Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold556
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: 56277
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.31
Warning! 3069 characters in sequence are not A, C, G, or T
Found at i:125 original size:43 final size:42
Alignment explanation
Indices: 4--296 Score: 248
Period size: 43 Copynumber: 6.8 Consensus size: 42
1 GGT
* *
4 CAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTATGG
1 CAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGG
* * * ** *
46 AAAAAGCGCCACTAAATATCATAGTCTTTAGTGGCGTTTGTGG
1 -CAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGG
* *
89 TCAAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTGAGGG
1 -CAAAGCGCCGCTAAAGATCAGGGTCT-TTAGCGGCGTTTG-TGG
* * * ** * * *
133 GAAAGCGCTGCTAAAGACCCTGATCTTTAGTGGCGTTTTTGG
1 CAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGG
* * * *
175 GAGAAGCGCCGCTAAAGATAAGGGTCTTTAGTGGCGTTTGAGAG
1 CA-AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTG-G
* * **
219 -AGAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTCTCC
1 CA-AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGG
* *
261 CAAAAACGCCGCTAAAGATCAAGGTCTTTAGCGGCG
1 C-AAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCG
297 CATTCATTAG
Statistics
Matches: 199, Mismatches: 44, Indels: 14
0.77 0.17 0.05
Matches are distributed among these distances:
42 6 0.03
43 187 0.94
44 6 0.03
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (42 bp):
CAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGG
Found at i:147 original size:86 final size:85
Alignment explanation
Indices: 1--296 Score: 298
Period size: 86 Copynumber: 3.4 Consensus size: 85
* * *
1 GGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTT-ATGGAAAAAGCGCCACTAAATAT
1 GGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGA-GGAGAAAGCGCCGCTAAAGAT
65 CATAGTCTTTAGTGGCGTTTGT
65 CAT-GTCTTTAGTGGCGTTTGT
* * * * *
87 GGTCAAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTGAGGGGAAAGCGCTGCTAAAGAC
1 GGTCAAAGCGCCGCTAAAGATAAGGGTCT-TTAGCGGCGTTTGAGGAGAAAGCGCCGCTAAAGAT
* *
151 CCTGATCTTTAGTGGCGTTTTT
65 CATG-TCTTTAGTGGCGTTTGT
* *
173 GG-GAGAAGCGCCGCTAAAGATAAGGGTCTTTAGTGGCGTTTGA-GAGAGAAGCGCCGCTAAAGA
1 GGTCA-AAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGAGGAGA-AAGCGCCGCTAAAGA
* * * *
236 TCAGGGTCTTTAGCGGCGCTTCT
64 TCA-TGTCTTTAGTGGCGTTTGT
** *
259 -CCCAAAAACGCCGCTAAAGATCAA-GGTCTTTAGCGGCG
1 GGTC-AAAGCGCCGCTAAAGAT-AAGGGTCTTTAGCGGCG
297 CATTCATTAG
Statistics
Matches: 174, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
85 7 0.04
86 160 0.92
87 7 0.04
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (85 bp):
GGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGAGGAGAAAGCGCCGCTAAAGATC
ATGTCTTTAGTGGCGTTTGT
Found at i:275 original size:129 final size:128
Alignment explanation
Indices: 27--296 Score: 274
Period size: 129 Copynumber: 2.1 Consensus size: 128
17 AAGATAAGGG
* * * *
27 TCTTTAGCGGCGTTTATGGAAAAAGCGCCACTAAATATCATAGTCTTTAGTGGCGTTTGTGGTCA
1 TCTTTAGCGGCGTTTATGGAAAAAGCGCCACTAAAGATAAGAGTCTTTAGTGGCGTTTGAGG-CA
* * * **** * *
92 AAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGGGAAAGCGCTGCTAAAGACCCTGA
65 AAGCGCCGCTAAAGATCAGGGTCTATTGCGGCGCTTCACCCAAAAACGCCGCTAAAGACCCTGA
* * * * * *
156 TCTTTAGTGGCGTTTTTGGGAGAAGCGCCGCTAAAGATAAGGGTCTTTAGTGGCGTTTGAGAG-A
1 TCTTTAGCGGCGTTTATGGAAAAAGCGCCACTAAAGATAAGAGTCTTTAGTGGCGTTTGAG-GCA
* * **
220 GAAGCGCCGCTAAAGATCAGGGTCT-TTAGCGGCGCTTCTCCCAAAAACGCCGCTAAAGATCAAG
65 -AAGCGCCGCTAAAGATCAGGGTCTATT-GCGGCGCTTCACCCAAAAACGCCGCTAAAGACCCTG
*
284 G
128 A
285 TCTTTAGCGGCG
1 TCTTTAGCGGCG
297 CATTCATTAG
Statistics
Matches: 113, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
128 3 0.03
129 109 0.96
