Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 12 of 128
Found at i:3476412 original size:22 final size:21
Alignment explanation
Indices: 3476387--3476428 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3476377 GGAGTTCTTC
3476387 AATGCCCAATTACAGTCTCTAA
1 AATGCCCAATTA-AGTCTCTAA
* *
3476409 AATGTCTAATTAAGTCTCTA
1 AATGCCCAATTAAGTCTCTA
3476429 CCAAGCCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (21 bp):
AATGCCCAATTAAGTCTCTAA
Found at i:3479865 original size:76 final size:75
Alignment explanation
Indices: 3479740--3479882 Score: 223
Period size: 76 Copynumber: 1.9 Consensus size: 75
3479730 TGAATCGTAC
* * *
3479740 TGTTATTCAAGCTTAGTGCCTAGAGGTTTAGTGTCGGTGTTATTCAAGCTTAGTGCCTAGCAGGC
1 TGTTATTCAAGCTTAGTGCCTAGAGGCTTAGTGTCGCTATTATTCAAGCTTAGTGCCTAGCAGGC
3479805 TTTGTGTTGG
66 TTTGTGTTGG
* * *
3479815 TGTTATTCAAGCTTTGTGTCTAGTAGGCTTAGTGTCGCTATTATTTAAGCTTAGTGCCTAGCAGG
1 TGTTATTCAAGCTTAGTGCCTAG-AGGCTTAGTGTCGCTATTATTCAAGCTTAGTGCCTAGCAGG
3479880 CTT
65 CTT
3479883 ATAGTCGGTG
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 21 0.34
76 40 0.66
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (75 bp):
TGTTATTCAAGCTTAGTGCCTAGAGGCTTAGTGTCGCTATTATTCAAGCTTAGTGCCTAGCAGGC
TTTGTGTTGG
Found at i:3479883 original size:38 final size:38
Alignment explanation
Indices: 3479740--3479892 Score: 202
Period size: 38 Copynumber: 4.1 Consensus size: 38
3479730 TGAATCGTAC
*
3479740 TGTTATTCAAGCTTAGTGCCTAG-AGGTTTAGTGTCGG
1 TGTTATTCAAGCTTAGTGCCTAGCAGGCTTAGTGTCGG
* *
3479777 TGTTATTCAAGCTTAGTGCCTAGCAGGCTTTGTGTTGG
1 TGTTATTCAAGCTTAGTGCCTAGCAGGCTTAGTGTCGG
* * * *
3479815 TGTTATTCAAGCTTTGTGTCTAGTAGGCTTAGTGTCGC
1 TGTTATTCAAGCTTAGTGCCTAGCAGGCTTAGTGTCGG
* *
3479853 TATTATTTAAGCTTAGTGCCTAGCAGGCTTA-TAGTCGG
1 TGTTATTCAAGCTTAGTGCCTAGCAGGCTTAGT-GTCGG
3479891 TG
1 TG
3479893 CAATAAAGGT
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
37 24 0.24
38 74 0.76
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.39
Consensus pattern (38 bp):
TGTTATTCAAGCTTAGTGCCTAGCAGGCTTAGTGTCGG
Found at i:3485884 original size:50 final size:51
Alignment explanation
Indices: 3485756--3486047 Score: 309
Period size: 50 Copynumber: 5.9 Consensus size: 51
3485746 TCGTATATCG
* * *
3485756 GTGCCGATGCCATGTCCCGGATATGGTCTTACACTGGCA--CTCATC--T-A
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACT-GCACTCTCATCGGTCT
** * * * *
3485803 AAGCTGATGCCATGTCCCAAACATGGTCTTACACTG-ACTCTCATCTGTCC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGCACTCTCATCGGTCT
* *
3485853 GTGCCAATGCCATGTCCCAGACAAGGTCTTACACTAGCACT-T-ATCGGTCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACT-GCACTCTCATCGGTCT
* * *
3485903 GTGCCGATGCCATGTCCCAGACATGGTCTTACACT-AACTCTCCTCTGTCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGCACTCTCATCGGTCT
* *
3485953 GTGCCGATACCATGTCCTAGACATGGTCTTACACTAGCACTC-C-TCGGTCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACT-GCACTCTCATCGGTCT
* *
3486003 GTGCCGATGCCATGTACCAGACATGGTCTTACACTGGCACACTCA
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACT-GCACTCTCA
3486048 CTGCCATGGT
Statistics
Matches: 203, Mismatches: 29, Indels: 21
0.80 0.11 0.08
Matches are distributed among these distances:
45 1 0.00
46 1 0.00
47 35 0.17
48 3 0.01
49 2 0.01
50 150 0.74
51 4 0.02
52 7 0.03
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.27
Consensus pattern (51 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGCACTCTCATCGGTCT
Found at i:3485943 original size:100 final size:100
Alignment explanation
Indices: 3485808--3486037 Score: 361
Period size: 100 Copynumber: 2.3 Consensus size: 100
3485798 ATCTAAAGCT
* * *
3485808 GATGCCATGTCCCAAACATGGTCTTACACTGACTCTCATCTGTCCGTGCCAATGCCATGTCCCAG
1 GATGCCATGTCCCAGACATGGTCTTACACTAACTCTCATCTGTCCGTGCCAATACCATGTCCCAG
*
3485873 ACAAGGTCTTACACTAGCACTTATCGGTCTGTGCC
66 ACAAGGTCTTACACTAGCACTCATCGGTCTGTGCC
* * * *
3485908 GATGCCATGTCCCAGACATGGTCTTACACTAACTCTCCTCTGTCTGTGCCGATACCATGTCCTAG
1 GATGCCATGTCCCAGACATGGTCTTACACTAACTCTCATCTGTCCGTGCCAATACCATGTCCCAG
* *
3485973 ACATGGTCTTACACTAGCACTCCTCGGTCTGTGCC
66 ACAAGGTCTTACACTAGCACTCATCGGTCTGTGCC
*
3486008 GATGCCATGTACCAGACATGGTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
3486038 GGCACACTCA
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 119 1.00
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.28
Consensus pattern (100 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAACTCTCATCTGTCCGTGCCAATACCATGTCCCAG
ACAAGGTCTTACACTAGCACTCATCGGTCTGTGCC
Found at i:3487763 original size:299 final size:299
Alignment explanation
Indices: 3487212--3487806 Score: 937
Period size: 299 Copynumber: 2.0 Consensus size: 299
3487202 GCTGTTACAG
* **
3487212 AATCACTCGTTCTGATTGCCCGTCAGTCTGAGGATGAAATGCAGTGTTGAAATTAAGCTTAGTGC
1 AATCACTCATTCTGATTGCCCGTCAGTCTGAGGATGAAATGCAGTACTGAAATTAAGCTTAGTGC
* * * * *
3487277 TTAAAGCCTCGTAAAGTTTGCTCCAAAATCTTGATGTAAATCTCGGATCTCGATCTAAAATAATA
66 TTAAAGCCTCATAAAGTTTGCTCCAAAATCTCGATGTAAATATCAGATCTCAATCTAAAATAATA
* *
3487342 GATGTCGAAACTCCGTGTAATCTCACAATCTCAAACACATATAGTTCTGCTAATCTCTCAAGGGT
131 GATGTCGAAACTCCATGTAATCTCACAATCTCAAACACATATAATTCTGCTAATCTCTCAAGGGT
* *
3487407 GTAGTATATTCTAATTGGAATAAAATGTGCCGACTTTGTCAATTTGTCAACAATCACCC-GTATT
196 GTAGTATATTCTAATTGGAATAAAATGTGCCGACTTTGTCAATCTGTCAAAAATCACCCAG-ATT
3487471 GAATCTTTCTTTCTCGGAGTTACAAGTAAACCAGATAAAA
260 GAATCTTTCTTTCTCGGAGTTACAAGTAAACCAGATAAAA
*
3487511 AATCATTCATTCTGATTGCCCGTCAGTCTGAGGATGAAATGCAGTACTGAAATTAAGCTTAGTGC
1 AATCACTCATTCTGATTGCCCGTCAGTCTGAGGATGAAATGCAGTACTGAAATTAAGCTTAGTGC
*
3487576 TTAAAGCCTCATTAAGTTTGCTCCAAAATCTCGATGTAAATATCAGATCTCAAT-TCAAAATAAT
66 TTAAAGCCTCATAAAGTTTGCTCCAAAATCTCGATGTAAATATCAGATCTCAATCT-AAAATAAT
* *
3487640 AGATGTCGGAACTCCATGTAATCTCACAATCT-AAGATACATATAATTCTGCTAATCTCTCAAGG
130 AGATGTCGAAACTCCATGTAATCTCACAATCTCAA-ACACATATAATTCTGCTAATCTCTCAAGG
* *
3487704 GTGTAGTCTGTTCTAATTGGAATAAAATGTGCCGA-TTTCGTCAATCTGTCAAAAATCACCCAGA
194 GTGTAGTATATTCTAATTGGAATAAAATGTGCCGACTTT-GTCAATCTGTCAAAAATCACCCAGA
* * *
3487768 TTGAATCTTTCTTTGTCGGAGTTATAGGTAAACCAGATA
258 TTGAATCTTTCTTTCTCGGAGTTACAAGTAAACCAGATA
3487807 CGAAATCCAT
Statistics
Matches: 271, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
298 6 0.02
299 264 0.97
300 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (299 bp):
AATCACTCATTCTGATTGCCCGTCAGTCTGAGGATGAAATGCAGTACTGAAATTAAGCTTAGTGC
TTAAAGCCTCATAAAGTTTGCTCCAAAATCTCGATGTAAATATCAGATCTCAATCTAAAATAATA
GATGTCGAAACTCCATGTAATCTCACAATCTCAAACACATATAATTCTGCTAATCTCTCAAGGGT
GTAGTATATTCTAATTGGAATAAAATGTGCCGACTTTGTCAATCTGTCAAAAATCACCCAGATTG
AATCTTTCTTTCTCGGAGTTACAAGTAAACCAGATAAAA
Found at i:3491885 original size:39 final size:38
Alignment explanation
Indices: 3491830--3492111 Score: 224
Period size: 39 Copynumber: 7.2 Consensus size: 38
3491820 CATACACCGG
* *
3491830 CACACATCCTGCTAGGCATATAGCCCGAATAATCATCGA
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCA-CGA
* * * * *
3491869 AACACAGACTACTAGGCACATAGCCCGAATAATTACCGG
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCA-CGA
* ** ** * *
3491908 CACACAGTCTGGAAGATACATAGCCTGAATAATCACCA
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACGA
* * * *
3491946 GCATACAGCCAGCTAGGCACATAGCCCGAATATTCACTA
1 -CACACAGCCTGCTAGGCACATAGCCCGAATAATCACGA
* *
3491985 GCACACAGCCTGCTAGGCATATAGCCCGAATAATCATCGG
1 -CACACAGCCTGCTAGGCACATAGCCCGAATAATCA-CGA
* *
3492025 CA-AGCAGCCGGCTAGGCACATAGCCCGAATAATCACCTA
1 CACA-CAGCCTGCTAGGCACATAGCCCGAATAATCA-CGA
** * * * * *
3492064 CATGCAGCTTGCTAGGAACGTAGCCTGAATAATCACCA
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACGA
3492102 GCACACAGCC
1 -CACACAGCC
3492112 CAAATAATCA
Statistics
Matches: 188, Mismatches: 50, Indels: 10
0.76 0.20 0.04
Matches are distributed among these distances:
38 4 0.02
39 183 0.97
40 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.17
Consensus pattern (38 bp):
CACACAGCCTGCTAGGCACATAGCCCGAATAATCACGA
Found at i:3492046 original size:117 final size:117
Alignment explanation
Indices: 3491840--3492111 Score: 291
Period size: 117 Copynumber: 2.3 Consensus size: 117
3491830 CACACATCCT
* * * * *
3491840 GCTAGGCATATAGCCCGAATAATCA-TCGAAACACAGACTACTAGGCACATAGCCCGAATAATTA
1 GCTAGGCACATAGCCCGAATAATCACTAG-CACACAGCCTACTAGGCACATAGCCCGAATAATCA
* * *
3491904 CCGGCACACAGTCTGGAAGATACATAGCCTGAATAATCACC-AGCATACAGCCA
65 CCGGCACACAGTCCGGAAGACACATAGCCCGAATAATCACCTA-CATACAGCCA
* * * *
3491957 GCTAGGCACATAGCCCGAATATTCACTAGCACACAGCCTGCTAGGCATATAGCCCGAATAATCAT
1 GCTAGGCACATAGCCCGAATAATCACTAGCACACAGCCTACTAGGCACATAGCCCGAATAATCAC
* * * **
3492022 CGGCA-AGCAG-CCGGCTAGGCACATAGCCCGAATAATCACCTACATGCAGCTT
66 CGGCACA-CAGTCCGG-AAGACACATAGCCCGAATAATCACCTACATACAGCCA
* * * *
3492074 GCTAGGAACGTAGCCTGAATAATCACCAGCACACAGCC
1 GCTAGGCACATAGCCCGAATAATCACTAGCACACAGCC
3492112 CAAATAATCA
Statistics
Matches: 129, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
116 4 0.03
117 122 0.95
118 3 0.02
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.17
Consensus pattern (117 bp):
GCTAGGCACATAGCCCGAATAATCACTAGCACACAGCCTACTAGGCACATAGCCCGAATAATCAC
CGGCACACAGTCCGGAAGACACATAGCCCGAATAATCACCTACATACAGCCA
Found at i:3492111 original size:78 final size:77
Alignment explanation
Indices: 3491880--3492111 Score: 252
Period size: 78 Copynumber: 3.0 Consensus size: 77
3491870 ACACAGACTA
* ** * * *
3491880 CTAGGCACATAGCCCGAATAATTACCGGCACACAGTCTG-GAAGATACATAGCCTGAATAATCAC
1 CTAGGCACATAGCCCGAATAATCACTAGCACACAGCCTGCTAGGA-ACATAGCCTGAATAATCAC
3491944 CAGCATACAGCCAG
65 CAGCA-ACAGCCAG
* * * * *
3491958 CTAGGCACATAGCCCGAATATTCACTAGCACACAGCCTGCTAGGCATATAGCCCGAATAATCATC
1 CTAGGCACATAGCCCGAATAATCACTAGCACACAGCCTGCTAGGAACATAGCCTGAATAATCACC
* *
3492023 GGCAAGCAGCCGG
66 AGCAA-CAGCCAG
** * *
3492036 CTAGGCACATAGCCCGAATAATCACCTA-CATGCAGCTTGCTAGGAACGTAGCCTGAATAATCAC
1 CTAGGCACATAGCCCGAATAATCA-CTAGCACACAGCCTGCTAGGAACATAGCCTGAATAATCAC
3492100 CAGCACACAGCC
65 CAGCA-ACAGCC
3492112 CAAATAATCA
Statistics
Matches: 127, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
77 1 0.01
78 120 0.94
79 6 0.05
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (77 bp):
CTAGGCACATAGCCCGAATAATCACTAGCACACAGCCTGCTAGGAACATAGCCTGAATAATCACC
AGCAACAGCCAG
Found at i:3492117 original size:23 final size:23
Alignment explanation
Indices: 3492091--3492135 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3492081 ACGTAGCCTG
3492091 AATAATCA-CCAGCACACAGCCCA
1 AATAATCATCC-GCACACAGCCCA
3492114 AATAATCATCCGCACACAGCCC
1 AATAATCATCCGCACACAGCCC
3492136 GCTAGGCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.40, C:0.40, G:0.09, T:0.11
Consensus pattern (23 bp):
AATAATCATCCGCACACAGCCCA
Found at i:3494653 original size:299 final size:298
Alignment explanation
Indices: 3494115--3494993 Score: 1249
Period size: 299 Copynumber: 2.9 Consensus size: 298
3494105 CCAAAATTTG
* * * *
3494115 AATCACTCGTTCTGATTGCCCGTCAATCTGAGGATGAAACGCAGTGTTGAAATTAAGCTTAGTGC
1 AATCACTCGTTCTGATTGCCCGTCAGTCTGAGGATGAATCGCGGTGCTGAAATTAAGCTTAGTGC
* * ** * *
3494180 CTAAAGCCTCGTGAAGTTTT-CTCCAAAATCTCGATGTAGATCTTGGATCTCAATCCAAAATAAT
66 CTAAAGCCTCATGAA-TTTTGCTCCAAAATCTCGATGTAAATCTCAGATCTCGATCCGAAATAAT
* * *
