Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 18 of 204
Found at i:5311165 original size:81 final size:78
Alignment explanation
Indices: 5311070--5311218 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 78
5311060 CACTTATCTG
* * *
5311070 ATCAAGTGACAAAGTAATAAGTGGTAGCTTTAGCTACACTTATTTGATCAAGTGAGA-AAGTGAT
1 ATCAAGTGACAAAGTAATAAATGGTAG-TCTAGCTACACTTATCTGATC-A--GAGACAAGTGAT
5311134 AAGTGGTAGCTTTACTT
62 AAGTGGTAGCTTTACTT
* *
5311151 ATCAAGTGAGAAAGTGATAAATGGTAGTCTAGCTACACTTATCTGATCAGAGACAAGTGATAAGT
1 ATCAAGTGACAAAGTAATAAATGGTAGTCTAGCTACACTTATCTGATCAGAGACAAGTGATAAGT
5311216 GGT
66 GGT
5311219 TGCCTAGCTA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
77 4 0.06
78 14 0.23
79 1 0.02
80 19 0.31
81 24 0.39
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (78 bp):
ATCAAGTGACAAAGTAATAAATGGTAGTCTAGCTACACTTATCTGATCAGAGACAAGTGATAAGT
GGTAGCTTTACTT
Found at i:5311184 original size:40 final size:35
Alignment explanation
Indices: 5311116--5311193 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 35
5311106 CACTTATTTG
* **
5311116 ATCAAGTGAGAAAGTGATAAGTGGTAGCTTTACTT
1 ATCAAGTGAGAAAGTGATAAGTGCTAGCTACACTT
5311151 ATCAAGTGAGAAAGTGATAAATGGTAGTCTAGCTACACTT
1 ATCAAGTGAGAAAGTGAT-AA--GT-G-CTAGCTACACTT
5311191 ATC
1 ATC
5311194 TGATCAGAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 18 0.51
36 2 0.06
38 2 0.06
39 1 0.03
40 12 0.34
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (35 bp):
ATCAAGTGAGAAAGTGATAAGTGCTAGCTACACTT
Found at i:5311211 original size:170 final size:169
Alignment explanation
Indices: 5310898--5311242 Score: 459
Period size: 170 Copynumber: 2.0 Consensus size: 169
5310888 TGAGTACTTT
*
5310898 TGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGA
1 TGATCAAGTGACAAAGTAATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGA
* * **
5310963 TAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTCACTTATCTGATCA
66 TAAGTGGTAGCTTTAGCTACACTCAACTGAGAAAGTGAGAAAGTGATAAGTCACTTATCTGATCA
* *
5311028 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATC
131 AGAGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATC
* *
5311068 TGATCAAGTGACAAAGTAATAAGTGGTAGCTTTAGCTACACTTATTTGATCAAGTGAGAAAGTGA
1 TGATCAAGTGACAAAGTAATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGA
* * * *
5311133 TAAGTGGTAGCTTTA-CT-TA-TCAAGTGAGAAAGTGATAAA-TGGTAGTCTAGCTACACTTATC
66 TAAGTGGTAGCTTTAGCTACACTCAACTGAGAAAGTGAGAAAGT-G-A-T-AAG-T-CACTTATC
*
5311194 TGATC-AGAGAC-AAGTGATAAGTGGTTGCCTAGCTACACTTATC
125 TGATCAAGAGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATC
5311237 TGATCA
1 TGATCA
5311243 GGGACAAGTG
Statistics
Matches: 155, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
166 1 0.01
167 15 0.10
168 2 0.01
169 23 0.15
170 95 0.61
171 6 0.04
172 13 0.08
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (169 bp):
TGATCAAGTGACAAAGTAATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGA
TAAGTGGTAGCTTTAGCTACACTCAACTGAGAAAGTGAGAAAGTGATAAGTCACTTATCTGATCA
AGAGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATC
Found at i:5312303 original size:14 final size:14
Alignment explanation
Indices: 5312286--5312316 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5312276 ATGTAAAAAG
*
5312286 ATATATGTATGTAT
1 ATATATGTATATAT
5312300 ATATATGTATATAT
1 ATATATGTATATAT
5312314 ATA
1 ATA
5312317 AGTTATAAAA
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:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
ATATATGTATATAT
Found at i:5312395 original size:41 final size:41
Alignment explanation
Indices: 5312293--5312396 Score: 97
Period size: 41 Copynumber: 2.5 Consensus size: 41
5312283 AAGATATATG
*
5312293 TATGTATATATATGTATATATATAAGTTATAAAATATAAAAAA
1 TATGTATATAGA--TATATATATAAGTTATAAAATATAAAAAA
* * * *
5312336 TATTTACA-AG-TATGTATATATATTTATGAAAACTA-AAAAAA
1 TATGTATATAGATATATATATA-AGTTAT-AAAA-TATAAAAAA
5312377 TATGTATATAGATATATATA
1 TATGTATATAGATATATATA
5312397 GATATGTATA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
39 9 0.19
40 5 0.10
41 16 0.33
42 5 0.10
43 13 0.27
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (41 bp):
TATGTATATAGATATATATATAAGTTATAAAATATAAAAAA
Found at i:5312407 original size:92 final size:96
Alignment explanation
Indices: 5312297--5312478 Score: 248
Period size: 92 Copynumber: 1.9 Consensus size: 96
5312287 TATATGTATG
* * * *
5312297 TATATATATGTATATATATAAGTTATAAAATATAAAAAATATTTACAAGTATGTAT-ATATATTT
1 TATATATATGTATATATATAAATTATAAAATATAAAAAAAATATACAAGTATGTATAATATATAT
*
5312361 ATGAA-AACT-A-AAAAAATATGTATATAGA
66 ATGAATAAATCATAAAAAATATGTATATAGA
* *
5312389 TATATATA-GATATGTATATAAATTATAAAATATAAAAAAAATATATAAGTATGTATGAATATAT
1 TATATATATG-TATATATATAAATTATAAAATATAAAAAAAATATACAAGTATGTAT-AATATAT
5312453 ATATGAATAAATCATAAAAAATATGT
64 ATATGAATAAATCATAAAAAATATGT
5312479 GTACGTATAT
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
91 1 0.01
92 49 0.64
94 12 0.16
95 3 0.04
96 1 0.01
97 11 0.14
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (96 bp):
TATATATATGTATATATATAAATTATAAAATATAAAAAAAATATACAAGTATGTATAATATATAT
ATGAATAAATCATAAAAAATATGTATATAGA
Found at i:5312586 original size:24 final size:21
Alignment explanation
Indices: 5312559--5312620 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 21
5312549 GTAAAAAGTT
5312559 ATAATAAAAATAAGGTAAGTAATA
1 ATAATAAAAATAA--T-AGTAATA
5312583 ATAATAAACACAATAATAGTAATA
1 ATAAT-AA-A-AATAATAGTAATA
*
5312607 ATAGTAAAAATAAT
1 ATAATAAAAATAAT
5312621 GATAACACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
21 6 0.18
22 1 0.03
23 2 0.06
24 16 0.47
25 3 0.09
26 1 0.03
27 5 0.15
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (21 bp):
ATAATAAAAATAATAGTAATA
Found at i:5313026 original size:36 final size:36
Alignment explanation
Indices: 5312977--5313068 Score: 148
Period size: 39 Copynumber: 2.5 Consensus size: 36
5312967 AGGTTAAAGC
*
5312977 CAAAACGACGTCGTTTTGGTACCTGGGAGGCCTGCT
1 CAAAACGATGTCGTTTTGGTACCTGGGAGGCCTGCT
5313013 CAAAACGATGTCGTCGTTTTGGTACCTGGGAGGCCTGCT
1 CAAAACGA--T-GTCGTTTTGGTACCTGGGAGGCCTGCT
5313052 CAAAACGATGTCGTTTT
1 CAAAACGATGTCGTTTT
5313069 AGGGGGCCTA
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
36 16 0.31
37 1 0.02
39 35 0.67
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (36 bp):
CAAAACGATGTCGTTTTGGTACCTGGGAGGCCTGCT
Found at i:5313036 original size:39 final size:39
Alignment explanation
Indices: 5312985--5313065 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
5312975 GCCAAAACGA
5312985 CGTCGTTTTGGTACCTGGGAGGCCTGCTCAAAACGATGT
1 CGTCGTTTTGGTACCTGGGAGGCCTGCTCAAAACGATGT
5313024 CGTCGTTTTGGTACCTGGGAGGCCTGCTCAAAACGATGT
1 CGTCGTTTTGGTACCTGGGAGGCCTGCTCAAAACGATGT
5313063 CGT
1 CGT
5313066 TTTAGGGGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.28
Consensus pattern (39 bp):
CGTCGTTTTGGTACCTGGGAGGCCTGCTCAAAACGATGT
Found at i:5317078 original size:45 final size:45
Alignment explanation
Indices: 5317014--5317102 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
5317004 ACTCAACCAG
*
5317014 GTTCGACCCAATATGTCACGATGGCAGCTCCGCCAAACCCTGCTA
1 GTTCGACCCAATATGTCACGATGGCAGCTCCACCAAACCCTGCTA
* * *
5317059 GTTCGATCCAATATGTCACGGTGGCAGCTGCACCAAACCCTGCT
1 GTTCGACCCAATATGTCACGATGGCAGCTCCACCAAACCCTGCT
5317103 TCTGCAGAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (45 bp):
GTTCGACCCAATATGTCACGATGGCAGCTCCACCAAACCCTGCTA
Found at i:5319606 original size:21 final size:21
Alignment explanation
Indices: 5319580--5319620 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5319570 ATCTGCTCAA
* *
5319580 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5319601 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5319621 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5327821 original size:54 final size:54
Alignment explanation
Indices: 5327731--5327840 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 54
5327721 CATTAGAGGA
* *
5327731 TTAGTGGTGGGGTTAATTGTTGGAGCTTCTGGTTTGATTCTTGGCCTAGGTTTG
1 TTAGTGGTGGGGTTAATTGTTGGAGCTTCTGCTTTGATTCTTGGCCTAGGTGTG
* *
5327785 TTAGTGGTGGGGTTAATTGTTGGAGCTTGTGCTTTGATTTTTGGCCTAGGTGTG
1 TTAGTGGTGGGGTTAATTGTTGGAGCTTCTGCTTTGATTCTTGGCCTAGGTGTG
5327839 TT
1 TT
5327841 CTTGTGGTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.11, C:0.08, G:0.35, T:0.45
Consensus pattern (54 bp):
TTAGTGGTGGGGTTAATTGTTGGAGCTTCTGCTTTGATTCTTGGCCTAGGTGTG
Found at i:5333245 original size:26 final size:26
Alignment explanation
Indices: 5333216--5333265 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5333206 AAATAACATA
* *
5333216 GAAAGCAATTTAAA-TAGGTAATATAT
1 GAAA-CAACTTAAAGTAGCTAATATAT
5333242 GAAACAACTTAAAGTAGCTAATAT
1 GAAACAACTTAAAGTAGCTAATAT
5333266 CAAACATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (26 bp):
GAAACAACTTAAAGTAGCTAATATAT
Found at i:5335206 original size:45 final size:45
Alignment explanation
Indices: 5335051--5335578 Score: 208
Period size: 44 Copynumber: 11.7 Consensus size: 45
5335041 GTTTTAATTC
* * * *
5335051 GCTCCACTGTAACTTTAGGGAGATAAGATTAG-TAGCTTCAATAC-
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGTTATCTTCAAT-CT
*
5335095 GCTCCACTGCAACTTCAGGGAGATAATG-TTTGTTA-CTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAA-GATTTGTTATCTTCAATCT
* * * * * *
5335139 ACTTCACTGCAACTTCAAGGAGATAAGTTTTGTTATCTTTAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGTTATCTTCAATCT
* * *
5335184 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGGTTTAAT-T
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGTTA---T--CTTCAATCT
* * * * ** *
5335233 CGAC-CTACTGCAACTTCAGAGG-TATAGGATTTATCGT-TTTAATCCT
1 -G-CTCCACTGCAACTTCAG-GGAGATAAGATTTGTTATCTTCAAT-CT
* * ** *
5335279 -CTCCACTGCAACTTTAGGGAGATAGGATTACTT-GCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGTTATCTTCAATCT
* * *
5335322 GCTCCACTGCAACTTTAGGGAGATAAGA-TTGGTATCCTC--TCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGTTATCTTCAATCT
* * ** * * * * *
5335364 GTTTCACTGCAACGCCAGGGAAATAAGTTTTGTTGTTGTTGCTTTAATTT
1 GCTCCACTGCAACTTCAGGGAGATAAG--AT-TTGTT-AT-CTTCAATCT
* * * * * **
5335414 GTTCCACTGCAACGTT-AGGGAAATAAGGTTTGCTGTCTTTGATCT
1 GCTCCACTGCAAC-TTCAGGGAGATAAGATTTGTTATCTTCAATCT
* * ** * * * ** *
5335459 GTTCCACTACTGCTT-AGGAAGACAGGATCAG-TAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGTTATCTTCAATCT
* * * *
5335502 GCTCCACTGCAACTTTAGGGAGATAAGACTTG-TATCTTTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGTTATCTTCAATCT
*** * *
5335546 GCTTTTCTGCAACTTCAGTGAGATAAGGTTTGT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGT
5335579 GTTTTTAATT
Statistics
Matches: 361, Mismatches: 92, Indels: 61
0.70 0.18 0.12
Matches are distributed among these distances:
42 24 0.07
43 28 0.08
44 180 0.50
45 56 0.16
46 6 0.02
47 6 0.02
48 4 0.01
49 1 0.00
50 53 0.15
51 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (45 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTTGTTATCTTCAATCT
Found at i:5335667 original size:88 final size:88
Alignment explanation
Indices: 5335566--5336161 Score: 543
Period size: 88 Copynumber: 6.8 Consensus size: 88
5335556 AACTTCAGTG
* ** * *
5335566 AGATAAGGTTTGTGTTTTTAATTTGCTTCACTGTCAGTACAGGAAGACAAGATCTGCAATCTTCA
1 AGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAATCTTCA
* * *
5335631 ACTTACTCCACTTCTGCTCAGAA
66 ACCTACTCCACTGCTGCTCAGGA
* * * * * * *
5335654 AGATAAGGCTTGTGTTTTTGATCTGTTTCACTACCAGTGCAGGAAGATAAGACCTGCAATCTTTA
1 AGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAATCTTCA
* * * *
5335719 ACCTATTTCACTGCTACTTAAGG-
66 ACCTACTCCACTGCTGC-TCAGGA
* * *
5335742 AGATAAGGCTTGT-TATTTCGATCTGTTTCACTGCCAATACAGGAAGACAAGATTTGCAATCTTC
1 AGATAAGGCTTGTGT-TTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAATCTTC
* * *
5335806 AACCTATTCCACTGCTTCTCTGGA
65 AACCTACTCCACTGCTGCTCAGGA
* * *
5335830 AGATAAGG-TTGGTGTTTTCGATCTGCTTCACTGCCAGTATAGGAAGACAAAATCTTCAATCTTC
1 AGATAAGGCTT-GTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAATCTTC
5335894 AACCTACTCCACTGCTGCTCAGGA
65 AACCTACTCCACTGCTGCTCAGGA
* * * *
5335918 AGATAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATTTGCAAACTTTA
1 AGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAATCTTCA
* * *
5335983 ACCCACTCCACTACTGCTCAGGG
66 ACCTACTCCACTGCTGCTCAGGA
** * * ** ** * * * * **
5336006 AGATAAGGCAGGTATCTTCGATCTATTTTGCTGCCAATACAGGAAGAAAAAATTTGTTATCTTCA
1 AGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAATCTTCA
* * * *
5336071 ACCTGCTCCGCTG-TAAACTCAGGG
66 ACCTACTCCACTGCT--GCTCAGGA
*** * * * * * * **
5336095 AGGCGAGGCTGGTGTCTTCGATCTACTTCACTGCCAATGCAGGAAAACAAGATCTGTTATCTTCA
1 AGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAATCTTCA
5336160 AC
66 AC
5336162 TTGCTCCGCT
Statistics
Matches: 420, Mismatches: 80, Indels: 15
0.82 0.16 0.03
Matches are distributed among these distances:
87 7 0.02
88 347 0.83
89 66 0.16
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (88 bp):
AGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAATCTTCA
ACCTACTCCACTGCTGCTCAGGA
Found at i:5335875 original size:44 final size:44
Alignment explanation
Indices: 5335827--5335964 Score: 109
Period size: 44 Copynumber: 3.1 Consensus size: 44
5335817 CTGCTTCTCT
*
5335827 GGAAGATAAGGTTGGTGTTTTCGATCTGCTTCACTGCCAGTATA
1 GGAAGATAAGGTTGGTGTTTTCGATCTGCTTCACTGCCAGTACA
* ** **** * * * * * *
5335871 GGAAGACAAAATCTTCAATCTTCAACCTACTCCACTG-CTGCT-CA
1 GGAAGATAAGGT-TGGTGTTTTCGATCTGCTTCACTGCCAG-TACA
*
5335915 GGAAGATAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAGTACA
1 GGAAGATAAGGTTGGTGTTTTCGATCTGCTTCACTGCCAGTACA
5335959 GGAAGA
1 GGAAGA
5335965 CAAGATTTGC
Statistics
Matches: 62, Mismatches: 28, Indels: 8
0.63 0.29 0.08
Matches are distributed among these distances:
43 16 0.26
44 30 0.48
45 16 0.26
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (44 bp):
GGAAGATAAGGTTGGTGTTTTCGATCTGCTTCACTGCCAGTACA
Found at i:5336042 original size:264 final size:264
Alignment explanation
Indices: 5335566--5336074 Score: 678
Period size: 264 Copynumber: 1.9 Consensus size: 264
5335556 AACTTCAGTG
* * * * *
5335566 AGATAAGGTTTGTGTTTTTAATTTGCTTCACTGTCAGTACAGGAAGACAAGATCTGCAATCTTCA
1 AGATAAGGTTGGTGTTTTCAATCTGCTTCACTGCCAGTACAGGAAGACAAAATCTGCAATCTTCA
* * * * * *
5335631 ACTTACTCCACTTCTGCTCAGAAAGATAAGGCTTGTGTTTTTGATCTGTTTCACTACCAGTGCAG
66 ACCTACTCCACTGCTGCTCAGAAAGATAAGGCTGGTGTTTTCGATCTGCTTCACTACCAGTACAG
* * * * * * * * *
5335696 GAAGATAAGACCTGCAATCTTTAACCTATTTCACTGCTACTTAAGGAGATAAGGCTTGTTATTTC
131 GAAGACAAGACCTGCAAACTTTAACCCACTCCACTACTACTCAAGGAGATAAGGCTAGGTATTTC
* * *
5335761 GATCTGTTTCACTGCCAATACAGGAAGACAAGATTTGCAATCTTCAACCTATTCCACTGCTTCTC
196 GATCTATTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCTATTCCACTGCTTCTC
5335826 TGGA
261 TGGA
* * *
5335830 AGATAAGGTTGGTGTTTTCGATCTGCTTCACTGCCAGTATAGGAAGACAAAATCTTCAATCTTCA
1 AGATAAGGTTGGTGTTTTCAATCTGCTTCACTGCCAGTACAGGAAGACAAAATCTGCAATCTTCA
* *
5335895 ACCTACTCCACTGCTGCTCAGGAAGATAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAGTACAG
66 ACCTACTCCACTGCTGCTCAGAAAGATAAGGCTGGTGTTTTCGATCTGCTTCACTACCAGTACAG
** * *
5335960 GAAGACAAGATTTGCAAACTTTAACCCACTCCACTACTGCTCAGGGAGATAAGGC-AGGTATCTT
131 GAAGACAAGACCTGCAAACTTTAACCCACTCCACTACTACTCAAGGAGATAAGGCTAGGTAT-TT
** **
5336024 CGATCTATTTTGCTGCCAATACAGGAAGAAAAAATTTGTTATCTTCAACCT
195 CGATCTATTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCT
5336075 GCTCCGCTGT
Statistics
Matches: 208, Mismatches: 36, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
263 4 0.02
264 204 0.98
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (264 bp):
AGATAAGGTTGGTGTTTTCAATCTGCTTCACTGCCAGTACAGGAAGACAAAATCTGCAATCTTCA
ACCTACTCCACTGCTGCTCAGAAAGATAAGGCTGGTGTTTTCGATCTGCTTCACTACCAGTACAG
GAAGACAAGACCTGCAAACTTTAACCCACTCCACTACTACTCAAGGAGATAAGGCTAGGTATTTC
GATCTATTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCTATTCCACTGCTTCTC
TGGA
Found at i:5336129 original size:89 final size:89
Alignment explanation
Indices: 5335591--5336228 Score: 355
Period size: 88 Copynumber: 7.2 Consensus size: 89
5335581 TTTTAATTTG
* * * * * * *** **
5335591 CTTCACTGTCAGTACAGGAAGACAAGATCTGCAATCTTCAACTTACTCCACT-TCTGCTCAGAAA
1 CTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCTACTCCACTGTAAACTCAGGGA
* * * * *
5335655 GATAAGGCTTGTGTTTTTGATCTG
66 GACAAGGCTGGTGTCTTCGATCTA
* * * * * * ** * * * * *
5335679 TTTCACTACCAGTGCAGGAAGATAAGACCTGCAATCTTTAACCTATTTCACTGCT--ACTTAAGG
1 CTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCTACTCCACTG-TAAACTCAGGG
* * * *
5335742 AGATAAGGCTTGT-TATTTCGATCTG
65 AGACAAGGCTGGTGT-CTTCGATCTA
* * * * * * *
5335767 TTTCACTGCCAATACAGGAAGACAAGATTTGCAATCTTCAACCTATTCCACTGCT--TCTCTGGA
1 CTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCTACTCCACTG-TAAACTCAGGG
* * * *
5335830 AGATAAGGTTGGTGTTTTCGATCTG
65 AGACAAGGCTGGTGTCTTCGATCTA
* * * *
5335855 CTTCACTGCCAGTATAGGAAGACAAAATCTT-CAATCTTCAACCTACTCCACTGCT--GCTCAGG
1 CTTCACTGCCAATACAGGAAGAAAAAAT-TTGCAATCTTCAACCTACTCCACTG-TAAACTCAGG
* * * *
5335917 AAGATAAGGCTGGTGTTTTCGATCTG
64 GAGACAAGGCTGGTGTCTTCGATCTA
* * * * * * **
5335943 CTTCACTGCCAGTACAGGAAGACAAGATTTGCAAACTTTAACCCACTCCAC--TACTGCTCAGGG
1 CTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCTACTCCACTGTA-AACTCAGGG
* * *
5336006 AGATAAGGCAGGTATCTTCGATCTA
65 AGACAAGGCTGGTGTCTTCGATCTA
* ** ** * *
5336031 TTTTGCTGCCAATACAGGAAGAAAAAATTTGTTATCTTCAACCTGCTCCGCTGTAAACTCAGGGA
1 CTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCTACTCCACTGTAAACTCAGGGA
* *
5336096 GGCGAGGCTGGTGTCTTCGATCTA
66 GACAAGGCTGGTGTCTTCGATCTA
* * * ** * * * * *
5336120 CTTCACTGCCAATGCAGGAA-AACAAGATCTGTTATCTTCAACTTGCTCCGCTGCAAACTCAAGG
1 CTTCACTGCCAATACAGGAAGAA-AAAATTTGCAATCTTCAACCTACTCCACTGTAAACTCAGGG
* * *
5336184 AGGCGAGGCTGGTGTCTTTGATCTA
65 AGACAAGGCTGGTGTCTTCGATCTA
*
5336209 CTTCGCTGCCAATACAGGAA
1 CTTCACTGCCAATACAGGAA
5336229 TACAAGATCT
Statistics
Matches: 457, Mismatches: 81, Indels: 23
0.81 0.14 0.04
Matches are distributed among these distances:
85 1 0.00
87 3 0.01
88 326 0.71
89 124 0.27
90 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (89 bp):
CTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCTACTCCACTGTAAACTCAGGGA
GACAAGGCTGGTGTCTTCGATCTA
Found at i:5336234 original size:89 final size:89
Alignment explanation
Indices: 5336011--5336238 Score: 323
Period size: 89 Copynumber: 2.6 Consensus size: 89
5336001 CAGGGAGATA
* * * * * *
5336011 AGGCAGGTATCTTCGATCTATTTTGCTGCCAATACAGGAAGAA-AAAATTTGTTATCTTCAACCT
1 AGGCTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAA-AACAAGATCTGTTATCTTCAACCT
* *
5336075 GCTCCGCTGTAAACTCAGGGAGGCG
65 GCTCCGCTGCAAACTCAAGGAGGCG
* * *
5336100 AGGCTGGTGTCTTCGATCTACTTCACTGCCAATGCAGGAAAACAAGATCTGTTATCTTCAACTTG
1 AGGCTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAAACAAGATCTGTTATCTTCAACCTG
5336165 CTCCGCTGCAAACTCAAGGAGGCG
66 CTCCGCTGCAAACTCAAGGAGGCG
* *
5336189 AGGCTGGTGTCTTTGATCTACTTCGCTGCCAATACAGGAATACAAGATCT
1 AGGCTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAAACAAGATCT
5336239 ACCATAATGA
Statistics
Matches: 123, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
88 2 0.02
89 121 0.98
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (89 bp):
AGGCTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAAACAAGATCTGTTATCTTCAACCTG
CTCCGCTGCAAACTCAAGGAGGCG
Found at i:5337195 original size:5 final size:5
Alignment explanation
Indices: 5337185--5337224 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
5337175 TTCGCCTTGG
5337185 TCTTT TCTTT T-TTT TC-TT T-TTT TCTTTT TCTTT TCTTT TC
1 TCTTT TCTTT TCTTT TCTTT TCTTT TC-TTT TCTTT TCTTT TC
5337225 ATGAAACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 10 0.32
5 16 0.52
6 5 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (5 bp):
TCTTT
Found at i:5337202 original size:14 final size:14
Alignment explanation
Indices: 5337185--5337223 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
5337175 TTCGCCTTGG
5337185 TCTTTTCTTTTTTT
1 TCTTTTCTTTTTTT
5337199 TCTTTT-TTTCTTTT
1 TCTTTTCTTT-TTTT
5337213 TCTTTTCTTTT
1 TCTTTTCTTTT
5337224 CATGAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.13
14 17 0.74
15 3 0.13
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:5339912 original size:22 final size:23
Alignment explanation
Indices: 5339885--5339927 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5339875 AAAAGTGATT
*
5339885 TTTTTAATAAA-AATTTGATTTG
1 TTTTTAAGAAACAATTTGATTTG
*
5339907 TTTTTAAGAAACGATTTGATT
1 TTTTTAAGAAACAATTTGATT
5339928 ATATTAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (23 bp):
TTTTTAAGAAACAATTTGATTTG
Found at i:5345255 original size:9 final size:9
Alignment explanation
Indices: 5345241--5345271 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5345231 GTTAAACGAA
5345241 TCGAGTTAT
1 TCGAGTTAT
*
5345250 TCGAGTTAA
1 TCGAGTTAT
5345259 TCGAGTTAT
1 TCGAGTTAT
5345268 TCGA
1 TCGA
5345272 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:5345342 original size:9 final size:9
Alignment explanation
Indices: 5345325--5345361 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5345315 TGAGTTTTCG
5345325 AATTCGAAT
1 AATTCGAAT
*
5345334 AACTCGAAT
1 AATTCGAAT
5345343 AATTCGAAT
1 AATTCGAAT
5345352 AATTCGAAT
1 AATTCGAAT
5345361 A
1 A
5345362 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5351986 original size:18 final size:18
Alignment explanation
Indices: 5351940--5351986 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
5351930 ATTATTCTAA
*
5351940 TATTTGATTTA-TTATTT
1 TATTTTATTTATTTATTT
*
5351957 TATTTTACTTATTTATTT
1 TATTTTATTTATTTATTT
5351975 TAATTTT-TTTAT
1 T-ATTTTATTTAT
5351987 CTGACTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 11 0.44
19 5 0.20
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
TATTTTATTTATTTATTT
Found at i:5354675 original size:45 final size:45
Alignment explanation
