Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005639.1 Hibiscus syriacus cultivar Beakdansim tig00013144_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: 74359
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2104 original size:63 final size:63
Alignment explanation
Indices: 2037--2163 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
2027 TACAAACGTT
2037 ATAATTTTTAATTATAACGAGATTAAAAAAATCTTATCAAGTGACAATCTATTAATATAAAAA
1 ATAATTTTTAATTATAACGAGATTAAAAAAATCTTATCAAGTGACAATCTATTAATATAAAAA
2100 ATAATTTTTAATTATAACGAGATTAAAAAAATCTTATCAAGTGACAATCTATTAATATAAAAA
1 ATAATTTTTAATTATAACGAGATTAAAAAAATCTTATCAAGTGACAATCTATTAATATAAAAA
2163 A
1 A
2164 AATGTAGACC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (63 bp):
ATAATTTTTAATTATAACGAGATTAAAAAAATCTTATCAAGTGACAATCTATTAATATAAAAA
Found at i:2641 original size:30 final size:30
Alignment explanation
Indices: 2607--2665 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
2597 AAGAGTTATA
* *
2607 CTTACTTTTACTGTTTTTTATCACATTCTT
1 CTTACATTTACTGTTTTTAATCACATTCTT
2637 CTTACATTTACTGTTTTTAATCACATTCT
1 CTTACATTTACTGTTTTTAATCACATTCT
2666 AACCCGTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.56
Consensus pattern (30 bp):
CTTACATTTACTGTTTTTAATCACATTCTT
Found at i:2957 original size:14 final size:14
Alignment explanation
Indices: 2940--2966 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2930 CCATCAGATA
2940 TCTTATATTATTAC
1 TCTTATATTATTAC
2954 TCTTATATTATTA
1 TCTTATATTATTA
2967 TCGGAATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (14 bp):
TCTTATATTATTAC
Found at i:5258 original size:10 final size:10
Alignment explanation
Indices: 5243--5272 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5233 TTTCGTTCTA
*
5243 ATTTCATTGT
1 ATTTCATGGT
5253 ATTTCATGGT
1 ATTTCATGGT
5263 ATTTCATGGT
1 ATTTCATGGT
5273 TTTACCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.53
Consensus pattern (10 bp):
ATTTCATGGT
Found at i:8353 original size:29 final size:30
Alignment explanation
Indices: 8295--8369 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 30
8285 GGGGCTGGAT
*
8295 TGCATGGCGACCTACCTAGGTTGTTGGGCG
1 TGCATGGCGACCTACCTAGGTCGTTGGGCG
**
8325 TGCATGGCGACCT-GGTAGGTCGTTGGGCG
1 TGCATGGCGACCTACCTAGGTCGTTGGGCG
8354 TGCATGGCGACCTACC
1 TGCATGGCGACCTACC
8370 CTATCTAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 26 0.67
30 13 0.33
ACGTcount: A:0.13, C:0.25, G:0.37, T:0.24
Consensus pattern (30 bp):
TGCATGGCGACCTACCTAGGTCGTTGGGCG
Found at i:8417 original size:14 final size:14
Alignment explanation
Indices: 8398--8426 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8388 CGGAGCACCT
8398 GGCGACCTATATGA
1 GGCGACCTATATGA
8412 GGCGACCTATATGA
1 GGCGACCTATATGA
8426 G
1 G
8427 CAATTAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (14 bp):
GGCGACCTATATGA
Found at i:9760 original size:23 final size:23
Alignment explanation
Indices: 9734--9779 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
9724 GCCATCTGAC
** *
9734 CGAGGCCATTCGAGCGAGCTATG
1 CGAGGCCAGCCGAACGAGCTATG
*
9757 CGAGGGCAGCCGAACGAGCTATG
1 CGAGGCCAGCCGAACGAGCTATG
9780 TAAGGGAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.37, T:0.13
Consensus pattern (23 bp):
CGAGGCCAGCCGAACGAGCTATG
Found at i:20481 original size:21 final size:21
Alignment explanation
Indices: 20452--20496 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
20442 AATATGTAAA
20452 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
20473 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
20494 TCG
1 TCG
20497 TAACGCGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:20504 original size:21 final size:21
Alignment explanation
Indices: 20387--20520 Score: 78
Period size: 20 Copynumber: 6.6 Consensus size: 21
20377 AAATGACCAA
* *
20387 CAAATTCGCAACGTGA-ATTC
1 CAAATTCGCAACGCGATTTTC
* * *
20407 CAATTTCGCAAC-CAAGTTTC
1 CAAATTCGCAACGCGATTTTC
* * * *
20427 CAATTTCGCAACGCGAATATG
1 CAAATTCGCAACGCGATTTTC
* **
20448 TAAA-TCGCATTGCGATTTTC
1 CAAATTCGCAACGCGATTTTC
***
20468 CAAATTCGCGTTGCGATTTTC
1 CAAATTCGCAACGCGATTTTC
* **
20489 CAAATTCGTAACGCGATAGT-
1 CAAATTCGCAACGCGATTTTC
20509 CAAATTCGCAAC
1 CAAATTCGCAAC
20521 ACGAAAGTCA
Statistics
