Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 98 of 187
Found at i:29098981 original size:26 final size:29
Alignment explanation
Indices: 29098952--29099004 Score: 76
Period size: 26 Copynumber: 1.9 Consensus size: 29
29098942 TTGTTTATAC
*
29098952 TTAAATTTTAA-TAAAA-A-TTTAAAATA
1 TTAAATTTAAATTAAAACATTTTAAAATA
29098978 TTAAATTTAAATTAAAACATTTTAAAA
1 TTAAATTTAAATTAAAACATTTTAAAA
29099005 AAATATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 5 0.22
28 1 0.04
29 7 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TTAAATTTAAATTAAAACATTTTAAAATA
Found at i:29099227 original size:39 final size:39
Alignment explanation
Indices: 29099184--29099267 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
29099174 TTTAAACTAA
*
29099184 ATTGA-ATAA-ATATTATTCTACAAAATTTATTTAATAATT
1 ATTGAGATAATAT-TTATTC-AAAAAATTTATTTAATAATT
* **
29099223 ATTGAGCTTTTATTTATTCAAAAAATTTATTTAATAATT
1 ATTGAGATAATATTTATTCAAAAAATTTATTTAATAATT
29099262 ATTGAG
1 ATTGAG
29099268 CTTCTATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 30 0.77
40 7 0.18
41 2 0.05
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (39 bp):
ATTGAGATAATATTTATTCAAAAAATTTATTTAATAATT
Found at i:29099268 original size:39 final size:40
Alignment explanation
Indices: 29099196--29099278 Score: 141
Period size: 39 Copynumber: 2.1 Consensus size: 40
29099186 TGAATAAATA
* *
29099196 TTATTCTACAAAATTTATTTAATAATTATTGAGCTTTTAT
1 TTATTCTAAAAAATTTATTTAATAATTATTGAGCTTCTAT
29099236 TTATTC-AAAAAATTTATTTAATAATTATTGAGCTTCTAT
1 TTATTCTAAAAAATTTATTTAATAATTATTGAGCTTCTAT
29099275 TTAT
1 TTAT
29099279 GTGAAAAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 35 0.85
40 6 0.15
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (40 bp):
TTATTCTAAAAAATTTATTTAATAATTATTGAGCTTCTAT
Found at i:29099964 original size:16 final size:14
Alignment explanation
Indices: 29099926--29099959 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29099916 TTATAAAACA
*
29099926 TTATAAATATATAT
1 TTATAACTATATAT
*
29099940 TTATTACTATATAT
1 TTATAACTATATAT
29099954 TTATAA
1 TTATAA
29099960 AACTAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATAACTATATAT
Found at i:29103022 original size:9 final size:9
Alignment explanation
Indices: 29103008--29103044 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
29102998 TATAGTTTAA
29103008 TATTCGAAT
1 TATTCGAAT
29103017 TATTCGAAT
1 TATTCGAAT
*
29103026 TATTCGAGT
1 TATTCGAAT
29103035 TATTCGAAT
1 TATTCGAAT
29103044 T
1 T
29103045 CAAAAACTCA
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:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:29106912 original size:165 final size:165
Alignment explanation
Indices: 29106653--29107042 Score: 540
Period size: 165 Copynumber: 2.4 Consensus size: 165
29106643 TTTAATACTC
* * * * * * * *
29106653 GTTGATCATTATAATTATTCTTCTTATGTTTTTTTACCAGCTATTCTT-CT-TAAAGTTAAGGGA
1 GTTGATCTTTATAAATATTCTTCTTATGATTTTTTACTAGTTGTTCTTACTCTAGAGTTAAGAGA
* *
29106716 ATAACACCTTAATTATCGGGAGATAAGTATGTATTGATAACTTGTTGAGACCAAATGTTAAGCAA
66 ATAACACCTTAATTATCGGCAAATAAGTATGTATTGATAACTTGTTGAGACCAAATGTTAAGCAA
29106781 TTGTGGTTTATA-TTCAGAGACATATGTTCCTTCAT
131 TTGTGGTTTATATTTC-GAGACATATGTTCCTTCAT
* * *
29106816 GTTGATCTTTATAAATATTATTCTTATGCTTTTTTACTAGTTGTTCTTAATCTAGAGTTGAA-AG
1 GTTGATCTTTATAAATATTCTTCTTATGATTTTTTACTAGTTGTTCTTACTCTAGAGTT-AAGAG
* *
29106880 AATAATACCTTAATTATC-GCACAATAAGTATGTATTGATAACTTGTTGAGACCAAATGTTGAGC
65 AATAACACCTTAATTATCGGCA-AATAAGTATGTATTGATAACTTGTTGAGACCAAATGTTAAGC
29106944 AATTGTGGTTTATATTTCGAGACATATGTTCCTTCAT
129 AATTGTGGTTTATATTTCGAGACATATGTTCCTTCAT
* * *
29106981 GTTTATTTTTATAAATATTCGTCTTAT-ATTCTTTTACTAGTTGTTCTTACTCTAGAGTTAAG
1 GTTGATCTTTATAAATATTCTTCTTATGATT-TTTTACTAGTTGTTCTTACTCTAGAGTTAAG
29107043 GGAAGAAGAA
Statistics
Matches: 200, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
163 41 0.20
164 7 0.04
165 147 0.74
166 5 0.03
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (165 bp):
GTTGATCTTTATAAATATTCTTCTTATGATTTTTTACTAGTTGTTCTTACTCTAGAGTTAAGAGA
ATAACACCTTAATTATCGGCAAATAAGTATGTATTGATAACTTGTTGAGACCAAATGTTAAGCAA
TTGTGGTTTATATTTCGAGACATATGTTCCTTCAT
Found at i:29107703 original size:164 final size:164
Alignment explanation
Indices: 29107196--29108092 Score: 1124
Period size: 164 Copynumber: 5.5 Consensus size: 164
29107186 TAAATGTGAA
* * * *
29107196 TAAGCACATTCGTTCCTTT-ATATTGATCATTATAAATATTCTTGTTATATTTTTTTACCAGTTG
1 TAAG-ACATACGTT-CTTTCATGTTGATCATTATAAATATTCTTCTTAT-GTTTTTTACCAGTTG
* * * * * * * * *
29107260 TTCTTGCCCTAGGGTTGAGGGAATAATACCATACTTACCGTGCGGTACGTATATATTTAAAACTT
63 TTCTTGCCCTAGAGTTGAGGGAATAATACCTTAATTACAGCGCGGTAAGTATCTATTGATAACTT
*
29107325 GTTGAGACCAAATGTTGAGCAATTGAGGTTTATATTC
128 GTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTC
* * * * * * * * *
29107362 AAAGACATGCATTCCTTCATGTTGGTCATTATAAATATTCTTTTTATTTTTTTTACCAATTATTC
1 TAAGACATACGTTCTTTCATGTTGATCATTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTC
* * * *
29107427 TTGCTCTAGAGTTGAGAGAATAATGCCTTAATTACAGCGC-G---GTATGTATTGATAACTTGTT
66 TTGCCCTAGAGTTGAGGGAATAATACCTTAATTACAGCGCGGTAAGTATCTATTGATAACTTGTT
* * *
29107488 AAGACCAAATTTTGAGCAATTGTAGTTTATATTC
131 GAGACCAAATGTTGAGCAATTGTGGTTTATATTC
* * * * * *
29107522 TAATACATACATTCTTTCACGTTGATCATTATAAATATTATTCTTATGTTTTTTACCAGTTCTTT
1 TAAGACATACGTTCTTTCATGTTGATCATTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTC
* * * *
29107587 TTGCCCAAGAGTTGAGGGAATAATACCTTAAGTACAGCACGGTAAGTATCTATTGATAACTTCTT
66 TTGCCCTAGAGTTGAGGGAATAATACCTTAATTACAGCGCGGTAAGTATCTATTGATAACTTGTT
* *
29107652 GAGACCAAATGTTGAACAATAGTGGTTTATATTC
131 GAGACCAAATGTTGAGCAATTGTGGTTTATATTC
*
29107686 TAAGACATACGTTCTTTCATGTTGATCATTATAAATATTCTTCTTATATTTTTTACCAGTTGTTC
1 TAAGACATACGTTCTTTCATGTTGATCATTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTC
* * * * *
29107751 TTGCCCAAGAGTTGAGGGAATAATACATTAATTACAGCACGGTAAGTATCTATTTATAACTTCTT
66 TTGCCCTAGAGTTGAGGGAATAATACCTTAATTACAGCGCGGTAAGTATCTATTGATAACTTGTT
* *
29107816 GAGACCAAATGTTGAACAATAGTGGTTTATATTC
131 GAGACCAAATGTTGAGCAATTGTGGTTTATATTC
* * *
29107850 TAAGACATATGTTCTTTCATGTTGATCATTATAAATATTCTTCTTATGCTTTTTACCAGTTGTTT
1 TAAGACATACGTTCTTTCATGTTGATCATTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTC
* * * *
29107915 TTACCCCTAGAGTTGAGGGAATAATACCTTAATTACTGCGCGGTAAGTAT-GATTGATAAGTTGT
66 TT-GCCCTAGAGTTGAGGGAATAATACCTTAATTACAGCGCGGTAAGTATCTATTGATAACTTGT
29107979 TGAGACCAAATGTTGAGCAATTGTGGTTTATATTC
130 TGAGACCAAATGTTGAGCAATTGTGGTTTATATTC
* * * * *
29108014 CAAGACATATGTTCCTTCACGTTGATC-TTCATAAATATTCTTCTTATGTTTTTTTACTAGTTGT
1 TAAGACATACGTTCTTTCATGTTGATCATT-ATAAATATTCTTCTTATG-TTTTTTACCAGTTGT
*
29108078 TCTTGCTCTAGAGTT
64 TCTTGCCCTAGAGTT
29108093 TATGGAAGAA
Statistics
Matches: 641, Mismatches: 82, Indels: 18
0.87 0.11 0.02
Matches are distributed among these distances:
160 134 0.21
161 1 0.00
163 3 0.00
164 409 0.64
165 91 0.14
166 3 0.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.41
Consensus pattern (164 bp):
TAAGACATACGTTCTTTCATGTTGATCATTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTC
TTGCCCTAGAGTTGAGGGAATAATACCTTAATTACAGCGCGGTAAGTATCTATTGATAACTTGTT
GAGACCAAATGTTGAGCAATTGTGGTTTATATTC
Found at i:29108846 original size:164 final size:164
Alignment explanation
Indices: 29108511--29109369 Score: 684
Period size: 164 Copynumber: 5.2 Consensus size: 164
29108501 ATTACCCGAG
* * * * *
29108511 GTTGAGACCAAATGTGGGGAAATTGTGGTTTATATTACGAGGCATACGTTCCTTCACGTTGATCA
1 GTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGGCATACGTTCCTTCATGTTGATCA
* * * ** * * * * * *
29108576 TTATAAATCTTCTTCTAATGTTTTTTTCCAGTTATTATCACTCAAGTGTTGTGAGAAGGATAACG
66 TTATAAATCTTCTTCTAATGTTTTTTACCAGTTGTTCTTGCTCAAGAGTTGAGGGAAGAAAAAAG
* * *
29108641 TAAGT-AT-TGAGCGATAAGTATGTATTGATGACTT
131 TAATTAATCTG-G-GGTAAGTATGTATTGATAACTT
* * * *
29108675 ATTGAGACCAAATGTTGAGCAATTCTGGTTTATATTTCGAGGCATACGTTCCTTCATATTGATTA
1 GTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGGCATACGTTCCTTCATGTTGATCA
* * * * * * *
29108740 TTATAAATCTTCTACTAATGTTTTTTGCTAGATCTTCTTGCTCTAGAGTTGAGGCAAGAAAAAAG
66 TTATAAATCTTCTTCTAATGTTTTTTACCAGTTGTTCTTGCTCAAGAGTTGAGGGAAGAAAAAAG
* *
29108805 TAATTAATCTGGGGTAAATATGCATTGATAACTT
131 TAATTAATCTGGGGTAAGTATGTATTGATAACTT
* * * *
29108839 GTTGAGACCAAATATTAAGCAAATT-TGGTTTATATTCTGCTAATGTTTTTTGC-TA-GAT-CTT
1 GTTGAGACCAAATGTTGAGC-AATTGTGGTTTATATT-T-C-GA-G------GCATACGTTCCTT
* * * * * *
29108900 CATATTGATCATTGTAAATCTTCTTCTTTTTATGTTTTTTACCAGTTGTTCTTTCTCCAGAGTGG
55 CATGTTGATCATTATAAATCTTCTTC---TAATGTTTTTTACCAGTTGTTCTTGCTCAAGAGTTG
* * ** * ** * *
29108965 AGGGAA-TAATACCTAAATTACAGC-GCAGTCAGTATGTATAGATAACTT
117 AGGGAAGAAAAAAGT-AATTA-ATCTGGGGTAAGTATGTATTGATAACTT
* * * *
29109013 GTTGAGACCAAATGTTGAGCAATTGTGATTTATATTTCGAGACATACGTTCTTTCATGTTGATCT
1 GTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGGCATACGTTCCTTCATGTTGATCA
* * * *
29109078 TTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTTTTGCTCAAGAGTTGAGGGAAGAAGAAAG
66 TTATAAATCTTCTTCTAATGTTTTTTACCAGTTGTTCTTGCTCAAGAGTTGAGGGAAGAAAAAAG
* * * *
29109143 TAATTAATCCGAGGTAAGTCTATATTGATAACTT
131 TAATTAATCTGGGGTAAGTATGTATTGATAACTT
* * * * * * * *
29109177 GTTGAGACCAAATATTGAG-AGAATGTGATTTATATTTTGAGACATACGTTTCTTCATGTTGGTA
1 GTTGAGACCAAATGTTGAGCA-ATTGTGGTTTATATTTCGAGGCATACGTTCCTTCATGTTGATC
* * * * * * *
29109241 ATTATAAATCTTCTTCTTAT-TTTTTTACCAGTTGTTCTTTCTCCAGAGTTGGGGGAATAATACA
65 ATTATAAATCTTCTTCTAATGTTTTTTACCAGTTGTTCTTGCTCAAGAGTTGAGGGAAGAAAAAA
* ** * **
29109305 TTAATT-A-C-GATGT-ACTATGTATTGACCACTT
130 GTAATTAATCTGGGGTAAGTATGTATTGATAACTT
*
29109336 GTTGAGACCAAATGTTGAGTAATTGTGGTTTATA
1 GTTGAGACCAAATGTTGAGCAATTGTGGTTTATA
29109370 ATTCTAAGAC
Statistics
Matches: 558, Mismatches: 111, Indels: 57
0.77 0.15 0.08
Matches are distributed among these distances:
159 42 0.08
160 5 0.01
161 1 0.00
162 1 0.00
163 45 0.08
164 290 0.52
165 13 0.02
166 5 0.01
167 25 0.04
168 1 0.00
170 1 0.00
171 27 0.05
172 3 0.01
173 11 0.02
174 86 0.15
175 2 0.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.40
Consensus pattern (164 bp):
GTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGGCATACGTTCCTTCATGTTGATCA
TTATAAATCTTCTTCTAATGTTTTTTACCAGTTGTTCTTGCTCAAGAGTTGAGGGAAGAAAAAAG
TAATTAATCTGGGGTAAGTATGTATTGATAACTT
Found at i:29109211 original size:338 final size:323
Alignment explanation
Indices: 29108657--29109369 Score: 822
Period size: 338 Copynumber: 2.2 Consensus size: 323
29108647 TTGAGCGATA
* * * *
29108657 AGTATGTATTGATGACTTATTGAGACCAAATGTTGAGCAATTCTGGTTTATATTTCGAGGCATAC
1 AGTATGTATTGATAACTTGTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGACATAC
* * * *
29108722 GTTCCTTCATATTGATTATTATAAATCTTCTACTAATGTTTTTTGCTAGATCTTCTTGCTCTAGA
66 GTTCCTTCATATTGATTATTATAAATATTCTACTAATGTTTTTTACCAGATCTTCTTGCTCAAGA
* * *
29108787 GTTGAGGCAAGAAAAAAGTAATTAATCTGGGGTAAATATGCATTGATAACTTGTTGAGACCAAAT
131 GTTGAGGCAAGAAAAAAGTAATTAATCCGAGGTAAATATACATTGATAACTTGTTGAGACCAAAT
* * *** ** * *
29108852 ATTAAGCAAATTTGGTTTATATTCTGCTAATGTTTTTTGCTAGATCTTCATATTGATCATTGTAA