Indices: 5354624--5354755 Score: 160
Period size: 45 Copynumber: 3.0 Consensus size: 45
5354614 TACGTATACC
*
5354624 GGGTACCATTAATTATAAATGTGGTTGCTATGTGCTGATTCCACT
1 GGGTACCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACT
* *
5354669 GGGTACCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
1 GGGTACCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACT
* * * * * * *
5354714 GAGTATCATTGACTATAAGGGTGG-TGCTGTGTGCAGA-TCCAC
1 GGGTACCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCAC
5354756 CGTGTATCTA
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 5 0.06
44 11 0.14
45 62 0.79
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (45 bp):
GGGTACCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACT
Found at i:5357511 original size:19 final size:20
Alignment explanation
Indices: 5357469--5357511 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5357459 TCATACTTTC
* *
5357469 TATTCACATTTTCATATTCA
1 TATTCACATATTCAAATTCA
5357489 -ATTCACATATTCAAATT-A
1 TATTCACATATTCAAATTCA
5357507 TATTC
1 TATTC
5357512 CACAATCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTCACATATTCAAATTCA
Found at i:5357752 original size:42 final size:41
Alignment explanation
Indices: 5357693--5357837 Score: 109
Period size: 42 Copynumber: 3.5 Consensus size: 41
5357683 CAGAAGCAGT
*
5357693 ATACGGCACATAAAGTGCCTAAAACGACACACGTGGTGTCTA
1 ATACGACACATAAAGTGCCTAAAACGACACACGTGGTG-CTA
* * * ** * **
5357735 ATACGACACATATAGTGCCTGGTAAATGTA-TTA-GAAGCAG-T-
1 ATACGACACATAAAGTGCCT--AAAACG-ACACACG-TGGTGCTA
5357776 ATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCCTA
1 ATACGACACATAAAGTGCCTAAAACGACACACGTGGTG-CTA
* *
5357818 ATACGACGCATATAGTGCCT
1 ATACGACACATAAAGTGCCT
5357838 GATCGGCAAA
Statistics
Matches: 75, Mismatches: 19, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
38 1 0.01
39 7 0.09
40 1 0.01
41 20 0.27
42 37 0.49
43 1 0.01
44 7 0.09
45 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (41 bp):
ATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCTA
Found at i:5357823 original size:83 final size:83
Alignment explanation
Indices: 5357684--5357838 Score: 283
Period size: 83 Copynumber: 1.9 Consensus size: 83
5357674 TCAATATATC
* *
5357684 AGAAGCAGTATACGGCACATAAAGTGCCTAAAACGACACACGTGGTGTCTAATACGACACATATA
1 AGAAGCAGTATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCCTAATACGACACATATA
5357749 GTGCCTGGTAAATGTATT
66 GTGCCTGGTAAATGTATT
*
5357767 AGAAGCAGTATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCCTAATACGACGCATATA
1 AGAAGCAGTATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCCTAATACGACACATATA
5357832 GTGCCTG
66 GTGCCTG
5357839 ATCGGCAAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 69 1.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (83 bp):
AGAAGCAGTATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCCTAATACGACACATATA
GTGCCTGGTAAATGTATT
Found at i:5357835 original size:21 final size:21
Alignment explanation
Indices: 5357776--5357837 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
5357766 TAGAAGCAGT
*
5357776 ATACGACACATAAAGTGCCTA
1 ATACGACACATATAGTGCCTA
* ** *
5357797 AAACGACACACGTGGTGCCTA
1 ATACGACACATATAGTGCCTA
*
5357818 ATACGACGCATATAGTGCCT
1 ATACGACACATATAGTGCCT
5357838 GATCGGCAAA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
ATACGACACATATAGTGCCTA
Found at i:5358038 original size:29 final size:29
Alignment explanation
Indices: 5358004--5358060 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
5357994 ACTAATCAAT
*
5358004 ATTCAATTCAATATTAACACATATTTCTC
1 ATTCAATTCAATACTAACACATATTTCTC
5358033 ATTCAATTCAATACTAACACATATTTCT
1 ATTCAATTCAATACTAACACATATTTCT
5358061 GTAATATCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.40
Consensus pattern (29 bp):
ATTCAATTCAATACTAACACATATTTCTC
Found at i:5360188 original size:23 final size:24
Alignment explanation
Indices: 5360145--5360191 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5360135 CTTTTGAGTT
*
5360145 AATAAATTCTCTTGAGTTTTTTTC
1 AATAAATTCCCTTGAGTTTTTTTC
*
5360169 AATAATTTCCCTTGAGTTTTTTT
1 AATAAATTCCCTTGAGTTTTTTT
5360192 TTAGAAGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (24 bp):
AATAAATTCCCTTGAGTTTTTTTC
Found at i:5365482 original size:26 final size:27
Alignment explanation
Indices: 5365449--5365511 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
5365439 ATAAAAAATA
5365449 ACCAAAATATTAT-AACTTTTTTATTT
1 ACCAAAATATTATAAACTTTTTTATTT
*
5365475 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAACTTTTTTATTT
5365502 ACCAAAATAT
1 ACCAAAATAT
5365512 ACAAAAAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 13 0.37
27 22 0.63
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (27 bp):
ACCAAAATATTATAAACTTTTTTATTT
Found at i:5365534 original size:17 final size:17
Alignment explanation
Indices: 5365504--5365537 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5365494 TTTTATTTAC
*
5365504 CAAAATATACAAAAAAA
1 CAAAAAATACAAAAAAA
*
5365521 CAAAAAATAGAAAAAAA
1 CAAAAAATACAAAAAAA
5365538 AACCTTCACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (17 bp):
CAAAAAATACAAAAAAA
Found at i:5365598 original size:27 final size:26
Alignment explanation
Indices: 5365568--5365670 Score: 109
Period size: 27 Copynumber: 3.8 Consensus size: 26
5365558 CACCCTGGTC
*
5365568 GTGCCAAGATGATTGGCGGCACCAAAG
1 GTGCCAA-ATGATTGGCGGCACCAATG
* *
5365595 GTGCCAAAGTTATTGGCGGCACCGATG
1 GTGCCAAA-TGATTGGCGGCACCAATG
*
5365622 GTGTCAAGGA-GATTGGCGGCACCAATG
1 GTGCCAA--ATGATTGGCGGCACCAATG
*
5365649 GTGCCATACTGATTGGCGGCAC
1 GTGCCA-AATGATTGGCGGCAC
5365671 TACTCGTGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
26 1 0.02
27 60 0.95
28 1 0.02
29 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.34, T:0.19
Consensus pattern (26 bp):
GTGCCAAATGATTGGCGGCACCAATG
Found at i:5365901 original size:3 final size:3
Alignment explanation
Indices: 5365893--5365924 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5365883 TTTTAGTTAG
*
5365893 TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5365925 AGATGTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5366815 original size:18 final size:18
Alignment explanation
Indices: 5366773--5366815 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
5366763 TTGATATAGT
* *
5366773 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
* *
5366791 TGCTGGCGAAGGAGAAGG
1 TGGTGGCGAAGAAGAAGG
5366809 TGGTGGC
1 TGGTGGC
5366816 AATCATTGGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.07, G:0.49, T:0.19
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:5372503 original size:4 final size:4
Alignment explanation
Indices: 5372482--5372600 Score: 83
Period size: 4 Copynumber: 30.0 Consensus size: 4
5372472 CTCCTTTCCT
*
5372482 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC
* * *
5372527 -TTC TTTC TTT- TTTT TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC TTTC
5372573 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
5372601 CCTCTCCTTC
Statistics
Matches: 96, Mismatches: 5, Indels: 28
0.74 0.04 0.22
Matches are distributed among these distances:
3 19 0.20
4 58 0.60
5 11 0.11
6 8 0.08
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:5372514 original size:41 final size:40
Alignment explanation
Indices: 5372457--5372590 Score: 177
Period size: 41 Copynumber: 3.4 Consensus size: 40
5372447 CTTCCTTCCC
5372457 TCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTT
1 TCTTTTTTTT-TCTTCTCCTTTCCTTTTCTTTCCTTCTTTT
* *
5372498 TCTTTCTTTTTTCTTCTCCTTTCCTCTTC-TT-CTT-TCTT
1 TCTTT-TTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTT
*
5372536 T-TTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTT
1 TCTTTTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTT
5372575 TCTTTCTTTCTTTCTT
1 TCTTT-TTT-TTTCTT
5372591 TCTTTCTTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
36 21 0.26
37 5 0.06
38 7 0.09
39 7 0.09
40 5 0.06
41 25 0.31
42 10 0.12
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (40 bp):
TCTTTTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTT
Found at i:5372518 original size:36 final size:34
Alignment explanation
Indices: 5372428--5372601 Score: 142
Period size: 35 Copynumber: 4.9 Consensus size: 34
5372418 AAAAATTACC
* * *
5372428 TTTTTTTCTTTTTTTTTTCC--TTCCTTCCCTCT
1 TTTTTTTCTTTTTTCTTTCCTTTTCTTTCCTTCT
* *
5372460 TTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCT
1 TTTTTTTCT-TTTTTCTTTCCTTTTCTTTCCTTCT
*
5372495 TTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTCTTTCT
1 TTTT-TTTCTTTTTTCTT-TCCTTT--TC-T-TTCCTTCT
5372535 TTTTTTT-TTCTCTTCTCCTTTCCTTTTCTTTCCTTCT
1 TTTTTTTCTT-T-TT-T-CTTTCCTTTTCTTTCCTTCT
5372572 TTTTCTTTCTTTCTTTCTTT-C-TTTCTTTCC
1 TTTT-TTTCTTT-TTTCTTTCCTTTTCTTTCC
5372602 CTCTCCTTCT
Statistics
Matches: 118, Mismatches: 9, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
32 9 0.08
33 8 0.07
34 9 0.08
35 21 0.18
36 15 0.13
37 12 0.10
38 12 0.10
39 9 0.08
40 13 0.11
41 7 0.06
42 3 0.03
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (34 bp):
TTTTTTTCTTTTTTCTTTCCTTTTCTTTCCTTCT
Found at i:5372679 original size:27 final size:27
Alignment explanation
Indices: 5372641--5372692 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5372631 TATTATAACA
* * *
5372641 TTGGTGCCGCCAATGACTTTGGCACCT
1 TTGGTGCAGCCAATCACCTTGGCACCT
5372668 TTGGTGCAGCCAATCACCTTGGCAC
1 TTGGTGCAGCCAATCACCTTGGCAC
5372693 GACCAGGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.17, C:0.31, G:0.25, T:0.27
Consensus pattern (27 bp):
TTGGTGCAGCCAATCACCTTGGCACCT
Found at i:5372781 original size:26 final size:27
Alignment explanation
Indices: 5372751--5372813 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 27
5372741 TGTTTTTGGT
5372751 ATATTTTGGTAAATAAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
5372777 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
5372804 ATATTTTGGT
1 ATATTTTGGT
5372814 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 21 0.58
27 15 0.42
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:5372990 original size:24 final size:24
Alignment explanation
Indices: 5372961--5373008 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5372951 AATAAAAAAT
5372961 AATATTATTCTAAAGATCTTATAA
1 AATATTATTCTAAAGATCTTATAA
5372985 AATATTATTCTAAAGATCTTATAA
1 AATATTATTCTAAAGATCTTATAA
5373009 TAGTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (24 bp):
AATATTATTCTAAAGATCTTATAA
Found at i:5380537 original size:25 final size:26
Alignment explanation
Indices: 5380487--5380537 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
5380477 CGAAACTTAT
*
5380487 CAGAATAGTTTGTAGCCAAGCTGCCA
1 CAGAATAGTTTATAGCCAAGCTGCCA
5380513 CAGAATAGTTTATAG-CAAGCTGCCA
1 CAGAATAGTTTATAGCCAAGCTGCCA
5380538 ATATATCGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (26 bp):
CAGAATAGTTTATAGCCAAGCTGCCA
Found at i:5380917 original size:32 final size:31
