Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397283.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_31.0, 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: 1333793
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 10515 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:599571 original size:2 final size:2
Alignment explanation
Indices: 599564--599599 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
599554 GATGGGTCAA
*
599564 CT CT CT CT CT CT CT CT CT AT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
599600 GTGGTGCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:606682 original size:16 final size:16
Alignment explanation
Indices: 606661--606699 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
606651 CAAAGAGATA
606661 AGAGAGAGCA-AGACAG
1 AGAGAGAG-AGAGACAG
606677 AGAGAGAGAGAGACAG
1 AGAGAGAGAGAGACAG
606693 AGAGAGA
1 AGAGAGA
606700 AAGGTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.51, C:0.08, G:0.41, T:0.00
Consensus pattern (16 bp):
AGAGAGAGAGAGACAG
Found at i:608864 original size:20 final size:22
Alignment explanation
Indices: 608831--608870 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
608821 AGATAGACCT
608831 TTTTGTTGTAAGTT-TTTTTTC
1 TTTTGTTGTAAGTTCTTTTTTC
*
608852 TTTT-TTGTCAGTTCTTTTT
1 TTTTGTTGTAAGTTCTTTTT
608871 GTTATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.07, C:0.07, G:0.12, T:0.72
Consensus pattern (22 bp):
TTTTGTTGTAAGTTCTTTTTTC
Found at i:611219 original size:67 final size:68
Alignment explanation
Indices: 611110--611243 Score: 234
Period size: 67 Copynumber: 2.0 Consensus size: 68
611100 TCGGGGGTTT
**
611110 TAGCATGCTGGAAATAAGAGAATGCTGCTAAGAGGATACTTGGACTTCAGGGATTATTAGAACCA
1 TAGCATGCTGGAAATAAGAGAATGCTGCTAAGAGGATACTTGGACTTCAGGGATTACGAGAACCA
611175 ATA
66 ATA
*
611178 TAGCATGCTGGAAATAAGA-AATGCTGCTAAGAGGATACTTGGACTTGAGGGATTACGAGAACCA
1 TAGCATGCTGGAAATAAGAGAATGCTGCTAAGAGGATACTTGGACTTCAGGGATTACGAGAACCA
611242 AT
66 AT
611244 GTAGTTAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
67 44 0.70
68 19 0.30
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (68 bp):
TAGCATGCTGGAAATAAGAGAATGCTGCTAAGAGGATACTTGGACTTCAGGGATTACGAGAACCA
ATA
Found at i:611853 original size:50 final size:49
Alignment explanation
Indices: 611799--611946 Score: 208
Period size: 48 Copynumber: 3.0 Consensus size: 49
611789 TTTTTTTAGC
* * *
611799 TAGTAATGCTTTTCATCCATCTTTACTCTCTGTCCTCCCTTCGCTCATCT
1 TAGTAATGCTTTTCATCCATCTTTATTTTCTGT-CTCCCTTCTCTCATCT
** * *
611849 TAGTAATGCTTTTTGTCCATCTTTATTTTCTGTCT-ACTCCTCTCATCT
1 TAGTAATGCTTTTCATCCATCTTTATTTTCTGTCTCCCTTCTCTCATCT
611897 TAGTAATGCTTTTCATCCATCTTTATTTTCTGTACTCCCTTCTCTCATCT
1 TAGTAATGCTTTTCATCCATCTTTATTTTCTGT-CTCCCTTCTCTCATCT
611947 CCATCCCCTC
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
48 41 0.48
49 4 0.05
50 40 0.47
ACGTcount: A:0.15, C:0.29, G:0.07, T:0.49
Consensus pattern (49 bp):
TAGTAATGCTTTTCATCCATCTTTATTTTCTGTCTCCCTTCTCTCATCT
Found at i:613673 original size:15 final size:15
Alignment explanation
Indices: 613653--613686 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
613643 GGTTTGTCAC
613653 TGCTGTTTTGCACGG
1 TGCTGTTTTGCACGG
613668 TGCTGTTTTGCACGG
1 TGCTGTTTTGCACGG
613683 TGCT
1 TGCT
613687 AGGGTGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.21, G:0.32, T:0.41
Consensus pattern (15 bp):
TGCTGTTTTGCACGG
Found at i:616860 original size:2 final size:2
Alignment explanation
Indices: 616853--616885 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
616843 TTATTCAGTC
616853 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 A
616886 ACACAATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:629711 original size:2 final size:2
Alignment explanation
Indices: 629704--629741 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
629694 ATCAACATTG
629704 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
629742 TTATGCTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:635551 original size:2 final size:2
Alignment explanation
Indices: 635544--635588 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
635534 ATCAAGCAGG
635544 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
635585 GA GA
1 GA GA
635589 AATGTGTTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:635801 original size:15 final size:14
Alignment explanation
Indices: 635781--635814 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
635771 AGAAATTTTT
635781 AAAAAAAATAAAAGG
1 AAAAAAAATAAAA-G
635796 AAAAAAAATAAAAG
1 AAAAAAAATAAAAG
635810 AAAAA
1 AAAAA
635815 GTTAGTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (14 bp):
AAAAAAAATAAAAG
Found at i:642849 original size:21 final size:21
Alignment explanation
Indices: 642821--642864 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
642811 TCGTTGAAGC
*
642821 AAAGGCAAATACTA-GAACAG
1 AAAGGCAAAAACTAGGAACAG
*
642841 AAAGCGCAAAAATTAGGAACAG
1 AAAG-GCAAAAACTAGGAACAG
642863 AA
1 AA
642865 GAATGCGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 8 0.40
22 8 0.40
ACGTcount: A:0.57, C:0.14, G:0.20, T:0.09
Consensus pattern (21 bp):
AAAGGCAAAAACTAGGAACAG
Found at i:652141 original size:39 final size:39
Alignment explanation
Indices: 652098--652240 Score: 105
Period size: 39 Copynumber: 3.6 Consensus size: 39
652088 GAGCTTAATA
*
652098 ATATGATGAATATTGATTTATGAATGATTTGGTTTACTT
1 ATATGACGAATATTGATTTATGAATGATTTGGTTTACTT
* * *
652137 ATATGATGGAAAATTGGATTT-TCAAATGATTTGAGTTATAC--
1 ATATGA-CGAATATT-GATTTAT-GAATGATTTG-GTT-TACTT
* * * *
652178 ATATGACGAACATTG-TTCTATGAATGCTTTGGTTAATTT
1 ATATGACGAATATTGATT-TATGAATGATTTGGTTTACTT
* **
652217 ATGTGACGAATATCAATTTATGAA
1 ATATGACGAATATTGATTTATGAA
652241 CGAAAGGAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
37 1 0.01
38 5 0.06
39 33 0.41
40 16 0.20
41 20 0.25
42 3 0.04
43 3 0.04
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (39 bp):
ATATGACGAATATTGATTTATGAATGATTTGGTTTACTT
Found at i:658596 original size:32 final size:32
Alignment explanation
Indices: 658555--658620 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
658545 CAAAACGTTT
* *
658555 ATTCTGTGATTGATGAGTTGTATATGTATTAA
1 ATTCTGTGATTGATGAGTTGTACATGCATTAA
658587 ATTCTGTGATTGATGAGTTGTACATGCATTAA
1 ATTCTGTGATTGATGAGTTGTACATGCATTAA
658619 AT
1 AT
658621 GTTCTCTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (32 bp):
ATTCTGTGATTGATGAGTTGTACATGCATTAA
Found at i:662722 original size:21 final size:21
Alignment explanation
Indices: 662689--662728 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
662679 AAGTTGGGTT
*
662689 CTTGGTACAGAAATTGATGAG
1 CTTGGTACAGAAAGTGATGAG
662710 CTTGGTA-AGGAAAGTGATG
1 CTTGGTACA-GAAAGTGATG
662729 TCATTTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (21 bp):
CTTGGTACAGAAAGTGATGAG
Found at i:681973 original size:21 final size:22
Alignment explanation
Indices: 681940--681980 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
681930 CAGGCTGAGG
* *
681940 TGTCTCCTGCGTCTG-CGTATC
1 TGTCGCCTCCGTCTGACGTATC
681961 TGTCGCCTCCGTCTGACGTA
1 TGTCGCCTCCGTCTGACGTA
681981 GAAGTGCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.07, C:0.34, G:0.24, T:0.34
Consensus pattern (22 bp):
TGTCGCCTCCGTCTGACGTATC
Found at i:687672 original size:13 final size:13
Alignment explanation
Indices: 687654--687679 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
687644 ACACAAACTC
687654 AAAAACAAAAAAA
1 AAAAACAAAAAAA
687667 AAAAACAAAAAAA
