Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 18 of 32
Found at i:2322099 original size:31 final size:33
Alignment explanation
Indices: 2322045--2322109 Score: 98
Period size: 31 Copynumber: 2.0 Consensus size: 33
2322035 TATGAACAGT
2322045 ATATAAATATATCAACATATCAAAATTTAAATA
1 ATATAAATATATCAACATATCAAAATTTAAATA
* *
2322078 ATATAAATAT-T-AATATATCAAAATTTATATA
1 ATATAAATATATCAACATATCAAAATTTAAATA
2322109 A
1 A
2322110 ACATATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 19 0.63
32 1 0.03
33 10 0.33
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (33 bp):
ATATAAATATATCAACATATCAAAATTTAAATA
Found at i:2322461 original size:28 final size:25
Alignment explanation
Indices: 2322429--2322499 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 25
2322419 ATCAAAATTT
*
2322429 ATATAAATATAAAATATTTTAAATATG
1 ATATAAATATAAAATA--TAAAATATG
2322456 ATTATAATATAATAAAATATAAAATATG
1 A-TATAA-AT-ATAAAATATAAAATATG
*
2322484 ATATGAATATACAAAT
1 ATATAAATATA-AAAT
2322500 TGTGAGACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 3 0.08
26 6 0.16
27 5 0.13
28 14 0.37
29 2 0.05
30 8 0.21
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (25 bp):
ATATAAATATAAAATATAAAATATG
Found at i:2322727 original size:2 final size:2
Alignment explanation
Indices: 2322720--2322751 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2322710 TTAAAAGGTT
2322720 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2322752 AAATTGACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2322871 original size:15 final size:16
Alignment explanation
Indices: 2322827--2322889 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 16
2322817 ATATACGTAT
2322827 TTATATTTAATTTAAGA
1 TTATATTTAATTTAA-A
* *
2322844 TAAAATTTTTAATTTAAA
1 T--TATATTTAATTTAAA
2322862 TTA-ATTTAATTTAAA
1 TTATATTTAATTTAAA
2322877 TTATTATTTAATT
1 TTA-TATTTAATT
2322890 AATAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 14 0.37
16 1 0.03
17 9 0.24
18 2 0.05
19 12 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TTATATTTAATTTAAA
Found at i:2323074 original size:16 final size:16
Alignment explanation
Indices: 2323053--2323108 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
2323043 AACTTTAAAA
2323053 ATAAATTTTAAAATAT
1 ATAAATTTTAAAATAT
* *
2323069 ATAAATATTAATAATAA
1 ATAAATTTTAA-AATAT
2323086 ATAATATTTTAAAATAT
1 ATAA-ATTTTAAAATAT
*
2323103 TTAAAT
1 ATAAAT
2323109 AATAAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 12 0.36
17 15 0.45
18 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAATTTTAAAATAT
Found at i:2323191 original size:16 final size:14
Alignment explanation
Indices: 2323169--2323203 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
2323159 GTAAAACATT
2323169 TTTATTTAAGTTTAA
1 TTTATTTAA-TTTAA
2323184 TATTATTTAATTTAA
1 T-TTATTTAATTTAA
2323199 TTTAT
1 TTTAT
2323204 AAATTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 7 0.37
16 8 0.42
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TTTATTTAATTTAA
Found at i:2323319 original size:19 final size:19
Alignment explanation
Indices: 2323292--2323329 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2323282 ATAATTAAAT
2323292 TTAAATAAA-TATATATTTA
1 TTAAATAAATTATA-ATTTA
*
2323311 TTAATTAAATTATAATTTA
1 TTAAATAAATTATAATTTA
2323330 AATTAGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAATAAATTATAATTTA
Found at i:2328592 original size:3 final size:3
Alignment explanation
Indices: 2328586--2328621 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2328576 TTATTATATG
2328586 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2328622 AATGATGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2329591 original size:2 final size:2
Alignment explanation
Indices: 2329584--2329614 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2329574 TAACTTTTAT
2329584 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
2329615 TACTTTTGAG
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:2330091 original size:22 final size:21
Alignment explanation
Indices: 2330036--2330102 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
2330026 ATTAATATTT
*
2330036 TTAATAAAATAAAAAATACTTAA
1 TTAATAAATTAAAAAAT--TTAA
**
2330059 TTAA-ATTTTAAAAAATTTATA
1 TTAATAAATTAAAAAATTTA-A
2330080 TTAATAAATTAAAAAA-TTAA
1 TTAATAAATTAAAAAATTTAA
2330100 TTA
1 TTA
2330103 TCATGTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 7 0.19
21 8 0.22
22 18 0.49
23 4 0.11
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAATAAATTAAAAAATTTAA
Found at i:2330488 original size:20 final size:20
Alignment explanation
Indices: 2330463--2330502 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2330453 TTATAAAATT
*
2330463 AATTTAATTTAATTTTATTA
1 AATTTAATTTAATTTGATTA
* *
2330483 AATTTATTTTTATTTGATTA
1 AATTTAATTTAATTTGATTA
2330503 TGTAGGTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
AATTTAATTTAATTTGATTA
Found at i:2334191 original size:27 final size:29
Alignment explanation
Indices: 2334161--2334218 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
2334151 AAATGTTATA
* *
2334161 TATATTAATA-TTG-TATATGTATTATTT
1 TATAATAATAGTTGTTAAATGTATTATTT
* *
2334188 TATAATCATAGTTGTTAAATGTATTTTTT
1 TATAATAATAGTTGTTAAATGTATTATTT
2334217 TA
1 TA
2334219 CTTTATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 8 0.32
28 3 0.12
29 14 0.56
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.57
Consensus pattern (29 bp):
TATAATAATAGTTGTTAAATGTATTATTT
Found at i:2334776 original size:23 final size:22
Alignment explanation
Indices: 2334725--2334786 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
2334715 ACTCAAAAAT
*
2334725 TAATTTTTTTAATTTATTAATA
1 TAATTTTTTTAATTAATTAATA
2334747 TAATTTTTTTAAACTTAATTAA-A
1 TAATTTTTTT-AA-TTAATTAATA
* *
2334770 TATTTTTATTTTATTAA
1 TAATTTT-TTTAATTAA
2334787 AAATAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 14 0.41
23 10 0.29
24 10 0.29
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TAATTTTTTTAATTAATTAATA
Found at i:2340055 original size:47 final size:49
Alignment explanation
Indices: 2340004--2340098 Score: 140
Period size: 50 Copynumber: 2.0 Consensus size: 49
2339994 ATTTTGGGAG
* **
2340004 AGTACAATTTTCTGCTTAA-TT-TTAACTGCATTAATTATTATATGTAA
1 AGTACAATTTCCTGCTTAATTTATTAACTGCAGCAATTATTATATGTAA
2340051 AGTACAATTTCCTGCTTAATTTTATTAACTGCAGCAATTATTATATGT
1 AGTACAATTTCCTGCTTAA-TTTATTAACTGCAGCAATTATTATATGT
2340099 TAATCCATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 18 0.43
49 2 0.05
50 22 0.52
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (49 bp):
AGTACAATTTCCTGCTTAATTTATTAACTGCAGCAATTATTATATGTAA
Found at i:2344911 original size:7 final size:7
Alignment explanation
Indices: 2344899--2344924 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2344889 TGAGTCTCTT
2344899 ATATATA
1 ATATATA
2344906 ATATATA
1 ATATATA
2344913 ATATATA
1 ATATATA
2344920 ATATA
1 ATATA
2344925 CATATATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATATA
Found at i:2345440 original size:2 final size:2
Alignment explanation
Indices: 2345428--2345462 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2345418 GGGGTGAAAC
*
2345428 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2345463 CATGAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2345578 original size:12 final size:12
Alignment explanation
Indices: 2345563--2345599 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2345553 ATGATTATTG
*
2345563 TTTTAATTAAGT
1 TTTTAATTAAAT
*
2345575 TTTTAAATAAAT
1 TTTTAATTAAAT
2345587 TTTTAATTAAAT
1 TTTTAATTAAAT
2345599 T
1 T
2345600 GATATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (12 bp):
TTTTAATTAAAT
Found at i:2357643 original size:17 final size:17
Alignment explanation
Indices: 2357623--2357709 Score: 75
Period size: 17 Copynumber: 4.9 Consensus size: 17
2357613 AGTTTAACGA
2357623 TTTAAAATAATTAAAAT
1 TTTAAAATAATTAAAAT
* *
2357640 TTTAAAGTAATTAGAAT
1 TTTAAAATAATTAAAAT
*
2357657 TTAAAAAATAATTACAAGAT
1 TT-TAAAATAATTA-AA-AT
* ***
2357677 TATATCCTAAATTAAAAT
1 TTTAAAAT-AATTAAAAT
2357695 TTTAAAATAATTAAA
1 TTTAAAATAATTAAA
2357710 CGATTACAAC
