Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3199
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: 91379
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:9156 original size:9 final size:9
Alignment explanation
Indices: 9142--9211 Score: 68
Period size: 9 Copynumber: 7.3 Consensus size: 9
9132 AAAAAATTGC
9142 TTTTTTAAT
1 TTTTTTAAT
9151 TTTTTTAAT
1 TTTTTTAAT
*
9160 AATTTTTAAT
1 -TTTTTTAAT
**
9170 TTTAAAATAAT
1 TTT--TTTAAT
9181 TTTTTTATAT
1 TTTTTTA-AT
9191 TTTTTTAAT
1 TTTTTTAAT
*
9200 TTTTTAAAT
1 TTTTTTAAT
9209 TTT
1 TTT
9212 AAAAAATATT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 26 0.52
10 17 0.34
11 7 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:9197 original size:40 final size:39
Alignment explanation
Indices: 9114--9217 Score: 131
Period size: 39 Copynumber: 2.6 Consensus size: 39
9104 CATTATCTAA
9114 TTAATTATTTTAATTTTAAAAAAATTGCTTTTTTAATTTTT
1 TTAATT-TTTTAATTTTAAAAAAATT-CTTTTTTAATTTTT
*
9155 TTAATAATTTTTAATTTTAAAATAA-T-TTTTTTATATTTTT
1 TTAAT--TTTTTAATTTTAAAAAAATTCTTTTTTA-ATTTTT
9195 TTAATTTTTTAAATTTTAAAAAA
1 TTAATTTTTT-AATTTTAAAAAA
9218 TATTAATTCA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
38 5 0.09
39 18 0.32
40 11 0.19
41 6 0.11
42 16 0.28
43 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (39 bp):
TTAATTTTTTAATTTTAAAAAAATTCTTTTTTAATTTTT
Found at i:9369 original size:13 final size:14
Alignment explanation
Indices: 9346--9374 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9336 GTTTGAGAGC
9346 TAAAAAGATAAAAA
1 TAAAAAGATAAAAA
9360 TAAAAA-ATAAAAA
1 TAAAAAGATAAAAA
9373 TA
1 TA
9375 GAGAGCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (14 bp):
TAAAAAGATAAAAA
Found at i:12239 original size:5 final size:5
Alignment explanation
Indices: 12229--12257 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12219 ATTTAAAAAC
12229 AATAT AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATA
12258 GGCACAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:12651 original size:31 final size:31
Alignment explanation
Indices: 12608--12682 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
12598 TGCTATACGG
* *
12608 ACATGCCTGTGTGGTTCAGGCCGTGTGGCCA
1 ACATGCCTGTGTGGTTCAGGCCATGTGACCA
12639 ACATG-CTCGTGTGGTTCAGGCCATGTGACCA
1 ACATGCCT-GTGTGGTTCAGGCCATGTGACCA
* *
12670 ATACGCCTGTGTG
1 ACATGCCTGTGTG
12683 ACTTACCTCG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 2 0.05
31 34 0.89
32 2 0.05
ACGTcount: A:0.16, C:0.25, G:0.32, T:0.27
Consensus pattern (31 bp):
ACATGCCTGTGTGGTTCAGGCCATGTGACCA
Found at i:13030 original size:21 final size:21
Alignment explanation
Indices: 12997--13040 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12987 CAACTTTTAA
* *
12997 ATATGTTCAATAT-TCAATTT
1 ATATGTTAAATATCTAAATTT
13017 ATATGGTTAAATATCTAAATTT
1 ATAT-GTTAAATATCTAAATTT
13039 AT
1 AT
13041 CAATCAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 8 0.40
22 8 0.40
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (21 bp):
ATATGTTAAATATCTAAATTT
Found at i:17093 original size:25 final size:25
Alignment explanation
Indices: 17065--17143 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
17055 TGTATATAGC
17065 ATTCTTATATGTAATATTATCTATA
1 ATTCTTATATGTAATATTATCTATA
* * * * **
17090 ATTC-CATATCCTTAAT-GTATATAGC
1 ATTCTTATAT--GTAATATTATCTATA
17115 ATTCTTATATGTAATATTATCTATA
1 ATTCTTATATGTAATATTATCTATA
17140 ATTC
1 ATTC
17144 CACTATTTAC
Statistics
Matches: 38, Mismatches: 12, Indels: 8
0.66 0.21 0.14
Matches are distributed among these distances:
24 8 0.21
25 22 0.58
26 8 0.21
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.48
Consensus pattern (25 bp):
ATTCTTATATGTAATATTATCTATA
Found at i:17115 original size:50 final size:50
Alignment explanation
Indices: 17040--17146 Score: 205
Period size: 50 Copynumber: 2.1 Consensus size: 50
17030 CCTCCTCTCC
17040 ATTCCACATCCTTAATGTATATAGCATTCTTATATGTAATATTATCTATA
1 ATTCCACATCCTTAATGTATATAGCATTCTTATATGTAATATTATCTATA
*
17090 ATTCCATATCCTTAATGTATATAGCATTCTTATATGTAATATTATCTATA
