Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2770
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: 217587
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:3061 original size:21 final size:22
Alignment explanation
Indices: 3015--3061 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3005 TCATTTTCTT
*
3015 TTCTTTTTCACTCTCTCTCAAT
1 TTCTTTTTCACTCTCTCTCAAA
* *
3037 TTCTTTTTCAGT-TCTTTCAAA
1 TTCTTTTTCACTCTCTCTCAAA
3058 TTCT
1 TTCT
3062 CCAAAGATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.15, C:0.26, G:0.02, T:0.57
Consensus pattern (22 bp):
TTCTTTTTCACTCTCTCTCAAA
Found at i:7156 original size:24 final size:25
Alignment explanation
Indices: 7129--7182 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
7119 ATGAGTGATA
*
7129 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
7153 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
7177 AAAAAA
1 AAAAAA
7183 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:13382 original size:15 final size:15
Alignment explanation
Indices: 13362--13397 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
13352 TTGTATGCAA
*
13362 TTTTTTT-AATAATT
1 TTTTTTTCAAAAATT
13376 TTTTTTTCAAAAATT
1 TTTTTTTCAAAAATT
13391 TTTTTTT
1 TTTTTTT
13398 GAACTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTTCAAAAATT
Found at i:13741 original size:22 final size:22
Alignment explanation
Indices: 13711--13754 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
13701 TTTGGTATTT
13711 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
13733 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
13755 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:16025 original size:30 final size:30
Alignment explanation
Indices: 15991--16087 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
15981 AGCTCACTCA
15991 TAGCTC-ACATTCAGCTCACGAGCTAAACCT
1 TAGCTCAAC-TTCAGCTCACGAGCTAAACCT
* * * * *
16021 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
16051 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
16081 TAGCTCA
1 TAGCTCA
16088 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 50 0.96
31 2 0.04
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:36639 original size:30 final size:30
Alignment explanation
Indices: 36605--36701 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
36595 TAAACTAAAA
*
36605 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * * *
36635 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTAAGCTAAAGT
* *
36665 TGAGCTAAGGTTTAGCTCGTAAGTCGAAAG-
1 TGAGCTAAGCTTTAGCTCGTAAG-CTAAAGT
36695 TGAGCTA
1 TGAGCTA
36702 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:37397 original size:16 final size:16
Alignment explanation
Indices: 37365--37402 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
37355 CATTAAACAC
*
37365 TTTTTTTTCAGATTTT
1 TTTTTTTTCAGAATTT
37381 TTTTCTTTTC-GAATTT
1 TTTT-TTTTCAGAATTT
37397 TTTTTT
1 TTTTTT
37403 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 13 0.65
17 5 0.25
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTTTTTTCAGAATTT
Found at i:37425 original size:10 final size:11
Alignment explanation
Indices: 37381--37423 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 11
37371 TTCAGATTTT
37381 TTTTCTTTTCGAA
1 TTTT-TTTT-GAA
37394 TTTTTTTTTGAA
1 -TTTTTTTTGAA
37406 TTTTTTTTGAA
1 TTTTTTTTGAA
37417 TTTTTTT
1 TTTTTTT
37424 GACTTGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 18 0.62
12 3 0.10
13 4 0.14
14 4 0.14
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:40410 original size:14 final size:14
Alignment explanation
Indices: 40391--40421 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40381 CTATTTGAAC
40391 CTTTCTTAACCTTT
1 CTTTCTTAACCTTT
*
40405 CTTTCTTAGCCTTT
1 CTTTCTTAACCTTT
40419 CTT
1 CTT
40422 CAACTATCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.29, G:0.03, T:0.58
Consensus pattern (14 bp):
CTTTCTTAACCTTT
Found at i:41879 original size:14 final size:14
Alignment explanation
Indices: 41845--41879 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41835 TATATGTTCT
41845 TTTTTTTATACGAA
1 TTTTTTTATACGAA
* *
41859 ATTTTTTGTACGAA
1 TTTTTTTATACGAA
41873 TTTTTTT
1 TTTTTTT
41880 CACTGAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.09, T:0.63
Consensus pattern (14 bp):
TTTTTTTATACGAA
Found at i:43014 original size:16 final size:17
Alignment explanation
Indices: 42984--43015 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42974 TAGACACATT
42984 AAACATATATTAATATG
1 AAACATATATTAATATG
43001 AAACATAT-TTAATAT
1 AAACATATATTAATAT
43016 ACTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
AAACATATATTAATATG
Found at i:49945 original size:21 final size:21
Alignment explanation
Indices: 49900--49962 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
49890 TTTGAACCAT
* *
49900 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
49922 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
