Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001443.1 Hibiscus syriacus cultivar Beakdansim tig00002792_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: 68414
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:18976 original size:42 final size:42
Alignment explanation
Indices: 18917--18999 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
18907 CCGTCTTAGC
*
18917 AGATGATATTCCATCAGCCCTACCAGACATAAGATTCGTCCA
1 AGATGATATTCCATCAGCCCTACAAGACATAAGATTCGTCCA
*
18959 AGATGATATTCCATCAGCCCTACAAGCCATAAGATTCGTCC
1 AGATGATATTCCATCAGCCCTACAAGACATAAGATTCGTCC
19000 TATTGATCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (42 bp):
AGATGATATTCCATCAGCCCTACAAGACATAAGATTCGTCCA
Found at i:20411 original size:36 final size:36
Alignment explanation
Indices: 20371--20445 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
20361 CTTCTTCGTA
* *
20371 TTCCTCCTCCTCCACTTCCACCTCATACTCTTCTTC
1 TTCCTCCTCCTCCACCTCCACATCATACTCTTCTTC
* *
20407 TTCCTTCTCCTCCTCCTCCACATCATACTCTTCTTC
1 TTCCTCCTCCTCCACCTCCACATCATACTCTTCTTC
20443 TTC
1 TTC
20446 TTCTTCTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.11, C:0.48, G:0.00, T:0.41
Consensus pattern (36 bp):
TTCCTCCTCCTCCACCTCCACATCATACTCTTCTTC
Found at i:20446 original size:42 final size:42
Alignment explanation
Indices: 20357--20451 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
20347 GTCGTCGTCG
* * *
20357 TCTTCTTCTTCGTATTCCTCCTCCTCCACTTCCACCTCATAC
1 TCTTCTTCTTCCTATTCCTCCTCCTCCACATCCAACTCATAC
*
20399 TCTTCTTCTTCCT-TCTCCTCCTCCTCCACAT-CATACTC-TTC
1 TCTTCTTCTTCCTAT-TCCTCCTCCTCCACATCCA-ACTCATAC
20440 TTCTTCTTCTTC
1 -TCTTCTTCTTC
20452 TTCATCAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
41 5 0.11
42 41 0.89
ACGTcount: A:0.09, C:0.44, G:0.01, T:0.45
Consensus pattern (42 bp):
TCTTCTTCTTCCTATTCCTCCTCCTCCACATCCAACTCATAC
Found at i:22641 original size:31 final size:30
Alignment explanation
Indices: 22573--22648 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
22563 TTAGAAATTT
* * *
22573 GTTGCAACTTAAAATGTAATGGAAAAGTAT
1 GTTGCAACTTAAAATGCAATAGAAAAGTAG
*
22603 GTTGCAACTTAAAATGACAACTATAAAA-TAG
1 GTTGCAACTTAAAATG-CAA-TAGAAAAGTAG
22634 GTTGCAACTTTAAAA
1 GTTGCAAC-TTAAAA
22649 AGGGTAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 16 0.41
31 12 0.31
32 11 0.28
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (30 bp):
GTTGCAACTTAAAATGCAATAGAAAAGTAG
Found at i:27728 original size:103 final size:103
Alignment explanation
Indices: 27544--27761 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
27534 GTCGAGGGTC
* *
27544 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
* *
27609 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
*
27647 TATGTGGTCCTTCGGGACATATATGTATTCTTTGTAACATGTATGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
* *
27712 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
27750 TATGTGGTCCTT
1 TATGTGGTCCTT
27762 ATGGATATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
Found at i:29316 original size:36 final size:36
Alignment explanation
Indices: 29237--29316 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
29227 TGAAATAGCT
* **
29237 GGATCATCAGACAATGAAGTCATCCCCGAAGAAGTT
1 GGATCATCAGACAATGAAGTCATCACCGAAGAAGCC
* * * *
29273 GGGTCATCAGGCAATGAAGTTATCACCGAAGGAGCC
1 GGATCATCAGACAATGAAGTCATCACCGAAGAAGCC
29309 GGATCATC
1 GGATCATC
29317 GAACGATGGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.19
Consensus pattern (36 bp):
GGATCATCAGACAATGAAGTCATCACCGAAGAAGCC
Found at i:29945 original size:55 final size:55
