Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold597
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: 59232
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.22
Warning! 17838 characters in sequence are not A, C, G, or T
Found at i:392 original size:25 final size:26
Alignment explanation
Indices: 346--395 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
336 ATACAAATAC
346 ATTTTTATAATATACACTTATTTTTTT
1 ATTTTTATAATATACAC-TATTTTTTT
373 ATTTATTATAA-ATACA-TATTTTT
1 ATTT-TTATAATATACACTATTTTT
396 ATGTTTCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.32
27 9 0.41
28 6 0.27
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTTATAATATACACTATTTTTTT
Found at i:13292 original size:44 final size:45
Alignment explanation
Indices: 13175--13466 Score: 201
Period size: 44 Copynumber: 6.6 Consensus size: 45
13165 ATTATACAGG
* * *
13175 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGTAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGGTA-A
* *
13221 TCTTATCTCCCTGAGATTATAGCGGAGCAGATCAAAG-ATGGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGGTAA
* * * * *
13265 TCCTATCTCCCTGATATTACAGTGGAGCGGATTAAA-ACCAAGG--A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGA--ATGGTAA
* ** * ** *
13309 TCTTATCTCTCTGA-AGTTACAGCAGAGTAGATC-GCGCCA-GG---
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAG-AATGGTAA
* ** ** * * *
13350 TCTTATTTCCCTGAGATTACAGTGGAATAGGCCGAAGAATTGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGGTA-A
*
13396 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-ATGGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGGTAA
* *
13440 TCCTATCTCCCTGATATTACAGTGGAG
1 TCTTATCTCCCTGAGATTACAGTGGAG
13467 TGGATTAAAA
Statistics
Matches: 188, Mismatches: 45, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
41 25 0.13
42 5 0.03
43 2 0.01
44 81 0.43
45 9 0.05
46 66 0.35
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (45 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGGTAA
Found at i:13418 original size:87 final size:87
Alignment explanation
Indices: 13307--13604 Score: 243
Period size: 87 Copynumber: 3.4 Consensus size: 87
13297 TAAAACCAAG
* *
13307 GATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGCCAGGTCTTATTTCCCTGAGATTACAG
1 GATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGCGCCAGGTCTTATTTCCCTGAGATTACAG
*
13372 TGGAATAGGCCGAAGAATTGCA
66 TGGAATAGGCCGAAGAATTCCA
* ** * * *
13394 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCAAAG--ATGGTAATCCTATCTCCCTGATA
1 GATCTTATCTCCCTGAAG-TTACAGCAGAGCAGATC-GCGCCA-GG---TCTTATTTCCCTGAGA
* ***
13456 TTACAGTGGAGT-GGATTAA-AA--CCAA
60 TTACAGTGGAATAGGCCGAAGAATTCC-A
* * * * * **
13481 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATTGCACCTTGTCTTATTTCCCTGAGATTACA
1 -GATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGCGCCAGGTCTTATTTCCCTGAGATTACA
* * *
13546 GTGGAACAGACCGAAGAATTTCA
65 GTGGAATAGGCCGAAGAATTCCA
*
13569 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCG
1 GATCTTATCTCCCTGAAG-TTACAGCAGAGCAGATCG
13605 AAGACACTAT
Statistics
Matches: 157, Mismatches: 38, Indels: 32
0.69 0.17 0.14
Matches are distributed among these distances:
85 23 0.15
86 9 0.06
87 62 0.39
88 32 0.20
89 7 0.04
90 24 0.15
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (87 bp):
GATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGCGCCAGGTCTTATTTCCCTGAGATTACAG
TGGAATAGGCCGAAGAATTCCA
