGTTAT
*
66082 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
66147 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66208 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
66273 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66334 T-CCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
66398 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
66459 TCCCCGAGGGACATGAATGACATAATAGGGTAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
66524 GCACCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66585 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
66650 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66711 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
66776 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66812 CCGATTATAG
Statistics
Matches: 596, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
125 125 0.21
126 471 0.79
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:66533 original size:251 final size:252
Alignment explanation
Indices: 66082--66811 Score: 1408
Period size: 251 Copynumber: 2.9 Consensus size: 252
66072 TTTAAGTTAT
*
66082 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
66147 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
66212 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
131 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
*
66277 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
196 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66334 T-CCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
66398 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTGTCCC
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
* *
66463 CGAGGGACATGAATGACATAATAGGGTAATGATAATATTCTCTGACGAAATAATGGAAGGCGCAC
131 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
66528 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
196 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66585 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
66650 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
66715 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
131 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
66780 CCCCGGGAACGCGCCTTCACGTGAATAGTGAA
196 CCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66812 CCGATTATAG
Statistics
Matches: 469, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
251 246 0.52
252 223 0.48
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (252 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:66892 original size:8 final size:8
Alignment explanation
Indices: 66879--66919 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
66869 TCACAATCTT
66879 TCAAATTC
1 TCAAATTC
66887 TCAAATTC
1 TCAAATTC
* *
66895 CCAAACTC
1 TCAAATTC
66903 T-AAATTC
1 TCAAATTC
66910 TCAAATTC
1 TCAAATTC
66918 TC
1 TC
66920 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:69944 original size:12 final size:13
Alignment explanation
Indices: 69911--69948 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
69901 AAATACATAA
69911 ATATATTTAATAT
1 ATATATTTAATAT
*
69924 ATTTATTTAATAT
1 ATATATTTAATAT
69937 A-ATATTTAATAT
1 ATATATTTAATAT
69949 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:70000 original size:23 final size:23
Alignment explanation
Indices: 69962--70019 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
69952 TAGTTATAAT
69962 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
69983 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
70006 TTTTACATAATATA
1 TTTTACATAATATA
70020 TTATTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:71871 original size:6 final size:6
Alignment explanation
Indices: 71860--71895 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
71850 TTTTCGTCCA
71860 TATTTT TATTTT TATTTTT TATTTTT TATTTT TATT
1 TATTTT TATTTT TA-TTTT TA-TTTT TATTTT TATT
71896 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 16 0.55
7 13 0.45
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:71878 original size:7 final size:7
Alignment explanation
Indices: 71862--71892 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
71852 TTCGTCCATA
71862 TTTTTA-
1 TTTTTAT
71868 TTTTTAT
1 TTTTTAT
71875 TTTTTAT
1 TTTTTAT
71882 TTTTTAT
1 TTTTTAT
71889 TTTT
1 TTTT
71893 ATTATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:71878 original size:13 final size:13
Alignment explanation
Indices: 71860--71895 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
71850 TTTTCGTCCA
71860 TATTTTTA-TTTT
1 TATTTTTATTTTT
71872 TATTTTTTATTTTT
1 TA-TTTTTATTTTT
71886 TATTTTTATT
1 TATTTTTATT
71896 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 14 0.64
14 6 0.27
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:72009 original size:36 final size:36
Alignment explanation
Indices: 71958--72130 Score: 214
Period size: 34 Copynumber: 4.8 Consensus size: 36
71948 AATATATAAT
71958 TTTTAGAAAACGGATTTCGAAAATATATATTATATAG
1 TTTT-GAAAACGGATTTCGAAAATATATATTATATAG
*
71995 TTTTGAAAACGGATTTCG-GAA-ATATATTATATAG
1 TTTTGAAAACGGATTTCGAAAATATATATTATATAG
72029 TTTTGAAAACGG-TATTCGAAAATATATATATCATATAG
1 TTTTGAAAACGGAT-TTCGAAAATATATAT-T-ATATAG
*
72067 TTTTG-AAACGGTTTTCGAAAATATATATATTATATAG
1 TTTTGAAAACGGATTTCG-AAA-ATATATATTATATAG
* *
72104 TTTTGAAAA--TATTTTGAAAATATATAT
1 TTTTGAAAACGGATTTCGAAAATATATAT
72131 ATAATGAAAA
Statistics
Matches: 122, Mismatches: 5, Indels: 21
0.82 0.03 0.14
Matches are distributed among these distances:
33 1 0.01
34 37 0.30
35 7 0.06
36 24 0.20
37 26 0.21
38 19 0.16
39 8 0.07
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTTGAAAACGGATTTCGAAAATATATATTATATAG
Found at i:72085 original size:37 final size:37
Alignment explanation
Indices: 71949--72133 Score: 224
Period size: 37 Copynumber: 5.1 Consensus size: 37
71939 TTTTGAAAAA
* *
71949 ATATATA-ATTTTTAGAAAACGGATTTCGAAAATATAT
1 ATATATATAGTTTT-GAAAACGGTTTTCGAAAATATAT
* *
71986 AT-TATATAGTTTTGAAAACGGATTTCG-GAA-ATAT
1 ATATATATAGTTTTGAAAACGGTTTTCGAAAATATAT
*
72020 AT-TATATAGTTTTGAAAACGGTATTCGAAAATATAT
1 ATATATATAGTTTTGAAAACGGTTTTCGAAAATATAT
72056 ATATCATATAGTTTTG-AAACGGTTTTCGAAAATATAT
1 ATAT-ATATAGTTTTGAAAACGGTTTTCGAAAATATAT
**
72093 ATATTATATAGTTTTGAAAA-TATTTT-GAAAATATAT
1 ATA-TATATAGTTTTGAAAACGGTTTTCGAAAATATAT
72129 ATATA
1 ATATA
72134 ATGAAAATAT
Statistics
Matches: 133, Mismatches: 8, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
34 29 0.22
35 6 0.05
36 37 0.28
37 46 0.35
38 15 0.11
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (37 bp):
ATATATATAGTTTTGAAAACGGTTTTCGAAAATATAT
Found at i:72138 original size:17 final size:17
Alignment explanation
Indices: 72118--72150 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
72108 GAAAATATTT
72118 TGAAAATATATATATAA
1 TGAAAATATATATATAA
72135 TGAAAATATATATATA
1 TGAAAATATATATATA
72151 TTATATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
