Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015911.1 Corchorus olitorius cultivar O-4 contig15944, 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: 99431
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:1298 original size:29 final size:29
Alignment explanation
Indices: 1262--1322 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
1252 GCATCCATGT
* *
1262 TTAAATTTTATACTTCTTTAGGTTGTTAA
1 TTAAATTTTATACCTCTTCAGGTTGTTAA
*
1291 TTAAATTTTATACCTCTTCATGTTGTTAA
1 TTAAATTTTATACCTCTTCAGGTTGTTAA
1320 TTA
1 TTA
1323 TGCCATGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (29 bp):
TTAAATTTTATACCTCTTCAGGTTGTTAA
Found at i:8206 original size:136 final size:140
Alignment explanation
Indices: 8044--8412 Score: 458
Period size: 136 Copynumber: 2.6 Consensus size: 140
8034 TTCAAAATCA
* * *
8044 AAAATCTTGCTCAAGGTCGAGTTTGCATTTGTAAGTCCTCCTGGCTCAATTTCAGAAACCTCCGG
1 AAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGTCCTCCGGGCACAATTTCAGAAACCTCCGG
* * * * * * **
8109 GTATTAATTCTGATAAATCCTTCGGGTTTCATTTCATTTCATCAAG-TTCAA-CAAGGTTGTGTT
66 GTATTAATTCTGATAAATCCTCCAGGTATCATCTCATTTCATCAAGTTTCAATCAAAGTCGCATT
8172 TAAG-TT-TC
131 TAAGTTTATC
* * * **
8180 AAAACCTTGCTTAAGGTTGAGTTTGCATTTGTAAGTCCTCCGGGCACCATTTCAGAAACCTTTGG
1 AAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGTCCTCCGGGCACAATTTCAGAAACCTCCGG
*
8245 GTATTAATTCTGATAAATCCTCCAGGTATCATCTCATTTCATCAAGTTTTTAATCAAAGTCGCAT
66 GTATTAATTCTGATAAATCCTCCAGGTATCATCTCATTTCATCAAG-TTTCAATCAAAGTCGCAT
8310 TTAAGTTTCAAAGTC
130 TTAAGTTT---A-TC
* * *
8325 AAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTACGGGCACAATATCAGAAACCTCCGG
1 AAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGTCCTCCGGGCACAATTTCAGAAACCTCCGG
* * *
8390 GTGTTAATTCTGACAAGTCCTCC
66 GTATTAATTCTGATAAATCCTCC
8413 GGGCATTCTA
Statistics
Matches: 196, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
136 99 0.51
138 4 0.02
139 12 0.06
140 2 0.01
145 79 0.40
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (140 bp):
AAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGTCCTCCGGGCACAATTTCAGAAACCTCCGG
GTATTAATTCTGATAAATCCTCCAGGTATCATCTCATTTCATCAAGTTTCAATCAAAGTCGCATT
TAAGTTTATC
Found at i:8548 original size:40 final size:40
Alignment explanation
Indices: 8501--8879 Score: 419
Period size: 40 Copynumber: 9.6 Consensus size: 40
8491 AGTCAATTTT
*
8501 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAG
*
8541 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAG
* *
8581 AACCCTACTT-AGGATCATTGCTTTATCAAATTAA--TCAC
1 AATCCTA-TTCAGGATCATTGCTTTATCAAATTAATTTCAG
* *
8619 AATCCTACTCAGTATCATTGCTTTATCAAATTAATTTCAG
1 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAG
* * *
8659 AATCCTATTCAAGATTATTGCTTTATCAGATTAATTTCAG
1 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAG
* ** * *** * *
8699 AATCATGCTCAGGATCATTTCTTTA-CCGGTCAA--TCAC
1 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAG
* * ** *
8736 AATCCTACTCAGGATCATTGCTTTTTCAGGTGAATTTCAG
1 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAG
* * * *
8776 AATCCTAATCAGGATCATTGCTTTATCAGATTGATTTCAA
1 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAG
* * * *
8816 AATCCTACTCGGGATCATTGCTTTATCAAGTGAATTTCAG
1 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAG
*
8856 AATCCTATTTAGGATCATTGCTTT
1 AATCCTATTCAGGATCATTGCTTT
8880 TCGAATCCTA
Statistics
Matches: 288, Mismatches: 44, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
37 25 0.09
38 38 0.13
39 5 0.02
40 218 0.76
41 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (40 bp):
AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAG
Found at i:8796 original size:117 final size:118
Alignment explanation
Indices: 8501--8879 Score: 481
Period size: 117 Copynumber: 3.2 Consensus size: 118
8491 AGTCAATTTT
* *
8501 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAAAATCCTATTCAGGATCATTGCTTTA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTATTCAGGATCATTGCTTTA
* * * *
8566 TCAAATTAATTTCAAAACCCTACTTAGGATCATTGCTTTATCAAATTAATCAC
66 TCAGATTAATTTCAAAATCCTACTCAGGATCATTGCTTTATCAAATCAATCAC
* * *
8619 AATCCTACTCAGTATCATTGCTTTATCAAATTAATTTCAGAATCCTATTCAAGATTATTGCTTTA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTATTCAGGATCATTGCTTTA
* * * * ***
8684 TCAGATTAATTTCAGAATCATGCTCAGGATCATTTCTTTA-CCGGTCAATCAC
66 TCAGATTAATTTCAAAATCCTACTCAGGATCATTGCTTTATCAAATCAATCAC
* ** * *
8736 AATCCTACTCAGGATCATTGCTTTTTCAGGTGAATTTCAGAATCCTAATCAGGATCATTGCTTTA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTATTCAGGATCATTGCTTTA
* * * * *
8801 TCAGATTGATTTCAAAATCCTACTCGGGATCATTGCTTTATCAAGTGAATTTCAG
66 TCAGATTAATTTCAAAATCCTACTCAGGATCATTGCTTTATCAAATCAA--TCAC
* *
8856 AATCCTATTTAGGATCATTGCTTT
1 AATCCTACTCAGGATCATTGCTTT
8880 TCGAATCCTA
Statistics
Matches: 222, Mismatches: 36, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
117 99 0.45
118 98 0.44
120 25 0.11
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (118 bp):
AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTATTCAGGATCATTGCTTTA
TCAGATTAATTTCAAAATCCTACTCAGGATCATTGCTTTATCAAATCAATCAC
Found at i:8885 original size:27 final size:27
Alignment explanation
Indices: 8850--8961 Score: 156
Period size: 27 Copynumber: 4.1 Consensus size: 27
8840 ATCAAGTGAA
8850 TTTCAGAATCCTATTTAGGATCATTGCT
1 TTTCAGAATCCTATTTAGGATCATTG-T
*
8878 TTTC-GAATCCTATTCAGGATCATTGCT
1 TTTCAGAATCCTATTTAGGATCATTG-T
*
8905 TTCTCA-AATGCTATTTAGGATCATTGT
1 TT-TCAGAATCCTATTTAGGATCATTGT
*
8932 TTTCTGAATCCTATTTAGGATCATTGT
1 TTTCAGAATCCTATTTAGGATCATTGT
8959 TTT
1 TTT
8962 ATCAGTTAAT
Statistics
Matches: 76, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
26 2 0.03
27 50 0.66
28 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (27 bp):
TTTCAGAATCCTATTTAGGATCATTGT
Found at i:8999 original size:39 final size:39
Alignment explanation
Indices: 8937--9012 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
8927 ATTGTTTTCT
* * *
8937 GAATCCTATTTAGGATCATTGTTTTATCAGTTAATTTAA
1 GAATCCTATTCAGGATCAATGTTTTATCAGTGAATTTAA
* * *
8976 GAATCCTGTTCAGGGTCAATGTTTTCTCAGTGAATTT
1 GAATCCTATTCAGGATCAATGTTTTATCAGTGAATTT
9013 CAAAGTCTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (39 bp):
GAATCCTATTCAGGATCAATGTTTTATCAGTGAATTTAA
Found at i:16803 original size:29 final size:29
Alignment explanation
Indices: 16764--16824 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
16754 GCATCCATGT
* *
16764 TTAAATTTTATACTTCTTTATGTTGTTAA
1 TTAAATGTTATACTTCTTCATGTTGTTAA
16793 TTAAATGTTATACTTCTTCATGTTGTTAA
1 TTAAATGTTATACTTCTTCATGTTGTTAA
16822 TTA
1 TTA
16825 TGCCATGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (29 bp):
TTAAATGTTATACTTCTTCATGTTGTTAA
Found at i:22165 original size:18 final size:18
Alignment explanation
Indices: 22142--22206 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 18
22132 AATAAATATG
22142 CAAAACAAAAAACAAAAA
1 CAAAACAAAAAACAAAAA
22160 CAAAAC-AAAAACAAAAA
1 CAAAACAAAAAACAAAAA
**
22177 -AAGGCAAAAAA-ACAAAA
1 CAAAACAAAAAACA-AAAA
*
22194 GAAAACGAAAAAA
1 CAAAAC-AAAAAA
22207 GAAGTAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 4 0.10
17 20 0.51
18 9 0.23
19 6 0.15
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (18 bp):
CAAAACAAAAAACAAAAA
Found at i:22166 original size:11 final size:11
Alignment explanation
Indices: 22150--22175 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
22140 TGCAAAACAA
22150 AAAACAAAAAC
1 AAAACAAAAAC
22161 AAAACAAAAAC
1 AAAACAAAAAC
22172 AAAA
1 AAAA
22176 AAAGGCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAC
Found at i:22193 original size:6 final size:6
Alignment explanation
Indices: 22143--22176 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
22133 ATAAATATGC
22143 AAAACAA AAAACA AAAAC- AAAACA AAAACA AAAA
1 AAAAC-A AAAACA AAAACA AAAACA AAAACA AAAA
22177 AAGGCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.62
7 5 0.19
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:22198 original size:10 final size:9
Alignment explanation
Indices: 22148--22206 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
22138 TATGCAAAAC
22148 AAAAAACAA
1 AAAAAACAA
*
22157 AAACAA-AA
1 AAAAAACAA
*
22165 CAAAAACAA
1 AAAAAACAA
*
22174 AAAAAGGC-A
1 AAAAA-ACAA
22183 AAAAAACAA
1 AAAAAACAA
22192 AAGAAAACGAA
1 AA-AAAAC-AA
22203 AAAA
1 AAAA
22207 GAAGTAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
8 7 0.18
9 20 0.51
10 8 0.21
11 4 0.10
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:23633 original size:147 final size:145
