Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 66 of 356
Found at i:20923385 original size:23 final size:23
Alignment explanation
Indices: 20923303--20923389 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
20923293 CCTGATCAGT
*
20923303 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* * *
20923325 A-ATGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
20923345 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
20923368 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
20923390 TCAGTAAAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 32 0.60
22 1 0.02
23 19 0.36
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:20927733 original size:28 final size:28
Alignment explanation
Indices: 20927702--20927763 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
20927692 ATTATTATTT
20927702 TTTACAATTTTTTAGATTA-TTTATATAA
1 TTTA-AATTTTTTAGATTATTTTATATAA
** **
20927730 TTTAGTTTTTTTATTTTATTTTATATAA
1 TTTAAATTTTTTAGATTATTTTATATAA
20927758 TTTAAA
1 TTTAAA
20927764 AGAAAAATAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (28 bp):
TTTAAATTTTTTAGATTATTTTATATAA
Found at i:20931628 original size:31 final size:32
Alignment explanation
Indices: 20931579--20931655 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
20931569 ACTCATTTTT
20931579 TTAAAAAAAAAGTGTTAAGTTCAAATA-CTAAA
1 TTAAAAAAAAAGTGTTAAGTTCAAATATC-AAA
* *
20931611 TTAAGAAAAAA-TTTTAAGTTCAAATATCAAA
1 TTAAAAAAAAAGTGTTAAGTTCAAATATCAAA
*
20931642 TT-ATAAAAAAGTGT
1 TTAAAAAAAAAGTGT
20931656 CAAATTTAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
30 7 0.18
31 21 0.54
32 11 0.28
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (32 bp):
TTAAAAAAAAAGTGTTAAGTTCAAATATCAAA
Found at i:20948691 original size:14 final size:14
Alignment explanation
Indices: 20948672--20948699 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20948662 ATTTACAAAT
20948672 GGAATTTCAATCTA
1 GGAATTTCAATCTA
20948686 GGAATTTCAATCTA
1 GGAATTTCAATCTA
20948700 CTCTTATAGC
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:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
GGAATTTCAATCTA
Found at i:20951210 original size:20 final size:20
Alignment explanation
Indices: 20951185--20951226 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
20951175 CATGTGTTAG
20951185 TTGAATTAGCAGTTCTTCCA
1 TTGAATTAGCAGTTCTTCCA
20951205 TTGAATTAGCAGTTCTTCCA
1 TTGAATTAGCAGTTCTTCCA
20951225 TT
1 TT
20951227 TAACTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (20 bp):
TTGAATTAGCAGTTCTTCCA
Found at i:20956729 original size:11 final size:11
Alignment explanation
Indices: 20956711--20956764 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
20956701 CCGGAAACCC
20956711 TATTTTATTTT
1 TATTTTATTTT
*
20956722 TCTTTTATTTT
1 TATTTTATTTT
*
20956733 TATTTTATGTT
1 TATTTTATTTT
* *
20956744 TAATTTAATTT
1 TATTTTATTTT
* *
20956755 AATTTAATTT
1 TATTTTATTT
20956765 GTTGATCTTT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:20957204 original size:16 final size:16
Alignment explanation
Indices: 20957183--20957213 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20957173 CATATTAGAG
20957183 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
20957199 CATATATATTTGAAA
1 CATATAAATTTGAAA
20957214 ACTTATTTAG
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:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:20957285 original size:12 final size:11
Alignment explanation
Indices: 20957268--20957302 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
20957258 TTTAACTTTC
20957268 TTTATATATTTT
1 TTTATA-ATTTT
20957280 TTTATAA-TTT
1 TTTATAATTTT
20957290 TTTATAATTTT
1 TTTATAATTTT
20957301 TT
1 TT
20957303 AAAGATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATAATTTT
Found at i:20957300 original size:9 final size:10
Alignment explanation
Indices: 20957272--20957303 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
20957262 ACTTTCTTTA
*
20957272 TATATTTTTT
1 TATAATTTTT
20957282 TATAATTTTT
1 TATAATTTTT
20957292 TATAATTTTT
1 TATAATTTTT
20957302 TA
1 TA
20957304 AAGATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATAATTTTT
Found at i:20957343 original size:19 final size:19
Alignment explanation
Indices: 20957308--20957363 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 19
20957298 TTTTTAAAGA
*
20957308 TATAAAT-TTTGAAATTTT
1 TATAAATATTTTAAATTTT
20957326 TATAAATATTTTAAA-TTT
1 TATAAATATTTTAAATTTT
*
20957344 TAAAAATAATTTTAAATTTT
1 TATAAAT-ATTTTAAATTTT
20957364 ATTTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 16 0.48
19 14 0.42
20 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:20957364 original size:19 final size:19
Alignment explanation
Indices: 20957312--20957364 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
20957302 TAAAGATATA
*
20957312 AATTTTGAAATTTTTATAAAT
1 AATTTT-AAA-TTTTAAAAAT
20957333 -ATTTTAAATTTTAAAAAT
1 AATTTTAAATTTTAAAAAT
20957351 AATTTTAAATTTTA
1 AATTTTAAATTTTA
20957365 TTTTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 9 0.30
19 16 0.53
20 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
AATTTTAAATTTTAAAAAT
Found at i:20964010 original size:55 final size:54
Alignment explanation
Indices: 20963866--20964010 Score: 202
Period size: 54 Copynumber: 2.7 Consensus size: 54
20963856 AAAAAAGAAT
* * * *
20963866 TTTTTTTTGTACTGGTCTGTCAATGGCCGGCACCAATAATTTTAAAAAAATTAA
1 TTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAGTAATTTTAAAAAAATTAA
* *
20963920 TTTTTTTTGTGCTGGCCTATCAATAGTCGGCACCAGTAA-TTTAAAAAAATTTAAA
1 TTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAGTAATTTTAAAAAAA-TT-AA
*
20963975 TTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAG
1 TTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAG
20964011 AATACGAGTT
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
53 10 0.12
54 35 0.44
55 35 0.44
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (54 bp):
TTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAGTAATTTTAAAAAAATTAA
Found at i:20964053 original size:54 final size:54
Alignment explanation
Indices: 20963979--20964117 Score: 233
Period size: 54 Copynumber: 2.6 Consensus size: 54
20963969 TTTAAATTTT
* * *
20963979 TTTGGTGCTGGCCTATCAATGGCCGGCACCAGAATACGAGTTTTTAAAAAAAAA
1 TTTGGTGCTGGCCTATCAATGGCTGGCACCAGAATACAAGTTTTCAAAAAAAAA
*
20964033 TTTGGTGCTGGCCTGTCAATGGCTGGCACCAGAATACAAGTTTTCAAAAAAAAA
1 TTTGGTGCTGGCCTATCAATGGCTGGCACCAGAATACAAGTTTTCAAAAAAAAA
*
20964087 TTTGGTGTTGGCCTATCAATGGCTGGCACCA
1 TTTGGTGCTGGCCTATCAATGGCTGGCACCA
20964118 ATATTAAAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (54 bp):
TTTGGTGCTGGCCTATCAATGGCTGGCACCAGAATACAAGTTTTCAAAAAAAAA
Found at i:20966158 original size:32 final size:32
Alignment explanation
Indices: 20966102--20966210 Score: 96
Period size: 30 Copynumber: 3.7 Consensus size: 32
20966092 CCTTTTATTT
*
20966102 TTCATTTTA-ATT-TTATTTTATTTTTTTCAA
1 TTCATTTTATATTATTATTTTCTTTTTTTCAA
*
20966132 TTCATTTCATATTATTATTTTC--TTTTTCATA
1 TTCATTTTATATTATTATTTTCTTTTTTTCA-A
20966163 TT-ATTTT-TCA-TATTA---T-TTTTTTTCAA
1 TTCATTTTAT-ATTATTATTTTCTTTTTTTCAA
*
20966189 TTCATTTTATATTATTTTTTTC
1 TTCATTTTATATTATTATTTTC
20966211 AAATTAATTA
Statistics
Matches: 62, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
26 4 0.06
27 13 0.21
28 5 0.08
29 6 0.10
30 20 0.32
31 7 0.11
32 7 0.11
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (32 bp):
TTCATTTTATATTATTATTTTCTTTTTTTCAA
Found at i:20966192 original size:57 final size:55
Alignment explanation
Indices: 20966094--20966210 Score: 162
Period size: 57 Copynumber: 2.1 Consensus size: 55
20966084 TTATCAACCC
* * *
20966094 TTTTATTTTTCATTTTAATTTTATTTTATTTTTTTCAATTCATTTCATATTATTA
1 TTTTCTTTTTCATATTAATTTTATATTATTTTTTTCAATTCATTTCATATTATTA
* * *
20966149 TTTTCTTTTTCATATTATTTTTCATATTATTTTTTTTCAATTCATTTTATATTATTT
1 TTTTCTTTTTCATATTAATTTT-ATATTA-TTTTTTTCAATTCATTTCATATTATTA
20966206 TTTTC
1 TTTTC
20966211 AAATTAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 19 0.35
56 5 0.09
57 30 0.56
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (55 bp):
TTTTCTTTTTCATATTAATTTTATATTATTTTTTTCAATTCATTTCATATTATTA
Found at i:20966196 original size:14 final size:15
Alignment explanation
Indices: 20966144--20966196 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 15
20966134 CATTTCATAT
20966144 TATTATTTTCTTTTTCA
