Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 388 of 410
Found at i:117649508 original size:126 final size:126
Alignment explanation
Indices: 117649270--117649520 Score: 367
Period size: 126 Copynumber: 2.0 Consensus size: 126
117649260 TATTTTGACC
* * * *
117649270 CTGAAAAAATAATTTTAAGAAGACGTTTCTGAACCAGTAGTATCAAAAACGTTTCAAGAAGAATG
1 CTGAAAAAATAATTTTAAGAAGACATTTCTGAACAAATAGTATCAAAAACGCTTCAAGAAGAATG
* * ** * *
117649335 CATTGTCAACAAAATTACAGAAAAATGTTCTCATGTGGACACTCTTTTTCTACAGTAGTTA
66 CATTGTCAACAAAATTACAGAAAAATGCTCCCACATAGACACCCTTTTTCTACAGTAGTTA
* * *
117649396 CTGAAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGTATG
1 CTGAAAAAATAATTTTAAGAAGACATTTCTGAACAAATAGTATCAAAAACGCTTCAAGAAGAATG
* *
117649461 CATTGTCAGCAAAATTACAGAAAAATGCTCCCACATAGACGCCCTTTTTCTACAGTAGTT
66 CATTGTCAACAAAATTACAGAAAAATGCTCCCACATAGACACCCTTTTTCTACAGTAGTT
117649521 CATGCTTGGC
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
126 110 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (126 bp):
CTGAAAAAATAATTTTAAGAAGACATTTCTGAACAAATAGTATCAAAAACGCTTCAAGAAGAATG
CATTGTCAACAAAATTACAGAAAAATGCTCCCACATAGACACCCTTTTTCTACAGTAGTTA
Found at i:117651582 original size:26 final size:26
Alignment explanation
Indices: 117651553--117651636 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 26
117651543 ATAAAAAATT
*
117651553 ATAAAATAAAAATTAATTAAAATTAC
1 ATAAAATAAAAATTAAATAAAATTAC
*
117651579 ATAAATGATAAAATATTAAATAATATT-C
1 ATAAA--ATAAAA-ATTAAATAAAATTAC
* *
117651607 A-AAAATTAAAATTAACTAAAATTAC
1 ATAAAATAAAAATTAAATAAAATTAC
117651632 ATAAA
1 ATAAA
117651637 TGAAAAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
24 11 0.23
25 7 0.15
26 8 0.17
27 3 0.06
28 8 0.17
29 11 0.23
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.31
Consensus pattern (26 bp):
ATAAAATAAAAATTAAATAAAATTAC
Found at i:117651635 original size:53 final size:54
Alignment explanation
Indices: 117651555--117651672 Score: 184
Period size: 54 Copynumber: 2.2 Consensus size: 54
117651545 AAAAAATTAT
* * *
117651555 AAAATAAAAATTAATTAAAATTACATAAATG-ATAAAATATTAAATAATATTCA
1 AAAATTAAAATTAACTAAAATTACATAAATGAAAAAAATATTAAATAATATTCA
*
117651608 AAAATTAAAATTAACTAAAATTACATAAATGAAAAAAATATTAAATAATATTTA
1 AAAATTAAAATTAACTAAAATTACATAAATGAAAAAAATATTAAATAATATTCA
*
117651662 AAATTTAAAAT
1 AAAATTAAAAT
117651673 AAACCATTAC
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
53 29 0.49
54 30 0.51
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (54 bp):
AAAATTAAAATTAACTAAAATTACATAAATGAAAAAAATATTAAATAATATTCA
Found at i:117654922 original size:12 final size:12
Alignment explanation
Indices: 117654905--117654929 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
117654895 AAAATTGAAA
117654905 AAATTTTAAAAT
1 AAATTTTAAAAT
117654917 AAATTTTAAAAT
1 AAATTTTAAAAT
117654929 A
1 A
117654930 CGATCCATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTTTAAAAT
Found at i:117655509 original size:25 final size:23
Alignment explanation
Indices: 117655481--117655763 Score: 160
Period size: 24 Copynumber: 11.4 Consensus size: 23
117655471 AATTGAAGAC
117655481 AAATGAATA-AAAAATATTTAAAAGT
1 AAAT-AATATAAAAA-ATTTAAAA-T
**
117655506 AAATAATATAACAAGGTTTAAAAT
1 AAATAATATAA-AAAATTTAAAAT
* *
117655530 AAATGATA-AATGAAACCATTTAAAGT
1 AAATAATATAA--AAA--ATTTAAAAT
* *
117655556 AAAAAATATAAAAAGTTTAAAAT
1 AAATAATATAAAAAATTTAAAAT
117655579 AAATAATATATAAAAAATTTAAAAT
1 AAAT-A-ATATAAAAAATTTAAAAT
** * *
117655604 AAATAAAATATGAAATGATTCAGAAT
1 AAAT--AATAT-AAAAAATTTAAAAT
* * *
117655630 AAACAATATATATAAATTCTAACAT
1 AAATAATATA-AAAAATT-TAAAAT
*
117655655 AAATAAAATATAAAACAATTTGAAAT
1 AAAT--AATATAAAA-AATTTAAAAT
* *
117655681 AAATAATTTATAAAGCAATTTAAAGT
1 AAATAA--TATAAA-AAATTTAAAAT
117655707 AAATAATATAAAATAATTTAAAA-
1 AAATAATATAAAA-AATTTAAAAT
*
117655730 ATAATAATACAAAACAGA-TTAAAAT
1 A-AATAATATAAAA-A-ATTTAAAAT
117655755 AAATAATAT
1 AAATAATAT
117655764 GATAAAACAA
Statistics
Matches: 200, Mismatches: 36, Indels: 45
0.71 0.13 0.16
Matches are distributed among these distances:
23 14 0.07
24 65 0.32
25 49 0.25
26 60 0.30
27 12 0.06
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (23 bp):
AAATAATATAAAAAATTTAAAAT
Found at i:117655682 original size:51 final size:49
Alignment explanation
Indices: 117655491--117656044 Score: 192
Period size: 50 Copynumber: 11.0 Consensus size: 49
117655481 AAATGAATAA
** * *
117655491 AAAATATTTAAAAGTAAAT--AATATAACAAGGTTTAAAATAAATGATAAAT
1 AAAA-ATTTAAAA-TAAATAAAATATAA-AAAATTTAAAATAAATAATATAT
* * *
117655541 GAAACCATTTAAAGT-AA-AAAATATAAAAAGTTTAAAATAAATAATATAT
1 -AAA-AATTTAAAATAAATAAAATATAAAAAATTTAAAATAAATAATATAT
** * * *
117655590 AAAAAATTTAAAATAAATAAAATATGAAATGATTCAGAATAAACAATATAT
1 -AAAAATTTAAAATAAATAAAATAT-AAAAAATTTAAAATAAATAATATAT
* * * *
117655641 ATAAATTCTAACATAAATAAAATATAAAACAATTTGAAATAAATAATTTAT
1 AAAAATT-TAAAATAAATAAAATATAAAA-AATTTAAAATAAATAATATAT
* *
117655692 AAAGCAATTTAAAGTAAAT--AATATAAAATAATTTAAAA-ATAATAATACA-
1 AAA--AATTTAAAATAAATAAAATATAAAA-AATTTAAAATA-AATAATATAT
* * * *
117655741 AAACAGA-TTAAAATAAATAATATGATAAAACAAATACTATATGAAA-AAA-ACTTTAA
1 AAA-A-ATTTAAAATAAATAAAAT-AT-AAA-AAAT--T-TA--AAATAAATAATATAT
** * *
117655797 AAAAATAAACAAATAAAATAAAA-A-AATAAAATTGTTCAAAATAAATACTAT-G
1 AAAAATTTA-AAATAA-ATAAAATATAA-AAAA-T-TT-AAAATAAATAATATAT
* * * * * * *
117655849 AAAGATTTATAATAAATGAAATA-AATAAGTTTAAAAATGAATAACATAT
1 AAAAATTTAAAATAAATAAAATATAAAAAATTT-AAAATAAATAATATAT
** * * * *
117655898 GAAAAGACCTAAAAT-GATAAAATA-AATAAGTTTAATATAAATAATATAT
1 -AAAA-ATTTAAAATAAATAAAATATAAAAAATTTAAAATAAATAATATAT
* * * ** * *
117655947 GAGATATTTAAAAATAAATAAAATA-AATAAGCTTAATACAAATAATATAT
1 -AAAAATTT-AAAATAAATAAAATATAAAAAATTTAAAATAAATAATATAT
* * ** *
117655997 GAGATATTTAAAAATAAATAAAATA-AATGAATTTAATATAAATAATAT
1 -AAAAATTT-AAAATAAATAAAATATAAAAAATTTAAAATAAATAATAT
117656045 CTGAGAAAGA
Statistics
Matches: 393, Mismatches: 73, Indels: 75
0.73 0.13 0.14
Matches are distributed among these distances:
48 35 0.09
49 54 0.14
50 151 0.38
51 81 0.21
52 24 0.06
53 16 0.04
54 4 0.01
55 8 0.02
56 11 0.03
57 9 0.02
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (49 bp):
AAAAATTTAAAATAAATAAAATATAAAAAATTTAAAATAAATAATATAT
Found at i:117655684 original size:26 final size:25
Alignment explanation
Indices: 117655542--117655773 Score: 142
Period size: 25 Copynumber: 9.2 Consensus size: 25
117655532 ATGATAAATG
*
117655542 AAACCATTTAAAGT-AA-AAAATATA
1 AAACAATTTAAA-TAAATAAAATATA
* *
117655566 AAA-AGTTTAAAATAAATAATATATA
1 AAACAATTT-AAATAAATAAAATATA
*
117655591 AAA-AATTTAAAATAAATAAAATATG
1 AAACAATTT-AAATAAATAAAATATA
** * * *
117655616 AAATGATTCAGAATAAACAATATAT-
1 AAACAATTTA-AATAAATAAAATATA
*
117655641 ATA-AATTCTAACATAAATAAAATATA
1 AAACAATT-TAA-ATAAATAAAATATA
**
117655667 AAACAATTTGAAATAAATAATTTATA
1 AAACAATTT-AAATAAATAAAATATA
*
117655693 AAGCAATTTAAAGTAAAT--AATATA
1 AAACAATTTAAA-TAAATAAAATATA
* *
117655717 AAATAATTT-AA-AAATAATAATACA
1 AAACAATTTAAATAAATAA-AATATA
* *
117655741 AAACAGATTAAAATAAATAATATGATA
1 AAACA-ATTTAAATAAATAAAAT-ATA
117655768 AAACAA
1 AAACAA
117655774 ATACTATATG
Statistics
Matches: 162, Mismatches: 28, Indels: 34
0.72 0.12 0.15
Matches are distributed among these distances:
21 4 0.02
23 6 0.04
24 32 0.20
25 53 0.33
26 48 0.30
27 19 0.12
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.28
Consensus pattern (25 bp):
AAACAATTTAAATAAATAAAATATA
Found at i:117655814 original size:13 final size:13
Alignment explanation
Indices: 117655798--117655828 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
117655788 AAACTTTAAA
*
117655798 AAAATAAACAAAT
1 AAAATAAAAAAAT
117655811 AAAATAAAAAAAT
1 AAAATAAAAAAAT
117655824 AAAAT
1 AAAAT
117655829 TGTTCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:117656042 original size:50 final size:50
Alignment explanation
Indices: 117655914--117656050 Score: 231
Period size: 50 Copynumber: 2.7 Consensus size: 50
117655904 ACCTAAAATG
117655914 ATAAAATAAATAAGTTTAATATAAATAATATATGAGATATTTAAAAATAA
1 ATAAAATAAATAAGTTTAATATAAATAATATATGAGATATTTAAAAATAA
* *
117655964 ATAAAATAAATAAGCTTAATACAAATAATATATGAGATATTTAAAAATAA
1 ATAAAATAAATAAGTTTAATATAAATAATATATGAGATATTTAAAAATAA
*
117656014 ATAAAATAAATGAA-TTTAATATAAATAATATCTGAGA
1 ATAAAATAAAT-AAGTTTAATATAAATAATATATGAGA
117656051 AAGAAAATTT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 79 0.98
51 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (50 bp):
ATAAAATAAATAAGTTTAATATAAATAATATATGAGATATTTAAAAATAA
Found at i:117659365 original size:21 final size:22
Alignment explanation
Indices: 117659323--117659365 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
117659313 CGCCTATACA
*
117659323 ATATAAAAATAATTAATTTTTT
1 ATATAAAAATAATTAATATTTT
* *
117659345 ATATAATAA-AATTACTATTTT
1 ATATAAAAATAATTAATATTTT
117659366 CATTTATAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATAAAAATAATTAATATTTT
Found at i:117678719 original size:23 final size:23
Alignment explanation
Indices: 117678687--117678738 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
117678677 TTAGAAAGGA
117678687 GAAA-AACGCAGTAGAAATAACC
1 GAAATAACGCAGTAGAAATAACC
*
117678709 GAAATAACGCAGTAGAAATAACT
1 GAAATAACGCAGTAGAAATAACC
117678732 GAAATAA
1 GAAATAA
117678739 TTTCTTGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.56, C:0.13, G:0.17, T:0.13
Consensus pattern (23 bp):
GAAATAACGCAGTAGAAATAACC
