Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005546.1 Hibiscus syriacus cultivar Beakdansim tig00012840_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: 1755203
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:253049 original size:55 final size:55
Alignment explanation
Indices: 252938--253089 Score: 193
Period size: 55 Copynumber: 2.8 Consensus size: 55
252928 CTATACAGGA
* *** *
252938 ATTCATCAACTCATGTTGAATTTCT-TGGGCA-GCACAC-ATAGTGCTTGTACGATG
1 ATTCATCAACTCATGATGAA-TTCTGTGAATATGCACACGA-AGTGCGTGTACGATG
*
252992 ATTCATCAACTCATGATGAATTCTGTGAATATGCACACGAAGTGCGTGTACGGTG
1 ATTCATCAACTCATGATGAATTCTGTGAATATGCACACGAAGTGCGTGTACGATG
* *
253047 ATTCATCAACTCATGATGAATTCCGTGAATATACACACGAAGT
1 ATTCATCAACTCATGATGAATTCTGTGAATATGCACACGAAGT
253090 TCCTGTAGTA
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
53 4 0.05
54 22 0.25
55 60 0.69
56 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCTGTGAATATGCACACGAAGTGCGTGTACGATG
Found at i:257573 original size:49 final size:49
Alignment explanation
Indices: 257517--257858 Score: 540
Period size: 49 Copynumber: 7.0 Consensus size: 49
257507 AAATGAATGG
* * * * *
257517 ATGAAAGTTAAATGCACAACGGCGCATTCCAGCATAAAAGGTGCCACTG
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
** *
257566 ATGAAAGTTAAATGCATAACAATGCATTTCGGCATAAAATGTGCCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
* *
257615 ATGAAATTTAAATGCATAACGATGCATTTCGGCATAAAAGGTGCCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
257664 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
*
257713 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGTCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
* *
257762 ATGAAAGTTAAATGCATAACGGTGCATTTCGGAATAAAAGATGCCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
* * *
257811 ATGAAAGTTAAATGCATAACGGTGCATTTTGACATAAAAGATGCCACT
1 ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
257859 CATGGTATTC
Statistics
Matches: 273, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 273 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (49 bp):
ATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTA
Found at i:260360 original size:14 final size:14
Alignment explanation
Indices: 260341--260390 Score: 86
Period size: 13 Copynumber: 3.7 Consensus size: 14
260331 CTTCCTAACG
260341 TGGAAAGCTTCATT
1 TGGAAAGCTTCATT
260355 TGGAAAGCTTCATT
1 TGGAAAGCTTCATT
260369 TGG-AAGCTTCATT
1 TGGAAAGCTTCATT
260382 T-GAAAGCTT
1 TGGAAAGCTT
260391 AATATATGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 1 0.03
13 17 0.49
14 17 0.49
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (14 bp):
TGGAAAGCTTCATT
Found at i:263508 original size:36 final size:36
Alignment explanation
Indices: 263461--263533 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
263451 AATAATTTAA
263461 AATTTTCGTATTTACACCTAAGTCCCTCCTATAAAT
1 AATTTTCGTATTTACACCTAAGTCCCTCCTATAAAT
263497 AATTTTCGTATTTACACCTAAGTCCCTCCTATAAAT
1 AATTTTCGTATTTACACCTAAGTCCCTCCTATAAAT
263533 A
1 A
263534 CAACCCATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (36 bp):
AATTTTCGTATTTACACCTAAGTCCCTCCTATAAAT
Found at i:264464 original size:5 final size:5
Alignment explanation
Indices: 264407--265033 Score: 696
Period size: 5 Copynumber: 124.4 Consensus size: 5
264397 AAATATTAAT
*
264407 ATATA ATAATA ATATA A-AT- ATATA TATACA AGTAT- A-ATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA -ATATA A-TATA ATATA ATATA
* * * *
264451 CTTTA ATATA ATAT- ATA-A CA-ATA ATATGTT ATATA ATAT- ATCTA
1 ATATA ATATA ATATA ATATA -ATATA ATA--TA ATATA ATATA ATATA
* * *
264495 ACAATA CTATA CTATA ATAATA ATAATA ATATA TACTATA TATATA ATAT-
1 A-TATA ATATA ATATA AT-ATA AT-ATA ATATA -A-TATA -ATATA ATATA
*
264545 ATACTA CTATA TATATA TATATA CTATATA ATATA TATATA ATACTA A-ATA
1 ATA-TA ATATA -ATATA -ATATA --ATATA ATATA -ATATA ATA-TA ATATA
264596 ATAT- ATATA ATAT- ATATA ATAT- ATATA A-AT- ATAATA ATATA TATATAA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA -ATAT-A
264644 TATATA ATATA ATATA ATAT- ATATA ATATA ATAT- ATATA ATATA ATATA
1 -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
264693 ATATA ATATA ATATA ATATA ATATA ATATA ATATAA TATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA
264745 ATATA ATATA ATATA ATATA ATATA ATATA ATATA A-ATA ATATA ATATAA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT-A
264795 TATATA ATATA ATATA ATATA A-ATA ATATA ATATA A-ATA ATAT- A-ATA
1 -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
264842 ATATA ATATA ATA-A TATATA ATATA ATATA ATATA ATATA ATATA A-ATA
1 ATATA ATATA ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA
264891 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA TATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA ATATA
264942 ATATAA TATATA ATATA ATAT- ATAT- ATATA ATATA ATATA ATATA ATATA
1 ATAT-A -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
264992 ATATA TATATA ATATA ATAT- ATATA ATATA ATATA ATATA AT
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
265034 GTCCTGAACG
Statistics
Matches: 553, Mismatches: 16, Indels: 106
0.82 0.02 0.16
Matches are distributed among these distances:
3 6 0.01
4 72 0.13
5 368 0.67
6 73 0.13
7 34 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:264517 original size:71 final size:70
Alignment explanation
Indices: 264511--265031 Score: 471
Period size: 71 Copynumber: 7.3 Consensus size: 70
264501 CTATACTATA
* * *
264511 ATAATAATAATAATATATACTATAT-ATATAATATATACTACT-ATATATATATATATACTATAT
1 ATAAT-ATAAT-ATATATAATATATAATATAATA-ATAATA-TAATATA-ATATA-ATA-TATAA
264574 AATATATATATAAT
59 AATA-ATAT-TAAT
264588 ACTAA-ATAATATATATAATATATATAATATATATAA-ATATAATAATATATATATAATATATAA
1 A-TAATATAATATATAT-A-ATATATAATATA-ATAATA-AT-ATAATATA-ATATAATATATAA
*
264651 TATAATA-TAAT
59 AATAATATTAAT
264662 AT-ATATAATATA-AT-ATATATAATATAAT-ATAATATAATATAATATAATATAATATAATATA
1 ATAATATAATATATATAATATATAATATAATAATAATATAATATAATATAATAT-ATA-AA-ATA
*
264723 ATATAATAT
63 ATATTA-AT
*
264732 ATAATATAATATA-AT-ATAATATAATATAAT-ATAATATAATATAATATAAATAATATAATATA
1 ATAATATAATATATATAAT-ATATAATATAATAATAATATAATATAATAT-AAT-ATATAAAATA
264794 ATATATAAT
63 ATAT-TAAT
*
264803 ATAATATAATATAAAT-A-ATATAATATAAATAAT-ATAATAATATAATATAATAATATATAATA
1 ATAATATAATATATATAATATATAATAT-AATAATAAT-ATAATATAATATAAT-ATATA-AA-A
264865 TAATA-TAAT
61 TAATATTAAT
* *
264874 ATAATATAATATAAATAATATAATATAATATAAT-ATAATATAATATAATATAATATAT-ATATA
1 ATAATATAATATATAT-A-AT-ATATAATATAATAATAATATAATATAATATAATATATAAAATA
264937 ATA-TAAT
63 ATATTAAT
*
264944 ATAATAT-ATA-ATATAATATATATATATAAT-ATAATATAATATAATATAATATAT-ATATAAT
1 ATAATATAATATATATAATATATA-ATATAATAATAATATAATATAATATAATATATAAAATAAT
265005 A-TAAT
65 ATTAAT
265010 AT-ATATAATATAATATAATATA
1 ATAATATAATAT-ATATAATATA
265032 ATGTCCTGAA
Statistics
Matches: 397, Mismatches: 11, Indels: 81
0.81 0.02 0.17
Matches are distributed among these distances:
65 18 0.05
66 61 0.15
67 5 0.01
68 22 0.06
69 16 0.04
70 30 0.08
71 71 0.18
72 52 0.13
73 25 0.06
74 25 0.06
75 11 0.03
76 18 0.05
77 14 0.04
78 14 0.04
79 15 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (70 bp):
ATAATATAATATATATAATATATAATATAATAATAATATAATATAATATAATATATAAAATAATA
TTAAT
Found at i:264639 original size:66 final size:65
Alignment explanation
Indices: 264406--265031 Score: 648
Period size: 61 Copynumber: 9.6 Consensus size: 65
264396 AAAATATTAA
* * * *
264406 TATATAATAATAATATAA-AT-AT-ATATATACAA-GTATA-ATAATATACTTTAATATA-ATAT
1 TATATAAT-ATAATATAATATAATAATATATATAATATATATATAATATAATATAATATATATAT
264465 A
65 A
* * * * *
264466 TA-ACAATA-ATATGTTATATAAT-ATATCTAACAATACTATACTATAATAATAATAATAATATA
1 TATATAATATA-ATATAATATAATAATATAT-ATAATA-TATA-TATAAT-ATAAT-ATAATATA
264528 TACTATA
60 TA-TATA
264535 TATATAATATATACTACTATATATATATATATACTATATAATATATATATAATACTAA-ATAATA
1 TATATAATATA-A-TA-TA-ATATA-ATA-ATA-TATATAATATATATATAATA-TAATATAATA
264599 TATATAATA
58 TATAT-ATA
264608 TATATAATAT-ATATAAATATAATAATATATAT-ATA-ATATATAATATAATATAATATATATA-
1 TATATAATATAATAT-AATATAATAATATATATAATATATATATAATATAATATAATATATATAT
264669 A
65 A
264670 TATAATATATATAATATAATATAAT-ATA-ATATAATATA-ATATAATATAATATAATATA-ATA
1 TAT-ATA-ATATAATATAATATAATAATATATATAATATATATATAATATAATATAATATATATA
264731 TA
64 TA
264733 TAATATAATATAATATAATATAAT-ATA-ATATAATATA-ATATAATATAA-ATAATATA-ATAT
1 T-ATATAATATAATATAATATAATAATATATATAATATATATATAATATAATATAATATATATAT
264793 AA
65 -A
264795 TATATAATATAATATAATATAAATAATATAATATAA-ATAATATAATAATATAATATAATAATAT
1 TATATAATATAATATAATAT-AATAATAT-ATATAATAT-ATAT-ATAATATAATATAAT-ATAT
264859 ATAATA
61 AT-ATA
264865 TAATATAATATAATATAATATAAATAATATAATATAATATA-ATATAATATAATATAATATA-AT
1 T-ATATAATATAATATAATAT-AATAATAT-ATATAATATATATATAATATAATATAATATATAT
264928 ATA
63 ATA
264931 TATATAATATAATATAATAT-ATAATATA-AT-ATATATATATAATATAATATAATATA-ATATA
1 TATATAATATAATATAATATAATAATATATATAATATATATATAATATAATATAATATATATATA
264992 -ATATATATATAATATAATATATATAATATAATATAATATA
1 TATATA-ATATAATATAATATA-ATAATAT-ATATAATATA
265032 ATGTCCTGAA
Statistics
Matches: 501, Mismatches: 12, Indels: 100
0.82 0.02 0.16
Matches are distributed among these distances:
57 1 0.00
58 5 0.01
59 6 0.01
60 19 0.04
61 76 0.15
62 58 0.12
63 59 0.12
64 39 0.08
65 40 0.08
66 20 0.04
67 21 0.04
68 12 0.02
69 30 0.06
70 14 0.03
71 42 0.08
72 4 0.01
73 24 0.05
74 6 0.01
75 11 0.02
76 4 0.01
77 8 0.02
78 2 0.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (65 bp):
TATATAATATAATATAATATAATAATATATATAATATATATATAATATAATATAATATATATATA
Found at i:266364 original size:2 final size:2
Alignment explanation
Indices: 266357--266432 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
266347 TGAAACATGC
266357 AT AT AT AT 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 AT
266399 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
266433 TCATGGGGTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:267001 original size:12 final size:12
Alignment explanation
Indices: 266980--267012 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
266970 GATTTGACCC
*
266980 TAAACTTTAATA
1 TAAACCTTAATA
266992 TAAACCTTAATA
1 TAAACCTTAATA
267004 TAAA-CTTAA
1 TAAACCTTAA
267013 AAAAACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAACCTTAATA
Found at i:267310 original size:20 final size:20
Alignment explanation
Indices: 267285--267359 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
267275 TATCATCTTG
267285 CTCGAAAGACTTATAGATGA
1 CTCGAAAGACTTATAGATGA
* * *
267305 CTCGAAGGATTTA-AGCATCA
1 CTCGAAAGACTTATAG-ATGA
* *
267325 TGCTCGAAAGACTTATTGATGG
1 --CTCGAAAGACTTATAGATGA
* *
267347 CCCGAATGACTTA
1 CTCGAAAGACTTA
267360 CTCATCAAGA
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.05
20 25 0.61
22 13 0.32
23 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (20 bp):
CTCGAAAGACTTATAGATGA
Found at i:267366 original size:42 final size:41
Alignment explanation
Indices: 267253--267366 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 41
267243 ACCCGAAGGT
* *
267253 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
* * * *
267294 CTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGA
* *
267336 CTTATTGATGGCCCGAATGACTTACTCATCA
1 CTTATAGATGGCCCGAAGGACTTA-TCATCA
267367 AGAAACCCTT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 20 0.34
42 39 0.66
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:267590 original size:53 final size:53
Alignment explanation
Indices: 267420--267957 Score: 569
Period size: 53 Copynumber: 10.0 Consensus size: 53
267410 TTACATTTAT
* * * *
267420 CATCAAGAAACCCCTGAAAACCAGGCTTAGCTTCTTTCAAAATTGATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGATTCTTTC-AAATTCATTTGAAAA
* * *
267474 CATTAAGAAACCCCTGAAAATCAGGCTTA-ACTTCTTTGAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGA-TTCTTT-CAAATTCATTTGAAAA
* * *
267528 CATCAAGAAACCCCTAACAATTAGGCTTAGATTCTTTCAAATTCAATTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGATTCTTTCAAATTCATTTGAAAA
* *
267581 CATCAAGAAACCCCTGAAAATCAGGCTTA-ACTTTTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGA-TTCTTTCAAATTCATTTGAAAA
* *
267634 CATCAAGAAACCCCTAAAAATTAGGCTTAGATTCTCTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGATTCTTTCAAATTCATTTGAAAA
* * ** * * * * *
267687 CATCAAGAAACCGCTAAAAATTATACCTAGCTTCTCTCAAATGCATTTTAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGATTCTTTCAAATTCATTTGAAAA
* *
267740 CATCAAGAAACCCTTAAAAATCAGGCTTAGATTCCTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGATTCTTTCAAATTCATTTGAAAA
* * * * *
267793 CATAAAGAAACCCCTAAAAATTAGTCTTAGCTTCTTTCAAATTCATTGTAAATAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGATTCTTTCAAATTCATT-TGAA-AA
* * * * *
