Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 190 of 313
Found at i:58333658 original size:51 final size:51
Alignment explanation
Indices: 58333579--58333680 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
58333569 CCAATCGGCC
**
58333579 AGGAATACCATCTTCATCGGTGGTGTCGACAGTGCTTCCCCACGCTTTCAA
1 AGGAATACCATCTTCATCGGTGAAGTCGACAGTGCTTCCCCACGCTTTCAA
* *
58333630 AGGAATGCCATCTTCATCGGTTAAGTCGACAGTGCTTCCCCACGCTTTCAA
1 AGGAATACCATCTTCATCGGTGAAGTCGACAGTGCTTCCCCACGCTTTCAA
58333681 TAGAAGAGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (51 bp):
AGGAATACCATCTTCATCGGTGAAGTCGACAGTGCTTCCCCACGCTTTCAA
Found at i:58338929 original size:16 final size:16
Alignment explanation
Indices: 58338908--58338974 Score: 89
Period size: 16 Copynumber: 4.2 Consensus size: 16
58338898 GGCTCACTGG
*
58338908 AATGGAATAGAGCTAT
1 AATGGAATAGAGCTGT
58338924 AATGGAATAGAGCTGT
1 AATGGAATAGAGCTGT
* *
58338940 AATGGAATAAAGTTGT
1 AATGGAATAGAGCTGT
* *
58338956 AATGTAATAGAGGTGT
1 AATGGAATAGAGCTGT
58338972 AAT
1 AAT
58338975 CAGAAATTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.42, C:0.03, G:0.27, T:0.28
Consensus pattern (16 bp):
AATGGAATAGAGCTGT
Found at i:58346186 original size:18 final size:19
Alignment explanation
Indices: 58346155--58346197 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
58346145 GCTAATGTGT
*
58346155 TAAAAACAGTAGCTAAAAA
1 TAAAAACAGAAGCTAAAAA
**
58346174 TAAAAACA-AAGCTTGAAA
1 TAAAAACAGAAGCTAAAAA
58346192 TAAAAA
1 TAAAAA
58346198 TATAAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.16
Consensus pattern (19 bp):
TAAAAACAGAAGCTAAAAA
Found at i:58346621 original size:48 final size:48
Alignment explanation
Indices: 58346550--58346646 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
58346540 TTTATTAATT
*
58346550 ATATGAGAAATAATTTAATAAATTGTATACTTAAATGTGTAATATAAA
1 ATATGAGAAATAATTTAATAAATTGTATAATTAAATGTGTAATATAAA
* * *
58346598 ATATGATAAATAATTTAATAAATTGTATAATTTAATTTGTAATATAAA
1 ATATGAGAAATAATTTAATAAATTGTATAATTAAATGTGTAATATAAA
58346646 A
1 A
58346647 GATAATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (48 bp):
ATATGAGAAATAATTTAATAAATTGTATAATTAAATGTGTAATATAAA
Found at i:58348345 original size:22 final size:22
Alignment explanation
Indices: 58348320--58348365 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
58348310 GGCATATTTT
*
58348320 TTATTTGATATTTTGTATG-TGA
1 TTATTT-ATATTATGTATGTTGA
*
58348342 TTATTTTTATTATGTATGTTGA
1 TTATTTATATTATGTATGTTGA
58348364 TT
1 TT
58348366 TCATTTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (22 bp):
TTATTTATATTATGTATGTTGA
Found at i:58349340 original size:21 final size:21
Alignment explanation
Indices: 58349308--58349350 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
58349298 ATTTATTAAC
* *
58349308 AAATTAAGCAATGTT-TAAAT
1 AAATTAAACAATATTCTAAAT
58349328 AAATCTAAACAATATTCTAAAT
1 AAAT-TAAACAATATTCTAAAT
58349350 A
1 A
58349351 GTGTGTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (21 bp):
AAATTAAACAATATTCTAAAT
Found at i:58358868 original size:28 final size:27
Alignment explanation
Indices: 58358802--58358886 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 27
58358792 TAAAATGGAA
*
58358802 AATTTTTAAATTAATAAAAATAAAATT
1 AATTTTTAAAATAATAAAAATAAAATT
* * * * *
58358829 AACATTTAAAAATATTAAAAATTTAATTT
1 AA-TTTTTAAAATAATAAAAA-TAAAATT
* *
58358858 AATTTTTAAAATTATAAATATATAAATT
1 AATTTTTAAAATAATAAAAATA-AAATT
58358886 A
1 A
58358887 TTAAAATTAT
Statistics
Matches: 42, Mismatches: 13, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
27 3 0.07
28 32 0.76
29 7 0.17
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (27 bp):
AATTTTTAAAATAATAAAAATAAAATT
Found at i:58358885 original size:29 final size:28
Alignment explanation
Indices: 58358802--58358885 Score: 66
Period size: 29 Copynumber: 3.0 Consensus size: 28
58358792 TAAAATGGAA
*
58358802 AATTTTT-AAATTAATAAAA-ATAAAATT
1 AATTTTTAAAATT-ATAAAATATAAATTT
** * *
58358829 AACATTTAAAAATATTAAAA-ATTTAATTT
1 AATTTTTAAAATTA-TAAAATA-TAAATTT
58358858 AATTTTTAAAATTATAAATATATAAATT
1 AATTTTTAAAATTATAAA-ATATAAATT
58358886 ATTAAAATTA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
27 6 0.14
28 14 0.33
29 22 0.51
30 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTTTTAAAATTATAAAATATAAATTT
Found at i:58362208 original size:21 final size:21
Alignment explanation
Indices: 58362150--58362211 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
58362140 CTATTAGACC
58362150 CAACGTGAGCAGGAGAGTCAA
1 CAACGTGAGCAGGAGAGTCAA
* * * *
58362171 C-A--TTAGGATGAGGGTCAA
1 CAACGTGAGCAGGAGAGTCAA
58362189 CAACGTGAGCAGGAGAGTCAA
1 CAACGTGAGCAGGAGAGTCAA
58362210 CA
1 CA
58362212 TTGAGATGAG
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
18 13 0.43
19 1 0.03
20 1 0.03
21 15 0.50
ACGTcount: A:0.37, C:0.18, G:0.32, T:0.13
Consensus pattern (21 bp):
CAACGTGAGCAGGAGAGTCAA
Found at i:58362222 original size:18 final size:18
Alignment explanation
Indices: 58362162--58362228 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
58362152 ACGTGAGCAG
58362162 GAGAGTCAACATT-AGGAT
1 GAGAGTCAACATTGA-GAT
* * *
58362180 GAGGGTCAACAACGTGAGCAG
1 GAGAGTCAAC-A-TTGAG-AT
58362201 GAGAGTCAACATTGAGAT
1 GAGAGTCAACATTGAGAT
*
58362219 GAGAATCAAC
1 GAGAGTCAAC
58362229 TATCGGCAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 19 0.50
19 5 0.13
20 3 0.08
21 11 0.29
ACGTcount: A:0.39, C:0.15, G:0.30, T:0.16
Consensus pattern (18 bp):
GAGAGTCAACATTGAGAT
Found at i:58362228 original size:39 final size:39
Alignment explanation
Indices: 58362150--58362228 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 39
58362140 CTATTAGACC
**
58362150 CAACGTGAGCAGGAGAGTCAACATTAGGATGAGGGTCAA
1 CAACGTGAGCAGGAGAGTCAACATTAGGATGAGAATCAA
58362189 CAACGTGAGCAGGAGAGTCAACATT-GAGATGAGAATCAA
1 CAACGTGAGCAGGAGAGTCAACATTAG-GATGAGAATCAA
58362228 C
1 C
58362229 TATCGGCAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.38, C:0.16, G:0.30, T:0.15
Consensus pattern (39 bp):
CAACGTGAGCAGGAGAGTCAACATTAGGATGAGAATCAA
Found at i:58368175 original size:19 final size:20
Alignment explanation
Indices: 58368148--58368186 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
58368138 AGATGTGCTT
58368148 TTTAGTTCTTTTAT-ATTTG
1 TTTAGTTCTTTTATAATTTG
*
58368167 TTTATTTCTTTTATAATTTG
1 TTTAGTTCTTTTATAATTTG
58368187 ATAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTAGTTCTTTTATAATTTG
Found at i:58368323 original size:17 final size:17
Alignment explanation
Indices: 58368258--58368324 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 17
58368248 ATTATACGCT
*
58368258 TTTTATATATATTTTTA
1 TTTTATATATATTTATA
* * *
58368275 TTGTATATATTTTTCTA
1 TTTTATATATATTTATA
*
58368292 TTTT-TATAAATTTATA
1 TTTTATATATATTTATA
*
58368308 TTTTATATTTATTTATA
1 TTTTATATATATTTATA
58368325 ATAATAATCT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
16 13 0.32
17 27 0.68
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (17 bp):
TTTTATATATATTTATA
Found at i:58369130 original size:18 final size:17
Alignment explanation
Indices: 58369100--58369133 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
58369090 TAATTTTTTT
*
58369100 AATATTTTAAATTTATA
1 AATATTTAAAATTTATA
58369117 AATATTTAATAATTTAT
1 AATATTTAA-AATTTAT
58369134 TTAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATTTAAAATTTATA
Found at i:58378992 original size:43 final size:43
Alignment explanation
Indices: 58378839--58378994 Score: 126
Period size: 43 Copynumber: 3.7 Consensus size: 43
58378829 GGCTCATACA
* *
58378839 ATGCCAACGTCCCAGATGTGGTCTTACAGGTA-ATCAC-ATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTATA-CACAAT-TCG
* ** *
58378882 ATGCC-ACTGTCCTAGACAG-GGTCTTACACAAAT-CA-AATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTATACACAATTCG
* * * * *
58378923 ATGCCAATGTCCCAGCCATAGCCTTACACGTATACACAATTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTATACACAATTCG
*
58378966 ATGCCAACGTCCCAGACGTGTTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
58378995 AAAAATACAT
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
41 24 0.29
42 9 0.11
43 50 0.60
44 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTATACACAATTCG
Found at i:58381147 original size:22 final size:23
Alignment explanation
Indices: 58381122--58381178 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
58381112 TGCACTAATG
*
58381122 AACAGAGAGCACTAAA-GTGCTA
1 AACAGAGAGCACTAAATGTACTA
58381144 AACAGAGAGCAC-AAATGTACTA
1 AACAGAGAGCACTAAATGTACTA
* *
58381166 AACGGAGAACACT
1 AACAGAGAGCACT
58381179 GTCGTGCTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACTAAATGTACTA
Found at i:58382157 original size:5 final size:5
Alignment explanation
Indices: 58382147--58382339 Score: 379
Period size: 5 Copynumber: 38.8 Consensus size: 5
58382137 TGTTTGTTTT
58382147 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
58382197 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
58382247 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
58382297 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
58382340 CTTAACTTTT
Statistics
Matches: 187, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
4 4 0.02
5 183 0.98
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:58383064 original size:18 final size:18
Alignment explanation
Indices: 58383041--58383085 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
58383031 ATACAACTAT
58383041 TAAACTTGAGACGATCAC
1 TAAACTTGAGACGATCAC
58383059 TAAACTTGAGACGATCAC
1 TAAACTTGAGACGATCAC
*
58383077 TAACCTTGA
1 TAAACTTGA
58383086 AATAGTAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (18 bp):
TAAACTTGAGACGATCAC
Found at i:58389812 original size:37 final size:37
