Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3598
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: 50740
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:208 original size:29 final size:28
Alignment explanation
Indices: 165--236 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
155 TCATGAGATT
* *
165 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGAGTTGAAA--GTACA
195 -GCACTAAGTGTGCGAGTTGAAAGTACA
1 GGCACTAAGTGTGCGAGTTGAAAGTACA
222 TGGCACTAAGTGTGC
1 -GGCACTAAGTGTGC
237 ACGGTTGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 5 0.13
29 33 0.87
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (28 bp):
GGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:481 original size:174 final size:175
Alignment explanation
Indices: 195--521 Score: 491
Period size: 174 Copynumber: 1.9 Consensus size: 175
185 AAATTGTACA
* * *
195 GCACTAAGTGTGCGAGTTGAAAGTACATGGCACTAAGTGTGCACGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTGAAAGTACATGGCACAAAGTGTGCACGGTTGATTACTAAACACTATG
* *
260 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTT-CCGAGTCGG
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTC-A
324 ATTTTGGACAGCAAAAAGGTAAGTGTTGCGCAACTTGAAATGCATG
130 ATTTTGGACAGCAAAAAGGTAAGTGTTGCGCAACTTGAAATGCATG
* * * ** *
370 GCACTAAGTGTGTGAGTT-TAAGTGCATGG-ACAAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTGAAAGTACATGGCACAAAGTGTGCACGGTTGATTACTAAACACTATG
433 TGTGC-AACCCAGTATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTC
66 TGTGCGAACCCA--ATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTC
*
497 AATTTTGGACAGCGAAAAGGTAAGT
129 AATTTTGGACAGCAAAAAGGTAAGT
522 ACCATTGAGT
Statistics
Matches: 137, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
172 6 0.04
173 33 0.24
174 74 0.54
175 24 0.18
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (175 bp):
GCACTAAGTGTGCGAGTTGAAAGTACATGGCACAAAGTGTGCACGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCAAAAAGGTAAGTGTTGCGCAACTTGAAATGCATG
Found at i:8001 original size:29 final size:28
Alignment explanation
Indices: 7965--8042 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
7955 TCATGAGATT
7965 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
7995 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
8022 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
8043 GATTATTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:8256 original size:172 final size:172
Alignment explanation
Indices: 7995--8318 Score: 542
Period size: 172 Copynumber: 1.9 Consensus size: 172
7985 AAATTGTACA
* *
7995 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAACACTATGT
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCACGGTTGATTATAAACACTATGT
* *
8060 GTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGAT
66 GTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
8125 TTTGGACAGCGGAAAAGTAAGTGTGCGAACTTGAAATGCATG
131 TTTGGACAGCGGAAAAGTAAGTGTGCGAACTTGAAATGCATG
* * * *
8167 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCATGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCACGGTTGATTA-TAAACACTATG
*
8232 TGTGC-AACCCAGTATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
65 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
*
8296 TTTTGGACAGCGGAAAGGTAAGT
130 TTTTGGACAGCGGAAAAGTAAGT
8319 ACCTTGAGTT
Statistics
Matches: 141, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
172 127 0.90
173 14 0.10