3494244 AAATGCTGGAACTCCGTGTAATCTCACAATCTCAGACACATATAGTTTTGCTAATCTCTCAAGGG
130 AGATG-TGAAACTCCGTGTAATCTCACAATCTCAGACACATATAGTTCTGCTAATCTCTCAAGGG
* *
3494309 TGTAGTCTATTCTGATTGGAGTAAAATGTTCCGATTTCATCAATCTGTCAACAATCATCCAGATT
194 TGTAGTCTGTTCTGATTGGAATAAAATGTTCCGATTTCATCAATCTGTCAACAATCATCCAGATT
* * * *
3494374 CAGTCTTTATTTCTCGGAGTTACAGGTAAACCAAATATGA
259 GAATCTTTCTTTCTCGGAGTTACAGGTAAACCAAATACGA
*
3494414 AATCACTCGTTCTGATTGCCCGTCAGTCTGAAGATGAATCGCGGTGCTGAAATTAAGCTTAGTGC
1 AATCACTCGTTCTGATTGCCCGTCAGTCTGAGGATGAATCGCGGTGCTGAAATTAAGCTTAGTGC
* * *
3494479 GTAAAGCCTCATGAATTTTGTTCCAAAATCTCAATGTAAATCTCAGATCTCGATCCGAAATAATA
66 CTAAAGCCTCATGAATTTTGCTCCAAAATCTCGATGTAAATCTCAGATCTCGATCCGAAATAATA
* ** *
3494544 GATGTTGAAACTTCGTGTAATCTCACAATCTCAGACACATATAGTTCTATTAATCTCTCAAGGTT
131 GATG-TGAAACTCCGTGTAATCTCACAATCTCAGACACATATAGTTCTGCTAATCTCTCAAGGGT
* * *
3494609 GTAGTCTGTTCTAATTGGAATAAAATGTGCCGATTTCATCAATCTATCAACAATCATCCAGATTG
195 GTAGTCTGTTCTGATTGGAATAAAATGTTCCGATTTCATCAATCTGTCAACAATCATCCAGATTG
* *
3494674 AATCTTTCTTTCTCAGAGTTACAGGTAAACCAGATACGA
260 AATCTTTCTTTCTCGGAGTTACAGGTAAACCAAATACGA
* * * *
3494713 AATCACTCGTTTTGATTACCGGTCAGTCTGAGGATGAATCGTGGTGCTGAAATTAAGCTTAGTGC
1 AATCACTCGTTCTGATTGCCCGTCAGTCTGAGGATGAATCGCGGTGCTGAAATTAAGCTTAGTGC
* ** * *
3494778 CTAAAGCCTCATGAAGTTTGCTATAAAATCTCGATGTAAATTTCAGATCTCGATTCGAAATAATA
66 CTAAAGCCTCATGAATTTTGCTCCAAAATCTCGATGTAAATCTCAGATCTCGATCCGAAATAATA
* *
3494843 GATGTCAGAACTCCGTGTAATCTCACAATCTCAGACCCATATAGTTCTGCTAATCTCTCAAGGGT
131 GATGTGA-AACTCCGTGTAATCTCACAATCTCAGACACATATAGTTCTGCTAATCTCTCAAGGGT
* * * * * * *
3494908 ATAGTATGTTCTGATTAGAATAAAATGTTTCGTTTTCGTCAATCTGTCAACAATC-CCTCAGATT
195 GTAGTCTGTTCTGATTGGAATAAAATGTTCCGATTTCATCAATCTGTCAACAATCATC-CAGATT
3494972 GAATCTTTCTTTCTCGGAGTTA
259 GAATCTTTCTTTCTCGGAGTTA
3494994 TAGACCAGAT
Statistics
Matches: 514, Mismatches: 63, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
298 7 0.01
299 507 0.99
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (298 bp):
AATCACTCGTTCTGATTGCCCGTCAGTCTGAGGATGAATCGCGGTGCTGAAATTAAGCTTAGTGC
CTAAAGCCTCATGAATTTTGCTCCAAAATCTCGATGTAAATCTCAGATCTCGATCCGAAATAATA
GATGTGAAACTCCGTGTAATCTCACAATCTCAGACACATATAGTTCTGCTAATCTCTCAAGGGTG
TAGTCTGTTCTGATTGGAATAAAATGTTCCGATTTCATCAATCTGTCAACAATCATCCAGATTGA
ATCTTTCTTTCTCGGAGTTACAGGTAAACCAAATACGA
Found at i:3497313 original size:38 final size:39
Alignment explanation
Indices: 3497264--3497337 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 39
3497254 AATATATTTA
*
3497264 TTTTTTTAATTTTAAAATATTTTT-ACATACTTTTTAAT
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAT
3497302 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTT
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTT
3497338 TTTATGGGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 24 0.71
39 10 0.29
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (39 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAT
Found at i:3500452 original size:39 final size:39
Alignment explanation
Indices: 3500406--3500822 Score: 485
Period size: 39 Copynumber: 10.7 Consensus size: 39
3500396 CGACACAACT
* * * *
3500406 TGCTAGGCATATAGCCCGAATAATCATCGGCACACAACT
1 TGCTAGGCACATAGCCCGAATAATCACCGGCACACAGCC
*
3500445 TGCTAGGCACATAACCCGAATAATCACCGGCACACAGCC
1 TGCTAGGCACATAGCCCGAATAATCACCGGCACACAGCC
* *
3500484 TGCTAGGCACAAAGCCCGAATAATCACCAGCACACAGCC
1 TGCTAGGCACATAGCCCGAATAATCACCGGCACACAGCC
** * *
3500523 TGCTAGGCACATAGCTTGAATAATCATCGGCACACACCC
1 TGCTAGGCACATAGCCCGAATAATCACCGGCACACAGCC
*
3500562 TGCTAGGCACATAGCCCGAATAATCACTGGCACACAGCC
1 TGCTAGGCACATAGCCCGAATAATCACCGGCACACAGCC
** * *
3500601 TGCTAGGCACATAGCCTTAATAATCACCGGCACTCAACC
1 TGCTAGGCACATAGCCCGAATAATCACCGGCACACAGCC
* * *** *
3500640 TGCTAGGCACACAGCCCGAATAATCACCTGCGTGCATCC
1 TGCTAGGCACATAGCCCGAATAATCACCGGCACACAGCC
* * *
3500679 TGCTAGGCACATAGACCGAATAATCACCCGCACACAACC
1 TGCTAGGCACATAGCCCGAATAATCACCGGCACACAGCC
* * * * *
3500718 TGCTAGGCTCATAACCCGAATAATCATTC-GCACCCAGCT
1 TGCTAGGCACATAGCCCGAATAATCA-CCGGCACACAGCC
* * * * * *
3500757 TGCTAGGTACAAAACCTGAATAATCATCGACACACAGCC
1 TGCTAGGCACATAGCCCGAATAATCACCGGCACACAGCC
*
3500796 TGCTAGGCACATAGCCCGAACAATCAC
1 TGCTAGGCACATAGCCCGAATAATCAC
3500823 TGTATTTCTA
Statistics
Matches: 317, Mismatches: 59, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
38 2 0.01
39 314 0.99
40 1 0.00
ACGTcount: A:0.32, C:0.33, G:0.18, T:0.17
Consensus pattern (39 bp):
TGCTAGGCACATAGCCCGAATAATCACCGGCACACAGCC
Found at i:3506804 original size:20 final size:20
Alignment explanation
Indices: 3506779--3506819 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3506769 TCATAAAATG
3506779 TTAGCCCAAATTAAAAGTGA
1 TTAGCCCAAATTAAAAGTGA
3506799 TTAGCCCAAATTAAAAGTGA
1 TTAGCCCAAATTAAAAGTGA
3506819 T
1 T
3506820 CTAATTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
TTAGCCCAAATTAAAAGTGA
Found at i:3514113 original size:92 final size:92
Alignment explanation
Indices: 3513840--3514384 Score: 702
Period size: 92 Copynumber: 5.9 Consensus size: 92
3513830 GTATATGTTT
* * *
3513840 TATACATTGCCGAATTGATTTGTATAAAGATATACATTGGCGAATTTGATTTGTTTATAGATATA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATA
* *
3513905 CATTGCCGAAATTGATTTGTTTATAGA
66 CATTGCCGAATTTGATTTGTATATAGA
* ** * * * *
3513932 TATACATTGCCGAAGTTGAATTGCT-TATAGATATACATTGTTGAATTAGAATTGTTTGTAGATA
1 TATACATTGCCGAA-TTGATTTG-TATATAGATATACATTGCCGAATTTGATTTGTATATAGATA
* *
3513996 TACATTGTCAAATTTGATTTGTATATAGA
64 TACATTGCCGAATTTGATTTGTATATAGA
* * * * * *
3514025 TATACATTGTCAAATTTGATTTCTATATGGATATATATTGCCGAA-TTGATTTGTATATAAATAT
1 TATACATTGCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATAT
3514089 ACATTGCCGAATTTGATTTGTATATAGA
65 ACATTGCCGAATTTGATTTGTATATAGA
* ** * *
3514117 TATACATTGCTGAATTTGATTTGTATATTA-ATATACATTGCTAAATTTGATTTGTATATGGTTA
1 TATACATTGCCGAA-TTGATTTGTATA-TAGATATACATTGCCGAATTTGATTTGTATATAGATA
* *
3514181 TACATTGTCGAATTTGATTTGTATATGGA
64 TACATTGCCGAATTTGATTTGTATATAGA
* *
3514210 TATACATTGCCGAATTGATTTGTCTATAGATATACATTGTCGAATTTGATTTGTATATAGATATA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATA
*
3514275 CATTGCCGAATTTGATTTGTATATGGA
66 CATTGCCGAATTTGATTTGTATATAGA
* * * *
3514302 TATTCATTGCCAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTCGTATATGGATATA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATA
*
3514367 TATTGCCGAA-TTGATTTG
66 CATTGCCGAATTTGATTTG
3514385 AGCATTGGAT
Statistics
Matches: 392, Mismatches: 55, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
91 10 0.03
92 226 0.58
93 155 0.40
94 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.43
Consensus pattern (92 bp):
TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATA
CATTGCCGAATTTGATTTGTATATAGA
Found at i:3514117 original size:154 final size:152
Alignment explanation
Indices: 3513840--3514384 Score: 736
Period size: 154 Copynumber: 3.5 Consensus size: 152
3513830 GTATATGTTT
* * * * * *
3513840 TATACATTGCCGAATTGATTTGTATAAAGATATACATTGGCGAATTTGATTTGTTTATAGATATA
1 TATACATTGCCAAATTGATTTGTATATAGATATACATTGTCGAATTTGATTTCTATATGGATATA
* * *
3513905 CATTGCCGAAATTGATTTGTTTATAGATATACATTGCCGAAGTTGAATTGCT-TATAGATATACA
66 CATTGCCG-AATTGATTTGTATATAGATATACATTGCCGAATTTGATTTG-TATATAGATATACA
* * *
3513969 TTGTTGAATTAGAATTGTTTGTAGA
129 TTGCTGAATTTGATTTGTTT-TAGA
* *
3513994 TATACATTGTCAAATTTGATTTGTATATAGATATACATTGTCAAATTTGATTTCTATATGGATAT
1 TATACATTGCCAAA-TTGATTTGTATATAGATATACATTGTCGAATTTGATTTCTATATGGATAT
* *
3514059 ATATTGCCGAATTGATTTGTATATAAATATACATTGCCGAATTTGATTTGTATATAGATATACAT
65 ACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATACAT
3514124 TGCTGAATTTGATTTGTATATTA-A
130 TGCTGAATTTGATTTGT-T-TTAGA
* * * *
3514148 TATACATTGCTAAATTTGATTTGTATATGGTTATACATTGTCGAATTTGATTTGTATATGGATAT
1 TATACATTGCCAAA-TTGATTTGTATATAGATATACATTGTCGAATTTGATTTCTATATGGATAT
* *
3514213 ACATTGCCGAATTGATTTGTCTATAGATATACATTGTCGAATTTGATTTGTATATAGATATACAT
65 ACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATACAT
* * *
3514278 TGCCGAATTTGATTTGTATATGGA
130 TGCTGAATTTGATTTGT-TTTAGA
* *
3514302 TATTCATTGCCAAATTGATTTGTATATAGATATACATTGCCGAATTTGA-TTCGTATATGGATAT
1 TATACATTGCCAAATTGATTTGTATATAGATATACATTGTCGAATTTGATTTC-TATATGGATAT
*
3514366 ATATTGCCGAATTGATTTG
65 ACATTGCCGAATTGATTTG
3514385 AGCATTGGAT
Statistics
Matches: 349, Mismatches: 36, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
152 2 0.01
153 63 0.18
154 228 0.65
155 55 0.16
156 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.43
Consensus pattern (152 bp):
TATACATTGCCAAATTGATTTGTATATAGATATACATTGTCGAATTTGATTTCTATATGGATATA
CATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATACATT
GCTGAATTTGATTTGTTTTAGA
Found at i:3514394 original size:31 final size:31
Alignment explanation
Indices: 3513840--3514384 Score: 643
Period size: 31 Copynumber: 17.7 Consensus size: 31
3513830 GTATATGTTT
**
3513840 TATACATTGCCGAA-TTGATTTGTATAAAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
3513870 TATACATTGGCGAATTTGATTTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
3513901 TATACATTGCCGAAATTGATTTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
3513932 TATACATTGCCGAAGTTGAATTGCT-TATAGA
1 TATACATTGCCGAATTTGATTTG-TATATGGA
** * * * * *
3513963 TATACATTGTTGAATTAGAATTGTTTGTAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
3513994 TATACATTGTCAAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
3514025 TATACATTGTCAAATTTGATTTCTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* **
3514056 TATATATTGCCGAA-TTGATTTGTATATAAA
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
3514086 TATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* **
3514117 TATACATTGCTGAATTTGATTTGTATATTAA
1 TATACATTGCCGAATTTGATTTGTATATGGA
** *
3514148 TATACATTGCTAAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
3514179 TATACATTGTCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
3514210 TATACATTGCCGAA-TTGATTTGTCTATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
3514240 TATACATTGTCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
3514271 TATACATTGCCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
3514302 TATTCATTGCC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
3514332 TATACATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
3514363 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
3514385 AGCATTGGAT
Statistics
Matches: 454, Mismatches: 55, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
30 101 0.22
31 352 0.78
32 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.43
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATGGA
Found at i:3516134 original size:20 final size:18
Alignment explanation
Indices: 3516109--3516148 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 18
3516099 ACCTAACATG
3516109 AATTAAATTTAAACCATATT
1 AATTAAA-TTAAA-CATATT
3516129 AATTAAATTAAACATATT
1 AATTAAATTAAACATATT
3516147 AA
1 AA
3516149 CATCTCAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAATTAAACATATT
Found at i:3517727 original size:5 final size:5
Alignment explanation
Indices: 3517700--3517765 Score: 71
Period size: 5 Copynumber: 12.8 Consensus size: 5
3517690 GTACATATGC
* * *
