Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003313.1 Hibiscus syriacus cultivar Beakdansim tig00006975_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: 86139
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:967 original size:3 final size:3
Alignment explanation
Indices: 959--997 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
949 TATTTTTTAA
*
959 ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
998 TTAATACCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3612 original size:85 final size:85
Alignment explanation
Indices: 3464--3655 Score: 219
Period size: 85 Copynumber: 2.3 Consensus size: 85
3454 CATGAATCTC
* * * * **
3464 AGATGACACGCAATTGTGCGTCATGAATTTATGATGCGCATTTATGACGCTCATTGCGCGTCATT
1 AGATGACACACATTTGTGTGTCATAAATTTATGACACGCATTTATGACGCTCATTGCGCGTCATT
* * *
3529 GAAGCCCCCGTCA-TA-AATGA
66 GAAGCACACGCCATTAGAA--A
* * *
3549 AGATGACACACATTTGTGTGTCATAAATTTATGACATGCATTTATGAC-TTACATTGCGTGTCAT
1 AGATGACACACATTTGTGTGTCATAAATTTATGACACGCATTTATGACGCT-CATTGCGCGTCAT
3613 TGAAGCACACGCCATTAGAAA
65 TGAAGCACACGCCATTAGAAA
*
3634 AGATGACACACATTCGTGTGTC
1 AGATGACACACATTTGTGTGTC
3656 GTGATTCTAT
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
84 1 0.01
85 86 0.95
86 2 0.02
87 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (85 bp):
AGATGACACACATTTGTGTGTCATAAATTTATGACACGCATTTATGACGCTCATTGCGCGTCATT
GAAGCACACGCCATTAGAAA
Found at i:3682 original size:2 final size:2
Alignment explanation
Indices: 3675--3716 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3665 TGTTGTAAAT
3675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3716 T
1 T
3717 TGTAGATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9337 original size:3 final size:3
Alignment explanation
Indices: 9324--9363 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
9314 TATTTTTTAA
9324 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9364 TTAATACCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:10522 original size:10 final size:10
Alignment explanation
Indices: 10507--10545 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
10497 TCAAAAGGGA
10507 AAAATTAAAT
1 AAAATTAAAT
10517 AAAATTAAAT
1 AAAATTAAAT
*
10527 AAAATTAAAG
1 AAAATTAAAT
*
10537 AGAATTAAA
1 AAAATTAAA
10546 AGGAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (10 bp):
AAAATTAAAT
Found at i:11974 original size:35 final size:35
Alignment explanation
Indices: 11904--12070 Score: 95
Period size: 34 Copynumber: 4.9 Consensus size: 35
11894 ATATATATAA
11904 AAAATATTTTCCAAAACCTATATAATATATATTTTT
1 AAAATATTTT-CAAAACCTATATAATATATATTTTT
* *
11940 AAAATATTTT-AAAA-TTATATATTATATACTTTTTT
1 AAAATATTTTCAAAACCTATATAATATATA--TTTTT
* * **
11975 AAAAAAATGTTTTCAAAA--T-TAT-ATA-GT-TTTCA
1 ---AAAATATTTTCAAAACCTATATAATATATATTTTT
* * * * *
12007 AAAATGTTTTTAAAA-CTATATATTATATGTTTTC
1 AAAATATTTTCAAAACCTATATAATATATATTTTT
12041 AAAATGA-TTTCAAAA-CTATATAATATATAT
1 AAAAT-ATTTTCAAAACCTATATAATATATAT
12071 ATGTTTTCAA
Statistics
Matches: 103, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
29 14 0.14
30 1 0.01
31 3 0.03
32 5 0.05
33 13 0.13
34 32 0.31
35 6 0.06
36 12 0.12
37 3 0.03
38 10 0.10
39 4 0.04
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.46
Consensus pattern (35 bp):
AAAATATTTTCAAAACCTATATAATATATATTTTT
Found at i:12056 original size:34 final size:36
Alignment explanation
Indices: 11992--12084 Score: 118
Period size: 38 Copynumber: 2.5 Consensus size: 36
11982 TGTTTTCAAA
* *
11992 ATTATATAGTTTTCAAAAATGTTTTTAAAAC-TAT-AT
1 ATTATAT-GTTTTC-AAAATGATTTCAAAACATATAAT
12028 ATTATATGTTTTCAAAATGATTTCAAAACTATATAAT
1 ATTATATGTTTTCAAAATGATTTCAAAAC-ATATAAT
12065 ATATATATGTTTTCAAAATG
1 AT-TATATGTTTTCAAAATG
12085 TTTTTTTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
34 14 0.27
35 6 0.12
36 10 0.20
37 4 0.08
38 17 0.33
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (36 bp):
ATTATATGTTTTCAAAATGATTTCAAAACATATAAT
Found at i:12304 original size:36 final size:36
Alignment explanation
Indices: 12111--12311 Score: 205
Period size: 37 Copynumber: 5.4 Consensus size: 36
12101 ATAAAAGAAT
*
12111 CTATATATTATAT-TAATTCTCAAAATGTTTTTAAAAA
1 CTATATATTATATATAATTTTCAAAATG-TTTT-AAAA
*
12148 CTATATAATATATAT-ATTTTCAAAAATGTTTTGAAAA
1 CTATATATTATATATAATTTTC-AAAATGTTTT-AAAA
12185 CTATATATTATAT-TAATTTTCAAAATGTTTTAAAA
1 CTATATATTATATATAATTTTCAAAATGTTTTAAAA
* * *
12220 AT-TATATAATATATAAATGTTTTGAAACATGTTTTCAAAA
1 CTATATATTATATAT-AA--TTTTCAAA-ATGTTTT-AAAA
*
12260 CTATATATTATATATACATTTT-AAAATGTTTTCAAA
1 CTATATATTATATATA-ATTTTCAAAATGTTTTAAAA
**
12296 CTGCATATTATATATA
1 CTATATATTATATATA
12312 TATATATGTA
Statistics
Matches: 141, Mismatches: 12, Indels: 23
0.80 0.07 0.13
Matches are distributed among these distances:
34 9 0.06
35 6 0.04
36 30 0.21
37 50 0.35
38 17 0.12
39 11 0.08
40 6 0.04
41 12 0.09
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
CTATATATTATATATAATTTTCAAAATGTTTTAAAA
Found at i:12308 original size:75 final size:71
Alignment explanation
Indices: 12111--12314 Score: 219
Period size: 75 Copynumber: 2.7 Consensus size: 71
12101 ATAAAAGAAT
* * *
12111 CTATATATTATATTAATTCTCAAAATGTTTTTAAAAACTATATAATATATATATTTTCAAAAATG
1 CTATATATTATATTAATT-TTAAAATG-TTTT-AAAACTATATTATATAAATATTTTCAAAAATG
*
12176 TTTTGAAAA
63 TTTTCAAAA
* * * *
12185 CTATATATTATATTAATTTTCAAAATGTTTTAAAAATTATATAATATATAAATGTTTTGAAACAT
1 CTATATATTATATTAATTTT-AAAATGTTTT-AAAACTATAT--TATATAAATATTTTCAAAAAT