Found at i:13462 original size:175 final size:175
Alignment explanation
Indices: 13171--13645 Score: 765
Period size: 175 Copynumber: 2.7 Consensus size: 175
13161 GTTCATTATA
* * *
13171 CAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGTAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAG
* *
13236 ATTATAGCGGAGCAGATCAAAGATGGTAATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAA
66 ATTACAGCGGAGCAGATCAAAGATGGTAATCCTATCTCCCTGATATTACAGTGGAGTGGATTAAA
*
13301 ACCAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGC
131 ACCAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCAC
* *
13346 CAGGTCTTATTTCCCTGAGATTACAGTGGAATAGGCCGAAGAATTGCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAG
13411 ATTACAGCGGAGCAGATCAAAGATGGTAATCCTATCTCCCTGATATTACAGTGGAGTGGATTAAA
66 ATTACAGCGGAGCAGATCAAAGATGGTAATCCTATCTCCCTGATATTACAGTGGAGTGGATTAAA
* *
13476 ACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATTGCAC
131 ACCAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCAC
** *
13521 CTTGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAG
* *** * *
13586 ATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AGTGCAGTGGAGTGGATT
66 ATTACAGCGGAGCAGATCAAAGATGGTAATCCTATCTCCCTGATATTACAGTGGAGTGGATT
13646 GAAGCAACAA
Statistics
Matches: 279, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
173 16 0.06
174 15 0.05
175 248 0.89
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (175 bp):
CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAG
ATTACAGCGGAGCAGATCAAAGATGGTAATCCTATCTCCCTGATATTACAGTGGAGTGGATTAAA
ACCAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCAC
Found at i:13491 original size:44 final size:43
Alignment explanation
Indices: 13268--13516 Score: 125
Period size: 44 Copynumber: 5.7 Consensus size: 43
13258 ATGGTAATCC
**
13268 TATCTCCCTGATATTACAGTGGAGCGGATTAAAACCAAGGATCT
1 TATCTCCCTGA-ATTACAGTGGAGTAGATTAAAACCAAGGATCT
* ** ****
13312 TATCTCTCTGAAGTTACAGCAGAGTAGA-TCGCGCC-AGG-TCT
1 TATCTCCCTGAA-TTACAGTGGAGTAGATTAAAACCAAGGATCT
* * *** *
13353 TATTTCCCTGAGATTACAGTGGAATAGGCCGAAGAATTGC-A-GATCT
1 TATCTCCCTGA-ATTACAGTGGAGTA-GATTAA-AA--CCAAGGATCT
* * * * * *
13399 TATCTCCCTGAGATTACAGCGGAGCAGA-TCAAA-GATGGTAATCC
1 TATCTCCCTGA-ATTACAGTGGAGTAGATTAAAACCAAGG--ATCT
*
13443 TATCTCCCTGATATTACAGTGGAGTGGATTAAAACCAAGGATCT
1 TATCTCCCTGA-ATTACAGTGGAGTAGATTAAAACCAAGGATCT
* *
13487 TATCTCTCTGAAGTTACAGTAGAGTAGATT
1 TATCTCCCTGAA-TTACAGTGGAGTAGATT
13517 GCACCTTGTC
Statistics
Matches: 148, Mismatches: 42, Indels: 30
0.67 0.19 0.14
Matches are distributed among these distances:
41 22 0.15
42 6 0.04
43 7 0.05
44 77 0.52
45 6 0.04
46 30 0.20
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGAATTACAGTGGAGTAGATTAAAACCAAGGATCT
Found at i:15999 original size:108 final size:108
Alignment explanation
Indices: 15810--16216 Score: 595
Period size: 108 Copynumber: 3.7 Consensus size: 108
15800 NNNNNNNNNN
*
15810 TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCCACC-A
1 TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCAACCAA
* *
15874 ATTGACTTAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATA
66 ATAG-CTAAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATA
*
15918 TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCGACCAA
1 TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCAACCAA
* *
15983 ATAGCTAAATATCCTTTT-AAAAACTTTTAAAAAAATAAGGCAATG