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (172 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCACGGTTGATTATAAACACTATGT
GTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
TTTGGACAGCGGAAAAGTAAGTGTGCGAACTTGAAATGCATG
Found at i:12108 original size:24 final size:24
Alignment explanation
Indices: 12053--12109 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
12043 TTCTACATCT
* *
12053 TTTCTTTTTGTTTCTTTTTTCTAA
1 TTTCTTTTTCTTTCTTTCTTCTAA
*
12077 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTTCT-TTCTTTCTTCTAA
12100 TTTCTTTTTC
1 TTTCTTTTTC
12110 ACTCTCAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTCTTTTTCTTTCTTTCTTCTAA
Found at i:14307 original size:38 final size:39
Alignment explanation
Indices: 14257--14365 Score: 148
Period size: 38 Copynumber: 2.8 Consensus size: 39
14247 TATTATAGTT
* *
14257 TGAGTATTTAATTATGCCATAATTTTAACATCATTAATA
1 TGAGTATTTAATTATGTCATAATTTGAACATCATTAATA
* *
14296 TGAGT-TTTAATTATGTCATAATCTGAACATCTTTAATA
1 TGAGTATTTAATTATGTCATAATTTGAACATCATTAATA
* * *
14334 TGGGTCTTTAATTATGTCATAGTTTGAACATC
1 TGAGTATTTAATTATGTCATAATTTGAACATC
14366 TTCAATACTT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 33 0.53
39 29 0.47
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (39 bp):
TGAGTATTTAATTATGTCATAATTTGAACATCATTAATA
Found at i:14362 original size:39 final size:38
Alignment explanation
Indices: 14257--14372 Score: 151
Period size: 39 Copynumber: 3.0 Consensus size: 38
14247 TATTATAGTT
* * *
14257 TGAGTATTTAATTATGCCATAATTTTAACATCATTAATA
1 TGAGT-TTTAATTATGTCATAATTTGAACATCTTTAATA
*
14296 TGAGTTTTAATTATGTCATAATCTGAACATCTTTAATA
1 TGAGTTTTAATTATGTCATAATTTGAACATCTTTAATA
* * *
14334 TGGGTCTTTAATTATGTCATAGTTTGAACATCTTCAATA
1 TGAGT-TTTAATTATGTCATAATTTGAACATCTTTAATA
14373 CTTGTTTTCA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 33 0.49
39 35 0.51
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (38 bp):
TGAGTTTTAATTATGTCATAATTTGAACATCTTTAATA
Found at i:14458 original size:23 final size:23
Alignment explanation
Indices: 14432--14481 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
14422 TTCCTACAAA
** *
14432 TTAAAGTGTGTTTAAACCTTGTC
1 TTAAAGTGCATTTAAACATTGTC
*
14455 TTAATGTGCATTTAAACATTGTC
1 TTAAAGTGCATTTAAACATTGTC
14478 TTAA
1 TTAA
14482 TGTTGTCCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (23 bp):
TTAAAGTGCATTTAAACATTGTC
Found at i:16737 original size:23 final size:23
Alignment explanation
Indices: 16707--16755 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
16697 TAAATTTTAA
16707 TCTATTTGTGAGTTATTCAACTC
1 TCTATTTGTGAGTTATTCAACTC
16730 TCTATTTGTGAGTTATTCAACTC
1 TCTATTTGTGAGTTATTCAACTC
16753 TCT
1 TCT
16756 TTGTTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.49
Consensus pattern (23 bp):
TCTATTTGTGAGTTATTCAACTC
Found at i:17446 original size:26 final size:27
Alignment explanation
Indices: 17373--17452 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
17363 AACACGTTAG
* *
17373 GAAAGAAAAAGCCTTTGTGGTATAATAT
1 GAAAG-AAAAGCCTTTGTGGCATAACAT
17401 GAAAGAAAAGCCTTTGTGGCATAACAT
1 GAAAGAAAAGCCTTTGTGGCATAACAT
* *
17428 G-AAGGAATGCCTTTGTGGCA-AACAT
1 GAAAGAAAAGCCTTTGTGGCATAACAT
17453 CTAAATGGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
25 5 0.10
26 17 0.35
27 21 0.44
28 5 0.10
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (27 bp):
GAAAGAAAAGCCTTTGTGGCATAACAT
Found at i:21100 original size:31 final size:32
Alignment explanation
Indices: 21064--21143 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 32
21054 CGGATTACTC