12250 GTTTTCAAAA
62 GTTTTCAAAA
* *
12260 CTATATATTATATATACATTTTAAAATGTTTTCAAACTGCATATTATATATATAT
1 CTATATATTATAT-TA-ATTTTAAAATGTTTTAAAACT--ATATTATATAAATAT
12315 ATATGTAAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 13
0.82 0.09 0.10
Matches are distributed among these distances:
73 15 0.14
74 24 0.22
75 51 0.46
76 12 0.11
77 9 0.08
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (71 bp):
CTATATATTATATTAATTTTAAAATGTTTTAAAACTATATTATATAAATATTTTCAAAAATGTTT
TCAAAA
Found at i:13052 original size:165 final size:164
Alignment explanation
Indices: 12752--14718 Score: 1604
Period size: 165 Copynumber: 11.9 Consensus size: 164
12742 GTAAATTTGG
* * * * *
12752 TGTGCTCTCGAAGTTGAGTGTAATTGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTTGACTTAA
1 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
*
12817 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTC-TTGGTGACAGA
66 GCTATGCTGCAAATGATGTGCCTTCGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
* * * *
12881 TAACCCTTCTTGCCTTGAGTTATGCTATAAATGA
131 TAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * * *
12915 TGTGCCCTCGAAGCTAAGTGTAATCGAACTCGAGGGCCTTTGGCAGATAGCCCTTCACGACTTAA
1 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
* * *
12980 GCTATGCTGCAAATGATGCGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAG
66 GCTATGCTGCAAATGATGTGCCTTCGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGG-TGACAG
* * *
13045 ATAACCCTTCTCGATTTAAGTTATACTGCAAATGA
130 ATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * * * * * * * *
13080 TATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGTCACAGATAACCCTTCTAGCC
1 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCG-AGGGTCTTTGG---CAGATAACCCTTCTCGAC
* * * * * *
13144 TTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTCA-TTGAACTAGAAGGTCTTTGGT
62 TTAAGCTATGCTGCAAATGATGTGCCTTCG-AGCTGAGTGT-AGTCGAACTCGAAGGTCTTTGG-
* *
13208 TGGCAGATATCCCTTCTCGACTTAAGTTATGCTACAAATGA
124 TGACAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * * *
13249 TGTGCTCTCGAAGCTGAGTGCAATCGAACTCGAGGGTCTTTGACAGATAGCCCTTCTCGACTTAA
1 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
* * * * * * * * *
13314 GCTTTGTTGCAAATGATGTACCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCATAA
66 GCTATGCTGCAAATGATGTGCCTTCGAGCTGAGTGTAGTCGAACTCGAAGGTC-TTTGGTGACAG
* * * **
13379 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
130 ATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * *
13414 TGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTTAGTAGATAACCCTTCTCGAC
1 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G---GCAGATAACCCTTCTCGAC
* * * * * *
13479 TTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGCCTTTGGT-
62 TTAAGCTATGCTGCAAATGATGTGCCTTCG-AGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTG
*
13543 --AGATAACCCTTCTCGACTTAAGCTATGCTACAAATGA
126 ACAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * * * * * * * * *
13580 TGTG-CCTTGGAGCTGAGCGTAGTCGAACACGAAGGTATTTTGGTCATAGATAACCCTACTAGCC
1 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGT-CTTTGG-C--AGATAACCCTTCTCGAC
* * * ** * * * *
13644 TTGAGTTGTGCTATAAATTATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTT
62 TTAAGCTATGCTGCAAATGATGTGCCTTCG-AGCTGAGTGTAGTCGAACTCGAAGGTCTTTGG-T
* *
13709 GGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGA
125 GACAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* *
13749 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCATATAGCCCTTCTCGACTTAA
1 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
* * * * * *
13814 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTTGAAGGTCTTTTGGTCATAG
66 GCTATGCTGCAAATGATGTGCCTTCGAGCTGAGTGTAGTCGAACTCGAAGGTC-TTTGGTGACAG
* * * * *
13879 ATAACCCTTCTAGCCTTGAGTTATGCAATAAATGA
130 ATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * * *
13914 TGTACCCTTGAAGCTGAGTGTAATCAAACTTGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
1 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
* * * * * *
13979 ACTATGCTACAAATGATGTGCCCTCGAAGATGAGTGTAATCGAACTCG-AGGATATTT-G-G-CA
66 GCTATGCTGCAAATGATGTGCCTTCG-AGCTGAGTGTAGTCGAACTCGAAGG-TCTTTGGTGACA
* * *
14040 GATAACCCTTCTCGACTTAAGCTATGGTGCAAATGA
129 GATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * * * * * * * *
14076 TGTG-TCTTGGAGCTTAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCC
1 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGG---CAGATAACCCTTCTCGAC
* * * * * * * * *
14140 TTGAGTTATGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTATTTGGT-
62 TTAAGCTATGCTGCAAATGATGTGCCTTCG-AGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTG
* *
14204 --AGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGA
126 ACAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * * * * * * *
14241 TATG-CCTTGGAGCTGA-TCGTAGTCGAACTCGAAGGTCTTTTGGTCACAAATAACCCTTCTAGC
1 TGTGCCCTCGAAGCTGAGT-GTAATCGAACTCGAGGGTC-TTTGG---CAGATAACCCTTCTCGA
* * * * * * * * *
14304 CTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCTTT-G-
61 CTTAAGCTATGCTGCAAATGATGTGCCTTCG-AGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGT
* * * * *
14367 G-CAGATAGCCCTTCTTGACTTAAGCTATGTTGCAAATGA
125 GACAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
** * * * ** * * ** *
14406 TACG-CTTTGGAGCTGAGCATAGTCGAACTTGAAAGTCTTTGGTTGGCAGATAACCCTTCTCGAT
1 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAACCCTTCTCGAC
** * * * * * *
14470 TTAAATTATGCTACAAATTATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTGGTTG
62 TTAAGCTATGCTGCAAATGATGTGCCTTCGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGG-TG
* * * * *
14535 GCAGATAGCCCTTCAT-GACTTAAGGTATGTTGCAAATGA
126 ACAGATAACCCTTC-TCGACTTAAGTTATGCTACAAATGA
* ** * * * * *
14574 TGT-TCCTTTAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTTAGCAGATAACCCATCTTGA
1 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTT-G---GCAGATAACCCTTCTCGA
* * * ** *
14638 CTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTATTTTGGT
61 CTTAAGCTATGCTGCAAATGATGTGCCTTCGAGCTGAGTGTAGTCGAACTCGAAGGT-CTTTGGT
* *
14703 CACAAATAACCCTTCT
125 GACAGATAACCCTTCT
14719 AGCTTTGAGT
Statistics
Matches: 1488, Mismatches: 263, Indels: 101
0.80 0.14 0.05
Matches are distributed among these distances:
161 25 0.02
162 38 0.03
163 108 0.07
164 54 0.04
165 689 0.46
166 143 0.10
167 3 0.00
168 107 0.07
169 245 0.16
170 76 0.05
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (164 bp):
TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
GCTATGCTGCAAATGATGTGCCTTCGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
TAACCCTTCTCGACTTAAGTTATGCTACAAATGA
Found at i:13223 original size:85 final size:85
Alignment explanation
Indices: 12791--14694 Score: 1582
Period size: 85 Copynumber: 22.9 Consensus size: 85
12781 TCGAGGGTCT
* * * *
12791 TTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
12855 TCGAACTCGAAGGTC-TTGG
66 TCGAACTCGAAGGTCTTTGG
* * * * ** * * *
12874 -TGACAGATAACCCTTCTTGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTAAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
* *
12938 TCGAACTCG-AGGGC-CT--
66 TCGAACTCGAAGGTCTTTGG
* * * * *
12954 TTGGCAGATAGCCCTTCACGACTTAAGCTATGCTGCAAATGATGCG-CCTT-AGAGCTGAGCGTA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGA-AGCTGAGTGTA
13017 GTCGAACTCGAAGGTCTTTGG
65 GTCGAACTCGAAGGTCTTTGG
* * * * * *
13038 TTGACAGATAACCCTTCTCGATTTAAGTTATACTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
*
13102 TCGAACTCGAAGGTTTTTTGG
66 TCGAACTCGAAGG-TCTTTGG
** * * * * *
13123 -TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTCA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGT-A
* *
13187 -TTGAACTAGAAGGTCTTTGG
65 GTCGAACTCGAAGGTCTTTGG
* * * * * *
13207 TTGGCAGATATCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCTCTCGAAGCTGAGTGCAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
*
13272 TCGAACTCGAGGGTC--T--
66 TCGAACTCGAAGGTCTTTGG
* * * * * * *
13288 TTGACAGATAGCCCTTCTCGACTTAAGCTT-TGTTGCAAATGATGT-ACCTTGGAGTTGAGCGTA
1 TTGGCAGATAACCCTTCTCGACTTAAG-TTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTA
13351 GTCGAACTCGAAGGTCTTTTGG
65 GTCGAACTCGAAGGTC-TTTGG
*** * * * * * * *
13373 -TCATAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
*
13437 TCAAACTCGAAGGTCTTTGG
66 TCGAACTCGAAGGTCTTTGG
* * * * *
13457 TTAGTAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
* *
13522 TCGAACTCGAGGGCCTTTGG
66 TCGAACTCGAAGGTCTTTGG
* * * *
13542 -T---AGATAACCCTTCTCGACTTAAGCTATGCTACAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
* *
13602 TCGAACACGAAGGTATTTTGG
66 TCGAACTCGAAGGT-CTTTGG
*** * * * * * ** * * *
13623 -TCATAGATAACCCTACTAGCCTTGAGTTGTGCTATAAATTATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
*
13687 TCAAACTCGAAGGTCTTTGG
66 TCGAACTCGAAGGTCTTTGG
* * * *
13707 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
*
13772 TCGAACTCGAGGGTC--T--
66 TCGAACTCGAAGGTCTTTGG
* * * * *
13788 TTGGCATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
* *
13852 TCAAACTTGAAGGTCTTTTGG
66 TCGAACTCGAAGGTC-TTTGG
*** * * * *** * *
13873 -TCATAGATAACCCTTCTAGCCTTGAGTTATGCAATAAATGATGTACCCTTGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
* * *
13937 TCAAACTTGAGGGTC--T--
66 TCGAACTCGAAGGTCTTTGG
** * * * *
13953 TTGGCAGATAACCCTTCTCGACTTAAACTATGCTACAAATGATGTGCCCTCGAAGATGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
* *
14018 TCGAACTCG-AGG-ATAT--
66 TCGAACTCGAAGGTCTTTGG
* * * * * *
14034 TTGGCAGATAACCCTTCTCGACTTAAGCTATGGTGCAAATGATGTG-TCTTGGAGCTTAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
14098 TCGAACTCGAAGGTCTTTTGG
66 TCGAACTCGAAGGTC-TTTGG
** * * * * * * *
14119 -TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
* * *
14183 TCAAACTCGAGGGTATTTGG
66 TCGAACTCGAAGGTCTTTGG
* * * * *
14203 -T---AGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATATG-CCTTGGAGCTGA-TCGTA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGT-GTA
14262 GTCGAACTCGAAGGTCTTTTGG
65 GTCGAACTCGAAGGTC-TTTGG
** * * * * * * * * * *
14284 -TCACAAATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGTTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
*
14348 TCGAACTCGAGGGTC--T--
66 TCGAACTCGAAGGTCTTTGG
* * * * ** * * **
14364 TTGGCAGATAGCCCTTCTTGACTTAAGCTATGTTGCAAATGATACG-CTTTGGAGCTGAGCATAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
* *
14428 TCGAACTTGAAAGTCTTTGG
66 TCGAACTCGAAGGTCTTTGG
* * * * * * *
14448 TTGGCAGATAACCCTTCTCGATTTAAATTATGCTACAAATTATATG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
*
14512 TCGAACTCGAAGGTTTTTGG
66 TCGAACTCGAAGGTCTTTGG
* * * * * *
14532 TTGGCAGATAGCCCTTCAT-GACTTAAGGTATGTTGCAAATGATGT-TCCTTTAAGCTGAGCGTA
1 TTGGCAGATAACCCTTC-TCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTA
14595 GTCGAACTCGAAGGTCTTTTGG
65 GTCGAACTCGAAGGTC-TTTGG
* * * * * **
14617 TTAGCAGATAACCCATCTTGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCATAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
14681 TCGAACTCGAAGGT
66 TCGAACTCGAAGGT
14695 ATTTTGGTCA
Statistics
Matches: 1455, Mismatches: 306, Indels: 118
0.77 0.16 0.06
Matches are distributed among these distances:
79 2 0.00
80 167 0.11
81 338 0.23
82 49 0.03
83 31 0.02
84 427 0.29
85 439 0.30
86 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (85 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAG
TCGAACTCGAAGGTCTTTGG
Found at i:13356 original size:250 final size:249
Alignment explanation
Indices: 12752--14664 Score: 2223
Period size: 250 Copynumber: 7.7 Consensus size: 249
12742 GTAAATTTGG
* * * *
12752 TGTGCTCTCGAAGTTGAGTGTAATTGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTTGACTTAA
1 TGTGC-CTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
* *
12817 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTC--TTGGTGACAG
65 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAG
* * * *
12880 ATAACCCTTCTTGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTAAGTGTAATCGAACT
130 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACT
* * * * * *
12945 CG-AGGGC-CT--TTGGCAGATAGCCCTTCACGACTTAAGCTATGCTGCAAATGA
195 CGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * * * * *
12996 TGCGCCT-TAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGAT
1 TGTGCCTCGA-AGCTGAGTGTAATCGAACTCGAGGGTCTTT-G--G-CAGATAACCCTTCTCGAC
* * * *
13060 TTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGTC
61 TTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
* **
13125 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTCATTG
126 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCA
* *
13190 AACTAGAAGGTCTTTGGTTGGCAGATATCCCTTCTCGACTTAAGTTATGCTACAAATGA
191 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * *
13249 TGTGCTCTCGAAGCTGAGTGCAATCGAACTCGAGGGTCTTTGACAGATAGCCCTTCTCGACTTAA
1 TGTGC-CTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
* * * * * *
13314 GCTTTGTTGCAAATGATGTACCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCATAA
65 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAG
13379 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACT
130 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACT
* * **
13444 CGAAGGTCTTTGGTTAGTAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGA
195 CGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* *
13499 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGCCTTTGGTAGATAACCCTTCTCGACTTAA
1 TGTG-CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
* * * *
13564 GCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACACGAAGGTATTTTGGTCATAG
65 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAG
* * * *
13629 ATAACCCTACTAGCCTTGAGTTGTGCTATAAATTATGTGCCCTCGAAGCTGAGTGTAATCAAACT
130 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACT
*
13694 CGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGA
195 CGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* *
13749 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCATATAGCCCTTCTCGACTTAA
1 TGTG-CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
* * *
13814 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTTGAAGGTCTTTTGGTCATAG
65 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAG
** * *
13879 ATAACCCTTCTAGCCTTGAGTTATGCAATAAATGATGTACCCTTGAAGCTGAGTGTAATCAAACT
130 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACT
* * **
13944 TGAGGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAACTATGCTACAAATGA
195 CGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * *
13995 TGTGCCCTCGAAGATGAGTGTAATCGAACTCGAGGATATTTGGCAGATAACCCTTCTCGACTTAA
1 TGTG-CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAA
* * *
14060 GCTATGGTGCAAATGATGTGTCTTGGAGCTTAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAG
65 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAG
*
14125 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCAAACT
130 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACT
* * * *
14190 CGAGGGTATTTGG-T---AGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGA
195 CGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * * * * * * *
14241 TATGCCTTGGAGCTGA-TCGTAGTCGAACTCGAAGGTCTTTTGGTCACAAATAACCCTTCTAGCC
1 TGTGCCTCGAAGCTGAGT-GTAATCGAACTCGAGGGTC-TTTGG---CAGATAACCCTTCTCGAC
* * * * * * * * * * *
14305 TTGAGTTATGTTGTAAATGATGTTCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTC-TTTGG-
61 TTAAGCTATGCTGCAAATGATG-TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGT
* * * * * * * ** * * * ** *
14368 --CAGATAGCCCTTCTTGACTTAAGCTATGTTGCAAATGATACG-CTTTGGAGCTGAGCATAGTC
125 CACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATC
* * * * * *
14430 GAACTTGAAAGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAATTATGCTACAAATTA
190 AAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
* * * * * * * *
14490 TATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTGGTTGGCAGATAGCCCTTCAT-GAC
1 TGTGCCTCGAAGCTGAGTGTAATCGAACTCG-AGG-GTCT--TTGGCAGATAACCCTTC-TCGAC
* * * ** *
14554 TTAAGGTATGTTGCAAATGATGTTCCTTTAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTT
61 TTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
* * * * * *
14619 AGCAGATAACCCATCTTGACTTAAGTTATGCTGCAAATGATATGCC
126 A-CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCC
14665 TTGGAGCTGA
Statistics
Matches: 1440, Mismatches: 189, Indels: 70
