Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 56 of 145
Found at i:19480995 original size:136 final size:137
Alignment explanation
Indices: 19480816--19481088 Score: 539
Period size: 136 Copynumber: 2.0 Consensus size: 137
19480806 CACTCGCCCT
19480816 ATCTTACATAATAATAATAATAATAATAATAATAATAATAATAATAAACTCAAGTTAAAAATTTA
1 ATCTTACATAATAATAATAATAATAATAATAATAATAATAATAATAAACTCAAGTTAAAAATTTA
19480881 AGATTATTGTTACCAATTGTTTTTAACATCGTAGGAATTTGGAGTCAATTTTACAGTCAACACTC
66 AGATTATTGTTACCAATTGTTTTTAACATCGTAGGAATTTGGAGTCAATTTTACAGTCAACACTC
19480946 GACATGA
131 GACATGA
19480953 ATCTTACAT-ATAATAATAATAATAATAATAATAATAATAATAATAAACTCAAGTTAAAAATTTA
1 ATCTTACATAATAATAATAATAATAATAATAATAATAATAATAATAAACTCAAGTTAAAAATTTA
19481017 AGATTATTGTTACCAATTGTTTTTAACATCGTAGGAATTTGGAGTCAATTTTACAGTCAACACTC
66 AGATTATTGTTACCAATTGTTTTTAACATCGTAGGAATTTGGAGTCAATTTTACAGTCAACACTC
19481082 GACATGA
131 GACATGA
19481089 CATGTCCACA
Statistics
Matches: 136, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
136 127 0.93
137 9 0.07
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (137 bp):
ATCTTACATAATAATAATAATAATAATAATAATAATAATAATAATAAACTCAAGTTAAAAATTTA
AGATTATTGTTACCAATTGTTTTTAACATCGTAGGAATTTGGAGTCAATTTTACAGTCAACACTC
GACATGA
Found at i:19482623 original size:3 final size:3
Alignment explanation
Indices: 19482615--19482639 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19482605 CCACACACTG
19482615 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
19482640 TGTCCTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19495098 original size:26 final size:26
Alignment explanation
Indices: 19495069--19495118 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
19495059 AAAGATTGTT
*
19495069 AAAACTCTTTTAAAAG-AAACTCAAGA
1 AAAACTC-TTGAAAAGAAAACTCAAGA
*
19495095 AAAATTCTTGAAAAGAAAACTCAA
1 AAAACTCTTGAAAAGAAAACTCAA
19495119 AGAGAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.56, C:0.14, G:0.08, T:0.22
Consensus pattern (26 bp):
AAAACTCTTGAAAAGAAAACTCAAGA
Found at i:19495220 original size:85 final size:86
Alignment explanation
Indices: 19495117--19495287 Score: 335
Period size: 85 Copynumber: 2.0 Consensus size: 86
19495107 AAGAAAACTC
19495117 AAAGAGAATTTATTAACTCAAAAAAGAAGTTGAATAATAATGAATTAAATGATTTGTGCACAATG
1 AAAGAGAATTTATTAACTCAAAAAAGAAGTTGAATAATAATGAATTAAATGATTTGTGCACAATG
19495182 CAAAGGCCTATATATAGGCTA
66 CAAAGGCCTATATATAGGCTA
19495203 AAAGAGAA-TTATTAACTCAAAAAAGAAGTTGAATAATAATGAATTAAATGATTTGTGCACAATG
1 AAAGAGAATTTATTAACTCAAAAAAGAAGTTGAATAATAATGAATTAAATGATTTGTGCACAATG
19495267 CAAAGGCCTATATATAGGCTA
66 CAAAGGCCTATATATAGGCTA
19495288 TCTAAATAAA
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 77 0.91
86 8 0.09
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.27
Consensus pattern (86 bp):
AAAGAGAATTTATTAACTCAAAAAAGAAGTTGAATAATAATGAATTAAATGATTTGTGCACAATG
CAAAGGCCTATATATAGGCTA
Found at i:19501505 original size:21 final size:21
Alignment explanation
Indices: 19501479--19501518 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19501469 GTTCTTAGAT
19501479 AAATTAGTTTAGTAATTTTGA
1 AAATTAGTTTAGTAATTTTGA
19501500 AAATTAGTTTAGTAATTTT
1 AAATTAGTTTAGTAATTTT
19501519 AGATTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
AAATTAGTTTAGTAATTTTGA
Found at i:19501764 original size:5 final size:6
Alignment explanation
Indices: 19501748--19501789 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
19501738 TAATTTAGCC
* *
19501748 ATTTTT ATTTTT ATTTTT ATTTTTT AGTTTA ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT A-TTTTT ATTTTT ATTTTT ATTTT
19501790 CTAATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:19501771 original size:19 final size:19
Alignment explanation
Indices: 19501749--19501789 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
19501739 AATTTAGCCA
* *
19501749 TTTTTATTTTTATTTTTAT
1 TTTTTAGTTTAATTTTTAT
19501768 TTTTTAGTTTAATTTTTAT
1 TTTTTAGTTTAATTTTTAT
19501787 TTT
1 TTT
19501790 CTAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTAGTTTAATTTTTAT
Found at i:19528593 original size:25 final size:26
Alignment explanation
Indices: 19528558--19528621 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
19528548 TTTCAAATTC
19528558 ATAT-TTTTATAA-TATATATTATA-G
1 ATATATTTTATAATTAT-TATTATAGG
* *
19528582 ATATATTTTATAATTATTTTTCTAGG
1 ATATATTTTATAATTATTATTATAGG
19528608 A-ATATTTTATAATT
1 ATATATTTTATAATT
19528622 TCATAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 4 0.11
25 26 0.74
26 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (26 bp):
ATATATTTTATAATTATTATTATAGG
Found at i:19528599 original size:11 final size:12
Alignment explanation
Indices: 19528558--19528601 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 12
19528548 TTTCAAATTC
19528558 ATAT-TTTTATA
1 ATATATTTTATA
*
19528569 ATATATATTATA
1 ATATATTTTATA
19528581 GATATATTTTATA
1 -ATATATTTTATA
19528594 AT-TATTTT
1 ATATATTTT
19528602 TCTAGGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.34
12 8 0.28
13 11 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
ATATATTTTATA
Found at i:19531031 original size:26 final size:26
Alignment explanation
Indices: 19531000--19531050 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
19530990 CATTGAAGTT
* * *
19531000 TGGTTTATCTTTTTACATGCATGAAG
1 TGGTTTATATTTATACACGCATGAAG
19531026 TGGTTTATATTTATACACGCATGAA
1 TGGTTTATATTTATACACGCATGAA
19531051 ATCATAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (26 bp):
TGGTTTATATTTATACACGCATGAAG
Found at i:19542692 original size:30 final size:31
Alignment explanation
Indices: 19542656--19542727 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 31
19542646 GTTATTATAG
*
19542656 TAATTTTTTTAAAATTTTAAAT-TA-AATTAA
1 TAATTTTTTTAAAATTTAAAATATATAA-TAA
**
19542686 TAA-TTTTAAAAAATTTAAAATATATAATAA
1 TAATTTTTTTAAAATTTAAAATATATAATAA
19542716 TAATTTTGTTTA
1 TAATTTT-TTTA
19542728 TTTAATCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
29 15 0.45
30 11 0.33
31 5 0.15
32 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (31 bp):
TAATTTTTTTAAAATTTAAAATATATAATAA
Found at i:19543046 original size:108 final size:110
Alignment explanation
Indices: 19542917--19543134 Score: 422
Period size: 108 Copynumber: 2.0 Consensus size: 110
19542907 TTGTACTTTT
19542917 ATATTATTTTTAAGTAAAACAATTAAAAATTACAAGTCTTAGAATTAAAGGCATGTTCAATAATA
1 ATATTATTTTTAAGTAAAACAATTAAAAATTACAAGTCTTAGAATTAAAGGCATGTTCAATAATA
19542982 TTAAAATATAAATTTATTATCATTCCACTTTTATATATTATTTAA
66 TTAAAATATAAATTTATTATCATTCCACTTTTATATATTATTTAA
19543027 ATATTA-TTTT-AGTAAAACAATTAAAAATTACAAGTCTTAGAATTAAAGGCATGTTCAATAATA
1 ATATTATTTTTAAGTAAAACAATTAAAAATTACAAGTCTTAGAATTAAAGGCATGTTCAATAATA
19543090 TTAAAATATAAATTTATTATCATTCCACTTTTATATATTATTTAA
66 TTAAAATATAAATTTATTATCATTCCACTTTTATATATTATTTAA
19543135 TAAATTTTAA
Statistics
Matches: 108, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
108 98 0.91
109 4 0.04
110 6 0.06
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (110 bp):
ATATTATTTTTAAGTAAAACAATTAAAAATTACAAGTCTTAGAATTAAAGGCATGTTCAATAATA
TTAAAATATAAATTTATTATCATTCCACTTTTATATATTATTTAA
Found at i:19548218 original size:15 final size:15
Alignment explanation
Indices: 19548194--19548250 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
19548184 ACATAAATTT
19548194 GTTTTATTTTCATTA
1 GTTTTATTTTCATTA
* * *
19548209 GTTTTGTTTTTTATTTT
1 GTTTT-ATTTTCA-TTA
19548226 GTTTTATTTTCATTA
1 GTTTTATTTTCATTA
*
19548241 GTTTTGTTTT
1 GTTTTATTTT
19548251 TTTATTATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 16 0.48
16 10 0.30
17 7 0.21
