Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1980
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: 147833
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:10554 original size:45 final size:43
Alignment explanation
Indices: 10490--10578 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 43
10480 AATCTAGAAA
10490 TATAAATTATGACTCATAATCCTTTTTTAAAAATTTTTAATGATT
1 TATAAATTATGACTCATAATCC-TTTTT-AAAATTTTTAATGATT
*
10535 TATAAATTATGACTCATAATTCTTTTTAAAATTTTTAATGATT
1 TATAAATTATGACTCATAATCCTTTTTAAAATTTTTAATGATT
10578 T
1 T
10579 CCTAAATTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
43 17 0.40
44 5 0.12
45 21 0.49
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (43 bp):
TATAAATTATGACTCATAATCCTTTTTAAAATTTTTAATGATT
Found at i:11167 original size:15 final size:16
Alignment explanation
Indices: 11147--11176 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11137 AAATAACAAC
11147 ATTATA-TCATAAATA
1 ATTATACTCATAAATA
11162 ATTATACTCATAAAT
1 ATTATACTCATAAAT
11177 TATCATCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTATACTCATAAATA
Found at i:11241 original size:24 final size:24
Alignment explanation
Indices: 11214--11268 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
11204 TATACAGAGT
* * *
11214 CAGATGTGTGTTCATAATCAGATA
1 CAGATGCGTATTCAGAATCAGATA
*
11238 CAGATGCGTATTCAGATTCAGATA
1 CAGATGCGTATTCAGAATCAGATA
*
11262 CAAATGC
1 CAGATGC
11269 AGACACAGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (24 bp):
CAGATGCGTATTCAGAATCAGATA
Found at i:13719 original size:48 final size:48
Alignment explanation
Indices: 13648--13743 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
13638 ACATGAGTAA
* *
13648 GCTTTAATAGAGCTTAGTAAGTTCAACAGTTGAATCAATAAAACTTAC
1 GCTTTAATAGAGCCTAGCAAGTTCAACAGTTGAATCAATAAAACTTAC
* *
13696 GCTTTAATAGAGCCTAGCAAGTTCAACGGTTGAATTAATAAAACTTAC
1 GCTTTAATAGAGCCTAGCAAGTTCAACAGTTGAATCAATAAAACTTAC
13744 CATATAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (48 bp):
GCTTTAATAGAGCCTAGCAAGTTCAACAGTTGAATCAATAAAACTTAC
Found at i:16257 original size:50 final size:50
Alignment explanation
Indices: 16193--16325 Score: 194
Period size: 50 Copynumber: 2.7 Consensus size: 50
16183 CACTGTCATA
** * * *
16193 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCCTG
1 TCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
** *
16243 TCCCAGATATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
16293 TCCCAGATATGGTCTTACATGGGACCTCTCATA
1 TCCCAGATATGGTCTTACATGGGACCTCTCATA
16326 ACCTCAATGA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
TCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
Found at i:23837 original size:50 final size:50
Alignment explanation
Indices: 23783--23903 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
23773 CCATATATGA
** ** *
23783 TCTTACATGAGAGTTCTCATATCGGTGCCCCTA-CCATGTCCCAAACATGG
1 TCTTACATGAGACCTCTCATATCGGTG-CCAAAGCAATGTCCCAAACATGG
** * *
23833 TCTTACGGGGGACCTCTCATCTCGGTGCCAAAGCAATGTCCCAAACATGG
1 TCTTACATGAGACCTCTCATATCGGTGCCAAAGCAATGTCCCAAACATGG
*
23883 TCTTACATGGGACCTCTCATA
1 TCTTACATGAGACCTCTCATA
23904 ACCTCAATGA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
49 3 0.05
50 55 0.95
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (50 bp):
TCTTACATGAGACCTCTCATATCGGTGCCAAAGCAATGTCCCAAACATGG
Found at i:23928 original size:56 final size:50
Alignment explanation
Indices: 23816--23955 Score: 145
Period size: 56 Copynumber: 2.7 Consensus size: 50
23806 GGTGCCCCTA
** *
23816 CCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAAG
1 CCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGATGCCAAAG
* **
23866 CAATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCCAATT
1 CCATGTCCCAAACATGGTCTTACATGGGACCTCTCAT---CTC---GATGCCAAAG
** *
23922 CCATGTCCCTGACATGGTCTTACATGGGATCTCT
1 CCATGTCCCAAACATGGTCTTACATGGGACCTCT
23956 TTACTCAAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
50 34 0.46
53 3 0.04
56 37 0.50
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (50 bp):
CCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGATGCCAAAG
Found at i:30720 original size:30 final size:30
Alignment explanation
Indices: 30684--30750 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
30674 CTATTATCTT
30684 CATTTTTATTTTATTTCCTTCATCTTCCAC
1 CATTTTTATTTTATTTCCTTCATCTTCCAC
30714 CATTTTTATTTTATTTCCTTCATCTTCCAC
1 CATTTTTATTTTATTTCCTTCATCTTCCAC
30744 CATTTTT
1 CATTTTT
30751 CATCACTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.58
Consensus pattern (30 bp):
CATTTTTATTTTATTTCCTTCATCTTCCAC
Found at i:31383 original size:18 final size:20
Alignment explanation
Indices: 31362--31405 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
31352 TGTGTTTTAA
31362 ATTTTATAG-T-TTAATTTT
1 ATTTTATAGTTATTAATTTT
*
31380 ATTTTGTAGTTATTAATTTT
1 ATTTTATAGTTATTAATTTT
31400 -TTTTAT
1 ATTTTAT
31406 CTTTTAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 8 0.36
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (20 bp):
ATTTTATAGTTATTAATTTT
Found at i:51439 original size:35 final size:35
Alignment explanation
Indices: 51400--51484 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
51390 TTAGCGAGAT
**
51400 AAATGGTTTATAGGCTCTATGGAGCAACACCATGG
1 AAATGGTTTATAGGCTCTACAGAGCAACACCATGG
* * * * *
51435 AAATGGTCTACAGGTTCTACAGAGCAACACCGTGT
1 AAATGGTTTATAGGCTCTACAGAGCAACACCATGG
51470 AAATGGTTTATAGGC
1 AAATGGTTTATAGGC
51485 ACTTCAAAGC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (35 bp):
AAATGGTTTATAGGCTCTACAGAGCAACACCATGG
Found at i:51842 original size:218 final size:218
Alignment explanation
Indices: 51433--51857 Score: 638
Period size: 218 Copynumber: 1.9 Consensus size: 218
51423 GCAACACCAT
* *
51433 GGAAATGGTCTACAGGTTCTACAGAGCAACACCGTGTAAATGGTTTATAGGCACTTCAAAGCGAC
1 GGAAACGGTCTACAGGTTCTACAGAGCAACACCATGTAAATGGTTTATAGGCACTTCAAAGCGAC
* * * * *
51498 ACCTCGTAAGGGGTTCACTGACTCCTCGAAGTAAAAAGTCCATGGCAAGCCATGGCATGATCCAG
66 ACCTCGAAAGAGGTTCACTGACTCCTCGAAGTAAAAAGTCCATAGCAAACCATGGCATGATCCAA
* ** *
51563 TGGAGGATAGGTACATCTTATGGAAAAAATGAAGTTTGTCGGAGCAATAAATAGAGAAGCCCGTC
131 TGGAGGATAGGTACACCTTATGGAAAAAATGAAGTTCATCGAAGCAATAAATAGAGAAGCCCGTC
*
51628 GGTGAATATATGAGAAGACTTGA
196 GGGGAATATATGAGAAGACTTGA
* *
51651 GGAAACGGTCTACAGTTTCTACAGAGCGACACCATGTAAATGGTTTATAGGCACTTCAAAGCGAC
1 GGAAACGGTCTACAGGTTCTACAGAGCAACACCATGTAAATGGTTTATAGGCACTTCAAAGCGAC
* * *
51716 ACCTCGAAAGAGGTTCACTGACTTCTCTG-AGTAAAAAGTCCATAGCAAACTATGGTATGATCCA
66 ACCTCGAAAGAGGTTCACTGACTCCTC-GAAGTAAAAAGTCCATAGCAAACCATGGCATGATCCA
* * *
51780 ATGGAGGATAGGTACGCCTTATGGAAAAAATGAAGTTCATCGAAGCCATGAATA-AGGAAGCCCG
130 ATGGAGGATAGGTACACCTTATGGAAAAAATGAAGTTCATCGAAGCAATAAATAGA-GAAGCCCG
51844 TCGGGGAATATATG
194 TCGGGGAATATATG
51858 CAAAGACCAT
Statistics
Matches: 185, Mismatches: 20, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
217 1 0.01
218 183 0.99
219 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (218 bp):
GGAAACGGTCTACAGGTTCTACAGAGCAACACCATGTAAATGGTTTATAGGCACTTCAAAGCGAC
ACCTCGAAAGAGGTTCACTGACTCCTCGAAGTAAAAAGTCCATAGCAAACCATGGCATGATCCAA
TGGAGGATAGGTACACCTTATGGAAAAAATGAAGTTCATCGAAGCAATAAATAGAGAAGCCCGTC
GGGGAATATATGAGAAGACTTGA
Found at i:53941 original size:17 final size:17
Alignment explanation
Indices: 53919--53978 Score: 120
Period size: 17 Copynumber: 3.5 Consensus size: 17
53909 CATGTTGTCA
53919 GGTCGTGTGTGTCACAC
1 GGTCGTGTGTGTCACAC
53936 GGTCGTGTGTGTCACAC
1 GGTCGTGTGTGTCACAC
53953 GGTCGTGTGTGTCACAC
1 GGTCGTGTGTGTCACAC