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
17 24 0.46
18 15 0.29
19 5 0.10
20 8 0.15
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TTTAAAATAATTAAAAT
Found at i:2357730 original size:31 final size:30
Alignment explanation
Indices: 2357695--2357762 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
2357685 AAATTAAAAT
2357695 TTTAAAATAATTAAACGATTACAACCGTTAA
1 TTTAAAATAATTAAACGATTACAA-CGTTAA
* *
2357726 TTTAAAATAATTAAACGATTATAACTTTAA
1 TTTAAAATAATTAAACGATTACAACGTTAA
2357756 -TTAAAAT
1 TTTAAAAT
2357763 TTTAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 7 0.20
30 5 0.14
31 23 0.66
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (30 bp):
TTTAAAATAATTAAACGATTACAACGTTAA
Found at i:2357885 original size:23 final size:22
Alignment explanation
Indices: 2357859--2357908 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
2357849 GAAATAATTT
*
2357859 TTTTAATAAT-ATAACTATTATTA
1 TTTTAATAATAATAA-TA-TAATA
*
2357882 TTTTTATAATAATAATATAATA
1 TTTTAATAATAATAATATAATA
2357904 TTTTA
1 TTTTA
2357909 TCAATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 8 0.35
23 11 0.48
24 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTTAATAATAATAATATAATA
Found at i:2357993 original size:17 final size:17
Alignment explanation
Indices: 2357973--2358009 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2357963 ATAAAAACCT
*
2357973 TAACAATATTATTAAAA
1 TAACAATAATATTAAAA
*
2357990 TAACAATAATATTATAA
1 TAACAATAATATTAAAA
2358007 TAA
1 TAA
2358010 AATTATAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (17 bp):
TAACAATAATATTAAAA
Found at i:2359241 original size:18 final size:17
Alignment explanation
Indices: 2359194--2359251 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
2359184 ATTTTTTTTA
2359194 AAATTTATAT-AATA-T
1 AAATTTATATAAATATT
2359209 AAA-TTAT-TAATATATCT
1 AAATTTATATAA-ATAT-T
*
2359226 AAATTTATATAAATATA
1 AAATTTATATAAATATT
*
2359243 AAAATTATA
1 AAATTTATA
2359252 AAGATAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
13 1 0.03
14 5 0.14
15 6 0.17
17 12 0.34
18 8 0.23
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTATATAAATATT
Found at i:2359483 original size:12 final size:13
Alignment explanation
Indices: 2359465--2359513 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
2359455 AAAAATTAAT
2359465 TATTTATTATAAA
1 TATTTATTATAAA
2359478 -ATTTATTAATAAA
1 TATTTATT-ATAAA
* **
2359491 TTTTTAAAATAAA
1 TATTTATTATAAA
2359504 TATTTATTAT
1 TATTTATTAT
2359514 TTAATTATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
12 7 0.25
13 17 0.61
14 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTTATTATAAA
Found at i:2359508 original size:27 final size:28
Alignment explanation
Indices: 2359462--2359535 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 28
2359452 TAAAAAAATT
* *
2359462 AATTATTTATTATAAA-ATTTATTAATA
1 AATTATTAAATATAAATATTTATTAATA
* * *
2359489 AATTTTTAAA-ATAAATATTTATTATTT
1 AATTATTAAATATAAATATTTATTAATA
2359516 AATTATTAAATATAATATAT
1 AATTATTAAATATAA-ATAT
2359536 GATAAATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 5 0.13
27 25 0.66
28 4 0.11
29 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AATTATTAAATATAAATATTTATTAATA
Found at i:2359926 original size:14 final size:15
Alignment explanation
Indices: 2359902--2359930 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2359892 TAATTAATAA
2359902 TAATTTATTATATTT
1 TAATTTATTATATTT
2359917 TAATTT-TTATATTT
1 TAATTTATTATATTT
2359931 ATTTTACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TAATTTATTATATTT
Found at i:2360729 original size:20 final size:20
Alignment explanation
Indices: 2360704--2360850 Score: 96
Period size: 20 Copynumber: 6.8 Consensus size: 20
2360694 TTTTTACTAA
2360704 TTTATAAATAAAATATTTAT
1 TTTATAAATAAAATATTTAT
*
2360724 TTTATATATAAAATAAAATTTAAT
1 TTTATAAATAAAAT---ATTT-AT
* * * *
2360748 TTTAATAATTATAATTTTTAA
1 TTT-ATAAATAAAATATTTAT
*
2360769 TTTATAAATCAAATATTTAT
1 TTTATAAATAAAATATTTAT
*
2360789 TTTATATATAAAATAAAATTTAAT
1 TTTATAAATAAAAT---ATTT-AT
* * * *
2360813 TTTAATAATTATAATTTTTAA
1 TTT-ATAAATAAAATATTTAT
*
2360834 TTTATAAATCAAATATT
1 TTTATAAATAAAATATT
2360851 AAATTAAACT
Statistics
Matches: 95, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
20 47 0.49
21 8 0.08
22 6 0.06
23 8 0.08
24 10 0.11
25 16 0.17
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTATAAATAAAATATTTAT
Found at i:2360770 original size:65 final size:65
Alignment explanation
Indices: 2360701--2360850 Score: 291
Period size: 65 Copynumber: 2.3 Consensus size: 65
2360691 ATTTTTTTAC
*
2360701 TAATTTATAAATAAAATATTTATTTTATATATAAAATAAAATTTAATTTTAATAATTATAATTTT
1 TAATTTATAAATCAAATATTTATTTTATATATAAAATAAAATTTAATTTTAATAATTATAATTTT
2360766 TAATTTATAAATCAAATATTTATTTTATATATAAAATAAAATTTAATTTTAATAATTATAATTTT
1 TAATTTATAAATCAAATATTTATTTTATATATAAAATAAAATTTAATTTTAATAATTATAATTTT
2360831 TAATTTATAAATCAAATATT
1 TAATTTATAAATCAAATATT
2360851 AAATTAAACT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 84 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (65 bp):
TAATTTATAAATCAAATATTTATTTTATATATAAAATAAAATTTAATTTTAATAATTATAATTTT
Found at i:2361995 original size:105 final size:105
Alignment explanation
Indices: 2361807--2362023 Score: 303
Period size: 105 Copynumber: 2.1 Consensus size: 105
2361797 TATTTTAAAA
* *
2361807 AAATAAAATAAGTAATAATTTAGTTAAGTGAAAAGAGATTTAAATTTTTTAAAATAATTTTATAT
1 AAAT-AAATAAATAATAATTTAGTTAAGTGAAAAGAGATTCAAATTTTTTAAAATAATTTTATAT
* * *
2361872 TTCGTTTAAGATTGAAATAGTCATTCAGTA-AGAGAGATATT
65 TTCATTTAAGATTAAAATAGTCATTCAGTAGA-AGAAATATT
* * *
2361913 AAATAAATAAATAATAATTTGGTTAAGTGAAAAGAGATTCGAATTTTTTAAAATAATTTTGTATT
1 AAATAAATAAATAATAATTTAGTTAAGTGAAAAGAGATTCAAATTTTTTAAAATAATTTTATATT
* *
2361978 TTATTTCAAG-TTAAAATAGTCATTTAGTAGAAGAAATATT
66 TCATTT-AAGATTAAAATAGTCATTCAGTAGAAGAAATATT
2362018 AAATAA
1 AAATAA
2362024 TTATTTGAAG
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
105 91 0.92
106 8 0.08
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (105 bp):
AAATAAATAAATAATAATTTAGTTAAGTGAAAAGAGATTCAAATTTTTTAAAATAATTTTATATT
TCATTTAAGATTAAAATAGTCATTCAGTAGAAGAAATATT
Found at i:2362190 original size:9 final size:10
Alignment explanation
Indices: 2362173--2362199 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2362163 ATATGCGTGA
2362173 TTAAAAAAAG
1 TTAAAAAAAG
2362183 TTAAAAAAAG
1 TTAAAAAAAG
2362193 TTAAAAA
1 TTAAAAA
2362200 GAGTATGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (10 bp):
TTAAAAAAAG
Found at i:2364195 original size:17 final size:18
Alignment explanation
Indices: 2364173--2364212 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2364163 AATTTATATA
2364173 ATAAAAATT-AT-TAACAT
1 ATAAAAATTAATATAA-AT
2364190 ATAAAAATTAATATAAAT
1 ATAAAAATTAATATAAAT
2364208 ATAAA
1 ATAAA
2364213 CACAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 9 0.43
19 3 0.14
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAAAATTAATATAAAT
Found at i:2364248 original size:18 final size:19
Alignment explanation
Indices: 2364225--2364260 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2364215 CAATTAAAAT
*
2364225 ATGATA-AAATATATAAAC
1 ATGATATAAATACATAAAC
2364243 ATGATATAAATACATAAA
1 ATGATATAAATACATAAA
2364261 TTATAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (19 bp):
ATGATATAAATACATAAAC
Found at i:2365514 original size:3 final size:3
Alignment explanation
Indices: 2365506--2365552 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
2365496 TTTCAGCATT
2365506 TTA TTA TTA TTA TTA TTA TTAA TT- TT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
2365550 TTA
1 TTA
2365553 ATTTTAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2365554 original size:26 final size:26
Alignment explanation
Indices: 2365504--2365557 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
2365494 ATTTTCAGCA
2365504 TTTTATTATTATTATTATTATTAATT
1 TTTTATTATTATTATTATTATTAATT
2365530 TTTTATTATTATTATTATTATTAATT
1 TTTTATTATTATTATTATTATTAATT
2365556 TT
1 TT
2365558 AATTTGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTTATTATTATTATTATTATTAATT
Found at i:2366767 original size:22 final size:20
Alignment explanation
