Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold321
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: 1060354
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 5 of 6
Found at i:841785 original size:42 final size:42
Alignment explanation
Indices: 841694--841780 Score: 133
Period size: 41 Copynumber: 2.1 Consensus size: 42
841684 AAAAATTGTG
*
841694 TTTTTAAAAGAAATAAAAAAATTATTGGAGTAAAAGATTGTA
1 TTTTTAAAAGAAATAAAAAAATTATTGGAGTAAAAGATAGTA
* *
841736 TTTTTAAAAGAAAT-AAAAAATTATTTGAGTAAATGA-AGTA
1 TTTTTAAAAGAAATAAAAAAATTATTGGAGTAAAAGATAGTA
841776 TTTTT
1 TTTTT
841781 TTAAATAGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
40 8 0.19
41 20 0.48
42 14 0.33
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (42 bp):
TTTTTAAAAGAAATAAAAAAATTATTGGAGTAAAAGATAGTA
Found at i:849540 original size:3 final size:3
Alignment explanation
Indices: 849534--849568 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
849524 CATCATCATC
849534 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
849569 AGTTTCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:852019 original size:2 final size:2
Alignment explanation
Indices: 852014--852044 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
852004 TGTGTGTGTG
852014 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
852045 TTATGTATGC
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:852786 original size:14 final size:16
Alignment explanation
Indices: 852755--852787 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
852745 ACTACTCAAA
852755 AAAATATTGTTTTATT
1 AAAATATTGTTTTATT
852771 AAAATATT-TTTT-TT
1 AAAATATTGTTTTATT
852785 AAA
1 AAA
852788 TTTAAGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 4 0.24
16 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AAAATATTGTTTTATT
Found at i:853189 original size:22 final size:20
Alignment explanation
Indices: 853147--853192 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
853137 ATACATAATT
*
853147 TATATAAATAAATAATTAAA
1 TATATAAATAAATAAATAAA
*
853167 TATATTAATTAAATTAAATAAA
1 TATA-TAAATAAA-TAAATAAA
853189 TATA
1 TATA
853193 CATCGTATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 7 0.32
22 11 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATATAAATAAATAAATAAA
Found at i:853240 original size:25 final size:26
Alignment explanation
Indices: 853206--853269 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
853196 CGTATCAAAA
*
853206 TTATAAAAATATATAAAATTTAAT-T
1 TTATATAAATATATAAAATTTAATAT
* *
853231 TTATATAAATATA-AATATTTTATAT
1 TTATATAAATATATAAAATTTAATAT
* *
853256 ATATATATATATAT
1 TTATATAAATATAT
853270 TATCACCTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 8 0.25
25 24 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTATATAAATATATAAAATTTAATAT
Found at i:853250 original size:19 final size:19
Alignment explanation
Indices: 853228--853272 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
853218 ATAAAATTTA
853228 ATTTTATATAAATATAAAT
1 ATTTTATATAAATATAAAT
* *
853247 ATTTTATATATATATATAT
1 ATTTTATATAAATATAAAT
*
853266 ATATTAT
1 ATTTTAT
853273 CACCTACACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTATATAAATATAAAT
Found at i:860621 original size:24 final size:23
Alignment explanation
Indices: 860594--860638 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
860584 ATAATAAAGT
*
860594 AAAATTTTAAATTAATTTATTTTA
1 AAAAATTTAAATTAA-TTATTTTA
860618 AAAAATTTAAATTAATTATTT
1 AAAAATTTAAATTAATTATTT
860639 AACTAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAAAATTTAAATTAATTATTTTA
Found at i:861316 original size:20 final size:21
Alignment explanation
Indices: 861284--861322 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
861274 ACGATGCATA
861284 ATTAATATTTTAATATATATG
1 ATTAATATTTTAATATATATG
*
861305 ATTAAT-TTTTAATTTATA
1 ATTAATATTTTAATATATA
861323 AAAATTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
ATTAATATTTTAATATATATG
Found at i:861484 original size:18 final size:19
Alignment explanation
Indices: 861444--861485 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
861434 AAATAATTAA
*
861444 TAAAATTAATATATTATAT
1 TAAAATTAATATATTATAC
* *
861463 TAAATTTAATA-ATTCTAC
1 TAAAATTAATATATTATAC
861481 TAAAA
1 TAAAA
861486 AGAATTAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAAATTAATATATTATAC
Found at i:862760 original size:2 final size:2
Alignment explanation
Indices: 862753--862778 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
862743 ATCTCCGTAA
862753 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
862779 GATTAGACAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:863267 original size:19 final size:19
Alignment explanation
Indices: 863243--863281 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
863233 TTTTAATATT
863243 TTAATA-ATTTATATTATAA
1 TTAATATATTTAT-TTATAA
863262 TTAATATATTTATTTATAA
1 TTAATATATTTATTTATAA
863281 T
1 T
863282 CATATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAATATATTTATTTATAA
Found at i:867783 original size:24 final size:22
Alignment explanation
Indices: 867751--867835 Score: 82
Period size: 24 Copynumber: 3.7 Consensus size: 22
867741 ACTTGATAAT
867751 ATTAAATATAATATAAAAAAATA
1 ATTAAATATAATAT-AAAAAATA
*
867774 ATTAAAATATAATATATAAAATA
1 ATT-AAATATAATATAAAAAATA
* * *
867797 AATATATA-AATATAAAATATA
1 ATTAAATATAATATAAAAAATA
*
867818 TTTTAAATATAATTATAA
1 -ATTAAATATAA-TATAA
867836 TTTAATAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 11 0.22
22 9 0.18
23 14 0.28
24 16 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTAAATATAATATAAAAAATA
Found at i:867791 original size:31 final size:32
Alignment explanation
Indices: 867748--867817 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
867738 TTGACTTGAT
*
867748 AATATTAAATATAATATAAAAAAAT-AAT-TAA
1 AATA-TAAATATAAAATAAAAAAATAAATATAA
* *
867779 AATATAATATATAAAATAAATATATAAATATAA
1 AATATAA-ATATAAAATAAAAAAATAAATATAA
867812 AATATA
1 AATATA
867818 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 3 0.09
31 18 0.55
32 3 0.09
33 9 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (32 bp):
AATATAAATATAAAATAAAAAAATAAATATAA
Found at i:867798 original size:19 final size:19
Alignment explanation
Indices: 867748--867829 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
867738 TTGACTTGAT
* *
867748 AATATTAAATATAATATAAA
1 AATATAAAATA-AATATATA
* *
867768 AAAAT-AATTAAA-ATATA
1 AATATAAAATAAATATATA
867785 ATATATAAAATAAATATATA
1 A-ATATAAAATAAATATATA
* *
867805 AATATAAAATATAT-TTTA
1 AATATAAAATAAATATATA
867823 AATATAA
1 AATATAA
867830 TTATAATTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
17 5 0.10
18 15 0.29
19 22 0.42
20 10 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AATATAAAATAAATATATA
Found at i:867802 original size:13 final size:13
Alignment explanation
Indices: 867761--867817 Score: 66
Period size: 13 Copynumber: 4.4 Consensus size: 13
867751 ATTAAATATA
867761 ATATAAAA-AAAT
1 ATATAAAATAAAT
867773 A-ATTAAAATATAAT
1 ATA-TAAAATA-AAT
867787 ATATAAAATAAAT
1 ATATAAAATAAAT
867800 ATATAAATATAAA-
1 ATATAAA-ATAAAT
867813 ATATA
1 ATATA
867818 TTTTAAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.03
12 6 0.15
13 16 0.40
14 16 0.40
15 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATAAAATAAAT
Found at i:867807 original size:26 final size:27
Alignment explanation
Indices: 867746--867817 Score: 91
Period size: 24 Copynumber: 2.9 Consensus size: 27
867736 GATTGACTTG
867746 ATAATAT-TAAATATAATATA-AAAAA
1 ATAATATATAAATATAATATATAAAAA
*
867771 ATAAT-TA-AAATATAATATATAAAAT
1 ATAATATATAAATATAATATATAAAAA
*
867796 A-AATATATAAATATAAAATATA
1 ATAATATATAAATATAATATATA
867818 TTTTAAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 16 0.39
25 12 0.29
26 13 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
ATAATATATAAATATAATATATAAAAA
Found at i:867834 original size:17 final size:18