Found at i:117694716 original size:20 final size:20
Alignment explanation
Indices: 117694673--117694720 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
117694663 ACTGTTTTGT
117694673 TATGGGCCAACTGTATTGAA
1 TATGGGCCAACTGTATTGAA
*
117694693 -ATGGGCCCAACTGTGTT-AA
1 TATGGG-CCAACTGTATTGAA
117694712 TAT-GGCCAA
1 TATGGGCCAA
117694721 GGCCCAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 12 0.48
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (20 bp):
TATGGGCCAACTGTATTGAA
Found at i:117696046 original size:24 final size:24
Alignment explanation
Indices: 117695995--117696040 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
117695985 TTTCTAGAAG
* *
117695995 ATTTAGTATTTACTAGTATAATAA
1 ATTTAGCATTTACTAGCATAATAA
*
117696019 ATTTAGCATTTATTAGCATAAT
1 ATTTAGCATTTACTAGCATAAT
117696041 TTATTTGACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (24 bp):
ATTTAGCATTTACTAGCATAATAA
Found at i:117703242 original size:52 final size:52
Alignment explanation
Indices: 117703127--117703329 Score: 209
Period size: 52 Copynumber: 3.9 Consensus size: 52
117703117 CATATCATAG
* * *
117703127 CGATGCCATATCCCAGATATGGTCTTATAC-GGAAGCACATTATCAC-AT-CATAC
1 CGATGCCATAGCCCAGCTATGGTCTTATACGGGCAG-ACA-TATCACAATGC--AC
* * * *
117703180 CAATGCCATAGCCCAGCCATGGTTTTATA-GGGGAGTACATATCACAATGCAC
1 CGATGCCATAGCCCAGCTATGGTCTTATACGGGCAG-ACATATCACAATGCAC
**
117703232 CGATGCCATAGCCCAGCTATGGTCTTATACGGGCAGACATATCACAATTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTATACGGGCAGACATATCACAATGCAC
* * *
117703284 CGATTCCATAGCCCAACTATGGTCTTATACAGGC-GCACATATCACA
1 CGATGCCATAGCCCAGCTATGGTCTTATACGGGCAG-ACATATCACA
117703330 TTTATCCCGT
Statistics
Matches: 129, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
51 1 0.01
52 89 0.69
53 38 0.29
54 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (52 bp):
CGATGCCATAGCCCAGCTATGGTCTTATACGGGCAGACATATCACAATGCAC
Found at i:117703324 original size:104 final size:105
Alignment explanation
Indices: 117703127--117703329 Score: 250
Period size: 104 Copynumber: 1.9 Consensus size: 105
117703117 CATATCATAG
*
117703127 CGATGCCATATCCCAGATATGGTCTTATACGGAAGCACATTATCACATCATACCAATGCCATAGC
1 CGATGCCATAGCCCAGATATGGTCTTATACGGAAGCACATTATCACATCATACCAATGCCATAGC
* * ** *
117703192 CCAGCCATGGTTTTATAGGGGAGTACATATCACAATGCAC
66 CCAACCATGGTCTTATACAGGAGCACATATCACAATGCAC
* * * * *
117703232 CGATGCCATAGCCCAGCTATGGTCTTATACGGGCAG-ACA-TATCACAAT-TTACCGATTCCATA
1 CGATGCCATAGCCCAGATATGGTCTTATAC-GGAAGCACATTATCAC-ATCATACCAATGCCATA
* *
117703294 GCCCAACTATGGTCTTATACAGGCGCACATATCACA
64 GCCCAACCATGGTCTTATACAGGAGCACATATCACA
117703330 TTTATCCCGT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
104 46 0.55
105 33 0.40
106 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (105 bp):
CGATGCCATAGCCCAGATATGGTCTTATACGGAAGCACATTATCACATCATACCAATGCCATAGC
CCAACCATGGTCTTATACAGGAGCACATATCACAATGCAC
Found at i:117707355 original size:29 final size:26
Alignment explanation
Indices: 117707303--117707356 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
117707293 CTATTAATTA
* *
117707303 AATAATAAAATATCTTATATTAAAAT
1 AATAATAAAATATCTTACAATAAAAT
117707329 AATAATAAAATAATCTTAACCAATAAAA
1 AATAATAAAAT-ATCTT-A-CAATAAAA
117707357 ATCTAACACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 11 0.48
27 5 0.22
28 1 0.04
29 6 0.26
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (26 bp):
AATAATAAAATATCTTACAATAAAAT
Found at i:117708041 original size:13 final size:13
Alignment explanation
Indices: 117708023--117708060 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
117708013 TTTGGCAATG
117708023 CTTTTGAAAAGTA
1 CTTTTGAAAAGTA
*
117708036 CTTTTGAAAAGTG
1 CTTTTGAAAAGTA
117708049 CTTTTGAAAAGT
1 CTTTTGAAAAGT
117708061 TTGGTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:117709154 original size:20 final size:20
Alignment explanation
Indices: 117709129--117709179 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
117709119 ATTAATTATT
117709129 TATAAAATATAATTTAAATA
1 TATAAAATATAATTTAAATA
* * *
117709149 TATAAACTATATTTTAGATA
1 TATAAAATATAATTTAAATA
117709169 T-TAAAATATAA
1 TATAAAATATAA
117709180 CCAATTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
TATAAAATATAATTTAAATA
Found at i:117712254 original size:22 final size:22
Alignment explanation
Indices: 117712229--117712274 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
117712219 AAAAAAGATT
*
117712229 AATTGGGAGCGAAGAA-AAGAAG
1 AATTAGGAG-GAAGAAGAAGAAG
*
117712251 AATTAGGAGGAAGAAGAGGAAG
1 AATTAGGAGGAAGAAGAAGAAG
117712273 AA
1 AA
117712275 AAAGATCAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.52, C:0.02, G:0.37, T:0.09
Consensus pattern (22 bp):
AATTAGGAGGAAGAAGAAGAAG
Found at i:117714147 original size:100 final size:101
Alignment explanation
Indices: 117713943--117714147 Score: 250
Period size: 100 Copynumber: 2.0 Consensus size: 101
117713933 ATTGAACATT
*
117713943 AACATCATTTACAGTCTAGAGCAATTAGTTTGAATGCCCCCCCTAATATTTAAAATTCTACCTTT
1 AACATCATTTACAGTCTAGAACAATTAGTTTGAATG--CCCCCTAATATTTAAAATTCTACCTTT
* * * * **
117714008 CTGAGCTGAAAACTTAAATGGGGATTTAAATTGTGATC
64 CTGAGATGAAAACTCAAATGGAGATTTAAAGTGCAATC
* ** ** *
117714046 AACATCATTTTCAGTCTTTAACAATTAGTTTGAATG-CCTTTAATATTTAAAATTCTACCTTTTT
1 AACATCATTTACAGTCTAGAACAATTAGTTTGAATGCCCCCTAATATTTAAAATTCTACCTTTCT
* *
117714110 GAGATGACAACTCAATTGGAGATTTAAAGTGCAATC
66 GAGATGAAAACTCAAATGGAGATTTAAAGTGCAATC
117714146 AA
1 AA
117714148 GATTGCATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
100 55 0.63
103 32 0.37
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (101 bp):
AACATCATTTACAGTCTAGAACAATTAGTTTGAATGCCCCCTAATATTTAAAATTCTACCTTTCT
GAGATGAAAACTCAAATGGAGATTTAAAGTGCAATC
Found at i:117716946 original size:41 final size:41
Alignment explanation
Indices: 117716900--117716981 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
117716890 GCATTACAAT
117716900 TGAAATGTGGTTATTTTATCAATTATATCAATCTTTAACAG
1 TGAAATGTGGTTATTTTATCAATTATATCAATCTTTAACAG
117716941 TGAAATGTGGTTATTTTATCAATTATATCAATCTTTAACAG
1 TGAAATGTGGTTATTTTATCAATTATATCAATCTTTAACAG
117716982 AAAAATTGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (41 bp):
TGAAATGTGGTTATTTTATCAATTATATCAATCTTTAACAG
Found at i:117722935 original size:18 final size:19
Alignment explanation
Indices: 117722904--117722941 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
117722894 TACTTTCAAT
117722904 AAATAAATATATAAA-TAA
1 AAATAAATATATAAACTAA
117722922 AAATAAAT-TAATAAACTAA
1 AAATAAATAT-ATAAACTAA
117722941 A
1 A
117722942 CTCAACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 13 0.72
19 4 0.22
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATAAATATATAAACTAA
Found at i:117723316 original size:22 final size:23
Alignment explanation
Indices: 117723264--117723317 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
117723254 AAGTATATAA
*
117723264 ATTAAGAAATTATAATTAAACATT
1 ATTAA-AAATTATAATTAAAAATT
* *
117723288 -TCAAAAAATATAATTAAAAATT
1 ATTAAAAATTATAATTAAAAATT
117723310 ATTAAAAA
1 ATTAAAAA
117723318 AAAAAACTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (23 bp):
ATTAAAAATTATAATTAAAAATT
Found at i:117725831 original size:31 final size:31
Alignment explanation
Indices: 117725773--117725831 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
117725763 TAAATATTTC
**
117725773 TTAAATGTGTAGTTTGAATTCTTTGTTGCAG
1 TTAAATGTGTAGTTTGAATTCAGTGTTGCAG
*
117725804 TTAACTGTGTAGTTTGAATTCAGTGTTG
1 TTAAATGTGTAGTTTGAATTCAGTGTTG
117725832 TTTTATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.47
Consensus pattern (31 bp):
TTAAATGTGTAGTTTGAATTCAGTGTTGCAG
Found at i:117730535 original size:31 final size:31
Alignment explanation
Indices: 117730495--117730562 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
117730485 GGTGCAATTA
*
117730495 TATAAATGAAAATTTAATTGT-AGTTCAAATG
1 TATACATGAAAATTTAATTGTGAG-TCAAATG
* * * *
117730526 TATACATGAAACTTTGATTTTGAGTCAACTG
1 TATACATGAAAATTTAATTGTGAGTCAAATG
117730557 TATACA
1 TATACA
117730563 CTTGAAGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (31 bp):
TATACATGAAAATTTAATTGTGAGTCAAATG
Found at i:117730940 original size:36 final size:35
Alignment explanation
Indices: 117730868--117730937 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
117730858 AATAGACCGG
*
117730868 TAATTATAATTTAATTTACAATTATTAATTAAAAA
1 TAATTATAATTTAATTTACAATTATTAATAAAAAA
*
117730903 TAATTATGATTTAATTTTGAC-ATTATT-ATAAAAAA
1 TAATTATAATTTAA-TTT-ACAATTATTAATAAAAAA
117730938 ATATTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 20 0.65
36 9 0.29
37 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (35 bp):
TAATTATAATTTAATTTACAATTATTAATAAAAAA
Found at i:117733035 original size:18 final size:18
Alignment explanation
Indices: 117732981--117733041 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
117732971 TTGTTCATTA
*
117732981 TTTTT-AAAGTTTTATATT
1 TTTTTGAAAATTTTAT-TT
* *
117732999 TTTTTGGAATTTTTAATTT
1 TTTTTGAAAATTTT-ATTT
117733018 TTTTTGAAAATTTTATTT
1 TTTTTGAAAATTTTATTT
117733036 ATTTTT
1 -TTTTT
117733042 TCATTTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.25
19 25 0.69
20 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.69
Consensus pattern (18 bp):
TTTTTGAAAATTTTATTT
Found at i:117739055 original size:23 final size:23
Alignment explanation
Indices: 117739009--117739070 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
