Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2811
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: 87583
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2407 original size:42 final size:42
Alignment explanation
Indices: 2316--2454 Score: 145
Period size: 43 Copynumber: 3.2 Consensus size: 42
2306 TTGAGATCCG
* * * *
2316 TGTCTGGGACATAGGCCTCGATTTGAGATTTACGTGTAAGACAA
1 TGTCTGGGACATAGGCATC-ATATCAGATTT-CGTGTAAGACCA
*
2360 TGTCTGGGACATAGGCATCATATCAGATTTCGTGTAAGACCC
1 TGTCTGGGACATAGGCATCATATCAGATTTCGTGTAAGACCA
* * * * *
2402 TGTCTGGGACAAAGGCATTGATA-CTGAATTACTTGTAAGACCA
1 TGTCTGGGACATAGGCA-TCATATCAG-ATTTCGTGTAAGACCA
2445 TGTCTGGGAC
1 TGTCTGGGAC
2455 GTCGGCATTG
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
42 28 0.34
43 36 0.44
44 18 0.22
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (42 bp):
TGTCTGGGACATAGGCATCATATCAGATTTCGTGTAAGACCA
Found at i:9770 original size:42 final size:43
Alignment explanation
Indices: 9674--9822 Score: 142
Period size: 42 Copynumber: 3.5 Consensus size: 43
9664 TGACATATCA
* * *
9674 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTTGAGATTTACG
1 TGTAAGACCATGTCTGGGACACAGGCATCGATCT-AGATTTACG
* * *
9718 TGCAAGACCATGTTTGGGACATAGGCATCGTATCT-GATTT-CG
1 TGTAAGACCATGTCTGGGACACAGGCATCG-ATCTAGATTTACG
* * * *
9760 TGTAAGACCATGTCTAGGACAGAGGCATCGATACTA-AATTACA
1 TGTAAGACCATGTCTGGGACACAGGCATCGAT-CTAGATTTACG
**
9803 TGTAAGACCACATCTGGGAC
1 TGTAAGACCATGTCTGGGAC
9823 GTTGGCATTG
Statistics
Matches: 86, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
41 2 0.02
42 33 0.38
43 23 0.27
44 25 0.29
45 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACACAGGCATCGATCTAGATTTACG
Found at i:13926 original size:22 final size:22
Alignment explanation
Indices: 13900--13975 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
13890 GAATGTATAT
13900 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * *
13922 ATGTGATGAACGTG-AGCAT-GCATA
1 ATGTGAT-AA-G-GCCGAATGGC-CA
13946 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
13969 ATGTGAT
1 ATGTGAT
13976 GAATGTGAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 15 0.37
23 9 0.22
24 9 0.22
25 8 0.20
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:13965 original size:47 final size:47
Alignment explanation
Indices: 13896--14021 Score: 234
Period size: 47 Copynumber: 2.7 Consensus size: 47
13886 TGATGAATGT
13896 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAACGTGAGCATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAACGTGAGCATGC
*
13943 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAACGTGAGCATGC
*
13990 ATATGTGTGATAAGGCCGAATGGCCAATGTGA
1 ATATATGTGATAAGGCCGAATGGCCAATGTGA
14022 ATATGAACAT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 77 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (47 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAACGTGAGCATGC
Found at i:14063 original size:42 final size:42
Alignment explanation
Indices: 13898--14064 Score: 165
Period size: 47 Copynumber: 3.7 Consensus size: 42
13888 ATGAATGTAT
* *
13898 ATATGTGATAAGGCCGAATGGCCAATGTG-ATGAACGTGAGCATGC
1 ATATGTGGTAAGGCCGAATGGCCAATGTGAAT--A--TGAACATGC
* * *
13943 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCATGC
1 --ATATGTGGTAAGGCCGAATGGCCAA--TG-TGAATATGAACATGC
13990 ATATGTGTGATAAGGCCGAATGGCCAATGTGAATATGAACATGC
1 ATATGTG-G-TAAGGCCGAATGGCCAATGTGAATATGAACATGC
* *
14034 ATATGTGGTAAAGCCGAATGGTCAATGTGAA
1 ATATGTGGTAAGGCCGAATGGCCAATGTGAA
14065 ATATATATAT
Statistics
Matches: 108, Mismatches: 6, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
42 21 0.19
43 1 0.01
44 20 0.19
45 9 0.08
47 51 0.47
49 2 0.02
50 2 0.02