TGAAAATATATATATAA
Found at i:72265 original size:7 final size:7
Alignment explanation
Indices: 72252--72296 Score: 53
Period size: 6 Copynumber: 7.0 Consensus size: 7
72242 TATATATATA
72252 TATTATT
1 TATTATT
72259 TATTA-T
1 TATTATT
72265 T-TTATT
1 TATTATT
72271 TATT-TT
1 TATTATT
72277 TATT-TT
1 TATTATT
72283 TATTATT
1 TATTATT
*
72290 CATTATT
1 TATTATT
72297 CCTTTTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
5 3 0.09
6 16 0.47
7 15 0.44
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTATT
Found at i:72275 original size:16 final size:16
Alignment explanation
Indices: 72252--72296 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
72242 TATATATATA
72252 TATTATTTATTA-TTT
1 TATTATTTATTATTTT
72267 TATTTATTT-TTATTTT
1 TA-TTATTTATTATTTT
*
72283 TATTATTCATTATT
1 TATTATTTATTATT
72297 CCTTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTATTTATTATTTT
Found at i:73651 original size:31 final size:31
Alignment explanation
Indices: 73579--73655 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
73569 AGTTACGTCG
* *
73579 GGGACCATATTACAAATGCACTAAATGTTGA
1 GGGACCATATTGCAAATGCACTAAATATTGA
* *
73610 GGGACCATATTGCAAATGGACTAAATATTGG
1 GGGACCATATTGCAAATGCACTAAATATTGA
**
73641 GGGATTATATTGCAA
1 GGGACCATATTGCAA
73656 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.27
Consensus pattern (31 bp):
GGGACCATATTGCAAATGCACTAAATATTGA
Found at i:74898 original size:31 final size:31
Alignment explanation
Indices: 74843--74918 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
74833 CTTTTAAAAC
** * *
74843 TTGCAATATAATCCCCCAATATTTAG-TCCCT
1 TTGCAATATGGTCCCCCAACATTTAGAT-CAT
*
74874 TTGCAATATGGTCCCTCAACATTTAGATCAT
1 TTGCAATATGGTCCCCCAACATTTAGATCAT
*
74905 TTGCAATACGGTCC
1 TTGCAATATGGTCC
74919 TTGTAACTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGATCAT
Found at i:75121 original size:9 final size:9
Alignment explanation
Indices: 75091--75120 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
75081 TCAGTATGTT
75091 TTTTATTTG
1 TTTTATTTG
75100 TTTTATTTG
1 TTTTATTTG
75109 TTTTATTT-
1 TTTTATTTG
75117 TTTT
1 TTTT
75121 TCACTTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (9 bp):
TTTTATTTG
Found at i:75162 original size:7 final size:7
Alignment explanation
Indices: 75150--75215 Score: 132
Period size: 7 Copynumber: 9.4 Consensus size: 7
75140 TTTTATTACT
75150 TTTAAAA
1 TTTAAAA
75157 TTTAAAA
1 TTTAAAA
75164 TTTAAAA
1 TTTAAAA
75171 TTTAAAA
1 TTTAAAA
75178 TTTAAAA
1 TTTAAAA
75185 TTTAAAA
1 TTTAAAA
75192 TTTAAAA
1 TTTAAAA
75199 TTTAAAA
1 TTTAAAA
75206 TTTAAAA
1 TTTAAAA
75213 TTT
1 TTT
75216 TTAATTTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TTTAAAA
Found at i:75313 original size:25 final size:25
Alignment explanation
Indices: 75285--75335 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
75275 TTTCATTGAT
* *
75285 TTATTTAATATTTATTT-CTTATTTA
1 TTATCTAACATTTATTTACTT-TTTA
*
75310 TTATCTAACATTTTTTTACTTTTTA
1 TTATCTAACATTTATTTACTTTTTA
75335 T
1 T
75336 GAATACTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (25 bp):
TTATCTAACATTTATTTACTTTTTA
Found at i:76378 original size:22 final size:21
Alignment explanation
Indices: 76344--76386 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
76334 TAAATTATTT
76344 AAAAATTTAAATAAAAATATAA
1 AAAAATTTAAATAAAAA-ATAA
76366 AAAACATTT-AATAAAAAATAA
1 AAAA-ATTTAAATAAAAAATAA
76387 TTTTTATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAATTTAAATAAAAAATAA
Found at i:79285 original size:12 final size:12
Alignment explanation
Indices: 79268--79295 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
79258 TTACTAATAG
79268 AATTTTTTTATT
1 AATTTTTTTATT
79280 AATTTTTTTATT
1 AATTTTTTTATT
79292 AATT
1 AATT
79296 ATAATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
AATTTTTTTATT
Found at i:80165 original size:29 final size:30
Alignment explanation
Indices: 80130--80197 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
80120 TTGGACTAAT
* ** *
80130 GACTAAAATGTAAGTTTTG-AAAGTTTAGG
1 GACTAAAATATAAACTTTGAAAAGTGTAGG
* *
80159 GGCTAAAGTATAAACTTTGAAAAGTGTAGG
1 GACTAAAATATAAACTTTGAAAAGTGTAGG
80189 GACTAAAAT
1 GACTAAAAT
80198 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (30 bp):
GACTAAAATATAAACTTTGAAAAGTGTAGG
Found at i:82378 original size:36 final size:36
Alignment explanation
Indices: 82321--82460 Score: 235
Period size: 36 Copynumber: 3.9 Consensus size: 36
82311 AGTTGAGTAT
**
82321 TATCAGCTTTAATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
82357 TATCAGCTTTGGTACACTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
82393 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
82429 TATTAGCTTTGGTACATTCATGTATCAATGTT
1 TATCAGCTTTGGTACATTCGTGTATCAATGTT
82461 CAGCACCATT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 98 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:84910 original size:74 final size:71
Alignment explanation
Indices: 84811--85065 Score: 257
Period size: 74 Copynumber: 3.5 Consensus size: 71
84801 TTAATTAGGA
* * * *
84811 AATAACAATTAAAAATATATGAAAATATTTAAAATTATAGTTAATAAGTAAAATTTAAAAATTAT
1 AATAAAAATTAAAAATATA-AAAAATA-TAAAAATTATAATTAATAAGTAAAA-TTAAAAATTAT
84876 TTTTCCATT
63 TTTTCCATT
* * * *
84885 AATAATAATTTAAAAATATAAAAAATATAAAAATTATAATTAATAAATAAAA--ATAAATCATTT
1 AATAA-AAATTAAAAATATAAAAAATATAAAAATTATAATTAATAAGTAAAATTAAAAATTATTT
84948 CTTCCATT
65 -TTCCATT
* * * *** *
84956 AACAAAAATTGAAAATATAAAAAAATGTTGTGAATTATAATTAATAAGTAAAAGTTAAGAA-TAT
1 AATAAAAATTAAAAATAT-AAAAAAT-ATAAAAATTATAATTAATAAGTAAAA-TTAAAAATTAT
85020 TTTCTCCATT
63 TTT-TCCATT
*
85030 AATAAAAATTAAAAATAT-AAGAATATAAAAATTATA
1 AATAAAAATTAAAAATATAAAAAATATAAAAATTATA
85066 GTAAATTATA
Statistics
Matches: 147, Mismatches: 26, Indels: 19
0.77 0.14 0.10
Matches are distributed among these distances:
70 20 0.14
71 26 0.18
72 26 0.18
73 23 0.16
74 37 0.25
75 15 0.10
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (71 bp):
AATAAAAATTAAAAATATAAAAAATATAAAAATTATAATTAATAAGTAAAATTAAAAATTATTTT
TCCATT
Found at i:85586 original size:4 final size:4
Alignment explanation
Indices: 85577--85602 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
85567 ATTAGAGGAA
85577 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
85603 GAAAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:88300 original size:17 final size:19
Alignment explanation
Indices: 88275--88312 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
88265 TTTTACAGAC
*
88275 ATATTGATATG-ATAA-AA
1 ATATGGATATGCATAAGAA
88292 ATATGGATATGCATAAGAA
1 ATATGGATATGCATAAGAA
88311 AT
1 AT
88313 GTTAGTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 4 0.22
19 4 0.22
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.32
Consensus pattern (19 bp):
ATATGGATATGCATAAGAA
Found at i:89914 original size:24 final size:24
Alignment explanation
