Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003300.1 Hibiscus syriacus cultivar Beakdansim tig00006942_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 130599
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2815 original size:18 final size:19
Alignment explanation
Indices: 2792--2827 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2782 AAAATATAAT
2792 ATATATA-ATTTTGAAAAC
1 ATATATAGATTTTGAAAAC
*
2810 ATATATAGTTTTTGAAAA
1 ATATATAGATTTTGAAAA
2828 TATAATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (19 bp):
ATATATAGATTTTGAAAAC
Found at i:2860 original size:45 final size:42
Alignment explanation
Indices: 2776--2863 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 42
2766 TTTTAAACGA
* *
2776 TTTTTGAAAATATAATATATATAATTTTGAAAACATATATAG
1 TTTTTGAAAATATAATATACATAATTTTGAAAAAATATATAG
2818 TTTTTGAAAATATAATATGTTACATAATTTT-AAATAAATATATAG
1 TTTTTGAAAATATAATA---TACATAATTTTGAAA-AAATATATAG
2863 T
1 T
2864 ACTTATTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
42 17 0.43
44 3 0.08
45 20 0.50
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (42 bp):
TTTTTGAAAATATAATATACATAATTTTGAAAAAATATATAG
Found at i:4822 original size:30 final size:30
Alignment explanation
Indices: 4782--4839 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
4772 TAACCTTGTT
* *
4782 TTTTTTAAGGTGTTCGTGTTCGTTTATTAA
1 TTTTTAAAGGTGTTCATGTTCGTTTATTAA
4812 TTTTTAAAGGTGTTCATGTTCGTTTATT
1 TTTTTAAAGGTGTTCATGTTCGTTTATT
4840 TATTGTGCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.17, C:0.07, G:0.19, T:0.57
Consensus pattern (30 bp):
TTTTTAAAGGTGTTCATGTTCGTTTATTAA
Found at i:4896 original size:11 final size:11
Alignment explanation
Indices: 4877--4962 Score: 82
Period size: 11 Copynumber: 7.8 Consensus size: 11
4867 TCACGAATAT
*
4877 GTTCATTTAGC
1 GTTCGTTTAGC
*
4888 GTTCGTTTAGT
1 GTTCGTTTAGC
*
4899 ATTCGTTTAGC
1 GTTCGTTTAGC
4910 GTTCGTTTAGC
1 GTTCGTTTAGC
* *
4921 GTTCATTTAGT
1 GTTCGTTTAGC
* **
4932 GTTTGTTTATT
1 GTTCGTTTAGC
*
4943 GTTCGTTTATC
1 GTTCGTTTAGC
*
4954 GTTCATTTA
1 GTTCGTTTA
4963 TATATTCAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 62 1.00
ACGTcount: A:0.14, C:0.13, G:0.20, T:0.53
Consensus pattern (11 bp):
GTTCGTTTAGC
Found at i:4910 original size:22 final size:22
Alignment explanation
Indices: 4876--4962 Score: 93
Period size: 22 Copynumber: 4.0 Consensus size: 22
4866 TTCACGAATA
*
4876 TGTTCATTTAGCGTTCGTTTAG
1 TGTTCGTTTAGCGTTCGTTTAG
*
4898 TATTCGTTTAGCGTTCGTTTAG
1 TGTTCGTTTAGCGTTCGTTTAG
* * * * *
4920 CGTTCATTTAGTGTTTGTTTAT
1 TGTTCGTTTAGCGTTCGTTTAG
* *
4942 TGTTCGTTTATCGTTCATTTA
1 TGTTCGTTTAGCGTTCGTTTA
4963 TATATTCAAT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.14, C:0.13, G:0.20, T:0.54
Consensus pattern (22 bp):
TGTTCGTTTAGCGTTCGTTTAG
Found at i:4919 original size:33 final size:33
Alignment explanation
Indices: 4877--4962 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
4867 TCACGAATAT
* *
4877 GTTCATTTAGCGTTCGTTTAGTATTCGTTTAGC
1 GTTCGTTTAGCGTTCATTTAGTATTCGTTTAGC
* * **
4910 GTTCGTTTAGCGTTCATTTAGTGTTTGTTTATT
1 GTTCGTTTAGCGTTCATTTAGTATTCGTTTAGC
*
4943 GTTCGTTTATCGTTCATTTA
1 GTTCGTTTAGCGTTCATTTA
4963 TATATTCAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.14, C:0.13, G:0.20, T:0.53
Consensus pattern (33 bp):
GTTCGTTTAGCGTTCATTTAGTATTCGTTTAGC
Found at i:14489 original size:19 final size:19
Alignment explanation
Indices: 14465--14511 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
14455 AAACAAGGGG
14465 GCTAAAATGCTAAAAAAAA
1 GCTAAAATGCTAAAAAAAA
14484 GCTAAAATGCTAAAAAAAA
1 GCTAAAATGCTAAAAAAAA
14503 GCTAAAATG
1 GCTAAAATG
14512 ACCATTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.60, C:0.11, G:0.13, T:0.17
Consensus pattern (19 bp):
GCTAAAATGCTAAAAAAAA
Found at i:14738 original size:16 final size:15
Alignment explanation
Indices: 14717--14747 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
14707 TAAAATTATT
14717 TTTTTTAAAACCTTAA
1 TTTTTT-AAACCTTAA
14733 TTTTTTAAACCTTAA
1 TTTTTTAAACCTTAA
14748 AAACCCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTTTAAACCTTAA
Found at i:15671 original size:9 final size:9
Alignment explanation
Indices: 15657--15730 Score: 61
Period size: 9 Copynumber: 8.7 Consensus size: 9
15647 TTTTATATTT
15657 TTATATTAA
1 TTATATTAA
15666 TTATA-TATA
1 TTATATTA-A
*
15675 TAATATT--
1 TTATATTAA
*
15682 TTATATTAT
1 TTATATTAA
15691 TTATATTAA
1 TTATATTAA
15700 TTATA-TATA
1 TTATATTA-A
*
15709 TAATATT--
1 TTATATTAA
15716 TTATATTAA
1 TTATATTAA
15725 TTATAT
1 TTATAT
15731 AATACAAATC
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
7 12 0.23
8 4 0.08
9 34 0.65
10 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATATTAA
Found at i:15699 original size:34 final size:34
Alignment explanation
Indices: 15634--15730 Score: 178
Period size: 34 Copynumber: 2.9 Consensus size: 34
15624 GCCCTGATTA
15634 TATATATATAATATTTTATATT-TTTATATTAAT
1 TATATATATAATATTTTATATTATTTATATTAAT
15667 TATATATATAATATTTTATATTATTTATATTAAT
1 TATATATATAATATTTTATATTATTTATATTAAT
*
15701 TATATATATAATATTTTATATTAATTATAT
1 TATATATATAATATTTTATATTATTTATAT
15731 AATACAAATC
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
33 22 0.35
34 40 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATATATATAATATTTTATATTATTTATATTAAT
Found at i:15705 original size:25 final size:25
Alignment explanation
Indices: 15649--15730 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 25
15639 ATATAATATT
*
15649 TTATATTTTTATATTAATTATA-TATA
1 TTATA-TTTTATATTATTTATATTA-A
*
15675 TAATATTTTATATTATTTATATTAA
1 TTATATTTTATATTATTTATATTAA
* *
15700 TTATA-TATATAATATTTTATATTAA
1 TTATATTTTATATTA-TTTATATTAA
15725 TTATAT
1 TTATAT
15731 AATACAAATC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
24 7 0.15
25 35 0.73
26 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATATTTTATATTATTTATATTAA
Found at i:26835 original size:58 final size:61
Alignment explanation
Indices: 26791--26923 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 61
26781 CTACATTTTT
* * *
26791 AATTAGTCCCTAAACTT-T-AATATTCAAATTTCATCCTCAAACTATTATACTCAATTCTA
1 AATTAGTCCCTAAAATTGTGAACATTCAAATTTCATCCTCAAACTATGATACTCAATTCTA
* ** * **
26850 AATTAGTCCTTAAAATTGTGAACATTCTGATTTCATCCTTAAACTATGACCCTC-ATTCTA
1 AATTAGTCCCTAAAATTGTGAACATTCAAATTTCATCCTCAAACTATGATACTCAATTCTA
*
26910 AATTGGTCCC-AAAA
1 AATTAGTCCCTAAAA
26924 CATTTAAATC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
59 19 0.31
60 15 0.25
61 27 0.44
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (61 bp):
AATTAGTCCCTAAAATTGTGAACATTCAAATTTCATCCTCAAACTATGATACTCAATTCTA
Found at i:30566 original size:14 final size:14
Alignment explanation
Indices: 30547--30575 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
30537 TGTCAGGGTT
30547 TGGATTACGATCCA
1 TGGATTACGATCCA
30561 TGGATTACGATCCA
1 TGGATTACGATCCA
30575 T
1 T
30576 ATTTGGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (14 bp):
TGGATTACGATCCA
Found at i:33349 original size:78 final size:78
Alignment explanation
Indices: 33220--33376 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 78
33210 TCTTTATGGA
*
33220 GAGAAATGTTATCTCTTTACCGATCATAAAAGCCTGAAGTACTTGTTAACTCAAAAAGATCTAAT
1 GAGAAACGTTATCTCTTTACCGATCATAAAAGCCTGAAGTACTTGTTAACTCAAAAAGATCTAAT
33285 CTTTGTCAAAGAT
66 CTTTGTCAAAGAT
33298 GAGAAACGTTATCTCTTTACCGATCATAAAAGCCTGAAGTACTTGTTAACTCAAAAAGATCTAAT
1 GAGAAACGTTATCTCTTTACCGATCATAAAAGCCTGAAGTACTTGTTAACTCAAAAAGATCTAAT
33363 CTTTGTCAAAGAT
66 CTTTGTCAAAGAT
33376 G
1 G
33377 TTTGATGGAA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (78 bp):
GAGAAACGTTATCTCTTTACCGATCATAAAAGCCTGAAGTACTTGTTAACTCAAAAAGATCTAAT
CTTTGTCAAAGAT
Found at i:38334 original size:43 final size:43
Alignment explanation
Indices: 38217--38395 Score: 144
Period size: 43 Copynumber: 4.1 Consensus size: 43
38207 GCTAAAGTTT
* *
38217 GCGGCGTTTGTGGAAAAAAAACGCCGTAATAGGT-TATGATATATA
1 GCGGCGTTTGT--AATAAAAACGCCGTAATAGGTGT-TGATATTTA
* * * * *
38262 GCGGCATTTATATTACAAATGCCGTAATAGGTGTTGATATTTA
1 GCGGCGTTTGTAATAAAAACGCCGTAATAGGTGTTGATATTTA
* * * *
38305 GCGGCGTTTGTAATAAAAACACCGCAATAGGTGGTGATGTTTA
1 GCGGCGTTTGTAATAAAAACGCCGTAATAGGTGTTGATATTTA
* * * *** * * *
38348 GTGGCATTTTTCCCACAAACGCCGTAATAGTTGTTGAAATTTA
1 GCGGCGTTTGTAATAAAAACGCCGTAATAGGTGTTGATATTTA
38391 GCGGC
1 GCGGC
38396 ATTTTTATTG
Statistics
Matches: 103, Mismatches: 30, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
43 93 0.90
44 1 0.01
45 9 0.09
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (43 bp):
GCGGCGTTTGTAATAAAAACGCCGTAATAGGTGTTGATATTTA
Found at i:38354 original size:86 final size:87
Alignment explanation
Indices: 38217--38395 Score: 207
Period size: 86 Copynumber: 2.1 Consensus size: 87
38207 GCTAAAGTTT
* * * ** *
38217 GCGGCGTTTGTGGAAAAAAAACGCCGTAATAGGTTATGATATATAGCGGCATTTATATTACAAAT
1 GCGGCGTTTGT-GAAAAAAAACACCGCAATAGGTGATGATATATAGCGGCATTTATACCACAAAC
*
38282 GCCGTAATAGGTGTTGATATTTA
65 GCCGTAATAGGTGTTGAAATTTA
* * * * * * *
38305 GCGGCGTTTGT-AATAAAAACACCGCAATAGGTGGTGATGTTTAGTGGCATTTTTCCCACAAACG
1 GCGGCGTTTGTGAAAAAAAACACCGCAATAGGTGATGATATATAGCGGCATTTATACCACAAACG
*
38369 CCGTAATAGTTGTTGAAATTTA
66 CCGTAATAGGTGTTGAAATTTA
38391 GCGGC
1 GCGGC
38396 ATTTTTATTG
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
86 65 0.86
88 11 0.14
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (87 bp):
GCGGCGTTTGTGAAAAAAAACACCGCAATAGGTGATGATATATAGCGGCATTTATACCACAAACG