267848 TCATCAAGAAACCCCTGAAAATCAGACTTA-ATTTCTTTGAAAGCTCATTTAAAAA
1 -CATCAAGAAACCCCTAAAAATCAGGCTTAGA-TTCTTTCAAA-TTCATTTGAAAA
** * ** * * *
267903 TCATCAAGAAACTTCTGAAAATCAAACTTAGTTTCTTTAAAAGCTCATTTGAAAA
1 -CATCAAGAAACCCCTAAAAATCAGGCTTAGATTCTTTCAAA-TTCATTTGAAAA
267958 TTGTCAAGAA
Statistics
Matches: 415, Mismatches: 58, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
52 1 0.00
53 236 0.57
54 82 0.20
55 53 0.13
56 38 0.09
57 5 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.29
Consensus pattern (53 bp):
CATCAAGAAACCCCTAAAAATCAGGCTTAGATTCTTTCAAATTCATTTGAAAA
Found at i:267932 original size:55 final size:55
Alignment explanation
Indices: 267809--268164 Score: 410
Period size: 55 Copynumber: 6.5 Consensus size: 55
267799 GAAACCCCTA
* * * * * * **
267809 AAAATTAGTCTTAGCTTCTTTCAAA-TTCATTGTAAATAATCATCAAGAAACCCCTG
1 AAAATCAGACTTAGTTTCTTTAAAAGCTCATT-TAAA-AATAATCAAGAAACTTCTG
* * *
267865 AAAATCAGACTTAATTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACTTCTG
1 AAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATAATCAAGAAACTTCTG
* * ** *
267920 AAAATCAAACTTAGTTTCTTTAAAAGCTCATTTGAAAATTGTCAAGAAACTTTTG
1 AAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATAATCAAGAAACTTCTG
* *
267975 AAAATCATACTTAGTTTCTTTAAAAGCTCATTTAAAAATGATCAAGAAACTTCTG
1 AAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATAATCAAGAAACTTCTG
* * * *
268030 AAAATCGGACTTAGTTTCTTTAAAATCTC-TTTTAAAATAATCAAGAAACTTTTG
1 AAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATAATCAAGAAACTTCTG
* * * * **
268084 AAAATCATATTTAGTTTCTTTGAAAGCTTATTTAAAAATAATCAAGAAACTTCCA
1 AAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATAATCAAGAAACTTCTG
*
268139 AAAATCAGACTTAGTTTTTTTTAAAA
1 AAAATCAGACTTAG-TTTCTTTAAAA
268165 TCGCTTTAAC
Statistics
Matches: 257, Mismatches: 40, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
54 45 0.18
55 174 0.68
56 33 0.13
57 5 0.02
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (55 bp):
AAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATAATCAAGAAACTTCTG
Found at i:272762 original size:106 final size:106
Alignment explanation
Indices: 272577--272786 Score: 420
Period size: 106 Copynumber: 2.0 Consensus size: 106
272567 GTGCGATGTA
272577 ATCCTTATTATTAGCACATTAGTAATGCGTTCTATAGTACTTGTGCTATGAAATGAATAAAAGTG
1 ATCCTTATTATTAGCACATTAGTAATGCGTTCTATAGTACTTGTGCTATGAAATGAATAAAAGTG
272642 AAATGTATGGGTTTGAAATGGAATGAAAAGTACAAGAATAC
66 AAATGTATGGGTTTGAAATGGAATGAAAAGTACAAGAATAC
272683 ATCCTTATTATTAGCACATTAGTAATGCGTTCTATAGTACTTGTGCTATGAAATGAATAAAAGTG
1 ATCCTTATTATTAGCACATTAGTAATGCGTTCTATAGTACTTGTGCTATGAAATGAATAAAAGTG
272748 AAATGTATGGGTTTGAAATGGAATGAAAAGTACAAGAAT
66 AAATGTATGGGTTTGAAATGGAATGAAAAGTACAAGAAT
272787 TGAAGTGAGA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (106 bp):
ATCCTTATTATTAGCACATTAGTAATGCGTTCTATAGTACTTGTGCTATGAAATGAATAAAAGTG
AAATGTATGGGTTTGAAATGGAATGAAAAGTACAAGAATAC
Found at i:274631 original size:3 final size:3
Alignment explanation
Indices: 274623--274713 Score: 75
Period size: 3 Copynumber: 30.7 Consensus size: 3
274613 CTTGCTAATT
* *
274623 TTA TTA TTA TTA TTA TTA TTA TT- TAA TTA TTA GTTA -TA TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* *
274667 TTA TTA TTG TTA TT- TTA TTA TATA TT- TATA TTA TCT- TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA TTA T-TA TTA TTA TTA
274712 TT
1 TT
274714 TCTGCAGGCC
Statistics
Matches: 71, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
2 7 0.10
3 56 0.79
4 8 0.11
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:274663 original size:32 final size:33
Alignment explanation
Indices: 274627--274714 Score: 90
Period size: 35 Copynumber: 2.6 Consensus size: 33
274617 CTAATTTTAT
274627 TATTATTATTATTATTATTTAATTAT-TAGTTA
1 TATTATTATTATTATTATTTAATTATATAGTTA
* * *
274659 TATTATTTTTATTATTGTTATTTTATTATATATTTA
1 TATTA---TTATTATTATTATTTAATTATATAGTTA
*
274695 TATTATCT-TTATTTTTATTT
1 TATTAT-TATTATTATTATTT
274715 CTGCAGGCCC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
32 5 0.11
33 12 0.26
34 1 0.02
35 19 0.40
36 10 0.21
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.68
Consensus pattern (33 bp):
TATTATTATTATTATTATTTAATTATATAGTTA
Found at i:275777 original size:131 final size:131
Alignment explanation
Indices: 275533--275928 Score: 508
Period size: 131 Copynumber: 3.0 Consensus size: 131
275523 ATAAATAACA
* * * * * * * *
275533 CTCGAATTAATATCGAATTCTGAGATGAAATAGTAACATCTATTCATTTTGATTGAAATAATAAA
1 CTCGAATTAATATTGAATTTTGGGATGAAATAGTAATATCTCTTCATTTCGAATGAAGTAATAAA
* * * *
275598 TGACTCCTTTAAGGCATGAGAGGTCATTTATTATCGATTGAAAATAATTAGATATTATCGTTTTC
66 TGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
275663 T
131 T
* * * *
275664 CTTGAATTAATTTTGAATTTTGGGATGAAATAGGAATACCTCTTCATTTCGAATGAAGTAATAAA
1 CTCGAATTAATATTGAATTTTGGGATGAAATAGTAATATCTCTTCATTTCGAATGAAGTAATAAA
* * * *
275729 TGATTGCTTTAAGGCATGAGATGTCAATTATTCTCGATTGGAAGTAATTAGATATTATTGTTTTC
66 TGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
275794 T
131 T
* * *
275795 CTCGAATTAATATTGAATTTTAGGATGAAATAGTAATATCACTTCATTTCG-ATTAGAGTAATAA
1 CTCGAATTAATATTGAATTTTGGGATGAAATAGTAATATCTCTTCATTTCGAATGA-AGTAATAA
* * * **
275859 AT-AGTTGTTTTAAGGCATTAGAGGTCATTTATTCTCAACAGGAAATAATTAGATATTATCGTTT
65 ATGA-TTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTT
275923 TCT
129 TCT
275926 CTC
1 CTC
275929 TTAAAAATTC
Statistics
Matches: 227, Mismatches: 36, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
130 4 0.02
131 223 0.98
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (131 bp):
CTCGAATTAATATTGAATTTTGGGATGAAATAGTAATATCTCTTCATTTCGAATGAAGTAATAAA
TGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
T
Found at i:284832 original size:23 final size:23
Alignment explanation
Indices: 284802--284857 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
284792 AACAAAAAGT
*
284802 TCACTGATTGCGAGGCAAGGTAC
1 TCACTGATTGCAAGGCAAGGTAC
284825 TCACTGATTGCAAGGCAAGGTAC
1 TCACTGATTGCAAGGCAAGGTAC
*
284848 TCACCGATTG
1 TCACTGATTG
284858 AAAAGTAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (23 bp):
TCACTGATTGCAAGGCAAGGTAC
Found at i:287397 original size:134 final size:134
Alignment explanation
Indices: 287154--287438 Score: 364
Period size: 134 Copynumber: 2.2 Consensus size: 134
287144 GATCCCCTTT
* * *
287154 CTTTTTCTAGATTTGTTCTTCCCTGAAGAAGCAGTGGAACAAGTCTGCCTCGATAAAAATTTCCC
1 CTTTTTCCAGATTTGATCTTCCCTGAAGAAGCAGTGGAACAAGTATGCCTCGATAAAAATTTCCC
* * * * *
287219 TGAAGAACAGTGGAATAAATCAACGTTACCATATTTGTTTTACCCTAAAAAAATAGTGGAGCAAA
66 TGAAGAACAATGGAATAAATCAACCTTACCATATATGATATACCCTAAAAAAATAGTGGAGCAAA
287284 ACCC
131 ACCC
* ** *
287288 CTTTTTCCATATTTGATCTTCCCTGAAGAAGCAGTGGAACAAGTATGCCTCGATCCAATTTTCCC
1 CTTTTTCCAGATTTGATCTTCCCTGAAGAAGCAGTGGAACAAGTATGCCTCGATAAAAATTTCCC
* * **
287353 TGAAGAACAATGGAATAAATCAACACTT-TCATATATGATATACCCT-AAAGAGCAGTGGAGC-A
66 TGAAGAACAATGGAATAAATCAAC-CTTACCATATATGATATACCCTAAAAAAATAGTGGAGCAA
*
287415 TACCC
130 AACCC
*
287420 C-TTTT-CAGATTCGATCTTC
1 CTTTTTCCAGATTTGATCTTC
287439 AAAAATCTTT
Statistics
Matches: 131, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
130 12 0.09
131 4 0.03
132 6 0.05
133 12 0.09
134 95 0.73
135 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (134 bp):
CTTTTTCCAGATTTGATCTTCCCTGAAGAAGCAGTGGAACAAGTATGCCTCGATAAAAATTTCCC
TGAAGAACAATGGAATAAATCAACCTTACCATATATGATATACCCTAAAAAAATAGTGGAGCAAA
ACCC
Found at i:289301 original size:61 final size:61
Alignment explanation
Indices: 289170--289303 Score: 139
Period size: 61 Copynumber: 2.2 Consensus size: 61
289160 TAAATATGTT
* * * ** *
289170 CATTTTTGTCACTTTTGCACTTTTTTTATTTTAAATTTTGATATGTTGATTTATTTGTTTA
1 CATTTTAGTCACGTTTGCACTTTTTTTATTTTAAATTTTGACATGCCGATTTATTTATTTA
* *
289231 CATTCTAGTCACGTTTGCATTTTGTTTTATTTT-AATTTTG-CATGCCGCATTTATGTTATTT-
1 CATTTTAGTCACGTTTGCACTTT-TTTTATTTTAAATTTTGACATGCCG-ATTTAT-TTATTTA
*
289292 TATTTTAGTCAC
1 CATTTTAGTCAC
289304 AAATTAGTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
60 4 0.07
61 42 0.70
62 14 0.23
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.57
Consensus pattern (61 bp):
CATTTTAGTCACGTTTGCACTTTTTTTATTTTAAATTTTGACATGCCGATTTATTTATTTA
Found at i:291638 original size:12 final size:13
Alignment explanation
Indices: 291621--291652 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
291611 TTGACGAACA
291621 AGCTCGTTTA-TG
1 AGCTCGTTTATTG
291633 AGCTCGTTTATTG
1 AGCTCGTTTATTG
291646 A-CTCGTT
1 AGCTCGTT
291653 CATTTATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (13 bp):
AGCTCGTTTATTG
Found at i:296253 original size:20 final size:20
Alignment explanation
Indices: 296215--296253 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
296205 CAAATTCAAC
*
296215 TATACTCACTTAAATCATCT
1 TATACTCACTTAAAACATCT
296235 TATA-TCACTTGAAAACATC
1 TATACTCACTT-AAAACATC
296254 ATAATATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (20 bp):
TATACTCACTTAAAACATCT
Found at i:296709 original size:19 final size:19
Alignment explanation
Indices: 296685--296722 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
296675 TCCCTTACTA
296685 AATGACTATTATTCCCCTT
1 AATGACTATTATTCCCCTT
*
296704 AATGACTATTATTTCCCTT
1 AATGACTATTATTCCCCTT
296723 CCTCTTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (19 bp):
AATGACTATTATTCCCCTT
Found at i:298520 original size:55 final size:55
Alignment explanation
Indices: 298446--298881 Score: 631
Period size: 55 Copynumber: 7.9 Consensus size: 55
298436 TTCCAATATG
* *
298446 GAAATTCATATACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACA
1 GAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACA
*
298501 GAAATTCATAAACTCATTATGAATTTCTTAGTTTTACACACAAAGTGCCCATACA
1 GAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACA
* * *
298556 AAAATTCATAAACTCATTATGAATTTATTAGTTTTGCACACAAAGTGCCCATACG
1 GAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACA
**
298611 GAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATATG
1 GAAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCCATACA
* *
298667 GAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACAGAAAGTGCCTATACA
1 GAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACA
* * * **
298722 AAAATTCATAAACTCATTATGAATTTCTTAGTTTTGTACACAAAGTTCCCATATG
1 GAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACA
* * * *
298777 GAAATTCTTAAACTTATTATGAATTTCTTAGTTTTGCACATAAAGTGCCCATA-T
1 GAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACA
* * * *
298831 GAAAATTCATAAACTTATTATGAATTGCTTAGTTTTTCCACACACAGTGCC
1 G-AAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTGCC
298882 ATTTGGTAAT
Statistics
Matches: 345, Mismatches: 33, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
54 1 0.00
55 275 0.80
56 69 0.20
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (55 bp):
GAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACA
Found at i:298824 original size:221 final size:221
Alignment explanation
Indices: 298441--298881 Score: 693
Period size: 221 Copynumber: 2.0 Consensus size: 221
298431 CCCATTTCCA
* * *
298441 ATATGGAAATTCATATACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAAAT
1 ATATGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAAAAAT
298506 TCATAAACTCATTATGAATTTCTTAGTTTTACACACAAAGTGCCCATACAAAAATTCATAAACTC
66 TCATAAACTCATTATGAATTTCTTAGTTTTACACACAAAGTGCCCATACAAAAATTCATAAACTC
*
298571 ATTATGAATTTATTAGTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATT
131 ATTATGAATTTATTAGTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTCATTATGAATT
* *
298636 TCTTAGTTTTTGCACACAAAGTGCCC
196 GCTTAGTTTTTCCACACAAAGTGCCC
* *
298662 ATATGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACAGAAAGTGCCTATACAAAAAT
1 ATATGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAAAAAT
** * *** * *
298727 TCATAAACTCATTATGAATTTCTTAGTTTTGTACACAAAGTTCCCATATGGAAATTCTTAAACTT
66 TCATAAACTCATTATGAATTTCTTAGTTTTACACACAAAGTGCCCATACAAAAATTCATAAACTC
* * * *
298792 ATTATGAATTTCTTAGTTTTGCACATAAAGTGCCCATATGAAAATTCATAAACTTATTATGAATT
131 ATTATGAATTTATTAGTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTCATTATGAATT
*
298857 GCTTAGTTTTTCCACACACAGTGCC
196 GCTTAGTTTTTCCACACAAAGTGCC
298882 ATTTGGTAAT
Statistics
Matches: 199, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
221 199 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (221 bp):
ATATGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAAAAAT
TCATAAACTCATTATGAATTTCTTAGTTTTACACACAAAGTGCCCATACAAAAATTCATAAACTC
ATTATGAATTTATTAGTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTCATTATGAATT
GCTTAGTTTTTCCACACAAAGTGCCC
Found at i:303841 original size:21 final size:21