Indices: 2366740--2366792 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
2366730 TTATTTTAAA
* *
2366740 ATTTAAATTTATTTATTATTT
1 ATTTAAATTTATATA-TAATT
2366761 ATATTAAATTTATATATAATT
1 AT-TTAAATTTATATATAATT
2366782 ATTTAAATTTA
1 ATTTAAATTTA
2366793 AATTCGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 9 0.31
21 8 0.28
22 12 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTAAATTTATATATAATT
Found at i:2366771 original size:11 final size:10
Alignment explanation
Indices: 2366740--2366792 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
2366730 TTATTTTAAA
2366740 ATTTAAATTT
1 ATTTAAATTT
*
2366750 ATTTATTATTT
1 ATTTA-AATTT
2366761 ATATTAAATTT
1 AT-TTAAATTT
*
2366772 ATATATAA-TT
1 ATTTA-AATTT
2366782 ATTTAAATTT
1 ATTTAAATTT
2366792 A
1 A
2366793 AATTCGAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 2 0.06
10 16 0.46
11 14 0.40
12 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:2369910 original size:2 final size:2
Alignment explanation
Indices: 2369897--2369937 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2369887 CGATGGATCT
* *
2369897 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2369938 GAATGCTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2370477 original size:3 final size:3
Alignment explanation
Indices: 2370469--2370499 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2370459 TAGTGTTTTT
2370469 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2370500 CAATTAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2375464 original size:30 final size:30
Alignment explanation
Indices: 2375429--2375488 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2375419 GTTGTGTCGA
2375429 AGTAGATAGAATGTATATCAAATGAAAAGT
1 AGTAGATAGAATGTATATCAAATGAAAAGT
2375459 AGTAGATAGAATGTATATCAAATGAAAAGT
1 AGTAGATAGAATGTATATCAAATGAAAAGT
2375489 GAAGATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.27
Consensus pattern (30 bp):
AGTAGATAGAATGTATATCAAATGAAAAGT
Found at i:2375916 original size:16 final size:16
Alignment explanation
Indices: 2375895--2375929 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2375885 TGAACTTAAT
2375895 TAACCTAAAT-TCGAAA
1 TAACCTAAATAT-GAAA
2375911 TAACCTAAATATGAAA
1 TAACCTAAATATGAAA
2375927 TAA
1 TAA
2375930 TTCAAACTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.94
17 1 0.06
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (16 bp):
TAACCTAAATATGAAA
Found at i:2376655 original size:23 final size:23
Alignment explanation
Indices: 2376629--2376697 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 23
2376619 ACTTTTAATT
2376629 ATTTTATAATTAT-TATTATAAAA
1 ATTTTA-AATTATATATTATAAAA
* *
2376652 ATTTTAAAATATATATT-TTAAA
1 ATTTTAAATTATATATTATAAAA
*
2376674 ATTTTAAATATATATTTTATAAAA
1 ATTTTAAAT-TATATATTATAAAA
2376698 TTTAATTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 17 0.45
23 17 0.45
24 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTAAATTATATATTATAAAA
Found at i:2376677 original size:22 final size:22
Alignment explanation
Indices: 2376649--2376702 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
2376639 TATTATTATA
2376649 AAAATTTTAAAATATATATTTT
1 AAAATTTTAAAATATATATTTT
2376671 AAAATTTT-AAATATATATTTT
1 AAAATTTTAAAATATATATTTT
*
2376692 ATAAAATTTAA
1 A-AAATTTTAA
2376703 TTAATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 14 0.48
22 14 0.48
23 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAATTTTAAAATATATATTTT
Found at i:2376684 original size:21 final size:21
Alignment explanation
Indices: 2376649--2376702 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
2376639 TATTATTATA
2376649 AAAATTTTAAAATATATATTTT
1 AAAATTTT-AAATATATATTTT
2376671 AAAATTTTAAATATATATTTT
1 AAAATTTTAAATATATATTTT
*
2376692 ATAAAATTTAA
1 A-AAATTTTAA
2376703 TTAATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAAATTTTAAATATATATTTT
Found at i:2376698 original size:23 final size:22
Alignment explanation
Indices: 2376629--2376700 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 22
2376619 ACTTTTAATT
*
2376629 ATTTTATAAT-TATTATTATAAAA
1 ATTTTAAAATATATT-TTAT-AAA
2376652 ATTTTAAAATATATATTT-TAAA
1 ATTTTAAAATATAT-TTTATAAA
2376674 ATTTTAAATATATATTTTATAAA
1 ATTTTAAA-ATATATTTTATAAA
2376697 ATTT
1 ATTT
2376701 AATTAATTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
22 14 0.32
23 24 0.55
24 5 0.11
25 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTAAAATATATTTTATAAA
Found at i:2387341 original size:56 final size:56
Alignment explanation
Indices: 2387255--2387367 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
2387245 CTTGAACAAC
*
2387255 TGCAGATCGTAAAAATTATTTGAATATCAAGAAATGCATGCCAAACACAATTATAT
1 TGCAGATCGTAAAAATTATTTAAATATCAAGAAATGCATGCCAAACACAATTATAT
2387311 TGCAGATCGTAAAAATTATTTAAATATCAAGAAATGCATGCCAAACACAATTATAT
1 TGCAGATCGTAAAAATTATTTAAATATCAAGAAATGCATGCCAAACACAATTATAT
2387367 T
1 T
2387368 TGGGGGAAAG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (56 bp):
TGCAGATCGTAAAAATTATTTAAATATCAAGAAATGCATGCCAAACACAATTATAT
Found at i:2391190 original size:24 final size:24
Alignment explanation
Indices: 2391149--2391197 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
2391139 ATTTTTATAC
2391149 TTTAATAATTTATATTATATAAAT
1 TTTAATAATTTATATTATATAAAT
*
2391173 TTTAATAAATTTAT-TTATTTAAAT
1 TTTAAT-AATTTATATTATATAAAT
2391197 T
1 T
2391198 ATATTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTAATAATTTATATTATATAAAT
Found at i:2391199 original size:33 final size:32
Alignment explanation
Indices: 2391119--2391201 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 32
2391109 TATTAAATAA
* *
2391119 TATTT-TTTAAATTTATATAAATTTTTATACTT
1 TATTTATTTAAA-TTATATAAATTTTAATAATT
* * *
2391151 TAATAATTTATATTATATAAATTTTAATAAATT
1 TATTTATTTAAATTATATAAATTTTAAT-AATT
2391184 TATTTATTTAAATTATAT
1 TATTTATTTAAATTATAT
2391202 TTAAATTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 18 0.44
33 23 0.56
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTTATTTAAATTATATAAATTTTAATAATT
Found at i:2391254 original size:25 final size:27
Alignment explanation
Indices: 2391199--2391255 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
2391189 ATTTAAATTA
**
2391199 TATTTA-AATTATTTTTATTTTATGTG
1 TATTTATAATTATTTTTATACTATGTG
2391225 T-TTTATAATTA-TTTTATACTAT-TG
1 TATTTATAATTATTTTTATACTATGTG
2391249 TATTTAT
1 TATTTAT
2391256 TTTTTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 3 0.11
25 18 0.67
26 6 0.22
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTTATAATTATTTTTATACTATGTG
Found at i:2391826 original size:21 final size:22
Alignment explanation
Indices: 2391795--2391839 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2391785 TTAAAAATAA
* *
2391795 AAATAATTTTTTATTAATATAT
1 AAATAATTTTTTATAAATAAAT
2391817 AAAT-ATTTTTTATAAATAAAT
1 AAATAATTTTTTATAAATAAAT
2391838 AA
1 AA
2391840 TTTTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATAATTTTTTATAAATAAAT
Found at i:2392061 original size:27 final size:26
Alignment explanation
Indices: 2392018--2392109 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 26
2392008 TTAAAAATTC
*
2392018 TTTATATATATACTATATTTATATTTT
1 TTTATATATA-AATATATTTATATTTT
* *
2392045 TTTATATATTAAATATAATTATA-TTA
1 TTTATATA-TAAATATATTTATATTTT
* *
2392071 ATTATATTAAAAATATATATT-TAATTTT
1 TTTATA-TATAAATATAT-TTAT-ATTTT
*
2392099 TTTATTTATAA
1 TTTATATATAA
2392110 TTTAATTTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
26 15 0.30
27 27 0.54
28 8 0.16
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTATATATAAATATATTTATATTTT
Found at i:2394175 original size:2 final size:2
Alignment explanation
Indices: 2394168--2394198 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2394158 CAATATAATC
2394168 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
2394199 TTTAAAAATA
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:2394765 original size:20 final size:20
Alignment explanation
Indices: 2394736--2394811 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
2394726 TTTTTATCCA
2394736 GATGTATCGATACATTTTTC
1 GATGTATCGATACATTTTTC
* * *
2394756 GATATATCGATACATGTAT-
1 GATGTATCGATACATTTTTC
