Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015245.1 Kokia drynarioides strain JFW-HI SEQ_130290, 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: 767229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 115 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:792 original size:36 final size:36
Alignment explanation
Indices: 751--823 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
741 AGTTATTAGT
751 AAATTTCGAATAATATTAAGAATGTTTAATTATTGA
1 AAATTTCGAATAATATTAAGAATGTTTAATTATTGA
787 AAATTTCGAATAATATTAAGAATGTTTAATTATTGA
1 AAATTTCGAATAATATTAAGAATGTTTAATTATTGA
823 A
1 A
824 TTAATATGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (36 bp):
AAATTTCGAATAATATTAAGAATGTTTAATTATTGA
Found at i:3746 original size:98 final size:98
Alignment explanation
Indices: 3586--4066 Score: 602
Period size: 98 Copynumber: 4.9 Consensus size: 98
3576 TCGAGGTAGA
* * * * ** * **
3586 AAATTCGCCATTGCGGCTCCAATTTTTCCCAGCATGTTTCTGAGGTATAAGGTTTGTTGTTGCGA
1 AAATTCGCCGTTACGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTTGCCGTTGCGA
*
3651 CTTAAACCTTTCCCTCCATATCTTCGTGGTACT
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * ** *
3684 AGATTCGCTGTTACGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCTA
1 AAATTCGCCGTTACGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTTGCCGTTGCGA
*
3749 CTTAAACCTTTCCCTCCATATCTTCATGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * ** * * *
3782 AAATTCACCGTTACGGCCTCAATCTTTCCCAACATGTTTTTGAGGTACAATGTTTGCCTTTGCGA
1 AAATTCGCCGTTACGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTTGCCGTTGCGA
*
3847 CTTAAACCTTTCCCTCCATATCTTTGTGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * ** * * * *
3880 AGATTCGTCGTTGCTACTTCAATCTTTCCCTTTATGTTTCTAAGGTACAAGGTTTACCGTTGTGA
1 AAATTCGCCGTTACGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTTGCCGTTGCGA
** *
3945 CTTAAACCTTTCCCTTTATATCTTTGTGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* *
3978 AAATTCGCCGTTGCGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAATGTTTGCCGTTGCGA
1 AAATTCGCCGTTACGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTTGCCGTTGCGA
*
4043 CTTAAAACCTTTCCCTCTATATCT
66 CTT-AAACCTTTCCCTCCATATCT
4067 ATAGAATGGA
Statistics
Matches: 324, Mismatches: 58, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
98 305 0.94
99 19 0.06
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (98 bp):
AAATTCGCCGTTACGGCTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTTGCCGTTGCGA
CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
Found at i:3760 original size:49 final size:49
Alignment explanation
Indices: 3618--4058 Score: 275
Period size: 49 Copynumber: 9.0 Consensus size: 49
3608 TTTTTCCCAG
* * ** *
3618 CATGTTTCTGAGGTATAAGGTTTGTTGTTGCGACTTAAACCTTTCCCTC
1 CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* * * * * * * * *
3667 CATATCTTC-GTGGTACTAGATTCGCTGTTACGGCTTCAATCTTTCCCTT
1 CATGT-TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* * *
3716 CATGTTTCTGAGGTACAAGGTTCACCGTTGCTACTTAAACCTTTCCCTC
1 CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* * * * * * * * **
3765 CATATCTTC--ATGGTACCAA-ATTCACCGTTACGGCCTCAATCTTTCCCAA
1 CATGT-TTCTGA-GGTA-CAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* * * * *
3814 CATGTTTTTGAGGTACAATGTTTGCCTTTGCGACTTAAACCTTTCCCTC
1 CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* * * * * * * *
3863 CATATCTT-TGTGGTACCAGATTCGTCGTTGCTACTTCAATCTTTCCCTT
1 CATGT-TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* * ** *
3912 TATGTTTCTAAGGTACAAGGTTTACCGTTGTGACTTAAACCTTTCCCTT
1 CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* * * * * * *
3961 TATATCTT-TGTGGTACCAA-ATTCGCCGTTGCGGCTTCAATCTTTCCCTT
1 CATGT-TTCTGAGGTA-CAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* *
4010 CATGTTTCTGAGGTACAATGTTTGCCGTTGCGACTTAAAACCTTTCCCT
1 CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTT-AAACCTTTCCCT
4059 CTATATCTAT
Statistics
Matches: 287, Mismatches: 90, Indels: 29
0.71 0.22 0.07
Matches are distributed among these distances:
48 16 0.06
49 244 0.85
50 27 0.09
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.39
Consensus pattern (49 bp):
CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
Found at i:15112 original size:112 final size:113
Alignment explanation
Indices: 14928--15246 Score: 525
Period size: 114 Copynumber: 2.8 Consensus size: 113
14918 AGGAACATAC
* * *
14928 TCGATTATGCAAATTCTACAAAAAATCACATCCAACACGTTAGGGCACAATTCTTCGAAGTTTTC
1 TCGATTGTGCAAATTCTAC-AAAAATCACACCCAACACGTTAGGGCACAATTCTTCGAAGTTTCC
* *
14993 ACACAAAAGGATATTGCCTCGATTTAAAAAAAA-ATAAAGGGAGGATAA
65 ACACAAAAGAATATTGTCTCGATTTAAAAAAAATATAAAGGGAGGATAA
*
15041 TCGATTGTGCAAATTCTACAAAAATCACACCCAACACGTTAGGGCATAATTCTTCGAAGTTTCCA
1 TCGATTGTGCAAATTCTACAAAAATCACACCCAACACGTTAGGGCACAATTCTTCGAAGTTTCCA
* *
15106 CACAAAAGAATATTGTCTCGATTTTAAAAAAAATTTTAAGGGAGGATAA
66 CACAAAAGAATATTGTCTCGA-TTTAAAAAAAATATAAAGGGAGGATAA
15155 TCGATTGTGCAAATTCTACAAAAATCACACCCAACACGTTAGGGCACAATTCTTCGAAGTTTCCA
1 TCGATTGTGCAAATTCTACAAAAATCACACCCAACACGTTAGGGCACAATTCTTCGAAGTTTCCA
*
15220 CACAAAATAATATTGTCTC-ATTTAAAA
66 CACAAAAGAATATTGTCTCGATTTAAAA
15247 GTATTTATGT
Statistics
Matches: 194, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
112 69 0.36
113 30 0.15
114 95 0.49
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (113 bp):
TCGATTGTGCAAATTCTACAAAAATCACACCCAACACGTTAGGGCACAATTCTTCGAAGTTTCCA
CACAAAAGAATATTGTCTCGATTTAAAAAAAATATAAAGGGAGGATAA
Found at i:16085 original size:21 final size:22
Alignment explanation
Indices: 16037--16085 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
16027 AATGTTTGGA
* * *
16037 TTTTTTTTGTTTCTTTAATCTG
1 TTTTTTTTATTTCTTAAATCAG
*
16059 TCTTTTTTATTTCTTAAAT-AG
1 TTTTTTTTATTTCTTAAATCAG
16080 TTTTTT
1 TTTTTT
16086 ACTTAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.14, C:0.08, G:0.06, T:0.71
Consensus pattern (22 bp):
TTTTTTTTATTTCTTAAATCAG
Found at i:16267 original size:17 final size:17
Alignment explanation
Indices: 16245--16278 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16235 TTCGGAATCC
16245 CTCACGAACATGGGCGA
1 CTCACGAACATGGGCGA
16262 CTCACGAACATGGGCGA
1 CTCACGAACATGGGCGA
16279 GTTCGGAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.12
Consensus pattern (17 bp):
CTCACGAACATGGGCGA
Found at i:18100 original size:6 final size:6
Alignment explanation
Indices: 18089--18120 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
18079 TTCTGCACCA
18089 GCCCCT GCCCCT GCCCCT GCCCCT GCCCCT GC
1 GCCCCT GCCCCT GCCCCT GCCCCT GCCCCT GC
18121 AGTTCAGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.19, T:0.16
Consensus pattern (6 bp):
GCCCCT
Found at i:18273 original size:51 final size:51
Alignment explanation
Indices: 18190--18290 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 51
18180 CTCAATGGCG
* * *
18190 GTTTCAGGGTGGGATTCATGCTTTCACTCCGGGGACTCAACCAGC-AGGGCA
1 GTTTCACGGTGGGATTCATGCTTCCACACCGGGGACTCAACC-GCAAGGGCA
18241 GTTTCACGGTGGGA-TCTATGCTTCCACACCGGGGACTCAACCGCAAGGGC
1 GTTTCACGGTGGGATTC-ATGCTTCCACACCGGGGACTCAACCGCAAGGGC
18291 TAAGCAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
50 4 0.09
51 41 0.91
ACGTcount: A:0.20, C:0.28, G:0.31, T:0.22
Consensus pattern (51 bp):
GTTTCACGGTGGGATTCATGCTTCCACACCGGGGACTCAACCGCAAGGGCA
Found at i:19077 original size:11 final size:11
Alignment explanation
Indices: 19063--19087 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19053 TTTATTTAAG
19063 TTTTTAAAATT
1 TTTTTAAAATT
19074 TTTTTAAAATT
1 TTTTTAAAATT
19085 TTT
1 TTT
19088 AATTAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTAAAATT
Found at i:19118 original size:33 final size:33
Alignment explanation
Indices: 19081--19156 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
19071 ATTTTTTTAA
**
19081 AATTTTTAATTAGTAATGATAAAATTAC-ATTTT
1 AATTTTTAATTAAAAATGATAAAATTACGA-TTT
*
19114 AA-TTTTATATTAAAAATGATAAAATTTCGATTT
1 AATTTTTA-ATTAAAAATGATAAAATTACGATTT
19147 AATATTTTAA
1 AAT-TTTTAA
19157 AATTTATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
32 5 0.14
33 24 0.67
34 2 0.06
35 5 0.14
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (33 bp):
AATTTTTAATTAAAAATGATAAAATTACGATTT
Found at i:20184 original size:23 final size:23
Alignment explanation
Indices: 20158--20206 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
20148 ATTACAAGAG
20158 AATATTCACTGTTTATGCCAAAA
1 AATATTCACTGTTTATGCCAAAA
* *
20181 AATATTTACTGTTTATGCTAAAA
1 AATATTCACTGTTTATGCCAAAA
20204 AAT
1 AAT
20207 CTCACTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (23 bp):
AATATTCACTGTTTATGCCAAAA
Found at i:20220 original size:22 final size:22
Alignment explanation
Indices: 20163--20240 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 22
20153 AAGAGAATAT
* * *
20163 TCACTGTTTATGCCAAAAAATAT
1 TCACTATTCATGCCAAAAAAT-C
* * * *
20186 TTACTGTTTATGCTAAAAAATC
1 TCACTATTCATGCCAAAAAATC
* *
20208 TCACTATTCATGCCAGAGAATC
1 TCACTATTCATGCCAAAAAATC
*
20230 TTACTATTCAT
1 TCACTATTCAT
20241 TTCAAATTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 26 0.58
23 19 0.42
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (22 bp):
TCACTATTCATGCCAAAAAATC
Found at i:22381 original size:23 final size:23
Alignment explanation
Indices: 22244--22441 Score: 154
Period size: 23 Copynumber: 8.5 Consensus size: 23
22234 AGTGTTGGGT
* * * *
22244 AACAGAGGGTACCCAAAGTGTTA
1 AACAGAGGGCACACACAGTGCTA
* *
22267 ATCAGAGGGCGCACGA-AGTGCTAA
1 AACAGAGGGCACAC-ACAGTGCT-A
* *
22291 TAACAGTGGGCACACACAGTGCTG
1 -AACAGAGGGCACACACAGTGCTA
22315 AACAGAGGGCACGA-AGC-GTGCTA
1 AACAGAGGGCAC-ACA-CAGTGCTA
22338 AACAGAGGGCACGA-AGC-GTGCTA
1 AACAGAGGGCAC-ACA-CAGTGCTA
*
22361 AACAGAGGGCACACACAGTGCTG
1 AACAGAGGGCACACACAGTGCTA
* * *
22384 ACCAGAGAGCACACACAGTGCTG
1 AACAGAGGGCACACACAGTGCTA
* *
22407 ACCAGAGAGCACACACAGTGCTA
1 AACAGAGGGCACACACAGTGCTA
* *
22430 ATCAGAGAGCAC
1 AACAGAGGGCAC
22442 GCTAGTGTTC
Statistics
Matches: 151, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.01
23 127 0.84
24 5 0.03
25 17 0.11
ACGTcount: A:0.35, C:0.24, G:0.29, T:0.11
Consensus pattern (23 bp):
AACAGAGGGCACACACAGTGCTA
Found at i:23961 original size:180 final size:180
Alignment explanation
Indices: 23659--24018 Score: 693
Period size: 180 Copynumber: 2.0 Consensus size: 180
23649 TATTGAAATC
*
23659 CCATAATTCTATTTCAATCCCTATACTCTTTAATACTTCAAAAGGAAATCTACAAGAAAATTAAG
1 CCATAATTCTAATTCAATCCCTATACTCTTTAATACTTCAAAAGGAAATCTACAAGAAAATTAAG
*
23724 GTGTCTACTAGCCCTCTATGTCTTTCTTAAGGAAATTTCAAAGAAAATGGAGGATTTTGAAGCTT
66 GTGTCTACTAGCCCTCTATGCCTTTCTTAAGGAAATTTCAAAGAAAATGGAGGATTTTGAAGCTT
23789 GGAGGGTTTAACAATGGTGGAAGGACTTAATTGAAATAAAAGCAAAAGTT
131 GGAGGGTTTAACAATGGTGGAAGGACTTAATTGAAATAAAAGCAAAAGTT
*
23839 CCATAATTCTAATTCAATCCCTATACTCTTTAATACTTCAAAAGGAAATCTGCAAGAAAATTAAG
1 CCATAATTCTAATTCAATCCCTATACTCTTTAATACTTCAAAAGGAAATCTACAAGAAAATTAAG
23904 GTGTCTACTAGCCCTCTATGCCTTTCTTAAGGAAATTTCAAAGAAAATGGAGGATTTTGAAGCTT
66 GTGTCTACTAGCCCTCTATGCCTTTCTTAAGGAAATTTCAAAGAAAATGGAGGATTTTGAAGCTT
23969 GGAGGGTTTAACAATGGTGGAAGGACTTAATTGAAATAAAAGCAAAAGTT
131 GGAGGGTTTAACAATGGTGGAAGGACTTAATTGAAATAAAAGCAAAAGTT
24019 GGATGGAGAG
Statistics
Matches: 177, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
180 177 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (180 bp):
CCATAATTCTAATTCAATCCCTATACTCTTTAATACTTCAAAAGGAAATCTACAAGAAAATTAAG
GTGTCTACTAGCCCTCTATGCCTTTCTTAAGGAAATTTCAAAGAAAATGGAGGATTTTGAAGCTT
GGAGGGTTTAACAATGGTGGAAGGACTTAATTGAAATAAAAGCAAAAGTT
Found at i:28591 original size:23 final size:23
Alignment explanation
Indices: 28561--28700 Score: 115
Period size: 23 Copynumber: 6.0 Consensus size: 23
28551 CTGGGTAACG
*
28561 GAGGGCACACAAAGTTCTAATCA
1 GAGGGCACACAAAGTGCTAATCA
*
28584 GAGGGCACACGAAGTGCTAATAACA
1 GAGGGCACACAAAGTGCTAAT--CA
*
28609 GAGGGCACACACAGTGCTGAA-CA