1 TATTA-TTT-TTTTTCA
20966161 TATTA---TTTTTCA
1 TATTATTTTTTTTCA
20966173 TATTATTTTTTTTCA
1 TATTATTTTTTTTCA
20966188 -ATTCATTTT
1 TATT-ATTTT
20966197 ATATTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 12 0.38
14 3 0.09
15 12 0.38
17 5 0.16
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTTTTTCA
Found at i:20966208 original size:12 final size:12
Alignment explanation
Indices: 20966154--20966182 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20966144 TATTATTTTC
20966154 TTTTTCATATTA
1 TTTTTCATATTA
20966166 TTTTTCATATTA
1 TTTTTCATATTA
20966178 TTTTT
1 TTTTT
20966183 TTTCAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTCATATTA
Found at i:20966215 original size:25 final size:25
Alignment explanation
Indices: 20966111--20966209 Score: 103
Period size: 25 Copynumber: 3.7 Consensus size: 25
20966101 TTTCATTTTA
*
20966111 ATTTTATTTTA-TTTTTTTCAATTC
1 ATTTTATATTATTTTTTTTCAATTC
20966135 ATTTCATATTATTATTTTCTTTTTCATATT-
1 ATTT--TA-TATTA-TTT-TTTTTCA-ATTC
20966165 ATTTTTCATATTATTTTTTTTCAATTC
1 A-TTTT-ATATTATTTTTTTTCAATTC
20966192 ATTTTATATTATTTTTTT
1 ATTTTATATTATTTTTTT
20966210 CAAATTAATT
Statistics
Matches: 64, Mismatches: 1, Indels: 19
0.76 0.01 0.23
Matches are distributed among these distances:
24 4 0.06
25 13 0.20
26 9 0.14
27 12 0.19
28 3 0.05
29 8 0.12
30 9 0.14
31 6 0.09
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (25 bp):
ATTTTATATTATTTTTTTTCAATTC
Found at i:20966520 original size:5 final size:5
Alignment explanation
Indices: 20966512--20966588 Score: 82
Period size: 5 Copynumber: 14.6 Consensus size: 5
20966502 ACTCTTTTTT
* *
20966512 TTTCA TTTCT TTTCA TTTTCA TTTCA TCTTCA TTTTA TTTCA TTTCAA
1 TTTCA TTTCA TTTCA -TTTCA TTTCA T-TTCA TTTCA TTTCA TTTC-A
* *
20966560 CTTCA TTTCA TTCTAA TTTCA TTTCA TTT
1 TTTCA TTTCA TT-TCA TTTCA TTTCA TTT
20966589 AAAATTTTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
5 42 0.70
6 18 0.30
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTCA
Found at i:20966569 original size:16 final size:16
Alignment explanation
Indices: 20966512--20966588 Score: 86
Period size: 16 Copynumber: 4.8 Consensus size: 16
20966502 ACTCTTTTTT
* *
20966512 TTTCATTTCTTTTCAT
1 TTTCATTTCATTTCAA
20966528 TTTCATTTCATCTTC-A
1 TTTCATTTCAT-TTCAA
*
20966544 TTTTATTTCATTTCAA
1 TTTCATTTCATTTCAA
*
20966560 CTTCATTTCA-TTCTAA
1 TTTCATTTCATTTC-AA
20966576 TTTCATTTCATTT
1 TTTCATTTCATTT
20966589 AAAATTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
15 6 0.12
16 40 0.78
17 5 0.10
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTCATTTCATTTCAA
Found at i:20966601 original size:17 final size:19
Alignment explanation
Indices: 20966581--20966620 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
20966571 TCTAATTTCA
20966581 TTTC-ATTTAAAATT-TTT
1 TTTCAATTTAAAATTATTT
*
20966598 TTTCAATTTAAATTTATTT
1 TTTCAATTTAAAATTATTT
20966617 TTTC
1 TTTC
20966621 TCAATTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTCAATTTAAAATTATTT
Found at i:20966618 original size:21 final size:20
Alignment explanation
Indices: 20966592--20966651 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
20966582 TTCATTTAAA
20966592 ATTTTTTTTCAATTTAAATTT
1 ATTTTTTTTCAATTT-AATTT
* *
20966613 ATTTTTTCTCAA-TTCATTT
1 ATTTTTTTTCAATTTAATTT
*
20966632 ATATTTTTT-AATTTTAATTT
1 ATTTTTTTTCAA-TTTAATTT
20966652 TAATTTTTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.34
20 8 0.25
21 11 0.34
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTTTTTCAATTTAATTT
Found at i:20966659 original size:40 final size:41
Alignment explanation
Indices: 20966595--20966687 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
20966585 ATTTAAAATT
* *
20966595 TTTTTTCAA-TTTAAATTT-ATTTTTTCTCAATTCATTTATA
1 TTTTTT-AATTTTAAATTTAATTTTTCCTCAATTCATTTAAA
* * *
20966635 TTTTTTAATTTTAATTTTAATTTTTCCTTATTTCATTTAAA
1 TTTTTTAATTTTAAATTTAATTTTTCCTCAATTCATTTAAA
*
20966676 TTTTTTATTTTT
1 TTTTTTAATTTT
20966688 CAATGCAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.04
40 14 0.31
41 29 0.64
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.68
Consensus pattern (41 bp):
TTTTTTAATTTTAAATTTAATTTTTCCTCAATTCATTTAAA
Found at i:20966688 original size:20 final size:20
Alignment explanation
Indices: 20966625--20966689 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
20966615 TTTTTCTCAA
* *
20966625 TTCATTTATATTTTTTAATT
1 TTCATTTAAATTTTTTATTT
* * **
20966645 TTAATTTTAATTTTTCCTTAT
1 TTCATTTAAATTTTTTATT-T
20966666 TTCATTTAAATTTTTTATTT
1 TTCATTTAAATTTTTTATTT
20966686 TTCA
1 TTCA
20966690 ATGCAATTTT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCATTTAAATTTTTTATTT
Found at i:20966843 original size:27 final size:25
Alignment explanation
Indices: 20966809--20966947 Score: 90
Period size: 27 Copynumber: 5.4 Consensus size: 25
20966799 TTTCTTTCAA
20966809 ATTTAATTTCATTTTTTTCTCATTTC
1 ATTTAATTT-ATTTTTTTCTCATTTC
* *
20966835 ATTTCAATTAAATTTTTTCCTCATTTC
1 ATTT-AATT-TATTTTTTTCTCATTTC
* *
20966862 TTTTGAATTTATCTTTCTTTC-AATTTTC
1 ATTT-AATTTAT-TTT-TTTCTCA-TTTC
* * **
20966890 ATTTAA---ATTTTGTAC-CGCTTC
1 ATTTAATTTATTTTTTTCTCATTTC
20966911 ATTTCAATTTATTTTTTTCTCATTTC
1 ATTT-AATTTATTTTTTTCTCATTTC
*
20966937 ATTTAAATTAT
1 ATTTAATTTAT
20966948 CAATTTTTCC
Statistics
Matches: 85, Mismatches: 18, Indels: 21
0.69 0.15 0.17
Matches are distributed among these distances:
21 7 0.08
22 4 0.05
23 3 0.04
24 2 0.02
25 13 0.15
26 14 0.16
27 32 0.38
28 10 0.12
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (25 bp):
ATTTAATTTATTTTTTTCTCATTTC
Found at i:20966850 original size:26 final size:26
Alignment explanation
Indices: 20966821--20966955 Score: 75
Period size: 26 Copynumber: 5.2 Consensus size: 26
20966811 TTAATTTCAT
20966821 TTTTTTCTCATTTCATTTCAATTAAA
1 TTTTTTCTCATTTCATTTCAATTAAA
* *
20966847 TTTTTTCCTCATTTCTTTTGAATT---
1 TTTTTT-CTCATTTCATTTCAATTAAA
* * *
20966871 TATCTT-TC-TTTCAATTTTCATTTAAA
1 TTTTTTCTCATTTC-A-TTTCAATTAAA
* ** * *
20966897 TTTTGTAC-CGCTTCATTTCAATTTAT
1 TTTT-TTCTCATTTCATTTCAATTAAA
*
20966923 TTTTTTCTCATTTCATTTAAATTATCAA
1 TTTTTTCTCATTTCATTTCAATTA--AA
20966951 TTTTT
1 TTTTT
20966956 CCATGTAATT
Statistics
Matches: 77, Mismatches: 20, Indels: 22
0.65 0.17 0.18
Matches are distributed among these distances:
21 4 0.05
22 2 0.03
23 6 0.08
24 4 0.05
25 2 0.03
26 32 0.42
27 18 0.23
28 9 0.12
ACGTcount: A:0.22, C:0.16, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTTTCTCATTTCATTTCAATTAAA
Found at i:20966880 original size:76 final size:74
Alignment explanation
Indices: 20966698--20966945 Score: 192
Period size: 75 Copynumber: 3.4 Consensus size: 74
20966688 CAATGCAATT
** * * *
20966698 TTAAATTTTTTTGTCATTTCTTTTAAA-TTATCTATCTTTC-CATTTA--T-TTTTTTTCTCATC
1 TTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAAATTTATTTATTTTTTTCTCAT-
*
20966758 TT-ATTTAAA
65 TTCATTTCAA
* * * *
20966767 TTAAAAGTTTCTCC-CA-TTCATTTAAATTTGTATTTCTTTCAAATTTAATTTCATTTTTTTCTC
1 TT-AAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAAATTT-ATTT-ATTTTTTTCTC
20966830 ATTTCATTTCAA
63 ATTTCATTTCAA
* * * * *
20966842 TTAAATTTTTTCCTCATTTCTTTTGAATTTATCTTTCTTTCAATTTTCATTTAAATTTTGTAC-C
1 TTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAAATTT-ATTT--ATTTTTTTCTC
**
20966906 GCTTCATTTCAA
63 ATTTCATTTCAA
* *
20966918 TT-TATTTTTTTCTCATTTCATTTAAATT
1 TTAAATTTTTTCCTCATTTCATTTAAATT
20966946 ATCAATTTTT
Statistics
Matches: 140, Mismatches: 27, Indels: 18
0.76 0.15 0.10
Matches are distributed among these distances:
68 9 0.06
69 14 0.10
70 11 0.08
71 1 0.01
73 1 0.01
74 11 0.08
75 44 0.31
76 42 0.30
77 7 0.05
ACGTcount: A:0.24, C:0.15, G:0.02, T:0.59
Consensus pattern (74 bp):
TTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAAATTTATTTATTTTTTTCTCATT
TCATTTCAA
Found at i:20968767 original size:20 final size:20
Alignment explanation
Indices: 20968742--20968796 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
20968732 AGGGGCACAC
20968742 GCCCGTGTGGCCTAGG-ACAT
1 GCCCGTGTGGCCT-GGAACAT
20968762 GCCCGTGTGGCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAT
20968782 GCCCGTGTGGCCTGG
1 GCCCGTGTGGCCTGG
20968797 CCGTAGGCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 2 0.06
20 32 0.94
ACGTcount: A:0.11, C:0.31, G:0.38, T:0.20
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGAACAT
Found at i:20970959 original size:3 final size:3