Indices: 89887--89950 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
89877 ATTTGAATTA
*
89887 TGATATGATACTTGACATGGATTT
1 TGATATGATACTTGACATGGATTC
89911 TGATATGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACATGGATTC
89935 TGATATGATACTTGAC
1 TGATATGATACTTGAC
89951 TTGAATTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
23 1 0.03
24 35 0.95
25 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:90174 original size:2 final size:2
Alignment explanation
Indices: 90167--90199 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
90157 GGGATGGGGG
90167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
90200 GTTTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92653 original size:14 final size:13
Alignment explanation
Indices: 92629--92662 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
92619 TTCCCATTAC
92629 AGACGTGCATATGA
1 AGAC-TGCATATGA
92643 ATGACTGCATATGA
1 A-GACTGCATATGA
92657 AGACTG
1 AGACTG
92663 TTCAACTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 11 0.58
15 3 0.16
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (13 bp):
AGACTGCATATGA
Found at i:92962 original size:30 final size:30
Alignment explanation
Indices: 92926--93187 Score: 203
Period size: 30 Copynumber: 8.8 Consensus size: 30
92916 TTCAAATTTT
* *
92926 TATTTTTTCTATTTAAGTTCTTTAACTTTC
1 TATTTTTTCTATTTTAGTCCTTTAACTTTC
92956 TATTTTTTCTATTTTAGTCCTTTAACTTT-
1 TATTTTTTCTATTTTAGTCCTTTAACTTTC
**
92985 TATTTTAGCTATTTTAGTCCTTTAACTTTC
1 TATTTTTTCTATTTTAGTCCTTTAACTTTC
* ** * *
93015 TATCTTAACTATTTTAGTCCCTTAAGTTTC
1 TATTTTTTCTATTTTAGTCCTTTAACTTTC
* * *
93045 TATTTTTTGTTATTTTAGTCCTTTAAATGTC
1 TATTTTTT-CTATTTTAGTCCTTTAACTTTC
* * *
93076 T-TTTTGT-TATTTTAGTCCTTTAAATGTC
1 TATTTTTTCTATTTTAGTCCTTTAACTTTC
* * * *
93104 TATATTTGCTA-TTTA-TACCCTTAAGTTTC
1 TATTTTTTCTATTTTAGT-CCTTTAACTTTC
* * * * *
93133 -AGTTTTTACTGTTTTAGCCCTTTAAGTTTA
1 TA-TTTTTTCTATTTTAGTCCTTTAACTTTC
* * * *
93163 TGTTTTTGCTATTTAAGTCTTTTAA
1 TATTTTTTCTATTTTAGTCCTTTAA
93188 ATCGAATATG
Statistics
Matches: 189, Mismatches: 34, Indels: 18
0.78 0.14 0.07
Matches are distributed among these distances:
28 24 0.13
29 49 0.26
30 97 0.51
31 19 0.10
ACGTcount: A:0.20, C:0.14, G:0.08, T:0.58
Consensus pattern (30 bp):
TATTTTTTCTATTTTAGTCCTTTAACTTTC
Found at i:92997 original size:59 final size:59
Alignment explanation
Indices: 92923--93187 Score: 209
Period size: 59 Copynumber: 4.5 Consensus size: 59
92913 CCCTTCAAAT
* * * *
92923 TTTTATTTTTTCTATTTAAGTTCTTTAACTTTCTATTTTTTCTATTTTAGTCCTTTAAC
1 TTTTATTTTTGCTATTTTAGTCCTTTAACTTTCTATTTTATCTATTTTAGTCCTTTAAC
* * * * *
92982 TTTTATTTTAGCTATTTTAGTCCTTTAACTTTCTATCTTAACTATTTTAGTCCCTTAAG
1 TTTTATTTTTGCTATTTTAGTCCTTTAACTTTCTATTTTATCTATTTTAGTCCTTTAAC
* * * * *
93041 TTTCTATTTTTTGTTATTTTAGTCCTTTAAATGTCT-TTTTGT-TATTTTAGTCCTTTAAA
1 TTT-TA-TTTTTGCTATTTTAGTCCTTTAACTTTCTATTTTATCTATTTTAGTCCTTTAAC
* * * * * * *
93100 TGTCTATATTTGCTA-TTTA-TACCCTTAAGTTTC-AGTTTT-TACTGTTTTAGCCCTTTAAG
1 T-TTTATTTTTGCTATTTTAGT-CCTTTAACTTTCTA-TTTTAT-CTATTTTAGTCCTTTAAC
* * *
93159 TTTATGTTTTTGCTATTTAAGTCTTTTAA
1 TTT-TATTTTTGCTATTTTAGTCCTTTAA
93188 ATCGAATATG
Statistics
Matches: 162, Mismatches: 33, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
56 1 0.01
57 14 0.09
58 12 0.07
59 95 0.59
60 14 0.09
61 26 0.16
ACGTcount: A:0.20, C:0.14, G:0.08, T:0.58
Consensus pattern (59 bp):
TTTTATTTTTGCTATTTTAGTCCTTTAACTTTCTATTTTATCTATTTTAGTCCTTTAAC
Found at i:93049 original size:89 final size:86
Alignment explanation
Indices: 92947--93189 Score: 238
Period size: 89 Copynumber: 2.7 Consensus size: 86
92937 TTTAAGTTCT
* * *
92947 TTAACTTTCTATTTTTTCTATTTTAGTCCTTTAACTTTTATTTTAGCTATTTTAGTCCTTTAACT
1 TTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAATTTT-TTTT-GCTATTTTAGTCCTTTAAAT
* *
93012 TTCTATCTTAACTATTT-TAGTCCC
64 GTCTATATTAACTATTTATA--CCC
* * *
93036 TTAAGTTTCTATTTTTTGTTATTTTAGTCCTTTAAATGTCTTTTTGTTATTTTAGTCCTTTAAAT
1 TTAAGTTTCTATTTTTT-CTATTTTAGTCCTTTAAAT-TTTTTTTGCTATTTTAGTCCTTTAAAT
**
93101 GTCTATATTTGCTATTTATACCC
64 GTCTATATTAACTATTTATACCC
* * * * * *
93124 TTAAGTTTC-AGTTTTTACTGTTTTAGCCCTTTAAGTTTATGTTTTTGCTATTTAAGTCTTTTAA
1 TTAAGTTTCTA-TTTTTTCTATTTTAGTCCTTTAA-ATT-T-TTTTTGCTATTTTAGTCCTTTAA
93188 AT
62 AT
93190 CGAATATGAT
Statistics
Matches: 128, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
87 16 0.12
88 18 0.14
89 69 0.54
90 23 0.18
91 2 0.02
ACGTcount: A:0.21, C:0.14, G:0.08, T:0.57
Consensus pattern (86 bp):
TTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAATTTTTTTTGCTATTTTAGTCCTTTAAATGT
CTATATTAACTATTTATACCC
Found at i:93086 original size:28 final size:28
Alignment explanation
Indices: 93048--93104 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
93038 AAGTTTCTAT
93048 TTTTTGTTATTTTAGTCCTTTAAATGTC
1 TTTTTGTTATTTTAGTCCTTTAAATGTC
93076 TTTTTGTTATTTTAGTCCTTTAAATGTC
1 TTTTTGTTATTTTAGTCCTTTAAATGTC
93104 T
1 T
93105 ATATTTGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.61
Consensus pattern (28 bp):
TTTTTGTTATTTTAGTCCTTTAAATGTC
Found at i:94682 original size:3 final size:3
Alignment explanation
Indices: 94670--94706 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
94660 ACATTATTTA
94670 ATT A-T ATT ATT ATT ATT ATT ATT ATT AATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT A
94707 CATTTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:94689 original size:22 final size:22
Alignment explanation
Indices: 94662--94706 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
94652 TCTACAAAAC
94662 ATTATT-TAATTATATTATTATT
1 ATTATTATAATTA-ATTATTATT
*
94684 ATTATTATTATTAATTATTATT
1 ATTATTATAATTAATTATTATT
94706 A
1 A
94707 CATTTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTATTATAATTAATTATTATT
Found at i:95070 original size:16 final size:17
Alignment explanation
Indices: 95049--95083 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
95039 CGAATTTCAG
95049 CTTGATTCAAGC-CGAA
1 CTTGATTCAAGCTCGAA
95065 CTTGATTCAAGCTCGAA
1 CTTGATTCAAGCTCGAA
95082 CT
1 CT
95084 CAAGCTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (17 bp):
CTTGATTCAAGCTCGAA
Found at i:96810 original size:19 final size:18
Alignment explanation
Indices: 96781--96819 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
96771 TGTTCCTTTT
96781 GACACTCATTAATCCAAA
1 GACACTCATTAATCCAAA
96799 GACACATCATTAATCCAAA
1 GACAC-TCATTAATCCAAA
96818 GA
1 GA
96820 GATGGCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.46, C:0.26, G:0.08, T:0.21
Consensus pattern (18 bp):
GACACTCATTAATCCAAA
Found at i:97281 original size:17 final size:17
Alignment explanation
Indices: 97259--97291 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
97249 TTAGTGTTCC
97259 TTCAATT-TGTGCTTGTT
1 TTCAATTGTGT-CTTGTT
97276 TTCAATTGTGTCTTGT
1 TTCAATTGTGTCTTGT
97292 AATTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (17 bp):
TTCAATTGTGTCTTGTT
Found at i:100473 original size:15 final size:15
