Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1115
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: 495024
ACGTcount: A:0.19, C:0.08, G:0.09, T:0.18
Warning! 230474 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:434037 original size:22 final size:22
Alignment explanation
Indices: 434009--434051 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
433999 GGGGTTGTTT
*
434009 CAGTTAAAGTTATATATACATC
1 CAGTTAAAATTATATATACATC
*
434031 CAGTTAAAATTATATGTACAT
1 CAGTTAAAATTATATATACAT
434052 TAGTTATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (22 bp):
CAGTTAAAATTATATATACATC
Found at i:434315 original size:22 final size:22
Alignment explanation
Indices: 434259--434315 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
434249 ATGAAAAGTT
*
434259 ATATGTACATTCAGTTAAAATC
1 ATATGTACATTTAGTTAAAATC
* *
434281 ATATGTACGTTTAGTTATAATC
1 ATATGTACATTTAGTTAAAATC
*
434303 ATATGTATATTTA
1 ATATGTACATTTA
434316 ATTTTATTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.44
Consensus pattern (22 bp):
ATATGTACATTTAGTTAAAATC
Found at i:434636 original size:22 final size:22
Alignment explanation
Indices: 434582--434628 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
434572 TAAAGTCATA
* * *
434582 TATATTCAGTTATAATTATATG
1 TATATACAATTATAATCATATG
434604 TATATACAATTATAATCATATG
1 TATATACAATTATAATCATATG
434626 TAT
1 TAT
434629 GTTTAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (22 bp):
TATATACAATTATAATCATATG
Found at i:434783 original size:43 final size:43
Alignment explanation
Indices: 434704--434816 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 43
434694 AAAATATTAT
* * * *
434704 ATATTAAATATGTTTTAAATTTTTTTAAATAGTAATTCAGGACTTA
1 ATATAAAATAT-TTTTAAA--TTTTTAAACAATAATTCAAGACTTA
* * * *
434750 ATAT-AAATTTTTTTATTATTTTTAAACAATAATTTAAGATTTA
1 ATATAAAATATTTTTA-AATTTTTAAACAATAATTCAAGACTTA
434793 ATATAAAATATTTTTAAATTTTTA
1 ATATAAAATATTTTTAAATTTTTA
434817 TTATCTTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
43 31 0.55
44 15 0.27
45 6 0.11
46 4 0.07
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (43 bp):
ATATAAAATATTTTTAAATTTTTAAACAATAATTCAAGACTTA
Found at i:434815 original size:53 final size:52
Alignment explanation
Indices: 434758--435456 Score: 491
Period size: 52 Copynumber: 13.0 Consensus size: 52
434748 TAATATAAAT
* *
434758 TTTTTTATTATTTTTAAACAATAATTTAAGATTTAATATAAAATATTTTTAA
1 TTTTTTATTATTTTTAAATAGTAATTTAAGATTTAATATAAAATATTTTTAA
* * *
434810 ATTTTTATTATCTTTAAATAGTAATTCAAGATTTAATATAAAATATTTTTTTAA
1 TTTTTTATTATTTTTAAATAGTAATTTAAGATTTAATATAAAATA--TTTTTAA
*
434864 ATTTTTATTATTTTT-AATAGTAATTTAAGATTTAATATAAAATATTTTTAA
1 TTTTTTATTATTTTTAAATAGTAATTTAAGATTTAATATAAAATATTTTTAA
* * * * *
434915 TTTTTTATTATTTTTTTAAGAGTAACTCAAGATTTAATAAAAAATATTTTTAA
1 TTTTTTATTA-TTTTTAAATAGTAATTTAAGATTTAATATAAAATATTTTTAA
* * * * ***
434968 TTTTTTATTATTTTTAAATAGTATTTATAAAATTTTTTATTTGTTATCATTTTTAAA
1 TTTTTTATTATTTTTAAATAGTAATT-TAAGA--TTTAATATAAAAT-ATTTTT-AA
* * ** * ** * * *
435025 TAATAATTCAGGATTTAATGTAAA-A-TAATTCTCAA-ATAGTAATTCATAATTTAATATAAA
1 T--T-TTTTATTATTT--T-TAAATAGTAATT-T-AAGAT-TTAA-T-ATAAAATATTTTTAA
* * ** * * * * * ** *** *
435085 TTATTTATTTTATTATTATTTTGAAATAGT-A-ATTCAAAATTTAATATAAAATAT
1 TT-TTT-TATTATTTTTAAATAGTAAT-TTAAGATTTAATATAAAATAT-TTTTAA
*
435139 TTTTATTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATTTTTAA
1 TTTT-TTATTATTTTTAAATAGTAATTTAAGATTTAATATAAAATATTTTTAA
* * * *
435192 ATTTTTATTATTTTTAAATAATAATTTAATATTTAAGATAAAATATGATTTTAA
1 TTTTTTATTATTTTTAAATAGTAATTTAAGATTTAATATAAAATAT--TTTTAA
*
435246 TTTTTTA-T-TTTTTAAATAGTAATTT-GGTATTTAATATAAAATATTTTTAA