49943 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
49963 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:56146 original size:46 final size:45
Alignment explanation
Indices: 56000--56169 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 45
55990 GGTTGAGCAT
* *
56000 CCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGAGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACGC
* * *
56045 CCGAACTCGTTGAGTTGAGT-CGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAC---GC
56089 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACGC
*
56137 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
56170 GGGGCGGTTA
Statistics
Matches: 105, Mismatches: 9, Indels: 21
0.78 0.07 0.16
Matches are distributed among these distances:
41 2 0.02
42 4 0.04
44 9 0.09
45 20 0.19
46 52 0.50
47 7 0.07
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACGC
Found at i:59910 original size:13 final size:13
Alignment explanation
Indices: 59892--59920 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
59882 CGGCTAACCT
59892 ACATAATTAAATA
1 ACATAATTAAATA
59905 ACATAATTAAATA
1 ACATAATTAAATA
59918 ACA
1 ACA
59921 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:61532 original size:30 final size:30
Alignment explanation
Indices: 61498--61594 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
61488 TAAACTAAAA
61498 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
61528 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
61558 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
61588 TGAGCTA
1 TGAGCTA
61595 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:63989 original size:15 final size:14
Alignment explanation
Indices: 63949--63994 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
63939 CTCTTGCCTC
*
63949 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
63964 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
63979 TCTTTTGCTTTTTCT
1 TCTTTT-CTTTTTCT
63994 T
1 T
63995 TTCTTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 14 0.50
16 10 0.36
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.76
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:64001 original size:16 final size:16
Alignment explanation
Indices: 63949--64011 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 16
63939 CTCTTGCCTC
* *
63949 TCTTTTCTTTTT-ATT
1 TCTTTGCTTTTTCTTT
* *
63964 TCGTTTTCTTTTTCTTC
1 TC-TTTGCTTTTTCTTT
63981 T-TTTGCTTTTTCTTT
1 TCTTTGCTTTTTCTTT
63996 TCTTTG-TTTTCTCTTT
1 TCTTTGCTTTT-TCTTT
64012 ACAAAAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 19 0.47
16 19 0.47
17 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (16 bp):
TCTTTGCTTTTTCTTT
Found at i:66631 original size:30 final size:31
Alignment explanation
Indices: 66537--66633 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
66527 TAAACTAAAA
*
66537 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
* * * * * *
66567 TGTGCTGAGGTTAAACTCCTAAGCTG-AAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
*
66597 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
66627 TGAGCTA
1 TGAGCTA
66634 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 48 0.94
31 3 0.06
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (31 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
Found at i:66919 original size:21 final size:20
Alignment explanation
Indices: 66895--66943 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
66885 AAAAAGGAAT
*
66895 GAGCTGAAACGAGCTAAATAC
1 GAGCTCAAACGAGCTAAA-AC
* *
66916 GAGCTCAAATGAGTTAAAAC
1 GAGCTCAAACGAGCTAAAAC
66936 GAGCTCAA
1 GAGCTCAA
66944 GTGAGCTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.16
Consensus pattern (20 bp):
GAGCTCAAACGAGCTAAAAC
Found at i:66939 original size:20 final size:21
Alignment explanation
Indices: 66895--66950 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
66885 AAAAAGGAAT
* *
66895 GAGCTGAAACGAGCTAAATAC
1 GAGCTCAAATGAGCTAAATAC
*
66916 GAGCTCAAATGAGTTAAA-AC
1 GAGCTCAAATGAGCTAAATAC
*
66936 GAGCTCAAGTGAGCT
1 GAGCTCAAATGAGCT
66951 GATGGGAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (21 bp):
GAGCTCAAATGAGCTAAATAC
Found at i:70496 original size:30 final size:30
Alignment explanation
Indices: 70410--70507 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 30
70400 TTAAACTAAA
* *
70410 ATGAGCTAAGCTTTAGCTCATGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
* * * * * *
70440 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
* * * *
70470 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
70500 ATGAGCTA
1 ATGAGCTA
70508 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCATGAGCTGAAG
Found at i:76041 original size:13 final size:14
Alignment explanation
Indices: 76023--76054 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
76013 CATAAATCAC
76023 TTTTTTT-G-ATTT
1 TTTTTTTCGAATTT
76035 TTTTTTTCGAATTT
1 TTTTTTTCGAATTT
