Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006505.1 Hibiscus syriacus cultivar Beakdansim tig00015834_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: 95247
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:3460 original size:31 final size:31
Alignment explanation
Indices: 3425--3499 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
3415 CATATACACA
*
3425 TTCATATCACATAGGCATATAAGCTCATAGC
1 TTCATATCACATAGGCATACAAGCTCATAGC
3456 TTCATATCACATAGGCATACAAGCTCATAGC
1 TTCATATCACATAGGCATACAAGCTCATAGC
3487 TTCATATCACATA
1 TTCATATCACATA
3500 TATCATGTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (31 bp):
TTCATATCACATAGGCATACAAGCTCATAGC
Found at i:6437 original size:23 final size:23
Alignment explanation
Indices: 6384--6427 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
6374 AATTATATGG
*
6384 CACTTCAGTGCAAACCTATGTAA
1 CACTTCGGTGCAAACCTATGTAA
6407 CACTTCGGTGCAAACCTATGT
1 CACTTCGGTGCAAACCTATGT
6428 GGTCCTTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (23 bp):
CACTTCGGTGCAAACCTATGTAA
Found at i:7838 original size:22 final size:22
Alignment explanation
Indices: 7813--7874 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 22
7803 CCATAGTAAG
7813 AAACAAGGAAATGATGATTACA
1 AAACAAGGAAATGATGATTACA
*
7835 AAAC-ATG-AATG-T-ATT-CA
1 AAACAAGGAAATGATGATTACA
**
7852 TTA-AAGGAAATGATGATTACA
1 AAACAAGGAAATGATGATTACA
7873 AA
1 AA
7875 CAGTATACCA
Statistics
Matches: 29, Mismatches: 6, Indels: 11
0.63 0.13 0.24
Matches are distributed among these distances:
17 5 0.17
18 7 0.24
19 2 0.07
20 7 0.24
21 4 0.14
22 4 0.14
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (22 bp):
AAACAAGGAAATGATGATTACA
Found at i:8708 original size:4 final size:4
Alignment explanation
Indices: 8699--9179 Score: 925
Period size: 4 Copynumber: 121.2 Consensus size: 4
8689 GAATAAATTA
8699 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
8747 TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
8793 TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
8839 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
8887 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
8935 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
8983 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9031 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9079 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9127 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
9175 CATG T
1 TATG T
9180 TTTCATGTTT
Statistics
Matches: 471, Mismatches: 2, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
2 4 0.01
4 467 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:9331 original size:3 final size:3
Alignment explanation
Indices: 9323--9348 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9313 CTATTTGTAA
9323 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
9349 ATTAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:10110 original size:53 final size:53
Alignment explanation
Indices: 10016--10117 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
10006 TCCACCTTCG
* * * **
10016 AAAGTGTTCATGTTTTGTTCATTTAACACTCGTGAGTATGTTCATTTATTCTA
1 AAAGTATTCATGTTTTGTTCATTTAACACTCATAAACATGTTCATTTATTCTA
* *
10069 AAAGTATTCATGTTTTGTTCATTTAACATTCATAAACATGTTTATTTAT
1 AAAGTATTCATGTTTTGTTCATTTAACACTCATAAACATGTTCATTTAT
10118 GTATTCGTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (53 bp):
AAAGTATTCATGTTTTGTTCATTTAACACTCATAAACATGTTCATTTATTCTA
Found at i:12832 original size:69 final size:69
Alignment explanation
Indices: 12740--12871 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 69
12730 ATTGCATGAA
* * *
12740 TCTAGAAATGAACACATCGTTAATGTATGATGA-ATCATCATTATTATCTTCTTCTTCTTCTTGC