1 ATTCCACATCCTTAATGTATATAGCATTCTTATATGTAATATTATCTATA
17140 ATTCCAC
1 ATTCCAC
17147 TATTTACATC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.44
Consensus pattern (50 bp):
ATTCCACATCCTTAATGTATATAGCATTCTTATATGTAATATTATCTATA
Found at i:19906 original size:15 final size:15
Alignment explanation
Indices: 19886--19915 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19876 GGGAGATTAC
19886 TCGTATTATGTAATT
1 TCGTATTATGTAATT
19901 TCGTATTATGTAATT
1 TCGTATTATGTAATT
19916 GTGCAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (15 bp):
TCGTATTATGTAATT
Found at i:21190 original size:48 final size:48
Alignment explanation
Indices: 21134--21245 Score: 145
Period size: 48 Copynumber: 2.3 Consensus size: 48
21124 GATTCAACTC
* * * *
21134 CGCACACATAGTGCCAAATAATTCCGCACACATAGTGCCTTAC-ATATA
1 CGCACACATAGTGCCAAACAAATACGCACACATAGTGCCATACGA-ATA
* * *
21182 TGCACACATAGTGCCATACAAATATGCACACATAGTGCCATACGAATA
1 CGCACACATAGTGCCAAACAAATACGCACACATAGTGCCATACGAATA
21230 CGCACACATAGTGCCA
1 CGCACACATAGTGCCA
21246 CTTAAATCCG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 54 0.98
49 1 0.02
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.21
Consensus pattern (48 bp):
CGCACACATAGTGCCAAACAAATACGCACACATAGTGCCATACGAATA
Found at i:21257 original size:24 final size:23
Alignment explanation
Indices: 21134--21257 Score: 108
Period size: 24 Copynumber: 5.2 Consensus size: 23
21124 GATTCAACTC
* * *
21134 CGCACACATAGTGCCAAATAATTC
1 CGCACACATAGTGCC-ATTAAATA
21158 CGCACACATAGTGCC-TTACATATA
1 CGCACACATAGTGCCATTA-A-ATA
* *
21182 TGCACACATAGTGCCATACAAATA
1 CGCACACATAGTGCCAT-TAAATA
*
21206 TGCACACATAGTGCCA-TACGAATA
1 CGCACACATAGTGCCATTA--AATA
*
21230 CGCACACATAGTGCCACTTAAATC
1 CGCACACATAGTGCCA-TTAAATA
21254 CGCA
1 CGCA
21258 TATCTAGTAA
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
22 3 0.04
23 1 0.01
24 75 0.89
25 2 0.02
26 3 0.04
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (23 bp):
CGCACACATAGTGCCATTAAATA
Found at i:21727 original size:15 final size:15
Alignment explanation
Indices: 21703--21732 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21693 TATTTCCATT
*
21703 ACACATACATATATA
1 ACACACACATATATA
21718 ACACACACATATATA
1 ACACACACATATATA
21733 TATATTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (15 bp):
ACACACACATATATA
Found at i:25936 original size:46 final size:47
Alignment explanation
Indices: 25873--26193 Score: 413
Period size: 46 Copynumber: 7.0 Consensus size: 47
25863 TTCGACATGA
* * * * * * *
25873 TGCCATAGTGTCTTTCAACTATGGTCTTACCCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGT
* ** *** *
25919 TGCCATGGTATCATTCAACCATGGTCTTATTCA-TTTCCCCGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTT-CATATCAGGT
* *
25966 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGT
26012 TGCCATGGTATCTTTCAACCATGGTCTTACAC-GTTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGT
*
26058 TGCCATGGTATCTTTCAACCGTGGTCTTACAC-GTTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGT
*
26104 TGCTATGGTATCTTTCAACCATGGTCTTACAC-GTTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGT
*
26150 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAG
26194 AGAGCACACT
Statistics
Matches: 251, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
45 3 0.01
46 205 0.82
47 43 0.17
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGT
Found at i:28345 original size:11 final size:11
Alignment explanation
Indices: 28329--28380 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
28319 TATACTAAAT
28329 AAATAATAATA
1 AAATAATAATA
*
28340 AAATAAT-ATT
1 AAATAATAATA
* *
28350 AAATATCTCATA
1 AAATA-ATAATA
*
28362 AAATATTAATA
1 AAATAATAATA
28373 AAATAATA
1 AAATAATA
28381 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:32474 original size:24 final size:24
Alignment explanation
Indices: 32422--32533 Score: 152
Period size: 24 Copynumber: 4.7 Consensus size: 24
32412 GATTCAACTC
* * * * *
32422 CGCACATATAGTGCCAAATAATTC
