Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008283.1 Hibiscus syriacus cultivar Beakdansim tig00110945_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: 2862730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 14
Found at i:493458 original size:21 final size:21
Alignment explanation
Indices: 493432--493475 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
493422 CCAGATTCGT
493432 AACGCGAACATCGACTATCGC
1 AACGCGAACATCGACTATCGC
*
493453 AACGCGAACTTCGACTATCGC
1 AACGCGAACATCGACTATCGC
493474 AA
1 AA
493476 TGTGATTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (21 bp):
AACGCGAACATCGACTATCGC
Found at i:493583 original size:63 final size:63
Alignment explanation
Indices: 493484--493647 Score: 310
Period size: 63 Copynumber: 2.6 Consensus size: 63
493474 AATGTGATTC
*
493484 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTGTTCCAAATTCGCGTTGCGATAGTCCAAGTTT
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTGTTCCAAATTCGCGTTGCGATAGTCCAAGTTT
493547 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTGTTCCAAATTCGCGTTGCGATAGTCCAAGTTT
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTGTTCCAAATTCGCGTTGCGATAGTCCAAGTTT
*
493610 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAA
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTGTTCCAA
493648 GTTCATTGCG
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 99 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (63 bp):
GTTGCGATAGTCGAAGTTCGCGTTGCGATTTGTTCCAAATTCGCGTTGCGATAGTCCAAGTTT
Found at i:493662 original size:105 final size:106
Alignment explanation
Indices: 493483--493833 Score: 444
Period size: 105 Copynumber: 3.3 Consensus size: 106
493473 CAATGTGATT
* * * *
493483 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTGTTCCAAATTCGCGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATAGTCCAAGTTC-CGTTGCGA-TAG-TCGAAGTTCGCGTTGCGATTTATTCCAAGTT
* *
493546 TGTTGCGATAGTCGAAGTTCGCGTTGCGATTTGTTCCAAATTCG
63 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
493590 CGTTGCGATAGTCCAAGTT-TGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCAT
1 CGTTGCGATAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
* *
493654 TGCGATAGTTGAAGTTCGCGTTGCAATTTATTCCAAATT--
66 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * * **
493693 CATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTATAAGTTCG
1 CGTTGCGATAGTCCAAGTTC-CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
493758 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
65 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
493800 CGTTGCGATTTATTCCAAGTT-TGTTGCGATAGTC
1 CGTTGCGA--TAGTCCAAGTTCCGTTGCGATAGTC
493834 CAAAATCACA
Statistics
Matches: 212, Mismatches: 24, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
103 33 0.16
104 2 0.01
105 130 0.61
107 38 0.18
109 9 0.04
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (106 bp):
CGTTGCGATAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:493677 original size:63 final size:62
Alignment explanation
Indices: 493481--493671 Score: 285
Period size: 63 Copynumber: 3.1 Consensus size: 62
493471 CGCAATGTGA
*
493481 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTGTTCCAAATTCGCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTGTTCCAAATTC-CGTTGCGATAGTCCAAG
*
493544 TTTGTTGCGATAGTCGAAGTTCGCGTTGCGATTTGTTCCAAATTCGCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTGTTCCAAATTC-CGTTGCGATAGTCCAAG
* * * * **
493607 TTTGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT-CATTGCGATAGTTGAAG
1 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTGTTCCAAATTCCGTTGCGATAGTCCAAG
493668 TTCG
1 TTCG
493672 CGTTGCAATT
Statistics
Matches: 120, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
61 17 0.14
63 103 0.86
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (62 bp):
TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTGTTCCAAATTCCGTTGCGATAGTCCAAG
Found at i:493762 original size:63 final size:63
Alignment explanation
Indices: 493653--493833 Score: 254
Period size: 63 Copynumber: 2.8 Consensus size: 63
493643 TCCAAGTTCA
* * * *
493653 TTGCGATAGTTGAAGTTCGCGTTGCAATTTATTCCAAATTCATTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
* **
493716 TTGCGATAGTCGAAGTTTGCGTTGCGATTTATTATAAGTTCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
* * *
493779 TTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAGTTTGTTGCGATAGTC
1 TTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
493834 CAAAATCACA
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 62 0.60
65 41 0.40
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.38
Consensus pattern (63 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
Found at i:493836 original size:42 final size:40
Alignment explanation
Indices: 493481--493836 Score: 261
Period size: 42 Copynumber: 8.4 Consensus size: 40
493471 CGCAATGTGA
* *
493481 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTGTTCCAAA
1 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGA-TAG-TCCAAG
* *
493523 TTCGCGTTGCGATAGTCCAAGTT--TGTTGCGATAGTCGAAG
1 TT--CGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAG
* *
493563 TTCGCGTTGCGATTTGTTCCAAATTCGCGTTGCGATAGTCCAAG
1 TT--CGTTGCGA-TAG-TCCAAGTTCGCGTTGCGATAGTCCAAG
* * *
493607 TTTGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAG
1 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCCAAG
* ** * * *
493649 TTCATTGCGATAGTTGAAGTTCGCGTTGCAATTTATTCCAAA
1 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCCAAG
* * *
493691 TTCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAG
* ** *
493731 TTTGCGTTGCGATTTATTATAAGTT--CGTTGCGATAGTCGAAG
1 -TT-CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATAGTCCAAG
* *
493773 TTCGCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAG
1 TT--CGTTGCGA--TAGTCCAAGTTCGCGTTGCGA--TAGTCCAAG
*
493819 TTTGTTGCGATAGTCCAA
1 TTCGTTGCGATAGTCCAA
493837 AATCACAACG
Statistics
Matches: 264, Mismatches: 33, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
40 38 0.14
41 10 0.04
42 148 0.56
44 59 0.22
46 9 0.03
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (40 bp):
TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAG
Found at i:494736 original size:21 final size:20
Alignment explanation
Indices: 494707--494883 Score: 155
Period size: 21 Copynumber: 8.6 Consensus size: 20
494697 TTTGAAATAA
494707 ATCGCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTCGACT
*
494728 ATCTCAA-CGAACTTCGACT
1 ATCGCAAGCGAACTTCGACT
*
494747 ATCTCAA-CGAACTTCGACT
1 ATCGCAAGCGAACTTCGACT
494766 ATCGCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTCGACT
* * *
494787 ATCGCAA-TGAACTTGGAAT
1 ATCGCAAGCGAACTTCGACT
494806 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTCGACT
* * *
494829 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTCGACT
*
494848 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAA-GCGAACTTCGACT
*
494871 ATCTCAATGCGAA
1 ATCGCAA-GCGAA
494884 TATGTAAATC
Statistics
Matches: 131, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
19 55 0.42
21 57 0.44
23 19 0.15
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAAGCGAACTTCGACT
Found at i:494740 original size:19 final size:19
Alignment explanation
Indices: 494716--494839 Score: 149
Period size: 19 Copynumber: 6.2 Consensus size: 19
494706 AATCGCAACG
*
494716 CGAACTTCGACTATCTCAA
1 CGAACTTCGACTATCGCAA
*
494735 CGAACTTCGACTATCTCAA
1 CGAACTTCGACTATCGCAA
494754 CGAACTTCGACTATCGCAA
1 CGAACTTCGACTATCGCAA
494773 CGCGAACTTCGACTATCGCAA
1 --CGAACTTCGACTATCGCAA
* * *
494794 TGAACTTGGAATAAATCGCAA
1 CGAACTTCGACT--ATCGCAA
494815 CGCGAACTTCGACTATCGCAA
1 --CGAACTTCGACTATCGCAA
494836 CGAA
1 CGAA
494840 TTTGGAATAA
Statistics
Matches: 92, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
19 50 0.54
21 33 0.36
23 9 0.10
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (19 bp):
CGAACTTCGACTATCGCAA
Found at i:494799 original size:59 final size:61
Alignment explanation
Indices: 494707--494837 Score: 185
Period size: 59 Copynumber: 2.1 Consensus size: 61
494697 TTTGAAATAA
* * *
494707 ATCGCAACGCGAACTTCGACTATCTCAACGAACTTCGACT-ATCTCAA-CGAACTTCGACT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTCGAATAATCGCAACCGAACTTCGACT
* *
494766 ATCGCAACGCGAACTTCGACTATCGCAATGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTCGAAT-AATCGCAAC-CGAACTTCGACT
494829 ATCGCAACG
1 ATCGCAACG
494838 AATTTGGAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
59 36 0.57
61 6 0.10
63 21 0.33
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (61 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAACTTCGAATAATCGCAACCGAACTTCGACT
Found at i:494825 original size:42 final size:42
Alignment explanation
Indices: 494735--494873 Score: 210
Period size: 42 Copynumber: 3.4 Consensus size: 42
494725 ACTATCTCAA
* * *
494735 CGAACTTCGACTATCTCAACGAACTTCGACT--ATCGCAACG
1 CGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACG
*
494775 CGAACTTCGACTATCGCAATGAACTTGGAATAAATCGCAACG
1 CGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACG
*
494817 CGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACG
1 CGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACG
*
494859 CGAACTTGGACTATC
1 CGAACTTCGACTATC
494874 TCAATGCGAA
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 27 0.30
42 63 0.70
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (42 bp):
CGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACG
Found at i:504073 original size:57 final size:55
Alignment explanation
Indices: 503962--504073 Score: 120
Period size: 57 Copynumber: 2.0 Consensus size: 55
503952 TTGATGCACG
****
503962 AAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTTGTGCATC
1 AAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCAT-GAAAATGCATC
*
504018 AAATGCATTCGATGTTTTCATAAA-ATCCAGAGTGTGCATCGATGCAT-AAAATGCAT
1 AAATGCATTCGATG-TTTCA-AAATAGCCAGA--GTGCATCGATGCATGAAAATGCAT
504074 TATATGTTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
56 14 0.30
57 16 0.34
58 3 0.06
59 14 0.30
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (55 bp):
AAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGAAAATGCATC
Found at i:506336 original size:23 final size:22
Alignment explanation
Indices: 506306--506387 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 22
506296 GCATGGCCTT
506306 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
506328 CGTGCATCGGTGCACTTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* * *
506350 GTGTATCGATTCATATTCAAGGG
1 GTGCATCGATGCACATTCAA-GG
*
506373 GATGCATCAATGCAC
1 G-TGCATCGATGCAC
506388 TGTTAGGTGT
Statistics
Matches: 43, Mismatches: 13, Indels: 5
0.70 0.21 0.08
Matches are distributed among these distances:
21 13 0.30
22 3 0.07
23 18 0.42
24 9 0.21
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:506368 original size:44 final size:44
Alignment explanation
Indices: 506310--506406 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
506300 GGCCTTGTGC
**
506310 ATCGATGCACATTCAAGGCG-TGCATCGGTGCACT-TTCATGGTGT
1 ATCGATGCACATTCAAGGCGATGCATCAATGCACTGTT-A-GGTGT
* * *
506354 ATCGATTCATATTCAAGGGGATGCATCAATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGCGATGCATCAATGCACTGTTAGGTGT
506398 ATCGATGCA
1 ATCGATGCA
506407 TTAAGCACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 30 0.67
45 13 0.29
46 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCGATGCATCAATGCACTGTTAGGTGT
Found at i:512542 original size:21 final size:23
Alignment explanation
Indices: 512502--512543 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
512492 AATTAAATCG
512502 AAAATACTTAGAAAATCATTTGT
1 AAAATACTTAGAAAATCATTTGT
*
512525 AAAAT-CTTA-AAATTCATTT
1 AAAATACTTAGAAAATCATTT
512544 AAACTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (23 bp):
AAAATACTTAGAAAATCATTTGT
Found at i:514652 original size:55 final size:55
Alignment explanation
Indices: 514580--514683 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
514570 TTCAAAGGAA
*
514580 ATCTTCAATCAACTTCAAATTTCTTCATGCATCGGATCTCTTTCTTCATAGATCT
1 ATCTTCAATCAACTTCAAATTTCTTCATGCATCGGATCTCCTTCTTCATAGATCT
** * *
514635 ATCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTCCTTCTTCAT
1 ATCTTCAATCAACTTCAAATTTCTTCATGCATCGGATCTCCTTCTTCAT
514684 GAACCATTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.24, C:0.25, G:0.08, T:0.43
Consensus pattern (55 bp):
ATCTTCAATCAACTTCAAATTTCTTCATGCATCGGATCTCCTTCTTCATAGATCT
Found at i:518564 original size:3 final size:3
