Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008075.1 Hibiscus syriacus cultivar Beakdansim tig00110577_pilon, whole genome shotgun sequence
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: 1947163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:223800 original size:22 final size:22
Alignment explanation
Indices: 223769--223840 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
223759 CTGAGTGGCA
223769 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
223792 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
223814 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
223835 TATGAA
1 TATGAA
223841 ACCCTCAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.44
22 22 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:223825 original size:21 final size:21
Alignment explanation
Indices: 223777--223839 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
223767 CATATGAAAT
* *
223777 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
223799 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
223820 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
223840 AACCCTCAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:225317 original size:64 final size:64
Alignment explanation
Indices: 225217--225377 Score: 209
Period size: 64 Copynumber: 2.5 Consensus size: 64
225207 TAATGAAGGT
* * *
225217 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
225280 GG
63 GC
* *
225282 ATGCATCGATGCACTACTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
225346 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
225378 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 57 0.67
65 25 0.29
66 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:227593 original size:114 final size:114
Alignment explanation
Indices: 227393--227612 Score: 361
Period size: 114 Copynumber: 1.9 Consensus size: 114
227383 GATCATGCAG
* * * * * *
227393 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCAAATGATTGATTCTGGGGTTCATACCAAATCAGACCAGATAACTCAAAGA
227458 ACACTTCCAGAAGATGCTATTGGGTC-TCTTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTC-TTATTTCTACTATGAGCAAA
*
227507 TTCATCTTTCAAATCAAATGATTGATTTTGGGGTTCATACCAAATCAGACCAGATAACTCAAAGA
1 TTCATCTTTCAAATCAAATGATTGATTCTGGGGTTCATACCAAATCAGACCAGATAACTCAAAGA
227572 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
227613 CGAGAACGTG
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
114 96 0.98
115 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCAAATGATTGATTCTGGGGTTCATACCAAATCAGACCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:231733 original size:27 final size:27
Alignment explanation
Indices: 231699--231758 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
231689 AAATGTAATT
*
231699 ATGT-AAAAATGAAAATGTAAATACAA
1 ATGTAAAAAATGAAAACGTAAATACAA
* *
231725 ATGTAAAAAATGCAAACGTAAATGCAA
1 ATGTAAAAAATGAAAACGTAAATACAA
231752 ATGTAAA
1 ATGTAAA
231759 TATGTGAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.58, C:0.07, G:0.13, T:0.22
Consensus pattern (27 bp):
ATGTAAAAAATGAAAACGTAAATACAA
Found at i:231836 original size:15 final size:15
Alignment explanation
Indices: 231818--231856 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
231808 ATAAAAGTAT
*
231818 AAATACAAAAATGAA
1 AAATGCAAAAATGAA
* *
231833 AAATGCAAAGATGCA
1 AAATGCAAAAATGAA
231848 AAATGCAAA
1 AAATGCAAA
231857 TGTATGTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.64, C:0.10, G:0.13, T:0.13
Consensus pattern (15 bp):
AAATGCAAAAATGAA
Found at i:234045 original size:143 final size:142
Alignment explanation
Indices: 233854--234112 Score: 357
Period size: 143 Copynumber: 1.8 Consensus size: 142
233844 AAGAAAATCT
*
233854 ATTAATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATG-ACTTCT
1 ATTAATATATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAA-GAACTTCT
** * * *
233918 AGGTTCCTTAAGACAGCTCTTTTCTTAA-A-AATAAATAAATATTAAAATAACATCTTTCTAAAA
65 AGGTGACTTAAGACAGCCCATTTCTTAATATAAAAAATAAATATTAAAATAACATCTTTCTAAAA
233981 ATAATTAAAATAA
130 ATAATTAAAATAA
233994 ATTAATATATATATAATTTATAAA-AATATGATATTTATTTATTTA-AGAATATCAGAAAAGAAC
1 ATTAATATATATAT-ATTTATAAATAA-A--ATATTTATTTATTTAGA-AATATCAGAAAAGAAC
*
234057 TTCTAGGTGATTTAAGACAGCCCATTTCTTAATATTAAAAAATAAATATTAAAATA
61 TTCTAGGTGACTTAAGACAGCCCATTTCTTAATA-TAAAAAATAAATATTAAAATA
234113 TGATTATTTT
Statistics
Matches: 103, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
140 15 0.15
141 10 0.10
142 2 0.02
143 56 0.54
144 1 0.01
146 19 0.18
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (142 bp):
ATTAATATATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGAACTTCTA
GGTGACTTAAGACAGCCCATTTCTTAATATAAAAAATAAATATTAAAATAACATCTTTCTAAAAA
TAATTAAAATAA
Found at i:234839 original size:13 final size:13
Alignment explanation
Indices: 234817--234868 Score: 86
Period size: 13 Copynumber: 4.0 Consensus size: 13
234807 CCGGTGACCG
*
234817 GCCGGTCACCGTC
1 GCCGGCCACCGTC
234830 GCCGGCCACCGTC
1 GCCGGCCACCGTC
234843 GCCGGCCACCGTC
1 GCCGGCCACCGTC
*
234856 GCCGCCCACCGTC
1 GCCGGCCACCGTC
234869 CACGGTGGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.08, C:0.54, G:0.29, T:0.10
Consensus pattern (13 bp):
GCCGGCCACCGTC
Found at i:239790 original size:15 final size:15
Alignment explanation
Indices: 239747--239793 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
239737 ATAATAAAAT
239747 AAAATATCTAAATTC
1 AAAATATCTAAATTC
*
239762 AAACATAT-TCAAATTT
1 AAA-ATATCT-AAATTC
*
239778 ACAATATCTAAATTC
1 AAAATATCTAAATTC
239793 A
1 A
239794 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAATATCTAAATTC
Found at i:241913 original size:20 final size:20
Alignment explanation
Indices: 241890--241986 Score: 122
Period size: 20 Copynumber: 4.8 Consensus size: 20
241880 ATTCGCGTTG
241890 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* * *
241910 CATTTCGCGTCGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
241931 AAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTC
241951 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
241971 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
241987 AGTCTACAGT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
20 49 0.78
21 14 0.22
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:248740 original size:31 final size:30
Alignment explanation
Indices: 248702--248794 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 30
248692 TGCCTTTATC
248702 TTTGTTTCCTTTGTTTTTGTTGTGATGGGTT
1 TTTGTTTCCTTTG-TTTTGTTGTGATGGGTT
* * **
248733 TTTGTTTCCTTTGCTTGTATTGTGATTAGTT
1 TTTGTTTCCTTTG-TTTTGTTGTGATGGGTT
* * * * *
248764 TCTATTTTCTTTGGTTTGCTGTGATGGGTT
1 TTTGTTTCCTTTGTTTTGTTGTGATGGGTT
248794 T
1 T
248795 CTATTTCTTT
Statistics
Matches: 48, Mismatches: 14, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
30 12 0.25
31 36 0.75
ACGTcount: A:0.06, C:0.09, G:0.24, T:0.61
Consensus pattern (30 bp):
TTTGTTTCCTTTGTTTTGTTGTGATGGGTT
Found at i:249206 original size:73 final size:73
Alignment explanation
Indices: 249087--249231 Score: 281
Period size: 73 Copynumber: 2.0 Consensus size: 73
249077 CCCATACATG
249087 TGATGAATAACATAGACGAGAAGTATTATTCTCTCTTTTTCTGCGTCTGCAGTCCTAAACCAAGT
1 TGATGAATAACATAGACGAGAAGTATTATTCTCTCTTTTTCTGCGTCTGCAGTCCTAAACCAAGT
249152 GCACATAT
66 GCACATAT
*
249160 TGATGAATAACATAGACGAGAAGTATTATTCTCTCTTTTTCTGCGTCTGCAGTCCTAAACCAGGT
1 TGATGAATAACATAGACGAGAAGTATTATTCTCTCTTTTTCTGCGTCTGCAGTCCTAAACCAAGT
249225 GCACATA
66 GCACATA
249232 CTTGTGAGAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (73 bp):
TGATGAATAACATAGACGAGAAGTATTATTCTCTCTTTTTCTGCGTCTGCAGTCCTAAACCAAGT
GCACATAT
Found at i:261843 original size:24 final size:24
Alignment explanation
Indices: 261816--261875 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
261806 CAAGAAAGCT
261816 ATTTTTTTTATAAATAAAAAAATG
1 ATTTTTTTTATAAATAAAAAAATG
261840 ATTTTTTTTATAAATAAAAAAATG
1 ATTTTTTTTATAAATAAAAAAATG
261864 ATTTTTTTTATA
1 ATTTTTTTTATA
261876 TCCTAAAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (24 bp):
ATTTTTTTTATAAATAAAAAAATG
Found at i:268400 original size:22 final size:23
Alignment explanation
Indices: 268359--268401 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
268349 GGTTTTTCCT
268359 AATATTTATTTTAGATATTTTTA
1 AATATTTATTTTAGATATTTTTA
268382 AATATTT-TTTTATGA-ATTTT
1 AATATTTATTTTA-GATATTTT
268402 CTTTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (23 bp):
AATATTTATTTTAGATATTTTTA
Found at i:271049 original size:61 final size:61
Alignment explanation
Indices: 270954--271075 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
270944 GTAATTAGTA
270954 AATGAAGACAAGTACACGAGTGACAACAAGGTGGAGCTAAGTAATTTATATAGGGAATGGG
1 AATGAAGACAAGTACACGAGTGACAACAAGGTGGAGCTAAGTAATTTATATAGGGAATGGG
271015 AATGAAGACAAGTACACGAGTGACAACAAGGTGGAGCTAAGTAATTTATATAGGGAATGGG
1 AATGAAGACAAGTACACGAGTGACAACAAGGTGGAGCTAAGTAATTTATATAGGGAATGGG
271076 TAAATGCTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.41, C:0.10, G:0.30, T:0.20
Consensus pattern (61 bp):
AATGAAGACAAGTACACGAGTGACAACAAGGTGGAGCTAAGTAATTTATATAGGGAATGGG
Found at i:273304 original size:52 final size:52
Alignment explanation
Indices: 273207--273309 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 52