0.85 0.11 0.04
Matches are distributed among these distances:
242 1 0.00
243 27 0.02
244 6 0.00
245 51 0.04
246 302 0.21
247 67 0.05
248 30 0.02
249 207 0.14
250 632 0.44
251 3 0.00
252 4 0.00
253 80 0.06
254 29 0.02
255 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (249 bp):
TGTGCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAG
CTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGA
TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTC
GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
Found at i:14700 original size:85 final size:84
Alignment explanation
Indices: 12794--14745 Score: 1597
Period size: 84 Copynumber: 23.5 Consensus size: 84
12784 AGGGTCTTTG
* * * * *
12794 GCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGA
*
12859 ACTCGAAGGTC-TTGGTGA
66 ACTCGAAGGTCTTTGGTTA
* * * ** * * * *
12877 -CAGATAACCCTTCTTGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTAAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCG
* *
12941 AACTCGAGGGCCTTT-G---
65 AACTCGAAGGTCTTTGGTTA
* * * *
12957 GCAGATAGCCCTTCACGACTTAAGCTATGCTGCAAATGATGCGCCTT-AGAGCTGAGCGTAGTCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGA-AGCTGAGCGTAGTCG
13021 AACTCGAAGGTCTTTGGTT-
65 AACTCGAAGGTCTTTGGTTA
* * * *
13040 GACAGATAACCCTTCTCGATTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCG
1 G-CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCG
* *
13105 AACTCGAAGGTTTTTTGGTCA
65 AACTCGAAGG-TCTTTGGTTA
* * * * * * *
13126 -CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTCA-TT
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGT-AGTC
* *
13189 GAACTAGAAGGTCTTTGGTTG
64 GAACTCGAAGGTCTTTGGTTA
* * * * * *
13210 GCAGATATCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCTCTCGAAGCTGAGTGCAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC-CTTGAAGCTGAGCGTAGTCG
*
13275 AACTCGAGGGTCTTT-G--A
65 AACTCGAAGGTCTTTGGTTA
* * * * *
13292 -CAGATAGCCCTTCTCGACTTAAGCTT-TGTTGCAAATGATGTACCTTGGAGTTGAGCGTAGTCG
1 GCAGATAACCCTTCTCGACTTAAG-TTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCG
*
13355 AACTCGAAGGTCTTTTGGTCA
65 AACTCGAAGGTC-TTTGGTTA
* * * * * * * * * *
13376 -TAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCG
13440 AACTCGAAGGTCTTTGGTTA
65 AACTCGAAGGTCTTTGGTTA
* * * * *
13460 GTAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCG
* *
13525 AACTCGAGGGCCTTTGG-T-
65 AACTCGAAGGTCTTTGGTTA
* * *
13543 --AGATAACCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGA
* * *
13606 ACACGAAGGTATTTTGGTCA
66 ACTCGAAGGT-CTTTGGTTA
* * * * * * ** * * * * *
13626 -TAGATAACCCTACTAGCCTTGAGTTGTGCTATAAATTATGTGCCCTCGAAGCTGAGTGTAATCA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCG
*
13690 AACTCGAAGGTCTTTGGTTG
65 AACTCGAAGGTCTTTGGTTA
* * * * *
13710 GCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCG
*
13775 AACTCGAGGGTCTTT-G---
65 AACTCGAAGGTCTTTGGTTA
* * * * *
13791 GCATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGA
* *
13856 ACTTGAAGGTCTTTTGGTCA
66 ACTCGAAGGTC-TTTGGTTA
* * * * *** * * * *
13876 -TAGATAACCCTTCTAGCCTTGAGTTATGCAATAAATGATGTACCCTTGAAGCTGAGTGTAATCA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT-GCCTTGAAGCTGAGCGTAGTCG
* *
13940 AACTTGAGGGTCTTT-G---
65 AACTCGAAGGTCTTTGGTTA
** * * * * *
13956 GCAGATAACCCTTCTCGACTTAAACTATGCTACAAATGATGTGCCCTCGAAGATGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCG
*
14021 AACTCG-AGGATATTT-G---
65 AACTCGAAGG-TCTTTGGTTA
* * * * *
14037 GCAGATAACCCTTCTCGACTTAAGCTATGGTGCAAATGATGTGTCTTGGAGCTTAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGA
*
14102 ACTCGAAGGTCTTTTGGTCA
66 ACTCGAAGGTC-TTTGGTTA
* * * * * * * * *
14122 -CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG-TGCCTTGAAGCTGAGCGTAGTCG
* *
14186 AACTCGAGGGTATTTGG-T-
65 AACTCGAAGGTCTTTGGTTA
* * * * * *
14204 --AGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATATGCCTTGGAGCTGATCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGA
*
14267 ACTCGAAGGTCTTTTGGTCA
66 ACTCGAAGGTC-TTTGGTTA
* * * * * * * * * * *
14287 -CAAATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGTTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG-TGCCTTGAAGCTGAGCGTAGTCG
*
14351 AACTCGAGGGTCTTT-G---
65 AACTCGAAGGTCTTTGGTTA
* * * * ** * * *
14367 GCAGATAGCCCTTCTTGACTTAAGCTATGTTGCAAATGATACGCTTTGGAGCTGAGCATAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGA
* * *
14432 ACTTGAAAGTCTTTGGTTG
66 ACTCGAAGGTCTTTGGTTA
* * * * * *
14451 GCAGATAACCCTTCTCGATTTAAATTATGCTACAAATTATATGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGA
* *
14516 ACTCGAAGGTTTTTGGTTG
66 ACTCGAAGGTCTTTGGTTA
* * * * *
14535 GCAGATAGCCCTTCAT-GACTTAAGGTATGTTGCAAATGATGTTCCTTTAAGCTGAGCGTAGTCG
1 GCAGATAACCCTTC-TCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCG
14599 AACTCGAAGGTCTTTTGGTTA
65 AACTCGAAGGTC-TTTGGTTA
* * * * *
14620 GCAGATAACCCATCTTGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGA
* *
14685 ACTCGAAGGTATTTTGGTCA
66 ACTCGAAGGT-CTTTGGTTA
* * * * *
14705 -CAAATAACCCTTCTAG-CTTTGAGTTATGTTGTAAATGATGT
1 GCAGATAACCCTTCTCGAC-TTAAGTTATGCTGCAAATGATGT
14746 CCTAAAAAAT
Statistics
Matches: 1500, Mismatches: 308, Indels: 121
0.78 0.16 0.06
Matches are distributed among these distances:
79 1 0.00
80 179 0.12
81 333 0.22
82 41 0.03
83 34 0.02
84 460 0.31
85 451 0.30
86 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGA
ACTCGAAGGTCTTTGGTTA
Found at i:15956 original size:83 final size:85