Alignment explanation
Indices: 100447--100487 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
100437 ATTTTGGAAA
100447 TTGTTAGTGTTGTCTT
1 TTGTT-GTGTTGTCTT
100463 TTGTTGTGTTGTCTT
1 TTGTTGTGTTGTCTT
100478 TTGTTGTGTT
1 TTGTTGTGTT
100488 TTCAAAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.02, C:0.05, G:0.27, T:0.66
Consensus pattern (15 bp):
TTGTTGTGTTGTCTT
Found at i:101585 original size:7 final size:6
Alignment explanation
Indices: 101561--101593 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
101551 ATCGATACAT
101561 TTTGCA TTTGCA TTTGCA TTATGCA -TTGCA TTT
1 TTTGCA TTTGCA TTTGCA TT-TGCA TTTGCA TTT
101594 ATTTAAACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.16
6 17 0.68
7 4 0.16
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (6 bp):
TTTGCA
Found at i:102153 original size:27 final size:27
Alignment explanation
Indices: 102114--102179 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
102104 AATATCGAAT
102114 GAATTATAGATTCTTTTAATTCTTCAA
1 GAATTATAGATTCTTTTAATTCTTCAA
* * *
102141 GAATTATATATTCTTTTAGTTCTTTAA
1 GAATTATAGATTCTTTTAATTCTTCAA
102168 GAATTATAGATT
1 GAATTATAGATT
102180 TTTGACATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (27 bp):
GAATTATAGATTCTTTTAATTCTTCAA
Found at i:102959 original size:14 final size:15
Alignment explanation
Indices: 102931--102988 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
102921 AAATCAAAGC
*
102931 AAAGAGAAAAGAATT
1 AAAGAGAAAAAAATT
102946 AAAGA-AAAAAAATT
1 AAAGAGAAAAAAATT
* *
102960 GCAAAGAG-GAAAAATC
1 --AAAGAGAAAAAAATT
102976 AAAGAGAAAAAAA
1 AAAGAGAAAAAAA
102989 AGCAAAGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 14 0.40
15 10 0.29
16 11 0.31
ACGTcount: A:0.71, C:0.03, G:0.17, T:0.09
Consensus pattern (15 bp):
AAAGAGAAAAAAATT
Found at i:102967 original size:31 final size:31
Alignment explanation
Indices: 102929--102988 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
102919 TCAAATCAAA
*
102929 GCAAAGAGAAAAGAATTAAAGA-AAAAAAATT
1 GCAAAGAGAAAA-AATCAAAGAGAAAAAAATT
*
102960 GCAAAGAGGAAAAATCAAAGAGAAAAAAA
1 GCAAAGAGAAAAAATCAAAGAGAAAAAAA
102989 AGCAAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.68, C:0.05, G:0.18, T:0.08
Consensus pattern (31 bp):
GCAAAGAGAAAAAATCAAAGAGAAAAAAATT
Found at i:102984 original size:32 final size:31
Alignment explanation
Indices: 102946--103018 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 31
102936 GAAAAGAATT
*
102946 AAAGAAAAAAAATTGCAAA-G-AGGAAAAATCA
1 AAAGAAAAAAAA--GCAAAGGAAGGAAAAAACA
102977 AAGAGAAAAAAAAGCAAAGGAAAGGAAAAAACA
1 AA-AGAAAAAAAAGCAAAGG-AAGGAAAAAACA
103010 AAAGAAAAA
1 AAAGAAAAA
103019 GCAAGGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
30 5 0.14
31 3 0.08
32 17 0.46
33 12 0.32
ACGTcount: A:0.73, C:0.05, G:0.18, T:0.04
Consensus pattern (31 bp):
AAAGAAAAAAAAGCAAAGGAAGGAAAAAACA
Found at i:102989 original size:16 final size:16
Alignment explanation
Indices: 102930--103018 Score: 55
Period size: 15 Copynumber: 5.8 Consensus size: 16
102920 CAAATCAAAG
*
102930 CAAAGAG-AAAAGAAT
1 CAAAGAGAAAAAAAAT
* *
102945 TAAAGA-AAAAAAATT
1 CAAAGAGAAAAAAAAT
*
102960 GCAAAGAG--GAAAAAT
1 -CAAAGAGAAAAAAAAT
*
102975 CAAAGAGAAAAAAAAG
1 CAAAGAGAAAAAAAAT
*
102991 CAAAG-GAAAGGAAAAAA
1 CAAAGAGAAA--AAAAAT
103008 CAAA-AGAAAAA
1 CAAAGAGAAAAA
103019 GCAAGGAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
14 7 0.12
15 22 0.39
16 15 0.26
17 13 0.23
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.06
Consensus pattern (16 bp):
CAAAGAGAAAAAAAAT
Found at i:104382 original size:36 final size:33
Alignment explanation
Indices: 104301--104402 Score: 123
Period size: 33 Copynumber: 3.0 Consensus size: 33
104291 ATTTCTTTTG
* * *
104301 AAAAATCTTTGAATCTGTTTCAGTTTAAACAAA
1 AAAAATCTTTGAGTCTGTTTCACTTGAAACAAA
*
104334 AAAAATCATTGAGTCTGTTTCACTTGAAACAAA
1 AAAAATCTTTGAGTCTGTTTCACTTGAAACAAA
* *
104367 ATGCAAAATCTTTGAGTTTGTTTCCCTTGAAACAAA
1 A---AAAATCTTTGAGTCTGTTTCACTTGAAACAAA
104403 GTGTTATCTC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
33 30 0.51
36 29 0.49
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (33 bp):
AAAAATCTTTGAGTCTGTTTCACTTGAAACAAA
Found at i:104590 original size:61 final size:61
Alignment explanation
Indices: 104468--104588 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 61
104458 AACAAAACAA
* *
104468 AAAAATCTTTGAGTCTGTTTCTTTGGTAAAAAAATTGTCTCTTTTGAGACAGTTTCTTTTG
1 AAAAATCTTTGAGTCTGTTTCTTTGGTAAAAAAATTGTCTCTCTTGAGACAGTATCTTTTG
****
104529 AAAAATCTTTGAGTCTGTTTCTTTGG-AAATTTTTTTTGTCTCTCTTGAGACAGTATCTTT
1 AAAAATCTTTGAGTCTGTTTCTTTGGTAAA--AAAATTGTCTCTCTTGAGACAGTATCTTT
104589 GATTTTGTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
60 3 0.06
61 26 0.50
62 23 0.44
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (61 bp):
AAAAATCTTTGAGTCTGTTTCTTTGGTAAAAAAATTGTCTCTCTTGAGACAGTATCTTTTG
Found at i:104620 original size:30 final size:30
Alignment explanation
Indices: 104584--104640 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
104574 TGAGACAGTA
* *
104584 TCTTTGATTTTGTTTCTATTGAAACAAAAG
1 TCTTTGAGTCTGTTTCTATTGAAACAAAAG
104614 TCTTTGAGTCTGTTTCTATTGAAACAA
1 TCTTTGAGTCTGTTTCTATTGAAACAA
104641 TAAATCATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (30 bp):
TCTTTGAGTCTGTTTCTATTGAAACAAAAG
Found at i:104657 original size:34 final size:30
Alignment explanation
Indices: 104583--104646 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
104573 TTGAGACAGT
* *
104583 ATCTTTGATTTTGTTTCTATTGAAACAAAA
1 ATCTTTGAGTCTGTTTCTATTGAAACAAAA
*
104613 GTCTTTGAGTCTGTTTCTATTGAAACAATAA
1 ATCTTTGAGTCTGTTTCTATTGAAACAA-AA
104644 ATC
1 ATC
104647 ATCTTTGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (30 bp):
ATCTTTGAGTCTGTTTCTATTGAAACAAAA
Found at i:104772 original size:65 final size:60
Alignment explanation
Indices: 104658--104928 Score: 176
Period size: 65 Copynumber: 4.3 Consensus size: 60
104648 TCTTTGAGTC
* * *
104658 GTTTTCCTAGAAACGAA-TTGTCTCTTGAGAC-ATTTCTCTTAAAACAAAATAATATTAAAGTTT
1 GTTTTCCTTGAAACAAATTTGTCTCTTGAGACAATTTCT-TTGAAA-AAAAT-AT-TT-AAGTTT
* * *
104721 GTTTTCCTTGAAACAAATGTTGTCGCTTGAGACAATTTCTTGTGAAAAAAATCTTTGAGTTT
1 GTTTTCCTTGAAACAAAT-TTGTCTCTTGAGACAATTTCTT-TGAAAAAAATATTTAAGTTT
* * * * *
104783 G-TTTCTTTGGAAACAAAATTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAATCTTTGAGTC
1 GTTTTCCTT-GAAAC-AAATT-TGTCTCTTGAGACAATTTC-TTT--GAAAAAAATATTTAAGTT
104847 T
60 T
* * * *
104848 G-TTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAGATTT-TTGAGAAAAAAATCTTTGAGT
1 GTTTTCCTT-GAAACAAA--TTTG--TCTCTTGAGACA-ATTTCTT-TGAAAAAAATATTTAAGT
104911 TT
59 TT
104913 G-TTTCTCTTGAAACAA
1 GTTTTC-CTTGAAACAA
104929 TCATCTTTGA
Statistics
Matches: 177, Mismatches: 14, Indels: 32
0.79 0.06 0.14
Matches are distributed among these distances:
61 6 0.03
62 12 0.07
63 39 0.22
64 6 0.03
65 82 0.46
66 16 0.09
67 12 0.07
68 4 0.02