Alignment explanation
Indices: 58389761--58389868 Score: 102
Period size: 37 Copynumber: 2.9 Consensus size: 37
58389751 ATTCAAAAAA
*
58389761 TAATATTATTTTAATAGTTTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTTTAATATTAAATTTAATAT
*
58389797 TAATACTTATCTTAATAGTATT-TTATT-AATTTAATAT
1 TAATA-TTATCTTAATAGT-TTAATATTAAATTTAATAT
*
58389834 TAAAGTGTTTATCTTAATA--TTAA-ATTAAATTTAAT
1 T-AA-T-ATTATCTTAATAGTTTAATATTAAATTTAAT
58389869 GTTTATCTAC
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
36 18 0.30
37 26 0.43
38 4 0.07
39 12 0.20
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTAATATTAAATTTAATAT
Found at i:58389947 original size:17 final size:17
Alignment explanation
Indices: 58389907--58389947 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
58389897 TTTTAATAAG
*
58389907 ATTTAATATTAAATTTA
1 ATTTAATATTAAATTAA
* *
58389924 ATCTAATATTAGATTAA
1 ATTTAATATTAAATTAA
58389941 ATTTAAT
1 ATTTAAT
58389948 TACTTGCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
ATTTAATATTAAATTAA
Found at i:58394096 original size:13 final size:13
Alignment explanation
Indices: 58394063--58394100 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
58394053 GATATATTTG
*
58394063 TAATTTGAAAACT
1 TAATTTGAAAAAT
58394076 TAAATTTGAAAAAT
1 T-AATTTGAAAAAT
58394090 TAATTTGAAAA
1 TAATTTGAAAA
58394101 TTTGTAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAAAT
Found at i:58394388 original size:35 final size:35
Alignment explanation
Indices: 58394337--58394443 Score: 144
Period size: 35 Copynumber: 3.1 Consensus size: 35
58394327 TTCACTTGTC
* *
58394337 TTTTCTTGCAGGGAATCTTTCCTGTTCATGCATTA
1 TTTTCTTGCAGGGAATCTTTCCTGTTCATACATCA
* *
58394372 TTTTGTTGCAGGGAATCTTTCCTGTTCACACATCA
1 TTTTCTTGCAGGGAATCTTTCCTGTTCATACATCA
* * *
58394407 -TTTCTTACAGGGAATCTCTCCTATTCATACATCA
1 TTTTCTTGCAGGGAATCTTTCCTGTTCATACATCA
58394441 TTT
1 TTT
58394444 CTGGTATTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 29 0.47
35 33 0.53
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (35 bp):
TTTTCTTGCAGGGAATCTTTCCTGTTCATACATCA
Found at i:58394423 original size:34 final size:34
Alignment explanation
Indices: 58394338--58394445 Score: 144
Period size: 34 Copynumber: 3.1 Consensus size: 34
58394328 TCACTTGTCT
* *
58394338 TTTCTTGCAGGGAATCTTTCCTGTTCATGCATTA
1 TTTCTTGCAGGGAATCTTTCCTGTTCATACATCA
* *
58394372 TTTTGTTGCAGGGAATCTTTCCTGTTCACACATCA
1 -TTTCTTGCAGGGAATCTTTCCTGTTCATACATCA
* * *
58394407 TTTCTTACAGGGAATCTCTCCTATTCATACATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCATACATCA
58394441 TTTCT
1 TTTCT
58394446 GGTATTATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
34 34 0.53
35 30 0.47
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (34 bp):
TTTCTTGCAGGGAATCTTTCCTGTTCATACATCA
Found at i:58396387 original size:34 final size:34
Alignment explanation
Indices: 58396344--58396451 Score: 144
Period size: 34 Copynumber: 3.1 Consensus size: 34
58396334 AAATAATACC
* * *
58396344 AGAAATGATGTATGAATAGGAGAGATTCCCTGTA
1 AGAAATGATGTATGAACAGGAAAGATTCCCTGCA
*
58396378 AGAAATGATGTGTGAACAGGAAAGATTCCCTGCA
1 AGAAATGATGTATGAACAGGAAAGATTCCCTGCA
* * *
58396412 ACAAAATAATGCATGAACAGGAAAGATTCCCTGCA
1 A-GAAATGATGTATGAACAGGAAAGATTCCCTGCA
58396447 AGAAA
1 AGAAA
58396452 AGACAAGTGA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 34 0.53
35 30 0.47
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (34 bp):
AGAAATGATGTATGAACAGGAAAGATTCCCTGCA
Found at i:58396434 original size:35 final size:34
Alignment explanation
Indices: 58396346--58396452 Score: 133
Period size: 35 Copynumber: 3.1 Consensus size: 34
58396336 ATAATACCAG
* * * *
58396346 AAATGATGTATGAATAGGAGAGATTCCCTGTAAG
1 AAATGATGTATGAACAGGAAAGATTCCCTGCAAA
*
58396380 AAATGATGTGTGAACAGGAAAGATTCCCTGCAACA
1 AAATGATGTATGAACAGGAAAGATTCCCTGCAA-A
* *
58396415 AAATAATGCATGAACAGGAAAGATTCCCTGCAAGA
1 AAATGATGTATGAACAGGAAAGATTCCCTGCAA-A
58396450 AAA
1 AAA
58396453 GACAAGTGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
34 29 0.46
35 34 0.54
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (34 bp):
AAATGATGTATGAACAGGAAAGATTCCCTGCAAA
Found at i:58396719 original size:14 final size:14
Alignment explanation
Indices: 58396689--58396725 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
58396679 AGTTTACAAA
*
58396689 TTTTCAAA-TTAAT
1 TTTTCAAATTTAAG
58396702 TTTTCAAATTTAAG
1 TTTTCAAATTTAAG
58396716 TTTTCAAATT
1 TTTTCAAATT
58396726 ACAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (14 bp):
TTTTCAAATTTAAG
Found at i:58400995 original size:21 final size:23
Alignment explanation
Indices: 58400953--58400995 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
58400943 TAATTAATTA
*
58400953 TAAACAGAAGCAAATCTCTTTTC
1 TAAACAGAAGCAAATATCTTTTC
*
58400976 TAAA-AGAAG-AAATATGTTTT
1 TAAACAGAAGCAAATATCTTTT
58400996 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (23 bp):
TAAACAGAAGCAAATATCTTTTC
Found at i:58401040 original size:21 final size:21
Alignment explanation
Indices: 58401016--58401071 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
58401006 TGGAACAATT
*
58401016 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
58401037 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
58401057 AAGAAATAGAATCAA
1 AAGAAAAAG-ATCAA
58401072 TAATTTGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:58401057 original size:20 final size:23
Alignment explanation
Indices: 58401027--58401071 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
58401017 AGAAAAAGAG
58401027 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
58401048 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
58401070 AA
1 AA
58401072 TAATTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:58402990 original size:11 final size:12
Alignment explanation
Indices: 58402974--58403006 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
58402964 AAATATAATC
*
58402974 TAATATTAGA-T
1 TAATATTAAATT
58402985 TAATATTAAATT
1 TAATATTAAATT
58402997 TAATATTAAA
1 TAATATTAAA
58403007 AAGATTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
TAATATTAAATT
Found at i:58404273 original size:24 final size:25
Alignment explanation
Indices: 58404246--58404301 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
58404236 TTTGGTTCAT
58404246 AATCAGCAGCAGTTTCAACAAC-AC
1 AATCAGCAGCAGTTTCAACAACAAC
*
58404270 AATCAGCAGCATTTTCAACAACAAC
1 AATCAGCAGCAGTTTCAACAACAAC
58404295 AA-CAGCA
1 AATCAGCA
58404302 TCAACAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.45, C:0.29, G:0.11, T:0.16
Consensus pattern (25 bp):
AATCAGCAGCAGTTTCAACAACAAC
Found at i:58404302 original size:21 final size:20
Alignment explanation
Indices: 58404252--58404313 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 20
58404242 TCATAATCAG
*
58404252 CAGCAGTTTCAACAACACAATCAG
1 CAGCA-TTTCAAC-A-ACAA-CAA
58404276 CAGCATTTTCAACAACAACAA
1 CAGCA-TTTCAACAACAACAA
58404297 CAGCA--TCAACAACAACA
1 CAGCATTTCAACAACAACA
58404314 GCAGTGGCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 12 0.33
21 7 0.19
22 4 0.11
23 1 0.03
24 12 0.33
ACGTcount: A:0.47, C:0.31, G:0.08, T:0.15
Consensus pattern (20 bp):
CAGCATTTCAACAACAACAA
Found at i:58404308 original size:15 final size:15
Alignment explanation
Indices: 58404288--58404316 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58404278 GCATTTTCAA
58404288 CAACAACAACAGCAT
1 CAACAACAACAGCAT
58404303 CAACAACAACAGCA
1 CAACAACAACAGCA
58404317 GTGGCTCAGG
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:0.55, C:0.34, G:0.07, T:0.03
Consensus pattern (15 bp):
CAACAACAACAGCAT
Found at i:58409137 original size:4 final size:4
Alignment explanation
Indices: 58409128--58409156 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
58409118 GTTTGGTACC
58409128 GTCT GTCT GTCT GTCT GTCT GTCT GTCT G
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT G
58409157 ATCATGGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.28, T:0.48
Consensus pattern (4 bp):
GTCT
Found at i:58413323 original size:23 final size:23
Alignment explanation
Indices: 58413297--58413352 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
58413287 TGCACATAGA
* *
58413297 TATGAAAGTCTTTTTATAGGTAG
1 TATGAAAGTCTCTTTAAAGGTAG
*
58413320 TATGAAAG-CCCTTTAAAGGTAG
1 TATGAAAGTCTCTTTAAAGGTAG
*
58413342 TATGAGAGTCT
1 TATGAAAGTCT
58413353 GAGGAGTCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (23 bp):
TATGAAAGTCTCTTTAAAGGTAG
Found at i:58413672 original size:28 final size:28
Alignment explanation
Indices: 58413618--58413683 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
58413608 AAAAGGACAA
* *
58413618 TCTTTCAAGTGAGAGTCCATCAGGACTG
1 TCTTACAAGTGAGAGTCCATCAAGACTG
* *
58413646 TCTTATAAGTGAGAGTCCGTCAAGACTG
1 TCTTACAAGTGAGAGTCCATCAAGACTG
58413674 TCTTACAAGT
1 TCTTACAAGT
58413684 ATGAATCTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (28 bp):
TCTTACAAGTGAGAGTCCATCAAGACTG
Found at i:58417995 original size:5 final size:6
Alignment explanation
Indices: 58417966--58417993 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
58417956 ACACATGGTA
58417966 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
58417994 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:58418173 original size:16 final size:16
Alignment explanation
Indices: 58418152--58418199 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
58418142 ATTATTGTCT
58418152 TAAAATTTAAAATATA
1 TAAAATTTAAAATATA
* * *
58418168 TAAAATCTAAAAAATT
1 TAAAATTTAAAATATA
*
58418184 TAAAATATTAGAATAT
1 TAAAAT-TTAAAATAT
58418200 TATTTAACAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAAATTTAAAATATA
Found at i:58423250 original size:22 final size:21
Alignment explanation