Alignment explanation
Indices: 20970938--20970978 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
20970928 TTATCTCAAT
*
20970938 TAA TAGA TAA -AA T-A TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20970979 GTAAATATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:20972893 original size:55 final size:52
Alignment explanation
Indices: 20972760--20972941 Score: 213
Period size: 54 Copynumber: 3.4 Consensus size: 52
20972750 TTTAGTGCTG
* * *
20972760 GCCATTGATAGGCCAA-CACCAAAAAAATTTAATTTTTTTTTAATACTGGTGCC
1 GCCATTGACAGG-CAAGCACAAAAAAAATTCAA-TTTTTTTTAATACTGGTGCC
* * *
20972813 TGCCATTGACAAGCTACCACCAAAAAAAATTCAATTTTTTTTAATACTGGTGCC
1 -GCCATTGACAGGCAAGCA-CAAAAAAAATTCAATTTTTTTTAATACTGGTGCC
* *
20972867 GACCATTGACAGGCCAGCACTAAAAAAATTTCAAATTTTTTTTAAATACTGGTGCC
1 G-CCATTGACAGGCAAGCAC-AAAAAAAATTC-AATTTTTTTT-AATACTGGTGCC
20972923 GCCATTGACAGGCAAGCAC
1 GCCATTGACAGGCAAGCAC
20972942 CAATTTTTTT
Statistics
Matches: 112, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
53 4 0.04
54 56 0.50
55 39 0.35
56 13 0.12
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (52 bp):
GCCATTGACAGGCAAGCACAAAAAAAATTCAATTTTTTTTAATACTGGTGCC
Found at i:20977342 original size:36 final size:36
Alignment explanation
Indices: 20977302--20977419 Score: 200
Period size: 36 Copynumber: 3.3 Consensus size: 36
20977292 ACTGCCACCA
20977302 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
1 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
*
20977338 CCAGCTCCACTTATTCCAAACCCCTTTCAGCCTCCT
1 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
* *
20977374 CCAGCTCCTCTTATTCCAAACCCTTTTCAGCCTCCT
1 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
*
20977410 CCAGCCCCAC
1 CCAGCTCCAC
20977420 CGGCTCCACT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 77 1.00
ACGTcount: A:0.19, C:0.47, G:0.06, T:0.27
Consensus pattern (36 bp):
CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
Found at i:20977552 original size:45 final size:45
Alignment explanation
Indices: 20977371--20977558 Score: 250
Period size: 45 Copynumber: 4.2 Consensus size: 45
20977361 CTTTCAGCCT
* * * *
20977371 CCTCCAGCTCCTCTTATTCCAAACCCTTTTCAGCCTCCTCCAGCC
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
* * *
20977416 CCACCGGCTCCACTTATTCCAAACCCTTTTCAGCCTCCTCCCGCA
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
* *
20977461 CCACCGGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
* * * * *
20977506 CCTCCAGCTCCATTTATCCCAAACCCCTTCCAGCCTCCTTCGGCA
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
20977551 CCTCCAGC
1 CCTCCAGC
20977559 ACCTCCAGCA
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 130 1.00
ACGTcount: A:0.17, C:0.50, G:0.09, T:0.24
Consensus pattern (45 bp):
CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
Found at i:20986611 original size:13 final size:13
Alignment explanation
Indices: 20986593--20986634 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
20986583 ATATGACGTG
20986593 ATTTTTTTGGTTC
1 ATTTTTTTGGTTC
* *
20986606 ATTTTTTT-ATGC
1 ATTTTTTTGGTTC
20986618 ACTTTTTTTGGTTC
1 A-TTTTTTTGGTTC
20986632 ATT
1 ATT
20986635 AATGTGACGT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.67
Consensus pattern (13 bp):
ATTTTTTTGGTTC
Found at i:20990807 original size:33 final size:33
Alignment explanation
Indices: 20990770--20990848 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
20990760 TAGCCTTGCC
* *
20990770 ATGGTCTTACACTC-GTAATGTCATAACCCATTT
1 ATGGTCTTACACTCAG-AATGCCATAACCCAATT
*
20990803 ATGGTCTTATCA-TCAGGATGCCATAACCCAATT
1 ATGGTCTTA-CACTCAGAATGCCATAACCCAATT
20990836 ATGGTCTTACACT
1 ATGGTCTTACACT
20990849 TATACATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.05
33 35 0.88
34 3 0.08
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (33 bp):
ATGGTCTTACACTCAGAATGCCATAACCCAATT
Found at i:20990903 original size:105 final size:101
Alignment explanation
Indices: 20990788--20990985 Score: 254
Period size: 105 Copynumber: 1.9 Consensus size: 101
20990778 ACACTCGTAA
* * **
20990788 TGTCATAACCCATTTATGGTCTTATCA-TCAGGATGCCATAACCCAATTATGGTCTTACACTTAT
1 TGTCATAACCCAGTTATAGTCTTATCACT-AAAATGCCATAACCCAATTATGGTCTTACA-TT-T
*
20990852 ACATATACTACCATGGTCTAACCATGGTCTTATGTTCATGG
63 A-A-ACACTACCATGGTCTAACCATGGTCTTATGTTCATGG
* * *
20990893 TGTCATAACCCAGTTATAGTCTTTTCACTAAAATGCCATAGCCCAGTTATGGTCTTACATTTAAA
1 TGTCATAACCCAGTTATAGTCTTATCACTAAAATGCCATAACCCAATTATGGTCTTACATTTAAA
* *
20990958 CATTACCATGGTCTAACCATTGTCTTAT
66 CACTACCATGGTCTAACCATGGTCTTAT
20990986 CCATCAATTC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
101 26 0.32
102 1 0.01
103 2 0.02
104 2 0.02
105 50 0.61
106 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (101 bp):
TGTCATAACCCAGTTATAGTCTTATCACTAAAATGCCATAACCCAATTATGGTCTTACATTTAAA
CACTACCATGGTCTAACCATGGTCTTATGTTCATGG
Found at i:20995067 original size:21 final size:21
Alignment explanation
Indices: 20995043--20995084 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20995033 CTTTTCTAAA
** *
20995043 GTTAAAATTCAAAATTATTAT
1 GTTAAAAGGCAAAACTATTAT
20995064 GTTAAAAGGCAAAACTATTAT
1 GTTAAAAGGCAAAACTATTAT
20995085 TGTTTATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (21 bp):
GTTAAAAGGCAAAACTATTAT
Found at i:20995508 original size:60 final size:60
Alignment explanation
Indices: 20995436--20995559 Score: 230
Period size: 60 Copynumber: 2.1 Consensus size: 60
20995426 TCTTTTAGAT
20995436 ATATCAATATTAGCTCTTCTAGAGCTTTAAACTAAATCTGTACACCCAAATATTGCATTA
1 ATATCAATATTAGCTCTTCTAGAGCTTTAAACTAAATCTGTACACCCAAATATTGCATTA
* *
20995496 ATATCAATATTAGCTCTTCTAGAGCTTTAAACTAAATTTGTACACCCAGATATTGCATTA
1 ATATCAATATTAGCTCTTCTAGAGCTTTAAACTAAATCTGTACACCCAAATATTGCATTA
20995556 ATAT
1 ATAT
20995560 TGGTTTATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (60 bp):
ATATCAATATTAGCTCTTCTAGAGCTTTAAACTAAATCTGTACACCCAAATATTGCATTA
Found at i:20995892 original size:3 final size:3
Alignment explanation
Indices: 20995882--20995917 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
20995872 TATGTCCATG
20995882 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
20995918 GTTTACATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20997711 original size:52 final size:51
Alignment explanation
Indices: 20997639--20997849 Score: 181
Period size: 53 Copynumber: 4.0 Consensus size: 51
20997629 ATATCATACC
* * * *
20997639 GATGCCATATCCCAGATATGGTCTTACACGGGAGCACTTATCACTTTTCTCT
1 GATGCCATAGCCCAGCTATGGTCTTATACGGGATCACTTATCACTTTT-TCT
* * *
20997691 GATGCCATAGCCTAGCTATGGTCTTATAC-GGATCACTTGTATCACTTTAATCC
1 GATGCCATAGCCCAGCTATGGTCTTATACGGGATCAC-T-TATCACTTT-TTCT
* * * ** *
20997744 GAAGCTATAGCCTAGCTATGGTCTTATACAGAAATCACTTATCACTTGTTTTT
1 GATGCCATAGCCCAGCTATGGTCTTATAC-GGGATCACTTATCACTT-TTTCT
* * **
20997797 CGATGCTATAGCCCAGCTATGGTCTTGTACGAATATCACTTATCACTTGTTTC
1 -GATGCCATAGCCCAGCTATGGTCTTATACG-GGATCACTTATCACTT-TTTC
20997850 CATGGTCCAA
Statistics
Matches: 132, Mismatches: 19, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
51 6 0.05
52 26 0.20
53 48 0.36
54 47 0.36
55 5 0.04
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.35
Consensus pattern (51 bp):
GATGCCATAGCCCAGCTATGGTCTTATACGGGATCACTTATCACTTTTTCT
Found at i:20997848 original size:54 final size:52
Alignment explanation
Indices: 20997655--20997844 Score: 195
Period size: 54 Copynumber: 3.6 Consensus size: 52
20997645 ATATCCCAGA
* ** * * *
20997655 TATGGTCTTACACGGGAGCACTTATCAC-TTTTCTCTGATGCCATAGCCTAGC
1 TATGGTCTTATACGAAATCACTTATCACTTTTTTTC-GATGCTATAGCCTAGC
* ** * *
20997707 TATGGTCTTATACG-GATCACTTGTATCACTTTAATCCGAAGCTATAGCCTAGC
1 TATGGTCTTATACGAAATCAC-T-TATCACTTTTTTTCGATGCTATAGCCTAGC
*
20997760 TATGGTCTTATACAGAAATCACTTATCACTTGTTTTTCGATGCTATAGCCCAGC
1 TATGGTCTTATAC-GAAATCACTTATCACTT-TTTTTCGATGCTATAGCCTAGC
*
20997814 TATGGTCTTGTACGAATATCACTTATCACTT
1 TATGGTCTTATACGAA-ATCACTTATCACTT
20997845 GTTTCCATGG
Statistics
Matches: 116, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
51 5 0.04
52 14 0.12
53 44 0.38
54 48 0.41
55 5 0.04
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (52 bp):
TATGGTCTTATACGAAATCACTTATCACTTTTTTTCGATGCTATAGCCTAGC
Found at i:21005428 original size:54 final size:52
Alignment explanation
Indices: 21005265--21005454 Score: 215
Period size: 54 Copynumber: 3.6 Consensus size: 52
21005255 ATATCCTGAA
* * * * *