1 TTTTTTATTATTTTTAAATAGTAATTTAAG-ATTTAATATAAAATATTTTTAA
* * *
435296 TTTTTTATTA-TTTTAAATAGTAATTTGATATTTAATATAAAATATGCTTTTCAT
1 TTTTTTATTATTTTTAAATAGTAATTTAAGATTTAATATAAAATAT--TTTT-AA
* ** * *
435350 TTTTTTATTATTTTTAATTAACAATTCAAGATTTAATATAAAATATATTTTTTA
1 TTTTTTATTATTTTTAAATAGTAATTTAAGATTTAATAT-AAA-ATATTTTTAA
** *
435404 TTTTTTATTATTGTTTAAATTTTAATTTAAGGTTTAATATAAAATATTTTTAA
1 TTTTTTATTATT-TTTAAATAGTAATTTAAGATTTAATATAAAATATTTTTAA
435457 AATTTTATGA
Statistics
Matches: 502, Mismatches: 105, Indels: 79
0.73 0.15 0.12
Matches are distributed among these distances:
50 13 0.03
51 49 0.10
52 127 0.25
53 113 0.23
54 76 0.15
55 56 0.11
56 14 0.03
57 8 0.02
58 8 0.02
59 5 0.01
60 12 0.02
61 10 0.02
62 7 0.01
63 4 0.01
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (52 bp):
TTTTTTATTATTTTTAAATAGTAATTTAAGATTTAATATAAAATATTTTTAA
Found at i:435091 original size:50 final size:50
Alignment explanation
Indices: 435037--435187 Score: 128
Period size: 50 Copynumber: 3.1 Consensus size: 50
435027 ATAATTCAGG
* *
435037 ATTTAATGTAAAATAATTCTCAAATAGTAATTCATAATTTAATATAAATT
1 ATTTAATGTAAAATAATTCTCAAATAGTAATTCAAAATTTAATATAAAAT
* * ** * * *
435087 ATTTATTTTATTATTATTTTGAAATAGTAATTCAAAATTTAATATAAAAT
1 ATTTAATGTAAAATAATTCTCAAATAGTAATTCAAAATTTAATATAAAAT
** * * * ** *
435137 ATTT--T-TATTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAAT
1 ATTTAATGTAAAATAATTCTCAAATAGTAATTCAAAATTTAATATAAAAT
435184 ATTT
1 ATTT
435188 TTAAATTTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
47 42 0.48
48 1 0.01
50 45 0.51
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (50 bp):
ATTTAATGTAAAATAATTCTCAAATAGTAATTCAAAATTTAATATAAAAT
Found at i:438092 original size:41 final size:41
Alignment explanation
Indices: 438047--438131 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
438037 ATTAGAATCT
*
438047 AAGCGTAATATGGAAAAAAGATAAACATTTTTAATCAATGA
1 AAGCGTAATATGGAAAAAAAATAAACATTTTTAATCAATGA
438088 AAGCGTAATATGGAAAAAAAATAAACATTTTTAATCAATGA
1 AAGCGTAATATGGAAAAAAAATAAACATTTTTAATCAATGA
438129 AAG
1 AAG
438132 TAAAACTATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (41 bp):
AAGCGTAATATGGAAAAAAAATAAACATTTTTAATCAATGA
Found at i:438142 original size:42 final size:41
Alignment explanation
Indices: 438053--438142 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
438043 ATCTAAGCGT
* **
438053 AATATGGAAAAAAGATAAACATTTTTAATCAATGAAAGCGT
1 AATATGGAAAAAAAATAAACATTTTTAATCAATGAAAGCAA
*
438094 AATATGGAAAAAAAATAAACATTTTTAATCAATGAAAGTAA
1 AATATGGAAAAAAAATAAACATTTTTAATCAATGAAAGCAA
438135 AACTATGG
1 AA-TATGG
438143 CTATGATTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 39 0.89
42 5 0.11
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (41 bp):
AATATGGAAAAAAAATAAACATTTTTAATCAATGAAAGCAA
Found at i:438172 original size:2 final size:2
Alignment explanation
Indices: 438165--438193 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
438155 TTATAAATAA
438165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
438194 AGCACTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:442854 original size:18 final size:17
Alignment explanation
Indices: 442808--442855 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
442798 GGATTTATGC
*
442808 ATGTATGAAGCATGGAAA
1 ATGTATGAA-CATGAAAA
*
442826 ATGCATGGAACATAGAAAA
1 ATGTAT-GAACAT-GAAAA
442845 ATGTATGAACA
1 ATGTATGAACA
442856 AAGGCTGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.21
Consensus pattern (17 bp):
ATGTATGAACATGAAAA
Found at i:443771 original size:44 final size:43
Alignment explanation
Indices: 443716--443804 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
