Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 168 of 332
Found at i:55525218 original size:20 final size:19
Alignment explanation
Indices: 55525172--55525209 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55525162 CATCCAAACA
55525172 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
55525191 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
55525210 TTTAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:55526376 original size:22 final size:22
Alignment explanation
Indices: 55526351--55526393 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
55526341 AAACATGTTT
55526351 AAAACAT-CAACCTTTCCACATC
1 AAAACATGCAA-CTTTCCACATC
* *
55526373 AAAATATGCAAGTTTCCACAT
1 AAAACATGCAACTTTCCACAT
55526394 TCACAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.42, C:0.28, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAACATGCAACTTTCCACATC
Found at i:55527111 original size:42 final size:42
Alignment explanation
Indices: 55526957--55527154 Score: 243
Period size: 43 Copynumber: 4.7 Consensus size: 42
55526947 TACCATGCCA
* * * *
55526957 ATGCCATATCCTAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * * * *
55526999 ATGCCAATACCCCAGCTATGGTCTTACATGTAATCTCGTATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
55527042 ATGCCAATACCCCAGCTATGGTCTTACACGAAATCTCACATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
55527085 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
*
55527127 ATGTCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
55527155 ATAGTCTCAG
Statistics
Matches: 142, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
42 64 0.45
43 78 0.55
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:55532670 original size:10 final size:10
Alignment explanation
Indices: 55532650--55532685 Score: 58
Period size: 9 Copynumber: 3.8 Consensus size: 10
55532640 CTATCCCTAT
55532650 AAAAT-ATTA
1 AAAATAATTA
55532659 AAAATAATTA
1 AAAATAATTA
55532669 AAAATAA-TA
1 AAAATAATTA
55532678 AAAATAAT
1 AAAATAAT
55532686 AGTATAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 14 0.56
10 11 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATAATTA
Found at i:55532848 original size:33 final size:31
Alignment explanation
Indices: 55532797--55532861 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 31
55532787 TAAAAAAAAT
*
55532797 AAAAAAAATAGAATTAAAAGCTTTGATATGGA
1 AAAAAAAACAGAATTAAAAGCTTTGAT-TGGA
*
55532829 AAAATAAAACAGAATTAAAAGGTTTGATTGGA
1 AAAA-AAAACAGAATTAAAAGCTTTGATTGGA
55532861 A
1 A
55532862 TTTTGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 9 0.30
33 21 0.70
ACGTcount: A:0.55, C:0.03, G:0.17, T:0.25
Consensus pattern (31 bp):
AAAAAAAACAGAATTAAAAGCTTTGATTGGA
Found at i:55533411 original size:46 final size:45
Alignment explanation
Indices: 55533344--55533430 Score: 165
Period size: 46 Copynumber: 1.9 Consensus size: 45
55533334 TACGAATTCT
55533344 AAGCCTCAAGAACCCTTTTGTGGATTTTTTTTTGACAACCTTCGTA
1 AAGCCTCAAGAACCCTTTTGTGGA-TTTTTTTTGACAACCTTCGTA
55533390 AAGCCTCAAGAACCCTTTTGTGGATTTTTTTTGACAACCTT
1 AAGCCTCAAGAACCCTTTTGTGGATTTTTTTTGACAACCTT
55533431 TGGCTAGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 17 0.41
46 24 0.59
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (45 bp):
AAGCCTCAAGAACCCTTTTGTGGATTTTTTTTGACAACCTTCGTA
Found at i:55534929 original size:40 final size:40
Alignment explanation
Indices: 55534859--55535076 Score: 325
Period size: 40 Copynumber: 5.5 Consensus size: 40
55534849 AAACCAAGTA
* *
55534859 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
55534898 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55534938 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55534978 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
55535018 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
55535058 CCTTCGGGACCTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
55535077 TTATCATTCG
Statistics
Matches: 166, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
39 15 0.09
40 151 0.91
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55541041 original size:40 final size:40
Alignment explanation
Indices: 55540824--55541046 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
55540814 AAGCCAAGTA
* * * *
55540824 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
55540863 CCTTCGGGACATAGCCCGAATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
55540903 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55540943 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55540983 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
55541023 CCTTCGGGACTTAGCCCGGTTATA
1 CCTTCGGGACTTAGCCCGGATATA
55541047 TTCCAAATAT
Statistics
Matches: 165, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 13 0.08
40 151 0.92
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55546357 original size:40 final size:40
Alignment explanation
Indices: 55546287--55546544 Score: 396
Period size: 40 Copynumber: 6.5 Consensus size: 40
55546277 AAACCAAGTA
* *
55546287 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
55546326 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55546366 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55546406 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55546446 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
55546486 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
55546526 CCTTCGGGACCTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
55546545 TTATCATTCG
Statistics
Matches: 206, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
39 15 0.07
40 191 0.93
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55548291 original size:10 final size:10
Alignment explanation
Indices: 55548258--55548308 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
55548248 ATTAAATTCT
*
55548258 TAAAGATATA
1 TAAAGATAAA
55548268 TACAA-ATAAA
1 TA-AAGATAAA
*
55548278 TAAAGATAAT
1 TAAAGATAAA
55548288 TAAAGATAAA
1 TAAAGATAAA
55548298 TGAAA-ATAAA
1 T-AAAGATAAA
55548308 T
1 T
55548309 CTTAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (10 bp):
TAAAGATAAA
Found at i:55549222 original size:119 final size:119
Alignment explanation
Indices: 55549084--55549309 Score: 335
Period size: 119 Copynumber: 1.9 Consensus size: 119
55549074 CTAGTTAGCT
* * *
55549084 GAGTTTTACCCATCACGTCACACAACCTTTTGACGCGAAGTAGAATGATAACCCAAGCACCCTAC
1 GAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAAGGACAACCCAAGCACCCTAC
* * * *
55549149 CCCGGTTACTTAATCAGTCACGTTCTGAGCTGTACTTATAACCTCGGGTTAACG
66 CCCGGTTACTCAATCAGTCACGTTCTAAGCTGCACTCATAACCTCGGGTTAACG
* * * *
55549203 GAGTTTTACCTAACACGTCACAGAACTTTTTGACGCGAAGTAGAAGGACAACCCAAGCACCTTAC
1 GAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAAGGACAACCCAAGCACCCTAC
* *
55549268 CCCGGTTACTCAGTCAGTCACGTTTTAAGCTGCACTCATAAC
66 CCCGGTTACTCAATCAGTCACGTTCTAAGCTGCACTCATAAC
55549310 TATGGAAACA
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
119 94 1.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (119 bp):
GAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAAGGACAACCCAAGCACCCTAC
CCCGGTTACTCAATCAGTCACGTTCTAAGCTGCACTCATAACCTCGGGTTAACG
Found at i:55550205 original size:8 final size:7
Alignment explanation
Indices: 55550194--55550248 Score: 58
Period size: 8 Copynumber: 7.3 Consensus size: 7
55550184 TTAATATTCA
55550194 AATAAAGT
1 AATAAA-T
55550202 AATAAAT
1 AATAAAT
55550209 AATAAAAT
1 AAT-AAAT
55550217 AAAATAAAGT
1 --AATAAA-T
55550227 AATAAAT
1 AATAAAT
55550234 AA-AAAT
1 AATAAAT
55550240 AATAAAT
1 AATAAAT
55550247 AA
1 AA
55550249 AATAAAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.14
7 13 0.31
8 16 0.38
9 3 0.07
10 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:55550219 original size:5 final size:5
Alignment explanation
Indices: 55550209--55550260 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
55550199 AGTAATAAAT
* *
55550209 AATAA AATAA AATAA AGTAATA AATAA AA-AT AAT-A AATAA AATAA AATAA
1 AATAA AATAA AATAA AAT-A-A AATAA AATAA AATAA AATAA AATAA AATAA
55550259 AA
1 AA
55550261 ATAGAAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 6 0.15
5 28 0.72
6 2 0.05
7 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:55550224 original size:17 final size:17
Alignment explanation
Indices: 55550202--55550268 Score: 77
Period size: 17 Copynumber: 3.9 Consensus size: 17
55550192 CAAATAAAGT
55550202 AATAAATAATAAAATAA
1 AATAAATAATAAAATAA
55550219 AATAAAGTAAT-AAATAA
1 AATAAA-TAATAAAATAA
55550236 AA-ATAATAAATAAAATAA
1 AATA-AAT-AATAAAATAA
55550254 AATAAA-AATAGAAAT
1 AATAAATAATA-AAAT
55550269 TGGGTAGCCT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.14
17 23 0.52
18 14 0.32
19 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AATAAATAATAAAATAA
Found at i:55550225 original size:25 final size:25
Alignment explanation
Indices: 55550193--55550263 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
55550183 ATTAATATTC
*
55550193 AAATAAAGTAATAAATAATAA-AAT
1 AAATAAAGTAATAAATAAAAATAAT
55550217 AAAATAAAGTAATAAATAAAAATAAT
1 -AAATAAAGTAATAAATAAAAATAAT
*
55550243 AAATAAAAT-A-AAATAAAAATA
1 AAATAAAGTAATAAATAAAAATA
55550264 GAAATTGGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.26
24 1 0.02
25 28 0.65
26 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (25 bp):
AAATAAAGTAATAAATAAAAATAAT
Found at i:55550250 original size:12 final size:12
Alignment explanation
Indices: 55550193--55550253 Score: 70
Period size: 12 Copynumber: 4.9 Consensus size: 12
55550183 ATTAATATTC
*
55550193 AAATAAAGTAAT
1 AAATAAAATAAT
55550205 AAATAATAA-AAT
1 AAATAA-AATAAT
*
55550217 AAAATAAAGTAAT
1 -AAATAAAATAAT
55550230 AAATAAAAATAAT
1 AAAT-AAAATAAT
55550243 AAATAAAATAA
1 AAATAAAATAA
55550254 AATAAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 21 0.50
13 21 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:55551993 original size:46 final size:45
Alignment explanation
Indices: 55551881--55552006 Score: 141
Period size: 45 Copynumber: 2.8 Consensus size: 45
55551871 AGTATATCTG
* *
55551881 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCG
1 TGCCGATGCCATGTCCCAGACATGATCTTACACTGACACATCTCA
* * *
55551926 TAGCCGATG-CATGTCCCAGACAT-ATTTTACA-TAGCACTCGTCTCAA
1 T-GCCGATGCCATGTCCCAGACATGATCTTACACT-G-ACACATCTC-A
*
55551972 TGCCGATGCCATGTCCCAGACATGGTCTTACACTG
1 TGCCGATGCCATGTCCCAGACATGATCTTACACTG
55552007 GCTCTCATAA
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
43 1 0.01
44 7 0.10
45 29 0.43
46 22 0.33
47 7 0.10
48 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (45 bp):
