Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_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: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 24
Found at i:5576546 original size:12 final size:12
Alignment explanation
Indices: 5576495--5576553 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 12
5576485 TTAACCCTTA
5576495 TTATTTATATGTAT
1 TTATTTATA--TAT
* *
5576509 ATATGTATATAT
1 TTATTTATATAT
*
5576521 TTAATTATAT-T
1 TTATTTATATAT
*
5576532 TTATTTATTTAT
1 TTATTTATATAT
5576544 TTA-TTATATA
1 TTATTTATATA
5576554 ATTTTTTTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
11 15 0.42
12 14 0.39
14 7 0.19
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (12 bp):
TTATTTATATAT
Found at i:5576680 original size:2 final size:2
Alignment explanation
Indices: 5576673--5576717 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5576663 TTCCTAACGT
5576673 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
5576715 TA T
1 TA T
5576718 TCTTACTTTA
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:5576785 original size:14 final size:13
Alignment explanation
Indices: 5576675--5576897 Score: 62
Period size: 13 Copynumber: 16.8 Consensus size: 13
5576665 CCTAACGTTA
5576675 TATATATATATATAT
1 TATAT-TATAT-TAT
5576690 ATATATATATATATAT
1 -TATAT-TATAT-TAT
*
5576706 ATATATATATATTCT
1 -TATAT-TATATTAT
5576721 TACT-TTAT-TTATT
1 TA-TATTATATTA-T
* *
5576734 TATATTTCTATGAT
1 TATA-TTATATTAT
* *
5576748 TACTATTTTTTTAGT
1 TA-TATTATATTA-T
5576763 TAATATTATATGTAT
1 T-ATATTATAT-TAT
*
5576778 TTTA-T-TATTAT
1 TATATTATATTAT
5576789 TATATTATTATTAT
1 TATATTA-TATTAT
*
5576803 TACTATT-TAGTAT
1 TA-TATTATATTAT
*
5576816 TTTATTATATTA-
1 TATATTATATTAT
* * *
5576828 TACA-TACATTTT
1 TATATTATATTAT
5576840 TAT-TTATATATAT
1 TATATTATAT-TAT
5576853 T-T-TTATTATTAT
1 TATATTA-TATTAT
*
5576865 T-TATTTATACTAT
1 TATA-TTATATTAT
5576878 T-TATT-TATT-T
1 TATATTATATTAT
5576888 T-TATTATATT
1 TATATTATATT
5576898 TTTAGTTTCT
Statistics
Matches: 163, Mismatches: 23, Indels: 47
0.70 0.10 0.20
Matches are distributed among these distances:
10 6 0.04
11 18 0.11
12 30 0.18
13 31 0.19
14 27 0.17
15 21 0.13
16 30 0.18
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (13 bp):
TATATTATATTAT
Found at i:5576787 original size:3 final size:3
Alignment explanation
Indices: 5576766--5576828 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
5576756 TTTTAGTTAA
*
5576766 TAT TA- TAT GTAT T-T TAT TAT TAT TA- TAT TAT TAT TAT TAC TATT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
*
5576810 TAG TAT T-T TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
5576829 ACATACATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
2 10 0.20
3 34 0.69
4 5 0.10
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:5576789 original size:11 final size:11
Alignment explanation
Indices: 5576775--5576897 Score: 58
Period size: 11 Copynumber: 10.8 Consensus size: 11
5576765 ATATTATATG
*
5576775 TATTTTATTAT
1 TATTATATTAT
5576786 TATTATATTAT
1 TATTATATTAT
*
5576797 TA-T-TATTAC
1 TATTATATTAT
5576806 TATTTAGTATT-T
1 TA-TTA-TATTAT
5576818 TATTATATTA-
1 TATTATATTAT
* * *
5576828 TACATACATTTT
1 TA-TTATATTAT
5576840 TATTTATATATAT
1 TA-TTATAT-TAT
*
5576853 TTTTATTATTATT
1 TATTA-TATTA-T
*
5576866 TATTTATACTATT
1 TA-TTATATTA-T
*
5576879 TATT-TATTTT
1 TATTATATTAT
5576889 TATTATATT
1 TATTATATT
5576898 TTTAGTTTCT
Statistics
Matches: 85, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
9 7 0.08
10 12 0.14
11 28 0.33
12 15 0.18
13 20 0.24
14 3 0.04
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (11 bp):
TATTATATTAT
Found at i:5576791 original size:20 final size:19
Alignment explanation
Indices: 5576765--5576829 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 19
5576755 TTTTTAGTTA
5576765 ATATTATATGTATTTTATT
1 ATATTATATGTATTTTATT
5576784 ATTATTATAT-TATTATTATT
1 A-TATTATATGTATT-TTATT
5576804 ACTATT-TA-GTATTTTATT
1 A-TATTATATGTATTTTATT
5576822 ATATTATA
1 ATATTATA
5576830 CATACATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 4 0.10
18 8 0.20
19 11 0.27
20 18 0.44
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.62
Consensus pattern (19 bp):
ATATTATATGTATTTTATT