66 ATAGCTAAATATCCTTTTCAAAAA-TTTT--CAAAATAAGGCAATA
* *
16028 TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGAGTGTCGATTTTTCTCGTTCAACC
1 TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGA--TTTCTCGTTCAACC
* *
16093 AAAGAGCTAAATATCCTTTTCAACAA-TTTCAAAATAAGGCAATA
64 AAATAGCTAAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATA
* * * *
16137 TTTTGTGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCACGTTTAGCCAA
1 TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCAACCAA
* *
16202 ATTGCTAAATCTCCT
66 ATAGCTAAATATCCT
16217 CTTGAATTTT
Statistics
Matches: 271, Mismatches: 21, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
107 30 0.11
108 79 0.29
109 63 0.23
110 60 0.22
111 3 0.01
112 32 0.12
113 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (108 bp):
TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCAACCAA
ATAGCTAAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATA
Found at i:16188 original size:219 final size:218
Alignment explanation
Indices: 15810--16216 Score: 658
Period size: 219 Copynumber: 1.9 Consensus size: 218
15800 NNNNNNNNNN
* * *
15810 TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCCACCAA
1 TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGAGTGTCGATTTCTCGTTCAACCAA
* *
15875 TTGACTTAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGG
66 TAGACTAAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGG
*
15940 AACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCGA-CCAAATAGCTAAATATCCTTTTAAA
131 AACGTGCCCTAAGGTACTGGGTTTCGATTTCACGTT-GAGCCAAATAGCTAAATATCCTTTTAAA
16004 AACTTTTAAAAAAATAAGGCAATG
195 AACTTTTAAAAAAATAAGGCAATG
16028 TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGAGTGTCGATTTTTCTCGTTCAACC
1 TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGAGTGTCGA--TTTCTCGTTCAACC
* *
16093 AA-AGAGCTAAATATCCTTTTCAACAA-TTTCAAAATAAGGCAATATTTTGTGTTTGGAAATTCG
64 AATAGA-CTAAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCG
* * *
16156 AGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCACGTTTAGCCAAATTGCTAAATCTCCT
128 AGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCACGTTGAGCCAAATAGCTAAATATCCT
16217 CTTGAATTTT
Statistics
Matches: 174, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
218 48 0.28
219 93 0.53
220 33 0.19
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (218 bp):
TTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGAGTGTCGATTTCTCGTTCAACCAA
TAGACTAAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGG
AACGTGCCCTAAGGTACTGGGTTTCGATTTCACGTTGAGCCAAATAGCTAAATATCCTTTTAAAA
ACTTTTAAAAAAATAAGGCAATG
Found at i:17658 original size:18 final size:19
Alignment explanation
Indices: 17620--17658 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17610 TGACGTTTGG
* *
17620 GGACTCAATTTAGTCAAAA
1 GGACTAAATTTAGTAAAAA
17639 GGACTAAATTT-GTAAAAA
1 GGACTAAATTTAGTAAAAA
17657 GG
1 GG
17659 CAAAAGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (19 bp):
GGACTAAATTTAGTAAAAA
Found at i:35966 original size:50 final size:50
Alignment explanation
Indices: 35907--36085 Score: 261
Period size: 50 Copynumber: 3.6 Consensus size: 50
35897 ATCCTCTAGC
35907 AGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTA
1 AGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTA
* **
35957 AGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTA
1 AGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTA
* * **