TGCCGATGCCATGTCCCAGACATGATCTTACACTGACACATCTCA
Found at i:55555405 original size:10 final size:10
Alignment explanation
Indices: 55555385--55555420 Score: 58
Period size: 9 Copynumber: 3.8 Consensus size: 10
55555375 CTATCCCTAT
55555385 AAAAT-ATTA
1 AAAATAATTA
55555394 AAAATAATTA
1 AAAATAATTA
55555404 AAAATAA-TA
1 AAAATAATTA
55555413 AAAATAAT
1 AAAATAAT
55555421 AGTATAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 14 0.56
10 11 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATAATTA
Found at i:55556342 original size:10 final size:10
Alignment explanation
Indices: 55556315--55556374 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
55556305 TTAAATTTTA
55556315 AAAGATAAAT
1 AAAGATAAAT
55556325 ACAA-ATAAAT
1 A-AAGATAAAT
*
55556335 AAAGATAATT
1 AAAGATAAAT
*
55556345 AAAGATAATT
1 AAAGATAAAT
55556355 AAAGATAAAT
1 AAAGATAAAT
55556365 GAAA-ATAAAT
1 -AAAGATAAAT
55556375 CCTAAAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:55557650 original size:137 final size:137
Alignment explanation
Indices: 55557454--55557728 Score: 532
Period size: 137 Copynumber: 2.0 Consensus size: 137
55557444 GCCCATTCAA
*
55557454 GTAATAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTC
1 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTC
55557519 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
66 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
55557584 CATTTGG
131 CATTTGG
*
55557591 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
1 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTC
55557656 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
66 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
55557721 CATTTGG
131 CATTTGG
55557728 G
1 G
55557729 GAGACTACTC
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 136 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTC
AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
CATTTGG
Found at i:55557686 original size:64 final size:64
Alignment explanation
Indices: 55557476--55557686 Score: 142
Period size: 64 Copynumber: 3.2 Consensus size: 64
55557466 CTGGGCCAGA
* *
55557476 GCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
55557540 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
55557602 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
55557613 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
55557677 GCCCATTTCA
1 GCCCATTTCA
55557687 AAATACATGC
Statistics
Matches: 102, Mismatches: 28, Indels: 34
0.62 0.17 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.25
65 5 0.05
66 1 0.01
67 10 0.10
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:55558013 original size:25 final size:27
Alignment explanation
Indices: 55557976--55558028 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
55557966 TCAAACATGC
55557976 ATTTAGGTCAATTTAACT-CTAGGGGT
1 ATTTAGGTCAATTTAACTACTAGGGGT
* *
55558002 ATTTCGGT-AATTTATCTACTAGGGGT
1 ATTTAGGTCAATTTAACTACTAGGGGT
55558028 A
1 A
55558029 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTACTAGGGGT
Found at i:55559543 original size:26 final size:26
Alignment explanation
Indices: 55559507--55559616 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
55559497 CATGAAATTC
55559507 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
55559533 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
55559559 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
55559585 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
55559611 TTATCA
1 TTATCA
55559617 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:55563544 original size:137 final size:137
Alignment explanation
Indices: 55563348--55563622 Score: 523
Period size: 137 Copynumber: 2.0 Consensus size: 137
55563338 GCCCATTCAA
*
55563348 GTAATAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTC
1 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTC
55563413 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
66 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
55563478 CATTTGG
131 CATTTGG
*
55563485 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
1 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTC
*
55563550 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATTCAACATCAGTAAACATATGCAAGCC
66 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
55563615 CATTTGG
131 CATTTGG
55563622 G
1 G
55563623 GAGACTACTC
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTC
AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
CATTTGG
Found at i:55563580 original size:64 final size:64
Alignment explanation
Indices: 55563370--55563580 Score: 142
Period size: 64 Copynumber: 3.2 Consensus size: 64
55563360 CTGGGCCAGA
* *
55563370 GCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
55563434 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
55563496 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
55563507 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
55563571 GCCCATTTCA
1 GCCCATTTCA
55563581 AAATACATTC
Statistics
Matches: 102, Mismatches: 28, Indels: 34
0.62 0.17 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.25
65 5 0.05
66 1 0.01
67 10 0.10
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:55566031 original size:94 final size:93
Alignment explanation
Indices: 55565868--55566860 Score: 1010
Period size: 94 Copynumber: 10.3 Consensus size: 93
55565858 CCCTTCGGGA
* * *
55565868 CTTATCACATTTATACACT-TCCACATCCAT--CATTGGCCATTCGG-CTTATCACATATATACA
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACA-ATATACA
55565929 CTTTCACATTCATCACATTGGCCATTCGGC
64 CTTTCACATTCATCACATTGGCCATTCGGC
* * * *
55565959 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCAATTCGGCCTTATCAC-ACATACACT
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAATATACAC-
55566023 TGTTCACATTCATCACATTGGCCATTCGGC
65 T-TTCACATTCATCACATTGGCCATTCGGC
* * * *
55566053 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCAATTCGGCCTTATCAC-ACATACACA
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAATATACAC-
55566117 TGTTCACATTCATCACATTGGCCATTCGGC
65 T-TTCACATTCATCACATTGGCCATTCGGC
* * * *
55566147 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCA-
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACA-ATATACAC
* **
55566211 TGTTCACACATACACATGTTCACATTCATCACATT-GGC
65 T-TT--CACAT--TCA---TCACATT-GGC-CATTCGGC
* * * ** * *
55566249 CAT-TCGGCCT-TATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTC
1 CTTATC-ACATATAT-ACATGTTCACA--TT--CA----TCACATTGGCCATTCGGCCTTATCAC
* *
55566312 ATATATGCA-TGTTCACATTCATCACATCGGCCATTCGGC
56 A-ATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
55566351 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--A-ATATAC
55566416 ACTTTCACATTCATCACATTGGCCATTCGGC
63 ACTTTCACATTCATCACATTGGCCATTCGGC
* *
55566447 CTTATCTCATATAT-CACGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC-ATATACACA
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAATATACAC-
55566510 TGTTCACATTCATCACATTGGCCATTCGGC
65 T-TTCACATTCATCACATTGGCCATTCGGC
*
55566540 CTTATCACATATATACACTTTCACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
1 CTTATCACATATATACA---T-----GTTCACATTCATCACATTGGCCATTCGGCCTTATCACA-
* *
55566605 ATATACACTTTCACATTCATCACATCGGCCATTAGGC
57 ATATACACTTTCACATTCATCACATTGGCCATTCGGC
* ** *
55566642 CTTATCACATATATACACT-TTCACATTCATCACATCGGCTGTTAGGCCTTATCACATATATACA
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACA-ATATACA
* *
55566706 CTTTCACATTCATCACATCGGCCATTAGGC
64 CTTTCACATTCATCACATTGGCCATTCGGC
* * *
55566736 CTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTAGCCCTTATCACATATATATA
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC----A-ATA
*
55566800 TACACTTTCACATTCATCACATTGGCCATTAGGC
60 TACACTTTCACATTCATCACATTGGCCATTCGGC
55566834 CTTATCACATATATACACT-TTCACATT
1 CTTATCACATATATACA-TGTTCACATT
55566861 TATTCAAATA
Statistics
Matches: 792, Mismatches: 60, Indels: 93
0.84 0.06 0.10
Matches are distributed among these distances:
90 1 0.00
91 31 0.04
92 8 0.01
93 55 0.07
94 332 0.42
95 39 0.05
96 56 0.07
97 1 0.00
98 69 0.09
100 3 0.00
101 15 0.02
102 109 0.14
103 15 0.02
104 10 0.01
106 4 0.01
108 5 0.01
110 39 0.05
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (93 bp):
CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAATATACACT
TTCACATTCATCACATTGGCCATTCGGC
Found at i:55566078 original size:141 final size:140
Alignment explanation
Indices: 55565868--55566860 Score: 1168
Period size: 141 Copynumber: 6.9 Consensus size: 140
55565858 CCCTTCGGGA
* *
55565868 CTTATCACATTTATACACT-TCCACATCCAT--CATTGGCCATTCGG-CTTATCACATATATACA
1 CTTATCACA--TATACACTGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
* *
55565929 CT-TTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCA-TGTTCACATTCATCAC
64 -TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCAC
*
55565992 ATTGGCAATTCGGC
127 ATTGGCCATTCGGC
* * *
55566006 CTTATCACACATACACTTGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCAT
1 CTTATCACATATACAC-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAT
* * *
55566071 GTTCACATTCATCACATTGGCAATTCGGCCTTATCACACATACACA-TGTTCACATTCATCACAT
65 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCACAT
55566135 TGGCCATTCGGC
129 TGGCCATTCGGC
*
55566147 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCAT
1 CTTATCACATATACAC-TGTTCACATTCATCACATTGGCCATTCGGCCTTA--TC----A--CA-
* * *
55566212 GTTCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA-TG
56 --T-----ATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-
55566276 TTCACATTCATCACATTGGCCATTCGGC
113 TTCACATTCATCACATTGGCCATTCGGC
* * * *
55566304 CTTATCTCATATATGCA-TGTTCACATTCATCACATCGGCCATTCGGCCTTATCACACATACACA
1 CTTATCACATATA--CACTGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
55566368 TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCAC
64 TGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCATCAC
55566433 ATTGGCCATTCGGC
127 ATTGGCCATTCGGC
* *
55566447 CTTATCTCATATATCAC-GTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACACAT
1 CTTATCACATATA-CACTGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAT
55566511 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACACTTTCACATTC
65 GTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATAT--A---T-ACACTTTCACATTC
55566576 ATCACATTGGCCATTCGGC
122 ATCACATTGGCCATTCGGC
* *
55566595 CTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CTTATCAC--ATATACACTGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
