Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007224.1 Hibiscus syriacus cultivar Beakdansim tig00019116_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: 66456
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:444 original size:12 final size:12
Alignment explanation
Indices: 427--453 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
417 TTATAACTTA
427 GGGTTTTAAGTT
1 GGGTTTTAAGTT
439 GGGTTTTAAGTT
1 GGGTTTTAAGTT
451 GGG
1 GGG
454 GTAGGTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (12 bp):
GGGTTTTAAGTT
Found at i:672 original size:14 final size:14
Alignment explanation
Indices: 655--688 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
645 AAAATTAAAG
655 TTTATGATTTAAGA
1 TTTATGATTTAAGA
* *
669 TTTAAGATTTAAGC
1 TTTATGATTTAAGA
683 TTTATG
1 TTTATG
689 CTTTGAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTATGATTTAAGA
Found at i:1980 original size:31 final size:30
Alignment explanation
Indices: 1940--2044 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
1930 ATAAATTTTC
* * *
1940 ATAATTTTAAGGACTATTTTATAATAATTTG
1 ATAAGTTTAATGACTATTTTGTAAT-ATTTG
* *
1971 ATAAGTTTAATTACTATGTTGTAACTATTTG
1 ATAAGTTTAATGACTATTTTGTAA-TATTTG
*
2002 ATAAAGTTTAATGACTTTTTTGTAATTATTTG
1 AT-AAGTTTAATGACTATTTTGTAA-TATTTG
2034 A-AGAGTTTAAT
1 ATA-AGTTTAAT
2045 AATCATTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
30 1 0.02
31 34 0.55
32 27 0.44
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (30 bp):
ATAAGTTTAATGACTATTTTGTAATATTTG
Found at i:2025 original size:32 final size:32
Alignment explanation
Indices: 1966--2044 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
1956 TTTTATAATA
*
1966 ATTTGAT-AAGTTTAATTACTATGTTGTAACT
1 ATTTGATAAAGTTTAATGACTATGTTGTAACT
* * *
1997 ATTTGATAAAGTTTAATGACTTTTTTGTAATT
1 ATTTGATAAAGTTTAATGACTATGTTGTAACT
*
2029 ATTTGA-AGAGTTTAAT
1 ATTTGATAAAGTTTAAT
2045 AATCATTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 16 0.38
32 26 0.62
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (32 bp):
ATTTGATAAAGTTTAATGACTATGTTGTAACT
Found at i:2339 original size:16 final size:17
Alignment explanation
Indices: 2301--2340 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
2291 GTTTCCTATC
2301 ATTTTTGTTCTTGTGAT
1 ATTTTTGTTCTTGTGAT
2318 ATTTTTGTTCTTGTGAT
1 ATTTTTGTTCTTGTGAT
2335 ATTTTT
1 ATTTTT
2341 ACATCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.05, G:0.15, T:0.68
Consensus pattern (17 bp):
ATTTTTGTTCTTGTGAT
Found at i:11704 original size:54 final size:54
Alignment explanation
Indices: 11622--11729 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
11612 TACAAGTTTT
11622 TAAGTCGAACTCTATTTTAAAATTTTCAAGTTGAGTCAAGAGAAACAATATTAG
1 TAAGTCGAACTCTATTTTAAAATTTTCAAGTTGAGTCAAGAGAAACAATATTAG
11676 TAAGTCGAACTCTATTTTAAAATTTTCAAGTTGAGTCAAGAGAAACAATATTAG
1 TAAGTCGAACTCTATTTTAAAATTTTCAAGTTGAGTCAAGAGAAACAATATTAG
11730 AACTCGACTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (54 bp):
TAAGTCGAACTCTATTTTAAAATTTTCAAGTTGAGTCAAGAGAAACAATATTAG
Found at i:12006 original size:22 final size:22
Alignment explanation
Indices: 11964--12011 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
11954 TAGTCTCTCG
* *
11964 TTTCCTTTGTTTATCTATTTCT
1 TTTCCCTTGTTTATCTATTTCA
*
11986 TTTCCCTTGTTTTTC-ATTTTCA
1 TTTCCCTTGTTTATCTA-TTTCA
12008 TTTC
1 TTTC
12012 TTCAATTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.08, C:0.21, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTCCCTTGTTTATCTATTTCA
Found at i:16541 original size:13 final size:14
Alignment explanation
Indices: 16513--16541 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16503 ATATTTTATA
16513 ATATTTTTACTATT
1 ATATTTTTACTATT
16527 ATATTTTTACT-TT
1 ATATTTTTACTATT
16540 AT
1 AT
16542 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:16756 original size:110 final size:111
