Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 92 of 311
Found at i:29578816 original size:31 final size:31
Alignment explanation
Indices: 29578778--29578887 Score: 177
Period size: 31 Copynumber: 3.5 Consensus size: 31
29578768 TTTAATGGTT
29578778 ACTGGGCCAAAGCCTTTTCATAAATCATATC
1 ACTGGGCCAAAGCCTTTTCATAAATCATATC
* *
29578809 ACTGGGCCGAAGCCTTATCATAAATCATATC
1 ACTGGGCCAAAGCCTTTTCATAAATCATATC
*
29578840 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCAAAGCCTTTTCATAAATCATATC
29578871 ACTGGG-CAGAAGCCTTT
1 ACTGGGCCA-AAGCCTTT
29578888 ACTGTAAACG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
30 1 0.01
31 73 0.99
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (31 bp):
ACTGGGCCAAAGCCTTTTCATAAATCATATC
Found at i:29579127 original size:13 final size:13
Alignment explanation
Indices: 29579109--29579134 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29579099 TTTAATAACA
29579109 GGGGCAAAGCCCT
1 GGGGCAAAGCCCT
29579122 GGGGCAAAGCCCT
1 GGGGCAAAGCCCT
29579135 TTTTGGTAAA
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:0.23, C:0.31, G:0.38, T:0.08
Consensus pattern (13 bp):
GGGGCAAAGCCCT
Found at i:29579181 original size:25 final size:25
Alignment explanation
Indices: 29579120--29579186 Score: 109
Period size: 24 Copynumber: 2.7 Consensus size: 25
29579110 GGGCAAAGCC
*
29579120 CTGGGGCAAAGCCCTTTTTGGTAAA
1 CTGGGGCAAAGCCCTTTTCGGTAAA
29579145 CT-GGGCAAAGCCCTTTTCGGTAAA
1 CTGGGGCAAAGCCCTTTTCGGTAAA
*
29579169 CTGGGGCATAGCCCTTTT
1 CTGGGGCAAAGCCCTTTT
29579187 AGCACTTCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
24 23 0.59
25 16 0.41
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (25 bp):
CTGGGGCAAAGCCCTTTTCGGTAAA
Found at i:29580054 original size:27 final size:27
Alignment explanation
Indices: 29579992--29580056 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
29579982 GGGCATATTC
29579992 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
29580019 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
*
29580046 GTCTTTTTACC
1 GTCATTTTACC
29580057 TATTAAGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:29580214 original size:27 final size:27
Alignment explanation
Indices: 29580087--29580296 Score: 138
Period size: 27 Copynumber: 7.7 Consensus size: 27
29580077 TTTCATCCTA
* * * *
29580087 CAAGGGTATTTTGGTAAATCTACTAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
*** ** *
29580114 CAAGGGTATTTCAATAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
29580141 CAATGGTATTTCT-ATAATTTTTAGAAAGT
1 CAAGGGTATTT-TGGTAA-TTTTACAAA-T
* * **
29580170 CAAGGGAATTTTTGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
29580197 C-AGGGATATTTTGGTAATTTTACAAAT
1 CAAGGG-TATTTTGGTAATTTTACAAAT
** * * *
29580224 TGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
29580251 CAATGGTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
29580277 CTAGGGGTATTTTGGTAATT
1 C-AAGGGTATTTTGGTAATT
29580297 CTACCCTATA
Statistics
Matches: 143, Mismatches: 33, Indels: 14
0.75 0.17 0.07
Matches are distributed among these distances:
26 5 0.03
27 107 0.75
28 19 0.13
29 12 0.08
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:29580336 original size:27 final size:27
Alignment explanation
Indices: 29580194--29580362 Score: 105
Period size: 27 Copynumber: 6.3 Consensus size: 27
29580184 TAATTTTGTA
* * *
29580194 AATC-AGGGATATTTTGGTAATTTTAC
1 AATCGAGGGGTATTTCGGTAATTTCAC
*
29580220 AAATTGA-GGGTATTTCGGTAATTTCAC
1 -AATCGAGGGGTATTTCGGTAATTTCAC
* * ** * *
29580247 AAACCAATGGTATTTTGGTAATTTTAC
1 AATCGAGGGGTATTTCGGTAATTTCAC
* * * *
29580274 AAACTAGGGGTATTTTGGTAATTCTACCC
1 AATCGAGGGGTATTTCGGTAATT-T-CAC
* *
29580303 TAT--AGGGGTATTTCAGTAATTTCAC
1 AATCGAGGGGTATTTCGGTAATTTCAC
***
29580328 AATCGA-GGGTAAAACGGTAATTTCAC
1 AATCGAGGGGTATTTCGGTAATTTCAC
29580354 AATCGAGGG
1 AATCGAGGG
29580363 TAAAACAGTA
Statistics
Matches: 110, Mismatches: 25, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
25 4 0.04
26 26 0.24
27 76 0.69
28 2 0.02
29 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35
Consensus pattern (27 bp):
AATCGAGGGGTATTTCGGTAATTTCAC
Found at i:29580347 original size:26 final size:26
Alignment explanation
Indices: 29580316--29580401 Score: 120
Period size: 26 Copynumber: 3.3 Consensus size: 26
29580306 AGGGGTATTT
29580316 CAGTAATTTCACAATCGAGGGTAAAA
1 CAGTAATTTCACAATCGAGGGTAAAA
*
29580342 CGGTAATTTCACAATCGAGGGTAAAA
1 CAGTAATTTCACAATCGAGGGTAAAA
* *
29580368 CAGTAATTTGTA-AATCAAGGGTAAAA
1 CAGTAATTT-CACAATCGAGGGTAAAA
*
29580394 TAGTAATT
1 CAGTAATT
29580402 CTATAAATCG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
26 53 0.98
27 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.27
Consensus pattern (26 bp):
CAGTAATTTCACAATCGAGGGTAAAA
Found at i:29580416 original size:27 final size:26
Alignment explanation
Indices: 29580328--29580417 Score: 110
Period size: 26 Copynumber: 3.4 Consensus size: 26
29580318 GTAATTTCAC
* *
29580328 AATCGAGGGTAAAACGGTAATTTCA-C
1 AATCGAGGGTAAAACAGTAATTT-ATA
*
29580354 AATCGAGGGTAAAACAGTAATTTGTA
1 AATCGAGGGTAAAACAGTAATTTATA
* *
29580380 AATCAAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAACAGTAATT-TATA
29580407 AATCGAGGGTA
1 AATCGAGGGTA
29580418 CTTTGGTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
26 42 0.76
27 13 0.24
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.26
Consensus pattern (26 bp):
AATCGAGGGTAAAACAGTAATTTATA
Found at i:29582438 original size:20 final size:20
Alignment explanation
Indices: 29582413--29582457 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
29582403 AGAGACTAAA
* *
29582413 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
29582433 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
29582453 ATGAA
1 ATGAA
29582458 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:29586482 original size:16 final size:16
Alignment explanation
Indices: 29586463--29586493 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29586453 CTTCTTCACT
29586463 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
29586479 TACTTACTTACTTAA
1 TACTCACTTACTTAA
29586494 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:29586499 original size:20 final size:20
Alignment explanation
Indices: 29586460--29586499 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29586450 AAACTTCTTC
* *
29586460 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
29586480 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
29586500 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:29586870 original size:55 final size:54
Alignment explanation
Indices: 29586680--29586934 Score: 215
Period size: 55 Copynumber: 4.8 Consensus size: 54
29586670 ACGCGGGTAC
* * * *
29586680 CTTACCATTGCCATGACTTGTCATGGTCTTACATGGTA----T-CCTT-TTGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTTGCCTTATAG-AA
* * *
29586729 CTTACCATTGCCATGTCTTGATATGGTCTTACATGGTATCC-TTGCCTTAT-GAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTTGCCTTATAGAA
* * * * *
29586782 CTCAGCAATGCCATGCCTTGGCATTGTCTTACATGGGACCTTTGCCTTATAGCAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTTGCCTTATAG-AA
* * * * *
29586837 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTT-CCTTAGA-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATG-GTACCTTTGCCTTATAGAA
*
29586890 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTA-CCTT
29586935 AAACCCTAAT
Statistics
Matches: 168, Mismatches: 25, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
49 35 0.21
52 2 0.01
53 44 0.26
54 14 0.08
55 68 0.40
56 5 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTTGCCTTATAGAA
Found at i:29586871 original size:108 final size:110
Alignment explanation
Indices: 29586727--29586927 Score: 291
Period size: 108 Copynumber: 1.8 Consensus size: 110
29586717 ATCCTTTTGA
* * * *
29586727 AACTTACCATTGCCATGTCTTGATATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCAGCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
*
29586790 -TGCCATGCCTTGGCATTGTCTTACATGGGACCTTTGCCTTATAGC
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGC
* * * *
29586835 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTTCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
29586900 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
29586928 TATCCTTAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 1 0.01
108 47 0.58
109 6 0.07
110 27 0.33
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGC
Found at i:29588474 original size:38 final size:38
Alignment explanation
Indices: 29588423--29588501 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
29588413 TTTAACCGGA
29588423 GGTCTTTATCTCCTTCAGTGACCTGTGTGGGTAGTTCT
1 GGTCTTTATCTCCTTCAGTGACCTGTGTGGGTAGTTCT
29588461 GGTCTTTATCTCCTTCAGTGACCTGTGTGGGTAGTTCT
1 GGTCTTTATCTCCTTCAGTGACCTGTGTGGGTAGTTCT
29588499 GGT
1 GGT
29588502 AAACCCAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.10, C:0.20, G:0.28, T:0.42
Consensus pattern (38 bp):
GGTCTTTATCTCCTTCAGTGACCTGTGTGGGTAGTTCT
Found at i:29590857 original size:30 final size:30
Alignment explanation
Indices: 29590821--29590881 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
29590811 AAGCTGAGCC
29590821 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
29590851 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
29590881 T
1 T
29590882 GAGTTAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:29604357 original size:19 final size:20
Alignment explanation
Indices: 29604327--29604364 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
29604317 TTTAAGAGCC