273197 ATACTTATAC
* *
273207 TTATATATGAATCATATCAATTTAAATTATAATAAATTCAAAAAAAATATTA
1 TTATATATGAATCATATCAATTTAAACTATAATAAAATCAAAAAAAATATTA
* *
273259 TTATATATGAATTATATCAATTTAAACTATAGTAAAAAT-AGAAAAAAATAT
1 TTATATATGAATCATATCAATTTAAACTATAAT-AAAATCA-AAAAAAATAT
273310 AAATAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
52 31 0.69
53 14 0.31
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (52 bp):
TTATATATGAATCATATCAATTTAAACTATAATAAAATCAAAAAAAATATTA
Found at i:283913 original size:18 final size:18
Alignment explanation
Indices: 283890--283942 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
283880 ATTTTGGGGA
283890 TGCAAAATCAGCCACGTC
1 TGCAAAATCAGCCACGTC
**
283908 TGC-AAATGTGTTCCACGTC
1 TGCAAAATCAG--CCACGTC
283927 TGCAAAATCAGCCACG
1 TGCAAAATCAGCCACG
283943 ACGAGCGACG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 5 0.18
18 8 0.29
19 10 0.36
20 5 0.18
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (18 bp):
TGCAAAATCAGCCACGTC
Found at i:295622 original size:23 final size:23
Alignment explanation
Indices: 295569--295629 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
295559 ATCATATATT
* *
295569 TATTT-TTTTAAAAATAAATTAA
1 TATTTATTTTATAAATAAATAAA
** *
295591 TATCAATTTTATAAATATATAAA
1 TATTTATTTTATAAATAAATAAA
*
295614 TATTTATTTAATAAAT
1 TATTTATTTTATAAAT
295630 TTAATTTTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTTATTTTATAAATAAATAAA
Found at i:300082 original size:23 final size:23
Alignment explanation
Indices: 300025--300084 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
300015 TATTTGTCTC
* *
300025 TTAAAATTTTACAAATTTTTTAT
1 TTAAAATTTTATAAATTTATTAT
300048 TTAAAATTTTATAAATTTATTAT
1 TTAAAATTTTATAAATTTATTAT
300071 TTAAAATTTTATAA
1 TTAAAATTTTATAA
300085 TCGCCCTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAAATTTTATAAATTTATTAT
Found at i:301668 original size:22 final size:22
Alignment explanation
Indices: 301643--301707 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
301633 ACCCGAATCG
301643 TTGACAGGTCTGACCGTTGACC
1 TTGACAGGTCTGACCGTTGACC
* **
301665 TTGACAGGTCAT-ATCGTTGATT
1 TTGACAGGTC-TGACCGTTGACC
* *
301687 TTGACCGGTCAGACCGTTGAC
1 TTGACAGGTCTGACCGTTGAC
301708 TTTCACATTG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (22 bp):
TTGACAGGTCTGACCGTTGACC
Found at i:310399 original size:28 final size:28
Alignment explanation
Indices: 310315--310399 Score: 107
Period size: 28 Copynumber: 3.0 Consensus size: 28
310305 TCGTCGTTGC
* * * * *
310315 TTTCAAATACTAGCTCGATAACGTAATG
1 TTTCAAGTACTAACTGGACAACATAATG
*
310343 CTTCAAGTACTAACTGGACAACATAATG
1 TTTCAAGTACTAACTGGACAACATAATG
*
310371 TTTCAAGTACTAACTGGGCAACATAATG
1 TTTCAAGTACTAACTGGACAACATAATG
310399 T
1 T
310400 AACGAATATC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (28 bp):
TTTCAAGTACTAACTGGACAACATAATG
Found at i:315009 original size:13 final size:13
Alignment explanation
Indices: 314991--315021 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
314981 TTTCAAGTTA
314991 TAATTATTTCCAT
1 TAATTATTTCCAT
315004 TAATTATTTCCAT
1 TAATTATTTCCAT
315017 TAATT
1 TAATT
315022 TCACTAGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATTATTTCCAT
Found at i:320165 original size:20 final size:21
Alignment explanation
Indices: 320128--320179 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
320118 TTGAGGTAAT
*
320128 ATGTTGTAAATT-ATTGTTTGA
1 ATGTTG-AAATTGATTGTTAGA
*
320149 GTGTTGAAATTGA-TGTTAGA
1 ATGTTGAAATTGATTGTTAGA
320169 ATG-TGAAATTG
1 ATGTTGAAATTG
320180 GGTCATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.30
20 13 0.48
21 6 0.22
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (21 bp):
ATGTTGAAATTGATTGTTAGA
Found at i:320377 original size:14 final size:14
Alignment explanation
Indices: 320360--320386 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
320350 CATCGAAAGA
320360 ATTTTTAGGAAATT
1 ATTTTTAGGAAATT
320374 ATTTTTAGGAAAT
1 ATTTTTAGGAAAT
320387 GTAAAAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
ATTTTTAGGAAATT
Found at i:322846 original size:22 final size:22
Alignment explanation
Indices: 322819--322887 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
322809 TAATCGTTAC
322819 ATATGATGTGTATCATGAACAT
1 ATATGATGTGTATCATGAACAT
322841 ATATGATGTGTATCATGAACAT
1 ATATGATGTGTATCATGAACAT
* *
322863 ATATGATATTTATCATGAATCAT
1 ATATGATGTGTATCATGAA-CAT
322886 AT
1 AT
322888 TTCGGGTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
22 39 0.89
23 5 0.11
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (22 bp):
ATATGATGTGTATCATGAACAT
Found at i:323122 original size:30 final size:30
Alignment explanation
Indices: 323035--323182 Score: 170
Period size: 30 Copynumber: 4.8 Consensus size: 30
323025 TAATCGGATT
*
323035 AACACTATAGTGTGTAAGGACACTTAGTGC
1 AACACTATAGTGTGTAAGGACACTTAGTAC
* * *
323065 ATATGGTACTATGGTGCGTAAGGACACTTAGTAC
1 A-A---CACTATAGTGTGTAAGGACACTTAGTAC
* * *
323099 AATATTATAGTGTGTAAGTACACTTAGTAC
1 AACACTATAGTGTGTAAGGACACTTAGTAC
* *
323129 AACACTGTAGTGTGTAAGGAAACTTAGTAC
1 AACACTATAGTGTGTAAGGACACTTAGTAC
*
323159 AACACTGTAGTGTGTAAGGACACT
1 AACACTATAGTGTGTAAGGACACT
323183 CAATGTATAT
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
30 73 0.73
31 1 0.01
33 1 0.01
34 25 0.25
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (30 bp):
AACACTATAGTGTGTAAGGACACTTAGTAC
Found at i:323713 original size:24 final size:24
Alignment explanation
Indices: 323686--323734 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
323676 TTAAATAAAT
*
323686 ATTACTATATTAAATTATA-TTTTA
1 ATTACTA-ATTAAATTAGACTTTTA
*
323710 ATTATTAATTAAATTAGACTTTTA
1 ATTACTAATTAAATTAGACTTTTA
323734 A
1 A
323735 ACCAGACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTACTAATTAAATTAGACTTTTA
Found at i:325998 original size:9 final size:9
Alignment explanation
Indices: 325984--326042 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
325974 TATATATATA
325984 ATTTTTTAT
1 ATTTTTTAT
325993 ATTTTTTAT
1 ATTTTTTAT
**
326002 ATTAATTAT
1 ATTTTTTAT
* *
326011 ATATATATAT
1 AT-TTTTTAT
*
326021 AATATTTTAT
1 -ATTTTTTAT
326031 ATTTTTTAT
1 ATTTTTTAT
326040 ATT
1 ATT
326043 AATTATATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
9 29 0.73
10 9 0.22
11 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:326021 original size:38 final size:38
Alignment explanation
Indices: 325970--326053 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 38
325960 CTCGATTATA
*
325970 TATATATATATATAATTTTTTATATTTTTTATATTAAT
1 TATATATATATATAATATTTTATATTTTTTATATTAAT
326008 TATATATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATATATAATATTTTATATTTTTTATATTAAT
326046 TATATATA
1 TATATATA
326054 AAATATTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (38 bp):
TATATATATATATAATATTTTATATTTTTTATATTAAT
Found at i:326479 original size:31 final size:31
Alignment explanation
Indices: 326444--326511 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
326434 TTAAAAAACA
*
326444 TAAGATATAG-TCACTTTCATTTTTATTTAAT
1 TAAGATAT-GTTCACCTTCATTTTTATTTAAT
326475 TAAGATATGTTCACCTTCATTTTTATTTAAT
1 TAAGATATGTTCACCTTCATTTTTATTTAAT
326506 TAAGAT
1 TAAGAT
326512 GTGATCATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.50
Consensus pattern (31 bp):
TAAGATATGTTCACCTTCATTTTTATTTAAT
Found at i:326659 original size:27 final size:26
Alignment explanation
Indices: 326627--326694 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 26
326617 AAATTTTAAC
326627 ATAAAATATATATTTTTAAATGAAAAT
1 ATAAAA-ATATATTTTTAAATGAAAAT
* *
326654 A-AAAAA-ATATTTTTAAATTAAATT
1 ATAAAAATATATTTTTAAATGAAAAT
326678 AATAATAAAATATATTT
1 -AT-A-AAAATATATTT
326695 AATAAGCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
24 16 0.47
25 2 0.06
26 4 0.12
27 2 0.06
28 4 0.12
29 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
ATAAAAATATATTTTTAAATGAAAAT
Found at i:327554 original size:18 final size:18
Alignment explanation
Indices: 327531--327571 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
327521 AATATTGTTG
*
327531 AATAAAAGT-ATTAAAGAT
1 AATAAAAGTAAATAAA-AT
327549 AATAAAAGTAAATAAAAT
1 AATAAAAGTAAATAAAAT
327567 AATAA
1 AATAA
327572 TAAAAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (18 bp):
AATAAAAGTAAATAAAAT
Found at i:327751 original size:26 final size:25
Alignment explanation
Indices: 327694--327754 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
327684 TTATTTTAAA
* *
327694 AGTTAAATAATATTTTAACCCTTTG
1 AGTTGAATTATATTTTAACCCTTTG
327719 AGTTGAATTATATTTTAACCCTTTTG
1 AGTTGAATTATATTTTAACCC-TTTG
327745 AGTTGAATTA
1 AGTTGAATTA
327755 AACTCTAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (25 bp):
AGTTGAATTATATTTTAACCCTTTG
Found at i:330120 original size:12 final size:13
Alignment explanation
Indices: 330094--330126 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
330084 ATGATGGATG
330094 TTTAAAAATTGGT
1 TTTAAAAATTGGT
*
330107 TTTAATAATT-GT
1 TTTAAAAATTGGT
330119 TTTAAAAA
1 TTTAAAAA
330127 GAAAATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (13 bp):
TTTAAAAATTGGT
Found at i:333411 original size:15 final size:15
Alignment explanation
Indices: 333393--333425 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