Alignment explanation
Indices: 23378--23764 Score: 576
Period size: 147 Copynumber: 2.7 Consensus size: 145
23368 TTTGGTAAGT
* *
23378 TTTTTAGCAAAGTTGTGTTTAAGTTTCAAAATCAAAAAACCTTGCTCAAGGTCGAGTTTGCATTT
1 TTTTTAACAAAGCTGTGTTTAAGTTTCAAAATC-AAAAACCTTGCTCAAGGTCGAGTTTGCATTT
* * * *
23443 GTATGTCCTCCGGACTCCATTTCAGAAACCTCCAGGTATTAATTCTGATAAATCCTCTGGGTATC
65 GTAAGTCCTCCGGGCTCCATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATC
23508 ATTTTCATTTCATCAAG
130 A-TTTCATTTCATCAAG
23525 TTTTTAATCAAAGCTGTGTTTAAGTTTCAAAATCAAAAACCTTGCTCAAGGTCGAGTTTGCATTT
1 TTTTTAA-CAAAGCTGTGTTTAAGTTTCAAAATCAAAAACCTTGCTCAAGGTCGAGTTTGCATTT
*
23590 GTAAGTCCTCCGGGCTCCATTTCAGAAAACTCCGGGTATTAATTCTGATAAATCCTCCGGGTATC
65 GTAAGTCCTCCGGGCTCCATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATC
23655 ATTTCATTTCATCAAG
130 ATTTCATTTCATCAAG
* * *
23671 --TTCAACAAGGCTGTGTTTAAG-TT-----TC-AAAACCTTGCTCAAGGTTGAGTTTGCATTTG
1 TTTTTAACAAAGCTGTGTTTAAGTTTCAAAATCAAAAACCTTGCTCAAGGTCGAGTTTGCATTTG
* *
23727 TAAGTCCTCCGGGCACCATTTTAGAAACCTCCGGGTAT
66 TAAGTCCTCCGGGCTCCATTTCAGAAACCTCCGGGTAT
23765 CATCTCATTT
Statistics
Matches: 226, Mismatches: 13, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
136 65 0.29
137 2 0.01
142 2 0.01
143 15 0.07
144 4 0.02
146 15 0.07
147 98 0.43
148 25 0.11
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (145 bp):
TTTTTAACAAAGCTGTGTTTAAGTTTCAAAATCAAAAACCTTGCTCAAGGTCGAGTTTGCATTTG
TAAGTCCTCCGGGCTCCATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCA
TTTCATTTCATCAAG
Found at i:23765 original size:111 final size:115
Alignment explanation
Indices: 23643--23882 Score: 310
Period size: 120 Copynumber: 2.1 Consensus size: 115
23633 TCTGATAAAT
* * *
23643 CCTCCGGGTATCATTTCATTTCATCAAG-TTCAA-C-AAGGCTGTGTTTAAG-TT-TCAAAACCT
1 CCTCCGGGTATCATCTCATTTCATCAAGTTTCAATCAAAGTC-GTATTTAAGTTTATCAAAACCT
* * * *
23703 TGCTCAAGGTTGAGTTTGCATTTGTAAGTCCTCCGGGCACCATTTTAGAAA
65 TGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAA
*
23754 CCTCCGGGTATCATCTCATTTCATCAAGTTTTTAATCAAAGTCGTATTTAAGTTTCAAAGTCAAA
1 CCTCCGGGTATCATCTCATTTCATCAAG-TTTCAATCAAAGTCGTATTTAAGTTT---A-TCAAA
*
23819 ACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGTGCACAATTTCAGAAA
61 ACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAA
23874 CCTCCGGGT
1 CCTCCGGGT
23883 GTTAATTCTG
Statistics
Matches: 110, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
111 27 0.25
113 4 0.04
114 9 0.08
115 6 0.05
120 64 0.58
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (115 bp):
CCTCCGGGTATCATCTCATTTCATCAAGTTTCAATCAAAGTCGTATTTAAGTTTATCAAAACCTT
GCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAA
Found at i:24044 original size:40 final size:40
Alignment explanation
Indices: 23992--24337 Score: 360
Period size: 40 Copynumber: 8.8 Consensus size: 40
23982 AGTAAATTTT
* *
23992 AATCCTATTCAGGATCATTACTTTATCAAATTAATTTCAA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
24032 AATCCTACTCAGGATCATTGCTTTATCAAATTAA--TCAC
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
24070 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAT
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * * * *
24110 AATCCTATTCAGGATTATTGCTTTGTCAGATTAATTTCAG
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * * *** * *
24150 AATCATGCTCAGGATCATTTCTTTA-CCGGTCAA--TCAC
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * ** * *
24187 AATCGTACTCAGGATCTTTGCTTTATCAGGTGAATTTCAG
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * *
24227 AATCCTATTCAGGATCATTGCTTTATCAGATTGATTTCAA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * * * *
24267 AATCATACTCGGGATCATTGCTTTATCAAGTGAATTTCAT
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
24307 AATCCTATTCAGGATCATTGCTTTCTCAAAT
1 AATCCTACTCAGGATCATTGCTTTATCAAAT
24338 GCTATTTAGG
Statistics
Matches: 255, Mismatches: 46, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
37 24 0.09
38 43 0.17
39 5 0.02
40 183 0.72
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (40 bp):
AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
Found at i:24231 original size:117 final size:118
Alignment explanation
Indices: 23992--24338 Score: 444
Period size: 117 Copynumber: 2.9 Consensus size: 118
23982 AGTAAATTTT
* * *
23992 AATCCTATTCAGGATCATTACTTTATCAAATTAATTTCAAAATCCTACTCAGGATCATTGCTTTA
1 AATCCTATTCAGGATCATTGCTTTATCAGATTAATTTCAAAATCATACTCAGGATCATTGCTTTA
* * *
24057 TCAAATTAATCACAATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAT
66 TCAAATCAATCACAATCCTACTCAGGATCATTGCTTTATCAAATGAATTTCAG
* * * * *
24110 AATCCTATTCAGGATTATTGCTTTGTCAGATTAATTTCAGAATCATGCTCAGGATCATTTCTTTA
1 AATCCTATTCAGGATCATTGCTTTATCAGATTAATTTCAAAATCATACTCAGGATCATTGCTTTA
*** * * **
24175 -CCGGTCAATCACAATCGTACTCAGGATCTTTGCTTTATCAGGTGAATTTCAG
66 TCAAATCAATCACAATCCTACTCAGGATCATTGCTTTATCAAATGAATTTCAG
* *
24227 AATCCTATTCAGGATCATTGCTTTATCAGATTGATTTCAAAATCATACTCGGGATCATTGCTTTA
1 AATCCTATTCAGGATCATTGCTTTATCAGATTAATTTCAAAATCATACTCAGGATCATTGCTTTA
* * * * *
24292 TCAAGTGAATTTCATAATCCTATTCAGGATCATTGCTTTCTCAAATG
66 TCAAATCAA--TCACAATCCTACTCAGGATCATTGCTTTATCAAATG
24339 CTATTTAGGA
Statistics
Matches: 191, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
117 100 0.52
118 62 0.32
120 29 0.15
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (118 bp):
AATCCTATTCAGGATCATTGCTTTATCAGATTAATTTCAAAATCATACTCAGGATCATTGCTTTA
TCAAATCAATCACAATCCTACTCAGGATCATTGCTTTATCAAATGAATTTCAG
Found at i:24342 original size:28 final size:27
Alignment explanation
Indices: 24307--24436 Score: 179
Period size: 28 Copynumber: 4.7 Consensus size: 27
24297 TGAATTTCAT
*
24307 AATCCTATTCAGGATCATTGCTTTCTCA
1 AATCCTATTTAGGATCATTGCTTTCT-A
* * *
24335 AATGCTATTTAGGATCATTGTTTTCTG
1 AATCCTATTTAGGATCATTGCTTTCTA
24362 AATCCTATTTAGGATCATTGCTTTCTCA
1 AATCCTATTTAGGATCATTGCTTTCT-A
* * *
24390 AATGCTATTTAGGATCATTGTTTTCTG
1 AATCCTATTTAGGATCATTGCTTTCTA
24417 AATCCTATTTAGGATCATTG
1 AATCCTATTTAGGATCATTG
24437 TTTTATCAGT
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
27 43 0.48
28 47 0.52
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.44
Consensus pattern (27 bp):
AATCCTATTTAGGATCATTGCTTTCTA
Found at i:24391 original size:55 final size:55
Alignment explanation
Indices: 24307--24436 Score: 251
Period size: 55 Copynumber: 2.4 Consensus size: 55
24297 TGAATTTCAT
*
24307 AATCCTATTCAGGATCATTGCTTTCTCAAATGCTATTTAGGATCATTGTTTTCTG
1 AATCCTATTTAGGATCATTGCTTTCTCAAATGCTATTTAGGATCATTGTTTTCTG
24362 AATCCTATTTAGGATCATTGCTTTCTCAAATGCTATTTAGGATCATTGTTTTCTG
1 AATCCTATTTAGGATCATTGCTTTCTCAAATGCTATTTAGGATCATTGTTTTCTG
24417 AATCCTATTTAGGATCATTG
1 AATCCTATTTAGGATCATTG
24437 TTTTATCAGT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 74 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.44
Consensus pattern (55 bp):
AATCCTATTTAGGATCATTGCTTTCTCAAATGCTATTTAGGATCATTGTTTTCTG
Found at i:24437 original size:27 final size:28
Alignment explanation
Indices: 24307--24440 Score: 191
Period size: 27 Copynumber: 4.9 Consensus size: 28
24297 TGAATTTCAT
* *
24307 AATCCTATTCAGGATCATTGCTTTCTCA
1 AATCCTATTTAGGATCATTGTTTTCTCA
* *
24335 AATGCTATTTAGGATCATTGTTTTCT-G
1 AATCCTATTTAGGATCATTGTTTTCTCA
*
24362 AATCCTATTTAGGATCATTGCTTTCTCA
1 AATCCTATTTAGGATCATTGTTTTCTCA
* *
24390 AATGCTATTTAGGATCATTGTTTTCT-G
1 AATCCTATTTAGGATCATTGTTTTCTCA
24417 AATCCTATTTAGGATCATTGTTTT
1 AATCCTATTTAGGATCATTGTTTT
24441 ATCAGTTAAT
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
27 47 0.50
28 47 0.50
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (28 bp):
AATCCTATTTAGGATCATTGTTTTCTCA
Found at i:24478 original size:39 final size:39
Alignment explanation
Indices: 24411--24493 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
24401 GGATCATTGT
* * * *
24411 TTTCTGAATCCTATTTAGGATCATTGTTTTATCAGTTAA
1 TTTCAGAATCCTATTCAGGATCAATGTTTTATCAGTGAA
* * *
24450 TTTCAGAATCCTGTTCAGGGTCAATGTTTTCTCAGTGAA
1 TTTCAGAATCCTATTCAGGATCAATGTTTTATCAGTGAA
24489 TTTCA
1 TTTCA
24494 AAGTCTTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (39 bp):
TTTCAGAATCCTATTCAGGATCAATGTTTTATCAGTGAA
Found at i:27634 original size:29 final size:29
Alignment explanation
Indices: 27598--27658 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
27588 GCATCCATGT
27598 TTAAATTTTATACTTCTTTATGTTGTTAA
1 TTAAATTTTATACTTCTTTATGTTGTTAA
27627 TTAAATTTTATACTTCTTTATGTTGTTAA
1 TTAAATTTTATACTTCTTTATGTTGTTAA
27656 TTA
1 TTA
27659 TGCCATGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (29 bp):
