Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 20 of 172
Found at i:6388724 original size:17 final size:18
Alignment explanation
Indices: 6388702--6388736 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6388692 GATATGATAC
*
6388702 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
6388719 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
6388737 AAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:6389047 original size:19 final size:19
Alignment explanation
Indices: 6389019--6389090 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
6389009 AATCATATCT
6389019 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
6389038 TCTAAAATTG--TATCA-A
1 TCTAAGATTGCATATCATA
6389054 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
6389073 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
6389091 TGAAGATTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
16 10 0.21
17 5 0.10
18 5 0.10
19 28 0.58
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:6389098 original size:17 final size:19
Alignment explanation
Indices: 6389022--6389098 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
6389012 CATATCTTCT
*
6389022 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
* *
6389041 AAAATTG--TATCA-ATCT
1 AAGATTGCATATCATATCG
*
6389057 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
6389076 AAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCG
6389093 AAGATT
1 AAGATT
6389099 ATATTTCCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
16 10 0.19
17 11 0.21
18 6 0.12
19 25 0.48
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:6390000 original size:82 final size:82
Alignment explanation
Indices: 6389870--6390022 Score: 272
Period size: 82 Copynumber: 1.9 Consensus size: 82
6389860 ATCTTAAAGG
*
6389870 TTTCTTAATTTCTCCAAGATTGGGTTTCTCTTTCAACACAAGCTCAAGAATTCTATGGGTGGCAT
1 TTTCTTAACTTCTCCAAGATTGGGTTTCTCTTTCAACACAAGCTCAAGAATTCTATGGGTGGCAT
6389935 AAAAAAAAATTTAAACA
66 AAAAAAAAATTTAAACA
*
6389952 TTTCTTAACTTCTCCATGATTGGGTTTCTCTTTCAA-AGCAAGCTCAAGAATTCTATGGGTGGCA
1 TTTCTTAACTTCTCCAAGATTGGGTTTCTCTTTCAACA-CAAGCTCAAGAATTCTATGGGTGGCA
6390016 TAAAAAA
65 TAAAAAA
6390023 TTCAGTGTTG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
81 1 0.01
82 67 0.99
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (82 bp):
TTTCTTAACTTCTCCAAGATTGGGTTTCTCTTTCAACACAAGCTCAAGAATTCTATGGGTGGCAT
AAAAAAAAATTTAAACA
Found at i:6392859 original size:3 final size:3
Alignment explanation
Indices: 6392851--6392876 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6392841 AAAAGGTCTG
6392851 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
6392877 AATATCTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:6395313 original size:131 final size:128
Alignment explanation
Indices: 6395015--6395346 Score: 415
Period size: 130 Copynumber: 2.6 Consensus size: 128
6395005 TTGCCACTAA
* * * *
6395015 CAAGAGTGAAGATTGAATCTTCGAGCTGTTTAACCTTTGATTTT-TATTTTCAGAAAAG-AAAAG
1 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCAGAAAAGAAAAAG
* * *
6395078 --AGAAGGCCTGCTTGGTCCCTTTACCTAAGAAAATGCTCTTCCTGATTGGTATTCAATCACCAG
66 AAAAAAGGCCTGCTTGGTCCC--TACCTAAGAAAATACTCTTCCTGATTGATATTCAATCACCAG
6395141 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCAGAAAAAGAAAGA
1 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCAG-AAAAGAAA-A
* * * *
6395206 AGAAAAAAGGCCTGCTTGGTGCCC-ATCTAAGAAATTACTCTTGCTGATTGATATTCGATCACCA
64 AGAAAAAAGGCCTGCTTGGT-CCCTACCTAAGAAAATACTCTTCCTGATTGATATTCAATCACCA
6395270 G
128 G
* * * *
6395271 CAAGGTGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGC-TTAGAATTCTCAGGAAAAGAAAA
1 CAA-GAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCA-GAAAAGAAAA
*
6395335 GGAAAAAAGGCC
64 AGAAAAAAGGCC
6395347 ATCTTGTTGT
Statistics
Matches: 181, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
126 41 0.23
127 8 0.04
128 5 0.03
129 14 0.08
130 58 0.32
131 37 0.20
132 15 0.08
133 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (128 bp):
CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCAGAAAAGAAAAAG
AAAAAAGGCCTGCTTGGTCCCTACCTAAGAAAATACTCTTCCTGATTGATATTCAATCACCAG
Found at i:6395382 original size:130 final size:130
Alignment explanation
Indices: 6395015--6395421 Score: 395
Period size: 130 Copynumber: 3.2 Consensus size: 130
6395005 TTGCCACTAA
* * * ** *
6395015 CAAGAGTGAAGATTGAATCTTCGAGCTGTTTAACCTTTGATTT-TTATTTTCAG-AAAAG-AA-A
1 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTAGAATTATCAGAAAAAGAAAGA
* * * *
6395076 AG--AGAAGGCCTGCTTGGT-CCCTTTACCTAAGAAAATGCTCTTCCTGATTGGTATTCAATCAC
66 AGAAAAAAGGCCTGCTTGGTGCCC---ATCTAAGAAAATGCTCTTGCTGATTGATATTCAATCAC
6395138 CAG
128 CAG
* *
6395141 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCAGAAAAAGAAAGA
1 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTAGAATTATCAGAAAAAGAAAGA
* * *
6395206 AGAAAAAAGGCCTGCTTGGTGCCCATCTAAGAAATTACTCTTGCTGATTGATATTCGATCACCAG
66 AGAAAAAAGGCCTGCTTGGTGCCCATCTAAGAAAATGCTCTTGCTGATTGATATTCAATCACCAG
* * *
6395271 CAAGGTGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGC-TTAGAATTCTCAGGAAAAGAAA-
1 CAA-GAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTAGAATTATCAGAAAAAGAAAG
* * * * ** * ** *
6395334 AGGAAAAAAGGCCAT-CTTGTTGTCCGTGCCT-AGAAAATGCTCCAGCTGATTGGTGGTCAACCA
65 AAGAAAAAAGGCC-TGCTTGGTGCCCAT--CTAAGAAAATGCTCTTGCTGATTGATATTCAATCA
*
6395397 CTAG
127 CCAG
* *
6395401 CAAGAGCAAACATTGAATCTT
1 CAAGAGTAAAGATTGAATCTT
6395422 CGAGTAACAA
Statistics
Matches: 236, Mismatches: 34, Indels: 19
0.82 0.12 0.07
Matches are distributed among these distances:
126 40 0.17
127 8 0.03
128 5 0.02
129 38 0.16
130 89 0.38
131 38 0.16
132 15 0.06
133 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (130 bp):
CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTAGAATTATCAGAAAAAGAAAGA
AGAAAAAAGGCCTGCTTGGTGCCCATCTAAGAAAATGCTCTTGCTGATTGATATTCAATCACCAG
Found at i:6398480 original size:30 final size:32
Alignment explanation
Indices: 6398446--6398516 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
6398436 ACATTTTGAT
6398446 TAATTTTT-AAA-AGTTTAATAAATATTT-TTA
1 TAATTTTTAAAATAGTTTAA-AAATATTTCTTA
*
6398476 TAATTTTTAAAATTATTTTAAAAATATTTCTTA
1 TAATTTTTAAAA-TAGTTTAAAAATATTTCTTA
6398509 TAATTTTT
1 TAATTTTT
6398517 TTAATTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 8 0.22
31 3 0.08
32 8 0.22
33 17 0.47
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (32 bp):
TAATTTTTAAAATAGTTTAAAAATATTTCTTA
Found at i:6406658 original size:9 final size:9
Alignment explanation
Indices: 6406644--6406677 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
6406634 GATCAAGCAA
6406644 AATTAAATT
1 AATTAAATT
6406653 AATTAAATT
1 AATTAAATT
*
6406662 AATCAAATT
1 AATTAAATT
6406671 AATTAAA
1 AATTAAA
6406678 ATAAATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
AATTAAATT
Found at i:6407175 original size:20 final size:19
Alignment explanation
Indices: 6407128--6407182 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
6407118 AATTTAATAC
**
6407128 TTATCTTAATATTATTGTA
1 TTATCTTAATATTAAAGTA
6407147 TTAAT-TTAATATTAAAGTGA
1 TT-ATCTTAATATTAAAGT-A
6407167 TTATCTTAATATTAAA
1 TTATCTTAATATTAAA
6407183 TTTAATCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (19 bp):
TTATCTTAATATTAAAGTA
Found at i:6407194 original size:68 final size:69
Alignment explanation
Indices: 6407104--6407238 Score: 200
Period size: 68 Copynumber: 2.0 Consensus size: 69
6407094 TGTAATAAAT
* * * * *
6407104 TTAATATTTAATTTAATTTAATACTTATCTTAAT-ATTATTGTATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATCTAATACTTATCTTAATAAGTATTATATTAATTTAATAATAAAGTGAT
6407168 TATC
66 TATC
* *
6407172 TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATAATAAAGTGAT
1 TTAATATTAAATTTAATCTAATACTTATCTTAATAAGTATTATATTAATTTAATAATAAAGTGAT
6407237 TA
66 TA
6407239 AATTTAATCA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
68 30 0.51
69 29 0.49
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (69 bp):
TTAATATTAAATTTAATCTAATACTTATCTTAATAAGTATTATATTAATTTAATAATAAAGTGAT
TATC
Found at i:6407399 original size:26 final size:26
Alignment explanation
Indices: 6407370--6407421 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
6407360 TTAGAAAATT
*
6407370 TATAAAGATATTTTTCATATTTACAA
1 TATAAAGATATTTTCCATATTTACAA
6407396 TATAAAGATATTTTCCATATTTACAA
1 TATAAAGATATTTTCCATATTTACAA
6407422 CTTGATCCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (26 bp):
TATAAAGATATTTTCCATATTTACAA
Found at i:6409996 original size:26 final size:27
Alignment explanation
Indices: 6409958--6410010 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
6409948 TTTTTATTTC
* *
6409958 ATTTTATTTTAA-TAATAAGTTAAAAT
1 ATTTTATTTTAATTAAAAAGTAAAAAT
6409984 ATTTT-TTTCTAATTAAAAAGTAAAAAT
1 ATTTTATTT-TAATTAAAAAGTAAAAAT
6410011 TAATTGTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.13
26 8 0.35
27 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (27 bp):
ATTTTATTTTAATTAAAAAGTAAAAAT
Found at i:6410909 original size:32 final size:32
Alignment explanation
Indices: 6410873--6410942 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
6410863 ATTTTAGGGA
** *
6410873 GGTGAATGTTCTTATTTATGTGTGTATATTTT
1 GGTGAATGTTCTTATCGATGTGTGCATATTTT
*
6410905 GGTGATTGTTCTTATCGATGTGTGCATATTTT
1 GGTGAATGTTCTTATCGATGTGTGCATATTTT
6410937 GGTGAA
1 GGTGAA
