Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 202 of 208
Found at i:62416636 original size:89 final size:86
Alignment explanation
Indices: 62416498--62416761 Score: 233
Period size: 88 Copynumber: 3.0 Consensus size: 86
62416488 GTCCCTCTGT
* * * * * * * * * *
62416498 TTTTTTTTTACACTCAATTGAGCACTTAAACTTTTAAAATGTATCAAAAATATCTTTACACTTCT
1 TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAAACCTTAACACTTCT
62416563 TCAAAAAAAGCAATTAAACCCCCC
66 TCAAAAAAA-CAATT-AA-CCCCC
* *** *
62416587 TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAAACCTTAATTTTTTT
1 TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAAACCTTAACACTTCT
* * *
62416652 TCAAAGAAACAATTAAGCCTC
66 TCAAAAAAACAATTAACCCCC
** ** *
62416673 TATTTTTTCCCCACTCAATTTGGGTACTTGAACTTTCATAATGCATCAAAAAGGCCTTAA-ATTT
1 T-TTTTTTTTCCACTCAA-TTGGGTACTTGAACTTTCATAATGCATCAAAAAAACCTTAACA-CT
* * *
62416737 TTTTCAAAAAAGCAATTAAGCCCC
63 TCTTCAAAAAAACAATTAACCCCC
62416761 T
1 T
62416762 ACTCTTATTA
Statistics
Matches: 145, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
86 4 0.03
87 16 0.11
88 67 0.46
89 58 0.40
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (86 bp):
TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAAACCTTAACACTTCT
TCAAAAAAACAATTAACCCCC
Found at i:62416696 original size:88 final size:87
Alignment explanation
Indices: 62416596--62416758 Score: 265
Period size: 88 Copynumber: 1.9 Consensus size: 87
62416586 CTTTTTTTTT
*
62416596 CCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAAACCTTAATTTTTTTTCAAAGAAA
1 CCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAAACCTTAAATTTTTTTCAAA-AAA
62416661 -CAATTAAGCCTCTATTTTTTCC
65 GCAATTAAGCCTCTATTTTTTCC
* **
62416683 CCACTCAATTTGGGTACTTGAACTTTCATAATGCATCAAAAAGGCCTTAAATTTTTTTCAAAAAA
1 CCACTCAA-TTGGGTACTTGAACTTTCATAATGCATAAAAAAAACCTTAAATTTTTTTCAAAAAA
62416748 GCAATTAAGCC
65 GCAATTAAGCC
62416759 CCTACTCTTA
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
87 11 0.16
88 59 0.84
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (87 bp):
CCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAAACCTTAAATTTTTTTCAAAAAAG
CAATTAAGCCTCTATTTTTTCC
Found at i:62416823 original size:20 final size:20
Alignment explanation
Indices: 62416790--62416837 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
62416780 AAAAAGAATC
*
62416790 ATAAAAA-TAATAAATTTTA
1 ATAAAAATTATTAAATTTTA
62416809 GA-AAAAATTATTAAATTTTA
1 -ATAAAAATTATTAAATTTTA
62416829 ATAAAAATT
1 ATAAAAATT
62416838 TAAAAACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
ATAAAAATTATTAAATTTTA
Found at i:62417206 original size:19 final size:18
Alignment explanation
Indices: 62417163--62417240 Score: 75
Period size: 19 Copynumber: 4.2 Consensus size: 18
62417153 TATGACTTTA
* *
62417163 TAAAATTTTATAATTCTT
1 TAAATTTTTATAATTTTT
* *
62417181 TATATTTCTATATATTTTT
1 TAAATTTTTATA-ATTTTT
**
62417200 TAAATTTTTATAAAATTT
1 TAAATTTTTATAATTTTT
62417218 TACAATTTTTATATATTTTT
1 TA-AATTTTTATA-ATTTTT
62417238 TAA
1 TAA
62417241 TAATTTTTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
18 15 0.32
19 26 0.55
20 6 0.13
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
TAAATTTTTATAATTTTT
Found at i:62417213 original size:10 final size:10
Alignment explanation
Indices: 62417159--62417237 Score: 60
Period size: 10 Copynumber: 8.3 Consensus size: 10
62417149 TTCTTATGAC
*
62417159 TTTATAAAAT
1 TTTATAAATT
62417169 TTTAT-AATT
1 TTTATAAATT
62417178 CTTTAT--ATT
1 -TTTATAAATT
* *
62417187 TCTATATATT
1 TTTATAAATT
62417197 TTT-TAAATT
1 TTTATAAATT
*
62417206 TTTATAAAAT
1 TTTATAAATT
*
62417216 TTTA-CAATT
1 TTTATAAATT
*
62417225 TTTATATATT
1 TTTATAAATT
62417235 TTT
1 TTT
62417238 TAATAATTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
8 4 0.07
9 21 0.38
10 30 0.55
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTATAAATT
Found at i:62417225 original size:28 final size:27
Alignment explanation
Indices: 62417194--62417274 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
62417184 ATTTCTATAT
62417194 ATTTTTTAAATTTTTATAAAATTTTACA
1 ATTTTTTAAATTTTTATAAAATTTT-CA
* *
62417222 ATTTTTATATATTTTT-TAATAATTTTTA
1 ATTTTT-TAAATTTTTATAA-AATTTTCA
* * *
62417250 ATATTTGAATTTTTTATTAAAATTT
1 ATTTTTTAAATTTTTA-TAAAATTT
62417275 AATAATATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
27 6 0.14
28 20 0.47
29 17 0.40
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (27 bp):
ATTTTTTAAATTTTTATAAAATTTTCA
Found at i:62417237 original size:11 final size:10
Alignment explanation
Indices: 62417192--62417255 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
62417182 ATATTTCTAT
62417192 ATATTTTTTA
1 ATATTTTTTA
62417202 A-ATTTTTATA
1 ATATTTTT-TA
* **
62417212 AAATTTTACA
1 ATATTTTTTA
*
62417222 AT-TTTTAT-
1 ATATTTTTTA
62417230 ATATTTTTTA
1 ATATTTTTTA
*
62417240 ATAATTTTTA
1 ATATTTTTTA
62417250 ATATTT
1 ATATTT
62417256 GAATTTTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
8 2 0.05
9 16 0.37
10 20 0.47
11 5 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
ATATTTTTTA
Found at i:62418184 original size:17 final size:17
Alignment explanation
Indices: 62418162--62418195 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62418152 ATCCACTAAT
*
62418162 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62418179 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62418196 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62422823 original size:17 final size:17
Alignment explanation
Indices: 62422801--62422834 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62422791 ATCCACTAAT
*
62422801 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62422818 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62422835 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62424095 original size:28 final size:29
Alignment explanation
Indices: 62424062--62424123 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
62424052 TACAAAATTC
62424062 TAAAAATTAAAAAT-TAAATGAAAGT-AGA
1 TAAAAATTAAAAATATAAAT-AAAGTGAGA
**
62424090 TAAAAATTTCAAATATAAATAAAGTGAGA
1 TAAAAATTAAAAATATAAATAAAGTGAGA
*
62424119 GAAAA
1 TAAAA
62424124 TGAGGAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (29 bp):
TAAAAATTAAAAATATAAATAAAGTGAGA
Found at i:62425094 original size:24 final size:23
Alignment explanation
Indices: 62425066--62425111 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
62425056 ATATATAAAG
62425066 AATAAAAAATAACATCTTAATTTA
1 AATAAAAAATAA-ATCTTAATTTA
** *
62425090 AATAATTAATAAATTTTAATTT
1 AATAAAAAATAAATCTTAATTT
62425112 GAAAAAAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
AATAAAAAATAAATCTTAATTTA
Found at i:62426035 original size:62 final size:61
Alignment explanation
Indices: 62425960--62426084 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 61
62425950 AAATGTTTAG
*
62425960 TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTGAACTATCAATATG-TGTTATTATTA
1 TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTAAACTATCAATA-GATGTT-TTATTA
* * *
62426022 TGGTACATGTACTTTGAAAATGTTTAATGTGGTACCTAAACTATCAATAGATGTTTTATTA
1 TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTAAACTATCAATAGATGTTTTATTA
62426083 TG
1 TG
62426085 ATACTTGGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 9 0.16
62 49 0.84
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.40
Consensus pattern (61 bp):
TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTAAACTATCAATAGATGTTTTATTA
Found at i:62426255 original size:31 final size:32
Alignment explanation
Indices: 62426219--62426302 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
62426209 AGCCCCCAAA
62426219 ATTTTTGAAAATTTTCATTATA-C-CTTTTAATT
1 ATTTTTGAAAATTTTCATTA-AGCACTTTTAA-T
* *
62426251 TTTTTTGAAAATTTTAATTAAGCACTTTTAA-
1 ATTTTTGAAAATTTTCATTAAGCACTTTTAAT
* *
62426282 AATTTTGAAAATTCTCATTAA
1 ATTTTTGAAAATTTTCATTAA
62426303 TCTCACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
31 18 0.41
32 19 0.43
33 7 0.16
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (32 bp):
ATTTTTGAAAATTTTCATTAAGCACTTTTAAT
Found at i:62427922 original size:17 final size:17
Alignment explanation
Indices: 62427900--62427933 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62427890 ATCCACTAAT
*
62427900 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62427917 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62427934 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62432563 original size:17 final size:17
Alignment explanation
Indices: 62432541--62432574 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62432531 ATCCACTAAT
*
62432541 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62432558 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62432575 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62440591 original size:5 final size:5
Alignment explanation
Indices: 62440581--62440638 Score: 50
Period size: 5 Copynumber: 12.0 Consensus size: 5
62440571 TGACAAAACC
* * * *
62440581 TAAAA TAAAA TAAAA TCAAAA TTAAA T-AAA TCAAT TAAAA T-AAA T-AAC
1 TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
62440629 TAAAA TAAAA
1 TAAAA TAAAA
62440639 AAATAAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 11 0.25
5 28 0.64
6 5 0.11
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:62440607 original size:11 final size:10
Alignment explanation
Indices: 62440581--62440638 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 10
