Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2783
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: 61022
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4596 original size:49 final size:49
Alignment explanation
Indices: 4527--4622 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
4517 AACGTAGGGA
4527 AATCGAACTGTGTAAACATATTAGTTGTTCATTGTTTTTCTACTTTGGG
1 AATCGAACTGTGTAAACATATTAGTTGTTCATTGTTTTTCTACTTTGGG
4576 AATCGAACTGTGTAAACATATTAGTTGTTCATTGTTTTTCTACTTTG
1 AATCGAACTGTGTAAACATATTAGTTGTTCATTGTTTTTCTACTTTG
4623 TTCTTTACTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (49 bp):
AATCGAACTGTGTAAACATATTAGTTGTTCATTGTTTTTCTACTTTGGG
Found at i:6860 original size:22 final size:21
Alignment explanation
Indices: 6835--6876 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
6825 TTTATTTATT
6835 TTAATTAATCAAGTTAAATAAA
1 TTAATTAATCAA-TTAAATAAA
**
6857 TTAATTTCTCAATTAAATAA
1 TTAATTAATCAATTAAATAA
6877 TTTTCTCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAATTAATCAATTAAATAAA
Found at i:6879 original size:16 final size:18
Alignment explanation
Indices: 6853--6885 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6843 TCAAGTTAAA
6853 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
6870 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
6886 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:11362 original size:39 final size:40
Alignment explanation
Indices: 11278--11355 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
11268 AAAATGTCGG
*
11278 TAAAAATCGAGCATTAGCGGCGCTTTAAGAAAATCGCCAC
1 TAAAAATCGAGCATTAGCGGCGCTTTAAGAAAAACGCCAC
* *
11318 TAAAAAT-GAGCATTAGCGGCGTTTTTAGGAAAAACGCC
1 TAAAAATCGAGCATTAGCGGCG-CTTTAAGAAAAACGCC
11356 GCAAAAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 14 0.41
40 20 0.59
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (40 bp):
TAAAAATCGAGCATTAGCGGCGCTTTAAGAAAAACGCCAC
Found at i:11452 original size:41 final size:41
Alignment explanation
Indices: 11402--11555 Score: 188
Period size: 41 Copynumber: 3.8 Consensus size: 41
11392 CTTTGGGGGA
*
11402 TTTAGCGGCGTTTCT-GTAGAAGCGCCGCTAATGCTGGGGTC
1 TTTAGCGGCGTTTTTAGTA-AAGCGCCGCTAATGCTGGGGTC
* *
11443 TTTAGCGGCGTTTTT-GATAAAGCGCCGCTAGTGCTGGGATC
1 TTTAGCGGCGTTTTTAG-TAAAGCGCCGCTAATGCTGGGGTC
* * * *
11484 TTTAGCGGCATTTTTGGTAAAGCGCCACTAATGCTGAGGTC
1 TTTAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCTGGGGTC
*
11525 TGTAGCGGCGTTTTTAG-AGAAGCGCCGCTAA
1 TTTAGCGGCGTTTTTAGTA-AAGCGCCGCTAA
11556 AAATATTTTG
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
40 1 0.01
41 94 0.96
42 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCTGGGGTC
Found at i:11539 original size:82 final size:82
Alignment explanation
Indices: 11402--11554 Score: 220
Period size: 82 Copynumber: 1.9 Consensus size: 82
11392 CTTTGGGGGA
* * * *
11402 TTTAGCGGCGTTTCTGTAGAAGCGCCGCTAATGCTGGGGTCTTTAGCGGCGTTTTT-GATAAAGC
1 TTTAGCGGCATTTCTGTAGAAGCGCCACTAATGCTGAGGTCTGTAGCGGCGTTTTTAGA-AAAGC
11466 GCCGCTAGTGCTGGGATC