* *
2394775 GAATGTATCGATATATTCTTC
1 G-ATGTATCGATACATTTTTC
*
2394796 AATGTATCGATACATT
1 GATGTATCGATACATT
2394812 ATATCTTTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.02
20 43 0.98
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (20 bp):
GATGTATCGATACATTTTTC
Found at i:2394849 original size:16 final size:16
Alignment explanation
Indices: 2394828--2394858 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2394818 TTTTACCTAG
2394828 ATGTATCGATACATCA
1 ATGTATCGATACATCA
2394844 ATGTATCGATACATC
1 ATGTATCGATACATC
2394859 TAGTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (16 bp):
ATGTATCGATACATCA
Found at i:2407446 original size:17 final size:17
Alignment explanation
Indices: 2407424--2407469 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
2407414 TTTTTAGTAT
*
2407424 TATTTATTTAG-TATATA
1 TATTTATTTAGAT-TAAA
2407441 TATTTAATTT-GATTAAA
1 TATTT-ATTTAGATTAAA
2407458 TATTTATTTAGA
1 TATTTATTTAGA
2407470 CAAGAATTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.16
17 16 0.64
18 5 0.20
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (17 bp):
TATTTATTTAGATTAAA
Found at i:2407677 original size:41 final size:38
Alignment explanation
Indices: 2407631--2407711 Score: 92
Period size: 41 Copynumber: 2.1 Consensus size: 38
2407621 TTCTAAAAAA
*
2407631 ATTAAAAAAATTATTATT-TTATTTATTTATTTTAATTTATG
1 ATTAAAAAAATTA-TATTATTATTT-TTAATTTT-ATTT-TG
**
2407672 ATTAAATTAATTATATTATTATTTTTAATTTTATTTTG
1 ATTAAAAAAATTATATTATTATTTTTAATTTTATTTTG
2407710 AT
1 AT
2407712 AATGAGTACA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 4 0.11
39 4 0.11
40 11 0.31
41 17 0.47
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (38 bp):
ATTAAAAAAATTATATTATTATTTTTAATTTTATTTTG
Found at i:2410386 original size:22 final size:22
Alignment explanation
Indices: 2410359--2410411 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
2410349 TGATCTTTAA
*
2410359 TAATTAAAAATTTATTTAA-ATT
1 TAATTAAAAATATA-TTAATATT
2410381 TAATTATAAAATATATTAATATT
1 TAATTA-AAAATATATTAATATT
2410404 TATATTAA
1 TA-ATTAA
2410412 TATAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 10 0.37
23 13 0.48
24 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATTAAAAATATATTAATATT
Found at i:2410457 original size:28 final size:30
Alignment explanation
Indices: 2410371--2410457 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 30
2410361 ATTAAAAATT
*
2410371 TATTTAAATTTAATTAT-AA-AATATATTAA
1 TATTTATA-TTAATTATAAATAATATATTAA
*
2410400 TATTTATATTAA-TATAAAATAATATTTTAA
1 TATTTATATTAATTAT-AAATAATATATTAA
*
2410430 T-TTT-TATTAATTATAAATAATAAATTAA
1 TATTTATATTAATTATAAATAATATATTAA
2410458 ATCATATGGG
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
27 3 0.06
28 22 0.44
29 15 0.30
30 10 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TATTTATATTAATTATAAATAATATATTAA
Found at i:2410672 original size:2 final size:2
Alignment explanation
Indices: 2410665--2410699 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2410655 TCTATACATG
2410665 TA TA TA 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
2410700 AGGGATCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2413465 original size:2 final size:2
Alignment explanation
Indices: 2413458--2413484 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2413448 AACAGAACAA
2413458 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
2413485 CCACTCATTG
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:2415608 original size:2 final size:2
Alignment explanation
Indices: 2415601--2415635 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2415591 TATGTATGTA
2415601 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2415636 TGAACAATTT
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2415767 original size:189 final size:189
Alignment explanation
Indices: 2415447--2415805 Score: 682
Period size: 189 Copynumber: 1.9 Consensus size: 189
2415437 GCATTCAACA
2415447 TGAACAATTTGAGTCCAAAGTTAAATTTCTGAATGCAGAATCATAAAACAAAACATATGCACCAT
1 TGAACAATTTGAGTCCAAAGTTAAATTTCTGAATGCAGAATCATAAAACAAAACATATGCACCAT
2415512 TTATGTATCAATTCAGGCAACTAGCTATATAAATATTTATCAATTCCAAGGATATTTGAGAAGAT
66 TTATGTATCAATTCAGGCAACTAGCTATATAAATATTTATCAATTCCAAGGATATTTGAGAAGAT
2415577 TTCACATATGTATGTATGTATGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
131 TTCACATATGTATGTATGTATGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
2415636 TGAACAATTTGAGTCCAAAGTTAAATTTCTGAATGCAGAATCATAAAACAAAACATATGCACCAT
1 TGAACAATTTGAGTCCAAAGTTAAATTTCTGAATGCAGAATCATAAAACAAAACATATGCACCAT
2415701 TTATGTATCAATTCAGGCAACTAGCTATATAAATATTTATCAATTCCAAGGATATTTGAGAAGAT
66 TTATGTATCAATTCAGGCAACTAGCTATATAAATATTTATCAATTCCAAGGATATTTGAGAAGAT
* * * *
2415766 TTCACATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
131 TTCACATATGTATGTATGTATGTATGTGTGTGTGTGTGTG
2415806 ATGCAGACAG
Statistics
Matches: 166, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
189 166 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.36
Consensus pattern (189 bp):
TGAACAATTTGAGTCCAAAGTTAAATTTCTGAATGCAGAATCATAAAACAAAACATATGCACCAT
TTATGTATCAATTCAGGCAACTAGCTATATAAATATTTATCAATTCCAAGGATATTTGAGAAGAT
TTCACATATGTATGTATGTATGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
Found at i:2415781 original size:2 final size:2
Alignment explanation
Indices: 2415774--2415805 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2415764 ATTTCACATA
2415774 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2415806 ATGCAGACAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2427103 original size:44 final size:44
Alignment explanation
Indices: 2427040--2427129 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
2427030 AACTTAGCGT
2427040 AAATCAATATTCTCAATAGAAATTACTAAAACTCAAATCCTAAC
1 AAATCAATATTCTCAATAGAAATTACTAAAACTCAAATCCTAAC
2427084 AAATCAATATTCTCAATAGAAATTACTAAAACTCAAATCCTAAC
1 AAATCAATATTCTCAATAGAAATTACTAAAACTCAAATCCTAAC
2427128 AA
1 AA
2427130 TTGCTTCCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (44 bp):
AAATCAATATTCTCAATAGAAATTACTAAAACTCAAATCCTAAC
Found at i:2427897 original size:2 final size:2
Alignment explanation
Indices: 2427884--2427938 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
2427874 TTGTATCCAC
* *
2427884 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2427925 AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT
2427939 TTATCGATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2427936 original size:29 final size:29
Alignment explanation
Indices: 2427894--2427960 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
2427884 ATATAGATAT
* *
2427894 ATATATATATATATATATATATATTATAA
1 ATATAAATATATATATATATAGATTATAA
* *
2427923 ATATAAATATATATATTTATCGATTATAA
1 ATATAAATATATATATATATAGATTATAA
2427952 ATATAAATA
1 ATATAAATA
2427961 AGACATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (29 bp):
ATATAAATATATATATATATAGATTATAA
Found at i:2428061 original size:15 final size:15
Alignment explanation
Indices: 2428041--2428070 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2428031 TTGAATAGTA
*
2428041 TAATATTTTTATTTT
1 TAATATATTTATTTT
2428056 TAATATATTTATTTT
1 TAATATATTTATTTT
2428071 AATTAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TAATATATTTATTTT
Found at i:2428469 original size:9 final size:9
Alignment explanation
Indices: 2428441--2428473 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2428431 ATTAACAATA
2428441 ATTTATTAT
1 ATTTATTAT
2428450 ATTT-TTAT
1 ATTTATTAT
*
2428458 ATTTATTTT
1 ATTTATTAT
2428467 ATTTATT
1 ATTTATT
2428474 GAATGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
ATTTATTAT
Found at i:2428752 original size:16 final size:16
Alignment explanation
Indices: 2428733--2428763 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2428723 ATATATATTT
2428733 TAATTAAAAAAATTAC
1 TAATTAAAAAAATTAC
*
2428749 TAATTTAAAAAATTA
1 TAATTAAAAAAATTA
2428764 TTTCTTTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATTAAAAAAATTAC
Found at i:2429717 original size:14 final size:14
Alignment explanation
Indices: 2429700--2429726 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2429690 AAAAGTAGTA