Alignment explanation
Indices: 15852--16075 Score: 222
Period size: 95 Copynumber: 2.5 Consensus size: 85
15842 TGGCTAGTGG
*
15852 ATCCATAAAGCCA-GGGCGTTTAACCAAATGCTCTAGAGAGACAACTTA-ATA-TATAAACACCT
1 ATCCATAAAG-CAGGGGCGTTTAACCAATTGCTCTAGAGAGACAACTTATATAGTATAAACACCT
* *
15914 TTATCAGGTTAGCTGAATCTT
65 TTATCAGGCTAGCTGAATATT
*
15935 ATCCATAAAGCAGGGGCGTTTAACCAATTGC-CTTAGAGGGATAGCTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCAGGGGCGTTTAACCAATTGCTC-TAGA--G--AG-ACAA-C-TTA---TATAGT
* **
15999 ATTATTACCTTTATCAGGCTAGCTGAATATT
55 ATAAACACCTTTATCAGGCTAGCTGAATATT
* * *
16030 ATCCATAAAGTAGGGGCGTTTAACCAATTTCTCTAGAGGGACAACT
1 ATCCATAAAGCAGGGGCGTTTAACCAATTGCTCTAGAGAGACAACT
16076 CAAGCTTTAT
Statistics
Matches: 115, Mismatches: 11, Indels: 25
0.76 0.07 0.17
Matches are distributed among these distances:
82 3 0.03
83 31 0.27
85 1 0.01
87 2 0.02
88 4 0.03
89 2 0.02
90 6 0.05
91 1 0.01
93 1 0.01
94 3 0.03
95 60 0.52
96 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (85 bp):
ATCCATAAAGCAGGGGCGTTTAACCAATTGCTCTAGAGAGACAACTTATATAGTATAAACACCTT
TATCAGGCTAGCTGAATATT
Found at i:16078 original size:95 final size:95
Alignment explanation
Indices: 15910--16091 Score: 294
Period size: 95 Copynumber: 1.9 Consensus size: 95
15900 ATATATAAAC
* *
15910 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCAGGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCAGGGGCGTTTAACCAATTGCCTTAGAGGG
* *
15975 ATAGCTCAAGCTTTATTGTATAGTATTATT
66 ACAACTCAAGCTTTATTGTATAGTATTATT
* *
16005 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTAGGGGCGTTTAACCAATT-TCTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCAGGGGCGTTTAACCAATTGCCT-TAGAGG
16069 GACAACTCAAGCTTTATTGTATA
65 GACAACTCAAGCTTTATTGTATA
16092 TATATAATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 2 0.03
95 78 0.98
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCAGGGGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATAGTATTATT
Found at i:19423 original size:12 final size:12
Alignment explanation
Indices: 19406--19432 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19396 TTAATTGCGA
19406 AAATTAAAAATT
1 AAATTAAAAATT
19418 AAATTAAAAATT
1 AAATTAAAAATT
19430 AAA
1 AAA
19433 AGTATTCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTAAAAATT
Found at i:19658 original size:15 final size:16
Alignment explanation
Indices: 19626--19659 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19616 AAATAAAATT
*
19626 AAAGAGAAAAACAGGA
1 AAAGAAAAAAACAGGA
19642 AAAGAAAAAAACA-GA
1 AAAGAAAAAAACAGGA
19657 AAA
1 AAA
19660 TACAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAACAGGA
Found at i:20754 original size:33 final size:33
Alignment explanation
Indices: 20710--20773 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
20700 CATGTTGTTT
20710 GTGATACCGGCCATCCCGAGATGGGTCAGTCTC
1 GTGATACCGGCCATCCCGAGATGGGTCAGTCTC
* * *
20743 GTGATATCGGCCATCTCGGGATGGGTCAGTC
1 GTGATACCGGCCATCCCGAGATGGGTCAGTC
20774 CAGAGATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.17, C:0.27, G:0.33, T:0.23
Consensus pattern (33 bp):
GTGATACCGGCCATCCCGAGATGGGTCAGTCTC
Found at i:21049 original size:34 final size:35
Alignment explanation
Indices: 21005--21154 Score: 118
Period size: 34 Copynumber: 4.4 Consensus size: 35
20995 TCCAAAACCA
*
21005 ATATAATATATATTTTTAAAAAT-ATTTTAAAATT
1 ATATAATATATATTTTTAAAAATGATTTTAAAACT
* *
21039 ATATATTATATACTTTTTTTAAAAAAATG-TTTTCAAA--
1 ATATA--ATATA-TATTTTT--AAAAATGATTTTAAAACT
* * *
21076 AT-T-ATATA-GTTTTCAAAAATGTTTTTAAAACT
1 ATATAATATATATTTTTAAAAATGATTTTAAAACT
* * *
21108 ATATATTATATGTTTTT-AAAATGATTTCAAAACT
1 ATATAATATATATTTTTAAAAATGATTTTAAAACT
21142 ATATAATATATAT
1 ATATAATATATAT
21155 ATATATATAT
Statistics
Matches: 93, Mismatches: 11, Indels: 24
0.73 0.09 0.19
Matches are distributed among these distances:
29 7 0.08
30 7 0.08
31 4 0.04
32 2 0.02
33 6 0.06
34 35 0.38
35 5 0.05
36 6 0.06
37 8 0.09
39 13 0.14
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (35 bp):
ATATAATATATATTTTTAAAAATGATTTTAAAACT
Found at i:24987 original size:25 final size:25
Alignment explanation
Indices: 24951--25006 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 25
24941 AGAAGAGCAA
24951 CAAAA-AAAAATA-GACAAATATCT
1 CAAAATAAAAATAGGACAAATATCT
** *
24974 CAAAATAATAAATAGGTTACATATCT
1 CAAAATAA-AAATAGGACAAATATCT
25000 CAAAATA
1 CAAAATA
25007 TAAGTGAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 5 0.19
24 2 0.07
25 5 0.19
26 15 0.56
ACGTcount: A:0.59, C:0.12, G:0.05, T:0.23
Consensus pattern (25 bp):
CAAAATAAAAATAGGACAAATATCT
Found at i:26277 original size:21 final size:21
Alignment explanation
Indices: 26227--26277 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
26217 TTCACTGAAC
*
26227 ATTTTAAATATTTTATAATAT
1 ATTTAAAATATTTTATAATAT
* * *
26248 A-TAATAAATATTTTATATTTT
1 ATTTA-AAATATTTTATAATAT
26269 ATTTAAAAT
1 ATTTAAAAT
26278 TATATATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
20 1 0.04
21 20 0.87
22 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTAAAATATTTTATAATAT
Found at i:28773 original size:21 final size:21
Alignment explanation
Indices: 28734--28782 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28724 GCAAAATCAC
* *
28734 ATATATTCATATTAATATTAA
1 ATATCTTCGTATTAATATTAA
* *
28755 ATCTCTTCGTATTAGTATTAA
1 ATATCTTCGTATTAATATTAA
28776 ATATCTT
1 ATATCTT
28783 TATGTTAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (21 bp):