3517700 TCTTC TCTTCT TCTTCT TTTTT TCTTT TCTTT TCTTT TTTTT TC-TT TCTTT
1 TCTTT TCTT-T TCTT-T TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT
3517751 GTCTTT TCTTT TCTT
1 -TCTTT TCTTT TCTT
3517766 CTTTTTTTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
4 4 0.08
5 35 0.66
6 14 0.26
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:3517729 original size:19 final size:18
Alignment explanation
Indices: 3517702--3517774 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 18
3517692 ACATATGCTC
*
3517702 TTCTCTTCTTCTTCTTTTT
1 TTCTTTTCTTCTT-TTTTT
3517721 TTCTTTTCTTTTCTTTTTTT
1 TTCTTTTC--TTCTTTTTTT
* *
3517741 TTC-TTTC-T-TTGTCTT
1 TTCTTTTCTTCTTTTTTT
3517756 TTCTTTTCTTCTTTTTTT
1 TTCTTTTCTTCTTTTTTT
3517774 T
1 T
3517775 CACGAGCATT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
15 8 0.18
16 5 0.11
17 1 0.02
18 6 0.14
19 11 0.25
20 8 0.18
21 5 0.11
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.79
Consensus pattern (18 bp):
TTCTTTTCTTCTTTTTTT
Found at i:3517773 original size:11 final size:10
Alignment explanation
Indices: 3517710--3517773 Score: 74
Period size: 10 Copynumber: 6.2 Consensus size: 10
3517700 TCTTCTCTTC
3517710 TTCTTCTTTTT
1 TTCTT-TTTTT
*
3517721 TTCTTTTCTT
1 TTCTTTTTTT
3517731 TTCTTTTTTT
1 TTCTTTTTTT
*
3517741 TTCTTTCTTT
1 TTCTTTTTTT
* *
3517751 GTCTTTTCTT
1 TTCTTTTTTT
3517761 TTCTTCTTTTT
1 TTCTT-TTTTT
3517772 TT
1 TT
3517774 TCACGAGCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
10 33 0.75
11 11 0.25
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:3519052 original size:3 final size:3
Alignment explanation
Indices: 3519044--3519143 Score: 200
Period size: 3 Copynumber: 33.3 Consensus size: 3
3519034 CTCTATGGGA
3519044 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3519092 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3519140 TCT T
1 TCT T
3519144 TCGAGATCCT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:3520628 original size:14 final size:16
Alignment explanation
Indices: 3520597--3520638 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
3520587 TGCAAAGTTG
3520597 ATTATAATTAATATAT
1 ATTATAATTAATATAT
*
3520613 ATTATAATAAATATAT
1 ATTATAATTAATATAT
3520629 -TTATATATTA
1 ATTATA-ATTA
3520639 GTTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATAATTAATATAT
Found at i:3525763 original size:21 final size:21
Alignment explanation
Indices: 3525721--3525775 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
3525711 CGGAGATTTG
* *
3525721 TAGCAAGGAACT-TAACAAAC
1 TAGCAAGGAAGTGGAACAAAC
* *
3525741 TAGTAAGGAAGTGGAACAGAC
1 TAGCAAGGAAGTGGAACAAAC
3525762 TAGCAAGGAAGTGG
1 TAGCAAGGAAGTGG
3525776 CAGAAAATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.44, C:0.13, G:0.29, T:0.15
Consensus pattern (21 bp):
TAGCAAGGAAGTGGAACAAAC
Found at i:3527240 original size:110 final size:110
Alignment explanation
Indices: 3527047--3527633 Score: 800
Period size: 110 Copynumber: 5.4 Consensus size: 110
3527037 TAGTTGATTA
* *
3527047 TGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
1 TGGTCGAACGAGAAAAATCGAAACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
3527112 AACATTGCCTTATTTTGAAATTTTTGAAAAGGATATTTAGCTATT
66 AACATTGCCTTATTTTGAAATTTTTGAAAAGGATATTTAGCTATT
* *
3527157 TGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCCAAACGC-
1 TGGTCGAACGAGAAAAATCGAAACCCAGTACCTTAGGGCATGTTTTCTCGAATTT-CCAAACGCA
*
3527221 AAACATTGCCTTATTTTGAAATTTTTGAAAAGGATACTTAGCTATT
65 AAACATTGCCTTATTTTGAAATTTTTGAAAAGGATATTTAGCTATT
* * *
3527267 TGGTTGAACGAGAAAACTCGACACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
1 TGGTCGAACGAGAAAAATCGAAACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
*
3527332 AACATTGCCTTATTTTGAAAATTTTTGAAAAGGATATTAAG-TCATT
66 AACATTGCCTTATTTTG-AAATTTTTGAAAAGGATATTTAGCT-ATT
* * * *
3527378 TGGTCGAACGAG--AAATCGAAACCCAGTACCTTAAGGCACG-TTCCTCGAATTTCCAAATGCAA
1 TGGTCGAACGAGAAAAATCGAAACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
* * *
3527440 AACATTGCCATATTTTTTAAAAGTTTTTTAAAAGGATATTTAGCTATT
66 AACATTGCC-T-TATTTTGAAA-TTTTTGAAAAGGATATTTAGCTATT
* * * * * *
3527488 TGGTCGAAC-A-AGAAATTGAAACCCAGTACCTTAGGGCACG-TTCCTCAAATTTTCAAACGCAA
1 TGGTCGAACGAGAAAAATCGAAACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
* * *
3527550 AATATTGCCTTATTTTGAAAATTTTTGAAAAGAATATTAAG-TCATT
66 AACATTGCCTTATTTTG-AAATTTTTGAAAAGGATATTTAGCT-ATT
3527596 TGGTCGAACGAG--AAATCGAAACCCAGTACCTTAGGGCA
1 TGGTCGAACGAGAAAAATCGAAACCCAGTACCTTAGGGCA
3527634 CAATATTGCC
Statistics
Matches: 436, Mismatches: 27, Indels: 30
0.88 0.05 0.06
Matches are distributed among these distances:
107 1 0.00
108 88 0.20
109 42 0.10
110 261 0.60
111 44 0.10
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (110 bp):
TGGTCGAACGAGAAAAATCGAAACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
AACATTGCCTTATTTTGAAATTTTTGAAAAGGATATTTAGCTATT
Found at i:3527579 original size:218 final size:219
Alignment explanation
Indices: 3527047--3527634 Score: 839
Period size: 218 Copynumber: 2.7 Consensus size: 219
3527037 TAGTTGATTA
* * * *
3527047 TGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
1 TGGTCGAACAAGAAAACTCGAAACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
* *
3527112 AACATTGCCTTATTTTG-AAATTTTTGAAAAGGATATTTAG-CTATTTGGTTGAACGAGAAAAAT
66 AACATTGCCTTATTTTGAAAATTTTTGAAAAGGATATTAAGTC-ATTTGGTCGAACGAG--AAAT
* * * *
3527175 CGACACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCCAAACGCAAACATTGCCTTATTTTGA
128 CGAAACCCAGTACCTTAGGGCACGTTTCCTCGAATTTCCCAAACGCAAACATTGCCTTATTTTAA
3527240 AATTTTTGAAAAGGATACTTAGCTATT
193 AATTTTTGAAAAGGATACTTAGCTATT
* * *
3527267 TGGTTGAACGAGAAAACTCGACACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
1 TGGTCGAACAAGAAAACTCGAAACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
3527332 AACATTGCCTTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCGAACGAGAAATCGA
66 AACATTGCCTTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCGAACGAGAAATCGA
* * *
3527397 AACCCAGTACCTTAAGGCACG-TTCCTCGAATTT-CCAAATGCAAAACATTGCCATATTTTTTAA
131 AACCCAGTACCTTAGGGCACGTTTCCTCGAATTTCCCAAACGC-AAACATTGCC-T-TATTTTAA
* *
3527460 AAGTTTTTTAAAAGGATATTTAGCTATT
193 AA-TTTTTGAAAAGGATACTTAGCTATT
* * * * *
3527488 TGGTCGAACAAG-AAA-TTGAAACCCAGTACCTTAGGGCACG-TTCCTCAAATTTTCAAACGCAA
1 TGGTCGAACAAGAAAACTCGAAACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
* *
3527550 AATATTGCCTTATTTTGAAAATTTTTGAAAAGAATATTAAGTCATTTGGTCGAACGAGAAATCGA
66 AACATTGCCTTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCGAACGAGAAATCGA
3527615 AACCCAGTACCTTAGGGCAC
131 AACCCAGTACCTTAGGGCAC
3527635 AATATTGCCT
Statistics
Matches: 339, Mismatches: 23, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
217 7 0.02
218 122 0.36
219 48 0.14
220 92 0.27
221 69 0.20
222 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (219 bp):
TGGTCGAACAAGAAAACTCGAAACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
AACATTGCCTTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCGAACGAGAAATCGA
AACCCAGTACCTTAGGGCACGTTTCCTCGAATTTCCCAAACGCAAACATTGCCTTATTTTAAAAT
TTTTGAAAAGGATACTTAGCTATT
Found at i:3528024 original size:19 final size:18
Alignment explanation
Indices: 3527987--3528029 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3527977 AAATATGCAT
*
3527987 ATATATATATAATAAAAA
1 ATATATATATAAGAAAAA
* *
3528005 ATTATATATATTAGATAAA
1 A-TATATATATAAGAAAAA
3528024 ATATAT
1 ATATAT
3528030 GTAATGTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATATATATATAAGAAAAA
Found at i:3528133 original size:3 final size:3
Alignment explanation
Indices: 3528112--3528160 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
3528102 TAATGAAAAT
* *
3528112 ATA ATG ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3528160 A
1 A
3528161 AAACACGCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3529700 original size:95 final size:94
Alignment explanation
Indices: 3529528--3529708 Score: 290
Period size: 95 Copynumber: 1.9 Consensus size: 94
3529518 TAAGATCTGA
3529528 AATCTTCAATCTATTCCACTACCAACCAGGGAATAGAATTATCGGCTTCAATGTACTCCACTATA
1 AATCTTCAATCTATTCCACTACCAACCAGGGAATAGAATTATCGGCTTCAATGTACTCCACTATA
* * *
3529593 GTCATAGTGAGGTAAAATCTGCCATCTTC
66 ATCACAGGGAGGTAAAATCTGCCATCTTC
* * * *
3529622 AATCTTCAATCTATTCCACTGCCAATCAGGGAGATAGAATTTTCGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTACCAACCAGGGA-ATAGAATTATCGGCTTCAATGTACTCCACTAT
3529687 AATCACAGGGAGGTAAAATCTG
65 AATCACAGGGAGGTAAAATCTG
3529709 AAATTCTTTG
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 30 0.38
95 49 0.62
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (94 bp):
AATCTTCAATCTATTCCACTACCAACCAGGGAATAGAATTATCGGCTTCAATGTACTCCACTATA
ATCACAGGGAGGTAAAATCTGCCATCTTC
Found at i:3531572 original size:8 final size:7
Alignment explanation
Indices: 3531522--3531568 Score: 69
Period size: 7 Copynumber: 6.6 Consensus size: 7
3531512 TTGGCCTCTC
3531522 CATTTTT
1 CATTTTT
3531529 CATTTTT
1 CATTTTT
3531536 CATTTTT
1 CATTTTT
3531543 CA-TTTT
1 CATTTTT
3531549 CATTTTTT
1 CA-TTTTT
3531557 CATTCTTT
1 CATT-TTT
3531565 CATT
1 CATT
3531569 CTTTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.16
7 18 0.49
8 13 0.35
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:3531575 original size:21 final size:20
Alignment explanation
Indices: 3531531--3531577 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 20
3531521 CCATTTTTCA
3531531 TTTTTCATTTTTCATTTTCAT
1 TTTTTCATTTTTCATTTT-AT
3531552 TTTTTCATTCTTTCATTCTT-T
1 TTTTTCATT-TTTCATT-TTAT
3531573 TTTTT
1 TTTTT
3531578 TTACTCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 15 0.62
22 7 0.29
23 2 0.08
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTCATTTTTCATTTTAT
Found at i:3532424 original size:21 final size:22
Alignment explanation
Indices: 3532398--3532453 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
3532388 TGACCTCTCC
3532398 TTTTTCCTTTTCT-TTTTTTCT
1 TTTTTCCTTTTCTCTTTTTTCT
*
3532419 TTTTT-CTTTTTTCTTTTTTCT
1 TTTTTCCTTTTCTCTTTTTTCT
* *
3532440 TCTTTCTTTTTCTC
1 TTTTTCCTTTTCTC
3532454 CTATTTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.21
21 17 0.59
22 6 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTCCTTTTCTCTTTTTTCT
Found at i:3532431 original size:14 final size:14
Alignment explanation
Indices: 3532405--3532450 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
3532395 TCCTTTTTCC
3532405 TTTTCTTTTTTTCTT
1 TTTTC-TTTTTTCTT
3532420 TTTTCTTTTTTCTT
1 TTTTCTTTTTTCTT
*
3532434 TTTTCTTCTTTCTT
1 TTTTCTTTTTTCTT
3532448 TTT
1 TTT
3532451 CTCCTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 25 0.83
15 5 0.17
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTCTTTTTTCTT
Found at i:3533214 original size:17 final size:18
Alignment explanation
Indices: 3533182--3533218 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3533172 TCTGCACAGT
3533182 ATGATTATGAATGAAAGA
1 ATGATTATGAATGAAAGA
*
3533200 ATGATT-TGGATGAAAGA
1 ATGATTATGAATGAAAGA
3533217 AT
1 AT
3533219 AAAAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (18 bp):
ATGATTATGAATGAAAGA
Found at i:3542045 original size:48 final size:48
