Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003077.1 Hibiscus syriacus cultivar Beakdansim tig00006417_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: 69486
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:8584 original size:15 final size:17
Alignment explanation
Indices: 8564--8595 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
8554 CTAAGTAGTT
8564 TAATAAA-TAAA-ATAA
1 TAATAAACTAAAGATAA
8579 TAATAAACTAAAGATAA
1 TAATAAACTAAAGATAA
8596 GATAATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (17 bp):
TAATAAACTAAAGATAA
Found at i:9629 original size:2 final size:2
Alignment explanation
Indices: 9622--9660 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9612 ATCCCAAATT
9622 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9661 TCCTTAATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14478 original size:13 final size:13
Alignment explanation
Indices: 14460--14490 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
14450 GGTGAGATTT
14460 AAATTAAAGTAAA
1 AAATTAAAGTAAA
*
14473 AAATTAAATTAAA
1 AAATTAAAGTAAA
14486 AAATT
1 AAATT
14491 GACGTACGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (13 bp):
AAATTAAAGTAAA
Found at i:21952 original size:3 final size:3
Alignment explanation
Indices: 21944--21987 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
21934 ATGGGTTTTC
*
21944 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAA GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
21988 AACGTGTACG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:30197 original size:45 final size:45
Alignment explanation
Indices: 30143--30234 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 45
30133 GGTATAATGG
*
30143 CAAAAAAAAAA-AAGTCTTTAACTTCGGTAACTTTTGTTAATTGTA
1 CAAAAAAAAAATAAGTCTTCAACTTCGGTAACTTTT-TTAATTGTA
* *
30188 CAAAGAAAAAATAAGTCTTCAACTTCGGTCACTTTTTTAATTGTA
1 CAAAAAAAAAATAAGTCTTCAACTTCGGTAACTTTTTTAATTGTA
30233 CA
1 CA
30235 TTTAAAGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 21 0.49
46 22 0.51
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (45 bp):
CAAAAAAAAAATAAGTCTTCAACTTCGGTAACTTTTTTAATTGTA
Found at i:33274 original size:18 final size:18
Alignment explanation
Indices: 33251--33298 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
33241 ATTGAATCTA
33251 TTGTTAGAGATCACTTAG
1 TTGTTAGAGATCACTTAG
33269 TTGTTAGAGATCACTTAG
1 TTGTTAGAGATCACTTAG
33287 TTGGTT-GAGATC
1 TT-GTTAGAGATC
33299 TTCCATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 26 0.90
19 3 0.10
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (18 bp):
TTGTTAGAGATCACTTAG
Found at i:35369 original size:22 final size:23
Alignment explanation
Indices: 35326--35369 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
35316 ATTTTTACTT
* *
35326 AAATATATATTTTTATTGAATAA
1 AAATATATATTTTTAATAAATAA
35349 AAATA-ATATTTTTAATAAATA
1 AAATATATATTTTTAATAAATA
35370 TATAATTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATATATATTTTTAATAAATAA
Found at i:37070 original size:31 final size:31
Alignment explanation
Indices: 37032--37125 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
37022 CCCGAAGGAC
* * *
37032 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
37063 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
37094 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
37125 C
1 C
37126 CCTCGACCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:37701 original size:19 final size:21
Alignment explanation
Indices: 37659--37701 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
37649 TTCATAATCA
37659 CATATTCATATAGTTTATTAT