51 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (42 bp):
ATATGTGGTAAGGCCGAATGGCCAATGTGAATATGAACATGC
Found at i:14090 original size:94 final size:90
Alignment explanation
Indices: 13892--14063 Score: 222
Period size: 94 Copynumber: 1.9 Consensus size: 90
13882 TATGTGATGA
* *
13892 ATGTATATATGTGATAAGGCCGAATGGCCAATGTG-ATGAACGTGAGCATGCATATATGTGATAA
1 ATGTATATGTGTGATAAGGCCGAATGGCCAATGTGAAT--A--TGAACATGCA-ATATGTGATAA
* *
13956 GGCCGAATGGCCAATGTGATGAATGTGAGC
61 AGCCGAATGGCCAATGTGATGAATATGAGC
* *
13986 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGAATATGAACATGC-ATATGTGGTAAAGCCG
1 ATGTATATGTGTGATAAGGCCGAATGGCCAATGTGAATATGAACATGCAATATGTGATAAAGCCG
*
14050 AATGGTCAATGTGA
66 AATGGCCAATGTGA
14064 AATATATATA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
89 27 0.38
91 8 0.11
93 1 0.01
94 33 0.46
95 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (90 bp):
ATGTATATGTGTGATAAGGCCGAATGGCCAATGTGAATATGAACATGCAATATGTGATAAAGCCG
AATGGCCAATGTGATGAATATGAGC
Found at i:14317 original size:37 final size:37
Alignment explanation
Indices: 14267--14337 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
14257 GGAAATATAT
*
14267 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTATG
*
14304 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATT
14338 TCGTCTGAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTATG
Found at i:15884 original size:40 final size:40
Alignment explanation
Indices: 15601--15872 Score: 391
Period size: 40 Copynumber: 6.8 Consensus size: 40
15591 GAGAATTGAG
* * *
15601 AGTGATATATCCGGGCTAAATCCTGAAGATCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
15641 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
15681 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
15721 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
15761 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * **
15801 AGGGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
15841 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
15873 ATCATGCTGG
Statistics
Matches: 212, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 212 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:16089 original size:25 final size:25
Alignment explanation
Indices: 16048--16099 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
16038 TGTGTAATAA
16048 TGAATGAATAAGAGCACTATGTGTG
1 TGAATGAATAAGAGCACTATGTGTG
* *
16073 TGAATG-ATTAGAGGCACTGTGTGTG
1 TGAATGAATAAGA-GCACTATGTGTG
16098 TG
1 TG
16100 CGAATTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (25 bp):
TGAATGAATAAGAGCACTATGTGTG
Found at i:20154 original size:25 final size:25
Alignment explanation
Indices: 20126--20204 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 25
20116 CGAATGACCA
20126 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
* * * *
20151 ATGTGGT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-TGAACAT-GCATAT
20173 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
*
20198 GTGTGAT
1 ATGTGAT
20205 AAGGCCGAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 14
0.62 0.15 0.23
Matches are distributed among these distances:
22 7 0.18
23 9 0.24
24 9 0.24
25 13 0.34
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (25 bp):
ATGTGATGAATGTGAACATGCATAT
Found at i:20174 original size:47 final size:47
Alignment explanation
Indices: 20101--20225 Score: 205
Period size: 47 Copynumber: 2.7 Consensus size: 47
20091 TTTATGTGTT
* *
20101 TATATGAGATAAGGCCGAATGACCAATGTGATGAATGTGAACATGCA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
*
20148 TATATGTGGTAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
* *
20195 TATGTGTGATAAGGCCGAATGGCTAATGTGA
1 TATATGTGATAAGGCCGAATGGCCAATGTGA