196 ATTAAGCAAATGTGATTTATATT-T--TAA-GACATACG-T--ATCTTCATATTGATAATTATAA
*
29108917 ATCTTCTTCTTTTTATGTTTTTTACCAGTTGTTCTTTCTCCAGAG-TGGAGGGAATAATACCTAA
254 ATCTTCTTC---TTAT-TTTTTTACCAGTTGTTCTTTCTCCAGAGTTGG-GGGAATAATACATAA
29108981 ATTACAGCGCA-GT
314 ATT--A-CG-ATGT
* *
29108994 CAGTATGTATAGATAACTTGTTGAGACCAAATGTTGAGCAATTGTGATTTATATTTCGAGACATA
1 -AGTATGTATTGATAACTTGTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGACATA
* * * * * * *
29109059 CGTTCTTTCATGTTGATCT-TTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTTTTGCTCAA
65 CGTTCCTTCATATTGAT-TATTATAAATATTCTACTAATGTTTTTTACCAGATCTTCTTGCTCAA
* * * * *
29109123 GAGTTGAGGGAAGAAGAAAGTAATTAATCCGAGGTAAGTCTATATTGATAACTTGTTGAGACCAA
129 GAGTTGAGGCAAGAAAAAAGTAATTAATCCGAGGTAAATATACATTGATAACTTGTTGAGACCAA
* * * * *
29109188 ATATTGAG-AGAATGTGATTTATATTTTGAGACATACGTTTCTTCATGTTGGTAATTATAAATCT
194 ATATTAAGCA-AATGTGATTTATATTTTAAGACATACGTATCTTCATATTGATAATTATAAATCT
*
29109252 TCTTCTTATTTTTTTACCAGTTGTTCTTTCTCCAGAGTTGGGGGAATAATACATTAATTACGATG
258 TCTTCTTATTTTTTTACCAGTTGTTCTTTCTCCAGAGTTGGGGGAATAATACATAAATTACGATG
29109317 T
323 T
* ** *
29109318 ACTATGTATTGACCACTTGTTGAGACCAAATGTTGAGTAATTGTGGTTTATA
1 AGTATGTATTGATAACTTGTTGAGACCAAATGTTGAGCAATTGTGGTTTATA
29109370 ATTCTAAGAC
Statistics
Matches: 324, Mismatches: 47, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
323 47 0.15
324 4 0.01
325 1 0.00
327 44 0.14
328 7 0.02
331 26 0.08
333 1 0.00
334 3 0.01
335 2 0.01
337 2 0.01
338 186 0.57
339 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.41
Consensus pattern (323 bp):
AGTATGTATTGATAACTTGTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGACATAC
GTTCCTTCATATTGATTATTATAAATATTCTACTAATGTTTTTTACCAGATCTTCTTGCTCAAGA
GTTGAGGCAAGAAAAAAGTAATTAATCCGAGGTAAATATACATTGATAACTTGTTGAGACCAAAT
ATTAAGCAAATGTGATTTATATTTTAAGACATACGTATCTTCATATTGATAATTATAAATCTTCT
TCTTATTTTTTTACCAGTTGTTCTTTCTCCAGAGTTGGGGGAATAATACATAAATTACGATGT
Found at i:29113020 original size:23 final size:23
Alignment explanation
Indices: 29112994--29113044 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
29112984 CCATTAACAT
29112994 TGTAACACCCCGAAAATTACTAC
1 TGTAACACCCCGAAAATTACTAC
* *
29113017 TGTAATACCCTGAAAATTACTAC
1 TGTAACACCCCGAAAATTACTAC
*
29113040 AGTAA
1 TGTAA
29113045 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (23 bp):
TGTAACACCCCGAAAATTACTAC
Found at i:29115502 original size:22 final size:21
Alignment explanation
Indices: 29115474--29115521 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
29115464 AACCCTGAAT
29115474 CCTAAA-CTCCAAATCTATAAAC
1 CCTAAACCT-CAAATCT-TAAAC
*
29115496 CCTAAACCTTAAATCTTAAAC
1 CCTAAACCTCAAATCTTAAAC
29115517 CCTAA
1 CCTAA
29115522 TACTTAAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 10 0.42
22 12 0.50
23 2 0.08
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (21 bp):
CCTAAACCTCAAATCTTAAAC
Found at i:29115789 original size:28 final size:28
Alignment explanation
Indices: 29115758--29115813 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
29115748 AAATATTTGT
29115758 TTATAATTTAAAAAATTAATTATTTTAA
1 TTATAATTTAAAAAATTAATTATTTTAA
29115786 TTATAATTTAAAAAATTAATTATTTTAA
1 TTATAATTTAAAAAATTAATTATTTTAA
29115814 GTAATTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TTATAATTTAAAAAATTAATTATTTTAA
Found at i:29119792 original size:28 final size:28
Alignment explanation
Indices: 29119760--29119815 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
29119750 TGGTGCAATA
29119760 GATAAAATATTTTTTTAAATAAATCCTT
1 GATAAAATATTTTTTTAAATAAATCCTT
29119788 GATAAAATATTTTTTTAAATAAATCCTT
1 GATAAAATATTTTTTTAAATAAATCCTT
29119816 TTTTGTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (28 bp):
GATAAAATATTTTTTTAAATAAATCCTT
Found at i:29121108 original size:20 final size:20
Alignment explanation
Indices: 29121083--29121121 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29121073 TTAAACTTAA
29121083 ATATATATATT-TTAATTTTT
1 ATATAT-TATTATTAATTTTT
*
29121103 ATATATTTTTATTAATTTT
1 ATATATTATTATTAATTTT
29121122 AAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATATATTATTATTAATTTTT
Found at i:29123512 original size:12 final size:12
Alignment explanation
Indices: 29123497--29123523 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29123487 TGGAAGAAGG
29123497 AGATGAAGACGA
1 AGATGAAGACGA
29123509 AGATGAAGACGA
1 AGATGAAGACGA
29123521 AGA
1 AGA
29123524 CGGGGGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.33, T:0.07
Consensus pattern (12 bp):
AGATGAAGACGA
Found at i:29127493 original size:42 final size:43
Alignment explanation
Indices: 29127446--29127601 Score: 187
Period size: 42 Copynumber: 3.7 Consensus size: 43
29127436 ATCGAGATTA
29127446 CGTGTAAGACCATATCTGGGATA-TGGCATCGATATGAGAATT
1 CGTGTAAGACCATATCTGGGATATTGGCATCGATATGAGAATT
* * * *
29127488 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTT
1 CGTGTAAGACCATATCTGGGATATTGGCATCGATATGAGAATT
* * *
29127531 CGTG-AAGACCATGGT-TGGGCTATTGGCATCGATACGAG-ATT
1 CGTGTAAGACCAT-ATCTGGGATATTGGCATCGATATGAGAATT
*
29127572 ACATGTAAGACCATATCTGGGATA-TGGCAT
1 -CGTGTAAGACCATATCTGGGATATTGGCAT
29127602 TGTTATGGTA
Statistics
Matches: 97, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.02
42 58 0.60
43 37 0.38
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (43 bp):
CGTGTAAGACCATATCTGGGATATTGGCATCGATATGAGAATT
Found at i:29128302 original size:34 final size:34
Alignment explanation
Indices: 29128259--29128326 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
29128249 GAAACGGTGT
29128259 AAGCAAAAGAATCTTGTATTATGAGATATTTGAA
1 AAGCAAAAGAATCTTGTATTATGAGATATTTGAA
29128293 AAGCAAAAGAATCTTGTATTATGAGATATTTGAA
1 AAGCAAAAGAATCTTGTATTATGAGATATTTGAA
29128327 TTTTTGTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (34 bp):
AAGCAAAAGAATCTTGTATTATGAGATATTTGAA
Found at i:29134051 original size:6 final size:6
Alignment explanation
Indices: 29134040--29134067 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29134030 GGGAGCTTAT
29134040 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
29134068 TAAGAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.54
Consensus pattern (6 bp):
ATTTGG
Found at i:29134553 original size:3 final size:3
Alignment explanation
Indices: 29134542--29134573 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
29134532 CTTGAAAAAA
29134542 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
29134574 GTAGAGGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29135621 original size:21 final size:21
Alignment explanation
Indices: 29135591--29135662 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
29135581 AATTTTTTCA
*
29135591 AACC-TGAACCCTGAATCCTG
1 AACCTTGAACCCTAAATCCTG
* * *
29135611 AACTTTGAACCTTAAATCCCG
1 AACCTTGAACCCTAAATCCTG
*
29135632 AACCTTGAACCCTAAATTC-G
1 AACCTTGAACCCTAAATCCTG
29135652 AACCTTGAACC
1 AACCTTGAACC
29135663 TCGAATCCTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.33, C:0.32, G:0.11, T:0.24
Consensus pattern (21 bp):
AACCTTGAACCCTAAATCCTG
Found at i:29135717 original size:21 final size:20
Alignment explanation
Indices: 29135693--29135746 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
29135683 TCAAGCTTAG
29135693 GGTTCAAGATTTAGGATTTAA
1 GGTTCAAGATTTAGGATTT-A
*
29135714 GGTTC-AGAGTTTGGGATTTA
1 GGTTCAAGA-TTTAGGATTTA
*
29135734 GGATTCAAAATTT
1 GG-TTCAAGATTT
29135747 TCAAAGTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 6 0.21
21 20 0.71
22 2 0.07
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.39
Consensus pattern (20 bp):
GGTTCAAGATTTAGGATTTA
Found at i:29135845 original size:21 final size:21
Alignment explanation
Indices: 29135821--29135860 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29135811 ATTATGTATC
29135821 AATGACATAAAAAAATTATTA
1 AATGACATAAAAAAATTATTA
* * *
29135842 AATGTCATTAAATAATTAT
1 AATGACATAAAAAAATTAT
29135861 AAAGAGATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (21 bp):
AATGACATAAAAAAATTATTA
Found at i:29142396 original size:29 final size:29
Alignment explanation
Indices: 29142354--29142415 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
29142344 ATAAATTATT
*
29142354 CTCTATATTTCTTTTTCTTGCATGGAGAA
1 CTCTATATTTCTTTTTCTTGCATGCAGAA
*
29142383 CTCTATATTTCTTTTTCTTGCTTGCAGAA
1 CTCTATATTTCTTTTTCTTGCATGCAGAA
29142412 CTCT
1 CTCT
29142416 TAATATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (29 bp):
CTCTATATTTCTTTTTCTTGCATGCAGAA
Found at i:29142987 original size:25 final size:26
Alignment explanation
Indices: 29142941--29142999 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
29142931 ATGTTTGTAT
*
29142941 TTTTTTTTAATTTAAAGGGATTAG-TA
1 TTTTTTTTAA-TTAAAGAGATTAGTTA
29142967 TTTTTTTTAA-TAGAAGAGATTAGTTA
1 TTTTTTTTAATTA-AAGAGATTAGTTA
*
29142993 TTCTTTT
1 TTTTTTT
29143000 ATGTAGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 2 0.07
25 9 0.31
26 18 0.62
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.56
Consensus pattern (26 bp):
TTTTTTTTAATTAAAGAGATTAGTTA
Found at i:29143154 original size:95 final size:92
Alignment explanation
Indices: 29143055--29143375 Score: 333
Period size: 83 Copynumber: 3.5 Consensus size: 92
29143045 ATTAGTAATT
29143055 ATTATAAATTGTTTGTGTTTAGTTTAGTGTTTATTGTGATTTTAATTTTTTTTAAAAAACTTTTT
1 ATTATAAATTGTTTGTGTTTAGTTTAGTGTTTATTGTGATTTTAATTTTTTTT-AAAAA-TTTTT
*
29143120 AATGTTATTTTGTCAGTAATTTATGATTAG
64 AAT-TTATTTTGTTAGTAATTTATGATTAG
* * *
29143150 ATTATATATTGTTTGTGTTTAGTTTAGTGTTTATTGTGATCTTAAATTTTTTT----A-----AA
1 ATTATAAATTGTTTGTGTTTAGTTTAGTGTTTATTGTGATTTTAATTTTTTTTAAAAATTTTTAA
29143206 TTTATTTTGTTAGTAATTTATGATTAG
66 TTTATTTTGTTAGTAATTTATGATTAG
*
29143233 GTTATAAATTGTTTGTGTTTAGTTTAGTGTTTA-TGTGATTTTTTATGAATGCAATTTTTTTAAA
1 ATTATAAATTGTTTGTGTTTAGTTTAGTGTTTATTGTGA---TTT-T-AAT----TTTTTTTAAA
*
29143297 AATTATTTAAAAATTATTTTGTTAGTAATTTATGATTAG
57 AATT-TTT--AATTTATTTTGTTAGTAATTTATGATTAG
* * * *
29143336 ATTATAAATT-ATT-TCTTTAGTTTAATGTGTATTGTGATTT
1 ATTATAAATTGTTTGTGTTTAGTTTAGTGTTTATTGTGATTT
29143376 GTTATAATGT
Statistics
Matches: 190, Mismatches: 14, Indels: 40
0.78 0.06 0.16
Matches are distributed among these distances:
82 5 0.03
83 56 0.29
84 3 0.02
85 2 0.01
86 1 0.01
87 2 0.01
90 1 0.01
91 7 0.04
95 51 0.27
99 3 0.02
101 15 0.08
102 7 0.04
103 37 0.19
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.57
Consensus pattern (92 bp):
ATTATAAATTGTTTGTGTTTAGTTTAGTGTTTATTGTGATTTTAATTTTTTTTAAAAATTTTTAA
TTTATTTTGTTAGTAATTTATGATTAG
Found at i:29143309 original size:12 final size:11
Alignment explanation
Indices: 29143291--29143315 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29143281 ATGCAATTTT
29143291 TTTAAAAATTA
1 TTTAAAAATTA
29143302 TTTAAAAATTA
1 TTTAAAAATTA
29143313 TTT
1 TTT
29143316 TGTTAGTAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAAATTA
Found at i:29143397 original size:103 final size:103
Alignment explanation
Indices: 29143193--29143391 Score: 278
Period size: 103 Copynumber: 2.0 Consensus size: 103
29143183 TTGTGATCTT
* * * * * *
29143193 AAATTTTTTTAAATTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTT
1 AAATTATTTAAAAATTATTTTGTTAGTAATTTATGATTAGATTATAAATTGATTGTCTTTAGTTT
* * *
29143258 AGTGTTTATGTGATTTTTTATGAATGCAATTTTTTTAA
66 AATGTGTATGTGATTTGTTATGAATGCAATTTTTTTAA
29143296 AAATTATTTAAAAATTATTTTGTTAGTAATTTATGATTAGATTATAAATT-ATT-TCTTTAGTTT
1 AAATTATTTAAAAATTATTTTGTTAGTAATTTATGATTAGATTATAAATTGATTGTCTTTAGTTT
*
29143359 AATGTGTATTGTGATTTGTTAT-AATGTAATTTT
66 AATGTGTA-TGTGATTTGTTATGAATGCAATTTT
29143392 ATTTTATTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
101 25 0.29
102 14 0.16
103 46 0.54
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (103 bp):
AAATTATTTAAAAATTATTTTGTTAGTAATTTATGATTAGATTATAAATTGATTGTCTTTAGTTT
AATGTGTATGTGATTTGTTATGAATGCAATTTTTTTAA
Found at i:29145887 original size:49 final size:49
Alignment explanation
Indices: 29145801--29146121 Score: 427
Period size: 49 Copynumber: 6.6 Consensus size: 49
29145791 CAAAAATACC
* * * *
29145801 AACTTCGTAATTTAAATT-AAATTAATTGCAGCATTAAAAATTGGAACA
1 AACTTTGTAATTTAAATTGAGATTCATTGCAACATTAAAAATTGGAACA
*
29145849 AACTTTGTAATTTAGATTGAGATTCATTGCAACATTAAAAATTGGAACA
1 AACTTTGTAATTTAAATTGAGATTCATTGCAACATTAAAAATTGGAACA
** *
29145898 AACTTCATAATTTAAATTGAGATTCACTGCAACATTAAAAATTGGAACA
1 AACTTTGTAATTTAAATTGAGATTCATTGCAACATTAAAAATTGGAACA
* * *
29145947 AACTTCGTAATTTCAATTGAGATTCATTACAACATTAAAAATTGGAACA
1 AACTTTGTAATTTAAATTGAGATTCATTGCAACATTAAAAATTGGAACA
* * * *
29145996 AATTTTGTAATTTAAATT-ATGATTCATTACAACATTAAAATTTGGAATA
1 AACTTTGTAATTTAAATTGA-GATTCATTGCAACATTAAAAATTGGAACA
* *
29146045 AACTTTATAATTTAAATT-AGATTAATTGCAACATT-AAAA-TGATGAACA
1 AACTTTGTAATTTAAATTGAGATTCATTGCAACATTAAAAATTG--GAACA
29146093 AACTTTGTAATTTAAATTGAGATTCATTG
1 AACTTTGTAATTTAAATTGAGATTCATTG
29146122 GAGTACATTA
Statistics
Matches: 242, Mismatches: 26, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
46 2 0.01
47 3 0.01
48 52 0.21
49 185 0.76
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (49 bp):
AACTTTGTAATTTAAATTGAGATTCATTGCAACATTAAAAATTGGAACA
Found at i:29145941 original size:25 final size:25
Alignment explanation
Indices: 29145864--29145941 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
29145854 TGTAATTTAG
*
29145864 ATTGAGATTCATTGCAACATTAAAA
1 ATTGAGATTCACTGCAACATTAAAA
* * *
29145889 ATTG-GA-ACAAACTTCATA-ATT-TAA
1 ATTGAGATTC--ACTGCA-ACATTAAAA
29145913 ATTGAGATTCACTGCAACATTAAAA
1 ATTGAGATTCACTGCAACATTAAAA
29145938 ATTG
1 ATTG
29145942 GAACAAACTT
Statistics
Matches: 39, Mismatches: 7, Indels: 14
0.65 0.12 0.23
Matches are distributed among these distances:
23 2 0.05
24 16 0.41
25 19 0.49
26 2 0.05
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.32
Consensus pattern (25 bp):
ATTGAGATTCACTGCAACATTAAAA
Found at i:29149003 original size:17 final size:17
Alignment explanation
Indices: 29148981--29149016 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29148971 TCCTTTAATC
29148981 TTCTCTACTAATTTTTT
1 TTCTCTACTAATTTTTT
* *
29148998 TTCTCTTCTACTTTTTT
1 TTCTCTACTAATTTTTT
29149015 TT
1 TT
29149017 ACTACTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCTCTACTAATTTTTT
Found at i:29149111 original size:27 final size:27
Alignment explanation
Indices: 29149081--29149154 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
29149071 CCTCTCAAAT
* *
29149081 AGGGGCCACTAGTGCCGCGTACCTAAG
1 AGGGGTCACTAGTGCCGCCTACCTAAG
** *
29149108 AGGGGTCACTAGTGTTGCCTACTTAAG
1 AGGGGTCACTAGTGCCGCCTACCTAAG
*
29149135 AGGGGTCACTAGTACCGCCT
1 AGGGGTCACTAGTGCCGCCT
29149155 CTTTGAGAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.22, C:0.26, G:0.31, T:0.22
Consensus pattern (27 bp):
AGGGGTCACTAGTGCCGCCTACCTAAG
Found at i:29151993 original size:13 final size:13
Alignment explanation
Indices: 29151975--29152000 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29151965 AAAATTAAAA
29151975 TTTCAAGATAATT
1 TTTCAAGATAATT
29151988 TTTCAAGATAATT
1 TTTCAAGATAATT
29152001 CTTTAATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTCAAGATAATT
Found at i:29156568 original size:14 final size:14
Alignment explanation
Indices: 29156549--29156594 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
29156539 TTTTATAATC
29156549 TTCACATTCATTCA
1 TTCACATTCATTCA
29156563 TTCACATTCATTCA
1 TTCACATTCATTCA
* *
29156577 TTCACGTTTATTCA
1 TTCACATTCATTCA
29156591 TTCA
1 TTCA
29156595 TAAGAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.46
Consensus pattern (14 bp):
TTCACATTCATTCA
Found at i:29157974 original size:41 final size:39
Alignment explanation
Indices: 29157867--29157975 Score: 96
Period size: 41 Copynumber: 2.6 Consensus size: 39
29157857 AGTTAATCAC
29157867 TTTAATATTAAAATTATTAAATTAATAGAATATTATCTTAA
1 TTTAATATTAAAA-TATTAAA-TAATAGAATATTATCTTAA
* * * *
29157908 TATAATATTAAAAATACTATTATAATA-AGTATTA-CATTAAA
1 TTTAATATT-AAAATATTA-AATAATAGAATATTATC-TT-AA
29157949 TTTAATATTAAATATATTAGAATAATA
1 TTTAATATTAAA-ATATTA-AATAATA
29157976 TTACTTTTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
39 1 0.02
40 11 0.20
41 38 0.69
42 5 0.09
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (39 bp):
TTTAATATTAAAATATTAAATAATAGAATATTATCTTAA
Found at i:29160329 original size:13 final size:13
Alignment explanation
Indices: 29160311--29160336 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29160301 CGTTTTTCCA
29160311 AAAACCATTTGTT
1 AAAACCATTTGTT
29160324 AAAACCATTTGTT
1 AAAACCATTTGTT
29160337 TGCATAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:29165989 original size:17 final size:16
Alignment explanation
Indices: 29165952--29165991 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
29165942 TTAAAATGAT
29165952 CCAATTTATTTAAAAA
1 CCAATTTATTTAAAAA
* *
29165968 CCAATTTTTTTCAAAA
1 CCAATTTATTTAAAAA
29165984 CACAATTT
1 C-CAATTT
29165992 GCAACGCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (16 bp):
CCAATTTATTTAAAAA
Found at i:29171670 original size:42 final size:42
Alignment explanation
Indices: 29171602--29171999 Score: 476
Period size: 42 Copynumber: 9.3 Consensus size: 42
29171592 ATGTCGTAAA
* *
29171602 CTTTTGCGGCGCTTACAGAAAAAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAATAAACGCCACTAAAGATCATGTT
* *
29171646 CTTTAGCGGCGCTTAGAAAGAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTT
* * *
29171688 CTTTAACGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCT-TAGAAATAAACGCCACTAAAGATCATGTT
* * * *
29171731 CTTTAGCGGCGCTAAAAAATAAATGCCACTAAAGACCATGTT
1 CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTT
* * *
29171773 CTTTAGCGACGCTTAAAAATAAACGCCACTAAAGAGCATGTT
1 CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTT
*
29171815 CTTTAGTGGCGCTTAGAAATAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTT
* * *
29171857 CTTTAGCGGCGCTAAGGAAATAAATGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-GAAATAAACGCCACTAAAGATCATGTT
*
29171900 CTTTAGCGGCGCTTAGGACAA-AAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-GA-AATAAACGCCACTAAAGATCATGTT
* * * * *
29171943 CTTTAGCGGCACTTTGAAAGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGAAA-TAAACGCCACTAAAGA-TCATGTT
* *
29171986 CTATAGCGGTGCTT
1 CTTTAGCGGCGCTT
29172000 GTTTAAAAAC
Statistics
Matches: 316, Mismatches: 32, Indels: 13
0.88 0.09 0.04
Matches are distributed among these distances:
41 2 0.01
42 157 0.50
43 142 0.45
44 15 0.05
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTT
Found at i:29171903 original size:169 final size:169
Alignment explanation
Indices: 29171620--29171999 Score: 505
Period size: 169 Copynumber: 2.2 Consensus size: 169
29171610 GCGCTTACAG
* *
29171620 AAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCCGCTAAAGATCAT
1 AAAAAAACGCCACTAAAGAGCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCCACTAAAGATCAT
29171685 GTTCTTTAACGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGC-TA-AAA
66 GTTCTTTAACGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAA
*
29171748 AATAAATGCCACTAAAGACCATGTTCTTTAGCGACGCTTA
131 AA-AAACGCCACTAAAGACCATGTTCTTTAGCGACGCTTA
* *
29171788 AAAATAAACGCCACTAAAGAGCATGTTCTTTAGTGGCGCTTAGAAATAAACGCCACTAAAGATCA
1 AAAA-AAACGCCACTAAAGAGCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCCACTAAAGATCA
* ** * * *
29171853 TGTTCTTTAGCGGCGCTAAGGAAATAAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGA
65 TGTTCTTTAACGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
* * * * *
29171918 CAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTTGA
130 AAAAAACGCCACTAAAGACCATGTTCTTTAGCGACGC-TT-A
* * * * *
29171960 AAGAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGTGCTT
1 AAAAAAACGCCACTAAAGAG-CATGTTCTTTAGCGGCGCTT
29172000 GTTTAAAAAC
Statistics
Matches: 184, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
168 4 0.02
169 110 0.60
170 33 0.18
171 33 0.18
172 4 0.02
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (169 bp):
AAAAAAACGCCACTAAAGAGCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCCACTAAAGATCAT
GTTCTTTAACGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAA
AAAAACGCCACTAAAGACCATGTTCTTTAGCGACGCTTA
Found at i:29172492 original size:12 final size:12
Alignment explanation
Indices: 29172473--29172536 Score: 64
Period size: 12 Copynumber: 5.6 Consensus size: 12
29172463 TCTGCTTCAA
29172473 TCGCTGCTTCTC
1 TCGCTGCTTCTC
*
29172485 TCGTTGCTTCTC
1 TCGCTGCTTCTC
29172497 -CTGCTGCTTCTC
1 TC-GCTGCTTCTC
**
29172509 TCGCTGCAGC-C
1 TCGCTGCTTCTC
29172520 T--CTGCTTCTC
1 TCGCTGCTTCTC
29172530 TCGCTGC
1 TCGCTGC
29172537 GGCCTCTGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
9 5 0.12
10 2 0.05
11 3 0.07
12 30 0.73
13 1 0.02
ACGTcount: A:0.02, C:0.41, G:0.19, T:0.39
Consensus pattern (12 bp):
TCGCTGCTTCTC
Found at i:29172526 original size:21 final size:21
Alignment explanation
Indices: 29172500--29172568 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
29172490 GCTTCTCCTG
29172500 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
29172521 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
29172542 CTGCTTCTCTCGTTGCTGCCT
1 CTGCTTCTCTCGCTGCAGCCT
29172563 CTGCTT
1 CTGCTT
29172569 TAAGTTGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.01, C:0.41, G:0.20, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:29178050 original size:9 final size:9
Alignment explanation
Indices: 29178036--29178340 Score: 104
Period size: 9 Copynumber: 35.0 Consensus size: 9
29178026 AAGATATACA
29178036 TTATGTAAG
1 TTATGTAAG
29178045 TTATGTAAG
1 TTATGTAAG
*
29178054 TTGTGTAAG
1 TTATGTAAG
**
29178063 TTGCGTAAG
1 TTATGTAAG
* *
29178072 ATGTGT-A-
1 TTATGTAAG
* *
29178079 TTATGAAAC
1 TTATGTAAG
29178088 TTATGTAAG
1 TTATGTAAG
* *
29178097 TTATCT--C
1 TTATGTAAG
29178104 TTATGTAAG
1 TTATGTAAG
*
29178113 TTATGTAAA
1 TTATGTAAG
*
29178122 ATATGT-A-
1 TTATGTAAG
*
29178129 TTATTTACA-
1 TTATGTA-AG
*
29178138 -CATGTAAG
1 TTATGTAAG
*
29178146 TTATGT--C
1 TTATGTAAG
29178153 TTATGTAAG
1 TTATGTAAG
**
29178162 TTGCGTAAG
1 TTATGTAAG
*
29178171 TTGTGT-A-
1 TTATGTAAG
*
29178178 TTATGAAAG
1 TTATGTAAG
*
29178187 TTATGT--C
1 TTATGTAAG
29178194 TTATGTAAG
1 TTATGTAAG
*
29178203 TTATGTAGG
