Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001026.1 Hibiscus syriacus cultivar Beakdansim tig00002045_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: 80510
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6936 original size:6 final size:6
Alignment explanation
Indices: 6840--6934 Score: 172
Period size: 6 Copynumber: 15.8 Consensus size: 6
6830 CATGTATCGT
6840 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC
1 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC
* *
6888 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGT GTATGT GTATG
1 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATG
6935 TGAATGCCAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 88 1.00
ACGTcount: A:0.17, C:0.14, G:0.34, T:0.36
Consensus pattern (6 bp):
GTATGC
Found at i:10348 original size:17 final size:17
Alignment explanation
Indices: 10326--10359 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
10316 CGTACATCGC
10326 AAATTTGCAATGAACTT
1 AAATTTGCAATGAACTT
10343 AAATTTGCAATGAACTT
1 AAATTTGCAATGAACTT
10360 TGATCGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
AAATTTGCAATGAACTT
Found at i:33318 original size:23 final size:23
Alignment explanation
Indices: 33269--33319 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
33259 GTGTTATATT
**
33269 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
33292 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
33315 ATATT
1 ATATT
33320 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:33331 original size:19 final size:18
Alignment explanation
Indices: 33307--33399 Score: 62
Period size: 19 Copynumber: 5.0 Consensus size: 18
33297 TTAAATATCT
33307 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTA-A
* * *
33326 TTATTAGATTAATATTAA
1 TTATTAAAATATTATTAA
* * *
33344 ATATAAATAATATTATTCA
1 TTATTAA-AATATTATTAA
* *
33363 TTATTAAATATATAAATAA
1 TTATTAAA-ATATTATTAA
*
33382 TTTATT-ATATATTATTAA
1 -TTATTAAAATATTATTAA
33400 AATAAAATTA
Statistics
Matches: 54, Mismatches: 17, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
18 14 0.26
19 35 0.65
20 5 0.09
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (18 bp):
TTATTAAAATATTATTAA
Found at i:33359 original size:30 final size:30
Alignment explanation
Indices: 33325--33405 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 30
33315 ATATTATTAG
*
33325 ATTATTAGATTAATATTAAATATAAATAAT
1 ATTATTACATTAATATTAAATATAAATAAT
*
33355 ATTATT-CATT-AT-TAAATATATAAATAAT
1 ATTATTACATTAATATTAA-ATATAAATAAT
* *
33383 -TTATTATA-TATTATTAAA-ATAAA
1 ATTATTACATTAATATTAAATATAAA
33406 ATTATAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
27 14 0.33
28 16 0.38
29 6 0.14
30 6 0.14
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
ATTATTACATTAATATTAAATATAAATAAT
Found at i:33477 original size:17 final size:18
Alignment explanation
Indices: 33451--33484 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33441 TTTATTATAA
33451 TATTAAAAATA-TAATAT
1 TATTAAAAATATTAATAT
*
33468 TATTAGAAATATTAATA
1 TATTAAAAATATTAATA
33485 AATATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TATTAAAAATATTAATAT
Found at i:34323 original size:20 final size:21
Alignment explanation
Indices: 34298--34390 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
34288 TTTTCCCAAT
*
34298 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
34318 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
34339 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
34359 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
34380 TCGCAATGCGA
1 TCGCAATGCGA
34391 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:34405 original size:41 final size:41
Alignment explanation
Indices: 34298--34390 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
34288 TTTTCCCAAT
34298 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
34339 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
34380 TCGCAATGCGA
1 TCGCAATGCGA
34391 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:34425 original size:21 final size:20
Alignment explanation
Indices: 34376--34426 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
34366 GCGAATTGGG
* *
34376 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
34396 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
34417 AAAATCGCAA
1 AAAATCGCAA
34427 CGAGATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:34442 original size:16 final size:16
Alignment explanation