Alignment explanation
Indices: 16616--16836 Score: 363
Period size: 110 Copynumber: 2.0 Consensus size: 111
16606 TGGAAATCAT
* *
16616 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * * *
16681 TATTTAGTT-ATTTATTTAATGCATGATTATTATATTAATAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
* *
16726 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTACATTATTATTAA
1 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
16791 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
16837 TTTTTTTGTA
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 69 0.68
111 33 0.32
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:22137 original size:15 final size:15
Alignment explanation
Indices: 22117--22147 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
22107 CAAATCAGTT
22117 CCCAGAATCGCAACG
1 CCCAGAATCGCAACG
22132 CCCAGAATCGCAACG
1 CCCAGAATCGCAACG
22147 C
1 C
22148 GATTATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.42, G:0.19, T:0.06
Consensus pattern (15 bp):
CCCAGAATCGCAACG
Found at i:22161 original size:21 final size:21
Alignment explanation
Indices: 22137--22249 Score: 81
Period size: 21 Copynumber: 5.5 Consensus size: 21
22127 CAACGCCCAG
22137 AATCGCAACGCGATTATGAAT
1 AATCGCAACGCGATTATGAAT
* *
22158 AATCGCAATGCGA-TA-GTAAA
1 AATCGCAACGCGATTATG-AAT
** * **
22178 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGATTATGAAT
* *
22200 AATCGCAACGTGAATATGAA-
1 AATCGCAACGCGATTATGAAT
* *
22220 AATCGCAACGCGATTCTGACT
1 AATCGCAACGCGATTATGAAT
22241 -ATCGCAACG
1 AATCGCAACG
22250 AGTATCCGTA
Statistics
Matches: 69, Mismatches: 18, Indels: 11
0.70 0.18 0.11
Matches are distributed among these distances:
19 1 0.01
20 31 0.45
21 33 0.48
22 4 0.06
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (21 bp):
AATCGCAACGCGATTATGAAT
Found at i:22225 original size:20 final size:20
Alignment explanation
Indices: 22200--22432 Score: 144
Period size: 20 Copynumber: 11.5 Consensus size: 20
22190 GATTTTCCAT
* **
22200 AATCGCAACGTGAATATGAA
1 AATCGCAACGAGAATCCGAA
* * * *
22220 AATCGCAACGCGATTCTGAC
1 AATCGCAACGAGAATCCGAA
* *
22240 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGAGAATCCG-AA
* * *
22261 AATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATCCGAA
* *
22281 AATCGCAACGACAATACGTAA
1 AATCGCAACGAGAATCCG-AA
* * *
22302 AATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATCCGAA
* *
22322 AATCGCAACGAGAATACGTA
1 AATCGCAACGAGAATCCGAA
* * *
22342 AATCGCAACGACAATACGTA
1 AATCGCAACGAGAATCCGAA
* * * *
22362 AATCGCAA-TACGTATCTGTA
1 AATCGCAACGA-GAATCCGAA
* *
22382 AATCGCAACGACAATACGTAA
1 AATCGCAACGAGAATCCG-AA
* * *
22403 AATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATCCGAA
22423 AATCGCAACG
1 AATCGCAACG
22433 CGATTTTTAA
Statistics
Matches: 165, Mismatches: 43, Indels: 10
0.76 0.20 0.05
Matches are distributed among these distances:
19 1 0.01
20 116 0.70
21 48 0.29
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGAGAATCCGAA
Found at i:22263 original size:41 final size:41
Alignment explanation
Indices: 22200--22369 Score: 197
Period size: 41 Copynumber: 4.2 Consensus size: 41
22190 GATTTTCCAT
* * *
22200 AATCGCAACGTGAATATG-AAAATCGCAACGCG-ATTC-TGA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT-A
* * *
22239 CTATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
22281 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* *
22322 AATCGCAACGAGAATACGT-AAATCGCAACGAC-AATACGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACG-CGTATCCGTA
22362 AATCGCAA
1 AATCGCAA
22370 TACGTATCTG
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
40 38 0.34
41 70 0.62
42 4 0.04
43 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
Found at i:22284 original size:61 final size:61
Alignment explanation
