Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 22 of 190
Found at i:3450755 original size:21 final size:22
Alignment explanation
Indices: 3450713--3450764 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
3450703 ACCCGAATTA
3450713 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
3450735 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
3450756 AT-AAATATT
1 ATAAAATATT
3450765 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:3450772 original size:30 final size:30
Alignment explanation
Indices: 3450737--3450797 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3450727 TTTAAAATAT
* * * *
3450737 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATAATTA
*
3450767 AAAATATCATTATATAAATATATATAATTA
1 AAAATATCATTATATAAATATAAATAATTA
3450797 A
1 A
3450798 TTAATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATAATTA
Found at i:3451147 original size:11 final size:10
Alignment explanation
Indices: 3451128--3451159 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
3451118 ATATGTGAGA
3451128 TTTTTAAATT
1 TTTTTAAATT
3451138 TTTTTGAAATT
1 TTTTT-AAATT
3451149 TTTTTAAATT
1 TTTTTAAATT
3451159 T
1 T
3451160 ATAAATCGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:3452451 original size:3 final size:3
Alignment explanation
Indices: 3452438--3452480 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
3452428 AGAGGGACCG
3452438 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3452481 AAAATATTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3453705 original size:44 final size:41
Alignment explanation
Indices: 3453634--3453719 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 41
3453624 TTTTTTTCTT
*
3453634 TTTTTTTAAATAATAAATAAATAAATAATTTTTATATTAAAAA
1 TTTTTTTAAATAATAAATAAATAAATAATATTT-T-TTAAAAA
* ** *
3453677 TTTTTTTAAATACCTAAATATTTTAATAATATTTTTTAAAAA
1 TTTTTTTAAATA-ATAAATAAATAAATAATATTTTTTAAAAA
3453719 T
1 T
3453720 ATACTTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 8 0.22
43 13 0.35
44 16 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (41 bp):
TTTTTTTAAATAATAAATAAATAAATAATATTTTTTAAAAA
Found at i:3453753 original size:25 final size:29
Alignment explanation
Indices: 3453698--3453750 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
3453688 ACCTAAATAT
*
3453698 TTTAATAATATTTTTTAAAAATATACTTA
1 TTTAATAATATTTTTAAAAAATATACTTA
3453727 TTTAA-AA-ATTTTTAAAAAAT-TACT
1 TTTAATAATATTTTTAAAAAATATACT
3453751 ATTCGGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 12 0.52
28 2 0.09
29 5 0.22
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTAATAATATTTTTAAAAAATATACTTA
Found at i:3453891 original size:16 final size:17
Alignment explanation
Indices: 3453870--3453903 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3453860 TAAACATTAT
*
3453870 TATTTATT-TCAAAATA
1 TATTTATTATAAAAATA
3453886 TATTTATTATAAAAATA
1 TATTTATTATAAAAATA
3453903 T
1 T
3453904 TATTGACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTATTATAAAAATA
Found at i:3453941 original size:10 final size:10
Alignment explanation
Indices: 3453917--3453947 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
3453907 TGACATAAAT
3453917 AATATAAATAA
1 AATATAAA-AA
3453928 AATATAAAAA
1 AATATAAAAA
3453938 AATATAAAAA
1 AATATAAAAA
3453948 TTGTGCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.60
11 8 0.40
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AATATAAAAA
Found at i:3455262 original size:82 final size:82
Alignment explanation
Indices: 3455161--3455323 Score: 299
Period size: 82 Copynumber: 2.0 Consensus size: 82
3455151 ATTTATTATA
*
3455161 ATTTAGTTGATTTTCATCCTTTGTTGAATTAAAAATCTTTTGAGTACATTTCTCCGAAAGGGAAA
1 ATTTACTTGATTTTCATCCTTTGTTGAATTAAAAATCTTTTGAGTACATTTCTCCGAAAGGGAAA
3455226 GTCTTGGATTCAAATTC
66 GTCTTGGATTCAAATTC
* *
3455243 ATTTACTTGATTTTCATCCTTTGTTGAATTAAAAGTCTTTTGAGTACATTTCTCTGAAAGGGAAA
1 ATTTACTTGATTTTCATCCTTTGTTGAATTAAAAATCTTTTGAGTACATTTCTCCGAAAGGGAAA
3455308 GTCTTGGATTCAAATT
66 GTCTTGGATTCAAATT
3455324 AATTGATGGG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (82 bp):
ATTTACTTGATTTTCATCCTTTGTTGAATTAAAAATCTTTTGAGTACATTTCTCCGAAAGGGAAA
GTCTTGGATTCAAATTC
Found at i:3464587 original size:2 final size:2
Alignment explanation
Indices: 3464580--3464619 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3464570 TCCTTTCTTT
3464580 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3464620 AGAGAAAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3465863 original size:27 final size:25
Alignment explanation
Indices: 3465825--3465905 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 25
3465815 TAGTAGATAA
3465825 ATTTTTT--ATTAAATAATATAAATT
1 ATTTTTTAAATTAAATAATATAAA-T
* * *
3465849 ATTATTTTAAATTAATTAAAATTAAT
1 ATT-TTTTAAATTAAATAATATAAAT
* *
3465875 ATTTTTTAAATATATATAATAATATAT
1 ATTTTTTAAAT-TAAATAAT-ATAAAT
3465902 ATTT
1 ATTT
3465906 ATAAAATATT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
24 3 0.07
25 12 0.27
26 9 0.20
27 20 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTTTTAAATTAAATAATATAAAT
Found at i:3465897 original size:23 final size:23
Alignment explanation
Indices: 3465828--3465899 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 23
3465818 TAGATAAATT
*
3465828 TTTTATTAAATA-ATATAA-ATTA
1 TTTT-TTAAATATATATAATAATA
*
3465850 TTATTTTAAAT-TAATTAAAATTAATA
1 TT-TTTTAAATAT-A-TATAA-TAATA
3465876 TTTTTTAAATATATATAATAATA
1 TTTTTTAAATATATATAATAATA
3465899 T
1 T
3465900 ATATTTATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
22 8 0.20
23 9 0.22
24 8 0.20
25 9 0.22
26 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTTTAAATATATATAATAATA
Found at i:3475757 original size:3 final size:3
Alignment explanation
Indices: 3475739--3475790 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
3475729 TTATACACCA
* * *
3475739 TAT TA- TAT TA- TAT TAT TAT CAT T-G TAC TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3475784 TAT TAT T
1 TAT TAT T
3475791 TCTTTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
2 5 0.12
3 36 0.88
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3476644 original size:18 final size:17
Alignment explanation
Indices: 3476618--3476687 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 17
3476608 CAATCGTAGG
*
3476618 TTTTCTTTTTTGATTTTA
1 TTTTATTTTTT-ATTTTA
**
3476636 TTTTATTTTTTAAGCTTA
1 TTTTATTTTTT-ATTTTA
3476654 TTTTA--TTTTATTTTA
1 TTTTATTTTTTATTTTA
3476669 TTTTTAATTTTTTATTTTA
1 -TTTT-ATTTTTTATTTTA
3476688 CTGATTTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
15 4 0.10
16 8 0.19
17 1 0.02
18 19 0.45
19 10 0.24
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTATTTTTTATTTTA
Found at i:3476662 original size:28 final size:24
Alignment explanation
Indices: 3476623--3476687 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 24
3476613 GTAGGTTTTC
3476623 TTTTTTGATTTTATTTTATTTTTTAA
1 TTTTTT-ATTTTATTTTA-TTTTTAA
3476649 GCTTATTTTATTTTATTTTATTTTTAA
1 --TT-TTTTATTTTATTTTATTTTTAA
3476676 TTTTTTATTTTA
1 TTTTTTATTTTA
3476688 CTGATTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.28
25 2 0.06
27 7 0.19
28 13 0.36
29 4 0.11
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (24 bp):
TTTTTTATTTTATTTTATTTTTAA
Found at i:3476722 original size:28 final size:28
Alignment explanation
Indices: 3476661--3476723 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
3476651 TTATTTTATT
**
3476661 TTATTTTATTTTTAATTTTTTATTTTAC
1 TTATTTTATTTTTAATTTTAAATTTTAC
*
3476689 TGATTTTATTTTT-ATTTGATAAATTTTA-
1 TTATTTTATTTTTAATTT--TAAATTTTAC
3476717 TTATTTT
1 TTATTTT
3476724 GTAAAAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 4 0.14
28 18 0.62
29 7 0.24
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (28 bp):
TTATTTTATTTTTAATTTTAAATTTTAC
Found at i:3476868 original size:16 final size:18
Alignment explanation
Indices: 3476837--3476874 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3476827 TAAATAATAA
*
3476837 AAAAATTTCTTTC-AAAT
1 AAAAATTTCTTACAAAAT
3476854 AAAAATTT-TTACAAAAT
1 AAAAATTTCTTACAAAAT
3476871 AAAA
1 AAAA
3476875 TCATGAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTTCTTACAAAAT
Found at i:3477750 original size:19 final size:19
Alignment explanation
Indices: 3477728--3477765 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3477718 TTTCATTGCT
*
3477728 TATATTTGTTATTCATTTA
1 TATATTTGTCATTCATTTA
3477747 TATATTTGTCATTCATTTA