Alignment explanation
Indices: 303817--303856 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
303807 TGTTGGGTAA
*
303817 TTTCTCTCATGATTTTTCAGT
1 TTTCTCTCATGATTCTTCAGT
303838 TTTCTCTCATGATTCTTCA
1 TTTCTCTCATGATTCTTCA
303857 ATTCTCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTCTCTCATGATTCTTCAGT
Found at i:303861 original size:19 final size:20
Alignment explanation
Indices: 303818--303863 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
303808 GTTGGGTAAT
* *
303818 TTCTCTCATGATTTTTCAGTT
1 TTCTCTCATGATTCTTCAG-A
303839 TTCTCTCATGATTCTTCA-A
1 TTCTCTCATGATTCTTCAGA
303858 TTCTCT
1 TTCTCT
303864 TAAGGCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
21 17 0.74
ACGTcount: A:0.15, C:0.24, G:0.07, T:0.54
Consensus pattern (20 bp):
TTCTCTCATGATTCTTCAGA
Found at i:307410 original size:55 final size:55
Alignment explanation
Indices: 307336--307660 Score: 533
Period size: 55 Copynumber: 5.9 Consensus size: 55
307326 TATAATATGG
* * *
307336 AAATTCTTATACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGA
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGA
* * *
307391 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACAGAAAATGCCCATACAA
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGA
307446 AAATTCATAAACTCATTATGAATTTCTTAGGTTTTGCACACAAAGTGCCCATACGA
1 AAATTCATAAACTCATTATGAATTTCTTA-GTTTTGCACACAAAGTGCCCATACGA
* *
307502 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACATAAAGTGCCCATACGG
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGA
*
307557 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCAAACAAAGTGCCCATACGA
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGA
* *
307612 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCC
1 AAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTGCC
307661 ATTTGGTAAT
Statistics
Matches: 251, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
55 183 0.73
56 68 0.27
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (55 bp):
AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGA
Found at i:307624 original size:166 final size:166
Alignment explanation
Indices: 307336--307660 Score: 542
Period size: 166 Copynumber: 2.0 Consensus size: 166
307326 TATAATATGG
* * *
307336 AAATTCTTATACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCATAA
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCATAA
* *
307401 ACTCATTATGAATTTCTTAGTTTTGCACAGAAAATGCCCATACAAAAATTCATAAACTCATTATG
66 ACTCATTATGAATTTCTTAGTTTTGCAAACAAAATGCCCATACAAAAATTCATAAACTCATTATG
307466 AATTTCTTAGGTTTTGCACACAAAGTGCCCATACGA
131 AATTTCTTAGGTTTTGCACACAAAGTGCCCATACGA
* *
307502 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACATAAAGTGCCCATACGGAAATTCATAA
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCATAA
* * *
307567 ACTCATTATGAATTTCTTAGTTTTGCAAACAAAGTGCCCATACGAAAATTCATAAACTTATTATG
66 ACTCATTATGAATTTCTTAGTTTTGCAAACAAAATGCCCATACAAAAATTCATAAACTCATTATG
* *
307632 AATTTCTTAGTTTTTGCACACACAGTGCC
131 AATTTCTTAGGTTTTGCACACAAAGTGCC
307661 ATTTGGTAAT
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
166 147 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (166 bp):
AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCATAA
ACTCATTATGAATTTCTTAGTTTTGCAAACAAAATGCCCATACAAAAATTCATAAACTCATTATG
AATTTCTTAGGTTTTGCACACAAAGTGCCCATACGA
Found at i:307659 original size:111 final size:110
Alignment explanation
Indices: 307334--307660 Score: 537
Period size: 111 Copynumber: 3.0 Consensus size: 110
307324 TTTATAATAT
* * *
307334 GGAAATTCTTATACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCAT
1 GGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCAT
* *
307399 AAACTCATTATGAATTTCTTAGTTTTGCACAGAAAATGCCCATAC
66 AAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATAC
**
307444 AAAAATTCATAAACTCATTATGAATTTCTTAGGTTTTGCACACAAAGTGCCCATACGAAAATTCA
1 GGAAATTCATAAACTCATTATGAATTTCTTA-GTTTTGCACACAAAGTGCCCATACGAAAATTCA
*
307509 TAAACTCATTATGAATTTCTTAGTTTTGCACATAAAGTGCCCATAC
65 TAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATAC
*
307555 GGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCAAACAAAGTGCCCATACGAAAATTCAT
1 GGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCAT
* *
307620 AAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCC
66 AAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTGCC
307661 ATTTGGTAAT
Statistics
Matches: 202, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
110 80 0.40
111 122 0.60
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (110 bp):
GGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCAT
AAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATAC
Found at i:310572 original size:21 final size:21
Alignment explanation
Indices: 310533--310623 Score: 83
Period size: 23 Copynumber: 4.1 Consensus size: 21
310523 CACCAAAGTG
*
310533 CCACATACAATGTCCTGAAGGA
1 CCACATA-GATGTCCTGAAGGA
*
310555 CCACATAGATGTCTTGAAGGA
1 CCACATAGATGTCCTGAAGGA
* * *
310576 CCGCGTAGAAATGTCCCGAAGGA
1 CCACATAG--ATGTCCTGAAGGA
*
310599 CCACATAGAATTGTCCTAAAGGA
1 CCACATAG-A-TGTCCTGAAGGA
310622 CC
1 CC
310624 GCGTATAACC
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.32
22 9 0.16
23 29 0.52
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (21 bp):
CCACATAGATGTCCTGAAGGA
Found at i:310604 original size:44 final size:46
Alignment explanation
Indices: 310541--310628 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 46
310531 TGCCACATAC
* * *
310541 AATGTCCTGAAGGACCACATAG-A-TGTCTTGAAGGACCGCGTAGA
1 AATGTCCCGAAGGACCACATAGAATTGTCCTAAAGGACCGCGTAGA
310585 AATGTCCCGAAGGACCACATAGAATTGTCCTAAAGGACCGCGTA
1 AATGTCCCGAAGGACCACATAGAATTGTCCTAAAGGACCGCGTA
310629 TAACCCTCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 21 0.54
45 1 0.03
46 17 0.44
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (46 bp):
AATGTCCCGAAGGACCACATAGAATTGTCCTAAAGGACCGCGTAGA
Found at i:310812 original size:16 final size:18
Alignment explanation
Indices: 310791--310832 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
310781 TCTTATATGT
310791 TCACATAG-ATAATA-TA
1 TCACATAGAATAATAGTA
310807 TCACATAGAATAATATGTA
1 TCACATAGAATAATA-GTA
310826 TCACATA
1 TCACATA
310833 TCTTATCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.35
17 6 0.26
19 9 0.39
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (18 bp):
TCACATAGAATAATAGTA
Found at i:310829 original size:19 final size:18
Alignment explanation
Indices: 310785--310832 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
310775 ATACCTTCTT
310785 ATATGT-TCACATAGATA
1 ATATGTATCACATAGATA
310802 ATA--TATCACATAGAATA
1 ATATGTATCACATAG-ATA
310819 ATATGTATCACATA
1 ATATGTATCACATA
310833 TCTTATCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 8 0.30
17 9 0.33
19 9 0.33
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.33
Consensus pattern (18 bp):
ATATGTATCACATAGATA
Found at i:310874 original size:15 final size:15
Alignment explanation
Indices: 310854--310882 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
310844 AAACATGTAT
310854 TCACATAGCTTATAA
1 TCACATAGCTTATAA
310869 TCACATAGCTTATA
1 TCACATAGCTTATA
310883 TCATTTCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (15 bp):
TCACATAGCTTATAA
Found at i:315266 original size:23 final size:22
Alignment explanation
Indices: 315240--315309 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 22
315230 CCTAAAAACC
*
315240 AAATTAAAGTTAAATAATAGA-AA
1 AAATTAAA-TTAAATAA-AAATAA
315263 AAATTAAATTAAATAAAAATAA
1 AAATTAAATTAAATAAAAATAA
* *
315285 AATATTAAATTAAATTAAATTAA
1 AA-ATTAAATTAAATAAAAATAA
315308 AA
1 AA
315310 GAAATATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 2 0.05
22 12 0.29
23 28 0.67
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (22 bp):
AAATTAAATTAAATAAAAATAA
Found at i:315273 original size:5 final size:5
Alignment explanation
Indices: 315263--315308 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
315253 ATAATAGAAA
* * *
315263 AAATT AAATT AAATA AAAAT AAA-- ATATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAA
315309 AGAAATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
3 2 0.06
5 32 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
AAATT
Found at i:315282 original size:28 final size:26
Alignment explanation
Indices: 315251--315303 Score: 54
Period size: 28 Copynumber: 1.9 Consensus size: 26
315241 AATTAAAGTT
315251 AAATAATAGAAAAAATTAAATTAAATAA
1 AAATAATA-AAAAAATTAAATTAAA-AA
*
315279 AAATAA-AATATTAAATTAAATTAAA
1 AAATAATAA-A-AAAATTAAATTAAA
315304 TTAAAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 1 0.05
27 2 0.09
28 19 0.86
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (26 bp):
AAATAATAAAAAAATTAAATTAAAAA
Found at i:315304 original size:28 final size:27
Alignment explanation
Indices: 315263--315330 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 27
315253 ATAATAGAAA
315263 AAATTAAATTAAATAAAAATAAAATATT
1 AAATTAAATTAAATAAAAA-AAAATATT
* *
315291 AAATTAAATTAAATTAAAAGAAATATT
1 AAATTAAATTAAATAAAAAAAAATATT
*
315318 AAA-AAAATTAAAT
1 AAATTAAATTAAAT
315331 TGGAAAACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 9 0.24
27 10 0.27
28 18 0.49
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (27 bp):
AAATTAAATTAAATAAAAAAAAATATT
Found at i:316559 original size:7 final size:7
Alignment explanation
Indices: 316547--316760 Score: 130
Period size: 7 Copynumber: 29.0 Consensus size: 7
316537 ATATACTTTA
316547 ATATAAT
1 ATATAAT
316554 ATATAAT
1 ATATAAT
316561 AATAATAAT
1 -AT-ATAAT
316570 ACTATAAT
1 A-TATAAT
*
316578 ATATATT
1 ATATAAT
316585 ATATAAT
1 ATATAAT
**
316592 AAATACTGCT
1 --ATA-TAAT
316602 ATATAAT
1 ATATAAT
316609 ATATAAT
1 ATATAAT
316616 ATATAAT
1 ATATAAT
316623 ACATATACAAT
1 --ATAT--AAT
*
316634 ATATACT
1 ATATAAT
316641 ATATAATAT
1 ATAT-A-AT
316650 ATATAAT
1 ATATAAT
* *
316657 GTATATT
1 ATATAAT
*
316664 ACTATATT
1 A-TATAAT
*
316672 ATATATT
1 ATATAAT
316679 ATATAAT
1 ATATAAT
*
316686 TTATAAT
1 ATATAAT
*
316693 ATGTAAT
1 ATATAAT
* *
316700 CTAT-AC
1 ATATAAT
316706 A-ATAAT
1 ATATAAT
316712 A-ATAAT
1 ATATAAT
*
316718 ACTATACT
1 A-TATAAT
316726 ATA-ATAT
1 ATATA-AT
316733 ATATAAT
1 ATATAAT
*
316740 ATATACT
1 ATATAAT
*
316747 ACATAAT
1 ATATAAT
316754 ATATAAT
1 ATATAAT
316761 GTCCTGGACG
Statistics
Matches: 163, Mismatches: 26, Indels: 36
0.72 0.12 0.16
Matches are distributed among these distances:
5 2 0.01
6 10 0.06
7 97 0.60
8 27 0.17
9 22 0.13
10 2 0.01
11 3 0.02
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:316571 original size:29 final size:29
Alignment explanation
Indices: 316531--316760 Score: 102
Period size: 31 Copynumber: 7.7 Consensus size: 29
316521 ATATATAAGT
* *
316531 ATAAGAAT-ATACTTTAATATAATATATA
1 ATAATAATAATACTATAATATAATATATA
316559 ATAATAATAATACTATAATATATATTATATA
1 ATAATAATAATACTATAATATA-A-TATATA
* **
316590 ATAAATACTGCTA-TATAATATATAATATATA
1 AT-AATAATAATACTAT-A-ATATAATATATA
*
316621 ATACATATACAATA-TATACTATATAATATAT-
1 ATA-ATA-ATAATACTATA--ATATAATATATA
* * *
316652 ATAATGTATATTACTATATTAT-ATAT-TA
1 ATAAT-AATAATACTATAATATAATATATA
* * * *
316680 TATAATTTATAATA-TGTAATCT-ATACAATA
1 -ATAA-TAATAATACTATAATATAATA-TATA
316710 ATAATAATACTATACTATAATAT-ATATAATA
1 ATAATAATA--ATACTATAATATAATAT-ATA
*
316741 TATACTACATAATA-TATAAT
1 -ATAATA-ATAATACTATAAT
316761 GTCCTGGACG
Statistics
Matches: 157, Mismatches: 23, Indels: 42
0.71 0.10 0.19
Matches are distributed among these distances:
27 1 0.01
28 23 0.15
29 29 0.18
30 20 0.13
31 45 0.29
32 31 0.20
33 8 0.05
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (29 bp):
ATAATAATAATACTATAATATAATATATA
Found at i:321035 original size:25 final size:23
Alignment explanation
Indices: 321007--321101 Score: 95
Period size: 24 Copynumber: 3.9 Consensus size: 23
320997 TGTTTTTAAA
*
321007 ATAAAATATTAGAATAAAATAAAAG
1 ATAAAATAATA-AAT-AAATAAAAG
321032 ATAAAATAAATAAATAAATAAAAG
1 ATAAAAT-AATAAATAAATAAAAG
*
321056 ATAAGAATAATATAA-AAGAT-AAGG
1 ATAA-AATAATA-AATAA-ATAAAAG
321080 ATAAAATAAATAAATAAATAAA
1 ATAAAAT-AATAAATAAATAAA
321102 TTTAAAGTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
23 7 0.11
24 34 0.56
25 17 0.28
26 3 0.05
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (23 bp):
ATAAAATAATAAATAAATAAAAG
Found at i:321037 original size:12 final size:12
Alignment explanation
Indices: 321020--321065 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
321010 AAATATTAGA
321020 ATAAAATAAAAG
1 ATAAAATAAAAG
*
321032 ATAAAATAAATAA
1 ATAAAATAAA-AG
321045 AT-AAATAAAAG
1 ATAAAATAAAAG
321056 ATAAGAATAA
1 ATAA-AATAA
321066 TATAAAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 3 0.10
12 18 0.62
