Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000528.1 Hibiscus syriacus cultivar Beakdansim tig00001012_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: 73520
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:73 original size:14 final size:14
Alignment explanation
Indices: 37--75 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
27 ATTTTGAATT
*
37 TTAATTTAATTAATA
1 TTAA-TTAAATAATA
52 TT-ATTAAATAATA
1 TTAATTAAATAATA
65 TTAATTAAATA
1 TTAATTAAATA
76 TAACAATGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 11 0.50
14 9 0.41
15 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATTAAATAATA
Found at i:2060 original size:21 final size:21
Alignment explanation
Indices: 2036--2077 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2026 ATTGGTCCCA
*
2036 TAAAAT-GTATATAATAAGTAT
1 TAAAATAGT-TATAAAAAGTAT
*
2057 TAAATTAGTTATAAAAAGTAT
1 TAAAATAGTTATAAAAAGTAT
2078 AGTACCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TAAAATAGTTATAAAAAGTAT
Found at i:8161 original size:32 final size:32
Alignment explanation
Indices: 8123--8199 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
8113 CCTAAGGTTG
*
8123 CCTTGGGTAGGCTCTAAGGCCCCAAGGTACTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTACTC
* * * *
8155 CTTTGGGTAGGCTCTTAGGCCCTAATGTACTC
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTACTC
*
8187 CCTTGAGTAGGCT
1 CCTTGGGTAGGCT
8200 TGTACGACCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGGTACTC
Found at i:14567 original size:37 final size:36
Alignment explanation
Indices: 14499--14634 Score: 148
Period size: 37 Copynumber: 3.7 Consensus size: 36
14489 AAACAAAGGG
*
14499 TCGTCTCGCTTGAGACAAGTTTTCTTAAAAAACAAATT
1 TCGTCTCGCTTGAGAC-AGTTTTCCT-AAAAACAAATT
* *
14537 TTGTCTCGCTTGAGACAGTTTTCGCTAAAAATAAATT
1 TCGTCTCGCTTGAGACAGTTTTC-CTAAAAACAAATT
* * * * *
14574 TGGTCTCGTTTGAGACA-ATTTCTCTCAAAACAAAAT
1 TCGTCTCGCTTGAGACAGTTTTC-CTAAAAACAAATT
*
14610 TCGTCTCGCTTGAGACATTTTTCCT
1 TCGTCTCGCTTGAGACAGTTTTCCT
14635 TTGAGAAACA
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
36 31 0.37
37 36 0.43
38 16 0.19
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (36 bp):
TCGTCTCGCTTGAGACAGTTTTCCTAAAAACAAATT
Found at i:14623 original size:36 final size:36
Alignment explanation
Indices: 14499--14626 Score: 141
Period size: 36 Copynumber: 3.5 Consensus size: 36
14489 AAACAAAGGG
14499 TCGTCTCGCTTGAGACAAGTTT-TCTTAAAAAACAAATT
1 TCGTCTCGCTTGAGACAA-TTTCTC-T-AAAAACAAATT
* * * *
14537 TTGTCTCGCTTGAGACAGTTTTCGCTAAAAATAAATT
1 TCGTCTCGCTTGAGACA-ATTTCTCTAAAAACAAATT
* * * *
14574 TGGTCTCGTTTGAGACAATTTCTCTCAAAACAAAAT
1 TCGTCTCGCTTGAGACAATTTCTCTAAAAACAAATT
14610 TCGTCTCGCTTGAGACA
1 TCGTCTCGCTTGAGACA
14627 TTTTTCCTTT
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
36 29 0.39
37 25 0.33
38 20 0.27
39 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (36 bp):