Alignment explanation
Indices: 29841--29946 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 55
29831 ATTTTTTTAA
* *
29841 AAAAATATAAAATAAAATAACAAAGCCTATGAGTTTATTAAAGATAATAAATTTT
1 AAAAATATAAAATAAAATAACAAAGCCCATGAGTTTATTAAAGAAAATAAATTTT
* * *
29896 AAAAATATAAAATAAAATAA-TAGGTCCCATTA-TTTATTAAAGTAAAATAAA
1 AAAAATATAAAATAAAATAACAAAG-CCCATGAGTTTATTAAAG-AAAATAAA
29947 AATTAAGCGT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
54 12 0.27
55 32 0.73
ACGTcount: A:0.58, C:0.06, G:0.07, T:0.30
Consensus pattern (55 bp):
AAAAATATAAAATAAAATAACAAAGCCCATGAGTTTATTAAAGAAAATAAATTTT
Found at i:32569 original size:53 final size:53
Alignment explanation
Indices: 32506--32612 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
32496 TGTGGAAAGG
*
32506 TGGGATAAATGTTTCCGAGTATCTTTTGGTTCATACAATTACCAATAGAATAC
1 TGGGATAAATGTTTCCAAGTATCTTTTGGTTCATACAATTACCAATAGAATAC
32559 TGGGATAAATGTTTCCAAGTATCTTTTGGTTCATACAATTACCAATAGAATAC
1 TGGGATAAATGTTTCCAAGTATCTTTTGGTTCATACAATTACCAATAGAATAC
32612 T
1 T
32613 TTCATATCCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (53 bp):
TGGGATAAATGTTTCCAAGTATCTTTTGGTTCATACAATTACCAATAGAATAC
Found at i:35708 original size:69 final size:71
Alignment explanation
Indices: 35583--35742 Score: 173
Period size: 69 Copynumber: 2.3 Consensus size: 71
35573 GATGATTCAG
* * *
35583 GAGTCTTCAACCCCATCACCGACCGAGGCTTCAACCCCATCACCGACTGAGGCTTCAAGCCAATC
1 GAGTCTTCAACCCCATCTCCGA-CGAGGCTTCAACCCCATCACCAACTGAGGCTTCAACCCAATC
35648 TCCGA-T
65 TCCGACT
* * * * * *
35654 CGAGTCTTCAACCGCATCTCC-A-GAGTCTTCAACCCCATCCCCAATTGAGTCTTCAACCCCATC
1 -GAGTCTTCAACCCCATCTCCGACGAGGCTTCAACCCCATCACCAACTGAGGCTTCAACCCAATC
*
35717 TCTGACT
65 TCCGACT
* *
35724 GAGTCTTCAAACTCATCTC
1 GAGTCTTCAACCCCATCTC
35743 GGAATGAGAA
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
69 55 0.73
70 1 0.01
71 1 0.01
72 18 0.24
ACGTcount: A:0.24, C:0.39, G:0.14, T:0.23
Consensus pattern (71 bp):
GAGTCTTCAACCCCATCTCCGACGAGGCTTCAACCCCATCACCAACTGAGGCTTCAACCCAATCT
CCGACT
Found at i:35740 original size:24 final size:24
Alignment explanation
Indices: 35583--35789 Score: 145
Period size: 24 Copynumber: 8.8 Consensus size: 24
35573 GATGATTCAG
* * **
35583 GAGTCTTCAACCCCATCACCGACC
1 GAGTCTTCAACCCCATCTCGGAAT
* * * *
35607 GAGGCTTCAACCCCATCACCGACT
1 GAGTCTTCAACCCCATCTCGGAAT
* * * *
35631 GAGGCTTCAAGCCAATCTCCG-AT
1 GAGTCTTCAACCCCATCTCGGAAT
* *
35654 CGAGTCTTCAACCGCATCTC--CA-
1 -GAGTCTTCAACCCCATCTCGGAAT
**
35676 GAGTCTTCAACCCCATC-CCCAATT
1 GAGTCTTCAACCCCATCTCGGAA-T
* *
35700 GAGTCTTCAACCCCATCTCTGACT
1 GAGTCTTCAACCCCATCTCGGAAT
* *
35724 GAGTCTTCAAACTCATCTCGGAAT
1 GAGTCTTCAACCCCATCTCGGAAT
**
35748 GAGAATTCAACCCCATCTCGGAAT
1 GAGTCTTCAACCCCATCTCGGAAT
* *
35772 GAGTCTCCAACCTCATCT
1 GAGTCTTCAACCCCATCT
35790 AATAAAAGTT
Statistics
Matches: 149, Mismatches: 27, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
20 1 0.01
21 16 0.11
22 1 0.01
23 2 0.01
24 127 0.85
25 2 0.01
ACGTcount: A:0.26, C:0.37, G:0.14, T:0.23
Consensus pattern (24 bp):
GAGTCTTCAACCCCATCTCGGAAT
Found at i:35757 original size:93 final size:93
Alignment explanation
Indices: 35583--35766 Score: 219
Period size: 93 Copynumber: 2.0 Consensus size: 93
35573 GATGATTCAG
* *
35583 GAGTCTTCAACCCCATCACCGACCGAGGCTTCAACCCCATCACCGACTGAGGCTTCAAGCCAATC
1 GAGTCTTCAACCCCATCACCAACCGAGGCTTCAACCCCATCACCGACTGAGGCTTCAAACCAATC
** *
35648 TCCGATCGAGTCTTCAACCGCATCTCCA
66 TCCGATCGAGAATTCAACCCCATCTCCA
* ** * * * *
35676 GAGTCTTCAACCCCATCCCCAATTGAGTCTTCAACCCCATCTCTGACTGAGTCTTCAAACTC-AT