21005265 TATGGTCTTACACGGGAGCACTTATCACTTTTCTCCGATGCCATAGCCCAGC
1 TATGGTCTTATACGGAATCACTTATCACTTTTATCCAATGCCATAGCCCAGC
21005317 TATGGTCTTATACGG-ATCACTTGTATCA-TTTTAATCCGAA-GCCATAGCCCAGC
1 TATGGTCTTATACGGAATCAC-T-TATCACTTTT-ATCC-AATGCCATAGCCCAGC
* * * *
21005370 TATGGTATTATATGGAAATCACTTATCACTTGTTTTCCAATGCCATAGCCCAGT
1 TATGGTCTTATACGG-AATCACTTATCACTT-TTATCCAATGCCATAGCCCAGC
21005424 TATGGTCTTATACGGATATCACTTATCACTT
1 TATGGTCTTATACGGA-ATCACTTATCACTT
21005455 GTTGCCATGG
Statistics
Matches: 118, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
51 4 0.03
52 19 0.16
53 42 0.36
54 46 0.39
55 7 0.06
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (52 bp):
TATGGTCTTATACGGAATCACTTATCACTTTTATCCAATGCCATAGCCCAGC
Found at i:21019076 original size:2 final size:2
Alignment explanation
Indices: 21019021--21019057 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21019011 AAAAGCAAAA
21019021 AG AG AG 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 AG AG AG A
21019058 AATGGGAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21032647 original size:18 final size:18
Alignment explanation
Indices: 21032615--21032650 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21032605 AAAACCCTAA
**
21032615 ATTTTCTTTTTCTTTTTC
1 ATTTTCTTTCCCTTTTTC
21032633 ATTTTCTTTCCCTTTTTC
1 ATTTTCTTTCCCTTTTTC
21032651 CCTCCTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTCTTTCCCTTTTTC
Found at i:21032787 original size:17 final size:16
Alignment explanation
Indices: 21032757--21032809 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 16
21032747 ATTATAATTA
*
21032757 TATAATATAC-TATAT
1 TATAATTTACTTATAT
21032772 TATAATTTACTTTATAT
1 TATAATTTAC-TTATAT
*
21032789 TATTATTTACTTATAT
1 TATAATTTACTTATAT
*
21032805 AATAA
1 TATAA
21032810 GTAAATACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 9 0.28
16 9 0.28
17 14 0.44
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TATAATTTACTTATAT
Found at i:21057837 original size:33 final size:33
Alignment explanation
Indices: 21057784--21057853 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
21057774 ATTATTTAAA
* *
21057784 TATGATTTGAAAATGCTTTTGAGTATGTTTAGG
1 TATGATTTGAAAATACTTTTGAGAATGTTTAGG
* * * *
21057817 TATGATTTGAACATATTTTTGGGAATGTTTTGG
1 TATGATTTGAAAATACTTTTGAGAATGTTTAGG
21057850 TATG
1 TATG
21057854 GTTGATAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (33 bp):
TATGATTTGAAAATACTTTTGAGAATGTTTAGG
Found at i:21066379 original size:3 final size:3
Alignment explanation
Indices: 21066373--21066399 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
21066363 AATAATAATA
21066373 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
21066400 TGCATCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:21067928 original size:15 final size:15
Alignment explanation
Indices: 21067908--21067936 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21067898 AATTAAAATT
21067908 TTATTATTTTATTTA
1 TTATTATTTTATTTA
21067923 TTATTATTTTATTT
1 TTATTATTTTATTT
21067937 TGTTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTATTTTATTTA
Found at i:21070300 original size:15 final size:14
Alignment explanation
Indices: 21070280--21070318 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
21070270 TCTTGCTCTT
21070280 TCATATTATATCATA
1 TCATATTATAT-ATA
21070295 TCATATTATATATA
1 TCATATTATATATA
*
21070309 T-ATATAATAT
1 TCATATTATAT
21070319 TATAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.35
14 4 0.17
15 11 0.48
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (14 bp):
TCATATTATATATA
Found at i:21087919 original size:11 final size:11
Alignment explanation
Indices: 21087899--21087931 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
21087889 TCCCAAAATT
21087899 GAAAAGAAAAA
1 GAAAAGAAAAA
*
21087910 GAAGAGAAAAA
1 GAAAAGAAAAA
21087921 GAAAAGAAAAA
1 GAAAAGAAAAA
21087932 TGTTGTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:21090014 original size:48 final size:47
Alignment explanation
Indices: 21089940--21090122 Score: 199
Period size: 48 Copynumber: 3.7 Consensus size: 47
21089930 TTTTCACCTT
* *
21089940 AAGTGCCAATATCATAGCCCGAAGCCAACTCAATAAATCATGCACTCG
1 AAGTGCAAATATCATGGCCCGAAGCCAACTCAATAAATCATGCAC-CG
* * *
21089988 AAGTGCAAATATCATGGCTCGTAGCCAACTCAATAAATCATGCACCCA
1 AAGTGCAAATATCATGGCCCGAAGCCAACTCAATAAATCATGCA-CCG
*
21090036 AAGTGCAAATATCATGGCCC-ATAGCTAACTCAATATATAT-ATCTCGCACCTG
1 AAGTGCAAATATCATGGCCCGA-AGCCAACTCAATA-A-ATCA--T-GCACC-G
* *
21090088 AAGTGCCAATATCATGGCCTGAAGCCAACTCAATA
1 AAGTGCAAATATCATGGCCCGAAGCCAACTCAATA
21090123 TATCCCTAAT
Statistics
Matches: 114, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
48 72 0.63
49 3 0.03
50 2 0.02
51 3 0.03
52 33 0.29
53 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.22
Consensus pattern (47 bp):
AAGTGCAAATATCATGGCCCGAAGCCAACTCAATAAATCATGCACCG
Found at i:21090701 original size:21 final size:20
Alignment explanation
Indices: 21090673--21090711 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
21090663 CAAAACTTGT
21090673 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
21090693 ATAATCTATCATTAAACAT
1 ATAA-CTATCATCAAACAT
21090712 CAAAATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:21091661 original size:96 final size:95
Alignment explanation
Indices: 21091490--21091678 Score: 288
Period size: 96 Copynumber: 2.0 Consensus size: 95
21091480 TAAGATGATT
*
21091490 AAATATCTCATGACTTGATTCGCAATTGTTGATATTGAATATCGAGAATTGGACTGAAATGAATA
1 AAATATCTCATGACTTGATTCGCAATTGTTGATATTAAATATCGAGAATTGGACTGAAATGAATA
*
21091555 AAATATAAATAAGCATGATAACAAATTGAAA
66 AAATAGAAATAAGCATGAT-ACAAATTGAAA
* ** * * *
21091586 AAATGTCTCATGACTTGATTCGTGATTGTTGATATTAAATGTTGAGAATTGGATTGAAATGAATA
1 AAATATCTCATGACTTGATTCGCAATTGTTGATATTAAATATCGAGAATTGGACTGAAATGAATA
*
21091651 AAATAGAAATAAGCATGATATAAATTGA
66 AAATAGAAATAAGCATGATACAAATTGA
21091679 TAAGTGTCTT
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 8 0.10
96 76 0.90
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.32
Consensus pattern (95 bp):
AAATATCTCATGACTTGATTCGCAATTGTTGATATTAAATATCGAGAATTGGACTGAAATGAATA
AAATAGAAATAAGCATGATACAAATTGAAA
Found at i:21091932 original size:19 final size:19
Alignment explanation
Indices: 21091909--21091963 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
21091899 GTGTGGGTTT
*
21091909 ATGCACTTCGTGTGCCAGT
1 ATGCACTTCGTGTGCCAGG
* *
21091928 TTGCACTTTGTGTGCCAGG
1 ATGCACTTCGTGTGCCAGG
*
21091947 ATGCATTTCG-GTGCCAG
1 ATGCACTTCGTGTGCCAG
21091964 ATTGGTGTCG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.33
Consensus pattern (19 bp):
ATGCACTTCGTGTGCCAGG
Found at i:21093011 original size:44 final size:45
Alignment explanation
Indices: 21092951--21093044 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 45
21092941 TTTAAATATT
* * *
21092951 AATATATTAACTCTTTTGGAGCTTTCAACTAATTTTGTACTACCC
1 AATATATTAACTCTTTTGGAGCTTTAAACTAAATTTGTACTACCA
* *
21092996 AATA-ATTAGCTCTTTTGGAGCTTTAAACTAAATTTGTAGTACCA
1 AATATATTAACTCTTTTGGAGCTTTAAACTAAATTTGTACTACCA
21093040 AATAT
1 AATAT
21093045 TGCATTAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 39 0.91
45 4 0.09
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (45 bp):
AATATATTAACTCTTTTGGAGCTTTAAACTAAATTTGTACTACCA
Found at i:21097221 original size:16 final size:17
Alignment explanation
Indices: 21097190--21097222 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21097180 TTCATAAGTA
21097190 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
21097207 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
21097223 GCTCTATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:21097827 original size:46 final size:46
Alignment explanation
Indices: 21097503--21097826 Score: 470
Period size: 46 Copynumber: 7.0 Consensus size: 46
21097493 TTATCTTTGA
* * * * * *
21097503 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATAT
21097549 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
*
21097595 CACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
* * ***
21097641 CACGTTGCCATGGTATCTTCCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
*
21097687 CATGATGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
**
21097733 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
* **
21097779 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
21097825 CA
1 CA
21097827 GAGAACACAC
Statistics
