Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003762.1 Hibiscus syriacus cultivar Beakdansim tig00008061_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: 67199
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5417 original size:14 final size:15
Alignment explanation
Indices: 5394--5423 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5384 ATAACGTCCA
5394 CGACATCCGCAACCG
1 CGACATCCGCAACCG
5409 CGACA-CCGCAACCG
1 CGACATCCGCAACCG
5423 C
1 C
5424 ATTCGCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.27, C:0.50, G:0.20, T:0.03
Consensus pattern (15 bp):
CGACATCCGCAACCG
Found at i:15701 original size:32 final size:30
Alignment explanation
Indices: 15660--15729 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 30
15650 TTGAAAAAAA
15660 TTTATATTCTTTTTGTATTGAA-TTTTATTCACT
1 TTTA-ATTCTTTTT-TATTGAATTTTTA-T-ACT
*
15693 TTTAATTCTTTTTTATTGTATTTTTATACT
1 TTTAATTCTTTTTTATTGAATTTTTATACT
15723 TTTAATT
1 TTTAATT
15730 ACAATTGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
30 10 0.29
31 7 0.20
32 14 0.40
33 4 0.11
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.67
Consensus pattern (30 bp):
TTTAATTCTTTTTTATTGAATTTTTATACT
Found at i:19433 original size:18 final size:18
Alignment explanation
Indices: 19410--19462 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
19400 CATAGAAATT
*
19410 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
19428 TGTCCCGAAGGACCACTC
1 TGTCCCGAAGGACCACTA
19446 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
19463 GATAATCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:23687 original size:18 final size:18
Alignment explanation
Indices: 23672--23788 Score: 189
Period size: 18 Copynumber: 6.5 Consensus size: 18
23662 TTTGTCCTGT
*
23672 AGGACCACTATGTCCTGA
1 AGGACCACTATGTCCCGA
*
23690 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
*
23708 AGAACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
23726 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
23744 AGGACCACTATGTCCCAA
1 AGGACCACTATGTCCCGA
*
23762 AGGACCACTATGTCCCAA
1 AGGACCACTATGTCCCGA
23780 AGGACCACT
1 AGGACCACT
23789 GATAATCCCT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 93 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:26429 original size:17 final size:17
Alignment explanation
Indices: 26407--26443 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
26397 CCATTACAAG
26407 GAATCTAAACGTGCTTT
1 GAATCTAAACGTGCTTT
26424 GAATCTAAACGTGCTTT
1 GAATCTAAACGTGCTTT
26441 GAA
1 GAA
26444 GAGATGGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (17 bp):
GAATCTAAACGTGCTTT
Found at i:27524 original size:12 final size:13
Alignment explanation
Indices: 27498--27522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27488 TTTTTGAAAC
27498 TTTAATAAAAAAA
1 TTTAATAAAAAAA
27511 TTTAATAAAAAA
1 TTTAATAAAAAA
27523 TTAGTGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTAATAAAAAAA
Found at i:29178 original size:2 final size:2
Alignment explanation
Indices: 29171--29202 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29161 ATTAAATAAA
29171 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
29203 TGTTTGTCTT
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):
AT
Found at i:32445 original size:20 final size:22
Alignment explanation
Indices: 32416--32455 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
32406 TGTAATTGAT
32416 TTTCTAG-AAAATGAATTATAA
1 TTTCTAGAAAAATGAATTATAA
32437 TTTCT-GAAAAATGAATTAT
1 TTTCTAGAAAAATGAATTAT
32456 GGAAAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (22 bp):
TTTCTAGAAAAATGAATTATAA
Found at i:35199 original size:12 final size:12
Alignment explanation
Indices: 35182--35231 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
35172 AACGGTCAAC
35182 GGTCAACGGTCG
1 GGTCAACGGTCG
35194 GGTCAACGGTCG
1 GGTCAACGGTCG
*
35206 GGTC--GGGTCG
1 GGTCAACGGTCG
35216 GGTCAACGGTCG
1 GGTCAACGGTCG
35228 GGTC
1 GGTC