Indices: 22241--22412 Score: 240
Period size: 61 Copynumber: 2.8 Consensus size: 61
22231 GATTCTGACT
* * *
22241 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AAATCGCAACGAGAATACGTAAATCGCAACGACAATACGTAAA
*
22303 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGACAATACGT-AA
1 ATCGCAACGAGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGACAATACGTAAA
* * *
22363 ATCGCAA-TACGTATCTGTAAATCGCAACGACAATACGTAAAATCGCAACG
1 ATCGCAACGA-GTATCCGTAAATCGCAACGAGAATACGT-AAATCGCAACG
22413 CGTATCCGTA
Statistics
Matches: 100, Mismatches: 8, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
60 35 0.35
61 48 0.48
62 17 0.17
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (61 bp):
ATCGCAACGAGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGACAATACGTAAA
Found at i:22400 original size:101 final size:102
Alignment explanation
Indices: 22241--22432 Score: 323
Period size: 101 Copynumber: 1.9 Consensus size: 102
22231 GATTCTGACT
** * *
22241 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATC
1 ATCGCAACGACAATACGTAAAATCGCAACACGTATCCGTAAATCGCAACGACAATACGTAAAATC
22306 GCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
66 GCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* *
22343 ATCGCAACGACAATACGT-AAATCGCAATACGTATCTGTAAATCGCAACGACAATACGTAAAATC
1 ATCGCAACGACAATACGTAAAATCGCAACACGTATCCGTAAATCGCAACGACAATACGTAAAATC
22407 GCAACGCGTATCCGTAAATCGCAACG
66 GCAACGCGTATCCGTAAATCGCAACG
22433 CGATTTTTAA
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 69 0.82
102 15 0.18
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.18
Consensus pattern (102 bp):
ATCGCAACGACAATACGTAAAATCGCAACACGTATCCGTAAATCGCAACGACAATACGTAAAATC
GCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
Found at i:22418 original size:41 final size:39
Alignment explanation
Indices: 22241--22435 Score: 180
Period size: 41 Copynumber: 4.8 Consensus size: 39
22231 GATTCTGACT
* * *
22241 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTAT-CGT-AAATCGCAACGCGAATACGTAA
* * *
22282 ATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACG-CGTAT-CGT-AAATCGCAACGCGAATACGTAA
* *
22323 ATCGCAACGAGAATACGTAAATCGCAACGAC-AATACGTAA
1 ATCGCAACGCGTAT-CGTAAATCGCAACG-CGAATACGTAA
**
22363 ATCGCAATACGTATCTGTAAATCGCAACGAC-AATACGTAAA
1 ATCGCAACGCGTATC-GTAAATCGCAACG-CGAATACGT-AA
22404 ATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 ATCGCAACGCGTAT-CGTAAATCGCAACGCGA
22436 TTTTTAAAGC
Statistics
Matches: 135, Mismatches: 12, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
39 1 0.01
40 51 0.38
41 82 0.61
42 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (39 bp):
ATCGCAACGCGTATCGTAAATCGCAACGCGAATACGTAA
Found at i:22433 original size:20 final size:20
Alignment explanation
Indices: 22241--22434 Score: 196
Period size: 20 Copynumber: 9.6 Consensus size: 20
22231 GATTCTGACT
*
22241 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
22262 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
22282 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
22303 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
22323 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* *
22343 ATCGCAACGAC-AATACGTAA
1 ATCGCAACG-CGTATCCGTAA
** *
22363 ATCGCAATACGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* *
22383 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
22404 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
22424 ATCGCAACGCG
1 ATCGCAACGCG
22435 ATTTTTAAAG
Statistics
Matches: 144, Mismatches: 21, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.01
20 92 0.64
21 51 0.35
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:23020 original size:20 final size:19
Alignment explanation
Indices: 22995--23066 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