Found at i:5576843 original size:27 final size:31
Alignment explanation
Indices: 5576777--5576863 Score: 76
Period size: 32 Copynumber: 2.9 Consensus size: 31
5576767 ATTATATGTA
*
5576777 TTTTATTATTATTATATTATTATTATTACTAT
1 TTTTATT-TTATTATATTATTATCATTACTAT
*
5576809 TTAGTATTTTATTATATTA-TA-CA-TAC-AT
1 TT-TTATTTTATTATATTATTATCATTACTAT
* *
5576837 TTTTA-TTTATATATATTTTTATTATTA
1 TTTTATTTTAT-TATATTATTATCATTA
5576864 TTTATTTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
26 5 0.11
27 8 0.18
28 6 0.13
29 4 0.09
30 3 0.07
31 2 0.04
32 13 0.29
33 4 0.09
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (31 bp):
TTTTATTTTATTATATTATTATCATTACTAT
Found at i:5576873 original size:44 final size:43
Alignment explanation
Indices: 5576787--5576901 Score: 103
Period size: 44 Copynumber: 2.6 Consensus size: 43
5576777 TTTTATTATT
*
5576787 ATTATATTA-TTATTATTACTATTTAGTATTTTATTATATTATACATA
1 ATTAT-TTATTTA-TATTA-TATTT-TTATTTTATTATATTATAC-TA
5576834 CATT-TTTATTTATA-TATATTTTTATTATTATT-TATTTATACTA
1 -ATTATTTATTTATATTATATTTTTATT-TTATTATA-TTATACTA
* *
5576877 TTTATTTATTTTTATTATATTTTTA
1 ATTATTTATTTATATTATATTTTTA
5576902 GTTTCTTTGT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
42 2 0.03
43 17 0.29
44 26 0.44
45 2 0.03
46 5 0.08
47 4 0.07
48 3 0.05
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (43 bp):
ATTATTTATTTATATTATATTTTTATTTTATTATATTATACTA
Found at i:5588708 original size:10 final size:10
Alignment explanation
Indices: 5588693--5588717 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5588683 TTCATCACTA
5588693 CAAATTCTCT
1 CAAATTCTCT
5588703 CAAATTCTCT
1 CAAATTCTCT
5588713 CAAAT
1 CAAAT
5588718 ACTATCTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:5588802 original size:18 final size:19
Alignment explanation
Indices: 5588764--5588802 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5588754 ATATTATGTA
5588764 TTTAATTTATTTAAGTATT
1 TTTAATTTATTTAAGTATT
*
5588783 TTTACTTTATTTAA-TATT
1 TTTAATTTATTTAAGTATT
5588801 TT
1 TT
5588803 ACTAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTAATTTATTTAAGTATT
Found at i:5590884 original size:18 final size:18
Alignment explanation
Indices: 5590847--5590887 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5590837 ACCTGCTCAG
*
5590847 GATGACGACGACAATAAC
1 GATGACGACGACAACAAC
* *
5590865 GATGACGACGACGACGAC
1 GATGACGACGACAACAAC
5590883 GATGA
1 GATGA
5590888 TGGTGATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.29, T:0.10
Consensus pattern (18 bp):
GATGACGACGACAACAAC
Found at i:5591091 original size:26 final size:24
Alignment explanation
Indices: 5591020--5591091 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
5591010 TTATATTTGT
5591020 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
5591045 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
5591067 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
5591092 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:5598455 original size:20 final size:20
Alignment explanation
Indices: 5598432--5598471 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5598422 AATTGTAATA
*
5598432 TTATTTTTTC-AATTAAAATT
1 TTATTTTATCGAA-TAAAATT
5598452 TTATTTTATCGAATAAAATT
1 TTATTTTATCGAATAAAATT
5598472 AATAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
TTATTTTATCGAATAAAATT
Found at i:5599128 original size:21 final size:20
Alignment explanation
Indices: 5599104--5599328 Score: 154
Period size: 21 Copynumber: 10.8 Consensus size: 20
5599094 CATATTCGCA
*
5599104 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAATTC-CG
* * *
5599125 TTGCCATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATTC-CG
*
5599146 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAATTCCG
*
5599167 TTGCGATAGTCCAAGTTCCCG
1 TTGCGATAGTCCAAATT-CCG
* *
5599188 TTACGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAATTCCG
*
5599209 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAATTCCG
*
5599230 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAATTC-CG
*
5599251 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAATTCCG
* *
5599272 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATTC-CG
*