Matches: 87, Mismatches: 24, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
19 1 0.01
20 51 0.59
21 35 0.40
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (21 bp):
CAAATTCGCAACGCGATTTTC
Found at i:20514 original size:20 final size:20
Alignment explanation
Indices: 20489--20541 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
20479 TGCGATTTTC
* * *
20489 CAAATTCGTAACGCGATAGT
1 CAAATTCGCAACACGAAAGT
20509 CAAATTCGCAACACGAAAGT
1 CAAATTCGCAACACGAAAGT
20529 CAAATTCGCAACA
1 CAAATTCGCAACA
20542 GGTTTTAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACACGAAAGT
Found at i:21460 original size:24 final size:24
Alignment explanation
Indices: 21433--21486 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
21423 GTATTCGAAA
21433 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
21457 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
21481 TTTGAT
1 TTTGAT
21487 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:21669 original size:3 final size:3
Alignment explanation
Indices: 21661--21700 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
21651 ATATAACCCT
* *
21661 GAA GAA GAA GAA AAA GAA AAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
21701 TCCCCGAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:24271 original size:25 final size:25
Alignment explanation
Indices: 24243--24294 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
24233 AACAAATCAA
*
24243 TTAAACATTATTGTGGGTACATTAT
1 TTAAACATTATTATGGGTACATTAT
*
24268 TTAAACATTGTTATGGGTACATTAT
1 TTAAACATTATTATGGGTACATTAT
24293 TT
1 TT
24295 GGAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (25 bp):
TTAAACATTATTATGGGTACATTAT
Found at i:24690 original size:24 final size:25
Alignment explanation
Indices: 24663--24725 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
24653 TTTCAAATTC
*
24663 ATTTCATATGT-AATTGGAGTTTAA
1 ATTTCAAATGTAAATTGGAGTTTAA
* * *
24687 ATTT-AAATTTAAATTTGAGTTTGA
1 ATTTCAAATGTAAATTGGAGTTTAA
*
24711 ATTTC-AATATAAATT
1 ATTTCAAATGTAAATT
24726 TCGGCTCCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (25 bp):
ATTTCAAATGTAAATTGGAGTTTAA
Found at i:24726 original size:24 final size:24
Alignment explanation
Indices: 24674--24726 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
24664 TTTCATATGT
* *
24674 AATTGGAGTTTAAATTTAAATTTA
1 AATTTGAGTTTAAATTTAAATATA
* *
24698 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTAAATTTAAATATA
24722 AATTT
1 AATTT
24727 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTAAATTTAAATATA
Found at i:25073 original size:39 final size:39
Alignment explanation
Indices: 25030--25116 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
25020 TCCGATGCTC
*
25030 ATCAAAATCCAAAACTCATATGTTGCCAAGCAAAAGAAA
1 ATCAAAATCCAAAACTCATATGGTGCCAAGCAAAAGAAA
* *
25069 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAACTCATATGGTGCCAAGCAAAAGAAA
25108 ATCAAAATC
1 ATCAAAATC
25117 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAACTCATATGGTGCCAAGCAAAAGAAA
Found at i:25333 original size:20 final size:20
Alignment explanation
Indices: 25284--25326 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
25274 ATGTTGCGAT
*
25284 CAACGCGAAAGTTAAATTCG
1 CAACGCGAAAGTCAAATTCG
25304 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
25324 CAA
1 CAA
25327 ACCGAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:28663 original size:13 final size:13
Alignment explanation
Indices: 28645--28676 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28635 GGGTTTTTTC
28645 AACAAAAAGACAA
1 AACAAAAAGACAA
*
28658 AACAAAAAGGCAA
1 AACAAAAAGACAA
28671 AACAAA
1 AACAAA
28677 GACAAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.75, C:0.16, G:0.09, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:28915 original size:22 final size:22
Alignment explanation
Indices: 28885--28931 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
28875 GATGGAGATA
*
28885 GACGGATTTCGTCAGAAATGGG
1 GACGAATTTCGTCAGAAATGGG
* *
28907 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGTCAGAAATGGG
28929 GAC
1 GAC
28932 AGATGTCGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (22 bp):
GACGAATTTCGTCAGAAATGGG
Found at i:29088 original size:20 final size:20
Alignment explanation