TCGTCTCGCTTGAGACAATTTCTCTAAAAACAAATT
Found at i:15157 original size:3 final size:3
Alignment explanation
Indices: 15149--15195 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
15139 ATATTATAAT
15149 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
15195 T
1 T
15196 ATTTACATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:15164 original size:19 final size:19
Alignment explanation
Indices: 15140--15195 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
15130 GTCTAAAAAA
*
15140 TATTATAATTTATTATTAT
1 TATTATTATTTATTATTAT
15159 TATTATTATTTATTATTAT
1 TATTATTATTTATTATTAT
15178 TATTATTA-TTATTATTAT
1 TATTATTATTTATTATTAT
15196 ATTTACATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 10 0.28
19 26 0.72
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TATTATTATTTATTATTAT
Found at i:16572 original size:30 final size:30
Alignment explanation
Indices: 16524--16608 Score: 134
Period size: 30 Copynumber: 2.8 Consensus size: 30
16514 CCTCTGAGTT
*
16524 TTTTTGCTATTATGGTCCTTTAAATTTCTA
1 TTTTTGCTATTTTGGTCCTTTAAATTTCTA
* * *
16554 TTTTTGATATTTTAGTCCTTTAAGTTTCTA
1 TTTTTGCTATTTTGGTCCTTTAAATTTCTA
16584 TTTTTGCTATTTTGGTCCTTTAAAT
1 TTTTTGCTATTTTGGTCCTTTAAAT
16609 CGAATATGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.59
Consensus pattern (30 bp):
TTTTTGCTATTTTGGTCCTTTAAATTTCTA
Found at i:25223 original size:11 final size:11
Alignment explanation
Indices: 25207--25232 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25197 AGCAAATAAA
25207 ACATAATAATT
1 ACATAATAATT
25218 ACATAATAATT
1 ACATAATAATT
25229 ACAT
1 ACAT
25233 GCCACTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (11 bp):
ACATAATAATT
Found at i:25714 original size:40 final size:40
Alignment explanation
Indices: 25670--25751 Score: 148
Period size: 40 Copynumber: 2.0 Consensus size: 40
25660 ACCGTAGTGC
25670 TACACATAAGGTCGTGCCCACCATATACACCG-AAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGTAA-TGTAT
25710 TACACATAAGGTCGTGCCCACCATATACACCGTAATGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGTAATGTAT
25750 TA
1 TA
25752 TAAACCTCAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 39 0.95
41 2 0.05
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGTAATGTAT
Found at i:32285 original size:24 final size:26
Alignment explanation
Indices: 32240--32291 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
32230 CGTTCGTGAA
**
32240 CGTTCGATTATATGTTTGTTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
32266 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
32290 CG
1 CG
32292 AACAAATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 3 0.12
26 5 0.21
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.56
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:32584 original size:24 final size:24
Alignment explanation
Indices: 32553--32605 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