Indices: 58423225--58423267 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
58423215 TTTGAAGCTG
58423225 TCAAATATCACTCT-TTTATACT
1 TCAAA-ATCA-TCTATTTATACT
*
58423247 TCAAAATTATCTATTTATACT
1 TCAAAATCATCTATTTATACT
58423268 CCTATACTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 11 0.58
22 5 0.26
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.47
Consensus pattern (21 bp):
TCAAAATCATCTATTTATACT
Found at i:58430244 original size:66 final size:66
Alignment explanation
Indices: 58430171--58430303 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
58430161 GCATCGTTCA
58430171 AATACATAGAAAATAATTACATGTTTACTACAATATGAACACGTTTCCCAACATTACCCTCATAG
1 AATACATAGAAAATAATTACATGTTTACTACAATATGAACACGTTTCCCAACATTACCCTCATAG
58430236 G
66 G
** * * * *
58430237 AATACATAGAAAATAATTTTATGTTTACTACAATATGGACATGTTTCTCAATATTACCCTCATAG
1 AATACATAGAAAATAATTACATGTTTACTACAATATGAACACGTTTCCCAACATTACCCTCATAG
58430302 G
66 G
58430303 A
1 A
58430304 TATCTTTAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (66 bp):
AATACATAGAAAATAATTACATGTTTACTACAATATGAACACGTTTCCCAACATTACCCTCATAG
G
Found at i:58433755 original size:21 final size:23
Alignment explanation
Indices: 58433698--58433745 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
58433688 TTTTTTATCA
58433698 TTTTATAATATATACATAAATTT
1 TTTTATAATATATACATAAATTT
58433721 TTTTATAATATATACAT-AATTT
1 TTTTATAATATATACATAAATTT
58433743 TTT
1 TTT
58433746 AAGATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTATAATATATACATAAATTT
Found at i:58439631 original size:6 final size:6
Alignment explanation
Indices: 58439620--58439681 Score: 63
Period size: 6 Copynumber: 9.7 Consensus size: 6
58439610 TGAGTCAAAA
*
58439620 AAAATG AAAATG AAAAATG ATAAAATG AAAATG AAAAATG AAAAATG AAAA-A
1 AAAATG AAAATG -AAAATG --AAAATG AAAATG -AAAATG -AAAATG AAAATG
58439672 AAAATG AAAA
1 AAAATG AAAA
58439682 AGTAAAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
5 4 0.08
6 20 0.41
7 19 0.39
8 6 0.12
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:58439636 original size:7 final size:7
Alignment explanation
Indices: 58439619--58439691 Score: 86
Period size: 7 Copynumber: 11.0 Consensus size: 7
58439609 TTGAGTCAAA
58439619 AAAAATG
1 AAAAATG
58439626 -AAAATG
1 AAAAATG
58439632 AAAAATG
1 AAAAATG
58439639 ATAAAATG
1 A-AAAATG
58439647 -AAAATG
1 AAAAATG
58439653 AAAAATG
1 AAAAATG
58439660 AAAAATG
1 AAAAATG
58439667 -AAAA--
1 AAAAATG
58439671 AAAAATG
1 AAAAATG
58439678 AAAAA-G
1 AAAAATG
58439684 TAAAAATG
1 -AAAAATG
58439692 GTGAGGCTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 15
0.79 0.00 0.21
Matches are distributed among these distances:
5 4 0.07
6 17 0.29
7 30 0.52
8 7 0.12
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:58441025 original size:100 final size:100
Alignment explanation
Indices: 58440857--58441040 Score: 242
Period size: 100 Copynumber: 1.8 Consensus size: 100
58440847 TGCAGTGGAG
* ** * * **
58440857 CAGATTAAAGCTACGACGATGAATCTTGCTTCCCTGATTTTGCAATTTAAAAGATCGAAGCCGTA
1 CAGATTAAAGCTACGACGACGAATCTTGCTTCCCTGACATTGCAATTAAAAAGATCAAAGCCACA
*
58440922 ACGACGAATCTTATTTTCCTGGCAATGTAGTGAAA
66 ACGACGAATCTTACTTTCCTGGCAATGTAGTGAAA
* * * * *
58440957 CAGATTAAATCTACGACGGCGAATCTTGTTTCCCTGACATTGCAATTAAAAAGATTAAAGTCACA
1 CAGATTAAAGCTACGACGACGAATCTTGCTTCCCTGACATTGCAATTAAAAAGATCAAAGCCACA
*
58441022 ACGATGAATCTTACTTTCC
66 ACGACGAATCTTACTTTCC
58441041 CTGAGATTGC
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
100 70 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (100 bp):
CAGATTAAAGCTACGACGACGAATCTTGCTTCCCTGACATTGCAATTAAAAAGATCAAAGCCACA
ACGACGAATCTTACTTTCCTGGCAATGTAGTGAAA
Found at i:58441318 original size:44 final size:45
Alignment explanation
Indices: 58441207--58441538 Score: 163
Period size: 44 Copynumber: 7.6 Consensus size: 45
58441197 AAGCAAGTCT
* * * *
58441207 TATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGTTGAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGTGAATCC
* * * *
58441252 TATCTCTCTG-AGTTTGCAGTGGAGCAGATTGTAGCTGGT-AATCC
1 TATCTCCCTGAAG-TTGCAGTGGAGCAGACTGAAGATGGTGAATCC
* * ** *
58441296 TATCTCCCTGAAGTTGTAGTGGAGCGGA-TCGAA-ATAAT-AGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATGGTGA-ATCC
* * * * * * * *
58441340 TATCTCTCTGAAGTTTCAGTAGAGTAGA-T-CACATCAG-G--TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-GGTGAATCC
* ** * * * *
58441381 TATCTCCCTGAGGTTAG-AGCAGAGCAGACCGAAGA-AG-CAAGTCT
1 TATCTCCCTGAAGTT-GCAGTGGAGCAGACTGAAGATGGTGAA-TCC
* * *
58441425 TATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGTGAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGTGAATCC
* * * ** *
58441470 TATCTCCCTG-AGTTTGCAGTGAAGCAGATTGTAGCCGAT-AATCC
1 TATCTCCCTGAAG-TTGCAGTGGAGCAGACTGAAGATGGTGAATCC
58441514 TATCTCCCTGAAGTTGCAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
58441539 GGATTGAAAT
Statistics
Matches: 218, Mismatches: 51, Indels: 37
0.71 0.17 0.12
Matches are distributed among these distances:
41 27 0.12
42 1 0.00
43 9 0.04
44 114 0.52
45 65 0.30
46 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGTGAATCC
Found at i:58441425 original size:218 final size:217
Alignment explanation
Indices: 58441026--58441593 Score: 915
Period size: 218 Copynumber: 2.6 Consensus size: 217
58441016 GTCACAACGA
* * *
58441026 TGAATCTTACTTTCCCTGAGATTGCAGTGGAGCAGATTGTAGACGATAATCCTATCTCCTTGAAG
1 TGAATCTTA-TCTCCCTGAGTTTGCAGTGGAGCAGATTGTAG-CGATAATCCTATCTCCCTGAAG
* *
58441091 TTGCAGTGGAGCGGATTAAAATAATAGATCTTATCTCTCTG-AGTTTACAGTAAAGTAGATCACA
64 TTGCAGTGGAGCGGATTGAAATAATAGATCTTATCTCTCTGAAGTTT-CAGTAGAGTAGATCACA
* * **
58441155 TCAGGTCTTATCTCTCTGAGGTTGCAGCGGAGTGGACCGAAGAAGCAAGTCTTATCCCCCTGAAG
128 TCAGGTCTTATCTCCCTGAGGTTGCAGCAGAGCAGACCGAAGAAGCAAGTCTTATCCCCCTGAAG
*
58441220 TTGCAGTGGGGCAGACTGAAGATGT
193 TTGCAGTGGGGCAGACTGAAGATGG
* *
58441245 TGAATCTTATCTCTCTGAGTTTGCAGTGGAGCAGATTGTAGCTGGTAATCCTATCTCCCTGAAGT
1 TGAATCTTATCTCCCTGAGTTTGCAGTGGAGCAGATTGTAGC-GATAATCCTATCTCCCTGAAGT
* *
58441310 TGTAGTGGAGCGGATCGAAATAATAGATCTTATCTCTCTGAAGTTTCAGTAGAGTAGATCACATC
65 TGCAGTGGAGCGGATTGAAATAATAGATCTTATCTCTCTGAAGTTTCAGTAGAGTAGATCACATC
58441375 AGGTCTTATCTCCCTGAGGTTAG-AGCAGAGCAGACCGAAGAAGCAAGTCTTATCCCCCTGAAGT
130 AGGTCTTATCTCCCTGAGGTT-GCAGCAGAGCAGACCGAAGAAGCAAGTCTTATCCCCCTGAAGT
58441439 TGCAGTGGGGCAGACTGAAGATGG
194 TGCAGTGGGGCAGACTGAAGATGG
*
58441463 TGAATCTTATCTCCCTGAGTTTGCAGTGAAGCAGATTGTAGCCGATAATCCTATCTCCCTGAAGT
1 TGAATCTTATCTCCCTGAGTTTGCAGTGGAGCAGATTGTAG-CGATAATCCTATCTCCCTGAAGT
* *
58441528 TGCAGTGGAGCGGATTGAAATAATAGATTTTATCTCTCTGAAGTTGCAGTAGAGTAGATCACATC
65 TGCAGTGGAGCGGATTGAAATAATAGATCTTATCTCTCTGAAGTTTCAGTAGAGTAGATCACATC
58441593 A
130 A
58441594 AGCCTTGCCT
Statistics
Matches: 324, Mismatches: 21, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
217 1 0.00
218 307 0.95
219 16 0.05
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (217 bp):
TGAATCTTATCTCCCTGAGTTTGCAGTGGAGCAGATTGTAGCGATAATCCTATCTCCCTGAAGTT
GCAGTGGAGCGGATTGAAATAATAGATCTTATCTCTCTGAAGTTTCAGTAGAGTAGATCACATCA
GGTCTTATCTCCCTGAGGTTGCAGCAGAGCAGACCGAAGAAGCAAGTCTTATCCCCCTGAAGTTG
CAGTGGGGCAGACTGAAGATGG
Found at i:58441742 original size:87 final size:87
Alignment explanation
Indices: 58441593--58441912 Score: 496
Period size: 87 Copynumber: 3.7 Consensus size: 87
58441583 AGATCACATC
* * * * *
58441593 AAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAACAGATCTTACCTTCTTGCGTTA
1 AAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTA
*
58441658 ACAGCGAAGCAGACCGAAAACA
66 ACAGCGAAGCAGATCGAAAACA
* *
58441680 AAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTA
1 AAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTA
58441745 ACAGCGAAGCAGATCGAAAACA
66 ACAGCGAAGCAGATCGAAAACA
*
58441767 AAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGATAGCAGATCTTGTCTTCCTGCGTTA
1 AAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTA
* *
58441832 ACGGCGAAGTAGATCGAAAACA
66 ACAGCGAAGCAGATCGAAAACA
* * * * *
58441854 AAGTCTTGACTCCATCGGTTGCAGTAGAACTGATTAAAGATAGCAGATCTTGTCTTCCT
1 AAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
58441913 AAGCACTAGC
Statistics
Matches: 218, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 218 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (87 bp):
AAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTA
ACAGCGAAGCAGATCGAAAACA
Found at i:58442083 original size:43 final size:43
Alignment explanation
Indices: 58442035--58442149 Score: 112
Period size: 44 Copynumber: 2.7 Consensus size: 43
58442025 TTACAAGTCT
58442035 TATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAAGA-AATCA-ATCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCA-AA-ACAAT-AGATCC
* * * * *
58442078 TATCTCCCTGAAGTTA-CAGTGGAGCGGATTAAAACAATAGATCT
1 TATCTCCCT-AAG-CAGTAGTGGAGCAGATCAAAACAATAGATCC
58442122 TATCTCCCTAAGCAGTAGTGGAGCAGAT
1 TATCTCCCTAAGCAGTAGTGGAGCAGAT
58442150 TGCATTGGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
42 1 0.02
43 25 0.43
44 30 0.52
45 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (43 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAACAATAGATCC
Found at i:58442221 original size:44 final size:44
Alignment explanation
Indices: 58442158--58442263 Score: 158
Period size: 44 Copynumber: 2.4 Consensus size: 44
58442148 ATTGCATTGG
* * * *
58442158 GTCTTATCTCCTTGAAGTTGCAGCGAAGTAGACTGAGAAAATAA
1 GTCTTATCTCCCTGAAGTTGCAGCGAAGCAGAATGAGAAAACAA
*
58442202 GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGAATGAGAAAACAA
1 GTCTTATCTCCCTGAAGTTGCAGCGAAGCAGAATGAGAAAACAA
*
58442246 GTCTTATCCCCCTGAAGT
1 GTCTTATCTCCCTGAAGT
58442264 CACAGTGGGG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (44 bp):
GTCTTATCTCCCTGAAGTTGCAGCGAAGCAGAATGAGAAAACAA