1 CGCACACATAGTGCCATACAAATA
* *
32446 CGCACACATAGTGCCTTACATATA
1 CGCACACATAGTGCCATACAAATA
*
32470 TGCACACATAGTGCCATACAAATA
1 CGCACACATAGTGCCATACAAATA
32494 CGCACACATAGTGCCATACAAATA
1 CGCACACATAGTGCCATACAAATA
32518 CGCACACATAGTGCCA
1 CGCACACATAGTGCCA
32534 CTTAAATCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 77 1.00
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.21
Consensus pattern (24 bp):
CGCACACATAGTGCCATACAAATA
Found at i:35569 original size:37 final size:37
Alignment explanation
Indices: 35504--35649 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
35494 TACGTATGAT
* *
35504 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
35539 CACCTATCACTTTGTTTCTTGATCACATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
35576 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
35613 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
35650 TAAAGCTATC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 90 0.88
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:35666 original size:46 final size:46
Alignment explanation
Indices: 35613--35881 Score: 358
Period size: 46 Copynumber: 5.6 Consensus size: 46
35603 TAAGTGTAGC
* **
35613 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
35659 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
35705 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
35757 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
35809 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
35855 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
35882 AGTACTCAAA
Statistics
Matches: 207, Mismatches: 9, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
46 112 0.54
49 1 0.00
50 1 0.00
51 3 0.01
52 90 0.43
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:35732 original size:52 final size:52
Alignment explanation
Indices: 35656--35875 Score: 326
Period size: 52 Copynumber: 4.3 Consensus size: 52
35646 TAGCTAAAGC
* *
35656 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
35709 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
35761 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
35813 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
35859 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
35876 ATCAGAAGTA
Statistics
Matches: 152, Mismatches: 8, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
46 43 0.28
50 1 0.01
52 93 0.61
53 15 0.10
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:35735 original size:98 final size:97
Alignment explanation
Indices: 35613--35881 Score: 350
Period size: 98 Copynumber: 2.7 Consensus size: 97
35603 TAAGTGTAGC
* ** *
35613 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTT-TCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACT
35678 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
64 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
35712 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTG
1 CAC-TTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC--T----TTG
* *
35777 TCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
59 TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
35816 CAC--T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTATCACTTG
1 CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTG
35876 ATCAGA
66 ATCAGA
35882 AGTACTCAAA
Statistics
Matches: 155, Mismatches: 8, Indels: 21
0.84 0.04 0.11
Matches are distributed among these distances:
92 15 0.10
96 1 0.01
98 86 0.55
99 7 0.05
100 3 0.02
101 1 0.01
104 42 0.27
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (97 bp):
CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTG
ATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:39372 original size:42 final size:43
Alignment explanation
Indices: 39325--39452 Score: 110
Period size: 42 Copynumber: 3.1 Consensus size: 43
39315 TAGTGCTAAC
*
39325 GAAAACCCTTAAGGGTTAAAC-AGAAGCTCATAAGAGCTGAA-T
1 GAAAACCCTTAAGGGTTAAACTA-AAACTCATAAGAGCTGAACT
* *