* ** *
55566659 CT-TTCACATTCATCACATCGGCTGTTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 -TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
* *
55566723 TCGGCCATTAGGC
128 TTGGCCATTCGGC
* * *
55566736 CTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTAGCCCTTATCACATATATATA
1 CTTATCAC--ATATACACTGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC----ATATA
*
55566800 TACACT-TTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATT
60 TACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATT
55566861 TATTCAAATA
Statistics
Matches: 774, Mismatches: 39, Indels: 77
0.87 0.04 0.09
Matches are distributed among these distances:
136 6 0.01
137 1 0.00
138 18 0.02
140 15 0.02
141 264 0.34
142 91 0.12
143 50 0.06
144 2 0.00
145 64 0.08
147 5 0.01
148 40 0.05
149 81 0.10
150 6 0.01
151 1 0.00
152 1 0.00
155 2 0.00
157 125 0.16
159 2 0.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (140 bp):
CTTATCACATATACACTGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATG
TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTG
GCCATTCGGC
Found at i:55566220 original size:110 final size:110
Alignment explanation
Indices: 55566104--55566328 Score: 450
Period size: 110 Copynumber: 2.0 Consensus size: 110
55566094 TTCGGCCTTA
55566104 TCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTC
1 TCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTC
55566169 ACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGT
66 ACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGT
55566214 TCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTC
1 TCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTC
55566279 ACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGT
66 ACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGT
55566324 TCACA
1 TCACA
55566329 TTCATCACAT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 115 1.00
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.32
Consensus pattern (110 bp):
TCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTC
ACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGT
Found at i:55566237 original size:47 final size:46
Alignment explanation
Indices: 55565898--55566859 Score: 705
Period size: 47 Copynumber: 19.9 Consensus size: 46
55565888 CCACATCCAT
* *
55565898 CATTGGCCATTCGG-CTTATCACATATATACACT-TTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACA-TGTTCACA-TCATCA
* * **
55565944 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACA-TCATCA
* *
55565991 CATTGGCAATTCGGCCTTATCACACATACACTTGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACA-TCATCA
* * **
55566038 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACA-TCATCA
*
55566085 CATTGGCAATTCGGCCTTATCACACATACACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACA-TCATCA
55566132 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACA-TCATCA
* * **
55566179 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACA-CATACA
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACATCAT-CA
* ** * * ** *
55566225 CA-TGTTCACATTCATCACATTGGCCATTCGGC-CTTATCACACATACACATGTTCA-CA
1 CATTG-GC-CATTCGGC-C-TT----A-TC-ACACATA-CACATGTTCACA---TCATCA
* * **
55566282 TTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 -------CATTGGCCATTCGGCCTTATCACACATACACATGTTCACA-TCATCA
*
55566336 CATCGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACA-TCATCA
* *
55566383 CATTGGCCATTCGGCCTTATCACATATATATACACT-TTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCAC--ACATACACA-TGTTCACA-TCATCA
* *
55566432 CATTGGCCATTCGGCCTTATCTCATATATCAC--GTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATA-CACATGTTCACA-TCATCA
*
55566478 CATTGGCCATTCGGCCTTATCACATATACACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACA-TCATCA
*
55566525 CATTGGCCATTCGGCCTTATCACATATATACACTTTCACACT-TTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCAC------ACA--TACACA-TGTTCACA-TCATCA
* *
55566580 CATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACA-TGTTCACA-TCATCA
* * * *
55566627 CATCGGCCATTAGGCCTTATCACATATATACACT-TTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACA-TGTTCACA-TCATCA
* ** * * *
55566674 CATCGGCTGTTAGGCCTTATCACATATATACACT-TTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACA-TGTTCACA-TCATCA
* * * *
55566721 CATCGGCCATTAGGCCTTATCACATATATACACT-TTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACACA-TGTTCACA-TCATCA
* * * * *
55566768 CATCGGCCATTAGCCCTTATCACATATATATATACACT-TTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCAC----ACATACACA-TGTTCACA-TCATCA
* * *
55566819 CATTGGCCATTAGGCCTTATCACATATATACACT-TTCACAT
1 CATTGGCCATTCGGCCTTATCACACATACACA-TGTTCACAT
55566860 TTATTCAAAT
Statistics
Matches: 797, Mismatches: 71, Indels: 96
0.83 0.07 0.10
Matches are distributed among these distances:
45 8 0.01
46 61 0.08
47 539 0.68
48 3 0.00
49 46 0.06
50 1 0.00
51 45 0.06
53 7 0.01
54 6 0.01
55 57 0.07
56 5 0.01
57 3 0.00
59 2 0.00
61 2 0.00
62 1 0.00
63 6 0.01
64 3 0.00
65 2 0.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (46 bp):
CATTGGCCATTCGGCCTTATCACACATACACATGTTCACATCATCA
Found at i:55566261 original size:63 final size:63
Alignment explanation
Indices: 55566151--55566281 Score: 226
Period size: 63 Copynumber: 2.1 Consensus size: 63
55566141 TTCGGCCTTA
* * **
55566151 TCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGT
1 TCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGT
55566214 TCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGT
1 TCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGT
55566277 TCACA
1 TCACA
55566282 TTCATCACAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (63 bp):
TCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGT
Found at i:55568244 original size:85 final size:85
Alignment explanation
Indices: 55568115--55568293 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
55568105 TATTTTATTG
*
55568115 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
55568180 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
55568200 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
55568265 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
55568285 CCCATGCTC
1 CCCATGCTC
55568294 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:55569594 original size:40 final size:40
Alignment explanation
Indices: 55569549--55569948 Score: 560
Period size: 40 Copynumber: 10.1 Consensus size: 40
55569539 CGAATACACG
* * * *
55569549 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * * *
55569589 ACACCAGCACGAATGCTCTTCGGG--TTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
55569627 TCACTAGCACGAATGCTCTTC-GAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
55569666 TCACTAGCATGAATGCTCTTC-GGACTTAAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTT-AGCCCGGATACA
* *
55569706 TCACTAGCACGAATGCTCTCGTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCT--TCGGGACTTAGCCCGGATACA
*
55569748 TCACTAGCATGAATGCTCTT-GGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
55569787 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
55569827 TCACTAGCATGAATTGCTCTTCAGGACTTAGCCCGGATACA
1 TCACTAGCATGAA-TGCTCTTCGGGACTTAGCCCGGATACA
55569868 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
55569908 TCACTAGCATGAATGCTCTTCGGGACTTAGCTCGGAT-CA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
55569947 TC
1 TC
55569949 GTCGAGACCT
Statistics
Matches: 331, Mismatches: 21, Indels: 17
0.90 0.06 0.05
Matches are distributed among these distances:
37 1 0.00
38 31 0.09
39 79 0.24
40 145 0.44
41 38 0.11
42 32 0.10
43 5 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:55569778 original size:121 final size:118
Alignment explanation
Indices: 55569549--55569948 Score: 572
Period size: 121 Copynumber: 3.4 Consensus size: 118
55569539 CGAATACACG
* * * * * * *
55569549 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGG-G
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAC
* * * *
55569613 TTAGCACGGATATATCACTAGCACGAATGCTCTTCGAACTTAGCCCGGATACA
66 TTAGCCCGGATACATCACTAGCATGAATGCTCTTGGAACTTAGCCCGGATACA
55569666 TCACTAGCATGAATGCTCTTC-GGACTTAAGCCCGGATACATCACTAGCACGAATGCTCTCGTCG
1 TCACTAGCATGAATGCTCTTCGGGACTT-AGCCCGGATACATCACTAGCACGAATGCTCT--TCG
55569730 GAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTGGAACTTAGCCCGGATACA
63 G-ACTTAGCCCGGATACATCACTAGCATGAATGCTCTTGGAACTTAGCCCGGATACA
* * *
55569787 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATTGCTCTTCAGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA-TGCTCTTC-GG
*
55569852 ACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
64 ACTTAGCCCGGATACATCACTAGCATGAATGCTCTT-GGAACTTAGCCCGGATACA
*
55569908 TCACTAGCATGAATGCTCTTCGGGACTTAGCTCGGAT-CATC
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATC
55569949 GTCGAGACCT
Statistics
Matches: 256, Mismatches: 18, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
116 5 0.02
117 47 0.18
119 4 0.02
120 42 0.16
121 147 0.57
122 11 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (118 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAC
TTAGCCCGGATACATCACTAGCATGAATGCTCTTGGAACTTAGCCCGGATACA
Found at i:55569856 original size:81 final size:79
Alignment explanation
Indices: 55569562--55569948 Score: 575
Period size: 81 Copynumber: 4.9 Consensus size: 79
55569552 CCAGCATGAT
* * * * * * * * *
55569562 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGG-GTTAGCACGGATAT
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATAC
55569626 ATCACTAGCACGAA
66 ATCACTAGCACGAA
55569640 TGCTCTTC-GAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGACTTAAGCCCGGATA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGACTT-AGCCCGGATA
55569704 CATCACTAGCACGAA
65 CATCACTAGCACGAA
55569719 TGCTCTCGTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTT-GGAACTTAGCCCGGA
1 TGCTCT--TCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGG-ACTTAGCCCGGA
55569783 TACATCACTAGCACGAA
63 TACATCACTAGCACGAA
55569800 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATTGCTCTTCAGGACTTAGCCCGGAT
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA-TGCTCTTC-GGACTTAGCCCGGAT
*
55569865 ACATCACTAGCATGAA
64 ACATCACTAGCACGAA
* *
55569881 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCTCGGAT-
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATA
55569945 CATC
65 CATC
55569949 GTCGAGACCT
Statistics
Matches: 287, Mismatches: 13, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