Alignment explanation
Indices: 5380879--5380950 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
5380869 CCCGTGTGGG
* *
5380879 CCCACATGCCCATATTGGCCCT-GCTCGTGTGA
1 CCCACATGCCCAAATCGG-CCTAGCT-GTGTGA
5380911 CCCACATGCCCAAATCGGCCTAGGCTGTGTGA
1 CCCACATGCCCAAATCGGCCTA-GCTGTGTGA
5380943 CCCACATG
1 CCCACATG
5380951 GCCACATACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 3 0.08
32 30 0.83
33 3 0.08
ACGTcount: A:0.19, C:0.38, G:0.22, T:0.21
Consensus pattern (31 bp):
CCCACATGCCCAAATCGGCCTAGCTGTGTGA
Found at i:5389513 original size:17 final size:17
Alignment explanation
Indices: 5389491--5389524 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5389481 AGAGTTGAAA
5389491 ACAAAACTCAAAAATTG
1 ACAAAACTCAAAAATTG
* *
5389508 ACAAAATTCTAAAATTG
1 ACAAAACTCAAAAATTG
5389525 TTCATTAACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
ACAAAACTCAAAAATTG
Found at i:5394618 original size:25 final size:25
Alignment explanation
Indices: 5394590--5394657 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
5394580 CATGTAATTA
* *
5394590 GGAAGCTCTTCTGAGCCATGTAACG
1 GGAAGCTCTTCTGAGCCATATAAAG
* * **
5394615 GGAAGCTCATGTGAGCTGTATAAAG
1 GGAAGCTCTTCTGAGCCATATAAAG
5394640 GGAAGCTCTTGC-GAGCCA
1 GGAAGCTCTT-CTGAGCCA
5394658 GTTATCGAGA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (25 bp):
GGAAGCTCTTCTGAGCCATATAAAG
Found at i:5394792 original size:25 final size:25
Alignment explanation
Indices: 5394764--5394847 Score: 96
Period size: 25 Copynumber: 3.4 Consensus size: 25
5394754 CATTAATCGA
*
5394764 GAAGCTCATGAGAGCCAATTATCAG
1 GAAGCTCATGAGAGCCAAATATCAG
* * * *
5394789 GAAGCTCGTAAGGGCCAAATAACAG
1 GAAGCTCATGAGAGCCAAATATCAG
* *
5394814 GAAGCTCGTGAGAGCCAAATATCGG
1 GAAGCTCATGAGAGCCAAATATCAG
*
5394839 GACGCTCAT
1 GAAGCTCAT
5394848 AAGATCTGTG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (25 bp):
GAAGCTCATGAGAGCCAAATATCAG
Found at i:5395191 original size:61 final size:61
Alignment explanation
Indices: 5395114--5395233 Score: 231
Period size: 61 Copynumber: 2.0 Consensus size: 61
5395104 AATCCGATAC
*
5395114 TTTTTCTTTTCCTCAATCCAATTCCGTACTAGGTCTATCTAGATCTATACAAATGAATTAT
1 TTTTTCTTTTCATCAATCCAATTCCGTACTAGGTCTATCTAGATCTATACAAATGAATTAT
5395175 TTTTTCTTTTCATCAATCCAATTCCGTACTAGGTCTATCTAGATCTATACAAATGAATT
1 TTTTTCTTTTCATCAATCCAATTCCGTACTAGGTCTATCTAGATCTATACAAATGAATT
5395234 TTAACTTAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.42
Consensus pattern (61 bp):
TTTTTCTTTTCATCAATCCAATTCCGTACTAGGTCTATCTAGATCTATACAAATGAATTAT
Found at i:5400894 original size:25 final size:25
Alignment explanation
Indices: 5400840--5400894 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
5400830 AAACATTAAA
*
5400840 TTTAATTTAATATTAAGATAATGAC
1 TTTAATTTAATATTAAGAAAATGAC
*
5400865 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATGAC
5400889 TATTAA
1 T-TTAA
5400895 GATAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATGAC
Found at i:5400921 original size:17 final size:18
Alignment explanation
Indices: 5400899--5400933 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5400889 TATTAAGATA
5400899 AATATTAAACTA-AATTT
1 AATATTAAACTATAATTT
5400916 AATATTAAACTATAATTT
1 AATATTAAACTATAATTT
5400934 GAGGTCAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATTAAACTATAATTT
Found at i:5410057 original size:27 final size:27
Alignment explanation
Indices: 5410026--5410086 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
5410016 CTAGTTTATG
*
5410026 AATTTATACATTAATAAT-ATATATAAT
1 AATTTATACAATAA-AATAATATATAAT
* * *
5410053 AATTTCTTCAATAAACTAATATATAAT
1 AATTTATACAATAAAATAATATATAAT
5410080 AATTTAT
1 AATTTAT
5410087 TTATTTACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTTATACAATAAAATAATATATAAT
Found at i:5417008 original size:16 final size:16
Alignment explanation
Indices: 5416987--5417020 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5416977 CTATTCATGC
*
5416987 AAAATATAAAAGATAG
1 AAAATACAAAAGATAG
5417003 AAAATACAAAAGATAG
1 AAAATACAAAAGATAG
5417019 AA
1 AA
5417021 TAGTGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.12, T:0.15
Consensus pattern (16 bp):
AAAATACAAAAGATAG
Found at i:5418872 original size:40 final size:39
Alignment explanation
Indices: 5418824--5418919 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 39
5418814 GAAATTGAGA
5418824 TTGA-TACTGAATTGAATTATGGAA-TACTGAATATTGTTT
1 TTGAGTACTGAATTGAATTAT-GAAGTACTGAATATTG-TT
5418863 TTGAGTACTGAATTGAATTATGAAGTTACTGAATATTGTT
1 TTGAGTACTGAATTGAATTATGAAG-TACTGAATATTGTT
* * *
5418903 ATGTGTACTGCATTGAA
1 TTGAGTACTGAATTGAA
5418920 CTGTGAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
39 7 0.14
40 32 0.63
41 12 0.24
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (39 bp):
TTGAGTACTGAATTGAATTATGAAGTACTGAATATTGTT
Found at i:5418904 original size:21 final size:20
Alignment explanation
Indices: 5418834--5418912 Score: 56
Period size: 21 Copynumber: 3.9 Consensus size: 20
5418824 TTGATACTGA
*
5418834 ATTGAATTATGGAATACTGAAT
1 ATTG-ATTAT-GAGTACTGAAT
* *
5418856 ATTGTTTTTGAGTACTG-A-
1 ATTGATTATGAGTACTGAAT
5418874 ATTGAATTATGAAGTTACTGAAT
1 ATTG-ATTATG-AG-TACTGAAT
*
5418897 ATTG-TTATGTGTACTG
1 ATTGATTATGAGTACTG
5418913 CATTGAACTG
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
18 4 0.09
19 10 0.22
20 10 0.22
21 13 0.28
22 5 0.11
23 4 0.09
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (20 bp):
ATTGATTATGAGTACTGAAT
Found at i:5419229 original size:6 final size:6
Alignment explanation
Indices: 5419218--5419262 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
5419208 GTTTGTTGAA
** *
5419218 TACTGT TACTGT TACTGT TACTAC TACCGT TACTGAT TACTGT TA
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT TA
5419263 AGGTGTTGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:5419237 original size:45 final size:45
Alignment explanation
Indices: 5419134--5419238 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
5419124 TAATGCCGAC
* * *
5419134 TACTGTTACTATTACCGATTCGACACTTTGTGTGTTGAATATTGT
1 TACTGTTACTGTTACAGATTCGACACTTTGTGTGTTGAATACTGT
** * *
5419179 TACCATTATTGTTACAGATTC-AGCACTTTGTTTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGA-CACTTTGTGTGTTGAATACTGT
5419224 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
5419239 TACTACCGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
44 1 0.02
45 48 0.98
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGACACTTTGTGTGTTGAATACTGT
Found at i:5432201 original size:22 final size:22
Alignment explanation
Indices: 5432176--5432267 Score: 96
Period size: 22 Copynumber: 4.0 Consensus size: 22
5432166 TGCACTAATG
*
5432176 AACAGATAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
*
5432198 AACAGAGAGCAC-AGAATTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
*
5432220 AACAGAGAGCACTAACGTGCTAAA
1 AACAGAGAGCACTAAAGTGCT--A
* *
5432244 AATCAGAGAGCACTGATGTGCTA
1 AA-CAGAGAGCACTAAAGTGCTA
5432267 A
1 A
5432268 TAATCAGAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.02
22 35 0.59
23 3 0.05
24 3 0.05
25 17 0.29
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:5432253 original size:25 final size:25
Alignment explanation
Indices: 5432222--5432280 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
5432212 AATTGCTAAA
5432222 CAGAGAGCACTAACGTGCTAAAAAT
1 CAGAGAGCACTAACGTGCTAAAAAT
* * *
5432247 CAGAGAGCACTGATGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAAAAAT
5432272 CAGAGAGCA
1 CAGAGAGCA
5432281 TGCTAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.17
Consensus pattern (25 bp):
CAGAGAGCACTAACGTGCTAAAAAT
Found at i:5449378 original size:7 final size:7
Alignment explanation
Indices: 5449366--5449395 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5449356 AATTATTTAA
5449366 ATATTAT
1 ATATTAT
5449373 ATATTAT
1 ATATTAT
5449380 ATATTAT
1 ATATTAT
5449387 ATATTAT
1 ATATTAT
5449394 AT
1 AT
5449396 TATTCTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTAT
Found at i:5449549 original size:28 final size:29
Alignment explanation
Indices: 5449481--5449549 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
5449471 AGCACGATTC
*
5449481 AAGTTCAAGTACCAATTAGGTCAAAAAAAA
1 AAGTT-AAGTACAAATTAGGTCAAAAAAAA
** *
5449511 AAGTTGGGTACAAATTAGGT-TAAAAAAA
1 AAGTTAAGTACAAATTAGGTCAAAAAAAA
*
5449539 AATTTAAGTAC
1 AAGTTAAGTAC
5449550 CAAGTAAGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
28 15 0.47
29 12 0.38
30 5 0.16
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.25
Consensus pattern (29 bp):
AAGTTAAGTACAAATTAGGTCAAAAAAAA
Found at i:5449684 original size:26 final size:26
Alignment explanation
Indices: 5449645--5449699 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
5449635 TAGAATAAAC
5449645 AAAATTGTGCTAATTTTATT-TTTAA
1 AAAATTGTGCTAATTTTATTATTTAA
*
5449670 AAAAGTTGTGTTAATTTTATTGATTTAA
1 AAAA-TTGTGCTAATTTTATT-ATTTAA
5449698 AA
1 AA
5449700 TAGAATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 15 0.58
28 7 0.27
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (26 bp):
AAAATTGTGCTAATTTTATTATTTAA
Found at i:5453044 original size:20 final size:19
Alignment explanation
Indices: 5453019--5453058 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5453009 ACATCTTTCA
*
5453019 TTTTATTTATAGTTCATTTG
1 TTTTATGTATA-TTCATTTG
*
5453039 TTTTATGTATATTGATTTG
1 TTTTATGTATATTCATTTG
5453058 T
1 T
5453059 GCATATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (19 bp):
TTTTATGTATATTCATTTG
Found at i:5458037 original size:11 final size:11
Alignment explanation
Indices: 5457990--5458037 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
5457980 GTTTTCTCCC
*
5457990 TATTTTGTTAC
1 TATTTTGTTAT
* *
5458001 CATTTTATTAT
1 TATTTTGTTAT
* *
5458012 TATGTTGCTAT
1 TATTTTGTTAT
5458023 TATTTTGTTAT
1 TATTTTGTTAT
5458034 TATT
1 TATT
5458038 GTTCGGATAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.21, C:0.06, G:0.08, T:0.65
Consensus pattern (11 bp):
TATTTTGTTAT
Found at i:5459723 original size:18 final size:18
Alignment explanation
Indices: 5459690--5459747 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
5459680 ATTCTTCTGT
*
5459690 TAATGTTATAATATATTATT
1 TAAT-TTAT-ATATATTATA
*
5459710 TTATTTATATATATTATA
1 TAATTTATATATATTATA
*
5459728 TAATTTATA-ATAATATA
1 TAATTTATATATATTATA
5459745 TAA
1 TAA
5459748 ATAAACATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.29
18 17 0.50
19 4 0.12
20 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTTATATATATTATA
Found at i:5463291 original size:22 final size:22
Alignment explanation
Indices: 5463265--5463309 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
5463255 GAAAAAAGAA
*
5463265 AACATTGACGTAAAAGAGTGGG
1 AACATTAACGTAAAAGAGTGGG
5463287 AACATTAACGTAAAAGAGTGGG
1 AACATTAACGTAAAAGAGTGGG
5463309 A
1 A
5463310 GACCCAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.29, T:0.18
Consensus pattern (22 bp):