Alignment explanation
Indices: 518556--518589 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
518546 GCATGTAAAT
*
518556 TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
518590 TTATTAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:518597 original size:9 final size:9
Alignment explanation
Indices: 518554--518600 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
518544 CTGCATGTAA
518554 ATTAATAAT
1 ATTAATAAT
*
518563 AATAATAAT
1 ATTAATAAT
*
518572 AATAATAAT
1 ATTAATAAT
518581 -TTAATAAT
1 ATTAATAAT
*
518589 ATTATTAAT
1 ATTAATAAT
518598 ATT
1 ATT
518601 TTTGACCCGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 7 0.21
9 27 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATTAATAAT
Found at i:524772 original size:31 final size:30
Alignment explanation
Indices: 524737--524809 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
524727 CTTTTAGAAA
524737 TTATACTTTTAGT-CTCTAAATATTT-ACAACT
1 TTATACTTTTAGTCCTC-AAA-ATTTCA-AACT
*
524768 TTATAC-TTTAGTCCTCAAACTTTCAAACT
1 TTATACTTTTAGTCCTCAAAATTTCAAACT
524797 TTATA-TTTTAGTC
1 TTATACTTTTAGTC
524810 ACTAGTCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 19 0.50
30 10 0.26
31 9 0.24
ACGTcount: A:0.30, C:0.18, G:0.04, T:0.48
Consensus pattern (30 bp):
TTATACTTTTAGTCCTCAAAATTTCAAACT
Found at i:530080 original size:13 final size:13
Alignment explanation
Indices: 530054--530107 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 13
530044 AGGTCTTGTG
530054 ATAAT-TTA-ATA
1 ATAATATTATATA
530065 ATAATATTATATA
1 ATAATATTATATA
530078 ATAATA--ATATA
1 ATAATATTATATA
530089 ATATATTATTATATA
1 ATA-A-TATTATATA
530104 ATAA
1 ATAA
530108 ATAATAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
11 13 0.35
12 4 0.11
13 11 0.30
14 1 0.03
15 8 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATATTATATA
Found at i:530081 original size:16 final size:16
Alignment explanation
Indices: 530054--530114 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
530044 AGGTCTTGTG
*
530054 ATAATTTAATAATAAT
1 ATAATATAATAATAAT
*
530070 ATTATATAATAATAAT
1 ATAATATAATAATAAT
* *
530086 ATAATAT-ATTATTAT
1 ATAATATAATAATAAT
530101 ATAATA-AATAATAA
1 ATAATATAATAATAA
530115 AAAATGACAC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
15 17 0.46
16 20 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAATATAATAATAAT
Found at i:530523 original size:91 final size:91
Alignment explanation
Indices: 530368--530576 Score: 337
Period size: 91 Copynumber: 2.3 Consensus size: 91
530358 TAATAAACTT
* * *
530368 CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAATAATCTGTTTTACTACTCTTCCGTGAA
1 CACTACTCTTACGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
* * * *
530433 GATCATATTTAATATTAATTTGTTTC
66 GATCAGATTCAAGATTAATTTGCTTC
530459 CACTACTCTTACGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
1 CACTACTCTTACGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
*
530524 GATCAGATTCAAGATTGATTTGCTTC
66 GATCAGATTCAAGATTAATTTGCTTC
*
530550 CACTACTCTTTCGTGAAGGTTGGAAAT
1 CACTACTCTTACGTGAAGGTTGGAAAT
530577 AATAAACTTC
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 109 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (91 bp):
CACTACTCTTACGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
GATCAGATTCAAGATTAATTTGCTTC
Found at i:530594 original size:127 final size:127
Alignment explanation
Indices: 530459--531098 Score: 545
Period size: 127 Copynumber: 4.9 Consensus size: 127
530449 AATTTGTTTC
*
530459 CACTACTCTTACGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
1 CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
*
530524 GATCAGATTCAAGATTGATTTGCTTCCACTACTCTTTCGTGAAGGTTGGAAATAATAAACTT
66 GATCAGATTCAAGATTGATTTGCTTCCACTACTCTTCCGTGAAGGTTGGAAATAATAAACTT
* * *
530586 CACTACTCTTCCGTGAATGTTGGAAATGATACTGAGAAGAATCTGTTTTACTACTCTTTCGTGAA
1 CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
* * *
530651 GATCATATTCAAGATTGATTTACTTCCACTACTCTTCCGTGAAGGTTGGAAAAAATATTGAGAAG
66 GATCAGATTCAAGATTGATTTGCTTCCACTACTCTTCCGTGAAGGTTGG----AA-A-T---AAT
*
530716 AATATGTTT
122 AA-A--CTT
* * * * * * * *
530725 CACTACTCTTCCGTGAA-GAT---CA-GATTC-AAGATTG-ATTTGTTTCTACTAGTCTTCTGTG
1 CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGA-AGAATCTGTTTC-ACTACTCTTCCGTG
* * * * * * * *
530783 AAGGTTGGAAATGATACTGAGA-AGAATCTG-TTTCACTACTCTTCCGTGAAGATCAGATT-CAA
64 AA-GAT---CA-GATTC-AAGATTG-ATTTGCTTCCACTACTCTTCCGTGAAG----G-TTGGAA
* ***
530845 GATTGATTTGCTT
117 -A-TAATAAACTT
* *
530858 CCACTAGTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTATTCC----
1 -CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGA
* * *
530919 -GATCAAATTCAAGATTGATTTGCTTCCACTACTCTTTCGTGAAGGTTGGAAATAACAAACTT
65 AGATCAGATTCAAGATTGATTTGCTTCCACTACTCTTCCGTGAAGGTTGGAAATAATAAACTT
* * * *
530981 CACTACTCTTTCGTGAATGTTGGAAACGATACTGAGAAGAATCTGTTTCACTACTCTTTCGTGAA
1 CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
* * *
531046 GATCAGATTCAAGATTGATTTACTTCCACTACTGTTCCATGAAGGTTGGAAAT
66 GATCAGATTCAAGATTGATTTGCTTCCACTACTCTTCCGTGAAGGTTGGAAAT
531099 GATATTGAGA
Statistics
Matches: 399, Mismatches: 72, Indels: 84
0.72 0.13 0.15
Matches are distributed among these distances:
122 54 0.14
123 5 0.01
124 3 0.01
125 3 0.01
127 155 0.39
128 7 0.02
129 23 0.06
130 1 0.00
131 2 0.01
132 1 0.00
133 15 0.04
134 34 0.09
135 5 0.01
136 5 0.01
137 1 0.00
138 4 0.01
139 61 0.15
140 17 0.04
143 1 0.00
144 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (127 bp):
CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
GATCAGATTCAAGATTGATTTGCTTCCACTACTCTTCCGTGAAGGTTGGAAATAATAAACTT
Found at i:530715 original size:218 final size:218
Alignment explanation
Indices: 530323--530794 Score: 741
Period size: 218 Copynumber: 2.2 Consensus size: 218
530313 GGCTAAGAAC
* * **
530323 GATTTACTT-CACTACTCTTCCGCAAAGGTTGGAAATAATAAACTTCACTACTCTTCCGTGAAGG
1 GATTTGCTTCCACTACTCTTTCGTGAAGGTTGGAAATAATAAACTTCACTACTCTTCCGTGAAGG
* * *
530387 TTGGAAATGATACTGAGAATAATCTGTTTTACTACTCTTCCGTGAAGATCATATTTAATATTAAT
66 TTGGAAATGATACTGAGAAGAATCTGTTTTACTACTCTTCCGTGAAGATCATATTCAAGATTAAT
** ** *
530452 TTGTTTCCACTACTCTTACGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTT
131 TTACTTCCACTACTCTTACGTGAAGGTTGGAAAAAATACTGAGAAGAATATGTTTCACTACTCTT
530517 CCGTGAAGATCAGATTCAAGATT
196 CCGTGAAGATCAGATTCAAGATT
*
530540 GATTTGCTTCCACTACTCTTTCGTGAAGGTTGGAAATAATAAACTTCACTACTCTTCCGTGAATG
1 GATTTGCTTCCACTACTCTTTCGTGAAGGTTGGAAATAATAAACTTCACTACTCTTCCGTGAAGG
* *
530605 TTGGAAATGATACTGAGAAGAATCTGTTTTACTACTCTTTCGTGAAGATCATATTCAAGATTGAT
66 TTGGAAATGATACTGAGAAGAATCTGTTTTACTACTCTTCCGTGAAGATCATATTCAAGATTAAT
* *
530670 TTACTTCCACTACTCTTCCGTGAAGGTTGGAAAAAATATTGAGAAGAATATGTTTCACTACTCTT
131 TTACTTCCACTACTCTTACGTGAAGGTTGGAAAAAATACTGAGAAGAATATGTTTCACTACTCTT
530735 CCGTGAAGATCAGATTCAAGATT
196 CCGTGAAGATCAGATTCAAGATT
* * *
530758 GATTTGTTTCTACTAGTC-TTCTGTGAAGGTTGGAAAT
1 GATTTGCTTCCACTACTCTTTC-GTGAAGGTTGGAAAT
530795 GATACTGAGA
Statistics
Matches: 233, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
217 11 0.05
218 222 0.95
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Consensus pattern (218 bp):
GATTTGCTTCCACTACTCTTTCGTGAAGGTTGGAAATAATAAACTTCACTACTCTTCCGTGAAGG
TTGGAAATGATACTGAGAAGAATCTGTTTTACTACTCTTCCGTGAAGATCATATTCAAGATTAAT
TTACTTCCACTACTCTTACGTGAAGGTTGGAAAAAATACTGAGAAGAATATGTTTCACTACTCTT
CCGTGAAGATCAGATTCAAGATT
Found at i:530741 original size:91 final size:91
Alignment explanation
Indices: 530586--530971 Score: 584
Period size: 91 Copynumber: 4.3 Consensus size: 91
530576 TAATAAACTT
* * *
530586 CACTACTCTTCCGTGAATGTTGGAAATGATACTGAGAAGAATCTGTTTTACTACTCTTTCGTGAA
1 CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
* *
530651 GATCATATTCAAGATTGATTTACTTC
66 GATCAGATTCAAGATTGATTTGCTTC
** * *
530677 CACTACTCTTCCGTGAAGGTTGGAAAAAATATTGAGAAGAATATGTTTCACTACTCTTCCGTGAA
1 CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
*
530742 GATCAGATTCAAGATTGATTTGTTTC
66 GATCAGATTCAAGATTGATTTGCTTC
* * *
530768 TACTAGTCTTCTGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
1 CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
530833 GATCAGATTCAAGATTGATTTGCTTC
66 GATCAGATTCAAGATTGATTTGCTTC
* *
530859 CACTAGTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTATTCC-----
1 CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
*
530919 GATCAAATTCAAGATTGATTTGCTTC
66 GATCAGATTCAAGATTGATTTGCTTC
*
530945 CACTACTCTTTCGTGAAGGTTGGAAAT
1 CACTACTCTTCCGTGAAGGTTGGAAAT
530972 AACAAACTTC
Statistics
Matches: 271, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
86 50 0.18
91 221 0.82
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (91 bp):
CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
GATCAGATTCAAGATTGATTTGCTTC
Found at i:530784 original size:43 final size:42
Alignment explanation
Indices: 530629--530876 Score: 138
Period size: 43 Copynumber: 5.5 Consensus size: 42
530619 GAGAAGAATC
* * *
530629 TGTTTTACTACTCTTTCGTGAAGATCATATTCAAGATTGATT
1 TGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGATTGATT
* * * ** *** * *
530671 TACTTCCACTACTCTTCCGTGAAGGTTGGAAAAAATATTGAGAAGAATA
1 T-GTTTCACTACTCTTCCGTGAAGATCAGATTCAAGATT-----G-ATT
530720 TGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGATTGATT
1 TGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGATTGATT
* * * * * * * *
530762 TGTTTCTACTAGTCTTCTGTGAAGGTTGGAAATGATACTGAGA-AGAATC
1 TGTTTC-ACTACTCTTCCGTGAA-GAT---CA-GATTC-AAGATTG-ATT
530811 TGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGATTGATT
1 TGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGATTGATT
* *
530853 TGCTTCCACTAGTCTTCCGTGAAG
1 TG-TTTCACTACTCTTCCGTGAAG
530877 GTTGGAAATG
Statistics
Matches: 148, Mismatches: 41, Indels: 33
0.67 0.18 0.15
Matches are distributed among these distances:
42 16 0.11
43 64 0.43
44 3 0.02
47 3 0.02
48 48 0.32
49 14 0.09
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (42 bp):
TGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGATTGATT
Found at i:531121 original size:395 final size:395
Alignment explanation
Indices: 530368--531371 Score: 1549
Period size: 395 Copynumber: 2.5 Consensus size: 395
530358 TAATAAACTT
* * * *
530368 CACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAATAATCTGTTTTACTACTCTTCCGTGAA
1 CACTAGTCTTCTGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
* * * * *
530433 GATCATATTTAATATTAATTTGTTTCCACTACTCTTACGTGAAGGTTGGAAATGATACTGAGAAG
66 GATCAGATTCAAGATTAATTTGCTTCCACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAG
*
530498 AATCTGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGATTGATTTGCTTCCACTACTCTTTCG
131 AATCTGTTTCACTACTATTCC-----GATCAGATTCAAGATTGATTTGCTTCCACTACTCTTTCG
* *
530563 TGAAGGTTGGAAATAATAAACTTCACTACTCTTCCGTGAATGTTGGAAATGATACTGAGAAGAAT
191 TGAAGGTTGGAAATAACAAACTTCACTACTCTTCCGTGAATGTTGGAAACGATACTGAGAAGAAT
* * *
530628 CTGTTTTACTACTCTTTCGTGAAGATCATATTCAAGATTGATTTACTTCCACTACTCTTCCGTGA
256 CTGTTTCACTACTCTTTCGTGAAGATCAGATTCAAGATTGATTTACTTCCACTACTCTTCCATGA
*
530693 AGGTTGGAAAAAATATTGAGAAGAATATGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGATT
321 AGGTTGGAAAAAATATTGAGAAGAATATGTTTCACTACTCTTCCGTGAAGATCAAATTCAAGATT
*
530758 GATTTGTTTC
386 GATTTGATTC
*
530768 TACTAGTCTTCTGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
1 CACTAGTCTTCTGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
* *
530833 GATCAGATTCAAGATTGATTTGCTTCCACTAGTCTTCCGTGAAGGTTGGAAATGATACTGAGAAG
66 GATCAGATTCAAGATTAATTTGCTTCCACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAG
*
530898 AATCTGTTTCACTACTATTCCGATCAAATTCAAGATTGATTTGCTTCCACTACTCTTTCGTGAAG
131 AATCTGTTTCACTACTATTCCGATCAGATTCAAGATTGATTTGCTTCCACTACTCTTTCGTGAAG
*
530963 GTTGGAAATAACAAACTTCACTACTCTTTCGTGAATGTTGGAAACGATACTGAGAAGAATCTGTT
196 GTTGGAAATAACAAACTTCACTACTCTTCCGTGAATGTTGGAAACGATACTGAGAAGAATCTGTT
*
531028 TCACTACTCTTTCGTGAAGATCAGATTCAAGATTGATTTACTTCCACTACTGTTCCATGAAGGTT
261 TCACTACTCTTTCGTGAAGATCAGATTCAAGATTGATTTACTTCCACTACTCTTCCATGAAGGTT
** * * *
531093 GGAAATGATATTGAGAAGAATCTGTTTCATTACTCTTTCGTGAAGATCAAATTCAAGATTGATTT
326 GGAAAAAATATTGAGAAGAATATGTTTCACTACTCTTCCGTGAAGATCAAATTCAAGATTGATTT
531158 GATTC
391 GATTC
* * *
531163 CACTAGTCTTCTGTGAAGGTTGGAAATGATACTGAGAAGAATATGTTTCACTTCTCTTCCGTTAA
1 CACTAGTCTTCTGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
* * * *
531228 GATCAGATTCAAGATTTATTTACTTCCACTACTCTTCAGTGAAGGTTGGAAATGATACTAAGAAG
66 GATCAGATTCAAGATTAATTTGCTTCCACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAG
* * * * * *
531293 AATTTGTTTCACTACTCTTTCAAGAGGACCAGATTCAAGATTGATTTGCTTTCACTACTCTTCCG