333383 AAATTCTAAA
333393 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
333408 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
333423 TAT
1 TAT
333426 ATTTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:335871 original size:12 final size:12
Alignment explanation
Indices: 335854--335880 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
335844 CATTATCACC
335854 TGGGTTCAACTG
1 TGGGTTCAACTG
335866 TGGGTTCAACTG
1 TGGGTTCAACTG
335878 TGG
1 TGG
335881 TTTCTCAGAG
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:0.15, C:0.15, G:0.37, T:0.33
Consensus pattern (12 bp):
TGGGTTCAACTG
Found at i:337581 original size:20 final size:21
Alignment explanation
Indices: 337556--337599 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
337546 CCGAAAATAT
* *
337556 TAAAAATATTGAT-TTTTAAA
1 TAAAAATAATAATATTTTAAA
337576 TAAAAATAATAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
337597 TAA
1 TAA
337600 TTTTTTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:337868 original size:18 final size:19
Alignment explanation
Indices: 337842--337885 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
337832 TTTTAAATTT
337842 TTTTATTAAA-ATATTATG
1 TTTTATTAAATATATTATG
*
337860 TTTTGTTAAATATATTATG
1 TTTTATTAAATATATTATG
337879 TTATTAT
1 TT-TTAT
337886 AATTTCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 10 0.45
20 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTTATTAAATATATTATG
Found at i:338167 original size:3 final size:3
Alignment explanation
Indices: 338161--338226 Score: 60
Period size: 3 Copynumber: 22.0 Consensus size: 3
338151 TGCTATGTTG
* * * * * *
338161 TTA TTA TTA TTA TTA TTA TTA TTA TCA TAA TAA TAA TCA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
338209 ATA TTT TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
338227 CTACCATGTA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:344857 original size:2 final size:2
Alignment explanation
Indices: 344844--344883 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
344834 TTAGTCTCCC
*
344844 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
344884 CTACAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:352625 original size:2 final size:2
Alignment explanation
Indices: 352618--352646 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
352608 CACGTCAGTA
352618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
352647 AATTATTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:355381 original size:89 final size:88
Alignment explanation
Indices: 355222--355419 Score: 310
Period size: 89 Copynumber: 2.2 Consensus size: 88
355212 GTTATTGGAT
*
355222 AGTTAG-AGAATACG-ACTTTTTCATTGACACGTAAACAAATAGCAGTTTTAATATTCTGTTTTA
1 AGTTAGTA-AATACGTA-TTTTTCATTGACACGTAAACAAATAGCAGTGTTAATATTCTGTTTTA
*
355285 CGAAAGAAAAAACTTGTAGAAAATTG
64 CGAAAG-AAAAACTCGTAGAAAATTG
* *
355311 AGTTGGTAAATACGTATTTTTCATTGACACGTAAACAAATAGCAGTGTTAATCTTCTGTTTTACG
1 AGTTAGTAAATACGTATTTTTCATTGACACGTAAACAAATAGCAGTGTTAATATTCTGTTTTACG
355376 AAAGAAAAACTCGTAGAAAATTG
66 AAAGAAAAACTCGTAGAAAATTG
*
355399 AGTTAGTAAATATGTATTTTT
1 AGTTAGTAAATACGTATTTTT
355420 GTTGACAGTA
Statistics
Matches: 101, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
88 37 0.37
89 62 0.61
90 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (88 bp):
AGTTAGTAAATACGTATTTTTCATTGACACGTAAACAAATAGCAGTGTTAATATTCTGTTTTACG
AAAGAAAAACTCGTAGAAAATTG
Found at i:359164 original size:2 final size:2
Alignment explanation
Indices: 359157--359193 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
359147 AAATCTATTA
359157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
359194 AGATATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:359568 original size:21 final size:21
Alignment explanation
Indices: 359540--359589 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
359530 ATGACTACAT
359540 AATA-ATAACA-ATAATAATTA
1 AATATATAACATATAA-AATTA
359560 AATATATAAACATATAAAATTA
1 AATATAT-AACATATAAAATTA
359582 AA-ATATAA
1 AATATATAA
359590 ATAAACAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 6 0.22
21 6 0.22
22 11 0.41
23 4 0.15
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (21 bp):
AATATATAACATATAAAATTA
Found at i:359590 original size:21 final size:22
Alignment explanation
Indices: 359546--359590 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
359536 ACATAATAAT
359546 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAATATATA
359568 AACATATAA-AATTAAA-ATATA
1 AACA-ATAATAATTAAATATATA
359589 AA
1 AA
359591 TAAACAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AACAATAATAATTAAATATATA
Found at i:359622 original size:16 final size:16
Alignment explanation
Indices: 359573--359646 Score: 51
Period size: 19 Copynumber: 4.1 Consensus size: 16
359563 ATATAAACAT
359573 ATAAAATTAAAATATAA
1 ATAAAATTAAAA-ATAA
*
359590 ATAAACAATGACTAAAATAA
1 AT-AA-AATTA--AAAATAA
359610 ATAAAATTAAAAAGT-A
1 ATAAAATTAAAAA-TAA
359626 ATAAAACTTGTAAAAATAA
1 ATAAAA--T-TAAAAATAA
359645 AT
1 AT
359647 GAAAGTAGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
16 11 0.24
17 3 0.07
18 8 0.17
19 15 0.33
20 6 0.13
21 3 0.07
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:361068 original size:3 final size:3
Alignment explanation
Indices: 361060--361146 Score: 52
Period size: 3 Copynumber: 29.3 Consensus size: 3
361050 GTAATATGTT
* * * * *
361060 ATA ATA ATA TTTA TTA ATA ATA A-A AAA AT- ATA ATA TTA ATA ATT
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
361104 ATT ATA ATA ATC ATA ATA ATA AAA AAA ATA AAA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
361147 AAAAGGCCAA
Statistics
Matches: 66, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
2 4 0.06
3 60 0.91
4 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:361740 original size:124 final size:122
Alignment explanation
Indices: 361507--362167 Score: 796
Period size: 124 Copynumber: 5.5 Consensus size: 122
361497 TTAAGGCAAG
* *
361507 GTTGAACAAGTCCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTGTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
** * *
361571 ACACT-TCTGGAAATGTTGATGCTGATATATCTCATTCTGTGATAGAATCGAGCAAAAA
66 ACTTTATCTGGAAATATTGATG-TGAT-TATCTCCTTCTGTGATAGAATCGAGCAAAAA
361629 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
361694 ACTTTATCTGGAAATATTGATGATGATTTATCTCCTTCTGTGATAGAATCGAGCAAAAA
66 ACTTTATCTGGAAATATTGATG-TGA-TTATCTCCTTCTGTGATAGAATCGAGCAAAAA
*
361753 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
361818 ACTTTATCTAGAAATATTGATGTTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAA
66 ACTTTATCTGGAAATATTGATG-TGAT-TATCTCCTTCTGTGATAGAATCGAGCAAAAA
361877 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * *
361942 ACTTCT-TCTGGAAA-A--G-T-TG---A--TCCATCGAGTGAT-GAATTCAAGCAAAAG
66 ACTT-TATCTGGAAATATTGATGTGATTATCTCCTTC-TGTGATAGAA-TCGAGCAAAAA
* * * * * *
361990 GTTAAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCATATGAGTTATTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * * * *
362055 ACTCTACCTGG-CA-A-TG-T-TG---A--TCCATCAAGTGAT-GAATTTGAGCAAAAG
66 ACTTTATCTGGAAATATTGATGTGATTATCTCCTTC-TGTGATAGAA-TCGAGCAAAAA
* * *
362103 GTTGAACAAGTTCTTCCCATTATGAACTTCTTCTTCTTTCTTCATATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
362168 CCTCTACCTG
Statistics
Matches: 495, Mismatches: 35, Indels: 27
0.89 0.06 0.05
Matches are distributed among these distances:
112 11 0.02
113 168 0.34
114 1 0.00
118 2 0.00
120 1 0.00
121 1 0.00
122 32 0.06
123 35 0.07
124 242 0.49
125 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (122 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTATCTGGAAATATTGATGTGATTATCTCCTTCTGTGATAGAATCGAGCAAAAA
Found at i:361998 original size:113 final size:113
Alignment explanation
Indices: 361745--362206 Score: 532
Period size: 113 Copynumber: 4.0 Consensus size: 113
361735 GATAGAATCG
* * *
361745 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
* * * * ** *
361810 CATTATGAACTTTATCTAGAAATATTGATGTTGATCTATCTCCTTCTGTGATAGAA-TCG
66 CATTATGAACTCTACCT-G-GA-A---ATGTTGATCCA--T-C--GAGTGAT-GAATTCA
* *
361869 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
* *
361934 CATTATGAACTTCT-TCTGGAAAAGTTGATCCATCGAGTGATGAATTCA
66 CATTATGAAC-TCTACCTGGAAATGTTGATCCATCGAGTGATGAATTCA
* * * * *
361982 AGCAAAAGGTTAAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCATATGAGTTATTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
* * **
362047 CATTATGAACTCTACCTGGCAATGTTGATCCATCAAGTGATGAATTTG
66 CATTATGAACTCTACCTGGAAATGTTGATCCATCGAGTGATGAATTCA
* *
362095 AGCAAAAGGTTGAACAAGTTCTTCCCATTATGAACTTCTTCTTCTTTCTTCATATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
* * * *
362160 CATTATGACCTCTACCTGGTAATGCTGATCCATCGAATGATGAATTC
66 CATTATGAACTCTACCTGGAAATGTTGATCCATCGAGTGATGAATTC
362207 GAATCTTTGC
Statistics
Matches: 301, Mismatches: 34, Indels: 17
0.86 0.10 0.05
Matches are distributed among these distances:
112 6 0.02
113 202 0.67
115 1 0.00
116 1 0.00
118 9 0.03
121 1 0.00
122 1 0.00
123 1 0.00
124 77 0.26
125 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
CATTATGAACTCTACCTGGAAATGTTGATCCATCGAGTGATGAATTCA
Found at i:362037 original size:24 final size:23
