Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000663.1 Hibiscus syriacus cultivar Beakdansim tig00001292_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: 73931
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3555 original size:29 final size:29
Alignment explanation
Indices: 3513--3584 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
3503 ATGGATTGTC
3513 GAAATAACTAGTCTAGTGTAATATTTGAT
1 GAAATAACTAGTCTAGTGTAATATTTGAT
3542 GAAATAACTAGTCTAGTGTAATATTTGAT
1 GAAATAACTAGTCTAGTGTAATATTTGAT
*
3571 AAAATAACTAGTCT
1 GAAATAACTAGTCT
3585 GTTGTGAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.36
Consensus pattern (29 bp):
GAAATAACTAGTCTAGTGTAATATTTGAT
Found at i:6563 original size:21 final size:21
Alignment explanation
Indices: 6537--6582 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
6527 AGGAATTCTC
6537 TGGCTGATACTAGCTTATCTT
1 TGGCTGATACTAGCTTATCTT
6558 TGGCTGATACTAGCTTATCTT
1 TGGCTGATACTAGCTTATCTT
6579 TGGC
1 TGGC
6583 ATCCTCTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (21 bp):
TGGCTGATACTAGCTTATCTT
Found at i:21246 original size:2 final size:2
Alignment explanation
Indices: 21241--21268 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21231 AGTTTTTTTT
21241 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
21269 ACTTGCCGTG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31521 original size:15 final size:15
Alignment explanation
Indices: 31490--31531 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
31480 GAAATTATAA
31490 AATATT-TAATTATATT
1 AATATTATAA-TA-ATT
*
31506 ATTATTATAATAATT
1 AATATTATAATAATT
31521 AATATTATAAT
1 AATATTATAAT
31532 TAATATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 13 0.57
16 7 0.30
17 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATTATAATAATT
Found at i:31530 original size:12 final size:12
Alignment explanation
Indices: 31490--31537 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
31480 GAAATTATAA
31490 AATATT-TAATT
1 AATATTATAATT
*
31501 -ATATTATTATT
1 AATATTATAATT
31512 -ATA--ATAATT
1 AATATTATAATT
31521 AATATTATAATT
1 AATATTATAATT
31533 AATAT
1 AATAT
31538 ATTTTAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 5 0.16
10 8 0.26
11 7 0.23
12 11 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AATATTATAATT
Found at i:32201 original size:28 final size:26
Alignment explanation
Indices: 32129--32201 Score: 69
Period size: 28 Copynumber: 2.8 Consensus size: 26
32119 TGAATAGATC
**
32129 AAAGAAAAAATGTAGA-AAATAAAAA
1 AAAGAAAAAAAATAGATAAATAAAAA
* *
32154 AAAGAAAAATAATCA-TTAAATCAAAAA
1 AAAGAAAAAAAAT-AGATAAAT-AAAAA
32181 AAAGGAAAAAAAATAGATAAA
1 AAA-GAAAAAAAATAGATAAA
32202 ATAGAGAGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
25 10 0.27
26 5 0.14
27 9 0.24
28 13 0.35
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.14
Consensus pattern (26 bp):
AAAGAAAAAAAATAGATAAATAAAAA
Found at i:32956 original size:17 final size:17
Alignment explanation
Indices: 32934--32967 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
32924 ACCTTCGGTA
32934 TTTTTT-GGTATTTGTTT
1 TTTTTTGGGT-TTTGTTT
32951 TTTTTTGGGTTTTGTTT
1 TTTTTTGGGTTTTGTTT
32968 CTGTATTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.03, C:0.00, G:0.21, T:0.76
Consensus pattern (17 bp):
TTTTTTGGGTTTTGTTT
Found at i:33670 original size:18 final size:19
Alignment explanation
Indices: 33627--33672 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
33617 ACCTAAAAAA
* *
33627 AAAAAAAAAACGAGTAAAT
1 AAAAAATAAACAAGTAAAT
*
33646 -AATAATAAACAAG-AAAT
1 AAAAAATAAACAAGTAAAT
33663 AAAAAATAAA
1 AAAAAATAAA
33673 ATACTACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (19 bp):
AAAAAATAAACAAGTAAAT