22985 TTCTAAACTT
22995 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
*
23015 AAAATCGCAACACGTAAATG
1 AAAATCGCAACA-GAAAATG
** *
23035 ACTATCACAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
23056 AAAATCGCAAC
1 AAAATCGCAAC
23067 GAGAGAATCG
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:23077 original size:14 final size:14
Alignment explanation
Indices: 23058--23128 Score: 79
Period size: 14 Copynumber: 4.7 Consensus size: 14
23048 GAGAAATGAA
23058 AATCGCAACGAGAG
1 AATCGCAACGAGAG
23072 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
23086 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
23105 AATCGCAACGAGAT
1 AATCGCAACGAGAG
23119 AATCGCAACG
1 AATCGCAACG
23129 CGAAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 34 0.68
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 10 0.20
ACGTcount: A:0.44, C:0.23, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:23114 original size:33 final size:33
Alignment explanation
Indices: 23072--23144 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
23062 GCAACGAGAG
**
23072 AATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAACGCGAAACCAA
*
23105 AATCGCAACGAGATAATCGCAACGCGAAACCAA
1 AATCGCAACGAGAGAATCGCAACGCGAAACCAA
23138 AATCGCA
1 AATCGCA
23145 TTGCAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.45, C:0.25, G:0.21, T:0.10
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAACGCGAAACCAA
Found at i:23187 original size:19 final size:19
Alignment explanation
Indices: 23140--23285 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
23130 GAAACCAAAA
* *
23140 TCGCATTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
23159 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
23178 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
23192 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
23211 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
23225 TCTCGTTGCAATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
23245 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
23264 CTCTCGTTACGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
23284 TC
1 TC
23286 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 19 0.19
16 5 0.05
17 5 0.05
19 41 0.41
20 30 0.30
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:23200 original size:14 final size:14
Alignment explanation
Indices: 23181--23233 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
23171 TTTAATTTCG
23181 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
23195 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
23214 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
23228 CGTTGC
1 CGTTGC
23234 AATAGTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 16 0.50
16 3 0.09
17 3 0.09
19 10 0.31
ACGTcount: A:0.08, C:0.26, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:23204 original size:33 final size:33
Alignment explanation
Indices: 23162--23257 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
23152 TTTCATTTCG
23162 CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
*
23195 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
* * * *
23228 CGTTGCAATAGTCATTTTCGCGTTGCGATT
1 CGTTGCGAT-TTTAATTTCGCGTTGCGATT
23258 TTCATTCTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 40 0.71
34 16 0.29
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
Found at i:25374 original size:21 final size:20
Alignment explanation
Indices: 25315--25375 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 20
25305 CTCGAGAGTC
25315 CCCTCCCACCATTCAAGAGG
1 CCCTCCCACCATTCAAGAGG
* ** * * *
25335 CTACTGTCATCGTTGAAGAGG
1 C-CCTCCCACCATTCAAGAGG
25356 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCATTCAAGAG
25376 CCCGATTCAC
Statistics
Matches: 27, Mismatches: 12, Indels: 3
