Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008162.1 Hibiscus syriacus cultivar Beakdansim tig00110733_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3688897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 16
Found at i:2758821 original size:15 final size:15
Alignment explanation
Indices: 2758733--2758837 Score: 72
Period size: 16 Copynumber: 6.7 Consensus size: 15
2758723 TTTTGTCCCT
*
2758733 TTTTC-TTTTTGATTT
1 TTTTCTTTTTTG-TTC
*
2758748 TTGTTCTTTCTTTTTTC
1 TT-TTCTTT-TTTGTTC
* *
2758765 TTTTGTTTTGTTCTTTC
1 TTTTCTTTT-TT-GTTC
2758782 TTTT-TTCTTTTGTT-
1 TTTTCTT-TTTTGTTC
2758796 TTCTTCTTTTTTGCTTC
1 TT-TTCTTTTTTG-TTC
*
2758813 TTTTCTTTTTTGTTT
1 TTTTCTTTTTTGTTC
2758828 TTTTCTTTTT
1 TTTTCTTTTT
2758838 GTTATGATTG
Statistics
Matches: 75, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
14 2 0.03
15 24 0.32
16 28 0.37
17 18 0.24
18 3 0.04
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTTGTTC
Found at i:2761594 original size:73 final size:72
Alignment explanation
Indices: 2761475--2761628 Score: 290
Period size: 73 Copynumber: 2.1 Consensus size: 72
2761465 GTCCCCAGCA
2761475 GAGTCGCCAAGCTGTCGCAACCATCTTTCGGTTGGGCCCCGGAATTGGGCTTCGACTTGAAAAAT
1 GAGTCGCCAAGCTGTCGCAACCATCTTTCGGTTGGGCCCCGGAATTGGGCTTCGACTTG-AAAAT
2761540 GTGGATTG
65 GTGGATTG
*
2761548 GAGTCGCCAAGCTGTCGCAACCGTCTTTCGGTTGGGCCCCGGAATTGGGCTTCGACTTGAAAATG
1 GAGTCGCCAAGCTGTCGCAACCATCTTTCGGTTGGGCCCCGGAATTGGGCTTCGACTTGAAAATG
2761613 TGGATTG
66 TGGATTG
2761620 GAGTCGCCA
1 GAGTCGCCA
2761629 CCGATCATTT
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
72 22 0.28
73 58 0.73
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.25
Consensus pattern (72 bp):
GAGTCGCCAAGCTGTCGCAACCATCTTTCGGTTGGGCCCCGGAATTGGGCTTCGACTTGAAAATG
TGGATTG
Found at i:2761903 original size:18 final size:19
Alignment explanation
Indices: 2761865--2761959 Score: 72
Period size: 19 Copynumber: 5.0 Consensus size: 19
2761855 TGTTAGAGAG
*
2761865 AAAAAAATGAATAAATGAA
1 AAAAAAATGAATAAATAAA
*
2761884 AAAAAAATGAA-GAATAAA
1 AAAAAAATGAATAAATAAA
2761902 AATAAGTAAA--AATAAATAAA
1 AA-AA--AAATGAATAAATAAA
* *
2761922 AATAAAAGGAA-AAATAAA
1 AAAAAAATGAATAAATAAA
* *
2761940 TAAATAAATAAATAAATAAA
1 -AAAAAAATGAATAAATAAA
2761960 TAAATGAAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
17 3 0.05
18 14 0.23
19 25 0.42
20 15 0.25
21 3 0.05
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (19 bp):
AAAAAAATGAATAAATAAA
Found at i:2761913 original size:10 final size:10
Alignment explanation
Indices: 2761896--2761963 Score: 68
Period size: 10 Copynumber: 6.6 Consensus size: 10
2761886 AAAAATGAAG
2761896 AATAAAAATA
1 AATAAAAATA
*
2761906 AGTAAAAATA
1 AATAAAAATA
2761916 AATAAAAATAA
1 AATAAAAAT-A
*
2761927 AAGGAAAAATA
1 AA-TAAAAATA
2761938 AAT--AAATA
1 AATAAAAATA
2761946 AATAAATAAATA
1 AAT-AA-AAATA
2761958 AATAAA
1 AATAAA
2761964 TGAAATATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
8 8 0.17
10 18 0.38
11 8 0.17
12 14 0.29
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.19
Consensus pattern (10 bp):
AATAAAAATA
Found at i:2761927 original size:16 final size:16
Alignment explanation
Indices: 2761877--2761959 Score: 62
Period size: 16 Copynumber: 5.1 Consensus size: 16
2761867 AAAAATGAAT
*
2761877 AAATGAAAAAAAAATGAA
1 AAAT-AAAAATAAAT-AA
* *
2761895 GAATAAAAATAAGTAA
1 AAATAAAAATAAATAA
2761911 AAATAAATAA-AAATAA
1 AAATAAA-AATAAATAA
**
2761927 AAGGAAAAATAAATAA
1 AAATAAAAATAAATAA
*
2761943 ATAA-ATAAATAAATAA
1 A-AATAAAAATAAATAA
2761959 A
1 A
2761960 TAAATGAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.04
16 37 0.70
17 11 0.21
18 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (16 bp):
AAATAAAAATAAATAA
Found at i:2761937 original size:22 final size:20
Alignment explanation
Indices: 2761896--2761943 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 20
2761886 AAAAATGAAG
*
2761896 AATAAAAATAAGTAAAAATA
1 AATAAAAATAAGGAAAAATA
2761916 AATAAAAATAAAAGGAAAAATA
1 AATAAAAAT--AAGGAAAAATA
2761938 AATAAA
1 AATAAA
2761944 TAAATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 9 0.36
22 16 0.64
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (20 bp):
AATAAAAATAAGGAAAAATA
Found at i:2761940 original size:4 final size:4
Alignment explanation
Indices: 2761933--2761970 Score: 67
Period size: 4 Copynumber: 9.2 Consensus size: 4
2761923 ATAAAAGGAA
2761933 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A
2761971 TTAATATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2761953 original size:38 final size:35
Alignment explanation
Indices: 2761865--2761959 Score: 93
Period size: 38 Copynumber: 2.6 Consensus size: 35
2761855 TGTTAGAGAG
* * *
2761865 AAAA-AAATGAATAAATGAAAAAAAAATGAAGAATA
1 AAAATAAATAAATAAAT-AAAAAAAAAGGAAAAATA
*
2761900 AAAATAAGTAAAAATAAATAAAAATAAAAGGAAAAATAA
1 AAAATAA--ATAAATAAATAAAAA-AAAAGGAAAAAT-A
2761939 ATAAATAAATAAATAAATAAA
1 A-AAATAAATAAATAAATAAA
2761960 TAAATGAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
35 4 0.08
36 2 0.04
37 5 0.10
38 30 0.61
39 2 0.04
40 6 0.12
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (35 bp):
AAAATAAATAAATAAATAAAAAAAAAGGAAAAATA
Found at i:2762075 original size:18 final size:18
Alignment explanation
Indices: 2762042--2762104 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
2762032 ATAATGATAG
*
2762042 TAATATAAA-AATATAATA
1 TAATATAAACAA-ATAAAA
2762060 TAATATAAACAAATAAAA
1 TAATATAAACAAATAAAA
* * *
2762078 AAATAAAAACAAAAACAAA
1 TAATATAAACAAATA-AAA
2762097 TAAATATA
1 T-AATATA
2762105 TAAATCAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 26 0.72
19 5 0.14
20 5 0.14
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (18 bp):
TAATATAAACAAATAAAA
Found at i:2762272 original size:2 final size:2
Alignment explanation
Indices: 2762265--2762331 Score: 56
Period size: 2 Copynumber: 36.5 Consensus size: 2
2762255 AAATATTTAA
* * *
2762265 AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT CT A- AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2762304 AT AT AT GT AT AT AT A- AT A- AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2762332 GTGTAAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
1 6 0.11
2 48 0.89
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2762317 original size:37 final size:37
Alignment explanation
Indices: 2762267--2762341 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
2762257 ATATTTAAAT
2762267 ATATATATATATATATATATATAATA-ATA-TCTAAAAA
1 ATATATATATATATA-ATA-ATAATATATAGTCTAAAAA
* *
2762304 ATATATGTATATATAATAATAATATATAGTGTAAAAA
1 ATATATATATATATAATAATAATATATAGTCTAAAAA
2762341 A
1 A
2762342 ATCAATTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 6 0.18
36 6 0.18
37 22 0.65
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (37 bp):
ATATATATATATATAATAATAATATATAGTCTAAAAA
Found at i:2765360 original size:313 final size:312
Alignment explanation
Indices: 2764793--2765418 Score: 1234
Period size: 313 Copynumber: 2.0 Consensus size: 312
2764783 ATTCCTCTCC
2764793 TCCCATACACAGTAGATGTAAGCACACCAAGCAACTCTAAGAATAAACACAGGAAATATTTTCCT
1 TCCCATACACAGTAGATGTAAGCACACCAAGCAACTCTAAGAATAAACACAGGAAATATTTTCCT
2764858 CTAAACCACGAAATAGCCCAGCTCAACTCCTCCTCCCAAGTCCCCACAGCTCTGTTAACATTGCA
66 CTAAACCACGAAATAGCCCAGCTCAACTCCTCCTCCCAAGTCCCCACAGCTCTGTTAACATTGCA
2764923 CAGTTGTGCAATTTCCTCCCAAACAGCCTTCGAGAACTAGCATTCAAAGAAAATATGGCTACGAG
131 CAGTTGTGCAATTTCCTCCCAAACAGCCTTCGAGAACTAGCATTCAAAGAAAATATGGCTACGAG
2764988 TCTCAGGCGCAGCTTCACACAATCTGCATTTTTCATTCACCTCAATTCTCAAACGAGCAAGCCTA
196 TCTCAGGCGCAGCTTCACACAATCTGCATTTTTCATTCACCTCAATTCTCAAACGAGCAAGCCTA
2765053 TCAGCAGTTGGCAGCCTATCTAAAATAGCCATCCAAGCAATAAGCGAGTGTT
261 TCAGCAGTTGGCAGCCTATCTAAAATAGCCATCCAAGCAATAAGCGAGTGTT
2765105 TCCCATACACAGTAGATGTAAGCACACCAAGCAACTCTAAGAATAAACACAGGGAAATATTTTCC
1 TCCCATACACAGTAGATGTAAGCACACCAAGCAACTCTAAGAATAAACACA-GGAAATATTTTCC
*
2765170 TCTAAACCGCGAAATAGCCCAGCTCAACTCCTCCTCCCAAGTCCCCACAGCTCTGTTAACATTGC
65 TCTAAACCACGAAATAGCCCAGCTCAACTCCTCCTCCCAAGTCCCCACAGCTCTGTTAACATTGC
2765235 ACAGTTGTGCAATTTCCTCCCAAACAGCCTTCGAGAACTAGCATTCAAAGAAAATATGGCTACGA
130 ACAGTTGTGCAATTTCCTCCCAAACAGCCTTCGAGAACTAGCATTCAAAGAAAATATGGCTACGA
2765300 GTCTCAGGCGCAGCTTCACACAATCTGCATTTTTCATTCACCTCAATTCTCAAACGAGCAAGCCT
195 GTCTCAGGCGCAGCTTCACACAATCTGCATTTTTCATTCACCTCAATTCTCAAACGAGCAAGCCT
2765365 ATCAGCAGTTGGCAGCCTATCTAAAATAGCCATCCAAGCAATAAGCGAGTGTT
260 ATCAGCAGTTGGCAGCCTATCTAAAATAGCCATCCAAGCAATAAGCGAGTGTT
2765418 T
1 T
2765419 TGGTATGTGC
Statistics
Matches: 312, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
312 51 0.16
313 261 0.84
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (312 bp):
TCCCATACACAGTAGATGTAAGCACACCAAGCAACTCTAAGAATAAACACAGGAAATATTTTCCT
CTAAACCACGAAATAGCCCAGCTCAACTCCTCCTCCCAAGTCCCCACAGCTCTGTTAACATTGCA
CAGTTGTGCAATTTCCTCCCAAACAGCCTTCGAGAACTAGCATTCAAAGAAAATATGGCTACGAG
TCTCAGGCGCAGCTTCACACAATCTGCATTTTTCATTCACCTCAATTCTCAAACGAGCAAGCCTA
TCAGCAGTTGGCAGCCTATCTAAAATAGCCATCCAAGCAATAAGCGAGTGTT
Found at i:2768249 original size:11 final size:11
Alignment explanation
Indices: 2768225--2768256 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
2768215 AATTTTCATC
2768225 TATATATAATAT
1 TATATAT-ATAT
2768237 TATATATATAT
1 TATATATATAT
2768248 TATATATAT
1 TATATATAT
2768257 TTTAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATATATATAT
Found at i:2769406 original size:13 final size:13
Alignment explanation
Indices: 2769388--2769454 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
2769378 ATATATTGTT
2769388 TTTTATTTTTTTA
1 TTTTATTTTTTTA
**
2769401 TTTTATTTTCCTA
1 TTTTATTTTTTTA
*
2769414 -TTT-TGTTTTTA
1 TTTTATTTTTTTA
*
2769425 TTTT-TGTTTTTTC
1 TTTTAT-TTTTTTA
*
2769438 TTTAATTTTATTTA
1 TTTTATTTT-TTTA
2769452 TTT
1 TTT
2769455 CCATTATTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
11 5 0.12
12 7 0.17
13 22 0.54
14 7 0.17
ACGTcount: A:0.13, C:0.04, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:2769613 original size:42 final size:42
Alignment explanation
Indices: 2769528--2769614 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