117738999 AAATTTTAAG
* *
117739009 TTAAAAATAATT-AAA-GTATTT
1 TTAAAAAGAATTAAAACATATTT
117739030 TTAAAAAGAATTAAAACATATTT
1 TTAAAAAGAATTAAAACATATTT
117739053 TTAAAAAGAATTAAAACA
1 TTAAAAAGAATTAAAACA
117739071 AAGGCTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.30
22 3 0.08
23 23 0.62
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (23 bp):
TTAAAAAGAATTAAAACATATTT
Found at i:117739079 original size:23 final size:23
Alignment explanation
Indices: 117739030--117739079 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
117739020 TAAAGTATTT
* ***
117739030 TTAAAAAGAATTAAAACATATTT
1 TTAAAAAGAATTAAAACAAAGGC
117739053 TTAAAAAGAATTAAAACAAAGGC
1 TTAAAAAGAATTAAAACAAAGGC
117739076 TTAA
1 TTAA
117739080 TGATAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (23 bp):
TTAAAAAGAATTAAAACAAAGGC
Found at i:117740305 original size:12 final size:13
Alignment explanation
Indices: 117740282--117740316 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
117740272 AATACGTTAT
*
117740282 TTATTGAATAATA
1 TTATTAAATAATA
117740295 TTA-TAAATAATA
1 TTATTAAATAATA
117740307 TTATTAAATA
1 TTATTAAATA
117740317 TTGATAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (13 bp):
TTATTAAATAATA
Found at i:117743351 original size:23 final size:21
Alignment explanation
Indices: 117743310--117743353 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
117743300 TAATTGATTT
117743310 TATTTTTTTTATAAAAATAAA
1 TATTTTTTTTATAAAAATAAA
117743331 TATTTTATATTTA-AAATAATAAA
1 TATTTT-T-TTTATAAA-AATAAA
117743354 AATAAGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.30
22 4 0.20
23 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTTTTTTATAAAAATAAA
Found at i:117744818 original size:16 final size:17
Alignment explanation
Indices: 117744778--117744818 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
117744768 ACAAACTTTC
117744778 TTTTTATTATATTGAAT
1 TTTTTATTATATTGAAT
117744795 TTTGTTATT-T-TTGAAT
1 TTT-TTATTATATTGAAT
117744811 ATTTTTAT
1 -TTTTTAT
117744819 AATTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.45
17 7 0.32
18 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (17 bp):
TTTTTATTATATTGAAT
Found at i:117747817 original size:6 final size:6
Alignment explanation
Indices: 117747808--117747833 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
117747798 GGAACTTGAA
117747808 CTGGAT CTGGAT CTGGAT CTGGAT CT
1 CTGGAT CTGGAT CTGGAT CTGGAT CT
117747834 CTCTCTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.31, T:0.35
Consensus pattern (6 bp):
CTGGAT
Found at i:117760463 original size:20 final size:20
Alignment explanation
Indices: 117760431--117760479 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
117760421 AGATAACTAT
117760431 ATAAAAAA-A-TTTTAAAAA
1 ATAAAAAATATTTTTAAAAA
117760449 ATAAAAAATATTTTTAAAAA
1 ATAAAAAATATTTTTAAAAA
*
117760469 ATAAAGAATAT
1 ATAAAAAATAT
117760480 AAATGAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 8 0.29
19 1 0.04
20 19 0.68
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
ATAAAAAATATTTTTAAAAA
Found at i:117762941 original size:11 final size:11
Alignment explanation
Indices: 117762906--117762941 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
117762896 TTTTGCTACA
117762906 ATTTTACTATT
1 ATTTTACTATT
*
117762917 ATATTACTATT
1 ATTTTACTATT
*
117762928 ATTTTACTGTT
1 ATTTTACTATT
117762939 ATT
1 ATT
117762942 GTTTGAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.61
Consensus pattern (11 bp):
ATTTTACTATT
Found at i:117773579 original size:54 final size:52
Alignment explanation
Indices: 117773518--117773725 Score: 258
Period size: 54 Copynumber: 3.9 Consensus size: 52
117773508 CCATGGCAAC
*
117773518 AAGTGATAAGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA
1 AAGTGATAAGTGA-TTCCATATAAGACCATAGCTGGGCTATGGCATCGGAAAA
* * **
117773571 CAAGTGATAAGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGATTA
1 -AAGTGATAAGTGA-TTCCATATAAGACCATAGCTGGGCTATGGCATCGGAAAA
*
117773625 AAGTGATACAAGTGA-TCCATATAAGACCATAGCTGGGCTATGGCATCGGAGAA
1 AAGTGAT--AAGTGATTCCATATAAGACCATAGCTGGGCTATGGCATCGGAAAA
* * * *
117773678 AAGTGATAAGTG-CTCCAATGTAAGACCATATCTGGGATATGGCATCGG
1 AAGTGATAAGTGATTCC-ATATAAGACCATAGCTGGGCTATGGCATCGG
117773726 TATGATATAT
Statistics
Matches: 140, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
51 8 0.06
52 28 0.20
53 48 0.34
54 50 0.36
55 6 0.04
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (52 bp):
AAGTGATAAGTGATTCCATATAAGACCATAGCTGGGCTATGGCATCGGAAAA
Found at i:117775639 original size:16 final size:17
Alignment explanation
Indices: 117775608--117775641 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
117775598 AGAAATGAGC
117775608 AAATGCAAGGGAAAAGA
1 AAATGCAAGGGAAAAGA
*
117775625 AAATGCAA-TGAAAAGA
1 AAATGCAAGGGAAAAGA
117775641 A
1 A
117775642 TTAGAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.62, C:0.06, G:0.24, T:0.09
Consensus pattern (17 bp):
AAATGCAAGGGAAAAGA
Found at i:117777576 original size:132 final size:132
Alignment explanation
Indices: 117777334--117777601 Score: 491
Period size: 132 Copynumber: 2.0 Consensus size: 132
117777324 ATAATATTTA
*
117777334 TGTAGTGGTACCAATGTGTGATAAATTTTGCTATGTTATATGTCCATGTAGTGTAAGCATATATA
1 TGTAGTGGTACCAATGTGTAATAAATTTTGCTATGTTATATGTCCATGTAGTGTAAGCATATATA
*
117777399 TAACTAAACTAGGTCACATGGGTATCTGGTTGAATGAGCATTAAATGACATATAGATTATGAGCT
66 TAACTAAACTAGGTCACATGGGTATCTGGTTGAATGAGCACTAAATGACATATAGATTATGAGCT
117777464 AT
131 AT
*
117777466 TGTAGTGGTACCAATGTGTAATAGATTTTGCTATGTTATATGTCCATGTAGTGTAAGCATATATA
1 TGTAGTGGTACCAATGTGTAATAAATTTTGCTATGTTATATGTCCATGTAGTGTAAGCATATATA
* *
117777531 TAACTAAACTAGGTCACATGGGTATGTGGTTGAATGAGCACTAAATGGCATATAGATTATGAGCT
66 TAACTAAACTAGGTCACATGGGTATCTGGTTGAATGAGCACTAAATGACATATAGATTATGAGCT
117777596 AT
131 AT
117777598 TGTA
1 TGTA
117777602 TGCCAGAGAG
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 131 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.35
Consensus pattern (132 bp):
TGTAGTGGTACCAATGTGTAATAAATTTTGCTATGTTATATGTCCATGTAGTGTAAGCATATATA
TAACTAAACTAGGTCACATGGGTATCTGGTTGAATGAGCACTAAATGACATATAGATTATGAGCT
AT
Found at i:117783523 original size:43 final size:44
Alignment explanation
Indices: 117783459--117783550 Score: 168
Period size: 43 Copynumber: 2.1 Consensus size: 44
117783449 AAGAGTTGTT
117783459 TAAATGTTATTTTAATATTGTACATTGTACATAATCTCAAAATG
1 TAAATGTTATTTTAATATTGTACATTGTACATAATCTCAAAATG
*
117783503 TAAATGTTA-TTTAATATTGTACATTGTGCATAATCTCAAAATG
1 TAAATGTTATTTTAATATTGTACATTGTACATAATCTCAAAATG
117783546 TAAAT
1 TAAAT
117783551 TTTGTATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 38 0.81
44 9 0.19
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (44 bp):
TAAATGTTATTTTAATATTGTACATTGTACATAATCTCAAAATG
Found at i:117789552 original size:2 final size:2
Alignment explanation
Indices: 117789545--117789573 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
117789535 TTGAATATTC
117789545 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
117789574 AAAGGATGTT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:117789821 original size:29 final size:29
Alignment explanation
Indices: 117789778--117789839 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
117789768 ATATTATAAT
* * *
117789778 TTTTTAATAATTAAATTAAAATTTAATTA
1 TTTTTAAGAAATAAAGTAAAATTTAATTA
* **
117789807 TTTTTAAGAAATAAAGTATAATTTTTTTA
1 TTTTTAAGAAATAAAGTAAAATTTAATTA
117789836 TTTT
1 TTTT
117789840 AAAATTTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTTTAAGAAATAAAGTAAAATTTAATTA
Found at i:117790779 original size:29 final size:29
Alignment explanation
Indices: 117790733--117790793 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
117790723 CTAGTAAAAT
* *
117790733 AATAAAATTATATTTTTACTATC-GTAAA
1 AATAAAATTATAATTTTAATATCTGTAAA
* *
117790761 AATATAAATTTTAATTTTAATTTCTGTAAA
1 AATA-AAATTATAATTTTAATATCTGTAAA
117790791 AAT
1 AAT
117790794 TTTTCTAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.15
29 15 0.56
30 8 0.30
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (29 bp):
AATAAAATTATAATTTTAATATCTGTAAA
Found at i:117791131 original size:26 final size:26
Alignment explanation
Indices: 117791095--117791144 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
117791085 CCGGAGGCGC
117791095 GACCATTCGCGCCTGCTGCAGGGGTG
1 GACCATTCGCGCCTGCTGCAGGGGTG
117791121 GACCATTCGCGCCTGCTGCAGGGG
1 GACCATTCGCGCCTGCTGCAGGGG
117791145 CGTGACTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.32, G:0.38, T:0.18
Consensus pattern (26 bp):
GACCATTCGCGCCTGCTGCAGGGGTG
Found at i:117794482 original size:11 final size:11
Alignment explanation
Indices: 117794468--117794495 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
117794458 ACATTATATC
117794468 AAAATTACATT
1 AAAATTACATT
117794479 AAAATTACATT
1 AAAATTACATT
117794490 AAAATT
1 AAAATT
117794496 TCTTACTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATTACATT
Found at i:117795579 original size:3 final size:3
Alignment explanation
Indices: 117795565--117795619 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
117795555 CTTTCTCCCC
* *
117795565 CTT CTC CTT CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
117795613 CTT -TT CT
1 CTT CTT CT
117795620 CTTTTTACTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:117795891 original size:24 final size:22