35232 GGGTCAGACC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 9 0.26
12 25 0.74
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:35217 original size:22 final size:22
Alignment explanation
Indices: 35189--35236 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
35179 AACGGTCAAC
35189 GGTCGGGTCAACGGTCGGGTCG
1 GGTCGGGTCAACGGTCGGGTCG
35211 GGTCGGGTCAACGGTCGGGTCG
1 GGTCGGGTCAACGGTCGGGTCG
35233 GGTC
1 GGTC
35237 AGACCGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (22 bp):
GGTCGGGTCAACGGTCGGGTCG
Found at i:35257 original size:19 final size:18
Alignment explanation
Indices: 35235--35281 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 18
35225 TCGGGTCGGG
35235 TCAGACCGGTCAAACCGGC
1 TCAGACCGGTCAAA-CGGC
*
35254 TCAGACCGGTCAAACGGG
1 TCAGACCGGTCAAACGGC
35272 TCAGACCGGT
1 TCAGACCGGT
35282 TCGAACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.26, C:0.32, G:0.30, T:0.13
Consensus pattern (18 bp):
TCAGACCGGTCAAACGGC
Found at i:35312 original size:9 final size:9
Alignment explanation
Indices: 35233--35311 Score: 59
Period size: 9 Copynumber: 8.3 Consensus size: 9
35223 GGTCGGGTCG
*
35233 GGTCAGACC
1 GGTCAAACC
35242 GGTCAAACC
1 GGTCAAACC
*
35251 GGCTCAGACC
1 GG-TCAAACC
*
35261 GGTCAAACG
1 GGTCAAACC
*
35270 GGTCAGACC
1 GGTCAAACC
*
35279 GGTTCGAACC
1 GG-TCAAACC
*
35289 GGTTGAAAACC
1 GG-T-CAAACC
*
35300 GGTTAAACC
1 GGTCAAACC
35309 GGT
1 GGT
35312 TTCCAGCAGC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
9 32 0.57
10 18 0.32
11 6 0.11
ACGTcount: A:0.27, C:0.28, G:0.30, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:42473 original size:17 final size:17
Alignment explanation
Indices: 42451--42511 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
42441 AACGGTCAAC
42451 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
42468 GGTCAACGGTCGGGTTGGGTCG
1 GGTCAACGGTC-----GGGTCG
*
42490 GGTCAACTGTCGGGTCG
1 GGTCAACGGTCGGGTCG
42507 GGTCA
1 GGTCA
42512 GACCGGTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 22 0.58
22 16 0.42
ACGTcount: A:0.11, C:0.21, G:0.46, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:42490 original size:22 final size:22
Alignment explanation
Indices: 42444--42510 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
42434 GAAAGTCAAC
*
42444 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
*
42468 GGTCAACGGTCGGGTTGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
42490 GGTCAACTGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
42511 AGACCGGTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 28 0.72
24 11 0.28
ACGTcount: A:0.12, C:0.22, G:0.45, T:0.21
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:42574 original size:19 final size:19
Alignment explanation
Indices: 42509--42563 Score: 94
Period size: 18 Copynumber: 2.9 Consensus size: 19
42499 TCGGGTCGGG
42509 TCAGACCGGTCAAACCGGC
1 TCAGACCGGTCAAACCGGC
*
42528 TCAGACCGGTCAAA-CGGG
1 TCAGACCGGTCAAACCGGC
42546 TCAGACCGGTCAAACCGG
1 TCAGACCGGTCAAACCGG
42564 TTCGAACCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 17 0.50
19 17 0.50
ACGTcount: A:0.27, C:0.33, G:0.29, T:0.11
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGC
Found at i:42593 original size:20 final size:21
Alignment explanation
Indices: 42557--42595 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42547 CAGACCGGTC
*
42557 AAACCGGTTCGAACCGGTTGA
1 AAACCGGTTCAAACCGGTTGA
42578 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCAAACCGGTT
42596 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.21
Consensus pattern (21 bp):
AAACCGGTTCAAACCGGTTGA
Found at i:42595 original size:9 final size:9
Alignment explanation
Indices: 42507--42594 Score: 77
Period size: 9 Copynumber: 9.3 Consensus size: 9
42497 TGTCGGGTCG
*
42507 GGTCAGACC
1 GGTCAAACC
42516 GGTCAAACC
1 GGTCAAACC
*
42525 GGCTCAGACC
1 GG-TCAAACC
*
42535 GGTCAAACG
1 GGTCAAACC
*
42544 GGTCAGACC
1 GGTCAAACC
42553 GGTCAAACC
1 GGTCAAACC
*
42562 GGTTCGAACC
1 GG-TCAAACC
*
42572 GGTTGAAAACC