ATATCTTCGTATTAATATTAA
Found at i:36425 original size:18 final size:18
Alignment explanation
Indices: 36404--36438 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
36394 CTATTTTATA
36404 ACTCAAATATTATTTAAC
1 ACTCAAATATTATTTAAC
36422 ACTCAAATATTATTTAA
1 ACTCAAATATTATTTAA
36439 AACTTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (18 bp):
ACTCAAATATTATTTAAC
Found at i:36621 original size:40 final size:39
Alignment explanation
Indices: 36577--36668 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 39
36567 AACCATATAT
* *
36577 AATATACATATATATACTTCTTCATATTTTTTTCATATGC
1 AATATACATGTATATACTACTTCATATTTTTTT-ATATGC
* *
36617 AATATACATGTA-CTCCTACTTCATATTTTTTTATATGC
1 AATATACATGTATATACTACTTCATATTTTTTTATATGC
36655 AATATACATGTATA
1 AATATACATGTATA
36669 GGAGTATCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 18 0.39
39 17 0.37
40 11 0.24
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.47
Consensus pattern (39 bp):
AATATACATGTATATACTACTTCATATTTTTTTATATGC
Found at i:41648 original size:12 final size:12
Alignment explanation
Indices: 41633--41673 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
41623 TTTCTAAAAA
*
41633 AATATTTATTTT
1 AATAATTATTTT
41645 AATAATTATTTT
1 AATAATTATTTT
*
41657 AATAGATTATCTT
1 AATA-ATTATTTT
41670 AATA
1 AATA
41674 GTTAGAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (12 bp):
AATAATTATTTT
Found at i:41671 original size:13 final size:13
Alignment explanation
Indices: 41638--41674 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
41628 AAAAAAATAT
41638 TTATTTTAATA-A
1 TTATTTTAATAGA
41650 TTATTTTAATAGA
1 TTATTTTAATAGA
*
41663 TTATCTTAATAG
1 TTATTTTAATAG
41675 TTAGAAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (13 bp):
TTATTTTAATAGA
Found at i:52389 original size:25 final size:25
Alignment explanation
Indices: 52361--52471 Score: 204
Period size: 25 Copynumber: 4.4 Consensus size: 25
52351 CGAGTCAGTC
52361 GAGTCAACTCGTTAGTTAACCCGTT
1 GAGTCAACTCGTTAGTTAACCCGTT
52386 GAGTCAACTCGTTAGTTAACCCGTT
1 GAGTCAACTCGTTAGTTAACCCGTT
52411 GAGTCAACTCGTTAGTTAACCCGTT
1 GAGTCAACTCGTTAGTTAACCCGTT
* *
52436 GAGTCAACTCGTTAGTCAACCTGTT
1 GAGTCAACTCGTTAGTTAACCCGTT
52461 GAGTCAACTCG
1 GAGTCAACTCG
52472 GATAGAGTCA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 84 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (25 bp):
GAGTCAACTCGTTAGTTAACCCGTT
Found at i:54911 original size:13 final size:13
Alignment explanation
Indices: 54889--54932 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
54879 TCATAACCCG
54889 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
54902 ACCTGACCCGTTT
1 ACCCGACCCGTTT
*
54915 ACCCGACCCGTTG
1 ACCCGACCCGTTT
54928 ACCCG
1 ACCCG
54933 TTGACCCGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.16, C:0.45, G:0.18, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:54950 original size:15 final size:15
Alignment explanation
Indices: 54919--54962 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
54909 CCGTTTACCC
54919 GACCCGTTGACCCGTT
1 GACCCGTTGA-CCGTT
54935 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
54950 GACCCGTTGACCG
1 GACCCGTTGACCG
54963 GCGTTGACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 18 0.64
16 10 0.36
ACGTcount: A:0.14, C:0.36, G:0.27, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:54952 original size:23 final size:24
Alignment explanation
Indices: 54922--54971 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
54912 TTTACCCGAC
54922 CCGTTGACCCGTTGACC-CGTTGA
1 CCGTTGACCCGTTGACCGCGTTGA
54945 CCGTTGACCCGTTGACCGGCGTTGA
1 CCGTTGACCCGTTGACC-GCGTTGA
54970 CC
1 CC
54972 ACTGTTGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 17 0.68
25 8 0.32
ACGTcount: A:0.12, C:0.36, G:0.28, T:0.24
Consensus pattern (24 bp):
CCGTTGACCCGTTGACCGCGTTGA
Found at i:54969 original size:10 final size:8
Alignment explanation
Indices: 54919--54981 Score: 83
Period size: 8 Copynumber: 7.5 Consensus size: 8
54909 CCGTTTACCC
54919 GACCCGTT
1 GACCCGTT
54927 GACCCGTT
1 GACCCGTT
54935 GACCCGTT
1 GACCCGTT
54943 GA-CCGTT
1 GACCCGTT
54950 GACCCGTT
1 GACCCGTT
54958 GACCGGCGTT
1 GACC--CGTT
54968 GACCACTGTT
1 GACC-C-GTT
54978 GACC
1 GACC
54982 AAAACTTTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
7 7 0.14
8 27 0.54
9 1 0.02
10 15 0.30
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:56295 original size:18 final size:18
Alignment explanation
Indices: 56269--56303 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56259 TCGAAAGGAC
*
56269 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
56287 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
56304 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:57439 original size:24 final size:24
Alignment explanation
Indices: 57412--57526 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
57402 TTCGATTTGA
57412 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
57436 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
57460 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
57484 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
* *
57507 ATTCCGATCTGTTACTTGAC
1 ATTCTGATCTGATACTTGAC
57527 CTGATTTATG
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
23 21 0.25
24 61 0.73
25 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:59622 original size:13 final size:13
Alignment explanation
Indices: 59604--59648 Score: 90
Period size: 13 Copynumber: 3.5 Consensus size: 13