36007 AGACCATGTCTGGGACATGGCA-TGGATACCGACATGAGAACATCCCATGTA
1 AGACCATGTCTGGGACATGGCATTGG-CACCGAGATGAG-AGGTCCCATGTA
*
36058 AGACCATGTCTGGGACATGGCTTTGGCA
1 AGACCATGTCTGGGACATGGCATTGGCA
36086 TGTTATTATC
Statistics
Matches: 114, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
49 3 0.03
50 78 0.68
51 30 0.26
52 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTA
Found at i:46593 original size:207 final size:205
Alignment explanation
Indices: 46238--47266 Score: 1452
Period size: 207 Copynumber: 5.0 Consensus size: 205
46228 TATCTCCTGT
* * * *
46238 TTTTTTTAGCTATTTAGACTTTCCACTCAACCTAATAATTTACCGCATCATTTTTTGTATCAAAC
1 TTTTTTTAGCTATTTAGATTTTCCACTCAACCTAATAATTTACCACATCA-ATTTTGTATCAGA-
* * * *
46303 CCTAATCAGATCTTAGGACTTCTATTGGAAATCACTTTTAAGCTATGACTGGACATACAAGAGGT
64 GCTAATTAGATCTTAGGACTTATATTGGAAATCACTTTTAAGCCATGACTGGACATACAAGAGGT
* **
46368 CAAGGAAAAGAAAATCAAAGCCAACAAATAGAGTTGTCAGAGATGAGGCCCATGATAGAAGAATT
129 CAAGGAAGAGAAAATCAAAGCCAACAAATAGAGTTGTCAGAGATGAGGCGTATGATAGAAGAATT
*
46433 GTTGCATTTTAA
194 GTCGCATTTTAA
* *
46445 TTTTTTTAGCTATTTAGATTTTCCACTCAACCAAATAATTTACCACATCAATTTTGATATCAAAG
1 TTTTTTTAGCTATTTAGATTTTCCACTCAACCTAATAATTTACCACATCAATTTTG-TATCAGAG
* * * *
46510 TCTAATTAGATCCTAAGACTTATATTGGAAATCGCTTTTAAGCCATGACTGAACATACAAGAGGT
65 -CTAATTAGATCTTAGGACTTATATTGGAAATCACTTTTAAGCCATGACTGGACATACAAGAGGT
* * * * ** *
46575 TAAGGAAGAGAAAATCAAAACCAACAAATAAAGTTGTCAGGGATGAGATGCATGATAGAAGAATT
129 CAAGGAAGAGAAAATCAAAGCCAACAAATAGAGTTGTCAGAGATGAGGCGTATGATAGAAGAATT
* *
46640 GTCCCATTCTAA
194 GTCGCATTTTAA
*
46652 TTTTTTTAGCTATTTAGATTTTCCACTCAACCTAATAATTTACCACATCATTTTTGGTATCAGAG
1 TTTTTTTAGCTATTTAGATTTTCCACTCAACCTAATAATTTACCACATCAATTTT-GTATCAGAG
46717 CATAATTAGATCTTAGGACTTATATTGGAAATCACTTTTAAGCCATGACTGGACATACAAGAGGT
65 C-TAATTAGATCTTAGGACTTATATTGGAAATCACTTTTAAGCCATGACTGGACATACAAGAGGT
* * * *
46782 AAAGTAAGAGAAAATCAAAGCCAAAAAATAGAGTTGTCAGAGATGAGGCGTATGATAGAAAAATT
129 CAAGGAAGAGAAAATCAAAGCCAACAAATAGAGTTGTCAGAGATGAGGCGTATGATAGAAGAATT
46847 GTCGCATTTTAA
194 GTCGCATTTTAA
*
46859 TTTTTTTTAACTATTTAGATTTTCCACTCAACCTAATAATTTA-CAGCATCAATTTTTGTATCAG
1 -TTTTTTTAGCTATTTAGATTTTCCACTCAACCTAATAATTTACCA-CATCAA-TTTTGTATCAG
* * *
46923 AGTCTAATTAGATCTTATGACTTATATTGAAAATCACTTTTAAGCCATGATTGGACATACAAGAG
63 AG-CTAATTAGATCTTAGGACTTATATTGGAAATCACTTTTAAGCCATGACTGGACATACAAGAG
*
46988 GTCAAGGAAGAGAAAATCAAAGCCAACAAATAGAGTTGTCAAAGATGAGGC-TATGATAGAAGAA
127 GTCAAGGAAGAGAAAATCAAAGCCAACAAATAGAGTTGTCAGAGATGAGGCGTATGATAGAAGAA
* *
47052 TTGACACATTTTAA
192 TTGTCGCATTTTAA
* * * *
47066 TTTTTTTAGCTATTTAGGTTTTTCACTCAACCAAATAATTTACCACATCAGTTTTGGTATCAGAG
1 TTTTTTTAGCTATTTAGATTTTCCACTCAACCTAATAATTTACCACATCAATTTT-GTATCAGAG
* * * * *
47131 CTTAATTAGATCCTATGACTTATATTAGAAATCACTTTTAAGCCATGAATAGG-CATATAAGAGG
65 C-TAATTAGATCTTAGGACTTATATTGGAAATCACTTTTAAGCCATGACT-GGACATACAAGAGG
* * * *
47195 TCAAGGAAGAGAAAATCAAAGCCAAGAAATAGAGTTGTCAAAGATGAGGCGTATGATTGAAGATT
128 TCAAGGAAGAGAAAATCAAAGCCAACAAATAGAGTTGTCAGAGATGAGGCGTATGATAGAAGAAT
47260 TGTCGCA
193 TGTCGCA
47267 AGCTATACTA
Statistics
Matches: 740, Mismatches: 69, Indels: 26
0.89 0.08 0.03
Matches are distributed among these distances:
205 5 0.01
206 161 0.22
207 408 0.55
208 161 0.22
209 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (205 bp):
TTTTTTTAGCTATTTAGATTTTCCACTCAACCTAATAATTTACCACATCAATTTTGTATCAGAGC
TAATTAGATCTTAGGACTTATATTGGAAATCACTTTTAAGCCATGACTGGACATACAAGAGGTCA