443706 GTATCGATGC
* * * *
443716 ATTGAAGAATGTATTGATACATTTGGTTTAAAAACCCAGAATGT
1 ATTGAAAAATGTATCGATACATTTGG-GTAAAAACCCAAAATGT
* *
443760 ATTGAAAAATGTATCGATACTTTTGGGTCAAAACCCAAAATGT
1 ATTGAAAAATGTATCGATACATTTGGGTAAAAACCCAAAATGT
443803 AT
1 AT
443805 CGATACAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 16 0.41
44 23 0.59
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (43 bp):
ATTGAAAAATGTATCGATACATTTGGGTAAAAACCCAAAATGT
Found at i:449160 original size:13 final size:13
Alignment explanation
Indices: 449139--449170 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
449129 TCGATAGATT
*
449139 ATACTTTGTATCG
1 ATACATTGTATCG
449152 ATACATTGTATCG
1 ATACATTGTATCG
449165 ATACAT
1 ATACAT
449171 GCTCATTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (13 bp):
ATACATTGTATCG
Found at i:449200 original size:20 final size:19
Alignment explanation
Indices: 449154--449211 Score: 89
Period size: 19 Copynumber: 3.0 Consensus size: 19
449144 TTGTATCGAT
*
449154 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGA
*
449173 TCATTGTATCGATACATGA
1 ACATTGTATCGATACATGA
449192 ACAATTGTATCGATACATGA
1 AC-ATTGTATCGATACATGA
449212 GATTGGCAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGA
Found at i:449278 original size:13 final size:13
Alignment explanation
Indices: 449260--449308 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
449250 CATGGGACAA
449260 TGTATCGATACAT
1 TGTATCGATACAT
449273 TGTATCGATACA-
1 TGTATCGATACAT
449285 TG-AT-GA-A-AT
1 TGTATCGATACAT
449294 TGTATCGATACAT
1 TGTATCGATACAT
449307 TG
1 TG
449309 CTTGTAACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 4 0.13
12 3 0.10
13 16 0.52
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:449281 original size:33 final size:34
Alignment explanation
Indices: 449239--449308 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
449229 CTATCACTGT
449239 TTGTATCGATACATG-GGACAA-TGTATCGATACA
1 TTGTATCGATACATGAGGA-AATTGTATCGATACA
*
449272 TTGTATCGATACATGATGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTGTATCGATACA
449306 TTG
1 TTG
449309 CTTGTAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTGTATCGATACA
Found at i:452498 original size:28 final size:27
Alignment explanation
Indices: 452431--452503 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
452421 TTTCACAATC
*
452431 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
452458 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
*
452486 GGGGATATTCCAACCCCG
1 GGGGATACTCCAACCCCG
452504 ACTTTATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:452551 original size:51 final size:52
Alignment explanation
Indices: 452486--452707 Score: 184
Period size: 51 Copynumber: 4.3 Consensus size: 52
452476 TTATTTCTGA
* * ***
452486 GGGGATA-TTCCAACCCCGACTTTATTTCCAAAATATTGATTTTT-CATAATC
1 GGGGATACTT-CAACCCCGATTTTATTTCCAAAACACCAATTTTTCCATAATC
* * * * * *
452537 GGGGATACTTCAACCCTGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTTCAACCCCGATTTTATTTCCAAAACACCAATTTTTCCATAATC
* ** * * *
452589 -GGGATACTCCAACCGTGGTTTTATTTTCAAAACACCAATTTTTCCTTTAATC
1 GGGGATACTTCAACCCCGATTTTATTTCCAAAACACCAATTTTTCC-ATAATC
* *
452641 GGGGATAC-TCTAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CATAATC
1 GGGGATACTTC-AACCCCGATTTTATTTCC-AAAACACCAATTTTTCCATAATC
* *
452693 GAGGATACTCCAACC
1 GGGGATACTTCAACC
452708 TCGTTATCTC
Statistics
Matches: 136, Mismatches: 28, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
51 72 0.53
52 28 0.21
53 22 0.16
54 14 0.10
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (52 bp):
GGGGATACTTCAACCCCGATTTTATTTCCAAAACACCAATTTTTCCATAATC