Alignment explanation
Indices: 867787--867840 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
867777 AAAATATAAT
867787 ATATAAAATA-AATATATAA
1 ATATAAAATATAAT-T-TAA
*
867806 ATATAAAATATATTTTAA
1 ATATAAAATATAATTTAA
*
867824 ATAT-AATTATAATTTAA
1 ATATAAAATATAATTTAA
867841 TAAAACATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 11 0.35
18 7 0.23
19 11 0.35
20 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAAAATATAATTTAA
Found at i:868634 original size:20 final size:21
Alignment explanation
Indices: 868604--868656 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
868594 GAATTTGAAT
*
868604 AATTTTTTTAATTTTAATT-A
1 AATTATTTTAATTTTAATTAA
*
868624 TATTATTTTAA-TTTAATTAA
1 AATTATTTTAATTTTAATTAA
868644 AATTATTATTAAT
1 AATTATT-TTAAT
868657 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 7 0.26
20 16 0.59
21 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTATTTTAATTTTAATTAA
Found at i:870237 original size:16 final size:16
Alignment explanation
Indices: 870213--870278 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
870203 GATAATTATT
870213 TTATGAAATATTAATA
1 TTATGAAATATTAATA
* * *
870229 TTATTAAATAAATATTA
1 TTATGAAAT-ATTAATA
* *
870246 ATATGATAT-TTAATAA
1 TTATGAAATATTAAT-A
*
870262 TTATGAAATTTTAATA
1 TTATGAAATATTAATA
870278 T
1 T
870279 ATAATAAAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
15 3 0.08
16 18 0.49
17 16 0.43
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (16 bp):
TTATGAAATATTAATA
Found at i:870361 original size:13 final size:13
Alignment explanation
Indices: 870340--870386 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 13
870330 CTTTTAATAA
870340 TATTAATATAAAT
1 TATTAATATAAAT
*
870353 TATT--TATATAT
1 TATTAATATAAAT
870364 T-TTAATA-AAAT
1 TATTAATATAAAT
870375 TA-TAATATAAAT
1 TATTAATATAAAT
870387 ATTTATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 6 0.21
13 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATTAATATAAAT
Found at i:870367 original size:32 final size:33
Alignment explanation
Indices: 870331--870392 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
870321 TGATGTTGAC
*
870331 TTTTAATAATA-T-TAATATAAATTATTTATATA
1 TTTTAATAAAATTATAATATAAA-TATTTATATA
870363 TTTTAATAAAATTATAATATAAATATTTAT
1 TTTTAATAAAATTATAATATAAATATTTAT
870393 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 10 0.37
33 8 0.30
34 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TTTTAATAAAATTATAATATAAATATTTATATA
Found at i:870382 original size:21 final size:23
Alignment explanation
Indices: 870333--870383 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
870323 ATGTTGACTT
870333 TTAATA-ATATTAATATAAATTA
1 TTAATATATATTAATATAAATTA
* *
870355 TTTATATATTTTAATA-AAATTA
1 TTAATATATATTAATATAAATTA
870377 -TAATATA
1 TTAATATA
870384 AATATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 11 0.44
23 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATATATATTAATATAAATTA
Found at i:871083 original size:2 final size:2
Alignment explanation
Indices: 871072--871103 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
871062 ATGGCTGCCT
871072 TA TA -A 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 T
871104 TCTTGGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:873616 original size:2 final size:2
Alignment explanation
Indices: 873609--873645 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
873599 TGGTGTTTCT
873609 TA 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 TA T
873646 TATTGTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:879437 original size:22 final size:21
Alignment explanation
Indices: 879380--879439 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
879370 TCAAACACAT
879380 TTTATATATC-AATTCATA-TA
1 TTTATATATCTAATT-ATATTA
*
879400 -TT-TATATCGTATTTATATTA
1 TTTATATATC-TAATTATATTA
879420 TTTATATATCATAATTATAT
1 TTTATATATC-TAATTATAT
879440 ATAAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 6 0.19
19 5 0.16
20 5 0.16
21 2 0.06
22 14 0.44
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTATATATCTAATTATATTA
Found at i:879480 original size:18 final size:19
Alignment explanation
Indices: 879457--879497 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
879447 ATTATCTAAA
*
879457 TTATAACATAATAATA-AT
1 TTATAAAATAATAATATAT
*
879475 TTATAAAATTATAATATAT
1 TTATAAAATAATAATATAT
879494 TTAT
1 TTAT
879498 TTTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATAAAATAATAATATAT
Found at i:880693 original size:16 final size:16
Alignment explanation
Indices: 880667--880734 Score: 93
Period size: 16 Copynumber: 4.2 Consensus size: 16
880657 TCATTGTTAA
*
880667 ATTTAGATTATTTCAGG
1 ATTTAAATTATTTC-GG
* *
880684 -TTTAAGTTATTTTGG
1 ATTTAAATTATTTCGG
880699 ATTTAAATTATTTCGG
1 ATTTAAATTATTTCGG
880715 ATTTAAATTATTTCGG
1 ATTTAAATTATTTCGG
880731 ATTT
1 ATTT
880735 GGGTTAATCA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
15 2 0.04
16 43 0.96
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.53
Consensus pattern (16 bp):
ATTTAAATTATTTCGG
Found at i:880703 original size:32 final size:32
Alignment explanation
Indices: 880667--880751 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
880657 TCATTGTTAA
* *
880667 ATTTAGATTATTTCAGGTTTAAGTTATTTTGG
1 ATTTAGATTATTTCAGGTTTAAATTATTTCGG
*
880699 ATTTAAATTATTTC-GGATTTAAATTATTTCGG
1 ATTTAGATTATTTCAGG-TTTAAATTATTTCGG
* * *
880731 ATTTGGGTTA-ATCAGGTTTAA
1 ATTTAGATTATTTCAGGTTTAA
880752 TACTTGGATT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 9 0.20
32 35 0.80
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (32 bp):
ATTTAGATTATTTCAGGTTTAAATTATTTCGG
Found at i:880844 original size:6 final size:6
Alignment explanation
Indices: 880833--880857 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
880823 TTCAAGTCAT
880833 TTTAAG TTTAAG TTTAAG TTTAAG T
1 TTTAAG TTTAAG TTTAAG TTTAAG T
880858 CAACCAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TTTAAG
Found at i:881583 original size:16 final size:16
Alignment explanation
Indices: 881562--881631 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 16
881552 GTTAATTGTC
881562 CGGATCATTTTAAGTT
1 CGGATCATTTTAAGTT
**
881578 CGGATCATTTCATTTTGGATT
1 CGGATCA--T--TTTAAG-TT
* *
881599 CAGATCATTTCAAGTT
1 CGGATCATTTTAAGTT
881615 CGGATCATTTTAAGTT
1 CGGATCATTTTAAGTT
881631 C
1 C
881632 AAATCATTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
16 24 0.59
17 3 0.07
18 1 0.02
19 1 0.02
20 4 0.10
21 8 0.20
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (16 bp):
CGGATCATTTTAAGTT
Found at i:881592 original size:21 final size:21
Alignment explanation
Indices: 881566--881610 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
881556 ATTGTCCGGA
*
881566 TCATTTTA-AGTTCGGATCATT
1 TCATTTTAGA-TTCAGATCATT
*
881587 TCATTTTGGATTCAGATCATT
1 TCATTTTAGATTCAGATCATT
881608 TCA
1 TCA
881611 AGTTCGGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (21 bp):
TCATTTTAGATTCAGATCATT
Found at i:881637 original size:16 final size:16
Alignment explanation
Indices: 881597--881643 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
881587 TCATTTTGGA
881597 TTCAGATCATTTCAAG
1 TTCAGATCATTTCAAG
* *
881613 TTCGGATCATTTTAAG
1 TTCAGATCATTTCAAG
*
881629 TTCAAATCATTTCAA
1 TTCAGATCATTTCAA
881644 ATTTCGAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (16 bp):
TTCAGATCATTTCAAG
Found at i:881733 original size:22 final size:24
Alignment explanation
Indices: 881690--881737 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
881680 CATCAATTCA
881690 AATTAAATTAAATTTAAATTTAAATT
1 AATTAAATTAAATTT--ATTTAAATT
881716 AATT-AATTAAATTT-TTTAAATT
1 AATTAAATTAAATTTATTTAAATT
881738 CAAATCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
25 10 0.45
26 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTAAATTAAATTTATTTAAATT
Found at i:882697 original size:8 final size:8
Alignment explanation