13 8 0.28
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:321044 original size:4 final size:4
Alignment explanation
Indices: 321035--321102 Score: 50
Period size: 4 Copynumber: 16.0 Consensus size: 4
321025 ATAAAAGATA
* *
321035 AAAT AAAT AAAT AAAT AAA- AGAT AAGAAT AATAT AAA- AGAT AAGGAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -A-AAT AA-AT AAAT AAAT AA--AT
321082 AAAAT AAAT AAAT AAAT AAAT
1 -AAAT AAAT AAAT AAAT AAAT
321103 TTAAAGTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
3 4 0.08
4 34 0.65
5 8 0.15
6 4 0.08
7 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:321053 original size:42 final size:44
Alignment explanation
Indices: 321005--321097 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 44
320995 ATTGTTTTTA
* *
321005 AAATAAAATATTAGAATAAAATAAAAGATAA-AAT-AAATAAAT
1 AAATAAAAGATAAGAATAAAATAAAAGATAAGAATAAAATAAAT
* *
321047 AAATAAAAGATAAGAATAATATAAAAGATAAGGATAAAATAAAT
1 AAATAAAAGATAAGAATAAAATAAAAGATAAGAATAAAATAAAT
321091 AAATAAA
1 AAATAAA
321098 TAAATTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 28 0.62
43 2 0.04
44 15 0.33
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (44 bp):
AAATAAAAGATAAGAATAAAATAAAAGATAAGAATAAAATAAAT
Found at i:321055 original size:24 final size:24
Alignment explanation
Indices: 321023--321101 Score: 108
Period size: 24 Copynumber: 3.3 Consensus size: 24
321013 TATTAGAATA
321023 AAATAAAAGATAAAATAAATAAAT
1 AAATAAAAGATAAAATAAATAAAT
321047 AAATAAAAGATAAGAATAATATAAA-
1 AAATAAAAGATAA-AATAA-ATAAAT
* *
321072 AGAT-AAGGATAAAATAAATAAAT
1 AAATAAAAGATAAAATAAATAAAT
321095 AAATAAA
1 AAATAAA
321102 TTTAAAGTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
22 5 0.10
23 8 0.17
24 22 0.46
25 8 0.17
26 5 0.10
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (24 bp):
AAATAAAAGATAAAATAAATAAAT
Found at i:321072 original size:18 final size:17
Alignment explanation
Indices: 321044--321089 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
321034 AAAATAAATA
321044 AATAAATAAAAGATAAG
1 AATAAATAAAAGATAAG
321061 AATAATATAAAAGATAAG
1 AATAA-ATAAAAGATAAG
*
321079 GATAAAATAAA
1 AAT-AAATAAA
321090 TAAATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 19 0.73
19 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.20
Consensus pattern (17 bp):
AATAAATAAAAGATAAG
Found at i:326455 original size:17 final size:18
Alignment explanation
Indices: 326422--326455 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
326412 AATGTGATAA
*
326422 ATTTTATTTTATTATTCT
1 ATTTGATTTTATTATTCT
326440 ATTTGATTTT-TTATTC
1 ATTTGATTTTATTATTC
326456 AATTATCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (18 bp):
ATTTGATTTTATTATTCT
Found at i:328071 original size:31 final size:30
Alignment explanation
Indices: 328014--328075 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
328004 AATTAAAGTT
328014 AAATAATAAAATAAAATAAAATTAAAATGAA
1 AAATAATAAAATAAAATAAAATTAAAA-GAA
* *
328045 AAATACTAAATTAAAAT-AAATATAAAAGAA
1 AAATAATAAAATAAAATAAAAT-TAAAAGAA
328075 A
1 A
328076 GATTAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.23
Consensus pattern (30 bp):
AAATAATAAAATAAAATAAAATTAAAAGAA
Found at i:329307 original size:9 final size:8
Alignment explanation
Indices: 329263--329521 Score: 63
Period size: 7 Copynumber: 31.9 Consensus size: 8
329253 AAGAAAATAT
329263 TAATATAA
1 TAATATAA
329271 TAATA-ATA
1 TAATATA-A
329279 TAA-ATGATA
1 TAATAT-A-A
329288 TACATAT-A
1 TA-ATATAA
329296 TAAGTATAA
1 TAA-TATAA
*
329305 TAATATACTT
1 TAATATA--A
329315 TAATATAA
1 TAATATAA
329323 T-ATA-AA
1 TAATATAA
329329 -ACA-ATAA
1 TA-ATATAA
329336 T-ATATAA
1 TAATATAA
*
329343 TACTATAA
1 TAATATAA
329351 T-ATATAA
1 TAATATAA
*
329358 T-ATATAC
1 TAATATAA
*
329365 TACTAT-A
1 TAATATAA
329372 TAATAT-A
1 TAATATAA
329379 TAATAT-A
1 TAATATAA
329386 TACACTAT-A
1 TA-A-TATAA
329395 TAATAT-A
1 TAATATAA
329402 T-ATATAGA
1 TAATATA-A
329410 TATATATATA
1 TA-ATATA-A
329420 TAATACTACA
1 TAATA-TA-A
*
329430 TTATAT-A
1 TAATATAA
*
329437 TATATTTACA
1 TA-ATATA-A
329447 TAGATAT-A
1 TA-ATATAA
*
329455 TAATCTATA
1 TAATATA-A
329464 TAATATATA
1 TAATATA-A
*
329473 CTATTATAA
1 -TAATATAA
* *
329482 T-CTATAC
1 TAATATAA
329489 TATATATTAA
1 TA-ATA-TAA
329499 TAATAATAA
1 TAAT-ATAA
*
329508 T-ATATTA
1 TAATATAA
329515 TAATATA
1 TAATATA
329522 TACTACGTAA
Statistics
Matches: 193, Mismatches: 24, Indels: 68
0.68 0.08 0.24
Matches are distributed among these distances:
6 8 0.04
7 60 0.31
8 46 0.24
9 37 0.19
10 40 0.21
11 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (8 bp):
TAATATAA
Found at i:329335 original size:13 final size:15
Alignment explanation
Indices: 329319--329425 Score: 69
Period size: 15 Copynumber: 6.9 Consensus size: 15
329309 ATACTTTAAT
329319 ATAATATA-AA-ACA
1 ATAATATATAATACA
*
329332 ATAATATATAATACT
1 ATAATATATAATACA
*
329347 ATAATATATAATATA
1 ATAATATATAATACA
* *
329362 TACTACTATATAATA-T
1 -A-TAATATATAATACA
*
329378 ATAATATATACACTA-T
1 ATAATATATA-A-TACA
*
329394 ATAATATATATATAGA
1 ATAATATATA-ATACA
329410 TATATATATATAATAC
1 -ATA-ATATATAATAC
329426 TACATTATAT
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
13 8 0.11
14 10 0.13
15 19 0.25
16 15 0.20
17 17 0.22
18 7 0.09
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (15 bp):
ATAATATATAATACA
Found at i:329412 original size:6 final size:6
Alignment explanation
Indices: 329335--329523 Score: 110
Period size: 5 Copynumber: 33.5 Consensus size: 6
329325 TAAAACAATA
329335 ATATAT A-ATACT ATA-AT ATATA- ATATAT ACTACTAT ATA-AT ATATA-
1 ATATAT ATATA-T ATATAT ATATAT ATATAT A-TA-TAT ATATAT ATATAT
* * *
329381 ATATAT ACACTAT ATA-AT ATATAT ATAGAT ATATAT ATATA- ATACTAC
1 ATATAT ATA-TAT ATATAT ATATAT ATATAT ATATAT ATATAT ATA-TAT
* * * *
329429 AT-TAT ATATAT ATTTAC ATAGAT ATATA- ATCTAT ATA-AT ATATACT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATA-T
*
329475 AT-TAT A-ATCT ATACTAT ATAT-T A-ATA- ATA-AT A-ATAT AT-TAT
1 ATATAT ATATAT ATA-TAT ATATAT ATATAT ATATAT ATATAT ATATAT
329516 A-ATAT ATA
1 ATATAT ATA
329524 CTACGTAATA
Statistics
Matches: 142, Mismatches: 15, Indels: 52
0.68 0.07 0.25
Matches are distributed among these distances:
4 5 0.04
5 63 0.44
6 50 0.35
7 20 0.14
8 4 0.03
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (6 bp):
ATATAT
Found at i:329537 original size:2 final size:2
Alignment explanation
Indices: 329335--329523 Score: 110
Period size: 2 Copynumber: 100.5 Consensus size: 2
329325 TAAAACAATA
329335 AT AT AT A- AT ACT AT A- AT AT AT A- AT AT AT ACT ACT AT AT A-
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T A-T AT AT AT
* *
329374 AT AT AT A- AT AT AT AC ACT AT AT A- AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
329415 AT AT AT A- AT ACT AC AT -T AT AT AT AT AT TT AC AT AG AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
329456 A- AT CT AT AT A- AT AT AT ACT AT -T AT A- AT CT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT
329496 -T A- AT A- AT A- AT A- AT AT AT -T AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
329524 CTACGTAATA
Statistics
Matches: 146, Mismatches: 16, Indels: 50
0.69 0.08 0.24
Matches are distributed among these distances:
1 19 0.13
2 113 0.77
3 14 0.10
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:331093 original size:2 final size:2
Alignment explanation
Indices: 331086--331135 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
331076 ATGAACATGC
331086 AT AT AT AT 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 AT
331128 AT AT AT AT
1 AT AT AT AT
331136 TCATGGGATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:334964 original size:42 final size:41
Alignment explanation
Indices: 334846--334970 Score: 108
Period size: 42 Copynumber: 3.0 Consensus size: 41
334836 ATCATGTGAA
* * * * * *
334846 AACATCATACCCAAAGGTCTTATGGATGGCCCGAAGGACTT
1 AACATCATGCTCAAAAGACTTATAGATGGCCTGAAGGACTT
* * * * * *
334887 ATCATCTTGCTCAAAATACTTATAGATGACGTGAAGGATTT
1 AACATCATGCTCAAAAGACTTATAGATGGCCTGAAGGACTT
*
334928 AAACATCATGCTCGAAAGACTTACT-GATGGCCTGAAGGACTT
1 -AACATCATGCTCAAAAGACTTA-TAGATGGCCTGAAGGACTT
334970 A
1 A
334971 CTCATCAAGC
Statistics
Matches: 63, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
41 30 0.48
42 32 0.51
43 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (41 bp):
AACATCATGCTCAAAAGACTTATAGATGGCCTGAAGGACTT
Found at i:334977 original size:42 final size:41
Alignment explanation
Indices: 334864--334977 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
334854 ACCCAAAGGT
* * * *
334864 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAATA
1 CTTATAGATGGCCTGAAGGACTTATCATCATGCTCAAAAGA
* * * * *
334905 CTTATAGATGACGTGAAGGATTTAAACATCATGCTCGAAAGA
1 CTTATAGATGGCCTGAAGGACTT-ATCATCATGCTCAAAAGA
334947 CTTACT-GATGGCCTGAAGGACTTACTCATCA
1 CTTA-TAGATGGCCTGAAGGACTTA-TCATCA
334978 AGCAACCCTT
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
41 19 0.33
42 37 0.65
43 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (41 bp):
CTTATAGATGGCCTGAAGGACTTATCATCATGCTCAAAAGA
Found at i:336445 original size:76 final size:76
Alignment explanation
Indices: 336355--336497 Score: 277
Period size: 76 Copynumber: 1.9 Consensus size: 76
336345 TTAAAGGTGC
336355 ATTTAAACAAACTTATAAGACATTGATCAATAACAAGAAACAACAATCAACAAGAATCAATAGAG
1 ATTTAAACAAACTTATAAGACATTGATCAATAACAAGAAACAACAATCAACAAGAATCAATAGAG
336420 AATCAAAGAGT
66 AATCAAAGAGT
*
336431 ATTTAAACAAACTTATAAGACATTGATCAATATCAAGAAACAACAATCAACAAGAATCAATAGAG
1 ATTTAAACAAACTTATAAGACATTGATCAATAACAAGAAACAACAATCAACAAGAATCAATAGAG
336496 AA
66 AA
336498 AGCATCAAAC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.20
Consensus pattern (76 bp):
ATTTAAACAAACTTATAAGACATTGATCAATAACAAGAAACAACAATCAACAAGAATCAATAGAG
AATCAAAGAGT
Found at i:341890 original size:21 final size:20
Alignment explanation
Indices: 341825--341891 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
341815 TTGTGCTTCA
341825 TGCATCGATACACCT-AACAG
1 TGCATCGATACACCTGAA-AG
*
341845 TGCATCGATGA-ATCCTTGAATG
1 TGCATCGAT-ACA-CC-TGAAAG
*
341867 TGCATCGATACACCATGAAGG
1 TGCATCGATACACC-TGAAAG
341888 TGCA
1 TGCA
341892 CCAATGTACG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 10 0.26
21 15 0.38
22 12 0.31
23 2 0.05
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (20 bp):
TGCATCGATACACCTGAAAG
Found at i:343505 original size:21 final size:21
Alignment explanation
Indices: 343465--343506 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
343455 TTCGGGAGCA
*
343465 AGCTCTTCACGAGCTGCTCCT
1 AGCTCTTCACGAGCTCCTCCT
* *
343486 AGCTCTTCTCGTGCTCCTCCT
1 AGCTCTTCACGAGCTCCTCCT
343507 CCTCCTCTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.40, G:0.17, T:0.33
Consensus pattern (21 bp):
AGCTCTTCACGAGCTCCTCCT
Found at i:343859 original size:14 final size:15
Alignment explanation
Indices: 343834--343862 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
343824 TTGTTTTTGA
343834 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
343849 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
343863 AAATGCTTAA
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:344601 original size:64 final size:64
Alignment explanation
Indices: 344530--344655 Score: 159
Period size: 65 Copynumber: 2.0 Consensus size: 64
344520 ATGCACCAAT
344530 CCATGCATCGATGCACAATGA-ATTAAATTG-AAA-ATCGAATGCATTTCATGCATCGATGCACA
1 CCATGCATCGAT--ACAATGAGATTAAA-TGAAAACATCGAATGCATTTCATGCATCGATGCACA
344592 TA
63 TA
* ** *
344594 CCATGCATCGATACAGTGAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCAC
1 CCATGCATCGATACAATGA-GATTAAATGAAAACATCGAATGCATTTCATGCATCGATGCAC
344656 TCTGGCTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
62 6 0.11
63 2 0.04
64 19 0.35
65 27 0.50
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
CCATGCATCGATACAATGAGATTAAATGAAAACATCGAATGCATTTCATGCATCGATGCACATA
Found at i:344648 original size:46 final size:45
Alignment explanation
Indices: 344596--344702 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
344586 TGCACATACC
* * *
344596 ATGCATCGATACAGTGAGGAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATACACTCAGGATATTT-TG-AAACATCGAATGCACTTG
* * *
344642 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATACACTCAGGATATTTTGAAACATCGAATGCACTTG
*
344687 ATGCATCGATGCACTC
1 ATGCATCGATACACTC
344703 TTAGTACACC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 33 0.61
46 18 0.33
47 3 0.06
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (45 bp):
ATGCATCGATACACTCAGGATATTTTGAAACATCGAATGCACTTG
Found at i:348937 original size:42 final size:41
Alignment explanation
Indices: 348828--348937 Score: 104
Period size: 38 Copynumber: 2.7 Consensus size: 41