Alignment explanation
Indices: 117795851--117795912 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 22
117795841 AATTTTAAAA
117795851 ATTATTAAAATATAATAAAATAATAAT
1 ATTATTAAAA-A-AATAAAAT--T-AT
117795878 ATT-TTAAAAAAATAAAATTAT
1 ATTATTAAAAAAATAAAATTAT
117795899 ATTATTAAAAAAAT
1 ATTATTAAAAAAAT
117795913 GGGTCGCCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.15
22 11 0.32
24 8 0.24
25 1 0.03
26 6 0.18
27 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTATTAAAAAAATAAAATTAT
Found at i:117796356 original size:24 final size:23
Alignment explanation
Indices: 117796311--117796356 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
117796301 TTTATAATAA
*
117796311 TAAAATTAATTTTTATATTTCTC
1 TAAAATTAATTTTTATAATTCTC
117796334 TAAAATTAAATTATTT-TAATTCT
1 TAAAATT-AATT-TTTATAATTCT
117796357 TTTGTAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 10 0.50
25 3 0.15
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (23 bp):
TAAAATTAATTTTTATAATTCTC
Found at i:117798806 original size:59 final size:59
Alignment explanation
Indices: 117798741--117798875 Score: 243
Period size: 59 Copynumber: 2.3 Consensus size: 59
117798731 TAATTTACAG
* *
117798741 TTTTTAAATTTAAGTATTGATTAGATTCAAAAATAAAAATTTAAATACCAAGTTTACCA
1 TTTTTAAATTTAAATATTAATTAGATTCAAAAATAAAAATTTAAATACCAAGTTTACCA
*
117798800 TTTTTAAATTTAAATATTAATTAGATTCAAAAATAAAAATTTAAATACCAAGTTTACTA
1 TTTTTAAATTTAAATATTAATTAGATTCAAAAATAAAAATTTAAATACCAAGTTTACCA
117798859 TTTTTAAATTTAAATAT
1 TTTTTAAATTTAAATAT
117798876 ATAAAAATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 73 1.00
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (59 bp):
TTTTTAAATTTAAATATTAATTAGATTCAAAAATAAAAATTTAAATACCAAGTTTACCA
Found at i:117799723 original size:21 final size:22
Alignment explanation
Indices: 117799699--117799739 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
117799689 ATATTTGTAA
*
117799699 ATATTTATATAT-AATAAATAT
1 ATATTTAAATATCAATAAATAT
117799720 ATATTTAAATATCAATAAAT
1 ATATTTAAATATCAATAAAT
117799740 TCAAAACTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATTTAAATATCAATAAATAT
Found at i:117801007 original size:311 final size:310
Alignment explanation
Indices: 117800443--117801019 Score: 764
Period size: 311 Copynumber: 1.9 Consensus size: 310
117800433 ATTTAGAATT
* ** * *
117800443 TATATGTGTTTAAAAATAATATACAATAAACAATATGTGTATGGTTTGAAATTAATTAATTATGA
1 TATATGTGTTTAAAAATAACATACAATAAACAATAAATGTATGGTTTGAAACTAATTAATTATAA
* * * * * *
117800508 TAACACATAAAATATATACAATATTAAAATAAAAAAAGATTAATTTGTGAGGAAAAAATAAAATT
66 TAACAAATAAAATATATACAATATTAAAAAAAAAAAAGATTAAATTATGAAGAAAAAACAAAATT
* * * *
117800573 TAAACCACAAATATATCATATTAACAACACTAAATGCACTATAATTATTTATCATGGTGTTGTCA
131 TAAACCACAAATACATCATATAAACAACACTAAATGCACTATAATCATTTATCATGATGTTGTCA
* * * * * * *
117800638 TCAATTGTGAGTTAGTGTTGAGTTGACTTATGGCACCAACTCAATTAACAATATTATTAATATAT
196 TAAATTGTAAATTAGTGTTAAGTTAACTTATGACACCAACTCAATTAACAACATTATTAATATAT
117800703 A-AATTCTATCACATATATATGCGTGCGGAAATCACAAATTTAGAACACA
261 ACAATTCTATCACATATATATGCGTGCGGAAATCACAAATTTAGAACACA
* *
117800752 TATATGTGTTTAAAAATAACGTATAATAAACAATAAAATGTATGGTTTGAAACTAATTAATTATA
1 TATATGTGTTTAAAAATAACATACAATAAACAAT-AAATGTATGGTTTGAAACTAATTAATTATA
* * * ** *
117800817 ATAGCAAATGAAATATGTACGTTATTAAAAGAAAAAAATAGATTAAATTAT-AAG-TAAAACAAA
65 ATAACAAATAAAATATATACAATATTAAAA-AAAAAAA-AGATTAAATTATGAAGAAAAAACAAA
* * * *
117800880 ATTTAAACACATAAATACATCATATAAACGATACTAAATGCACTATAATCATTTATCATGATTTT
128 ATTTAAAC-CACAAATACATCATATAAACAACACTAAATGCACTATAATCATTTATCATGATGTT
* * *
117800945 GTCATAAATTGTAAATTAGTGTTAAGTTAACTTATGATATCGACTCAATTAACAACATTATTAAT
192 GTCATAAATTGTAAATTAGTGTTAAGTTAACTTATGACACCAACTCAATTAACAACATTATTAAT
117801010 ATATACAATT
257 ATATACAATT
117801020 GATGAAGATA
Statistics
Matches: 226, Mismatches: 37, Indels: 7
0.84 0.14 0.03
Matches are distributed among these distances:
309 31 0.14
310 65 0.29
311 116 0.51
312 14 0.06
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (310 bp):
TATATGTGTTTAAAAATAACATACAATAAACAATAAATGTATGGTTTGAAACTAATTAATTATAA
TAACAAATAAAATATATACAATATTAAAAAAAAAAAAGATTAAATTATGAAGAAAAAACAAAATT
TAAACCACAAATACATCATATAAACAACACTAAATGCACTATAATCATTTATCATGATGTTGTCA
TAAATTGTAAATTAGTGTTAAGTTAACTTATGACACCAACTCAATTAACAACATTATTAATATAT
ACAATTCTATCACATATATATGCGTGCGGAAATCACAAATTTAGAACACA
Found at i:117801963 original size:29 final size:30
Alignment explanation
Indices: 117801894--117801969 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
117801884 AATCTCAAAA
* * *
117801894 TTATACATAAACTTTGATTTAATGTGCAGT
1 TTATACATGAACTTTAATTTAATGTGCAAT
*
117801924 TTCATATATGAACTTTAATTT-A-GTGCAAT
1 TT-ATACATGAACTTTAATTTAATGTGCAAT
117801953 TATATACATGAAACTTT
1 T-TATACATG-AACTTT
117801970 GATTGTGGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 13 0.34
30 10 0.26
31 15 0.39
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (30 bp):
TTATACATGAACTTTAATTTAATGTGCAAT
Found at i:117803752 original size:18 final size:19
Alignment explanation
Indices: 117803729--117803768 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
117803719 TTCCACCCTG
*
117803729 AAAAAGAAGGAAAA-AAAA
1 AAAAAGAAAGAAAAGAAAA
117803747 AAAAAGAAAGAAAAGAAAA
1 AAAAAGAAAGAAAAGAAAA
117803766 AAA
1 AAA
117803769 GCTGCTTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAGAAAAGAAAA
Found at i:117829433 original size:14 final size:14
Alignment explanation
Indices: 117829388--117829433 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
117829378 TGAAAAATAG
117829388 AAAAATTAAATTCTT
1 AAAAATTAAATT-TT
* * *
117829403 AAAAATAAAAATAT
1 AAAAATTAAATTTT
117829417 AAAAATTAAATTTT
1 AAAAATTAAATTTT
117829431 AAA
1 AAA
117829434 TTTATAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATTAAATTTT
Found at i:117832244 original size:18 final size:19
Alignment explanation
Indices: 117832213--117832264 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
117832203 AAAATATTTA
*
117832213 TATTATAATATTTTATAAT
1 TATTATAATTTTTTATAAT
*
117832232 T-TTATAATTTTTT-TATT
1 TATTATAATTTTTTATAAT
117832249 TATTA-AATTTTTTATA
1 TATTATAATTTTTTATA
117832265 CAGTATCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 12 0.41
18 16 0.55
19 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTATAATTTTTTATAAT
Found at i:117836223 original size:58 final size:59
Alignment explanation
Indices: 117836121--117836239 Score: 154
Period size: 58 Copynumber: 2.0 Consensus size: 59
117836111 TGGTGATCAT
* * *
117836121 TTTGTAACTTTTTATAGTTAGGTGTCTTAAAAAGAAATTTACTAATAATTGAGTGACTA
1 TTTGTAACTTTTTATAATTAGATGACTTAAAAAGAAATTTACTAATAATTGAGTGACTA
* *
117836180 TTTGTAACTTTTTATAATT-GAATGAC-TAAAAACG-AATTTACTAATAGTTGAGTGATTA
1 TTTGTAACTTTTTATAATTAG-ATGACTTAAAAA-GAAATTTACTAATAATTGAGTGACTA
117836238 TT
1 TT
117836240 AGTGGATTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
58 31 0.58
59 22 0.42
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (59 bp):
TTTGTAACTTTTTATAATTAGATGACTTAAAAAGAAATTTACTAATAATTGAGTGACTA
Found at i:117841018 original size:22 final size:22
Alignment explanation
Indices: 117840993--117841049 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
117840983 ATATTCAAAC
117840993 AATAACAACAAAA-TAATAATG-A
1 AATAACAACAAAACT-ATAA-GAA
* *
117841015 AATACCAATAAAACTATAAGAA
1 AATAACAACAAAACTATAAGAA
*
117841037 AACAACAACAAAA
1 AATAACAACAAAA
117841050 AAAGCAACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.68, C:0.14, G:0.04, T:0.14
Consensus pattern (22 bp):
AATAACAACAAAACTATAAGAA
Found at i:117849057 original size:22 final size:23
Alignment explanation
Indices: 117849027--117849073 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
117849017 ATAATATCCA
117849027 AACATTAATAATAAAA-TAGTAGC
1 AACATTAATAATAAAATTA-TAGC
*
117849050 AACA-TAATAGTAAAATTATAGC
1 AACATTAATAATAAAATTATAGC
117849072 AA
1 AA
117849074 AATAGTGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (23 bp):
AACATTAATAATAAAATTATAGC
Found at i:117849867 original size:16 final size:16
Alignment explanation
Indices: 117849846--117849879 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
117849836 TGCATATTTA
*
117849846 ATCATTTATATAATAT
1 ATCATTTACATAATAT
*
117849862 ATCATTTACATATTAT
1 ATCATTTACATAATAT
117849878 AT
1 AT
117849880 TTATTTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (16 bp):
ATCATTTACATAATAT
Found at i:117851269 original size:26 final size:26
Alignment explanation
Indices: 117851232--117851282 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
117851222 AGGGAAAAAC
*
117851232 AAAAGAGAATAAAAATAAAAAAATTT
1 AAAAGAGAATAAAAAGAAAAAAATTT
117851258 AAAAGA-ACATAAAAAGAAAAAAATT
1 AAAAGAGA-ATAAAAAGAAAAAAATT
117851283 AAATTACTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.16
Consensus pattern (26 bp):
AAAAGAGAATAAAAAGAAAAAAATTT
Found at i:117851468 original size:15 final size:15
Alignment explanation
Indices: 117851422--117851474 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
117851412 ATAATACGTT
117851422 AATATAAATGACTAA
1 AATATAAATGACTAA
* * *
117851437 AACAT-AAT-ATTTTA
1 AATATAAATGA-CTAA
117851451 AATATAAATGACTAA
1 AATATAAATGACTAA
117851466 AATATAAAT
1 AATATAAAT
117851475 CAAAAGAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
13 1 0.03
14 9 0.31
15 18 0.62
16 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (15 bp):
AATATAAATGACTAA