Matches: 256, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 252 0.98
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
Found at i:21100022 original size:29 final size:30
Alignment explanation
Indices: 21099970--21100038 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
21099960 CCACCCTTAA
* * *
21099970 CATATTTGCACTATTAGTCCTTCAACTTTT
1 CATATTTACACTATTAATCCTTCAAATTTT
21100000 CATATTTACACT-TTAATCCTTCAAATTTT
1 CATATTTACACTATTAATCCTTCAAATTTT
*
21100029 GAGTATTTAC
1 CA-TATTTAC
21100039 TCTTGGGCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.47
30 18 0.53
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (30 bp):
CATATTTACACTATTAATCCTTCAAATTTT
Found at i:21104888 original size:27 final size:26
Alignment explanation
Indices: 21104850--21104965 Score: 124
Period size: 27 Copynumber: 4.3 Consensus size: 26
21104840 AGCATGGCTG
* *
21104850 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
21104876 TCAGATACAGATAATTGTGGCAGAGCCA
1 CCAGA-ACAGATAA-TGTGGCAGAGCCA
21104904 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * * *
21104931 CCAGATCAGATATTTGTGGCATAACCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
*
21104958 CCAAAACA
1 CCAGAACA
21104966 CTTCCTCCAT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.05
27 57 0.74
28 16 0.21
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:21104914 original size:54 final size:54
Alignment explanation
Indices: 21104850--21104965 Score: 153
Period size: 54 Copynumber: 2.1 Consensus size: 54
21104840 AGCATGGCTG
* * *
21104850 CCAGAACAGATA-ATGTGACAGAGTCATCAGATACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATTGTGGCAGAACCA
* * *
21104904 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAACCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATTGTGGCAGAACCA
*
21104958 CCAAAACA
1 CCAGAACA
21104966 CTTCCTCCAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATTGTGGCAGAACCA
Found at i:21106607 original size:26 final size:26
Alignment explanation
Indices: 21106571--21106680 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
21106561 CATGAAATTC
21106571 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
21106597 TTATCATGAAACATTTACCTAACTCA
1 TTATCATGAAACATTTACCTAACCCA
* *
21106623 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
21106649 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
21106675 TTATCA
1 TTATCA
21106681 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 77 0.97
27 2 0.03
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:21106691 original size:10 final size:10
Alignment explanation
Indices: 21106676--21106700 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
21106666 CCTAACCTAT
21106676 TATCAATTTG
1 TATCAATTTG
21106686 TATCAATTTG
1 TATCAATTTG
21106696 TATCA
1 TATCA
21106701 TAAATTATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (10 bp):
TATCAATTTG
Found at i:21107379 original size:20 final size:18
Alignment explanation
Indices: 21107350--21107394 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
21107340 AACGAAAAGC
21107350 AGGG-AAAGAAAGAAAGAA
1 AGGGAAAAGAAAG-AAGAA
21107368 AGGAGAAAAGAAAGAAGAA
1 AGG-GAAAAGAAAGAAGAA
21107387 AGGGAAAA
1 AGGGAAAA
21107395 TTTAAGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGGGAAAAGAAAGAAGAA
Found at i:21110656 original size:27 final size:28
Alignment explanation
Indices: 21110621--21110677 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
21110611 ATATAAAAAG
* *
21110621 TATAAATAATATAAAGCTCTAC-TTTAA
1 TATAAATAATATAAAACTATACTTTTAA
*
21110648 TATACATAATATAAAACTATACTTTTAA
1 TATAAATAATATAAAACTATACTTTTAA
21110676 TA
1 TA
21110678 AATATTAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.39
Consensus pattern (28 bp):
TATAAATAATATAAAACTATACTTTTAA
Found at i:21115156 original size:8 final size:8
Alignment explanation
Indices: 21115140--21115174 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
21115130 TTTCATTTGC
*
21115140 TTTGGTTT
1 TTTGTTTT
21115148 TTTGTTTT
1 TTTGTTTT
21115156 TTTGTTTT
1 TTTGTTTT
21115164 TTT-TTTT
1 TTTGTTTT
21115171 TTTG
1 TTTG
21115175 GCAAAGAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (8 bp):
TTTGTTTT
Found at i:21115164 original size:15 final size:15
Alignment explanation
Indices: 21115144--21115174 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21115134 ATTTGCTTTG
21115144 GTTTTTTGTTTTTTT
1 GTTTTTTGTTTTTTT
*
21115159 GTTTTTTTTTTTTTT
1 GTTTTTTGTTTTTTT
21115174 G
1 G
21115175 GCAAAGAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
GTTTTTTGTTTTTTT
Found at i:21120064 original size:24 final size:23
Alignment explanation
Indices: 21120020--21120064 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
21120010 GGTACTGTAG
*
21120020 TTCATTTCATGTTATTTTGGTAT
1 TTCATTTCATGTTATTATGGTAT
* *
21120043 TTCATTTTCTTGTTCTTATGGT
1 TTCA-TTTCATGTTATTATGGT
21120065 CAATTTCAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.62
Consensus pattern (23 bp):
TTCATTTCATGTTATTATGGTAT
Found at i:21129427 original size:30 final size:30
Alignment explanation
Indices: 21129393--21129451 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
21129383 AGTTCATACC
21129393 CCAAATATGCCATTCAAGTGCCATACATAA
1 CCAAATATGCCATTCAAGTGCCATACATAA
*
21129423 CCAAATATGCCATTCAAGTTCCATACATA
1 CCAAATATGCCATTCAAGTGCCATACATA
21129452 TAGCTTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.25
Consensus pattern (30 bp):
CCAAATATGCCATTCAAGTGCCATACATAA
Found at i:21133419 original size:51 final size:51
Alignment explanation
Indices: 21133336--21133454 Score: 143
Period size: 51 Copynumber: 2.3 Consensus size: 51
21133326 TAAAAAATAT
* * *
21133336 TTTTTATTTGGTGTTGGCTTTCCTGAATCCAGCACCAGTTTTTTTATTGAAA
1 TTTTT-TTTGGTGTTGGCTTTCCTGAATCCAGCACCAGTGTTGTTAATGAAA
* * *
21133388 TTTTTTTTGGTGTTGGCTTTCTTG-TTGCCAGCACCAGTGTTGTTAATGCAA
1 TTTTTTTTGGTGTTGGCTTTCCTGAAT-CCAGCACCAGTGTTGTTAATGAAA
21133439 TTTTCTTTT-GTGTTGG
1 TTTT-TTTTGGTGTTGG
21133455 TGTTCTCGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.02
51 49 0.83
52 9 0.15
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (51 bp):
TTTTTTTTGGTGTTGGCTTTCCTGAATCCAGCACCAGTGTTGTTAATGAAA
Found at i:21133473 original size:51 final size:51
Alignment explanation
Indices: 21133336--21133474 Score: 133
Period size: 51 Copynumber: 2.7 Consensus size: 51
21133326 TAAAAAATAT
* * * *
21133336 TTTTTATTTGGTGTTGGCTTTC-CTGAAT-CCAGCACCAGTTTTTTTATTGAAA
1 TTTTT-TTTGGTGTTGGCTTTCTC-G-TTGCCAGCACCAGTGTTGTTAATGAAA
* *
21133388 TTTTTTTTGGTGTTGGCTTTCTTGTTGCCAGCACCAGTGTTGTTAATGCAA
1 TTTTTTTTGGTGTTGGCTTTCTCGTTGCCAGCACCAGTGTTGTTAATGAAA
* *
21133439 TTTTCTTTT-GTGTTGG-TGTTCTCGTTGTCGGCACCA
1 TTTT-TTTTGGTGTTGGCT-TTCTCGTTGCCAGCACCA
21133475 CCAGGCTATA
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
50 2 0.03
51 63 0.85
52 9 0.12
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.48
Consensus pattern (51 bp):
TTTTTTTTGGTGTTGGCTTTCTCGTTGCCAGCACCAGTGTTGTTAATGAAA
Found at i:21140741 original size:2 final size:2
Alignment explanation
Indices: 21140734--21140760 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21140724 TTATTTCTTG
21140734 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
21140761 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21142486 original size:46 final size:44
Alignment explanation
Indices: 21142382--21142489 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
21142372 TGTCTTTGAC
** * * *
21142382 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
21142426 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
21142472 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
21142490 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:21143381 original size:4 final size:4
Alignment explanation
Indices: 21143372--21143399 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
21143362 CCTTTTTCTT
21143372 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
21143400 CTTCCTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:21143473 original size:9 final size:9
Alignment explanation
Indices: 21143459--21143492 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
21143449 TTCTATTCTG
21143459 TTTCTTTTC
1 TTTCTTTTC
21143468 TTTCTTTT-
1 TTTCTTTTC
*
21143476 TTTCTATTC
1 TTTCTTTTC
21143485 TTTCTTTT
1 TTTCTTTT
21143493 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:21143485 original size:17 final size:17