Indices: 34421--34451 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34411 TAATAAAAAA
34421 TCGCAACGAGATACTT
1 TCGCAACGAGATACTT
*
34437 TCGCAACGCGATACT
1 TCGCAACGAGATACT
34452 GACTTTCGCA
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:0.29, G:0.19, T:0.23
Consensus pattern (16 bp):
TCGCAACGAGATACTT
Found at i:35070 original size:19 final size:19
Alignment explanation
Indices: 35048--35232 Score: 138
Period size: 19 Copynumber: 10.1 Consensus size: 19
35038 GAAACCAAAA
* *
35048 TCGCATTGCGATTTTCTTT
1 TCGCGTTGCGATTTTCATT
35067 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
35086 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
35105 TCGCGGTTGCAATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
35125 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
** **
35141 T-G-GTCACGATAGTCATT
1 TCGCGTTGCGATTTTCATT
35158 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
35172 TCTCGTTACGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
35191 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
35211 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
35231 TC
1 TC
35233 AACCAAAAGA
Statistics
Matches: 131, Mismatches: 22, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 57 0.44
20 47 0.36
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:35125 original size:39 final size:38
Alignment explanation
Indices: 35048--35137 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 38
35038 GAAACCAAAA
* *
35048 TCGCATTGCGATTTTCTTTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCTTTTCGCGTTGCAATTTTCATT
35086 TCGCGTTGCGATTTT-TATTTCGCGGTTGCAATTTTCATT
1 TCGCGTTGCGATTTTCT-TTTCGC-GTTGCAATTTTCATT
35125 TCGCGTTGCGATT
1 TCGCGTTGCGATT
35138 GTCTGGTCAC
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
37 1 0.02
38 20 0.42
39 27 0.56
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCTTTTCGCGTTGCAATTTTCATT
Found at i:35202 original size:34 final size:33
Alignment explanation
Indices: 35120--35207 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
35110 GTTGCAATTT
* *
35120 TCATTTCGCGTTGCGATTGTCTGGTCACGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
*
35153 TCATTTCGCGTTGCGATTCTCTCGTTACGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
35186 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
35208 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:0.14, C:0.25, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
Found at i:35209 original size:20 final size:20
Alignment explanation
Indices: 35186--35232 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
35176 GTTACGATAG
35186 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
35206 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
35226 TCATTTC
1 TCATTTC
35233 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:36913 original size:18 final size:18
Alignment explanation
Indices: 36890--36935 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
36880 TTTACTCGTA
36890 ATTTCACTTAAATTAACC
1 ATTTCACTTAAATTAACC
36908 ATTTCACTTAAATTAACC
1 ATTTCACTTAAATTAACC
36926 ATTTCACTTA
1 ATTTCACTTA
36936 GATTGCTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTCACTTAAATTAACC
Found at i:37311 original size:42 final size:42
Alignment explanation
Indices: 37251--37373 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
37241 GCCCGACTCG
* * *
37251 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
37293 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
37335 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
37374 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:37331 original size:21 final size:21
Alignment explanation
Indices: 37307--37373 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
37297 TCATTCCTCG
37307 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
37328 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
37349 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
37370 AGAG
1 AGAG
37374 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:38751 original size:14 final size:14
Alignment explanation
Indices: 38732--38767 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
38722 ATTGTTTAAT
38732 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
38746 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
38760 TGATTTGT
1 TGATTTGT
38768 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:38938 original size:20 final size:19
Alignment explanation
Indices: 38891--38939 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