1 GG-T-CAAACC
*
42583 GGTTAAACC
1 GGTCAAACC
42592 GGT
1 GGT
42595 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
9 40 0.62
10 19 0.29
11 6 0.09
ACGTcount: A:0.27, C:0.28, G:0.30, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:43711 original size:18 final size:18
Alignment explanation
Indices: 43670--43713 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
43660 AAAAAAAATT
*
43670 GATGAGAGAAAGAGAGTC
1 GATGAGAGAAAGAGAGCC
*
43688 GGTGAG-GAACAGAGAGCC
1 GATGAGAGAA-AGAGAGCC
43706 GATGAGAG
1 GATGAGAG
43714 GTGGAGGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 17 0.81
19 1 0.05
ACGTcount: A:0.39, C:0.09, G:0.43, T:0.09
Consensus pattern (18 bp):
GATGAGAGAAAGAGAGCC
Found at i:43765 original size:10 final size:10
Alignment explanation
Indices: 43750--43781 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
43740 GGTGGAGAGC
43750 AGTGAATATT
1 AGTGAATATT
43760 AGTGAATA--
1 AGTGAATATT
43768 AGTGAATATT
1 AGTGAATATT
43778 AGTG
1 AGTG
43782 TGGGCTCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (10 bp):
AGTGAATATT
Found at i:44436 original size:3 final size:3
Alignment explanation
Indices: 44430--44485 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
44420 AAAATACATA
44430 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
44478 AAT AAT AA
1 AAT AAT AA
44486 AGTATGAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:44521 original size:21 final size:21
Alignment explanation
Indices: 44495--44537 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
44485 AAGTATGAAT
44495 AAAAATTAGAAATAAAATTTC
1 AAAAATTAGAAATAAAATTTC
44516 AAAAATTAGAAATAAAATTTC
1 AAAAATTAGAAATAAAATTTC
44537 A
1 A
44538 CACTCAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAAATTAGAAATAAAATTTC
Found at i:46858 original size:31 final size:30
Alignment explanation
Indices: 46782--46858 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 30
46772 ACTTTTAAAA
* * *
46782 TTTACAATACAGTCCCCTAACATTAATCCG
1 TTTACAATATAGTCCCCCAACATTAATACG
** * * *
46812 TTTGTAATATGGTCCCCCAACATTTAGTATG
1 TTTACAATATAGTCCCCCAACA-TTAATACG
46843 TTTACAATATAGTCCC
1 TTTACAATATAGTCCC
46859 TGACCGTTGA
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (30 bp):
TTTACAATATAGTCCCCCAACATTAATACG
Found at i:48838 original size:31 final size:30
Alignment explanation
Indices: 48795--48899 Score: 147
Period size: 31 Copynumber: 3.4 Consensus size: 30
48785 TTAAACGGCT
* *
48795 GGGGACCATATTGCAAACAGACTAAATGTTA
1 GGGGACCGTATTGCAAAC-GACTAAATGTTG
48826 GGGGACCGTATTGCAAACGAACTAAATGTTG
1 GGGGACCGTATTGCAAACG-ACTAAATGTTG
*
48857 GGGGACCGTATTGCAAACGGACTAAATATTG
1 GGGGACCGTATTGCAAAC-GACTAAATGTTG
*
48888 GGGGACTGTATT
1 GGGGACCGTATT
48900 ACAAGTTTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
30 1 0.01
31 66 0.97
32 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (30 bp):
GGGGACCGTATTGCAAACGACTAAATGTTG
Found at i:49269 original size:24 final size:24
Alignment explanation
Indices: 49213--49271 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
49203 AACCAAATAT
* *
49213 AAAGACTCCAAAATGATAAATGAA
1 AAAGACTCTAAAATGATAAATAAA
49237 AAAGACTCTAAAATGATAAATAAA
1 AAAGACTCTAAAATGATAAATAAA
49261 AAAGACTCTAA
1 AAAGACTCTAA
49272 GAATACAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.59, C:0.12, G:0.10, T:0.19
Consensus pattern (24 bp):
AAAGACTCTAAAATGATAAATAAA
Found at i:54965 original size:13 final size:15
Alignment explanation
Indices: 54935--54966 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
54925 AGTGAGAAAA
54935 AGAAAAACATACGAG
1 AGAAAAACATACGAG
54950 AGAAAAA-ATA-GAG
1 AGAAAAACATACGAG
54963 AGAA
1 AGAA
54967 TTGAGAGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.66, C:0.06, G:0.22, T:0.06
Consensus pattern (15 bp):
AGAAAAACATACGAG
Found at i:60492 original size:17 final size:16
Alignment explanation
Indices: 60451--60493 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
60441 TAACGACACA
60451 TTAATATTTAATTATTT
1 TTAA-ATTTAATTATTT