5599293 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAATTCCG
5599314 TTGCGATAGTCCAAA
1 TTGCGATAGTCCAAA
5599329 ATCGCAACGA
Statistics
Matches: 167, Mismatches: 23, Indels: 30
0.76 0.10 0.14
Matches are distributed among these distances:
19 34 0.20
21 99 0.59
23 34 0.20
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCCAAATTCCG
Found at i:5599211 original size:63 final size:63
Alignment explanation
Indices: 5599144--5599278 Score: 252
Period size: 63 Copynumber: 2.1 Consensus size: 63
5599134 TCGAAGTTCG
5599144 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCCCGTTACGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCCCGTTACGATTTATTCCAAATT
* *
5599207 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCCCGTTACGATTTATTCCAAATT
5599270 CGTTGCGAT
1 CGTTGCGAT
5599279 AGTCGAAGTT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (63 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCCCGTTACGATTTATTCCAAATT
Found at i:5599233 original size:105 final size:105
Alignment explanation
Indices: 5599123--5599320 Score: 351
Period size: 105 Copynumber: 1.9 Consensus size: 105
5599113 TCCAAGTTCG
*
5599123 CGTTGCCATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCCCG
1 CGTTGCCATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCCCG
5599188 TTACGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
66 TTACGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* * *
5599228 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCCATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCCCG
*
5599293 TTGCGATTTATTCCAAATTCGTTGCGAT
66 TTACGATTTATTCCAAATTCGTTGCGAT
5599321 AGTCCAAAAT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 88 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (105 bp):
CGTTGCCATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCCCG
TTACGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
Found at i:5599253 original size:42 final size:42
Alignment explanation
Indices: 5599207--5599327 Score: 233
Period size: 42 Copynumber: 2.9 Consensus size: 42
5599197 ATTCCAAATT
5599207 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
*
5599249 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
5599291 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
5599328 AATCGCAACG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (42 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:5599316 original size:63 final size:61
Alignment explanation
Indices: 5599144--5599320 Score: 196
Period size: 63 Copynumber: 2.8 Consensus size: 61
5599134 TCGAAGTTCG
* * *
5599144 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCCCGTTACGATTTATTCCAAATT
1 CGTTGCGA-TTAGTCCAAATTCGTTGCGATAGTCCAAATT-CCGTTGCGATTTATTCCAAATT
* *
5599207 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGA-TTAGTCCAAATTCGTTGCGATAGTCCAAATTC-CGTTGCGATTTATTCCAAATT
* * *
5599270 CGTTGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT-CGTTGCGAT
1 CGTTGCGATTAGTCCAAATT--CGTTGCGA--TAGTCCAAATTCCGTTGCGAT
5599321 AGTCCAAAAT
Statistics
Matches: 103, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
61 8 0.08
62 1 0.01
63 85 0.83
65 9 0.09
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (61 bp):
CGTTGCGATTAGTCCAAATTCGTTGCGATAGTCCAAATTCCGTTGCGATTTATTCCAAATT
Found at i:5599954 original size:6 final size:6
Alignment explanation
Indices: 5599945--5599969 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5599935 GTCGTGGTCG
5599945 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
5599970 ACGTGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:5600898 original size:21 final size:22
Alignment explanation
Indices: 5600859--5600911 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
5600849 ATCATATCCA
5600859 TATCTTATTCCATTTTTTTCTC
1 TATCTTATTCCATTTTTTTCTC
*
5600881 TATCTTATTCGA-TTTTTTCTC
1 TATCTTATTCCATTTTTTTCTC
5600902 TATCTCTATT
1 TATCT-TATT
5600912 ATTTTATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.15, C:0.21, G:0.02, T:0.62
Consensus pattern (22 bp):
TATCTTATTCCATTTTTTTCTC
Found at i:5603264 original size:21 final size:21
Alignment explanation
Indices: 5603231--5603293 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
