Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold153
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: 3137677
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 19 of 24
Found at i:2482583 original size:13 final size:13
Alignment explanation
Indices: 2482567--2482591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2482557 AAAATTTAGA
2482567 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
2482580 AAAAAAAAAAAA
1 AAAAAAAAAAAA
2482592 AGATGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:2482794 original size:16 final size:16
Alignment explanation
Indices: 2482770--2482822 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2482760 AAGTTTTTAA
2482770 AATAATATTTATTTTT
1 AATAATATTTATTTTT
* * ***
2482786 AATACTATTAAATTAAA
1 AATAATATT-TATTTTT
2482803 AATAATATTTATTTTT
1 AATAATATTTATTTTT
2482819 AATA
1 AATA
2482823 TAATTAAAAA
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
AATAATATTTATTTTT
Found at i:2482810 original size:33 final size:34
Alignment explanation
Indices: 2482768--2482841 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
2482758 AAAAGTTTTT
*
2482768 AAAATAATATTTATTTTTAATACT-ATT-AAATTA
1 AAAATAATATTTATTTTTAATA-TAATTAAAAATA
2482801 AAAATAATATTTATTTTTAATATAATTAAAAATA
1 AAAATAATATTTATTTTTAATATAATTAAAAATA
2482835 AAAATAA
1 AAAATAA
2482842 AAATATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
32 1 0.03
33 25 0.66
34 12 0.32
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (34 bp):
AAAATAATATTTATTTTTAATATAATTAAAAATA
Found at i:2483662 original size:19 final size:20
Alignment explanation
Indices: 2483638--2483675 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2483628 TCATAATAAA
2483638 TTTACA-GTCATAA-CTTCAC
1 TTTACATGT-ATAAGCTTCAC
2483657 TTTACATGTATAAGCTTCA
1 TTTACATGTATAAGCTTCA
2483676 ACTCCATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (20 bp):
TTTACATGTATAAGCTTCAC
Found at i:2486889 original size:2 final size:2
Alignment explanation
Indices: 2486884--2486925 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2486874 AATGAATGAA
2486884 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2486926 ATTTAAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2487004 original size:13 final size:13
Alignment explanation
Indices: 2486986--2487011 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2486976 TTTTTTAAAA
2486986 AATATTTATATTT
1 AATATTTATATTT
2486999 AATATTTATATTT
1 AATATTTATATTT
2487012 GAGATATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:2487330 original size:20 final size:20
Alignment explanation
Indices: 2487298--2487336 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2487288 ATGTTTTTTA
2487298 AAATTTAATTATAAAAATAT
1 AAATTTAATTATAAAAATAT
2487318 AAATATTAA-TATAAAAATA
1 AAAT-TTAATTATAAAAATA
2487337 ATTTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTTAATTATAAAAATAT
Found at i:2487674 original size:4 final size:4
Alignment explanation
Indices: 2487665--2487689 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2487655 CAATTACGAT
2487665 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
2487690 ACTTGAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2488187 original size:21 final size:22
Alignment explanation
Indices: 2488124--2488187 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
2488114 ACATTTTTCA
*
2488124 AAAAATATTAA-TAAAAATTATT
1 AAAAATATAAATTAAAAA-TATT
* * *
2488146 AAAAATATATATT-TAATTATT
1 AAAAATATAAATTAAAAATATT
2488167 AAAAAT-TAAATTAAAAATATT
1 AAAAATATAAATTAAAAATATT
2488188 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
20 5 0.15
21 16 0.48
22 11 0.33
23 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAATATAAATTAAAAATATT
Found at i:2488705 original size:21 final size:22
Alignment explanation
Indices: 2488665--2488706 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2488655 GTATAATTAT
* *
2488665 TTTTTATATTTCAAATTATAAG
1 TTTTTATATATCAAAATATAAG
2488687 TTTTTATATAT-AAAATATAA
1 TTTTTATATATCAAAATATAA
2488707 TATTAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTTATATATCAAAATATAAG
Found at i:2489436 original size:10 final size:11
Alignment explanation
Indices: 2489421--2489449 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2489411 ATTAACTATA
2489421 TTTATTTTA-T
1 TTTATTTTATT
2489431 TTTATTTTATT
1 TTTATTTTATT
2489442 TTTATTTT
1 TTTATTTT
2489450 TATGAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:2491044 original size:164 final size:167
Alignment explanation
Indices: 2490751--2491058 Score: 401
Period size: 164 Copynumber: 1.9 Consensus size: 167
2490741 CTTCGGATGC
* * * * *
2490751 ATTTCATAGATTGTGTTTTGACTGGCCTGTGATTTTCGGATTTTTTTCAATTCTATCCATCAATG
1 ATTTCATAGATTGTGTTTTGACTAGCCTGTGATTTTCGGACTTTTGTCAATACCATCCATCAATG
* * **
2490816 GTTGTCAGCTTAGGAATTGTTGCTTCATGGGCTTCAAGACATGAGTCAGATCCACAATTTTATTG
66 GTTGTCAGCTTAGGAATTGTTGCTTCAAGGGCATCAAGACATGAGAAAGATCCACAATTTTATTG
2490881 TCATCAGGATAGAATGCTGTATCAATACTTTGTTAAT
131 TCATCAGGATAGAATGCTGTATCAATACTTTGTTAAT
* * *
2490918 ATTTCATAGATTGTGTTTTGTC-AGCCTGTGA-TTTCTGG-CTTTTGTCGATACCATCCGTCAAT
1 ATTTCATAGATTGTGTTTTGACTAGCCTGTGATTTTC-GGACTTTTGTCAATACCATCCATCAAT
* * * ** *
2490980 GGTTGTCGGC-TGGGCATTGTTTTTTCAAGGGCATCAGGACATGAGAAAGATCCAC-ATCTTTAT
65 GGTTGTCAGCTTAGGAATTGTTGCTTCAAGGGCATCAAGACATGAGAAAGATCCACAAT-TTTAT
2491043 TGTCATCAGGATAGAA
129 TGTCATCAGGATAGAA
2491059 CCCTGTATGA
Statistics
Matches: 121, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
163 2 0.02
164 57 0.47
165 31 0.26
166 10 0.08
167 21 0.17
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.39
Consensus pattern (167 bp):
ATTTCATAGATTGTGTTTTGACTAGCCTGTGATTTTCGGACTTTTGTCAATACCATCCATCAATG
GTTGTCAGCTTAGGAATTGTTGCTTCAAGGGCATCAAGACATGAGAAAGATCCACAATTTTATTG
TCATCAGGATAGAATGCTGTATCAATACTTTGTTAAT
Found at i:2494620 original size:13 final size:14
Alignment explanation
Indices: 2494595--2494622 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2494585 TTATTTCGTG
2494595 AAAAATAATTTTTA
1 AAAAATAATTTTTA
2494609 AAAAATAATTTTTA
1 AAAAATAATTTTTA
2494623 TTTATTAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAAATAATTTTTA
Found at i:2496257 original size:22 final size:23
Alignment explanation
Indices: 2496232--2496281 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
2496222 AATGTAATAA
2496232 AATATTTTAAAAATTTTAT-ATT
1 AATATTTTAAAAATTTTATAATT
* *
2496254 AATA-TTTATATATTTTATAATT
1 AATATTTTAAAAATTTTATAATT
2496276 AA-ATTT
1 AATATTT
2496282 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTTTAAAAATTTTATAATT
Found at i:2505258 original size:1 final size:1
Alignment explanation
Indices: 2505248--2505341 Score: 71
Period size: 1 Copynumber: 94.0 Consensus size: 1
2505238 TGGCAATTGG
* * * ** * * * *
2505248 AAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAAGAAAAAAACAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * *
2505313 GGAAAAAGAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2505342 GTGAAGATTT
Statistics
Matches: 71, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:2505297 original size:37 final size:37
Alignment explanation
Indices: 2505248--2505341 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 37
2505238 TGGCAATTGG
2505248 AAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAGAA
1 AAAAAGAAAAAAACAAAAC-AAAAAAAAGGAAAAAGAA
2505286 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAA
1 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAA
* *
2505323 AAAAAAAACAAAAAAAAAA
1 AAAAAGAA-AAAAACAAAA
2505342 GTGAAGATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
37 25 0.47
38 28 0.53
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (37 bp):
AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAA
Found at i:2505331 original size:27 final size:29
Alignment explanation
Indices: 2505286--2505339 Score: 94
Period size: 27 Copynumber: 1.9 Consensus size: 29
2505276 GGAAAAAGAA
2505286 AAAAAGAAAAAAACAAAACAAAAAAAAGG
1 AAAAAGAAAAAAACAAAACAAAAAAAAGG
2505315 AAAAAG-AAAAAA-AAAACAAAAAAAA
1 AAAAAGAAAAAAACAAAACAAAAAAAA
2505340 AAGTGAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 13 0.52
28 6 0.24
29 6 0.24
ACGTcount: A:0.87, C:0.06, G:0.07, T:0.00
Consensus pattern (29 bp):
AAAAAGAAAAAAACAAAACAAAAAAAAGG
Found at i:2505341 original size:30 final size:30
Alignment explanation
Indices: 2505246--2505341 Score: 104
Period size: 37 Copynumber: 3.0 Consensus size: 30
2505236 CATGGCAATT
*
2505246 GGAAAAAGAAAAAAACAAA-ACAAAAAAAAA
1 GGAAAAAGAAAAAAA-AAACAAAAAAAAAAA
2505276 GGAAAAAGAAAAAAAGAAAAAAACAAAACAAAAAAAA
1 GGAAAAAG----AAA-AAAAAAAC-AAA-AAAAAAAA
2505313 GGAAAAAGAAAAAAAAAACAAAAAAAAAA
1 GGAAAAAGAAAAAAAAAACAAAAAAAAAA
2505342 GTGAAGATTT
Statistics
Matches: 57, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
30 15 0.26
31 3 0.05
32 8 0.14
33 3 0.05
34 6 0.11
35 4 0.07
36 2 0.04
37 16 0.28
ACGTcount: A:0.84, C:0.05, G:0.10, T:0.00
Consensus pattern (30 bp):
GGAAAAAGAAAAAAAAAACAAAAAAAAAAA
Found at i:2507537 original size:13 final size:14
Alignment explanation
Indices: 2507518--2507570 Score: 63
Period size: 13 Copynumber: 3.7 Consensus size: 14
2507508 AACTCTGTCA
2507518 ATTATTTTATGATT
1 ATTATTTTATGATT
*
2507532 -TTATTTTATTATT
1 ATTATTTTATGATT
2507545 ATTAATATTTATGATT
1 ATT-AT-TTTATGATT
*
2507561 AATATTTTAT
1 ATTATTTTAT
2507571 TATAATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 12 0.36
14 7 0.21
15 4 0.12
16 10 0.30
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (14 bp):
ATTATTTTATGATT
Found at i:2507576 original size:13 final size:14
Alignment explanation
Indices: 2507540--2507584 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
2507530 TTTTATTTTA
2507540 TTATTATTAATA-T
1 TTATTATTAATATT
*
2507553 TTATGATTAATATT
1 TTATTATTAATATT
2507567 TTATTA-TAATATT
1 TTATTATTAATATT
2507580 ATTAT
1 -TTAT
2507585 AACAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTATTATTAATATT
Found at i:2508346 original size:29 final size:29
Alignment explanation
Indices: 2508260--2508346 Score: 72
Period size: 29 Copynumber: 2.9 Consensus size: 29
2508250 CAAAATTTTA
2508260 TTTTATTATTTAAGATAAT-ATTTAAAAATTAT
1 TTTTATTATTTAA-ATAATAATTT--AAA-TAT
* * **
2508292 TTTTA-TAATTAAAT-TTAAATAAAAATAT
1 TTTTATTATTTAAATAAT-AATTTAAATAT
2508320 TTTTATTATTTAAATAATAATTTAAAT
1 TTTTATTATTTAAATAATAATTTAAAT
2508347 TAATTTAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
28 8 0.19
29 19 0.44
30 3 0.07
31 8 0.19
32 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
TTTTATTATTTAAATAATAATTTAAATAT
Found at i:2510939 original size:8 final size:8
Alignment explanation
Indices: 2510926--2510950 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2510916 AAATCCACAA
2510926 GCATGATT
1 GCATGATT
2510934 GCATGATT
1 GCATGATT
2510942 GCATGATT
1 GCATGATT
2510950 G
1 G
2510951 ATTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (8 bp):
GCATGATT
Found at i:2511205 original size:20 final size:20
Alignment explanation
Indices: 2511163--2511205 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2511153 AAAATTTATT
* *
2511163 TAAATTTAATTATAAATATA
1 TAAATTTAATTATAAAAAAA
2511183 TAAATATTAA-TATAAAAAAA
1 TAAAT-TTAATTATAAAAAAA
2511203 TAA
1 TAA
2511206 TTCTATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAATTTAATTATAAAAAAA
Found at i:2511785 original size:15 final size:15
Alignment explanation
Indices: 2511765--2511797 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2511755 AGCAATTAAG
2511765 CTTAATCAGAACATT
1 CTTAATCAGAACATT
*
2511780 CTTAATCAGAATATT
1 CTTAATCAGAACATT
2511795 CTT
1 CTT
2511798 TAAGGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
CTTAATCAGAACATT
Found at i:2515844 original size:16 final size:17
Alignment explanation
Indices: 2515807--2515865 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
2515797 GTTGTGTATA
* *
2515807 TAAATATATTTAATTTTT
1 TAAAT-TATTTTATATTT
2515825 TAAATTATTTTATA-TT
1 TAAATTATTTTATATTT
2515841 TAAA-TA-TTTATATTT
1 TAAATTATTTTATATTT
*
2515856 TTAATTATTT
1 TAAATTATTT
2515866 ATTGAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
14 6 0.17
15 7 0.20
16 8 0.23
17 9 0.26
18 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TAAATTATTTTATATTT
Found at i:2515866 original size:16 final size:16
Alignment explanation
Indices: 2515821--2515867 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
2515811 TATATTTAAT
2515821 TTTTTAAATTATTT-TA
1 TTTTT-AATTATTTATA
* *
2515837 TATTTAAATATTTATA
1 TTTTTAATTATTTATA
2515853 TTTTTAATTATTTAT
1 TTTTTAATTATTTAT
2515868 TGAATATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTAATTATTTATA
Found at i:2518875 original size:15 final size:15
Alignment explanation
Indices: 2518855--2518885 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2518845 TATAAAATAA
2518855 AATATGAATATATTT
1 AATATGAATATATTT
2518870 AATATGAATATATTT
1 AATATGAATATATTT
2518885 A
1 A
2518886 TTTTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
AATATGAATATATTT
Found at i:2519286 original size:26 final size:25
Alignment explanation
Indices: 2519249--2519309 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
2519239 ATAAATTATG
*
2519249 AAATAT-TATAAAAATAAGTATAATAT
1 AAATATAT-TAAAAATAA-TATAAAAT
* *
2519275 AAATATATTAAAATTTATATAAAAT
1 AAATATATTAAAAATAATATAAAAT
2519300 AAAT-TATTAA
1 AAATATATTAA
2519310 TATATCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 6 0.19
25 11 0.35
26 13 0.42
27 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AAATATATTAAAAATAATATAAAAT
Found at i:2528028 original size:20 final size:22
Alignment explanation
Indices: 2527986--2528030 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
2527976 TAATAATTGT
2527986 TTAATTATATTTTTTAAAAAATA
1 TTAATTATATTTTTT-AAAAATA
2528009 TTAATTATA-TTTTT-AAAATA
1 TTAATTATATTTTTTAAAAATA
2528029 TT
1 TT
2528031 TTTTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
22 5 0.23
23 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTATATTTTTTAAAAATA
Found at i:2528264 original size:18 final size:19
Alignment explanation
Indices: 2528217--2528280 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 19
2528207 TTTCTTATTT
* *
2528217 ATTTTAATTAAATTTAATA
1 ATTTTTATTATATTTAATA
*
2528236 ATTTATATTATATTT-ATA
1 ATTTTTATTATATTTAATA
* *
2528254 TTTTTTATTATATTATAATT
1 ATTTTTATTATATT-TAATA
2528274 ATTTTTA
1 ATTTTTA
2528281 AAATATTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 15 0.42
19 13 0.36
20 8 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTATTATATTTAATA
Found at i:2528397 original size:12 final size:12
Alignment explanation
Indices: 2528363--2528401 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2528353 TTACATATTT
2528363 TATTTAT-ATTA
1 TATTTATAATTA
2528374 TATTAATATAATTA
1 TATT--TATAATTA
2528388 TATTTATAATTA
1 TATTTATAATTA
2528400 TA
1 TA
2528402 AAAATCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.16
12 10 0.40
13 3 0.12
14 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTTATAATTA
Found at i:2528411 original size:26 final size:25
Alignment explanation
Indices: 2528363--2528412 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
2528353 TTACATATTT
**
2528363 TATTTATATTATATTAATATAATTA
1 TATTTATATTATAAAAATATAATTA
*
2528388 TATTTATAATTATAAAAATCTAATT
1 TATTTAT-ATTATAAAAATATAATT
2528413 TTAGCGTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTTATATTATAAAAATATAATTA
Found at i:2528798 original size:9 final size:9
Alignment explanation