2429700 AATATTTATATATC
1 AATATTTATATATC
2429714 AATATTTATATAT
1 AATATTTATATAT
2429727 TTTTTATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
AATATTTATATATC
Found at i:2430973 original size:20 final size:21
Alignment explanation
Indices: 2430935--2430974 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2430925 AGTATTTTGA
* *
2430935 TAAAATGATAATTTTATTAAT
1 TAAAATAATAATTTAATTAAT
2430956 TAAAATAAT-ATTTAATTAA
1 TAAAATAATAATTTAATTAA
2430975 CTCGTGGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TAAAATAATAATTTAATTAAT
Found at i:2431359 original size:22 final size:21
Alignment explanation
Indices: 2431326--2431366 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2431316 GGTGATTGAA
2431326 TAATTTTTTAAAATAATTTGT
1 TAATTTTTTAAAATAATTTGT
*
2431347 TAATTATTTTAAAATTATTT
1 TAATT-TTTTAAAATAATTT
2431367 TATTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TAATTTTTTAAAATAATTTGT
Found at i:2431372 original size:23 final size:21
Alignment explanation
Indices: 2431326--2431372 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
2431316 GGTGATTGAA
*
2431326 TAATTTTTTAAAATAATTTGT
1 TAATTTTTTAAAATAATTTAT
*
2431347 TAATTATTTTAAAATTATTTTAT
1 TAATT-TTTTAAAA-TAATTTAT
2431370 TAA
1 TAA
2431373 AATATTCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 8 0.36
23 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TAATTTTTTAAAATAATTTAT
Found at i:2431998 original size:17 final size:18
Alignment explanation
Indices: 2431962--2431999 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2431952 TAAATTTTAT
*
2431962 ATATTTTTTATGAAAATA
1 ATATTTATTATGAAAATA
*
2431980 ATATTTATTAT-ATAATA
1 ATATTTATTATGAAAATA
2431997 ATA
1 ATA
2432000 GAAAAACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATTTATTATGAAAATA
Found at i:2436369 original size:67 final size:67
Alignment explanation
Indices: 2436261--2436390 Score: 251
Period size: 67 Copynumber: 1.9 Consensus size: 67
2436251 CACGACATGC
*
2436261 ATACACAGTTTGCAAGTCTACTTAATACTAGCTTATCATGATCCAAATCTGTGTTGGAGGTTTAA
1 ATACACAGTTTGCAAGTCTACTTAATACTAGCTTATCATGATCCAAATCTGTGATGGAGGTTTAA
2436326 CA
66 CA
2436328 ATACACAGTTTGCAAGTCTACTTAATACTAGCTTATCATGATCCAAATCTGTGATGGAGGTTT
1 ATACACAGTTTGCAAGTCTACTTAATACTAGCTTATCATGATCCAAATCTGTGATGGAGGTTT
2436391 GACACATTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (67 bp):
ATACACAGTTTGCAAGTCTACTTAATACTAGCTTATCATGATCCAAATCTGTGATGGAGGTTTAA
CA
Found at i:2437390 original size:1 final size:1
Alignment explanation
Indices: 2437386--2437410 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2437376 GAAAAAATGC
2437386 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
2437411 TTGCATCTAG
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2437448 original size:21 final size:21
Alignment explanation
Indices: 2437424--2437463 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2437414 CATCTAGGTG
2437424 TGTCCAAATGGGTCTTGATCA
1 TGTCCAAATGGGTCTTGATCA
*
2437445 TGTCCAAATGTGTCTTGAT
1 TGTCCAAATGGGTCTTGAT
2437464 GTGTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (21 bp):
TGTCCAAATGGGTCTTGATCA
Found at i:2439369 original size:16 final size:15
Alignment explanation
Indices: 2439348--2439377 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
2439338 GTGGATTTTT
2439348 TAAAATATATAAAATA
1 TAAAATA-ATAAAATA
2439364 TAAAATAATAAAAT
1 TAAAATAATAAAAT
2439378 TATTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAATAATAAAATA
Found at i:2439541 original size:17 final size:17
Alignment explanation
Indices: 2439504--2439542 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2439494 TTTGTTATTT
*
2439504 TTTATTTTTATTAATAT
1 TTTATTTTTATTAATAA
2439521 TTTATTTTTA-TATATAA
1 TTTATTTTTATTA-ATAA
2439538 TTTAT
1 TTTAT
2439543 AAAAGGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATTTTTATTAATAA
Found at i:2440075 original size:13 final size:16
Alignment explanation
Indices: 2440023--2440071 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
2440013 AAATATTAAA
* *
2440023 ATATTCTTTAATTACAT
1 ATATTTTTTAAATA-AT
*
2440040 ATATATTTTAAATAAT
1 ATATTTTTTAAATAAT
2440056 ATATTTTTTAAATAAT
1 ATATTTTTTAAATAAT
2440072 TTTTATAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTTTTAAATAAT
Found at i:2440524 original size:30 final size:31
Alignment explanation
Indices: 2440490--2440569 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
2440480 TGATAAAATA
*
2440490 TTTTAAAATATTATTAAT-TATAAATATAAT
1 TTTTAAAATATTATTAATAAATAAATATAAT
*
2440520 TTTTATAAA-A-TATGAATAAATAAATATAAT
1 TTTTA-AAATATTATTAATAAATAAATATAAT
* *
2440550 TTTTAATAT-TTATTCATAAA
1 TTTTAAAATATTATTAATAAA
2440570 AGTGAAGGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
29 8 0.20
30 30 0.73
31 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (31 bp):
TTTTAAAATATTATTAATAAATAAATATAAT
Found at i:2445266 original size:2 final size:2
Alignment explanation
Indices: 2445259--2445294 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2445249 TTCAATAAGA
2445259 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
2445295 TCCAAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2445869 original size:2 final size:2
Alignment explanation
Indices: 2445864--2445899 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2445854 TTTGTGTGTG
2445864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2445900 ATTTAAGAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2449119 original size:15 final size:15
Alignment explanation
Indices: 2449089--2449134 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
2449079 TGGACTGATC
*
2449089 AGATTAGTTTCGGATT
1 AGATTA-TTTCAGATT
2449105 AGATTATTTCAGATT
1 AGATTATTTCAGATT
*
2449120 AGATTAATTCAGATT
1 AGATTATTTCAGATT
2449135 TTAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 22 0.79
16 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (15 bp):
AGATTATTTCAGATT
Found at i:2449188 original size:16 final size:16
Alignment explanation
Indices: 2449164--2449210 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2449154 TTCGAATTCG
*
2449164 AGTTTGGATCATTTCA
1 AGTTCGGATCATTTCA
**
2449180 AGTTCGGATTGTTTCA
1 AGTTCGGATCATTTCA
*
2449196 AGTTCAGATCATTTC
1 AGTTCGGATCATTTC
2449211 GAATTTGGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (16 bp):
AGTTCGGATCATTTCA
Found at i:2450101 original size:32 final size:32
Alignment explanation
Indices: 2450050--2450120 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
2450040 TCGAGTTTGA
*
2450050 ATCA-TTTCGATTCGAGTTATTTCAAGTTCAG
1 ATCATTTTAGATTCGAGTTATTTCAAGTTCAG
* *
2450081 ATCATTTTAGATTCGGGTTATTTCAGGTTCAG
1 ATCATTTTAGATTCGAGTTATTTCAAGTTCAG
*
2450113 ATTATTTT
1 ATCATTTT
2450121 CGAGTTCAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 4 0.11
32 31 0.89
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (32 bp):
ATCATTTTAGATTCGAGTTATTTCAAGTTCAG
Found at i:2450117 original size:16 final size:16
Alignment explanation
Indices: 2450066--2450119 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
2450056 TCGATTCGAG
*
2450066 TTATTTCAAGTTCAGA
1 TTATTTCAGGTTCAGA
* * * * *
2450082 TCATTTTAGATTCGGG
1 TTATTTCAGGTTCAGA
2450098 TTATTTCAGGTTCAGA
1 TTATTTCAGGTTCAGA
2450114 TTATTT
1 TTATTT
2450120 TCGAGTTCAG
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (16 bp):
TTATTTCAGGTTCAGA
Found at i:2455963 original size:458 final size:458
Alignment explanation
Indices: 2455106--2456024 Score: 1748
Period size: 458 Copynumber: 2.0 Consensus size: 458
2455096 TCCCAAATAG
2455106 CTATAAACGACTATAATTTCAAATGCATGTATTGAAACATTATGAATTGTATCGATACATAGCAA
1 CTATAAACGACTATAATTTCAAATGCATGTATTGAAACATTATGAATTGTATCGATACATAGCAA
2455171 CGAGAATGCATGGAAATAAGCACCTAATAAGACAACAATGACTACAAACACAATCATTCAATCAC
66 CGAGAATGCATGGAAATAAGCACCTAATAAGACAACAATGACTACAAACACAATCATTCAATCAC
2455236 CAACGAGTATATCAATATTCAAGACTATAAATTTGAGTTTCCAACAGCTGAATATGAAGAGAATC
131 CAACGAGTATATCAATATTCAAGACTATAAATTTGAGTTTCCAACAGCTGAATATGAAGAGAATC
2455301 CATCAAGAAACACCAAGAGATCAAAGCATTCAAAGTTTTACTTATTTTCTCATTTCAAGAGCTTT
196 CATCAAGAAACACCAAGAGATCAAAGCATTCAAAGTTTTACTTATTTTCTCATTTCAAGAGCTTT
* *
2455366 TATTCTCATTGTTGTCATTTTTTGAAAGCTTTTTGTATTTGATTTGTGTTTATTCTTTCACAAAC