CCGTAATAGGTGTTGAAATTTA
Found at i:38397 original size:43 final size:43
Alignment explanation
Indices: 38235--38468 Score: 209
Period size: 43 Copynumber: 5.4 Consensus size: 43
38225 TGTGGAAAAA
* * *
38235 AAACGCCGTAATAGGT-TATGATATATAGCGGCATTTATATTAC
1 AAACGCCGTAATAGGTGT-TGATATTTAGCGGCATTTTTACTAC
* * * * *
38278 AAATGCCGTAATAGGTGTTGATATTTAGCGGCGTTTGTAATAA
1 AAACGCCGTAATAGGTGTTGATATTTAGCGGCATTTTTACTAC
* * * * * * *
38321 AAACACCGCAATAGGTGGTGATGTTTAGTGGCATTTTTCCCAC
1 AAACGCCGTAATAGGTGTTGATATTTAGCGGCATTTTTACTAC
* * * *
38364 AAACGCCGTAATAGTTGTTGAAATTTAGCGGCATTTTTATTGC
1 AAACGCCGTAATAGGTGTTGATATTTAGCGGCATTTTTACTAC
* * * * * * *
38407 AAACGCCATAATAAGTTTTGAGATTTAGCTGCATTTTTCCCAC
1 AAACGCCGTAATAGGTGTTGATATTTAGCGGCATTTTTACTAC
*
38450 AAACGCCGCAATAGGTGTT
1 AAACGCCGTAATAGGTGTT
38469 TGAGCTTTCG
Statistics
Matches: 147, Mismatches: 43, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
43 146 0.99
44 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (43 bp):
AAACGCCGTAATAGGTGTTGATATTTAGCGGCATTTTTACTAC
Found at i:38488 original size:43 final size:43
Alignment explanation
Indices: 38355--38489 Score: 103
Period size: 43 Copynumber: 3.1 Consensus size: 43
38345 TTAGTGGCAT
** * * *
38355 TTTTCCCACAAACGCCGTAAT-AGTTGTTGAAATTTAGCGGCAT
1 TTTTCCCACAAACGCCACAATAAGTT-TTGAGATTTAGCTGCAG
**** * *
38398 TTTTATTGCAAACGCCATAATAAGTTTTGAGATTTAGCTGCAT
1 TTTTCCCACAAACGCCACAATAAGTTTTGAGATTTAGCTGCAG
* * * *
38441 TTTTCCCACAAACGCCGCAATAGGTGTTTGAGCTTTCGCTGC-G
1 TTTTCCCACAAACGCCACAATAAGT-TTTGAGATTTAGCTGCAG
38484 TTTTCC
1 TTTTCC
38490 GGTATATAAC
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
43 55 0.75
44 18 0.25
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (43 bp):
TTTTCCCACAAACGCCACAATAAGTTTTGAGATTTAGCTGCAG
Found at i:38976 original size:21 final size:21
Alignment explanation
Indices: 38891--38962 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
38881 TGGTATGTTT
* *
38891 CTTCTCTCTATGCTGTCGTTG
1 CTTCTCTCTATGATGTCGCTG
* * *
38912 CTTCTCTCTTTGATGCCACTG
1 CTTCTCTCTATGATGTCGCTG
*
38933 TTTCTCTCTATGATGTCGCTG
1 CTTCTCTCTATGATGTCGCTG
38954 CTTCTCTCT
1 CTTCTCTCT
38963 GTGCTTCCGC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.07, C:0.31, G:0.15, T:0.47
Consensus pattern (21 bp):
CTTCTCTCTATGATGTCGCTG
Found at i:38983 original size:42 final size:42
Alignment explanation
Indices: 38894--38984 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 42
38884 TATGTTTCTT
* * * * *
38894 CTCTCTATGCTGTCGTTGCTTCTCTCTTTGATGCCACTGTTT
1 CTCTCTATGATGTCGCTGCTTCTCTCTGTGATGCCACTGCTG
* * *
38936 CTCTCTATGATGTCGCTGCTTCTCTCTGTGCTTCCGCTGCTG
1 CTCTCTATGATGTCGCTGCTTCTCTCTGTGATGCCACTGCTG
*
38978 GTCTCTA
1 CTCTCTA
38985 CTTCCCTTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.07, C:0.31, G:0.19, T:0.44
Consensus pattern (42 bp):
CTCTCTATGATGTCGCTGCTTCTCTCTGTGATGCCACTGCTG
Found at i:47761 original size:3 final size:3
Alignment explanation
Indices: 47753--47793 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
47743 ATGTTTACTT
47753 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
47794 TAACCATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:50176 original size:22 final size:22
Alignment explanation
Indices: 50145--50188 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
50135 CATTCACATA
*
50145 TTTACATTTACATTTGCATTTT
1 TTTACATTTACATTTACATTTT
* *
50167 TTTACGTTTATATTTACATTTT
1 TTTACATTTACATTTACATTTT
50189 CATAATTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.05, T:0.61
Consensus pattern (22 bp):
TTTACATTTACATTTACATTTT
Found at i:55264 original size:116 final size:115
Alignment explanation
Indices: 54875--55335 Score: 773
Period size: 115 Copynumber: 4.0 Consensus size: 115
54865 AGCAAGTGCC
* *
54875 ATGTGCTCATAGTAGAAATAAGAATACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* * *
54940 ATATGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAA
66 ATATGGTTTGGTATGAACCCGAAAAACCAATCATTGGATTTAAAAGATGA
54990 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
55055 ATATGGTTTGGTATGAACCCGAAAAACCAATCATTGGATTTAAAAGATGA
66 ATATGGTTTGGTATGAACCCGAAAAACCAATCATTGGATTTAAAAGATGA
*
55105 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGATGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* * *
55170 ATCTGGTTTGGCATGAACCCTGAAAAACCAATCATTGGATTTGAAAGATGA
66 ATATGGTTTGGTATGAACCC-GAAAAACCAATCATTGGATTTAAAAGATGA
55221 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* * * *
55286 ATCTGGTTCGGTAGGAA-CC-ACAAAACCAATCATTGGAATTAAAAGATGA
66 ATATGGTTTGGTATGAACCCGA-AAAACCAATCATTGGATTTAAAAGATGA
55335 A
1 A
55336 CTGCATGATC
Statistics
Matches: 329, Mismatches: 15, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