ACGTcount: A:0.12, C:0.04, G:0.11, T:0.74
Consensus pattern (15 bp):
GTTTTATTTTCATTA
Found at i:19548232 original size:32 final size:32
Alignment explanation
Indices: 19548191--19548252 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
19548181 GATACATAAA
19548191 TTTGTTTTATTTTCATTAGTTTTGTTTTTTAT
1 TTTGTTTTATTTTCATTAGTTTTGTTTTTTAT
19548223 TTTGTTTTATTTTCATTAGTTTTGTTTTTT
1 TTTGTTTTATTTTCATTAGTTTTGTTTTTT
19548253 TATTATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.11, C:0.03, G:0.10, T:0.76
Consensus pattern (32 bp):
TTTGTTTTATTTTCATTAGTTTTGTTTTTTAT
Found at i:19548251 original size:16 final size:16
Alignment explanation
Indices: 19548200--19548251 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
19548190 ATTTGTTTTA
19548200 TTTTCATTAGTTTTGT
1 TTTTCATTAGTTTTGT
* * *
19548216 TTTTTATTTTGTTTT-A
1 TTTTCA-TTAGTTTTGT
19548232 TTTTCATTAGTTTTGT
1 TTTTCATTAGTTTTGT
19548248 TTTT
1 TTTT
19548252 TTATTATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 7 0.25
16 14 0.50
17 7 0.25
ACGTcount: A:0.12, C:0.04, G:0.10, T:0.75
Consensus pattern (16 bp):
TTTTCATTAGTTTTGT
Found at i:19548258 original size:26 final size:29
Alignment explanation
Indices: 19548191--19548261 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 29
19548181 GATACATAAA
*
19548191 TTTGTTTTATTTTCATTAGTTTTGTTTTTTAT
1 TTTGTATTATTTTCATTAGTTTTG---TTTAT
*
19548223 TTTGTTTTATTTTCATTAGTTTTG-TT-T
1 TTTGTATTATTTTCATTAGTTTTGTTTAT
19548250 TTT-TATTATTTT
1 TTTGTATTATTTT
19548262 ACTATTTTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 8 0.21
27 4 0.11
28 2 0.05
32 24 0.63
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.76
Consensus pattern (29 bp):
TTTGTATTATTTTCATTAGTTTTGTTTAT
Found at i:19552499 original size:94 final size:94
Alignment explanation
Indices: 19552338--19552549 Score: 291
Period size: 94 Copynumber: 2.3 Consensus size: 94
19552328 TAAAACCATA
* * *
19552338 AATCCTATACCCCTAAAGTTACAGTGGGATGAATTGAAGCCATCATGACGAATCTTATCTCCCTG
1 AATCCTATACCCCTAAAGTTGCAGTGGGATGAATTAAAGCCATCATGACGAATATTATCTCCCTG
* *
19552403 AAGTTGCAGTGGAGCAGATTGAAGCCACT
66 AAGATGCAGTGGAGCAGACTGAAGCCACT
* * **
19552432 AATCCTATACCCCTAAAGTTGCAGTGGGATGGATTAAAGTCATCATGGTGAATATTATCTCCCTG
1 AATCCTATACCCCTAAAGTTGCAGTGGGATGAATTAAAGCCATCATGACGAATATTATCTCCCTG
*
19552497 AAGATGCAGTGGAGTAGACTGAAGCCACT
66 AAGATGCAGTGGAGCAGACTGAAGCCACT
* * *
19552526 -AGCCTTATATCCCTGAAGTTGCAG
1 AATCC-TATACCCCTAAAGTTGCAG
19552550 CGGAGCAACT
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
93 3 0.03
94 101 0.97
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (94 bp):
AATCCTATACCCCTAAAGTTGCAGTGGGATGAATTAAAGCCATCATGACGAATATTATCTCCCTG
AAGATGCAGTGGAGCAGACTGAAGCCACT
Found at i:19552749 original size:143 final size:143
Alignment explanation
Indices: 19552486--19552843 Score: 506
Period size: 143 Copynumber: 2.5 Consensus size: 143
19552476 ATGGTGAATA
* * * * * * *
19552486 TTATCTCCCTGAAGATGCAGTGGAGTAGACTGAAGCCACTAGCCTTATATCCCTGAAGTTGCAGC
1 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCCTGAAGTTGTAGT
*
19552551 GGAGCA-ACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTACAA
66 GGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAAATTAAAGCTACAA
19552615 ATTAT-GACGGATC
131 ATTATGGA-GGATC
* * * *
19552628 TTATCTTCCTAAAGTTGCAGTGGAGCAGATTTAAGCCACTGGCCTTATCTCCCTGAAATTGTAGT
1 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCCTGAAGTTGTAGT
* *
19552693 GGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAGATTAAAGTTACAA
66 GGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAAATTAAAGCTACAA
19552758 ATTATGGAGGATC
131 ATTATGGAGGATC
* * * * *
19552771 TTATCTTCTTGAAGTTGCAGTGGAGCATATTGAAGCCACCAATCC-TATCTCCCTGAAGTTATAG
1 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CTAGCCTTATCTCCCTGAAGTTGTAG
19552835 TGGAGCAGA
65 TGGAGCAGA
19552844 TTAAAACGGT
Statistics
Matches: 190, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
142 60 0.32
143 125 0.66
144 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (143 bp):
TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCCTGAAGTTGTAGT
GGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAAATTAAAGCTACAA
ATTATGGAGGATC
Found at i:19553150 original size:18 final size:20
Alignment explanation
Indices: 19553127--19553169 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
19553117 CTGGGCCCAA
*
19553127 CAAAAT-AA-ATTACAAAGC
1 CAAAATAAACATTACAAACC
19553145 CAAAATAAACATTACAAACC
1 CAAAATAAACATTACAAACC
19553165 CAAAA
1 CAAAA
19553170 ATTAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 2 0.09
20 14 0.64
ACGTcount: A:0.63, C:0.21, G:0.02, T:0.14
Consensus pattern (20 bp):
CAAAATAAACATTACAAACC
Found at i:19553343 original size:16 final size:17
Alignment explanation
Indices: 19553316--19553349 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
19553306 CACACAAAGC
19553316 AGCAATAGAGAAACAAT
1 AGCAATAGAGAAACAAT
*
19553333 AGCAA-AGAGAAATAAT
1 AGCAATAGAGAAACAAT
19553349 A
1 A
19553350 AACAATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.62, C:0.09, G:0.18, T:0.12
Consensus pattern (17 bp):
AGCAATAGAGAAACAAT
Found at i:19555617 original size:21 final size:21
Alignment explanation
Indices: 19555593--19555632 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
19555583 ATATACATGG
*
19555593 ATTGCTACGTAGATGACAGGT
1 ATTGCCACGTAGATGACAGGT
19555614 ATTGCCACGTAGATGACAG
1 ATTGCCACGTAGATGACAG
19555633 ATCAATATTT
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:0.17, G:0.28, T:0.25
Consensus pattern (21 bp):
ATTGCCACGTAGATGACAGGT
Found at i:19559177 original size:13 final size:13
Alignment explanation
Indices: 19559145--19559170 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19559135 TTTTACCTTC
19559145 TGTTTTTTTATTT
1 TGTTTTTTTATTT
19559158 TGTTTTTTTATTT
1 TGTTTTTTTATTT
19559171 ATTTTTTAAA
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:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (13 bp):
TGTTTTTTTATTT
Found at i:19559951 original size:30 final size:28
Alignment explanation
Indices: 19559889--19559964 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 28
19559879 TTGTTGTTGT
* *
19559889 TATTATAATTATTATTATTACTACTTTC
1 TATTATTATTAATATTATTACTACTTTC
19559917 -ATTATTATTAATATTATTACTA-TTACTGC
1 TATTATTATTAATATTATTACTACTT--T-C
19559946 TATTATTGA-TAATATTATT
1 TATTATT-ATTAATATTATT
19559965 TGCTTATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 2 0.05
27 20 0.49
28 1 0.02
29 1 0.02
30 16 0.39
31 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (28 bp):
TATTATTATTAATATTATTACTACTTTC
Found at i:19560043 original size:29 final size:28
Alignment explanation
Indices: 19560010--19560073 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
19560000 TATTAACATC
*
19560010 TTTAATTCATTTCAACTTATTTTAATAT
1 TTTAATTCATTTAAACTTATTTTAATAT
* *
19560038 TGTTAATTTATTTAAATTTATTTTAATAT
1 T-TTAATTCATTTAAACTTATTTTAATAT
19560067 TTTAATT
1 TTTAATT
19560074 TACATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 7 0.22
29 25 0.78
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTAATTCATTTAAACTTATTTTAATAT
Found at i:19560088 original size:29 final size:29
Alignment explanation
Indices: 19560026--19560089 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
19560016 TCATTTCAAC
**
19560026 TTATTTTAATATTGTTAATTTATTTAAAT
1 TTATTTTAATATTGTTAATTTACATAAAT
*
19560055 TTATTTTAATATT-TTAATTTACATATAT
1 TTATTTTAATATTGTTAATTTACATAAAT
19560083 TATATTT
1 T-TATTT
19560090 ATTTCTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (29 bp):
TTATTTTAATATTGTTAATTTACATAAAT
