Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008917.1 Hibiscus syriacus cultivar Beakdansim tig00112221_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: 766343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:750821 original size:6 final size:6
Alignment explanation
Indices: 750810--750844 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
750800 CACGTATTAT
750810 CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
750845 TACGAGACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:751332 original size:5 final size:5
Alignment explanation
Indices: 751326--751441 Score: 151
Period size: 5 Copynumber: 22.0 Consensus size: 5
751316 GCCGTCCGTC
* * *
751326 TCGTC TCGTC TCGTC TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG
1 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG
751376 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTG TCGTG TCGTG TCGTG TCGTG TCGT-G TCGT-G TCGT-G TCGT-G
751425 TCGTGG TCGTGG TCGTG
1 TCGT-G TCGT-G TCGTG
751442 GTAATACGTG
Statistics
Matches: 109, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
5 74 0.68
6 35 0.32
ACGTcount: A:0.00, C:0.22, G:0.41, T:0.38
Consensus pattern (5 bp):
TCGTG
Found at i:751641 original size:21 final size:21
Alignment explanation
Indices: 751615--751657 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
751605 TTGCGATAAC
751615 GCGAACTTCGACTATCGCATT
1 GCGAACTTCGACTATCGCATT
751636 GCGAACTTCGACTATCGCATT
1 GCGAACTTCGACTATCGCATT
751657 G
1 G
751658 TGATTTACAT
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:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCATT
Found at i:751695 original size:21 final size:21
Alignment explanation
Indices: 751669--751723 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
751659 GATTTACATA
751669 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
751690 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
751711 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
751724 TCTGGAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:757486 original size:42 final size:42
Alignment explanation
Indices: 757439--757557 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
757429 TTCCCCGAAA
* * *
757439 TCCCGTGTTTGTTTTATGCAATTCGTTTTCCGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
*
757481 TCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
*
757523 TCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAA
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
757558 TGTAATTCAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.46
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
Found at i:757756 original size:21 final size:23
Alignment explanation
Indices: 757713--757763 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
757703 CATTTTCATC
757713 AAAATATTATTTATTAAAATATTT
1 AAAATATTATTTATT-AAATATTT
757737 AAAATA-TATTTATT-AATATTT
1 AAAATATTATTTATTAAATATTT
757758 AAAATA
1 AAAATA
757764 ATATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.48
23 8 0.30
24 6 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATATTATTTATTAAATATTT
Found at i:757756 original size:29 final size:28
Alignment explanation
Indices: 757724--757786 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
757714 AAATATTATT
*
757724 TATTAAAATATTTAAAATA-TATTTATTAA
1 TATTAAAATA-ATAAAATATTATTT-TTAA
*
757753 TATTTAAAATAATATAATATTATTTTTAA
1 TA-TTAAAATAATAAAATATTATTTTTAA
757782 TATTA
1 TATTA
757787 TATAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.10
29 14 0.47
30 13 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TATTAAAATAATAAAATATTATTTTTAA
Found at i:757772 original size:53 final size:53
Alignment explanation
Indices: 757715--757822 Score: 132
Period size: 53 Copynumber: 2.0 Consensus size: 53
757705 TTTTCATCAA
* **
757715 AATATTATTTATTAA-AATATTTAAAATATATTTATTAATATT-TAA-AATAATAT
1 AATATTATTT-TTAATAATATATAAAATA-ATCAATT-ATATTATAATAATAATAT
*
757768 AATATTATTTTTAATATTATATAAAATAATCAATTATATTATAATAATAATAT
1 AATATTATTTTTAATAATATATAAAATAATCAATTATATTATAATAATAATAT
757821 AA
1 AA
757823 GATATTATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
51 5 0.10
52 12 0.25
53 31 0.65
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (53 bp):
AATATTATTTTTAATAATATATAAAATAATCAATTATATTATAATAATAATAT
Found at i:757780 original size:22 final size:22
Alignment explanation
Indices: 757730--757791 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
757720 TATTTATTAA
*
757730 AATATTTAAAATATAT-TTATT
1 AATATTTAAAATATATAATATT
757751 AATATTTAAAATAATATAATATT
1 AATATTTAAAAT-ATATAATATT
* *
757774 -ATTTTTAATATTATATAA
1 AATATTTAA-AATATATAA
757792 AATAATCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 12 0.34
22 17 0.49
23 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTAAAATATATAATATT
Found at i:757795 original size:29 final size:30
Alignment explanation
Indices: 757749--757853 Score: 81
Period size: 31 Copynumber: 3.5 Consensus size: 30
757739 AATATATTTA
*
757749 TTAATATT-TAAAATAATATAATATTAT-TT
1 TTAATATTATATAA-AATATAATATTATATT
*
757778 TTAATATTATATAAAATAATCA-ATTATATT
1 TTAATATTATATAAAAT-ATAATATTATATT
* * * * *
757808 ATAATAATAATATAAGATATTATATTTTTATT
1 TTAAT-ATTATATAAAATATAATA-TTATATT
*
757840 TTAATAATATATAA
1 TTAATATTATATAA
757854 TAATTTTTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
29 16 0.27
30 16 0.27
31 18 0.30
32 10 0.17
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (30 bp):