Found at i:459562 original size:17 final size:17
Alignment explanation
Indices: 459540--459573 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
459530 CAGAGGTAAG
*
459540 AAGGAAGGCAAAGTCAA
1 AAGGAAGCCAAAGTCAA
*
459557 AAGGAAGCCATAGTCAA
1 AAGGAAGCCAAAGTCAA
459574 GAATCGATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.15, G:0.26, T:0.09
Consensus pattern (17 bp):
AAGGAAGCCAAAGTCAA
Found at i:464878 original size:12 final size:12
Alignment explanation
Indices: 464870--464919 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
464860 AAAAAAAAGC
464870 AAAAG-AAAAAA
1 AAAAGCAAAAAA
*
464881 AAAAGGAAAAAA
1 AAAAGCAAAAAA
464893 AAAA-CAAAAAA
1 AAAAGCAAAAAA
*
464904 ACAAAACAAAGAAA
1 A-AAAGCAAA-AAA
464918 AA
1 AA
464920 GAGAGAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 12 0.35
12 13 0.38
13 5 0.15
14 4 0.12
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAGCAAAAAA
Found at i:464880 original size:17 final size:17
Alignment explanation
Indices: 464858--464936 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 17
464848 CCTTCTCTTC
464858 AAAAAAAAAAGCAAAAG
1 AAAAAAAAAAGCAAAAG
* *
464875 AAAAAAAAAAGGAAAAAA
1 AAAAAAAAAA-GCAAAAG
* *
464893 AAAACAAAAAAACAAAAC
1 AAAA-AAAAAAGCAAAAG
464911 AAAGAAAAAGAGAG-AAAAG
1 AAA-AAAAA-A-AGCAAAAG
464930 AAAAAAA
1 AAAAAAA
464937 CCTACTTAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
17 10 0.20
18 24 0.48
19 15 0.30
20 1 0.02
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGCAAAAG
Found at i:464881 original size:8 final size:8
Alignment explanation
Indices: 464870--464936 Score: 50
Period size: 8 Copynumber: 8.5 Consensus size: 8
464860 AAAAAAAAGC
464870 AAAAGAAA
1 AAAAGAAA
464878 AAAA-AAA
1 AAAAGAAA
*
464885 GGAAA-AAA
1 -AAAAGAAA
*
464893 AAAACAAA
1 AAAAGAAA
*
464901 AAAACAAA
1 AAAAGAAA
464909 ACAAAGAAA
1 A-AAAGAAA
* *
464918 AAGAG-AG
1 AAAAGAAA
464925 AAAAGAAA
1 AAAAGAAA
464933 AAAA
1 AAAA
464937 CCTACTTAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
7 11 0.23
8 30 0.62
9 7 0.15
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:464884 original size:11 final size:11
Alignment explanation
Indices: 464870--464904 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
464860 AAAAAAAAGC
464870 AAAAGAAAAAA
1 AAAAGAAAAAA
464881 AAAAGGAAAAAA
1 AAAA-GAAAAAA
*
464893 AAAACAAAAAA
1 AAAAGAAAAAA
464904 A
1 A
464905 CAAAACAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:464890 original size:28 final size:28
Alignment explanation
Indices: 464859--464937 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
464849 CTTCTCTTCA
464859 AAAAAAAAAGCAAAAGAAAAAAA-AAAGG
1 AAAAAAAAAGCAAAAGAAAAAAACAAA-G
*
464887 AAAAAAAAAACAAAA-AAACAAAACAAAG
1 AAAAAAAAAGCAAAAGAAA-AAAACAAAG
* *
464915 AAAAAGAGAG-AAAAGAAAAAAAC
1 AAAAAAAAAGCAAAAGAAAAAAAC
464938 CTACTTAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 12 0.27
28 29 0.66
29 3 0.07
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.00
Consensus pattern (28 bp):
AAAAAAAAAGCAAAAGAAAAAAACAAAG
Found at i:464902 original size:36 final size:38
Alignment explanation
Indices: 464859--464936 Score: 99
Period size: 36 Copynumber: 2.1 Consensus size: 38
464849 CTTCTCTTCA
* *
464859 AAAAAAAAAGCAAAAGAAA-AAAAAAAG-GAAAA-AAA
1 AAAAAAAAAACAAAACAAAGAAAAAAAGAGAAAAGAAA
*
464894 AAACAAAAAAACAAAACAAAGAAAAAGAGAGAAAAGAAA
1 AAA-AAAAAAACAAAACAAAGAAAAAAAGAGAAAAGAAA
464933 AAAA
1 AAAA
464937 CCTACTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 3 0.08
36 14 0.39
37 7 0.19
38 6 0.17
39 6 0.17
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (38 bp):