Found at i:33812 original size:31 final size:33
Alignment explanation
Indices: 33738--33816 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
33728 CCATTTACTA
* * *
33738 TATAATTTTAAAAAATGTTTTAAAACTATATGT
1 TATAGTTTTCAAAAACGTTTTAAAACTATATGT
33771 TATAGTTTTCAAAAACGTTTTAAAACTATA--T
1 TATAGTTTTCAAAAACGTTTTAAAACTATATGT
33802 TATA-TGTTTCAAAAA
1 TATAGT-TTTCAAAAA
33817 AAATTTCAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 1 0.02
31 14 0.33
33 27 0.64
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (33 bp):
TATAGTTTTCAAAAACGTTTTAAAACTATATGT
Found at i:33818 original size:33 final size:33
Alignment explanation
Indices: 33684--33818 Score: 88
Period size: 33 Copynumber: 4.2 Consensus size: 33
33674 TACTACATAT
*
33684 AAAAATGTTTTAAAACTATA-TATA--TTTCAA
1 AAAAACGTTTTAAAACTATATTATATGTTTCAA
* * * * **
33714 AAATAC-TTTCAAAACCAT-TTACTATATAATTTTA
1 AAAAACGTTTTAAAACTATATTA-TATGT--TTCAA
*
33748 AAAAATGTTTTAAAACTATATGT-TATAGTTTTC--
1 AAAAACGTTTTAAAACTATAT-TATAT-G-TTTCAA
33781 AAAAACGTTTTAAAACTATATTATATGTTTCAA
1 AAAAACGTTTTAAAACTATATTATATGTTTCAA
33814 AAAAA
1 AAAAA
33819 ATTTCAACTA
Statistics
Matches: 78, Mismatches: 13, Indels: 25
0.67 0.11 0.22
Matches are distributed among these distances:
29 12 0.15
30 6 0.08
31 4 0.05
32 3 0.04
33 28 0.36
34 7 0.09
35 15 0.19
36 1 0.01
37 2 0.03
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (33 bp):
AAAAACGTTTTAAAACTATATTATATGTTTCAA
Found at i:33910 original size:37 final size:38
Alignment explanation
Indices: 33743--34038 Score: 215
Period size: 38 Copynumber: 8.3 Consensus size: 38
33733 TACTATATAA
* *
33743 TTTTAAAAAATG-TTTT-AAAACTATAT-GT-TATA-G
1 TTTTCAAAAATGATTTTAAAAACTATATAATATATATG
*
33776 TTTTCAAAAACG-TTTT-AAAAC--TAT-AT-TATATG
1 TTTTCAAAAATGATTTTAAAAACTATATAATATATATG
* * * * *
33808 -TTTCAAAAA-AAATTT--CAACTATATATTATATA-A
1 TTTTCAAAAATGATTTTAAAAACTATATAATATATATG
* * * *
33841 ATTTC-AAAATGATTTT-AAAACTATTTATTATATAAG
1 TTTTCAAAAATGATTTTAAAAACTATATAATATATATG
* *
33877 TTTTC-GAAATGGTTTTAAAAACTATATAATATATATG
1 TTTTCAAAAATGATTTTAAAAACTATATAATATATATG
* *
33914 GTTTCAAAAAT-ATCTTCAAAAACTATATAATATATATG
1 TTTTCAAAAATGAT-TTTAAAAACTATATAATATATATG
*
33952 TTTTCAAAAAAATG-TTTTCAAAAC--TATAATATATATG
1 TTTTC--AAAAATGATTTTAAAAACTATATAATATATATG
* * *
33989 TTTTCAAAAATGATTTTAAAAATTATATATTATATATA
1 TTTTCAAAAATGATTTTAAAAACTATATAATATATATG
*
34027 TTTTCTAAAATG
1 TTTTCAAAAATG
34039 TGTTTTTTTT
Statistics
Matches: 213, Mismatches: 31, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
30 3 0.01
31 20 0.09
32 4 0.02
33 24 0.11
34 12 0.06
35 22 0.10
36 21 0.10
37 40 0.19
38 53 0.25
39 7 0.03
40 7 0.03
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.43
Consensus pattern (38 bp):
TTTTCAAAAATGATTTTAAAAACTATATAATATATATG
Found at i:33938 original size:38 final size:37
Alignment explanation
Indices: 33700--34037 Score: 164
Period size: 38 Copynumber: 9.5 Consensus size: 37
33690 GTTTTAAAAC
* * * *
33700 TATATAT-ATTTCAAAAATACTTTC-AAAACCATTTAC
1 TATATATGTTTTCAAAAATA-TTTCAAAAACTATATAA
* * * * *
33736 TATATA-ATTTTAAAAAATGTTT-TAAAACTATAT-G
1 TATATATGTTTTCAAAAATATTTCAAAAACTATATAA
** *
33770 T-TATA-GTTTTCAAAAACGTTT-TAAAAC--TAT-A
1 TATATATGTTTTCAAAAATATTTCAAAAACTATATAA
* *
33801 T-TATATG-TTTCAAAAAAAATTTC---AACTATATAT
1 TATATATGTTTTC-AAAAATATTTCAAAAACTATATAA
** * * *
33834 TATATA-AATTTC-AAAATGATTT-TAAAACTATTTAT
1 TATATATGTTTTCAAAAAT-ATTTCAAAAACTATATAA
* * * *
33869 TATATAAGTTTTC-GAAATGGTTTTAAAAACTATATAA
1 TATATATGTTTTCAAAAAT-ATTTCAAAAACTATATAA
*
33906 TATATATGGTTTCAAAAATATCTTCAAAAACTATATAA
1 TATATATGTTTTCAAAAATAT-TTCAAAAACTATATAA
*
33944 TATATATGTTTTCAAAAAAATGTTTTC-AAAAC--TATAA
1 TATATATGTTTTC--AAAAAT-ATTTCAAAAACTATATAA
* * *
33981 TATATATGTTTTCAAAAATGATTTTAAAAATTATATAT