Alignment explanation
Indices: 362002--362046 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
361992 TAAACAAATT
*
362002 CTTCTCATTATGAATTTATTCTTC
1 CTTCTCATTATG-AGTTATTCTTC
362026 CTTCTTCA-TATGAGTTATTCT
1 CTTC-TCATTATGAGTTATTCT
362047 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (23 bp):
CTTCTCATTATGAGTTATTCTTC
Found at i:362620 original size:22 final size:22
Alignment explanation
Indices: 362559--362622 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
362549 AGATCCAATA
* * *
362559 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
*
362581 AATATATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
362603 AATCTATCATCTTTGAAGAG
1 AATCTATCATCTTTGAAGAG
362623 TATAGATGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:365905 original size:64 final size:63
Alignment explanation
Indices: 365836--366020 Score: 198
Period size: 64 Copynumber: 2.9 Consensus size: 63
365826 TTATATGAAT
* *
365836 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTATTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAGGTAGTGCATCGATGCACCCA--TTAATAATAAA-ACATCGAATGCAA-T
365899 C-
62 CG
* * *
365900 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCG
1 GTGCATCGATGCATAGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
** **
365964 GTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAACAATAATACTACATCGAAT
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAAT
366021 ACCTTTGATG
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
63 2 0.02
64 94 0.90
65 6 0.06
66 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCACCCATTAATAATAAAACATCGAATGCAATCG
Found at i:366050 original size:64 final size:64
Alignment explanation
Indices: 365884--366057 Score: 190
Period size: 64 Copynumber: 2.7 Consensus size: 64
365874 TAAAATAAAG
* ** *
365884 ACATCGAATGCAATTCG-TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAA
1 ACATCGAATACAA-TCGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAACAATAATGAA
* * * *
365948 ACATCGAATGCAATCGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAACAATAAT-ACT
1 ACATCGAATACAATCGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAACAATAATGA-A
** * * * *
366012 ACATCGAATACCTTTGATGCACCGATACATCAGTAGTGCATCGATG
1 ACATCGAATACAATCGATGCATCGATGCATAAGTAGTGCATCGATG
366058 AATTCCTTCA
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 4 0.04
64 90 0.96
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (64 bp):
ACATCGAATACAATCGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAACAATAATGAA
Found at i:366386 original size:12 final size:12
Alignment explanation
Indices: 366369--366415 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
366359 ATATATGTTC
366369 ATGTGATATGAT
1 ATGTGATATGAT
366381 ATGTGATATGAT
1 ATGTGATATGAT
*
366393 ATGTGATATGAC
1 ATGTGATATGAT
*
366405 ATGTAATATGA
1 ATGTGATATGA
366416 GAACATGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.38
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:366590 original size:15 final size:15
Alignment explanation
Indices: 366560--366637 Score: 138
Period size: 15 Copynumber: 5.1 Consensus size: 15
366550 GAGGGTATAA
366560 TAGTCCTTCGGGGATG
1 TAGTCCTTC-GGGATG
366576 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
*
366591 TAATCCTTCGGGATG
1 TAGTCCTTCGGGATG
366606 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
366621 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
366636 TA
1 TA
366638 ATAGTCCTAC
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
15 51 0.85
16 9 0.15
ACGTcount: A:0.15, C:0.19, G:0.32, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:372910 original size:64 final size:63
Alignment explanation
Indices: 372841--373025 Score: 198
Period size: 64 Copynumber: 2.9 Consensus size: 63
372831 TTATATGAAT
* *
372841 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTATTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAGGTAGTGCATCGATGCACCCA--TTAATAATAAA-ACATCGAATGCAA-T
372904 C-
62 CG
* * *
372905 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCG
1 GTGCATCGATGCATAGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
** **
372969 GTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAACAATAATACTACATCGAAT
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAAT
373026 ACCTTTGATG
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
63 2 0.02
64 94 0.90
65 6 0.06
66 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCACCCATTAATAATAAAACATCGAATGCAATCG
Found at i:373055 original size:64 final size:64
Alignment explanation
Indices: 372889--373062 Score: 190
Period size: 64 Copynumber: 2.7 Consensus size: 64
372879 TAAAATAAAG
* ** *
372889 ACATCGAATGCAATTCG-TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAA
1 ACATCGAATACAA-TCGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAACAATAATGAA
* * * *
372953 ACATCGAATGCAATCGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAACAATAAT-ACT
1 ACATCGAATACAATCGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAACAATAATGA-A
** * * * *
373017 ACATCGAATACCTTTGATGCACCGATACATCAGTAGTGCATCGATG
1 ACATCGAATACAATCGATGCATCGATGCATAAGTAGTGCATCGATG
373063 AATTCCTTCA
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 4 0.04
64 90 0.96
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (64 bp):
ACATCGAATACAATCGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAACAATAATGAA
Found at i:373391 original size:12 final size:12
Alignment explanation
Indices: 373374--373408 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
373364 ATATATGTTC
373374 ATGTGATATGAT
1 ATGTGATATGAT
373386 ATGTGATATGAT
1 ATGTGATATGAT
373398 ATGTGATATGA
1 ATGTGATATGA
373409 CATGAGCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:373552 original size:15 final size:15
Alignment explanation
Indices: 373534--373595 Score: 124
Period size: 15 Copynumber: 4.1 Consensus size: 15
373524 GAGGGTATAA
373534 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
373549 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
373564 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
373579 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
373594 TA
1 TA
373596 ATGGTCCTAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.15, C:0.19, G:0.32, T:0.34
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:376798 original size:3 final size:3
Alignment explanation
Indices: 376790--376874 Score: 82
Period size: 3 Copynumber: 28.3 Consensus size: 3
376780 GTAATATGTT
* * *
376790 ATA ATA ATA TTTA TTA ATA ATA ATA ATA ATA AT- ATA ATA TTA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
376835 ATT ATT ATA ATA ATC ATA ATA ATT ATT ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
376875 AAAAGCCAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
2 2 0.03
3 66 0.94
4 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (3 bp):
ATA
Found at i:376811 original size:26 final size:27
Alignment explanation
Indices: 376781--376855 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 27
376771 TTTGGGCTTG
* *
376781 TAATATGTTATAATAATAT-TTATTAA
1 TAATATATTATAATAATATAATATTAA
*
376807 TAATA-ATAATAATAATATAATATTAA
1 TAATATATTATAATAATATAATATTAA
376833 TAAT-TATTATAATAATCATAATA
1 TAATATATTATAATAAT-ATAATA
376856 ATTATTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.26
26 25 0.60
27 6 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (27 bp):
TAATATATTATAATAATATAATATTAA
Found at i:378001 original size:9 final size:9
Alignment explanation
Indices: 377987--378011 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
377977 ATCTAAATAA
377987 AAAATCCCG
1 AAAATCCCG
377996 AAAATCCCG
1 AAAATCCCG
378005 AAAATCC
1 AAAATCC
378012 GGGATTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.32, G:0.08, T:0.12
Consensus pattern (9 bp):
AAAATCCCG
Found at i:385501 original size:4 final size:4
Alignment explanation
Indices: 385494--385531 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
385484 ATACATCAAC
*
385494 ACAT ACAT ACAT ATAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
385532 GATACATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:385503 original size:16 final size:16
Alignment explanation
Indices: 385482--385526 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
385472 GATTGAGAAA
385482 ACATACATCA-ACACAT
1 ACATACAT-ATACACAT
*
385498 ACATACATATATACAT
1 ACATACATATACACAT
*
385514 ACATACACATACA
1 ACATACATATACA
385527 TACATGATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.04
16 24 0.96
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (16 bp):
ACATACATATACACAT
Found at i:385917 original size:36 final size:35
Alignment explanation
Indices: 385854--385961 Score: 117
Period size: 38 Copynumber: 2.9 Consensus size: 35
385844 TCTTATTAAA
* * * *
385854 AAAAACAAAGTGTCGTCTCACTAGAGACAGTTTTCTT
1 AAAAACAAA-TTTTGTCTCGCTTGAGACA-TTTTCTT
385891 AAAAACAAATTTTGTCTCGCTTGAGACAACTTTCTCTT
1 AAAAACAAATTTTGTCTCGCTTGAGAC-A-TTT-TCTT
* *
385929 TAAAACAAATTATGTCTCGCTTGAGACATTTTC
1 AAAAACAAATTTTGTCTCGCTTGAGACATTTTC
385962 CACAAACTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
35 2 0.03
36 17 0.27
37 14 0.23
38 29 0.47