53970 GGTCGTGTG
1 GGTCGTGTG
53979 ACAGCCCGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.10, C:0.22, G:0.38, T:0.30
Consensus pattern (17 bp):
GGTCGTGTGTGTCACAC
Found at i:61220 original size:54 final size:54
Alignment explanation
Indices: 61161--61267 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
61151 TCCTAAATCG
* * *
61161 TGTAACTCACTGACTTGGGTCACAC-AGTCGTGTCGTAGGTCGTGTGCCAGACCA
1 TGTAACTCACTGACTTGGGTCACACGA-CCGTATCGCAGGTCGTGTGCCAGACCA
* * *
61215 TGTAACTCTCTGACTTGTGTCACACGACCGTATCGCAGGTCGTGTGCTAGACC
1 TGTAACTCACTGACTTGGGTCACACGACCGTATCGCAGGTCGTGTGCCAGACC
61268 GTGTCGCAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 45 0.98
55 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (54 bp):
TGTAACTCACTGACTTGGGTCACACGACCGTATCGCAGGTCGTGTGCCAGACCA
Found at i:61294 original size:24 final size:24
Alignment explanation
Indices: 61240--61295 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
61230 TGTGTCACAC
* *
61240 GACCGTATCGCAGGTCGTGTGCTA
1 GACCGTGTCGCAGGCCGTGTGCTA
61264 GACCGTGTCGCAGGCCGTGTGCTA
1 GACCGTGTCGCAGGCCGTGTGCTA
*
61288 GATCGTGT
1 GACCGTGT
61296 AACTCACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (24 bp):
GACCGTGTCGCAGGCCGTGTGCTA
Found at i:68147 original size:2 final size:2
Alignment explanation
Indices: 68140--68164 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
68130 CAAAGATGAC
68140 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
68165 TTATTTGTTA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:71015 original size:173 final size:175
Alignment explanation
Indices: 70724--71055 Score: 456
Period size: 173 Copynumber: 1.9 Consensus size: 175
70714 AACAAGGTAT
* * * *
70724 GATAAGATTATGCAAAAAAAAAAAATTATATTAGTAGTTATTTAATCATGAGTTTTTTTTATCAT
1 GATAAGATTATGCAAAAAAAAAAAATTATATTAGTAGTCATTCAATCATGAGATTATTTTATCAT
* * * *
70789 TAAATTATGAAAAATTACAATATGATTATTTAACTATTCAATTTTGTATTATTCTAGCCACGT-A
66 TAAATTATGAAAAATTACAATATAATCATTTAACTATTCAAATTTATATTATTCTAGCCAC-TAA
70853 ACTATATTAAATTTTAGAGTGCTTCCATTTCTATGTAACATGCTAG
130 ACTATATTAAATTTTAGAGTGCTTCCATTTCTATGTAACATGCTAG
* *
70899 GATAAGATTATG-AAAAAAAACTAGATTATATTAGTAGTCATTCAATCAT-A-ATTATTTTATCA
1 GATAAGATTATGCAAAAAAAA-AAAATTATATTAGTAGTCATTCAATCATGAGATTATTTTATCA
* * * * *
70961 TTCAATTATGAAAATTTACAATATAATCATTTAATTATTCAAATTTATATTATTCTGGTCACTAA
65 TTAAATTATGAAAAATTACAATATAATCATTTAACTATTCAAATTTATATTATTCTAGCCACTAA
* * *
71026 ACTATATTAGATTTTAGAGTGTTTTCATTT
130 ACTATATTAAATTTTAGAGTGCTTCCATTT
71056 TACGTTAGTC
Statistics
Matches: 137, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
172 1 0.01
173 91 0.66
174 9 0.07
175 36 0.26
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (175 bp):
GATAAGATTATGCAAAAAAAAAAAATTATATTAGTAGTCATTCAATCATGAGATTATTTTATCAT
TAAATTATGAAAAATTACAATATAATCATTTAACTATTCAAATTTATATTATTCTAGCCACTAAA
CTATATTAAATTTTAGAGTGCTTCCATTTCTATGTAACATGCTAG
Found at i:78706 original size:28 final size:27
Alignment explanation
Indices: 78674--78751 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 27
78664 CAATTAATTT
78674 ATTATTTAAAATTTAAAAAATTATAAAA
1 ATTATTTAAAA-TTAAAAAATTATAAAA
* *
78702 ATTATTTAAAAAAATT-AAAACTTATTAAA
1 ATTATTT---AAAATTAAAAAATTATAAAA
*
78731 ATTATTTTAAAAATAAAAAAT
1 ATTA-TTTAAAATTAAAAAAT
78752 ATGTTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
27 5 0.12
28 12 0.29
29 15 0.37
30 5 0.12
31 4 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
ATTATTTAAAATTAAAAAATTATAAAA
Found at i:78720 original size:20 final size:21
Alignment explanation
Indices: 78684--78731 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
78674 ATTATTTAAA
*
78684 ATTTAAAAAATTATAAAAATT
1 ATTTAAAAAAATATAAAAATT
*
78705 ATTTAAAAAAAT-TAAAACTT
1 ATTTAAAAAAATATAAAAATT