65 GCCGCTAGTGCTGGGATC
* *
11484 TTTAGCGGCATTTTTGGTA-AAGCGCCACTAATGCTGAGGTCTGTAGCGGCGTTTTTAGAGAAGC
1 TTTAGCGGCATTTCT-GTAGAAGCGCCACTAATGCTGAGGTCTGTAGCGGCGTTTTTAGAAAAGC
11548 GCCGCTA
65 GCCGCTA
11555 AAAATATTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
82 58 0.92
83 5 0.08
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.30
Consensus pattern (82 bp):
TTTAGCGGCATTTCTGTAGAAGCGCCACTAATGCTGAGGTCTGTAGCGGCGTTTTTAGAAAAGCG
CCGCTAGTGCTGGGATC
Found at i:11768 original size:25 final size:27
Alignment explanation
Indices: 11713--11768 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
11703 AATCCCTAAT
* * *
11713 CTTCAGACTTTTCTTCACTCCCGTTTT
1 CTTCAGACTTTTCATCACTCCCGCTTC
11740 CTTCAGACTTTTCAT-A-TCCCGCTTC
1 CTTCAGACTTTTCATCACTCCCGCTTC
11765 CTTC
1 CTTC
11769 TCATTATCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 11 0.42
26 1 0.04
27 14 0.54
ACGTcount: A:0.12, C:0.36, G:0.07, T:0.45
Consensus pattern (27 bp):
CTTCAGACTTTTCATCACTCCCGCTTC
Found at i:15328 original size:43 final size:43
Alignment explanation
Indices: 15263--15463 Score: 197
Period size: 43 Copynumber: 4.7 Consensus size: 43
15253 AAGTCATGCT
* * * * *
15263 TTTAGCGGTGTTTGTGAGAAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGGTCTTGATC
* * * * *
15306 TTTAGTGGTGTTTGTAAAAAAAGTGCTGCTAAAGGTCTTGACC
1 TTTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGGTCTTGATC
* *
15349 TTTAGCGGCATTTGTGAGAAAAA-CGCCGCTAAAGGTCTTGATC
1 TTTAGCGGCGTTTGT-AAAAAAAGCGCCGCTAAAGGTCTTGATC
* *** * *
15392 TTTACCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGGTCTTGATC
* **
15435 TTTAGCGGCGTTTGTGAGCAAAGCGCCGC
1 TTTAGCGGCGTTTGTAAAAAAAGCGCCGC
15464 AAATACTTTT
Statistics
Matches: 131, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
42 4 0.03
43 121 0.92
44 6 0.05
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGGTCTTGATC
Found at i:15387 original size:86 final size:86
Alignment explanation
Indices: 15263--15463 Score: 249
Period size: 86 Copynumber: 2.3 Consensus size: 86
15253 AAGTCATGCT
* * * ** *
15263 TTTAGCGGTGTTTGTGAGAAAAGCGTCGCTAAAGGTCTTGGTCTTTAGTGGTGTTTGTAAAAAAA
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGATCTTTACCGGCGTTTGTAAAAAAA
* *
15328 GTGCTGCTAAAGGTCTTGACC
66 GCGCCGCTAAAGGTCTTGACC
* * *** *
15349 TTTAGCGGCATTTGTGAGAAAAACGCCGCTAAAGGTCTTGATCTTTACCGGCGTTTGTGGGATAA
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGATCTTTACCGGCGTTTGTAAAAAAA
**
15414 GCGCCGCTAAAGGTCTTGGTC
66 GCGCCGCTAAAGGTCTTGACC
*
15435 TTTAGCGGCGTTTGTGAGCAAAGCGCCGC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGC
15464 AAATACTTTT
Statistics
Matches: 96, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
86 96 1.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGATCTTTACCGGCGTTTGTAAAAAAA
GCGCCGCTAAAGGTCTTGACC
Found at i:16200 original size:145 final size:145
Alignment explanation
Indices: 15937--16226 Score: 580
Period size: 145 Copynumber: 2.0 Consensus size: 145
15927 CCACCCTTAA