32543 TGTGTTTGTG
*
32553 TTGTTCGTTTATGTTCGTTTATGT
1 TTGTTCGTTTATGTTCGTTTACGT
*
32577 TTGTTCGTTTGTGTTCGTTTACGT
1 TTGTTCGTTTATGTTCGTTTACGT
32601 TTGTT
1 TTGTT
32606 TATCATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.06, C:0.09, G:0.23, T:0.62
Consensus pattern (24 bp):
TTGTTCGTTTATGTTCGTTTACGT
Found at i:32695 original size:16 final size:16
Alignment explanation
Indices: 32674--32706 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
32664 AAAACTTTTT
32674 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
32690 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
32706 T
1 T
32707 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:32826 original size:12 final size:12
Alignment explanation
Indices: 32809--33087 Score: 123
Period size: 12 Copynumber: 23.5 Consensus size: 12
32799 GTTGTATTAC
32809 ATATTATAGTATAT
1 ATATTATAG--TAT
32823 ATTATTATATGGTAT
1 A-TATTATA--GTAT
*
32838 ATATTATATTA-
1 ATATTATAGTAT
32849 ATA-TATAGTAT
1 ATATTATAGTAT
32860 ATATT-TAGTATT
1 ATATTATAGTA-T
32872 ATATTATAGTAT
1 ATATTATAGTAT
*
32884 GT-TCTATTA-TAT
1 ATAT-TA-TAGTAT
32896 ATATTAT-GT-T
1 ATATTATAGTAT
*
32906 ATA-TATATTATT
1 ATATTATAGTA-T
32918 ATATTATTA-TAT
1 ATATTA-TAGTAT
*
32930 CTATTATA-T-T
1 ATATTATAGTAT
*
32940 ATATTATATTAT
1 ATATTATAGTAT
* *
32952 AGCATT-TATTAT
1 A-TATTATAGTAT
*
32964 ATATCATAGTAT
1 ATATTATAGTAT
*
32976 AT-TATGTAGTAT
1 ATAT-TATAGTAT
32988 CATATTATA-TAT
1 -ATATTATAGTAT
*
33000 -TTTATATAGTAT
1 ATAT-TATAGTAT
*
33012 -TA-TATAATAT
1 ATATTATAGTAT
33022 ATAATATATAGTAT
1 AT-AT-TATAGTAT
*
33036 ATATTATATTAT
1 ATATTATAGTAT
33048 -TATT-TA-TAT
1 ATATTATAGTAT
* *
33057 -TATTATATTAC
1 ATATTATAGTAT
33068 ATATTATAGTTATT
1 ATATTATAG-TA-T
33082 ATATTA
1 ATATTA
33088 CATTATTTTT
Statistics
Matches: 209, Mismatches: 22, Indels: 68
0.70 0.07 0.23
Matches are distributed among these distances:
9 10 0.05
10 32 0.15
11 32 0.15
12 73 0.35
13 24 0.11
14 26 0.12
15 11 0.05
17 1 0.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (12 bp):
ATATTATAGTAT
Found at i:32838 original size:22 final size:20
Alignment explanation
Indices: 32809--33085 Score: 107
Period size: 19 Copynumber: 14.2 Consensus size: 20
32799 GTTGTATTAC
32809 ATAT-TATAGTATATATTATT
1 ATATGTATA-TATATATTATT
*
32829 ATATGGTATATATTATATTAAT
1 ATAT-GTATATA-TATATTATT
* *
32851 ATATAGTATATATTTAGTATT
1 ATAT-GTATATATATATTATT
*
32872 ATAT-TATAGTATGT-TCTATT
1 ATATGTATA-TATATAT-TATT
*
32892 ATA--TATAT-TATGTTA-T
1 ATATGTATATATATATTATT
*
32908 ATATAT-TAT-TATATTATT
1 ATATGTATATATATATTATT
*
32926 ATATCTAT-TATAT-TATATT
1 ATATGTATATATATAT-TATT
**
32945 ATAT-TATA-GCAT-TTATT
1 ATATGTATATATATATTATT
32962 ATA--TATCATAGTATATTATGT
1 ATATGTAT-ATA-TATATTAT-T
*
32983 AGTAT-CATATTATATATT-TT
1 A-TATGTATA-TATATATTATT
*
33003 ATATAGTAT-TATATAATA-T
1 ATAT-GTATATATATATTATT
*
33022 ATA-ATATATAGTATA-TATT
1 ATATGTATATA-TATATTATT
*