131 AATCTGTTTCACTACT-ATTC----CGATCAGATTCAAGATTGATTTGCTTCCACTACTCTTTCG
531358 TGAAGGTTGGAAAT
191 TGAAGGTTGGAAAT
531372 GATACTGAGA
Statistics
Matches: 555, Mismatches: 44, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
395 365 0.66
396 3 0.01
400 187 0.34
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (395 bp):
CACTAGTCTTCTGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTCCGTGAA
GATCAGATTCAAGATTAATTTGCTTCCACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAG
AATCTGTTTCACTACTATTCCGATCAGATTCAAGATTGATTTGCTTCCACTACTCTTTCGTGAAG
GTTGGAAATAACAAACTTCACTACTCTTCCGTGAATGTTGGAAACGATACTGAGAAGAATCTGTT
TCACTACTCTTTCGTGAAGATCAGATTCAAGATTGATTTACTTCCACTACTCTTCCATGAAGGTT
GGAAAAAATATTGAGAAGAATATGTTTCACTACTCTTCCGTGAAGATCAAATTCAAGATTGATTT
GATTC
Found at i:531136 original size:91 final size:91
Alignment explanation
Indices: 530977--531447 Score: 658
Period size: 91 Copynumber: 5.2 Consensus size: 91
530967 GAAATAACAA
* * *
530977 ACTT-CACTACTCTTTCGTGAATGTTGGAAACGATACTGAGAAGAATCTGTTTCACTACTCTTTC
1 ACTTCCACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTTC
531041 GTGAAGATCAGATTCAAGATTGATTT
66 GTGAAGATCAGATTCAAGATTGATTT
* * * *
531067 ACTTCCACTACTGTTCCATGAAGGTTGGAAATGATATTGAGAAGAATCTGTTTCATTACTCTTTC
1 ACTTCCACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTTC
*
531132 GTGAAGATCAAATTCAAGATTGATTT
66 GTGAAGATCAGATTCAAGATTGATTT
* * * * *
531158 GA-TTCCACTAGTCTTCTGTGAAGGTTGGAAATGATACTGAGAAGAATATGTTTCACTTCTCTTC
1 -ACTTCCACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTT
* *
531222 CGTTAAGATCAGATTCAAGATTTATTT
65 CGTGAAGATCAGATTCAAGATTGATTT
* * *
531249 ACTTCCACTACTCTTCAGTGAAGGTTGGAAATGATACTAAGAAGAATTTGTTTCACTACTCTTTC
1 ACTTCCACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTTC
** * *
531314 AAGAGGACCAGATTCAAGATTGATTT
66 GTGAAGATCAGATTCAAGATTGATTT
* * * *
531340 GCTTTCACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATTTGTTTCACTACTCTTCC
1 ACTTCCACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTTC
**
531405 GTGAAGATCAGATTCAAGATCAATTT
66 GTGAAGATCAGATTCAAGATTGATTT
*
531431 GCTTCCACTACTCTTCC
1 ACTTCCACTACTCTTCC
531448 TTAGCGACCT
Statistics
Matches: 334, Mismatches: 44, Indels: 5
0.87 0.11 0.01
Matches are distributed among these distances:
90 5 0.01
91 328 0.98
92 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (91 bp):
ACTTCCACTACTCTTCCGTGAAGGTTGGAAATGATACTGAGAAGAATCTGTTTCACTACTCTTTC
GTGAAGATCAGATTCAAGATTGATTT
Found at i:541984 original size:8 final size:8
Alignment explanation
Indices: 541971--542041 Score: 56
Period size: 8 Copynumber: 8.8 Consensus size: 8
541961 TCGGGTCTTG
*
541971 TAATAATT
1 TAATAATA
541979 TAATAATA
1 TAATAATA
541987 TAATTATATGA
1 TAA-TA-AT-A
541998 TAATAATA
1 TAATAATA
542006 TAAT-ATA
1 TAATAATA
* *
542013 TTATTATA
1 TAATAATA
* *
542021 TTATTATA
1 TAATAATA
542029 TAATAA-A
1 TAATAATA
542036 TAATAA
1 TAATAA
542042 AAACGACACT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
7 13 0.24
8 30 0.55
9 4 0.07
10 4 0.07
11 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (8 bp):
TAATAATA
Found at i:546185 original size:39 final size:39
Alignment explanation
Indices: 546141--546827 Score: 973
Period size: 39 Copynumber: 17.7 Consensus size: 39
546131 AGGTTGAATA
* * * * *
546141 AGTTCTTCAGATTATGAATTTCTTCTTCCTCTTCATATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* *
546180 AGTTCTTCAAACTATAAACTCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* *
546219 AGTTCTTCAAACTATGAAATCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* * *
546258 AGTTCTTCAGATTATGAACTCATTCTT-C-CTTCATACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* *
546295 AATTCTTCAGACTATGAACTCCTTCTTCCTCTTCATACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* * *
546334 AATTCTTCAGACTATGAACTCCTTCTTCCTCTTCATATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
*
546373 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
*
546412 AGTTCTTCAGGCTATGAACTCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
*
546451 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* * *
546490 AGTTCTTCAGATTATGAACTCTTTCTTTCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* * * * *
546529 AGTTCTTCATATTATGAACTCTTTCTTCTTCTTCAGATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* * * *
546568 AGTTCTTCAAATTATGAACTCATTCTTCCTCTTTAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* * *
546607 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCATATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* * *
546646 AGTTCTTCAGACTTTGAACTCATTCTTCCTCTTCTGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* *
546685 AGTTCTTCAGACTATGAACTCATTATTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
*
546724 AGTTCTTTAGACTATGAACTCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* *
546763 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCATACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
546802 AGTTCTTCAGACTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTCCTTCT
546828 GGAAATGTTT
Statistics
Matches: 588, Mismatches: 58, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
37 32 0.05
38 2 0.00
39 554 0.94
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (39 bp):
AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
Found at i:546322 original size:20 final size:20
Alignment explanation
Indices: 546297--546361 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
546287 TTCATACGAA
546297 TTCTTCAGACTATGAACTCC
1 TTCTTCAGACTATGAACTCC
** * ***
546317 TTCTTC-CTCT-TCATACGAA
1 TTCTTCAGACTATGA-ACTCC
546336 TTCTTCAGACTATGAACTCC
1 TTCTTCAGACTATGAACTCC
546356 TTCTTC
1 TTCTTC
546362 CTCTTCATAT
Statistics
Matches: 30, Mismatches: 12, Indels: 6
0.62 0.25 0.12
Matches are distributed among these distances:
18 2 0.07
19 10 0.33
20 16 0.53
21 2 0.07
ACGTcount: A:0.22, C:0.31, G:0.08, T:0.40
Consensus pattern (20 bp):
TTCTTCAGACTATGAACTCC
Found at i:546932 original size:72 final size:73
Alignment explanation
Indices: 546833--547165 Score: 526
Period size: 73 Copynumber: 4.6 Consensus size: 73
546823 CTTCTGGAAA
* * * * *
546833 TGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAATTTTCTCCAGTGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCTAGCGAG
546898 AAACAGTT
66 AAACAGTT
*
546906 TGTTTTAAG-AAAACAATCTCAAGTGAGATAAATTGCTATTT-AAGGTGAAACTTTCTCAAGCGA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAA-GTGAAACTTTCTCTAGCGA
*
546969 GAAATAGTT
65 GAAACAGTT
* *
546978 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTAAAACTTTCTCTAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCTAGCGAG
*
547043 AAACATTT
66 AAACAGTT
*
547051 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCTAACGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCTAGCGAG
*
547116 AAACATTT
66 AAACAGTT
*
547124 TGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTGCTATTT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
547166 GAAAATATCC
Statistics
Matches: 242, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
71 1 0.00
72 64 0.26
73 175 0.72
74 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCTAGCGAG
AAACAGTT
Found at i:547065 original size:36 final size:35
Alignment explanation
Indices: 546953--547137 Score: 138
Period size: 36 Copynumber: 5.1 Consensus size: 35
546943 ATTTAAGGTG
*
546953 AAACTTTCTCAAGCGAGAAATAGTTTGTTTTAAGAA
1 AAACTTTCTCAAGCGAGAAA-ATTTTGTTTTAAGAA
** * * * * *
546989 AAACAATCTCAAGTGAGATAAATTACTATTTCAAGTA
1 AAACTTTCTCAAGCGAGA-AAATT-TTGTTTTAAGAA
*
547026 AAACTTTCTCTAGCGAGAAACATTTTGTTTTAAGAA
1 AAACTTTCTCAAGCGAGAAA-ATTTTGTTTTAAGAA
** * * * * **
547062 AAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTG
1 AAACTTTCTCAAGCGAGA-AAATT-TTGTTTTAAGAA
547099 AAACTTTCTCTAA-CGAGAAACATTTTGTTTTAAGAA
1 AAACTTTCTC-AAGCGAGAAA-ATTTTGTTTTAAGAA
547135 AAA
1 AAA
547138 TAATCTCAAG
Statistics
Matches: 109, Mismatches: 33, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
36 56 0.51
37 51 0.47
38 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (35 bp):
AAACTTTCTCAAGCGAGAAAATTTTGTTTTAAGAA
Found at i:548813 original size:118 final size:118
Alignment explanation
Indices: 548603--548890 Score: 423
Period size: 118 Copynumber: 2.4 Consensus size: 118
548593 AAAATAAACT
* * *
548603 TTCAAAATGCCTCACATGAATCATTTCTGTCTAAAATGGGCCTTCAAAATGCCCCAACATTTGCT
1 TTCAAAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCCTTCAAAATGCCCCAACATTTGCT
* *
548668 TCTTGCTAATATGAGCTTTCAAAAATGCCCAAATATTCATACTGACATGGACC
66 TCTTGCTAATATGAGCTTTCAAAAATGCCCAAATATTCATAATGACATAGACC
* * * *
548721 TTCAAAACGCCCCACATGGATCATTTCTGTTTGAAATGGGCCTTCGAGATGCCCCAACATTTGCT
1 TTCAAAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCCTTCAAAATGCCCCAACATTTGCT
* * **
548786 TCTTGCTAATATGAGCTTTCAACAATGCTCAAATATTCATAATGATGTAGACC
66 TCTTGCTAATATGAGCTTTCAAAAATGCCCAAATATTCATAATGACATAGACC
* * * *
548839 TTCAAAATACCCCACATGGGTCATTTCTGTCTGAAATGGGTCTTTAAAATGC
1 TTCAAAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCCTTCAAAATGC
548891 TTTAATATTC
Statistics
Matches: 149, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
118 149 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (118 bp):
TTCAAAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCCTTCAAAATGCCCCAACATTTGCT
TCTTGCTAATATGAGCTTTCAAAAATGCCCAAATATTCATAATGACATAGACC
Found at i:553237 original size:42 final size:43
Alignment explanation
Indices: 553190--553274 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
553180 TGGTATATCA
* *
553190 AACAAAACTTTACATATA-GGGATAGATTTCACTCCTAACTTC
1 AACAAAACTTTACATATAGGGGATAAACTTCACTCCTAACTTC
*
553232 AACAAAACTTTATATATAGGGGATAAACTTCACTCCTAACTTC
1 AACAAAACTTTACATATAGGGGATAAACTTCACTCCTAACTTC
553275 TCTAAAGCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 17 0.44
43 22 0.56
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (43 bp):
AACAAAACTTTACATATAGGGGATAAACTTCACTCCTAACTTC
Found at i:566007 original size:21 final size:19
Alignment explanation
Indices: 565979--566024 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
565969 TCATTGAATC
565979 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
565999 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
566018 ACTTAGT
1 A-TTAGT
566025 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:568072 original size:134 final size:135
Alignment explanation
Indices: 567780--568256 Score: 424
Period size: 136 Copynumber: 3.6 Consensus size: 135
567770 TATCGAGGAT
* * * *
567780 TGTTGACTCATTCCACTATTCTTCAGGGAATATTGAATCGAGGTAGACTTGTTCCACTATTACTC
1 TGTTGATTCATTCCACTTTTCTTCAGGGAAGATTGAATCGAGGTAGACTTATTCCACTATTACTC
* * *
567845 AAGGAATATCAAATCTGGAAAAAAAGAATGATATATTCCACTACTTCTTGAGGGAAAATCATATA
66 AAGGAAGATCAAATCTGG-AAAAAAGAATGACATATTCCACTACTTCTTGAGGGAAAATCAAATA
567910 TGAAAA
130 TGAAAA
* *
567916 TATTGATTCATTCCA-TTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTATTCCACTATTCCT
1 TGTTGATTCATTCCACTT-TTCTTCAGGGAAGATTGAATCGAGGTAGACTTATTCCACTATTACT
* * * **
567980 CAGGGAAGATCAAATCTGG-GAAAAGAATGACATGTTCCACTGTTTCTTGAGGGAAAATCAAATA
65 CAAGGAAGATCAAATCTGGAAAAAAGAATGACATATTCCACTACTTCTTGAGGGAAAATCAAATA
*
568044 TGGAAA
130 TGAAAA
* * *
568050 TGTTGATTCATTCCACTTTTCTTTA-GGCAGACTTG--T-----T--AC--ATT--GC---TACT
1 TGTTGATTCATTCCACTTTTCTTCAGGGAAGA-TTGAATCGAGGTAGACTTATTCCACTATTACT
* * * * *** * *
568098 CAGGGAAGATCAAATCTGAAAAAAAAAAAGGGATC-TATTTTGCTGCTTCTTGAGGGAAAATCAG
65 CAAGGAAGATCAAATCTG-GAAAAAAGAA-TGA-CATATTCCACTACTTCTTGAGGGAAAATCAA
*
568162 ATCT-AAAA
127 ATATGAAAA
* *
568170 TGTTGATTCATTCCACTGTTCTTCAGGG-AGTATTGAATCGAGGTAGACTTATTCCATTGA-TAC
1 TGTTGATTCATTCCACTTTTCTTCAGGGAAG-ATTGAATCGAGGTAGACTTATTCCACT-ATTAC
* *
568233 TCAGGGAAGATCAATTCTTGGAAA
64 TCAAGGAAGATCAAATC-TGGAAA
568257 GATAGGGGAT
Statistics
Matches: 277, Mismatches: 38, Indels: 52
0.75 0.10 0.14
Matches are distributed among these distances:
118 21 0.08
120 37 0.13
121 32 0.12
122 2 0.01
123 3 0.01
125 2 0.01
127 2 0.01
129 2 0.01
131 3 0.01
132 1 0.00
133 5 0.02
134 67 0.24
135 3 0.01
136 95 0.34
137 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (135 bp):
TGTTGATTCATTCCACTTTTCTTCAGGGAAGATTGAATCGAGGTAGACTTATTCCACTATTACTC
AAGGAAGATCAAATCTGGAAAAAAGAATGACATATTCCACTACTTCTTGAGGGAAAATCAAATAT
GAAAA
Found at i:576851 original size:131 final size:130
Alignment explanation
Indices: 576523--576885 Score: 399
Period size: 130 Copynumber: 2.8 Consensus size: 130
576513 TTAAGAGAAA
* * *
576523 AAACGATAATATCTAATTATTTCCAAACGAGAATAAATGACCTTTCATGCCTTAAAACAAACATT