1 GAGGGCACACAAAGTGCT-AATCA
* *
28632 GAGGGCACTA-AACGTGCTAAACA
1 GAGGGCAC-ACAAAGTGCTAATCA
* *
28655 GAGGACACACACAGTGCTGAA-CA
1 GAGGGCACACAAAGTGCT-AATCA
* * * *
28678 AAGAGCACACACAGTGCTGATCA
1 GAGGGCACACAAAGTGCTAATCA
28701 AAGAGTGCGT
Statistics
Matches: 96, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
22 4 0.04
23 69 0.72
24 3 0.03
25 18 0.19
26 2 0.02
ACGTcount: A:0.39, C:0.24, G:0.26, T:0.12
Consensus pattern (23 bp):
GAGGGCACACAAAGTGCTAATCA
Found at i:28613 original size:48 final size:48
Alignment explanation
Indices: 28532--28697 Score: 146
Period size: 48 Copynumber: 3.5 Consensus size: 48
28522 CGAAGTACTT
* ** * *
28532 AACAGAGGGCACATAAGTGCTGGGTAACGGAGGGCACACAAAGTTCT-
1 AACAGAGGGCACAGAAGTGCTGAATAACAGAGGGCACACAAAGTGCTG
*
28579 AATCAGAGGGCACACGAAGTGCT-AATAACAGAGGGCACACACAGTGCTG
1 AA-CAGAGGGCACA-GAAGTGCTGAATAACAGAGGGCACACAAAGTGCTG
* *
28628 AACAGAGGGCACTA-AACGTGCT--A-AACAGAGGACACACACAGTGCTG
1 AACAGAGGGCAC-AGAA-GTGCTGAATAACAGAGGGCACACAAAGTGCTG
* * *
28674 AACAAAGAGCACACACAGTGCTGA
1 AACAGAGGGCACAGA-AGTGCTGA
28698 TCAAAGAGTG
Statistics
Matches: 101, Mismatches: 9, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
45 1 0.01
46 38 0.38
47 6 0.06
48 46 0.46
49 10 0.10
ACGTcount: A:0.38, C:0.22, G:0.28, T:0.12
Consensus pattern (48 bp):
AACAGAGGGCACAGAAGTGCTGAATAACAGAGGGCACACAAAGTGCTG
Found at i:28616 original size:25 final size:24
Alignment explanation
Indices: 28531--28672 Score: 109
Period size: 23 Copynumber: 5.9 Consensus size: 24
28521 CCGAAGTACT
* **
28531 TAACAGAGGGCACATAAGTGCTGGG
1 TAACAGAGGGCACACAAGTGCT-AA
* *
28556 TAACGGAGGGCACACAAAGTTCTAA
1 TAACAGAGGGCACAC-AAGTGCTAA
28581 T--CAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACAC-AAGTGCTAA
28604 TAACAGAGGGCACACACAGTGCT--
1 TAACAGAGGGCACACA-AGTGCTAA
*
28627 GAACAGAGGGCACTA-AACGTGCT-A
1 TAACAGAGGGCAC-ACAA-GTGCTAA
*
28651 -AACAGAGGACACACACAGTGCT
1 TAACAGAGGGCACACA-AGTGCT
28673 GAACAAAGAG
Statistics
Matches: 98, Mismatches: 10, Indels: 20
0.77 0.08 0.16
Matches are distributed among these distances:
22 2 0.02
23 55 0.56
24 3 0.03
25 32 0.33
26 6 0.06
ACGTcount: A:0.37, C:0.22, G:0.28, T:0.13
Consensus pattern (24 bp):
TAACAGAGGGCACACAAGTGCTAA
Found at i:28695 original size:46 final size:48
Alignment explanation
Indices: 28588--28695 Score: 134
Period size: 46 Copynumber: 2.3 Consensus size: 48
28578 TAATCAGAGG
* * *
28588 GCACACGA-AGTGCTAATAACAGAGGGCACACACAGTGCTGAACAGAGG
1 GCACAC-ACAGTGCTAATAACAGAGGACACACACAGTGCTGAACAAAGA
*
28636 GCACTAAAC-GTGCT-A-AACAGAGGACACACACAGTGCTGAACAAAGA
1 GCAC-ACACAGTGCTAATAACAGAGGACACACACAGTGCTGAACAAAGA
28682 GCACACACAGTGCT
1 GCACACACAGTGCT
28696 GATCAAAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
45 3 0.06
46 37 0.71
47 1 0.02
48 10 0.19
49 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (48 bp):
GCACACACAGTGCTAATAACAGAGGACACACACAGTGCTGAACAAAGA
Found at i:30996 original size:28 final size:26
Alignment explanation
Indices: 30965--31018 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
30955 CACATTACAA
30965 AAAC-AATACAAAATAAATAAAAAGGATT
1 AAACAAATA-AAAA-AAA-AAAAAGGATT
*
30993 AAACAAATAAAAAAAACAAAAGGATT
1 AAACAAATAAAAAAAAAAAAAGGATT
31019 TAATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 9 0.38
27 3 0.12
28 8 0.33
29 4 0.17
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (26 bp):
AAACAAATAAAAAAAAAAAAAGGATT
Found at i:31977 original size:24 final size:25
Alignment explanation
Indices: 31949--31999 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
31939 ACTCAATAGA
31949 AAAGTCAAC-GGTCAATGGTC-AATC
1 AAAGTCAACGGGTCAA-GGTCGAATC
31973 AAAGTCAACGGGTCAAGGTCGAATC
1 AAAGTCAACGGGTCAAGGTCGAATC
31998 AA
1 AA
32000 CTAATTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.18
Consensus pattern (25 bp):
AAAGTCAACGGGTCAAGGTCGAATC
Found at i:38447 original size:47 final size:47
Alignment explanation
Indices: 38350--38894 Score: 475
Period size: 47 Copynumber: 11.6 Consensus size: 47
38340 TTCTTCTGTA
* * * *
38350 GCTTCAATCTGCCCCTCTGGATTTAGGGGTATAAGATTGGATTTGGTG
1 GCTTCAATCTACCCCTCTGGATTT-GGGGTATAAGACTAGATGTGGTG
* * * *
38398 GCTTCAATCTATCCCTCTAGATTTGGGGTATAAGACTAGATATGATG
1 GCTTCAATCTACCCCTCTGGATTTGGGGTATAAGACTAGATGTGGTG
* * * * * *
38445 GCTTCAATATGCCCTTCTGAATTTAGGGTATAAGATTAGATGTGGTG
1 GCTTCAATCTACCCCTCTGGATTTGGGGTATAAGACTAGATGTGGTG
* * * * *
38492 GCTTTAATCTACCCCTCTTGATTTGGGATATAAGATTGGATGTGGTG
1 GCTTCAATCTACCCCTCTGGATTTGGGGTATAAGACTAGATGTGGTG
* ** * * * *
38539 GCTTCAATCTGCCATTCTCGATTTAGGGTATAAGATTGGA--TGGTG
1 GCTTCAATCTACCCCTCTGGATTTGGGGTATAAGACTAGATGTGGTG
* * * * *
38584 GCTTTAATCTGA-CCCTTTGGATTTGGGGTATAAGATTGGATGTGATG
1 GCTTCAATCT-ACCCCTCTGGATTTGGGGTATAAGACTAGATGTGGTG
* * *** * ** * ** *
38631 ACTTTAATCTGTGCCTTTTAATTTGGGGTATAAGACTGGATACGATG
1 GCTTCAATCTACCCCTCTGGATTTGGGGTATAAGACTAGATGTGGTG
* * * * *
38678 GCTTCAATCTGCCCTTCTGGATTTGAGGTATAAGACTAGATGTGATA
1 GCTTCAATCTACCCCTCTGGATTTGGGGTATAAGACTAGATGTGGTG
* * * *
38725 GCTTCAATCTGCCCCTCTGGATTTGAGGTATAAGACTAAATGCGGTG
1 GCTTCAATCTACCCCTCTGGATTTGGGGTATAAGACTAGATGTGGTG
** * * *
38772 GCTTCAATCTGTCCCTCTGGATTTGAGGTATAAGACTAGATGTGATA
1 GCTTCAATCTACCCCTCTGGATTTGGGGTATAAGACTAGATGTGGTG
* * * *
38819 GCTTCAATCTACCTCTTTGGATTTGGGGTATAAGATTGGATGTGGTG
1 GCTTCAATCTACCCCTCTGGATTTGGGGTATAAGACTAGATGTGGTG
* * *
38866 GCTTCAATTTGCCCCTCTAGATTTGGGGT
1 GCTTCAATCTACCCCTCTGGATTTGGGGT
38895 GTAACACTCA
Statistics
Matches: 407, Mismatches: 86, Indels: 9
0.81 0.17 0.02
Matches are distributed among these distances:
45 37 0.09
47 349 0.86
48 21 0.05
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (47 bp):
GCTTCAATCTACCCCTCTGGATTTGGGGTATAAGACTAGATGTGGTG
Found at i:38501 original size:94 final size:94
Alignment explanation
Indices: 38350--38894 Score: 571
Period size: 94 Copynumber: 5.8 Consensus size: 94
38340 TTCTTCTGTA
* * *
38350 GCTTCAATCTGCCCCTCTGGATTTAGGGGTATAAGATTGGATTTGGTGGCTTCAATCTATCCCTC
1 GCTTCAATCTGCCCTTCTGGATTTA-GGGTATAAGATTGGATGTGGTGGCTTCAATCTACCCCTC
* *
38415 TAGATTTGGGGTATAAGACTAGATATGATG
65 TGGATTTGGGGTATAAGACTAGATGTGATG
* * * *
38445 GCTTCAATATGCCCTTCTGAATTTAGGGTATAAGATTAGATGTGGTGGCTTTAATCTACCCCTCT
1 GCTTCAATCTGCCCTTCTGGATTTAGGGTATAAGATTGGATGTGGTGGCTTCAATCTACCCCTCT
* * * * *
38510 TGATTTGGGATATAAGATTGGATGTGGTG
66 GGATTTGGGGTATAAGACTAGATGTGATG
* * * *
38539 GCTTCAATCTGCCATTCTCGATTTAGGGTATAAGATTGGA--TGGTGGCTTTAATCTGA-CCCTT
1 GCTTCAATCTGCCCTTCTGGATTTAGGGTATAAGATTGGATGTGGTGGCTTCAATCT-ACCCCTC
* *
38601 TGGATTTGGGGTATAAGATTGGATGTGATG
65 TGGATTTGGGGTATAAGACTAGATGTGATG
* * * ** * * ** * * *
38631 ACTTTAATCTGTGCCTT-TTAATTTGGGGTATAAGACTGGATACGATGGCTTCAATCTGCCCTTC
1 GCTTCAATCTG-CCCTTCTGGATTTAGGGTATAAGATTGGATGTGGTGGCTTCAATCTACCCCTC
* *
38695 TGGATTTGAGGTATAAGACTAGATGTGATA
65 TGGATTTGGGGTATAAGACTAGATGTGATG
* * ** * **
38725 GCTTCAATCTGCCCCTCTGGATTT-GAGGTATAAGACTAAATGCGGTGGCTTCAATCTGTCCCTC
1 GCTTCAATCTGCCCTTCTGGATTTAG-GGTATAAGATTGGATGTGGTGGCTTCAATCTACCCCTC
* *
38789 TGGATTTGAGGTATAAGACTAGATGTGATA
65 TGGATTTGGGGTATAAGACTAGATGTGATG
* * * *
38819 GCTTCAATCTACCTCTT-TGGATTTGGGGTATAAGATTGGATGTGGTGGCTTCAATTTGCCCCTC
1 GCTTCAATCTGCC-CTTCTGGATTTAGGGTATAAGATTGGATGTGGTGGCTTCAATCTACCCCTC
*
38883 TAGATTTGGGGT
65 TGGATTTGGGGT
38895 GTAACACTCA
Statistics
Matches: 379, Mismatches: 62, Indels: 19
0.82 0.13 0.04
Matches are distributed among these distances:
92 74 0.20
93 8 0.02
94 272 0.72
95 25 0.07
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (94 bp):
GCTTCAATCTGCCCTTCTGGATTTAGGGTATAAGATTGGATGTGGTGGCTTCAATCTACCCCTCT
GGATTTGGGGTATAAGACTAGATGTGATG
Found at i:38782 original size:233 final size:235
Alignment explanation
Indices: 38348--38894 Score: 669
Period size: 233 Copynumber: 2.3 Consensus size: 235
38338 TTTTCTTCTG
* * * * *
38348 TAGCTTCAATCTGCCCCTCTGGATTTAGGGGTATAAGATTGGATTTGGTGGCTTCAATCTATCCC
1 TAGCTTCAATCTGACCCTTTGGATTT-GGGGTATAAGATTGGATGTGATGACTTCAATCTATCCC
*
38413 TCTAGATTTGGGGTATAAGACTAGATATGATGGCTTCAATATGCCCTTCTGAATTTAGGGTATAA
65 TCTAGATTTGGGGTATAAGACTAGATACGATGGCTTCAATATGCCCTTCTGAATTTAGGGTATAA
* * * * * * ** *
38478 GATTAGATGTGGTGGCTTTAATCTACCCCTCTTGATTTGGGATATAAGATTGGATGTGGTGGCTT
130 GACTAGATGTGATAGCTTCAATCTACCCCTCTGGATTTGGGATATAAGACTAAATGCGGTGGCTT
* * *
38543 CAATCTG-CCATTCTCGATTT-AGGGTATAAGATTGGATG-G-
195 CAATCTGTCC-CTCTCGATTTGA-GGTATAAGACTAGATGTGA
* * * * *
38582 TGGCTTTAATCTGACCCTTTGGATTTGGGGTATAAGATTGGATGTGATGACTTTAATCTGTGCCT
1 TAGCTTCAATCTGACCCTTTGGATTTGGGGTATAAGATTGGATGTGATGACTTCAATCTAT-CCC
* * * *
38647 TTTA-ATTTGGGGTATAAGACTGGATACGATGGCTTCAATCTGCCCTTCTGGATTT-GAGGTATA
65 TCTAGATTTGGGGTATAAGACTAGATACGATGGCTTCAATATGCCCTTCTGAATTTAG-GGTATA
*
38710 AGACTAGATGTGATAGCTTCAATCTGCCCCTCTGGATTTGAGG-TATAAGACTAAATGCGGTGGC
129 AGACTAGATGTGATAGCTTCAATCTACCCCTCTGGATTTG-GGATATAAGACTAAATGCGGTGGC
*
38774 TTCAATCTGTCCCTCTGGATTTGAGGTATAAGACTAGATGTGA
193 TTCAATCTGTCCCTCTCGATTTGAGGTATAAGACTAGATGTGA
* * * **
38817 TAGCTTCAATCT-ACCTCTTTGGATTTGGGGTATAAGATTGGATGTGGTGGCTTCAATTTGCCCC
1 TAGCTTCAATCTGACC-CTTTGGATTTGGGGTATAAGATTGGATGTGATGACTTCAATCTATCCC
38881 TCTAGATTTGGGGT
65 TCTAGATTTGGGGT
38895 GTAACACTCA
Statistics
Matches: 266, Mismatches: 38, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
232 1 0.00
233 165 0.62
234 41 0.15
235 59 0.22
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (235 bp):
TAGCTTCAATCTGACCCTTTGGATTTGGGGTATAAGATTGGATGTGATGACTTCAATCTATCCCT
CTAGATTTGGGGTATAAGACTAGATACGATGGCTTCAATATGCCCTTCTGAATTTAGGGTATAAG
ACTAGATGTGATAGCTTCAATCTACCCCTCTGGATTTGGGATATAAGACTAAATGCGGTGGCTTC
AATCTGTCCCTCTCGATTTGAGGTATAAGACTAGATGTGA
Found at i:38803 original size:141 final size:141
Alignment explanation
Indices: 38350--38890 Score: 545
Period size: 141 Copynumber: 3.8 Consensus size: 141
38340 TTCTTCTGTA
* * * *
38350 GCTTCAATCTGCCCCTCTGGATTTAGGGGTATAAGATTGGATTTGGTGGCTTCAATCTATCCC-T
1 GCTTCAATCTGCCCCTCTGGATTT-GGGGTATAAGACTGGATGTGATGGCTTCAATCT-GCCCTT
* * * * * *
38414 CTAGATTTGGGGTATAAGACTAGATATGATGGCTTCAATATGCCCTTCTGAATTT-AGGGTATAA
64 CTGGATTTGAGGTATAAGACTAGATGTGATGGCTTCAATCTGCCCCTCTGGATTTGA-GGTATAA
38478 GATTAGATGTGGTG
128 GATTAGATGTGGTG
* * * * * * *
38492 GCTTTAATCTACCCCTCTTGATTTGGGATATAAGATTGGATGTGGTGGCTTCAATCTGCCATTCT
1 GCTTCAATCTGCCCCTCTGGATTTGGGGTATAAGACTGGATGTGATGGCTTCAATCTGCCCTTCT
* * * * * * *
38557 CGATTT-AGGGTATAAGATTGGATG-G-TGGCTTTAATCTGACCCTTTGGATTTGGGGTATAAGA
66 GGATTTGA-GGTATAAGACTAGATGTGATGGCTTCAATCTGCCCCTCTGGATTTGAGGTATAAGA
* *
38619 TTGGATGTGATG
130 TTAGATGTGGTG
* * ** * ** **
38631 ACTTTAATCTGTGCCTTTTAATTTGGGGTATAAGACTGGATACGATGGCTTCAATCTGCCCTTCT
1 GCTTCAATCTGCCCCTCTGGATTTGGGGTATAAGACTGGATGTGATGGCTTCAATCTGCCCTTCT
* *
38696 GGATTTGAGGTATAAGACTAGATGTGATAGCTTCAATCTGCCCCTCTGGATTTGAGGTATAAGAC
66 GGATTTGAGGTATAAGACTAGATGTGATGGCTTCAATCTGCCCCTCTGGATTTGAGGTATAAGAT
* *
38761 TAAATGCGGTG
131 TAGATGTGGTG
* * * * *
38772 GCTTCAATCTGTCCCTCTGGATTTGAGGTATAAGACTAGATGTGATAGCTTCAATCTACCTCTT-
1 GCTTCAATCTGCCCCTCTGGATTTGGGGTATAAGACTGGATGTGATGGCTTCAATCTGCC-CTTC
* * * * * *
38836 TGGATTTGGGGTATAAGATTGGATGTGGTGGCTTCAATTTGCCCCTCTAGATTTG
65 TGGATTTGAGGTATAAGACTAGATGTGATGGCTTCAATCTGCCCCTCTGGATTTG
38891 GGGTGTAACA
Statistics
Matches: 327, Mismatches: 65, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
139 111 0.34
140 5 0.02
141 187 0.57
142 24 0.07
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (141 bp):
GCTTCAATCTGCCCCTCTGGATTTGGGGTATAAGACTGGATGTGATGGCTTCAATCTGCCCTTCT
GGATTTGAGGTATAAGACTAGATGTGATGGCTTCAATCTGCCCCTCTGGATTTGAGGTATAAGAT
TAGATGTGGTG
Found at i:40309 original size:37 final size:37
Alignment explanation
Indices: 40268--40411 Score: 207
Period size: 37 Copynumber: 3.9 Consensus size: 37
40258 AATCATCAAG
*
40268 CATTATGCTCTAACCGAGACGTAAGCCTTCCATATAA
1 CATTACGCTCTAACCGAGACGTAAGCCTTCCATATAA
* * * * *
40305 CATTACGCTCTAATCGAGATGTGAGTCTTACATATAA
1 CATTACGCTCTAACCGAGACGTAAGCCTTCCATATAA
*
40342 CATTACGCTCTAACCGAGACGTAAGCTTTCCATATAA