TTAAATTTTATACTTCTTTATGTTGTTAA
Found at i:42754 original size:29 final size:29
Alignment explanation
Indices: 42703--42928 Score: 216
Period size: 29 Copynumber: 7.8 Consensus size: 29
42693 ACATAGAGTA
42703 TGCAAAAATGACCAAACTG-CCCTAGAATG
1 TGCAAAAATGACCAAA-TGCCCCTAGAATG
* *
42732 TG-TAAAATGACCATAATGCCCCT-GGATG
1 TGCAAAAATGACCA-AATGCCCCTAGAATG
***
42760 AATAAAAATGACCAAAATGCCCCTAG-ATG
1 TGCAAAAATGACC-AAATGCCCCTAGAATG
*
42789 TGCAAAAATGACCATAATACCCCTAG-ATG
1 TGCAAAAATGACCA-AATGCCCCTAGAATG
* *
42818 TGCAAAAATGACCAAACTGCTCC-AGAATA
1 TGCAAAAATGACCAAA-TGCCCCTAGAATG
42847 TGCAAAAATGACCAAAATGCCCCTA-AATG
1 TGCAAAAATGACC-AAATGCCCCTAGAATG
* * * *
42876 TGCAAAAATGACCAAAATACCTC-AAAATA
1 TGCAAAAATGACC-AAATGCCCCTAGAATG
42905 TGCAAAAATGACCAAAATGCCCCT
1 TGCAAAAATGACC-AAATGCCCCT
42929 GAGCGTGCGA
Statistics
Matches: 166, Mismatches: 19, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
28 22 0.13
29 138 0.83
30 6 0.04
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.19
Consensus pattern (29 bp):
TGCAAAAATGACCAAATGCCCCTAGAATG
Found at i:42797 original size:58 final size:59
Alignment explanation
Indices: 42703--42928 Score: 264
Period size: 58 Copynumber: 3.9 Consensus size: 59
42693 ACATAGAGTA
* * * * *
42703 TGCAAAAATGACCAAACTG-CCCTAGAATGTG-TAAAATGACCATAATGCCCCTGGATG
1 TGCAAAAATGACCAAAATGCCCCTAGAATATGCAAAAATGACCAAAATGCCCCTAGATG
*** * * *
42760 AATAAAAATGACCAAAATGCCCCTAG-ATGTGCAAAAATGACCATAATACCCCTAGATG
1 TGCAAAAATGACCAAAATGCCCCTAGAATATGCAAAAATGACCAAAATGCCCCTAGATG
* * *
42818 TGCAAAAATGACCAAACTGCTCC-AGAATATGCAAAAATGACCAAAATGCCCCTAAATG
1 TGCAAAAATGACCAAAATGCCCCTAGAATATGCAAAAATGACCAAAATGCCCCTAGATG
* * *
42876 TGCAAAAATGACCAAAATACCTC-AAAATATGCAAAAATGACCAAAATGCCCCT
1 TGCAAAAATGACCAAAATGCCCCTAGAATATGCAAAAATGACCAAAATGCCCCT
42929 GAGCGTGCGA
Statistics
Matches: 145, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
57 22 0.15
58 123 0.85
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.19
Consensus pattern (59 bp):
TGCAAAAATGACCAAAATGCCCCTAGAATATGCAAAAATGACCAAAATGCCCCTAGATG
Found at i:42826 original size:87 final size:84
Alignment explanation
Indices: 42703--42930 Score: 255
Period size: 87 Copynumber: 2.6 Consensus size: 84
42693 ACATAGAGTA
* * *
42703 TGCAAAAATGACCAAACT-GCCCTAGAATGTG-TAAAATGACCATAATGCCCCTGGATGAAT-AA
1 TGCAAAAATGACCAAA-TACCCCTAG-ATGTGCAAAAATGACCA-AATGCCCCTGAAT--ATCAA
*
42765 AAATGACCAAAATGCCCCTAGATG
61 AAATGACCAAAATGCCCCTAAATG
* *
42789 TGCAAAAATGACCATAATACCCCTAGATGTGCAAAAATGACCAAACTGCTCCAGAATATGCAAAA
1 TGCAAAAATGACCA-AATACCCCTAGATGTGCAAAAATGACCAAA-TGCCCCTGAATAT-CAAAA
42854 ATGACCAAAATGCCCCTAAATG
63 ATGACCAAAATGCCCCTAAATG
* * * *
42876 TGCAAAAATGACCAAAATACCTCAAAATATGCAAAAATGACCAAAATGCCCCTGA
1 TGCAAAAATGACC-AAATACCCCTAGATGTGCAAAAATGACC-AAATGCCCCTGA
42931 GCGTGCGAAT
Statistics
Matches: 122, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
85 2 0.02
86 22 0.18
87 94 0.77
88 4 0.03
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.18
Consensus pattern (84 bp):
TGCAAAAATGACCAAATACCCCTAGATGTGCAAAAATGACCAAATGCCCCTGAATATCAAAAATG
ACCAAAATGCCCCTAAATG
Found at i:43311 original size:60 final size:59
Alignment explanation
Indices: 43173--43687 Score: 732
Period size: 60 Copynumber: 8.7 Consensus size: 59
43163 TGAAACATAG
* * **
43173 ACTCTCAAACAGAGACCTCGACCAGGA-TTTAAA-ACAAGACGAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAAA
* *
43230 ACTCTCTAACAGAGATCTCGAACATGATTTTAAAGACAAGATAAGATTTTGAATTGAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTG-AAA
* * *
43290 ACTCTCTAGCAGAGACCTCGAACAGGATTTTTAAAAACAAGATAATATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA-TTTTAAAGACAAGATAAGATTTTGAATTGAAA
* *
43350 ACTCTCTAATAGAGACCTTGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAACA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAA-A
* * * *
43410 ACTCTCTAGCAGAGACATCAAATAGGATTTTAAAGACAAGATAAGATTTTGAATTGAACA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAA-A
* * *
43470 ACTCTCTAGCAGAGACCTCAAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAAA
*
43529 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGA-TTTTGAATTGAAA
* * **
43589 ACTCTCTAACAGAGACCTCGAACAGGATTTTTAAA-ACAGGATAGGATTCCGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA-TTTTAAAGACAAGATAAGATTTTGAATTGAAA
*
43648 ACTCTCTAACAGAGACCTCGAACAGGATTTT-GAGACAAGA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGA
43688 AAAGGGAATT
Statistics
Matches: 417, Mismatches: 33, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
57 24 0.06
58 15 0.04
59 131 0.31
60 213 0.51
61 34 0.08
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.26
Consensus pattern (59 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAAA
Found at i:44172 original size:2 final size:2
Alignment explanation
Indices: 44165--44190 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44155 GAGAACACGC
44165 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
44191 GAAAGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44578 original size:35 final size:34
Alignment explanation
Indices: 44527--44643 Score: 128
Period size: 36 Copynumber: 3.3 Consensus size: 34
44517 CCTCCTATTT
* *
44527 GTTTTT-TTTTCTGACCTCTCTCTGTTTTAGGCCAA
1 GTTTTTCTTTTC-GACCTCTTTCTATTTTAGGCC-A
* *
44562 GTTTTTCTTTTCGACCTCTTTCTAATTTAGATCCA
1 GTTTTTCTTTTCGACCTCTTTCTATTTTAG-GCCA
*
44597 GTTTTTCTTTTTCGACATCTTTCTATTTTAGGTCCA
1 GTTTTTC-TTTTCGACCTCTTTCTATTTTAGG-CCA
*
44633 GTTTTTTTTTT
1 GTTTTTCTTTT
44644 TTAGCTCCTT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
35 33 0.47
36 37 0.53
ACGTcount: A:0.13, C:0.20, G:0.11, T:0.56
Consensus pattern (34 bp):
GTTTTTCTTTTCGACCTCTTTCTATTTTAGGCCA
Found at i:44656 original size:35 final size:36
Alignment explanation
Indices: 44561--44656 Score: 90
Period size: 36 Copynumber: 2.7 Consensus size: 36
44551 TTTTAGGCCA
* * *
44561 AGTTTTTC-TTTTCGACCTCTTTCTAATTTAGATCC
1 AGTTTTTCTTTTTAGACATCCTTCTAATTTAGATCC
* * * *
44596 AGTTTTTCTTTTTCGACATCTTTCTATTTTAGGTCC
1 AGTTTTTCTTTTTAGACATCCTTCTAATTTAGATCC
*
44632 AGTTTTTTTTTTTTAG-C-TCCTTCTA
1 AG-TTTTTCTTTTTAGACATCCTTCTA
44657 GGCATAGTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
35 15 0.28
36 27 0.51
37 11 0.21
ACGTcount: A:0.15, C:0.20, G:0.09, T:0.56
Consensus pattern (36 bp):
AGTTTTTCTTTTTAGACATCCTTCTAATTTAGATCC
Found at i:46662 original size:12 final size:13
Alignment explanation
Indices: 46644--46673 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
46634 GTTTTCTTTA
46644 ATTTTCTTGATTG
1 ATTTTCTTGATTG
46657 -TTTTCTTGATTG
1 ATTTTCTTGATTG
46669 ATTTT
1 ATTTT
46674 AATTGCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:54215 original size:21 final size:20
Alignment explanation
Indices: 54186--54238 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
54176 TTACTAGAAT
* * *
54186 AGCGACGTTTTTTTTTCATAC
1 AGCGGCGTTTTATTTT-AAAC
*
54207 AGCGGCGTTTCTATTTTAAAT
1 AGCGGCGTTT-TATTTTAAAC
54228 AGCGGCGTTTT
1 AGCGGCGTTTT
54239 CTGTTGCGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 21 0.78
22 5 0.19
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (20 bp):
AGCGGCGTTTTATTTTAAAC
Found at i:54458 original size:32 final size:32
Alignment explanation
Indices: 54417--54479 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
54407 TTTAGGAATT
*
54417 GCGGCGTTTCCTTAAAAAAACGCCACTATTTA
1 GCGGCGTTTCCGTAAAAAAACGCCACTATTTA
* * *
54449 GCGGCGTTTCCGTACAGAAACGCCGCTATTT
1 GCGGCGTTTCCGTAAAAAAACGCCACTATTT
54480 TGCCTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (32 bp):
GCGGCGTTTCCGTAAAAAAACGCCACTATTTA
Found at i:58596 original size:13 final size:13
Alignment explanation
Indices: 58561--58912 Score: 116
Period size: 13 Copynumber: 24.2 Consensus size: 13
58551 AATAGGTCAT
* *
58561 AAATTATAATGAG
1 AAATTATATTTAG
*
58574 AAAATAATATTTAG
1 -AAATTATATTTAG
*
58588 AAATGATATATGTAATG
1 AAAT--TATAT-TTA-G
*
58605 AAATTATAATTAG
1 AAATTATATTTAG
* *
58618 GAATTATATTTAT
1 AAATTATATTTAG
58631 AAATTATATATGTAATG
1 AAATTATAT-T-T-A-G
58648 AAA-TATTATTTAG
1 AAATTA-TATTTAG
*
58661 AAAATGATATTTAG
1 -AAATTATATTTAG
*
58675 AAACTATATATGTGAAG
1 AAA-T-TATAT-T-TAG
*
58692 AAATTATAATTAG
1 AAATTATATTTAG
* *
58705 GAATTATA-TTAT
1 AAATTATATTTAG
58717 AAATTATATATGTAATG
1 AAATTATAT-T-T-A-G
58734 AAA-TATTATTTAG
1 AAATTA-TATTTAG
58747 AAATTATATATGTATTG
1 AAATTATAT-T-TA--G
*
58764 AAATTATAATTAG
1 AAATTATATTTAG
*
58777 AAAATAATATTTAG
1 -AAATTATATTTAG
*
58791 AAATTAACAATTTTTAG
1 AAATT----ATATTTAG
*