76049 TTTTTT
1 TTTTTT
76055 AAACTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 1 0.06
14 10 0.56
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.81
Consensus pattern (14 bp):
TTTTTTTCGAATTT
Found at i:79888 original size:30 final size:30
Alignment explanation
Indices: 79854--79950 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
79844 TAAACTAAAA
*
79854 TGAGCTAAGCTTTAGCTCGTGCGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
79884 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
79914 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
79944 TGAGCTA
1 TGAGCTA
79951 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:81829 original size:20 final size:20
Alignment explanation
Indices: 81806--81852 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
81796 AGCTCCGTCC
81806 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTCAGCTCATTTG
*** *
81826 AGCTTGTTTCAGCTCGTTTG
1 AGCTCAATTCAGCTCATTTG
81846 AGCTCAA
1 AGCTCAA
81853 CCGAGCTTAC
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (20 bp):
AGCTCAATTCAGCTCATTTG
Found at i:84354 original size:13 final size:14
Alignment explanation
Indices: 84336--84372 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
84326 TCCTCTTGTA
*
84336 AAAAGAAAATGA-G
1 AAAAGAAAAAGACG
84349 AAAAGAAAAAGACG
1 AAAAGAAAAAGACG
84363 AAAAGAAAAA
1 AAAAGAAAAA
84373 AGAGATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAGACG
Found at i:84358 original size:14 final size:13
Alignment explanation
Indices: 84336--84377 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
84326 TCCTCTTGTA
*
84336 AAAAGAAAATGAG
1 AAAAGAAAAAGAG
84349 AAAAGAAAAAGACG
1 AAAAGAAAAAGA-G
84363 AAAAGAAAAAAGAG
1 AAAAG-AAAAAGAG
84377 A
1 A
84378 TCAAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.42
14 8 0.31
15 7 0.27
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAAGAG
Found at i:84388 original size:15 final size:15
Alignment explanation
Indices: 84336--84392 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 15
84326 TCCTCTTGTA
*
84336 AAAAGAAAA-TGA-G
1 AAAAGAAAAGAGACG
84349 AAAAGAAAA-AGACG
1 AAAAGAAAAGAGACG
84363 AAAAGAAAAAAGAGATC-
1 AAAAG--AAAAGAGA-CG
84380 AAAAGAAAAGAGA
1 AAAAGAAAAGAGA
84393 GGCAAGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 11 0.29
14 6 0.16
15 8 0.21
16 4 0.11
17 8 0.21
18 1 0.03
ACGTcount: A:0.72, C:0.04, G:0.21, T:0.04
Consensus pattern (15 bp):
AAAAGAAAAGAGACG
Found at i:84527 original size:12 final size:12
Alignment explanation
Indices: 84486--84528 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
84476 GAGAGGAAAC
*
84486 AAAATGAGATTG
1 AAAAAGAGATTG
*
84498 AAAAACAGATTG
1 AAAAAGAGATTG
*
84510 AAAAAGAGAATG
1 AAAAAGAGATTG
84522 AAAAAGA
1 AAAAAGA
84529 AAAAGAGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.63, C:0.02, G:0.21, T:0.14
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:86205 original size:30 final size:30
Alignment explanation
Indices: 86129--86206 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
86119 TTTAGCTCAC
86129 GAGCTAAACCTTAGCTCAACTGCAGCTTAG
1 GAGCTAAACCTTAGCTCAACTGCAGCTTAG
* *
86159 GAG-TATAATCTCAGCTCAACTGCAGCTTAAG
1 GAGCTA-AACCTTAGCTCAACTGCAGCTT-AG
*
86190 G-GCTAAAGCTTAGCTCA
1 GAGCTAAACCTTAGCTCA
86207 TTTTAGCTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 2 0.05
30 34 0.83
31 5 0.12
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (30 bp):
GAGCTAAACCTTAGCTCAACTGCAGCTTAG
Found at i:88249 original size:20 final size:20
Alignment explanation
Indices: 88203--88249 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
88193 AGCTCGTTTC
*
88203 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
88223 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
88243 CAGCTCA
1 CAGCTCA
88250 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:89679 original size:12 final size:11
Alignment explanation
Indices: 89662--89692 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
89652 TTCGTAACGT
*
89662 AAAAAAAGTCA
1 AAAAAAAATCA
89673 AAAAAAAATCA
1 AAAAAAAATCA
89684 AAAAAAAAT
1 AAAAAAAAT
89693 TGAGTTGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:90954 original size:48 final size:47
Alignment explanation
Indices: 90875--90980 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
90865 GAGTGTCATG
*
90875 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
90923 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
90971 GAAAAAGAAA
1 GAAAAAGAAA
90981 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:92697 original size:20 final size:20
Alignment explanation
Indices: 92651--92697 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
92641 AGCTCGTTTC
*
92651 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
92671 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
92691 CAGCTCA
1 CAGCTCA
92698 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:103023 original size:21 final size:20