1 TCTAGAAATGAACACATCATTAATGTATG-TGACATCATCATCATCATCTTCTTCTTCTTCTTGC
12804 GGGAG
65 GGGAG
* * * *
12809 TCTAGAAATGAACCCATTATTAATGTATGTGATCATTATCATCATCATCTTTTTCTTCTTCTT
1 TCTAGAAATGAACACATCATTAATGTATGTGA-CATCATCATCATCATCTTCTTCTTCTTCTT
12872 CTTCTTCTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
68 3 0.06
69 26 0.48
70 25 0.46
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (69 bp):
TCTAGAAATGAACACATCATTAATGTATGTGACATCATCATCATCATCTTCTTCTTCTTCTTGCG
GGAG
Found at i:13159 original size:66 final size:66
Alignment explanation
Indices: 13053--13177 Score: 180
Period size: 66 Copynumber: 1.9 Consensus size: 66
13043 TGCCCTGACG
* * *
13053 ATTTCGTCTATTTCAGTCTTATCAAGTGCAACTTTTCTGCTC-TTAGTATAAACAGGCTTATGGA
1 ATTTCGTCTATTTCAGTCGTATCAAGTGCAAATTTTCTGCTCGTAAG-ATAAACAGGCTTATGGA
13117 CA
65 CA
* * *
13119 ATTTCGTCTATTTCAGTCGTATCAGGTTCAAATTTTCTGCTCGTAAGATAATCAGGCTT
1 ATTTCGTCTATTTCAGTCGTATCAAGTGCAAATTTTCTGCTCGTAAGATAAACAGGCTT
13178 CGCACAATCC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 49 0.94
67 3 0.06
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (66 bp):
ATTTCGTCTATTTCAGTCGTATCAAGTGCAAATTTTCTGCTCGTAAGATAAACAGGCTTATGGAC
A
Found at i:13937 original size:105 final size:105
Alignment explanation
Indices: 13755--13963 Score: 418
Period size: 105 Copynumber: 2.0 Consensus size: 105
13745 GCCGTTGCAC
13755 TCGCTTTTACAGAGACCACATATGAAAATATGATCTACAACAAGGATGAGAAACTGTTGACATAT
1 TCGCTTTTACAGAGACCACATATGAAAATATGATCTACAACAAGGATGAGAAACTGTTGACATAT
13820 GTGAAACCACAGCTGTTTCTCCATAGGCGATTCAGCACAA
66 GTGAAACCACAGCTGTTTCTCCATAGGCGATTCAGCACAA
13860 TCGCTTTTACAGAGACCACATATGAAAATATGATCTACAACAAGGATGAGAAACTGTTGACATAT
1 TCGCTTTTACAGAGACCACATATGAAAATATGATCTACAACAAGGATGAGAAACTGTTGACATAT
13925 GTGAAACCACAGCTGTTTCTCCATAGGCGATTCAGCACA
66 GTGAAACCACAGCTGTTTCTCCATAGGCGATTCAGCACA
13964 TGTTTTGTGG
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (105 bp):
TCGCTTTTACAGAGACCACATATGAAAATATGATCTACAACAAGGATGAGAAACTGTTGACATAT
GTGAAACCACAGCTGTTTCTCCATAGGCGATTCAGCACAA
Found at i:17557 original size:12 final size:12
Alignment explanation
Indices: 17528--17556 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17518 ATATCATATT
17528 TAAAAATAAAAC
1 TAAAAATAAAAC
17540 TAAAAATAAAA-
1 TAAAAATAAAAC
17551 TAAAAA
1 TAAAAA
17557 AATCGAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (12 bp):
TAAAAATAAAAC
Found at i:21095 original size:22 final size:22
Alignment explanation
Indices: 21070--21113 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21060 TTATATAATT
21070 TCTTATTAATTT-ATATATTAAA
1 TCTTA-TAATTTCATATATTAAA
*
21092 TCTTATAATTTCATTTATTAAA
1 TCTTATAATTTCATATATTAAA
21114 AATTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (22 bp):
TCTTATAATTTCATATATTAAA
Found at i:21121 original size:21 final size:20
Alignment explanation
Indices: 21075--21123 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
21065 TAATTTCTTA
**
21075 TTAATTTATATATTAAATCT
1 TTAATTTATATATTAAAAAT
*
21095 TATAATTTCATTTATTAAAAAT
1 T-TAATTT-ATATATTAAAAAT
21117 TTAATTT
1 TTAATTT
21124 GAATTATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 12 0.50
22 11 0.46
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATTTATATATTAAAAAT
Found at i:22346 original size:2 final size:2
Alignment explanation
Indices: 22339--22386 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
22329 CTTTAATTTA
*
22339 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT ACT -T TT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT CT CT
22381 CT CT CT
1 CT CT CT
22387 GTTTGATGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:25715 original size:2 final size:2
Alignment explanation
Indices: 25708--25752 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
25698 TAGGTATGCT
