Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015288.1 Kokia drynarioides strain JFW-HI SEQ_130333, 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: 637797
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 464 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:347871 original size:15 final size:15
Alignment explanation
Indices: 347851--347882 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
347841 GGCAAAGGCC
347851 GTGGTAGAGGTGATG
1 GTGGTAGAGGTGATG
*
347866 GTGGTAGAGGTGCTG
1 GTGGTAGAGGTGATG
347881 GT
1 GT
347883 CAACATGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.03, G:0.53, T:0.28
Consensus pattern (15 bp):
GTGGTAGAGGTGATG
Found at i:352662 original size:19 final size:20
Alignment explanation
Indices: 352638--352685 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
352628 TAAAACAAAT
352638 AAAATGCAAAGACAA-TAAA
1 AAAATGCAAAGACAATTAAA
*
352657 AAAATGCAATGACAATTAAA
1 AAAATGCAAAGACAATTAAA
352677 ATAAATGCA
1 A-AAATGCA
352686 TGCAACTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 14 0.54
20 5 0.19
21 7 0.27
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (20 bp):
AAAATGCAAAGACAATTAAA
Found at i:359246 original size:18 final size:17
Alignment explanation
Indices: 359219--359253 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
359209 ACTGTGTCTG
359219 GGTCTGTGATCGCATAT
1 GGTCTGTGATCGCATAT
359236 GGTCATGTGATCGCATAT
1 GGTC-TGTGATCGCATAT
359254 TATCTGGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (17 bp):
GGTCTGTGATCGCATAT
Found at i:365846 original size:128 final size:128
Alignment explanation
Indices: 365618--365876 Score: 455
Period size: 128 Copynumber: 2.0 Consensus size: 128
365608 TACTAGCGAC
* * *
365618 TAAGGTACGCCACTTGTTTGAATTAATTGGTGGGCGATATTCATGAAAATTATTTTTTAATACTA
1 TAAGGTACGCCACTTATTTGAATTAATTGGTGGGCGATATGCATGAAAATTATTGTTTAATACTA
365683 TTTAATTGAGACTTAATTGGTGTTAATAAATTCAATTGAAGGTATATGAATATGTATGGTATT
66 TTTAATTGAGACTTAATTGGTGTTAATAAATTCAATTGAAGGTATATGAATATGTATGGTATT
* * *
365746 TAAGGTACGCCACTTATTTTAATTAATTGGTGGGTGATATGCATGAAAATTATTGTTTAATATTA
1 TAAGGTACGCCACTTATTTGAATTAATTGGTGGGCGATATGCATGAAAATTATTGTTTAATACTA
*
365811 TTTAATTGAGGCTTAATTGGTGTTAATAAATTCAATTGAAGGTATATGAATATGTATGGTATT
66 TTTAATTGAGACTTAATTGGTGTTAATAAATTCAATTGAAGGTATATGAATATGTATGGTATT
365874 TAA
1 TAA
365877 TCATAGTTAA
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 124 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (128 bp):
TAAGGTACGCCACTTATTTGAATTAATTGGTGGGCGATATGCATGAAAATTATTGTTTAATACTA
TTTAATTGAGACTTAATTGGTGTTAATAAATTCAATTGAAGGTATATGAATATGTATGGTATT
Found at i:367824 original size:16 final size:18
Alignment explanation
Indices: 367785--367818 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
367775 TAAGTTTATA
367785 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
367802 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
367819 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:371589 original size:80 final size:81
Alignment explanation
Indices: 371439--371597 Score: 221
Period size: 80 Copynumber: 2.0 Consensus size: 81
371429 AGCCAAATGG
** ** * *
371439 AACCAATCATTTTATTATTCATCAATTATCACAAAGATTATTGTTCTAGTGATAGAAACCAAAGC
1 AACCAATCATTTTATTATTCATCAATTATCACAAAGACAATCATTCTACTGATAGAAAACAAAGC
371504 AGAGTCAAGATCCAAC
66 AGAGTCAAGATCCAAC
* * * *
371520 AACCATTCATTTTATTATTCGTCCATTATCAGAAA-ACAATCATTCTACTGATAGAAAACAAAGC
1 AACCAATCATTTTATTATTCATCAATTATCACAAAGACAATCATTCTACTGATAGAAAACAAAGC
371584 AGAGTCAAGATCCA
66 AGAGTCAAGATCCA
371598 GCACCTTGCA
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 37 0.54
81 31 0.46
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (81 bp):
AACCAATCATTTTATTATTCATCAATTATCACAAAGACAATCATTCTACTGATAGAAAACAAAGC
AGAGTCAAGATCCAAC
Found at i:378164 original size:17 final size:17
Alignment explanation
Indices: 378142--378174 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
378132 CATTGGGATG
378142 GAACT-GAGGAATGAAAT
1 GAACTGGAGGAA-GAAAT
378159 GAACTGGAGGAAGAAA
1 GAACTGGAGGAAGAAA
378175 ACTTTATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.33, T:0.12
Consensus pattern (17 bp):
GAACTGGAGGAAGAAAT
Found at i:379844 original size:18 final size:16
Alignment explanation
Indices: 379813--379851 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
379803 TAATTTTGAC
*
379813 GATGATGAAGGATGGT
1 GATGATGAAGGATGAT
379829 GATGATGCATAGGATGAT
1 GATGATG-A-AGGATGAT
379847 GATGA
1 GATGA
379852 AATAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.33, C:0.03, G:0.38, T:0.26
Consensus pattern (16 bp):
GATGATGAAGGATGAT
Found at i:381957 original size:26 final size:26
Alignment explanation
Indices: 381909--381962 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
381899 AAGTTGTACA
*
381909 TCAAAAAAATATCTTTAGAAATTTTC
1 TCAAAAAAATATCTTTAAAAATTTTC
*
381935 TCAAAAAAAT-TTTTTAAAGAATTTTC
1 TCAAAAAAATATCTTTAAA-AATTTTC
381961 TC
1 TC
381963 TTAACAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (26 bp):
TCAAAAAAATATCTTTAAAAATTTTC
Found at i:382145 original size:59 final size:61
Alignment explanation
Indices: 382075--382192 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 61
382065 ATTACTTTAA
* * *
382075 TATTAAATTAATATAATACTTATCAAC-ATAT-ATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTATCAACAATATAACATTAAATTAAATTTAATATTAAATCT
* *
382134 TATTAAATTAATAGAATATTTATCTACAATATAAACATTAAATTAAATTTAATATTAAA
1 TATTAAATTAATAGAATACTTATCAACAATAT-AACATTAAATTAAATTTAATATTAAA
382193 ATAATCACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
59 24 0.47
60 4 0.08
62 23 0.45
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (61 bp):
TATTAAATTAATAGAATACTTATCAACAATATAACATTAAATTAAATTTAATATTAAATCT
Found at i:382192 original size:17 final size:17
Alignment explanation
Indices: 382170--382259 Score: 71
Period size: 17 Copynumber: 5.4 Consensus size: 17
382160 CAATATAAAC
382170 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
* * *
382187 ATTAAAAT-AA-TCACT
1 ATTAAATTAAATTTAAT
*
382202 -TTAATATTAAATTTAAA
1 ATTAA-ATTAAATTTAAT
** *
382219 ATTCTATTAAA-ATAATT
1 ATTAAATTAAATTTAA-T
382236 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
382253 ATTAAAT
1 ATTAAAT
382260 ATATTAAAAT
Statistics
Matches: 53, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
14 4 0.08
15 5 0.09
16 7 0.13
17 32 0.60
18 5 0.09
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTAAATTAAATTTAAT
Found at i:386214 original size:9 final size:9
Alignment explanation
Indices: 386200--386230 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
386190 GATCAAGTAA
386200 AATTAAATT
1 AATTAAATT
386209 AATTAAATT
1 AATTAAATT
386218 AATTAAAATT
1 AATT-AAATT
386228 AAT
1 AAT
386231 ATGATACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:386801 original size:59 final size:60
Alignment explanation
Indices: 386701--386815 Score: 171
Period size: 59 Copynumber: 1.9 Consensus size: 60
386691 AGTGATTATC
* *
386701 TTAATATTAAATTTAATTAATAGAATATTATAGATAAATATTCTATTAATTTAATAAGAT
1 TTAATATTAAATTTAATTAATAGAATATTAAAGATAAATATTATATTAATTTAATAAGAT
**
386761 TTAATATTAAATTTAATATAATA-TTTA-TAAAGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAAT-TAATAGAATATTAAAGATAAATATTATATTAATTTAATA
386816 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 26 0.52
60 19 0.38
61 5 0.10
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (60 bp):
TTAATATTAAATTTAATTAATAGAATATTAAAGATAAATATTATATTAATTTAATAAGAT
Found at i:389337 original size:52 final size:52
Alignment explanation
Indices: 389094--389341 Score: 318
Period size: 52 Copynumber: 4.8 Consensus size: 52
389084 ATTTCACTTC
* * * * ** *
389094 ATTCATATACTCACAATGACACATAGCCACCAGACCTTATAATCCACAAGGG
1 ATTCATATACTCACGATGACACATAGTCATCAGACCTTTTAATCCGTAAAGG
* * **
389146 ATTCGTATACTCACGATGACACAGAGTCATC-GAACCCCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCAG-ACCTTTTAATCCGTAAAGG
* * * *
389198 ATCCATATACTCACGATGATACTTAGTCATCGGACCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCAGACCTTTTAATCCGTAAAGG
*
389250 ATTCATATACTCACGATGACACTTAGTCATCAGACCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCAGACCTTTTAATCCGTAAAGG
* *
389302 ATTCATATACTCACGATGACACATAGCCATAAGACCTTTT
1 ATTCATATACTCACGATGACACATAGTCATCAGACCTTTT
389342 CGTTTATGAT
Statistics
Matches: 170, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
51 1 0.01
52 168 0.99
53 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGTCATCAGACCTTTTAATCCGTAAAGG
Found at i:394199 original size:35 final size:35
Alignment explanation
Indices: 394158--394227 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
394148 ACTTTATTCA
394158 TGATTTGACCTCAAATTTATATCATTTTTTCTACT
1 TGATTTGACCTCAAATTTATATCATTTTTTCTACT
394193 TGATTTGACCTCAAATTTATATCATTTTTTCTACT
1 TGATTTGACCTCAAATTTATATCATTTTTTCTACT
394228 GTAATACCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (35 bp):
TGATTTGACCTCAAATTTATATCATTTTTTCTACT
Found at i:398318 original size:31 final size:30
Alignment explanation
Indices: 398280--398338 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
398270 AACGATGGTG
398280 GTTCAGATAGTAGTAAAAATATGGATGATTA
1 GTTCAGATAGTAGTAAAAA-ATGGATGATTA
*
398311 GTTCAGATAGTAGTAAAAAATGTATGAT
1 GTTCAGATAGTAGTAAAAAATGGATGAT
398339 CATTCTGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.32
Consensus pattern (30 bp):
GTTCAGATAGTAGTAAAAAATGGATGATTA
Found at i:400844 original size:60 final size:61
Alignment explanation
Indices: 400728--400895 Score: 250
Period size: 60 Copynumber: 2.7 Consensus size: 61
400718 TTTGTTATTT
*
400728 ATTTATTT-ATCTATATTCATAAAATAATAAATAAATAATAAAATAAGATTATTATTATTTTAC
1 ATTTATTTAAT-TATATTCATAAAATAATAAATAAATAAT-AAA-AAGATTAATATTATTTTAC
* *
400791 ATTTATTTAATTATATTCATACAATAATAAATAAATAATAAAAA-ATTAATATTATTTTAT
1 ATTTATTTAATTATATTCATAAAATAATAAATAAATAATAAAAAGATTAATATTATTTTAC
*
400851 ATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAAAAA
1 ATTTATTTAATTATATTCATAAAATAATAAATAAAT-AATAAAAA
400896 TAAAAATAAT
Statistics
Matches: 98, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
60 48 0.49
61 10 0.10
62 3 0.03
63 35 0.36
64 2 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (61 bp):
ATTTATTTAATTATATTCATAAAATAATAAATAAATAATAAAAAGATTAATATTATTTTAC
Found at i:401488 original size:40 final size:40
Alignment explanation
Indices: 401422--401809 Score: 319
Period size: 40 Copynumber: 9.8 Consensus size: 40
401412 TATAGTTTTA
* * *
401422 GGGGTAAAAGATTGGATCGT-TTCAATCTGCCCCATGGTC
1 GGGGTAAGAGATCGGATGGTCTTCAATCTGCCCCATGGTC
* * *
401461 GGGGTAAGAGATCGAATGGTCTTCAATCTGCCCTC-TAGTT
1 GGGGTAAGAGATCGGATGGTCTTCAATCTGCCC-CATGGTC
* * * **
401501 AGGGTAAAATATTAGAT--TCCTTCAATCTGCCCCATGGTC
1 GGGGTAAGAGATCGGATGGT-CTTCAATCTGCCCCATGGTC
* * *
401540 GGGGTAAGAGATCGGATGGTCTTCAATTTGCCCTC-TAGTT
1 GGGGTAAGAGATCGGATGGTCTTCAATCTGCCC-CATGGTC
* * * * **
401580 AGGGTAAAAGATTGGATTG-CTTCAATCTAACCCATGGT-
1 GGGGTAAGAGATCGGATGGTCTTCAATCTGCCCCATGGTC
* * * * *
401618 AGGGTAAAAGATCGGATTG-CTTCAATCTACCCCATGGTT
1 GGGGTAAGAGATCGGATGGTCTTCAATCTGCCCCATGGTC
* *
401657 GGGGTAAGAGATCGGATGGTCTTTAATCTGCCTTC-TGGTC
1 GGGGTAAGAGATCGGATGGTCTTCAATCTGCC-CCATGGTC
* * * *
401697 GAGGTAAAAGATTGGATGGTCTTCTATCTGCCCCATGGTC
1 GGGGTAAGAGATCGGATGGTCTTCAATCTGCCCCATGGTC
* *
401737 GGGGTAAGAGATCAGATGATCTTCAATCTGCCCTC-TGGTC
1 GGGGTAAGAGATCGGATGGTCTTCAATCTGCCC-CATGGTC
* * * * *
401777 AGAGTAAGAGATTGAATGGTCTTCAATTTGCCC
1 GGGGTAAGAGATCGGATGGTCTTCAATCTGCCC
401810 ATTTCAGCTT
Statistics
Matches: 278, Mismatches: 58, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
38 39 0.14
39 74 0.27
40 160 0.58
41 5 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (40 bp):
GGGGTAAGAGATCGGATGGTCTTCAATCTGCCCCATGGTC
Found at i:401559 original size:79 final size:79
Alignment explanation
Indices: 401423--401809 Score: 324
Period size: 79 Copynumber: 4.9 Consensus size: 79
401413 ATAGTTTTAG
* * *
401423 GGGTAAAAGATTGGA-TCGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAA
1 GGGTAAAAGATTAGATTC-CTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAA
401487 TCTGCCCTCTAGTTA
65 TCTGCCCTCTAGTTA
*
401502 GGGTAAAATATTAGATTCCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTAGATTCCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
*
401567 TTGCCCTCTAGTTA
66 CTGCCCTCTAGTTA
* * ** * * *
401581 GGGTAAAAGATTGGATTGCTTCAATCTAACCCATGGT-AGGGTAAAAGATCGGATTG-CTTCAAT
1 GGGTAAAAGATTAGATTCCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
* * *
401644 CTACCC-CATGGTTG
66 CTGCCCTC-TAGTTA
* ** * * * * *
401658 GGGTAAGAGATCGGATGGT-CTTTAATCTGCCTTC-TGGTCGAGGTAAAAGATTGGATGGTCTTC
1 GGGTAAAAGATTAGAT--TCCTTCAATCTGCC-CCATGGTCGGGGTAAGAGATCGGATGGTCTTC
* * **
401721 TATCTGCCC-CATGGTCG
63 AATCTGCCCTC-TAGTTA
* * * * * *
401738 GGGTAAGAGATCAGATGAT-CTTCAATCTGCCCTC-TGGTCAGAGTAAGAGATTGAATGGTCTTC
1 GGGTAAAAGATTAGAT--TCCTTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGGATGGTCTTC
*
401801 AATTTGCCC
63 AATCTGCCC
401810 ATTTCAGCTT
Statistics
Matches: 259, Mismatches: 41, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
76 1 0.00
77 29 0.11
78 29 0.11
79 120 0.46
80 80 0.31
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (79 bp):
GGGTAAAAGATTAGATTCCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
CTGCCCTCTAGTTA
Found at i:401643 original size:117 final size:118
Alignment explanation
Indices: 401422--401809 Score: 358
Period size: 117 Copynumber: 3.3 Consensus size: 118
401412 TATAGTTTTA
* * * * * * * * *
401422 GGGGTAAAAGATTGGATCGT-TTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGAATGGTCTTC
1 GGGGTAAGAGATCGGATGGTCTTCAATTTGCCCTC-TGGTAGAGGTAAAAGATTGGATGGTCTTC
* * * * * *
401485 AATCT-GCCCTCTAGTTAGGGTAAAATATTAGATTCCTTCAATCTGCCCCATGGTC
65 AATCTAACCC-AT-GGTAGGGTAAAAGATCAGATTGCTTCAATCTGCCCCATGGTC
* *
401540 GGGGTAAGAGATCGGATGGTCTTCAATTTGCCCTCTAGTTAG-GGTAAAAGATTGGATTG-CTTC
1 GGGGTAAGAGATCGGATGGTCTTCAATTTGCCCTCT-GGTAGAGGTAAAAGATTGGATGGTCTTC
* * *
401603 AATCTAACCCATGGTAGGGTAAAAGATCGGATTGCTTCAATCTACCCCATGGTT
65 AATCTAACCCATGGTAGGGTAAAAGATCAGATTGCTTCAATCTGCCCCATGGTC
* * * * *
401657 GGGGTAAGAGATCGGATGGTCTTTAATCTGCCTTCTGGTCGAGGTAAAAGATTGGATGGTCTTCT
1 GGGGTAAGAGATCGGATGGTCTTCAATTTGCCCTCTGGTAGAGGTAAAAGATTGGATGGTCTTCA
** * *
401722 ATCTGCCCCATGGTCGGGGTAAGAGATCAGA-TGATCTTCAATCTGCCCTC-TGGTC
66 ATCTAACCCATGGT-AGGGTAAAAGATCAGATTG--CTTCAATCTGCCC-CATGGTC
* * * *
401777 AGAGTAAGAGATTGAATGGTCTTCAATTTGCCC
1 GGGGTAAGAGATCGGATGGTCTTCAATTTGCCC
401810 ATTTCAGCTT
Statistics
Matches: 220, Mismatches: 40, Indels: 18
0.79 0.14 0.06
Matches are distributed among these distances:
116 3 0.01
117 84 0.38
118 45 0.20
119 41 0.19
120 46 0.21
121 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (118 bp):
GGGGTAAGAGATCGGATGGTCTTCAATTTGCCCTCTGGTAGAGGTAAAAGATTGGATGGTCTTCA
ATCTAACCCATGGTAGGGTAAAAGATCAGATTGCTTCAATCTGCCCCATGGTC
Found at i:401886 original size:50 final size:50
Alignment explanation
Indices: 401831--401973 Score: 200
Period size: 50 Copynumber: 2.9 Consensus size: 50
401821 AAGAGTATAC
*
401831 GATTCATCC-TTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGA-ATGA
1 GATTCA-CCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGT-ATATGA
401881 GATTCACCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGTATATGA
1 GATTCACCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGTATATGA
* * ** *
401931 GATTCGCCATTGTGGCTTCAATCTGTTCCTTTACAGCTTTAGG
1 GATTCACCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGG
401974 GGTATAGGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
49 3 0.04
50 82 0.96
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (50 bp):
GATTCACCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGTATATGA
Found at i:406725 original size:31 final size:30
Alignment explanation
Indices: 406674--406753 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
406664 CGTCTTTCTC
* *
406674 AAACTTT-TAATGTATGAAAATGCGATGCA
1 AAACTTTATAATGCATGAAAATGCAATGCA
*
406703 AAACTTTATAAATGCATGAAAATGCAATGCG
1 AAACTTTAT-AATGCATGAAAATGCAATGCA
*
406734 AAATTTTATGAATGCATGAA
1 AAACTTTAT-AATGCATGAA
406754 TGCATATGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 7 0.16
30 1 0.02
31 36 0.82
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (30 bp):
AAACTTTATAATGCATGAAAATGCAATGCA
Found at i:409079 original size:23 final size:25
Alignment explanation
Indices: 409053--409098 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
409043 CCAATTAGAG
409053 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
409076 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
409099 TGGATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:409515 original size:15 final size:15
Alignment explanation
Indices: 409478--409516 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
409468 TTATGTGTGC
*
409478 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
409493 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
409507 TTAATTCTTG
1 TTAATTCTTG
409517 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:412379 original size:6 final size:6
Alignment explanation
Indices: 412361--412411 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
412351 AATTAGTATA
* * * *
412361 TTTATT TTCATT TTTATT TTTAGT TTTATT TTATTTT TTTAAT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TT-TATT TTTATT TTTATT
412410 TT
1 TT
412412 AATTATGCAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:412392 original size:5 final size:5
Alignment explanation
Indices: 412361--412412 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
412351 AATTAGTATA
*
412361 TTTAT TTTCATT TTTATT TTTAGT TTTAT TTTAT TTT-T TTAAT TTTAT
1 TTTAT TTT-A-T TTTA-T TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT
412409 TTTA
1 TTTA
412413 ATTATGCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 3 0.07
5 21 0.51
6 13 0.32
7 4 0.10
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:413338 original size:16 final size:16
Alignment explanation
Indices: 413318--413398 Score: 78
Period size: 15 Copynumber: 5.1 Consensus size: 16
413308 ATTGTTTAGA
*
413318 AAAAAAGAAAAAAGA-
1 AAAAAAGAAAAAAAAG
*
413333 AAAAAAG-TAAAAAAG
1 AAAAAAGAAAAAAAAG
*
413348 AAAAATTGAAAAAAAAG
1 AAAAA-AGAAAAAAAAG
*
413365 AAAATTGAGAAAAAAAAG
1 AAAA--AAGAAAAAAAAG
413383 -AAAAAGAAAAAAAAG
1 AAAAAAGAAAAAAAAG
413398 A
1 A
413399 CAAGTGTGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
14 5 0.09
15 23 0.43
16 1 0.02
17 14 0.26
18 10 0.19
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAG
Found at i:413348 original size:23 final size:24
Alignment explanation
Indices: 413318--413362 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
413308 ATTGTTTAGA
413318 AAAAAAGAAAAA-AGAAAAAAAGT
1 AAAAAAGAAAAATAGAAAAAAAGT
*
413341 AAAAAAGAAAAATTGAAAAAAA
1 AAAAAAGAAAAATAGAAAAAAA
413363 AGAAAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (24 bp):
AAAAAAGAAAAATAGAAAAAAAGT
Found at i:413367 original size:33 final size:33
Alignment explanation
Indices: 413315--413398 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 33
413305 TTTATTGTTT
*
413315 AGAAAAA-AAGAAAAAAGAAAA-AAAG-TAAAAA
1 AGAAAAAGAA-AAAAAAGAAAATAAAGAAAAAAA
**
413346 AGAAAAATTGAAAAAAAAGAAAATTGAGAAAAAAA
1 AGAAAAA--GAAAAAAAAGAAAATAAAGAAAAAAA
413381 AGAAAAAGAAAAAAAAGA
1 AGAAAAAGAAAAAAAAGA
413399 CAAGTGTGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
31 7 0.16
33 22 0.49
34 4 0.09
35 12 0.27
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (33 bp):
AGAAAAAGAAAAAAAAGAAAATAAAGAAAAAAA
Found at i:413398 original size:9 final size:9
Alignment explanation
Indices: 413317--413396 Score: 55
Period size: 9 Copynumber: 9.4 Consensus size: 9
413307 TATTGTTTAG
413317 AAAAAAAG-
1 AAAAAAAGA
413325 -AAAAAAG-
1 AAAAAAAGA
413332 AAAAAAAG-
1 AAAAAAAGA
*
413340 TAAAAAAG-
1 AAAAAAAGA
**
413348 AAAAATTGA