0.64 0.29 0.07
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (20 bp):
CCCTCCCACCATTCAAGAGG
Found at i:26740 original size:14 final size:15
Alignment explanation
Indices: 26721--26757 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
26711 ATTTTTTAAT
26721 TGATTTGTTAAA-GA
1 TGATTTGTTAAATGA
*
26735 TGATTTG-TAAATGT
1 TGATTTGTTAAATGA
26749 TGATTTGTT
1 TGATTTGTT
26758 TAATTGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 15 0.75
15 1 0.05
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (15 bp):
TGATTTGTTAAATGA
Found at i:26935 original size:20 final size:19
Alignment explanation
Indices: 26869--26945 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
26859 TCGCAACGTG
*
26869 GAAATGAAAATTGCAATGC
1 GAAATGAAAATCGCAATGC
26888 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
26905 G-AGTG--AATCGCAATGC
1 GAAATGAAAATCGCAATGC
*
26921 GGAAATGAAAATCGCAACGC
1 -GAAATGAAAATCGCAATGC
26941 GAAAT
1 GAAAT
26946 CATTTCCGCG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.17
16 4 0.08
17 3 0.06
18 3 0.06
19 20 0.42
20 10 0.21
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:26974 original size:20 final size:20
Alignment explanation
Indices: 26949--26988 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
26939 GCGAAATCAT
*
26949 TTCCGCGTTGCGATAGTCAA
1 TTCCGCATTGCGATAGTCAA
26969 TTCCGCATTGCGATAGTCAA
1 TTCCGCATTGCGATAGTCAA
26989 ATGAATGTCT
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:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (20 bp):
TTCCGCATTGCGATAGTCAA
Found at i:27268 original size:20 final size:19
Alignment explanation
Indices: 27205--27277 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
27195 AGAGGAAAAG
*
27205 ATGAAAATCGTAATGCGAA
1 ATGAAAATCGCAATGCGAA
27224 ATGAAAATCGCAA--CG-A
1 ATGAAAATCGCAATGCGAA
*
27240 GTG--AATCGCAATGCGAAA
1 ATGAAAATCGCAATGCG-AA
*
27258 ATGAAAATCGCAACGCGAA
1 ATGAAAATCGCAATGCGAA
27277 A
1 A
27278 CTAATTTCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 8 0.18
16 5 0.11
17 2 0.05
18 3 0.07
19 15 0.34
20 11 0.25
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:27345 original size:18 final size:18
Alignment explanation
Indices: 27281--27384 Score: 119
Period size: 18 Copynumber: 5.9 Consensus size: 18
27271 CGCGAAACTA
*
27281 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
27300 ATTTTCGCA-TGCGA-TTC
1 A-TTTCGCATTGCGATTTC
*
27317 A-CTCG--TTGCGATTTC
1 ATTTCGCATTGCGATTTC
27332 ATTTCGCATTGCGATTTC
1 ATTTCGCATTGCGATTTC
*
27350 ATTTAGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
27369 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
27385 CTCTCGTTGC
Statistics
Matches: 73, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
14 5 0.07
15 7 0.10
16 3 0.04
17 4 0.05
18 25 0.34
19 23 0.32
20 6 0.08
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (18 bp):
ATTTCGCATTGCGATTTC
Found at i:27373 original size:37 final size:34
Alignment explanation
Indices: 27289--27384 Score: 117
Period size: 37 Copynumber: 2.8 Consensus size: 34
27279 TAATTTCGCG
*
27289 TTGCGATTTTCATTTTCGCA-TGCGA-TTCACTCG
1 TTGCGATTTTCA-TTTCGCATTGCGATTTCACTCA
*
27322 TTGCGA-TTTCATTTCGCATTGCGATTTCATTTAGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTCA-CT--CA
27358 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
27385 CTCTCGTTGC
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
31 7 0.13
32 10 0.18
33 10 0.18
34 1 0.02
36 7 0.13
37 20 0.36
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.45
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCACTCA
Found at i:27420 original size:20 final size:20
Alignment explanation
Indices: 27397--27443 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
27387 CTCGTTGCAT
* *
27397 TAGTCATTTCCGCGTTGCGA
1 TAGTCAATTCCGCATTGCGA
*