6410943 ATATTAAGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.50
Consensus pattern (32 bp):
GGTGAATGTTCTTATCGATGTGTGCATATTTT
Found at i:6427727 original size:50 final size:50
Alignment explanation
Indices: 6427673--6427774 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
6427663 ATTATAGATG
6427673 TATGGAATTCATTTCATAATGTATGCCGTGTTTCATAGATATTATATTTT
1 TATGGAATTCATTTCATAATGTATGCCGTGTTTCATAGATATTATATTTT
6427723 TATGGAATTCATTTCATAATGTATGCCGTGTTTCATAGATATTATATTTT
1 TATGGAATTCATTTCATAATGTATGCCGTGTTTCATAGATATTATATTTT
6427773 TA
1 TA
6427775 AGTTATCTAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (50 bp):
TATGGAATTCATTTCATAATGTATGCCGTGTTTCATAGATATTATATTTT
Found at i:6428657 original size:24 final size:25
Alignment explanation
Indices: 6428624--6428691 Score: 95
Period size: 24 Copynumber: 2.8 Consensus size: 25
6428614 AAGTCTGTCT
* *
6428624 GGAGAAGATTTAGAAGCTGAA-AAG
1 GGAGAGGATTTAGGAGCTGAATAAG
*
6428648 GGAGAGGATTTAGGAGCT-AATCAG
1 GGAGAGGATTTAGGAGCTGAATAAG
6428672 GGAGAGGATTTAGGAGCTGA
1 GGAGAGGATTTAGGAGCTGA
6428692 TTAGGGTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
23 2 0.05
24 36 0.92
25 1 0.03
ACGTcount: A:0.37, C:0.06, G:0.38, T:0.19
Consensus pattern (25 bp):
GGAGAGGATTTAGGAGCTGAATAAG
Found at i:6430192 original size:29 final size:27
Alignment explanation
Indices: 6430133--6430220 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 27
6430123 GAAGCGTCCC
*
6430133 GGTGGCTATGCCACAATTATCTGATCT
1 GGTGGCTTTGCCACAATTATCTGATCT
* *
6430160 GGTGGCTTTGCCACATATATATCTGTTTT
1 GGTGGCTTTGCCACA-AT-TATCTGATCT
*
6430189 GGTGG-TTCTGCCACGATTATCTGTATCT
1 GGTGGCTT-TGCCACAATTATCTG-ATCT
6430217 GGTG
1 GGTG
6430221 ACTCTATCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 20 0.39
28 12 0.24
29 19 0.37
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (27 bp):
GGTGGCTTTGCCACAATTATCTGATCT
Found at i:6433099 original size:18 final size:18
Alignment explanation
Indices: 6433076--6433117 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
6433066 GTTAAGGACC
6433076 ATTGATGATAGTGACGCT
1 ATTGATGATAGTGACGCT
6433094 ATTGATGATAGTGACGCT
1 ATTGATGATAGTGACGCT
6433112 ATTGAT
1 ATTGAT
6433118 CGTGACCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (18 bp):
ATTGATGATAGTGACGCT
Found at i:6436903 original size:24 final size:24
Alignment explanation
Indices: 6436870--6436943 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
6436860 AAGTCTGTCT
*
6436870 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
6436894 GGAGAGGATTTAGGAACTGATCAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
6436918 GGAGAGAATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
6436942 GG
1 GG
6436944 TGAACTGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.39, T:0.22
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:6438417 original size:27 final size:27
Alignment explanation
Indices: 6438377--6438490 Score: 106
Period size: 27 Copynumber: 4.1 Consensus size: 27
6438367 AGGAAGCATC
*
6438377 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTTTGCCACAATTATCTGAT
* *
6438404 CTGGTGGCTTTGCCACATATATATATGTT
1 CTGGTGGCTTTGCCACA-AT-TATCTGAT
*
6438433 CTGGTGG-TTCTGCCACGATTATCTGTAT
1 CTGGTGGCTT-TGCCACAATTATCTG-AT
* * * *
6438461 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTTTGCCACAATTATCTGAT
6438487 CTGG
1 CTGG
6438491 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
26 5 0.07
27 29 0.40
28 18 0.25
29 20 0.28
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.39
Consensus pattern (27 bp):
CTGGTGGCTTTGCCACAATTATCTGAT
Found at i:6439549 original size:45 final size:45
Alignment explanation
Indices: 6439498--6439586 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
6439488 TTACCCATGT
6439498 TGGAATTTTAAGAATTAGTGAAGTTTGTTG-AGATTGTCATTGTAG
1 TGGAATTTTAAGAATTAGTGAAGTTTG-TGAAGATTGTCATTGTAG
*
6439543 TGGAATTTTAAGAATTAGTGAAGTTTGTGAAGATTTTCATTGTA
1 TGGAATTTTAAGAATTAGTGAAGTTTGTGAAGATTGTCATTGTA
6439587 AGGAAACTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 2 0.05
45 40 0.95
ACGTcount: A:0.30, C:0.02, G:0.25, T:0.43
Consensus pattern (45 bp):
TGGAATTTTAAGAATTAGTGAAGTTTGTGAAGATTGTCATTGTAG
Found at i:6442742 original size:18 final size:19
Alignment explanation
Indices: 6442719--6442760 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
6442709 ATGTGACCCC
6442719 TGTTTTCCC-AAATTTTCA
1 TGTTTTCCCAAAATTTTCA
6442737 TGTTTTCCCAAAATTTTCA
1 TGTTTTCCCAAAATTTTCA
6442756 TGTTT
1 TGTTT
6442761 GTTTCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.52
Consensus pattern (19 bp):
TGTTTTCCCAAAATTTTCA
Found at i:6443323 original size:38 final size:38
Alignment explanation
Indices: 6443199--6443309 Score: 152
Period size: 38 Copynumber: 2.9 Consensus size: 38
6443189 ACAAAATTTG
* * *
6443199 CATGTTTACTGTTAATAATAAATTTG-GTACGTGTTAAA
1 CATGTCTACTGTTAATAATGAA-TTGAGTACATGTTAAA
* *
6443237 CATGTCTACTGTTAATGATGAATTGAGTAGATGTTAAA
1 CATGTCTACTGTTAATAATGAATTGAGTACATGTTAAA
*
6443275 CATGTCTACTGTTAATAATGAATTGAGCACATGTT
1 CATGTCTACTGTTAATAATGAATTGAGTACATGTT
6443310 GTACCTGTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
37 3 0.05
38 61 0.95
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (38 bp):
CATGTCTACTGTTAATAATGAATTGAGTACATGTTAAA
Found at i:6444787 original size:38 final size:38
Alignment explanation
Indices: 6444670--6444794 Score: 153
Period size: 38 Copynumber: 3.3 Consensus size: 38
6444660 ACATAATTTG
* *
6444670 CATGTCTACTGTTAATAATAAATTAAGTACTTGTTAAA
1 CATGTCTACTGTTAATAATGAATTAAGTACATGTTAAA
* * * *
6444708 CATGTCTACTATTAATGATGAATTAAGTATATATTAAA
1 CATGTCTACTGTTAATAATGAATTAAGTACATGTTAAA
* **
6444746 CATGTCTACTGTTAATAATGAATTGAA-CACATGTTGTA
1 CATGTCTACTGTTAATAATGAATT-AAGTACATGTTAAA
6444784 CATGTCTACTG
1 CATGTCTACTG
6444795 CTACTGTTGA
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 71 0.97
39 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (38 bp):
CATGTCTACTGTTAATAATGAATTAAGTACATGTTAAA
Found at i:6445084 original size:89 final size:89
Alignment explanation
Indices: 6444917--6445087 Score: 200
Period size: 89 Copynumber: 1.9 Consensus size: 89
6444907 CTAGAAGCAA
* * * * **
6444917 ATTTTATTTACGAGATTTTTCTGTGTATCCACAGCCAAAGGTAGATTCTAATTTTGGGATAATTG
1 ATTTTATCTACGAGATTTTTCTGTGCATCCACAGCCAAAGGCAGATTCTAACTGCGGGATAATTG
** *
6444982 TTGTGTTTTCATAGCCAGAGGCTG
66 TTGTGCGTCCATAGCCAGAGGCTG
* * * * *
6445006 ATTTTATCTGCGAGATTTTTGTTGTGCATCCATAGCCAGAGGCAGATTCTAACTGCGGGAT-TTT
1 ATTTTATCTACGAGATTTTT-CTGTGCATCCACAGCCAAAGGCAGATTCTAACTGCGGGATAATT
6445070 GTTGTGCGTCCATAGCCA
65 GTTGTGCGTCCATAGCCA
6445088 CTGACAGTTT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
89 35 0.52
90 32 0.48
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (89 bp):
ATTTTATCTACGAGATTTTTCTGTGCATCCACAGCCAAAGGCAGATTCTAACTGCGGGATAATTG
TTGTGCGTCCATAGCCAGAGGCTG
Found at i:6445085 original size:44 final size:45
Alignment explanation
Indices: 6444991--6445087 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
6444981 GTTGTGTTTT
* * *
6444991 CATAGCCAGAGGCTGATTTTATCTGCGAGATTTTTGTTGTGCATC
1 CATAGCCAGAGGCAGATTCTAACTGCGAGATTTTTGTTGTGCATC
* *
6445036 CATAGCCAGAGGCAGATTCTAACTGCGGGA-TTTTGTTGTGCGTC
1 CATAGCCAGAGGCAGATTCTAACTGCGAGATTTTTGTTGTGCATC
6445080 CATAGCCA
1 CATAGCCA
6445088 CTGACAGTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 21 0.45
45 26 0.55
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (45 bp):
CATAGCCAGAGGCAGATTCTAACTGCGAGATTTTTGTTGTGCATC
Found at i:6447003 original size:11 final size:11
Alignment explanation
Indices: 6446987--6447012 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6446977 AAAACTAATC
6446987 TTAATTAATAA
1 TTAATTAATAA
6446998 TTAATTAATAA
1 TTAATTAATAA
6447009 TTAA
1 TTAA
6447013 AATAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTAATTAATAA
Found at i:6450611 original size:6 final size:7
Alignment explanation
Indices: 6450593--6450618 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6450583 ATAACGGGTA
6450593 ATTTTTT
1 ATTTTTT
6450600 ATTTTTT
1 ATTTTTT
6450607 ATTTTTT
1 ATTTTTT
6450614 ATTTT
1 ATTTT
6450619 GTAATATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:6456702 original size:7 final size:7
Alignment explanation
Indices: 6456690--6456714 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6456680 CATTTCTAAA
6456690 CATCCCT
1 CATCCCT
6456697 CATCCCT
1 CATCCCT
6456704 CATCCCT
1 CATCCCT
6456711 CATC
1 CATC
6456715 ATTCATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.56, G:0.00, T:0.28
Consensus pattern (7 bp):
CATCCCT
Found at i:6464432 original size:27 final size:27
Alignment explanation
Indices: 6464393--6464446 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
6464383 AAAAAGACTA
6464393 AGTGATGCAGTAATGGGAATGAACATG
1 AGTGATGCAGTAATGGGAATGAACATG
**
6464420 AGTGATGTGGTAATGGGAATGAACATG
1 AGTGATGCAGTAATGGGAATGAACATG
6464447 TCTAGGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (27 bp):
AGTGATGCAGTAATGGGAATGAACATG
Found at i:6465400 original size:117 final size:117
Alignment explanation
Indices: 6465194--6465425 Score: 428
Period size: 117 Copynumber: 2.0 Consensus size: 117
6465184 CAAAAAGGAA
* * *
6465194 AAATGTATGAGCTTAAGTTCAAAATAAGTTTGGGGGTGTTCTAAAGGTTCGCTTAAAGAAAAAGG
1 AAATGCATGAGCTTAAGTTCAAAATAAGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAAGG
6465259 TTGTATTACGAGAAAACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAACTG
66 TTGTATTACGAGAAAACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAACTG
*
6465311 AAATGCATGAGCTTAAGTTCAAAATATGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAAGG
1 AAATGCATGAGCTTAAGTTCAAAATAAGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAAGG
6465376 TTGTATTACGAGAAAACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAAC
66 TTGTATTACGAGAAAACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAAC
6465426 CAAAATGTCC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 111 1.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (117 bp):
AAATGCATGAGCTTAAGTTCAAAATAAGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAAGG
TTGTATTACGAGAAAACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAACTG
Found at i:6466673 original size:19 final size:19
Alignment explanation
Indices: 6466646--6466687 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
6466636 CATCTCTAAA
*
6466646 TTCTCTTAGCATTCTTCTT
1 TTCTATTAGCATTCTTCTT
6466665 TTCTATTAGCATTCTTCTT
1 TTCTATTAGCATTCTTCTT
6466684 TTCT
1 TTCT
6466688 CCCCACGCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.12, C:0.24, G:0.05, T:0.60
Consensus pattern (19 bp):
TTCTATTAGCATTCTTCTT
Found at i:6467481 original size:19 final size:22
Alignment explanation
Indices: 6467448--6467487 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
6467438 AGTTTATTTA
6467448 TGTTATAATTGTTGC-AAAATG
1 TGTTATAATTGTTGCTAAAATG
6467469 TGTT-TAATT-TTGCTAAAAT
1 TGTTATAATTGTTGCTAAAAT
6467488 CTATTTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (22 bp):
TGTTATAATTGTTGCTAAAATG
Found at i:6468500 original size:25 final size:25
Alignment explanation
Indices: 6468400--6468493 Score: 68
Period size: 24 Copynumber: 3.8 Consensus size: 25
6468390 GGTTGTATAA
**
6468400 CAGGAAGCTCATAAGAGCCA-TAAT
1 CAGGAAGCTCCGAAGAGCCATTAAT
* * * *
6468424 CAGAAAGCTCATGTA-AGCCAATAA-
1 CAGGAAGCTC-CGAAGAGCCATTAAT
* *
6468448 CGGGTAGCTCCGAAGAGCCATTAAT
1 CAGGAAGCTCCGAAGAGCCATTAAT
* *
6468473 CAGGAAGCTCCGGATAGCCAT
1 CAGGAAGCTCCGAAGAGCCAT
6468494 ATATCAGAAG
Statistics
Matches: 52, Mismatches: 14, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
23 2 0.04
24 29 0.56
25 21 0.40
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.17
Consensus pattern (25 bp):
CAGGAAGCTCCGAAGAGCCATTAAT
Found at i:6477373 original size:17 final size:16
Alignment explanation
Indices: 6477337--6477382 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
6477327 TTTAGTATAG
6477337 ATATTTATAAAAACAT
1 ATATTTATAAAAACAT
6477353 ATATTTATGAAACAA-AT
1 ATATTTAT-AAA-AACAT
6477370 ATATTTATAAAAA
1 ATATTTATAAAAA
6477383 AAGTAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.07
16 11 0.39
17 13 0.46
18 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (16 bp):
ATATTTATAAAAACAT
Found at i:6478615 original size:21 final size:21
Alignment explanation
Indices: 6478589--6478630 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
6478579 AGTTTCATTG
6478589 TTAGCACCATTGCATTCTTTT
1 TTAGCACCATTGCATTCTTTT
6478610 TTAGCACCATTGCATTCTTTT
1 TTAGCACCATTGCATTCTTTT
6478631 GTTAAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.48
Consensus pattern (21 bp):
TTAGCACCATTGCATTCTTTT
Found at i:6478662 original size:47 final size:47
Alignment explanation
Indices: 6478609--6478705 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
6478599 TGCATTCTTT
6478609 TTTAGCACCATTGCATTCTTTTGTTAAATTTGTCGAGTGTCTTGAAA
1 TTTAGCACCATTGCATTCTTTTGTTAAATTTGTCGAGTGTCTTGAAA
6478656 TTTAGCACCATTGCATTCTTTTGTTAAATTTGTCGAGTGTCTTGAAA
1 TTTAGCACCATTGCATTCTTTTGTTAAATTTGTCGAGTGTCTTGAAA
6478703 TTT
1 TTT
6478706 TTAAAAAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.46
Consensus pattern (47 bp):
TTTAGCACCATTGCATTCTTTTGTTAAATTTGTCGAGTGTCTTGAAA
Found at i:6481568 original size:18 final size:18
Alignment explanation
Indices: 6481545--6481579 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6481535 ATGTGTCCCT
6481545 TCCACAAGGGCGCGTGTC
1 TCCACAAGGGCGCGTGTC
* *
6481563 TCCACACGGGCGTGTGT
1 TCCACAAGGGCGCGTGT
6481580 AGCTTTCACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.31, G:0.34, T:0.20
Consensus pattern (18 bp):
TCCACAAGGGCGCGTGTC
Found at i:6481626 original size:19 final size:19
Alignment explanation
Indices: 6481602--6481640 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6481592 GGCATGTAGG
*
6481602 CTTCCACACGGCCAAGGCA
1 CTTCCACACAGCCAAGGCA
6481621 CTTCCACACAGCCAAGGCA
1 CTTCCACACAGCCAAGGCA
6481640 C
1 C
6481641 ACAACTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.44, G:0.18, T:0.10
Consensus pattern (19 bp):
CTTCCACACAGCCAAGGCA
Found at i:6483673 original size:16 final size:16
Alignment explanation
Indices: 6483652--6483708 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
6483642 TTTGGTTCGC
*
6483652 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
6483668 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
6483684 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
6483700 TGTAATGGA
1 TGTAATGGA
6483709 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:6483975 original size:18 final size:17
Alignment explanation
Indices: 6483954--6483988 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6483944 TTATTATTAA
*
6483954 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
6483972 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
6483989 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:6486373 original size:12 final size:12
Alignment explanation
Indices: 6486356--6486381 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6486346 TACAAAAAAT
6486356 AGAAGCTGCTAC
1 AGAAGCTGCTAC
6486368 AGAAGCTGCTAC
1 AGAAGCTGCTAC
6486380 AG
1 AG
6486382 CAATAACCAA
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:0.35, C:0.23, G:0.27, T:0.15
Consensus pattern (12 bp):
AGAAGCTGCTAC
Found at i:6492114 original size:16 final size:17
Alignment explanation
Indices: 6492082--6492114 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6492072 ATTTTATAAG
6492082 TTTAATACAAAGGTTAA
1 TTTAATACAAAGGTTAA
*
6492099 TTTAATA-AATGGTTAA
1 TTTAATACAAAGGTTAA
6492115 ATGTAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.39
Consensus pattern (17 bp):
TTTAATACAAAGGTTAA
Found at i:6493465 original size:35 final size:35
Alignment explanation
Indices: 6493363--6493465 Score: 109
Period size: 35 Copynumber: 2.9 Consensus size: 35
6493353 CAATGTTATC
* * *
6493363 TGGCGTGCTGGATGGTACTGGCTCTAATGAACAAT
1 TGGCGTGCTGGATGGTACTGACTCTTATGAGCAAT
* * * *
6493398 TGGTGTGCTAGATGGTACTGACT-TTCACGAGCAGT
1 TGGCGTGCTGGATGGTACTGACTCTT-ATGAGCAAT
* *
6493433 TGGCGTGTTGGATGGTACTGCCTCTTATGAGCA
1 TGGCGTGCTGGATGGTACTGACTCTTATGAGCA
6493466 TCTAGTATGT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
34 1 0.02
35 51 0.94
36 2 0.04
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.31
Consensus pattern (35 bp):
TGGCGTGCTGGATGGTACTGACTCTTATGAGCAAT
Found at i:6496144 original size:17 final size:18
Alignment explanation
Indices: 6496131--6496990 Score: 373
Period size: 18 Copynumber: 48.9 Consensus size: 18
6496121 TAATCTTCAA
6496131 TGATATGCAATCTTAGATG
1 TGATATGCAATCTTAGA-G
6496150 TGATATGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496167 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496186 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496202 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496221 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496237 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496256 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496272 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496291 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496307 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496326 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496342 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496361 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496377 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496396 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496412 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496431 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496447 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496466 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496482 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496501 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496517 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496536 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496552 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496571 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496587 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496606 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496622 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496641 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496657 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496676 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496692 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496711 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496727 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496746 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496762 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496781 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496797 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496816 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496832 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496851 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496867 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496886 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496902 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