113 1 0.00
114 27 0.08
115 194 0.59
116 107 0.33
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (115 bp):
ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
ATATGGTTTGGTATGAACCCGAAAAACCAATCATTGGATTTAAAAGATGA
Found at i:55277 original size:231 final size:229
Alignment explanation
Indices: 54875--55335 Score: 789
Period size: 231 Copynumber: 2.0 Consensus size: 229
54865 AGCAAGTGCC
*
54875 ATGTGCTCATAGTAGAAATAAGAATACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTG
*
54940 ATATGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAAATGTGCTCATAGTAG
66 ATATGGTTTGGCATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAAATGTGCTCATAGTAG
* *
55005 AAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGGTATG
131 AAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTCGGTAGG
*
55070 AACC-CGAAAAACCAATCATTGGATTTAAAAGATGA
196 AACCAC--AAAACCAATCATTGGAATTAAAAGATGA
* *
55105 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGATGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTG
* * *
55170 ATCTGGTTTGGCATGAACCCTGAAAAACCAATCATTGGATTTGAAAGATGAATGTGCTCATAGTA
66 ATATGGTTTGGCATGAACCC-CAAAAACCAATCATTGGATTTGAAAGATAAATGTGCTCATAGTA
*
55235 GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAG
130 GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTCGGTAG
55300 GAACCACAAAACCAATCATTGGAATTAAAAGATGA
195 GAACCACAAAACCAATCATTGGAATTAAAAGATGA
55335 A
1 A
55336 CTGCATGATC
Statistics
Matches: 218, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
230 108 0.50
231 109 0.50
232 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (229 bp):
ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTG
ATATGGTTTGGCATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAAATGTGCTCATAGTAG
AAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTCGGTAGG
AACCACAAAACCAATCATTGGAATTAAAAGATGA
Found at i:56586 original size:76 final size:75
Alignment explanation
Indices: 56491--56657 Score: 208
Period size: 76 Copynumber: 2.2 Consensus size: 75
56481 CGAATGTTGT
* * * * *
56491 GGCATGCTAAAAACCCCTTTCAATCAGAATCAGGAATATTGAAGTATTCTGAATATTTATATCAG
1 GGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTGAAGCATTCTGAACACTTATATCAG
56556 CAAAATGCTGG
66 C-AAATGCTGG
* * * * *
56567 GGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGACTATTGATGCATTTTGAACACTTGTATTAG
1 GGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTGAAGCATTCTGAACACTTATATCAG
* *
56632 CCAATGTTGG
66 CAAATGCTGG
*
56642 GGCATGCTGAAGGCCC
1 GGCATGCTGAAAGCCC
56658 ATATCATCCT
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 22 0.28
76 56 0.72
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (75 bp):
GGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTGAAGCATTCTGAACACTTATATCAG
CAAATGCTGG
Found at i:57599 original size:54 final size:51
Alignment explanation
Indices: 57532--57679 Score: 165
Period size: 50 Copynumber: 2.9 Consensus size: 51
57522 ATCTTGGCAT
* * * *
57532 AAGCCACAAAAAAGGATAAATGTGTTGTCAAATGCTTTACGAACATCTAAGCAG
1 AAGCCACAGAAAAGGATGAATGTATTGTCAAATGTTTTACGAAC-TC-AA-CAG
* * * *
57586 AAGCCACAGAAAAGGATGAAGGTATTGTCAAGTGTTTTAC-ATCTCGACAG
1 AAGCCACAGAAAAGGATGAATGTATTGTCAAATGTTTTACGAACTCAACAG
*
57636 AAACCACAGGAAAA-GATGAATGTATTGTCAAATGTTTTACGAAC
1 AAGCCACA-GAAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
57680 CAGTGATTAT
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
50 34 0.43
51 8 0.10
52 2 0.03
53 2 0.03
54 34 0.43
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (51 bp):
AAGCCACAGAAAAGGATGAATGTATTGTCAAATGTTTTACGAACTCAACAG
Found at i:58527 original size:115 final size:113
Alignment explanation
Indices: 58395--58632 Score: 350
Period size: 115 Copynumber: 2.1 Consensus size: 113
58385 GTGCCAGTTA
* * * *
58395 GAGAAGAACTTATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAATAACTTGTTCAACTTTTTGT
1 GAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
*
58460 TTGAATTCATCATTTGATGGATCAACATCCCCAGTGAAAGAGTTCATAAT
66 TTGAATTCATCATTCGATGGATCAACATCCCCAG-G-AAGAGTTCATAAT
*
58510 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
1 GAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
* ** **
58575 TTGAATTCATCATTCGATGGATCATCATTGCCAGGGCGAGTTCATAAT
66 TTGAATTCATCATTCGATGGATCAACATCCCCAGGAAGAGTTCATAAT
*
58623 GAGAAAAACT
1 GAGAAGAACT
58633 TGGTCAACTT
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
113 20 0.18
114 1 0.01
115 90 0.81
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
GAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
TTGAATTCATCATTCGATGGATCAACATCCCCAGGAAGAGTTCATAAT
Found at i:58622 original size:73 final size:73
Alignment explanation