33041 ATAT-TATTATTTATATTATT
1 ATATGTA-TATATATATTATT
*
33061 ATAT-TACATATTATAGTTATT
1 ATATGTATATA-TATA-TTATT
33082 ATAT
1 ATAT
33086 TACATTATTT
Statistics
Matches: 204, Mismatches: 21, Indels: 63
0.71 0.07 0.22
Matches are distributed among these distances:
16 7 0.03
17 24 0.12
18 21 0.10
19 52 0.25
20 38 0.19
21 26 0.13
22 32 0.16
23 4 0.02
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (20 bp):
ATATGTATATATATATTATT
Found at i:32845 original size:24 final size:24
Alignment explanation
Indices: 32813--33074 Score: 152
Period size: 24 Copynumber: 10.6 Consensus size: 24
32803 TATTACATAT
* *
32813 TATAGTATATATTATTATATGGTA
1 TATATTATATATTATTATATAGTA
*
32837 TATA-T-TATATTAATATATAGTA
1 TATATTATATATTATTATATAGTA
32859 TATATT-TAGTATTA-TATTATAGTA
1 TATATTATA-TATTATTA-TATAGTA
* *
32883 TGT-TCTATTATATATATTATGTTA-TA
1 TATAT-TA-TATAT-TATTAT-ATAGTA
*
32909 TATATTATTATATTATTATAT-CTA
1 TATATTA-TATATTATTATATAGTA
* *
32933 TTATATTATAT-TATATTATAGCA-TT
1 -TATATTATATAT-TATTATA-TAGTA
*
32958 TATTATATATCATAGTATATTATGTAGTA
1 TA-TAT-TAT-ATA-T-TATTATATAGTA
32987 TCATATTATATATT-TTATATAGTA
1 T-ATATTATATATTATTATATAGTA
* *
33011 TTATATAATATA-TAATATATAGTA
1 -TATATTATATATTATTATATAGTA
*
33035 TATATTATATTATTATT-TATATTA
1 TATATTATA-TATTATTATATAGTA
*
33059 TTATATTACATATTAT
1 -TATATTATATATTAT
33075 AGTTATTATA
Statistics
Matches: 193, Mismatches: 18, Indels: 54
0.73 0.07 0.20
Matches are distributed among these distances:
22 19 0.10
23 17 0.09
24 75 0.39
25 33 0.17
26 21 0.11
27 10 0.05
28 4 0.02
29 13 0.07
30 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (24 bp):
TATATTATATATTATTATATAGTA
Found at i:32847 original size:5 final size:5
Alignment explanation
Indices: 32809--33106 Score: 137
Period size: 5 Copynumber: 60.2 Consensus size: 5
32799 GTTGTATTAC
* * * *
32809 ATATT ATAGT ATA-T ATTATT ATATG GTA-T ATATT ATATT A-ATAT ATAGT
1 ATATT ATATT ATATT A-TATT ATATT ATATT ATATT ATATT ATAT-T ATATT
* * * *
32858 ATA-T AT-TT AGTATT ATATT ATAGT ATGTT CTATT ATA-T ATATT ATGTT
1 ATATT ATATT A-TATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
* **
32906 ATATAT ATTATT ATATT ATTATAT CTATT ATATT ATATT ATATT ATAGC
1 ATAT-T A-TATT ATATT A-TAT-T ATATT ATATT ATATT ATATT ATATT
* * * * *
32955 AT-TT AT-TAT ATATC ATAGT ATATT AT-GT AGTATC ATATT ATA-T ATTTT
1 ATATT ATAT-T ATATT ATATT ATATT ATATT A-TATT ATATT ATATT ATATT
* *
33003 ATA-T AGTATT ATATA ATA-T ATAAT ATA-T AGTA-T ATATT ATATT ATTATT
1 ATATT A-TATT ATATT ATATT ATATT ATATT A-TATT ATATT ATATT A-TATT
* *
33052 -TA-T ATTATT ATATT ACATATT ATAGT -TATT ATATT ACATT AT-TT
1 ATATT A-TATT ATATT --ATATT ATATT ATATT ATATT ATATT ATATT
* *
33096 TTATT TTATT A
1 ATATT ATATT A
33107 ATAATTGTCT
Statistics
Matches: 224, Mismatches: 38, Indels: 62
0.69 0.12 0.19
Matches are distributed among these distances:
3 1 0.00
4 40 0.18
5 148 0.66
6 26 0.12
7 9 0.04