TTAATATTATATAAAATATAATATTATATT
Found at i:757851 original size:24 final size:25
Alignment explanation
Indices: 757819--757885 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 25
757809 TAATAATAAT
*
757819 ATAAGATATTATATTTTTAT-TTTA
1 ATAATATATTATATTTTTATATTTA
*
757843 ATAATATATAATAATTTTTTTATATTTA
1 ATAATATAT--T-ATATTTTTATATTTA
757871 ATAATGA-ATTATATT
1 ATAAT-ATATTATATT
757886 ATGAGAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
24 8 0.23
25 4 0.11
26 2 0.06
27 9 0.26
28 11 0.31
29 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (25 bp):
ATAATATATTATATTTTTATATTTA
Found at i:757868 original size:29 final size:33
Alignment explanation
Indices: 757801--757875 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 33
757791 AAATAATCAA
*
757801 TTATATTATAATAATAATATAAGATATTATATT
1 TTATATTTTAATAATAATATAAGATATTATATT
*
757834 TT-TATTTTAATAAT-ATATAATA-ATT-T-TT
1 TTATATTTTAATAATAATATAAGATATTATATT
757862 TTATA-TTTAATAAT
1 TTATATTTTAATAAT
757876 GAATTATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 13 0.33
29 3 0.08
30 3 0.08
31 7 0.18
32 11 0.28
33 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (33 bp):
TTATATTTTAATAATAATATAAGATATTATATT
Found at i:758119 original size:20 final size:20
Alignment explanation
Indices: 758094--758362 Score: 294
Period size: 20 Copynumber: 13.4 Consensus size: 20
758084 GATTTTCCAT
* ** *
758094 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
758114 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
758134 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
758154 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
758174 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
758194 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
758214 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
758234 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
758254 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
758274 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
758294 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
758314 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
758334 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
758354 AATCACAAC
1 AATCGCAAC
758363 ACTGAAATTT
Statistics
Matches: 213, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.01
20 207 0.97
21 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:759071 original size:24 final size:24
Alignment explanation
Indices: 759032--759078 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
759022 AAATTTGGTC
759032 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
759056 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
759079 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:761590 original size:19 final size:19
Alignment explanation
Indices: 761568--761873 Score: 349
Period size: 19 Copynumber: 17.4 Consensus size: 19
761558 CGGAAAATAC
*
761568 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
761587 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
761601 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
761621 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
761635 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
761653 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
761672 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
761686 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
761705 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
761724 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
761738 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
761757 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
761776 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
761795 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
761814 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
761828 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
761847 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
761866 AATCGCAA
1 AATCGCAA
761874 CGAGATAATC
Statistics
Matches: 247, Mismatches: 13, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 16 0.06
17 15 0.06
18 22 0.09
19 132 0.53
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:761640 original size:14 final size:15
Alignment explanation
Indices: 761621--761698 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 15
761611 CGGAAATGAA
761621 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
*
761635 AATCGCAATGCGAAATG
1 AATCGCAA-GCGAGA-G
*
761652 AAATCGCAATGCGAAATGAA
1 -AATCGCAA-GCG--A-GAG
761672 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
761686 AATCGCAATGCGA
1 AATCGCAA-GCGA
761699 AATGAAAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.14
17 3 0.06
18 12 0.24
19 8 0.16
20 1 0.02
21 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (15 bp):
AATCGCAAGCGAGAG
Found at i:761693 original size:33 final size:33
Alignment explanation
Indices: 761652--761854 Score: 180
Period size: 33 Copynumber: 5.8 Consensus size: 33
761642 ATGCGAAATG
761652 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
* * *
761685 GAATCGCAATGCGAAATGAAAATCGCAATGCG-
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
* ** *
761717 AAAT-GAAAAT-CGAACCGACATAATCGCAATGCGAAATTA
1 AAATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GA
*
761756 AAATCGCAATACGAAATGAAAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GA