*
60468 TATTAATTTAATTATGTT
1 T-TAAATTTAATTAT-TT
60486 TTAAATTT
1 TTAAATTT
60494 TTGAATTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTAAATTTAATTATTT
Found at i:62065 original size:10 final size:10
Alignment explanation
Indices: 62032--62064 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
62022 GTCTGTTTGG
62032 TTTTAATTTA
1 TTTTAATTTA
*
62042 ATTTAATTTA
1 TTTTAATTTA
62052 TTTT-ATTTA
1 TTTTAATTTA
62061 TTTT
1 TTTT
62065 TTAGAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:62914 original size:30 final size:30
Alignment explanation
Indices: 62863--62941 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
62853 TAGATGAACT
** *
62863 TAATTAATTTTTTGGCT-AAGTTCGAGGGCC
1 TAATTAATTTTTT-TATAAAGTTCGAGGACC
* *
62893 TAATTAATTTTTTTATAAAGTTTGAGGACT
1 TAATTAATTTTTTTATAAAGTTCGAGGACC
*
62923 TATTTAATTTTTTTATAAA
1 TAATTAATTTTTTTATAAA
62942 AAATAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 1 0.02
30 41 0.98
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.49
Consensus pattern (30 bp):
TAATTAATTTTTTTATAAAGTTCGAGGACC
Found at i:63028 original size:22 final size:22
Alignment explanation
Indices: 62976--63029 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
62966 AATATAAAAT
*
62976 ATAAAC-AATTATTAATATTCA
1 ATAAACTAAATATTAATATTCA
* *
62997 ATACATTAAATATTAA-ATTACA
1 ATAAACTAAATATTAATATT-CA
63019 ATAAACTAAAT
1 ATAAACTAAAT
63030 TAGTTAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAAACTAAATATTAATATTCA
Found at i:63202 original size:22 final size:20
Alignment explanation
Indices: 63159--63208 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
63149 GACCAACAAA
63159 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* *
63179 TTTGCAACGCGAATTTCCCAAT
1 TTCGCAACGCGAA-CT-CCAAT
63201 TTCGCAAC
1 TTCGCAAC
63209 TCAGTTTCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.48
21 1 0.04
22 12 0.48
ACGTcount: A:0.28, C:0.32, G:0.14, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:63485 original size:22 final size:21
Alignment explanation
Indices: 63460--63528 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
63450 TCTCTATGGC
* *
63460 GACATTCGTCCTCATCTCCGGT
1 GACATCCGTCC-CATATCCGGT
* *
63482 GACATCCGTCCCCATATCTGGC
1 GACATCCGT-CCCATATCCGGT
63504 GACATCCGTCCCTATATCCGGT
1 GACATCCGTCCC-ATATCCGGT
63526 GAC
1 GAC
63529 CCCCCTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 3 0.08
22 34 0.87
23 2 0.05
ACGTcount: A:0.17, C:0.38, G:0.19, T:0.26
Consensus pattern (21 bp):
GACATCCGTCCCATATCCGGT
Found at i:65427 original size:42 final size:42
Alignment explanation
Indices: 65368--65466 Score: 171
Period size: 42 Copynumber: 2.4 Consensus size: 42
65358 CCCCCCACTT
* * *
65368 CGAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
65410 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
65452 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
65467 ATTTCATCAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.27, C:0.37, G:0.19, T:0.16
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
Found at i:65610 original size:21 final size:21
Alignment explanation
Indices: 65581--65630 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
65571 GTTAGGGAAG
*
65581 TTACATGATGAGGTCAGTACT
1 TTACGTGATGAGGTCAGTACT
* *
65602 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
65623 TTACGTGA
1 TTACGTGA
65631 CGACAACTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:66075 original size:21 final size:21
Alignment explanation
Indices: 66049--66124 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
66039 ATTCACCTGT
*
66049 CATCGTTCAAGAGGCCCCTTC
1 CATCGTTCAAGAGGCCCCTCC
**
66070 CATCGTTCAAGAGGCATCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
66091 CATCGTTCAATAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
66112 CACCGTTCAAGAG
1 CATCGTTCAAGAG
66125 CCCGATTCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.22
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Done.