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (60 bp):
GTTTTCCTTGAAACAAATTTGTCTCTTGAGACAATTTCTTTGAAAAAAATATTTAAGTTT
Found at i:105090 original size:43 final size:43
Alignment explanation
Indices: 105023--105116 Score: 143
Period size: 43 Copynumber: 2.2 Consensus size: 43
105013 GCCAAACCTT
*
105023 CTCATCACATAAGAGTCACATCAACCCTAAATAACCAGCCATC
1 CTCATCACACAAGAGTCACATCAACCCTAAATAACCAGCCATC
** * *
105066 CTCATCACACAAGAGTTGCTTCAACCCTAAATAACTAGCCATC
1 CTCATCACACAAGAGTCACATCAACCCTAAATAACCAGCCATC
105109 CTCATCAC
1 CTCATCAC
105117 GTAAAAACCG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.36, C:0.35, G:0.07, T:0.21
Consensus pattern (43 bp):
CTCATCACACAAGAGTCACATCAACCCTAAATAACCAGCCATC
Found at i:105249 original size:42 final size:40
Alignment explanation
Indices: 105157--105259 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 40
105147 GCATATCGTT
105157 CTCATCGCGTAGGAACCGTGTCATCCTCCGACCAGACCTC
1 CTCATCGCGTAGGAACCGTGTCATCCTCCGACCAGACCTC
* *
105197 CTCATAGCGTAGGAGCCGTGTCA-CC-CCTGATAACCAG-CCATC
1 CTCATCGCGTAGGAACCGTGTCATCCTCC-G---ACCAGACC-TC
105239 CTCATCGCGTAGGAACCGTGT
1 CTCATCGCGTAGGAACCGTGT
105260 TATCACTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
38 2 0.04
39 3 0.06
40 21 0.39
41 2 0.04
42 26 0.48
ACGTcount: A:0.21, C:0.36, G:0.22, T:0.20
Consensus pattern (40 bp):
CTCATCGCGTAGGAACCGTGTCATCCTCCGACCAGACCTC
Found at i:105354 original size:134 final size:131
Alignment explanation
Indices: 105157--105619 Score: 441
Period size: 134 Copynumber: 3.5 Consensus size: 131
105147 GCATATCGTT
* * *
105157 CTCATCGCGTAGGAACCGTGTCATCCTCCGACCAGACCTCCTCAT-AGCGTAGGAGCCGTGTCAC
1 CTCATCACGTAGGAACCATGTCATCC-CCGACCAGACCTCCTCATCA-CGTAGGAGCCATGTCAC
*
105221 CCCTGATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCACTCTTCCTAAAGATGGCCTGC
64 CCATGATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCAC-CTTCCTAAAGATGGCCTGC
*
105286 CATC
128 AATC
** * *
105290 CTCATCACGTAGGAACTGTGTCATTCCCCTGACCAGACCTCCTCACCACGTAGGAGTCATGTCAC
1 CTCATCACGTAGGAACCATGTCA-TCCCC-GACCAGACCTCCTCATCACGTAGGAGCCATGTCAC
* * ** * ** *
105355 TCATGATAACCAGCCGTTTTCATCACGTAGGAACCGTGTTATCA--TTCCTAAAGATGGTATGCT
64 CCATGATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCTGCA
*
105418 GTC
129 ATC
* *** * *
105421 CTTATTGTGTAGGAACCATGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACT
1 CTCATCACGTAGGAACCATGTCATCCCC-GACCAGACCTCCTCATCACGTAGGAGCCATGTCACC
* * * * * ** *
105486 CTTAGATAATCAACCATCCTCATTGCGAAGGAACCGTGTTATCACCCTTTTTAAAGATGGCCAG-
65 CAT-GATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCA-CCTTCCTAAAGATGGCCTGC
105550 AACTC
128 AA-TC
* * ** * * *
105555 TTCATCACGTA-TAAGCCATGTCATTCCCCGACCAGATTTCCTTATCACGTAGGAGTCATGCCAC
1 CTCATCACGTAGGAA-CCATGTCA-TCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCAC
105619 C
64 C
105620 TTTAGACGAC
Statistics
Matches: 267, Mismatches: 53, Indels: 19
0.79 0.16 0.06
Matches are distributed among these distances:
130 41 0.15
131 67 0.25
133 25 0.09
134 128 0.48
135 6 0.02
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (131 bp):
CTCATCACGTAGGAACCATGTCATCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCC
ATGATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCTGCAAT
C
Found at i:105520 original size:131 final size:131
Alignment explanation
Indices: 105096--105530 Score: 450
Period size: 130 Copynumber: 3.3 Consensus size: 131
105086 TCAACCCTAA
* * ** * ** * *
105096 ATAACTAGCCATCCTCATCACGTAAAAACCGTGTTATTA--TCGCTAATA-ATGGCATATCGTTC
1 ATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCACTTC-CTAA-AGATGGCATGCCATCC
*
105158 TCATCGCGTAGGAACCGTGTCATCCTCC-GACCAGACCTCCTCAT-AGCGTAGGAGCCGTGTCAC
64 TCATCACGTAGGAACCGTGTCATCC-CCTGACCAGACCTCCTCATCA-CGTAGGAGCCGTGTCAC
* *
105221 CCCTG
127 TCATG
*
105226 ATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCACTCTTCCTAAAGATGGCCTGCCATCC
1 ATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCA--CTTCCTAAAGATGGCATGCCATCC
* * * *
105291 TCATCACGTAGGAACTGTGTCATTCCCCTGACCAGACCTCCTCACCACGTAGGAGTCATGTCACT
64 TCATCACGTAGGAACCGTGTCA-TCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACT
105356 CATG
128 CATG
* ** * * ** *
105360 ATAACCAGCCGTTTTCATCACGTAGGAACCGTGTTATCA-TTCCTAAAGATGGTATGCTGTCCTT
1 ATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCACTTCCTAAAGATGGCATGCCATCCTC
*** * *
105424 ATTGTGTAGGAACCATGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACTCTT
66 ATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACTCAT
105489 AG
131 -G
* * * *
105491 ATAATCAACCATCCTCATTGCGAAGGAACCGTGTTATCAC
1 ATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCAC
105531 CCTTTTTAAA
Statistics
Matches: 252, Mismatches: 43, Indels: 18
0.81 0.14 0.06
Matches are distributed among these distances:
130 75 0.30
131 67 0.27
132 1 0.00
133 35 0.14
134 73 0.29
135 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.26
Consensus pattern (131 bp):
ATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCACTTCCTAAAGATGGCATGCCATCCTC
ATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACTCAT
G
Found at i:105938 original size:3 final size:3
Alignment explanation
Indices: 105918--105962 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
105908 TCTACAAAAA
105918 TAT TAT T-T TAAT TA- TAT TAT TAT ATAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
105963 ATTTTTTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.11
3 29 0.76
4 5 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:107972 original size:16 final size:18
Alignment explanation
Indices: 107953--107992 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
107943 TTATTTCGAG
107953 TATTTTTTA-TCAT-TTT
1 TATTTTTTATTCATATTT
*
107969 TATTTTTTATTCTTATTT
1 TATTTTTTATTCATATTT
107987 TATTTT
1 TATTTT
107993 ATTTTTGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 3 0.14
18 9 0.43
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (18 bp):
TATTTTTTATTCATATTT
Found at i:109405 original size:16 final size:17
Alignment explanation
Indices: 109384--109426 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
109374 TCTCTTGTAA
109384 GGATGAA-AACACTTTT
1 GGATGAATAACACTTTT
*
109400 GGATGAATGTAACTCTTTT
1 GGATGAA--TAACACTTTT
109419 GGATGAAT
1 GGATGAAT
109427 GAAACTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 7 0.30
17 1 0.04
19 15 0.65
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (17 bp):
GGATGAATAACACTTTT
Found at i:109419 original size:19 final size:19
Alignment explanation
Indices: 109390--109436 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
109380 GTAAGGATGA
*
109390 AAACACTTTTGGATGAATG
1 AAACTCTTTTGGATGAATG
*
109409 TAACTCTTTTGGATGAATG
1 AAACTCTTTTGGATGAATG
109428 AAACTCTTT
1 AAACTCTTT
109437 CTAAGAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (19 bp):
AAACTCTTTTGGATGAATG
Found at i:112473 original size:66 final size:60