Found at i:19560090 original size:28 final size:29
Alignment explanation
Indices: 19560026--19560090 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
19560016 TCATTTCAAC
**
19560026 TTAT-TTTAATATTGTTAATTTATTTAAA
1 TTATATTTAATATTGTTAATTTACATAAA
*
19560054 TT-TATTTTAATATT-TTAATTTACATATA
1 TTATA-TTTAATATTGTTAATTTACATAAA
19560082 TTATATTTA
1 TTATATTTA
19560091 TTTCTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
28 19 0.61
29 11 0.35
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (29 bp):
TTATATTTAATATTGTTAATTTACATAAA
Found at i:19563978 original size:15 final size:17
Alignment explanation
Indices: 19563958--19563989 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
19563948 TGAAAAAGTT
19563958 GAAAAT-AATT-TTTCA
1 GAAAATCAATTCTTTCA
19563973 GAAAATCAATTCTTTCA
1 GAAAATCAATTCTTTCA
19563990 ATCAAACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (17 bp):
GAAAATCAATTCTTTCA
Found at i:19565502 original size:25 final size:24
Alignment explanation
Indices: 19565433--19565503 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 24
19565423 AATTTTCTCG
19565433 AAATTTTACCGATGGTAAAATCGTCA
1 AAATTTTA-CGAT-GTAAAATCGTCA
* * *
19565459 AAATTTTACTAGGGGAAAATCGTCA
1 AAATTTTACGA-TGTAAAATCGTCA
19565484 AAATTTTATCGATGTAAAAT
1 AAATTTTA-CGATGTAAAAT
19565504 TGTGATGAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
25 27 0.73
26 10 0.27
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (24 bp):
AAATTTTACGATGTAAAATCGTCA
Found at i:19566941 original size:8 final size:8
Alignment explanation
Indices: 19566928--19566957 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
19566918 AAAAATAGGG
19566928 CCCAAAAA
1 CCCAAAAA
19566936 CCCAAAAA
1 CCCAAAAA
19566944 CCCAAAAA
1 CCCAAAAA
19566952 CCCAAA
1 CCCAAA
19566958 CCTTAAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (8 bp):
CCCAAAAA
Found at i:19568147 original size:11 final size:12
Alignment explanation
Indices: 19568133--19568161 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
19568123 TTAATTAATA
19568133 ATATTATTATT-
1 ATATTATTATTG
19568144 ATATTATTATTG
1 ATATTATTATTG
19568156 ATATTA
1 ATATTA
19568162 CAATCAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
ATATTATTATTG
Found at i:19568834 original size:8 final size:8
Alignment explanation
Indices: 19568821--19568894 Score: 84
Period size: 8 Copynumber: 9.4 Consensus size: 8
19568811 AGACTAAAAA
19568821 AAAAAATC
1 AAAAAATC
19568829 AAAAAAATC
1 -AAAAAATC
19568838 AAAAAATC
1 AAAAAATC
19568846 AAAAAAAATC
1 --AAAAAATC
19568856 AAAAAATC
1 AAAAAATC
19568864 -AAAAAT-
1 AAAAAATC
19568870 -AAAAATC
1 AAAAAATC
*
19568877 -AAAAATA
1 AAAAAATC
19568884 AAAAAATC
1 AAAAAATC
19568892 AAA
1 AAA
19568895 GTCAAAAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
6 6 0.10
7 12 0.20
8 25 0.42
9 8 0.14
10 8 0.14
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATC
Found at i:19568834 original size:10 final size:10
Alignment explanation
Indices: 19568819--19568861 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
19568809 TCAGACTAAA
19568819 AAAAAAAATC
1 AAAAAAAATC
19568829 -AAAAAAATC
1 AAAAAAAATC
19568838 --AAAAAATC
1 AAAAAAAATC
19568846 AAAAAAAATC
1 AAAAAAAATC
19568856 AAAAAA
1 AAAAAA
19568862 TCAAAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.26
9 9 0.29
10 14 0.45
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:19568843 original size:18 final size:18
Alignment explanation
Indices: 19568820--19568894 Score: 77
Period size: 18 Copynumber: 4.2 Consensus size: 18
19568810 CAGACTAAAA
19568820 AAAAAAATCAAAAAAATC
1 AAAAAAATCAAAAAAATC
19568838 -AAAAAATCAAAAAAAATC
1 AAAAAAATC-AAAAAAATC
*
19568856 -AAAAAATCAAAAATAA-A
1 AAAAAAATCAAAAA-AATC
19568873 AATCAAAAAT-AAAAAAATC
1 AA--AAAAATCAAAAAAATC
19568892 AAA
1 AAA
19568895 GTCAAAAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
17 14 0.29
18 22 0.45
19 7 0.14
20 6 0.12
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAAAAATCAAAAAAATC
Found at i:19568854 original size:27 final size:28
Alignment explanation
Indices: 19568817--19568894 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
19568807 GTTCAGACTA
19568817 AAAAAAAAAATCAAAAAAATCAAAAAAT
1 AAAAAAAAAATCAAAAAAATCAAAAAAT
*
19568845 -CAAAAAAAATC-AAAAAATC-AAAAAT
1 AAAAAAAAAATCAAAAAAATCAAAAAAT
19568870 AAAAATCAAAAAT-AAAAAAATCAAA
1 AAAAA--AAAAATCAAAAAAATCAAA
19568895 GTCAAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
25 6 0.14
26 11 0.26
27 10 0.23
28 14 0.33
29 2 0.05
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (28 bp):
AAAAAAAAAATCAAAAAAATCAAAAAAT
Found at i:19568886 original size:6 final size:7
Alignment explanation
Indices: 19568849--19568903 Score: 60
Period size: 7 Copynumber: 7.9 Consensus size: 7
19568839 AAAAATCAAA
19568849 AAAAATC
1 AAAAATC
19568856 AAAAAATC
1 -AAAAATC
19568864 AAAAAT-
1 AAAAATC
19568870 AAAAATC
1 AAAAATC
*
19568877 AAAAATAA
1 AAAAAT-C
19568885 AAAAATC
1 AAAAATC
*
19568892 -AAAGTC
1 AAAAATC
19568898 AAAAAT
1 AAAAAT
19568904 AGGAGAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 11 0.28
7 16 0.40
8 13 0.32
ACGTcount: A:0.75, C:0.09, G:0.02, T:0.15
Consensus pattern (7 bp):
AAAAATC
Found at i:19568888 original size:21 final size:22
Alignment explanation
Indices: 19568849--19568904 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
19568839 AAAAATCAAA
*
19568849 AAAAATCAAAAA-ATCAAAAAT
1 AAAAATCAAAAATATAAAAAAT
19568870 AAAAATCAAAAATA-AAAAAAT
1 AAAAATCAAAAATATAAAAAAT
* *
19568891 CAAAGTCAAAAATA
1 AAAAATCAAAAATA
19568905 GGAGAAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.75, C:0.09, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAAATCAAAAATATAAAAAAT
Found at i:19568903 original size:28 final size:28
Alignment explanation
Indices: 19568822--19568894 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
19568812 GACTAAAAAA
*
19568822 AAAAATCAAAAAAATCAAAAAATCAAAA--
1 AAAAAT-AAAAAAATC-AAAAATAAAAATC
**
19568850 AAAATCAAAA-AATCAAAAATAAAAATC
1 AAAAATAAAAAAATCAAAAATAAAAATC
19568877 AAAAATAAAAAAATCAAA
1 AAAAATAAAAAAATCAAA
19568895 GTCAAAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
25 10 0.27
26 4 0.11
27 12 0.32
28 11 0.30
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (28 bp):
AAAAATAAAAAAATCAAAAATAAAAATC
Found at i:19568916 original size:6 final size:6
Alignment explanation
Indices: 19568907--19568948 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
19568897 CAAAAATAGG
*
19568907 AGAAAA AGAAAA A-AAAG A-AAAA AGAAAA AGAAAA AGAAAA AG
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AG
19568949 GAGAGGTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 8 0.24
6 25 0.76
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:19569136 original size:23 final size:23
Alignment explanation
Indices: 19569110--19569163 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
19569100 GATCATTAAT
19569110 TACTTCATCAAATGGATAGAGGC
1 TACTTCATCAAATGGATAGAGGC
19569133 TACTTCATCAAATGGATAGAGGC
1 TACTTCATCAAATGGATAGAGGC
19569156 TACTTCAT
1 TACTTCAT
19569164 GGATCAAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (23 bp):
TACTTCATCAAATGGATAGAGGC
Found at i:19569833 original size:7 final size:8
Alignment explanation
Indices: 19569816--19569848 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
19569806 TGAAAAAATG
19569816 AATGAAAA
1 AATGAAAA
19569824 AATG-AAA
1 AATGAAAA
19569831 AATGAAAAA
1 AATG-AAAA
19569840 AATGAAAA
1 AATGAAAA
19569848 A
1 A
19569849 GTAAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.30
8 9 0.39