Indices: 882684--882796 Score: 55
Period size: 8 Copynumber: 14.1 Consensus size: 8
882674 GTGATTTATT
882684 TATATTTA
1 TATATTTA
882692 TATATTT-
1 TATATTTA
882699 TATATATTA
1 TATAT-TTA
882708 TA-A-TTA
1 TATATTTA
*
882714 TGTA-TTA
1 TATATTTA
*
882721 AATA-TTA
1 TATATTTA
882728 TATATTTA
1 TATATTTA
882736 TATAAAATTTA
1 TAT---ATTTA
882747 -ATATTT-
1 TATATTTA
882753 TAATATTT-
1 T-ATATTTA
*
882761 TAT-GTTA
1 TATATTTA
882768 TATTAATTTTGA
1 TA-T-A-TTT-A
882780 TATATTTA
1 TATATTTA
882788 TATATTTA
1 TATATTTA
882796 T
1 T
882797 TTTGTATTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 30
0.70 0.05 0.25
Matches are distributed among these distances:
6 6 0.07
7 25 0.30
8 34 0.40
9 5 0.06
10 3 0.04
11 8 0.10
12 3 0.04
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (8 bp):
TATATTTA
Found at i:882709 original size:22 final size:21
Alignment explanation
Indices: 882681--882739 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
882671 TTGGTGATTT
**
882681 ATTTATATTTATATATTTTAT
1 ATTTATATTTATATATTAAAT
* *
882702 ATATTATAATTATGTATTAAAT
1 AT-TTATATTTATATATTAAAT
882724 ATTATATATTTATATA
1 ATT-TATATTTATATA
882740 AAATTTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTATATTTATATATTAAAT
Found at i:882743 original size:20 final size:20
Alignment explanation
Indices: 882702--882752 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
882692 TATATTTTAT
* *
882702 ATATTATA-ATTATGTATTAA
1 ATATTATATATT-TATATAAA
882722 ATATTATATATTTATATAAA
1 ATATTATATATTTATATAAA
882742 AT-TTA-ATATTT
1 ATATTATATATTT
882753 TAATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.21
19 3 0.11
20 16 0.57
21 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATATTATATATTTATATAAA
Found at i:882814 original size:22 final size:22
Alignment explanation
Indices: 882766--882816 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
882756 TATTTTATGT
882766 TATATTAATTTTGATATATTTA
1 TATATTAATTTTGATATATTTA
*
882788 TATATTTATTTTG-TAT-TTATA
1 TATATTAATTTTGATATATT-TA
882809 TAATATTA
1 T-ATATTA
882817 TATCATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 2 0.08
21 6 0.24
22 17 0.68
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TATATTAATTTTGATATATTTA
Found at i:883340 original size:2 final size:2
Alignment explanation
Indices: 883333--883358 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
883323 AAGTTACGAC
883333 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
883359 GATTTAAGTT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:883727 original size:14 final size:14
Alignment explanation
Indices: 883710--883749 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
883700 AAATAGTTTT
883710 TTTAAAATTTATAA
1 TTTAAAATTTATAA
883724 TTTAAAA-TTATAA
1 TTTAAAATTTATAA
*
883737 ATTATAAATTTAT
1 TTTA-AAATTTAT
883750 TGAATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 9 0.39
14 10 0.43
15 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAAATTTATAA
Found at i:889797 original size:19 final size:19
Alignment explanation
Indices: 889775--889817 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
889765 TAATTTTTAT
889775 ATATAAATAATTTTAAAAA
1 ATATAAATAATTTTAAAAA
** *
889794 ATATATTTATTTTTAAAAA
1 ATATAAATAATTTTAAAAA
*
889813 TTATA
1 ATATA
889818 CATTTTATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATAAATAATTTTAAAAA
Found at i:889962 original size:19 final size:19
Alignment explanation
Indices: 889928--889970 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
889918 GGATAGAATT
*
889928 ATTTTTTAAAATTT-AAAA
1 ATTTATTAAAATTTAAAAA
889946 ATTTATTAAATATTTAAAAA
1 ATTTATTAAA-ATTTAAAAA
889966 ATTTA
1 ATTTA
889971 AATAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 4 0.18
20 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTATTAAAATTTAAAAA
Found at i:890244 original size:2 final size:2
Alignment explanation
Indices: 890237--890289 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
890227 TCTCTATCTC
*
890237 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
890279 AT AT AT GT AT A
1 AT AT AT AT AT A
890290 AAGAGAAGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:891044 original size:37 final size:39
Alignment explanation
Indices: 890975--891065 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 39
890965 ATTTAAAAAT
* * *
890975 TTAAAATTATTTATATAAATTATATAATAATTAGTATTTAA
1 TTAAAA-TATTTAAATAAATTATATAATAATTAATATGT-A
891016 TTAAAATATTTAAATAAA-TATAT-A-AATTAATATGTA
1 TTAAAATATTTAAATAAATTATATAATAATTAATATGTA
*
891052 TTTAAAT-TTTAAAT
1 TTAAAATATTTAAAT
891066 GTTAAATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
35 7 0.15
36 7 0.15
37 9 0.20
38 1 0.02
39 5 0.11
40 11 0.24
41 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (39 bp):
TTAAAATATTTAAATAAATTATATAATAATTAATATGTA
Found at i:891127 original size:15 final size:16
Alignment explanation
Indices: 891101--891130 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
891091 AAAATAATTT
891101 ATCAATATATTTTTAA
1 ATCAATATATTTTTAA
891117 ATCAA-ATATTTTTA
1 ATCAATATATTTTTA
891131 TTGATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (16 bp):
ATCAATATATTTTTAA
Found at i:891424 original size:2 final size:2
Alignment explanation
Indices: 891417--891456 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
891407 GGTACAAATT
*
891417 TA TA TA TA TA TA TA TA T- TT TCA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
891457 AACACACCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:891977 original size:2 final size:2
Alignment explanation
Indices: 891964--891999 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
891954 CGGCTTGAGC
*
891964 AT AT AA 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
892000 TTCAATCAAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:895326 original size:34 final size:34
Alignment explanation
Indices: 895283--895500 Score: 250
Period size: 34 Copynumber: 6.4 Consensus size: 34
895273 TTGATAAAAA
*
895283 CTACCATTTAATCAACAATGGCAACCTACCAAAT
1 CTACCATTTAATCAACAATGGTAACCTACCAAAT
* *
895317 CTACCATTTAGTCAATAATGGTAAGCC-ACCAAAT
1 CTACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
895351 C-ACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CTA-CCATTTAATCAACAATGGTAACCTACCAAAT
* *
895385 -TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CTAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
895419 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 CTACCATTTAATCAACAATGG-TAACCTACCAAAT
*
895453 C-ACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CTA-CCATTTAATCAACAATGGTAACCTACCAAAT
895487 C-ACCATTTAATCAA
1 CTACCATTTAATCAA
895501 GAATTCTCCC
Statistics
Matches: 160, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
33 18 0.11
34 135 0.84
35 7 0.04
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CTACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:895405 original size:68 final size:67
Alignment explanation
Indices: 895286--895500 Score: 279
Period size: 68 Copynumber: 3.2 Consensus size: 67
895276 ATAAAAACTA
* * * *
895286 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAATAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
895351 CAC
65 CAC
* * * *
895354 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
895419 CTC
65 CAC
* * * *
895422 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
895487 CA-
65 CAC
895489 CCATTTAATCAA
1 CCATTTAATCAA
895501 GAATTCTCCC
Statistics
Matches: 127, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 13 0.10
68 113 0.89
69 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:895463 original size:102 final size:101
Alignment explanation
Indices: 895285--895500 Score: 333
Period size: 102 Copynumber: 2.1 Consensus size: 101
895275 GATAAAAACT
* * *
895285 ACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAATAATGGTAAGCCACCAAA
1 ACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAA
* * *
895350 TCACCCATTTAATCAATAATGGTAAGCTACCAAATT
66 TCACCCATTTAATCAACAATGGTAAACTACCAAATC
* * * *
895386 TCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
1 AC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
895451 ATCACCCATTTAATCAACAATGGTAAACTACCAAATC
65 ATCACCCATTTAATCAACAATGGTAAACTACCAAATC
895488 ACCATTTAATCAA
1 ACCATTTAATCAA
895501 GAATTCTCCC
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 12 0.12
102 91 0.88
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
ACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAA
TCACCCATTTAATCAACAATGGTAAACTACCAAATC
Found at i:896424 original size:34 final size:34
Alignment explanation
Indices: 896355--896570 Score: 161
Period size: 34 Copynumber: 6.3 Consensus size: 34
896345 TGTCTCCAGA
896355 TAATCAACAATGG-ACAACCTACCAAATCTAC-CATT
1 TAATCAACAATGGTA-AACC-ACCAAAT-TACTCATT
* *
896390 TAGTCAACAATGGTAAGCCACCAAATTACTCATT
1 TAATCAACAATGGTAAACCACCAAATTACTCATT
* * *** **
896424 TAATCAATAATGATAAGTTACCAAATTTTTCATT
1 TAATCAACAATGGTAAACCACCAAATTACTCATT
* * *
896458 TAATCAACAATGGTAAGCTACCAAATCT-CCCATT
1 TAATCAACAATGGTAAACCACCAAAT-TACTCATT
* ** * * *
896492 TAGTCAACAATGACAAACCTACCGAATCACCCATT
1 TAATCAACAATGGTAAACC-ACCAAATTACTCATT
* * * *
896527 TAATTAACAATAGTAAACTACCAAATCA-TCATT
1 TAATCAACAATGGTAAACCACCAAATTACTCATT
896560 TAATCAACAAT
1 TAATCAACAAT
896571 CATAATAATA
Statistics
Matches: 146, Mismatches: 30, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
33 17 0.12
34 87 0.60
35 41 0.28
36 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (34 bp):
TAATCAACAATGGTAAACCACCAAATTACTCATT
Found at i:896559 original size:102 final size:103
Alignment explanation
Indices: 896355--896570 Score: 258
Period size: 102 Copynumber: 2.1 Consensus size: 103
896345 TGTCTCCAGA
** * * *
896355 TAATCAACAATGGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATTACT
1 TAATCAACAATGGACAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAAATCACC
* ** **
896420 CATTTAATCAATAATGATAAGTTACCAAATTTTTCATT
66 CATTTAATCAACAATGATAAACTACCAAATTCATCATT
* * * *
896458 TAATCAACAATGG-TAAGCTACCAAATCTCCCATTTAGTCAACAATGACAAACCTACCGAATCAC
1 TAATCAACAATGGACAACCTACCAAATCTACCATTTAGTCAACAATGACAAACC-ACCAAATCAC
*
896522 CCATTTAATTAACAAT-AGTAAACTACCAAA-TCATCATT
65 CCATTTAATCAACAATGA-TAAACTACCAAATTCATCATT
896560 TAATCAACAAT
1 TAATCAACAAT
896571 CATAATAATA
Statistics
Matches: 96, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
102 52 0.54
103 44 0.46
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (103 bp):
TAATCAACAATGGACAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAAATCACC
CATTTAATCAACAATGATAAACTACCAAATTCATCATT
Found at i:898578 original size:19 final size:19
Alignment explanation
Indices: 898534--898579 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
898524 AATATAATAT
*
898534 AAATTT-TTTAAAAATTTA
1 AAATTTATTAAAAAATTTA
*
898552 AATTTTTATTAAAAAATTTA
1 AA-ATTTATTAAAAAATTTA
898572 AAATTTAT
1 AAATTTAT
898580 AATATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 2 0.09
19 8 0.35
20 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATTTATTAAAAAATTTA
Found at i:900809 original size:38 final size:39
Alignment explanation
Indices: 900757--900835 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 39
900747 AATTGAAACG
900757 AACAGGTATTCTTCTTGTTTGTACCATCTTATGGTGTCA
1 AACAGGTATTCTTCTTGTTTGTACCATCTTATGGTGTCA
900796 AACAGGT-TTCTTCTTGTTTGTACCATCTTATGGTGTCA
1 AACAGGTATTCTTCTTGTTTGTACCATCTTATGGTGTCA
900834 AA
1 AA
900836 GATTCTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 33 0.82
39 7 0.17
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.43
Consensus pattern (39 bp):
AACAGGTATTCTTCTTGTTTGTACCATCTTATGGTGTCA
Found at i:909191 original size:2 final size:2
Alignment explanation
Indices: 909186--909212 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
909176 AGAAAAAATA
909186 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
909213 CATACAACTC
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:911002 original size:23 final size:24
Alignment explanation
Indices: 910972--911021 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
910962 AAAATTTTAT
*
910972 TAAAATATAATTATA-TTAAATAA
1 TAAAATATAATTATATTTAAAAAA
*
910995 TAAAATATATTTATATTTAAAAAA
1 TAAAATATAATTATATTTAAAAAA
911019 TAA
1 TAA
911022 TAAACTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAAATATAATTATATTTAAAAAA
Found at i:911280 original size:22 final size:23
Alignment explanation
Indices: 911252--911296 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
911242 TTTCACTTAA
911252 ATTATTT-ATTTAATAATAAAAT
1 ATTATTTAATTTAATAATAAAAT
*
911274 ATTATTTAAATTTAATTATAAAA
1 ATTATTT-AATTTAATAATAAAA
911297 ATATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTATTTAATTTAATAATAAAAT
Found at i:911333 original size:33 final size:33
Alignment explanation
Indices: 911249--911333 Score: 79
Period size: 34 Copynumber: 2.6 Consensus size: 33
911239 TAGTTTCACT
*
911249 TAAA-TTA-TTTATTTAATA-ATAAAATATTATT
1 TAAATTTATTTTA-TTAATATATAAAATATTATA
* * *
911280 TAAATTTA-ATTATAAAAATATATAAATATTAATA
1 TAAATTTATTTTATTAATATATA-AAATATT-ATA
911314 TAAATTTATTTTATTAATAT
1 TAAATTTATTTTATTAATAT
911334 TTTAATAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
31 8 0.19
32 9 0.21
33 7 0.17
34 10 0.24
35 8 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
TAAATTTATTTTATTAATATATAAAATATTATA
Found at i:912814 original size:3 final size:3
Alignment explanation
Indices: 912794--912834 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
912784 ACCTCGTCAT
* *
912794 CAC CAT CAC CAT CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
912835 TCATCGTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.34, C:0.61, G:0.00, T:0.05
Consensus pattern (3 bp):
CAC
Found at i:912818 original size:9 final size:9
Alignment explanation
Indices: 912748--912834 Score: 66
Period size: 9 Copynumber: 9.3 Consensus size: 9
912738 TTCATCCTCC
*
912748 CCACCACCT
1 CCACCACCA
*
912757 CCACCTCCA
1 CCACCACCA
*
912766 CCATCACCA
1 CCACCACCA
* *
912775 GCAACACCAA
1 CCACCACC-A
* *
912785 CCTCGTCATCA
1 CCAC--CACCA
*
912796 CCATCACCA
1 CCACCACCA
*
912805 TCACCACCA
1 CCACCACCA
912814 CCACCACCA
1 CCACCACCA
912823 CCACCACCA
1 CCACCACCA
912832 CCA
1 CCA
912835 TCATCGTCAT
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
9 51 0.86
10 2 0.03
11 3 0.05
12 3 0.05
ACGTcount: A:0.31, C:0.57, G:0.02, T:0.09
Consensus pattern (9 bp):
CCACCACCA
Found at i:912870 original size:9 final size:9
Alignment explanation
Indices: 912794--912872 Score: 61
Period size: 9 Copynumber: 8.8 Consensus size: 9
912784 ACCTCGTCAT
912794 CACCATCAC
1 CACCATCAC
* *
912803 CATCACCAC
1 CACCATCAC
*
912812 CACCACCAC
1 CACCATCAC
*
912821 CACCACCAC
1 CACCATCAC
*
912830 CACCATCAT
1 CACCATCAC
**
912839 CGTCATCAC
1 CACCATCAC
**
912848 CATTACTC-C
1 CACCA-TCAC
912857 CACCATCAC
1 CACCATCAC
912866 CACCATC
1 CACCATC
912873 CTCATCTAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
8 2 0.04
9 52 0.93
10 2 0.04
ACGTcount: A:0.30, C:0.54, G:0.01, T:0.14
Consensus pattern (9 bp):
CACCATCAC
Found at i:915866 original size:2 final size:2
Alignment explanation
Indices: 915854--915890 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
915844 GTTGCTTCCC
*
915854 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
915891 ACTCTACCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:919536 original size:2 final size:2
Alignment explanation
Indices: 919518--919564 Score: 53
Period size: 2 Copynumber: 23.0 Consensus size: 2
919508 TTGCTAAGCA
919518 AT AT AT CAT ACT A- AT AT AT ACT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
919559 AT AT AT
1 AT AT AT
919565 GCTGTTGGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 2 0.05
2 33 0.82
3 5 0.12
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:928083 original size:29 final size:31