1 AAAAAAAGA
413357 AAAAAAAGA
1 AAAAAAAGA
***
413366 AAATTGAGA
1 AAAAAAAGA
413375 AAAAAAAGA
1 AAAAAAAGA
413384 AAAAGAAA-A
1 AAAA-AAAGA
413393 AAAA
1 AAAA
413397 GACAAGTGTG
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
7 7 0.12
8 19 0.33
9 28 0.49
10 3 0.05
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:413742 original size:9 final size:9
Alignment explanation
Indices: 413728--413754 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
413718 ACCTTAAACA
413728 CTTTGAGTG
1 CTTTGAGTG
413737 CTTTGAGTG
1 CTTTGAGTG
413746 CTTTGAGTG
1 CTTTGAGTG
413755 AATCTTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (9 bp):
CTTTGAGTG
Found at i:414904 original size:15 final size:15
Alignment explanation
Indices: 414867--414905 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
414857 TTATGTGTGC
*
414867 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
414882 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
414896 TTAATTCTTG
1 TTAATTCTTG
414906 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:417835 original size:25 final size:23
Alignment explanation
Indices: 417794--417839 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
417784 TCAATTAGAG
417794 AATTATCGTTTAGATTTAATTCT
1 AATTATCGTTTAGATTTAATTCT
*
417817 AATTATCTTTTTAGAATTTAATT
1 AATTATC-GTTTAG-ATTTAATT
417840 TGGATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 5 0.25
25 8 0.40
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATCGTTTAGATTTAATTCT
Found at i:419519 original size:21 final size:22
Alignment explanation
Indices: 419493--419534 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
419483 TTATATTCAA
*
419493 AAAAATAATAA-ATAAATAAAT
1 AAAAATAATAAGAAAAATAAAT
419514 AAAAATAATAAGAAAAATAAA
1 AAAAATAATAAGAAAAATAAA
419535 ATTGGATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (22 bp):
AAAAATAATAAGAAAAATAAAT
Found at i:419529 original size:12 final size:11
Alignment explanation
Indices: 419491--419533 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
419481 ATTTATATTC
419491 AAAAAAATAAT
1 AAAAAAATAAT
*
419502 AAATAAATAA-
1 AAAAAAATAAT
*
419512 ATAAAAATAAT
1 AAAAAAATAAT
419523 AAGAAAAATAA
1 AA-AAAAATAA
419534 AATTGGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.31
11 10 0.38
12 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:423504 original size:18 final size:21
Alignment explanation
Indices: 423476--423517 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
423466 TCTATATGAA
423476 AAAAATAAAATTA-TTTT-AT
1 AAAAATAAAATTACTTTTGAT
423495 AAAAAT-AAATTACTTTTGAT
1 AAAAATAAAATTACTTTTGAT
423515 AAA
1 AAA
423518 TTGAAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 10 0.48
20 5 0.24
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAATAAAATTACTTTTGAT
Found at i:423893 original size:18 final size:18
Alignment explanation
Indices: 423870--423911 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
423860 TTTTTAAAAT
423870 TATTTTTA-TAATTTTTAA
1 TATTTTTAGT-ATTTTTAA
423888 TATTTTTAGTATTTTTAA
1 TATTTTTAGTATTTTTAA
*
423906 AATTTT
1 TATTTT
423912 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TATTTTTAGTATTTTTAA
Found at i:424422 original size:43 final size:43
Alignment explanation
Indices: 424294--424453 Score: 177
Period size: 41 Copynumber: 3.8 Consensus size: 43
424284 CGCAAAAGGT
* *
424294 AAACGTCGCAAAAGGTAAAGAGCAATAGCGGCGTTTATGAG-A
1 AAACGCCGCAAAAGGTAAAGAGCAATAGCGGCGTTTATGGGAA
* * * *
424336 AAACGCCGCAAAAGATAAA-A-CAATAACGGCGTTTATAGAAA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGCGGCGTTTATGGGAA
* * *
424377 AAACGCCACAAAAGGTAAAGAGCATTAGTGGCGTTTATGGGAA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGCGGCGTTTATGGGAA
* * *
424420 AAACGCCGCTAAAGGT-TA-AGCAATAGCGACGTTT
1 AAACGCCGCAAAAGGTAAAGAGCAATAGCGGCGTTT
424454 TCCAAATAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
40 15 0.16
41 32 0.33
42 19 0.20
43 30 0.31
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.17
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTAAAGAGCAATAGCGGCGTTTATGGGAA
Found at i:438372 original size:43 final size:43
Alignment explanation
Indices: 438270--438570 Score: 388
Period size: 43 Copynumber: 7.0 Consensus size: 43
438260 CCGTTAAGTA
*
438270 TGTGGGAAAAGCGACGCTAAAGACCATGTTCTATAGC-GCGTT
1 TGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTT
* * * *
438312 TGTGGAAAAAACGCCGCTAAAAACCATGCTCTATAGCGGCGTT
1 TGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTT
* * * *
438355 TGTGGGAAAAGCACCGCTAAAAACCATGCTCTAGAGCGGCGTT
1 TGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTT
* * * *
438398 TGTGAGAAAAACGCCACTAAAGACCATGTTCTATAGCGGCATT
1 TGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTT
* * *
438441 TGTGGGAAAAGCGCTGCTAAAGACCATGCTCTATAGCGGCATT
1 TGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTT
* * *
438484 TGTGAGAAAAACGCCGCTAAAGACCATGTTCTATAGCGGTGTT
1 TGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTT
* * * *
438527 TGTGGGAAAAGCGTCACTAAAGATCATGTTCTATAGCGGTGTT
1 TGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTT
438570 T
1 T
438571 TCTCATATAA
Statistics
Matches: 225, Mismatches: 33, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
42 32 0.14
43 193 0.86
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (43 bp):
TGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTT
Found at i:438999 original size:11 final size:11
Alignment explanation
Indices: 438969--439005 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
438959 AACAAACCTT
*
438969 AAAATTTGCAA
1 AAAATTTACAA
438980 AACAATTTACAA
1 AA-AATTTACAA
438992 AAAATTTACAA
1 AAAATTTACAA
439003 AAA
1 AAA
439006 TAACGTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.62, C:0.11, G:0.03, T:0.24
Consensus pattern (11 bp):
AAAATTTACAA
Found at i:439073 original size:16 final size:19
Alignment explanation
Indices: 439036--439075 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
439026 ATTACTAATT
439036 TTTTAATATATATTAGAAA
1 TTTTAATATATATTAGAAA
439055 TTTTAATAT-T-TTA-AAA
1 TTTTAATATATATTAGAAA
439071 TTTTA
1 TTTTA
439076 TAAATCACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 3 0.14
18 1 0.05
19 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTTAATATATATTAGAAA
Found at i:439135 original size:16 final size:18
Alignment explanation
Indices: 439111--439149 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
439101 TTTGTAACCT
*
439111 AAAATTT-TAAATATATA
1 AAAATTTATAATTATATA
*
439128 AAAATTTATAATTATTTA
1 AAAATTTATAATTATATA
439146 AAAA
1 AAAA
439150 AACTTTACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTTATAATTATATA
Found at i:439156 original size:21 final size:21
Alignment explanation
Indices: 439127--439167 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
439117 TTAAATATAT
439127 AAAAATTTA-TAATTATTTAA
1 AAAAATTTACTAATTATTTAA
*
439147 AAAAACTTTACTAATTTTTTA
1 AAAAA-TTTACTAATTATTTA
439168 TATTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAAATTTACTAATTATTTAA
Found at i:439196 original size:16 final size:18
Alignment explanation
Indices: 439153--439197 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
439143 TTAAAAAAAC
439153 TTTACTAATTTTTTATATT
1 TTTAC-AATTTTTTATATT
*
439172 TTTA-TATTTTTTA-A-T
1 TTTACAATTTTTTATATT
439187 TTTACAATTTT
1 TTTACAATTTT
439198 ACATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 8 0.35
19 4 0.17
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTACAATTTTTTATATT
Found at i:441077 original size:48 final size:48
Alignment explanation
Indices: 441006--441104 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
440996 GTTTTGTTAT
441006 AACAACTAATTATAACTTTAGTTAAAATAGTAAAGCCAAATGATTAGC
1 AACAACTAATTATAACTTTAGTTAAAATAGTAAAGCCAAATGATTAGC
441054 AACAACTAATTATAACTTTAGTTAAAATAGTAAAGCCAAATGATTAGC
1 AACAACTAATTATAACTTTAGTTAAAATAGTAAAGCCAAATGATTAGC
441102 AAC
1 AAC
441105 CATAATGTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.28
Consensus pattern (48 bp):
AACAACTAATTATAACTTTAGTTAAAATAGTAAAGCCAAATGATTAGC
Found at i:442372 original size:23 final size:21
Alignment explanation
Indices: 442344--442384 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
442334 GAAAAAATAT
*
442344 ATATATACTAAAAATTTTAAA
1 ATATATATTAAAAATTTTAAA
*
442365 ATATATATTAGAAATTTTAA
1 ATATATATTAAAAATTTTAA
442385 TGTTGTCTCT
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:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATATATTAAAAATTTTAAA
Found at i:449024 original size:5 final size:5
Alignment explanation
Indices: 449011--449067 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
449001 TGAAATTTTC
* * * *
449011 TCGAA TCGAT TCGAA TTGAA TCGAG TCGAA T-GAGA TGGAA TTCGAA TCGAA
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGA-A TCGAA -TCGAA TCGAA
449062 TCGAA T
1 TCGAA T
449068 ATATTTGTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
4 2 0.05
5 34 0.81
6 6 0.14
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (5 bp):
TCGAA
Found at i:450233 original size:38 final size:39
Alignment explanation
Indices: 450187--450281 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 39
450177 TATCAAACTT
*
450187 TAAT-AAAAATATAAAATATAT-TTAAA-TTTTACTAAAAA
1 TAATAAAAAATATAAAATA-ATCGTAAACTTTTA-TAAAAA
*
450225 T-TTAAAAAATATATAAA-AATCGTAAACTTTTATAAAAA
1 TAATAAAAAATATA-AAATAATCGTAAACTTTTATAAAAA
450263 TAATAAAAAATTATAAAAT
1 TAATAAAAAA-TATAAAAT
450282 GCATAAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
37 3 0.06
38 22 0.47
39 18 0.38
40 4 0.09
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (39 bp):
TAATAAAAAATATAAAATAATCGTAAACTTTTATAAAAA
Found at i:450241 original size:29 final size:29
Alignment explanation
Indices: 450158--450241 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
450148 AATAAAAATC
*
450158 AATAAAAGTTATAAAAAA-ATATCAAACTTT
1 AATAAAAATT-TAAAAAATATAT-AAACTTT
* * * *