AACATTAACGTAAAAGAGTGGG
Found at i:5464774 original size:12 final size:12
Alignment explanation
Indices: 5464754--5464785 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5464744 GGCTGCGAGC
5464754 AGAAGCAGGGCG
1 AGAAGCAGGGCG
*
5464766 AGGAGCAGGGCG
1 AGAAGCAGGGCG
5464778 AGAAGCAG
1 AGAAGCAG
5464786 ACCTTCCTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.50, T:0.00
Consensus pattern (12 bp):
AGAAGCAGGGCG
Found at i:5465544 original size:9 final size:9
Alignment explanation
Indices: 5465530--5465560 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5465520 GTTAAACGAA
5465530 TCGAGTTAT
1 TCGAGTTAT
*
5465539 TCGAGTTAA
1 TCGAGTTAT
5465548 TCGAGTTAT
1 TCGAGTTAT
5465557 TCGA
1 TCGA
5465561 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:5465628 original size:9 final size:9
Alignment explanation
Indices: 5465614--5465641 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5465604 TAAGTTTTCG
5465614 AATTCGAAT
1 AATTCGAAT
5465623 AATTCGAAT
1 AATTCGAAT
5465632 AATTCGAAT
1 AATTCGAAT
5465641 A
1 A
5465642 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5467064 original size:43 final size:43
Alignment explanation
Indices: 5466995--5467218 Score: 290
Period size: 43 Copynumber: 5.3 Consensus size: 43
5466985 TTTTAGAAAT
*
5466995 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
5467038 AAACGACGCTATAGATCAGGAGCTTTAGCGGCGCTTTT-ACAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
5467080 AAACGTCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-ACAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
5467122 AAACGCCGCCATAGCTCAAGATCTTTAGCGACGCTTATCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
5467165 AAACGCCGCTATAGGTCATGACTTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
5467208 AAACGCCGCTA
1 AAACGCCGCTA
5467219 AAAACATATA
Statistics
Matches: 158, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
42 74 0.47
43 84 0.53
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:5467166 original size:85 final size:85
Alignment explanation
Indices: 5466995--5467216 Score: 302
Period size: 85 Copynumber: 2.6 Consensus size: 85
5466985 TTTTAGAAAT
* * *
5466995 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGACGCTATAGATCAGGAG
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCCATAGATCAAGAG
* *
5467060 CTTTAGCGGCGCTTTTACAC
66 CTTTAGCGACGCTTTCACAC
* * * * *
5467080 AAACGTCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-ACACAAACGCCGCCATAGCTCAAGAT
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCCATAGATCAAGAG
*
5467144 CTTTAGCGACGCTTATCCCAC
66 CTTTAGCGACGCTT-TCACAC
* * *
5467165 AAACGCCGCTATAGGTCATGACTTTTAGCGGCACTTTTCCCACAAACGCCGC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
5467217 TAAAAACATA
Statistics
Matches: 118, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
84 33 0.28
85 73 0.62
86 12 0.10
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (85 bp):
AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCCATAGATCAAGAG
CTTTAGCGACGCTTTCACAC
Found at i:5467447 original size:9 final size:9
Alignment explanation
Indices: 5467433--5467458 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5467423 AATAAATATC
5467433 ATGCTTATA
1 ATGCTTATA
5467442 ATGCTTATA
1 ATGCTTATA
5467451 ATGCTTAT
1 ATGCTTAT
5467459 TGAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (9 bp):
ATGCTTATA
Found at i:5470106 original size:281 final size:276
Alignment explanation
Indices: 5469474--5470097 Score: 838
Period size: 282 Copynumber: 2.2 Consensus size: 276
5469464 TAAAGATATA
* *
5469474 ATAAAAGGTCTCAGACATCCAAGGAAGGATAAAAGCAGCACAAGCTCTTAAGCCCGGCGAAAAGC
1 ATAAAAGGTCTCAGACATCCAAGGAAGGA-AGAAGCAGCACAAGCTCTCAAG-CC-GC--AAAGC
*
5469539 AAAAGCTCTCAGGCAGCCACTGCGAATGTTTTGAGAAACAAGCCTTACACCTTATCATCATAAAC
61 GAAAGCTCTCAGGCAGCCACTGCGAATGTTTTGAGAAACAAGCCTTACA-CTTATCATCATAAAC
** *
5469604 CCATACACATGAAATATATTATCATTTGACTCAATTTTATGAATATCGTTTATCAATGGAACTGA
125 CCATACACAACAAATATATTATCATTTGACTCAATTTTAAGAATATCGTTTATCAATGGAACTGA
* * *
5469669 AAAAAAAGGGAAACATATACAACCAGATTTCTGAGAAAATAATTGGATTTTCAAGCGCAAATAAT
190 AAAAAAAGGGAAAAATATACAACCAGATTTCTGAGAAAATAACTGGATTTTCAAGCACAAATAAT
5469734 GAAAAACAACTATATACAAGTC
255 GAAAAACAACTATATACAAGTC
5469756 ATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCCGGCGAAAGGC
1 ATAAAAGGTCTCAGACATCCAAGGAAGGAA-GAAGCAGCACAAGCTCTCAAG-CC-GC-AAA-GC
* * **
5469821 GAAAGCTCTTAGGCGGCCACTGCGAATGTTTTGAGAAACAAGCCTTTGGA-TTATCATCATAAAC
61 GAAAGCTCTCAGGCAGCCACTGCGAATGTTTTGAGAAACAAGCC-TTACACTTATCATCATAAAC
* * * *
5469885 CCATACACAACAAATATATTTTCCTTTGACTGAATTTTAAGAATATCGTTTATCAATTGAACTGA
125 CCATACACAACAAATATATTATCATTTGACTCAATTTTAAGAATATCGTTTATCAATGGAACTG-
* * * * *
5469950 AAAAAAAAAAAGGGAAAAAATGTACAACCAGATTTCTGAGGAAGTGACTGGGTTTTCAAGCACAA
189 ---AAAAAAAAGGG-AAAAATATACAACCAGATTTCTGAGAAAATAACTGGATTTTCAAGCACAA
*
5470015 ATAATG-AAAACAACAATCATATAGAAGTC
250 ATAATGAAAAACAAC--T-ATATACAAGTC
5470044 ATAAAAGGTCTCAGACATCCAAGGAAGGAAGGAAGCAGCACAAGCTCTCAAGCC
1 ATAAAAGGTCTCAGACATCCAAGGAAGGAA-GAAGCAGCACAAGCTCTCAAGCC
5470098 AAGCGAAAGG
Statistics
Matches: 306, Mismatches: 25, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
281 75 0.25
282 97 0.32
283 3 0.01
285 19 0.06
286 48 0.16
287 3 0.01
288 61 0.20
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (276 bp):
ATAAAAGGTCTCAGACATCCAAGGAAGGAAGAAGCAGCACAAGCTCTCAAGCCGCAAAGCGAAAG
CTCTCAGGCAGCCACTGCGAATGTTTTGAGAAACAAGCCTTACACTTATCATCATAAACCCATAC
ACAACAAATATATTATCATTTGACTCAATTTTAAGAATATCGTTTATCAATGGAACTGAAAAAAA
AGGGAAAAATATACAACCAGATTTCTGAGAAAATAACTGGATTTTCAAGCACAAATAATGAAAAA
CAACTATATACAAGTC
Found at i:5471598 original size:21 final size:22
Alignment explanation
Indices: 5471574--5471628 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
5471564 GACCCCGAAT
*
5471574 CTCTAAACCTTAAATCACTAA-
1 CTCTAAACCTTAAACCACTAAC
* **
5471595 CTCTTAACCCCAAACCACTAAC
1 CTCTAAACCTTAAACCACTAAC
5471617 CTCTAAACCTTA
1 CTCTAAACCTTA
5471629 TTTAGTATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.25
Consensus pattern (22 bp):
CTCTAAACCTTAAACCACTAAC
Found at i:5471703 original size:7 final size:7
Alignment explanation
Indices: 5471691--5471720 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5471681 CGACCCCAAT
5471691 CCCTAAC
1 CCCTAAC
5471698 CCCTAAC
1 CCCTAAC
5471705 CCCTAAC
1 CCCTAAC
5471712 CCCTAAC
1 CCCTAAC
5471719 CC
1 CC
5471721 ATAAACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.60, G:0.00, T:0.13
Consensus pattern (7 bp):
CCCTAAC
Found at i:5472317 original size:41 final size:41
Alignment explanation
Indices: 5472259--5472414 Score: 240
Period size: 41 Copynumber: 3.8 Consensus size: 41
5472249 AAATGTTTTT
*
5472259 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
5472300 GCGGCGCTTTCTAAAAAATGCCGCTAAATATATGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
5472341 GCGGCGCTTTCTCAAAATCGCCGCTAAAGATCTAAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
5472382 GTGGCGCTTTCTCAAAAACGCCGCTAAAGATCT
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCT
5472415 AAAAGGTACA
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 102 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:5472545 original size:40 final size:39
Alignment explanation
Indices: 5472470--5472583 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 39
5472460 TTTTTCCAAA
* *
5472470 AAACGCCGCTAATGCT-AATTTTTAGCGGCGCTTTACTGG
1 AAACGCCGCTAATGCTCGATTTTTAGCGGCGTTTTAC-GG
* *
5472509 AAACGCCGCTAATGCTCGATCTTTAGCGGCGTTTTACGT
1 AAACGCCGCTAATGCTCGATTTTTAGCGGCGTTTTACGG
**
5472548 AAAGCGCCGCTAATGCTCGATTTTTAATGGCGTTTT
1 AAA-CGCCGCTAATGCTCGATTTTTAGCGGCGTTTT
5472584 TTATCCAAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 20 0.30
40 46 0.70
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (39 bp):
AAACGCCGCTAATGCTCGATTTTTAGCGGCGTTTTACGG
Found at i:5475764 original size:43 final size:44
Alignment explanation
Indices: 5475703--5476687 Score: 308
Period size: 44 Copynumber: 22.4 Consensus size: 44
5475693 GATCTGTAAT
* *
5475703 CTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAG
* * ** * * * *
5475746 CTTCAATGTACTCTACTGTAACCTCAGGGAGGA-AAAATCTGCCAT
1 CTTCAATCTACTCCACTGTTGCCT-AGGGA-GATAGAATCTACTAG
* * ** * *
5475791 CTTCGATCTGCTCCACTACTGCTTAGGGAGATA-AGATCTA-TAAT
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGA-ATCTACT-AG
* *
5475835 CTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAG
* ** * * ** *
5475878 CTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAATCCGCTAT
1 CTTCAATCTACTCCACTGTTGCC-TAGGGAGATAGAATCTACTAG
* ** ** * * *
5475923 CTTCGATCTGTTCCACTACTGCTTAGGGAGATA-AGATCT-GTAAT
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGA-ATCTACT-AG
* * * * *
5475967 CTTTAATCTATTTCACTGTTGCCTAGGGAGATAGAA-ATACTGG
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAG
* ** * * ** * *
5476010 CTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTGTTGCCT-AGGGAGATAGAATCTACTAG
* * * ** * * * *
5476055 CTTCGATCTGCTCCTCTACTGCTTATGGAGATA-AGATCT-GTAAT
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGA-ATCTACT-AG
* * *
5476099 CTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAG
* ** * * * * * *
5476142 CTTCAATGTACTCCACTGTAACCTCAGAGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGTTGCCT-AGGGAGATAGAATCTACTAG
* * ** * * * *
5476187 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTGTA--AT
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGAT-AGAATCTACTAG
* *
5476230 CTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAG
* * ** * * ** * *
5476273 CTTCTATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAC
1 CTTCAATCTACTCCACTGTTGCCT-AGGGAGATAGAATCTACTAG
* * ** * * * * *
5476318 CTTCGATCTGCTCCACTACTGCTTATGTAGATA-AGATCT-GTAAT
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGA-ATCTACT-AG
* * *
5476362 CTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAG
* ** * * ** *
5476405 CTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCTAT
1 CTTCAATCTACTCCACTGTTGCCT-AGGGAGATAGAATCTACTAG
* * ** * * * *
5476450 CTTCGATCTGCTCCACTACTGCTTATGGAGATA-AGATCT-GTAAT
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGA-ATCTACT-AG
* * * * *
5476494 CTTCAATCTATTCCACTGCTGCCCAAGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAG
* * ** * * * * * *
5476537 CTTCAATGTACTCCACTATAACCTCAGGAAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGTTGCCT-AGGGAGATAGAATCTACTAG
* * * * * *
5476582 CTTCGATCTGCTCCACT-TCTGCTTATGGAGATA-AGATCT-GTAAT
1 CTTCAATCTACTCCACTGT-TGCCTAGGGAGATAGA-ATCTACT-AG
* * * * *
5476626 CTTCAATCTATTCCACTGCTGCCCAGGGATATAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAG
*
5476669 CTTCAATGTACTCCACTGT
1 CTTCAATCTACTCCACTGT
5476688 ATCCTCAGGG
Statistics
Matches: 648, Mismatches: 249, Indels: 90
0.66 0.25 0.09
Matches are distributed among these distances:
41 2 0.00
42 4 0.01
43 191 0.29
44 319 0.49