2769518 TAGTGGTTTG
* * *
2769528 ATTATTTTAATAGGTGTAGTGGTTTAGGGTGTATTTGATTTA
1 ATTATTTTAATAGGTGTAGTGATTTAGGGTGAATTTGAGTTA
* *
2769570 ATTATTTTAATAGGTGTAGTGATTTAGGTTGAATTTGGGTTA
1 ATTATTTTAATAGGTGTAGTGATTTAGGGTGAATTTGAGTTA
2769612 ATT
1 ATT
2769615 TTATTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (42 bp):
ATTATTTTAATAGGTGTAGTGATTTAGGGTGAATTTGAGTTA
Found at i:2769671 original size:13 final size:11
Alignment explanation
Indices: 2769642--2769679 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
2769632 TTTCGTATCA
2769642 TTTTTTTC-TT
1 TTTTTTTCATT
*
2769652 TTTTTTCCATT
1 TTTTTTTCATT
2769663 TTTTATTTCATT
1 TTTT-TTTCATT
2769675 TTTTT
1 TTTTT
2769680 CTTTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 7 0.29
11 7 0.29
12 10 0.42
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTCATT
Found at i:2769934 original size:18 final size:18
Alignment explanation
Indices: 2769895--2769934 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2769885 TATTAATATT
* *
2769895 AATATTTTTTCTTTTTTC
1 AATATTTTTTATTTTTAC
2769913 -ATATTTTTTATTTTTAC
1 AATATTTTTTATTTTTAC
2769930 AATAT
1 AATAT
2769935 AACATTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (18 bp):
AATATTTTTTATTTTTAC
Found at i:2774008 original size:99 final size:99
Alignment explanation
Indices: 2773888--2774089 Score: 316
Period size: 99 Copynumber: 2.0 Consensus size: 99
2773878 TTATAATATT
* *
2773888 ATATATATACAATAAAGCTTGAGATGTCCCTCTAAATCAATTAGTTAAACACCCCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTAGTTAAACACCCCAGCTTTATGG
2773953 ATAAGATTC-AGCTAACCTGATAAAGGTGATTATA
66 ATAAGATTCGA-CTAACCTGATAAAGGTGATTATA
* * * * *
2773987 ATATCTATACAATAAAGCTTGAGCTGTCCCTCTAAGGCAATTGGTTAAACGCCCCAGCTTTATGG
1 ATATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTAGTTAAACACCCCAGCTTTATGG
*
2774052 ATAAGATTCGACTAGCCTGATAAAGGTGATTATA
66 ATAAGATTCGACTAACCTGATAAAGGTGATTATA
2774086 ATAT
1 ATAT
2774090 TGAGTTGTCC
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 93 0.99
100 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTAGTTAAACACCCCAGCTTTATGG
ATAAGATTCGACTAACCTGATAAAGGTGATTATA
Found at i:2775590 original size:57 final size:59
Alignment explanation
Indices: 2775508--2775665 Score: 194
Period size: 57 Copynumber: 2.7 Consensus size: 59
2775498 CTTACAAAAT
* **
2775508 ATTGGATTTCAACTTCACAAGGAAGGATATCCAACTCAAAGCCAA-ACAAT-ATTCAAG
1 ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATACAATGAAACAAG
* ****
2775565 ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAACAAG
1 ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATACAATGAAACAAG
* * * *
2775624 ATTTGATTTCAGCTTCAGAACGAAGGATATCCAATTCAAAGC
1 ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC
2775666 TCAGCTTCAC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
57 43 0.50
58 1 0.01
59 42 0.49
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (59 bp):
ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATACAATGAAACAAG
Found at i:2776093 original size:85 final size:84
Alignment explanation
Indices: 2775963--2776189 Score: 276
Period size: 85 Copynumber: 2.7 Consensus size: 84
2775953 CAGCATAGCT
* * * * *
2775963 CAAGGTGAGTAGGGCTATCTATCAACCAAAACCTTTGAGTTCGATTACATTCAGCTCAAAGCCAT
1 CAAGGCGAGAAGGGCTATCTGTCAA-CAAAACCTTCGAGTTCGATTCCATTCAGCTCAAAGCCAT
*
2776028 ATTAAATTTACAGTATAACG
65 ATTAAATTTACAGAATAACG
* * *
2776048 CAAGGCGAGAAGGGTTATCTGTCAACAAATACCTTCGAGTTCGATTCCATTCAGCTCAAGGGCAT
1 CAAGGCGAGAAGGGCTATCTGTCAACAAA-ACCTTCGAGTTCGATTCCATTCAGCTCAAAGCCAT
* *
2776113 GTTAAATTTACAGAATAACT
65 ATTAAATTTACAGAATAACG
* * **
2776133 TAAGTCGAGAAAAGCTATCTGTCAACGAAAA-CTGTCGAGTTCGATTCCATTCAGCTC
1 CAAGGCGAGAAGGGCTATCTGTCAAC-AAAACCT-TCGAGTTCGATTCCATTCAGCTC
2776190 GATGACACAT
Statistics
Matches: 123, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
84 6 0.05
85 114 0.93
86 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (84 bp):
CAAGGCGAGAAGGGCTATCTGTCAACAAAACCTTCGAGTTCGATTCCATTCAGCTCAAAGCCATA
TTAAATTTACAGAATAACG
Found at i:2778124 original size:14 final size:14
Alignment explanation
Indices: 2778105--2778243 Score: 63
Period size: 14 Copynumber: 9.8 Consensus size: 14
2778095 TATATTGTAT
2778105 TTTTATTTTTTTTA
1 TTTTATTTTTTTTA
**
2778119 TTTTA-TTTTACTA
1 TTTTATTTTTTTTA
*
2778132 TTTTATTTTTGTT-
1 TTTTATTTTTTTTA
* *
2778145 TTTTCTTTAATTTTA
1 TTTTATTT-TTTTTA
2778160 -TTTATTTTCATTATTAAA
1 TTTTATTTT--TT-TT--A
** * * *
2778178 TACTATGTTATATA
1 TTTTATTTTTTTTA
* *
2778192 TATTATTTTTATT-
1 TTTTATTTTTTTTA
*
2778205 TTTTATTTTTTTTT
1 TTTTATTTTTTTTA
2778219 TTTTATTTTTTATT-
1 TTTTATTTTTT-TTA
2778233 TTTTATTTTTT
1 TTTTATTTTTT
2778244 CTTTTAATTT
Statistics
Matches: 93, Mismatches: 21, Indels: 22
0.68 0.15 0.16
Matches are distributed among these distances:
13 29 0.31
14 50 0.54
15 4 0.04
16 3 0.03
17 1 0.01
18 1 0.01
19 5 0.05
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTTTTA
Found at i:2778207 original size:1 final size:1
Alignment explanation
Indices: 2778197--2778248 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
2778187 ATATATATTA
* * * * * *
2778197 TTTTTATTTTTTATTTTTTTTTTTTTATTTTTTATTTTTTATTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2778249 AATTTTGCAG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.10, C:0.02, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:2778209 original size:7 final size:7
Alignment explanation
Indices: 2778197--2778248 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
2778187 ATATATATTA
2778197 TTTTTAT
1 TTTTTAT
2778204 TTTTTAT
1 TTTTTAT
*
2778211 TTTTTTT
1 TTTTTAT
2778218 TTTTTAT
1 TTTTTAT
2778225 TTTTTAT
1 TTTTTAT
2778232 TTTTTAT
1 TTTTTAT
*
2778239 TTTTTCT
1 TTTTTAT
2778246 TTT
1 TTT
2778249 AATTTTGCAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.10, C:0.02, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:2778314 original size:42 final size:42
Alignment explanation
Indices: 2778266--2778355 Score: 137
Period size: 42 Copynumber: 2.1 Consensus size: 42
2778256 CAGTGGTTTG
* *
2778266 ATTATTTTAATAGGTGTAGTGGTTTAGGGTGTATTT-GATTTA
1 ATTATTTTAATAGGTGTAGTGGTTTAAGGTGAATTTGGA-TTA
*
2778308 ATTATTTTAATAGGTGTAGTGGTTTAAGTTGAATTTGGATTA
1 ATTATTTTAATAGGTGTAGTGGTTTAAGGTGAATTTGGATTA
2778350 ATTATT
1 ATTATT
2778356 ATCATTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 42 0.95
43 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (42 bp):
ATTATTTTAATAGGTGTAGTGGTTTAAGGTGAATTTGGATTA
Found at i:2778637 original size:10 final size:10
Alignment explanation
Indices: 2778622--2778665 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
2778612 TATATTAATA
*
2778622 TTTTTTTCTT
1 TTTTTTTATT
*
2778632 TTTTTTTCTT
1 TTTTTTTATT
*
2778642 TTTTTCATATT
1 TTTTT-TTATT
2778653 TTTTTTTATT
1 TTTTTTTATT
2778663 TTT
1 TTT
2778666 ACAATAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:2778891 original size:92 final size:92
Alignment explanation
Indices: 2778778--2778963 Score: 363
Period size: 92 Copynumber: 2.0 Consensus size: 92
2778768 CAACCTGCAA
2778778 ATTAATTGGTACCGAAAGGGTAGTTCAAAGGTGCTAATCCTTCATTGACTGTAACCGACTCCCGA
1 ATTAATTGGTACCGAAAGGGTAGTTCAAAGGTGCTAATCCTTCATTGACTGTAACCGACTCCCGA
2778843 ACCCGACACATTTCTGGTAAAACGCAT
66 ACCCGACACATTTCTGGTAAAACGCAT
*
2778870 ATTAATTGGTACCGAAAGGGTAGTTCAAGGGTGCTAATCCTTCATTGACTGTAACCGACTCCCGA
1 ATTAATTGGTACCGAAAGGGTAGTTCAAAGGTGCTAATCCTTCATTGACTGTAACCGACTCCCGA
2778935 ACCCGACACATTTCTGGTAAAACGCAT
66 ACCCGACACATTTCTGGTAAAACGCAT
2778962 AT
1 AT
2778964 CAGGTAAGAT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (92 bp):
ATTAATTGGTACCGAAAGGGTAGTTCAAAGGTGCTAATCCTTCATTGACTGTAACCGACTCCCGA
ACCCGACACATTTCTGGTAAAACGCAT
Found at i:2781411 original size:12 final size:14
Alignment explanation
Indices: 2781382--2781429 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
2781372 ACATCAAAAA
2781382 ATTTTAAAATATAT
1 ATTTTAAAATATAT
*
2781396 ATTTTAAATAATATTTTT
1 ATTTT-AA-AATA--TAT
2781414 ATTTTAAAATATAT
1 ATTTTAAAATATAT
2781428 AT
1 AT
2781430 ATAAATGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 2 0.07
16 8 0.29
17 2 0.07
18 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTTAAAATATAT
Found at i:2794347 original size:16 final size:15
Alignment explanation
Indices: 2794326--2794359 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2794316 GCATTCAACA
2794326 AATATAAGCATGATAC
1 AATATAAGCATGA-AC
*
2794342 AATATAATCATGAAC
1 AATATAAGCATGAAC
2794357 AAT
1 AAT
2794360 TACAACCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (15 bp):
AATATAAGCATGAAC
Found at i:2802855 original size:20 final size:21
Alignment explanation
Indices: 2802811--2802858 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2802801 CCGGAAGGGG
*
2802811 GTATCGGTACCATAGTATAGAA
1 GTATCGGTACCA-AGGATAGAA
*
2802833 GTATCGGTACC-AGGATAGTA
1 GTATCGGTACCAAGGATAGAA
2802853 GTATCG
1 GTATCG
2802859 ATACTATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (21 bp):
GTATCGGTACCAAGGATAGAA
Found at i:2803315 original size:34 final size:34
Alignment explanation
Indices: 2803276--2803570 Score: 149
Period size: 34 Copynumber: 7.7 Consensus size: 34
2803266 CCATAGCTGA
*
2803276 AATGCATATGGGTGCATTATCGGCTTAAAAGAAT
1 AATGCATATGGGTGCATTATTGGCTTAAAAGAAT
* *
2803310 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCGTAGCT
1 AATGCATATGGGTGCATTATTGGC-TTAAA--A----G-A-AT
* *
2803353 GAAATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATTGGCTTAAAAGAAT
* *
2803389 AATGCATATCGGTGCATTATTGGCATAAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATTGGC-TTAAA--A-G--A-A--T
* *
2803432 GAAATGCATATGGGTACATTATTGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATTGGCTTAAAAGAAT
* *
2803468 AATGCATATAGGTGCATTATTGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATTGGC-TTAAA--A-G--A-A--T
* *** *
2803511 GAAATGCATATGGGAGCATTATCATCATAAAAGAAT
1 --AATGCATATGGGTGCATTATTGGCTTAAAAGAAT
2803547 AATGCATATGGGTGCATTATTGGC
1 AATGCATATGGGTGCATTATTGGC
2803571 ATGAAAGGAT
Statistics
Matches: 198, Mismatches: 30, Indels: 66
0.67 0.10 0.22
Matches are distributed among these distances:
34 87 0.44
35 10 0.05
36 3 0.02
37 4 0.02
38 5 0.03
39 2 0.01
40 2 0.01
41 5 0.03
42 4 0.02
43 3 0.02
44 9 0.05
45 64 0.32
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATTGGCTTAAAAGAAT
Found at i:2803630 original size:34 final size:34
Alignment explanation
Indices: 2803592--2803660 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
2803582 TCATAGCTGA
2803592 AATGCATATAGGTGCATTATTGGCATAAAAGAAT
1 AATGCATATAGGTGCATTATTGGCATAAAAGAAT
* * *
2803626 AATGCATATGGGTGCATTATTGGTATGAAAGAAT
1 AATGCATATAGGTGCATTATTGGCATAAAAGAAT
2803660 A
1 A
2803661 CTATAGCTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (34 bp):
AATGCATATAGGTGCATTATTGGCATAAAAGAAT
Found at i:2803690 original size:79 final size:79
Alignment explanation
Indices: 2803221--2803680 Score: 731
Period size: 79 Copynumber: 5.8 Consensus size: 79
2803211 ATATGAATGA
* *
2803221 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATTAAGGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
2803286 GGTGCATTATCGGC
66 GGTGCATTATCGGC
* * *
2803300 TTAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCGTAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
2803365 GGTGCATTATCGGC
66 GGTGCATTATCGGC
* *
2803379 ATAAAAGAATAATGCATATCGGTGCATTATTGGCATAAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
* *
2803444 GGTACATTATTGGC
66 GGTGCATTATCGGC
*
2803458 ATAAAAGAATAATGCATATAGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
* **
2803523 GGAGCATTATCATC
66 GGTGCATTATCGGC
* *
2803537 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATA
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
*
2803602 GGTGCATTATTGGC
66 GGTGCATTATCGGC
* * * * *
2803616 ATAAAAGAATAATGCATATGGGTGCATTATTGGTATGAAAGAATACTATAGCTGAAATACATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
2803681 AATGTATTAT
Statistics
Matches: 348, Mismatches: 33, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 348 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
GGTGCATTATCGGC
Found at i:2803746 original size:56 final size:56
Alignment explanation
Indices: 2803626--2803746 Score: 156
Period size: 56 Copynumber: 2.2 Consensus size: 56
2803616 ATAAAAGAAT
* * *
2803626 AATGCA-TATGGGTGCATTATTGGTATGAAAGAATACTATAGCTGAAATACATATG
1 AATGCATTATGGGTGCATTATTGGAATGAAAGAATACCATAGATGAAATACATATG
* *
2803681 AATGTATTATGGGTGCATTATTGGAATGAAATG-ATCCCATAGATGAAATACATATG
1 AATGCATTATGGGTGCATTATTGGAATGAAA-GAATACCATAGATGAAATACATATG
**
2803737 GGTGCATTAT
1 AATGCATTAT
2803747 CGGCATAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
55 5 0.09
56 50 0.89
57 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.32
Consensus pattern (56 bp):
AATGCATTATGGGTGCATTATTGGAATGAAAGAATACCATAGATGAAATACATATG
Found at i:2803779 original size:34 final size:34
Alignment explanation
Indices: 2803731--2803871 Score: 95
Period size: 34 Copynumber: 3.8 Consensus size: 34
2803721 AGATGAAATA
*
2803731 CATATGGGTGCATTATCGGCATAAAAGAATAATG
1 CATATGGGTACATTATCGGCATAAAAGAATAATG
*
2803765 CATATGGGTACATTATTGGCATGAAATGACGCCATAGCTGAAATG
1 CATATGGGTACATTATCGGCAT-AAA--A-G--A-A--T--AATG
** *
2803810 CATATGGGTGTATTATCGTCAATAAAAGAATAATG
1 CATATGGGTACATTATCGGC-ATAAAAGAATAATG
* *
2803845 CATATGGGTGA-ATTATTGGCATGAAAG
1 CATATGGGT-ACATTATCGGCATAAAAG
2803872 GATGCCATAA
Statistics
Matches: 84, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
34 26 0.31
35 23 0.27
37 2 0.02
38 1 0.01
39 1 0.01
40 2 0.02
41 1 0.01
42 1 0.01
43 2 0.02
45 23 0.27
46 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (34 bp):
CATATGGGTACATTATCGGCATAAAAGAATAATG
Found at i:2803802 original size:135 final size:135
Alignment explanation
Indices: 2803553--2803825 Score: 386
Period size: 135 Copynumber: 2.0 Consensus size: 135
2803543 GAATAATGCA
* ** * * *
2803553 TATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATAGGTGCATTATTGGCAT
1 TATGGGTGCATTATTGGAATGAAAGGATCCCATAGATGAAATACATATAGGTGCATTATCGGCAT
* * * *
2803618 AAAAGAATAATGCATATGGGTGCATTATTGGTATGAAAGAATACTATAGCTGAAATACATATGAA
66 AAAAGAATAATGCATATGGGTACATTATTGGCATGAAAGAACACCATAGCTGAAATACATATGAA
2803683 TGTAT
131 TGTAT
* *
2803688 TATGGGTGCATTATTGGAATGAAATGATCCCATAGATGAAATACATATGGGTGCATTATCGGCAT
1 TATGGGTGCATTATTGGAATGAAAGGATCCCATAGATGAAATACATATAGGTGCATTATCGGCAT
* * *
2803753 AAAAGAATAATGCATATGGGTACATTATTGGCATGAAATG-ACGCCATAGCTGAAATGCATATGG
66 AAAAGAATAATGCATATGGGTACATTATTGGCATGAAA-GAACACCATAGCTGAAATACATATGA
*
2803817 GTGTAT
130 ATGTAT
2803823 TAT
1 TAT
2803826 CGTCAATAAA
Statistics
Matches: 121, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
135 120 0.99
136 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (135 bp):
TATGGGTGCATTATTGGAATGAAAGGATCCCATAGATGAAATACATATAGGTGCATTATCGGCAT
AAAAGAATAATGCATATGGGTACATTATTGGCATGAAAGAACACCATAGCTGAAATACATATGAA
TGTAT
Found at i:2803819 original size:79 final size:80
Alignment explanation
Indices: 2803688--2803880 Score: 275
Period size: 79 Copynumber: 2.4 Consensus size: 80
2803678 ATGAATGTAT
* *
2803688 TATGGGTGCATTATTGGAATGAAATGATC-CCATAGATGAAATACATATGGGTGCATTATCGGC-
1 TATGGGTACATTATTGGCATGAAATGA-CGCCATAGATGAAATACATATGGGTGCATTATCGGCA
2803751 ATAAAAGAATAATGCA
65 ATAAAAGAATAATGCA
* * * *
2803767 TATGGGTACATTATTGGCATGAAATGACGCCATAGCTGAAATGCATATGGGTGTATTATCGTCAA
1 TATGGGTACATTATTGGCATGAAATGACGCCATAGATGAAATACATATGGGTGCATTATCGGCAA
2803832 TAAAAGAATAATGCA
66 TAAAAGAATAATGCA
* *
2803847 TATGGGTGA-ATTATTGGCATGAAAGGATGCCATA
1 TATGGGT-ACATTATTGGCATGAAATGACGCCATA
2803881 AATAAAATGC
Statistics
Matches: 103, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
78 1 0.01
79 55 0.53
80 46 0.45
81 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (80 bp):
TATGGGTACATTATTGGCATGAAATGACGCCATAGATGAAATACATATGGGTGCATTATCGGCAA
TAAAAGAATAATGCA
Found at i:2803889 original size:80 final size:79
Alignment explanation
Indices: 2803688--2803892 Score: 286
Period size: 80 Copynumber: 2.6 Consensus size: 79
2803678 ATGAATGTAT
* * * *
2803688 TATGGGTGCATTATTGGAATGAAATGATCCCATAGATGAAATACATATGGGTGCATTATCGGCAT
1 TATGGGTGAATTATTGGCATGAAATGATGCCATAGATGAAATGCATATGGGTGCATTATCGGCAT
2803753 AAAAGAATAATGCA
66 AAAAGAATAATGCA
* * * *
2803767 TATGGGT-ACATTATTGGCATGAAATGACGCCATAGCTGAAATGCATATGGGTGTATTATCGTCA
1 TATGGGTGA-ATTATTGGCATGAAATGATGCCATAGATGAAATGCATATGGGTGCATTATCGGC-
2803831 ATAAAAGAATAATGCA
64 ATAAAAGAATAATGCA
* * *
2803847 TATGGGTGAATTATTGGCATGAAAGGATGCCATAAATAAAATGCAT
1 TATGGGTGAATTATTGGCATGAAATGATGCCATAGATGAAATGCAT
2803893 GAAAGGATGC
Statistics
Matches: 110, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
79 54 0.49
80 55 0.50
81 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (79 bp):
TATGGGTGAATTATTGGCATGAAATGATGCCATAGATGAAATGCATATGGGTGCATTATCGGCAT
AAAAGAATAATGCA
Found at i:2803918 original size:80 final size:80
Alignment explanation
Indices: 2803688--2803920 Score: 197
Period size: 80 Copynumber: 2.9 Consensus size: 80
2803678 ATGAATGTAT
* * * * * * * * ***
2803688 TATGGGTGCATTATTGGAATGAAATGATC-CCATAGATGAAATACATATGGGTGCATTATCGGC-
1 TATGGGTACATTATTGGCATGAAAGGA-CGCCATAAATAAAATGCATAAGGATGCATTATAATCA
2803751 ATAAAAGAATAATGCA
65 ATAAAAGAATAATGCA
* ** * * * * **
2803767 TATGGGTACATTATTGGCATGAAATGACGCCATAGCTGAAATGCATATGGGTGTATTATCGTCAA
1 TATGGGTACATTATTGGCATGAAAGGACGCCATAAATAAAATGCATAAGGATGCATTATAATCAA
2803832 TAAAAGAATAATGCA
66 TAAAAGAATAATGCA
*
2803847 TATGGGTGA-ATTATTGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTA-AAT
1 TATGGGT-ACATTATTGGCATGAAAGGACGCCATAAATAAAATGCAT--AAGGATGCATTATAAT
*
2803910 C-ATGAAAGAAT
63 CAATAAAAGAAT
2803921 GGAAAAATTA
Statistics
Matches: 132, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
78 1 0.01
79 55 0.42
80 64 0.48
81 3 0.02
82 9 0.07
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (80 bp):
TATGGGTACATTATTGGCATGAAAGGACGCCATAAATAAAATGCATAAGGATGCATTATAATCAA
TAAAAGAATAATGCA
Found at i:2823879 original size:26 final size:26
Alignment explanation
Indices: 2823845--2823898 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
2823835 AAATATTTGG
*
2823845 TATAATTACACATTTGATCATTGTTA
1 TATAATTACACATTTGATCAATGTTA
2823871 TATAATTACACATTTGATCAATGTTA
1 TATAATTACACATTTGATCAATGTTA
2823897 TA
1 TA
2823899 CATTCTATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (26 bp):
TATAATTACACATTTGATCAATGTTA
Found at i:2831916 original size:22 final size:22
Alignment explanation
Indices: 2831859--2831909 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2831849 GATGGAGATA
2831859 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
2831881 AACGAATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2831903 GACGGAT
1 GACGGAT
2831910 GTTGCCGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.41, T:0.18
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2832051 original size:20 final size:20
Alignment explanation
Indices: 2832026--2832077 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2832016 GTGTTTTGAA
2832026 TTCGAAAATAAAATTCGCGT
1 TTCGAAAATAAAATTCGCGT
2832046 TTCGAAAATAAAATTCGCGT
1 TTCGAAAATAAAATTCGCGT
*
2832066 TGCGAAAATAAA
1 TTCGAAAATAAA
2832078 CGCGCTTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (20 bp):
TTCGAAAATAAAATTCGCGT
Found at i:2832931 original size:21 final size:21
Alignment explanation
Indices: 2832898--2832950 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2832888 GTTAGGGGAG
*
2832898 TTACGTGACGAGGTCAGTGCT
1 TTACGTGACGAGGTCAGTACT
* * *
2832919 TTGCGTGATGAGGTCGGTACT
1 TTACGTGACGAGGTCAGTACT
2832940 TTACGTGACGA
1 TTACGTGACGA
2832951 CAATGGTGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.30
Consensus pattern (21 bp):
TTACGTGACGAGGTCAGTACT
Found at i:2833044 original size:21 final size:21
Alignment explanation
Indices: 2833020--2833059 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2833010 ATGACAATGG
* *
2833020 TACTTTACGTGGTGAGGTATC
1 TACTTTACATGATGAGGTATC
2833041 TACTTTACATGATGAGGTA
1 TACTTTACATGATGAGGTA
2833060 GTCGCTCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (21 bp):
TACTTTACATGATGAGGTATC
Found at i:2833376 original size:21 final size:21
Alignment explanation