1 TATATATGTTTTCAAAAAT-ATTTCAAAAACTATATAA
* *
34019 TATATATATTTTCTAAAAT
1 TATATATGTTTTCAAAAAT
34038 GTGTTTTTTT
Statistics
Matches: 242, Mismatches: 36, Indels: 46
0.75 0.11 0.14
Matches are distributed among these distances:
30 3 0.01
31 12 0.05
32 16 0.07
33 28 0.12
34 9 0.04
35 36 0.15
36 31 0.13
37 40 0.17
38 52 0.21
39 5 0.02
40 9 0.04
41 1 0.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (37 bp):
TATATATGTTTTCAAAAATATTTCAAAAACTATATAA
Found at i:34038 original size:38 final size:38
Alignment explanation
Indices: 33824--34101 Score: 206
Period size: 38 Copynumber: 7.4 Consensus size: 38
33814 AAAAAATTTC
*
33824 AACTATATATTATATA-AATTTC-AAAATGATTTT-AA
1 AACTATATATTATATATATTTTCAAAAATGATTTTAAA
* * *
33859 AACTATTTATTATATA-AGTTTTC-GAAATGGTTTTAAA
1 AACTATATATTATATATA-TTTTCAAAAATGATTTTAAA
* ** *
33896 AACTATATAATATATATGGTTTCAAAAAT-ATCTTCAAA
1 AACTATATATTATATATATTTTCAAAAATGAT-TTTAAA
* * *
33934 AACTATATAATATATATGTTTTCAAAAAAATG-TTTTCAA
1 AACTATATATTATATATATTTTC--AAAAATGATTTTAAA
*
33973 AACTATA-A-TATATATGTTTTCAAAAATGATTTTAAA
1 AACTATATATTATATATATTTTCAAAAATGATTTTAAA
* * * **
34009 AATTATATATTATATATATTTTCTAAAATGTGTTTTTTTTTTA
1 AACTATATATTATATATATTTTC-AAAA-ATG---ATTTTAAA
*
34052 AACTATATATTATATA-GTTTT-AAAAACT-A--TTAAA
1 AACTATATATTATATATATTTTCAAAAA-TGATTTTAAA
34086 AACTATATATTATATA
1 AACTATATATTATATA
34102 CGTAGTTTCA
Statistics
Matches: 199, Mismatches: 27, Indels: 35
0.76 0.10 0.13
Matches are distributed among these distances:
34 19 0.10
35 23 0.12
36 25 0.13
37 35 0.18
38 44 0.22
39 15 0.08
40 14 0.07
42 4 0.02
43 20 0.10
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (38 bp):
AACTATATATTATATATATTTTCAAAAATGATTTTAAA
Found at i:34043 original size:75 final size:75
Alignment explanation
Indices: 33842--34044 Score: 229
Period size: 75 Copynumber: 2.7 Consensus size: 75
33832 ATTATATAAA
* *
33842 TTTC-AAAATGATTTT-AAAACTATTTATTATATA-AGTTTTCGAAATG-GTTTTAAAAACTATA
1 TTTCAAAAATGATTTTAAAAACTATATATTATATATA-TTTTCAAAATGTGTTTTAAAAAC-ATA
33903 TAATATATATGG
64 TAATATATATGG
* * * ** *
33915 TTTCAAAAAT-ATCTTCAAAAACTATATAATATATATGTTTTCAAAAAAATGTTTTCAAAAC-TA
1 TTTCAAAAATGAT-TTTAAAAACTATATATTATATATATTTTC-AAAATGTGTTTTAAAAACATA
*
33978 TAATATATATGT
64 TAATATATATGG
*
33990 TTTCAAAAATGATTTTAAAAATTATATATTATATATATTTTCTAAAATGTGTTTT
1 TTTCAAAAATGATTTTAAAAACTATATATTATATATATTTTC-AAAATGTGTTTT
34045 TTTTTTAAAC
Statistics
Matches: 107, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
73 6 0.06
74 7 0.07
75 79 0.74
76 5 0.05
77 10 0.09
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.44
Consensus pattern (75 bp):
TTTCAAAAATGATTTTAAAAACTATATATTATATATATTTTCAAAATGTGTTTTAAAAACATATA
ATATATATGG
Found at i:34974 original size:165 final size:165
Alignment explanation
Indices: 34702--35536 Score: 1221
Period size: 165 Copynumber: 5.0 Consensus size: 165
34692 TGACAAATAG
* * * * * * * * * * *
34702 CCCTTCTTGCCTTGAGCTATGTTGTAACTGATATGACCTCGAAGTTGAGTGTAATCGAACCCAGG
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
* *
34767 GGTCTTTGGCAGATAGCCCTTATCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
34832 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAA
131 GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
*
34867 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTC-AGAGCTGAGTGTAGTCGAACTCGG
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA-AGCTGAGTGTAATCGAACTCGG
* *
34931 GGGTCTTTGGCAGATAGCCCTTATCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAG
65 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
* *
34996 CGTAGTCGAACTCAAAGGTATTTGGTTGGCAGATAA
130 CGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
* * *