* *
21064 CCCCCTTG-AAGTGCATGTATATAAATGTTCA-
1 CCCCCTTGTAA-TACATGTACATAAATGTTCAT
**
21095 CCCCCTTGTAATACATGTACATGGATGTTCAT
1 CCCCCTTGTAATACATGTACATAAATGTTCAT
* *
21127 CCCCCTTATAATGCATG
1 CCCCCTTGTAATACATG
21144 AATCTTCCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 24 0.59
32 17 0.41
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (32 bp):
CCCCCTTGTAATACATGTACATAAATGTTCAT
Found at i:23329 original size:29 final size:29
Alignment explanation
Indices: 23292--23461 Score: 132
Period size: 29 Copynumber: 5.9 Consensus size: 29
23282 TTTTAGAGTC
* *
23292 TCACCATAAAGGCATCATTTTAACAGAGA
1 TCACCATAAAGGCTTCCTTTTAACAGAGA
* *
23321 TCACTAT-AAGGCTTCCCTTTAACAGAGA
1 TCACCATAAAGGCTTCCTTTTAACAGAGA
*
23349 TCACCACAAAGGCTTCCTTTTAACAGAGA
1 TCACCATAAAGGCTTCCTTTTAACAGAGA
** * * * * *
23378 TTGCCACAAGGGCATCCTTTTAATAGAAA
1 TCACCATAAAGGCTTCCTTTTAACAGAGA
* * *
23407 T-AGCCACAAAGGCTTCCTGTTAATAGAGA
1 TCA-CCATAAAGGCTTCCTTTTAACAGAGA
* * *
23436 T-AGCCACAAAAGATTCC-TTTAACAGA
1 TCA-CCATAAAGGCTTCCTTTTAACAGA
23462 AATTGGTGTT
Statistics
Matches: 117, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
28 30 0.26
29 87 0.74
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (29 bp):
TCACCATAAAGGCTTCCTTTTAACAGAGA
Found at i:23370 original size:57 final size:58
Alignment explanation
Indices: 23292--23464 Score: 156
Period size: 58 Copynumber: 3.0 Consensus size: 58
23282 TTTTAGAGTC
* * * * * * *
23292 TCACCATAAAGGCATCATTTTAACAGAGATCACTATAA-GGCTTCCCTTTAACAGAGA
1 TCACCACAAAGGCTTCCTTTTAACAGAGATCACCACAAGGGCATCCCTTTAACAGAAA
** * *
23349 TCACCACAAAGGCTTCCTTTTAACAGAGATTGCCACAAGGGCATCCTTTTAATAGAAA
1 TCACCACAAAGGCTTCCTTTTAACAGAGATCACCACAAGGGCATCCCTTTAACAGAAA
* * ** *
23407 T-AGCCACAAAGGCTTCCTGTTAATAGAGAT-AGCCACAAAAG-ATTCCTTTAACAGAAA
1 TCA-CCACAAAGGCTTCCTTTTAACAGAGATCA-CCACAAGGGCATCCCTTTAACAGAAA
23464 T
1 T
23465 TGGTGTTTTT
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
57 46 0.49
58 48 0.51
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (58 bp):
TCACCACAAAGGCTTCCTTTTAACAGAGATCACCACAAGGGCATCCCTTTAACAGAAA
Found at i:23965 original size:227 final size:227
Alignment explanation
Indices: 23561--24012 Score: 690
Period size: 227 Copynumber: 2.0 Consensus size: 227
23551 AATTTTTAAA
* * * *
23561 ATATGATGCCATAGCCTAGCCATGGTCTTAGACTATATGGTCTTTAGAGTGCCATGGGCTTTTCC
1 ATATGATGCCATAGCCCAGCCATGGTCTTAGACTATATGGTCTTCAGAATGCCATGGACTTTTCC
* * *
23626 TTTCAGAGATTCATGTTTTTGTTCTCGAAGAACCCCTTTAGACAACACAAATAGTTCATGCAGAC
66 TTTAAGAGATTCATGTTTTTATTCTCGAAGAACCCCTTTAGACAACACAAACAGTTCATGCAGAC
*
23691 TCATACTTAACAAACTCATCCACATATGACTTACACATGATAGACTCTTTCACAATAGACTTGTT
131 TCATACTTAACAAACTCATCCACATATGACTTACACATGACAGACTCTTTCACAATAGACTTGTT
* *
23756 CATATCTTCCATACACACATTGATACACTTCC
196 CATATCCTCAATACACACATTGATACACTTCC
23788 ATATGATGCCATAGCCCAGCCATGGTCTTAGACTATATGGTCTTCAGAATGCCATGGACTTTTCC
1 ATATGATGCCATAGCCCAGCCATGGTCTTAGACTATATGGTCTTCAGAATGCCATGGACTTTTCC
* * * * *
23853 TTTAAGAGATTCATGTTTTTATTCTTGATAG-ACCCTTTTAGACGACATAAACATTTCATGCAGA
66 TTTAAGAGATTCATGTTTTTATTCTCGA-AGAACCCCTTTAGACAACACAAACAGTTCATGCAGA
* * * * * *
23917 CTTATACTTGACAGACTTATTCACATATGACTTACTCATGACAGACTCTTTCACAATAGACTTGT
130 CTCATACTTAACAAACTCATCCACATATGACTTACACATGACAGACTCTTTCACAATAGACTTGT
*
23982 TCATTTCCTCAATACACACATTGATACACTT
195 TCATATCCTCAATACACACATTGATACACTT
24013 TAGACACTAA
Statistics
Matches: 202, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
227 200 0.99
228 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (227 bp):