Indices: 2833347--2833422 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
2833337 ATTCACTTGT
2833347 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * **
2833368 CATCATTCAAGATGCCCCTGT
1 CATCGTTCAAGAGGCCCCTCC
**
2833389 CATCGTTCAAGAGGTTCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
2833410 CACCGTTCAAGAG
1 CATCGTTCAAGAG
2833423 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:2833391 original size:42 final size:41
Alignment explanation
Indices: 2833344--2833425 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 41
2833334 CTGATTCACT
*
2833344 TGTCATCGTTCAAGAGGCCCCTCCCATCATTCAAGATGCCCC
1 TGTCATCGTTCAAGAGGCCCCTCCCACCATTCAAGA-GCCCC
** *
2833386 TGTCATCGTTCAAGAGGTTCCTCCCACCGTTCAAGAGCCC
1 TGTCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGCCC
2833426 GATTCACATG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 4 0.11
42 32 0.89
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (41 bp):
TGTCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGCCCC
Found at i:2835005 original size:29 final size:29
Alignment explanation
Indices: 2834907--2835006 Score: 69
Period size: 29 Copynumber: 3.5 Consensus size: 29
2834897 AACGCAAATC
** *
2834907 AAATTCACGTTGCGATTGTTACGAAAGTA
1 AAATTCACAATGCGATTGTTGCGAAAGTA
** ** * *
2834936 AAATTTGCAATGC-A-AATAGCGAAAGTC
1 AAATTCACAATGCGATTGTTGCGAAAGTA
****
2834963 AAATTCGTGTTGCGATTGTTGCGAAAGTA
1 AAATTCACAATGCGATTGTTGCGAAAGTA
2834992 AAATTCACAATGCGA
1 AAATTCACAATGCGA
2835007 AAGTCAAATT
Statistics
Matches: 48, Mismatches: 21, Indels: 4
0.66 0.29 0.05
Matches are distributed among these distances:
27 17 0.35
28 2 0.04
29 29 0.60
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (29 bp):
AAATTCACAATGCGATTGTTGCGAAAGTA
Found at i:2835087 original size:20 final size:20
Alignment explanation
Indices: 2835015--2835090 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
2835005 GAAAGTCAAA
* * *
2835015 TTCGTGTTGTGAATTTGATTT
1 TTCGCGTTGCGAATTTGA-CT
**
2835036 TTCGCGTTTTGAATTTGACT
1 TTCGCGTTGCGAATTTGACT
*** *
2835056 TTCGCAACGCGAATTTGAGT
1 TTCGCGTTGCGAATTTGACT
2835076 TTCGCGTTGCGAATT
1 TTCGCGTTGCGAATT
2835091 CAAGGAAAAC
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.17, C:0.14, G:0.24, T:0.45
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTGACT
Found at i:2835315 original size:18 final size:18
Alignment explanation
Indices: 2835292--2835327 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2835282 AAGCCGGTTA
2835292 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
2835310 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
2835328 CCTTTTGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:2838665 original size:20 final size:21
Alignment explanation
Indices: 2838560--2838673 Score: 87
Period size: 20 Copynumber: 5.6 Consensus size: 21
2838550 AAATAAAACC
*
2838560 TGTTGCGAAATT-ATAATTCA-
1 TGTTGCGAATTTGA-AATTCAG
* *
2838580 TGTTGCGAATTCGAAAATC-G
1 TGTTGCGAATTTGAAATTCAG
* * *
2838600 AGTTACGAATTCAGAAA-TC-G
1 TGTTGCGAATT-TGAAATTCAG
*
2838620 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTCAG
* *
2838641 TGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTCAG
2838661 TGTTGCGAATTTG
1 TGTTGCGAATTTG
2838674 GAAAATCGCA
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
19 4 0.05
20 56 0.72
21 18 0.23
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (21 bp):
TGTTGCGAATTTGAAATTCAG
Found at i:2839311 original size:19 final size:19
Alignment explanation
Indices: 2839289--2839353 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 19
2839279 CCATAAATAC
2839289 ATCAAACTAACATATTACA
1 ATCAAACTAACATATTACA
* *
2839308 ATCAAAGTAACA-ATCCACA
1 ATCAAACTAACATAT-TACA
2839327 TATACACCAACTAACATATTACA
1 -AT-CA--AACTAACATATTACA
2839350 ATCA
1 ATCA
2839354 TTCATGAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
18 2 0.06
19 14 0.39
20 2 0.06
21 4 0.11
22 2 0.06
23 10 0.28
24 2 0.06
ACGTcount: A:0.51, C:0.25, G:0.02, T:0.23
Consensus pattern (19 bp):
ATCAAACTAACATATTACA
Found at i:2839349 original size:42 final size:43
Alignment explanation
Indices: 2839272--2839353 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 43
2839262 TAATATAAAA
*
2839272 TAACAATCCATAAATACATCAAACTAACATATTACAATCAAAG
1 TAACAATCCACAAATACATCAAACTAACATATTACAATCAAAG
* *
2839315 TAACAATCCACATATACA-CCAACTAACATATTACAATCA
1 TAACAATCCACAAATACATCAAACTAACATATTACAATCA
2839354 TTCATGAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 20 0.56
43 16 0.44
ACGTcount: A:0.51, C:0.24, G:0.01, T:0.23
Consensus pattern (43 bp):
TAACAATCCACAAATACATCAAACTAACATATTACAATCAAAG
Found at i:2842622 original size:49 final size:48
Alignment explanation
Indices: 2842563--2842816 Score: 258
Period size: 49 Copynumber: 5.2 Consensus size: 48
2842553 TCATGTCGAT
* * *
2842563 AATGCACCGTTCTTCATCTAACTTGTATTAGAGACACCTTTTTGCCAAA
1 AATGCACCGTT-TTCATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
** * * * *
2842612 AATGCACCGTTAGGCATTTACCTTGAATTAGTGACACCTTTCTGCCAAG
1 AATGCACCGTT-TTCATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
* * * * *
2842661 AATGCATCATTTTCATCTAACTTGCATTAGTGGCACATTTCTGCAAAA
1 AATGCACCGTTTTCATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
* * * * *
2842709 AATGCACCGTTAGGT-ATTTAACTTGCATTAGTGGCACCTTTCTACCAAG
1 AATGCACCGTT--TTCATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
* * * *
2842758 AATGCATCATTTTCATCTAACTTTCATTAGTGACACCTTTATGCCAAA
1 AATGCACCGTTTTCATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
2842806 AATGCACCGTT
1 AATGCACCGTT
2842817 AGGTATTTAA
Statistics
Matches: 163, Mismatches: 39, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
47 1 0.01
48 74 0.45
49 87 0.53
50 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (48 bp):
AATGCACCGTTTTCATCTAACTTGCATTAGTGACACCTTTCTGCCAAA
Found at i:2842741 original size:97 final size:97
Alignment explanation
Indices: 2842575--2842826 Score: 387
Period size: 97 Copynumber: 2.6 Consensus size: 97
2842565 TGCACCGTTC
* * * * *
2842575 TTCATCTAACTTGTATTAGAGACACCTTTTTGCCAAAAATGCACCGTTAGGCATTTACCTTGAAT
1 TTCATCTAACTTGCATTAGTGACACCTTTATGCCAAAAATGCACCGTTAGGTATTTAACTTGAAT
*
2842640 TAGTGACACCTTTCTGCCAAGAATGCATCATT
66 TAGTGACACCTTTCTACCAAGAATGCATCATT
* * * * *
2842672 TTCATCTAACTTGCATTAGTGGCACATTTCTGCAAAAAATGCACCGTTAGGTATTTAACTTGCAT
1 TTCATCTAACTTGCATTAGTGACACCTTTATGCCAAAAATGCACCGTTAGGTATTTAACTTGAAT
*
2842737 TAGTGGCACCTTTCTACCAAGAATGCATCATT
66 TAGTGACACCTTTCTACCAAGAATGCATCATT
*
2842769 TTCATCTAACTTTCATTAGTGACACCTTTATGCCAAAAATGCACCGTTAGGTATTTAA
1 TTCATCTAACTTGCATTAGTGACACCTTTATGCCAAAAATGCACCGTTAGGTATTTAA
2842827 AAGAGGTTGC
Statistics
Matches: 139, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 139 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (97 bp):
TTCATCTAACTTGCATTAGTGACACCTTTATGCCAAAAATGCACCGTTAGGTATTTAACTTGAAT
TAGTGACACCTTTCTACCAAGAATGCATCATT
Found at i:2842900 original size:54 final size:54
Alignment explanation
Indices: 2842831--2843121 Score: 440
Period size: 54 Copynumber: 5.4 Consensus size: 54
2842821 ATTTAAAAGA
* * * **
2842831 GGTTGCACACTTAGTGCCTATACAGTTGTTCATCAACATATGATGAATTTTGTG
1 GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
* *
2842885 AGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTG
1 GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
* *
2842939 GGTTGCACAAATAGTGCCTATACGGTCGTTCATCAACATATGGTGAATTCCGTG
1 GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
* *
2842993 GGTTGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTCCGTC
1 GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
* * *
2843047 GGTTGCACATATA-TGCCTACACGGTCGTTCATCAACATATGATGAATTCCATG
1 GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
*
2843100 GGTTGTACACATAGTGCCTATA
1 GGTTGCACACATAGTGCCTATA
2843122 GTACACTTAA
Statistics
Matches: 215, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
53 47 0.22
54 168 0.78
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (54 bp):
GGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTG
Found at i:2842923 original size:27 final size:27
Alignment explanation
Indices: 2842893--2842978 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
2842883 TGAGTTGCAC
2842893 ACATAGTGCCTATACGGTCGTTCATCA
1 ACATAGTGCCTATACGGTCGTTCATCA
** * *
2842920 ACATATGATGAAT-TTC-GTGGGTTGCA-CA
1 ACATA-G-TGCCTATACGGT-CGTT-CATCA
2842948 A-ATAGTGCCTATACGGTCGTTCATCA
1 ACATAGTGCCTATACGGTCGTTCATCA
2842974 ACATA
1 ACATA
2842979 TGGTGAATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
25 5 0.12
26 9 0.21
27 15 0.35
28 9 0.21
29 5 0.12
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (27 bp):
ACATAGTGCCTATACGGTCGTTCATCA
Found at i:2849655 original size:14 final size:14
Alignment explanation
Indices: 2849617--2849657 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
2849607 AAATATTGAT
*
2849617 TTAATTTTGGACTG
1 TTAATTTTGGGCTG
2849631 TTAATTTTGGGCTG
1 TTAATTTTGGGCTG
2849645 TTAATTTTGGGCT
1 TTAATTTTGGGCT
2849658 AGTTTGTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.51
Consensus pattern (14 bp):
TTAATTTTGGGCTG
Found at i:2852425 original size:3 final size:3
Alignment explanation
Indices: 2852417--2852442 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2852407 AACGGTGCCA
2852417 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
2852443 ATGATGCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:2853147 original size:14 final size:15
Alignment explanation
Indices: 2853119--2853155 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2853109 ACACTAACAT
2853119 AATATAATTCCATAA
1 AATATAATTCCATAA
*
2853134 AATA-AATTCTATAA
1 AATATAATTCCATAA
2853148 AATATAAT
1 AATATAAT
2853156 CGATGCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATAATTCCATAA
Found at i:2864585 original size:28 final size:28
Alignment explanation
Indices: 2864551--2864613 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
2864541 TCATCTCATG
2864551 AGTGATAAGGAAGCCAATAAGTTCATCA
1 AGTGATAAGGAAGCCAATAAGTTCATCA
*
2864579 AGTGATAAGGGAGCCAATAAGTTCATCA
1 AGTGATAAGGAAGCCAATAAGTTCATCA
2864607 AGTGATA