AGGAAGAGAAAATCAAAGCCAACAAATAGAGTTGTCAGAGATGAGGCGTATGATAGAAGAATTGT
CGCATTTTAA
Found at i:51459 original size:18 final size:18
Alignment explanation
Indices: 51433--51473 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
51423 CCCGAAATAT
*
51433 AGGCATGAAATTTTGCCC
1 AGGCCTGAAATTTTGCCC
51451 AGGCCTGAAATTTTGCCC
1 AGGCCTGAAATTTTGCCC
51469 AGGCC
1 AGGCC
51474 CGGCCCGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (18 bp):
AGGCCTGAAATTTTGCCC
Found at i:51889 original size:26 final size:27
Alignment explanation
Indices: 51842--51912 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
51832 TTAAGATTCA
*
51842 AAATATTTATAAAAATT-TTAAATTTT
1 AAATATTTATAAAAATTATAAAATTTT
*
51868 AAATTTTTA-AAAAATATATAAAATTTTT
1 AAATATTTATAAAAAT-TATAAAA-TTTT
* *
51896 AAAAATTTCTAAAAATT
1 AAATATTTATAAAAATT
51913 GTATAAAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 6 0.17
26 9 0.25
27 4 0.11
28 11 0.31
29 6 0.17
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATATTTATAAAAATTATAAAATTTT
Found at i:52152 original size:15 final size:14
Alignment explanation
Indices: 52119--52157 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
52109 TAATTTTTTT
*
52119 AATTTAACTCGAAC
1 AATTTGACTCGAAC
*
52133 AATTTGACTCGATTC
1 AATTTGACTCGA-AC
52148 AATTTGACTC
1 AATTTGACTC
52158 AACTTGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (14 bp):
AATTTGACTCGAAC
Found at i:53539 original size:28 final size:29
Alignment explanation
Indices: 53508--53570 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
53498 AAATACTAAA
* *
53508 ATAATTTTGTTAAATTTTAAT-TTTTTTT
1 ATAATTTTATTAAATTTTAATGTTTTCTT
* * *
53536 ATAATTTTATTGATTTTTTATGTTTTCTT
1 ATAATTTTATTAAATTTTAATGTTTTCTT
53565 ATAATT
1 ATAATT
53571 CTAAAATGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (29 bp):
ATAATTTTATTAAATTTTAATGTTTTCTT
Found at i:55171 original size:13 final size:14
Alignment explanation
Indices: 55153--55182 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55143 TAATATTTAG
55153 GGTTCGA-GTTCAA
1 GGTTCGAGGTTCAA
55166 GGTTCGAGGTTCAA
1 GGTTCGAGGTTCAA
55180 GGT
1 GGT
55183 AAAATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.20, C:0.13, G:0.37, T:0.30
Consensus pattern (14 bp):
GGTTCGAGGTTCAA
Found at i:55253 original size:32 final size:32
Alignment explanation
Indices: 55208--55276 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
55198 ATTATGTGTC
*
55208 AATGACATGGAAAAAATTGCACAAAAGTTACT
1 AATGTCATGGAAAAAATTGCACAAAAGTTACT
*
55240 AATGTCATTGAAAAAATTGCACAAAAGTTACT
1 AATGTCATGGAAAAAATTGCACAAAAGTTACT
55272 AATGT
1 AATGT
55277 TTTTCTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (32 bp):
AATGTCATGGAAAAAATTGCACAAAAGTTACT
Found at i:58343 original size:58 final size:59
Alignment explanation
Indices: 58233--58364 Score: 176
Period size: 58 Copynumber: 2.2 Consensus size: 59
58223 ATAGAAATGG
* *
58233 TGAAAATGGAGAAAATGGAGAAATGTGAAACATTCGGAAATGATTATAGTTTTCTCCAAAA
1 TGAAAAT-GA-AAAATGGAGAAATGTGAAACATTCAGAAATGAATATAGTTTTCTCCAAAA
* * * * *
58294 TGAAAATGAAAAATGGATAAATG-GAATCATTTAGAAATGAATGTGGTTTTCTCCAAAA
1 TGAAAATGAAAAATGGAGAAATGTGAAACATTCAGAAATGAATATAGTTTTCTCCAAAA
58352 TGAAAATGAAAAA
1 TGAAAATGAAAAA
58365 AAAAAGAATG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
58 42 0.66
59 13 0.20
60 2 0.03
61 7 0.11
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (59 bp):
TGAAAATGAAAAATGGAGAAATGTGAAACATTCAGAAATGAATATAGTTTTCTCCAAAA
Done.