ATATGATGCCATAGCCCAGCCATGGTCTTAGACTATATGGTCTTCAGAATGCCATGGACTTTTCC
TTTAAGAGATTCATGTTTTTATTCTCGAAGAACCCCTTTAGACAACACAAACAGTTCATGCAGAC
TCATACTTAACAAACTCATCCACATATGACTTACACATGACAGACTCTTTCACAATAGACTTGTT
CATATCCTCAATACACACATTGATACACTTCC
Found at i:26898 original size:42 final size:42
Alignment explanation
Indices: 26847--26942 Score: 156
Period size: 42 Copynumber: 2.3 Consensus size: 42
26837 GGTTCCCATA
*
26847 TTAAGCATGCCAACTGTATTAATTATAAATTTGATTCACATG
1 TTAAGCATGCCAACTATATTAATTATAAATTTGATTCACATG
* * *
26889 TTTAGCATGCCAACTATGTTGATTATAAATTTGATTCACATG
1 TTAAGCATGCCAACTATATTAATTATAAATTTGATTCACATG
26931 TTAAGCATGCCA
1 TTAAGCATGCCA
26943 CTAAAAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (42 bp):
TTAAGCATGCCAACTATATTAATTATAAATTTGATTCACATG
Found at i:28182 original size:12 final size:12
Alignment explanation
Indices: 28165--28193 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
28155 GCCACATGCT
28165 CGTGTGCTAGGC
1 CGTGTGCTAGGC
28177 CGTGTGCTAGGC
1 CGTGTGCTAGGC
28189 CGTGT
1 CGTGT
28194 AACTACCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.24, G:0.41, T:0.28
Consensus pattern (12 bp):
CGTGTGCTAGGC
Found at i:28785 original size:20 final size:20
Alignment explanation
Indices: 28762--28986 Score: 127
Period size: 20 Copynumber: 11.2 Consensus size: 20
28752 GAAGTATAAA
28762 CAGGGGCACGTAAGTGCAAT
1 CAGGGGCACGTAAGTGCAAT
* ** *
28782 CAGGGGTATCG-AAGCACAAA
1 CAGGGGCA-CGTAAGTGCAAT
*
28802 CAAGGGCACGTAAGTGCAAT
1 CAGGGGCACGTAAGTGCAAT
* * * *
28822 CAAGGGTAC-TGAAGTACAAA
1 CAGGGGCACGT-AAGTGCAAT
* **
28842 AAATGGCACGTAAGTGCAAT
1 CAGGGGCACGTAAGTGCAAT
* ** *
28862 CAGGGGTACCAAAGTACAAAT
1 CAGGGGCACGTAAGTGC-AAT
*
28883 -AGGGGCACGTAAGTGAAAT
1 CAGGGGCACGTAAGTGCAAT
* * * *
28902 TAGGGGTAC-TGAAGTACAAA
1 CAGGGGCACGT-AAGTGCAAT
* *
28922 CAGGGGCACATAAGTGCAGT
1 CAGGGGCACGTAAGTGCAAT
* * *
28942 CAGGGGTACCG-AAGTACAAA
1 CAGGGGCA-CGTAAGTGCAAT
*
28962 CAGGGGCACGTAAGTGCAGT
1 CAGGGGCACGTAAGTGCAAT
28982 CAGGG
1 CAGGG
28987 TATAATTTAC
Statistics
Matches: 148, Mismatches: 47, Indels: 20
0.69 0.22 0.09
Matches are distributed among these distances:
19 9 0.06
20 131 0.89
21 8 0.05
ACGTcount: A:0.36, C:0.17, G:0.32, T:0.15
Consensus pattern (20 bp):
CAGGGGCACGTAAGTGCAAT
Found at i:28809 original size:40 final size:39
Alignment explanation
Indices: 28751--28986 Score: 301
Period size: 40 Copynumber: 5.9 Consensus size: 39
28741 TTGAAATTAC
*
28751 CGAAGTATAAACAGGGGCACGTAAGTGCAATCAGGGGTA
1 CGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTA
* * *
28790 TCGAAGCACAAACAAGGGCACGTAAGTGCAATCAAGGGTA
1 -CGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTA
* **
28830 CTGAAGTACAAAAAATGGCACGTAAGTGCAATCAGGGGTA
1 C-GAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTA
* * * *
28870 CCAAAGTACAAATAGGGGCACGTAAGTGAAATTAGGGGTA
1 -CGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTA
* *
28910 CTGAAGTACAAACAGGGGCACATAAGTGCAGTCAGGGGTA
1 C-GAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTA
*
28950 CCGAAGTACAAACAGGGGCACGTAAGTGCAGTCAGGG
1 -CGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGG
28987 TATAATTTAC
Statistics
Matches: 171, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 2 0.01
40 167 0.98
41 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.31, T:0.15
Consensus pattern (39 bp):
CGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTA
Found at i:36624 original size:51 final size:51
Alignment explanation
Indices: 36557--36698 Score: 169