1 AGTGATA
2864614 GAGTTTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (28 bp):
AGTGATAAGGAAGCCAATAAGTTCATCA
Found at i:2866103 original size:63 final size:62
Alignment explanation
Indices: 2866004--2866128 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 62
2865994 ACTTCAGGAC
2866004 CAAATGTTCAAAATAAAATGTGCATGGCCATGACATTTTGTTAATATTTTCTTCTATTCTTTG
1 CAAATGTTCAAAATAAAATGTGCATGGCCATGACATTTTGTTAATA-TTTCTTCTATTCTTTG
2866067 CAAATGTTCAAAATAAAATGTGCATGGCCATGACATTTTGTTAATATTTCTTCTATTCTTTG
1 CAAATGTTCAAAATAAAATGTGCATGGCCATGACATTTTGTTAATATTTCTTCTATTCTTTG
2866129 TCACTCCCTC
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 16 0.26
63 46 0.74
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (62 bp):
CAAATGTTCAAAATAAAATGTGCATGGCCATGACATTTTGTTAATATTTCTTCTATTCTTTG
Found at i:2867299 original size:29 final size:29
Alignment explanation
Indices: 2867237--2867320 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
2867227 ACCGTTGACT
* ***
2867237 GGTGATATTCTGGGAATTAATTTGATTTTA
1 GGTGCTATTCTGGGAATTAATTT-AAAATA
2867267 -GTGCTATTCTGGGAATTAATTTAAAATA
1 GGTGCTATTCTGGGAATTAATTTAAAATA
* * *
2867295 GGTGCTATTTTGGTAATT-TTTTAAAA
1 GGTGCTATTCTGGGAATTAATTTAAAA
2867321 AGGGGTGCTG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 10 0.22
29 36 0.78
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTTAAAATA
Found at i:2868733 original size:17 final size:18
Alignment explanation
Indices: 2868711--2868745 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2868701 CTGTATTATT
2868711 AATATTT-TGTTCTATAC
1 AATATTTATGTTCTATAC
2868728 AATATTTAATGTTCTATA
1 AATATTT-ATGTTCTATA
2868746 AGTTATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (18 bp):
AATATTTATGTTCTATAC
Found at i:2874183 original size:223 final size:223
Alignment explanation
Indices: 2873797--2874238 Score: 852
Period size: 223 Copynumber: 2.0 Consensus size: 223
2873787 TGGAAATCAG
2873797 AAACCAATTCCTCCCAAATTCCCTCTCCCAACCTCAACTTCCGACGACGATCATGACGCCGTCTG
1 AAACCAATTCCTCCCAAATTCCCTCTCCCAACCTCAACTTCCGACGACGATCATGACGCCGTCTG
2873862 AATTCGATAGCCGTTTTGAAAGTACATCGTGTTCGTTATCAAGTCAGGAACAATCCCCTTAAATT
66 AATTCGATAGCCGTTTTGAAAGTACATCGTGTTCGTTATCAAGTCAGGAACAATCCCCTTAAATT
2873927 AATTGAAGCGAAACGTTGCCAAACGCCGTGAATTTCAAGTCAAAGCATCGACATTTTTTTAGCTC
131 AATTGAAGCGAAACGTTGCCAAACGCCGTGAATTTCAAGTCAAAGCATCGACATTTTTTTAGCTC
2873992 AATCGCCTAG-AAATCA-AAATTCCAGA
196 AATCGCCTAGAAAATCATAAATTCCAGA
2874018 AAACCAATTCCTCCCAAATTCCCTCTCCCAACCTCAACTTCCGACGACGATCATGACGCCGTCTG
1 AAACCAATTCCTCCCAAATTCCCTCTCCCAACCTCAACTTCCGACGACGATCATGACGCCGTCTG
2874083 AATTCCGATAGCCGTTTTGAAAGTACCATCGTGTTCGTTATCAAGTCAGGAACAATCCCCTTAAA
66 AATT-CGATAGCCGTTTTGAAAGTA-CATCGTGTTCGTTATCAAGTCAGGAACAATCCCCTTAAA
2874148 TTAATTGAAGCGAAACGTTGCCAAACGCCGTGAATTTCAAGTCAAAGCATCGACATTTTTTTAGC
129 TTAATTGAAGCGAAACGTTGCCAAACGCCGTGAATTTCAAGTCAAAGCATCGACATTTTTTTAGC
2874213 TCAATCGCCTAGAAAATCATAAATTC
194 TCAATCGCCTAGAAAATCATAAATTC
2874239 ATCGTCGATC
Statistics
Matches: 217, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
221 69 0.32
222 20 0.09
223 116 0.53
224 6 0.03
225 6 0.03
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.26
Consensus pattern (223 bp):
AAACCAATTCCTCCCAAATTCCCTCTCCCAACCTCAACTTCCGACGACGATCATGACGCCGTCTG
AATTCGATAGCCGTTTTGAAAGTACATCGTGTTCGTTATCAAGTCAGGAACAATCCCCTTAAATT
AATTGAAGCGAAACGTTGCCAAACGCCGTGAATTTCAAGTCAAAGCATCGACATTTTTTTAGCTC
AATCGCCTAGAAAATCATAAATTCCAGA
Found at i:2874439 original size:32 final size:33
Alignment explanation
Indices: 2874374--2874441 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
2874364 GTTTCTGATA
2874374 TGATGAAATCGAGCTCTATGCTGTTCAAAAATT
1 TGATGAAATCGAGCTCTATGCTGTTCAAAAATT
2874407 TGATGAAATCGAGCTCTATGCTG-TCAAAAATT
1 TGATGAAATCGAGCTCTATGCTGTTCAAAAATT
2874439 TGA
1 TGA
2874442 ACCGATCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 12 0.34
33 23 0.66
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (33 bp):
TGATGAAATCGAGCTCTATGCTGTTCAAAAATT
Found at i:2874650 original size:22 final size:22
Alignment explanation
Indices: 2874625--2874684 Score: 76
Period size: 17 Copynumber: 3.0 Consensus size: 22
2874615 GAACCGGTCC
2874625 GACCCGACCCGACCGTTGACCT
1 GACCCGACCCGACCGTTGACCT
2874647 -----GACCCGACCGTTGACCT
1 GACCCGACCCGACCGTTGACCT
*
2874664 GACCCGACCCGATCGTTGACC
1 GACCCGACCCGACCGTTGACC
2874685 GTTAACCGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
17 17 0.53
22 15 0.47
ACGTcount: A:0.18, C:0.43, G:0.23, T:0.15
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCT
Found at i:2874684 original size:17 final size:17
Alignment explanation
Indices: 2874625--2874672 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
2874615 GAACCGGTCC
*
2874625 GACCCGACCCGACCGTT
1 GACCTGACCCGACCGTT
2874642 GACCTGACCCGACCGTT
1 GACCTGACCCGACCGTT
2874659 GACCTGACCCGACC
1 GACCTGACCCGACC
2874673 CGATCGTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (17 bp):
GACCTGACCCGACCGTT
Found at i:2875928 original size:117 final size:117
Alignment explanation
Indices: 2875718--2876001 Score: 410
Period size: 117 Copynumber: 2.4 Consensus size: 117
2875708 GTATTTCAGG
* * * *
2875718 CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTCACTGGTGTACAGGTGGGTGTATGGTTCTGGGGAA
1 CTCCTTTGCTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGAGGAA
* * * *
2875783 CCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGA
66 CCTACACATTGTAGTGAGTGAAGCGACTGGATGGAGAACTTATTACTGCAGA
* *
2875835 CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAAGTGGGTGTATGGTTCTGAGGAA
1 CTCCTTTGCTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGAGGAA
* *
2875900 CCTACACATTGTAGTGA-TGAAAGCGACTGGATGGAGACCTTATTACTGCAGG
66 CCTACACATTGTAGTGAGTG-AAGCGACTGGATGGAGAACTTATTACTGCAGA
**
2875952 CTCCTCAGCT-TCGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTG
1 CTCCTTTGCTGT-GTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTG
2876002 CATTTTTCGG
Statistics
Matches: 149, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
116 3 0.02
117 146 0.98
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (117 bp):
CTCCTTTGCTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGAGGAA
CCTACACATTGTAGTGAGTGAAGCGACTGGATGGAGAACTTATTACTGCAGA
Found at i:2876908 original size:20 final size:19
Alignment explanation
Indices: 2876883--2876937 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
2876873 ATTGGAATAG
2876883 GGGGTTTAGAAACCAAGAAA
1 GGGGTTTAGAAACCAAG-AA
*
2876903 GGGGTTTAGAAACCAAGCA
1 GGGGTTTAGAAACCAAGAA
*
2876922 GGTGGTTTTGAAACCA
1 GG-GGTTTAGAAACCA
2876938 TAAGGAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (19 bp):
GGGGTTTAGAAACCAAGAA
Found at i:2878833 original size:24 final size:24
Alignment explanation
Indices: 2878816--2878916 Score: 125
Period size: 24 Copynumber: 4.2 Consensus size: 24
2878806 ATCAAAACAT
2878816 AATTCAGGTCAAGTATCAGATCAG
1 AATTCAGGTCAAGTATCAGATCAG
*
2878840 AA-TCTAGGTCATGTATCAGATCAG
1 AATTC-AGGTCAAGTATCAGATCAG
* *
2878864 AATCCATGTC-AGTATCAGATCAG
1 AATTCAGGTCAAGTATCAGATCAG
* * *
2878887 AATCCAGGTCAAGTATCATAACAG
1 AATTCAGGTCAAGTATCAGATCAG
2878911 AATTCA
1 AATTCA
2878917 AATCAGAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
23 23 0.35
24 42 0.64
25 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (24 bp):
AATTCAGGTCAAGTATCAGATCAG
Found at i:2891160 original size:34 final size:32
Alignment explanation
Indices: 2891070--2891161 Score: 80
Period size: 34 Copynumber: 2.8 Consensus size: 32
2891060 TGTAATGCCC
*
2891070 ATTC-TTC-CTGTATTGTTTCTTATTATTGTACT
1 ATTCTTTCACTGTATTG-TTCTT-TTAATGTACT
** * *
2891102 ATTCTTTTTCTGTACTGTTCCTTTTAATGTATT
1 ATTCTTTCACTGTATTGTT-CTTTTAATGTACT
2891135 ATTCATTTCACTGTATTGTATCTTTTA
1 ATTC-TTTCACTGTATTGT-TCTTTTA
2891162 CTATACAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
32 4 0.08
33 16 0.33
34 27 0.56
35 1 0.02
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (32 bp):
ATTCTTTCACTGTATTGTTCTTTTAATGTACT
Found at i:2891509 original size:40 final size:39
Alignment explanation
Indices: 2891454--2891554 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 39
2891444 CGTGAAACCC
2891454 ATAATGCACATGTAGTGTCATAACGCAAATAAAGTGCCA
1 ATAATGCACATGTAGTGTCATAACGCAAATAAAGTGCCA
* * * **
2891493 GATAATGTACATGTAGTGTCAGATCGCACTTAAAGTGCCA
1 -ATAATGCACATGTAGTGTCATAACGCAAATAAAGTGCCA
*
2891533 A-AATGCACATATAGTG-CATAAC
1 ATAATGCACATGTAGTGTCATAAC
2891555 ATATGCACAC
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
37 4 0.08
38 13 0.25
39 1 0.02
40 34 0.65
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (39 bp):
ATAATGCACATGTAGTGTCATAACGCAAATAAAGTGCCA
Found at i:2893631 original size:20 final size:22
Alignment explanation
Indices: 2893582--2893632 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2893572 CCATAAACCC
*
2893582 TAACCTTTACCAATTTCATCTT
1 TAACCATTACCAATTTCATCTT
* *
2893604 TAAACATTACCAA-TTGAT-TT
1 TAACCATTACCAATTTCATCTT
2893624 TAACCATTA
1 TAACCATTA
2893633 TTCAAGCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 10 0.40
21 4 0.16
22 11 0.44
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (22 bp):
TAACCATTACCAATTTCATCTT
Found at i:2899147 original size:3 final size:3
Alignment explanation
Indices: 2899126--2899163 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2899116 GTTAACCATA
* *
2899126 TTC TTC TTT TTC TTA TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2899164 TTTTACATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:2899240 original size:15 final size:16
Alignment explanation
Indices: 2899215--2899246 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2899205 TCATTAACTC
2899215 TATTCTTTCTTCTTCT
1 TATTCTTTCTTCTTCT
2899231 TATT-TTTCTTCTTCT
1 TATTCTTTCTTCTTCT
2899246 T
1 T
2899247 TTTCACATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTCTTTCTTCTTCT
Found at i:2901384 original size:13 final size:14
Alignment explanation
Indices: 2901356--2901388 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2901346 TTCATAAATA
2901356 ATAATATTTATAAT
1 ATAATATTTATAAT
*
2901370 ATAATA-TTATTAT
1 ATAATATTTATAAT
2901383 ATAATA