9 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AATGAAAA
Found at i:19569841 original size:16 final size:15
Alignment explanation
Indices: 19569816--19569861 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
19569806 TGAAAAAATG
19569816 AATGAAAAAATGAAA
1 AATGAAAAAATGAAA
19569831 AATGAAAAAAATGAAA
1 AATG-AAAAAATGAAA
*
19569847 AA-GTAAAAATAGAAA
1 AATGAAAAAAT-GAAA
19569862 GGCTAAAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 6 0.21
15 9 0.32
16 13 0.46
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AATGAAAAAATGAAA
Found at i:19571053 original size:46 final size:46
Alignment explanation
Indices: 19570991--19571594 Score: 872
Period size: 46 Copynumber: 13.1 Consensus size: 46
19570981 ACAGATCAAT
*
19570991 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * * *
19571037 GATGATAGCAGATCTTGTCTTCCTATAATTGGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
**
19571083 GAAGATAGCAGATCTTGTCTTTTTGTATTTGGCAGCGGAAGG-GATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGG-AGGAGATC
* *
19571129 AAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * *
19571175 GAAGATAGCAGATCTTATTTTCCTGTAATTGGCAGCGGAAGG-GATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGG-AGGAGATC
* *
19571221 GAAGATAGCAAATCTTGTCTTCCTGTATTTGGCAGCGAAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * *
19571267 GAAGATAGCAGATCTTGTCTTCTTGTATTTGGCAGCGGAAGAGGTC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* *
19571313 GAAGGTAGCAGATCTTGTCTTCCTGTATTTGGCAACGGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * *
19571359 GAAGATAGCAGATCTTGTTTTCCTGTATTTGACAGCGGAAGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * *
19571405 GAAGATAGTAGATCTTGTTTTCCTGTATTTGACAGCGGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
*
19571451 GAAGATAGCAGA-CATTGTCTTCCTGTATTTGGCAGCGGAGTAGATC
1 GAAGATAGCAGATC-TTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
*
19571497 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
* * * * *
19571543 GAAGATAGCAGATCTTGTCTTTCTGTATTTAGTAGTGGAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
19571589 GAAGAT
1 GAAGAT
19571595 GGTGAATCTT
Statistics
Matches: 501, Mismatches: 51, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
45 7 0.01
46 487 0.97
47 7 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.30
Consensus pattern (46 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
Found at i:19571931 original size:132 final size:125
Alignment explanation
Indices: 19571647--19571934 Score: 321
Period size: 126 Copynumber: 2.2 Consensus size: 125
19571637 GCCATTAGTC
*
19571647 CTATCACCCTAAGCAGTAGTGGAGCAAATCGAAAATGGTGAATCTTATCTTCCCAATACAAGTGG
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAAATGGTGAATCTTATCTTCCCAATACAAGTGG
* * ** *
19571712 AGTAAGTTAAAAATTACAGATCTTCCCTAAGCAGAGTGGGGTAGGTTGAAGATTGCAGATT
66 AGAAAGTTAAAAATTA-AGATCTTCCCTAAGCAGAGTGGAGTAGGTCAAAGACTGCAGATT
* *
19571773 CTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATAC-AGTGG
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAAATGGTGAATCTTATCTTCCCAATACAAGTGG
** * * *
19571837 AGAAGCAGATTTAAGCCATT-AG-TCCTATCACTCTAAGTAGTAGTGGAGTATGTCAAAGACTGT
66 AGAA--AG--TTAA-AAATTAAGAT-CT-TC-C-CTAAGCAG-AGTGGAGTAGGTCAAAGACTGC
19571900 AGATT
121 AGATT
* *
19571905 CTATCCCCCTAATCAGTAGTGGAGCAGATC
1 CTATCACCCTAAGCAGTAGTGGAGCAGATC
19571935 AACAATAACG
Statistics
Matches: 136, Mismatches: 16, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
125 8 0.06
126 56 0.41
127 3 0.02
128 4 0.03
129 6 0.04
130 4 0.03
131 7 0.05
132 48 0.35
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (125 bp):
CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAAATGGTGAATCTTATCTTCCCAATACAAGTGG
AGAAAGTTAAAAATTAAGATCTTCCCTAAGCAGAGTGGAGTAGGTCAAAGACTGCAGATT
Found at i:19573113 original size:11 final size:12
Alignment explanation
Indices: 19573099--19573127 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
19573089 TTAATTAATA
19573099 ATATTATTATT-
1 ATATTATTATTG
19573110 ATATTATTATTG
1 ATATTATTATTG
19573122 ATATTA
1 ATATTA
19573128 CAATCAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
ATATTATTATTG
Found at i:19575643 original size:19 final size:21
Alignment explanation
Indices: 19575610--19575649 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
19575600 AGATTTCAAC
19575610 CTTTGTCAATAATAT-CAAAA
1 CTTTGTCAATAATATACAAAA
*
19575630 CTTTGTTAAT-ATATACAAAA
1 CTTTGTCAATAATATACAAAA
19575650 AATATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
CTTTGTCAATAATATACAAAA
Found at i:19576004 original size:31 final size:32
Alignment explanation
Indices: 19575943--19576004 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 32
19575933 AAAATTCACA
* * *
19575943 ATATTTATATTACAAAAATGTATTAGGAATGC
1 ATATTTAAATTACAAAAATGTAATACGAATGC
19575975 ATATTTAAATTAC-AAAATGTAA-ATCGAATG
1 ATATTTAAATTACAAAAATGTAATA-CGAATG
19576005 AAAATACCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 1 0.04
31 13 0.50
32 12 0.46
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.35
Consensus pattern (32 bp):
ATATTTAAATTACAAAAATGTAATACGAATGC
Found at i:19579584 original size:126 final size:125
Alignment explanation
Indices: 19579178--19579744 Score: 689
Period size: 126 Copynumber: 4.5 Consensus size: 125
19579168 GATAAAATCA
* * * * * * *
19579178 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCGCGGCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
19579243 AGGTCCT-AGAAAAATAATTTCGACTTGACGTTTTTGAGCAAATAGTTTAAA-AACGCTTC
66 AGGTCCTGA-AAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTAAAACAACGCTTC
* * *
19579302 AAGTAAGATGCTTTATGAGAAGAATTTGT-AAATTCGCGCCCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAA-TCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * * * * *
19579366 TTGGTCCTGGAAGAAATAATTTCGAGTCGACGTTTTTGAGCAAATAGTTAAAAAAAACGCTTC
65 TAGGTCCT-GAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTT-AAAACAACGCTTC
* * * *
19579429 AAGCAGGATGATTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGTGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
19579494 GGGTCCTGAAAAAATAATTTTGAATTGACGTTCCTGAGCAAATAGTATAAAACAACGCTGC
66 AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGT-TAAAACAACGCTTC
* * * *
19579555 AAGCAGCATGCTATT-TGAGAAGAGTTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTACTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * * *
19579619 TAGGTCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAATAGTATAAATC-A--TTTC
65 TAGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGT-TAAAACAACGCTTC
* *
19579678 TAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACACGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
19579743 AG
66 AG
19579745 CATGTTTAGG
Statistics
Matches: 382, Mismatches: 52, Indels: 19
0.84 0.11 0.04
Matches are distributed among these distances:
122 2 0.01
123 62 0.16
124 58 0.15
125 36 0.09
126 150 0.39
127 72 0.19
128 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTAAAACAACGCTTC
Found at i:19582943 original size:22 final size:22
Alignment explanation
Indices: 19582891--19583365 Score: 506
Period size: 22 Copynumber: 22.0 Consensus size: 22
19582881 TCAAATTATA
*
19582891 TTTAAGTTAA-GGGTTAGGGCT
1 TTTAAGTTAAGGGGTTAGGGTT
* * *
19582912 TTTAATTTAATGGTTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
19582934 TTAAAGTTAA-GGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
19582955 TTTAAGTTAA-GGGTTAAGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* * *
19582976 TTTAGGTTAAGGGTTTATGAG-T
1 TTTAAGTTAAGGGGTTA-GGGTT
* * *