Indices: 2528784--2528808 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2528774 AATTTTTTAA
2528784 AAAAATTTT
1 AAAAATTTT
2528793 AAAAATTTT
1 AAAAATTTT
2528802 AAAAATT
1 AAAAATT
2528809 ATAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAAAATTTT
Found at i:2529230 original size:29 final size:29
Alignment explanation
Indices: 2529195--2529363 Score: 88
Period size: 29 Copynumber: 6.0 Consensus size: 29
2529185 CAAATATTTT
2529195 TTTATATAATTATATTTAA-ATATTATATA
1 TTTATATAA-TATATTTAATATATTATATA
*
2529224 TTTATATAA-ATA-TTAATAAATTATA-A
1 TTTATATAATATATTTAATATATTATATA
* *
2529250 TTTATATTATAAAAATTTTAATATATT-TATA
1 TTTATA-TA-ATATA-TTTAATATATTATATA
** * * * *
2529281 TTTATATTTTATTTTTTAT-TATTTTTTA
1 TTTATATAATATATTTAATATATTATATA
* * * *
2529309 -ATATATCATA-ATTTAATAATTTTTTATA
1 TTTATATAATATATTTAAT-ATATTATATA
*
2529337 TTTATATTATAT-TTTAA-ATTATTATAT
1 TTTATATAATATATTTAATA-TATTATAT
2529364 TTGAACAAAT
Statistics
Matches: 106, Mismatches: 21, Indels: 27
0.69 0.14 0.18
Matches are distributed among these distances:
26 16 0.15
27 24 0.23
28 22 0.21
29 25 0.24
30 3 0.03
31 16 0.15
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTATATAATATATTTAATATATTATATA
Found at i:2529233 original size:19 final size:21
Alignment explanation
Indices: 2529196--2529248 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
2529186 AAATATTTTT
*
2529196 TTATATAATTATATTTAAATA
1 TTATATAATTATATATAAATA
2529217 TTATAT-ATT-TATATAAATA
1 TTATATAATTATATATAAATA
2529236 TTA-ATAAATTATA
1 TTATAT-AATTATA
2529249 ATTTATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.07
19 12 0.43
20 6 0.21
21 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATATAATTATATATAAATA
Found at i:2529271 original size:31 final size:31
Alignment explanation
Indices: 2529214--2529288 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
2529204 TTATATTTAA
*
2529214 ATATTATATATTTATATAAATATTAATAAA-TT
1 ATATT-TATA-TTATAAAAATATTAATAAATTT
* *
2529246 ATAATTTATATTATAAAAATTTTAATATATTT
1 AT-ATTTATATTATAAAAATATTAATAAATTT
2529278 ATATTTATATT
1 ATATTTATATT
2529289 TTATTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 25 0.66
32 10 0.26
33 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
ATATTTATATTATAAAAATATTAATAAATTT
Found at i:2530547 original size:22 final size:22
Alignment explanation
Indices: 2530517--2530579 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
2530507 ATTTTTATTT
* * *
2530517 AATAATAATAATAAAATTATTTA
1 AATATTAAT-ATAAAAATATATA
2530540 AAT-TTAATTATAAAAATATATA
1 AATATTAA-TATAAAAATATATA
2530562 AATATTAATATAAAAATA
1 AATATTAATATAAAAATA
2530580 ATTTTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATATTAATATAAAAATATATA
Found at i:2533923 original size:17 final size:17
Alignment explanation
Indices: 2533884--2533917 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2533874 AATATAAAAA
2533884 TAAA-ATATATTTATAT
1 TAAATATATATTTATAT
2533900 TAAATATATATTTATAT
1 TAAATATATATTTATAT
2533917 T
1 T
2533918 TGATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATATATATTTATAT
Found at i:2534386 original size:23 final size:23
Alignment explanation
Indices: 2534286--2534401 Score: 63
Period size: 23 Copynumber: 5.2 Consensus size: 23
2534276 AATAAAATAA
*
2534286 ATTATTTATATTATTATATAAAAAT
1 ATTATATATATTATTATAT--AAAT
* * *
2534311 AATTGTATA-ATATATAATACAAAT
1 -ATTATATATAT-TATTATATAAAT
2534335 GA-TATAT-TA-TATTATAT-AAT
1 -ATTATATATATTATTATATAAAT
2534355 -TT-TA-A-ATTATTATATAAAT
1 ATTATATATATTATTATATAAAT
*
2534374 ATTATATATATTA-CATATAAAAT
1 ATTATATATATTATTATAT-AAAT
2534397 ATTAT
1 ATTAT
2534402 TAAAAATAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 25
0.67 0.09 0.24
Matches are distributed among these distances:
17 1 0.01
18 10 0.14
19 4 0.06
20 5 0.07
21 8 0.11
22 5 0.07
23 18 0.26
24 5 0.07
25 2 0.03
26 12 0.17
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTATATATATTATTATATAAAT
Found at i:2536487 original size:33 final size:34
Alignment explanation
Indices: 2536386--2536497 Score: 99
Period size: 32 Copynumber: 3.4 Consensus size: 34
2536376 ATATGACTGA
* * * *
2536386 ATTT-AATAATAATTTAAAAATCTTTTAAATTTTTT
1 ATTTAAAT-ATAAATTAAAAA-ATTTTAAAATTATT
* *
2536421 ATTTACATATAAATTTAAAAA-TTT-AAATTATT
1 ATTTAAATATAAATTAAAAAATTTTAAAATTATT
*
2536453 ATTTAAATATTAA-TAAAAAATTTTAAAATTATT
1 ATTTAAATATAAATTAAAAAATTTTAAAATTATT
*
2536486 ATTCAAAT-TAAA
1 ATTTAAATATAAA
2536498 AATTTGAATT
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
31 6 0.10
32 23 0.37
33 18 0.29
35 14 0.22
36 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (34 bp):
ATTTAAATATAAATTAAAAAATTTTAAAATTATT
Found at i:2538014 original size:3 final size:3
Alignment explanation
Indices: 2538006--2538049 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2537996 TCTAGCTGTT
2538006 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2538050 TTACATAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2540831 original size:18 final size:18
Alignment explanation
Indices: 2540808--2540842 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2540798 AAAGGCAAAA
*
2540808 ACATAATAAGGGAAACTC
1 ACATAACAAGGGAAACTC
*
2540826 ACATAACAAGGGTAACT
1 ACATAACAAGGGAAACT
2540843 TGAGTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (18 bp):
ACATAACAAGGGAAACTC
Found at i:2543973 original size:2 final size:2
Alignment explanation
Indices: 2543968--2543999 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2543958 TATGTGTGTG
*
2543968 TA TA TA TA CA 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
2544000 ATTATGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2549016 original size:17 final size:17
Alignment explanation
Indices: 2548994--2549028 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2548984 AAAAATTTGA
*
2548994 ATATATTTATATCGAAT
1 ATATATTCATATCGAAT
*
2549011 ATATATTCATATCTAAT
1 ATATATTCATATCGAAT
2549028 A
1 A
2549029 CGCATGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (17 bp):
ATATATTCATATCGAAT
Found at i:2549517 original size:20 final size:20
Alignment explanation
Indices: 2549480--2549543 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
2549470 TAATAAAACA
*
2549480 AAAAAAAAATGAAAAGAAAGT
1 AAAAGAAAA-GAAAAGAAAGT
2549501 ATAAAGAAAAG-AAAGAAAAGT
1 A-AAAGAAAAGAAAAG-AAAGT
* *
2549522 AAAGGAAAGGAAAAGAAAGT
1 AAAAGAAAAGAAAAGAAAGT
2549542 AA
1 AA
2549544 GATTGGGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 18 0.49
21 12 0.32
22 7 0.19
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (20 bp):
AAAAGAAAAGAAAAGAAAGT
Found at i:2549518 original size:25 final size:25
Alignment explanation
Indices: 2549481--2549540 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
2549471 AATAAAACAA
* *
2549481 AAAAAAAATGAAAAG-AAAGTATAAAG
1 AAAAGAAA-GAAAAGTAAAGGA-AAAG
*
2549507 AAAAGAAAGAAAAGTAAAGGAAAGG
1 AAAAGAAAGAAAAGTAAAGGAAAAG
2549532 AAAAGAAAG
1 AAAAGAAAG
2549541 TAAGATTGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.60
26 12 0.40
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.07
Consensus pattern (25 bp):
AAAAGAAAGAAAAGTAAAGGAAAAG
Found at i:2549799 original size:20 final size:20
Alignment explanation
Indices: 2549771--2549810 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2549761 AGTAAAAGTA
2549771 TTATCTAAAATCATTATTTT
1 TTATCTAAAATCATTATTTT
* * *
2549791 TTATTTAAAGTTATTATTTT
1 TTATCTAAAATCATTATTTT
2549811 AGATAAGTTA
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:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (20 bp):
TTATCTAAAATCATTATTTT
Found at i:2552226 original size:30 final size:29
Alignment explanation
Indices: 2552190--2552249 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