38881 TGCGAAATTA
** *
38891 GCGTTGCGATTTTCATTTC
1 GCGTTGCGATAGTAATTTC
*
38910 GCATTGCGATAGTAATTTCC
1 GCGTTGCGATAGTAATTT-C
38930 GCGTTGCGAT
1 GCGTTGCGAT
38940 GGACATTAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.39
Consensus pattern (19 bp):
GCGTTGCGATAGTAATTTC
Found at i:41225 original size:12 final size:12
Alignment explanation
Indices: 41208--41232 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41198 TCTTCGGGGA
41208 CTTTTTCTTCTT
1 CTTTTTCTTCTT
41220 CTTTTTCTTCTT
1 CTTTTTCTTCTT
41232 C
1 C
41233 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:41441 original size:24 final size:24
Alignment explanation
Indices: 41407--41460 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
41397 CTGAAACATC
* *
41407 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
41431 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
41455 ATCAAA
1 ATCAAA
41461 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:42544 original size:20 final size:20
Alignment explanation
Indices: 42519--42569 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
42509 ATTCATTTGA
42519 CTATCGCAACGCAAAAATGG
1 CTATCGCAACGCAAAAATGG
*
42539 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCAAAAATGG
*
42559 TTATCGCAACG
1 CTATCGCAACG
42570 AGAAAATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCAAAAATGG
Found at i:42574 original size:20 final size:20
Alignment explanation
Indices: 42519--42576 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
42509 ATTCATTTGA
42519 CTATCGCAACGCA-AAAATGG
1 CTATCGCAACG-AGAAAATGG
*
42539 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
42559 TTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
42577 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:42636 original size:19 final size:19
Alignment explanation
Indices: 42595--42662 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
42585 GAAATGAAAA
42595 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
42611 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
42628 TCGTATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
42647 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
42663 TCATTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:42681 original size:19 final size:19
Alignment explanation
Indices: 42623--42695 Score: 66
Period size: 19 Copynumber: 4.1 Consensus size: 19
42613 GTTGCGATTT
* **
42623 TCATTTCGTATTGCGATTT
1 TCATTTCGCATTGCGATAG
42642 TCATTTCGCATTGCG--A-
1 TCATTTCGCATTGCGATAG
*
42658 T--TTTCTCATTGCGATAG
1 TCATTTCGCATTGCGATAG
*
42675 TCATTTCGCGTTGCGATAG
1 TCATTTCGCATTGCGATAG
42694 TC
1 TC
42696 TGTTTTGCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
14 11 0.25
16 2 0.05
17 1 0.02
19 30 0.68
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:44703 original size:20 final size:19
Alignment explanation
Indices: 44668--44734 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
44658 GAAACTTAAA
44668 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
44687 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
44707 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
44726 ATCGCAACG
1 ATCGCAACG
44735 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:44742 original size:14 final size:14
Alignment explanation
Indices: 44723--44780 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
44713 ATGCGAAATG
44723 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
44737 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
44753 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
44769 AAAATCGCAACG
1 AAAATCGCAACG
44781 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:44765 original size:32 final size:33
Alignment explanation
Indices: 44707--44785 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
44697 GGAAATGGCT
*
44707 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
44740 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
44772 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
44786 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:44837 original size:14 final size:14
Alignment explanation
Indices: 44814--44871 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
44804 TTTCATTTCG
*
44814 CGTTGTGATTTTGT
1 CGTTGCGATTTTGT
*
44828 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
44844 CGCATTACGATTTTGT
1 CG--TTGCGATTTTGT
44860 CGTTGCGATTTT
1 CGTTGCGATTTT
44872 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.54