1 AAAAACAAAAAAA
687680 TTAAGATAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAA
Found at i:693826 original size:32 final size:31
Alignment explanation
Indices: 693785--693848 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
693775 GTTTTAATTG
*
693785 TATTTTTTAAGGATAATTAATATTA-AAAAATA
1 TATTGTTTAA-GATAA-TAATATTAGAAAAATA
* *
693817 TATTGTTTAATATAATAATTTTAGAAAAATA
1 TATTGTTTAAGATAATAATATTAGAAAAATA
693848 T
1 T
693849 TTTTAGAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 7 0.25
31 12 0.43
32 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (31 bp):
TATTGTTTAAGATAATAATATTAGAAAAATA
Found at i:697806 original size:2 final size:2
Alignment explanation
Indices: 697799--697833 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
697789 TAAGATTCTT
697799 TA TA TA TA 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 TA TA TA TA T
697834 CTTCTGGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:705602 original size:43 final size:43
Alignment explanation
Indices: 705534--705617 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
705524 GCCAAAATGG
*
705534 AACAACAGAATTCCAAATTAAAGGCAAGGTCACAGACCATATT
1 AACAAAAGAATTCCAAATTAAAGGCAAGGTCACAGACCATATT
* * * *
705577 AACAAAAGAATTCTAAGTTACAGGCAAGGTCACGGACCATA
1 AACAAAAGAATTCCAAATTAAAGGCAAGGTCACAGACCATA
705618 GTAAGCATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (43 bp):
AACAAAAGAATTCCAAATTAAAGGCAAGGTCACAGACCATATT
Found at i:712308 original size:15 final size:15
Alignment explanation
Indices: 712290--712318 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
712280 AAAGGGCAAA
712290 AAAGTAAAATAATTT
1 AAAGTAAAATAATTT
712305 AAAGTAAAATAATT
1 AAAGTAAAATAATT
712319 AAAAAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
AAAGTAAAATAATTT
Found at i:719243 original size:18 final size:18
Alignment explanation
Indices: 719220--719257 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
719210 CGGCATGATC
719220 TGGTAACCAAGAGCAATT
1 TGGTAACCAAGAGCAATT
*
719238 TGGTAATCAAGAGCAATT
1 TGGTAACCAAGAGCAATT
719256 TG
1 TG
719258 ATTAACATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (18 bp):
TGGTAACCAAGAGCAATT
Found at i:720510 original size:16 final size:17
Alignment explanation
Indices: 720484--720518 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
720474 ATTGCTTCAA
720484 TTAAGTCCCTCTAACAT
1 TTAAGTCCCTCTAACAT
*
720501 TTAA-TCCCTCTCACAT
1 TTAAGTCCCTCTAACAT
720517 TT
1 TT
720519 TTCATCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.26, C:0.31, G:0.03, T:0.40
Consensus pattern (17 bp):
TTAAGTCCCTCTAACAT
Found at i:720629 original size:152 final size:151
Alignment explanation
Indices: 720347--720654 Score: 370
Period size: 152 Copynumber: 2.0 Consensus size: 151
720337 AATTATTTCA
* * * *
720347 ATTTAGTCTCTCTAACATTTTTCGTCTAAATTAATTGTTACAGTGTGGAAGTCAACATTGATGTG
1 ATTTAATCCCTCTAACATTTTTCATCTAAATTAATTGTTACACTGTGG-AGTCAACATTGATGTG
* * * * * * *
720412 ACGTATAGAAGGGGTTTTGGTTACTGATATGGCAGTGCCATGTCACATTTCAAGATCGGAGAATT
65 ACATATAAAAGGGGTTTTGATTACTGATATGACAGTGCCATATCACATTTCAAGATCGAAAAATT
720477 GCTTCAA-TTAAGTCCCTCTAAC
130 GCTTCAATTTAA-TCCCTCTAAC
* *
720499 ATTTAATCCCTCTCACATTTTTCATCTAAATTAATTGTTATACTGCTGCG-GTCAACATTGATGT
1 ATTTAATCCCTCTAACATTTTTCATCTAAATTAATTGTTACACTG-TG-GAGTCAACATTGATGT
* * * *
720563 GACATATAAAATGGGTTTTGATTGCTGATATGATAGTGTCATATCACACTTT-AAGATCGAAAAA
64 GACATATAAAAGGGGTTTTGATTACTGATATGACAGTGCCATATCACA-TTTCAAGATCGAAAAA
* * *
720627 TTGTTTCAATTTAATCCCTTTAAT
128 TTGCTTCAATTTAATCCCTCTAAC
720651 ATTT
1 ATTT
720655 TTTATCTAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
152 122 0.92
153 9 0.07
154 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (151 bp):
ATTTAATCCCTCTAACATTTTTCATCTAAATTAATTGTTACACTGTGGAGTCAACATTGATGTGA
CATATAAAAGGGGTTTTGATTACTGATATGACAGTGCCATATCACATTTCAAGATCGAAAAATTG
CTTCAATTTAATCCCTCTAAC
Found at i:721345 original size:55 final size:55
Alignment explanation
Indices: 721279--721387 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 55
721269 ACACCAGCAA
*
721279 CCAAAACCCCTTTGTATGCCACGTCACAATATCGGTCAATTTGAACAAAAAAAAT
1 CCAAAACCCCTTTGTATGCCACGTCACAATAACGGTCAATTTGAACAAAAAAAAT
* * *
721334 CCAAAACCCCTTTGTATGTCACGTCATAATAACGGTTAATTTGAACAAAAAAAA
1 CCAAAACCCCTTTGTATGCCACGTCACAATAACGGTCAATTTGAACAAAAAAAA
721388 ATATTAGAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (55 bp):
CCAAAACCCCTTTGTATGCCACGTCACAATAACGGTCAATTTGAACAAAAAAAAT
Found at i:734841 original size:11 final size:12
Alignment explanation
Indices: 734818--734842 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
734808 AATATTTACG
734818 TTTAAAAATTTT
1 TTTAAAAATTTT
734830 TTTAAAAATTTT
1 TTTAAAAATTTT
734842 T
1 T
734843 ATTTATCGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAAAAATTTT
Found at i:735508 original size:52 final size:52
Alignment explanation
Indices: 735452--735558 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
735442 TTAAAACTAT
735452 ATTTTAAACAAAGTAAATTTTAATAAAGCACATTAATTATAAATGATTAATA
1 ATTTTAAACAAAGTAAATTTTAATAAAGCACATTAATTATAAATGATTAATA
735504 ATTTTAAACAAAGTAAATTTTAATAAAGCACATTAATTATAAATGATTAATA
1 ATTTTAAACAAAGTAAATTTTAATAAAGCACATTAATTATAAATGATTAATA
735556 ATT
1 ATT
735559 AAAAATATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (52 bp):
ATTTTAAACAAAGTAAATTTTAATAAAGCACATTAATTATAAATGATTAATA
Found at i:742852 original size:24 final size:25
Alignment explanation
Indices: 742812--742858 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
742802 TAGTGAAAAA
742812 AAATATTATAGATATTT-TATATTT
1 AAATATTATAGATATTTATATATTT
*
742836 AAATATTA-ATATCATTTATATAT
1 AAATATTATAGAT-ATTTATATAT
742859 AATATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 12 0.60
25 5 0.25
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
AAATATTATAGATATTTATATATTT
Found at i:742855 original size:34 final size:34
Alignment explanation
Indices: 742817--742895 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 34
742807 AAAAAAAATA
*
742817 TTATAGAT-AT-TTTATATTTAAATATTAATATCAT
1 TTATAGATAATATTTAT-TTTAAAAATTAATAT-AT
* *
742851 TTATATATAATATTTATTTTAAAAATTAATGTAT
1 TTATAGATAATATTTATTTTAAAAATTAATATAT
*
742885 TTATATATAAT
1 TTATAGATAAT
742896 TATGATTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
34 20 0.50
35 15 0.38
36 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
TTATAGATAATATTTATTTTAAAAATTAATATAT
Found at i:743423 original size:22 final size:23
Alignment explanation
Indices: 743375--743428 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
743365 CTGATTTAAT
* *
743375 AATTTTTTAAATTTAAATTATGT
1 AATTTTTAAAATTTAAATTATGA
743398 AATTTTTAAAATTTTAAA-TAT-A
1 AATTTTTAAAA-TTTAAATTATGA
*
743420 AATTATTAA
1 AATTTTTAA
743429 TAATAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.30
23 13 0.48
24 6 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AATTTTTAAAATTTAAATTATGA
Found at i:744526 original size:9 final size:9
Alignment explanation
Indices: 744497--744571 Score: 50
Period size: 9 Copynumber: 8.2 Consensus size: 9
744487 CTTGAAACAT
744497 ATAAAT-AA
1 ATAAATAAA
744505 ATAGAATAGAA
1 ATA-AATA-AA
744516 ATGAAA-AAA
1 AT-AAATAAA
744525 ATAAATAAA
1 ATAAATAAA
*
744534 AT-AATAAT
1 ATAAATAAA
744542 ATAAATTAAA
1 ATAAA-TAAA
*
744552 A-AATTAAAA
1 ATAAAT-AAA
*
744561 AAAAATAAA
1 ATAAATAAA
744570 AT
1 AT
744572 TGATTGAGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 17
0.71 0.07 0.23
Matches are distributed among these distances:
8 14 0.26
9 24 0.45
10 8 0.15
11 6 0.11
12 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (9 bp):
ATAAATAAA
Found at i:750550 original size:20 final size:21
Alignment explanation
Indices: 750514--750557 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
750504 GCACAATGTT
750514 AGAAATATTTGAGAAGAAAGA
1 AGAAATATTTGAGAAGAAAGA
*
750535 AGAAAT-TTTTAGAAGAAAGA
1 AGAAATATTTGAGAAGAAAGA
750555 AGA
1 AGA
750558 GTATGACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (21 bp):
AGAAATATTTGAGAAGAAAGA
Found at i:751983 original size:21 final size:20
Alignment explanation
Indices: 751959--752002 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
751949 TGAGATTCTT
751959 AGAAATATTTGA-AAAGAAAGA
1 AGAAAT-TTTGAGAAA-AAAGA
*
751980 AGAAATTTTTAGAAAAAAGA
1 AGAAATTTTGAGAAAAAAGA
752000 AGA
1 AGA
752003 GTATGACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.20
Consensus pattern (20 bp):
AGAAATTTTGAGAAAAAAGA
Found at i:754340 original size:15 final size:16
Alignment explanation
Indices: 754313--754342 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
754303 TTATTTACGG
754313 AAAAATATCTACCAAT
1 AAAAATATCTACCAAT
754329 AAAAATAT-TACCAA
1 AAAAATATCTACCAA
754343 GTGTCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATATCTACCAAT
Found at i:756885 original size:15 final size:14
Alignment explanation
Indices: 756865--756908 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
756855 ATAATAAAAT
756865 ATAATAATTTAATTA
1 ATAATAA-TTAATTA
756880 ATAATAATTAATTA
1 ATAATAATTAATTA
*
756894 ACTAATTATTAATTA
1 A-TAATAATTAATTA
756909 TAAAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAATAATTAATTA
Found at i:761915 original size:3 final size:3
Alignment explanation
Indices: 761907--761945 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
761897 AATAGACAGA
761907 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
761946 GTTTAGTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:762318 original size:21 final size:24
Alignment explanation
Indices: 762292--762346 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
762282 GATTTGGTCT
762292 AAAAAATAA-ATAA-ATAA-ATAA
1 AAAAAATAATATAATATAATATAA
762313 ATAAAAATAATATAATATAATATAA
1 A-AAAAATAATATAATATAATATAA
*
762338 AAAGAATAA
1 AAAAAATAA
762347 GACCCAGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.03
22 8 0.28
23 4 0.14
24 11 0.38
25 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAAAATAATATAATATAATATAA
Found at i:772724 original size:30 final size:30
Alignment explanation
Indices: 772620--772724 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
772610 TCAAAAAATT
* *
772620 TTAAATAAGTCTTTATACTTTTA--TTGCA-
1 TTAAATAAGTCCTTATATTTTTATTTTG-AG
* *
772648 TTTAATCAAGTCTTTATATTTTTATTTTGAG
1 TTAAAT-AAGTCCTTATATTTTTATTTTGAG
* *
772679 TCAAATAA-ACTCTTATATTTTTATTTTGAG
1 TTAAATAAGTC-CTTATATTTTTATTTTGAG
772709 TTAAATAAGTCCTTAT
1 TTAAATAAGTCCTTAT
772725 TACTAATGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
28 5 0.08
29 17 0.27
30 33 0.52
31 8 0.13
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (30 bp):
TTAAATAAGTCCTTATATTTTTATTTTGAG
Found at i:778312 original size:21 final size:21
Alignment explanation
Indices: 778288--778328 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
778278 CAACTCCCTG
778288 ATTTGGTGCAACGTTCACTTT
1 ATTTGGTGCAACGTTCACTTT
778309 ATTTGGTGCAACGTTCACTT
1 ATTTGGTGCAACGTTCACTT
778329 CATTCATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (21 bp):
ATTTGGTGCAACGTTCACTTT
Found at i:793076 original size:2 final size:2
Alignment explanation
Indices: 793064--793101 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
793054 CTTTTTCCTT
793064 TA TA CTA TA TA 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 TA TA TA TA TA T
793102 CTATTTGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:794193 original size:2 final size:2
Alignment explanation
Indices: 794186--794211 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
794176 TTTGAAAGAA
794186 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
794212 GAGGTGGGTT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:796782 original size:28 final size:28
Alignment explanation
Indices: 796730--796783 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
796720 ATATACATAG
* ** *
796730 TTAATAGTATCGTAATGTAATTGTATTA
1 TTAAGAGTATCGTAATCAAACTGTATTA
796758 TTAAGAGTATCGTAATCAAACTGTAT
1 TTAAGAGTATCGTAATCAAACTGTAT
796784 AATGATGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (28 bp):
TTAAGAGTATCGTAATCAAACTGTATTA
Found at i:808971 original size:28 final size:29
Alignment explanation
Indices: 808936--809000 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
808926 AATCTTAAAT
808936 TATTTTTAAAAAATT-AAATAAATCTTTA
1 TATTTTTAAAAAATTCAAATAAATCTTTA
** * *
808964 TATTTTTATTACATTCAAATAAATTTTTA
1 TATTTTTAAAAAATTCAAATAAATCTTTA
808993 TATTTTTA
1 TATTTTTA
809001 TTTTGAGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 12 0.38
29 20 0.62
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (29 bp):
TATTTTTAAAAAATTCAAATAAATCTTTA
Found at i:809022 original size:30 final size:30
Alignment explanation
Indices: 808979--809084 Score: 149
Period size: 30 Copynumber: 3.5 Consensus size: 30
808969 TTATTACATT
*
808979 CAAATAAATTTTTATATTTTTATTTTGAGC
1 CAAATAAACTTTTATATTTTTATTTTGAGC
** *
809009 CAAATATGCTTTTATACTTTTATTTTGAGC
1 CAAATAAACTTTTATATTTTTATTTTGAGC
* * *
809039 CAAATAAACTCTTATATTTTTATTTTTAGT
1 CAAATAAACTTTTATATTTTTATTTTGAGC
809069 CAAATAAACTTTTATA
1 CAAATAAACTTTTATA
809085 ACTAATACTT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (30 bp):
CAAATAAACTTTTATATTTTTATTTTGAGC
Found at i:814216 original size:51 final size:51
Alignment explanation
Indices: 814152--814257 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
814142 AAACTCTAAA
* * *
814152 CATTTTGAGCATTTTAAAGT-GATTTTTGATACACG-AAAAAAACCTTATGAG
1 CATTTTAAACATTTTAAAGTAG-TTTTTAATACACGAAAAAAAACCTT-TGAG
* * *
814203 CATTTTAAACATTTTAGAGTAGTTTTTAATAGATGAAAAAAAACCTTTGAG
1 CATTTTAAACATTTTAAAGTAGTTTTTAATACACGAAAAAAAACCTTTGAG
814254 CATT
1 CATT
814258 CTTCATCAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 35 0.74
52 12 0.26
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (51 bp):
CATTTTAAACATTTTAAAGTAGTTTTTAATACACGAAAAAAAACCTTTGAG
Found at i:814666 original size:22 final size:22
Alignment explanation
Indices: 814616--814668 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
814606 AATGATTAAG
*
814616 TCACACAATATTTAAAAACTAA
1 TCACACAATACTTAAAAACTAA
* *
814638 TCTCACAATACTTAAAAATTAA
1 TCACACAATACTTAAAAACTAA
*
814660 TGACACAAT
1 TCACACAAT
814669 GTCTAAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.28
Consensus pattern (22 bp):
TCACACAATACTTAAAAACTAA
Found at i:829969 original size:4 final size:4
Alignment explanation
Indices: 829960--829994 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
829950 AAATTCGAGA
829960 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
829995 ATTAGAATCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:836062 original size:4 final size:4
Alignment explanation
Indices: 836053--836083 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
836043 AGAGGGAAGG
836053 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
836084 CGTATACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:837372 original size:9 final size:9
Alignment explanation