77 35 0.12
78 10 0.03
79 67 0.23
80 29 0.10
81 102 0.36
82 44 0.15
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATAC
ATCACTAGCACGAA
Found at i:55570071 original size:38 final size:38
Alignment explanation
Indices: 55570002--55570076 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
55569992 GAATTTTAAT
*
55570002 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
* *
55570040 CCGGACATAATCTCT-TCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTGT-ACATAGCCAGCGGGTCTTTA
55570077 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
Found at i:55572589 original size:14 final size:12
Alignment explanation
Indices: 55572561--55572585 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55572551 GGCCTTATCA
55572561 CATATATCACAT
1 CATATATCACAT
55572573 CATATATCACAT
1 CATATATCACAT
55572585 C
1 C
55572586 TCATCGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (12 bp):
CATATATCACAT
Found at i:55572684 original size:47 final size:47
Alignment explanation
Indices: 55572629--55573161 Score: 781
Period size: 47 Copynumber: 11.3 Consensus size: 47
55572619 CTTATCATAC
*
55572629 ACAT-TTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATAT
1 ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT
* * *
55572675 GCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATAC
1 ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT
* *
55572722 ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATAC
1 ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT
* *
55572769 ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATAC
1 ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT
* *
55572816 ACATGTTCACATTCATCACATTGGCCATTCGACCTTATCTCATATAT
1 ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT
* * *
55572863 GCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATAC
1 ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT
55572910 ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATGTAT
1 ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATA--TAT
55572959 ACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT
1 ACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT
* *
55573006 ACACT-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
1 ACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT
* *
55573053 ACACT-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 ACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATAT
*
55573102 ACACT-TTCACATTCATCACATTGGCCATTAGGCCTTATCACATATAT
1 ACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT
55573149 ACACT-TTCACATT
1 ACA-TGTTCACATT
55573162 TATTCAAATA
Statistics
Matches: 461, Mismatches: 20, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
46 3 0.01
47 367 0.80
49 90 0.20
50 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (47 bp):
ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT
Found at i:55572715 original size:107 final size:103
Alignment explanation
Indices: 55572519--55573149 Score: 362
Period size: 94 Copynumber: 6.5 Consensus size: 103
55572509 TATCACATTT
*
55572519 ATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATCACATCATATATCACA
1 ATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATAT---AGCATATATCACA
*
55572584 TCTCATCGCATTGGACATTCATCACATTCATCAGGCTTATC
63 TCTCATCACATTGGACATTCATCACATTCATCAGGCTTATC
* * * *
55572625 ATACACATTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATAT-GCATGT-TCACAT-
1 ATACAC-TTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATAGCATATATCACATC
* **
55572687 TCATCACATTGGCCATTCGGC-C-TT-ATCA--C--A-C
65 TCATCACATTGGACATTCATCACATTCATCAGGCTTATC
* * * * *
55572718 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACA-CATGT-TCACAT
1 ATACAC-T-TCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATAGCATATATCACAT
* **
55572781 -TCATCACATTGGCCATTCGGC-C-TT-ATCA--C--A-C
64 CTCATCACATTGGACATTCATCACATTCATCAGGCTTATC
* * * * *
55572812 ATACACATGTTCACATTCATCACATTGGCCATTCGACCTTATCTCATATAT-GCATGT-TCACAT
1 ATACAC-T-TCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATAGCATATATCACAT
* **
55572875 -TCATCACATTGGCCATTCGGC-C-TT-ATCA--C--A-C
64 CTCATCACATTGGACATTCATCACATTCATCAGGCTTATC
* *
55572906 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATGTATA-CACT-T-TCA
1 ATACAC-T-TCCACATCCATCACATTGGCCATTCGGCCTTATCACATA--TATAGCA-TATATCA
* ** *
55572968 CAT-TCATCACATTGGCCATTCGGC-C-TT-ATCA--CATAT-
61 CATCTCATCACATTGGACATTCATCACATTCATCAGGCTTATC
* * * *
55573004 ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA-CACT-T-TCACAT-
1 ATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATAGCA-TATATCACATC
* * *
55573065 TCATCACATCGGCCATT-AGGC-C-TT-ATCA--CATATAT-
65 TCATCACATTGGACATTCA-TCACATTCATCAGGC-T-TATC
* * *
55573100 ATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
1 ATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATA
55573150 CACTTTCACA
Statistics
Matches: 487, Mismatches: 24, Indels: 38
0.89 0.04 0.07
Matches are distributed among these distances:
93 9 0.02
94 258 0.53
96 131 0.27
97 2 0.00
98 11 0.02
99 2 0.00
100 1 0.00
101 17 0.03
102 6 0.01
103 4 0.01
106 6 0.01
107 40 0.08
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (103 bp):
ATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATAGCATATATCACATCT
CATCACATTGGACATTCATCACATTCATCAGGCTTATC
Found at i:55573079 original size:143 final size:141
Alignment explanation
Indices: 55572624--55573161 Score: 809
Period size: 143 Copynumber: 3.8 Consensus size: 141
55572614 TCAGGCTTAT
* *
55572624 CATACACAT-TTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATT
1 CATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATT
* *
55572688 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCG
66 CATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCG
55572753 GCCTTATCACA
131 GCCTTATCACA
* *
55572764 CATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATT
1 CATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATT
* * *
55572829 CATCACATTGGCCATTCGACCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCG
66 CATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCG
55572894 GCCTTATCACA
131 GCCTTATCACA
55572905 CATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATGTATACACT-TTCAC
1 CATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATA--TATACA-TGTTCAC
*
55572969 ATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCACATCGGCCA
63 ATTCATCACATTGGCCATTCGGCCTTATCACATATATACA-TGTTCACATTCATCACATTGGCCA
*
55573033 TTAGGCCTTATCACA
127 TTCGGCCTTATCACA
* * * *
55573048 TATATACACT-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACT-TTCA
1 CATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACA-TGTTCA
*
55573111 CATTCATCACATTGGCCATTAGGCCTTATCACATATATACACT-TTCACATT
62 CATTCATCACATTGGCCATTCGGCCTTATCACATATATACA-TGTTCACATT
55573162 TATTCAAATA
Statistics
Matches: 369, Mismatches: 21, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
140 9 0.02
141 170 0.46
143 184 0.50
144 3 0.01
145 3 0.01
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (141 bp):
CATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATT
CATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCG
GCCTTATCACA
Found at i:55574550 original size:85 final size:85
Alignment explanation
Indices: 55574421--55574599 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
55574411 TATTTTATTG
*
55574421 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
55574486 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
55574506 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
55574571 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
55574591 CCCATGCTC
1 CCCATGCTC
55574600 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:55576316 original size:26 final size:26
Alignment explanation
Indices: 55576278--55576361 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
55576268 CATGAAATTC
* *
55576278 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
55576304 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
55576330 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
55576356 TTATCA
1 TTATCA
55576362 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:55582676 original size:26 final size:26
Alignment explanation
Indices: 55582640--55582694 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
55582630 TAAAATATGC
*
55582640 TCTCTTTGCTCTCATATTCTCTTTGT
1 TCTCTTTGCTCTCACATTCTCTTTGT
*
55582666 TCTCTTTGCTCTCCCATTCTCTTTGT
1 TCTCTTTGCTCTCACATTCTCTTTGT
55582692 TCT
1 TCT
55582695 TTATTCTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.05, C:0.31, G:0.07, T:0.56
Consensus pattern (26 bp):
TCTCTTTGCTCTCACATTCTCTTTGT
Found at i:55583774 original size:23 final size:24
Alignment explanation
Indices: 55583742--55583791 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
55583732 AAATTATATT
*
55583742 TAATTATTTTCTAA-ATTT-TTTCA
1 TAATTATTTT-TAACATTTCTTTAA
*
55583765 TAATTTTTTTTAACATTTCTTTAA
1 TAATTATTTTTAACATTTCTTTAA
55583789 TAA
1 TAA
55583792 AATGGATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 13 0.57
24 7 0.30
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATTATTTTTAACATTTCTTTAA
Found at i:55583884 original size:16 final size:17
Alignment explanation
Indices: 55583865--55583897 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
55583855 CTAGATTGAA
55583865 TTTAAAAAAT-AATATT
1 TTTAAAAAATAAATATT
*
55583881 TTTAAAATATAAATATT
1 TTTAAAAAATAAATATT
55583898 ATAATAGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAAAAATAAATATT
Found at i:55585527 original size:6 final size:6
Alignment explanation
Indices: 55585516--55585554 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
55585506 ATAAATAAAA
55585516 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAA
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAA
55585555 ATCACATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
TAATAT
Found at i:55588614 original size:13 final size:13
Alignment explanation
Indices: 55588596--55588621 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55588586 TCGGTCGATT
55588596 AAAGAAGAATAAA
1 AAAGAAGAATAAA
55588609 AAAGAAGAATAAA
1 AAAGAAGAATAAA
55588622 TGAAGTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (13 bp):
AAAGAAGAATAAA
Found at i:55590288 original size:46 final size:45
Alignment explanation
Indices: 55590220--55590316 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 45
55590210 GACTCACCAC
* *
55590220 AGCTCATATGAGCTTACTGATTCAACTCG-TAAGAGCTTACTATTTT