Indices: 58540--58705 Score: 224
Period size: 73 Copynumber: 2.3 Consensus size: 73
58530 AGGAAGAAGA
* * * * * *
58540 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCATCATTG
1 AGTTCATAATGAGAAGAACTTGGTCAACTTTTCGCTCGAATTCATCACTAGATAGATCAACATTG
* *
58605 CCAGGGCG
66 CCAGAGAG
* * * *
58613 AGTTCATAATGAGAAAAACTTGGTCAACTTTTTGCTCGAATTCATCACTAGATAGATCAACTTTT
1 AGTTCATAATGAGAAGAACTTGGTCAACTTTTCGCTCGAATTCATCACTAGATAGATCAACATTG
58678 CCAGAGAG
66 CCAGAGAG
58686 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
58706 CATCTGAAGA
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 80 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (73 bp):
AGTTCATAATGAGAAGAACTTGGTCAACTTTTCGCTCGAATTCATCACTAGATAGATCAACATTG
CCAGAGAG
Found at i:58999 original size:123 final size:123
Alignment explanation
Indices: 58661--59170 Score: 778
Period size: 123 Copynumber: 4.2 Consensus size: 123
58651 AATTCATCAC
* * *
58661 TAGAT-AG-ATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAA
1 TAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAA
* * *
58724 GAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGCATGACTCTATCACAGAAGGAGA
65 GAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCATAACTCTATCACAGAAGGAGA
* * *
58783 TAAATCATCATCAA-TATTTCC--AGAAAGTTCATAATGAGAAGAACTTATCTGAAAAGGAAGAA
1 TAGATCAGCATCAACT-TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAA
* *
58845 GAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGA
65 GAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCATAACTCTATCACAGAAGGAGA
58904 TAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 TAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
* **
58969 AAGTTCATAATGAGAAGAGCTTATTTAACCTTTTGTTTAACTCTATCACAGAAGGAGA
66 AAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCATAACTCTATCACAGAAGGAGA
*
59027 TAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGTGGAAGAAG
1 TAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
* ** *
59092 AAGTTCATAATGAGAAGAGCTTATTTAACCTTTTGTTTAACTCTATCACAGAAGCAGA
66 AAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCATAACTCTATCACAGAAGGAGA
* *
59150 TAGATCAACATCAACATTTCC
1 TAGATCAGCATCAACTTTTCC
59171 GAGTGAAGAT
Statistics
Matches: 363, Mismatches: 19, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
121 82 0.23
122 35 0.10
123 236 0.65
124 10 0.03
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (123 bp):
TAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
AAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCATAACTCTATCACAGAAGGAGA
Found at i:59315 original size:19 final size:18
Alignment explanation
Indices: 59282--59322 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
59272 TTTTCATTTG
*
59282 ATTATTATTTATATTATT
1 ATTATTATATATATTATT
59300 ATTATTATGATATATTATT
1 ATTATTAT-ATATATTATT
59319 ATTA
1 ATTA
59323 AATAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTATTATATATATTATT
Found at i:60791 original size:3 final size:3
Alignment explanation
Indices: 60783--60814 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
60773 ATGTTTACTT
*
60783 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
60815 TAACCATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:60798 original size:12 final size:12
Alignment explanation
Indices: 60777--60814 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
60767 TTTTATATGT
*
60777 TTACTTTTATTA
1 TTACTATTATTA
60789 TTACTATTATTA
1 TTACTATTATTA
*
60801 TTATTATTATTA
1 TTACTATTATTA
60813 TT
1 TT
60815 TAACCATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (12 bp):
TTACTATTATTA
Found at i:61165 original size:42 final size:39
Alignment explanation
Indices: 61098--61176 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 39
61088 AATAAATATT
*
61098 TTATAAATTAATATATATATATTTTTTTTAAAAATAGGA
1 TTATAAATTAATATATATATATTTTTTCTAAAAATAGGA
* * *
61137 TTATAAATTTAATATATCTTTGAATTTTTTCTAATAATAG
1 TTATAAA-TTAATATATATAT--ATTTTTTCTAAAAATAG
61177 AGACAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 7 0.21
40 11 0.33
42 15 0.45
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (39 bp):
TTATAAATTAATATATATATATTTTTTCTAAAAATAGGA
Found at i:63562 original size:42 final size:42
Alignment explanation
Indices: 63219--63560 Score: 477
Period size: 42 Copynumber: 8.1 Consensus size: 42
63209 CCCTATTACA
* ** * * *
63219 GCGTTTGAACTATAAACAACGCTATATTACTACTTTATTACA
1 GCGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCG
* * *
63261 GCGTTTGAGCTATAAACACCGCTATATTACTATTATATTGCG
1 GCGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCG
63303 GCGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCG
1 GCGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCG
*
63345 GCGTTTGAGCTATAAACGCTGCTATATTACTACTCTATTGCG
1 GCGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCG
* *
63387 ACATTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCG
1 GCGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCG
* * * *
63429 GCGTTTGAGATATAAATGCCGCTATATTACGACTCTATTACG
1 GCGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCG
*
63471 GCGTTTGAGCTATAAACGCCGTTATATTACTACTCTATTGCG
1 GCGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCG
* ** * * *
63513 ACGTTTTTGTTATAAACACTGCTATATTACTACTCTATTGCG
1 GCGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCG
63555 GCGTTT
1 GCGTTT
63561 TTTACAACAA
Statistics
Matches: 268, Mismatches: 32, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 268 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (42 bp):
GCGTTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCG
Found at i:64609 original size:22 final size:22
Alignment explanation
Indices: 64563--64611 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
64553 CACGTTTTCA
*
64563 AAAGCTATTATTTTTCCTATTCG
1 AAAGCTATTATTTTTCCCA-TCG
64586 AAAGCTATTATTTTTCTCCA-CG
1 AAAGCTATTATTTTTC-CCATCG
64608 AAAG
1 AAAG
64612 TAGAAAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 16 0.67
24 2 0.08
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (22 bp):
AAAGCTATTATTTTTCCCATCG
Found at i:65260 original size:83 final size:82
Alignment explanation
Indices: 65086--65261 Score: 212
Period size: 83 Copynumber: 2.1 Consensus size: 82
65076 TTTTTAGCAC
* * *
65086 AAACGCCACTATAAACAACTCTATTGCGGTGTTTGTATAAAAATACCGCTAAATTACTAATCTAT
1 AAACGCCACTATAAACAACTATATTGCGGCGTTTGTATAAAAACACCGCTAAATTACTAATCTAT
* *
65151 TACGGCATTTTTTGTAA
66 TACGGCATTTGTTGAAA
* * * *
65168 AAACACCACTATAAACAACTATATTTCGGCGTTTG-AGCTATAAACGCCGCTAAATTAC-AACTC
1 AAACGCCACTATAAACAACTATATTGCGGCGTTTGTA--TAAAAACACCGCTAAATTACTAA-TC
*
65231 TATTACGGCGTTTGTTGAAA
63 TATTACGGCATTTGTTGAAA
*
65251 AAATGCCACTA
1 AAACGCCACTA
65262 AAGTATCATT
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
81 1 0.01
82 33 0.42
83 45 0.57
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (82 bp):
AAACGCCACTATAAACAACTATATTGCGGCGTTTGTATAAAAACACCGCTAAATTACTAATCTAT
TACGGCATTTGTTGAAA
Found at i:65263 original size:42 final size:41
Alignment explanation
Indices: 65100--65263 Score: 102
Period size: 42 Copynumber: 4.0 Consensus size: 41
65090 GCCACTATAA
* * * *
65100 ACAACTCTATTGCGGTGTTTGT-ATAAAAATACCGCTAAATT
1 ACAACTCTATTACGGCGTTTGTGA-AAAAACACCACTAAATT
* * *
65141 ACTAA-TCTATTACGGCATTTTTTGTAAAAACACCACTATAA--
1 AC-AACTCTATTACGGC-GTTTGTGAAAAAACACCACTA-AATT
* * * * * * *
65182 ACAACTATATTTCGGCGTTTGAGCTATAAACGCCGCTAAATT
1 ACAACTCTATTACGGCGTTTGTG-AAAAAACACCACTAAATT
**
65224 ACAACTCTATTACGGCGTTTGTTGAAAAAATGCCACTAAA
1 ACAACTCTATTACGGCGTTTG-TGAAAAAACACCACTAAA
65264 GTATCATTTT
Statistics
Matches: 92, Mismatches: 22, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
40 8 0.09
41 33 0.36
42 48 0.52
43 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (41 bp):
ACAACTCTATTACGGCGTTTGTGAAAAAACACCACTAAATT
Found at i:76314 original size:19 final size:20
Alignment explanation
Indices: 76290--76340 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
76280 CGGCCAAGAG
* *
76290 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
76309 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
76329 CATGTATTTTCA
1 CATGTATTTTCA
76341 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:80490 original size:19 final size:20
Alignment explanation
Indices: 80466--80516 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
80456 CGGCCAAGAG
* *
80466 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
80485 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
80505 CATGTATTTTCA
1 CATGTATTTTCA
80517 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:86003 original size:42 final size:42
Alignment explanation
Indices: 85944--86050 Score: 151
Period size: 42 Copynumber: 2.5 Consensus size: 42
85934 GGAATGTTGG
*
85944 GGCATGTTGAAAGCCCATTTCAGTCAGAAATAATCTATGTGA
1 GGCATGTTGAAAGCCCATTTCAGTCAGAAACAATCTATGTGA
* * * * *
85986 GGCATGCTGAAGGCCCATTTTAGTCAGAAACAATTTATGTGG
1 GGCATGTTGAAAGCCCATTTCAGTCAGAAACAATCTATGTGA
*
86028 GGCATTTTGAAAGCCCATTTCAG
1 GGCATGTTGAAAGCCCATTTCAG
86051 ACAAAAATGA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (42 bp):
GGCATGTTGAAAGCCCATTTCAGTCAGAAACAATCTATGTGA
Found at i:86817 original size:22 final size:22
Alignment explanation
Indices: 86789--86837 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
86779 ATTCTGCAAG
86789 GATGATAGATTCTCTCTTCAAA
1 GATGATAGATTCTCTCTTCAAA
*
86811 GATGATAGATTCTCTTTTCAAA