25708 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
25750 TA T
1 TA T
25753 TCATTAATAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27747 original size:23 final size:23
Alignment explanation
Indices: 27721--27767 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
27711 CACCACAGCT
27721 CGTATAAATGCACCGAAATGCCA
1 CGTATAAATGCACCGAAATGCCA
* *
27744 CGTATAATTGCACCGAAGTGCCA
1 CGTATAAATGCACCGAAATGCCA
27767 C
1 C
27768 ATAGAATTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (23 bp):
CGTATAAATGCACCGAAATGCCA
Found at i:27775 original size:23 final size:23
Alignment explanation
Indices: 27729--27812 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
27719 CTCGTATAAA
* *
27729 TGCACCGAAATGCCACGTATAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
27752 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
27775 TGCACC-ATAGTGCCGCGTAGAAT
1 TGCACCGA-AGTGCCACGTAGAAT
* *
27798 TGCACTGTAGTGCCA
1 TGCACCGAAGTGCCA
27813 TATAATAATG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 1 0.02
23 50 0.98
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:28752 original size:21 final size:21
Alignment explanation
Indices: 28720--28762 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
28710 TATTTGTTTA
28720 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
28741 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
28762 A
1 A
28763 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:32629 original size:2 final size:2
Alignment explanation
Indices: 32622--32671 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
32612 TATGTAACAA
*
32622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
32664 AC AT AT AT
1 AT AT AT AT
32672 GTCCTTATCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:33005 original size:23 final size:23
Alignment explanation
Indices: 32987--33093 Score: 133
Period size: 23 Copynumber: 4.7 Consensus size: 23
32977 CTCGTATAAA
32987 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
33010 TTCACCGAAGTGCCACGTATAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
33033 TACACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
33056 TGCACAGTAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
33079 TGCAACGTAGTGCCA
1 TGCACCGAAGTGCCA
33094 TATAATAATG
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:34040 original size:21 final size:21
Alignment explanation
Indices: 34008--34050 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
33998 TGTTTGTTTA
34008 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
34029 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
34050 A
1 A
34051 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:35865 original size:18 final size:18
Alignment explanation
Indices: 35842--35902 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
35832 AGGAATAAAG
35842 AAGAAAGGAGAAGAGAAT
1 AAGAAAGGAGAAGAGAAT
*
35860 AAGAAATGAGAAGAGAAT
1 AAGAAAGGAGAAGAGAAT
* *
35878 AAGAAATGAGAAGAGAAG
1 AAGAAAGGAGAAGAGAAT
35896 AAGAAAG
1 AAGAAAG
35903 ATTGGAGATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.07
Consensus pattern (18 bp):
AAGAAAGGAGAAGAGAAT
Found at i:41626 original size:20 final size:20
Alignment explanation
Indices: 41601--41671 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
41591 TTATTGTGCC
41601 TATGATAAATTTTATCTCGA
1 TATGATAAATTTTATCTCGA
41621 TATGATAAATATTT-T-TC-A
1 TATGATAAAT-TTTATCTCGA
* *
41639 T-TCA-AACTTTTTATCTCGA
1 TATGATAA-ATTTTATCTCGA
*
41658 TATAATAAATTTTA
1 TATGATAAATTTTA
41672 ATAAAAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
16 5 0.12
17 4 0.10
18 4 0.10
19 4 0.10
20 18 0.45
21 5 0.12
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (20 bp):
TATGATAAATTTTATCTCGA