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:32908 original size:63 final size:63
Alignment explanation
Indices: 32809--33066 Score: 175
Period size: 63 Copynumber: 4.3 Consensus size: 63
32799 GTTGTATTAC
* *
32809 ATATTATAGTATATATTATTATATGGTATATATTATATTAATATATAGTATA-TATT-TA-GTAT
1 ATATTATAGTATATATTATTATATGATATATATTATA-T-ATAT-TAGTATATTATTATATCTAT
32871 T
63 T
* * *
32872 ATATTATAGTATGT-TCTATTATAT-ATATTATGTTATATATATTATTATATTATTATATCTATT
1 ATATTATAGTATATAT-TATTATATGATA-TATATTATATATATTAGTATATTATTATATCTATT
32935 ATA-T-TA-TAT-TA-TATTATA-GCAT-T-TATTATATATCA-TAGTATATTATGTAGTATCAT
1 ATATTATAGTATATATTATTATATG-ATATATATTATATAT-ATTAGTATATTAT-TA-TATC-T
32991 ATT
61 ATT
** *
32994 ATA-TATTTTATATAGTATTATAT-A-ATATA-TA-ATATA-TAGTATA-TATTATAT-TATT
1 ATATTATAGTATATATTATTATATGATATATATTATATATATTAGTATATTATTATATCTATT
*
33049 AT-TTATATTATTATATTA
1 ATATTATAGTA-TATATTA
33067 CATATTATAG
Statistics
Matches: 164, Mismatches: 10, Indels: 49
0.74 0.04 0.22
Matches are distributed among these distances:
55 12 0.07
56 25 0.15
57 7 0.04
58 13 0.08
59 14 0.09
60 18 0.11
61 17 0.10
62 13 0.08
63 45 0.27
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (63 bp):
ATATTATAGTATATATTATTATATGATATATATTATATATATTAGTATATTATTATATCTATT
Found at i:33005 original size:7 final size:7
Alignment explanation
Indices: 32803--33085 Score: 125
Period size: 7 Copynumber: 38.1 Consensus size: 7
32793 TATAGTGTTG
*
32803 TATTACA
1 TATTATA
32810 TATTATA
1 TATTATA
32817 GTA-TATA
1 -TATTATA
32824 TTATTATA
1 -TATTATA
**
32832 TGGTATA
1 TATTATA
32839 TATTATA
1 TATTATA
*
32846 TTAATATA
1 -TATTATA
*
32854 TAGTATA
1 TATTATA
32861 TATT-TA
1 TATTATA
32867 GTATTATA
1 -TATTATA
32875 T-TATAGTA
1 TAT-TA-TA
* *
32883 TGTTCTA
1 TATTATA
32890 T-TATATA
1 TAT-TATA
*
32897 TATTATG
1 TATTATA
32904 T-TATATA
1 TAT-TATA
32911 TATTATTA
1 TATTA-TA
32919 TATTATTA
1 TATTA-TA
32927 TATCTATTA
1 TAT-TA-TA
32936 TATTATA
1 TATTATA
32943 T-TATATTA
1 TAT-TA-TA
** *
32951 TAGCATT
1 TATTATA
32958 TATTATA
1 TATTATA
32965 TATCATAGTA
1 TAT--TA-TA
*
32975 TATTATG
1 TATTATA
*
32982 TAGTATCA
1 TATTAT-A
32990 TATTATA
1 TATTATA
32997 TATT-T-
1 TATTATA
33002 TA-TATA
1 TATTATA
33008 GTATTATA
1 -TATTATA
*
33016 TAATATA
1 TATTATA
*
33023 TAATATA
1 TATTATA
*
33030 TAGTATA
1 TATTATA
33037 TATTATA
1 TATTATA
33044 TTATTATTTA
1 -TATTA--TA
33054 TATTATTA
1 TATTA-TA
*
33062 TATTACA
1 TATTATA
33069 TATTATA
1 TATTATA
33076 GTTATTATA
1 --TATTATA
33085 T
1 T
33086 TACATTATTT
Statistics
Matches: 218, Mismatches: 28, Indels: 60
0.71 0.09 0.20
Matches are distributed among these distances:
4 1 0.00
5 3 0.01
6 7 0.03
7 114 0.52
8 63 0.29
9 23 0.11
10 7 0.03
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (7 bp):
TATTATA
Found at i:33080 original size:21 final size:21
Alignment explanation
Indices: 33033--33104 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
33023 TAATATATAG