35032 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTC-AGAGTTGAGTGTAGTCGAACTCGA
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA-AGCTGAGTGTAATCGAACTCGG
* * * **
35096 AGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAGAG
65 GGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAG
* *
35161 CTGAGTGTAGTCGAACTCGAAGGTCTTTAGTTGGCAGATAA
125 CTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
*
35202 CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
35267 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
**
35332 GTAGTCGAACTCGAAGGTCTTTTGG-TCACAGATAA
131 GTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAA
* * * *
35367 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
*
35432 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
35497 GTAGTCGAACTCGAAGGTC-TTGG-TGGCAGATAG
131 GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
35530 CCCTTCT
1 CCCTTCT
35537 GGCCTTGAGC
Statistics
Matches: 615, Mismatches: 47, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
163 18 0.03
164 1 0.00
165 398 0.65
166 48 0.08
167 1 0.00
168 1 0.00
169 42 0.07
170 105 0.17
171 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (165 bp):
CCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
Found at i:35115 original size:85 final size:84
Alignment explanation
Indices: 34772--35536 Score: 946
Period size: 85 Copynumber: 9.2 Consensus size: 84
34762 CCAGGGGTCT
* * * * * *
34772 TTGGCAGATAGCCCTTATCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAG
*
34836 TCGAACTCAAAGGTCTTTGG
66 TCGAACTCGAAGGTCTTT-G
* *
34856 TTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCAGAGCTGAGTGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAG
**
34921 TCGAACTCGGGGGTC--T-
66 TCGAACTCGAAGGTCTTTG
* * * * * *
34937 TTGGCAGATAGCCCTTATCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAG
* *
35001 TCGAACTCAAAGGTATTTGG
66 TCGAACTCGAAGGTCTTT-G
* * *
35021 TTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCAGAGTTGAGTGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAG
35086 TCGAACTCGAAGGTCTTTAG
66 TCGAACTCGAAGGTCTTT-G
*
35106 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAGAGCTGAGTGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAG
35171 TCGAACTCGAAGGTCTTTAG
66 TCGAACTCGAAGGTCTTT-G
* *
35191 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAG
**
35256 TCGAACTCGGGGGTC--T-
66 TCGAACTCGAAGGTCTTTG
* * * *
35272 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAG
35336 TCGAACTCGAAGGTCTTTTG
66 TCGAACTCGAAGGTC-TTTG
* ** * * * * * *
35356 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAG
**
35421 TCGAACTCGGGGGTC--T-
66 TCGAACTCGAAGGTCTTTG
* * * * *
35437 TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAG
35501 TCGAACTCGAAGGTC-TTG
66 TCGAACTCGAAGGTCTTTG
* *
35519 GTGGCAGATAGCCCTTCT
1 TTGGCAGATAACCCTTCT
35537 GGCCTTGAGC
Statistics
Matches: 586, Mismatches: 82, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
80 80 0.14
81 122 0.21
82 19 0.03
83 3 0.01
84 119 0.20
85 243 0.41
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (84 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAG
TCGAACTCGAAGGTCTTTG
Found at i:35438 original size:335 final size:329
Alignment explanation
Indices: 34702--35536 Score: 1246
Period size: 335 Copynumber: 2.5 Consensus size: 329
34692 TGACAAATAG
* * * * * * *
34702 CCCTTCTTGCCTTGAGCTATGTTGTAACTGATATGACCTCGAAGTTGAGTGTAATCGAACCCAGG
1 CCCTTCTTGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGGG
* *
34767 GGTCTTTGGCAGATAGCCCTTATCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
34832 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATG
131 GTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
*