1 AGCTCATATGAGCTTACCGATTCAACTCGAT-AGAGCTTACT-GTTT
* *
55590266 AGCTCAT-TGGAGCTTCCCGATTCAGCTCGATAGAGCTTACTGTTT
1 AGCTCATAT-GAGCTTACCGATTCAACTCGATAGAGCTTACTGTTT
55590311 AGCTCA
1 AGCTCA
55590317 ACAGAGCTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
45 10 0.22
46 34 0.76
47 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (45 bp):
AGCTCATATGAGCTTACCGATTCAACTCGATAGAGCTTACTGTTT
Found at i:55606744 original size:23 final size:23
Alignment explanation
Indices: 55606718--55606769 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
55606708 GGACTCACCA
*
55606718 TAGCTTGTATGAGCTTACTGA-TT
1 TAGCTCGTATGAGCTTACT-ATTT
55606741 TAGCTCGTATGAGCTTACTATTT
1 TAGCTCGTATGAGCTTACTATTT
55606764 TAGCTC
1 TAGCTC
55606770 ATTGGAGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.42
Consensus pattern (23 bp):
TAGCTCGTATGAGCTTACTATTT
Found at i:55606777 original size:23 final size:22
Alignment explanation
Indices: 55606728--55606849 Score: 93
Period size: 23 Copynumber: 5.3 Consensus size: 22
55606718 TAGCTTGTAT
*
55606728 GAGCTTACTGATTTAGCTC-GTA
1 GAGCTTACT-ATTTAGCTCAATA
* *
55606750 TGAGCTTACTATTTTAGCTCATTG
1 -GAGCTTACTA-TTTAGCTCAATA
* * * *
55606774 GAGCTTATTGATTCAACTCGATA
1 GAGCTTACT-ATTTAGCTCAATA
* *
55606797 GAGCTTACTGTTTAGCTCAATG
1 GAGCTTACTATTTAGCTCAATA
*
55606819 GAGCTTACCATTTTCAGCTCAATA
1 GAGCTTACTA-TTT-AGCTCAATA
55606843 GAGCTTA
1 GAGCTTA
55606850 TTGTTTATCA
Statistics
Matches: 77, Mismatches: 17, Indels: 9
0.75 0.17 0.09
Matches are distributed among these distances:
22 17 0.22
23 43 0.56
24 17 0.22
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (22 bp):
GAGCTTACTATTTAGCTCAATA
Found at i:55606786 original size:46 final size:45
Alignment explanation
Indices: 55606728--55606826 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 45
55606718 TAGCTTGTAT
* * * *
55606728 GAGCTTACTGATTTAGCTCG-TATGAGCTTACTATTTTAGCTCATTG
1 GAGCTTACTGATTCAACTCGATA-GAGCTTACT-GTTTAGCTCAATG
*
55606774 GAGCTTATTGATTCAACTCGATAGAGCTTACTGTTTAGCTCAATG
1 GAGCTTACTGATTCAACTCGATAGAGCTTACTGTTTAGCTCAATG
55606819 GAGCTTAC
1 GAGCTTAC
55606827 CATTTTCAGC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 18 0.39
46 26 0.57
47 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.37
Consensus pattern (45 bp):
GAGCTTACTGATTCAACTCGATAGAGCTTACTGTTTAGCTCAATG
Found at i:55606844 original size:46 final size:44
Alignment explanation
Indices: 55606751--55606856 Score: 115
Period size: 46 Copynumber: 2.3 Consensus size: 44
55606741 TAGCTCGTAT
* * *
55606751 GAGCTTACTATTTTAGCTCATTGGAGCTTATTGATTCAACTCGATA
1 GAGCTTACT-GTTTAGCTCAATGGAGCTTATT-ATTCAACTCAATA
*
55606797 GAGCTTACTGTTTAGCTCAATGGAGCTTACCATT-TTCAGCTCAATA
1 GAGCTTACTGTTTAGCTCAATGGAGCTT---ATTATTCAACTCAATA
*
55606843 GAGCTTATTGTTTA
1 GAGCTTACTGTTTA
55606857 TCAGCTCAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
45 17 0.33
46 32 0.62
48 3 0.06
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (44 bp):
GAGCTTACTGTTTAGCTCAATGGAGCTTATTATTCAACTCAATA
Found at i:55611623 original size:26 final size:26
Alignment explanation
Indices: 55611594--55611645 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
55611584 CTTCGATCAT
55611594 GTAAAGGAATCTATAACCTATCAATC
1 GTAAAGGAATCTATAACCTATCAATC
55611620 GTAAAGGAATCTATAACCTATCAATC
1 GTAAAGGAATCTATAACCTATCAATC
55611646 TCTCAAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (26 bp):
GTAAAGGAATCTATAACCTATCAATC
Found at i:55615564 original size:44 final size:42
Alignment explanation
Indices: 55615499--55615666 Score: 149
Period size: 43 Copynumber: 3.9 Consensus size: 42
55615489 TAGGATTCAA
55615499 ATATGTGATTTCGTGTAAGACCACATCTGGGACATTGGCATC
1 ATATGTGATTTCGTGTAAGACCACATCTGGGACATTGGCATC
* ** *
55615541 AATTTGTGATTTGCGTGTAAGACCATGTCTGGGACATCGGCATC
1 -ATATGTGATTT-CGTGTAAGACCACATCTGGGACATTGGCATC
* * * * * * *
55615585 GTATATGAGTTCGTGTAAAACC-CTATCTGAGATAGTGGCATC
1 ATATGTGATTTCGTGTAAGACCAC-ATCTGGGACATTGGCATC
* * * * *
55615627 GATATGTGATTGCATGTAAGATCACGTCTGGGACGTTGGC
1 -ATATGTGATTTCGTGTAAGACCACATCTGGGACATTGGC
55615667 TTGTACGAGT
Statistics
Matches: 94, Mismatches: 27, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
42 23 0.24
43 42 0.45
44 29 0.31
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (42 bp):
ATATGTGATTTCGTGTAAGACCACATCTGGGACATTGGCATC
Found at i:55617320 original size:46 final size:46
Alignment explanation
Indices: 55617219--55617306 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
55617209 TGTAACCTAC
* * *
55617219 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
* *
55617265 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTC
55617307 AACCATCCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:55623465 original size:20 final size:20
Alignment explanation
Indices: 55623427--55623463 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55623417 AGGGAAGAAG
*
55623427 AAAAGAAAAATGAAGAAATA
1 AAAAGAAAAATGAAAAAATA
55623447 AAAAGAAAAA-GAAAAAA
1 AAAAGAAAAATGAAAAAA
55623464 ATTAAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAATGAAAAAATA
Found at i:55625598 original size:31 final size:30
Alignment explanation
Indices: 55625563--55625636 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
55625553 TTAATGGTTC
* *
55625563 AGTGACTAAAATGTTACAACATTT-TAACGTA
1 AGTGACTAAAATGTT--AACATTTCAAACATA
*
55625594 AGTGACTAAAACG-TAACATTTCAAACATA
1 AGTGACTAAAATGTTAACATTTCAAACATA
55625623 AGTGACTAAAATGT
1 AGTGACTAAAATGT
55625637 AATTTAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 7 0.19
29 17 0.46
30 1 0.03
31 12 0.32
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (30 bp):
AGTGACTAAAATGTTAACATTTCAAACATA
Found at i:55629331 original size:3 final size:3
Alignment explanation
Indices: 55629323--55629352 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
55629313 AATAAACTTT
55629323 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55629353 AAGACAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55636245 original size:22 final size:21
Alignment explanation
Indices: 55636204--55636245 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
55636194 CACTTTTTCA
*
55636204 TTATGTTTTTTATGTTTTCTT
1 TTATGTTTTTTATGTCTTCTT
55636225 TTATAGTTTTTTCAT-TCTTCT
1 TTAT-GTTTTTT-ATGTCTTCT
55636246 GAATTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 12 0.67
23 2 0.11
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (21 bp):
TTATGTTTTTTATGTCTTCTT
Found at i:55636442 original size:23 final size:22
Alignment explanation
Indices: 55636394--55636449 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
55636384 ACATACACAT
* * *
55636394 TATTATTTTTTAAGATAATTTA
1 TATTTTTTTTTAAAAAAATTTA
55636416 -ATTTTTTTTTAAAAAATATTTA
1 TATTTTTTTTTAAAAAA-ATTTA
55636438 TATTTATTTTTT
1 TATTT-TTTTTT
55636450 TTATGTGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 13 0.46
22 5 0.18
23 4 0.14
24 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTTTTTTTTAAAAAAATTTA
Found at i:55643029 original size:40 final size:40
Alignment explanation
Indices: 55642992--55643216 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
55642982 GCTACTCGTT
* *
55642992 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
55643032 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
55643072 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** *
55643112 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
** * * * *
55643152 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
*
55643192 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
55643217 CATCATTCAA
Statistics
Matches: 171, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 19 0.11
40 150 0.88
41 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:55651141 original size:38 final size:39
Alignment explanation
Indices: 55650977--55651200 Score: 267
Period size: 40 Copynumber: 5.7 Consensus size: 39
55650967 GCTACTCGTT
* *
55650977 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
*
55651017 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
*
55651057 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
* *
55651097 CAAATGCCTTC-GGATCTTAGTCCGGATTAGT-ACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTAGTAACTCGCA
* * * *
55651135 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
55651176 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55651201 CATCATTCAA
Statistics
Matches: 168, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
38 33 0.20
39 11 0.07
40 113 0.67
41 11 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:55651160 original size:118 final size:120
Alignment explanation
Indices: 55650977--55651200 Score: 287
Period size: 118 Copynumber: 1.9 Consensus size: 120
55650967 GCTACTCGTT
*
55650977 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
55651042 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * **
55651097 CAAATGCCTTC-GGATCTTAGTCCGGAT-TAGT-ACTCGTACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
55651158 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
55651201 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
117 3 0.03
118 52 0.58
119 15 0.17
120 20 0.22
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:55654240 original size:68 final size:68
Alignment explanation
Indices: 55654121--55654276 Score: 217
Period size: 68 Copynumber: 2.3 Consensus size: 68
55654111 GTGAAAGTTT
* * *
55654121 GCCAAGACATTAAACATGGGGATTACAGGTGTAAGACCATAGCTCAGCTATGGCA-ACCAATTGA
1 GCCAAGACATTAAACATGAGGATTACAGGTGTAAGACCATAACTCAGCTATGG-AGACCAATAGA
55654185 GTCC
65 GTCC
* * *
55654189 GCCAGGACATTAGACATGAGGATTACAGGTGTAAGACCATAACTC-GACTATGGAGACCAGTAGA
1 GCCAAGACATTAAACATGAGGATTACAGGTGTAAGACCATAACTCAG-CTATGGAGACCAATAGA
*
55654253 GTCT
65 GTCC
55654257 GCCAAGACATTAAACATGAG
1 GCCAAGACATTAAACATGAG
55654277 ACATGATGAG
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
67 2 0.03
68 75 0.97
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (68 bp):
GCCAAGACATTAAACATGAGGATTACAGGTGTAAGACCATAACTCAGCTATGGAGACCAATAGAG
TCC
Found at i:55657523 original size:22 final size:23
Alignment explanation
Indices: 55657498--55657549 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
55657488 TATAAAACCT
55657498 AATAAAAA-TAAG-CTTAAAGAAA
1 AATAAAAAGT-AGTCTTAAAGAAA
**
55657520 AATAAAAAGTAGTCTTAAATTAA
1 AATAAAAAGTAGTCTTAAAGAAA
55657543 AATAAAA
1 AATAAAA
55657550 GGAACAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.23
Consensus pattern (23 bp):
AATAAAAAGTAGTCTTAAAGAAA
Found at i:55660310 original size:17 final size:17