27417 TAGTTAATTCCGCATTGCGA
1 TAGTCAATTCCGCATTGCGA
27437 TAGTCAA
1 TAGTCAA
27444 ATGAATATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
TAGTCAATTCCGCATTGCGA
Found at i:27684 original size:19 final size:19
Alignment explanation
Indices: 27660--27811 Score: 245
Period size: 19 Copynumber: 8.1 Consensus size: 19
27650 AGAGGAAAAG
27660 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
27679 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
27698 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
27717 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
*
27736 ATGAAAATCGTAATGCGAA
1 ATGAAAATCGCAATGCGAA
* *
27755 ATGAAAATCGTAATGTGAA
1 ATGAAAATCGCAATGCGAA
27774 ATG--AATCGCAATGCGAAA
1 ATGAAAATCGCAATGCG-AA
*
27792 ATGAAAATCGCAACGCGAA
1 ATGAAAATCGCAATGCGAA
27811 A
1 A
27812 CTAATTTCGC
Statistics
Matches: 125, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.08
18 5 0.04
19 99 0.79
20 11 0.09
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.17
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:27878 original size:33 final size:33
Alignment explanation
Indices: 27821--27905 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
27811 ACTAATTTCG
*
27821 CGTTACGATTTTCATTTTCGCATTGCAATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCAATTCACT
* *
27855 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCAATTCACT
**
27888 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
27906 CGCGTTGCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 33 0.72
34 13 0.28
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCAATTCACT
Found at i:27913 original size:20 final size:20
Alignment explanation
Indices: 27888--27942 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
27878 GCGATTCTCT
*
27888 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
*
27908 CGTTGCGATAGTCAATTCTG
1 CGTTGCGATAGTCAATTCCG
*
27928 CATTGCGATAGTCAA
1 CGTTGCGATAGTCAA
27943 ATGAATGTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:30386 original size:24 final size:24
Alignment explanation
Indices: 30359--30405 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
30349 CAAAATCCGA
30359 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
30383 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
30406 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:30414 original size:24 final size:24
Alignment explanation
Indices: 30363--30414 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
30353 ATCCGAGTAT
** *
30363 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
30387 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
30411 TGAC
1 TGAC
30415 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:31321 original size:60 final size:60
Alignment explanation
Indices: 31255--31525 Score: 310
Period size: 60 Copynumber: 4.5 Consensus size: 60
31245 GTCAGAATCT
* * * *
31255 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACAGATTCA
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
* * *
31315 CATTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
* * * * * * * *
31375 CGTTGCGATTTACGTATTCTCGTTGCGATTTACAG-ATACGCATTGCGATTTACATATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTAC-GTATTCGCATTGCGATTTACAGATACG
* ** * *
31435 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCGCATTGCGATTTACAGATACG
* *
31496 CGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGA-TTTACGGATACGCATTGCGAT
31526 AGTCAGAATC
Statistics
Matches: 177, Mismatches: 30, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
60 126 0.71
61 32 0.18
62 19 0.11
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
Found at i:31445 original size:40 final size:40
Alignment explanation
Indices: 31257--31586 Score: 333
Period size: 40 Copynumber: 8.2 Consensus size: 40
31247 CAGAATCTCG