29604327 ACACGTCCATGTGGCTAGGG
1 ACACGTCCATGTGGCTAGGG
*
29604347 ACACG-CCATGTGGGTAGG
1 ACACGTCCATGTGGCTAGG
29604365 CCGTGTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.21, C:0.24, G:0.37, T:0.18
Consensus pattern (20 bp):
ACACGTCCATGTGGCTAGGG
Found at i:29605402 original size:42 final size:42
Alignment explanation
Indices: 29605351--29605471 Score: 116
Period size: 43 Copynumber: 2.9 Consensus size: 42
29605341 CATACAATAC
* * *
29605351 CATACCAATGCCATATCCCAAATATGGTCTCACATGGGATCT
1 CATATCAATGCCATATCCCAAATATGGTCTTACATGAGATCT
* * * * * *
29605393 CATATCAATGCCAATAGCCCAACTATGGTGTTAAACGAGTTCT
1 CATATCAATGCC-ATATCCCAAATATGGTCTTACATGAGATCT
** * *
29605436 CATATTGATGCAATATCCCAGATATGGTCTTACATG
1 CATATCAATGCCATATCCCAAATATGGTCTTACATG
29605472 TAATCTTAGT
Statistics
Matches: 60, Mismatches: 18, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
42 29 0.48
43 31 0.52
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (42 bp):
CATATCAATGCCATATCCCAAATATGGTCTTACATGAGATCT
Found at i:29622622 original size:23 final size:23
Alignment explanation
Indices: 29622593--29622652 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
29622583 TGTCCCCAAG
29622593 CACACGGGCGTGTGCATTGCCTC
1 CACACGGGCGTGTGCATTGCCTC
* *
29622616 CATACGGGCGTGTGCATTTCCTC
1 CACACGGGCGTGTGCATTGCCTC
*
29622639 CACACGGGCATGTG
1 CACACGGGCGTGTG
29622653 AGGCTTTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.15, C:0.32, G:0.30, T:0.23
Consensus pattern (23 bp):
CACACGGGCGTGTGCATTGCCTC
Found at i:29627625 original size:27 final size:27
Alignment explanation
Indices: 29627595--29627799 Score: 241
Period size: 27 Copynumber: 7.6 Consensus size: 27
29627585 ATATTGAGTC
* * * *
29627595 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* * *
29627622 CGCACACTTAGTGCTACGTAATCGAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29627649 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29627677 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
** **
29627704 CGCACACTTAGTGC-ATCATTTTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29627731 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29627758 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29627785 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29627800 GTACAATTTA
Statistics
Matches: 154, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
27 130 0.84
28 24 0.16
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29635849 original size:48 final size:48
Alignment explanation
Indices: 29635770--29635942 Score: 213
Period size: 48 Copynumber: 3.6 Consensus size: 48
29635760 TCTGTGGGCT
*
29635770 AGTGTAAGACCATGTCTGGGACATGGAATCGGCCTCAATATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATGTGAGCC
* * * * ** *** * *
29635818 ACTGTAAGACCATGTTTGGAACATGTCATCGGTATTGTTATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATGTGAGCC
*
29635866 AGTGTAAGACCATGTCTGGGACATGGCATCGACCTCAATATGT-AGGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATGTGA-GCC
29635914 AGTGTAAGACCATGTCTGGGACATGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCAT
29635943 TGACATTTTA
Statistics
Matches: 100, Mismatches: 24, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
47 1 0.01
48 99 0.99
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATGTGAGCC
Found at i:29641149 original size:64 final size:64
Alignment explanation
Indices: 29641045--29641252 Score: 190
Period size: 67 Copynumber: 3.2 Consensus size: 64
29641035 CATCATGTGT
*
29641045 ACAAGAGAGCTACAAGACATTATTATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TA-TATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
29641110 TAG
62 TAG
* * * * *
29641113 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTAC-AGGTGAAGGACACCATG
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGT-GATACTA--TG-TGTACACCATG
29641177 TAG
62 TAG
* * * * * *
29641180 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCAGCATGT-G
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAG
29641242 TACAAGAGAGC
1 -ACAAGAGAGC
29641253 CAAACTATAT
Statistics
Matches: 117, Mismatches: 16, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
62 1 0.01
63 18 0.15
64 23 0.20
65 10 0.09
66 19 0.16
67 33 0.28
68 13 0.11
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
Found at i:29644643 original size:27 final size:27
Alignment explanation
Indices: 29644613--29644669 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
29644603 TTCCCCAATT
29644613 CTATTTTCTGTGAATTCTTAGCTTAGG
1 CTATTTTCTGTGAATTCTTAGCTTAGG
29644640 CTATTTTCTGTGAATTCTTAGCTTAGG
1 CTATTTTCTGTGAATTCTTAGCTTAGG
29644667 CTA
1 CTA
29644670 GATAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (27 bp):
CTATTTTCTGTGAATTCTTAGCTTAGG
Found at i:29649131 original size:82 final size:81
Alignment explanation
Indices: 29649015--29649170 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
29649005 AAATTGTACA
* * * *
29649015 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
29649079 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29649096 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
29649161 TGCGAGTTGA
65 TGCGAATTGA
29649171 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29649138 original size:55 final size:52
Alignment explanation
Indices: 29649014--29649167 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
29649004 TAAATTGTAC
* *
29649014 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
29649067 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
29649122 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
29649168 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:29649172 original size:27 final size:27
Alignment explanation
Indices: 29649015--29649170 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
29649005 AAATTGTACA
*
29649015 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
29649042 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
29649069 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
29649096 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
29649124 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
29649151 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
29649171 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:29649181 original size:27 final size:27
Alignment explanation
Indices: 29649007--29649191 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
29648997 GCGGGATTAA
*
29649007 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
29649034 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
29649061 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
29649088 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
29649116 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
29649143 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
29649170 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
29649192 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:29649182 original size:82 final size:81
Alignment explanation
Indices: 29649007--29649191 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
29648997 GCGGGATTAA
* * * *
29649007 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
29649072 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
29649088 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
29649152 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
29649170 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
29649192 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:29655552 original size:17 final size:17
Alignment explanation
Indices: 29655530--29655566 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
29655520 TAGGAAAGAT
29655530 GATAGATGAATTATAAG
1 GATAGATGAATTATAAG
29655547 GATAGATGAATTATAAG
1 GATAGATGAATTATAAG
29655564 GAT
1 GAT
29655567 TAATTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (17 bp):
GATAGATGAATTATAAG
Found at i:29657188 original size:82 final size:81
Alignment explanation
Indices: 29657072--29657227 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
29657062 AAATTGTACA
* * * *
29657072 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
29657136 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29657153 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
29657218 TGCGAGTTGA
65 TGCGAATTGA
29657228 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29657195 original size:55 final size:52
Alignment explanation
Indices: 29657071--29657224 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
29657061 TAAATTGTAC
* *
29657071 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
29657124 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
29657179 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
29657225 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:29657229 original size:27 final size:27
Alignment explanation
Indices: 29657072--29657227 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
29657062 AAATTGTACA
*
29657072 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
29657099 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
29657126 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
29657153 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
29657181 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
29657208 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
29657228 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:29657238 original size:27 final size:27
Alignment explanation
Indices: 29657064--29657248 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