15937 CCCCAATTATAAAAAATAATAATATTTTAGGATTTTACTTAAAAACACCATTTGAACTTGTCATG
1 CCCCAATTATAAAAAATAATAATATTTTAGGATTTTACTTAAAAACACCATTTGAACTTGTCATG
16002 ATTTTCTTTCGAGAAAAATCGACGTCTTAATTAAAAATAAATTAAAAAGATTTTAACAATACTTT
66 ATTTTCTTTCGAGAAAAATCGACGTCTTAATTAAAAATAAATTAAAAAGATTTTAACAATACTTT
16067 GACCTACCAAAATTT
131 GACCTACCAAAATTT
16082 CCCCAATTATAAAAAATAATAATATTTTAGGATTTTACTTAAAAACACCATTTGAACTTGTCATG
1 CCCCAATTATAAAAAATAATAATATTTTAGGATTTTACTTAAAAACACCATTTGAACTTGTCATG
16147 ATTTTCTTTCGAGAAAAATCGACGTCTTAATTAAAAATAAATTAAAAAGATTTTAACAATACTTT
66 ATTTTCTTTCGAGAAAAATCGACGTCTTAATTAAAAATAAATTAAAAAGATTTTAACAATACTTT
16212 GACCTACCAAAATTT
131 GACCTACCAAAATTT
16227 TCATAATTAA
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (145 bp):
CCCCAATTATAAAAAATAATAATATTTTAGGATTTTACTTAAAAACACCATTTGAACTTGTCATG
ATTTTCTTTCGAGAAAAATCGACGTCTTAATTAAAAATAAATTAAAAAGATTTTAACAATACTTT
GACCTACCAAAATTT
Found at i:20951 original size:33 final size:33
Alignment explanation
Indices: 20891--20958 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
20881 GAAACAGTAG
* *
20891 AATGTGCACACATATACGACATTTACTCAACAA
1 AATGTGCACACAGATACGACATCTACTCAACAA
* * * *
20924 AATGTGCATACAGATGCGTCATCTACTCAGCAA
1 AATGTGCACACAGATACGACATCTACTCAACAA
20957 AA
1 AA
20959 ATAGCAGCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.24
Consensus pattern (33 bp):
AATGTGCACACAGATACGACATCTACTCAACAA
Found at i:31896 original size:33 final size:33
Alignment explanation
Indices: 31833--31919 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
31823 TTTCTTTATA
* * *
31833 ATTTAGAGTTTAGTATTTTAAATTATTATTTATG
1 ATTTAGAATTTAGTA-TTTAAATTAATATTTAAG
* **
31867 GTTTATTATTTAGTATTTAAATTAATATTTAAG
1 ATTTAGAATTTAGTATTTAAATTAATATTTAAG
31900 ATTTAGAATTTAGTATTTAA
1 ATTTAGAATTTAGTATTTAA
31920 TATTTAAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 33 0.75
34 11 0.25
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (33 bp):
ATTTAGAATTTAGTATTTAAATTAATATTTAAG
Found at i:31898 original size:7 final size:7
Alignment explanation
Indices: 31868--31930 Score: 53
Period size: 7 Copynumber: 9.4 Consensus size: 7
31858 TTATTTATGG
*
31868 TTTATTA
1 TTTAATA
*
31875 TTTAGTA
1 TTTAATA
31882 TTTAA-A
1 TTTAATA
31888 -TTAATA
1 TTTAATA
*
31894 TTTAAGA
1 TTTAATA
31901 TTTAGA-A
1 TTTA-ATA
*
31908 TTTAGTA
1 TTTAATA
31915 TTTAATA
1 TTTAATA
31922 TTTAA-A
1 TTTAATA
31928 TTT
1 TTT
31931 TAGCTGTTAG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.09
6 6 0.13
7 36 0.77
8 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (7 bp):
TTTAATA
Found at i:31940 original size:28 final size:27
Alignment explanation
Indices: 31874--31930 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
31864 ATGGTTTATT
* *
31874 ATTTAGTATTTA-AATTAATATTTAAG
1 ATTTAGAATTTAGATTTAATATTTAAG
31900 ATTTAGAATTTAGTATTTAATATTTAA-
1 ATTTAGAATTTAG-ATTTAATATTTAAG
31927 ATTT
1 ATTT
31931 TAGCTGTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 4 0.15
28 12 0.44
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (27 bp):