Indices: 837358--837395 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
837348 TCCAGGGACA
837358 ATTATTATG
1 ATTATTATG
837367 ATTATTATG
1 ATTATTATG
837376 ATTATTATG
1 ATTATTATG
*
837385 ATTATGATG
1 ATTATTATG
837394 AT
1 AT
837396 AGATAATGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (9 bp):
ATTATTATG
Found at i:838836 original size:2 final size:2
Alignment explanation
Indices: 838829--838858 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
838819 AGTGATTTGA
*
838829 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
838859 TTTCTTCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:839104 original size:3 final size:3
Alignment explanation
Indices: 839096--839120 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
839086 TCTGGCGACG
839096 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
839121 CAACAACACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:842166 original size:2 final size:2
Alignment explanation
Indices: 842161--842187 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
842151 TCTCTTGCTT
842161 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
842188 GTGTTTTCTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:850111 original size:13 final size:13
Alignment explanation
Indices: 850076--850117 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
850066 TCAGTATGTC
850076 ATATCATTAT-TTA
1 ATAT-ATTATATTA
* *
850089 TTATAATATATTA
1 ATATATTATATTA
850102 ATATATTATATTA
1 ATATATTATATTA
850115 ATA
1 ATA
850118 ACGTGTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATTATATTA
Found at i:850194 original size:25 final size:25
Alignment explanation
Indices: 850161--850216 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
850151 AATATTTGAT
850161 TTAAA-ATAA-AAATATAAAAATTTA
1 TTAAATATAATAAA-ATAAAAATTTA
*
850185 TTAAATATAATAAAATAATAATTTA
1 TTAAATATAATAAAATAAAAATTTA
850210 TATAAAT
1 T-TAAAT
850217 TTTTTGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 5 0.18
25 15 0.54
26 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TTAAATATAATAAAATAAAAATTTA
Found at i:853085 original size:3 final size:3
Alignment explanation
Indices: 853079--853103 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
853069 CAGGCACGAA
853079 CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC C
853104 GTGGAAGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:853516 original size:1 final size:1
Alignment explanation
Indices: 853510--853534 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
853500 TCATTTTGGA
853510 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
853535 ACTCTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:854110 original size:11 final size:11
Alignment explanation
Indices: 854094--854123 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
854084 TGAAGATTGA
854094 AAAAAAATAAT
1 AAAAAAATAAT
854105 AAAAAAATAAT
1 AAAAAAATAAT
854116 AAAAAAAT
1 AAAAAAAT
854124 GGAGTGCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:874210 original size:4 final size:4
Alignment explanation
Indices: 874201--874225 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
874191 AATATGTAAG
874201 GCTA GCTA GCTA GCTA GCTA GCTA G
1 GCTA GCTA GCTA GCTA GCTA GCTA G
874226 AACAGATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (4 bp):
GCTA
Found at i:878306 original size:22 final size:21
Alignment explanation
Indices: 878272--878318 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
878262 TCCCCGCTCC
*
878272 CTTTTTTTTTTTTTCCCTTTT
1 CTTTTTTTGTTTTTCCCTTTT
*
878293 CTTTGTTTTGTTTTTCTCTTTT
1 CTTT-TTTTGTTTTTCCCTTTT
878315 -TTTT
1 CTTTT
878319 CCTCTTCTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 7 0.30
22 15 0.65
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (21 bp):
CTTTTTTTGTTTTTCCCTTTT
Found at i:878932 original size:5 final size:5
Alignment explanation
Indices: 878922--878955 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
878912 AAATTAGAGG
*
878922 AAAGA AAAGA AAAGA AAAGA AAA-A AAAAA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
878956 GATAATCAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:885076 original size:2 final size:2
Alignment explanation
Indices: 885069--885098 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
885059 TATTCTTTAA
885069 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
885099 GGGAGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:885255 original size:96 final size:96
Alignment explanation
Indices: 885152--885439 Score: 567
Period size: 96 Copynumber: 3.0 Consensus size: 96
885142 ATTAAGTGTG
*
885152 TATGATATTTAGTTTCCATTTAAAAAAAGTTTGTATATATAATCTATTTTTTCTATTAATTATAA
1 TATGATATTTAGTTTCCATTAAAAAAAAGTTTGTATATATAATCTATTTTTTCTATTAATTATAA
885217 ATTTTTCATAAATAACTTAGTGTGAAGTCTT
66 ATTTTTCATAAATAACTTAGTGTGAAGTCTT
885248 TATGATATTTAGTTTCCATTAAAAAAAAGTTTGTATATATAATCTATTTTTTCTATTAATTATAA
1 TATGATATTTAGTTTCCATTAAAAAAAAGTTTGTATATATAATCTATTTTTTCTATTAATTATAA
885313 ATTTTTCATAAATAACTTAGTGTGAAGTCTT
66 ATTTTTCATAAATAACTTAGTGTGAAGTCTT
885344 TATGATATTTAGTTTCCATTAAAAAAAAGTTTGTATATATAATCTATTTTTTCTATTAATTATAA
1 TATGATATTTAGTTTCCATTAAAAAAAAGTTTGTATATATAATCTATTTTTTCTATTAATTATAA
885409 ATTTTTCATAAATAACTTAGTGTGAAGTCTT
66 ATTTTTCATAAATAACTTAGTGTGAAGTCTT
885440 GTGGATAAAT
Statistics
Matches: 191, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 191 1.00
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.48
Consensus pattern (96 bp):
TATGATATTTAGTTTCCATTAAAAAAAAGTTTGTATATATAATCTATTTTTTCTATTAATTATAA
ATTTTTCATAAATAACTTAGTGTGAAGTCTT
Found at i:886627 original size:18 final size:18
Alignment explanation
Indices: 886606--886645 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
886596 AAGGTACTCA
*
886606 TTTTTCTTTCTTTTT-TC
1 TTTTTTTTTCTTTTTGTC
*
886623 TTTTTTTTTTTTTTTGTC
1 TTTTTTTTTCTTTTTGTC
886641 TTTTT
1 TTTTT
886646 GAATTACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.88
Consensus pattern (18 bp):
TTTTTTTTTCTTTTTGTC
Found at i:892027 original size:22 final size:23
Alignment explanation
Indices: 892002--892045 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
891992 AAAAATTGAG
892002 TTTTAATATTT-AAAACTGTATC
1 TTTTAATATTTAAAAACTGTATC
*
892024 TTTTAATGTTTAAAAACTGTAT
1 TTTTAATATTTAAAAACTGTAT
892046 GTACACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (23 bp):
TTTTAATATTTAAAAACTGTATC
Found at i:893716 original size:5 final size:5
Alignment explanation
Indices: 893702--893733 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
893692 GGAAAAAAAA
893702 GAAA- GAAAG GAAAG GAAAG GAAAG GAAAG GAA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAA
893734 TGAGTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:899235 original size:42 final size:42
Alignment explanation
Indices: 899159--899243 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
899149 GTTGCAGTAG
* *
899159 ACAGCAAGAGATATAACACTCACTGTCCTCAAGTTTTTAAAC
1 ACAGCAAGAGATATAACACTCACTATCCTCAAGTTTCTAAAC
* *
899201 ACAGCAAGAGATATAAC-C-CCCTTCATCCTTAAGTTTCTAAAC
1 ACAGCAAGAGATATAACACTCAC-T-ATCCTCAAGTTTCTAAAC
899243 A
1 A
899244 GAGACAACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 2 0.05
41 2 0.05
42 33 0.89
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.26
Consensus pattern (42 bp):
ACAGCAAGAGATATAACACTCACTATCCTCAAGTTTCTAAAC
Found at i:901709 original size:12 final size:12
Alignment explanation
Indices: 901692--901719 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
