Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold517
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: 36973
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:644 original size:20 final size:19
Alignment explanation
Indices: 602--656 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
592 ATCATTTTTC
*
602 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TATCA
622 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTA-TCA
* *
642 ATGTTTTGATACATT
1 ATGTATCGATACATT
657 CTATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:727 original size:20 final size:20
Alignment explanation
Indices: 671--718 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
661 TTTTTTTACC
*
671 CAATGTATCGATACATTTTT
1 CAATGTATCGATACATTTAT
691 CAATGTATCGATACATTTAT
1 CAATGTATCGATACATTTAT
*
711 GAATGTAT
1 CAATGTAT
719 TTATACATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (20 bp):
CAATGTATCGATACATTTAT
Found at i:2432 original size:10 final size:11
Alignment explanation
Indices: 2417--2445 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2407 CCACTAGATG
2417 ATTTTTCAAA-
1 ATTTTTCAAAC
2427 ATTTTTCAAAC
1 ATTTTTCAAAC
2438 ATTTTTCA
1 ATTTTTCA
2446 TAAAAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTTCAAAC
Found at i:4860 original size:13 final size:13
Alignment explanation
Indices: 4842--4898 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
4832 TAAAAGTGTT
4842 TGTATCGATACAA
1 TGTATCGATACAA
4855 TGTATCGATACATAA
1 TGTATCGATAC--AA
4870 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
4887 TGTATCGATACA
1 TGTATCGATACA
4899 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4879 original size:19 final size:18
Alignment explanation
Indices: 4818--4917 Score: 76
Period size: 19 Copynumber: 5.8 Consensus size: 18
4808 TTTTCAATGA
4818 TTTGTATCGATACATAAAAGTG
1 TTTGTATCGATACAT--AA--G
4840 TTTGTATCGATAC--AA-
1 TTTGTATCGATACATAAG
4855 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
4871 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
4887 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
4903 TTTTGTATCGATACA
1 -TTTGTATCGATACA
4918 ATGTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 27
0.71 0.00 0.29
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 2 0.03
18 2 0.03
19 23 0.35
22 13 0.20
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:4882 original size:32 final size:32
Alignment explanation
Indices: 4820--4922 Score: 170
Period size: 32 Copynumber: 3.1 Consensus size: 32
4810 TTCAATGATT
4820 TGTATCGATACATAAAAGTGTTTGTATCGATACAA
1 TGTATCGATACAT--AAGTG-TTGTATCGATACAA
4855 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
4887 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
4919 TGTA
1 TGTA
4923 AGCTATCTGC
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
32 49 0.73
33 5 0.07
35 13 0.19
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:5158 original size:53 final size:52
Alignment explanation
Indices: 4980--5158 Score: 285
Period size: 50 Copynumber: 3.5 Consensus size: 52
4970 CACTGATCTT
*
4980 TGTATCGATACATGCAGGCAAATTTGCCCAGAT-AATACGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTAT-CGATACACTATAAAA
5032 TGTATCGATACATGCA-GCAAATTTGCCCAGATGTATCGATAC-CTAT-AAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
5081 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTAT-AAAA
*
5134 TGTATCGATACATGCAGGCGAATTT
1 TGTATCGATACATGCAGGCAAATTT
5159 TCATATTTCG
Statistics
Matches: 119, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
49 19 0.16
50 29 0.24
51 26 0.22
52 18 0.15
53 27 0.23
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:6035 original size:20 final size:20
Alignment explanation
