Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2587
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: 129897
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:4363 original size:28 final size:28
Alignment explanation
Indices: 4325--4531 Score: 328
Period size: 28 Copynumber: 7.5 Consensus size: 28
4315 AATTGTACAA
*
4325 CACTATGTGTGCGAGCTTGATTATGTAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
*
4353 CACTAACTGTGCGAGCTTGATTATGTAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
*
4381 CACTAAGTGTGCAAGCTTGATTATGTAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
*
4409 CACTAAGTGTGCGAGCTTGGTTATGTAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
4437 CACTAAGTGTGCGAGCTTGATTATGTAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
*
4465 CACTAAGTGTGCGAG-TTGATTATATAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
* *
4492 CAGTAAGTGTGCGAG-TTGATTATATAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
*
4519 CACTGAGTGTGCG
1 CACTAAGTGTGCG
4532 GACTTAATAT
Statistics
Matches: 168, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
27 48 0.29
28 120 0.71
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (28 bp):
CACTAAGTGTGCGAGCTTGATTATGTAG
Found at i:12560 original size:28 final size:27
Alignment explanation
Indices: 12507--12686 Score: 258
Period size: 26 Copynumber: 6.6 Consensus size: 27
12497 TAAATTGTAC
12507 AGCACTAAGTGTGCGAGCTTG--TATGT
1 AGCACTAAGTGTGCGAG-TTGATTATGT
12533 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGATTATGT
12561 AGCACTAAGTGTGC-AGTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
12587 AGCACTAAGTGTGCGAGTTGATTGATATGT
1 AGCACTAAGTGTGCGAGTTGA-T--TATGT
*
12617 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAG-TTGATTATGT
*
12645 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
12672 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12687 GACTTAATAT
Statistics
Matches: 145, Mismatches: 2, Indels: 13
0.91 0.01 0.08
Matches are distributed among these distances:
26 45 0.31
27 32 0.22
28 41 0.28
30 23 0.16
31 4 0.03
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:12628 original size:84 final size:81
Alignment explanation
Indices: 12507--12686 Score: 272
Period size: 84 Copynumber: 2.2 Consensus size: 81
12497 TAAATTGTAC
* *
12507 AGCACTAAGTGTGCGAGCTTGTATGTAGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTG
1 AGCACTAAGTGTGCGAGATTGTATGTAGCACTAAGTGTGCGAGCTTGATTATATAGCACTAAGTG
*
12572 TGC-AGTTGATTATGT
66 TGCGAGTTGATTATAT
*
12587 AGCACTAAGTGTGCGAGTTGATTGATATGTAGCACTAAGTGTGCGAGTTTGATTATATAGCACTA
1 AGCACTAAGTGTGCGA---GATTG-TATGTAGCACTAAGTGTGCGAGCTTGATTATATAGCACTA
12652 AGTGTGCGAGTTGATTATAT
62 AGTGTGCGAGTTGATTATAT
*
12672 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12687 GACTTAATAT
Statistics
Matches: 90, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
80 16 0.18
83 4 0.04
84 45 0.50
85 25 0.28
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (81 bp):
AGCACTAAGTGTGCGAGATTGTATGTAGCACTAAGTGTGCGAGCTTGATTATATAGCACTAAGTG
TGCGAGTTGATTATAT
Found at i:20735 original size:28 final size:28
Alignment explanation
Indices: 20697--20904 Score: 346
Period size: 28 Copynumber: 7.5 Consensus size: 28
20687 AATTGTACAA
20697 CACTAAGTGTGCGAGCTTGATTATGTAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
20725 CACTAAGTGTGCGAGCTTGATTATGTAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
*
20753 CACTAAGTGTGCAAGCTTGATTATGTAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
*
20781 CACTAAGTGTGCGAGCTTGGTTATGTAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
20809 CACTAAGTGTGCGAGCTTGATTATGTAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
* *
20837 CACTAAGTGTGCGAGTTTGATTATATAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
* *
20865 CAGTAAGTGTGCGAG-TTGATTATATAG
1 CACTAAGTGTGCGAGCTTGATTATGTAG
*
20892 CACTGAGTGTGCG
1 CACTAAGTGTGCG
20905 GACTTAATAT
Statistics
Matches: 171, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