348818 ATCCGAAGGT
* * *
348828 CTTATGGATGG-CTCGAAGGACTTA-TCATCTTGCTCGAAAGA
1 CTTAT-GATGGCCT-GAAGGACTTACTCATCATACTCAAAAGA
* * *
348869 CTTATGA---CCCGAAGGATTTACACATCATACTCAAAAGA
1 CTTATGATGGCCTGAAGGACTTACTCATCATACTCAAAAGA
348907 CTTACTGATGGCCTGAAGGACTTACTCATCA
1 CTTA-TGATGGCCTGAAGGACTTACTCATCA
348938 AGCAAATCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
37 9 0.17
38 18 0.33
39 3 0.06
40 2 0.04
41 5 0.09
42 17 0.31
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (41 bp):
CTTATGATGGCCTGAAGGACTTACTCATCATACTCAAAAGA
Found at i:350960 original size:64 final size:64
Alignment explanation
Indices: 350859--351009 Score: 266
Period size: 64 Copynumber: 2.4 Consensus size: 64
350849 ACTTACTAAC
* *
350859 TAAGAAACTTTAGGAATCGTTTTCTTACTTTTCGAAAGAAATTAATTTTCAGAAAATATTTAAA
1 TAAGAAACTTTGGGAATCGTTTTCTTACTTTTCGAAAGAAATTAATTTTCAAAAAATATTTAAA
350923 TAAGAAACTTTGGGAATCGTTTTCTTACTTTTCGAAAGAAATTAATTTTCAAAAAATATTTAAA
1 TAAGAAACTTTGGGAATCGTTTTCTTACTTTTCGAAAGAAATTAATTTTCAAAAAATATTTAAA
**
350987 TAAGAAACTTTGAAAATCGTTTT
1 TAAGAAACTTTGGGAATCGTTTT
351010 TTCATTTTTT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 83 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.39
Consensus pattern (64 bp):
TAAGAAACTTTGGGAATCGTTTTCTTACTTTTCGAAAGAAATTAATTTTCAAAAAATATTTAAA
Found at i:351346 original size:53 final size:53
Alignment explanation
Indices: 351226--351706 Score: 513
Period size: 53 Copynumber: 9.1 Consensus size: 53
351216 TATGATTAAT
* * * ** * *
351226 AAACCCCCAAAAATTATGATTACCTTGTTTCAAATTCA-TTGGAAACATCAAG
1 AAACCCCTAAAAATTAGGCTTAGATTCTTTCAAATTCATTTGAAAACATCAAG
* * * *
351278 AAACCCCTAAAAATTAGGCTGAGATTCTTTAAAATTCATTAGAAAATATCAAG
1 AAACCCCTAAAAATTAGGCTTAGATTCTTTCAAATTCATTTGAAAACATCAAG
* * * *
351331 AAACCCCTAATAATTAGGCTTAGGTTTTTTAAAATTCATTTGAAAACATCAAG
1 AAACCCCTAAAAATTAGGCTTAGATTCTTTCAAATTCATTTGAAAACATCAAG
* * * * * *
351384 AAACCCCTGAAAGTAAGGCTTGGCTTCTTTCAAATTCATTTGAAAACATAAAG
1 AAACCCCTAAAAATTAGGCTTAGATTCTTTCAAATTCATTTGAAAACATCAAG
* * * * *
351437 AAACTCCGAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTAAAAATATCAAG
1 AAACCCCTAAAAATTAGGCTTAGATTCTTTCAAATTCATTTGAAAACATCAAG
* * * * *
351490 AAACCCATGAAATTTAGGCTCAAATTC-TTCTAAATTCATTTGAAAACATCAAG
1 AAACCCCTAAAAATTAGGCTTAGATTCTTTC-AAATTCATTTGAAAACATCAAG
* *
351543 AAACCCCTAAAAATTATGCTTAGCA-TCTTTCAAATTCATTTGAAACCATCAAG
1 AAACCCCTAAAAATTAGGCTTAG-ATTCTTTCAAATTCATTTGAAAACATCAAG
* * *
351596 AAACCCCTGAAAATAAGGCTTAGATTCTTTCAAATAT-ATTTGAAAACATAAAG
1 AAACCCCTAAAAATTAGGCTTAGATTCTTTCAAAT-TCATTTGAAAACATCAAG
* * * * *
351649 AAACCCCTAAAAATTAGACTTA-ATTTCTTTGAAAGCTCATTTTAAAATATCAAG
1 AAACCCCTAAAAATTAGGCTTAGA-TTCTTTCAAA-TTCATTTGAAAACATCAAG
351703 AAAC
1 AAAC
351707 TTATGAAAAT
Statistics
Matches: 355, Mismatches: 65, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
52 35 0.10
53 298 0.84
54 22 0.06
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (53 bp):
AAACCCCTAAAAATTAGGCTTAGATTCTTTCAAATTCATTTGAAAACATCAAG
Found at i:351716 original size:54 final size:54
Alignment explanation
Indices: 351656--351845 Score: 222
Period size: 54 Copynumber: 3.5 Consensus size: 54
351646 AAGAAACCCC
* * *
351656 TAAAAATTAGACTTAATTTCTTTGAAAGCTCATTTTAAAAT-ATCAAGAAACTTA
1 TAAAAATCAGACTTAGTTTCTTTAAAAGCTCA-TTTAAAATAATCAAGAAACTTA
* * * * * *
351710 TGAAAATCAAACTTAGTTTCTTTAAAAGCTTATTTAAAATCATCAGGAATCTTA
1 TAAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAATAATCAAGAAACTTA
* * * *
351764 TAAAAATTAGACATAGTTTCTTCAAAAGCTCATTTAAAGATAATAAAGAAACTTCA
1 TAAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAA-ATAATCAAGAAACTT-A
351820 -AAAAATCAGACTTAGTTTCTTTAAAA
1 TAAAAATCAGACTTAGTTTCTTTAAAA
351846 ATCACGTTAA
Statistics
Matches: 112, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
53 8 0.07
54 69 0.62
55 34 0.30
56 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (54 bp):
TAAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAATAATCAAGAAACTTA
Found at i:376987 original size:3 final size:3
Alignment explanation
Indices: 376969--377015 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
376959 CTTGTTAATT
376969 TTA TTGA TTAA TTA TTA TT- TCTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TT-A TT-A TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
377015 T
1 T
377016 ATACTTGTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 3 0.08
3 29 0.74
4 7 0.18
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:378176 original size:108 final size:109
Alignment explanation
Indices: 378026--378236 Score: 266
Period size: 108 Copynumber: 1.9 Consensus size: 109
378016 TACCCCTAAG
* * *
378026 TTAGTTGTGTTTTGTATGTTGGTCACATACGAGGACCTAAGTTGCTAAGTATCCATTTTCATGCA
1 TTAGTTGTGTTTTGCATGTTGGTCACATACGAGGACCAAAGTTGCTAAGTACCCATTTTCATGCA
* **
378091 TGTTATATA-TATTTGGGATATTTTCTGTTTAATCCCCCATAGT
66 TGTTATATATTATTTGGAATATTTGATGTTTAATCCCCCATAGT
* * * **
378134 TTAG-TGTGTTTGTGCATGTTGGTCACTTA-TAGTGACCAAAGTTGTTATTTACCCATTTTCATG
1 TTAGTTGTGTTT-TGCATGTTGGTCACATACGAG-GACCAAAGTTGCTAAGTACCCATTTTCATG
* *
378197 CATGTTATGTATTTTTTGGAATATTTGATGTTTAATCCCC
64 CATGTTATATATTATTTGGAATATTTGATGTTTAATCCCC
378237 TTTTTTAGGC
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
107 9 0.10
108 54 0.62
109 24 0.28
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (109 bp):
TTAGTTGTGTTTTGCATGTTGGTCACATACGAGGACCAAAGTTGCTAAGTACCCATTTTCATGCA
TGTTATATATTATTTGGAATATTTGATGTTTAATCCCCCATAGT
Found at i:379271 original size:131 final size:130
Alignment explanation
Indices: 379037--379432 Score: 596
Period size: 131 Copynumber: 3.0 Consensus size: 130
379027 TAAATAACAT
* * *
379037 TCGAATTAATATCGAATTTTGGGATGAAATAGTAATATCTCTTCATTTCGATTGAAATAATAAAT
1 TCGAATTAATATTGAATTTTGGGATGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAAT
*
379102 GACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAAATATTATCATTTTCT
66 -ACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCT
379167 C
130 C
*
379168 TCGAATTAATATTGAATTTTGGGATGAAATAGTAATACCTCTTCATTTCGATTGGAGTAATAAAC
1 TCGAATTAATATTGAATTTTGGGATGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAA-
* *
379233 TATTGCTTTAAGGCATGAGATGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTTC
65 TACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCA-TTTTC
379298 TC
129 TC
* * * * * *
379300 TTGAATTAATATT-AGATTTTAGGAAGAAATAGTAATATCTCTTCATTTTGGTTTGAGTAATAAA
1 TCGAATTAATATTGA-ATTTTGGGATGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAA
* * *
379364 TAGCTGCTTTAAGGCATGAGAGGTCATTTATTCTCGACTGTAAATAATTAGATATTATCGTTTTC
65 TA-CTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTC
379429 TC
129 TC
379431 TC
1 TC
379433 TTAAAATTTC
Statistics
Matches: 241, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
131 126 0.52
132 115 0.48
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (130 bp):
TCGAATTAATATTGAATTTTGGGATGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAAT
ACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTC
Found at i:379372 original size:132 final size:132
Alignment explanation
Indices: 379039--379434 Score: 559
Period size: 132 Copynumber: 3.0 Consensus size: 132
379029 AATAACATTC
* * * *
379039 GAATTAATATCGAATTTTGGGATGAAATAGTAATATCTCTTCA-TTTCGATTGAAATAATAAAT-
1 GAATTAATATTGAATTTTGGGATGAAATAGTAATATCTCTTCATTTTGGTTTG-AGTAATAAATA
*
379102 GACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAAATATTATCA-TTTTC
65 G-CTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTTC
*
379166 TCTC
129 TCTT
* * * *
379170 GAATTAATATTGAATTTTGGGATGAAATAGTAATACCTCTTCATTTCGATTGGAGTAATAAACTA
1 GAATTAATATTGAATTTTGGGATGAAATAGTAATATCTCTTCATTTTGGTTTGAGTAATAAA-TA
* *
379235 -TTGCTTTAAGGCATGAGATGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTTCT
65 GCTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTTCT
379299 CTT
130 CTT
* *
379302 GAATTAATATT-AGATTTTAGGAAGAAATAGTAATATCTCTTCATTTTGGTTTGAGTAATAAATA
1 GAATTAATATTGA-ATTTTGGGATGAAATAGTAATATCTCTTCATTTTGGTTTGAGTAATAAATA
* * *
379366 GCTGCTTTAAGGCATGAGAGGTCATTTATTCTCGACTGTAAATAATTAGATATTATCGTTTTCTC
65 GCTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTT-TC
379431 TCTT
129 TCTT
379435 AAAATTTCAA
Statistics
Matches: 235, Mismatches: 23, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
131 106 0.45
132 123 0.52
133 6 0.03
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (132 bp):
GAATTAATATTGAATTTTGGGATGAAATAGTAATATCTCTTCATTTTGGTTTGAGTAATAAATAG
CTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTTCTC
TT
Found at i:385455 original size:18 final size:19
Alignment explanation
Indices: 385426--385470 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
385416 CGAGACAAAC
385426 TTCCACAAGAAAA-ATT-AA
1 TTCCA-AAGAAAATATTGAA
385444 TTTCCAAAGAAAATATTGAA
1 -TTCCAAAGAAAATATTGAA
385464 TTCCAAA
1 TTCCAAA
385471 ACTTCCAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.29
19 15 0.62
20 2 0.08
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.27
Consensus pattern (19 bp):
TTCCAAAGAAAATATTGAA
Found at i:385928 original size:132 final size:132
Alignment explanation
Indices: 385573--385946 Score: 330
Period size: 132 Copynumber: 2.8 Consensus size: 132
385563 GCAAATCAAA
* * * * *
385573 CTCGATTCAATCATCCCTGAAGAACAGTGGAATGAATCAACATTTCCATATATGATTTACCCTGA
1 CTCGATTCAATCTTCCTTGAAGAATAGTGGAATGAATCAACATTTCCAGATATGATATACCCTGA
* * *
385638 ATAAGCAACGGGACATATCCCCTTTCTTTTTTTCAGATTTGATCTTCCCTGAAGAAGTAGTGGAA
66 A-AAGCAGC-GGATATAT-CCC---CTTTTTCT-AGATTTGATCTTCCCTGAAGAAGTAGTGGAA
*
385703 CAAGTCTGC
124 CAAGTCTAC
* ** * ** *
385712 CTCGATTCAAT-TTTCTCTGAAGAACT-GTGGAATGAATCAATGTTTCTAGATCGGTTATACCCT
1 CTCGATTCAATCTTCCT-TGAAGAA-TAGTGGAATGAATCAACATTTCCAGATATGATATACCCT
** * * * * *
385775 -AAAATATAGTGGATGAAATCCCCTTTTTCTAGATTTGATCTTCCTTG-AGTAGTAGTGGAACAT
64 GAAAA-GCAGCGGAT-ATATCCCCTTTTTCTAGATTTGATCTTCCCTGAAGAAGTAGTGGAACAA
385838 GTCTAC
127 GTCTAC
* * *
385844 CTCGATTCAATCTTCCTTGAAGAATAGTGGAATGAATCAACACTTCGAGATATGATATATCCTGA
1 CTCGATTCAATCTTCCTTGAAGAATAGTGGAATGAATCAACATTTCCAGATATGATATACCCTGA
* * *
385909 AGAGCAGCGCAATATAT-CCC-TTTTC-AGATTCGATCTTC
66 AAAGCAGCG-GATATATCCCCTTTTTCTAGATTTGATCTTC
385947 AAAAATCTCT
Statistics
Matches: 188, Mismatches: 39, Indels: 26
0.74 0.15 0.10
Matches are distributed among these distances:
129 12 0.06
130 5 0.03
131 4 0.02
132 72 0.38
133 25 0.13
134 7 0.04
137 8 0.04
138 8 0.04
139 47 0.25
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (132 bp):
CTCGATTCAATCTTCCTTGAAGAATAGTGGAATGAATCAACATTTCCAGATATGATATACCCTGA
AAAGCAGCGGATATATCCCCTTTTTCTAGATTTGATCTTCCCTGAAGAAGTAGTGGAACAAGTCT
AC
Found at i:386146 original size:3 final size:3
Alignment explanation
Indices: 386132--386201 Score: 65
Period size: 3 Copynumber: 23.3 Consensus size: 3
386122 CTTGTTAATT
* *
386132 TTA TTAA TTA TTA TTA TT- TAA TTA TTA TT- TCTA TTA TTT TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
*
386177 TTA TT- TTA TTA TATA TTA ATA TTA T
1 TTA TTA TTA TTA T-TA TTA TTA TTA T
386202 CTTTTTTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
2 4 0.07
3 44 0.80
4 7 0.13
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:386157 original size:11 final size:10
Alignment explanation
Indices: 386132--386193 Score: 63
Period size: 11 Copynumber: 5.8 Consensus size: 10
386122 CTTGTTAATT
*
386132 TTATTAATTA
1 TTATTATTTA
386142 TTATTATTTAA
1 TTATTATTT-A
386153 TTATTATTTCTA
1 TTATTA-TT-TA
386165 TTATT-TTTA
1 TTATTATTTA
386174 TTATTATTTTA
1 TTATTA-TTTA
386185 TTATATATT
1 TTAT-TATT
386194 AATATTATCT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
9 7 0.16
10 10 0.22
11 17 0.38
12 10 0.22
13 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTATTTA
Found at i:387263 original size:108 final size:107
Alignment explanation
Indices: 387085--387313 Score: 300
Period size: 108 Copynumber: 2.1 Consensus size: 107
387075 TCCCCCTAAC
* *
387085 TTAGTCGTGTTTTTGCATGTTCGTCACCTGCGAGTACCAACGTTGTTATTTACCCGTGTTCATGC
1 TTAG-CGTGTTTTTGCATGTTCGTCACCTGCGAGTACCAAAGTTGTTATTTACCCATGTTCATGC
* *
387150 ATGTTATATATTTTTGGGATATTTGTTGTTTAGTC-CCCTATAGT
65 ATGTTATATATTTTTGGAATAATTGTTGTTTAGTCACCCT-TA-T
* * * * *
387194 TTAGCGTGTTTTTGTATGTTGGTCACCTG-TAGTGACCAAATTTGTTATTTACCCATTTTCATGC
1 TTAGCGTGTTTTTGCATGTTCGTCACCTGCGAGT-ACCAAAGTTGTTATTTACCCATGTTCATGC
* *
387258 ATGTTATGTATTTTTGGAATAATTGTTGTTTAGTCACGCTTAT
65 ATGTTATATATTTTTGGAATAATTGTTGTTTAGTCACCCTTAT
387301 TTAGGCGTGTTTT
1 TTA-GCGTGTTTT
387314 CCATTTCAGT
Statistics
Matches: 106, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
107 7 0.07
108 92 0.87
109 7 0.07
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (107 bp):