29657054 GCGGGATTAA
*
29657064 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
29657091 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
29657118 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
29657145 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
29657173 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
29657200 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
29657227 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
29657249 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:29657239 original size:82 final size:81
Alignment explanation
Indices: 29657064--29657248 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
29657054 GCGGGATTAA
* * * *
29657064 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
29657129 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
29657145 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
29657209 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
29657227 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
29657249 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:29658651 original size:46 final size:46
Alignment explanation
Indices: 29658598--29658770 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
29658588 GGGTGTTACA
29658598 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
*** *
29658644 GAACTCGTTGAGTTGAGTCCGAGTTC-GGGA--GATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCC
* * *
29658691 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
*
29658737 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29658771 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 2 0.02
46 62 0.58
47 28 0.26
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
Found at i:29662133 original size:56 final size:56
Alignment explanation
Indices: 29662066--29662177 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
29662056 CACACGGGAA
29662066 AAAATTAGGGAACACGGGCGTGTCCCCTGGCCGTGTGTCCCAAAATCTATAAATAC
1 AAAATTAGGGAACACGGGCGTGTCCCCTGGCCGTGTGTCCCAAAATCTATAAATAC
29662122 AAAATTAGGGAACACGGGCGTGTCCCCTGGCCGTGTGTCCCAAAATCTATAAATAC
1 AAAATTAGGGAACACGGGCGTGTCCCCTGGCCGTGTGTCCCAAAATCTATAAATAC
29662178 CCTTCACCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (56 bp):
AAAATTAGGGAACACGGGCGTGTCCCCTGGCCGTGTGTCCCAAAATCTATAAATAC
Found at i:29677179 original size:48 final size:48
Alignment explanation
Indices: 29677116--29677279 Score: 177
Period size: 48 Copynumber: 3.4 Consensus size: 48
29677106 TAAGGTTATT
* * *
29677116 TGTGGGCTAGTGTAAGACCATGTTCGGGACATGGCATCAACCTCAATA
1 TGTGAGCTAGTGTAAGACCATGTTCGGGACATGACATCAGCCTCAATA
* * * * ***
29677164 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGACATCAGCATTGTTA
1 TGTGAGCTAGTGTAAGACCATGTTCGGGACATGACATCAGCCTCAATA
* * ** *
29677212 TGAGAGCTAGTGTAAGACCATG-TCTGGGACACGACATTGGTCTCAATA
1 TGTGAGCTAGTGTAAGACCATGTTC-GGGACATGACATCAGCCTCAATA
29677260 TGTGAGCTAGTGTAAGACCA
1 TGTGAGCTAGTGTAAGACCA
29677280 AGTATCAACA
Statistics
Matches: 92, Mismatches: 23, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
47 1 0.01
48 91 0.99
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (48 bp):
TGTGAGCTAGTGTAAGACCATGTTCGGGACATGACATCAGCCTCAATA
Found at i:29677374 original size:84 final size:84
Alignment explanation
Indices: 29677199--29677362 Score: 213
Period size: 84 Copynumber: 2.0 Consensus size: 84
29677189 GGAACATGAC
* * * * ** * *
29677199 ATCAGCATTGTTATGAGAGCTAGTGTAAGACCATGTCTGGGACACGACATTGGTCTCAATATGTG
1 ATCAACATTGTTATGAGAGCTAATATAAGACCATGTCCGGGACACGACATCAGCCTCAATATGTA
*
29677264 AGCTAGTGTAAGACCAAGT
66 AGCCAGTGTAAGACCAAGT
** *
29677283 ATCAACATTGTTATGAGAGCTAATATAAGACTGTGTCCGGGACATGACATCAGCCTCAATATGTA
1 ATCAACATTGTTATGAGAGCTAATATAAGACCATGTCCGGGACACGACATCAGCCTCAATATGTA
29677348 AGCCAGTG-AAGACCA
66 AGCCAGTGTAAGACCA
29677363 TGTCTGGAAC
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
83 7 0.10
84 61 0.90
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (84 bp):
ATCAACATTGTTATGAGAGCTAATATAAGACCATGTCCGGGACACGACATCAGCCTCAATATGTA
AGCCAGTGTAAGACCAAGT
Found at i:29680318 original size:2 final size:2
Alignment explanation
Indices: 29680311--29680353 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
29680301 ACCTTTTTAG
* * *
29680311 TA TA TA TA TA AA TA TA TA TT TA TG TA TA TA TA TA GTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
29680354 CTTTTATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29682055 original size:43 final size:42
Alignment explanation
Indices: 29681966--29682066 Score: 100
Period size: 43 Copynumber: 2.4 Consensus size: 42
29681956 TAATACCATG
* * *
29681966 TCTGGGACATTGGCATCATATATGATTTTCTATAAGACCCTG
1 TCTGGGACAGTGGCATCATATATGATTTACTATAAGACCCTA
* *
29682008 TCTGGGACAGTGGCATCGATATTTGA-TTACATGTAAGACCAC-A
1 TCTGGGACAGTGGCATC-ATATATGATTTAC-TATAAGACC-CTA
29682051 TCTGGGA-AGTTGGCAT
1 TCTGGGACAG-TGGCAT
29682067 TCTATGAGCT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
42 21 0.42
43 28 0.56
44 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (42 bp):
TCTGGGACAGTGGCATCATATATGATTTACTATAAGACCCTA
Found at i:29692767 original size:25 final size:25
Alignment explanation
Indices: 29692739--29692786 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29692729 TTATATTATG
* * *
29692739 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACCGTTATACCCCTAGGTA
29692764 AAAATGACCGTTATACCCCTAGG
1 AAAATGACCGTTATACCCCTAGG
29692787 GTTTACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (25 bp):
AAAATGACCGTTATACCCCTAGGTA
Found at i:29692847 original size:20 final size:20
Alignment explanation
Indices: 29692822--29692868 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
29692812 ATTTTGATAT
29692822 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
29692842 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
29692862 ACATGAT
1 ACATGAT
29692869 GTATTTTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:29692994 original size:51 final size:51
Alignment explanation
Indices: 29692903--29692999 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
29692893 GAGGAAGTGC
**
29692903 AAAAGGGCTATGCCCCAATTTATTGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTATGCCCCAATTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
29692954 AAAAGGGCTTATG-CCCAAGTTTACCGAAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGC-TATGCCCCAA-TTTACCGAAAAGGGCTTATGCCCCAGTT
29693000 ACTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
51 23 0.55
52 19 0.45
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (51 bp):
AAAAGGGCTATGCCCCAATTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:29692999 original size:25 final size:26
Alignment explanation
Indices: 29692903--29692999 Score: 144
Period size: 26 Copynumber: 3.8 Consensus size: 26
29692893 GAGGAAGTGC
*
29692903 AAAAGGGC-TATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
29692928 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
29692954 AAAAGGGCTTATGCCCAAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
29692980 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
29693000 ACTAAAAGAG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
25 17 0.26
26 49 0.74
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:29698430 original size:15 final size:15
Alignment explanation
Indices: 29698406--29698435 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29698396 CTAATGTATT
29698406 TTTTGAGGTTTCGGC
1 TTTTGAGGTTTCGGC
*
29698421 TTTTGTGGTTTCGGC
1 TTTTGAGGTTTCGGC
29698436 ACAAGTGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.33, T:0.50
Consensus pattern (15 bp):
TTTTGAGGTTTCGGC
Found at i:29703602 original size:40 final size:40
Alignment explanation
Indices: 29703518--29703740 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
29703508 TTGAATGATG
* * * *
29703518 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
** *
29703558 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
29703598 TCCGGG-TAAG--CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
*
29703635 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
*
29703675 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTA-AA
* *
29703716 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
29703741 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 14
0.87 0.05 0.07
Matches are distributed among these distances:
37 32 0.19
38 4 0.02
39 4 0.02
40 113 0.68
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:29703758 original size:80 final size:78
Alignment explanation
Indices: 29703518--29703773 Score: 247
Period size: 80 Copynumber: 3.3 Consensus size: 78
29703508 TTGAATGATG
* * * * * *
29703518 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
29703581 TTGTGCGAGATACTAA
64 TTGTGCGAG-GACTAA
* *
29703597 TTCCGGG-TAAG--CCGAAGGCATTTGTGCGAGATACTA-AATCCGGGTTAAGTCCCGAAGGCAT
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCAT
*
29703658 TTGTGCGAGTTACTAAA
64 TTGTGCGAG-GACT-AA
*
29703675 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
**
29703740 GAACGAGGAGCTATA
66 GTGCGAGGA-CTA-A
* *
29703755 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
29703774 TACGTGATTT
Statistics
Matches: 150, Mismatches: 16, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
76 2 0.01
77 50 0.33
78 13 0.09
79 20 0.13
80 63 0.42
81 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGGACTAA
Found at i:29711515 original size:40 final size:40
Alignment explanation
Indices: 29711455--29711627 Score: 249
Period size: 40 Copynumber: 4.3 Consensus size: 40
