Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1126
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: 70468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:10907 original size:40 final size:39
Alignment explanation
Indices: 10863--11046 Score: 221
Period size: 40 Copynumber: 4.7 Consensus size: 39
10853 GCTCCTCGTT
* *
10863 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
*
10903 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
* *
10943 CAAATGCCTTCGGG-CTTAGCCCGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
* * * *
10981 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
11022 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
11047 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
37 2 0.02
38 23 0.18
39 19 0.15
40 69 0.55
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:10989 original size:78 final size:81
Alignment explanation
Indices: 10863--11044 Score: 230
Period size: 78 Copynumber: 2.3 Consensus size: 81
10853 GCTCCTCGTT
* **
10863 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
10927 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
10943 CAAATGCCTTCGGG-CTTAGCCCGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
11006 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
11022 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
11045 GACATCATTC
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
77 3 0.03
78 46 0.52
79 26 0.29
80 14 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:15237 original size:44 final size:44
Alignment explanation
Indices: 15165--15437 Score: 159
Period size: 44 Copynumber: 6.2 Consensus size: 44
15155 AGCAATAGCA
** *
15165 GAGCAGATCAAAGATGGTGGATCTTATCTCCCTGAGATTACAGCG
1 GAGCAGATTGAAGATGGT-AATCTTATCTCCCTGAGATTACAGCG
* * ** *
15210 GAGCAGATTGAAGCTGGTAATCCTATCTCTTTGAGATTACAGTG
1 GAGCAGATTGAAGATGGTAATCTTATCTCCCTGAGATTACAGCG
* * **
15254 GAGCAGATT-AAAATAAAGG--ATCTTATCTCTCTGA-AGTTACAGTA
1 GAGCAGATTGAAGAT---GGTAATCTTATCTCCCTGAGA-TTACAGCG
* * * *
15298 GAGTAGATCG--CAT--TATGTCTTATCTCCCTGAGATTACAGTC-
1 GAGCAGATTGAAGATGGTA-ATCTTATCTCCCTGAGATTACAG-CG
** * ** * *
15339 GAATAGACTGAAGAATTTTAGATCTTATCTTCTTGAGATTACAGCG
1 GAGCAGATTGAAG-ATGGTA-ATCTTATCTCCCTGAGATTACAGCG
* * *
15385 GAGCAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTACAGTG
1 GAGCAGATTGAAGATGGTAATCTTATCTCCCTGAGATTACAGCG
*
15429 GAGCGGATT
1 GAGCAGATT
15438 AAAATAAAGG
Statistics
Matches: 174, Mismatches: 38, Indels: 33
0.71 0.16 0.13
Matches are distributed among these distances:
41 26 0.15
42 1 0.01
43 6 0.03
44 88 0.51
45 19 0.11
46 34 0.20
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (44 bp):
GAGCAGATTGAAGATGGTAATCTTATCTCCCTGAGATTACAGCG
Found at i:15456 original size:44 final size:42
Alignment explanation
Indices: 15183--15479 Score: 147
Period size: 44 Copynumber: 6.8 Consensus size: 42
15173 CAAAGATGGT
* **
15183 GGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATA
* **
15225 GGTAATCCTATCTCTTTGAGATTACAGTGGAGCAGATTAAAATAAA
1 GG--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT--A
* * * *** *
15271 GGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATTA
1 GGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATA
* * ** *
15313 TG-TCTTATCTCCCTGAGATTACAGTCGAATAGACTGAAGAATTTTA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA---TA
* * * **
15359 -GATCTTATCTTCTTGAGATTACAGCGGAGCAGATTGAAGCT-
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATA
* *
15400 GGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 GG--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT--A
* * * *
15446 GGATCTTATCTCTCTGA-AGTACAGTAGAGTAGAT
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGAT
15480 CGCATCAGGT
Statistics
Matches: 191, Mismatches: 44, Indels: 39