Alignment explanation
Indices: 3541971--3542086 Score: 162
Period size: 48 Copynumber: 2.4 Consensus size: 48
3541961 CTAACAAATT
* *
3541971 CAAAATTTTGGCCTGCACTTGGTCTAAACCACGGCCCACACAG-ATGCC
1 CAAAATTATGGCCTGCACTTGCTCTAAACCACGGCCCACA-AGAATGCC
* * *
3542019 CAAAATTCTGGCTTGCACTTGCTCTAAACCACGGCCCACATGAATGCC
1 CAAAATTATGGCCTGCACTTGCTCTAAACCACGGCCCACAAGAATGCC
*
3542067 CATAATTATGGCCTGCACTT
1 CAAAATTATGGCCTGCACTT
3542087 AGTTCCACAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 1 0.02
48 59 0.98
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (48 bp):
CAAAATTATGGCCTGCACTTGCTCTAAACCACGGCCCACAAGAATGCC
Found at i:3550994 original size:12 final size:12
Alignment explanation
Indices: 3550977--3551009 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3550967 CGGCCTGCCC
3550977 ATATTAATTTTT
1 ATATTAATTTTT
3550989 ATATT-ATTTTT
1 ATATTAATTTTT
3551000 ATA-TAATTTT
1 ATATTAATTTT
3551010 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:3551045 original size:18 final size:20
Alignment explanation
Indices: 3551010--3551050 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
3551000 ATATAATTTT
*
3551010 AAAATATATATAATACATCA
1 AAAATATATATAAAACATCA
3551030 AAAATAT-TA-AAAACATCA
1 AAAATATATATAAAACATCA
3551048 AAA
1 AAA
3551051 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 2 0.10
20 7 0.35
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATATATATAAAACATCA
Found at i:3551167 original size:30 final size:30
Alignment explanation
Indices: 3551133--3551195 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
3551123 ACTTAACAAG
3551133 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
3551163 CAAATATCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
3551193 CAA
1 CAA
3551196 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:3551319 original size:22 final size:22
Alignment explanation
Indices: 3551277--3551319 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
3551267 AAATAGGGAG
* *
3551277 AAAACAACAAGAAAATAATATT
1 AAAACAACAAAAAAAAAATATT
3551299 AAAA-AACAAAAAAAAACATAT
1 AAAACAACAAAAAAAAA-ATAT
3551320 ATTTTTTGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAACAACAAAAAAAAAATATT
Found at i:3551321 original size:24 final size:24
Alignment explanation
Indices: 3551277--3551322 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3551267 AAATAGGGAG
* *
3551277 AAAACAACAAGAAAATAATATTAA
1 AAAACAAAAAAAAAATAATATTAA
3551301 AAAACAAAAAAAAACAT-ATATT
1 AAAACAAAAAAAAA-ATAATATT
3551323 TTTTGCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (24 bp):
AAAACAAAAAAAAAATAATATTAA
Found at i:3554464 original size:28 final size:27
Alignment explanation
Indices: 3554398--3554465 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
3554388 TTATAGCATG
*
3554398 TTTATT-TTTATTTTAAAAATAGGAATT
1 TTTATTATTT-TTTTAAAAATAGGAACT
*
3554425 TTTATAGTATTTTTTTAAACATAGGAAACT
1 TTTAT--TATTTTTTTAAAAATAGG-AACT
3554455 TTTATTATTTT
1 TTTATTATTTT
3554466 ATTAGTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 5 0.14
28 6 0.17
29 13 0.37
30 11 0.31
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (27 bp):
TTTATTATTTTTTTAAAAATAGGAACT
Found at i:3555614 original size:39 final size:43
Alignment explanation
Indices: 3555569--3555676 Score: 125
Period size: 46 Copynumber: 2.5 Consensus size: 43
3555559 TTTCCTTATG
* * *
3555569 CTATTACACCTCTATTCCATT-C-AACCAAATACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTACTAACCAAACAAAAGAATTAC
*
3555609 C-ATTACGCATCTATTCCATTACATTTAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATTCCATTAC---TAACCAAACAAAAGAATTAC
3555654 CTATTACGCCTCTATTCCATTAC
1 CTATTACGCCTCTATTCCATTAC
3555677 GCCTCTATTC
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
39 17 0.30
40 2 0.04
44 13 0.23
45 4 0.07
46 20 0.36
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.31
Consensus pattern (43 bp):
CTATTACGCCTCTATTCCATTACTAACCAAACAAAAGAATTAC
Found at i:3555669 original size:46 final size:44
Alignment explanation
Indices: 3555586--3555676 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 44
3555576 ACCTCTATTC
* *
3555586 CATTCAACCAAATACAAGAATACCATTACGCATCTATTCCATTA
1 CATTCAACCAAACAAAAGAATACCATTACGCATCTATTCCATTA
* *
3555630 CATTTAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAA-TACC-ATTACGCATCTATTCCATTA
3555676 C
1 C
3555677 GCCTCTATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 17 0.41
45 4 0.10
46 20 0.49
ACGTcount: A:0.40, C:0.27, G:0.04, T:0.29
Consensus pattern (44 bp):
CATTCAACCAAACAAAAGAATACCATTACGCATCTATTCCATTA
Found at i:3555677 original size:16 final size:16
Alignment explanation
Indices: 3555656--3555692 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
3555646 AGAATTACCT
3555656 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
3555672 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
3555688 ATTAC
1 ATTAC
3555693 AGCGAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:3559351 original size:32 final size:32
Alignment explanation
Indices: 3559315--3559379 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
3559305 CTAGAACTTG
* * *
3559315 AAACTTGAATTACTTG-TTTGAGTTGACTCGAA
1 AAACTCGAATAACTTGATTTGA-TTAACTCGAA
3559347 AAACTCGAATAACTTGATTTGATTAACTCGAA
1 AAACTCGAATAACTTGATTTGATTAACTCGAA
3559379 A
1 A
3559380 TTCTAATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (32 bp):
AAACTCGAATAACTTGATTTGATTAACTCGAA
Found at i:3561121 original size:15 final size:15
Alignment explanation
Indices: 3561101--3561173 Score: 76
Period size: 15 Copynumber: 4.7 Consensus size: 15
3561091 ATACTACAAA
3561101 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
3561116 ATATTTATAATTTAAT
1 ATATTTATTA-TTAAT
*
3561132 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
*
3561149 ATA-TTAATATTGAAT
1 ATATTTATTATT-AAT
3561164 ATATTTATTA
1 ATATTTATTA
3561174 ATATGTATGT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
14 7 0.15
15 17 0.36
16 10 0.21
17 4 0.09
18 9 0.19
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:3561141 original size:33 final size:32
Alignment explanation
Indices: 3561099--3561173 Score: 100
Period size: 33 Copynumber: 2.4 Consensus size: 32
3561089 TTATACTACA
* * *
3561099 AAATATTTATTATTAATATATTTATAATTTAAT
1 AAATATTTATTATTAAAATATTAAT-ATTGAAT
3561132 AAATATTTATTATTAAAATATTAATATTGAAT
1 AAATATTTATTATTAAAATATTAATATTGAAT
3561164 --ATATTTATTA
1 AAATATTTATTA
3561174 ATATGTATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 10 0.26
32 6 0.15
33 23 0.59
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (32 bp):
AAATATTTATTATTAAAATATTAATATTGAAT
Found at i:3563397 original size:22 final size:23
Alignment explanation
Indices: 3563348--3563404 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
3563338 CTCCCGATTT
*
3563348 CTCTTCCTGTTTCATCCATCGGC
1 CTCTTCCTGTTTCATCCATCAGC
**
3563371 CTCTTCCTGTTTCA-CTTTCAGC
1 CTCTTCCTGTTTCATCCATCAGC
3563393 CTCTTCCTGTTT
1 CTCTTCCTGTTT
3563405 AATTTCTTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.07, C:0.37, G:0.11, T:0.46
Consensus pattern (23 bp):
CTCTTCCTGTTTCATCCATCAGC
Found at i:3565440 original size:20 final size:20
Alignment explanation
Indices: 3565404--3565442 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3565394 AAATTTTTAA
*
3565404 AAATATATTTATAATATAAT
1 AAATATATTAATAATATAAT
3565424 AAATATA-TAATACATATAA
1 AAATATATTAATA-ATATAA
3565443 ATTTAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATTAATAATATAAT
Found at i:3566991 original size:16 final size:16
Alignment explanation
Indices: 3566957--3567010 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
3566947 TTGATTTGCT
* *
3566957 ATTACATCTCTAATCC
1 ATTACACCTCTATTCC
*
3566973 ATTACACCTCTATTTC
1 ATTACACCTCTATTCC
* *
3566989 ATTACGCCTCTATTCA
1 ATTACACCTCTATTCC
3567005 ATTACA
1 ATTACA
3567011 GCGAACCAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:3573858 original size:18 final size:18
Alignment explanation
Indices: 3573835--3573880 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
3573825 ATAATTTTAG
3573835 TAAATTCATATA-TTCTAT
1 TAAATT-ATATATTTCTAT
*
3573853 TAAATTATATATTTTTAT
1 TAAATTATATATTTCTAT
3573871 TAAATTATAT
1 TAAATTATAT
3573881 TTAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAATTATATATTTCTAT
Found at i:3574056 original size:18 final size:19
Alignment explanation
Indices: 3574033--3574098 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
3574023 ACACACACTC
3574033 CACCGCT-GTATCCAATCT
1 CACCGCTAGTATCCAATCT
3574051 CACCGCTACAGTATCCAATCT
1 CACCGCT--AGTATCCAATCT
* *
3574072 CACCGCTACAGTAACTAATCT
1 CACCGCT--AGTATCCAATCT
3574093 CACCGC
1 CACCGC
3574099 CACCGCTGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 7 0.16
21 36 0.84
ACGTcount: A:0.27, C:0.39, G:0.11, T:0.23
Consensus pattern (19 bp):
CACCGCTAGTATCCAATCT
Found at i:3574066 original size:21 final size:21
Alignment explanation
Indices: 3574040--3574098 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
3574030 CTCCACCGCT
3574040 GTATCCAATCTCACCGCTACA
1 GTATCCAATCTCACCGCTACA
3574061 GTATCCAATCTCACCGCTACA
1 GTATCCAATCTCACCGCTACA
* *
3574082 GTAACTAATCTCACCGC
1 GTATCCAATCTCACCGC
3574099 CACCGCTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.29, C:0.37, G:0.10, T:0.24
Consensus pattern (21 bp):
GTATCCAATCTCACCGCTACA
Found at i:3581516 original size:147 final size:147
Alignment explanation
Indices: 3581249--3581549 Score: 491
Period size: 147 Copynumber: 2.0 Consensus size: 147
3581239 AATGCCCCAG
* *
3581249 CAACCTCTATGAGATGTATAACAGCTATTTTTGTTGACATGTTAGAAGAAGGCTTGGATGTATTT
1 CAACCTTTATGAGATGTATAACAGCTATTTTTGCTGACATGTTAGAAGAAGGCTTGGATGTATTT
*
3581314 ATGGATGATTTCTCAGTATATGGAGATTCATTTCAAGAATTTTGGACAATCTTAAAAAAGTCTTG
66 ATGGATGATTTCTCAGTATATGGAGATTCATTTCAAGAATTTTGGACAATCTTAAAAAAGTCTTA
3581379 CAGAGATGCAA-AA-AAAC
131 CAGAGAT--AAGAAGAAAC
* **
3581396 CAACCTTTATGAGATGTATGATGGCTATTTTTGCTGACATGTTAGAAGAAGGCTTGGATGTATTT
1 CAACCTTTATGAGATGTATAACAGCTATTTTTGCTGACATGTTAGAAGAAGGCTTGGATGTATTT
3581461 ATGGATGATTTCTCAGTATAT-GAGATTCATTTCAAGAATGTTTGGACAATCTTAAAAAAGTCTT
66 ATGGATGATTTCTCAGTATATGGAGATTCATTTCAAGAAT-TTTGGACAATCTTAAAAAAGTCTT
*
3581525 ATAGAGATAAGAAGAAAC
130 ACAGAGATAAGAAGAAAC
3581543 CAACCTT
1 CAACCTT
3581550 GTATTAAACT
Statistics
Matches: 144, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
145 2 0.01
146 20 0.14
147 122 0.85
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (147 bp):
CAACCTTTATGAGATGTATAACAGCTATTTTTGCTGACATGTTAGAAGAAGGCTTGGATGTATTT
ATGGATGATTTCTCAGTATATGGAGATTCATTTCAAGAATTTTGGACAATCTTAAAAAAGTCTTA
CAGAGATAAGAAGAAAC
Found at i:3587346 original size:38 final size:38
Alignment explanation
Indices: 3587295--3587562 Score: 266
Period size: 38 Copynumber: 6.9 Consensus size: 38
3587285 AACGTAACGT
* **
3587295 TATTCGGGCTCCGTGCCTAGCAGGCTTTGTGTTGGTGA
1 TATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTGA
* * *
3587333 TATTCGAGCTCCGTGCCTAGCAGGCTTTATGCCGGTGA
1 TATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTGA
* *
3587371 TATTCGGGCTCTGTGCCTAGTAGGCTTTGTGCTGGTGA
1 TATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTGA
* * * *