Alignment explanation
Indices: 102989--103032 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
102979 ACAGTCTTGT
102989 AAAGAGAAAACAAAGAAAAGA
1 AAAGAGAAAACAAA-AAAAGA
*
103010 AAAGA-AAAAGCAAAAGAAGA
1 AAAGAGAAAA-CAAAAAAAGA
103030 AAA
1 AAA
103033 ACAAACGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAGAGAAAACAAAAAAAGA
Found at i:103133 original size:12 final size:12
Alignment explanation
Indices: 103124--103148 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
103114 TTTAAAAAGC
103124 AAAAAGAAAATG
1 AAAAAGAAAATG
103136 AAAAAGAAAATG
1 AAAAAGAAAATG
103148 A
1 A
103149 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:103145 original size:18 final size:18
Alignment explanation
Indices: 103117--103173 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
103107 AAAAGCCTTT
103117 AAAAAGCAAAAAGAAAATG
1 AAAAAG-AAAAAGAAAATG
* * *
103136 AAAAAGAAAATGAGATTG
1 AAAAAGAAAAAGAAAATG
* *
103154 AAAAAGAGAACGAAAA-G
1 AAAAAGAAAAAGAAAATG
103171 AAA
1 AAA
103174 TTTGAGAGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.68
19 6 0.19
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.07
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAATG
Found at i:103158 original size:30 final size:31
Alignment explanation
Indices: 103124--103205 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
103114 TTTAAAAAGC
*
103124 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
103154 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
**
103184 AAAAAGAAGTTGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
103206 TGAAAAAGAG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 25 0.60
31 9 0.21
ACGTcount: A:0.63, C:0.01, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:103199 original size:12 final size:12
Alignment explanation
Indices: 103182--103227 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
103172 AATTTGAGAG
*
103182 TGAAAAAGAAGT
1 TGAAAAAGAAAT
103194 TGAAAAAGAAAT
1 TGAAAAAGAAAT
*
103206 TGAAAAAGAGAT
1 TGAAAAAGAAAT
*
103218 T-AAAGAGAAA
1 TGAAAAAGAAA
103228 GAAATTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 7 0.23
12 23 0.77
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (12 bp):
TGAAAAAGAAAT
Found at i:104516 original size:14 final size:14
Alignment explanation
Indices: 104497--104541 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
104487 AACTCATCTT
*
104497 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
104511 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
104524 AATTTAATTTAATG
1 AGTTTAATTTAATG
104538 AGTT
1 AGTT
104542 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:113328 original size:13 final size:13
Alignment explanation
Indices: 113274--113329 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 13
113264 TTTTATATAC
113274 TTCG-ATTTTTTT
1 TTCGAATTTTTTT
113286 TT--AATTTTTTT
1 TTCGAATTTTTTT
113297 TT-G-ATTTTTTT
1 TTCGAATTTTTTT
*
113308 TTCAAATTTTTTT
1 TTCGAATTTTTTT
113321 TTCGAATTT
1 TTCGAATTT
113330 CTTCTCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 20 0.53
12 2 0.05
13 16 0.42
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (13 bp):
TTCGAATTTTTTT
Found at i:118102 original size:20 final size:19
Alignment explanation
Indices: 118079--118143 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
118069 AAGCTCAAAC
118079 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
118099 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
118119 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
118139 GAGCT
1 GAGCT
118144 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:119957 original size:33 final size:33
Alignment explanation
Indices: 119919--119981 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
119909 GATTACTCAC
119919 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
119952 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
119982 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:120004 original size:15 final size:13
Alignment explanation
Indices: 119978--120034 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
119968 TCAAGCTCTC
*
119978 TTTCAATTTCTTT
1 TTTCATTTTCTTT
119991 TTTCACTTTT-TCTT
1 TTTCA-TTTTCT-TT
120005 TTTCAATTTTCTTT
1 TTTC-ATTTTCTTT
120019 TCTTCATTTTCTTT
1 T-TTCATTTTCTTT
120033 TT
1 TT
120035 CTCTCACTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 7 0.18
14 26 0.68
15 5 0.13
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCATTTTCTTT
Found at i:120008 original size:27 final size:27
Alignment explanation
Indices: 119978--120035 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
119968 TCAAGCTCTC
119978 TTTCAA-TTTCTTTT-TTCACTTTTTCTT
1 TTTCAATTTTCTTTTCTTCA--TTTTCTT
120005 TTTCAATTTTCTTTTCTTCATTTTCTT
1 TTTCAATTTTCTTTTCTTCATTTTCTT
120032 TTTC
1 TTTC
120036 TCTCACTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 17 0.59
28 8 0.28
29 4 0.14
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTCAATTTTCTTTTCTTCATTTTCTT