0.70 0.16 0.14
Matches are distributed among these distances:
41 26 0.14
42 8 0.04
43 21 0.11
44 101 0.53
45 2 0.01
46 33 0.17
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (42 bp):
GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATA
Found at i:15616 original size:162 final size:162
Alignment explanation
Indices: 15334--15833 Score: 725
Period size: 162 Copynumber: 3.0 Consensus size: 162
15324 CCTGAGATTA
* * * *
15334 CAGTCGAATAGACTGAAGAATTTTAGATCTTATCTTCTTGAGATTACAGCGGAGCAGATTGAAGC
1 CAGTGGAATAGACCGAAGAATTTCAGATCTTAT-TTCCTGAGATTACAGCGGAGCAGATTGAAGC
15399 TGGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAA
65 TGGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAA
15464 GTACAGTAGAGTAGATCGCATCAGGTCTTATCT
130 GTACAGTAGAGTAGATCGCATCAGGTCTTATCT
* *
15497 CAGTGGAATTGACCGAAGAATTTCAGATCTTATTTCCTGAGAATACAGCGGAGCAGATTGAAGCT
1 CAGTGGAATAGACCGAAGAATTTCAGATCTTATTTCCTGAGATTACAGCGGAGCAGATTGAAGCT
*
15562 GGTAATCCTATCTCTCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAG
66 GGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAG
* *
15627 TGACGGTAGAGTAGATCGCATCAGGTCATATCT
131 T-ACAGTAGAGTAGATCGCATCAGGTCTTATCT
*
15660 CCCTGAGATTACAATGGAATAGACCGAAGAATTTCAGATCTTATCTCCTTGAGATTACAGCGGAG
1 --C--AG-------TGGAATAGACCGAAGAATTTCAGATCTTATTTCC-TGAGATTACAGCGGAG
*
15725 CAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGTATCTT
54 CAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
* * *
15790 A--TCTCAGAAGTTACAGTAGAGCAGATCGTATCAGGTCTTATCT
119 ATCTCTCTGAAG-TACAGTAGAGTAGATCGCATCAGGTCTTATCT
15833 C
1 C
15834 CCTGAGATTA
Statistics
Matches: 304, Mismatches: 19, Indels: 20
0.89 0.06 0.06
Matches are distributed among these distances:
162 95 0.31
163 58 0.19
165 1 0.00
167 2 0.01
171 1 0.00
173 35 0.12
174 33 0.11
175 79 0.26
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (162 bp):
CAGTGGAATAGACCGAAGAATTTCAGATCTTATTTCCTGAGATTACAGCGGAGCAGATTGAAGCT
GGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAG
TACAGTAGAGTAGATCGCATCAGGTCTTATCT
Found at i:15793 original size:44 final size:44
Alignment explanation
Indices: 15697--15794 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
15687 AGAATTTCAG
* ** *
15697 ATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTGGTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAAATAGTA
* * *
15741 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAAAGT-
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAAAT--AGTA
15785 ATCTTATCTC
1 ATCTTATCTC
15795 AGAAGTTACA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
43 3 0.07
44 39 0.89
45 2 0.05
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (44 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAAATAGTA
Found at i:15950 original size:173 final size:173
Alignment explanation
Indices: 15500--15906 Score: 523
Period size: 173 Copynumber: 2.3 Consensus size: 173
15490 CTTATCTCAG
* * * * * * *
15500 TGGAATTGACCGAAGAATTTCAGATCTTA-TTTCCTGAGAATACAGCGGAGCAGATTGAAGCTGG
1 TGGAATAGACCGAAGAATTACAGATCTTACCTCCCTAAG-ATACAGCGGAGCAGATCGAAGCTCG
* * *
15564 TAATCCTATCTCTCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTG
65 TAATCCTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTA-CTCTCAGAAGTG
* *
15629 ACGGTAGAGTAGATCGCATCAGGTCATATCTCCCTGAGATTACAA
129 ACAGTAGAGCAGATCGCATCAGGTCATATCTCCCTGAGATTACAA
* * * * * *
15674 TGGAATAGACCGAAGAATTTCAGATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTGG
1 TGGAATAGACCGAAGAATTACAGATCTTACCTCCCTAAGA-TACAGCGGAGCAGATCGAAGCTCG
* * *
15739 TAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGTATCTTA-TCTCAGAAGTTA
65 TAATCCTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTACTCTCAGAAGTGA
* * *
15803 CAGTAGAGCAGATCGTATCAGGTCTTATCTCCCTGAGATTACAG
130 CAGTAGAGCAGATCGCATCAGGTCATATCTCCCTGAGATTACAA
* *