ATTTAGAATTTAGATTTAATATTTAAG
Found at i:31976 original size:20 final size:21
Alignment explanation
Indices: 31951--31991 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31941 ATTTTTTTAG
31951 ATGTAAA-GTTAGGATTTAAA
1 ATGTAAATGTTAGGATTTAAA
* *
31971 ATGTAAATTTTAGTATTTAAA
1 ATGTAAATGTTAGGATTTAAA
31992 GTTTAACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (21 bp):
ATGTAAATGTTAGGATTTAAA
Found at i:32017 original size:14 final size:14
Alignment explanation
Indices: 31985--32024 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31975 AAATTTTAGT
31985 ATTTAAAGTTTAAC
1 ATTTAAAGTTTAAC
* *
31999 ATTTAAAATTTAAG
1 ATTTAAAGTTTAAC
*
32013 GTTTAAAGTTTA
1 ATTTAAAGTTTA
32025 TTGTTTAGAA
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:0.03, G:0.10, T:0.45
Consensus pattern (14 bp):
ATTTAAAGTTTAAC
Found at i:32024 original size:21 final size:21
Alignment explanation
Indices: 31985--32024 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31975 AAATTTTAGT
*
31985 ATTTAAAGTTTAACATTTAAA
1 ATTTAAAGTTTAAAATTTAAA
* *
32006 ATTTAAGGTTTAAAGTTTA
1 ATTTAAAGTTTAAAATTTA
32025 TTGTTTAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (21 bp):
ATTTAAAGTTTAAAATTTAAA
Found at i:33621 original size:20 final size:21
Alignment explanation
Indices: 33596--33634 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
33586 TCAAATACTC
33596 GAAATA-CA-ATTTATATATAT
1 GAAATATCAGATTTA-ATATAT
33616 GAAATATCAGATTTAATAT
1 GAAATATCAGATTTAATAT
33635 TTGATGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (21 bp):
GAAATATCAGATTTAATATAT
Found at i:37749 original size:23 final size:24
Alignment explanation
Indices: 37722--37770 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
37712 GTGGGTGGAG
*
37722 AAGAAAAGGAGAGGA-AAGAAAGA
1 AAGAAAAGGAAAGGAGAAGAAAGA
*
37745 AAGAAAAGGAAAGGAGGAGAAAGA
1 AAGAAAAGGAAAGGAGAAGAAAGA
37769 AA
1 AA
37771 AAGAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (24 bp):
AAGAAAAGGAAAGGAGAAGAAAGA
Found at i:37756 original size:14 final size:14
Alignment explanation
Indices: 37725--37791 Score: 57
Period size: 14 Copynumber: 4.7 Consensus size: 14
37715 GGTGGAGAAG
*
37725 AAAAGGAGAGGAAAG
1 AAAAGGA-AAGAAAG
37740 -AAA-GAAAGAAAAG
1 AAAAGGAAAG-AAAG
* *
37753 GAAAGGAGGAGAAAG
1 AAAAGGA-AAGAAAG
*
37768 AAAAAGAAAGAAAG
1 AAAAGGAAAGAAAG
37782 AAAAGGAAAG
1 AAAAGGAAAG
37792 GAGGAGAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
12 2 0.05
13 6 0.14
14 21 0.50
15 11 0.26
16 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AAAAGGAAAGAAAG
Found at i:37767 original size:20 final size:20
Alignment explanation
Indices: 37742--37805 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
37732 GAGGAAAGAA
37742 AGAAAGAAAAGGAAAGGAGG
1 AGAAAGAAAAGGAAAGGAGG
*
37762 AGAAAG--AA--AAA-GA-A
1 AGAAAGAAAAGGAAAGGAGG
37776 AGAAAGAAAAGGAAAGGAGG
1 AGAAAGAAAAGGAAAGGAGG
37796 AGAAAGAAAA
1 AGAAAGAAAA
37806 AAAAAAGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
14 6 0.17
15 2 0.06
16 5 0.14
18 5 0.14
19 2 0.06