Found at i:58448452 original size:8 final size:8
Alignment explanation
Indices: 58448430--58448462 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
58448420 GAGTAAAATC
58448430 ATGTA-AT
1 ATGTATAT
*
58448437 ATGCATAT
1 ATGTATAT
58448445 ATGTATAT
1 ATGTATAT
58448453 ATGTATAT
1 ATGTATAT
58448461 AT
1 AT
58448463 TTCAGAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.45
Consensus pattern (8 bp):
ATGTATAT
Found at i:58451230 original size:29 final size:29
Alignment explanation
Indices: 58451189--58451319 Score: 87
Period size: 30 Copynumber: 4.6 Consensus size: 29
58451179 ACTATTTTTG
* *
58451189 AAAGGATGTCTTTGTGGCTATCTCAGTTA
1 AAAGGAAGCCTTTGTGGCTATCTCAGTTA
* *
58451218 AAAGTG-AGCCTTTGTGG-TAGTTTCCG-T-
1 AAAG-GAAGCCTTTGTGGCTA-TCTCAGTTA
*
58451245 -AAGGAAGCCTTTGTGGCTATCTCTGTTAA
1 AAAGGAAGCCTTTGTGGCTATCTCAGTT-A
* *
58451274 AAAGGAAGTCC-TTGTGGCAATCTCTA-ATA
1 AAAGGAAG-CCTTTGTGGCTATCTC-AGTTA
*
58451303 AAAAGAATGCCTTTGTG
1 AAAGGAA-GCCTTTGTG
58451320 ACTTTTTCTG
Statistics
Matches: 80, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
25 1 0.01
26 18 0.22
27 3 0.04
28 3 0.04
29 26 0.32
30 27 0.34
31 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (29 bp):
AAAGGAAGCCTTTGTGGCTATCTCAGTTA
Found at i:58451281 original size:30 final size:29
Alignment explanation
Indices: 58451161--58451380 Score: 113
Period size: 26 Copynumber: 7.8 Consensus size: 29
58451151 TTATTTTTCG
* *
58451161 TAAAAGGATGCCTTTGTGACTAT-T-T-T
1 TAAAAGGAAGCCTTTGTGGCTATCTCTGT
* * * *
58451187 TGAAAGGATGTCTTTGTGGCTATCTCAGT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTGT
* *
58451216 TAAAAGTG-AGCCTTTGTGG-TAGTTTCCG-
1 TAAAAG-GAAGCCTTTGTGGCTA-TCTCTGT
58451244 T--AAGGAAGCCTTTGTGGCTATCTCTGT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTGT
* **
58451271 TAAAAAGGAAGTCC-TTGTGGCAATCTCTAA
1 T-AAAAGGAAG-CCTTTGTGGCTATCTCTGT
* * * *
58451301 TAAAAAGAATGCCTTTGTGACTTTTTCTGT
1 TAAAAGGAA-GCCTTTGTGGCTATCTCTGT
* * *** *
58451331 TAGAAGGATGCC-TTGTGG-TAAGACT-C
1 TAAAAGGAAGCCTTTGTGGCTATCTCTGT
58451357 TAAAAGGAAAGCCTTTGTGGCTAT
1 TAAAAGG-AAGCCTTTGTGGCTAT
58451381 TTTTGGAAGG
Statistics
Matches: 144, Mismatches: 33, Indels: 31
0.69 0.16 0.15
Matches are distributed among these distances:
25 1 0.01
26 44 0.31
27 11 0.08
28 14 0.10
29 33 0.23
30 39 0.27
31 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (29 bp):
TAAAAGGAAGCCTTTGTGGCTATCTCTGT
Found at i:58458830 original size:45 final size:45
Alignment explanation
Indices: 58458766--58458859 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
58458756 ATTAGTAATA
* * *
58458766 TAAAACTTAATATTATCTTGCTTTTATTATTAAACATACGAAAAT
1 TAAAACTTAATATTATCTTGCATTTATTAGTAAACATACCAAAAT
* *
58458811 TAAAACTTAATATTATCTTGCATTTATTAGTAGATATACCAAAAT
1 TAAAACTTAATATTATCTTGCATTTATTAGTAAACATACCAAAAT
58458856 TAAA
1 TAAA
58458860 GTACCTTGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (45 bp):
TAAAACTTAATATTATCTTGCATTTATTAGTAAACATACCAAAAT
Found at i:58460227 original size:13 final size:13
Alignment explanation
Indices: 58460209--58460239 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58460199 ATTTTAAAAA
*
58460209 ATAAATATTAATT
1 ATAAATATTAAAT
58460222 ATAAATATTAAAT
1 ATAAATATTAAAT
58460235 ATAAA
1 ATAAA
58460240 AACATCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAAATATTAAAT
Found at i:58461268 original size:31 final size:31
Alignment explanation
Indices: 58461232--58461295 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
58461222 TCCATCAAAG
*
58461232 TTTTACCACTCTCATATGTACGAAGACGGGT
1 TTTTACCACTCTCATATGCACGAAGACGGGT
58461263 TTTTACCACTCTCATATGCACGAAGACGGGT
1 TTTTACCACTCTCATATGCACGAAGACGGGT
58461294 TT
1 TT
58461296 GATTCCACTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (31 bp):
TTTTACCACTCTCATATGCACGAAGACGGGT
Found at i:58462346 original size:19 final size:19
Alignment explanation
Indices: 58462322--58462369 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
58462312 CACATCTACG
*
58462322 AGCTCATCCAAAGATGCAA
1 AGCTCATCCAAAGATACAA
**
58462341 AGCTCA-CCAAATTTACAA
1 AGCTCATCCAAAGATACAA
58462359 A-CTCATCCAAA
1 AGCTCATCCAAA
58462370 ATTGTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.44, C:0.29, G:0.08, T:0.19
Consensus pattern (19 bp):
AGCTCATCCAAAGATACAA
Found at i:58466044 original size:18 final size:19
Alignment explanation
Indices: 58466017--58466054 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
58466007 AAGCAAATAA
*
58466017 ATTATTAAAA-ATAAAAAT
1 ATTATAAAAATATAAAAAT
58466035 ATTATAAAAATTATAAAAAT
1 ATTATAAAAA-TATAAAAAT
58466055 CGGTTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATTATAAAAATATAAAAAT
Found at i:58469116 original size:19 final size:19
Alignment explanation
Indices: 58469092--58469128 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
58469082 TCTCTCAACA
58469092 AAAATAATTT-TAAAAATTC
1 AAAAT-ATTTATAAAAATTC
58469111 AAAATATTTATAAAAATT
1 AAAATATTTATAAAAATT
58469129 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATATTTATAAAAATTC
Found at i:58469137 original size:18 final size:18
Alignment explanation
Indices: 58469097--58469140 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
58469087 CAACAAAAAT
58469097 AATTT-TAAAAATTCAAA
1 AATTTATAAAAATTCAAA
**
58469114 ATATTTATAAAAATTTTAA
1 A-ATTTATAAAAATTCAAA
58469133 AATTTATA
1 AATTTATA
58469141 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 11 0.48
19 11 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTATAAAAATTCAAA
Found at i:58469863 original size:17 final size:18
Alignment explanation
Indices: 58469841--58469895 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
58469831 TTCATATTTT
58469841 AAATAAAAAAT-TTTAAA
1 AAATAAAAAATATTTAAA
**
58469858 AAATAAAAAAATATGAAAA
1 AAAT-AAAAAATATTTAAA
* *
58469877 AAATAAAAACTCTTTAAA
1 AAATAAAAAATATTTAAA
58469895 A
1 A
58469896 TTCAAAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 4 0.13
18 18 0.60
19 8 0.27
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (18 bp):
AAATAAAAAATATTTAAA
Found at i:58469919 original size:17 final size:17
Alignment explanation
Indices: 58469841--58469920 Score: 58
Period size: 17 Copynumber: 4.7 Consensus size: 17
58469831 TTCATATTTT
*
58469841 AAATA-AAAAATTTTAAA
1 AAATATAAAAA-TATAAA
*
58469858 AAATAAAAAAATATGAAA
1 AAATATAAAAATAT-AAA
* **
58469876 AAA-ATAAAAACTCTTTA
1 AAATATAAAAA-TATAAA
*
58469893 AAAT-TCAAAATATAAA
1 AAATATAAAAATATAAA
58469909 AAATATAAAAAT
1 AAATATAAAAAT
58469921 TCTAACATTC
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
16 7 0.15
17 28 0.58
18 13 0.27
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (17 bp):
AAATATAAAAATATAAA
Found at i:58469931 original size:32 final size:34
Alignment explanation
Indices: 58469865--58469932 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
58469855 AAAAAATAAA
*
58469865 AAAATATGAAAAAAATAAAAACTCTTTAAAATTC
1 AAAATATGAAAAAAATAAAAACTCTCTAAAATTC
*
58469899 AAAATAT-AAAAAATATAAAAA-T-TCTAACATTC
1 AAAATATGAAAAAA-ATAAAAACTCTCTAAAATTC
58469931 AA
1 AA
58469933 TATTATCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.32
33 7 0.23
34 14 0.45
ACGTcount: A:0.63, C:0.09, G:0.01, T:0.26
Consensus pattern (34 bp):
AAAATATGAAAAAAATAAAAACTCTCTAAAATTC
Found at i:58470331 original size:24 final size:25
Alignment explanation
Indices: 58470303--58470349 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
58470293 GATAACATTG
58470303 AATTTTTATATATTTA-AAAAAGAT
1 AATTTTTATATATTTATAAAAAGAT
* *
58470327 AATTTTTATTTTTTTATAAAAAG
1 AATTTTTATATATTTATAAAAAG
58470350 TTCTTGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
AATTTTTATATATTTATAAAAAGAT
Found at i:58470598 original size:14 final size:15
Alignment explanation
Indices: 58470571--58470602 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
58470561 TTTTTAGAAT
58470571 TTTTTAATATTTTTA
1 TTTTTAATATTTTTA
58470586 TTTTTAATA-TTTTA
1 TTTTTAATATTTTTA
58470600 TTT
1 TTT
58470603 GCCTTGAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTAATATTTTTA
Found at i:58470826 original size:241 final size:240
Alignment explanation
Indices: 58470540--58471271 Score: 1279
Period size: 241 Copynumber: 3.0 Consensus size: 240
58470530 TGAAACCAAG
58470540 TTAAAAAACCAGTTGAACCAATTTTTAGAATTTTTTA-ATATTTTTATTTTTAATATTTTATTTG
1 TTAAAAAACCAGTTGAACCAATTTTTAGAATTTTTTAGA-ATTTTTATTTTTAATATTTTATTTG
* ** * * * * * * *
58470604 CCTTGAACTTGTCAGATTGGTTGCTTTGGGAACCAATTTGTTAGGCCAATTCGAAATCGATTCAA
65 CTTTGAACTTGTTGGACTAGTTGCTTTGGAAACCAATTCGTCAAGCCAATTCGAAATCGGTTCAA
* * * *
58470669 CTT-TAATTCAATCGGTTTTTAGCTCAGTTGAACCAATCTGTACCGGTTCGCTTATTTACTTTCA
130 -TTCTAATTCAATC-GATTTTAGCTCGGTTCAACCAATTTGTACCGGTTCGCTTATTTACTTTCA
58470733 AAGTTTTATTATTTCTATTTCTTGAAGATTTACCACTATAAATTTAAA
193 AAGTTTTATTATTTCTATTTCTTGAAGATTTACCACTATAAATTTAAA
58470781 TTAAAAAACCAGTTGAACCAATTTTTAGAATTTTTTAGAATTTTTATTTTTAATATTTTATTTGC
1 TTAAAAAACCAGTTGAACCAATTTTTAGAATTTTTTAGAATTTTTATTTTTAATATTTTATTTGC
58470846 TTTGAACTTGTTGGACTAGTTGCTTTGGAAACCAATTCGTCAAGCCAATTCGAAATCGGTTCAAT
66 TTTGAACTTGTTGGACTAGTTGCTTTGGAAACCAATTCGTCAAGCCAATTCGAAATCGGTTCAAT
58470911 TGCTAATTCAATCGATTTTAGCTCGGTTCAACCAATTTGTACCGGTTCGCTTATTTACTTTCAAA
131 T-CTAATTCAATCGATTTTAGCTCGGTTCAACCAATTTGTACCGGTTCGCTTATTTACTTTCAAA
58470976 GTTTTATTATTTCTATTTCTTGAAGATTTACCACTATAAATTTAAA
195 GTTTTATTATTTCTATTTCTTGAAGATTTACCACTATAAATTTAAA
58471022 TTAAAAAACCAGTTGAACCAATTTTTAGAATTTTTTAGAATTTTTATTTTTAATATTTTATTTGC
1 TTAAAAAACCAGTTGAACCAATTTTTAGAATTTTTTAGAATTTTTATTTTTAATATTTTATTTGC
58471087 TTTGAACTTGTTGGACTAGTTGCTTTGGAAACCAATTCGTCAAGCCAATTCGAAATCGGTTCAAT
66 TTTGAACTTGTTGGACTAGTTGCTTTGGAAACCAATTCGTCAAGCCAATTCGAAATCGGTTCAAT
58471152 TGCTAATTCAATCGATTTTAGCTCGGTTCAACCAATTTGTACCGGTTCGCTTATTTACTTTCAAA