901682 GACAGAACAC
901692 CCCTCTCTCTCT
1 CCCTCTCTCTCT
901704 CCCTCTCTCTCT
1 CCCTCTCTCTCT
901716 CCCT
1 CCCT
901720 GTTTTAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (12 bp):
CCCTCTCTCTCT
Found at i:912882 original size:45 final size:45
Alignment explanation
Indices: 912816--912905 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
912806 TGATGTTGTT
* *
912816 ACATGTCTTTCATTAGTTTCTTGTTTAATCTGGCAAAAGCTCATG
1 ACATGTCTTTCATTAGCTTCTTGTTTAATCCGGCAAAAGCTCATG
912861 ACATGTCTTTCATTAGCTTCTTGTTTAATCCGGCAAAAGCTCATG
1 ACATGTCTTTCATTAGCTTCTTGTTTAATCCGGCAAAAGCTCATG
912906 CCTTAATCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (45 bp):
ACATGTCTTTCATTAGCTTCTTGTTTAATCCGGCAAAAGCTCATG
Found at i:914158 original size:22 final size:25
Alignment explanation
Indices: 914112--914159 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
914102 TAATAGTTTA
914112 TAATTAATAATTATTTAATTATTAT
1 TAATTAATAATTATTTAATTATTAT
*
914137 TAATTAA-AA-TA-TTAATTGTTAT
1 TAATTAATAATTATTTAATTATTAT
914159 T
1 T
914160 CTATATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 11 0.50
23 2 0.09
24 2 0.09
25 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TAATTAATAATTATTTAATTATTAT
Found at i:914322 original size:22 final size:22
Alignment explanation
Indices: 914297--914344 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
914287 TGTCATATAA
914297 TAACAAGTGATATGGTAATTAT
1 TAACAAGTGATATGGTAATTAT
914319 TAACAAGTGATATGGTAATTAT
1 TAACAAGTGATATGGTAATTAT
914341 TAAC
1 TAAC
914345 TGTTAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (22 bp):
TAACAAGTGATATGGTAATTAT
Found at i:914579 original size:15 final size:15
Alignment explanation
Indices: 914554--914594 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
914544 TATAATTTTT
*
914554 TAAAA-ATTTTAATA
1 TAAAATATTTTAAAA
914568 TAAAATATTTTAAAA
1 TAAAATATTTTAAAA
914583 TCAAAAT-TTTTA
1 T-AAAATATTTTA
914595 TTTTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 14 0.58
16 5 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAATATTTTAAAA
Found at i:924615 original size:19 final size:20
Alignment explanation
Indices: 924583--924620 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
924573 TATGCTTGGC
*
924583 AAATCAAAATTTTTAAAATA
1 AAATCAAAAATTTTAAAATA
*
924603 AAAT-AAAAATTTTGAAAT
1 AAATCAAAAATTTTAAAAT
924621 TATCAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (20 bp):
AAATCAAAAATTTTAAAATA
Found at i:925335 original size:55 final size:55
Alignment explanation
Indices: 925268--925377 Score: 157
Period size: 55 Copynumber: 2.0 Consensus size: 55
925258 GATAGCAGAT
* * *
925268 GGAATTGGTCTCAAGCAAGAATTCAAAATAAACGTTGTGTTCCAAGTCGTTTAAA
1 GGAATTGATCTCAAGCAAGAATTCAAAATAAACCTTGTGATCCAAGTCGTTTAAA
** * *
925323 GGAATTGATCTCAAGCAAGAATTTGAGATAAACCTTGTGATCCAAGTTGTTTAAA
1 GGAATTGATCTCAAGCAAGAATTCAAAATAAACCTTGTGATCCAAGTCGTTTAAA
925378 TTTAACCACG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (55 bp):
GGAATTGATCTCAAGCAAGAATTCAAAATAAACCTTGTGATCCAAGTCGTTTAAA
Found at i:927016 original size:2 final size:2
Alignment explanation
Indices: 927009--927043 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
926999 GGATAAGTTT
927009 TA TA TA TA 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 TA TA TA TA T
927044 GTAAATTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:942909 original size:22 final size:19
Alignment explanation
Indices: 942883--942933 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 19
942873 ATAATATGTT
942883 ATAAAAATTAAGACGATAACTA
1 ATAAAAATTAAGA-G-TAA-TA
942905 ATAAAATTATTAAGAGTAATA
1 ATAAAA--ATTAAGAGTAATA
942926 ATAAAAAT
1 ATAAAAAT
942934 AAAATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.07
21 8 0.30
22 9 0.33
23 1 0.04
24 7 0.26
ACGTcount: A:0.61, C:0.04, G:0.08, T:0.27
Consensus pattern (19 bp):
ATAAAAATTAAGAGTAATA
Found at i:942927 original size:21 final size:24
Alignment explanation
Indices: 942889--942931 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
942879 TGTTATAAAA
942889 ATTAAGACGATAACTAATAAAATT
1 ATTAAGACGATAACTAATAAAATT
942913 ATTAAGA-G-TAA-TAATAAAA
1 ATTAAGACGATAACTAATAAAA
942932 ATAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 1 0.05
24 7 0.37
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (24 bp):
ATTAAGACGATAACTAATAAAATT
Found at i:943150 original size:214 final size:219
Alignment explanation
Indices: 942763--943194 Score: 590
Period size: 214 Copynumber: 2.0 Consensus size: 219
942753 TAATTATAAA
* * *
942763 ATATATATAATGTATTACTTTATTATATATATGAAATTAATGATATAGCTTATATATTATAATAT
1 ATATATATAATATATTACTTTATTATATATATGAAATTAA-GATATAGCTAAAATATTATAATAT
* * *
942828 TTTAATTTTTATGTCAAAATTTATATAAATAATAATTAATTATAAATAATATGTTATAAAAATTA
65 TATAATTTTTATATCAAAATTTATATAAATAATAACTAATTATAAATAATATGTTATAAAAATTA
*
942893 AGACGATAACTAATAAAATTATTAAGAGTAATAATAAAAATAAAATTTATTATAAGTTATAGTAA
130 AGACGATAACTAATAAAATTATTAAGAGTAATAATAAAAATAAAATTTATTATAAGTTATAATAA
942958 TGCTTATGTATAAATTAAATATATGT
195 T-CTTATGTATAAATTAAATATATGT
*
942984 ATATATATAATATATTACTTTATTATATATATGAAATT-A-ATA-A-C-AAAAT-TTAT-ATGTT
1 ATATATATAATATATTACTTTATTATATATATGAAATTAAGATATAGCTAAAATATTATAATATT
* *
943042 ATAATGTTTTATATCAAAGTTTATATAAATAATAACTAATTATAAATAATATGTTGTAAAAATTA
66 ATAAT-TTTTATATCAAAATTTATATAAATAATAACTAATTATAAATAATATGTTATAAAAATTA
** * * * * * * * *
943107 AGGTGATAATTAATGAGATTATTAAGTGTAATTATATAAATAAAGTTTATTATAAGTTATAATGA
130 AGACGATAACTAATAAAATTATTAAGAGTAATAATAAAAATAAAATTTATTATAAGTTATAATAA
* *
943172 TTTTATGTCTAAATTAAATATAT
195 TCTTATGTATAAATTAAATATAT
943195 ATGTAATGTT
Statistics
Matches: 188, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
213 28 0.15
214 114 0.61
215 3 0.02
216 1 0.01
217 1 0.01
218 3 0.02
220 1 0.01
221 37 0.20
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (219 bp):
ATATATATAATATATTACTTTATTATATATATGAAATTAAGATATAGCTAAAATATTATAATATT
ATAATTTTTATATCAAAATTTATATAAATAATAACTAATTATAAATAATATGTTATAAAAATTAA
GACGATAACTAATAAAATTATTAAGAGTAATAATAAAAATAAAATTTATTATAAGTTATAATAAT
CTTATGTATAAATTAAATATATGT
Found at i:943469 original size:15 final size:16
Alignment explanation
Indices: 943451--943483 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
943441 TTAATATATT
943451 TTAAATATA-TATTAA
1 TTAAATATATTATTAA
*
943466 TTAAATGTATTATTAA
1 TTAAATATATTATTAA
943482 TT
1 TT
943484 TTTTAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TTAAATATATTATTAA
Found at i:943476 original size:26 final size:27
Alignment explanation
Indices: 943429--943481 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
943419 TTGTATACGT
943429 ATATATAATAAATTAATATATT-TTAA
1 ATATATAATAAATTAATATATTATTAA
* *
943455 ATATAT-ATTAATTAAATGTATTATTAA
1 ATATATAATAAATT-AATATATTATTAA
943482 TTTTTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 6 0.26
26 13 0.57
27 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
ATATATAATAAATTAATATATTATTAA
Found at i:943513 original size:21 final size:20
Alignment explanation
Indices: 943484--943522 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
943474 ATTATTAATT
943484 TTTTAATA-TATATAAAAATA
1 TTTTAATATTA-ATAAAAATA
943504 TTTTATATATTAATAAAAA
1 TTTTA-ATATTAATAAAAA
943523 ATATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 10 0.59
22 2 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTAATATTAATAAAAATA
Found at i:945273 original size:2 final size:2
Alignment explanation