1 ATAATA
2901389 ATCATCACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAATATTTATAAT
Found at i:2901896 original size:43 final size:45
Alignment explanation
Indices: 2901797--2901898 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
2901787 AATCTAATTT
* * * *
2901797 CACTACTCTTCCGT-GAATATCAAATTCAAAGTTGAATTTGCTTC
1 CACTACTCTTTCGTGGAATATCAAACTCAAACTTGAATTTACTTC
* * *
2901841 CACTACTTTTTCGTGGAATTTCAAACTCAAACTTGGA-TTAC-TC
1 CACTACTCTTTCGTGGAATATCAAACTCAAACTTGAATTTACTTC
2901884 CACTACTCTTTCGTG
1 CACTACTCTTTCGTG
2901899 AAGTTCTCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 16 0.33
44 15 0.31
45 18 0.37
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (45 bp):
CACTACTCTTTCGTGGAATATCAAACTCAAACTTGAATTTACTTC
Found at i:2901934 original size:46 final size:43
Alignment explanation
Indices: 2901882--2902032 Score: 136
Period size: 46 Copynumber: 3.5 Consensus size: 43
2901872 CTTGGATTAC
2901882 TCCACTACTCTTTCGTGAAGTTCTCATACTTTGCTGAAAACTCTGT
1 TCCACTACTCTTTCGTGAAGTT-TCATACTTTGCTGAAAA-TC-GT
* * ***
2901928 TCCACTACTCTTTCATGGAG-TTCATA-TTTGCT-TTTA-C-T
1 TCCACTACTCTTTCGTGAAGTTTCATACTTTGCTGAAAATCGT
2901966 T-CACTACTCTTAT-GTGAAGATTTCATACTTTGCTGAAAAATCCGT
1 TCCACTACTCTT-TCGTGAAG-TTTCATACTTTGCTG-AAAAT-CGT
*
2902011 TCCACTACTCTTTCGTGGAGTT
1 TCCACTACTCTTTCGTGAAGTT
2902033 CAAATTTTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
37 14 0.17
38 3 0.04
39 6 0.07
40 7 0.08
42 2 0.02
43 6 0.07
44 6 0.07
45 6 0.07
46 33 0.40
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (43 bp):
TCCACTACTCTTTCGTGAAGTTTCATACTTTGCTGAAAATCGT
Found at i:2901983 original size:83 final size:83
Alignment explanation
Indices: 2901878--2902039 Score: 247
Period size: 83 Copynumber: 2.0 Consensus size: 83
2901868 CAAACTTGGA
* *
2901878 TTACTCCACTACTCTTTCGTGAAG-TTCTCATACTTTGCTGAAAACTCTGTTCCACTACTCTTTC
1 TTACTCCACTACTCTTTCGTGAAGATT-TCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTC
*
2901942 ATGGAGTTCATATTTGCTT
65 ATGGAGTTCAAATTTGCTT
*
2901961 TTACTTCACTACTCTTAT-GTGAAGATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTC
1 TTACTCCACTACTCTT-TCGTGAAGATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTC
*
2902025 GTGGAGTTCAAATTT
65 ATGGAGTTCAAATTT
2902040 TTATTTTGCT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
83 69 0.96
84 3 0.04
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (83 bp):
TTACTCCACTACTCTTTCGTGAAGATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTCA
TGGAGTTCAAATTTGCTT
Found at i:2902600 original size:22 final size:22
Alignment explanation
Indices: 2902575--2902623 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2902565 AATAAAGCTT
*
2902575 TCATCTTTGAAAAGAGAATCTA
1 TCATCGTTGAAAAGAGAATCTA
2902597 TCATCGTTGAAAAGAGAATCTA
1 TCATCGTTGAAAAGAGAATCTA
2902619 TCATC
1 TCATC
2902624 CTTGCAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (22 bp):
TCATCGTTGAAAAGAGAATCTA
Found at i:2902828 original size:56 final size:56
Alignment explanation
Indices: 2902713--2902829 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 56
2902703 GAAACAGATT
* *
2902713 ACAAGAAGGATTTATCCTAATTCCTTTCATGTGTCCACATCTAATCTAATCTTTTA
1 ACAAGAAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCTAATCTTTGA
* *
2902769 ACAAGAATGATTTTATCTTAATTCCTTTCATGTCTCCACATCTAATC-AGAT-TTTGA
1 ACAAGAAGGA-TTTATCCTAATTCCTTTCATGTCTCCACATCTAATCTA-ATCTTTGA
2902825 ACAAG
1 ACAAG
2902830 GTTTTCCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
56 19 0.35
57 36 0.65
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (56 bp):
ACAAGAAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCTAATCTTTGA
Found at i:2910844 original size:65 final size:65
Alignment explanation
Indices: 2910711--2910918 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 65
2910701 TGTACTAAAA
* * *
2910711 GTGCATCGATGCATAAAATGCACTCGATG-TTTCAAAATAGCCTGAGTGTATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGCTG
* *
2910775 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGGATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCGATGCATGGCT
*
2910838 AT
65 -G
* * * *
2910840 GTGCATCGATGCATGAAATGCATTCGATG--TTCAATTTATTCCATG-GTGCATCGATGCATGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAA--AATACCCTGAGTGCATCGATGCATGG-
*
2910902 TTG
63 CTG
2910905 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2910919 GGATTGGTGC
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 44 0.35
65 71 0.57
66 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGCTG
Found at i:2910908 original size:20 final size:20
Alignment explanation
Indices: 2910883--2910938 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
2910873 ATTTATTCCA
2910883 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
2910903 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
*
2910923 TGGTGCATCGGTGCAT
1 TGGTGCATCGATGCAT
2910939 TACTTTGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:2913635 original size:23 final size:22
Alignment explanation
Indices: 2913605--2913686 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
2913595 GCATGGCCTT
2913605 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
2913627 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
2913649 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
2913672 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
2913687 TGTTAAGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 19 0.40
24 12 0.25
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:2913697 original size:44 final size:44
Alignment explanation
Indices: 2913609--2913706 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 44
2913599 GGCCTTGTGC
* *
2913609 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATAGTGT
*
2913653 ATCGATGCACATTCAAAGG-GATGCATCGATGCA-CTGTTA-AGTGT
1 ATCGATGCACATTC-AAGGCG-TGCATCGATGCACCT-TCATAGTGT
2913697 ATCGATGCAC
1 ATCGATGCAC
2913707 TAAGCACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 31 0.65
45 17 0.35
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATAGTGT
Found at i:2915567 original size:398 final size:398
Alignment explanation
Indices: 2914831--2915630 Score: 1600
Period size: 398 Copynumber: 2.0 Consensus size: 398
2914821 CCATCATGCT
2914831 CATCTCGAATTCACTTTGCATTAGCTTAGAAATTTCTTGACAAAGAACCTCATTAGTAGAACCAA
1 CATCTCGAATTCACTTTGCATTAGCTTAGAAATTTCTTGACAAAGAACCTCATTAGTAGAACCAA
2914896 ATATTATATCATCAACATAAATTTGAACTACTAATAAATATTTACCTTTATTCTTTAAAAACAAT
66 ATATTATATCATCAACATAAATTTGAACTACTAATAAATATTTACCTTTATTCTTTAAAAACAAT
2914961 GTATTGTCAACCTTCCATTTGGAAAAACCTTTTTCAATTAAAAAGTTTGACAATATTTCATACCG
131 GTATTGTCAACCTTCCATTTGGAAAAACCTTTTTCAATTAAAAAGTTTGACAATATTTCATACCG
2915026 AGCTCTAGGTGCTTGTTTTAAGCCATAAAGCACTTTTATCAATTTAAGAACATGATTTGGAAATT
196 AGCTCTAGGTGCTTGTTTTAAGCCATAAAGCACTTTTATCAATTTAAGAACATGATTTGGAAATT
2915091 TTAAATCTTCAAAACCAGGAGGTTGTTCCACATACACTTCTTCCTTTATAAAACCATTTAAAATG
261 TTAAATCTTCAAAACCAGGAGGTTGTTCCACATACACTTCTTCCTTTATAAAACCATTTAAAATG
2915156 CACTTTTAACATCCATTTGATATAATTTAAATTCATGAAAACATGCAAATGCTAATAACATTCTA
326 CACTTTTAACATCCATTTGATATAATTTAAATTCATGAAAACATGCAAATGCTAATAACATTCTA
2915221 ATTGCTTC
391 ATTGCTTC
2915229 CATCTCGAATTCACTTTGCATTAGCTTAGAAATTTCTTGACAAAGAACCTCATTAGTAGAACCAA
1 CATCTCGAATTCACTTTGCATTAGCTTAGAAATTTCTTGACAAAGAACCTCATTAGTAGAACCAA
2915294 ATATTATATCATCAACATAAATTTGAACTACTAATAAATATTTACCTTTATTCTTTAAAAACAAT
66 ATATTATATCATCAACATAAATTTGAACTACTAATAAATATTTACCTTTATTCTTTAAAAACAAT
2915359 GTATTGTCAACCTTCCATTTGGAAAAACCTTTTTCAATTAAAAAGTTTGACAATATTTCATACCG
131 GTATTGTCAACCTTCCATTTGGAAAAACCTTTTTCAATTAAAAAGTTTGACAATATTTCATACCG
2915424 AGCTCTAGGTGCTTGTTTTAAGCCATAAAGCACTTTTATCAATTTAAGAACATGATTTGGAAATT
196 AGCTCTAGGTGCTTGTTTTAAGCCATAAAGCACTTTTATCAATTTAAGAACATGATTTGGAAATT
2915489 TTAAATCTTCAAAACCAGGAGGTTGTTCCACATACACTTCTTCCTTTATAAAACCATTTAAAATG
261 TTAAATCTTCAAAACCAGGAGGTTGTTCCACATACACTTCTTCCTTTATAAAACCATTTAAAATG
2915554 CACTTTTAACATCCATTTGATATAATTTAAATTCATGAAAACATGCAAATGCTAATAACATTCTA
326 CACTTTTAACATCCATTTGATATAATTTAAATTCATGAAAACATGCAAATGCTAATAACATTCTA
2915619 ATTGCTTC
391 ATTGCTTC
2915627 CATC
1 CATC
2915631 CTAGCTACGG
Statistics
Matches: 402, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
398 402 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (398 bp):
CATCTCGAATTCACTTTGCATTAGCTTAGAAATTTCTTGACAAAGAACCTCATTAGTAGAACCAA
ATATTATATCATCAACATAAATTTGAACTACTAATAAATATTTACCTTTATTCTTTAAAAACAAT
GTATTGTCAACCTTCCATTTGGAAAAACCTTTTTCAATTAAAAAGTTTGACAATATTTCATACCG
AGCTCTAGGTGCTTGTTTTAAGCCATAAAGCACTTTTATCAATTTAAGAACATGATTTGGAAATT
TTAAATCTTCAAAACCAGGAGGTTGTTCCACATACACTTCTTCCTTTATAAAACCATTTAAAATG
CACTTTTAACATCCATTTGATATAATTTAAATTCATGAAAACATGCAAATGCTAATAACATTCTA
ATTGCTTC
Found at i:2919915 original size:63 final size:65
Alignment explanation
Indices: 2919846--2919967 Score: 176
Period size: 63 Copynumber: 1.9 Consensus size: 65
2919836 ACTAAGAGTG
* * *
2919846 CATCGATGCATAAAATGCATTGGATG-TTTCA-AAATAACTGAGTGTATCGATGCATGGCTGGTT
1 CATCGATGCATAAAATGCATTCGATGTTTTCATAAAGAACTGAGTGCATCGATGCATGGCTGGTT
* **
2919909 CATCGATGCATCAAATGCATTCGATGTTTTCATAAAGCCCTGAGTGCATCGATGCATGG
1 CATCGATGCATAAAATGCATTCGATGTTTTCATAAAGAACTGAGTGCATCGATGCATGG
2919968 TATATGCATC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
63 24 0.47
64 5 0.10
65 22 0.43
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (65 bp):
CATCGATGCATAAAATGCATTCGATGTTTTCATAAAGAACTGAGTGCATCGATGCATGGCTGGTT
Found at i:2920001 original size:65 final size:65
Alignment explanation
Indices: 2919844--2919984 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 65
2919834 GCACTAAGAG
* * * *
2919844 TGCATCGATGCATAAAATGCATTGGATG-TTTCAAAATAACTGAGTGTATCGATGCATGGCTGGT
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAGAACTGAGTGCATCGATGCATGGCTGAT
* **
2919908 T-CATCGATGCATCAAATGCATTCGATGTTTTCATAAAGCCCTGAGTGCATCGATGCATGG-T-A
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAAGAACTGAGTGCATCGATGCATGGCTGA
2919970 T
65 T
2919971 ATGCATCGATGCAT
1 -TGCATCGATGCAT
2919985 GAAGTGCTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
63 25 0.38
64 8 0.12
65 33 0.50