58808 AAACTATATTTAG
1 AAATTATATTTAG
* **
58821 AAAATAATAAATAG
1 -AAATTATATTTAG
*
58835 CAATTATATATGTAATG
1 AAATTATAT-T-T-A-G
*
58852 AAATTATAATTAG
1 AAATTATATTTAG
* *
58865 AAAATAATATTTCG
1 -AAATTATATTTAG
58879 AAATTTTAAAATATTTAG
1 AAA--TT---ATATTTAG
58897 AAATTATATTTAG
1 AAATTATATTTAG
58910 AAA
1 AAA
58913 ATAAAATTTG
Statistics
Matches: 253, Mismatches: 43, Indels: 85
0.66 0.11 0.22
Matches are distributed among these distances:
12 10 0.04
13 76 0.30
14 62 0.25
15 28 0.11
16 17 0.07
17 50 0.20
18 10 0.04
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.39
Consensus pattern (13 bp):
AAATTATATTTAG
Found at i:58687 original size:87 final size:86
Alignment explanation
Indices: 58572--58749 Score: 306
Period size: 87 Copynumber: 2.1 Consensus size: 86
58562 AATTATAATG
58572 AGAAAATAATATTTAGAAATGATATATGT-AATGAAATTATAATTAGGAATTATATTTATAAATT
1 AGAAAATAATATTTAGAAATGATATATGTGAA-GAAATTATAATTAGGAATTATA-TTATAAATT
58636 ATATATGTAATGAAATATTATTT
64 ATATATGTAATGAAATATTATTT
*
58659 AGAAAATGATATTTAGAAACT-ATATATGTGAAGAAATTATAATTAGGAATTATATTATAAATTA
1 AGAAAATAATATTTAGAAA-TGATATATGTGAAGAAATTATAATTAGGAATTATATTATAAATTA
58723 TATATGTAATGAAATATTATTT
65 TATATGTAATGAAATATTATTT
58745 AGAAA
1 AGAAA
58750 TTATATATGT
Statistics
Matches: 88, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
86 37 0.42
87 48 0.55
88 3 0.03
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.39
Consensus pattern (86 bp):
AGAAAATAATATTTAGAAATGATATATGTGAAGAAATTATAATTAGGAATTATATTATAAATTAT
ATATGTAATGAAATATTATTT
Found at i:58768 original size:17 final size:17
Alignment explanation
Indices: 58717--58771 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
58707 ATTATATTAT
*
58717 AAATTATATATGTAATG
1 AAATTATATATGTATTG
*
58734 AAA-TAT-TAT-T-TAG
1 AAATTATATATGTATTG
58747 AAATTATATATGTATTG
1 AAATTATATATGTATTG
58764 AAATTATA
1 AAATTATA
58772 ATTAGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 6 0.19
16 4 0.13
17 13 0.42
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
AAATTATATATGTATTG
Found at i:58777 original size:30 final size:30
Alignment explanation
Indices: 58619--58867 Score: 120
Period size: 30 Copynumber: 8.5 Consensus size: 30
58609 TATAATTAGG
* *
58619 AATTATATTTATAAATTATATATGTAATGA
1 AATTATAATTAGAAATTATATATGTAATGA
* *
58649 AA-TATTATTTAGAAA--ATGATAT-TTA-GA
1 AATTA-TAATTAGAAATTAT-ATATGTAATGA
* *
58676 AACTATATATGTGAAGAAATTATA-AT-T-A-GG
1 AATTATA-AT-T--AGAAATTATATATGTAATGA
*
58706 AATTAT-ATTATAAATTATATATGTAATGA
1 AATTATAATTAGAAATTATATATGTAATGA
* *
58735 AA-TATTATTTAGAAATTATATATGTATTGA
1 AATTA-TAATTAGAAATTATATATGTAATGA
* *
58765 AATTATAATTAGAAAATA-ATAT-TTA-GA
1 AATTATAATTAGAAATTATATATGTAATGA
* *
58792 AATTAACAATTTTTAGAAACTATAT-T-T-A-GAA
1 AATT-ATAA---TTAGAAATTATATATGTAATG-A
* * *
58823 AATAATAAATAGCAATTATATATGTAATGA
1 AATTATAATTAGAAATTATATATGTAATGA
58853 AATTATAATTAGAAA
1 AATTATAATTAGAAA
58868 ATAATATTTC
Statistics
Matches: 169, Mismatches: 24, Indels: 52
0.69 0.10 0.21
Matches are distributed among these distances:
25 9 0.05
26 2 0.01
27 24 0.14
28 17 0.10
29 16 0.09
30 70 0.41
31 26 0.15
32 3 0.02
33 2 0.01
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (30 bp):
AATTATAATTAGAAATTATATATGTAATGA
Found at i:58821 original size:44 final size:43
Alignment explanation
Indices: 58734--58921 Score: 164
Period size: 44 Copynumber: 4.3 Consensus size: 43
58724 ATATGTAATG
* * *
58734 AAATATTATTTAGAAATTATATATGTATT-GAAATTATAATTAGA
1 AAATAATATTTAGAAATTA-AAAT-TTTTAGAAATTATAATTAGA
* *
58778 AAATAATATTTAGAAATTAACAATTTTTAGAAACTATATTTAGA
1 AAATAATATTTAGAAATTAA-AATTTTTAGAAATTATAATTAGA
** * * * *
58822 AAATAATAAATAGCAATT-ATATATGTAATGAAATTATAATTAGA
1 AAATAATATTTAGAAATTAAAAT-TTTTA-GAAATTATAATTAGA
* * *
58866 AAATAATATTTCGAAATTTTAAAATATTTAGAAATTATATTTAGA
1 AAATAATATTTAGAAA--TTAAAATTTTTAGAAATTATAATTAGA
*
58911 AAATAAAATTT
1 AAATAATATTT
58922 GAATATAGCG
Statistics
Matches: 114, Mismatches: 23, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
42 2 0.02
43 8 0.07
44 73 0.64
45 24 0.21
46 4 0.04
47 3 0.03
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (43 bp):
AAATAATATTTAGAAATTAAAATTTTTAGAAATTATAATTAGA
Found at i:58843 original size:88 final size:88
Alignment explanation
Indices: 58748--58916 Score: 277
Period size: 88 Copynumber: 1.9 Consensus size: 88
58738 ATTATTTAGA
* *
58748 AATTATATATGTATTGAAATTATAATTAGAAAATAATATTTAGAAA-TTAACAATTTTTAGAAAC
1 AATTATATATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTTAA-AATATTTAGAAAC
58812 TATATTTAGAAAATAATAAATAGC
65 TATATTTAGAAAATAATAAATAGC
* *
58836 AATTATATATGTAATGAAATTATAATTAGAAAATAATATTTCGAAATTTTAAAATATTTAGAAAT
1 AATTATATATGTAATGAAATTATAATTAGAAAATAATATTTAGAAA-TTTAAAATATTTAGAAAC
58901 TATATTTAGAAAATAA
65 TATATTTAGAAAATAA
58917 AATTTGAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
88 44 0.59
89 27 0.36
90 4 0.05
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.38
Consensus pattern (88 bp):
AATTATATATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTTAAAATATTTAGAAACT
ATATTTAGAAAATAATAAATAGC
Found at i:58858 original size:116 final size:116
Alignment explanation
Indices: 58624--58855 Score: 272
Period size: 116 Copynumber: 2.0 Consensus size: 116
58614 TTAGGAATTA
* * * *
58624 TATTTATAAATTATATATGTAATGAAATATTATTTAGAAAATGATATTTAGAAACTATATATGTG
1 TATTTAGAAATTATATATGTAATGAAATATTAATTAGAAAATAATATTTAGAAACTATAAATGTG
* * * *
58689 AAGAAATTATAATTAGGAATTATATTATAAATTATATATGTAATGAAATAT
66 AAGAAACTATAATTAGAAATAATATAATAAATTATATATGTAATGAAATAT
* * *
58740 TATTTAGAAATTATATATGTATTGAAAT-TATAATTAGAAAATAATATTTAGAAATTA-ACAATT
1 TATTTAGAAATTATATATGTAATGAAATAT-TAATTAGAAAATAATATTTAGAAACTATA-AATG
** *
58803 TTTAGAAACTATATTTAGAAAATAATA-AATAGCAATTATATATGTAATGAAAT
64 TGAAGAAACTATAATTAG-AAATAATATAATA--AATTATATATGTAATGAAAT
58856 TATAATTAGA
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
115 2 0.02
116 69 0.71
117 6 0.06
118 20 0.21
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (116 bp):
TATTTAGAAATTATATATGTAATGAAATATTAATTAGAAAATAATATTTAGAAACTATAAATGTG
AAGAAACTATAATTAGAAATAATATAATAAATTATATATGTAATGAAATAT
Found at i:66165 original size:29 final size:29
Alignment explanation
Indices: 66125--66349 Score: 226
Period size: 29 Copynumber: 7.8 Consensus size: 29
66115 ACCTAGAGTA
*
66125 TGCAAAAATGACCAAACTGCCCCAGAATG
1 TGCAAAAATGACCAAAATGCCCCAGAATG
* * * *
66154 TGTAAAAATGACCATAATGCCCCTGGATG
1 TGCAAAAATGACCAAAATGCCCCAGAATG
* * *
66183 AGTAAAAATGACCAAAATGCCTCTAG-ATG
1 TGCAAAAATGACCAAAATGCC-CCAGAATG
* * *
66212 CGCAAAAATGACCATAATACCCCTAG-ATG
1 TGCAAAAATGACCAAAATGCCCC-AGAATG
* * *
66241 TGCAAAAATGACCAAACTGCTCCAGAATA
1 TGCAAAAATGACCAAAATGCCCCAGAATG
*
66270 TGCAAGAATGACCAAAATGCCCCTA-AATG
1 TGCAAAAATGACCAAAATGCCCC-AGAATG
*
66299 TGC-AAAATGACCAAAATGCCCCTA-AATA
1 TGCAAAAATGACCAAAATGCCCC-AGAATG
*
66327 TGCAAAAATGACCAAAATACCCC
1 TGCAAAAATGACCAAAATGCCCC
66350 TGATCGTGCG
Statistics
Matches: 164, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
28 29 0.18
29 132 0.80
30 3 0.02
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (29 bp):
TGCAAAAATGACCAAAATGCCCCAGAATG
Found at i:66704 original size:60 final size:60
Alignment explanation
Indices: 66566--67202 Score: 867
Period size: 60 Copynumber: 10.7 Consensus size: 60
66556 TTAAACATAG
* * **
66566 ACTCTCAAACAGAGACCTCGACCAGGATTTTAAA-ACAAGACGAGATTTTGAATTG-AAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAAAA
* * *
66624 ACTCTCTAACAGAGATCTCGAACATGATTTTAAAGACAATATAAGATTTTGAATTGAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAAAA
* * * * * *
66684 ACTCGCTAGCAGAGACCTCGAATAAGATTTTTAAAAACAAGATAATATTTTGAATT-AAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA-TTTTAAAGACAAGATAAGATTTTGAATTGAAAA
* * *
66744 ACTCTCTAACAGAGACCTCGAACAAGATTTTAAAGACAAGGTAAGATTTTGAATTGAACA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAAAA
* * *
66804 ACTCTCTAGCAGAGACCTCGAACAAGATTTTAAAGACAAGATAAGATTTTGAATTGAACA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAAAA
* * * *
66864 ACTCTCTAGCAGAGACTTCGAACAAGATTTTAAAAACAAGATAAGATTTTGAATT-AAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAAAA
* *
66923 ACTCTCTAACAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTTTAATTG-AAA
1 ACTCTCTAACAGAGACCTCGAACAGGA-TTTTAAAGACAAGATAAGA-TTTTGAATTGAAAA
*
66984 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAACA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAAAA
* * ** *
67044 ACTCTCTAGCAGAGACCACGAACAGGATACTAAAGACAAGATAAGATTTTGAATTGAACA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAAAA
* * * *
67104 ACTCTCTAGCAGAGACCTCGAACAGGATTTTTAAA-ACAGGATAGGATTCTGAATTG-AAA
1 ACTCTCTAACAGAGACCTCGAACAGGA-TTTTAAAGACAAGATAAGATTTTGAATTGAAAA
67163 ACTCTCTAACAGAGACCTCGAACAGGATTTT-AAGACAAGA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGA
67203 AAAGGGAATT
Statistics
Matches: 522, Mismatches: 47, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
57 2 0.00
58 39 0.07
59 107 0.20
60 306 0.59
61 68 0.13
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (60 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAGACAAGATAAGATTTTGAATTGAAAA
Found at i:68118 original size:36 final size:36
Alignment explanation
Indices: 68063--68144 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 36
68053 TTTTAGGCCA
*
68063 AGTTTTTC-TTTTCGACCTCTTTCTATTATAGGTCC
1 AGTTTTTCTTTTTCAACCTCTTTCTATTATAGGTCC
*
68098 AGTTTTTCTTTTTCAACCTCTTTCTATTTTAGGTCC
1 AGTTTTTCTTTTTCAACCTCTTTCTATTATAGGTCC
68134 AGTTTTT-TTTT
1 AGTTTTTCTTTT
68145 AAAGCAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
35 12 0.27
36 32 0.73
ACGTcount: A:0.13, C:0.20, G:0.10, T:0.57
Consensus pattern (36 bp):
AGTTTTTCTTTTTCAACCTCTTTCTATTATAGGTCC
Found at i:71913 original size:36 final size:35
Alignment explanation
Indices: 71873--72770 Score: 1016
Period size: 36 Copynumber: 25.1 Consensus size: 35
71863 TAATGTCCCC
* * *
71873 ACTTAATTATCCTGAATTAAGTTTTTTATTGACTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGA-TTT
* * *
71909 ACTTAATTA-CCTCGAATTAAGTTTATTGACT-CTTT
1 ACTTAATTACCCT-GAATTAAGTCT-TTGATTGATTT
* * *
71944 ACTTAATTACCCTGAATTGAGTCCTTGACT-ACTTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGA--TTT
* *
71980 ACTTAATTACCCTGAATTAAGTTTTTG-CTGATTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGATTT
* *
72014 ACTTAATTTCCTTGAAATTAAGTCTTT-ACTTGATTT
1 ACTTAATTACCCTG-AATTAAGTCTTTGA-TTGATTT
* * *
72050 ACTTAATTTCCTTGAAATTAAGTCTTTGCTTGATTT
1 ACTTAATTACCCTG-AATTAAGTCTTTGATTGATTT
* * *
72086 ACTTAATTACCTTGAATTAAGTCTTTGCTCGATTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGATTT
* *
72121 ATTTAATTACCCTGAATTAAGT-TTGTGCTTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTT-TGATTGA-TTT
* * * * * *
72157 ACCTAATTTCCTTGAAATTAATTCCTTGCTTGATTT
1 ACTTAATTACCCTG-AATTAAGTCTTTGATTGATTT
* *
72193 ACTTAATTACCTTGAATTAAGTCTTTGATTGCTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGATTT
* *
72228 ACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTT
* *
72264 ACTTAATCACCCTGAATTAAGTCTTTGCTTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGA-TTT
* *
72300 ACTTAATTACCCTGGATTAAGTTTTTGATTGTATTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTT
* * *
72336 ACTTAATCACCCTGAATTAAGTCTTTGATCGCTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGATTT
* *
72371 ACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTT
* * *
72407 ACTTAATTACCCTAAATTAAGTCGTTGCTTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGA-TTT
*
72443 ACTTAATTGCCCTGAATTAAGTCTTTGATTGTATTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTT
* *
72479 ACTTAATCACCCTGAATTAAGTCTTTGATTGCTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGATTT
* *
72514 ACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTT
*
72550 ACTTAATTACCCTGAATTAAGTCTTTGCTTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGA-TTT
* **
72586 ACTTAATTGCCCTGAATTAAGTCTTTGCCTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGA-TTT
*
72622 ACTTAATTACCCTGAGTTAAGTCTTTGATTGTATTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTT
* * *
72658 ACTTAATCACTCTGAATTAAGTCTTTAATTGATTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGATTT
72693 CACTTAATTACCCTGAATTAAGTCTTTGATTGATTTT
1 -ACTTAATTACCCTGAATTAAGTCTTTGATTGA-TTT
* *
72730 ACTTAATTACCCTAAATTAAGTCTTTGATTGTAATT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTT
72766 ACTTA
1 ACTTA
72771 CTGCATTGAT
Statistics
Matches: 757, Mismatches: 79, Indels: 52
0.85 0.09 0.06
Matches are distributed among these distances:
34 23 0.03
35 199 0.26
36 509 0.67
37 25 0.03
38 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.46
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTCTTTGATTGATTT
Found at i:71994 original size:107 final size:105
Alignment explanation
Indices: 71873--72770 Score: 924
Period size: 107 Copynumber: 8.4 Consensus size: 105
71863 TAATGTCCCC
* * *
71873 ACTTAATTATCCTGAATTAAGTTTTTTATTGACTTTACTTAATTA-CCTCGAATTAAG-TTT-AT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGA-TTTACTTAATTACCCT-GAATTAAGTTTTGAT
* *
71935 TGACTCTTTACTTAATTACCCTGAATTGAGTCCTTGACTACTTTT
64 TGA-T-TTTACTTAATTACCCTGAATTAAGTCTTTGACTA-TTTT
* * * *
71980 ACTTAATTACCCTGAATTAAGTTTTTG-CTGATTTACTTAATTTCCTTGAAATTAAGTCTTT-AC
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGATTTACTTAATTACCCTG-AATTAAGT-TTTGA-
* *
72043 TTGA-TTTACTTAATTTCCTTGAAATTAAGTCTTTG-CT-TGATTT
63 TTGATTTTACTTAATTACCCTG-AATTAAGTCTTTGACTAT--TTT
* * * * *
72086 ACTTAATTACCTTGAATTAAGTCTTTGCTCGATTTATTTAATTACCCTGAATTAAGTTTGTGCTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGATTTACTTAATTACCCTGAATTAAGTTT-TGATT
* * * * *
72151 GATTTTACCTAATTTCCTTGAAATTAATTCCTTG-CT-TGATTT
65 GATTTTACTTAATTACCCTG-AATTAAGTCTTTGACTAT--TTT
* * *
72193 ACTTAATTACCTTGAATTAAGTCTTTGATTGCTTTACTTAATCACCCTGAATTAAGTCTTTGATT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGATTTACTTAATTACCCTGAATTAAGT-TTTGATT
*
72258 G-TGTTTACTTAATCACCCTGAATTAAGTCTTTG-CTTGATTTT
65 GAT-TTTACTTAATTACCCTGAATTAAGTCTTTGAC-T-ATTTT
* * *
72300 ACTTAATTACCCTGGATTAAGTTTTTGATTGTATTTACTTAATCACCCTGAATTAAGTCTTTGAT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTTACTTAATTACCCTGAATTAAGT-TTTGAT
* * * * *
72365 CG-CTTTACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTT
64 TGATTTTACTTAATTACCCTGAATTAAGTCTTTGACTAT-TTT
* * * *
72407 ACTTAATTACCCTAAATTAAGTCGTTGCTTGATTTTACTTAATTGCCCTGAATTAAGTCTTTGAT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGA-TTTACTTAATTACCCTGAATTAAGT-TTTGAT
* * **
72472 TG-TATTTACTTAATCACCCTGAATTAAGTCTTTGATTGCTTT
64 TGAT-TTTACTTAATTACCCTGAATTAAGTCTTTGACTATTTT
* * *
72514 ACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTTACTTAATTACCCTGAATTAAGTCTTTGCT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTTACTTAATTACCCTGAATTAAGT-TTTGAT
* *
72579 TGATTTTACTTAATTGCCCTGAATTAAGTCTTTGCCTGATTTT
64 TGATTTTACTTAATTACCCTGAATTAAGTCTTTGACT-ATTTT
* * * *
72622 ACTTAATTACCCTGAGTTAAGTCTTTGATTGTATTTACTTAATCACTCTGAATTAAGTCTTTAAT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTTACTTAATTACCCTGAATTAAGT-TTTGAT
* *
72687 TGATTTCACTTAATTACCCTGAATTAAGTCTTTGATTGATTTT
64 TGATTTTACTTAATTACCCTGAATTAAGTCTTTGACT-ATTTT
* *
72730 ACTTAATTACCCTAAATTAAGTCTTTGATTGTAATTACTTA
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTTACTTA
72771 CTGCATTGAT
Statistics
Matches: 689, Mismatches: 77, Indels: 49
0.85 0.09 0.06
Matches are distributed among these distances:
104 1 0.00
105 14 0.02
106 85 0.12
107 372 0.54
108 212 0.31
109 5 0.01
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.46
Consensus pattern (105 bp):
ACTTAATTACCCTGAATTAAGTCTTTGATTGATTTACTTAATTACCCTGAATTAAGTTTTGATTG
ATTTTACTTAATTACCCTGAATTAAGTCTTTGACTATTTT
Found at i:72063 original size:18 final size:18
Alignment explanation
Indices: 72008--72100 Score: 55
Period size: 18 Copynumber: 5.2 Consensus size: 18
71998 AAGTTTTTGC
72008 TGATTTACTTAATTTCCT
1 TGATTTACTTAATTTCCT
* ** * *
72026 TGAAATTAAGT-CTTTACT
1 TG-ATTTACTTAATTTCCT
72044 TGATTTACTTAATTTCCT
1 TGATTTACTTAATTTCCT
* ** * *
72062 TGAAATTAAGT-CTTTGCT
1 TG-ATTTACTTAATTTCCT
*
72080 TGATTTACTTAATTACCT
1 TGATTTACTTAATTTCCT
72098 TGA
1 TGA
72101 ATTAAGTCTT
Statistics
Matches: 50, Mismatches: 21, Indels: 8
0.63 0.27 0.10
Matches are distributed among these distances:
17 10 0.20
18 30 0.60
19 10 0.20
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (18 bp):
TGATTTACTTAATTTCCT
Found at i:72195 original size:143 final size:142
Alignment explanation
Indices: 71873--72770 Score: 1128
Period size: 143 Copynumber: 6.3 Consensus size: 142
71863 TAATGTCCCC
** * ** *
71873 ACTTAATTATCCTGAATTAAGTTTTTTATTGACTTTACTTAATTA-CCTCGAATTAAGTTTATTG
1 ACTTAATTGCCCTGAATTAAGTCTTTGCTTGA-TTTACTTAATTACCCT-GAATTAAGTCT-TTG
* * * * **
71937 ACT-CTTTACTTAATTACCCTGAATTGAGTCCTTGACTACT-TTTACTTAATTACCCTGAATTAA
63 ATTGCTTTACTTAATCACCCTGAATTAAGTCTTTGA-TTGTGTTTACTTAATTACCCTGAATTAA
*
72000 GTTTTTGC-TGA-TTT
127 GTCTTTGCTTGATTTT
* * * * * *
72014 ACTTAATTTCCTTGAAATTAAGTCTTTACTTGATTTACTTAATTTCCTTGAAATTAAGTCTTTGC