Indices: 29063--29102 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29053 TCGTAAAAAC
29063 ATTTGACTTTTGCGTTGCGA
1 ATTTGACTTTTGCGTTGCGA
*
29083 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTTTTGCGTTGCGA
29103 TTTACAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.47
Consensus pattern (20 bp):
ATTTGACTTTTGCGTTGCGA
Found at i:29163 original size:20 final size:20
Alignment explanation
Indices: 29109--29184 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
29099 GCGATTTACA
*
29109 AATTCACGTTGCGAAATTGG
1 AATTCGCGTTGCGAAATTGG
* *
29129 AA-ACTGGGTTGCGAAATTGG
1 AATTC-GCGTTGCGAAATTGG
* *
29149 AATTCGCGTTACG-AATTTG
1 AATTCGCGTTGCGAAATTGG
29168 AGA-TCGCGTTGC-AAATT
1 A-ATTCGCGTTGCGAAATT
29185 TGTTGGTCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
19 19 0.43
20 24 0.55
21 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.30
Consensus pattern (20 bp):
AATTCGCGTTGCGAAATTGG
Found at i:29706 original size:31 final size:33
Alignment explanation
Indices: 29639--29706 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
29629 TTAAGTAACG
29639 TTTAATATTAACATTTTTAATAGAAAAATAATAT
1 TTTAATATTAACATTTTTAATA-AAAAATAATAT
29673 TTTAATATTAACA-TTTTAAGT-AAAAA-AATAT
1 TTTAATATTAACATTTTTAA-TAAAAAATAATAT
29704 TTT
1 TTT
29707 CTGTCACCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
31 8 0.24
32 5 0.15
33 6 0.18
34 14 0.42
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (33 bp):
TTTAATATTAACATTTTTAATAAAAAATAATAT
Found at i:29887 original size:29 final size:29
Alignment explanation
Indices: 29842--29899 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
29832 GTGTTGGCCG
*
29842 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
29871 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
29900 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:29952 original size:10 final size:10
Alignment explanation
Indices: 29939--29989 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 10
29929 ACACGCTAGG
29939 CATCCGAGGC
1 CATCCGAGGC
29949 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
29963 CATCCGAGAG-
1 CATCCGAG-GC
29973 CATCCGAGGC
1 CATCCGAGGC
29983 CATCCGA
1 CATCCGA
29990 ACGAACTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
9 1 0.03
10 21 0.60
11 3 0.09
13 2 0.06
14 8 0.23
ACGTcount: A:0.24, C:0.39, G:0.27, T:0.10
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:29961 original size:14 final size:14
Alignment explanation
Indices: 29942--29969 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29932 CGCTAGGCAT
29942 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
29956 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
29970 GAGCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:30014 original size:33 final size:33
Alignment explanation
Indices: 29937--30047 Score: 132
Period size: 33 Copynumber: 3.3 Consensus size: 33
29927 CAACACGCTA
* * *
29937 GGCATCCGAGGCCATCCGACCGAGGCCATCCGAG
1 GGCATCCGAGGCCATCCGAACGA-GCTATGCGAG
* *
29971 AGCATCCGAGGCCATCCGAACGAACTATGCGAG
1 GGCATCCGAGGCCATCCGAACGAGCTATGCGAG
* * *
30004 GGCATCCGAGGGCAACCGAGCGAGCTATGCGAG
1 GGCATCCGAGGCCATCCGAACGAGCTATGCGAG
*
30037 GGAATCCGAGG
1 GGCATCCGAGG
30048 GAAACCGAGC
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
33 45 0.68
34 21 0.32
ACGTcount: A:0.25, C:0.31, G:0.34, T:0.10
Consensus pattern (33 bp):
GGCATCCGAGGCCATCCGAACGAGCTATGCGAG
Found at i:30048 original size:33 final size:33
Alignment explanation
Indices: 29974--30060 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
29964 ATCCGAGAGC
* * * * *
29974 ATCCGAGGCCATCCGAACGAACTATGCGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
30007 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
*
30040 ATCCGAGGGAAACCGAGCGAG
1 ATCCGAGGGCAACCGAGCGAG
30061 GGTAGGTCGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.29, C:0.26, G:0.36, T:0.09
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
Found at i:33087 original size:12 final size:12
Alignment explanation
Indices: 33070--33094 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33060 TATTAAATAA
33070 TAATAATATTTT
1 TAATAATATTTT
33082 TAATAATATTTT
1 TAATAATATTTT
33094 T
1 T