Indices: 945268--945298 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
945258 AAATAAATCT
945268 TA TA 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 TA TA T
945299 GATCTTTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:946499 original size:20 final size:22
Alignment explanation
Indices: 946470--946512 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
946460 CAAAAAATAA
*
946470 AAAATTATTTAA-A-TTTTTTT
1 AAAATAATTTAAGAGTTTTTTT
946490 AAAATAATTTAAGAGTTTTTTT
1 AAAATAATTTAAGAGTTTTTTT
946512 A
1 A
946513 GATATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
AAAATAATTTAAGAGTTTTTTT
Found at i:959986 original size:2 final size:2
Alignment explanation
Indices: 959979--960011 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
959969 AGCTTAACAA
959979 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 A
960012 AAACAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:963440 original size:2 final size:2
Alignment explanation
Indices: 963423--963456 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
963413 TATTGAACCC
* *
963423 AT AT AC AT AC 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
963457 TTTGTTTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:964657 original size:2 final size:2
Alignment explanation
Indices: 964650--964674 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
964640 AATCATTTAG
964650 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 A
964675 GCAGGAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:973287 original size:2 final size:2
Alignment explanation
Indices: 973280--973306 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
973270 AGATATGCAG
973280 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
973307 CATGAAAAAT
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:997860 original size:24 final size:24
Alignment explanation
Indices: 997828--997878 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
997818 AATTGTTGAG
997828 TTAGTTGAAATATCACTTTTTGTT
1 TTAGTTGAAATATCACTTTTTGTT
997852 TTAGTTGAAATATCACTTTTTGTT
1 TTAGTTGAAATATCACTTTTTGTT
997876 TTA
1 TTA
997879 TATCAAGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.55
Consensus pattern (24 bp):
TTAGTTGAAATATCACTTTTTGTT
Found at i:998815 original size:17 final size:17
Alignment explanation
Indices: 998789--998821 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
998779 TGTCATATTA
*
998789 TGTAACATATTTAATTT
1 TGTAAAATATTTAATTT
998806 TGTAAAATATTTAATT
1 TGTAAAATATTTAATT
998822 AATCATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (17 bp):
TGTAAAATATTTAATTT
Found at i:1019514 original size:29 final size:31
Alignment explanation
Indices: 1019462--1019525 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
1019452 AAAAAACTTT
*
1019462 ATAAATATTATATAAATTTTTTTTGTGGAAA
1 ATAAATATTATATAAATTTTTTTTGTGAAAA
*
1019493 ATAAATATTATAT-CA-TTTTTTTGTGAAAA
1 ATAAATATTATATAAATTTTTTTTGTGAAAA
1019522 ATAA
1 ATAA
1019526 TTTACTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 17 0.55
30 1 0.03
31 13 0.42
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (31 bp):
ATAAATATTATATAAATTTTTTTTGTGAAAA
Found at i:1019580 original size:16 final size:16
Alignment explanation
Indices: 1019559--1019591 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1019549 AAGGATGAGA
1019559 TAATTTTAGATAATTT
1 TAATTTTAGATAATTT
1019575 TAATTTTAGATAATTT
1 TAATTTTAGATAATTT
1019591 T
1 T
1019592 TAATAGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TAATTTTAGATAATTT
Found at i:1065753 original size:25 final size:26
Alignment explanation
Indices: 1065702--1065753 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
1065692 TTAAAAAATA
* *
1065702 TTATTTATTATAAAAATAGAACTTAT
1 TTATTAATTATAAAAATAGAACATAT
* *
1065728 TTATTAATTA-AAAAATATAAGATAT
1 TTATTAATTATAAAAATAGAACATAT
1065753 T
1 T
1065754 ATATGAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (26 bp):
TTATTAATTATAAAAATAGAACATAT
Found at i:1085855 original size:2 final size:2
Alignment explanation
Indices: 1085848--1085900 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1085838 TTGACTTCGA
1085848 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1085890 AT TT AT AT AT A
1 AT AT AT AT AT A
1085901 CAACAATTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1093270 original size:29 final size:29
Alignment explanation
Indices: 1093212--1093270 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1093202 GAAATAAATC
*
1093212 AAAAGCAAGATGAAAATTTAAAAAACAAA
1 AAAAGCAAGATGAAAATTCAAAAAACAAA
*
1093241 AAAAGCAAAGATG-AAATTC-AAGAACAAA
1 AAAAGC-AAGATGAAAATTCAAAAAACAAA
1093269 AA
1 AA
1093271 TGCGATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 10 0.37
29 11 0.41
30 6 0.22
ACGTcount: A:0.68, C:0.08, G:0.12, T:0.12
Consensus pattern (29 bp):
AAAAGCAAGATGAAAATTCAAAAAACAAA
Found at i:1093766 original size:29 final size:29
Alignment explanation
Indices: 1093734--1093789 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1093724 ATTCAAGAAA
1093734 ATTTAATTAAATCTTTATATATTTATTAT
1 ATTTAATTAAATCTTTATATATTTATTAT
* *
1093763 ATTTAATTAAATTTTTATATTTTTATT
1 ATTTAATTAAATCTTTATATATTTATT
1093790 TTGAGTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTAATTAAATCTTTATATATTTATTAT
Found at i:1097769 original size:59 final size:57
Alignment explanation
Indices: 1097706--1097890 Score: 167
Period size: 59 Copynumber: 3.1 Consensus size: 57
1097696 ATGTTTAGTG
*
1097706 AAATATTTTTTTGGAATAGAATATTTATTTTGAAAGCTATTAACCAACGTGTTCAAT-GA
1 AAATATTTTTTT-GAATAGAGTATTTATTTTGAAA-CTATTAACCAACGTGTT-AATAGA
** * * *
1097765 AAATATTCTTTTAAAATAGAGTATTTATTTTGAACACTAATTGACCTACATG-TAATTAGA
1 AAATATT-TTTTTGAATAGAGTATTTATTTTGAA-ACT-ATTAACCAACGTGTTAA-TAGA
* * * * * *
1097825 AAATATTTTTTTGAAAATGAGTGTTTATTTTGAAAACTATTAACTAATGTGTTGATCGA
1 AAATATTTTTTTGAATA-GAGTATTTATTTTG-AAACTATTAACCAACGTGTTAATAGA
1097884 AAATATT
1 AAATATT
1097891 CTTTGGAGAG
Statistics
Matches: 101, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
58 2 0.02
59 55 0.54
60 42 0.42
61 2 0.02
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (57 bp):
AAATATTTTTTTGAATAGAGTATTTATTTTGAAACTATTAACCAACGTGTTAATAGA
Found at i:1097925 original size:119 final size:119
Alignment explanation
Indices: 1097706--1097940 Score: 278
Period size: 119 Copynumber: 2.0 Consensus size: 119
1097696 ATGTTTAGTG
* *
1097706 AAATATTTTTTTGGAATAGAATATTTATTTTGAAAGCTATTAACCAACGTGTTCAATGAAAATAT
1 AAATATTTTTTTGAAATAGAATATTTATTTTGAAAACTATTAACCAACGTGTTCAATGAAAATAT
* * * *
1097771 TCTTTTAAAATAGAGTATTTATTTTGAACACTAATTGACCTACATGTAATTAGA
66 TCTTTGAAAAGAGAGTATTTATTTTAAAAACTAATTGACCTACATGTAATTAGA
* * * * *
1097825 AAATATTTTTTTGAAA-ATGAGTGTTTATTTTGAAAACTATTAACTAATGTGTT-GATCGAAAAT
1 AAATATTTTTTTGAAATA-GAATATTTATTTTGAAAACTATTAACCAACGTGTTCAAT-GAAAAT
* * * * *
1097888 ATTCTTTGGAGAG-GAAGTGTTTATTTTAAAAAGTAATTGATCTACATGTAATT
64 ATTCTTTGAAAAGAG-AGTATTTATTTTAAAAACTAATTGACCTACATGTAATT
1097941 GTGGTTAAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 4 0.04
119 93 0.96
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.41
Consensus pattern (119 bp):
AAATATTTTTTTGAAATAGAATATTTATTTTGAAAACTATTAACCAACGTGTTCAATGAAAATAT
TCTTTGAAAAGAGAGTATTTATTTTAAAAACTAATTGACCTACATGTAATTAGA
Found at i:1101851 original size:23 final size:23
Alignment explanation
Indices: 1101825--1101879 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
1101815 CATTATAAAA
1101825 CAGCTTATTAAGCATGATAGCTG
1 CAGCTTATTAAGCATGATAGCTG