1 CATTACGCTCTAACCGAGACGTAAGCCTTCCATATAA
**
40379 CATTACAATCTAACCGAGACGTAAGCCTTCCAT
1 CATTACGCTCTAACCGAGACGTAAGCCTTCCAT
40412 CAAAGTAGTT
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 92 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (37 bp):
CATTACGCTCTAACCGAGACGTAAGCCTTCCATATAA
Found at i:42774 original size:47 final size:47
Alignment explanation
Indices: 42723--43234 Score: 380
Period size: 47 Copynumber: 10.9 Consensus size: 47
42713 AATGCGGTGA
*
42723 CTTCAATCTTTCCCTTTAGATTTAGGGTATAAGACTAGATGTGATAG
1 CTTCAATCTTCCCCTTTAGATTTAGGGTATAAGACTAGATGTGATAG
* * * * *
42770 CTTCAAAT-TGCCCCTCTAGATTTAAGGTATAAGACTGGATGTGAAAG
1 CTTC-AATCTTCCCCTTTAGATTTAGGGTATAAGACTAGATGTGATAG
* * * **
42817 CTTCAATC-TACCCTTCTAGATTT-GAGGTATCAGACTCGATACGATAG
1 CTTCAATCTTCCCCTT-TAGATTTAG-GGTATAAGACTAGATGTGATAG
* * * * *
42864 CTTCAAT-TTGCTCCTCT-GAATTTGGGGTTTAAGACTAGATGTGATAA
1 CTTCAATCTT-CCCCTTTAG-ATTTAGGGTATAAGACTAGATGTGATAG
** * * * * *
42911 CTTCAAT-TTGCCTTTTTGGATTTTGGGTATAAGATTGGATGTGATGG
1 CTTCAATCTT-CCCCTTTAGATTTAGGGTATAAGACTAGATGTGATAG
* *
42958 CTTCAAT-TCACCCCTCTAGATTT-GTGGTATAAGACTAGATGTGATTA-
1 CTTCAATCT-TCCCCTTTAGATTTAG-GGTATAAGACTAGATGTGA-TAG
* * * *
43005 CTTTAATCTT-CCCTTCTAGATTTAGGGTATGAGATTTTGATGTGATAG
1 CTTCAATCTTCCCCTT-TAGATTTAGGGTATAAGA-CTAGATGTGATAG
* **
43053 CTTCAATCTGCCTTTTTAGATTTAGGGTATAAGACTAGATGTGATAG
1 CTTCAATCTTCCCCTTTAGATTTAGGGTATAAGACTAGATGTGATAG
* * * * * * * * * *
43100 ATTCATTCTACCCCTCTAAATTTGGGGTAAAAAATTAGATGTGATGG
1 CTTCAATCTTCCCCTTTAGATTTAGGGTATAAGACTAGATGTGATAG
** * * * *
43147 CTTCAATCTGACCCTTTAAATTTGGGGTATAAGACTGGATGTGATGG
1 CTTCAATCTTCCCCTTTAGATTTAGGGTATAAGACTAGATGTGATAG
* * *
43194 CTTCAATCTGCCCCTCTAGATTT-GAGGTATAAGATTAGATG
1 CTTCAATCTTCCCCTTTAGATTTAG-GGTATAAGACTAGATG
43235 GTCACTAGAC
Statistics
Matches: 365, Mismatches: 81, Indels: 38
0.75 0.17 0.08
Matches are distributed among these distances:
46 14 0.04
47 304 0.83
48 44 0.12
49 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (47 bp):
CTTCAATCTTCCCCTTTAGATTTAGGGTATAAGACTAGATGTGATAG
Found at i:42863 original size:94 final size:93
Alignment explanation
Indices: 42723--43234 Score: 460
Period size: 94 Copynumber: 5.4 Consensus size: 93
42713 AATGCGGTGA
* *
42723 CTTCAATCTTTCCCTT-TAGATTT-AGGGTATAAGACTAGATGTGATAGCTTCAAATTGCCCCTC
1 CTTCAATC-TACCCTTCTAGATTTGA-GGTATAAGATTAGATGTGATAGCTTC-AATTGCCCCTC
** * *
42786 TAGATTTAAGGTATAAGACTGGATGTGAAAG
63 TAGATTTGGGGTATAAGACTAGATGTGATAG
* * * ** *
42817 CTTCAATCTACCCTTCTAGATTTGAGGTATCAGACTCGATACGATAGCTTCAATTTGCTCCTCT-
1 CTTCAATCTACCCTTCTAGATTTGAGGTATAAGATTAGATGTGATAGCTTCAA-TTGCCCCTCTA
* *
42881 GAATTTGGGGTTTAAGACTAGATGTGATAA
65 G-ATTTGGGGTATAAGACTAGATGTGATAG
* * * * * * * *
42911 CTTCAATTTGCCTTTTTGGATTTTG-GGTATAAGATTGGATGTGATGGCTTCAATTCACCCCTCT
1 CTTCAATCTACCCTTCTAGA-TTTGAGGTATAAGATTAGATGTGATAGCTTCAATT-GCCCCTCT
*
42975 AGATTTGTGGTATAAGACTAGATGTGATTA-
64 AGATTTGGGGTATAAGACTAGATGTGA-TAG
* * * * ** *
43005 CTTTAATCTTCCCTTCTAGATTT-AGGGTATGAGATTTTGATGTGATAGCTTCAATCTGCCTTTT
1 CTTCAATCTACCCTTCTAGATTTGA-GGTATAAGA-TTAGATGTGATAGCTTCAAT-TGCCCCTC
*
43069 TAGATTTAGGGTATAAGACTAGATGTGATAG
63 TAGATTTGGGGTATAAGACTAGATGTGATAG
* * * * * * * * * *
43100 ATTCATTCTACCCCTCTAAATTTGGGGTAAAAAATTAGATGTGATGGCTTCAATCTGACCCTTTA
1 CTTCAATCTACCCTTCTAGATTTGAGGTATAAGATTAGATGTGATAGCTTCAAT-TGCCCCTCTA
* * *
43165 AATTTGGGGTATAAGACTGGATGTGATGG
65 GATTTGGGGTATAAGACTAGATGTGATAG
* *
43194 CTTCAATCTGCCCCTCTAGATTTGAGGTATAAGATTAGATG
1 CTTCAATCTACCCTTCTAGATTTGAGGTATAAGATTAGATG
43235 GTCACTAGAC
Statistics
Matches: 336, Mismatches: 68, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
93 14 0.04
94 243 0.72
95 78 0.23
96 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (93 bp):
CTTCAATCTACCCTTCTAGATTTGAGGTATAAGATTAGATGTGATAGCTTCAATTGCCCCTCTAG
ATTTGGGGTATAAGACTAGATGTGATAG
Found at i:43234 original size:141 final size:141
Alignment explanation
Indices: 42723--43234 Score: 489
Period size: 141 Copynumber: 3.6 Consensus size: 141
42713 AATGCGGTGA
* *
42723 CTTCAATCTTTCCCTTTAGATTTAGGGTATAAGACTAGATGTGATAGCTTCAAAT-TGCCCCTCT
1 CTTCAATCTGTCCCTTTAAATTTAGGGTATAAGACTAGATGTGATAGCTTC-AATCTGCCCCTCT
* * * * * *
42787 AGATTTAAGGTATAAGACTGGATGTGAAAGCTTCAATCTACCCTTCTAGATTTGAGGTATCAGAC
65 AGATTTGAGGTATAAGACTAGATGTGATAGCTTCATTCTACCCCTCTAGATTTGAGGTATAAGAC
* **
42852 TCGATACGATAG
130 TAGATGTGATAG
* * * * * * * ** *
42864 CTTCAATTTG-CTCCTCTGAATTTGGGGTTTAAGACTAGATGTGATAACTTCAATTTGCCTTTTT
1 CTTCAATCTGTC-CCTTTAAATTTAGGGTATAAGACTAGATGTGATAGCTTCAATCTGCCCCTCT
* * * * *
42928 GGATTTTG-GGTATAAGATTGGATGTGATGGCTTCAATTC-ACCCCTCTAGATTTGTGGTATAAG
65 AGA-TTTGAGGTATAAGACTAGATGTGATAGCTTC-ATTCTACCCCTCTAGATTTGAGGTATAAG
42991 ACTAGATGTGATTA-
128 ACTAGATGTGA-TAG
* * * * * ** *
43005 CTTTAATCT-TCCCTTCTAGATTTAGGGTATGAGATTTTGATGTGATAGCTTCAATCTGCCTTTT
1 CTTCAATCTGTCCCTT-TAAATTTAGGGTATAAGA-CTAGATGTGATAGCTTCAATCTGCCCCTC
* * * * *
43069 TAGATTT-AGGGTATAAGACTAGATGTGATAGATTCATTCTACCCCTCTAAATTTGGGGTAAAAA
64 TAGATTTGA-GGTATAAGACTAGATGTGATAGCTTCATTCTACCCCTCTAGATTTGAGGTATAAG
* *
43133 ATTAGATGTGATGG
128 ACTAGATGTGATAG
* * * *
43147 CTTCAATCTGACCCTTTAAATTTGGGGTATAAGACTGGATGTGATGGCTTCAATCTGCCCCTCTA
1 CTTCAATCTGTCCCTTTAAATTTAGGGTATAAGACTAGATGTGATAGCTTCAATCTGCCCCTCTA
*
43212 GATTTGAGGTATAAGATTAGATG
66 GATTTGAGGTATAAGACTAGATG
43235 GTCACTAGAC
Statistics
Matches: 299, Mismatches: 58, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
140 7 0.02
141 175 0.59
142 112 0.37
143 5 0.02
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (141 bp):
CTTCAATCTGTCCCTTTAAATTTAGGGTATAAGACTAGATGTGATAGCTTCAATCTGCCCCTCTA
GATTTGAGGTATAAGACTAGATGTGATAGCTTCATTCTACCCCTCTAGATTTGAGGTATAAGACT
AGATGTGATAG
Found at i:47360 original size:21 final size:21
Alignment explanation
Indices: 47280--47377 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
47270 GGAGCACTGA
**
47280 AGTGCAATACAGGGGCA-TTG
1 AGTGCAATACAGGGGCACCAG
* *
47300 AAGTGCAATATAGGGGCACTAG
1 -AGTGCAATACAGGGGCACCAG
*
47322 AGTGCAATATAGGGGCACCAG
1 AGTGCAATACAGGGGCACCAG
*
47343 AGTGCAATACAGGGGCACCAA
1 AGTGCAATACAGGGGCACCAG
* *
47364 AGTGTATTACAGGG
1 AGTGCAATACAGGG
47378 TTCTTACTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 67 0.97
22 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.33, T:0.17
Consensus pattern (21 bp):
AGTGCAATACAGGGGCACCAG
Found at i:51769 original size:21 final size:22
Alignment explanation
Indices: 51745--51790 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
51735 TTGTATGGTG
* *
51745 TGAA-TAAAAATGTTTGTCAAA
1 TGAATTAAAAATATTTGCCAAA
*
51766 TGAATTTAAAATATTTGCCAAA
1 TGAATTAAAAATATTTGCCAAA
51788 TGA
1 TGA
51791 GACAGAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.35
Consensus pattern (22 bp):
TGAATTAAAAATATTTGCCAAA
Found at i:52347 original size:59 final size:58
Alignment explanation
Indices: 52255--52371 Score: 173
Period size: 59 Copynumber: 2.0 Consensus size: 58
52245 TAGGGGTCGC
*
52255 ATTGGTTCTACATAGAATGGCAACACAACACAGGCGTCGAATTGGTTCTAATACAGCTT
1 ATTGGTTCTACATAG-ATGGCAACACAACACAGGCGTCAAATTGGTTCTAATACAGCTT
* *
52314 ATTGGTTCTACATAG-TGCAGCGACATAACACAGGCGTCAAATTGGTTCTAATACAGCT
1 ATTGGTTCTACATAGATG--GCAACACAACACAGGCGTCAAATTGGTTCTAATACAGCT
52372 CTTTATATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
57 2 0.04
59 51 0.96
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (58 bp):
ATTGGTTCTACATAGATGGCAACACAACACAGGCGTCAAATTGGTTCTAATACAGCTT
Found at i:57555 original size:12 final size:13
Alignment explanation
Indices: 57535--57567 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
57525 ATAAAATGGA
57535 TTTTT-TTTTA-T
1 TTTTTATTTTATT
57546 TTTTTATTTTATT
1 TTTTTATTTTATT
57559 TTTTTATTT
1 TTTTTATTT
57568 GGGTTTCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 5 0.25
13 10 0.50
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:58992 original size:39 final size:40
Alignment explanation
Indices: 58949--59170 Score: 233
Period size: 39 Copynumber: 5.7 Consensus size: 40
58939 CTAGTAGTTC
* * *
58949 TTACAGTGTCACTACTACTTCAGTATAGCATTATGA-TGT
1 TTACAGTGTCACTACCAGTTCAGTATAGCACTATGAGTGT
* * *
58988 TTACAATATCACCACCAGTTCAGTATAGCA-T-TGCAGTGT
1 TTACAGTGTCACTACCAGTTCAGTATAGCACTATG-AGTGT
* * *
59027 TTATAGTGTCACTACCAGTTTAGTATAGCACTA-CAGTGT
1 TTACAGTGTCACTACCAGTTCAGTATAGCACTATGAGTGT
* * *
59066 TTATAGTGTCACTACCAGTTCAGTATAGCACTA-CAATGT
1 TTACAGTGTCACTACCAGTTCAGTATAGCACTATGAGTGT
* * * *
59105 GTACAGTGTCACTGCTAGTTCAATATAGCA-T-TGTAGTGT
1 TTACAGTGTCACTACCAGTTCAGTATAGCACTATG-AGTGT
59144 TTACAGTGTCACTACCAGTTCAGTATA
1 TTACAGTGTCACTACCAGTTCAGTATA
59171 TATTCTTAAG
Statistics
Matches: 153, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
37 2 0.01
38 3 0.02
39 147 0.96
40 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (40 bp):
TTACAGTGTCACTACCAGTTCAGTATAGCACTATGAGTGT
Found at i:59054 original size:22 final size:22
Alignment explanation
Indices: 59028--59093 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
59018 TTGCAGTGTT
59028 TATAGTGTCACTACCAGTTTAG
1 TATAGTGTCACTACCAGTTTAG
59050 TATA--G-CACTA-CAGTGTT--
1 TATAGTGTCACTACCAGT-TTAG
*
59067 TATAGTGTCACTACCAGTTCAG
1 TATAGTGTCACTACCAGTTTAG
59089 TATAG
1 TATAG
59094 CACTACAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
17 4 0.11
18 4 0.11
19 8 0.22
20 7 0.19
21 4 0.11
22 9 0.25
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (22 bp):
TATAGTGTCACTACCAGTTTAG
Found at i:59058 original size:19 final size:19
Alignment explanation
Indices: 59036--59099 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
59026 TTTATAGTGT
59036 CACTACCAGTTTAGTATAG
1 CACTACCAGTTTAGTATAG
59055 CACTA-CAGTGTT--TATAGTG
1 CACTACCAGT-TTAGTATA--G
*
59074 TCACTACCAGTTCAGTATAG
1 -CACTACCAGTTTAGTATAG
59094 CACTAC
1 CACTAC
59100 AATGTGTACA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
17 4 0.11
18 4 0.11
19 14 0.38
20 7 0.19
21 4 0.11
22 4 0.11
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (19 bp):
CACTACCAGTTTAGTATAG
Found at i:59067 original size:78 final size:77
Alignment explanation
Indices: 58950--59170 Score: 262
Period size: 78 Copynumber: 2.8 Consensus size: 77
58940 TAGTAGTTCT
* * * * *
58950 TACAGTGTCACTACTACTTCAGTATAGCATTATGATGTTTACAATATCACCACCAGTTCAGTATA
1 TACAGTGTCACTACTAGTTCAGTATAGCATTAAG-TGTTTACAGTGTCACTACCAGTTCAGTATA
* * * *
59015 GCATTGCAGTGTT
65 GCACTACAATGTG
* * * * *
59028 TATAGTGTCACTACCAGTTTAGTATAGCACTACAGTGTTTATAGTGTCACTACCAGTTCAGTATA
1 TACAGTGTCACTACTAGTTCAGTATAGCATTA-AGTGTTTACAGTGTCACTACCAGTTCAGTATA
59093 GCACTACAATGTG
65 GCACTACAATGTG
* * *
59106 TACAGTGTCACTGCTAGTTCAATATAGCATTGTAGTGTTTACAGTGTCACTACCAGTTCAGTATA
1 TACAGTGTCACTACTAGTTCAGTATAGCATT-AAGTGTTTACAGTGTCACTACCAGTTCAGTATA
59171 TATTCTTAAG
Statistics
Matches: 119, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
78 118 0.99
79 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (77 bp):
TACAGTGTCACTACTAGTTCAGTATAGCATTAAGTGTTTACAGTGTCACTACCAGTTCAGTATAG
CACTACAATGTG
Found at i:59078 original size:20 final size:20
Alignment explanation
Indices: 59021--59080 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
59011 TATAGCATTG
59021 CAGTGTTTATAGTGTCACTA
1 CAGTGTTTATAGTGTCACTA
59041 CCA--GTTTAGTA-TAG-CACTA
1 -CAGTGTTTA-TAGT-GTCACTA
59060 CAGTGTTTATAGTGTCACTA
1 CAGTGTTTATAGTGTCACTA
59080 C
1 C
59081 CAGTTCAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
18 2 0.06
19 14 0.42
20 15 0.45
21 2 0.06
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (20 bp):
CAGTGTTTATAGTGTCACTA
Found at i:59143 original size:117 final size:117
Alignment explanation
Indices: 58953--59170 Score: 301
Period size: 117 Copynumber: 1.9 Consensus size: 117
58943 TAGTTCTTAC
* * ** * *
58953 AGTGTCACTACTACTTCAGTATAGCATTATGATGTTTACAATATCACCACCAGTTCAGTATAGCA
1 AGTGTCACTACCACTTCAGTATAGCACTACAATGTGTACAATATCACCACCAGTTCAATATAGCA
* *
59018 TTGCAGTGTTTATAGTGTCACTACCAGTTTAGTATAGCACTACAGTGTTTAT