19582998 TTTAATTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* *
19583020 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* *
19583042 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* * *
19583064 TTAAAGTTAA-AGGTTAGTGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
19583085 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
19583107 TTTAAGTTAAGGGGTTAGGTTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
19583129 TTTAAGTTAA-GGGTTAGGATT
1 TTTAAGTTAAGGGGTTAGGGTT
19583150 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
19583172 TTTAAGTTAA-GGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
19583193 TTTAAGTTAA-GGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* ** *
19583214 TTTAGGTTAATAGTTTATGGG-T
1 TTTAAGTTAAGGGGTTA-GGGTT
* *
19583236 TTTAAGTTAAAGGTTTAGGG-T
1 TTTAAGTTAAGGGGTTAGGGTT
19583257 TTTAGAGTTAA-GGGTTAGGGTT
1 TTTA-AGTTAAGGGGTTAGGGTT
* *
19583279 TTTAGGTTAATGGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* *
19583301 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* * *
19583323 TTTAGGTTAAGGGTTTAGGATT
1 TTTAAGTTAAGGGGTTAGGGTT
* *
19583345 TTTAATTTAA-GGGTTAAGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
19583366 AGGGTTTTTA
Statistics
Matches: 394, Mismatches: 49, Indels: 22
0.85 0.11 0.05
Matches are distributed among these distances:
21 156 0.40
22 234 0.59
23 4 0.01
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (22 bp):
TTTAAGTTAAGGGGTTAGGGTT
Found at i:19582951 original size:43 final size:43
Alignment explanation
Indices: 19582891--19583359 Score: 574
Period size: 43 Copynumber: 10.8 Consensus size: 43
19582881 TCAAATTATA
* * *
19582891 TTTAAGTTAAGGGTTAGGGCTTTTAATTTAATGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
19582934 TTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
19582976 TTTAGGTTAAGGGTTTATGAG-TTTTAATTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGG-TTA-GGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
19583020 TTTAATTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
19583064 TTAAAGTTAAAGGTTAGTGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
19583107 TTTAAGTTAAGGGGTTAGGTTTTTTAAGTTAAGGG-TTAGGATT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
19583150 TTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* **
19583193 TTTAAGTTAAGGGTTAGGGTTTTTAGGTTAATAGTTTATGGG-T
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTA-GGGTT
*
19583236 TTTAAGTTAAAGGTTTAGGG-TTTTAGAGTTAAGGG-TTAGGGTT
1 TTTAAGTT-AAGGGTTAGGGTTTTTA-AGTTAAGGGTTTAGGGTT
* *
19583279 TTTAGGTTAATGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
19583323 TTTAGGTTAAGGGTTTAGGATTTTTAATTTAAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTT
19583360 AAGGTTAGGG
Statistics
Matches: 373, Mismatches: 39, Indels: 27
0.85 0.09 0.06
Matches are distributed among these distances:
42 44 0.12
43 191 0.51
44 138 0.37
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
Found at i:19583034 original size:65 final size:63
Alignment explanation
Indices: 19582891--19583365 Score: 576
Period size: 65 Copynumber: 7.3 Consensus size: 63
19582881 TCAAATTATA
* * *
19582891 TTTAAGTTAAGGGTTAGGGCTTTTAATTTAATGGTTTAGGGTTTTAAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTT-AAGTTAAGGGTTAGGGTT
* * * * *
19582955 TTTAAGTTAAGGGTTAAGGTTTTTAGGTTAAGGGTTTATGAGTTTTAATTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTA-GGGTTTTAAGTTAAGGG-TTAGGGTT
* * * *
19583020 TTTAATTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTAAAGTTAAAGGTTAGTGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTT-AAGTTAAGGGTTAGGGTT
* * *
19583085 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGGTTAGGTTTTTTAAGTTAAGGGTTAGGATT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGG-GTTTTAAGTTAAGGGTTAGGGTT
19583150 TTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG-TTTTAAGTTAAGGGTTAGGGTT
* * * *
19583214 TTTAGGTTAATAGTTTATGGG-TTTTAAGTTAAAGGTTTAGGGTTTTAGAGTTAAGGGTTAGGGT
1 TTTAAGTTAA-GGGTTA-GGGTTTTTAAGTTAAGGGTTTAGGGTTTTA-AGTTAAGGGTTAGGGT
19583278 T
63 T
* * * *
19583279 TTTAGGTTAATGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTAAGGGTTTAGGAT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGTTT-AGGGTTTTAAGTTAAGGG-TTAGGGT
19583344 T
63 T
* *
19583345 TTTAATTTAAGGGTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTT
19583366 AGGGTTTTTA
Statistics
Matches: 360, Mismatches: 38, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
64 102 0.28
65 198 0.55
66 60 0.17
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (63 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAGTTAAGGGTTAGGGTT
Found at i:19583353 original size:27 final size:27
Alignment explanation
Indices: 19583327--19583393 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
19583317 AAGGTTTTTA
19583327 GGTTAAGGGTTTAGGATTTTTAATTTAAG
1 GGTTAA-GG-TTAGGATTTTTAATTTAAG
* **
19583356 GGTTAAGGTTAGGGTTTTTAGGTTAAG
1 GGTTAAGGTTAGGATTTTTAATTTAAG
*
19583383 TGTTTAAGGTT
1 -GGTTAAGGTT
19583394 TGTCAATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 16 0.48
28 11 0.33
29 6 0.18
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (27 bp):
GGTTAAGGTTAGGATTTTTAATTTAAG
Found at i:19583678 original size:21 final size:21
Alignment explanation
Indices: 19583652--19583698 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
19583642 GCGGCGGTTG
* *
19583652 TGGTTCTTCCAGT-GGGGATTC
1 TGGTTCTCCCAGTAGGGCA-TC
19583673 TGGTTCTCCCAGTAGGGCATC
1 TGGTTCTCCCAGTAGGGCATC
19583694 TGGTT
1 TGGTT
19583699 GTCGGAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.11, C:0.21, G:0.32, T:0.36
Consensus pattern (21 bp):
TGGTTCTCCCAGTAGGGCATC
Found at i:19584823 original size:20 final size:20
Alignment explanation
Indices: 19584786--19584823 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19584776 TTTATTTTTA
*
19584786 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
19584806 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
19584824 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:19585822 original size:11 final size:11
Alignment explanation
Indices: 19585808--19585884 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
19585798 ATAAATATGG
19585808 ATTTGAGAGAA
1 ATTTGAGAGAA
*
19585819 ATTTTGA-AGGA
1 A-TTTGAGAGAA
19585830 ATTTGAGAGCAA
1 ATTTGAGAG-AA
19585842 A-TTGAGAGGAA
1 ATTTGAGA-GAA
19585853 ATTT-AGAAGAA
1 ATTTGAG-AGAA
19585864 A-TTGAGAGAAA
1 ATTTGAGAG-AA
19585875 ATTTGAGAGA
1 ATTTGAGAGA
19585885 GGATTAGTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
10 9 0.16
11 28 0.51
12 18 0.33
ACGTcount: A:0.45, C:0.01, G:0.27, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:19585847 original size:33 final size:33
Alignment explanation
Indices: 19585808--19585884 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
19585798 ATAAATATGG
* * *
19585808 ATTTGAGAGAAATTTTGAAGGAATTTGAGAGCAA
1 ATTTGAGAGAAATTTAGAA-GAAATTGAGAGAAA
19585842 A-TTGAGAGGAAATTTAGAAGAAATTGAGAGAAA
1 ATTTGAGA-GAAATTTAGAAGAAATTGAGAGAAA
19585875 ATTTGAGAGA
1 ATTTGAGAGA
19585885 GGATTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 21 0.55
34 17 0.45
ACGTcount: A:0.45, C:0.01, G:0.27, T:0.26
Consensus pattern (33 bp):
ATTTGAGAGAAATTTAGAAGAAATTGAGAGAAA
Found at i:19593905 original size:3 final size:3
Alignment explanation
Indices: 19593897--19593956 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
19593887 AACTTAATGT
19593897 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19593945 ATA ATA ATA ATA
1 ATA ATA ATA ATA