1 CATATTCATATAGTTTATTAT
*
37680 CATA-TCATATGGTTTA-TAT
1 CATATTCATATAGTTTATTAT
37699 CAT
1 CAT
37702 CATAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (21 bp):
CATATTCATATAGTTTATTAT
Found at i:37710 original size:22 final size:20
Alignment explanation
Indices: 37665--37711 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
37655 ATCACATATT
*
37665 CATATAGTTTATTATCATAT
1 CATATAGTTTATTATCATAA
*
37685 CATATGGTTTATATCATCATAA
1 CATATAGTTTAT-T-ATCATAA
37707 CATAT
1 CATAT
37712 CACATATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 11 0.48
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (20 bp):
CATATAGTTTATTATCATAA
Found at i:38163 original size:21 final size:21
Alignment explanation
Indices: 38139--38183 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38129 TTTTGTTCGT
* *
38139 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
38160 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
38181 TTG
1 TTG
38184 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:39349 original size:42 final size:41
Alignment explanation
Indices: 39314--39503 Score: 127
Period size: 37 Copynumber: 4.9 Consensus size: 41
39304 AAAAATATTT
39314 TAAAACTATAT-A-TATTTTCAAACATGTTTTTAAAAAAACTA
1 TAAAA-TATATAATTATTTTCAAA-ATGTTTTTAAAAAAACTA
* *
39355 TATAATATATAATTATTTTCAAAATGTTTTT---AAAATTA
1 TAAAATATATAATTATTTTCAAAATGTTTTTAAAAAAACTA
* * * *
39393 TATATTATATAA--GTTTTCAAAATG-ATTT-AAAAAACTA
1 TAAAATATATAATTATTTTCAAAATGTTTTTAAAAAAACTA
* *
39430 TATATTATAT-A-TATTTTCAAAATAAGTTTTT--AAAAACTA
1 TAAAATATATAATTATTTTCAAAAT--GTTTTTAAAAAAACTA
* * * * * *
39469 TATAATTTATAAATGTTTTCAAAATATTTTCAAAA
1 TAAAATATATAATTATTTTCAAAATGTTTTTAAAA
39504 CTGTATATTA
Statistics
Matches: 124, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
35 3 0.02
36 12 0.10
37 26 0.21
38 17 0.14
39 21 0.17
40 9 0.07
41 26 0.21
42 10 0.08
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (41 bp):
TAAAATATATAATTATTTTCAAAATGTTTTTAAAAAAACTA
Found at i:39480 original size:114 final size:114
Alignment explanation
Indices: 39320--39528 Score: 298
Period size: 114 Copynumber: 1.8 Consensus size: 114
39310 ATTTTAAAAC
* *
39320 TATATATATTTTCAAACATGTTTTTAAAAAAACTATATAATATATAATTATTTTCAAAATGTTTT
1 TATATATATTTTCAAACATGTTTTT-AAAAAACTATATAATATATAAATATTTTCAAAATATTTT
* *
39385 TAAAATTATATATTATATA-AGTTTTCAAAATGATTTAAAAAACTATATAT
65 CAAAACTATATATTATATATA-TTTTCAAAATGATTTAAAAAACTATATAT
* *
39435 TATATATATTTTCAAA-ATAAGTTTTT-AAAAACTATATAATTTATAAATGTTTTCAAAATATTT
1 TATATATATTTTCAAACAT--GTTTTTAAAAAACTATATAATATATAAATATTTTCAAAATATTT
*
39498 TCAAAACTGTATATTATATATATTTTCAAAA
64 TCAAAACTATATATTATATATATTTTCAAAA
39529 ATTATATATT
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
114 61 0.73
115 17 0.20
116 6 0.07
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (114 bp):
TATATATATTTTCAAACATGTTTTTAAAAAACTATATAATATATAAATATTTTCAAAATATTTTC
AAAACTATATATTATATATATTTTCAAAATGATTTAAAAAACTATATAT
Found at i:39511 original size:77 final size:73
Alignment explanation
Indices: 39320--39528 Score: 235
Period size: 77 Copynumber: 2.7 Consensus size: 73
39310 ATTTTAAAAC
* *
39320 TATATATA-TTTTCAAACATGTTTTTAAAAAAACTATATAATATATAATTATTTTCAAAATGTTT
1 TATATA-AGTTTTCAAA-ATG-ATTT-AAAAAACTATATATTATAT-A-TATTTTCAAAATGTTT
*
39384 TTAAAATTATATAT
60 TTAAAACTATATAT
39398 TATATAAGTTTTCAAAATGATTTAAAAAACTATATATTATATATATTTTCAAAATAAGTTTTTAA
1 TATATAAGTTTTCAAAATGATTTAAAAAACTATATATTATATATATTTTCAAAAT--GTTTTT-A
39463 AAACTATATAAT
63 AAACTATAT-AT
** *
39475 T-TATAAATGTTTTCAAAAT-ATTTTCAAAACTGTATATTATATATATTTTCAAAA
1 TATAT-AA-GTTTTCAAAATGATTTAAAAAACTATATATTATATATATTTTCAAAA
39529 ATTATATATT