Alignment explanation
Indices: 21143459--21143492 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21143449 TTCTATTCTG
*
21143459 TTTCTTTTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
21143476 TTTCTATTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
21143493 GTTTTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTATTCTTTCTTTT
Found at i:21143514 original size:5 final size:5
Alignment explanation
Indices: 21143501--21143573 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
21143491 TTGTTTTATG
21143501 TATATA TATAA TATAA TATAA TAT-A T-TAA TGATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
21143549 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
21143574 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:21143526 original size:19 final size:19
Alignment explanation
Indices: 21143502--21143544 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
21143492 TGTTTTATGT
21143502 ATATATATAAT-ATAATATA
1 ATATAT-TAATGATAATATA
21143521 ATATATTAATGATAATATA
1 ATATATTAATGATAATATA
21143540 ATATA
1 ATATA
21143545 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATATTAATGATAATATA
Found at i:21143554 original size:24 final size:24
Alignment explanation
Indices: 21143508--21143572 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
21143498 ATGTATATAT
* * *
21143508 ATAATATAATATAATATATTAATG
1 ATAATATAATATAATAAAATAATC
21143532 ATAATATAATATAA-AAACATAATC
1 ATAATATAATATAATAAA-ATAATC
*
21143556 ATTACTATAATATAATA
1 A-TAATATAATATAATA
21143573 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 19 0.56
25 12 0.35
26 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATC
Found at i:21148729 original size:46 final size:44
Alignment explanation
Indices: 21148625--21148732 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
21148615 TGTCTTTGAC
** * * *
21148625 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
21148669 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
21148715 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
21148733 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:21149624 original size:4 final size:4
Alignment explanation
Indices: 21149615--21149642 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
21149605 CCTTTTTCTT
21149615 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
21149643 CTTCCTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:21149716 original size:9 final size:9
Alignment explanation
Indices: 21149702--21149735 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
21149692 TTCTATTCTG
21149702 TTTCTTTTC
1 TTTCTTTTC
21149711 TTTCTTTT-
1 TTTCTTTTC
*
21149719 TTTCTATTC
1 TTTCTTTTC
21149728 TTTCTTTT
1 TTTCTTTT
21149736 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:21149728 original size:17 final size:17
Alignment explanation
Indices: 21149702--21149735 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21149692 TTCTATTCTG
*
21149702 TTTCTTTTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
21149719 TTTCTATTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
21149736 GTTTTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTATTCTTTCTTTT
Found at i:21149755 original size:5 final size:5
Alignment explanation
Indices: 21149747--21149814 Score: 63
Period size: 5 Copynumber: 13.8 Consensus size: 5
21149737 TTTTATGTAT
*
21149747 ATATA ATATA ATATA ATAT- AT-TA ATGATA ATATA ATATA A-A-A ACATA
1 ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA ATATA
*
21149794 ATCATTA CTATA ATATA ATAT
1 AT-A-TA ATATA ATATA ATAT
21149815 TTTTTTAACA
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.06
4 6 0.11
5 35 0.66
6 6 0.11
7 3 0.06
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:21149776 original size:19 final size:19
Alignment explanation
Indices: 21149744--21149785 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
21149734 TTGTTTTATG
21149744 TATATATAATATAATATAA
1 TATATATAATATAATATAA
21149763 TATAT-TAATGATAATATAA
1 TATATATAAT-ATAATATAA
21149782 TATA
1 TATA
21149786 AAAACATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TATATATAATATAATATAA
Found at i:21149795 original size:24 final size:24
Alignment explanation
Indices: 21149749--21149813 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
21149739 TTATGTATAT
* * *
21149749 ATAATATAATATAATATATTAATG
1 ATAATATAATATAATAAAATAATC
21149773 ATAATATAATATAA-AAACATAATC
1 ATAATATAATATAATAAA-ATAATC
*
21149797 ATTACTATAATATAATA
1 A-TAATATAATATAATA
21149814 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 19 0.56
25 12 0.35
26 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATC
Found at i:21150341 original size:21 final size:21
Alignment explanation
Indices: 21150315--21150354 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21150305 GAACAAAAAT
*
21150315 GACATGTTGAACAGGTTTCAG
1 GACATGTTGAACAAGTTTCAG
21150336 GACATGTTGAACAAGTTTC
1 GACATGTTGAACAAGTTTC
21150355 TAGGTAAATG
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:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (21 bp):
GACATGTTGAACAAGTTTCAG
Found at i:21151386 original size:22 final size:23
Alignment explanation
Indices: 21151361--21151420 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
21151351 TGGACTGAAT
21151361 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
21151383 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
21151405 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
21151421 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:21151388 original size:4 final size:4
Alignment explanation
Indices: 21151370--21151403 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
21151360 TATAAAAATT
21151370 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
21151404 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:21152821 original size:18 final size:18
Alignment explanation
Indices: 21152800--21152838 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
21152790 TTTCTTCAAC
* *
21152800 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
21152818 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
21152836 TTC
1 TTC
21152839 ACTCGCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:21155194 original size:22 final size:23
Alignment explanation
Indices: 21155169--21155228 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
21155159 TGGACTGAAT
21155169 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
21155191 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
21155213 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
21155229 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:21155196 original size:4 final size:4
Alignment explanation
Indices: 21155178--21155211 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
21155168 TATAAAAATT
21155178 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
21155212 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:21156631 original size:10 final size:10
Alignment explanation
Indices: 21156612--21156671 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
21156602 TGAAATTCTA
21156612 AAAGATAAAT
1 AAAGATAAAT
21156622 ACAA-ATAAAT
1 A-AAGATAAAT
*
21156632 AAAGATAATT
1 AAAGATAAAT
21156642 AAAGATAAAT
1 AAAGATAAAT
21156652 AAAGATAAAT
1 AAAGATAAAT
21156662 GAAA-ATAAAT
1 -AAAGATAAAT
21156672 CCTAAAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:21157670 original size:29 final size:30
Alignment explanation
Indices: 21157606--21157672 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
21157596 TAAATTGGCC
21157606 CTAAATTTTTAAAATTAAGAAGTAGAGGAA
1 CTAAATTTTTAAAATTAAGAAGTAGAGGAA
*
21157636 CTAAATTCTTTAAAA-TAA-AATTAG-GGAAA
1 CTAAATT-TTTAAAATTAAGAAGTAGAGG-AA
21157665 CTAAATTT
1 CTAAATTT
21157673 CGACTGTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 3 0.09
29 14 0.41
30 10 0.29
31 7 0.21
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (30 bp):
CTAAATTTTTAAAATTAAGAAGTAGAGGAA
Found at i:21158132 original size:4 final size:4
Alignment explanation
Indices: 21158125--21158250 Score: 234
Period size: 4 Copynumber: 31.5 Consensus size: 4
21158115 TAAATAAATA
21158125 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
21158173 ATAC ATAC ATAC ATAC ATGC ATAC ATGC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