Found at i:120062 original size:18 final size:18
Alignment explanation
Indices: 120041--120098 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
120031 TTTTCTCTCA
120041 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
120059 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
120077 C-TTTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
120094 GTTTT
1 CTTTT
120099 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 13 0.39
18 20 0.61
ACGTcount: A:0.05, C:0.16, G:0.07, T:0.72
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:120087 original size:11 final size:11
Alignment explanation
Indices: 120068--120102 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
120058 TCTTTTGCAA
*
120068 TTTCTTTTTCT
1 TTTCGTTTTCT
120079 TTTCGTTTTCT
1 TTTCGTTTTCT
*
120090 TTTTGTTTTCT
1 TTTCGTTTTCT
120101 TT
1 TT
120103 CAATTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (11 bp):
TTTCGTTTTCT
Found at i:120115 original size:6 final size:6
Alignment explanation
Indices: 119996--120102 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
119986 TCTTTTTTCA
* * * **
119996 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
120047 CGATTT CTTTTT CTTTTG CAATTT CTTTTT C-TTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
120094 -GTTTT CTTT
1 CTTTTT CTTT
120103 CAATTTCTTT
Statistics
Matches: 73, Mismatches: 24, Indels: 8
0.70 0.23 0.08
Matches are distributed among these distances:
5 9 0.12
6 52 0.71
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:121190 original size:30 final size:28
Alignment explanation
Indices: 121133--121195 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 28
121123 TTAAACTTGA
*
121133 TTTTTTTTGCTCACCTTTTTTTTCTTTTCT
1 TTTTTTTTGCTCA-CTTTTTTTACTTTT-T
121163 TTTTTTTTGCTCGA-TTTTTTTCACTTTTT
1 TTTTTTTTGCTC-ACTTTTTTT-ACTTTTT
121192 TTTT
1 TTTT
121196 CAATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 12 0.40
30 17 0.57
31 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.75
Consensus pattern (28 bp):
TTTTTTTTGCTCACTTTTTTTACTTTTT
Found at i:121230 original size:13 final size:12
Alignment explanation
Indices: 121177--121247 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 12
121167 TTTTGCTCGA
*
121177 TTTTTTTCACTT
1 TTTTTTTCAATT
121189 TTTTTTTCAATTT
1 TTTTTTTCAA-TT
121202 TTTTTTCAATCCAATT
1 TTTTTT---T-CAATT
121218 TTTTTTTCGAATT
1 TTTTTTTC-AATT
*
121231 TTTTTTT-GATT
1 TTTTTTTCAATT
121242 TTTTTT
1 TTTTTT
121248 GTTACTCCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
11 9 0.18
12 10 0.20
13 20 0.39
16 9 0.18
17 3 0.06
ACGTcount: A:0.14, C:0.10, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:122727 original size:20 final size:20
Alignment explanation
Indices: 122704--122768 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
122694 AAGCTCAAAC
* *
122704 GAGCTAAAGTAAGCTAAATT
1 GAGCTCAAGTGAGCTAAATT
*
122724 GAGCTCAAGCGAGCTAAATT
1 GAGCTCAAGTGAGCTAAATT
* * *
122744 AAGCTCATGTGAGCTAAATC
1 GAGCTCAAGTGAGCTAAATT
122764 GAGCT
1 GAGCT
122769 GGGAAAAACT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (20 bp):
GAGCTCAAGTGAGCTAAATT
Found at i:122767 original size:30 final size:29
Alignment explanation
Indices: 122695--122768 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
122685 ACTTAATCCA
122695 AGCTCAAACGAGCTAAAGTAAGCTAAATTG
1 AGCT-AAACGAGCTAAAGTAAGCTAAATTG
* * *
122725 AGCTCAAGCGAGCTAAATTAAGCT-CATGTG
1 AGCT-AAACGAGCTAAAGTAAGCTAAAT-TG
122755 AGCTAAATCGAGCT
1 AGCTAAA-CGAGCT
122769 GGGAAAAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 4 0.11
30 34 0.89
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (29 bp):
AGCTAAACGAGCTAAAGTAAGCTAAATTG
Found at i:123107 original size:18 final size:18
Alignment explanation
Indices: 123084--123133 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
123074 GAAAGAAAAA
*
123084 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
123102 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
123120 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
123134 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:123110 original size:24 final size:24
Alignment explanation
Indices: 123077--123158 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
123067 AAGAAATGAA
123077 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
123101 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
123125 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
*
123149 AGAGAAAGAA
1 AGAAAAAGAA
123159 TGTGAGCAAG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:125632 original size:14 final size:13
Alignment explanation
Indices: 125613--125657 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
125603 AACTCACCTT
125613 AGTTTAATTAAATG
1 AGTTTAATT-AATG
*
125627 AGTTTAATTGATG
1 AGTTTAATTAATG
*
125640 AATTTAATTTAATG
1 AGTTTAA-TTAATG
125654 AGTT
1 AGTT
125658 GCTTCTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (13 bp):