66 TTGCAGTGTTTACAGTGTCACTACCAGTTCAGTATAGCACTACAGTGTTTAT
* * * ** *
59070 AGTGTCACTACCAGTTCAGTATAGCACTACAATGTGTACAGTGTCACTGCTAGTTCAATATAGCA
1 AGTGTCACTACCACTTCAGTATAGCACTACAATGTGTACAATATCACCACCAGTTCAATATAGCA
*
59135 TTGTAGTGTTTACAGTGTCACTACCAGTTCAGTATA
66 TTGCAGTGTTTACAGTGTCACTACCAGTTCAGTATA
59171 TATTCTTAAG
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
117 86 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (117 bp):
AGTGTCACTACCACTTCAGTATAGCACTACAATGTGTACAATATCACCACCAGTTCAATATAGCA
TTGCAGTGTTTACAGTGTCACTACCAGTTCAGTATAGCACTACAGTGTTTAT
Found at i:67184 original size:39 final size:39
Alignment explanation
Indices: 67137--67379 Score: 351
Period size: 39 Copynumber: 6.2 Consensus size: 39
67127 GTATTACTAC
* *
67137 TTCAGTATAGTATTGCGGTGTTTACAGTGTCACTGCCAG
1 TTCAGTATAGCATTGCAGTGTTTACAGTGTCACTGCCAG
* * * *
67176 TTCAGTATAGCATTACAGTGTTTATAGTGTCACTGTCAA
1 TTCAGTATAGCATTGCAGTGTTTACAGTGTCACTGCCAG
67215 TTCAGTATAGCATTGCAGTGTTTACAGTGTCACTGCCAG
1 TTCAGTATAGCATTGCAGTGTTTACAGTGTCACTGCCAG
* * * *
67254 TTCAATATAGCATTACAGTGTTCACAGTGTCAATGCCAG
1 TTCAGTATAGCATTGCAGTGTTTACAGTGTCACTGCCAG
* * *
67293 TTCAGTATAGCATTGTAGTGTTTACAATGTCACTGCCAA
1 TTCAGTATAGCATTGCAGTGTTTACAGTGTCACTGCCAG
* *
67332 TTCAGTATAGCATTGCAGTGTTTATAGTATCACTGCCAG
1 TTCAGTATAGCATTGCAGTGTTTACAGTGTCACTGCCAG
67371 TTCAGTATA
1 TTCAGTATA
67380 TATTCATAAA
Statistics
Matches: 178, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 178 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (39 bp):
TTCAGTATAGCATTGCAGTGTTTACAGTGTCACTGCCAG
Found at i:71419 original size:36 final size:36
Alignment explanation
Indices: 71366--71502 Score: 213
Period size: 36 Copynumber: 3.8 Consensus size: 36
71356 TGGTAACAGG
71366 CATGACCTTT-GGCTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTAGG-TCAACAGGGAGTAAAATGAGCAT
* *
71402 TATGACCTTTAGGTCAACAGGGAGTAAAGTGAGCAT
1 CATGACCTTTAGGTCAACAGGGAGTAAAATGAGCAT
*
71438 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTAGGTCAACAGGGAGTAAAATGAGCAT
* *
71474 CATGACCTTTAGCTCAATAGGGAGTAAAA
1 CATGACCTTTAGGTCAACAGGGAGTAAAA
71503 CGAATAACAA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
36 90 0.98
37 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (36 bp):
CATGACCTTTAGGTCAACAGGGAGTAAAATGAGCAT
Found at i:71483 original size:72 final size:72
Alignment explanation
Indices: 71366--71501 Score: 236
Period size: 72 Copynumber: 1.9 Consensus size: 72
71356 TGGTAACAGG
* *
71366 CATGACCTTTGGCTCAACAGGGAGTAAAATGAGCATTATGACCTTTAGGTCAACAGGGAGTAAAG
1 CATGACCTTTGGCTCAACAGGGAGTAAAATGAGCATCATGACCTTTAGCTCAACAGGGAGTAAAG
71431 TGAGCAT
66 TGAGCAT
* *
71438 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATCATGACCTTTAGCTCAATAGGGAGTAAA
1 CATGACCTTTGGCTCAACAGGGAGTAAAATGAGCATCATGACCTTTAGCTCAACAGGGAGTAAA
71502 ACGAATAACA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (72 bp):
CATGACCTTTGGCTCAACAGGGAGTAAAATGAGCATCATGACCTTTAGCTCAACAGGGAGTAAAG
TGAGCAT
Found at i:72204 original size:21 final size:21
Alignment explanation
Indices: 72170--72220 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
72160 TAGATGCTTG
* *
72170 ACTTGTTTCGGTAAAAAAGTC
1 ACTTGTATCAGTAAAAAAGTC
* **
72191 TCTTGTATCAGTAAAACTGTC
1 ACTTGTATCAGTAAAAAAGTC
72212 ACTTGTATC
1 ACTTGTATC
72221 GGTAGAAGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (21 bp):
ACTTGTATCAGTAAAAAAGTC
Found at i:73870 original size:39 final size:39
Alignment explanation
Indices: 73821--73950 Score: 115
Period size: 39 Copynumber: 3.3 Consensus size: 39
73811 CCATTAACCA
*
73821 ATCTCTTACCCCGCGACAGGGGCAGATTGTAACCATCCG
1 ATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATCCG
* * * * *
73860 ATCTTTTA-CCC-CGATCATAGGGCAGA-T-CACCGTCAGCCA
1 ATCTCTTACCCCGCGA-CA-GGGGCAGATTGCAAC--CATCCG
* *
73899 ATCTCTTACCCCGCGACAGGGGCATATTGCAACCATTCG
1 ATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATCCG
*
73938 ATCTTTTACCCCG
1 ATCTCTTACCCCG
73951 ATCATGAGGC
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
37 5 0.07
38 6 0.09
39 46 0.67
40 6 0.09
41 6 0.09
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATCCG
Found at i:73940 original size:78 final size:78
Alignment explanation
Indices: 73818--74354 Score: 687
Period size: 78 Copynumber: 6.9 Consensus size: 78
73808 TCACCATTAA
* * *
73818 CCAATCTCTTACCCCGCGACAGGGGCAGATTGTAACCATCCGATCTTTTACCCCGATCATAGGGC
1 CCAATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATTCGATCTTTTACCCCGATCATGGGGC
73883 AGATCACCGTCAG
66 AGATCACCGTCAG
* *
73896 CCAATCTCTTACCCCGCGACAGGGGCATATTGCAACCATTCGATCTTTTACCCCGATCATGAGGC
1 CCAATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATTCGATCTTTTACCCCGATCATGGGGC
*
73961 ATATCACCGTCAG
66 AGATCACCGTCAG
* ** * * * *
73974 CCAGTCTCTTACCCCGTAATAGGGGCAGATTGTAACTATCCGATCTTTTACCCCGATCATGGGGC
1 CCAATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATTCGATCTTTTACCCCGATCATGGGGC
* *
74039 AGATCACCATCAA
66 AGATCACCGTCAG
* * * * * *
74052 CCAATCTCTTACCCCACAACAGGGGTAGATTGCAACCATTTGATATTTTAACCCGATCATGGGGC
1 CCAATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATTCGATCTTTTACCCCGATCATGGGGC
*
74117 AGATCACTGTCAG
66 AGATCACCGTCAG
* * * * *
74130 CCAATCTCTTACCTCACGACAAGTGCAGATTGCAACCATTCGATCTTTTACCCCAATCATGGGGC
1 CCAATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATTCGATCTTTTACCCCGATCATGGGGC
*
74195 AGATCACCGTCAA
66 AGATCACCGTCAG
* * * ** * * *** *
74208 TCAATCTCTTACCCCACGATAAAGGCAGATTGCAACCATTCGATCTTTTACACCAATCATTATGT
1 CCAATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATTCGATCTTTTACCCCGATCATGGGGC
74273 AGATCACCGTCAG
66 AGATCACCGTCAG
* * * *
74286 TCAATCTCTTACCCCGCGACAGGGGCAAATTGCAACCATTCGATCTTTTACTCTGATCATGGGGC
1 CCAATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATTCGATCTTTTACCCCGATCATGGGGC
74351 AGAT
66 AGAT
74355 TGAAGACATC
Statistics
Matches: 393, Mismatches: 66, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 393 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (78 bp):
CCAATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATTCGATCTTTTACCCCGATCATGGGGC
AGATCACCGTCAG
Found at i:74064 original size:39 final size:39
Alignment explanation
Indices: 73854--74222 Score: 135
Period size: 39 Copynumber: 9.5 Consensus size: 39
73844 AGATTGTAAC
* * * *
73854 CATCCGATCTTTTACCCCGATCATAGGGCAGATCACCGT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATCACCAT
* * ** * *
73893 CAGCCAATCTCTTACCCCGCGA-CA-GGGGCATATTGCAAC
1 CATCCAATCTCTTA-CCC-CGATCATGGGGCAGATCACCAT
* * * * * *
73932 CATTCGATCTTTTACCCCGATCATGAGGCATATCACCGT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATCACCAT
* * * * *
73971 CAGCCAGTCTCTTACCCCG-TAATAGGGGCAGATTGTAAC-T
1 CATCCAATCTCTTACCCCGATCAT-GGGGCAGA-T-CACCAT
* *
74011 -ATCCGATCTTTTACCCCGATCATGGGGCAGATCACCAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATCACCAT
* * * * ** * *
74049 CAACCAATCTCTTACCCCACAACA-GGGGTAGATTGCAAC
1 CATCCAATCTCTTACCCC-GATCATGGGGCAGATCACCAT
*** * * * **
74088 CATTTGATATTTTAACCCGATCATGGGGCAGATCACTGT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATCACCAT
* * * ** * *
74127 CAGCCAATCTCTTACCTCACGA-CA-AGTGCAGATTGCAAC
1 CATCCAATCTCTTACC-C-CGATCATGGGGCAGATCACCAT
* * * * *
74166 CATTCGATCTTTTACCCCAATCATGGGGCAGATCACCGT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATCACCAT
74205 CAAT-CAATCTCTTACCCC
1 C-ATCCAATCTCTTACCCC
74223 ACGATAAAGG
Statistics
Matches: 223, Mismatches: 90, Indels: 34
0.64 0.26 0.10
Matches are distributed among these distances:
37 7 0.03
38 16 0.07
39 174 0.78
40 18 0.08
41 8 0.04
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (39 bp):
CATCCAATCTCTTACCCCGATCATGGGGCAGATCACCAT
Found at i:74375 original size:42 final size:42
Alignment explanation
Indices: 74328--74461 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 42
74318 CAACCATTCG
* *
74328 ATCTTTTACTCTGATCATGGGGCAGATTGAAGACATCATCTA
1 ATCTTTTACCCTGATCATGGGGCAGATTGAAGACATCATCCA
* * *
74370 ATCTTTTACCCTAATCA-GAGGGCAGATTAAATACA-CA-CCA
1 ATCTTTTACCCTGATCATG-GGGCAGATTGAAGACATCATCCA
* * *
74410 ATCTCTTACCCCGATCATAGGGCAGATTGAAGACATCATCCA
1 ATCTTTTACCCTGATCATGGGGCAGATTGAAGACATCATCCA
*
74452 ATCTTCTACC
1 ATCTTTTACC
74462 TCTAAATCAA
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
40 30 0.40
41 5 0.07
42 40 0.53
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (42 bp):
ATCTTTTACCCTGATCATGGGGCAGATTGAAGACATCATCCA
Found at i:74420 original size:40 final size:42
Alignment explanation
Indices: 74347--74455 Score: 132
Period size: 40 Copynumber: 2.6 Consensus size: 42
74337 TCTGATCATG
* * * *
74347 GGGCAGATTGAAGACATCATCTAATCTTTTACCCTAATCAGA
1 GGGCAGATTAAAGACATCATCCAATCTCTTACCCCAATCAGA
* * *
74389 GGGCAGATTAAATACA-CA-CCAATCTCTTACCCCGATCATA
1 GGGCAGATTAAAGACATCATCCAATCTCTTACCCCAATCAGA
*
74429 GGGCAGATTGAAGACATCATCCAATCT
1 GGGCAGATTAAAGACATCATCCAATCT
74456 TCTACCTCTA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
40 31 0.55
41 4 0.07
42 21 0.38
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (42 bp):
GGGCAGATTAAAGACATCATCCAATCTCTTACCCCAATCAGA
Found at i:76493 original size:30 final size:30
Alignment explanation
Indices: 76406--76793 Score: 314
Period size: 29 Copynumber: 13.1 Consensus size: 30
76396 ACATTATTGA
* **
76406 CCCT-AACTTTTCCAAAATTTTATTTTAAC
1 CCCTAAACTTTTCTAAAATTACATTTTAAC
* *
76435 CCCTAAAC-TTTCTAAAA-AATCACGTTTAAC
1 CCCTAAACTTTTCTAAAATTA-CA-TTTTAAC
* *
76465 CCCCAAACTTTTCTAAAATGACATTTTAAAC
1 CCCTAAACTTTTCTAAAATTACATTTT-AAC
* *
76496 CCTTAAACTTTTCCAAAATTACATTTTAAC
1 CCCTAAACTTTTCTAAAATTACATTTTAAC
* * * *
76526 GCTTAAACTTTT-TCAAAAATACATTTTGAC
1 CCCTAAACTTTTCT-AAAATTACATTTTAAC
* *
76556 CCCTTAACTTTT-T-AAATTACATTTTGA-
1 CCCTAAACTTTTCTAAAATTACATTTTAAC
* ** *
76583 CCCTAAACTTCTCCGAAATCACATTTTAAC
1 CCCTAAACTTTTCTAAAATTACATTTTAAC
* *
76613 CTCTAAACTCTTCTAGAAA-TACATTTTGAA-
1 CCCTAAACTTTTCTA-AAATTACATTTT-AAC
* *
76643 CCCTAAACTTTCCTAAAATCACATTTTAA-
1 CCCTAAACTTTTCTAAAATTACATTTTAAC
* * * *
76672 CCCTAAACTTCTCCAAAGTCACATTTTAA-
1 CCCTAAACTTTTCTAAAATTACATTTTAAC
* *
76701 CCCTAAACTTTTCCAAAACTACATTTTAA-
1 CCCTAAACTTTTCTAAAATTACATTTTAAC
* *
76730 CCCTAAACTTTCCTAAAATTACATTTTTAC
1 CCCTAAACTTTTCTAAAATTACATTTTAAC
** **
76760 TACTAAACTTTTTCTAAAATTATGTTTTAAC
1 CCCTAAAC-TTTTCTAAAATTACATTTTAAC
76791 CCC
1 CCC
76794 GTATTCTCCA
Statistics
Matches: 289, Mismatches: 55, Indels: 28
0.78 0.15 0.08
Matches are distributed among these distances:
27 10 0.03
28 13 0.04
29 105 0.36
30 99 0.34
31 61 0.21
32 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
CCCTAAACTTTTCTAAAATTACATTTTAAC
Found at i:80175 original size:23 final size:23
Alignment explanation
Indices: 80148--80198 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
80138 GAACAGTGAG
* *
80148 ATTCTCTGGCATGAATAGTAAAT
1 ATTCTCTAGCATAAATAGTAAAT
80171 ATTCTCTAGCATAAATAGTAAAT
1 ATTCTCTAGCATAAATAGTAAAT
80194 ATTCT
1 ATTCT
80199 TTTAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (23 bp):
ATTCTCTAGCATAAATAGTAAAT
Found at i:80699 original size:17 final size:17
Alignment explanation
Indices: 80679--80711 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
80669 TTTAAGGACT
80679 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
80696 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
80712 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:80975 original size:50 final size:50
Alignment explanation
Indices: 80908--81063 Score: 163
Period size: 50 Copynumber: 3.1 Consensus size: 50
80898 TAACATCCAT
*
80908 TAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAG
1 TAACTCACATG-TTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAG
* * * * * *
80959 TAACTTACATGTTAGTTAAATATGCATCATAAAT-CTTATCATGCATTATG
1 TAACTCACATGTTAGTTAAGTTTGCATCATAAATAATGA-CATGCATTAAG
* * *
81009 TAACTCCCATGTTAGTTAAAGTTTGCATCATTAAATCAA-GTCATGCATTTAG
1 TAACTCACATGTTAGTT-AAGTTTGCATCA-TAAAT-AATGACATGCATTAAG
