Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold514
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: 141623
ACGTcount: A:0.22, C:0.10, G:0.11, T:0.23
Warning! 47999 characters in sequence are not A, C, G, or T
Found at i:2330 original size:38 final size:38
Alignment explanation
Indices: 2212--2332 Score: 140
Period size: 38 Copynumber: 3.2 Consensus size: 38
2202 ATACTTATGT
2212 TAAATTATATTTTATAGCATTATATATTATGATTTTAG
1 TAAATTATATTTTATAGCATTATATATTATGATTTTAG
* * * *
2250 TAAATTCATA--TCATAACATT-TAATATTAAGAATTTTAT
1 TAAATT-ATATTTTATAGCATTAT-ATATTATG-ATTTTAG
* *
2288 TAAATTATATTTTATAGTATTATATATTATGATCTTAG
1 TAAATTATATTTTATAGCATTATATATTATGATTTTAG
2326 TAAATTA
1 TAAATTA
2333 ATAAGAGACT
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
36 1 0.01
37 18 0.27
38 30 0.45
39 17 0.25
40 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (38 bp):
TAAATTATATTTTATAGCATTATATATTATGATTTTAG
Found at i:10278 original size:29 final size:29
Alignment explanation
Indices: 10245--10302 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
10235 TTAAAGTTTG
10245 ACATCTTCTTTTAACATTCATATTATATT
1 ACATCTTCTTTTAACATTCATATTATATT
*
10274 ACATCTTCTTTTAATATTCATATTATATT
1 ACATCTTCTTTTAACATTCATATTATATT
10303 TAGTCTAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (29 bp):
ACATCTTCTTTTAACATTCATATTATATT
Found at i:11126 original size:30 final size:30
Alignment explanation
Indices: 11066--11127 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
11056 CATGGTCATA
* *
11066 TGACACACACGGTCGGACTACACGATTGTG
1 TGACACACACGGTCGAACTACACGACTGTG
* *
11096 TGACACACACGGTCTAACTACACGGCTGTG
1 TGACACACACGGTCGAACTACACGACTGTG
11126 TG
1 TG
11128 TCATTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.21
Consensus pattern (30 bp):
TGACACACACGGTCGAACTACACGACTGTG
Found at i:11214 original size:54 final size:54
Alignment explanation
Indices: 11156--11288 Score: 142
Period size: 54 Copynumber: 2.5 Consensus size: 54
11146 TGCAAGTTAT
* * *
11156 ACACGGCCTGCGACATGGCCGTGTGACCCAAGTCAGTGAGTTACTCGATCTG-G
1 ACACGGCCTGCGACATGGCCGTGTGACACAAGTCAGTGAGCTACACGATCTGAG
* * * * * *
11209 CACACGGCTTGCAACATGGCTGTGTGACATAAGTTAGTGAGCTACACGATTTGAG
1 -ACACGGCCTGCGACATGGCCGTGTGACACAAGTCAGTGAGCTACACGATCTGAG
* * *
11264 ACATGGGCTGGGACATGGCCGTGTG
1 ACACGGCCTGCGACATGGCCGTGTG
11289 TCCTATTGTT
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
54 62 0.98
55 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.23
Consensus pattern (54 bp):
ACACGGCCTGCGACATGGCCGTGTGACACAAGTCAGTGAGCTACACGATCTGAG
Found at i:14130 original size:21 final size:21
Alignment explanation
Indices: 14092--14137 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
14082 AATAAACACC
*
14092 AAAAATTTATTTTAAAAATAA
1 AAAAAATTATTTTAAAAATAA
14113 TAAAAAATTATTTT-AAAATAA
1 -AAAAAATTATTTTAAAAATAA
14134 AAAA
1 AAAA
14138 TAAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 7 0.30
22 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAATTATTTTAAAAATAA
Found at i:15355 original size:21 final size:21
Alignment explanation
Indices: 15317--15362 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
15307 AATAAACACC
*
15317 AAAAATTTATTTTAAAAATAA
1 AAAAAATTATTTTAAAAATAA
15338 TAAAAAATTATTTT-AAAATAA
1 -AAAAAATTATTTTAAAAATAA
15359 AAAA
1 AAAA
15363 TAAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 7 0.30
22 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAATTATTTTAAAAATAA
Found at i:16516 original size:20 final size:20
Alignment explanation
Indices: 16491--16603 Score: 76
Period size: 20 Copynumber: 5.9 Consensus size: 20
16481 TACAAATGAT
16491 TTTTTAATAAATTTTTATGG
1 TTTTTAATAAATTTTTATGG
* *