1 GAGTCTTCAACCCCATCACCAACCGAGGCTTCAACCCCATCACCGACTGAGGCTTCAAAC-CAAT
*
35740 CTCGGAAT-GAGAATTCAACCCCATCTC
65 CTCCG-ATCGAGAATTCAACCCCATCTC
35767 GGAATGAGTC
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
93 73 0.96
94 3 0.04
ACGTcount: A:0.26, C:0.38, G:0.14, T:0.23
Consensus pattern (93 bp):
GAGTCTTCAACCCCATCACCAACCGAGGCTTCAACCCCATCACCGACTGAGGCTTCAAACCAATC
TCCGATCGAGAATTCAACCCCATCTCCA
Found at i:39299 original size:24 final size:24
Alignment explanation
Indices: 39272--39351 Score: 142
Period size: 24 Copynumber: 3.3 Consensus size: 24
39262 AGGTAACTCT
39272 GCTTATCCCGATAAGTGCATGACC
1 GCTTATCCCGATAAGTGCATGACC
39296 GCTTATCCCGATAAGTGCATGACC
1 GCTTATCCCGATAAGTGCATGACC
* *
39320 GCTTATCCCGATAAGTGAATGACT
1 GCTTATCCCGATAAGTGCATGACC
39344 GCTTATCC
1 GCTTATCC
39352 GCTTATCGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (24 bp):
GCTTATCCCGATAAGTGCATGACC
Found at i:39820 original size:20 final size:21
Alignment explanation
Indices: 39796--39844 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
39786 AAGTATAATT
39796 ATAAATTAGTTAAAATAAA-A
1 ATAAATTAGTTAAAATAAATA
* *
39816 GTAAATTATTTAAAATAAATA
1 ATAAATTAGTTAAAATAAATA
39837 ATAAATTA
1 ATAAATTA
39845 TGCTAGTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
ATAAATTAGTTAAAATAAATA
Found at i:41301 original size:16 final size:16
Alignment explanation
Indices: 41280--41310 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41270 TATAAATTAA
*
41280 ATTAATGGTGCTCATT
1 ATTAATAGTGCTCATT
41296 ATTAATAGTGCTCAT
1 ATTAATAGTGCTCAT
41311 CGATAATCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (16 bp):
ATTAATAGTGCTCATT
Found at i:44855 original size:14 final size:16
Alignment explanation
Indices: 44836--44869 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
44826 GCATTAAAAA
44836 AAAATTAAAA-ATA-G
1 AAAATTAAAATATATG
44850 AAAATTAAAATATATG
1 AAAATTAAAATATATG
44866 AAAA
1 AAAA
44870 ACAAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 3 0.17
16 5 0.28
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAATTAAAATATATG
Found at i:48841 original size:27 final size:26
Alignment explanation
Indices: 48745--48846 Score: 66
Period size: 27 Copynumber: 3.8 Consensus size: 26
48735 AATATAATAA
*
48745 ATTA-TTAATA-AAATTTATATTATTT
1 ATTATTTAATATAAA-TAATATTATTT
* *
48770 ATTAATTTTATAGAAATAATATTA-TT
1 ATT-ATTTAATATAAATAATATTATTT
** *
48796 AAAATATTAATAATGAATAATATTATTT
1 ATTAT-TTAAT-ATAAATAATATTATTT
48824 ATGTATTTAATATTAATATAATA
1 AT-TATTTAATA-TAA-ATAATA
48847 ATAATATAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
25 5 0.09
26 8 0.14
27 24 0.41
28 13 0.22
29 8 0.14
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
ATTATTTAATATAAATAATATTATTT
Found at i:48845 original size:11 final size:11
Alignment explanation
Indices: 48831--48909 Score: 56
Period size: 11 Copynumber: 7.2 Consensus size: 11
48821 TTTATGTATT
*
48831 TAATATTAATA
1 TAATAATAATA
48842 TAATAATAATA
1 TAATAATAATA
* *
48853 TAATAATATTT
1 TAATAATAATA
48864 TAA-AATAATA
1 TAATAATAATA
**
48874 CTTTTTAA-AATA
1 --TAATAATAATA
*
48886 TATTTAA-AATA
1 TA-ATAATAATA
48897 TAATAATAATA
1 TAATAATAATA
48908 TA
1 TA
48910 TTTAAAATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
10 9 0.17
11 38 0.70
12 5 0.09
13 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (11 bp):
TAATAATAATA
Found at i:48872 original size:13 final size:13
Alignment explanation
Indices: 48854--48896 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 13
48844 ATAATAATAT
48854 AATAATATTTTAA
1 AATAATATTTTAA