130 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (128 bp):
TCTTTAGCGGCGTTTATGGAAAAAGCGCCACTAAAGATAAGAGTCTTTAGTGGCGTTTGAGGCAA
AGCGCCGCTAAAGATCAGGGTCTATTGCGGCGCTTCACCCAAAAACGCCGCTAAAGACCCTGA
Found at i:1938 original size:25 final size:25
Alignment explanation
Indices: 1909--1981 Score: 146
Period size: 25 Copynumber: 2.9 Consensus size: 25
1899 TATTAGCTCA
1909 ATTTTTATTATTTCATTTAACAATT
1 ATTTTTATTATTTCATTTAACAATT
1934 ATTTTTATTATTTCATTTAACAATT
1 ATTTTTATTATTTCATTTAACAATT
1959 ATTTTTATTATTTCATTTAACAA
1 ATTTTTATTATTTCATTTAACAA
1982 AATCCTGTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTTATTATTTCATTTAACAATT
Found at i:4033 original size:51 final size:51
Alignment explanation
Indices: 3907--4042 Score: 197
Period size: 50 Copynumber: 2.7 Consensus size: 51
3897 AGTGAAAGTG
3907 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAATGAT
* * *
3958 A-GGTCGCATGTGTAGTACTATGTGCATGCTACTACGTGTA-TCGG-ATGGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACT-GGAATGAT
*
4007 AATGGTCACATGTGTAGTACAATGTGCAGGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
4043 TGTGAACCGA
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
49 5 0.07
50 40 0.53
51 31 0.41
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAATGAT
Found at i:4104 original size:45 final size:45
Alignment explanation
Indices: 4048--4139 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
4038 TACTATGTGA
* *
4048 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
* *
4093 ACCGGACATCATTGATTAATAAGGTGGTTGTTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
4138 AC
1 AC
4140 TGAGTATCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:6689 original size:21 final size:21
Alignment explanation
Indices: 6665--6707 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
6655 TAAGTTAATT
6665 TACTC-GTAATTTTTCTATTTA
1 TACTCTGTAATTTTTC-ATTTA
* *
6686 TACTCTTTTATTTTTCATTTA
1 TACTCTGTAATTTTTCATTTA
6707 T
1 T
6708 TTTATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.14, G:0.02, T:0.63
Consensus pattern (21 bp):
TACTCTGTAATTTTTCATTTA
Found at i:8006 original size:18 final size:17
Alignment explanation
Indices: 7962--8011 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
7952 GTCCGATTCG
7962 ATTAAATAAAATATTAAAA
1 ATTAAAT-AAA-ATTAAAA
*
7981 ATT-TATAAAATTAAAA
1 ATTAAATAAAATTAAAA
7997 ATATAAATAAAATTA
1 AT-TAAATAAAATTA
8012 GATTAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.33
17 4 0.15
18 11 0.41
19 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAAATAAAATTAAAA
Found at i:11278 original size:31 final size:31
Alignment explanation
Indices: 11243--11306 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
11233 GCCATTGATG
*
11243 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTTAAA
*
11274 AAAATATAAAAAAAATTATAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTTAAA
11305 AA
1 AA
11307 CGAGAGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAAAAATTAAAATTATTTTAAA
Found at i:11343 original size:22 final size:22
Alignment explanation
Indices: 11317--11385 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
11307 CGAGAGTTTA
*
11317 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
**
11339 AGAGAATTTTTGAAGGACTTTG
1 AGAGAATTTTTGAAGGAAATTG
*
11361 AGAGAATTTTTGAATGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
11383 AGA
1 AGA
11386 TAGGATTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.39, C:0.01, G:0.28, T:0.32
Consensus pattern (22 bp):
AGAGAATTTTTGAAGGAAATTG
Found at i:11659 original size:29 final size:27
Alignment explanation
Indices: 11618--11671 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
11608 CGGGGAAAAT
11618 GGCCCATTCCGGTAAATAATTAAAAAACC
1 GGCCCATTCCGGTAAAT--TTAAAAAACC