Indices: 5988--6035 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
5978 GTTAACAGCC
* **
5988 CATGATTCATGCATTTTGAG
1 CATGTTTCATGCATTTACAG
6008 CTATGTTTCATGCATTTACAG
1 C-ATGTTTCATGCATTTACAG
6029 CATGTTT
1 CATGTTT
6036 AGCACCTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (20 bp):
CATGTTTCATGCATTTACAG
Found at i:12775 original size:21 final size:22
Alignment explanation
Indices: 12730--12776 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
12720 TTGCAAGATG
12730 AAATAAGAAGTTAGCTAATGAA
1 AAATAAGAAGTTAGCTAATGAA
12752 AAATAATG-AGTTAGCTAA-GAA
1 AAATAA-GAAGTTAGCTAATGAA
12773 AAAT
1 AAAT
12777 GAAAACTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.29
22 16 0.67
23 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.17, T:0.23
Consensus pattern (22 bp):
AAATAAGAAGTTAGCTAATGAA
Found at i:16705 original size:13 final size:13
Alignment explanation
Indices: 16687--16718 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
16677 CTTTGCTATC
16687 GATACATTGTATT
1 GATACATTGTATT
16700 GATACATTGTATT
1 GATACATTGTATT
16713 GATACA
1 GATACA
16719 GGGTGATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (13 bp):
GATACATTGTATT
Found at i:19195 original size:20 final size:19
Alignment explanation
Indices: 19141--19195 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
19131 AAAACCCTTA
*
19141 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
19161 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
19181 AATGTATCGATACAT
1 AAAGTATCGATACAT
19196 GAAAAAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:19296 original size:32 final size:31
Alignment explanation
Indices: 19237--19296 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
19227 AGCCAAACTT
* **
19237 GTATCGATACACCAAGTATGTATCGATATAA
1 GTATCGATACACAAACAATGTATCGATATAA
19268 GTATCGATACACAAACAATTGTATCGATA
1 GTATCGATACACAAACAA-TGTATCGATA
19297 CATTGGCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (31 bp):
GTATCGATACACAAACAATGTATCGATATAA
Found at i:28910 original size:16 final size:19
Alignment explanation
Indices: 28889--28930 Score: 70
Period size: 17 Copynumber: 2.3 Consensus size: 19
28879 GCGTCCTCCG
28889 CAAAAAAAAACAA-AA-AA
1 CAAAAAAAAACAACAACAA
28906 CAAAAAAAAACAACAACAA
1 CAAAAAAAAACAACAACAA
28925 CAAAAA
1 CAAAAA
28931 GGGTCCGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 8 0.35
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAACAACAACAA
Found at i:30398 original size:29 final size:29
Alignment explanation
Indices: 30359--30682 Score: 219
Period size: 29 Copynumber: 10.9 Consensus size: 29
30349 ATTCCTCACC
30359 TTTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTTCAAAGCCCACAAGTCAGTGGCATCTT
30388 TTTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTTCAAAGCCCACAAGTCAGTGGCATCTT
* *
30417 TTTCAAAGTCCACAAGTCAGTGGCAAC--
1 TTTCAAAGCCCACAAGTCAGTGGCATCTT
* * *
30444 CTTCAAAGCCCACAAATCAGTGGCACCCTT
1 TTTCAAAGCCCACAAGTCAGTGGCA-TCTT
* * * *
30474 TTCCGAAGCCCACAAGTCGGTAGCATC-T
1 TTTCAAAGCCCACAAGTCAGTGGCATCTT
* * * *
30502 TTTCTAAAGTCCACAACTCCGTGGCACTTTT
1 TTTC-AAAGCCCACAAGTCAGTGGCA-TCTT
* * * * * *
30533 TTTCTTTTGTAAGCTCACAACTCCGTAGCACTATT
1 TTTC-----AAAGCCCACAAGTCAGTGGCA-TCTT
* * * *
30568 TTTCCTTTTAAGCCCACAAGTTAGTGGCACCCT
1 TTT-C---AAAGCCCACAAGTCAGTGGCATCTT
* *
30601 TTTCAAAAGCCCACAAGTCAGTGGCAAC-C
1 TTTC-AAAGCCCACAAGTCAGTGGCATCTT
* *
30630 TTTAAAAGCCCACAAGTCAGTAGCAATC--
1 TTTCAAAGCCCACAAGTCAGTGGC-ATCTT
*
30658 TTTAAAAGCCCACAAGTCAGTGGCA
1 TTTCAAAGCCCACAAGTCAGTGGCA
30683 ACCTTCAAAA
Statistics
Matches: 239, Mismatches: 44, Indels: 26
0.77 0.14 0.08
Matches are distributed among these distances:
27 23 0.10
28 47 0.20
29 76 0.32
30 40 0.17
31 5 0.02
32 1 0.00
33 4 0.02
34 18 0.08
35 24 0.10