78725 A-TTAAAA
1 ATTTAAAA
78732 TTATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.24
20 8 0.32
21 11 0.44
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTTAAAAAAATATAAAAATT
Found at i:78750 original size:29 final size:27
Alignment explanation
Indices: 78674--78751 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 27
78664 CAATTAATTT
*
78674 ATTATTTAAAATTTAAAAAATTATAAAA
1 ATTATTTAAAA-ATAAAAAATTATAAAA
*
78702 ATTATTTAAAAA-AATTAAAACTTATTAAA
1 ATTATTTAAAAATAA--AAAA-TTATAAAA
78731 ATTATTTTAAAAATAAAAAAT
1 ATTA-TTTAAAAATAAAAAAT
78752 ATGTTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
26 2 0.05
28 16 0.37
29 15 0.35
30 8 0.19
31 2 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
ATTATTTAAAAATAAAAAATTATAAAA
Found at i:81125 original size:16 final size:15
Alignment explanation
Indices: 81101--81145 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
81091 TTTTTAAAGT
81101 AAAAA-TAATAAATG
1 AAAAATTAATAAATG
81115 AAAAAATTAATAAAATG
1 -AAAAATTAAT-AAATG
81132 AAAAATATAATAAA
1 AAAAAT-TAATAAA
81146 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.19
16 13 0.48
17 9 0.33
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (15 bp):
AAAAATTAATAAATG
Found at i:81132 original size:17 final size:17
Alignment explanation
Indices: 81101--81152 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
81091 TTTTTAAAGT
81101 AAAAA-TAAT-AAATGA
1 AAAAATTAATAAAATGA
81116 AAAAATTAATAAAATG-
1 AAAAATTAATAAAATGA
*
81132 AAAAATATAATAAAAAGA
1 AAAAAT-TAATAAAATGA
81150 AAA
1 AAA
81153 GAAAAGAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
15 5 0.16
16 10 0.31
17 14 0.44
18 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (17 bp):
AAAAATTAATAAAATGA
Found at i:83801 original size:39 final size:39
Alignment explanation
Indices: 83758--83902 Score: 182
Period size: 39 Copynumber: 3.7 Consensus size: 39
83748 TTCACTTTTG
* * *
83758 AGCATATATCACATTACACATATAATCACATAACATTTA
1 AGCATATATCACAATACTCATATAATCACATAACATTCA
* ** **
83797 AGCATATATCATAATACTCATATAATTGCATAATGTTCA
1 AGCATATATCACAATACTCATATAATCACATAACATTCA
* * *
83836 AGCACATATCGCAATACTCATATGATCACATAACATTCA
1 AGCATATATCACAATACTCATATAATCACATAACATTCA
*
83875 AGCATATATCCCAATACTCATATAATCA
1 AGCATATATCACAATACTCATATAATCA
83903 TTTTATAGGA
Statistics
Matches: 87, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 87 1.00
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (39 bp):
AGCATATATCACAATACTCATATAATCACATAACATTCA
Found at i:95760 original size:17 final size:18
Alignment explanation
Indices: 95720--95760 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
95710 AATTTTGGGT
*
95720 CCACATGCCCGTGTTGGC
1 CCACACGCCCGTGTTGGC
*
95738 CGACACGCCCGTG-TGGC
1 CCACACGCCCGTGTTGGC
95755 CCACAC
1 CCACAC
95761 ACCAAAATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.15, C:0.44, G:0.27, T:0.15
Consensus pattern (18 bp):
CCACACGCCCGTGTTGGC
Found at i:101825 original size:38 final size:38
Alignment explanation
Indices: 101783--101855 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
101773 CTTATTAAAT
*
101783 ATACAGAGATATTAATGAATGAATGTTTTATTTTCTTA
1 ATACAAAGATATTAATGAATGAATGTTTTATTTTCTTA
101821 ATACAAAGATATTAATGAATGAATGTTTTATTTTC
1 ATACAAAGATATTAATGAATGAATGTTTTATTTTC
101856 ATTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.44
Consensus pattern (38 bp):
ATACAAAGATATTAATGAATGAATGTTTTATTTTCTTA
Found at i:102616 original size:21 final size:21
Alignment explanation
Indices: 102583--102633 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
102573 GGCTTATCTA
* *
102583 AGTGA-AAATGCTTTTTCTGT
1 AGTGAGAAATGCTTTCTCTGC
*
102603 AGTGAGAAGTGCTTTCTCTGC
1 AGTGAGAAATGCTTTCTCTGC
102624 AGTGAGAAAT
1 AGTGAGAAAT