* * * *
31257 TTGCGATTTACAGATTCGCATTGCGATTTAC-GTATTCGCA
1 TTGCGATTTACATATTCTCGTTGCGATTTACAG-ATACGCA
* * * *
31297 TTGCGATTTACAGATTCACATTGCGATTTACGGATACGCA
1 TTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCA
* *
31337 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
1 TTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCA
*
31377 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCA
1 TTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCA
* *
31417 TTGCGATTTACATATTCTCGTTGCGATTTACGGATACGCG
1 TTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCA
* * * *
31457 TTGCGATTTTACGTATTATCGTTGCGATTTACGGATACGCG
1 TTGCGA-TTTACATATTCTCGTTGCGATTTACAGATACGCA
** * *
31498 TTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCGCA
1 TTGCGA-TTTACATATTCTCGTTGCGAT-TTACAGATA-CGCA
* * * * * * * *
31539 TTACGATTTATATGTTCGCGTTGCGATTTTCATATTCGCG
1 TTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCA
31579 TTGCGATT
1 TTGCGATT
31587 ATGGAAAATC
Statistics
Matches: 252, Mismatches: 32, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
39 1 0.00
40 181 0.72
41 69 0.27
42 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCA
Found at i:31576 original size:20 final size:20
Alignment explanation
Indices: 31255--31586 Score: 280
Period size: 20 Copynumber: 16.5 Consensus size: 20
31245 GTCAGAATCT
31255 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTACAGATTCG
*
31275 CATTGCGATTTAC-GTATTCG
1 CGTTGCGATTTACAG-ATTCG
* *
31295 CATTGCGATTTACAGATTCA
1 CGTTGCGATTTACAGATTCG
* * *
31315 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACAGATTCG
* *
31335 CATTGCGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATTCG
*
31355 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTACAGATTCG
*
31375 CGTTGCGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATTCG
*
31395 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTACAGATTCG
* * *
31415 CATTGCGATTTACATATTCT
1 CGTTGCGATTTACAGATTCG
* *
31435 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACAGATTCG
**
31455 CGTTGCGATTTTAC-GTATTAT
1 CGTTGCGA-TTTACAG-ATTCG
* *
31476 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACAGATTCG
* * *
31496 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACAGATTCG
* *
31517 CGTTGCGATAGT-CAGAATCG
1 CGTTGCGAT-TTACAGATTCG
* * *
31537 CATTACGATTTATATG-TTCG
1 CGTTGCGATTTACA-GATTCG
* *
31557 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACAGATTCG
31577 CGTTGCGATT
1 CGTTGCGATT
31587 ATGGAAAATC
Statistics
Matches: 253, Mismatches: 45, Indels: 28
0.78 0.14 0.09
Matches are distributed among these distances:
19 4 0.02
20 209 0.83
21 40 0.16
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTTACAGATTCG
Found at i:32236 original size:47 final size:49
Alignment explanation
Indices: 32167--32274 Score: 159
Period size: 47 Copynumber: 2.2 Consensus size: 49
32157 GTTATACAAA
*
32167 ACGCGGTACCTGCCCTGCGCTATAT-AAAATTA-T-GGAGTAAAGGTAT
1 ACGCGGTACCTGCCCCGCGCTATATAAAAATTATTAGGAGTAAAGGTAT
*
32213 GACGCGGTACCTGCCCCGTGCTATATAAAAATTATTAGGAGTAAAGGTAT
1 -ACGCGGTACCTGCCCCGCGCTATATAAAAATTATTAGGAGTAAAGGTAT
32263 AGCGCGGTACCT
1 A-CGCGGTACCT
32275 AATCCGCGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
47 23 0.42
48 7 0.13
49 2 0.04
50 23 0.42
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (49 bp):
ACGCGGTACCTGCCCCGCGCTATATAAAAATTATTAGGAGTAAAGGTAT
Found at i:32329 original size:41 final size:41
Alignment explanation
Indices: 32278--32371 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
32268 GGTACCTAAT
*
32278 CCGCGATATACCCCTACGTGGAGTATAGCGCGCTGCAGGGG
1 CCGCGCTATACCCCTACGTGGAGTATAGCGCGCTGCAGGGG
* *
32319 CCGTGCTATACCCCTACGTGGCGTATAGCGCGCTGCAGGGG
1 CCGCGCTATACCCCTACGTGGAGTATAGCGCGCTGCAGGGG
32360 CCGCGCTATACC
1 CCGCGCTATACC