131 T-CTAATTCAATCGATTTTAGCTCGGTTCAACCAATTTGTACCGGTTCGCTTATTTACTTTCAAA
58471217 GTTTTATTATTTCTATTTCTTGAAGATTTACCACTATAAATTTAAA
195 GTTTTATTATTTCTATTTCTTGAAGATTTACCACTATAAATTTAAA
58471263 TTAAAAAAC
1 TTAAAAAAC
58471272 TAAAAATAAT
Statistics
Matches: 474, Mismatches: 14, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
240 2 0.00
241 461 0.97
242 11 0.02
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (240 bp):
TTAAAAAACCAGTTGAACCAATTTTTAGAATTTTTTAGAATTTTTATTTTTAATATTTTATTTGC
TTTGAACTTGTTGGACTAGTTGCTTTGGAAACCAATTCGTCAAGCCAATTCGAAATCGGTTCAAT
TCTAATTCAATCGATTTTAGCTCGGTTCAACCAATTTGTACCGGTTCGCTTATTTACTTTCAAAG
TTTTATTATTTCTATTTCTTGAAGATTTACCACTATAAATTTAAA
Found at i:58478326 original size:37 final size:37
Alignment explanation
Indices: 58478276--58478350 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 37
58478266 TCACTGAAAT
* *
58478276 CTTTATGTCGGAGTCGGGATTGTCTTGGATGCTGAAC
1 CTTTATGTCGGAGTCGGGATTGTCCTGGACGCTGAAC
58478313 CTTTATG-CTGGAGTCGGGATTGTCCTGGACGCTGAAC
1 CTTTATGTC-GGAGTCGGGATTGTCCTGGACGCTGAAC
58478350 C
1 C
58478351 GAGACTCTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 1 0.03
37 34 0.97
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (37 bp):
CTTTATGTCGGAGTCGGGATTGTCCTGGACGCTGAAC
Found at i:58478758 original size:21 final size:20
Alignment explanation
Indices: 58478712--58478785 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 20
58478702 CCTGATCAGT
*
58478712 ATACGACACATAAGTGCCTG
1 ATACGACACAGAAGTGCCTG
* * *
58478732 AAACGACACACGAGGTGTCTG
1 ATACGACACA-GAAGTGCCTG
58478753 ATACGACAC-GTAAAGTGCCTGAG
1 ATACGACACAG--AAGTGCCT--G
58478776 ATACGACACA
1 ATACGACACA
58478786 TAAAATGCCT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
19 1 0.02
20 9 0.22
21 21 0.51
23 10 0.24
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.16
Consensus pattern (20 bp):
ATACGACACAGAAGTGCCTG
Found at i:58478782 original size:23 final size:23
Alignment explanation
Indices: 58478752--58478797 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
58478742 CGAGGTGTCT
* *
58478752 GATACGACACGTAAAGTGCCTGA
1 GATACGACACATAAAATGCCTGA
58478775 GATACGACACATAAAATGCCTGA
1 GATACGACACATAAAATGCCTGA
58478798 TCGGCAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (23 bp):
GATACGACACATAAAATGCCTGA
Found at i:58478798 original size:44 final size:41
Alignment explanation
Indices: 58478712--58478798 Score: 93
Period size: 44 Copynumber: 2.0 Consensus size: 41
58478702 CCTGATCAGT
* ** *
58478712 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGTCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAATGCCTG
* *
58478753 ATACGACACGTAAAGTGCCTGAGATACGACACATAAAATGCCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAATGCCTG
58478797 AT
1 AT
58478799 CGGCAAAGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
41 10 0.27
42 10 0.27
43 1 0.03
44 16 0.43
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAATGCCTG
Found at i:58479125 original size:16 final size:17
Alignment explanation
Indices: 58479104--58479135 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
58479094 TAATAATAAT
58479104 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
58479120 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
58479136 GCTTACCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:58479830 original size:14 final size:14
Alignment explanation
Indices: 58479788--58479822 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
58479778 TCCTCTGTTC
58479788 TTTCTTTCTTTT-T
1 TTTCTTTCTTTTGT
58479801 GTTTCTTTCTTTTGT
1 -TTTCTTTCTTTTGT
58479816 TTTCTTT
1 TTTCTTT
58479823 TATTTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 19 0.95
15 1 0.05
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (14 bp):
TTTCTTTCTTTTGT
Found at i:58479994 original size:14 final size:17
Alignment explanation
Indices: 58479975--58480012 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
58479965 ATTTATTTCT
58479975 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
58479989 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
58480006 TAATATA
1 TAATATA
58480013 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:58480030 original size:11 final size:11
Alignment explanation
Indices: 58479992--58480030 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
58479982 ATATTTATAA
58479992 TATAATTAATT
1 TATAATTAATT
*
58480003 TAATAATATACTT
1 T-ATAAT-TAATT
58480016 TATAATTAATT
1 TATAATTAATT
58480027 TATA
1 TATA
58480031 TATTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:58495021 original size:8 final size:8
Alignment explanation
Indices: 58495008--58495033 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
58494998 AATGCAATCT
58495008 TCAACTTG
1 TCAACTTG
58495016 TCAACTTG
1 TCAACTTG
58495024 TCAACTTG
1 TCAACTTG
58495032 TC
1 TC
58495034 TTTAGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (8 bp):
TCAACTTG
Found at i:58499305 original size:23 final size:23
Alignment explanation
Indices: 58499279--58499323 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
58499269 GAAAATAGGC
*
58499279 CTACACGACCTACTTTGCCCAGT
1 CTACACGACCTACTTGGCCCAGT
58499302 CTACACGACCTACTTGGCCCAG
1 CTACACGACCTACTTGGCCCAG
58499324 CCCGTGAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.22
Consensus pattern (23 bp):
CTACACGACCTACTTGGCCCAGT
Found at i:58500576 original size:14 final size:14
Alignment explanation
Indices: 58500557--58500584 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58500547 GGTACAATCA
58500557 AAGTCTATTTGGTT
1 AAGTCTATTTGGTT
58500571 AAGTCTATTTGGTT
1 AAGTCTATTTGGTT
58500585 GGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (14 bp):
AAGTCTATTTGGTT
Found at i:58501131 original size:13 final size:13
Alignment explanation
Indices: 58501113--58501139 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58501103 TTTATTTAGT
58501113 GTTTAGGGTTTAA
1 GTTTAGGGTTTAA
58501126 GTTTAGGGTTTAA
1 GTTTAGGGTTTAA
58501139 G
1 G
58501140 GTTAAGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (13 bp):
GTTTAGGGTTTAA
Found at i:58503268 original size:3 final size:3
Alignment explanation
Indices: 58503260--58503311 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
58503250 TATTTTAGTG
* * * *
58503260 TTA TTA TTA TTA TTA CTG TTA TTA TTA TTA CTA CTA TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
58503306 TTA TTA
1 TTA TTA
58503312 GTTTTATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:58503279 original size:18 final size:18
Alignment explanation
Indices: 58503248--58503311 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
58503238 TGTTTAATTA
*
58503248 ATTATT-TTAGTGTTATT
1 ATTATTATTACTGTTATT
58503265 ATTATTATTACTGTTATT
1 ATTATTATTACTGTTATT
* *
58503283 ATTATTACTACTATTATT
1 ATTATTATTACTGTTATT
58503301 AATTATTATTA
1 -ATTATTATTA
58503312 GTTTTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.15
18 26 0.63
19 9 0.22
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (18 bp):
ATTATTATTACTGTTATT
Found at i:58503283 original size:15 final size:15
Alignment explanation
Indices: 58503261--58503311 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
58503251 ATTTTAGTGT
58503261 TATTATTATTATTAC
1 TATTATTATTATTAC
*
58503276 TGTTATTATTATTAC
1 TATTATTATTATTAC
* *
58503291 TACTATTATTAATTAT
1 TATTATTATT-ATTAC
58503307 TATTA
1 TATTA
58503312 GTTTTATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 22 0.73
16 8 0.27
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:58513124 original size:9 final size:9
Alignment explanation
Indices: 58513107--58513143 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
58513097 TGAGTTTTCG
58513107 AATTCGAAT
1 AATTCGAAT
*
58513116 AACTCGAAT
1 AATTCGAAT
58513125 AATTCGAAT
1 AATTCGAAT
58513134 AATTCGAAT
1 AATTCGAAT
58513143 A
1 A
58513144 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:58513390 original size:30 final size:31
Alignment explanation
Indices: 58513356--58513415 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
58513346 AAACCTTTTA
*
58513356 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
58513386 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
58513416 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:58522791 original size:23 final size:23
Alignment explanation
Indices: 58522764--58522810 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
58522754 TCAAATCGAG
58522764 TTAGGATGATAAAATACGATTTT
1 TTAGGATGATAAAATACGATTTT
*
58522787 TTAGGATGATAAAATATGATTTT
1 TTAGGATGATAAAATACGATTTT
58522810 T
1 T
58522811 CAACTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (23 bp):
TTAGGATGATAAAATACGATTTT
Found at i:58524586 original size:17 final size:17
Alignment explanation
Indices: 58524564--58524600 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
58524554 AATGACATGA
*
58524564 GTTCACATATCATAAGG
1 GTTCACATATCACAAGG
58524581 GTTCACATATCACAAGG
1 GTTCACATATCACAAGG
58524598 GTT
1 GTT
58524601 TGCAAATCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (17 bp):
GTTCACATATCACAAGG
Found at i:58529068 original size:169 final size:170
Alignment explanation
Indices: 58528788--58529167 Score: 412
Period size: 169 Copynumber: 2.2 Consensus size: 170
58528778 TACCGAAAAA
*
58528788 CTATACTAGCACACACAATGCATCATCGAATATACTGAAACAACTATACTAGCACACACAATGCA
1 CTATACTAGCACACACAATGCATCATCGAATATACTCAAACAACTATACTAGCACACACAATGCA
* * * * * *
58528853 TTATCGAATATACTAAAGCAACTATACTGGCACACACAGTGCATCATCGGATAAACTGAAGCAAA
66 TCATCGAATAAACCAAAGCAAATATACTAGCACACACAGTGCATCATCAGATAAACTGAAGCAAA
*
58528918 TATACTGGCACACAGTGCATAATCAGATATGTCAAAGCAT
131 TATACTGACACACAGTGCATAATCAGATATGTCAAAGCAT
* * * * *