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.34
Consensus pattern (35 bp):
AAAAACAAATTTTGTCTCGCTTGAGACATTTTCTT
Found at i:386049 original size:90 final size:93
Alignment explanation
Indices: 385884--386050 Score: 243
Period size: 92 Copynumber: 1.8 Consensus size: 93
385874 CTAGAGACAG
* * * *
385884 TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAACTTTCTCTTTAAAACAAATTATGTCTCGC
1 TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAACTTTATCGTCAAAACAAATTATGTCTCAC
385949 TTGAGACATTTTCCACAAACTTTGAGAT
66 TTGAGACATTTTCCACAAACTTTGAGAT
*
385977 TTTTC-TAAAAACAAATTTTGTCTCGCTTGAGGCAA-TTTAT-GTCAAAACAAATT-TCGTCTCA
1 TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAACTTTATCGTCAAAACAAATTAT-GTCTCA
*
386038 TTTGAGACATTTT
65 CTTGAGACATTTT
386051 TTTCCTTTGA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
89 1 0.01
90 28 0.42
91 4 0.06
92 29 0.43
93 5 0.07
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (93 bp):
TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAACTTTATCGTCAAAACAAATTATGTCTCAC
TTGAGACATTTTCCACAAACTTTGAGAT
Found at i:386217 original size:36 final size:35
Alignment explanation
Indices: 386162--386255 Score: 109
Period size: 34 Copynumber: 2.7 Consensus size: 35
386152 ATCGTTTTCT
* * *
386162 CAAACTTTGTCTCGCTTGAGACAATTTCTCTAAAAA
1 CAAATTTTGTCTCGCTTGAGAC-ATGTATCTAAAAA
** * *
386198 CAAATTTTGTCTCATTTGAGAC-TGTATCTTAAAG
1 CAAATTTTGTCTCGCTTGAGACATGTATCTAAAAA
386232 CAAATTTTGTCTCGCTTGAGACAT
1 CAAATTTTGTCTCGCTTGAGACAT
386256 CATTTTCTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
34 28 0.58
35 1 0.02
36 19 0.40
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (35 bp):
CAAATTTTGTCTCGCTTGAGACATGTATCTAAAAA
Found at i:386567 original size:29 final size:27
Alignment explanation
Indices: 386508--386660 Score: 188
Period size: 27 Copynumber: 5.6 Consensus size: 27
386498 TCTTTTGAGG
386508 AAAAAATCTTTGAGTTTGTTCCTCTT-A
1 AAAAAATCTTTGAGTTTGTTCCT-TTGA
386535 AAAAAATCTTTGAGTTTGTTCCTCTTG-
1 AAAAAATCTTTGAGTTTGTTCCT-TTGA
386562 AAAAAATCTTTGAGTTTGTTCCTTTTGA
1 AAAAAATCTTTGAGTTTGTTCC-TTTGA
*
386590 ATAAAAATCTTGGAGTTTGTTCCTTTGGA
1 A-AAAAATCTTTGAGTTTGTTCCTTT-GA
* *
386619 ATAAAAATCTGTGAG-TTGTTTCGTTTG-
1 A-AAAAATCTTTGAGTTTG-TTCCTTTGA
386646 AAAAAATCTTTGAGT
1 AAAAAATCTTTGAGT
386661 CTATTTACTT
Statistics
Matches: 114, Mismatches: 5, Indels: 14
0.86 0.04 0.11
Matches are distributed among these distances:
26 12 0.11
27 52 0.46
28 9 0.08
29 41 0.36
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.43
Consensus pattern (27 bp):
AAAAAATCTTTGAGTTTGTTCCTTTGA
Found at i:386798 original size:67 final size:67
Alignment explanation
Indices: 386724--387245 Score: 923
Period size: 67 Copynumber: 7.9 Consensus size: 67
386714 TTTGAGATTG
386724 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
386789 AA
66 AA
*
386791 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
386856 AA
66 AA
*
386858 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
386923 AA
66 AA
*
386925 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
386990 AA
66 AA
*
386992 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
387057 AA
66 AA
387059 TTTCTTTTGAAAC--AAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
387122 AA
66 AA
387124 -TTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAAGA
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTT-AAGA
*
387188 CAA
65 TAA
*
387191 TTTCTTTTG--A-AAAAATCTCTGAGTTTGTTTCCTTT-GAAACAAAATTTTGTCTCTC
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTT-CTTTGGAAACAAAATTTTGTCTCTC
387246 GAGACAACTT
Statistics
Matches: 446, Mismatches: 4, Indels: 12
0.97 0.01 0.03
Matches are distributed among these distances:
64 12 0.03
65 90 0.20
66 50 0.11
67 286 0.64
68 8 0.02
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:387108 original size:28 final size:29
Alignment explanation
Indices: 387059--387174 Score: 94
Period size: 28 Copynumber: 3.8 Consensus size: 29
387049 TTTAAGATAA
*
387059 TTTCTTTTGAAAC-AAATCTTTGAGTTTG
1 TTTCTTTGGAAACAAAATCTTTGAGTTTG
**
387087 TTTCTTTGGAAACAAAAT-TTTGTCTCTCTTAAG
1 TTTCTTTGGAAACAAAATCTTTG--AGT-TT--G
*
387120 ATAATTCTTTTGAAACAAAAATCTTTGAGTTTG
1 -T--TTCTTTGGAAAC-AAAATCTTTGAGTTTG
387153 TTTCTTTGGAAACAAAAT-TTTG
1 TTTCTTTGGAAACAAAATCTTTG
387175 TCTCTCTTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
28 20 0.29
29 9 0.13
30 12 0.17
31 2 0.03
32 1 0.01
33 2 0.03
34 1 0.01
35 2 0.03
36 12 0.17
37 5 0.07
38 4 0.06
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (29 bp):
TTTCTTTGGAAACAAAATCTTTGAGTTTG
Found at i:387302 original size:40 final size:40
Alignment explanation
Indices: 387247--387326 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
387237 TTGTCTCTCG
*
387247 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
*
387287 AGACAACTTCTTTTGAAAATACCCACATTTGATATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
387327 CTATTAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:387760 original size:35 final size:36
Alignment explanation
Indices: 387694--387768 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
387684 TATTTCTTTG
* *
387694 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
*
387730 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCTGTTTCCCTT
387765 GAAA
1 GAAA
387769 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
Found at i:387920 original size:63 final size:67
Alignment explanation
Indices: 387744--387921 Score: 179
Period size: 66 Copynumber: 2.7 Consensus size: 67
387734 CAAAATAAAC
* * * *
387744 ATCTTTGAGATCGTTTCTC-TTGAAATGAATTTTGTCTCATTTGAGCCAATTCCTCATGAAACAC
1 ATCTTTGAGAACGTTTCCCTTTGAAACGAATTTTGTCTCATTTGAGACAATTCCTCATGAAACAC
387808 CG
66 CG
** * ** * *
387810 ATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGGTTGAGACAATTCC-CTTTAAACAC
1 ATCTTTGAGAACGTTTCCCTTTGAAACGAATTTTGTCTCATTTGAGACAATTCCTCATGAAACAC
387874 CG
66 CG
***
387876 -TCTTTG-GGTTGTTT-CCTTTGAAACGAATTTTGTCTC-TTTCGAGACA
1 ATCTTTGAGAACGTTTCCCTTTGAAACGAATTTTGTCTCATTT-GAGACA
387922 GTTGCTTTGG
Statistics
Matches: 92, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
62 2 0.02
63 25 0.27
64 5 0.05
65 6 0.07
66 27 0.29
67 27 0.29
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (67 bp):
ATCTTTGAGAACGTTTCCCTTTGAAACGAATTTTGTCTCATTTGAGACAATTCCTCATGAAACAC
CG
Found at i:388090 original size:28 final size:28
Alignment explanation
Indices: 388040--388093 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
388030 TCAAAATCCA
* *
388040 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
388068 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
388094 CATTATCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:388175 original size:46 final size:45
Alignment explanation
Indices: 388124--388305 Score: 146
Period size: 46 Copynumber: 4.2 Consensus size: 45
388114 GCCATCCTCG
*
388124 TCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 TCACGTAGGAACCATGTCATCACC-TTAGATGGCCAGAACTCTTCA
* * * * *
388170 TCACGTATGAGCCGTGTCATC-CC-CAGA---CCAGATCTCTTCA
1 TCACGTAGGAACCATGTCATCACCTTAGATGGCCAGAACTCTTCA
* * * ** * * *
388210 TCACGTAGGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCCTCG
1 TCACGTAGGAACCATGTCATCACCTTAGATGGCCAGAAC-TCTTCA
*
388253 TCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 TCACGTAGGAACCATGTCATCACC-TTAGATGGCCAGAACTCTTCA
388299 TCACGTA
1 TCACGTA
388306 TGAGTCGTGT
Statistics
Matches: 106, Mismatches: 20, Indels: 20
0.73 0.14 0.14
Matches are distributed among these distances:
39 2 0.02
40 33 0.31
42 1 0.01
43 27 0.25
45 5 0.05
46 37 0.35
47 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (45 bp):
TCACGTAGGAACCATGTCATCACCTTAGATGGCCAGAACTCTTCA
Found at i:388212 original size:40 final size:40
Alignment explanation
Indices: 388157--388357 Score: 161
Period size: 40 Copynumber: 4.8 Consensus size: 40
388147 CTTTAGATGG
*
388157 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCAGA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAGA
* * **
388197 CCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAG---A
* * * * * * *
388240 CCAG-CCGTCCTCGTCACGTAGGAACCATGTTATCACCTTTAGA
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTGTCATC-CC--CAGA
* *
388283 TGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCAGA
1 ---CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAGA
* *
388326 CCAGATCTCCTCATCACGTAGGAGCCGTGTCA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCA
388358 CCTTTAGACG
Statistics
Matches: 124, Mismatches: 26, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
40 62 0.50
42 1 0.01
43 30 0.24
44 1 0.01
45 2 0.02
46 27 0.22
47 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAGA
Found at i:388340 original size:129 final size:129
Alignment explanation
Indices: 388105--388357 Score: 479
Period size: 129 Copynumber: 2.0 Consensus size: 129
388095 ATTATCCTAG
388105 AGATAACCAGCCATCCTCGTCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCATCCTCGTCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
*
388170 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
*
388234 AGATAACCAGCCGTCCTCGTCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCATCCTCGTCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