34897 ATGTGCCCTCAGAGCTGAGTGTAGTCGAACTCGGGGGTCTTTGGCAGATAGCCCTTATCGACTTA
195 ATGTGCCCTCAGAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTATCGACTTA
**
34962 AGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTATTTGGTTGGCA
260 AGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTATTTGGTTCACA
35027 GATAA
325 GATAA
* * * * *
35032 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTC-AGAGTTGAGTGTAGTCGAACTCGA
1 CCCTTCTTGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA-AGTTGAGTGTAATCGAACTCGG
* * * **
35096 AGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAGAG
65 GGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAG
*
35161 CTGAGTGTAGTCGAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTG
125 CTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTG
*
35226 CAAATGATGTGCCCTC-GAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCT
189 CAAATGATGTGCCCTCAG-AGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTAT
* * *
35290 CGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
253 CGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGT-ATTT
35355 GG-TCACAGATAA
317 GGTTCACAGATAA
* *
35367 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTTGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGGG
*
35432 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
35497 GTAGTCGAACTCGAAGGTC-TTGGTGGCAGATAGCCCTTCT
131 GTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT
35537 GGCCTTGAGC
Statistics
Matches: 450, Mismatches: 46, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
328 17 0.04
329 3 0.01
330 84 0.19
331 43 0.10
332 1 0.00
333 1 0.00
334 43 0.10
335 252 0.56
336 6 0.01
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (329 bp):
CCCTTCTTGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGGG
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
TGTGCCCTCAGAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTATCGACTTAA
GCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTATTTGGTTCACAG
ATAA
Found at i:38906 original size:18 final size:19
Alignment explanation
Indices: 38865--38909 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
38855 AGTTAATGTG
38865 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
* *
38884 AATGCACAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
38902 AATGCAAA
1 AATGCAAA
38910 ATGTCTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.64, C:0.11, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:41477 original size:17 final size:17
Alignment explanation
Indices: 41455--41488 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
41445 ACCTTCGGTA
41455 TTTTTT-GGTATTTGTTT
1 TTTTTTGGGT-TTTGTTT
41472 TTTTTTGGGTTTTGTTT
1 TTTTTTGGGTTTTGTTT
41489 CTGTATTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.03, C:0.00, G:0.21, T:0.76
Consensus pattern (17 bp):
TTTTTTGGGTTTTGTTT
Found at i:42191 original size:18 final size:19
Alignment explanation
Indices: 42148--42193 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
42138 ACCTAAAAAA
* *
42148 AAAAAAAAAACGAGTAAAT
1 AAAAAATAAACAAGTAAAT
*
42167 -AATAATAAACAAG-AAAT
1 AAAAAATAAACAAGTAAAT
42184 AAAAAATAAA
1 AAAAAATAAA
42194 ATACTACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (19 bp):
AAAAAATAAACAAGTAAAT
Found at i:42333 original size:31 final size:33
Alignment explanation
Indices: 42259--42337 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
42249 CCATTTACTA
* * *
42259 TATAATTTTAAAAAATGTTTTAAAACTATATGT
1 TATAGTTTTCAAAAACGTTTTAAAACTATATGT
42292 TATAGTTTTCAAAAACGTTTTAAAACTATA--T
1 TATAGTTTTCAAAAACGTTTTAAAACTATATGT
42323 TATA-TGTTTCAAAAA
1 TATAGT-TTTCAAAAA
42338 AAATTTCAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 1 0.02
31 14 0.33