Alignment explanation
Indices: 928034--928093 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
928024 TAAGAATTAG
*
928034 ATTTAAAAATAAAATTTTAAAATATT-TAAT
1 ATTTAAAAATAAAATCTTAAAATATTATAAT
*
928064 ATTTAAAAATAATA-CTTAAAATATTATAAT
1 ATTTAAAAATAAAATCTTAAAATATTATAAT
928094 TATTATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (31 bp):
ATTTAAAAATAAAATCTTAAAATATTATAAT
Found at i:928243 original size:95 final size:95
Alignment explanation
Indices: 928136--928333 Score: 296
Period size: 95 Copynumber: 2.1 Consensus size: 95
928126 GATATAAAAT
* *
928136 ATATA-TAAAAAATAAACTAATTCAAATATAAATATAAAATAAAAAGC-AAAATTTTAAATTAAA
1 ATATAGTATAAAATAAACTAATTCAAATATAAATACAAAATAAAAA-CAAAAATTTTAAATTAAA
*
928199 GGATATTTAAAAAATTGA-AAAATGAATAATA
65 GGATATTT-AAAAATTAATAAAATGAATAATA
* *
928230 A-ATTAGTATAAAATAAACTTATTTAAATATAAATACAAAATAAAAACAAAAATTTTAAATTAAA
1 ATA-TAGTATAAAATAAACTAATTCAAATATAAATACAAAATAAAAACAAAAATTTTAAATTAAA
928294 GGATATTTAAAAATTAATAAAATGAATAATA
65 GGATATTTAAAAATTAATAAAATGAATAATA
928325 ATATAGTAT
1 ATATAGTAT
928334 GATGAAAGGT
Statistics
Matches: 94, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
93 1 0.01
94 12 0.13
95 80 0.85
96 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (95 bp):
ATATAGTATAAAATAAACTAATTCAAATATAAATACAAAATAAAAACAAAAATTTTAAATTAAAG
GATATTTAAAAATTAATAAAATGAATAATA
Found at i:929688 original size:32 final size:32
Alignment explanation
Indices: 929611--929690 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
929601 AATTAGACAT
* *
929611 AATTTTTTATAAATTTTATGAATATTAAATAA
1 AATTATTTATAAATTTTATGAATAATAAATAA
*
929643 AATTAATCT-TAAATTTTATGAATAATAAATAA
1 AATT-ATTTATAAATTTTATGAATAATAAATAA
929675 AATTATTTATAAATTT
1 AATTATTTATAAATTT
929691 GATAATTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.07
32 37 0.88
33 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (32 bp):
AATTATTTATAAATTTTATGAATAATAAATAA
Found at i:930242 original size:6 final size:6
Alignment explanation
Indices: 930231--930255 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
930221 AGAAAGAGAT
930231 AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA A
930256 GCCCTAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:930461 original size:6 final size:6
Alignment explanation
Indices: 930450--930481 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
930440 TTTCATTCTT
930450 AAAGAA AAAGAA AAAGAA AAAGAA AAA-AA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
930482 CACTTGTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:935473 original size:2 final size:2
Alignment explanation
Indices: 935463--935514 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
935453 TAATACACAC
* * *
935463 AT AT GT AT AT AT AT AT GT AT GT 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
935505 AT AT AT AT AT
1 AT AT AT AT AT
935515 TACTTAAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:937062 original size:24 final size:27
Alignment explanation
Indices: 937030--937081 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
937020 AATATTTAAA
*
937030 TTTATTA-TTTAAATTTGTTT-TATAT
1 TTTATTATTTTAAATTTATTTATATAT
*
937055 TTTA-TATTTTATATTTATTTATATAT
1 TTTATTATTTTAAATTTATTTATATAT
937081 T
1 T
937082 ATTTTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.09
25 15 0.65
26 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
TTTATTATTTTAAATTTATTTATATAT
Found at i:937507 original size:20 final size:20
Alignment explanation
Indices: 937482--937574 Score: 75
Period size: 21 Copynumber: 4.5 Consensus size: 20
937472 TATTGAGTTA
* *
937482 AATTTAAATATTTTATATTT
1 AATTTAAATATTTTAAAATT
937502 AATTTAAATAATTTATAAAATT
1 AATTTAAAT-ATTT-TAAAATT
*
937524 AA-TTAAATATTTT-TAATT
1 AATTTAAATATTTTAAAATT
* *
937542 AATATTATAAAATTAT-AAATT
1 AAT-TTA-AATATTTTAAAATT
937563 AGATTTAAATAT
1 A-ATTTAAATAT
937575 AAATAATTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
18 6 0.10
19 1 0.02
20 20 0.33
21 24 0.40
22 9 0.15
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
AATTTAAATATTTTAAAATT
Found at i:937530 original size:41 final size:41
Alignment explanation
Indices: 937483--937574 Score: 111
Period size: 41 Copynumber: 2.2 Consensus size: 41
937473 ATTGAGTTAA
*
937483 ATTTAAATATTTTATATTTAAT-TTA-AATAATTTATAAAATTA-
1 ATTTAAATATTTT-TAATTAATATTATAA-AA-TTAT-AAATTAG
937525 A-TTAAATATTTTTAATTAATATTATAAAATTATAAATTAG
1 ATTTAAATATTTTTAATTAATATTATAAAATTATAAATTAG
937565 ATTTAAATAT
1 ATTTAAATAT
937575 AAATAATTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
39 6 0.13
40 12 0.27
41 24 0.53
42 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (41 bp):
ATTTAAATATTTTTAATTAATATTATAAAATTATAAATTAG
Found at i:937906 original size:16 final size:17
Alignment explanation
Indices: 937887--937927 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
937877 AATTTATATT
937887 TAAATAAATTAT-TTTA
1 TAAATAAATTATATTTA
*
937903 TAAATTAAATTTTATTTA
1 TAAA-TAAATTATATTTA
937921 -AAATAAA
1 TAAATAAA
937928 AATAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 10 0.45
18 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATAAATTATATTTA
Found at i:937944 original size:34 final size:32
Alignment explanation
Indices: 937875--937958 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 32
937865 TATTTAATTC
* *
937875 TTAATTTATATTT-AAATAAATTATTTTATAAA
1 TTAATTT-TATTTAAAATAAAATAATTTATAAA
937907 TTAAATTTTATTTAAAATAAAAATAATTTA-AAGA
1 TT-AATTTTATTTAAAAT-AAAATAATTTATAA-A
937941 TTAATATTTATTTAAAAT
1 TTAAT-TTTATTTAAAAT
937959 TTTTTAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
32 7 0.16
33 14 0.31
34 24 0.53
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
TTAATTTTATTTAAAATAAAATAATTTATAAA
Found at i:949115 original size:167 final size:167
Alignment explanation
Indices: 948833--949172 Score: 617
Period size: 167 Copynumber: 2.0 Consensus size: 167
948823 CGATTGACTG
* * *
948833 AAGCCCTTACTCTGTCACCGAGGAACTCCAAAGTCTAGGACATAATGAAGAAATATGGAAGATAA
1 AAGCCATTACTCTGTCACCAAGGAACACCAAAGTCTAGGACATAATGAAGAAATATGGAAGATAA
*
948898 TCAGTAGAGGAAAAGCTCGACCAAATTAGTTGGGAAAAATTTGCTAATTAAAATGAAAAGCCTGA
66 TCAGTAAAGGAAAAGCTCGACCAAATTAGTTGGGAAAAATTTGCTAATTAAAATGAAAAGCCTGA
948963 AACAAGCTGAAGAAGAAAAGCATGTTATTTAGAATAC
131 AACAAGCTGAAGAAGAAAAGCATGTTATTTAGAATAC
949000 AAGCCATTACTCTGTCACCAAGGAACACCAAAGTCTAGGACATAATGAAGAAATATGGAAGATAA
1 AAGCCATTACTCTGTCACCAAGGAACACCAAAGTCTAGGACATAATGAAGAAATATGGAAGATAA
* *
949065 TCAGTAAAGGAAAAGCTCGACCAAATTAGTTGGGAAAACTTTGCTAATTAAAATGAAAAGTCTGA
66 TCAGTAAAGGAAAAGCTCGACCAAATTAGTTGGGAAAAATTTGCTAATTAAAATGAAAAGCCTGA
*
949130 AACATGCTGAAGAAGAAAAGCATGTTATTTAGAATAC
131 AACAAGCTGAAGAAGAAAAGCATGTTATTTAGAATAC
949167 AAGCCA
1 AAGCCA
949173 GGTCTAACAA
Statistics
Matches: 166, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
167 166 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (167 bp):
AAGCCATTACTCTGTCACCAAGGAACACCAAAGTCTAGGACATAATGAAGAAATATGGAAGATAA
TCAGTAAAGGAAAAGCTCGACCAAATTAGTTGGGAAAAATTTGCTAATTAAAATGAAAAGCCTGA
AACAAGCTGAAGAAGAAAAGCATGTTATTTAGAATAC
Found at i:951042 original size:2 final size:2
Alignment explanation
Indices: 951035--951064 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
951025 TTCTTTTGTA
*
951035 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
951065 GTTTACGTAT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:960346 original size:14 final size:14
Alignment explanation
Indices: 960266--960346 Score: 57
Period size: 14 Copynumber: 6.1 Consensus size: 14
960256 AATTATTTTA
*
960266 TATTATATTTATA-
1 TATTATAATTATAT
*
960279 TATT-TTATTATAT
1 TATTATAATTATAT
*
960292 TA--A-AATTATTT
1 TATTATAATTATAT
* *
960303 TAATATAAATATAT
1 TATTATAATTATAT
960317 TATTATAATT-TAAT
1 TATTATAATTAT-AT
*
960331 TATTTTAATTATAT
1 TATTATAATTATAT
960345 TA
1 TA
960347 CAATTATGCT
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
11 8 0.15
12 6 0.12