3587409 TATTCGGGCTCTGTGCCTAACAAGCTTTGTGTCAGTGA
1 TATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTGA
* * *
3587447 TATTTGGGCTCTGTGCCTAGCAGGTTTTGTGCCAGTGTA
1 TATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTG-A
* * * * *
3587486 TTATATCAGGCTCTGTGTCTAGCAGGCTTCGTGTCAGTGTA
1 -TAT-TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTG-A
* * * *
3587527 GTATATCAGGATTTGTGCCTAGCAGGCTTCGTGCCG
1 -TAT-TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCG
3587563 ATGTATTATA
Statistics
Matches: 195, Mismatches: 32, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
38 131 0.67
39 1 0.01
40 3 0.02
41 60 0.31
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.34
Consensus pattern (38 bp):
TATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTGA
Found at i:3587387 original size:22 final size:22
Alignment explanation
Indices: 3587362--3587425 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
3587352 GCAGGCTTTA
3587362 TGCCGGTGATATTCGGGCTCTG
1 TGCCGGTGATATTCGGGCTCTG
*
3587384 TGCC--T-AGTA----GGCTTTG
1 TGCCGGTGA-TATTCGGGCTCTG
*
3587400 TGCTGGTGATATTCGGGCTCTG
1 TGCCGGTGATATTCGGGCTCTG
3587422 TGCC
1 TGCC
3587426 TAACAAGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 16
0.60 0.08 0.32
Matches are distributed among these distances:
16 9 0.30
18 3 0.10
19 2 0.07
20 3 0.10
22 13 0.43
ACGTcount: A:0.09, C:0.22, G:0.34, T:0.34
Consensus pattern (22 bp):
TGCCGGTGATATTCGGGCTCTG
Found at i:3587508 original size:41 final size:41
Alignment explanation
Indices: 3587340--3587620 Score: 204
Period size: 41 Copynumber: 7.1 Consensus size: 41
3587330 TGATATTCGA
* ** * *
3587340 GCTCCGTGCCTAGCAGGCTTTATGCCGGTG-A-TAT-TCGG
1 GCTCTGTGCCTAGCAGGCTTCGTGCCAGTGTATTATATCAG
* * ** *
3587378 GCTCTGTGCCTAGTAGGCTTTGTGCTGGTG-A-TAT-TCGG
1 GCTCTGTGCCTAGCAGGCTTCGTGCCAGTGTATTATATCAG
* * * * **
3587416 GCTCTGTGCCTAACAAGCTTTGTGTCAGTG-A-TAT-TTGG
1 GCTCTGTGCCTAGCAGGCTTCGTGCCAGTGTATTATATCAG
* *
3587454 GCTCTGTGCCTAGCAGGTTTTGTGCCAGTGTATTATATCAG
1 GCTCTGTGCCTAGCAGGCTTCGTGCCAGTGTATTATATCAG
* * *
3587495 GCTCTGTGTCTAGCAGGCTTCGTGTCAGTGTAGTATATCAG
1 GCTCTGTGCCTAGCAGGCTTCGTGCCAGTGTATTATATCAG
* *
3587536 GATTTGTGCCTAGCAGGCTTCGTGCC-GATGTATTATATCAG
1 GCTCTGTGCCTAGCAGGCTTCGTGCCAG-TGTATTATATCAG
* * * * * * * *
3587577 CCTTTATGCCTAGTAAGCTTTGTGCCGGAGTATTATATCAG
1 GCTCTGTGCCTAGCAGGCTTCGTGCCAGTGTATTATATCAG
3587618 GCT
1 GCT
3587621 TCGAGTATGC
Statistics
Matches: 203, Mismatches: 35, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
38 91 0.45
39 1 0.00
40 4 0.02
41 106 0.52
42 1 0.00
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.35
Consensus pattern (41 bp):
GCTCTGTGCCTAGCAGGCTTCGTGCCAGTGTATTATATCAG
Found at i:3588116 original size:21 final size:21
Alignment explanation
Indices: 3588090--3588130 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3588080 ATATGTGAGA
3588090 AATTTA-CTTAAGTTATGGATG
1 AATTTATC-TAAGTTATGGATG
*
3588111 AATTTATCTAGGTTATGGAT
1 AATTTATCTAAGTTATGGAT
3588131 AAATACCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (21 bp):
AATTTATCTAAGTTATGGATG
Found at i:3593228 original size:38 final size:38
Alignment explanation
Indices: 3593173--3593273 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 38
3593163 TATTTGGGCT
** *
3593173 CCAGTGATATTTGGGCTCTGTGCCTAGCAAGCTTTGTG
1 CCAGTGATATTCAGGCTCTGTGCCTAACAAGCTTTGTG
* *
3593211 CCGGTGATATTCAGGCTCTGTGCCTAACAGGCTTTGTG
1 CCAGTGATATTCAGGCTCTGTGCCTAACAAGCTTTGTG
*
3593249 CTAGTGTATTATATCAGGCTCTGTG
1 CCAGTG-A-TAT-TCAGGCTCTGTG
3593274 TACAGTCGGC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 37 0.70
39 1 0.02
40 3 0.06
41 12 0.23
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.35
Consensus pattern (38 bp):
CCAGTGATATTCAGGCTCTGTGCCTAACAAGCTTTGTG
Found at i:3593351 original size:41 final size:41
Alignment explanation
Indices: 3593186--3593350 Score: 164
Period size: 41 Copynumber: 4.1 Consensus size: 41
3593176 GTGATATTTG
* *
3593186 GGCTCTGTGCCTAGCAAGCTTTGTGCCGGTG-A-TAT-TCA
1 GGCTCTGTGCCTAGCAGGCTTTGTGTCGGTGTATTATATCA
* *
3593224 GGCTCTGTGCCTAACAGGCTTTGTG-CTAGTGTATTATATCA
1 GGCTCTGTGCCTAGCAGGCTTTGTGTC-GGTGTATTATATCA
* *
3593265 GGCTCTGTGTAC-AGTC-GGCTTCGT-TCCGGTGTATTATATCA
1 GGCTCTGTG-CCTAG-CAGGCTTTGTGT-CGGTGTATTATATCA
* * *
3593306 GGCTTTGTGCCTAGTAGGCTTTGTGTCGGTGTATTATATTA
1 GGCTCTGTGCCTAGCAGGCTTTGTGTCGGTGTATTATATCA
3593347 GGCT
1 GGCT
3593351 TCGAGCATGG
Statistics
Matches: 104, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
37 1 0.01
38 26 0.25
39 1 0.01
40 4 0.04
41 68 0.65
42 4 0.04
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (41 bp):
GGCTCTGTGCCTAGCAGGCTTTGTGTCGGTGTATTATATCA
Found at i:3593370 original size:41 final size:41
Alignment explanation
Indices: 3593291--3593370 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
3593281 GGCTTCGTTC
* * * *
3593291 CGGTGTATTATATCAGGCTTTGTGCCTAGTAGGCTTTGTGT
1 CGGTGTATTATATCAGGCTTCGAGCATAGTAGGATTTGTGT
* * *
3593332 CGGTGTATTATATTAGGCTTCGAGCATGGTAGTATTTGT
1 CGGTGTATTATATCAGGCTTCGAGCATAGTAGGATTTGT
3593371 ACCGATGTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.17, C:0.12, G:0.29, T:0.41
Consensus pattern (41 bp):
CGGTGTATTATATCAGGCTTCGAGCATAGTAGGATTTGTGT
Found at i:3596517 original size:13 final size:13
Alignment explanation
Indices: 3596501--3596531 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3596491 AAATGTGTAA
3596501 ATGAAATGGTTAT
1 ATGAAATGGTTAT
3596514 ATGAAATGGTTAT
1 ATGAAATGGTTAT
3596527 ATGAA
1 ATGAA
3596532 TATATACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (13 bp):
ATGAAATGGTTAT
Found at i:3598775 original size:13 final size:13
Alignment explanation
Indices: 3598745--3598807 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
3598735 AAATTTTTGG
* *
3598745 CTTTTCAAAAGCA
1 CTTTTGAAAAACA
*
3598758 TTTTTGAAAAACA
1 CTTTTGAAAAACA
*
3598771 CTTTTGAAAAATA
1 CTTTTGAAAAACA
3598784 CTTTTGAAAAACA
1 CTTTTGAAAAACA
*
3598797 CTTCTGAAAAA
1 CTTTTGAAAAA
3598808 GAGAAGCTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.33
Consensus pattern (13 bp):
CTTTTGAAAAACA
Found at i:3600918 original size:272 final size:273
Alignment explanation
Indices: 3600431--3600976 Score: 1085
Period size: 272 Copynumber: 2.0 Consensus size: 273
3600421 ATATAAAAAC
3600431 CTTTAAATTTTTATTTTATAATTTAACATAAATAAATGGAAAGAGTATACACCACCAATTTAAAA
1 CTTTAAATTTTTATTTTATAATTTAACATAAATAAATGGAAAGAGTATACACCACCAATTTAAAA
3600496 GAGATTACAAATAAGGTTTTTTTTTTTTTCTTTTTTGTAGTTTTAAGACACAACATTTAATTTTT
66 GAGATTACAAATAAGGTTTTTTTTTTTTTCTTTTTTGTAGTTTTAAGACACAACATTTAATTTTT
3600561 AATAGTAAAAAAAAAATCATATCATGGATGGACCATGAATAATACGATATGAAGGTGATAGTTGT
131 AATAGTAAAAAAAAAATCATATCATGGATGGACCATGAATAATACGATATGAAGGTGATAGTTGT
3600626 GGTCCCTATTAAAGATAAGCTTTTCTTTTAATTAAAATTTAACCACACCTTTCAAAATCGTATAA
196 GGTCCCTATTAAAGATAAGCTTTTCTTTTAATTAAAATTTAACCACACCTTTCAAAATCGTATAA
3600691 CTAACAAGTGTTA
261 CTAACAAGTGTTA
3600704 CTTTAAA-TTTTATTTTATAATTTAACATAAATAAATGGAAAGAGTATACACCACCAATTTAAAA
1 CTTTAAATTTTTATTTTATAATTTAACATAAATAAATGGAAAGAGTATACACCACCAATTTAAAA
3600768 GAGATTACAAATAAGGTTTTTTTTTTTTTCTTTTTTGTAGTTTTAAGACACAACATTTAATTTTT
66 GAGATTACAAATAAGGTTTTTTTTTTTTTCTTTTTTGTAGTTTTAAGACACAACATTTAATTTTT
3600833 AATAGTAAAAAAAAAATCATATCATGGATGGACCATGAATAATACGATATGAAGGTGATAGTTGT
131 AATAGTAAAAAAAAAATCATATCATGGATGGACCATGAATAATACGATATGAAGGTGATAGTTGT
3600898 GGTCCCTATTAAAGATAAGCTTTTCTTTTAATTAAAATTTAACCACACCTTTCAAAATCGTATAA
196 GGTCCCTATTAAAGATAAGCTTTTCTTTTAATTAAAATTTAACCACACCTTTCAAAATCGTATAA
3600963 CTAACAAGTGTTA
261 CTAACAAGTGTTA
3600976 C
1 C
3600977 CAATGTTATG
Statistics
Matches: 273, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
272 266 0.97
273 7 0.03
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (273 bp):
CTTTAAATTTTTATTTTATAATTTAACATAAATAAATGGAAAGAGTATACACCACCAATTTAAAA
GAGATTACAAATAAGGTTTTTTTTTTTTTCTTTTTTGTAGTTTTAAGACACAACATTTAATTTTT
AATAGTAAAAAAAAAATCATATCATGGATGGACCATGAATAATACGATATGAAGGTGATAGTTGT
GGTCCCTATTAAAGATAAGCTTTTCTTTTAATTAAAATTTAACCACACCTTTCAAAATCGTATAA
CTAACAAGTGTTA
Found at i:3601380 original size:34 final size:34
Alignment explanation
Indices: 3601343--3601463 Score: 118
Period size: 34 Copynumber: 3.6 Consensus size: 34
3601333 ATTTTTGGTA
*
3601343 GGTTTAGAGTTTTTTAAAAAAATTAATTAAACTAG
1 GGTTTAG-GTTTTTTAAAAAAATTAATTAAATTAG
* * * * * * *
3601378 GTTTTTGG-GTTTTAAATAACTAAATAAAATTAG
1 GGTTTAGGTTTTTTAAAAAAATTAATTAAATTAG
* * *
3601411 GGTTTAGGGTTTTTAAGAAAATTAATTAAATTAT
1 GGTTTAGGTTTTTTAAAAAAATTAATTAAATTAG
*
3601445 GGTTTAGTTTTTTTAAAAA
1 GGTTTAGGTTTTTTAAAAA
3601464 TAAATTTGTG
Statistics
Matches: 65, Mismatches: 20, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
33 25 0.38
34 35 0.54
35 5 0.08
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.44
Consensus pattern (34 bp):
GGTTTAGGTTTTTTAAAAAAATTAATTAAATTAG
Found at i:3601464 original size:32 final size:34
Alignment explanation
Indices: 3601343--3601469 Score: 100
Period size: 33 Copynumber: 3.8 Consensus size: 34
3601333 ATTTTTGGTA
* * * *
3601343 GGTTTAGAGTTTTTTAAAAAAATTAATTAAACTAG
1 GGTTTAG-GGTTTTTAAGAAAATAAATTAAATTAG
* * * *
3601378 GTTTTTGGG-TTTTAA-ATAACTAAATAAAATTAG
1 GGTTTAGGGTTTTTAAGA-AAATAAATTAAATTAG
* *
3601411 GGTTTAGGGTTTTTAAGAAAATTAATTAAATTAT
1 GGTTTAGGGTTTTTAAGAAAATAAATTAAATTAG
* *
3601445 GGTTTA-GTTTTTTTA-AAAATAAATT
1 GGTTTAGGGTTTTTAAGAAAATAAATT
3601470 TGTGTTTGGG
Statistics
Matches: 73, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
32 10 0.14
33 32 0.44
34 25 0.34
35 6 0.08
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (34 bp):
GGTTTAGGGTTTTTAAGAAAATAAATTAAATTAG
Found at i:3601750 original size:126 final size:126
Alignment explanation
Indices: 3601518--3601916 Score: 552
Period size: 126 Copynumber: 3.2 Consensus size: 126
3601508 ATTTTGTTTT
* * * * *
3601518 TTTTTCTACAGTAATTTCTGAAAAAATAATTTTGAGAAGACGATTCTGAAA-AGATAATGTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCT-AAACAAATAATGTAAAA
* * *
3601582 AACGCTTCAAGCAAGATACACTGTCAGCAAAATTACTGAAAAAAGCTCCTACGTGGACGCTC
65 AAAGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCTACGTGGATGCTC
*
3601644 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAACAAATATTGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAACAAATAATGT-AAAA
* * *
3601709 AAAGCTTCAAGCAAGATGTACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGATGCTC
65 AAAGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCTACGTGGATGCTC
* * * * *
3601771 TTTTTCTACAGTAGTCCCTGAAAAAATAATTTTAAGAAGACAGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAACAAATAATGTAAAAA
* * * *
3601836 ATGCTTCAAG-TAGAATGCACTGTCAGCAAAATTACTGAAAAAGGCT-CTCACGTGGATGTTC
66 AAGCTTCAAGCAAG-ATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCT-ACGTGGATGCTC
3601897 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
3601917 TTTGGCCTTA
Statistics
Matches: 244, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
125 6 0.02
126 122 0.50
127 116 0.48
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAACAAATAATGTAAAAA
AAGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCTACGTGGATGCTC
Found at i:3605446 original size:18 final size:18
Alignment explanation