Statistics
Matches: 118, Mismatches: 6, Indels: 15
0.85 0.04 0.11
Matches are distributed among these distances:
73 12 0.10
74 1 0.01
75 24 0.20
76 15 0.13
77 41 0.35
78 25 0.21
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (73 bp):
TATATAAGTTTTCAAAATGATTTAAAAAACTATATATTATATATATTTTCAAAATGTTTTTAAAA
CTATATAT
Found at i:39524 original size:25 final size:26
Alignment explanation
Indices: 39492--39548 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
39482 TGTTTTCAAA
*
39492 ATATTTTC-AAAACTGTATATTATAT
1 ATATTTTCAAAAACTATATATTATAT
*
39517 ATATTTTCAAAAATTATATATTATAT
1 ATATTTTCAAAAACTATATATTATAT
39543 A-ATTTT
1 ATATTTT
39549 TTAAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (26 bp):
ATATTTTCAAAAACTATATATTATAT
Found at i:39567 original size:36 final size:39
Alignment explanation
Indices: 39517--39592 Score: 131
Period size: 36 Copynumber: 2.0 Consensus size: 39
39507 TATATTATAT
39517 ATATTTTCAAAAATTATATATTATATA-AT-TTTTTAAA
1 ATATTTTCAAAAATTATATATTATATATATATTTTTAAA
39554 ATATTTT-AAAAATTATATATTATATATATATTTTTAAA
1 ATATTTTCAAAAATTATATATTATATATATATTTTTAAA
39592 A
1 A
39593 ATCATTTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
36 19 0.51
37 9 0.24
38 9 0.24
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (39 bp):
ATATTTTCAAAAATTATATATTATATATATATTTTTAAA
Found at i:39573 original size:62 final size:64
Alignment explanation
Indices: 39456--39582 Score: 170
Period size: 62 Copynumber: 2.0 Consensus size: 64
39446 TCAAAATAAG
* * *
39456 TTTTTAAAAACTATATAATTTATAAATGTTTTCAAAATATTTTCAAAACTGTATATTATATATA
1 TTTTCAAAAACTATATAATTTATAAATGTTTTCAAAATATTTTAAAAACTATATATTATATATA
* * *
39520 TTTTCAAAAATTATAT-A-TTATATAAT-TTTTTAAAATATTTTAAAAATTATATATTATATATA
1 TTTTCAAAAACTATATAATTTATA-AATGTTTTCAAAATATTTTAAAAACTATATATTATATATA
39582 T
1 T
39583 ATTTTTAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
62 38 0.68
63 4 0.07
64 14 0.25
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (64 bp):
TTTTCAAAAACTATATAATTTATAAATGTTTTCAAAATATTTTAAAAACTATATATTATATATA
Found at i:39583 original size:64 final size:64
Alignment explanation
Indices: 39456--39594 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 64
39446 TCAAAATAAG
* * *
39456 TTTTTAAAAACTATATAATTTATAAATGTTTTCAAAATATTTTCAAAACTGTATATTATATATA
1 TTTTTAAAAATTATATAATTTATAAATGTTTTCAAAATATTTTAAAAACTATATATTATATATA
* * *
39520 TTTTCAAAAATTATAT-A-TTATATAAT-TTTTTAAAATATTTTAAAAATTATATATTATATATA
1 TTTTTAAAAATTATATAATTTATA-AATGTTTTCAAAATATTTTAAAAACTATATA-T-TATATA
39582 TA
63 TA
39584 TTTTTAAAAAT
1 TTTTTAAAAAT
39595 CATTTGTAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
62 28 0.43
63 5 0.08
64 32 0.49
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (64 bp):
TTTTTAAAAATTATATAATTTATAAATGTTTTCAAAATATTTTAAAAACTATATATTATATATA
Found at i:39616 original size:38 final size:36
Alignment explanation
Indices: 39517--39617 Score: 98
Period size: 39 Copynumber: 2.7 Consensus size: 36
39507 TATATTATAT
* *
39517 ATATTTTCAAAAATTATATAT-TATATAATTTTTTAAA
1 ATATTTT--AAAATTATAAATATATATAATTTTTAAAA
*
39554 ATATTTTAAAAATTATATATTATATATATATTTTTAAAA
1 ATATTTT-AAAATTATA-AATATATATA-ATTTTTAAAA
39593 ATCATTTGT-AAATTATAAATATATA
1 AT-ATTT-TAAAATTATAAATATATA
39618 AAAAATGTAG
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
36 10 0.18
37 8 0.15
38 13 0.24
39 19 0.35
40 4 0.07
41 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (36 bp):
ATATTTTAAAATTATAAATATATATAATTTTTAAAA
Found at i:45609 original size:334 final size:336
Alignment explanation
Indices: 44995--45668 Score: 1307
Period size: 334 Copynumber: 2.0 Consensus size: 336
44985 AAACCACGCC