33095 TTTATCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAATAATATTTT
Found at i:36581 original size:15 final size:15
Alignment explanation
Indices: 36561--36666 Score: 57
Period size: 15 Copynumber: 7.5 Consensus size: 15
36551 TATCGATGAT
36561 TTTTTATAGAAATAA
1 TTTTTATAGAAATAA
**
36576 TTTTTATTTAAAT-A
1 TTTTTATAGAAATAA
* *
36590 -TATTATCG--ATGAA
1 TTTTTATAGAAAT-AA
36603 TTTTTATAGAAATAA
1 TTTTTATAGAAATAA
**
36618 TTTTTATTTAAAT-A
1 TTTTTATAGAAATAA
* *
36632 -TATTATCG--ATGAA
1 TTTTTATAGAAAT-AA
*
36645 TTTTTATATAAATAA
1 TTTTTATAGAAATAA
36660 TTTTTAT
1 TTTTTAT
36667 TTAAATATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 20
0.65 0.15 0.20
Matches are distributed among these distances:
11 4 0.06
13 12 0.18
14 13 0.20
15 33 0.50
16 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTTTATAGAAATAA
Found at i:36592 original size:42 final size:42
Alignment explanation
Indices: 36544--36674 Score: 244
Period size: 42 Copynumber: 3.1 Consensus size: 42
36534 ATAATAAAGT
*
36544 AATATATTATCGATGATTTTTTATAGAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
36586 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
*
36628 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
36670 AATAT
1 AATAT
36675 TTAGAATTCA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (42 bp):
AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
Found at i:38890 original size:16 final size:16
Alignment explanation
Indices: 38845--38891 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
38835 GTTTACTTCA
*
38845 AAATGATTAAG-CGCT
1 AAATGATTAAGATGCT
38860 AAATGATTCAA-ATGCT
1 AAATGATT-AAGATGCT
*
38876 GAATGATTAAGATGCT
1 AAATGATTAAGATGCT
38892 CTGTATGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (16 bp):
AAATGATTAAGATGCT
Found at i:49272 original size:21 final size:21
Alignment explanation
Indices: 49192--49273 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
49182 CGCAAATCAG
*
49192 TTTCCATATTCGCAACGCGAT
1 TTTCCATATTCGCAATGCGAT
* *
49213 TAT-GACTA-TCGCAATGCGAT
1 TTTCCA-TATTCGCAATGCGAT
* **
49233 TTTCCATTTTCGCGTTGCGAT
1 TTTCCATATTCGCAATGCGAT
49254 TTTCCCA-ATTCGCAATGCGA
1 TTT-CCATATTCGCAATGCGA
49274 ATAAGTAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
20 15 0.33
21 28 0.61
22 3 0.07
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (21 bp):
TTTCCATATTCGCAATGCGAT
Found at i:49288 original size:20 final size:21
Alignment explanation
Indices: 49263--49314 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
49253 TTTTCCCAAT
*
49263 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
49283 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
49304 TCGCAATGCGA
1 TCGCAATGCGA
49315 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:49293 original size:41 final size:41
Alignment explanation
Indices: 49248--49540 Score: 195
Period size: 41 Copynumber: 7.2 Consensus size: 41
49238 ATTTTCGCGT
* *
49248 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* *** * *
49289 TGCGAATTTGGAAAATCGCAATGCG-ATAC-TGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGT-A-AATCGCAA
* * * * **
49330 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATACGTAAATCGCAA
*
49371 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* *** *
49412 CGCGA-TTAAGTAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* *** * * *
49452 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TACGTAAATCGCAA
* * * * * *
49493 TGCGA-ATACGTAAATCGCAATGCGAAT-CTTACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTA-AATCGCAA
49533 TGCGATTT
1 TGCGATTT
49541 ACATAGCGCC
Statistics
Matches: 202, Mismatches: 41, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
39 2 0.01
40 79 0.39
41 117 0.58
43 3 0.01
44 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
Found at i:49358 original size:21 final size:21
Alignment explanation
Indices: 49324--49396 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
49314 ATACTGACTA
* *
49324 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
49345 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
49365 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
49386 TCGCAATGCGA
1 TCGCAATGCGA
49397 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:49411 original size:20 final size:20