1 AAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAAACATT
* * * * * * *
576588 TATTACTCTAA-TCGAAATGAAGATATATTATTATTTTGTCTTAAAATTCAATATTGATTCGAGT
66 TATTACTCCAACT-AAAATGAAGAGATATTATTATTCTGTCTTAAAAATCAATATTGATCCGAGA
576652 G
130 G
* * ** * * *
576653 AAACAATAATATCTAATGATTTCCAATCGAGAATAAATAATGTCTCATACCTTAAAGCAGACATT
1 AAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAAACATT
* *
576718 TATTGCTCCAACTAAAATGAAGAGATATCATTATTCTGTCTTAAAAATCAATATTGATCCGAGAG
66 TATTACTCCAACTAAAATGAAGAGATATTATTATTCTGTCTTAAAAATCAATATTGATCCGAGAG
* * * ****
576783 AAA-ATGGTAAT-TTTGAATTATTTCCAATCGAGAATAAATGACCTCCCATGCCTTAAAATTTTC
1 AAACA--ATAATATCT-AATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAAAC
* * * *
576846 ATTTATTACTCCAACCAAAATAAAAAGATATTACTATTCT
63 ATTTATTACTCCAACTAAAATGAAGAGATATTATTATTCT
576886 TAATATCAAT
Statistics
Matches: 191, Mismatches: 38, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
129 1 0.01
130 114 0.60
131 76 0.40
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (130 bp):
AAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAAACATT
TATTACTCCAACTAAAATGAAGAGATATTATTATTCTGTCTTAAAAATCAATATTGATCCGAGAG
Found at i:578040 original size:20 final size:20
Alignment explanation
Indices: 578017--578054 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
578007 GCCTACTTTT
*
578017 GGCCGCCTTTCTCTACCCCC
1 GGCCGCCTTGCTCTACCCCC
578037 GGCCGCCTTGCTCTACCC
1 GGCCGCCTTGCTCTACCC
578055 TCGATCGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.53, G:0.18, T:0.24
Consensus pattern (20 bp):
GGCCGCCTTGCTCTACCCCC
Found at i:578996 original size:3 final size:3
Alignment explanation
Indices: 578988--579046 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
578978 TGCACAAAGA
* ** *
578988 AAT AAT AAT AAT ATT AAT -AT AAT AAT AAT GTT AAT AAT ATT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
579036 AAT AAT AAT AA
1 AAT AAT AAT AA
579047 CGGGACGAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:581184 original size:67 final size:67
Alignment explanation
Indices: 581102--581313 Score: 268
Period size: 66 Copynumber: 3.2 Consensus size: 67
581092 AGGAAAAAAT
*
581102 AATTTATTTGAAAATTATTAACCGAACCGAATTAACCAAATTTTTCTTTAACCATTAATCGAACC
1 AATTTATTTGAAAATTATTAACCGAACCAAATTAACCAAATTTTTCTTTAACCATTAATCGAACC
581167 AA
66 AA
* * * * *** * *
581169 AATTTATTTGGAAATTATTAACTGAA-TAAAATAAATTAGTTTTTCTTTAACCGTTAATCGAACC
1 AATTTATTTGAAAATTATTAACCGAACCAAATTAACCAAATTTTTCTTTAACCATTAATCGAACC
581233 AA
66 AA
*
581235 AATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTTCTTTAA-CATTAATCGA
1 AATTTATTTGAAAATTATTAACCGAACCAAATTAACC-AA--ATTTTTCTTTAACCATTAATCGA
*
581299 ACCGA
63 ACCAA
581304 AA-TTATTTGA
1 AATTTATTTGA
581314 CCGTTAATCG
Statistics
Matches: 121, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
66 56 0.46
67 30 0.25
68 9 0.07
69 15 0.12
70 11 0.09
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (67 bp):
AATTTATTTGAAAATTATTAACCGAACCAAATTAACCAAATTTTTCTTTAACCATTAATCGAACC
AA
Found at i:581425 original size:89 final size:88
Alignment explanation
Indices: 581218--581519 Score: 365
Period size: 89 Copynumber: 3.4 Consensus size: 88
581208 TTTTTCTTTA
*
581218 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTT
1 ACCGTTAATCGAACC-AAATTTATTTGAAAATTATTAATC-AACCAAATTAACCG-A----TTTT
581283 CTTTAACATTAATCGAACCGAAATTATTTG
59 CTTTAACATTAATCGAACCGAAATTATTTG
581313 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAATCAAACCAAATTAACCGATTTT-TTTA
1 ACCGTTAATCGAACC-AAATTTATTTGAAAATTATTAATC-AACCAAATTAACCGATTTTCTTTA
*
581377 ACATTAATCGAACCGAAATTATTTC
64 ACATTAATCGAACCGAAATTATTTG
* *
581402 ACCGTTAATCGAACCAAATTTTATTTGAAAATTA-T--T-AACCGAATT-----TTTTTCTTTAA
1 ACCGTTAATCGAACCAAA-TTTATTTGAAAATTATTAATCAACCAAATTAACCGATTTTCTTTAA
*
581458 CCACTAATCGAA-CGAAAATTATTTG
65 -CATTAATCGAACCG-AAATTATTTG
581483 ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTA
1 ACCGTTAATCGAA-CCAAATTTATTTGAAAATTATTA
581520 TTCGAATAAA
Statistics
Matches: 192, Mismatches: 8, Indels: 26
0.85 0.04 0.12
Matches are distributed among these distances:
79 4 0.02
80 7 0.04
81 47 0.24
82 6 0.03
84 8 0.04
86 1 0.01
88 4 0.02
89 58 0.30
90 4 0.02
94 1 0.01
95 52 0.27
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (88 bp):
ACCGTTAATCGAACCAAATTTATTTGAAAATTATTAATCAACCAAATTAACCGATTTTCTTTAAC
ATTAATCGAACCGAAATTATTTG
Found at i:581526 original size:81 final size:79
Alignment explanation
Indices: 581369--581519 Score: 234
Period size: 81 Copynumber: 1.9 Consensus size: 79
581359 AATTAACCGA
*
581369 TTTTTTTAACATTAATCGAACCGAAATTATTTCACCGTTAATCGAACCAAATTTTATTTGAAAAT
1 TTTTTTTAACACTAATCGAACCGAAATTATTTCACCGTTAATCGAACCAAATTTTATTTGAAAAT
581434 TATTAACCGAATTT
66 TATTAACCGAATTT
*
581448 TTTTCTTTAACCACTAATCGAA-CGAAAATTATTTGACCGTTAATCGAACCCAAA-TTTATTTGA
1 TTTT-TTTAA-CACTAATCGAACCG-AAATTATTTCACCGTTAATCGAA-CCAAATTTTATTTGA
581511 AAATTATTA
62 AAATTATTA
581520 TTCGAATAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
79 4 0.06
80 7 0.11
81 50 0.76
82 5 0.08
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (79 bp):
TTTTTTTAACACTAATCGAACCGAAATTATTTCACCGTTAATCGAACCAAATTTTATTTGAAAAT
TATTAACCGAATTT
Found at i:581609 original size:66 final size:66
Alignment explanation
Indices: 581487--581629 Score: 178
Period size: 66 Copynumber: 2.1 Consensus size: 66
581477 TATTTGACCG
** ** * * *
581487 TTAATCGAACCCAAATTTATTTGAAAATTATTATTCGAATAAAATAAATTATTTTTTCTTTAACC
1 TTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACAAAATAAATGATTTTTTCTTTAACA
*
581552 C
66 A
* *
581553 TTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACCAAATCAATCGATTTTTTTCTTTAA
1 TTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACAAAATAAAT-GA-TTTTTTCTTTAA
581618 CAA
64 CAA
581621 TTAATCGAA
1 TTAATCGAA
581630 TCGAAATTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 42 0.65
67 1 0.02
68 22 0.34
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (66 bp):
TTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACAAAATAAATGATTTTTTCTTTAACA
A
Found at i:581628 original size:160 final size:160
Alignment explanation
Indices: 581156--581801 Score: 684
Period size: 160 Copynumber: 4.0 Consensus size: 160
581146 TCTTTAACCA
*
581156 TTAATCGAACCAAAATTTATTTGGAAATTATTAA-CTGAATAAAATAAATTAGTTTTTCTTTAAC
1 TTAATCGAACCAAAATTTATTTGAAAATTATTAATC-GAATAAAATAAATTA-TTTTTCTTTAAC
*
581220 CGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTTCT
64 CGTTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAA-TTTTTTTCT
581285 TTAA-CATTAATCGAACCGAAATTATTTGACCG
128 TTAACCATTAATCGAACCGAAATTATTTGACCG
* * * * ***
581317 TTAATCGAACCGAAATTTATTTGAAAATTATTAATCAAACCAAATTAACCGA-TTTT-TTTAA-C
1 TTAATCGAACCAAAATTTATTTGAAAATTATTAATCGAA-TAAAATAAATTATTTTTCTTTAACC
* * ***
581379 ATTAATCGAACCGAAATTATTTCACCGTTAATCGAACCAAATT-TTATTTGAA--AATTATTAAC
65 GTTAATCGAA-C-AAA-AATTT-A---TT--T-G-A--AAATTATTAACCGAACCAA--ATTAAC
*
581441 CGAATTTTTTTCTTTAACCACTAATCGAA-CGAAAATTATTTGACCG
115 CGAATTTTTTTCTTTAACCATTAATCGAACCG-AAATTATTTGACCG
* *
581487 TTAATCGAACCCAAATTTATTTGAAAATTATTATTCGAATAAAATAAATTATTTTTTCTTTAACC
1 TTAATCGAACCAAAATTTATTTGAAAATTATTAATCGAATAAAATAAATTA-TTTTTCTTTAACC
* * *
581552 CTTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACCAAATCAATCG-ATTTTTTTCTTT
65 GTTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTCTTT
* * **
581616 AACAATTAATCGAATCGAAATTATTTGATAG
130 AACCATTAATCGAACCGAAATTATTTGACCG
* * * *
581647 TTAATCGAATCAAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTCCTTAATCG
1 TTAATCGAACCAAAATTTATTTGAAAATTATTAATCGAATAAAATAAATTATTTTTCTTTAACCG
* ** * * * *
581712 TTATTCGAACCGAAATTTATTTGAAAATTATTAACTGAATCGAATTAACCGAA-TTTTTTCTATA
66 TTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTCTTTA
* *
581776 ACCATTAATTGAACTGAAATTTATTT
131 ACCATTAATCGAACCGAAA-TTATTT
581802 AACCAAATAA
Statistics
Matches: 402, Mismatches: 54, Indels: 59
0.78 0.10 0.11
Matches are distributed among these distances:
158 10 0.02
159 85 0.21
160 101 0.25
161 52 0.13
162 10 0.02
163 3 0.01
164 1 0.00
165 2 0.00
166 2 0.00
167 1 0.00
168 3 0.01
169 24 0.06
170 80 0.20
171 12 0.03
172 6 0.01
173 10 0.02
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (160 bp):
TTAATCGAACCAAAATTTATTTGAAAATTATTAATCGAATAAAATAAATTATTTTTCTTTAACCG
TTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTCTTTA
ACCATTAATCGAACCGAAATTATTTGACCG
Found at i:582371 original size:13 final size:13
Alignment explanation
Indices: 582338--582376 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
582328 CTAAAAAGTA
*
582338 ATTATATTAATA-
1 ATTATATAAATAT
*
582350 ATAATATAAATAT
1 ATTATATAAATAT
582363 ATTATATAAATAT
1 ATTATATAAATAT
582376 A
1 A
582377 CTAATGATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTATATAAATAT
Found at i:583510 original size:15 final size:16
Alignment explanation
Indices: 583490--583531 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
583480 ATTTTAACAT
583490 ATATATAAT-ATTTAA
1 ATATATAATAATTTAA
583505 ATATATAATAATTTAA
1 ATATATAATAATTTAA
583521 AT-T-TAATAATT
1 ATATATAATAATT
583532 CAATTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.31
15 10 0.38
16 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATAATAATTTAA
Found at i:583515 original size:18 final size:18
Alignment explanation
Indices: 583482--583516 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
583472 GATCGAAAAT
583482 TTTAACATATATATAATA
1 TTTAACATATATATAATA
583500 TTTAA-ATATATAATAAT
1 TTTAACATATAT-ATAAT
583517 TTAAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAACATATATATAATA
Found at i:584587 original size:31 final size:31
Alignment explanation
Indices: 584541--584606 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
584531 AGTTACGTCG
* *
584541 GGGACTATATTGCAAACGGAATAAATGTTGA
1 GGGACCATATAGCAAACGGAATAAATGTTGA
* * *
584572 GGGACCATATAGCAAATGGACTAAATGTTGG
1 GGGACCATATAGCAAACGGAATAAATGTTGA
584603 GGGA
1 GGGA
584607 TTATATTGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.23
Consensus pattern (31 bp):
GGGACCATATAGCAAACGGAATAAATGTTGA
Found at i:587214 original size:21 final size:21
Alignment explanation
Indices: 587184--587231 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
587174 AATTTTCAAA
*
587184 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
587205 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
587226 ACATTG
1 ACATTG
587232 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:591862 original size:21 final size:21
Alignment explanation
Indices: 591832--591879 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
591822 TAATTTTCAA
*
591832 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
591853 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
591874 ACATTG
1 ACATTG
591880 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:594973 original size:2 final size:2
Alignment explanation
Indices: 594966--595052 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
594956 CGAAGTCGTT
594966 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
595008 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
595050 TA T
1 TA T
595053 TTGATAAAAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:596661 original size:17 final size:18
Alignment explanation
Indices: 596639--596672 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
596629 TCAGCCGGTC
596639 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
596656 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
596673 CTAATAGCGG
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:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:600869 original size:14 final size:14
Alignment explanation
Indices: 600850--600893 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
600840 ATGGAGAGTA
600850 TTATTTATGGAAAG
1 TTATTTATGGAAAG
* *
600864 TTATTT-TTGAAAA
1 TTATTTATGGAAAG
600877 TATATTTATGGAAAG
1 T-TATTTATGGAAAG
600892 TT
1 TT
600894 GAAAAGTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 6 0.25
14 12 0.50
15 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (14 bp):
TTATTTATGGAAAG
Found at i:602663 original size:36 final size:37
Alignment explanation
Indices: 602603--602720 Score: 157
Period size: 36 Copynumber: 3.1 Consensus size: 37
602593 AACTCTTTTA
*
602603 CTATTAGACTCAAAAACTAATAAGCATTGAACATGTAT
1 CTATTAAACTC-AAAACTAATAAGCATTGAACATGTAT
602641 CTATTAAACTC-AAACTAATAAGCATTGAACATGTAT
1 CTATTAAACTCAAAACTAATAAGCATTGAACATGTAT
*
602677 CTATTAGACTCAAAAACTAACTAATAAGCATTGAACATGTAT
1 CTATTAAACTC---AA--AACTAATAAGCATTGAACATGTAT
602719 CT
1 CT
602721 CCTTATTTTC