2552180 AGAGAATACG
*
2552190 ATTATTTTAAA-TTATTATTTAATTAATAAA
1 ATTATTTTAAATTTA-AATTTAATT-ATAAA
*
2552220 ATTATTTTATATTTAAATTTAATTATAAA
1 ATTATTTTAAATTTAAATTTAATTATAAA
2552249 A
1 A
2552250 ATATATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 6 0.22
30 18 0.67
31 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTATTTTAAATTTAAATTTAATTATAAA
Found at i:2552258 original size:22 final size:22
Alignment explanation
Indices: 2552228--2552274 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
2552218 AAATTATTTT
*
2552228 ATATTTAAAT-TTAATTATAAAA
1 ATATATAAATATTAA-TATAAAA
2552250 ATATATAAATATTAATATAAAA
1 ATATATAAATATTAATATAAAA
2552272 ATA
1 ATA
2552275 AAAATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATATAAATATTAATATAAAA
Found at i:2552262 original size:30 final size:30
Alignment explanation
Indices: 2552206--2552262 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
2552196 TTAAATTATT
* **
2552206 ATTTAATTAATAAAATTATTTTATATTTAA
1 ATTTAATTAATAAAAATATTAAATATTTAA
2552236 ATTTAATT-ATAAAAATATATAAATATT
1 ATTTAATTAATAAAAATAT-TAAATATT
2552263 AATATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 9 0.39
30 14 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTAATTAATAAAAATATTAAATATTTAA
Found at i:2553240 original size:17 final size:16
Alignment explanation
Indices: 2553199--2553241 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
2553189 ATTTGAAATA
2553199 TTTATTAA-AATATTT
1 TTTATTAATAATATTT
2553214 TTTAATTTAATAATTATTT
1 TTT-A-TTAATAA-TATTT
2553233 TTTATTAAT
1 TTTATTAAT
2553242 TAAATTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.12
16 1 0.04
17 9 0.38
18 3 0.12
19 8 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATTAATAATATTT
Found at i:2553247 original size:19 final size:19
Alignment explanation
Indices: 2553197--2553248 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
2553187 TGATTTGAAA
* *
2553197 TATTTATTAAAATATTTTT
1 TATTAATTAAATTATTTTT
2553216 TAATTTAA-T-AATTATTTTT
1 T-A-TTAATTAAATTATTTTT
2553235 TATTAATTAAATTA
1 TATTAATTAAATTA
2553249 CATTTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 4 0.15
18 2 0.07
19 16 0.59
20 2 0.07
21 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTAATTAAATTATTTTT
Found at i:2554061 original size:30 final size:34
Alignment explanation
Indices: 2554005--2554070 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 34
2553995 CTCTTTAATT
2554005 TTTTTTAAATAAAATTTTTATATTTT-A-TTATA
1 TTTTTTAAATAAAATTTTTATATTTTAATTTATA
*
2554037 TTTTTT-AATAAAA-TTTTATCTTTTAATTTATA
1 TTTTTTAAATAAAATTTTTATATTTTAATTTATA
2554069 TT
1 TT
2554071 AAAATAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 10 0.32
31 8 0.26
32 13 0.42
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (34 bp):
TTTTTTAAATAAAATTTTTATATTTTAATTTATA
Found at i:2554077 original size:30 final size:30
Alignment explanation
Indices: 2553998--2554084 Score: 99
Period size: 30 Copynumber: 2.9 Consensus size: 30
2553988 GAAAAACCTC
2553998 TTTAATTT-TTTTTAAATAAAATTTTTATAT
1 TTTAATTTATTTTTAAATAAAA-TTTTATAT
* *
2554028 TTT-ATTATATTTTTTAATAAAATTTTATCT
1 TTTAATT-TATTTTTAAATAAAATTTTATAT
* *
2554058 TTTAATTTATATTAAAAT-AAATTTTAT
1 TTTAATTTATTTTTAAATAAAATTTTAT
2554085 TTTAAATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
29 12 0.24
30 22 0.45
31 15 0.31
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTAATTTATTTTTAAATAAAATTTTATAT
Found at i:2555153 original size:32 final size:32
Alignment explanation
Indices: 2555081--2555160 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
2555071 CATATTTAAG
*
2555081 GTATTATATATTCATATAAATTTTAACAAGTTA
1 GTATT-TATATTCATATAAATATTAACAAGTTA
* * *
2555114 ATAATTTATATT-ATATAAATATTAACATATTTT
1 GT-ATTTATATTCATATAAATATTAACA-AGTTA
2555147 GTATTTATA-TCATA
1 GTATTTATATTCATA
2555161 CTCATATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
31 1 0.03
32 24 0.62
33 11 0.28
34 3 0.08
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (32 bp):
GTATTTATATTCATATAAATATTAACAAGTTA
Found at i:2555574 original size:2 final size:2
Alignment explanation
Indices: 2555567--2555594 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2555557 ATGAGTTTTC
2555567 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
2555595 GGGAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2559354 original size:18 final size:16
Alignment explanation
Indices: 2559323--2559358 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
2559313 TTTAAACTCA
2559323 AATGTAATATTTCTTT
1 AATGTAATATTTCTTT
2559339 AATGCTAATCATTTCTTT
1 AATG-TAAT-ATTTCTTT
2559357 AA
1 AA
2559359 AAATATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 4 0.22
18 10 0.56
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (16 bp):
AATGTAATATTTCTTT
Found at i:2560586 original size:3 final size:3
Alignment explanation
Indices: 2560578--2560628 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
2560568 TAGATACAGT
* * * *
2560578 ACC ACC ACC ACC ACC ACC ACC ACC ACC AAC ACC AAC ACC AAC ACC AAC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
2560626 ACC
1 ACC
2560629 GCCCCGTACC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.41, C:0.59, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:2564526 original size:208 final size:204
Alignment explanation
Indices: 2564134--2564548 Score: 492
Period size: 208 Copynumber: 2.0 Consensus size: 204
2564124 AAACCATTCC
** * * ** ** *
2564134 ACATCCAATGATCACCTAAATCATATTCTGTTAGTGGCTGAAATATCAATCCGCATTTTTCTTTA
1 ACATCCAATGATCACCTAAATCATATTCTGTTAGCAGCTGAAACAGCAATCCAAAGATTTCTTCA
* * * **
2564199 ACAAACAACAAGTTTCAAGATTACTCATTCGCCCTTCGCTGCCTAGTATTCAAAAAATTTGACTC
66 ACAAACAACAAGTTTCAAGATTACTCACTCGCCCTTCACTGCCTAGTAGTCAAAAAATTCAACTC
* * * * * *
2564264 ACATACACGAACACCCACATTACAAATTCTCTACCACCAGACAATATTGACCTCTTTTATTCCTC
131 ACATACACAAACACCAACATTACAAATTCTCCACCACCACACAATATCGACCTCTATTATTCCTC
*
2564329 ACAACCAAA
196 AAAACCAAA
* *
2564338 ACATCCAATGATCAGCTAAATCATATTCTTTTAGCAGCT-AAACACGCAAATCCAAAGATTTCTT
1 ACATCCAATGATCACCTAAATCATATTCTGTTAGCAGCTGAAACA-GC-AATCCAAAGATTTCTT
* * * *
2564402 CAATAAACAACACATTTTCAAGATTGCTCAGCT-GCCCTTCATTGCCTAGTAGTCAAAAATAATT
64 CAACAAACAACA-AGTTTCAAGATTACTCA-CTCGCCCTTCACTGCCTAGTAGTC-AAAA-AATT
* *
2564466 CAACTCGCCTACACAAACACCAACATTACAAATTCTCCACCACCACACAATATCGACCTCTATTA
125 CAACTCACATACACAAACACCAACATTACAAATTCTCCACCACCACACAATATCGACCTCTATTA
*
2564531 TTTCTCAAAACCAAA
190 TTCCTCAAAACCAAA
2564546 ACA
1 ACA
2564549 ACTAAACCAT
Statistics
Matches: 175, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
203 4 0.02
204 36 0.21
205 22 0.13
206 33 0.19
207 5 0.03
208 75 0.43
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (204 bp):
ACATCCAATGATCACCTAAATCATATTCTGTTAGCAGCTGAAACAGCAATCCAAAGATTTCTTCA
ACAAACAACAAGTTTCAAGATTACTCACTCGCCCTTCACTGCCTAGTAGTCAAAAAATTCAACTC
ACATACACAAACACCAACATTACAAATTCTCCACCACCACACAATATCGACCTCTATTATTCCTC
AAAACCAAA
Found at i:2566117 original size:16 final size:16
Alignment explanation
Indices: 2566098--2566181 Score: 56
Period size: 16 Copynumber: 5.5 Consensus size: 16
2566088 TACTATTTAA
2566098 TTAAAATATTAACAAT
1 TTAAAATATTAACAAT
* *
2566114 TTAAAA-ATAAAATAAT
1 TTAAAATAT-TAACAAT
*
2566130 TT-AAAT-TTAATAAT
1 TTAAAATATTAACAAT
2566144 TTAAAATCA--AATCAAT
1 TTAAAAT-ATTAA-CAAT
*
2566160 TTAAAAT-TTTA-AAT
1 TTAAAATATTAACAAT
2566174 TTAAAATA
1 TTAAAATA
2566182 ATTTAATCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 19
0.69 0.06 0.24
Matches are distributed among these distances:
14 18 0.33
15 12 0.22
16 24 0.44
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAATATTAACAAT
Found at i:2566117 original size:20 final size:20
Alignment explanation
Indices: 2566047--2566117 Score: 53
