Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2365
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: 29749
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:5545 original size:27 final size:28
Alignment explanation
Indices: 5515--5570 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
5505 CATCTCTTCT
* *
5515 AAAGAGATCATTGATGAAGATT-AATTC
1 AAAGAGATCAATCATGAAGATTCAATTC
*
5542 AAAGAGATTAATCATGAAGATTCAATTC
1 AAAGAGATCAATCATGAAGATTCAATTC
5570 A
1 A
5571 TTATTTGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.29
Consensus pattern (28 bp):
AAAGAGATCAATCATGAAGATTCAATTC
Found at i:9609 original size:29 final size:28
Alignment explanation
Indices: 9577--9644 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
9567 TAAAGATTTG
9577 TTTAGATATAAATTAAAAGTTAGAT-TTTA
1 TTTAG-TATAAATTAAAAGTTA-ATGTTTA
** **
9606 TTTAGGTGCAAATTAATTGTTAATGTTTA
1 TTTA-GTATAAATTAAAAGTTAATGTTTA
9635 TTTAGTATAA
1 TTTAGTATAA
9645 TAAAATATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
28 6 0.19
29 24 0.77
30 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.47
Consensus pattern (28 bp):
TTTAGTATAAATTAAAAGTTAATGTTTA
Found at i:9949 original size:2 final size:2
Alignment explanation
Indices: 9942--9982 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
9932 TTAAAAACTT
*
9942 TA TA TA TA TA TA TA TA -A TA TA TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9983 ATGATAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:9976 original size:25 final size:25
Alignment explanation
Indices: 9942--9992 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
9932 TTAAAAACTT
9942 TATATATATATATATAAT-ATATAAA
1 TATATATATATATATAATGATA-AAA
9967 TATATATATATATATAATGATAAAA
1 TATATATATATATATAATGATAAAA
9992 T
1 T
9993 TCAAAAACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TATATATATATATATAATGATAAAA
Found at i:13076 original size:50 final size:50
Alignment explanation
Indices: 13015--13210 Score: 293
Period size: 50 Copynumber: 3.9 Consensus size: 50
13005 AGTTGCTTAA
* * *
13015 AGTCAAAAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAATAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
13065 AGTCAATAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAATAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* *
13115 AGTCAATAATTATGGTCACCTTTCTCGATTGTCAAAGGTTAGTGAAGAAT
1 AGTCAATAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * * * *
13165 AGTCAACAATTATGGTCAACTCTTTCTATTATCAAAGGTTGGTGAA
1 AGTCAATAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAA
13211 AACCACCAAA
Statistics
Matches: 132, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 132 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (50 bp):
AGTCAATAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:17428 original size:20 final size:20
Alignment explanation
Indices: 17403--17463 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
17393 TTGCCATCAC
17403 GTGAAGCTTGTAGAAAACAT
1 GTGAAGCTTGTAGAAAACAT
*
17423 GTGAAGCATGTAGAAAACAT
1 GTGAAGCTTGTAGAAAACAT
17443 GTGAAGCTTGTAGAAAACAT
1 GTGAAGCTTGTAGAAAACAT
17463 G
1 G
17464 AAATGATGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.41, C:0.10, G:0.26, T:0.23
Consensus pattern (20 bp):
GTGAAGCTTGTAGAAAACAT
Found at i:18587 original size:14 final size:14
Alignment explanation
Indices: 18568--18594 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18558 TACAAAATTA
18568 AAAATAATAAAAAT
1 AAAATAATAAAAAT
18582 AAAATAATAAAAA
1 AAAATAATAAAAA
18595 ATTCTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATAATAAAAAT
Found at i:21067 original size:36 final size:36
Alignment explanation
Indices: 21026--21128 Score: 84
Period size: 36 Copynumber: 3.2 Consensus size: 36
21016 CCTTTTTCTT
21026 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
* * * *
21062 TCAAAG---A-GC-AG--GAT-GCTTTTTCT--T-T
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
*
21087 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
21123 TCAAAG
1 TCAAAG
21129 AGCAGGACAC
Statistics
Matches: 47, Mismatches: 9, Indels: 22
0.60 0.12 0.28
Matches are distributed among these distances:
25 6 0.13
26 1 0.02
28 9 0.19
29 3 0.06
30 2 0.04
31 2 0.04
32 3 0.06
33 8 0.17
35 1 0.02
36 12 0.26
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (36 bp):
TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
Found at i:21171 original size:55 final size:55
Alignment explanation
Indices: 21026--22424 Score: 1778
Period size: 55 Copynumber: 24.9 Consensus size: 55
21016 CCTTTTTCTT
* * * *
21026 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C----ACCTC
21087 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
21142 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
*
21197 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
*
21252 TCAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * *
21307 TTAAAGCCCACACAAGTTGGTGGCACCTTTT--AGTCCCCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGCAGGACACCTC
*
21362 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
*
21417 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * *
21472 TCAAAGCCCACACAAGTTGGTGGCACCTTT-C-GTCCCCAAAGAGCAGGACGCCTTC
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACC-TC
* * * * *