AAAAAAAAAACAAAACAAAGAAAAAAAGAGAAAAGAAA
Found at i:466638 original size:55 final size:55
Alignment explanation
Indices: 465898--466646 Score: 892
Period size: 55 Copynumber: 13.4 Consensus size: 55
465888 TCTCCTTCCG
*
465898 CTTTTTAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
465953 -TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* *
466008 CCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
466063 -TTTTCCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
466118 -TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
466173 -TTTTCCAATCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
466228 C-CTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAACCCACACAAGTTGGCGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
466287 C-CTTCAGTCCTCAAAGAG-TGAGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAG-GACACC-TTTC----AAAGCCCACACAAGTTGGTGGCA
* * * *
466346 C-CTTCAGTCCTCAAAGAGCATGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
466406 CCTTTCAGTCCCCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
466461 CCTTTCAGTCCCCAAAGAGCAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
466516 -TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * *
466571 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
466626 CTTTTTACTCCTCAATGAGCA
1 CTTTTCAGTCCTCAAAGAGCA
466647 TGATACACTT
Statistics
Matches: 620, Mismatches: 43, Indels: 62
0.86 0.06 0.09
Matches are distributed among these distances:
54 34 0.05
55 437 0.70
56 12 0.02
58 3 0.00
59 86 0.14
60 23 0.04
61 20 0.03
64 4 0.01
65 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23
Consensus pattern (55 bp):
CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:466646 original size:110 final size:110
Alignment explanation
Indices: 465904--466630 Score: 982
Period size: 110 Copynumber: 6.5 Consensus size: 110
465894 TCCGCTTTTT
465904 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
465969 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
66 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
466014 AGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
*
466079 GAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
66 GAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
466124 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAGA
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
466189 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACC-TTC
66 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * **
466233 AGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAACCCACACAAGTTGGCGGCACCTT-CAGTCC
1 AGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
* * *
466297 TCAAAGAG-TGAGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACC-TTC
61 TCAAAGAGCAG-GACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
466351 AGTCCTCAAAGAGCATGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGT
1 AGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGT
* * *
466415 CCCCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
59 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
466467 AGTCCCCAAAGAGCAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
466532 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
66 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
466577 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
466631 TACTCCTCAA
Statistics
Matches: 549, Mismatches: 42, Indels: 51
0.86 0.07 0.08
Matches are distributed among these distances:
109 29 0.05
110 327 0.60
111 6 0.01
112 1 0.00
113 17 0.03
114 28 0.05
115 26 0.05
116 21 0.04
117 1 0.00
118 45 0.08
119 24 0.04