13 8 0.15
14 29 0.56
15 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTATAATTATAT
Found at i:962311 original size:18 final size:19
Alignment explanation
Indices: 962252--962314 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 19
962242 CATTTTAATC
962252 ATATTTAAATATAA-ATATT
1 ATATTT-AATATAATATATT
* * * *
962271 ATGTTTATTATAATTTTTT
1 ATATTTAATATAATATATT
962290 ATATTTAATA-AATATATT
1 ATATTTAATATAATATATT
962308 ATATTTA
1 ATATTTA
962315 TATTATTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 19 0.54
19 16 0.46
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATATTTAATATAATATATT
Found at i:962315 original size:37 final size:37
Alignment explanation
Indices: 962252--962329 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 37
962242 CATTTTAATC
* *
962252 ATATTTAAATATAAATATTATGTTTATTATAATTTTTT
1 ATATTTAAATATAAATATTATATTTA-TATAATTTTTG
*
962290 ATATTT-AATA-AATATATTATATTTATATTATTTTTG
1 ATATTTAAATATAA-ATATTATATTTATATAATTTTTG
962326 ATAT
1 ATAT
962330 CACATTCTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 15 0.42
37 15 0.42
38 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.58
Consensus pattern (37 bp):
ATATTTAAATATAAATATTATATTTATATAATTTTTG
Found at i:963372 original size:17 final size:18
Alignment explanation
Indices: 963352--963394 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
963342 TCTTTTTTAA
963352 TAAAAAATAATT-TTT-TT
1 TAAAAAA-AATTCTTTCTT
*
963369 TAAAAAAATTTCTTTCTT
1 TAAAAAAAATTCTTTCTT
963387 TAAAAAAA
1 TAAAAAAA
963395 TCAACCGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 10 0.43
18 10 0.43
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAAAAAATTCTTTCTT
Found at i:964010 original size:13 final size:14
Alignment explanation
Indices: 963980--964015 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
963970 AATATTTAAC
*
963980 AAATTAAATATGAT
1 AAATTAAATATAAT
963994 AAATTAAATA-AAT
1 AAATTAAATATAAT
964007 AAATTAAAT
1 AAATTAAAT
964016 CATAGTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
AAATTAAATATAAT
Found at i:964444 original size:23 final size:23
Alignment explanation
Indices: 964393--964445 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
964383 CATTAATTTT
964393 AACAAG-GACAAAATAAAAACAC
1 AACAAGAGACAAAATAAAAACAC
* * *
964415 AAGAAGAGA-AAAATTAAAACCTC
1 AACAAGAGACAAAA-TAAAAACAC
964438 AACAAGAG
1 AACAAGAG
964446 TCCCTTCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.64, C:0.15, G:0.13, T:0.08
Consensus pattern (23 bp):
AACAAGAGACAAAATAAAAACAC
Found at i:966334 original size:2 final size:2
Alignment explanation
Indices: 966327--966378 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
966317 TCAAAGTGGC
*
966327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT A- AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
966369 AT AT A- AT AT A
1 AT AT AT AT AT A
966379 AAATTATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 41 0.91
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:968433 original size:13 final size:12
Alignment explanation
Indices: 968415--968474 Score: 65
Period size: 11 Copynumber: 5.2 Consensus size: 12
968405 TAATAATTTT
968415 AATATAATATACA
1 AATATAATATA-A
968428 AATATAATATAA
1 AATATAATATAA
968440 AA-ATAAT-TAA
1 AATATAATATAA
*
968450 AATTTAATATAA
1 AATATAATATAA
*
968462 TATA-AATA-AA
1 AATATAATATAA
968472 AAT
1 AAT
968475 TTTAAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 9 0.22
11 13 0.32
12 8 0.20
13 11 0.27
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
AATATAATATAA
Found at i:968481 original size:40 final size:41
Alignment explanation
Indices: 968390--968507 Score: 107
Period size: 40 Copynumber: 2.8 Consensus size: 41
968380 TAATTATAAT
*
968390 TTTTAAAAATAAATTTAATAATTTTAATATAATATACAAATATAA
1 TTTTAAAAAT-AA-TTAA-AA-TTTAATATAATATACAAATAAAA
*
968435 -TATAAAAATAATTAAAATTTAATATAATAT--AAATAAAAA
1 TTTTAAAAATAATTAAAATTTAATATAATATACAAAT-AAAA
* * *
968474 TTTTAAAATTAATTTAATTTTAATTATTAATATA
1 TTTTAAAAATAATTAAAATTTAA-TA-TAATATA
968508 TTTAAAATTT
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
38 4 0.06
39 3 0.05
40 31 0.50
41 4 0.06
42 10 0.16
43 2 0.03
44 8 0.13
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (41 bp):
TTTTAAAAATAATTAAAATTTAATATAATATACAAATAAAA
Found at i:968634 original size:18 final size:18
Alignment explanation
Indices: 968590--968632 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
968580 TATTAATTTT
968590 TAAATTTATTAATAAAAA
1 TAAATTTATTAATAAAAA
*
968608 TAAATTTATTAATATAAA
1 TAAATTTATTAATAAAAA
968626 TATAATT
1 TA-AATT
968633 ATATAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATTTATTAATAAAAA
Found at i:968656 original size:23 final size:24
Alignment explanation
Indices: 968617--968675 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 24
968607 ATAAATTTAT
968617 TAATATAAATATAATTATATAAAAA-A
1 TAATATAAA-AT-ATTATA-AAAAATA
968643 TAAT-TAAAATATTATAAAAAATA
1 TAATATAAAATATTATAAAAAATA
968666 TAATATAAAA
1 TAATATAAAA
968676 ATAAAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.16
23 11 0.35
24 7 0.23
25 4 0.13
26 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
TAATATAAAATATTATAAAAAATA
Found at i:968679 original size:11 final size:12
Alignment explanation
Indices: 968617--968679 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
968607 ATAAATTTAT
968617 TAATATAAATATAA
1 TAATATAAA-AT-A
* *
968631 TTATATAAAAAA
1 TAATATAAAATA
968643 TAAT-TAAAATA
1 TAATATAAAATA
* *
968654 TTATAAAAAATA
1 TAATATAAAATA
968666 TAATATAAAA-A
1 TAATATAAAATA
968677 TAA
1 TAA
968680 AAATATAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
11 13 0.32
12 18 0.45
13 1 0.03
14 8 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATATAAAATA
Found at i:968682 original size:21 final size:21
Alignment explanation
Indices: 968618--968682 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
968608 TAAATTTATT
** *
968618 AATATAAATATAATTATATAAA
1 AATAT-AATATAAAAATAAAAA
968640 AA-ATAAT-TAAAATATTATAAAA
1 AATATAATATAAAA-A-TA-AAAA
968662 AATATAATATAAAAATAAAAA
1 AATATAATATAAAAATAAAAA
968683 TATAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
19 3 0.09
20 4 0.11
21 8 0.23
22 9 0.26
23 6 0.17
24 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AATATAATATAAAAATAAAAA
Found at i:968717 original size:49 final size:48
Alignment explanation
Indices: 968609--968717 Score: 112
Period size: 49 Copynumber: 2.2 Consensus size: 48
968599 TAATAAAAAT
* **
968609 AAATTTATTAATATAAATATAATTATATAAAAAATAATTAAAATATTATA
1 AAATTTA-TAATATAAAAATAAAAATATAAAAAATAATT-AAATATTATA
** * *
968659 AAAAATATAATATAAAAATAAAAATATAAAAAAATATATT-AATTTTTTA
1 AAATTTATAATATAAAAATAAAAATAT-AAAAAATA-ATTAAATATTATA
968708 AAATTTATAA
1 AAATTTATAA
968718 AATTTTAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
49 32 0.67
50 13 0.27
51 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (48 bp):
AAATTTATAATATAAAAATAAAAATATAAAAAATAATTAAATATTATA
Found at i:968752 original size:26 final size:25
Alignment explanation
Indices: 968705--968757 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
968695 TATTAATTTT
* *
968705 TTAAAATTTATAAAATTTTAAATATA
1 TTAAAATTAATAAAATTATAAA-ATA
968731 TTAAAATTAATATAAA-TATAAAATA
1 TTAAAATTAATA-AAATTATAAAATA
968756 TT
1 TT
968758 TTAAATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.21
26 16 0.67
27 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAAAATTAATAAAATTATAAAATA
Found at i:969914 original size:18 final size:18
Alignment explanation
Indices: 969891--969926 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
969881 ACGTGAGGGT
*
969891 GGATATGGCGGTGGTGGA
1 GGATATGGCGATGGTGGA
969909 GGATATGGCGATGGTGGA
1 GGATATGGCGATGGTGGA
969927 TACGGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.53, T:0.22
Consensus pattern (18 bp):
GGATATGGCGATGGTGGA
Found at i:972534 original size:2 final size:2
Alignment explanation