Alignment explanation
Indices: 49386--49537 Score: 189
Period size: 20 Copynumber: 7.5 Consensus size: 20
49376 TTTTCATAAT
49386 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
49406 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
49426 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
49446 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
49466 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
49487 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
49507 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
49527 TCGCAATGCGA
1 TCGCAATGCGA
49538 TTTACATAGC
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
19 3 0.03
20 92 0.81
21 18 0.16
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:49430 original size:40 final size:40
Alignment explanation
Indices: 49386--49519 Score: 214
Period size: 40 Copynumber: 3.3 Consensus size: 40
49376 TTTTCATAAT
49386 TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
49426 TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
* * * * *
49466 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAA
49507 TCGCAATGCGAAT
1 TCGCAATGCGAAT
49520 CTTACTATCG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 53 0.60
41 35 0.40
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
Found at i:49436 original size:61 final size:62
Alignment explanation
Indices: 49263--49519 Score: 204
Period size: 61 Copynumber: 4.2 Consensus size: 62
49253 TTTTCCCAAT
* * *
49263 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACT--A
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATATTCA-TAAA
*** * * * * * * ** * *
49324 TCGCAATGC-AATTTTCCTAATTCGCATTGCGATTTACG-TATTCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGAA--TAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATATTCATAAA
* * * * * *
49386 TCGCAATGCGAATACGTAAATCGCAACGCG-ATTAAGTAAATCGCAATGCGA-ATACGTAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATATTCATAAA
* * * *
49446 TCGCAACGCGATTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGA-ATACGTAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATATTCATAAA
49507 TCGCAATGCGAAT
1 TCGCAATGCGAAT
49520 CTTACTATCG
Statistics
Matches: 150, Mismatches: 39, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
60 38 0.25
61 84 0.56
62 26 0.17
63 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (62 bp):
TCGCAATGCGAATAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATATTCATAAA
Found at i:49839 original size:9 final size:9
Alignment explanation
Indices: 49825--49850 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
49815 AGGGTTAGTT
49825 TTTTTTTTG
1 TTTTTTTTG
49834 TTTTTTTTG
1 TTTTTTTTG
49843 TTTTTTTT
1 TTTTTTTT
49851 TTAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:50142 original size:33 final size:33
Alignment explanation
Indices: 50103--50190 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
50093 AACGCGATTT
50103 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAA
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAA
* *
50136 TTATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAA
50169 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
50191 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTGCGATAA
Found at i:50192 original size:20 final size:20
Alignment explanation
Indices: 50158--50215 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
50148 GCGATTCTCT
**
50158 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
50178 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
50198 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
50216 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:53798 original size:14 final size:14
Alignment explanation
Indices: 53779--53812 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
53769 TGTTTAATTT
53779 ATTTGTAAAAGGTG
1 ATTTGTAAAAGGTG
*
53793 ATTTGTAAAAGTTG
1 ATTTGTAAAAGGTG
53807 ATTTGT
1 ATTTGT
53813 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGGTG
Found at i:53943 original size:19 final size:19
Alignment explanation
Indices: 53919--53965 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
53909 AAAAAGTACT
*
53919 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