Alignment explanation
Indices: 112261--112479 Score: 228
Period size: 65 Copynumber: 3.5 Consensus size: 60
112251 TATCAGGATC
* * *
112261 CTTTTAGTTGTTTCTCTTGAAAC-AAATTTTGTCTCTCGAGACAGTTTCTTTAAAAAAAGT
1 CTTTGAGTTGTTTCTCTTGAAACAAAATTTTGTCTCTCGAGACAGTTTTTTTGAAAAAA-T
* * *
112321 CTTTGAGTCTGTTTCTCTGGAAACAAAATTTTGTCTCTATTGAGACAATTTCTTTTGAGAAAAAT
1 CTTTGAGT-TGTTTCTCTTGAAACAAAATTTTGTCTC--TCGAGACAGTTT-TTTTGA-AAAAAT
112386 CTTTGAGTTTGTTTC-CTTTGAAACAAAATTTTGTCTCTCGAGACAGTTTATTTTGAAAACACTT
1 CTTTGAG-TTGTTTCTC-TTGAAACAAAATTTTGTCTCTCGAGACAGTTT-TTTTGAAAA-A---
112450 AT
59 AT
112452 CTTTGAGATTGTTT-TCCTTGAAACAAAA
1 CTTTGAG-TTGTTTCT-CTTGAAACAAAA
112480 CAAACCCTCT
Statistics
Matches: 134, Mismatches: 11, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
60 7 0.05
61 14 0.10
62 15 0.11
63 17 0.13
64 11 0.08
65 37 0.28
66 32 0.24
67 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (60 bp):
CTTTGAGTTGTTTCTCTTGAAACAAAATTTTGTCTCTCGAGACAGTTTTTTTGAAAAAAT
Found at i:117580 original size:134 final size:133
Alignment explanation
Indices: 117108--117573 Score: 505
Period size: 134 Copynumber: 3.5 Consensus size: 133
117098 GATGGCATGC
*
117108 CATCCTCATCGCGTATGAACCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGT
1 CATCCTCATCACGTATGAACCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGT
** * * * *
117173 CATCCC-TGATAAAAAACCGTCCTCATCGCATAGGAATCGTGTTATCACCCTTTCTAAAGATGGC
66 CA-CCCTTGATAACCAACCGTCCTCATCGCGTAGGAACCGTGTTATTACCCTTCCTAAAGATGGC
*
117237 CTG-T
130 C-GAA
* * ** *
117241 CGTCCTCATCATGTAAAAACCGTGTCATTCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATG
1 CATCCTCATCACGTATGAACCGTGTCA-TCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTG
* * * ** * * *
117306 TCACCCATGATAATCAGCCGTCCTCATTACGTAAGAACCGTGTTA-T--CATCCCTAAAGATGGC
65 TCACCCTTGATAACCAACCGTCCTCATCGCGTAGGAACCGTGTTATTACCCTTCCTAAAGATGGC
* *
117368 CTAC
130 CGAA
* * * * **
117372 CATCCTCATCACGTAGGAACTGTGTCAT-CCCTGACCATACCTCCTCATCACGTACAAGCCGTGT
1 CATCCTCATCACGTATGAACCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGT
117436 CACCCTTAGATAACCAACCGTCCTCATCGCGTAGGAACCGTGTTATTACCCTTCCTAAAGATGGC
66 CACCCTT-GATAACCAACCGTCCTCATCGCGTAGGAACCGTGTTATTACCCTTCCTAAAGATGGC
117501 CAGAA
130 C-GAA
* ** ** * **
117506 C-TCTTCATCACGTATGAGTCGTGTCATCTACCAACCAGATTTCCTCATCACGTAGGAGCCGTGT
1 CATCCTCATCACGTATGAACCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGT
117570 CACC
66 CACC
117574 TTTAGATGAC
Statistics
Matches: 270, Mismatches: 54, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
129 37 0.14
130 33 0.12
131 37 0.14
133 61 0.23
134 102 0.38
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (133 bp):
CATCCTCATCACGTATGAACCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGT
CACCCTTGATAACCAACCGTCCTCATCGCGTAGGAACCGTGTTATTACCCTTCCTAAAGATGGCC
GAA
Found at i:117781 original size:3 final size:3
Alignment explanation
Indices: 117773--117831 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
117763 ATACCAAAAA
* * *
117773 TAT TAT TA- TAT TAT AAA TAT TAAT TA- TAT TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
117817 TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT T
117832 TACATGTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 6 0.13
3 37 0.80
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:118800 original size:15 final size:16
Alignment explanation
Indices: 118780--118819 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
118770 TAAGAGCTAA
118780 TAGCATGTTTGGT-CC
1 TAGCATGTTTGGTCCC
118795 TAGCATGTTTGGTCCC
1 TAGCATGTTTGGTCCC
118811 T-GCATGTTT
1 TAGCATGTTT
118820 AACCTTACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.42
Consensus pattern (16 bp):
TAGCATGTTTGGTCCC
Found at i:119473 original size:29 final size:29
Alignment explanation
Indices: 119260--119537 Score: 190
Period size: 30 Copynumber: 9.5 Consensus size: 29
119250 GTAATTACTG
* *
119260 TTTAGCCCTTCAAATTT-T-TTTT-CTAT
1 TTTAGTCCTTTAAATTTCTATTTTACTAT
* * * *
119286 TTAAGTTCTTTAACTTTATATTTTTACTAT
1 TTTAGTCCTTTAAATTTCTA-TTTTACTAT
*
119316 TTTAGTCCTTTAACTTTCTATTTTAGCTAT
1 TTTAGTCCTTTAAATTTCTATTTTA-CTAT
* *
119346 TTTAGTCCTTTAAATTTTTGTTTTATCTAT
1 TTTAGTCCTTTAAATTTCTATTTTA-CTAT
* * **
119376 TTTAGTCCCTTAAGTTTCTATTTTTGTTAT
1 TTTAGTCCTTTAAATTTCTA-TTTTACTAT
* *
119406 TTTAGTCCTTTAAATGTCTATTTT-TTATT
1 TTTAGTCCTTTAAATTTCTATTTTACTA-T
* *
119435 TTTTGTCCTTTAAATATCTATATTTACTA-
1 TTTAGTCCTTTAAATTTCTAT-TTTACTAT
* ** *
119464 TTTAGACCTTTATGTTTC-ATTTTTACTGT
1 TTTAGTCCTTTAAATTTCTA-TTTTACTAT
* * * * *
119493 TTTAGCCCTTTAAGTTTATGGTTTTTCTAT
1 TTTAGTCCTTTAAATTTCT-ATTTTACTAT
* *
119523 TTAAGTCTTTTAAAT
1 TTTAGTCCTTTAAAT
119538 CGAATATGAT
Statistics
Matches: 199, Mismatches: 40, Indels: 22
0.76 0.15 0.08
Matches are distributed among these distances:
26 12 0.06
27 1 0.01
28 10 0.05
29 62 0.31
30 108 0.54
31 6 0.03
ACGTcount: A:0.21, C:0.13, G:0.07, T:0.59
Consensus pattern (29 bp):
TTTAGTCCTTTAAATTTCTATTTTACTAT
Found at i:119569 original size:2 final size:2
Alignment explanation
Indices: 119562--119588 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
119552 CCTTATTTTG
119562 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
119589 TTCATTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123258 original size:20 final size:20
Alignment explanation
Indices: 123233--123270 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
123223 TGTTTTGACC
123233 AGAAGTTTCGAAACTTTCAA
1 AGAAGTTTCGAAACTTTCAA
*
123253 AGAAGTTTTGAAACTTTC
1 AGAAGTTTCGAAACTTTC
123271 TAAAACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (20 bp):
AGAAGTTTCGAAACTTTCAA
Found at i:123319 original size:19 final size:19
Alignment explanation
Indices: 123297--123340 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
123287 TGAGTTTCAA
* *
123297 AACTTCACAAGAGTTTTGT
1 AACTTCACAAAAGTTTTGG
*
123316 AACTTTCATAAAAGTTTTGG
1 AAC-TTCACAAAAGTTTTGG
123336 AACTT
1 AACTT
123341 TACTTGAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (19 bp):
AACTTCACAAAAGTTTTGG
Found at i:125710 original size:9 final size:9
Alignment explanation
Indices: 125668--125702 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
125658 ATTTTTTTTC
125668 AAAAAAACAA
1 AAAAAAAC-A
125678 AAAAAAACA
1 AAAAAAACA
125687 AAAAAAACA
1 AAAAAAACA
125696 AAAAAAA
1 AAAAAAA
125703 AACTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:125710 original size:10 final size:10
Alignment explanation
Indices: 125668--125703 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
125658 ATTTTTTTTC
125668 AAAAAAACAA
1 AAAAAAACAA
125678 AAAAAAAC-A
1 AAAAAAACAA
125687 AAAAAAACAA
1 AAAAAAACAA
125697 AAAAAAA
1 AAAAAAA
125704 ACTAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:134507 original size:18 final size:17
Alignment explanation
Indices: 134483--134529 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