21527 TTATTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAAGACGCCTTC
1 -----TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC-TC
** *
21588 TCCTTTTAAAGCCCACACAAGTTGGTGGCATCCTCCAGTCCTCAAAGAGCAGGACACCTT
1 T-C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
*
21648 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
*
21703 TCAAAGCCCGCACAAGTTGGTGGCACCTTTT---GTCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGCAGGACACCTC
*
21757 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
21812 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * * * *
21867 TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAAGATACTTTTTCTTT
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC-----C-TC
*
21928 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* *
21983 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * *
22038 TTAAAGCCCACACAAGTTTGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * * *
22093 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGTAGGACGCCTTTTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC---TC
* ** * ** *
22151 TTTTAAAGCCCACACAAGTTGGTGGCA-CCTCCAGTCCTCAAAAAGTGGGACGCCTTTTC
1 --TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC---TC
22210 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1 --TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * *
22267 TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTC
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * * * *
22322 TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGTAGGACGCCTT
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTC
* ** * * * *
22377 TCAAAGCCTACACGTGTTTGTGGCATTTT-TACTCCTCAATGAGCAGGA
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA
22425 TACACTTTAT
Statistics
Matches: 1211, Mismatches: 89, Indels: 83
0.88 0.06 0.06
Matches are distributed among these distances:
52 4 0.00
53 4 0.00
54 83 0.07
55 804 0.66
56 11 0.01
57 10 0.01
58 1 0.00
59 58 0.05
60 77 0.06
61 159 0.13
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (55 bp):
TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
Found at i:23285 original size:19 final size:19
Alignment explanation
Indices: 23261--23328 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
23251 AATTCAACGA
23261 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
23280 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
23295 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
23312 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
23329 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:23299 original size:32 final size:32
Alignment explanation
Indices: 23263--23325 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
23253 TTCAACGATT
*
23263 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
23295 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
23326 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:23300 original size:13 final size:13
Alignment explanation
Indices: 23282--23306 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23272 ACATAAGTTT
23282 TGTATCGATACAA
1 TGTATCGATACAA
23295 TGTATCGATACA
1 TGTATCGATACA
23307 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:23386 original size:13 final size:13
Alignment explanation
Indices: 23368--23393 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23358 CATTTTTCTG
23368 TGTATCGATACAT
1 TGTATCGATACAT
23381 TGTATCGATACAT
1 TGTATCGATACAT
23394 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:23390 original size:33 final size:33
Alignment explanation
Indices: 23348--23414 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
23338 GCCAAGGAAA
***
23348 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
23381 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
23414 T
1 T
23415 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:25938 original size:28 final size:27
Alignment explanation
Indices: 25868--25943 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
25858 TTTCTTCACA
*
25868 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACTCCGTTAATC
*
25895 ATCGGGGATACTCCAACTCCGTT-ATT
1 ATCGGGGATACTCCAACTCCGTTAATC
*
25921 TTCGAGGGGATACTCCAACTCCG
1 ATC--GGGGATACTCCAACTCCG
25944 GTTTTATCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.09
27 22 0.50
28 18 0.41
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (27 bp):
ATCGGGGATACTCCAACTCCGTTAATC
Found at i:25977 original size:107 final size:106
Alignment explanation
Indices: 25821--26209 Score: 326
Period size: 107 Copynumber: 3.6 Consensus size: 106
25811 ATAATCGGGA
* *
25821 ATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACC
1 ATACTCCAACTCCGGTTTTA-TTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCCAACC
25886 CCGTTAATCATCGGGGATACTCCAACTCCGTTATTTTCGAGGGG
63 CCGTTAATCATCGGGGATACTCCAACTCCGTTATTTTCGAGGGG
* *
25930 ATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCC
1 ATACTCCAACTCCGGTTTTATTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCCAA-CC
** * ** * * * * **
25994 TGGTTTTATTTTC---AAAACGCCAATTTTCC-TT-TAATC--GGGG
63 CCG-TTAATCATCGGGGATACTCCAA--CTCCGTTATTTTCGAGGGG
* * * *
26034 ATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAACCTC
1 ATACTCCAACTCCGGTTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCC
* * * *