19593957 GTTAGTGGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:19597667 original size:26 final size:26
Alignment explanation
Indices: 19597617--19597667 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
19597607 AAAATGTATA
* * * *
19597617 CAATTATTGATAACATAATACATACG
1 CAATTATTGATAAAAAAAAAAATACG
19597643 CAATTATTGATAAAAAAAAAAATAC
1 CAATTATTGATAAAAAAAAAAATAC
19597668 ATGAGAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (26 bp):
CAATTATTGATAAAAAAAAAAATACG
Found at i:19598857 original size:15 final size:15
Alignment explanation
Indices: 19598837--19598866 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19598827 ATATGCTTTT
19598837 TTTAATGTTTTTTAA
1 TTTAATGTTTTTTAA
*
19598852 TTTAATTTTTTTTAA
1 TTTAATGTTTTTTAA
19598867 AAAAATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTAATGTTTTTTAA
Found at i:19599664 original size:15 final size:15
Alignment explanation
Indices: 19599617--19599667 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
19599607 TCCACCAAAT
19599617 AAAATATTATTGTTT-
1 AAAATATTATT-TTTA
* ** *
19599632 AAAATTTTAAATTAA
1 AAAATATTATTTTTA
19599647 AAAATATTATTTTTA
1 AAAATATTATTTTTA
19599662 AAAATA
1 AAAATA
19599668 AAAAACACAT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 2 0.07
15 25 0.93
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
AAAATATTATTTTTA
Found at i:19601231 original size:15 final size:14
Alignment explanation
Indices: 19601210--19601245 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
19601200 ATAATCCTTA
*
19601210 ATAATTATCTTAAT
1 ATAATTATCCTAAT
19601224 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
19601239 ATAATTA
1 ATAATTA
19601246 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:19605214 original size:36 final size:33
Alignment explanation
Indices: 19605138--19605220 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 33
19605128 AGTTTGTTCC
* *
19605138 AAGTTTGTTGCAATGAATCTAATTTAAGTTACA
1 AAGTTTGTTCCAATGAATCTAATTTAAGATACA
*
19605171 AAATTTGTTCCAATGAATCTCAATTAAATAA-ATACA
1 AAGTTTGTTCCAATGAATCT-AATT---TAAGATACA
19605207 AAGTTTGTTCCAAT
1 AAGTTTGTTCCAAT
19605221 TTTGTTCCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 18 0.43
34 4 0.10
36 17 0.40
37 3 0.07
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (33 bp):
AAGTTTGTTCCAATGAATCTAATTTAAGATACA
Found at i:19608699 original size:19 final size:19
Alignment explanation
Indices: 19608671--19608859 Score: 200
Period size: 19 Copynumber: 9.7 Consensus size: 19
19608661 AATTTTTGAG
*
19608671 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
**
19608690 GATATACAATCCAAGATAT
1 GATATACAATCTTAGATAT
* *
19608709 GATATATGCAATCCTAAATAT
1 GATATA--CAATCTTAGATAT
*
19608730 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
19608749 GATATATAATCTTAGATATT
1 GATATACAATCTTAGATA-T
**
19608769 GATATACAA-CCAAGATAT
1 GATATACAATCTTAGATAT
* *
19608787 GATATATGCAATCCTAAATAT
1 GATATA--CAATCTTAGATAT
*
19608808 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
19608827 GATATATAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
19608846 GATATGCAATCTTA
1 GATATACAATCTTA
19608860 AAATATATGA
Statistics
Matches: 142, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
18 7 0.05
19 95 0.67
20 12 0.08
21 28 0.20
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:19608738 original size:59 final size:58
Alignment explanation
Indices: 19608671--19608859 Score: 233
Period size: 59 Copynumber: 3.2 Consensus size: 58
19608661 AATTTTTGAG
**
19608671 GATATGCAATCTTAGATATGATATACAATCCAAGATATGATATATGCAATCCTAAATAT
1 GATATGCAATCTTAGATATGATATACAATCTTAGATATGATATAT-CAATCCTAAATAT
*
19608730 GATATGCAATCTTAGATATGATATATAATCTTAGATATTGATATA-CAA-CC-AAGATAT
1 GATATGCAATCTTAGATATGATATACAATCTTAGATA-TGATATATCAATCCTAA-ATAT
* * * * *
19608787 GATATATGCAATCCTAAATATGATATGCAATCTTAGATATGATATAT-AATCTTAGATAT
1 G--ATATGCAATCTTAGATATGATATACAATCTTAGATATGATATATCAATCCTAAATAT
19608846 GATATGCAATCTTA
1 GATATGCAATCTTA
19608860 AAATATATGA
Statistics
Matches: 113, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
56 2 0.02
57 19 0.17
58 12 0.11
59 72 0.64
60 8 0.07
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (58 bp):
GATATGCAATCTTAGATATGATATACAATCTTAGATATGATATATCAATCCTAAATAT
Found at i:19608795 original size:78 final size:78
Alignment explanation
Indices: 19608678--19608856 Score: 333
Period size: 78 Copynumber: 2.3 Consensus size: 78
19608668 GAGGATATGC
19608678 AATCTTAGATATGATATACAATCCAAGATATGATATATGCAATCCTAAATATGATATGCAATCTT
1 AATCTTAGATATGATATACAATCCAAGATATGATATATGCAATCCTAAATATGATATGCAATCTT
19608743 AGATATGATATAT
66 AGATATGATATAT
19608756 AATCTTAGATATTGATATACAA-CCAAGATATGATATATGCAATCCTAAATATGATATGCAATCT
1 AATCTTAGATA-TGATATACAATCCAAGATATGATATATGCAATCCTAAATATGATATGCAATCT
19608820 TAGATATGATATAT
65 TAGATATGATATAT
*
19608834 AATCTTAGATATGATATGCAATC
1 AATCTTAGATATGATATACAATC
19608857 TTAAAATATA
Statistics
Matches: 98, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
77 9 0.09
78 79 0.81
79 10 0.10
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (78 bp):
AATCTTAGATATGATATACAATCCAAGATATGATATATGCAATCCTAAATATGATATGCAATCTT
AGATATGATATAT
Found at i:19618896 original size:19 final size:19
Alignment explanation
Indices: 19618874--19618914 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
19618864 ATGCAAACTA
*
19618874 AGATATGATATATAATCTT
1 AGATATGATATACAATCTT
*
19618893 AGATATGATATGCAATCTT
1 AGATATGATATACAATCTT
19618912 AGA
1 AGA
19618915 ATATATGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (19 bp):
AGATATGATATACAATCTT
Found at i:19621677 original size:3 final size:3
Alignment explanation
Indices: 19621671--19621724 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
19621661 CGTCGTCATC
19621671 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19621719 ATT ATT
1 ATT ATT
19621725 GTTGTTGTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19622191 original size:18 final size:20
Alignment explanation
Indices: 19622157--19622194 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
19622147 GTACACAATA
19622157 AATTAATCATAATAATTTAT
1 AATTAATCATAATAATTTAT
19622177 AATTAAT-AT-ATAATTTAT
1 AATTAATCATAATAATTTAT
19622195 TTATTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTAATCATAATAATTTAT
Found at i:19622895 original size:23 final size:23
Alignment explanation
Indices: 19622866--19622909 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19622856 TGTATATATT
* *
19622866 TGTTGAGGAAAAATTATATTTCA
1 TGTTGAGCAAAAATAATATTTCA
*
19622889 TGTTGAGCTAAAATAATATTT
1 TGTTGAGCAAAAATAATATTT
19622910 TGCATCGCCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.41
Consensus pattern (23 bp):
TGTTGAGCAAAAATAATATTTCA
Found at i:19630466 original size:16 final size:16
Alignment explanation
Indices: 19630423--19630468 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
19630413 AAGTGCCTTG
19630423 GAAAACACATTTTTTC
1 GAAAACACATTTTTTC
19630439 GAAAA-ACATTTTTTAC
1 GAAAACACATTTTTT-C
*
19630455 -AAAACACGTTTTTT
1 GAAAACACATTTTTT
19630469 GTTAACTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (16 bp):
GAAAACACATTTTTTC
Found at i:19631038 original size:28 final size:27
Alignment explanation
Indices: 19631007--19631066 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
19630997 GTTTTTGCTT
* * * *
19631007 TTAATTAATAAATTTTTATTTATATAGA
1 TTAAATAATAAATATGTAATTATAT-GA
*
19631035 TTAAATATTAAATATGTAATTATATGA
1 TTAAATAATAAATATGTAATTATATGA
19631062 TTAAA
1 TTAAA
19631067 ATATATATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (27 bp):