1 TATATTTGTCATTCATTTA
3477766 CATGTGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (19 bp):
TATATTTGTCATTCATTTA
Found at i:3482680 original size:86 final size:86
Alignment explanation
Indices: 3482582--3482743 Score: 236
Period size: 86 Copynumber: 1.9 Consensus size: 86
3482572 CTTACGAGCT
* * * * *
3482582 TAAAATCTTTACGAATCTAGAATCTTTGCAAAACTTGAAATCTTGTGAATCTTTCT-TTCTTGCG
1 TAAAATCTTTACGAATCTAAAACCTTTACAAAACTTGAAATCCTGCGAATCTTT-TATTCTTGCG
3482646 AATCTAAAAACCCTTATGAACC
65 AATCTAAAAACCCTTATGAACC
*
3482668 TAAAATCTTTACGAATCTAAAACCTTTACGAAACTTGAAATCCTGCGAATCTTTTATTCTTGCGA
1 TAAAATCTTTACGAATCTAAAACCTTTACAAAACTTGAAATCCTGCGAATCTTTTATTCTTGCGA
* *
3482733 ATTTGAAAACC
66 ATCTAAAAACC
3482744 TTTGTAAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
85 1 0.01
86 66 0.99
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (86 bp):
TAAAATCTTTACGAATCTAAAACCTTTACAAAACTTGAAATCCTGCGAATCTTTTATTCTTGCGA
ATCTAAAAACCCTTATGAACC
Found at i:3482687 original size:17 final size:17
Alignment explanation
Indices: 3482644--3482699 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
3482634 TTCTTTCTTG
*
3482644 CGAATCTAAAAACCCTTA
1 CGAATCT-AAAACCTTTA
* * *
3482662 TGAACCTAAAATCTTTA
1 CGAATCTAAAACCTTTA
3482679 CGAATCTAAAACCTTTA
1 CGAATCTAAAACCTTTA
3482696 CGAA
1 CGAA
3482700 ACTTGAAATC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 26 0.84
18 5 0.16
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (17 bp):
CGAATCTAAAACCTTTA
Found at i:3484428 original size:58 final size:58
Alignment explanation
Indices: 3484326--3484546 Score: 317
Period size: 57 Copynumber: 3.8 Consensus size: 58
3484316 TTGTGTAGGA
* * *
3484326 AAAATTGATACTTTCAACTTTTCCCCAAAAGTA-TTTTTTAGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTTTAAGG
3484383 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTTTAAGG
***
3484441 AAAATTGATACTTTCAACTTTT-CCTCAAAAA-CCCTTTTT-GAAATTTATTTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTGGAAATTTA-TTTTTAAGG
3484498 AAAATTGATACTTTCAACTTTTCCCT-AAAATATTTTTTCCTGGAAATTT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT--TGGAAATTT
3484547 TGATTTTTTA
Statistics
Matches: 147, Mismatches: 9, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
56 12 0.08
57 74 0.50
58 53 0.36
59 1 0.01
60 7 0.05
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTTTAAGG
Found at i:3484458 original size:115 final size:115
Alignment explanation
Indices: 3484326--3484546 Score: 356
Period size: 115 Copynumber: 1.9 Consensus size: 115
3484316 TTGTGTAGGA
** *
3484326 AAAATTGATACTTTCAACTTTTCCCCAAAAGTATTTTTTAGAAATTTA-TTTTTAAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAACACTTTTT-GAAATTTATTTTTTAAGGAAAATTG
3484390 ATACTTTCAACTTTTCCCTAAAAATATTTTTT-TGGAAATTTATTTTTAAGG
65 ATACTTTCAACTTTTCCCT-AAAATATTTTTTCTGGAAATTTATTTTTAAGG
* *
3484441 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTGAAATTTATTTTTTAAGGAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAACACTTTTTGAAATTTATTTTTTAAGGAAAATTGA
3484506 TACTTTCAACTTTTCCCTAAAATATTTTTTCCTGGAAATTT
66 TACTTTCAACTTTTCCCTAAAATATTTTTT-CTGGAAATTT
3484547 TGATTTTTTA
Statistics
Matches: 98, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
114 20 0.20
115 69 0.70
116 9 0.09
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.45
Consensus pattern (115 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAACACTTTTTGAAATTTATTTTTTAAGGAAAATTGA
TACTTTCAACTTTTCCCTAAAATATTTTTTCTGGAAATTTATTTTTAAGG
Found at i:3485499 original size:4 final size:4
Alignment explanation
Indices: 3485492--3485701 Score: 68
Period size: 4 Copynumber: 53.2 Consensus size: 4
3485482 ATATTATAGG
* * * * * *
3485492 ATAA ATAA ATAA AAAA AT-A AT-A ACAG ATAT ATAA TTAG ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
*
3485538 ATAA A-AT ATAA A-ATA AT-A AT-A AT-A AT-A ATAAA ATATA ATATA
1 ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA AT-AA ATA-A ATA-A
* * * * *
3485580 AT-A ATAA ATAT ATAA CTAT ATAA ATAAA ATACA TATAA AT-A TTAA CAGAA
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATA-A -ATAA ATAA ATAA -ATAA
* * * * * * *
3485630 AGAA A-AA ATAA ATAA ATAA ATAA ATAA AGAT ATAC ATAT ATTA ATAC
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
3485677 ATAGTA AT-A ATAA ATAA AT-A ATAA A
1 ATA--A ATAA ATAA ATAA ATAA ATAA A
3485702 ATACATAAAA
Statistics
Matches: 156, Mismatches: 32, Indels: 36
0.70 0.14 0.16
Matches are distributed among these distances:
3 34 0.22
4 98 0.63
5 19 0.12
6 5 0.03
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:3485510 original size:38 final size:38
Alignment explanation
Indices: 3485468--3485543 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
3485458 TAGAACAGAT
*
3485468 AAATAAAAAAAAATATATTA-TAGGATAAATAAATAAAA
1 AAATAAAAAAAAATATATAATTA-GATAAATAAATAAAA
* * *
3485506 AAATAATAACAGATATATAATTAGATAAATAAATAAAA
1 AAATAAAAAAAAATATATAATTAGATAAATAAATAAAA
3485544 TATAAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 31 0.94
39 2 0.06
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.25
Consensus pattern (38 bp):
AAATAAAAAAAAATATATAATTAGATAAATAAATAAAA
Found at i:3485557 original size:3 final size:3
Alignment explanation
Indices: 3485537--3485586 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
3485527 TAGATAAATA
3485537 AAT AA- AAT -AT AA- AAT AAT AAT AAT AAT AAT AA- AAT -AT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3485579 AAT AAT AA
1 AAT AAT AA
3485587 ATATATAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
2 12 0.29
3 29 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3485560 original size:34 final size:33
Alignment explanation
Indices: 3485430--3485607 Score: 113
Period size: 34 Copynumber: 5.2 Consensus size: 33
3485420 AATAAAAATC
* *
3485430 AAATAAATAGAAA-AAAATAATAGATAATTAGA-
1 AAATAAATAAAAATAAAATAATATATAA-TAGAT
3485462 ACAGATAAATAAAAA-AAAAT-ATAT-T-ATAGGAT
1 A-A-ATAAATAAAAATAAAATAATATATAATA-GAT
*
3485494 AAATAAATAAAAAAATAATAACAGATATATAATTAGAT
1 AAATAAAT--AAAAATAA-AATA-ATATATAA-TAGAT
3485532 AAATAAATAAAATATAAAATAATA-ATAATA-AT
1 AAATAAATAAAA-ATAAAATAATATATAATAGAT
* *
3485564 -AATAAAATATAATATAATAATAAATATATAACTATAT
1 AAAT-AAATA-AAAATAA-AAT-AATATATAA-TAGAT
3485601 AAATAAA
1 AAATAAA
3485608 ATACATATAA
Statistics
Matches: 119, Mismatches: 5, Indels: 39
0.73 0.03 0.24
Matches are distributed among these distances:
30 8 0.07
31 7 0.06
32 19 0.16
33 13 0.11
34 25 0.21
35 7 0.06
36 13 0.11
37 10 0.08
38 15 0.13
39 2 0.02
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (33 bp):
AAATAAATAAAAATAAAATAATATATAATAGAT
Found at i:3485600 original size:27 final size:25
Alignment explanation
Indices: 3485518--3485610 Score: 88
Period size: 25 Copynumber: 3.7 Consensus size: 25
3485508 ATAATAACAG
3485518 ATATATAAT-TAGATAAATAAATAA-A
1 ATATATAATATA-AT-AATAAATAATA
*
3485543 ATATAAAATAATAATAAT-AATAATA
1 ATATATAAT-ATAATAATAAATAATA
*
3485568 AAATATAATATAATAATAAATATATA
1 ATATATAATATAATAATAAATA-ATA
3485594 ACTATATAA-ATAA-AATA
1 A-TATATAATATAATAATA
3485611 CATATAAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
24 13 0.22
25 27 0.47
26 10 0.17
27 8 0.14
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (25 bp):
ATATATAATATAATAATAAATAATA
Found at i:3485941 original size:16 final size:14
Alignment explanation
Indices: 3485898--3485960 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 14
3485888 AACATTTTCA
3485898 TTTTTTTGATTTTT-
1 TTTTTTTG-TTTTTG
*
3485912 TTTATATT-TTTTTG
1 TTT-TTTTGTTTTTG
3485926 TTTGCTTTTGTTTTTG
1 TTT--TTTTGTTTTTG
3485942 TTTTTTTGTTTTT-
1 TTTTTTTGTTTTTG
3485955 TTTTTT
1 TTTTTT
3485961 AACCAAAGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
13 11 0.26
14 16 0.38
15 6 0.14
16 9 0.21
ACGTcount: A:0.05, C:0.02, G:0.10, T:0.84
Consensus pattern (14 bp):
TTTTTTTGTTTTTG
Found at i:3485955 original size:10 final size:10
Alignment explanation
Indices: 3485898--3485958 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
3485888 AACATTTTCA
*
3485898 TTTTTTTGAT
1 TTTTTTTGTT
* *
3485908 TTTTTTTATA
1 TTTTTTTGTT
3485918 TTTTTTTGTT
1 TTTTTTTGTT
*
3485928 TGCTTTTGTTTTT
1 T--TTTT-TTGTT
3485941 GTTTTTTTGTT
1 -TTTTTTTGTT
3485952 TTTTTTT
1 TTTTTTT
3485959 TTAACCAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
10 23 0.57
11 4 0.10
12 8 0.20
13 4 0.10
14 1 0.03
ACGTcount: A:0.05, C:0.02, G:0.10, T:0.84