450188 AATAAAAATATAAAATATATTTAAATTTT
1 AATAAAAATTTAAAAAATATATAAACTTT
*
450217 ACTAAAAATTTAAAAAATATATAAA
1 AATAAAAATTTAAAAAATATATAAA
450242 AATCGTAAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 33 0.75
30 11 0.25
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (29 bp):
AATAAAAATTTAAAAAATATATAAACTTT
Found at i:450243 original size:19 final size:18
Alignment explanation
Indices: 450134--450244 Score: 64
Period size: 19 Copynumber: 5.9 Consensus size: 18
450124 GACATGTGAC
*
450134 AAAAAAATATAAAAA-AT
1 AAAAAAATATAAAAATTT
* *
450151 AAAAATCA-ATAAAAGTTAT
1 AAAAA-AATATAAAAATT-T
* *
450170 AAAAAAATATCAAACTTT
1 AAAAAAATATAAAAATTT
450188 AATAAAAATATAAAATATATT
1 AA-AAAAATATAAAA-AT-TT
* ***
450209 TAAATTTTACTAAAAATTT
1 AAAAAAATA-TAAAAATTT
450228 AAAAAATATATAAAAAT
1 AAAAAA-ATATAAAAAT
450245 CGTAAACTTT
Statistics
Matches: 69, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
17 11 0.16
18 5 0.07
19 36 0.52
20 9 0.13
21 8 0.12
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.30
Consensus pattern (18 bp):
AAAAAAATATAAAAATTT
Found at i:450857 original size:39 final size:39
Alignment explanation
Indices: 450814--450894 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
450804 ATTTTCAGCT
450814 TTAGTTTGATC-CAATCTGTTAATGGCCCAATTAATAAAC
1 TTAGTTTGA-CACAATCTGTTAATGGCCCAATTAATAAAC
* * *
450853 TTAGTTTGACACAATCTGTTTATGGTCCAATTAATAAGC
1 TTAGTTTGACACAATCTGTTAATGGCCCAATTAATAAAC
450892 TTA
1 TTA
450895 TTGTTAGTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (39 bp):
TTAGTTTGACACAATCTGTTAATGGCCCAATTAATAAAC
Found at i:451591 original size:22 final size:22
Alignment explanation
Indices: 451566--451610 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
451556 ATTTTTTATT
*
451566 ATTTTATTATGATTTTT-ATAAA
1 ATTTT-TTATAATTTTTAATAAA
*
451588 ATTTTTTCTAATTTTTAATAAA
1 ATTTTTTATAATTTTTAATAAA
451610 A
1 A
451611 ATTAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTTTTTATAATTTTTAATAAA
Found at i:451630 original size:29 final size:29
Alignment explanation
Indices: 451586--451652 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
451576 GATTTTTATA
451586 AAAT-TTTTTCTAATTTTTAATAAAAATT
1 AAATATTTTTCTAATTTTTAATAAAAATT
* *
451614 AAATATTTTTC-ATATTTTTAATAAGATTT
1 AAATATTTTTCTA-ATTTTTAATAAAAATT
*
451643 AATTATTTTT
1 AAATATTTTT
451653 AAAATAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (29 bp):
AAATATTTTTCTAATTTTTAATAAAAATT
Found at i:456872 original size:14 final size:15
Alignment explanation
Indices: 456853--456890 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
456843 AGCACGAATG
456853 AATAAATAT-AAAAA
1 AATAAATATGAAAAA
*
456867 AATAAATATGAGAAA
1 AATAAATATGAAAAA
456882 AATGAAATA
1 AAT-AAATA
456891 AGAATTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 7 0.33
16 5 0.24
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (15 bp):
AATAAATATGAAAAA
Found at i:457141 original size:29 final size:29
Alignment explanation
Indices: 457070--457328 Score: 210
Period size: 30 Copynumber: 9.0 Consensus size: 29
457060 CACTTTGGGA
*
457070 AAGTTCGAGG-TAAAAATG--ATTTTTGG
1 AAGTTCGGGGATAAAAATGTAATTTTTGG
* *
457096 TAGTTCGAGGATAAAAATGTAATTTTTGAG
1 AAGTTCGGGGATAAAAATGTAATTTTTG-G
* *
457126 AAGTTCGGGGATAAAAATATGATTTTTGG
1 AAGTTCGGGGATAAAAATGTAATTTTTGG
* * * *
457155 AATTTTGGGGACAAAAATGTAATTTTTAAG
1 AAGTTCGGGGATAAAAATGTAATTTTT-GG
* * * *
457185 AAGTTTGGGGGTAAAAATATGATTTTTGG
1 AAGTTCGGGGATAAAAATGTAATTTTTGG
* *
457214 AAGTTCAGGGAT-AAAATGTAATTTTTTAG
1 AAGTTCGGGGATAAAAATGTAA-TTTTTGG
457243 AAGTTCGAGGG-TAAAATATG--ATTTTTGG
1 AAGTTCG-GGGATAAAA-ATGTAATTTTTGG
* * *
457271 AAGTTCAGAGG-CAAAAATGTAAGTTTTGAG
1 AAGTTC-GGGGATAAAAATGTAATTTTTG-G
* * *
457301 AAGTTTGGGGGTAAAAATGTGATTTTTG
1 AAGTTCGGGGATAAAAATGTAATTTTTG
457329 TACAGTTAAG
Statistics
Matches: 186, Mismatches: 33, Indels: 24
0.77 0.14 0.10
Matches are distributed among these distances:
26 9 0.05
27 11 0.06
28 25 0.13
29 64 0.34
30 74 0.40
31 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
AAGTTCGGGGATAAAAATGTAATTTTTGG
Found at i:457171 original size:59 final size:59
Alignment explanation
Indices: 457081--457328 Score: 317
Period size: 59 Copynumber: 4.3 Consensus size: 59
457071 AGTTCGAGGT
* * *
457081 AAAA-ATGATTTTTGGTAGTTCGAGGATAAAAATGTAATTTTTGAGAAGTTCGGGGATA
1 AAAATATGATTTTTGGAAGTTCGAGGACAAAAATGTAATTTTTGAGAAGTTCGGGGGTA
* * * * *
457139 AAAATATGATTTTTGGAATTTTGGGGACAAAAATGTAATTTTTAAGAAGTTTGGGGGTA
1 AAAATATGATTTTTGGAAGTTCGAGGACAAAAATGTAATTTTTGAGAAGTTCGGGGGTA
* * *
457198 AAAATATGATTTTTGGAAGTTC-AGGGA-TAAAATGTAATTTTTTAGAAGTTCGAGGGT-
1 AAAATATGATTTTTGGAAGTTCGA-GGACAAAAATGTAATTTTTGAGAAGTTCGGGGGTA
* *
457255 AAAATATGATTTTTGGAAGTTCAGAGG-CAAAAATGTAAGTTTTGAGAAGTTTGGGGGTA
1 AAAATATGATTTTTGGAAGTTC-GAGGACAAAAATGTAATTTTTGAGAAGTTCGGGGGTA
*
457314 AAAATGTGATTTTTG
1 AAAATATGATTTTTG
457329 TACAGTTAAG
Statistics
Matches: 163, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
57 22 0.13
58 57 0.35
59 84 0.52
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (59 bp):
AAAATATGATTTTTGGAAGTTCGAGGACAAAAATGTAATTTTTGAGAAGTTCGGGGGTA
Found at i:457286 original size:28 final size:28
Alignment explanation
Indices: 457070--457286 Score: 119
Period size: 29 Copynumber: 7.6 Consensus size: 28
457060 CACTTTGGGA
457070 AAGTTC-GAGGTAAAA-ATGATTTTTGG
1 AAGTTCAGAGGTAAAATATGATTTTTGG
*
457096 TAGTTC-GAGGATAAAA-ATGTAATTTTTGAG
1 AAGTTCAGAGG-TAAAATATG--ATTTTTG-G
*
457126 AAGTTC-GGGGATAAAAATATGATTTTTGG
1 AAGTTCAGAGG-T-AAAATATGATTTTTGG
** * * *
457155 AA-TTTTG-GGGACAAAAATGTAATTTTTAAG
1 AAGTTCAGAGGTA-AAATATG--ATTTTT-GG
** *
457185 AAGTTTGGGGGTAAAAATATGATTTTTGG
1 AAGTTCAGAGGT-AAAATATGATTTTTGG
* * *
457214 AAGTTCAG-GGATAAAATGTAATTTTTTAG
1 AAGTTCAGAGG-TAAAATATGA-TTTTTGG
457243 AAGTTC-GAGGGTAAAATATGATTTTTGG
1 AAGTTCAGA-GGTAAAATATGATTTTTGG
*
457271 AAGTTCAGAGGCAAAA
1 AAGTTCAGAGGTAAAA
457287 ATGTAAGTTT
Statistics
Matches: 152, Mismatches: 20, Indels: 36
0.73 0.10 0.17
Matches are distributed among these distances:
26 10 0.07
27 14 0.09
28 32 0.21
29 47 0.31
30 29 0.19
31 8 0.05
32 11 0.07
33 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (28 bp):
AAGTTCAGAGGTAAAATATGATTTTTGG
Found at i:458969 original size:18 final size:17
Alignment explanation
Indices: 458939--459031 Score: 141
Period size: 17 Copynumber: 5.4 Consensus size: 17
458929 CTTTTTATAT
458939 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
458956 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
* * *
458974 TTTAAACTTAAGATGAA
1 TTTAAATTTAAAATAAA
458991 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
459008 TTTAAACTTTAAAATAAA
1 TTTAAA-TTTAAAATAAA
459026 TTTAAA
1 TTTAAA
459032 AATGAGTTCA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
17 35 0.51
18 33 0.49
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:458993 original size:35 final size:36
Alignment explanation
Indices: 458939--459031 Score: 88
Period size: 35 Copynumber: 2.7 Consensus size: 36
458929 CTTTTTATAT
*
458939 TTTAAATTT-AAAATAAATTTAAA-TTTAAAAATAAA
1 TTTAAATTTAAAAATAAATTTAAACCTT-AAAATAAA
* * * *
458974 TTTAAACTT-AAGATGAATTTAAA-TTTAAAATAAA
1 TTTAAATTTAAAAATAAATTTAAACCTTAAAATAAA
459008 TTTAAACTTT-AAAATAAATTTAAA
1 TTTAAA-TTTAAAAATAAATTTAAA
459032 AATGAGTTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
34 14 0.27
35 37 0.73
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (36 bp):
TTTAAATTTAAAAATAAATTTAAACCTTAAAATAAA
Found at i:459018 original size:7 final size:6
Alignment explanation
Indices: 458939--459031 Score: 70
Period size: 6 Copynumber: 16.0 Consensus size: 6
458929 CTTTTTATAT
* ** *
458939 TTTAAA TTTAAA -ATAAA TTTAAA TTTAAA AATAAA TTTAAA CTTAAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
* * *
458987 --TGAA TTTAAA TTTAAA -ATAAA TTTAAA CTTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA
459032 AATGAGTTCA
Statistics
Matches: 67, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
4 1 0.01
5 14 0.21
6 45 0.67
7 7 0.10
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:459045 original size:52 final size:52
Alignment explanation
Indices: 458939--459045 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 52
458929 CTTTTTATAT
** *
458939 TTTAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAAACTTAAGATGAA
1 TTTAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAAAAATAAGATCAA
* *
458991 TTTAAATTTAAAATAAATTTAAACTTT-AAAATAAATTTAAAAATGAGTTCAA
1 TTTAAATTTAAAATAAATTTAAA-TTTAAAAATAAATTTAAAAATAAGATCAA
459043 TTT
1 TTT
459046 GGGCCCGAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
52 46 0.94
53 3 0.06
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAAAAATAAGATCAA
Found at i:459466 original size:39 final size:39
Alignment explanation
Indices: 459423--459783 Score: 236
Period size: 39 Copynumber: 9.3 Consensus size: 39
459413 CCATGATCAA
* *
459423 GGTAAGAGATTGGTTGATGATGATCTGCCCTAAGCTCGG
1 GGTAAGAGATTGGATGATGATGATCTGCCCCAAGCTCGG
* * * *
459462 GGTAAAAGATTGAATGACTGCA--ATCTGCCTCATGCTCGG
1 GGTAAGAGATTGGATGA-TG-ATGATCTGCCCCAAGCTCGG
* * *
459501 GGTAAGAGATTTGTTGATGATGATCTGCCCCAGGCTCGG
1 GGTAAGAGATTGGATGATGATGATCTGCCCCAAGCTCGG
* * * * *
459540 GGTCAGAGATCGGATG--GTTGCAATTTGCCCCAAGCTTGG
1 GGTAAGAGATTGGATGATGATG--ATCTGCCCCAAGCTCGG
* * * * *
459579 GGTAAGAGATTGGTTTATGGTGATCTACCCCAAGCTCAG
1 GGTAAGAGATTGGATGATGATGATCTGCCCCAAGCTCGG
*** * *
459618 GGTAAGAGATCAAATG--GCTGCAATCTGCCCCAGGCTCGG
1 GGTAAGAGATTGGATGATGATG--ATCTGCCCCAAGCTCGG
*
459657 GGTAAGAGATT-GACTGATGATGATCTGCCCCAAGCTCGA
1 GGTAAGAGATTGGA-TGATGATGATCTGCCCCAAGCTCGG
*** * ** * * *
459696 GGTAAGAGATCAAATGGCT-ACAATCTGTCCCATGATCGG
1 GGTAAGAGATTGGAT-GATGATGATCTGCCCCAAGCTCGG
* * * *
459735 GGTAAGAGATTGGCTGAT-AGTGATTTGCCCCAGGCTCGA
1 GGTAAGAGATTGGATGATGA-TGATCTGCCCCAAGCTCGG
459774 GGTAAGAGAT
1 GGTAAGAGAT
459784 CAAATGACTG
Statistics
Matches: 242, Mismatches: 64, Indels: 32
0.72 0.19 0.09