62440571 TGACAAAACC
62440581 TAAAATAAAA
1 TAAAATAAAA
62440591 TAAAATCAAAA
1 TAAAAT-AAAA
*
62440602 TTAAAT-AAA
1 TAAAATAAAA
* *
62440611 TCAATTAAAA
1 TAAAATAAAA
*
62440621 T-AAAT-AAC
1 TAAAATAAAA
62440629 TAAAATAAAA
1 TAAAATAAAA
62440639 AAATAAATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
8 3 0.08
9 14 0.37
10 12 0.32
11 9 0.24
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:62440613 original size:15 final size:16
Alignment explanation
Indices: 62440582--62440638 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
62440572 GACAAAACCT
62440582 AAAATAAAATAAAATC
1 AAAATAAAATAAAATC
*
62440598 AAAATTAAAT-AAATC
1 AAAATAAAATAAAATC
* *
62440613 -AATTAAAATAAATAAC
1 AAAATAAAATAAA-ATC
62440629 TAAAATAAAA
1 -AAAATAAAA
62440639 AAATAAATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 7 0.22
15 7 0.22
16 11 0.34
18 7 0.22
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAAAATAAAATC
Found at i:62440645 original size:13 final size:14
Alignment explanation
Indices: 62440581--62440645 Score: 62
Period size: 13 Copynumber: 4.6 Consensus size: 14
62440571 TGACAAAACC
62440581 TAAAATAAAATAAAA
1 TAAAATAAAAT-AAA
*
62440596 TCAAAATTAAATAAA
1 T-AAAATAAAATAAA
* *
62440611 TCAATTAAAATAAA
1 TAAAATAAAATAAA
*
62440625 T-AACTAAAATAAA
1 TAAAATAAAATAAA
62440638 -AAAATAAA
1 TAAAATAAA
62440646 TCAAAGATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
13 17 0.40
14 11 0.26
15 5 0.12
16 9 0.21
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAAATAAAATAAA
Found at i:62443553 original size:14 final size:16
Alignment explanation
Indices: 62443534--62443569 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
62443524 ACCCATAGAA
62443534 TATTTTTTT-AT-TTT
1 TATTTTTTTCATATTT
62443548 TATTTTTTTCATATTT
1 TATTTTTTTCATATTT
62443564 TATTTT
1 TATTTT
62443570 ATTTTTTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 9 0.45
15 2 0.10
16 9 0.45
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (16 bp):
TATTTTTTTCATATTT
Found at i:62445743 original size:11 final size:11
Alignment explanation
Indices: 62445688--62445743 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
62445678 AAAACTTATT
*
62445688 AAAAATTAGAA
1 AAAAATTATAA
* *
62445699 AAAAATTTTAG
1 AAAAATTATAA
* *
62445710 AAAAATCATCA
1 AAAAATTATAA
*
62445721 AAAAA-TAAAA
1 AAAAATTATAA
62445731 AAAAATTATAA
1 AAAAATTATAA
62445742 AA
1 AA
62445744 TTTTATAAAA
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
10 7 0.21
11 26 0.79
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:62446040 original size:28 final size:28
Alignment explanation
Indices: 62445999--62446072 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
62445989 TTACATTTTG
*
62445999 TATAATTTTCTTATGACTT-TATAAAATTT
1 TATAATTTT-TTAT-AATTCTATAAAATTT
* *
62446028 TATAATTTTTTATAATTCTATATATTTT
1 TATAATTTTTTATAATTCTATAAAATTT
*
62446056 TATAATTTTTTAAAATT
1 TATAATTTTTTATAATT
62446073 TTTATAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 3 0.08
28 28 0.70
29 9 0.22
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (28 bp):
TATAATTTTTTATAATTCTATAAAATTT
Found at i:62446044 original size:18 final size:18
Alignment explanation
Indices: 62446023--62446105 Score: 64
Period size: 18 Copynumber: 4.6 Consensus size: 18
62446013 GACTTTATAA
62446023 AATTTTATAATTTTTTAT
1 AATTTTATAATTTTTTAT
*
62446041 AATTCTAT-ATATTTTTAT
1 AATTTTATAAT-TTTTTAT
* *
62446059 AATTTTTTAAAATTTTTAT
1 AATTTTAT-AATTTTTTAT
* * *
62446078 AAATTTCACAATTTTATA-
1 -AATTTTATAATTTTTTAT
62446096 AATTTT-TAAT
1 AATTTTATAAT
62446106 AAATTTTTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
16 3 0.06
17 7 0.14
18 20 0.40
19 14 0.28
20 6 0.12
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTTATAATTTTTTAT
Found at i:62446109 original size:11 final size:11
Alignment explanation
Indices: 62446089--62446117 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
62446079 AATTTCACAA
62446089 TTTT-ATAAAT
1 TTTTAATAAAT
62446099 TTTTAATAAAT
1 TTTTAATAAAT
62446110 TTTTAATA
1 TTTTAATA
62446118 TTTGAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAATAAAT
Found at i:62451134 original size:19 final size:19
Alignment explanation
Indices: 62451090--62451153 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
62451080 AGAAAAAATC
* *
62451090 ATAAAAATAATAAATTTTA
1 ATAAAATTATTAAATTTTA
*
62451109 GAAAAAATTATTAAATTTTA
1 -ATAAAATTATTAAATTTTA
*
62451129 ATAAAAATT-TAAAATTTTA
1 AT-AAAATTATTAAATTTTA
*
62451148 TTAAAA
1 ATAAAA
62451154 ATTAGAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
18 4 0.11
19 11 0.30
20 22 0.59
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
ATAAAATTATTAAATTTTA
Found at i:62451153 original size:18 final size:19
Alignment explanation
Indices: 62451101--62451164 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 19
62451091 TAAAAATAAT
*
62451101 AAATTTT-AGAAAAAATTA
1 AAATTTTAATAAAAAATTA
*
62451119 TTAAATTTTAATAAAAATTTA
1 --AAATTTTAATAAAAAATTA
*
62451140 AAATTTT-ATTAAAAATTA
1 AAATTTTAATAAAAAATTA
*
62451158 GAATTTT
1 AAATTTT
62451165 TTTAGAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
18 15 0.39
19 7 0.18
20 7 0.18
21 9 0.24
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AAATTTTAATAAAAAATTA
Found at i:62451154 original size:19 final size:20
Alignment explanation
Indices: 62451090--62451157 Score: 79
Period size: 19 Copynumber: 3.5 Consensus size: 20
62451080 AGAAAAAATC
*
62451090 ATAAAAATAAT-AAATTTTA
1 ATAAAAATTATAAAATTTTA
*
62451109 GA-AAAAATTATTAAATTTTA
1 -ATAAAAATTATAAAATTTTA
62451129 ATAAAAATT-TAAAATTTTA
1 ATAAAAATTATAAAATTTTA
*
62451148 TTAAAAATTA
1 ATAAAAATTA
62451158 GAATTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 26 0.62
20 16 0.38
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
ATAAAAATTATAAAATTTTA
Found at i:62451464 original size:9 final size:9
Alignment explanation
Indices: 62451444--62451541 Score: 65
Period size: 10 Copynumber: 10.3 Consensus size: 9
62451434 TTCTTATAAC
62451444 TTTATAAAAT
1 TTTAT-AAAT
62451454 TTTATAAAT
1 TTTATAAAT
*
62451463 TTT-TATAT
1 TTTATAAAT
*
62451471 TTCTATATAT
1 TT-TATAAAT
62451481 TTTA-AAAT
1 TTTATAAAT
*
62451489 TTTTTAAAATT
1 TTTAT-AAA-T
62451500 TTTATAAAAT
1 TTTAT-AAAT
* *
62451510 TTTACAATT
1 TTTATAAAT
*
62451519 TTTATATATT
1 TTTATA-AAT
62451529 TTTAATAAAT
1 TTT-ATAAAT
62451539 TTT
1 TTT
62451542 TAATATTTGA
Statistics
Matches: 73, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
8 12 0.16
9 18 0.25
10 31 0.42
11 12 0.16
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTATAAAT
Found at i:62451509 original size:21 final size:21
Alignment explanation
Indices: 62451483--62451543 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 21
62451473 CTATATATTT
62451483 TAAAATTTTTTAAAATTTTTA
1 TAAAATTTTTTAAAATTTTTA
*
62451504 TAAAA--TTTTACAATTTTTA
1 TAAAATTTTTTAAAATTTTTA
* *
62451523 T-ATATTTTTAATAAATTTTTA
1 TAAAATTTTTTA-AAATTTTTA
62451544 ATATTTGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.06
19 14 0.42
20 4 0.12
21 13 0.39
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TAAAATTTTTTAAAATTTTTA
Found at i:62451527 original size:47 final size:48
Alignment explanation
Indices: 62451439--62451549 Score: 129
Period size: 46 Copynumber: 2.4 Consensus size: 48
62451429 TAATTTTCTT
* * * *
62451439 ATAACTTTATAAAA-TTTTATAAATTTTTATATTTCTATATA-TTTTA
1 ATAAATTTTTAAAATTTTTATAAAATTTTAAATTTCTATATATTTTTA
* *
62451485 A-AATTTTTTAAAATTTTTATAAAATTTTACAATTTTTATATATTTTTA
1 ATAAATTTTTAAAATTTTTATAAAATTTTA-AATTTCTATATATTTTTA
*
62451533 ATAAATTTTTAATATTT
1 ATAAATTTTTAAAATTT
62451550 GATTTTTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
45 10 0.19
46 15 0.28
47 10 0.19
48 6 0.11
49 13 0.24
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (48 bp):
ATAAATTTTTAAAATTTTTATAAAATTTTAAATTTCTATATATTTTTA
Found at i:62451529 original size:10 final size:10
Alignment explanation
Indices: 62451453--62451549 Score: 62
Period size: 9 Copynumber: 10.2 Consensus size: 10
62451443 CTTTATAAAA
*
62451453 TTTTATA-AA
1 TTTTATATAT
62451462 TTTT-TATAT
1 TTTTATATAT
*
62451471 TTCTATATAT
1 TTTTATATAT
* *
62451481 TTTAAAAT-T
1 TTTTATATAT
*
62451490 TTTTA-AAAT
1 TTTTATATAT
* *
62451499 TTTTATAAAA
1 TTTTATATAT
*
62451509 TTTTACA-AT
1 TTTTATATAT
62451518 TTTTATATAT
1 TTTTATATAT
*
62451528 TTTTAATAAAT
1 TTTT-ATATAT
62451539 TTTTA-ATAT
1 TTTTATATAT
62451548 TT
1 TT
62451550 GATTTTTTAT
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
8 3 0.04
9 31 0.45
10 26 0.38
11 9 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTATATAT
Found at i:62451729 original size:96 final size:98
Alignment explanation
Indices: 62451617--62451798 Score: 271
Period size: 99 Copynumber: 1.9 Consensus size: 98
62451607 AATTTTTAAT
* * *
62451617 AAAATTAGGGGGTTAATTGCTTTTTTT-TAA-GTTTGAGGG-TCTTTTTGATGCATTTTGAAAGT
1 AAAAGTAGGGGCTTAATTGCTTTTTTTAAAATGTTTGAGGGCT-TTTTTGATGCATTTTGAAAGT
*
62451679 TCAAGTACCCAATTGACTGCAAAACAAAAAGAAA
65 TCAAGTACCCAAATGACTGCAAAACAAAAAGAAA
*
62451713 AAAAGTAGGGGCTTAATTGCTTTTTTTGAAAATGTTTGAGGGCTTTTTTGATGTATTTTGAAAGT
1 AAAAGTAGGGGCTTAATTGCTTTTTTT-AAAATGTTTGAGGGCTTTTTTGATGCATTTTGAAAGT
*
62451778 TCAAGTACCCAAATGAGTGCA
65 TCAAGTACCCAAATGACTGCA
62451799 TAAAAAGAAC
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
96 25 0.33
98 2 0.03
99 48 0.63
100 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (98 bp):
AAAAGTAGGGGCTTAATTGCTTTTTTTAAAATGTTTGAGGGCTTTTTTGATGCATTTTGAAAGTT