58528958 CTATACTGGCACACATAGTGCATCATCGAAT-TAC-CAAAGCAACTATAC-AGGCACACATAGTG
1 CTATACTAGCACACACAATGCATCATCGAATATACTCAAA-CAACTATACTA-GCACACACAATG
* * * * *
58529020 CATCATC-AGATAAACCAAAGTAAATATACTAGCACATACAGTGCATCATCATATATATTGAAGC
64 CATCATCGA-ATAAACCAAAGCAAATATACTAGCACACACAGTGCATCATCAGATAAACTGAAGC
* * ** ** *
58529084 AACTATACTGACACACATAGTGCATCATTGGATATACCGAAA-CAA
128 AAATATACTGACACAC--AGTGCATAATCAGATATGTC-AAAGCAT
* * *
58529129 CTATACTAGCACACACAATGTATCATTGGATATAC-CAAA
1 CTATACTAGCACACACAATGCATCATCGAATATACTCAAA
58529168 GGACACAGTG
Statistics
Matches: 172, Mismatches: 31, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
168 5 0.03
169 87 0.51
170 28 0.16
171 42 0.24
172 10 0.06
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (170 bp):
CTATACTAGCACACACAATGCATCATCGAATATACTCAAACAACTATACTAGCACACACAATGCA
TCATCGAATAAACCAAAGCAAATATACTAGCACACACAGTGCATCATCAGATAAACTGAAGCAAA
TATACTGACACACAGTGCATAATCAGATATGTCAAAGCAT
Found at i:58529143 original size:212 final size:212
Alignment explanation
Indices: 58528747--58529143 Score: 491
Period size: 212 Copynumber: 1.9 Consensus size: 212
58528737 ATACGAAGTG
* *
58528747 TATACTAGCACACATAATGCTTCATCGGATATACCGAAAAACTATACTAGCACACACAATGCATC
1 TATACTAGCACACATAATGCATCATCGAATATACCGAAAAACTATACTAGCACACACAATGCATC
* * * *
58528812 ATCGAATATACTGAAACAACTATACTAGCACACACAATGCATTATCGAATATACTAAAGCAACTA
66 ATCGAATAAACTCAAACAAATATACTAGCACACACAATGCATCATCGAATATACTAAAGCAACTA
* * * *
58528877 TACTGGCACACACAGTGCATCATCGGATAAACTGAAGCAAATATACTGGCACACAGTGCATAATC
131 TACTGACACACACAGTGCATCATCGGATAAACCGAAACAAATATACTAGCACACAGTGCATAATC
58528942 AGATATGTCAAAGCATC
196 AGATATGTCAAAGCATC
* * * *
58528959 TATACTGGCACACATAGTGCATCATCGAAT-TACC-AAAGCAACTATAC-AGGCACACATAGTGC
1 TATACTAGCACACATAATGCATCATCGAATATACCGAAA--AACTATACTA-GCACACACAATGC
* * * * *
58529021 ATCATC-AGATAAAC-CAAAGTAAATATACTAGCACATACAGTGCATCATC-ATATATATTGAAG
63 ATCATCGA-ATAAACTCAAA-CAAATATACTAGCACACACAATGCATCATCGA-ATATACTAAAG
* * * *
58529083 CAACTATACTGACACACATAGTGCATCATTGGATATACCGAAACAACTATACTAGCACACA
125 CAACTATACTGACACACACAGTGCATCATCGGATAAACCGAAACAAATATACTAGCACACA
58529144 CAATGTATCA
Statistics
Matches: 156, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
210 3 0.02
211 10 0.06
212 143 0.92
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.22
Consensus pattern (212 bp):
TATACTAGCACACATAATGCATCATCGAATATACCGAAAAACTATACTAGCACACACAATGCATC
ATCGAATAAACTCAAACAAATATACTAGCACACACAATGCATCATCGAATATACTAAAGCAACTA
TACTGACACACACAGTGCATCATCGGATAAACCGAAACAAATATACTAGCACACAGTGCATAATC
AGATATGTCAAAGCATC
Found at i:58529164 original size:43 final size:43
Alignment explanation
Indices: 58528747--58529164 Score: 336
Period size: 43 Copynumber: 9.8 Consensus size: 43
58528737 ATACGAAGTG
* *
58528747 TATACTAGCACACATAATGCTTCATCGGATATACCGAAA-AAC
1 TATACTAGCACACACAATGCATCATCGGATATACCGAAACAAC
* *
58528789 TATACTAGCACACACAATGCATCATCGAATATACTGAAACAAC
1 TATACTAGCACACACAATGCATCATCGGATATACCGAAACAAC
* * *
58528832 TATACTAGCACACACAATGCATTATCGAATATA-CTAAAGCAAC
1 TATACTAGCACACACAATGCATCATCGGATATACCGAAA-CAAC
* * * * * *
58528875 TATACTGGCACACACAGTGCATCATCGGATAAACTGAAGCAAA
1 TATACTAGCACACACAATGCATCATCGGATATACCGAAACAAC
* * * * ** *
58528918 TATACT-G-GCACACAGTGCATAATCAGATATGTC-AAAGCATC
1 TATACTAGCACACACAATGCATCATCGGATATACCGAAA-CAAC
* * * *
58528959 TATACTGGCACACATAGTGCATCATCGAAT-TACC-AAAGCAAC
1 TATACTAGCACACACAATGCATCATCGGATATACCGAAA-CAAC
* * * * * *
58529001 TATAC-AGGCACACATAGTGCATCATCAGATAAACC-AAAGTAAA
1 TATACTA-GCACACACAATGCATCATCGGATATACCGAAA-CAAC
* * ** ** *
58529044 TATACTAGCACATACAGTGCATCATCATATATATTGAAGCAAC
1 TATACTAGCACACACAATGCATCATCGGATATACCGAAACAAC
*
58529087 TATACT-G-ACACACATAGTGCATCATTGGATATACCGAAACAAC
1 TATACTAGCACACACA-A-TGCATCATCGGATATACCGAAACAAC
* *
58529130 TATACTAGCACACACAATGTATCATTGGATATACC
1 TATACTAGCACACACAATGCATCATCGGATATACC
58529165 AAAGGACACA
Statistics
Matches: 304, Mismatches: 58, Indels: 27
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.01
41 33 0.11
42 76 0.25
43 179 0.59
44 7 0.02
45 7 0.02
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (43 bp):
TATACTAGCACACACAATGCATCATCGGATATACCGAAACAAC
Found at i:58529213 original size:72 final size:72
Alignment explanation
Indices: 58529102--58529242 Score: 158
Period size: 72 Copynumber: 2.0 Consensus size: 72
58529092 TGACACACAT
** * ** * *
58529102 AGTGCATCATTGGATATACCGAAACAACTATACTAGCACACACAATGTATCATTGGATATACCAA
1 AGTGCATCATTAAATATACCGAAACAAATATACTAGCACACACAATACATCATCGAATATACCAA
58529167 AGGACAC
66 AGGACAC
* * * * *
58529174 AGTGCATCATTAAATATATCGAAGA-AAATATATTGGCACACATAGTACATCATCGAATATACCA
1 AGTGCATCATTAAATATACCGAA-ACAAATATACTAGCACACACAATACATCATCGAATATACCA
58529238 AAGGA
65 AAGGA
58529243 TAACCTGTAC
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
72 55 0.98
73 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (72 bp):
AGTGCATCATTAAATATACCGAAACAAATATACTAGCACACACAATACATCATCGAATATACCAA
AGGACAC
Found at i:58533179 original size:35 final size:35
Alignment explanation
Indices: 58533110--58533237 Score: 175
Period size: 35 Copynumber: 3.6 Consensus size: 35
58533100 ATTACATCGA
*
58533110 CAATCCAACCAAAACACACCAGATGCTCACAAGAGC
1 CAATCCAACCAAAACACACCA-ATGCTCATAAGAGC
* *
58533146 CAATCCATCCGAAACACACCAATGCTCATAAGAGC
1 CAATCCAACCAAAACACACCAATGCTCATAAGAGC
* **
58533181 TAATCCTTCCAAAACACACCAATGCTCATAAGAGC
1 CAATCCAACCAAAACACACCAATGCTCATAAGAGC
* *
58533216 TAATCCAACCGAAACACACCAA
1 CAATCCAACCAAAACACACCAA
58533238 AACAGAGAAC
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 64 0.77
36 19 0.23
ACGTcount: A:0.43, C:0.34, G:0.09, T:0.13
Consensus pattern (35 bp):
CAATCCAACCAAAACACACCAATGCTCATAAGAGC
Found at i:58534578 original size:35 final size:35
Alignment explanation
Indices: 58534527--58534708 Score: 188
Period size: 35 Copynumber: 5.2 Consensus size: 35
58534517 GTTGTTACAG
* *
58534527 GTGTTGTGGCGAAATATTAAATGAGTGAAGTAATA
1 GTGTTGTGGCGGAATATTAAATGAATGAAGTAATA
* **
58534562 GTTTTGTGGCGGAATATTAAATGAATGAAGTAAGG
1 GTGTTGTGGCGGAATATTAAATGAATGAAGTAATA
*** *
58534597 GTGTTGTGGTAAAATATTAAAAT-AATGAAGTAACA
1 GTGTTGTGGCGGAATATT-AAATGAATGAAGTAATA
* *
58534632 GTGTTGTGGCGGGATATTAAATGAATGAAGT-ATCG
1 GTGTTGTGGCGGAATATTAAATGAATGAAGTAAT-A
* * * * *
58534667 GTGTTGTGGCGGTATGTTAAAAGAATGAAGTATTG
1 GTGTTGTGGCGGAATATTAAATGAATGAAGTAATA
58534702 GTGTTGT
1 GTGTTGT
58534709 AATGGGATGT
Statistics
Matches: 122, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
34 5 0.04
35 112 0.92
36 5 0.04
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (35 bp):
GTGTTGTGGCGGAATATTAAATGAATGAAGTAATA
Found at i:58534687 original size:70 final size:70
Alignment explanation
Indices: 58534526--58534741 Score: 236
Period size: 70 Copynumber: 3.1 Consensus size: 70
58534516 GGTTGTTACA
* * *
58534526 GGTGTTGTGGCGAAATATT-AAATGAGTGAAGTAATAGTTTTGTGGCGGAATATTAAATGAATGA
1 GGTGTTGTGGCGAAATATTAAAAT-AATGAAGTAATAGTGTTGTGGCGGGATATTAAATGAATGA
**
58534590 AGTAAG
65 AGTATC
** *
58534596 GGTGTTGTGGTAAAATATTAAAATAATGAAGTAACAGTGTTGTGGCGGGATATTAAATGAATGAA
1 GGTGTTGTGGCGAAATATTAAAATAATGAAGTAATAGTGTTGTGGCGGGATATTAAATGAATGAA
58534661 GTATC
66 GTATC
** * * * * *** * * *
58534666 GGTGTTGTGGCGGTATGTTAAAAGAATGAAGTATTGGTGTTGTAATGGGATGTTAATTGAAAGAA
1 GGTGTTGTGGCGAAATATTAAAATAATGAAGTAATAGTGTTGTGGCGGGATATTAAATGAATGAA
58534731 GTATC
66 GTATC
58534736 GGTGTT
1 GGTGTT
58534742 CTAACGAAAT
Statistics
Matches: 122, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
70 118 0.97
71 4 0.03
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (70 bp):
GGTGTTGTGGCGAAATATTAAAATAATGAAGTAATAGTGTTGTGGCGGGATATTAAATGAATGAA
GTATC
Found at i:58534719 original size:35 final size:35
Alignment explanation
Indices: 58534616--58534747 Score: 131
Period size: 35 Copynumber: 3.8 Consensus size: 35
58534606 TAAAATATTA
* * ** *
58534616 AAAT-AATGAAGTAACAGTGTTGTGGCGGGATATT
1 AAATGAATGAAGTATCGGTGTTGTAACGGGATGTT
** *
58534650 AAATGAATGAAGTATCGGTGTTGTGGCGGTATGTT
1 AAATGAATGAAGTATCGGTGTTGTAACGGGATGTT
* * *
58534685 AAAAGAATGAAGTATTGGTGTTGTAATGGGATGTT
1 AAATGAATGAAGTATCGGTGTTGTAACGGGATGTT
* * *
58534720 AATTGAAAGAAGTATCGGTGTTCTAACG
1 AAATGAATGAAGTATCGGTGTTGTAACG
58534748 AAATTTTAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
34 4 0.05
35 77 0.95
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (35 bp):
AAATGAATGAAGTATCGGTGTTGTAACGGGATGTT
Found at i:58544102 original size:357 final size:356
Alignment explanation
Indices: 58543385--58544034 Score: 857
Period size: 357 Copynumber: 1.8 Consensus size: 356
58543375 TTTTAATAAA
*
58543385 AGCAAATGATAAATTGACCACCTTGGAAGGAAGCCATATGGACACTTGACCTTCTAAGTTCTAAA
1 AGCAAATGATAAATTGACCACCTCGGAAGGAAG-C--ATGGACACTTGACC-TCTAAGTTCTAAA
* *
58543450 TAGGTGTATTGCCAGTAGAAGATTAGAGAGTAAATGCCATGAAGGAATTTAAATTCAAGTTTACA
62 TAGGTGTATTGCCAGTACAAGATTAGAGAGTAAATGCCATGAAGGAATTCAAATTCAAGTTTACA
* * * *
58543515 AATGAGAAAATAAGAAGCTGTAATCTTAGATTATTACATAAAATGGTAAATAGAAGATCAGCATT
127 AATGAGAAAATAAGAAGCTGCAATCTAAGATTATTACACAAAATGGAAAATAGAAGATCAGCATT
* *
58543580 CAATAAGGAATAAGTACAAAGCTAGCAGCTACCAGAGAAAGTAGAATTTTGCATAGCATCAATGG
192 CAATAAGGAATAAGTACAAAGCTAGCAGCTACCAGAGAAAATAGAATTTAGCATAGCATC-A--G
*
58543645 GTTATAATGAAACTGCAGCCACTTAAGGAGATAAGAAATGCATATAAAAGCAATAAAAATAAGGT
254 GATATAATGAAACTGCAGCCACTTAAGGAGATAAGAAATGCATATAAAAGCAATAAAAATAAGGT
** * *
58543710 AGGCTTCAATCATTGGATGAAGTGACAATTTGACATTT
319 ACACTTCAATCATTAGATGAAGCGACAATTTGACATTT
* * * *
58543748 AGCAAATGATAAATTGACCATCTCGGAATGAAG-ATGGACAGTTGA-C-CTAAGTTCTAACATTG
1 AGCAAATGATAAATTGACCACCTCGGAAGGAAGCATGGACACTTGACCTCTAAGTTCTAA-ATAG
* * * *
58543810 GTGTATTGCCAGTACAAGATTAGAGAGTAAATGCTATGGAGGAATTCAACTTCAAGTTTACAGAT
65 GTGTATTGCCAGTACAAGATTAGAGAGTAAATGCCATGAAGGAATTCAAATTCAAGTTTACAAAT