1 TTATGTAAG
*
29178212 GTATGTATTA-
1 TTATGTA--AG
*
29178222 TTATGTAAC
1 TTATGTAAG
* *
29178231 TTATTTAAT
1 TTATGTAAG
*
29178240 TTATGTAGG
1 TTATGTAAG
*
29178249 GTATGTATTA-
1 TTATGTA--AG
*
29178259 TTATGTAAC
1 TTATGTAAG
* *
29178268 TTATTTAAT
1 TTATGTAAG
*
29178277 TTATGTAGG
1 TTATGTAAG
*
29178286 GTATGTATTA-
1 TTATGTA--AG
*
29178296 TTATGTAAC
1 TTATGTAAG
* *
29178305 TTATTTAAT
1 TTATGTAAG
*
29178314 TTATGTAGG
1 TTATGTAAG
*
29178323 GTATGTAAG
1 TTATGTAAG
29178332 TTATGTAAG
1 TTATGTAAG
29178341 CTCTGTATTA
Statistics
Matches: 215, Mismatches: 58, Indels: 46
0.67 0.18 0.14
Matches are distributed among these distances:
7 29 0.13
8 12 0.06
9 156 0.73
10 18 0.08
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29178095 original size:25 final size:25
Alignment explanation
Indices: 29178067--29178132 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
29178057 TGTAAGTTGC
*
29178067 GTAAGATGTGTATTATGAAACTTAT
1 GTAAGATATGTATTATGAAACTTAT
* * * * *
29178092 GTAAGTTATCTCTTATGTAAGTTAT
1 GTAAGATATGTATTATGAAACTTAT
*
29178117 GTAAAATATGTATTAT
1 GTAAGATATGTATTAT
29178133 TTACACATGT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.44
Consensus pattern (25 bp):
GTAAGATATGTATTATGAAACTTAT
Found at i:29178160 original size:16 final size:16
Alignment explanation
Indices: 29178139--29178208 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 16
29178129 TTATTTACAC
29178139 ATGTAAGTTATGTCTT
1 ATGTAAGTTATGTCTT
29178155 ATGTAAG-T-TG-C--
1 ATGTAAGTTATGTCTT
* *
29178166 --GTAAGTTGTGTATT
1 ATGTAAGTTATGTCTT
*
29178180 ATGAAAGTTATGTCTT
1 ATGTAAGTTATGTCTT
29178196 ATGTAAGTTATGT
1 ATGTAAGTTATGT
29178209 AGGGTATGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
9 5 0.12
10 1 0.02
11 2 0.05
13 1 0.02
14 2 0.05
15 1 0.02
16 30 0.71
ACGTcount: A:0.27, C:0.04, G:0.23, T:0.46
Consensus pattern (16 bp):
ATGTAAGTTATGTCTT
Found at i:29178187 original size:25 final size:25
Alignment explanation
Indices: 29178141--29178188 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29178131 ATTTACACAT
* *
29178141 GTAAGTTATGTCTTATGTAAGTTGC
1 GTAAGTTATGTATTATGAAAGTTGC
*
29178166 GTAAGTTGTGTATTATGAAAGTT
1 GTAAGTTATGTATTATGAAAGTT
29178189 ATGTCTTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.04, G:0.25, T:0.44
Consensus pattern (25 bp):
GTAAGTTATGTATTATGAAAGTTGC
Found at i:29178244 original size:37 final size:37
Alignment explanation
Indices: 29178193--29178329 Score: 256
Period size: 37 Copynumber: 3.7 Consensus size: 37
29178183 AAAGTTATGT
* *
29178193 CTTATGTAAGTTATGTAGGGTATGTATTATTATGTAA
1 CTTATTTAATTTATGTAGGGTATGTATTATTATGTAA
29178230 CTTATTTAATTTATGTAGGGTATGTATTATTATGTAA
1 CTTATTTAATTTATGTAGGGTATGTATTATTATGTAA
29178267 CTTATTTAATTTATGTAGGGTATGTATTATTATGTAA
1 CTTATTTAATTTATGTAGGGTATGTATTATTATGTAA
29178304 CTTATTTAATTTATGTAGGGTATGTA
1 CTTATTTAATTTATGTAGGGTATGTA
29178330 AGTTATGTAA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 98 1.00
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (37 bp):
CTTATTTAATTTATGTAGGGTATGTATTATTATGTAA
Found at i:29182017 original size:21 final size:21
Alignment explanation
Indices: 29181973--29182017 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29181963 CTTAAATCCC
* * *
29181973 CCTAACCCCTAAATCATAACA
1 CCTAACCCCTAAACCACAAAA
*
29181994 CCTAACCCTTAAACCACAAAA
1 CCTAACCCCTAAACCACAAAA
29182015 CCT
1 CCT
29182018 TGAACTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.18
Consensus pattern (21 bp):
CCTAACCCCTAAACCACAAAA
Found at i:29182340 original size:96 final size:96
Alignment explanation
Indices: 29182229--29182403 Score: 296
Period size: 96 Copynumber: 1.8 Consensus size: 96
29182219 TAAATCCCTG
* * * *
29182229 AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAAACCCTGAAAGCTAAGAAAACGGTGTCGTTG
1 AGCATTAGCGACGCTTTACTAAAAACGCCGCTAAAACCCCGAAAGCAAAGAAAACGGTGTCGTTG
29182294 GGTTTAATTTTTTTTGCGGCGATTTTATGCC
66 GGTTTAATTTTTTTTGCGGCGATTTTATGCC
* *
29182325 AGCATTAGCGACGCTTTACTAAAAACGCCGCTAAACCCCCGAAAGCAAAGAAGACGGTGTCGTTG
1 AGCATTAGCGACGCTTTACTAAAAACGCCGCTAAAACCCCGAAAGCAAAGAAAACGGTGTCGTTG
29182390 GGTTTAATTTTTTT
66 GGTTTAATTTTTTT
29182404 GCGTCGCTTC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 73 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (96 bp):
AGCATTAGCGACGCTTTACTAAAAACGCCGCTAAAACCCCGAAAGCAAAGAAAACGGTGTCGTTG
GGTTTAATTTTTTTTGCGGCGATTTTATGCC
Found at i:29183725 original size:18 final size:18
Alignment explanation
Indices: 29183697--29183731 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29183687 ACAAAACTAA
29183697 ATTTAAAAAATCTAATTTT
1 ATTTAAAAAATC-AATTTT
29183716 ATTT-AAAAATCAATTT
1 ATTTAAAAAATCAATTT
29183732 ATTATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTAAAAAATCAATTTT
Found at i:29194430 original size:30 final size:30
Alignment explanation
Indices: 29194375--29194435 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
29194365 TTCTTCCTTC
29194375 ACATTACTTATCTTATACTTTTATATATAT
1 ACATTACTTATCTTATACTTTTATATATAT
* *
29194405 ACATTA-TTATTTTATCCTTTATATATATAT
1 ACATTACTTATCTTATACTTT-TATATATAT
29194435 A
1 A
29194436 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (30 bp):
ACATTACTTATCTTATACTTTTATATATAT
Found at i:29194431 original size:2 final size:2
Alignment explanation
Indices: 29194424--29194458 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29194414 TTTTATCCTT
29194424 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29194459 CCTTTTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29199020 original size:20 final size:20
Alignment explanation
Indices: 29198975--29199022 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29198965 GTTCATATGG
* * *
29198975 GATTGCACTTCGGTGTCTTT
1 GATTGCACTTCAGTGCCTCT
*
29198995 GTTTGCACTTCAGTGCCTCT
1 GATTGCACTTCAGTGCCTCT
29199015 GATTGCAC
1 GATTGCAC
29199023 AATCATGCCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (20 bp):
GATTGCACTTCAGTGCCTCT
Found at i:29202718 original size:33 final size:33
Alignment explanation
Indices: 29202668--29202808 Score: 119
Period size: 33 Copynumber: 4.3 Consensus size: 33
29202658 TTGACTACTA
* * *
29202668 GGGAAGGTGATGTTGAAGGGGTAGAATTTGATG
1 GGGAGGGTGATGATGAAGGGGTAGAATCTGATG
29202701 GGGAGGGTGATGATGAAGGGGTAGAATCTGATG
1 GGGAGGGTGATGATGAAGGGGTAGAATCTGATG
** * * *
29202734 GTAAAGGTGAT-CTGGAAAGGGTAGAATCT-ATTG
1 GGGAGGGTGATGAT-GAAGGGGTAGAATCTGA-TG
* * *
29202767 GGGAGGGTGATGGA-GGAGAGGTACAAGT-TGATG
1 GGGAGGGTGAT-GATGAAGGGGTAGAA-TCTGATG
29202800 GGGAGGGTG
1 GGGAGGGTG
29202809 TGTCTGTTAT
Statistics
Matches: 86, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
32 2 0.02
33 82 0.95
34 2 0.02
ACGTcount: A:0.28, C:0.03, G:0.47, T:0.23
Consensus pattern (33 bp):
GGGAGGGTGATGATGAAGGGGTAGAATCTGATG
Found at i:29202799 original size:66 final size:66
Alignment explanation
Indices: 29202671--29202800 Score: 149
Period size: 66 Copynumber: 2.0 Consensus size: 66
29202661 ACTACTAGGG
* * * * * *
29202671 AAGGTGATGTTGAAGGGGTAGAATTTGATGGGGAGGGTGATGATGAAGGGGTAGAATCTGATGGT
1 AAGGTGATCTGGAAAGGGTAGAATCTGATGGGGAGGGTGATGATGAAGAGGTACAATCTGATGGT
29202736 A
66 A
*
29202737 AAGGTGATCTGGAAAGGGTAGAATCT-ATTGGGGAGGGTGATGGA-GGAGAGGTACAAGT-TGAT
1 AAGGTGATCTGGAAAGGGTAGAATCTGA-TGGGGAGGGTGAT-GATGAAGAGGTACAA-TCTGAT
29202799 GG
63 GG
29202801 GGAGGGTGTG
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
65 1 0.02
66 50 0.93
67 3 0.06
ACGTcount: A:0.29, C:0.03, G:0.44, T:0.24
Consensus pattern (66 bp):
AAGGTGATCTGGAAAGGGTAGAATCTGATGGGGAGGGTGATGATGAAGAGGTACAATCTGATGGT
A
Found at i:29202991 original size:51 final size:51
Alignment explanation
Indices: 29202915--29203018 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
29202905 AAGTTGTTGT
* *
29202915 TGATGAATATGCTGTTGATTTTGCAACATTAGATGGAGTAGATAATGATGC
1 TGATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTAGATAATGATGC
* *
29202966 TGATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGC
1 TGATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTAGATAATGATGC
29203017 TG
1 TG
29203019 CTACAAGTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.29, C:0.09, G:0.28, T:0.35
Consensus pattern (51 bp):
TGATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTAGATAATGATGC
Found at i:29203910 original size:14 final size:14
Alignment explanation
Indices: 29203891--29203919 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29203881 AAGCTTGGTA
29203891 TTGTTTTTTTTATT
1 TTGTTTTTTTTATT
29203905 TTGTTTTTTTTATT
1 TTGTTTTTTTTATT
29203919 T
1 T
29203920 AACTAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (14 bp):
TTGTTTTTTTTATT
Found at i:29208390 original size:37 final size:34
Alignment explanation
Indices: 29208280--29208390 Score: 98
Period size: 37 Copynumber: 3.0 Consensus size: 34
29208270 ATTCCAAAAA
*
29208280 TAATATTATATTAATAGTTTAATATTAAATTTAAT-T
1 TAATATTATCTTAATA--TTAA-ATTAAATTTAATAT
* **
29208316 TAATACTTATCTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATCTTAATATTAAATTA--AATTTAATAT
29208353 TAAAGTGATTATCTTAATATTAAATTAAATTTAATAT
1 T-AA-T-ATTATCTTAATATTAAATTAAATTTAATAT
29208390 T
1 T
29208391 TATCTAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
34 3 0.05
35 2 0.03
36 13 0.21
37 23 0.38
38 2 0.03
39 17 0.28
40 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (34 bp):
TAATATTATCTTAATATTAAATTAAATTTAATAT
Found at i:29217774 original size:22 final size:21
Alignment explanation
Indices: 29217749--29217814 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 21
29217739 TGCGTGCTTG
29217749 TCTAGGTTTGCACTTCGGTGCC
1 TCTA-GTTTGCACTTCGGTGCC
** * *
29217771 TCTA-TTCACAGTTCGGTGTC
1 TCTAGTTTGCACTTCGGTGCC
*
29217791 TC-AGTTTGCACTACGGTGCC
1 TCTAGTTTGCACTTCGGTGCC
29217811 TCTA
1 TCTA
29217815 ATTGCACAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.82
21 1 0.03
22 4 0.12
ACGTcount: A:0.14, C:0.27, G:0.23, T:0.36
Consensus pattern (21 bp):
TCTAGTTTGCACTTCGGTGCC
Found at i:29229989 original size:26 final size:25
Alignment explanation
Indices: 29229960--29230033 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
29229950 ACATATTTCC
29229960 TCAAAATTTTAAC-AGGGGTAAAATCA
1 TCAAAATTTT-ACTA-GGGTAAAATCA
* *
29229986 TCAAAATATTACTAGGGTAAAATCG
1 TCAAAATTTTACTAGGGTAAAATCA
* *
29230011 TTAAAATTTTTCTAGGGTAAAAT
1 TCAAAATTTTACTAGGGTAAAAT
29230034 AGGGATGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 32 0.76
26 10 0.24
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (25 bp):
TCAAAATTTTACTAGGGTAAAATCA
Found at i:29237333 original size:1 final size:1
Alignment explanation
Indices: 29237327--29237351 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
29237317 CTCTCTCTCC
29237327 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
29237352 GCTTATCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29242988 original size:17 final size:19
Alignment explanation
Indices: 29242950--29242989 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
29242940 TCTTTGTTCC
*
29242950 CAATACATTTCATCTTTAT
1 CAATACATTTCATCTGTAT