1101848 CAGCTTATTAAGCATGATAGCTG
1 CAGCTTATTAAGCATGATAGCTG
1101871 CAGCTTATT
1 CAGCTTATT
1101880 CTTCCTCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (23 bp):
CAGCTTATTAAGCATGATAGCTG
Found at i:1111988 original size:2 final size:2
Alignment explanation
Indices: 1111981--1112014 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1111971 AAAGCTATGC
1111981 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
1112015 GACCTTAATT
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:1117922 original size:2 final size:2
Alignment explanation
Indices: 1117915--1117943 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1117905 TTTTGTTGAT
1117915 TA 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 TA T
1117944 TTTAGACGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1128002 original size:15 final size:15
Alignment explanation
Indices: 1127971--1128159 Score: 74
Period size: 16 Copynumber: 12.3 Consensus size: 15
1127961 TATATAAAAA
1127971 ATAAAAT-AAAATAT
1 ATAAAATAAAAATAT
1127985 ATAAAATAAAAATTTAT
1 ATAAAATAAAAA--TAT
* *
1128002 ATAATATAGGTAAAATAAA
1 ATAAAATA---AAAAT-AT
* *
1128021 ATAAACT-AAATTAT
1 ATAAAATAAAAATAT
*
1128035 ATAATATAAAAAATAT
1 ATAAAAT-AAAAATAT
1128051 ATTAAAAATATAAAATAT
1 A-T-AAAATA-AAAATAT
*
1128069 A-AAAATAGAATAATAA
1 ATAAAATA-AA-AATAT
1128085 ATAAAA-ATAAAATAT
1 ATAAAATA-AAAATAT
* *
1128100 ATGACATTAAAAATAT
1 AT-AAAATAAAAATAT
**
1128116 ATTTAA-AAAAATAT
1 ATAAAATAAAAATAT
*
1128130 -T-ATATAAAAAT-T
1 ATAAAATAAAAATAT
*
1128142 A-ATAATAAAAA-AT
1 ATAAAATAAAAATAT
1128155 ATAAA
1 ATAAA
1128160 TATATTACAT
Statistics
Matches: 130, Mismatches: 24, Indels: 42
0.66 0.12 0.21
Matches are distributed among these distances:
12 2 0.02
13 16 0.12
14 23 0.18
15 23 0.18
16 26 0.20
17 17 0.13
18 13 0.10
19 6 0.05
20 4 0.03
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (15 bp):
ATAAAATAAAAATAT
Found at i:1128005 original size:26 final size:25
Alignment explanation
Indices: 1127954--1128072 Score: 86
Period size: 25 Copynumber: 4.8 Consensus size: 25
1127944 ATAATTAAAA
* * *
1127954 TAAAATATAT-ATA-AAAAATAAAA
1 TAAAATATATAAAATAAAAATATAC
*
1127977 TAAAATATATAAAATAAAAATTTA-
1 TAAAATATATAAAATAAAAATATAC
* *
1128001 TATAATATAGGTAAAAT-AAAATAAAC
1 TAAAATATA--TAAAATAAAAATATAC
* * *
1128027 TAAATTATATAATATAAAAAATATAT
1 TAAAATATATAAAAT-AAAAATATAC
1128053 TAAAA-ATATAAAATATAAAA
1 TAAAATATATAAAATA-AAAA
1128073 ATAGAATAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
23 10 0.13
24 16 0.21
25 25 0.33
26 24 0.32
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (25 bp):
TAAAATATATAAAATAAAAATATAC
Found at i:1128048 original size:31 final size:29
Alignment explanation
Indices: 1127971--1128086 Score: 85
Period size: 31 Copynumber: 3.9 Consensus size: 29
1127961 TATATAAAAA
* *
1127971 ATAAAATAAAATATATAAAATAAAAATTTAT
1 ATAATATAAAA-A-ATAAAATAAAAAATTAT
*
1128002 ATAATATAGGTAAAATAAAATAAACTAAATTAT
1 ATAATATA--AAAAATAAAATAAA--AAATTAT
* *
1128035 ATAATATAAAAAAT-ATATTAAAAA-TAT
1 ATAATATAAAAAATAAAATAAAAAATTAT
* * *
1128062 AAAATAT-AAAAATAGAATAATAAAT
1 ATAATATAAAAAATAAAATAAAAAAT
1128087 AAAAATAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
26 6 0.09
27 15 0.22
28 3 0.04
30 5 0.07
31 22 0.32
32 1 0.01
33 16 0.24
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (29 bp):
ATAATATAAAAAATAAAATAAAAAATTAT
Found at i:1128092 original size:75 final size:73
Alignment explanation
Indices: 1127958--1128098 Score: 169
Period size: 75 Copynumber: 1.9 Consensus size: 73
1127948 TTAAAATAAA
* **
1127958 ATATATATAAAAAATAAAATAAAATATATAAAATAAAAATTTATATAATATAGGTAAAATAAAAT
1 ATATATATAAAAAATAAAATAAAATATATAAAATAAAAA--TATAGAATATAAATAAAATAAAAT
1128023 AAACTAAATT
64 AAACTAAATT
* *
1128033 ATATAATATAAAAAATATATTAAAA-ATATAAAATATAAAA-ATAGAATAATAAATAAAAATAAA
1 ATAT-ATATAAAAAATAAAATAAAATATATAAAATA-AAAATATAGAAT-ATAAAT-AAAATAAA
1128096 ATA
62 ATA
1128099 TATGACATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
73 6 0.11
74 4 0.07
75 25 0.44
76 22 0.39
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (73 bp):
ATATATATAAAAAATAAAATAAAATATATAAAATAAAAATATAGAATATAAATAAAATAAAATAA
ACTAAATT
Found at i:1128112 original size:65 final size:63
Alignment explanation
Indices: 1128015--1128170 Score: 170
Period size: 65 Copynumber: 2.4 Consensus size: 63
1128005 ATATAGGTAA
* * * * *
1128015 AATAAAATAAACTAAATTATATAATATAAAAAATATA-TTAAAAATATAAAATATAAAAATAGAA
1 AATAAAA-AAAATAAA-TATATGACATTAAAAATATATTTAAAAAAATAAAATATAAAAAT-GAA
1128079 T
63 T
** *
1128080 AATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAAAAAATATTATATAAAAATTAAT
1 AATAAA-AAAAAT-AAATATATGACATTAAAAATATATTTAAAAAAATAAAATATAAAAATGAAT
* *
1128145 AATAAAAAATATAAATATATTACATT
1 AATAAAAAAAATAAATATATGACATT
1128171 TATATTTTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
63 13 0.17
64 5 0.06
65 36 0.46
66 24 0.31
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.31
Consensus pattern (63 bp):
AATAAAAAAAATAAATATATGACATTAAAAATATATTTAAAAAAATAAAATATAAAAATGAAT
Found at i:1128151 original size:27 final size:28
Alignment explanation
Indices: 1128033--1128156 Score: 106
Period size: 27 Copynumber: 4.7 Consensus size: 28
1128023 AAACTAAATT
1128033 ATATAAT-ATAAAAAATAT-AT-TAAAA
1 ATATAATAATAAAAAATATGATATAAAA
1128058 ATATAA-AATATAAAAATA-GA-ATAATAA
1 ATATAATAATA-AAAAATATGATATAA-AA
* *
1128085 ATA-AA-AATAAAATATATGACATTAAAA
1 ATATAATAATAAAAAATATGATA-TAAAA
* * *
1128112 ATATATTTA-AAAAAATATTATATAAAA
1 ATATAATAATAAAAAATATGATATAAAA
1128139 AT-TAATAATAAAAAATAT
1 ATATAATAATAAAAAATAT
1128157 AAATATATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
25 15 0.19
26 23 0.29
27 27 0.34
28 14 0.17
29 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (28 bp):
ATATAATAATAAAAAATATGATATAAAA
Found at i:1128276 original size:16 final size:16
Alignment explanation
Indices: 1128255--1128308 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
1128245 TAATGTTATT
1128255 TTATTTATATATAATA
1 TTATTTATATATAATA
* *
1128271 TTATTTTTTTATAATA
1 TTATTTATATATAATA
*
1128287 ATATTTATTATAATAATA
1 TTATTTA-TAT-ATAATA
1128305 TTAT
1 TTAT
1128309 AAATAATCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
16 19 0.63
17 2 0.07
18 9 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTTATATATAATA
Found at i:1128295 original size:20 final size:21
Alignment explanation
Indices: 1128245--1128291 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1128235 TCAAACGCTG
*
1128245 TAATGTTATTTTATTTATATA
1 TAATATTATTTTATTTATATA
1128266 TAATATTATTTT-TTTATA-A
1 TAATATTATTTTATTTATATA
1128285 TAATATT
1 TAATATT
1128292 TATTATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 8 0.32
20 6 0.24
21 11 0.44
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TAATATTATTTTATTTATATA
Found at i:1128299 original size:15 final size:15
Alignment explanation
Indices: 1128256--1128306 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
1128246 AATGTTATTT
*
1128256 TATTTATATATAATAT
1 TATTTAT-TATAATAA
*
1128272 TATTTTTTTATAATAA
1 TA-TTTATTATAATAA
1128288 TATTTATTATAATAA
1 TATTTATTATAATAA
1128303 TATT
1 TATT
1128307 ATAAATAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 16 0.52
16 11 0.35
17 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTATTATAATAA
Found at i:1128314 original size:15 final size:16
Alignment explanation
Indices: 1128259--1128323 Score: 55
Period size: 15 Copynumber: 4.2 Consensus size: 16
1128249 GTTATTTTAT