Found at i:46745 original size:197 final size:194
Alignment explanation
Indices: 46406--46790 Score: 662
Period size: 197 Copynumber: 2.0 Consensus size: 194
46396 CTGCAGACAG
* *
46406 TGTCCACGTTTAATTTTTAAAATTCATTATTTCAATATATTATTAATTTAAATATTTAATCAAAA
1 TGTCCACGTTTAATTTTTAAAATTCATTATTTCAATATAATATTAATTTAAATATCTAATCAAAA
* *
46471 AATATTAATTTAAATATTATATTTATATGGTTTAATTATATCGTAATTTAAGGTAAATGCCATAT
66 AATATTAATTTAAATATTATATTTATATGGTTTAATTATATCATAATTTAAGGTAAATGCCATAC
* *
46536 TTAATCTCTTAATTATTATTTTGACTTCATTTTAGTCACCTATCGTCAAAAAATAAACAGAAAAC
131 TTAATATCTTAATTATTATTTTGACTTCATTTTA-TCACCTATCATCAAAAAATAAACAGAAAAC
46601 TGTCCACGTTTAATTTTTAAAATTCATTATCTTCAATATAATATTAATTTAAATATCTAATCAAA
1 TGTCCACGTTTAATTTTTAAAATTCATTAT-TTCAATATAATATTAATTTAAATATCTAATC-AA
*
46666 AAAATATTAATTTAAATATTATATTTATATGGTTTAATTATATCATAATTTAAGGTAAATTCCAT
64 AAAATATTAATTTAAATATTATATTTATATGGTTTAATTATATCATAATTTAAGGTAAATGCCAT
* *
46731 ACTTAATATCTTAATTATTATTTTGACTTCGTTTTATCACCTATCATCAAAAAGTAAACA
129 ACTTAATATCTTAATTATTATTTTGACTTCATTTTATCACCTATCATCAAAAAATAAACA
46791 AACATAAAAT
Statistics
Matches: 179, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
195 30 0.17
196 51 0.28
197 98 0.55
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (194 bp):
TGTCCACGTTTAATTTTTAAAATTCATTATTTCAATATAATATTAATTTAAATATCTAATCAAAA
AATATTAATTTAAATATTATATTTATATGGTTTAATTATATCATAATTTAAGGTAAATGCCATAC
TTAATATCTTAATTATTATTTTGACTTCATTTTATCACCTATCATCAAAAAATAAACAGAAAAC
Found at i:52220 original size:17 final size:17
Alignment explanation
Indices: 52198--52236 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
52188 AATTCTTATT
52198 ATATATAAAA-ATATATA
1 ATATATAAAATA-ATATA
*
52215 ATATATAAAGTAATATA
1 ATATATAAAATAATATA
52232 ATATA
1 ATATA
52237 GAGTTAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
ATATATAAAATAATATA
Found at i:53136 original size:81 final size:81
Alignment explanation
Indices: 53009--53183 Score: 341
Period size: 81 Copynumber: 2.2 Consensus size: 81
52999 TAAAAAAGGA
*
53009 GTTTACCAAACACTAAAAATGGAGGGTTTACTACTAATCAACTGTTTATGCTCAAATAAGCTAAA
1 GTTTACCAAACACTAAAAACGGAGGGTTTACTACTAATCAACTGTTTATGCTCAAATAAGCTAAA
53074 AGTTCTTCAAAAAGTT
66 AGTTCTTCAAAAAGTT
53090 GTTTACCAAACACTAAAAACGGAGGGTTTACTACTAATCAACTGTTTATGCTCAAATAAGCTAAA
1 GTTTACCAAACACTAAAAACGGAGGGTTTACTACTAATCAACTGTTTATGCTCAAATAAGCTAAA
53155 AGTTCTTCAAAAAGTT
66 AGTTCTTCAAAAAGTT
53171 GTTTACCAAACAC
1 GTTTACCAAACAC
53184 CCCCAATATT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 93 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (81 bp):
GTTTACCAAACACTAAAAACGGAGGGTTTACTACTAATCAACTGTTTATGCTCAAATAAGCTAAA
AGTTCTTCAAAAAGTT
Found at i:60389 original size:4 final size:4
Alignment explanation
Indices: 60380--60409 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
60370 GGCTAATGAT
*
60380 ATAC ATAC ATAC ATAC ATAC ATGC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
60410 GCATGCATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:60410 original size:8 final size:8
Alignment explanation
Indices: 60380--60422 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
60370 GGCTAATGAT
*
60380 ATACATAC
1 ATACATGC
*
60388 ATACATAC
1 ATACATGC
60396 ATACATGC
1 ATACATGC
60404 ATACATGC
1 ATACATGC
*
60412 ATGCATGC
1 ATACATGC
60420 ATA
1 ATA
60423 AGACAAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (8 bp):
ATACATGC
Found at i:60414 original size:12 final size:12
Alignment explanation
Indices: 60380--60422 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
60370 GGCTAATGAT
*
60380 ATACATACATAC
1 ATACATACATGC
60392 ATACATACATGC
1 ATACATACATGC
*
60404 ATACATGCATGC
1 ATACATACATGC
*
60416 ATGCATA
1 ATACATA
60423 AGACAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (12 bp):
ATACATACATGC