29242969 CAATACATTTC-TC-GTAT
1 CAATACATTTCATCTGTAT
29242986 CAAT
1 CAAT
29242990 TATCTATGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 2 0.10
19 11 0.55
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.42
Consensus pattern (19 bp):
CAATACATTTCATCTGTAT
Found at i:29244200 original size:16 final size:16
Alignment explanation
Indices: 29244179--29244214 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
29244169 AAATGGAAAG
29244179 TATATAGATATACATA
1 TATATAGATATACATA
29244195 TATATAGATATACATA
1 TATATAGATATACATA
29244211 TATA
1 TATA
29244215 AAAAAGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TATATAGATATACATA
Found at i:29245819 original size:85 final size:86
Alignment explanation
Indices: 29245711--29246163 Score: 262
Period size: 85 Copynumber: 5.3 Consensus size: 86
29245701 TTTTAGTCTA
* * * *
29245711 CTCCACTGCAACTTCAGGGAGATAAGGCTGGATGCGATCTGCTCTACCGTAACTTCATAGATATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACCGCAACTTCAGAGAGATA
* **
29245776 TGATTCAT-T-ATTTTAATTTG
66 AGA-TCATGTGATTTTAATCCG
* *
29245796 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACCGCAACTTCAGAGAGATA
* *
29245861 AGATCTTGTGGTTTTAATCCG
66 AGATCATGTGATTTTAATCCG
* * *** * * * ** *
29245882 CTCCACTGCAACTTCAGGAAGATAGGATTGCTTTTTTTC-ATCTTCTCCACTACTACTT-AGAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA---C-TGGATGCGATCTGCTCTACCGCAACTTCAGAGA
*** *
29245945 GATAAGA-C-TG-GA-TGCGATCTG
62 GATAAGATCATGTGATTTTAATCCG
* * ** * *** * * * *
29245966 CTCTACTACAACTTCAAAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATGCGATCTGCTCTACCGCAACTTCAGAGAG
* * ** *
29246031 ATAGGAT--TG-GTTTCTTCTGTCTG
63 ATAAGATCATGTGATT-TT-AATCCG
* * * * **
29246054 CTCCACTGCAACTTCAGGGAGATAAGGCTGGATGTGATCTGCTGTACTGTGACTTCAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACCGCAACTTCAGAGAGATA
* *
29246119 AGATCTTGTGGTTTTAATCCG
66 AGATCATGTGATTTTAATCCG
**
29246140 CTCCACTAAAACTTCAGGGAGATA
1 CTCCACTGCAACTTCAGGGAGATA
29246164 GGATTGGTTT
Statistics
Matches: 282, Mismatches: 70, Indels: 31
0.74 0.18 0.08
Matches are distributed among these distances:
82 1 0.00
83 4 0.01
84 44 0.16
85 107 0.38
86 61 0.22
87 6 0.02
88 41 0.15
89 16 0.06
90 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (86 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACCGCAACTTCAGAGAGATA
AGATCATGTGATTTTAATCCG
Found at i:29246175 original size:130 final size:129
Alignment explanation
Indices: 29245794--29246297 Score: 760
Period size: 129 Copynumber: 3.9 Consensus size: 129
29245784 TATTTTAATT
*
29245794 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGA
1 TGCTCCACTACAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGA
* * * *
29245859 TAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTGCTTT-TTTTCAT
66 TAAGATC-TGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT-GT
29245923 C
129 C
* * * * * *
29245924 TTCTCCACTACTACTT-AGAGAGATAAGACTGGATGCGATCTGCTCTACTACAACTTCAAAGAGA
1 TGCTCCACTACAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGA
29245988 TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
66 TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
* * * **
29246052 TGCTCCACTGCAACTTCAGGGAGATAAGGCTGGATGTGATCTGCTGTACTGTGACTTCAGAGAGA
1 TGCTCCACTACAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGA
**
29246117 TAAGATCTTGTGGTTTTAATCCGCTCCACTAAAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
66 TAAGATC-TGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
* * *
29246182 TCCTCCACTACAACTTCAGGGAGATAAGATTGGATGTGATCTGCTCTACCGCAACTTCAGAGAGA
1 TGCTCCACTACAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGA
* *
29246247 TAAGATCTGTGATTTTAATCCGTTCCACTGCAACTTCAGGGAGATAGGATT
66 TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
29246298 TGTGACTCTT
Statistics
Matches: 335, Mismatches: 36, Indels: 7
0.89 0.10 0.02
Matches are distributed among these distances:
128 62 0.19
129 141 0.42
130 132 0.39
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (129 bp):
TGCTCCACTACAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGA
TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
Found at i:29246644 original size:129 final size:129
Alignment explanation
Indices: 29246400--29246655 Score: 318
Period size: 129 Copynumber: 2.0 Consensus size: 129
29246390 ATAAAGTCTA
* * * * * *
29246400 ATGCGATCTGCTCTATTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTTCACTGCAA
1 ATGCGATCTGCTCTACTGCAACATCAGAGAGACAAGATCCATCATTTGAATCCACTCCACTGCAA
* * *
29246465 CTTCAGGAAGATATGATTGGTTTCTTCAATCTGCTCCACTGCAACTTCAGGG-AGATAAGATTGG
66 CTTCAGGAAGATAGGATTGGCTTCTTCAATCTGCTCAACTGCAACTTCAGGGAAG-TAAGATTGG
* ** **
29246529 ATGCGATCTGCTCTACTGCAACATCAGAGAGACGAGATCTGTGGTTTGAATCCACTCCACTGCAA
1 ATGCGATCTGCTCTACTGCAACATCAGAGAGACAAGATCCATCATTTGAATCCACTCCACTGCAA
* * * *
29246594 CTTCAGGGAGATAGGATTGGCTTCTTCAATCTGTTTAACTGTAA-TGTCAGGGAAGTAAGATT
66 CTTCAGGAAGATAGGATTGGCTTCTTCAATCTGCTCAACTGCAACT-TCAGGGAAGTAAGATT
29246656 CGCTGTCGTA
Statistics
Matches: 107, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
128 1 0.01
129 104 0.97
130 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (129 bp):
ATGCGATCTGCTCTACTGCAACATCAGAGAGACAAGATCCATCATTTGAATCCACTCCACTGCAA
CTTCAGGAAGATAGGATTGGCTTCTTCAATCTGCTCAACTGCAACTTCAGGGAAGTAAGATTGG
Found at i:29246755 original size:100 final size:100
Alignment explanation
Indices: 29246617--29246937 Score: 462
Period size: 100 Copynumber: 3.2 Consensus size: 100
29246607 GGATTGGCTT
* * * * * * *
29246617 CTTCAATCTGTTTAACTGTAATGTCAGGGAAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCCA
1 CTTCAATCT-TTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
* * * *
29246682 CTACACCACCAGGGAACGTAAGATTCGCCGTTGTGG
65 CTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* * * *
29246718 TTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTTACCGTTGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
* *
29246783 TGCACCGCCTGGGAAAGTAAAATTCACCGTTGTGG
66 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
29246818 CTTCAATCTTTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
* *
29246883 TGCACCGCCTGGGAAAATAAGATTTGCCGTTGTGG
66 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
29246918 CTTCAATCTTTTAATTGCAA
1 CTTCAATCTTTTAATTGCAA
29246938 ACTATGGTTT
Statistics
Matches: 195, Mismatches: 25, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
100 187 0.96
101 8 0.04
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (100 bp):
CTTCAATCTTTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
Found at i:29246762 original size:49 final size:49
Alignment explanation
Indices: 29246701--29246875 Score: 188
Period size: 49 Copynumber: 3.5 Consensus size: 49
29246691 CAGGGAACGT
* * *
29246701 AAGATTCGCCGTTGTGGTTTCAATCTTTTAATTGCAATGTCGGGGAAGC
1 AAGATTCACCGTTGTAGCTTCAATCTTTTAATTGCAATGTCGGGGAAGC
* * ** * ** * * *
29246750 GAGATTTACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAGT
1 AAGATTCACCGTTGTAGCTTCAATCT-TTTAATTGCAATGTC-GGGGAAGC
* * *
29246801 AAAATTCACCGTTGTGGCTTCAATCTTTTAATTGCAATGTCAGGGAAGC
1 AAGATTCACCGTTGTAGCTTCAATCTTTTAATTGCAATGTCGGGGAAGC
29246850 AAGATTCACCGTTGTAGCTTCAATCT
1 AAGATTCACCGTTGTAGCTTCAATCT
29246876 GTTCCACTGC
Statistics
Matches: 96, Mismatches: 28, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
49 50 0.52
50 18 0.19
51 28 0.29
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (49 bp):
AAGATTCACCGTTGTAGCTTCAATCTTTTAATTGCAATGTCGGGGAAGC
Found at i:29246815 original size:51 final size:51
Alignment explanation
Indices: 29246646--29246926 Score: 219
Period size: 51 Copynumber: 5.6 Consensus size: 51
29246636 AATGTCAGGG
* * * * * * *
29246646 AAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCCACTACACCACCAGGGA
1 AAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
* * * * ** * ** * *
29246697 ACGTAAGATTCGCCGTTGTGGTTTCAATCT-TTTAATTGCAATGTC-GGGG
1 AAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
** *
29246746 AAGCGAGATTTACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
1 AAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
* * ** * ** * *
29246797 AAGTAAAATTCACCGTTGTGGCTTCAATCT-TTTAATTGCAATGTCAGGG-
1 AAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
*
29246846 AAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
1 AAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
* ** *
29246897 AAATAAGATTTGCCGTTGTGGCTTCAATCT
1 AAGTAAGATTCACCGTTGTAGCTTCAATCT
29246927 TTTAATTGCA
Statistics
Matches: 171, Mismatches: 55, Indels: 8
0.73 0.24 0.03
Matches are distributed among these distances:
49 53 0.31
50 40 0.23
51 78 0.46
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (51 bp):
AAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGA
Found at i:29247042 original size:46 final size:46
Alignment explanation
Indices: 29246992--29247725 Score: 1049
Period size: 46 Copynumber: 16.0 Consensus size: 46
29246982 AGATCTACAG
* * * *
29246992 TCTTCGATCTACTCCGCTGCCAAATACAAGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
* * *
29247038 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGATAAGATCTTCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
*
29247084 TCTTCGATCTCCTCCACTACCAAATACAGGAAGATAAGATCTGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
* * * *
29247130 TCTTTGATCTCATTCACTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
*
29247176 TCTTCGATCTCCTCCACTGCCAAATACAGAAAGATAAGATCTGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
* ** *
29247222 TCTTCGA-CCCACTCTGCTGCCAAATACAGGAAGATAAGATCTTCTA
1 TCTTCGATCTC-CTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
*
29247268 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
*
29247314 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCCGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
* * *
29247360 TCTTCGATCTCCTCC-GTGCCAAATACAGTAAGATAAGATCCGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
* * * * *
29247405 TCTTTGATCTCCTCCTCTGCCAAATACAAGAAGACAATATCTGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
* * *
29247451 TTTTTGATCTCCTCCGCTGCCAAATACAGGAAGATAAGATCTGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
* * ** *
29247497 TTTTTGATCTCCTCTGCTGCCAAATACAGGAAGATAAGATCCGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
* *
29247543 TCTTCGATCTCCTCTACTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
* *
29247589 TCTTCGATCTACTCCACTGCCAAATACAGGAAGATAAGATCCGCTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
* *
29247635 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCCGTTA
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
* **
29247681 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACGAGATCTGCT
1 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCT
29247726 GCTTCTAGTC
Statistics
Matches: 624, Mismatches: 61, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
45 44 0.07
46 578 0.93
47 2 0.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (46 bp):
TCTTCGATCTCCTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