Statistics
Matches: 72, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
36 35 0.49
38 10 0.14
40 1 0.01
42 26 0.36
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (37 bp):
CTATTAAACTCAAAACTAATAAGCATTGAACATGTAT
Found at i:602775 original size:14 final size:14
Alignment explanation
Indices: 602758--602785 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
602748 ATCAATCATT
602758 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
602772 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
602786 CCTTTTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTTTGTTTTTTTG
Found at i:602916 original size:2 final size:2
Alignment explanation
Indices: 602911--602947 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
602901 TATCACACAC
602911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
602948 CTCTTTTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:603539 original size:27 final size:27
Alignment explanation
Indices: 603495--603575 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
603485 CTAGTTTAAG
**
603495 AATAAATACTATGCTTTAATTATATTTT
1 AATAAATA-TATTATTTAATTATATTTT
* * * *
603523 ACT-AATATTATTATTTAATCAAATTTA
1 AATAAATA-TATTATTTAATTATATTTT
*
603550 AATAAATATATTTTTTAATT-TATTTT
1 AATAAATATATTATTTAATTATATTTT
603576 TATTTAATTT
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
26 4 0.10
27 30 0.75
28 6 0.15
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (27 bp):
AATAAATATATTATTTAATTATATTTT
Found at i:604362 original size:193 final size:190
Alignment explanation
Indices: 604069--604677 Score: 788
Period size: 194 Copynumber: 3.3 Consensus size: 190
604059 TATTGAAATT
* * ** * * * * * * *
604069 TGTATCGATACTTTTCTAATTATATCTACCAAATTATTGATACTTTAGGAATTTAAAATAATTGC
1 TGTATCAATACTTTTATAAGAATATGTATCATATTATCGATACTTTAAGAATTTAAAAGAATTAC
*
604134 AATAATAGCGCCTATAAAGTATCAATACTTTATAAACATGTATCGATACATGACAATATAACAGG
66 AATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACATGACAATATAACA-G
604199 TAAAAATATGACAAAACCAGTTTTAATATGACAAAACCGGTAAAGAGATACAAGATATGTTGAA
130 T-AAAATATGACAAAACCAG-TTTAATATGACAAAACCGGTAAAGAGATAC-AGATATGTTGAA
** *
604263 TGTATTGATACTTTTATAAGAATATGTATCATGTTATCGATACTTTAAGAATTT-AAAGAATTAC
1 TGTATCAATACTTTTATAAGAATATGTATCATATTATCGATACTTTAAGAATTTAAAAGAATTAC
604327 AATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACATGACAATATAACAG-
66 AATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACATGACAATATAACAGT
604391 -----AT------A-CA----AATATGACAAAACCGGTAAAGAGATACCAGATATGTTGAA
131 AAAATATGACAAAACCAGTTTAATATGACAAAACCGGTAAAGAGATA-CAGATATGTTGAA
* * *
604436 GGTATCAATACTTTTATAAGCATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTAC
1 TGTATCAATACTTTTATAAGAATATGTATCATATTATCGATACTTTAAGAATTTAAAAGAATTAC
604501 AATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACATGACAATATAACAAG
66 AATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACATGACAATATAAC-AG
* * *
604566 TTAAAATATGACAAAACCAGTTTCAATATGACAAAACCGGTAAAGCGCTACTGTATATGTTGAA
130 -TAAAATATGACAAAACCAGTTT-AATATGACAAAACCGGTAAAGAGATACAG-ATATGTTGAA
* *
604630 TGTATCAATACTTTAATAAGTAA-ATGCATCATATTATCGATACTTTAA
1 TGTATCAATACTTTTATAAG-AATATGTATCATATTATCGATACTTTAA
604678 AAAAATGAGA
Statistics
Matches: 364, Mismatches: 27, Indels: 48
0.83 0.06 0.11
Matches are distributed among these distances:
173 86 0.24
174 73 0.20
175 2 0.01
178 2 0.01
179 1 0.00
182 2 0.01
185 2 0.01
188 1 0.00
189 2 0.01
192 1 0.00
193 72 0.20
194 119 0.33
195 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (190 bp):
TGTATCAATACTTTTATAAGAATATGTATCATATTATCGATACTTTAAGAATTTAAAAGAATTAC
AATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACATGACAATATAACAGT
AAAATATGACAAAACCAGTTTAATATGACAAAACCGGTAAAGAGATACAGATATGTTGAA
Found at i:604581 original size:174 final size:173
Alignment explanation
Indices: 604223--604583 Score: 625
Period size: 173 Copynumber: 2.1 Consensus size: 173
604213 AACCAGTTTT
* **
604223 AATATGACAAAACCGGTAAAGAGATACAAGATATGTTGAATGTATTGATACTTTTATAAGAATAT
1 AATATGACAAAACCGGTAAAGAGATACAAGATATGTTGAAGGTATCAATACTTTTATAAGAATAT
*
604288 GTATCATGTTATCGATACTTTAAGAATTTAAAGAATTACAATAATAGCGCCTATAAAGTATCGAT
66 GTATCATATTATCGATACTTTAAGAATTTAAAGAATTACAATAATAGCGCCTATAAAGTATCGAT
604353 ACTTTATAAACATGTATCGATACATGACAATATAACAGATACA
131 ACTTTATAAACATGTATCGATACATGACAATATAACAGATACA
* *
604396 AATATGACAAAACCGGTAAAGAGATACCAGATATGTTGAAGGTATCAATACTTTTATAAGCATAT
1 AATATGACAAAACCGGTAAAGAGATACAAGATATGTTGAAGGTATCAATACTTTTATAAGAATAT
*
604461 GTATCATATTATCGATACTTTAGGAATTTAAAAGAATTACAATAATAGCGCCTATAAAGTATCGA
66 GTATCATATTATCGATACTTTAAGAATTT-AAAGAATTACAATAATAGCGCCTATAAAGTATCGA
*
604526 TACTTTATAAACATGTATCGATACATGACAATATAACAAGTTA-A
130 TACTTTATAAACATGTATCGATACATGACAATATAAC-AGATACA
604570 AATATGACAAAACC
1 AATATGACAAAACC
604584 AGTTTCAATA
Statistics
Matches: 178, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
173 87 0.49
174 87 0.49
175 4 0.02
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (173 bp):
AATATGACAAAACCGGTAAAGAGATACAAGATATGTTGAAGGTATCAATACTTTTATAAGAATAT
GTATCATATTATCGATACTTTAAGAATTTAAAGAATTACAATAATAGCGCCTATAAAGTATCGAT
ACTTTATAAACATGTATCGATACATGACAATATAACAGATACA
Found at i:605280 original size:19 final size:19
Alignment explanation
Indices: 605258--605335 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 19
605248 CAATTAGAGT
*
605258 TAGAAAATGATATTATAGG
1 TAGAAAATAATATTATAGG
* *
605277 TAGAAAATAAATATCGATA-C
1 TAGAAAAT-AATAT-TATAGG
* * *
605297 TTGCATATAATATTATAGG
1 TAGAAAATAATATTATAGG
* *
605316 TAGAAAATGATATTGTAGG
1 TAGAAAATAATATTATAGG
605335 T
1 T
605336 TGTATAAATG
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
18 3 0.07
19 28 0.65
20 9 0.21
21 3 0.07
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (19 bp):
TAGAAAATAATATTATAGG
Found at i:605339 original size:231 final size:225
Alignment explanation
Indices: 604931--605392 Score: 615
Period size: 231 Copynumber: 2.0 Consensus size: 225
604921 GTACATTGTT
* * * * *
604931 GAAACCCTAGTTTTTTTATTATTACAATAATCGAAAATAGAGGTTTTATGGATTTGGGGTTTTTT
1 GAAACCCTAGTTTTTTTAATATTACAATAATCGAAAAGAGAGGGTTTATGGATTTGGGGATTTTG
* * *
604996 AAGTAAAGAAACATTTGAGACCGATTACAGGTAGAAAGCGATATTCAAGGTGTAAAATAAATATC
66 AAGCAAAGAAACATTTGAGACCAATTACAGGTAGAAAACGATATTCAAGGTGTAAAATAAATATC
**
605061 GATACTTTTATAAAATATTATAGGTAGAAAATGATATTGTAGGTTGTATAAATGTACCAATACTT
131 GATACTTGCATAAAATATTATAGGTAGAAAATGATATTGTAGGTTGTATAAATGTACCAATACTT
605126 GTAGTAGAGAGTATTCTCATTCGTTTGAAG
196 GTAGTAGAGAGTATTCTCATTCGTTTGAAG
* *
605156 GAAACCCTAGTTTTTTTTAATATTACAGTAATCAGAAATAGAGATTAGGGTTTATGGGTTTGGGG
1 GAAACCCTAG-TTTTTTTAATATTACAATAATC-GAAA-AGAG---AGGGTTTATGGATTTGGGG
* * * *
605221 ATTTTGAAGCAAAG-AACGATTTGGGACCAATTAGAGTTAGAAAATGATATT-ATAGGTAG-AAA
60 ATTTTGAAGCAAAGAAAC-ATTTGAGACCAATTACAGGTAGAAAACGATATTCA-AGGT-GTAAA
*
605283 ATAAATATCGATACTTGCATATAATATTATAGGTAGAAAATGATATTGTAGGTTGTATAAATGTA
122 ATAAATATCGATACTTGCATAAAATATTATAGGTAGAAAATGATATTGTAGGTTGTATAAATGTA
** * * * *
605348 CTGATATTTGTAGTATAGAGTATTCTGATTCTTTTGAAG
187 CCAATACTTGTAGTAGAGAGTATTCTCATTCGTTTGAAG
605387 GAAACC
1 GAAACC
605393 GTTTTACTAT
Statistics
Matches: 205, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
225 10 0.05
226 20 0.10
227 4 0.02
228 3 0.01
230 4 0.02
231 163 0.80
232 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (225 bp):
GAAACCCTAGTTTTTTTAATATTACAATAATCGAAAAGAGAGGGTTTATGGATTTGGGGATTTTG
AAGCAAAGAAACATTTGAGACCAATTACAGGTAGAAAACGATATTCAAGGTGTAAAATAAATATC
GATACTTGCATAAAATATTATAGGTAGAAAATGATATTGTAGGTTGTATAAATGTACCAATACTT
GTAGTAGAGAGTATTCTCATTCGTTTGAAG
Found at i:610638 original size:179 final size:179
Alignment explanation
Indices: 610383--610947 Score: 650
Period size: 179 Copynumber: 3.1 Consensus size: 179
610373 AAGAGTATCA
* * * * *
610383 ATACTTTTTGTCCAGTATGCATCCCAAATGTGATGCACGCAGAAAGTTTCGATACATGTATGAAA
1 ATACTTTTTGTCCAATATGCATCCCAAACGAGATGCACACAGAAAGTATCGATACATGTATGAAA
* **
610448 AGTATCGATTCTTAAAACTTCGAAATCGATTAGTATACTGTAATAGGTAAATTTACAATGTAAGC
66 AGTATCGATTCTTAAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAAGC
* * * * *
610513 GGTAAAAATATACTGGTTTAATGAGAAAATACGTATACATAAAGTATTG
131 GATAAAAATATACCGGTTTAATGACAAAATAAGTAAACATAAAGTATTG
*
610562 ATACTTTTTGTCCAATATGCATCCCAAACGAGATGCACACAGAATGTATCGATACATGTATGAAA
1 ATACTTTTTGTCCAATATGCATCCCAAACGAGATGCACACAGAAAGTATCGATACATGTATGAAA
*
610627 AGTATCGATTCTTAAAACTTTGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAAGC
66 AGTATCGATTCTTAAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAAGC
**
610692 GATAAAAATATACCGGTTTAATGACAAAATAAGTAAACATAAAGTATCA
131 GATAAAAATATACCGGTTTAATGACAAAATAAGTAAACATAAAGTATTG
* * * *
610741 ATACATTTTGTAAGAGTATCGATATTTTTTGTCCAGTATGCATGCCAAACGAGATGTATACAGAA
1 ATAC-TTTT-T----G--TCCA-A---TATG--C---AT-C---CCAAACGAGATGCACACAGAA
* * * *
610806 AGTATCGATATATGTATGAGAAGTATCGATTCTTAAAACTTAGAAATCGA-T--TATAAAGTAAT
45 AGTATCGATACATGTATGAAAAGTATCGATTCTTAAAACTTCGAAACCGATTAGTATAAAGTAAT
* * * *
610868 AGGCAAATTTACAATGTAAGCGGTAAAAATAAACCGGTTTAATGACAAAATATGTAAACATAAAG
110 AGGTAAATTTACAATGTAAGCGATAAAAATATACCGGTTTAATGACAAAATAAGTAAACATAAAG
*
610933 TATCG
175 TATTG
610938 ATACTTTTTG
1 ATACTTTTTG
610948 AATGAGTATC
Statistics
Matches: 334, Mismatches: 31, Indels: 30
0.85 0.08 0.08
Matches are distributed among these distances:
179 166 0.50
180 4 0.01
181 1 0.00
185 1 0.00
187 3 0.01
188 1 0.00
191 4 0.01
193 1 0.00
195 1 0.00
196 6 0.02
197 81 0.24
199 1 0.00
200 64 0.19
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (179 bp):
ATACTTTTTGTCCAATATGCATCCCAAACGAGATGCACACAGAAAGTATCGATACATGTATGAAA
AGTATCGATTCTTAAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAAGC
GATAAAAATATACCGGTTTAATGACAAAATAAGTAAACATAAAGTATTG
Found at i:610927 original size:197 final size:199
Alignment explanation
Indices: 610555--610977 Score: 654
Period size: 197 Copynumber: 2.1 Consensus size: 199
610545 GTATACATAA
* * * *
610555 AGTATTGATACTTTTTGTCCAATATGCATCCCAAACGAGATGCACACAGAATGTATCGATACATG
1 AGTATCGATATTTTTTGTCCAGTATGCATCCCAAACGAGATGCACACAGAAAGTATCGATACATG
* *
610620 TATGAAAAGTATCGATTCTTAAAACTTTGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAA
66 TATGAAAAGTATCGATTCTTAAAACTTAGAAACCGATTA-TATAAAGTAATAGGCAAATTTACAA
*
610685 TGTAAGCGATAAAAATATACCGGTTTAATGACAAAATAAGTAAACATAAAGTATCAATACATTTT
130 TGTAAGCGATAAAAATAAACCGGTTTAATGACAAAATAAGTAAACATAAAGTATCAATACATTTT
610750 GTAA-G
195 G-AATG
* * * *
610755 AGTATCGATATTTTTTGTCCAGTATGCATGCCAAACGAGATGTATACAGAAAGTATCGATATATG
1 AGTATCGATATTTTTTGTCCAGTATGCATCCCAAACGAGATGCACACAGAAAGTATCGATACATG
* *
610820 TATGAGAAGTATCGATTCTTAAAACTTAGAAATCGA-T-TATAAAGTAATAGGCAAATTTACAAT
66 TATGAAAAGTATCGATTCTTAAAACTTAGAAACCGATTATATAAAGTAATAGGCAAATTTACAAT
* * * *
610883 GTAAGCGGTAAAAATAAACCGGTTTAATGACAAAATATGTAAACATAAAGTATCGATACTTTTTG
131 GTAAGCGATAAAAATAAACCGGTTTAATGACAAAATAAGTAAACATAAAGTATCAATACATTTTG
610948 AATG
196 AATG
610952 AGTATCGATATTTTTTGTCCAGTATG
1 AGTATCGATATTTTTTGTCCAGTATG
610978 AAAACATCGA
Statistics
Matches: 205, Mismatches: 17, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
196 2 0.01
197 112 0.55
199 1 0.00
200 90 0.44
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (199 bp):
AGTATCGATATTTTTTGTCCAGTATGCATCCCAAACGAGATGCACACAGAAAGTATCGATACATG
TATGAAAAGTATCGATTCTTAAAACTTAGAAACCGATTATATAAAGTAATAGGCAAATTTACAAT
GTAAGCGATAAAAATAAACCGGTTTAATGACAAAATAAGTAAACATAAAGTATCAATACATTTTG
AATG
Found at i:612167 original size:18 final size:16
Alignment explanation
Indices: 612146--612184 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
612136 CATTGACCAT
612146 GAAGACCACCAACCGATG
1 GAAGACCA-CAA-CGATG
612164 GAAGA-CACAACGATG
1 GAAGACCACAACGATG
612179 GAAGAC
1 GAAGAC
612185 GTTACATCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.50
16 3 0.15
17 2 0.10
18 5 0.25
ACGTcount: A:0.44, C:0.26, G:0.26, T:0.05
Consensus pattern (16 bp):
GAAGACCACAACGATG
Found at i:613864 original size:6 final size:6
Alignment explanation
Indices: 613846--613929 Score: 89
Period size: 6 Copynumber: 14.0 Consensus size: 6
613836 TTTAAGACTG
* * * *
613846 AATTTC -ATGTTC AATTTC AATTTT AATTTG AGTTTG AATTTC AATTTC
1 AATTTC AAT-TTC AATTTC AATTTC AATTTC AATTTC AATTTC AATTTC
* * *
613894 AATTTC AATTTG AATTTG AATTTC AATTTT AATTTC
1 AATTTC AATTTC AATTTC AATTTC AATTTC AATTTC
613930 GGCTCCACTA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
5 2 0.03
6 63 0.94
7 2 0.03
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (6 bp):
AATTTC
Found at i:613864 original size:36 final size:35
Alignment explanation
Indices: 613824--613910 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 35