Period size: 20 Copynumber: 3.8 Consensus size: 20
2566037 CATGAGAGAC
* *
2566047 ATATTAA-AACTTATTTAAA
1 ATATTAACAATTTAATTAAA
* *
2566066 AT-TAAAAAATTTAATTTAAA
1 ATATTAACAATTTAA-TTAAA
*
2566086 A-A-T-ACTATTTAATTAAA
1 ATATTAACAATTTAATTAAA
2566103 ATATTAACAATTTAA
1 ATATTAACAATTTAA
2566118 AAATAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 11
0.68 0.12 0.19
Matches are distributed among these distances:
17 6 0.15
18 11 0.28
19 8 0.21
20 14 0.36
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATTAACAATTTAATTAAA
Found at i:2566147 original size:30 final size:30
Alignment explanation
Indices: 2566077--2566179 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 30
2566067 TTAAAAAATT
** *
2566077 TAATTTAAAAATACTATTTAATTAAAATATTAA
1 TAATTTAAAAATA--AAATAATTTAAAT-TTAA
*
2566110 CAATTTAAAAATAAAATAATTTAAATTTAA
1 TAATTTAAAAATAAAATAATTTAAATTTAA
* *
2566140 TAATTT-AAAATCAAATCAATTTAAAATTTTA
1 TAATTTAAAAATAAAAT-AATTT-AAATTTAA
2566171 -AATTTAAAA
1 TAATTTAAAA
2566180 TAATTTAATC
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
29 9 0.15
30 19 0.32
31 20 0.33
33 12 0.20
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (30 bp):
TAATTTAAAAATAAAATAATTTAAATTTAA
Found at i:2566173 original size:7 final size:7
Alignment explanation
Indices: 2566098--2566180 Score: 51
Period size: 7 Copynumber: 11.0 Consensus size: 7
2566088 TACTATTTAA
2566098 TTAAAAT
1 TTAAAAT
2566105 ATTAACAAT
1 -TTAA-AAT
2566114 TTAAAA-
1 TTAAAAT
*
2566120 ATAAAAT
1 TTAAAAT
*
2566127 AATTTAAAT
1 --TTAAAAT
2566136 TTAATAAT
1 TTAA-AAT
2566144 TTAAAAT
1 TTAAAAT
**
2566151 CAAATCAAT
1 TTAA--AAT
2566160 TTAAAAT
1 TTAAAAT
*
2566167 TTTAAAT
1 TTAAAAT
2566174 TTAAAAT
1 TTAAAAT
2566181 AATTTAATCT
Statistics
Matches: 58, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
6 5 0.09
7 25 0.43
8 15 0.26
9 13 0.22
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (7 bp):
TTAAAAT
Found at i:2566194 original size:30 final size:30
Alignment explanation
Indices: 2566094--2566195 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
2566084 AAAATACTAT
*
2566094 TTAA-TTAAAATATTAACAATTTAAAAATAAA
1 TTAATTTAAAAT-TTAATAATTT-AAAATAAA
*
2566125 ATAATTT-AAATTTAATAATTTAAAATCAAA
1 TTAATTTAAAATTTAATAATTTAAAAT-AAA
* * *
2566155 TCAATTTAAAATTTTA-AATTTAAAATAAT
1 TTAATTTAAAATTTAATAATTTAAAATAAA
2566184 TTAATCTTAAAA
1 TTAAT-TTAAAA
2566196 CCTCTCCTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
29 11 0.18
30 33 0.55
31 14 0.23
32 2 0.03
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (30 bp):
TTAATTTAAAATTTAATAATTTAAAATAAA
Found at i:2566544 original size:18 final size:17
Alignment explanation
Indices: 2566504--2566574 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 17
2566494 TCTCTCCCTG
* *
2566504 ATATATAAATTT-TAAT
1 ATATAAAAATTTATATT
*
2566520 ATTTAAATAATTTATATT
1 ATATAAA-AATTTATATT
*
2566538 ATAT-AAAATTTAAATT
1 ATATAAAAATTTATATT
* * *
2566554 ATTTATAAATTTTTATT
1 ATATAAAAATTTATATT
2566571 ATAT
1 ATAT
2566575 TAATAATTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
16 17 0.40
17 19 0.45
18 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATAAAAATTTATATT
Found at i:2566565 original size:33 final size:34
Alignment explanation
Indices: 2566504--2566574 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 34
2566494 TCTCTCCCTG
*
2566504 ATATATAAATTTTAATATTTAAATAATTTATATT
1 ATATATAAATTTAAATATTTAAATAATTTATATT
* *
2566538 ATATA-AAATTTAAATTATTTATA-AATTTTTATT
1 ATATATAAATTTAAA-TATTTAAATAATTTATATT
2566571 ATAT
1 ATAT
2566575 TAATAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 21 0.64
34 12 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
ATATATAAATTTAAATATTTAAATAATTTATATT
Found at i:2566611 original size:16 final size:16
Alignment explanation
Indices: 2566567--2566615 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2566557 TATAAATTTT
*
2566567 TATTATATTAATAATTA
1 TATTATATT-TTAATTA
2566584 -ATT-T-TTTT-ATTA
1 TATTATATTTTAATTA
2566596 TATTATATTTTAATTA
1 TATTATATTTTAATTA
2566612 TATT
1 TATT
2566616 TACATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
12 4 0.15
13 4 0.15
14 3 0.11
15 5 0.19
16 11 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTATATTTTAATTA
Found at i:2566628 original size:11 final size:10
Alignment explanation
Indices: 2566597--2566630 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
2566587 TTTTTATTAT
2566597 ATTATATTTTA
1 ATTATA-TTTA
2566608 ATTATATTTA
1 ATTATATTTA
2566618 CATTATATTTA
1 -ATTATATTTA
2566629 AT
1 AT
2566631 ATTATTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTATATTTA
Found at i:2566756 original size:18 final size:19
Alignment explanation
Indices: 2566734--2566785 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
2566724 TATTTATAAA
2566734 ATTTTAAATAAAAATAATT
1 ATTTTAAATAAAAATAATT
* *
2566753 -TTTTAATTTAAAAT-ATT
1 ATTTTAAATAAAAATAATT
*
2566770 ATTTTAAATAATAATA
1 ATTTTAAATAAAAATA
2566786 TAAATTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTTAAATAAAAATAATT
Found at i:2566792 original size:19 final size:18
Alignment explanation
Indices: 2566732--2566795 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
2566722 ACTATTTATA
2566732 AAATTTTAAATAAAA-AT
1 AAATTTTAAATAAAATAT
* *
2566749 AATTTTTTAATTTAAAATAT
1 AA-ATTTTAA-ATAAAATAT
*
2566769 -TATTTTAAATAATAATAT
1 AAATTTTAAATAA-AATAT
2566787 AAATTTTAA
1 AAATTTTAA
2566796 GCCATATATC
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
17 5 0.14
18 17 0.47
19 12 0.33
20 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTTTAAATAAAATAT
Found at i:2576753 original size:8 final size:9
Alignment explanation
Indices: 2576728--2576782 Score: 64
Period size: 8 Copynumber: 6.3 Consensus size: 9
2576718 AAATAAGAGT
2576728 AATATAATA
1 AATATAATA
2576737 AATATAATA
1 AATATAATA
2576746 AA-ATAAT-
1 AATATAATA
2576753 AATAT-ATA
1 AATATAATA
2576761 AATATAATA
1 AATATAATA
2576770 TGAATAT-ATA
1 --AATATAATA
2576780 AAT
1 AAT
2576783 TATTTTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
7 4 0.10
8 15 0.37
9 14 0.34
10 3 0.07
11 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (9 bp):
AATATAATA
Found at i:2576764 original size:19 final size:19
Alignment explanation
Indices: 2576731--2576782 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2576721 TAAGAGTAAT
2576731 ATAATAA-ATAT-AATAAA
1 ATAATAATATATAAATAAA
*
2576748 ATAATAATATATAAATATA
1 ATAATAATATATAAATAAA
2576767 AT-ATGAATATATAAAT
1 ATAAT-AATATATAAAT
2576783 TATTTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 7 0.23
18 6 0.19
19 18 0.58
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
ATAATAATATATAAATAAA
Found at i:2576764 original size:42 final size:41
Alignment explanation
Indices: 2576685--2576764 Score: 92
Period size: 42 Copynumber: 1.9 Consensus size: 41
2576675 TGAATGAATA
2576685 TAATACAAAAATATATATAAATAGTATAAATAAAAATAAGAG
1 TAATACAAAAATATATATAAATAG-ATAAATAAAAATAAGAG
* *
2576727 TAATATAATAAATATA-ATAAAATA-ATAATATATAAATA
1 TAATACAA-AAATATATAT-AAATAGATAA-ATAAAAATA
2576765 TAATATGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
41 4 0.12
42 17 0.52
43 12 0.36
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (41 bp):
TAATACAAAAATATATATAAATAGATAAATAAAAATAAGAG
Found at i:2576838 original size:10 final size:11
Alignment explanation
Indices: 2576681--2576844 Score: 74
Period size: 11 Copynumber: 14.6 Consensus size: 11
2576671 GATATGAATG
*
2576681 AATATAATACA
1 AATATAATATA
*
2576692 AAAATATATATA
1 AATATA-ATATA
*
2576704 AATAGTATAAATA
1 AATA-TA-ATATA
* *
2576717 AAAATAAGAGT-
1 AATATAATA-TA
2576728 AATAT-A-ATA
1 AATATAATATA
2576737 AATATAATA-A
1 AATATAATATA
2576747 AATAATAATATATA
1 AAT-AT-A-ATATA
2576761 AATATAATATGA