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:3485959 original size:20 final size:20
Alignment explanation
Indices: 3485898--3485960 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
3485888 AACATTTTCA
*
3485898 TTTTTTTGATTTTTTTTATATTT
1 TTTTTTTG-TTTTTTTT-T-TTG
* *
3485921 TTTTGTTTGCTTTTGTTTTTG
1 TTTT-TTTGTTTTTTTTTTTG
3485942 TTTTTTTGTTTTTTTTTTT
1 TTTTTTTGTTTTTTTTTTT
3485961 AACCAAAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 13 0.38
21 6 0.18
22 1 0.03
23 10 0.29
24 4 0.12
ACGTcount: A:0.05, C:0.02, G:0.10, T:0.84
Consensus pattern (20 bp):
TTTTTTTGTTTTTTTTTTTG
Found at i:3486062 original size:41 final size:41
Alignment explanation
Indices: 3485968--3486262 Score: 430
Period size: 41 Copynumber: 7.1 Consensus size: 41
3485958 TTTAACCAAA
* * * *
3485968 GCTCCTCTAAACAGAGACTCAACAACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-ATAAATT
*
3486011 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
*
3486052 GCTCCTCTAAACAGAGGCACCACGACTTCGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
* * *
3486093 GCTCTTCTAAACAAAGGCACCACGACTTCGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
* ** *
3486134 GCTCCTCTAAATAGAGGCATTATGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
3486175 GCTCCTCTAAACAGAGGCACCACGA-TTTCGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAATAAATT
*
3486216 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
3486257 GCTCCT
1 GCTCCT
3486263 TGACGATCAT
Statistics
Matches: 229, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
40 3 0.01
41 193 0.84
42 6 0.03
43 27 0.12
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
Found at i:3487485 original size:11 final size:12
Alignment explanation
Indices: 3487464--3487511 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 12
3487454 TTCTACCAAA
3487464 ATCTCTTTTTTTC
1 ATCT-TTTTTTTC
3487477 AT-TTTTTTTTC
1 ATCTTTTTTTTC
3487488 -TCTTTTTTTTC
1 ATCTTTTTTTTC
3487499 ATCATCTTTTTTT
1 ATC-T-TTTTTTT
3487512 TCTTGCTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 1 0.03
11 17 0.55
12 3 0.10
13 3 0.10
14 7 0.23
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (12 bp):
ATCTTTTTTTTC
Found at i:3487524 original size:15 final size:14
Alignment explanation
Indices: 3487475--3487525 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
3487465 TCTCTTTTTT
3487475 TCATTTTTTT-TTC
1 TCATTTTTTTCTTC
* *
3487488 TCTTTTTTTTCATC
1 TCATTTTTTTCTTC
*
3487502 ATCTTTTTTTTCTTGC
1 -TCATTTTTTTCTT-C
3487518 TCATTTTT
1 TCATTTTT
3487526 CATCCATTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 9 0.29
14 2 0.06
15 19 0.61
16 1 0.03
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.73
Consensus pattern (14 bp):
TCATTTTTTTCTTC
Found at i:3491468 original size:57 final size:57
Alignment explanation
Indices: 3491405--3491617 Score: 245
Period size: 57 Copynumber: 3.7 Consensus size: 57
3491395 TTGTGTAGGA
* *
3491405 AAAATTGATACTTTTAACTTTTTCCC-AAAAGTATTTTTTGGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTGGAAATTTATTTTTAAGG
* *
3491462 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGGAAA-TTT-ATTTTTAAGG
* *** *
3491523 AAAATTGATACTTTTAACTTTT-CCTCAAAAACCCTTTTT-GAAATTTATTTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTGGAAATTTA-TTTTTAAGG
*
3491580 AAAATTAATACTTTCAACTTTTCCCT-AAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
3491618 CCTGAAAATT
Statistics
Matches: 132, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
56 17 0.13
57 53 0.40
58 6 0.05
59 15 0.11
60 6 0.05
61 35 0.27
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTTTAAGG
Found at i:3491552 original size:118 final size:118
Alignment explanation
Indices: 3491405--3491635 Score: 351
Period size: 118 Copynumber: 2.0 Consensus size: 118
3491395 TTGTGTAGGA
** * * *
3491405 AAAATTGATACTTTTAACTTTTTCCCAAAAGTATTTTTTGGAAATTTA-TTTTTAAGGAAAATTG
1 AAAATTGATACTTTTAACTTTTTCCCAAAAACACTTTTT-GAAATTTATTTTTTAAGAAAAATTA
*
3491469 ATACTTTCAACTTTTCCCTAAAAATATTTTTT-TTGAAAATTTTGATTTTCAAGG
65 ATACTTTCAACTTTTCCCT-AAAATATTTTTTCCTGAAAATTTTGATTTTCAAGG
*
3491523 AAAATTGATACTTTTAAC-TTTTCCTCAAAAACCCTTTTTGAAATTTATTTTTTAAGAAAAATTA
1 AAAATTGATACTTTTAACTTTTTCC-CAAAAACACTTTTTGAAATTTATTTTTTAAGAAAAATTA
3491587 ATACTTTCAACTTTTCCCTAAAATATTTTTTCCTGAAAATTTTGATTTT
65 ATACTTTCAACTTTTCCCTAAAATATTTTTTCCTGAAAATTTTGATTTT
3491636 TTATTTAAAG
Statistics
Matches: 103, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
117 26 0.25
118 77 0.75
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (118 bp):
AAAATTGATACTTTTAACTTTTTCCCAAAAACACTTTTTGAAATTTATTTTTTAAGAAAAATTAA
TACTTTCAACTTTTCCCTAAAATATTTTTTCCTGAAAATTTTGATTTTCAAGG
Found at i:3491730 original size:10 final size:10
Alignment explanation
Indices: 3491715--3491745 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3491705 TCGGATCGTA
3491715 GCTCGGCTTG
1 GCTCGGCTTG
*
3491725 GCTCGGCTCG
1 GCTCGGCTTG
3491735 GCTCGGCTTG
1 GCTCGGCTTG
3491745 G
1 G
3491746 AGGGGGCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.42, T:0.26
Consensus pattern (10 bp):
GCTCGGCTTG
Found at i:3492547 original size:4 final size:4
Alignment explanation
Indices: 3492540--3492748 Score: 66
Period size: 4 Copynumber: 52.2 Consensus size: 4
3492530 ATATTATAGG
* * *
3492540 ATAA ATAA ATAA AAAA AT-A ATAA CGATATA A-AA TTAG ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA --ATA-A ATAA ATAA ATAA ATAA ATAA
*
3492589 A-AT ATAA A-ATA AT-A AT-A AT-A AT-A ATAA ATTATA ATATA AT-A
1 ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA A-TA-A ATA-A ATAA
* * * * *
3492630 ATAA ATAT ATAA CTAT ATAA ATAAA ATACA TATAA AT-A TTAA CAGAA
1 ATAA ATAA ATAA ATAA ATAA AT-AA ATA-A -ATAA ATAA ATAA -ATAA
* * * * * * *
3492677 AGAA A-AA ATAA ATAA ATAA ATAA ATAA AGAT ATAC ATAT ATTA ATAC
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
3492724 ATAGTA AT-A ATAA ATAA AT-A ATAA A
1 ATA--A ATAA ATAA ATAA ATAA ATAA A
3492749 ATACATAAAA
Statistics
Matches: 156, Mismatches: 27, Indels: 44
0.69 0.12 0.19
Matches are distributed among these distances:
3 33 0.21
4 95 0.61
5 17 0.11
6 10 0.06
7 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:3492582 original size:25 final size:22
Alignment explanation
Indices: 3492554--3492641 Score: 72
Period size: 25 Copynumber: 3.7 Consensus size: 22
3492544 ATAAATAAAA
*
3492554 AAATAATAACGATATAAAATTAGAT
1 AAATAATAA-AATATAAAA-TA-AT
3492579 AAATAAATAAAATATAAAATAAT
1 AAAT-AATAAAATATAAAATAAT
*
3492602 -AATAATAATAATA-AATTATAAT
1 AAATAATAA-AATATAA-AATAAT
3492624 ATAATAATAAATATATAA
1 A-AATAATAAA-ATATAA
3492642 CTATATAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
21 7 0.13
22 12 0.22
23 3 0.06
24 13 0.24
25 14 0.26
26 5 0.09
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATAATAAAATATAAAATAAT
Found at i:3492604 original size:3 final size:3
Alignment explanation
Indices: 3492584--3492633 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
3492574 TAGATAAATA
*
3492584 AAT AA- AAT -AT AA- AAT AAT AAT AAT AAT AAT AAAT TAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
3492626 AAT AAT AA
1 AAT AAT AA
3492634 ATATATAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 8 0.20
3 29 0.73
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3492618 original size:44 final size:45
Alignment explanation
Indices: 3492540--3492641 Score: 108
Period size: 44 Copynumber: 2.3 Consensus size: 45
3492530 ATATTATAGG
* *
3492540 ATAAAT-AAATA-AAAAAATAATAACGATATAAAATTA-GATA-A
1 ATAAATAAAATATAAAAAATAATAACAATATAAAATTATAATATA
*
3492581 ATAAATAAAATATAAAATAATAATAATAATA-ATAAATTATAATATA
1 ATAAATAAAATATAAAA-AATAATAACAATATA-AAATTATAATATA
3492627 AT-AATAAATATATAA
1 ATAAATAAA-ATATAA
3492642 CTATATAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
41 6 0.12
42 5 0.10
43 5 0.10
44 17 0.33
45 9 0.18
46 9 0.18
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (45 bp):
ATAAATAAAATATAAAAAATAATAACAATATAAAATTATAATATA
Found at i:3493283 original size:18 final size:17
Alignment explanation
Indices: 3493256--3493289 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3493246 GATCGTAGAT
*
3493256 TTTCTTTTTTCTATTTTA
1 TTTCTATTTT-TATTTTA
3493274 TTTCTATTTTTATTTT
1 TTTCTATTTTTATTTT
3493290 TTGATTTTAT
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:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTATTTTTATTTTA
Found at i:3496184 original size:31 final size:32
Alignment explanation