48867 AATAATACTTTTTAA
1 AATAATA--TTTTAA
48882 AAT-ATA-TTTAA
1 AATAATATTTTAA
48893 AATA
1 AATA
48897 TAATAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 8 0.30
13 7 0.26
14 3 0.11
15 9 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
AATAATATTTTAA
Found at i:48908 original size:22 final size:22
Alignment explanation
Indices: 48882--48986 Score: 99
Period size: 22 Copynumber: 4.7 Consensus size: 22
48872 TACTTTTTAA
48882 AATATATTTAAAATATAATAAT
1 AATATATTTAAAATATAATAAT
*
48904 AATATATTTAAAATATATTAAAT
1 AATATATTTAAAATATAAT-AAT
*
48927 AATACTTTTTAAAATAT-ATAAT
1 AATA-TATTTAAAATATAATAAT
* *
48949 ATTATTATTT-TAATA-AATAATT
1 AATA-TATTTAAAATATAATAA-T
* *
48971 AATAAATTTATAATAT
1 AATATATTTAAAATAT
48987 TTTTATTTCA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
21 12 0.18
22 37 0.54
23 8 0.12
24 11 0.16
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
AATATATTTAAAATATAATAAT
Found at i:48926 original size:9 final size:11
Alignment explanation
Indices: 48877--48945 Score: 77
Period size: 11 Copynumber: 6.1 Consensus size: 11
48867 AATAATACTT
48877 TTTAAAATATA
1 TTTAAAATATA
48888 TTTAAAATATA
1 TTTAAAATATA
*
48899 -ATAATAATATA
1 TTTAA-AATATA
48910 TTTAAAATATA
1 TTTAAAATATA
* *
48921 TTAAATAATACTT
1 TTTAA-AATA-TA
48934 TTTAAAATATA
1 TTTAAAATATA
48945 T
1 T
48946 AATATTATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
10 3 0.06
11 29 0.60
12 11 0.23
13 5 0.10
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (11 bp):
TTTAAAATATA
Found at i:48941 original size:57 final size:55
Alignment explanation
Indices: 48838--48945 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 55
48828 ATTTAATATT
* *
48838 AATATAATAATAATATAATAATATTTTAAAATAATACTTTTTAAAATATATTTAA
1 AATATAATAATAATATAAAAATATATTAAAATAATACTTTTTAAAATATATTTAA
48893 AATATAATAATAATATATTTAAAATATATT-AAATAATACTTTTTAAAATATAT
1 AATATAATAATAATATA---AAAATATATTAAAATAATACTTTTTAAAATATAT
48946 AATATTATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
55 17 0.35
57 23 0.48
58 8 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (55 bp):
AATATAATAATAATATAAAAATATATTAAAATAATACTTTTTAAAATATATTTAA
Found at i:48959 original size:24 final size:23
Alignment explanation
Indices: 48882--48959 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 23
48872 TACTTTTTAA
*
48882 AATATATTT-AAA-ATATAATAAT
1 AATATTTTTAAAATATATAAT-AT
*
48904 AATATATTTAAAATATATTAA-AT
1 AATATTTTTAAAATATA-TAATAT
48927 AATACTTTTTAAAATATATAATATT
1 AATA-TTTTTAAAATATATAATA-T
*
48952 ATTATTTT
1 AATATTTT
48960 AATAAATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
22 9 0.19
23 12 0.25
24 20 0.42
25 7 0.15
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (23 bp):
AATATTTTTAAAATATATAATAT
Found at i:50923 original size:19 final size:19
Alignment explanation
Indices: 50899--50935 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
50889 AGCACCGTCG
*
50899 TTCTCAACTCAGCTTCCGT
1 TTCTCAACTCAGATTCCGT
50918 TTCTCAACTCAGATTCCG
1 TTCTCAACTCAGATTCCG
50936 CTTCAAGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.35, G:0.11, T:0.35
Consensus pattern (19 bp):
TTCTCAACTCAGATTCCGT
Found at i:54118 original size:11 final size:11
Alignment explanation
Indices: 54102--54131 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
54092 CACAATCTTC
54102 TTCTTCTTTAT
1 TTCTTCTTTAT
54113 TTCTTCTTTAT
1 TTCTTCTTTAT
54124 TT-TTCTTT
1 TTCTTCTTT
54132 TCATGGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTCTTTAT
Found at i:54648 original size:17 final size:17