AGTTTAATTAATG
Found at i:131010 original size:12 final size:12
Alignment explanation
Indices: 130993--131026 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
130983 AGGAAATTTG
130993 AAAAAAAAATTC
1 AAAAAAAAATTC
131005 -AAAAAAAATTC
1 AAAAAAAAATTC
131016 AAAAAAAAATT
1 AAAAAAAAATT
131027 GAAGTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:142936 original size:21 final size:21
Alignment explanation
Indices: 142888--142936 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
142878 CCTCGTCTTT
*
142888 TTCTTTTTTTCTTTTTCTAAC
1 TTCTTTTCTTCTTTTTCTAAC
142909 -TCATTTTCTTCTTTCTTC-AAC
1 TTC-TTTTCTTCTTT-TTCTAAC
142930 TTCTTTT
1 TTCTTTT
142937 TCAATTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 17 0.71
22 5 0.21
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.67
Consensus pattern (21 bp):
TTCTTTTCTTCTTTTTCTAAC
Found at i:144927 original size:21 final size:21
Alignment explanation
Indices: 144879--144928 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
144869 CCTCGTCTTT
*
144879 TTCTTTTTTTCTTTTTCTAAC
1 TTCTTTTCTTCTTTTTCTAAC
144900 -TCATTTTCTTCTTTCTTC-AAC
1 TTC-TTTTCTTCTTT-TTCTAAC
144921 TTCTTTTC
1 TTCTTTTC
144929 AATTTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 18 0.72
22 5 0.20
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.66
Consensus pattern (21 bp):
TTCTTTTCTTCTTTTTCTAAC
Found at i:146943 original size:17 final size:18
Alignment explanation
Indices: 146918--146955 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
146908 TTTCTTCAAC
* *
146918 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
146935 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
146953 TTC
1 TTC
146956 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:149308 original size:6 final size:6
Alignment explanation
Indices: 149297--149322 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
149287 GTAAATAAAT
149297 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
149323 CTTTACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:151255 original size:42 final size:42
Alignment explanation
Indices: 151196--151343 Score: 287
Period size: 42 Copynumber: 3.5 Consensus size: 42
151186 CATTTAAGCC
151196 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
151238 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
151280 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
151322 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
151344 TATTTAATGA
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
42 95 0.90
43 10 0.10
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:151345 original size:14 final size:14
Alignment explanation
Indices: 151326--151370 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
151316 AACTCATCTT
*
151326 AGTTTAATTAAATG
1 AGTTTAATTTAATG
151340 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
151353 AATTTAATTTAATG
1 AGTTTAATTTAATG
151367 AGTT
1 AGTT
151371 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:155915 original size:31 final size:32
Alignment explanation
Indices: 155862--155921 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
155852 AATTCGTTCA
* *
155862 CACCTATGTTCACATGGCAAGACTGTTCAGTT
1 CACCTATGTTCACATAGCAAGACTCTTCAGTT
155894 CACCT-TGTTCACACTAG-AAGACTCTTCA
1 CACCTATGTTCACA-TAGCAAGACTCTTCA
155922 ACATTCGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (32 bp):
CACCTATGTTCACATAGCAAGACTCTTCAGTT
Found at i:160119 original size:12 final size:12
Alignment explanation
Indices: 160103--160134 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
160093 TTTCTTTTTG
160103 CTTTTCAAAGGC
1 CTTTTCAAAGGC
*
160115 TTTTTCAAAGGC
1 CTTTTCAAAGGC
160127 CTTTTCAA
1 CTTTTCAA
160135 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (12 bp):
CTTTTCAAAGGC
Found at i:160192 original size:5 final size:5
Alignment explanation
Indices: 160182--160238 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
160172 CTCTTGCCTC
*
160182 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTT TGCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-CTTT T-CTTT
160229 TCTTT TCTTT
1 TCTTT TCTTT
160239 GTTTTCTCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.56
6 15 0.33
7 1 0.02
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:160248 original size:16 final size:16
Alignment explanation
Indices: 160180--160249 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
160170 GCCTCTTGCC
160180 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTAT
*
160196 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTAT
* **
160212 TCT-TTTGCTTTTGCT
1 TCTCTTTTCTTTTTAT
*
160227 TTTCTTTTCTTTGTT-T
1 TCTCTTTTCTTT-TTAT
160243 TCTCTTT
1 TCTCTTT
160250 ACAAGAATGT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 14 0.33
16 27 0.63
17 2 0.05
ACGTcount: A:0.03, C:0.19, G:0.04, T:0.74
Consensus pattern (16 bp):
TCTCTTTTCTTTTTAT
Found at i:161179 original size:12 final size:12