Found at i:117853564 original size:60 final size:58
Alignment explanation
Indices: 117853431--117853583 Score: 175
Period size: 60 Copynumber: 2.6 Consensus size: 58
117853421 ATACATTTTT
* * *
117853431 GGTACCTAAACTTGGCTTCAAGGTTCAAATTGGTACCAAGGCTTTTTTGGTCCAATTA
1 GGTACCTGAACTTGGCTTTAAGGTTCAAATTGGTACCAAAGCTTTTTTGGTCCAATTA
* * * * *
117853489 AGTTCTTGAACTTGGCTTTAAGGTTCAATTTGGTACCTAAAG-TTTAGTTTTGTCCAATTA
1 GGTACCTGAACTTGGCTTTAAGGTTCAAATTGGTACC-AAAGCTTT--TTTGGTCCAATTA
*
117853549 GGTACCTGAACTTGGCTTCTTA-GTTCAAATTGGTA
1 GGTACCTGAACTTGGCTT-TAAGGTTCAAATTGGTA
117853584 GCTGAAATTG
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
58 34 0.44
59 3 0.04
60 39 0.50
61 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (58 bp):
GGTACCTGAACTTGGCTTTAAGGTTCAAATTGGTACCAAAGCTTTTTTGGTCCAATTA
Found at i:117853609 original size:31 final size:31
Alignment explanation
Indices: 117853536--117853612 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
117853526 TAAAGTTTAG
* *
117853536 TTTTGTCCAATTAGGTACCTGAACTTGGCTT
1 TTTTGTCAAATTAGGTACCTGAAATTGGCTT
* * *
117853567 CTTAGTTCAAATT-GGTAGCTGAAATTGGCTT
1 TTTTG-TCAAATTAGGTACCTGAAATTGGCTT
117853598 TTTTGTGCAAATTAG
1 TTTTGT-CAAATTAG
117853613 TACTTACAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
30 1 0.03
31 28 0.78
32 7 0.19
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (31 bp):
TTTTGTCAAATTAGGTACCTGAAATTGGCTT
Found at i:117854827 original size:14 final size:14
Alignment explanation
Indices: 117854808--117854836 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
117854798 GATAGAGACG
117854808 TATGTTACTATCAC
1 TATGTTACTATCAC
117854822 TATGTTACTATCAC
1 TATGTTACTATCAC
117854836 T
1 T
117854837 GTTCATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (14 bp):
TATGTTACTATCAC
Found at i:117858813 original size:12 final size:12
Alignment explanation
Indices: 117858798--117858827 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
117858788 AGTTTTCTTC
117858798 TTTTTTTTTTAT
1 TTTTTTTTTTAT
*
117858810 TTTTATTTTTAT
1 TTTTTTTTTTAT
117858822 TTTTTT
1 TTTTTT
117858828 ATATGTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTTAT
Found at i:117858874 original size:2 final size:2
Alignment explanation
Indices: 117858867--117858904 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
117858857 TAGTTAGGTT
117858867 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
117858905 AAAAGATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:117862384 original size:16 final size:16
Alignment explanation
Indices: 117862348--117862382 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
117862338 TTTAGGTTTG
117862348 AAAATTTTAATTAATT
1 AAAATTTTAATTAATT
*
117862364 AAAATTTT-TTTAATT
1 AAAATTTTAATTAATT
117862379 AAAA
1 AAAA
117862383 ATCTATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAATTTTAATTAATT
Found at i:117868523 original size:12 final size:12
Alignment explanation
Indices: 117868506--117868531 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
117868496 TTAATTTGGT
117868506 TCTACCACGTTA
1 TCTACCACGTTA
117868518 TCTACCACGTTA
1 TCTACCACGTTA
117868530 TC
1 TC
117868532 AGAAGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.35, G:0.08, T:0.35
Consensus pattern (12 bp):
TCTACCACGTTA
Found at i:117884715 original size:6 final size:6
Alignment explanation
Indices: 117884704--117884743 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
117884694 TGTTGCACAA
117884704 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
117884744 GATAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:117892212 original size:22 final size:23
Alignment explanation
Indices: 117892157--117892247 Score: 76
Period size: 25 Copynumber: 3.8 Consensus size: 23
117892147 ATATTACGTA
* *
117892157 TATATATATATATATATATTACATGT
1 TATAT-TATGTATATATTTTACA--T
*
117892183 TATCTTATGTATATATTTTA-AT
1 TATATTATGTATATATTTTACAT
* *
117892205 TATATTATGTATGTATTTTTTACAC
1 TATATTATGTA--TATATTTTACAT
*
117892230 TATATTATGTACATATTT
1 TATATTATGTATATATTT
117892248 CAAAGGTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
22 11 0.20
23 5 0.09
24 9 0.17
25 25 0.46
26 4 0.07
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (23 bp):
TATATTATGTATATATTTTACAT
Found at i:117893135 original size:21 final size:19
Alignment explanation
Indices: 117893092--117893149 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
117893082 AAATTTATTC
**
117893092 AAATTA-AAATAAACATT-
1 AAATTATAAATAAATTTTA
117893109 AAATTATAGGAATAAATTTTA
1 AAATTATA--AATAAATTTTA
*
117893130 AAATTATATATAAATTTTA
1 AAATTATAAATAAATTTTA
117893149 A
1 A
117893150 TTTAATATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 6 0.18
18 1 0.03
19 11 0.32
20 8 0.24
21 8 0.24
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATTATAAATAAATTTTA
Found at i:117897741 original size:16 final size:15
Alignment explanation
Indices: 117897701--117897742 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
117897691 TGAAAAATTT
*
117897701 AGTACTGAATTTTTA
1 AGTACTAAATTTTTA
*
117897716 A-TATTAAATTTTATA
1 AGTACTAAATTTT-TA
117897731 AGTACTAAATTT
1 AGTACTAAATTT
117897743 ATATTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 9 0.41
15 4 0.18
16 9 0.41
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (15 bp):
AGTACTAAATTTTTA
Found at i:117897849 original size:39 final size:39
Alignment explanation
Indices: 117897805--117897882 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
117897795 TTAATAAAAG
117897805 TAAATACTTATTTTTAGTATTTATTCTTTTAATTTTCAT
1 TAAATACTTATTTTTAGTATTTATTCTTTTAATTTTCAT
117897844 TAAATACTTATTTTTAGTATTTATTCTTTTAATTTTCAT
1 TAAATACTTATTTTTAGTATTTATTCTTTTAATTTTCAT
117897883 CTTATTAGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (39 bp):
TAAATACTTATTTTTAGTATTTATTCTTTTAATTTTCAT
Found at i:117903613 original size:20 final size:20
Alignment explanation
Indices: 117903571--117903611 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
117903561 CACAAAATAA
*
117903571 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATAATTTACT
117903591 TTTCTGG-AAATAATTTA-T
1 TTTCTGGAAAATAATTTACT
117903609 TTT
1 TTT
117903612 TTTGGTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 9 0.45
20 7 0.35
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTCTGGAAAATAATTTACT
Found at i:117905184 original size:43 final size:42
Alignment explanation
Indices: 117905119--117905207 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 42
117905109 ATGATATATT
*
117905119 TTTTTCAATAATTTAATATCACAT-AGGTAATTTTATCTTAAA
1 TTTTTCAATAATTTAATATCACATCA-GTAATTTCATCTTAAA
* *
117905161 CTTTTTCAATAGTTTAATGTCACATCAGTAATTTCATCTTAAA
1 -TTTTTCAATAATTTAATATCACATCAGTAATTTCATCTTAAA
117905204 TTTT
1 TTTT
117905208 AATATTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 4 0.10
43 37 0.88
44 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (42 bp):
TTTTTCAATAATTTAATATCACATCAGTAATTTCATCTTAAA
Found at i:117905836 original size:21 final size:21
Alignment explanation
Indices: 117905810--117905849 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
117905800 CAAAACAACG
*
117905810 TAGTTTTGCCTTTTAACTTGA
1 TAGTTTTGACTTTTAACTTGA
117905831 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
117905850 TAGAAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.55
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTGA
Found at i:117911693 original size:3 final size:3
Alignment explanation
Indices: 117911685--117911737 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
117911675 ATATATTTAC
117911685 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
117911731 TCTA TTA
1 T-TA TTA
117911738 ATTGAGATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.09
3 40 0.85
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:117912932 original size:37 final size:38
Alignment explanation
Indices: 117912890--117912986 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 38
117912880 CGGATAGATT
*
117912890 CGATGAGGCGTTGGTCGCCAC-TTTGCTTCG-GCTTAGC
1 CGATGAGGCGTTGGTCGCCACTTTTGCTTCGAAC-TAGC
* * *
117912927 CGATGAGACGTTGGTCGTCACTTATTTGCTTCGAACTATC
1 CGATGAGGCGTTGGTCGCCAC-T-TTTGCTTCGAACTAGC
117912967 CGATGAGGCGTTGGTCGCCA
1 CGATGAGGCGTTGGTCGCCA
117912987 TTCTGGTGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
37 19 0.38
40 30 0.60
41 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.30, T:0.30
Consensus pattern (38 bp):
CGATGAGGCGTTGGTCGCCACTTTTGCTTCGAACTAGC
Found at i:117914307 original size:33 final size:34
Alignment explanation
Indices: 117914260--117914325 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
117914250 TTTTTAATTA
* * *
117914260 AATTTTACCCTCAACCTTTT-AAAAAGTGTTAAT
1 AATTTGACCATCAACCTTTTGAAAAAGAGTTAAT
117914293 AATTTGACCATCAACCTTTTGAAAAAGAGTTAA
1 AATTTGACCATCAACCTTTTGAAAAAGAGTTAA
117914326 ATTGATGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.62
34 11 0.38
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (34 bp):
AATTTGACCATCAACCTTTTGAAAAAGAGTTAAT
Found at i:117916309 original size:13 final size:13
Alignment explanation
Indices: 117916291--117916315 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
117916281 GATTTTTTGA
117916291 ATTTTTTTATTTC
1 ATTTTTTTATTTC
117916304 ATTTTTTTATTT
1 ATTTTTTTATTT
117916316 TTATTAATGA