*
388299 TCACGTATGAGTCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
66 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
388358 CCTTTAGACG
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 121 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (129 bp):
AGATAACCAGCCATCCTCGTCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
Found at i:388386 original size:129 final size:129
Alignment explanation
Indices: 388118--388388 Score: 420
Period size: 129 Copynumber: 2.1 Consensus size: 129
388108 TAACCAGCCA
*
388118 TCCTCGTCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
1 TCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
* * **
388183 GTGTCATCCCCAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
66 GTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGAGAACCAAACG
* *
388247 TCCTCGTCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGTC
1 TCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
* *
388312 GTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTC-ACCTTTAGACGACCCAAAC
66 GTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC-ATAGA-GAACCAAAC
388376 -
129 G
*
388376 TCTTCATCACGTA
1 TCCTCATCACGTA
388389 TGAGCAGTGT
Statistics
Matches: 131, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
128 3 0.02
129 123 0.94
130 5 0.04
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (129 bp):
TCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
GTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGAGAACCAAACG
Found at i:389042 original size:9 final size:9
Alignment explanation
Indices: 389028--389052 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
389018 ATCTAAATAA
389028 AAAATCCCG
1 AAAATCCCG
389037 AAAATCCCG
1 AAAATCCCG
389046 AAAATCC
1 AAAATCC
389053 GGGATTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.32, G:0.08, T:0.12
Consensus pattern (9 bp):
AAAATCCCG
Found at i:391875 original size:3 final size:3
Alignment explanation
Indices: 391864--391921 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
391854 GTTTTTTTCG
*
391864 TTA TT- TTA TTA TTA TTA TTA TTA TTAA CTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
391908 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
391922 TAATATATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
2 4 0.08
3 45 0.88
4 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:391930 original size:12 final size:11
Alignment explanation
Indices: 391870--391930 Score: 54
Period size: 12 Copynumber: 5.4 Consensus size: 11
391860 TTCGTTATTT
*
391870 TATTATTATTA
1 TATTATTAATA
391881 TTATTATTAACTA
1 -TATTATTAA-TA
391894 TATTATT-AT-
1 TATTATTAATA
*
391903 TATTATTATTA
1 TATTATTAATA
391914 TTATTATTTAATA
1 -TATTA-TTAATA
391927 TATT
1 TATT
391931 TTTACATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
9 7 0.17
10 2 0.05
11 1 0.02
12 24 0.59
13 7 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATTAATA
Found at i:391930 original size:15 final size:15
Alignment explanation
Indices: 391879--391930 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
391869 TTATTATTAT
391879 TATTATTA-TTAACTA
1 TATTATTATTTAA-TA
*
391894 TATTATTATTATTATTA
1 TATTATTA-T-TTAATA
391911 TTATTATTATTTAATA
1 -TATTATTATTTAATA
391927 TATT
1 TATT
391931 TTTACATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 12 0.39
16 5 0.16
17 3 0.10
18 11 0.35
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTATTTAATA
Found at i:399656 original size:18 final size:18
Alignment explanation
Indices: 399615--399656 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
399605 CAGATCGAGA
399615 AAACATACATATATACAC
1 AAACATACATATATACAC
*
399633 ATACATACATA-ATACATC
1 AAACATACATATATACA-C
399651 AAACAT
1 AAACAT
399657 TTAACATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (18 bp):
AAACATACATATATACAC
Found at i:400259 original size:156 final size:153
Alignment explanation
Indices: 399967--400250 Score: 362
Period size: 156 Copynumber: 1.8 Consensus size: 153
399957 AATTCAGTCT
* * * * * * *
399967 CTTGAGACATTTTTTCTTTGGGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTC
1 CTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGGTTCACATAAAACAAAATTAATCTC
* *
400032 ATTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCACAAATTTTG
66 ACTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACACTTTTCCAC--A-TTTG
400097 AGAATTTTAAAACAAATTGTGTTTCG
128 AGAATTTTAAAACAAATTGTGTTTCG
400123 CTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGGTTCAC-TAAAAACAAAATTAATCT
1 CTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGGTTCACAT-AAAACAAAATTAATCT
* * * *
400187 CACCTT-AGATTCTTGTTTCTTTCAAAACAAATTTCGTCTCGCTTGAGAC-CTTTTCC-C-TTTG
65 CA-CTTGAGA-TCGTATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACACTTTTCCACATTTG
400248 AGA
128 AGA
400251 TCCAAATTTC
Statistics
Matches: 112, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
151 7 0.06
155 2 0.02
156 66 0.59
157 37 0.33
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (153 bp):
CTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGGTTCACATAAAACAAAATTAATCTC
ACTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACACTTTTCCACATTTGAGA
ATTTTAAAACAAATTGTGTTTCG
Found at i:400334 original size:36 final size:36
Alignment explanation
Indices: 400311--400408 Score: 101
Period size: 36 Copynumber: 2.8 Consensus size: 36
400301 TCGTTTCCTC
400311 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCACT
1 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCACT
* ** * *
400347 AAAAACAAATTTTGTCTCATTTGAGACTATAT--CT
1 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCACT
* * * *
400381 TAAAGCAAATTTTGTCTCACTTGAGACA
1 AAAAACAAACTTTGTCTCGCTTGAGACA
400409 TCATTTTCTC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 26 0.49
36 27 0.51
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (36 bp):
AAAAACAAACTTTGTCTCGCTTGAGACAATTTCACT
Found at i:400715 original size:28 final size:28
Alignment explanation
Indices: 400652--400753 Score: 125
Period size: 29 Copynumber: 3.6 Consensus size: 28
400642 TCTGGAGACA
* * *
400652 GTTTCTCTTGAGATAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAAAATCTTTGAGTCT
*
400680 GTTCCTTTTGAATAAAAATCTTTGAGT-T
1 GTTTCTTTTGAA-AAAAATCTTTGAGTCT
400708 GTTTCTTTTGAAACAAATATCTTTGAGTCT
1 GTTTCTTTTGAAA-AAA-ATCTTTGAGTCT
*
400738 ATTTCTTTTGAAAAAA
1 GTTTCTTTTGAAAAAA
400754 TTTATCTCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
27 1 0.02
28 24 0.38
29 26 0.41
30 13 0.20
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (28 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTCT
Found at i:400808 original size:60 final size:63
Alignment explanation
Indices: 400709--400846 Score: 151
Period size: 62 Copynumber: 2.2 Consensus size: 63
400699 CTTTGAGTTG
*
400709 TTTCTTTTGAAACAAATATCTTTGAGTCTATTTCTTTTG-AA-AAAATTTATCTC-CTAAAGACA
1 TTTCTTTTG-AA-AAATATCTTTGAGTCTATTTCCTTTGAAACAAAATTT-TCTCTCTAAAGACA
400771 A
63 A
* * **
400772 TTTCTTTTGAAAAA-ATCTTTGAGT-TGGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAA
1 TTTCTTTTGAAAAATATCTTTGAGTCT-ATTTCCTTTGAAACAAAATTTTCTCTCTAAAGACAA
*
400834 CTTCTTTTGAAAA
1 TTTCTTTTGAAAA
400847 TACCCACCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
59 1 0.02
60 18 0.28
61 8 0.12
62 29 0.45
63 9 0.14
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
TTTCTTTTGAAAAATATCTTTGAGTCTATTTCCTTTGAAACAAAATTTTCTCTCTAAAGACAA
Found at i:400986 original size:15 final size:15
Alignment explanation
Indices: 400963--401006 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
400953 TTTTGAGTCG
*
400963 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
400978 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
400993 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
401007 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:401487 original size:40 final size:40
Alignment explanation
Indices: 401429--401793 Score: 211
Period size: 40 Copynumber: 8.7 Consensus size: 40
401419 CCAGTCGTCC
* * *
401429 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCATCCCTAGACCAGATCTCT
* * * * *
401469 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATC-TCT
* * * *
401512 TCATCACATAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATC-CC--TAGA---CCAGATCTCT
* *
401558 TCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCA-TCCCTAGACCAGATCTCT
* * *
401598 TCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATC-TCT
* * *
401640 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATC-CC--TAGA---CCAGATCTCT
* *
401686 TCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCA-TCCCTAGACCAGATCTCT
* * *
401726 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCA-AACTCT
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATCTCT
* * *
401768 TCATCACGTACGAGCAGTGTCGTCCC
1 TCATCACGTAGGAGCCGTGTCATCCC
401794 CAACAACCAA
Statistics
Matches: 250, Mismatches: 45, Indels: 58
0.71 0.13 0.16
Matches are distributed among these distances:
38 3 0.01
39 3 0.01
40 85 0.34
41 1 0.00
42 53 0.21
43 37 0.15
44 3 0.01
46 59 0.24
47 6 0.02
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (40 bp):
TCATCACGTAGGAGCCGTGTCATCCCTAGACCAGATCTCT