26099 GTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGG
65 GTTA-ATCATCGGGGATACTCCAACTCCGTTATTTTCGAGGGG
* * * * *** * * *
26142 ATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
1 ATACTCCAACTCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCG
26207 TTA
66 TTA
26210 TTTTCGAAGG
Statistics
Matches: 218, Mismatches: 46, Indels: 34
0.73 0.15 0.11
Matches are distributed among these distances:
102 2 0.01
103 7 0.03
104 44 0.20
105 16 0.07
106 22 0.10
107 75 0.34
108 28 0.13
109 24 0.11
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (106 bp):
ATACTCCAACTCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCG
TTAATCATCGGGGATACTCCAACTCCGTTATTTTCGAGGGG
Found at i:25999 original size:52 final size:51
Alignment explanation
Indices: 25926--26095 Score: 175
Period size: 52 Copynumber: 3.3 Consensus size: 51
25916 TTATTTTCGA
*
25926 GGGGATACTCCAACTCCGGTTTTATCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATC-CTAAAACACCAATTTTTCCACAATC
** * **
25978 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATCCT-AAAACACCAATTTTTCC-ACAATC
* * *
26030 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTA--TCCTAAAACACCAATTTTTCCACAATC
*
26082 GAGGATACTCCAAC
1 GGGGATACTCCAAC
26096 CTCGTTATTT
Statistics
Matches: 96, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
51 10 0.10
52 69 0.72
53 12 0.12
54 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGGTTTTATCCTAAAACACCAATTTTTCCACAATC
Found at i:26079 original size:104 final size:103
Alignment explanation
Indices: 25759--26094 Score: 297
Period size: 104 Copynumber: 3.2 Consensus size: 103
25749 ATCAATTCTC
* * * * *
25759 CACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGAAT
1 CACAATCGAGGATACTCCAA-TCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
*
25823 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * * * ** * * * * **
25864 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA--CTCCGTTATTTTCGA
1 CACAATCGAGGATACTCCAATCCGGTTTTATTTTC---AAAACACCAATTTTCC-TT-TAATC--
* * *
25926 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTT
59 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT
* *
25970 CCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGAGGATACTCCAATCC-GGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
*
26035 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
26075 CACAATCGAGGATACTCCAA
1 CACAATCGAGGATACTCCAA
26095 CCTCGTTATT
Statistics
Matches: 178, Mismatches: 37, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
103 6 0.03
104 45 0.25
105 33 0.19
106 21 0.12
107 41 0.23
108 5 0.03
109 27 0.15
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (103 bp):
CACAATCGAGGATACTCCAATCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:26115 original size:28 final size:28
Alignment explanation
Indices: 26079--26155 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
26069 ATTTTTCACA
* * *
26079 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
26107 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
26135 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
26156 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:26141 original size:212 final size:212
Alignment explanation
Indices: 25757--26162 Score: 611
Period size: 212 Copynumber: 1.9 Consensus size: 212
25747 TTATCAATTC
* *
25757 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGAA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGAA
* *
25822 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * * * *
25887 CGTTAATCATCGGGGATACTCCAACTCCGTTATTTTCGAGGGGATACTCCAACTCCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
25952 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * * *
25969 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
26033 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 AATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
26096 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
26161 AT
193 AT
26163 TCCCAAAATA
Statistics
Matches: 174, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
211 31 0.18
212 109 0.63
213 34 0.20
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGAA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:26288 original size:77 final size:79
Alignment explanation
Indices: 26109--26309 Score: 230
Period size: 77 Copynumber: 2.6 Consensus size: 79
26099 GTTATTTCAT
* * * *
26109 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
* * *
26174 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * ** *
26188 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCC-GATTT-TTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAAT-A
26250 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* *
26265 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
26310 TGTTATTATC
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
76 8 0.08
77 51 0.49
78 4 0.04
79 41 0.39
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.28
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:29708 original size:2 final size:2
Alignment explanation
Indices: 29695--29730 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
29685 AGTTCCAATC
*
29695 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29731 TATTGAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.