20 16 0.44
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AGAAAGAAAAGGAAAGGAGG
Found at i:37775 original size:34 final size:34
Alignment explanation
Indices: 37736--37806 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
37726 AAAGGAGAGG
37736 AAAGAAAGAAAGAAAAGGAAAGGAGGAGAAAGAA
1 AAAGAAAGAAAGAAAAGGAAAGGAGGAGAAAGAA
37770 AAAGAAAGAAAGAAAAGGAAAGGAGGAGAAAGAA
1 AAAGAAAGAAAGAAAAGGAAAGGAGGAGAAAGAA
37804 AAA
1 AAA
37807 AAAAAGGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (34 bp):
AAAGAAAGAAAGAAAAGGAAAGGAGGAGAAAGAA
Found at i:37819 original size:20 final size:23
Alignment explanation
Indices: 37762--37819 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
37752 GGAAAGGAGG
* *
37762 AGAAAGAAAAAGAAAGAAAGAAA
1 AGAAAGGAGAAGAAAGAAAGAAA
*
37785 AGGAAAGGAGGAGAAAGAAA-AAA
1 A-GAAAGGAGAAGAAAGAAAGAAA
37808 A-AAAGG-GAAGAA
1 AGAAAGGAGAAGAA
37820 GAAGGGTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.17
21 5 0.17
23 5 0.17
24 15 0.50
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (23 bp):
AGAAAGGAGAAGAAAGAAAGAAA
Found at i:38135 original size:21 final size:20
Alignment explanation
Indices: 38111--38160 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 20
38101 TGGCCAGTAC
38111 AAATAACAAAAACAATAGC-AA
1 AAATAACAAAAA-AA-AGCAAA
38132 AAATAACAAAAAAAAGCAGAA
1 AAATAACAAAAAAAAGCA-AA
38153 AAATAACA
1 AAATAACA
38161 GCACCAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.11
20 2 0.07
21 22 0.81
ACGTcount: A:0.74, C:0.12, G:0.06, T:0.08
Consensus pattern (20 bp):
AAATAACAAAAAAAAGCAAA
Found at i:38713 original size:26 final size:25
Alignment explanation
Indices: 38666--38714 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
38656 TTTGACTCTA
*
38666 ATTTTTTTTAAATTTCTCTCAATTT
1 ATTTTTTTTAAATTTATCTCAATTT
*
38691 ATTTTTTTTAACTTTATCGTCAAT
1 ATTTTTTTTAAATTTATC-TCAAT
38715 ACGCTTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.61
Consensus pattern (25 bp):
ATTTTTTTTAAATTTATCTCAATTT
Found at i:40111 original size:303 final size:304
Alignment explanation
Indices: 39448--40207 Score: 1291
Period size: 304 Copynumber: 2.5 Consensus size: 304
39438 AAAAATTGTA
*
39448 TATTTAAAAAACACACTAAA-TTA-ATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
*
39511 TAAAATTAGAAAATATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGG
66 TAAAATTAGAAAATATGATATTTTTTAAAGTAATAAAATTCGG-GAAAAAAATACGAACAAATGG
* *
39576 CCGAAGTAAGGGTTTTTTACTAAATTAAAAAATAGAAATAATTAATACATTTCAAACATAATGTA
130 CCGAAATAAGTGTTTTTTACTAAATTAAAAAATAGAAATAATTAATACATTTCAAACATAATGTA
*
39641 CTAAGATAAATTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAATCGG
195 CTAAGATAAAGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAATCGG
* *
39706 GAAAAAAATACGAGCAAAGGGCCGAAATAAGGGTTTTTTTTAATT
260 GAAAAAAATACGAGCAAAGGGCCGAAATAAGGGTTTCTTTAAATT
39751 TATTTAAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATA
1 TATTT-AAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATA
* *
39816 ATAAAATTA-AAAATA-GTATATTTTTTAAAGTAATAAATTTC-GGAAAAAAATACGAACAAAGG