Found at i:401777 original size:128 final size:129
Alignment explanation
Indices: 401429--401761 Score: 589
Period size: 128 Copynumber: 2.6 Consensus size: 129
401419 CCAGTCGTCC
* * *
401429 TCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
*
401493 CATAGATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
401558 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
*
401622 CTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
401686 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
401751 ATAGATAACCA
66 ATAGATAACCA
401762 AACTCTTCAT
Statistics
Matches: 195, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
128 125 0.64
129 65 0.33
130 5 0.03
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:401955 original size:3 final size:3
Alignment explanation
Indices: 401944--401998 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
401934 GTTTTTTTCG
*
401944 TTA TT- TTA TTA TTA TTA TTA TTA TTAA CTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
401988 TTA TTA TTA TT
1 TTA TTA TTA TT
401999 TAATATATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
2 4 0.08
3 42 0.88
4 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:402007 original size:12 final size:11
Alignment explanation
Indices: 401950--402007 Score: 52
Period size: 12 Copynumber: 5.4 Consensus size: 11
401940 TTCGTTATTT
*
401950 TATTATTATTA
1 TATTATTAATA
401961 TTATTATTAACTA
1 -TATTATTAA-TA
401974 TATTATT-AT-
1 TATTATTAATA
401983 TATTATT-AT-
1 TATTATTAATA
401992 TATTATTTAATA
1 TATTA-TTAATA
402004 TATT
1 TATT
402008 TTTACATATT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
9 14 0.34
10 3 0.07
11 3 0.07
12 19 0.46
13 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATTAATA
Found at i:402007 original size:15 final size:14
Alignment explanation
Indices: 401949--402007 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 14
401939 TTTCGTTATT
401949 TTATTATT-AT-TA
1 TTATTATTAATATA
401961 TTATTATTAACTATA
1 TTATTATTAA-TATA
*
401976 TTATTATTATTATTA
1 TTATTATTAATA-TA
401991 TTATTATTTAATATA
1 TTATTA-TTAATATA
402006 TT
1 TT
402008 TTTACATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 8 0.20
13 1 0.03
14 3 0.08
15 23 0.57
16 5 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATTATTAATATA
Found at i:407895 original size:21 final size:23
Alignment explanation
Indices: 407866--407918 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 23
407856 TTTTAATTTT
*
407866 TTATAAAAATTATA-TTA-AATA
1 TTATAAAAAGTATATTTATAATA
*
407887 TTCTAAAAAGTATATTTATAATA
1 TTATAAAAAGTATATTTATAATA
407910 TTATAAAAA
1 TTATAAAAA
407919 AATCTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 12 0.44
22 3 0.11
23 12 0.44
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TTATAAAAAGTATATTTATAATA
Found at i:407975 original size:22 final size:23
Alignment explanation
Indices: 407941--407987 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
407931 ATATTTGTTT
*
407941 TTTTAAATCATATT-ATTAATTTA
1 TTTTAAATAATATTAATT-ATTTA
407964 TTTT-AATAATATTAATTATTTA
1 TTTTAAATAATATTAATTATTTA
407986 TT
1 TT
407988 AAAATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTAAATAATATTAATTATTTA
Found at i:408019 original size:23 final size:24
Alignment explanation
Indices: 407989--408046 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
407979 TTATTTATTA
407989 AAAT-TTATTTTAAAT-AACTAATT
1 AAATATTATTTTAAATAAAC-AATT
*
408012 -AATATTATTTAAAATAAACAATT
1 AAATATTATTTTAAATAAACAATT
*
408035 AAATATAATTTT
1 AAATATTATTTT
408047 TAAAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.10
23 14 0.48
24 12 0.41
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATATTATTTTAAATAAACAATT
Found at i:410604 original size:64 final size:66
Alignment explanation
Indices: 410495--410703 Score: 236
Period size: 65 Copynumber: 3.2 Consensus size: 66
410485 TTTCAATGTG
* * * *
410495 ATGCACCGATGCAC-CAATCCATGCATCGATGCAC-CATGGAATTAATTG-AACATCGAATGCAG
1 ATGCATCGATGCACTC--TCCATGCATCGATGCACTCAGGGTATTAATTGAAACATCGAATGCAC
410557 TTC
64 TTC
* *
410560 ATGCATCGATGCACTCTCCATGCATCGATGCACTC-GGGTTTTAA-TGAAAACATCGAATGCATT
1 ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGGTATTAATTG-AAACATCGAATGCACT
*
410623 TT
65 TC
* * *
410625 ATGCATCGATGCACAT-ACCATGCATCGATGCACTCAGGCTATT--TTGAAACATTGAATGCACT
1 ATGCATCGATGCAC-TCTCCATGCATCGATGCACTCAGGGTATTAATTGAAACATCGAATGCACT
410687 TC
65 TC
410689 ATGCATCGATGCACT
1 ATGCATCGATGCACT
410704 AAGGGTCCAA
Statistics
Matches: 125, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
63 3 0.02
64 52 0.42
65 63 0.50
66 7 0.06
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (66 bp):
ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGGTATTAATTGAAACATCGAATGCACTT
C
Found at i:416457 original size:21 final size:22
Alignment explanation
Indices: 416411--416486 Score: 84
Period size: 21 Copynumber: 3.5 Consensus size: 22
416401 ACACCTAACA
* *
416411 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATACACCCTTGAAT
* *
416433 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATACACCCTTGAAT
416454 GTGCA-CTGATACACGCCTTGAAT
1 GTGCATC-GATACAC-CCTTGAAT
416477 GTGCATCGAT
1 GTGCATCGAT
416487 GCACAAGGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.02
21 17 0.38
22 12 0.27
23 14 0.31
24 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (22 bp):
GTGCATCGATACACCCTTGAAT
Found at i:416480 original size:23 final size:21
Alignment explanation
Indices: 416395--416486 Score: 82
Period size: 21 Copynumber: 4.3 Consensus size: 21
416385 TGCTTAATGT
*
416395 ATCGATACACC-T-AACAGTGC
1 ATCGATACACCTTGAA-TGTGC
*
416415 ATCGATGCATCCTTGAATGTGC
1 ATCGATACA-CCTTGAATGTGC
* *
416437 ATCGATACACCATGAAGGTGC
1 ATCGATACACCTTGAATGTGC
416458 A-CTGATACACGCCTTGAATGTGC
1 ATC-GATACA--CCTTGAATGTGC
416481 ATCGAT
1 ATCGAT
416487 GCACAAGGTC
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
20 9 0.16
21 19 0.33
22 13 0.22
23 16 0.28
24 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (21 bp):
ATCGATACACCTTGAATGTGC
Found at i:418427 original size:14 final size:15
Alignment explanation
Indices: 418402--418430 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
418392 TTGATTTTGA
418402 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
418417 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
418431 AAATGTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:419134 original size:45 final size:45
Alignment explanation
Indices: 419061--419150 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
419051 GATGCACCAA
419061 TCCATGCATCGATGCACCATGGAATTAATTG-AACATCGAATGCAG
1 TCCATGCATCGATGCACCATGGAATTAA-TGAAACATCGAATGCAG
* **
419106 TCCATGCATCGATGCA-CTTGGGTTTTAATGAAAACATCGAATGCA
1 TCCATGCATCGATGCACCAT-GGAATTAATG-AAACATCGAATGCA
419151 TTTGATGCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
44 4 0.10
45 22 0.56
46 13 0.33
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (45 bp):
TCCATGCATCGATGCACCATGGAATTAATGAAACATCGAATGCAG
Found at i:419232 original size:17 final size:19
Alignment explanation
Indices: 419204--419252 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
419194 TATTTTGAAA
419204 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
419222 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
419241 CACCGATGCACT
1 CATCGATGCACT
419253 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:420641 original size:15 final size:15
Alignment explanation
Indices: 420620--420658 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
420610 GTCTTTATCT
420620 ATCTTTATTATATTA
1 ATCTTTATTATATTA
* *
420635 GTCTTTATTATCTTA
1 ATCTTTATTATATTA
420650 ATCTTTATT
1 ATCTTTATT
420659 CTTGATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.03, T:0.62
Consensus pattern (15 bp):
ATCTTTATTATATTA
Found at i:425496 original size:34 final size:35
Alignment explanation
Indices: 425453--425554 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
425443 TTTCGTCATA
*
425453 TTAGGATTCAAACTCCTAAAAATATGATAGAA-TT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
425487 TTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
425522 TGCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 T--TAGGATTCAAACTCCTAAAAATAGGATAGA
425555 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (35 bp):
TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:425578 original size:37 final size:37
Alignment explanation
Indices: 425454--425589 Score: 152
Period size: 37 Copynumber: 3.8 Consensus size: 37
425444 TTCGTCATAT
* *
425454 TAGGATTCAAACTCCTAAAAATATGATAGAATT-T--
1 TAGGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
* *
425488 TAGGATTCAAACTCCTAAAAATAGGATAAAATTTTGC
1 TAGGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
* *
425525 TAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTAC
1 TAGGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
** * * *
425562 TATTATTTAAATTCCTAAAGATAGGATA
1 TAGGATTCAAACTCCTAAAAATAGGATA
425590 CACACTATAA
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
34 31 0.35
35 1 0.01
37 56 0.64
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (37 bp):
TAGGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