5603221 ACCCCTATTT
* *
5603231 TCTTTTCTATTTTCTTTTTCC
1 TCTTTCCTTTTTTCTTTTTCC
**
5603252 TCTTTCCTTTTTT-TTTCTTAA
1 TCTTTCCTTTTTTCTTT-TTCC
*
5603273 TTTTTCCTTTTTTCTTTTTCC
1 TCTTTCCTTTTTTCTTTTTCC
5603294 ATTTTTCTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (21 bp):
TCTTTCCTTTTTTCTTTTTCC
Found at i:5603290 original size:14 final size:14
Alignment explanation
Indices: 5603228--5603302 Score: 59
Period size: 14 Copynumber: 5.5 Consensus size: 14
5603218 TGAACCCCTA
*
5603228 TTTTC-TTTT-CTA
1 TTTTCTTTTTCCTT
*
5603240 TTTTCTTTTTCCTC
1 TTTTCTTTTTCCTT
*
5603254 TTTCCTTTTT--TT
1 TTTTCTTTTTCCTT
*
5603266 TTCTTAATTTTTCCTT
1 TT-TT-CTTTTTCCTT
*
5603282 TTTTCTTTTTCCAT
1 TTTTCTTTTTCCTT
5603296 TTTTCTT
1 TTTTCTT
5603303 CAAGTGTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
12 8 0.16
13 5 0.10
14 31 0.62
15 2 0.04
16 4 0.08
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTCTTTTTCCTT
Found at i:5609998 original size:17 final size:19
Alignment explanation
Indices: 5609976--5610014 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5609966 ATATTATTTT
5609976 TATTTAA-T-AAAAATAAA
1 TATTTAATTGAAAAATAAA
*
5609993 TATTTAATTGAAAAATATA
1 TATTTAATTGAAAAATAAA
5610012 TAT
1 TAT
5610015 AAGGGGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TATTTAATTGAAAAATAAA
Found at i:5614228 original size:11 final size:11
Alignment explanation
Indices: 5614168--5614256 Score: 65
Period size: 11 Copynumber: 7.9 Consensus size: 11
5614158 AATATTTGAT
*
5614168 AAAATAAAAAA
1 AAAATAAAATA
5614179 GAAAATAAAAT-
1 -AAAATAAAATA
* *
5614190 AAACTAAGAATG
1 AAAATAA-AATA
* *
5614202 AATAT-AAATG
1 AAAATAAAATA
5614212 AAAATAAAATTA
1 AAAATAAAA-TA
* *
5614224 TAATATAATATA
1 -AAAATAAAATA
5614236 AAAATAAAATA
1 AAAATAAAATA
5614247 AAAATAAAAT
1 AAAATAAAAT
5614257 GTTTCGGAGA
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
10 14 0.23
11 26 0.42
12 15 0.24
13 7 0.11
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:5615102 original size:20 final size:20
Alignment explanation
Indices: 5615066--5615103 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5615056 ATCCTATTCT
**
5615066 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
5615086 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
5615104 ATGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:5619065 original size:21 final size:21
Alignment explanation
Indices: 5619040--5619083 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5619030 ACAATTGCCA
5619040 CACGAG-AATTGCCTTGGACCC
1 CACGAGCAATT-CCTTGGACCC
* *
5619061 CACGAGCACTTCCTTGGAGCC
1 CACGAGCAATTCCTTGGACCC
5619082 CA
1 CA
5619084 TGCACATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.18
Consensus pattern (21 bp):
CACGAGCAATTCCTTGGACCC
Found at i:5622064 original size:10 final size:10
Alignment explanation
Indices: 5622049--5622074 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5622039 CAAAGAAGGG
5622049 CAAGAACCTC
1 CAAGAACCTC
5622059 CAAGAACCTC
1 CAAGAACCTC
5622069 CAAGAA
1 CAAGAA
5622075 AAGAGGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.35, G:0.12, T:0.08
Consensus pattern (10 bp):
CAAGAACCTC
Found at i:5629918 original size:20 final size:20
Alignment explanation
Indices: 5629893--5629939 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
5629883 TTTTCAACAT
5629893 GAAGTATTGATCTATTCATG
1 GAAGTATTGATCTATTCATG
5629913 GAAGTATTGATCTATTCATG
1 GAAGTATTGATCTATTCATG
5629933 GAAGTAT
1 GAAGTAT
5629940 CAATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (20 bp):
GAAGTATTGATCTATTCATG
Found at i:5632436 original size:210 final size:210
Alignment explanation
Indices: 5632074--5632493 Score: 840
Period size: 210 Copynumber: 2.0 Consensus size: 210
5632064 AATACATGCC
5632074 CCTAGATTTTAAAAGTACTCTTATAAGCATAAAATTTTGATGGTGTTTTCTCTCATTGACAAGAT
1 CCTAGATTTTAAAAGTACTCTTATAAGCATAAAATTTTGATGGTGTTTTCTCTCATTGACAAGAT
5632139 TTATAGAAAGTGTTGTGGTGGATGGTTCCAAGTGTAGTCTTGAGGGTAGGGTTAGGAGTCGTTCC
66 TTATAGAAAGTGTTGTGGTGGATGGTTCCAAGTGTAGTCTTGAGGGTAGGGTTAGGAGTCGTTCC
5632204 TCCCATCCTAGTAATGTTAGCGATGAGTTCCTTCATAAGATATAGGTTCATAGGTATCAGTTGAT
131 TCCCATCCTAGTAATGTTAGCGATGAGTTCCTTCATAAGATATAGGTTCATAGGTATCAGTTGAT