44995 ATTTGATTAAGACAAAATTACAGAATCACCCCCGCCACTGTTTGCGTCAAAATATCCAAACGCCC
1 ATTTGATTAAGACAAAATTACAGAATCACCCCCGCCACTGTTTGCGTCAAAATATCCAAACGCCC
45060 CGTGAGGCTGTCCACAGAACTGGCCGGATACACCCTCGTTCGGACGTGTTTCAAATTGCCTCCAT
66 CGTGAGGCTGTCCACAGAACTGGCCGGATACACCCTCGTTCGGACGTGTTTCAAATTGCCTCCAT
*
45125 GTTCGCCACGTGTCTCGTACTGCCCCTCCGTCAACATCCTCTTCCATTCCAGAATTTTAACAGTG
131 GTTCGCCACGTGTCTCGTACTCCCCCTCCGTCAACATCCTCTTCCATTCCAGAATTTTAACAGTG
*
45190 CCGACAATGGAGGAGGAACCGTTGGGCCTCGGATGGCAGACTCGGTAATAATGAAGAAATCGATG
196 CCGACAATGGAGGAGGAACCGTTGGGCCTCGGATGGCAGACTCGGTAATAATGAAGAAATCAATG
45255 GCATTTACGTTAAAAGAGATTCCCAGTA-TTTTTTTATTTTCTTGAATTATTATATATATTCTTT
261 GCATTTACGTTAAAAGAGATTCCCAGTATTTTTTTTATTTTCTTGAATTATTATATATATTCTTT
45319 TTGACCAAAAG
326 TTGACCAAAAG
45330 ATTT-ATTAAGACAAAATTACAGAATCACCCCCGCCACTGTTTGCGTCAAAATATCCAAACGCCC
1 ATTTGATTAAGACAAAATTACAGAATCACCCCCGCCACTGTTTGCGTCAAAATATCCAAACGCCC
45394 CGTGAGGCTGTCCACAGAACTGGCCGGATACACCCTCGTTCGGACGTGTTTCAAATTGCCTCCAT
66 CGTGAGGCTGTCCACAGAACTGGCCGGATACACCCTCGTTCGGACGTGTTTCAAATTGCCTCCAT
*
45459 GTTCGCCACGTGTCTCGTACTCCCCCTCCGTCAACATCCTCTTCCATTCCAGAGTTTTAACAGTG
131 GTTCGCCACGTGTCTCGTACTCCCCCTCCGTCAACATCCTCTTCCATTCCAGAATTTTAACAGTG
45524 CCGACAATGGAGGAGGAACCGTTGGGCCTCGGATGGCAGACTCGGTAATAATGAAGAAATCAATG
196 CCGACAATGGAGGAGGAACCGTTGGGCCTCGGATGGCAGACTCGGTAATAATGAAGAAATCAATG
45589 GCATTTACGTTAAAAGAGATTCCCAGTATTTTTTTTATTTTCTTGAATTATTATATATATTCTTT
261 GCATTTACGTTAAAAGAGATTCCCAGTATTTTTTTTATTTTCTTGAATTATTATATATATTCTTT
45654 TTGACCAAAAG
326 TTGACCAAAAG
45665 ATTT
1 ATTT
45669 TTTGCAGGGA
Statistics
Matches: 335, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
334 280 0.84
335 55 0.16
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (336 bp):
ATTTGATTAAGACAAAATTACAGAATCACCCCCGCCACTGTTTGCGTCAAAATATCCAAACGCCC
CGTGAGGCTGTCCACAGAACTGGCCGGATACACCCTCGTTCGGACGTGTTTCAAATTGCCTCCAT
GTTCGCCACGTGTCTCGTACTCCCCCTCCGTCAACATCCTCTTCCATTCCAGAATTTTAACAGTG
CCGACAATGGAGGAGGAACCGTTGGGCCTCGGATGGCAGACTCGGTAATAATGAAGAAATCAATG
GCATTTACGTTAAAAGAGATTCCCAGTATTTTTTTTATTTTCTTGAATTATTATATATATTCTTT
TTGACCAAAAG
Found at i:52903 original size:40 final size:40
Alignment explanation
Indices: 52854--52940 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 40
52844 TGGGTCTTGT
* * *
52854 TAAGTGCTGGCTTCCTGGACTC-TCTGTGTCTGGGACTCAC
1 TAAGAGCTGGCTTCCTGAACTCTTCTGTATCTGGG-CTCAC
* *
52894 TAAGAGCTGGTTTTCTGAACTCTTTCTGTATCTGGGCTCAC
1 TAAGAGCTGGCTTCCTGAACTC-TTCTGTATCTGGGCTCAC
52935 TAAGAG
1 TAAGAG
52941 ATTGTTTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
40 18 0.45
41 11 0.28
42 11 0.28
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.34
Consensus pattern (40 bp):
TAAGAGCTGGCTTCCTGAACTCTTCTGTATCTGGGCTCAC
Found at i:62691 original size:3 final size:3
Alignment explanation
Indices: 62685--62722 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
62675 TTCTTTTTTT
62685 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
62723 TCTTTATGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:65670 original size:2 final size:2
Alignment explanation
Indices: 65663--65694 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
65653 ATTTCCCGGT
65663 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
65695 ATGAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65708 original size:16 final size:16
Alignment explanation
Indices: 65689--65720 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
65679 TATATATATA
65689 TATATAATGAATTATT
1 TATATAATGAATTATT
*
65705 TATATTATGAATTATT
1 TATATAATGAATTATT
65721 AGATTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TATATAATGAATTATT
Done.