*
33033 TATA-TATTATATTA-TTATT
1 TATATTATTATATTACATATT
33052 TATATTATTATATTACATA-T
1 TATATTATTATATTACATATT
33072 TATAGTTATTATATTACATTATT
1 TATA-TTATTATATTACA-TATT
*
33095 TTTATT-TTAT
1 TATATTATTAT
33105 TAATAATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.09
20 15 0.33
21 19 0.41
22 4 0.09
23 4 0.09
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (21 bp):
TATATTATTATATTACATATT
Found at i:46199 original size:5 final size:5
Alignment explanation
Indices: 46174--46470 Score: 143
Period size: 5 Copynumber: 60.4 Consensus size: 5
46164 GTTATATTAC
* *
46174 ATATT ATA-T ATATG GTA-T ATATT ATATT A-ATAT ATAGTAT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATAT-T ATA-T-T ATATT
* * * *
46219 ATA-T AT-TT AGTATT ATGTT ATAGT ATGTT CTATT ATA-T AGTATT ATATT
1 ATATT ATATT A-TATT ATATT ATATT ATATT ATATT ATATT A-TATT ATATT
46268 ATA-T ATATT AGTATT -T-TT AGTA-T ATTATT ATATT ATTATAT ATATT
1 ATATT ATATT A-TATT ATATT A-TATT A-TATT ATATT A-TAT-T ATATT
* * ** * *
46314 ATAGT A-AAT ATATT ATAGC AT-TT AT-TAT ATATC ATAGT ATATT ATA-T
1 ATATT ATATT ATATT ATATT ATATT ATAT-T ATATT ATATT ATATT ATATT
* *
46361 AGTATT ATATT ATA-T ATATT ATA-T ATTTT ATA-T AGTA-T ATATT ATAAT
1 A-TATT ATATT ATATT ATATT ATATT ATATT ATATT A-TATT ATATT ATATT
*
46409 ATATT ATTATT -TA-T ATTATT AAATT ATATT ATATT ATTATT -TA-T
1 ATATT A-TATT ATATT A-TATT ATATT ATATT ATATT A-TATT ATATT
*
46453 ATTATT ATATT ACATT AT
1 A-TATT ATATT ATATT AT
46471 TTTTATTTTA
Statistics
Matches: 225, Mismatches: 32, Indels: 70
0.69 0.10 0.21
Matches are distributed among these distances:
3 4 0.02
4 43 0.19
5 136 0.60
6 34 0.15
7 8 0.04
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:46213 original size:22 final size:22
Alignment explanation
Indices: 46146--46222 Score: 82
Period size: 22 Copynumber: 3.3 Consensus size: 22
46136 TGACACCTTT
* *
46146 TTATATTTATATTATAGTGTTATA
1 TTATATTAATA-TATAGT-ATATA
*
46170 TTACATATTATATATATGGTATATA
1 TT--ATATTA-ATATATAGTATATA
46195 TTATATTAATATATAGTATATA
1 TTATATTAATATATAGTATATA
46217 TTATAT
1 TTATAT
46223 ATTTAGTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 19 0.41
23 6 0.13
24 2 0.04
25 6 0.13
26 10 0.22
27 3 0.07
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.53
Consensus pattern (22 bp):
TTATATTAATATATAGTATATA
Found at i:46454 original size:17 final size:17
Alignment explanation
Indices: 46149--46457 Score: 124
Period size: 18 Copynumber: 16.7 Consensus size: 17
46139 CACCTTTTTA
* *
46149 TATTTATATTATAGTGT
1 TATTTATATTATATTAT
46166 TATATTACATATTATATATAT
1 TAT-TT--ATATTATAT-TAT
** * *
46187 GGTATATATTATATTAA
1 TATTTATATTATATTAT
*
46204 TATATAGTA-TATATTAT
1 TATTTA-TATTATATTAT
*
46221 ATATTTAGTATTATGTTAT
1 -TATTTA-TATTATATTAT
*
46240 AGTATGTTCTATTATATAGTAT
1 --TAT-TTATATTATAT--TAT
*
46262 TATATTATA-TATATTAG
1 TAT-TTATATTATATTAT
* *
46279 TATTTTTAGTATATTAT
1 TATTTATATTATATTAT