1 AATATAATAT-A
*
2576773 ATATATAA-ATT
1 A-ATATAATATA
* * *
2576784 ATTTTATTATA
1 AATATAATATA
2576795 AATAT-ATA-A
1 AATATAATATA
*
2576804 AATAAAATTTATA
1 AATATAA--TATA
2576817 AATATAATATA
1 AATATAATATA
*
2576828 AATA-CATATA
1 AATATAATATA
2576838 AATATAA
1 AATATAA
2576845 AATTAATGAG
Statistics
Matches: 116, Mismatches: 19, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
8 1 0.01
9 11 0.09
10 21 0.18
11 33 0.28
12 18 0.16
13 28 0.24
14 4 0.03
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (11 bp):
AATATAATATA
Found at i:2578496 original size:17 final size:18
Alignment explanation
Indices: 2578471--2578505 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2578461 AAATTTTAAC
2578471 TTTTATTTT-AATTTTTT
1 TTTTATTTTAAATTTTTT
*
2578488 TTTTGTTTTAAATTTTTT
1 TTTTATTTTAAATTTTTT
2578506 ATAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTATTTTAAATTTTTT
Found at i:2578853 original size:24 final size:26
Alignment explanation
Indices: 2578811--2578863 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
2578801 CTAATTTTTA
* *
2578811 ATTTTATTTAAAAATTTATATT-ATT
1 ATTTTATTAAAAAAATTATATTAATT
*
2578836 ATTTT-TTAAAAAAATTATTTTAATT
1 ATTTTATTAAAAAAATTATATTAATT
2578861 ATT
1 ATT
2578864 ATAATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTTTATTAAAAAAATTATATTAATT
Found at i:2581112 original size:30 final size:29
Alignment explanation
Indices: 2581045--2581119 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
2581035 AGCTAAAATA
* *
2581045 CTAAAAAAGCCCTTATCCTTTTATTGTAC
1 CTAAATAAGCCCTTATCCTTTGATTGTAC
* *
2581074 CCAAATAAGCCCTTATCCTTTGATTTTTAC
1 CTAAATAAGCCCTTATCCTTTGA-TTGTAC
* *
2581104 TTAAATAAGACCTTAT
1 CTAAATAAGCCCTTAT
2581120 TTCAAATGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 20 0.53
30 18 0.47
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (29 bp):
CTAAATAAGCCCTTATCCTTTGATTGTAC
Found at i:2581215 original size:30 final size:30
Alignment explanation
Indices: 2581181--2581247 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
2581171 CATTAGGACT
* *
2581181 TTATTTGGGTACAAGTTAAAGATTAAGGGC
1 TTATTTGGGTACAAATTAAAGACTAAGGGC
*
2581211 TTATTTGGGTACAAATTAAAGGCTAAGGGC
1 TTATTTGGGTACAAATTAAAGACTAAGGGC
2581241 TTATTTG
1 TTATTTG
2581248 AGTGTAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36
Consensus pattern (30 bp):
TTATTTGGGTACAAATTAAAGACTAAGGGC
Found at i:2586006 original size:2 final size:2
Alignment explanation
Indices: 2585999--2586026 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2585989 TCTAGAATGA
2585999 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
2586027 GTTTCAGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2586206 original size:2 final size:2
Alignment explanation
Indices: 2586199--2586233 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2586189 GAATTTTGCT
2586199 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2586234 TCATTTATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2586823 original size:30 final size:29
Alignment explanation
Indices: 2586761--2586824 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
2586751 AGTACTTTGT
* **
2586761 TAAAAAACAGTGGACAGAACGAAAATGAA
1 TAAAAAACAGTGGACAGAACCAAAACAAA
* *
2586790 TAAAAAACAGTGGACATATCCAAAACAAGA
1 TAAAAAACAGTGGACAGAACCAAAACAA-A
2586820 TAAAA
1 TAAAA
2586825 TAAAAGTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.59, C:0.12, G:0.16, T:0.12
Consensus pattern (29 bp):
TAAAAAACAGTGGACAGAACCAAAACAAA
Found at i:2588009 original size:18 final size:20
Alignment explanation
Indices: 2587988--2588078 Score: 64
Period size: 18 Copynumber: 4.3 Consensus size: 20
2587978 TTTATATTTT
*
2587988 TATAATAAAA-AT-TATTAA
1 TATAATAAAATATATATAAA
*
2588006 TATATTAAAATATATATAAA
1 TATAATAAAATATATATAAA
2588026 TATAAAATATTTTAAATAT-TATAATA
1 TAT--AATA----AAATATATATAA-A
2588052 TTATAATAAAATATATA-AAA
1 -TATAATAAAATATATATAAA
2588072 TATAATA
1 TATAATA
2588079 TTAATACATA
Statistics
Matches: 59, Mismatches: 3, Indels: 21
0.71 0.04 0.25
Matches are distributed among these distances:
18 9 0.15
19 9 0.15
20 9 0.15
21 8 0.14
22 5 0.08
25 9 0.15
26 7 0.12
27 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATAATAAAATATATATAAA
Found at i:2588013 original size:8 final size:8
Alignment explanation
Indices: 2587995--2588059 Score: 51
Period size: 8 Copynumber: 7.8 Consensus size: 8
2587985 TTTTATAATA
2587995 AAAATTATT
1 AAAA-TATT
*
2588004 AATATATT
1 AAAATATT
2588012 AAAATATAT
1 AAAATAT-T
2588021 ATAAATA-T
1 A-AAATATT
2588029 AAAATATTT
1 AAAATA-TT
*
2588038 TAAATATT
1 AAAATATT
*
2588046 ATAATATT
1 AAAATATT
*
2588054 ATAATA
1 AAAATA
2588060 AAATATATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
7 5 0.11
8 26 0.55
9 11 0.23
10 5 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AAAATATT
Found at i:2588043 original size:16 final size:16
Alignment explanation
Indices: 2587992--2588044 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
2587982 TATTTTTATA
2587992 ATAAAA-ATTATTAATAT
1 ATAAAATATT-TTAA-AT
*
2588009 ATTAAAATATATATAAAT
1 A-TAAAATAT-TTTAAAT
2588027 ATAAAATATTTTAAAT
1 ATAAAATATTTTAAAT
2588043 AT
1 AT
2588045 TATAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 8 0.26
17 9 0.29
18 8 0.26
19 5 0.16
20 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATATTTTAAAT
Found at i:2588068 original size:20 final size:20
Alignment explanation
Indices: 2588004--2588097 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 20
2587994 AAAAATTATT
*
2588004 AATATATTAAAATAT-ATATA
1 AATATA-TAAATTATAATATA
*
2588024 AATATA-AAA-TAT--TTTA
1 AATATATAAATTATAATATA
2588040 AATATTATAATATTATAATA-A
1 AATA-TATAA-ATTATAATATA
* *
2588061 AATATATAAAATATAATATT
1 AATATATAAATTATAATATA
*
2588081 AATACATAAATTATAAT
1 AATATATAAATTATAAT
2588098 TCAACATTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
16 7 0.11
17 5 0.08
18 5 0.08
19 9 0.15
20 29 0.48
21 5 0.08
22 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATATAAATTATAATATA
Found at i:2588090 original size:65 final size:65
Alignment explanation
Indices: 2587957--2588096 Score: 144
Period size: 65 Copynumber: 2.1 Consensus size: 65
2587947 AATATTATAC
* * * * * *
2587957 AAATGTATACAATTTTTAAATTTTATATTTTTATAATAAAAATTATTAATATATTAAAATATATA
1 AAAT-TATAAAATTTTTAAATATTATAATATTATAATAAAAATTATTAAAATATTAAAATATACA
2588022 T
65 T
*
2588023 AAA-TATAAAATATTTTAAATATTATAATATTATAAT-AAAA-TATATAAAATA-TAATATTAAT
1 AAATTATAAAAT-TTTTAAATATTATAATATTATAATAAAAATTAT-TAAAATATTAA-AAT-AT
2588084 ACAT
62 ACAT
2588088 AAATTATAA
1 AAATTATAA
2588097 TTCAACATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
63 6 0.10
64 19 0.31
65 29 0.47
66 8 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (65 bp):
AAATTATAAAATTTTTAAATATTATAATATTATAATAAAAATTATTAAAATATTAAAATATACAT
Found at i:2588096 original size:27 final size:27
Alignment explanation
Indices: 2588004--2588095 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 27
2587994 AAAAATTATT
*
2588004 AATATATTAAAATAT-ATA-TAAATATAA
1 AATATA-TAAAATATAATATTATA-ATAA
*
2588031 AATATTTTAAATATTATAATATTATAATAA
1 AATA-TATAAA-A-TATAATATTATAATAA
2588061 AATATATAAAATATAATATTAATACATAA
1 AATATATAAAATATAATATT-ATA-ATAA
*
2588090 ATTATA
1 AATATA
2588096 ATTCAACATT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
27 17 0.31
28 6 0.11
29 17 0.31
30 11 0.20
31 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (27 bp):
AATATATAAAATATAATATTATAATAA
Found at i:2588462 original size:15 final size:15
Alignment explanation
Indices: 2588429--2588472 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2588419 AATTATGCCA
* *
2588429 TATTATAAATATAAT
1 TATTTTAAAAATAAT
2588444 TATTTTAATAAATAA-
1 TATTTTAA-AAATAAT
2588459 TATTTTAAAAATAA