Indices: 3605420--3605462 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3605410 GACTGGGAAA
* *
3605420 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
*
3605438 AGGATACATATATGGGCT
1 AGGATACATATAAGGGCT
3605456 AGGATAC
1 AGGATAC
3605463 GGACCTAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:3607043 original size:20 final size:21
Alignment explanation
Indices: 3607018--3607056 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3607008 ATAAATTAAA
3607018 ATTAAATAA-ATGGAAAAAAT
1 ATTAAATAATATGGAAAAAAT
*
3607038 ATTAAATAATATTGAAAAA
1 ATTAAATAATATGGAAAAA
3607057 TTAACCCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (21 bp):
ATTAAATAATATGGAAAAAAT
Found at i:3607257 original size:9 final size:11
Alignment explanation
Indices: 3607223--3607273 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
3607213 AGAGAGTTTT
3607223 GAGAAATTTAGA
1 GAGAAATTT-GA
3607235 GAGAAATTTGA
1 GAGAAATTTGA
*
3607246 GAGAAATTAGA
1 GAGAAATTTGA
*
3607257 GAGAAAATTGA
1 GAGAAATTTGA
3607268 -AGAAAT
1 GAGAAAT
3607274 AGTGTACGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 5 0.14
11 21 0.60
12 9 0.26
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (11 bp):
GAGAAATTTGA
Found at i:3622413 original size:12 final size:12
Alignment explanation
Indices: 3622396--3622422 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3622386 TTAGTAAAAG
3622396 AATAGGTTTTTA
1 AATAGGTTTTTA
3622408 AATAGGTTTTTA
1 AATAGGTTTTTA
3622420 AAT
1 AAT
3622423 TTTACTGTCA
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:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (12 bp):
AATAGGTTTTTA
Found at i:3631444 original size:19 final size:19
Alignment explanation
Indices: 3631414--3631464 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
3631404 AGAAAACAAG
*
3631414 AGAACAAATCTAAACCTAA
1 AGAAAAAATCTAAACCTAA
* *
3631433 AGATAGAATCTAAACCTAA
1 AGAAAAAATCTAAACCTAA
3631452 AGAAAAAATCTAA
1 AGAAAAAATCTAA
3631465 GCTAATGGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.59, C:0.16, G:0.08, T:0.18
Consensus pattern (19 bp):
AGAAAAAATCTAAACCTAA
Found at i:3644193 original size:20 final size:20
Alignment explanation
Indices: 3644146--3644203 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
3644136 AATAATTTAA
* *
3644146 ATTG-AGCTTAAACGAGCTG
1 ATTGAAGCTCAAATGAGCTG
* *
3644165 ATTTAAGCTCAAGTGAGCTG
1 ATTGAAGCTCAAATGAGCTG
* *
3644185 ATTGGAGCTGAAATGAGCT
1 ATTGAAGCTCAAATGAGCT
3644204 TGGGAAGCTG
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (20 bp):
ATTGAAGCTCAAATGAGCTG
Found at i:3654169 original size:40 final size:40
Alignment explanation
Indices: 3654125--3654228 Score: 136
Period size: 40 Copynumber: 2.6 Consensus size: 40
3654115 AGATAAACTG
* * * *
3654125 CAGTAATGTGGACAGGCCACCAGTGTTGCAGACAAGTTGC
1 CAGTAATGTGGACAAGCCACCAGTGTTACAGAAAAGCTGC
*
3654165 CAGTAATGTGGACAAGCCACTAGTGTTACAGAAAAGCTGC
1 CAGTAATGTGGACAAGCCACCAGTGTTACAGAAAAGCTGC
* * *
3654205 TAATAATGTGGAAAAGCCACCAGT
1 CAGTAATGTGGACAAGCCACCAGT
3654229 AATGTAGATA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (40 bp):
CAGTAATGTGGACAAGCCACCAGTGTTACAGAAAAGCTGC
Found at i:3654298 original size:60 final size:60
Alignment explanation
Indices: 3654190--3654303 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
3654180 GCCACTAGTG
* * * **
3654190 TTACAGAAAAGCTGCTAATAATGTGGAAAAGCCACCAGTAATGTAGATAAACTGTCAGTA
1 TTACAGAAAAGCTGCCAATAATATGGAAAAGCCACCAATAATACAGATAAACTGTCAGTA
* * *
3654250 TTACAGAAAAGCTGCCAGTATTATGGACAAA-CCTCCAATAATACAGATAAACTG
1 TTACAGAAAAGCTGCCAATAATATGGA-AAAGCCACCAATAATACAGATAAACTG
3654304 CTAGTACTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
60 42 0.93
61 3 0.07
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (60 bp):
TTACAGAAAAGCTGCCAATAATATGGAAAAGCCACCAATAATACAGATAAACTGTCAGTA
Found at i:3656878 original size:51 final size:51
Alignment explanation
Indices: 3656815--3657004 Score: 208
Period size: 51 Copynumber: 3.7 Consensus size: 51
3656805 TATCGATGAA
*
3656815 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCTATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCTATAAATATTGGT
* * * * * * *
3656866 CACATGTATAGTACTAAGTGAAGCCTACTATGTGTACCGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCTATAAA--TATTGGT
* * * *
3656917 CACGTGTGTAGTACTATGTGAAGGCTACTACGCG-AACTGTAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCTATAAATA-TTGGT
*
3656967 CATGTGTGTAGTACTATGTGAAGGCTACTACGTGTATC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATC
3657005 GAATGATAAT
Statistics
Matches: 112, Mismatches: 21, Indels: 12
0.77 0.14 0.08
Matches are distributed among these distances:
50 41 0.37
51 70 0.62
52 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCTATAAATATTGGT
Found at i:3663174 original size:3 final size:3
Alignment explanation
Indices: 3663166--3663192 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3663156 CTAGGAAAAA
3663166 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
3663193 ATTTTTATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3685800 original size:43 final size:42
Alignment explanation
Indices: 3685750--3685862 Score: 131
Period size: 43 Copynumber: 2.6 Consensus size: 42
3685740 GTGTTTTCGA
* *
3685750 GTAAGACCACGTCTGGGACGTTGGCATCGA-CTTGTGTTTACAT
1 GTAAGACCACGTCTGGGACG-TGGCATCGATC-TGTGATCACAT
* *
3685793 GTAAGACC-CTATTTGGGACAGTGGCATCGATCTGTGATCACAT
1 GTAAGACCAC-GTCTGGGAC-GTGGCATCGATCTGTGATCACAT
3685836 GTAAGACCACGTCTGGGACGCTGGCAT
1 GTAAGACCACGTCTGGGACG-TGGCAT
3685863 TGTACGAGCT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.03
43 54 0.92
44 3 0.05
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (42 bp):
GTAAGACCACGTCTGGGACGTGGCATCGATCTGTGATCACAT
Found at i:3686838 original size:21 final size:22
Alignment explanation
Indices: 3686808--3686848 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
3686798 TGTATGGTGT
3686808 GATTTGGTTT-TGGTATTATATA
1 GATTTGGTTTATGGT-TTATATA
3686830 GATTT-GTTTATGGTTTATA
1 GATTTGGTTTATGGTTTATA
3686849 AGTATAGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (22 bp):
GATTTGGTTTATGGTTTATATA
Found at i:3713141 original size:151 final size:151
Alignment explanation
Indices: 3712867--3713169 Score: 606
Period size: 151 Copynumber: 2.0 Consensus size: 151
3712857 GGGACCACAA
3712867 ATACGAGTCAAAAAATATTTTAATATTATTTTGTGTGTTTATTATGTGTGAATTTGATTGTGTGA
1 ATACGAGTCAAAAAATATTTTAATATTATTTTGTGTGTTTATTATGTGTGAATTTGATTGTGTGA
3712932 AATTTTCGTGTTTAAATTTTATCATTTGAATGACCGATTAAAGAAAATGACTAAATCACGTAAAA
66 AATTTTCGTGTTTAAATTTTATCATTTGAATGACCGATTAAAGAAAATGACTAAATCACGTAAAA
3712997 TGAAAATTTAGGGTTAAATTT
131 TGAAAATTTAGGGTTAAATTT
3713018 ATACGAGTCAAAAAATATTTTAATATTATTTTGTGTGTTTATTATGTGTGAATTTGATTGTGTGA
1 ATACGAGTCAAAAAATATTTTAATATTATTTTGTGTGTTTATTATGTGTGAATTTGATTGTGTGA
3713083 AATTTTCGTGTTTAAATTTTATCATTTGAATGACCGATTAAAGAAAATGACTAAATCACGTAAAA
66 AATTTTCGTGTTTAAATTTTATCATTTGAATGACCGATTAAAGAAAATGACTAAATCACGTAAAA
3713148 TGAAAATTTAGGGTTAAATTT
131 TGAAAATTTAGGGTTAAATTT
3713169 A
1 A
3713170 AAAGCACCTA
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 152 1.00
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.42
Consensus pattern (151 bp):
ATACGAGTCAAAAAATATTTTAATATTATTTTGTGTGTTTATTATGTGTGAATTTGATTGTGTGA
AATTTTCGTGTTTAAATTTTATCATTTGAATGACCGATTAAAGAAAATGACTAAATCACGTAAAA
TGAAAATTTAGGGTTAAATTT
Found at i:3726542 original size:18 final size:19
Alignment explanation
Indices: 3726527--3726562 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3726517 AGAATATTTT
3726527 ATTTTTGA-AAAATATTCG
1 ATTTTTGATAAAATATTCG
*
3726545 ATTTTTGATAAAAAATTC
1 ATTTTTGATAAAATATTC
3726563 AATTAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (19 bp):
ATTTTTGATAAAATATTCG
Found at i:3733738 original size:94 final size:95
Alignment explanation
Indices: 3733603--3733784 Score: 278
Period size: 94 Copynumber: 1.9 Consensus size: 95
3733593 TGAGATATAT
* * *
3733603 ACAAATCTCACAAAAGCCCATGCTCTCAAGGAGCACACAAAGTGAGGCTCACAAATA-CTCATGT
1 ACAAAACTCAAAAAAGCCCATGCTCTCAAGGAGCACACAAAGTGAGGCTCACAAA-AGCTCATAT
3733667 T-TCAAAGGAACACACAGAGTGAGACTTATC
65 TCTCAAAGGAACACACAGAGTGAGACTTATC
* *
3733697 ACAAAACTCAAAAAATCCCATGCTCTCAAGGAGCACGCAAAGTGAGGCTCACAAAAGCTCATATT
1 ACAAAACTCAAAAAAGCCCATGCTCTCAAGGAGCACACAAAGTGAGGCTCACAAAAGCTCATATT
**
3733762 CTCAAAGGAACACGTAGAGTGAG
66 CTCAAAGGAACACACAGAGTGAG
3733785 TTTTAACAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
93 1 0.01
94 58 0.73
95 20 0.25
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.17
Consensus pattern (95 bp):
ACAAAACTCAAAAAAGCCCATGCTCTCAAGGAGCACACAAAGTGAGGCTCACAAAAGCTCATATT
CTCAAAGGAACACACAGAGTGAGACTTATC
Found at i:3741543 original size:19 final size:19
Alignment explanation
Indices: 3741496--3741552 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
3741486 TTAGAATTTT
*
3741496 TTTTATAAAAATCGTAAAA
1 TTTTATAAAAATTGTAAAA
*** *
3741515 AAGTAAAAAAATTGTAAAA
1 TTTTATAAAAATTGTAAAA
*
3741534 TTTTATAAAAATTATAAAA
1 TTTTATAAAAATTGTAAAA
3741553 AATTAGCGAC
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (19 bp):
TTTTATAAAAATTGTAAAA
Found at i:3742346 original size:20 final size:20
Alignment explanation
Indices: 3742321--3742377 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
3742311 TACGATAATT
3742321 TTTATAATTTTTTTACGAAA
1 TTTATAATTTTTTTACGAAA
* **
3742341 TTTAT-ATTTCTTTAC-ATT
1 TTTATAATTTTTTTACGAAA
*
3742359 TTGTATAATTTTCTTACGA
1 TT-TATAATTTTTTTACGA
3742378 CTTTATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.10
19 12 0.41
20 13 0.45
21 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTATAATTTTTTTACGAAA
Found at i:3742580 original size:22 final size:22
Alignment explanation
Indices: 3742552--3742624 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
3742542 ATTGCTTTTA
3742552 TTTTTGAAAAGGTTTAAGAGTC
1 TTTTTGAAAAGGTTTAAGAGTC
* * *
3742574 TTTTTGATACA-TTTTAAAAGT-
1 TTTTTGA-AAAGGTTTAAGAGTC
* * *
3742595 TTTTGTTAAAAGGTTTAAGGGCC
1 TTTT-TGAAAAGGTTTAAGAGTC
3742618 TTTTTGA
1 TTTTTGA
3742625 TACATTTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 6 0.16
22 25 0.68
23 6 0.16
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (22 bp):
TTTTTGAAAAGGTTTAAGAGTC
Found at i:3742599 original size:20 final size:20
Alignment explanation
Indices: 3742574--3742643 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
3742564 TTTAAGAGTC
3742574 TTTTTGATACATTTTAAAAG
1 TTTTTGATACATTTTAAAAG
* * * **
3742594 TTTTTGTTAAAAGGTTTAAGGG
1 TTTTTGAT-ACA-TTTTAAAAG
3742616 CCTTTTTGATACATTTTAAAAG
1 --TTTTTGATACATTTTAAAAG
3742638 TTTTTG
1 TTTTTG
3742644 TATTTTTGTA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
20 13 0.36
21 2 0.06
22 12 0.33
23 2 0.06
24 7 0.19
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.50
Consensus pattern (20 bp):
TTTTTGATACATTTTAAAAG
Found at i:3742613 original size:44 final size:44
Alignment explanation
Indices: 3742558--3742644 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
3742548 TTTATTTTTG
*
3742558 AAAAGGTTTAAGAGTCTTTTTGATACATTTTAAAAGTTTTTGTT
1 AAAAGGTTTAAGAGCCTTTTTGATACATTTTAAAAGTTTTTGTT
*
3742602 AAAAGGTTTAAGGGCCTTTTTGATACATTTTAAAAGTTTTTGT