Matches are distributed among these distances:
37 7 0.03
38 6 0.02
39 217 0.90
40 5 0.02
41 7 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (39 bp):
GGTAAGAGATTGGATGATGATGATCTGCCCCAAGCTCGG
Found at i:459525 original size:78 final size:78
Alignment explanation
Indices: 459393--459856 Score: 489
Period size: 78 Copynumber: 5.9 Consensus size: 78
459383 CTTTATTGCT
* * ** *
459393 TCAAATGACTACAATCTGCCCCATGATCAAGGTAAGAGATTGGTTGATGATGATCTGCCCTAAGC
1 TCAAATGACTGCAATCTGCCCCATGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
*
459458 TCGGGGTAAAAGA
66 TCGGGGTAAGAGA
** * * *
459471 TTGAATGACTGCAATCTGCCTCATGCTCGGGGTAAGAGATTTGTTGATGATGATCTGCCCCAGGC
1 TCAAATGACTGCAATCTGCCCCATGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
*
459536 TCGGGGTCAGAGA
66 TCGGGGTAAGAGA
** ** * * * * * *
459549 TCGGATGGTTGCAATTTGCCCCAAGCTTGGGGTAAGAGATTGGTTTATGGTGATCTACCCCAAGC
1 TCAAATGACTGCAATCTGCCCCATGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
*
459614 TCAGGGTAAGAGA
66 TCGGGGTAAGAGA
* * **
459627 TCAAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGATGATCTGCCCCAAGC
1 TCAAATGACTGCAATCTGCCCCATGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
*
459692 TCGAGGTAAGAGA
66 TCGGGGTAAGAGA
* * * * * * *
459705 TCAAATGGCTACAATCTGTCCCATGATCGGGGTAAGAGATTGGCTGAT-AGTGATTTGCCCCAGG
1 TCAAATGACTGCAATCTGCCCCATGCTCGGGGTAAGAGATTGGTTGATGA-TGATCTGCCCCAAG
*
459769 CTCGAGGTAAGAGA
65 CTCGGGGTAAGAGA
* * * * * * * * * * *
459783 TCAAATGACTGCAATTTGTCCTAGGCTCGGGGTAAGAGATTAGCTAATGGTGATTTGTCCCAGGC
1 TCAAATGACTGCAATCTGCCCCATGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
459848 TCGGGGTAA
66 TCGGGGTAA
459857 AGGATCGAAA
Statistics
Matches: 326, Mismatches: 58, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
77 1 0.00
78 325 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (78 bp):
TCAAATGACTGCAATCTGCCCCATGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
TCGGGGTAAGAGA
Found at i:459800 original size:39 final size:39
Alignment explanation
Indices: 459445--459822 Score: 201
Period size: 39 Copynumber: 9.7 Consensus size: 39
459435 GTTGATGATG
* * * **
459445 ATCTGCCCTAAGCTCGGGGTAAAAGATTGAATGACTGCA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGACTGCA
* * ****
459484 ATCTGCCTCATGCTCGGGGTAAGAGATTTGTTGA-TG-A
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGACTGCA
* ** **
459521 TGATCTGCCCCAGGCTCGGGGTCAGAGATCGGATGGTTGCA
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGACTGCA
* * * **** * **
459562 ATTTGCCCCAAGCTTGGGGTAAGAGATTGGTTTA-TGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGACT-GCA
* * * *
459601 ATCTACCCCAAGCTCAGGGTAAGAGATCAAATGGCTGCA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGACTGCA
** *
459640 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGA-TG-A
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGACTGCA
* * * *
459677 TGATCTGCCCCAAGCTCGAGGTAAGAGATCAAATGGCTACA
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGACTGCA
* * * **** **
459718 ATCTGTCCCATGATCGGGGTAAGAGATTGGCTGA-TAGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGACT-GCA
* *
459757 ATTTGCCCCAGGCTCGAGGTAAGAGATCAAATGACTGCA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGACTGCA
* * *
459796 ATTTGTCCTAGGCTCGGGGTAAGAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
459823 TAGCTAATGG
Statistics
Matches: 251, Mismatches: 76, Indels: 24
0.72 0.22 0.07
Matches are distributed among these distances:
37 2 0.01
38 6 0.02
39 236 0.94
40 5 0.02
41 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGACTGCA
Found at i:467931 original size:36 final size:36
Alignment explanation
Indices: 467890--467961 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
467880 CAACTGCACT
*
467890 TGCATTTCCTTTTGAATTTGCTCTAGCAC-TTGCTCC
1 TGCATTTCCTTTTGAATTTGATCTAGC-CTTTGCTCC
467926 TGCATTTCCTTTTGAATTTGATCTAGCCTTTGCTCC
1 TGCATTTCCTTTTGAATTTGATCTAGCCTTTGCTCC
467962 ATAGCTTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.14, C:0.26, G:0.14, T:0.46
Consensus pattern (36 bp):
TGCATTTCCTTTTGAATTTGATCTAGCCTTTGCTCC
Found at i:470619 original size:11 final size:11
Alignment explanation
Indices: 470603--470630 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
470593 AAACGGAAGT
470603 GAAAACTTCAC
1 GAAAACTTCAC
470614 GAAAACTTCAC
1 GAAAACTTCAC
470625 GAAAAC
1 GAAAAC
470631 ATGGGTATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.25, G:0.11, T:0.14
Consensus pattern (11 bp):
GAAAACTTCAC
Found at i:471828 original size:29 final size:28
Alignment explanation
Indices: 471794--472079 Score: 232
Period size: 29 Copynumber: 9.8 Consensus size: 28
471784 AAAGTTTAAC
**
471794 GGTAAAAATGTAATTTTGGGAAAGTTCGG
1 GGTAAAAATGTAATTTTTAG-AAGTTCGG
* ** * *
471823 GATAAAAACATGATTTTTAAGAAGTTCAG
1 GGTAAAAATGTAATTTTT-AGAAGTTCGG
* * * *
471852 GGCAAAAATATAATTTTTGAAAAATTCGAG
1 GGTAAAAATGTAATTTTT-AGAAGTTCG-G
* * * *
471882 TGTAAAAATGTTATTTTTAAAAGTTTGAG
1 GGTAAAAATGTAATTTTTAGAAGTTCG-G
**
471911 GGTAAAAATGTAATTTTTAGAAGTTTAAG
1 GGTAAAAATGTAATTTTTAGAAG-TTCGG
* *
471940 GGTAAAAATGTAATTTTTGAGAAATTTGAG
1 GGTAAAAATGTAATTTTT-AGAAGTTCG-G
* * *
471970 GGTAAAAACGTGATTTTTGGAAGTTCGAG
1 GGTAAAAATGTAATTTTTAGAAGTTCG-G
* * *
471999 AGTAAAAATGTAATTTTTGGAAGTTTAGG
1 GGTAAAAATGTAATTTTTAGAAG-TTCGG
472028 GGTAAAAATGTAATTTTTAGAAGTTCGG
1 GGTAAAAATGTAATTTTTAGAAGTTCGG
472056 AGGTAAAAATG-AGATTTTTAGAAG
1 -GGTAAAAATGTA-ATTTTTAGAAG
472080 AAAACAAGGG
Statistics
Matches: 208, Mismatches: 41, Indels: 16
0.78 0.15 0.06
Matches are distributed among these distances:
28 5 0.02
29 161 0.77
30 42 0.20
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.35
Consensus pattern (28 bp):
GGTAAAAATGTAATTTTTAGAAGTTCGG
Found at i:471831 original size:59 final size:59
Alignment explanation
Indices: 471768--471927 Score: 146
Period size: 59 Copynumber: 2.7 Consensus size: 59
471758 ATTTGGGGTT
* * *
471768 AAAACATAATTTTAAAAAAGTTTAACGGTAAAAATGTAATTTTGGGAAAGTTCG-G-GATA
1 AAAACATAATTTT-AAAAAGTTTAAGGGTAAAAATGTAATTTTGGAAAAATTCGAGTG-TA
* * * * * *
471827 AAAACATGATTTTTAAGAAG-TTCAGGGCAAAAATATAATTTTTGAAAAATTCGAGTGTA
1 AAAACAT-AATTTTAAAAAGTTTAAGGGTAAAAATGTAATTTTGGAAAAATTCGAGTGTA
** * * *
471886 AAAATGTTATTTTTAAAAGTTTGAGGGTAAAAATGTAATTTT
1 AAAACATAATTTTAAAAAGTTTAAGGGTAAAAATGTAATTTT
471928 TAGAAGTTTA
Statistics
Matches: 79, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
58 34 0.43
59 39 0.49
60 6 0.08
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.34
Consensus pattern (59 bp):
AAAACATAATTTTAAAAAGTTTAAGGGTAAAAATGTAATTTTGGAAAAATTCGAGTGTA
Found at i:471887 original size:88 final size:85
Alignment explanation
Indices: 471794--472066 Score: 271
Period size: 88 Copynumber: 3.1 Consensus size: 85
471784 AAAGTTTAAC
** * * *
471794 GGTAAAAATGTAATTTTGGGAAAGTTCGGGATAAAAACATGATTTTTAAGAAGTTCAGGGCAAAA
1 GGTAAAAATGTAATTTT-GGAAAGTTCGGGATAAAAATGTAATTTTT-AGAAGTTAAGGGTAAAA
* *
471859 ATATAATTTTTGAAAAATTCGA
64 ATGTAATTTTTGAGAAATTCGA
* ** * *
471881 GTGTAAAAATGTTATTTTTAAAAGTTTGAGGGTAAAAATGTAATTTTTAGAAGTTTAAGGGTAAA
1 G-GTAAAAATGTAATTTTGGAAAGTTCG-GGATAAAAATGTAATTTTTAGAAG-TTAAGGGTAAA
*
471946 AATGTAATTTTTGAGAAATTTGA
63 AATGTAATTTTTGAGAAATTCGA
* * * * *
471969 GGGTAAAAACGTGATTTTTGG-AAGTTCGAGAGTAAAAATGTAATTTTTGGAAGTTTAGGGGTAA
1 -GGTAAAAATGT-AATTTTGGAAAGTTCGGGA-TAAAAATGTAATTTTTAGAAG-TTAAGGGTAA
*
472033 AAATGTAATTTTT-AGAAGTTCGGA
62 AAATGTAATTTTTGAGAAATTC-GA
472057 GGTAAAAATG
1 GGTAAAAATG
472067 AGATTTTTAG
Statistics
Matches: 153, Mismatches: 26, Indels: 14
0.79 0.13 0.07
Matches are distributed among these distances:
87 29 0.19
88 119 0.78
89 5 0.03
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (85 bp):
GGTAAAAATGTAATTTTGGAAAGTTCGGGATAAAAATGTAATTTTTAGAAGTTAAGGGTAAAAAT
GTAATTTTTGAGAAATTCGA
Found at i:471946 original size:117 final size:116
Alignment explanation
Indices: 471774--472052 Score: 285
Period size: 117 Copynumber: 2.4 Consensus size: 116
471764 GGTTAAAACA
* * ** * *
471774 TAATTTTAAAAAAGTTTAACGGTAAAAATGTAATTTTGGGAAAG-TTCGGGATAAAAACATGATT
1 TAATTTT-TAAAAGTTT-AGGGTAAAAATGTAATTTTTAG-AAGTTTAGGGATAAAAACATAATT
* *
471838 TTTAAG-AAGTTCAGGGCAAAAATATAATTTTTGAAAAATTCGAGTGTAAAAATG
63 TTTAAGAAAGTTCAGGGCAAAAACATAATTTTTG-AAAATTCGAGAGTAAAAATG
* **
471892 TTATTTTTAAAAGTTTGAGGGTAAAAATGTAATTTTTAGAAGTTTAAGGG-TAAAAATGTAATTT
1 TAATTTTTAAAAGTTT-AGGGTAAAAATGTAATTTTTAGAAGTTT-AGGGATAAAAACATAATTT
* * * * * * * *
471956 TTGAGAAATTTGAGGGTAAAAACGTGATTTTTGGAAGTTCGAGAGTAAAAATG
64 TTAAGAAAGTTCAGGGCAAAAACATAATTTTTGAAAATTCGAGAGTAAAAATG
**
472009 TAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTAGAAGTT
1 TAATTTTTAAAAGTTTA-GGGTAAAAATGTAATTTTTAGAAGTT
472053 CGGAGGTAAA
Statistics
Matches: 134, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
116 4 0.03
117 100 0.75
118 30 0.22
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (116 bp):
TAATTTTTAAAAGTTTAGGGTAAAAATGTAATTTTTAGAAGTTTAGGGATAAAAACATAATTTTT
AAGAAAGTTCAGGGCAAAAACATAATTTTTGAAAATTCGAGAGTAAAAATG
Found at i:473876 original size:6 final size:6
Alignment explanation
Indices: 473865--473955 Score: 59
Period size: 6 Copynumber: 16.0 Consensus size: 6
473855 TATTTTATAT
** * *
473865 TTTAAA TTTAAA AATAAA TTTAAA CTCAAA --TAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
473911 -ATAAA TTTAAA CTTAAGA --TGAA TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
473956 AATGGGTTCA
Statistics
Matches: 64, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
4 4 0.06
5 10 0.16
6 49 0.77
7 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.38
Consensus pattern (6 bp):
TTTAAA
Found at i:473908 original size:34 final size:34
Alignment explanation
Indices: 473865--473955 Score: 148
Period size: 34 Copynumber: 2.7 Consensus size: 34
473855 TATTTTATAT
473865 TTTAAATTTAAAAATAAATTTAAACTCAA-ATAAA
1 TTTAAATTT-AAAATAAATTTAAACTCAAGATAAA
* *
473899 TTTAAATTTAAAATAAATTTAAACTTAAGATGAA
1 TTTAAATTTAAAATAAATTTAAACTCAAGATAAA
