Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010075.1 Kokia drynarioides strain JFW-HI SEQ_124853, 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: 198805
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:24 original size:3 final size:3
Alignment explanation
Indices: 16--84 Score: 50
Period size: 3 Copynumber: 22.7 Consensus size: 3
6 AAATGGTTAT
* ** * *
16 TAA TAA TAA TAT TAA TAA TAA TAA -ATA TTG TAA TAA TGA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* *
61 TAA TTAA TAT TAA TAT TAA TAA TA
1 TAA -TAA TAA TAA TAA TAA TAA TA
85 GTAAAAAAGT
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
2 1 0.02
3 45 0.92
4 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:30 original size:12 final size:12
Alignment explanation
Indices: 13--81 Score: 58
Period size: 12 Copynumber: 6.2 Consensus size: 12
3 ATTAAATGGT
13 TATTAATAATAA
1 TATTAATAATAA
25 TATTAATAATAA
1 TATTAATAATAA
**
37 TA--AAT-ATTG
1 TATTAATAATAA
* *
46 TAATAATGATAA
1 TATTAATAATAA
58 TATTAAT--TAA
1 TATTAATAATAA
*
68 TATTAATATTAA
1 TATTAATAATAA
80 TA
1 TA
82 ATAGTAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 4 0.09
10 13 0.28
11 3 0.06
12 27 0.57
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (12 bp):
TATTAATAATAA
Found at i:52 original size:27 final size:27
Alignment explanation
Indices: 19--71 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
9 TGGTTATTAA
19 TAATAAT-ATTAATAATAATAAATATTG
1 TAATAATGA-TAATAATAATAAATATTG
* *
46 TAATAATGATAATATTAATTAATATT
1 TAATAATGATAATAATAATAAATATT
72 AATATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATAATGATAATAATAATAAATATTG
Found at i:1199 original size:30 final size:30
Alignment explanation
Indices: 1124--1265 Score: 170
Period size: 29 Copynumber: 4.9 Consensus size: 30
1114 TAAAATCCTA
*
1124 TTTTGACCTCGAAACTTCCAAAAATCCCAT
1 TTTTGACCTCGAAACTTCCAAAAATCTCAT
*
1154 TTTT-ACC-CCAAACTTCCAAAAATCTCAT
1 TTTTGACCTCGAAACTTCCAAAAATCTCAT
*
1182 TTTTGACCTCGAAACTTCCAAAAAT-TCCGT
1 TTTTGACCTCGAAACTTCCAAAAATCT-CAT
1212 TTTT-ACTCTCG-AACTTCCAAAAATCTCA-
1 TTTTGAC-CTCGAAACTTCCAAAAATCTCAT
* * *
1240 TTTTGACCCCAAAACTTCTAAAAATC
1 TTTTGACCTCGAAACTTCCAAAAATC
1266 CCAATTTTAC
Statistics
Matches: 97, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
28 29 0.30
29 38 0.39
30 30 0.31
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (30 bp):
TTTTGACCTCGAAACTTCCAAAAATCTCAT
Found at i:1277 original size:29 final size:28
Alignment explanation
Indices: 1115--1278 Score: 166
Period size: 29 Copynumber: 5.7 Consensus size: 28
1105 TAAACTATCT
* * *
1115 AAAATCCTATTTTGACCTCGAAACTTCCA
1 AAAATCCCATTTTTACC-CCAAACTTCCA
1144 AAAATCCCATTTTTACCCCAAACTTCCA
1 AAAATCCCATTTTTACCCCAAACTTCCA
* *
1172 AAAATCTCATTTTTGACCTCGAAACTTCCA
1 AAAATCCCATTTTT-ACC-CCAAACTTCCA
* * * *
1202 AAAATTCCGTTTTTACTCTCGAACTTCCA
1 AAAATCCCATTTTTAC-CCCAAACTTCCA
* * *
1231 AAAATCTCATTTTGACCCCAAAACTTCTA
1 AAAATCCCATTTTTACCCC-AAACTTCCA
*
1260 AAAATCCCAATTTTACCCC
1 AAAATCCCATTTTTACCCC
1279 CGAATGTCTA
Statistics
Matches: 110, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
28 25 0.23
29 63 0.57
30 22 0.20
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAATCCCATTTTTACCCCAAACTTCCA
Found at i:1292 original size:58 final size:59
Alignment explanation
Indices: 1115--1301 Score: 224
Period size: 58 Copynumber: 3.2 Consensus size: 59
1105 TAAACTATCT
*
1115 AAAATC-CTATTTTGACCTCGAAACTTCCAAAAATCCCATTTTTA-CCCCAAACTTCCA
1 AAAATCTCTATTTTGACCTCGAAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCA
* * * *
1172 AAAATCTC-ATTTTTGACCTCGAAACTTCCAAAAATTCCGTTTTTACTCTCGAACTTCCA
1 AAAATCTCTA-TTTTGACCTCGAAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCA
* * * * *
1231 AAAATCTC-ATTTTGACCCCAAAACTTCTAAAAATCCCAATTTTACCCCCGAA-TGTCTA
1 AAAATCTCTATTTTGACCTCGAAACTTCCAAAAATCCCATTTTTACCCCCGAACT-TCCA
1289 AAAAT-TCTATTTT
1 AAAATCTCTATTTT
1302 TAAACCCCGA
Statistics
Matches: 111, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
57 10 0.09
58 82 0.74
59 19 0.17
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (59 bp):
AAAATCTCTATTTTGACCTCGAAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCA
Found at i:1302 original size:29 final size:30
Alignment explanation
Indices: 1256--1313 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
1246 CCCCAAAACT
*
1256 TCTAAAAATCCCAATTTT-ACCCCCGAATG
1 TCTAAAAATCCCAATTTTAAACCCCGAATG
* * *
1285 TCTAAAAATTCTATTTTTAAACCCCGAAT
1 TCTAAAAATCCCAATTTTAAACCCCGAAT
1314 ATTCCCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (30 bp):
TCTAAAAATCCCAATTTTAAACCCCGAATG
Found at i:1302 original size:87 final size:87
Alignment explanation
Indices: 1115--1303 Score: 215
Period size: 87 Copynumber: 2.2 Consensus size: 87
1105 TAAACTATCT
* * * *
1115 AAAATCCTATTTTGACCTCGAAACTTCCAAAAATCCCATTTTTACCCCAAACTTCCAAAAATCTC
1 AAAATTCTATTTTTACCTCGAAACTTCCAAAAATCCCATTTTGACCCCAAACTTCCAAAAATCCC
* *
1180 ATTTTTGACCTCGAAACTTCCA
66 AATTTTGACCCCGAAACTTCCA
** * *
1202 AAAATTCCGTTTTTACTCTCG-AACTTCCAAAAATCTCATTTTGACCCCAAAACTTCTAAAAATC
1 AAAATTCTATTTTTAC-CTCGAAACTTCCAAAAATCCCATTTTGACCCC-AAACTTCCAAAAATC
*
1266 CCAATTTT-ACCCCCG-AA-TGTCTA
64 CCAATTTTGA-CCCCGAAACT-TCCA
1289 AAAATTCTATTTTTA
1 AAAATTCTATTTTTA
1304 AACCCCGAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
86 1 0.01
87 56 0.66
88 28 0.33
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (87 bp):
AAAATTCTATTTTTACCTCGAAACTTCCAAAAATCCCATTTTGACCCCAAACTTCCAAAAATCCC
AATTTTGACCCCGAAACTTCCA
Found at i:1681 original size:96 final size:96
Alignment explanation
Indices: 1564--1755 Score: 255
Period size: 96 Copynumber: 2.0 Consensus size: 96
1554 AAAGCTTTAC
*
1564 AATCGAGGCAATATTCTTTTAT-TTCGAGTTTCAAAAAT-TTGTGCCTTAACTCACTAGGTGCAA
1 AATCGAGGCAATATTCTTTTATCTTCGA--TTCAAAAATATTGCGCCTTAACTCACTAGGTGCAA
*
1627 TTTTTCTTCAAATCGAAATAATCGAATACCCTT
64 CTTTTCTTCAAATCGAAATAATCGAATACCCTT