33 27 0.64
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (33 bp):
TATAGTTTTCAAAAACGTTTTAAAACTATATGT
Found at i:42339 original size:33 final size:33
Alignment explanation
Indices: 42205--42339 Score: 88
Period size: 33 Copynumber: 4.2 Consensus size: 33
42195 TACTACATAT
*
42205 AAAAATGTTTTAAAACTATA-TATA--TTTCAA
1 AAAAACGTTTTAAAACTATATTATATGTTTCAA
* * * * **
42235 AAATAC-TTTCAAAACCAT-TTACTATATAATTTTA
1 AAAAACGTTTTAAAACTATATTA-TATGT--TTCAA
*
42269 AAAAATGTTTTAAAACTATATGT-TATAGTTTTC--
1 AAAAACGTTTTAAAACTATAT-TATAT-G-TTTCAA
42302 AAAAACGTTTTAAAACTATATTATATGTTTCAA
1 AAAAACGTTTTAAAACTATATTATATGTTTCAA
42335 AAAAA
1 AAAAA
42340 ATTTCAACTA
Statistics
Matches: 78, Mismatches: 13, Indels: 25
0.67 0.11 0.22
Matches are distributed among these distances:
29 12 0.15
30 6 0.08
31 4 0.05
32 3 0.04
33 28 0.36
34 7 0.09
35 15 0.19
36 1 0.01
37 2 0.03
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (33 bp):
AAAAACGTTTTAAAACTATATTATATGTTTCAA
Found at i:42391 original size:35 final size:34
Alignment explanation
Indices: 42257--42560 Score: 128
Period size: 38 Copynumber: 8.5 Consensus size: 34
42247 AACCATTTAC
*
42257 TATATAATTTTAAAAAATG-TTTTAAAACTA-TAT
1 TATATAATTTT-CAAAATGATTTTAAAACTATTAT
* *
42290 GT-TATAGTTTTCAAAAACG-TTTTAAAACTA-TAT
1 -TATATAATTTTC-AAAATGATTTTAAAACTATTAT
* ** * *
42323 TATAT--GTTTCAAAAAAAATTT-CAACTATATAT
1 TATATAATTTTCAAAATGATTTTAAAACTAT-TAT
*
42355 TATATAAATTTCAAAATGATTTTAAAACTATTTAT
1 TATATAATTTTCAAAATGATTTTAAAACTA-TTAT
* *
42390 TATATAAGTTTTCGAAATGGTTTTTAAAAACTA-TAT
1 TATATAA-TTTTCAAAAT-GATTTT-AAAACTATTAT
* * *
42426 AATATATATGGTTTCAAAAAT-ATCTTCAAAAACTATATAA
1 TATATA-AT--TTTC-AAAATGAT-TT-TAAAACTAT-TAT
* *
42466 TATATATGTTTTCAAAAAAATG-TTTTCAAAACTA-TAA
1 TATATA-ATTTTC---AAAATGATTTT-AAAACTATTAT
* *
42503 TATATATGTTTTCAAAAATGATTTTAAAAATTATATAT
1 TATATA-ATTTTC-AAAATGATTTT-AAAACTAT-TAT
42541 TATATATATTTTCTAAAATG
1 TATATA-ATTTTC-AAAATG
42561 TGTTTTTTTT
Statistics
Matches: 214, Mismatches: 29, Indels: 50
0.73 0.10 0.17
Matches are distributed among these distances:
30 9 0.04
31 7 0.03
32 9 0.04
33 30 0.14
34 13 0.06
35 22 0.10
36 28 0.13
37 23 0.11
38 44 0.21
39 13 0.06
40 16 0.07
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.43
Consensus pattern (34 bp):
TATATAATTTTCAAAATGATTTTAAAACTATTAT
Found at i:42393 original size:98 final size:96
Alignment explanation
Indices: 42205--42393 Score: 229
Period size: 98 Copynumber: 1.9 Consensus size: 96
42195 TACTACATAT
* * * * *
42205 AAAAATGTTTTAAAACTATATATATTTCAAAAATACTTTCAAAACCATTTACTATATAATTTTAA
1 AAAAACGTTTTAAAACTATATATATTTCAAAAAAAATTTC-AAACCATATACTATATAAATTTAA
*
42270 AAAATGTTTTAAAACTATATGTTATAGTTTTC
65 AAAATGTTTTAAAACTATATATTATAGTTTTC
* *
42302 AAAAACGTTTTAAAACTATATTATATGTTTCAAAAAAAATTTC-AACTATATATTATATAAATTT
1 AAAAACGTTTTAAAACTATA-TATA--TTTCAAAAAAAATTTCAAACCATATACTATATAAATTT
* *
42366 -CAAAATGATTTTAAAACTATTTATTATA
63 AAAAAATG-TTTTAAAACTATATATTATA
42394 TAAGTTTTCG
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
97 25 0.32
98 39 0.50
100 14 0.18
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (96 bp):
AAAAACGTTTTAAAACTATATATATTTCAAAAAAAATTTCAAACCATATACTATATAAATTTAAA
AAATGTTTTAAAACTATATATTATAGTTTTC
Found at i:42432 original size:38 final size:37
Alignment explanation
Indices: 42345--42566 Score: 184
Period size: 38 Copynumber: 5.9 Consensus size: 37
42335 AAAAAATTTC
* ** *
42345 AACTATATATTATATA-AATTTCAAAATGATTTT-AA
1 AACTATATAATATATATGTTTTCAAAATGTTTTTAAA
* * * *
42380 AACTATTTATTATATAAGTTTTCGAAATGGTTTTTAAA
1 AACTATATAATATATATGTTTTCAAAAT-GTTTTTAAA
* * * *
42418 AACTATATAATATATATGGTTTCAAAAATATCTTCAAA
1 AACTATATAATATATATGTTTTC-AAAATGTTTTTAAA
*
42456 AACTATATAATATATATGTTTTCAAAAAAATG-TTTTCAA