53938 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
53957 ATCGCAACG
1 ATCGCAACG
53966 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:54012 original size:19 final size:19
Alignment explanation
Indices: 53990--54140 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
53980 CGAAATTAAA
53990 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
54009 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * *
54024 -CCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
* *
54042 TTCGCATTGCGA----AAT
1 TTCGCGTTGCGATTTTCAT
54057 -TCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
54075 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
54090 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
54108 TTCGCATTGCGATAGTAATT
1 TTCGCGTTGCGATTTTCA-T
54128 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
54141 AGACATTAAG
Statistics
Matches: 94, Mismatches: 22, Indels: 31
0.64 0.15 0.21
Matches are distributed among these distances:
14 26 0.28
15 2 0.02
16 5 0.05
17 6 0.06
18 2 0.02
19 40 0.43
20 13 0.14
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:54036 original size:33 final size:32
Alignment explanation
Indices: 53994--54120 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
53984 ATTAAATTCG
*
53994 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* *
54027 CGTTGCGATTTTTATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
54060 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
54093 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
54121 AGTAATTTTC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:54072 original size:66 final size:66
Alignment explanation
Indices: 53987--54119 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
53977 ATGCGAAATT
* *
53987 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTTATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
54052 G
66 G
*
54053 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
54118 G
66 G
54119 A
1 A
54120 TAGTAATTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:55954 original size:21 final size:21
Alignment explanation
Indices: 55930--55990 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
55920 AACGGTGGGT
*
55930 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
55951 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
*
55972 GGGGACTCTTGAGGAATGA
1 GGGGACTCTTGAGGGATGA
55991 CAGGTGAGTC
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.13, G:0.41, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:55957 original size:42 final size:42
Alignment explanation
Indices: 55902--55990 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
55892 CCTCTTCAAC
* * * *
55902 AATGACAGTGGCCTCTTGAACGGTGGGTGGGGACTCTTGAGG
1 AATGATAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
* *
55944 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 AATGATAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
55986 AATGA
1 AATGA
55991 CAGGTGAGTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.22, C:0.15, G:0.39, T:0.24
Consensus pattern (42 bp):
AATGATAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:56380 original size:19 final size:19
Alignment explanation
Indices: 56353--56403 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
56343 ACACGAAACT
*
56353 TACTTTCGCAACGCCAAAA
1 TACTATCGCAACGCCAAAA
**
56372 TACTATCGCAACGCGGAAA
1 TACTATCGCAACGCCAAAA
56391 TGACTATCGCAAC
1 T-ACTATCGCAAC
56404 ACGGAAATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (19 bp):
TACTATCGCAACGCCAAAA
Found at i:56398 original size:20 final size:20
Alignment explanation
Indices: 56358--56443 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
56348 AAACTTACTT
**
56358 TCGCAACGCCAAAAT-ACTA
1 TCGCAACGCGGAAATGACTA
56377 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
56397 TCGCAACACGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
56417 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
56436 TCGCAACG
1 TCGCAACG
56444 ACAAAATCGC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 27 0.48
20 29 0.52
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:56401 original size:39 final size:39
Alignment explanation