Found at i:29248150 original size:24 final size:24
Alignment explanation
Indices: 29248097--29248152 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
29248087 ATTGCCCTCT
29248097 ACTGTAATCTTCAGAGTTCAATCC
1 ACTGTAATCTTCAGAGTTCAATCC
** *
29248121 GTTGTAATCTTCA-AGGTTCAGTCC
1 ACTGTAATCTTCAGA-GTTCAATCC
29248145 ACTGTAAT
1 ACTGTAAT
29248153 TTTGGGACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (24 bp):
ACTGTAATCTTCAGAGTTCAATCC
Found at i:29248784 original size:97 final size:97
Alignment explanation
Indices: 29248618--29248920 Score: 362
Period size: 97 Copynumber: 3.0 Consensus size: 97
29248608 GTAAAATGCT
*
29248618 TGAAAAAGATTATCA-ATATGGACAAGATGAAATTTTATTGAGAACAAAGCTCAAAATGAATAAA
1 TGAAAAAGATTATCACA-ATGGACAAGATGAAATTTTATTGAGAACAAAGCTCAAAATAAATAAA
*
29248682 TTAATCAAGATAACAAATTTTGCTAAGATAAGA
65 TTAATCAAGATAGCAAATTTTGCTAAGATAAGA
* * * *
29248715 TGAAAAAGATTATCACAATGGGA-AAGATGAAATTTTATTGAGAGCAGAGCTCTAAACAAATAAA
1 TGAAAAAGATTATCACAAT-GGACAAGATGAAATTTTATTGAGAACAAAGCTCAAAATAAATAAA
*
29248779 TTAATCAGGATAGCAAATTTTGCTAAGATTCAAAATGAA
65 TTAATCAAGATAGCAAATTTTGCTAAGA-T---AA-G-A
**
29248818 TAAGATGAAAATGATTATCACAATGGACAAGATGAAATTTTATTGAGAACAAAGCTCGCAATAAA
1 T--GA--AAAA-GATTATCACAATGGACAAGATGAAATTTTATTGAGAACAAAGCTCAAAATAAA
* *
29248883 TAAA-TAATCAAGATAGCAAA-TTTGCTAAGTTACGA
61 TAAATTAATCAAGATAGCAAATTTTGCTAAGATAAGA
29248918 TGA
1 TGA
29248921 GAATAAATTA
Statistics
Matches: 177, Mismatches: 15, Indels: 27
0.81 0.07 0.12
Matches are distributed among these distances:
97 79 0.45
98 7 0.04
100 2 0.01
101 3 0.02
102 2 0.01
103 2 0.01
105 3 0.02
106 9 0.05
107 22 0.12
108 48 0.27
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (97 bp):
TGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAACAAAGCTCAAAATAAATAAAT
TAATCAAGATAGCAAATTTTGCTAAGATAAGA
Found at i:29248834 original size:108 final size:106
Alignment explanation
Indices: 29248709--29248911 Score: 309
Period size: 108 Copynumber: 1.9 Consensus size: 106
29248699 TTTTGCTAAG
* * *
29248709 ATAAGATGAAAAAGATTATCACAATGGGA-AAGATGAAATTTTATTGAGAGCAGAGCTCTAAACA
1 ATAAGATGAAAAAGATTATCACAAT-GGACAAGATGAAATTTTATTGAGAACAAAGCTCGAAACA
*
29248773 AATAAATTAATCAGGATAGCAAATTTTGCTAAGATTCAAAATGA
65 AATAAA-TAATCAAGATAGCAAA-TTTGCTAAGATTCAAAATGA
* * *
29248817 ATAAGATGAAAATGATTATCACAATGGACAAGATGAAATTTTATTGAGAACAAAGCTCGCAATAA
1 ATAAGATGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAACAAAGCTCGAAACAA
29248882 ATAAATAATCAAGATAGCAAATTTGCTAAG
66 ATAAATAATCAAGATAGCAAATTTGCTAAG
29248912 TTACGATGAG
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
106 9 0.10
107 18 0.21
108 60 0.69
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.26
Consensus pattern (106 bp):
ATAAGATGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAACAAAGCTCGAAACAA
ATAAATAATCAAGATAGCAAATTTGCTAAGATTCAAAATGA
Found at i:29254050 original size:11 final size:11
Alignment explanation
Indices: 29254034--29254073 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
29254024 CGCAAATACG
29254034 TATAAATATTA
1 TATAAATATTA
29254045 TATAAATATATA
1 TATAAATAT-TA
29254057 TATATAATA-TA
1 TATA-AATATTA
29254068 TATAAA
1 TATAAA
29254074 AATGTGCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
12 6 0.22
13 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATAAATATTA
Found at i:29254113 original size:16 final size:16
Alignment explanation
Indices: 29254092--29254123 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29254082 TGTGAGATAT
29254092 AAATAAAATAAAAATA
1 AAATAAAATAAAAATA
*
29254108 AAATAAGATAAAAATA
1 AAATAAAATAAAAATA
29254124 TATATATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAATAAAATAAAAATA
Found at i:29263724 original size:4 final size:4
Alignment explanation
Indices: 29263715--29263747 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
29263705 GGGGTGTTAT
29263715 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
29263748 AATCAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:29264666 original size:23 final size:22
Alignment explanation
Indices: 29264606--29264666 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
29264596 ATAATTTTGA
29264606 TATTTTATAATATATAAACAATTT
1 TATTTTAT-ATA-ATAAACAATTT
* * *
29264630 TATTTCAATGTAATAATCAATTT
1 TATTT-TATATAATAAACAATTT
29264653 TACTTTTATATAAT
1 TA-TTTTATATAAT
29264667 GATAATAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
23 18 0.60
24 10 0.33
25 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTTTATATAATAAACAATTT
Found at i:29266396 original size:20 final size:20
Alignment explanation
Indices: 29266342--29266396 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
29266332 GATACTAACT
* **
29266342 TAAAAATATCGATAATTTTA
1 TAAAAATATCGATACTCGTA
* *
29266362 TAAAAATATCAATACTCGTG
1 TAAAAATATCGATACTCGTA
29266382 TAAAAATATCGATAC
1 TAAAAATATCGATAC
29266397 CACTAACGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (20 bp):
TAAAAATATCGATACTCGTA
Found at i:29271338 original size:23 final size:23
Alignment explanation
Indices: 29271312--29271371 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
29271302 ATTTTTTATA
* *
29271312 TAAATCTAATCATAATAATTAAC
1 TAAATATAATAATAATAATTAAC
* *
29271335 TAAATATAATAATTATAATTACC
1 TAAATATAATAATAATAATTAAC
*
29271358 ATAATTATAATAAT
1 -TAAATATAATAAT
29271372 TTTTGACCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAATATAATAATAATAATTAAC
Found at i:29274814 original size:8 final size:8
Alignment explanation
Indices: 29274799--29274831 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
29274789 ATAAAATGTG
29274799 AAAA-AAA
1 AAAAGAAA
29274806 AAAAGAAA
1 AAAAGAAA
29274814 AAAAGAAAA
1 AAAAG-AAA
29274823 AAAAGAAA
1 AAAAGAAA
29274831 A
1 A
29274832 CATGATATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 4 0.17
8 12 0.50
9 8 0.33
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:29274814 original size:9 final size:9
Alignment explanation
Indices: 29274802--29274831 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29274792 AAATGTGAAA
29274802 AAAAAAAAG
1 AAAAAAAAG
29274811 -AAAAAAAG
1 AAAAAAAAG
29274819 AAAAAAAAG
1 AAAAAAAAG
29274828 AAAA
1 AAAA
29274832 CATGATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:29278622 original size:12 final size:12
Alignment explanation
Indices: 29278607--29278634 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
29278597 AAAATGTAAA
29278607 AAAAAAAAAAAG
1 AAAAAAAAAAAG
29278619 AAAAAAAAAAAG
1 AAAAAAAAAAAG
29278631 AAAA
1 AAAA
29278635 CATGATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:29278865 original size:11 final size:10
Alignment explanation
Indices: 29278838--29278862 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29278828 TTTATATTCA
29278838 TAATTATTTT
1 TAATTATTTT
29278848 TAATTATTTT
1 TAATTATTTT
29278858 TAATT
1 TAATT
29278863 TATAACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TAATTATTTT
Found at i:29280660 original size:21 final size:20
Alignment explanation
Indices: 29280636--29280699 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
29280626 GTGGGGGTCA
* *
29280636 ACACGCCCATGTGAAGGAGGC
1 ACACACCCATGTGAA-GAAGC
*
29280657 ACACACCCGTGTGAAGAAGC
1 ACACACCCATGTGAAGAAGC
* *
29280677 ACACACTCGTGTGAAGAAGC
1 ACACACCCATGTGAAGAAGC
29280697 ACA
1 ACA
29280700 AGCCTGTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 26 0.67
21 13 0.33
ACGTcount: A:0.34, C:0.28, G:0.27, T:0.11
Consensus pattern (20 bp):
ACACACCCATGTGAAGAAGC
Found at i:29280680 original size:20 final size:20
Alignment explanation
Indices: 29280645--29280699 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
29280635 AACACGCCCA
*
29280645 TGTGAAGGAGGCACACACCCG
1 TGTGAA-GAAGCACACACCCG
*
29280666 TGTGAAGAAGCACACACTCG
1 TGTGAAGAAGCACACACCCG
29280686 TGTGAAGAAGCACA
1 TGTGAAGAAGCACA
29280700 AGCCTGTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.35, C:0.24, G:0.29, T:0.13
Consensus pattern (20 bp):
TGTGAAGAAGCACACACCCG
Found at i:29286209 original size:26 final size:26
Alignment explanation
Indices: 29286179--29286231 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
29286169 TTCCAAAATT
*
29286179 TAGTCCAA-ATTAGTACTTTACAAAAA
1 TAGTCCAAGATTA-AACTTTACAAAAA
*
29286205 TAGTCCAAGATTAAAGTTTACAAAAA
1 TAGTCCAAGATTAAACTTTACAAAAA
29286231 T
1 T
29286232 CTGGAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.30
Consensus pattern (26 bp):
TAGTCCAAGATTAAACTTTACAAAAA
Found at i:29291480 original size:13 final size:13
Alignment explanation
Indices: 29291454--29291493 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
29291444 CACCATTTGT
29291454 AAACAGACATACAG
1 AAACAGA-ATACAG
29291468 AAACAGAATACAG
1 AAACAGAATACAG
*
29291481 AACCAGAAATACA
1 AAACAG-AATACA
29291494 CACATTCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.60, C:0.20, G:0.12, T:0.07
Consensus pattern (13 bp):
AAACAGAATACAG
Found at i:29291801 original size:20 final size:20
Alignment explanation
Indices: 29291776--29291813 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29291766 AGTCACATGA
*
29291776 CTGTGTGAAGATGCACTCGC
1 CTGTGTGAAGAAGCACTCGC
29291796 CTGTGTGAAGAAGCACTC
1 CTGTGTGAAGAAGCACTC
29291814 ACCCATGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (20 bp):
CTGTGTGAAGAAGCACTCGC
Found at i:29291822 original size:20 final size:20
Alignment explanation
Indices: 29291779--29291823 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29291769 CACATGACTG
* * **
29291779 TGTGAAGATGCACTCGCCTG
1 TGTGAAGAAGCACTCACCCA
29291799 TGTGAAGAAGCACTCACCCA
1 TGTGAAGAAGCACTCACCCA
29291819 TGTGA
1 TGTGA
29291824 GAGGAGGCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (20 bp):
TGTGAAGAAGCACTCACCCA
Found at i:29294961 original size:14 final size:15
Alignment explanation
Indices: 29294940--29294977 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
29294930 AATTGAATGA
29294940 ATAAATTTTGTATAC
1 ATAAATTTTGTATAC
*
29294955 A-AAA-TTTGTATAT
1 ATAAATTTTGTATAC
29294968 ATAAATTTTG
1 ATAAATTTTG
29294978 AATATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 9 0.45
14 6 0.30
15 5 0.25
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (15 bp):
ATAAATTTTGTATAC
Found at i:29294977 original size:15 final size:15
Alignment explanation
Indices: 29294940--29294983 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
29294930 AATTGAATGA
*
29294940 ATAAATTTTGTATAC
1 ATAAATTTTGTATAT
29294955 A-AAA-TTTGTATAT
1 ATAAATTTTGTATAT
*
29294968 ATAAATTTTGAATAT
1 ATAAATTTTGTATAT
29294983 A
1 A
29294984 AAAAGTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 9 0.36
14 6 0.24
15 10 0.40
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (15 bp):
ATAAATTTTGTATAT
Found at i:29297568 original size:30 final size:30
Alignment explanation
Indices: 29297523--29297610 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
29297513 ATTTTAGGAG
*
29297523 CCACGCGGGCTGGGCACACACCCATGTGAC
1 CCACACGGGCTGGGCACACACCCATGTGAC
* * *
29297553 CCATACGGTCTGGGCACACGA-CTATGTGAC
1 CCACACGGGCTGGGCACAC-ACCCATGTGAC