1 AACTATATAATATATATGTTTTC---AAAATGTTTTTAAA
*
42495 AAC--TATAATATATATGTTTTCAAAAATGATTTTAAA
1 AACTATATAATATATATGTTTTC-AAAATGTTTTTAAA
* * *
42531 AATTATATATTATATATATTTTCTAAAATGTGTTTT
1 AACTATATAATATATATGTTTTC-AAAATGT-TTTT
42567 TTTTTTAAAC
Statistics
Matches: 153, Mismatches: 24, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
35 22 0.14
36 16 0.10
37 23 0.15
38 71 0.46
39 15 0.10
40 6 0.04
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (37 bp):
AACTATATAATATATATGTTTTCAAAATGTTTTTAAA
Found at i:42446 original size:75 final size:76
Alignment explanation
Indices: 42221--42546 Score: 234
Period size: 75 Copynumber: 4.6 Consensus size: 76
42211 GTTTTAAAAC
* * * *
42221 TATATAT-ATTTCAAAAAT-ACTTTCAAAACCATTTACTATATAA-TTTT--AAAAAATGTTTT-
1 TATATATGATTTCAAAAATGA-TTTTAAAACTATATATTATATAAGTTTTCAAAAAAATGTTTTA
*
42280 AAAACTATAT-G
65 AAAACTATATAA
* * *
42291 T-TATA-GTTTTCAAAAACG-TTTTAAAAC--TATATTATAT--G-TTTCAAAAAAA--ATTT--
1 TATATATGATTTCAAAAATGATTTTAAAACTATATATTATATAAGTTTTCAAAAAAATGTTTTAA
* *
42344 CAACTATATAT
66 AAACTATATAA
* * * ***
42355 TATATA-AATTTC-AAAATGATTTTAAAACTATTTATTATATAAGTTTTCGAAATGGT-TTTTAA
1 TATATATGATTTCAAAAATGATTTTAAAACTATATATTATATAAGTTTTCAAAAAAATGTTTTAA
42417 AAACTATATAA
66 AAACTATATAA
* * * *
42428 TATATATGGTTTCAAAAAT-ATCTTCAAAAACTATATAATATATATGTTTTCAAAAAAATGTTTT
1 TATATATGATTTCAAAAATGAT-TT-TAAAACTATATATTATATAAGTTTTCAAAAAAATGTTTT
*
42492 CAAAAC--TATAA
64 AAAAACTATATAA
* *
42503 TATATATGTTTTCAAAAATGATTTTAAAAATTATATATTATATA
1 TATATATGATTTCAAAAATGATTTT-AAAACTATATATTATATA
42547 TATTTTCTAA
Statistics
Matches: 199, Mismatches: 34, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
63 8 0.04
64 12 0.06
65 17 0.09
66 14 0.07
67 9 0.05
68 8 0.04
69 14 0.07
70 8 0.04
71 3 0.02
73 15 0.08
74 6 0.03
75 48 0.24
76 28 0.14
77 9 0.05
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (76 bp):
TATATATGATTTCAAAAATGATTTTAAAACTATATATTATATAAGTTTTCAAAAAAATGTTTTAA
AAACTATATAA
Found at i:42547 original size:75 final size:73
Alignment explanation
Indices: 42268--42623 Score: 242
Period size: 75 Copynumber: 4.9 Consensus size: 73
42258 ATATAATTTT
* *
42268 AAAAAATGTTTT-AAAACTATATGT-TATAGTTTTCAAAAACG-TTTTAAAAC--TATA-T-TAT
1 AAAAAAT-TTTTCAAAACTATATATATATAGTTTTCAAAAATGATTTTAAAACTATATATTATAT
42326 ATG-TTTCA
65 ATGTTTTCA
* ** *
42334 AAAAAA-ATTTC--AACTATATATTATATAAATTTC-AAAATGATTTTAAAACTATTTATTATAT
1 AAAAAATTTTTCAAAACTATATA-TATATAGTTTTCAAAAATGATTTTAAAACTATATATTATAT
* *
42395 AAGTTTTCG
65 ATGTTTTCA
*** * * * *
42404 AAATGGTTTTTAAAAACTATATAATATATATGGTTTCAAAAAT-ATCTTCAAAAACTATATAATA
1 AAAAAATTTTTCAAAACTATAT-ATATATA-GTTTTCAAAAATGAT-TT-TAAAACTATATATTA
42468 TATATGTTTTCA
62 TATATGTTTTCA
*
42480 AAAAAATGTTTTCAAAACTATA-ATATATATGTTTTCAAAAATGATTTTAAAAATTATATATTAT
1 AAAAAAT-TTTTCAAAACTATATATATATA-GTTTTCAAAAATGATTTT-AAAACTATATATTAT
*
42544 ATATATTTTCTA
63 ATATGTTTTC-A
*** ** *
42556 AAATGTGTTTTTTTTTTAAACTATATATTATATAGTTTT-AAAAACT-A-TTAAAAACTATATAT
1 AAA----AAATTTTTCAAAACTATATA-TATATAGTTTTCAAAAA-TGATTTTAAAACTATATAT
42618 TATATA
60 TATATA
42624 CGTAGTTTCA
Statistics
Matches: 226, Mismatches: 36, Indels: 45
0.74 0.12 0.15
Matches are distributed among these distances:
63 8 0.04
64 9 0.04
65 17 0.08
66 6 0.03
67 3 0.01
68 1 0.00
69 5 0.02
70 7 0.03
71 3 0.01
73 14 0.06
74 7 0.03
75 50 0.22
76 32 0.14
77 30 0.13
78 2 0.01
79 18 0.08
80 8 0.04
81 6 0.03
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (73 bp):
AAAAAATTTTTCAAAACTATATATATATAGTTTTCAAAAATGATTTTAAAACTATATATTATATA
TGTTTTCA
Found at i:55442 original size:21 final size:19
Alignment explanation
Indices: 55418--55457 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
55408 TGAAAAATTA
55418 CTCCCCCTTACTAAAACACTT