761794 AAATCGCAATGCGAAATGAAAATCGCAACGA-A
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
761826 AGAATCGCAATGCGAAATGAAAATCGCAA
1 A-AATCGCAATGCGAAATGAAAATCGCAA
761855 TGCGAAATGA
Statistics
Matches: 143, Mismatches: 15, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
31 7 0.05
32 9 0.06
33 64 0.45
34 1 0.01
35 1 0.01
36 2 0.01
38 44 0.31
39 8 0.06
40 7 0.05
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGA
Found at i:761708 original size:52 final size:53
Alignment explanation
Indices: 761596--761873 Score: 349
Period size: 52 Copynumber: 5.2 Consensus size: 53
761586 AAATCCCAAC
*
761596 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
761649 ATG-AAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
761700 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
761752 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
761809 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
761861 ATGAAAATCGCAA
1 ATGAAAATCGCAA
761874 CGAGATAATC
Statistics
Matches: 210, Mismatches: 8, Indels: 15
0.90 0.03 0.06
Matches are distributed among these distances:
51 41 0.20
52 128 0.61
53 5 0.02
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:761771 original size:71 final size:71
Alignment explanation
Indices: 761568--761911 Score: 314
Period size: 71 Copynumber: 4.9 Consensus size: 71
761558 CGGAAAATAC
* * *
761568 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA-AATCGCAATGCGGAAATGAAAATCGCAA--
1 AATCGCAATGCGAAATGAAAATCGCAACGA--AATAATCGCAATGC-GAAATTAAAATCGCAATG
*
761629 CG--A-GAG
63 CGAAATGAA
* *
761635 AATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAAT---AATCGCAATGCGAAATTAAAATCGCAA
761694 TGCGAAATGAA
61 TGCGAAATGAA
* *
761705 AATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTAAAATCGCAATACG
1 AATCGCAATGCGAAATGAAAATCGCAA-CGAAATAATCGCAATGCGAAATTAAAATCGCAATGCG
761769 AAATGAA
65 AAATGAA
*
761776 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAAT---AATCGCAATGCGAAATTAAAATCGCAA
761836 TGCGAAATGAA
61 TGCGAAATGAA
* *
761847 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAAATTA-AAATCGCAATGCG
761911 A
65 A
761912 TTTTCATTTC
Statistics
Matches: 232, Mismatches: 16, Indels: 54
0.77 0.05 0.18
Matches are distributed among these distances:
65 10 0.04
66 25 0.11
67 20 0.09
68 6 0.03
69 15 0.06
70 22 0.09
71 113 0.49
72 4 0.02
73 7 0.03
74 2 0.01
76 8 0.03
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAAATTAAAATCGCAATGCGA
AATGAA
Found at i:761821 original size:142 final size:136
Alignment explanation
Indices: 761568--761905 Score: 486
Period size: 142 Copynumber: 2.4 Consensus size: 136
761558 CGGAAAATAC
* * * *
761568 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAAC-CGAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
761631 AGAGAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATG
63 AGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATG
761696 CGAAATGAA
128 CGAAATGAA
761705 AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACCGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
761770 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 -A-GAAAATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
761835 ATGCGAAATGAA
125 ATGCGAAATGAA
761847 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACCGA-ATAATCGCAATGCGAAATTA-AAATCGCA
761906 TTGCGATTTT
Statistics
Matches: 184, Mismatches: 7, Indels: 15
0.89 0.03 0.07
Matches are distributed among these distances:
135 2 0.01
136 18 0.10
137 33 0.18
138 3 0.02
140 1 0.01
141 19 0.10
142 103 0.56
143 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (136 bp):
AATCGCAATGCGAAATGAAAATCGAACCGAATAATCGCAATGCGAAATTAAAATCGCAAACGAGA
AAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:762011 original size:19 final size:19
Alignment explanation
Indices: 761902--762003 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
761892 AAATTATAAA
761902 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
761921 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
761941 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
761957 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
761974 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
761993 CGCATTGCGAT
1 CGCATTGCGAT
762004 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:762129 original size:14 final size:14
Alignment explanation
Indices: 762110--762146 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
762100 CATCAATTAC
762110 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
762124 ACAAATCATCTTTT
1 ACAAATCAACTTTT
762138 ACAAATCAA
1 ACAAATCAA
762147 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:762175 original size:38 final size:38
Alignment explanation
Indices: 762127--762199 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
762117 AACTTTTACA
*
762127 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
762165 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
762200 CAATCAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:762217 original size:52 final size:51
Alignment explanation
Indices: 762113--762227 Score: 137
Period size: 52 Copynumber: 2.2 Consensus size: 51
762103 CAATTACACA
* **
762113 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCATATTAAACAAATCAA-TAAACAATCAAAAATTG
762165 AATCAACTTTTACAAATCA-ATTAAAC-AATCAA-AAACAATCAATTAACTATTG
1 AATCAACTTTTACAAATCATATTAAACAAATCAATAAACAATCAA--AA--ATTG