473933 TTTAAATTTAAAATAAATTTAAA
1 TTTAAATTTAAAATAAATTTAAA
473956 AATGGGTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 18 0.33
34 36 0.67
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.38
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATTTAAACTCAAGATAAA
Found at i:473914 original size:17 final size:17
Alignment explanation
Indices: 473865--473955 Score: 121
Period size: 17 Copynumber: 5.4 Consensus size: 17
473855 TATTTTATAT
473865 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
473883 TTTAAA-CTCAAATAAA
1 TTTAAATTTAAAATAAA
473899 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* * *
473916 TTTAAACTTAAGATGAA
1 TTTAAATTTAAAATAAA
473933 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
473950 TTTAAA
1 TTTAAA
473956 AATGGGTTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
16 13 0.21
17 43 0.69
18 6 0.10
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.38
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:475015 original size:28 final size:29
Alignment explanation
Indices: 474966--475026 Score: 99
Period size: 27 Copynumber: 2.1 Consensus size: 29
474956 TTTAATTAAT
474966 TTTTAAAAATTCAAAAAATTATAAAAAATA
1 TTTTAAAAATTCAAAAAATTAT-AAAAATA
474996 TTTTAAAAA-T-AAAAAATTATAAAAATA
1 TTTTAAAAATTCAAAAAATTATAAAAATA
475023 TTTT
1 TTTT
475027 TTTAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 11 0.35
28 10 0.32
29 1 0.03
30 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
TTTTAAAAATTCAAAAAATTATAAAAATA
Found at i:475018 original size:16 final size:17
Alignment explanation
Indices: 474989--475022 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
474979 AAAAATTATA
*
474989 AAAAATATTTTAAAAAT
1 AAAAATATTATAAAAAT
475006 AAAAA-ATTATAAAAAT
1 AAAAATATTATAAAAAT
475022 A
1 A
475023 TTTTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATATTATAAAAAT
Found at i:475027 original size:28 final size:29
Alignment explanation
Indices: 474963--475027 Score: 98
Period size: 28 Copynumber: 2.2 Consensus size: 29
474953 TCATTTAATT
474963 AATTTTTAAAAATTCAAAAAATTATAAAA
1 AATTTTTAAAAATTCAAAAAATTATAAAA
474992 AATATTTTAAAAA-T-AAAAAATTATAAAA
1 AAT-TTTTAAAAATTCAAAAAATTATAAAA
475020 ATATTTTT
1 A-ATTTTT
475028 TTAATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 19 0.56
29 6 0.18
30 9 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AATTTTTAAAAATTCAAAAAATTATAAAA
Found at i:478319 original size:29 final size:30
Alignment explanation
Indices: 478281--478341 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
478271 TAATTTTTAT
478281 AATAATAAAAATATAATTTTTAAAAAATTA
1 AATAATAAAAATATAATTTTTAAAAAATTA
* * *
478311 AATAA-AAAATTATTATTTTTAAAAGATTA
1 AATAATAAAAATATAATTTTTAAAAAATTA
478340 AA
1 AA
478342 GTATAACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
AATAATAAAAATATAATTTTTAAAAAATTA
Found at i:481013 original size:21 final size:21
Alignment explanation
Indices: 480963--481022 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
480953 TTTTTCTATT
480963 GAGTTAATTTTTTTAGATAATTA
1 GAGTT-ATTTTTTTA-ATAATTA
* *
480986 CATTTATTTTTTTAA-AATTAA
1 GAGTTATTTTTTTAATAATT-A
481007 GAGTTATTTTTTTAAT
1 GAGTTATTTTTTTAAT
481023 TTAATGTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 4 0.13
21 15 0.48
22 9 0.29
23 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (21 bp):
GAGTTATTTTTTTAATAATTA
Found at i:481034 original size:21 final size:20
Alignment explanation
Indices: 480989--481046 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
480979 ATAATTACAT
*
480989 TTATTTTTTTAAAATTAAGAG
1 TTATTTTTTT-AATTTAAGAG
481010 TTATTTTTTTAATTTAATGTA-
1 TTATTTTTTTAATTTAA-G-AG
*
481031 TTATTTATTTAATTTA
1 TTATTTTTTTAATTTA
481047 TTATTTTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.18
21 26 0.79
22 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTATTTTTTTAATTTAAGAG
Found at i:481042 original size:16 final size:16
Alignment explanation
Indices: 481021--481052 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
481011 TATTTTTTTA
481021 ATTTAATGTATTATTT
1 ATTTAATGTATTATTT
*
481037 ATTTAATTTATTATTT
1 ATTTAATGTATTATTT
481053 TCCACATGTA
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:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
ATTTAATGTATTATTT
Found at i:482004 original size:29 final size:30
Alignment explanation
Indices: 481964--482020 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
481954 AATTTGACAT
*
481964 TTTTTTTCTTAA-TTTGATACTTAAATTTAA
1 TTTTTTTCTTAAGTTAG-TACTTAAATTTAA
481994 TTTTTTT-TTAAGTTAGTACTTAAATTT
1 TTTTTTTCTTAAGTTAGTACTTAAATTT
482021 TTTGGGATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTTTTCTTAAGTTAGTACTTAAATTTAA
Found at i:485187 original size:22 final size:24
Alignment explanation
Indices: 485146--485189 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
485136 GATTGATATA
485146 TAATCTTTAGAAGATATGATTTTG
1 TAATCTTTAGAAGATATGATTTTG
*
485170 TAAT-TTTAG-AGATTTGATTT
1 TAATCTTTAGAAGATATGATTT
485190 GTAGATAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 5 0.26
24 4 0.21
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (24 bp):
TAATCTTTAGAAGATATGATTTTG
Found at i:508437 original size:20 final size:21
Alignment explanation
Indices: 508397--508437 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
508387 AAGATTGGAA
*
508397 ATCTTAGATTTGATAGGTAAT
1 ATCTTAGATTTGATAGATAAT
*
508418 ATCTTAGA-TTGATATATAAT
1 ATCTTAGATTTGATAGATAAT
508438 CTTTAGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (21 bp):
ATCTTAGATTTGATAGATAAT
Found at i:508475 original size:22 final size:23
Alignment explanation
Indices: 508434--508480 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
508424 GATTGATATA
508434 TAATCTTTAGAAGATATGATTGTG
1 TAATCTTTAGAAGATATGATT-TG
*
508458 TAATC-TTAG-AGATTTGATTTG
1 TAATCTTTAGAAGATATGATTTG
508479 TA
1 TA
508481 GATAGCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 9 0.41
23 4 0.18
24 5 0.23
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (23 bp):
TAATCTTTAGAAGATATGATTTG
Found at i:511252 original size:74 final size:74
Alignment explanation
Indices: 511131--511297 Score: 264
Period size: 74 Copynumber: 2.3 Consensus size: 74
511121 AATTCAGGCT
511131 ACTAACCAAGGTGACAGAGGTGGCAAAATCCGGATGGATGAAAGTAAGATTCAAGCTATTGTTAA
1 ACTAACCAAGGTGACAGAGGTGGCAAAATCCGGATGGATGAAAGTAAGATTCAAGCTATTGTTAA
*
511196 GTGAGAGCC
66 GTGAGAACC
* * * *
511205 ACTAA-CATAGGTGACGGAGGTGGCAAAATTCGGATGGATGAAAGTAAGATTCAAGTTGTTGTTA
1 ACTAACCA-AGGTGACAGAGGTGGCAAAATCCGGATGGATGAAAGTAAGATTCAAGCTATTGTTA
511269 AGTGAGAACC
65 AGTGAGAACC
*
511279 ACTAACCAAGGTGATAGAG
1 ACTAACCAAGGTGACAGAG
511298 TTACGGTCTT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
73 2 0.02
74 80 0.95
75 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.22
Consensus pattern (74 bp):
ACTAACCAAGGTGACAGAGGTGGCAAAATCCGGATGGATGAAAGTAAGATTCAAGCTATTGTTAA
GTGAGAACC
Found at i:513564 original size:22 final size:24
Alignment explanation
Indices: 513520--513571 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 24
513510 CTTAGATTTA
513520 TATGTAATCTTTAAATGATATGAT
1 TATGTAATCTTTAAATGATATGAT
*
513544 TATGTAATC-TTAGA-GATATGAT
1 TATGTAATCTTTAAATGATATGAT
513566 T-TGTAA
1 TATGTAA
513572 ATAGCTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 5 0.19
22 9 0.33
23 4 0.15
24 9 0.33
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (24 bp):
TATGTAATCTTTAAATGATATGAT
Found at i:515646 original size:21 final size:21
Alignment explanation
Indices: 515622--515675 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
515612 CATAAGACAG
*
515622 TTCTACCGATACAAGTGA-GAC
1 TTCTACCGATACAAGTCATG-C
* *
515643 TTCTATCGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATGC
515664 TTCTACCGATAC
1 TTCTACCGATAC
515676 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATGC
Found at i:524479 original size:37 final size:37
Alignment explanation
Indices: 524438--524508 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
524428 AAAAATAATT
524438 TTATTTTAATAGT-TTAATATTAAATTTAAT-TTAATAC
1 TTATTTTAATAGTATT-ATATT-AATTTAATATTAATAC
*
524475 TTATTTTAATAGTATTTTATTAATTTAATATTAA
1 TTATTTTAATAGTATTATATTAATTTAATATTAA
524509 AGTGTTTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 8 0.26
37 21 0.68
38 2 0.06
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (37 bp):
TTATTTTAATAGTATTATATTAATTTAATATTAATAC
Found at i:526718 original size:32 final size:32
Alignment explanation
Indices: 526656--526718 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
526646 CCGCTCATTG
* * *
526656 AATTCTTTTTCCAACTTTTAAGAGACCTAAAT
1 AATTCTTTTTCCAAATTTTAAAAAACCTAAAT
*
526688 AATT-TTTTCTCCAAATTTTAAAAAATCTAAA
1 AATTCTTTT-TCCAAATTTTAAAAAACCTAAA
526719 ACTTCCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.41
Consensus pattern (32 bp):
AATTCTTTTTCCAAATTTTAAAAAACCTAAAT
Found at i:527729 original size:14 final size:15
Alignment explanation
Indices: 527700--527732 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
527690 TCGAGTTTAA
527700 GGTTTAAAAGTTTGG
1 GGTTTAAAAGTTTGG
*
527715 GGTTTAAGA-TTTGG
1 GGTTTAAAAGTTTGG
527729 GGTT
1 GGTT
527733 ATATTATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.42
Consensus pattern (15 bp):
GGTTTAAAAGTTTGG
Found at i:527772 original size:21 final size:21
Alignment explanation
Indices: 527744--527783 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
527734 TATTATATGA
527744 GTTTAGGGTTTGG-GTTTAAG
1 GTTTAGGGTTTGGAGTTTAAG
527764 GTTTAAGGGTTTGGAGTTTA
1 GTTT-AGGGTTTGGAGTTTA
527784 GATTTTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (21 bp):
GTTTAGGGTTTGGAGTTTAAG
Found at i:528164 original size:21 final size:22
Alignment explanation
Indices: 528129--528169 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
528119 TAAGATAACC
528129 ATATATAAAATTTTAATTAAAAA
1 ATATATAAAATTTT-ATTAAAAA
528152 ATATAT-AAA-TTTATTAAA
1 ATATATAAAATTTTATTAAA