46296 TATATTATTATATATATTAT
1 TAT-TTA-TAT-TATATTAT
** **
46316 AGTAAATATATTATAGCATT
1 --TATTTATATTATATTA-T
*
46336 TATTATATATCATAGTATAT
1 TATT-TATATTATA-T-TAT
*
46356 TATATAGTATTATATTAT
1 TATTTA-TATTATATTAT
*
46374 ATATATTATA-TATTTTAT
1 -TAT-TTATATTATATTAT
*
46392 ATAGTATATATTATAATATAT
1 -TA-TTTATATTAT-AT-TAT
46413 TA-TTAT-TTATATTAT
1 TATTTATATTATATTAT
*
46428 TAAATTATATTATATTAT
1 T-ATTTATATTATATTAT
46446 TATTTATATTAT
1 TATTTATATTAT
46458 TATATTACAT
Statistics
Matches: 223, Mismatches: 38, Indels: 62
0.69 0.12 0.19
Matches are distributed among these distances:
15 4 0.02
16 7 0.03
17 49 0.22
18 55 0.25
19 39 0.17
20 53 0.24
21 11 0.05
22 5 0.02
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.55
Consensus pattern (17 bp):
TATTTATATTATATTAT
Found at i:46463 original size:17 final size:17
Alignment explanation
Indices: 46149--46477 Score: 107
Period size: 17 Copynumber: 18.6 Consensus size: 17
46139 CACCTTTTTA
*
46149 TATTTATATTA-TAGTGT
1 TATTTATATTATTA-TAT
*
46166 TATATTACA-TATTATAT
1 TAT-TTATATTATTATAT
*
46183 ATATGGTATA-TATTATAT
1 -TAT-TTATATTATTATAT
46201 TAATATATAGTATATATTATA-
1 T-AT-T-TA-TAT-TATTATAT
*
46222 TATTTAGTATTATGTTATAG
1 TATTTA-TATTA--TTATAT
*
46242 TATGTTCTATTATATAGTAT
1 TAT-TTATATTAT-TA-TAT
46262 TATATTATATATATTAGTAT
1 TAT-TTATAT-TATTA-TAT
*
46282 TTTTAGTATATTATTATAT
1 TATT--TATATTATTATAT
*
46301 TA-TTATATATATTATAG
1 TATTTATAT-TATTATAT
* *
46318 TA--AATA-TATTATAG
1 TATTTATATTATTATAT
* *
46332 CATTTATTATATATCATAGT
1 TATTTA-TAT-TATTATA-T
*
46352 ATATTATATAGTATTATAT
1 -TATT-TATATTATTATAT
*
46371 TATATATATTA-TATA-
1 TATTTATATTATTATAT
*
46386 T-TTTATA-TAGTATA-
1 TATTTATATTATTATAT
*
46400 TA-TTATAATA-TATTAT
1 TATTTATATTATTA-TAT
*
46416 TATTTATATTATTAAAT
1 TATTTATATTATTATAT
46433 TATATTATATTATTAT-T
1 TAT-TTATATTATTATAT
*
46450 TATATTAT-TATATTACAT
1 TAT-TTATAT-TATTATAT
*
46468 TATTTTTATT
1 TATTTATATT
46478 TTAAGTGTCT
Statistics
Matches: 245, Mismatches: 30, Indels: 74
0.70 0.09 0.21
Matches are distributed among these distances:
13 2 0.01
14 26 0.11
15 5 0.02
16 16 0.07
17 57 0.23
18 51 0.21
19 22 0.09
20 41 0.17
21 16 0.07
22 9 0.04
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (17 bp):
TATTTATATTATTATAT
Found at i:48522 original size:32 final size:32
Alignment explanation
Indices: 48486--48547 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
48476 TCGATTTTCA
* * *
48486 GGTCAAATTAATATATGATTGATCCATTTTTG
1 GGTCAAATAAATATATGATCGATCAATTTTTG
* *
48518 GGTCAAGTAAATATCTGATCGATCAATTTT
1 GGTCAAATAAATATATGATCGATCAATTTT
48548 CACTTCAGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (32 bp):
GGTCAAATAAATATATGATCGATCAATTTTTG
Found at i:48810 original size:18 final size:19
Alignment explanation
Indices: 48777--48813 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
48767 AAGAAATAAA
*
48777 ATTTTTAATTATAAATTTT
1 ATTTTCAATTATAAATTTT