Alignment explanation
Indices: 55660288--55660322 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55660278 TGTGTTATTC
55660288 GAATTAC-AGGCTTGAAG
1 GAATTACGA-GCTTGAAG
55660305 GAATTACGAGCTTGAAG
1 GAATTACGAGCTTGAAG
55660322 G
1 G
55660323 GTGATTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.34, C:0.11, G:0.31, T:0.23
Consensus pattern (17 bp):
GAATTACGAGCTTGAAG
Found at i:55663663 original size:13 final size:13
Alignment explanation
Indices: 55663645--55663669 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55663635 CTTAGCTGGG
55663645 ACACGCCCGTGTT
1 ACACGCCCGTGTT
55663658 ACACGCCCGTGT
1 ACACGCCCGTGT
55663670 GCGATTACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
ACACGCCCGTGTT
Found at i:55665253 original size:79 final size:82
Alignment explanation
Indices: 55665142--55665326 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
55665132 GCTACTCGTT
* *
55665142 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
55665205 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
55665222 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
55665285 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
55665302 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55665327 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:55665326 original size:40 final size:40
Alignment explanation
Indices: 55665123--55665326 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
55665113 CGGAATTTAA
** *
55665123 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55665163 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
55665203 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55665242 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
55665282 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
55665322 CCGGA
1 CCGGA
55665327 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:55669318 original size:22 final size:22
Alignment explanation
Indices: 55669290--55669411 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
55669280 TTCCACATCC
55669290 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
55669312 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
55669336 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
55669359 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
55669383 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
55669406 ATCACA
1 ATCACA
55669412 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:55669325 original size:47 final size:47
Alignment explanation
Indices: 55669262--55669565 Score: 425
Period size: 47 Copynumber: 6.4 Consensus size: 47
55669252 CCCTTCGGGA
* * *
55669262 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
55669309 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
55669356 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
55669403 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
55669450 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
55669497 CTTATCACGCATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCA--CATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
55669546 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
55669566 GTACATCAAT
Statistics
Matches: 239, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 197 0.82
49 40 0.17
50 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:55675448 original size:24 final size:23
Alignment explanation
Indices: 55675421--55675525 Score: 69
Period size: 24 Copynumber: 4.6 Consensus size: 23
55675411 GAGTCATGGT
55675421 CAGTAAGCTCCT-TTGAGCTAAAAA
1 CAGTAAGCTCCTATTGAGCT--AAA
* *
55675445 CAGTAAACT-CTATTGAGCTGAA
1 CAGTAAGCTCCTATTGAGCTAAA
*
55675467 CAGTAAGCT-CT-TTCGAGATAAA
1 CAGTAAGCTCCTATT-GAGCTAAA
* *
55675489 TC-GATAAGCTTC-AATGAGCTGAAA
1 -CAG-TAAGCTCCTATTGAGCT-AAA
55675513 CAGTAAGCTCCTA
1 CAGTAAGCTCCTA
55675526 CAAGCTGTAG
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
21 2 0.03
22 19 0.30
23 21 0.33
24 22 0.34
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (23 bp):
CAGTAAGCTCCTATTGAGCTAAA
Found at i:55691049 original size:56 final size:56
Alignment explanation
Indices: 55690958--55691080 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
55690948 GAGATTGGCG
* * *
55690958 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
55691015 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
55691070 CTGAGTGTGCG
1 CTAAGTGTGCG
55691081 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:55691067 original size:27 final size:28
Alignment explanation
Indices: 55690958--55691080 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
55690948 GAGATTGGCG
* * * *
55690958 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
55690987 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
55691015 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
55691043 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
55691070 CTGAGTGTGCG
1 CTAAGTGTGCG
55691081 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:55691091 original size:27 final size:27
Alignment explanation
Indices: 55690983--55691093 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
55690973 TAAATTGTAC
* * *
55690983 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
55691011 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
55691039 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
55691066 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
55691093 A
1 A
55691094 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:55699248 original size:56 final size:56
Alignment explanation
Indices: 55699157--55699279 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
55699147 GAGATTGGCG
* * *
55699157 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
55699214 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
55699269 CTGAGTGTGCG
1 CTAAGTGTGCG
55699280 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:55699266 original size:27 final size:28
Alignment explanation
Indices: 55699157--55699279 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
55699147 GAGATTGGCG
* * * *
55699157 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
55699186 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
55699214 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
55699242 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
55699269 CTGAGTGTGCG
1 CTAAGTGTGCG
55699280 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:55699290 original size:27 final size:27
Alignment explanation
Indices: 55699182--55699292 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
55699172 TAAATTGTAC
* * *
55699182 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
55699210 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
55699238 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
55699265 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
55699292 A
1 A
55699293 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:55706245 original size:20 final size:20
Alignment explanation
Indices: 55706222--55706259 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55706212 ATGTATATGT
*
55706222 ATATATAAATATAAATATCA
1 ATATATAAAGATAAATATCA
55706242 ATATATAAAGATAAATAT
1 ATATATAAAGATAAATAT
55706260 TATATAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (20 bp):
ATATATAAAGATAAATATCA
Found at i:55710744 original size:25 final size:24
Alignment explanation
Indices: 55710716--55710830 Score: 107
Period size: 23 Copynumber: 4.9 Consensus size: 24
55710706 TAAGCTCCTC
* *
55710716 TGAGCTGATAAATAGTAAGGTCTAT
1 TGAGCTGA-AAACAGTAAGCTCTAT
*
55710741 TGAGCTGAAAACGGTAAGCTCTAT
1 TGAGCTGAAAACAGTAAGCTCTAT
*
55710765 TTAGCT--AAACAGTAAGCTCT-T
1 TGAGCTGAAAACAGTAAGCTCTAT
* *
55710786 TCGAGCTG-AATCAGTAAGCT-TCAA
1 T-GAGCTGAAAACAGTAAGCTCT-AT
55710810 TGAGCTG-AAACAGTAAGCTCT
1 TGAGCTGAAAACAGTAAGCTCT
55710831 TACAAGCTGT
Statistics
Matches: 76, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
21 2 0.03
22 18 0.24
23 28 0.37
24 20 0.26
25 8 0.11
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (24 bp):
TGAGCTGAAAACAGTAAGCTCTAT
Found at i:55710838 original size:23 final size:23
Alignment explanation
Indices: 55710767--55710839 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
55710757 AGCTCTATTT
* *
55710767 AGCT-AAACAGTAAGCTCTTTCG
1 AGCTGAAACAGTAAGCTCTTACA
* *
55710789 AGCTGAATCAGTAAGCT-TCA-A
1 AGCTGAAACAGTAAGCTCTTACA
55710810 TGAGCTGAAACAGTAAGCTCTTACA
1 --AGCTGAAACAGTAAGCTCTTACA
55710835 AGCTG
1 AGCTG
55710840 TGGTGAGTCC
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
22 5 0.12
23 32 0.80
24 2 0.05
25 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (23 bp):
AGCTGAAACAGTAAGCTCTTACA
Found at i:55718233 original size:37 final size:37
Alignment explanation
Indices: 55718174--55718282 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
55718164 AGCTCAGACG
* *
55718174 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
55718211 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
55718248 TAATCTCCATACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
55718283 ATATATTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:55718487 original size:50 final size:50
Alignment explanation
Indices: 55718433--55718529 Score: 151
Period size: 50 Copynumber: 1.9 Consensus size: 50
55718423 ATCGCCTACG
55718433 TATTTCACACTAG-CCATTCGGCTTTACCACATATACATATCTCATATATA
1 TATTTCACA-TAGACCATTCGGCTTTACCACATATACATATCTCATATATA
* * *
55718483 TATTTCACATTGACCATTCGGCTTTACCACGTATGCATATCTCATAT
1 TATTTCACATAGACCATTCGGCTTTACCACATATACATATCTCATAT
55718530 TCATCACATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 2 0.05
50 41 0.95
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (50 bp):
TATTTCACATAGACCATTCGGCTTTACCACATATACATATCTCATATATA
Found at i:55718586 original size:47 final size:47
Alignment explanation
Indices: 55718487--55718679 Score: 246
Period size: 47 Copynumber: 4.1 Consensus size: 47
55718477 TATATATATT
* * * * *
55718487 TCACATTGACCATTCGGCTTTA-C-CACGTATGCATATCTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCAT-GCTCACATTCA
55718533 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
* *
55718580 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
* * * ** *
55718627 TCACATTGGCCATTCGGCCTTATCTCATATATACATATTCACTTTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
55718674 TCACAT
1 TCACAT
55718680 AAAATCCTAA
Statistics
Matches: 134, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
46 20 0.15
47 104 0.78