20226 AACATGTATG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
Found at i:20264 original size:48 final size:48
Alignment explanation
Indices: 20148--20329 Score: 228
Period size: 48 Copynumber: 3.8 Consensus size: 48
20138 TGAACATGCA
* * * *
20148 TATATGTGGTAAGGCCGAATGGCCAATGTGATGA-ATG--TGA-ACATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGA-AATATGTATGAGATATG
* * *
20193 CATATGTGTGATAAGGCCGAATGGCTAATGTGAAACATGTATGAGATATG
1 TATATGTG-G-TAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
*
20243 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
*
20291 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
20330 GGCGATGTGC
Statistics
Matches: 123, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
45 7 0.06
46 2 0.02
47 24 0.20
48 75 0.61
49 4 0.03
50 11 0.09
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:20584 original size:37 final size:37
Alignment explanation
Indices: 20476--20584 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
20466 GGAAATATAT
*
20476 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
20513 TTCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
20550 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
20585 CGTCTGAGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:24383 original size:43 final size:43
Alignment explanation
Indices: 24331--24426 Score: 131
Period size: 43 Copynumber: 2.2 Consensus size: 43
24321 TACATGTAAT
*
24331 CACAAATCGATGCCACTGTCCCAAATAG-GGTCTTACACAAGAA
1 CACATATCGATGCCACTGTCCCAAA-AGTGGTCTTACACAAGAA
* * * *
24374 CACATATCGATGCCAGTGTCCCAGACGTGGTCTTACACGAGAA
1 CACATATCGATGCCACTGTCCCAAAAGTGGTCTTACACAAGAA
24417 CACATATCGA
1 CACATATCGA
24427 AAATCCTATG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.02
43 46 0.98
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (43 bp):
CACATATCGATGCCACTGTCCCAAAAGTGGTCTTACACAAGAA
Found at i:25093 original size:14 final size:15
Alignment explanation
Indices: 25076--25104 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25066 ACACTAAAAT
25076 TTCACACAT-ATAAA
1 TTCACACATAATAAA
25090 TTCACACATAATAAA
1 TTCACACATAATAAA
25105 CACAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:29013 original size:53 final size:53
Alignment explanation
Indices: 28933--29039 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
28923 CCAAGACCTT
* * *
28933 AGTTAATCCAAACAACATCACCAAAAACTCATAATGTCTATACCGAGTCTAAA
1 AGTTAATCCAAACAACATCACCAAAAACTCATAATGCCCATACCGAGTCCAAA
* *
28986 AGTTAATCCAAACAGCATCACTAAAAACTCATAATGCCCATACCGAGTCCAAA
1 AGTTAATCCAAACAACATCACCAAAAACTCATAATGCCCATACCGAGTCCAAA
29039 A
1 A
29040 AGCAGTTTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.45, C:0.26, G:0.08, T:0.21
Consensus pattern (53 bp):
AGTTAATCCAAACAACATCACCAAAAACTCATAATGCCCATACCGAGTCCAAA
Found at i:37489 original size:21 final size:21
Alignment explanation
Indices: 37448--37500 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
37438 AAAATTTAGA
*
37448 ATATTATATTTGTATATAAGT
1 ATATTATATATGTATATAAGT
*
37469 ATATT-TATATGTATGTAAAGT
1 ATATTATATATGTATAT-AAGT
*
37490 ATAATATATAT
1 ATATTATATAT
37501 ATAATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.33
21 13 0.48
22 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (21 bp):
ATATTATATATGTATATAAGT
Found at i:40234 original size:20 final size:20
Alignment explanation
Indices: 40188--40244 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
40178 TCAACAACTA
* *
40188 TTTCACTCGATCCAAATATG
1 TTTCAATCGATCTAAATATG
* *
40208 CTACAATCGATCTAAATATG
1 TTTCAATCGATCTAAATATG
* *
40228 TTTCAATTGATTTAAAT
1 TTTCAATCGATCTAAAT
40245 CAGTTACAAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.39