48796 ATTTTCAATTA-AAATTTT
1 ATTTTCAATTATAAATTTT
48814 CAAGTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTCAATTATAAATTTT
Found at i:49286 original size:16 final size:16
Alignment explanation
Indices: 49273--49311 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
49263 TTGTTTTCGT
49273 TTTAGGTTAATTTCAA
1 TTTAGGTTAATTTCAA
* **
49289 TTTAGGTTACTTTTTA
1 TTTAGGTTAATTTCAA
49305 TTTAGGT
1 TTTAGGT
49312 CAAATCGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.56
Consensus pattern (16 bp):
TTTAGGTTAATTTCAA
Found at i:49768 original size:24 final size:24
Alignment explanation
Indices: 49723--49768 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
49713 ATGATTTACG
* *
49723 GCAATTCATTCATAGATTTGGGGT
1 GCAATTCATGCATAGATATGGGGT
*
49747 GCAATTCATGCATGGATATGGG
1 GCAATTCATGCATAGATATGGG
49769 AAGTTCACGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (24 bp):
GCAATTCATGCATAGATATGGGGT
Found at i:59256 original size:23 final size:23
Alignment explanation
Indices: 59230--59274 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
59220 CACAACAGCT
59230 CGTATAAATT-CACCGAAGTGCCA
1 CGTA-AAATTACACCGAAGTGCCA
*
59253 CGTAGAATTACACCGAAGTGCC
1 CGTAAAATTACACCGAAGTGCC
59275 GCATAGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
CGTAAAATTACACCGAAGTGCCA
Found at i:59295 original size:23 final size:23
Alignment explanation
Indices: 59236--59284 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
59226 AGCTCGTATA
*
59236 AATT-CACCGAAGTGCCACGTAG
1 AATTACACCGAAGTGCCACATAG
*
59258 AATTACACCGAAGTGCCGCATAG
1 AATTACACCGAAGTGCCACATAG
59281 AATT
1 AATT
59285 GTACCGTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (23 bp):
AATTACACCGAAGTGCCACATAG
Found at i:59546 original size:31 final size:30
Alignment explanation
Indices: 59501--59560 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
59491 TATTGTATAG
*
59501 ACATATAATTTCCATACCTT-TATCACATAA
1 ACATATAATTTCCAT-CATTGTATCACATAA
*
59531 ACATATCATGTTCCATCATTGTATCACATA
1 ACATATAAT-TTCCATCATTGTATCACATA
59561 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCATTGTATCACATAA
Found at i:60558 original size:10 final size:10
Alignment explanation
Indices: 60543--60567 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
60533 CTTCACGTTG
60543 AAGAAGAAGA
1 AAGAAGAAGA
60553 AAGAAGAAGA
1 AAGAAGAAGA
60563 AAGAA
1 AAGAA
60568 ATCTGGAAAC
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAGAAGAAGA
Found at i:66128 original size:23 final size:23
Alignment explanation
Indices: 66095--66162 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
66085 ACCACAGCTT
* * *
66095 GTATAAATGCACTGAATTGCCAC
1 GTATAATTGCACCGAAGTGCCAC
* *
66118 GTATAATTGCACCGAAGTGTCGC
1 GTATAATTGCACCGAAGTGCCAC
* *
66141 GTAGAATTGCACCGTAGTGCCA
1 GTATAATTGCACCGAAGTGCCA
66163 TATAAGATTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (23 bp):
GTATAATTGCACCGAAGTGCCAC
Done.