15847 TGGAATAGACCGAAGAATTACAGATCTTGCCTCCCTAAGA-AGTAGCGGAGCAGATCGAAG
1 TGGAATAGACCGAAGAATTACAGATCTTACCTCCCTAAGATA-CAGCGGAGCAGATCGAAG
15907 ACATCGAATC
Statistics
Matches: 210, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
171 1 0.00
172 16 0.08
173 84 0.40
174 29 0.14
175 80 0.38
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (173 bp):
TGGAATAGACCGAAGAATTACAGATCTTACCTCCCTAAGATACAGCGGAGCAGATCGAAGCTCGT
AATCCTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTACTCTCAGAAGTGAC
AGTAGAGCAGATCGCATCAGGTCATATCTCCCTGAGATTACAA
Found at i:26079 original size:25 final size:25
Alignment explanation
Indices: 26037--26090 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
26027 TTTTCTCAAA
*
26037 AATTTAATTAATATAAAATATTA-AT
1 AATTTAATAAATATAAAA-ATTAGAT
26062 AATTTAATAAAT-TGAAAAATTAGAT
1 AATTTAATAAATAT-AAAAATTAGAT
26087 AATT
1 AATT
26091 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
AATTTAATAAATATAAAAATTAGAT
Found at i:40128 original size:17 final size:17
Alignment explanation
Indices: 40096--40133 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
40086 TTCCATTCTA
40096 ATTTGACCCAAAAAATTT
1 ATTTGACCCAAAAAA-TT
*
40114 ATTTTACCC-AAAAATT
1 ATTTGACCCAAAAAATT
40130 ATTT
1 ATTT
40134 AAAACTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 5 0.26
18 8 0.42
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTTGACCCAAAAAATT
Found at i:61899 original size:47 final size:47
Alignment explanation
Indices: 61772--62102 Score: 567
Period size: 47 Copynumber: 7.1 Consensus size: 47
61762 GAAATGATAG
*
61772 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
61819 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
61865 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
61912 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
61959 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
62006 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
62053 -AGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
62099 TAAG
1 TAAG
62103 TCCGAAGGGC
Statistics
Matches: 272, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
46 83 0.31
47 189 0.69
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:64184 original size:29 final size:29
Alignment explanation
Indices: 64149--64222 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
64139 GTTGTGAGAT
* *
64149 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
* *
64178 TGGCACTAAGTGTGTGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
64207 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
64223 TGGTTGATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:64676 original size:80 final size:79
Alignment explanation
Indices: 64533--64728 Score: 216
Period size: 80 Copynumber: 2.5 Consensus size: 79
64523 TCGAATGATG
* **
64533 TCCGGGCTAAGTCCCGAAG-GCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATCATGCT-AGTGACCATATCCGGACTAAGATCCGAAGGCATT
* *
64597 GGTGCGAGTTACTAAA
65 CGTGCGAGTGA-TAAA
** * *
64613 TCCGGGCTAAGTCCCGAAGAGCATCATGCTAGTGA-TGTATCCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATCATGCTAGTGACCATATCCGGACTAAGATCCGAAG-GCATT
* *
64677 CGTGCTAGTGATATA
65 CGTGCGAGTGATAAA
* * *
64692 TCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGAC
1 TCCGGGCTAAGTCCCGAAGAGC-ATCATGCTAGTGAC
64729 GTGTATTCGG
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
79 42 0.43
80 49 0.50
81 7 0.07
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGAGCATCATGCTAGTGACCATATCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTGATAAA
Found at i:64694 original size:40 final size:41
Alignment explanation
Indices: 64533--64728 Score: 190
Period size: 40 Copynumber: 4.9 Consensus size: 41
64523 TCGAATGATG
* *
64533 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGACTATA
* * * * *