120 22 0.04
121 1 0.00
124 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23
Consensus pattern (110 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:467496 original size:19 final size:19
Alignment explanation
Indices: 467472--467539 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
467462 AATTCAACAA
467472 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
467491 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
467506 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
467523 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
467540 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:467511 original size:13 final size:13
Alignment explanation
Indices: 467493--467517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
467483 ACATAAGTTT
467493 TGTATCGATACAA
1 TGTATCGATACAA
467506 TGTATCGATACA
1 TGTATCGATACA
467518 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:467515 original size:32 final size:32
Alignment explanation
Indices: 467474--467536 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
467464 TTCAACAATT
*
467474 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
467506 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
467537 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:467597 original size:13 final size:13
Alignment explanation
Indices: 467579--467604 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
467569 CATTTTTCTG
467579 TGTATCGATACAT
1 TGTATCGATACAT
467592 TGTATCGATACAT
1 TGTATCGATACAT
467605 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:467601 original size:33 final size:33
Alignment explanation
Indices: 467559--467625 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
467549 GCCAAGGAAA
***
467559 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
467592 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
467625 T
1 T
467626 TGAAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:476397 original size:20 final size:20
Alignment explanation
Indices: 476372--476423 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
476362 AAAACCCAGA
476372 TGTATCGATACAACATTCCT
1 TGTATCGATACAACATTCCT
476392 TGTATCGATACAACATTCCT
1 TGTATCGATACAACATTCCT
476412 TGTATCGATACA
1 TGTATCGATACA
476424 TTGGGTACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAACATTCCT
Found at i:478777 original size:32 final size:33
Alignment explanation
Indices: 478717--478781 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
478707 CACACCCAGA
** *
478717 TGTATCGATACATTTTGCTTTGTATTGATACAT
1 TGTATCGATACATGCTGCATTGTATTGATACAT
478750 TGTATCGATACATGCT-CATTGTATTGATACAT
1 TGTATCGATACATGCTGCATTGTATTGATACAT
478782 GGACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATGCTGCATTGTATTGATACAT
Found at i:478792 original size:20 final size:19
Alignment explanation
Indices: 478746--478802 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
478736 TTGTATTGAT
478746 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* * *
478765 TCATTGTATTGATACATGG
1 ACATTGTATCGATACATGC
478784 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
478803 AGATTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:478879 original size:21 final size:21
Alignment explanation
Indices: 478832--478886 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
478822 TACCCACTGT
478832 TTGTATCGATACATGGGATAA
1 TTGTATCGATACATGGGATAA
*
478853 -TGTATCGATACATGATGA-AA
1 TTGTATCGATACATG-GGATAA
478873 TTGTATCGATACAT
1 TTGTATCGATACAT
478887 TGCTTGTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (21 bp):
TTGTATCGATACATGGGATAA
Found at i:479777 original size:31 final size:31