* * *
29297583 CCACACGGGCTAGACACACGCCCATGTG
1 CCACACGGGCTGGGCACACACCCATGTG
29297611 CCAGCTCGTG
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
30 45 0.98
31 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.27, T:0.14
Consensus pattern (30 bp):
CCACACGGGCTGGGCACACACCCATGTGAC
Found at i:29302247 original size:4 final size:4
Alignment explanation
Indices: 29302238--29302310 Score: 79
Period size: 4 Copynumber: 19.8 Consensus size: 4
29302228 CCTTTTTCTT
*
29302238 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTCTT TTTA -TTA TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA
29302284 TTTA -TTA -TTA -TTA -TTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
29302311 TTCATTTCTC
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
3 21 0.34
4 38 0.61
5 3 0.05
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:29302277 original size:3 final size:3
Alignment explanation
Indices: 29302259--29302301 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
29302249 ATTTATTTAT
* *
29302259 TTA TTA TTC TTT TTA TTA TTTA TTA TTTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TT
29302302 TATTTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:29302277 original size:23 final size:23
Alignment explanation
Indices: 29302246--29302309 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
29302236 TTTTTATTTA
*
29302246 TTTATTTATTTATTTATTATTCTT
1 TTTA-TTATTTATTTATTATTATT
29302270 TTTATTATTTA-TTATTTATTATT
1 TTTATTATTTATTTA-TTATTATT
*
29302293 ATTATTATTTATTTATT
1 TTTATTATTTATTTATT
29302310 TTTCATTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
22 3 0.08
23 26 0.72
24 7 0.19
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTATTATTTATTTATTATTATT
Found at i:29302435 original size:20 final size:19
Alignment explanation
Indices: 29302398--29302436 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
29302388 TTGTTATCCA
*
29302398 TTTTTATTTTTTTCTTTGT
1 TTTTTATTTTTTTATTTGT
29302417 TTTTTATTTTTATTATTTGT
1 TTTTTATTTTT-TTATTTGT
29302437 ATTAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.82
Consensus pattern (19 bp):
TTTTTATTTTTTTATTTGT
Found at i:29304111 original size:21 final size:21
Alignment explanation
Indices: 29304087--29304127 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29304077 TTCTTTTCTT
29304087 TTTAGTTTTAGTTTTATTTTC
1 TTTAGTTTTAGTTTTATTTTC
* *
29304108 TTTATTTTTATTTTTATTTT
1 TTTAGTTTTAGTTTTATTTT
29304128 TAGTTGTTTT
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:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTAGTTTTAGTTTTATTTTC
Found at i:29304115 original size:27 final size:27
Alignment explanation
Indices: 29304072--29304144 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
29304062 GATCATTGAG
*
29304072 TTTA-TTTCTTTTCTTTTTAGTTTTAGT
1 TTTATTTTC-TTTATTTTTAGTTTTAGT
* *
29304099 TTTATTTTCTTTATTTTTATTTTTATT
1 TTTATTTTCTTTATTTTTAGTTTTAGT
*
29304126 TTTAGTTGT-TTTATTTTTA
1 TTTA-TTTTCTTTATTTTTA
29304145 TGTCCTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 33 0.82
28 7 0.17
ACGTcount: A:0.14, C:0.04, G:0.05, T:0.77
Consensus pattern (27 bp):
TTTATTTTCTTTATTTTTAGTTTTAGT
Found at i:29304116 original size:15 final size:14
Alignment explanation
Indices: 29304092--29304145 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
29304082 TTCTTTTTAG
*
29304092 TTTTAGTTTTATTT
1 TTTTATTTTTATTT
29304106 TCTTTATTTTTA--T
1 T-TTTATTTTTATTT
*
29304119 TTTTATTTTTAGTTG
1 TTTTATTTTTA-TTT
29304134 TTTTATTTTTAT
1 TTTTATTTTTAT
29304146 GTCCTTAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 10 0.29
13 2 0.06
14 2 0.06
15 20 0.59
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.78
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:29304143 original size:6 final size:6
Alignment explanation
Indices: 29304080--29304145 Score: 51
Period size: 6 Copynumber: 10.0 Consensus size: 6
29304070 AGTTTATTTC
* * *
29304080 TTTTCT TTTTAG TTTTAGT TTTATTT TCTTTAT TTTTAT TTTTAT TTTTAGTT
1 TTTTAT TTTTAT TTTTA-T TTT-TAT T-TTTAT TTTTAT TTTTAT TTTTA--T
29304133 GTTTTAT TTTTAT
1 -TTTTAT TTTTAT
29304146 GTCCTTAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
6 31 0.63
7 9 0.18
8 4 0.08
9 5 0.10
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:29316413 original size:26 final size:26
Alignment explanation
Indices: 29316356--29316432 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 26
29316346 ACACCAATAT
* * * * *
29316356 CGCAGCAGAGCTGCCAGTGATAATGA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
*
29316382 CACAGCAAAGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
* *
29316408 CGCAGCAACGCTGCCCGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAACAGTA
29316433 TATGTGGCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.34, C:0.29, G:0.25, T:0.13
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:29316628 original size:27 final size:27
Alignment explanation
Indices: 29316605--29316758 Score: 170
Period size: 27 Copynumber: 5.7 Consensus size: 27
29316595 AGGGGTATAA
*
29316605 CAGTTATTTTACCCTTCGGAGGTATTT
1 CAGTAATTTTACCCTTCGGAGGTATTT
* * *
29316632 CGGTAATTTTATCCTTCGGGGGTATTT
1 CAGTAATTTTACCCTTCGGAGGTATTT
29316659 CAGTAATTTTACCCTTC-GAGAGTATTT
1 CAGTAATTTTACCCTTCGGAG-GTATTT
* *
29316686 CAGTAATTTTACCCTT-TGAGGGTGTTT
1 CAGTAATTTTACCCTTCGGA-GGTATTT
** *
29316713 TGGTAATTTTTCCCTTC-GAGGGTATTT
1 CAGTAATTTTACCCTTCGGA-GGTATTT
*
29316740 TAGTAATTTTACCCTTCGG
1 CAGTAATTTTACCCTTCGG
29316759 TAATCTTACT
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.02
27 104 0.96
28 2 0.02
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (27 bp):
CAGTAATTTTACCCTTCGGAGGTATTT
Found at i:29316684 original size:54 final size:54
Alignment explanation
Indices: 29316596--29316758 Score: 193
Period size: 54 Copynumber: 3.0 Consensus size: 54
29316586 TCAACTACTA
** * * *
29316596 GGGGTATAACAGTTATTTTACCCTTCG-GAGGTATTTCGGTAATTTTATCCTTCG
1 GGGGTATTTCAGTAATTTTACCCTTCGAGA-GTATTTCAGTAATTTTACCCTTCG
*
29316650 GGGGTATTTCAGTAATTTTACCCTTCGAGAGTATTTCAGTAATTTTACCCTTTG
1 GGGGTATTTCAGTAATTTTACCCTTCGAGAGTATTTCAGTAATTTTACCCTTCG
* * ** * * *
29316704 AGGGTGTTTTGGTAATTTTTCCCTTCGAGGGTATTTTAGTAATTTTACCCTTCG
1 GGGGTATTTCAGTAATTTTACCCTTCGAGAGTATTTCAGTAATTTTACCCTTCG
29316758 G
1 G
29316759 TAATCTTACT
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
54 91 0.98
55 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (54 bp):
GGGGTATTTCAGTAATTTTACCCTTCGAGAGTATTTCAGTAATTTTACCCTTCG
Found at i:29316745 original size:81 final size:81
Alignment explanation
Indices: 29316605--29316757 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
29316595 AGGGGTATAA
* *
29316605 CAGTTATTTTACCCTTCGGAGGTATTTCGGTAATTTTATCCTTCGGGGGTATTTCAGTAATTTTA
1 CAGTAATTTTACCCTTCGGAGGTATTTCGGTAATTTTATCCTTCGAGGGTATTTCAGTAATTTTA
29316670 CCCTTCGAGAGTATTT
66 CCCTTCGAGAGTATTT
* * * *
29316686 CAGTAATTTTACCCTT-TGAGGGTGTTTTGGTAATTTT-TCCCTTCGAGGGTATTTTAGTAATTT
1 CAGTAATTTTACCCTTCGGA-GGTATTTCGGTAATTTTAT-CCTTCGAGGGTATTTCAGTAATTT
29316749 TACCCTTCG
64 TACCCTTCG
29316758 GTAATCTTAC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
80 3 0.05
81 61 0.95
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (81 bp):
CAGTAATTTTACCCTTCGGAGGTATTTCGGTAATTTTATCCTTCGAGGGTATTTCAGTAATTTTA
CCCTTCGAGAGTATTT
Found at i:29316762 original size:43 final size:43
Alignment explanation
Indices: 29316714--29316801 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
29316704 AGGGTGTTTT
* * * *
29316714 GGTAATTTTTCCCTTCGAGGGTATTTTAGTAATTTTACCCTTC
1 GGTAATCTTACCCTTCGAGGATATTTCAGTAATTTTACCCTTC
* *
29316757 GGTAATCTTACTCTTTGAGGATATTTCAGTAATTTTACCCTTC
1 GGTAATCTTACCCTTCGAGGATATTTCAGTAATTTTACCCTTC
29316800 GG
1 GG
29316802 GAATAATTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.44
Consensus pattern (43 bp):
GGTAATCTTACCCTTCGAGGATATTTCAGTAATTTTACCCTTC
Found at i:29316789 original size:70 final size:70
Alignment explanation
Indices: 29316688--29316827 Score: 165
Period size: 70 Copynumber: 2.0 Consensus size: 70
29316678 GAGTATTTCA
* * * ** * * * * *
29316688 GTAATTTTACCCTTTGAGGGTGTTTTGGTAATTTTTCCCTTCGAGG-GTATTTTAGTAATTTTAC
1 GTAATCTTACCCTTTGAGGATATTTCAGTAATTTTACCCTTCG-GGAATAATTCAATAATTTTAC
29316752 CCTTCG
65 CCTTCG
*
29316758 GTAATCTTACTCTTTGAGGATATTTCAGTAATTTTACCCTTCGGGAATAATTCAATAATTTTACC
1 GTAATCTTACCCTTTGAGGATATTTCAGTAATTTTACCCTTCGGGAATAATTCAATAATTTTACC
29316823 CTTCG
66 CTTCG
29316828 TGGGTAAGTC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
69 2 0.03
70 56 0.97
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (70 bp):
GTAATCTTACCCTTTGAGGATATTTCAGTAATTTTACCCTTCGGGAATAATTCAATAATTTTACC
CTTCG
Found at i:29317380 original size:18 final size:19
Alignment explanation
Indices: 29317343--29317380 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
29317333 AATGGCCAAC
**
29317343 AAGAGAAGAAGAAACTAAA
1 AAGAGAAGAAGAAAAGAAA
29317362 AAGA-AAGAAGAAAAGAAA
1 AAGAGAAGAAGAAAAGAAA
29317380 A
1 A
29317381 GATGAGGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (19 bp):
AAGAGAAGAAGAAAAGAAA
Found at i:29323105 original size:20 final size:20
Alignment explanation
Indices: 29323067--29323105 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29323057 AACTTAGACT
*
29323067 TGTTGATAAAATTCATTTCA
1 TGTTGATAAAACTCATTTCA
*
29323087 TGTTGATAAAACTCGTTTC
1 TGTTGATAAAACTCATTTC
29323106 GTTATTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
TGTTGATAAAACTCATTTCA
Found at i:29324037 original size:27 final size:27
Alignment explanation
Indices: 29324007--29324177 Score: 193
Period size: 27 Copynumber: 6.3 Consensus size: 27
29323997 TATAACAGTT
*
29324007 ATTTTA-CCTTTCGGGGGTATTTTAGTA
1 ATTTTACCCTTT-GAGGGTATTTTAGTA
* *
29324034 ATTTTACCCTTTAAGGGCATTTTAGTA
1 ATTTTACCCTTTGAGGGTATTTTAGTA
* *
29324061 ATTTTACCCTTTGAGGGTATTTCAATA
1 ATTTTACCCTTTGAGGGTATTTTAGTA
29324088 ATTTTACCCTTTGAGGGTATTTTAGTA
1 ATTTTACCCTTTGAGGGTATTTTAGTA
* * * **
29324115 ATTTTACTCTTTAAGGGTAATTCGGTA
1 ATTTTACCCTTTGAGGGTATTTTAGTA
* * *
29324142 ATTTTACCCTTCGAGGGTAATTT-GATC
1 ATTTTACCCTTTGAGGGTATTTTAG-TA
29324169 ATTTTACCC
1 ATTTTACCC
29324178 ATGATTCACA
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
26 1 0.01
27 117 0.95
28 5 0.04
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTTTGAGGGTATTTTAGTA
Found at i:29324115 original size:81 final size:82
Alignment explanation
Indices: 29324007--29324177 Score: 231
Period size: 81 Copynumber: 2.1 Consensus size: 82
29323997 TATAACAGTT
* * *
29324007 ATTTTA-CCTTTCGGGGGTATTTTAGTAATTTTACCCTTTAAGGGCATTTTAGTAATTTTACCCT
1 ATTTTACCCTTTCGAGGGTATTTTAGTAATTTTACCCTTTAAGGGCAATTCAGTAATTTTACCCT
*
29324071 TTGAGGGT-ATTTCAATA
66 TCGAGGGTAATTT-AATA
* * *
29324088 ATTTTACCCTTT-GAGGGTATTTTAGTAATTTTACTCTTTAAGGGTAATTCGGTAATTTTACCCT
1 ATTTTACCCTTTCGAGGGTATTTTAGTAATTTTACCCTTTAAGGGCAATTCAGTAATTTTACCCT
* *
29324152 TCGAGGGTAATTTGATC
66 TCGAGGGTAATTTAATA
29324169 ATTTTACCC
1 ATTTTACCC
29324178 ATGATTCACA
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