29711445 GGACTAAGAT
* * *
29711455 CCGAAGGCCTTTGTGTGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* *
29711495 CCAAAGGCATTTGTGCGAGATACTAAATCTGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
*
29711535 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * *
29711575 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTA-AATCCGGGTTAAGTC
29711615 CCGAAGGCATTTG
1 CCGAAGGCATTTG
29711628 AATGAGGAGC
Statistics
Matches: 122, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
40 120 0.98
41 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:29711645 original size:80 final size:80
Alignment explanation
Indices: 29711476--29711660 Score: 214
Period size: 80 Copynumber: 2.3 Consensus size: 80
29711466 TGTGTGAGAT
* * * *
29711476 ACTAATTCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGATACTAAATCTGGGTTAAGTCCCGAAG
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAG
** *
29711541 GCATTTGTGCGAGTT
66 GCATTTGAACGAGTG
* *
29711556 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAA
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTA-AATCCGGGCTAAGTCCCGAA
*
29711620 GGCATTTGAATGAG-G
65 GGCATTTGAACGAGTG
* * *
29711635 AGCTATATCC-GGTTAAATTCCGAAGG
1 A-CTAAATCCGGGTTAAGTCCCGAAGG
29711661 TACGTGATTT
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
79 15 0.17
80 73 0.81
81 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (80 bp):
ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAG
GCATTTGAACGAGTG
Found at i:29714277 original size:26 final size:26
Alignment explanation
Indices: 29714248--29714355 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
29714238 TGGAACAAAT
29714248 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
29714274 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29714300 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29714326 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29714352 TGAT
1 TGAT
29714356 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29715990 original size:27 final size:26
Alignment explanation
Indices: 29715950--29716090 Score: 151
Period size: 27 Copynumber: 5.2 Consensus size: 26
29715940 AGGAAGCGTC
*
29715950 CTGGTGGCTATGCCATAATTATCTGAT
1 CTGGTGGCTCTGCCA-AATTATCTGAT
*
29715977 CTGGTGGCTCTGCCACATATATCTG-T
1 CTGGTGGCTCTGCCAAAT-TATCTGAT
*
29716003 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCA-AATTATCTGAT
* * *
29716031 CTGATGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCAAAT-TATCTGAT
29716058 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCA-AATTATCTG-AT
29716085 CTGGTG
1 CTGGTG
29716091 ACTCCATCAC
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
26 11 0.11
27 81 0.84
28 4 0.04
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCAAATTATCTGAT
Found at i:29716029 original size:54 final size:54
Alignment explanation
Indices: 29715947--29716090 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
29715937 TGGAGGAAGC
*
29715947 GTCCTGGTGGCTATGCCATAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
*
29716001 GTCCTGGTGGCTATGCCACAATTATCTGATCTGATGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
* *
29716055 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
29716091 ACTCCATCAC
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
53 6 0.07
54 78 0.93
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:29716101 original size:27 final size:26
Alignment explanation
Indices: 29715969--29716108 Score: 82
Period size: 27 Copynumber: 5.2 Consensus size: 26
29715959 ATGCCATAAT
* * **
29715969 TATCTGATCTGGTGGCTCTGCCACATA
1 TATCTGTTCTGGTGACTCCACCACA-A
* * ***
29715996 TATCTGTCCTGGTGGCTATGCCACAA
1 TATCTGTTCTGGTGACTCCACCACAA
* * * **
29716022 TTATCTGATCTGATGGCTCTGCCACATA
1 -TATCTGTTCTGGTGACTCCACCACA-A
* **
29716050 TATCTGTTCTGGTGGCTCTGCCACAA
1 TATCTGTTCTGGTGACTCCACCACAA
*
29716076 TATCTGTATCTGGTGACTCCATCACAA
1 TATCTGT-TCTGGTGACTCCACCACAA
29716103 TATCTG
1 TATCTG
29716109 GTAGCCCCAC
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
26 9 0.09
27 87 0.90
28 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (26 bp):
TATCTGTTCTGGTGACTCCACCACAA
Found at i:29720500 original size:46 final size:46
Alignment explanation
Indices: 29720392--29720731 Score: 288
Period size: 46 Copynumber: 7.6 Consensus size: 46
29720382 AAGCTGACGC
* * * ** *
29720392 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCTTGA-GGTCGATG
1 CATGTCCCAGACATGTCTTACACTAGC-TCTA-GTCTCAATGCT-GATG
* *
29720440 CATGTCCCAGACATGTCTTGCACTAGCTCTAGTCTCAATGCTGGTG
1 CATGTCCCAGACATGTCTTACACTAGCTCTAGTCTCAATGCTGATG
29720486 CATGTCCCAGACATGTCTT--AC-A---CTAG-CTC--T-C-GATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTAGTCTCAATGCTGATG
*
29720521 CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTAGTCTCAATGCTGATG
* * *
29720567 CATGTCCCAAACATGTCTTACACTGGCTC---TCAT-AATGTGGTCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTAGTC-TCAA--TGCT-GATG
*
29720613 CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTAGTCTCAATGCTGATG
* * *
29720659 CATGTCCCAAACATGTCTTACACTGGCTC---TCAT-AATGTGGTCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTAGTC-TCAA--TGCT-GATG
*
29720705 CATGTCCCAGACATGTCTTACAGTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
29720732 ACACATATGT
Statistics
Matches: 246, Mismatches: 22, Indels: 50
0.77 0.07 0.16
Matches are distributed among these distances:
35 22 0.09
36 1 0.00
37 3 0.01
38 1 0.00
39 3 0.01
40 4 0.02
41 3 0.01
42 3 0.01
43 9 0.04
44 5 0.02
45 7 0.03
46 147 0.60
47 8 0.03
48 26 0.11
49 4 0.02
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTAGTCTCAATGCTGATG
Found at i:29720523 original size:35 final size:35
Alignment explanation
Indices: 29720484--29720552 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
29720474 TCAATGCTGG
29720484 TGCATGTCCCAGACATGTCTTACACTAGCTCTCGA
1 TGCATGTCCCAGACATGTCTTACACTAGCTCTCGA
29720519 TGCATGTCCCAGACATGTCTTACACTAGCTCTCG
1 TGCATGTCCCAGACATGTCTTACACTAGCTCTCG
29720553 TCTCAATGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.22, C:0.32, G:0.17, T:0.29
Consensus pattern (35 bp):
TGCATGTCCCAGACATGTCTTACACTAGCTCTCGA
Found at i:29720569 original size:81 final size:81
Alignment explanation
Indices: 29720434--29720689 Score: 359
Period size: 81 Copynumber: 3.0 Consensus size: 81
29720424 TATCTTGAGG
* * * *
29720434 TCGATGCATGTCCCAGACATGTCTTGCACTAGCTCTAGTCTCAATGCTGGTGCATGTCCCAGACA
1 TCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGCATGTCCCAAACA
*
29720499 TGTCTTACACTAGCTC
66 TGTCTTACACTGGCTC
29720515 TCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGCATGTCCCAAACA
1 TCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGCATGTCCCAAACA
29720580 TGTCTTACACTGGCTC
66 TGTCTTACACTGGCTC
*
29720596 TCATAATGTGGTCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGCA
1 TC--GA--T-G-C-ATG--T--CCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGCA
29720661 TGTCCCAAACATGTCTTACACTGGCTC
55 TGTCCCAAACATGTCTTACACTGGCTC
29720688 TC
1 TC
29720690 ATAATGTGGT
Statistics
Matches: 158, Mismatches: 6, Indels: 11
0.90 0.03 0.06
Matches are distributed among these distances:
81 78 0.49
83 1 0.01
85 1 0.01
86 1 0.01
87 1 0.01
88 3 0.02
90 1 0.01
92 72 0.46
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (81 bp):
TCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGCATGTCCCAAACA
TGTCTTACACTGGCTC
Found at i:29720643 original size:92 final size:92
Alignment explanation
Indices: 29720515--29720731 Score: 425
Period size: 92 Copynumber: 2.4 Consensus size: 92
29720505 ACACTAGCTC
29720515 TCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGCATGTCCCAAACA
1 TCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGCATGTCCCAAACA
29720580 TGTCTTACACTGGCTCTCATAATGTGG
66 TGTCTTACACTGGCTCTCATAATGTGG
29720607 TCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGCATGTCCCAAACA
1 TCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGCATGTCCCAAACA
29720672 TGTCTTACACTGGCTCTCATAATGTGG
66 TGTCTTACACTGGCTCTCATAATGTGG
*
29720699 TCGATGCATGTCCCAGACATGTCTTACAGTAGC
1 TCGATGCATGTCCCAGACATGTCTTACACTAGC
29720732 ACACATATGT
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 124 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (92 bp):
TCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGCATGTCCCAAACA
TGTCTTACACTGGCTCTCATAATGTGG
Found at i:29725392 original size:25 final size:25
Alignment explanation
Indices: 29725324--29725385 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
29725314 ACGAGCTGTA
*
29725324 AACGATAAGCTCCTTCGAGATGAAT
1 AACGGTAAGCTCCTTCGAGATGAAT
*
29725349 AACGGTAAGCTCCTTCGAGTTGAAT
1 AACGGTAAGCTCCTTCGAGATGAAT
29725374 AACGGTAAGCTC
1 AACGGTAAGCTC
29725386 ATACGAGCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (25 bp):
AACGGTAAGCTCCTTCGAGATGAAT
Found at i:29729552 original size:25 final size:25
Alignment explanation
Indices: 29729524--29729589 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
29729514 CCATTTTAAC
29729524 AGCTTGTGTGAGCATAACGATTCAT
1 AGCTTGTGTGAGCATAACGATTCAT
* *
29729549 AGCTTATGTGAGCATATCGATTCAT
1 AGCTTGTGTGAGCATAACGATTCAT
* *
29729574 AGCTTGTCTAAGCATA
1 AGCTTGTGTGAGCATA
29729590 CCATTTCACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (25 bp):
AGCTTGTGTGAGCATAACGATTCAT
Found at i:29729612 original size:25 final size:24
Alignment explanation
Indices: 29729522--29729615 Score: 80
Period size: 25 Copynumber: 3.8 Consensus size: 24
29729512 GCCCATTTTA
* *
29729522 ACAGCTTGTGTGAGCATAACGATTC
1 ACAGCTTATGTGAGCAT-ACCATTC
* *
29729547 ATAGCTTATGTGAGCATATCGATTC