Alignment explanation
Indices: 161155--161206 Score: 67
Period size: 11 Copynumber: 4.7 Consensus size: 12
161145 CATAAATCAC
161155 TTTTTTTC--AT
1 TTTTTTTCGAAT
161165 TTTTTTT-GAAT
1 TTTTTTTCGAAT
161176 TTTTTTTCGAAT
1 TTTTTTTCGAAT
*
161188 TTTTTTTCG-GT
1 TTTTTTTCGAAT
161199 TTTTTTTC
1 TTTTTTTC
161207 AAACTTGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
10 7 0.18
11 18 0.47
12 13 0.34
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.75
Consensus pattern (12 bp):
TTTTTTTCGAAT
Found at i:162385 original size:13 final size:13
Alignment explanation
Indices: 162367--162391 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
162357 AATAGTTGTG
162367 TGTTATTTAATTA
1 TGTTATTTAATTA
162380 TGTTATTTAATT
1 TGTTATTTAATT
162392 TTGTAGGTTA
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:166183 original size:14 final size:14
Alignment explanation
Indices: 166125--166183 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
166115 ACCTAAATCG
*
166125 ACCAATTCGTTCAT
1 ACCATTTCGTTCAT
*
166139 ATCCCTTT-GTTCAT
1 A-CCATTTCGTTCAT
*
166153 ACCATTTCATTTC-T
1 ACCATTTC-GTTCAT
*
166167 ACCATTTCGTTCGT
1 ACCATTTCGTTCAT
166181 ACC
1 ACC
166184 CCTCTTTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 21 0.58
15 7 0.19
ACGTcount: A:0.20, C:0.31, G:0.07, T:0.42
Consensus pattern (14 bp):
ACCATTTCGTTCAT
Found at i:167955 original size:56 final size:56
Alignment explanation
Indices: 167850--167956 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
167840 ATTAATGCCG
* * * * *
167850 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGTCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGTCGT
167906 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
167957 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGTCGT
Found at i:168596 original size:20 final size:20
Alignment explanation
Indices: 168565--168636 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
168555 AGCTAATAAC
* *
168565 GAGCTC-AATGAGTTAAATT
1 GAGCTCGAATGAGCTAACTT
* *
168584 GAGCTTGAATGAGCTGACTT
1 GAGCTCGAATGAGCTAACTT
* *
168604 GAGCACGAATGAGCTAACCT
1 GAGCTCGAATGAGCTAACTT
168624 GAGCTCGAATGAG
1 GAGCTCGAATGAG
168637 TTGAACCACA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 5 0.12
20 38 0.88
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.24
Consensus pattern (20 bp):
GAGCTCGAATGAGCTAACTT
Found at i:169960 original size:15 final size:16
Alignment explanation
Indices: 169921--169961 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
169911 AACAACACTC
169921 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
169937 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
169951 CTTTCTTTTTC
1 CTTTCTTTTTC
169962 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:170155 original size:17 final size:15
Alignment explanation
Indices: 170118--170156 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
170108 TATCTCCCAC
170118 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
170134 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
170151 TCATTT
1 TCATTT
170157 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:171174 original size:12 final size:12
Alignment explanation
Indices: 171157--171202 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
171147 ATTGAATACA
171157 AATTTTTTTTTG
1 AATTTTTTTTTG
171169 AA-TTTTTTTTG
1 AATTTTTTTTTG
**
171180 AATTTTTTTTCA
1 AATTTTTTTTTG
171192 AATTTTTTTTT
1 AATTTTTTTTT
171203 CCTTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:171176 original size:10 final size:11
Alignment explanation
Indices: 171160--171201 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
171150 GAATACAAAT
171160 TTTTTTTTGAA
1 TTTTTTTTGAA
171171 TTTTTTTTGAA
1 TTTTTTTTGAA
*
171182 TTTTTTTTCAAA
1 TTTTTTTT-GAA
171194 TTTTTTTT
1 TTTTTTTT
171202 TCCTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:171183 original size:23 final size:23
Alignment explanation
Indices: 171157--171201 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
171147 ATTGAATACA
**
171157 AATTTTTTTTTGAATTTTTTTTG
1 AATTTTTTTTCAAATTTTTTTTG
171180 AATTTTTTTTCAAATTTTTTTT
1 AATTTTTTTTCAAATTTTTTTT
171202 TCCTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (23 bp):
AATTTTTTTTCAAATTTTTTTTG
Found at i:172572 original size:56 final size:56
Alignment explanation
Indices: 172467--172573 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
172457 ATTAATGTCG
* * * * *
172467 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
172523 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
172574 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
Found at i:173223 original size:20 final size:20
Alignment explanation
Indices: 173198--173252 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
173188 ACGAGTTAAA
* *
173198 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
173218 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