1 CTCCCCCTTA--AAAACACTT
*
55439 CTCCCCTTTAAAAACACTT
1 CTCCCCCTTAAAAACACTT
55458 AACACTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.30, C:0.40, G:0.00, T:0.30
Consensus pattern (19 bp):
CTCCCCCTTAAAAACACTT
Found at i:61424 original size:22 final size:21
Alignment explanation
Indices: 61382--61421 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61372 GAGTTTATTT
*
61382 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
61403 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
61422 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:63304 original size:18 final size:17
Alignment explanation
Indices: 63250--63298 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
63240 TTGGACCCTT
* *
63250 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
63268 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
63286 AGTGCATTCGATG
1 AGTGCA-TCGATG
63299 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:63348 original size:56 final size:57
Alignment explanation
Indices: 63279--63397 Score: 154
Period size: 56 Copynumber: 2.1 Consensus size: 57
63269 AGTGCATCGA
*
63279 TGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCA-GAGTGCATCGATGCATGG-TTGG
1 TGCATCAAATGCATTCGATGTTT-AAAATAAGCCATG-GTGCATCGATGCATGGATTGG
** **
63335 TGCATCAAATGCATTCGATGTTTAATTTAATTCATGGTGCATCGATGCATGGATTGG
1 TGCATCAAATGCATTCGATGTTTAAAATAAGCCATGGTGCATCGATGCATGGATTGG
63392 TGCATC
1 TGCATC
63398 GGTGCATCAC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
55 3 0.05
56 41 0.75
57 11 0.20
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (57 bp):
TGCATCAAATGCATTCGATGTTTAAAATAAGCCATGGTGCATCGATGCATGGATTGG
Found at i:64184 original size:21 final size:21
Alignment explanation
Indices: 64159--64199 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
64149 ATATAAATTG
64159 TGTATCGATGCACTACTACAT
1 TGTATCGATGCACTACTACAT
*
64180 TGTATCGATGCACTGCTACA
1 TGTATCGATGCACTACTACA
64200 GTAACTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (21 bp):
TGTATCGATGCACTACTACAT
Found at i:67325 original size:27 final size:24
Alignment explanation
Indices: 67270--67316 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
67260 TGATTCAGTA
*
67270 CTAATTAATTTAATAAAAAAATAT
1 CTAAATAATTTAATAAAAAAATAT
67294 -TAAATAATTTAATAAAAAAATAT
1 CTAAATAATTTAATAAAAAAATAT
67317 ATTCTAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
CTAAATAATTTAATAAAAAAATAT
Found at i:72718 original size:21 final size:20
Alignment explanation
Indices: 72669--72724 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
72659 TTATTGGATT
*
72669 AAATTAAA-ATAAAAATAAA
1 AAATTAAATATATAAATAAA
72688 ATTAATTAAATATATAAATAATA
1 A--AATTAAATATATAAATAA-A
72711 AAATTAAATATATA
1 AAATTAAATATATA
72725 TTTATGATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.03
21 20 0.62
22 9 0.28
23 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTAAATATATAAATAAA
Found at i:72725 original size:25 final size:24
Alignment explanation
Indices: 72677--72725 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
72667 TTAAATTAAA
*
72677 ATAAAAATAAAATTAATTAAATAT
1 ATAAAAATAAAATTAAATAAATAT
*
72701 ATAAATAATAAAATTAAATATATAT
1 ATAAA-AATAAAATTAAATAAATAT
72726 TTATGATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAAAATAAAATTAAATAAATAT
Found at i:73764 original size:16 final size:18
Alignment explanation
Indices: 73743--73777 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
73733 AGATTTTGCG
73743 TGCTTT-TAGCTA-CATT
1 TGCTTTATAGCTACCATT
73759 TGCTTTATAGCTACCATT
1 TGCTTTATAGCTACCATT
73777 T
1 T
73778 TCTTGGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 6 0.35
18 5 0.29
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (18 bp):
TGCTTTATAGCTACCATT
Done.