36 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCTT
Found at i:30476 original size:56 final size:57
Alignment explanation
Indices: 30359--30691 Score: 197
Period size: 56 Copynumber: 5.6 Consensus size: 57
30349 ATTCCTCACC
* * * * *
30359 TTTCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTTCAAAGCCCACAAGTCAGTGGCAAC-TCTTCAAAGCCCACAAATCAGTGGCACCCT
*
30417 TTTCAAAGTCCACAAGTCAGTGGCAAC-CTTCAAAGCCCACAAATCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAATCAGTGGCACCCT
* * * * * * * * *
30473 TTTCCGAAGCCCACAAGTCGGTAGCATCTTTTCTAAAGTCCACAACTCCGTGGCACTTTTTTTCT
1 TTT-CAAAGCCCACAAGTCAGTGGCAACTCTTC-AAAGCCCACAAATCAGTGGCAC------CCT
** * * * * * ** * *
30538 TTTGTAAGCTCACAACTCCGTAGCACTATTTTTCCTTTTAAGCCCACAAGTTAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCA--A---CT-CTTCAAAGCCCACAAATCAGTGGCACCCT
* * * **
30601 TTTCAAAAGCCCACAAGTCAGTGGCAAC-CTTTAAAAGCCCACAAGTCAGTAGCAATC-
1 TTTC-AAAGCCCACAAGTCAGTGGCAACTC-TTCAAAGCCCACAAATCAGTGGCACCCT
*
30658 TTTAAAAGCCCACAAGTCAGTGGCAAC-CTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCAACTCTTCAAA
30692 AGCACATAAG
Statistics
Matches: 212, Mismatches: 46, Indels: 37
0.72 0.16 0.13
Matches are distributed among these distances:
55 5 0.02
56 52 0.25
57 23 0.11
58 49 0.23
59 19 0.09
62 1 0.00
63 5 0.02
64 33 0.16
65 5 0.02
69 18 0.08
70 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (57 bp):
TTTCAAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAATCAGTGGCACCCT
Found at i:30501 original size:86 final size:85
Alignment explanation
Indices: 30360--30527 Score: 239
Period size: 86 Copynumber: 2.0 Consensus size: 85
30350 TTCCTCACCT
* * * *
30360 TTCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTT-TCAAA
1 TTCAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTAGCATCTTTTCT-AAA
*
30424 GTCCACAAGTCAGTGGCAACC
65 GTCCACAACTCAGTGGCAACC
* *
30445 TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTAGCATCTTTTCTAAA
1 TTCAAAGCCCACAAATCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTAGCATCTTTTCTAAA
*
30510 GTCCACAACTCCGTGGCA
65 GTCCACAACTCAGTGGCA
30528 CTTTTTTTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
85 23 0.32
86 49 0.67
87 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (85 bp):
TTCAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTAGCATCTTTTCTAAAG
TCCACAACTCAGTGGCAACC
Found at i:30586 original size:34 final size:35
Alignment explanation
Indices: 30512--30586 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
30502 TTTCTAAAGT
* * *
30512 CCACAACTCCGTGGCACTTTTTTTCTTTTGTAAGC
1 CCACAACTCCGTAGCACTATTTTTCCTTTGTAAGC
*
30547 TCACAACTCCGTAGCACTATTTTTCCTTT-TAAGC
1 CCACAACTCCGTAGCACTATTTTTCCTTTGTAAGC
30581 CCACAA
1 CCACAA
30587 GTTAGTGGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
34 10 0.29
35 25 0.71
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.36
Consensus pattern (35 bp):
CCACAACTCCGTAGCACTATTTTTCCTTTGTAAGC
Found at i:30645 original size:28 final size:28
Alignment explanation
Indices: 30577--30728 Score: 173
Period size: 28 Copynumber: 5.3 Consensus size: 28
30567 TTTTCCTTTT
* *
30577 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTT-AA
30607 AAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
* *
30635 AAGCCCACAAGTCAGTAGCAATCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
30663 AAGCCCACAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
* * *
30691 AAGCACATAAGT-TGAT-GCAAACCTTTCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTT-AA
30720 AAGCCCACA
1 AAGCCCACA
30729 CAAGTTGGTG
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
27 3 0.03
28 70 0.66
29 12 0.11
30 21 0.20
ACGTcount: A:0.37, C:0.28, G:0.16, T:0.19
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTTAA
Found at i:30816 original size:48 final size:49
Alignment explanation
Indices: 30748--31087 Score: 427
Period size: 48 Copynumber: 7.0 Consensus size: 49
30738 GGCGTCTTCT
* * *
30748 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-GTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
30796 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
30844 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT--CATC
*
30896 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
30945 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGTACC-TCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
30993 TTTAAGCCCAATATCGCTGGCCTTGAAACAGCATATTGGCACCTT-GTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
31041 TTTAAGACCAATGTCGCCGGCCTTGAATCAGCACATTGTCACCTTCA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
31088 AGTCTAACTG
Statistics
Matches: 252, Mismatches: 33, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
47 3 0.01
48 158 0.63
49 43 0.17
50 2 0.01
51 2 0.01
52 44 0.17
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (49 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
Found at i:30996 original size:149 final size:145
Alignment explanation
Indices: 30748--31087 Score: 493
Period size: 149 Copynumber: 2.3 Consensus size: 145
30738 GGCGTCTTCT
* * *
30748 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGTCCAATGTAG
1 TTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* * * *
30812 CTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
66 CTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGCCCAATATCGCTGGCCTTGAAACAGCA
*
30877 TATTGGCGCCTTTGGCACC
131 TATTGGCACC-TT-G--CC
* *
30896 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
*
30961 CTGGCCTTGAATCAGCACATTGGTACCTCACCTTTAAGCCCAATATCGCTGGCCTTGAAACAGCA
66 CTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGCCCAATATCGCTGGCCTTGAAACAGCA
*
31026 TATTGGCACCTTGTC
131 TATTGGCACCTTGCC
* * * *
31041 TTTAAGACCAATGTCGCCGGCCTTGAATCAGCACATTGTCACCTTCA
1 TTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
31088 AGTCTAACTG
Statistics
Matches: 174, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
145 42 0.24
147 1 0.01
148 44 0.25
149 87 0.50
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (145 bp):
TTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGCCCAATATCGCTGGCCTTGAAACAGCA
TATTGGCACCTTGCC
Found at i:31860 original size:13 final size:13
Alignment explanation
Indices: 31842--31869 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31832 TACATAAACT
31842 ATTGTATTGATAC
1 ATTGTATTGATAC
31855 ATTGTATTGATAC
1 ATTGTATTGATAC
31868 AT
1 AT
31870 AAATTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (13 bp):
ATTGTATTGATAC
Found at i:31865 original size:33 final size:32
Alignment explanation
Indices: 31823--31887 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
31813 TTTCAACGAT
*
31823 TTGTATTGATACATAAACTATTGTATTGATACA
1 TTGTATTGATACATAAA-TATTGTATCGATACA
*
31856 TTGTATTGATACATAAATTTTGTATCGATACA
1 TTGTATTGATACATAAATATTGTATCGATACA
31888 ATTTAAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (32 bp):
TTGTATTGATACATAAATATTGTATCGATACA
Found at i:32089 original size:52 final size:51
Alignment explanation
Indices: 31943--32090 Score: 233
Period size: 51 Copynumber: 2.9 Consensus size: 51
31933 GTCGATACAT
***
31943 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
31995 TGTATGGATACATTATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
32046 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTAT-AAATGTATCGATACATGCAGGCAAATTT
32091 TCATATTTCG
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 48 0.55
52 40 0.45
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Done.