Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007192.1 Hibiscus syriacus cultivar Beakdansim tig00018955_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: 51112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1185 original size:3 final size:3
Alignment explanation
Indices: 1167--1253 Score: 132
Period size: 3 Copynumber: 31.0 Consensus size: 3
1157 CCATTTGTTT
1167 TTA TT- TTA TT- TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1212 TT- TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1254 ACATTTTAGG
Statistics
Matches: 78, Mismatches: 0, Indels: 12
0.87 0.00 0.13
Matches are distributed among these distances:
2 12 0.15
3 66 0.85
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1192 original size:17 final size:17
Alignment explanation
Indices: 1167--1253 Score: 121
Period size: 17 Copynumber: 5.4 Consensus size: 17
1157 CCATTTGTTT
1167 TTATT-TTATT-TTATTA
1 TTATTATTATTATT-TTA
*
1183 TTATTATTATTATTATA
1 TTATTATTATTATTTTA
1200 TTATTATTATTATTTTA
1 TTATTATTATTATTTTA
1217 TTATTATTATTA--TTA
1 TTATTATTATTATTTTA
1232 -TATTATTATTATTTTA
1 TTATTATTATTATTTTA
1248 TTATTA
1 TTATTA
1254 ACATTTTAGG
Statistics
Matches: 64, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
14 11 0.17
15 3 0.05
16 8 0.12
17 40 0.62
18 2 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTATTATTATTTTA
Found at i:1201 original size:14 final size:15
Alignment explanation
Indices: 1167--1253 Score: 132
Period size: 14 Copynumber: 6.2 Consensus size: 15
1157 CCATTTGTTT
1167 TTATT-TTATT-TTA
1 TTATTATTATTATTA
1180 TTATTATTATTATTA
1 TTATTATTATTATTA
1195 TTA-TATTATTATTA
1 TTATTATTATTATTA
1209 TTATT-TTATTATTA
1 TTATTATTATTATTA
1223 TTATTATTA-TATTA
1 TTATTATTATTATTA
1237 TTATTATT-TTATTA
1 TTATTATTATTATTA
1251 TTA
1 TTA
1254 ACATTTTAGG
Statistics
Matches: 69, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.07
14 54 0.78
15 10 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTATTATTATTA
Found at i:2825 original size:17 final size:18
Alignment explanation
Indices: 2805--2840 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2795 TTTATAAAAA
2805 TATAAAAAAT-ATATATT
1 TATAAAAAATAATATATT
*
2822 TATAAAAATTAATATATT
1 TATAAAAAATAATATATT
2840 T
1 T
2841 TCTTGGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAAAATAATATATT
Found at i:2830 original size:149 final size:148
Alignment explanation
Indices: 2557--2832 Score: 346
Period size: 149 Copynumber: 1.9 Consensus size: 148
2547 TATTAATATT
*
2557 TATTTATTTATTTATTAATTTTAAGAAGGGGTTGTCTTAAAGCAACTAGAAGTCATTTTCTGATA
1 TATTTATTTATTTATTAATATTAAGAAGGGGTTGTCTTAAAGCAACTAGAAGTCATTTTCTGATA
* * * * * * *
2622 TTTTAAAAATAAATAAATATCATACTTTTATAATTATATATATTAGTTTATTTTTAAAATTATTT
66 TTTT-AAAATAAATAAATATCATACTTTTAAAAATATAAAAAATAGTATATTTTAAAAATTATTT
2687 TTAGAAAATATTTTATTAA
130 TTAGAAAATATTTTATTAA
* *
2706 TATTTATTTATTTTTTAATATTAAGAACGGGGATT-TCTTAAAGCAACTATAAGTCATTTTCT-A
1 TATTTATTTATTTATTAATATTAAGAA-GGGG-TTGTCTTAAAGCAACTAGAAGTCATTTTCTGA
* *
2769 TTATTTCT-AAGTAAATAAATATCTTA-TTTATAAAAATATAAAAAATA-TATATTTATAAAAAT
64 -TATTT-TAAAATAAATAAATATCATACTTT-TAAAAATATAAAAAATAGTATATTT-TAAAAAT
2831 TA
125 TA
2833 ATATATTTTC
Statistics
Matches: 109, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