48 10 0.07
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
Found at i:55718607 original size:22 final size:22
Alignment explanation
Indices: 55718532--55718650 Score: 59
Period size: 23 Copynumber: 5.1 Consensus size: 22
55718522 TCTCATATTC
55718532 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
55718554 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGGCCTT
55718578 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * *
55718601 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
55718625 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
55718648 ATC
1 ATC
55718651 TCATATATAC
Statistics
Matches: 71, Mismatches: 10, Indels: 32
0.63 0.09 0.28
Matches are distributed among these distances:
22 18 0.25
23 19 0.27
24 19 0.27
25 15 0.21
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:55720488 original size:96 final size:95
Alignment explanation
Indices: 55720338--55720676 Score: 385
Period size: 96 Copynumber: 3.5 Consensus size: 95
55720328 GACCATGGCG
* * * ***
55720338 ATATGAGAGCCAGTGTAAGACCATGTATGGGACATGGCATCGGCCTCGATATGTGTCAGTGTAAG
1 ATATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTTTATGTGTCAGTGTAAG
*
55720403 ACCATGTCTAGGACATGGCATCGGCACCGGT
66 ACCATGTCTGGGACATGGCATCGGCACC-GT
* * * * * *
55720434 ATATGCGAGCTAGTGTAAGACCATGTTTGGAACATGGTATCGACATTTTTATGTGAGCCAGAGTA
1 ATATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTTTATGT--GTCAGTGTA
* *
55720499 AGACCATGCCTGGGACATGGCATCGGC-CTC-A
64 AGACCATGTCTGGGACATGGCATCGGCAC-CGT
** * *
55720530 ATATTCGAGCTAGCGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTGTATGTGTCAGTGTA
1 ATATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATT-TT-TATGTGTCAGTGTA
*
55720595 AGACCATGTCTGGGACATGGCATCGACACCGAT
64 AGACCATGTCTGGGACATGGCATCGGCACCG-T
* ** *
55720628 GTATGAGAGCCAGTGTAAGACCATGTCCGGAACATGGCATCAGCATTTT
1 ATATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTT
55720677 ACCCTTTTTT
Statistics
Matches: 203, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
96 120 0.59
97 6 0.03
98 77 0.38
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (95 bp):
ATATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTTTATGTGTCAGTGTAAG
ACCATGTCTGGGACATGGCATCGGCACCGT
Found at i:55720517 original size:48 final size:48
Alignment explanation
Indices: 55720339--55720676 Score: 186
Period size: 48 Copynumber: 7.0 Consensus size: 48
55720329 ACCATGGCGA
* * * * * * ***
55720339 TATGAGAGCCAGTGTAAGACCATGTATGGGACATGGCATCGGCCTCGA
1 TATGTGAGCCAGAGTAAGACCATGTCTGGAACATGGCATCGACATTTT
* * *** *
55720387 TATGT--GTCAGTGTAAGACCATGTCTAGG-ACATGGCATCGGCACCGGTA
1 TATGTGAGCCAGAGTAAGACCATGTCT-GGAACATGGCATC-G-ACATTTT
* * * * *
55720435 TATGCGAGCTAGTGTAAGACCATGTTTGGAACATGGTATCGACATTTT
1 TATGTGAGCCAGAGTAAGACCATGTCTGGAACATGGCATCGACATTTT
* * * * ***
55720483 TATGTGAGCCAGAGTAAGACCATGCCTGGGACATGGCATCGGCCTCAA
1 TATGTGAGCCAGAGTAAGACCATGTCTGGAACATGGCATCGACATTTT
* * * *
55720531 TAT-TCGAGCTAGCGTAAGACCATGTTTGGAACATGGCATCGGCATTGTT
1 TATGT-GAGCCAGAGTAAGACCATGTCTGGAACATGGCATCGACATT-TT
* * * ** *
55720580 GTATGT--GTCAGTGTAAGACCATGTCTGGGACATGGCATCGACACCGATG
1 -TATGTGAGCCAGAGTAAGACCATGTCTGGAACATGGCATCGACA--TTTT
* * *
55720629 TATGAGAGCCAGTGTAAGACCATGTCCGGAACATGGCATC-AGCATTTT
1 TATGTGAGCCAGAGTAAGACCATGTCTGGAACATGGCATCGA-CATTTT
55720677 ACCCTTTTTT
Statistics
Matches: 222, Mismatches: 53, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
46 28 0.13
47 4 0.02
48 123 0.55
49 5 0.02
50 61 0.27
51 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (48 bp):
TATGTGAGCCAGAGTAAGACCATGTCTGGAACATGGCATCGACATTTT
Found at i:55721475 original size:15 final size:15
Alignment explanation
Indices: 55721455--55721484 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55721445 CTAGTTACAA
55721455 ATGCTTTTTACATAT
1 ATGCTTTTTACATAT
55721470 ATGCTTTTTACATAT
1 ATGCTTTTTACATAT
55721485 TTTATAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (15 bp):
ATGCTTTTTACATAT
Found at i:55723116 original size:29 final size:27
Alignment explanation
Indices: 55723098--55723167 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
55723088 ATATTAAGTC
55723098 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
55723125 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
55723153 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
55723168 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:55723161 original size:28 final size:28
Alignment explanation
Indices: 55723098--55723195 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
55723088 ATATTAAGTC
*
55723098 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
55723125 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
55723153 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
55723182 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55723196 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55733951 original size:42 final size:42
Alignment explanation
Indices: 55733832--55733962 Score: 127
Period size: 42 Copynumber: 3.1 Consensus size: 42
55733822 CACATAGTGC
* * * * * *
55733832 CATACCAATGCCATATCCCAAATATAGTCTTACATGTAATCT
1 CATACCGATACCATATCCCAGATATGGTCTTACACGAAATCT
* ** * *
55733874 CATACCGATGCCAATAGACCAGCTATGGTCTTACACGAAATTT
1 CATACCGATACC-ATATCCCAGATATGGTCTTACACGAAATCT
* * *
55733917 CATATCGATACCATATCCCAGATATGGTTTTACACAAAATCT
1 CATACCGATACCATATCCCAGATATGGTCTTACACGAAATCT
55733959 CATA
1 CATA
55733963 ATGATGTCAT
Statistics
Matches: 71, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 39 0.55
43 32 0.45
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (42 bp):
CATACCGATACCATATCCCAGATATGGTCTTACACGAAATCT
Found at i:55733974 original size:42 final size:42
Alignment explanation
Indices: 55733842--55733994 Score: 119
Period size: 42 Copynumber: 3.6 Consensus size: 42
55733832 CATACCAATG
* * *** * *
55733842 CCATATCCCAAATATAGTCTTACATGTAATCTCATACCGATG
1 CCATATCCCAGATATGGTCTTACACAAAATCTCATATCGATA
** * * *
55733884 CCAATAGACCAGCTATGGTCTTACACGAAATTTCATATCGATA
1 CC-ATATCCCAGATATGGTCTTACACAAAATCTCATATCGATA
* *
55733927 CCATATCCCAGATATGGTTTTACACAAAATCTCATAAT-GATG
1 CCATATCCCAGATATGGTCTTACACAAAATCTCAT-ATCGATA
* ** *
55733969 TCATATTTCACATATGGTCTTACACA
1 CCATATCCCAGATATGGTCTTACACA
55733995 TAACCTCGGT
Statistics
Matches: 87, Mismatches: 22, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
42 53 0.61
43 34 0.39
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (42 bp):
CCATATCCCAGATATGGTCTTACACAAAATCTCATATCGATA
Found at i:55734222 original size:19 final size:19
Alignment explanation
Indices: 55734182--55734224 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
55734172 CACTTTTTAC
* * *
55734182 AATTTAGTCCTTTTTGCTA
1 AATTTAGTCATTTTTACAA
55734201 AATTTAGTCATTTTTACAA
1 AATTTAGTCATTTTTACAA
55734220 AATTT
1 AATTT
55734225 TCACAAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (19 bp):
AATTTAGTCATTTTTACAA
Found at i:55738348 original size:2 final size:2
Alignment explanation
Indices: 55738341--55738370 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55738331 ACTAAGTTCA
55738341 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
55738371 CTTTGAATGT
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:55738742 original size:13 final size:13
Alignment explanation
Indices: 55738702--55738743 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
55738692 AACAATTAAA
*
55738702 TCACATTAATATT
1 TCACATTAAAATT
* *
55738715 ACACATTAAATTT
1 TCACATTAAAATT
55738728 TCACATTAAAATT
1 TCACATTAAAATT
55738741 TCA
1 TCA
55738744 ATTTTCACAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (13 bp):
TCACATTAAAATT
Found at i:55740605 original size:40 final size:40
Alignment explanation
Indices: 55740561--55740641 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
55740551 CAACTGGTTC
55740561 TTTAGTGGGAGATAAAATAATTGCCAATGGATGGTTTTGA
1 TTTAGTGGGAGATAAAATAATTGCCAATGGATGGTTTTGA
55740601 TTTAGTGGGAGATAAAATAATTGCCAATGGATGGTTTTGA
1 TTTAGTGGGAGATAAAATAATTGCCAATGGATGGTTTTGA
55740641 T
1 T
55740642 ATGGTTGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (40 bp):
TTTAGTGGGAGATAAAATAATTGCCAATGGATGGTTTTGA
Found at i:55741546 original size:19 final size:19
Alignment explanation
Indices: 55741522--55741560 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
55741512 GAGTTAACAT
55741522 AACCTTTTCATGTATTTGG
1 AACCTTTTCATGTATTTGG
*
55741541 AACCTTTTCATGTTTTTGG
1 AACCTTTTCATGTATTTGG
55741560 A
1 A
55741561 GGGTCATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (19 bp):
AACCTTTTCATGTATTTGG
Found at i:55747294 original size:33 final size:36
Alignment explanation
Indices: 55747225--55747308 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 36
55747215 CTATACCCAT
* * *
55747225 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCATA-ACACATACACATATGTTCAC
55747262 CTATGCCGAATGCAT-ACACATA-A-ATATGTTCAC
1 CTATGCCGAATGCATAACACATACACATATGTTCAC
55747295 CTATGCCGAATGCA
1 CTATGCCGAATGCA
55747309 ACATATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 22 0.50
34 1 0.02
35 6 0.14
37 15 0.34
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (36 bp):
CTATGCCGAATGCATAACACATACACATATGTTCAC
Found at i:55747582 original size:41 final size:41
Alignment explanation
Indices: 55747537--55747733 Score: 308
Period size: 41 Copynumber: 4.8 Consensus size: 41
55747527 ACCGGCTCTT
*
55747537 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
55747578 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
55747619 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
*
55747660 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCGTTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
55747701 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
55747734 TAACGATAAA
Statistics
Matches: 147, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
39 2 0.01
40 2 0.01
41 138 0.94
42 2 0.01
43 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:55749591 original size:21 final size:22
Alignment explanation
Indices: 55749565--55749611 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
55749555 CTCTGCTCAA
*
55749565 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
55749586 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
55749608 ACTC
1 ACTC
55749612 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:55755367 original size:13 final size:12
Alignment explanation
Indices: 55755344--55755406 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
55755334 AATAATTTTA
55755344 TATTAAAATTAT
1 TATTAAAATTAT