1 TATTTTAAAAATAA
2588473 ATAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 6 0.23
15 15 0.58
16 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTTAAAAATAAT
Found at i:2590173 original size:20 final size:20
Alignment explanation
Indices: 2590136--2590173 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2590126 TAACTTCTTC
* *
2590136 AATTATAATTTGAGTTATTT
1 AATTATAATTTCAATTATTT
2590156 AATTATAATTTCAATTAT
1 AATTATAATTTCAATTAT
2590174 AAGTTTCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
AATTATAATTTCAATTATTT
Found at i:2590443 original size:24 final size:23
Alignment explanation
Indices: 2590391--2590453 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
2590381 TATTTATATA
* * *
2590391 ATAAATTTTATTTAAATTAATTT
1 ATAAATATTAATTAAAATAATTT
2590414 ATAAATATTAATATAAAATAATTT
1 ATAAATATTAAT-TAAAATAATTT
*
2590438 -TAAAATTTTAATTAAA
1 AT-AAATATTAATTAAA
2590454 TTTAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAATATTAATTAAAATAATTT
Found at i:2591984 original size:18 final size:18
Alignment explanation
Indices: 2591961--2591997 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2591951 TTTTATTAGT
2591961 ATAAATAGAA-AAATAAAA
1 ATAAATA-AATAAATAAAA
2591979 ATAAATAAATAAATAAAA
1 ATAAATAAATAAATAAAA
2591997 A
1 A
2591998 CAAAATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (18 bp):
ATAAATAAATAAATAAAA
Found at i:2594765 original size:2 final size:2
Alignment explanation
Indices: 2594752--2594785 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2594742 AATGTTTTTG
*
2594752 AT AT AC 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
2594786 GAGAATAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2595167 original size:24 final size:23
Alignment explanation
Indices: 2595140--2595185 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
2595130 AATTAGATTG
*
2595140 ATTTAATCAATTTTAATATATTTT
1 ATTTAATAAATTTTAAT-TATTTT
2595164 ATTTAATAAATTTTAATTATTT
1 ATTTAATAAATTTTAATTATTT
2595186 AAAAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
ATTTAATAAATTTTAATTATTTT
Found at i:2595424 original size:44 final size:44
Alignment explanation
Indices: 2595373--2595470 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 44
2595363 TCATTTTTTA
2595373 TAATTGATTAATTTTAAAATCAAATAAAATAAAATAAATTAATT
1 TAATTGATTAATTTTAAAATCAAATAAAATAAAATAAATTAATT
* *
2595417 TAATTGATTAATTTTAAAATTAAATAAAATAAATTAAATTAATT
1 TAATTGATTAATTTTAAAATCAAATAAAATAAAATAAATTAATT
2595461 TAATTTGATT
1 TAA-TTGATT
2595471 GGTTCGATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 45 0.88
45 6 0.12
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (44 bp):
TAATTGATTAATTTTAAAATCAAATAAAATAAAATAAATTAATT
Found at i:2595613 original size:27 final size:29
Alignment explanation
Indices: 2595556--2595613 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
2595546 TTTTTACATG
*
2595556 ATAAAAAAATTAATATAAATTATAATTAT
1 ATAAAAAAATTAATATAAATTATAATAAT
2595585 ATAAAAAAA-T-ATATAAA-TATATATAAT
1 ATAAAAAAATTAATATAAATTATA-ATAAT
2595612 AT
1 AT
2595614 TTTCTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 13 0.48
28 1 0.04
29 9 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
ATAAAAAAATTAATATAAATTATAATAAT
Found at i:2597404 original size:2 final size:2
Alignment explanation
Indices: 2597399--2597429 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2597389 AAAATAAAAA
2597399 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2597430 AACCCTTCGT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2607675 original size:18 final size:18
Alignment explanation
Indices: 2607654--2607751 Score: 58
Period size: 18 Copynumber: 5.3 Consensus size: 18
2607644 AAAAGCATTG
2607654 TAATTTATATTATATATT
1 TAATTTATATTATATATT
* *
2607672 TAATTAAATTTTAATATATTTT
1 TAATT-TATATT-ATATA--TT
*
2607694 TATATTTTTATTATATATAT
1 TA-ATTTATATTATATAT-T
* * *
2607714 T-ATTTTTATCATA-AAT
1 TAATTTATATTATATATT
*
2607730 TATTTTATATTATAT-TT
1 TAATTTATATTATATATT
2607747 TAATT
1 TAATT
2607752 ATTATATTTA
Statistics
Matches: 60, Mismatches: 12, Indels: 17
0.67 0.13 0.19
Matches are distributed among these distances:
16 2 0.03
17 15 0.25
18 16 0.27
19 5 0.08
20 7 0.12
21 5 0.08
22 7 0.12
23 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (18 bp):
TAATTTATATTATATATT
Found at i:2607756 original size:14 final size:15
Alignment explanation
Indices: 2607737--2607770 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2607727 AATTATTTTA
*
2607737 TATTATATTT-TAAT
1 TATTATATTTAAAAT
2607751 TATTATATTTAAAAT
1 TATTATATTTAAAAT
2607766 TATTA
1 TATTA
2607771 AATATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATATTTAAAAT
Found at i:2607786 original size:7 final size:7
Alignment explanation
Indices: 2607774--2607798 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2607764 ATTATTAAAT
2607774 ATAATAA
1 ATAATAA
2607781 ATAATAA
1 ATAATAA
2607788 ATAATAA
1 ATAATAA
2607795 ATAA
1 ATAA
2607799 AGGCATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAA
Found at i:2607838 original size:11 final size:10
Alignment explanation
Indices: 2607822--2607863 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
2607812 CTCACTTATA
2607822 TTTAATTGAAT
1 TTTAATT-AAT
2607833 TTTAA-TAAT
1 TTTAATTAAT
*
2607842 TTAAATTAAT
1 TTTAATTAAT
2607852 TTTAAATTAAT
1 TTT-AATTAAT
2607863 T
1 T
2607864 ATTTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 7 0.26
10 7 0.26
11 13 0.48
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (10 bp):
TTTAATTAAT
Found at i:2607910 original size:25 final size:26
Alignment explanation
Indices: 2607861--2607911 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
2607851 TTTTAAATTA
2607861 ATTATTTATATATAAAAATTATTTTT
1 ATTATTTATATATAAAAATTATTTTT
*
2607887 ATTATTTA-ATATAAATA-TATTTTT
1 ATTATTTATATATAAAAATTATTTTT
2607911 A
1 A
2607912 ATATAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 8 0.33
25 8 0.33
26 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTATTTATATATAAAAATTATTTTT
Found at i:2607913 original size:17 final size:18
Alignment explanation
Indices: 2607886--2607920 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2607876 AAATTATTTT
2607886 TATTATTTAATATAAATA
1 TATTATTTAATATAAATA
2607904 TATT-TTTAATATAAATA
1 TATTATTTAATATAAATA
2607921 AAATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATTTAATATAAATA
Found at i:2609194 original size:6 final size:6
Alignment explanation
Indices: 2609177--2609258 Score: 64
Period size: 6 Copynumber: 13.7 Consensus size: 6
2609167 CTATACTTAA
*
2609177 TATATAT TATATT TATATT TAAAATT TA-A-- TATATT TAATAATT TATA-T
1 TATAT-T TATATT TATATT T-ATATT TATATT TATATT T-AT-ATT TATATT
* * *
2609225 TACATT TATAAT TATATT TATATC TATATT TATA
1 TATATT TATATT TATATT TATATT TATATT TATA
2609259 CTATTGATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
3 2 0.03
4 1 0.02
5 5 0.08
6 35 0.57
7 14 0.23
8 4 0.07
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (6 bp):
TATATT
Found at i:2609211 original size:16 final size:17
Alignment explanation
Indices: 2609190--2609221 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2609180 ATATTATATT
2609190 TATATTTAA-AATTTAA
1 TATATTTAATAATTTAA
2609206 TATATTTAATAATTTA
1 TATATTTAATAATTTA
2609222 TATTACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTTAATAATTTAA
Found at i:2609386 original size:22 final size:21
Alignment explanation
Indices: 2609348--2609389 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2609338 ATATTTTATT
2609348 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
2609369 TAAATATTAA-TATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
2609389 T
1 T
2609390 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:2609842 original size:24 final size:22