TTAGCGTGTTTTTGCATGTTCGTCACCTGCGAGTACCAAAGTTGTTATTTACCCATGTTCATGCA
TGTTATATATTTTTGGAATAATTGTTGTTTAGTCACCCTTAT
Found at i:389663 original size:45 final size:41
Alignment explanation
Indices: 389567--390066 Score: 247
Period size: 34 Copynumber: 12.6 Consensus size: 41
389557 TATGGCGTCA
389567 TTTCATGCCAATAATGCACCCATATGCA-TTA--T----TC
1 TTTCATGCCAATAATGCACCCATATGCATTTAGCTAGCATC
* * * *
389601 TTTTATTCACGATAATGCACCGATATGCATTTCAGCTACGACATCC
1 TTTCATGC-CAATAATGCACCCATATGCATTT-AGCTA-G-CAT-C
*
389647 TTTCATGCCAATAATGCACCTATATGCA-TTA--T----TC
1 TTTCATGCCAATAATGCACCCATATGCATTTAGCTAGCATC
* * * *
389681 TTTTATGCCGATAATGTACCCATATGTATTTCAGCTATGGCATCC
1 TTTCATGCCAATAATGCACCCATATGCATTT-AGCTA--GCAT-C
*
389726 TTTCATTCCAATAATGCACCCATATGCA-TTA--T----TC
1 TTTCATGCCAATAATGCACCCATATGCATTTAGCTAGCATC
* *
389760 TTTTATGCCGATAATGCACCCATATGCATTTTAGCTATGGCATCC
1 TTTCATGCCAATAATGCACCCATATGCA-TTTAGCTA--GCAT-C
* *
389805 TTTCATGCCAATAATACACCTATATGCA-TTA--T----TC
1 TTTCATGCCAATAATGCACCCATATGCATTTAGCTAGCATC
* *
389839 TTTTATGCCGATAATGCACCCATATGCATTTCAGCTATGGCATAC
1 TTTCATGCCAATAATGCACCCATATGCATTT-AGCTA--GCAT-C
389884 TTTCATGCCAATAATGCACCCATATGCA-TTA--T----TC
1 TTTCATGCCAATAATGCACCCATATGCATTTAGCTAGCATC
* * * * *
389918 TTTTAAGCCGATAATGCACCCATATGTATTTAAGTTAGGCATCC
1 TTTCATGCCAATAATGCACCCATATGCATTT-AGCTA-GCAT-C
* *
389962 TTTCATGTCAATAATGCACCCAAATGCA-TTA--T----TC
1 TTTCATGCCAATAATGCACCCATATGCATTTAGCTAGCATC
* * * *
389996 TTTTATGCCGATAATTCATCCATATGCATTTTAGCTATGGCATCC
1 TTTCATGCCAATAATGCACCCATATGCA-TTTAGCTA--GCAT-C
390041 TTTCATGCCAATAATGCACCCATATG
1 TTTCATGCCAATAATGCACCCATATG
390067 TGTTATTCTT
Statistics
Matches: 349, Mismatches: 51, Indels: 121
0.67 0.10 0.23
Matches are distributed among these distances:
34 129 0.37
35 29 0.08
36 11 0.03
37 1 0.00
38 5 0.01
39 1 0.00
40 1 0.00
41 4 0.01
42 1 0.00
43 9 0.03
44 33 0.09
45 118 0.34
46 7 0.02
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (41 bp):
TTTCATGCCAATAATGCACCCATATGCATTTAGCTAGCATC
Found at i:389737 original size:79 final size:79
Alignment explanation
Indices: 389557--390080 Score: 807
Period size: 79 Copynumber: 6.6 Consensus size: 79
389547 GCATTTTATT
* * *
389557 TATGGCGTCATTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATTCACGATAATGCACC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGC-CGATAATGCACC
*
389622 GATATGCATTTCAGC
65 CATATGCATTTCAGC
* * * *
389637 TACGACATCCTTTCATGCCAATAATGCACCTATATGCATTATTCTTTTATGCCGATAATGTACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
*
389702 ATATGTATTTCAGC
66 ATATGCATTTCAGC
*
389716 TATGGCATCCTTTCATTCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
*
389781 ATATGCATTTTAGC
66 ATATGCATTTCAGC
* *
389795 TATGGCATCCTTTCATGCCAATAATACACCTATATGCATTATTCTTTTATGCCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
389860 ATATGCATTTCAGC
66 ATATGCATTTCAGC
* *
389874 TATGGCATACTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAAGCCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
* * *
389939 ATATGTATTTAAGT
66 ATATGCATTTCAGC
* * * *
389953 TA-GGCATCCTTTCATGTCAATAATGCACCCAAATGCATTATTCTTTTATGCCGATAATTCATCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
*
390017 ATATGCATTTTAGC
66 ATATGCATTTCAGC
**
390031 TATGGCATCCTTTCATGCCAATAATGCACCCATATGTGTTATTCTTTTAT
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT
390081 TCATTCGTTC
Statistics
Matches: 403, Mismatches: 40, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
78 69 0.17
79 288 0.71
80 46 0.11
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.37
Consensus pattern (79 bp):
TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
ATATGCATTTCAGC
Found at i:390643 original size:21 final size:21
Alignment explanation
Indices: 390617--390673 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
390607 ATACTACATC
390617 ATCAGTATCAATACTGATTGA
1 ATCAGTATCAATACTGATTGA
*
390638 ATCAGTATCCATACTGATTGA
1 ATCAGTATCAATACTGATTGA
*
390659 ATCAGTATCGATACT
1 ATCAGTATCAATACT
390674 ACTCGGCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (21 bp):
ATCAGTATCAATACTGATTGA
Found at i:394884 original size:80 final size:79
Alignment explanation
Indices: 394812--394965 Score: 263
Period size: 80 Copynumber: 1.9 Consensus size: 79
394802 GCATTTTATT
* *
394812 TATGGCATCCTTTCATGCCAATAATGTACCCATATGCATTATTCTTTTATTGACGATAATGCACC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTA-TGACGAAAATGCACC
394877 CATATGCATTTCAGC
65 CATATGCATTTCAGC
* *
394892 TATGGCATCCTTTCATGCCAATAATGCACCTATATGCATTATTCTTTTATGCCGAAAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGACGAAAATGCACCC
394957 ATATGCATT
66 ATATGCATT
394966 ATTCTTTTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
79 23 0.33
80 47 0.67
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (79 bp):
TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGACGAAAATGCACCC
ATATGCATTTCAGC
Found at i:394944 original size:34 final size:34
Alignment explanation
Indices: 394901--395078 Score: 187
Period size: 34 Copynumber: 4.9 Consensus size: 34
394891 CTATGGCATC
* *
394901 CTTTCATGCCAATAATGCACCTATATGCATTATT
1 CTTTTATGCCAATAATGCACCCATATGCATTATT
394935 CTTTTATGCCGAA-AATGCACCCATATGCATTATT
1 CTTTTATGCC-AATAATGCACCCATATGCATTATT
* *
394969 CTTTTATTCCGATAATGCACCCATATGCATTTGAGCTAT
1 CTTTTATGCCAATAATGCACCCATATGCA-TT-A--T-T
395008 GGCATCCTTTCATGCCAATAATGCACCCATATGCATTATT
1 --C-T--TTT-ATGCCAATAATGCACCCATATGCATTATT
* *
395048 CTTTTATGTCAATAATGCACACATATGCATT
1 CTTTTATGCCAATAATGCACCCATATGCATT
395079 TCAGCTATGG
Statistics
Matches: 123, Mismatches: 8, Indels: 26
0.78 0.05 0.17
Matches are distributed among these distances:
33 1 0.01
34 78 0.63
35 7 0.06
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 1 0.01
44 5 0.04
45 22 0.18
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (34 bp):
CTTTTATGCCAATAATGCACCCATATGCATTATT
Found at i:395010 original size:113 final size:114
Alignment explanation
Indices: 394821--395078 Score: 430
Period size: 113 Copynumber: 2.3 Consensus size: 114
394811 TTATGGCATC
* *
394821 CTTTCATGCCAATAATGTACCCATATGCATTATTCTTTTATTGACGATAATGCACCCATATGCAT
1 CTTTTATGCCAATAATGCACCCATATGCATTATTCTTTTATTGACGATAATGCACCCATATGCAT
*
394886 TTCAGCTATGGCATCCTTTCATGCCAATAATGCACCTATATGCATTATT
66 TTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATT
*
394935 CTTTTATGCCGAA-AATGCACCCATATGCATTATTCTTTTATT-CCGATAATGCACCCATATGCA
1 CTTTTATGCC-AATAATGCACCCATATGCATTATTCTTTTATTGACGATAATGCACCCATATGCA
*
394998 TTTGAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATT
65 TTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATT
* *
395048 CTTTTATGTCAATAATGCACACATATGCATT
1 CTTTTATGCCAATAATGCACCCATATGCATT
395079 TCAGCTATGG
Statistics
Matches: 135, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
112 2 0.01
113 94 0.70
114 37 0.27
115 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (114 bp):
CTTTTATGCCAATAATGCACCCATATGCATTATTCTTTTATTGACGATAATGCACCCATATGCAT
TTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATT
Found at i:395023 original size:79 final size:79
Alignment explanation
Indices: 394935--395135 Score: 307
Period size: 79 Copynumber: 2.5 Consensus size: 79
394925 ATGCATTATT
* * *
394935 CTTTTATGCCGAA-AATGCACCCATATGCATTATTCTTTTATTCCGATAATGCACCCATATGCAT
1 CTTTCATGCC-AATAATGCACCCATATGCATTATTCTTTTATTCCAATAATGCACACATATGCAT
*
394999 TTGAGCTATGGCATC
65 TTCAGCTATGGCATC
395014 CTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGT-CAATAATGCACACATATGCAT
1 CTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT-TCCAATAATGCACACATATGCAT
*
395078 TTCAGCTATGGTATC
65 TTCAGCTATGGCATC
* *
395093 CTTTCATTCCAATAATGCACCCATATGCATTACTCTTTTATTC
1 CTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATTC
395136 ATTCGTTCTA
Statistics
Matches: 112, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
78 3 0.03
79 108 0.96
80 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.37
Consensus pattern (79 bp):
CTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATTCCAATAATGCACACATATGCATT
TCAGCTATGGCATC
Found at i:395031 original size:45 final size:44
Alignment explanation
Indices: 394980--395123 Score: 164
Period size: 45 Copynumber: 3.5 Consensus size: 44
394970 TTTTATTCCG
394980 ATAATGCACCCATATGCATTTGAGCTATGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTT-AGCTATGGCATCCTTTCATGCCA
*
395025 ATAATGCACCCATATGCA-TTA--T-T--C-T--TTT-ATGTCA
1 ATAATGCACCCATATGCATTTAGCTATGGCATCCTTTCATGCCA
* * *
395059 ATAATGCACACATATGCATTTCAGCTATGGTATCCTTTCATTCCA
1 ATAATGCACCCATATGCATTT-AGCTATGGCATCCTTTCATGCCA
395104 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
395124 ACTCTTTTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
34 22 0.27
35 5 0.06
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
44 5 0.06
45 41 0.50
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (44 bp):
ATAATGCACCCATATGCATTTAGCTATGGCATCCTTTCATGCCA
Found at i:396759 original size:131 final size:130
Alignment explanation
Indices: 396479--396762 Score: 363
Period size: 131 Copynumber: 2.2 Consensus size: 130
396469 GGGGTATTAC
* * *
396479 ATTAGATATTATTGTTTTCTCTCTAATTAATATTGGATTTGGGACGAAATAGTAATATCTCTTCA
1 ATTAGATATTATTGTTTTCTCTCGAATTAATATTGAATTTAGGACGAAATAGTAATATCTCTTCA
* * *
396544 TTTCGATTGAAGTAATAAATGAATGCTTTAAGGCATGAGAGTTCATTTATTCTCGATTGAAAATA
66 TTTCGATTGAAGTAATAAATGAATGCTTTAAGGAATGAGAGGTCATTTATTCTCAATTGAAAATA
** * * * *
396609 ATTAGATATTATCATTTTCTCTCGAATTAATATTGAATTTTAGGACGGAATCGTAATATTTCTTT
1 ATTAGATATTATTGTTTTCTCTCGAATTAATATTGAA-TTTAGGACGAAATAGTAATATCTCTTC
* * * * * *
396674 ATTTTGATTGGAGTAATAAAT-AGTTTCTTTAAGGAATGAGAGGTCATTTATTTTCAATTGGAAA
65 ATTTCGATTGAAGTAATAAATGA-ATGCTTTAAGGAATGAGAGGTCATTTATTCTCAATTGAAAA
396738 TA
129 TA
* *
396740 ATTATATATTATTGCTTTCTCTC
1 ATTAGATATTATTGTTTTCTCTC
396763 TTAAAAATTA
Statistics
Matches: 130, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
130 34 0.26
131 96 0.74
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (130 bp):
ATTAGATATTATTGTTTTCTCTCGAATTAATATTGAATTTAGGACGAAATAGTAATATCTCTTCA
TTTCGATTGAAGTAATAAATGAATGCTTTAAGGAATGAGAGGTCATTTATTCTCAATTGAAAATA
Found at i:413725 original size:54 final size:54
Alignment explanation
Indices: 413372--413710 Score: 484
Period size: 54 Copynumber: 6.3 Consensus size: 54
413362 TTACCAAATA
* *
413372 GACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
1 GACACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
413426 GATACTAAGTGTGCATTTCAC-GTAATTCATCCTATGTGGAGGAATAACCGTTTT
1 GACACTAAGTGTGCATTTCACAG-AATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
413480 GATACTAAGTGTGCATTTCACAGAATTCATCATATGTGGAGGAATAACTGTTTC
1 GACACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
413534 GACACTAAGTGGGCATTTCACAGAATTCATCCTATGTGGATGAATAACTGTTTC
1 GACACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
*
413588 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GACACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
413642 AACACTAAGTGTGCATTTCAC-GTAATTCATCATATGTGGATGAATAACCATTTA
1 GACACTAAGTGTGCATTTCACAG-AATTCATCCTATGTGGATGAATAACCGTTTC
* *
413696 GGCACTATGTGTGCA
1 GACACTAAGTGTGCA
413711 AAGCAAGAAA
Statistics
Matches: 260, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
53 2 0.01
54 257 0.99
55 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (54 bp):
GACACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:419948 original size:95 final size:95
Alignment explanation
Indices: 419823--420009 Score: 234
Period size: 95 Copynumber: 2.0 Consensus size: 95
419813 TGATTCAATC
* * *
419823 AGTATCGATACCATGAAAGGGTATCGATACCAAGAAACATTGAATCC-AAAATCGATATCGATA-
1 AGTATAGATACCATGAAAGGGTATCAATACCAAGAAACATCGAA-CCTAAAATCGATATCGATAT
* * *
419886 CTGGAAGGGGGTATCGGTACCATAGTATTGT
65 CAGGAAGGGGATATCGATACCATAGTATTGT
* * * * *
419917 AGTATAGATACCATGGTAAGGGTATCAATACCAGGAAACATCGAACCTAAATTTGGTATCGATAT
1 AGTATAGATACCAT-GAAAGGGTATCAATACCAAGAAACATCGAACCTAAAATCGATATCGATAT
*
419982 CAGTAAGGGGATATCGATACCATAGTAT
65 CAGGAAGGGGATATCGATACCATAGTAT
420010 AGAAGTATCG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
94 15 0.19
95 39 0.50
96 24 0.31
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (95 bp):
AGTATAGATACCATGAAAGGGTATCAATACCAAGAAACATCGAACCTAAAATCGATATCGATATC
AGGAAGGGGATATCGATACCATAGTATTGT
Found at i:420025 original size:96 final size:95
Alignment explanation
Indices: 419823--420030 Score: 240
Period size: 96 Copynumber: 2.2 Consensus size: 95
419813 TGATTCAATC
* * *
419823 AGTATCGATACCAT-GAAAGGGTATCGATACCAAGAAACATTGAATCCAAAATCGATATCGATAC
1 AGTATCGATACCATGGTAAGGGTATCAATACCAAGAAACATCGAATCCAAAATCGATATCGATAC
* * * * *
419887 TGGAAGGGGGTATCGGTACCATAGTATTGT