1 ACAGCTTATGTGAGCATA-CCATTC
* * * *
29729572 ATAGCTTGTCTAAGCATACCATTTC
1 ACAGCTTATGTGAGCATACCA-TTC
*
29729597 ACAGCTCATGTGAGCATAC
1 ACAGCTTATGTGAGCATAC
29729616 ATGTACAAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
24 3 0.05
25 53 0.95
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (24 bp):
ACAGCTTATGTGAGCATACCATTC
Found at i:29732892 original size:30 final size:30
Alignment explanation
Indices: 29732846--29732905 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29732836 TTCCCGAGCC
* *
29732846 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAAATGTAATTATGCAAAAGTT
* *
29732876 TAGGGGAAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGAAAAAATGTAATTATGCAAAAGTT
29732906 CGTATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGAAAAAATGTAATTATGCAAAAGTT
Found at i:29741116 original size:42 final size:42
Alignment explanation
Indices: 29741069--29741181 Score: 156
Period size: 43 Copynumber: 2.7 Consensus size: 42
29741059 TACCATACCA
* *
29741069 ATGCCATATCCTAGATATGGTCTTACA-TAGGATCTCATATCG
1 ATGCCATATCCTAGATATGGTCTTACACAAAG-TCTCATATCG
* * *
29741111 ATGCCAATAGCCCAGCTATGGTCTTACACAAAGTCTCATATCG
1 ATGCC-ATATCCTAGATATGGTCTTACACAAAGTCTCATATCG
29741154 ATGCCATATCCTAGATATGGTCTTACAC
1 ATGCCATATCCTAGATATGGTCTTACAC
29741182 GTAATCTTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 25 0.41
43 34 0.56
44 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCTAGATATGGTCTTACACAAAGTCTCATATCG
Found at i:29746139 original size:27 final size:27
Alignment explanation
Indices: 29746109--29746170 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
29746099 ATTTACTAAA
*
29746109 ATACCCCTAAGTATG-ATAATTACCACT
1 ATACCCCTAAG-ATGCAAAATTACCACT
* *
29746136 ATACCCCT-AGGTGCAAAATTACCATT
1 ATACCCCTAAGATGCAAAATTACCACT
29746162 ATACCCCTA
1 ATACCCCTA
29746171 GGGTTAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.07
26 20 0.67
27 8 0.27
ACGTcount: A:0.35, C:0.29, G:0.08, T:0.27
Consensus pattern (27 bp):
ATACCCCTAAGATGCAAAATTACCACT
Found at i:29746318 original size:28 final size:28
Alignment explanation
Indices: 29746275--29746390 Score: 157
Period size: 28 Copynumber: 4.2 Consensus size: 28
29746265 GGAGGAAGCG
*
29746275 TTCTGGTGGCTATGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
*
29746303 TTCTGGTGGCTCTGCCACAAATATCTGA
1 TTCTGGTGGCTCTGCCACAAATATCTGT
*
29746331 TTCTGGTGGCACTGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* * *
29746359 ATCTGGTGACTCTGTCAC-AATA-CTG-
1 TTCTGGTGGCTCTGCCACAAATATCTGT
29746384 TTCTGGT
1 TTCTGGT
29746391 AGCCATGCTG
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
25 6 0.08
26 3 0.04
27 4 0.05
28 66 0.84
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAAATATCTGT
Found at i:29755613 original size:13 final size:13
Alignment explanation
Indices: 29755595--29755619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29755585 AAATTGGATG
29755595 TTATTATTATTTA
1 TTATTATTATTTA
29755608 TTATTATTATTT
1 TTATTATTATTT
29755620 TGTATGTCTA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:29757305 original size:8 final size:8
Alignment explanation
Indices: 29757292--29757329 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
29757282 CTAGATCGGC
29757292 AAAAGCCG
1 AAAAGCCG
29757300 AAAAGCCG
1 AAAAGCCG
* *
29757308 AAATGCTG
1 AAAAGCCG
29757316 AAAAGCCG
1 AAAAGCCG
29757324 AAAAGC
1 AAAAGC
29757330 TGACATCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.50, C:0.21, G:0.24, T:0.05
Consensus pattern (8 bp):
AAAAGCCG
Found at i:29757320 original size:16 final size:16
Alignment explanation
Indices: 29757292--29757332 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
29757282 CTAGATCGGC
*
29757292 AAAAGCCGAAAAGCCG
1 AAAAGCTGAAAAGCCG
*
29757308 AAATGCTGAAAAGCCG
1 AAAAGCTGAAAAGCCG
29757324 AAAAGCTGA
1 AAAAGCTGA
29757333 CATCTTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.20, G:0.24, T:0.07
Consensus pattern (16 bp):
AAAAGCTGAAAAGCCG
Found at i:29762575 original size:13 final size:13
Alignment explanation
Indices: 29762557--29762581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29762547 AAATTGGATG
29762557 TTATTATTATTTT
1 TTATTATTATTTT
29762570 TTATTATTATTT
1 TTATTATTATTT
29762582 CGTATGTCTA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTATTATTTT
Found at i:29764574 original size:27 final size:27
Alignment explanation
Indices: 29764544--29764605 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
29764534 ATTTACTAAA
29764544 ATACCCCTAAGTATG-AAAATTACCACT
1 ATACCCCTAAG-ATGCAAAATTACCACT
* *
29764571 ATACCCCT-AGGTGCAAAATTACCATT
1 ATACCCCTAAGATGCAAAATTACCACT
29764597 ATACCCCTA
1 ATACCCCTA
29764606 GGGTTAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 21 0.68
27 8 0.26
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (27 bp):
ATACCCCTAAGATGCAAAATTACCACT
Found at i:29764712 original size:28 final size:28
Alignment explanation
Indices: 29764678--29764762 Score: 113
Period size: 28 Copynumber: 3.1 Consensus size: 28
29764668 TGCTATGATA
29764678 TGGTGGCTCTGCCACAAATATCTGATTC
1 TGGTGGCTCTGCCACAAATATCTGATTC
*
29764706 TGGTGGCACTGCCACAAATATCTGTATT-
1 TGGTGGCTCTGCCACAAATATCTG-ATTC
* *
29764734 TGGTGACTCTGTCAC-AATATCTG-TTC
1 TGGTGGCTCTGCCACAAATATCTGATTC
29764760 TGG
1 TGG
29764763 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.06
27 8 0.16
28 35 0.69
29 3 0.06
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (28 bp):
TGGTGGCTCTGCCACAAATATCTGATTC
Found at i:29770788 original size:13 final size:13
Alignment explanation
Indices: 29770770--29770795 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29770760 AAATTGGATG
29770770 TTATTATTATTTT
1 TTATTATTATTTT
29770783 TTATTATTATTTT
1 TTATTATTATTTT
29770796 GTATGTCTAG
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTATTATTTT
Found at i:29772665 original size:26 final size:27
Alignment explanation
Indices: 29772636--29772696 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
29772626 ATTTACTAAA
29772636 ATACCCCTAAGTATG-AAAA-TACCATT
1 ATACCCCTAAG-ATGCAAAATTACCATT
*
29772662 ATACCCCT-AGGTGCAAAATTACCATT
1 ATACCCCTAAGATGCAAAATTACCATT
29772688 ATACCCCTA
1 ATACCCCTA
29772697 GGGTTAGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 2 0.06
25 6 0.19
26 23 0.74
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (27 bp):
ATACCCCTAAGATGCAAAATTACCATT
Found at i:29772859 original size:28 final size:28
Alignment explanation
Indices: 29772803--29772860 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
29772793 AGAAGCGTTC
**
29772803 TGGTGGCTATGCCACAAATATCTGTTTT
1 TGGTGGCTATGCCACAAATATCTAATTT
*
29772831 TGGTGGCTCTGCCACAAATATCTAATTT
1 TGGTGGCTATGCCACAAATATCTAATTT
29772859 TG
1 TG
29772861 TGCCACAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (28 bp):
TGGTGGCTATGCCACAAATATCTAATTT
Found at i:29778597 original size:42 final size:43
Alignment explanation
Indices: 29778528--29778646 Score: 143
Period size: 44 Copynumber: 2.8 Consensus size: 43
29778518 CCAAATATCT
* * *
29778528 ATGCCACTATCCCAGACAGGGTCTTACACGAAATCA-AA-TACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCATAAGT-CG
** *
29778570 ATGCTGATGTCTCAGACATGGTCTTACACGTAAATCATAAGTCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AAATCATAAGTCG
*
29778614 ATGCCAATGTCCCAGACATGGTCTTGCACGAAA
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAA
29778647 ACACATATCG
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 24 0.38
43 9 0.14
44 30 0.47
45 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCATAAGTCG
Found at i:29778630 original size:44 final size:42
Alignment explanation
Indices: 29778485--29778643 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 42
29778475 AGCCCATACA
* * * * * *
29778485 ATGCCAACGTCCCAAACGTGGTCTTACATGT-AACCAAATATCT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATC-AA-ATCG
* * *
29778528 ATGCCACTATCCCAGACAGGGTCTTACACG-AAATCAAATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCAAAT-CG
** *
29778570 ATGCTGATGTCTCAGACATGGTCTTACACGTAAATCATAAGTCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCA-AA-TCG
*
29778614 ATGCCAATGTCCCAGACATGGTCTTGCACG
1 ATGCCAATGTCCCAGACATGGTCTTACACG
29778644 AAAACACATA
Statistics
Matches: 92, Mismatches: 19, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
41 2 0.02
42 27 0.29
43 32 0.35
44 30 0.33
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCAAATCG
Found at i:29783470 original size:33 final size:33
Alignment explanation
Indices: 29783428--29783494 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
29783418 TACCCATGAT
*
29783428 AGCTGAATTATTATAATGCCCCTAGTAGCCCAC
1 AGCTGAATTACTATAATGCCCCTAGTAGCCCAC
29783461 AGCTGAATTACTATAATGCCCCTAGTAGCCCAC
1 AGCTGAATTACTATAATGCCCCTAGTAGCCCAC
29783494 A
1 A
29783495 TTTATTAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (33 bp):
AGCTGAATTACTATAATGCCCCTAGTAGCCCAC
Found at i:29793092 original size:20 final size:20
Alignment explanation
Indices: 29793067--29793111 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
29793057 AAGGACTAAA
* *
29793067 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
29793087 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
29793107 ATGAA
1 ATGAA
29793112 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:29793761 original size:57 final size:57
Alignment explanation
Indices: 29793621--29793768 Score: 149
Period size: 57 Copynumber: 2.6 Consensus size: 57
29793611 ATTGATCTTG
* * *
29793621 TTATAGAAAGGATTTAGCCTGGACGGGTAATCCCGATAAAATACCTCTTGAGCATACA
1 TTATATAAAGGATTTAGCCTGGACTGGTAAT-CCGATAAAATACCTCTTAAGCATACA