CAAGTACCCAAATGACTGCAAAACAAAAAGAAA
Found at i:62454227 original size:54 final size:54
Alignment explanation
Indices: 62454169--62454278 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
62454159 ATATATATAT
* * *
62454169 ATATAAAAGAAAACACATTTTTATGAAATATAAGATTTTGTTAAAAGAAAGAGC
1 ATATAAAAGAAAACACATTTTTATGAAATACAAGATTTTGCTAAAAGAAAAAGC
* * *
62454223 ATATAAAAGCATACACGTTTTTATGAAATACAAGATTTTGCTAAAAGAAAAAGC
1 ATATAAAAGAAAACACATTTTTATGAAATACAAGATTTTGCTAAAAGAAAAAGC
62454277 AT
1 AT
62454279 CCAATTTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (54 bp):
ATATAAAAGAAAACACATTTTTATGAAATACAAGATTTTGCTAAAAGAAAAAGC
Found at i:62454812 original size:17 final size:17
Alignment explanation
Indices: 62454790--62454823 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62454780 ATCCACTAAT
*
62454790 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62454807 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62454824 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62459451 original size:17 final size:17
Alignment explanation
Indices: 62459429--62459462 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62459419 ATCCACTAAT
*
62459429 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62459446 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62459463 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62460354 original size:72 final size:72
Alignment explanation
Indices: 62460265--62460720 Score: 747
Period size: 72 Copynumber: 6.3 Consensus size: 72
62460255 CTTGAGACGC
62460265 AACCAATTGAGTGGACAAATTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTT
1 AACCAATTGAGTGGACAAATTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTT
62460330 GTC-GTGG
66 GTCAG-GG
*
62460337 AACCGATTGAGTGGACAAATTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTT
1 AACCAATTGAGTGGACAAATTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTT
*
62460402 GTCAGAG
66 GTCAGGG
*
62460409 AACCAATTGAGGGGACAAATTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTT
1 AACCAATTGAGTGGACAAATTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTT
62460474 GTC-GTGG
66 GTCAG-GG
* * *
62460481 AACCGATTGAGTGGACAAATTCCAATATCATTGGGGAGCCTCTTGCAACTCACTCATTTAGACTT
1 AACCAATTGAGTGGACAAATTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTT
62460546 GTC-GTGG
66 GTCAG-GG
* * *
62460553 AACCGATTGAGTGGACAAATTCCAAGATCATTGGGGAATCTCTTGCAACTCACTCAATTAGACTT
1 AACCAATTGAGTGGACAAATTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTT
*
62460618 GTCAGAG
66 GTCAGGG
* **
62460625 AACCAATTGAGTGGACAAATTCCAAGATCATTGGGGAACCACTTGCAACTCACTGTTTTAGACTT
1 AACCAATTGAGTGGACAAATTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTT
62460690 GTCAGGG
66 GTCAGGG
62460697 AACCAATTGAGTGGACAAATTCCA
1 AACCAATTGAGTGGACAAATTCCA
62460721 TTGTCAATTC
Statistics
Matches: 360, Mismatches: 21, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
71 1 0.00
72 357 0.99
73 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (72 bp):
AACCAATTGAGTGGACAAATTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTT
GTCAGGG
Found at i:62463179 original size:30 final size:30
Alignment explanation
Indices: 62463143--62463202 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
62463133 AGGAAACAAG
62463143 ACCATGTCAAAATTTCCAAAAATTAGTCAT
1 ACCATGTCAAAATTTCCAAAAATTAGTCAT
62463173 ACCATGTCAAAATTTCCAAAAATTAGTCAT
1 ACCATGTCAAAATTTCCAAAAATTAGTCAT
62463203 TCATTTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (30 bp):
ACCATGTCAAAATTTCCAAAAATTAGTCAT
Found at i:62463958 original size:87 final size:87
Alignment explanation
Indices: 62463792--62463998 Score: 220
Period size: 87 Copynumber: 2.4 Consensus size: 87
62463782 AGTCCCTCTT
* * * * *
62463792 TTTTTTTTTACACTCAATTGAGTACTTAAACTTTTAAAATGTATCAAAAATATCTTAACACTTCT
1 TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTTAAAATGCATCAAAAATACCTTAACACTTCT
62463857 TCAAAAAAAGCAATTAAACCCC
66 TCAAAAAAAGCAATTAAACCCC
* * ***
62463879 TTTTTTTTTCCGCTCAATTGGGTACTTGAA-TTTTCATAATGCATCAAAAATACCTTAATTTTTT
1 TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTT-AAAATGCATCAAAAATACCTTAA-CACTT
* * * *
62463943 TTTCAAAGAAA-CAATTAAGCCTC
64 CTTCAAAAAAAGCAATTAAACCCC
* * *
62463966 TATTTTTTTCCTACTCAACTAGGTACTTGAACT
1 TTTTTTTTTCC-ACTCAATTGGGTACTTGAACT
62463999 GTCAAAAAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
86 4 0.04
87 66 0.67
88 27 0.28
89 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (87 bp):
TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTTAAAATGCATCAAAAATACCTTAACACTTCT
TCAAAAAAAGCAATTAAACCCC
Found at i:62464078 original size:10 final size:10
Alignment explanation
Indices: 62464042--62464162 Score: 72
Period size: 10 Copynumber: 12.4 Consensus size: 10
62464032 AAAATTAGAA
*
62464042 AAAAAATCAT
1 AAAAAATTAT
* *
62464052 -AAAAATAAA
1 AAAAAATTAT
*
62464061 AAAAAATTAG
1 AAAAAATTAT
62464071 AAAAAATTAT
1 AAAAAATTAT
* **
62464081 TAAATTTTA-
1 AAAAAATTAT
62464090 ATAAAAATT-T
1 A-AAAAATTAT
*
62464100 AAAAACTTAT
1 AAAAAATTAT
* *
62464110 TAAAAATTAG
1 AAAAAATTAT
*
62464120 AAAAAATTTT
1 AAAAAATTAT
*
62464130 AGAAAAATTGT
1 A-AAAAATTAT
*
62464141 CAAAAA--AT
1 AAAAAATTAT
62464149 AAAAAATTAT
1 AAAAAATTAT
62464159 AAAA
1 AAAA
62464163 TTTTATAATT
Statistics
Matches: 82, Mismatches: 22, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
8 6 0.07
9 13 0.16
10 55 0.67
11 8 0.10
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.28
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:62464086 original size:49 final size:49
Alignment explanation
Indices: 62464033--62464127 Score: 111
Period size: 49 Copynumber: 1.9 Consensus size: 49
62464023 CTCTTATTAA
62464033 AAATTAGAAAAAAAATCATAAAAA-TAAAAAAAAATTAGAAAAAATTATT
1 AAATTAGAAAAAAAAT-ATAAAAACTAAAAAAAAATTAGAAAAAATTATT
** * * * **
62464082 AAATTTTAATAAAAATTTAAAAACTTATTAAAAATTAGAAAAAATT
1 AAATTAGAAAAAAAATATAAAAACTAAAAAAAAATTAGAAAAAATT
62464128 TTAGAAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
48 6 0.16
49 32 0.84
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.28
Consensus pattern (49 bp):
AAATTAGAAAAAAAATATAAAAACTAAAAAAAAATTAGAAAAAATTATT
Found at i:62464124 original size:29 final size:28
Alignment explanation
Indices: 62464042--62464162 Score: 84
Period size: 29 Copynumber: 4.1 Consensus size: 28
62464032 AAAATTAGAA
* * *
62464042 AAAAAATCA-TAAAAATAAAAAAAAATTAG
1 AAAAAATTATTAAAAAT-TAAAAAAATT-T
**
62464071 AAAAAATTATTAAATTTTAATAAAAATTT
1 AAAAAATTATTAAAAATTAA-AAAAATTT
*
62464100 AAAAACTTATTAAAAATTAGAAAAAATTTT
1 AAAAAATTATTAAAAATTA-AAAAAA-TTT
* * *
62464130 AGAAAAATTGTCAAAAAAT-AAAAAATTAT
1 A-AAAAATTATTAAAAATTAAAAAAATT-T
62464159 AAAA
1 AAAA
62464163 TTTTATAATT
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
28 5 0.07
29 39 0.53
30 17 0.23
31 13 0.18
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.28
Consensus pattern (28 bp):
AAAAAATTATTAAAAATTAAAAAAATTT
Found at i:62466833 original size:36 final size:34
Alignment explanation
Indices: 62466793--62466873 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 34
62466783 AATTTAATTT
62466793 ATATTTTATTATTTGATTCA-AATATAATCTGTAAAA
1 ATATTTTATTATTTGATT-AGAATATAAT-T-TAAAA
*
62466829 ATATTTTGA-TATTTTATTATGAATATAATTTAAAA
1 ATATTTT-ATTATTTGATTA-GAATATAATTTAAAA
62466864 ATATTTTATT
1 ATATTTTATT
62466874 GTATATTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
34 1 0.03
35 14 0.35
36 16 0.40
37 9 0.22
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (34 bp):
ATATTTTATTATTTGATTAGAATATAATTTAAAA
Found at i:62467040 original size:19 final size:18
Alignment explanation
Indices: 62466998--62467043 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
62466988 ATATAATTGT
*
62466998 AATAATTTTTAATTATTT
1 AATAATTTTTAATTATTA
* *
62467016 ATTAATTTTGTAATTGTTA
1 AATAATTTT-TAATTATTA
62467035 AATAATTTT
1 AATAATTTT
62467044 AAAAACTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (18 bp):
AATAATTTTTAATTATTA
Found at i:62467183 original size:21 final size:21
Alignment explanation
Indices: 62467155--62467209 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
62467145 ACCGCTGTTT
62467155 CTAATCTCACCGCTACAGTATC
1 CTAATCTCACCGCTACAGTA-C
62467177 C-AATCTCACCGCTACAGTAC
1 CTAATCTCACCGCTACAGTAC
62467197 CTAATCTCACCGC
1 CTAATCTCACCGC
62467210 CACCGCTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.27, C:0.40, G:0.09, T:0.24
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAC
Found at i:62470525 original size:84 final size:84
Alignment explanation
Indices: 62470376--62470556 Score: 314
Period size: 84 Copynumber: 2.2 Consensus size: 84
62470366 TATCAAAGAA
*
62470376 TTCC-AATC-CAAATCACTAGAATATTTATATCTAAACAATAATAATCTTAGTGGTGTGATAGAG
1 TTCCAAATCTCAAATCACTAGAATATTTATATCTAAACAATAATAATCTTAGTGGTGTCATAGAG
62470439 TTTAGCATGTTCTCAAACC
66 TTTAGCATGTTCTCAAACC
*
62470458 TTCCAAATCTCAAATCACTAGAATATTTATTTCTAAACAATAATAATCTTAGTGGTGTCATAGAG
1 TTCCAAATCTCAAATCACTAGAATATTTATATCTAAACAATAATAATCTTAGTGGTGTCATAGAG
*
62470523 TTTCGCATGTTCTCAAACC
66 TTTAGCATGTTCTCAAACC
62470542 TTCCAAATCT-AAATC
1 TTCCAAATCTCAAATC
62470557 TTCTCGACCT
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
82 4 0.04
83 9 0.10
84 81 0.86
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (84 bp):
TTCCAAATCTCAAATCACTAGAATATTTATATCTAAACAATAATAATCTTAGTGGTGTCATAGAG
TTTAGCATGTTCTCAAACC
Found at i:62471557 original size:20 final size:20
Alignment explanation