TTAAATAATAAATATGTAATTATATGA
Found at i:19631081 original size:32 final size:32
Alignment explanation
Indices: 19631039--19631108 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
19631029 TATAGATTAA
*
19631039 ATATTAAATATGTAAT-TAT-ATGATTAAAATAT
1 ATATTTAATATGTAATGTATAAT-ATT-AAATAT
*
19631071 ATATTTAATATTTAATGTATAATATTAAATAT
1 ATATTTAATATGTAATGTATAATATTAAATAT
19631103 AT-TTTA
1 ATATTTA
19631109 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 4 0.12
32 22 0.65
33 6 0.18
34 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (32 bp):
ATATTTAATATGTAATGTATAATATTAAATAT
Found at i:19631423 original size:14 final size:13
Alignment explanation
Indices: 19631406--19631442 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
19631396 ATAATAAATT
19631406 AAAAGAAAAAAAGG
1 AAAAGAAAAAAA-G
19631420 AAAAGAATAAAAAG
1 AAAAGAA-AAAAAG
19631434 AAAAGAAAA
1 AAAAGAAAA
19631443 TTGCCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 15 0.68
15 5 0.23
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:19632414 original size:43 final size:43
Alignment explanation
Indices: 19632366--19632531 Score: 269
Period size: 43 Copynumber: 3.9 Consensus size: 43
19632356 TTATGTGAAA
*
19632366 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
* **
19632409 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGCCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
* *
19632452 AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGTTTTTATCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
*
19632495 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTT
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTT
19632532 AGCCACAAAC
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 112 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
Found at i:19632468 original size:86 final size:86
Alignment explanation
Indices: 19632366--19632543 Score: 302
Period size: 86 Copynumber: 2.1 Consensus size: 86
19632356 TTATGTGAAA
19632366 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAACAAACGCCGCTAAAGAACATGAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAACAAACGCCGCTAAAGAACATGAC
*
19632431 CTTTAGCGGCGCTTTTGCCAC
66 CTTTAGCGGCGCTTTAGCCAC
* * * * *
19632452 AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGTTTTTATCACAAACGCCGCTAAAGATCGTGAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAACAAACGCCGCTAAAGAACATGAC
19632517 CTTTAGCGGCGCTTTAGCCAC
66 CTTTAGCGGCGCTTTAGCCAC
19632538 AAACGC
1 AAACGC
19632544 TTTAGATACA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAACAAACGCCGCTAAAGAACATGAC
CTTTAGCGGCGCTTTAGCCAC
Found at i:19639495 original size:26 final size:26
Alignment explanation
Indices: 19639466--19639516 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
19639456 AACAAATATT
* *
19639466 TTTCTATGTTTTTTTATTTCAAATTA
1 TTTCTATGTGTTATTATTTCAAATTA
19639492 TTTCTATGTGTTATTATTTCAAATT
1 TTTCTATGTGTTATTATTTCAAATT
19639517 TATCCATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.08, G:0.06, T:0.63
Consensus pattern (26 bp):
TTTCTATGTGTTATTATTTCAAATTA
Found at i:19639603 original size:19 final size:19
Alignment explanation
Indices: 19639563--19639605 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
19639553 AATTTTAATT
*
19639563 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
19639582 AATAGTAAAT-AACAGATAA
1 AATA-TAAATAAACAAATAA
19639601 AATAT
1 AATAT
19639606 TTTTGCGGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.71
20 5 0.24
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:19639667 original size:41 final size:41
Alignment explanation
Indices: 19639610--19639767 Score: 253
Period size: 41 Copynumber: 3.9 Consensus size: 41
19639600 AAATATTTTT
* *
19639610 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
19639651 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
19639692 GCGCCGCTTTTTTAAAAACGCTGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
19639733 GCGGCGCTTTTTTAAAAACGCCGCTAAAGACCTGA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGA
19639768 TAGGTCAAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 109 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:19639852 original size:41 final size:39
Alignment explanation
Indices: 19639807--19639898 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 39
19639797 GGTTTTTTTT
19639807 GCGGCGTTTTTCCAAAAAACGCCGCTAATGCTTGATCTTTA
1 GCGGCGTTTTT--AAAAAACGCCGCTAATGCTTGATCTTTA
** ** *
19639848 GCGGCGTTTTGTGTAAAGGGCCGCTAATGCTTGATTTTTA
1 GCGGCGTTTT-TAAAAAACGCCGCTAATGCTTGATCTTTA
19639888 GCGGCGTTTTT
1 GCGGCGTTTTT
19639899 TGTCCAAACG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
39 1 0.02
40 33 0.73
41 10 0.22
42 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (39 bp):
GCGGCGTTTTTAAAAAACGCCGCTAATGCTTGATCTTTA
Found at i:19643730 original size:39 final size:40
Alignment explanation
Indices: 19643609--19643730 Score: 142
Period size: 40 Copynumber: 3.1 Consensus size: 40
19643599 GCGGCATTTT
* *
19643609 AAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTCA-A
1 AAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTTGAGA
* * *
19643648 AAATCGCCGCTAAAGATCCAGCATTAGCGGCCCTTTTTG-GA
1 AAA-CGCCGCTAAAAATCAAGCATTAGCGG-CGTTTTTGAGA
* *
19643689 AAACGCCGCTAAAAAT-GAGCATTAGTGGCGTTTTTGAGA
1 AAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTTGAGA
19643728 AAA
1 AAA
19643731 GCTCCGCAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
38 7 0.10
39 18 0.26
40 36 0.51
41 9 0.13
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (40 bp):
AAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTTGAGA
Found at i:19643841 original size:41 final size:41
Alignment explanation
Indices: 19643781--19644096 Score: 418
Period size: 41 Copynumber: 7.7 Consensus size: 41
19643771 CCTTTAGAGG
*
19643781 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAAAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* * * *
19643822 CTTTACCGGCGTTTATGGAAAAGTGCCGCTAATGCTCATAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* * * * *
19643863 CTTTAGCGACGTTTTT-GAAAACCGACGCTAATGCTTAAAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* * *
19643903 CTTTAGCGGCGTTTTTGAAAAATCGCCGCTAATGCTCAGAG
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* *
19643944 CTTTAGCGGCGTTTTTGGAAAATCGCCGCTAATGCTCAGAG
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* *
19643985 CTTTAGCGGCATTTTTGGAAAAGCGCCGCTAATGCTCAGAG
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* *
19644026 CTTTAGCGGCGTTTATGGAAAAGAGCCGCTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
** *
19644067 CTTTAGCGGTTTTTTTTGAAAAAGCGCCGC
1 CTTTAGCGG-CGTTTTTGGAAAAGCGCCGC
19644097 AAAAACATTT
Statistics
Matches: 242, Mismatches: 31, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
40 34 0.14
41 193 0.80
42 15 0.06
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
Found at i:19644348 original size:14 final size:15
Alignment explanation
Indices: 19644320--19644352 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
19644310 ATGACTGATA
19644320 GATTATGGAATTAGG
1 GATTATGGAATTAGG
19644335 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
19644349 GATT
1 GATT
19644353 CTAGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:19644554 original size:7 final size:7
Alignment explanation
Indices: 19644498--19644564 Score: 55
Period size: 7 Copynumber: 9.6 Consensus size: 7
19644488 TAAATAATGT
19644498 TTAGGGG
1 TTAGGGG
*
19644505 TTGGGGG
1 TTAGGGG
*
19644512 CTAGGGG
1 TTAGGGG
**
19644519 TTAGTAG
1 TTAGGGG
*
19644526 TTAGGGA