59594 AACCTGACCT
59604 GACCCGTTTACCC
1 GACCCGTTTACCC
59617 GACCCGTTTACCC
1 GACCCGTTTACCC
59630 GACCCGTTTACCC
1 GACCCGTTTACCC
59643 GACCCG
1 GACCCG
59649 ACCTGTTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.16, C:0.47, G:0.18, T:0.20
Consensus pattern (13 bp):
GACCCGTTTACCC
Found at i:59634 original size:18 final size:18
Alignment explanation
Indices: 59626--59680 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
59616 CGACCCGTTT
*
59626 ACCCGACCCGTTTACCCG
1 ACCCGACCCGTTGACCCG
*
59644 ACCCGACCTGTTGACCCG
1 ACCCGACCCGTTGACCCG
59662 ACCCGTTGACCCGTTGACC
1 ACCC---GACCCGTTGACC
59681 GTTGACCCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 20 0.65
21 11 0.35
ACGTcount: A:0.16, C:0.45, G:0.20, T:0.18
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:59648 original size:31 final size:31
Alignment explanation
Indices: 59613--59674 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
59603 TGACCCGTTT
* *
59613 ACCCGACCCGTTTACCCGACCCGTTTACCCG
1 ACCCGACCCGTTGACCCGACCCGTTGACCCG
*
59644 ACCCGACCTGTTGACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCGACCCGTTGACCCG
59675 TTGACCGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.47, G:0.19, T:0.18
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGTTGACCCG
Found at i:59659 original size:13 final size:13
Alignment explanation
Indices: 59598--59674 Score: 73
Period size: 13 Copynumber: 5.5 Consensus size: 13
59588 GGTCATAACC
*
59598 TGACCTGACCCGT
1 TGACCCGACCCGT
*
59611 TTACCCGACCCGT
1 TGACCCGACCCGT
*
59624 TTACCCGACCCGTT
1 TGACCCGACCCG-T
*
59638 TACCCGACCCGACCTGT
1 T----GACCCGACCCGT
59655 TGACCCGACCCGT
1 TGACCCGACCCGT
59668 TGACCCG
1 TGACCCG
59675 TTGACCGTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
13 41 0.76
14 2 0.04
17 2 0.04
18 9 0.17
ACGTcount: A:0.16, C:0.44, G:0.19, T:0.21
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:59672 original size:26 final size:26
Alignment explanation
Indices: 59598--59674 Score: 73
Period size: 31 Copynumber: 2.8 Consensus size: 26
59588 GGTCATAACC
* *
59598 TGACCTGACCCGTTTACCCGACCCGT
1 TGACCCGACCCGTTGACCCGACCCGT
* *
59624 TTACCCGACCCGTTTACCCGACCCGACCTGT
1 TGACCCGACCCG-TT----GACCCGACCCGT
59655 TGACCCGACCCGTTGACCCG
1 TGACCCGACCCGTTGACCCG
59675 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
26 16 0.39
27 2 0.05
30 2 0.05
31 21 0.51
ACGTcount: A:0.16, C:0.44, G:0.19, T:0.21
Consensus pattern (26 bp):
TGACCCGACCCGTTGACCCGACCCGT
Found at i:59684 original size:15 final size:15
Alignment explanation
Indices: 59664--59696 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
59654 TTGACCCGAC
59664 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
59679 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
59694 CCG
1 CCG
59697 GCGTTGACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.36, G:0.27, T:0.24
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:59703 original size:10 final size:8
Alignment explanation
Indices: 59661--59705 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
59651 CTGTTGACCC
59661 GACCCGTT
1 GACCCGTT
59669 GACCCGTT
1 GACCCGTT
59677 GA-CCGTT
1 GACCCGTT
59684 GACCCGTT
1 GACCCGTT
59692 GACCGGCGTT
1 GACC--CGTT
59702 GACC
1 GACC
59706 ACTGTTGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.21
8 19 0.56
10 8 0.24
ACGTcount: A:0.13, C:0.36, G:0.29, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:61022 original size:18 final size:18
Alignment explanation
Indices: 60999--61036 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
60989 TGTTCGAAAG
*
60999 GATTGAAGTAAATGATAA
1 GATTGAAGTAAATAATAA
*
61017 GATTGAATTAAATAATAA
1 GATTGAAGTAAATAATAA
61035 GA
1 GA
61037 CCGGATGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (18 bp):
GATTGAAGTAAATAATAA
Found at i:62171 original size:24 final size:24
Alignment explanation
Indices: 62144--62261 Score: 150
Period size: 24 Copynumber: 5.0 Consensus size: 24
62134 TTCGATTTGA
62144 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
62168 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
62192 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
62216 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
* * *
62239 ATTCCGATATGTTACTTGACATG
1 ATTCTGATCTGATACTTGACATG
62262 ATTTATGTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
23 21 0.25
24 61 0.73
25 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:64612 original size:18 final size:17
Alignment explanation
Indices: 64584--64617 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
64574 TGAAGCTGAT
*
64584 CAGTTTTGTTGTTTCAC
1 CAGTTTTGTTGCTTCAC
64601 CAGTTGTTGTTGCTTCA
1 CAGTT-TTGTTGCTTCA
64618 GTTGTTGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.50
Consensus pattern (17 bp):
CAGTTTTGTTGCTTCAC
Found at i:64947 original size:2 final size:2
Alignment explanation
Indices: 64940--64964 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64930 ATAATGAACT
64940 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
64965 TTAAAACCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68692 original size:2 final size:2
Alignment explanation
Indices: 68685--68746 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
68675 TATTAATCAT
68685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
68727 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
68747 AACAATGATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.