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:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
ATTTTTTTATTTC
Found at i:117924012 original size:34 final size:34
Alignment explanation
Indices: 117923943--117924019 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
117923933 TATTCAAATA
*
117923943 TTTTTATTTAAGTTATTGAATTATTTAAAAGTTT
1 TTTTTATTTAAGTTATTGAACTATTTAAAAGTTT
*
117923977 TTTTTATTTAAGTTATTGAGCT-TTT--AAG-TT
1 TTTTTATTTAAGTTATTGAACTATTTAAAAGTTT
117924007 TTTTT-TTTAAGTT
1 TTTTTATTTAAGTT
117924020 CCGTTAGCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
29 8 0.20
30 7 0.17
31 3 0.07
33 3 0.07
34 20 0.49
ACGTcount: A:0.26, C:0.01, G:0.10, T:0.62
Consensus pattern (34 bp):
TTTTTATTTAAGTTATTGAACTATTTAAAAGTTT
Found at i:117924016 original size:29 final size:32
Alignment explanation
Indices: 117923926--117924019 Score: 97
Period size: 34 Copynumber: 3.0 Consensus size: 32
117923916 TTTTTTTGCC
* * *
117923926 ATTGAACTATTCAAA-TATTTTTATTTAAGTT
1 ATTGAACTATTTAAAGTTTTTTTTTTTAAGTT
*
117923957 ATTGAATTATTTAAAAGTTTTTTTTATTTAAGTT
1 ATTGAACTATTT-AAAGTTTTTTTT-TTTAAGTT
*
117923991 ATTGAGCT-TTT-AAG-TTTTTTTTTTAAGTT
1 ATTGAACTATTTAAAGTTTTTTTTTTTAAGTT
117924020 CCGTTAGCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 8 0.15
30 7 0.13
31 13 0.24
32 3 0.06
33 9 0.17
34 14 0.26
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (32 bp):
ATTGAACTATTTAAAGTTTTTTTTTTTAAGTT
Found at i:117951022 original size:30 final size:30
Alignment explanation
Indices: 117950980--117951044 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
117950970 TCAAATAATA
*
117950980 TATTA-AATTTTTATATTTTTATTCAAAGC
1 TATTATAACTTTTATATTTTTATTCAAAGC
117951009 TATTATAACTTTTATATTTTTATTCAAAGC
1 TATTATAACTTTTATATTTTTATTCAAAGC
117951039 TATTAT
1 TATTAT
117951045 CAATTGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (30 bp):
TATTATAACTTTTATATTTTTATTCAAAGC
Found at i:117952665 original size:20 final size:20
Alignment explanation
Indices: 117952636--117952676 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
117952626 AGCTTCCTTC
* * *
117952636 TAACATCAAGGAGTTGCTTG
1 TAACACCAAGAAGTTGATTG
117952656 TAACACCAAGAAGTTGATTG
1 TAACACCAAGAAGTTGATTG
117952676 T
1 T
117952677 TGGAAAATCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (20 bp):
TAACACCAAGAAGTTGATTG
Found at i:117957365 original size:34 final size:34
Alignment explanation
Indices: 117957295--117957367 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 34
117957285 AAATATCAAT
*
117957295 TTTTATTTAAAAATAAATAAATTTTAATATTTTA
1 TTTTATTTAAAAATAAATAAATTTTAATATTCTA
*
117957329 TTTTATTTAAAAA-AAAT-CATTATTAATGATTCTA
1 TTTTATTTAAAAATAAATAAATT-TTAAT-ATTCTA
117957363 TTTTA
1 TTTTA
117957368 GTTGGTTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 3 0.09
33 9 0.26
34 23 0.66
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (34 bp):
TTTTATTTAAAAATAAATAAATTTTAATATTCTA
Found at i:117960931 original size:42 final size:42
Alignment explanation
Indices: 117960849--117960931 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
117960839 AGAAACAGGG
* *
117960849 GACACACGACCGTGTCCCTGCCCGTGTAACTCACTGACTTGA
1 GACACACGACCGTGTCCCAGCCCGTGTAACTCACTAACTTGA
* * * *
117960891 GACATACGACCGTGTCCCAGCCTGTGTAATTTACTAACTTG
1 GACACACGACCGTGTCCCAGCCCGTGTAACTCACTAACTTG
117960932 GGTCACATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.25
Consensus pattern (42 bp):
GACACACGACCGTGTCCCAGCCCGTGTAACTCACTAACTTGA
Found at i:117964148 original size:19 final size:19
Alignment explanation
Indices: 117964124--117964163 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
117964114 GACTTAAATT
117964124 CTAGTATTGTGTGTCGTGA
1 CTAGTATTGTGTGTCGTGA
117964143 CTAGTATTGTGTGTCGTGA
1 CTAGTATTGTGTGTCGTGA
117964162 CT
1 CT
117964164 TTGAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.12, G:0.30, T:0.42
Consensus pattern (19 bp):
CTAGTATTGTGTGTCGTGA
Found at i:117971228 original size:49 final size:50
Alignment explanation
Indices: 117971173--117971268 Score: 176
Period size: 50 Copynumber: 1.9 Consensus size: 50
117971163 AATCGAACAA
*
117971173 AACTTAAAA-TTAACTTTTAATACAAAAATCTTCACGATACTTATTATAT
1 AACTTAAAAGTTAACTTTTAATACAAAAATCTTCACGACACTTATTATAT
117971222 AACTTAAAAGTTAACTTTTAATACAAAAATCTTCACGACACTTATTA
1 AACTTAAAAGTTAACTTTTAATACAAAAATCTTCACGACACTTATTA
117971269 CATGATATCT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 9 0.20
50 36 0.80
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (50 bp):
AACTTAAAAGTTAACTTTTAATACAAAAATCTTCACGACACTTATTATAT
Found at i:117976980 original size:29 final size:30
Alignment explanation
Indices: 117976937--117977001 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
117976927 TGCAACAATC
* * *
117976937 AAAAGAAAGCAAAAT-AAAATAAAAAGGTA
1 AAAAGAAAACAAAATAAAAATAAAAACGAA
*
117976966 AAAAGAAAACGAAATAAAAATAAAAACGAA
1 AAAAGAAAACAAAATAAAAATAAAAACGAA
117976996 AAAAGA
1 AAAAGA
117977002 TCTAGTGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.75, C:0.05, G:0.12, T:0.08
Consensus pattern (30 bp):
AAAAGAAAACAAAATAAAAATAAAAACGAA
Found at i:117976998 original size:24 final size:23
Alignment explanation
Indices: 117976953--117976997 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
117976943 AAGCAAAATA
117976953 AAATAAAAAGGTAAAAAGAAAACG
1 AAATAAAAA-GTAAAAAGAAAACG
117976977 AAATAAAAA-TAAAAACGAAAA
1 AAATAAAAAGTAAAAA-GAAAA
117976998 AAGATCTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 9 0.45
ACGTcount: A:0.76, C:0.04, G:0.11, T:0.09
Consensus pattern (23 bp):
AAATAAAAAGTAAAAAGAAAACG
Found at i:117979377 original size:18 final size:18
Alignment explanation
Indices: 117979327--117979377 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
117979317 ATTATATACA
* *
117979327 TTATATCTTATTATGTGTT
1 TTATATATTATT-TATGTT
*
117979346 TTAT-TATTCTTTTATGTT
1 TTATATATT-ATTTATGTT
117979364 TTATATATTATTTA
1 TTATATATTATTTA
117979378 AGCTATCATG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (18 bp):
TTATATATTATTTATGTT
Found at i:117980468 original size:130 final size:131
Alignment explanation
Indices: 117980302--117980687 Score: 492
Period size: 132 Copynumber: 2.9 Consensus size: 131
117980292 TTTAGAGATT
* * * **
117980302 ATGAGTGAAGTTCTAAAGGAATATTCGATTGTTTTGAGTGAACGGAG-AATTGCAACCCAGCACG
1 ATGAGTGAAATTCTAAAGGGATATTCGATTATTTTGAGCAAACGGAGAAATTGCAACCCAGCACG
* * * * *
117980366 ATAGGGCACGATTCCCGAATTGCCAAACATCGAGTATTACCTTTGTTTTAAAGAGTTTTAGAAAA
66 TTAGGGCACGATTCCCGAATTGCCAAATATCGAATATCACCTTTGTTTTAAAGAATTTTAGAAAA
117980431 C
131 C
* *
117980432 ATGAATGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAAC-GAGAAATTGCAACCCAGCACG
1 ATGAGTGAAATTCTAAAGGGATATTCGATTATTTTGAGCAAACGGAGAAATTGCAACCCAGCACG
* * * * *
117980496 TTAGGGCACGATTCCGCAAATTTCCAAATATCGAACATCGCATTTGTTTTAAA-ATATTTTTAGA
66 TTAGGGCACGATTCC-CGAATTGCCAAATATCGAATATCACCTTTGTTTTAAAGA-A-TTTTAGA
*
117980560 AGAC
128 AAAC
* *
117980564 ATGAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACGG-GAAATTGCAACCCAGCACG
1 ATGAGTGAAATTCTAAAGGGATATTCGATTATTTTGAGCAAACGGAGAAATTGCAACCCAGCACG
* * * *
117980628 TTAGGGCAAGATTTCGCGAATTGCCAAATATCGAATCTCACCTTCGTTTTAAAGAATTTT
66 TTAGGGCACGA-TTCCCGAATTGCCAAATATCGAATATCACCTTTGTTTTAAAGAATTTT
117980688 TAAACGAATA
Statistics
Matches: 218, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
129 3 0.01
130 68 0.31
131 33 0.15
132 109 0.50
133 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (131 bp):
ATGAGTGAAATTCTAAAGGGATATTCGATTATTTTGAGCAAACGGAGAAATTGCAACCCAGCACG
TTAGGGCACGATTCCCGAATTGCCAAATATCGAATATCACCTTTGTTTTAAAGAATTTTAGAAAA
C
Found at i:117982882 original size:50 final size:51
Alignment explanation
Indices: 117982820--117982925 Score: 153
Period size: 51 Copynumber: 2.1 Consensus size: 51
117982810 AAAGTGATAA
* *
117982820 GCTACACTTATCTGATCAAGGA-AAAGTGA-AAGTGATAAGTGATAGCTTCG
1 GCTACACTTATCTGATCAAGGACAAA-TGACAAGTGAAAAGTGATAGCTCCG
* *
117982870 GCTACACTTATCTGATCAATGACAAATGACAAGTGAAAAGTGGTAGCTCCG
1 GCTACACTTATCTGATCAAGGACAAATGACAAGTGAAAAGTGATAGCTCCG
117982921 GCTAC
1 GCTAC
117982926 CTGATCAGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
50 24 0.48
51 26 0.52
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (51 bp):
GCTACACTTATCTGATCAAGGACAAATGACAAGTGAAAAGTGATAGCTCCG
Found at i:117982939 original size:31 final size:31
Alignment explanation
Indices: 117982901--117983018 Score: 202
Period size: 31 Copynumber: 3.8 Consensus size: 31
117982891 ACAAATGACA
117982901 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
117982932 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
117982963 AGTGAAAAGTGGTAG-TACCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCT-CCGGCTACCTGATC
* *
117982994 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGGCTAC
117983019 AAGTGACAAG
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
30 1 0.01
31 81 0.98
32 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:117983122 original size:47 final size:46
Alignment explanation
Indices: 117983041--117983250 Score: 212
Period size: 47 Copynumber: 4.6 Consensus size: 46
117983031 ATTTCCGTAC
* * * * * *
117983041 AAGACCATATCTGGGATATGACATCGGTGTGATATATGCTACTGTAT
1 AAGACCATAGCTGGGATATGGCATCAGTGTGATATGTGATAC-GTGT
* * *
117983088 AAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATTCGTGT
1 AAGACCATAGCTGGGATATGGCATCAGTGTGATATGTGATACGTGT
* *
117983134 AAGACCATAGCTGGGTTATGGCATCGATATGTGATATGTGATTACGTGT