Period size: 51 Copynumber: 2.8 Consensus size: 51
36547 TTATTATCAT
* *
36557 TCGATAGACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCT-
1 TCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTA
* * * ** *
36607 TCTGGTACACATGGTAGCCTGCACATAGTACTACACATGTGACCATTATCTA
1 TC-GATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTA
* * *
36659 TCGATACACGTAGTAACCTGCACTTAGTACTACACACGTG
1 TCGATACACATAGTAGCCTGCACATAGTACTACACACGTG
36699 TGTATAGGCA
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
50 2 0.03
51 72 0.95
52 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (51 bp):
TCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTA
Found at i:41159 original size:27 final size:27
Alignment explanation
Indices: 41129--41306 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41119 ATATTGAGTC
* * * *
41129 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41156 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41183 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41211 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41238 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41265 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41292 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41307 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41268 original size:82 final size:81
Alignment explanation
Indices: 41150--41305 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41140 TGCTATATAA
* *
41150 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41215 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41232 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41296 CACTTAGTGC
65 CACTTAGTGC
41306 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:49336 original size:27 final size:27
Alignment explanation
Indices: 49295--49470 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
49285 ATATTGAGTC
* * * *
49295 CGCACAC-CAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
49321 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
49348 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
49376 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
49403 CGCACACTTAGTGCATCACAT--TC-ATT
1 CGCACACTTAGTGC-T-ACATAGTCAAAT
*
49429 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
49456 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
49471 GTACAATTTA
Statistics
Matches: 128, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
24 4 0.03
26 26 0.20
27 72 0.56
28 23 0.18
29 3 0.02
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:49453 original size:53 final size:53
Alignment explanation
Indices: 49295--49470 Score: 196
Period size: 53 Copynumber: 3.3 Consensus size: 53
49285 ATATTGAGTC
* * * * *
49295 CGCACAC-CAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACAT-ATCAACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
49348 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATA-TC-AACTCGCACACTTAGTGCAACATAGTCAAAT
*
49403 CGCACACTTAGTGCATCACAT-TC-ATTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGC-T-ACATATCAACTCGCACACTTAGTGCAACATAGTCAAAT
49456 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
49471 GTACAATTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
52 1 0.01
53 47 0.45
54 11 0.10
55 41 0.39
56 1 0.01
57 4 0.04
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (53 bp):
CGCACACTTAGTGCTACATATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Done.