Indices: 972520--972560 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
972510 GATGATAAAA
972520 AT AT AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
972561 GAAATATACC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:985385 original size:30 final size:29
Alignment explanation
Indices: 985343--985456 Score: 115
Period size: 30 Copynumber: 3.9 Consensus size: 29
985333 TTCTCCATCG
*
985343 TCATCATTATCTTCTTCTAATTCTTCTTCA
1 TCATCATCATCTTCTTCT-ATTCTTCTTCA
* * * *
985373 TCATCAACATCTTCTTC-A-TCGTCATCG
1 TCATCATCATCTTCTTCTATTCTTCTTCA
*
985400 TCATCATCATCTTCTTCTTCTTCTTCTTCA
1 TCATCATCATCTTCTTC-TATTCTTCTTCA
* *
985430 TCGTCATCATCTTCTTCTCCTTCTTCT
1 TCATCATCATCTTCTTCT-ATTCTTCT
985457 ACTTCTTCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
27 22 0.32
28 1 0.01
29 1 0.01
30 45 0.65
ACGTcount: A:0.16, C:0.32, G:0.03, T:0.49
Consensus pattern (29 bp):
TCATCATCATCTTCTTCTATTCTTCTTCA
Found at i:985389 original size:33 final size:33
Alignment explanation
Indices: 985329--985467 Score: 106
Period size: 33 Copynumber: 4.3 Consensus size: 33
985319 TCGTTACGTT
* *
985329 CTTCTTCTCCATCGTCATCAT-TATCTTCTTCTA
1 CTTCTTCTTCATCATCATCATCT-TCTTCTTCTA
* * *
985362 ATTCTTCTTCATCATCAACATCTTCTTC--AT-
1 CTTCTTCTTCATCATCATCATCTTCTTCTTCTA
* * * * *
985392 CGTCATCGTCATCATCATCTTCTTCTTCTTCTT
1 CTTCTTCTTCATCATCATCATCTTCTTCTTCTA
* * * * *
985425 CTTCATCGTCATCATCTTCTTCTCCTTCTTCTA
1 CTTCTTCTTCATCATCATCATCTTCTTCTTCTA
985458 CTTCTTCTTC
1 CTTCTTCTTC
985468 TTCCCCGTTA
Statistics
Matches: 84, Mismatches: 18, Indels: 8
0.76 0.16 0.07
Matches are distributed among these distances:
30 22 0.26
31 1 0.01
32 1 0.01
33 59 0.70
34 1 0.01
ACGTcount: A:0.14, C:0.34, G:0.03, T:0.49
Consensus pattern (33 bp):
CTTCTTCTTCATCATCATCATCTTCTTCTTCTA
Found at i:985392 original size:9 final size:9
Alignment explanation
Indices: 985364--985470 Score: 56
Period size: 9 Copynumber: 11.6 Consensus size: 9
985354 TTCTTCTAAT
985364 TCTTCTTCA
1 TCTTCTTCA
* **
985373 TCATCAACA
1 TCTTCTTCA
985382 TCTTCTTCA
1 TCTTCTTCA
*
985391 TCGTCATCGTCA
1 TC-T--TCTTCA
* * *
985403 TCATCATCT
1 TCTTCTTCA
*
985412 TCTTCTTCT
1 TCTTCTTCA
985421 TCTTCTTCA
1 TCTTCTTCA
* *
985430 TCGTCATCA
1 TCTTCTTCA
985439 TCTTCTTC-
1 TCTTCTTCA
985447 TCCTTCTTC-
1 T-CTTCTTCA
*
985456 TACTTCTTCT
1 T-CTTCTTCA
985466 TCTTC
1 TCTTC
985471 CCCGTTAACC
Statistics
Matches: 75, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
8 1 0.01
9 65 0.87
10 2 0.03
12 7 0.09
ACGTcount: A:0.13, C:0.35, G:0.03, T:0.50
Consensus pattern (9 bp):
TCTTCTTCA
Found at i:985415 original size:3 final size:3
Alignment explanation
Indices: 985409--985470 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
985399 GTCATCATCA
* * * * *
985409 TCT TCT TCT TCT TCT TCT TCA TCG TCA TCA TCT TCT TCT CCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
985457 ACT TCT TCT TCT TC
1 TCT TCT TCT TCT TC
985471 CCCGTTAACC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.06, C:0.35, G:0.02, T:0.56
Consensus pattern (3 bp):
TCT
Found at i:985452 original size:27 final size:27
Alignment explanation
Indices: 985328--985455 Score: 112
Period size: 27 Copynumber: 4.6 Consensus size: 27
985318 ATCGTTACGT
* * * *
985328 TCTTCTTCTCCATCGTCATCATTATCT
1 TCTTCTTCTCCTTCTTCATCATCATCA
** * *
985355 TCTTCTAATTCTTCTTCATCATCAACA
1 TCTTCTTCTCCTTCTTCATCATCATCA
* * *
985382 TCTTCTTCATCGTCATCGTCATCATCATCT
1 TCTTCTTC-TC--CTTCTTCATCATCATCA
* *
985412 TCTTCTTCTTCTTCTTCATCGTCATCA
1 TCTTCTTCTCCTTCTTCATCATCATCA
985439 TCTTCTTCTCCTTCTTC
1 TCTTCTTCTCCTTCTTC
985456 TACTTCTTCT
Statistics
Matches: 77, Mismatches: 21, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
27 54 0.70
28 1 0.01
29 1 0.01
30 21 0.27
ACGTcount: A:0.15, C:0.34, G:0.03, T:0.48
Consensus pattern (27 bp):
TCTTCTTCTCCTTCTTCATCATCATCA
Found at i:986652 original size:2 final size:2
Alignment explanation
Indices: 986645--986678 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
986635 AAATGCATGC
986645 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
986679 TTCTTCTTAG
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:988062 original size:23 final size:24
Alignment explanation
Indices: 988036--988082 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
988026 ATTATTTTAA
* *
988036 AAATATTAATATTTTTAAA-ATTT
1 AAATATCAATATTTATAAATATTT
988059 AAATATCAATATTTATAAATATTT
1 AAATATCAATATTTATAAATATTT
988083 TTATTCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
AAATATCAATATTTATAAATATTT
Found at i:988064 original size:17 final size:17
Alignment explanation
Indices: 988028--988060 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
988018 TTATCGTAAT
988028 TATTTTAAAAATATTAA
1 TATTTTAAAAATATTAA
*
988045 TATTTTTAAAAT-TTAA
1 TATTTTAAAAATATTAA
988061 ATATCAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTTTAAAAATATTAA
Found at i:991862 original size:18 final size:19
Alignment explanation
Indices: 991836--991871 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
991826 ATTTAATATA
991836 AATTATTTAAA-ATTTTAT
1 AATTATTTAAATATTTTAT
*
991854 AATTTTTTAAATATTTTA
1 AATTATTTAAATATTTTA
991872 AAATATCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTATTTAAATATTTTAT
Found at i:992918 original size:17 final size:18
Alignment explanation
Indices: 992875--992931 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
992865 GTTTCGAGAC
992875 ATATATTATAATTATATTT
1 ATATATT-TAATTATATTT
* *
992894 AAAAATTTAA-TATATTT
1 ATATATTTAATTATATTT
992911 ATATATTTATATTATAATTT
1 ATATATTTA-ATTAT-ATTT
992931 A
1 A
992932 ATTATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 14 0.45
18 4 0.13
19 8 0.26
20 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATTTAATTATATTT
Found at i:993242 original size:19 final size:20
Alignment explanation
Indices: 993206--993289 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 20
993196 AGTAAGGTAT
*
993206 ATATAATAATATTAAATATG
1 ATATAATAATATTAAATATA
*
993226 ATATAATTATA-TAAATATA
1 ATATAATAATATTAAATATA
*
993245 ATATAAATAAAACAATTATAATATA
1 ATAT-AAT--AA-TATTA-AATATA
*
993270 ATATAATAA-AATAAATATA
1 ATATAATAATATTAAATATA
993289 A
1 A
993290 AATGTAAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
19 18 0.34
20 16 0.30
22 3 0.06
23 1 0.02
24 5 0.09
25 10 0.19
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (20 bp):
ATATAATAATATTAAATATA
Found at i:993247 original size:5 final size:5
Alignment explanation
Indices: 993206--993289 Score: 61
Period size: 5 Copynumber: 17.2 Consensus size: 5
993196 AGTAAGGTAT
* *
993206 ATATA ATAATA TTA-A ATATG ATATA AT-T- ATATAA ATATA ATATA A-ATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA
* * *
993254 AAACA ATTATA ATATA ATATA ATAAA ATA-A ATATA A
1 ATATA A-TATA ATATA ATATA ATATA ATATA ATATA A
993290 AATGTAAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
3 2 0.03
4 13 0.21
5 37 0.59
6 11 0.17
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (5 bp):
ATATA
Found at i:993261 original size:28 final size:29
Alignment explanation
Indices: 993230--993284 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
993220 AATATGATAT
993230 AATTAT-ATA-AATATAATATAAATAAAAC
1 AATTATAATATAATATAATA-AAATAAAAC
993258 AATTATAATATAATATAATAAAATAAA
1 AATTATAATATAATATAATAAAATAAA
993285 TATAAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 6 0.24
29 10 0.40
30 9 0.36
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (29 bp):
AATTATAATATAATATAATAAAATAAAAC
Found at i:993270 original size:25 final size:24
Alignment explanation
Indices: 993234--993289 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
993224 TGATATAATT
993234 ATATAAATATAATATAAATAAAACAA
1 ATAT-AATATAATAT-AATAAAACAA
* *
993260 TTATAATATAATATAATAAAATAA
1 ATATAATATAATATAATAAAACAA
993284 ATATAA
1 ATATAA
993290 AATGTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 14 0.52
25 10 0.37