6496921 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
6496937 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
*
6496956 TGAT-TGCAATCTTAGATA
1 TGATATGCAATCTTAGA-G
*
6496974 TGATATACAATCTTAGA
1 TGATATGCAATCTTAGA
6496991 AGATATGATT
Statistics
Matches: 679, Mismatches: 47, Indels: 230
0.71 0.05 0.24
Matches are distributed among these distances:
15 44 0.06
16 24 0.04
17 255 0.38
18 259 0.38
19 51 0.08
20 46 0.07
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (18 bp):
TGATATGCAATCTTAGAG
Found at i:6496200 original size:35 final size:35
Alignment explanation
Indices: 6496138--6496990 Score: 1670
Period size: 35 Copynumber: 24.3 Consensus size: 35
6496128 CAATGATATG
*
6496138 CAATCTTAGATGTGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
6496174 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496209 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496244 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496279 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496314 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496349 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496384 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496419 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496454 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496489 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496524 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496559 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496594 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496629 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496664 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496699 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496734 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496769 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496804 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496839 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496874 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496909 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
6496944 CAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
6496981 CAATCTTAGA
1 CAATCTTAGA
6496991 AGATATGATT
Statistics
Matches: 814, Mismatches: 1, Indels: 3
1.00 0.00 0.00
Matches are distributed among these distances:
35 786 0.97
36 15 0.02
37 13 0.02
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:6499273 original size:25 final size:25
Alignment explanation
Indices: 6499239--6499289 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
6499229 CTACTTGTTT
6499239 GCCAATCTTTCTTTCAAGGTAATCA
1 GCCAATCTTTCTTTCAAGGTAATCA
6499264 GCCAATCTTTCTTTCAAGGTAATCA
1 GCCAATCTTTCTTTCAAGGTAATCA
6499289 G
1 G
6499290 AGCAACTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (25 bp):
GCCAATCTTTCTTTCAAGGTAATCA
Found at i:6502212 original size:1 final size:1
Alignment explanation
Indices: 6502206--6502270 Score: 58
Period size: 1 Copynumber: 65.0 Consensus size: 1
6502196 CTTCTATTTC
* * * * * * * *
6502206 AAAAAAAAAAAGAAAAAAGAAAAAAAAGAAAAGAAAAAGAGAAAAAAAAGAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6502271 TGGAGAGGCC
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:6502237 original size:22 final size:23
Alignment explanation
Indices: 6502206--6502264 Score: 90
Period size: 21 Copynumber: 2.7 Consensus size: 23
6502196 CTTCTATTTC
6502206 AAAAAA-AAAAAGAAAAA-AGAA
1 AAAAAAGAAAAAGAAAAAGAGAA
6502227 AAAAAAG-AAAAGAAAAAGAGAA
1 AAAAAAGAAAAAGAAAAAGAGAA
6502249 AAAAAAGAAAAA-AAAA
1 AAAAAAGAAAAAGAAAA
6502265 GAAAAATGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
21 16 0.46
22 15 0.43
23 4 0.11
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAAAGAAAAAGAGAA
Found at i:6502245 original size:27 final size:27
Alignment explanation
Indices: 6502210--6502270 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 27
6502200 TATTTCAAAA
* *
6502210 AAAAAAAGAAAAAAGAAAAAAAAGAAAAG
1 AAAAAGAGAAAAAA-AAGAAAAA-AAAAG
6502239 AAAAAGAGAAAAAAAAGAAAAAAAAAG
1 AAAAAGAGAAAAAAAAGAAAAAAAAAG
6502266 AAAAA
1 AAAAA
6502271 TGGAGAGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 10 0.33
28 7 0.23
29 13 0.43
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (27 bp):
AAAAAGAGAAAAAAAAGAAAAAAAAAG
Found at i:6503369 original size:79 final size:81
Alignment explanation
Indices: 6503261--6503415 Score: 251
Period size: 79 Copynumber: 1.9 Consensus size: 81
6503251 TTAAATTTGC
* *
6503261 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGA-A-GACTCGCCTAAATCCCCTAAGTAGT
1 AGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAGACGACTCGCCTAAATCCCCTAAGCAGT
6503324 AGGGTAACAGGTTCGT
66 AGGGTAACAGGTTCGT
* *
6503340 AGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGATGACTACTCGCCTTAATCCCCTAAGCAG
1 AGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGA-GACGACTCGCCTAAATCCCCTAAGCAG
6503405 TAGGGTAACAG
65 TAGGGTAACAG
6503416 ATCTTATCCC
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
79 36 0.52
81 1 0.01
82 32 0.46
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (81 bp):
AGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAGACGACTCGCCTAAATCCCCTAAGCAGT
AGGGTAACAGGTTCGT
Found at i:6503848 original size:206 final size:206
Alignment explanation
Indices: 6503494--6504901 Score: 2568
Period size: 206 Copynumber: 6.8 Consensus size: 206
6503484 TAGACCAAAG
* * * * *
6503494 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTG
1 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
*
6503559 CTTATAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
66 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
6503624 AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
131 AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
6503689 GAGGGCAGACA
196 GAGGGCAGACA
6503700 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
1 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
6503765 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
66 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
6503830 AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
131 AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
6503895 GAGGGCAGACA
196 GAGGGCAGACA
6503906 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
1 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
6503971 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
66 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
6504036 AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
131 AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
6504101 GAGGGCAGACA
196 GAGGGCAGACA
6504112 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
1 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
6504177 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
66 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
6504242 AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
131 AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
6504307 GAGGGCAGACA
196 GAGGGCAGACA
6504318 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
1 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
6504383 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
66 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
6504448 AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
131 AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
6504513 GAGGGCAGACA
196 GAGGGCAGACA
6504524 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
1 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
* ** *
6504589 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCGA-GTGCTTACGCCGAAGCAAGTC
66 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTC-ACGTGTTTACGATGAAGCAAATC
* * * * * *
6504653 TAAGATAATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCGCCTCCATATTCGAC
130 TAAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGAC
*
6504718 GGAGGGTAGACA
195 GGAGGGCAGACA
*
6504730 CATAGCAGCTCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
1 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
* * * * *
6504795 CTTACAAGGAGAAAATCGAAGACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGAAGCAAACCT
66 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
*
6504860 AAGATGATTTGGCATCTCTGTATTGTCA-AGAAACAAATCGAA
131 AAGATGATTTGGCATATCTGTATTGTCAGAG-AACAAATCGAA
6504902 GAAGCAGATT
Statistics
Matches: 1174, Mismatches: 25, Indels: 6
0.97 0.02 0.00
Matches are distributed among these distances:
205 2 0.00
206 1171 1.00
207 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (206 bp):
CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
GAGGGCAGACA
Found at i:6505322 original size:19 final size:19
Alignment explanation
Indices: 6505297--6505387 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