102634 TGCACACTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (21 bp):
AGTGAGAAATGCTTTCTCTGC
Found at i:104797 original size:14 final size:14
Alignment explanation
Indices: 104778--104813 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
104768 GGAAAGTAAG
104778 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
* *
104792 TCATTTTTCAGAAG
1 TCATTTTCCAGAAA
104806 TCATTTTC
1 TCATTTTC
104814 TGTAAAACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.44
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:105431 original size:7 final size:7
Alignment explanation
Indices: 105419--105452 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
105409 ATATAATAAC
105419 AAATTTT
1 AAATTTT
105426 AAATTTT
1 AAATTTT
*
105433 AAACTTT
1 AAATTTT
*
105440 AAACTTT
1 AAATTTT
105447 AAATTT
1 AAATTT
105453 CAATTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTT
Found at i:107097 original size:23 final size:22
Alignment explanation
Indices: 107071--107145 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 22
107061 GTAGCCATTT
107071 AGGCGTTATAGAATACGCCACAA
1 AGGC-TTATAGAATACGCCACAA
* *
107094 AGGCTTAATAGATTATGCCACAA
1 AGGCTT-ATAGAATACGCCACAA
*
107117 AGGCTCTACTAG-ATACACCACAA
1 AGGCT-TA-TAGAATACGCCACAA
107140 AGGCTT
1 AGGCTT
107146 CACAAATATC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 3 0.07
23 37 0.84
24 4 0.09
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (22 bp):
AGGCTTATAGAATACGCCACAA
Found at i:110560 original size:6 final size:6
Alignment explanation
Indices: 110549--110575 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
110539 GTATTAACTG
110549 TGACCA TGACCA TGACCA TGACCA TGA
1 TGACCA TGACCA TGACCA TGACCA TGA
110576 ACACACAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (6 bp):
TGACCA
Found at i:115991 original size:12 final size:12
Alignment explanation
Indices: 115974--116001 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
115964 AAATGAGAGG
115974 AATTTTAAAGGA
1 AATTTTAAAGGA
115986 AATTTTAAAGGA
1 AATTTTAAAGGA
115998 AATT
1 AATT
116002 GAGGGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (12 bp):
AATTTTAAAGGA
Found at i:121088 original size:25 final size:25
Alignment explanation
Indices: 121019--121095 Score: 100
Period size: 25 Copynumber: 3.1 Consensus size: 25
121009 GAGTAGACTG
* *
121019 ATTTTCATAGATCGTGTGAACATTT
1 ATTTTCATAGCTCGTGTGAGCATTT
* *
121044 ACTTTCATAGCTCATGTGAGCATTT
1 ATTTTCATAGCTCGTGTGAGCATTT
* *
121069 GTTTTCATAGCTCGTGTGAGCAATT
1 ATTTTCATAGCTCGTGTGAGCATTT
121094 AT
1 AT
121096 AGTTATAACT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.42
Consensus pattern (25 bp):
ATTTTCATAGCTCGTGTGAGCATTT
Found at i:122961 original size:29 final size:29
Alignment explanation
Indices: 122926--122985 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
122916 TTTTGACATG
122926 ATTGATTATTGGAAGGTTTTATTTATGAT
1 ATTGATTATTGGAAGGTTTTATTTATGAT
122955 ATTGATTATTGGAAGGTTTTATTTATGAT
1 ATTGATTATTGGAAGGTTTTATTTATGAT
122984 AT
1 AT
122986 AATTGATCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (29 bp):
ATTGATTATTGGAAGGTTTTATTTATGAT
Found at i:129916 original size:21 final size:22
Alignment explanation
Indices: 129877--129917 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
129867 TTTAAGTTAT
129877 TTATTAAATTACAAGTTTAATC
1 TTATTAAATTACAAGTTTAATC
129899 TTATT-AATTAACAA-TTTAA
1 TTATTAAATT-ACAAGTTTAA
129918 AACACATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (22 bp):
TTATTAAATTACAAGTTTAATC
Found at i:133893 original size:13 final size:13
Alignment explanation
Indices: 133875--133899 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
133865 TAATAATTAT
133875 TTAATATATATAA
1 TTAATATATATAA
133888 TTAATATATATA
1 TTAATATATATA