* *
11647 GGCCTATTTCGGTAAATTTAAAAAA
1 GGCCCATTCCGGTAAATTTAAAAAA
11672 AAGGGCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
29 15 0.65
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (27 bp):
GGCCCATTCCGGTAAATTTAAAAAACC
Found at i:20729 original size:16 final size:15
Alignment explanation
Indices: 20688--20730 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
20678 AAAGATGATA
20688 ATATTAATATATAATT
1 ATATTAAT-TATAATT
**
20704 ATATCCATTATAATAT
1 ATATTAATTATAAT-T
20720 ATATTAATTAT
1 ATATTAATTAT
20731 TATCAGCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTAATTATAATT
Found at i:21311 original size:20 final size:20
Alignment explanation
Indices: 21283--21321 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
21273 AATTTTTCTC
21283 CTAAATTTT-AATTTTATTAT
1 CTAAATTTTCAA-TTTATTAT
*
21303 CTAATTTTTCAATTTATTA
1 CTAAATTTTCAATTTATTA
21322 AATTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (20 bp):
CTAAATTTTCAATTTATTAT
Found at i:22318 original size:25 final size:25
Alignment explanation
Indices: 22258--22318 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
22248 CTCCTAAATT
*
22258 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTAAATTATCTAATTTTTCAA
* *
22283 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTAAATTATCTAAT-TTTTCA-A
22308 TTAATTAAATT
1 TTAATTAAATT
22319 TTTGATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTCAA
Found at i:30812 original size:33 final size:33
Alignment explanation
Indices: 30774--30844 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
30764 ACCTGTATCT
* *
30774 CAGTCACATAGGT-CTCCTTCACCTGTCCCACTA
1 CAGTCACATAGGTCCTCC-TCACCTGCCCCACAA
*
30807 CAGTCACATATGTCCTCCTCACCTGCCCCACAA
1 CAGTCACATAGGTCCTCCTCACCTGCCCCACAA
30840 CAGTC
1 CAGTC
30845 CTCCATCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 30 0.88
34 4 0.12
ACGTcount: A:0.23, C:0.42, G:0.11, T:0.24
Consensus pattern (33 bp):
CAGTCACATAGGTCCTCCTCACCTGCCCCACAA
Found at i:32577 original size:19 final size:19
Alignment explanation
Indices: 32546--32583 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
32536 GGAATGTTAG
*
32546 AGTAGTTAGTAAAGCTGTT
1 AGTAGTTAGTAAAACTGTT
32565 AGTAGTT-GTTAAAACTGTT
1 AGTAGTTAG-TAAAACTGTT
32584 GTACGGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (19 bp):
AGTAGTTAGTAAAACTGTT
Found at i:38427 original size:2 final size:2
Alignment explanation
Indices: 38422--38446 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38412 AAAAAAAAAA
38422 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 A
38447 CAAAGAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39376 original size:30 final size:30
Alignment explanation
Indices: 39342--39404 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
39332 ACTTAACAAG
39342 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
39372 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
39402 CAA
1 CAA
39405 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:41654 original size:2 final size:2
Alignment explanation
Indices: 41647--41681 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
41637 AAATTACCAA
*
41647 AT AT AT AT AT AT AT AT AT AT GT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41682 TAAAACTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42831 original size:2 final size:2
Alignment explanation
Indices: 42824--42849 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42814 TGCATTTCAA
42824 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
42850 TGAGGAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:42905 original size:3 final size:3
Alignment explanation
Indices: 42885--42934 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
42875 AAATTGATGA