134473 TGTTTATGAG
134483 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
134501 TGAATTGGAATCTGTTA
1 GGAATTGGAATCTGTAA
134518 GGAATTGGAATC
1 GGAATTGGAATC
134530 CAATTCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:137797 original size:25 final size:25
Alignment explanation
Indices: 137746--137797 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
137736 AATTAACGAT
** *
137746 TTAAATAAATATTATTTTTGTAAAA
1 TTAAATAAATATTATAATAGTAAAA
137771 TTAAATAAA-ATTATAATAGTAATAA
1 TTAAATAAATATTATAATAGTAA-AA
137796 TT
1 TT
137798 GTATCAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
TTAAATAAATATTATAATAGTAAAA
Found at i:138219 original size:20 final size:20
Alignment explanation
Indices: 138194--138233 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
138184 TTGTATTATC
*
138194 TTATAAAATTAATAAATTTT
1 TTATAAAATAAATAAATTTT
* *
138214 TTATAACATAAATGAATTTT
1 TTATAAAATAAATAAATTTT
138234 ATTTCTATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
TTATAAAATAAATAAATTTT
Found at i:143657 original size:2 final size:2
Alignment explanation
Indices: 143650--143679 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
143640 TTAAATGATA
143650 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
143680 TAATTATAAG
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:144054 original size:23 final size:24
Alignment explanation
Indices: 144013--144071 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
144003 ATATTTTATA
*
144013 TATATTAACTTTAAGAAATATTTT
1 TATATTAACTTTAAGAAATATATT
144037 TATATTAA-TTT-AGTAAATATATT
1 TATATTAACTTTAAG-AAATATATT
144060 TATTATTAACTT
1 TA-TATTAACTT
144072 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 2 0.06
23 13 0.42
24 14 0.45
25 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (24 bp):
TATATTAACTTTAAGAAATATATT
Found at i:144065 original size:26 final size:25
Alignment explanation
Indices: 143995--144086 Score: 72
Period size: 25 Copynumber: 3.7 Consensus size: 25
143985 ACATAACTTA
143995 AATTTAT-AATAT-TTTATATATATT
1 AATTTATAAATATATTTAT-TATATT
144019 AACTTTA-AGAA-ATATTT-TTATATT
1 AA-TTTATA-AATATATTTATTATATT
144043 AATTTAGTAAATATATTTATTATTAACTT
1 AATTTA-TAAATATATTTATTA-T-A-TT
144072 AATTTA-AAAT-TATTT
1 AATTTATAAATATATTT
144087 TATCTTTATT
Statistics
Matches: 57, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
23 4 0.07
24 12 0.21
25 14 0.25
26 13 0.23
27 5 0.09
28 1 0.02
29 8 0.14
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
AATTTATAAATATATTTATTATATT
Found at i:144089 original size:27 final size:26
Alignment explanation
Indices: 144041--144114 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 26
144031 TATTTTTATA
144041 TTAATTTAGTAAATATATTTAT-TATTAAC
1 TTAATTTA--AAATAT-TTTATCT-TTAAC
**
144070 TTAATTTAAAATTATTTTATCTTTATT
1 TTAATTTAAAA-TATTTTATCTTTAAC
144097 TTAATTTAAAAATATTTT
1 TTAATTT-AAAATATTTT
144115 TTTGTGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
27 24 0.60
28 8 0.20
29 8 0.20
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (26 bp):
TTAATTTAAAATATTTTATCTTTAAC
Found at i:147294 original size:14 final size:14
Alignment explanation
Indices: 147275--147307 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
147265 AGGTAAGTTG
147275 ATTTCAATTGGTTA
1 ATTTCAATTGGTTA
147289 ATTTCAATTGGTTA
1 ATTTCAATTGGTTA
147303 ATTTC
1 ATTTC
147308 TTGAATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (14 bp):
ATTTCAATTGGTTA
Found at i:147853 original size:21 final size:21
Alignment explanation
Indices: 147785--147861 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
147775 TTGATGCATG
* *
147785 GGGTATCGATACCTGTATGAA
1 GGGTATCGATACCTATATGGA
**
147806 AAGTATCGATACC-ATATGGA
1 GGGTATCGATACCTATATGGA
*
147826 GGAGGTATCGATACCTATGTGGA
1 -G-GGTATCGATACCTATATGGA
147849 GGGTATCGATACC
1 GGGTATCGATACC
147862 CAGGGAACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.11
21 23 0.50
22 12 0.26
23 6 0.13
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.26
Consensus pattern (21 bp):
GGGTATCGATACCTATATGGA
Found at i:148882 original size:28 final size:28
Alignment explanation
Indices: 148836--148940 Score: 174
Period size: 28 Copynumber: 3.8 Consensus size: 28
148826 TCGAGGGTTC
* * *
148836 TATGTGGTCCTTCGAGACATATGTATTA
1 TATGTGGTCCTTTGGGACATATGTGTTA
*
148864 TATGTGGTCCTTTAGGACATATGTGTTA
1 TATGTGGTCCTTTGGGACATATGTGTTA
148892 TATGTGGTCCTTTGGGACATATGTGTTA
1 TATGTGGTCCTTTGGGACATATGTGTTA
148920 TATGTGGTCCTTTGGGACATA
1 TATGTGGTCCTTTGGGACATA
148941 GTGGTCATTC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 72 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (28 bp):
TATGTGGTCCTTTGGGACATATGTGTTA
Found at i:149382 original size:20 final size:20
Alignment explanation
Indices: 149354--149402 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
149344 GTAATGATAA
*
149354 GTATGTAGATAATGATTTAT
1 GTATGTAGATAATAATTTAT
* *
149374 GTATATAGATGATAATTTAT
1 GTATGTAGATAATAATTTAT
149394 GTATGTAGA
1 GTATGTAGA
149403 CAAGTATTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (20 bp):
GTATGTAGATAATAATTTAT
Found at i:152275 original size:22 final size:21
Alignment explanation
Indices: 152247--152298 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
152237 GTATGAACAA
152247 TATCGATATCATATGAAGGA-GG
1 TATCGATA-CATATG-AGGAGGG
* *
152269 TATCGATACCTATGTGGAGGG
1 TATCGATACATATGAGGAGGG
152290 TATCGATAC
1 TATCGATAC
152299 CCGGGGAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 16 0.59
22 8 0.30
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (21 bp):
TATCGATACATATGAGGAGGG
Found at i:152347 original size:19 final size:20
Alignment explanation
Indices: 152323--152375 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
152313 AGCTAATTTT
152323 GGTATCGGTACCT-GAGTAG-
1 GGTATCGGTACCTAGA-TAGA
*
152342 GGTATCAGTACCCTAGCATAGA
1 GGTATCGGTA-CCTAG-ATAGA
152364 GGTATCGGTACC
1 GGTATCGGTACC
152376 CTAAGGGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 9 0.32
20 3 0.11
21 6 0.21
22 10 0.36
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (20 bp):
GGTATCGGTACCTAGATAGA
Found at i:156733 original size:41 final size:41
Alignment explanation
Indices: 156612--156829 Score: 231
Period size: 41 Copynumber: 5.3 Consensus size: 41
156602 CTATAAACAT
* *
156612 GCGGCGTTTGTAAACACAAATGCCACTAAAGTATGAGTCTATA
1 GCGGCGTTTGTATA-A-AAATGCCACTAAAGTATGAGTCTTTA
* * * * *
156655 GCGACATTTGTATAAAAAATTCCACTAAAGCATGAGTCTATA
1 GCGGCGTTTGTAT-AAAAATGCCACTAAAGTATGAGTCTTTA
* * *
156697 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTG
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTA
* * * * * *
156738 GTGGCATATGTATAAAAGTGCCACTAAAGTACGATTCTTTA
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTA
* *
156779 GCGGCGTTTGT-CAAAAATGCCACTAAAGTATGAGTATTTA
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTA
*
156819 GCAGCGTTTGT
1 GCGGCGTTTGT
156830 TCTAAAAACG