528170 TATTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 3 0.17
23 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATAAAATTTTATTAAAAA
Found at i:528192 original size:16 final size:15
Alignment explanation
Indices: 528143--528193 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
528133 ATAAAATTTT
528143 AATTAAAAAATATATA
1 AATT-AAAAATATATA
*
528159 AATTTATTAAATAT-TA
1 AA-TTA-AAAATATATA
528175 AATTAAAAATCATATA
1 AATTAAAAAT-ATATA
528191 AAT
1 AAT
528194 ACATATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.14
15 5 0.17
16 12 0.41
17 8 0.28
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTAAAAATATATA
Found at i:528725 original size:28 final size:29
Alignment explanation
Indices: 528676--528735 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
528666 TATCAATTTT
*
528676 TTTAAATAATACATATTTTTATAATTAAA
1 TTTAAATAATACATATTATTATAATTAAA
* *
528705 TTTAAAT-ATA-ATATGTATTATTATTTAA
1 TTTAAATAATACATAT-TATTATAATTAAA
528733 TTT
1 TTT
528736 GAATTCAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 16 0.59
29 7 0.26
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (29 bp):
TTTAAATAATACATATTATTATAATTAAA
Found at i:530327 original size:20 final size:19
Alignment explanation
Indices: 530295--530346 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
530285 GTGTAATTAT
* * *
530295 AAAAATATTAAATTCTAAA
1 AAAAATATAAAAATATAAA
530314 AAAAATATAAAAATATAAA
1 AAAAATATAAAAATATAAA
*
530333 AAAAGTACTAAAAA
1 AAAAATA-TAAAAA
530347 AAAAAAATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAATATAAAAATATAAA
Found at i:530352 original size:19 final size:18
Alignment explanation
Indices: 530311--530353 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
530301 ATTAAATTCT
530311 AAAAAAAATATAAAAATA
1 AAAAAAAATATAAAAATA
*
530329 TAAAAAAAGTACTAAAAA-A
1 -AAAAAAAATA-TAAAAATA
530348 AAAAAA
1 AAAAAA
530354 TAGAAACGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 10 0.45
20 6 0.27
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (18 bp):
AAAAAAAATATAAAAATA
Found at i:531683 original size:22 final size:24
Alignment explanation
Indices: 531632--531686 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
531622 TAGTAAAGTA
* *
531632 TTAAAAGTATTAAAAATTGGTGTAT
1 TTAAAAATATTAAAAATT-GTGAAT
531657 TTAAAAATATTAAAAATT-T-AAT
1 TTAAAAATATTAAAAATTGTGAAT
531679 TTAAAAAT
1 TTAAAAAT
531687 TTATTCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 10 0.36
23 1 0.04
25 17 0.61
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (24 bp):
TTAAAAATATTAAAAATTGTGAAT
Found at i:533859 original size:15 final size:16
Alignment explanation
Indices: 533831--533869 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
533821 AATTTAATCT
533831 AATATTTATCTTAA-TA
1 AATA-TTATCTTAATTA
*
533847 AATATTATGTTAATTA
1 AATATTATCTTAATTA
533863 AATATTA
1 AATATTA
533870 AAATGATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (16 bp):
AATATTATCTTAATTA
Found at i:548906 original size:37 final size:37
Alignment explanation
Indices: 548721--548898 Score: 241
Period size: 37 Copynumber: 4.8 Consensus size: 37
548711 GTTATTGGAT
*
548721 CACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
* *
548758 CACCGGCACAAA-ACTAGCTAGGCACATAACCTGAATA
1 CACCGGCACAAAGCCT-GCTAGGCACATAGCCTGAATA
* * *
548795 CACCGGCACAAAGCCTGCTGGGCACATGGCCTGAGTA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
**
548832 CATTGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
* * *
548869 TACCGGCACAAAGTCTTCTAGGCACATAGC
1 CACCGGCACAAAGCCTGCTAGGCACATAGC
548899 TCGAATATTG
Statistics
Matches: 121, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
36 2 0.02
37 117 0.97
38 2 0.02
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.16
Consensus pattern (37 bp):
CACCGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
Found at i:564347 original size:123 final size:123
Alignment explanation
Indices: 564125--564347 Score: 326
Period size: 123 Copynumber: 1.8 Consensus size: 123
564115 GATGAGATAT
* *
564125 AGAGAAGTGGAGCAAAATAATAAAGTAGAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCTT
1 AGAGAAGTGGACCAAAATAATAAAGGAGAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCTT
* *
564190 GATAAGATACAGATAAGTGGATCAAAATAATGAAGCGGTCATATTCTTAATCAAGTAC
66 GATAAGATACAGAAAAGTGGATCAAAACAATGAAGCGGTCATATTCTTAATCAAGTAC
*
564248 AGAGAAGTGGACCAAAATAATGAAGCGA-AGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCC
1 AGAGAAGTGGACCAAAATAATAAAG-GAGAGCTCAATGTGAGTGAAACTTCAAACCCCATCTT-C
* * *
564312 TT-ATGAGATACAGAGAAAG-GGATTAAAACATTGAAG
64 TTGATAAGATACAGA-AAAGTGGATCAAAACAATGAAG
564348 TAGAGCTCAA
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
123 82 0.92
124 7 0.08
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (123 bp):
AGAGAAGTGGACCAAAATAATAAAGGAGAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCTT
GATAAGATACAGAAAAGTGGATCAAAACAATGAAGCGGTCATATTCTTAATCAAGTAC
Found at i:564588 original size:75 final size:74
Alignment explanation
Indices: 564448--564641 Score: 237
Period size: 75 Copynumber: 2.6 Consensus size: 74
564438 ATGAAGCAGT
* * ** *
564448 CATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAAAAAAGCGGAGCTTAATATGAATGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTGGATC-AAACAAAGAAGCAAAGCTTAACATGAATGAAA
*
564513 CTTCAAACCT
65 CTTCAAACCC
* * * *
564523 TATCTTCCTGATGAGATACAGAGAAGTGGATCAAGACAATGAAGCAAAGTTTAACGTGAGA-GAA
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAA-ACAAAGAAGCAAAGCTTAACATGA-ATGAA
564587 ACTTCAAACCC
64 ACTTCAAACCC
* * *
564598 CATCTTCCTGATGAGATACAAAAAAGTGGATCAAACAACGAAGC
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAACAAAGAAGC
564642 GATCATCTTC
Statistics
Matches: 103, Mismatches: 14, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
74 11 0.11
75 91 0.88
76 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.21
Consensus pattern (74 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGATCAAACAAAGAAGCAAAGCTTAACATGAATGAAAC
TTCAAACCC
Found at i:564672 original size:122 final size:122
Alignment explanation
Indices: 564524--564754 Score: 336
Period size: 122 Copynumber: 1.9 Consensus size: 122
564514 TTCAAACCTT
* * * * * *
564524 ATCTTCCTGATGAGATACAGAGAAGTGGATCAAGACAATGAAGCAAAGTTTAACGTGAGAGAAAC
1 ATCTTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCAAAGCTCAACGAGAGAGAAAC
* *
564589 TTCAAACCCCATCTTCCTGATGAGATACAAAAAAGTGGATCAAACAACGAAGCGATC
66 TTCAAACCCCAACTTCCTGATGAGATACAAAAAAGTGGACCAAACAACGAAGCGATC
* ** * *
564646 ATCTTCCTAATGAGATACAGAGAAGTGGACCAAAATAATGAAGCGGAGCTCAATGAGAGTGAAAC
1 ATCTTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCAAAGCTCAACGAGAGAGAAAC
*
564711 TTCAAACCCCAACTTCCTGATGAGATACAAAGAAGTGGACCAAA
66 TTCAAACCCCAACTTCCTGATGAGATACAAAAAAGTGGACCAAA
564755 AGATGAAGGT
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
122 95 1.00
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (122 bp):
ATCTTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCAAAGCTCAACGAGAGAGAAAC
TTCAAACCCCAACTTCCTGATGAGATACAAAAAAGTGGACCAAACAACGAAGCGATC
Found at i:564729 original size:197 final size:198
Alignment explanation
Indices: 564386--564749 Score: 536
Period size: 197 Copynumber: 1.8 Consensus size: 198
564376 TGAGTAGAGT
* * * * *
564386 GAAACTTCAAACCCCATCTTCCTTATGAGATATAGAGAAGTGGATCAAAACAATGAAGCAGTCAT
1 GAAACTTCAAACCCCATCTTCCTGATGAGATACAAAAAAGTGGATCAAAACAACGAAGCAGTCAT
* * * *
564451 CTTCCTGATGAGATATAGAGAAGTGGATCAAAACAAAAAAGCGGAGCTTAATATGAATGAAACTT
66 CTTCCTAATGAGATACAGAGAAGTGGACCAAAACAAAAAAGCGGAGCTCAATATGAATGAAACTT
** * *
564516 CAAACCTTATCTTCCTGATGAGATACAGAGAAGTGGATCAAGACAATGAAGCAAAGTTTAACGTG
131 CAAACCCCAACTTCCTGATGAGATACAAAGAAGTGGATCAAGACAATGAAGCAAAGTTTAACGTG
564581 AGA
196 AGA
564584 GAAACTTCAAACCCCATCTTCCTGATGAGATACAAAAAAGTGGATC-AAACAACGAAGC-GATCA
1 GAAACTTCAAACCCCATCTTCCTGATGAGATACAAAAAAGTGGATCAAAACAACGAAGCAG-TCA
* ** *
564647 TCTTCCTAATGAGATACAGAGAAGTGGACCAAAATAATGAAGCGGAGCTCAATGA-GAGTGAAAC
65 TCTTCCTAATGAGATACAGAGAAGTGGACCAAAACAAAAAAGCGGAGCTCAAT-ATGAATGAAAC
564711 TTCAAACCCCAACTTCCTGATGAGATACAAAGAAGTGGA
129 TTCAAACCCCAACTTCCTGATGAGATACAAAGAAGTGGA
564750 CCAAAAGATG
Statistics
Matches: 147, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
196 1 0.01
197 103 0.70
198 43 0.29
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (198 bp):
GAAACTTCAAACCCCATCTTCCTGATGAGATACAAAAAAGTGGATCAAAACAACGAAGCAGTCAT
CTTCCTAATGAGATACAGAGAAGTGGACCAAAACAAAAAAGCGGAGCTCAATATGAATGAAACTT
CAAACCCCAACTTCCTGATGAGATACAAAGAAGTGGATCAAGACAATGAAGCAAAGTTTAACGTG
AGA
Found at i:567897 original size:12 final size:11
Alignment explanation
Indices: 567876--567931 Score: 50
Period size: 9 Copynumber: 5.5 Consensus size: 11
567866 AAGGTCCTTT
*
567876 TCTTTATTCTC
1 TCTTTCTTCTC
567887 ATCTTTCTTCTC
1 -TCTTTCTTCTC
*
567899 TCCTTCTTCT-
1 TCTTTCTTCTC
567909 TC-TTCTTCT-
1 TCTTTCTTCTC
567918 TC-TTCTTCT-
1 TCTTTCTTCTC
567927 TCTTT
1 TCTTT
567932 TTTTTCTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
9 18 0.44
10 4 0.10
11 9 0.22
12 10 0.24
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (11 bp):
TCTTTCTTCTC
Found at i:567907 original size:3 final size:3
Alignment explanation
Indices: 567891--567945 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
567881 ATTCTCATCT
* * *
567891 TTC TTC -TC TCC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTT TTT TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
567938 TTC TTC TT
1 TTC TTC TT
567946 ATTCCTTCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:590249 original size:51 final size:51
Alignment explanation
Indices: 590173--590364 Score: 321
Period size: 51 Copynumber: 3.8 Consensus size: 51
590163 CACTGGCACA
* * *
590173 AAGCCTGCTTAAAGTCATCGGCTCAAGGCCTGCTATTTAATCACAGACTCG
1 AAGCCTGCTAAAAGTCACCGGCTCAAGGCCTGCTATTTAATCACCGACTCG
590224 AAGCCTGCTAAAAGTCACCGGCTCAAGGCCTGCTATTTAATCACCGACTCG