Indices: 62471532--62471581 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
62471522 TGGCTTAAAA
62471532 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
62471552 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
62471569 GTGGTAGTGGATT
1 TTGGTAGTGGATT
62471582 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:62476196 original size:20 final size:20
Alignment explanation
Indices: 62476171--62476220 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
62476161 TGGCTTAAAA
62476171 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
62476191 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
62476208 GTGGTAGTGGATT
1 TTGGTAGTGGATT
62476221 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:62478680 original size:90 final size:93
Alignment explanation
Indices: 62478498--62478689 Score: 241
Period size: 93 Copynumber: 2.1 Consensus size: 93
62478488 AAGCAATTAA
* * * *
62478498 GGCCTTTTTCATGCATTATGAAAGTTCAAGTACCGAATTGAGTGCAAGAAAAAAAAAGTAGGGGC
1 GGCCTTTTTGATGCATTATGAAAGTTCAAGTACCCAAATGAGTGCAAGAAAAAAAAAGCAGGGGC
** *
62478563 TTAATTGCTTTTTTTGAAAATGTTTGAG
66 TTAATTGCCATTTTTGAAAAAGTTTGAG
* * * *
62478591 GGCCTTTTTGATGTATTTTGAAAGTTCAAGTACCCAAATGAGTGC-A-TAAAAAGAA-CAGGGG-
1 GGCCTTTTTGATGCATTATGAAAGTTCAAGTACCCAAATGAGTGCAAGAAAAAAAAAGCAGGGGC
62478652 TTCAATTGCCATTTTTGAAAAAGTTTGAG
66 TT-AATTGCCATTTTTGAAAAAGTTTGAG
62478681 GG-CTTTTTG
1 GGCCTTTTTG
62478690 CACCCTTAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
89 9 0.10
90 30 0.34
91 7 0.08
92 1 0.01
93 40 0.46
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (93 bp):
GGCCTTTTTGATGCATTATGAAAGTTCAAGTACCCAAATGAGTGCAAGAAAAAAAAAGCAGGGGC
TTAATTGCCATTTTTGAAAAAGTTTGAG
Found at i:62480136 original size:22 final size:21
Alignment explanation
Indices: 62480100--62480140 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
62480090 GTTAAAAATG
62480100 ATTTTTTTAAAAAAATATTTTT
1 ATTTTTTTAAAAAAA-ATTTTT
**
62480122 ATTTTTTTATTAAAAATTT
1 ATTTTTTTAAAAAAAATTT
62480141 AGAATTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTTTAAAAAAAATTTTT
Found at i:62484209 original size:62 final size:61
Alignment explanation
Indices: 62484134--62484258 Score: 178
Period size: 62 Copynumber: 2.0 Consensus size: 61
62484124 AAATGTCTAG
* * *
62484134 TGGTACAAGTACTTTGAAAATATATAATGTGGCACCTGAACTATCAATATGTGTTATTATTA
1 TGGTACAAGTACTTTGAAAATATATAATGTGGCACCTAAACTATCAATATATATT-TTATTA
* * * *
62484196 TGGTACATGTACTTTGAAAATGTTTAATGTGGTACCTAAACTATCAATATATATTTTATTA
1 TGGTACAAGTACTTTGAAAATATATAATGTGGCACCTAAACTATCAATATATATTTTATTA
62484257 TG
1 TG
62484259 ATACTTGATA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
61 8 0.14
62 48 0.86
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.40
Consensus pattern (61 bp):
TGGTACAAGTACTTTGAAAATATATAATGTGGCACCTAAACTATCAATATATATTTTATTA
Found at i:62484426 original size:30 final size:30
Alignment explanation
Indices: 62484359--62484472 Score: 90
Period size: 31 Copynumber: 3.7 Consensus size: 30
62484349 TTTCCTTTAA
* **
62484359 AATTTTTAGAAAA-TTTCAATTAAGCCCTCAA
1 AATTTTT-GAAAATTTTC-ATTAAGCACTCTT
*
62484390 AATTTTTGAAAATTTTCATTATA-C-CTTTT
1 AATTTTTGAAAATTTTCATTA-AGCACTCTT
* *
62484419 AATTTTTTAAAAAATTTTAATTAAGCACTCTT
1 AA-TTTTT-GAAAATTTTCATTAAGCACTCTT
* *
62484451 AAATTTTGAAAATTCTCATTAA
1 AATTTTTGAAAATTTTCATTAA
62484473 TCTCACAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
29 4 0.06
30 28 0.42
31 29 0.43
32 6 0.09
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.45
Consensus pattern (30 bp):
AATTTTTGAAAATTTTCATTAAGCACTCTT
Found at i:62484426 original size:61 final size:61
Alignment explanation
Indices: 62484352--62484471 Score: 161
Period size: 61 Copynumber: 2.0 Consensus size: 61
62484342 TTTGTTTTTT
* * *
62484352 CCTTTAAAATTTTTAGAAAATTTCAATTAAGCCCTC-AAAATTTTTGAAAATTTTCATTATA
1 CCTTTAAAATTTTTAAAAAATTTCAATTAAGCACTCTAAAA-TTTTGAAAATTCTCATTATA
* * * *
62484413 CCTTTTAATTTTTTAAAAAATTTTAATTAAGCACTCTTAAATTTTGAAAATTCTCATTA
1 CCTTTAAAATTTTTAAAAAATTTCAATTAAGCACTCTAAAATTTTGAAAATTCTCATTA
62484472 ATCTCACAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 48 0.94
62 3 0.06
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.45
Consensus pattern (61 bp):
CCTTTAAAATTTTTAAAAAATTTCAATTAAGCACTCTAAAATTTTGAAAATTCTCATTATA
Found at i:62491139 original size:61 final size:61
Alignment explanation
Indices: 62491072--62491203 Score: 158
Period size: 61 Copynumber: 2.1 Consensus size: 61
62491062 GTCTAATAAC
* * * *
62491072 AAATTTAGCCCTAAATGTTAACAAAACTT-GTCATTTTAGTTCAAATTCTAAAAATTTTAAT
1 AAATTTAACCCTAAATATTAACAAAAATTAG-CAATTTAGTTCAAATTCTAAAAATTTTAAT
* ** *
62491133 AAATTTAACCCTTAATATTTTCAAAAATTAGCAATTTAGTTCTAATTCTAAAAATTTTAAT
1 AAATTTAACCCTAAATATTAACAAAAATTAGCAATTTAGTTCAAATTCTAAAAATTTTAAT
62491194 ATATATTTAA
1 A-A-ATTTAA
62491204 AAAAATATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 52 0.87
62 2 0.03
63 6 0.10
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (61 bp):
AAATTTAACCCTAAATATTAACAAAAATTAGCAATTTAGTTCAAATTCTAAAAATTTTAAT
Found at i:62494494 original size:79 final size:79
Alignment explanation
Indices: 62494363--62494522 Score: 320
Period size: 79 Copynumber: 2.0 Consensus size: 79
62494353 CAATGTTTCT
62494363 GAAAATAAACTCCATGGTCAGATTCCTCAAGGCAAACAGTTCAACACATTTGGAAATGATTCATA
1 GAAAATAAACTCCATGGTCAGATTCCTCAAGGCAAACAGTTCAACACATTTGGAAATGATTCATA
62494428 TGAAGGAAACAAGG
66 TGAAGGAAACAAGG
62494442 GAAAATAAACTCCATGGTCAGATTCCTCAAGGCAAACAGTTCAACACATTTGGAAATGATTCATA
1 GAAAATAAACTCCATGGTCAGATTCCTCAAGGCAAACAGTTCAACACATTTGGAAATGATTCATA
62494507 TGAAGGAAACAAGG
66 TGAAGGAAACAAGG
62494521 GA
1 GA
62494523 TTATGTGGAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.21
Consensus pattern (79 bp):
GAAAATAAACTCCATGGTCAGATTCCTCAAGGCAAACAGTTCAACACATTTGGAAATGATTCATA
TGAAGGAAACAAGG
Found at i:62495116 original size:26 final size:26
Alignment explanation
Indices: 62495087--62495139 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
62495077 GGTAAAAATT
62495087 ATATGAATAAACTTTTATAAATATAA
1 ATATGAATAAACTTTTATAAATATAA
62495113 ATATGAATAAACTTTTATAAATATAA
1 ATATGAATAAACTTTTATAAATATAA
62495139 A
1 A
62495140 GTGTAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
ATATGAATAAACTTTTATAAATATAA
Found at i:62497036 original size:24 final size:24
Alignment explanation
Indices: 62497004--62497050 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
62496994 GTCTATCAGA
62497004 AAGTTTTTCCTATGGTGAAAAGTG
1 AAGTTTTTCCTATGGTGAAAAGTG
62497028 AAGTTTTTCCTATGGTGAAAAGT
1 AAGTTTTTCCTATGGTGAAAAGT
62497051 TGCATTGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (24 bp):
AAGTTTTTCCTATGGTGAAAAGTG
Found at i:62497439 original size:21 final size:21
Alignment explanation
Indices: 62497413--62497452 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
62497403 AAAGAGGAAG
62497413 TAGTTGTTAACCTTTTCGATT
1 TAGTTGTTAACCTTTTCGATT
62497434 TAGTTGTTAACCTTTTCGA
1 TAGTTGTTAACCTTTTCGA
62497453 AAGTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (21 bp):
TAGTTGTTAACCTTTTCGATT
Found at i:62500836 original size:19 final size:19
Alignment explanation
Indices: 62500801--62500837 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
62500791 AATATAATGT
*
62500801 TAAAATATTTATATAATAC
1 TAAAATATTTAGATAATAC
*
62500820 TAAAATATTTAGGTAATA
1 TAAAATATTTAGATAATA
62500838 TATGCGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
TAAAATATTTAGATAATAC
Found at i:62513624 original size:17 final size:17
Alignment explanation
Indices: 62513602--62513635 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62513592 ATCCACTAAT
*
62513602 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62513619 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62513636 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62515330 original size:72 final size:72
Alignment explanation
Indices: 62515220--62515807 Score: 887
Period size: 72 Copynumber: 8.1 Consensus size: 72
62515210 GAATTGACAA
* * *
62515220 TGGAATTTGTCCACTCAATTGGTTCATCGACAAGTGTAAATGAGTGAGATGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
62515285 ATGATCT
66 ATGATCT
* * * *
62515292 TGGAATTTTTCCACTCAATTGGTTCACCGGCAACTGTAAATGAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
62515357 ATGATCT
66 ATGATCT
* *
62515364 TGGAATTTGTCCGCTCAATTGGTTCACCGATAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
62515429 ATGATCT
66 ATGATCT
*
62515436 CGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
62515501 ATGATCT
66 ATGATCT
62515508 TGGAATTTGTCCACTCAATTGGTTCACCGACAAG--TAAATGAGTGAGTTGCAAGATGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGA-G-------
*
62515571 ATGATCCCCAATGATCT
58 --GTTCCCCAATGATCT
* *
62515588 TGGAATTTGTCCACTCAATTGGTTCATCGACAAATCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
62515653 ATGATCT
66 ATGATCT
*
62515660 TGGAATTTGTCCACTCAATTGGTTC-CACGACAAGTCTAAATGAGTGAGTTGAAAGAGGTTCCCC
1 TGGAATTTGTCCACTCAATTGGTTCAC-CGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCC
*
62515724 AATAATCT
65 AATGATCT
**
62515732 TGGAATTTGTCCACTCAATTGGTTCTGCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTT-CCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
*
62515796 GTGATCT
66 ATGATCT
62515803 TGGAA
1 TGGAA
62515808 CCGGTCCTGA
Statistics
Matches: 475, Mismatches: 27, Indels: 29
0.89 0.05 0.05
Matches are distributed among these distances:
70 20 0.04
71 15 0.03
72 373 0.79
80 46 0.10
81 1 0.00
82 20 0.04
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (72 bp):
TGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
ATGATCT
Found at i:62515746 original size:296 final size:286
Alignment explanation
Indices: 62515220--62515807 Score: 901
Period size: 296 Copynumber: 2.0 Consensus size: 286
62515210 GAATTGACAA
* *
62515220 TGGAATTTGTCCACTCAATTGGTTCATCGACAAGTGTAAATGAGTGAGATGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGACAAG-GTAAATGAGTGAGATGCAAGAGGATCCCCA
* * * *
62515285 ATGATCTTGGAATTTTTCCACTCAATTGGTTCACCGGCAACTGTAAATGAGTGAGTTGCAAGAGG
65 ATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAATCTAAATGAGTGAGTTGCAAGAGG
* *
62515350 TTCCCCAATGATCTTGGAATTTGTCCGCTCAATTGGTTCACCGATAAGTCTAAATGAGTGAGTTG
130 TTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTG
* *
62515415 CAAGAGGTTCCCCAATGATCTCGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAG
195 AAAGAGGTTCCCCAATAATCTCGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAG
62515480 TGAGTTGCAAGAGGTTCCCCAATGATCT
260 TGAGTTGCAAGAGGTT-CCCAATGATCT
*
62515508 TGGAATTTGTCCACTCAATTGGTTCACCGACAA-GTAAATGAGTGAGTTGCAAGATGTTCCCCAA
1 TGGAATTTGTCCACTCAATTGGTTCACCGACAAGGTAAATGAGTGAGATGCAAGA-G--------
*
62515572 TGATCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCATCGACAAATCTAAATGAGTGAGT
57 -GATCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAATCTAAATGAGTGAGT
62515637 TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTC-CACGACAAGTCTAAAT
121 TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCAC-CGACAAGTCTAAAT
* **
62515701 GAGTGAGTTGAAAGAGGTTCCCCAATAATCTTGGAATTTGTCCACTCAATTGGTTCTGCGACAAG
185 GAGTGAGTTGAAAGAGGTTCCCCAATAATCTCGGAATTTGTCCACTCAATTGGTTCACCGACAAG
*
62515766 TCTAAATGAGTGAGTTGCAAGAGGTTCCCAGTGATCT
250 TCTAAATGAGTGAGTTGCAAGAGGTTCCCAATGATCT
62515803 TGGAA
1 TGGAA
62515808 CCGGTCCTGA
Statistics
Matches: 273, Mismatches: 16, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
286 20 0.07
287 1 0.00
288 32 0.12
295 16 0.06
296 204 0.75
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (286 bp):
TGGAATTTGTCCACTCAATTGGTTCACCGACAAGGTAAATGAGTGAGATGCAAGAGGATCCCCAA
TGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAATCTAAATGAGTGAGTTGCAAGAGGT
TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGA
AAGAGGTTCCCCAATAATCTCGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGT
GAGTTGCAAGAGGTTCCCAATGATCT
Found at i:62519892 original size:18 final size:20
Alignment explanation
Indices: 62519871--62519907 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
62519861 TATTTTGTTT
62519871 TATTT-ATTTCTA-AACTCA
1 TATTTCATTTCTATAACTCA
*
62519889 TATTTCTTTTCTATAACTC
1 TATTTCATTTCTATAACTC
62519908 CAATTATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 6 0.38
20 5 0.31
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTCATTTCTATAACTCA
Found at i:62520755 original size:3 final size:3
Alignment explanation
Indices: 62520749--62520787 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
62520739 ATTGTTGTTG
62520749 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62520788 ACACCACTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:62521047 original size:20 final size:20
Alignment explanation
Indices: 62521022--62521071 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
62521012 TGGCTTAAAA
62521022 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
62521042 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
62521059 GTGGTAGTGGATT
1 TTGGTAGTGGATT
62521072 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:62525686 original size:20 final size:20
Alignment explanation
Indices: 62525661--62525710 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
62525651 TGGCTTAAAA
62525661 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
62525681 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
62525698 GTGGTAGTGGATT
1 TTGGTAGTGGATT
62525711 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:62529960 original size:30 final size:29
Alignment explanation
Indices: 62529922--62530041 Score: 120
Period size: 30 Copynumber: 4.1 Consensus size: 29
62529912 TAAAAAAAAA
* *
62529922 TTTA-AAAATTGTATTTTGACCTCTGAACT
1 TTTATAAAATTATATTTTGACC-CTAAACT
* *
62529951 TTTCTAAAATT-TCATTTTGACCCTTAAATT
1 TTTATAAAATTAT-ATTTTGACCC-TAAACT
*
62529981 TTTATAAAATTATATTTTAACCCTTAATA-T
1 TTTATAAAATTATATTTTGACCC-TAA-ACT
*
62530011 TTTTTAAAATTATATTTTGACCCTAAACT
1 TTTATAAAATTATATTTTGACCCTAAACT
62530040 TT
1 TT
62530042 CTCGAAATTA
Statistics
Matches: 78, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
28 1 0.01
29 11 0.14
30 64 0.82
31 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.49
Consensus pattern (29 bp):
TTTATAAAATTATATTTTGACCCTAAACT
Found at i:62529991 original size:60 final size:59
Alignment explanation
Indices: 62529922--62530034 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 59
62529912 TAAAAAAAAA
* * *
62529922 TTTAAAAATTGTATTTTGACCTCTGAA-CTTTTCTAAAATT-TCATTTTGACCCTTAAATT
1 TTTAAAAATTATATTTTAACC-CTGAATATTTTCTAAAATTAT-ATTTTGACCCTTAAATT
* *
62529981 TTTATAAAATTATATTTTAACCCTTAATATTTTTTAAAATTATATTTTGACCCT
1 TTTA-AAAATTATATTTTAACCCTGAATATTTTCTAAAATTATATTTTGACCCT
62530035 AAACTTTCTC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
59 8 0.17
60 37 0.80
61 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (59 bp):
TTTAAAAATTATATTTTAACCCTGAATATTTTCTAAAATTATATTTTGACCCTTAAATT
Found at i:62530277 original size:9 final size:9
Alignment explanation
Indices: 62530260--62530296 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
62530250 TGAGTTTTCG
62530260 AATTCGAAT
1 AATTCGAAT
*
62530269 AACTCGAAT
1 AATTCGAAT
62530278 AATTCGAAT
1 AATTCGAAT
62530287 AATTCGAAT
1 AATTCGAAT
62530296 A
1 A
62530297 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:62530545 original size:30 final size:31
Alignment explanation
Indices: 62530511--62530570 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
62530501 AAACCTTTTA
*
62530511 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
62530541 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
62530571 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:62531213 original size:5 final size:5
Alignment explanation
Indices: 62531203--62531228 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
62531193 GAACAAATAT
62531203 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
62531229 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:62536198 original size:61 final size:61
Alignment explanation
Indices: 62536133--62536252 Score: 152
Period size: 61 Copynumber: 2.0 Consensus size: 61
62536123 TTTGTGAGAT
* * *
62536133 TAATGAGAATTTTC-AAAATTTAAGAGTGCTTAATTAAAATTTTCAAAAAAATTAAAAGGTA
1 TAATGAAAATTTTCAAAAATTT-AGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGGTA
* * * * *
62536194 TAATGAAAATTTTCAAAAATTTTGAGGGCCTAATTGAAATTTTCTAAAAATTTTAAAGG
1 TAATGAAAATTTTCAAAAATTTAGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGG
62536253 AAAAAACAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
61 43 0.86
62 7 0.14
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (61 bp):
TAATGAAAATTTTCAAAAATTTAGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGGTA
Found at i:62536264 original size:61 final size:61
Alignment explanation
Indices: 62536140--62536265 Score: 137
Period size: 61 Copynumber: 2.1 Consensus size: 61
62536130 GATTAATGAG
* * * * **
62536140 AATTTTCAAAATTTAAGAGTGCTTAATTAAAATTTTCAAAAAAATTAAAAGGTATAATGAA
1 AATTTTCAAAATTTAAGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGGAAAAAACAA
* * * * *
62536201 AATTTTCAAAAATTT-TGAGGGCCTAATTGAAATTTTCTAAAAATTTTAAAGGAAAAAACAA
1 AATTTTC-AAAATTTAAGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGGAAAAAACAA
62536262 AATT
1 AATT
62536266 CTTCGATTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 46 0.87
62 7 0.13
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.34
Consensus pattern (61 bp):
AATTTTCAAAATTTAAGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGGAAAAAACAA
Found at i:62537681 original size:21 final size:21
Alignment explanation
Indices: 62537642--62537682 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
62537632 AATTAAGCTC
* * *
62537642 TCAATGTTTATATATTATGTG
1 TCAATGTTAATAGAATATGTG
62537663 TCAATGTTAATAGAATATGT
1 TCAATGTTAATAGAATATGT
62537683 AATTGTTGCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (21 bp):
TCAATGTTAATAGAATATGTG
Found at i:62539939 original size:50 final size:50
Alignment explanation
Indices: 62539862--62539982 Score: 172
Period size: 50 Copynumber: 2.4 Consensus size: 50
62539852 TACAAATTTA
* * * *
62539862 ACTATCAATTGTTTATTGACTATACTTTTAACTCCAC-AAAAAGGGCTAAG
1 ACTATCAATTGTCTATTGACTACAC-TTTAACTCCACAAAAAAAGACTAAG
*
62539912 ACTATCAATTGTCTATTGACTACACTTTAACTCGACAAAAAAAGACTAAG
1 ACTATCAATTGTCTATTGACTACACTTTAACTCCACAAAAAAAGACTAAG
*
62539962 ACTATCAGTTGTCTATTGACT
1 ACTATCAATTGTCTATTGACT
62539983 TCACACTTGC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 10 0.16
50 54 0.84
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (50 bp):
ACTATCAATTGTCTATTGACTACACTTTAACTCCACAAAAAAAGACTAAG
Found at i:62541951 original size:89 final size:89
Alignment explanation
Indices: 62541754--62541952 Score: 280
Period size: 89 Copynumber: 2.3 Consensus size: 89
62541744 TAATAAGAGT
62541754 AGGGGCTTAATTGC-TTTTTTG-AAAAAAAATAAAGGCCTTTTTGATGCATTATGAAAGTTCAAG
1 AGGGGCTTAATTGCTTTTTTTGAAAAAAAAATAAAGGCCTTTTTGATGCATTATGAAAGTTCAAG
* *
62541817 TACCCAATTGAGTGGGAAAAAAAT