Indices: 3496135--3496208 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
3496125 ATTATAAAAA
3496135 TTAT-TAAAAATTTATATATT-T-ATATTATATT
1 TTATATAAAAA-TTATATATTATAAT-TTATATT
3496166 TTATATAAAAATTATATATTATAATTTATATT
1 TTATATAAAAATTATATATTATAATTTATATT
*
3496198 GT-TATAAAAAT
1 TTATATAAAAAT
3496209 ATAAAATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 22 0.56
32 15 0.38
33 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (32 bp):
TTATATAAAAATTATATATTATAATTTATATT
Found at i:3496290 original size:11 final size:11
Alignment explanation
Indices: 3496261--3496303 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
3496251 AAATTTTAAA
3496261 TTATATTATTT
1 TTATATTATTT
3496272 TATATATT-TTAT
1 T-TATATTATT-T
3496284 TTATATTATTT
1 TTATATTATTT
3496295 TTATATTAT
1 TTATATTAT
3496304 ATTATCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATATTATTT
Found at i:3496703 original size:15 final size:16
Alignment explanation
Indices: 3496685--3496715 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3496675 ATTTTTCTGA
3496685 TAATT-ATTTAAAATT
1 TAATTAATTTAAAATT
3496700 TAATTAATTTAAAATT
1 TAATTAATTTAAAATT
3496716 AAATCGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTAATTTAAAATT
Found at i:3496934 original size:16 final size:18
Alignment explanation
Indices: 3496915--3496947 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3496905 TATTGATATA
3496915 TTTTAAT-TAT-TTTTAT
1 TTTTAATATATATTTTAT
3496931 TTTTAATATATATTTTA
1 TTTTAATATATATTTTA
3496948 AAATATATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTAATATATATTTTAT
Found at i:3498675 original size:6 final size:6
Alignment explanation
Indices: 3498664--3498691 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3498654 AATTATATGT
3498664 GTAAAA GTAAAA GTAAAA GTAAAA GTAA
1 GTAAAA GTAAAA GTAAAA GTAAAA GTAA
3498692 TTATTGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (6 bp):
GTAAAA
Found at i:3500063 original size:13 final size:12
Alignment explanation
Indices: 3500044--3500097 Score: 74
Period size: 13 Copynumber: 4.4 Consensus size: 12
3500034 TGATAATTTT
3500044 AAATATAATATA
1 AAATATAATATA
3500056 ATAATATAATATA
1 A-AATATAATATA
*
3500069 AAATATAAAATA
1 AAATATAATATA
3500081 TAAATATAA-ATA
1 -AAATATAATATA
3500093 AAATA
1 AAATA
3500098 ATTTAAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
11 5 0.13
12 14 0.36
13 20 0.51
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATAATATA
Found at i:3500072 original size:25 final size:24
Alignment explanation
Indices: 3500043--3500098 Score: 53
Period size: 27 Copynumber: 2.3 Consensus size: 24
3500033 TTGATAATTT
*
3500043 TAAATATAATATAATAATATAATATA
1 TAAATAAAATATAA-AATATAA-ATA
*
3500069 AAATATAAAATAT-AAATATAAATA
1 TAA-ATAAAATATAAAATATAAATA
3500093 -AAATAA
1 TAAATAA
3500099 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 4 0.15
23 2 0.07
24 3 0.11
25 7 0.26
26 3 0.11
27 8 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
TAAATAAAATATAAAATATAAATA
Found at i:3500073 original size:20 final size:20
Alignment explanation
Indices: 3500043--3500104 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
3500033 TTGATAATTT
3500043 TAAATAT-AATATAATAATA
1 TAAATATAAATATAATAATA
3500062 T-AATATAAAATATAA-AATA
1 TAAATAT-AAATATAATAATA
* *
3500081 TAAATATAAATAAAATAATT
1 TAAATATAAATATAATAATA
3500101 TAAA
1 TAAA
3500105 ATTTTAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 5 0.14
19 13 0.35
20 19 0.51
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATATAAATATAATAATA
Found at i:3500075 original size:7 final size:7
Alignment explanation
Indices: 3500050--3500090 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
3500040 TTTTAAATAT
3500050 AATATAA
1 AATATAA
3500057 TAATAT--
1 -AATATAA
3500063 AATATAA
1 AATATAA
3500070 AATATAA
1 AATATAA
3500077 AATAT-A
1 AATATAA
3500083 AATATAA
1 AATATAA
3500090 A
1 A
3500091 TAAAATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
5 5 0.17
6 6 0.20
7 14 0.47
8 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATATAA
Found at i:3500144 original size:29 final size:28
Alignment explanation
Indices: 3500088--3500151 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
3500078 ATATAAATAT
3500088 AAATA-AAATAATTTAAAATTTTAATAAA
1 AAATATAAATAATTTAAAATTTT-ATAAA
*
3500116 AATTATAAATAATTTAATAAATTTT-TAAA
1 AAATATAAATAATTT-A-AAATTTTATAAA
3500145 AAATATA
1 AAATATA
3500152 TTTTATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 4 0.13
29 19 0.61
30 1 0.03
31 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
AAATATAAATAATTTAAAATTTTATAAA
Found at i:3502634 original size:17 final size:16
Alignment explanation
Indices: 3502606--3502639 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3502596 TTGAGGTTTC
*
3502606 CATTTCATTTTTTATT
1 CATTTCATTTTTAATT
3502622 CATTTCAATTTTTAATT
1 CATTTC-ATTTTTAATT
3502639 C
1 C
3502640 TTATAATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (16 bp):
CATTTCATTTTTAATT
Found at i:3516314 original size:26 final size:26
Alignment explanation
Indices: 3516255--3516320 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
3516245 AATATTATTT
3516255 TTAA-TAAAAATATAAAATTAAATAA
1 TTAATTAAAAATATAAAATTAAATAA
*
3516280 AT-ATATAAAAATATAAAATTAAATAA
1 TTAAT-TAAAAATATAAAATTAAATAA
3516306 TTAATTAAAAA-ATAA
1 TTAATTAAAAATATAA
3516321 TTTTTTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
24 1 0.03
25 5 0.14
26 28 0.78
27 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (26 bp):
TTAATTAAAAATATAAAATTAAATAA
Found at i:3520804 original size:19 final size:19
Alignment explanation
Indices: 3520775--3520819 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3520765 AATAATTTTA
3520775 TATAA-TTAATTAATA-AAT
1 TATAATTTAATTAA-ACAAT
3520793 TATAATTTAATTAAACAAT
1 TATAATTTAATTAAACAAT
3520812 TA-AATTTA
1 TATAATTTA
3520820 CACACAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAATTTAATTAAACAAT
Found at i:3522818 original size:52 final size:51
Alignment explanation
Indices: 3522735--3522880 Score: 168
Period size: 52 Copynumber: 2.8 Consensus size: 51
3522725 AACTTGTAAA
* *
3522735 AAAATAATTATAAGAGAAATAAGATTTTTAATAGGTAAGTTTCACTTACAAG
1 AAAAGAATTATAAGAGAAA-AAGATTCTTAATAGGTAAGTTTCACTTACAAG
* * * ** *
3522787 AGAAA-AATTCTAAGAGGAAAAAGATTCTTAATAGGTAAATTTGACTTGTAGG
1 A-AAAGAATTATAAGA-GAAAAAGATTCTTAATAGGTAAGTTTCACTTACAAG
*
3522839 AAAAGAATTTTAAGAGAAAAGAGATTCTTAATAGGTAAGTTT
1 AAAAGAATTATAAGAGAAAA-AGATTCTTAATAGGTAAGTTT
3522881 TTATCGTTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
51 8 0.10
52 66 0.81
53 7 0.09
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.31
Consensus pattern (51 bp):
AAAAGAATTATAAGAGAAAAAGATTCTTAATAGGTAAGTTTCACTTACAAG
Found at i:3526075 original size:2 final size:2
Alignment explanation
Indices: 3526068--3526099 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3526058 CATCTTGAGC
3526068 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
3526100 TCAAACATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3531023 original size:11 final size:11
Alignment explanation
Indices: 3530994--3531023 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3530984 ATTGTCAGTG
*
3530994 ATATTTTAGTA
1 ATATTTTGGTA
3531005 ATATTTTGGTA
1 ATATTTTGGTA
3531016 ATATTTTG
1 ATATTTTG
3531024 ATTGATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (11 bp):
ATATTTTGGTA
Found at i:3531141 original size:97 final size:99
Alignment explanation
Indices: 3531034--3531217 Score: 311
Period size: 97 Copynumber: 1.9 Consensus size: 99
3531024 ATTGATTTGA
*
3531034 TATTAATTTAGAGAATATTATATATTGATTTAGTTGATTATAAGAATTGATTTAGTCATTATTT-
1 TATTAATTTAGAGAATATTAGATATTGATTTAGTTGATTATAAGAATTGATTTAGTCATTATTTC
*
3531098 TCATTGATTGTAT-TTTT-TTTTATTTTATAACAT
66 T-ATTGACTGTATGTTTTATTTTATTTTATAACAT
*
3531131 TATTAATTTAGAGAATATTAGATATTGATTTAGTTGATTATAAGAATTGATTTAGTTATTATTTC
1 TATTAATTTAGAGAATATTAGATATTGATTTAGTTGATTATAAGAATTGATTTAGTCATTATTTC
3531196 TATTGACTGTATGTTTTATTTT
66 TATTGACTGTATGTTTTATTTT
3531218 GTAACATTTT
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
97 72 0.89
98 5 0.06
99 4 0.05
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.54
Consensus pattern (99 bp):
TATTAATTTAGAGAATATTAGATATTGATTTAGTTGATTATAAGAATTGATTTAGTCATTATTTC
TATTGACTGTATGTTTTATTTTATTTTATAACAT
Found at i:3531200 original size:21 final size:22
Alignment explanation
Indices: 3531153--3531201 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