1 AAGCCTGCTAAAAGTCACCGGCTCAAGGCCTGCTATTTAATCACCGACTCG
* * *
590275 AAGCCTGTTAAAAGTCACTGGCTCAAGGCCTGCTATTTAATCACCGGCTCG
1 AAGCCTGCTAAAAGTCACCGGCTCAAGGCCTGCTATTTAATCACCGACTCG
*
590326 AAGCCTGCTAAAAGTCACCGACTCAAGGCCTGCTATTTA
1 AAGCCTGCTAAAAGTCACCGGCTCAAGGCCTGCTATTTA
590365 TCTCTTATTT
Statistics
Matches: 132, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 132 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (51 bp):
AAGCCTGCTAAAAGTCACCGGCTCAAGGCCTGCTATTTAATCACCGACTCG
Found at i:590360 original size:25 final size:25
Alignment explanation
Indices: 590175--590360 Score: 150
Period size: 25 Copynumber: 7.3 Consensus size: 25
590165 CTGGCACAAA
* *
590175 GCCTGCTTAAAGTCATCGGCTCAAG
1 GCCTGCTAAAAGTCACCGGCTCAAG
* * *
590200 GCCTGCTATTTAA-TCACAGACTCGAA-
1 GCCTGCTA--AAAGTCACCGGCTC-AAG
590226 GCCTGCTAAAAGTCACCGGCTCAAG
1 GCCTGCTAAAAGTCACCGGCTCAAG
* *
590251 GCCTGCTATTTAA-TCACCGACTCGAA-
1 GCCTGCTA--AAAGTCACCGGCTC-AAG
* *
590277 GCCTGTTAAAAGTCACTGGCTCAAG
1 GCCTGCTAAAAGTCACCGGCTCAAG
*
590302 GCCTGCTATTTAA-TCACCGGCTCGAA-
1 GCCTGCTA--AAAGTCACCGGCTC-AAG
*
590328 GCCTGCTAAAAGTCACCGACTCAAG
1 GCCTGCTAAAAGTCACCGGCTCAAG
590353 GCCTGCTA
1 GCCTGCTA
590361 TTTATCTCTT
Statistics
Matches: 127, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
24 12 0.09
25 55 0.43
26 48 0.38
27 12 0.09
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (25 bp):
GCCTGCTAAAAGTCACCGGCTCAAG
Found at i:591802 original size:53 final size:53
Alignment explanation
Indices: 591722--591830 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
591712 AAAGGTTACA
591722 ATCACGAAAATAGTTTGGCACATTGTATTGTTCCCTATTCTTTCCCTTTTAGT
1 ATCACGAAAATAGTTTGGCACATTGTATTGTTCCCTATTCTTTCCCTTTTAGT
591775 ATCACGAAAATAGTTTGGCACATTGTATTGTTCCCTATTCTTTCCCTTTTAGT
1 ATCACGAAAATAGTTTGGCACATTGTATTGTTCCCTATTCTTTCCCTTTTAGT
591828 ATC
1 ATC
591831 TCATTCCCTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (53 bp):
ATCACGAAAATAGTTTGGCACATTGTATTGTTCCCTATTCTTTCCCTTTTAGT
Found at i:595028 original size:24 final size:23
Alignment explanation
Indices: 594985--595029 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
594975 ATCCCATTCC
594985 CTCTCACCTCCTTATTTCTCCTT
1 CTCTCACCTCCTTATTTCTCCTT
*
595008 CTCTTACCTTCCTT-TTCTCTCC
1 CTCTCACC-TCCTTATT-TCTCC
595030 ACTTAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.07, C:0.44, G:0.00, T:0.49
Consensus pattern (23 bp):
CTCTCACCTCCTTATTTCTCCTT
Found at i:595256 original size:19 final size:19
Alignment explanation
Indices: 595232--595268 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
595222 TATTATTAAT
*
595232 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
595251 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
595269 TTAATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:595682 original size:19 final size:19
Alignment explanation
Indices: 595646--595682 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
595636 ATTACTTATA
* *
595646 TATTTTTTATTAACCAAAC
1 TATTTTTTATAAAACAAAC
595665 TATTTTTTATAAAACAAA
1 TATTTTTTATAAAACAAA
595683 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTTTTTATAAAACAAAC
Found at i:609896 original size:23 final size:23
Alignment explanation
Indices: 609869--609922 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
609859 TCGAACTCAA
* *
609869 AACTCGAATTACT-TATTCGAGTT
1 AACTCGAATAACTCGATTCGA-TT
*
609892 GACTCGAATAACTCGATTCGATT
1 AACTCGAATAACTCGATTCGATT
609915 AACTCGAA
1 AACTCGAA
609923 ATTCAATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (23 bp):
AACTCGAATAACTCGATTCGATT
Found at i:613611 original size:53 final size:53
Alignment explanation
Indices: 613483--613731 Score: 329
Period size: 53 Copynumber: 4.7 Consensus size: 53
613473 TCCGCATTTG
* * * * * * *
613483 ATAACTCATGATGACACAGAGTCATCGAACCTTTAATCCATGAT-GGTTTCGT
1 ATAACTCACGATGACACAAAGTCATTGGACCTTTAATCCGTGATAGGATTCAT
* * * *
613535 GTAACTCACGATGACACAAAGTCATTAGACCTTTAATCCGTAATAGAATTCAT
1 ATAACTCACGATGACACAAAGTCATTGGACCTTTAATCCGTGATAGGATTCAT
* * * * *
613588 AAAACTCACGATGACACATAGTCATCGAACCTTTAATCCATGATAGGATTCAT
1 ATAACTCACGATGACACAAAGTCATTGGACCTTTAATCCGTGATAGGATTCAT
*
613641 ATAACTCACGATGACACAGAGTCATTGGACCTTTAATCCGTGATAGGATTCAT
1 ATAACTCACGATGACACAAAGTCATTGGACCTTTAATCCGTGATAGGATTCAT
*
613694 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATC
1 ATAACTCACGATGACACAAAGTCATTGGACCTTTAATC
613732 TTCGGCACAA
Statistics
Matches: 169, Mismatches: 27, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
52 36 0.21
53 133 0.79
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (53 bp):
ATAACTCACGATGACACAAAGTCATTGGACCTTTAATCCGTGATAGGATTCAT
Found at i:613692 original size:106 final size:105
Alignment explanation
Indices: 613485--613731 Score: 377
Period size: 106 Copynumber: 2.3 Consensus size: 105
613475 CGCATTTGAT
* * * * *
613485 AACTCATGATGACACAGAGTCATCGAACCTTTAATCCATGATGGTTTCGTGTAACTCACGATGAC
1 AACTCACGATGACACAAAGTCATCGAACCTTTAATCCATGATGGATTCATATAACTCACGATGAC
613550 ACAAAGTCATTAGACCTTTAATCCGTAATAGAATTCATAA
66 ACAAAGTCATTAGACCTTTAATCCGTAATAGAATTCATAA
*
613590 AACTCACGATGACACATAGTCATCGAACCTTTAATCCATGATAGGATTCATATAACTCACGATGA
1 AACTCACGATGACACAAAGTCATCGAACCTTTAATCCATGAT-GGATTCATATAACTCACGATGA
* * * * *
613655 CACAGAGTCATTGGACCTTTAATCCGTGATAGGATTCATAT
65 CACAAAGTCATTAGACCTTTAATCCGTAATAGAATTCATAA
*
613696 AACTCACGATGACACAAAGTCATCGGACCTTTAATC
1 AACTCACGATGACACAAAGTCATCGAACCTTTAATC
613732 TTCGGCACAA
Statistics
Matches: 129, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
105 40 0.31
106 89 0.69
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (105 bp):
AACTCACGATGACACAAAGTCATCGAACCTTTAATCCATGATGGATTCATATAACTCACGATGAC
ACAAAGTCATTAGACCTTTAATCCGTAATAGAATTCATAA
Found at i:621616 original size:24 final size:24
Alignment explanation
Indices: 621584--621645 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
621574 CAAGTATACA
621584 AACTACCGATACTTCTATA-CACAT
1 AACTACCGATACTTCTA-AGCACAT
621608 AACTACCGATACTTCTAAGCACAT
1 AACTACCGATACTTCTAAGCACAT
621632 AACTACCGATACTT
1 AACTACCGATACTT
621646 GATATTCAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.27
Consensus pattern (24 bp):
AACTACCGATACTTCTAAGCACAT
Found at i:622330 original size:53 final size:53
Alignment explanation
Indices: 622201--622396 Score: 259
Period size: 53 Copynumber: 3.7 Consensus size: 53
622191 TTCGCATTTG
* * *
622201 ATAACTAACGATGACAAAAAGTCATCGGACCTTTAATCCATGAT-GGATTCTT
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCAT
* * * * * *
622253 GTAACTCATGATGACACAAAGTCATCAGACCTTTAATCCGTAATAGAATTCAT
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCAT
* * *
622306 ATAACTCACAATGACACATAGTCATCGAACCTTTAATCCATGATAGGATTCAT
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCAT
* *
622359 ATAACTCACGATAACATAAAGTCATCGGACCTTTAATC
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATC
622397 TTTGGCACAA
Statistics
Matches: 120, Mismatches: 23, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
52 37 0.31
53 83 0.69
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (53 bp):
ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCAT
Found at i:627909 original size:36 final size:35
Alignment explanation
Indices: 627856--627953 Score: 151
Period size: 36 Copynumber: 2.7 Consensus size: 35
627846 CTATTTGTTT
627856 TACTACCTGTTGACCCAAAGGTCATGATACTCATTA
1 TACT-CCTGTTGACCCAAAGGTCATGATACTCATTA
*
627892 TACTCACTGTTGACCCAAAGGTCATGATGCTCATTA
1 TACTC-CTGTTGACCCAAAGGTCATGATACTCATTA
*
627928 TATTCCTTGTTGACCCAAAGGTCATG
1 TACTCC-TGTTGACCCAAAGGTCATG
627954 CCTGTTACCG
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
35 2 0.03
36 56 0.97
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (35 bp):
TACTCCTGTTGACCCAAAGGTCATGATACTCATTA
Found at i:635554 original size:19 final size:19
Alignment explanation
Indices: 635501--635676 Score: 183
Period size: 19 Copynumber: 9.3 Consensus size: 19
635491 CAGTACAGTA
* *
635501 TATTGCTCTCACGAGCTAG
1 TATTGCTCTTACGAGCCAG
*
635520 TAACT-CTCTTACGAGCCAG
1 T-ATTGCTCTTACGAGCCAG
* * *
635539 TAATGCTATTATGAGCCAG
1 TATTGCTCTTACGAGCCAG
* *
635558 TATTGCTCTTGCGAGCCAA
1 TATTGCTCTTACGAGCCAG
*
635577 TATTGCTCTTGCGAGCCAG
1 TATTGCTCTTACGAGCCAG
* *
635596 TATTGCCCTTATGAGCCAG
1 TATTGCTCTTACGAGCCAG
* * **
635615 TATTTCTATCGCGAGCCAG
1 TATTGCTCTTACGAGCCAG
* *
635634 TATTGCTCTTACCAGTCAG
1 TATTGCTCTTACGAGCCAG
635653 TATTGCTCTTACGAGCCAG
1 TATTGCTCTTACGAGCCAG
635672 TATTG
1 TATTG
635677 TATTCCTTTT
Statistics
Matches: 126, Mismatches: 29, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
18 2 0.02
19 122 0.97
20 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (19 bp):
TATTGCTCTTACGAGCCAG
Found at i:635586 original size:57 final size:57
Alignment explanation
Indices: 635525--635676 Score: 205
Period size: 57 Copynumber: 2.7 Consensus size: 57
635515 GCTAGTAACT
* * * *
635525 CTCTTACGAGCCAGTAATGCTATTATGAGCCAGTATTGCTCTTGCGAGCCAATATTG
1 CTCTTACGAGCCAGTATTGCTCTTATGAGCCAGTATTGCTATCGCGAGCCAATATTG
* * * *
635582 CTCTTGCGAGCCAGTATTGCCCTTATGAGCCAGTATTTCTATCGCGAGCCAGTATTG
1 CTCTTACGAGCCAGTATTGCTCTTATGAGCCAGTATTGCTATCGCGAGCCAATATTG
* * *
635639 CTCTTACCAGTCAGTATTGCTCTTACGAGCCAGTATTG
1 CTCTTACGAGCCAGTATTGCTCTTATGAGCCAGTATTG
635677 TATTCCTTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 81 1.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (57 bp):
CTCTTACGAGCCAGTATTGCTCTTATGAGCCAGTATTGCTATCGCGAGCCAATATTG
Found at i:636321 original size:17 final size:18
Alignment explanation
Indices: 636279--636340 Score: 97
Period size: 18 Copynumber: 3.4 Consensus size: 18
636269 AATTTGAATA
***
636279 TTCAAAAATAACGAGTAA
1 TTCAAAAATAACGAGCCT
636297 TTCAAAAATAACGAGCCT
1 TTCAAAAATAACGAGCCT
636315 TTCAAAAATAACGAGCCT
1 TTCAAAAATAACGAGCCT
636333 TTCAAAAA
1 TTCAAAAA
636341 AATCTCATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.50, C:0.18, G:0.10, T:0.23
Consensus pattern (18 bp):
TTCAAAAATAACGAGCCT
Done.