* ** *
1660 AATCGAGGCAATGTT-TCTTTATCTTCGATTCTGAAATATTGCGCCTTAACTTACTAGGTGCAAC
1 AATCGAGGCAATATTCT-TTTATCTTCGATTCAAAAATATTGCGCCTTAACTCACTAGGTGCAAC
* * *
1724 TTTTCTTCAAATTGAGATAATCGAATATCCTT
65 TTTTCTTCAAATCGAAATAATCGAATACCCTT
1756 TTCTCAAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
95 8 0.10
96 71 0.85
97 5 0.06
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTCTTTTATCTTCGATTCAAAAATATTGCGCCTTAACTCACTAGGTGCAACT
TTTCTTCAAATCGAAATAATCGAATACCCTT
Found at i:6763 original size:27 final size:27
Alignment explanation
Indices: 6731--6786 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
6721 ACCTATCTTA
6731 GTGTTATTTAAGTATACGTGTGTGTGT
1 GTGTTATTTAAGTATACGTGTGTGTGT
6758 GTGTTATTTAAGTATACGTGTGTGTGT
1 GTGTTATTTAAGTATACGTGTGTGTGT
6785 GT
1 GT
6787 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.04, G:0.30, T:0.48
Consensus pattern (27 bp):
GTGTTATTTAAGTATACGTGTGTGTGT
Found at i:10814 original size:14 final size:14
Alignment explanation
Indices: 10775--10828 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
10765 AGTCGTAATG
* *
10775 AAATTAAAATTTGA
1 AAATTTAAATTTTA
* *
10789 AAACTTATATTTTA
1 AAATTTAAATTTTA
* *
10803 AAATTTGAATTTTT
1 AAATTTAAATTTTA
10817 AAATTTAAATTT
1 AAATTTAAATTT
10829 AATTTTGAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (14 bp):
AAATTTAAATTTTA
Found at i:10822 original size:22 final size:21
Alignment explanation
Indices: 10799--10852 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
10789 AAACTTATAT
10799 TTTAAAATTTGAATTTTTAAA
1 TTTAAAATTTGAATTTTTAAA
*
10820 TTT-AAATTT-AATTTTGAAA
1 TTTAAAATTTGAATTTTTAAA
**
10839 GCTAAAACTTTGAA
1 TTTAAAA-TTTGAA
10853 GAAACTTTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 10 0.37
20 9 0.33
21 6 0.22
22 2 0.07
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (21 bp):
TTTAAAATTTGAATTTTTAAA
Found at i:11131 original size:22 final size:22
Alignment explanation
Indices: 11074--11133 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
11064 ATCTTGTTAG
* * *
11074 AGAATCTCACTATTCACGTCAG
1 AGAATCTCACTGTTCACATCAA
11096 AGAATCTCACTGTTCACATCAA
1 AGAATCTCACTGTTCACATCAA
*
11118 AGAATCTCAATGTTCA
1 AGAATCTCACTGTTCA
11134 TTTTTTTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (22 bp):
AGAATCTCACTGTTCACATCAA
Found at i:11222 original size:22 final size:22
Alignment explanation
Indices: 11159--11224 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
11149 AGAATATTGC
* * *
11159 AGGGAATCTCACTGTTCACGTA
1 AGGGAATATCACTGTTCACTTT
*
11181 AGGGAATATCACTGTGCACTTT
1 AGGGAATATCACTGTTCACTTT
11203 AGGGAATATCACTGTTCACTTT
1 AGGGAATATCACTGTTCACTTT
11225 GTTTTTTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (22 bp):
AGGGAATATCACTGTTCACTTT
Found at i:23235 original size:14 final size:14
Alignment explanation
Indices: 23216--23245 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
23206 TTCTAGCCTT
23216 TATTTGAGGAAGGA
1 TATTTGAGGAAGGA
23230 TATTTGAGGAAGGA
1 TATTTGAGGAAGGA
23244 TA
1 TA
23246 AATACATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (14 bp):
TATTTGAGGAAGGA
Found at i:33344 original size:21 final size:21
Alignment explanation
Indices: 33316--33366 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
33306 ATAATAGCAT
33316 AATCCAAATATAAAATTTAGA
1 AATCCAAATATAAAATTTAGA
* * *
33337 AATTCAAACATAAAATTTATA
1 AATCCAAATATAAAATTTAGA
33358 AATCCAAAT
1 AATCCAAAT
33367 TACATAATCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (21 bp):
AATCCAAATATAAAATTTAGA
Found at i:35663 original size:19 final size:19
Alignment explanation
Indices: 35628--35666 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
35618 AAAGTTTGTT
*
35628 ATTAATAAATTTTTATTGG
1 ATTAATAAATTTCTATTGG
35647 ATTAA-AAATTTACTATTGG
1 ATTAATAAATTT-CTATTGG
35666 A
1 A
35667 GTTTAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (19 bp):
ATTAATAAATTTCTATTGG
Found at i:38152 original size:14 final size:15
Alignment explanation
Indices: 38129--38168 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
38119 TTATTTTAAA
*
38129 TAAAAGATTATAA-T
1 TAAAAAATTATAACT
38143 TAAAAAATTATAACTT
1 TAAAAAATTATAAC-T
38159 TAAAAAATTA
1 TAAAAAATTA
38169 AAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.52
16 11 0.48
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (15 bp):
TAAAAAATTATAACT
Found at i:47812 original size:36 final size:36
Alignment explanation
Indices: 47772--47874 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
47762 ATATAATCAA
* * *
47772 TCACATGACATGAAGAACATACTCACATATTTTTTG
1 TCACATGGCATGAAGAACATACCCACATATTTGTTG
47808 TCACATGGCATGAAGAACATACCCACATATTTGTTG
1 TCACATGGCATGAAGAACATACCCACATATTTGTTG
* *
47844 TTACACGGCATGAAGAACATACCCACATATT
1 TCACATGGCATGAAGAACATACCCACATATT
47875 CATTTTCACA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (36 bp):
TCACATGGCATGAAGAACATACCCACATATTTGTTG
Found at i:47989 original size:23 final size:23
Alignment explanation
Indices: 47954--48150 Score: 232
Period size: 23 Copynumber: 8.6 Consensus size: 23
47944 ATCTTAATTC
*
47954 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
*
47977 TTTAATCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * ** *
48000 TTTGAGCACAAATCTTAATAATA
1 TTTAAGCATAAATCACATTAATA
*
48023 TTTACGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
48046 ATTAAGCACAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
48069 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
48092 CTTAAGCAAAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
48115 TTTAAGTATAAATCACATTAACA
1 TTTAAGCATAAATCACATTAATA
* *
48138 CTTAAGCACAAAT
1 TTTAAGCATAAAT
48151 AATCATCTTT
Statistics
Matches: 142, Mismatches: 32, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 142 1.00
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (23 bp):
TTTAAGCATAAATCACATTAATA