3531143 GAATATTAGA
*
3531153 TATTGATTTAGTTGATTATAAG
1 TATTGATTTAGTTGATTATAAC
* **
3531175 AATTGATTTAGTT-ATTATTTC
1 TATTGATTTAGTTGATTATAAC
3531196 TATTGA
1 TATTGA
3531202 CTGTATGTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (22 bp):
TATTGATTTAGTTGATTATAAC
Found at i:3538402 original size:12 final size:13
Alignment explanation
Indices: 3538380--3538422 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
3538370 ATGTTGAGAT
*
3538380 AAATTATAATTAA
1 AAATAATAATTAA
3538393 AAA-AATAATTAA
1 AAATAATAATTAA
*
3538405 AAATATTAAATTAA
1 AAATAAT-AATTAA
3538419 AAAT
1 AAAT
3538423 TAGATGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 11 0.42
13 5 0.19
14 10 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATAATAATTAA
Found at i:3538418 original size:14 final size:14
Alignment explanation
Indices: 3538382--3538422 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3538372 GTTGAGATAA
3538382 ATTATAATTAAAAA-
1 ATTA-AATTAAAAAT
*
3538396 AAT-AATTAAAAAT
1 ATTAAATTAAAAAT
3538409 ATTAAATTAAAAAT
1 ATTAAATTAAAAAT
3538423 TAGATGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 12 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTAAATTAAAAAT
Found at i:3540575 original size:51 final size:51
Alignment explanation
Indices: 3540499--3540598 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
3540489 AAGGCATTGA
*
3540499 AAATGTTTGCCTTAGATCTCACAATGGTATTATTAAGACACTTTGTCATGT
1 AAATGTTTGCCTTAGATCTCACAATGATATTATTAAGACACTTTGTCATGT
*
3540550 AAATGTTT-CTCTTAGATCTCACAATGATATTATTACGACACTTTGTCAT
1 AAATGTTTGC-CTTAGATCTCACAATGATATTATTAAGACACTTTGTCAT
3540599 ATAAGGTAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 1 0.02
51 45 0.98
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (51 bp):
AAATGTTTGCCTTAGATCTCACAATGATATTATTAAGACACTTTGTCATGT
Found at i:3541921 original size:19 final size:19
Alignment explanation
Indices: 3541894--3541933 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3541884 AAATATGTTA
*
3541894 AAGTCAAAATTTTTTTCTT
1 AAGTCAAAACTTTTTTCTT
*
3541913 AAGTTAAAACTTTTTTCTT
1 AAGTCAAAACTTTTTTCTT
3541932 AA
1 AA
3541934 ACTCCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (19 bp):
AAGTCAAAACTTTTTTCTT
Found at i:3548150 original size:43 final size:47
Alignment explanation
Indices: 3548094--3548183 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 47
3548084 ACTATTAAAG
* **
3548094 ATATTTGATTAAAATTTATGTATAA-TAAAAATT-TTAAATTATTTT
1 ATATTTGATTAAAATTCATAAATAATTAAAAATTATTAAATTATTTT
3548139 ATATTT-A-TAAAATTCATAAATAATTAAAAATTATTAAATTATTTT
1 ATATTTGATTAAAATTCATAAATAATTAAAAATTATTAAATTATTTT
3548184 TATGATAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 13 0.32
44 9 0.22
45 18 0.45
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (47 bp):
ATATTTGATTAAAATTCATAAATAATTAAAAATTATTAAATTATTTT
Found at i:3548706 original size:21 final size:22
Alignment explanation
Indices: 3548662--3548706 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
3548652 TGATAAAATG
* * *
3548662 TTGTATTTTTAATTTTTATGAT
1 TTGTATTTTAAATTTTAATAAT
3548684 TTGTA-TTTAAATTTTAATAAT
1 TTGTATTTTAAATTTTAATAAT
3548705 TT
1 TT
3548707 AAGAACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (22 bp):
TTGTATTTTAAATTTTAATAAT
Found at i:3549193 original size:21 final size:21
Alignment explanation
Indices: 3549169--3549209 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3549159 CTATGATTTT
3549169 TAATTTCAAAAAATAAAAAAA
1 TAATTTCAAAAAATAAAAAAA
* *
3549190 TAATTTTAAAATATAAAAAA
1 TAATTTCAAAAAATAAAAAA
3549210 TTTTAGAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAATTTCAAAAAATAAAAAAA
Found at i:3549364 original size:31 final size:30
Alignment explanation
Indices: 3549266--3549368 Score: 81
Period size: 31 Copynumber: 3.4 Consensus size: 30
3549256 AAAGACAAAA
* *
3549266 AAAATATATAA-ATTTA-ATAAAACTCAAAAT
1 AAAATATATAATTTTTATATAAAA-T-ATAAT
3549296 AAAA-ATATTATATTTTT-TAT-AAATATAAATT
1 AAAATATA-TA-ATTTTTATATAAAATAT-AA-T
*
3549327 ATAATATATAATTTTTATATAAAATATAAT
1 AAAATATATAATTTTTATATAAAATATAAT
3549357 ACAAATATATAA
1 A-AAATATATAA
3549369 ATTACTAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
29 4 0.07
30 17 0.29
31 24 0.41
32 14 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAATATATAATTTTTATATAAAATATAAT
Found at i:3550005 original size:21 final size:21
Alignment explanation
Indices: 3549979--3550021 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3549969 AGGACAAACG
3549979 TAATTAATATCCGACCCCAGC
1 TAATTAATATCCGACCCCAGC
3550000 TAATTAATATCCGACCCCAGC
1 TAATTAATATCCGACCCCAGC
3550021 T
1 T
3550022 TAAACAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.26
Consensus pattern (21 bp):
TAATTAATATCCGACCCCAGC
Found at i:3555830 original size:110 final size:112
Alignment explanation
Indices: 3555612--3555837 Score: 314
Period size: 114 Copynumber: 2.0 Consensus size: 112
3555602 TTGGCTCAAA
* * *
3555612 TCTAGTCATTTTTACTTTAATTCAGTTTAGTTACCTTTATTTTCGATCTTTGCTCAGTCCAGTCA
1 TCTAGTCATTTTGACCTTAATTCAGTTTAGTTACCTTTATTTTCGATCTTTGCTCAGTCCAATCA
*
3555677 CTTTTATTTTTTGACCCTGACTTAGTTCGGTCGCCTTCATTTTTTTAC
66 C-TTTATTTTTTGACCCTGACTTAGTTCGGTCACCTTCATTTTTTTAC
* * * ** *
3555725 TCTAGTCATTTTCGACCTTAGTTTAGTTTCGTTACCTTTATTTTTTATCTTTGCTTAGT-CAATC
1 TCTAGTCATTTT-GACCTTAATTCAGTTTAGTTACCTTTATTTTCGATCTTTGCTCAGTCCAATC
*
3555789 AC-TTATTTTTTGACCC-GGCTTAGTTCGGTCACCTTCATTTTTTTAC
65 ACTTTATTTTTTGACCCTGACTTAGTTCGGTCACCTTCATTTTTTTAC
3555835 TCT
1 TCT
3555838 TGTTTAGTCC
Statistics
Matches: 101, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
110 31 0.31
111 14 0.14
113 18 0.18
114 38 0.38
ACGTcount: A:0.16, C:0.21, G:0.12, T:0.51
Consensus pattern (112 bp):
TCTAGTCATTTTGACCTTAATTCAGTTTAGTTACCTTTATTTTCGATCTTTGCTCAGTCCAATCA
CTTTATTTTTTGACCCTGACTTAGTTCGGTCACCTTCATTTTTTTAC
Found at i:3571680 original size:2 final size:2
Alignment explanation
Indices: 3571675--3571700 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3571665 CCCCCCCCCA
3571675 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
3571701 TCCTCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3577805 original size:2 final size:2
Alignment explanation
Indices: 3577794--3577824 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3577784 AATTTATTAT
3577794 TA TA -A 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
3577825 GATACACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3579711 original size:15 final size:14
Alignment explanation
Indices: 3579691--3579720 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3579681 CAATACTTTA
3579691 TATTTATTATTTATT
1 TATTTATT-TTTATT
3579706 TATTTATTTTTATT
1 TATTTATTTTTATT
3579720 T
1 T
3579721 TTATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTATTTTTATT
Found at i:3579733 original size:20 final size:21
Alignment explanation
Indices: 3579693--3579733 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3579683 ATACTTTATA
**
3579693 TTTATTATTTATTTATTTATT
1 TTTATTATTTATTTAAATATT
3579714 TTTATT-TTTATTTAAATATT
1 TTTATTATTTATTTAAATATT
3579734 ATAGTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTATTATTTATTTAAATATT
Found at i:3579792 original size:29 final size:29
Alignment explanation
Indices: 3579759--3579836 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 29
3579749 ACTTTATATA
* **
3579759 AAATAAATTTTATTATATAATAAGTTAAT
1 AAATAAATTTTATTATATAACAAACTAAT
3579788 AAATAAATTGTATTATTATATAACAAACTAAT
1 AAATAAA-T-T-TTATTATATAACAAACTAAT
3579820 AAATAAATTTTAATTAT
1 AAATAAATTTT-ATTAT
3579837 TTATTAACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 9 0.21
30 7 0.17
31 2 0.05
32 24 0.57
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (29 bp):
AAATAAATTTTATTATATAACAAACTAAT
Found at i:3579809 original size:32 final size:33
Alignment explanation
Indices: 3579768--3579847 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
3579758 AAAATAAATT
* **
3579768 TTATTATATAATAAGTTAATAAATAAATTGT-A
1 TTATTATATAACAAACTAATAAATAAATTGTAA
*
3579800 TTATTATATAACAAACTAATAAATAAATTTTAA
1 TTATTATATAACAAACTAATAAATAAATTGTAA
3579833 TTATT-TATTAACAAA
1 TTATTATA-TAACAAA
3579848 TTTATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 29 0.69
33 13 0.31
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (33 bp):
TTATTATATAACAAACTAATAAATAAATTGTAA
Found at i:3579850 original size:21 final size:23
Alignment explanation