5632269 GCAAAAGTCATAGAG
196 GCAAAAGTCATAGAG
5632284 CCTAGATTTTAAAAGTACTCTTATAAGCATAAAATTTTGATGGTGTTTTCTCTCATTGACAAGAT
1 CCTAGATTTTAAAAGTACTCTTATAAGCATAAAATTTTGATGGTGTTTTCTCTCATTGACAAGAT
5632349 TTATAGAAAGTGTTGTGGTGGATGGTTCCAAGTGTAGTCTTGAGGGTAGGGTTAGGAGTCGTTCC
66 TTATAGAAAGTGTTGTGGTGGATGGTTCCAAGTGTAGTCTTGAGGGTAGGGTTAGGAGTCGTTCC
5632414 TCCCATCCTAGTAATGTTAGCGATGAGTTCCTTCATAAGATATAGGTTCATAGGTATCAGTTGAT
131 TCCCATCCTAGTAATGTTAGCGATGAGTTCCTTCATAAGATATAGGTTCATAGGTATCAGTTGAT
5632479 GCAAAAGTCATAGAG
196 GCAAAAGTCATAGAG
5632494 GTGATCTTAT
Statistics
Matches: 210, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
210 210 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (210 bp):
CCTAGATTTTAAAAGTACTCTTATAAGCATAAAATTTTGATGGTGTTTTCTCTCATTGACAAGAT
TTATAGAAAGTGTTGTGGTGGATGGTTCCAAGTGTAGTCTTGAGGGTAGGGTTAGGAGTCGTTCC
TCCCATCCTAGTAATGTTAGCGATGAGTTCCTTCATAAGATATAGGTTCATAGGTATCAGTTGAT
GCAAAAGTCATAGAG
Found at i:5635480 original size:15 final size:15
Alignment explanation
Indices: 5635432--5635474 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5635422 TTTTTCTTCT
* *
5635432 TTTTTCTTCCTC-TA
1 TTTTTCTTCTTCTTG
5635446 TTTTTCTTCTTCTTG
1 TTTTTCTTCTTCTTG
*
5635461 TTTTTCTTTTTCTT
1 TTTTTCTTCTTCTT
5635475 TCTTTTGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTCTTCTTCTTG
Found at i:5638094 original size:24 final size:24
Alignment explanation
Indices: 5638038--5638099 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
5638028 GTATATTTTA
* *
5638038 TTTTTTAATTATTTGCATTAACTT
1 TTTTTTTATTATTTTCATTAACTT
* *
5638062 TATTATTATTATTTTCATTAA-TAT
1 TTTTTTTATTATTTTCATTAACT-T
5638086 TTTTTTTATT-TTTT
1 TTTTTTTATTATTTT
5638100 AATGTCATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTTTTATTATTTTCATTAACTT
Found at i:5642133 original size:11 final size:10
Alignment explanation
Indices: 5642111--5642157 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
5642101 AAATTTTGGC
5642111 TTTTTGTTTT
1 TTTTTGTTTT
*
5642121 TTTTAGTTTT
1 TTTTTGTTTT
*
5642131 TTTTTGCCTTT
1 TTTTTG-TTTT
5642142 TTTTTGTTTT
1 TTTTTGTTTT
5642152 GTTTTT
1 -TTTTT
5642158 TTTGGAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 17 0.55
11 14 0.45
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.83
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:5642146 original size:16 final size:14
Alignment explanation
Indices: 5642111--5642161 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
5642101 AAATTTTGGC
5642111 TTTTTGTTTT-TTT
1 TTTTTGTTTTGTTT
*
5642124 TAGTTTTTTTTTGCCTTT
1 T--TTTTGTTTTG--TTT
5642142 TTTTTGTTTTGTTT
1 TTTTTGTTTTGTTT
5642156 TTTTTG
1 TTTTTG
5642162 GAAAAAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.03
14 9 0.29
15 8 0.26
16 9 0.29
18 4 0.13
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82
Consensus pattern (14 bp):
TTTTTGTTTTGTTT
Found at i:5642151 original size:28 final size:26
Alignment explanation
Indices: 5642104--5642160 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 26
5642094 TTTTTTGAAA
*
5642104 TTTTGGCTTTTTGTTTTTTTTAGTTTTT
1 TTTTGCCTTTTTG-TTTTTTT-GTTTTT
5642132 TTTTGCCTTTTT-TTTGTTTTGTTTTT
1 TTTTGCCTTTTTGTTT-TTTTGTTTTT
5642158 TTT
1 TTT
5642161 GGAAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 12 0.44
27 4 0.15
28 11 0.41
ACGTcount: A:0.02, C:0.05, G:0.12, T:0.81
Consensus pattern (26 bp):
TTTTGCCTTTTTGTTTTTTTGTTTTT
Found at i:5642931 original size:15 final size:17
Alignment explanation
Indices: 5642906--5642939 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5642896 TAAAGGTCCT
5642906 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
5642922 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
5642938 AA
1 AA
5642940 CATATCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:5643870 original size:43 final size:43
Alignment explanation
Indices: 5643812--5644099 Score: 337
Period size: 43 Copynumber: 6.7 Consensus size: 43
5643802 CAAAAAATGT
* * * *
5643812 CGCAATAGGTATTGATATTTAGCGGCGTTTGTCACACAAACGC
1 CGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACAC
5643855 CGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACAC
1 CGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACAC
* *
5643898 CGCAATAGGTGTTGATATTTAGCGGTGTTTGTTATAAAAACAC
1 CGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACAC
* **
5643941 CGCAATAGGTGTTGATATTTAGCGGTGTTTGTCATAAAAATGC
1 CGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACAC
* * * * * *
5643984 CGCAATAGGTGTTAATATTTAGCAGCATTTTTCAGACAAACAC
1 CGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACAC
* * * *
5644027 CGCAATAGGT-TATGATTTTTAGCGGCGTTTTTCGCT-AAAACGC
1 CGCAATAGGTGT-TGATATTTAGCGGCGTTTGTC-ATAAAAACAC
* * * *
5644070 CACAGTAGGTGTTGATGTTTTGCGGCGTTT
1 CGCAATAGGTGTTGATATTTAGCGGCGTTT
5644100 CTGTTAAAAA
Statistics
Matches: 212, Mismatches: 30, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
42 1 0.00
43 210 0.99
44 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (43 bp):
CGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACAC
Found at i:5644592 original size:21 final size:21
Alignment explanation
Indices: 5644511--5644592 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
5644501 CTGTTGATAT
* * *
5644511 GCTGCTTCTCTCTGTGCTGCC
1 GCTGCTGCTCTCTCTGCTTCC
** *
5644532 GCTGCTTTTTTCTCTGCTTCC
1 GCTGCTGCTCTCTCTGCTTCC
* ** *
5644553 ACTGCTGCTCTGGCTGCTTCT
1 GCTGCTGCTCTCTCTGCTTCC
5644574 GCTGCTGCTCTCTCTGCTT
1 GCTGCTGCTCTCTCTGCTT
5644593 TCCTTGCTTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.01, C:0.35, G:0.21, T:0.43
Consensus pattern (21 bp):
GCTGCTGCTCTCTCTGCTTCC
Found at i:5652458 original size:18 final size:18
Alignment explanation
Indices: 5652435--5652486 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
5652425 CTGGTGGTCG
5652435 TTGCGCTGGTGGAGAAGA
1 TTGCGCTGGTGGAGAAGA
* *
5652453 TTGCGCTGCTGGAGAAGG
1 TTGCGCTGGTGGAGAAGA
*
5652471 TTGCGCTGGTAGAGAA
1 TTGCGCTGGTGGAGAA
5652487 TGTTAGGAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.21, C:0.13, G:0.42, T:0.23
Consensus pattern (18 bp):
TTGCGCTGGTGGAGAAGA
Found at i:5653529 original size:41 final size:41
Alignment explanation
Indices: 5653486--5653686 Score: 280
Period size: 41 Copynumber: 4.9 Consensus size: 41
5653476 GTTTATACAA
* ** *
5653486 AAAAATGCCACTATTGATT-ACACTATTATGACGTTTGT-T
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
5653525 AAAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
1 -AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
* * * *
5653567 AAAAGCGCCACTATTGATTAACATTATTGCGGCATTTTTCT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
*
5653608 AAAAACGCCATTATTGATTAACACTATTGCGGCGTTTGTCT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
* *
5653649 AAAAATGCCACTATTGATTATCACTATTGCGGCGTTTG
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTG
5653687 AGGAATAAAC
Statistics
Matches: 143, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 18 0.13
41 124 0.87
42 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (41 bp):
AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
Found at i:5653861 original size:71 final size:71
Alignment explanation
Indices: 5653745--5653883 Score: 233
Period size: 71 Copynumber: 2.0 Consensus size: 71
5653735 AAACGCCGCT
* * * *
5653745 AATTTACCACTCTATTGCGGTGTTTTGGCTCAATTGCCACAAAATTTATACTCTATTGCGGCGTT
1 AATTTACCACTCTAATGCGGTGTTTTGGCTAAATCGCCACAAAATTTATACTCTATTACGGCGTT
5653810 TGTACC
66 TGTACC
*
5653816 AATTTACCACTCTAATGCGGTGTTTTGGCTAAATCGCCTCAAAATTTATACTCTATTACGGCGTT
1 AATTTACCACTCTAATGCGGTGTTTTGGCTAAATCGCCACAAAATTTATACTCTATTACGGCGTT
5653881 TGT
66 TGT
5653884 GGTATAAACG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (71 bp):
AATTTACCACTCTAATGCGGTGTTTTGGCTAAATCGCCACAAAATTTATACTCTATTACGGCGTT
TGTACC
Found at i:5653922 original size:42 final size:40
Alignment explanation
Indices: 5653858--5653964 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 40
5653848 ATCGCCTCAA
* *
5653858 AATTTA-TACTCTATTACGGCGTTTGTGGTATAAACGCCGCT
1 AATTTACTACTCTATTGCAGCGTTTGTGG-A-AAACGCCGCT
* *
5653899 AATTTACTACCCTATTGCAGCGTTTTTTGGAAAACGCCGCT
1 AATTTACTACTCTATTGCAGCG-TTTGTGGAAAACGCCGCT
* *
5653940 -ATATATCAACTCTATTGCAGCGTTT
1 AATTTA-CTACTCTATTGCAGCGTTT
5653965 TTACTACAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
40 7 0.12
41 30 0.54
42 13 0.23
43 6 0.11
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36