Found at i:48011 original size:46 final size:46
Alignment explanation
Indices: 47955--48150 Score: 293
Period size: 46 Copynumber: 4.3 Consensus size: 46
47945 TCTTAATTCT
* * *
47955 TTAAGCACAAATCACATTAATATTTAATCATAAATCACATTAATAT
1 TTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATAC
* * * * *
48001 TTGAGCACAAATCTTAATAATATTTACGCATAAATCACATTAATAA
1 TTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATAC
48047 TTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATAC
1 TTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATAC
* * *
48093 TTAAGCAAAAATCATATTAATATTTAAGTATAAATCACATTAACAC
1 TTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATAC
48139 TTAAGCACAAAT
1 TTAAGCACAAAT
48151 AATCATCTTT
Statistics
Matches: 134, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 134 1.00
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (46 bp):
TTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATAC
Found at i:52801 original size:193 final size:190
Alignment explanation
Indices: 52438--52802 Score: 462
Period size: 193 Copynumber: 1.9 Consensus size: 190
52428 CTGTACTATA
* * * * * *
52438 AATTGTTCCCTAATGATGCTGCTCACACGAGCTGTCTAGAGTATGCGTAAAGCATAGTCCCAACC
1 AATTATTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCCTAAAGCATAATCCCAACC
* * * * * *
52503 ATCGTAGGGCCTATAATTCATTTAGGATACATATCTCTTTCCTGAGTCACGATGCTGCTCACACA
66 ATCGTAGGGCATATAATCCATTTAGGATACATATCTCTTTCCCGACTCACGATACTACTCACACA
* *
52568 AGCTGTTGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATATGATATTTGTGCATAT
131 AGCTATCGAGGACTCGCAACA-ATGCGGTACCTCAGCCATCGATATGATATTTGTGCATAT
* * *
52629 AATTATTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCACTTATGCATAAATCTCAA
1 AATTATTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGC-CTAAAGCAT-AATCCCAA
* * * * *
52694 CCATCGTAGGGCATGTAATCCATTCTTGGATTCTTTTCTCATTTCCCGACTCACGATACTACTCA
64 CCATCGTAGGGCATATAATCCATT-TAGGATACATATCTC-TTTCCCGACTCACGATACTACTCA
* *
52759 CACGAGCTATCGAGGACTCGCAAC-ATGTGGTACCTCAGCCATCG
127 CACAAGCTATCGAGGACTCGCAACAATGCGGTACCTCAGCCATCG
52803 CGTTGGTTTC
Statistics
Matches: 146, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
191 42 0.29
192 6 0.04
193 46 0.32
194 11 0.08
195 41 0.28
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (190 bp):
AATTATTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCCTAAAGCATAATCCCAACC
ATCGTAGGGCATATAATCCATTTAGGATACATATCTCTTTCCCGACTCACGATACTACTCACACA
AGCTATCGAGGACTCGCAACAATGCGGTACCTCAGCCATCGATATGATATTTGTGCATAT
Found at i:56851 original size:7 final size:7
Alignment explanation
Indices: 56839--56882 Score: 63
Period size: 7 Copynumber: 6.1 Consensus size: 7
56829 ATATTTATTT
56839 TCTTTTC
1 TCTTTTC
56846 TCTTTTC
1 TCTTTTC
56853 TCTTTTC
1 TCTTTTC
56860 TTCTTCTT-
1 -TCTT-TTC
56868 TCTTTTC
1 TCTTTTC
56875 TCTTTTC
1 TCTTTTC
56882 T
1 T
56883 TTCTGTGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 2 0.06
7 26 0.76
8 4 0.12
9 2 0.06
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TCTTTTC
Found at i:56871 original size:22 final size:22
Alignment explanation
Indices: 56838--56883 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
56828 TATATTTATT
56838 TTCTTTTCTCTTTTCTCTTTTC
1 TTCTTTTCTCTTTTCTCTTTTC
56860 TTCTTCTT-TCTTTTCTCTTTTC
1 TTCTT-TTCTCTTTTCTCTTTTC
56882 TT
1 TT
56884 TCTGTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (22 bp):
TTCTTTTCTCTTTTCTCTTTTC
Found at i:58758 original size:11 final size:11
Alignment explanation
Indices: 58742--58769 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
58732 GAAGGGAAAG
58742 GTATCAGCTTA
1 GTATCAGCTTA
58753 GTATCAGCTTA
1 GTATCAGCTTA
58764 GTATCA
1 GTATCA
58770 CCATCACGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (11 bp):
GTATCAGCTTA
Found at i:60379 original size:27 final size:27
Alignment explanation
Indices: 60343--60397 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
60333 TACAAAAGAG
60343 ACAATGAATACACAAATTTAGGGAGAA
1 ACAATGAATACACAAATTTAGGGAGAA
*
60370 ACAATTAATACACAAATTTAGGGAGAA
1 ACAATGAATACACAAATTTAGGGAGAA
60397 A
1 A
60398 ATAGGTGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (27 bp):
ACAATGAATACACAAATTTAGGGAGAA
Found at i:62225 original size:40 final size:39
Alignment explanation
Indices: 62111--62225 Score: 124
Period size: 40 Copynumber: 2.9 Consensus size: 39
62101 GTAGTTTAGT
* * * *
62111 AGTGTTTACAGTATCACGGCTAG-TCAGTAATAATATTAC
1 AGTGTTTACAGTGTCACTGCCAGTTCAGT-ATAATATCAC
* * *
62150 AGTGTTTACAGTGTTACTGCCAGTTTAGTACTAATATCGC
1 AGTGTTTACAGTGTCACTGCCAGTTCAGTA-TAATATCAC
*
62190 AGTGTTTACAGTGTCACTACCAGTTCAGTGATAATA
1 AGTGTTTACAGTGTCACTGCCAGTTCAGT-ATAATA
62226 CTCCTAAGTA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
39 20 0.32
40 42 0.67
41 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGCCAGTTCAGTATAATATCAC
Found at i:62696 original size:56 final size:56
Alignment explanation
Indices: 62595--62705 Score: 125
Period size: 56 Copynumber: 2.0 Consensus size: 56
62585 CACTATTTCC
* * * * * *
62595 CAAAACAGTATGCACACACGATTTGACACATGCCCATGTGTCCAGCTCATGTGTCA
1 CAAAACAGTATACACACACGACTAGACACATGCCCATGTGCCCAGCCCATATGTCA
* **
62651 CAAAATAGTATACACACACGGACTAG-CACATGCCGGTGTGCCCAGCCCATATGTC
1 CAAAACAGTATACACACAC-GACTAGACACATGCCCATGTGCCCAGCCCATATGTC
62706 TCATGTGCCT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
56 41 0.91
57 4 0.09
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.21
Consensus pattern (56 bp):
CAAAACAGTATACACACACGACTAGACACATGCCCATGTGCCCAGCCCATATGTCA
Found at i:66139 original size:98 final size:98
Alignment explanation
Indices: 65970--66166 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
65960 CACTACCGAG
* *
65970 GCATTCGTTATTCCGAATGGCATAATCAGGAACTCGTAGTGGTAGTAACATGTTCATAAGGTCGT
1 GCATTCGTTATTCCGAATGGCATAACCAGGAACTCGTAGTGGTAGTAACATGTTCAGAAGGTCGT
*
66035 CTTATACATGTCTTTTTCCTTAACCTTAAGCTA