1 AAAAGGTTTAAGAGCCTTTTTGATACATTTTAAAAGTTTTTGT
3742645 ATTTTTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (44 bp):
AAAAGGTTTAAGAGCCTTTTTGATACATTTTAAAAGTTTTTGTT
Found at i:3764221 original size:35 final size:35
Alignment explanation
Indices: 3764147--3764229 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 35
3764137 TTTTGATTCG
* * * *
3764147 CATGTTGAGCATGCTATTATTCTAATTATGATTCG
1 CATGTTAAGCATGCCATTATTCTAATTATGACTCA
* * *
3764182 CATGTTAAGCATGCCATTATTTTGATTCTGACTCA
1 CATGTTAAGCATGCCATTATTCTAATTATGACTCA
*
3764217 CATGTTAAACATG
1 CATGTTAAGCATG
3764230 TCACAGTGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.40
Consensus pattern (35 bp):
CATGTTAAGCATGCCATTATTCTAATTATGACTCA
Found at i:3775257 original size:101 final size:102
Alignment explanation
Indices: 3775138--3775322 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
3775128 AAAGTGATGG
* *
3775138 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-C-CAAAATGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTAGCGCAAAATGAT-GGTCACATGTGTAGT
*
3775201 ACTATGTGAAGTCTACTATGCGTACCAGATAGTTTTGA
65 ACTATGTGAAGGCTACTATGCGTACCAGATAGTTTTGA
* * *
3775239 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTAGCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTAGCGCAAAATGATGGTCACATGTGTAGTA
3775304 CTATGTGAAGGCTACTATG
66 CTATGTGAAGGCTACTATG
3775323 TGAACCGATA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 36 0.47
102 34 0.45
103 6 0.08
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTAGCGCAAAATGATGGTCACATGTGTAGTA
CTATGTGAAGGCTACTATGCGTACCAGATAGTTTTGA
Found at i:3775258 original size:51 final size:51
Alignment explanation
Indices: 3775130--3775322 Score: 192
Period size: 51 Copynumber: 3.8 Consensus size: 51
3775120 TGAAAGTGAA
* * * * *
3775130 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCA-A-
1 AGTGATGATCACATGTGTAGTACTATGTGAAGGCTACTATGCGTACCAGAT
* * * *
3775179 AATGATAGGTCGCATGTGTAGTACTATGTGAAGTCTACTATGCGTACCAGAT
1 AGTGAT-GATCACATGTGTAGTACTATGTGAAGGCTACTATGCGTACCAGAT
** * * *** * *
3775231 AGTTTTGATCACGTGTGTAGTACTATGTGCAGGCTACTACATGTAGCGGAT
1 AGTGATGATCACATGTGTAGTACTATGTGAAGGCTACTATGCGTACCAGAT
*
3775282 AGTGATGGTCACATGTGTAGTACTATGTGAAGGCTACTATG
1 AGTGATGATCACATGTGTAGTACTATGTGAAGGCTACTATG
3775323 TGAACCGATA
Statistics
Matches: 114, Mismatches: 27, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
49 5 0.04
50 36 0.32
51 70 0.61
52 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (51 bp):
AGTGATGATCACATGTGTAGTACTATGTGAAGGCTACTATGCGTACCAGAT
Found at i:3775417 original size:46 final size:44
Alignment explanation
Indices: 3775329--3775418 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 44
3775319 TATGTGAACC
* *
3775329 GATATCATTAATTATAAGGGGGTTGCTATGTGCTGATCCCACCG
1 GATATCATTAATTAAAAGGGGGTTGATATGTGCTGATCCCACCG
* *
3775373 GATATCATTGATTACAAAGGGTGGTTGATGTGTGCTGAAT-CCACCG
1 GATATCATTAATTA-AAAGGG-GGTTGATATGTGCTG-ATCCCACCG
3775419 TGTATCTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 13 0.33
45 5 0.13
46 19 0.49
47 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (44 bp):
GATATCATTAATTAAAAGGGGGTTGATATGTGCTGATCCCACCG
Found at i:3775569 original size:16 final size:16
Alignment explanation
Indices: 3775548--3775579 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3775538 TGATTGAAAG
*
3775548 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
3775564 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
3775580 ACAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:3778509 original size:28 final size:28
Alignment explanation
Indices: 3778472--3778582 Score: 91
Period size: 28 Copynumber: 3.9 Consensus size: 28
3778462 TTAGATGGCG
*
3778472 CCACGAAGGCATTCCTTTTCAGAGATAA
1 CCACAAAGGCATTCCTTTTCAGAGATAA
* * **
3778500 CCATAAAGGC-TTCCTTATCTAGAGATTG
1 CCACAAAGGCATTCCTTTTC-AGAGATAA
* *
3778528 CCACAAAGGCA-TCCTTTTCATTAAGTACTCA
1 CCACAAAGGCATTCCTTTTCA--GAG-A-TAA
*
3778559 CCACAAAGGCTTTCCTTTTCAGAG
1 CCACAAAGGCATTCCTTTTCAGAG
3778583 TTTTTCCACA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
27 9 0.14
28 30 0.47
29 2 0.03
30 3 0.05
31 11 0.17
32 9 0.14
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (28 bp):
CCACAAAGGCATTCCTTTTCAGAGATAA
Found at i:3780778 original size:2 final size:2
Alignment explanation
Indices: 3780771--3780817 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
3780761 GTATGTGATC
* *
3780771 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3780813 GT AT A
1 AT AT A
3780818 ACTAATGTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3780869 original size:21 final size:20
Alignment explanation
Indices: 3780843--3780881 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3780833 TAAGGTAGTT
3780843 TTGAAATGGAAATGTATTGGA
1 TTGAAATGGAAA-GTATTGGA
*
3780864 TTGAAATGTAAAGTATTG
1 TTGAAATGGAAAGTATTG
3780882 CATGGTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGAAATGGAAAGTATTGGA
Found at i:3782006 original size:13 final size:13
Alignment explanation
Indices: 3781990--3782015 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3781980 GGAATGATTT
3781990 TGAGAAAATTTCG
1 TGAGAAAATTTCG
3782003 TGAGAAAATTTCG
1 TGAGAAAATTTCG
3782016 ACGTTTGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
TGAGAAAATTTCG
Found at i:3782457 original size:50 final size:50
Alignment explanation
Indices: 3782358--3782646 Score: 337
Period size: 50 Copynumber: 5.7 Consensus size: 50
3782348 ATGAGATCCA
** *
3782358 ATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGATTATGAGAGGTCTC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGC---ACCGAG---ATGAGAGGTCCC
* * *
3782414 ATGTAAGACCATGTCTCGGCCATGGCGTTGGCACCGAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCC
** *
3782464 ATGTAAGACCACATCTGGGACATGGCATTGGCACCAAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCC
* *
3782514 ATGTAAGACTATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCC
* * ** **
3782564 -TCGTAAGACCATGTCTGGGACATGGCATGGGCACTGTTATGAGAACTCCC
1 AT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCC
* *
3782614 ATGTAAGACCATATCTGGGATATGGCATTGGCA
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA
3782647 AAACAGAAAA
Statistics
Matches: 203, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.00
50 168 0.83
51 1 0.00
53 4 0.02
56 29 0.14
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.24
Consensus pattern (50 bp):
ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCC
Found at i:3782588 original size:150 final size:149
Alignment explanation
Indices: 3782402--3782695 Score: 376
Period size: 150 Copynumber: 2.0 Consensus size: 149
3782392 TATTGAGATT
* * * **
3782402 ATGAGAGGTCTCATGTAAGACCATGTCTCGGCCATGGCGTTGGCACCGAGATGAGAGGTCCCATG
1 ATGAGAGGTCTCATGTAAGACCATGTCTCGGACATGGCATGGGCACCGAGATGAGAACTCCCATG
** * **
3782467 TAAGACCACATCTGGGACATGGCATTGGCACCA-AGATGAGAGGTCCCATGTAAGACTATGTCTG
66 TAAGACCACATCTGGGACATGGCATTGGCAAAACAGA--AAACATCCCATGTAAGACTATGTCTG
*
3782531 GGACATGGCGTTGGCACCGAG
129 GGACATAGCGTTGGCACCGAG
* * * **
3782552 ATGAGAGGTC-CCTCGTAAGACCATGTCTGGGACATGGCATGGGCACTGTTATGAGAACTCCCAT
1 ATGAGAGGTCTCAT-GTAAGACCATGTCTCGGACATGGCATGGGCACCGAGATGAGAACTCCCAT
* *
3782616 GTAAGACCATATCTGGGATATGGCATTGGCAAAACAGAAAACATCCCATGTAAGACTATGTCTGG
65 GTAAGACCACATCTGGGACATGGCATTGGCAAAACAGAAAACATCCCATGTAAGACTATGTCTGG
*
3782681 GACATAGCTTTGGCA
130 GACATAGCGTTGGCA
3782696 TGTATTATCA
Statistics
Matches: 123, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
149 39 0.32
150 81 0.66
151 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22
Consensus pattern (149 bp):
ATGAGAGGTCTCATGTAAGACCATGTCTCGGACATGGCATGGGCACCGAGATGAGAACTCCCATG
TAAGACCACATCTGGGACATGGCATTGGCAAAACAGAAAACATCCCATGTAAGACTATGTCTGGG
ACATAGCGTTGGCACCGAG
Found at i:3782912 original size:12 final size:12
Alignment explanation
Indices: 3782895--3782933 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3782885 ATGAGTTATT
3782895 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
3782907 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
3782919 TAAGTGAGTAAG
1 TAAGTAAGCAAG
3782931 TAA
1 TAA
3782934 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:3785340 original size:28 final size:28
Alignment explanation
Indices: 3785297--3785350 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
3785287 TTTCAACTTT
*
3785297 AAATATGATTATCAAAATTGGTGGGACA
1 AAATATGATTAGCAAAATTGGTGGGACA
*
3785325 AAATATTATTAGCAAAATTGGTGGGA
1 AAATATGATTAGCAAAATTGGTGGGA
3785351 TACAATTGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.30
Consensus pattern (28 bp):
AAATATGATTAGCAAAATTGGTGGGACA
Found at i:3787191 original size:46 final size:46
Alignment explanation
Indices: 3787124--3787301 Score: 241
Period size: 46 Copynumber: 3.9 Consensus size: 46
3787114 TAGGTGAAAG
* * *
3787124 TAATAGTGTCTGGTTACCCATTTA-GGTTAAACCTACACAAATCGAA
1 TAATAGTGTCTGGTCACCCA-TTAGGGTTGAACCTACACAAATCAAA
* *
3787170 TAATAGTGTTTCGTCACCCATTAGGGTTGAACCTACACAAATCAAA
1 TAATAGTGTCTGGTCACCCATTAGGGTTGAACCTACACAAATCAAA
* * * * *
3787216 TAATAGTATTTTGTCACCCATTAGGGTTGAACATACACGAATCAAA
1 TAATAGTGTCTGGTCACCCATTAGGGTTGAACCTACACAAATCAAA
*
3787262 TAATAGTGTCTGGTCACCCGTTAGGGTTGAACCTACACAA
1 TAATAGTGTCTGGTCACCCATTAGGGTTGAACCTACACAA
3787302 CAAATATCCT
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 3 0.03
46 113 0.97
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (46 bp):
TAATAGTGTCTGGTCACCCATTAGGGTTGAACCTACACAAATCAAA
Found at i:3793747 original size:19 final size:18
Alignment explanation
Indices: 3793696--3793748 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
3793686 AATAATATGT
3793696 GATAAGTGGTCTTTTTAGG
1 GATAAGTGGT-TTTTTAGG
* * *
3793715 TATATGAGGTTTTTTAGG
1 GATAAGTGGTTTTTTAGG
*
3793733 GGTAAGTGGTATTTTT
1 GATAAGTGGT-TTTTT
3793749 TTGTGTGGTG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.47
Consensus pattern (18 bp):
GATAAGTGGTTTTTTAGG
Found at i:3795311 original size:20 final size:22
Alignment explanation
Indices: 3795286--3795328 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3795276 AAAAATAATC
*
3795286 AAAAT-ATTTTTT-ATTTTTTA
1 AAAATAATTTTTTGAATTTTTA
3795306 AAAATAATTTTTTGAATTTTTA
1 AAAATAATTTTTTGAATTTTTA
3795328 A
1 A
3795329 CTTTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AAAATAATTTTTTGAATTTTTA
Found at i:3798844 original size:14 final size:14
Alignment explanation
Indices: 3798825--3798852 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3798815 TACTTGAGAG
3798825 CAATATAATTAAAA
1 CAATATAATTAAAA
3798839 CAATATAATTAAAA
1 CAATATAATTAAAA
3798853 AAATGATGTA
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:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
CAATATAATTAAAA
Found at i:3806989 original size:18 final size:18
Alignment explanation
Indices: 3806966--3807024 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
3806956 TAAAACCTTC
*
3806966 TACAATTACTAAGATTCT
1 TACAATTAATAAGATTCT
* * ** *
3806984 TACAATCATTTTGCTTC-
1 TACAATTAATAAGATTCT
3807001 TACAATTAATAAGATTCT
1 TACAATTAATAAGATTCT
3807019 TACAAT
1 TACAAT
3807025 CATTTTGCCT
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (18 bp):