21158221 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
21158251 TGTTTAGATA
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 118 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:21158798 original size:17 final size:16
Alignment explanation
Indices: 21158774--21158811 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
21158764 TTATAAAAGT
*
21158774 ATAAAAT-ATCTTA-A
1 ATAAAATAATATTATA
21158788 ATAAAATAATATTATA
1 ATAAAATAATATTATA
21158804 ATAAAATA
1 ATAAAATA
21158812 TACAAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 5 0.24
16 9 0.43
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAAATAATATTATA
Found at i:21159635 original size:29 final size:28
Alignment explanation
Indices: 21159556--21159644 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 28
21159546 ATACTGATAA
* *
21159556 ATAATTTT--ATA-TTTGAATATTTATT
1 ATAATTTTAAATATTTTTAATAATTATT
*
21159581 ATGATTTTAAATATTTTTAATAAATTATT
1 ATAATTTTAAATATTTTTAAT-AATTATT
*
21159610 ATAATTCTTAAA-ATTTTTAAATAATTTTT
1 ATAATT-TTAAATATTTTT-AATAATTATT
21159639 ATAATT
1 ATAATT
21159645 AAATCGAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
25 7 0.13
27 3 0.06
28 6 0.11
29 29 0.55
30 8 0.15
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (28 bp):
ATAATTTTAAATATTTTTAATAATTATT
Found at i:21159801 original size:12 final size:12
Alignment explanation
Indices: 21159761--21159803 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
21159751 ATGTCATCAC
21159761 TTAATTATAAAAA
1 TTAATTA-AAAAA
* **
21159774 TAAATTAAAATT
1 TTAATTAAAAAA
21159786 TTAATTAAAAAA
1 TTAATTAAAAAA
21159798 TTAATT
1 TTAATT
21159804 TATTTTTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
12 18 0.75
13 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTAATTAAAAAA
Found at i:21162731 original size:49 final size:49
Alignment explanation
Indices: 21162659--21162756 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
21162649 AATAGGTTAA
21162659 ACTGTCGTCGTTTTGATGATTTTGATTTTAGGGGTTGGTGATTGAAGTT
1 ACTGTCGTCGTTTTGATGATTTTGATTTTAGGGGTTGGTGATTGAAGTT
21162708 ACTGTCGTCGTTTTGATGATTTTGATTTTAGGGGTTGGTGATTGAAGTT
1 ACTGTCGTCGTTTTGATGATTTTGATTTTAGGGGTTGGTGATTGAAGTT
21162757 TGAACAATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.16, C:0.06, G:0.31, T:0.47
Consensus pattern (49 bp):
ACTGTCGTCGTTTTGATGATTTTGATTTTAGGGGTTGGTGATTGAAGTT
Found at i:21163123 original size:20 final size:20
Alignment explanation
Indices: 21163098--21163163 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
21163088 CCAAGGGTCA
21163098 GTTTTACTATTAATTTCATG
1 GTTTTACTATTAATTTCATG
* * **
21163118 GTTTTACCTCTTGAGGTCA--
1 GTTTTA-CTATTAATTTCATG
21163137 GTTTTACTATTAATTTCATG
1 GTTTTACTATTAATTTCATG
21163157 GTTTTAC
1 GTTTTAC
21163164 CTCTTGAGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
20 13 0.37
21 8 0.23
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (20 bp):
GTTTTACTATTAATTTCATG
Found at i:21163147 original size:39 final size:39
Alignment explanation
Indices: 21163093--21163172 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
21163083 AAGGTCCAAG
21163093 GGTCAGTTTTACTATTAATTTCATGGTTTTACCTCTTGA
1 GGTCAGTTTTACTATTAATTTCATGGTTTTACCTCTTGA
21163132 GGTCAGTTTTACTATTAATTTCATGGTTTTACCTCTTGA
1 GGTCAGTTTTACTATTAATTTCATGGTTTTACCTCTTGA
21163171 GG
1 GG
21163173 GGTGTGATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.47
Consensus pattern (39 bp):
GGTCAGTTTTACTATTAATTTCATGGTTTTACCTCTTGA
Found at i:21166568 original size:39 final size:38
Alignment explanation
Indices: 21166525--21166633 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 38
21166515 ACCAGCTCGA
* *
21166525 AGCCTGCAGGACTTTAGCCCGAACGTAATTCCAGCATAT
1 AGCCTGC-GGACTTAAGCCCGAACATAATTCCAGCATAT
* *
21166564 AGCCTGCGGACCTTAAGTCCGGACATAATTCCAGCATAT
1 AGCCTGCGGA-CTTAAGCCCGAACATAATTCCAGCATAT
* * *
21166603 AGCCTGCGGACCTTAAGTCCGGATATAATTC
1 AGCCTGCGGA-CTTAAGCCCGAACATAATTC
21166634 ATCACTGAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 3 0.05
39 61 0.95
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (38 bp):
AGCCTGCGGACTTAAGCCCGAACATAATTCCAGCATAT
Found at i:21170233 original size:118 final size:118
Alignment explanation
Indices: 21170019--21170265 Score: 440
Period size: 118 Copynumber: 2.1 Consensus size: 118
21170009 TTTTCCTTAA
*
21170019 TTTAACTTACATTCTAACTTTTTACTAAATTACCCTTTAATATAACTTATAAAATTACTAAATCA
1 TTTAA-TTACATTCTAACTTTTCACTAAATTACCCTTTAATATAACTTATAAAATTACTAAATCA
21170084 TGTCCATAAATGTCCATAATATAAGTATATGGTATAATTACCATCTAAGGAAGG
65 TGTCCATAAATGTCCATAATATAAGTATATGGTATAATTACCATCTAAGGAAGG
* *
21170138 TTTAATTACATTCTAACTTTTCACTAAATTTCCCTTTAATATAACTTATAAAATTACTAACTCAT
1 TTTAATTACATTCTAACTTTTCACTAAATTACCCTTTAATATAACTTATAAAATTACTAAATCAT
* *
21170203 GTCGATAAATGTCCATAATATAAGTATATGGTATAATTACCCTCTAAGGAAGG
66 GTCCATAAATGTCCATAATATAAGTATATGGTATAATTACCATCTAAGGAAGG
21170256 TTTAATTACA
1 TTTAATTACA
21170266 CAATTGGTCT
Statistics
Matches: 123, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
118 118 0.96
119 5 0.04
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (118 bp):
TTTAATTACATTCTAACTTTTCACTAAATTACCCTTTAATATAACTTATAAAATTACTAAATCAT
GTCCATAAATGTCCATAATATAAGTATATGGTATAATTACCATCTAAGGAAGG
Found at i:21175958 original size:23 final size:25
Alignment explanation
Indices: 21175932--21175996 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 25
21175922 TTTAATATAT
21175932 TATTGCTATTATTTTTATG-T-TTC
1 TATTGCTATTATTTTTATGTTATTC
*
21175955 TATT--TA-TATTTATTTTGTTATTC
1 TATTGCTATTATTT-TTATGTTATTC
*
21175978 TAATGCTATTATTATTTAT
1 TATTGCTATTATT-TTTAT
21175997 CTAATTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
20 5 0.16
21 6 0.19
22 1 0.03
23 10 0.31
25 2 0.06
26 7 0.22
27 1 0.03
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (25 bp):
TATTGCTATTATTTTTATGTTATTC
Found at i:21176009 original size:15 final size:14
Alignment explanation
Indices: 21175941--21176069 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 14
21175931 TTATTGCTAT
21175941 TATTTTTATGTT-TC
1 TATTTTTAT-TTATC
*
21175955 TATTTATATTTAT-
1 TATTTTTATTTATC
*
21175968 T-TTGTTATTCTAATGC
1 TATTTTTATT-T-AT-C
*
21175984 TATTATTATTTATC
1 TATTTTTATTTATC
21175998 TAATTTTTATTTATC
1 T-ATTTTTATTTATC
* *
21176013 TATTTATATTTCTAC
1 TATTTTTATTTAT-C
*
21176028 TATTATTATATT-TC
1 TATTTTTAT-TTATC
*
21176042 TATTTATTATATT-TT
1 TATTT-TTAT-TTATC
*
21176057 TATTTCTATTTAT
1 TATTTTTATTTAT
21176070 ATACTAATAT
Statistics
Matches: 92, Mismatches: 12, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
12 6 0.07
13 6 0.07
14 32 0.35
15 37 0.40
16 4 0.04
17 7 0.08
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (14 bp):
TATTTTTATTTATC
Found at i:21176022 original size:29 final size:28
Alignment explanation
Indices: 21175941--21176048 Score: 78
Period size: 29 Copynumber: 3.8 Consensus size: 28
21175931 TTATTGCTAT
*
21175941 TATTTTTATGTTTCTATTTATATTTAT-
1 TATTTTTATATTTCTATTTATATTTATC
* * * *
21175968 TTTGTTATTCTAATGCTA-TTATTATTTATC
1 TAT-TT-TTATATTTCTATTTA-TATTTATC
*
21175998 TAATTTTTAT-TTATCTATTTATATTTCTAC
1 T-ATTTTTATATT-TCTATTTATATTTAT-C
*
21176028 TATTATTATATTTCTATTTAT
1 TATTTTTATATTTCTATTTAT
21176049 TATATTTTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
27 2 0.03
28 6 0.10
29 42 0.69
30 10 0.16
31 1 0.02
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (28 bp):
TATTTTTATATTTCTATTTATATTTATC
Found at i:21176054 original size:23 final size:24
Alignment explanation
Indices: 21176025--21176095 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 24
21176015 TTTATATTTC
21176025 TACTATTATTATATTTCTATTTAT
1 TACTATTATTATATTTCTATTTAT
21176049 TA-TATT-TT-TATTTCTATTTAT
1 TACTATTATTATATTTCTATTTAT
*
21176070 ATACTAATATTAT-TTTC-A-TTAT
1 -TACTATTATTATATTTCTATTTAT
21176092 TACT
1 TACT
21176096 TTTTTCCTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
21 17 0.40
22 8 0.19
23 8 0.19
24 8 0.19
25 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (24 bp):
TACTATTATTATATTTCTATTTAT
Found at i:21181143 original size:19 final size:20
Alignment explanation
Indices: 21181119--21181165 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
21181109 TTGTGAAACT
* *
21181119 TAATGCACATG-ATGTGATG
1 TAATGCAAATGCATGAGATG
21181138 TAATGCAAATGCATGAGATG
1 TAATGCAAATGCATGAGATG
21181158 -AATGCAAA
1 TAATGCAAA
21181166 ACTAAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (20 bp):