173238 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
173253 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:176079 original size:21 final size:20
Alignment explanation
Indices: 176040--176079 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
176030 ATCAGCTCAC
*
176040 TTGAGCTCGATTCAGCTCGT
1 TTGAGCTAGATTCAGCTCGT
*
176060 TTGAGCTAGAATTGAGCTCG
1 TTGAGCTAG-ATTCAGCTCG
176080 ATCTAGCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (20 bp):
TTGAGCTAGATTCAGCTCGT
Found at i:184265 original size:14 final size:14
Alignment explanation
Indices: 184242--184285 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
184232 GTAGAAAGAG
* *
184242 GGGTACGAACGGAA
1 GGGTAGGAACGAAA
*
184256 TGGTAGGAACGAAA
1 GGGTAGGAACGAAA
184270 GGGTAGGAAC-AAA
1 GGGTAGGAACGAAA
184283 GGG
1 GGG
184286 ATATGAACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.39, C:0.09, G:0.43, T:0.09
Consensus pattern (14 bp):
GGGTAGGAACGAAA
Found at i:184293 original size:14 final size:13
Alignment explanation
Indices: 184257--184296 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
184247 CGAACGGAAT
184257 GGTAGGAACGAAAG
1 GGTAGGAAC-AAAG
184271 GGTAGGAACAAAG
1 GGTAGGAACAAAG
*
184284 GGATATGAACAAA
1 GG-TAGGAACAAA
184297 TTGGTCGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.47, C:0.07, G:0.35, T:0.10
Consensus pattern (13 bp):
GGTAGGAACAAAG
Found at i:190283 original size:20 final size:20
Alignment explanation
Indices: 190260--190306 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
190250 TGGTTAAGAT
*
190260 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* *
190280 TGAG-TAGACTTGAGCTCGAG
1 TGAGCT-GAATTGAGCTCGAA
190300 TGAGCTG
1 TGAGCTG
190307 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.26, C:0.13, G:0.34, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:193140 original size:10 final size:9
Alignment explanation
Indices: 193127--193161 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
193117 TTTTCACTTT
193127 TTTTTTGTTC
1 TTTTTT-TTC
*
193137 TTTTTTTAC
1 TTTTTTTTC
193146 TTTTTTTTC
1 TTTTTTTTC
193155 TTTTTTT
1 TTTTTTT
193162 GCTCACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:193964 original size:21 final size:21
Alignment explanation
Indices: 193938--193992 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 21
193928 GCATCTATGT
193938 TGTTCACACTA-ACTTAAATTC
1 TGTTCACAC-AGACTTAAATTC
*
193959 TGTTCACACAGGTATTTAAATTC
1 TGTTCACACA-G-ACTTAAATTC
193982 TGTTCACACAG
1 TGTTCACACAG
193993 GTATTTAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.03
21 9 0.30
22 1 0.03
23 19 0.63
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (21 bp):
TGTTCACACAGACTTAAATTC
Found at i:193977 original size:23 final size:23
Alignment explanation
Indices: 193951--194000 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
193941 TCACACTAAC
193951 TTAAATTCTGTTCACACAGGTAT
1 TTAAATTCTGTTCACACAGGTAT
193974 TTAAATTCTGTTCACACAGGTAT
1 TTAAATTCTGTTCACACAGGTAT
193997 TTAA
1 TTAA
194001 CATGTTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (23 bp):
TTAAATTCTGTTCACACAGGTAT
Found at i:194006 original size:21 final size:21
Alignment explanation
Indices: 193959--194012 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 21
193949 ACTTAAATTC
193959 TGTTCACACAGGTATTTAAATT
1 TGTTCACACAGGTATTTAAA-T
193981 CTGTTCACACAGGTATTTAACA-
1 -TGTTCACACAGGTATTTAA-AT
194003 TGTTCACACA
1 TGTTCACACA
194013 AATAGCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.33
23 19 0.63
24 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTTCACACAGGTATTTAAAT
Found at i:202229 original size:13 final size:13
Alignment explanation
Indices: 202213--202255 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
202203 CTTTTTTTAA
202213 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
* *
202226 TTTTTTTTCAAAC
1 TTTTTTTTCGAAT
202239 TTTTTTTT-G-AT
1 TTTTTTTTCGAAT
202250 TTTTTT
1 TTTTTT
202256 AACTTGTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 7 0.27
13 19 0.73
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:204060 original size:27 final size:27
Alignment explanation
Indices: 204030--204093 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
204020 TTAGGACTTA
204030 TCTTTATTCTTGCTG-TTCAATTTCT-TT
1 TCTTTATTCTTGCTGTTTC-ATTT-TATT
204057 TCTTTATTCTTGCTGTTTCATTTTATT
1 TCTTTATTCTTGCTGTTTCATTTTATT
204084 TCTTTATTCT
1 TCTTTATTCT
204094 ACTTGTGCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
26 1 0.03
27 31 0.89
28 3 0.09
ACGTcount: A:0.11, C:0.17, G:0.06, T:0.66
Consensus pattern (27 bp):
TCTTTATTCTTGCTGTTTCATTTTATT
Found at i:207200 original size:12 final size:13
Alignment explanation
Indices: 207183--207211 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
207173 TTTAACTAAG
207183 TAAATAAAT-AAA
1 TAAATAAATAAAA
207195 TAAATAAATAAAA
1 TAAATAAATAAAA
207208 TAAA
1 TAAA
207212 AATAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Done.