** *
58543875 GAGAAAATAAGAAGCTGCAATCTAAGATTATTACACAAAATGGCAAACATTAGAAGATTGGGATT
130 GAGAAAATAAGAAGCTGCAATCTAAGATTATTACACAAAATGG-AAA-A-TAGAAGATCAGCATT
* *
58543940 C-ATAAGGAATAAGTGCAAAGCTAG-ATGCTACTAGA-AATAATAGAATTTAGCATAGCA-C-GG
192 CAATAAGGAATAAGTACAAAGCTAGCA-GCTACCAGAGAA-AATAGAATTTAGCATAGCATCAGG
* * *
58544000 ATATAATGAAATTGCGGCCGCTTAAGGAGATAAGA
255 ATATAATGAAACTGCAGCCACTTAAGGAGATAAGA
58544035 CGTGGTTACA
Statistics
Matches: 255, Mismatches: 26, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
354 33 0.13
356 11 0.04
357 102 0.40
358 7 0.03
359 59 0.23
360 13 0.05
363 30 0.12
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (356 bp):
AGCAAATGATAAATTGACCACCTCGGAAGGAAGCATGGACACTTGACCTCTAAGTTCTAAATAGG
TGTATTGCCAGTACAAGATTAGAGAGTAAATGCCATGAAGGAATTCAAATTCAAGTTTACAAATG
AGAAAATAAGAAGCTGCAATCTAAGATTATTACACAAAATGGAAAATAGAAGATCAGCATTCAAT
AAGGAATAAGTACAAAGCTAGCAGCTACCAGAGAAAATAGAATTTAGCATAGCATCAGGATATAA
TGAAACTGCAGCCACTTAAGGAGATAAGAAATGCATATAAAAGCAATAAAAATAAGGTACACTTC
AATCATTAGATGAAGCGACAATTTGACATTT
Found at i:58545737 original size:60 final size:60
Alignment explanation
Indices: 58545625--58545800 Score: 164
Period size: 60 Copynumber: 2.9 Consensus size: 60
58545615 AAAAAATACG
* * * * * *
58545625 GGTACTTAATTGTGACAAAAAAATAAACTCAAGTACCTAATTAAACACTGAAGCT-AAACTTA
1 GGTACTTAAATGGGAC--AAAAA-AAACTCAAGTACCAAATTGAACATTGAAGCTCAAACTCA
* *
58545687 GGTACTTAAATGGGACAAAGAAAAACTCAAGTACCAAAGTGAACTTTGAAG-TCAAACTCA
1 GGTACTTAAATGGGACAAA-AAAAACTCAAGTACCAAATTGAACATTGAAGCTCAAACTCA
* * * *
58545747 AGTAC-CAAATTGGGAC-AAAAAAACTCAAATACCGAATTGAACATTGAAGC-CAAA
1 GGTACTTAAA-TGGGACAAAAAAAACTCAAGTACCAAATTGAACATTGAAGCTCAAA
58545801 TTCATGTATC
Statistics
Matches: 96, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
58 31 0.32
59 6 0.06
60 43 0.45
61 2 0.02
62 14 0.15
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (60 bp):
GGTACTTAAATGGGACAAAAAAAACTCAAGTACCAAATTGAACATTGAAGCTCAAACTCA
Found at i:58546559 original size:25 final size:25
Alignment explanation
Indices: 58546514--58546562 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
58546504 TTTGACAAGT
58546514 TTAGGTACAAATTGAGAAAAAAAGC
1 TTAGGTACAAATTGAGAAAAAAAGC
58546539 TTAGGTACCAAATT-AGGAAAAAAA
1 TTAGGTA-CAAATTGA-GAAAAAAA
58546563 ATGTCAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.20
Consensus pattern (25 bp):
TTAGGTACAAATTGAGAAAAAAAGC
Found at i:58551270 original size:88 final size:87
Alignment explanation
Indices: 58551121--58551566 Score: 421
Period size: 88 Copynumber: 5.1 Consensus size: 87
58551111 AGAGTAGATC
* * * *
58551121 GGTTAAAAATAACAGATCTTGCCTTCCTGTGCCGACAGCGAAGCAGATCGAAGACGCCAGCCTTG
1 GGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGTAGATCGAAGAC-ACAGCCTTG
*
58551186 CCTCCCTGGGTTGCAGCGGAGCA
65 CCTCCCTGGGTGGCAGCGGAGCA
* *
58551209 GGTTAAAAATAGCAGATCTTACCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACATCAGCCTTG
1 GGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGTAGATCGAAGACA-CAGCCTTG
* * *
58551274 CCTCCCTAGGTTGCAGCAGAGCA
65 CCTCCCTGGGTGGCAGCGGAGCA
* * *
58551297 GGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCAAAGTAGATCGAAGACTCCAGCCTTA
1 GGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGTAGATCGAAGAC-ACAGCCTTG
* * * * * * *
58551362 TCTCCTTGAGTAGCTGTGGAGTA
65 CCTCCCTGGGTGGCAGCGGAGCA
* * ** * ** * * * * *
58551385 GGTTGAAAATTA-TAGATCTTATCTCCCTAAGCAG-TAGCGGAGTAGATTGAAGACACTAACCTT
1 GGTT-AAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGTAGATCGAAGACAC-AGCCTT
* *
58551448 GCCTCCCTTGGTGGCAG-GAGAACA
64 GCCTCCCTGGGTGGCAGCG-GAGCA
* * ** * *
58551472 GGTTAAAGATAGCAGATCTTGCCTTCTTGTACTGACAGTGAAGTAGATCGAAGACACTAGCCTTG
1 GGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGTAGATCGAAGACAC-AGCCTTG
* * *
58551537 CCTCCCTCGGTGGTAGTGGAGCA
65 CCTCCCTGGGTGGCAGCGGAGCA
58551560 GGTTAAA
1 GGTTAAA
58551567 GATTACATAT
Statistics
Matches: 288, Mismatches: 62, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
86 7 0.02
87 51 0.18
88 223 0.77
89 7 0.02
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.23
Consensus pattern (87 bp):
GGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGTAGATCGAAGACACAGCCTTGC
CTCCCTGGGTGGCAGCGGAGCA
Found at i:58551320 original size:44 final size:42
Alignment explanation
Indices: 58551182--58551325 Score: 110
Period size: 44 Copynumber: 3.3 Consensus size: 42
58551172 AGACGCCAGC
58551182 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCT-GGTTGCAGC-GAGCAGGTTAAAAATAGCAGAT
* * ** * ** * * * *
58551226 CTTACCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACATCAG-C
1 CTTGCCTCCCTG-GTTG-CAGCG-AGCAGGTTAAAAATAGCAGAT
58551270 CTTGCCTCCCTAGGTTGCAGCAGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCT-GGTTGCAGC-GAGCAGGTTAAAAATAGCAGAT
*
58551314 CTTGCCTTCCTG
1 CTTGCCTCCCTG
58551326 CGCCGACAGC
Statistics
Matches: 71, Mismatches: 23, Indels: 13
0.66 0.21 0.12
Matches are distributed among these distances:
43 19 0.27
44 34 0.48
45 18 0.25
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (42 bp):
CTTGCCTCCCTGGTTGCAGCGAGCAGGTTAAAAATAGCAGAT
Found at i:58551518 original size:175 final size:172
Alignment explanation
Indices: 58551121--58551608 Score: 528
Period size: 175 Copynumber: 2.8 Consensus size: 172
58551111 AGAGTAGATC
* * *
58551121 GGTTAAAAATAACAGATCTTGCCTTCCTGTGCCGACAGCGAAGCAGATCGAAGACGCCAGCCTTG
1 GGTTAAAAATAGCAGATCTTGCCTTCCTGTGCCGACAGCGAAGTAGATCGAAGACACCAGCCTTG
* * * * * * ** * * *
58551186 CCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTACCTTCCTGCGCCGACAGCGAA
66 CCT-CCTTGG-TGCTGTGGAGCAGGTTAAAATTA-CAGATCTTATCTCCCTAAGCAG-TAGCGGA
* * *
58551251 GCAGATCGAAGACATCAGCCTTGCCTCCCTAGGTTGCAGCAGAGCA
127 GCAGATCGAAGACATCAACCTTGCCTCCCTAGGTGGCAGCAGAACA
* * * *
58551297 GGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCAAAGTAGATCGAAGACTCCAGCCTTA
1 GGTTAAAAATAGCAGATCTTGCCTTCCTGTGCCGACAGCGAAGTAGATCGAAGACACCAGCCTTG
* * *
58551362 TCTCCTTGAGTAGCTGTGGAGTAGGTTGAAAATTATAGATCTTATCTCCCTAAGCAGTAGCGGAG
66 CCTCCTTG-GT-GCTGTGGAGCAGGTT-AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAG
* * * *
58551427 TAGATTGAAGACA-CTAACCTTGCCTCCCTTGGTGGCAGGAGAACA
128 CAGATCGAAGACATC-AACCTTGCCTCCCTAGGTGGCAGCAGAACA
* * * * * *
58551472 GGTTAAAGATAGCAGATCTTGCCTTCTTGTACTGACAGTGAAGTAGATCGAAGACACTAGCCTTG
1 GGTTAAAAATAGCAGATCTTGCCTTCCTGTGCCGACAGCGAAGTAGATCGAAGACACCAGCCTTG
* * * *
58551537 CCTCCCTCGGTGGTAGTGGAGCAGGTTAAAGATTACATATCTTATCTCCCTAAGCAGTAGTGGAG
66 CCT-CCTTGGTGCT-GTGGAGCAGGTTAAA-ATTACAGATCTTATCTCCCTAAGCAGTAGCGGAG
58551602 CAGATCG
128 CAGATCG
58551609 CATCCAGCCT
Statistics
Matches: 259, Mismatches: 46, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
174 6 0.02
175 153 0.59
176 94 0.36
177 6 0.02
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (172 bp):
GGTTAAAAATAGCAGATCTTGCCTTCCTGTGCCGACAGCGAAGTAGATCGAAGACACCAGCCTTG
CCTCCTTGGTGCTGTGGAGCAGGTTAAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAG
ATCGAAGACATCAACCTTGCCTCCCTAGGTGGCAGCAGAACA
Found at i:58551668 original size:44 final size:44
Alignment explanation
Indices: 58551619--58551716 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 44
58551609 CATCCAGCCT
* *
58551619 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCC
1 TATCTCCCTGGTCAGCAGGGGAATAGGTTGAAGATTGAGAATCC
*
58551663 TATCTCCCTGGTCAGCAGGGGAATAGGTTGAAGATTGAGAATCT
1 TATCTCCCTGGTCAGCAGGGGAATAGGTTGAAGATTGAGAATCC
58551707 TATCTCCCTG
1 TATCTCCCTG
58551717 AAGTTACAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (44 bp):
TATCTCCCTGGTCAGCAGGGGAATAGGTTGAAGATTGAGAATCC
Found at i:58551755 original size:44 final size:43
Alignment explanation
Indices: 58551702--58551809 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 43
58551692 GAAGATTGAG
* *
58551702 AATCTTATCTCCCTGAAGTTACAGTGGAGTAG-ATTAAAGCCAA
1 AATCTTATCTCCCTGAAGTTACAATGGAG-AGAATTAAAACCAA
* * *
58551745 TAATCCTATCTCCCTGAAGTTTCAATGGAGCGAATTAAAACCAA
1 -AATCTTATCTCCCTGAAGTTACAATGGAGAGAATTAAAACCAA
*
58551789 AGATCTTATCTCTCTGAAGTT
1 A-ATCTTATCTCCCTGAAGTT
58551810 GCAGATAGCA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 2 0.04
44 53 0.96
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTACAATGGAGAGAATTAAAACCAA
Found at i:58551932 original size:44 final size:43
Alignment explanation
Indices: 58551835--58551934 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 43
58551825 CATCTGGTCT
* * * *
58551835 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGTAAGAAAATCT
1 TATCTCCCTAAAATTGCAGTGGAGCAAACTGAG-AAGAAAATCC
* *
58551879 TATCCCCCTAAAATTGCAGTGGAGCAAACTGA-ATGAATAAGTCC
1 TATCTCCCTAAAATTGCAGTGGAGCAAACTGAGAAGAA-AA-TCC
58551923 TATCTCCCTAAA
1 TATCTCCCTAAA
58551935 GTTGTAGTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
42 4 0.09
43 2 0.04
44 41 0.87
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (43 bp):
TATCTCCCTAAAATTGCAGTGGAGCAAACTGAGAAGAAAATCC
Found at i:58553380 original size:14 final size:15
Alignment explanation
Indices: 58553346--58553380 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
58553336 TAAATCCATT
58553346 TTTATATTTAAGTAC
1 TTTATATTTAAGTAC
58553361 TTTATATTTAAGTA-
1 TTTATATTTAAGTAC
58553375 TTTATA
1 TTTATA
58553381 CAATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (15 bp):
TTTATATTTAAGTAC
Found at i:58557794 original size:2 final size:2
Alignment explanation
Indices: 58557781--58557811 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
58557771 CAAAGTTCCT
*
58557781 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
58557812 TATCAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:58561847 original size:6 final size:6
Alignment explanation
Indices: 58561838--58561864 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