27 23 0.13
28 148 0.87
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
CACTAAGTGTGCGAGCTTGATTATGTAG
Found at i:25056 original size:43 final size:42
Alignment explanation
Indices: 24974--25091 Score: 157
Period size: 43 Copynumber: 2.8 Consensus size: 42
24964 GATTTGAGAT
*
24974 TTACGTGTAAGACCATGTCTGGGAC-ATCGACATCATATTTGA
1 TTACGTGTAAGACCATGTCTGGGACAAT-GGCATCATATTTGA
**
25016 TTTTGTGTAAGACCATGTCTGGGACAATGGCATCGATATTTGA
1 TTACGTGTAAGACCATGTCTGGGACAATGGCATC-ATATTTGA
* * *
25059 TTACATGTAAGACCATGTCTGGGGCATTGGCAT
1 TTACGTGTAAGACCATGTCTGGGACAATGGCAT
25092 TGTACGAGCT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
42 28 0.42
43 38 0.58
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (42 bp):
TTACGTGTAAGACCATGTCTGGGACAATGGCATCATATTTGA
Found at i:29248 original size:23 final size:23
Alignment explanation
Indices: 29205--29248 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
29195 CATCATAATA
*
29205 TCATCTATTTCATATCACAAAAC
1 TCATCTATATCATATCACAAAAC
*
29228 TCATC-ATATCATCATCTCAAA
1 TCATCTATATCAT-ATCACAAA
29249 CCAAAGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (23 bp):
TCATCTATATCATATCACAAAAC
Found at i:33227 original size:17 final size:17
Alignment explanation
Indices: 33195--33245 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
33185 ACCATATAAT
*
33195 AACTCT-TATTTGGAAC
1 AACTCTATATTTAGAAC
*
33211 ACCTCTATATTTAGAAC
1 AACTCTATATTTAGAAC
*
33228 AACT-TACATTTAGAAC
1 AACTCTATATTTAGAAC
33244 AA
1 AA
33246 GTCAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 18 0.60
17 12 0.40
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (17 bp):
AACTCTATATTTAGAAC
Found at i:36124 original size:16 final size:16
Alignment explanation
Indices: 36083--36124 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
36073 AAAGTTGATA
36083 ATAATTAATATATATT
1 ATAATTAATATATATT
*
36099 ATAATGAATATA-ATT
1 ATAATTAATATATATT
36114 ATATATTAATA
1 ATA-ATTAATA
36125 ATTATCATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
ATAATTAATATATATT
Found at i:36817 original size:13 final size:13
Alignment explanation
Indices: 36799--36827 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
36789 GATTGTTTAT
36799 TAAACTAATTAAC
1 TAAACTAATTAAC
36812 TAAACTAATTAAC
1 TAAACTAATTAAC
36825 TAA
1 TAA
36828 TTAAACTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:36834 original size:17 final size:15
Alignment explanation
Indices: 36797--36837 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 15
36787 GGGATTGTTT
36797 ATTAAACTAATTAAC
1 ATTAAACTAATTAAC
36812 --TAAACTAATTAAC
1 ATTAAACTAATTAAC
36825 TAATTAAACTAAT
1 --ATTAAACTAAT
36838 GCACAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 13 0.59
17 9 0.41
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTAAACTAATTAAC
Found at i:69925 original size:40 final size:42
Alignment explanation
Indices: 69860--69956 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 42
69850 AAAGTCAGTA
*
69860 TCGCACACTTAGTGCC-TTATATAGCC-AAAGCTAT-GCCAAC
1 TCGCACACTTAGTGCCATTATATAGCCGAAA-CTATAGCAAAC
* **
69900 TCGCACACTTAGTGCCATT-TGTAGCCGAAACTATATTAAAC
1 TCGCACACTTAGTGCCATTATATAGCCGAAACTATAGCAAAC
69941 -CGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
69957 AGCATAGTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
40 42 0.84
41 8 0.16
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (42 bp):
TCGCACACTTAGTGCCATTATATAGCCGAAACTATAGCAAAC
Found at i:84867 original size:21 final size:21
Alignment explanation
Indices: 84843--84884 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
84833 TCATCAGATC
*
84843 TACAGCTTGAGGCATCGGGGG
1 TACAGCTTGAGGAATCGGGGG
*
84864 TACAGGTTGAGGAATCGGGGG
1 TACAGCTTGAGGAATCGGGGG
84885 AGGTTGGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.14, G:0.45, T:0.19
Consensus pattern (21 bp):
TACAGCTTGAGGAATCGGGGG
Found at i:86665 original size:47 final size:46
Alignment explanation
Indices: 86550--86670 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 46