45 132 0.20
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAG
Found at i:5475765 original size:132 final size:132
Alignment explanation
Indices: 5475611--5476767 Score: 1938
Period size: 132 Copynumber: 8.8 Consensus size: 132
5475601 GAGATAGGAT
* ** *
5475611 TGGCTTCAATGTACTCTACTGTAACCTCAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
*
5475676 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5475741 AC
131 AC
* * *
5475743 TGGCTTCAATGTACTCTACTGTAACCTCAGGGAGGAAAAATCTGCCATCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* *
5475808 ACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5475873 AC
131 AC
* * *
5475875 TGGCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAATCCGCTATCTTCGATCTGTTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* * * *
5475940 ACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTTCACTGTTGCCTAGGGAGATAGAAAT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5476005 AC
131 AC
*
5476007 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCTCT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
*
5476072 ACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5476137 AC
131 AC
* *
5476139 TGGCTTCAATGTACTCCACTGTAACCTCAGAGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
*
5476204 ACTGCTTAGGGAGATAAGA-CTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5476268 AC
131 AC
* *
5476270 TGGCTTCTATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCACCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* *
5476335 ACTGCTTATGTAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5476400 AC
131 AC
*
5476402 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* * *
5476467 ACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5476532 AC
131 AC
* * *
5476534 TGGCTTCAATGTACTCCACTATAACCTCAGGAAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* * * *
5476599 TCTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGATATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5476664 AC
131 AC
* *
5476666 TGGCTTCAATGTACTCCACTGTATCCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* *
5476731 ACTGCTTAAGGAGATAAGATCTGTAATCTTCGATCTA
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTA
5476768 CCTCACGCCA
Statistics
Matches: 968, Mismatches: 56, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
131 124 0.13
132 844 0.87
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (132 bp):
TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
AC
Found at i:5476606 original size:527 final size:528
Alignment explanation
Indices: 5475611--5476767 Score: 2001
Period size: 527 Copynumber: 2.2 Consensus size: 528
5475601 GAGATAGGAT
* * *
5475611 TGGCTTCAATGTACTCTACTGTAACCTCAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
5475676 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
* * *
5475741 ACTGGCTTCAATGTACTCTACTGTAACCTCAGGGAGGAAAAATCTGCCATCTTCGATCTGCTCCA
131 ACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGAAAAATCCGCCACCTTCGATCTGCTCCA
*
5475806 CTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAA
196 CTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAA
* *
5475871 TTACTGGCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAATCCGCTATCTTCGATCTGTTC
261 TTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTC
* * * * *
5475936 CACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTTCACTGTTGCCTAGGGAGATAG
326 CACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAG
* *
5476001 AAATACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGC
391 AAATACTGGCTTCAATGTACTCCACTATAACCTCAGGAAGGTAAAATCCGCCATCTTCGATCTGC
* *
5476066 TCCTCTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGAT
456 TCCACTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGAT
5476131 AGAATTAC
521 AGAATTAC
*
5476139 TGGCTTCAATGTACTCCACTGTAACCTCAGAGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
5476204 ACTGCTTAGGGAGATAAGA-CTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
* *
5476268 ACTGGCTTCTATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCACCTTCGATCTGCTCCA
131 ACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGAAAAATCCGCCACCTTCGATCTGCTCCA
* * *
5476333 CTACTGCTTATGTAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAA
196 CTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAA
5476398 TTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTC
261 TTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTC
*
5476463 CACTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAG
326 CACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAG
* *
5476528 AATTACTGGCTTCAATGTACTCCACTATAACCTCAGGAAGGTAAAATCTGCCATCTTCGATCTGC
391 AAATACTGGCTTCAATGTACTCCACTATAACCTCAGGAAGGTAAAATCCGCCATCTTCGATCTGC
* *
5476593 TCCACTTCTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGATAT
456 TCCACTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGAT
5476658 AGAATTAC
521 AGAATTAC
* * *
5476666 TGGCTTCAATGTACTCCACTGTATCCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
* *
5476731 ACTGCTTAAGGAGATAAGATCTGTAATCTTCGATCTA
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTA
5476768 CCTCACGCCA
Statistics
Matches: 593, Mismatches: 35, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
527 497 0.84
528 96 0.16
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (528 bp):
TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
ACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGAAAAATCCGCCACCTTCGATCTGCTCCA
CTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAA
TTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAG
AAATACTGGCTTCAATGTACTCCACTATAACCTCAGGAAGGTAAAATCCGCCATCTTCGATCTGC
TCCACTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGAT
AGAATTAC
Found at i:5476911 original size:89 final size:88
Alignment explanation
Indices: 5476784--5477027 Score: 301
Period size: 89 Copynumber: 2.8 Consensus size: 88
5476774 GCCAATACAT
* ** * * *
5476784 GAAGACAATATCTACTATCTTCGATCCACTTCATGCCAATATATGAAGACAAGATCTACTTTCTT
1 GAAGACAAGATCTGTTATCCTCGATCTACTTCATGCCAATATATGAAGACAAGATCTGCTTTCTT
5476849 CAATCTACTCCACCACCAGTATGG
66 C-ATCTACTCCACCACCAGTATGG
* * *
5476873 GGAGACAAGATCTGTTGTCC-CTGATCTACTTCATGCCAATATATGAAGACAAGATCTGTTTTCT
1 GAAGACAAGATCTGTTATCCTC-GATCTACTTCATGCCAATATATGAAGACAAGATCTGCTTTC-
* *
5476937 TTCATCTACTTCGCCACCAGTATGG
64 TTCATCTACTCCACCACCAGTATGG
* * * * * *
5476962 GAATACAATATCTGTTATCTTCGATCTACTTTATGCCAATACATGAAGACAGGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATCCTCGATCTACTTCATGCCAATATATGAAGACAAGATCTGCTTTCTT
5477027 C
66 C
5477028 CTAGCCTACT
Statistics
Matches: 132, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
88 4 0.03
89 124 0.94
90 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (88 bp):
GAAGACAAGATCTGTTATCCTCGATCTACTTCATGCCAATATATGAAGACAAGATCTGCTTTCTT
CATCTACTCCACCACCAGTATGG
Found at i:5477027 original size:44 final size:44
Alignment explanation
Indices: 5476757--5477027 Score: 199
Period size: 44 Copynumber: 6.1 Consensus size: 44
5476747 AGATCTGTAA
* * * * *
5476757 TCTTCGATCTACCTCACGCCAATACATGAAGACAATATCTACTA
1 TCTTCGATCTACTTCACGCCAATATATGAAGACAAGATCTGCTT
* * *
5476801 TCTTCGATCCACTTCATGCCAATATATGAAGACAAGATCTACTT
1 TCTTCGATCTACTTCACGCCAATATATGAAGACAAGATCTGCTT
* * * * ** *
5476845 TCTTCAATCTACTCCACCACCAGTATGGGGAGACAAGATCTG-TT
1 TCTTCGATCTACTTCA-CGCCAATATATGAAGACAAGATCTGCTT
* * *
5476889 GTC-CCTGATCTACTTCATGCCAATATATGAAGACAAGATCTGTTT
1 -TCTTC-GATCTACTTCACGCCAATATATGAAGACAAGATCTGCTT
* * * ** * *
5476934 TCTTTC-ATCTACTTCGCCACCAGTATGGGAATACAATATCTG-TT
1 TC-TTCGATCTACTTC-ACGCCAATATATGAAGACAAGATCTGCTT
* * * *
5476978 ATCTTCGATCTACTTTATGCCAATACATGAAGACAGGATCTGCTT
1 -TCTTCGATCTACTTCACGCCAATATATGAAGACAAGATCTGCTT
5477023 TCTTC
1 TCTTC
5477028 CTAGCCTACT
Statistics
Matches: 172, Mismatches: 45, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
44 110 0.64
45 61 0.35
46 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (44 bp):
TCTTCGATCTACTTCACGCCAATATATGAAGACAAGATCTGCTT
Found at i:5478230 original size:14 final size:13
Alignment explanation
Indices: 5478206--5478236 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
5478196 CCATTTTACG
5478206 TTTTCATTTTTCA
1 TTTTCATTTTTCA
5478219 TTTTCATCTTTTCA
1 TTTTCAT-TTTTCA
5478233 TTTT
1 TTTT
5478237 TTCATCTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:5478240 original size:16 final size:16
Alignment explanation
Indices: 5478206--5478253 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
5478196 CCATTTTACG
5478206 TTTTCAT-TTTTCA--
1 TTTTCATCTTTTCATT
5478219 TTTTCATCTTTTCATT
1 TTTTCATCTTTTCATT
**
5478235 TTTTCATCTCGTCATT
1 TTTTCATCTTTTCATT
5478251 TTT
1 TTT
5478254 CCGACTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
16 17 0.57
ACGTcount: A:0.12, C:0.19, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTCATCTTTTCATT
Found at i:5480702 original size:3 final size:3
Alignment explanation
Indices: 5480640--5480682 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
5480630 CTTGTTAACT
* *
5480640 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5480683 ATTTTCATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5480979 original size:24 final size:27
Alignment explanation
Indices: 5480952--5481003 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
5480942 TTTCTTTTTT
5480952 TATGTTCA-T-TTATGTATTT-GTTTA
1 TATGTTCATTCTTATGTATTTAGTTTA
*
5480976 TATGTTCATTCTTATGTTTTTAGTTTA
1 TATGTTCATTCTTATGTATTTAGTTTA
5481003 T
1 T
5481004 TTATTTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 8 0.33
25 1 0.04
26 9 0.38
27 6 0.25
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.63
Consensus pattern (27 bp):
TATGTTCATTCTTATGTATTTAGTTTA
Found at i:5481385 original size:110 final size:107
Alignment explanation
Indices: 5481126--5481434 Score: 460
Period size: 109 Copynumber: 2.8 Consensus size: 107
5481116 TCAAAAAAGG
* *
5481126 AAAATATTTCAAAATAAGGTAATGTTTTGCATTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAAA-ATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
*
5481191 GGTTTCGATTTCTCGTTCGACCAAATAACTTAATATCCTTTTC
65 GGTTTCGATTTCTCGTTCAACCAAATAACTTAATATCCTTTTC
* *
5481234 AAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACT
1 AAAAA-TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACT
* *
5481299 GGGTGTCGATTTTTCTCGTTCAACCAAATAGC-TAAGTATCCTTTTC
64 GGGTTTCGA--TTTCTCGTTCAACCAAATAACTTAA-TATCCTTTTC
* *
5481345 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCTCTAAGGTGCTGG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
5481410 GTTTCGATTTCTCG-TCTAACCAAAT
66 GTTTCGATTTCTCGTTC-AACCAAAT
5481435 TGACAAATAT
Statistics
Matches: 183, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
106 2 0.01
107 16 0.09
108 41 0.22
109 48 0.26
110 42 0.23
111 34 0.19
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (107 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