Indices: 56358--56450 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 39
56348 AAACTTACTT
**
56358 TCGCAACGCCAAAAT-ACTATCGCAACGCGGAAATGACTA
1 TCGCAACGCCAAAATGACTATCGCAACGC-GAAATGAAAA
* ** * *
56397 TCGCAACACGGAAATGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACGCCAAAATGACTATCGCAACGCGAAATGAAAA
*
56436 TCGCAACGACAAAAT
1 TCGCAACGCCAAAAT
56451 CGCAACGCGA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
39 31 0.74
40 11 0.26
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (39 bp):
TCGCAACGCCAAAATGACTATCGCAACGCGAAATGAAAA
Found at i:56491 original size:19 final size:18
Alignment explanation
Indices: 56469--56532 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
56459 GAAACACAAA
56469 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
* *
56488 TCGCGTTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
56504 TCG--TTGCGATTTTTATT
1 TCGCATTGCGA-TTTTATT
56521 TCGCATTGCGAT
1 TCGCATTGCGAT
56533 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
14 6 0.16
16 7 0.19
17 4 0.11
18 4 0.11
19 16 0.43
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:56540 original size:19 final size:20
Alignment explanation
Indices: 56518--56560 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
56508 TGCGATTTTT
56518 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
56537 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
56557 ATTT
1 ATTT
56561 TCGTGTTACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:57129 original size:18 final size:18
Alignment explanation
Indices: 57106--57153 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
57096 CGGGTCGATC
57106 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
57124 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
57142 AGGTGATGGCTC
1 AGGTGATGGCTC
57154 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:58450 original size:20 final size:20
Alignment explanation
Indices: 58425--58467 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
58415 AATAGTTTCT
58425 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
58445 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
58465 GAA
1 GAA
58468 TTTGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:59074 original size:41 final size:41
Alignment explanation
Indices: 58955--59092 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
58945 CGCTTTGAAA
* * *
58955 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
58996 ATTGAGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
59036 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
59077 ACCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
59093 CCAAATTCGC
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:59089 original size:20 final size:20
Alignment explanation
Indices: 58975--59088 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
58965 GATTATGTAT
*
58975 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
58995 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
59015 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
59035 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
59056 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
59076 TACCGCGTTGCGA
1 TATCGCGTTGCGA
59089 TTTTCCAAAT
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
19 3 0.04
20 57 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:59108 original size:41 final size:41
Alignment explanation
Indices: 59022--59189 Score: 196
Period size: 41 Copynumber: 4.1 Consensus size: 41
59012 AAGTATCGAG
* * ** * *
59022 TTGCGAAAGTCAGTATCGCGTTGCGATTTT-GTATTATCGCG
1 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-TCGCA
* *
59063 TTGCGATAGTCAGTACCGCGTTGCGATTTTCCAAATTCGCA
1 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
** *
59104 TTGCGATTTTCCA-AATTCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCAAATTCGCA
59146 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
59187 TTG
1 TTG
59190 TGATTTACTT
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
41 72 0.66
42 37 0.34
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
Found at i:59109 original size:21 final size:21
Alignment explanation
Indices: 59083--59212 Score: 167
Period size: 21 Copynumber: 6.3 Consensus size: 21