66 CTTATACATGTCTTTTTCCTTAACCATAAGCTA
*
66068 GCATTCGTTATTCCGAATGGCATAACCAGGAACTCGTAGTGGTAGTAACGTGTTCAGAAGGTCGT
1 GCATTCGTTATTCCGAATGGCATAACCAGGAACTCGTAGTGGTAGTAACATGTTCAGAAGGTCGT
*
66133 CTTATACATTTCTTTTTCCTTAACCATAAGCTA
66 CTTATACATGTCTTTTTCCTTAACCATAAGCTA
66166 G
1 G
66167 TGATAGCCCG
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (98 bp):
GCATTCGTTATTCCGAATGGCATAACCAGGAACTCGTAGTGGTAGTAACATGTTCAGAAGGTCGT
CTTATACATGTCTTTTTCCTTAACCATAAGCTA
Found at i:69070 original size:38 final size:40
Alignment explanation
Indices: 69008--69107 Score: 123
Period size: 38 Copynumber: 2.5 Consensus size: 40
68998 TGGTAGTCTA
* * * *
69008 GCAGTGTTTACAGTATCACGGCTAGTCAATTA-CAATATT
1 GCAGTGTTTACAGTGTCACTGCTAGTCAAGTAGCAATATC
** *
69047 GCAGTG-TTACAGTGTCACTGCTAGTTTAGTAGTAATATC
1 GCAGTGTTTACAGTGTCACTGCTAGTCAAGTAGCAATATC
69086 GCAGTGTTTACAGTGTCACTGC
1 GCAGTGTTTACAGTGTCACTGC
69108 CAATTCAATG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 20 0.38
39 17 0.33
40 15 0.29
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (40 bp):
GCAGTGTTTACAGTGTCACTGCTAGTCAAGTAGCAATATC
Found at i:69123 original size:40 final size:39
Alignment explanation
Indices: 69008--69123 Score: 101
Period size: 40 Copynumber: 2.9 Consensus size: 39
68998 TGGTAGTCTA
* * * * * *
69008 GCAGTGTTTACAGTATCAC-GGCTAGTCAATTACAATATT
1 GCAGTGTTTACAGTGTCACTGCCAATTCAA-TATAATATC
* * * *
69047 GCAGTG-TTACAGTGTCACTGCTAGTTTAGTAGTAATATC
1 GCAGTGTTTACAGTGTCACTGCCAATTCAATA-TAATATC
69086 GCAGTGTTTACAGTGTCACTGCCAATTCAATGATAATA
1 GCAGTGTTTACAGTGTCACTGCCAATTCAAT-ATAATA
69124 CTCCCAAGTG
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
38 13 0.22
39 20 0.34
40 25 0.42
41 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (39 bp):
GCAGTGTTTACAGTGTCACTGCCAATTCAATATAATATC
Found at i:71516 original size:2 final size:2
Alignment explanation
Indices: 71509--71564 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
71499 CAAGATCCGT
71509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71551 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
71565 ATTTTCAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:79485 original size:18 final size:18
Alignment explanation
Indices: 79462--79507 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
79452 CAAGGTCACG
79462 ATCAATAGT-GTCACTAGC
1 ATCAATA-TCGTCACTAGC
*
79480 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTAGC
79498 ATCAATATCG
1 ATCAATATCG
79508 ATATCATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (18 bp):
ATCAATATCGTCACTAGC
Found at i:79512 original size:15 final size:17
Alignment explanation
Indices: 79473--79519 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
79463 TCAATAGTGT
*
79473 CACTAGCATCAATATCG
1 CACTATCATCAATATCG
79490 TCACTATCATCAATATCG
1 -CACTATCATCAATATCG
79508 -A-TATCATCAATA
1 CACTATCATCAATA
79520 AGAAAACCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 11 0.39
16 1 0.04
18 16 0.57
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (17 bp):
CACTATCATCAATATCG
Found at i:82537 original size:18 final size:18
Alignment explanation
Indices: 82514--82550 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
82504 ACAATTCATA
82514 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
82532 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
82550 T
1 T
82551 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:84979 original size:21 final size:21
Alignment explanation
Indices: 84949--85037 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
84939 CTCACAAAGA
* *
84949 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
84969 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
84990 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
85011 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
85035 AAA
1 AAA
85038 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:85030 original size:24 final size:21
Alignment explanation
Indices: 84949--85017 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
84939 CTCACAAAGA
* * *
84949 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
84969 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
84990 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
85011 AAAAAGA
1 AAAAAGA
85018 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:99785 original size:26 final size:26
Alignment explanation
Indices: 99712--99816 Score: 79
Period size: 26 Copynumber: 4.0 Consensus size: 26
99702 TTACTACTAA
* * *
99712 TGTCGTTGCATGAGCATGTCCAAAAT
1 TGTCGCTGCATGAACATGTCCAGAAT
* * *
99738 TGTCGCTGTA-GAAACTTATCCAGAAT
1 TGTCGCTGCATG-AACATGTCCAGAAT
*
99764 TCTCGCTGCATGAACATGTCCA-AAGT
1 TGTCGCTGCATGAACATGTCCAGAA-T
* * * *
99790 TGTCGTTGTATGAGCATGTTCAGAAT
1 TGTCGCTGCATGAACATGTCCAGAAT
99816 T
1 T
99817 ACGCCTAAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
25 3 0.05
26 54 0.90
27 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTCCAGAAT
Found at i:127791 original size:3 final size:3
Alignment explanation
Indices: 127783--127823 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
127773 GCGAAAGCAC
* *
127783 AAG AAG AAG AAG AAG AAG AAT AAG AAG AAG AAT AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
127824 TCGTGACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (3 bp):
AAG
Found at i:127800 original size:12 final size:12
Alignment explanation
Indices: 127783--127823 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
127773 GCGAAAGCAC
*
127783 AAGAAGAAGAAG
1 AAGAAGAATAAG
127795 AAGAAGAATAAG
1 AAGAAGAATAAG
127807 AAGAAGAATAAG
1 AAGAAGAATAAG
127819 AAGAA
1 AAGAA
127824 TCGTGACGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (12 bp):
AAGAAGAATAAG
Found at i:141725 original size:78 final size:77
Alignment explanation
Indices: 141589--141733 Score: 211