613814 TTTATACAGT
613824 TTTCATTTTCAATTTAAGACTGAATTTC-ATGTTCAA
1 TTTCATTTT-AATTTAAGACTGAATTTCAAT-TTCAA
* **
613860 TTTCAATTTTAATTTGAGTTTGAATTTCAATTTCAA
1 TTTC-ATTTTAATTTAAGACTGAATTTCAATTTCAA
*
613896 TTTCAATTTGAATTT
1 TTTC-ATTTTAATTT
613911 GAATTTCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 38 0.84
37 7 0.16
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (35 bp):
TTTCATTTTAATTTAAGACTGAATTTCAATTTCAA
Found at i:613889 original size:30 final size:30
Alignment explanation
Indices: 613855--613929 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
613845 GAATTTCATG
* *
613855 TTCAATTTCAATTTTAATTTGAGTTTGAAT
1 TTCAATTTCAATTTCAATTTGAATTTGAAT
613885 TTCAATTTCAATTTCAATTTGAATTTGAAT
1 TTCAATTTCAATTTCAATTTGAATTTGAAT
*
613915 TTCAATTTTAATTTC
1 TTCAATTTCAATTTC
613930 GGCTCCACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (30 bp):
TTCAATTTCAATTTCAATTTGAATTTGAAT
Found at i:615331 original size:19 final size:19
Alignment explanation
Indices: 615307--615344 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
615297 ATTTATAAAT
615307 CGGTTAAAATTTGACAAAA
1 CGGTTAAAATTTGACAAAA
615326 CGGTTAAAATTTGACAAAA
1 CGGTTAAAATTTGACAAAA
615345 TTGATTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (19 bp):
CGGTTAAAATTTGACAAAA
Found at i:615693 original size:20 final size:20
Alignment explanation
Indices: 615668--615719 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
615658 AAAATAAAGC
615668 ATCGATACTTTTTTATGTGT
1 ATCGATACTTTTTTATGTGT
615688 ATCGATACTTTTTTATGTGT
1 ATCGATACTTTTTTATGTGT
615708 ATCGATACTTTT
1 ATCGATACTTTT
615720 CTCCAGCATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.12, G:0.13, T:0.54
Consensus pattern (20 bp):
ATCGATACTTTTTTATGTGT
Found at i:616362 original size:21 final size:21
Alignment explanation
Indices: 616336--616387 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
616326 AAACATCTAG
616336 AAAGTATCGATACCTTACACA
1 AAAGTATCGATACCTTACACA
616357 AAAGTATCGATACCTTACACA
1 AAAGTATCGATACCTTACACA
616378 AAAGTATCGA
1 AAAGTATCGA
616388 CACTTCAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (21 bp):
AAAGTATCGATACCTTACACA
Found at i:618277 original size:2 final size:2
Alignment explanation
Indices: 618270--618312 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
618260 ATGTATCGAT
618270 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
618312 A
1 A
618313 GACAGATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:618323 original size:2 final size:2
Alignment explanation
Indices: 618318--618351 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
618308 ACACAGACAG
618318 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
618352 TCTTACTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:619146 original size:226 final size:225
Alignment explanation
Indices: 618767--619237 Score: 714
Period size: 226 Copynumber: 2.1 Consensus size: 225
618757 ACAAATCAAG
* * * *
618767 TAATTAACCCGTTATGTTATCGTCGGATTTCTAAGGCTCTTTTAGCTTAAACTTTGGTAACATTT
1 TAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACATTT
* *
618832 CAGGCGTTACTTAATATGTTGATAATACCAATAACAAATTCAATAATTAACATATTTTGTTATCG
66 CAAGCGTTACCTAATATGTTGATAATACCAATAACAAATTCAATAATTAACATATTTTGTTATCG
* * * *
618897 TCGGGTTTCCAAAGGCCCATCAGTTTTAAAAAGGCGCTA-CCTATTACGTTATATAAGCGCTACC
131 TCGGATTTCCAAAGGCCCATCAGTTTTAAAAAGGCAC-AGCCTATTACATTATACAAGCGCTACC
*
618961 TAATATGTTATTATGCTTGATAATGTTTCCAA
195 TAATATGTTA-TATGCTTGATAATGCTTCCAA
* *
618993 TAATTAACCGGTTATGTTATCGTCAGATTTGTAAGGCTCTATCAGTTTAAACTTTGGTAACATTT
1 TAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACATTT
* * *
619058 TAAGCGTTACCTAATATGTTGATAATACTAATAACAAATT-AAGTAATTAACCTATTTTGTTATC
66 CAAGCGTTACCTAATATGTTGATAATACCAATAACAAATTCAA-TAATTAACATATTTTGTTATC
* *
619122 GTCGGATTTTCAAA-GCCTCATCAGTTTTAAAAAGGCACAGCCTATTACATTATACAAGCGCTGC
130 GTCGGATTTCCAAAGGCC-CATCAGTTTTAAAAAGGCACAGCCTATTACATTATACAAGCGCTAC
*
619186 CTAATATGTTATATGCTTGATAATGCTTCCAG
194 CTAATATGTTATATGCTTGATAATGCTTCCAA
619218 TAATTAACCGGTTATGTTAT
1 TAATTAACCGGTTATGTTAT
619238 TGTCGTATTT
Statistics
Matches: 223, Mismatches: 19, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
225 45 0.20
226 178 0.80
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (225 bp):
TAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACATTT
CAAGCGTTACCTAATATGTTGATAATACCAATAACAAATTCAATAATTAACATATTTTGTTATCG
TCGGATTTCCAAAGGCCCATCAGTTTTAAAAAGGCACAGCCTATTACATTATACAAGCGCTACCT
AATATGTTATATGCTTGATAATGCTTCCAA
Found at i:619268 original size:117 final size:118
Alignment explanation
Indices: 619099--619359 Score: 373
Period size: 117 Copynumber: 2.2 Consensus size: 118
619089 TAACAAATTA
** * *
619099 AGTAATTAACCTATTTTGTTATCGTCGGATTTTCAAAGCCTCATCAGTTTTAAAAAGGCAC-AGC
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTTCAAAGCCTCATCAGCTTTAAAAAGGCACTA-C
* *
619163 CTATTACATTATACAAGCGCTGCCTAATATGTTA-TATGCTTGATAATGCTTCC
65 CTATTACATTATACAAGCGCTACCTAATATGTTATTATGCTTGATAATACTTCC
* * *
619216 AGTAATTAACCGGTTATGTTATTGTCGTATTTTCAAAGCCTCATCAGCTTTAAAAAGGCGCTACC
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTTCAAAGCCTCATCAGCTTTAAAAAGGCACTACC
* * * *
619281 TATTACGTTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATATTTTC
66 TATTACATTATACAAGCGCTACCTAATATGTTATTATGCTTGATAATACTTCC
*
619334 AGTTATTAACCGGTTATGTTATCGTC
1 AGTAATTAACCGGTTATGTTATCGTC
619360 TATATTTTTT
Statistics
Matches: 127, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
117 86 0.68
118 41 0.32
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (118 bp):
AGTAATTAACCGGTTATGTTATCGTCGGATTTTCAAAGCCTCATCAGCTTTAAAAAGGCACTACC
TATTACATTATACAAGCGCTACCTAATATGTTATTATGCTTGATAATACTTCC
Found at i:619975 original size:14 final size:15
Alignment explanation
Indices: 619948--619977 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
619938 TTCGATCCGA
619948 AAATTATATTTTAAT
1 AAATTATATTTTAAT
619963 AAATTAT-TTTTAAT
1 AAATTATATTTTAAT
619977 A
1 A
619978 GAGATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATTATATTTTAAT
Found at i:620492 original size:45 final size:45
Alignment explanation
Indices: 620422--620530 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
620412 CAGAGAATGG
* * *
620422 AACCGACTACAACAACACAAGCACCGACGACCATAGCGCAGCTTA
1 AACCGACAACAACAACACAAACACCGACGACCAGAGCGCAGCTTA
* * * * *
620467 AACCGACAACAGCAACCCAAACACCGGCGACCGGAGCGCAGTTTA
1 AACCGACAACAACAACACAAACACCGACGACCAGAGCGCAGCTTA
620512 AGA-CGACAACAACAACACA
1 A-ACCGACAACAACAACACA
620531 GGTAGTTACG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 52 0.98
46 1 0.02
ACGTcount: A:0.41, C:0.35, G:0.17, T:0.06
Consensus pattern (45 bp):
AACCGACAACAACAACACAAACACCGACGACCAGAGCGCAGCTTA
Found at i:622319 original size:24 final size:24
Alignment explanation
Indices: 622291--622337 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
622281 TCAAATTAAA
622291 ATAATATTTATTTA-AGTTTGAATG
1 ATAAT-TTTATTTATAGTTTGAATG
* *
622315 ATAATTTTTTTTATATTTTGAAT
1 ATAATTTTATTTATAGTTTGAAT
622338 ATTTCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
ATAATTTTATTTATAGTTTGAATG
Found at i:626110 original size:190 final size:191
Alignment explanation
Indices: 625752--626155 Score: 503
Period size: 190 Copynumber: 2.1 Consensus size: 191
625742 ATTCATAGTC
* * * *
625752 CTTTTGACTATTGCAAATTAAAAGATAATTTTTAATTTGATTATTAGTATGATAATTACTCTTTT
1 CTTTTAACTATTGCAAATT-AAAGATAATTTTTAATTTGAATATTAGTAAGATAATTACTCTTTG
* * * * * *
625817 AATAAGTCGATTTAAAAAGGTATTTGTTATATTTTCAATTTTGAATATTAAAATATAAATATATA
65 AATAAGTCAACTTAAAAAGGTATTTGTTACATTTTCAACTGTGAATATTAAAAGATAAATATATA
** *
625882 CTTTTGTATAATTCAAATTAAAATAATATTTGTTTAAGTCTGAAT-AGTAAAAGGAG-ATTAT
130 CTTTTGTATAATTCAAATTAAAATAATACCTATTTAAGTCTGAATGA-TAAAAGGAGTATTAT
* *
625943 CTTTTAACTATTGCAAATTAAATAT-ATTATTTAATTTTAATATTAGTAAGATAATTACTCTTTG
1 CTTTTAACTATTGCAAATTAAAGATAATT-TTTAATTTGAATATTAGTAAGATAATTACTCTTTG
** * *
626007 AATATTTCAACTTAAAAAGGTATTTGTTACCTTTTCAACTGTGAATATT-AAAGATAATTATATA
65 AATAAGTCAACTTAAAAAGGTATTTGTTACATTTTCAACTGTGAATATTAAAAGATAAATATATA
* * * * *
626071 TTTTTGTATATTTTCAAATTAAAATAATACCTATTTAAGTTTGAATGATAAAATGAGTTTTAT
130 CTTTTGTATA-ATTCAAATTAAAATAATACCTATTTAAGTCTGAATGATAAAAGGAGTATTAT
*
626134 CTTTTGAA-TATTTCAAATTAAA
1 CTTTT-AACTATTGCAAATTAAA
626156 AAATATTGTT
Statistics
Matches: 183, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
189 25 0.14
190 115 0.63
191 41 0.22
192 2 0.01
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (191 bp):
CTTTTAACTATTGCAAATTAAAGATAATTTTTAATTTGAATATTAGTAAGATAATTACTCTTTGA
ATAAGTCAACTTAAAAAGGTATTTGTTACATTTTCAACTGTGAATATTAAAAGATAAATATATAC
TTTTGTATAATTCAAATTAAAATAATACCTATTTAAGTCTGAATGATAAAAGGAGTATTAT
Found at i:627704 original size:8 final size:8
Alignment explanation
Indices: 627683--627720 Score: 67
Period size: 8 Copynumber: 4.6 Consensus size: 8
627673 TTATACTTAG
627683 CTAACAACC
1 CTAACAA-C
627692 CTAACAAC
1 CTAACAAC
627700 CTAACAAC
1 CTAACAAC
627708 CTAACAAC
1 CTAACAAC
627716 CTAAC
1 CTAAC
627721 TGCACAACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 22 0.76
9 7 0.24
ACGTcount: A:0.47, C:0.39, G:0.00, T:0.13
Consensus pattern (8 bp):
CTAACAAC
Found at i:633373 original size:19 final size:19
Alignment explanation
Indices: 633349--633385 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
633339 ATTGTGTGAG
633349 GTCGAAGATTTTGGACATT
1 GTCGAAGATTTTGGACATT
*
633368 GTCGAAGTTTTTGGACAT
1 GTCGAAGATTTTGGACAT
633386 GGTCTGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (19 bp):
GTCGAAGATTTTGGACATT
Found at i:634033 original size:64 final size:65
Alignment explanation
Indices: 633957--634112 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 65
633947 ACACCCTAAT
* * * *
633957 TCGAATGCATTTTGTTTACCGATGCACA-ACCATGCATCGATGCACTCCT-GAT-TTTATTGAAA
1 TCGAATGTATTTTGTGTACCGATGCACAGACCATGCATCAATACACTCCTGGATCTTT-TT-AAA
634019 CA
64 CA
* * *
634021 TCGAATGTATTTTATGTACCGATGCATAGACCATGCATCAATACACTCCTGGCTCTTTTTAAACA
1 TCGAATGTATTTTGTGTACCGATGCACAGACCATGCATCAATACACTCCTGGATCTTTTTAAACA
* * *
634086 TTGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGTATTTTGTGTACCGATGCAC
634113 TCAAAGTGTA
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 24 0.31
65 46 0.60
66 4 0.05
67 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (65 bp):
TCGAATGTATTTTGTGTACCGATGCACAGACCATGCATCAATACACTCCTGGATCTTTTTAAACA
Found at i:639460 original size:23 final size:23
Alignment explanation
Indices: 639434--639504 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
639424 GAAAGTGTAC
* *
639434 CGATGCATTCCCTGAATATGCAT
1 CGATGCATTCCATGAATGTGCAT
* * * *
639457 CGATACA--CTATGAAGGTGCAC
1 CGATGCATTCCATGAATGTGCAT
*
639478 CGATGCATTCCTTGAATGTGCAT
1 CGATGCATTCCATGAATGTGCAT
639501 CGAT
1 CGAT
639505 ATACTATACA
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
21 15 0.43
23 20 0.57
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (23 bp):
CGATGCATTCCATGAATGTGCAT
Found at i:639480 original size:44 final size:44
Alignment explanation
Indices: 639409--639524 Score: 162
Period size: 44 Copynumber: 2.7 Consensus size: 44
639399 TTTGCTAAGC
*
639409 GCATCGATACACTATGAAAGTGTACCGATGCATTCCCTGAATAT
1 GCATCGATACACTATGAAAGTGCACCGATGCATTCCCTGAATAT
* * *
639453 GCATCGATACACTATGAAGGTGCACCGATGCATTCCTTGAATGT
1 GCATCGATACACTATGAAAGTGCACCGATGCATTCCCTGAATAT
* * *
639497 GCATCGATATACTAT-ACAGTGTACCGAT
1 GCATCGATACACTATGAAAGTGCACCGAT
639525 ACACTCGTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
43 10 0.16
44 54 0.84
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (44 bp):
GCATCGATACACTATGAAAGTGCACCGATGCATTCCCTGAATAT
Found at i:641466 original size:90 final size:89
Alignment explanation
Indices: 641310--641474 Score: 276
Period size: 90 Copynumber: 1.8 Consensus size: 89
641300 CTAACACACC
* * *
641310 CTTTTATAGCCAAGTTACCCTAATCATATTAGTGTTTTATTATTTTAAATTAATTAAATCTATAT
1 CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATAT
641375 TTAATTAATTGGAATTTAATAATT
66 TTAATTAATTGGAATTTAATAATT
*
641399 CTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATATATA
1 CTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATATA
*
641464 TTTCATTAATT
65 TTTAATTAATT
641475 AAAATTAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 32 0.46
90 38 0.54
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (89 bp):
CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATAT
TTAATTAATTGGAATTTAATAATT
Found at i:654779 original size:74 final size:75
Alignment explanation
Indices: 654456--654779 Score: 247