16511 TTTTTAGTAAA-TTGT-T--
1 TTTTTAATAAATTTTTATGG
*
16527 TTTTT-AT-AAGTTTTATGG
1 TTTTTAATAAATTTTTATGG
* *
16545 TTTTTAATTAATTTTTATTG
1 TTTTTAATAAATTTTTATGG
* * * *
16565 ATTTTAGTAAAATTTAATGG
1 TTTTTAATAAATTTTTATGG
**
16585 TTTTTTTTATAATTTTTAT
1 TTTTTAATA-AATTTTTAT
16604 ATGTTTTTTA
Statistics
Matches: 69, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
14 2 0.03
15 4 0.06
16 6 0.09
18 6 0.09
19 5 0.07
20 39 0.57
21 7 0.10
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (20 bp):
TTTTTAATAAATTTTTATGG
Found at i:31359 original size:3 final size:3
Alignment explanation
Indices: 31351--31383 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
31341 TTAAAATGTG
31351 TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA
31384 AAATAGCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:31374 original size:16 final size:16
Alignment explanation
Indices: 31353--31383 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31343 AAAATGTGTA
31353 TTATTATTATTATTAT
1 TTATTATTATTATTAT
31369 TTATTATTATTATTA
1 TTATTATTATTATTA
31384 AAATAGCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:38620 original size:24 final size:24
Alignment explanation
Indices: 38562--38622 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
38552 CCACTCATAT
*
38562 TATTTTTTAATTAAAAAGTATTTA
1 TATTTTTTATTTAAAAAGTATTTA
* * * *
38586 T-TTTATATATTTAATAATTTTTTA
1 TATTT-TTTATTTAAAAAGTATTTA
38610 TATTTTTTATTTA
1 TATTTTTTATTTA
38623 TTGTAACTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
23 3 0.10
24 23 0.79
25 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTTTTTATTTAAAAAGTATTTA
Found at i:39848 original size:30 final size:30
Alignment explanation
Indices: 39814--39871 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39804 AACAACTCAG
* *
39814 TGACTTGAATAAAAACTTTTGAATAGTTAC
1 TGACTTAAATAAAAACTTTCGAATAGTTAC
*
39844 TGACTTAAATGAAAACTTTCGAATAGTT
1 TGACTTAAATAAAAACTTTCGAATAGTT
39872 CAATGACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (30 bp):
TGACTTAAATAAAAACTTTCGAATAGTTAC
Found at i:39883 original size:30 final size:30
Alignment explanation
Indices: 39814--39892 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
39804 AACAACTCAG
* * * *
39814 TGACTTGAATAAAAACTTTTGAATAGTTAC
1 TGACTTAAATGAAAACTTTCGAATAGTTAA
39844 TGACTTAAATGAAAACTTTCGAATAGTTCAA
1 TGACTTAAATGAAAACTTTCGAATAGTT-AA
* *
39875 TGAC-TAAATTATAACTTT
1 TGACTTAAATGAAAACTTT
39893 TTTTTTAGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 37 0.88
31 5 0.12
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (30 bp):
TGACTTAAATGAAAACTTTCGAATAGTTAA
Found at i:42978 original size:29 final size:29
Alignment explanation
Indices: 42899--42983 Score: 68
Period size: 29 Copynumber: 3.0 Consensus size: 29
42889 GTTGGGTGAT
* *
42899 CATTTTGTAACTTTTCATAGTTTGATGAC
1 CATTTTATAACTTTTCATAGTTAGATGAC
** * * * *
42928 CA--AAAAAAATTTT-ACTAATTAGGTGAC
1 CATTTTATAACTTTTCA-TAGTTAGATGAC
42955 CATTTTATAACTTTTCATAGTTAGATGAC
1 CATTTTATAACTTTTCATAGTTAGATGAC
42984 AAAAAAAAAA
Statistics
Matches: 38, Mismatches: 14, Indels: 8
0.63 0.23 0.13
Matches are distributed among these distances:
26 1 0.03
27 17 0.45
29 19 0.50
30 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (29 bp):
CATTTTATAACTTTTCATAGTTAGATGAC
Found at i:57123 original size:18 final size:19
Alignment explanation
Indices: 57083--57124 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
57073 ACCTAATTGG
* *
57083 ACCAAAATAAACTTTAGAT
1 ACCAAAATAAACATTAGAA
*
57102 ACCAAATTAAACATTA-AA
1 ACCAAAATAAACATTAGAA
57120 ACCAA
1 ACCAA
57125 GTGCAAGTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.57, C:0.19, G:0.02, T:0.21