42885 AAG AA- AAG AAG AATG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
42930 AAG AA
1 AAG AA
42935 AAGGGGATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:47139 original size:24 final size:25
Alignment explanation
Indices: 47110--47162 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
47100 GGCTCTTTCG
*
47110 TGAAATTTAATACAAATG-ATGCAA
1 TGAAATGTAATACAAATGAATGCAA
* * *
47134 TGAAATGTAATGCAGATGAATGGAA
1 TGAAATGTAATACAAATGAATGCAA
47159 TGAA
1 TGAA
47163 TGCAAAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (25 bp):
TGAAATGTAATACAAATGAATGCAA
Found at i:51807 original size:44 final size:44
Alignment explanation
Indices: 51759--51885 Score: 114
Period size: 44 Copynumber: 2.9 Consensus size: 44
51749 CTTCAAAGGT
* * * * *
51759 ATAGGATTCATCGCTTTAATCC-GCTTCAATGCAACTTTAGGGAG
1 ATAGGATTAATAGCTTT-AGCCTGCTCCAATGCAACTTCAGGGAG
* *
51803 ATAGGATTAATAGCTTTAGCCTGCTCCACTGTAACTTCAGGGAG
1 ATAGGATTAATAGCTTTAGCCTGCTCCAATGCAACTTCAGGGAG
* * * * *
51847 ATAGGAATT-ATATCTTCAACCTGCCCCACTGCAACTTCA
1 ATAGG-ATTAATAGCTTTAGCCTGCTCCAATGCAACTTCA
51886 AAGGGATAAG
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 3 0.04
44 63 0.91
45 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
ATAGGATTAATAGCTTTAGCCTGCTCCAATGCAACTTCAGGGAG
Found at i:51909 original size:44 final size:44
Alignment explanation
Indices: 51861--51944 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
51851 GAATTATATC
* *
51861 TTCAACCTGCCCCACTGCAACTTCAAAGGGATAAGGTTTGTTAT
1 TTCAACCTACCCCACTGCAACTTCAAAGAGATAAGGTTTGTTAT
* * *
51905 TTCAACCTACTCTACTGCAACTTCAGAGAGATAAGGTTTG
1 TTCAACCTACCCCACTGCAACTTCAAAGAGATAAGGTTTG
51945 ATATAATCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
TTCAACCTACCCCACTGCAACTTCAAAGAGATAAGGTTTGTTAT
Found at i:53065 original size:45 final size:45
Alignment explanation
Indices: 53013--53099 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
53003 AGTTCGAAAT
* *
53013 GAATAAATTAATCAAGATAACAAATTTTTCCAAGATACGAAATGA
1 GAATAAATTAATCAAGATAACAAATTTTGCCAAAATACGAAATGA
* ** *
53058 GAATAAATTGATCAAGATGGCATATTTTGCCAAAATACGAAA
1 GAATAAATTAATCAAGATAACAAATTTTGCCAAAATACGAAA
53100 ACGAATAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.26
Consensus pattern (45 bp):
GAATAAATTAATCAAGATAACAAATTTTGCCAAAATACGAAATGA
Found at i:53380 original size:5 final size:5
Alignment explanation
Indices: 53370--53424 Score: 73
Period size: 5 Copynumber: 11.8 Consensus size: 5
53360 GGCCTCTACT
*
53370 TTTTC TTTTC TTTT- TCTTC TTTTC TTTTC -TTT- TTTTC TTTTC TTTT-
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
53416 TTTTC TTTT
1 TTTTC TTTT
53425 TTTAACATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 13 0.30
5 31 0.70
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:53391 original size:9 final size:9
Alignment explanation
Indices: 53377--53427 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
53367 ACTTTTTCTT
53377 TTCTTTTTC
1 TTCTTTTTC
*
53386 TTCTTTTCTT
1 TTCTTTT-TC
53396 TTCTTTTT-
1 TTCTTTTTC
53404 TTC-TTTTC
1 TTCTTTTTC
*
53412 TTTTTTTTC
1 TTCTTTTTC
53421 TT-TTTTT
1 TTCTTTTT
53428 AACATTCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
7 4 0.11
8 10 0.27
9 15 0.41
10 8 0.22
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:53391 original size:14 final size:13
Alignment explanation
Indices: 53372--53424 Score: 70
Period size: 14 Copynumber: 3.9 Consensus size: 13
53362 CCTCTACTTT
53372 TTCTTTTCTTTTTC
1 TTCTTTTC-TTTTC
53386 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
*
53399 TTTTTTTCTTTTC
1 TTCTTTTCTTTTC
*
53412 TTTTTTTTCTTTT
1 -TTCTTTTCTTTT
53425 TTTAACATTC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
13 17 0.46
14 20 0.54
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTCTTTTCTTTTC
Done.