Indices: 3579824--3579875 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 23
3579814 ACTAATAAAT
3579824 AAATTTTAATTATTT-ATTAAC-
1 AAATTTTAATTATTTAATTAACA
*
3579845 AAA-TTT-ATTATTTAATTTACA
1 AAATTTTAATTATTTAATTAACA
3579866 AAATTTTAAT
1 AAATTTTAAT
3579876 ATTGATCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 7 0.27
20 8 0.31
21 6 0.23
22 3 0.12
23 2 0.08
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
AAATTTTAATTATTTAATTAACA
Found at i:3587563 original size:14 final size:14
Alignment explanation
Indices: 3587524--3587556 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3587514 CAAAATTTTA
3587524 AAGAC-GACATAAT
1 AAGACAGACATAAT
3587537 AAGACAGACATAAT
1 AAGACAGACATAAT
3587551 AAGACA
1 AAGACA
3587557 ACGATAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (14 bp):
AAGACAGACATAAT
Found at i:3588071 original size:24 final size:24
Alignment explanation
Indices: 3588026--3588071 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3588016 TTTATAATGA
* *
3588026 GAAATCCAATAGCAAAATAAAATT
1 GAAATCCAAGAACAAAATAAAATT
3588050 GAAATCCAAGAACATAAA-AAAA
1 GAAATCCAAGAACA-AAATAAAA
3588072 GATAGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.63, C:0.13, G:0.09, T:0.15
Consensus pattern (24 bp):
GAAATCCAAGAACAAAATAAAATT
Found at i:3589941 original size:24 final size:24
Alignment explanation
Indices: 3589914--3589964 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3589904 TAAAAAAATT
*
3589914 AAATTAATAATATA-TTAATTAATA
1 AAATTAA-AATATACATAATTAATA
*
3589938 AAATTAAAATATACATATTTAATA
1 AAATTAAAATATACATAATTAATA
3589962 AAA
1 AAA
3589965 AATTAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAATTAAAATATACATAATTAATA
Found at i:3589944 original size:29 final size:26
Alignment explanation
Indices: 3589906--3589970 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 26
3589896 AAAATATATA
*
3589906 AAAAAATTAAATTAATA-ATATATTAATT
1 AAAAAATTAAAAT-ATACATAT-TTAA-T
3589934 AATAAAATTAAAATATACATATTTAAT
1 AA-AAAATTAAAATATACATATTTAAT
3589961 AAAAAATTAA
1 AAAAAATTAA
3589971 TATAAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
26 8 0.24
27 3 0.09
28 9 0.26
29 14 0.41
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAAATTAAAATATACATATTTAAT
Found at i:3589972 original size:24 final size:25
Alignment explanation
Indices: 3589914--3589974 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 25
3589904 TAAAAAAATT
*
3589914 AAATTAATA-ATATATTAATTAATA
1 AAATTAATATACATATTAATTAATA
3589938 AAATTAAAATATACATATTTAA-TAA-A
1 AAATT--AATATACATA-TTAATTAATA
3589964 AAATTAATATA
1 AAATTAATATA
3589975 AAAATTATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
24 11 0.34
26 10 0.31
27 7 0.22
28 4 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATTAATATACATATTAATTAATA
Found at i:3609576 original size:3 final size:3
Alignment explanation
Indices: 3609547--3609604 Score: 71
Period size: 3 Copynumber: 17.7 Consensus size: 3
3609537 ATAAAATATC
3609547 AAT AATT AAT AATT CAAT GAAT CAAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AA-T -AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT
3609594 AAT AAT AAT AA
1 AAT AAT AAT AA
3609605 ATACAATTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
3 37 0.74
4 11 0.22
5 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3609726 original size:28 final size:26
Alignment explanation
Indices: 3609695--3609755 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
3609685 TAAATATTTT
*
3609695 TATTTAAAATTATTTATAATAAATAAAA
1 TATTTAAAACTA--TATAATAAATAAAA
*
3609723 TA-TTCAAACTATATAATAAATAAAA
1 TATTTAAAACTATATAATAAATAAAA
*
3609748 -ATATAAAA
1 TATTTAAAA
3609756 AACAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
24 1 0.04
25 18 0.64
27 7 0.25
28 2 0.07
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (26 bp):
TATTTAAAACTATATAATAAATAAAA
Found at i:3610806 original size:34 final size:35
Alignment explanation
Indices: 3610768--3610839 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 35
3610758 GCTGTATTTC
3610768 TACGTATTAGGTGTT-GGAGGTGCTATTTGAGCAG
1 TACGTATTAGGTGTTGGGAGGTGCTATTTGAGCAG
3610802 TACGTATTAGGTGTTGGAGGAGGTGCTATTTGAGCAG
1 TACGTATTAGGTGTT-G-GGAGGTGCTATTTGAGCAG
3610839 T
1 T
3610840 TAATATCTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 15 0.43
37 20 0.57
ACGTcount: A:0.21, C:0.08, G:0.36, T:0.35
Consensus pattern (35 bp):
TACGTATTAGGTGTTGGGAGGTGCTATTTGAGCAG
Found at i:3612926 original size:22 final size:22
Alignment explanation
Indices: 3612901--3612944 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3612891 ATTTTCTGTC
3612901 CTTAATTCTAGGA-ATACAAATA
1 CTTAATTCTA-GATATACAAATA
*
3612923 CTTAATTTTAGATATACAAATA
1 CTTAATTCTAGATATACAAATA
3612945 TAAATAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (22 bp):
CTTAATTCTAGATATACAAATA
Found at i:3613668 original size:20 final size:21
Alignment explanation
Indices: 3613643--3613695 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
3613633 GATATTTTTA
3613643 AATATTTATATTTT-AAAAAT
1 AATATTTATATTTTAAAAAAT
3613663 AATATTTTATATTTTAAAAAAT
1 AATA-TTTATATTTTAAAAAAT
3613685 AATATTT-TATT
1 AATATTTATATT
3613696 AATTTCGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.26
21 13 0.42
22 10 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATATTTATATTTTAAAAAAT
Found at i:3613673 original size:21 final size:22
Alignment explanation
Indices: 3613643--3613694 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
3613633 GATATTTTTA
3613643 AATA-TTTATATTTT-AAAAAT
1 AATATTTTATATTTTAAAAAAT
3613663 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
3613685 AATATTTTAT
1 AATATTTTAT
3613695 TAATTTCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 10 0.33
22 16 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:3617378 original size:22 final size:22
Alignment explanation
Indices: 3617338--3617380 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3617328 ATCTTCTGTC
*
3617338 CTTAATTCTAGGGACACAAATA
1 CTTAATTCTAGAGACACAAATA
* *
3617360 CTTAATTCTAGATATACAAAT
1 CTTAATTCTAGAGACACAAAT
3617381 GTAAATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (22 bp):
CTTAATTCTAGAGACACAAATA
Found at i:3618682 original size:20 final size:20
Alignment explanation
Indices: 3618657--3618697 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3618647 TTTTCTAACG
3618657 ATGGTTTAGAACAGTTATAT
1 ATGGTTTAGAACAGTTATAT
3618677 ATGGTTTAGAACAGTTATAT
1 ATGGTTTAGAACAGTTATAT
3618697 A
1 A
3618698 GAACATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
ATGGTTTAGAACAGTTATAT
Found at i:3619253 original size:18 final size:18
Alignment explanation
Indices: 3619196--3619255 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
3619186 TACAGAAGAA
3619196 ATGTTTCAAAAACTGCTT
1 ATGTTTCAAAAACTGCTT
* * **
3619214 GTGTTTTAGCAA--GCATT
1 ATGTTTCAAAAACTGC-TT
3619231 AATGTTTCAAAAACTGCTT
1 -ATGTTTCAAAAACTGCTT
3619250 ATGTTT
1 ATGTTT
3619256 TAGGTAGCAT
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
16 2 0.07
17 2 0.07
18 22 0.73
19 2 0.07
20 2 0.07
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (18 bp):
ATGTTTCAAAAACTGCTT
Found at i:3624398 original size:18 final size:18
Alignment explanation
Indices: 3624375--3624411 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3624365 TAATATAGTA
**
3624375 ATTTTTTATTTTAAAAAT
1 ATTTTTTATAATAAAAAT
3624393 ATTTTTTATAATAAAAAT
1 ATTTTTTATAATAAAAAT
3624411 A
1 A
3624412 CTTCTTGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTTTATAATAAAAAT
Found at i:3625500 original size:14 final size:13
Alignment explanation
Indices: 3625481--3625511 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
3625471 TATAATAAAT
3625481 TTTATTTATTTATA
1 TTTATTTA-TTATA
3625495 TTTATTTATTATA
1 TTTATTTATTATA
3625508 TTTA
1 TTTA
3625512 ATAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTATTATA
Found at i:3629838 original size:41 final size:41
Alignment explanation
Indices: 3629781--3629862 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
3629771 AAACTAAGCA
*
3629781 GTGATTATGCTGGTAGACTCAGGCAGCACGTATAATTTTTT
1 GTGATTATGCTAGTAGACTCAGGCAGCACGTATAATTTTTT
* *
3629822 GTGATTATGCTAGTAGACTTAGGCAGCATGTATAATTTTTT
1 GTGATTATGCTAGTAGACTCAGGCAGCACGTATAATTTTTT
3629863 AAGTCAGGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (41 bp):
GTGATTATGCTAGTAGACTCAGGCAGCACGTATAATTTTTT
Found at i:3633902 original size:15 final size:15
Alignment explanation