148 9 0.08
149 62 0.57
150 35 0.32
151 3 0.03
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (148 bp):
TATTTATTTATTTATTAATATTAAGAAGGGGTTGTCTTAAAGCAACTAGAAGTCATTTTCTGATA
TTTTAAAATAAATAAATATCATACTTTTAAAAATATAAAAAATAGTATATTTTAAAAATTATTTT
TAGAAAATATTTTATTAA
Found at i:6618 original size:15 final size:15
Alignment explanation
Indices: 6598--6629 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
6588 GATCAATACC
6598 TTTTGCATACATTCA
1 TTTTGCATACATTCA
6613 TTTTGCATACATTCA
1 TTTTGCATACATTCA
6628 TT
1 TT
6630 ATTCATTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (15 bp):
TTTTGCATACATTCA
Found at i:9842 original size:11 final size:11
Alignment explanation
Indices: 9826--9855 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
9816 GAGCTAAAAC
9826 TGGGAAAGGTT
1 TGGGAAAGGTT
9837 TGGGAAAGGTT
1 TGGGAAAGGTT
9848 TGGGAAAG
1 TGGGAAAG
9856 AATCTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (11 bp):
TGGGAAAGGTT
Found at i:15407 original size:22 final size:22
Alignment explanation
Indices: 15344--15429 Score: 111
Period size: 22 Copynumber: 3.9 Consensus size: 22
15334 ACATCTACAT
*
15344 TCTTCAAAGATGATAGATACAT-
1 TCTTCAAAGATGATAGATTC-TC
15366 TCTTCAAAAGATGATAGATTCTC
1 TCTTC-AAAGATGATAGATTCTC
15389 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* * *
15411 TTTTCAAAGAAGAAAGATT
1 TCTTCAAAGATGATAGATT
15430 TATTGGATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
22 39 0.67
23 19 0.33
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:15992 original size:123 final size:123
Alignment explanation
Indices: 15827--16261 Score: 666
Period size: 123 Copynumber: 3.6 Consensus size: 123
15817 TTTCCGCGAG
*
15827 AGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAAAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
15891 AACCTTTTGC-TAGACTCTATCACAGAAGGAGATAGATCAACGTACACTTTTCCAGAGAA
65 AACCTTTTGCAT-GACTCTATCACAGAAGGAGATAGATCAACATACACTTTTCCAGAGAA
* * *
15950 AGTTCATAATGAGAATAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
16015 ACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATACACTTTTCCAGAGAA
66 ACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATACACTTTTCCAGAGAA
*
16073 AGTTCATAAT---AAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
** * * *
16135 ACCTTTTGCATGAAACTATCACAGAAGGAGATAGATCAACATAAACATTTCTAGA-AA
66 ACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATACACTTTTCCAGAGAA
* * * * *
16192 TGTTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAATTCATAACGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
16257 ACCTT
66 ACCTT
16262 GCCTTAATTC
Statistics
Matches: 289, Mismatches: 18, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
119 11 0.04
120 100 0.35
122 55 0.19
123 122 0.42
124 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (123 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATACACTTTTCCAGAGAA
Found at i:16640 original size:3 final size:3
Alignment explanation
Indices: 16634--16682 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
16624 TTTGGTTTTT
* *
16634 TTA TTA TTA TTA TTA CTA TTA TTTA TTA TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
16680 TTA
1 TTA