81 70 0.89
82 9 0.11
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (82 bp):
ATTTTACCCTTTCGAGGGTATTTTAGTAATTTTACCCTTTAAGGGCAATTCAGTAATTTTACCCT
TCGAGGGTAATTTAATA
Found at i:29325071 original size:17 final size:19
Alignment explanation
Indices: 29325035--29325074 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
29325025 AATTGGCAAC
*
29325035 AAGAGAAGAAGAAACTGAA
1 AAGAGAAGAAGAAACAGAA
29325054 AAGA-AAGAAGAAA-AGAA
1 AAGAGAAGAAGAAACAGAA
29325071 AAGA
1 AAGA
29325075 TGAGGGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.70, C:0.03, G:0.25, T:0.03
Consensus pattern (19 bp):
AAGAGAAGAAGAAACAGAA
Found at i:29336413 original size:50 final size:49
Alignment explanation
Indices: 29336355--29336505 Score: 146
Period size: 50 Copynumber: 3.0 Consensus size: 49
29336345 TAACTGTGAT
*
29336355 GTCTGGGAAGCAAGATTCGCCATTGCGGCTTCAATCTGTTCCACTGCACC
1 GTCTGGGAAGCAAGATTCGCC-TTGCGGCTTTAATCTGTTCCACTGCACC
* ** **
29336405 GTCTGGGAAGCAAAATTCG--TTGCAGTAGCTTTAATCT-TCTTAACTGCAAT
1 GTCTGGGAAGCAAGATTCGCCTTGC-G--GCTTTAATCTGT-TCCACTGCACC
* * *
29336455 GTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACC
1 GTCTGGGAAGCAAGATTCGCC-TTGCGGCTTTAATCTGTTCCACTGCACC
29336505 G
1 G
29336506 CCAAGGGAGT
Statistics
Matches: 79, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
47 4 0.05
48 1 0.01
49 1 0.01
50 68 0.86
51 1 0.01
52 1 0.01
53 3 0.04
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (49 bp):
GTCTGGGAAGCAAGATTCGCCTTGCGGCTTTAATCTGTTCCACTGCACC
Found at i:29336726 original size:46 final size:46
Alignment explanation
Indices: 29336673--29336791 Score: 166
Period size: 46 Copynumber: 2.6 Consensus size: 46
29336663 ATCTGCTCCG
* ** * *
29336673 CTGTAATCTCTGGGAGATAAGATTTGAGATTCCTCGATCTATTCCA
1 CTGTAATCTCAGGGAGATAAGACCTGAAATACCTCGATCTATTCCA
* * *
29336719 CTGTAATCTCAGGGAGATAAGACCTGAAATACTTTGGTCTATTCCA
1 CTGTAATCTCAGGGAGATAAGACCTGAAATACCTCGATCTATTCCA
29336765 CTGTAATCTCAGGGAGATAAGACCTGA
1 CTGTAATCTCAGGGAGATAAGACCTGA
29336792 TGCGATCTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (46 bp):
CTGTAATCTCAGGGAGATAAGACCTGAAATACCTCGATCTATTCCA
Found at i:29336876 original size:221 final size:221
Alignment explanation
Indices: 29336524--29336925 Score: 651
Period size: 221 Copynumber: 1.8 Consensus size: 221
29336514 GTAAGGTCTA
*
29336524 AAATTCTTCGGTCTATTCCACTATAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTAT
1 AAATACTTCGGTCTATTCCACTATAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTAT
**
29336589 AACTTCAGAGAGATAAGATCCTTTATGTTAATCCACTCCACTGTAATCTCAAGGAGATAGGATTA
66 AACTTCAGAGAGATAAGATCCTTTATGTTAATCCACTCCACAATAATCTCAAGGAGATAGGATTA
* * * *
29336654 CTAGCTTCAATCTGCTCCGCTGTAATCTCTGGGAGATAAGATTTGAGATTCCTCGATCTATTCCA
131 CTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCCTCGATCTATTCCA
29336719 CTGTAATCTCAGGGAGATAAGACCTG
196 CTGTAATCTCAGGGAGATAAGACCTG
* * *
29336745 AAATACTTTGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
1 AAATACTTCGGTCTATTCCACTATAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTAT
* *** *
29336810 AACTTCAGAGAGATAAGATCCTTTATTTTAATCTGGTCCACAATAATCTCAGGGAGATAGGATTA
66 AACTTCAGAGAGATAAGATCCTTTATGTTAATCCACTCCACAATAATCTCAAGGAGATAGGATTA
* *
29336875 CTGGCTTCAATCTGCTCCATTGTAATCTCAGGGAGATAAGATCTGAAATTC
131 CTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTC
29336926 TTTGGTCTAT
Statistics
Matches: 164, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
221 164 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (221 bp):
AAATACTTCGGTCTATTCCACTATAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTAT
AACTTCAGAGAGATAAGATCCTTTATGTTAATCCACTCCACAATAATCTCAAGGAGATAGGATTA
CTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCCTCGATCTATTCCA
CTGTAATCTCAGGGAGATAAGACCTG
Found at i:29345175 original size:14 final size:14
Alignment explanation
Indices: 29345156--29345185 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29345146 TATAAAAATG
*
29345156 TAAGTATGTATGTA
1 TAAGTATGTATATA
29345170 TAAGTATGTATATA
1 TAAGTATGTATATA
29345184 TA
1 TA
29345186 TAACATAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (14 bp):
TAAGTATGTATATA
Found at i:29346821 original size:130 final size:130
Alignment explanation
Indices: 29346545--29347580 Score: 1671
Period size: 130 Copynumber: 8.0 Consensus size: 130
29346535 TGTGGTTTTA
* * * * * *
29346545 GTCTACTCCACTGCAACTTCAGGGAGATAAGGCTGGATGCGATATGCTCTACCGCAACTTCATAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
* * ** * * ** *
29346610 ATATATGAT-TCATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTTT
66 AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
* *
29346674 GTCTGCTCCACTGCAACTTCAGGGAAATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
* * * *
29346739 AGATATGATCTTGTGGTTTTAATCCGCTCTACTGCAAATTCAGGTAGATAGGATTGGTTTCTTCT
66 AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
* *
29346804 GTCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
29346869 AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
66 AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
* *
29346934 GTCTGCTCCACTACAACTTCAGGGAGATAAGAGTGGATGTGATCTGCTCTACTGCAACTTCAGAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
* * *
29346999 AGATATGATCTTGTGGTTTTAATCCGCTCCACTGCAAATTCAGGGAGATAGGATTGGTTTCTTAT
66 AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
* *
29347064 GTCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGTGATCTACTCTACTGCAACTTCAGAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
*
29347129 AGATAAGATCTTGTGGTTTTAATCAGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
66 AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
*
29347194 GTCTGCTCCACTACAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
29347259 AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
66 AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
* * * *
29347324 GTCTGCTCCGCTGCAACTTTAGGGAGATAAGACTTGATGTGATTTGCTCTACTGCAACTTCAGAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
* * *
29347389 AAATAAGATCTTGTGGTTTTAATCCGTTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCT
66 AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
* * *
29347454 GTCTGCTCCACTACAACTTCAGGGAGATAAGACTGGATGTGATCTGTTCTACTGTAACTTCAGAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
*
29347519 AGATAAGAT-TTGTGGTTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTGGTTTCTT
66 AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTT
29347581 TCGTCTATTT
Statistics
Matches: 843, Mismatches: 63, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
129 115 0.14
130 728 0.86
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (130 bp):
GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
Found at i:29347715 original size:50 final size:50
Alignment explanation
Indices: 29347594--29347835 Score: 173
Period size: 50 Copynumber: 4.9 Consensus size: 50
29347584 TCTATTTAAC
* * * ** *
29347594 TGCAATGTCAGGGAAACAAGATTCACCGTCGTAGCTTCAAT-TTGTTCCAC
1 TGCAATATCAGGGAAGCAAGATTCACCATCGTAGCTTCAATCTT-TTAAAT
* ** * ** * *
29347644 TACACCACCAAAGAAGTAAGATTCACCATCGTGGCTTCAATCTTTTAAAT
1 TGCAATATCAGGGAAGCAAGATTCACCATCGTAGCTTCAATCTTTTAAAT
* * ** ** *
29347694 TGCAATATCAGGGAAGCAAGATTCGCCATCGTAGCTTTAATCTACTCCAC
1 TGCAATATCAGGGAAGCAAGATTCACCATCGTAGCTTCAATCTTTTAAAT
* * ** * * ** *
29347744 TGTACTGCCAGGGAAGTAAGATTCGCTGTCGTGGCTTCAAT-TTTTAAAT
1 TGCAATATCAGGGAAGCAAGATTCACCATCGTAGCTTCAATCTTTTAAAT
* *
29347793 TGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATCT
1 TGCAATATCAGGGAAGCAAGATTCACCATCGTAGCTTCAATCT
29347836 GCTCCACTGC
Statistics
Matches: 138, Mismatches: 52, Indels: 4
0.71 0.27 0.02
Matches are distributed among these distances:
49 35 0.25
50 101 0.73
51 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (50 bp):
TGCAATATCAGGGAAGCAAGATTCACCATCGTAGCTTCAATCTTTTAAAT
Found at i:29347828 original size:99 final size:100
Alignment explanation
Indices: 29347594--29347858 Score: 361
Period size: 100 Copynumber: 2.7 Consensus size: 100
29347584 TCTATTTAAC
* * * * * * ** **
29347594 TGCAATGTCAGGGAAACAAGATTCACCGTCGTAGCTTCAATTTGTTCCACTACACCACCAAAGAA
1 TGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAA
29347659 GTAAGATTCACCATCGTGGCTTCAATCTTTTAAAT
66 GTAAGATTCACCATCGTGGCTTCAATCTTTTAAAT
* * * *
29347694 TGCAATATCAGGGAAGCAAGATTCGCCATCGTAGCTTTAATCTACTCCACTGTACTGCCAGGGAA
1 TGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAA
* **
29347759 GTAAGATTCGCTGTCGTGGCTTCAAT-TTTTAAAT
66 GTAAGATTCACCATCGTGGCTTCAATCTTTTAAAT
*
29347793 TGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACTGCTAGGGAA
1 TGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAA
29347858 G
66 G
29347859 ATTGCTTCAT
Statistics
Matches: 143, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
99 69 0.48
100 74 0.52
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (100 bp):
TGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAA
GTAAGATTCACCATCGTGGCTTCAATCTTTTAAAT
Found at i:29348193 original size:24 final size:24
Alignment explanation
Indices: 29348155--29348211 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
29348145 CGGATTGCCC
**
29348155 CCACTGTAATTTTCAAAGTTCAAT
1 CCACTGTAAACTTCAAAGTTCAAT
* * *
29348179 CCGCTGTAAACTTCAAGGTTCAGT
1 CCACTGTAAACTTCAAAGTTCAAT
29348203 CCACTGTAA
1 CCACTGTAA
29348212 TTTAGGGACA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (24 bp):
CCACTGTAAACTTCAAAGTTCAAT
Found at i:29353820 original size:16 final size:16
Alignment explanation
Indices: 29353801--29353831 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29353791 AGTATAAATA
*
29353801 ATATATATCTAAGTAG
1 ATATATATATAAGTAG
29353817 ATATATATATAAGTA
1 ATATATATATAAGTA
29353832 AACTTGGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (16 bp):
ATATATATATAAGTAG
Found at i:29360283 original size:39 final size:38
Alignment explanation
Indices: 29360231--29360324 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 38
29360221 TAATTACCAT
* * * *
29360231 AATTATAATAATTATAATAATGTTTGACCAAAACATTAC
1 AATTACAATAATTATAATAATATTCGACCAAAA-ATTAA
* *
29360270 AATTACAATAATTATAATAATATTCGATCATAAATTAA
1 AATTACAATAATTATAATAATATTCGACCAAAAATTAA
29360308 AATTACAATAATTATAA
1 AATTACAATAATTATAA
29360325 CAAGGATTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (38 bp):
AATTACAATAATTATAATAATATTCGACCAAAAATTAA
Found at i:29364742 original size:37 final size:37
Alignment explanation
Indices: 29364690--29364791 Score: 102
Period size: 37 Copynumber: 2.7 Consensus size: 37
29364680 AAGCTAATAC
* *
29364690 AAGTTTGTATAAATTTTTAAATATTTTTAATATGTTTTAT
1 AAGTTTTTAT-AATTTTTAAATATTTTTAAT-T-TTATAT
*
29364730 -A-TTTTTATAATTTATT-AATTTTTTTAATTTTATAT
1 AAGTTTTTATAATTT-TTAAATATTTTTAATTTTATAT
*
29364765 AAGTTTTTATAATATTTATAATATTTT
1 AAGTTTTTATAATTTTTA-AATATTTT
29364792 ATGATTTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
35 5 0.10
36 4 0.08
37 27 0.52
38 15 0.29
39 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (37 bp):
AAGTTTTTATAATTTTTAAATATTTTTAATTTTATAT
Done.