6505287 ATGATCTTCA
6505297 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
6505316 TTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
6505335 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
6505352 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
6505370 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
6505388 AGATATGATT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 34 0.52
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:6505337 original size:14 final size:15
Alignment explanation
Indices: 6505318--6505373 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
6505308 TCTTAGATTT
6505318 GATATG-CAATCTTA
1 GATATGACAATCTTA
6505332 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
6505349 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
6505367 GATATGA
1 GATATGA
6505374 TATACAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:6505367 original size:35 final size:37
Alignment explanation
Indices: 6505305--6505394 Score: 134
Period size: 35 Copynumber: 2.5 Consensus size: 37
6505295 CAATGATATG
*
6505305 CAATCTTAGATTTGATATGCAATCTTAGATATG-ATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGAATA
6505341 CAATCTTAGATATGAT-TGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGA-ATA
6505378 CAATCTTAGA-A-GATATG
1 CAATCTTAGATATGATATG
6505395 ATTTTGTAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
35 19 0.38
36 18 0.36
37 13 0.26
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (37 bp):
CAATCTTAGATATGATATGCAATCTTAGATATGAATA
Found at i:6519889 original size:29 final size:30
Alignment explanation
Indices: 6519843--6519944 Score: 77
Period size: 29 Copynumber: 3.4 Consensus size: 30
6519833 ATTTGAGCAC
* *
6519843 TTTTGAAAAGGCTAGGCCCTTCTCTGACCA
1 TTTTGAAAAGGTTAGGCCCTTCTATGACCA
* * *
6519873 TTTTG-AAAGGTTTGG-CCTTCATTTGAGCA
1 TTTTGAAAAGGTTAGGCCCTTC-TATGACCA
* *
6519902 CTTTTGTAAAA-GTTAGGCTCTTATATGACCA
1 -TTTTG-AAAAGGTTAGGCCCTTCTATGACCA
*
6519933 TCTTG-AAAGGTT
1 TTTTGAAAAGGTT
6519945 TGGTTCTTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
28 8 0.14
29 17 0.30
30 14 0.25
31 11 0.20
32 6 0.11
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.37
Consensus pattern (30 bp):
TTTTGAAAAGGTTAGGCCCTTCTATGACCA
Found at i:6519907 original size:60 final size:59
Alignment explanation
Indices: 6519829--6519947 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 59
6519819 TTTGAGAAGC
* * *
6519829 CCTTATTTGAGCACTTTTG-AAAAGGCTAGGCCCTTCTCTGACCATTTTGAAAGGTTTGG
1 CCTTATTTGAGCACTTTTGTAAAA-GCTAGGCCCTTATATGACCATCTTGAAAGGTTTGG
* *
6519888 CCTTCATTTGAGCACTTTTGTAAAAGTTAGGCTCTTATATGACCATCTTGAAAGGTTTGG
1 CCTT-ATTTGAGCACTTTTGTAAAAGCTAGGCCCTTATATGACCATCTTGAAAGGTTTGG
6519948 TTCTTATATG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
59 4 0.08
60 45 0.85
61 4 0.08
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (59 bp):
CCTTATTTGAGCACTTTTGTAAAAGCTAGGCCCTTATATGACCATCTTGAAAGGTTTGG
Found at i:6519953 original size:29 final size:28
Alignment explanation
Indices: 6519867--6519958 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 28
6519857 GGCCCTTCTC
* *
6519867 TGACCATTTTGAAAGGTTTGGCCTTCATT
1 TGACCATTTTGAAAGGTTTGGTCTT-ATA
* * *
6519896 TGAGCACTTTTGTAAAAGTTAGGCTCTTATA
1 TGACCA-TTTTG-AAAGGTTTGG-TCTTATA
*
6519927 TGACCATCTTGAAAGGTTTGGTTCTTATA
1 TGACCATTTTGAAAGGTTTGG-TCTTATA
6519956 TGA
1 TGA
6519959 ACAACCCCTA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
29 23 0.46
30 9 0.18
31 15 0.30
32 3 0.06
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (28 bp):
TGACCATTTTGAAAGGTTTGGTCTTATA
Found at i:6520381 original size:6 final size:6
Alignment explanation
Indices: 6520370--6520404 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
6520360 CGGAGAAATT
6520370 ATTATG ATTATG ATTATG ATTATG ATTATG ATTAT
1 ATTATG ATTATG ATTATG ATTATG ATTATG ATTAT
6520405 TTTTTATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
ATTATG
Found at i:6525287 original size:9 final size:9
Alignment explanation
Indices: 6525273--6525306 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
6525263 GTTTTCGAAT
*
6525273 TCGAATAAC
1 TCGAATAAA
*
6525282 TCGAATAAT
1 TCGAATAAA
6525291 TCGAATAAA
1 TCGAATAAA
6525300 TCGAATA
1 TCGAATA
6525307 TCAAACTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (9 bp):
TCGAATAAA
Found at i:6525291 original size:18 final size:18
Alignment explanation
Indices: 6525270--6525306 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6525260 TGAGTTTTCG
*
6525270 AATTCGAATAACTCGAAT
1 AATTCGAATAAATCGAAT
6525288 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCGAAT
6525306 A
1 A
6525307 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (18 bp):
AATTCGAATAAATCGAAT
Found at i:6526781 original size:51 final size:51
Alignment explanation
Indices: 6526726--6526891 Score: 208
Period size: 57 Copynumber: 3.1 Consensus size: 51
6526716 GTCTTTTTCT
* * *
6526726 TTTTCTTTTTGGAGAAAACCACATTCATTTCCAAATGATTCCATTTCTCCA
1 TTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCATTTCTCCA
* *
6526777 TTTTCATTTTGGAGAAAACTATAATCATTTCCAAATGATTTCATTTCTCCATTTCCA
1 TTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCA-TT-T-C---TCCA
6526834 TTTTCATTTTGGAGAAAACCATAATCATTTCCAAAT-ATTTCCCATTTCTCCA
1 TTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGA-TT-CCATTTCTCCA
6526886 TTTTCA
1 TTTTCA
6526892 CCATTTCTAT
Statistics
Matches: 100, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
51 38 0.38
52 12 0.12
53 1 0.01
54 1 0.01
55 1 0.01
56 2 0.02
57 43 0.43
58 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.43
Consensus pattern (51 bp):
TTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCATTTCTCCA
Found at i:6532913 original size:17 final size:15
Alignment explanation
Indices: 6532889--6532925 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
6532879 AATAAAGAAT
6532889 TAATTTTTTTAAAAA
1 TAATTTTTTTAAAAA
6532904 GTAATATTTTTTAAAAA
1 -TAAT-TTTTTTAAAAA
6532921 TAATT
1 TAATT
6532926 ATAATTTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 8 0.40
17 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
TAATTTTTTTAAAAA
Found at i:6538402 original size:73 final size:72
Alignment explanation
Indices: 6538325--6538507 Score: 186
Period size: 73 Copynumber: 2.5 Consensus size: 72
6538315 GGCTGTATAG
* * * * *
6538325 CGGGAAGCTCATAAGAGCCATAATCAGGAAGCTCATGCGAGCCAATAACAAGTAGCTCCAAAGAG
1 CGGGAAGCTCAAAAGAGCCATAATCAGGAAGCTCAAGCGAGCC-ATAACAAGAAGCCCCAAAGAA
6538390 CCATTAAT
65 CCATTAAT
*** * * * * * *
6538398 CGGGAAGCTCCGGATAGCCATATATCAGGAAGTTCAAGTGAGCCATATCGAGAAGCCCCGAAGAA
1 CGGGAAGCTCAAAAGAGCCATA-ATCAGGAAGCTCAAGCGAGCCATAACAAGAAGCCCCAAAGAA
6538463 CCATTAAT
65 CCATTAAT
* *
6538471 CAGGAAGCTCACAAAGAGCCATTAATCGGGAAGCTCA
1 CGGGAAGCTCA-AAAGAGCCA-TAATCAGGAAGCTCA
6538508 CGAAGAGCCA
Statistics
Matches: 87, Mismatches: 20, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
73 50 0.57
74 35 0.40
75 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (72 bp):
CGGGAAGCTCAAAAGAGCCATAATCAGGAAGCTCAAGCGAGCCATAACAAGAAGCCCCAAAGAAC
CATTAAT
Found at i:6538408 original size:25 final size:25
Alignment explanation
Indices: 6538378--6538527 Score: 112
Period size: 26 Copynumber: 6.0 Consensus size: 25
6538368 AATAACAAGT
6538378 AGCTCCAAAGAGCCATTAATCGGGA
1 AGCTCCAAAGAGCCATTAATCGGGA
** * *
6538403 AGCTCCGGATAGCCA-TATATCAGGA
1 AGCTCCAAAGAGCCATTA-ATCGGGA
* * *
6538428 AG-TTCAAGTGAGCCA-T-ATCGAGA
1 AGCTCCAA-AGAGCCATTAATCGGGA
* * * *
6538451 AGCCCCGAAGAACCATTAATCAGGA
1 AGCTCCAAAGAGCCATTAATCGGGA
6538476 AGCTCACAAAGAGCCATTAATCGGGA
1 AGCTC-CAAAGAGCCATTAATCGGGA
*
6538502 AGCTCACGAAGAGCCATATAA-CGGGA
1 AGCTC-CAAAGAGCCAT-TAATCGGGA
6538528 CACTCATAAG
Statistics
Matches: 95, Mismatches: 23, Indels: 13
0.73 0.18 0.10
Matches are distributed among these distances:
23 12 0.13
24 7 0.07
25 35 0.37
26 38 0.40
27 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (25 bp):
AGCTCCAAAGAGCCATTAATCGGGA
Found at i:6542964 original size:5 final size:5
Alignment explanation
Indices: 6542956--6542987 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
6542946 AATCTTTTAA
6542956 TTATT TTATT TTATT TTATT TTATTT TTATT T
1 TTATT TTATT TTATT TTATT TTA-TT TTATT T
6542988 CAAAAAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:6544420 original size:22 final size:23
Alignment explanation
Indices: 6544393--6544446 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
6544383 AGCTTACCGA
* *
6544393 TTTCAGCTCGTATGAACTTACTG
1 TTTCAGCTCGAAAGAACTTACTG
* *
6544416 -TTCAGATCGAAAGAGCTTACTG
1 TTTCAGCTCGAAAGAACTTACTG
6544438 TTTCAGCTC
1 TTTCAGCTC
6544447 AATAGAGTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (23 bp):
TTTCAGCTCGAAAGAACTTACTG
Found at i:6544453 original size:23 final size:23
Alignment explanation
Indices: 6544381--6544485 Score: 92
Period size: 23 Copynumber: 4.6 Consensus size: 23
6544371 TCATCTCATA
* *
6544381 AGAGCTTACCGATTTCAGCTC-GT
1 AGAGCTTACTG-TTTCAGCTCAAT
* *
6544404 ATGAACTTACTG-TTCAGATCGAA-
1 A-GAGCTTACTGTTTCAGCTC-AAT
6544427 AGAGCTTACTGTTTCAGCTCAAT
1 AGAGCTTACTGTTTCAGCTCAAT
* *
6544450 AGAG-TGTACAGTTTCAGCTCATT
1 AGAGCT-TACTGTTTCAGCTCAAT
6544473 AGAGCTTACTGTT
1 AGAGCTTACTGTT
6544486 CATCAGCTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
22 19 0.29
23 38 0.58
24 9 0.14
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (23 bp):