16683 CATTTCAGGC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:16659 original size:19 final size:18
Alignment explanation
Indices: 16634--16682 Score: 89
Period size: 19 Copynumber: 2.7 Consensus size: 18
16624 TTTGGTTTTT
16634 TTATTATTATTATTACTA
1 TTATTATTATTATTACTA
16652 TTATTTATTATTATTACTA
1 TTA-TTATTATTATTACTA
16671 TTATTATTATTA
1 TTATTATTATTA
16683 CATTTCAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATTATTATTATTACTA
Found at i:17942 original size:2 final size:2
Alignment explanation
Indices: 17929--17968 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
17919 TGATTTAGTA
*
17929 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17969 TTATTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18247 original size:16 final size:17
Alignment explanation
Indices: 18226--18260 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
18216 TTTATAAAAA
18226 TATAAAAA-AATATATT
1 TATAAAAATAATATATT
18242 TATAAAAATTAATATATT
1 TATAAAAA-TAATATATT
18260 T
1 T
18261 TCTTGGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATAAAAATAATATATT
Found at i:20739 original size:37 final size:36
Alignment explanation
Indices: 20698--20933 Score: 214
Period size: 37 Copynumber: 6.4 Consensus size: 36
20688 TGAAAATATG
20698 TTTTGAAAACATATAATATATAGTTTTTAGAAAACGT
1 TTTTGAAAACATATAATATATAGTTTTTA-AAAACGT
* * *
20735 TTTTGAAAGCATATCATATATACTTTTTAAAAGAATCAGT
1 TTTTGAAAACATATAATATATAGTTTTT-AAA-AA-C-GT
* * *
20775 TTTTGAAAATATATAATAT-GA-TTTTGAAAATACGT
1 TTTTGAAAACATATAATATATAGTTTTTAAAA-ACGT
* * *
20810 TTTTGAAAACATATATTATATAGTTTTGAAAACACAT
1 TTTTGAAAACATATAATATATAGTTTTTAAAA-ACGT
* * *
20847 TTTTGAAAACGTATAATATACAG-TTTTAAAAATGAT
1 TTTTGAAAACATATAATATATAGTTTTTAAAAACG-T
*
20883 TTTTGAAAACGTATATAATATA-A--TTTTAAAAACAT
1 TTTTGAAAAC--ATATAATATATAGTTTTTAAAAACGT
20918 ATTTTGAAAACATATA
1 -TTTTGAAAACATATA
20934 TAGTTTTTTT
Statistics
Matches: 166, Mismatches: 22, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
34 5 0.03
35 21 0.13
36 40 0.24
37 64 0.39
38 16 0.10
39 2 0.01
40 18 0.11
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.40
Consensus pattern (36 bp):
TTTTGAAAACATATAATATATAGTTTTTAAAAACGT
Found at i:20830 original size:75 final size:72
Alignment explanation
Indices: 20698--20933 Score: 230
Period size: 72 Copynumber: 3.2 Consensus size: 72
20688 TGAAAATATG
* * *
20698 TTTTGAAAACATATAATATATAGTTTTTAGAAAACGTTTTTGAAAGCATATCA-TATATACTTTT
1 TTTTGAAAACATATAATATACAG-TTTTA-AAAACGTTTTTGAAAACATAT-ATTATATA-ATTT
*
20762 TAAAAGAATCAGT
62 TAAAA-AAACA-T
* * * *
20775 TTTTGAAAATATATAATAT-GA-TTTTGAAAATACGTTTTTGAAAACATATATTATATAGTTTTG
1 TTTTGAAAACATATAATATACAGTTTT-AAAA-ACGTTTTTGAAAACATATATTATATAATTTTA
*
20838 AAAACACAT
64 AAAAAACAT
* * * *
20847 TTTTGAAAACGTATAATATACAGTTTTAAAAATGATTTTTGAAAACGTATATAATATAATTTT--
1 TTTTGAAAACATATAATATACAGTTTTAAAAACG-TTTTTGAAAACATATATTATATAATTTTAA
20910 AAAAACAT
65 AAAAACAT
20918 ATTTTGAAAACATATA
1 -TTTTGAAAACATATA
20934 TAGTTTTTTT
Statistics
Matches: 136, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
71 7 0.05
72 34 0.25
73 33 0.24
74 19 0.14
75 24 0.18
76 1 0.01
77 18 0.13
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.40
Consensus pattern (72 bp):
TTTTGAAAACATATAATATACAGTTTTAAAAACGTTTTTGAAAACATATATTATATAATTTTAAA