Period size: 74 Copynumber: 4.4 Consensus size: 75
654446 TAGGATCATC
**
654456 TAAACCCACGAAG-GGAGTCATCTAAAGAATCAAGA-TCGACTTAAACTGCGAAGGGGAGTCATC
1 TAAACCCACGAAGAGGAGTCATCTAAAGAATCAAGACT-GACTTAAACCACGAAGGGGAGTCATC
*
654519 TCAATT-GACT
65 TCACTTGGACT
* * * * * * * *
654529 AAAACACGCGAAGAGGAGTCATCTAAAGCATCACGAC-AAGCTTAGACCCACGAA-GGGAGTCTT
1 TAAACCCACGAAGAGGAGTCATCTAAAGAATCAAGACTGA-CTTA-AACCACGAAGGGGAGTCAT
*
654592 CTCA-TTTGACT
64 CTCACTTGGACT
* * * * * * * ** ** *
654603 TAGACCCACGAAGGGGAGTCATCCAGAGAATTAAGAGTGGCTTAAGTCTTGAAGAGGAGTCATCT
1 TAAACCCACGAAGAGGAGTCATCTAAAGAATCAAGACTGACTTAAACCACGAAGGGGAGTCATC-
*
654668 TAAC-TGG-CT
65 TCACTTGGACT
* * * * *
654677 T--TCCCACAAAGGGGATTCATCTAAAGAATCAAGACTGACTTAAACCACAAAGGGGAGTCATCT
1 TAAACCCACGAAGAGGAGTCATCTAAAGAATCAAGACTGACTTAAACCACGAAGGGGAGTCATCT
*
654740 TACTTGGA-T
66 CACTTGGACT
*
654749 TAAACCCACGAAGAGGAGCCATCTAAAGAAT
1 TAAACCCACGAAGAGGAGTCATCTAAAGAAT
654780 TTTTCACCCG
Statistics
Matches: 187, Mismatches: 51, Indels: 25
0.71 0.19 0.10
Matches are distributed among these distances:
71 3 0.02
72 52 0.28
73 18 0.10
74 104 0.56
75 10 0.05
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (75 bp):
TAAACCCACGAAGAGGAGTCATCTAAAGAATCAAGACTGACTTAAACCACGAAGGGGAGTCATCT
CACTTGGACT
Found at i:655560 original size:223 final size:224
Alignment explanation
Indices: 654973--655672 Score: 670
Period size: 223 Copynumber: 3.1 Consensus size: 224
654963 GAAGAAAAAC
* * * * * * * * *
654973 CAGAATCGACTACATTCTAGCTTAACTTAGTGGCAAGGAGCTAATTCCCATTTAAAGCTTTTCAG
1 CAGAATCAACTATAGTCTAGCTTAACTCAGCGACAAAGAGATAATTCCCAGTTAAAG-TTTTCAG
* * *
655038 GCCAG--GTCAACTTCACGACAAAGGATACTTGACCCAAAAAAAGCATCCAGAATTGATTGCATT
65 GCCAGATTTCAACTTCACGACGAAGGATACTTGACCC-AAAAAAGCATCCAGAACTGATTGCATT
* * * * * * * *
655101 TTGGCTTAACTAAATGATGAGGAGCAATCTTCCAGTTAAATATTTTCGAAGTTAATTTCAACTCA
129 TTGGCTTAACTCAACGGTGAGGAGCCATCTTCTAGTAAAATATTTTC-AAGTCAATTTCAACTCC
* * * *
655166 ATGATGGAGGATATTGAATTCAAAAGTCAATT
193 ATAACGGAGGATATTGAGTTCAAAAGCCAATT
* * * * *
655198 TAGAATAAACTATAATCTAGCTTAACTCAGCGGCAAAGAGATAATTCCCAGTTGAAGTTTTCAGG
1 CAGAATCAACTATAGTCTAGCTTAACTCAGCGACAAAGAGATAATTCCCAGTTAAAGTTTTCAGG
* * * * * **
655263 CCAGATTTCAACTTCACGGCGAAGGATACTTGGCCTAGAAACGCATCCAGAACCAACTT-CATTT
66 CCAGATTTCAACTTCACGACGAAGGATACTTGACCCAAAAAAGCATCCAGAACTGA-TTGCATTT
* * * * *
655327 TGGGTTAACTCAACGGTGAGGAGCCATATTCTAGTCAAATCTTTTCAA-TCAGTTTCAACTCCAT
130 TGGCTTAACTCAACGGTGAGGAGCCATCTTCTAGTAAAATATTTTCAAGTCAATTTCAACTCCAT
* *
655391 TACGGAGGATATTGGGTTCAAAAGCCAATT
195 AACGGAGGATATTGAGTTCAAAAGCCAATT
* * * * * * * * *
655421 CAAAATCAACCACAGTCTAGCTTAACTCAGCGACGATGAGTTATTTTCCAGTTAAAGTTTTCATG
1 CAGAATCAACTATAGTCTAGCTTAACTCAGCGACAAAGAGATAATTCCCAGTTAAAGTTTTCAGG
* * * * * * * * *
655486 CTAGGTTTCAACTTAACGATGAAGGATACTTGACCCGAAAATGTATCCATAACTGATTGTATTTT
66 CCAGATTTCAACTTCACGACGAAGGATACTTGACCCAAAAAAGCATCCAGAACTGATTGCATTTT
* * * * * * * *
655551 GACTTAACTCAGCGGTGAAGAGCCATCTTCTAATAAAATATTTTTTAATTCAATTTTAACTCCAC
131 GGCTTAACTCAACGGTGAGGAGCCATCTTCTAGTAAAATA-TTTTCAAGTCAATTTCAACTCCAT
* **
655616 AACAGAGGATATTGAGTTTGAAAGCCAATT
195 AACGGAGGATATTGAGTTCAAAAGCCAATT
*
655646 CAGAATCGACTATAGTCTAGCTTAACT
1 CAGAATCAACTATAGTCTAGCTTAACT
655673 TAGTAGTGAG
Statistics
Matches: 381, Mismatches: 88, Indels: 12
0.79 0.18 0.02
Matches are distributed among these distances:
222 2 0.01
223 168 0.44
224 20 0.05
225 164 0.43
226 27 0.07
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (224 bp):
CAGAATCAACTATAGTCTAGCTTAACTCAGCGACAAAGAGATAATTCCCAGTTAAAGTTTTCAGG
CCAGATTTCAACTTCACGACGAAGGATACTTGACCCAAAAAAGCATCCAGAACTGATTGCATTTT
GGCTTAACTCAACGGTGAGGAGCCATCTTCTAGTAAAATATTTTCAAGTCAATTTCAACTCCATA
ACGGAGGATATTGAGTTCAAAAGCCAATT
Found at i:659206 original size:24 final size:24
Alignment explanation
Indices: 659157--659242 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 24
659147 CATATGTCTC
*
659157 GTTCGTTCAT-TTACGTTCGTGA-AT
1 GTTCGTTTATGTT-CGTTCG-GATAT
* * *
659181 GTTCGGTTATTTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGATAT
* *
659205 GTCCGTTTATGTTCGTTTGGATAT
1 GTTCGTTTATGTTCGTTCGGATAT
659229 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
659243 ATTCATTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 1 0.02
24 48 0.94
25 2 0.04
ACGTcount: A:0.12, C:0.14, G:0.23, T:0.51
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGATAT
Found at i:660388 original size:16 final size:16
Alignment explanation
Indices: 660367--660421 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
660357 TTTATGTTCG
660367 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCGTTTA
*
660383 TGTTCGTGTACGTTTA
1 TGTTCGTGTTCGTTTA
660399 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCGTTTA
660415 TGTTCGT
1 TGTTCGT
660422 TTATTTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.07, C:0.13, G:0.25, T:0.55
Consensus pattern (16 bp):
TGTTCGTGTTCGTTTA
Found at i:664157 original size:28 final size:28
Alignment explanation
Indices: 664126--664274 Score: 90
Period size: 28 Copynumber: 5.4 Consensus size: 28
664116 TTAGACTGAA
*
664126 GCACAGAGGTGCTCAGTCCTTTTTAACT
1 GCACAGAGGTGCTCAGTCCTTGTTAACT
* * * *
664154 GCACAGAGGTG-TCAGTTCTCGGTTGA-G
1 GCACAGAGGTGCTCAGTCCT-TGTTAACT
* ** * *
664181 GCACAGAGGTGCTCAATCAATCTTAGCT
1 GCACAGAGGTGCTCAGTCCTTGTTAACT
* * * * *
664209 ACACAGAGGTG-TCAGCTCCTGGCT-GCA
1 GCACAGAGGTGCTCAG-TCCTTGTTAACT
* *
664236 GCACAGAGGTGCTCAGTCATTTTTAACT
1 GCACAGAGGTGCTCAGTCCTTGTTAACT
*
664264 GTACAGAGGTG
1 GCACAGAGGTG
664275 TAAGTTCTCA
Statistics
Matches: 85, Mismatches: 30, Indels: 12
0.67 0.24 0.09
Matches are distributed among these distances:
27 39 0.46
28 46 0.54
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (28 bp):
GCACAGAGGTGCTCAGTCCTTGTTAACT
Found at i:664190 original size:55 final size:55
Alignment explanation
Indices: 664122--664363 Score: 254
Period size: 55 Copynumber: 4.4 Consensus size: 55
664112 GATTTTAGAC
* * * * *
664122 TGAAGCACAGAGGTGCTCAGTCCTTTTTAACTGCACAGAGGTGTCAGTTCTCGGT
1 TGAAGCACAGAGGTGCTCAATCATTTTTAACTACACAGAGGTGTCAGCTCTCGAT
* * * * **
664177 TGAGGCACAGAGGTGCTCAATCAATCTTAGCTACACAGAGGTGTCAGCTC-CTGGC
1 TGAAGCACAGAGGTGCTCAATCATTTTTAACTACACAGAGGTGTCAGCTCTC-GAT
* * ** * * *
664232 TGCAGCACAGAGGTGCTCAGTCATTTTTAACTGTACAGAGGTGTAAGTTCTCAAT
1 TGAAGCACAGAGGTGCTCAATCATTTTTAACTACACAGAGGTGTCAGCTCTCGAT
* * *
664287 TGAAGCAC-GAAGGTGCTCAATCACTTTTATCTACAAAGAGGTGTCAGCTCTCGAT
1 TGAAGCACAG-AGGTGCTCAATCATTTTTAACTACACAGAGGTGTCAGCTCTCGAT
*
664342 TGAAGTACAGAGGTGCTCAATC
1 TGAAGCACAGAGGTGCTCAATC
664364 GTTCATTCAA
Statistics
Matches: 150, Mismatches: 33, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
54 2 0.01
55 146 0.97
56 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (55 bp):
TGAAGCACAGAGGTGCTCAATCATTTTTAACTACACAGAGGTGTCAGCTCTCGAT
Found at i:664352 original size:110 final size:110
Alignment explanation
Indices: 664119--664360 Score: 326
Period size: 110 Copynumber: 2.2 Consensus size: 110
664109 CCAGATTTTA
* * ** *
664119 GACTGAAGCACAGAGGTGCTCAGTCCTTTTTAACTGCACAGAGGTGTCAGTTCTCGGTTGAGGCA
1 GACTGAAGCACAGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTAAGTTCTCAATTGAAGCA
*
664184 CAGAGGTGCTCAATCAATCTTAGCTACACAGAGGTGTCAGCTCCT
66 CAGAGGTGCTCAATCAATCTTAGCTACAAAGAGGTGTCAGCTCCT
* * *
664229 GGCTGCAGCACAGAGGTGCTCAGTCATTTTTAACTGTACAGAGGTGTAAGTTCTCAATTGAAGCA
1 GACTGAAGCACAGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTAAGTTCTCAATTGAAGCA
* * *
664294 C-GAAGGTGCTCAATCACTTTTATCTACAAAGAGGTGTCAGCT-CT
66 CAG-AGGTGCTCAATCAATCTTAGCTACAAAGAGGTGTCAGCTCCT
* *
664338 CGATTGAAGTACAGAGGTGCTCA
1 -GACTGAAGCACAGAGGTGCTCA
664361 ATCGTTCATT
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
109 3 0.03
110 111 0.97
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (110 bp):
GACTGAAGCACAGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTAAGTTCTCAATTGAAGCA
CAGAGGTGCTCAATCAATCTTAGCTACAAAGAGGTGTCAGCTCCT
Found at i:664615 original size:81 final size:81
Alignment explanation
Indices: 664480--664635 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 81
664470 CGAGTTACAA
* * *
664480 AGAATGGTTCGCACATGAAATGGTGGAGCAACAAGCTCTCATAGAGGTGAAGAGCAAGAAGCTAC
1 AGAATGGTTCGCACACGAAATGGTAGAGCAACAAGCTCTCACAGAGGTGAAGAGCAAGAAGCTAC
*
664545 TGAGCCGATTATACTG
66 CGAGCCGATTATACTG
* * * * *
664561 AGAATGTTTCGCACACGAAATGGTAGATCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTAC
1 AGAATGGTTCGCACACGAAATGGTAGAGCAACAAGCTCTCACAGAGGTGAAGAGCAAGAAGCTAC
664626 CGAGCCGATT
66 CGAGCCGATT
664636 GTACAAGATA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.19
Consensus pattern (81 bp):
AGAATGGTTCGCACACGAAATGGTAGAGCAACAAGCTCTCACAGAGGTGAAGAGCAAGAAGCTAC
CGAGCCGATTATACTG
Found at i:676000 original size:45 final size:45
Alignment explanation
Indices: 675936--676025 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
675926 TACATGGTCA
*
675936 AAGGATACCAAGTAAACCAGTCTAACGTGCCACATTAACCTCTTG
1 AAGGATACCAAGTAAACCAGTCTAACGTGCCACATGAACCTCTTG
675981 AAGGATACCAAGTAAACCAGTCTAACGTGCCACATGAACCTCTTG
1 AAGGATACCAAGTAAACCAGTCTAACGTGCCACATGAACCTCTTG
676026 TTATTGAGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.21
Consensus pattern (45 bp):
AAGGATACCAAGTAAACCAGTCTAACGTGCCACATGAACCTCTTG
Found at i:676742 original size:12 final size:13
Alignment explanation
Indices: 676712--676744 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
676702 TGCTTCTATC
676712 GATTATAATTTTTT
1 GATT-TAATTTTTT
676726 GATTTAATTTTTT
1 GATTTAATTTTTT
676739 -ATTTAA
1 GATTTAA
676745 CCAATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 9 0.47
14 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (13 bp):
GATTTAATTTTTT
Found at i:676943 original size:3 final size:3
Alignment explanation
Indices: 676935--677057 Score: 246
Period size: 3 Copynumber: 41.0 Consensus size: 3
676925 CTCCATAGAC
676935 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
676983 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
677031 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
677058 CAATCTCTCG
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 120 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:680223 original size:48 final size:48
Alignment explanation
Indices: 680167--680280 Score: 138
Period size: 48 Copynumber: 2.4 Consensus size: 48
680157 ATAACCTGAG
*
680167 TTAACCTCCGAGGAGGAACTCAACAAAAATAAAAAACATGATGGGGAA
1 TTAACCTCCGAGGAGAAACTCAACAAAAATAAAAAACATGATGGGGAA
* * * * * *
680215 TTAACCTCCGAGGAGAAACTCAATAGAATTCAGAAACATGATGGGGATG
1 TTAACCTCCGAGGAGAAACTCAACAAAAATAAAAAACATGATGGGGA-A
* *
680264 TTACCCTCCGAAGAGAA
1 TTAACCTCCGAGGAGAA
680281 TCCCTAGTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
48 41 0.73
49 15 0.27
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (48 bp):
TTAACCTCCGAGGAGAAACTCAACAAAAATAAAAAACATGATGGGGAA
Found at i:680523 original size:13 final size:13
Alignment explanation
Indices: 680505--680537 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
680495 GAAATTACTT
680505 AACATATGTGTCA
1 AACATATGTGTCA
680518 AACATATGTGTCA
1 AACATATGTGTCA
680531 AACATAT
1 AACATAT
680538 AGCATCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (13 bp):
AACATATGTGTCA
Found at i:681610 original size:21 final size:21
Alignment explanation
Indices: 681586--681625 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
681576 TTTAAATTCA
*
681586 GATTCAGATATTT-ATATATCC
1 GATTCA-AAATTTCATATATCC
681607 GATTCAAAATTTCATATAT
1 GATTCAAAATTTCATATAT
681626 ATGATGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (21 bp):
GATTCAAAATTTCATATATCC
Found at i:698755 original size:15 final size:15
Alignment explanation
Indices: 698730--698768 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
698720 GGCTAGTGAC
*
698730 TAAAA-TATAAGTTT
1 TAAAAGTATAAGTGT
698744 TAAAAGTATAAGTGT
1 TAAAAGTATAAGTGT
698759 T-AAAGTATAA
1 TAAAAGTATAA
698769 ACTTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (15 bp):
TAAAAGTATAAGTGT
Found at i:698763 original size:14 final size:14
Alignment explanation
Indices: 698730--698768 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
698720 GGCTAGTGAC
* *
698730 TAAAATATAAGTTT
1 TAAAGTATAAGTGT
698744 TAAAAGTATAAGTGT
1 T-AAAGTATAAGTGT
698759 TAAAGTATAA
1 TAAAGTATAA
698769 ACTTTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (14 bp):
TAAAGTATAAGTGT
Found at i:702277 original size:37 final size:37
Alignment explanation
Indices: 702236--702340 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
702226 TATCTTGTGG
* * *
702236 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