Indices: 3633882--3633913 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3633872 GAAACCCGTC
3633882 TTCTAAATCTCATTG
1 TTCTAAATCTCATTG
*
3633897 TTCTAACTCTCATTG
1 TTCTAAATCTCATTG
3633912 TT
1 TT
3633914 TTTGTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (15 bp):
TTCTAAATCTCATTG
Found at i:3636570 original size:17 final size:16
Alignment explanation
Indices: 3636531--3636571 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
3636521 ATTAATAATA
3636531 AACTATAAATAAAAAAT
1 AACT-TAAATAAAAAAT
3636548 AA-TTAAATTAAAAAAT
1 AACTTAAA-TAAAAAAT
3636564 AACTTAAA
1 AACTTAAA
3636572 AATAGACTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 11 0.50
17 7 0.32
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (16 bp):
AACTTAAATAAAAAAT
Found at i:3636942 original size:14 final size:13
Alignment explanation
Indices: 3636923--3636953 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
3636913 ATAATAAATT
3636923 TTTATTTATTTATA
1 TTTATTTA-TTATA
3636937 TTTATTTATTATA
1 TTTATTTATTATA
3636950 TTTA
1 TTTA
3636954 ATAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTATTATA
Found at i:3641278 original size:41 final size:41
Alignment explanation
Indices: 3641221--3641302 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
3641211 AAACTAAGCA
* *
3641221 GTGATTATGCTGGTAGACTCAGGCAGCACGTATAATTTTTT
1 GTGATTATGCTAGTAGACCCAGGCAGCACGTATAATTTTTT
*
3641262 GTGATTATGCTAGTAGACCCAGGCAGCATGTATAATTTTTT
1 GTGATTATGCTAGTAGACCCAGGCAGCACGTATAATTTTTT
3641303 AAGTCAGGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (41 bp):
GTGATTATGCTAGTAGACCCAGGCAGCACGTATAATTTTTT
Found at i:3648746 original size:26 final size:29
Alignment explanation
Indices: 3648699--3648751 Score: 76
Period size: 26 Copynumber: 1.9 Consensus size: 29
3648689 TTTTTTTACG
3648699 TTTTGATAATAAAAATCATAAAATTTTAA
1 TTTTGATAATAAAAATCATAAAATTTTAA
*
3648728 TTTT-ATAA-AAAAAT-TTAAAATTTT
1 TTTTGATAATAAAAATCATAAAATTTT
3648752 TTTAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 6 0.26
28 4 0.17
29 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TTTTGATAATAAAAATCATAAAATTTTAA
Found at i:3649358 original size:4 final size:4
Alignment explanation
Indices: 3649344--3649416 Score: 55
Period size: 4 Copynumber: 19.0 Consensus size: 4
3649334 TTTATATATA
* * * * *
3649344 AATT AAAT AATT AATT -ATT AAAT CA-T AATT AAAT AATT AATT AATA
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
*
3649390 AATT -A-T AATAT AATT AAAT AATT AATT
1 AATT AATT AAT-T AATT AATT AATT AATT
3649417 TCACACAATA
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
2 1 0.02
3 7 0.13
4 41 0.77
5 4 0.08
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (4 bp):
AATT
Found at i:3649376 original size:11 final size:10
Alignment explanation
Indices: 3649360--3649409 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
3649350 ATAATTAATT
3649360 ATTAAATCATA
1 ATTAAAT-ATA
3649371 ATTAAATAATTA
1 ATTAAAT-A-TA
3649383 ATT-AATA-A
1 ATTAAATATA
3649391 ATTATAATATA
1 ATTA-AATATA
3649402 ATTAAATA
1 ATTAAATA
3649410 ATTAATTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
8 4 0.12
10 9 0.26
11 16 0.47
12 5 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTAAATATA
Found at i:3649377 original size:26 final size:26
Alignment explanation
Indices: 3649344--3649415 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 26
3649334 TTTATATATA
*
3649344 AATTAAATAATTAATTATTAAATCAT
1 AATTAAATAATTAATTAATAAATCAT
*
3649370 AATTAAATAATTAATTAATAAATTAT
1 AATTAAATAATTAATTAATAAATCAT
* *
3649396 AATATAATTAAATAATTAAT
1 AAT-TAAATAATTAATTAAT
3649416 TTCACACAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 27 0.66
27 14 0.34
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTAAATAATTAATTAATAAATCAT
Found at i:3653763 original size:40 final size:41
Alignment explanation
Indices: 3653691--3653771 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
3653681 AATAGTAAAC
*
3653691 AAGAAAAAAATAATTCATTATAATATTTTTTTTTTCAATTA
1 AAGAAAAAAATAATTCATTATAATATTATTTTTTTCAATTA
3653732 AAGAAAAAAATAATTCATTATAATA-TATTTTTTTCAATTA
1 AAGAAAAAAATAATTCATTATAATATTATTTTTTTCAATTA
3653772 TAACTTTTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 14 0.36
41 25 0.64
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (41 bp):
AAGAAAAAAATAATTCATTATAATATTATTTTTTTCAATTA
Found at i:3654145 original size:15 final size:14
Alignment explanation
Indices: 3654122--3654151 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3654112 ATAAAAATAA
3654122 TTTTTTTTAACTTT
1 TTTTTTTTAACTTT
3654136 TTTTTCTTTAACTTT
1 TTTTT-TTTAACTTT
3654151 T
1 T
3654152 CTCTCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTTAACTTT
Found at i:3658722 original size:2 final size:2
Alignment explanation
Indices: 3658715--3658742 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3658705 CATTGTTATC
3658715 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
3658743 CTGTCAGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3664654 original size:20 final size:21
Alignment explanation
Indices: 3664625--3664664 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3664615 TAATAAAATC
*
3664625 TTTTAGTTT-ATTAATTTTAA
1 TTTTAATTTAATTAATTTTAA
*
3664645 TTTTAATTTAATTATTTTTA
1 TTTTAATTTAATTAATTTTA
3664665 GTAAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTTAATTTAATTAATTTTAA
Found at i:3667392 original size:19 final size:21
Alignment explanation
Indices: 3667349--3667404 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
3667339 ATTGCATGAA
*
3667349 TATTTTTATTTTA-GTTATCC
1 TATTTTTATTTTATTTTATCC
*
3667369 TA-TTTTATTTTATTTTATTC
1 TATTTTTATTTTATTTTATCC
*
3667389 -ATTTTTATTTAATTTT
1 TATTTTTATTTTATTTT
3667405 TATTTTCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTATTTTATTTTATCC
Found at i:3672194 original size:18 final size:18
Alignment explanation
Indices: 3672173--3672221 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3672163 ACAAAACAAC
3672173 ATAAA-TAAAATAAAAAAA
1 ATAAAGTAAAA-AAAAAAA
* *
3672191 ATAAAGTCAAAACAAAAA
1 ATAAAGTAAAAAAAAAAA
3672209 ATAAAGTGAAAAA
1 ATAAAGT-AAAAA
3672222 TAGAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (18 bp):
ATAAAGTAAAAAAAAAAA
Found at i:3672209 original size:19 final size:18
Alignment explanation
Indices: 3672186--3672220 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3672176 AATAAAATAA
3672186 AAAAAATAAAGTCAAAAC
1 AAAAAATAAAGTCAAAAC
*
3672204 AAAAAATAAAGTGAAAA
1 AAAAAATAAAGTCAAAA
3672221 ATAGAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.11
Consensus pattern (18 bp):
AAAAAATAAAGTCAAAAC
Found at i:3672221 original size:32 final size:32
Alignment explanation
Indices: 3672150--3672213 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
3672140 ATAATAAGAG
3672150 TAAATAAAAATAAACAAAACAACATAAATAAAA
1 TAAA-AAAAATAAACAAAACAACATAAATAAAA
3672183 TAAAAAAAATAAAGTCAAAACAA-A-AAATAAA
1 TAAAAAAAATAAA--CAAAACAACATAAATAAA
3672214 GTGAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 16 0.55
33 5 0.17
34 8 0.28
ACGTcount: A:0.77, C:0.08, G:0.02, T:0.14
Consensus pattern (32 bp):
TAAAAAAAATAAACAAAACAACATAAATAAAA
Found at i:3674425 original size:23 final size:22
Alignment explanation
Indices: 3674345--3674425 Score: 69
Period size: 21 Copynumber: 3.7 Consensus size: 22
3674335 TTTTTAAAAA
*
3674345 TTTTCAAATGAGAATCTTTG-AG
1 TTTTTAAATGAGAATC-TTGAAG
*
3674367 -TTTTAAAAGAGAATCTTGAAG
1 TTTTTAAATGAGAATCTTGAAG
**
3674388 TTTTTTTAT-ATGAATCTTGAAAG
1 TTTTTAAATGA-GAATCTTG-AAG
*
3674411 TTTTTGAATGAGAAT
1 TTTTTAAATGAGAAT
3674426 TTTTTAATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 3 0.06
21 16 0.34
22 13 0.28
23 14 0.30
24 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (22 bp):
TTTTTAAATGAGAATCTTGAAG
Found at i:3674712 original size:21 final size:21
Alignment explanation
Indices: 3674677--3674754 Score: 57
Period size: 22 Copynumber: 3.6 Consensus size: 21
3674667 TTTTGAATGA
*
3674677 GAATTTATGGAATTTTAAATTT
1 GAATTT-TTGAATTTTAAATTT
*** *
3674699 GAATTTTTGAATTTTGGGTGT
1 GAATTTTTGAATTTTAAATTT
* * *
3674720 GAATCTTTAGATTTTTTTAATTT
1 GAAT-TTTTGA-ATTTTAAATTT
3674743 GAATTTTTGAAT
1 GAATTTTTGAAT
3674755 GTTGGATATG
Statistics
Matches: 41, Mismatches: 13, Indels: 5
0.69 0.22 0.08
Matches are distributed among these distances:
21 15 0.37
22 16 0.39
23 10 0.24
ACGTcount: A:0.28, C:0.01, G:0.17, T:0.54
Consensus pattern (21 bp):