Alignment explanation
Indices: 54626--54660 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
54616 AATTATTTTC
54626 AGTTGCCACGACAATCG
1 AGTTGCCACGACAATCG
*
54643 AGTTGCCTCGACAATCG
1 AGTTGCCACGACAATCG
54660 A
1 A
54661 CTACTCAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (17 bp):
AGTTGCCACGACAATCG
Found at i:58737 original size:18 final size:18
Alignment explanation
Indices: 58686--58737 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 18
58676 CGACAATCAA
58686 GCAACTTATTTTATGGTT
1 GCAACTTATTTTATGGTT
* *
58704 G----TCATTTTA-AGTT
1 GCAACTTATTTTATGGTT
58717 GCAACTTATTTTATGGTT
1 GCAACTTATTTTATGGTT
58735 GCA
1 GCA
58738 TCACATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 10
0.64 0.10 0.26
Matches are distributed among these distances:
13 4 0.16
14 7 0.28
17 7 0.28
18 7 0.28
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (18 bp):
GCAACTTATTTTATGGTT
Found at i:58877 original size:17 final size:18
Alignment explanation
Indices: 58845--58893 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
58835 TTTTATTAAA
*
58845 AATATAAATATA-ATTTT
1 AATAAAAATATATATTTT
*
58862 ATTAAAAAT-TATA-TTT
1 AATAAAAATATATATTTT
58878 AATAAAAATATATATT
1 AATAAAAATATATATT
58894 AAAGTATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 13 0.50
17 12 0.46
18 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATAAAAATATATATTTT
Found at i:58883 original size:16 final size:17
Alignment explanation
Indices: 58845--58893 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
58835 TTTTATTAAA
*
58845 AATATAAATATA-ATTTT
1 AATAAAAATATATA-TTT
*
58862 ATTAAAAAT-TATATTT
1 AATAAAAATATATATTT
58878 AATAAAAATATATATT
1 AATAAAAATATATATT
58894 AAAGTATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAAAAATATATATTT
Found at i:58955 original size:53 final size:53
Alignment explanation
Indices: 58852--58951 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
58842 AAAAATATAA
* *
58852 ATATAATTTTATTAAAAATTATATTTAATAAAAATATATATTAAAGTATTTGT
1 ATATAATTTTATTAAAAATTATATTAAATAAAAATATATATAAAAGTATTTGT
*
58905 ATATAAATTTTATTAAAAA-TATA-TAAATTAGAAATA-ATA-AAAAGTAT
1 ATAT-AATTTTATTAAAAATTATATTAAA-TAAAAATATATATAAAAGTAT
58952 ATTTTCAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
51 7 0.17
52 6 0.14
53 15 0.36
54 14 0.33
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (53 bp):
ATATAATTTTATTAAAAATTATATTAAATAAAAATATATATAAAAGTATTTGT
Found at i:59611 original size:12 final size:12
Alignment explanation
Indices: 59596--59637 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
59586 TAATCCATCT
59596 ATTAATTGATTA
1 ATTAATTGATTA
**
59608 ATTAATCCATCT-
1 ATTAATTGAT-TA
59620 ATTAATTGATTA
1 ATTAATTGATTA
59632 ATTAAT
1 ATTAAT
59638 CCAAGCAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (12 bp):
ATTAATTGATTA
Found at i:59613 original size:24 final size:24
Alignment explanation
Indices: 59586--59640 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
59576 TTAGTTCAAC
59586 TAATCCATCTATTAATTGATTAAT
1 TAATCCATCTATTAATTGATTAAT
59610 TAATCCATCTATTAATTGATTAAT
1 TAATCCATCTATTAATTGATTAAT
59634 TAATCCA
1 TAATCCA
59641 AGCAATGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.44
Consensus pattern (24 bp):
TAATCCATCTATTAATTGATTAAT
Found at i:59746 original size:2 final size:2
Alignment explanation
Indices: 59739--59776 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
59729 ACCTTCATTC
59739 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
59777 GACCCTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.