66 TACCCAATTGAGTCGGAAAAAAAA
* * * ** *
62541841 AGAGGCTTAATTG-TTTCTTTGAAAAAAAAATTTAAGGTTTTTTTTATGCATTATGAAAGTTCAA
1 AGGGGCTTAATTGCTTTTTTTGAAAAAAAAA-TAAAGGCCTTTTTGATGCATTATGAAAGTTCAA
62541905 GTACCCAATTGAG-CGGAAAAAAAA
65 GTACCCAATTGAGTCGGAAAAAAAA
*
62541929 AGGGGTTTAATTGCTTTTTTTGAA
1 AGGGGCTTAATTGCTTTTTTTGAA
62541953 GAAGTGTAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
87 18 0.19
88 28 0.29
89 51 0.53
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.35
Consensus pattern (89 bp):
AGGGGCTTAATTGCTTTTTTTGAAAAAAAAATAAAGGCCTTTTTGATGCATTATGAAAGTTCAAG
TACCCAATTGAGTCGGAAAAAAAA
Found at i:62541971 original size:89 final size:87
Alignment explanation
Indices: 62541757--62542002 Score: 237
Period size: 89 Copynumber: 2.8 Consensus size: 87
62541747 TAAGAGTAGG
* ***
62541757 GGCTTAATTGCTTT-TTTGAAAAAAAATAAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTACC
1 GGCTTAATTG-TTTCTTTGAAAAAAATTAAAGATTTTTTTGATGCATTATGAAAGTTCAAGTACC
* *
62541821 CAATTGAGTGGGAAAAAAATAGA
65 CAATTGAGTCGGAAAAAAAAAGA
* * *
62541844 GGCTTAATTGTTTCTTTGAAAAAAAAATTTAAGGTTTTTTTTATGCATTATGAAAGTTCAAGTAC
1 GGCTTAATTGTTTCTTTG--AAAAAAATTAAAGATTTTTTTGATGCATTATGAAAGTTCAAGTAC
*
62541909 CCAATTGAG-CGGAAAAAAAAAGG
64 CCAATTGAGTCGGAAAAAAAAAGA
* * * * * * * * * *
62541932 GGTTTAATTGCTTTTTTTG-AAGAAGTGTAAAGATATTTTTGATACATTTTAAAAGTTTAAGTGC
1 GGCTTAATTG-TTTCTTTGAAAAAAAT-TAAAGATTTTTTTGATGCATTATGAAAGTTCAAGTAC
*
62541996 TCAATTG
64 CCAATTG
62542003 GGTAGAAAAA
Statistics
Matches: 132, Mismatches: 22, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
86 8 0.06
87 48 0.36
88 20 0.15
89 56 0.42
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36
Consensus pattern (87 bp):
GGCTTAATTGTTTCTTTGAAAAAAATTAAAGATTTTTTTGATGCATTATGAAAGTTCAAGTACCC
AATTGAGTCGGAAAAAAAAAGA
Found at i:62544311 original size:17 final size:17
Alignment explanation
Indices: 62544289--62544322 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62544279 ATCCACTAAT
*
62544289 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62544306 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62544323 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62547949 original size:17 final size:17
Alignment explanation
Indices: 62547927--62547960 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62547917 ATCCACTAAT
*
62547927 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62547944 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62547961 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62552587 original size:17 final size:17
Alignment explanation
Indices: 62552565--62552598 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62552555 ATCCACTAAT
*
62552565 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62552582 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62552599 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62554052 original size:17 final size:17
Alignment explanation
Indices: 62554030--62554063 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62554020 ATCCACTAAT
*
62554030 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62554047 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62554064 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62556487 original size:54 final size:54
Alignment explanation
Indices: 62556405--62556513 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
62556395 TTAAAATTGG
* * *
62556405 ATGCTTTTTCTTTTAGTAAAATCTTGTATTTCATAAAAACGTTTATACTTTTAT
1 ATGCTTTTTCTTTTAGCAAAATCTTGTATTTCATAAAAACGTGTATACTTATAT
* *
62556459 ATGCTTTTTCTTTTAGCAAGATCTTGTATTTCATAAAAATGTGTATACTTATAT
1 ATGCTTTTTCTTTTAGCAAAATCTTGTATTTCATAAAAACGTGTATACTTATAT
62556513 A
1 A
62556514 AATTCACGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (54 bp):
ATGCTTTTTCTTTTAGCAAAATCTTGTATTTCATAAAAACGTGTATACTTATAT
Found at i:62557381 original size:14 final size:15
Alignment explanation
Indices: 62557362--62557390 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62557352 TAATAAAAAT
62557362 AAAAA-TATTTTTAA
1 AAAAATTATTTTTAA
62557376 AAAAATTATTTTTAA
1 AAAAATTATTTTTAA
62557391 CCCTTTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAAATTATTTTTAA
Found at i:62558005 original size:50 final size:52
Alignment explanation
Indices: 62557921--62558043 Score: 135
Period size: 57 Copynumber: 2.3 Consensus size: 52
62557911 AGTTTGGTCC
*
62557921 CAATTGTCTATTGACTATAAATTTAACTCCAC-AAAAAG-GGCTAAGACTAT
1 CAATTGTCTATTGACTATAAATTTAACTCCACAAAAAAGAGACTAAGACTAT
* * *
62557971 CAATTGTCTATTGACTA-CACTTTAACTCAGACAAAAAAAGACAAAGACTAAGACTAT
1 CAATTGTCTATTGACTATAAATTTAACTC-CAC-AAAAAAG----AGACTAAGACTAT
62558028 CAATTGTCTATTGACT
1 CAATTGTCTATTGACT
62558044 TCACACTTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
49 9 0.15
50 19 0.31
52 6 0.10
57 27 0.44
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (52 bp):
CAATTGTCTATTGACTATAAATTTAACTCCACAAAAAAGAGACTAAGACTAT
Found at i:62561286 original size:61 final size:61
Alignment explanation
Indices: 62561166--62561288 Score: 140
Period size: 61 Copynumber: 2.0 Consensus size: 61
62561156 AATATATATA
* * * * *
62561166 TATTAAAATTTTTAGAATTAGAACTAAATTGCTAATTTTTGAAAATATTAAGGGTTAAATT
1 TATTAAAATTTTTAGAATTAGAACTAAAATGCCAAGTTTTGAAAACATTAAGGGCTAAATT
* * ** *
62561227 TATTAAATTTTTTAGAATTTGAACTAAAAT-CACAAGTTTTGTTAACATTCAGGGCTAAATT
1 TATTAAAATTTTTAGAATTAGAACTAAAATGC-CAAGTTTTGAAAACATTAAGGGCTAAATT
62561288 T
1 T
62561289 GTTGATTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 1 0.02
61 50 0.98
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (61 bp):
TATTAAAATTTTTAGAATTAGAACTAAAATGCCAAGTTTTGAAAACATTAAGGGCTAAATT
Found at i:62561465 original size:21 final size:21
Alignment explanation
Indices: 62561439--62561478 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
62561429 ATATTTACTT
62561439 TCGAAAAGGTTAACAACTAAA
1 TCGAAAAGGTTAACAACTAAA
62561460 TCGAAAAGGTTAACAACTA
1 TCGAAAAGGTTAACAACTA
62561479 CTTCCTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (21 bp):
TCGAAAAGGTTAACAACTAAA
Found at i:62561867 original size:24 final size:24
Alignment explanation
Indices: 62561840--62561886 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
62561830 TACCAATGCA
62561840 ACTTTTCACCATAGGAAAAACTTC
1 ACTTTTCACCATAGGAAAAACTTC
62561864 ACTTTTCACCATAGGAAAAACTT
1 ACTTTTCACCATAGGAAAAACTT
62561887 TCTGATAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (24 bp):
ACTTTTCACCATAGGAAAAACTTC
Found at i:62563777 original size:26 final size:26
Alignment explanation
Indices: 62563741--62563793 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
62563731 TAAATTACAC
62563741 TTTATATTTATAAAAGTTTATTCATA
1 TTTATATTTATAAAAGTTTATTCATA
62563767 TTTATATTTATAAAAGTTTATTCATA
1 TTTATATTTATAAAAGTTTATTCATA
62563793 T
1 T
62563794 AATTTTTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTATATTTATAAAAGTTTATTCATA
Found at i:62564489 original size:79 final size:79
Alignment explanation
Indices: 62564358--62564517 Score: 320
Period size: 79 Copynumber: 2.0 Consensus size: 79
62564348 ATCCACATAA
62564358 TCCCTTGTTTCCTTCATATGAATCATTTCCAAATGTGTTGAACTGTTTGCCTTGAGGAATCTGAC
1 TCCCTTGTTTCCTTCATATGAATCATTTCCAAATGTGTTGAACTGTTTGCCTTGAGGAATCTGAC
62564423 CATGGAGTTTATTT
66 CATGGAGTTTATTT
62564437 TCCCTTGTTTCCTTCATATGAATCATTTCCAAATGTGTTGAACTGTTTGCCTTGAGGAATCTGAC
1 TCCCTTGTTTCCTTCATATGAATCATTTCCAAATGTGTTGAACTGTTTGCCTTGAGGAATCTGAC
62564502 CATGGAGTTTATTT
66 CATGGAGTTTATTT
62564516 TC
1 TC
62564518 AGAAACATTG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (79 bp):
TCCCTTGTTTCCTTCATATGAATCATTTCCAAATGTGTTGAACTGTTTGCCTTGAGGAATCTGAC
CATGGAGTTTATTT
Found at i:62567773 original size:61 final size:61
Alignment explanation
Indices: 62567653--62567775 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 61
62567643 TTTAAATATA
* * * *
62567653 TATTAAAATTTTTAGAATTAGAACTAAATTGCTAATTTTTGAAAATATTAAGGGTTAAATT
1 TATTAAAATTTTTAGAATTAGAACTAAAATGCTAAGTTTTGAAAACATTAAGGGCTAAATT
* ** *
62567714 TATTAAAATTTTTAGAATTTGAACTAAAATGAC-AAGTTTTGTTAACATTTAGGGCTAAATT
1 TATTAAAATTTTTAGAATTAGAACTAAAATG-CTAAGTTTTGAAAACATTAAGGGCTAAATT
62567775 T
1 T
62567776 GTTATTAGAC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 52 0.98
62 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (61 bp):
TATTAAAATTTTTAGAATTAGAACTAAAATGCTAAGTTTTGAAAACATTAAGGGCTAAATT
Found at i:62579474 original size:61 final size:61
Alignment explanation
Indices: 62579409--62579528 Score: 161
Period size: 61 Copynumber: 2.0 Consensus size: 61
62579399 TTTGTGAGAT
* * *
62579409 TAATGAGAATTTTC-AAAATTTAAGAGTGCTTAATTAAAATTTTTTAAAAAATTAAAAGGTA
1 TAATGAAAATTTTCAAAAATTT-AGAGGGCTTAATTAAAATTTTCTAAAAAATTAAAAGGTA
* * * *
62579470 TAATGAAAATTTTCAAAAATTTTGAGGGCTTAATTGAAATTTTCTAAAAATTTTAAAGG
1 TAATGAAAATTTTCAAAAATTTAGAGGGCTTAATTAAAATTTTCTAAAAAATTAAAAGG
62579529 AAAAAACAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 44 0.86
62 7 0.14
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.38
Consensus pattern (61 bp):
TAATGAAAATTTTCAAAAATTTAGAGGGCTTAATTAAAATTTTCTAAAAAATTAAAAGGTA
Found at i:62579540 original size:61 final size:61
Alignment explanation
Indices: 62579416--62579541 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 61
62579406 GATTAATGAG
* * * * **
62579416 AATTTTCAAAATTTAAGAGTGCTTAATTAAAATTTTTTAAAAAATTAAAAGGTATAATGAA
1 AATTTTCAAAATTTAAGAGGGCTTAATTAAAATTTTCTAAAAAATTAAAAGGAAAAAACAA
* * * *
62579477 AATTTTCAAAAATTT-TGAGGGCTTAATTGAAATTTTCTAAAAATTTTAAAGGAAAAAACAA