Found at i:425982 original size:18 final size:17
Alignment explanation
Indices: 425943--425985 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
425933 ATTATATGGA
425943 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
425959 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
425977 TATTATTAT
1 TATTATTAT
425986 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:426010 original size:8 final size:9
Alignment explanation
Indices: 425980--426061 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 9
425970 ATGTTATTAT
*
425980 TATTATATG
1 TATTATATA
425989 TATATATATA
1 TAT-TATATA
425999 TATTATAT-
1 TATTATATA
*
426007 TATTCTCAT-
1 TATTAT-ATA
* *
426016 TCTTTTACTA
1 TATTATA-TA
*
426026 TATTTTAT-
1 TATTATATA
426034 TATTAT-TA
1 TATTATATA
426042 TA-TATATA
1 TATTATATA
426050 TA-TATATA
1 TATTATATA
426058 TATT
1 TATT
426062 TCTTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
7 4 0.07
8 25 0.42
9 17 0.28
10 14 0.23
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (9 bp):
TATTATATA
Found at i:426180 original size:17 final size:17
Alignment explanation
Indices: 426158--426192 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
426148 ATAGTTTATT
*
426158 TATATACCTATTATTAA
1 TATATACATATTATTAA
*
426175 TATATATATATTATTAA
1 TATATACATATTATTAA
426192 T
1 T
426193 TATTTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATACATATTATTAA
Found at i:426465 original size:38 final size:40
Alignment explanation
Indices: 426414--426493 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
426404 AGTGAGAGGG
*
426414 TAGCTTTTCTATTTT-TAAATA-TTTGGTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
426452 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
426492 TA
1 TA
426494 TTTTCCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:426569 original size:9 final size:9
Alignment explanation
Indices: 426548--426581 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
426538 TTTTTTTTCC
426548 TTTATCTTA-
1 TTTAT-TTAT
426557 TTTATTTAT
1 TTTATTTAT
426566 TTTATTTAT
1 TTTATTTAT
426575 TTTATTT
1 TTTATTT
426582 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:426570 original size:13 final size:14
Alignment explanation
Indices: 426548--426582 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
426538 TTTTTTTTCC
*
426548 TTTATCTTATTTA-
1 TTTATTTTATTTAT
426561 TTTATTTTATTTAT
1 TTTATTTTATTTAT
426575 TTTATTTT
1 TTTATTTT
426583 TCCCTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:429662 original size:22 final size:22
Alignment explanation
Indices: 429612--429665 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
429602 ATTCAATCAG
*
429612 AACAAAAAG-GGCAAAAAGAAA
1 AACAAAAAGAAGCAAAAAGAAA
429633 AA-AGAAAAGAAGCAAAAA-AAA
1 AACA-AAAAGAAGCAAAAAGAAA
429654 TAACAAAAAGAA
1 -AACAAAAAGAA
429666 AAAGGGACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
21 10 0.36
22 16 0.57
23 1 0.04
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.02
Consensus pattern (22 bp):
AACAAAAAGAAGCAAAAAGAAA
Found at i:430295 original size:22 final size:22
Alignment explanation
Indices: 430267--430310 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
430257 AGCTACCCCA
430267 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
430289 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
430311 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:430780 original size:18 final size:18
Alignment explanation
Indices: 430746--430781 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
430736 TCAACATCAA
* *
430746 ATATTGGGGTATTTTTGG
1 ATATTGGGGCATCTTTGG
430764 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
430782 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.33, T:0.44
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:431444 original size:36 final size:36
Alignment explanation
Indices: 431346--431471 Score: 216
Period size: 37 Copynumber: 3.4 Consensus size: 36
431336 ATTGAAAACA
*
431346 TTTCCCTTGAAATAAATTTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAA-TTTTGTCTCTCTTGAGACAG
*
431383 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-TAAATTTTGTCTCTCTTGAGACAG
431420 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
431456 TTTCCCTTGAAATAAA
1 TTTCCCTTGAAATAAA
431472 ATATTTGAAT
Statistics
Matches: 85, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
36 39 0.46
37 43 0.51
38 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
Found at i:431567 original size:138 final size:138
Alignment explanation
Indices: 431261--431672 Score: 490
Period size: 138 Copynumber: 3.0 Consensus size: 138
431251 TCACTAGAAG
* * * *
431261 AGTTTTGTCTCTCATGAAACAGTTTCCCTTGAAACAAA--TTGTCTCCCTTGAGACAGTTTCTCT
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCT
* * * * * * *
431324 TGAAATATAAACA-TTGAAAACA-TTTCCCTTGAAATAAATTTTTGTCTCTCTTGAGATAGTTTC
66 TGAAATA-AAATATTTGAATATATTTTCCC-TAAAACAAA-TTTTGTCTCCCTTGAGACAGTTTC
431387 CCTTGAAACAA
128 CCTTGAAACAA
* *
431398 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCT
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCT
* * * * **
431463 TGAAATAAAATATTTGAATATGTTTTCTCTAAAACAAATTTCGTCCCCCTTGAGACAGTTTCTTT
66 TGAAATAAAATATTTGAATATATTTTCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCT
* *
431528 TGGAACTA
131 TGAAACAA
* ** *
431536 AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTCCGTCTATCTTGAGACAGTTTCCCT
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCT
* * * * * *
431601 TGAAACAAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCT
66 TGAAATAAAATATTTGAATATATTTTCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCT
431666 TGAAACA
131 TGAAACA
431673 CAAAATCTTC
Statistics
Matches: 232, Mismatches: 39, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
137 34 0.15
138 150 0.65
139 43 0.19
140 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (138 bp):
AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCT
TGAAATAAAATATTTGAATATATTTTCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCT
TGAAACAA
Found at i:431594 original size:36 final size:36
Alignment explanation
Indices: 431511--431609 Score: 126
Period size: 36 Copynumber: 2.7 Consensus size: 36
431501 TTTCGTCCCC
* * * ** *
431511 CTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCT
1 CTTGAGACAGTTTCTCTTGAAAC-AAATTCCGTCTAT
431548 CTTGAGACAGTTTCTCTTGAAACAAATTCCGTCTAT
1 CTTGAGACAGTTTCTCTTGAAACAAATTCCGTCTAT
*
431584 CTTGAGACAGTTTCCCTTGAAACAAA
1 CTTGAGACAGTTTCTCTTGAAACAAA
431610 ATCTTTGAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 34 0.62
37 21 0.38
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.37
Consensus pattern (36 bp):
CTTGAGACAGTTTCTCTTGAAACAAATTCCGTCTAT
Found at i:432576 original size:105 final size:105
Alignment explanation
Indices: 432345--433005 Score: 958
Period size: 105 Copynumber: 6.3 Consensus size: 105
432335 GCCATCCGCG
* * * * * *
432345 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
432410 GGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
432454 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
432519 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
432559 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
432624 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
432664 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
432729 ACCGCTGCTTGTCAACAACAACTTCCCAATCTT-AGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TTCAGAGCCA
432769 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
432834 ACCGCTGCTTGTCAATAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
432869 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * * * *
432934 ACGGATGGTTGTCAACAAATAATTTCCCAGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
432975 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
433006 TGGAACAATG
Statistics
Matches: 511, Mismatches: 32, Indels: 21
0.91 0.06 0.04
Matches are distributed among these distances:
99 2 0.00
100 79 0.15
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 307 0.60
106 83 0.16
107 5 0.01
109 22 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:433597 original size:34 final size:36
Alignment explanation
Indices: 433553--433654 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
433543 TTTCGTCATA
*
433553 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
433588 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
433623 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
433655 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:433678 original size:37 final size:37
Alignment explanation
Indices: 433551--433688 Score: 156
Period size: 37 Copynumber: 3.8 Consensus size: 37
433541 TTTTTCGTCA
* *
433551 TACTAGGATTCAAACTCCTAAAAATATGATAGAATT-
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
*
433587 T--TAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
433622 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
** * * *
433659 TACTATTATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
433689 CCACACTATA
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
34 31 0.35
35 1 0.01
36 1 0.01
37 55 0.62
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
Done.