59073 CAGTACCGCG
59083 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
59104 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
59125 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
** *
59146 TTGCGATAGT-C-AGTATCGCA
1 TTGCGATTTTCCAAAT-TCGCA
59166 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
* * **
59187 TTGTGA-TTTACTTATTCGCA
1 TTGCGATTTTCCAAATTCGCA
59207 TTGCGA
1 TTGCGA
59213 ATTGTGAAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 30 0.32
21 61 0.64
22 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:59150 original size:83 final size:82
Alignment explanation
Indices: 59058--59212 Score: 238
Period size: 83 Copynumber: 1.9 Consensus size: 82
59048 TTTTGTATTA
* * *
59058 TCGCGTTGCGATAGTCAGTACCGCGTTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAATTCG
1 TCGCATTGCGATAGTCAGTACCGCATTGCGATTTTCCAAATTCGCATTGCGA-TTTACAAATTCG
59123 CATTGCGATTTTCCAAAT
65 CATTGCGATTTTCCAAAT
* * **
59141 TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCATTGTGATTTACTTATTCGC
1 TCGCATTGCGATAGTCAGTACCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACAAATTCGC
59206 ATTGCGA
66 ATTGCGA
59213 ATTGTGAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 17 0.26
83 48 0.74
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (82 bp):
TCGCATTGCGATAGTCAGTACCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACAAATTCGC
ATTGCGATTTTCCAAAT
Found at i:59206 original size:41 final size:41
Alignment explanation
Indices: 59083--59212 Score: 165
Period size: 41 Copynumber: 3.1 Consensus size: 41
59073 CAGTACCGCG
* *
59083 TTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCATTGCGA-TTTACTAATTCGCA
* *
59125 TTGCGATTTTCCAAATTCGCATTGCGA--TAGTCAGTATCGCA
1 TTGCGATTTTCCAAATTCGCATTGCGATTTACT-AAT-TCGCA
* *
59166 TTGCGATTTTCCAAATTCGCATTGTGATTTACTTATTCGCA
1 TTGCGATTTTCCAAATTCGCATTGCGATTTACTAATTCGCA
59207 TTGCGA
1 TTGCGA
59213 ATTGTGAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
39 1 0.01
40 2 0.03
41 42 0.55
42 28 0.37
43 3 0.04
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (41 bp):
TTGCGATTTTCCAAATTCGCATTGCGATTTACTAATTCGCA
Found at i:59226 original size:62 final size:62
Alignment explanation
Indices: 59094--59227 Score: 171
Period size: 62 Copynumber: 2.2 Consensus size: 62
59084 TGCGATTTTC
* *
59094 CAAATTCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAATTCGCATTGCGATAGT
1 CAAAATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTACAAATTCGCATTGCGATAGT
** * ** *
59156 CAGTATCGCATTGCGATTTTCCAAATTCGCATTGTGA-TTTACTTATTCGCATTGCGAATTGT
1 CAAAATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTACAAATTCGCATTGCG-ATAGT
*
59218 GAAAATCGCA
1 CAAAATCGCA
59228 ACGTGAAATT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 16 0.27
62 44 0.73
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (62 bp):
CAAAATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTACAAATTCGCATTGCGATAGT
Found at i:70165 original size:17 final size:19
Alignment explanation
Indices: 70136--70176 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
70126 CATGTTATAT
70136 TATTT-TGATATATATTG-
1 TATTTATGATATATATTGA
*
70153 TATTTATGA-ATATTTTGA
1 TATTTATGATATATATTGA
70171 TATTTA
1 TATTTA
70177 AATTTATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (19 bp):
TATTTATGATATATATTGA
Found at i:71077 original size:28 final size:29
Alignment explanation
Indices: 71022--71085 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
71012 TTTACATTGG
*
71022 GCTATAAAATAAAAAAGTGAATAATATAA
1 GCTATGAAATAAAAAAGTGAATAATATAA
* *
71051 GCTATGAAATGAAAAA-TGAA-AATTATAT
1 GCTATGAAATAAAAAAGTGAATAA-TATAA
71079 GCTATGA
1 GCTATGA
71086 CGTTTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 15 0.48
29 14 0.45
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (29 bp):
GCTATGAAATAAAAAAGTGAATAATATAA
Found at i:73573 original size:21 final size:21
Alignment explanation
Indices: 73534--73573 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
73524 CTAAATTTCT
**
73534 AATTTTAAAACCATTAACTCA
1 AATTTTAAAACCAAAAACTCA
*
73555 AATTTTAAATCCAAAAACT
1 AATTTTAAAACCAAAAACT
73574 ATAAATCTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTTAAAACCAAAAACTCA
Done.