Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2865
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: 38997
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:5974 original size:39 final size:39
Alignment explanation
Indices: 5896--6143 Score: 304
Period size: 40 Copynumber: 6.3 Consensus size: 39
5886 TCTTCGGAAT
* *
5896 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATA-AATCACTAGCACAAATGCCTTCGGGTC
* *
5935 TTAGCCCGGATATATCAACTCGCACAAATGCCTTC-GGTC
1 TTAGCCCGGATAAATC-ACTAGCACAAATGCCTTCGGGTC
*
5974 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-AAATCACTAGCACAAATGCCTTCGGGTC
* *
6014 TTAACCCGGATAAATCACTAGC-CAATTGCCTTCGGGTC
1 TTAGCCCGGATAAATCACTAGCACAAATGCCTTCGGGTC
* * * * *
6052 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAATC-ACTAGCACAAATGCCTTCGGGTC
* *
6092 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGAT-AAATCACTAGCACAAATGCCTTCGGGTC
6132 TTAGCCCGGATA
1 TTAGCCCGGATA
6144 TCATTCAAAT
Statistics
Matches: 182, Mismatches: 20, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
38 29 0.16
39 54 0.30
40 96 0.53
41 3 0.02
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (39 bp):
TTAGCCCGGATAAATCACTAGCACAAATGCCTTCGGGTC
Found at i:6022 original size:79 final size:79
Alignment explanation
Indices: 5896--6143 Score: 322
Period size: 79 Copynumber: 3.2 Consensus size: 79
5886 TCTTCGGAAT
* * * *
5896 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCAC
1 TTAGCCCGGATAAAACCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATC-ACTAGCAC
*
5960 AAATGCCTTC-GGTC
65 AATTGCCTTCGGGTC
* * *
5974 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATAAATCACTAGC-CA
1 TTAGCCCGGATAAAACCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCACTAGCACA
6038 ATTGCCTTCGGGTC
66 ATTGCCTTCGGGTC
* * * * * *
6052 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCAC
1 TTAGCCCGGATAAAACCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGAT-AAATCACTAGCAC
*
6117 AATTGCCTTCGGGAC
65 AATTGCCTTCGGGTC
6132 TTAGCCCGGATA
1 TTAGCCCGGATA
6144 TCATTCAAAT
Statistics
Matches: 146, Mismatches: 20, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
77 10 0.07
78 55 0.38
79 56 0.38
80 25 0.17
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (79 bp):
TTAGCCCGGATAAAACCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCACTAGCACA
ATTGCCTTCGGGTC
Found at i:6123 original size:118 final size:119
Alignment explanation
Indices: 5900--6144 Score: 395
Period size: 118 Copynumber: 2.1 Consensus size: 119
5890 CGGAATTTAG
* *
5900 CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATG
1 CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATG
*
5965 CCTTCGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAAC
66 CCTTCGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAAC
* * * *
6019 CCGGATA-AATCACTAGC-CAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACAAATG
1 CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATG
*
6082 CCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGC
66 CCTTC-GGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAAC
6137 CCGGATAT
1 CCGGATAT
6145 CATTCAAATG
Statistics
Matches: 116, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
117 47 0.41
118 62 0.53
119 7 0.06
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (119 bp):
CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATG
CCTTCGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAAC
Found at i:13855 original size:50 final size:50
Alignment explanation
Indices: 13731--14026 Score: 466
Period size: 50 Copynumber: 5.8 Consensus size: 50
13721 GATAATAACA
* ** * * *
13731 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
13782 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
13832 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
13882 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA---CCTCTCATCTCGG
13935 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
13985 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
14027 TTACCCAAAT
Statistics
Matches: 228, Mismatches: 14, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
50 145 0.64
51 33 0.14
53 50 0.22
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:13961 original size:103 final size:103
Alignment explanation
Indices: 13731--14025 Score: 470
Period size: 103 Copynumber: 2.9 Consensus size: 103
13721 GATAATAACA
** * * * *
13731 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGTTGGTGCCCATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAATGCCATGT
* *
13796 CCCAGACATGGTCTTATAGGGGA---CCTCTCATCTCGG
65 CCCAGACATGGTCTTACATGGGACCTCCTCTCATCTCGG
*
13832 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTC
13897 CCAGACATGGTCTTACATGGGACCTCCTCTCATCTCGG
66 CCAGACATGGTCTTACATGGGACCTCCTCTCATCTCGG
*
13935 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTC
14000 CCAGACATGGTCTTACATGGGACCTC
66 CCAGACATGGTCTTACATGGGACCTC
14026 TTTACCCAAA
Statistics
Matches: 181, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
100 42 0.23
101 36 0.20
103 103 0.57
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (103 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTC
CCAGACATGGTCTTACATGGGACCTCCTCTCATCTCGG
Found at i:14007 original size:153 final size:151
Alignment explanation
Indices: 13731--14026 Score: 484