81061 TAA
1 TAA
81064 TCCATTATTT
Statistics
Matches: 84, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
49 2 0.02
50 46 0.55
51 19 0.23
52 17 0.20
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAG
Found at i:83366 original size:19 final size:20
Alignment explanation
Indices: 83344--83381 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
83334 AATTTTTGAA
83344 ATTTTAAAATA-TAAAAATT
1 ATTTTAAAATATTAAAAATT
*
83363 ATTTTTAAATATTAAAAAT
1 ATTTTAAAATATTAAAAAT
83382 CATTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTTAAAATATTAAAAATT
Found at i:83394 original size:19 final size:18
Alignment explanation
Indices: 83372--83422 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
83362 TATTTTTAAA
*
83372 TATTAAAAATCATTAAATT
1 TATTAAAAAT-ATAAAATT
83391 TATTAAAAAGTATAAAATT
1 TATTAAAAA-TATAAAATT
83410 TATATAAAAATAT
1 TAT-TAAAAATAT
83423 TTTTAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
TATTAAAAATATAAAATT
Found at i:83394 original size:29 final size:29
Alignment explanation
Indices: 83325--83394 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
83315 AACATGTCAA
* * *
83325 CATTTAATTAATTTTTGAAATTTTAAAAT
1 CATTAAATTTATTTTTGAAATTTAAAAAT
* *
83354 -ATAAAAATTATTTTT-AAATATTAAAAAT
1 CATTAAATTTATTTTTGAAAT-TTAAAAAT
83382 CATTAAATTTATT
1 CATTAAATTTATT
83395 AAAAAGTATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
27 4 0.12
28 18 0.56
29 10 0.31
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (29 bp):
CATTAAATTTATTTTTGAAATTTAAAAAT
Found at i:89560 original size:177 final size:177
Alignment explanation
Indices: 89253--89595 Score: 600
Period size: 177 Copynumber: 1.9 Consensus size: 177
89243 GCACCAGCCC
*
89253 CTGCCCATGCCCCTGCAGTTCAGCCAATGGTGATCCCTTCTGGGCCCTGGAATCAACTGAGACCG
1 CTGCCCATGCCCCTGCAGTTCAGCCAATGGTGATCCCTTCTGGGCCCTGGAATCAACCGAGACCG
* * *
89318 GTTCTTGCAGCTCAATGGCGGTTTCAGGGTGTGATTCATGCTTTCACTCTGGGGACTCGACCACT
66 GTTCTTGCAGCTCAATGGCGGTTTCAGGGTGGGATTCATGCTTTCACTCCGGGGACTCAACCACT
*
89383 AGGGCAGTTTCACGGTGGGATCTATGCTTCCACACCTGGGGCATTTT
131 AGGGCAGTTTCACAGTGGGATCTATGCTTCCACACCTGGGGCATTTT
89430 CTGCACCA-GCCCCTGCAGTTCAGCCAATGGTGATCCCTTCTGGGCCCTGGAATCAACCGAGACC
1 CTGC-CCATGCCCCTGCAGTTCAGCCAATGGTGATCCCTTCTGGGCCCTGGAATCAACCGAGACC
*
89494 TGTTCTTGCAGCTCAATGGCGGTTTCAGGGTGGGAATT-ATGCTTTCACTCCGGGGACTCAACCA
65 GGTTCTTGCAGCTCAATGGCGGTTTCAGGGTGGG-ATTCATGCTTTCACTCCGGGGACTCAACCA
89558 CTAGGGCAGTTTCACAGTGGGATCTATGCTTCCACACC
129 CTAGGGCAGTTTCACAGTGGGATCTATGCTTCCACACC
89596 GGGAACTCAA
Statistics
Matches: 158, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
177 152 0.96
178 6 0.04
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.26
Consensus pattern (177 bp):
CTGCCCATGCCCCTGCAGTTCAGCCAATGGTGATCCCTTCTGGGCCCTGGAATCAACCGAGACCG
GTTCTTGCAGCTCAATGGCGGTTTCAGGGTGGGATTCATGCTTTCACTCCGGGGACTCAACCACT
AGGGCAGTTTCACAGTGGGATCTATGCTTCCACACCTGGGGCATTTT
Found at i:90686 original size:26 final size:25
Alignment explanation
Indices: 90657--90720 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 25
90647 ATCGATACAA
* *
90657 AAAATTTAATTTTAAATTTTATTATT
1 AAAATTTAATTTTAAAATATATT-TT
**
90683 AAAAAATAATTTTAAAATATATTTT
1 AAAATTTAATTTTAAAATATATTTT
*
90708 -AAATTTAAATTTA
1 AAAATTTAATTTTA
90721 CAAAATTCGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
24 10 0.32
25 2 0.06
26 19 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AAAATTTAATTTTAAAATATATTTT
Found at i:91826 original size:22 final size:22
Alignment explanation
Indices: 91763--91849 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 22
91753 ATAAATTACA
* *
91763 AGAGAATATTCACTATTTATGCC
1 AGAGAAT-CTCACTATTCATGCC
* * *
91786 AGAGAGTAT-TTACTGTTCATGTC
1 AGAGA--ATCTCACTATTCATGCC
*
91809 AGATAATCTCACTATTCATGCC
1 AGAGAATCTCACTATTCATGCC
91831 AGAGAATCTCACTATTCAT
1 AGAGAATCTCACTATTCAT
91850 TTCATTTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
21 2 0.04
22 29 0.56
23 19 0.37
25 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (22 bp):
AGAGAATCTCACTATTCATGCC
Found at i:98003 original size:47 final size:47
Alignment explanation
Indices: 97950--98039 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
97940 AAGAATGAAC
*
97950 ATGAGATATTCCCTA-CAAGAAAAAACGAAATGAACAGTGAGATAAAT
1 ATGAGATATTCCC-AGCAAGAAAAAACAAAATGAACAGTGAGATAAAT
97997 ATGAGATATTCCCAGCAAGAAAAAACAAAATGAACAGTGAGAT
1 ATGAGATATTCCCAGCAAGAAAAAACAAAATGAACAGTGAGAT
98040 TTTTTGGCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
46 1 0.02
47 40 0.98
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.18
Consensus pattern (47 bp):
ATGAGATATTCCCAGCAAGAAAAAACAAAATGAACAGTGAGATAAAT
Found at i:98617 original size:8 final size:8
Alignment explanation
Indices: 98595--98641 Score: 76
Period size: 8 Copynumber: 5.8 Consensus size: 8
98585 TTTTTATTAA
*
98595 AATTTAAT
1 AATTTTAT
98603 AATTTTTAT
1 AA-TTTTAT
98612 AATTTTAT
1 AATTTTAT
98620 AATTTTAT
1 AATTTTAT
98628 AATTTTAT
1 AATTTTAT
98636 AATTTT
1 AATTTT
98642 TATTGATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
8 30 0.81
9 7 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
AATTTTAT
Found at i:98629 original size:25 final size:26
Alignment explanation
Indices: 98586--98666 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 26
98576 CTTTATAGTT
*
98586 TTTTATTAAAATTTAATAATTTTTATAA
1 TTTTATT--AATTTTATAATTTTTATAA
98614 TTTTA-TAATTTTATAA-TTTTATAA
1 TTTTATTAATTTTATAATTTTTATAA
* *
98638 TTTTTATTGATTTT-T-ATTTTTATCA
1 -TTTTATTAATTTTATAATTTTTATAA
98663 TTTT
1 TTTT
98667 TTCGCCATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
24 13 0.28
25 22 0.47
26 6 0.13
27 1 0.02
28 5 0.11
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTTATTAATTTTATAATTTTTATAA
Found at i:98638 original size:33 final size:33
Alignment explanation
Indices: 98595--98666 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
98585 TTTTTATTAA
*
98595 AATTTAATAATTTTTA-TAATTTTATAATTTTAT
1 AATTTTATAATTTTTATTAATTTT-TAATTTTAT
* *
98628 AATTTTATAATTTTTATTGATTTTTATTTTTAT
1 AATTTTATAATTTTTATTAATTTTTAATTTTAT
*
98661 CATTTT
1 AATTTT
98667 TTCGCCATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (33 bp):
AATTTTATAATTTTTATTAATTTTTAATTTTAT
Found at i:98667 original size:16 final size:16
Alignment explanation
Indices: 98604--98668 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
98594 AAATTTAATA
*
98604 ATTTTTATAATTTTAT
1 ATTTTTATAATTTTTT
* *
98620 AATTTTATAATTTTATA
1 ATTTTTATAATTTT-TT
*
98637 ATTTTTATTGA-TTTTT
1 ATTTTTA-TAATTTTTT
*
98653 ATTTTTATCATTTTTT
1 ATTTTTATAATTTTTT
98669 CGCCATATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
15 2 0.05
16 26 0.67
17 9 0.23
18 2 0.05
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
ATTTTTATAATTTTTT
Found at i:98879 original size:89 final size:88
Alignment explanation
Indices: 98729--98964 Score: 323
Period size: 89 Copynumber: 2.7 Consensus size: 88
98719 ATTAGGGCTG
* *
98729 GTTCAAGTATCCAATTGAGTAC-AAAAAAATTAGGGGCTTAATTGCTTTTTTTGAAATAGTTTGA
1 GTTCAAGTACCCAATTGAGTACAAAAAAAATTA-GGGCTTAATTGCTTTTTTTGAAAAAGTTTGA
*
98793 GGGCCTTTTTGATGCATCTTGAAA
65 GGACCTTTTTGATGCATCTTGAAA
98817 GTTCAAGTACCCAATTGAGTACAAAAAAAATTAGGAGCTTAATTGCTTTTTTTGAAAAAGTTTGA
1 GTTCAAGTACCCAATTGAGTACAAAAAAAATTAGG-GCTTAATTGCTTTTTTTGAAAAAGTTTGA
* *
98882 GGACCTTTTTGATGCATTTTGATA
65 GGACCTTTTTGATGCATCTTGAAA
* * * * * *
98906 GTTTAAATACCAAATTGAGTGA-AAAAAAGAGTAATGGCTTAATTGCTTTTTTTGAAAAA
1 GTTCAAGTACCCAATTGAGT-ACAAAAAA-AATTAGGGCTTAATTGCTTTTTTTGAAAAA
98965 AAATTGATGA
Statistics
Matches: 133, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
88 23 0.17
89 105 0.79
90 5 0.04
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (88 bp):
GTTCAAGTACCCAATTGAGTACAAAAAAAATTAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAG
GACCTTTTTGATGCATCTTGAAA
Found at i:100658 original size:28 final size:28
Alignment explanation
Indices: 100618--100675 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
100608 TCAGAGCAAA
100618 AAAGTATGTTTCGGGTTACCTAATATAT
1 AAAGTATGTTTCGGGTTACCTAATATAT
*
100646 AAAGTATGTTTCGGGTTCCCTAATATAT
1 AAAGTATGTTTCGGGTTACCTAATATAT
100674 AA
1 AA
100676 TCTGACTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (28 bp):
AAAGTATGTTTCGGGTTACCTAATATAT
Found at i:104792 original size:95 final size:96
Alignment explanation
Indices: 104686--104876 Score: 303
Period size: 95 Copynumber: 2.0 Consensus size: 96
104676 AATTATATTT
* * * * *
104686 AATAAATAATAAATTAATTTAGACAATTTTATTAATTATGATTGATTGAATTTAGTATTTTTATG
1 AATAAACAATAAATTAATTTAAACAACTTTATTAAATATGATTGATTAAATTTAGTATTTTTATG
104751 ATAAATA-TTTTTTTCTTAAATGATTGATTG
66 ATAAATATTTTTTTTCTTAAATGATTGATTG
*
104781 AATAAACAATAAATTACTTTAAACAACTTTATTAAATATGATTGATTAAATTTAGTATTTTTATG
1 AATAAACAATAAATTAATTTAAACAACTTTATTAAATATGATTGATTAAATTTAGTATTTTTATG
*
104846 GTAAATATTTTTTTTTCTTAAATGATTGATT
66 ATAAATA-TTTTTTTTCTTAAATGATTGATT
104877 AATTAAAAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 65 0.75
97 22 0.25
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (96 bp):
AATAAACAATAAATTAATTTAAACAACTTTATTAAATATGATTGATTAAATTTAGTATTTTTATG
ATAAATATTTTTTTTCTTAAATGATTGATTG
Found at i:108438 original size:314 final size:315
Alignment explanation
Indices: 107827--108452 Score: 1103
Period size: 314 Copynumber: 2.0 Consensus size: 315
107817 TCGCGAAGGC
*
107827 AATAGTGAATAGAATGAGTAGTTTGCTAGATATATGTATTAATGAGGTGCATGGTGCTTTTATAC
1 AATAGTGAATAGAATGAGTAGTTTGCTAGATATATGTATTAATAAGGTGCATGGTGCTTTTATAC
* *
107892 CGAATCATCGAATCTTAGATAATACTCTTGTTTCTTATGATTTGCTTCATGTTCTAAAAACTAAG
66 CGAATCATCGAATCTTAGAGAATACTCTTGTTGCTTATGATTTGCTTCATGTTCTAAAAACTAAG
* *
107957 AAATGGGGTAAAAAAAGGTAGTTTTGCCCTGAAATTTAATATGATAAAGGCATACGATAGGGTAA
131 AAATGGGGTAAAAAAAGGTAGTTTTGCCCTGAAATTTAATATGAGAAAGGCATACAATAGGGTAA
*
108022 ATGGGTTTTTCTGGCAAGAATGATGATAAATCTAGGTTTTCATGTAAATTAAGTGGTTTGATAAT
196 ATGGGTTTTTCTAGCAAGAATGATGATAAATCTAGGTTTTCATGTAAATTAAGTGGTTTGATAAT
108087 GAGATGTGTAGCTTCGATCAACTATACAATGGGTTTCAATGGTTTTTGCTAAATG
261 GAGATGTGTAGCTTCGATCAACTATACAATGGGTTTCAATGGTTTTTGCTAAATG
108142 AATAGTGAATA-AATGAGTAGTTTGCTAGATATATGTATTAATAAGGTGCATGGTGCTTTTATAC
1 AATAGTGAATAGAATGAGTAGTTTGCTAGATATATGTATTAATAAGGTGCATGGTGCTTTTATAC
*
108206 CGAATCATTGAATCTTAGAGAATACTCTTGTTGCTTATGATTTGCTTCATGTTCTAAAAACTAAG
66 CGAATCATCGAATCTTAGAGAATACTCTTGTTGCTTATGATTTGCTTCATGTTCTAAAAACTAAG
* * *
108271 AAATGGGGTAAAAAAAGGTAGTTTTGCCTTGAAATTTAATGTGAGCAAGGCATACAATAGGGTAA
131 AAATGGGGTAAAAAAAGGTAGTTTTGCCCTGAAATTTAATATGAGAAAGGCATACAATAGGGTAA
* * **
108336 ATGGGTTTTTCTAGCAAGAATGATGATAAATCTGGGTTTTCATGTAGATTGGGTGGCTTTGATAA
196 ATGGGTTTTTCTAGCAAGAATGATGATAAATCTAGGTTTTCATGTAAATTAAGTGG-TTTGATAA
108401 TGAGATGTGTAGCTTCGATCAACTATACAAT-GGTTTCAATGGTTTTTGCTAA
260 TGAGATGTGTAGCTTCGATCAACTATACAATGGGTTTCAATGGTTTTTGCTAA
108453 GTATTGAGCC
Statistics
Matches: 296, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
314 246 0.83
315 50 0.17
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (315 bp):
AATAGTGAATAGAATGAGTAGTTTGCTAGATATATGTATTAATAAGGTGCATGGTGCTTTTATAC
CGAATCATCGAATCTTAGAGAATACTCTTGTTGCTTATGATTTGCTTCATGTTCTAAAAACTAAG
AAATGGGGTAAAAAAAGGTAGTTTTGCCCTGAAATTTAATATGAGAAAGGCATACAATAGGGTAA
ATGGGTTTTTCTAGCAAGAATGATGATAAATCTAGGTTTTCATGTAAATTAAGTGGTTTGATAAT
GAGATGTGTAGCTTCGATCAACTATACAATGGGTTTCAATGGTTTTTGCTAAATG
Found at i:128576 original size:21 final size:21
Alignment explanation
Indices: 128552--128602 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
128542 AGAAGGATAT
128552 GTTGTATCGGTAGATTGTAGG
1 GTTGTATCGGTAGATTGTAGG
128573 GTTGTATCGGTAGATTGTAGG
1 GTTGTATCGGTAGATTGTAGG
128594 GTTGTATCG
1 GTTGTATCG
128603 ATAAAACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.06, G:0.37, T:0.39
Consensus pattern (21 bp):
GTTGTATCGGTAGATTGTAGG
Found at i:129127 original size:17 final size:17
Alignment explanation