TAATGCAAATGCATGAGATG
Found at i:21184671 original size:16 final size:17
Alignment explanation
Indices: 21184650--21184688 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
21184640 GAATGATATT
21184650 AATAAAGG-CGA-GAATA
1 AATAAAGGCCGATG-ATA
21184666 AATAAAGGCCGATGATA
1 AATAAAGGCCGATGATA
21184683 AATAAA
1 AATAAA
21184689 ATGAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 12 0.57
18 1 0.05
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (17 bp):
AATAAAGGCCGATGATA
Found at i:21185076 original size:3 final size:3
Alignment explanation
Indices: 21185068--21185190 Score: 72
Period size: 3 Copynumber: 41.0 Consensus size: 3
21185058 AATGATATGG
* * * * * *
21185068 TAA TAA TAA TAG TGA TAA T-A CAA TAA TAA AAA TAA -AG TAGA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* * * * *
21185112 TAA CAA TAA TAA TAA TAGA -AA AAA TAGA AAA TAG TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* * *
21185158 TAA AAA TAA TAT TAA TAA TAA TAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21185191 CAAAAATTAA
Statistics
Matches: 87, Mismatches: 27, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
2 3 0.03
3 80 0.92
4 4 0.05
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:21186428 original size:36 final size:37
Alignment explanation
Indices: 21186388--21186465 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 37
21186378 AATATAATAC
*** *
21186388 ATTTTACTTTTTTTTTAAA-TTCGATAAATATTTTGA
1 ATTTTACTTTTTTAAAAAATTTCGATAAACATTTTGA
*
21186424 ATTTT-GTTTTTTAAAAAATTTCGATAAACATTTTGA
1 ATTTTACTTTTTTAAAAAATTTCGATAAACATTTTGA
*
21186460 AATTTA
1 ATTTTA
21186466 TATATTTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
35 9 0.26
36 25 0.74
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (37 bp):
ATTTTACTTTTTTAAAAAATTTCGATAAACATTTTGA
Found at i:21188668 original size:22 final size:22
Alignment explanation
Indices: 21188643--21188691 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
21188633 AAATAATTAA
*
21188643 ATTAATTATTTTTAATATT-TTT
1 ATTAATAATTTTTAA-ATTATTT
21188665 ATT-ATAATTTTTAAATTAATTT
1 ATTAATAATTTTTAAATT-ATTT
21188687 ATTAA
1 ATTAA
21188692 ATAAAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 10 0.43
22 9 0.39
23 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTAATAATTTTTAAATTATTT
Found at i:21215940 original size:16 final size:16
Alignment explanation
Indices: 21215914--21215960 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
21215904 TTGCAGGACT
21215914 GAAGC-AAGAAAAATC
1 GAAGCAAAGAAAAATC
* *
21215929 GAAGCAAAGAAAGAGC
1 GAAGCAAAGAAAAATC
*
21215945 AAAGCAAAGCAAAAAT
1 GAAGCAAAG-AAAAAT
21215961 TGATCAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.62, C:0.13, G:0.21, T:0.04
Consensus pattern (16 bp):
GAAGCAAAGAAAAATC
Found at i:21220502 original size:16 final size:16
Alignment explanation
Indices: 21220476--21220522 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
21220466 TTGCAGGACT
21220476 GAAGC-AAGAAAAATC
1 GAAGCAAAGAAAAATC
* *
21220491 GAAGCAAAGAAAGAGC
1 GAAGCAAAGAAAAATC
*
21220507 AAAGCAAAGCAAAAAT
1 GAAGCAAAG-AAAAAT
21220523 TGATCAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.62, C:0.13, G:0.21, T:0.04
Consensus pattern (16 bp):
GAAGCAAAGAAAAATC
Found at i:21225348 original size:50 final size:52
Alignment explanation
Indices: 21225289--21225387 Score: 139
Period size: 50 Copynumber: 1.9 Consensus size: 52
21225279 TTAATAAAGT
* * *
21225289 CATGCATTATGTATCTCTCATGTAAGTT-AAGTTTGCATCA-TAAATTATGA
1 CATGAATTATGTAACTCCCATGTAAGTTAAAGTTTGCATCATTAAATTATGA
* *
21225339 CATGAATTATGTAACTCCCATGTTAGTTAAAGTTTGCATTATTAAATTA
1 CATGAATTATGTAACTCCCATGTAAGTTAAAGTTTGCATCATTAAATTA
21225388 AGTCTTGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 24 0.57
51 11 0.26
52 7 0.17
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (52 bp):
CATGAATTATGTAACTCCCATGTAAGTTAAAGTTTGCATCATTAAATTATGA
Found at i:21225405 original size:52 final size:50
Alignment explanation
Indices: 21225289--21225407 Score: 121
Period size: 50 Copynumber: 2.3 Consensus size: 50
21225279 TTAATAAAGT
* * * * *
21225289 CATGCATTATGTATCTCTCATGTAAGTTAAGTTTGCATCATAAATTATGA
1 CATGAATTAAGTAACTCCCATGTAAGTTAAGTTTGCATCATAAATTAAGA
* * * *
21225339 CATGAATTATGTAACTCCCATGTTAGTTAAAGTTTGCATTATTAAATTAAGT
1 CATGAATTAAGTAACTCCCATGTAAGTT-AAGTTTGCATCA-TAAATTAAGA
* *
21225391 CTTGTATTAAGTAACTC
1 CATGAATTAAGTAACTC
21225408 ATTTGTTCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 24 0.42
51 11 0.19
52 22 0.39
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (50 bp):
CATGAATTAAGTAACTCCCATGTAAGTTAAGTTTGCATCATAAATTAAGA
Found at i:21228568 original size:26 final size:25
Alignment explanation
Indices: 21228539--21228587 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
21228529 AAACCTTAAA
21228539 CCCTTATTT-CTCCCTTTTCTTTCTTT
1 CCCTT-TTTCCTCCC-TTTCTTTCTTT
*
21228565 CCCTTTTTCCTTCCTTTCTTTCT
1 CCCTTTTTCCTCCCTTTCTTTCT
21228588 CCCCTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (25 bp):
CCCTTTTTCCTCCCTTTCTTTCTTT
Found at i:21228769 original size:23 final size:23
Alignment explanation
Indices: 21228715--21228762 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
21228705 TAATAAATAA
* *
21228715 ATATATATGTATTACAAATGTAC
1 ATATGTATTTATTACAAATGTAC
* *
21228738 ATATGTATTTATTACACATTTAC
1 ATATGTATTTATTACAAATGTAC
21228761 AT
1 AT
21228763 TATTATTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (23 bp):
ATATGTATTTATTACAAATGTAC
Found at i:21228834 original size:8 final size:8
Alignment explanation
Indices: 21228821--21228859 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
21228811 TTTAATTAAT
21228821 ATAATATA
1 ATAATATA
21228829 ATAATATA
1 ATAATATA
21228837 ATAATATA
1 ATAATATA
21228845 ATAATATA
1 ATAATATA
*
21228853 ATGATAT
1 ATAATAT
21228860 TTACTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
ATAATATA
Found at i:21234453 original size:101 final size:101
Alignment explanation
Indices: 21234278--21234480 Score: 325
Period size: 101 Copynumber: 2.0 Consensus size: 101
21234268 TAGCAGAAAA
* * * *
21234278 GTTTGTTGGAAAACGATTTTTGCTCATATTGGATTATGTGTGGAATGAATACCATTACAAGTGGG
1 GTTTGTTGGAAAACGATTTTTGCTCATATTGGATTATGTGTGAAATGAATACCATGACAAATGAG
* *
21234343 ACAGACTGAAGCAACCGCTATGGAGTGGACGAAGAG
66 ACAGACTGAAGCAACCGCTACGGAATGGACGAAGAG
*
21234379 GTTTGTTGGGAAACGATTTTTGCTCATATTGGATTATGTGTGAAATGAATACCATGACAAATGAG
1 GTTTGTTGGAAAACGATTTTTGCTCATATTGGATTATGTGTGAAATGAATACCATGACAAATGAG
**
21234444 ACAGACTGAAGCAAGTGCTACGGAATGGACGAAGAG
66 ACAGACTGAAGCAACCGCTACGGAATGGACGAAGAG
21234480 G
1 G
21234481 AAGTGAAGTC
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 93 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (101 bp):
GTTTGTTGGAAAACGATTTTTGCTCATATTGGATTATGTGTGAAATGAATACCATGACAAATGAG
ACAGACTGAAGCAACCGCTACGGAATGGACGAAGAG
Found at i:21243455 original size:43 final size:43
Alignment explanation
Indices: 21243373--21243547 Score: 128
Period size: 43 Copynumber: 4.1 Consensus size: 43
21243363 GGTTTATCCA
** *
21243373 ATGATGCACTATGTGTGTCAGTATAACTGTTTCGGTTTA-TCTG
1 ATGATGCACTATGTGTGTCAGTATAACTCCTTCGATTTATTC-G
* *
21243416 ATGATGCATTATGTGTGTCAGTAT-TCATCCTTCGATTTATTCG
1 ATGATGCACTATGTGTGTCAGTATAAC-TCCTTCGATTTATTCG
* * * * *
21243459 ATGATGCACTA--TGCG-CCGATATAACTACTTTGGTTTA-TCTG
1 ATGATGCACTATGTGTGTCAG-TATAACTCCTTCGATTTATTC-G
* * ** * *
21243500 ATGATGCACTATGTGTGCCAATATATTTCCTTCAATTTATCCG
1 ATGATGCACTATGTGTGTCAGTATAACTCCTTCGATTTATTCG
21243543 ATGAT
1 ATGAT
21243548 ACAATGCTGT
Statistics
Matches: 101, Mismatches: 22, Indels: 18
0.72 0.16 0.13
Matches are distributed among these distances:
40 4 0.04
41 27 0.27
42 2 0.02
43 64 0.63
44 4 0.04
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (43 bp):
ATGATGCACTATGTGTGTCAGTATAACTCCTTCGATTTATTCG
Found at i:21245264 original size:19 final size:19
Alignment explanation
Indices: 21245216--21245272 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
21245206 GATATATATA
21245216 AATAAT-TAATAAATAT-AT
1 AATAATATAA-AAATATAAT
21245234 AATACA-AGTAAAAATATAAT
1 AATA-ATA-TAAAAATATAAT
*
21245254 AATAATATAAAAAAATAAT
1 AATAATATAAAAATATAAT
21245273 GATGTAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
18 4 0.12
19 19 0.58
20 10 0.30
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AATAATATAAAAATATAAT
Done.