Period size: 78 Copynumber: 1.9 Consensus size: 77
141579 TGAATATTTT
*
141589 AAATACTAAGATTACGTTATTATGCCCCACAAGAATGATGGTCATGAGAGCAGCAATCTTGAATT
1 AAATACTAAGATTACGTTATTATGCCCCACAAGAATGATGGTCATGAGAGCAACAATCTTGAATT
141654 GATGATGACAAA
66 GATGATGACAAA
* * * * *
141666 AAATACTAAGATTACGTTATTATGCTCTCGCAAGATTGATGGTC-GGTAGAGCAACAATCTTGGA
1 AAATACTAAGATTACGTTATTATGC-CCCACAAGAATGATGGTCATG-AGAGCAACAATCTTGAA
141730 TTGA
64 TTGA
141734 CAATGACGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
77 26 0.43
78 34 0.57
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (77 bp):
AAATACTAAGATTACGTTATTATGCCCCACAAGAATGATGGTCATGAGAGCAACAATCTTGAATT
GATGATGACAAA
Found at i:142407 original size:13 final size:13
Alignment explanation
Indices: 142389--142415 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
142379 TTATTAGTTG
142389 TCCTTAAGAGGTA
1 TCCTTAAGAGGTA
142402 TCCTTAAGAGGTA
1 TCCTTAAGAGGTA
142415 T
1 T
142416 TTGTTTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCTTAAGAGGTA
Found at i:143066 original size:6 final size:6
Alignment explanation
Indices: 143057--143089 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
143047 TTATAAAACT
*
143057 AAATCA AAATTA AAATTA AAATTA AAATTA AAA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAA
143090 AATATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (6 bp):
AAATTA
Found at i:152569 original size:2 final size:2
Alignment explanation
Indices: 152564--152593 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
152554 TTATTTTTTA
152564 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
152594 TCTATTTTTT
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:156195 original size:20 final size:20
Alignment explanation
Indices: 156118--156200 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
156108 CCTTAACCAA
* *
156118 ATTT-TCAATATTTCTAAGG
1 ATTTATCAAAATTTCTAAAG
* *
156137 AATTATAAAAATTTCTAAA-
1 ATTTATCAAAATTTCTAAAG
* *
156156 ATTATATCAATATTTTTAAAG
1 ATT-TATCAAAATTTCTAAAG
156177 ATTTATCAAAATTTCTAAAG
1 ATTTATCAAAATTTCTAAAG
156197 ATTT
1 ATTT
156201 TCCTAGTGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
19 5 0.10
20 43 0.84
21 3 0.06
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTATCAAAATTTCTAAAG
Found at i:165277 original size:15 final size:15
Alignment explanation
Indices: 165257--165288 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
165247 TAAGCTTGAT
165257 ATGAGGTAGAAGATG
1 ATGAGGTAGAAGATG
*
165272 ATGAGGTTGAAGATG
1 ATGAGGTAGAAGATG
165287 AT
1 AT
165289 TTACACATCA
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:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (15 bp):
ATGAGGTAGAAGATG
Found at i:172000 original size:19 final size:19
Alignment explanation
Indices: 171978--172015 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
171968 TTTTTAAAAG
171978 TATAAATTTTTGGAATTTT
1 TATAAATTTTTGGAATTTT
* *
171997 TATATATTTTTTGAATTTT
1 TATAAATTTTTGGAATTTT
172016 GAAAACTATT
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:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (19 bp):
TATAAATTTTTGGAATTTT
Found at i:172237 original size:11 final size:11
Alignment explanation
Indices: 172221--172250 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
172211 CTCGAAATTT
172221 GATTTTTTTTC
1 GATTTTTTTTC
172232 GATTTTTTTTC
1 GATTTTTTTTC
*
172243 AATTTTTT
1 GATTTTTT
172251 AAAATCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (11 bp):
GATTTTTTTTC
Found at i:172936 original size:96 final size:96
Alignment explanation
Indices: 172762--172943 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
172752 GAGGACATTT
* ** **
172762 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAACATTTCGGGATCGAAGA
1 GATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAACATTTCGAAATCGAAGA
*
172827 TAAGGAAACATTGCCTCGATTAAGGGTATTC
66 TAAAGAAACATTGCCTCGATTAAGGGTATTC
* *
172858 GATTATTTCGATTCGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGAAATCTGAA
1 GATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAACA-TTTCGAAATC-GAA
*
172922 -ATAAA-AGAATATTGCCTCGATT
64 GATAAAGA-AACATTGCCTCGATT
172944 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 2 0.03
96 69 0.93
97 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (96 bp):
GATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAACATTTCGAAATCGAAGA
TAAAGAAACATTGCCTCGATTAAGGGTATTC
Found at i:173237 original size:29 final size:29
Alignment explanation
Indices: 173204--173538 Score: 283
Period size: 29 Copynumber: 11.5 Consensus size: 29
173194 AAAAAAAGGG
**
173204 ATTTTTGGAAGTTTAAGGGTAAAATGGTA
1 ATTTTTGGAAGTTTGGGGGTAAAATGGTA
* * * * *
173233 ATTTTCGAAAGGTTCGGGGTAAAAAATGG-G
1 ATTTTTGGAAGTTTGGGGGT--AAAATGGTA
*
173263 GTTTTTGGAAGTTTGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTTGGGGGTAAAATGGTA
* * * * *
173292 ATTTTTAGAAGGTTCGGGGTTAAATTGG-G
1 ATTTTTGGAA-GTTTGGGGGTAAAATGGTA
*
173321 GTTTTTGGAAGTTTGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTTGGGGGTAAAATGGTA
*
173350 ATTTTTGGAAAGTTT-GGGGTCAAAAATGG-G
1 ATTTTTGG-AAGTTTGGGGGT--AAAATGGTA
*
173380 ATTTTTGGAAATTTGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTTGGGGGTAAAATGGTA
* *
173409 A-TTTTGTAAAGTTT-GGGGTCAAAATGG-G
1 ATTTTTG-GAAGTTTGGGGGT-AAAATGGTA
173437 ATTTTTGGAAGTTTGGGGGTAAAAT-GTA
1 ATTTTTGGAAGTTTGGGGGTAAAATGGTA
* * * * *
173465 ATTTTTAGAAGGTTCGAGGTTAAAAATGG-G
1 ATTTTTGGAA-GTTTGGGGGT-AAAATGGTA
*
173495 ATTTTTGGAAGTTTAGGGGTAAAATGGTA
1 ATTTTTGGAAGTTTGGGGGTAAAATGGTA
*
173524 ATTTTTAGAAAGTTT
1 ATTTTT-GGAAGTTT
173539 AGGGTCAAAA
Statistics
Matches: 241, Mismatches: 45, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
27 1 0.00
28 66 0.27
29 90 0.37
30 69 0.29
31 15 0.06
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.37
Consensus pattern (29 bp):
ATTTTTGGAAGTTTGGGGGTAAAATGGTA
Found at i:173346 original size:58 final size:58