Consensus pattern (19 bp):
ACCAAAATAAACATTAGAA
Found at i:57683 original size:6 final size:6
Alignment explanation
Indices: 57672--57715 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
57662 AAAAATAGGT
* * * *
57672 AAAGGA AAAGGA GAAGGA GAAGGA AAAGGA GAAGGA GAAGGA AA
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AA
57716 TGACCCATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:57694 original size:12 final size:12
Alignment explanation
Indices: 57673--57713 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
57663 AAAATAGGTA
*
57673 AAGGAAAAGGAG
1 AAGGAGAAGGAG
*
57685 AAGGAGAAGGAA
1 AAGGAGAAGGAG
57697 AAGGAGAAGGAG
1 AAGGAGAAGGAG
57709 AAGGA
1 AAGGA
57714 AATGACCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (12 bp):
AAGGAGAAGGAG
Found at i:57696 original size:18 final size:18
Alignment explanation
Indices: 57673--57715 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
57663 AAAATAGGTA
57673 AAGGAAAAGGAGAAGGAG
1 AAGGAAAAGGAGAAGGAG
57691 AAGGAAAAGGAGAAGGAG
1 AAGGAAAAGGAGAAGGAG
57709 AAGGAAA
1 AAGGAAA
57716 TGACCCATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (18 bp):
AAGGAAAAGGAGAAGGAG
Found at i:61776 original size:14 final size:14
Alignment explanation
Indices: 61753--61792 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
61743 ACAGAAAAGT
*
61753 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
61767 AAATCATTTTACGG
1 AAAACATTTTACAG
61781 AAAACATTTTAC
1 AAAACATTTTAC
61793 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:61784 original size:34 final size:35
Alignment explanation
Indices: 61718--61784 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
61708 CAAACATCAG
* *
61718 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
61753 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
61785 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:62319 original size:22 final size:23
Alignment explanation
Indices: 62289--62331 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
62279 TTCAATTTAG
* *
62289 TTATCTATTATAAT-ATTTTATT
1 TTATATATTAAAATGATTTTATT
62311 TTATATATTAAAATGATTTTA
1 TTATATATTAAAATGATTTTA
62332 CACTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATATATTAAAATGATTTTATT
Found at i:71896 original size:20 final size:21
Alignment explanation
Indices: 71859--71898 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
71849 AAAAATATTA
71859 AAAATATTAAATATAAGTAGC
1 AAAATATTAAATATAAGTAGC
71880 AAAA-ATTAAAT-TGAAGTAG
1 AAAATATTAAATAT-AAGTAG
71899 AGTAGGGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 13 0.72
21 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (21 bp):
AAAATATTAAATATAAGTAGC
Found at i:73758 original size:5 final size:6
Alignment explanation
Indices: 73743--73767 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
73733 AAAAAATGCA
73743 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
73768 TACGGTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:81702 original size:113 final size:113
Alignment explanation
Indices: 81565--82090 Score: 426
Period size: 114 Copynumber: 4.6 Consensus size: 113
81555 CAACGTTCTG
* * *
81565 GTCTTGATGTATATTGGC-ATTAGTGGCGCTTATGAACAAACGCCGGTAATGTACAGTATTAGCG
1 GTCTTGATGTATATT-GCAATTAGTGGCGCTTATGAA-AAACGCCGCTAAAGTATAGTATTAGCG
* *
81629 GCGCTTAG-CGAAAGCACCGCAAAAGATGTTAACCAAAACGCAGAGTTTA
64 GCGCTTAGTCGAAAGCGCCGCAAAAGATCTTAACCAAAACGCAGAGTTTA
* *
81678 GTCTTGATGTATATTGCAATTAGTGGCGCTTATAAAGAAAACGCCGCTAATGTATAGTATTAGCG
1 GTCTTGATGTATATTGCAATTAGTGGCGCTTAT-GA-AAAACGCCGCTAAAGTATAGTATTAGCG
** * * * * * *
81743 GCGCAGAG-CGTTAAA-CGCCGCAAGATATCTTAATCAAAACGCACCATTTTG