762217 AATCAACTTTT
1 AATCAACTTTT
762228 GCAGCTCGAC
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
48 10 0.18
50 8 0.14
51 4 0.07
52 34 0.61
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (51 bp):
AATCAACTTTTACAAATCATATTAAACAAATCAATAAACAATCAAAAATTG
Found at i:764076 original size:14 final size:14
Alignment explanation
Indices: 764057--764113 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
764047 GCGAAATGAA
*
764057 AATCGCAACGACAG
1 AATCGCAACGAAAG
764071 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
764088 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
764104 AATCGCAACG
1 AATCGCAACG
764114 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:764084 original size:33 final size:33
Alignment explanation
Indices: 764038--764130 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
764028 GCGAAACCAA
*
764038 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
764071 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
764104 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
764131 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:764095 original size:19 final size:19
Alignment explanation
Indices: 764001--764135 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
763991 TAGTTTACTT
* *
764001 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
764021 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
764040 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
764059 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
764073 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
764092 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
764106 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
764125 TCGCAATGCGA
1 TCGCAACGCGA
764136 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:764153 original size:19 final size:19
Alignment explanation
Indices: 764131--764259 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
764121 AAAATCGCAA
764131 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
764150 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
764164 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
764183 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
764197 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
764216 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
764235 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
764255 TGCGA
1 TGCGA
764260 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:764173 original size:33 final size:33
Alignment explanation
Indices: 764131--764222 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
764121 AAAATCGCAA
764131 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
764164 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
764197 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
764223 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:764589 original size:92 final size:93
Alignment explanation
Indices: 764303--764661 Score: 644
Period size: 93 Copynumber: 3.9 Consensus size: 93
764293 TTGAATGGAT
764303 AAATTTACTTTCAACC-AAA-ACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
764366 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
764394 AAATTTACTTTCAACCAAAAGACAAAAC-AA-ACAAATACTATATTTCACAGTGTTAAAGAATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC--TATTTCACAGTGTTAAAGAATAC
764457 ACAGTTTAGCAGAATTGGCAGCAACCGAAC
64 ACAGTTTAGCAGAATTGGCAGCAACCGAAC
764487 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
764551 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
764579 AAATTTACTTTCAACCAAAAGAC-AAA-AAAGACAAATACTATTTCACAGTGTTAAAG-ATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
764641 AGTTTAGCAGAATTGGCAGCA
66 AGTTTAGCAGAATTGGCAGCA
764662 TTACTAAGCA
Statistics
Matches: 261, Mismatches: 0, Indels: 15
0.95 0.00 0.05
Matches are distributed among these distances:
90 38 0.15
91 45 0.17
92 81 0.31
93 88 0.34
94 2 0.01
95 7 0.03
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:764615 original size:185 final size:181
Alignment explanation
Indices: 764303--764661 Score: 650
Period size: 185 Copynumber: 2.0 Consensus size: 181
764293 TTGAATGGAT
764303 AAATTTACTTTCAACCAAAACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
1 AAATTTACTTTCAACCAAAACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
764368 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAACAAATACT
66 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAACAAATAC-
764433 ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130 -TATTTCACAGTGTTAAAG-ATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
764487 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACC-AAA-ACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
764551 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA-AAGACAAAT
64 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAA-ACAAAT
764615 ACTATTTCACAGTGTTAAAGATACACAGTTTAGCAGAATTGGCAGCA
128 ACTATTTCACAGTGTTAAAGATACACAGTTTAGCAGAATTGGCAGCA
764662 TTACTAAGCA
Statistics
Matches: 172, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
182 27 0.16
183 18 0.10
184 18 0.10
185 91 0.53
186 18 0.10
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (181 bp):
AAATTTACTTTCAACCAAAACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAACAAATACT
ATTTCACAGTGTTAAAGATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Done.