AGAGCTTACTGTTTCAGCTCAAT
Found at i:6545859 original size:11 final size:11
Alignment explanation
Indices: 6545843--6545867 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6545833 ATTTTTTTCC
6545843 AAAAATAAAAT
1 AAAAATAAAAT
6545854 AAAAATAAAAT
1 AAAAATAAAAT
6545865 AAA
1 AAA
6545868 GTAAGTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:6547575 original size:41 final size:41
Alignment explanation
Indices: 6547527--6547607 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
6547517 ATAGGACAAG
6547527 TCTAAATTTTGCTTGTCTAGAAATAAGGTCTTTAGGATCCA
1 TCTAAATTTTGCTTGTCTAGAAATAAGGTCTTTAGGATCCA
6547568 TCTAAATTTTGCTTGTCTAGAAATAAGGTCTTTAGGATCC
1 TCTAAATTTTGCTTGTCTAGAAATAAGGTCTTTAGGATCC
6547608 TTATAGTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (41 bp):
TCTAAATTTTGCTTGTCTAGAAATAAGGTCTTTAGGATCCA
Found at i:6551514 original size:117 final size:117
Alignment explanation
Indices: 6551308--6551605 Score: 587
Period size: 117 Copynumber: 2.5 Consensus size: 117
6551298 TAAATGTTGA
6551308 GAGCTAGATTTTTTAGAATCAAGACTAAATTAACTTAACGTATAAATATTGATGGTTAAAGTTAG
1 GAGCTAGATTTTTTAGAATCAAGACTAAATTAACTTAACGTATAAATATTGATGGTTAAAGTTAG
6551373 AAATCACCTATTTCTTTCCTTAATAAAGGATCTTGTGAGGCTCGAATCTTGT
66 AAATCACCTATTTCTTTCCTTAATAAAGGATCTTGTGAGGCTCGAATCTTGT
6551425 GAGCTAGATTTTTTAGAATCAAGACTAAATTAACTTAACGTATAAATATTGATGGTTAAAGTTAG
1 GAGCTAGATTTTTTAGAATCAAGACTAAATTAACTTAACGTATAAATATTGATGGTTAAAGTTAG
*
6551490 AAATCACTTATTTCTTTCCTTAATAAAGGATCTTGTGAGGCTCGAATCTTGT
66 AAATCACCTATTTCTTTCCTTAATAAAGGATCTTGTGAGGCTCGAATCTTGT
6551542 GAGCTAGATTTTTTAGAATCAAGACTAAATTAACTTAACGTATAAATATTGATGGTTAAAGTTA
1 GAGCTAGATTTTTTAGAATCAAGACTAAATTAACTTAACGTATAAATATTGATGGTTAAAGTTA
6551606 CTATTATGTC
Statistics
Matches: 180, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 180 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (117 bp):
GAGCTAGATTTTTTAGAATCAAGACTAAATTAACTTAACGTATAAATATTGATGGTTAAAGTTAG
AAATCACCTATTTCTTTCCTTAATAAAGGATCTTGTGAGGCTCGAATCTTGT
Found at i:6552745 original size:12 final size:12
Alignment explanation
Indices: 6552728--6552766 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
6552718 CGGCCCGCCC
6552728 ATATTAATTTTT
1 ATATTAATTTTT
*
6552740 ATATTATTTTTT
1 ATATTAATTTTT
*
6552752 ATATT-ATTTTA
1 ATATTAATTTTT
6552763 ATAT
1 ATAT
6552767 ATATATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:6552928 original size:29 final size:30
Alignment explanation
Indices: 6552886--6552947 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
6552876 ACTTAACAAG
* * *
6552886 CAAATGTTTCTAAAA-AATAACAAAATTAA
1 CAAATGTCTATAAAATAATAAAAAAATTAA
6552915 CAAATGTCTATAAAATAATAAAAAAATTAA
1 CAAATGTCTATAAAATAATAAAAAAATTAA
6552945 CAA
1 CAA
6552948 TAAAATAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.61, C:0.10, G:0.03, T:0.26
Consensus pattern (30 bp):
CAAATGTCTATAAAATAATAAAAAAATTAA
Found at i:6553002 original size:22 final size:22
Alignment explanation
Indices: 6552977--6553019 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6552967 TATCTAAACA
6552977 ATAAAAACAAAATAGTAGCAAC
1 ATAAAAACAAAATAGTAGCAAC
* **
6552999 ATAATAGTAAAATAGTAGCAA
1 ATAAAAACAAAATAGTAGCAA
6553020 AATAGAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAAAAACAAAATAGTAGCAAC
Found at i:6553023 original size:11 final size:11
Alignment explanation
Indices: 6552984--6553024 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
6552974 ACAATAAAAA
6552984 CAAAATAGTAG
1 CAAAATAGTAG
* *
6552995 CAACATAATAG
1 CAAAATAGTAG
*
6553006 TAAAATAGTAG
1 CAAAATAGTAG
6553017 CAAAATAG
1 CAAAATAG
6553025 AGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:6553032 original size:22 final size:22
Alignment explanation
Indices: 6552985--6553034 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
6552975 CAATAAAAAC
* *
6552985 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
6553007 AAAATAGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
6553029 AAAATA
1 AAAATA
6553035 ATAAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.60, C:0.06, G:0.16, T:0.18
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:6564240 original size:88 final size:88
Alignment explanation
Indices: 6564091--6564446 Score: 676
Period size: 88 Copynumber: 4.0 Consensus size: 88
6564081 CTTCTTTACC
*
6564091 CTTGGCAAGTAACTCAAACATTGACAATCTTCTATTTCCTTTGTGCCACTTCTTAGGAGTCCCAT
1 CTTGGCAAGTAACTCAAACTTTGACAATCTTCTATTTCCTTTGTGCCACTTCTTAGGAGTCCCAT
6564156 ATGTAAAGATTTCAATAAAGAGA
66 ATGTAAAGATTTCAATAAAGAGA
6564179 CTTGGCAAGTAACTCAAACTTTGACAATCTTCTATTTCCTTTGTGCCACTTCTTAGGAGTCCCAT
1 CTTGGCAAGTAACTCAAACTTTGACAATCTTCTATTTCCTTTGTGCCACTTCTTAGGAGTCCCAT
6564244 ATGTAAAGATTTCAATAAAGAGA
66 ATGTAAAGATTTCAATAAAGAGA
6564267 CTTGGCAAGTAACTCAAACTTTGACAATCTTCTATTTCCTTTGTGCCACTTCTTAGGAGTCCCAT
1 CTTGGCAAGTAACTCAAACTTTGACAATCTTCTATTTCCTTTGTGCCACTTCTTAGGAGTCCCAT
6564332 ATGTAAAGATTTCAATAAAGAGA
66 ATGTAAAGATTTCAATAAAGAGA
* *
6564355 CTTGGCAAGTAACTCAAACTTTGACAATCTTCTATTTCCTTTGTGCCACTTCCTAGGAGTCACAT
1 CTTGGCAAGTAACTCAAACTTTGACAATCTTCTATTTCCTTTGTGCCACTTCTTAGGAGTCCCAT
*
6564420 ATGTAAAGATTTTAATAAAGAGA
66 ATGTAAAGATTTCAATAAAGAGA
6564443 CTTG
1 CTTG
6564447 AAGAAGTTGA
Statistics
Matches: 264, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 264 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (88 bp):
CTTGGCAAGTAACTCAAACTTTGACAATCTTCTATTTCCTTTGTGCCACTTCTTAGGAGTCCCAT
ATGTAAAGATTTCAATAAAGAGA
Found at i:6571154 original size:25 final size:25
Alignment explanation
Indices: 6571120--6571173 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
6571110 CTAGAATACT
6571120 AATGGATGCCATGAAAATGGTTCTC
1 AATGGATGCCATGAAAATGGTTCTC
6571145 AATGGATGCCATGAAAATGGTTCTC
1 AATGGATGCCATGAAAATGGTTCTC
6571170 AATG
1 AATG
6571174 AATGAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (25 bp):
AATGGATGCCATGAAAATGGTTCTC
Found at i:6580575 original size:28 final size:29
Alignment explanation
Indices: 6580535--6580589 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
6580525 GCAATTACTT
* *
6580535 GTTAACATTTAAC-AA-ATTAAAAGAATA
1 GTTAACATATAACTAAGATAAAAAGAATA
6580562 GTTAGACATATAACTAAGATAAAAAGAA
1 GTTA-ACATATAACTAAGATAAAAAGAA
6580590 ATTTTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 8 0.35
29 2 0.09
30 9 0.39
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.25
Consensus pattern (29 bp):
GTTAACATATAACTAAGATAAAAAGAATA
Found at i:6580721 original size:12 final size:12
Alignment explanation
Indices: 6580702--6580745 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
6580692 TAATAATATG
6580702 ATATAATTT-AA
1 ATATAATTTAAA
6580713 ATAATAATTTAAA
1 AT-ATAATTTAAA
6580726 ATATAATTATAAA
1 ATATAATT-TAAA
6580739 CATATAA
1 -ATATAA
6580746 AACTTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.07
12 13 0.45
13 8 0.28
14 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATAATTTAAA
Found at i:6584154 original size:24 final size:24
Alignment explanation
Indices: 6584112--6584161 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
6584102 TTCCAGAAGG
* *
6584112 TAAAAGTGGGGCCTATGTATTTTT
1 TAAAAGTGGGCCCTATGTACTTTT
6584136 TAAAAGTGGGCCC-ATTGTACTTTT
1 TAAAAGTGGGCCCTA-TGTACTTTT
6584160 TA
1 TA
6584162 GGGATTACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (24 bp):
TAAAAGTGGGCCCTATGTACTTTT
Found at i:6588890 original size:40 final size:39
Alignment explanation
Indices: 6588830--6588964 Score: 162
Period size: 40 Copynumber: 3.4 Consensus size: 39
6588820 TAAATAACAG
* * * * *
6588830 GCTTTGTGCTAGTATATTTATCGGGCTTTGTGCTTAGCA
1 GCTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
* *
6588869 GACTTTGTGCTGGTGTGTTTATTGGGCTTTATGCCTAGTA
1 G-CTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
*
6588909 GGCTTTATGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
1 -GCTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
*
6588949 TGCCTTGTGCTGGTGT
1 -GCTTTGTGCTGGTGT
6588965 TGTCTATCAG
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 79 0.98
41 1 0.01
ACGTcount: A:0.11, C:0.15, G:0.30, T:0.44
Consensus pattern (39 bp):
GCTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
Found at i:6590789 original size:33 final size:33
Alignment explanation
Indices: 6590729--6590792 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
6590719 GAACTATCTT
* ** * *
6590729 TGTGTTTATTGTCCTAGTAGACTTTCTCTATTC
1 TGTGTTTATTGTCCCAACAAACATTCTCTATTC
6590762 TGTGTTTATTGTCCCAACAAACATTCTCTAT
1 TGTGTTTATTGTCCCAACAAACATTCTCTAT
6590793 GGGTTTCATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.47
Consensus pattern (33 bp):
TGTGTTTATTGTCCCAACAAACATTCTCTATTC
Found at i:6591493 original size:20 final size:20
Alignment explanation
Indices: 6591468--6591507 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6591458 CATGACGGAA
6591468 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
6591488 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
6591508 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:6597143 original size:32 final size:32
Alignment explanation
Indices: 6597096--6597159 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
6597086 TTAAAGGGAG
** *
6597096 ATAGTTTGTTGTGGATAATATAGTAAGAGCTC
1 ATAGTTTGTCATGGATAATAGAGTAAGAGCTC
*
6597128 ATAGTTTGTCATGGATATTAGAGTAAGAGCTC
1 ATAGTTTGTCATGGATAATAGAGTAAGAGCTC
6597160 CTTTTAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (32 bp):