GAATTTTTGAATTTTAAATTT
Found at i:3674778 original size:44 final size:44
Alignment explanation
Indices: 3674689--3674778 Score: 101
Period size: 44 Copynumber: 2.0 Consensus size: 44
3674679 ATTTATGGAA
* * * * *
3674689 TTTTAAATTTGAATTTTTGAATTTTGGGTGTGAATCTTTAGATT
1 TTTTAAATTTGAATTTTTGAATGTTGGATATGAACCTTCAGATT
* *
3674733 TTTTTAATTTGAATTTTTGAATGTTGGATATGAGCCTTGCA-ATT
1 TTTTAAATTTGAATTTTTGAATGTTGGATATGAACCTT-CAGATT
3674777 TT
1 TT
3674779 GATGTGAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 37 0.97
45 1 0.03
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.53
Consensus pattern (44 bp):
TTTTAAATTTGAATTTTTGAATGTTGGATATGAACCTTCAGATT
Found at i:3674848 original size:18 final size:17
Alignment explanation
Indices: 3674825--3674874 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
3674815 TCTTAAATGC
3674825 GAAACTGAAAATTCTTGT
1 GAAACT-AAAATTCTTGT
* *
3674843 GAAACTAAAAATCTAGT
1 GAAACTAAAATTCTTGT
*
3674860 GAATCT-AAATTCTTG
1 GAAACTAAAATTCTTG
3674875 CAAATTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 7 0.26
17 14 0.52
18 6 0.22
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (17 bp):
GAAACTAAAATTCTTGT
Found at i:3674954 original size:18 final size:18
Alignment explanation
Indices: 3674931--3675011 Score: 94
Period size: 18 Copynumber: 4.6 Consensus size: 18
3674921 TTCCGATCTC
3674931 AAATTCTTGTAAACCTGA
1 AAATTCTTGTAAACCTGA
*
3674949 AAATTCTTGTGAAA-CTAA
1 AAATTCTTGT-AAACCTGA
* *
3674967 AAATTCTTATAAATCTGA
1 AAATTCTTGTAAACCTGA
* *
3674985 AAATTCTTGCAAACTTGA
1 AAATTCTTGTAAACCTGA
3675003 AAATT-TTGT
1 AAATTCTTGT
3675012 GAATATTAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.11
18 44 0.83
19 3 0.06
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (18 bp):
AAATTCTTGTAAACCTGA
Found at i:3675007 original size:36 final size:36
Alignment explanation
Indices: 3674931--3674999 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
3674921 TTCCGATCTC
* *
3674931 AAATTCTTGTAAACCTGAAAATTCTTGTGAAACTAA
1 AAATTCTTATAAACCTGAAAATTCTTGTCAAACTAA
*
3674967 AAATTCTTATAAATCTGAAAATTCTTG-CAAACT
1 AAATTCTTATAAACCTGAAAATTCTTGTCAAACT
3675000 TGAAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 5 0.17
36 25 0.83
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (36 bp):
AAATTCTTATAAACCTGAAAATTCTTGTCAAACTAA
Found at i:3678886 original size:60 final size:58
Alignment explanation
Indices: 3678793--3679308 Score: 722
Period size: 60 Copynumber: 8.7 Consensus size: 58
3678783 TTTTTTGTAG
3678793 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTT--ATTTCT-AA
*
3678853 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAA-TTT-ATTTCT-AA
* ** *
3678913 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTTATTTCTAA
*
3678972 GGAAAATTGATACTTTCAACTCTTCCCCAAAAATA-TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTCTAA
*
3679029 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAATTTATTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA---TTTTTTTGGAAATTTA-TTTC---TAA
*
3679094 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGGAAATTTA-TTCTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTC-TAA
* * *
3679151 GGAAAATTGATACTTTCAACTTTT-CCCTAAAATATTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTTATTTCTAA
3679209 GGAAAATTGATACTTTCAACTTTTCCCCCAAAAATA-TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTT-CCCCAAAAATATTTTTTTGGAAATTTATTTCTAA
*
3679267 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
3679309 TTGGAATTTT
Statistics
Matches: 420, Mismatches: 19, Indels: 36
0.88 0.04 0.08
Matches are distributed among these distances:
56 8 0.02
57 90 0.21
58 90 0.21
59 44 0.10
60 102 0.24
61 44 0.10
62 4 0.01
65 38 0.09
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.45
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTCTAA
Found at i:3679219 original size:58 final size:57
Alignment explanation
Indices: 3678793--3679309 Score: 680
Period size: 58 Copynumber: 8.7 Consensus size: 57
3678783 TTTTTTGTAG
* *
3678793 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAT-TTTTTTTTGAAATTT--ATTTCT-AA
*
3678853 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAT-TTTTTTTTGAAA-TTT-ATTTCT-AA
* *
3678913 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAA-ATTTTTTTTTGAAATTTATTTCTAA
* * * *
3678972 GGAAAATTGATACTTTCAACTCTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATTTTTTTTTGAAATTTATTTCTAA
3679029 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAATTTATTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAA-A-TTTTTTTTT-GAAATTTA-TTTC---TAA
* *
3679094 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTA-TTCTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATTTTTTTTTGAAATTTATTTC-TAA
*
3679151 GGAAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAA-ATTTTTTTTTGAAATTTATTTCTAA
* * *
3679209 GGAAAATTGATACTTTCAACTTTTCCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTT-CCCTAAAAATTTTTTTTTGAAATTTATTTCTAA
3679267 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAT-TTTTTTTT
3679310 TGGAATTTTT
Statistics
Matches: 415, Mismatches: 26, Indels: 34
0.87 0.05 0.07
Matches are distributed among these distances:
57 92 0.22
58 102 0.25
59 45 0.11
60 93 0.22
61 34 0.08
62 13 0.03
63 1 0.00
64 4 0.01
65 31 0.07
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.45
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATTTTTTTTTGAAATTTATTTCTAA
Found at i:3679241 original size:238 final size:237
Alignment explanation
Indices: 3678793--3679314 Score: 871
Period size: 238 Copynumber: 2.2 Consensus size: 237
3678783 TTTTTTGTAG
*
3678793 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTTGGAAATTTCGATTTTCAAGGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTC-ATTTTCAAGGA
*
3678856 AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTTTCAAGGAAAATT
65 AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTTGATTTTCAAGGAAAATT
*
3678921 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTAAATTTATTTCTGAGGAAAATTGATACT
130 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCTGAGGAAAATTGATACT
3678986 TTCAACTCTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
195 TTCAACTCTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
3679029 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAATTT-ATTTTCTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTTGGAAATTTCATTTTC----A
*
3679093 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGGAAA-TTT-ATTCTT-AAGGA
61 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTTGATT-TTCAAGGA
3679154 AAATTGATACTTTCAACTTTTCCCT-AAAATATTTTTTTTTGAAATTTATTTCTGAGGAAAATTG
125 AAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCTGAGGAAAATTG
*
3679218 ATACTTTCAACTTTTCCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
190 ATACTTTCAACTCTT-CCCCAAAAATATTTTTTGGAAATTTATTTCTAA
3679267 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAA
3679315 TTTTTTATTT
Statistics
Matches: 272, Mismatches: 5, Indels: 17
0.93 0.02 0.06
Matches are distributed among these distances:
236 34 0.12
237 71 0.26
238 101 0.37
239 20 0.07
240 10 0.04
241 36 0.13
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (237 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTCATTTTCAAGGAA
AATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTTGATTTTCAAGGAAAATTG
ATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCTGAGGAAAATTGATACTT
TCAACTCTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
Found at i:3679402 original size:12 final size:11
Alignment explanation
Indices: 3679382--3679446 Score: 53
Period size: 12 Copynumber: 5.7 Consensus size: 11
3679372 AACCTAATCT
*
3679382 AATAAATAAAA
1 AATAAAAAAAA
3679393 AATAAAATAAACA
1 AATAAAA-AAA-A
*
3679406 AATAAACAAAGA
1 AATAAA-AAAAA
3679418 AAT-AAAAAAA
1 AATAAAAAAAA
*
3679428 ATTCAAAAAAAA
1 AAT-AAAAAAAA
3679440 AA-AAAAA
1 AATAAAAA
3679447 CCTGGAGCGG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
10 11 0.25
11 8 0.18
12 15 0.34
13 9 0.20
14 1 0.02
ACGTcount: A:0.82, C:0.05, G:0.02, T:0.12
Consensus pattern (11 bp):
AATAAAAAAAA
Found at i:3681190 original size:2 final size:2
Alignment explanation
Indices: 3681185--3681223 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3681175 GTATGTATAA
*
3681185 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3681224 ACAATCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Done.