AAAACAT
Found at i:20892 original size:36 final size:36
Alignment explanation
Indices: 20734--20933 Score: 162
Period size: 36 Copynumber: 5.4 Consensus size: 36
20724 TTAGAAAACG
* *
20734 TTTTTGAAAGCATATCATATATAC-TTTTTAAAAGAATCA
1 TTTTTGAAAACATAT-A-ATATACAGTTTT-AAA-AATCA
* * * *
20773 GTTTTTGAAAATATATAATAT-GA-TTTTGAAAATACG
1 -TTTTTGAAAACATATAATATACAGTTTTAAAAAT-CA
* *
20809 TTTTTGAAAACATATATTATATAGTTTTGAAAACA-CA
1 TTTTTGAAAACATATAATATACAGTTTT-AAAA-ATCA
* *
20846 TTTTTGAAAACGTATAATATACAGTTTTAAAAATGA
1 TTTTTGAAAACATATAATATACAGTTTTAAAAATCA
20882 TTTTTGAAAACGTATATAATATA-A-TTTTAAAAA-CA
1 TTTTTGAAAAC--ATATAATATACAGTTTTAAAAATCA
20917 TATTTTGAAAACATATA
1 T-TTTTGAAAACATATA
20934 TAGTTTTTTT
Statistics
Matches: 134, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
34 5 0.04
35 24 0.18
36 39 0.29
37 35 0.26
38 16 0.12
39 2 0.01
40 13 0.10
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.41
Consensus pattern (36 bp):
TTTTTGAAAACATATAATATACAGTTTTAAAAATCA
Found at i:21014 original size:17 final size:16
Alignment explanation
Indices: 20973--21014 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
20963 AACAAATAAT
20973 ATATAAT-TTTTGAAA
1 ATATAATATTTTGAAA
* *
20988 AGATATTATTTTCGAAA
1 ATATAATATTTT-GAAA
21005 ATATAATATT
1 ATATAATATT
21015 ATATAGTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (16 bp):
ATATAATATTTTGAAA
Found at i:21044 original size:30 final size:30
Alignment explanation
Indices: 21005--21103 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
20995 ATTTTCGAAA
21005 ATATAATATTATATAGTTT-TAT-TATATATT
1 ATATAATATTAT-TA-TTTATATCTATATATT
*
21035 ATATTATATTATTATTTATATCTATATATT
1 ATATAATATTATTATTTATATCTATATATT
*
21065 ATATCATA-TATT-TTTATAT-TATA-ATT
1 ATATAATATTATTATTTATATCTATATATT
*
21091 TTAT-AT-TTATTAT
1 ATATAATATTATTAT
21104 GTATTATTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
25 6 0.10
26 7 0.11
27 4 0.06
28 10 0.16
29 9 0.15
30 26 0.42
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (30 bp):
ATATAATATTATTATTTATATCTATATATT
Found at i:21046 original size:20 final size:20
Alignment explanation
Indices: 21010--21127 Score: 69
Period size: 20 Copynumber: 6.2 Consensus size: 20
21000 CGAAAATATA
*
21010 ATATTATA-TAGTTTTATTAT
1 ATATTATATTA-TATTATTAT
21030 ATATTATATTATATTA-T-T
1 ATATTATATTATATTATTAT
21048 AT-TTATATCTATA-TATTAT
1 ATATTATAT-TATATTATTAT
21067 ATCA-TATATT-T-TTA-TAT
1 AT-ATTATATTATATTATTAT
* *
21084 -TATAATTTTATATTTATTAT
1 ATATTATATTATA-TTATTAT
* * *
21104 GTATTAT-TTTTATTATTTT
1 ATATTATATTATATTATTAT
21123 ATATT
1 ATATT
21128 TTTTTTATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 27
0.70 0.06 0.24
Matches are distributed among these distances:
15 1 0.01
16 5 0.06
17 12 0.15
18 11 0.14
19 18 0.23
20 24 0.31
21 7 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
ATATTATATTATATTATTAT
Found at i:21047 original size:13 final size:13
Alignment explanation
Indices: 21010--21127 Score: 73
Period size: 13 Copynumber: 8.8 Consensus size: 13
21000 CGAAAATATA
21010 ATATTATA-TAGTT
1 ATATTATATTA-TT
*
21023 TTATTATA-TATT
1 ATATTATATTATT
21035 ATATTATATTATT
1 ATATTATATTATT
21048 AT-TTATATCTA-T
1 ATATTATAT-TATT
*
21060 ATATTATATCATAT
1 ATATTATATTAT-T
* *