64 GCGCTTAGTCG--AAAGCGCCGCAAAAGATCTTAACCAAAACGCA-GAGTTTA
* ** * * * *
81794 GTCTTGATGTATACTATAATTAGTGGCGTTTATGGAAAACGCCAG-TAAAGGATAGT-TATAGCA
1 GTCTTGATGTATATTGCAATTAGTGGCGCTTATGAAAAACGCC-GCTAAAGTATAGTAT-TAGCG
* * * * * * * * *
81857 GTGTTTTGTGGTAAGCGCCTCCAAATATCTTAACCAAAACGCAGAGTTTG
64 GCGCTTAGTCGAAAGCGCCGCAAAAGATCTTAACCAAAACGCAGAGTTTA
*
81907 GTCTTGA-GGAGTATTAG-AATTAGTGGCGCTTGATGAAAAACGCCGCTAAAGTATA-TCATTAG
1 GTCTTGATGTA-TATT-GCAATTAGTGGCGCTT-ATGAAAAACGCCGCTAAAGTATAGT-ATTAG
* * * * * *
81969 CGGCG-TTTGTGGAACGCGCTGC-AAAGTATCTTAACCAAAACACAGCGTTTA
62 CGGCGCTTAGTCGAAAGCGCCGCAAAAG-ATCTTAACCAAAACGCAGAGTTTA
* * ** * * *
82020 GTTCTTGATGTATACTGGAATTAGTGGCGCACATGGGAAAACGCCGCTGAAGCATAGTATTAGCG
1 G-TCTTGATGTATATTGCAATTAGTGGCGCTTAT-GAAAAACGCCGCTAAAGTATAGTATTAGCG
82085 GCGCTT
64 GCGCTT
82091 TTACCGAAAC
Statistics
Matches: 332, Mismatches: 58, Indels: 44
0.76 0.13 0.10
Matches are distributed among these distances:
112 7 0.02
113 101 0.30
114 156 0.47
115 32 0.10
116 36 0.11
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (113 bp):
GTCTTGATGTATATTGCAATTAGTGGCGCTTATGAAAAACGCCGCTAAAGTATAGTATTAGCGGC
GCTTAGTCGAAAGCGCCGCAAAAGATCTTAACCAAAACGCAGAGTTTA
Found at i:95297 original size:24 final size:24
Alignment explanation
Indices: 95191--95515 Score: 557
Period size: 24 Copynumber: 13.5 Consensus size: 24
95181 ATACGGAACA
* *
95191 AATA-CAGAGAGCACAAATGTGCT
1 AATATCAGAGAGCACCAACGTGCT
***
95214 AA-A-CAGAGAGCACTGGCGTGCT
1 AATATCAGAGAGCACCAACGTGCT
95236 AAATATCAGAGAGCACCAACGTGCT
1 -AATATCAGAGAGCACCAACGTGCT
95261 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
95286 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
95310 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
95335 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
95359 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
95383 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
95407 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
95431 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
95455 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
95479 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
95503 AATATCAGAGAGC
1 AATATCAGAGAGC
95516 GCGCTAAAGT
Statistics
Matches: 290, Mismatches: 7, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
22 16 0.06
23 4 0.01
24 206 0.71
25 64 0.22
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (24 bp):
AATATCAGAGAGCACCAACGTGCT
Found at i:96165 original size:13 final size:13
Alignment explanation
Indices: 96136--96173 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
96126 CCCGTTTTGC
96136 TCTCTGTTTCT-T
1 TCTCTGTTTCTAT
96148 TCTCTGTTTCTAT
1 TCTCTGTTTCTAT
*
96161 TCTCTTTTTCTAT
1 TCTCTGTTTCTAT
96174 CCTTTCTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.66
Consensus pattern (13 bp):
TCTCTGTTTCTAT
Found at i:104953 original size:87 final size:87
Alignment explanation
Indices: 104851--105011 Score: 220
Period size: 87 Copynumber: 1.9 Consensus size: 87
104841 GGCTTTAGCG
* *
104851 GCGTTTCTAGGAAAGCGCCGC-A-AAAATAACTAAGCCCAACGATGTCGTTTCCCGAGCTTTCAG
1 GCGTTTCTAGGAAAGCGCCGCTACAAAA-AACT-AGCCCAACGACGTCGTCTCCCGAGCTTTCAG
104914 GGATTTAGCGGCGCTTTATAGAAA
64 GGATTTAGCGGCGCTTTATAGAAA
** * *
104938 GCGTTTCT-GGAAAAGCGCCGCTACTTAAAACTGGCGCAACGACGTCGTCTCCCGAGCTTTCAGG
1 GCGTTTCTAGG-AAAGCGCCGCTACAAAAAACTAGCCCAACGACGTCGTCTCCCGAGCTTTCAGG
105002 GATTTAGCGG
65 GATTTAGCGG
105012 NNNNNNNNNN
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
86 2 0.03
87 56 0.86
88 5 0.08
89 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (87 bp):
GCGTTTCTAGGAAAGCGCCGCTACAAAAAACTAGCCCAACGACGTCGTCTCCCGAGCTTTCAGGG
ATTTAGCGGCGCTTTATAGAAA
Done.