TACAATTAATAAGATTCT
Found at i:3807008 original size:35 final size:35
Alignment explanation
Indices: 3806962--3807032 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
3806952 TAAATAAAAC
*
3806962 CTTCTACAATTACTAAGATTCTTACAATCATTTTG
1 CTTCTACAATTAATAAGATTCTTACAATCATTTTG
3806997 CTTCTACAATTAATAAGATTCTTACAATCATTTTG
1 CTTCTACAATTAATAAGATTCTTACAATCATTTTG
3807032 C
1 C
3807033 CTTACTACTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (35 bp):
CTTCTACAATTAATAAGATTCTTACAATCATTTTG
Found at i:3822445 original size:14 final size:14
Alignment explanation
Indices: 3822426--3822456 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3822416 ATGACTGCAA
*
3822426 TAACACTTTTGTGT
1 TAACACTTTTCTGT
3822440 TAACACTTTTCTGT
1 TAACACTTTTCTGT
3822454 TAA
1 TAA
3822457 AAAATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (14 bp):
TAACACTTTTCTGT
Found at i:3835101 original size:21 final size:20
Alignment explanation
Indices: 3835075--3835116 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
3835065 GCCGCTGCTG
3835075 CCTTG-CTACTCGCACCAACAC
1 CCTTGCCTA-TCGCACC-ACAC
3835096 CCTTGCCTATCGCACCACAC
1 CCTTGCCTATCGCACCACAC
3835116 C
1 C
3835117 ATCAAGACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 12 0.60
22 3 0.15
ACGTcount: A:0.21, C:0.50, G:0.10, T:0.19
Consensus pattern (20 bp):
CCTTGCCTATCGCACCACAC
Found at i:3846721 original size:43 final size:43
Alignment explanation
Indices: 3846660--3846831 Score: 344
Period size: 43 Copynumber: 4.0 Consensus size: 43
3846650 TTTAAGGAAA
3846660 ACAATTATGAAGATTTTCCTTAGTGTAAAATTCAATTCTCTTC
1 ACAATTATGAAGATTTTCCTTAGTGTAAAATTCAATTCTCTTC
3846703 ACAATTATGAAGATTTTCCTTAGTGTAAAATTCAATTCTCTTC
1 ACAATTATGAAGATTTTCCTTAGTGTAAAATTCAATTCTCTTC
3846746 ACAATTATGAAGATTTTCCTTAGTGTAAAATTCAATTCTCTTC
1 ACAATTATGAAGATTTTCCTTAGTGTAAAATTCAATTCTCTTC
3846789 ACAATTATGAAGATTTTCCTTAGTGTAAAATTCAATTCTCTTC
1 ACAATTATGAAGATTTTCCTTAGTGTAAAATTCAATTCTCTTC
3846832 TTTCATTTGA
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 129 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (43 bp):
ACAATTATGAAGATTTTCCTTAGTGTAAAATTCAATTCTCTTC
Found at i:3849396 original size:28 final size:28
Alignment explanation
Indices: 3849365--3849423 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3849355 TCTCGCCATG
3849365 AAGGCATCCTTTGACAAAG-ATTGCCACA
1 AAGGCATCCTTTGA-AAAGAATTGCCACA
* * *
3849393 AAGGCTTTCTTTTAAAAGATATTGCCACA
1 AAGGCATCCTTTGAAAAGA-ATTGCCACA
3849422 AA
1 AA
3849424 TGCTTCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 11 0.42
29 11 0.42
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (28 bp):
AAGGCATCCTTTGAAAAGAATTGCCACA
Found at i:3849421 original size:29 final size:29
Alignment explanation
Indices: 3849382--3849522 Score: 140
Period size: 29 Copynumber: 4.9 Consensus size: 29
3849372 CCTTTGACAA
* *
3849382 AGATTGCCACAAAGGCTTTCTTTTAAAAG
1 AGATCGCCACAAAGGCTTTCTTTTAATAG
* * * *
3849411 ATATTGCCACAAATGC-TTCATTTTAACAG
1 AGATCGCCACAAAGGCTTTC-TTTTAATAG
* * *
3849440 AGATCGTCACAAAAGCTTCCTTTTAATAG
1 AGATCGCCACAAAGGCTTTCTTTTAATAG
* *
3849469 AGATCGTCACAAAGGCTTCCTTTTAATAG
1 AGATCGCCACAAAGGCTTTCTTTTAATAG
* * *
3849498 AGATCACCACAAAGGCATTGTTTTA
1 AGATCGCCACAAAGGCTTTCTTTTA
3849523 TGAAAATTGA
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
28 3 0.03
29 90 0.95
30 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (29 bp):
AGATCGCCACAAAGGCTTTCTTTTAATAG
Found at i:3849600 original size:25 final size:27
Alignment explanation
Indices: 3849562--3849629 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 27
3849552 GTTGTGCCAT
3849562 AAAGGCATCTCCTTAT-AGA-TTACCAC
1 AAAGGCAT-TCCTTATAAGATTTACCAC
*
3849588 AAAGGTATTCCTTATCAGAGATTTACCAC
1 AAAGGCATTCCTTAT-A-AGATTTACCAC
*
3849617 AAAGACATTCCTT
1 AAAGGCATTCCTT
3849630 TAACAGAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 7 0.20
26 7 0.20
28 3 0.09
29 18 0.51
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (27 bp):
AAAGGCATTCCTTATAAGATTTACCAC
Found at i:3851228 original size:52 final size:51
Alignment explanation
Indices: 3851147--3851245 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 51
3851137 CCACAGCTCA
* *
3851147 TATGAGCTTACTGATTTCAGCTCGTGAGAGGC-TACTGATTCTTAGCTTTCT
1 TATGAGCTTACTGATTTCAGCTCGTGAGA-GCATACCGATTCATAGCTTTCT
*
3851198 TATGAGCTTTCTGATTTTCAGCTCGTGAGAGCATACCGATTCATAGCT
1 TATGAGCTTACTGA-TTTCAGCTCGTGAGAGCATACCGATTCATAGCT
3851246 CGTATGAGCA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
51 15 0.35
52 28 0.65
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (51 bp):
TATGAGCTTACTGATTTCAGCTCGTGAGAGCATACCGATTCATAGCTTTCT
Found at i:3859436 original size:15 final size:14
Alignment explanation
Indices: 3859411--3859459 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 14
3859401 TAACTTTCAA
3859411 AAAATAATTTCTAG
1 AAAATAATTTCTAG
*
3859425 AAAATAATTT-TCG
1 AAAATAATTTCTAG
3859438 AAAAATAATTTCTAG
1 -AAAATAATTTCTAG
3859453 AAAATAA
1 AAAATAA
3859460 CTTAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 2 0.06
14 27 0.87
15 2 0.06
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (14 bp):
AAAATAATTTCTAG
Found at i:3859436 original size:28 final size:28
Alignment explanation
Indices: 3859400--3859462 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
3859390 TTCACTGAAT
3859400 ATAACTTTCAAAAAATAATTTCTAGAAA
1 ATAACTTTCAAAAAATAATTTCTAGAAA
* *
3859428 ATAATTTTCGAAAAATAATTTCTAGAAA
1 ATAACTTTCAAAAAATAATTTCTAGAAA
3859456 ATAACTT
1 ATAACTT
3859463 AATTTTTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.35
Consensus pattern (28 bp):
ATAACTTTCAAAAAATAATTTCTAGAAA
Found at i:3871037 original size:27 final size:27
Alignment explanation
Indices: 3871002--3871401 Score: 402
Period size: 27 Copynumber: 14.9 Consensus size: 27
3870992 CGAAAAGGTT
*
3871002 GTAAAATGACCGTAATGACCCTGTAAG
1 GTAAAATGACCGTAATGACCCTGTAGG
* * *
3871029 GTAAAATGACTGTAATGCCCCTGTAAG
1 GTAAAATGACCGTAATGACCCTGTAGG
* *
3871056 GTAAAATGACCGTAATGCCCCTGTAAG
1 GTAAAATGACCGTAATGACCCTGTAGG
3871083 GTAAAATGACCGTAAT-ACCCCTGTAGG
1 GTAAAATGACCGTAATGA-CCCTGTAGG
* * *
3871110 GTAAAATTACCATAATGCCCCTGTAGG
1 GTAAAATGACCGTAATGACCCTGTAGG
* *
3871137 GTAAAATGACCGTAAT-AGCCATGTAAG
1 GTAAAATGACCGTAATGA-CCCTGTAGG
* * *
3871164 GTAAAATAATCATAAT-ACCCTTGTAGG
1 GTAAAATGACCGTAATGACCC-TGTAGG
* *
3871191 GTAAAATGACCGTAATGCCCCTATAGG
1 GTAAAATGACCGTAATGACCCTGTAGG
* * *
3871218 GTAAAATGACCATAGTGCCCCTGTAGG
1 GTAAAATGACCGTAATGACCCTGTAGG
* * *
3871245 GTAAAATAACTGTAAT-ACCCCTATAGG
1 GTAAAATGACCGTAATGA-CCCTGTAGG
* *
3871272 GTAAAATGACCGTAATGCCCCTGTACG
1 GTAAAATGACCGTAATGACCCTGTAGG
* *
3871299 GTAAAATGACCGTAA-CACTCTTGTAGG
1 GTAAAATGACCGTAATGAC-CCTGTAGG
*
3871326 GTAAAATGACCATAAT-ACCCCTGTAGG
1 GTAAAATGACCGTAATGA-CCCTGTAGG
* * *
3871353 GTAAAATGACCATAGT-ACTCTTGTAGG
1 GTAAAATGACCGTAATGAC-CCTGTAGG
*
3871380 GTAAAATGACTGTAATG-CCCTG
1 GTAAAATGACCGTAATGACCCTG
3871402 GTGGATAAAT
Statistics
Matches: 312, Mismatches: 49, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
26 7 0.02
27 301 0.96
28 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (27 bp):
GTAAAATGACCGTAATGACCCTGTAGG
Found at i:3871067 original size:54 final size:54
Alignment explanation
Indices: 3871002--3871399 Score: 490
Period size: 54 Copynumber: 7.4 Consensus size: 54
3870992 CGAAAAGGTT
* * * * * *
3871002 GTAAAATGACCGTAATGACCCTGTAAGGTAAAATGACTGTAATGCCCCTGTAAG
1 GTAAAATGACCATAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGG
* *
3871056 GTAAAATGACCGTAATGCCCCTGTAAGGTAAAATGACCGTAATACCCCTGTAGG
1 GTAAAATGACCATAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGG
* * * *
3871110 GTAAAATTACCATAATGCCCCTGTAGGGTAAAATGACCGTAATAGCCATGTAAG
1 GTAAAATGACCATAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGG
* * * * * *
3871164 GTAAAATAATCATAATACCCTTGTAGGGTAAAATGACCGTAATGCCCCTATAGG
1 GTAAAATGACCATAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGG
* * * *
3871218 GTAAAATGACCATAGTGCCCCTGTAGGGTAAAATAACTGTAATACCCCTATAGG
1 GTAAAATGACCATAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGG
* * * * *
3871272 GTAAAATGACCGTAATGCCCCTGTACGGTAAAATGACCGTAACACTCTTGTAGG
1 GTAAAATGACCATAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGG
* * * * *
3871326 GTAAAATGACCATAATACCCCTGTAGGGTAAAATGACCATAGTACTCTTGTAGG
1 GTAAAATGACCATAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGG
**
3871380 GTAAAATGACTGTAATGCCC
1 GTAAAATGACCATAATGCCC
3871400 TGGTGGATAA
Statistics
Matches: 299, Mismatches: 45, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 299 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (54 bp):
GTAAAATGACCATAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGG
Found at i:3871140 original size:81 final size:81
Alignment explanation
Indices: 3871002--3871399 Score: 494
Period size: 81 Copynumber: 4.9 Consensus size: 81
3870992 CGAAAAGGTT
* * *
3871002 GTAAAATGACCGTAATGA-CCCTGTAAGGTAAAATGACTGTAATGCCCCTGTAAGGTAAAATGAC
1 GTAAAATGACCGTAAT-ACCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGAC
3871066 CGTAATGCCCCTGTAAG
65 CGTAATGCCCCTGTAAG
* *
3871083 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATTACCATAATGCCCCTGTAGGGTAAAATGACC
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACC
*
3871148 GTAATAG-CCATGTAAG
66 GTAAT-GCCCCTGTAAG
* * * * *
3871164 GTAAAATAATCATAATACCCTTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACC
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACC
* * *
3871229 ATAGTGCCCCTGTAGG
66 GTAATGCCCCTGTAAG
* * * *
3871245 GTAAAATAACTGTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGTACGGTAAAATGACC
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACC
** * * *
3871310 GTAACACTCTTGTAGG
66 GTAATGCCCCTGTAAG
* * * * * * *
3871326 GTAAAATGACCATAATACCCCTGTAGGGTAAAATGACCATAGTACTCTTGTAGGGTAAAATGACT
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACC
3871391 GTAATGCCC
66 GTAATGCCC
3871400 TGGTGGATAA
Statistics
Matches: 270, Mismatches: 44, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
80 2 0.01
81 267 0.99
82 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (81 bp):
GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACC
GTAATGCCCCTGTAAG
Found at i:3871470 original size:24 final size:24
Alignment explanation
Indices: 3871435--3871493 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
3871425 CTCGAGGTCA
*
3871435 AATGACTGATTTGTCTGTG-TTTGG
1 AATGACTAATTTGTCTGTGATTT-G
*
3871459 TATGACTAATTTGTCTGTGATTTG
1 AATGACTAATTTGTCTGTGATTTG
3871483 AATGACTAATT
1 AATGACTAATT
3871494 CTGAGCATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (24 bp):
AATGACTAATTTGTCTGTGATTTG
Found at i:3871674 original size:26 final size:26
Alignment explanation
Indices: 3871619--3871674 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
3871609 ATACTATCAC
* *
3871619 TGGCACCTTTGCTGCGATACTGCTGC
1 TGGCACCTTTGCTGCGATACTACTGA
* *
3871645 TGGCAGCTTTGCTGCGATGCTACTGA
1 TGGCACCTTTGCTGCGATACTACTGA
3871671 TGGC
1 TGGC
3871675 TTTGTGTCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.12, C:0.27, G:0.30, T:0.30
Consensus pattern (26 bp):
TGGCACCTTTGCTGCGATACTACTGA
Done.