Alignment explanation
Indices: 173195--173533 Score: 461
Period size: 59 Copynumber: 5.8 Consensus size: 58
173185 GAAGGTTCGA
* ** *
173195 AAAAAAGGGATTTTTGGAAGTTTAAGGGTAAAATGGTAA-TTTTCGAAAGGTTCGGGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAG-AAGGTTCGGGGT
*
173253 AAAAAATGGGGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGT
1 -AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGT
* * * * * *
173312 TAAATTGGGGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGT
* *
173370 CAAAAATGGGATTTTTGGAAATTTGGGGGTAAAATGGTAATTTTGTA-AA-GTTTGGGGT
1 -AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTT-TAGAAGGTTCGGGGT
* *
173428 CAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAT-GTAATTTTTAGAAGGTTCGAGGTT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCG-GGGT
*
173486 AAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAA
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAA
173534 AGTTTAGGGT
Statistics
Matches: 252, Mismatches: 21, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
55 2 0.01
56 10 0.04
57 36 0.14
58 97 0.38
59 101 0.40
60 6 0.02
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.35
Consensus pattern (58 bp):
AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGT
Found at i:173818 original size:96 final size:96
Alignment explanation
Indices: 173644--173825 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
173634 GAGGACATTT
* ** **
173644 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAACATTTCGGGATCGAAGA
1 GATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAACATTTCGAAATCGAAGA
*
173709 TAAGGAAACATTGCCTCGATTAAGGGTATTC
66 TAAAGAAACATTGCCTCGATTAAGGGTATTC
* *
173740 GATTATTTCGATTCGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGAAATCTGAA
1 GATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAACA-TTTCGAAATC-GAA
*
173804 -ATAAA-AGAATATTGCCTCGATT
64 GATAAAGA-AACATTGCCTCGATT
173826 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 2 0.03
96 69 0.93
97 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (96 bp):
GATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAACATTTCGAAATCGAAGA
TAAAGAAACATTGCCTCGATTAAGGGTATTC
Found at i:174228 original size:58 final size:59
Alignment explanation
Indices: 174077--174586 Score: 674
Period size: 59 Copynumber: 8.7 Consensus size: 59
174067 GAAGGTTCGA
* ** * * *
174077 AAAAAAGGGATTTTTGGAAGTTTAAGGGTAAAATGGTAA-TTTTCGAAAGGTTCGGGGTA
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAG-AAGGTTTGGGGTC
* *
174136 AAAAATGGGGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGT-
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTC
* * * * *
174194 TAAATTGGGGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTC
*
174253 AAAAATGGGATTTTTGGAAATTTGGGGGTAAAATGGTAATTTTGTA-AA-GTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTT-TAGAAGGTTTGGGGTC
* * *
174311 -AAAATGGGATTTTTGGAAGTTTGGGGGTAAAAT-GTAATTTTTAGAAGGTTCGAGGTT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTC
* * *
174368 AAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGTC
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTC
* * * *
174427 -AAAATGGGATTTTTTGAAATTTAGGGGTAAAATGATAATTTTTAGAAGGTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTC
* * *
174485 AAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGTC
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTC
* * * *
174544 AAAAATGGTATTTTTGGAAATTCGAGGGTAAAATGGTAATTTT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTT
174587 GGGGAGTTTA
Statistics
Matches: 403, Mismatches: 40, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
55 2 0.00
56 10 0.02
57 39 0.10
58 148 0.37
59 198 0.49
60 6 0.01
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.36
Consensus pattern (59 bp):
AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTC
Found at i:174235 original size:117 final size:117
Alignment explanation
Indices: 174078--174587 Score: 679
Period size: 117 Copynumber: 4.4 Consensus size: 117
174068 AAGGTTCGAA
* ** *
174078 AAAAAGGGATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTCGA-AAGGTTCGGGGTAAAAAAT
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTT-GAGAAGGTTCGGGGTCAAAAAT
* * * ** *
174142 GGGGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTT
65 GGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGTC
* * * *
174195 AAATTGGGGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTG-GAAAGTTTGGGGTCAAAAAT
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAA-TTTTGAGAAGGTTCGGGGTCAAAAAT
* * *
174259 GGGATTTTTGGAAATTTGGGGGTAAAATGGTAA-TTTT-GTAAAGTTTGGGGTC
65 GGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAG-AAAGTTTAGGGTC
* * *
174311 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAAT-GTAATTTTTAGAAGGTTCGAGGTTAAAAATG
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTGAGAAGGTTCGGGGTCAAAAATG
174375 GGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGTC
66 GGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGTC
* * * * * *
174427 AAAATGGGATTTTTTGAAATTTAGGGGTAAAATGATAATTTTTAGAAGGTTTGGGGTCAAAAATG
1 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTGAGAAGGTTCGGGGTCAAAAATG
174492 GGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGTC
66 GGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGTC
* * * *
174544 AAAAATGGTATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTG
1 -AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTG
174588 GGGAGTTTAA
Statistics
Matches: 348, Mismatches: 37, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
114 4 0.01
115 52 0.15
116 91 0.26
117 161 0.46
118 40 0.11
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.36
Consensus pattern (117 bp):
AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTGAGAAGGTTCGGGGTCAAAAATG
GGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGTC
Found at i:174379 original size:882 final size:872
Alignment explanation
Indices: 172677--174432 Score: 3422
Period size: 882 Copynumber: 2.0 Consensus size: 872
172667 CTACGTCCAG
172677 TGAGTTAGGACACGACATTTCAAGATCCAGAAATAATGAGCTTTCCTTTGTAAAACCTTTTGAAA
1 TGAGTTAGGACACGACATTTCAAGATCCAGAAATAATGAGCTTTCCTTTGTAAAACCTTTTGAAA
172742 CTTTTGCGATGAGGACATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCG
66 CTTTTGCGATGAGGACATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCG
172807 CAACATTTCGGGATCGAAGATAAGGAAACATTGCCTCGATTAAGGGTATTCGATTATTTCGATTC
131 CAACATTTCGGGATCGAAGATAAGGAAACATTGCCTCGATTAAGGGTATTCGATTATTTCGATTC
172872 GAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAAATTTTCGAAATCTGAAATAAAAGAATATTGC
196 GAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAAATTTTCGAAATCTGAAATAAAAGAATATTGC
172937 CTCGATTTTAAAGTTTTTATGAAAAAAAATAATTTCGAAAACAAGCATGCGAGTTTAACAAGAAT
261 CTCGATTTTAAAGTTTTTATGAAAAAAAATAATTTCGAAAACAAGCATGCGAGTTTAACAAGAAT
173002 AAGCAGTCAAAGATGGATATTAAATAACGCGAAGCAAAATAAATGAGAGGACGAGTTATTCACGA
326 AAGCAGTCAAAGATGGATATTAAATAACGCGAAGCAAAATAAATGAGAGGACGAGTTATTCACGA
173067 AAGAAAACAAGGATGCAAAATGCAAGCGCAAAAAAAAAGTTAATGAGAGAGAAGAATGATGTAAT
391 AAGAAAACAAGGATGCAAAATGCAAGCGCAAAAAAAAAGTTAATGAGAGAGAAGAATGATGTAAT
173132 CTGAGTTCAAAACGAGACTTTTTGGATGCACGGGGTGCAAAATGGTAGTTTTGGAAGGTTCGAAA
456 CTGAGTTCAAAACGAGACTTTTTGGATGCACGGGGTGCAAAATGGTAGTTTTGGAAGGTTCGAAA
173197 AAAAGGGATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTCGAAAGGTTCGGGGTAAAAAATGG
521 AAAAGGGATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTCGAAAGGTTCGGGGTAAAAAATGG
173262 GGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTTAAATTGGGGTTTTT
586 GGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTTAAATTGGGGTTTTT
173327 GGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGGATTTTTGGAAAT
651 GGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGGATTTTTGGAAAT
173392 TTGGGGGTAAAATGGTAATTTTGTAAAGTTTGGGGTCAAAATGGGATTTTTGGAAGTTTGGGGGT
716 TTGGGGGTAAAATGGTAATTTTGTAAAGTTTGGGGTCAAAATGGGATTTTTGGAAGTTTGGGGGT
173457 AAAATGTAATTTTTAGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGG
781 AAAATGTAATTTTTAGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGG
173522 TAATTTTTAGAAAGTTTAGGGTCAAAA
846 TAATTTTTAGAAAGTTTAGGGTCAAAA
173549 NNNNNNNNNNTGAGTTAGGACACGACATTTCAAGATCCAGAAATAATGAGCTTTCCTTTGTAAAA
1 ----------TGAGTTAGGACACGACATTTCAAGATCCAGAAATAATGAGCTTTCCTTTGTAAAA
173614 CCTTTTGAAACTTTTGCGATGAGGACATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTA
56 CCTTTTGAAACTTTTGCGATGAGGACATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTA
173679 AGTTAAGGCGCAACATTTCGGGATCGAAGATAAGGAAACATTGCCTCGATTAAGGGTATTCGATT
121 AGTTAAGGCGCAACATTTCGGGATCGAAGATAAGGAAACATTGCCTCGATTAAGGGTATTCGATT
173744 ATTTCGATTCGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAAATTTTCGAAATCTGAAATAAA
186 ATTTCGATTCGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAAATTTTCGAAATCTGAAATAAA
173809 AGAATATTGCCTCGATTTTAAAGTTTTTATGAAAAAAAATAATTTCGAAAACAAGCATGCGAGTT
251 AGAATATTGCCTCGATTTTAAAGTTTTTATGAAAAAAAATAATTTCGAAAACAAGCATGCGAGTT
173874 TAACAAGAATAAGCAGTCAAAGATGGATATTAAATAACGCGAAGCAAAATAAATGAGAGGACGAG
316 TAACAAGAATAAGCAGTCAAAGATGGATATTAAATAACGCGAAGCAAAATAAATGAGAGGACGAG
173939 TTATTCACGAAAGAAAACAAGGATGCAAAATGCAAGCGCAAAAAAAAAGTTAATGAGAGAGAAGA
381 TTATTCACGAAAGAAAACAAGGATGCAAAATGCAAGCGCAAAAAAAAAGTTAATGAGAGAGAAGA
174004 ATGATGTAATCTGAGTTCAAAACGAGACTTTTTGGATGCACGGGGTGCAAAATGGTAGTTTTGGA
446 ATGATGTAATCTGAGTTCAAAACGAGACTTTTTGGATGCACGGGGTGCAAAATGGTAGTTTTGGA
174069 AGGTTCGAAAAAAAGGGATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTCGAAAGGTTCGGGG
511 AGGTTCGAAAAAAAGGGATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTCGAAAGGTTCGGGG
174134 TAAAAAATGGGGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTTAAAT
576 TAAAAAATGGGGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTTAAAT
174199 TGGGGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGGAT
641 TGGGGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGGAT
174264 TTTTGGAAATTTGGGGGTAAAATGGTAATTTTGTAAAGTTTGGGGTCAAAATGGGATTTTTGGAA
706 TTTTGGAAATTTGGGGGTAAAATGGTAATTTTGTAAAGTTTGGGGTCAAAATGGGATTTTTGGAA
174329 GTTTGGGGGTAAAATGTAATTTTTAGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTTAGG
771 GTTTGGGGGTAAAATGTAATTTTTAGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTTAGG
174394 GGTAAAATGGTAATTTTTAGAAAGTTTAGGGTCAAAA
836 GGTAAAATGGTAATTTTTAGAAAGTTTAGGGTCAAAA
174431 TG
1 TG
174433 GGATTTTTTG
Statistics
Matches: 874, Mismatches: 0, Indels: 10
0.99 0.00 0.01
Matches are distributed among these distances:
872 2 0.00
882 872 1.00
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.30
Consensus pattern (872 bp):
TGAGTTAGGACACGACATTTCAAGATCCAGAAATAATGAGCTTTCCTTTGTAAAACCTTTTGAAA
CTTTTGCGATGAGGACATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCG
CAACATTTCGGGATCGAAGATAAGGAAACATTGCCTCGATTAAGGGTATTCGATTATTTCGATTC
GAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAAATTTTCGAAATCTGAAATAAAAGAATATTGC
CTCGATTTTAAAGTTTTTATGAAAAAAAATAATTTCGAAAACAAGCATGCGAGTTTAACAAGAAT
AAGCAGTCAAAGATGGATATTAAATAACGCGAAGCAAAATAAATGAGAGGACGAGTTATTCACGA
AAGAAAACAAGGATGCAAAATGCAAGCGCAAAAAAAAAGTTAATGAGAGAGAAGAATGATGTAAT
CTGAGTTCAAAACGAGACTTTTTGGATGCACGGGGTGCAAAATGGTAGTTTTGGAAGGTTCGAAA
AAAAGGGATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTCGAAAGGTTCGGGGTAAAAAATGG
GGTTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTTAAATTGGGGTTTTT
GGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGGATTTTTGGAAAT
TTGGGGGTAAAATGGTAATTTTGTAAAGTTTGGGGTCAAAATGGGATTTTTGGAAGTTTGGGGGT
AAAATGTAATTTTTAGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGG
TAATTTTTAGAAAGTTTAGGGTCAAAA
Found at i:176911 original size:37 final size:38
Alignment explanation