Period size: 153 Copynumber: 1.9 Consensus size: 151
13721 GATAATAACA
** * * * *
13731 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGTTGGTGCCCATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATCTCGGTGCCAATGCCATGT
*
13796 CCCAGACATGGTCTTATAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTT
66 CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTT
13861 ACATGGGACCTCTCATCTCGG
131 ACATGGGACCTCTCATCTCGG
*
13882 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCCTCTCATCTCGGTGCCAATGCCAT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TCCTCTCATCTCGGTGCCAATGCCAT
* *
13947 GTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTC
64 GTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTC
14012 TTACATGGGACCTCT
129 TTACATGGGACCTCT
14027 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
151 36 0.27
153 97 0.73
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (151 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATCTCGGTGCCAATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTT
ACATGGGACCTCTCATCTCGG
Found at i:14142 original size:13 final size:13
Alignment explanation
Indices: 14121--14152 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
14111 GCTTGGATCA
*
14121 TCATCAAATAAAT
1 TCATAAAATAAAT
14134 TCATAAAATAAAT
1 TCATAAAATAAAT
14147 TCATAA
1 TCATAA
14153 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:16861 original size:39 final size:40
Alignment explanation
Indices: 16814--17062 Score: 290
Period size: 39 Copynumber: 6.3 Consensus size: 40
16804 TCTTCGGAAT
*
16814 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGG-C
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * *
16852 TTAGCCCGGATATATCAACTCGCACAAATGCCTTC-GGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * *
16891 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * * *
16931 TTAACCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * * * *
16971 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTC-GGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * * *
17010 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
17050 TTAGCCCGGATAT
1 TTAGCCCGGATAT
17063 CATTCAAATG
Statistics
Matches: 179, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
38 6 0.03
39 87 0.49
40 86 0.48
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
Found at i:16942 original size:40 final size:40
Alignment explanation
Indices: 16814--17061 Score: 301
Period size: 40 Copynumber: 6.3 Consensus size: 40
16804 TCTTCGGAAT
* * *
16814 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGG-C
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* *
16852 TTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTC-GGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
*
16891 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* *
16931 TTAACCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* * * * *
16971 TTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTC-GGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
* *
17010 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
17050 TTAGCCCGGATA
1 TTAGCCCGGATA
17062 TCATTCAAAT
Statistics
Matches: 181, Mismatches: 21, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
38 8 0.04
39 82 0.45
40 91 0.50
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
Found at i:17010 original size:79 final size:79
Alignment explanation
Indices: 16814--17061 Score: 306
Period size: 79 Copynumber: 3.2 Consensus size: 79
16804 TCTTCGGAAT
* * * * * *
16814 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGCTTAGCCCGGAT-ATATCAACTCGCAC
1 TTAGCCCGGATAAAAGCACTAGCACAAATGCCTTCGGTCTTAGCCCGGATAAAATC-ACTAGCAC
*
16877 AAATGCCTTC-GGTC
65 AATTGCCTTCGGGTC
* * *
16891 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATAAAATCACTAGCAC
1 TTAGCCCGGATAAAAGCACTAGCACAAATGCCTTC-GGTCTTAGCCCGGATAAAATCACTAGCAC
16956 AATTGCCTTCGGGTC
65 AATTGCCTTCGGGTC
* * * *
16971 TTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTCGGTCTTAGCCCGGATAAAATCACTAGCAC
1 TTAGCCCGGATAAAAGC-ACTAGCACAAATGCCTTCGGTCTTAGCCCGGATAAAATCACTAGCAC
*
17035 AATTGCCTTCGGGAC
65 AATTGCCTTCGGGTC
17050 TTAGCCCGGATA
1 TTAGCCCGGATA
17062 TCATTCAAAT
Statistics
Matches: 146, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
77 4 0.03
78 26 0.18
79 83 0.57
80 33 0.23
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (79 bp):
TTAGCCCGGATAAAAGCACTAGCACAAATGCCTTCGGTCTTAGCCCGGATAAAATCACTAGCACA
ATTGCCTTCGGGTC
Found at i:17028 original size:119 final size:118
Alignment explanation
Indices: 16818--17061 Score: 398
Period size: 119 Copynumber: 2.1 Consensus size: 118
16808 CGGAATTTAG
* * *
16818 CCGGATATAACCACAAGCACAAATGCCTTCGGGCTTAGCCCGGATATATCAACTCGCACAAATGC
1 CCGGATAAAACCACAAGCACAAATGCCTTCGGGCTTAACCCGGATATAGCAACTCGCACAAATGC
*
16883 CTTCGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAAC
66 CTTCGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAAC
* * * *
16936 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAACCACAAGCACAAATGCCTTCGGG-CTTAACCCGGATATAGCAACTCGCACAAATG
*
17001 CCTTCGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGC
65 CCTTCGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAAC
17055 CCGGATA
1 CCGGATA
17062 TCATTCAAAT
Statistics
Matches: 116, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
118 29 0.25