21074 ATTTTTATATTATA
1 A-TATTATATTATT
*
21088 ATTTTATATTTATT
1 ATATTATA-TTATT
*
21102 ATGTATTATTTTTATT
1 A--TATTA-TATTATT
*
21118 ATTTTATATT
1 ATATTATATT
21128 TTTTTTATTT
Statistics
Matches: 84, Mismatches: 11, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
12 19 0.23
13 33 0.39
14 12 0.14
15 9 0.11
16 10 0.12
17 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (13 bp):
ATATTATATTATT
Found at i:21065 original size:37 final size:33
Alignment explanation
Indices: 21024--21126 Score: 86
Period size: 37 Copynumber: 3.0 Consensus size: 33
21014 TATATAGTTT
21024 TATTATATATTATATTATATTATTATTTATATCTATA
1 TATTATATATTAT-TTATATTATTATTT-TA--TATA
* *
21061 TATTATATCATATATTTTTATATTATAATTTTATATT
1 TATTATAT-AT-TA--TTTATATTATTATTTTATATA
*
21098 TATTATGTATTA-TT-T-TTATTATTTTATAT
1 TATTATATATTATTTATATTATTATTTTATAT
21127 TTTTTTTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
30 13 0.22
31 1 0.02
32 2 0.03
35 2 0.03
36 2 0.03
37 18 0.31
38 2 0.03
39 4 0.07
40 13 0.22
41 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (33 bp):
TATTATATATTATTTATATTATTATTTTATATA
Found at i:21117 original size:9 final size:9
Alignment explanation
Indices: 21105--21144 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
21095 ATTTATTATG
21105 TATTATTTT
1 TATTATTTT
21114 TATTATTTT
1 TATTATTTT
*
21123 ATATTTTTTT
1 -TATTATTTT
21133 TATT-TTTT
1 TATTATTTT
21141 TATT
1 TATT
21145 TGGTCTACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 8 0.28
9 13 0.45
10 8 0.28
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TATTATTTT
Found at i:21119 original size:19 final size:19
Alignment explanation
Indices: 21023--21136 Score: 78
Period size: 20 Copynumber: 6.1 Consensus size: 19
21013 TTATATAGTT
*
21023 TTATTATATATTATATTATA
1 TTATTATATATTAT-TTTTA
* * *
21043 TTATTATTTA-TATCTATA
1 TTATTATATATTATTTTTA
21061 -TATTATATCATATATTTTTA
1 TTATTATAT-AT-TATTTTTA
*
21081 -TATTATA-A-T-TTTATA
1 TTATTATATATTATTTTTA
*
21096 TTTATTATGTATTATTTTTA
1 -TTATTATATATTATTTTTA
* *
21116 TTATTTTATATTTTTTTTA
1 TTATTATATATTATTTTTA
21135 TT
1 TT
21137 TTTTTATTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
15 5 0.07
16 1 0.01
17 13 0.17
18 7 0.09
19 22 0.29
20 27 0.36
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.66
Consensus pattern (19 bp):
TTATTATATATTATTTTTA
Found at i:21128 original size:30 final size:31
Alignment explanation
Indices: 21023--21127 Score: 101
Period size: 30 Copynumber: 3.4 Consensus size: 31
21013 TTATATAGTT
21023 TTATTATATATTATATTA-TATTATTATTTA
1 TTATTATATATTATATTATTATTATTATTTA
* *
21053 -TATCTATATATTATATCATATATTTTTATATTA
1 TTAT-TATATATTATATTAT-TATTATTAT-TTA
* *
21086 TAATTTTATATT-TATTATGTATTATT-TTTA
1 TTATTATATATTATATTAT-TATTATTATTTA
*
21116 TTATTTTATATT
1 TTATTATATATT
21128 TTTTTTATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
29 3 0.05
30 27 0.44
31 1 0.02
32 19 0.31
33 10 0.16
34 2 0.03
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (31 bp):
TTATTATATATTATATTATTATTATTATTTA
Found at i:21141 original size:19 final size:19
Alignment explanation
Indices: 21031--21143 Score: 61
Period size: 19 Copynumber: 5.6 Consensus size: 19
21021 TTTTATTATA
*
21031 TATTATATTATATTATTATT
1 TATTATTTTATATTATT-TT
* *