261 TATTCTCATTGTTGTCAATTTTTGAAAGCTTTTTGTATTTGATTTATGTTTATTCTTTCACAAAC
*
2455431 ATCAGCTTACTTAGAGACAATTTTCGTTTGTACAAATTTTTGAATTTTGTAAGGTTGCATTCAAC
326 ATCAGCTTACTTAGAGACAATTTTCATTTGTACAAATTTTTGAATTTTGTAAGGTTGCATTCAAC
*
2455496 TTTGGGTTACAATTTCTCAAGAATTAGGGGTATTATTCTTGGAGAGATTGTGAGGTTTTTATCTT
391 CTTGGGTTACAATTTCTCAAGAATTAGGGGTATTATTCTTGGAGAGATTGTGAGGTTTTTATCTT
2455561 AAC
456 AAC
* * *
2455564 CTATAAACGATTATAATTTCAAATGTATGTTTTGAAACATTATGAATTGTATCGATACATAGCAA
1 CTATAAACGACTATAATTTCAAATGCATGTATTGAAACATTATGAATTGTATCGATACATAGCAA
2455629 CGAGAATGCATGGAAATAAGCACCTAATAAGACAACAATGACTACAAACACAATCATTCAATCAC
66 CGAGAATGCATGGAAATAAGCACCTAATAAGACAACAATGACTACAAACACAATCATTCAATCAC
2455694 CAACGAGTATATCAATATTCAAGACTATAAATTTGAGTTTCCAACAGCTGAATATGAAGAGAATC
131 CAACGAGTATATCAATATTCAAGACTATAAATTTGAGTTTCCAACAGCTGAATATGAAGAGAATC
*
2455759 CATCAAGAAACACCAAGAGATCAAAGTATTCAAAGTTTTACTTATTTTCTCATTTCAAGAGCTTT
196 CATCAAGAAACACCAAGAGATCAAAGCATTCAAAGTTTTACTTATTTTCTCATTTCAAGAGCTTT
2455824 TATTCTCATTGTTGTCAATTTTTGAAAGCTTTTTGTATTTGATTTATGTTTATTCTTTCACAAAC
261 TATTCTCATTGTTGTCAATTTTTGAAAGCTTTTTGTATTTGATTTATGTTTATTCTTTCACAAAC
2455889 ATCAGCTTACTTAGAGACAATTTTCATTTGTACAAATTTTTGAATTTTGTAAGGTTGCATTCAAC
326 ATCAGCTTACTTAGAGACAATTTTCATTTGTACAAATTTTTGAATTTTGTAAGGTTGCATTCAAC
*
2455954 CTTGGGTTACAATTTCTCAAGAATTTGGGGTATTATTCTTGGAGAGATTGTGAGGTTTTTATCTT
391 CTTGGGTTACAATTTCTCAAGAATTAGGGGTATTATTCTTGGAGAGATTGTGAGGTTTTTATCTT
*
2456019 AGC
456 AAC
2456022 CTA
1 CTA
2456025 GAAAAGATAA
Statistics
Matches: 451, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
458 451 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (458 bp):
CTATAAACGACTATAATTTCAAATGCATGTATTGAAACATTATGAATTGTATCGATACATAGCAA
CGAGAATGCATGGAAATAAGCACCTAATAAGACAACAATGACTACAAACACAATCATTCAATCAC
CAACGAGTATATCAATATTCAAGACTATAAATTTGAGTTTCCAACAGCTGAATATGAAGAGAATC
CATCAAGAAACACCAAGAGATCAAAGCATTCAAAGTTTTACTTATTTTCTCATTTCAAGAGCTTT
TATTCTCATTGTTGTCAATTTTTGAAAGCTTTTTGTATTTGATTTATGTTTATTCTTTCACAAAC
ATCAGCTTACTTAGAGACAATTTTCATTTGTACAAATTTTTGAATTTTGTAAGGTTGCATTCAAC
CTTGGGTTACAATTTCTCAAGAATTAGGGGTATTATTCTTGGAGAGATTGTGAGGTTTTTATCTT
AAC
Found at i:2461222 original size:52 final size:52
Alignment explanation
Indices: 2461166--2461294 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2461156 CACTGATCTT
*
2461166 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGTAAATTTGACCAGATGTATCGATACACTATGAAA
* *
2461218 TGTATCGATACATACAGGCAAATTTGACCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGTAAATTTGACCAGATGTATCGATACACTATGAAA
2461270 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGTAAATTT
2461295 TCATATTTTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGTAAATTTGACCAGATGTATCGATACACTATGAAA
Found at i:2467207 original size:14 final size:14
Alignment explanation
Indices: 2467190--2467218 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2467180 AATGAAATAA
2467190 AACAATCTTTTTAT
1 AACAATCTTTTTAT
2467204 AACAATCTTTTTAT
1 AACAATCTTTTTAT
2467218 A
1 A
2467219 TTTATAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (14 bp):
AACAATCTTTTTAT
Found at i:2471698 original size:21 final size:21
Alignment explanation
Indices: 2471672--2471713 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2471662 AGCTACTGCC
2471672 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
2471693 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
2471714 GATCTTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:2474136 original size:52 final size:52
Alignment explanation
Indices: 2474069--2474202 Score: 182
Period size: 52 Copynumber: 2.6 Consensus size: 52
2474059 TTAAGTTTCT
*
2474069 CAATTGTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACAC
1 CAATT-TTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* *
2474120 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTCC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * *
2474173 CAATTTTTCACAATCGAGGATACTCCAACC
1 CAATTTTCCATAATCGGGGATACTCCAACC
2474203 TCGTTATTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
50 2 0.03
51 6 0.08
52 49 0.68
53 15 0.21
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31
Consensus pattern (52 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
Found at i:2474327 original size:107 final size:108
Alignment explanation
Indices: 2474136--2474340 Score: 259
Period size: 107 Copynumber: 1.9 Consensus size: 108
2474126 TCCTTTAATC
* *
2474136 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGACTTTATTTCCAAAAACACCAATTTCTCACAATCGAGGATACTCCAA
* **
2474201 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGA
66 CCCCGTTATTTCAGAGGGGATACTCCAACCCCGTTACCTCCGA
* * * ** * * * *
2474244 GGGGATACTCCAATTCCGGCTTTATTTCC-AAAATACTGATTTCTCATAATTGGGGATATTCCAA
1 GGGGATACTCCAACTCCGACTTTATTTCCAAAAACACCAATTTCTCACAATCGAGGATACTCCAA
* *
2474308 CCCCGTTATTTCCGAGGGGATACTCCAATCCCG
66 CCCCGTTATTTCAGAGGGGATACTCCAACCCCG
2474341 ATTTTATTTC
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
107 55 0.68
108 26 0.32
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.29
Consensus pattern (108 bp):
GGGGATACTCCAACTCCGACTTTATTTCCAAAAACACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCAGAGGGGATACTCCAACCCCGTTACCTCCGA
Found at i:2474395 original size:79 final size:79
Alignment explanation
Indices: 2474216--2474396 Score: 240
Period size: 79 Copynumber: 2.3 Consensus size: 79
2474206 TTATTTCATC
** * *
2474216 GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAATTCCGGCTTTATTTCCAAAATACT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGACTTTATTTCCAAAATACT
* *
2474281 GATTTCTCATAATT
66 GATTTCTCACAACT
* * *
2474295 GGGGATATTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTCC-TAAT-CA
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGACTTTATTTCCAAAATAC-
*
2474358 TCGATTTTTCACAACT
65 T-GATTTCTCACAACT
2474374 GGGGATACTCCAACCCCGTTATT
1 GGGGATACTCCAACCCCGTTATT
2474397 ATCTCTAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
77 1 0.01
78 4 0.04
79 84 0.94
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGACTTTATTTCCAAAATACT
GATTTCTCACAACT
Found at i:2476420 original size:2 final size:2
Alignment explanation
Indices: 2476413--2476452 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2476403 ATTCTCGATA
2476413 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
2476453 CCAAATGCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2478600 original size:30 final size:27
Alignment explanation
Indices: 2478544--2478604 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 27
2478534 ATAAATTATT
2478544 AATATTTTAAAATTTATATAAATATAA
1 AATATTTTAAAATTTATATAAATATAA
2478571 AATATTTTAAATATAATTATGAT-AATATAA
1 AATATTTTAAA-AT--TTAT-ATAAATATAA
2478601 AATA
1 AATA
2478605 CACAAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 11 0.37
28 2 0.07
30 15 0.50
31 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
AATATTTTAAAATTTATATAAATATAA
Found at i:2481540 original size:34 final size:34
Alignment explanation
Indices: 2481492--2481574 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
2481482 GTGAAGCACA
2481492 TTAGGTGTGTTAGGTGATGTATTTAGTGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTAGTGAGAATG
* *
2481526 TTAGATGTGTTAGGTGATGTATTTGGTGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTAGTGAGAATG
2481560 TTAGGTGTGTTAGGT
1 TTAGGTGTGTTAGGT
2481575 AATATGTTAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (34 bp):
TTAGGTGTGTTAGGTGATGTATTTAGTGAGAATG
Found at i:2481588 original size:34 final size:33
Alignment explanation
Indices: 2481492--2481589 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 33
2481482 GTGAAGCACA
*
2481492 TTAGGTGTGTTAGGTGATGTATTTA-GTGAGAATG
1 TTAGGTGTGTTAGGT-A-ATATTTAGGTGAGAATG
* *
2481526 TTAGATGTGTTAGGTGATGTATTT-GGTGAGAATG
1 TTAGGTGTGTTAGGT-A-ATATTTAGGTGAGAATG
2481560 TTAGGTGTGTTAGGTAATATGTTAGGTGAG
1 TTAGGTGTGTTAGGTAATAT-TTAGGTGAG
2481590 TAAGATATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
32 3 0.05
33 3 0.05
34 52 0.90
ACGTcount: A:0.23, C:0.00, G:0.36, T:0.41
Consensus pattern (33 bp):
TTAGGTGTGTTAGGTAATATTTAGGTGAGAATG
Found at i:2486357 original size:34 final size:34