16 8 0.23
18 8 0.23
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:44878 original size:33 final size:33
Alignment explanation
Indices: 44797--44887 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
44787 ACAAATCGCA
* *
44797 TTGCGATTTTCATTTCGCGTTGTGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
44830 TTGCGA-TTTCATTTCGCATTACGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
44862 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
44888 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.55
33 24 0.45
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:44906 original size:20 final size:19
Alignment explanation
Indices: 44872--44926 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
44862 TTGCGATTTT
*
44872 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
44891 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
44911 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
44927 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:45425 original size:18 final size:18
Alignment explanation
Indices: 45399--45443 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
45389 GTCGATCAGA
*
45399 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
45417 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
45435 TGATGGCTC
1 TGATGGCTC
45444 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:46836 original size:22 final size:22
Alignment explanation
Indices: 46811--46854 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
46801 GATTTAGATA
46811 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
46833 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
46855 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:47067 original size:20 final size:20
Alignment explanation
Indices: 47042--47135 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
47032 GATTATGTAT
47042 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
47062 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
47082 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
47103 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
47123 TATCGCATTGCGA
1 TATCGCGTTGCGA
47136 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:47136 original size:20 final size:20
Alignment explanation
Indices: 47022--47136 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
47012 CGCTTTGAAA
*
47022 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
47043 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
47063 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
47083 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
47104 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
47124 ATCGCATTGCGAT
1 ATCGCATTGCGAT
47137 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:47155 original size:41 final size:41
Alignment explanation
Indices: 47064--47198 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
47054 AAAGTCAGTA
* * * ** *
47064 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAAT
* * *
47104 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAAT
* **
47146 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCAAAT
47187 TCGCGTTGCGAT
1 TCGCGTTGCGAT
47199 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAAT
Found at i:47169 original size:20 final size:20
Alignment explanation
Indices: 47125--47217 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
47115 ATAGTCAGTA
* **
47125 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
47146 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
47166 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACTTAT
*
47187 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
47207 TCGCATTGCGA
1 TCGCATTGCGA
47218 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:47199 original size:41 final size:41
Alignment explanation
Indices: 47125--47217 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
47115 ATAGTCAGTA
*
47125 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACTTAT
47166 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACTTAT
47207 TCGCATTGCGA
1 TCGCATTGCGA
47218 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACTTAT
Found at i:59760 original size:33 final size:33
Alignment explanation
Indices: 59708--59794 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
59698 TTTTCATCCT
* *
59708 AAACCCGAATCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGAATATCAAACTTAAAA
**
59742 AAATTCGACCCGACCCGAATATCAAACTTAAAA