Alignment explanation
Indices: 2609815--2609861 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
2609805 TATTATGTTT
2609815 AATAATATTTAAATATAAATATAA
1 AATAATATTT--ATATAAATATAA
* *
2609839 AATATTATTTTTATAAATATAA
1 AATAATATTTATATAAATATAA
2609861 A
1 A
2609862 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
24 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAATATTTATATAAATATAA
Found at i:2609843 original size:21 final size:20
Alignment explanation
Indices: 2609818--2609879 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
2609808 TATGTTTAAT
2609818 AATATTTAAATATAAATATAA
1 AATATTTAAATATAAATAT-A
***
2609839 AATATTATTTTTATAAATATA
1 AATATT-TAAATATAAATATA
* *
2609860 AATTTTTAAAAAATAAATAT
1 AATATTT-AAATATAAATAT
2609880 GATCATATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 1 0.03
21 20 0.65
22 10 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTAAATATAAATATA
Found at i:2609855 original size:16 final size:17
Alignment explanation
Indices: 2609834--2609877 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
2609824 TAAATATAAA
*
2609834 TATAAAATAT-TATTTT
1 TATAAAATATAAATTTT
2609850 TAT-AAATATAAATTTT
1 TATAAAATATAAATTTT
2609866 TA-AAAA-ATAAAT
1 TATAAAATATAAAT
2609878 ATGATCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATAAAATATAAATTTT
Found at i:2609875 original size:15 final size:16
Alignment explanation
Indices: 2609845--2609877 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2609835 ATAAAATATT
*
2609845 ATTTTTATAAATATAA
1 ATTTTTATAAAAATAA
2609861 ATTTTTA-AAAAATAA
1 ATTTTTATAAAAATAA
2609876 AT
1 AT
2609878 ATGATCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTTATAAAAATAA
Found at i:2610119 original size:20 final size:18
Alignment explanation
Indices: 2610096--2610135 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
2610086 AATTAAAAAA
2610096 TATATTTTTATATTAATATT
1 TATATTTTTA-ATTAA-ATT
2610116 TATATTTTTAATTAAATT
1 TATATTTTTAATTAAATT
2610134 TA
1 TA
2610136 AATAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.25
19 5 0.25
20 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTTTTAATTAAATT
Found at i:2610532 original size:38 final size:38
Alignment explanation
Indices: 2610490--2610567 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
2610480 TTTAAGTAAA
2610490 AAATTAAA-TAAATT-TTATGT-TTATTAAATATAAAATTT
1 AAATTAAATTAAATTCTTAT-TATTATT--ATATAAAATTT
*
2610528 AAATTAAATTAAATTCTTATTATTATTATTTAAAATTT
1 AAATTAAATTAAATTCTTATTATTATTATATAAAATTT
2610566 AA
1 AA
2610568 TTTGATTTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
38 20 0.56
39 7 0.19
40 9 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (38 bp):
AAATTAAATTAAATTCTTATTATTATTATATAAAATTT
Found at i:2610620 original size:23 final size:24
Alignment explanation
Indices: 2610588--2610633 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2610578 TTTAATAATA
*
2610588 TTTATATTAATAA-TTATTTTTTAT
1 TTTATATTAA-AATTTATATTTTAT
2610612 TTTAT-TTAAAATTTATATTTTA
1 TTTATATTAAAATTTATATTTTA
2610634 AGCCAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 13 0.65
24 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTATATTAAAATTTATATTTTAT
Found at i:2610780 original size:2 final size:2
Alignment explanation
Indices: 2610773--2610803 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2610763 GGACCATCTG
*
2610773 TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2610804 TTGGTCTGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2610788 original size:14 final size:14
Alignment explanation
Indices: 2610769--2610799 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2610759 CTTAGGACCA
2610769 TCTGTCTCTCTCTC
1 TCTGTCTCTCTCTC
2610783 TCTGTCTCTCTCTC
1 TCTGTCTCTCTCTC
2610797 TCT
1 TCT
2610800 CTCTTTGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.42, G:0.06, T:0.52
Consensus pattern (14 bp):
TCTGTCTCTCTCTC
Found at i:2610987 original size:2 final size:2
Alignment explanation
Indices: 2610980--2611006 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2610970 AACTTTATTT
2610980 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2611007 CAATCTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2611275 original size:18 final size:18
Alignment explanation
Indices: 2611187--2611276 Score: 67
Period size: 18 Copynumber: 4.9 Consensus size: 18
2611177 TATTTTTTAT
*
2611187 ATTTAAA-TTAAAATTAA
1 ATTTAAATTTTAAATTAA
*
2611204 A-TTAAATTTTAAATTATT
1 ATTTAAATTTTAAATTA-A
* **
2611222 ATTTAAATATTAATAAAAA
1 ATTTAAATTTTAA-ATTAA
* *
2611241 TATTTATATTTTTAATTAA
1 -ATTTAAATTTTAAATTAA
*
2611260 ATTTAATTTTTAAATTA
1 ATTTAAATTTTAAATTA
2611277 TTAAATAATA
Statistics
Matches: 54, Mismatches: 14, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
16 5 0.09
17 9 0.17
18 15 0.28
19 13 0.24
20 12 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTAAATTTTAAATTAA
Found at i:2612130 original size:18 final size:18
Alignment explanation
Indices: 2612065--2612131 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
2612055 TTAAATTTAA
*
2612065 TAATAA-AAAATAATTAT
1 TAATAATAAAATAATTTT
2612082 TAAT-ATAAAATTAATTTT
1 TAATAATAAAA-TAATTTT
**
2612100 TAATAATTTAAT-ATTTT
1 TAATAATAAAATAATTTT
2612117 TAAATAATAAAATAA
1 T-AATAATAAAATAA
2612132 AATTATCAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
16 1 0.03
17 14 0.35
18 20 0.50
19 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATAAAATAATTTT
Found at i:2612372 original size:20 final size:21
Alignment explanation
Indices: 2612349--2612448 Score: 68
Period size: 24 Copynumber: 4.7 Consensus size: 21
2612339 TATAAAATTT
2612349 TATATAATATAAATTAT-TAA
1 TATATAATATAAATTATATAA
2612369 TATAT--TA-AAATTTATATAAA
1 TATATAATATAAA-TTATAT-AA
*
2612389 TATATAATATTTTAAA-TATAATTA
1 TATATAATA---TAAATTAT-ATAA
2612413 TATATAATATATGAATTATATAA
1 TATATAATATA--AATTATATAA
*
2612436 -ATACAATATAAAT
1 TATATAATATAAAT
2612449 ATGGATTATT
Statistics
Matches: 64, Mismatches: 3, Indels: 26
0.69 0.03 0.28
Matches are distributed among these distances:
17 3 0.05
18 6 0.09
19 1 0.02
20 15 0.23
21 2 0.03
22 11 0.17
23 5 0.08
24 16 0.25
25 2 0.03
26 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (21 bp):
TATATAATATAAATTATATAA
Found at i:2612424 original size:17 final size:17
Alignment explanation
Indices: 2612308--2612438 Score: 86
Period size: 17 Copynumber: 8.1 Consensus size: 17
2612298 ATAGCGGTAT
*
2612308 TATATAATTATAAAT-A
1 TATATAATTATATATAA
* *
2612324 TA-ATAAATATA-AAAA
1 TATATAATTATATATAA
* *
2612339 TATAAAATTTTATATAA
1 TATATAATTATATATAA
2612356 TATA-AATTAT-TA-ATA
1 TATATAATTATATATA-A
*
2612371 TATTAAAATT-TATATAAA
1 TA-TATAATTATATAT-AA
*
2612389 TATATAA-TAT-TTTAA
1 TATATAATTATATATAA
2612404 -ATATAATTATATATAA
1 TATATAATTATATATAA
2612420 TATATGAATTATATA-AA
1 TATAT-AATTATATATAA
2612437 TA
1 TA
2612439 CAATATAAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
14 8 0.09
15 21 0.23
16 23 0.25
17 26 0.29
18 12 0.13
19 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.44
Consensus pattern (17 bp):
TATATAATTATATATAA
Found at i:2612433 original size:26 final size:25
Alignment explanation
Indices: 2612380--2612457 Score: 65
Period size: 26 Copynumber: 3.2 Consensus size: 25
2612370 ATATTAAAAT
* *
2612380 TTATATAA-ATATATAATATTTTAA
1 TTATATAATATATATAATATATGAA
2612404 --ATATAATTATATATAATATATGAA
1 TTATATAA-TATATATAATATATGAA
* *
2612428 TTATATAAATACAATATAA-ATATGGA
1 TTATAT-AATA-TATATAATATATGAA
2612454 TTAT
1 TTAT
2612458 TAGATGTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
22 6 0.14
24 14 0.32
26 16 0.36
27 8 0.18
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (25 bp):
TTATATAATATATATAATATATGAA
Done.