1 AAGACCATAGCTGGGATATGGCATC-A-GTGTGATATGTGA-TACGTGT
* * * *
117983183 AAGACCATAGCTGGGCTATGGCATC-G-AT-ATATG-AATATGTGT
1 AAGACCATAGCTGGGATATGGCATCAGTGTGATATGTGATACGTGT
*
117983225 AAGACCATAGCTGGGCTATGGCATCA
1 AAGACCATAGCTGGGATATGGCATCA
117983251 TTATGTGAAG
Statistics
Matches: 142, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
42 31 0.22
43 1 0.01
44 5 0.04
45 1 0.01
46 26 0.18
47 37 0.26
48 11 0.08
49 30 0.21
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (46 bp):
AAGACCATAGCTGGGATATGGCATCAGTGTGATATGTGATACGTGT
Found at i:117983191 original size:49 final size:47
Alignment explanation
Indices: 117983087--117983258 Score: 205
Period size: 49 Copynumber: 3.7 Consensus size: 47
117983077 TGCTACTGTA
* * * *
117983087 TAAGACCATATCTGGGATATGGCATCA-GTGAGATATGTGATTCGTG
1 TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
*
117983133 TAAGACCATAGCTGGGTTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATT-CGTG
*
117983182 TAAGACCATAGCTGGGCTATGGCATCGATATATGA-A--T-A-T-GTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATTCGTG
117983224 TAAGACCATAGCTGGGCTATGGCATCATTATGTGA
1 TAAGACCATAGCTGGGCTATGGCATCA-TATGTGA
117983259 AGATGTGTAA
Statistics
Matches: 115, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
41 1 0.01
42 35 0.30
44 1 0.01
45 1 0.01
46 25 0.22
47 1 0.01
48 14 0.12
49 37 0.32
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (47 bp):
TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
Found at i:117983225 original size:42 final size:43
Alignment explanation
Indices: 117983130--117983293 Score: 181
Period size: 42 Copynumber: 3.7 Consensus size: 43
117983120 TATGTGATTC
* *
117983130 GTGTAAGACCATAGCTGGGTTATGGCATCGATATGTGATATG-TGATT
1 GTGTAAGACCATAGCTGGGCTATGGCATCG--AT-T-ATATGAAGA-T
*
117983177 ACGTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 --GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
*
117983221 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* **
117983263 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
117983294 GAAAATGAAG
Statistics
Matches: 104, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
41 1 0.01
42 64 0.62
43 1 0.01
44 6 0.06
45 2 0.02
47 1 0.01
49 29 0.28
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:117986635 original size:46 final size:46
Alignment explanation
Indices: 117986568--117986739 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
117986558 TGTAACCCGC
*
117986568 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
117986614 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * *
117986664 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTC--G-GATCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
117986704 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
117986740 ATGCCAACCA
Statistics
Matches: 107, Mismatches: 8, Indels: 23
0.78 0.06 0.17
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 1 0.01
42 2 0.02
43 27 0.25
46 35 0.33
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:117986732 original size:90 final size:92
Alignment explanation
Indices: 117986576--117986744 Score: 297
Period size: 90 Copynumber: 1.8 Consensus size: 92
117986566 GCCCATAAGT
*
117986576 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTC-GGCGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
117986641 CGAGTTCGGATGCCTAGTTACATCTCAC
65 CGAGTTCGGATGCCTAGTTACATCTCAC
*
117986669 GAACTCGGACTCAACTCAACGAGTTC-G-GATCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCGATCGCATCCATAAGTGAACTCGGACTCAACTCAAC
117986732 GAGTTCGGATGCC
66 GAGTTCGGATGCC
117986745 AACCATCCTA
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
90 48 0.65
91 1 0.01
93 25 0.34
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCGATCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:117989157 original size:29 final size:29
Alignment explanation
Indices: 117989118--117989205 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
117989108 CAAAGATAAC
*
117989118 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
117989147 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
117989176 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
117989206 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:117989176 original size:15 final size:15
Alignment explanation
Indices: 117989118--117989196 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
117989108 CAAAGATAAC
*
117989118 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
117989132 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
117989147 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
117989161 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
117989176 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
117989191 AAGAAA
1 AAGAAA
117989197 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:117989205 original size:15 final size:15
Alignment explanation
Indices: 117989129--117989205 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
117989119 AGAAAACCGA
117989129 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
117989144 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
117989158 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
117989172 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
117989188 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
117989203 ATA
1 ATA
117989206 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:117992211 original size:46 final size:46
Alignment explanation
Indices: 117992144--117992315 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
117992134 TGTAACCCGC
*
117992144 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
117992190 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * *
117992240 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTC--G-GATCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
117992280 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
117992316 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 8, Indels: 23
0.78 0.06 0.17
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 1 0.01
42 2 0.02
43 27 0.25
46 35 0.33
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:117992308 original size:90 final size:92
Alignment explanation
Indices: 117992152--117992319 Score: 295
Period size: 90 Copynumber: 1.8 Consensus size: 92
117992142 GCCCATAAGT
*
117992152 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTC-GGCGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
117992217 CGAGTTCGGATGCCTAGTTACATCTCAC
65 CGAGTTCGGATGCCTAGTTACATCTCAC
*
117992245 GAACTCGGACTCAACTCAACGAGTTC-G-GATCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCGATCGCATCCATAAGTGAACTCGGACTCAACTCAAC
117992308 GAGTTCGGATGC
66 GAGTTCGGATGC
117992320 TCAACCATCC
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
90 47 0.64
91 1 0.01
93 25 0.34
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCGATCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:117993916 original size:53 final size:53
Alignment explanation
Indices: 117993835--117993985 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
117993825 CTTACACGGT
* * * *
117993835 TCACATATCATACCGAAGCCATATCCCAGAC-ATGTTCTTATACGGAATCATATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
117993890 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
117993943 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
117993986 GCACACTTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.01
53 79 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:118001924 original size:19 final size:19
Alignment explanation
Indices: 118001900--118001945 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
118001890 AACACACACA
118001900 AGTAAGCTTATTGAAGCTT
1 AGTAAGCTTATTGAAGCTT
*
118001919 AGTAAGGTTATTGAAGCTT
1 AGTAAGCTTATTGAAGCTT
118001938 AGTAAGCT
1 AGTAAGCT
118001946 CATAGGCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.35
Consensus pattern (19 bp):
AGTAAGCTTATTGAAGCTT
Found at i:118002319 original size:53 final size:53
Alignment explanation
Indices: 118002238--118002388 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
118002228 CTTACACGGT
* *
118002238 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
118002293 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
118002346 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
118002389 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:118007639 original size:21 final size:22
Alignment explanation
Indices: 118007611--118007666 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
118007601 TAAATTTTTT
118007611 AGAA-AATATTTAAAATG-TAA
1 AGAATAATATTTAAAATGATAA
*
118007631 AGAATAATA-TTATAATGATAA
1 AGAATAATATTTAAAATGATAA
*
118007652 AGAATAACATTTAAA
1 AGAATAATATTTAAA
118007667 TTTATTTCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 11 0.37
21 15 0.50
22 4 0.13
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (22 bp):
AGAATAATATTTAAAATGATAA
Found at i:118009711 original size:20 final size:20
Alignment explanation
Indices: 118009688--118009728 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
118009678 TCAAACCATG
*
118009688 AATCTCAAA-CCCAAATCTTA
1 AATCACAAACCCCAAAT-TTA
118009708 AATCACAAACCCCAAATTTA
1 AATCACAAACCCCAAATTTA
118009728 A
1 A