Consensus pattern (40 bp):
AATTTACTACTCTATTGCAGCGTTTGTGGAAAACGCCGCT
Found at i:5654139 original size:32 final size:32
Alignment explanation
Indices: 5654103--5654167 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
5654093 GTGTGGGTGT
*
5654103 TAATCTATAAACATTTGTGTGTGCTTCATTTG
1 TAATCTACAAACATTTGTGTGTGCTTCATTTG
5654135 TAATCTACAAACATTTGTGTGTGCTTCATTTG
1 TAATCTACAAACATTTGTGTGTGCTTCATTTG
5654167 T
1 T
5654168 GCTAAACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (32 bp):
TAATCTACAAACATTTGTGTGTGCTTCATTTG
Found at i:5654174 original size:28 final size:29
Alignment explanation
Indices: 5654110--5654180 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 29
5654100 TGTTAATCTA
*
5654110 TAAACATTTGTGTGTGCTTCATTTGTAATC
1 TAAACATTTGTGTGTGCTTCATTTGT-AGC
5654140 TACAAACATTTGTGTGTGCTTCATTTGT-GC
1 T--AAACATTTGTGTGTGCTTCATTTGTAGC
5654170 TAAACATTTGT
1 TAAACATTTGT
5654181 ATGTATTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
28 10 0.26
30 3 0.08
32 25 0.66
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (29 bp):
TAAACATTTGTGTGTGCTTCATTTGTAGC
Found at i:5654527 original size:66 final size:68
Alignment explanation
Indices: 5654444--5654570 Score: 186
Period size: 66 Copynumber: 1.9 Consensus size: 68
5654434 AATATACTCG
* *
5654444 TTTATTGTATGTCATATTGTATCAAGCATGAGATGGG-T-TTAGGAAGAGGACACTGATTTATAT
1 TTTATTGTATGACATATTGTATCAAGCATGAGATGGGTTATTAGGAAGAGGACACTAATTTATAT
5654507 CCA
66 CCA
* * * *
5654510 TTTATTGTATGACATATTGTATTATGCTTGAGATGGGTTATTAGGAGGAGGACACTAATTT
1 TTTATTGTATGACATATTGTATCAAGCATGAGATGGGTTATTAGGAAGAGGACACTAATTT
5654571 TGTAGTATGC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 33 0.62
67 1 0.02
68 19 0.36
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.39
Consensus pattern (68 bp):
TTTATTGTATGACATATTGTATCAAGCATGAGATGGGTTATTAGGAAGAGGACACTAATTTATAT
CCA
Found at i:5656212 original size:46 final size:46
Alignment explanation
Indices: 5656143--5656400 Score: 399
Period size: 46 Copynumber: 5.6 Consensus size: 46
5656133 AAATGAATGA
* *
5656143 ATAAATGAAAATGCATAATGGTGCATTATTGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
** *
5656189 ATAAATGAAAATGCATAACGGTGCATTATCATCATGAAAGGATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
5656235 ATAAATGAAAATGCATAATGATGTATTATCGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
5656281 ATAAATGAAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
5656327 ATAAATGAAAATGCATAACAGTGCATTATTGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
5656373 ACAAATGAAAATGCATAACGGTGCATTA
1 ATAAATGAAAATGCATAACGGTGCATTA
5656401 ACGACATAAA
Statistics
Matches: 191, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 191 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:5659794 original size:2 final size:2
Alignment explanation
Indices: 5659787--5659833 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
5659777 TAAATTAATT
* *
5659787 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA AA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
5659830 TA TA
1 TA TA
5659834 AACAACATAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:5662443 original size:105 final size:108
Alignment explanation
Indices: 5662211--5662455 Score: 282
Period size: 105 Copynumber: 2.3 Consensus size: 108
5662201 AGCCAAGGTT
* *
5662211 GAACAAATTCTTCTCATTATGAACTCCTTCTCCCTTATTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACT-CTTCTCCCTTA-TGGACGAGTTCTTCTCATTATGAACTC
* * *
5662276 TCAACTGGAAATCTTGAACCAAATCCTTTTGCGGTGGACTTAGAAG
64 T-AACTGGAAATCTTGAACCAAATCCATCTGCGGTGAACTTAGAAG
* *
5662322 GAACATGTTTTTCTCATTATGAACT-TTCTCCCTTA-GGACGAGTTCTTCTCATTATGAACTCT-
1 GAACAAGTTCTTCTCATTATGAACTCTTCTCCCTTATGGACGAGTTCTTCTCATTATGAACTCTA
* * *** ** * *
5662384 TCTGGAAATGTTGGTTCACCTCCATCTGTGGTGAA-TTTGAAAG
66 ACTGGAAATCTTGAACCAAATCCATCTGCGGTGAACTTAG-AAG
5662427 GAACAAGTTCTTCTCATTATGAACTCTTC
1 GAACAAGTTCTTCTCATTATGAACTCTTC
5662456 ATTGGAAATG
Statistics
Matches: 114, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
104 3 0.03
105 50 0.44
106 3 0.03
107 26 0.23
109 10 0.09
111 22 0.19
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (108 bp):
GAACAAGTTCTTCTCATTATGAACTCTTCTCCCTTATGGACGAGTTCTTCTCATTATGAACTCTA