1 AATTTTC-AAAATTTAAGAGGGCTTAATTAAAATTTTCTAAAAAATTAAAAGGAAAAAACAA
62579538 AATT
1 AATT
62579542 CTCCAATTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 47 0.87
62 7 0.13
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (61 bp):
AATTTTCAAAATTTAAGAGGGCTTAATTAAAATTTTCTAAAAAATTAAAAGGAAAAAACAA
Found at i:62579708 original size:62 final size:61
Alignment explanation
Indices: 62579626--62579750 Score: 178
Period size: 62 Copynumber: 2.0 Consensus size: 61
62579616 TATCAAGTAT
* * *
62579626 CATAATAAAATATATATTGATAGTTTAGGTACCACATTAAACATTTTCAAAGTACATGTAC
1 CATAATAAAACACATATTGATAGTTCAGGTACCACATTAAACATTTTCAAAGTACATGTAC
* * * *
62579687 CATAATAATAACACATATTGATAGTTCAGGTGCCACATTATATATTTTCAAAGTACTTGTAC
1 CATAATAA-AACACATATTGATAGTTCAGGTACCACATTAAACATTTTCAAAGTACATGTAC
62579749 CA
1 CA
62579751 CTAGACATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
61 8 0.14
62 48 0.86
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.34
Consensus pattern (61 bp):
CATAATAAAACACATATTGATAGTTCAGGTACCACATTAAACATTTTCAAAGTACATGTAC
Found at i:62585554 original size:85 final size:85
Alignment explanation
Indices: 62585378--62585533 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
62585368 CCTTAATTGC
* * *
62585378 TTTTTGATGCATTATGAAAGTTCAAGTACCCAATTGAGTGGAAAAAAAATAGAGGCTTAATTGTT
1 TTTTTGATGCATTATGAAAGTTCAAGCACCCAATTGAGTCGAAAAAAAATAGAGGCTTAATCGTT
* *
62585443 TCTTTGAAAAAAAAAAGGTC
66 TCTTTGAAAAAAAAAAGATA
*
62585463 TTTTTGATGCATTATGAAAGTTCAAGCACCCAATTGAG-CGAAAAAAAA-AGA-GTTTAATCGCT
1 TTTTTGATGCATTATGAAAGTTCAAGCACCCAATTGAGTCGAAAAAAAATAGAGGCTTAATCG-T
*
62585525 TTTTTTGAA
65 TTCTTTGAA
62585534 GAAGTGTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
82 7 0.11
83 12 0.18
84 9 0.14
85 37 0.57
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (85 bp):
TTTTTGATGCATTATGAAAGTTCAAGCACCCAATTGAGTCGAAAAAAAATAGAGGCTTAATCGTT
TCTTTGAAAAAAAAAAGATA
Found at i:62590110 original size:61 final size:61
Alignment explanation
Indices: 62589976--62590098 Score: 151
Period size: 61 Copynumber: 2.0 Consensus size: 61
62589966 TATATGTATA
* * * *
62589976 TATTAAAATTTTTAGAATTAGAACTAAATCGCTAATTTTTGATAATATTAAGGGTTAAATT
1 TATTAAATTTTTTAGAATTAGAACTAAATCGCTAAGTTTTGATAACATTAAGGGCTAAATT
* * *
62590037 TATTAAATTTTTTAGAATTTGAACTAAAAT-GAC-AAGTTTTGTTAACATTCAGGGCTAAATT
1 TATTAAATTTTTTAGAATTAGAACT-AAATCG-CTAAGTTTTGATAACATTAAGGGCTAAATT
62590098 T
1 T
62590099 TTTGATTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 48 0.91
62 5 0.09
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (61 bp):
TATTAAATTTTTTAGAATTAGAACTAAATCGCTAAGTTTTGATAACATTAAGGGCTAAATT
Found at i:62591619 original size:21 final size:22
Alignment explanation
Indices: 62591593--62591647 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
62591583 AACAGCGGTG
62591593 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTGTA
62591614 GCGGTGAGATT-GGATACTGTA
1 GCGGTGAGATTAGGATACTGTA
62591635 GCGGTGAGATTAG
1 GCGGTGAGATTAG
62591648 AAACAGCGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.24, C:0.09, G:0.40, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTGTA
Found at i:62591782 original size:19 final size:18
Alignment explanation
Indices: 62591758--62591804 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
62591748 TAGAAGTTTT
*
62591758 AAAATTATTTAACAATTA
1 AAAATTATTAAACAATTA
* *
62591776 CAAAATTAATAAATAATTA
1 -AAAATTATTAAACAATTA
62591795 AAAATTATTA
1 AAAATTATTA
62591805 CAATTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTATTAAACAATTA
Found at i:62591907 original size:36 final size:34
Alignment explanation
Indices: 62591866--62591974 Score: 100
Period size: 36 Copynumber: 3.5 Consensus size: 34
62591856 GAAAAATTCA
62591866 AAAATATCAAAATATTTTACAGATTATATTCATAAT
1 AAAATATCAAAATATTTTA-A-ATTATATTCATAAT
*
62591902 AAAATATGAAAATATTTTAAA-TATA--C--AAT
1 AAAATATCAAAATATTTTAAATTATATTCATAAT
62591931 -AAA-AT----AT--TTTAAATTATATTCATAAT
1 AAAATATCAAAATATTTTAAATTATATTCATAAT
62591957 AAAATATCAAAATATTTT
1 AAAATATCAAAATATTTT
62591975 TACAGATTAT
Statistics
Matches: 59, Mismatches: 1, Indels: 28
0.67 0.01 0.32
Matches are distributed among these distances:
21 6 0.10
22 4 0.07
23 2 0.03
24 1 0.02
26 3 0.05
27 5 0.08
28 5 0.08
29 3 0.05
31 1 0.02
32 2 0.03
33 4 0.07
34 4 0.07
35 1 0.02
36 18 0.31
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (34 bp):
AAAATATCAAAATATTTTAAATTATATTCATAAT
Found at i:62592005 original size:36 final size:34
Alignment explanation
Indices: 62591928--62592007 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 34
62591918 TTAAATATAC
62591928 AATAAAATA-TTTTAAATTATATTCATAATAAAAT
1 AATAAAATATTTTTAAATTATATT-ATAATAAAAT
*
62591962 -ATCAAAATATTTTTACAGATTATATT-TGAATCAAAT
1 AAT-AAAATATTTTTA-A-ATTATATTAT-AATAAAAT
62591998 AATAAAATAT
1 AATAAAATAT
62592008 AAATTAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
33 2 0.05
34 6 0.15
35 6 0.15
36 15 0.38
37 10 0.26
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (34 bp):
AATAAAATATTTTTAAATTATATTATAATAAAAT
Found at i:62594902 original size:62 final size:61
Alignment explanation
Indices: 62594806--62594927 Score: 190
Period size: 62 Copynumber: 2.0 Consensus size: 61
62594796 GCCAAGTATC
* *
62594806 ATAATAAAACATATATTGATAGTTTAGGTACCACATTAAACATTTTCAAAGTACATGTACT
1 ATAATAAAACACATATTGATAGTTCAGGTACCACATTAAACATTTTCAAAGTACATGTACT
* * *
62594867 ATAATAATAACACATATTGATAGTTCAGGTACCACATTATATATTTTCAAAGTACTTGTAC
1 ATAATAA-AACACATATTGATAGTTCAGGTACCACATTAAACATTTTCAAAGTACATGTAC
62594928 CACTAGACAT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
61 7 0.13
62 48 0.87
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (61 bp):
ATAATAAAACACATATTGATAGTTCAGGTACCACATTAAACATTTTCAAAGTACATGTACT
Found at i:62597240 original size:28 final size:29
Alignment explanation
Indices: 62597200--62597261 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
62597190 ATTTCCCTGA
*
62597200 TTTTCTCTCACTTT-ATTTATATTTGAAAT
1 TTTTATCTCACTTTCATTTA-ATTTGAAAT
**
62597229 TTTTATCT-ACTTTCATTTAATTTTTAAT
1 TTTTATCTCACTTTCATTTAATTTGAAAT
62597257 TTTTA
1 TTTTA
62597262 GAATTTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTATCTCACTTTCATTTAATTTGAAAT
Found at i:62602226 original size:72 final size:72
Alignment explanation
Indices: 62602145--62602287 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 72
62602135 TTGACAATGG
*
62602145 AATTTGTCCACTCAATTGGTTCTGCC-ACAAGTCTAAATGAGTGAGTTGCAAAAGGTTCCCCAAT
1 AATTTGTCCACTCAATTGGTTC-ACCGACAAGTCTAAATGAGTGAGTTGCAAAAGGTTCCCCAAT
62602209 GATCTTGA
65 GATCTTGA
* *
62602217 AATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCAGTG
1 AATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAAAGGTTCCCCAATG
62602282 ATCTTG
66 ATCTTG
62602288 GAACCGGTCC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
71 2 0.03
72 65 0.97
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (72 bp):
AATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAAAGGTTCCCCAATG
ATCTTGA
Found at i:62609275 original size:21 final size:21
Alignment explanation
Indices: 62609233--62609275 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
62609223 GGTCAGCCTA
* *
62609233 TTGTTAAATGACACTTTGTAG
1 TTGTTAAATAACAATTTGTAG
62609254 TTGTTATAATAACAATTT-TAG
1 TTGTTA-AATAACAATTTGTAG
62609275 T
1 T
62609276 ATTTTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (21 bp):
TTGTTAAATAACAATTTGTAG
Found at i:62610146 original size:20 final size:21
Alignment explanation
Indices: 62610123--62610161 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
62610113 TTCTAATTCT
*
62610123 AAAT-TTTTAATAAAAAATAA
1 AAATATTTTAAAAAAAAATAA
62610143 AAATATTTTAAAAAAAAAT
1 AAATATTTTAAAAAAAAAT
62610162 CATTTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATTTTAAAAAAAAATAA
Found at i:62610161 original size:15 final size:17
Alignment explanation
Indices: 62610136--62610167 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
62610126 TTTTTAATAA
62610136 AAAATAAAAAT-ATTTT
1 AAAATAAAAATCATTTT
62610152 AAAA-AAAAATCATTTT
1 AAAATAAAAATCATTTT
62610168 TAACACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATAAAAATCATTTT
Found at i:62612902 original size:99 final size:99
Alignment explanation
Indices: 62612740--62612923 Score: 273
Period size: 99 Copynumber: 1.9 Consensus size: 99
62612730 GTTCTTTTTA
* ***
62612740 TGCACTCATTTGGGTACTTGAACTTTCAAAATACATCAAAAAAGCCCTCAAACATTTTCAAAAAA
1 TGCACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAAGCCCTCAAACATTAAAAAAAAA
* *
62612805 AGCAATTAAGCCCCTACTTTTTTTCTTTTTGTTT
66 AGCAATTAACCCCCTAATTTTTTTCTTTTTGTTT
* *
62612839 TGCAGTCAATTGGGTACTTGAACTTTCAAAATGCATC-AAAAAGACCCTCAAAC-TTAAAAAAAA
1 TGCACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAAG-CCCTCAAACATTAAAAAAAA
62612902 AAGCAATTAACCCCCTAATTTT
65 AAGCAATTAACCCCCTAATTTT
62612924 ATTAAAAATT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
98 33 0.43
99 43 0.57
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.32
Consensus pattern (99 bp):
TGCACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAAGCCCTCAAACATTAAAAAAAAA
AGCAATTAACCCCCTAATTTTTTTCTTTTTGTTT
Found at i:62613021 original size:10 final size:10
Alignment explanation
Indices: 62612991--62613086 Score: 53
Period size: 9 Copynumber: 10.2 Consensus size: 10
62612981 ATAAAAAATC
62612991 AAATAT-TAA
1 AAATATATAA
*
62613000 AAATTTATTAA
1 AAATATA-TAA
62613011 AAATATAT-A
1 AAATATATAA
*