Alignment explanation
Indices: 479732--479800 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
479722 CTTGCATGCA
* *
479732 AAGCAATGTAGCATGCAATCATGGGAGACAC
1 AAGCAAAGTAGCATGAAATCATGGGAGACAC
*
479763 ATGCAAAGTAGCATGAAATCATGGGAGACAC
1 AAGCAAAGTAGCATGAAATCATGGGAGACAC
479794 AAGCAAA
1 AAGCAAA
479801 TTGAAAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.14
Consensus pattern (31 bp):
AAGCAAAGTAGCATGAAATCATGGGAGACAC
Found at i:480368 original size:31 final size:30
Alignment explanation
Indices: 480333--480451 Score: 132
Period size: 31 Copynumber: 3.9 Consensus size: 30
480323 AGCTTCCAGT
*
480333 AGCTCGAGCGTCTT-CAAGCTTCCACGCTAGC
1 AGCTCGAGCCTCTTCCAA-CTTCCACGC-AGC
* * *
480364 AGCTCGAGCCTCTTCCAGCTTCCATGGCAGT
1 AGCTCGAGCCTCTTCCAACTTCCA-CGCAGC
*
480395 AGCTCGAGCCTCTTCCAACTTTCACGGCAGC
1 AGCTCGAGCCTCTTCCAACTTCCAC-GCAGC
* *
480426 AACTCGAACCTCTTCCAACTTCCACG
1 AGCTCGAGCCTCTTCCAACTTCCACG
480452 AACACGGCAG
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.01
31 69 0.93
32 4 0.05
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.24
Consensus pattern (30 bp):
AGCTCGAGCCTCTTCCAACTTCCACGCAGC
Found at i:480400 original size:62 final size:62
Alignment explanation
Indices: 480329--480449 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 62
480319 CACCAGCTTC
* * * *
480329 CAGTAGCTCGAGCGTCTT-CAAGCTTCCAC-GCTAGCAGCTCGAGCCTCTTCCAGCTTCCATGG
1 CAGTAGCTCGAGCCTCTTCCAA-CTTCCACGGC-AGCAACTCGAACCTCTTCCAACTTCCATGG
*
480391 CAGTAGCTCGAGCCTCTTCCAACTTTCACGGCAGCAACTCGAACCTCTTCCAACTTCCA
1 CAGTAGCTCGAGCCTCTTCCAACTTCCACGGCAGCAACTCGAACCTCTTCCAACTTCCA
480450 CGAACACGGC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 47 0.90
63 5 0.10
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (62 bp):
CAGTAGCTCGAGCCTCTTCCAACTTCCACGGCAGCAACTCGAACCTCTTCCAACTTCCATGG
Found at i:480478 original size:24 final size:24
Alignment explanation
Indices: 480446--480558 Score: 133
Period size: 24 Copynumber: 4.8 Consensus size: 24
480436 TCTTCCAACT
480446 TCCACGAACACGGCAGTAGCAGCA
1 TCCACGAACACGGCAGTAGCAGCA
**
480470 TCCACGAACACGGCAACAGCAGCA
1 TCCACGAACACGGCAGTAGCAGCA
* *
480494 TCCA-TAA-AC-ACAGTAGCAGCA
1 TCCACGAACACGGCAGTAGCAGCA
* * *
480515 TCCACGAACACGGCAGCATCACCA
1 TCCACGAACACGGCAGTAGCAGCA
*
480539 TCCACGAACACGACAGTAGC
1 TCCACGAACACGGCAGTAGC
480559 TAGAGCCTGT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
21 13 0.18
22 4 0.06
23 4 0.06
24 51 0.71
ACGTcount: A:0.36, C:0.35, G:0.19, T:0.09
Consensus pattern (24 bp):
TCCACGAACACGGCAGTAGCAGCA
Found at i:480524 original size:21 final size:21
Alignment explanation
Indices: 480459--480525 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
480449 ACGAACACGG
480459 CAGTAGCAGCATCCACGAACA
1 CAGTAGCAGCATCCACGAACA
** **
480480 CGGCAACAGCAGCATCCATAAACA
1 ---CAGTAGCAGCATCCACGAACA
480504 CAGTAGCAGCATCCACGAACA
1 CAGTAGCAGCATCCACGAACA
480525 C
1 C
480526 GGCAGCATCA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 18 0.51
24 17 0.49
ACGTcount: A:0.39, C:0.34, G:0.18, T:0.09
Consensus pattern (21 bp):
CAGTAGCAGCATCCACGAACA
Found at i:480549 original size:45 final size:45
Alignment explanation
Indices: 480459--480558 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
480449 ACGAACACGG
* *
480459 CAGTAGCAGCATCCACGAACACGGCAACAGCAGCATCCATAAACA
1 CAGTAGCAGCATCCACGAACACGGCAACAGCACCATCCACAAACA
* *
480504 CAGTAGCAGCATCCACGAACACGGCAGCATCACCATCCACGAACACGA
1 CAGTAGCAGCATCCACGAACACGGCAACAGCACCATCCAC-AA-AC-A
480552 CAGTAGC
1 CAGTAGC
480559 TAGAGCCTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
45 36 0.75
46 2 0.04
47 2 0.04
48 8 0.17