32372 ACGTGGCGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.17, C:0.33, G:0.32, T:0.18
Consensus pattern (41 bp):
CCGCGCTATACCCCTACGTGGAGTATAGCGCGCTGCAGGGG
Found at i:39051 original size:18 final size:20
Alignment explanation
Indices: 39020--39069 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
39010 ACTTTGCATG
39020 AGTATCGATACTCTTGGG-T
1 AGTATCGATACTCTTGGGCT
39039 AGTATCG-TACTCTTGGGCT
1 AGTATCGATACTCTTGGGCT
39058 AGTATCGATACT
1 AGTATCGATACT
39070 TTCAGTCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.34
19 15 0.52
20 4 0.14
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (20 bp):
AGTATCGATACTCTTGGGCT
Found at i:42755 original size:26 final size:27
Alignment explanation
Indices: 42718--42768 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
42708 ATCTGGTGAT
42718 TTTAAAATTTATT-T-TTTAAAAAATA
1 TTTAAAATTTATTATATTTAAAAAATA
42743 TTTAAAATATTATTATATTTAAAAAA
1 TTTAAAAT-TTATTATATTTAAAAAA
42769 CCATAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.35
26 5 0.22
27 1 0.04
28 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTAAAATTTATTATATTTAAAAAATA
Found at i:43842 original size:15 final size:16
Alignment explanation
Indices: 43822--43861 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
43812 ACAAAATACA
43822 ATATTCCCAGTAAT-T
1 ATATTCCCAGTAATCT
*
43837 ATATTCCCTGTAATCT
1 ATATTCCCAGTAATCT
*
43853 TTATTCCCA
1 ATATTCCCA
43862 CTGATAATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.28, C:0.25, G:0.05, T:0.42
Consensus pattern (16 bp):
ATATTCCCAGTAATCT
Found at i:45649 original size:3 final size:3
Alignment explanation
Indices: 45641--45673 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
45631 TCAAAGGTTT
45641 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45674 CGATCTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:47495 original size:26 final size:27
Alignment explanation
Indices: 47445--47496 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
47435 AACCAAATAA
* *
47445 GCCCTTAAACTTTAAAAAATCAATTTG
1 GCCCTCAAACTTAAAAAAATCAATTTG
47472 GCCCTCAAACTTAAAAAAAT-AATTT
1 GCCCTCAAACTTAAAAAAATCAATTT
47497 AATCCATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (27 bp):
GCCCTCAAACTTAAAAAAATCAATTTG
Found at i:48116 original size:18 final size:18
Alignment explanation
Indices: 48093--48140 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
48083 AAATTGTCCT
*
48093 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
48111 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
48128 TATTTATATATTT
1 TA-TTATATATTT
48141 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:62219 original size:21 final size:22
Alignment explanation
Indices: 62194--62246 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
62184 CAAAGGGAAT
62194 CGATTCCCCTCCAAGG-GGTAC
1 CGATTCCCCTCCAAGGAGGTAC
* *
62215 CGATTCCCAT--GAGGAGGTAC
1 CGATTCCCCTCCAAGGAGGTAC
62235 CGATT-CCCTCCA
1 CGATTCCCCTCCA
62247 CGCTCCAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
19 6 0.24
20 10 0.40
21 9 0.36
ACGTcount: A:0.21, C:0.36, G:0.23, T:0.21
Consensus pattern (22 bp):
CGATTCCCCTCCAAGGAGGTAC
Found at i:62392 original size:17 final size:16
Alignment explanation
Indices: 62366--62398 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
62356 AGCCATTGAT
62366 CAATAACAAGAATCAA
1 CAATAACAAGAATCAA
62382 CAATCAACAAGAATCAA
1 CAAT-AACAAGAATCAA
62399 GAGAGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.61, C:0.21, G:0.06, T:0.12
Consensus pattern (16 bp):
CAATAACAAGAATCAA
Found at i:64809 original size:2 final size:2
Alignment explanation
Indices: 64802--64829 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
64792 CATCGTTAGG
64802 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64830 GACTGAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.