*
1128259 TTATAT-ATAATATTA
1 TTATATAATAATAATA
* * *
1128274 TTTTTTTATAATAATA
1 TTATATAATAATAATA
*
1128290 TT-TATTATAATAATA
1 TTATATAATAATAATA
*
1128305 TTATA-AATAATCATA
1 TTATATAATAATAATA
1128320 TTAT
1 TTAT
1128324 CTGTAATTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
15 30 0.71
16 12 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATAATAATAATA
Found at i:1142127 original size:2 final size:2
Alignment explanation
Indices: 1142120--1142146 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1142110 AAGAAAAGTA
1142120 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 A
1142147 GAATTACATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1144017 original size:21 final size:21
Alignment explanation
Indices: 1143970--1144019 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1143960 ATCTCTTTTT
1143970 TTAATTATAAATAAATAAATA
1 TTAATTATAAATAAATAAATA
* * *
1143991 TAAATTA-AAATTATTAAATAA
1 TTAATTATAAATAAATAAAT-A
1144012 TTAATTAT
1 TTAATTAT
1144020 GAACCACTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAATTATAAATAAATAAATA
Found at i:1146051 original size:12 final size:10
Alignment explanation
Indices: 1146010--1146052 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
1146000 TAAAATATTC
1146010 AAAAATTATTA
1 AAAAATT-TTA
*
1146021 AAATATTTTA
1 AAAAATTTTA
1146031 AAAAATTTTA
1 AAAAATTTTA
1146041 AATAAACTTTTA
1 AA-AAA-TTTTA
1146053 TATTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 14 0.50
11 9 0.32
12 5 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:1168572 original size:49 final size:52
Alignment explanation
Indices: 1168516--1168635 Score: 149
Period size: 55 Copynumber: 2.3 Consensus size: 52
1168506 TTCGAATATA
*
1168516 AATAAGAAGATTAAGA-T-A-TATTTCATCCTAAATT-GAATATGAATGTGTG
1 AATAAGAAGATTAAGATTAACTATCTCATCCTAAATTAG-ATATGAATGTGTG
*
1168565 AATAAGAAGATTAAGATTAACACGTATCTCATCTTAAATTAGATATGAATGTGTG
1 AATAAGAAGATTAAGATT-A-AC-TATCTCATCCTAAATTAGATATGAATGTGTG
*
1168620 AATAAGAATATTAAGA
1 AATAAGAAGATTAAGA
1168636 CGTATCTCAT
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
49 16 0.26
50 1 0.02
53 1 0.02
55 42 0.69
56 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.33
Consensus pattern (52 bp):
AATAAGAAGATTAAGATTAACTATCTCATCCTAAATTAGATATGAATGTGTG
Found at i:1168639 original size:49 final size:49
Alignment explanation
Indices: 1168516--1168666 Score: 142
Period size: 49 Copynumber: 3.0 Consensus size: 49
1168506 TTCGAATATA
* ** * *
1168516 AATAAGAAGATTAAGATATATTTCATCCTAAATT-GAATATGAATGTGTG
1 AATAAGAATATTAAGACGTATCTCATCTTAAATTAG-ATATGAATGTGTG
*
1168565 AATAAGAAGATTAAGATTAACACGTATCTCATCTTAAATTAGATATGAATGTGTG
1 AATAAG-A-A-T---ATTAAGACGTATCTCATCTTAAATTAGATATGAATGTGTG
* * * *
1168620 AATAAGAATATTAAGACGTATCTCATTTTAGATCAGATACGAATGTG
1 AATAAGAATATTAAGACGTATCTCATCTTAAATTAGATATGAATGTG
1168667 AGAGTTAAGA
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
49 39 0.46
50 1 0.01
51 1 0.01
52 1 0.01
53 1 0.01
54 1 0.01
55 39 0.46
56 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.33
Consensus pattern (49 bp):
AATAAGAATATTAAGACGTATCTCATCTTAAATTAGATATGAATGTGTG
Found at i:1176827 original size:57 final size:57
Alignment explanation
Indices: 1176739--1176853 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
1176729 TGTGATTGGT
* *
1176739 GCCAATCAATCCAAACCTTACATGTTACATAATGAGGAACTTCTTCCACTTTGTCAA
1 GCCAATCAATCCAAACCTTACATGTTACATAACGAGGAACTTCTTCCACTTGGTCAA
*
1176796 GCCAATCAATGCAAACCTTACATGTTACATAACGAGGAACTTCTTCCACTTGGTCAA
1 GCCAATCAATCCAAACCTTACATGTTACATAACGAGGAACTTCTTCCACTTGGTCAA
1176853 G
1 G
1176854 GTCTAGTTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (57 bp):
GCCAATCAATCCAAACCTTACATGTTACATAACGAGGAACTTCTTCCACTTGGTCAA
Found at i:1182729 original size:11 final size:12
Alignment explanation
Indices: 1182713--1182745 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1182703 GGGAGAAGAC
1182713 GAGGAAGAG-GG
1 GAGGAAGAGAGG
1182724 GAGGAAGAGAGG
1 GAGGAAGAGAGG
*
1182736 GAAGAAGAGA
1 GAGGAAGAGA
1182746 AAGAGATGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (12 bp):
GAGGAAGAGAGG
Found at i:1182738 original size:20 final size:19
Alignment explanation
Indices: 1182703--1182740 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1182693 AGAAATGGAA
1182703 GGGAGAAGACGAGGAAGAG
1 GGGAGAAGACGAGGAAGAG
1182722 GGGAGGAAGA-GAGGGAAGA
1 GGGA-GAAGACGA-GGAAGA
1182741 AGAGAAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.55, T:0.00
Consensus pattern (19 bp):
GGGAGAAGACGAGGAAGAG
Found at i:1196944 original size:54 final size:54
Alignment explanation
Indices: 1196884--1197022 Score: 192
Period size: 54 Copynumber: 2.6 Consensus size: 54
1196874 CAGAGATATT
* * *
1196884 GATGGTGAGAGGAGAAGGGAGAAAGAGCGAGCAAGGAGCAGAGATAGAG-ACAT-
1 GATGGTGAAAGGAGAAGGGAGAAGGAGCGAGAAAGGAGCAGAGATAGAGAAC-TG
* *
1196937 GAGTGGTGAAAGGAGAAGGGAGAAGGAGCGAGAAAGGAGTAGGGATAGAGAACTG
1 GA-TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAAAGGAGCAGAGATAGAGAACTG
*
1196992 GACGGTGAAAGGAGAAGGGAGAAGGAGCGAG
1 GATGGTGAAAGGAGAAGGGAGAAGGAGCGAG
1197023 GGAAAAGCAG
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
53 2 0.03
54 71 0.92
55 4 0.05
ACGTcount: A:0.40, C:0.06, G:0.47, T:0.07
Consensus pattern (54 bp):
GATGGTGAAAGGAGAAGGGAGAAGGAGCGAGAAAGGAGCAGAGATAGAGAACTG
Found at i:1196971 original size:24 final size:24
Alignment explanation
Indices: 1196944--1197022 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 24
1196934 CATGAGTGGT
1196944 GAAAGGAGAAGGGAGAAGGAGCGA
1 GAAAGGAGAAGGGAGAAGGAGCGA
* *
1196968 GAAAGGAGTAGGGATAGAGAACTGGA-CGGT
1 GAAAGGAG-AAGG---GAGAA--GGAGC-GA
1196998 GAAAGGAGAAGGGAGAAGGAGCGA
1 GAAAGGAGAAGGGAGAAGGAGCGA
1197022 G
1 G
1197023 GGAAAAGCAG
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
24 13 0.30
25 4 0.09
26 5 0.12
28 5 0.12
29 4 0.09
30 12 0.28
ACGTcount: A:0.42, C:0.05, G:0.48, T:0.05
Consensus pattern (24 bp):
GAAAGGAGAAGGGAGAAGGAGCGA
Found at i:1197035 original size:54 final size:51
Alignment explanation
Indices: 1196887--1197070 Score: 165
Period size: 54 Copynumber: 3.4 Consensus size: 51
1196877 AGATATTGAT
* * * * *
1196887 GGTGAGAGGAGAAGGGAGAAAGAGCGAGCAAGGAGCAGAGATAGAG-ACATGA
1 GGTGAAAGGAGAAGGGAGAAGGAGCGAGGAA-AAGCAGGGATAGAGAAC-TGA
*
1196939 GTGGTGAAAGGAGAAGGGAGAAGGAGCGA-GAAAGGAGTAGGGATAGAGAACTGGA
1 --GGTGAAAGGAGAAGGGAGAAGGAGCGAGGAAA--AGCAGGGATAGAGAACT-GA
* *
1196994 CGGTGAAAGGAGAAGGGAGAAGGAGCGAGGGAAAAGCAGGGATAGGGATCTAGA
1 -GGTGAAAGGAGAAGGGAGAAGGAGCGA-GGAAAAGCAGGGATAGAGAACT-GA
* *
1197048 GAGTGGAAGGATAAGGGAGAAGG
1 G-GTGAAAGGAGAAGGGAGAAGG
1197071 TGCTTGATAG
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
53 3 0.03
54 99 0.90
55 4 0.04
56 4 0.04
ACGTcount: A:0.40, C:0.05, G:0.47, T:0.08
Consensus pattern (51 bp):
GGTGAAAGGAGAAGGGAGAAGGAGCGAGGAAAAGCAGGGATAGAGAACTGA
Found at i:1204300 original size:39 final size:40
Alignment explanation
Indices: 1204239--1204324 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 40
1204229 TTATAAGTGT
1204239 TTTATTAAGAATGTAATGTTAAT-T-TTTATAATTATTTTTA
1 TTTATTAAGAATGTAATGTTAATATATTTAT-A-TATTTTTA
*
1204279 TTTATTAA-AATGTAAAT-TTAATATATTTATATCTTTTTA
1 TTTATTAAGAATGT-AATGTTAATATATTTATATATTTTTA
1204318 -TTATTAA
1 TTTATTAA
1204325 TATTTATGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
38 7 0.17
39 17 0.40
40 13 0.31
41 5 0.12
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (40 bp):
TTTATTAAGAATGTAATGTTAATATATTTATATATTTTTA
Done.