1 ACTTAATTGCCCTG-AATTAAGTCTTTGCTTGATTTACTTAATTACCCTG-AATTAAGTCTTTGA
* * * * * * *
72079 TTGATTTACTTAATTACCTTGAATTAAGTCTTTGCTCG-ATTTATTTAATTACCCTGAATTAAGT
64 TTGCTTTACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTTACTTAATTACCCTGAATTAAGT
72143 -TTGTGCTTGATTTT
129 CTT-TGCTTGATTTT
* * * * * *
72157 ACCTAATTTCCTTGAAATTAATTCCTTGCTTGATTTACTTAATTACCTTGAATTAAGTCTTTGAT
1 ACTTAATTGCCCTG-AATTAAGTCTTTGCTTGATTTACTTAATTACCCTGAATTAAGTCTTTGAT
*
72222 TGCTTTACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTTACTTAATCACCCTGAATTAAGTC
65 TGCTTTACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTTACTTAATTACCCTGAATTAAGTC
72287 TTTGCTTGATTTT
130 TTTGCTTGATTTT
* * * * *
72300 ACTTAATTACCCTGGATTAAGTTTTTGATTGTATTTACTTAATCACCCTGAATTAAGTCTTTGAT
1 ACTTAATTGCCCTGAATTAAGTCTTTGCTTG-ATTTACTTAATTACCCTGAATTAAGTCTTTGAT
* *
72365 CGCTTTACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTTACTTAATTACCCTAAATTAAGTC
65 TGCTTTACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTTACTTAATTACCCTGAATTAAGTC
*
72430 GTTGCTTGATTTT
130 TTTGCTTGATTTT
* *
72443 ACTTAATTGCCCTGAATTAAGTCTTTGATTGTATTTACTTAATCACCCTGAATTAAGTCTTTGAT
1 ACTTAATTGCCCTGAATTAAGTCTTTGCTTG-ATTTACTTAATTACCCTGAATTAAGTCTTTGAT
72508 TGCTTTACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTTACTTAATTACCCTGAATTAAGTC
65 TGCTTTACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTTACTTAATTACCCTGAATTAAGTC
72573 TTTGCTTGATTTT
130 TTTGCTTGATTTT
* *
72586 ACTTAATTGCCCTGAATTAAGTCTTTGCCTGATTTTACTTAATTACCCTGAGTTAAGTCTTTGAT
1 ACTTAATTGCCCTGAATTAAGTCTTTGCTTGA-TTTACTTAATTACCCTGAATTAAGTCTTTGAT
* * * *
72651 TGTATTTACTTAATCACTCTGAATTAAGTCTTTAATTGAT-TTCACTTAATTACCCTGAATTAAG
65 TG-CTTTACTTAATCACCCTGAATTAAGTCTTTGATTG-TGTTTACTTAATTACCCTGAATTAAG
*
72715 TCTTTGATTGATTTT
128 TCTTTGCTTGATTTT
* * * *
72730 ACTTAATTACCCTAAATTAAGTCTTTGATTGTAATTACTTA
1 ACTTAATTGCCCTGAATTAAGTCTTTGCTTG-ATTTACTTA
72771 CTGCATTGAT
Statistics
Matches: 675, Mismatches: 67, Indels: 27
0.88 0.09 0.04
Matches are distributed among these distances:
140 2 0.00
141 55 0.08
142 115 0.17
143 396 0.59
144 105 0.16
145 2 0.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.46
Consensus pattern (142 bp):
ACTTAATTGCCCTGAATTAAGTCTTTGCTTGATTTACTTAATTACCCTGAATTAAGTCTTTGATT
GCTTTACTTAATCACCCTGAATTAAGTCTTTGATTGTGTTTACTTAATTACCCTGAATTAAGTCT
TTGCTTGATTTT
Found at i:74614 original size:17 final size:17
Alignment explanation
Indices: 74594--74647 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
74584 GCTGTATTAC
74594 TTTCTGTTCTGTTTCCT
1 TTTCTGTTCTGTTTCCT
74611 TTTCT-TTCATGTTT-CT
1 TTTCTGTTC-TGTTTCCT
*
74627 TTGTCCTG-CCTGTTTCCT
1 TT-T-CTGTTCTGTTTCCT
74645 TTT
1 TTT
74648 ATTTGTTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
16 7 0.23
17 17 0.55
18 7 0.23
ACGTcount: A:0.02, C:0.24, G:0.11, T:0.63
Consensus pattern (17 bp):
TTTCTGTTCTGTTTCCT
Found at i:81773 original size:77 final size:78
Alignment explanation
Indices: 81680--81846 Score: 255
Period size: 77 Copynumber: 2.1 Consensus size: 78
81670 TGACGACCGA
* *
81680 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGG-ATTGCTTTATCAAATTAAT
1 TCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTACTCAGGAATTGCTTTATCAAATTAAT
81744 TTCAGAATCCTAT
66 TTCAGAATCCTAT
* * *
81757 TCAGGATCATTGCTTTATCAGATTAATTTCAAAACCCTACTCAGGATCATTGTTTTATCAAGTTA
1 TCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTACTCAGGA--ATTGCTTTATCAAATTA
*
81822 ATTTCAGAATCCTGT
64 ATTTCAGAATCCTAT
81837 TCAGGATCAT
1 TCAGGATCAT
81847 CGGTCAATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
77 42 0.52
80 39 0.48
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (78 bp):
TCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTACTCAGGAATTGCTTTATCAAATTAAT
TTCAGAATCCTAT
Found at i:81782 original size:40 final size:40
Alignment explanation
Indices: 81680--81914 Score: 228
Period size: 40 Copynumber: 6.2 Consensus size: 40
81670 TGACGACCGA
* *
81680 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTAC
1 TCAGGATCATTGCTTTATCAGATTAATTTCAGAATCCTAT
*
81720 TCAGG---ATTGCTTTATCAAATTAATTTCAGAATCCTAT
1 TCAGGATCATTGCTTTATCAGATTAATTTCAGAATCCTAT
* * *
81757 TCAGGATCATTGCTTTATCAGATTAATTTCAAAACCCTAC
1 TCAGGATCATTGCTTTATCAGATTAATTTCAGAATCCTAT
* *
81797 TCAGGATCATTGTTTTATCA-AGTTAATTTCAGAATCCTGT
1 TCAGGATCATTGCTTTATCAGA-TTAATTTCAGAATCCTAT
* * *
81837 TCAGG---A-T-C---ATC-GGTCAATTTCAGAAACCTAT
1 TCAGGATCATTGCTTTATCAGATTAATTTCAGAATCCTAT
* * * *
81868 TCAGGATCATTGCTCTAT-TGGTTAATTTTAGAATCCTAT
1 TCAGGATCATTGCTTTATCAGATTAATTTCAGAATCCTAT
81907 TCAGGATC
1 TCAGGATC
81915 GTCAGTCAAT
Statistics
Matches: 163, Mismatches: 18, Indels: 29
0.78 0.09 0.14
Matches are distributed among these distances:
31 20 0.12
32 3 0.02
34 1 0.01
35 1 0.01
36 2 0.01
37 37 0.23
39 28 0.17
40 71 0.44
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (40 bp):
TCAGGATCATTGCTTTATCAGATTAATTTCAGAATCCTAT
Found at i:81856 original size:31 final size:31
Alignment explanation
Indices: 81821--81947 Score: 119
Period size: 31 Copynumber: 3.8 Consensus size: 31
81811 TTATCAAGTT
*
81821 AATTTCAGAATCCTGTTCAGGATCATCGGTC
1 AATTTCAGAATCCTATTCAGGATCATCGGTC
* *
81852 AATTTCAGAAACCTATTCAGGATCATTGCTCTATTGGTT
1 AATTTCAGAATCCTATTCAGGATCA----TC----GGTC
* * *
81891 AATTTTAGAATCCTATTCAGGATCGTCAGTC
1 AATTTCAGAATCCTATTCAGGATCATCGGTC
*
81922 AATTTCAGAATTCTATTCAGGATCAT
1 AATTTCAGAATCCTATTCAGGATCAT
81948 TGATCATCAG
Statistics
Matches: 77, Mismatches: 11, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
31 48 0.62
35 4 0.05
39 25 0.32
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (31 bp):
AATTTCAGAATCCTATTCAGGATCATCGGTC
Found at i:81910 original size:70 final size:71
Alignment explanation
Indices: 81781--81976 Score: 229
Period size: 70 Copynumber: 2.8 Consensus size: 71
81771 TTATCAGATT
* * * *
81781 AATTTCA-AAACCCTACTCAGGATCATTGTTTTATCAAGTTAATTTCAGAATCCTGTTCAGGATC
1 AATTTCAGAAA-CCTATTCAGGATCATTGCTCTATCAAGTTAATTTCAGAATCCTATTCAGGATC
*
81845 ATCGGTC
65 ATCAGTC
** * *
81852 AATTTCAGAAACCTATTCAGGATCATTGCTCTAT-TGGTTAATTTTAGAATCCTATTCAGGATCG
1 AATTTCAGAAACCTATTCAGGATCATTGCTCTATCAAGTTAATTTCAGAATCCTATTCAGGATCA
81916 TCAGTC
66 TCAGTC
** * **
81922 AATTTCAGAATTCTATTCAGGATCATTGATC-ATC-AGCCAATTTCAGAATCCTATT
1 AATTTCAGAAACCTATTCAGGATCATTGCTCTATCAAGTTAATTTCAGAATCCTATT
81977 TAGTATTATG
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
69 19 0.18
70 58 0.54
71 27 0.25
72 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (71 bp):
AATTTCAGAAACCTATTCAGGATCATTGCTCTATCAAGTTAATTTCAGAATCCTATTCAGGATCA
TCAGTC
Found at i:82096 original size:44 final size:43
Alignment explanation
Indices: 82040--82133 Score: 125
Period size: 44 Copynumber: 2.2 Consensus size: 43
82030 TGCGAGTTAA
82040 TTTCAAACTCTTATTTTAGGATCTCTTCCACTTTAAAAATTCGC
1 TTTCAAACTCTTATTTTAGGATCTCTTCCACTTT-AAAATTCGC
* * ** * *
82084 TTTCAAAGTCTTATTTTAGGGTCTCTTCTGCTTTATAATTCGT
1 TTTCAAACTCTTATTTTAGGATCTCTTCCACTTTAAAATTCGC
82127 TTTCAAA
1 TTTCAAA
82134 AAATCCTGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 14 0.32
44 30 0.68
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (43 bp):
TTTCAAACTCTTATTTTAGGATCTCTTCCACTTTAAAATTCGC
Found at i:84038 original size:44 final size:44
Alignment explanation
Indices: 83988--84083 Score: 174
Period size: 44 Copynumber: 2.2 Consensus size: 44
83978 GCATAGATAA
**
83988 AATTTAATTTCACAAAAGGATAATTTATTATGTTATTTTATATG
1 AATTTAATTTCACAAAAGGATAATTTATTATGTTATCCTATATG
84032 AATTTAATTTCACAAAAGGATAATTTATTATGTTATCCTATATG
1 AATTTAATTTCACAAAAGGATAATTTATTATGTTATCCTATATG
84076 AATTTAAT
1 AATTTAAT
84084 AATTGTTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (44 bp):
AATTTAATTTCACAAAAGGATAATTTATTATGTTATCCTATATG
Found at i:85559 original size:22 final size:22
Alignment explanation
Indices: 85442--85823 Score: 126
Period size: 22 Copynumber: 17.4 Consensus size: 22
85432 TAATTACACT
* *
85442 ATTTTTATGACCTTCTTATGAA
1 ATTTTGATAACCTTCTTATGAA
*
85464 ATTTTGATAACCTTCCTATGAA
1 ATTTTGATAACCTTCTTATGAA
* * ** * *
85486 ATTTTAATGACGAT-ATATGGA
1 ATTTTGATAACCTTCTTATGAA
* * * *
85507 ATTTCGAGAACCTTTTTAT-TA
1 ATTTTGATAACCTTCTTATGAA
**
85528 ATTTTTTTAACCTTCTTATGAA
1 ATTTTGATAACCTTCTTATGAA
* *
85550 ATTTTGTTAACC-TCACTATGAA
1 ATTTTGATAACCTTC-TTATGAA
**
85572 ATTTTGATAA-CTTCCCAATGAA
1 ATTTTGATAACCTT-CTTATGAA
* ** *
85594 ATTCTGATAACCAACACTATGAA
1 ATTTTGATAACCTTC-TTATGAA
* * *
85617 ATGTTGATAACCTCCATATG--
1 ATTTTGATAACCTTCTTATGAA
* * *
85637 ATATTGATAACC-ACATTATAAA
1 ATTTTGATAACCTTC-TTATGAA