Indices: 129105--129143 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
129095 CTCCACCTTG
129105 ACAAGAAATCTCAACGA
1 ACAAGAAATCTCAACGA
129122 ACAAGAAATCTCAACGA
1 ACAAGAAATCTCAACGA
129139 ACAAG
1 ACAAG
129144 TTCTTCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.23, G:0.13, T:0.10
Consensus pattern (17 bp):
ACAAGAAATCTCAACGA
Found at i:129476 original size:24 final size:24
Alignment explanation
Indices: 129444--129495 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
129434 TCTTTAGAAA
129444 CTTCGGTAATCGCCATGTACTCAG
1 CTTCGGTAATCGCCATGTACTCAG
129468 CTTCGGTAATCGCCATGTACTCAG
1 CTTCGGTAATCGCCATGTACTCAG
129492 CTTC
1 CTTC
129496 AGTGATAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (24 bp):
CTTCGGTAATCGCCATGTACTCAG
Found at i:135643 original size:20 final size:19
Alignment explanation
Indices: 135599--135664 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
135589 AAAAATATTC
*
135599 ATTTA-TTTATAATTTTAT
1 ATTTATTTTATAAATTTAT
* *
135617 ATGTATTTTGATAAATTTGT
1 ATTTATTTT-ATAAATTTAT
135637 ATTTATTTTA-AAATCTTAT
1 ATTTATTTTATAAAT-TTAT
*
135656 ATATATTTT
1 ATTTATTTT
135665 TATCGAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 8 0.21
19 15 0.38
20 16 0.41
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.61
Consensus pattern (19 bp):
ATTTATTTTATAAATTTAT
Found at i:135956 original size:63 final size:63
Alignment explanation
Indices: 135888--136018 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 63
135878 CCAATAGTAA
*
135888 AAAATATGGAGATAAAACTAAACCTCAAAACCCGAAAACAAAGAACCCTCAAAACGTAAATAC
1 AAAATATAGAGATAAAACTAAACCTCAAAACCCGAAAACAAAGAACCCTCAAAACGTAAATAC
135951 AAAATATAGAGATAAAACTAAACCTCAAAACCCGAAAACAAAGAACCCTCAAAACGTAAATAC
1 AAAATATAGAGATAAAACTAAACCTCAAAACCCGAAAACAAAGAACCCTCAAAACGTAAATAC
136014 AAAAT
1 AAAAT
136019 TCTTTAAAAG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.57, C:0.21, G:0.08, T:0.13
Consensus pattern (63 bp):
AAAATATAGAGATAAAACTAAACCTCAAAACCCGAAAACAAAGAACCCTCAAAACGTAAATAC
Found at i:136157 original size:24 final size:24
Alignment explanation
Indices: 136106--136157 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
136096 TTGGCAAGCC
* *
136106 AAATAAATTATGCTAATAAATGTA
1 AAATAAATTATACTAATAAATATA
* *
136130 AAATATATTATACTAATAAATATT
1 AAATAAATTATACTAATAAATATA
136154 AAAT
1 AAAT
136158 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATATA
Found at i:141186 original size:50 final size:51
Alignment explanation
Indices: 141107--141203 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 51
141097 GTGATTACAA
* *
141107 AATGTTTAAGCTCGTCAGCTATTCAGAATTAGAAT-AATCATGTTAGATAG
1 AATGTTTAAGCTCGTCAGCTATACAGAATTAAAATGAATCATGTTAGATAG
* * * *
141157 AATGTTTAAGCTTGTCAGTTATACTGAATTAAAATGATTCATGTTAG
1 AATGTTTAAGCTCGTCAGCTATACAGAATTAAAATGAATCATGTTAG
141204 GCTCTCCTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 30 0.75
51 10 0.25
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (51 bp):
AATGTTTAAGCTCGTCAGCTATACAGAATTAAAATGAATCATGTTAGATAG
Found at i:145722 original size:103 final size:104
Alignment explanation
Indices: 145566--145770 Score: 394
Period size: 103 Copynumber: 2.0 Consensus size: 104
145556 AAATAGTGCT
*
145566 TTCATGTGCGTCGACAAAAAGGAGATCTTTTATTCCTGCATAAAACTTAAAGAAAACG-AATTAA
1 TTCATGTGCGTCGACAAAAAGGAGATCTTTTATTCCTGCATAAAACTTAAAGAAAAAGAAATTAA
145630 AAGAAGACAAAAAGTAAAAATCAAAATTTTACAATGGCA
66 AAGAAGACAAAAAGTAAAAATCAAAATTTTACAATGGCA
145669 TTCATGTGCGTCGACAAAAAGGAGATCTTTTATTCCTGCATAAAACTTAAAGAAAAAGAAATTAA
1 TTCATGTGCGTCGACAAAAAGGAGATCTTTTATTCCTGCATAAAACTTAAAGAAAAAGAAATTAA
145734 AAGAAGACAAAAAGTAAAAATCAAAATTTTACAATGG
66 AAGAAGACAAAAAGTAAAAATCAAAATTTTACAATGG
145771 AATTATTAAG
Statistics
Matches: 100, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
103 57 0.57
104 43 0.43
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (104 bp):
TTCATGTGCGTCGACAAAAAGGAGATCTTTTATTCCTGCATAAAACTTAAAGAAAAAGAAATTAA
AAGAAGACAAAAAGTAAAAATCAAAATTTTACAATGGCA
Found at i:155933 original size:24 final size:24
Alignment explanation
Indices: 155882--155933 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
155872 TTCGTAAGGC
* *
155882 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
155906 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
155930 AAAT
1 AAAT
155934 CTTCTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:156394 original size:19 final size:19
Alignment explanation
Indices: 156358--156405 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
156348 ACTATTTTAA
156358 AATTAAAAATCATTAAATT
1 AATTAAAAATCATTAAATT
* *
156377 TATTAAAAAT-TTTAAAATT
1 AATTAAAAATCATT-AAATT
156396 AATTTAAAAA
1 AA-TTAAAAA
156406 AATTAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTAAAAATCATTAAATT
Found at i:156555 original size:17 final size:18
Alignment explanation
Indices: 156515--156556 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
156505 AATTATAGGT
*
156515 TTAAAAATTAAAATAAAC
1 TTAAAAATTAAAATAAAA
**
156533 GAAAAAATT-AAATAAAA
1 TTAAAAATTAAAATAAAA
156550 TTAAAAA
1 TTAAAAA
156557 AAAAAATCGT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
TTAAAAATTAAAATAAAA
Found at i:157188 original size:3 final size:3
Alignment explanation
Indices: 157180--157218 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
157170 TTTTATTTGA
* * *
157180 ATT ATT ATT ATT AAT AAT ATT ATT ATT ATT ATT AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
157219 TTCAAGAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:158966 original size:37 final size:38
Alignment explanation
Indices: 158870--158967 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 38
158860 ATTTTTGAAA
* *
158870 TGCACCCAAGACTGTCACTACATAAATATTCTTCACAT
1 TGCACCCAAGAATGTCACTGCATAAATATTCTTCACAT
* * ** *
158908 TGCATCCAA-AACTATTGCTGCATAAGTATTCTTCA-AT
1 TGCACCCAAGAA-TGTCACTGCATAAATATTCTTCACAT
158945 TGCACCCAAGAATGTCACTGCAT
1 TGCACCCAAGAATGTCACTGCAT
158968 GAACATGTAC
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
37 19 0.40
38 28 0.60
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.30
Consensus pattern (38 bp):
TGCACCCAAGAATGTCACTGCATAAATATTCTTCACAT
Found at i:167091 original size:17 final size:18
Alignment explanation
Indices: 167062--167116 Score: 69
Period size: 17 Copynumber: 3.0 Consensus size: 18
167052 AGCAATCATT
167062 TTTTTCTTCTTTTCTTTTC
1 TTTTTC-TCTTTTCTTTTC
167081 -TTTTCTCTTTTC-TTTC
1 TTTTTCTCTTTTCTTTTC
167097 TTTTTCTCATTTTCCTTTTC
1 TTTTTCTC-TTTT-CTTTTC
167117 AAGTGATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.12
17 14 0.44
18 9 0.28
19 1 0.03
20 4 0.12
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTCTCTTTTCTTTTC
Found at i:167384 original size:43 final size:43
Alignment explanation
Indices: 167323--167410 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
167313 TCTTTTATTT
167323 ATACAATGTTGCTGCAACTGGTCAGTTAGTTCAAGATTCAAAC
1 ATACAATGTTGCTGCAACTGGTCAGTTAGTTCAAGATTCAAAC
*
167366 ATACAATGTTGCTGCAACTGGTCAGTTAGTTCAAGATTTAAAC
1 ATACAATGTTGCTGCAACTGGTCAGTTAGTTCAAGATTCAAAC
167409 AT
1 AT
167411 TCACACTATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (43 bp):
ATACAATGTTGCTGCAACTGGTCAGTTAGTTCAAGATTCAAAC
Found at i:167831 original size:14 final size:14
Alignment explanation
Indices: 167812--167838 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
167802 AACAAAGTGC
167812 TAAAAAATAAAAAT
1 TAAAAAATAAAAAT
167826 TAAAAAATAAAAA
1 TAAAAAATAAAAA
167839 CTAACTCAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAAAAATAAAAAT
Found at i:174672 original size:6 final size:6
Alignment explanation
Indices: 174661--174694 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
174651 TAAAAGGATT
174661 AAATTA AAATTA AAATTA AAATTA AAATTA AAAT
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAAT
174695 CTCAGGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:176541 original size:37 final size:38
Alignment explanation
Indices: 176489--176607 Score: 118
Period size: 37 Copynumber: 3.2 Consensus size: 38
176479 TGGTCGGGGT
*
176489 AAGATTGCATGGCTTCAATCTGCCCTCTGAATGGGTAA
1 AAGATTGCATGGCTTCAATTTGCCCTCTGAATGGGTAA
* * * * * ***
176527 AAGATTG-TTTGCTTCCATTTGTCCCACGGTCGGGGT-A
1 AAGATTGCATGGCTTCAATTTG-CCCTCTGAATGGGTAA
*
176564 AA-ATTGCATGGCTTCAATTTGCCCTCTAAATGGGTAA
1 AAGATTGCATGGCTTCAATTTGCCCTCTGAATGGGTAA
176601 AAGATTG
1 AAGATTG
176608 GATGCTTTCA
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
36 12 0.20
37 27 0.46
38 20 0.34
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (38 bp):
AAGATTGCATGGCTTCAATTTGCCCTCTGAATGGGTAA
Found at i:176634 original size:74 final size:74
Alignment explanation
Indices: 176476--176640 Score: 231
Period size: 74 Copynumber: 2.2 Consensus size: 74
176466 TCAATCTGCT
* * **
176476 CCATGGTCGGGGTAAGATTGCATGGCTTCAATCTGCCCTCTGAATGGGTAAAAGATTGTTTGCTT
1 CCATGGTCGGGGTAAAATTGCATGGCTTCAATCTGCCCTCTAAATGGGTAAAAGATTGGATGCTT
* **
176541 CCATTTGTC
66 CCATCTACC
* *
176550 CCACGGTCGGGGTAAAATTGCATGGCTTCAATTTGCCCTCTAAATGGGTAAAAGATTGGATGCTT
1 CCATGGTCGGGGTAAAATTGCATGGCTTCAATCTGCCCTCTAAATGGGTAAAAGATTGGATGCTT
*
176615 TCATCTACC
66 CCATCTACC
*
176624 CCATGATCGGGGTAAAA
1 CCATGGTCGGGGTAAAA
176641 GATCGGTAGT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 79 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (74 bp):
CCATGGTCGGGGTAAAATTGCATGGCTTCAATCTGCCCTCTAAATGGGTAAAAGATTGGATGCTT
CCATCTACC
Found at i:176873 original size:40 final size:41
Alignment explanation
Indices: 176772--176877 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 41
176762 ATGGCTTCAC
* * *
176772 TCTACCTCATGATCAGGGTAAGAGATTGGACAATGTCTTTAG
1 TCTACCTCATGGTCAGGGTAAGATATT-GACAATGTCTTTAA
* * ***
176814 TCTGCCTCATGGGT-GGGGTAAGATATT-AGTGTGTCTTTAA
1 TCTACCTCAT-GGTCAGGGTAAGATATTGACAATGTCTTTAA
176854 TCTACCTCATGGTCAGGGTAAGAT
1 TCTACCTCATGGTCAGGGTAAGAT
176878 TTGGTGAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
39 3 0.06
40 27 0.52
42 20 0.38
43 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (41 bp):
TCTACCTCATGGTCAGGGTAAGATATTGACAATGTCTTTAA
Found at i:177469 original size:195 final size:195
Alignment explanation
Indices: 177195--177620 Score: 572
Period size: 195 Copynumber: 2.2 Consensus size: 195
177185 TTCCTATCAC
* * * * *
177195 GTACGAGGTTCATCATTATGGCTTCAACCTTTCCCTCCATATCTCCATGGTATAAGATTCACCGT
1 GTACAAGGTTCACCATTACGACTTCAACCTTTCCCTCCATATCTCCATGGTACAAGATTCACCGT
* *
177260 TATGGCTTTAATCTTTCCCATCACATCTTTAAGGTACA-AGGTTCGCCGTTGCGGCTTCAACCTT
66 TATGGCTGTAATCTTTCCCATCACATCTCTAAGGTACACA-GTTCGCCGTTGCGGCTTCAACCTT
* * * * * *
177324 TCCCTTCATATCTTCATGGTACAAGATTC-ATCGTTACGGCTTCAATCTTT-CCATCACATCTCT
130 TCACTCCATATCTTCATGGTACAAGATTCGCT-ATTACGACTTCAAT-TTTCCCATCACACCTCT
177387 AAG
193 AAG
*
177390 GTACAAGGTTCACCATTACGACTTCAACCTTTCCCTCCATATCTCCATGGTACAAGATAT-GCCG
1 GTACAAGGTTCACCATTACGACTTCAACCTTTCCCTCCATATCTCCATGGTACAAGAT-TCACCG
* * * * * *
177454 TTGTGGCTGTAATCTTTCCCATCACGTCTCTAAGGTATACAGTTCGCCTTTGTGTCTTCAACCTT
65 TTATGGCTGTAATCTTTCCCATCACATCTCTAAGGTACACAGTTCGCCGTTGCGGCTTCAACCTT
* *
177519 TCACTCCATATCTTCATGGTACAAGATTCGCTATTGCGACTTCAATTTTCCCATCACGCCTCTAA
130 TCACTCCATATCTTCATGGTACAAGATTCGCTATTACGACTTCAATTTTCCCATCACACCTCTAA
177584 G
195 G
* *
177585 GTACAAGGTTCGCCATTGCGACTTCAACCTTTCCCT
1 GTACAAGGTTCACCATTACGACTTCAACCTTTCCCT
177621 AAACCTTAAA
Statistics
Matches: 203, Mismatches: 24, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
194 3 0.01
195 197 0.97
196 3 0.01
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (195 bp):
GTACAAGGTTCACCATTACGACTTCAACCTTTCCCTCCATATCTCCATGGTACAAGATTCACCGT
TATGGCTGTAATCTTTCCCATCACATCTCTAAGGTACACAGTTCGCCGTTGCGGCTTCAACCTTT
CACTCCATATCTTCATGGTACAAGATTCGCTATTACGACTTCAATTTTCCCATCACACCTCTAAG
Found at i:177562 original size:49 final size:48
Alignment explanation
Indices: 177214--177620 Score: 243
Period size: 49 Copynumber: 8.4 Consensus size: 48
177204 TCATCATTAT