ACGTcount: A:0.37, C:0.35, G:0.19, T:0.09
Consensus pattern (45 bp):
CAGTAGCAGCATCCACGAACACGGCAACAGCACCATCCACAAACA
Found at i:481477 original size:16 final size:16
Alignment explanation
Indices: 481456--481487 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
481446 AAATATAATA
*
481456 AAAATAATAACAAAAT
1 AAAATAATAAAAAAAT
481472 AAAATAATAAAAAAAT
1 AAAATAATAAAAAAAT
481488 TATTTTCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAATAAAAAAAT
Found at i:485972 original size:22 final size:23
Alignment explanation
Indices: 485928--485972 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
485918 ATATTCATGG
*
485928 CATTCATTCAACATTTTCATAAT
1 CATTCATTCAACATTTGCATAAT
* *
485951 CATTCA-TCAATATTTGCTTAAT
1 CATTCATTCAACATTTGCATAAT
485973 TCCTAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.44
Consensus pattern (23 bp):
CATTCATTCAACATTTGCATAAT
Found at i:494051 original size:42 final size:42
Alignment explanation
Indices: 494002--494833 Score: 763
Period size: 42 Copynumber: 20.0 Consensus size: 42
493992 AAACTTTTGA
* * *
494002 AGACTTTCCTTCCCTTAGTCTGTCTGTCGGCTTTGACCTTGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * *
494044 AAACTTTCCTTCCCTTAGTCTACCTGTCGGCTTTGACCTTAG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* *
494086 AGACTTTCCTACCCTTAGTCTGCCTGTCAGCTTTGACCCTAG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * **
494128 AGACTTTCCTTCCTTTAGTCTGCCTGTCAGCTTTGACTTTAG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * *
494170 AGACTTTCCTACCCTTAGTTTGTCTGTCAGCTTTGACCCTGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * *
494212 AGACTTTCTTTCCCTTAGTCTGCCTATCGGCTTTGACCCTGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * **
494254 AGACTTT-CTTTCCTTA-TCCGCATGTCAGCTTTGACCCCGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * *
494294 AGACTTTCTTTCCCTTAGTCTACATGTCAGCTTTGACCCTAG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * *
494336 AGACTTTCCTACCCTTAGTCTGCCTGTCGACTTTGACCTTGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* *
494378 AGACTTTCCTTCCCTTAGTCTGCTTGTCGTCTTTGACCCTAG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
** * * *
494420 AGACTTTTTTTCCTTTAGTCTGCCTCTCAGCTTTGACCCTAG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * **
494462 AGACTTTACTACCTTTAGTCTACCTGTCGGCTTTGACCCGGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * *
494504 AGACTTTTCTTCCCTTAGTTTGCTTGTCAGTTTTGACCCT-G
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * *
494545 AAGAATTTCCTACCCTCAGTTTGCCTGTCGACTTTGACCCTAG
1 -AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
** *
494588 AGACTTT-CTAACCTTCAGTCTGCCTGTCGACTTTGACCCTAG
1 AGACTTTCCTTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTAG
* * * *
494630 AGATTTTCCTACCCTTAGTCTGCCCTTTCGGCTTTGACCCTGG
1 AGACTTTCCTTCCCTTAGTCTG-CCTGTCGGCTTTGACCCTAG
* * * * * *
494673 AGA-TTT-TTTTCCTTAGTCTGCCCGTCAGC-TTGA-CTTGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * * *
494711 AGACTTTTCTACCCTTAGTATGCCAGTCTGC-TTGACCTTAG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * *
494752 AGACTTT-CTACCCTTAGCCCTGCCT-ACTGG-TCTTGACCCT-G
1 AGACTTTCCTTCCCTTAG-TCTGCCTGTC-GGCT-TTGACCCTAG
* * * *
494793 AAGACTTTTCTACCCTCAGTCTGCCTGTCAGCTTTGACCCT
1 -AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCT
494834 GAAGACTACC
Statistics
Matches: 655, Mismatches: 117, Indels: 36
0.81 0.14 0.04
Matches are distributed among these distances:
38 7 0.01
39 7 0.01
40 64 0.10
41 49 0.07
42 489 0.75
43 39 0.06
ACGTcount: A:0.15, C:0.30, G:0.17, T:0.38
Consensus pattern (42 bp):
AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
Done.