702273 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
702310 ATCCTATTTTTATGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
702341 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:705407 original size:2 final size:2
Alignment explanation
Indices: 705400--705453 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
705390 TGTACAAAAT
705400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
705442 TA TA TA TA TA TA
1 TA TA TA TA TA TA
705454 CAATGATAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:706004 original size:28 final size:27
Alignment explanation
Indices: 705942--706005 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
705932 AGGAACGAAT
* *
705942 CTAAACTTATAAAATTTTAGAGGACAA
1 CTAAATTTATAAAATTTTAGAGGAAAA
*
705969 CTTGAATTTATAAAATTTTAAGAGGCAAAA
1 C-TAAATTTATAAAATTTT-AGAGG-AAAA
705999 C-AAATTT
1 CTAAATTT
706006 TCAGTAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
27 1 0.03
28 20 0.67
29 5 0.17
30 4 0.13
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (27 bp):
CTAAATTTATAAAATTTTAGAGGAAAA
Found at i:706277 original size:55 final size:55
Alignment explanation
Indices: 706121--706286 Score: 287
Period size: 55 Copynumber: 3.0 Consensus size: 55
706111 TCATACTTTG
*
706121 ATTTTAAAACCTTCTTATCTTTTAAATTTGGCTTATATGATAAATACGTATTTAA
1 ATTTTAAAACCTTCTTATCTTTTAAATTTGGCTTATATGATAAATATGTATTTAA
*
706176 ATTTTAAAACCTTCTTATCTTTTAAATTTGGCTTATACGATAAATATGTATTTAA
1 ATTTTAAAACCTTCTTATCTTTTAAATTTGGCTTATATGATAAATATGTATTTAA
* * *
706231 ATTTTAAAACCTTCTTATCTTTTAAATTTGGCTTGTATGATAAATATCTATATAA
1 ATTTTAAAACCTTCTTATCTTTTAAATTTGGCTTATATGATAAATATGTATTTAA
706286 A
1 A
706287 GTATATTATT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 105 1.00
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (55 bp):
ATTTTAAAACCTTCTTATCTTTTAAATTTGGCTTATATGATAAATATGTATTTAA
Found at i:709332 original size:14 final size:14
Alignment explanation
Indices: 709313--709397 Score: 54
Period size: 14 Copynumber: 5.9 Consensus size: 14
709303 TATTAACAAA
709313 AAATAAAATAAAAT
1 AAATAAAATAAAAT
709327 AAAT-AAATAATAAT
1 AAATAAAATAA-AAT
709341 ATTAATAAATATAAAAT
1 A--AATAAA-ATAAAAT
709358 -AAT-AAAT--AAT
1 AAATAAAATAAAAT
*
709368 AAATAATAATTTAAAT
1 AAATAA-AA-TAAAAT
*
709384 AATATATAATAAAA
1 AA-ATAAAATAAAA
709398 ATTATATAAC
Statistics
Matches: 57, Mismatches: 2, Indels: 23
0.70 0.02 0.28
Matches are distributed among these distances:
10 3 0.05
11 3 0.05
12 3 0.05
13 10 0.18
14 12 0.21
15 4 0.07
16 10 0.18
17 8 0.14
18 4 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:709338 original size:7 final size:7
Alignment explanation
Indices: 709323--709396 Score: 73
Period size: 7 Copynumber: 10.4 Consensus size: 7
709313 AAATAAAATA
709323 AAATAAAT
1 AAAT-AAT
709331 AAATAAT
1 AAATAAT
709338 AATATTAAT
1 AA-A-TAAT
709347 AAAT-AT
1 AAATAAT
709353 AAAATAAT
1 -AAATAAT
709361 AAATAAT
1 AAATAAT
709368 AAATAAT
1 AAATAAT
*
709375 -AAT-TT
1 AAATAAT
709380 AAATAAT
1 AAATAAT
*
709387 ATATAAT
1 AAATAAT
709394 AAA
1 AAA
709397 AATTATATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
5 1 0.02
6 8 0.14
7 33 0.59
8 8 0.14
9 6 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAATAAT
Found at i:709531 original size:45 final size:43
Alignment explanation
Indices: 709431--709542 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 43
709421 TCAAAAATAA
709431 TATGTTTTCAAAA--ACTATATATAT-TATATAAGTTTTCAAAAT
1 TATGTTTTCAAAACTA-TATATATATATATATAAGTTTTC-AAAT
*
709473 TA-GTTTTATAAAACTATATATATATATATATAAGTGTTTTC-AAT
1 TATGTTTT-CAAAACTATATATATATATATATAA--GTTTTCAAAT
709517 GTATGTTTTCAAAACTATAT-TATATA
1 -TATGTTTTCAAAACTATATATATATA
709543 CGTTTTCAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
41 5 0.08
42 6 0.10
43 9 0.15
44 17 0.28
45 12 0.20
46 11 0.18
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.46
Consensus pattern (43 bp):
TATGTTTTCAAAACTATATATATATATATATAAGTTTTCAAAT
Found at i:709602 original size:14 final size:14
Alignment explanation
Indices: 709583--709643 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
709573 TATATTATAC
709583 GTTTTCAAAAATGT
1 GTTTTCAAAAATGT
709597 GTTTTC-AAAAT-T
1 GTTTTCAAAAATGT
* * * *
709609 -ATAT--AATATAT
1 GTTTTCAAAAATGT
709620 GTTTTCAAAAATGT
1 GTTTTCAAAAATGT
709634 GTTTTCAAAA
1 GTTTTCAAAA
709644 CCATATTATA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
10 4 0.11
11 3 0.08
12 3 0.08
13 5 0.14
14 21 0.58
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (14 bp):
GTTTTCAAAAATGT
Found at i:709624 original size:37 final size:37
Alignment explanation
Indices: 709520--709765 Score: 200
Period size: 37 Copynumber: 6.6 Consensus size: 37
709510 TTTCAATGTA
* * *
709520 TGTTTTCAAAACTATATTATATACGTTTTCAAAAACCG
1 TGTTTTCAAAACTATATAATATATGTTTTCAAAAA-TG
* * *
709558 T-TTTTTAAAATTATATATATTATACGTTTTCAAAAATG
1 TGTTTTCAAAACTATATA-A-TATATGTTTTCAAAAATG
*
709596 TGTTTTCAAAATTATATAATATATGTTTTCAAAAATG
1 TGTTTTCAAAACTATATAATATATGTTTTCAAAAATG
* * *
709633 TGTTTTCAAAACCATAT--TATATATTTTCAAAAACCAG
1 TGTTTTCAAAACTATATAATATATGTTTTCAAAAA--TG
* * *
709670 T-TTTTAAAAACTATATATTATATGCTTTCAAAAAT-
1 TGTTTTCAAAACTATATAATATATGTTTTCAAAAATG
* * *
709705 TATTTTCTAAAAACTATATATTATATGGTTTT-AAAAA-A
1 TGTTTTC--AAAACTATATAATATAT-GTTTTCAAAAATG
* *
709743 TATTTTCTAAAACTATATTATAT
1 TGTTTTC-AAAACTATATAATAT
709766 TATTATTATA
Statistics
Matches: 176, Mismatches: 20, Indels: 25
0.80 0.09 0.11
Matches are distributed among these distances:
35 16 0.09
36 17 0.10
37 60 0.34
38 48 0.27
39 35 0.20
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (37 bp):
TGTTTTCAAAACTATATAATATATGTTTTCAAAAATG
Found at i:709699 original size:38 final size:36
Alignment explanation
Indices: 709522--709760 Score: 168
Period size: 38 Copynumber: 6.4 Consensus size: 36
709512 TCAATGTATG
* * *
709522 TTTTCAAAACTATAT-TATATACGTTTTCAAAAACCGTT
1 TTTTAAAAACTATATAT-TATATGTTTTCAAAAA-AG-T
* *
709560 TTTTAAAATTA-TATATATTATACGTTTTCAAAAATGT
1 TTTTAAAA--ACTATATATTATATGTTTTCAAAAAAGT
* * * *
709597 GTTTTCAAAATTATATAATATATGTTTTCAAAAATGT
1 -TTTTAAAAACTATATATTATATGTTTTCAAAAAAGT
* * *
709634 GTTTTCAAAAC--CATATTATATATTTTCAAAAACCAGT
1 -TTTTAAAAACTATATATTATATGTTTTCAAAAA--AGT
*
709671 TTTTAAAAACTATATATTATATGCTTTCAAAAATTA-T
1 TTTTAAAAACTATATATTATATGTTTTCAAAAA--AGT
709708 TTTCTAAAAACTATATATTATATGGTTTT-AAAAAA-T
1 TTT-TAAAAACTATATATTATAT-GTTTTCAAAAAAGT
*
709744 ATTTTCTAAAACTATAT
1 -TTTT-AAAAACTATAT
709761 TATATTATTA
Statistics
Matches: 170, Mismatches: 18, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
35 18 0.11
36 13 0.08
37 54 0.32
38 58 0.34
39 25 0.15
40 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATGTTTTCAAAAAAGT
Found at i:709723 original size:111 final size:110
Alignment explanation
Indices: 709519--709765 Score: 306
Period size: 111 Copynumber: 2.2 Consensus size: 110
709509 TTTTCAATGT
709519 ATGTTTTCAAAACTATATTATATACGTTTTCAAAAACCGTTTTTTAAAATTATATATATTATACG
1 ATGTTTTCAAAACTATATTATATAC-TTTTCAAAAACCGTTTTTTAAAA-TATATATATTATACG
* * *
709584 TTTTCAAAAATGTGTTTTCAAAATTATATAATATAT-GTTTTCAAAAA
64 CTTTCAAAAATGTATTTTCAAAACTATATAATATATGGTTTT-AAAAA
* * *
709631 TGTGTTTTCAAAACCATATTATATA-TTTTCAAAAACCAG-TTTTTAAAA-ACTATATATTATAT
1 -ATGTTTTCAAAACTATATTATATACTTTTCAAAAACC-GTTTTTTAAAATA-TATATATTATAC
*
709693 GCTTTCAAAAAT-TATTTTCTAAAAACTATATATTATATGGTTTTAAAAA
63 GCTTTCAAAAATGTATTTTC--AAAACTATATAATATATGGTTTTAAAAA
*
709742 ATATTTTCTAAAACTATATTATAT
1 ATGTTTTC-AAAACTATATTATAT
709766 TATTATTATA
Statistics
Matches: 118, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
109 7 0.06
110 28 0.24
111 55 0.47
112 6 0.05
113 22 0.19
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (110 bp):
ATGTTTTCAAAACTATATTATATACTTTTCAAAAACCGTTTTTTAAAATATATATATTATACGCT
TTCAAAAATGTATTTTCAAAACTATATAATATATGGTTTTAAAAA
Found at i:718047 original size:24 final size:24
Alignment explanation
Indices: 717974--718040 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
717964 GTTAGTTACA
*
717974 GAAGCTTGTGCTTTTGCAGCCGAT
1 GAAGCTTGTGCTTTTGCAGCAGAT
* *
717998 AAAGCTTGTACTTTTGCAGCAGAT
1 GAAGCTTGTGCTTTTGCAGCAGAT
718022 GAAG-TGTGTGCTTTTGCAG
1 GAAGCT-TGTGCTTTTGCAG
718041 TGGATGAGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.34
Consensus pattern (24 bp):
GAAGCTTGTGCTTTTGCAGCAGAT
Found at i:721843 original size:11 final size:11
Alignment explanation
Indices: 721827--721852 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
721817 CCCTTTCCCT
721827 TCTCTCTAAAC
1 TCTCTCTAAAC
721838 TCTCTCTAAAC
1 TCTCTCTAAAC
721849 TCTC
1 TCTC
721853 CCAACAGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (11 bp):
TCTCTCTAAAC
Found at i:722874 original size:18 final size:20
Alignment explanation
Indices: 722839--722878 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
722829 TTCAACAAAT
722839 AAATAATACTAATAAATATAA
1 AAATAATACTAATAAATA-AA
722860 AAATAATA-T-AT-AATAAA
1 AAATAATACTAATAAATAAA
722877 AA
1 AA
722879 CTATATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 2 0.11
20 1 0.05
21 8 0.42
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATAATACTAATAAATAAA
Found at i:722955 original size:2 final size:2
Alignment explanation
Indices: 722948--722974 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
722938 TTTCAAAAAC
722948 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
722975 GTTTTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:722998 original size:51 final size:50
Alignment explanation
Indices: 722909--723011 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 50
722899 TTTCAAAAAC
*
722909 TATATATTATATATTTTTTCAAAAATCGTTTTCAAAAACTATATATATATA
1 TATATATTATATATGTTTTCAAAAATCGTTTTCAAAAACTATATATAT-TA
*
722960 TATATATATATATATGTTTTCAAAATAT-GTTTT-TAAAACTATATATATTA
1 TATATAT-TATATATGTTTTCAAAA-ATCGTTTTCAAAAACTATATATATTA
723010 TA
1 TA
723012 GGTTTTCAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
50 4 0.08
51 21 0.44
52 21 0.44
53 2 0.04
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (50 bp):
TATATATTATATATGTTTTCAAAAATCGTTTTCAAAAACTATATATATTA
Found at i:723003 original size:39 final size:38
Alignment explanation
Indices: 722961--723086 Score: 136
Period size: 38 Copynumber: 3.3 Consensus size: 38
722951 ATATATATAT
722961 ATATATATATATATGTTTTCAAAATATGTTTTTAAAAC
1 ATATATATATATATGTTTTCAAAATATGTTTTTAAAAC
*
722999 -TATATATATTATAGGTTTTCAAAA-ATGTGTTTTCAAAAC
1 ATATATATA-TATATGTTTTCAAAATATGT-TTTT-AAAAC
* * *
723038 -TATATA-ATATATGTTATCAAAATCGTGTTTTCAAAAAC
1 ATATATATATATATGTTTTCAAAAT-ATGTTTT-TAAAAC
723076 ATAT-TATATAT
1 ATATATATATAT
723087 TCTAAAATCT
Statistics
Matches: 75, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
37 25 0.33
38 29 0.39
39 21 0.28
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (38 bp):
ATATATATATATATGTTTTCAAAATATGTTTTTAAAAC
Found at i:723085 original size:37 final size:37
Alignment explanation
Indices: 722962--723086 Score: 157
Period size: 37 Copynumber: 3.4 Consensus size: 37
722952 TATATATATA
* *
722962 TATATATATATATGTTTTCAAAATATGTTTTTAAAAC
1 TATATATATATATGTTTTCAAAATGTGTTTTCAAAAC
*
722999 TATATATATTATAGGTTTTCAAAAATGTGTTTTCAAAAC
1 TATATATA-TATATGTTTTC-AAAATGTGTTTTCAAAAC
*
723038 TATATA-ATATATGTTATCAAAATCGTGTTTTCAAAAAC
1 TATATATATATATGTTTTCAAAAT-GTGTTTTC-AAAAC
723076 -ATAT-TATATAT
1 TATATATATATAT
723087 TCTAAAATCT
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
36 5 0.06
37 35 0.45
38 16 0.21
39 22 0.28
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (37 bp):
TATATATATATATGTTTTCAAAATGTGTTTTCAAAAC
Found at i:731195 original size:31 final size:31
Alignment explanation
Indices: 731142--731201 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
731132 CAATGCCATA
* *
731142 TTTACCATTTAATACACTAACTTTCTCAATG
1 TTTACCATTTAACACACAAACTTTCTCAATG
* * *
731173 TTTACCATTTAGCACTCAAACTTTGTCAA
1 TTTACCATTTAACACACAAACTTTCTCAA
731202 CTTTCCAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (31 bp):
TTTACCATTTAACACACAAACTTTCTCAATG
Found at i:732498 original size:21 final size:21
Alignment explanation
Indices: 732472--732554 Score: 139
Period size: 21 Copynumber: 3.9 Consensus size: 21
732462 CTAGGACAGG
732472 GAGTATCGGTACTCCTTTAAT
1 GAGTATCGGTACTCCTTTAAT
*
732493 GAGTATCGATACTCCTTTAAT
1 GAGTATCGGTACTCCTTTAAT
*
732514 GAGTATAGGTACTCCTTTAAT
1 GAGTATCGGTACTCCTTTAAT
732535 GAGTATCGGTACTTCCTTTA
1 GAGTATCGGTAC-TCCTTTA
732555 TAATTTTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 50 0.88
22 7 0.12
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (21 bp):
GAGTATCGGTACTCCTTTAAT
Done.