64573 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCGTGCTAGTGACTATA
* *
64613 TCCGGGCTAAGTCCCGAAGAGCA-TCATGCTAGTGA-TGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACTATA
*
64652 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGA-TATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACTATA
* * * * *
64692 TCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGAC
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAC
64729 GTGTATTCGG
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
39 25 0.20
40 93 0.73
41 10 0.08
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACTATA
Found at i:64701 original size:79 final size:80
Alignment explanation
Indices: 64571--64727 Score: 210
Period size: 79 Copynumber: 2.0 Consensus size: 80
64561 TAAGTGACCA
* * *
64571 TATCCGGACTAAGATCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGAGC-
1 TATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTGACTAAATCCGGGCTAAATCCCGAAGAGCA
64635 ATCATGCTAGTGATG
66 ATCATGCTAGTGATG
* * * * *
64650 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGA-TATATCCGTGCTAAATCCCGAAGAGC
1 TATCCGGACTAAGATCCGAAG-GCATTCGTGCGAGTGACTAAATCCGGGCTAAATCCCGAAGAGC
*
64714 AATCATGCTGGTGA
65 AATCATGCTAGTGA
64728 CGTGTATTCG
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
79 42 0.63
80 25 0.37
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (80 bp):
TATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTGACTAAATCCGGGCTAAATCCCGAAGAGCA
ATCATGCTAGTGATG
Found at i:68186 original size:47 final size:46
Alignment explanation
Indices: 68075--68353 Score: 397
Period size: 46 Copynumber: 6.0 Consensus size: 46
68065 GAAATGATAG
* * *
68075 TAAGGCCTAATGGCGATGTG-TGAATGTGAAAGTGTATATGTGGGA
1 TAAGGCCTAATGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
68120 T-AGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGA
68166 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
68213 TAA-GCCTAATGGCCGATGTGATGAATGTGAAAGTGCATATATGTAA
1 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
68259 TAAGG-CTAATGGCGATGTGATGATATGTGAAAGTGTATATATTATGTGA
1 TAAGGCCTAATGCCGATGTGATGA-ATGTGAAAGTG--TATA-TATGTGA
68308 TAAGGCCTAATGGCCGATGTGA-GAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGA
68354 CGGGGCCGAG
Statistics
Matches: 214, Mismatches: 10, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
44 9 0.04
45 21 0.10
46 90 0.42
47 53 0.25
48 3 0.01
49 22 0.10
50 7 0.03
51 9 0.04
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (46 bp):
TAAGGCCTAATGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:68198 original size:93 final size:92
Alignment explanation
Indices: 68075--68353 Score: 420
Period size: 93 Copynumber: 3.0 Consensus size: 92
68065 GAAATGATAG
* * *
68075 TAAGGCCTAATGGCGATGTG-TGAATGTGAAAGTGTATATGTGGGATAGGCCTAATAGCCGATGT
1 TAAGGCCTAATGGCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGCCTAATGGCCGATGT
68139 GATGAATGTGAAAGTGTATATATGTGA
66 GATGAATGTGAAAGTGTATATATGTGA
* *
68166 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGCCTAATGGCCGATG
1 TAAGGCCTAAT-GGCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGCCTAATGGCCGATG
* *
68231 TGATGAATGTGAAAGTGCATATATGTAA
65 TGATGAATGTGAAAGTGTATATATGTGA
68259 TAAGG-CTAATGGCGATGTGATGATATGTGAAAGTGTATATATTATGTGATAAGGCCTAATGGCC
1 TAAGGCCTAATGGCGATGTGATGA-ATGTGAAAGTG--TATA-TATGTGAT-AGGCCTAATGGCC
68323 GATGTGA-GAATGTGAAAGTGTATATATGTGA
61 GATGTGATGAATGTGAAAGTGTATATATGTGA
68354 CGGGGCCGAG
Statistics
Matches: 170, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
91 23 0.14
92 24 0.14
93 70 0.41
94 4 0.02
95 30 0.18
96 19 0.11
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (92 bp):
TAAGGCCTAATGGCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGCCTAATGGCCGATGT
GATGAATGTGAAAGTGTATATATGTGA
Done.