Statistics
Matches: 145, Mismatches: 29, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
40 34 0.23
41 64 0.44
42 35 0.24
43 11 0.08
44 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTA
Found at i:162133 original size:11 final size:10
Alignment explanation
Indices: 162113--162192 Score: 56
Period size: 11 Copynumber: 7.7 Consensus size: 10
162103 AGTTTAAAAA
*
162113 ATTATAAAAT
1 ATTATTAAAT
162123 ACTTATTAAAT
1 A-TTATTAAAT
162134 -TTATTAAAAT
1 ATTATT-AAAT
*
162144 ATTATAAAATT
1 ATTATTAAA-T
*
162155 ATTAATAAAT
1 ATTATTAAAT
162165 -TTATCTAAAT
1 ATTAT-TAAAT
* *
162175 ACTATAAAAT
1 ATTATTAAAT
162185 AATTATTA
1 -ATTATTA
162193 TATTATCGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
9 8 0.15
10 18 0.33
11 28 0.52
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTATTAAAT
Found at i:162141 original size:31 final size:30
Alignment explanation
Indices: 162106--162192 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
162096 TCAATAAAGT
*
162106 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAATATTATAAAATA-TTATTAAATTTA
*
162137 TTAAAATATTATAAAATTATTAATAAATTTA
1 TTAAAATATTATAAAA-TATTATTAAATTTA
*
162168 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAATATTATAAAAT-ATTATTA
162193 TATTATCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 45 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
TTAAAATATTATAAAATATTATTAAATTTA
Found at i:162151 original size:19 final size:21
Alignment explanation
Indices: 162110--162159 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
162100 TAAAGTTTAA
162110 AAAATTA-TAAAATACTTATT
1 AAAATTATTAAAATACTTATT
*
162130 AAATTTATTAAAATA-TTA-T
1 AAAATTATTAAAATACTTATT
162149 AAAATTATTAA
1 AAAATTATTAA
162160 TAAATTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 9 0.33
21 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATTATTAAAATACTTATT
Found at i:165418 original size:9 final size:9
Alignment explanation
Indices: 165404--165472 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
165394 GCTACTGGAA
165404 ACCGGTTTG
1 ACCGGTTTG
*
165413 ACCGGTTTCA
1 ACCGGTTT-G
*
165423 ACCGGTTCG
1 ACCGGTTTG
*
165432 AACCGATTTG
1 -ACCGGTTTG
*
165442 ACCGGTCTG
1 ACCGGTTTG
165451 AACCGGTTTG
1 -ACCGGTTTG
*
165461 ACCGGTCTG
1 ACCGGTTTG
165470 ACC
1 ACC
165473 CGACCCGACC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 26 0.54
10 22 0.46
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:165445 original size:19 final size:20
Alignment explanation
Indices: 165423--165475 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
165413 ACCGGTTTCA
165423 ACCGGTTC-GAACCGATTTG
1 ACCGGTTCTGAACCGATTTG
*
165442 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTGAACCGATTTG
*
165461 ACCGG-TCTGACCCGA
1 ACCGGTTCTGAACCGA
165476 CCCGACCGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 2 0.07
19 28 0.93
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (20 bp):
ACCGGTTCTGAACCGATTTG
Found at i:165445 original size:29 final size:29
Alignment explanation
Indices: 165403--165458 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
165393 GGCTACTGGA
* *
165403 AACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGATTTGACCGGTCTCAACCGGTTCG
*
165432 AACCGATTTGACCGGTCTGAACCGGTT
1 AACCGATTTGACCGGTCTCAACCGGTT
165459 TGACCGGTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (29 bp):
AACCGATTTGACCGGTCTCAACCGGTTCG
Found at i:165528 original size:17 final size:17
Alignment explanation
Indices: 165468--165516 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
165458 TTGACCGGTC
165468 TGACCCGACCCGACCGG
1 TGACCCGACCCGACCGG
*
165485 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGG
165502 TGACCCGACCCGACC
1 TGACCCGACCCGACC
165517 CAACCGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.18, C:0.49, G:0.24, T:0.08
Consensus pattern (17 bp):
TGACCCGACCCGACCGG
Found at i:172515 original size:9 final size:9
Alignment explanation
Indices: 172498--172528 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
172488 CCCTGGAGGA
*
172498 CGCCTCACG
1 CGCCACACG
172507 CGCCACACG
1 CGCCACACG
172516 CGCCACACG
1 CGCCACACG
172525 CGCC
1 CGCC
172529 GCCGCAGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.16, C:0.58, G:0.23, T:0.03
Consensus pattern (9 bp):
CGCCACACG
Found at i:172578 original size:11 final size:11
Alignment explanation
Indices: 172562--172611 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 11
172552 AAACCGATTT
172562 AACCGGTTTTC
1 AACCGGTTTTC
*
172573 AACCGGTTCT-
1 AACCGGTTTTC
*
172583 GACCGG-TTTC
1 AACCGGTTTTC
*
172593 AACCGG-TTTG
1 AACCGGTTTTC
172603 AACCGGTTT
1 AACCGGTTT
172612 GACCGGTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 19 0.59
11 11 0.34
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (11 bp):
AACCGGTTTTC
Found at i:172589 original size:10 final size:9
Alignment explanation
Indices: 172574--172635 Score: 70
Period size: 10 Copynumber: 6.4 Consensus size: 9
172564 CCGGTTTTCA
172574 ACCGGTTCTG
1 ACCGGTT-TG
*
172584 ACCGGTTTCA
1 ACCGGTTT-G
172594 ACCGGTTTG
1 ACCGGTTTG
172603 AACCGGTTTG
1 -ACCGGTTTG
*
172613 ACCGGTCTG
1 ACCGGTTTG
172622 AACCGGTTTG
1 -ACCGGTTTG
172632 ACCG
1 ACCG
172636 ATCTGACCCG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
9 13 0.29
10 32 0.71
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:172592 original size:20 final size:21
Alignment explanation
Indices: 172562--172630 Score: 92
Period size: 20 Copynumber: 3.4 Consensus size: 21
172552 AAACCGATTT
172562 AACCGGTTTTCAACCGGTTCTG
1 AACCGG-TTTCAACCGGTTCTG
172584 -ACCGGTTTCAACCGGTT-TG
1 AACCGGTTTCAACCGGTTCTG
*
172603 AACCGGTTT-GACCGG-TCTG
1 AACCGGTTTCAACCGGTTCTG
172622 AACCGGTTT
1 AACCGGTTT
172631 GACCGATCTG
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
18 1 0.02
19 18 0.41
20 20 0.45
21 5 0.11
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
AACCGGTTTCAACCGGTTCTG
Found at i:172618 original size:19 final size:19
Alignment explanation
Indices: 172574--172635 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
172564 CCGGTTTTCA
*
172574 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTT-TGAACCGGTTT-G
172594 ACCGGTTTGAACCGGTTTG
1 ACCGGTTTGAACCGGTTTG
*
172613 ACCGGTCTGAACCGGTTTG
1 ACCGGTTTGAACCGGTTTG
172632 ACCG
1 ACCG
172636 ATCTGACCCG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
19 24 0.62
20 15 0.38
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.27
Consensus pattern (19 bp):
ACCGGTTTGAACCGGTTTG
Found at i:172640 original size:19 final size:19
Alignment explanation
Indices: 172601--172641 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
172591 TCAACCGGTT
*
172601 TGAACCGGTTTGACCGGTC
1 TGAACCGGTTTGACCGATC
172620 TGAACCGGTTTGACCGATC
1 TGAACCGGTTTGACCGATC
172639 TGA
1 TGA
172642 CCCGACCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (19 bp):
TGAACCGGTTTGACCGATC
Done.