118009729 GATTTTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (20 bp):
AATCACAAACCCCAAATTTA
Found at i:118015676 original size:18 final size:19
Alignment explanation
Indices: 118015628--118015676 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
118015618 TTGAATACTA
*
118015628 ATAAAATATTAAATTAATTT
1 ATAAAATA-TATATTAATTT
*
118015648 CTAAAAT-TATATTAA-TT
1 ATAAAATATATATTAATTT
118015665 ATAAAATATATA
1 ATAAAATATATA
118015677 AATTATAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 8 0.32
18 11 0.44
20 6 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAAATATATATTAATTT
Found at i:118015680 original size:16 final size:17
Alignment explanation
Indices: 118015649--118015683 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
118015639 AATTAATTTC
*
118015649 TAAAATTATATTAATTA
1 TAAAATTATATAAATTA
118015666 TAAAA-TATATAAATTA
1 TAAAATTATATAAATTA
118015682 TA
1 TA
118015684 GGTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTATATAAATTA
Found at i:118016181 original size:4 final size:4
Alignment explanation
Indices: 118016167--118016196 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
118016157 AATTAGAGGA
118016167 GATT GGATT GATT GATT GATT GATT GATT G
1 GATT -GATT GATT GATT GATT GATT GATT G
118016197 GGTTTCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (4 bp):
GATT
Found at i:118023662 original size:51 final size:50
Alignment explanation
Indices: 118023591--118023750 Score: 230
Period size: 51 Copynumber: 3.2 Consensus size: 50
118023581 TTGATCACAT
*
118023591 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAAGTTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGAGTAGCT-AAGCTACCACTTATCAC
**
118023642 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCGT
1 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAC
* * * *
118023692 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGAGTAGCT-AAGCTACCACTTATCAC
*
118023743 TTGTCACT
1 TTATCACT
118023751 GATCAGAAGT
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 44 0.44
51 55 0.56
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (50 bp):
TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAC
Found at i:118032331 original size:16 final size:17
Alignment explanation
Indices: 118032310--118032346 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
118032300 GGGTGGAAAG
118032310 AAAACTGAAAA-GAT-GA
1 AAAACT-AAAAGGATAGA
118032326 AAAACTAAAAGGATAGA
1 AAAACTAAAAGGATAGA
118032343 AAAA
1 AAAA
118032347 TAGAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 9 0.47
17 6 0.32
ACGTcount: A:0.68, C:0.05, G:0.16, T:0.11
Consensus pattern (17 bp):
AAAACTAAAAGGATAGA
Found at i:118038542 original size:14 final size:15
Alignment explanation
Indices: 118038520--118038553 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
118038510 AATTGAAAAT
*
118038520 TTAATATTATT-TTA
1 TTAAAATTATTCTTA
118038534 TTAAAATTATTCTTA
1 TTAAAATTATTCTTA
118038549 TTAAA
1 TTAAA
118038554 TAAATAACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAAAATTATTCTTA
Found at i:118039721 original size:5 final size:5
Alignment explanation
Indices: 118039704--118039736 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
118039694 AAAATAAAAT
118039704 ATTAA TATT-A ATTAA ATTAA ATTAA ATTAA ATT
1 ATTAA -ATTAA ATTAA ATTAA ATTAA ATTAA ATT
118039737 GTAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 3 0.12
5 20 0.77
6 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
ATTAA
Found at i:118042154 original size:12 final size:12
Alignment explanation
Indices: 118042137--118042163 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
118042127 AGCGTGTGAG
118042137 ACATGAACTCAA
1 ACATGAACTCAA
118042149 ACATGAACTCAA
1 ACATGAACTCAA
118042161 ACA
1 ACA
118042164 GGTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.15
Consensus pattern (12 bp):
ACATGAACTCAA
Found at i:118046656 original size:20 final size:19
Alignment explanation
Indices: 118046634--118046671 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
118046624 TAATTTTTGA
*
118046634 AAAATGATTTATTTTTCTG
1 AAAATGATTTACTTTTCTG
118046653 AAAATGATTTACTTTTCTG
1 AAAATGATTTACTTTTCTG
118046672 GTGTTTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (19 bp):
AAAATGATTTACTTTTCTG
Found at i:118054388 original size:132 final size:131
Alignment explanation
Indices: 118054121--118054762 Score: 639
Period size: 132 Copynumber: 4.9 Consensus size: 131
118054111 TAGAAAATAC
** * * *
118054121 GAGTGAAATTCCGAAGAGATATTCGATTATTTTGAACAAACGGGAGATTGCAACCCAGCACGATA
1 GAGTGAAATTTTGAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAGCACGATA
* * * *
118054186 GGGTACTATTCCCCGAATTGCCAAACATCGAACATTTCTTTCGTTTTAAA-GAGTTTTTAGAA-A
66 GGGCACGATT-CCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAAGGA-TTTTTAGAAGA
*
118054249 AAGT
129 CA-T
* ** * * * *
118054253 GAGTGAAATTTTGAAGGGATCTTCGATCGTTTCGAACAAATGAAAAAGTGCAACCCAGCACGATA
1 GAGTGAAATTTTGAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAGCACGATA
* * * *
118054318 GGGCACGATTCTCGAATTGCCAAACATTGAACATCGCCTTCGTTTTAAAGGGTTTTCTTA-ATA-
66 GGGCACGATTCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAA-GGATTT-TTAGA-AG
118054381 ACAT
128 ACAT
*** * * * * * **
118054385 GAGTGAAAACCTAAAGGAATATTCAATTGTTTTGAACAAATGAGAAATCACAACCCAGCACGATA
1 GAGTGAAATTTTGAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAGCACGATA
* * * ** * *
118054450 GGGCATGATTCCCGAATTGTCAAACACCGAGTATTGCCTTCGTTTTGAAGGATTTTTAGAAGACC
66 GGGCACGATTCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAAGGATTTTTAGAAGACA
118054515 T
131 T
* * * *
118054516 CAGTGAAATTTTGAAGGGATATTTGATTATTTTGAGA-AAACGAGAAATTGCAACCCAACACGTT
1 GAGTGAAATTTTGAAGGGATATTCGATTATTTTGA-ACAAACGAGAAATTGCAACCCAGCACGAT
* ** * *
118054580 AGGGCACGATTCCGCGAATTGCCAAATATTAAACATTGCCTTCGTTTTAAAGAATTTTTAAAAGA
65 AGGGCACGATTCC-CGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAAGGATTTTTAGAAGA
118054645 CAT
129 CAT
* * *
118054648 GAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACAC-ATT
1 GAGTGAAATTTTGAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAGCACGA-T
* * ** ** *
118054712 AGGGCACAATTCAACGAATCACCAAGTATCGAACATCGCCTTCGTTTTAAA
65 AGGGCACGATTC-CCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAA
118054763 TAATTGTGAA
Statistics
Matches: 415, Mismatches: 84, Indels: 22
0.80 0.16 0.04
Matches are distributed among these distances:
130 4 0.01
131 103 0.25
132 301 0.73
133 7 0.02
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (131 bp):
GAGTGAAATTTTGAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAGCACGATA
GGGCACGATTCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAAGGATTTTTAGAAGACA
T
Found at i:118054589 original size:263 final size:265
Alignment explanation
Indices: 118054139--118054762 Score: 643
Period size: 263 Copynumber: 2.4 Consensus size: 265
118054129 TTCCGAAGAG
* * * ** *
118054139 ATATTCGATTATTTTGAACAAACGGGAGATTGCAACCCAGCACGATAGGGTACTATTCCCCGAAT
1 ATATTCAATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACTATTCCCCGAAT
* * * * *
118054204 TGCCAAACATCGAACATTTCTTTCGTTTTAAAGAGTTTTTAGAAAAAGTGAGTGAAATTTTGAAG
66 TGCCAAACACCGAACATTGCCTTCGTTTTAAAGAGTTTTTAGAAAAACTCAGTGAAATTTTGAAG
* * * * *
118054269 GGATCTTCGATCGTTTCGAACAAATGAAAAAGTGCAACCCAGCACGATAGGGCACGATT-CTCGA
131 GGATATTCGATCATTTCGAACAAACGAAAAAGTGCAACCCAACACGATAGGGCACGATTCCGCGA
*
118054333 ATTGCCAAACATTGAACATCGCCTTCGTTTTAAAGGGTTTTCTTAATAACATGAGTGAAAACCTA
196 ATTGCCAAACATTAAACATCGCCTTCGTTTTAAAGGGTTTTCTTAATAACATGAGTGAAAACCTA
118054398 AAGGA
261 AAGGA
* *
118054403 ATATTCAATTGTTTTGAACAAATGAGAAATCACAACCCAGCACGATAGGGCA-TGATT-CCCGAA
1 ATATTCAATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACT-ATTCCCCGAA
* ** * * *
118054466 TTGTCAAACACCGAGTATTGCCTTCGTTTTGAAG-GATTTTTAGAAGACCTCAGTGAAATTTTGA
65 TTGCCAAACACCGAACATTGCCTTCGTTTTAAAGAG-TTTTTAGAAAAACTCAGTGAAATTTTGA
* * * * * *
118054530 AGGGATATTTGATTATTTTGAGA-AAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
129 AGGGATATTCGATCATTTCGA-ACAAACGAAAAAGTGCAACCCAACACGATAGGGCACGATTCCG
* * ** * *
118054594 CGAATTGCCAAATATTAAACATTGCCTTCGTTTTAAA-GAATTT-TTAAAAGACATGAGTGAAAT
193 CGAATTGCCAAACATTAAACATCGCCTTCGTTTTAAAGGGTTTTCTTAATA-ACATGAGTGAAAA
** * *
118054657 TTTGAAGGG
257 CCTAAAGGA
* * * ** * * **
118054666 ATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACAC-ATTAGGGCACAATTCAACGAA
1 ATATTCAATTATTTTGAACAAACGAGAAATCACAACCCAGCACGA-TAGGGCACTATTCCCCGAA
** ** * *
118054730 TCACCAAGTATCGAACATCGCCTTCGTTTTAAA
65 TTGCCAAACACCGAACATTGCCTTCGTTTTAAA
118054763 TAATTGTGAA
Statistics
Matches: 290, Mismatches: 62, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
262 7 0.02
263 173 0.60
264 110 0.38
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (265 bp):
ATATTCAATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACTATTCCCCGAAT
TGCCAAACACCGAACATTGCCTTCGTTTTAAAGAGTTTTTAGAAAAACTCAGTGAAATTTTGAAG
GGATATTCGATCATTTCGAACAAACGAAAAAGTGCAACCCAACACGATAGGGCACGATTCCGCGA
ATTGCCAAACATTAAACATCGCCTTCGTTTTAAAGGGTTTTCTTAATAACATGAGTGAAAACCTA
AAGGA
Found at i:118056143 original size:2 final size:2
Alignment explanation
Indices: 118056136--118056164 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
118056126 ACATGCAAAC
118056136 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
118056165 AATACATAAT
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
Done.