62613020 AAAT-TGTAA
1 AAATATATAA
* *
62613029 AATTTTATAA
1 AAATATATAA
*
62613039 AAAT-TTTAA
1 AAATATATAA
* *
62613048 AAA-ATTTTA
1 AAATATATAA
62613057 AAATATAT-A
1 AAATATATAA
*
62613066 GAA-ATATAA
1 AAATATATAA
*
62613075 AAATTTATAA
1 AAATATATAA
62613085 AA
1 AA
62613087 TTTTATAAAG
Statistics
Matches: 67, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
8 6 0.09
9 34 0.51
10 18 0.27
11 9 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
AAATATATAA
Found at i:62613070 original size:18 final size:17
Alignment explanation
Indices: 62613048--62613091 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
62613038 AAAATTTTAA
62613048 AAAATTTTAAAATATAT
1 AAAATTTTAAAATATAT
* * *
62613065 AGAAATATAAAAATTTAT
1 A-AAATTTTAAAATATAT
62613083 AAAATTTTA
1 AAAATTTTA
62613092 TAAAGTTATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AAAATTTTAAAATATAT
Found at i:62613076 original size:46 final size:47
Alignment explanation
Indices: 62612991--62613100 Score: 127
Period size: 46 Copynumber: 2.4 Consensus size: 47
62612981 ATAAAAAATC
* * * *
62612991 AAATATTAAAAATTTATTAAAAATATATAAAATTGTAAAATTTTATAA
1 AAATTTTAAAAAATTATTAAAAATATATAAAATTATAAAAATTTAT-A
62613039 AAATTTTAAAAAATT-TT-AAAATATATAGAAA-TATAAAAATTTATA
1 AAATTTTAAAAAATTATTAAAAATATATA-AAATTATAAAAATTTATA
* *
62613084 AAATTTTATAAAGTTAT
1 AAATTTTAAAAAATTAT
62613101 AAGAAAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
45 14 0.26
46 22 0.41
47 5 0.09
48 13 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (47 bp):
AAATTTTAAAAAATTATTAAAAATATATAAAATTATAAAAATTTATA
Found at i:62613091 original size:10 final size:10
Alignment explanation
Indices: 62613026--62613095 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
62613016 TATAAAATTG
62613026 TAAAATTTTA
1 TAAAATTTTA
62613036 TAAAAATTTTA
1 T-AAAATTTTA
*
62613047 -AAAAATTT-
1 TAAAATTTTA
*
62613055 TAAAA-TATA
1 TAAAATTTTA
62613064 TAGAAA---TA
1 TA-AAATTTTA
*
62613072 TAAAAATTTA
1 TAAAATTTTA
62613082 TAAAATTTTA
1 TAAAATTTTA
62613092 TAAA
1 TAAA
62613096 GTTATAAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
7 3 0.06
8 6 0.12
9 13 0.26
10 19 0.38
11 9 0.18
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (10 bp):
TAAAATTTTA
Found at i:62613171 original size:28 final size:28
Alignment explanation
Indices: 62613140--62613193 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
62613130 TAAATTTTGT
62613140 AAAA-AAA-ATTTATAAAAATTATTCTACC
1 AAAAGAAATATTT-TAAAAATT-TTCTACC
*
62613168 AAAAGAAATATTTTATAAATTTTCTA
1 AAAAGAAATATTTTAAAAATTTTCTA
62613194 TAACTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 9 0.39
29 10 0.43
30 4 0.17
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (28 bp):
AAAAGAAATATTTTAAAAATTTTCTACC
Found at i:62613421 original size:18 final size:19
Alignment explanation
Indices: 62613385--62613422 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
62613375 AAAAAATTCT
*
62613385 AATTTTTAATCAAATTTTA
1 AATTTTTAATCAAAATTTA
*
62613404 AATTTTT-ATTAAAATTTA
1 AATTTTTAATCAAAATTTA
62613422 A
1 A
62613423 TAAATTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTTTTAATCAAAATTTA
Found at i:62613436 original size:20 final size:21
Alignment explanation
Indices: 62613385--62613441 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 21
62613375 AAAAAATTCT
* *
62613385 AATTTTTAATCAAATTT--TA
1 AATTTTTACTAAAATTTAATA
*
62613404 AATTTTTATTAAAATTTAATA
1 AATTTTTACTAAAATTTAATA
62613425 AATTTTT-CTAAAATTTA
1 AATTTTTACTAAAATTTA
62613442 TTATTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.45
20 9 0.27
21 9 0.27
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTTTTACTAAAATTTAATA
Found at i:62613559 original size:69 final size:70
Alignment explanation
Indices: 62613483--62613622 Score: 205
Period size: 70 Copynumber: 2.0 Consensus size: 70
62613473 TAAGAGTAGG
62613483 GGCTTAATTGCTTT-TTTG-AAAAAAATTTAAGGCAT-TTTTGATGCATTATGAAAGTTCAAGTA
1 GGCTTAATTG-TTTCTTTGAAAAAAAATTTAAGG-ATCTTTTGATGCATTATGAAAGTTCAAGTA
62613545 CCCAATT
64 CCCAATT
* * * *
62613552 GGCTTAATTGTTTCTTTGAAAAAAAATTTAAGGTTCTTTTGTTTCATTATGAAAGTTTAAGTACC
1 GGCTTAATTGTTTCTTTGAAAAAAAATTTAAGGATCTTTTGATGCATTATGAAAGTTCAAGTACC
62613617 CAATT
66 CAATT
62613622 G
1 G
62613623 AGCGGAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
68 3 0.05
69 15 0.23
70 46 0.72
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (70 bp):
GGCTTAATTGTTTCTTTGAAAAAAAATTTAAGGATCTTTTGATGCATTATGAAAGTTCAAGTACC
CAATT
Found at i:62624100 original size:89 final size:89
Alignment explanation
Indices: 62623946--62624139 Score: 275
Period size: 89 Copynumber: 2.2 Consensus size: 89
62623936 TTTAAGGGTG
* * * *
62623946 CAAAAA-GCCCTCAAACTTTTTCAAAAATAGCAACTAAACCCCTTTTTTTTTTTGCACTCATTTG
1 CAAAAAGGCCCTCAAACCTTTTCAAAAAAAGCAACTAAACCCCTCTTTTTTTTTGCACTCAATTG
62624010 GGTACTTAAACTTTCAAAATACAT
66 GGTACTTAAACTTTCAAAATACAT
** *
62624034 CAAAAAGGCCCTCAAACCTTTTCAAAAAAAGCAGTTAAGCCCCTACTTTTTTTTT-CACTCAATT
1 CAAAAAGGCCCTCAAACCTTTTCAAAAAAAGCAACTAAACCCCT-CTTTTTTTTTGCACTCAATT
* *
62624098 GGGTACTTGAACTTTCAAAATGCAT
65 GGGTACTTAAACTTTCAAAATACAT
*
62624123 CAAAAAGACCCTCAAAC
1 CAAAAAGGCCCTCAAAC
62624140 ATAAAAAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
88 6 0.06
89 79 0.84
90 9 0.10
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (89 bp):
CAAAAAGGCCCTCAAACCTTTTCAAAAAAAGCAACTAAACCCCTCTTTTTTTTTGCACTCAATTG
GGTACTTAAACTTTCAAAATACAT
Found at i:62624256 original size:11 final size:11
Alignment explanation
Indices: 62624242--62624302 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 11
62624232 AAATTTAAAA
62624242 TATTAAAAATT
1 TATTAAAAATT
*
62624253 TATTAAAAATA
1 TATTAAAAATT
62624264 TA-TAAAAA-T
1 TATTAAAAATT
* *
62624273 T-GTAAAATTT
1 TATTAAAAATT
62624283 TA-TAAAAATT
1 TATTAAAAATT
*
62624293 T-TAAAAAATT
1 TATTAAAAATT
62624303 ATAAAATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 6 0.15
10 23 0.56
11 12 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TATTAAAAATT
Found at i:62624260 original size:19 final size:18
Alignment explanation
Indices: 62624235--62624329 Score: 66
Period size: 19 Copynumber: 5.0 Consensus size: 18
62624225 TTTAATAAAA
62624235 TTTAAAATATTAAAAATT
1 TTTAAAATATTAAAAATT
62624253 TATTAAAAATATATAAAAA-T
1 T-TT-AAAATAT-TAAAAATT
* * *
62624273 TGTAAAATTTTATAAAAAT
1 TTTAAAATATTA-AAAATT
* *
62624292 TTTAAAAAATTATAAAATA
1 TTTAAAATATTA-AAAATT
* *
62624311 TATAGAAATATAAAAAATT
1 TTTA-AAATATTAAAAATT
62624330 ATGAAATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
17 2 0.03
18 11 0.18
19 26 0.43
20 15 0.25
21 6 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TTTAAAATATTAAAAATT
Found at i:62624269 original size:10 final size:10
Alignment explanation
Indices: 62624238--62624328 Score: 68
Period size: 9 Copynumber: 9.5 Consensus size: 10
62624228 AATAAAATTT
62624238 AAAATAT-TA
1 AAAATATATA
*
62624247 AAAATTTATTA
1 AAAATATA-TA
62624258 AAAATATATA
1 AAAATATATA
*
62624268 AAAAT-TGTA
1 AAAATATATA
* *
62624277 AAATTTTATA
1 AAAATATATA
*
62624287 AAAAT-TTTA
1 AAAATATATA
62624296 AAAA-AT-TA
1 AAAATATATA
62624304 TAAAATATATA
1 -AAAATATATA
*
62624315 GAAATATA-A
1 AAAATATATA
62624324 AAAAT
1 AAAAT
62624329 TATGAAATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
8 2 0.03
9 30 0.45
10 23 0.35
11 11 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
AAAATATATA
Found at i:62624270 original size:29 final size:29
Alignment explanation
Indices: 62624237--62624328 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
62624227 TAATAAAATT
62624237 TAAAATATTAAAAATTTATTAAAAATATA
1 TAAAATATTAAAAATTTATTAAAAATATA
* *
62624266 TAAAA-ATTGTAAAATTT-TATAAAAAT-TT
1 TAAAATATT-AAAAATTTAT-TAAAAATATA
* * *
62624294 TAAAAAATTATAAAATATA-TAGAAATATA
1 TAAAATATTA-AAAATTTATTAAAAATATA
*
62624323 AAAAAT
1 TAAAAT
62624329 TATGAAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
28 16 0.33
29 33 0.67
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
TAAAATATTAAAAATTTATTAAAAATATA
Found at i:62624291 original size:56 final size:56
Alignment explanation
Indices: 62624215--62624344 Score: 158
Period size: 56 Copynumber: 2.3 Consensus size: 56
62624205 AATCAATAAT
* * *
62624215 ATTATTAAATTTTA-ATAAAA-TTTAAAATATTA-AAAATTTATTAAAAATATATAAAA
1 ATTATAAAATTTTATA-AAAATTTTAAAAAATTATAAAATATA-TAAAAATATA-AAAA
* *
62624271 ATTGTAAAATTTTATAAAAATTTTAAAAAATTATAAAATATATAGAAATATAAAAA
1 ATTATAAAATTTTATAAAAATTTTAAAAAATTATAAAATATATAAAAATATAAAAA
*
62624327 ATTATGAAATTTTATAAA
1 ATTATAAAATTTTATAAA
62624345 GTCATAAGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
56 36 0.56
57 21 0.33
58 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (56 bp):
ATTATAAAATTTTATAAAAATTTTAAAAAATTATAAAATATATAAAAATATAAAAA
Found at i:62624357 original size:56 final size:57
Alignment explanation
Indices: 62624259--62624382 Score: 144
Period size: 56 Copynumber: 2.2 Consensus size: 57
62624249 AATTTATTAA
* ** *
62624259 AAATATATAAAAATTGTAAAATTTTATAAAAATTTTAAAAAATTAT-AAAATATATAG
1 AAATATA-AAAAATTATAAAATTTTATAAAAATCATAAAAAATTATAAAAATATAAAG
* * *
62624316 AAATATAAAAAATTATGAAATTTTAT-AAAGTCATAAGAAAATTATACAAAATGTAAAG
1 AAATATAAAAAATTATAAAATTTTATAAAAATCATAA-AAAATTATA-AAAATATAAAG
62624374 AAATATAAA
1 AAATATAAA
62624383 TTTTTTATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
55 7 0.12
56 25 0.44
57 7 0.12
58 18 0.32
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (57 bp):
AAATATAAAAAATTATAAAATTTTATAAAAATCATAAAAAATTATAAAAATATAAAG
Done.