* * * * *
85659 AATTTAAAAACCTCCATAT-AA
1 ATTTTGATAACCTTCTTATGAA
* *
85680 ATTGTT-AGTAATCAC-AC-TCTGAA
1 ATT-TTGA-TAA-C-CTTCTTATGAA
* *
85703 ATATTGATAATCAC-AC-TATGAA
1 ATTTTGATAA-C-CTTCTTATGAA
* *
85725 ATTGTAATAACC-TCATTATGAA
1 ATTTTGATAACCTTC-TTATGAA
* *
85747 ATTTTGATAAACCTTCCTATAAA
1 ATTTTGAT-AACCTTCTTATGAA
* * *
85770 ATTTTGATAAACCTCCCTATAAA
1 ATTTTGAT-AACCTTCTTATGAA
*
85793 ATTTTGATAACCTCCTTATGAA
1 ATTTTGATAACCTTCTTATGAA
*
85815 ATCTTGATA
1 ATTTTGATA
85824 TGATTTTTTG
Statistics
Matches: 275, Mismatches: 64, Indels: 42
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.00
20 16 0.06
21 37 0.13
22 152 0.55
23 66 0.24
24 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
ATTTTGATAACCTTCTTATGAA
Found at i:85618 original size:23 final size:22
Alignment explanation
Indices: 85544--85823 Score: 180
Period size: 22 Copynumber: 12.7 Consensus size: 22
85534 TTAACCTTCT
*
85544 TATGAAATTTTGTTAACCTCAC
1 TATGAAATTTTGATAACCTCAC
* *
85566 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
85588 AATGAAATTCTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
*
85611 TATGAAATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * *
85632 ATATG--ATATTGATAACCACAT
1 -TATGAAATTTTGATAACCTCAC
* * * *
85653 TATAAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
85674 ATAT-AAATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* * * *
85697 TCTGAAATATTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* * *
85719 TATGAAATTGTAATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
85741 TATGAAATTTTGATAAACCTTC-C
1 TATGAAATTTTGAT-AACC-TCAC
* *
85764 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
*
85787 TATAAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
*
85808 TTATGAAATCTTGATA
1 -TATGAAATTTTGATA
85824 TGATTTTTTG
Statistics
Matches: 202, Mismatches: 41, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
20 15 0.07
21 7 0.03
22 118 0.58
23 60 0.30
24 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:85854 original size:22 final size:22
Alignment explanation
Indices: 85829--85948 Score: 102
Period size: 22 Copynumber: 5.5 Consensus size: 22
85819 TGATATGATT
*
85829 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTCACTATGAAA
* * *
85851 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTCACTATGAAA
* *
85873 TTTTGATCTA-CACACTATGAAA
1 TTTTGAT-AACCTCACTATGAAA
*
85895 TTTTGATAACCCTC-TTATGAAA
1 TTTTGATAA-CCTCACTATGAAA
* * *
85917 TTTTGA-AAACTAAACTAGGAAA
1 TTTTGATAACCT-CACTATGAAA
85939 TTTTGATAAC
1 TTTTGATAAC
85949 TTTCATATGA
Statistics
Matches: 76, Mismatches: 16, Indels: 11
0.74 0.16 0.11
Matches are distributed among these distances:
20 2 0.03
21 3 0.04
22 66 0.87
23 5 0.07
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGAAA
Found at i:85870 original size:57 final size:58
Alignment explanation
Indices: 85771--85879 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 58
85761 TCCTATAAAA
* *
85771 TTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTTATGAAATCTTGATATGATT
1 TTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCTATGAAATCTTGATATGATT
* * * * *
85829 TTTTGAT-AACCTCATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGAT
1 TTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCTATGAAATCTTGAT
85880 CTACACACTA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 37 0.84
58 7 0.16
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (58 bp):
TTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCTATGAAATCTTGATATGATT
Found at i:85877 original size:44 final size:44
Alignment explanation
Indices: 85844--85948 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
85834 ATAACCTCAT
* *
85844 TATGAAATTTTGTTAATCTCC-C-TATGAAATTTTGATCTACACAC
1 TATGAAATTTTGATAA-C-CCTCTTATGAAATTTTGATCAACACAC
* *
85888 TATGAAATTTTGATAACCCTCTTATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCCTCTTATGAAATTTTGATCAAC-ACAC
*
85932 TAGGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
85949 TTTCATATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
42 2 0.04
43 4 0.08
44 47 0.89
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCCTCTTATGAAATTTTGATCAACACAC
Found at i:86201 original size:66 final size:65
Alignment explanation
Indices: 86059--86210 Score: 155
Period size: 66 Copynumber: 2.3 Consensus size: 65
86049 CAGAAATACC
**
86059 ACTATGAAATTTTCGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCT
1 ACTATGAAATTTT-GTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACAA
*
86124 T
65 A
** * * * * *
86125 TTTATAAAATTTTGTTGA-CACCTTTATGAAATTTTGATAACCTCGTTT-TGAAATTTTGATAAG
1 ACTATGAAATTTTG-TAATCACATTT-TGAAAATTTGATAACCTC-TTTATGAAATTTTGATAAC
86188 AAA
63 AAA
86191 ACTATGAAATTTTGATAATC
1 ACTATGAAATTTTG-TAATC
86211 TTCCTATAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
65 7 0.10
66 56 0.84
67 4 0.06
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (65 bp):
ACTATGAAATTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACAAA
Found at i:86217 original size:22 final size:22
Alignment explanation
Indices: 86085--86476 Score: 129
Period size: 22 Copynumber: 17.6 Consensus size: 22
86075 AATCACATTT
* *
86085 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-CTA
**
86107 TGAAATTTTGATAACCTTTTTA
1 TGAAATTTTGATAACCTTCCTA
* *
86129 TAAAATTTTGTTGACACCTT--TA
1 TGAAATTTTGAT-A-ACCTTCCTA
* *
86151 TGAAATTTTGATAACC-TCGTTT
1 TGAAATTTTGATAACCTTC-CTA
*****
86173 TGAAATTTTGATAAGAAAACTA
1 TGAAATTTTGATAACCTTCCTA
*
86195 TGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAACCTTCCTA
*
86217 T-AAATTTTGATAATCCAATCTCTA
1 TGAAATTTTGATAA-CC-TTC-CTA
* *
86241 CGAAATTTCGATAATCAC-T-CTA
1 TGAAATTTTGATAA-C-CTTCCTA
*
86263 TGAGA-TTTGATAACCTT-CTA
1 TGAAATTTTGATAACCTTCCTA
* *
86283 TCAAATTTTGGT-A-C-TCCTCA
1 TGAAATTTTGATAACCTTCCT-A
* *
86303 TGAAATTGAGACTTTTATAACCTTCATA
1 TGAAA-T-----TTTGATAACCTTCCTA
* **
86331 TGGAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTC-CTA
** *
86353 AAAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTC-CTA
* *
86375 TGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTTCCTA
* *
86397 TGATATATT-AGTAACC-TCCTTA
1 TGAAATTTTGA-TAACCTTCC-TA
* *
86419 TGAAATTTTGTTAACC-ACACTA
1 TGAAATTTTGATAACCTTC-CTA
86441 TGAAATTCTT-ATAACC-TCGCTA
1 TGAAATT-TTGATAACCTTC-CTA
*
86463 TGACATTTTGATAA
1 TGAAATTTTGATAA
86477 TTTCTTTGAT
Statistics
Matches: 280, Mismatches: 56, Indels: 68
0.69 0.14 0.17
Matches are distributed among these distances:
18 1 0.00
19 5 0.02
20 17 0.06
21 33 0.12
22 177 0.63
23 9 0.03
24 9 0.03
25 13 0.05
26 5 0.02
27 2 0.01
28 6 0.02
29 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCCTA
Found at i:86427 original size:66 final size:65
Alignment explanation
Indices: 86355--86716 Score: 237
Period size: 66 Copynumber: 5.3 Consensus size: 65
86345 CAACACTAAA
*
86355 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGATATATTAGTAACCTCCTTAT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAAT-TTAGTAACCTCCTTAT
86420 G
65 G
* * * * *
86421 AAATTTTGTTAACCACACTATGAAATTCTT-ATAACCTCGCTATGACATTTTGATAATTTCTTTG
1 AAATTTTGATAACCACACTATGAAATT-TTGATAACCTCCCCATGAAATTTAG-TAA---C----
* * *
86485 ATAACCTTTCTAT
57 CT--CC-TTAT-G
* * * * * * *
86498 AAAATTGTGATAACCACACTATGAAA-TATCAGTAACCTTCCTAAGAAATTTTAATAACCTGATC
1 AA-ATTTTGATAACCACACTATGAAATTTTGA-TAACCTCCCCATGAAA-TTTAGTAACC---TC
86562 C-TATG
60 CTTATG
* * * * * * *
86567 AAATCTTGGTAACCACACTATGAAATTTTGATAACTTTCCCATGAAATTTTGATAACTTCCATAT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATTTAG-TAACCTCCTTAT
86632 G
65 G
* * * * *
86633 AAATTTTGGTAACTACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACCAT-CTTA
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATT-TAGTAACC-TCCTTA
86697 TG
64 TG
86699 AAATTTTGATAACCACAC
1 AAATTTTGATAACCACAC
86717 AGAGACAAGA
Statistics
Matches: 228, Mismatches: 43, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
65 6 0.03
66 116 0.51
67 7 0.03
68 37 0.16
69 6 0.03
70 2 0.01
72 2 0.01
73 1 0.00
74 1 0.00
75 3 0.01
76 4 0.02
77 4 0.02
78 36 0.16
79 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (65 bp):
AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATTTAGTAACCTCCTTATG
Found at i:86456 original size:44 final size:43
Alignment explanation
Indices: 86315--86712 Score: 182
Period size: 44 Copynumber: 9.2 Consensus size: 43
86305 AAATTGAGAC
* * **
86315 TTTTATAACCTTCA-TATGGAATTTTGATAACAACACTAAAAAA
1 TTTTATAACC-TCACTATGAAATTTTGATAACCACACTATGAAA