21051 TA-TATCTATATATTA-TAT
1 TATTAT-TTTATATTATTTT
*
21069 CATATATTTTTATATTATAATTT
1 TAT-TA-TTTTATATTAT--TTT
21092 TA-TATTTATTATGTATTATTTT
1 TATTA-TT-TTA--TATTATTTT
*
21114 TATTATTTTATATTTTTTT
1 TATTATTTTATATTATTTT
*
21133 TATTTTTTTAT
1 TATTATTTTAT
21144 TTGGTCTACA
Statistics
Matches: 73, Mismatches: 9, Indels: 23
0.70 0.09 0.22
Matches are distributed among these distances:
18 2 0.03
19 22 0.30
20 19 0.26
21 9 0.12
22 10 0.14
23 5 0.07
24 6 0.08
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (19 bp):
TATTATTTTATATTATTTT
Found at i:22403 original size:19 final size:18
Alignment explanation
Indices: 22375--22413 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
22365 AATTTGATCC
* *
22375 TTTAACATTTTCTTCATTT
1 TTTAAAATTTTATT-ATTT
22394 TTTAAAATTTTATTATTT
1 TTTAAAATTTTATTATTT
22412 TT
1 TT
22414 ATTTCTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTAAAATTTTATTATTT
Found at i:22535 original size:48 final size:50
Alignment explanation
Indices: 22477--22581 Score: 162
Period size: 48 Copynumber: 2.1 Consensus size: 50
22467 AATTTTCTTT
22477 ATTATTTATTTTAAATTTCTTTTA-AACTTT-ACATTTTCTT-AATTTTTA
1 ATTATTTATTTTAAATTTCTTTTATAA-TTTAACATTTTCTTCAATTTTTA
*
22525 ATTATTTATTTTAAATTTCTTTTATAATTTAACATTTTCTTCATTTTTTA
1 ATTATTTATTTTAAATTTCTTTTATAATTTAACATTTTCTTCAATTTTTA
*
22575 TTTATTT
1 ATTATTT
22582 CTCTTTTAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
48 27 0.52
49 12 0.23
50 13 0.25
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.65
Consensus pattern (50 bp):
ATTATTTATTTTAAATTTCTTTTATAATTTAACATTTTCTTCAATTTTTA
Found at i:31444 original size:2 final size:2
Alignment explanation
Indices: 31437--31472 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
31427 GCTTTGACTC
*
31437 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31473 CTTTTATAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33830 original size:509 final size:506
Alignment explanation
Indices: 32739--34040 Score: 2227
Period size: 509 Copynumber: 2.6 Consensus size: 506
32729 TAATTCCTTT
* *
32739 AAATTAACCC-CAACTTTTATCAAAATGATCATTTTGACTCCTATT-TCTTTTAGAGTATTTTAG
1 AAATTAACCCTCAACGTTTATCAAAATGATCATTTTGACTCCTATTCTCTTTTAGAGTATTTTGG
*
32802 CTCTAACATTTT-TGTAACACCCACGATCCGAATACGTATACTAATACAAGTTATAGATGTCACA
66 CTCTAACATTTTATGTAACACCCACGA-CCGAATACGTATACTAATACTAGTTATAGATGTCACA
* * * * *
32866 TTAATTATTTAAAACATTTTCTAACTCAAAAGTTATTAAAATTTTGTTTATTCTAACTTTTCAAA
130 TTAATTATTTAAAACATTTTCCAACTCAAAAGTGATTAAAAATTTGTTTCTTCTAACTTTCCAAA
* * *
32931 TCATAATCATTATTATAAAATATTAAATCACATAAAACAATACATAATATTTAAAACATATTTTA
195 TCGTAATCATTATTATAAAATATTAAATCGCATAAAACAACACATAATATTTAAAACATATTTTA
32996 ATATAAAATACGTCCCTTCATAA-AATTTTAAACTTTTAAGTACGTTTGTTTTCTCATTTTATAT
260 ATAT-AAATACGTCCCTTCATAATAA-TTTAAACTTTTAAGTACGTTTGTTTTCTCATTTTATAT
33060 TTAAACTTGTATCATATGACATTTTAATTTTATTTTCATTCCTGTAATCAACAGACAGTAGTTCT
323 TTAAACTTGTATCATATGACATTTTAATTTTATTTTCATTCCTGTAATCAACAGACAGTAGTTCT
*
33125 GTTTTAGAACAACTAAAAAATGACCTACAACTTCTAGACCCTTTCAATATCAATAAAGAAACACA
388 GTTTTAGAACAACTAAAAAATGACCTACAACTTCTAGACCCTTTCAATATCAATAAAGAAACAAA
*
33190 CTTATATATTCTAAACTCAACAATAAGTAACCTTAAAAAGTGAGGCATAATTCA
453 CTTATATATTCTAAACTCAACAATAAGTAACCCTAAAAAGTGAGGCATAATTCA