86540 GCCCATAAAC
* *
86550 GAACTCAGACTCAACTCAACGAGCTCGGGTGCTCGTATCCATAAGT
1 GAACTCAGACTCAACTCAACGAGCTCGGGTGCTAGTATACATAAGT
* *
86596 GAACTCAGACTCAACTCAACGAGCTCGGTTGCCTAGT-TACATCTCAG-
1 GAACTCAGACTCAACTCAACGAGCTCGGGTG-CTAGTATACA--TAAGT
* *
86643 GAACTCAGGCTCAACTCAACGAGTTCGG
1 GAACTCAGACTCAACTCAACGAGCTCGG
86671 AACTCAACCA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
46 33 0.50
47 30 0.45
48 3 0.05
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
GAACTCAGACTCAACTCAACGAGCTCGGGTGCTAGTATACATAAGT
Found at i:93828 original size:25 final size:25
Alignment explanation
Indices: 93781--93828 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
93771 TTACAATATG
* *
93781 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
*
93806 AAAATGACCATTATACCCGTAGG
1 AAAATGACCATTATACCCCTAGG
93829 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:94054 original size:47 final size:46
Alignment explanation
Indices: 93962--94063 Score: 159
Period size: 47 Copynumber: 2.2 Consensus size: 46
93952 AGGAAGTGCA
*
93962 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCACAGTTATTAAAGGGCTTATGCCCCAGTTATT
* *
94008 AAAGGGCTTATGCCACAGTTGTTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCACAGTTATT-AAAGGGCTTATGCCCCAGTTATT
94055 AAAGAGGCT
1 AAAG-GGCT
94064 AGGCCTCCAG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
46 21 0.41
47 26 0.51
48 4 0.08
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (46 bp):
AAAGGGCTTATGCCACAGTTATTAAAGGGCTTATGCCCCAGTTATT
Found at i:94063 original size:24 final size:23
Alignment explanation
Indices: 93962--94077 Score: 162
Period size: 23 Copynumber: 5.0 Consensus size: 23
93952 AGGAAGTGCA
93962 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
93985 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
94008 AAAGGGCTTATGCCACAGTTGTT
1 AAAGGGCTTATGCCCCAGTTATT
*
94031 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
*
94055 AAAGAGGC-TAGGCCTCCAGTTAT
1 AAAG-GGCTTATGCC-CCAGTTAT
94078 ACGATAAAGC
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
23 52 0.63
24 31 0.37
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:94307 original size:31 final size:31
Alignment explanation
Indices: 94269--94332 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
94259 CGTTTACAGT
*
94269 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAATAATATGAAATATGA
* **
94300 AAAGGCTTCGGCCTAATGTTATGAAATATGA
1 AAAGGCTTCGGCCCAATAATATGAAATATGA
94331 AA
1 AA
94333 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATAATATGAAATATGA
Found at i:117303 original size:55 final size:55
Alignment explanation
Indices: 117215--117334 Score: 222
Period size: 55 Copynumber: 2.2 Consensus size: 55
117205 TCTGGGGCAC
*
117215 CTATTCCCTTTTTATTCATTTTGTATTCTAGCAATGTTTGTTGACTGTGATTAAT
1 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
117270 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
1 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
*
117325 CTATTACCTT
1 CTATTCCCTT
117335 CAAATTTTGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.52
Consensus pattern (55 bp):
CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
Found at i:118015 original size:89 final size:88
Alignment explanation
Indices: 117843--118092 Score: 385
Period size: 89 Copynumber: 2.8 Consensus size: 88
117833 TCACCAGACC
* * * *
117843 TTAACCACCTAAGCAGTAGGGTAACAAGTTGAA-TTCATAGATCTTAACCCCCTAAGCAGTAGGG
1 TTAACCCCCTAAGTAGTAGGGTAACAAGTTGAAGTTCATAGATCTTATCACCCTAAGCAGTAGGG
*
117907 AAACAGATCGAAGGTGACGAGCT
66 AAACAGATCGAAGGGGACGAGCT
* *
117930 TTAACTCCCTAAGTAGTAGGGTAACAAGTTGAAGTTCATAAGATTTTATCACCCTAAGCAGTAGG
1 TTAACCCCCTAAGTAGTAGGGTAACAAGTTGAAGTTCAT-AGATCTTATCACCCTAAGCAGTAGG
*
117995 GAAACGGATCGAAGGGGACGAGCT
65 GAAACAGATCGAAGGGGACGAGCT
* *
118019 TTAACCCCCTAAGTAGTAGGGTAACAAGCTAAAGTTCATAGATCTTATCACCCTAAGCAGTAGGG
1 TTAACCCCCTAAGTAGTAGGGTAACAAGTTGAAGTTCATAGATCTTATCACCCTAAGCAGTAGGG
*
118084 AAGCAGATC