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAGAACTGAGTGCATCGATGCATGGCTGAT
Found at i:2922399 original size:21 final size:21
Alignment explanation
Indices: 2922366--2922406 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2922356 CTTGCATCTG
2922366 AATCGCGCATGTGTGCCTTGT
1 AATCGCGCATGTGTGCCTTGT
* *
2922387 AATCGGGCCTGTGTGCCTTG
1 AATCGCGCATGTGTGCCTTG
2922407 CTTTGTAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.32, T:0.32
Consensus pattern (21 bp):
AATCGCGCATGTGTGCCTTGT
Found at i:2924724 original size:65 final size:64
Alignment explanation
Indices: 2924655--2924779 Score: 182
Period size: 64 Copynumber: 1.9 Consensus size: 64
2924645 GAATGCATTT
*
2924655 CATGCATCGATGCACTC-AGATT-TTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCA
1 CATGCATCGATGCACTCTAG-TTGTTT-TG-AAACATCGAATGCATTTCATGCATCGATGCACCA
2924718 GC
63 GC
* *
2924720 CATGCATCGGTGCACTCTTGTTGTTTTGAAACATCGAATGCATTTCATGCATCGATGCAC
1 CATGCATCGATGCACTCTAGTTGTTTTGAAACATCGAATGCATTTCATGCATCGATGCAC
2924780 TCTTAGTGCA
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
64 31 0.56
65 20 0.36
66 4 0.07
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (64 bp):
CATGCATCGATGCACTCTAGTTGTTTTGAAACATCGAATGCATTTCATGCATCGATGCACCAGC
Found at i:2933312 original size:64 final size:63
Alignment explanation
Indices: 2933233--2933391 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
2933223 GAATAAATTG
*
2933233 AACATCGAATGCATTTCATGCATCGATGCACATACTATGCATC-ATGCACTCAGAG-T-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG
2933295 AA
63 -A
* * * *
2933297 AACATCGAATTCATTTGATGCATCGATGTACCAACCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGA
2933361 AACATCGAATGCATTTCATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
2933392 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 65 0.78
65 14 0.17
66 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGA
Found at i:2933407 original size:64 final size:63
Alignment explanation
Indices: 2933233--2933411 Score: 195
Period size: 64 Copynumber: 2.8 Consensus size: 63
2933223 GAATAAATTG
2933233 AACATCGAATGCATTTCATGCATCGATGCACATACTATGCATC-ATGCACTCAGAGTTTTATGAA
1 AACATCGAATGCATTTCATGCATCGATGCAC-T-CTATGCATCGATGCACTCAGAGTTTTATGAA
* * * * * *
2933297 AACATCGAATTCATTTGATGCATCGATGTACCAACCATGCATCGATGCACTCTG-GCTATTT-TG
1 AACATCGAATGCATTTCATGCATCGATGCA-C-TCTATGCATCGATGCACTCAGAG-T-TTTATG
2933360 -A
62 AA
*
2933361 AACATCGAATGCATTTCATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTC-TA-TGCATCGATGCACT
2933412 AAGGGTCTAA
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 77 0.79
65 14 0.14
66 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTATGCATCGATGCACTCAGAGTTTTATGAA
Found at i:2934357 original size:36 final size:36
Alignment explanation
Indices: 2934292--2934399 Score: 162
Period size: 36 Copynumber: 2.9 Consensus size: 36
2934282 TGATCTGATC
2934292 TTGCTTCACTACTCTCTTTTTTGTGAAGTCTTGATTTGCA
1 TTGCTTCACTA--CTC--TTTTGTGAAGTCTTGATTTGCA
*
2934332 TTGCTTCACTACTCTTTTGTGAAGTCTTGATTTGTA
1 TTGCTTCACTACTCTTTTGTGAAGTCTTGATTTGCA
*
2934368 TTGCTTCACTACTCTTTTGTGAAGGCTTGATT
1 TTGCTTCACTACTCTTTTGTGAAGTCTTGATT
2934400 AACTTGAGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
36 52 0.79
38 3 0.05
40 11 0.17
ACGTcount: A:0.16, C:0.19, G:0.17, T:0.49
Consensus pattern (36 bp):
TTGCTTCACTACTCTTTTGTGAAGTCTTGATTTGCA
Found at i:2937663 original size:24 final size:24
Alignment explanation
Indices: 2937636--2937707 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
2937626 GTAAACGGAG
*
2937636 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* * *
2937660 ATATCAGATATCAGAATAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
2937684 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
2937707 A
1 A
2937708 GGTAACGTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 14 0.35
24 26 0.65
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:2937708 original size:12 final size:12
Alignment explanation
Indices: 2937640--2937708 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
2937630 ACGGAGATAT
* *
2937640 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
2937652 CAGAATTCATAT
1 CAGAATTCAGAA
2937664 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
2937676 TAGAATCCAGAT
1 CAGAATTCAGAA
2937688 CAGAA-TCAGAA
1 CAGAATTCAGAA
2937699 CAGAATTCAG
1 CAGAATTCAG
2937709 GTAACGTATC
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
11 11 0.26
12 30 0.70
13 2 0.05
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:2940243 original size:18 final size:18
Alignment explanation
Indices: 2940217--2940253 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2940207 AACGGTAGGG
2940217 CAACAGGTCGGGTCGGGT
1 CAACAGGTCGGGTCGGGT
*
2940235 CAACGGGTCGGGTCGGGT
1 CAACAGGTCGGGTCGGGT
2940253 C
1 C
2940254 GGGTTGTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.24, G:0.46, T:0.16
Consensus pattern (18 bp):
CAACAGGTCGGGTCGGGT
Found at i:2940248 original size:13 final size:13
Alignment explanation
Indices: 2940175--2940230 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
2940165 CGCCGGTCAA
*
2940175 CGGGTCAATGGGT
1 CGGGTCAACGGGT
2940188 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
2940201 CGAGTCAAC-GGT
1 CGGGTCAACGGGT
* *
2940213 AGGG-CAACAGGT
1 CGGGTCAACGGGT
2940225 CGGGTC
1 CGGGTC
2940231 GGGTCAACGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 4 0.11
12 11 0.31
13 21 0.58
ACGTcount: A:0.20, C:0.21, G:0.43, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2942427 original size:24 final size:24
Alignment explanation
Indices: 2942400--2942485 Score: 104
Period size: 24 Copynumber: 3.6 Consensus size: 24
2942390 GTAAACGGAG
*
2942400 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
2942424 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
2942448 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
*
2942471 A-ATTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
2942486 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
22 1 0.02
23 18 0.34
24 34 0.64
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:2942431 original size:12 final size:12
Alignment explanation
Indices: 2942404--2942471 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
2942394 ACGGAGATAT
* *
2942404 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
2942416 CAGAATTCATAT
1 CAGAATTCAGAA
2942428 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
2942440 CAGAATCCAGAT
1 CAGAATTCAGAA
2942452 CAGAA-TCAGAA
1 CAGAATTCAGAA
2942463 CAGAATTCA
1 CAGAATTCA
2942472 ATTCGGAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 11 0.25
12 31 0.70
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:2943590 original size:18 final size:18
Alignment explanation
Indices: 2943569--2943603 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2943559 TGCCATCCGG
*
2943569 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
2943587 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
2943604 GTCCTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:2944949 original size:18 final size:18
Alignment explanation
Indices: 2944939--2944985 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
2944929 GTCGGGTCAA
2944939 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
2944957 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
2944975 CGGGTCGGGTC
1 CGGGTCGGGTC
2944986 GGGTTGTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:2944980 original size:13 final size:13
Alignment explanation
Indices: 2944920--2944962 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
2944910 GCCGGTCAAC
2944920 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2944933 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
2944946 GGTCAACAGGTCG
1 GGTCAACGGGTCG
2944959 GGTC
1 GGTC
2944963 GGGTCAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2960845 original size:33 final size:33
Alignment explanation
Indices: 2960807--2960901 Score: 136
Period size: 33 Copynumber: 2.9 Consensus size: 33
2960797 ATATGATAAA
* *
2960807 GATCTATGAGATCATACAAGAATGTTATAGAAG
1 GATCTATGAGATCATACAAGAATGTTACACAAG
* *
2960840 GATCTATAAGATCATACAAGAATGTTACACAAT
1 GATCTATGAGATCATACAAGAATGTTACACAAG
* *
2960873 GATCTATGAGGTCATACAAGAATGATACA
1 GATCTATGAGATCATACAAGAATGTTACA
2960902 AGTGGTGTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (33 bp):
GATCTATGAGATCATACAAGAATGTTACACAAG
Found at i:2961146 original size:21 final size:21
Alignment explanation
Indices: 2961094--2961192 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
2961084 TTAAGGAGTG
* * *
2961094 GTCCTTCGGAACATACATGTC
1 GTCCTTCGGGACATAGATGAC
* * *
2961115 GTTCTTTGGGACATATGAT-AG
1 GTCCTTCGGGACATA-GATGAC
*
2961136 GTCCTTCGGGACACAGATGAC
1 GTCCTTCGGGACATAGATGAC
* *
2961157 ATCCTTCGGGACATAGATGAT
1 GTCCTTCGGGACATAGATGAC
*
2961178 GTCCTTCGAGACATA
1 GTCCTTCGGGACATA
2961193 CATGTGGTCA
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 3 0.05
21 56 0.92
22 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.28
Consensus pattern (21 bp):
GTCCTTCGGGACATAGATGAC
Found at i:2961322 original size:21 final size:21
Alignment explanation
Indices: 2961296--2961372 Score: 100
Period size: 21 Copynumber: 3.6 Consensus size: 21
2961286 CTTAAGGAGT
*
2961296 GGTCCTTCAGGACATATACAA
1 GGTCCTTCGGGACATATACAA
2961317 GGTCCTTCGGGACATATACAA
1 GGTCCTTCGGGACATATACAA
* *
2961338 GTTGTACTTCGGGACATATACGA
1 G--GTCCTTCGGGACATATACAA
*
2961361 GATCCTTCGGGA
1 GGTCCTTCGGGA
2961373 TAATTTTACA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 30 0.61
23 19 0.39
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (21 bp):
GGTCCTTCGGGACATATACAA
Found at i:2961503 original size:30 final size:30
Alignment explanation
Indices: 2961469--2961532 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
2961459 GTTCTCAGTA
2961469 ATACATGGACCTA-CAAAAGATATCAAAAAT
1 ATACATGG-CCTATCAAAAGATATCAAAAAT
* * * *
2961499 ATACATGGGCTATTAAAAGATATTATAAAT
1 ATACATGGCCTATCAAAAGATATCAAAAAT
2961529 ATAC
1 ATAC
2961533 TGTATGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (30 bp):