ATAGTTTGTCATGGATAATAGAGTAAGAGCTC
Found at i:6602400 original size:22 final size:22
Alignment explanation
Indices: 6602372--6602413 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
6602362 ATTATATTAA
6602372 GAGTTAGATTGCATTTTGCTAG
1 GAGTTAGATTGCATTTTGCTAG
6602394 GAGTTAGATTGCATTTTGCT
1 GAGTTAGATTGCATTTTGCT
6602414 CTCTTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.43
Consensus pattern (22 bp):
GAGTTAGATTGCATTTTGCTAG
Found at i:6604948 original size:30 final size:29
Alignment explanation
Indices: 6604876--6604959 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
6604866 AAAATTATTA
6604876 TAAT-ATTATTATAATTTTTTATAACATTT
1 TAATAATT-TTATAATTTTTTATAACATTT
* * * * *
6604905 AAAAAAATCTATAATTTTTCTATTACATTT
1 TAATAATTTTATAATTTTT-TATAACATTT
6604935 TAATAATTTTATAATTTATTTATAA
1 TAATAATTTTATAATTT-TTTATAA
6604960 TTTTCTAACA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
29 12 0.29
30 28 0.67
31 2 0.05
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (29 bp):
TAATAATTTTATAATTTTTTATAACATTT
Found at i:6604996 original size:24 final size:23
Alignment explanation
Indices: 6604969--6605032 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
6604959 ATTTTCTAAC
6604969 AAAATTTTAATAATTTATATTTTT
1 AAAATTTTAATAATTT-TATTTTT
6604993 AAAA--TT-AT-A-TTTATTTTT
1 AAAATTTTAATAATTTTATTTTT
6605011 -AAATTTTAATAACTTTTTATTT
1 AAAATTTTAATAA--TTTTATTT
6605033 AAATAATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 4 0.12
20 3 0.09
21 3 0.09
22 2 0.06
24 11 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
AAAATTTTAATAATTTTATTTTT
Found at i:6605002 original size:14 final size:16
Alignment explanation
Indices: 6604973--6605004 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
6604963 TCTAACAAAA
6604973 TTTTAATAATTTATAT
1 TTTTAATAATTTATAT
6604989 TTTTAA-AA-TTATAT
1 TTTTAATAATTTATAT
6605003 TT
1 TT
6605005 ATTTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAATAATTTATAT
Found at i:6613612 original size:21 final size:21
Alignment explanation
Indices: 6613572--6613625 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
6613562 TTATTTAAAA
*
6613572 AATATTTTTTAGATAATTTT-
1 AATATTTTTTAAATAATTTTG
*
6613592 AATAATTTTTAAATAACTTTTG
1 AATATTTTTTAAATAA-TTTTG
6613614 AAT-TTTTTTAAA
1 AATATTTTTTAAA
6613626 ATTTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.48
21 12 0.41
22 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (21 bp):
AATATTTTTTAAATAATTTTG
Found at i:6620072 original size:43 final size:43
Alignment explanation
Indices: 6620007--6620088 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
6619997 AACGAAGGAA
* * *
6620007 GTATTAGCAGCTTGCTTGCACCGGTTAGTTGTTTATCCACACT
1 GTATTAGCAGCTTGCTTACACCGATTAGTGGTTTATCCACACT
*
6620050 GTATTAGTAGCTTG-TCTACACCGATTAGTGGTTTATCCA
1 GTATTAGCAGCTTGCT-TACACCGATTAGTGGTTTATCCA
6620089 TACCTATTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 33 0.97
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (43 bp):
GTATTAGCAGCTTGCTTACACCGATTAGTGGTTTATCCACACT
Found at i:6621660 original size:18 final size:20
Alignment explanation
Indices: 6621628--6621674 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
6621618 AGTGAGGGAT
* *
6621628 AAAAGCATAGCAATGA-TTA
1 AAAAGCATTGCAATGAGTGA
6621647 AAAAGCATTG-AATGAGTGA
1 AAAAGCATTGCAATGAGTGA
6621666 AAAA-CATTG
1 AAAAGCATTG
6621675 TGGGTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAAGCATTGCAATGAGTGA
Found at i:6625212 original size:21 final size:21
Alignment explanation
Indices: 6625188--6625232 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6625178 AAAATTTATA
* *
6625188 TTTCTTTAC-ATTTTGTATAAT
1 TTTC-TTACGATTTTATAAAAT
6625209 TTTCTTACGATTTTATAAAAT
1 TTTCTTACGATTTTATAAAAT
6625230 TTT
1 TTT
6625233 ATAAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTCTTACGATTTTATAAAAT
Found at i:6625233 original size:10 final size:10
Alignment explanation
Indices: 6625218--6625245 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6625208 TTTTCTTACG
6625218 ATTTTATAAA
1 ATTTTATAAA
6625228 ATTTTATAAA
1 ATTTTATAAA
6625238 ATTTTATA
1 ATTTTATA
6625246 TTTCTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATTTTATAAA
Found at i:6625269 original size:10 final size:9
Alignment explanation
Indices: 6625219--6625388 Score: 80
Period size: 9 Copynumber: 18.6 Consensus size: 9
6625209 TTTCTTACGA
*
6625219 TTTTATAAAA
1 TTTTAT-AAT
*
6625229 TTTTATAAAA
1 TTTTAT-AAT
6625239 TTTTAT-AT
1 TTTTATAAT
*
6625247 TTCTAT-AT
1 TTTTATAAT
6625255 ATTTTATAACT
1 -TTTTATAA-T
*
6625266 TTTTATGAT
1 TTTTATAAT
*
6625275 TTTTATAAAA
1 TTTTAT-AAT
*
6625285 TTTTACAAT
1 TTTTATAAT
*
6625294 TTTTCTAAT
1 TTTTATAAT
*
6625303 TTTTATAAA
1 TTTTATAAT
6625312 TTTTA-AAT
1 TTTTATAAT
*
6625320 ATTTA-AAT
1 TTTTATAAT
*
6625328 TTTTATTAAAA
1 TTTTA-T-AAT
*
6625339 TTTAATAAT
1 TTTTATAAT
* **
6625348 ATTTATAGC
1 TTTTATAAT
*
6625357 TTTTATTGAT
1 TTTTA-TAAT
* *
6625367 TTTAAT-TT
1 TTTTATAAT
6625375 TTTTATAAT
1 TTTTATAAT
6625384 TTTTA
1 TTTTA
6625389 ATAAAAGCAA
Statistics
Matches: 121, Mismatches: 30, Indels: 19
0.71 0.18 0.11
Matches are distributed among these distances:
8 27 0.22
9 51 0.42
10 36 0.30
11 7 0.06
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (9 bp):
TTTTATAAT
Found at i:6625285 original size:56 final size:59
Alignment explanation
Indices: 6625159--6625289 Score: 155
Period size: 58 Copynumber: 2.3 Consensus size: 59
6625149 TGATGCGATA
** * * *
6625159 ATTTTTATAACTTTTTTTCAAAATTTATATTTCTTTACATTTTGTATAATTTTCTTACG
1 ATTTTTATAAAATTTTATCAAAATTTATATTTCTATACATTTTGTATAACTTTCTTACG
* *
6625218 A-TTTTATAAAATTTTAT-AAAATTTTATATTTCTATATA-TTT-TATAACTTT-TTATG
1 ATTTTTATAAAATTTTATCAAAA-TTTATATTTCTATACATTTTGTATAACTTTCTTACG
6625273 ATTTTTATAAAATTTTA
1 ATTTTTATAAAATTTTA
6625290 CAATTTTTCT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
55 5 0.08
56 23 0.37
57 7 0.11
58 27 0.43
59 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (59 bp):
ATTTTTATAAAATTTTATCAAAATTTATATTTCTATACATTTTGTATAACTTTCTTACG
Found at i:6625315 original size:56 final size:53
Alignment explanation
Indices: 6625219--6625341 Score: 131
Period size: 56 Copynumber: 2.2 Consensus size: 53
6625209 TTTCTTACGA
* * * *
6625219 TTTTATAAAATTTTATAAAATTTTATATTTCTATATATTTTATAACTTTTTATGAT
1 TTTTATAAAATTTTACAAAATTTTATATTTCTATAAATTTTA-AA-TATTTA-AAT
* * *
6625275 TTTTATAAAATTTTAC-AATTTTTCTAATTTTTATAAATTTTAAATATTTAAAT
1 TTTTATAAAATTTTACAAAATTTTAT-ATTTCTATAAATTTTAAATATTTAAAT
6625328 TTTTATTAAAATTT
1 TTTTA-TAAAATTT
6625342 AATAATATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
53 7 0.12
54 13 0.22
55 9 0.16
56 29 0.50
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (53 bp):
TTTTATAAAATTTTACAAAATTTTATATTTCTATAAATTTTAAATATTTAAAT
Found at i:6625349 original size:28 final size:26
Alignment explanation
Indices: 6625219--6625352 Score: 92
Period size: 28 Copynumber: 4.9 Consensus size: 26
6625209 TTTCTTACGA
* *
6625219 TTTTATAAAATTTTATAAAATTTTATAT
1 TTTTATAAAATTTTA-AATA-TTTAAAT
* * * *
6625247 TTCTAT-ATATTTTATAACTTTTTATGAT
1 TTTTATAAAATTTTA-AA-TATTTA-AAT
* *
6625275 TTTTATAAAATTTTACAATTTTTCTAAT
1 TTTTATAAAATTTTA-AATATTT-AAAT
6625303 TTTTAT-AAATTTTAAATATTTAAAT
1 TTTTATAAAATTTTAAATATTTAAAT
*
6625328 TTTTATTAAAATTTAATAATATTTA
1 TTTTA-TAAAATTTTA-AATATTTA
6625353 TAGCTTTTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
25 8 0.09
26 7 0.08
27 29 0.34
28 33 0.38
29 9 0.10
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (26 bp):
TTTTATAAAATTTTAAATATTTAAAT
Found at i:6626363 original size:14 final size:14
Alignment explanation
Indices: 6626344--6626371 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6626334 TTTAGGATTT
6626344 TACCTAAAGTTGTC
1 TACCTAAAGTTGTC
6626358 TACCTAAAGTTGTC
1 TACCTAAAGTTGTC
6626372 AATCTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (14 bp):
TACCTAAAGTTGTC
Found at i:6630517 original size:16 final size:18
Alignment explanation
Indices: 6630478--6630519 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
6630468 GGAAATCAAG
*
6630478 GAAGGAAGAGATGAGAAA
1 GAAGAAAGAGATGAGAAA
6630496 -AAGAAAGAGA-GA-AAA
1 GAAGAAAGAGATGAGAAA
6630511 GAAGAAAGA
1 GAAGAAAGA
6630520 ATTCGGCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 10 0.45
17 9 0.41
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (18 bp):
GAAGAAAGAGATGAGAAA
Found at i:6636348 original size:34 final size:34
Alignment explanation
Indices: 6636301--6636371 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
6636291 TCTCTACCTT
* *
6636301 TTTTATTTGCATAATTAACATTGACTTTATAATA
1 TTTTATTTCCATAATTAACATTGACCTTATAATA
6636335 TTTTATTTCCATAATTAACATTGACCTTATAATA
1 TTTTATTTCCATAATTAACATTGACCTTATAATA
6636369 TTT
1 TTT
6636372 AGGTTCACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (34 bp):
TTTTATTTCCATAATTAACATTGACCTTATAATA
Found at i:6636781 original size:25 final size:23
Alignment explanation
Indices: 6636717--6636781 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 23
6636707 ATTATCACAC
*
6636717 TTTTATAAC-ATATAAATTATTT
1 TTTTATAACTTTATAAATTATTT
*
6636739 TTTATAATAA-TTTCTAAATATATTT
1 TTT-T-ATAACTTTATAAAT-TATTT
6636764 TTGTTATAACTTTATAAA
1 TT-TTATAACTTTATAAA
6636782 ATGCATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
22 3 0.09
23 1 0.03
24 14 0.41
25 15 0.44
26 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTATAACTTTATAAATTATTT
Found at i:6637930 original size:24 final size:23
Alignment explanation
Indices: 6637884--6637942 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
6637874 ATATTTATAG
6637884 AAATAAAATTAATTAAGTTAAATT
1 AAATAAAA-TAATTAAGTTAAATT
**
6637908 ATTTAAAATAATATAA-TTAAAATT
1 AAATAAAATAAT-TAAGTT-AAATT
6637932 AAATAAAATAA
1 AAATAAAATAA
6637943 AATTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATAAAATAATTAAGTTAAATT
Found at i:6640869 original size:115 final size:115
Alignment explanation
Indices: 6640688--6640898 Score: 341
Period size: 115 Copynumber: 1.8 Consensus size: 115
6640678 CAAAGTACAT
* * *
6640688 TAATGTTATCCATGAATAATTTTATTAACCAATCTGTTTGAAAAAATTATAAGTGTACAAATGAA
1 TAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAATGAA
*
6640753 TATACTACACTTAGGGTACCAGATCTAACAAGGACAACATACAAAAGGTA
66 TATACTACACTTAGGGCACCAGATCTAACAAGGACAACATACAAAAGGTA
* * *
6640803 TAATGTAATTCATGAATAATTTTACTAACTAGTCTGTTCGAAAAAATTATAAGTGTACAAATGAA
1 TAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAATGAA
* *
6640868 TATACTACATTTAGGGCACTAGATCTAACAA
66 TATACTACACTTAGGGCACCAGATCTAACAA
6640899 TCTTCAACTT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
115 87 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (115 bp):
TAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAATGAA
TATACTACACTTAGGGCACCAGATCTAACAAGGACAACATACAAAAGGTA
Found at i:6647333 original size:27 final size:26
Alignment explanation
Indices: 6647296--6647410 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
6647286 AGCATGGCTG
* *
6647296 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
6647322 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
6647350 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
6647377 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
6647404 CCAGAAC
1 CCAGAAC
6647411 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:6647355 original size:54 final size:54
Alignment explanation
Indices: 6647296--6647410 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
6647286 AGCATGGCTG
*
6647296 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
6647350 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
6647404 CCAGAAC
1 CCAGAAC
6647411 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:6649065 original size:26 final size:26
Alignment explanation
Indices: 6649029--6649137 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
6649019 ATGAAATTCC
6649029 TATCATGAAACATTTACCTAACCCAT
1 TATCATGAAACATTTACCTAACCCAT
6649055 TATCATGAAACATTTACCTAACCCAT
1 TATCATGAAACATTTACCTAACCCAT
* *
6649081 TATCATGGAACATTTACCTAACCTAT
1 TATCATGAAACATTTACCTAACCCAT
* *
6649107 TATCATGGAACATTTACCTAACCTAT
1 TATCATGAAACATTTACCTAACCCAT
6649133 TATCA
1 TATCA
6649138 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.33
Consensus pattern (26 bp):
TATCATGAAACATTTACCTAACCCAT
Found at i:6652159 original size:17 final size:15
Alignment explanation
Indices: 6652128--6652157 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6652118 CGCAACAAAA
6652128 AAAATTTTGTTTTTG
1 AAAATTTTGTTTTTG
6652143 AAAATCTTTGTTTTT
1 AAAAT-TTTGTTTTT
6652158 TGTAAACCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (15 bp):
AAAATTTTGTTTTTG
Found at i:6653434 original size:26 final size:26
Alignment explanation
Indices: 6653396--6653504 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
6653386 CATGAAATTC
* *
6653396 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
*
6653422 TTATAATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
6653448 TTATCATGGAACATTTA-CTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
6653473 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
6653499 TTATCA
1 TTATCA
6653505 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 25 0.32
26 53 0.68
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:6653483 original size:51 final size:52
Alignment explanation
Indices: 6653396--6653504 Score: 184
Period size: 51 Copynumber: 2.1 Consensus size: 52
6653386 CATGAAATTC
6653396 TTATCATGAAACATTTACCTAACCCATTATAATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCATTATAATGGAACATTTACCTAACCTA
* * *
6653448 TTATCATGGAACATTTA-CTAACCTATTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCATTATAATGGAACATTTACCTAACCTA
6653499 TTATCA
1 TTATCA
6653505 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 38 0.70
52 16 0.30
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (52 bp):
TTATCATGAAACATTTACCTAACCCATTATAATGGAACATTTACCTAACCTA
Found at i:6661484 original size:28 final size:28
Alignment explanation
Indices: 6661444--6661501 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
6661434 AACGGTCTGT
*
6661444 ATCACCGGTACATAGTACCTGCTAAATG
1 ATCACCGGCACATAGTACCTGCTAAATG
* *
6661472 ATCACCTGCACATAGTACCTTCTAAATG
1 ATCACCGGCACATAGTACCTGCTAAATG
6661500 AT
1 AT
6661502 TACCAGCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (28 bp):
ATCACCGGCACATAGTACCTGCTAAATG
Found at i:6662895 original size:15 final size:16
Alignment explanation
Indices: 6662875--6662912 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
6662865 ACTAACCACT
*
6662875 AATTCAATTAATT-AA
1 AATTCAATCAATTCAA
6662890 AATTC-ATCAATTCAA
1 AATTCAATCAATTCAA
6662905 AATTCAAT
1 AATTCAAT
6662913 ATAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 12 0.60
16 2 0.10
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTCAATCAATTCAA
Found at i:6672920 original size:21 final size:20
Alignment explanation
Indices: 6672896--6672937 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
6672886 AATTTTCAAA
6672896 AATTT-TCAAAGTTTTAATAAG
1 AATTTCTCAAA-TTTT-ATAAG
*
6672917 AATTTCTTAAATTTTATAAG
1 AATTTCTCAAATTTTATAAG
6672937 A
1 A
6672938 GGTTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (20 bp):
AATTTCTCAAATTTTATAAG
Found at i:6673074 original size:3 final size:3
Alignment explanation
Indices: 6673066--6673091 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6673056 GTTTGAAATG
6673066 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6673092 ATTTAAGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6673385 original size:20 final size:20
Alignment explanation
Indices: 6673343--6673396 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
6673333 AAAAATTTAT
6673343 AAAATATTAAATTTT-AGAA
1 AAAATATTAAATTTTAAGAA
*
6673362 AAAATATTAAATTTTAATAA
1 AAAATATTAAATTTTAAGAA
*
6673382 AAAAT-TTAAAATTTA
1 AAAATATTAAATTTTA
6673397 TTGAAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 24 0.75
20 8 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAATATTAAATTTTAAGAA
Found at i:6673403 original size:20 final size:21
Alignment explanation
Indices: 6673343--6673403 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 21
6673333 AAAAATTTAT
*
6673343 AAAATATT-AAATTTTA-GAA
1 AAAATATTAAAATTTAATGAA
*
6673362 AAAATATTAAATTTTAAT-AA
1 AAAATATTAAAATTTAATGAA
*
6673382 AAAAT-TTAAAATTTATTGAA
1 AAAATATTAAAATTTAATGAA
6673402 AA
1 AA
6673404 TTAGATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAATATTAAAATTTAATGAA
Found at i:6673647 original size:10 final size:10
Alignment explanation
Indices: 6673634--6673672 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
6673624 TTTTATGAAA
6673634 TTTATATTTC
1 TTTATATTTC
* *
6673644 TTTACATTTT
1 TTTATATTTC
6673654 TTTATATTTC
1 TTTATATTTC
*
6673664 TATATATTT
1 TTTATATTT
6673673 TATAATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATATTTC
Found at i:6673672 original size:20 final size:20
Alignment explanation
Indices: 6673634--6673693 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
6673624 TTTTATGAAA
* *
6673634 TTTATATTTCTTTACATTTT
1 TTTATATTTCTATATATTTT
6673654 TTTATATTTCTATATATTTT
1 TTTATATTTCTATATATTTT
* *
6673674 ATAATATTT-TATAATATTTT
1 TTTATATTTCTAT-ATATTTT
6673694 ATAATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.09
20 32 0.91
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATATTTCTATATATTTT
Found at i:6673680 original size:10 final size:10
Alignment explanation
Indices: 6673657--6673703 Score: 78
Period size: 10 Copynumber: 4.7 Consensus size: 10
6673647 ACATTTTTTT
6673657 ATATTTCTAT-
1 ATATTT-TATA
6673667 ATATTTTATA
1 ATATTTTATA
6673677 ATATTTTATA
1 ATATTTTATA
6673687 ATATTTTATA
1 ATATTTTATA
6673697 ATATTTT
1 ATATTTT
6673704 GAAAGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 3 0.08
10 33 0.92
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
ATATTTTATA
Found at i:6673857 original size:90 final size:88
Alignment explanation
Indices: 6673699--6673865 Score: 203
Period size: 90 Copynumber: 1.9 Consensus size: 88
6673689 ATTTTATAAT
* * * * ** *
6673699 ATTTTGAAAGTTTAAGTACCTAATTGAGTGCAAAAAAAATGTAGGGGCTTAATTGCTTTTTTTGA
1 ATTTTAAAAATTTAAGTACCCAAATGAGTGCAAAAAAAAAATAAGGGCTTAATT-CTTTTTTTG-
6673764 AAAAATTTGAGAGCCTTTTTGATGC
64 AAAAATTTGAGAGCCTTTTTGATGC
6673789 ATTTTAAAAATTTAAGTACCCAAATGAGTGTCAAAAAAAAAATAAGGG-TTCAATT-TTTATTTT
1 ATTTTAAAAATTTAAGTACCCAAATGAGTG-CAAAAAAAAAATAAGGGCTT-AATTCTTT-TTTT
*
6673852 TAAAAATTTGAGAG
63 GAAAAATTTGAGAG
6673866 ATTTTTACAC
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
89 16 0.24
90 32 0.48
91 18 0.27
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.37
Consensus pattern (88 bp):
ATTTTAAAAATTTAAGTACCCAAATGAGTGCAAAAAAAAAATAAGGGCTTAATTCTTTTTTTGAA
AAATTTGAGAGCCTTTTTGATGC
Done.