Alignment explanation
Indices: 2486319--2486401 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
2486309 GTGAAGCATA
*
2486319 TTAGGTGCGTTAGGTGATGTATTTGGTGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
*
2486353 TTAGGTGTGTTAAGTGATGTATTTGGTGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
2486387 TTAGGTGTGTTAGGT
1 TTAGGTGTGTTAGGT
2486402 AATATGTTAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.20, C:0.01, G:0.37, T:0.41
Consensus pattern (34 bp):
TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
Found at i:2486415 original size:34 final size:34
Alignment explanation
Indices: 2486305--2486416 Score: 134
Period size: 34 Copynumber: 3.3 Consensus size: 34
2486295 GTTAAGTGTG
* * *
2486305 TTAGGTGAAGCATATTAGGTGCGTTAGGTGATGTA
1 TTAGGTG-AGAATGTTAGGTGTGTTAGGTGATGTA
* *
2486340 TTTGGTGAGAATGTTAGGTGTGTTAAGTGATGTA
1 TTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTA
* * * *
2486374 TTTGGTGAGAATGTTAGGTGTGTTAGGTAATATG
1 TTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTA
2486408 TTAGGTGAG
1 TTAGGTGAG
2486417 TAAGATATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
34 61 0.91
35 6 0.09
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (34 bp):
TTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTA
Found at i:2490601 original size:531 final size:533
Alignment explanation
Indices: 2489575--2490631 Score: 1437
Period size: 531 Copynumber: 2.0 Consensus size: 533
2489565 AAGAATAGCT
*
2489575 CCATCCAAGAAGCGTTTTGAGTGAAGCAGTGACGCATTGAAAAAACATGGAAAATGAAATAGATC
1 CCATCCAAGAAGCGTTTTGAGTGAAGCAGTGACGCATTGAAAAAACATGGAAAATGAAACAGATC
* * * *
2489640 AACTGAGACACTAGCTCTAGAAAATAATCAATTATATGGGGCAAGAATTCATCTCGTTGACAATT
66 AACCGAGACACTAGCTCTAAAAAATAACCAATTATATGAGGCAAGAATTCATCTC--TG------
*
2489705 ACTATACTATGAAATTTATGAAGAGCAACAGATTCTTGATATACTAAGAATCAACTATCAGGTTG
123 ---ATAC-----AATTTATGAAGAGCAACAGATCCTTGATATACTAAGAATCAACTATCAGGTTG
* * *
2489770 TGCTTACATGGATCAGAGACAGCAGAGATAAAGACACCAGCCCTAATCATAAAGTATCAACTCAA
180 TGCTTACATGGATCAGAGACACCAGAGATAAAGAAACCAGCCCTAATCATAAAATATCAACTCAA
* * * **
2489835 AACAAGTATAGACCATTTGATAAAACAGCATTTCCTAGGAGTAAAAGAAGCAATACATAAGACAT
245 AACAAATATAGACCATTCGATAAAACAGCATATCCTAAAAGTAAAAGAAGCAATACATAAGACAT
*
2489900 GCAATTGGTAATTTCTTAAAGTGAGAAAAAGGGGAAATAAGATTTAGGCAAATTTTAGATTCCTA
310 GCAATTGGTAATTTCTTAAAGTGAGAAAAAAGGGAAATAAGATTTAGGCAAATTTTAGATTCCTA
* * * *
2489965 TCAAAATGCGGGATTTGTACAGTTAAGAAAAGAGATAGATCAAAATGCACATTCATGTAAACTTT
375 TCAAAATGCAGCATTTGTACAATTAAGAAAAGAGATAGATCAAAATGCACATTCACGTAAACTTT
* *
2490030 AGGTTCCTAGCTCAGGCCACCACGTTTGACACTACAAGAGAAT-AGTGTTG-AAAAA-AAATCCA
440 AGGTTCCTAGCTCACGCCACCACGTGTGACACTACAAGAGAATGA-TGTTGAAAAAAGAAATCCA
*
2490092 TGAAAGTTGGTGTATCAATGCACTAAAGCA
504 CGAAAGTTGGTGTATCAATGCACTAAAGCA
* * *
2490122 CCATCCAAGAAGCTTTTTGAGTGGAGCAGTGAGGCATTGAAAAAACATGGAAAATGAAACAGATC
1 CCATCCAAGAAGCGTTTTGAGTGAAGCAGTGACGCATTGAAAAAACATGGAAAATGAAACAGATC
* *
2490187 AACCGA-ACAGTAGCTCTAAAAAATAACCAATTATATGATGCAAGAATTCATCTC-G-TAC-ATT
66 AACCGAGACACTAGCTCTAAAAAATAACCAATTATATGAGGCAAGAATTCATCTCTGATACAATT
* * * *
2490248 TATGAAGAGTAACAGATCCTTGATATATTAAGAATCAACTATCAGGTTGTGGCTTGCATGGATTA
131 TATGAAGAGCAACAGATCCTTGATATACTAAGAATCAACTATCAGGTTGT-GCTTACATGGATCA
* * *
2490313 GAGACACCAGAGGTAAATAAACCAGCCTTACTAATCATAAAATGTCAACTCAAAACAAATATAGA
195 GAGACACCAGAGATAAAGAAACCAGCC---CTAATCATAAAATATCAACTCAAAACAAATATAGA
* * *
2490378 CCATTCGATAAAACAGCATATCCTAAAAGTAAAGGAAGCGATTCATAAGACATGCAATTGGTAAT
257 CCATTCGATAAAACAGCATATCCTAAAAGTAAAAGAAGCAATACATAAGACATGCAATTGGTAAT
* * * * * *
2490443 TTCTTAAAGTG-GAAAAGAAGGGAAATAGGGTTTAGGTATATTTTAGGTTCCTATGAAAATGCAG
322 TTCTTAAAGTGAGAAAA-AAGGGAAATAAGATTTAGGCAAATTTTAGATTCCTATCAAAATGCAG
*
2490507 CATTTGTACAATTAAGAGAAGAGATAGATCAAAATGCACATTCACGTAAACTTTAGGTTCCTAGC
386 CATTTGTACAATTAAGAAAAGAGATAGATCAAAATGCACATTCACGTAAACTTTAGGTTCCTAGC
* * *
2490572 TCACGCCATCACGTGTGACAGTCCAAGAGAATGATGTTGAAAAAAGAAATCCACGAAAGT
451 TCACGCCACCACGTGTGACACTACAAGAGAATGATGTTGAAAAAAGAAATCCACGAAAGT
2490632 GAATCAATGC
Statistics
Matches: 455, Mismatches: 47, Indels: 30
0.86 0.09 0.06
Matches are distributed among these distances:
527 50 0.11
528 35 0.08
530 5 0.01
531 233 0.51
532 6 0.01
533 16 0.04
543 1 0.00
546 43 0.09
547 66 0.15
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (533 bp):
CCATCCAAGAAGCGTTTTGAGTGAAGCAGTGACGCATTGAAAAAACATGGAAAATGAAACAGATC
AACCGAGACACTAGCTCTAAAAAATAACCAATTATATGAGGCAAGAATTCATCTCTGATACAATT
TATGAAGAGCAACAGATCCTTGATATACTAAGAATCAACTATCAGGTTGTGCTTACATGGATCAG
AGACACCAGAGATAAAGAAACCAGCCCTAATCATAAAATATCAACTCAAAACAAATATAGACCAT
TCGATAAAACAGCATATCCTAAAAGTAAAAGAAGCAATACATAAGACATGCAATTGGTAATTTCT
TAAAGTGAGAAAAAAGGGAAATAAGATTTAGGCAAATTTTAGATTCCTATCAAAATGCAGCATTT
GTACAATTAAGAAAAGAGATAGATCAAAATGCACATTCACGTAAACTTTAGGTTCCTAGCTCACG
CCACCACGTGTGACACTACAAGAGAATGATGTTGAAAAAAGAAATCCACGAAAGTTGGTGTATCA
ATGCACTAAAGCA
Found at i:2490680 original size:14 final size:15
Alignment explanation
Indices: 2490659--2490697 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
2490649 AAAAAAATAT
2490659 TATCTTTAAAAGTC-
1 TATCTTTAAAAGTCA
*
2490673 -ATCTTTTAAAGTCA
1 TATCTTTAAAAGTCA
2490687 TATCTTTAAAA
1 TATCTTTAAAA
2490698 AATATTGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 12 0.57
15 9 0.43
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (15 bp):
TATCTTTAAAAGTCA
Found at i:2492760 original size:31 final size:31
Alignment explanation
Indices: 2492722--2492805 Score: 159
Period size: 31 Copynumber: 2.7 Consensus size: 31
2492712 TAATAAATGT
2492722 ATAAATACTCCATTGTTATCTTAAGAGATAC
1 ATAAATACTCCATTGTTATCTTAAGAGATAC
*
2492753 ATAAATACTCCATCGTTATCTTAAGAGATAC
1 ATAAATACTCCATTGTTATCTTAAGAGATAC
2492784 ATAAATACTCCATTGTTATCTT
1 ATAAATACTCCATTGTTATCTT
2492806 CACTAGCTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (31 bp):
ATAAATACTCCATTGTTATCTTAAGAGATAC
Found at i:2499084 original size:24 final size:24
Alignment explanation
Indices: 2499056--2499102 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2499046 GTTTTTTTTA
2499056 TATTTTA-ATTTTTAAAATTTAAAT
1 TATTTTATATTTTT-AAATTTAAAT
*
2499080 TATTTTATATTTTTATATTTAAA
1 TATTTTATATTTTTAAATTTAAA
2499103 GGTGATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTTTATATTTTTAAATTTAAAT
Found at i:2499247 original size:18 final size:19
Alignment explanation
Indices: 2499226--2499264 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
2499216 TGTGTTTTGA
2499226 TTTTTTGAA-TTAA-ATTT
1 TTTTTTGAATTTAAGATTT
2499243 TTTTTTGAATTTAAGATTT
1 TTTTTTGAATTTAAGATTT
2499262 TTT
1 TTT
2499265 AAGTTTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
18 4 0.20
19 7 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTTTTGAATTTAAGATTT
Found at i:2499271 original size:16 final size:15
Alignment explanation
Indices: 2499176--2499275 Score: 53
Period size: 16 Copynumber: 6.3 Consensus size: 15
2499166 TTTATTTTTA
*
2499176 AGATTTTTTAAATTT
1 AGATTTTTTGAATTT
2499191 -GACTTATTTTGAATTT
1 AGA-TT-TTTTGAATTT
* **
2499207 AAATTTTTTTGTGTTT
1 AGA-TTTTTTGAATTT
*
2499223 TGATTTTTTGAA-TT
1 AGATTTTTTGAATTT
*
2499237 AAATTTTTTTTTGAATTT
1 AGA---TTTTTTGAATTT
2499255 AAGATTTTTT-AAGTTT
1 -AGATTTTTTGAA-TTT
2499271 AGATT
1 AGATT
2499276 GATCACAAGC
Statistics
Matches: 64, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
14 5 0.08
15 16 0.25
16 27 0.42
17 12 0.19
18 2 0.03
19 2 0.03
ACGTcount: A:0.27, C:0.01, G:0.11, T:0.61
Consensus pattern (15 bp):
AGATTTTTTGAATTT
Found at i:2499275 original size:15 final size:16
Alignment explanation
Indices: 2499172--2499264 Score: 59
Period size: 16 Copynumber: 5.8 Consensus size: 16
2499162 TATTTTTATT
*
2499172 TTTAAGATTTTTTAAA
1 TTTAAGATTTTTTGAA
2499188 TTT--GACTTATTTTGAA
1 TTTAAGA-TT-TTTTGAA
**
2499204 TTTAA-ATTTTTTTGTG
1 TTTAAGA-TTTTTTGAA
*
2499220 TTT-TGATTTTTTGAA
1 TTTAAGATTTTTTGAA
* **
2499235 TTAAATTTTTTTTTGAA
1 TTTAA-GATTTTTTGAA
2499252 TTTAAGATTTTTT
1 TTTAAGATTTTTT
2499265 AAGTTTAGAT
Statistics
Matches: 56, Mismatches: 14, Indels: 14
0.67 0.17 0.17
Matches are distributed among these distances:
14 2 0.04
15 11 0.20
16 27 0.48
17 16 0.29
ACGTcount: A:0.26, C:0.01, G:0.10, T:0.63