66 AGGAAGGGGATATCGATACCATAGTATAGA
* * * * *
419917 AGTATAGATACCATGGTAAGGGTATCAATACCAGGAAACATCGAA-CCTAAATTTGGTATCGATA
1 AGTATCGATACCATGGTAAGGGTATCAATACCAAGAAACATCGAATCC-AAAATCGATATCGATA
*
419981 TCAGTAAGGGGATATCGATACCATAGTATAGA
65 -CAGGAAGGGGATATCGATACCATAGTATAGA
* *
420013 AGTATCGGTACCAGGGTA
1 AGTATCGATACCATGGTA
420031 GTAGTATCGA
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
94 15 0.16
95 39 0.41
96 40 0.43
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.25
Consensus pattern (95 bp):
AGTATCGATACCATGGTAAGGGTATCAATACCAAGAAACATCGAATCCAAAATCGATATCGATAC
AGGAAGGGGATATCGATACCATAGTATAGA
Found at i:420426 original size:54 final size:54
Alignment explanation
Indices: 420363--420631 Score: 321
Period size: 54 Copynumber: 5.0 Consensus size: 54
420353 ATCAAATAGG
* *
420363 CACTAAGTGTGCATTTCACGAAATTCATCTTATGTGGATGAATAACTATTTCGA
1 CACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACTGTTTCGA
* * *
420417 CAGTAAGTGTGCATTTCACGAAATTCATCCTATGTGAAGGAATAA-TCGTTTCTG-
1 CACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACT-GTTTC-GA
* * * * ** * *
420471 TACTAAGTGTGCATTTCACGGAATTCATCATATATATAGGAATAACTGTTTCGG
1 CACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACTGTTTCGA
* * *
420525 CACTAAGTGTGCATTTCA-TAGAATTCATCCTACGTGGATGAATAACCGTTTC-A
1 CACTAAGTGTGCATTTCACGA-AATTCATCCTATGTGGATGAATAACTGTTTCGA
*
420578 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCG
1 -CACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACTGTTTCG
420632 GTACTATGTG
Statistics
Matches: 180, Mismatches: 27, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
53 2 0.01
54 176 0.98
55 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACTGTTTCGA
Found at i:420553 original size:108 final size:108
Alignment explanation
Indices: 420362--420642 Score: 375
Period size: 108 Copynumber: 2.6 Consensus size: 108
420352 TATCAAATAG
* * * * *
420362 GCACTAAGTGTGCATTTCACGAAATTCATCTTATGTGGATGAATAACTATTTCGACAGTAAGTGT
1 GCACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACTGTTTCGGCACTAAGTGT
* * * *
420427 GCATTTCACGAAATTCATCCTATGTGAAGGAATAATCGTTTCT
66 GCATTTCAAGAAATTCATCCTACGTGAAGGAATAACCGTTTCA
* * ** *
420470 GTACTAAGTGTGCATTTCACGGAATTCATCATATATATAGGAATAACTGTTTCGGCACTAAGTGT
1 GCACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACTGTTTCGGCACTAAGTGT
* *
420535 GCATTTCATAG-AATTCATCCTACGTGGATGAATAACCGTTTCA
66 GCATTTCA-AGAAATTCATCCTACGTGAAGGAATAACCGTTTCA
* * *
420578 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCGGTACTATGTGT
1 GCACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACTGTTTCGGCACTAAGTGT
420643 AAAGCAAGAA
Statistics
Matches: 148, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
108 147 0.99
109 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (108 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACTGTTTCGGCACTAAGTGT
GCATTTCAAGAAATTCATCCTACGTGAAGGAATAACCGTTTCA
Found at i:422030 original size:26 final size:25
Alignment explanation
Indices: 421973--422030 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
421963 AAAGGCACGG
421973 GTTTGAAATGGAATGAAAAGTACAA
1 GTTTGAAATGGAATGAAAAGTACAA
* *
421998 GAATTGAAAT-GAGATGGAAAAGTACAT
1 G-TTTGAAATGGA-AT-GAAAAGTACAA
422025 GTTTGA
1 GTTTGA
422031 TCTACTTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
25 3 0.11
26 13 0.48
27 11 0.41
ACGTcount: A:0.45, C:0.03, G:0.26, T:0.26
Consensus pattern (25 bp):
GTTTGAAATGGAATGAAAAGTACAA
Found at i:424650 original size:44 final size:43
Alignment explanation
Indices: 424608--424703 Score: 120
Period size: 46 Copynumber: 2.2 Consensus size: 43
424598 TTGGGACATA
424608 TATGTGGTCCTTTGGGATAATTCTACGTGGTCATTCGAGACATTTC
1 TATGTGGTCCTTTGGGATAA--CTACGTGGTCATTCGAGACA-TTC
* * * * *
424654 TACGTGATCCTTTGGGATAACTATGTGGTCCTTCGGGACATTC
1 TATGTGGTCCTTTGGGATAACTACGTGGTCATTCGAGACATTC
424697 TATGTGG
1 TATGTGG
424704 CACTTCGGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
43 8 0.19
44 17 0.40
46 18 0.42
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (43 bp):
TATGTGGTCCTTTGGGATAACTACGTGGTCATTCGAGACATTC
Found at i:424702 original size:22 final size:22
Alignment explanation
Indices: 424600--424724 Score: 78
Period size: 23 Copynumber: 5.7 Consensus size: 22
424590 GCAGTTCTTT
* *
424600 GGGACA-TATATGTGGTCCTTT
1 GGGACATTCTATGTGGTCCTTC
* * *
424621 GGGATAATTCTACGTGGTCATTC
1 GGGA-CATTCTATGTGGTCCTTC
* * * *
424644 GAGACATTTCTACGTGATCCTTT
1 GGGACA-TTCTATGTGGTCCTTC
* *
424667 GGGATA-ACTATGTGGTCCTTC
1 GGGACATTCTATGTGGTCCTTC
424688 GGGACATTCTATGTGG-CACTTC
1 GGGACATTCTATGTGGTC-CTTC
*
424710 GGTG-CATTTTATGTG
1 GG-GACATTCTATGTG
424725 AGCTATGGTG
Statistics
Matches: 79, Mismatches: 19, Indels: 11
0.72 0.17 0.10
Matches are distributed among these distances:
21 21 0.27
22 26 0.33
23 32 0.41
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (22 bp):
GGGACATTCTATGTGGTCCTTC
Found at i:427879 original size:57 final size:54
Alignment explanation
Indices: 427818--427924 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 54
427808 GCTCATAAGC
427818 TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCATAAGCTTATTATTA
1 TTATTTTTACCAAAATACTTACCA-TT--ATTCCATAAGCTCATAAGCTTATTATTA
** * * *
427875 TTATTTTTTTCAATATACTTGCCATTATTCCGTAAGCTCATAAGCTTATT
1 TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATT
427925 TGCATGGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 23 0.51
56 2 0.04
57 20 0.44
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.45
Consensus pattern (54 bp):
TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATTATTA
Found at i:432172 original size:23 final size:23
Alignment explanation
Indices: 432139--432193 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
432129 GGACATATAT
*
432139 GTGGTCTTTCAGGAAAATTCTAC
1 GTGGTCCTTCAGGAAAATTCTAC
* * *
432162 GTGGTCCTTCAGGACATTTTTAC
1 GTGGTCCTTCAGGAAAATTCTAC
*
432185 GCGGTCCTT
1 GTGGTCCTT
432194 TGGGACATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (23 bp):
GTGGTCCTTCAGGAAAATTCTAC
Found at i:432221 original size:21 final size:22
Alignment explanation
Indices: 432187--432227 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
432177 ATTTTTACGC
* *
432187 GGTCCTTTGGGACA-TCTATAT
1 GGTCCTTCGAGACATTCTATAT
432208 GGTCCTTCGAGACATTCTAT
1 GGTCCTTCGAGACATTCTAT
432228 GTGGCACTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (22 bp):
GGTCCTTCGAGACATTCTATAT
Found at i:432723 original size:21 final size:23
Alignment explanation
Indices: 432697--432738 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
432687 ATAATATATG
432697 TTTTGATCA-ATTT-TGTAAACC
1 TTTTGATCATATTTATGTAAACC
*
432718 TTTTGATTATATTTATGTAAA
1 TTTTGATCATATTTATGTAAA
432739 TTATTGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (23 bp):
TTTTGATCATATTTATGTAAACC
Found at i:434003 original size:26 final size:26
Alignment explanation
Indices: 433967--434016 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
433957 AATTTTATTA
433967 ATTAATATTATTTAATTA-TTATTTCT
1 ATTAATATTATTT-ATTATTTATTTCT
*
433993 ATTATTATTATTTATTATTTATTT
1 ATTAATATTATTTATTATTTATTT
434017 TAATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
ATTAATATTATTTATTATTTATTTCT
Found at i:434010 original size:22 final size:21
Alignment explanation
Indices: 433972--434050 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 21
433962 TATTAATTAA
*
433972 TATTATTTAATTATTATTTCTAT
1 TATTA-TTATTTATTATTTCT-T
*
433995 TATTATTATTTATTATTTATTT
1 TATTATTATTTATTATTT-CTT
*
434017 TAATATATATTTA-TATTATCTT
1 TATTAT-TATTTATTATT-TCTT
434039 TATT-TTATTTAT
1 TATTATTATTTAT
434051 GCATGCCCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 6 0.13
21 1 0.02
22 27 0.57
23 13 0.28
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTATTATTTATTATTTCTT
Found at i:437018 original size:24 final size:25
Alignment explanation
Indices: 436980--437027 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
436970 TGAATGTTGA
436980 ATGAGCATATAAAATGAACACGTTT
1 ATGAGCATATAAAATGAACACGTTT
437005 ATGAGCATAT-AAATGAACACGTT
1 ATGAGCATATAAAATGAACACGTT
437028 CGCGAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (25 bp):
ATGAGCATATAAAATGAACACGTTT
Found at i:441554 original size:11 final size:11
Alignment explanation
Indices: 441535--441575 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
441525 ATTTTGTTAG
441535 TAATAATAATA
1 TAATAATAATA
*
441546 TATTAATAATA
1 TAATAATAATA
*
441557 TAATAATATTA
1 TAATAATAATA
*
441568 TAACAATA
1 TAATAATA
441576 TTATTAGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
TAATAATAATA
Found at i:441575 original size:19 final size:19
Alignment explanation
Indices: 441537--441576 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
441527 TTTGTTAGTA
*
441537 ATAATAATATATTAATAAT
1 ATAATAATATATTAACAAT
441556 ATAATAATAT-TATAACAAT
1 ATAATAATATAT-TAACAAT
441575 AT
1 AT
441577 TATTAGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATAATATATTAACAAT
Found at i:442059 original size:67 final size:67
Alignment explanation
Indices: 441928--443364 Score: 2295
Period size: 67 Copynumber: 21.4 Consensus size: 67
441918 ATATGTTCTG
* * * *
441928 CTTACTCTGAAGGTAATAT-AAGATCTT-AAGGAATTTGATCCATTGAATTGGGGCAGACTTGTT
1 CTTACTCTGAAGGGAATATCAA-ATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTT
441991 CCA
65 CCA
* **
441994 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTAAATCGGAACAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442059 CA
66 CA
* ** * * *
442061 CTAACTCTGAAGGGAATATCAAATCTTGGAGGAACTTGATCCATTGAATCGAGGCAAACTTATTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442126 CA
66 CA
* * * * * * *
442128 CTTACTCTGAAGGGAATATCAAATATTAGAGGAGTTTAATCCATTGAATAGGGGTAGACTAGTTT
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442193 CA
66 CA
* *
442195 CTTACTCTGAAAGGAATGTCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442260 CA
66 CA
* *
442262 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATTGAGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442327 CA
66 CA
* *
442329 ATTACTCTAAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442394 CA
66 CA
* * *
442396 TTTACTCTGAAGGAAATATCAAATCTTGGAGGAGTTTGATCCATTTAATCGGGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442461 CA
66 CA
*
442463 CTTACTCTGAAAGGGAATATCAAATCTTGGAGGAATTTGATCCATTGAATCGGGGCAGACTTGTT
1 CTTACTCTG-AAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTT
442528 CCA
65 CCA
442531 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442596 CA
66 CA
* *
442598 CTTACTATGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCAGGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442663 CA
66 CA
* * *
442665 CTTACTCGGAAGGGAATATCAATTCTTGGAGGAATTTGATCCATTGAATCGGGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442730 CA
66 CA
* * *
442732 CTTACTCTGAAAGGGAATATCAAATCTTGGAGGAGTTTGTTCAATTGAATCGGGGAAGACTTGTT
1 CTTACTCTG-AAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTT
442797 CCA
65 CCA
* ** *
442800 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAATTTGATCCATTGAATTAGGGCTGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442865 CA
66 CA
*
442867 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATTGGGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442932 CA
66 CA
*
442934 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCAGGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
442999 CA
66 CA
*
443001 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAATTTGATCCATTGAATCGGGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
443066 CA
66 CA
* * * *
443068 CTTACTCTGAATGGAATATCAAATCTTGGAGGAGTTTGATCCACTGAAT-TGGCCAAGACTTGTT
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGC-AGACTTGTT
443132 CCA
65 CCA
* * *
443135 CTTACTATGAAGGAAATATCAAATCTTGGAGGAATTTGATCCATTGAATCGGGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
443200 CA
66 CA
* * *
443202 CTTACTCCGAAGGGAATATAAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGTAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
443267 CA
66 CA
* * *
443269 CTTACTCTAAAGGGAATATCAAATCTTGGAGGAATTTGATCCATTGAATTGGGGCAGACTTGTTC
1 CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
443334 CA
66 CA
443336 CTTACTCTGAAGGGAATATCAAATCTTGG
1 CTTACTCTGAAGGGAATATCAAATCTTGG
443365 GAAAGAGAGA
Statistics
Matches: 1258, Mismatches: 107, Indels: 11
0.91 0.08 0.01
Matches are distributed among these distances:
66 26 0.02
67 1103 0.88
68 129 0.10
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (67 bp):
CTTACTCTGAAGGGAATATCAAATCTTGGAGGAGTTTGATCCATTGAATCGGGGCAGACTTGTTC
CA
Found at i:450832 original size:24 final size:24