33244 AAATTAACCCTCAACGTTTATCAAAATGATCATTTTGACTCCTATTCTCTTTTAGAGTATTTTGG
1 AAATTAACCCTCAACGTTTATCAAAATGATCATTTTGACTCCTATTCTCTTTTAGAGTATTTTGG
* * *
33309 CTCTAACATTTTATGTAACACTCACGACATGAATACGTATACTAATATTAGTTATAGATGTCACA
66 CTCTAACATTTTATGTAACACCCACGAC-CGAATACGTATACTAATACTAGTTATAGATGTCACA
33374 TTAATTATTTAAAACA-TTTCCAACTCAAAAGTGATTAAAAATTTGTTTCTTCTAACTTTCCAAA
130 TTAATTATTTAAAACATTTTCCAACTCAAAAGTGATTAAAAATTTGTTTCTTCTAACTTTCCAAA
33438 TCGTAATCATTATTATAAAATATTAAATCGCATAAAACAACACATAATATTTAAAACATATTTTA
195 TCGTAATCATTATTATAAAATATTAAATCGCATAAAACAACACATAATATTTAAAACATATTTTA
* * *
33503 AAATAATATACGTCCCTTCATAATAATTTAAACTTTTAAGTACTTTTTTTTTCTCATTTTATATT
260 ATATAA-ATACGTCCCTTCATAATAATTTAAACTTTTAAGTACGTTTGTTTTCTCATTTTATATT
33568 TAAACTTGTATCATATGACATTTTAATTTTATTTTCATTCCTGTAATCAACAGACAAAGTAGTTC
324 TAAACTTGTATCATATGACATTTTAATTTTATTTTCATTCCTGTAATCAACAGAC--AGTAGTTC
33633 TGTTTTAGAACAACTAAAAAATGACCTACAACTTCTAGACCCTTTCAATATCAATAAAGAAACAA
387 TGTTTTAGAACAACTAAAAAATGACCTACAACTTCTAGACCCTTTCAATATCAATAAAGAAACAA
33698 ACTTATATATTCTAAACTCAACAATAAGTAACCCTAAAAAGTGAGGCATAATTCA
452 ACTTATATATTCTAAACTCAACAATAAGTAACCCTAAAAAGTGAGGCATAATTCA
* *
33753 AAATTAACCCTCAACGTTCATCAAAATAATCATTTTGACTCCTATTCTCTTTTAGAGTATTTTGG
1 AAATTAACCCTCAACGTTTATCAAAATGATCATTTTGACTCCTATTCTCTTTTAGAGTATTTTGG
* * * *
33818 CTCTAACATTTTATGCAAAACCCACGACCCGAATACGTGTACTAATACTAGTTATGGATGTCACA
66 CTCTAACATTTTATGTAACACCCACGA-CCGAATACGTATACTAATACTAGTTATAGATGTCACA
*
33883 TTAATTATTTAAAACATTTTGCAACTCAAAAGTGATTAAAAATTTGTTTCTTCTAACTTTCCAAA
130 TTAATTATTTAAAACATTTTCCAACTCAAAAGTGATTAAAAATTTGTTTCTTCTAACTTTCCAAA
*
33948 TCGTAATCATTATTATAAAATATTAAATCGTATAAAACCAACACATAATATTTAAAACATATTTT
195 TCGTAATCATTATTATAAAATATTAAATCGCATAAAA-CAACACATAATATTTAAAACATATTTT
* *
34013 AATATAAATGCATCCCTTCATAATAATT
259 AATATAAATACGTCCCTTCATAATAATT
34041 ATATTAGGTA
Statistics
Matches: 753, Mismatches: 33, Indels: 17
0.94 0.04 0.02
Matches are distributed among these distances:
505 10 0.01
506 36 0.05
507 246 0.33
508 64 0.08
509 261 0.35
510 103 0.14
511 33 0.04
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (506 bp):
AAATTAACCCTCAACGTTTATCAAAATGATCATTTTGACTCCTATTCTCTTTTAGAGTATTTTGG
CTCTAACATTTTATGTAACACCCACGACCGAATACGTATACTAATACTAGTTATAGATGTCACAT
TAATTATTTAAAACATTTTCCAACTCAAAAGTGATTAAAAATTTGTTTCTTCTAACTTTCCAAAT
CGTAATCATTATTATAAAATATTAAATCGCATAAAACAACACATAATATTTAAAACATATTTTAA
TATAAATACGTCCCTTCATAATAATTTAAACTTTTAAGTACGTTTGTTTTCTCATTTTATATTTA
AACTTGTATCATATGACATTTTAATTTTATTTTCATTCCTGTAATCAACAGACAGTAGTTCTGTT
TTAGAACAACTAAAAAATGACCTACAACTTCTAGACCCTTTCAATATCAATAAAGAAACAAACTT
ATATATTCTAAACTCAACAATAAGTAACCCTAAAAAGTGAGGCATAATTCA
Found at i:46702 original size:16 final size:16
Alignment explanation
Indices: 46636--46703 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
46626 GATATGATCT
*
46636 ATGTGATTATGTGAAA
1 ATGTGATTATATGAAA
* **
46652 ATGTGA-TATAAG-CT
1 ATGTGATTATATGAAA
*
46666 ATGTGA-TAT-TGAACT
1 ATGTGATTATATGAA-A
46681 ATGTGATTATATGAAA
1 ATGTGATTATATGAAA
46697 ATGTGAT
1 ATGTGAT
46704 AGAAGCTGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
13 1 0.02
14 9 0.22
15 11 0.27
16 16 0.39
17 4 0.10
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (16 bp):
ATGTGATTATATGAAA