39367 GAAAA-CC-TAGTAGGGTTAAACTAAAACTCGTAAGAGTTGAACT
1 GAAAACCCTTA--AGGGTTAAACTAAAACTCATAAGAGCTGAACT
* * *
39410 G-AAACCCATT-AGGGTT-AACTGAAACTCATATGAG-TTAACT
1 GAAAACCC-TTAAGGGTTAAACTAAAACTCATAAGAGCTGAACT
39450 GAA
1 GAA
39453 GCTCATGTGA
Statistics
Matches: 71, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
40 8 0.11
41 18 0.25
42 39 0.55
43 5 0.07
45 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (43 bp):
GAAAACCCTTAAGGGTTAAACTAAAACTCATAAGAGCTGAACT
Found at i:39457 original size:20 final size:20
Alignment explanation
Indices: 39385--39463 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
39375 AGTAGGGTTA
* * *
39385 AACTAAAACTCGTAAGAGTT
1 AACTGAAACTCATATGAGTT
* *
39405 GAACTGAAACCCAT-TAGGGTT
1 -AACTGAAACTCATAT-GAGTT
39426 AACTGAAACTCATATGAGTT
1 AACTGAAACTCATATGAGTT
* *
39446 AACTGAAGCTCATGTGAG
1 AACTGAAACTCATATGAG
39464 CTAAACGAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 32 0.68
21 15 0.32
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (20 bp):
AACTGAAACTCATATGAGTT
Found at i:49359 original size:21 final size:21
Alignment explanation
Indices: 49321--49360 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
49311 GACAGTTTTT
*
49321 ATTTATTTATTTTATATTTAG
1 ATTTATTTAATTTATATTTAG
49342 ATTTATTTTAATTT-TATTT
1 ATTTA-TTTAATTTATATTT
49361 CATAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
ATTTATTTAATTTATATTTAG
Found at i:49640 original size:10 final size:10
Alignment explanation
Indices: 49613--49648 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
49603 TGTAATATAT
49613 TATTTTCAAA
1 TATTTTCAAA
*
49623 TGATTTTCTAA
1 T-ATTTTCAAA
49634 TATTTTCAAA
1 TATTTTCAAA
49644 TATTT
1 TATTT
49649 GAAAAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (10 bp):
TATTTTCAAA
Found at i:50675 original size:35 final size:35
Alignment explanation
Indices: 50623--50692 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
50613 TTGCCCCATT
**
50623 CTCTGAAGAGATTGTAGCAATATATAAATACGTAA
1 CTCTGAAGAGAACGTAGCAATATATAAATACGTAA
50658 CTCTGAAGAGAACGTAGCAATATATAAATACGTAA
1 CTCTGAAGAGAACGTAGCAATATATAAATACGTAA
50693 TCTTTAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (35 bp):
CTCTGAAGAGAACGTAGCAATATATAAATACGTAA
Found at i:62193 original size:76 final size:76
Alignment explanation
Indices: 62113--62265 Score: 272
Period size: 76 Copynumber: 2.0 Consensus size: 76
62103 CTTAGATAAC
62113 ACGAGTACAAACCGGCTCATAAAATCATTTAGTATTCT-AAAGTACTCTCAAAACAGAAATAGAT
1 ACGAGTACAAACCGGCTCATAAAATCATTTAGTATTCTGAAA-TACTCTCAAAACAGAAATAGAT
62177 TAAGAAGTCAAT
65 TAAGAAGTCAAT
*
62189 ACGAGTACAAACCGGCTCATAAAATCATTTATTATTCTGAAATACTCTCAAAACAGAAATAGATT
1 ACGAGTACAAACCGGCTCATAAAATCATTTAGTATTCTGAAATACTCTCAAAACAGAAATAGATT
*
62254 AAGAAGTTAAT
66 AAGAAGTCAAT
62265 A
1 A
62266 AAGAGCTACC
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
76 71 0.96
77 3 0.04
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.26
Consensus pattern (76 bp):
ACGAGTACAAACCGGCTCATAAAATCATTTAGTATTCTGAAATACTCTCAAAACAGAAATAGATT
AAGAAGTCAAT
Found at i:63324 original size:3 final size:3
Alignment explanation
Indices: 63316--63341 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
63306 AAATGAGCAT
63316 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
63342 CCTATAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:65788 original size:20 final size:20
Alignment explanation
Indices: 65763--65801 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
65753 TTAGATTAAA
*
65763 TTTAATATTAAAATAATAAT
1 TTTAATATCAAAATAATAAT
*
65783 TTTAATATCAAATTAATAA
1 TTTAATATCAAAATAATAA
65802 AATACTATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTAATATCAAAATAATAAT
Found at i:71789 original size:14 final size:14
Alignment explanation
Indices: 71770--71799 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
71760 TTATATCGAG
71770 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
71784 ACCAATCCAATTCA
1 ACCAATCCAAATCA
71798 AC
1 AC
71800 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Done.