Consensus pattern (20 bp):
TTTCAATCGATCTAAATATG
Found at i:40301 original size:20 final size:19
Alignment explanation
Indices: 40220--40328 Score: 74
Period size: 20 Copynumber: 5.5 Consensus size: 19
40210 ACAATCGATC
* *
40220 TAAATATGTTTCAATTGATT
1 TAAATCTGTTACAATT-ATT
* **
40240 TAAATCAGTTACAACCAATT
1 TAAATCTGTTACAA-TTATT
* *
40260 TAAATCAGTTACAATGATT
1 TAAATCTGTTACAATTATT
*
40279 TAAATCTGTTTCAAATTATT
1 TAAATCTGTTAC-AATTATT
** *
40299 TAAATCTACTACAATCGATT
1 TAAATCTGTTACAAT-TATT
*
40319 TAAATTTGTT
1 TAAATCTGTT
40329 TCATCTTTAT
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
19 16 0.23
20 53 0.77
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (19 bp):
TAAATCTGTTACAATTATT
Found at i:40312 original size:59 final size:60
Alignment explanation
Indices: 40209--40323 Score: 146
Period size: 59 Copynumber: 1.9 Consensus size: 60
40199 CCAAATATGC
*
40209 TACAATCGATCTAAATATGTTTCAATTGATTTAAATCAGTTACAACCAATTTAAATCAGT
1 TACAATCGATCTAAATATGTTTCAATTGATTTAAATCAGCTACAACCAATTTAAATCAGT
* * * *
40269 TACAAT-GATTTAAATCTGTTTCAAATT-ATTTAAATCTA-CTACAATCGATTTAAAT
1 TACAATCGATCTAAATATGTTTC-AATTGATTTAAATC-AGCTACAACCAATTTAAAT
40324 TTGTTTCATC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
59 37 0.77
60 11 0.23
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (60 bp):
TACAATCGATCTAAATATGTTTCAATTGATTTAAATCAGCTACAACCAATTTAAATCAGT
Found at i:43060 original size:70 final size:68
Alignment explanation
Indices: 42939--43070 Score: 183
Period size: 70 Copynumber: 1.9 Consensus size: 68
42929 TAGAGTTTCA
* *
42939 TCACTTTTTGTATGTGTAAATGGTGCGGTGGTGAACTAATATCACTTTTTGTATGTAATTGTCAG
1 TCACTTTTTGTATGTGTAAATAGTGCGGTGGTGAACTAATATAACTTTTTGTATGTAATTGTCAG
43004 TTG
66 TTG
* * * * *
43007 TCACTTTTTTGTATGTGTAATTAAGTGTGGTGGTGGAGTAATTTAACTTTTTGTATGTAATTGT
1 TCAC-TTTTTGTATGTGTAAAT-AGTGCGGTGGTGAACTAATATAACTTTTTGTATGTAATTGT
43071 AGGATGATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 4 0.07
69 16 0.29
70 35 0.64
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.47
Consensus pattern (68 bp):
TCACTTTTTGTATGTGTAAATAGTGCGGTGGTGAACTAATATAACTTTTTGTATGTAATTGTCAG
TTG
Found at i:53516 original size:41 final size:41
Alignment explanation
Indices: 53465--53744 Score: 390
Period size: 41 Copynumber: 6.8 Consensus size: 41
53455 GAATGTAATA
*
53465 CAGACGTTAAGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
53506 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
53547 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
53588 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
53629 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* * *
53670 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAAT
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT--TT
* * **
53711 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
53745 ATCTGTTTAA
Statistics
Matches: 223, Mismatches: 9, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
39 3 0.01
40 8 0.04
41 210 0.94
42 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:61176 original size:41 final size:41
Alignment explanation
Indices: 61125--61403 Score: 381
Period size: 41 Copynumber: 6.8 Consensus size: 41
61115 GAATGTAATA
*
61125 CAGACGTTAAGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
61166 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
61207 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
61248 CAGAC-TTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
61288 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* * *
61329 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAAT
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT--TT
* * **