* * * * ** *
29793679 TTATCAT-TAGGGTTTAGCCTTGACTGGTAATCTGAATCAAGCT-CCTC-TAAGCTTACA
1 TTAT-ATAAAGGATTTAGCCTGGACTGGTAATCCG-AT-AAAATACCTCTTAAGCATACA
29793736 TTATATAAAGGATTTAGCCTGGACTGGTAATCC
1 TTATATAAAGGATTTAGCCTGGACTGGTAATCC
29793769 TGTTATATGA
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
56 2 0.03
57 36 0.50
58 30 0.42
59 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (57 bp):
TTATATAAAGGATTTAGCCTGGACTGGTAATCCGATAAAATACCTCTTAAGCATACA
Found at i:29806549 original size:41 final size:42
Alignment explanation
Indices: 29806440--29806560 Score: 140
Period size: 43 Copynumber: 2.9 Consensus size: 42
29806430 TACCATACTA
* *
29806440 ATGCCATATCCCAGATATGGTCTTACATG-GGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAG-TCTCATATCG
* *
29806482 ATGCCAATAGCCCAGCTATGGTCTTACACGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
* *
29806525 AT-TCATATCCCAGATATGATCTTACACGTAA-TCTCA
1 ATGCCATATCCCAGATATGGTCTTACACG-AAGTCTCA
29806561 ACTAACCCTA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
41 26 0.38
42 8 0.12
43 33 0.49
44 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
Found at i:29809993 original size:70 final size:70
Alignment explanation
Indices: 29809861--29809993 Score: 194
Period size: 70 Copynumber: 1.9 Consensus size: 70
29809851 ACGAATATAG
* * * * *
29809861 TGATTGGTAGTAATTCCACATATGTTGTGGACTATCGTAGCTCTGTGTGAGCATCGAGGTATAAG
1 TGATTGGTAGTAATTCCACATATGTTATGGACTACCGTAGCTCTATGTGAGCATCAAAGTATAAG
29809926 CTTAA
66 CTTAA
** *
29809931 TGATTGGTAGTAATTCTGCATATGTTATGGATTACCGTAGCTCTATGTGAGCATCAAAGTATA
1 TGATTGGTAGTAATTCCACATATGTTATGGACTACCGTAGCTCTATGTGAGCATCAAAGTATA
29809994 TGATTTTCCC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 55 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (70 bp):
TGATTGGTAGTAATTCCACATATGTTATGGACTACCGTAGCTCTATGTGAGCATCAAAGTATAAG
CTTAA
Found at i:29816254 original size:91 final size:93
Alignment explanation
Indices: 29816139--29816306 Score: 225
Period size: 91 Copynumber: 1.8 Consensus size: 93
29816129 ATATCAAGCT
* *
29816139 GATGCCATGTCCCAGACATGGTCTTACGCTAGCTTGCACAACG-CGACTGATGCATGTCCCAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTTGCACAACGTCGACT-ATACATGTCCCAGAC
*
29816203 ATCTCTTCCACTGCTCTTGTCTCAAAGTC
65 ATCTCTTACACTGCTCTTGTCTCAAAGTC
* * * * *
29816232 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTTTCACAATGTGGCCTATACATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTTGCACAACGTCGACTATACATGTCCCAGACA
*
29816295 TGTCTTACACTG
66 TCTCTTACACTG
29816307 GCACACATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
91 44 0.68
92 17 0.26
93 4 0.06
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (93 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTTGCACAACGTCGACTATACATGTCCCAGACA
TCTCTTACACTGCTCTTGTCTCAAAGTC
Found at i:30588941 original size:28 final size:28
Alignment explanation
Indices: 30588892--30588967 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
30588882 GATTCAAAAA
*
30588892 ATATATATTAAGTCCGCA-CACTCAGTGCT
1 ATATA-ATTAACT-CGCACCACTCAGTGCT
*
30588921 ATATAATTAACTCGCACCACTTAGTGCT
1 ATATAATTAACTCGCACCACTCAGTGCT
*
30588949 ATAATAATCAAACTCGCAC
1 AT-ATAAT-TAACTCGCAC
30588968 ACTTACTGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.10
28 18 0.44
29 10 0.24
30 9 0.22
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.29
Consensus pattern (28 bp):
ATATAATTAACTCGCACCACTCAGTGCT
Found at i:30588965 original size:30 final size:27
Alignment explanation
Indices: 30588906--30589005 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 27
30588896 ATATTAAGTC
* *
30588906 CGCACACTCAGTGCTATATAATTAACT
1 CGCACACTTAGTGCTATATAATAAACT
30588933 CGCACCACTTAGTGCTATAATAATCAAACT
1 CGCA-CACTTAGTGCTAT-ATAAT-AAACT
* * * *
30588963 CGCACACTTACTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA--TAAACT
30588992 CGCACACTTAGTGC
1 CGCACACTTAGTGC
30589006 CAATCTCATG
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
27 4 0.07
28 15 0.25
29 33 0.54
30 9 0.15
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATAAACT
Found at i:30596959 original size:27 final size:26
Alignment explanation
Indices: 30596929--30597003 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
30596919 GATTCAAAAA
*
30596929 TATATATTAAGTCCGCACACTCAGTGC
1 TATATATTAACT-CGCACACTCAGTGC
*
30596956 TATATAATTAACTCGCACACTTAGTGC
1 TATAT-ATTAACTCGCACACTCAGTGC
*
30596983 -ATATAATCAAACTCGCACACT
1 TATAT-AT-TAACTCGCACACT
30597004 TACTGCTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 7 0.16
27 30 0.70
28 6 0.14
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (26 bp):
TATATATTAACTCGCACACTCAGTGC
Found at i:30597004 original size:27 final size:27
Alignment explanation
Indices: 30596942--30597034 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 27
30596932 ATATTAAGTC
* *
30596942 CGCACACTCAGTGCTATATAATTAACT
1 CGCACACTTAGTGCTATATAATAAACT
30596969 CGCACACTTAGTGC-ATATAATCAAACT
1 CGCACACTTAGTGCTATATAAT-AAACT
* * * *
30596996 CGCACACTTACTGCTGTACACATTAAACC
1 CGCACACTTAGTGCTATATA-A-TAAACT
30597025 CGCACACTTA
1 CGCACACTTA
30597035 AGTTGCAATC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.12
27 30 0.54
28 3 0.05
29 15 0.27
30 1 0.02
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATAAACT
Found at i:30603902 original size:40 final size:40
Alignment explanation
Indices: 30603858--30603987 Score: 179
Period size: 40 Copynumber: 3.2 Consensus size: 40
30603848 ATAATTATTG
*
30603858 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTTCTTCGGTACCC
* * *
30603898 CTGAATGCACATATGTGCCCCTATTTGTTCTTCGATACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTTCTTCGGTACCC
* * * *
30603938 GTGGATGCACATACGTGCCCCTGTATGTTCTTCTGTACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTTCTTCGGTACCC
*
30603978 CTGGATGCAC
1 CTGAATGCAC
30603988 TAGCATGTGA
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.18, C:0.31, G:0.20, T:0.32
Consensus pattern (40 bp):
CTGAATGCACATACGTGCCCCTGTTTGTTCTTCGGTACCC
Found at i:30603918 original size:20 final size:20
Alignment explanation
Indices: 30603858--30603919 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
30603848 ATAATTATTG
30603858 CTGAATGCACATACGTGCCC
1 CTGAATGCACATACGTGCCC
** * * *
30603878 CTGTTTGTAC-TTCGGTACCC
1 CTGAATGCACATAC-GTGCCC
*
30603898 CTGAATGCACATATGTGCCC
1 CTGAATGCACATACGTGCCC
30603918 CT
1 CT
30603920 ATTTGTTCTT
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.29
Consensus pattern (20 bp):
CTGAATGCACATACGTGCCC
Found at i:30606147 original size:31 final size:31
Alignment explanation
Indices: 30606109--30606172 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
30606099 TAAGTAGATT
30606109 TCCCATATAAATACATCATTTAATTCATCAA
1 TCCCATATAAATACATCATTTAATTCATCAA
30606140 TCCCATATAAATACATCATTTAATTCATCAA
1 TCCCATATAAATACATCATTTAATTCATCAA
30606171 TC
1 TC
30606173 TTTTTATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (31 bp):
TCCCATATAAATACATCATTTAATTCATCAA
Found at i:30608380 original size:30 final size:30
Alignment explanation
Indices: 30608345--30608409 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
30608335 TCACACGGTC
*
30608345 GTGTGACACGCACGACCTGACGACACAACT
1 GTGTGACACACACGACCTGACGACACAACT
* **
30608375 GTGTGACACACACGGCCTGGTGACACAACT
1 GTGTGACACACACGACCTGACGACACAACT
30608405 GTGTG
1 GTGTG
30608410 TCATTTAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (30 bp):
GTGTGACACACACGACCTGACGACACAACT
Found at i:30615169 original size:4 final size:4
Alignment explanation
Indices: 30615152--30615182 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
30615142 TTTTTTTACT
30615152 TAAA TAATA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TA
30615183 TTGAAACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:30626522 original size:15 final size:15
Alignment explanation
Indices: 30626504--30626533 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30626494 AAGCAAATAA
30626504 AGAAATCCAAGATAG
1 AGAAATCCAAGATAG
*
30626519 AGAAATCCGAGATAG
1 AGAAATCCAAGATAG
30626534 GATACCATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.23, T:0.13
Consensus pattern (15 bp):
AGAAATCCAAGATAG
Found at i:30626985 original size:20 final size:20
Alignment explanation
Indices: 30626960--30626999 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
30626950 TTCACTGTGA
30626960 TTACCACATTCTTTCAATAT
1 TTACCACATTCTTTCAATAT
*
30626980 TTACCACATTCTTTTAATAT
1 TTACCACATTCTTTCAATAT
30627000 CGTATCTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (20 bp):
TTACCACATTCTTTCAATAT
Found at i:30636292 original size:25 final size:25
Alignment explanation
Indices: 30636263--30636504 Score: 198
Period size: 25 Copynumber: 9.7 Consensus size: 25
30636253 AAGATAATAC
* *
30636263 GATCGGCACAAATCCATCGATAACA
1 GATCGGCACAAAGCCATCAATAACA
* * *
30636288 GATCGACACATAGCCATCAATATCA
1 GATCGGCACAAAGCCATCAATAACA
* **
30636313 TATCGGCACAAAGCCATTGATAACA
1 GATCGGCACAAAGCCATCAATAACA
* * *
30636338 GATCGACACATAGCCATCAATATCA
1 GATCGGCACAAAGCCATCAATAACA
* * * *
30636363 TATCAGCACAAAGCCATCATTTACA
1 GATCGGCACAAAGCCATCAATAACA
*
30636388 GATCGGCACATAGCCATCAATAACA
1 GATCGGCACAAAGCCATCAATAACA
* * *
30636413 TATCGGCACAAAGCCATGAATAGCA
1 GATCGGCACAAAGCCATCAATAACA
* * * * *
30636438 TA-CTGGCACGAAGCCTTCAGTAGCA
1 GATC-GGCACAAAGCCATCAATAACA
* ** *
30636463 TATCGGCACAAAGCTTTCAATAGCA
1 GATCGGCACAAAGCCATCAATAACA
* *
30636488 TATCGGTACAAAGCCAT
1 GATCGGCACAAAGCCAT
30636505 AATTAGAATA
Statistics
Matches: 172, Mismatches: 43, Indels: 4
0.79 0.20 0.02
Matches are distributed among these distances:
24 1 0.01
25 170 0.99
26 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (25 bp):
GATCGGCACAAAGCCATCAATAACA
Found at i:30636339 original size:50 final size:50
Alignment explanation
Indices: 30636264--30636429 Score: 253
Period size: 50 Copynumber: 3.3 Consensus size: 50
30636254 AGATAATACG
* *
30636264 ATCGGCACAAATCCATCGATAACAGATCGACACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATTGATAACAGATCGACACATAGCCATCAATATCAT
30636314 ATCGGCACAAAGCCATTGATAACAGATCGACACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATTGATAACAGATCGACACATAGCCATCAATATCAT
* * * * *
30636364 ATCAGCACAAAGCCA-TCATTTACAGATCGGCACATAGCCATCAATAACAT
1 ATCGGCACAAAGCCATTGA-TAACAGATCGACACATAGCCATCAATATCAT
30636414 ATCGGCACAAAGCCAT
1 ATCGGCACAAAGCCAT
30636430 GAATAGCATA
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
49 2 0.02
50 104 0.98
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (50 bp):
ATCGGCACAAAGCCATTGATAACAGATCGACACATAGCCATCAATATCAT
Found at i:30636446 original size:50 final size:49
Alignment explanation
Indices: 30636264--30636476 Score: 227
Period size: 50 Copynumber: 4.3 Consensus size: 49
30636254 AGATAATACG
* *
30636264 ATCGGCACAAATCCATCG-ATAACAGATCGACACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCAT-GAAT-ACAGATCGGCACATAGCCATCAATATCAT
*
30636314 ATCGGCACAAAGCCATTG-ATAACAGATCGACACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCA-TGAAT-ACAGATCGGCACATAGCCATCAATATCAT
* * * *
30636364 ATCAGCACAAAGCCATCATTTACAGATCGGCACATAGCCATCAATAACAT
1 ATCGGCACAAAGCCATGA-ATACAGATCGGCACATAGCCATCAATATCAT
* * * *
30636414 ATCGGCACAAAGCCATGAATAGCATA-CTGGCACGA-AGCCTTCAGTAGCAT
1 ATCGGCACAAAGCCATGAATA-CAGATC-GGCAC-ATAGCCATCAATATCAT
30636464 ATCGGCACAAAGC
1 ATCGGCACAAAGC
30636477 TTTCAATAGC
Statistics
Matches: 144, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
49 4 0.03
50 137 0.95
51 3 0.02
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.19
Consensus pattern (49 bp):
ATCGGCACAAAGCCATGAATACAGATCGGCACATAGCCATCAATATCAT
Found at i:30636785 original size:26 final size:26
Alignment explanation
Indices: 30636756--30636813 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
30636746 AAAACGTCAT
30636756 TTTACCCTACAAGGGTATTTCAGTAA
1 TTTACCCTACAAGGGTATTTCAGTAA
*
30636782 TTTACCCTACAGGGGTATTTCAGTAA
1 TTTACCCTACAAGGGTATTTCAGTAA
30636808 TCTTAC
1 T-TTAC
30636814 AAACTTAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (26 bp):
TTTACCCTACAAGGGTATTTCAGTAA
Found at i:30645555 original size:119 final size:120
Alignment explanation
Indices: 30645377--30645601 Score: 314
Period size: 119 Copynumber: 1.9 Consensus size: 120
30645367 GCTACTCGTT
*
30645377 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
30645442 TTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
30645497 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCC
* * *
30645559 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
30645602 CATCATTCAA
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
118 4 0.04
119 67 0.72
120 22 0.24
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:30645601 original size:40 final size:40
Alignment explanation
Indices: 30645358--30645601 Score: 309
Period size: 40 Copynumber: 6.1 Consensus size: 40
30645348 CGGAATTTAA
** *
30645358 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
30645398 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
30645438 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
30645478 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
30645517 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
30645557 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
30645597 CCGGA
1 CCGGA
30645602 CATCATTCAA
Statistics
Matches: 181, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
38 2 0.01
39 33 0.18
40 134 0.74
41 12 0.07
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:30649603 original size:25 final size:25
Alignment explanation
Indices: 30649573--30649735 Score: 168
Period size: 25 Copynumber: 6.5 Consensus size: 25
30649563 CAATCTGCAT
*
30649573 AAAGCCATCGATAAT-AGATCGGCAC
1 AAAGCCATCAAT-ATCAGATCGGCAC
* * *
30649598 ATAGCCATCAATATCATATCGACAC
1 AAAGCCATCAATATCAGATCGGCAC
*
30649623 AAAGCCATCGATAAT-AGATCGGCAC
1 AAAGCCATCAAT-ATCAGATCGGCAC
* * *
30649648 ATAGCCATCAATATCATATCAGCAC
1 AAAGCCATCAATATCAGATCGGCAC
** *
30649673 AAAGCCATCGTTAACAGATCGGCAC
1 AAAGCCATCAATATCAGATCGGCAC
* *
30649698 ATAGCCATCAATATCATATCGGCAC
1 AAAGCCATCAATATCAGATCGGCAC
*
30649723 AAAGCCATGAATA
1 AAAGCCATCAATA
30649736 GCATACTGGC
Statistics
Matches: 110, Mismatches: 25, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
24 4 0.04
25 104 0.95
26 2 0.02
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.20
Consensus pattern (25 bp):
AAAGCCATCAATATCAGATCGGCAC
Found at i:30649632 original size:50 final size:50
Alignment explanation
Indices: 30649573--30649730 Score: 273
Period size: 50 Copynumber: 3.2 Consensus size: 50
30649563 CAATCTGCAT
30649573 AAAGCCATCGATAATAGATCGGCACATAGCCATCAATATCATATCGACAC
1 AAAGCCATCGATAATAGATCGGCACATAGCCATCAATATCATATCGACAC
30649623 AAAGCCATCGATAATAGATCGGCACATAGCCATCAATATCATATC-AGCAC
1 AAAGCCATCGATAATAGATCGGCACATAGCCATCAATATCATATCGA-CAC
* * *
30649673 AAAGCCATCGTTAACAGATCGGCACATAGCCATCAATATCATATCGGCAC
1 AAAGCCATCGATAATAGATCGGCACATAGCCATCAATATCATATCGACAC
30649723 AAAGCCAT
1 AAAGCCAT
30649731 GAATAGCATA
Statistics
Matches: 103, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
49 1 0.01
50 102 0.99
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.20
Consensus pattern (50 bp):
AAAGCCATCGATAATAGATCGGCACATAGCCATCAATATCATATCGACAC
Found at i:30649740 original size:25 final size:25
Alignment explanation
Indices: 30649590--30649805 Score: 191
Period size: 25 Copynumber: 8.6 Consensus size: 25
30649580 TCGATAATAG
* *
30649590 ATCGGCACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCAATAGCAT
* * ** *
30649615 ATCGACACAAAGCCATCGATAATAG
1 ATCGGCACAAAGCCATCAATAGCAT
* *
30649640 ATCGGCACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCAATAGCAT
* ** * *
30649665 ATCAGCACAAAGCCATCGTTAACAG
1 ATCGGCACAAAGCCATCAATAGCAT
* *
30649690 ATCGGCACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCAATAGCAT
*
30649715 ATCGGCACAAAGCCATGAATAGCAT
1 ATCGGCACAAAGCCATCAATAGCAT
* * * *
30649740 A-CTGGCACGAGGCCTTCAGTAGCAT
1 ATC-GGCACAAAGCCATCAATAGCAT
* **
30649765 ATCGACACAAAGCTTTCAATAGCAT
1 ATCGGCACAAAGCCATCAATAGCAT
*
30649790 ATCGGCAAAAAGCCAT
1 ATCGGCACAAAGCCAT
30649806 AATTAGAATA
Statistics
Matches: 148, Mismatches: 41, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
24 1 0.01
25 146 0.99
26 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (25 bp):
ATCGGCACAAAGCCATCAATAGCAT
Found at i:30649766 original size:100 final size:99
Alignment explanation
Indices: 30649573--30649777 Score: 265
Period size: 100 Copynumber: 2.1 Consensus size: 99
30649563 CAATCTGCAT
*
30649573 AAAGCCATCGATAATAGATCGGCACATAGCCATCAATATCATATCGACACAAAGCCATCGATAAT
1 AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACACAAAGCCATCGA-AAT
*
30649638 AGATCGGCACATAGCCATCAATATCATATC-AGCAC
65 AGATCGGCACATAGCCATCAATAGCATATCGA-CAC
* *
30649673 AAAGCCATCGTTAACAGATCGGCACATAGCCATCAATATCATATCGGCACAAAGCCAT-G-AATA
1 AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACACAAAGCCATCGAAATA
* * *
30649736 GCATACTGGCACGA-GGCCTTCAGTAGCATATCGACAC
66 G-AT-C-GGCAC-ATAGCCATCAATAGCATATCGACAC
30649773 AAAGC
1 AAAGC
30649778 TTTCAATAGC
Statistics
Matches: 93, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
97 5 0.05
98 2 0.02
99 2 0.02
100 82 0.88
101 2 0.02
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (99 bp):
AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACACAAAGCCATCGAAATA
GATCGGCACATAGCCATCAATAGCATATCGACAC
Found at i:30650090 original size:26 final size:27
Alignment explanation
Indices: 30650033--30650090 Score: 93
Period size: 25 Copynumber: 2.2 Consensus size: 27
30650023 GTAAAACATC
30650033 ATTTTACCCTACAAGGGTATTTTGGTA
1 ATTTTACCCTACAAGGGTATTTTGGTA
*
30650060 A-TTTACCTTAC-AGGGTATTTTGGTA
1 ATTTTACCCTACAAGGGTATTTTGGTA
30650085 ATTTTA
1 ATTTTA
30650091 TAAACCTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 15 0.52
26 13 0.45
27 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTACAAGGGTATTTTGGTA
Found at i:30657844 original size:26 final size:26
Alignment explanation
Indices: 30657809--30657879 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
30657799 TTCATTAATA
* *
30657809 CAAAACATACCATATA-TCATGCATAT
1 CAAAATATACCATAAACT-ATGCATAT
**
30657835 CAAAATATACTTTAAACTATGCATAT
1 CAAAATATACCATAAACTATGCATAT
**
30657861 CAAAATATACTTTAAACTA
1 CAAAATATACCATAAACTA
30657880 ACTTAACATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 39 0.98
27 1 0.03
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (26 bp):
CAAAATATACCATAAACTATGCATAT
Found at i:30669590 original size:21 final size:23
Alignment explanation
Indices: 30669561--30669602 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
30669551 TTCCCCTATA
*
30669561 ATCCTCTAATTTC-CTCCCACTT
1 ATCCTCTAAATTCACTCCCACTT
30669583 ATCC-CTAAATTCACTCCCAC
1 ATCCTCTAAATTCACTCCCAC
30669603 ACTTCCCCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.33
Consensus pattern (23 bp):
ATCCTCTAAATTCACTCCCACTT
Found at i:30673941 original size:25 final size:26
Alignment explanation
Indices: 30673913--30673964 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
30673903 GAGAATTTCG
30673913 ATTAAA-GGTTCTTTATGAACTTCCC
1 ATTAAATGGTTCTTTATGAACTTCCC
* *
30673938 ATTAAATTGGTTCTTTGTGAGCTTCCC