26 3 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
ATATAATATAATATAATAAAACAA
Found at i:993283 original size:8 final size:10
Alignment explanation
Indices: 993206--993289 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 10
993196 AGTAAGGTAT
993206 ATATAATAATA
1 ATATAAT-ATA
* *
993217 TTA-AATATG
1 ATATAATATA
993226 ATATAAT-T-
1 ATATAATATA
993234 ATATAAATATA
1 ATAT-AATATA
993245 ATATAA-ATA
1 ATATAATATA
* *
993254 AAACAATTATA
1 ATATAA-TATA
993265 ATATAATATA
1 ATATAATATA
*
993275 ATAAAATA-A
1 ATATAATATA
993284 ATATAA
1 ATATAA
993290 AATGTAAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
8 4 0.07
9 21 0.36
10 20 0.34
11 13 0.22
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (10 bp):
ATATAATATA
Found at i:993339 original size:20 final size:19
Alignment explanation
Indices: 993298--993353 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
993288 AAAATGTAAA
993298 TATATAAATTTATTAA-AATT
1 TATATAAA-TTA-TAATAATT
*
993318 TATATAAATATATAATATTT
1 TATATAAAT-TATAATAATT
*
993338 TAAATATAATTATAAT
1 TATATA-AATTATAAT
993354 TATTATTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 4 0.13
20 24 0.77
21 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATAAATTATAATAATT
Found at i:994099 original size:22 final size:23
Alignment explanation
Indices: 994069--994121 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
994059 ACTTAGAATT
*
994069 TAATTTAATTAATATAT-ATTTA
1 TAATTTAATAAATATATAATTTA
*
994091 -ATATTTAATAAATTTATAATTTA
1 TA-ATTTAATAAATATATAATTTA
994114 TAATTTAA
1 TAATTTAA
994122 ATTTTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.04
22 13 0.50
23 11 0.42
24 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAATTTAATAAATATATAATTTA
Found at i:994128 original size:30 final size:32
Alignment explanation
Indices: 994070--994149 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 32
994060 CTTAGAATTT
994070 AATTTAATTAATA-TAT-ATTTAATATTTAATA
1 AATTT-ATTAATATTATAATTTAATATTTAATA
994101 AATTTA-TAAT-TTATAATTTAA-ATTTTAATA
1 AATTTATTAATATTATAATTTAATA-TTTAATA
**
994131 TTTTTATTAATATTATAAT
1 AATTTATTAATATTATAAT
994150 CATAATTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
29 8 0.19
30 18 0.43
31 9 0.21
32 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
AATTTATTAATATTATAATTTAATATTTAATA
Found at i:994662 original size:16 final size:17
Alignment explanation
Indices: 994629--994661 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
994619 AATTTAATTT
*
994629 ATATAATATTT-TTAAA
1 ATATAATATTTAATAAA
994645 ATATAATATTTAATAAA
1 ATATAATATTTAATAAA
994662 TTTAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAATATTTAATAAA
Found at i:995101 original size:19 final size:20
Alignment explanation
Indices: 995056--995102 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
995046 AATAATTTAC
995056 ATATTTATAATATTAAATAG
1 ATATTTATAATATTAAATAG
* **
995076 A-AATTATAATA-TAAATTT
1 ATATTTATAATATTAAATAG
995094 ATATTTATA
1 ATATTTATA
995103 GATAAATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 6 0.27
19 15 0.68
20 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATTTATAATATTAAATAG
Found at i:996344 original size:22 final size:21
Alignment explanation
Indices: 996300--996352 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
996290 ATTATTTAAA
** *
996300 TATATTTAAATAATTTTATTT
1 TATATTTAAATAATAATAATT
996321 TAATATTTAAATAATAATAATT
1 T-ATATTTAAATAATAATAATT
996343 TATA-TTAAAT
1 TATATTTAAAT
996353 TTAGATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.21
21 4 0.14
22 18 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATTTAAATAATAATAATT
Found at i:1004215 original size:69 final size:70
Alignment explanation
Indices: 1004137--1004277 Score: 214
Period size: 69 Copynumber: 2.0 Consensus size: 70
1004127 CAGAAAGGAA
* *
1004137 TTTGAGAAATAACAAACAAAAGT-ATCTGAGATTAGTTTATTACTGTCCAAGAAATAACTATGTT
1 TTTGAGAAATAACAAACAAAA-TAACCTGAGATTAGTTGATTACTGTCCAAGAAATAACTATGTT
1004201 ATCTTT
65 ATCTTT
* *
1004207 TTTG-GAAATAACAAACAAAATAACCTGAGATTAGTTGATTACTTTCCAAGACATAACTATGTTA
1 TTTGAGAAATAACAAACAAAATAACCTGAGATTAGTTGATTACTGTCCAAGAAATAACTATGTTA
*
1004271 TGTTT
66 TCTTT
1004276 TT
1 TT
1004278 GCTTACTGGG
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
68 1 0.02
69 60 0.92
70 4 0.06
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (70 bp):
TTTGAGAAATAACAAACAAAATAACCTGAGATTAGTTGATTACTGTCCAAGAAATAACTATGTTA
TCTTT
Found at i:1005886 original size:95 final size:93
Alignment explanation
Indices: 1005741--1005915 Score: 262
Period size: 95 Copynumber: 1.9 Consensus size: 93
1005731 TTCGAGTCAC
*
1005741 TATATTTTATTATATTATAATACGTTAAGATATTTATTTTTTTATATTTATATAAAATTTAAAAT
1 TATATTTTATTATATTAAAATACGTTAAGATATTTATTTTTTTATATTTATATAAAATTTAAAAT
*
1005806 ATTAATAATTTATATTCGAATCATATTTA
66 ATTAAT-ATTCATATTCGAATCATATTTA
** * *
1005835 TATATTTTATTATATTAAAATCATTTTAAGATATTT-TATTTTTTATATTTATATAAAATTTGAT
1 TATATTTTATTATATTAAAAT-ACGTTAAGATATTTAT-TTTTTTATATTTATATAAAATTTAAA
1005899 ATATTAATATTCATATT
64 ATATTAATATTCATATT
1005916 ATATAAATTT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 29 0.40
95 44 0.60
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (93 bp):
TATATTTTATTATATTAAAATACGTTAAGATATTTATTTTTTTATATTTATATAAAATTTAAAAT
ATTAATATTCATATTCGAATCATATTTA
Found at i:1005936 original size:94 final size:93
Alignment explanation
Indices: 1005741--1005936 Score: 247
Period size: 95 Copynumber: 2.1 Consensus size: 93
1005731 TTCGAGTCAC
*
1005741 TATATTTTATTATATTATAATACGTTAAGATATTTATTTTTTTATATTTATATAAAATTTAAAAT
1 TATATTTTATTATATTAAAATACGTTAAGATATTTATTTTTTTATATTTATATAAAATTTAAAAT
* *
1005806 ATTAATAATTTATATTCGAATCATATTTA
66 ATTAATAATTCATATTC-AATCAAATTTA
** * *
1005835 TATATTTTATTATATTAAAATCATTTTAAGATATTT-TATTTTTTATATTTATATAAAATTTGAT
1 TATATTTTATTATATTAAAAT-ACGTTAAGATATTTAT-TTTTTTATATTTATATAAAATTTAAA
1005899 ATATTAAT-ATTCATATT-ATAT-AAATTTACA
64 ATATTAATAATTCATATTCA-ATCAAATTT--A
1005929 TATATTTT
1 TATATTTT
1005937 GAACGATCAA
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
92 6 0.07
93 2 0.02
94 38 0.42
95 44 0.49
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (93 bp):
TATATTTTATTATATTAAAATACGTTAAGATATTTATTTTTTTATATTTATATAAAATTTAAAAT
ATTAATAATTCATATTCAATCAAATTTA
Found at i:1013406 original size:23 final size:25
Alignment explanation
Indices: 1013360--1013417 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
1013350 TATATAAAAT
*
1013360 TTTTATATATTAATAATTTAATTTA
1 TTTTATATATTAATAATATAATTTA
*
1013385 TTTTATATATTTAT-ATAT-ATTTA
1 TTTTATATATTAATAATATAATTTA
* *
1013408 TGTCATATAT
1 TTTTATATAT
1013418 AAGTGATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 13 0.45
24 3 0.10
25 13 0.45
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTATATATTAATAATATAATTTA
Found at i:1013523 original size:23 final size:24
Alignment explanation
Indices: 1013497--1013549 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
1013487 AAAGTAAAAA
1013497 AATTATATAAATT-TTTATATGTT
1 AATTATATAAATTATTTATATGTT
* *
1013520 AATTAT-TAATTTATTTATATTTT
1 AATTATATAAATTATTTATATGTT
1013543 AA-TATAT
1 AATTATAT
1013550 TCATATATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
AATTATATAAATTATTTATATGTT
Found at i:1013584 original size:9 final size:9
Alignment explanation
Indices: 1013521--1013609 Score: 53
Period size: 8 Copynumber: 10.0 Consensus size: 9
1013511 TTATATGTTA
*
1013521 ATTATTAAT
1 ATTATTTAT
1013530 -TTATTTAT
1 ATTATTTAT
*
1013538 ATT-TTAAT
1 ATTATTTAT
*
1013546 A-TATTCAT
1 ATTATTTAT
*
1013554 A-TATTCAT
1 ATTATTTAT
1013562 ATTAAATTTAT
1 ATT--ATTTAT
*
1013573 ATTATTTTT
1 ATTATTTAT
1013582 ATT-TTATAT
1 ATTATT-TAT
*
1013591 ATTAATTAT
1 ATTATTTAT
1013600 ATATATTTAT
1 AT-TATTTAT
1013610 CTTAATACAC
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
7 1 0.02
8 27 0.42
9 21 0.33
10 7 0.11
11 8 0.12
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (9 bp):
ATTATTTAT
Done.