Consensus pattern (16 bp):
TTTAAGATTTTTTGAA
Found at i:2499550 original size:21 final size:21
Alignment explanation
Indices: 2499516--2499560 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2499506 AAGTTGTGAT
* *
2499516 ATATTTAAATTAATT-ATATTG
1 ATATTAAAAATAATTAAT-TTG
2499537 ATATTAAAAATAATTAATTTG
1 ATATTAAAAATAATTAATTTG
2499558 ATA
1 ATA
2499561 AATTTGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
ATATTAAAAATAATTAATTTG
Found at i:2499952 original size:18 final size:19
Alignment explanation
Indices: 2499926--2499961 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2499916 ATATAATTAT
2499926 ATAACATATAA-ATAATAC
1 ATAACATATAAGATAATAC
*
2499944 ATAATATATAAGATAATA
1 ATAACATATAAGATAATA
2499962 TTAAATTAGA
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:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (19 bp):
ATAACATATAAGATAATAC
Found at i:2501114 original size:27 final size:28
Alignment explanation
Indices: 2501083--2501161 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 28
2501073 TATTTTTATC
2501083 TTATTTAATA-AAAT-ATATATTAAAA-A
1 TTATTTAATATAAATAATA-ATTAAAATA
2501109 TATATTT-ATATAAATAATAATTAAAATA
1 T-TATTTAATATAAATAATAATTAAAATA
* *
2501137 TTATTT-ATATTAAAGAATAAATAAA
1 TTATTTAATA-TAAATAATAATTAAA
2501162 TTAATTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.09
27 24 0.52
28 18 0.39
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
TTATTTAATATAAATAATAATTAAAATA
Found at i:2501162 original size:27 final size:26
Alignment explanation
Indices: 2501105--2501161 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 26
2501095 ATATATATTA
* *
2501105 AAAATATATTTATATAAATAATAATT
1 AAAATATATTTATATAAAGAATAAAT
2501131 AAAATATTATTTATATTAAAGAATAAAT
1 AAAATA-TATTTATA-TAAAGAATAAAT
2501159 AAA
1 AAA
2501162 TTAATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 6 0.22
27 8 0.30
28 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAATATATTTATATAAAGAATAAAT
Found at i:2504912 original size:30 final size:32
Alignment explanation
Indices: 2504852--2504916 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
2504842 ATGATTGTTA
2504852 TTAAAAGTTTAATATAATTATTGTATTTATAT
1 TTAAAAGTTTAATATAATTATTGTATTTATAT
*
2504884 TTAAAATTTTAATAATAATT-TT-TA-TTATAT
1 TTAAAAGTTTAAT-ATAATTATTGTATTTATAT
2504914 TTA
1 TTA
2504917 TACTTACACA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 9 0.29
31 2 0.06
32 14 0.45
33 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (32 bp):
TTAAAAGTTTAATATAATTATTGTATTTATAT
Found at i:2509489 original size:20 final size:17
Alignment explanation
Indices: 2509447--2509490 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 17
2509437 TAAATCAAAT
2509447 TTAAATTAAAAACTATA
1 TTAAATTAAAAACTATA
*
2509464 TAAAATTGAATAAACTTATA
1 TTAAATT-AA-AAAC-TATA
2509484 TTAAATT
1 TTAAATT
2509491 TCATTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 2 0.09
19 4 0.18
20 10 0.45
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (17 bp):
TTAAATTAAAAACTATA
Found at i:2510546 original size:17 final size:18
Alignment explanation
Indices: 2510524--2510566 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
2510514 CCCAACATTC
2510524 TTTTTGTTTTACTTT-TT
1 TTTTTGTTTTACTTTATT
**
2510541 TTTTTGTTTTGTTTTATT
1 TTTTTGTTTTACTTTATT
2510559 TTTTTGTT
1 TTTTTGTT
2510567 AGGCCGTCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.05, C:0.02, G:0.09, T:0.84
Consensus pattern (18 bp):
TTTTTGTTTTACTTTATT
Found at i:2514067 original size:88 final size:88
Alignment explanation
Indices: 2513912--2514254 Score: 280
Period size: 88 Copynumber: 4.0 Consensus size: 88
2513902 TCTTTCATCT
* * * * * * * *
2513912 CATTAATCAAATATTTTCTGTCATGTTATAGAAGAAATCTAATACCTTATACGTTTGTCACACCT
1 CATTAGTCAAATATTTTCTGTCATGTCAGA-AAGAAATCTAATACC-CATGCATCTGTCACATCT
*
2513977 TTCAGGTTCTAAAAAATTTATTAAG
64 TTCAGGTTCTAAAAAATTTATTAGG
*
2514002 CATTAGTCAAATATTTAT-TGTCATGTCA-AAAGAAATCTAATACCTCATGTATCTGTCACATC-
1 CATTAGTCAAATATTT-TCTGTCATGTCAGAAAGAAATCTAATACC-CATGCATCTGTCACATCT
* *
2514064 -T----TTC--AAAAGTTTTTTAGG
64 TTCAGGTTCTAAAAAATTTATTAGG
* ** * * **
2514082 CATTAGTAAAATATTTT-TGTTGTGTTAG-AAGAAATTTAATACCCTATGCATCTGTCATGTCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAAATCTAATACCC-ATGCATCTGTCACATCTT
*
2514145 TCAGGTTCTAAGAAATTTATTAGG
65 TCAGGTTCTAAAAAATTTATTAGG
* * * * *
2514169 TATTAGTCAAATATTTTCTGTTATGTCAGAAA-AAATCTGATATCCCATACATTTGTCACATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAAATCTAATA-CCCATGCATCTGTCACATCTT
** * *
2514233 TTGGGTTCCAAGAAATTTATTA
65 TCAGGTTCTAAAAAATTTATTA
2514255 TACATATTTT
Statistics
Matches: 204, Mismatches: 35, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
78 1 0.00
79 35 0.17
80 26 0.13
81 1 0.00
82 3 0.01
85 3 0.01
86 1 0.00
87 26 0.13
88 77 0.38
89 6 0.03
90 24 0.12
91 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (88 bp):
CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAAATCTAATACCCATGCATCTGTCACATCTTT
CAGGTTCTAAAAAATTTATTAGG
Found at i:2514135 original size:79 final size:80
Alignment explanation
Indices: 2514001--2514147 Score: 190
Period size: 79 Copynumber: 1.9 Consensus size: 80
2513991 AATTTATTAA
* *
2514001 GCATTAGTCAAATATTTATTGTCATGTCAAAAGAAATCTAATACCTCATGTATCTGTCACATCTT
1 GCATTAGTAAAATATTTATTGTCATGTCAAAAGAAATCTAATACCTCATGCATCTGTCACATCTT
2514066 TCAAAAGTTTTTTAG
66 TCAAAAGTTTTTTAG
** * * * **
2514081 GCATTAGTAAAATATTT-TTGTTGTGTTAGAAGAAATTTAATACC-CTATGCATCTGTCATGTCT
1 GCATTAGTAAAATATTTATTGTCATGTCAAAAGAAATCTAATACCTC-ATGCATCTGTCACATCT
2514144 TTCA
65 TTCA
2514148 GGTTCTAAGA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
78 1 0.02
79 40 0.70
80 16 0.28
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (80 bp):
GCATTAGTAAAATATTTATTGTCATGTCAAAAGAAATCTAATACCTCATGCATCTGTCACATCTT
TCAAAAGTTTTTTAG
Found at i:2517535 original size:23 final size:23
Alignment explanation
Indices: 2517505--2517554 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2517495 TTCTAAATAA
* * *
2517505 AAAATTAAATTTAATAT-ATTTT
1 AAAATTTAATTTAAAATCAATTT
2517527 AAAATTTAATTTAAAATCAATTT
1 AAAATTTAATTTAAAATCAATTT
2517550 AAAAT
1 AAAAT
2517555 AAAAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATTTAATTTAAAATCAATTT
Found at i:2519503 original size:6 final size:6
Alignment explanation
Indices: 2519492--2519535 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
2519482 GCAATTGAGT
* * *
2519492 AGGTGG AGGTGG AGGTGG AGGTGG AGGTGG TGGCGG AGGAGG AG
1 AGGTGG AGGTGG AGGTGG AGGTGG AGGTGG AGGTGG AGGTGG AG
2519536 CTTTCTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.18, C:0.02, G:0.66, T:0.14
Consensus pattern (6 bp):
AGGTGG
Found at i:2520417 original size:2 final size:2
Alignment explanation
Indices: 2520406--2520443 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2520396 TAAGCCCGAT
*
2520406 TA TA -A TA TA TA TA TA TA TA TT TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2520444 AAAGAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2522323 original size:14 final size:16
Alignment explanation
Indices: 2522304--2522335 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2522294 ATTTGATAAA
2522304 TTTAATAT-TA-ATTT
1 TTTAATATATATATTT
2522318 TTTAATATATATATTT
1 TTTAATATATATATTT
2522334 TT
1 TT
2522336 AGTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAATATATATATTT
Found at i:2525574 original size:25 final size:25
Alignment explanation
Indices: 2525540--2525591 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
2525530 CTTACAACGG
2525540 GTGTTTTTGCTCCCCAGTATGCTTA
1 GTGTTTTTGCTCCCCAGTATGCTTA
*
2525565 GTGTTTTTGCTCCCCAGTGTGCTTA
1 GTGTTTTTGCTCCCCAGTATGCTTA
2525590 GT
1 GT
2525592 TTACTTAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (25 bp):
GTGTTTTTGCTCCCCAGTATGCTTA
Found at i:2525657 original size:16 final size:16
Alignment explanation
Indices: 2525624--2525658 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2525614 CCATTTGTTT
*
2525624 ATATAATATTTTAAAA
1 ATATAATATTTGAAAA
*
2525640 ATATAATATTTGATAA
1 ATATAATATTTGAAAA
2525656 ATA
1 ATA
2525659 AATTTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
ATATAATATTTGAAAA
Done.