Alignment explanation
Indices: 450800--450861 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
450790 GGTAATAATA
*
450800 AAAATAAAATAAAATTGTAATTAAAT
1 AAAA-AAAATAAAATAG-AATTAAAT
* *
450826 AAAAAAAATAATATAGGATTAAAT
1 AAAAAAAATAAAATAGAATTAAAT
*
450850 AAAAAATATAAA
1 AAAAAAAATAAA
450862 TTATTGGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 17 0.55
25 10 0.32
26 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (24 bp):
AAAAAAAATAAAATAGAATTAAAT
Found at i:451369 original size:20 final size:22
Alignment explanation
Indices: 451322--451369 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
451312 CACCAACCGA
451322 TTACTATTCCAGCCACCGTCAG
1 TTACTATTCCAGCCACCGTCAG
* *
451344 TCACTATT-CA-CCACCGTCGG
1 TTACTATTCCAGCCACCGTCAG
451364 TTACTA
1 TTACTA
451370 CTCCGGTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 14 0.61
21 2 0.09
22 7 0.30
ACGTcount: A:0.23, C:0.35, G:0.12, T:0.29
Consensus pattern (22 bp):
TTACTATTCCAGCCACCGTCAG
Found at i:452021 original size:11 final size:11
Alignment explanation
Indices: 452001--452042 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
451991 TTTATTGTTA
452001 ATAATAATAAT
1 ATAATAATAAT
*
452012 ATATTAATAAT
1 ATAATAATAAT
*
452023 ATAATAATATT
1 ATAATAATAAT
*
452034 ATAACAATA
1 ATAATAATA
452043 TTATTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:452042 original size:19 final size:19
Alignment explanation
Indices: 452004--452043 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
451994 ATTGTTAATA
*
452004 ATAATAATATATTAATAAT
1 ATAATAATATATTAACAAT
452023 ATAATAATAT-TATAACAAT
1 ATAATAATATAT-TAACAAT
452042 AT
1 AT
452044 TATTAGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATAATATATTAACAAT
Found at i:453895 original size:58 final size:58
Alignment explanation
Indices: 453773--453926 Score: 166
Period size: 59 Copynumber: 2.6 Consensus size: 58
453763 AGTATATACA
* * * *
453773 TATAATTTGGGATGCAATTGAAATATTCAAAAAGTTTGGGACCAATTTAAAATGAAGAT
1 TATAGTTTGGGATGAAATTGAAATATTC-AAAAGTTTGAGACCAATCTAAAATGAAGAT
* * * * ***
453832 CATAGTTTGGGGATG-AATTGAAATGTTCAAAAGTTTGAGACTAATCTAGAATGATTTT
1 TATAGTTT-GGGATGAAATTGAAATATTCAAAAGTTTGAGACCAATCTAAAATGAAGAT
*
453890 TATAGTTTAGGGATGAAATTGAAATATTTAAAAGTTT
1 TATAGTTT-GGGATGAAATTGAAATATTCAAAAGTTT
453927 AGGAACAATT
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
58 36 0.46
59 37 0.47
60 6 0.08
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (58 bp):
TATAGTTTGGGATGAAATTGAAATATTCAAAAGTTTGAGACCAATCTAAAATGAAGAT
Found at i:466391 original size:20 final size:20
Alignment explanation
Indices: 466366--466603 Score: 145
Period size: 20 Copynumber: 10.7 Consensus size: 20
466356 TAACTAAAAT
466366 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
466386 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
466406 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
466432 GCATGAAATGATACATTAAG
1 GCATGAAAGGATGCATTAAG
*
466452 GCATGAAAGGATGCCATAACTGAAATT
1 GCATGAAAGGATG-CAT---T--AA-G
* *
466479 G-ATGAAATGATGCATTAAA
1 GCATGAAAGGATGCATTAAG
* *
466498 GCATAAAAGGATGCAATAACTAAAAT
1 GCATGAAAGGATGC-AT---T--AAG
466524 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
466544 GCATGAAAGGATCCCATAACTAAAAT
1 GCATGAAAGGAT-GCAT---T--AAG
*
466570 GCATGAAAGGATGTATTAAG
1 GCATGAAAGGATGCATTAAG
466590 GCATGAAAGGATGC
1 GCATGAAAGGATGC
466604 CACAACTAAA
Statistics
Matches: 172, Mismatches: 20, Indels: 52
0.70 0.08 0.21
Matches are distributed among these distances:
19 1 0.01
20 87 0.51
21 11 0.06
22 4 0.02
24 4 0.02
25 10 0.06
26 54 0.31
27 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:466453 original size:46 final size:46
Alignment explanation
Indices: 466386--466615 Score: 354
Period size: 46 Copynumber: 5.0 Consensus size: 46
466376 ATGCATTAAG
466386 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* * *
466432 GCATGAAATGATACATTAAGGCATGAAAGGATGCCATAACTGAAATT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACT-AAAAT
* * * *
466479 G-ATGAAATGATGCATTAAAGCATAAAAGGATGCAATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
*
466524 GCATGAAAGGATGCATTAAGGCATGAAAGGATCCCATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* *
466570 GCATGAAAGGATGTATTAAGGCATGAAAGGATGCCACAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
466616 TAACGAATAT
Statistics
Matches: 166, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
45 5 0.03
46 156 0.94
47 5 0.03
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.21
Consensus pattern (46 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
Found at i:466527 original size:26 final size:25
Alignment explanation
Indices: 466341--466582 Score: 113
Period size: 20 Copynumber: 10.5 Consensus size: 25
466331 TATTATTAAG
*
466341 GCATGAAAGGATCCATAACTAAAAT
1 GCATGAAAGGATGCATAACTAAAAT
*
466366 GCATGAAAGGATGCAT---T--AAG
1 GCATGAAAGGATGCATAACTAAAAT
*
466386 GCATGAAAGGATGCAT---T--AAG
1 GCATGAAAGGATGCATAACTAAAAT
466406 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CATAACTAAAAT
* * *
466432 GCATGAAATGATACAT---T--AAG
1 GCATGAAAGGATGCATAACTAAAAT
*
466452 GCATGAAAGGATGCCATAACTGAAATT
1 GCATGAAAGGATG-CATAACT-AAAAT
*
466479 G-ATGAAATGATGCAT---T-AAA-
1 GCATGAAAGGATGCATAACTAAAAT
* *****
466498 GCATAAAAGGATGCAATAACTAAAAT
1 GCATGAAA-GGATGCATAACTAAAAT
*
466524 GCATGAAAGGATGCAT---T--AAG
1 GCATGAAAGGATGCATAACTAAAAT
*
466544 GCATGAAAGGATCCCATAACTAAAAT
1 GCATGAAAGGAT-GCATAACTAAAAT
466570 GCATGAAAGGATG
1 GCATGAAAGGATG
466583 TATTAAGGCA
Statistics
Matches: 162, Mismatches: 29, Indels: 52
0.67 0.12 0.21
Matches are distributed among these distances:
19 1 0.01
20 69 0.43
21 11 0.07
22 4 0.02
24 4 0.02
25 27 0.17
26 44 0.27
27 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (25 bp):
GCATGAAAGGATGCATAACTAAAAT
Found at i:468596 original size:104 final size:104
Alignment explanation
Indices: 468412--468621 Score: 296
Period size: 104 Copynumber: 2.0 Consensus size: 104
468402 AAGGCCAACG
** * *
468412 ATTCTTGAGTTGCCCAAATTGGTTTGAGGTTAGTTCATGTACATGTTAATTCTTTTGAGTTTATG
1 ATTCTTGAGTTGCCCAAATTGGTTCAAGGTTAGTTCATGTAAATGTTAATTCTGTTGAGTTTATG
* ** * * *
468477 AAATGTGATTTATATTGATTAGTTATTAAATTCTTCACC
66 AAATATGATGCATATTGATTAGTTATGAAATGCTTAACC
*
468516 ATTCTTCG-GTTGTCCAAATTGGTTCAAGGTTAGTTCATGTAAATGTTAATTCTGTTGAGTTTAT
1 ATTCTT-GAGTTGCCCAAATTGGTTCAAGGTTAGTTCATGTAAATGTTAATTCTGTTGAGTTTAT
*
468580 GAAATATGATGCATATTGGTTAGTTATGAAATGCTTAACC
65 GAAATATGATGCATATTGATTAGTTATGAAATGCTTAACC
468620 AT
1 AT
468622 GATTTGTTCT
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
104 92 0.99
105 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (104 bp):
ATTCTTGAGTTGCCCAAATTGGTTCAAGGTTAGTTCATGTAAATGTTAATTCTGTTGAGTTTATG
AAATATGATGCATATTGATTAGTTATGAAATGCTTAACC
Found at i:469197 original size:41 final size:40
Alignment explanation
Indices: 469151--469230 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
469141 ATGTACAGTT
* *
469151 ATATAAAGTTGACCAAAATTTTCATTCAA-AATTAACAAAAC
1 ATATAAAGTT-ACC-AAATTTCCATTCAATAATTAAAAAAAC
*
469192 ATATAAAGTTACCATATTTCCATTCAATAATTAAAAAAA
1 ATATAAAGTTACCAAATTTCCATTCAATAATTAAAAAAA
469231 TACATGAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 12 0.34
40 13 0.37
41 10 0.29
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (40 bp):
ATATAAAGTTACCAAATTTCCATTCAATAATTAAAAAAAC
Found at i:469408 original size:15 final size:16
Alignment explanation
Indices: 469371--469412 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
469361 GGTGGTGATG
469371 CCTGTTGTGTTGCTGA
1 CCTGTTGTGTTGCTGA
* *
469387 -CTATTGTGTTG-TTA
1 CCTGTTGTGTTGCTGA
469401 CCTGTTGTGTTG
1 CCTGTTGTGTTG
469413 GTGCCTCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.07, C:0.14, G:0.29, T:0.50
Consensus pattern (16 bp):
CCTGTTGTGTTGCTGA
Found at i:470836 original size:19 final size:19
Alignment explanation
Indices: 470809--470854 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
470799 TTTAAAAAGT
*
470809 GTTTACCTATAAACTTGTA
1 GTTTGCCTATAAACTTGTA
470828 GTTTGCCTATAAACTTGTA
1 GTTTGCCTATAAACTTGTA
470847 GTTTGCCT
1 GTTTGCCT
470855 TTGAGTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.43
Consensus pattern (19 bp):
GTTTGCCTATAAACTTGTA
Found at i:471591 original size:42 final size:41
Alignment explanation
Indices: 471472--471600 Score: 141
Period size: 42 Copynumber: 3.1 Consensus size: 41
471462 ACTCTCACTA
* *
471472 TCAGCCTTACCCTTAGCACCCTCACCCTCATTATTAGACTTC
1 TCAGCCTCACCCTCAGCACCCTCACCCTCATT-TTAGACTTC
* * *
471514 TCAACCTCACCCTCAGCATCATCACCCTCAGTTTTAGACTTC
1 TCAGCCTCACCCTCAGCACCCTCACCCTCA-TTTTAGACTTC
* * ** *
471556 TCAGCCTCACCATGAGCACCCTCAGTCTCACTTTTAAACTTC
1 TCAGCCTCACCCTCAGCACCCTCACCCTCA-TTTTAGACTTC
471598 TCA
1 TCA
471601 AGCTCTGTCT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 70 0.97
43 2 0.03
ACGTcount: A:0.23, C:0.40, G:0.08, T:0.29
Consensus pattern (41 bp):
TCAGCCTCACCCTCAGCACCCTCACCCTCATTTTAGACTTC
Found at i:474621 original size:54 final size:55
Alignment explanation
Indices: 474431--474623 Score: 316
Period size: 55 Copynumber: 3.5 Consensus size: 55
474421 ATGTATGATG
* *
474431 ATTTTCGTAAGGGGACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGA
1 ATTTCCGTAAGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGA
* *
474486 ATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTTTGA
1 ATTTCCGTAAGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGA
*
474541 ATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAG-TTATGA
1 ATTTCCGTAAGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGA
* *
474595 ATTTCTGTAAGGGCACTTTGTTTGCAAAA
1 ATTTCCGTAAGGGCACTTTGTGTGCAAAA
474624 TTATTTTATG
Statistics
Matches: 130, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
54 31 0.24
55 99 0.76
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (55 bp):
ATTTCCGTAAGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGA
Found at i:474826 original size:55 final size:55
Alignment explanation
Indices: 474628--474809 Score: 301
Period size: 55 Copynumber: 3.3 Consensus size: 55
474618 GCAAAATTAT
* * *
474628 TTTATGAATTTCCGTATGAGCACTTTGTGTGTAAAACTAAGAAATTCATAATAGG
1 TTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAG
* *
474683 TTTATGAATTTCCGTATGGGCACATTGTGTGCAAAGCTAAGAAATTCATAATAAG
1 TTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAG
* *
474738 TTTATGAATTTCCATACGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAG
1 TTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAG
474793 TTTATGAATTTCCGTAT
1 TTTATGAATTTCCGTAT
474810 TGGTAGTGGG
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 116 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (55 bp):
TTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAG
Found at i:485654 original size:22 final size:22
Alignment explanation
Indices: 485626--485682 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
485616 ACCAAATCTT
* *
485626 GAACTGAAGAAGAACATATATA
1 GAACTGAAGAAAAACATATACA
485648 GAACTGAAGAAAAACATATACA
1 GAACTGAAGAAAAACATATACA
485670 GAACTTGAA-AAAA
1 GAAC-TGAAGAAAA
485683 CTCTTCCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.58, C:0.11, G:0.16, T:0.16
Consensus pattern (22 bp):
GAACTGAAGAAAAACATATACA
Found at i:494911 original size:22 final size:24
Alignment explanation
Indices: 494881--494929 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
494871 ACCAAGGCCT
* *
494881 ATACTTAAA-AAACCCTAGCCC-A
1 ATACCTAAACAAACCCTAACCCTA
*
494903 ATACCTAAACTAACCCTAACCCTA
1 ATACCTAAACAAACCCTAACCCTA
494927 ATA
1 ATA
494930 TCTTCATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 8 0.36
23 10 0.45
24 4 0.18
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (24 bp):
ATACCTAAACAAACCCTAACCCTA
Found at i:498166 original size:103 final size:104
Alignment explanation
Indices: 497987--498195 Score: 411
Period size: 103 Copynumber: 2.0 Consensus size: 104
497977 AAACCCCTCT
497987 AAAACCTCCATCTTGGTCACCATGGTCAAATCTTGAGATTTTGGTCTTGAATTGAAGCTTTAGGG
1 AAAACCTCCATCTTGGTCACCATGGTCAAATCTTGAGATTTTGGTCTTGAATTGAAGCTTTAGGG
498052 GAGGGGTTATAAATCTTACCTTTGT-AATTTGGCCTAGC
66 GAGGGGTTATAAATCTTACCTTTGTAAATTTGGCCTAGC
498090 AAAACCTCCATCTTGGTCACCATGGTCAAATCTTGAGATTTTGGTCTTGAATTGAAGCTTTAGGG
1 AAAACCTCCATCTTGGTCACCATGGTCAAATCTTGAGATTTTGGTCTTGAATTGAAGCTTTAGGG
498155 GAGGGGTTATAAATCTTACCTTTGTAAATTTGGCCTAGC
66 GAGGGGTTATAAATCTTACCTTTGTAAATTTGGCCTAGC
498194 AA
1 AA
498196 CGTAGGGTAA
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
103 90 0.86
104 15 0.14
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (104 bp):
AAAACCTCCATCTTGGTCACCATGGTCAAATCTTGAGATTTTGGTCTTGAATTGAAGCTTTAGGG
GAGGGGTTATAAATCTTACCTTTGTAAATTTGGCCTAGC
Done.