GTTTCGATTTCTCGTTCAACCAAATAACTTAATATCCTTTTC
Found at i:5483468 original size:19 final size:20
Alignment explanation
Indices: 5483444--5483482 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5483434 AACTGTGTTT
* *
5483444 AATGCATATG-ATGTAATGA
1 AATGCAAATGCATGAAATGA
5483463 AATGCAAATGCATGAAATGA
1 AATGCAAATGCATGAAATGA
5483483 GTGTGAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.26
Consensus pattern (20 bp):
AATGCAAATGCATGAAATGA
Found at i:5486670 original size:14 final size:14
Alignment explanation
Indices: 5486648--5486686 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
5486638 CCAAAAAAGT
5486648 AAGTCATTTTCCAGA
1 AAGTCATTTTCC-GA
5486663 AA-TCATTTTCCGA
1 AAGTCATTTTCCGA
5486676 AAGTCATTTTC
1 AAGTCATTTTC
5486687 AGTGAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 17 0.74
15 2 0.09
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (14 bp):
AAGTCATTTTCCGA
Found at i:5487098 original size:14 final size:14
Alignment explanation
Indices: 5487079--5487126 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
5487069 AGGATGTTTC
*
5487079 TTTTGATTTGTATG
1 TTTTGATTTGAATG
5487093 TTTTGATTTGAATG
1 TTTTGATTTGAATG
*
5487107 TTTTTGTTTTGAAGTG
1 -TTTTGATTTGAA-TG
5487123 TTTT
1 TTTT
5487127 TTAATTGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 13 0.43
15 15 0.50
16 2 0.07
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.65
Consensus pattern (14 bp):
TTTTGATTTGAATG
Found at i:5487126 original size:16 final size:15
Alignment explanation
Indices: 5487079--5487127 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
5487069 AGGATGTTTC
*
5487079 TTTTGATTTGTATG-
1 TTTTGATTTGAATGT
5487093 TTTTGATTTGAATGT
1 TTTTGATTTGAATGT
*
5487108 TTTTGTTTTGAAGTGT
1 TTTTGATTTGAA-TGT
5487124 TTTT
1 TTTT
5487128 TAATTGTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 13 0.42
15 11 0.35
16 7 0.23
ACGTcount: A:0.14, C:0.00, G:0.20, T:0.65
Consensus pattern (15 bp):
TTTTGATTTGAATGT
Found at i:5487886 original size:29 final size:31
Alignment explanation
Indices: 5487837--5487896 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
5487827 GGCTACACAC
*
5487837 GAACTTTGATTCTATGTGCAATGTTATACAT
1 GAACTTTAATTCTATGTGCAATGTTATACAT
*
5487868 GAACTTTAATT-T-TGTGCAATTTTATACAT
1 GAACTTTAATTCTATGTGCAATGTTATACAT
5487897 TAAATGTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.59
30 1 0.04
31 10 0.37
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (31 bp):
GAACTTTAATTCTATGTGCAATGTTATACAT
Found at i:5491970 original size:24 final size:24
Alignment explanation
Indices: 5491935--5491999 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
5491925 TCCCTTTCTA
5491935 TTCTCTCTTTCTTTTCTCTTCTCTC
1 TTCTCT-TTTCTTTTCTCTTCTCTC
* * *
5491960 TTCTTTTTTCTTTTTTTTTCTCTC
1 TTCTCTTTTCTTTTCTCTTCTCTC
*
5491984 TTCTCTTCTCTTTTCT
1 TTCTCTTTTCTTTTCT
5492000 TGTTTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 29 0.85
25 5 0.15
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (24 bp):
TTCTCTTTTCTTTTCTCTTCTCTC
Found at i:5491987 original size:31 final size:30
Alignment explanation
Indices: 5491946--5492015 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 30
5491936 TCTCTCTTTC
*
5491946 TTTTCTCTTCTCTCTTCTTTTTTCTT-TTT
1 TTTTCTCTTCTCTCTTCTCTTTTCTTGTTT
5491975 TTTTCTC-TCTTCTCTTCTCTTTTCTTGTTT
1 TTTTCTCTTC-TCTCTTCTCTTTTCTTGTTT
5492005 TTTT-TCTTCTC
1 TTTTCTCTTCTC
5492016 GAAAGCCCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 2 0.05
29 26 0.70
30 9 0.24
ACGTcount: A:0.00, C:0.26, G:0.01, T:0.73
Consensus pattern (30 bp):
TTTTCTCTTCTCTCTTCTCTTTTCTTGTTT
Found at i:5492434 original size:29 final size:28
Alignment explanation
Indices: 5492383--5492500 Score: 119
Period size: 28 Copynumber: 4.1 Consensus size: 28
5492373 TAGATGACGC
** *
5492383 AAAAATTCTAAGGTTGAATTGTAATTTTA
1 AAAAATT-TAAGGTCAAAATGTAATTTTA
*
5492412 GGAAAATTTAAGGTCAAAATGTAATTTTA
1 -AAAAATTTAAGGTCAAAATGTAATTTTA
** *
5492441 AAAAATTGGAGGTCAAAATATAATTTTA
1 AAAAATTTAAGGTCAAAATGTAATTTTA
* *
5492469 AAAAAATTAGGGGTCAAAATGTAAATTTTA
1 AAAAATTTA-AGGTCAAAATGT-AATTTTA
5492499 AA
1 AA
5492501 TTTTATATAT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
28 30 0.41
29 28 0.38
30 15 0.21
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.34
Consensus pattern (28 bp):
AAAAATTTAAGGTCAAAATGTAATTTTA
Found at i:5492454 original size:28 final size:28
Alignment explanation
Indices: 5492402--5492500 Score: 119
Period size: 29 Copynumber: 3.4 Consensus size: 28
5492392 AAGGTTGAAT
* **
5492402 TGTAATTTTAGGAAAATTTAAGGTCAAAA
1 TGTAATTTTA-AAAAATTGGAGGTCAAAA
5492431 TGTAATTTTAAAAAATTGGAGGTCAAAA
1 TGTAATTTTAAAAAATTGGAGGTCAAAA
*
5492459 TATAATTTTAAAAAAATTAGG-GGTCAAAA
1 TGTAATTTT-AAAAAATT-GGAGGTCAAAA
5492488 TGTAAATTTTAAA
1 TGT-AATTTTAAA
5492501 TTTTATATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
28 23 0.37
29 31 0.50
30 8 0.13
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.34
Consensus pattern (28 bp):
TGTAATTTTAAAAAATTGGAGGTCAAAA
Found at i:5492537 original size:14 final size:15
Alignment explanation
Indices: 5492503--5492543 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
5492493 ATTTTAAATT
*
5492503 TTATATATTTTTCTGA
1 TTAT-TATTATTCTGA
5492519 TTATTATTATTCT-A
1 TTATTATTATTCTGA
5492533 TTATTATTATT
1 TTATTATTATT
5492544 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.50
15 8 0.33
16 4 0.17
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (15 bp):
TTATTATTATTCTGA
Found at i:5504321 original size:20 final size:20
Alignment explanation
Indices: 5504275--5504312 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5504265 TTGAATGTTT
*
5504275 CAAAAAATTCAATTTTAAAC
1 CAAAAAATTCAAATTTAAAC
*
5504295 CGAAAAA-TCAAATTTAAA
1 CAAAAAATTCAAATTTAAA
5504313 GGCAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (20 bp):
CAAAAAATTCAAATTTAAAC
Found at i:5506927 original size:114 final size:114
Alignment explanation
Indices: 5506727--5506956 Score: 424
Period size: 114 Copynumber: 2.0 Consensus size: 114
5506717 ATCGGTTTAA
*
5506727 AGAAGCTGCTCTATGGGGTTGAATTGACCTCCCAGGAAAGTCACCCATGCCCTAGGGGAATTGTA
1 AGAAGCAGCTCTATGGGGTTGAATTGACCTCCCAGGAAAGTCACCCATGCCCTAGGGGAATTGTA
5506792 ATAAAAGAAGTGAAAAAGTATAAACAAAACAAATCTTCCCTAAAGAATC
66 ATAAAAGAAGTGAAAAAGTATAAACAAAACAAATCTTCCCTAAAGAATC
5506841 AGAAGCAGCTCTATGGGGTTGAATTGACCTCCCAGGAAAGTCACCCATGCCCTAGGGGAATTGTA
1 AGAAGCAGCTCTATGGGGTTGAATTGACCTCCCAGGAAAGTCACCCATGCCCTAGGGGAATTGTA
* * *
5506906 ATAAATGGAGTGAAAAAGTATAAACAAAACAAATCTTCCTTAAAGAATC
66 ATAAAAGAAGTGAAAAAGTATAAACAAAACAAATCTTCCCTAAAGAATC
5506955 AG
1 AG
5506957 TCACAAGATG
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (114 bp):
AGAAGCAGCTCTATGGGGTTGAATTGACCTCCCAGGAAAGTCACCCATGCCCTAGGGGAATTGTA
ATAAAAGAAGTGAAAAAGTATAAACAAAACAAATCTTCCCTAAAGAATC
Found at i:5518416 original size:516 final size:505
Alignment explanation
Indices: 5517373--5518441 Score: 1520
Period size: 516 Copynumber: 2.1 Consensus size: 505
5517363 AACGGATTCC
* * *
5517373 ATAGCTACAAATCTAGAATCTAATTGTGCCAACGGAAAGATAGAAAGCCATTGAATCGAAAAACC
1 ATAGCTACAAAACTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGCCATTGAATCGAAAAACC
* * *
5517438 CAGATATCTTCATTCACTTACGTTTCATGAGTAGCCAAAGGGCACTTCTTACAACTTTTCGTGAC
66 CAGAAATCTTCATTCACTTACGTTTAACGAGTAGCCAAAGGGCACTTCTTACAACTTTTCGTGAC
* * *
5517503 ATTAACTGGAGAAAATTCCTTAAATAATAACCATACTTGTAGTCAACACCCTAATAAACAAGGGA
131 ACTAACTGGAGAAAATTCCTTAAATAATAACCATACTTGTAATCAACACCCTAATAAACAAGAGA
5517568 ACAAGAAATAACATTTCTACTTACGTATAACTATAACATTCAAAAGCTTTAGAAAATGAGATGGT
196 ACAAGAAATAACATTTCTACTTAC--ATAAC-ATAACATTCAAAAGCTTTAGAAAATGAGATGGT
*
5517633 TGCCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTTCAGAATCATTTGACATTAA
258 TGCCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTCCAGAATCATTTGACATTAA
* *
5517698 ATACAATGGTTGATTGTTAATGCAATGATTCACAATAAACCAACAGAACCTAATTATTATATATC
323 ATACAATGGTTGATTGTTAATGCAATGATTCACAATAAACCAACACAACCTAATTATTATACATC
* * *
5517763 ATAACAAACCAACCAAATTTTCCAAAAGAAGTTATCAACTACACGTGGCAAGTTTGCAAGTTAGA
388 ATAACAAACCAACCAAATTTGCCAAAAGAACTTATCAACTACACGTGACAAGTTTGCAAGTTAGA
* *
5517828 ATCAGGCATGAGCTAACTAAACTGGTACAATGAAACGGATTCCATTTTTGTTA
453 ATCAGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGTTA
* *
5517881 ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGTCATTGAATCGTAAAAC
1 ATAGCTACAAAA-CTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGCCATTGAATCGAAAAAC
* **
5517946 CCAGAAATCTTCATTCACTTAGGTTTAACG-GTAGCCAAAGGGCACTTCTTACGGCTTTTCGTGA
65 CCAGAAATCTTCATTCACTTACGTTTAACGAGTAGCCAAAGGGCACTTCTTACAACTTTTCGTGA
**
5518010 CACTGGCTGGAGAAAATTCCTTAAATAATGATCATGTATGGCACATGTTACTTGTAATCAACACC
130 CACTAACTGGAGAAAATTCCTTAAAT-A--AT-A---A---C-CA---TACTTGTAATCAACACC
* * *
5518075 CTAATAAACAAGAGAACAAGAAATATCATTTCTGCTTA-A-GA-ATAACATTCAAAAGCTTTAGA
181 CTAATAAACAAGAGAACAAGAAATAACATTTCTACTTACATAACATAACATTCAAAAGCTTTAGA
* ** *
5518137 AAATGAGATGGTTGCCCGATGCTAGATTGCATCAGAACTTTCAACGCAGTTCCACTTCCAGAATC
246 AAATGAGATGGTTGCCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTCCAGAATC
* * * *
5518202 TTTTGACATTAAATACAGTGGTTGATTGTTAATGCAATGATTCGCAATAAACCAACACAATCTAA
311 ATTTGACATTAAATACAATGGTTGATTGTTAATGCAATGATTCACAATAAACCAACACAACCTAA
** * *
5518267 TTATTATACATCATAATGAACTAACCAAATTTGCCAAAAGAACTTATCAACTACACGTGACAGGT
376 TTATTATACATCATAACAAACCAACCAAATTTGCCAAAAGAACTTATCAACTACACGTGACAAGT
* * *
5518332 TTGCCAAGTTAGAAT-ATGGCAAGAGCTAACTAAACTGGTTCAAAGAAATGGCTTCCATTTTTGT
441 TTG-CAAGTTAGAATCA-GGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGT
5518396 TA
504 TA
*
5518398 ATAGCTACAAAACTAGAATCTAATTGCAG-CAATGGAAAGATAAA
1 ATAGCTACAAAACTAGAATCTAATTG-TGCCAATGGAAAGATAAA
5518442 CAAAGAAAAG
Statistics
Matches: 500, Mismatches: 43, Indels: 28
0.88 0.08 0.05
Matches are distributed among these distances:
508 66 0.13
509 75 0.15
511 2 0.00
512 1 0.00
515 1 0.00
516 231 0.46
517 68 0.14
518 2 0.00
519 3 0.01
522 51 0.10
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (505 bp):
ATAGCTACAAAACTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGCCATTGAATCGAAAAACC
CAGAAATCTTCATTCACTTACGTTTAACGAGTAGCCAAAGGGCACTTCTTACAACTTTTCGTGAC
ACTAACTGGAGAAAATTCCTTAAATAATAACCATACTTGTAATCAACACCCTAATAAACAAGAGA
ACAAGAAATAACATTTCTACTTACATAACATAACATTCAAAAGCTTTAGAAAATGAGATGGTTGC
CCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTCCAGAATCATTTGACATTAAATA
CAATGGTTGATTGTTAATGCAATGATTCACAATAAACCAACACAACCTAATTATTATACATCATA
ACAAACCAACCAAATTTGCCAAAAGAACTTATCAACTACACGTGACAAGTTTGCAAGTTAGAATC
AGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGTTA
Found at i:5518458 original size:70 final size:70
Alignment explanation
Indices: 5518372--5518580 Score: 314
Period size: 70 Copynumber: 3.0 Consensus size: 70
5518362 TAAACTGGTT
* * *
5518372 CAAAGAAATGGCTTCCATTTTTGTTAATAGCTACAAAA-CTAGAATCTAATTGCAG-CAATGGAA