1 AAACCCGACCCGACCCGAATATCAAACTTAAAA
*
59775 AAACCCGACCCGACTCGAAT
1 AAACCCGACCCGACCCGAAT
59795 TCGAATTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 41 0.89
34 5 0.11
ACGTcount: A:0.43, C:0.32, G:0.10, T:0.15
Consensus pattern (33 bp):
AAACCCGACCCGACCCGAATATCAAACTTAAAA
Found at i:59849 original size:29 final size:31
Alignment explanation
Indices: 59784--59853 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
59774 AAAACCCGAC
* *
59784 CCGACTCGAATTCGAATTTTTTTAAAAAAAAT
1 CCGACCCG-ATTCGAATATTTTTAAAAAAAAT
*
59816 CCGACCCGATTCGAA-ATTTTTAAAAAAACT
1 CCGACCCGATTCGAATATTTTTAAAAAAAAT
59846 -CGACCCGA
1 CCGACCCGA
59854 ATATCATACT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 8 0.23
30 13 0.37
31 7 0.20
32 7 0.20
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (31 bp):
CCGACCCGATTCGAATATTTTTAAAAAAAAT
Found at i:59866 original size:28 final size:27
Alignment explanation
Indices: 59835--59897 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
59825 TTCGAAATTT
* * *
59835 TTAAAAAAACTCGACCCGAATATCATAC
1 TTAAAAAAAC-CAACCAGAATATCAAAC
*
59863 TT-AAAAAACCAACTAGAATATCAAAC
1 TTAAAAAAACCAACCAGAATATCAAAC
59889 TTAAAAAAA
1 TTAAAAAAA
59898 TGACCCAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 15 0.50
27 13 0.43
28 2 0.07
ACGTcount: A:0.56, C:0.19, G:0.05, T:0.21
Consensus pattern (27 bp):
TTAAAAAAACCAACCAGAATATCAAAC
Found at i:65954 original size:23 final size:23
Alignment explanation
Indices: 65928--65975 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
65918 ATAAAGTACA
*
65928 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
65951 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
65974 AT
1 AT
65976 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:66382 original size:21 final size:22
Alignment explanation
Indices: 66357--66408 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
66347 ACACTTTACA
*
66357 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
66380 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
66403 ATATAA
1 ATATAA
66409 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:66393 original size:23 final size:23
Alignment explanation
Indices: 66367--66429 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
66357 ATATAACCAC
66367 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
66390 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
66413 TACCTATTACATCATAT
1 TACCTATTACATTATAT
66430 GTTTACCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:67689 original size:33 final size:33
Alignment explanation
Indices: 67652--67717 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
67642 CATCTTAATA
*
67652 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
67685 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
67718 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:70043 original size:17 final size:18
Alignment explanation
Indices: 70021--70063 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
70011 ATATATCCGG
70021 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
70038 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
70058 TATCAT
1 TATCAT
70064 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:70081 original size:20 final size:19
Alignment explanation
Indices: 70026--70072 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
70016 TCCGGTATCA
70026 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
70045 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
70066 TTTTACC
1 TTTTACC
70073 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:70220 original size:20 final size:20
Alignment explanation
Indices: 70194--70239 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
70184 CACTTTTAAA
*
70194 TTTACCGGTTTTATCAT-TT
1 TTTACCGATTTTATCATATT
70213 TGTTACCGATTTTATCATATT
1 T-TTACCGATTTTATCATATT
70234 TTTACC
1 TTTACC
70240 TGGTATATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (20 bp):
TTTACCGATTTTATCATATT
Found at i:73080 original size:2 final size:2
Alignment explanation
Indices: 73073--73101 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
73063 CAGTTGAGAA
73073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73102 CATCAACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74681 original size:20 final size:20
Alignment explanation
Indices: 74658--74776 Score: 130
Period size: 20 Copynumber: 5.8 Consensus size: 20
74648 CTCAGTTTCC
* *
74658 AAAATCGCAGCGGGAATAGT