ATACATGGCCTATCAAAAGATATCAAAAAT
Found at i:2961681 original size:6 final size:6
Alignment explanation
Indices: 2961670--2961757 Score: 56
Period size: 6 Copynumber: 14.8 Consensus size: 6
2961660 AAATGGGTTC
* * * *
2961670 ATGATA ATGATA CTGATG TTGA-A ATGATA GA-GATC ATGATA ATGATA
1 ATGATA ATGATA ATGATA ATGATA ATGATA -ATGATA ATGATA ATGATA
* * * * *
2961717 TTGATG TTGATA ATGATA GA-GATC ATGATA ATGATA TTGAT
1 ATGATA ATGATA ATGATA -ATGATA ATGATA ATGATA ATGAT
2961758 GTTGAGAATG
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
5 5 0.08
6 56 0.89
7 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (6 bp):
ATGATA
Found at i:2961739 original size:36 final size:36
Alignment explanation
Indices: 2961668--2961802 Score: 227
Period size: 36 Copynumber: 3.8 Consensus size: 36
2961658 TTAAATGGGT
*
2961668 TCATGATAATGATACTGATGTTGA-AATGATAGAGA
1 TCATGATAATGATATTGATGTTGATAATGATAGAGA
2961703 TCATGATAATGATATTGATGTTGATAATGATAGAGA
1 TCATGATAATGATATTGATGTTGATAATGATAGAGA
* *
2961739 TCATGATAATGATATTGATGTTGAGAATGATAGAAA
1 TCATGATAATGATATTGATGTTGATAATGATAGAGA
*
2961775 TCATGATAACGATATTGATGTTGATAAT
1 TCATGATAATGATATTGATGTTGATAAT
2961803 AATGGTATTT
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 23 0.24
36 71 0.76
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.35
Consensus pattern (36 bp):
TCATGATAATGATATTGATGTTGATAATGATAGAGA
Found at i:2961799 original size:18 final size:18
Alignment explanation
Indices: 2961671--2961802 Score: 113
Period size: 18 Copynumber: 7.4 Consensus size: 18
2961661 AATGGGTTCA
*
2961671 TGATAATGATACTGATGT
1 TGATAATGATATTGATGT
** **
2961689 TGA-AATGATAGAGATCA
1 TGATAATGATATTGATGT
2961706 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
** **
2961724 TGATAATGATAGAGATCA
1 TGATAATGATATTGATGT
2961742 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
* *** **
2961760 TGAGAATGATAGAAATCA
1 TGATAATGATATTGATGT
*
2961778 TGATAACGATATTGATGT
1 TGATAATGATATTGATGT
2961796 TGATAAT
1 TGATAAT
2961803 AATGGTATTT
Statistics
Matches: 83, Mismatches: 30, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
17 13 0.16
18 70 0.84
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (18 bp):
TGATAATGATATTGATGT
Found at i:2964352 original size:7 final size:7
Alignment explanation
Indices: 2964340--2964427 Score: 74
Period size: 7 Copynumber: 11.9 Consensus size: 7
2964330 CTAAACAAAT
2964340 AAAAAAG
1 AAAAAAG
2964347 AAAAAAG
1 AAAAAAG
2964354 AAAAAA-
1 AAAAAAG
2964360 AAAAAA-
1 AAAAAAG
2964366 AAAGAAA-
1 AAA-AAAG
2964373 AAAAAAG
1 AAAAAAG
2964380 AAAAAAAG
1 -AAAAAAG
2964388 AAGAAGAAGG
1 AA-AA-AA-G
*
2964398 AAAAAACTAA
1 -AAAAA--AG
2964408 AAAAAAG
1 AAAAAAG
2964415 AAAAAAG
1 AAAAAAG
2964422 AAAAAA
1 AAAAAA
2964428 ATGAGAGATA
Statistics
Matches: 70, Mismatches: 2, Indels: 18
0.78 0.02 0.20
Matches are distributed among these distances:
6 12 0.17
7 35 0.50
8 9 0.13
9 8 0.11
10 3 0.04
11 3 0.04
ACGTcount: A:0.85, C:0.01, G:0.12, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:2964445 original size:1 final size:1
Alignment explanation
Indices: 2964340--2964428 Score: 61
Period size: 1 Copynumber: 89.0 Consensus size: 1
2964330 CTAAACAAAT
* * * * * * * ** *
2964340 AAAAAAGAAAAAAGAAAAAAAAAAAAAAAGAAAAAAAAAGAAAAAAAGAAGAAGAAGGAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
2964405 TAAAAAAAAGAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAA
2964429 TGAGAGATAC
Statistics
Matches: 65, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.85, C:0.01, G:0.12, T:0.01
Consensus pattern (1 bp):
A
Found at i:2964445 original size:35 final size:35
Alignment explanation
Indices: 2964340--2964428 Score: 105
Period size: 35 Copynumber: 2.7 Consensus size: 35
2964330 CTAAACAAAT
** **
2964340 AAAAAAG-AAAAAAGAA-AAAAAAAAAAAAAGAAA
1 AAAAAAGAAAAAAAGAAGAAAAAGGAAAAAACTAA
*
2964373 AAAAAAGAAAAAAAGAAGAAGAAGGAAAAAACTAA
1 AAAAAAGAAAAAAAGAAGAAAAAGGAAAAAACTAA
2964408 AAAAAAG-AAAAAAGAA-AAAAA
1 AAAAAAGAAAAAAAGAAGAAAAA
2964429 TGAGAGATAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
33 11 0.23
34 18 0.38
35 19 0.40
ACGTcount: A:0.85, C:0.01, G:0.12, T:0.01
Consensus pattern (35 bp):
AAAAAAGAAAAAAAGAAGAAAAAGGAAAAAACTAA
Found at i:2967527 original size:19 final size:19
Alignment explanation
Indices: 2967475--2967529 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
2967465 TTATATGACA
2967475 AAGATCTATGAGATCATAC
1 AAGATCTATGAGATCATAC
*
2967494 AAGA---AT--G-TTATAC
1 AAGATCTATGAGATCATAC
2967507 AAGATCTATGAGATCATAC
1 AAGATCTATGAGATCATAC
2967526 AAGA
1 AAGA
2967530 ATGTTACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
13 9 0.32
14 1 0.04
16 4 0.14
18 1 0.04
19 13 0.46
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (19 bp):
AAGATCTATGAGATCATAC
Found at i:2967551 original size:33 final size:33
Alignment explanation
Indices: 2967472--2967603 Score: 221
Period size: 33 Copynumber: 4.0 Consensus size: 33
2967462 GGGTTATATG
* *
2967472 ACAAAGATCTATGAGATCATACAAGAATGTTAT
1 ACAATGATCTATGAGATCATACAAGAATGTTAC
2967505 ACAA-GATCTATGAGATCATACAAGAATGTTAC
1 ACAATGATCTATGAGATCATACAAGAATGTTAC
2967537 ACAATGATCTATGAGATCATACAAGAATGTTAC
1 ACAATGATCTATGAGATCATACAAGAATGTTAC
* *
2967570 ACAATGATCTATGAGATCAGACAAGAATGATAC
1 ACAATGATCTATGAGATCATACAAGAATGTTAC
2967603 A
1 A
2967604 AGTGTTGTGA
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
32 31 0.33
33 64 0.67
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (33 bp):
ACAATGATCTATGAGATCATACAAGAATGTTAC
Found at i:2967558 original size:65 final size:66
Alignment explanation
Indices: 2967472--2967603 Score: 221
Period size: 65 Copynumber: 2.0 Consensus size: 66
2967462 GGGTTATATG
* * *
2967472 ACAAAGATCTATGAGATCATACAAGAATGTTATACAA-GATCTATGAGATCATACAAGAATGTTA
1 ACAAAGATCTATGAGATCATACAAGAATGTTACACAATGATCTATGAGATCAGACAAGAATGATA
2967536 C
66 C
*
2967537 ACAATGATCTATGAGATCATACAAGAATGTTACACAATGATCTATGAGATCAGACAAGAATGATA
1 ACAAAGATCTATGAGATCATACAAGAATGTTACACAATGATCTATGAGATCAGACAAGAATGATA
2967602 C
66 C
2967603 A
1 A
2967604 AGTGTTGTGA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
65 35 0.56
66 27 0.44
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (66 bp):
ACAAAGATCTATGAGATCATACAAGAATGTTACACAATGATCTATGAGATCAGACAAGAATGATA
C
Found at i:2967893 original size:21 final size:21
Alignment explanation
Indices: 2967796--2967894 Score: 101
Period size: 21 Copynumber: 4.7 Consensus size: 21
2967786 TTAAGGAGTA
*
2967796 GTCCTTCGGGACATACATGAC
1 GTCCTTCGGGACATAGATGAC
** * * *
2967817 GTTTTTTGGGGCATATGAT-AG
1 GTCCTTCGGGACATA-GATGAC
* *
2967838 GTCCTTCGAGACACAGATGAC
1 GTCCTTCGGGACATAGATGAC
*
2967859 ATCCTTCGGGACATAGATGAC
1 GTCCTTCGGGACATAGATGAC
2967880 GTCCTTCGGGACATA
1 GTCCTTCGGGACATA
2967895 CATGTGGTCA
Statistics
Matches: 59, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
20 3 0.05
21 54 0.92
22 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (21 bp):
GTCCTTCGGGACATAGATGAC
Found at i:2967908 original size:21 final size:21
Alignment explanation
Indices: 2967800--2967909 Score: 60
Period size: 21 Copynumber: 5.2 Consensus size: 21
2967790 GGAGTAGTCC
**
2967800 TTCGGGACATACATGACGTTT
1 TTCGGGACATACATGACGTCA
* * * * *
2967821 TTTGGGGCATATGAT-AGGTCC
1 TTCGGGACATA-CATGACGTCA
* * * * *
2967842 TTCGAGACACAGATGACATCC
1 TTCGGGACATACATGACGTCA
* *
2967863 TTCGGGACATAGATGACGTCC
1 TTCGGGACATACATGACGTCA
**
2967884 TTCGGGACATACATGTGGTCA
1 TTCGGGACATACATGACGTCA
2967905 TTCGG
1 TTCGG
2967910 ATATATATGT
Statistics
Matches: 68, Mismatches: 19, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.04
21 63 0.93
22 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (21 bp):
TTCGGGACATACATGACGTCA
Found at i:2968023 original size:21 final size:21
Alignment explanation
Indices: 2967997--2968039 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2967987 CTTAAAAAGT
2967997 GGTCCTTCGAAACATATACAA
1 GGTCCTTCGAAACATATACAA
**
2968018 GGTCCTTCGGGACATATACAA
1 GGTCCTTCGAAACATATACAA
2968039 G
1 G
2968040 TTGTCCTCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (21 bp):
GGTCCTTCGAAACATATACAA
Found at i:2968051 original size:23 final size:21
Alignment explanation
Indices: 2968008--2968059 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 21
2967998 GTCCTTCGAA
*
2968008 ACATATACAAGGTCCTTCGGG
1 ACATATACAAGGTCCTCCGGG
2968029 ACATATACAAGTTGTCCTCCGGG
1 ACATATACAAG--GTCCTCCGGG
2968052 ACATATAC
1 ACATATAC
2968060 GAGATCCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 11 0.39
23 17 0.61
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
ACATATACAAGGTCCTCCGGG
Found at i:2968397 original size:6 final size:6
Alignment explanation
Indices: 2968386--2968474 Score: 56
Period size: 6 Copynumber: 14.8 Consensus size: 6
2968376 AAATGGGTTC
* * * * *
2968386 ATGATA ATGATA TTGATG TTAATA ATGATA GA-GATC ATGATA ATGATA
1 ATGATA ATGATA ATGATA ATGATA ATGATA -ATGATA ATGATA ATGATA
* * * * *
2968434 TTGATG TTGATA ATGATA GA-GATC ATGATA ATGATA TTGAT
1 ATGATA ATGATA ATGATA -ATGATA ATGATA ATGATA ATGAT
2968475 GTTGAGAATG
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
5 2 0.03
6 60 0.94
7 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.37
Consensus pattern (6 bp):
ATGATA
Found at i:2968412 original size:18 final size:18
Alignment explanation
Indices: 2968387--2968522 Score: 119
Period size: 18 Copynumber: 7.6 Consensus size: 18
2968377 AATGGGTTCA
2968387 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
* ** **
2968405 TAATAATGATAGAGATCA
1 TGATAATGATATTGATGT
2968423 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
** **
2968441 TGATAATGATAGAGATCA
1 TGATAATGATATTGATGT
2968459 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
* *** **
2968477 TGAGAATGATAGAAATCA
1 TGATAATGATATTGATGT
**
2968495 TGATAACAATATTGATGT
1 TGATAATGATATTGATGT
2968513 TGATAATGAT
1 TGATAATGAT
2968523 GGTATTTATC
Statistics
Matches: 84, Mismatches: 34, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 84 1.00
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (18 bp):
TGATAATGATATTGATGT
Done.