61370 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
61404 ATCTGTTTAA
Statistics
Matches: 221, Mismatches: 9, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
39 3 0.01
40 48 0.22
41 168 0.76
42 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:61348 original size:122 final size:123
Alignment explanation
Indices: 61125--61404 Score: 383
Period size: 122 Copynumber: 2.3 Consensus size: 123
61115 GAATGTAATA
*
61125 CAGACGTTAAGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTTA
1 CAGACGTTAAGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTTA
*
61190 ATGCCGGTGATACATTTCAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACATTT
66 ATGCCGGTGATACATTTCAGACTATAAGTCTAGCAGGC-TAAGTGCCGGTGATACATTT
*
61248 CAGAC-TTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTATATGTCTAGCAGGCT
1 CAGACGTTAAGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTATAAGTCTAGCAGGCT
* *
61310 TAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTAAGTGCCGGTG-TAC-TGAAT
64 TAATGCCGGTGATACATTTCAGACTATAAGTCTAGCAGGCTAAGTGCCGGTGATACAT--TT
* * * **
61370 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGAA
1 CAGACGTTAAGTCTAGCAGGCTTAATGCCGGTGAA
61405 TCTGTTTAAA
Statistics
Matches: 141, Mismatches: 9, Indels: 13
0.87 0.06 0.08
Matches are distributed among these distances:
120 3 0.02
121 8 0.06
122 100 0.71
123 29 0.21
124 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (123 bp):
CAGACGTTAAGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTTA
ATGCCGGTGATACATTTCAGACTATAAGTCTAGCAGGCTAAGTGCCGGTGATACATTT
Found at i:69031 original size:43 final size:41
Alignment explanation
Indices: 68977--69210 Score: 226
Period size: 43 Copynumber: 5.5 Consensus size: 41
68967 GAATGTAATA
* * *
68977 CAGACGTTAAGTCTAGCAGGCTTAAATGCCGGGTAAGTA-ATTG
1 CAGACTTTAAGTCTAGCAGGCTT-AATGCC-GGTGA-TACATTT
*
69020 CAGACTTTAAGTCTAGCCGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
69061 CAGACTCTTAAGTCTAGCATAGGCTT-ATGCCGGTGATACATTTT
1 CAGACT-TTAAGTCTAGC--AGGCTTAATGCCGGTGATACA-TTT
69105 CAGACATTTAAGTCTAGCAGGC-TAATGCGCGGTGATACATTT
1 CAGAC-TTTAAGTCTAGCAGGCTTAATGC-CGGTGATACATTT
** *
69147 CAAAGACAATATCGTCT-GCAGGCTTAATGCC-GTGATGACATTT
1 C--AGACTTTA-AGTCTAGCAGGCTTAATGCCGGTGAT-ACATTT
* *
69190 CAGACCTATATGTCTAGCAGG
1 CAGA-CTTTAAGTCTAGCAGG
69211 GCTAAGTGCG
Statistics
Matches: 166, Mismatches: 10, Indels: 31
0.80 0.05 0.15
Matches are distributed among these distances:
40 2 0.01
41 21 0.13
42 43 0.26
43 61 0.37
44 38 0.23
45 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:73422 original size:3 final size:3
Alignment explanation
Indices: 73414--73447 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
73404 TTTGAAAAAG
*
73414 TTA TTA TTA TAA TTA TTA TTA TTA TTA TCTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
73448 AGTGGTGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:73855 original size:16 final size:16
Alignment explanation
Indices: 73825--73854 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
73815 ATGATGCAAC
73825 AATTATACTTATTTTG
1 AATTATACTTATTTTG
73841 AATTA-ACTTATTTT
1 AATTATACTTATTTT
73855 TATTTTTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (16 bp):
AATTATACTTATTTTG
Found at i:74783 original size:14 final size:15
Alignment explanation
Indices: 74765--74811 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
74755 AGTTCAATTT
74765 TATTTTAAATAATAA
1 TATTTTAAATAATAA
74780 -ATTTTAAA-AATAA
1 TATTTTAAATAATAA
* *
74793 TAATTTAAATAATAT
1 TATTTTAAATAATAA
74808 TATT
1 TATT
74812 CACATATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 5 0.19
14 15 0.56
15 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTTTAAATAATAA
Done.