* * * **
177214 GGCTTCAACCTTTCCCTCCATATCTCCATGGTATAAGATTCACCGTTAT
1 GGCTTCAACCTTTCCCT-CATATCTTCATGGTACAAGATTCGCCGTTGC
* * * * * *
177263 GGCTTTAATCTTTCCCATCACATCTTTAAGGTACAAGGTTCGCCGTTGC
1 GGCTTCAACCTTTCCC-TCATATCTTCATGGTACAAGATTCGCCGTTGC
** *
177312 GGCTTCAACCTTTCCCTTCATATCTTCATGGTACAAGATTCATCGTTAC
1 GGCTTCAACCTTTCCC-TCATATCTTCATGGTACAAGATTCGCCGTTGC
* * * * * * * *
177361 GGCTTCAATCTTTCCATCACATC-TCTAAGGTACAAGGTTCACCATTAC
1 GGCTTCAACCTTTCCCTCATATCTTC-ATGGTACAAGATTCGCCGTTGC
* * *
177409 GACTTCAACCTTTCCCTCCATATCTCCATGGTACAAGATAT-GCCGTTGT
1 GGCTTCAACCTTTCCCT-CATATCTTCATGGTACAAGAT-TCGCCGTTGC
* ** * * * *
177458 GGCTGT-AATCTTTCCCATCACGTC-TCTAAGGTATACAG-TTCGCCTTTGT
1 GGCT-TCAACCTTTCCC-TCATATCTTC-ATGGTACA-AGATTCGCCGTTGC
* * **
177507 GTCTTCAACCTTTCACTCCATATCTTCATGGTACAAGATTCGCTATTGC
1 GGCTTCAACCTTTCCCT-CATATCTTCATGGTACAAGATTCGCCGTTGC
* * ** * * * *
177556 GACTTCAA-TTTTCCCATCA-CGCCTCTAAGGTACAAGGTTCGCCATTGC
1 GGCTTCAACCTTTCCC-TCATATCTTC-ATGGTACAAGATTCGCCGTTGC
*
177604 GACTTCAACCTTTCCCT
1 GGCTTCAACCTTTCCCT
177621 AAACCTTAAA
Statistics
Matches: 274, Mismatches: 67, Indels: 35
0.73 0.18 0.09
Matches are distributed among these distances:
47 5 0.02
48 79 0.29
49 181 0.66
50 9 0.03
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.34
Consensus pattern (48 bp):
GGCTTCAACCTTTCCCTCATATCTTCATGGTACAAGATTCGCCGTTGC
Found at i:184511 original size:26 final size:27
Alignment explanation
Indices: 184455--184512 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
184445 AAGGTGAATT
*
184455 TTTTAAAAAAAATTCATTCTTCATTTCC
1 TTTTAAAAAAAA-TCATTCTTCATCTCC
184483 TTTTAAAAAAAA-CATTCTTTCATCT-C
1 TTTTAAAAAAAATCATTC-TTCATCTCC
184509 TTTT
1 TTTT
184513 CCACTCTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 10 0.36
27 6 0.21
28 12 0.43
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTTAAAAAAAATCATTCTTCATCTCC
Found at i:185978 original size:26 final size:26
Alignment explanation
Indices: 185941--185995 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
185931 TGCACCCAAG
185941 ATTGTCGCTGCATGAACATGTACAGA
1 ATTGTCGCTGCATGAACATGTACAGA
* * *
185967 ATTGTCGTTGCATGAACGTGTCCAGA
1 ATTGTCGCTGCATGAACATGTACAGA
185993 ATT
1 ATT
185996 ACGCTTAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (26 bp):
ATTGTCGCTGCATGAACATGTACAGA
Found at i:202569 original size:13 final size:13
Alignment explanation
Indices: 202553--202623 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 13
202543 GTATAAAAAC
*
202553 TTCATATAACTGT
1 TTCATATAACTAT
*
202566 TTCATATATCTACT
1 TTCATATAACTA-T
202580 TTCATAATAAC-AT
1 TTCAT-ATAACTAT
*
202593 TTCATGTAACTAT
1 TTCATATAACTAT
*
202606 TTCATCTAAGC-AT
1 TTCATATAA-CTAT
202619 TTCAT
1 TTCAT
202624 TTTACCAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
12 4 0.08
13 33 0.67
14 8 0.16
15 4 0.08
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.45
Consensus pattern (13 bp):
TTCATATAACTAT
Found at i:214615 original size:2 final size:2
Alignment explanation
Indices: 214608--214635 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
214598 CTAAGATTTA
214608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
214636 GTGTATTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:219275 original size:29 final size:30
Alignment explanation
Indices: 219234--219293 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
219224 AGGCGGAAAT
* *
219234 ATAAATTGCATAAAAATAAATA-ATAAATAA
1 ATAAATTGAAT-AAAATAAAAACATAAATAA
219264 ATAAA-TGAATAAAATAAAAACATAAATAA
1 ATAAATTGAATAAAATAAAAACATAAATAA
219293 A
1 A
219294 AATAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 9 0.33
29 13 0.48
30 5 0.19
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (30 bp):
ATAAATTGAATAAAATAAAAACATAAATAA
Found at i:219289 original size:36 final size:36
Alignment explanation
Indices: 219245--219318 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
219235 TAAATTGCAT
*
219245 AAAAATAAATAATAAAT-AAATAA-ATGAATAAAATA
1 AAAAATAAATAA-AAATAAAATAATACGAATAAAATA
219280 AAAACATAAATAAAAATAAAATAATACGAATAAAATA
1 AAAA-ATAAATAAAAATAAAATAATACGAATAAAATA
219317 AA
1 AA
219319 TAAAAAGGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
35 8 0.23
36 14 0.40
37 13 0.37
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (36 bp):
AAAAATAAATAAAAATAAAATAATACGAATAAAATA
Found at i:219319 original size:18 final size:17
Alignment explanation
Indices: 219258--219321 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
219248 AATAAATAAT
219258 AAATAAATAA-ATGAATA
1 AAATAAATAATA-GAATA
*
219275 AAATAAAAACATA-AATAA
1 AAATAAATA-ATAGAAT-A
219293 AAATAAAATAATACGAATA
1 AAAT-AAATAATA-GAATA
219312 AAATAAATAA
1 AAATAAATAA
219322 AAAGGATCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
17 11 0.28
18 15 0.38
19 10 0.26
20 3 0.08
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATAAATAATAGAATA
Found at i:219341 original size:4 final size:4
Alignment explanation
Indices: 219247--219322 Score: 54
Period size: 4 Copynumber: 18.8 Consensus size: 4
219237 AATTGCATAA
*
219247 AAAT AAAT -AAT AAAT AAAT AAAT GAAT AAAAT AAA- AACAT AAAT -AA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AA-AT AAAT AAAT
219293 AAAT AAA- ATAAT ACGAAT AAAAT AAAT AAA
1 AAAT AAAT A-AAT A--AAT -AAAT AAAT AAA
219323 AAGGATCAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
3 10 0.17
4 36 0.61
5 9 0.15
6 3 0.05
7 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:220397 original size:21 final size:21
Alignment explanation
Indices: 220363--220404 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
220353 TTTTATAGCA
220363 TGATTTTTTAATA-TATTTTT
1 TGATTTTTTAATATTATTTTT
*
220383 TGATTTTTTGTATATTATTTTT
1 TGATTTTTT-AATATTATTTTT
220405 GTCCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 3 0.16
22 7 0.37
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (21 bp):
TGATTTTTTAATATTATTTTT
Found at i:221384 original size:99 final size:100
Alignment explanation
Indices: 221220--221628 Score: 352
Period size: 101 Copynumber: 4.1 Consensus size: 100
221210 CAACTTCAGA
* * * **
221220 GATATAGGATTTGGGTTTGTAACTTCACTCCATTCCACTGCAACTTCAGTAAAGATTGAGATCTG
1 GATATAGGATTT-GG-ATGTAGCTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTG
* *
221285 CTACGATTAGTTTTG-GTCTGATCC-TTGCAA-CTTAAAG
64 CTACGATTAG--TTGAATCTGATCCACTG-AATCTTAAAG
* * *
221322 GATATATGATTTGG-TGTAGCTTCATTCCATTCCACTACAACATCAGTGGAGATTGAGATCTGCT
1 GATATAGGATTTGGATGTAGCTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCT
* *
221386 ACTATTAGTTGAATCTGATCCACTGAATCTTCAAG
66 ACGATTAGTTGAATCTGATCCACTGAATCTTAAAG
** * * ** *
221421 GATATAGGATTTGGAACTGGCTTAACTCCATTGAACTACAACTTCAGTGGAGATTGAGATATGCT
1 GATATAGGATTTGGATGTAGCTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCT
* * *
221486 ATTTG-TTAGTTGAAT-TCGATCCACT-ACATCTTTAGG
66 A--CGATTAGTTGAATCT-GATCCACTGA-ATCTTAAAG
* * * * * *
221522 GATACATGATTTGGATGT-GTATTCACTCCGTTCCACTACAACTTTCA-TGGAGACTGAGATATG
1 GATATAGGATTTGGATGTAG-CTTCACTCCATTCCACTACAAC-TTCAGTGGAGATTGAGATCTG
* * *
221585 CTATTTG-TTAGTTGAATCTGATCCACTGCATCTTCAAG
64 CTA--CGATTAGTTGAATCTGATCCACTGAATCTTAAAG
221623 GATATA
1 GATATA
221629 AGGCTTGGAT
Statistics
Matches: 256, Mismatches: 39, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
97 3 0.01
98 10 0.04
99 72 0.28
100 45 0.18
101 110 0.43
102 16 0.06
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (100 bp):
GATATAGGATTTGGATGTAGCTTCACTCCATTCCACTACAACTTCAGTGGAGATTGAGATCTGCT
ACGATTAGTTGAATCTGATCCACTGAATCTTAAAG
Found at i:221451 original size:199 final size:201
Alignment explanation
Indices: 221246--221628 Score: 445
Period size: 199 Copynumber: 1.9 Consensus size: 201
221236 TTGTAACTTC
* * * ***
221246 ACTCCATTCCACTGCAACTTCAGTAAAGATTGAGATCTGCTA-CGATTAGTTTTGGTCTGATCC-
1 ACTCCATTCAACTACAACTTCAGTAAAGATTGAGATATGCTATCG-TTAGTTGAAGTC-GATCCA
* * * * *
221309 TTGCAACTTAAAGGATATATGATTTGG-TGTAG-CTTCATTCCATTCCACTACAAC-ATCAGTGG
64 CTACAACTTAAAGGATACATGATTTGGATGT-GTATTCACTCCATTCCACTACAACTATCA-TGG
* *
221371 AGATTGAGATCTGCTA-CTATTAGTTGAATCTGATCCACTGAATCTTCAAGGATATAGGATTTGG
127 AGACTGAGATATGCTATCTATTAGTTGAATCTGATCCACTGAATCTTCAAGGATATAGGATTTGG
221435 AACTGGCTTA
192 AACTGGCTTA
* ** * *
221445 ACTCCATTGAACTACAACTTCAGTGGAGATTGAGATATGCTATTTGTTAGTTGAATTCGATCCAC
1 ACTCCATTCAACTACAACTTCAGTAAAGATTGAGATATGCTA-TCGTTAGTTGAAGTCGATCCAC
* * * * *
221510 TACATCTTTAGGGATACATGATTTGGATGTGTATTCACTCCGTTCCACTACAACTTTCATGGAGA
65 TACAACTTAAAGGATACATGATTTGGATGTGTATTCACTCCATTCCACTACAACTATCATGGAGA
* * *
221575 CTGAGATATGCTATTTGTTAGTTGAATCTGATCCACTGCATCTTCAAGGATATA
130 CTGAGATATGCTATCTATTAGTTGAATCTGATCCACTGAATCTTCAAGGATATA
221629 AGGCTTGGAT
Statistics
Matches: 151, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
199 41 0.27
200 30 0.20
201 40 0.26
202 40 0.26
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (201 bp):
ACTCCATTCAACTACAACTTCAGTAAAGATTGAGATATGCTATCGTTAGTTGAAGTCGATCCACT
ACAACTTAAAGGATACATGATTTGGATGTGTATTCACTCCATTCCACTACAACTATCATGGAGAC
TGAGATATGCTATCTATTAGTTGAATCTGATCCACTGAATCTTCAAGGATATAGGATTTGGAACT
GGCTTA
Found at i:224875 original size:18 final size:19
Alignment explanation
Indices: 224854--224894 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
224844 GCAACTACCA
224854 ATGTCAACACAACC-GATG
1 ATGTCAACACAACCTGATG
*
224872 ATGTCGACACAACCTGATG
1 ATGTCAACACAACCTGATG
224891 -TGTC
1 ATGTC
224895 CATACCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (19 bp):
ATGTCAACACAACCTGATG
Found at i:230344 original size:15 final size:15
Alignment explanation
Indices: 230309--230337 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
230299 GAAGAAGTGG
230309 AAGAAGAAGAAAGAA
1 AAGAAGAAGAAAGAA
230324 AAGAAGAAGAAAGA
1 AAGAAGAAGAAAGA
230338 GAGGAAGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGAAAGAA
Found at i:232868 original size:101 final size:101
Alignment explanation
Indices: 232691--233336 Score: 859
Period size: 101 Copynumber: 6.4 Consensus size: 101
232681 GTAAGATATT
* * *
232691 CATTCCTCTACAACTTCAGTGGAGATTGAGATATGC-AGCTTGTTAGTTGAATCTGATCCACTGC
1 CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTA-CTTGTTAATTGAATCTGATCCACTAC
*
232755 ATCTTTAGGGATATAGGATTTAGATGTGGCTTCACTC
65 ATCTTTAGGGATATAGGATTTGGATGTGGCTTCACTC
* * * * *
232792 CATTCTACTACAACTTCAGTGGATATTGAGTTATGTTGCTTGTTAATTGAATCTGATCCACTACA
1 CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTACTTGTTAATTGAATCTGATCCACTACA
*
232857 T-TTTCAAGGATATAGGATTTGGATGTGGCTTCACTC
66 TCTTT-AGGGATATAGGATTTGGATGTGGCTTCACTC
** * * * *
232893 CATTCCAAAACATCTTCAGTAGG-GATTAAGATCTGCTACTTGTTAATTGAATTTGATCCACTAC
1 CATTCCACTACAACTTCAGT-GGAGATTGAGATATGCTACTTGTTAATTGAATCTGATCCACTAC
232957 ATCTTTAGGGATATAGGATTTGGATGTGGCTTCACTC
65 ATCTTTAGGGATATAGGATTTGGATGTGGCTTCACTC
* * * * *
232994 CATTCCACTACATCTTCAGT-AAGGATTGAGATCTGCTACTTGTTAATTGAATTTGATCCACTAA
1 CATTCCACTACAACTTCAGTGGA-GATTGAGATATGCTACTTGTTAATTGAATCTGATCCACTAC
* *
233058 ATCTTTGGGGATATAGGATTTGGATGTGGCTTCACAC
65 ATCTTTAGGGATATAGGATTTGGATGTGGCTTCACTC
* * * * **
233095 CTTTCCACCACAACTTCAGTGGAGATTGAGATTTGCTACTTGTTAATTGAATTTGATCCACTGTA
1 CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTACTTGTTAATTGAATCTGATCCACTACA
* * *
233160 TTTTTAGGGATATAGGATTTCGATGTGGCTTCACTT
66 TCTTTAGGGATATAGGATTTGGATGTGGCTTCACTC
* * * * * * *
233196 TATTCCACTACAACTTTAATGGAGATTGAGATCTACTACTTGTTAATTGAATCTGATGCACTGCA
1 CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTACTTGTTAATTGAATCTGATCCACTACA
*
233261 TCTTTAGGGATATAGGATTTGGATGTGGCTCCACTC
66 TCTTTAGGGATATAGGATTTGGATGTGGCTTCACTC
*
233297 CATTCCACTACAACTTCAGTGAAGATTGAGATATGCTACT
1 CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTACT
233337 GCTTTGCTCC
Statistics
Matches: 477, Mismatches: 61, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
100 3 0.01
101 468 0.98
102 6 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (101 bp):
CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTACTTGTTAATTGAATCTGATCCACTACA
TCTTTAGGGATATAGGATTTGGATGTGGCTTCACTC
Found at i:233003 original size:48 final size:48
Alignment explanation
Indices: 232747--233009 Score: 129
Period size: 48 Copynumber: 5.3 Consensus size: 48
232737 TTGAATCTGA
* *
232747 TCCACTGCATCTTTAGGGATATAGGATTTAGATGTGGCTTCACTCCAT
1 TCCACTACATCTTTAGGGATATAGGATTTGGATGTGGCTTCACTCCAT
* * * * ** *** * * *
232795 TCTACTACAACTTCAGTGGATATTGAGTTATGTTGCTTGTTAATTGAATCTGA-
1 TCCACTACATCTTTAG-GGATA-T-AG-GAT-TTGGATGTGGCTTCACTC-CAT
*
232848 TCCACTACAT-TTTCAAGGATATAGGATTTGGATGTGGCTTCACTCCAT
1 TCCACTACATCTTT-AGGGATATAGGATTTGGATGTGGCTTCACTCCAT
** * * * *** * * **
232896 TCCAAAACATCTTCAGTAGGGAT-TAAGATCTGCTACTTGTTAATTGAATTTGA-
1 TCCACTACATCTT---TAGGGATATAGGATTTG-GA--TGTGGCTT-CACTCCAT
232949 TCCACTACATCTTTAGGGATATAGGATTTGGATGTGGCTTCACTCCAT
1 TCCACTACATCTTTAGGGATATAGGATTTGGATGTGGCTTCACTCCAT
232997 TCCACTACATCTT
1 TCCACTACATCTT
233010 CAGTAAGGAT
Statistics
Matches: 145, Mismatches: 52, Indels: 36
0.62 0.22 0.15
Matches are distributed among these distances:
47 4 0.03
48 49 0.34
49 9 0.06
50 18 0.12
51 16 0.11
52 10 0.07
53 35 0.24
54 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (48 bp):
TCCACTACATCTTTAGGGATATAGGATTTGGATGTGGCTTCACTCCAT
Found at i:234155 original size:20 final size:20
Alignment explanation
Indices: 234132--234186 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
234122 GAACAATGGC
234132 AAAAAATTGCAAACATTGGT
1 AAAAAATTGCAAACATTGGT
**
234152 AAAAAA-TGACAAATGTTGGT
1 AAAAAATTG-CAAACATTGGT
* *
234172 AAACAATAGCAAACA
1 AAAAAATTGCAAACA
234187 CTAATCAAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.20
Consensus pattern (20 bp):
AAAAAATTGCAAACATTGGT
Found at i:248720 original size:101 final size:100
Alignment explanation
Indices: 248543--249089 Score: 666
Period size: 101 Copynumber: 5.4 Consensus size: 100
248533 GTAAGATATT
* * * **
248543 CATTCCACTACAACTTTAGTGGAGATTGAGATATGC-AGCTAGTTAGTTGAATCTGATCCACTGT
1 CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTA-CTTGTTAATTGAATCTGATCCACTAC
*
248607 ATCTTTAGGGATATAGGATTTAGATGTGGCTTCACTC
65 AT-TTTAGGGATATAGGATTTGGATGTGGCTTCACTC
* * * * *
248644 CATTCTACTACAACTTCAGTTGATATTGAGATATGTTGCTTGTTAATTGAATCTGATCCACTACA
1 CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTACTTGTTAATTGAATCTGATCCACTACA
* *
248709 TTTTCAAGGATATAGGATTTGGATATGGCTTCACTC
66 TTTT-AGGGATATAGGATTTGGATGTGGCTTCACTC
* * * * * * *
248745 CATTCCATTACATCTTTAGT-AAGGATTAAGATCTGCTACTTGTTAATTGAATTTGATCCACTAC
1 CATTCCACTACAACTTCAGTGGA-GATTGAGATATGCTACTTGTTAATTGAATCTGATCCACTAC
248809 ATCTTTAGGGATATAGGATTTGGATGTGGCGCTTCACTC
65 AT-TTTAGGGATATAGGATTTGGATGT-G-GCTTCACTC
* * *
248848 CATTCCACTAAAACTTCAGTGGAGATTGAGATTTGTTACTTGTTAATTGAATCTGATCCACTACA
1 CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTACTTGTTAATTGAATCTGATCCACTACA
*
248913 TTTTTAGGGATATAAGATTTGGATGTGGCTTCACTC
66 -TTTTAGGGATATAGGATTTGGATGTGGCTTCACTC
* * * * * *
248949 CATTCCACTGCAACTTCAATGGAGATTGAGATCTGCTACTTGTTAATTGAATTTGATGCACTGCA
1 CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTACTTGTTAATTGAATCTGATCCACTACA
* * * * *
249014 TCTTCAAGGATATAAGATTTGGATGTGGCTCCCCTC
66 T-TTTAGGGATATAGGATTTGGATGTGGCTTCACTC
* *
249050 TATTCCATTACAACTTCAGTGGAGATTGAGATATGCTACT
1 CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTACT
249090 GCTTTGCTCC
Statistics
Matches: 384, Mismatches: 53, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
100 5 0.01
101 286 0.74
102 5 0.01
103 86 0.22
104 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (100 bp):
CATTCCACTACAACTTCAGTGGAGATTGAGATATGCTACTTGTTAATTGAATCTGATCCACTACA
TTTTAGGGATATAGGATTTGGATGTGGCTTCACTC
Found at i:248906 original size:204 final size:202
Alignment explanation
Indices: 248543--249089 Score: 711
Period size: 204 Copynumber: 2.7 Consensus size: 202
248533 GTAAGATATT
* * * * * * * * *
248543 CATTCCACTACAACTTTAGTGGAGATTGAGATATGC-AGCTAGTTAGTTGAATCTGATCCACTGT
1 CATTCCACTACAACTTCAATAGAGATTAAGATCTGCTA-CTTGTTAATTGAATTTGATCCACTGC
* * * *
248607 ATCTTTAGGGATATAGGATTTAGATGTGGCTTCACTCCATTCTACTACAACTTCAGTTGATATTG
65 ATCTTTAGGGATATAGGATTTGGATGTGGCTTCACTCCATTCCACTACAACTTCAGTGGAGATTG
* *
248672 AGATATGTTGCTTGTTAATTGAATCTGATCCACTACATTTTCAAGGATATAGGATTTGGATATGG
130 AGATATGTTACTTGTTAATTGAATCTGATCCACTACATTTTCAAGGATATAAGATTTGGATATGG
248737 CTTCACTC
195 CTTCACTC
* * * * *
248745 CATTCCATTACATCTTTAGTA-AGGATTAAGATCTGCTACTTGTTAATTGAATTTGATCCACTAC
1 CATTCCACTACAACTTCAATAGA-GATTAAGATCTGCTACTTGTTAATTGAATTTGATCCACTGC
*
248809 ATCTTTAGGGATATAGGATTTGGATGTGGCGCTTCACTCCATTCCACTAAAACTTCAGTGGAGAT
65 ATCTTTAGGGATATAGGATTTGGATGT-G-GCTTCACTCCATTCCACTACAACTTCAGTGGAGAT
* * * *
248874 TGAGATTTGTTACTTGTTAATTGAATCTGATCCACTACATTTTTAGGGATATAAGATTTGGATGT
128 TGAGATATGTTACTTGTTAATTGAATCTGATCCACTACATTTTCAAGGATATAAGATTTGGATAT
248939 GGCTTCACTC
193 GGCTTCACTC
* * * *
248949 CATTCCACTGCAACTTCAATGGAGATTGAGATCTGCTACTTGTTAATTGAATTTGATGCACTGCA
1 CATTCCACTACAACTTCAATAGAGATTAAGATCTGCTACTTGTTAATTGAATTTGATCCACTGCA
* * * * * * *
249014 TCTTCAAGGATATAAGATTTGGATGTGGCTCCCCTCTATTCCATTACAACTTCAGTGGAGATTGA
66 TCTTTAGGGATATAGGATTTGGATGTGGCTTCACTCCATTCCACTACAACTTCAGTGGAGATTGA
*
249079 GATATGCTACT
131 GATATGTTACT
249090 GCTTTGCTCC
Statistics
Matches: 300, Mismatches: 40, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
201 1 0.00
202 118 0.39
203 3 0.01
204 177 0.59
205 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (202 bp):
CATTCCACTACAACTTCAATAGAGATTAAGATCTGCTACTTGTTAATTGAATTTGATCCACTGCA
TCTTTAGGGATATAGGATTTGGATGTGGCTTCACTCCATTCCACTACAACTTCAGTGGAGATTGA
GATATGTTACTTGTTAATTGAATCTGATCCACTACATTTTCAAGGATATAAGATTTGGATATGGC
TTCACTC
Found at i:258575 original size:62 final size:62
Alignment explanation
Indices: 258478--258603 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 62
258468 AACCATAACA
* *
258478 ATAGGAAGAAGATGTAGCTGAAGAAAGTTAAGCAAAAGAAAATAAAGAAGACCAACTGTAGT
1 ATAGGAAGAAGATGCAGCTAAAGAAAGTTAAGCAAAAGAAAATAAAGAAGACCAACTGTAGT
258540 ATAGGAAGAAGATGCAGCTAAAGAAAGTTAAGCAAAAGAAAATAAAGAAGACCAACTGTAGT
1 ATAGGAAGAAGATGCAGCTAAAGAAAGTTAAGCAAAAGAAAATAAAGAAGACCAACTGTAGT
258602 AT
1 AT
258604 CATCTATGCC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.52, C:0.09, G:0.23, T:0.16
Consensus pattern (62 bp):
ATAGGAAGAAGATGCAGCTAAAGAAAGTTAAGCAAAAGAAAATAAAGAAGACCAACTGTAGT
Found at i:261143 original size:12 final size:12
Alignment explanation
Indices: 261126--261150 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
261116 TGTTATCATG
261126 ATGAATGCTATT
1 ATGAATGCTATT
261138 ATGAATGCTATT
1 ATGAATGCTATT
261150 A
1 A
261151 ATTCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:261204 original size:17 final size:17
Alignment explanation
Indices: 261182--261215 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
261172 ACATTCTTTA
261182 AGTGTTGGGTTGATTGT
1 AGTGTTGGGTTGATTGT
261199 AGTGTTGGGTTGATTGT
1 AGTGTTGGGTTGATTGT
261216 GTTTAATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.41, T:0.47
Consensus pattern (17 bp):
AGTGTTGGGTTGATTGT
Found at i:268070 original size:37 final size:38
Alignment explanation
Indices: 268020--268098 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
268010 CTCAAAGTAA
*
268020 TAAAGTGACACCTAGTGTCTCAT-CAACCTAGCCGAAG
1 TAAAGTGACACCTAGTATCTCATACAACCTAGCCGAAG
** * * *
268057 TAAAGTGGTACCTAGTATCTCATAGAATCTATCCGAAG
1 TAAAGTGACACCTAGTATCTCATACAACCTAGCCGAAG
268095 TAAA
1 TAAA
268099 ACAATGACAC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
37 20 0.57
38 15 0.43
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (38 bp):
TAAAGTGACACCTAGTATCTCATACAACCTAGCCGAAG
Found at i:268249 original size:18 final size:18
Alignment explanation
Indices: 268226--268262 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
268216 ACAATTCATA
268226 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
268244 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
268262 T
1 T
268263 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:268994 original size:14 final size:14
Alignment explanation
Indices: 268975--269016 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
268965 CATTTTCTTT
268975 TTCCTTCCCTTTTC
1 TTCCTTCCCTTTTC
268989 TTCCTTCCCTTTTC
1 TTCCTTCCCTTTTC
* *
269003 TCCCTTCCTTTTTC
1 TTCCTTCCCTTTTC
269017 ATTTAAGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (14 bp):
TTCCTTCCCTTTTC
Found at i:269061 original size:15 final size:15
Alignment explanation
Indices: 269025--269075 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
269015 TCATTTAAGC
*
269025 TTCTGTTCTTCTATTCT
1 TTCTTTTCTT-TATT-T
*
269042 TTCTTTTGTTTATTT
1 TTCTTTTCTTTATTT
*
269057 TTCTTTTCTTTATTC
1 TTCTTTTCTTTATTT
269072 TTCT
1 TTCT
269076 ATGTTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 18 0.60
16 4 0.13
17 8 0.27
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.73
Consensus pattern (15 bp):
TTCTTTTCTTTATTT
Found at i:279835 original size:18 final size:18
Alignment explanation
Indices: 279812--279848 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
279802 ACAATTCATA
279812 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
279830 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
279848 T
1 T
279849 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:280179 original size:17 final size:18
Alignment explanation
Indices: 280145--280180 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
280135 TGAATTTCTA
280145 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
280163 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
280180 T
1 T
280181 AAGTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:282951 original size:18 final size:18
Alignment explanation
Indices: 282930--282977 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
282920 GTTCTTGCAT
**
282930 TTGTGGTTGCAAACTTGA
1 TTGTGGTTGCAAACGCGA
* * *
282948 TTGTGGTGGTAATCGCGA
1 TTGTGGTTGCAAACGCGA
282966 TTGTGGTTGCAA
1 TTGTGGTTGCAA
282978 TTTACTATGT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.10, G:0.33, T:0.38
Consensus pattern (18 bp):
TTGTGGTTGCAAACGCGA
Found at i:292470 original size:21 final size:21
Alignment explanation
Indices: 292446--292488 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
292436 GCCTCGAGAA
*
292446 AGAGAGGAAATCCTATAAAAT
1 AGAGAGGAAATCCTAGAAAAT
292467 AGAGAGGAAATCCTAGAAAAT
1 AGAGAGGAAATCCTAGAAAAT
292488 A
1 A
292489 AGGGTCCGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.16
Consensus pattern (21 bp):
AGAGAGGAAATCCTAGAAAAT
Found at i:295824 original size:16 final size:17
Alignment explanation
Indices: 295803--295835 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
295793 GCCTAACTCG
295803 AAAAGAAAG-AAAGAAA
1 AAAAGAAAGAAAAGAAA
295819 AAAAGAAAGAAAAGAAA
1 AAAAGAAAGAAAAGAAA
295836 CCCAAACCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAGAAAGAAAAGAAA
Found at i:295825 original size:12 final size:13
Alignment explanation
Indices: 295802--295835 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
295792 AGCCTAACTC
295802 GAAAAGAAAGAAA
1 GAAAAGAAAGAAA
295815 GAAAA-AAAGAAA
1 GAAAAGAAAGAAA
295827 GAAAAGAAA
1 GAAAAGAAA
295836 CCCAAACCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAGAAA
Found at i:298643 original size:38 final size:38
Alignment explanation
Indices: 298601--298680 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
298591 GTCAGATGAG
* * *
298601 GCGATAATTCT-AGACGCAATTTTGGACGTGCTCATGCA
1 GCGATAATTCTGAG-CGCAATTCTAGACATGCTCATGCA
* *
298639 GCGATAATTCTGAGTGCAATTCTAGACATGCTCATTCA
1 GCGATAATTCTGAGCGCAATTCTAGACATGCTCATGCA
298677 GCGA
1 GCGA
298681 CATTAGTAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
38 34 0.94
39 2 0.06
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.29
Consensus pattern (38 bp):
GCGATAATTCTGAGCGCAATTCTAGACATGCTCATGCA
Done.