1 GATGATAGATTCTCTCTTCAAA
86833 GATGA
1 GATGA
86838 AAGCTTTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (22 bp):
GATGATAGATTCTCTCTTCAAA
Found at i:87618 original size:42 final size:42
Alignment explanation
Indices: 87571--87654 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
87561 CTCACAAATT
* * *
87571 TTTAAATCCTTCGGGTCATCTGTCAGTCTTTTGAGCATGATG
1 TTTAAATCATTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
*
87613 TTTAAATCATTTGGGTCATCTGTCAGTCTTTCGAGCAAGATG
1 TTTAAATCATTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
87655 ATAAGTCCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (42 bp):
TTTAAATCATTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
Found at i:87891 original size:18 final size:18
Alignment explanation
Indices: 87868--87967 Score: 89
Period size: 18 Copynumber: 5.3 Consensus size: 18
87858 CTGTTTTTTA
87868 TATATTACTATTATTAAT
1 TATATTACTATTATTAAT
87886 TATATTACTATTATT-AT
1 TATATTACTATTATTAAT
* *
87903 TATTATTATTGTTATTATTAT
1 TA-TATTACTATTATTA--AT
87924 TATATTACATATTTATT-AT
1 TATATTAC-TA-TTATTAAT
*
87943 ATATAATA-TATTATTATAT
1 -TATATTACTATTATTA-AT
87962 TATATT
1 TATATT
87968 TGCATTTACA
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
17 9 0.13
18 33 0.49
19 4 0.06
20 11 0.16
21 5 0.07
22 5 0.07
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (18 bp):
TATATTACTATTATTAAT
Found at i:87900 original size:3 final size:3
Alignment explanation
Indices: 87865--87964 Score: 80
Period size: 3 Copynumber: 32.3 Consensus size: 3
87855 TGTCTGTTTT
* *
87865 TTA TATA TTA CTA TTA TTAA TTA -TA TTA CTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
87911 TTG TTA TTA TTA TTA -TA TTA CATA TTTA TTA TATA TAA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA T-TA TTA T-TA TTA TTA
87959 -TA TTA T
1 TTA TTA T
87965 ATTTGCATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
2 6 0.08
3 57 0.73
4 15 0.19
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:87941 original size:16 final size:16
Alignment explanation
Indices: 87867--87963 Score: 78
Period size: 16 Copynumber: 6.0 Consensus size: 16
87857 TCTGTTTTTT
*
87867 ATATATTACTATTATTA
1 ATATATTATTA-TATTA
87884 AT-TA-TATTACTATT-
1 ATATATTATTA-TATTA
*
87898 AT-TATTATTATTATTG
1 ATATATTATTA-TATTA
*
87914 TTATTATTATTATATTA
1 ATA-TATTATTATATTA
87931 CATAT-TTATTATATATA
1 -ATATATTATTATAT-TA
87948 ATATATTATTATATTA
1 ATATATTATTATATTA
87964 TATTTGCATT
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.06
15 17 0.25
16 18 0.27
17 18 0.27
18 10 0.15
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (16 bp):
ATATATTATTATATTA
Found at i:91809 original size:2 final size:2
Alignment explanation
Indices: 91802--91827 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
91792 TTTAGTATGA
91802 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
91828 GACTAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92338 original size:25 final size:24
Alignment explanation
Indices: 92310--92382 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 24
92300 GAGATAGAAT
* *
92310 TAAAAGTGATGTAGTATGATTGAAA
1 TAAAA-TGATGTTGTAGGATTGAAA
92335 TAAAAATGATGTTGTAGGATTGAAA
1 T-AAAATGATGTTGTAGGATTGAAA
92360 TAAAATCGATGTTGTAGGATTGA
1 TAAAAT-GATGTTGTAGGATTGA
92383 TGAATGGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.11
25 35 0.80
26 4 0.09
ACGTcount: A:0.41, C:0.01, G:0.25, T:0.33
Consensus pattern (24 bp):
TAAAATGATGTTGTAGGATTGAAA
Found at i:97154 original size:11 final size:11
Alignment explanation
Indices: 97133--97167 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
97123 CCTTCCTTTC
*
97133 TCTTCTATTTT
1 TCTTTTATTTT
*
97144 TGTTTTATTTT
1 TCTTTTATTTT
97155 TCTTTTATTTT
1 TCTTTTATTTT
97166 TC
1 TC
97168 GTTCCTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.11, G:0.03, T:0.77
Consensus pattern (11 bp):
TCTTTTATTTT
Found at i:97972 original size:23 final size:21
Alignment explanation
Indices: 97924--97964 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
97914 GAGAATATTT
97924 TAAA-TTAGTTCTTCTCATTA
1 TAAATTTAGTTCTTCTCATTA
97944 TAAATTTA-TTCTTCCTCATTA
1 TAAATTTAGTTCTT-CTCATTA
97965 GATAAATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.51
Consensus pattern (21 bp):
TAAATTTAGTTCTTCTCATTA
Found at i:98538 original size:69 final size:69
Alignment explanation
Indices: 98448--98695 Score: 208
Period size: 69 Copynumber: 3.7 Consensus size: 69
98438 GGAAAATAAC
* *
98448 CTCAAGTGAGATAAAAATTTCTTGTTTAAAGTGAAACAATTTCGAAATTTATATTTCAAGAGAAA
1 CTCAAGTAAGATAAAAATTTCTTGTTTAAAGTGAAACAATTTCAAAATTTATATTTCAAGAGAAA
98513 GTGT
66 GTGT
* ** * * *
98517 CTCAAGTAAGATAAAATTTTCTTGTTTCGAGTTAAACAATTTCAAAATTTGTATTTTAAGAGAAA