133900 TTTTTTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAATATATATAA
Found at i:136257 original size:10 final size:10
Alignment explanation
Indices: 136254--136286 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
136244 TTTTTTTGGA
136254 TTTTTAGATT
1 TTTTTAGATT
136264 TTTTTAGATT
1 TTTTTAGATT
136274 TTTTATAG-TT
1 TTTT-TAGATT
136284 TTT
1 TTT
136287 AATATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 19 0.86
11 3 0.14
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (10 bp):
TTTTTAGATT
Found at i:136479 original size:21 final size:22
Alignment explanation
Indices: 136437--136479 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
136427 TTATTGTAAA
** *
136437 TATAAAATATTTATTTTTATAT
1 TATAAAATATTTAAATTAATAT
136459 TATAAAA-ATTTAAATTAATAT
1 TATAAAATATTTAAATTAATAT
136480 AAATTAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATAAAATATTTAAATTAATAT
Found at i:137228 original size:22 final size:21
Alignment explanation
Indices: 137198--137238 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
137188 TTTTATTTAA
137198 AAATATATTTAAAATTTTATCT
1 AAATATATTT-AAATTTTATCT
* *
137220 AAATCTATTTATATTTTAT
1 AAATATATTTAAATTTTAT
137239 AAATTACAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATATATTTAAATTTTATCT
Found at i:142713 original size:47 final size:47
Alignment explanation
Indices: 142629--142988 Score: 540
Period size: 47 Copynumber: 7.6 Consensus size: 47
142619 TATTTGAATA
142629 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
142678 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
142725 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
142774 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
142821 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
142868 AATGTGAAAGTGTATATATGCGACAGGGCCGAGTGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
142915 AATGTGAAAGTGTATATATGCGACAGGGCCGAATGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
142962 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
142989 TCCCGAAGGG
Statistics
Matches: 290, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
47 233 0.80
49 57 0.20
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:143208 original size:37 final size:37
Alignment explanation
Indices: 143107--143208 Score: 152
Period size: 37 Copynumber: 2.8 Consensus size: 37
143097 CCAAGCTCTA
*
143107 AAGACCCGATGACTAT-GTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACT-TCGTGTGGAGATTTTGTCCGGGT
*
143144 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACTTCGTGTGGAGATTTTGTCCGGGT
* *
143181 AAGACCCGATAACTTCATGTGGAGATTT
1 AAGACCCGATGACTTCGTGTGGAGATTT
143209 CGTCTGAGCT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (37 bp):
AAGACCCGATGACTTCGTGTGGAGATTTTGTCCGGGT
Found at i:144543 original size:40 final size:40
Alignment explanation
Indices: 144492--144668 Score: 239
Period size: 40 Copynumber: 4.4 Consensus size: 40
144482 AATGTCCAGG
* *
144492 CTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA
1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGA
* *
144532 CTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA
1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGA
*
144572 CTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTG-
1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCG-GA
** * * *
144612 CTAAACCCCGAAGAGCATTTGTGCTAGTGTTATATCCGGG
1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGA
*
144652 CTAGGTCCCGAAGAGCA
1 CTAAGTCCCGAAGAGCA
144669 ATCATGCTGG
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.01
40 122 0.98
41 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
CTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGA
Done.