66 AAACAGATC
118093 AAAAGACGGG
Statistics
Matches: 147, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
87 30 0.20
88 37 0.25
89 80 0.54
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (88 bp):
TTAACCCCCTAAGTAGTAGGGTAACAAGTTGAAGTTCATAGATCTTATCACCCTAAGCAGTAGGG
AAACAGATCGAAGGGGACGAGCT
Found at i:118073 original size:44 final size:44
Alignment explanation
Indices: 117850--118083 Score: 163
Period size: 44 Copynumber: 5.3 Consensus size: 44
117840 ACCTTAACCA
* * *
117850 CCTAAGCAGTAGGGTAACAAGTTGAA-TTCATAGATCTTAACCC
1 CCTAAGCAGTAGGGTAACAAGATGAAGTTCATAGATCTTATCAC
* * * * * * *
117893 CCTAAGCAGTAGGGAAAC-AGATCGAAGGTGA-CGAGCTTTAACTC
1 CCTAAGCAGTAGGGTAACAAGAT-GAAGTTCATAGATC-TTATCAC
* * *
117937 CCTAAGTAGTAGGGTAACAAGTTGAAGTTCATAAGATTTTATCAC
1 CCTAAGCAGTAGGGTAACAAGATGAAGTTCAT-AGATCTTATCAC
* * *** * * * *
117982 CCTAAGCAGTAGGGAAAC-GGATCGAAGGGGA-CGAGCTTTAACCC
1 CCTAAGCAGTAGGGTAACAAGAT-GAAGTTCATAGATC-TTATCAC
* * *
118026 CCTAAGTAGTAGGGTAACAAGCTAAAGTTCATAGATCTTATCAC
1 CCTAAGCAGTAGGGTAACAAGATGAAGTTCATAGATCTTATCAC
118070 CCTAAGCAGTAGGG
1 CCTAAGCAGTAGGG
118084 AAGCAGATCA
Statistics
Matches: 139, Mismatches: 42, Indels: 19
0.69 0.21 0.09
Matches are distributed among these distances:
42 3 0.02
43 25 0.18
44 75 0.54
45 34 0.24
46 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (44 bp):
CCTAAGCAGTAGGGTAACAAGATGAAGTTCATAGATCTTATCAC
Found at i:120015 original size:22 final size:23
Alignment explanation
Indices: 119990--120048 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
119980 TATATATACT
119990 TATATATTCTTATAGTTGTT-T-A
1 TATATATT-TTATAGTTGTTCTAA
*
120012 TATATATTATTATTGTTGTTCCTAA
1 TATATATT-TTATAGTTGTT-CTAA
120037 TATATATTTTAT
1 TATATATTTTAT
120049 GTATACATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 18 0.56
24 5 0.16
25 9 0.28
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (23 bp):
TATATATTTTATAGTTGTTCTAA
Found at i:120475 original size:24 final size:25
Alignment explanation
Indices: 120420--120475 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
120410 GTATGTTATG
* *
120420 TATATATTATGTATATGCTTTTAAA
1 TATATATTATATATATGATTTTAAA
* *
120445 TAT-TATTATATATCT-ATTTTCAA
1 TATATATTATATATATGATTTTAAA
120468 TATATATT
1 TATATATT
120476 TATGTAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.35
24 14 0.54
25 3 0.12
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (25 bp):
TATATATTATATATATGATTTTAAA
Found at i:129878 original size:40 final size:39
Alignment explanation
Indices: 129730--129879 Score: 194
Period size: 40 Copynumber: 3.8 Consensus size: 39
129720 GGATGATAAC
* * *
129730 CGGGCTAAGTCCCGAA-GCATTTGTGCTAGTGACTAATT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* * * *
129768 CTGGGCTAACTCCTGAAGGCATTTGTGCAAGTTACTATAT
1 C-GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
129808 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAAT
1 -CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
*
129849 CGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
129880 AGTTATATCC
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.13
40 79 0.81
41 4 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:129891 original size:80 final size:79
Alignment explanation
Indices: 129729--129875 Score: 215
Period size: 80 Copynumber: 1.8 Consensus size: 79
129719 CGGATGATAA
* * * *
129729 CCGGGCTAAGTCCCGAAGCATTTGTGCTAGTGACTAATTCTGGGCTAACTCCTGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGCATTTGTGCGAGTGACTAAATCTGGGCTAACTCCCGAAGGCATTTGA
129794 GCAAGTTACTATAT
66 GCAAGTTACTATAT
* *
129808 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAATC-GGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAA-GCATTTGTGCGAGTGACT-AAATCTGGGCTAACTCCCGAAGGCATTT
129872 GAGC
64 GAGC
129876 GAGTAGTTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
79 17 0.28
80 39 0.65
81 4 0.07
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGCATTTGTGCGAGTGACTAAATCTGGGCTAACTCCCGAAGGCATTTGA
GCAAGTTACTATAT
Done.