Found at i:46754 original size:44 final size:44
Alignment explanation
Indices: 46619--46760 Score: 185
Period size: 44 Copynumber: 3.2 Consensus size: 44
46609 TATATTTCAT
*
46619 GCTATGTGATATGATCTATGTGATTATGTGAAAATGTGATATAA
1 GCTATGTGATATGATCTATGTGATTATATGAAAATGTGATATAA
* *
46663 GCTATGTGATATTGAACTATGTGATTATATGAAAATGTGATAGAA
1 GCTATGTGATA-TGATCTATGTGATTATATGAAAATGTGATATAA
* * * *** *
46708 GCTGTGTGACATGATCTATGTGATTATTTGTCTATGTTATATAA
1 GCTATGTGATATGATCTATGTGATTATATGAAAATGTGATATAA
46752 GCTATGTGA
1 GCTATGTGA
46761 AAAGTTATAA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
44 45 0.54
45 39 0.46
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (44 bp):
GCTATGTGATATGATCTATGTGATTATATGAAAATGTGATATAA
Found at i:46871 original size:23 final size:23
Alignment explanation
Indices: 46837--46935 Score: 83
Period size: 23 Copynumber: 4.3 Consensus size: 23
46827 AAGTCGAAGG
* *
46837 TTCTACGCGGTCCTTCGGGACAA
1 TTCTATGCGGTCCTTCAGGACAA
* * * *
46860 TTCTACGTGGTCATTCAGGACAT
1 TTCTATGCGGTCCTTCAGGACAA
*
46883 TTCTATGCGGTCTTTCAGGACAA
1 TTCTATGCGGTCCTTCAGGACAA
* ** *
46906 TACTATAAGGTCCTTC-GAGACAT
1 TTCTATGCGGTCCTTCAG-GACAA
46929 TTCTATG
1 TTCTATG
46936 TGGCACTTCA
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 1 0.02
23 59 0.98
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (23 bp):
TTCTATGCGGTCCTTCAGGACAA
Found at i:48546 original size:22 final size:22
Alignment explanation
Indices: 48518--48581 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
48508 GTCTATTTCT
* *
48518 TTCAACGCATGACTCCTAATTG
1 TTCAACGCTTGGCTCCTAATTG
48540 TTCAACGCTTGGCTCCTAATTG
1 TTCAACGCTTGGCTCCTAATTG
48562 TTCAACGCTTGGCTCCTAAT
1 TTCAACGCTTGGCTCCTAAT
48582 AACGCTTATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (22 bp):
TTCAACGCTTGGCTCCTAATTG
Found at i:50953 original size:185 final size:188
Alignment explanation
Indices: 50655--51013 Score: 512
Period size: 186 Copynumber: 1.9 Consensus size: 188
50645 GGTGCAACCA
* * *
50655 TATTTCTTATATATGTTCATAAAATTTTCAATTTTAAACTTATTTTCTTATACTCGGATAATCCA
1 TATTTATTATATATGTTCATAAAATTTTCAAGTTTAAACTTATTTTCTTATACTAGGATAATCCA
* * * *
50720 AGACTCCATCCGCTTAAACTCTGATAATATTTTCGGTGCAAACTATTTT-ATTATTAAAAATATT
66 AGACTCCATCAGCTTAAAATCTAATAACATTTTCGGTGCAAACTATTTTAATTATTAAAAATATT
* * * * * *
50784 AACATTCCATATTAGAACCTGTTTTATTTTTTAGCCATGACATTTTTTGGCACAACTG
131 AACATTCCAGATTACAACCTATTTTAATTTTCAACCATGACATTTTTTGGCACAACTG
*
50842 TATTTATTATATATGTTCATAACATTTT-AAGTTTAAACTTA-TTTCTTATACTAGGATAATCCA
1 TATTTATTATATATGTTCATAAAATTTTCAAGTTTAAACTTATTTTCTTATACTAGGATAATCCA
* *
50905 AGGCTCCATCAGCTTAAAATC-AATAACATTTTC-GTCGCAACCCTATTTTAATTATTAAAAATA
66 AGACTCCATCAGCTTAAAATCTAATAACATTTTCGGT-GCAA-ACTATTTTAATTATTAAAAATA
*
50968 TTAACATTCTAGATTACAACCTATTTTAATTTTCAACCATGACATT
129 TTAACATTCCAGATTACAACCTATTTTAATTTTCAACCATGACATT
51014 ATTGGTGTGT
Statistics
Matches: 152, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
183 2 0.01
184 14 0.09
185 46 0.30
186 64 0.42
187 26 0.17
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (188 bp):
TATTTATTATATATGTTCATAAAATTTTCAAGTTTAAACTTATTTTCTTATACTAGGATAATCCA
AGACTCCATCAGCTTAAAATCTAATAACATTTTCGGTGCAAACTATTTTAATTATTAAAAATATT
AACATTCCAGATTACAACCTATTTTAATTTTCAACCATGACATTTTTTGGCACAACTG
Done.