1 AAAATCGCAACGTGAATAGT
*
74678 AAAAATCGGAACGTGAATAGT
1 -AAAATCGCAACGTGAATAGT
74699 AAATATCGCAACGTGAATAGT
1 AAA-ATCGCAACGTGAATAGT
* *
74720 AAAATAGCAACGTGAATGGT
1 AAAATCGCAACGTGAATAGT
** *
74740 AAAATCATAACGCGAATAGT
1 AAAATCGCAACGTGAATAGT
* *
74760 AAAATCACAACGCGAAT
1 AAAATCGCAACGTGAAT
74777 TTAGAAAATC
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
20 49 0.58
21 36 0.42
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGTGAATAGT
Found at i:74720 original size:42 final size:41
Alignment explanation
Indices: 74658--74763 Score: 124
Period size: 41 Copynumber: 2.6 Consensus size: 41
74648 CTCAGTTTCC
* * * *
74658 AAAATCGCAGCGGGAATAGTAAAAATCGGAACGTGAATAGT
1 AAAATCGCAACGCGAATAGTAAAAATAGCAACGTGAATAGT
* *
74699 AAATATCGCAACGTGAATAGT-AAAATAGCAACGTGAATGGT
1 AAA-ATCGCAACGCGAATAGTAAAAATAGCAACGTGAATAGT
**
74740 AAAATCATAACGCGAATAGTAAAA
1 AAAATCGCAACGCGAATAGTAAAA
74764 TCACAACGCG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 14 0.25
41 26 0.47
42 15 0.27
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGAATAGTAAAAATAGCAACGTGAATAGT
Found at i:74786 original size:21 final size:20
Alignment explanation
Indices: 74671--74790 Score: 109
Period size: 20 Copynumber: 5.8 Consensus size: 20
74661 ATCGCAGCGG
** *
74671 GAATAGTAAAAATCGGAACGT
1 GAATAGT-AAAATCACAACGC
* *
74692 GAATAGTAAATATCGCAACGT
1 GAATAGTAAA-ATCACAACGC
*
74713 GAATAGTAAAAT-AGCAACGT
1 GAATAGTAAAATCA-CAACGC
* *
74733 GAATGGTAAAATCATAACGC
1 GAATAGTAAAATCACAACGC
74753 GAATAGTAAAATCACAACGC
1 GAATAGTAAAATCACAACGC
74773 GAATTTAG-AAAATCACAA
1 GAA--TAGTAAAATCACAA
74791 AATCGCGTTG
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
20 47 0.54
21 37 0.43
22 3 0.03
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.20
Consensus pattern (20 bp):
GAATAGTAAAATCACAACGC
Found at i:75179 original size:20 final size:20
Alignment explanation
Indices: 75156--75247 Score: 91
Period size: 20 Copynumber: 4.6 Consensus size: 20
75146 TTACTATTCA
* *
75156 CGTTGCGAAATTAGAGTTCG
1 CGTTGCGAAATTTGACTTCG
75176 CGTTGCG-AATTTGACTATCG
1 CGTTGCGAAATTTGACT-TCG
* *
75196 CATTGC-AAATTTGACTTTTG
1 CGTTGCGAAATTTGAC-TTCG
*
75216 TGTTGCG-AATTTGACTATCG
1 CGTTGCGAAATTTGACT-TCG
75236 CGTTGCGAAATT
1 CGTTGCGAAATT
75248 GGAAACTGGG
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
19 8 0.14
20 45 0.78
21 5 0.09
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGAAATTTGACTTCG
Found at i:78214 original size:44 final size:44
Alignment explanation
Indices: 78151--78239 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
78141 AGACAACAGC
78151 TTATGACTTGTCACCTTTGACGAATTTTCTCAAGCTCCCTAGGA
1 TTATGACTTGTCACCTTTGACGAATTTTCTCAAGCTCCCTAGGA
78195 TTATGACTTGTCACCTTTGACGAATTTTCTCAAGCTCCCTAGGA
1 TTATGACTTGTCACCTTTGACGAATTTTCTCAAGCTCCCTAGGA
78239 T
1 T
78240 CAGTAACCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (44 bp):
TTATGACTTGTCACCTTTGACGAATTTTCTCAAGCTCCCTAGGA
Found at i:78759 original size:20 final size:21
Alignment explanation
Indices: 78734--78785 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
78724 TTTTCTCAAT
*
78734 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
78754 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
78775 TCGCAATGCGA
1 TCGCAATGCGA
78786 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:78779 original size:41 final size:40
Alignment explanation
Indices: 78734--78947 Score: 168
Period size: 41 Copynumber: 5.3 Consensus size: 40
78724 TTTTCTCAAT
* **
78734 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTACG-AAA
* * * * *
78775 TCGCAATGCG-AT-ACTGACTATCGCAATGCGATTTACGTAT
1 TCGCAATGCGAATAAGT-A-AATCGCAATGCGAATTACGAAA
** * * *
78815 TCGCGTTGCGATTTTCA-TAATTCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGA--ATAAGTAAATCGCAATGCGAATTACG-AAA
* * *
78856 TCGTAATGCGATTAAGTAAATCGCAATGCGAATTAGGGAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTA-CGAAA
*
78897 TCGCAATGCGAATACGTAAATCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTACG-AAA
78937 TCGCAATGCGA
1 TCGCAATGCGA
78948 TTTACATAGC
Statistics
Matches: 136, Mismatches: 26, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
39 6 0.04
40 47 0.35
41 78 0.57
42 2 0.01
43 2 0.01
44 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (40 bp):
TCGCAATGCGAATAAGTAAATCGCAATGCGAATTACGAAA
Found at i:78818 original size:20 final size:20
Alignment explanation
Indices: 78734--78949 Score: 177
Period size: 20 Copynumber: 10.7 Consensus size: 20
78724 TTTTCTCAAT
* *