1 ATTAAA-TGGTTCTTTATGAACTTCCC
30673965 GATCGTGCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
27 17 0.74
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (26 bp):
ATTAAATGGTTCTTTATGAACTTCCC
Found at i:30674030 original size:24 final size:24
Alignment explanation
Indices: 30674003--30674058 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
30673993 TGGCTATCAA
30674003 GAGCTTCCTGACATGG-TCTTTTGT
1 GAGCTTCCTGACATGGTTC-TTTGT
*
30674027 GAGCTTCCTGATATGGTTCTTTGT
1 GAGCTTCCTGACATGGTTCTTTGT
*
30674051 GAACTTCC
1 GAGCTTCC
30674059 CAATTATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.41
Consensus pattern (24 bp):
GAGCTTCCTGACATGGTTCTTTGT
Found at i:30680652 original size:40 final size:40
Alignment explanation
Indices: 30680600--30680783 Score: 160
Period size: 40 Copynumber: 4.6 Consensus size: 40
30680590 TAACTCATTC
* *
30680600 AATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCACACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAGAAACTCACACA
* * *
30680640 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGAAACTCACACA
* * * *
30680680 AAGGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGAAACTCACACA
* ** ** *
30680720 AAGGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAGAAACTCA-CACA
*
30680761 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
30680784 CAGCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 108 0.86
41 9 0.07
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGAAACTCACACA
Found at i:30680727 original size:80 final size:80
Alignment explanation
Indices: 30680603--30680783 Score: 192
Period size: 80 Copynumber: 2.3 Consensus size: 80
30680593 CTCATTCAAT
* * *
30680603 GCCTTCGGGACTTAACCCGGATTTTAAAACTCACACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCACACAAAGGCCTTC-GGATCTTAACCCGGATA-
*
30680666 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
* * * **
30680682 GGCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTA-AAACTCACACAAAGGCCTTCGGATCTTAACCCGGATA
30680746 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
30680763 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
30680784 CAGCATTCAA
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
79 6 0.07
80 69 0.80
81 10 0.12
82 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCACACAAAGGCCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:30685405 original size:21 final size:21
Alignment explanation
Indices: 30685371--30685410 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
30685361 TAATATAAAC
*
30685371 AATAATAGTAATAGATAAATG
1 AATAATAATAATAGATAAATG
* *
30685392 AATAATAATGATAGGTAAA
1 AATAATAATAATAGATAAA
30685411 CAAATTCGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (21 bp):
AATAATAATAATAGATAAATG
Found at i:30686513 original size:40 final size:39
Alignment explanation
Indices: 30686466--30686613 Score: 199
Period size: 40 Copynumber: 3.7 Consensus size: 39
30686456 TACTAGCACA
* * *
30686466 AAGCCTGCGGGACTTTAGGCCCGGATATA-GTACCAACACT
1 AAGCCTGCGGGA-TTTA-ACCCGGATATACTTACCAACACG
*
30686506 AAGCCTGCGGGATTTAACCCGGATATACTTTACCAGCACG
1 AAGCCTGCGGGATTTAACCCGGATATAC-TTACCAACACG
*
30686546 AAGCCTGCGGGCTTTAACCCGGATATACTTTACCAACACG
1 AAGCCTGCGGGATTTAACCCGGATATAC-TTACCAACACG
*
30686586 AAGCCTGCAGGATTTAACCCGGATATAC
1 AAGCCTGCGGGATTTAACCCGGATATAC
30686614 AATATATCGA
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
38 10 0.10
39 4 0.04
40 84 0.86
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (39 bp):
AAGCCTGCGGGATTTAACCCGGATATACTTACCAACACG
Found at i:30686580 original size:80 final size:80
Alignment explanation
Indices: 30686455--30686613 Score: 232
Period size: 80 Copynumber: 2.0 Consensus size: 80
30686445 CCGAATCCAG
* * * *
30686455 TTACTAGCACAAAGCCTGCGGGACTTTAGGCCCGGATATAGTACCAACACTAAGCCTGCGGGATT
1 TTACCAGCACAAAGCCTGCGGGACTTTAGACCCGGATATAGTACCAACACGAAGCCTGCAGGATT
30686520 TAACCCGGATATACT
66 TAACCCGGATATACT
* *
30686535 TTACCAGCACGAAGCCTGCGGG-CTTTA-ACCCGGATATACTTTACCAACACGAAGCCTGCAGGA
1 TTACCAGCACAAAGCCTGCGGGACTTTAGACCCGGATATA--GTACCAACACGAAGCCTGCAGGA
30686598 TTTAACCCGGATATAC
64 TTTAACCCGGATATAC
30686614 AATATATCGA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
78 10 0.14
79 5 0.07
80 56 0.79
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (80 bp):
TTACCAGCACAAAGCCTGCGGGACTTTAGACCCGGATATAGTACCAACACGAAGCCTGCAGGATT
TAACCCGGATATACT
Found at i:30689079 original size:13 final size:13
Alignment explanation
Indices: 30689061--30689085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30689051 TGTGGGTGCA
30689061 CACGGCCATGTCG
1 CACGGCCATGTCG
30689074 CACGGCCATGTC
1 CACGGCCATGTC
30689086 TGGCGTTGTT
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:0.28, T:0.16
Consensus pattern (13 bp):
CACGGCCATGTCG
Found at i:30695439 original size:42 final size:42
Alignment explanation
Indices: 30695378--30695544 Score: 244
Period size: 42 Copynumber: 4.0 Consensus size: 42
30695368 GAAAATATTT
*
30695378 GAGATAGCTTCGACTATGCATTGGCACTTAGTGTGCAAGATC
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
* *
30695420 GGGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCGAGATC
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
* * * *
30695462 AAGATAGCTTCAGCTATGCATTGGCACTTAGTGTGCATGATT
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
* * *
30695504 GAGTTAGCTTCGGCTACGTATTGGCACTTAGTGTGCAAGAT
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGAT
30695545 TCCCAAGTAA
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 110 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (42 bp):
GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
Found at i:30695676 original size:32 final size:32
Alignment explanation
Indices: 30695614--30695676 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
30695604 TATGAGATTG
* * *
30695614 GTACGATATGGTACAAGTATGTATGGAAATTT
1 GTACGAGATGGTACAAGTATGTACGAAAATTT
*
30695646 GTACGAGATGGTACAGGTATGTACGAAAATT
1 GTACGAGATGGTACAAGTATGTACGAAAATT
30695677 CAATTGAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (32 bp):
GTACGAGATGGTACAAGTATGTACGAAAATTT
Found at i:30699384 original size:19 final size:20
Alignment explanation
Indices: 30699357--30699396 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
30699347 ATGATTATGT
*
30699357 CAATGCATATTTTGT-AAAA
1 CAATACATATTTTGTGAAAA
30699376 CAATACATATTTTGTGAAAA
1 CAATACATATTTTGTGAAAA
30699396 C
1 C
30699397 GGACCTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (20 bp):
CAATACATATTTTGTGAAAA
Found at i:30699595 original size:49 final size:51
Alignment explanation
Indices: 30699462--30699595 Score: 191
Period size: 51 Copynumber: 2.7 Consensus size: 51
30699452 CTAAACACCA
* *
30699462 TTTGTGGACAAGCTACCACTGATTTGCAGATAAATTGCCAGTGATAACACT
1 TTTGTGGACAAGCTACCACTGATTTGCAGATATATTGCCACTGATAACACT
* * * *
30699513 TTTGTAGACAAGCCACCATTGATATGCAGATATATTGCCACTGATAA-A-T
1 TTTGTGGACAAGCTACCACTGATTTGCAGATATATTGCCACTGATAACACT
*
30699562 TTTGTGGACAAGCTACCACTGATTTGCAAATATA
1 TTTGTGGACAAGCTACCACTGATTTGCAGATATA
30699596 CTGTCACAGC
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 30 0.42
50 1 0.01
51 41 0.57
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (51 bp):
TTTGTGGACAAGCTACCACTGATTTGCAGATATATTGCCACTGATAACACT
Found at i:30703038 original size:93 final size:93
Alignment explanation
Indices: 30702912--30703082 Score: 247
Period size: 93 Copynumber: 1.8 Consensus size: 93
30702902 CCCATAATCG
* * ** *
30702912 AACTCGGGCTCAACTCAATGAGATCGGGTGTTCGCA-TCCATAAGTGAACT-GAGACTCAACTCA
1 AACTCGGACTCAACTCAACGAGATCGGACGTTCG-ATTCCATAAGTGAACTCG-GACTCAACTAA
30702975 ACGAGCTCGGATGCCTAGTTACATCTCACA
64 ACGAGCTCGGATGCCTAGTTACATCTCACA
*
30703005 AACTCGGACTCAACTCAACGAGTTCGGACGTTCGATTCCATAAGTGAACTCGGACTCAACTAAAC
1 AACTCGGACTCAACTCAACGAGATCGGACGTTCGATTCCATAAGTGAACTCGGACTCAACTAAAC
*
30703070 GAGTTCGGATGCC
66 GAGCTCGGATGCC
30703083 CAAATATCCG
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
92 1 0.01
93 67 0.97
94 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGATCGGACGTTCGATTCCATAAGTGAACTCGGACTCAACTAAAC
GAGCTCGGATGCCTAGTTACATCTCACA
Found at i:30708967 original size:46 final size:47
Alignment explanation
Indices: 30708799--30708974 Score: 193
Period size: 46 Copynumber: 3.8 Consensus size: 47
30708789 TGTAACCCGC
* * * *
30708799 CCATAAGTGAACTCGGATTCAACTCAACAAGCTC-AAGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAGCGTTCGCAT
*
30708845 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA-G-C--GTTCGCAT
* * *
30708895 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAGCGTTCGCAT
*
30708938 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
30708975 TGCCTAAATA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 2 0.02
46 61 0.55
47 29 0.26
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAGCGTTCGCAT
Found at i:30716502 original size:20 final size:19
Alignment explanation
Indices: 30716456--30716493 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
30716446 ATATTAATAC
30716456 ATTTTTATATAAAATTTAA
1 ATTTTTATATAAAATTTAA
30716475 ATATTTTA-ACTAAAATTTA
1 AT-TTTTATA-TAAAATTTA
30716494 TTATTTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTTATATAAAATTTAA
Found at i:30723043 original size:14 final size:15
Alignment explanation
Indices: 30723024--30723052 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30723014 AACTCTTTCC
30723024 ATTCTTTTT-GCTTT
1 ATTCTTTTTAGCTTT
30723038 ATTCTTTTTAGCTTT
1 ATTCTTTTTAGCTTT
30723053 CTGCTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.69
Consensus pattern (15 bp):
ATTCTTTTTAGCTTT
Done.