1 CAAAGAAAAGGATTCCA-TTTTGTTAATAGCTACAAAATCTAGAATCTAATTG-TGCCAATGGAA
5518435 AGATAAA
64 AGATAAA
* *
5518442 CAAAGAAAAGGATTCCATTTTGTTGATAGCTACAAAATCTAGAATCTAATTGTGTCAATGGAAAG
1 CAAAGAAAAGGATTCCATTTTGTTAATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAG
*
5518507 ATGAA
66 ATAAA
* *
5518512 CAAAGAAACGGATTCCATTTTGTTCATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAG
1 CAAAGAAAAGGATTCCATTTTGTTAATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAG
5518577 ATAA
66 ATAA
5518581 GAAGTCATTG
Statistics
Matches: 128, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
69 20 0.16
70 108 0.84
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (70 bp):
CAAAGAAAAGGATTCCATTTTGTTAATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAG
ATAAA
Found at i:5521168 original size:21 final size:21
Alignment explanation
Indices: 5521142--5521185 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5521132 CTAATTTCAT
*
5521142 CGCTACAGTATCCAATCTCAC
1 CGCTACAGTAACCAATCTCAC
*
5521163 CGCTACAGTAACTAATCTCAC
1 CGCTACAGTAACCAATCTCAC
5521184 CG
1 CG
5521186 TCACCGCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.36, G:0.11, T:0.23
Consensus pattern (21 bp):
CGCTACAGTAACCAATCTCAC
Found at i:5522916 original size:32 final size:31
Alignment explanation
Indices: 5522856--5522916 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
5522846 TCATGCTTGT
*
5522856 AATATAATTTTTACAAGTTAAACTTGTATAA
1 AATATAATTTTTACAAGTTAAACATGTATAA
5522887 AATATAACTTTTTA-AAGTTAAAACATGTAT
1 AATATAA-TTTTTACAAGTT-AAACATGTAT
5522917 GAGTGTTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (31 bp):
AATATAATTTTTACAAGTTAAACATGTATAA
Found at i:5524407 original size:15 final size:18
Alignment explanation
Indices: 5524363--5524406 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
5524353 TTTCTTGTTT
5524363 ATTTATTTTTATTTTTAGA
1 ATTT-TTTTTATTTTTAGA
5524382 ATTTTTATTTA-TTTTAG-
1 ATTTTT-TTTATTTTTAGA
5524399 ATTTTTTT
1 ATTTTTTT
5524407 AATAAAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 6 0.25
18 8 0.33
19 8 0.33
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (18 bp):
ATTTTTTTTATTTTTAGA
Found at i:5524407 original size:19 final size:19
Alignment explanation
Indices: 5524370--5524404 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
5524360 TTTATTTATT
5524370 TTTATTTTTAGAATTTTTA
1 TTTATTTTTAGAATTTTTA
5524389 TTTA-TTTTAG-ATTTTT
1 TTTATTTTTAGAATTTTT
5524405 TTAATAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (19 bp):
TTTATTTTTAGAATTTTTA
Found at i:5525570 original size:28 final size:27
Alignment explanation
Indices: 5525530--5525615 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 27
5525520 TTGTTCAACA
5525530 AAGCATG--TGGGTAGATTTATTTGAT
1 AAGCATGATTGGGTAGATTTATTTGAT
* * **
5525555 GAAGCATTATTGGGTAGATTGA-TCCA-
1 -AAGCATGATTGGGTAGATTTATTTGAT
*
5525581 AAGCATGATTGGGTGGATTTATTTGAT
1 AAGCATGATTGGGTAGATTTATTTGAT
5525608 AAAGCATG
1 -AAGCATG
5525616 TGAATAATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
25 18 0.39
26 8 0.17
27 2 0.04
28 18 0.39
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (27 bp):
AAGCATGATTGGGTAGATTTATTTGAT
Found at i:5532180 original size:3 final size:3
Alignment explanation
Indices: 5532172--5532217 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
5532162 TCTTCTGCAA
* * * *
5532172 CAT CAT CAT CAT CAT CAT CAT CTT CAT AAT CAC CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
5532218 TTCTGTACTC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:5535501 original size:13 final size:13
Alignment explanation
Indices: 5535483--5535507 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5535473 TAAAGGAACA
5535483 AGAAAAAAAATAG
1 AGAAAAAAAATAG
5535496 AGAAAAAAAATA
1 AGAAAAAAAATA
5535508 AAAAGAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (13 bp):
AGAAAAAAAATAG
Found at i:5538577 original size:43 final size:43
Alignment explanation
Indices: 5538529--5538681 Score: 200
Period size: 43 Copynumber: 3.6 Consensus size: 43
5538519 GGTTTTGTGC
* *
5538529 AAGACCATGTCTGGGACATTGGCATCGATATAAGATTACGTGT
1 AAGACCATGTCTGGGACATTGGCATCGATATGAGATTACATGT
* *
5538572 AAGACCATGTCCGGGATATTGGCATCGATATGAGATTACATGT
1 AAGACCATGTCTGGGACATTGGCATCGATATGAGATTACATGT
* * * * *
5538615 AAGACCCTGTCTGGAACAGTGGCATCGATATGTGATAACATGT
1 AAGACCATGTCTGGGACATTGGCATCGATATGAGATTACATGT
* *
5538658 AAGACCATATCTGGGATA-TGGCAT
1 AAGACCATGTCTGGGACATTGGCAT
5538682 TGTATGTGAT
Statistics
Matches: 95, Mismatches: 15, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
42 6 0.06
43 89 0.94
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
AAGACCATGTCTGGGACATTGGCATCGATATGAGATTACATGT
Found at i:5542248 original size:43 final size:42
Alignment explanation
Indices: 5542200--5542319 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 42
5542190 TATCGTACCA
** *
5542200 ATGCCAT-GTCCCAGAC-ATGGTCTTACATGGAAATCTCATATCG
1 ATGCCATAG-CCCAG-CTATGGTCTTACA-CAAAATCTCAAATCG
5542243 ATGCCAATAGCCCAGCTATGGTCTTACACAAAATCTCAAATCG
1 ATGCC-ATAGCCCAGCTATGGTCTTACACAAAATCTCAAATCG
* * *
5542286 ATGCCAATAGCGCAGCTTTGGTCTTACACGAAAT
1 ATGCC-ATAGCCCAGCTATGGTCTTACACAAAAT
5542320 TACACCTCGA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
43 49 0.72
44 18 0.26
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
ATGCCATAGCCCAGCTATGGTCTTACACAAAATCTCAAATCG
Found at i:5542264 original size:44 final size:43
Alignment explanation
Indices: 5542216--5542319 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 43
5542206 TGTCCCAGAC
** *
5542216 ATGGTCTTACATGGAAATCTCATATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACA-CAAAATCTCAAATCGATGCCAATAGCCCAGCT
*
5542260 ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCGCAGCT
1 ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCCAGCT
* *
5542303 TTGGTCTTACACGAAAT
1 ATGGTCTTACACAAAAT
5542320 TACACCTCGA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
43 43 0.80
44 11 0.20
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:5542574 original size:31 final size:31
Alignment explanation
Indices: 5542438--5542565 Score: 177
Period size: 31 Copynumber: 4.1 Consensus size: 31
5542428 ATATAATGCT
*
5542438 CAAATC-AATTCGGCAATATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATA-A-CCATATA
*
5542470 CGAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
* *
5542501 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
*
5542532 CAAATCAAATTCGGCAATGTATAAAACATATA
1 CAAATCAAATTCGGCAATGTAT-AACCATATA
5542564 CA
1 CA
5542566 TTTAAATTCA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
31 57 0.66
32 14 0.16
33 15 0.17
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATAACCATATA
Found at i:5544134 original size:25 final size:24
Alignment explanation
Indices: 5544106--5544177 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 24
5544096 TTCAAGCAAG
5544106 CAATGTCGGGAAGCTCATAAAGAGC
1 CAAT-TCGGGAAGCTCATAAAGAGC
* **
5544131 CAATTACCAGGAAGCTCACGAAGAGC
1 CAATT--CGGGAAGCTCATAAAGAGC
*
5544157 CATAATCGGGAAGCTCATAAA
1 CA-ATTCGGGAAGCTCATAAA
5544178 AGCTAAGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
24 1 0.03
25 16 0.43
26 18 0.49
27 2 0.05
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (24 bp):
CAATTCGGGAAGCTCATAAAGAGC
Found at i:5544143 original size:26 final size:25
Alignment explanation
Indices: 5544114--5544177 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
5544104 AGCAATGTCG
*
5544114 GGAAGCTCATAAAGAGCCAATTACCA
1 GGAAGCTCATAAAGAGCC-ATAACCA
** * *
5544140 GGAAGCTCACGAAGAGCCATAATCG
1 GGAAGCTCATAAAGAGCCATAACCA
5544165 GGAAGCTCATAAA
1 GGAAGCTCATAAA
5544178 AGCTAAGGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (25 bp):
GGAAGCTCATAAAGAGCCATAACCA
Found at i:5553171 original size:26 final size:27
Alignment explanation
Indices: 5553114--5553189 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 27
5553104 GAAGCTCCGG
* * *
5553114 AGAGCTTTTAATCAGAAAGCTCA-CAA
1 AGAGCCTTTAATCGGGAAGCTCATCAA
*
5553140 AGAGCCTTTAATCGGGAAGCTCATGAA
1 AGAGCCTTTAATCGGGAAGCTCATCAA
* *
5553167 A-AGCC-ATATATCGGGACGCTCAT
1 AGAGCCTTTA-ATCGGGAAGCTCAT
5553190 AAGAGTTGCG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
25 2 0.05
26 37 0.88
27 3 0.07
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (27 bp):
AGAGCCTTTAATCGGGAAGCTCATCAA
Found at i:5555494 original size:11 final size:11
Alignment explanation
Indices: 5555478--5555502 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5555468 GAATTTACGG
5555478 TAGAAATTGAA
1 TAGAAATTGAA
5555489 TAGAAATTGAA
1 TAGAAATTGAA
5555500 TAG
1 TAG
5555503 GAAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (11 bp):
TAGAAATTGAA
Found at i:5556218 original size:23 final size:23
Alignment explanation
Indices: 5556188--5556294 Score: 75
Period size: 23 Copynumber: 4.9 Consensus size: 23
5556178 AGCTTTGCCG
* *
5556188 ATCAGGCACTATATGTGTTGTAT
1 ATCAGGCACTATATGTGTCGCAT
*
5556211 ATCAGGCACTTTATGTGTCGCAT
1 ATCAGGCACTATATGTGTCGCAT
* **
5556234 TTCAGGCACCT-CGTGTGTCG--T
1 ATCAGGCA-CTATATGTGTCGCAT
*
5556255 ATCAGGCACCTA-GTGTGTCG--T
1 ATCAGGCA-CTATATGTGTCGCAT
*
5556276 TTCAGGCACT-TATGTGTCG
1 ATCAGGCACTATATGTGTCG
5556295 TATACTGATC
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
20 9 0.12
21 27 0.38
23 34 0.47
24 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (23 bp):
ATCAGGCACTATATGTGTCGCAT
Found at i:5556259 original size:21 final size:21
Alignment explanation
Indices: 5556235--5556297 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
5556225 GTGTCGCATT
*
5556235 TCAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTAGTGTGTCGTA
*
5556256 TCAGGCACCTAGTGTGTCGTT
1 TCAGGCACCTAGTGTGTCGTA
*
5556277 TCAGGCACTTA-TGTGTCGTA
1 TCAGGCACCTAGTGTGTCGTA
5556297 T
1 T
5556298 ACTGATCAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
20 9 0.24
21 29 0.76
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (21 bp):
TCAGGCACCTAGTGTGTCGTA
Found at i:5556272 original size:44 final size:41
Alignment explanation
Indices: 5556210--5556297 Score: 106
Period size: 44 Copynumber: 2.1 Consensus size: 41
5556200 ATGTGTTGTA
* *
5556210 TATCAGGCACTTTATGTGTCGCATTTCAGGCACCTCGTGTGTCG
1 TATCAGGCACTCTATGTGTCG--TTTCAGGCA-CTCATGTGTCG
*
5556254 TATCAGGCAC-CTAGTGTGTCGTTTCAGGCACTTATGTGTCG
1 TATCAGGCACTCTA-TGTGTCGTTTCAGGCACTCATGTGTCG
5556295 TAT
1 TAT
5556298 ACTGATCAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
41 12 0.30
42 9 0.22
43 2 0.05
44 17 0.43
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (41 bp):
TATCAGGCACTCTATGTGTCGTTTCAGGCACTCATGTGTCG
Found at i:5558815 original size:13 final size:13
Alignment explanation
Indices: 5558797--5558821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5558787 AAATTCAATG
5558797 TCAATTTCATATA
1 TCAATTTCATATA
5558810 TCAATTTCATAT
1 TCAATTTCATAT
5558822 CCAAACATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TCAATTTCATATA
Done.