* * * * *
86358 TTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGATA
1 TTTT-ATAACCTCACTATGAAATTTTGATAACCACACTATGAAA
* *
86402 TATTAGTAACCTC-CTTATGAAATTTTGTTAACCACACTATGAAA
1 TTTTA-TAACCTCAC-TATGAAATTTTGATAACCACACTATGAAA
* * **
86446 TTCTTATAACCTCGCTATGACATTTTGAT----A-A-T-T--TC
1 TT-TTATAACCTCACTATGAAATTTTGATAACCACACTATGAAA
* ** * *
86481 TTTGATAACCTTTCTATAAAATTGTGATAACCACACTATGAAA
1 TTTTATAACCTCACTATGAAATTTTGATAACCACACTATGAAA
* * * *
86524 TATCAGTAACCTTC-CTAAGAAATTTTAATAACCTGATC-CTATGAAA
1 TTTTA-TAACC-TCACTATGAAATTTTGATAACC--A-CACTATGAAA
** * ** *
86570 TCTTGGTAACCACACTATGAAATTTTGATAACTTTC-CCATGAAA
1 T-TTTATAACCTCACTATGAAATTTTGATAAC-CACACTATGAAA
* * * *
86614 TTTTGATAACTTC-CATATGAAATTTTGGTAACTACACTATGGAA
1 TTTT-ATAACCTCAC-TATGAAATTTTGATAACCACACTATGAAA
* * *
86658 TTTTGATAACCTC-CTCATGAAATTATAATAACCATC-TTATGAAA
1 TTTT-ATAACCTCACT-ATGAAATTTTGATAACCA-CACTATGAAA
86702 TTTTGATAACC
1 TTTT-ATAACC
86713 ACACAGAGAC
Statistics
Matches: 267, Mismatches: 60, Indels: 55
0.70 0.16 0.14
Matches are distributed among these distances:
34 20 0.07
35 2 0.01
37 1 0.00
38 2 0.01
39 2 0.01
40 2 0.01
41 1 0.00
43 17 0.06
44 180 0.67
45 7 0.03
46 31 0.12
47 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (43 bp):
TTTTATAACCTCACTATGAAATTTTGATAACCACACTATGAAA
Found at i:86555 original size:22 final size:22
Alignment explanation
Indices: 86481--86712 Score: 170
Period size: 22 Copynumber: 10.5 Consensus size: 22
86471 TGATAATTTC
* *
86481 TTTGATAACCTTTCTATAAAAT
1 TTTGATAACCTTCCTATGAAAT
* *
86503 TGTGATAACC-ACACTATGAAA-
1 TTTGATAACCTTC-CTATGAAAT
* * *
86524 TATCAGTAACCTTCCTAAGAAAT
1 TTTGA-TAACCTTCCTATGAAAT
*
86547 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAACCT--TCCTATGAAAT
* * *
86571 CTTGGTAACC-ACACTATGAAAT
1 TTTGATAACCTTC-CTATGAAAT
* *
86593 TTTGATAACTTTCCCATGAAAT
1 TTTGATAACCTTCCTATGAAAT
86615 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCTTCC-TATGAAAT
* * *
86637 TTTGGTAA-CTACACTATGGAAT
1 TTTGATAACCTTC-CTATGAAAT
86659 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCTTCCT-ATGAAAT
* * * *
86681 TATAATAACCATCTTATGAAAT
1 TTTGATAACCTTCCTATGAAAT
86703 TTTGATAACC
1 TTTGATAACC
86713 ACACAGAGAC
Statistics
Matches: 164, Mismatches: 33, Indels: 26
0.74 0.15 0.12
Matches are distributed among these distances:
21 10 0.06
22 127 0.77
23 10 0.06
24 17 0.10
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
TTTGATAACCTTCCTATGAAAT
Found at i:87187 original size:13 final size:13
Alignment explanation
Indices: 87151--87189 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
87141 TCTAAATTGA
87151 AATTTT-ATAATT
1 AATTTTAATAATT
87163 AATTTTTAAATAATT
1 AA-TTTT-AATAATT
87178 AATTTTAATAAT
1 AATTTTAATAAT
87190 GTCTATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 4 0.17
15 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTAATAATT
Found at i:88837 original size:129 final size:131
Alignment explanation
Indices: 88690--88950 Score: 366
Period size: 131 Copynumber: 2.0 Consensus size: 131
88680 CATTGTTTAA
* * *
88690 ACTTTTATAGTTTTACTCAACTAAAATCTGTA-TTTTTATTTAATT-TATCTAATATCCTTATAA
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAA
* * * * * * *
88753 ATA-TTTATTTTTTACCATTTTACTATTTTAATTAAAAACTTATATATATTAGAATTTTTTAAAT
66 ATATTTTA-TTGTTACCATTTTACTAATTCAATTAAAAACTAAGATATATTAGAAATTTTAAAAT
88817 AT
130 AT
*
88819 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAA
* * *
88884 CTATTTTATTGTTATCATTTTACTAATTCAATTGAAAACTAAGATATATTAGAAATTTTAAAATA
66 ATATTTTATTGTTACCATTTTACTAATTCAATTAAAAACTAAGATATATTAGAAATTTTAAAATA
88949 T
131 T
88950 A
1 A
88951 TATTTCTTAA
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
129 30 0.26
130 13 0.11
131 68 0.59
132 4 0.03
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.49
Consensus pattern (131 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAA
ATATTTTATTGTTACCATTTTACTAATTCAATTAAAAACTAAGATATATTAGAAATTTTAAAATA
T
Found at i:90094 original size:22 final size:22
Alignment explanation
Indices: 90054--90095 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
90044 GTTTATAATA
* *
90054 TTCTTGGGTCATCCGGGTTAAC
1 TTCTCGGGTCATCCAGGTTAAC
*
90076 TTCTCGGGTCATTCAGGTTA
1 TTCTCGGGTCATCCAGGTTA
90096 CTGATTTGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.38
Consensus pattern (22 bp):
TTCTCGGGTCATCCAGGTTAAC
Found at i:91290 original size:102 final size:102
Alignment explanation
Indices: 91114--91317 Score: 408
Period size: 102 Copynumber: 2.0 Consensus size: 102
91104 CCCACATACA
91114 AATGTTAGCAAACATGGTGATTTAATTACGAGGCGCAAATCGCCATGGATTTTGGAGTGAGTGAT
1 AATGTTAGCAAACATGGTGATTTAATTACGAGGCGCAAATCGCCATGGATTTTGGAGTGAGTGAT
91179 CATCAAACACCACATTAGTAATTGTAGTTGTGTTAGT
66 CATCAAACACCACATTAGTAATTGTAGTTGTGTTAGT
91216 AATGTTAGCAAACATGGTGATTTAATTACGAGGCGCAAATCGCCATGGATTTTGGAGTGAGTGAT
1 AATGTTAGCAAACATGGTGATTTAATTACGAGGCGCAAATCGCCATGGATTTTGGAGTGAGTGAT
91281 CATCAAACACCACATTAGTAATTGTAGTTGTGTTAGT
66 CATCAAACACCACATTAGTAATTGTAGTTGTGTTAGT
91318 TAATACGTGA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (102 bp):
AATGTTAGCAAACATGGTGATTTAATTACGAGGCGCAAATCGCCATGGATTTTGGAGTGAGTGAT
CATCAAACACCACATTAGTAATTGTAGTTGTGTTAGT
Found at i:93510 original size:67 final size:67
Alignment explanation
Indices: 93425--93558 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
93415 GATTTCTAAG
* *
93425 CCGATTATTATGTAGGCTATTTTATAGCAAATTTATTTTTTCCTTCTTTTCCTTTTAATTTACTT
1 CCGATTATTAGGTAGGCTATTTTATAGCAAATTTATTTCTTCCTTCTTTTCCTTTTAATTTACTT
93490 TA
66 TA
*
93492 CCGATTATTAGGTAGGCTATTTTGTAGCAAATTTATTTCTTCCTTCTTTTCCTTTTAATTTACTT
1 CCGATTATTAGGTAGGCTATTTTATAGCAAATTTATTTCTTCCTTCTTTTCCTTTTAATTTACTT
93557 TA
66 TA
93559 AGGGTTTATT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.54
Consensus pattern (67 bp):
CCGATTATTAGGTAGGCTATTTTATAGCAAATTTATTTCTTCCTTCTTTTCCTTTTAATTTACTT
TA
Found at i:95728 original size:7 final size:6
Alignment explanation
Indices: 95698--95774 Score: 59
Period size: 6 Copynumber: 12.2 Consensus size: 6
95688 GAGGCAACCC
*
95698 AATTTT AATTTT AATTTT AATTTT CAATTTTT AATTTTT AAAATTTT ATTTTT
1 AATTTT AATTTT AATTTT AATTTT -AA-TTTT AA-TTTT --AATTTT AATTTT
* *
95751 AACTTCT AA-CTT AATTTT -ATTTT A
1 AA-TTTT AATTTT AATTTT AATTTT A
95775 TAGGTCTCAT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
5 8 0.14
6 26 0.45
7 14 0.24
8 8 0.14
9 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:95748 original size:14 final size:14
Alignment explanation
Indices: 95698--95752 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
95688 GAGGCAACCC
95698 AATTTTAATTTT--
1 AATTTTAATTTTAA
*
95710 AATTTTAATTTTCA
1 AATTTTAATTTTAA
*
95724 ATTTTTAATTTTTAA
1 AATTTTAA-TTTTAA
*
95739 AATTTTATTTTTAA
1 AATTTTAATTTTAA
95753 CTTCTAACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
12 12 0.33
14 13 0.36
15 11 0.31
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
AATTTTAATTTTAA
Found at i:96576 original size:49 final size:49
Alignment explanation
Indices: 96519--96614 Score: 165
Period size: 49 Copynumber: 2.0 Consensus size: 49
96509 CTGAGTCATG
** *
96519 TGATTTGATTGTTTTTGGATTGATCTTTTATTTCCTCAATTTTTGAAAA
1 TGATTTGATTCATTTTGGATTGATCTTTTATTTCCCCAATTTTTGAAAA
96568 TGATTTGATTCATTTTGGATTGATCTTTTATTTCCCCAATTTTTGAA
1 TGATTTGATTCATTTTGGATTGATCTTTTATTTCCCCAATTTTTGAA
96615 GAATAAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.54
Consensus pattern (49 bp):
TGATTTGATTCATTTTGGATTGATCTTTTATTTCCCCAATTTTTGAAAA
Found at i:96632 original size:49 final size:48
Alignment explanation
Indices: 96531--96632 Score: 143
Period size: 49 Copynumber: 2.1 Consensus size: 48
96521 ATTTGATTGT
* * *
96531 TTTTGGATTGATCTTTTATTTCCTCAATTTTTGAAAATGATTTGATTCA
1 TTTTGGATTGATCTTTTATTTCCCCAATTTTTGAAAATAAATT-ATTCA
96580 TTTTGGATTGATCTTTTATTTCCCCAATTTTTGAAGAATAAATT-TTCAA
1 TTTTGGATTGATCTTTTATTTCCCCAATTTTTGAA-AATAAATTATTC-A
96629 TTTT
1 TTTT
96633 CAAAATTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
48 3 0.06
49 39 0.81
50 6 0.12
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (48 bp):
TTTTGGATTGATCTTTTATTTCCCCAATTTTTGAAAATAAATTATTCA
Found at i:97820 original size:18 final size:19
Alignment explanation
Indices: 97786--97824 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
97776 TGAAGATTTT
97786 TTGAAGATAATTTGAAGAA
1 TTGAAGATAATTTGAAGAA
*
97805 TTGAAGATCA-TTGAAGAA
1 TTGAAGATAATTTGAAGAA
97823 TT
1 TT
97825 ATTTCAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (19 bp):
TTGAAGATAATTTGAAGAA
Done.