119 87 0.75
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (118 bp):
CCGGATAAAACCACAAGCACAAATGCCTTCGGGCTTAACCCGGATATAGCAACTCGCACAAATGC
CTTCGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAAC
Found at i:20152 original size:46 final size:46
Alignment explanation
Indices: 20102--20274 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
20092 TGGTTTAGCA
*
20102 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
20148 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
20195 TCCGAACTCATTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
20241 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
20275 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:20258 original size:93 final size:93
Alignment explanation
Indices: 20099--20269 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
20089 GGATGGTTTA
* * *
20099 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
20164 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
20192 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
20257 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
20270 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:22179 original size:40 final size:40
Alignment explanation
Indices: 22124--22266 Score: 234
Period size: 40 Copynumber: 3.6 Consensus size: 40
22114 CGGATGATAA
* *
22124 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTATA-T
22164 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTATAT
* *
22204 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTATAT
22244 CCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
22267 GGAGCAAGTA
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 97 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTATAT
Found at i:22283 original size:80 final size:80
Alignment explanation
Indices: 22124--22300 Score: 234
Period size: 80 Copynumber: 2.2 Consensus size: 80
22114 CGGATGATAA
* * *
22124 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCATTGG
* *
22189 TGCGAGTCACTATAT
66 AGCAAGTCACTATAT
*
22204 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAGTCCCGAAGGCATTG
*
22268 GAGCAAGT-AGTTATAT
65 GAGCAAGTCA-CTATAT
* *
22284 TC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAG
22301 ATGCTTGGGT
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
79 17 0.20
80 69 0.80
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCATTGG
AGCAAGTCACTATAT
Found at i:22568 original size:22 final size:21
Alignment explanation
Indices: 22527--22570 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
22517 GAATGTGCAT
22527 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
22549 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
22571 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:30175 original size:40 final size:40
Alignment explanation
Indices: 30085--30225 Score: 225
Period size: 40 Copynumber: 3.6 Consensus size: 40
30075 TCGATGATAA
* *
30085 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGAC--TAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
30123 CCGGGCTAAGTCCCGAAGGCATTT-TGTCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTG-CGAGTTACTATAT
*
30163 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
30203 CCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
30226 GAGCAAGTAG
Statistics
Matches: 96, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
37 2 0.02
38 30 0.31
40 62 0.65
41 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:30249 original size:78 final size:78
Alignment explanation
Indices: 30085--30233 Score: 228
Period size: 78 Copynumber: 1.9 Consensus size: 78
30075 TCGATGATAA
* **
30085 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATCCGGGCTAAGTCCCGAAGGCATTTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATCCGGGCTAAGTCCCGAAGGCATTGAGT
*
30150 CGAGTTACTATAT
66 CAAGTTACTATAT
*
30163 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTGA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAT--CCGGGCTAAGTCCCGAAGGCATTGA
30228 G-CAAGT
64 GTCAAGT
30234 AGTTATATTC
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
78 36 0.56
79 4 0.06
80 24 0.38
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATCCGGGCTAAGTCCCGAAGGCATTGAGT
CAAGTTACTATAT
Found at i:30524 original size:22 final size:21
Alignment explanation
Indices: 30483--30526 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
30473 GAATGTGCAT
30483 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
30505 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
30527 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:38166 original size:40 final size:39
Alignment explanation
Indices: 38122--38263 Score: 196
Period size: 40 Copynumber: 3.6 Consensus size: 39
38112 AGATTGATAA
* *
38122 CCGGGATAAGTCCCGAAGGCATTTGTGCGAGTCACTATAT
1 CCGGGCTAAGTCCCGAA-GCATTTGTGCGAGTTACTATAT
*
38162 CCGGGCTAAGTCCCGAAGCATTTGTTCCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGCATTTG-TGCGAGTTACTATAT
*
38202 CCGGGCTAAGGTCCCGAAGCA-TTGTGCGAGGTTACTATAA
1 CCGGGCTAA-GTCCCGAAGCATTTGTGCGA-GTTACTATAT
*
38242 ACGGGCTAAGTCCCGAAGCATT
1 CCGGGCTAAGTCCCGAAGCATT
38264 GGAGCAAGTA
Statistics
Matches: 92, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
39 22 0.24
40 59 0.64
41 11 0.12
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGCATTTGTGCGAGTTACTATAT
Done.