ACTGGAAATCTTGAACCAAATCCATCTGCGGTGAACTTAGAAG
Found at i:5662674 original size:134 final size:134
Alignment explanation
Indices: 5662432--5662725 Score: 489
Period size: 134 Copynumber: 2.2 Consensus size: 134
5662422 GAAAGGAACA
* * *
5662432 AGTTCTTCTCATTATGAACTCTTCATTGGAAATGTCGATCCCTCAAGCGAGGCATCACTGATTCG
1 AGTTCTTCTCATTATGAACTC-TC-CTGAAAATGTCGATCCCTCAAGCGAGGCATCACTGATTCA
*
5662497 AAATGTCGTGAATCAAGTGATAGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGT
64 AAATGTCATGAATCAAGTGATAGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGT
*
5662562 CGGATG
129 CGAATG
**
5662568 AGTTCTTCTCATTATGAACTCTCCTGAAAATGTCGATCCCTCAAGCGAGGTGTCACTGATTCAAA
1 AGTTCTTCTCATTATGAACTCTCCTGAAAATGTCGATCCCTCAAGCGAGGCATCACTGATTCAAA
* *
5662633 ATGTCATGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCG
66 ATGTCATGAATCAAGTGATAGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCG
5662698 AATG
131 AATG
5662702 AGTTCTTCTCATTATGAACTCTCC
1 AGTTCTTCTCATTATGAACTCTCC
5662726 ATTGGAAATG
Statistics
Matches: 149, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
134 126 0.85
135 2 0.01
136 21 0.14
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (134 bp):
AGTTCTTCTCATTATGAACTCTCCTGAAAATGTCGATCCCTCAAGCGAGGCATCACTGATTCAAA
ATGTCATGAATCAAGTGATAGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCG
AATG
Found at i:5663640 original size:20 final size:18
Alignment explanation
Indices: 5663617--5663706 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 18
5663607 CCTTTTTCTC
5663617 TTTTCATTTTTTCATTTCTTT
1 TTTTCA-TTTTTCA-TT-TTT
5663638 TTTTCATTTTTCA-TTTT
1 TTTTCATTTTTCATTTTT
5663655 TTTTCATTTTTTTTCATTTTT
1 TTTTCA---TTTTTCATTTTT
5663676 TTTTC-TTTTTCATTTTT
1 TTTTCATTTTTCATTTTT
*
5663693 TTATC-TTTTT-ATTT
1 TTTTCATTTTTCATTT
5663707 GTTCCCTTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 13
0.82 0.01 0.17
Matches are distributed among these distances:
16 4 0.06
17 30 0.47
18 1 0.02
20 14 0.22
21 15 0.23
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCATTTTTCATTTTT
Found at i:5663648 original size:10 final size:10
Alignment explanation
Indices: 5663644--5663694 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
5663634 CTTTTTTTCA
5663644 TTTTTCATTT
1 TTTTTCATTT
5663654 TTTTTCATTT
1 TTTTTCATTT
5663664 TTTTTCA-TT
1 TTTTTCATTT
*
5663673 TTTTT--TTC
1 TTTTTCATTT
5663681 TTTTTCATTT
1 TTTTTCATTT
5663691 TTTT
1 TTTT
5663695 ATCTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 6 0.17
9 7 0.19
10 23 0.64
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:5663665 original size:27 final size:27
Alignment explanation
Indices: 5663635--5663706 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
5663625 TTTTCATTTC
5663635 TTTTTTTCATTTTTCATTT-TTTTTCAT
1 TTTTTTTCATTTTT-ATTTCTTTTTCAT
*
5663662 TTTTTTTCATTTTTTTTTCTTTTTCAT
1 TTTTTTTCATTTTTATTTCTTTTTCAT
5663689 TTTTTTATC-TTTTTATTT
1 TTTTTT-TCATTTTTATTT
5663707 GTTCCCTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 3 0.07
27 36 0.88
28 2 0.05
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTTTTCATTTTTATTTCTTTTTCAT
Found at i:5663701 original size:10 final size:9
Alignment explanation
Indices: 5663644--5663706 Score: 51
Period size: 8 Copynumber: 7.1 Consensus size: 9
5663634 CTTTTTTTCA
*
5663644 TTTTTCATT
1 TTTTTTATT
5663653 TTTTTTCATT
1 TTTTTT-ATT
5663663 TTTTTTCATT
1 TTTTTT-ATT
*
5663673 TTTTTT-TC
1 TTTTTTATT
*
5663681 TTTTTCA-T
1 TTTTTTATT
5663689 TTTTTTA-T
1 TTTTTTATT
*
5663697 CTTTTTATT
1 TTTTTTATT
5663706 T
1 T
5663707 GTTCCCTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 19 0.43
9 6 0.14
10 19 0.43
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTATT
Found at i:5675227 original size:2 final size:2
Alignment explanation
Indices: 5675220--5675269 Score: 61
Period size: 2 Copynumber: 26.0 Consensus size: 2
5675210 GTAAATTAAT
*
5675220 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA -A TA -A TA TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
5675261 TA -A TA TA TA
1 TA TA TA TA TA
5675270 AACATAGACC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 3 0.07
2 37 0.88
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Done.