55755356 TATT-AAA-TAT
1 TATTAAAATTAT
55755366 TATTAATAATTA-
1 TATTAA-AATTAT
*
55755378 TATTAAGAA-TGT
1 TATTAA-AATTAT
55755390 TATT-AAATTAT
1 TATTAAAATTAT
55755401 ATATTA
1 -TATTA
55755407 TTTTATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
10 9 0.22
11 8 0.20
12 22 0.54
13 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (12 bp):
TATTAAAATTAT
Found at i:55755371 original size:22 final size:23
Alignment explanation
Indices: 55755344--55755406 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 23
55755334 AATAATTTTA
55755344 TATTAAAATTATTATTA-AATAT
1 TATTAAAATTATTATTAGAATAT
*
55755366 TATTAATAATTA-TATTAAGAATGT
1 TATTAA-AATTATTATT-AGAATAT
55755390 TATT-AAATTATATATTA
1 TATTAAAATTAT-TATTA
55755407 TTTTATAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 15 0.43
23 8 0.23
24 12 0.34
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (23 bp):
TATTAAAATTATTATTAGAATAT
Found at i:55755413 original size:34 final size:33
Alignment explanation
Indices: 55755336--55755413 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
55755326 TTCTTAATAA
55755336 TAATTTTATATTAAAATTATTATTAAATATTAT
1 TAATTTTATATTAAAATTATTATTAAATATTAT
* *
55755369 TAATAATTATATTAAGAA-TGTTATTAAATTATATAT
1 TAAT-TTTATATTAA-AATTATTATTAAA-TAT-TAT
55755405 T-ATTTTATA
1 TAATTTTATA
55755414 AAATTGTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 4 0.11
34 23 0.61
35 7 0.18
36 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (33 bp):
TAATTTTATATTAAAATTATTATTAAATATTAT
Found at i:55755694 original size:16 final size:16
Alignment explanation
Indices: 55755673--55755726 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
55755663 TGAATTACTG
* *
55755673 ATTACAGCGCTATTCC
1 ATTACAGCTCTATTCA
*
55755689 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCA
*
55755705 ATTACATCTCTATTCA
1 ATTACAGCTCTATTCA
55755721 ATTACA
1 ATTACA
55755727 AACCTATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:55755718 original size:32 final size:32
Alignment explanation
Indices: 55755673--55755743 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
55755663 TGAATTACTG
* *
55755673 ATTACAGCGCTATTCCATTAC-AGCTCTATTCT
1 ATTACAGCGCTATTCAATTACAAAC-CTATTCT
* *
55755705 ATTACATCTCTATTCAATTACAAACCTATTCT
1 ATTACAGCGCTATTCAATTACAAACCTATTCT
55755737 ATTACAG
1 ATTACAG
55755744 TGAACCAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 31 0.94
33 2 0.06
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (32 bp):
ATTACAGCGCTATTCAATTACAAACCTATTCT
Found at i:55755799 original size:21 final size:21
Alignment explanation
Indices: 55755773--55755840 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
55755763 TATCTAAGTA
55755773 TATTTATTTTTAAAATAATAC
1 TATTTATTTTTAAAATAATAC
* * *
55755794 TATTTACTATATCAAAT-ATA-
1 TATTTA-TTTTTAAAATAATAC
*
55755814 TAGTTATTTTTAAAATAATAC
1 TATTTATTTTTAAAATAATAC
55755835 TATTTA
1 TATTTA
55755841 CTGTATTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 7 0.19
20 8 0.22
21 14 0.39
22 7 0.19
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (21 bp):
TATTTATTTTTAAAATAATAC
Found at i:55755821 original size:41 final size:41
Alignment explanation
Indices: 55755771--55755856 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
55755761 AATATCTAAG
*
55755771 TATATTTATTTTTAAAATAATACTATTTACTATATCAAATA
1 TATAGTTATTTTTAAAATAATACTATTTACTATATCAAATA
* *
55755812 TATAGTTATTTTTAAAATAATACTATTTACTGTATTAAATA
1 TATAGTTATTTTTAAAATAATACTATTTACTATATCAAATA
55755853 TATA
1 TATA
55755857 AAGAGTTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (41 bp):
TATAGTTATTTTTAAAATAATACTATTTACTATATCAAATA
Found at i:55755851 original size:22 final size:21
Alignment explanation
Indices: 55755785--55755852 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
55755775 TTTATTTTTA
*
55755785 AAATAATACTATTTACTATATC
1 AAATAATACTATTTACT-TATT
* *
55755807 AAAT-ATA-TAGTTA-TTTTT
1 AAATAATACTATTTACTTATT
55755825 AAAATAATACTATTTACTGTATT
1 -AAATAATACTATTTACT-TATT
55755848 AAATA
1 AAATA
55755853 TATAAAGAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
18 2 0.06
19 5 0.14
20 8 0.22
21 8 0.22
22 10 0.28
23 3 0.08
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (21 bp):
AAATAATACTATTTACTTATT
Found at i:55755982 original size:51 final size:51
Alignment explanation
Indices: 55755917--55756022 Score: 194
Period size: 51 Copynumber: 2.1 Consensus size: 51
55755907 AGTGACTAGC
* *
55755917 AAAAAAAAATTCAAAATTTGAAACGATTTGTAGGCATTTCAGATTAATAAG
1 AAAAAAAAACTCAAAATGTGAAACGATTTGTAGGCATTTCAGATTAATAAG
55755968 AAAAAAAAACTCAAAATGTGAAACGATTTGTAGGCATTTCAGATTAATAAG
1 AAAAAAAAACTCAAAATGTGAAACGATTTGTAGGCATTTCAGATTAATAAG
55756019 AAAA
1 AAAA
55756023 GGAGCTCCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.26
Consensus pattern (51 bp):
AAAAAAAAACTCAAAATGTGAAACGATTTGTAGGCATTTCAGATTAATAAG
Found at i:55756867 original size:22 final size:22
Alignment explanation
Indices: 55756841--55756889 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
55756831 ATATCCAAAC
55756841 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* * **
55756863 CATAATAGTAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
55756885 AATAA
1 AATAA
55756890 GGAGAAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.18
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:55756888 original size:11 final size:11
Alignment explanation
Indices: 55756849--55756888 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
55756839 ACAATAACAA
55756849 CAAAATAGTAG
1 CAAAATAGTAG
* *
55756860 CAACATAATAG
1 CAAAATAGTAG
*
55756871 TAAAATAGTAG
1 CAAAATAGTAG
55756882 CAAAATA
1 CAAAATA
55756889 AGGAGAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:55756897 original size:22 final size:22
Alignment explanation
Indices: 55756850--55756899 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
55756840 CAATAACAAC
* *
55756850 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
55756872 AAAATAGTAGCAAAATAAGGAG-
1 AAAATAGTAGCAAAATAA-GAGT
55756894 AAAATA
1 AAAATA
55756900 ATAAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.60, C:0.06, G:0.16, T:0.18
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:55757740 original size:30 final size:30
Alignment explanation
Indices: 55757704--55757764 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
55757694 ATTTTATTGT
* *
55757704 TAATTTTTTTATTATTTTAAAGACATTTGC
1 TAATTTTGTTACTATTTTAAAGACATTTGC
* *
55757734 TAATTTTGTTACTATTTTAGAGTCATTTGC
1 TAATTTTGTTACTATTTTAAAGACATTTGC
55757764 T
1 T
55757765 TGTTAAGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (30 bp):
TAATTTTGTTACTATTTTAAAGACATTTGC
Found at i:55757916 original size:12 final size:12
Alignment explanation
Indices: 55757881--55757918 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
55757871 GTTTATATAT
*
55757881 ATATTAAAATT-
1 ATATAAAAATTA
55757892 ATATAAAAA-TA
1 ATATAAAAATTA
55757903 ATATAAAAATTA
1 ATATAAAAATTA
55757915 ATAT
1 ATAT
55757919 GGGCAGGCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 1 0.04
11 17 0.71
12 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATAAAAATTA
Found at i:55759571 original size:15 final size:15
Alignment explanation
Indices: 55759551--55759579 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55759541 CAAAATTTAA
55759551 ATTTTGTTGAGGAAT
1 ATTTTGTTGAGGAAT
55759566 ATTTTGTTGAGGAA
1 ATTTTGTTGAGGAA
55759580 CCTTAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (15 bp):
ATTTTGTTGAGGAAT
Found at i:55759615 original size:19 final size:19
Alignment explanation
Indices: 55759591--55759627 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
55759581 CTTAAAATTC
55759591 AAAATTTT-AATTTTGATTA
1 AAAATTTTGAA-TTTGATTA
55759610 AAAATTTTGAATTTGATT
1 AAAATTTTGAATTTGATT
55759628 GAGGCATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
AAAATTTTGAATTTGATTA
Found at i:55760022 original size:22 final size:22
Alignment explanation
Indices: 55759995--55760037 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
55759985 ATATTTTTAT
55759995 TTTACTAAAAATAATTTAATTG
1 TTTACTAAAAATAATTTAATTG
55760017 TTTACTAAAAATAATTTAATT
1 TTTACTAAAAATAATTTAATT
55760038 TAAACAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTACTAAAAATAATTTAATTG
Found at i:55760236 original size:19 final size:18
Alignment explanation
Indices: 55760212--55760247 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
55760202 CCTAACTTTT
55760212 GTGATTCGATTTCGATTTG
1 GTGATTCGATTTC-ATTTG
*
55760231 GTGATTGGATTTCATTT
1 GTGATTCGATTTCATTT
55760248 TTTGTTTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.17, C:0.08, G:0.25, T:0.50
Consensus pattern (18 bp):
GTGATTCGATTTCATTTG
Found at i:55763257 original size:68 final size:68
Alignment explanation
Indices: 55763169--55763319 Score: 189
Period size: 68 Copynumber: 2.2 Consensus size: 68
55763159 GGAAGTCCGT
* * * * *
55763169 TAGGACATTAAA-ATTTGGGATTATAGGTATAAGACCATAGCTCAACTATGACATCCAATAGAG-
1 TAGGACATTAAACA-TAGGGATTACAAGTATAAGACCATAACTCAACTATGACAACCAATAGAGT
55763232 TCTGC
65 TC-GC
* * *
55763237 TAGGACATTAAACATAGGGATTACAAGTGTAAGACCATAACTCCACTATGGCAACCAATAGAGTT
1 TAGGACATTAAACATAGGGATTACAAGTATAAGACCATAACTCAACTATGACAACCAATAGAGTT
55763302 CGC
66 CGC
*
55763305 TAGAACATTAAACAT
1 TAGGACATTAAACAT
55763320 GGGGTATGAT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
68 69 0.96
69 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (68 bp):
TAGGACATTAAACATAGGGATTACAAGTATAAGACCATAACTCAACTATGACAACCAATAGAGTT
CGC
Found at i:55767580 original size:28 final size:28
Alignment explanation
Indices: 55767548--55767603 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
55767538 GTATATATGA
55767548 AAAAAAGGA-A-AATAAAAAGGAAAAAAAG
1 AAAAAAGGAGAGAA-AAAAA-GAAAAAAAG
55767576 AAAAAAGGAGAGAAAAAAAGAAAAAAAG
1 AAAAAAGGAGAGAAAAAAAGAAAAAAAG
55767604 CAAACGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 18 0.69
29 6 0.23
30 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (28 bp):
AAAAAAGGAGAGAAAAAAAGAAAAAAAG
Found at i:55767602 original size:21 final size:20
Alignment explanation
Indices: 55767546--55767603 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
55767536 GTGTATATAT
55767546 GAAAAAAAGGAAAATAAA-AAG
1 GAAAAAAA-GAAAA-AAAGAAG
*
55767567 GAAAAAAAG-AAAAAAGGAG
1 GAAAAAAAGAAAAAAAGAAG
55767586 AGAAAAAAAGAAAAAAAG
1 -GAAAAAAAGAAAAAAAG
55767604 CAAACGAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.09
19 5 0.15
20 10 0.30
21 15 0.45
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
GAAAAAAAGAAAAAAAGAAG
Done.