58561828 AGAAGGACAA
58561838 GGACTC GGACTC GGACTC GGACTC GGA
1 GGACTC GGACTC GGACTC GGACTC GGA
58561865 TTCAAGCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.37, T:0.15
Consensus pattern (6 bp):
GGACTC
Found at i:58563768 original size:13 final size:13
Alignment explanation
Indices: 58563752--58563776 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58563742 TTGAATTTTA
58563752 ATTTTTAAATTTC
1 ATTTTTAAATTTC
58563765 ATTTTTAAATTT
1 ATTTTTAAATTT
58563777 TAGGCTACTA
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTTAAATTTC
Found at i:58574230 original size:2 final size:2
Alignment explanation
Indices: 58574223--58574281 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
58574213 TCTATTCCCT
58574223 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
58574265 TC TT TC TT TC TT TC TC T
1 TC TC TC TC TC TC TC TC T
58574282 GTAAAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:58584692 original size:30 final size:30
Alignment explanation
Indices: 58584646--58584828 Score: 241
Period size: 30 Copynumber: 6.2 Consensus size: 30
58584636 GTATATGTTT
* *
58584646 TATATATTTCCGAATTGATTTGTATATGAA
1 TATACATTGCCGAATTGATTTGTATATGAA
** *
58584676 TATACATTTTCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGAA
*
58584706 TATACATCGCCGAATTGATTTGTATATGGAA
1 TATACATTGCCGAATTGATTTGTATAT-GAA
*
58584737 -ATACATTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGAA
*
58584766 TATACATTGCTGAATTGATTTGTATATGAA
1 TATACATTGCCGAATTGATTTGTATATGAA
*
58584796 TATACATTGTCG--TTGATTTGTATATG--
1 TATACATTGCCGAATTGATTTGTATATGAA
58584822 TATACAT
1 TATACAT
58584829 ATATATTGTT
Statistics
Matches: 138, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
26 7 0.05
28 14 0.10
29 2 0.01
30 113 0.82
31 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (30 bp):
TATACATTGCCGAATTGATTTGTATATGAA
Found at i:58584732 original size:60 final size:60
Alignment explanation
Indices: 58584655--58584828 Score: 268
Period size: 60 Copynumber: 3.0 Consensus size: 60
58584645 TTATATATTT
*
58584655 CCGAATTGATTTGTATATGAATATACATTTTCGAATTGATTTGTATATGGATATACATCG
1 CCGAATTGATTTGTATATGAATATACATTGTCGAATTGATTTGTATATGGATATACATCG
* *
58584715 CCGAATTGATTTGTATATGGAA-ATACATTGCCGAATTGATTTGTATATGGATATACATTG
1 CCGAATTGATTTGTATAT-GAATATACATTGTCGAATTGATTTGTATATGGATATACATCG
*
58584775 CTGAATTGATTTGTATATGAATATACATTGTCG--TTGATTTGTATAT-G-TATACAT
1 CCGAATTGATTTGTATATGAATATACATTGTCGAATTGATTTGTATATGGATATACAT
58584829 ATATATTGTT
Statistics
Matches: 107, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
56 7 0.07
57 1 0.01
58 13 0.12
59 3 0.03
60 80 0.75
61 3 0.03
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (60 bp):
CCGAATTGATTTGTATATGAATATACATTGTCGAATTGATTTGTATATGGATATACATCG
Found at i:58584846 original size:34 final size:30
Alignment explanation
Indices: 58584657--58584849 Score: 214
Period size: 30 Copynumber: 6.4 Consensus size: 30
58584647 ATATATTTCC
58584657 GAATTGATTTGTATATGAATATACATT-TT
1 GAATTGATTTGTATATGAATATACATTGTT
* * **
58584686 CGAATTGATTTGTATATGGATATACATCGCC
1 -GAATTGATTTGTATATGAATATACATTGTT
**
58584717 GAATTGATTTGTATATGGAA-ATACATTGCC
1 GAATTGATTTGTATAT-GAATATACATTGTT
* *
58584747 GAATTGATTTGTATATGGATATACATTGCT
1 GAATTGATTTGTATATGAATATACATTGTT
*
58584777 GAATTGATTTGTATATGAATATACATTGTC
1 GAATTGATTTGTATATGAATATACATTGTT
*
58584807 G--TTGATTTGTATATGTATACATATATATTGTT
1 GAATTGATTTGTATATG---A-ATATACATTGTT
58584839 GAATTGATTTG
1 GAATTGATTTG
58584850 AGCATTGGAT
Statistics
Matches: 141, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.10
29 2 0.01
30 103 0.73
31 3 0.02
32 11 0.08
34 8 0.06
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (30 bp):
GAATTGATTTGTATATGAATATACATTGTT
Found at i:58585021 original size:41 final size:40
Alignment explanation
Indices: 58584970--58585049 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 40
58584960 AAGGTGTGAT
* * *
58584970 TTCGTGTAAGACCATGTCTAGGACATTGGCATCGTATATGA
1 TTCGTATAAGACCATGCCTAGGACAGTGGCATCG-ATATGA
* *
58585011 TTCGTATAAGACCCTGCCTGGGACAGTGGCATCGATATG
1 TTCGTATAAGACCATGCCTAGGACAGTGGCATCGATATG
58585050 TGTTAACATG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 5 0.15
41 29 0.85
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (40 bp):
TTCGTATAAGACCATGCCTAGGACAGTGGCATCGATATGA
Found at i:58586857 original size:90 final size:90
Alignment explanation
Indices: 58586704--58586883 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
58586694 TTTTTTCCGT
58586704 TAATATTTAATTAGATTGCAAAATCTTTTATTTTTTAAAAAAGAATTCAAAACTCGACACTTGTA
1 TAATATTTAATTAGATTGCAAAATCTTTTATTTTTTAAAAAAGAATTCAAAACTCGACACTTGTA
58586769 GATATGAAGTTTAAGGTTACCCACA
66 GATATGAAGTTTAAGGTTACCCACA
*
58586794 TAATATTTAATTAGATTGCAACATCTTTTATTTTTTAAAAAAGAATTCAAAACTCGACACTTGTA
1 TAATATTTAATTAGATTGCAAAATCTTTTATTTTTTAAAAAAGAATTCAAAACTCGACACTTGTA
58586859 GATATGAAGTTTAAGGTTACCCACA
66 GATATGAAGTTTAAGGTTACCCACA
58586884 ATCGTTTCAA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (90 bp):
TAATATTTAATTAGATTGCAAAATCTTTTATTTTTTAAAAAAGAATTCAAAACTCGACACTTGTA
GATATGAAGTTTAAGGTTACCCACA
Found at i:58587468 original size:32 final size:32
Alignment explanation
Indices: 58587401--58587473 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
58587391 TAACAGTTGG
* * *
58587401 AACTGAATT-TTAAAATATAAAAAACTAGATG
1 AACTAAATTCTTAAAATATAAAAAACTAAATA
* *
58587432 AACTATATTCTTAAAATA-AATAAAATTAAATA
1 AACTAAATTCTTAAAATATAA-AAAACTAAATA
58587464 AACTAAATTC
1 AACTAAATTC
58587474 CAAATTTACG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
31 9 0.26
32 25 0.74
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (32 bp):
AACTAAATTCTTAAAATATAAAAAACTAAATA
Found at i:58589408 original size:19 final size:18
Alignment explanation
Indices: 58589384--58589443 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
58589374 TTTAACAAAA
58589384 TTTTTAAAACTTTATAAAT
1 TTTTTAAAACTTT-TAAAT
* *
58589403 TTTTTATAACTTTTATGAT
1 TTTTTAAAACTTTTA-AAT
*
58589422 TTTTTAATAATTTTTAAAT
1 TTTTTAA-AACTTTTAAAT
58589441 TTT
1 TTT
58589444 AGAAGAGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 2 0.06
19 25 0.74
20 7 0.21
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTAAAACTTTTAAAT
Found at i:58594130 original size:71 final size:70
Alignment explanation
Indices: 58594051--58594192 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 70
58594041 GATCCTTTTA
*
58594051 AGACCCAAATTGGAAAAGCTATGCCATTAGTAGTGTAATGGTTTATTTGAGTATGTGTAGGGACA
1 AGACCCAAATTGGAAAAGCTATGCCATTAGTAGTGTAATGGTTTATTTGAGTATGTGTAGGGAAA
58594116 TGACT
66 TGACT
58594121 ANGACCCAAATTGGAAAAGCTATGCCATTAGTAGTGTAATGGTTTATTTGAGTATGTGTAGGGAA
1 A-GACCCAAATTGGAAAAGCTATGCCATTAGTAGTGTAATGGTTTATTTGAGTATGTGTAGGGAA
58594186 ATGACT
65 ATGACT
58594192 A
1 A
58594193 TGGCCAGACC
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 1 0.01
71 69 0.99
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.31
Consensus pattern (70 bp):
AGACCCAAATTGGAAAAGCTATGCCATTAGTAGTGTAATGGTTTATTTGAGTATGTGTAGGGAAA
TGACT
Found at i:58599039 original size:20 final size:21
Alignment explanation
Indices: 58598999--58599046 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
58598989 TGATGTTATC
*
58598999 TATTTTTTATAATACGTTTCA
1 TATTTTTTATAATACGATTCA
58599020 TATTTTTTATAATAC-ATTCA
1 TATTTTTTATAATACGATTCA
58599040 TATTTTT
1 TATTTTT
58599047 CCCTCTTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTTTTATAATACGATTCA
Found at i:58600314 original size:14 final size:14
Alignment explanation
Indices: 58600292--58600340 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
58600282 CACGGATGGT
58600292 AATCAGAATATTAA
1 AATCAGAATATTAA
*
58600306 AATCTGAATATTATA
1 AATCAGAATATTA-A
58600321 TGAATCAGCAATATTAA
1 --AATCAG-AATATTAA
58600338 AAT
1 AAT
58600341 ATGTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 12 0.41
15 4 0.14
17 6 0.21
18 7 0.24
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (14 bp):
AATCAGAATATTAA
Found at i:58602455 original size:8 final size:8
Alignment explanation
Indices: 58602442--58602466 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
58602432 TATTATTTAA
58602442 ATTTTGAT
1 ATTTTGAT
58602450 ATTTTGAT
1 ATTTTGAT
58602458 ATTTTGAT
1 ATTTTGAT
58602466 A
1 A
58602467 ATTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (8 bp):
ATTTTGAT
Found at i:58604930 original size:22 final size:21
Alignment explanation
Indices: 58604900--58604944 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
58604890 ACACCAAAAC
*
58604900 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCG-TTTTTT
*
58604922 AGGCCTTTAGTGGCGTTTTTT
1 AGGCCTTTAGCGGCGTTTTTT
58604943 AG
1 AG
58604945 CGCCGCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.11, C:0.16, G:0.29, T:0.44
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGTTTTTT
Found at i:58606284 original size:28 final size:28
Alignment explanation
Indices: 58606244--58606304 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
58606234 AAAACAAGAA
*
58606244 TCAAATTAGTTCAA-CTCCAAGTCCTTAG
1 TCAAATCAGTTCAACCT-CAAGTCCTTAG
* *
58606272 TCAAATCAGTTCAACCTCAAGTTCTTTG
1 TCAAATCAGTTCAACCTCAAGTCCTTAG
58606300 TCAAA
1 TCAAA
58606305 AGAAAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (28 bp):
TCAAATCAGTTCAACCTCAAGTCCTTAG
Found at i:58609626 original size:18 final size:18
Alignment explanation
Indices: 58609603--58609642 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
58609593 AAATTATAAT
*
58609603 TTTTATTTTTTTATTTCA
1 TTTTATTTTTGTATTTCA
*
58609621 TTTTATTTTTGTATTTTA
1 TTTTATTTTTGTATTTCA
58609639 TTTT
1 TTTT
58609643 TTCTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTATTTTTGTATTTCA
Done.