1 CTCAAGTAAGATAAAAATTTCTTGTTTAAAGTGAAACAATTTCAAAATTTATATTTCAAGAGAAA
* *
98582 ATAT
66 GTGT
* ** * ** * *
98586 CTCTAGTGGGAT--AAA---GTT-TTTAAA-TGAAATGATTTCAAAATTTGTATTTGAAGAGAAA
1 CTCAAGTAAGATAAAAATTTCTTGTTTAAAGTGAAACAATTTCAAAATTTATATTTCAAGAGAAA
* *
98644 ATAT
66 GTGT
* * * * *
98648 CTTAAGTGAGACAAAAA-AT-TTGTTTCAAGTGAAACAATTTCAAAATTT
1 CTCAAGTAAGATAAAAATTTCTTGTTTAAAGTGAAACAATTTCAAAATTT
98696 GTGTTCCAAG
Statistics
Matches: 145, Mismatches: 28, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
62 42 0.29
63 4 0.03
64 5 0.03
65 2 0.01
66 5 0.03
67 19 0.13
69 68 0.47
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (69 bp):
CTCAAGTAAGATAAAAATTTCTTGTTTAAAGTGAAACAATTTCAAAATTTATATTTCAAGAGAAA
GTGT
Found at i:98892 original size:105 final size:105
Alignment explanation
Indices: 98630--98942 Score: 372
Period size: 105 Copynumber: 3.0 Consensus size: 105
98620 TCAAAATTTG
* * * * *
98630 TATTTGAAGAGAAA-ATATCTTAAGTGAGACAAAAAATTTGTTTCAAGTGAAACAATTTCAAAAT
1 TATTTCAAGAGAAACA-ATCTCAAGTGAGATAAAAAAATTGTTTCGAGTGAAACAATTTCAAAAT
* * *
98694 TTGTGTTCCAA-GGAGACTGTCTCAAGTGAGATGGAA--TTT
65 TTGTGTTTCAAGGGAAACTGTCTCAAGTGAGAT-AAATTTTT
***
98733 TATTTCACTTGAAAC---CTCAAGTGAGATAAAAAAATTGTTTCGAGTGAAACAATTTCAAAATT
1 TATTTCAAGAGAAACAATCTCAAGTGAGATAAAAAAATTGTTTCGAGTGAAACAATTTCAAAATT
* *
98795 TGTGTTTCAAGGGAAAATGTCTTAAGTGAGATAAATTTTT
66 TGTGTTTCAAGGGAAACTGTCTCAAGTGAGATAAATTTTT
* *
98835 TGTTTCAAGAGAAACAATCTCAAGTGAGATAAAAAAAAAT-TTTCGAGTGAAACAATTTCAAAAT
1 TATTTCAAGAGAAACAATCTCAAGTGAGAT-AAAAAAATTGTTTCGAGTGAAACAATTTCAAAAT
* * *
98899 TTGTGTTTCAAGGTAAACTGTCTCAAGCGAGACGAAATTTTT
65 TTGTGTTTCAAGGGAAACTGTCTCAAGTGAGA-TAAATTTTT
98941 TA
1 TA
98943 AGAAAACAAT
Statistics
Matches: 177, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
100 54 0.31
101 18 0.10
102 14 0.08
103 10 0.06
105 64 0.36
106 17 0.10
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (105 bp):
TATTTCAAGAGAAACAATCTCAAGTGAGATAAAAAAATTGTTTCGAGTGAAACAATTTCAAAATT
TGTGTTTCAAGGGAAACTGTCTCAAGTGAGATAAATTTTT
Found at i:106497 original size:21 final size:21
Alignment explanation
Indices: 106464--106516 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
106454 CTCTTCAACA
* *
106464 ATTA-AAAGCCAAGGCACACT
1 ATTACAAAGTCAAGGAACACT
* * *
106484 ATTGCAAAGTCAAGTAACATT
1 ATTACAAAGTCAAGGAACACT
106505 ATTACAAAGTCA
1 ATTACAAAGTCA
106517 TAGCTCATCT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (21 bp):
ATTACAAAGTCAAGGAACACT
Found at i:111156 original size:12 final size:13
Alignment explanation
Indices: 111138--111167 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
111128 TCATACAAAA
111138 GCATATGACCATT
1 GCATATGACCATT
111151 -CATATGACCATT
1 GCATATGACCATT
111163 GCATA
1 GCATA
111168 CATACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (13 bp):
GCATATGACCATT
Found at i:116658 original size:28 final size:28
Alignment explanation
Indices: 116626--116681 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
116616 GCCATCTGTT
* *
116626 CGAACGTAAATGAACGAACATAACCAAA
1 CGAACATAAATGAACGAACATAAACAAA
*
116654 CGAACATAAATGAACGAATATAAACAAA
1 CGAACATAAATGAACGAACATAAACAAA
116682 ACATATAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.12
Consensus pattern (28 bp):
CGAACATAAATGAACGAACATAAACAAA
Found at i:116669 original size:14 final size:14
Alignment explanation
Indices: 116626--116677 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
116616 GCCATCTGTT
*
116626 CGAACGTAAATGAA
1 CGAACATAAATGAA
***
116640 CGAACATAACCAAA
1 CGAACATAAATGAA
116654 CGAACATAAATGAA
1 CGAACATAAATGAA
*
116668 CGAATATAAA
1 CGAACATAAA
116678 CAAAACATAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.56, C:0.17, G:0.13, T:0.13
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:123980 original size:12 final size:12
Alignment explanation
Indices: 123945--123994 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
123935 ATTCACAAAC
*
123945 AAATTTATTTAT
1 AAATTTGTTTAT
*
123957 AATATTTTTTTAT
1 AA-ATTTGTTTAT
123970 AAATTTGTTTAT
1 AAATTTGTTTAT
*
123982 CAATTTG-TTAT
1 AAATTTGTTTAT
123993 AA
1 AA
123995 GTTCGTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 5 0.15
12 17 0.52
13 11 0.33
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (12 bp):
AAATTTGTTTAT
Found at i:124509 original size:18 final size:18
Alignment explanation
Indices: 124486--124522 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
124476 TTAAAATTTT
124486 AATAAATAAAAATAAATA
1 AATAAATAAAAATAAATA
* *
124504 AATAAATGAACATAAATA
1 AATAAATAAAAATAAATA
124522 A
1 A
124523 TATATTCAGA
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:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
AATAAATAAAAATAAATA
Done.