78734 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGATTACGTAAA
* ** *
78754 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCG-ATTACGTAAA
*
78775 TCGCAATGCGA-TAC-TGACTA
1 TCGCAATGCGATTACGT-A-AA
*
78795 TCGCAATGCGATTTACGT-AT
1 TCGCAATGCGA-TTACGTAAA
** * * *
78815 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGA-TTACGTAAA
*
78836 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
78856 TCGTAATGCGATTAAGTAAA
1 TCGCAATGCGATTACGTAAA
* *
78876 TCGCAATGCGAATTAGGGAAA
1 TCGCAATGCG-ATTACGTAAA
*
78897 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
*
78917 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
78937 TCGCAATGCGATT
1 TCGCAATGCGATT
78950 TACATAGCGC
Statistics
Matches: 156, Mismatches: 32, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.01
20 106 0.68
21 44 0.28
22 3 0.02
23 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:78864 original size:61 final size:61
Alignment explanation
Indices: 78734--78953 Score: 205
Period size: 61 Copynumber: 3.6 Consensus size: 61
78724 TTTTCTCAAT
* * ** *
78734 TCGCAATGCGAATAAGTAAATCGCAACGCGAATT-GGGAAAATCGCAATGCG-ATAC-TGACTA
1 TCGCAATGCGATTAAGTAAATCGCAATGCGAATTACAG-AAATCGCAATGCGAATACGT-A-AA
* * ** * * * *
78795 TCGCAATGCGATTTACGT-ATTCGCGTTGCGATTTTCATAATTCGCAATGCGAATACGTAAA
1 TCGCAATGCGA-TTAAGTAAATCGCAATGCGAATTACAGAAATCGCAATGCGAATACGTAAA
* **
78856 TCGTAATGCGATTAAGTAAATCGCAATGCGAATTAGGGAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTAAGTAAATCGCAATGCGAATTACAGAAATCGCAATGCGAATACGTAAA
* * *
78917 TCGCAATGCGAATACGTAAATCGCAATGCGATTTACA
1 TCGCAATGCGATTAAGTAAATCGCAATGCGAATTACA
78954 TAGCGCCATT
Statistics
Matches: 125, Mismatches: 29, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
60 5 0.04
61 110 0.88
62 9 0.07
63 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (61 bp):
TCGCAATGCGATTAAGTAAATCGCAATGCGAATTACAGAAATCGCAATGCGAATACGTAAA
Found at i:78900 original size:102 final size:102
Alignment explanation
Indices: 78716--78907 Score: 255
Period size: 102 Copynumber: 1.9 Consensus size: 102
78706 TCTACAGTGT
**
78716 CGTTGCGATTTTCTCAATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAA
1 CGTTGCGATTTTCTCAATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAAGAAAATCGCAA
* *
78781 TGCGATACTGACTATCGCAATGCGATTTACGTATTCG
66 TGCGATACGGACAATCGCAATGCGATTTACGTATTCG
* * * *
78818 CGTTGCGATTTTCAT-AATTCGCAATGCGAATACGTAAATCGTAATGCG-ATTAAGTAAATCGCA
1 CGTTGCGATTTTC-TCAATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAAGAAAATCGCA
*
78881 ATGCGAATTAGGGA-AATCGCAATGCGA
65 ATGCG-A-TACGGACAATCGCAATGCGA
78908 ATACGTAAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
101 17 0.22
102 56 0.72
103 5 0.06
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (102 bp):
CGTTGCGATTTTCTCAATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAAGAAAATCGCAA
TGCGATACGGACAATCGCAATGCGATTTACGTATTCG
Found at i:79503 original size:19 final size:19
Alignment explanation
Indices: 79466--79531 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
79456 TTCGAGAATG
79466 AAATCGCAACGCGGAAATAA
1 AAATCGCAACGC-GAAATAA
**
79486 CTATCGCAACGCGAAATAA
1 AAATCGCAACGCGAAATAA
**
79505 AAATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAATAA
79524 AAATCGCA
1 AAATCGCA
79532 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.11
Consensus pattern (19 bp):
AAATCGCAACGCGAAATAA
Found at i:79549 original size:19 final size:19
Alignment explanation
Indices: 79527--79619 Score: 79
Period size: 19 Copynumber: 5.1 Consensus size: 19
79517 GAAACCAAAA
*
79527 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
79546 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
79560 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
79579 CCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
79598 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
79618 TC
1 TC
79620 AACCAAAAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
14 10 0.17
16 2 0.03
17 3 0.05
19 27 0.47
20 16 0.28
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:79617 original size:39 final size:33
Alignment explanation
Indices: 79532--79594 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
79522 CAAAATCGCA
*
79532 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTCCGCGTTGCGATTCTCTCG
**
79565 TTGCGATAGTCATTCCGCGTTGCGATTCTC
1 TTGCGATTTTCATTCCGCGTTGCGATTCTC
79595 ATTATCTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.41
Consensus pattern (33 bp):
TTGCGATTTTCATTCCGCGTTGCGATTCTCTCG
Done.