Indices: 176836--176911 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
176826 TATATTCTAA
* * *
176836 TTTTATTTTTTTTACGATTTAATCCCTAAAATTCAAAT
1 TTTTATTTATTTTACAATTTAATCCCTAAAAGTCAAAT
*
176874 TTTTA-TTATTTTACAATTTAATTCCTCAAAAGT-AAAT
1 TTTTATTTATTTTACAATTTAATCCCT-AAAAGTCAAAT
176911 T
1 T
176912 ATTCAATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 23 0.70
38 10 0.30
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (38 bp):
TTTTATTTATTTTACAATTTAATCCCTAAAAGTCAAAT
Found at i:176983 original size:26 final size:26
Alignment explanation
Indices: 176943--176993 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
176933 CATTGGTTTT
*
176943 TTTAACTTTCGTTACCCTTAACCAAC
1 TTTAACTTTCATTACCCTTAACCAAC
*
176969 TTTAACTTTTATTACCCTTAACCAA
1 TTTAACTTTCATTACCCTTAACCAA
176994 ATAATGATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.41
Consensus pattern (26 bp):
TTTAACTTTCATTACCCTTAACCAAC
Found at i:180300 original size:24 final size:24
Alignment explanation
Indices: 180266--180317 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
180256 TTTTTAGAAG
*
180266 ATTTAATATTTATTAATATAATAT
1 ATTTAACATTTATTAATATAATAT
* *
180290 ATTTAACATTTATTAGTATAATTT
1 ATTTAACATTTATTAATATAATAT
180314 ATTT
1 ATTT
180318 GACCTACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTAACATTTATTAATATAATAT
Found at i:181406 original size:48 final size:48
Alignment explanation
Indices: 181292--181387 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
181282 AATTGGACAA
181292 AGAGGGTACATCAGGATGAGGGATTGAACGGGCATCATGCATGCTTAG
1 AGAGGGTACATCAGGATGAGGGATTGAACGGGCATCATGCATGCTTAG
181340 AGAGGGTACATCAGGATGAGGGATTGAACGGGCATCATGCATGCTTAG
1 AGAGGGTACATCAGGATGAGGGATTGAACGGGCATCATGCATGCTTAG
181388 GTTTGGGATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.21
Consensus pattern (48 bp):
AGAGGGTACATCAGGATGAGGGATTGAACGGGCATCATGCATGCTTAG
Found at i:186961 original size:31 final size:30
Alignment explanation
Indices: 186922--187022 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 30
186912 TTTACCCAAT
186922 TTTG-TACCTAAACTTGACACTTTTTTCTAA
1 TTTGATACCTAAACTTGACA-TTTTTTCTAA
* *
186952 TTTGATACCTAAACTT---TTTTTTATCCAA
1 TTTGATACCTAAACTTGACATTTTT-TCTAA
* *
186980 TTTGGTACATAAACTTGACATTTTTTCTTAA
1 TTTGATACCTAAACTTGACATTTTTTC-TAA
187011 TTTGATACCTAA
1 TTTGATACCTAA
187023 GCTTTTTTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
27 5 0.09
28 18 0.32
30 6 0.11
31 28 0.49
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.48
Consensus pattern (30 bp):
TTTGATACCTAAACTTGACATTTTTTCTAA
Found at i:186980 original size:59 final size:59
Alignment explanation
Indices: 186883--187031 Score: 196
Period size: 59 Copynumber: 2.5 Consensus size: 59
186873 AATTTGATAT
* * * * *
186883 TTTTTTTTTAATTT-AGTACTTAATC-TTTTTTTACCCAATTTTGTACCTAAACTTGACA
1 TTTTTTCTTAATTTGA-TACCTAAACTTTTTTTTACCCAATTTGGTACATAAACTTGACA
*
186941 CTTTTTTC-TAATTTGATACCTAAACTTTTTTTTATCCAATTTGGTACATAAACTTGACA
1 -TTTTTTCTTAATTTGATACCTAAACTTTTTTTTACCCAATTTGGTACATAAACTTGACA
*
187000 TTTTTTCTTAATTTGATACCTAAGCTTTTTTT
1 TTTTTTCTTAATTTGATACCTAAACTTTTTTT
187032 AAGATTCAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
58 20 0.25
59 60 0.75
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (59 bp):
TTTTTTCTTAATTTGATACCTAAACTTTTTTTTACCCAATTTGGTACATAAACTTGACA
Found at i:186982 original size:28 final size:27
Alignment explanation
Indices: 186942--187031 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 27
186932 AACTTGACAC
186942 TTTTTTCTAATTTGATACCTAAACTTT
1 TTTTTTCTAATTTGATACCTAAACTTT
* * * *
186969 TTTTTATCCAATTTGGTACATAAACTTGACA
1 TTTTT-TCTAATTTGATACCTAAACTT---T
*
187000 TTTTTTCTTAATTTGATACCTAAGCTTT
1 TTTTTTC-TAATTTGATACCTAAACTTT
187028 TTTT
1 TTTT
187032 AAGATTCAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
27 5 0.10
28 22 0.45
30 2 0.04
31 20 0.41
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53
Consensus pattern (27 bp):
TTTTTTCTAATTTGATACCTAAACTTT
Found at i:188269 original size:22 final size:22
Alignment explanation
Indices: 188230--188271 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
188220 TAAAAAATTC
*
188230 AAAAAAATATTAATAATTTATA
1 AAAAAAATATTAAAAATTTATA
188252 AAAAAAAT-TTATAAAATTTA
1 AAAAAAATATTA-AAAATTTA
188272 AGGAAACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAAAATATTAAAAATTTATA
Found at i:188856 original size:16 final size:16
Alignment explanation
Indices: 188835--188881 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
188825 TGAATTATTG
*
188835 ATTACAATTTTATTTC
1 ATTACAATTTTATTCC
*
188851 ATTACAGA-CTTATTCC
1 ATTACA-ATTTTATTCC
*
188867 ATTACAATTATATTC
1 ATTACAATTTTATTC
188882 AATTCTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTACAATTTTATTCC
Found at i:196043 original size:13 final size:13
Alignment explanation
Indices: 196027--196090 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
196017 CCATAAACAC
196027 AAATCCTAAACCT
1 AAATCCTAAACCT
*
196040 AAATACTAAACCCT
1 AAATCCTAAA-CCT
196054 -AAT-CTCAAACCT
1 AAATCCT-AAACCT
*
196066 CAAATCTTAAATCCT
1 -AAATCCTAAA-CCT
196081 AAATCC-AAAC
1 AAATCCTAAAC
196091 AAACCCCAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
12 6 0.14
13 18 0.43
14 14 0.33
15 4 0.10
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATCCTAAACCT
Found at i:196081 original size:27 final size:26
Alignment explanation
Indices: 196027--196090 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
196017 CCATAAACAC
196027 AAATCCTAAACCTAAATACTAAACCCT
1 AAATCC-AAACCTAAATACTAAACCCT
*
196054 -AATCTCAAACCTCAAAT-CTTAAATCCT
1 AAATC-CAAACCT-AAATAC-TAAACCCT
196081 AAATCCAAAC
1 AAATCCAAAC
196091 AAACCCCAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 11 0.34
27 17 0.53
28 4 0.12
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (26 bp):
AAATCCAAACCTAAATACTAAACCCT
Done.