65 ATAAAATTAGAAAATATG-ATATTTTTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAATG
*
39878 GCCGAAATAAGTGTTTTTTACTAAATTAAAAAAATAGAATTAATTAATACATTTCAAACATAATG
129 GCCGAAATAAGTGTTTTTTACTAAATT-AAAAAATAGAAATAATTAATACATTTCAAACATAATG
*
39943 TACTAAGATAAAGTAAAATAATAAAATATC-AAAATAATATATTTTTATTGAAAGTAATAAAATT
193 TACTAAGATAAAGTAAAATAATAAAATA-CGAAAATAATATATTTTTATTGAAAGTAATAAAAAT
*
40007 CGGGAAAAAAATACGAGCAAAGGGCCGAAATAATGGTTTCTTTAAATT
257 CGGGAAAAAAATACGAGCAAAGGGCCGAAATAAGGGTTTCTTTAAATT
40055 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
*
40120 TAAAATTAGAAAATATGATATTTTTTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAATGA
66 TAAAATTAGAAAATATGATA-TTTTTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAATGG
40185 CCGAAATAA-TGGTTTTTTACTAA
130 CCGAAATAAGT-GTTTTTTACTAA
40208 TTTTTTTTGA
Statistics
Matches: 431, Mismatches: 15, Indels: 19
0.93 0.03 0.04
Matches are distributed among these distances:
303 117 0.27
304 172 0.40
305 54 0.13
306 88 0.20
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.31
Consensus pattern (304 bp):
TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
TAAAATTAGAAAATATGATATTTTTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAATGGC
CGAAATAAGTGTTTTTTACTAAATTAAAAAATAGAAATAATTAATACATTTCAAACATAATGTAC
TAAGATAAAGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAATCGGG
AAAAAAATACGAGCAAAGGGCCGAAATAAGGGTTTCTTTAAATT
Found at i:42350 original size:77 final size:77
Alignment explanation
Indices: 42246--42484 Score: 390
Period size: 77 Copynumber: 3.1 Consensus size: 77
42236 AATTTATTTC
* * * *
42246 ACTTTTAATACCTTGATTTGGATACAATTGAAGCATAAGCATAAGCTGAATAAGTTTAATTATTC
1 ACTTTTTATACCTTAATTTGGATACAATTTAAGCATAAGCATAAGCTGAATAATTTTAATTATTC
*
42311 CAAATGAATTTT
66 CAAATGAATTAT
*
42323 ACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAGCTGAATAATTTTAATTATTC
1 ACTTTTTATACCTTAATTTGGATACAATTTAAGCATAAGCATAAGCTGAATAATTTTAATTATTC
*
42388 CAAATGAATCAT
66 CAAATGAATTAT
*
42400 -GTTTTTAATACCTTAATTTGGATACAATTTAAGCATAAGCATAAGCTGAATAATTTTAATTATT
1 ACTTTTT-ATACCTTAATTTGGATACAATTTAAGCATAAGCATAAGCTGAATAATTTTAATTATT
42464 CCAAATGAATTAT
65 CCAAATGAATTAT
42477 ACTTTTTA
1 ACTTTTTA
42485 CAACATTACA
Statistics
Matches: 149, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
76 5 0.03
77 139 0.93
78 5 0.03
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.40
Consensus pattern (77 bp):
ACTTTTTATACCTTAATTTGGATACAATTTAAGCATAAGCATAAGCTGAATAATTTTAATTATTC
CAAATGAATTAT
Found at i:45653 original size:22 final size:22
Alignment explanation
Indices: 45624--45686 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
45614 GTAACCATAA
45624 AGCAGCCCCATACCTCCACTAC
1 AGCAGCCCCATACCTCCACTAC
* *
45646 AGCGGCCCCATACCCCCACTAC
1 AGCAGCCCCATACCTCCACTAC
* *
45668 AGCAGTCCTATACCTCCAC
1 AGCAGCCCCATACCTCCAC
45687 AGCCCTCGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.25, C:0.49, G:0.11, T:0.14
Consensus pattern (22 bp):
AGCAGCCCCATACCTCCACTAC
Done.