Found at i:68233 original size:20 final size:20
Alignment explanation
Indices: 68208--68248 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
68198 TTCAAAACCC
68208 CTCCTTTTCTTCCATCTTGT
1 CTCCTTTTCTTCCATCTTGT
68228 CTCCTTTTCTTCCATCTTGT
1 CTCCTTTTCTTCCATCTTGT
68248 C
1 C
68249 AATTTGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.37, G:0.05, T:0.54
Consensus pattern (20 bp):
CTCCTTTTCTTCCATCTTGT
Found at i:70840 original size:34 final size:34
Alignment explanation
Indices: 70802--70875 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
70792 AACTAGAATA
*
70802 TTTCCCTAGCTTTTACACGGGATTAGCTAGAACC
1 TTTCCCTAGCTTTTACACGGGATAAGCTAGAACC
* *
70836 TTTCCCTAGCTTTTATACGGGATAAGCTAGAACT
1 TTTCCCTAGCTTTTACACGGGATAAGCTAGAACC
70870 TTTCCC
1 TTTCCC
70876 CTTTACAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (34 bp):
TTTCCCTAGCTTTTACACGGGATAAGCTAGAACC
Found at i:79205 original size:21 final size:21
Alignment explanation
Indices: 79179--79223 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
79169 CATAGTCAAT
79179 GGATCGGTATGAATGGGCAAG
1 GGATCGGTATGAATGGGCAAG
* *
79200 GGATCGGTATGGATGGGCATG
1 GGATCGGTATGAATGGGCAAG
79221 GGA
1 GGA
79224 CTCGAACCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.47, T:0.20
Consensus pattern (21 bp):
GGATCGGTATGAATGGGCAAG
Found at i:79551 original size:27 final size:27
Alignment explanation
Indices: 79485--79551 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
79475 GTTTGGTCGG
* *
79485 TTTCGGGTCGGGTGGAGGATGTAAAAT
1 TTTCGGGTAGGGTGGAGGAAGTAAAAT
* * * *
79512 TTTCTGTTGGGGTGGGGGAAGTAAAAT
1 TTTCGGGTAGGGTGGAGGAAGTAAAAT
79539 TTTCGGGTAGGGT
1 TTTCGGGTAGGGT
79552 CGGGTTGACC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.19, C:0.06, G:0.42, T:0.33
Consensus pattern (27 bp):
TTTCGGGTAGGGTGGAGGAAGTAAAAT
Found at i:81535 original size:47 final size:47
Alignment explanation
Indices: 81442--81542 Score: 125
Period size: 47 Copynumber: 2.1 Consensus size: 47
81432 CGATAAAAAA
*
81442 AACAAAATCAGTAGCGTTTTACCAAATCAAATAAAACGCCTAATAAT
1 AACAAAATCAGTAGCGTTTTACCAAATCAAATAAAACACCTAATAAT
* * * *
81489 AATAAAATCGGTAGCGTTTTACCAAATTC-GATAAAACACAC-GATAAT
1 AACAAAATCAGTAGCGTTTTACCAAA-TCAAATAAAACAC-CTAATAAT
81536 AACAAAA
1 AACAAAA
81543 ACGATAGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 43 0.93
48 3 0.07
ACGTcount: A:0.50, C:0.18, G:0.10, T:0.23
Consensus pattern (47 bp):
AACAAAATCAGTAGCGTTTTACCAAATCAAATAAAACACCTAATAAT
Found at i:86512 original size:18 final size:19
Alignment explanation
Indices: 86491--86526 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
86481 AAAATAAATA
86491 ATAAAA-ATAAAATCATTT
1 ATAAAATATAAAATCATTT
*
86509 ATAAAATTTAAAATCATT
1 ATAAAATATAAAATCATT
86527 AAAAAAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAAATATAAAATCATTT
Found at i:86709 original size:31 final size:29
Alignment explanation
Indices: 86652--86710 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
86642 TGTTTTGATT
*
86652 ATTAAAATTTTAAATTTTTTAAAATAATA
1 ATTAAAATTTTAAATTTTATAAAATAATA
*
86681 ATTAAATTTATTAAATTATTATAAAATAAT
1 ATTAAAATT-TTAAATT-TTATAAAATAAT
86711 TACTATGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 7 0.27
31 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTAAAATTTTAAATTTTATAAAATAATA
Found at i:87841 original size:31 final size:31
Alignment explanation
Indices: 87806--87878 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
87796 GTTAACATGT
87806 AGTGACCACT-TCTTAAATAAATAAAAATAAA
1 AGTGACCA-TATCTTAAATAAATAAAAATAAA
* * *
87837 AGTGATCATATCTTAATTAAATAAAAATGAA
1 AGTGACCATATCTTAAATAAATAAAAATAAA
* *
87868 TGTGAACATAT
1 AGTGACCATAT
87879 AAATCTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (31 bp):
AGTGACCATATCTTAAATAAATAAAAATAAA
Done.