1 TTAGGGG
*
19644533 TTAAGGGT
1 TT-AGGGG
19644541 TTA-GGG
1 TTAGGGG
*
19644547 TTGGGGG
1 TTAGGGG
19644554 TTAGGGG
1 TTAGGGG
19644561 TTAG
1 TTAG
19644565 ATTAATTGGT
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
6 4 0.09
7 35 0.78
8 6 0.13
ACGTcount: A:0.16, C:0.01, G:0.51, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:19644561 original size:21 final size:21
Alignment explanation
Indices: 19644496--19644562 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
19644486 ATTAAATAAT
*
19644496 GTTTAGGGGTTGGGGGCTAGGG
1 GTTTA-GGGTTGGGGGTTAGGG
* * * *
19644518 G-TTAGTAGTTAGGGATTAAGG
1 GTTTAG-GGTTGGGGGTTAGGG
19644539 GTTTAGGGTTGGGGGTTAGGG
1 GTTTAGGGTTGGGGGTTAGGG
19644560 GTT
1 GTT
19644563 AGATTAATTG
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.82
22 5 0.15
ACGTcount: A:0.15, C:0.01, G:0.51, T:0.33
Consensus pattern (21 bp):
GTTTAGGGTTGGGGGTTAGGG
Found at i:19648163 original size:39 final size:39
Alignment explanation
Indices: 19648086--19648163 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
19648076 CACTAAAGTT
* * *
19648086 TGAGCAATAGCGGCGTTTTTTAAAAAATGCAGCTAAAAA
1 TGAGCAATAGCGGCGTTTTTCAAAAAACGCAGCAAAAAA
*
19648125 TGAGCATTAGCGGCGTTTTTCAAAAAACGTC-GCAAAAAA
1 TGAGCAATAGCGGCGTTTTTCAAAAAACG-CAGCAAAAAA
19648164 CCTAAGCCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.97
40 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (39 bp):
TGAGCAATAGCGGCGTTTTTCAAAAAACGCAGCAAAAAA
Found at i:19648258 original size:41 final size:41
Alignment explanation
Indices: 19648198--19648564 Score: 493
Period size: 41 Copynumber: 9.0 Consensus size: 41
19648188 GGACCTTTCG
* * *
19648198 TGGTCTTTAGCGGCATTTTTGGAAAAGCGCCGCTACTGCTT
1 TGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
* *
19648239 TGGTCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTT
1 TGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
* *
19648280 TGGTCTTTCGCGGCATTTTTGGAAAAGCGCCGCTAATGCTC
1 TGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
* * * *
19648321 TGGTATTTAGCGGCGTTTTCGGAAAAGAGCCGCGAATGCTC
1 TGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
* * * *
19648362 TAGTCTTTAGCGGCGTTTGTGTAAAAGCGCCGCTAATGCTT
1 TGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
*
19648403 TGGTCTTTAGCGGCGTTTTTGGCAAAGCGCCGCTAATGCTC
1 TGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
* ** *
19648444 TAGTCTTTAATGGAG-TTTTGGAAAAGCGCCGCTAATGCTC
1 TGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
* *
19648484 TGGCCTTTAGCGGCGTTTTTTGGAGAAGCGCCGCTAATGCTC
1 TGGTCTTTAGCGGCG-TTTTTGGAAAAGCGCCGCTAATGCTC
* **
19648526 TGGTCTTTAGCGGCGTTTTTGCAAAAGCGCAACTAATGC
1 TGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGC
19648565 AAAATACTAT
Statistics
Matches: 282, Mismatches: 42, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
40 34 0.12
41 210 0.74
42 38 0.13
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (41 bp):
TGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
Found at i:19648951 original size:7 final size:7
Alignment explanation
Indices: 19648941--19648988 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
19648931 AATTTAAGGT
19648941 TTAGGGG
1 TTAGGGG
*
19648948 TTAGTGG
1 TTAGGGG
19648955 TTAGGGG
1 TTAGGGG
* *
19648962 TTAAGAG
1 TTAGGGG
*
19648969 TTAGGGAT
1 TTAGGG-G
19648977 TTAGGGG
1 TTAGGGG
19648984 TTAGG
1 TTAGG
19648989 ACTTAAGGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:19648998 original size:22 final size:22
Alignment explanation
Indices: 19648955--19648999 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19648945 GGGTTAGTGG
* *
19648955 TTAGGGGTTAAGAGTTAGGGAT
1 TTAGGGGTTAAGACTTAAGGAT
*
19648977 TTAGGGGTTAGGACTTAAGGAT
1 TTAGGGGTTAAGACTTAAGGAT
19648999 T
1 T
19649000 CAAGGGTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (22 bp):
TTAGGGGTTAAGACTTAAGGAT
Found at i:19649358 original size:19 final size:19
Alignment explanation
Indices: 19649311--19649356 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
19649301 AAATTATAAG
* *
19649311 AAATAAAATTAAAATACAA
1 AAATAAAAATGAAATACAA
19649330 AAATAAAAATGAAATA-AA
1 AAATAAAAATGAAATACAA
19649348 AAATAAAAA
1 AAATAAAAA
19649357 ATATAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (19 bp):
AAATAAAAATGAAATACAA
Found at i:19653223 original size:43 final size:43
Alignment explanation
Indices: 19653115--19653472 Score: 404
Period size: 43 Copynumber: 8.4 Consensus size: 43
19653105 ATGATATGTT
* * * * *
19653115 TTTAGCGGCGTTTTTG-CGAGAAGCGTCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGAC-AAAAGCGCCGCTAAAGGTCATGGTC
* *
19653157 TATAGCGGCGTTTGTAACAAAAGCGCCGCTAAAGGTCATGAG-C
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATG-GTC
* * *
19653200 TTTAGTGGCGTTTGTGATAAAAGCGTCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTC
* *
19653243 TTTAGCGGCGTTTGTTACAAAAGCGCAGCTAAAGGTCATGAG-C
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATG-GTC
* *
19653286 TTTAGCGGCGTTTGTGATAAAAGCGCAGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTC
* * *
19653329 TTTAACGGCG-TTGTGACAAAAGCGCCGTTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTC
** * * *
19653371 TTTAGCGGCGTTTGTTG-GTAAAGCACCACTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTG-TGACAAAAGCGCCGCTAAAGGTCATGGTC
* ** *
19653414 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTC
19653457 TTTAGCGGCGTTTGTG
1 TTTAGCGGCGTTTGTG
19653473 GGTAAAAACG
Statistics
Matches: 271, Mismatches: 36, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
42 70 0.26
43 198 0.73
44 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:19653361 original size:128 final size:128
Alignment explanation
Indices: 19653155--19653468 Score: 409
Period size: 128 Copynumber: 2.4 Consensus size: 128
19653145 AAAGGTTTGT
* * *
19653155 TCTATAGCGGCGTTTGTAACAAAAGCGCCGCTAAAGGTCATGAG-CTTTAGTGGCGTTTGTGATA
1 TCTATAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATG-GTCTTTAGCGGCG-TTGTGACA
* *
19653219 AAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTTACAAAAGC-GCAGCTAAAGGTCATG
64 AAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTTACAAAAGCACCA-CTAAAGGTCATG
19653283 AG
128 -G
* * * *
19653285 -CTTTAGCGGCGTTTGTGATAAAAGCGCAGCTAAAGGTCATGGTCTTTAACGGCGTTGTGACAAA
1 TCTATAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTGTGACAAA
* * *** *
19653349 AGCGCCGTTAAAGGTCGTGGTCTTTAGCGGCGTTTGTTGGTAAAGCACCACTAAAGGTCGTGG
66 AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTTACAAAAGCACCACTAAAGGTCATGG
** *
19653412 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTT
1 TCTATAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTT
19653469 TGTGGGTAAA
Statistics
Matches: 160, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
127 1 0.01
128 111 0.69
129 48 0.30
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (128 bp):
TCTATAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTGTGACAAA
AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTTACAAAAGCACCACTAAAGGTCATGG
Found at i:19654586 original size:18 final size:18
Alignment explanation
Indices: 19654563--19654622 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
19654553 ATGTAATTCT
19654563 AATGTAATTCTAATATAG
1 AATGTAATTCTAATATAG
* * **
19654581 AATGTAA-AC-AATTTTCT
1 AATGTAATTCTAA-TATAG
*
19654598 TATGTAATTCTAATATAG
1 AATGTAATTCTAATATAG
19654616 AATGTAA
1 AATGTAA
19654623 CTTGTTTTAA
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 2 0.07
17 9 0.31
18 16 0.55
19 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (18 bp):
AATGTAATTCTAATATAG
Found at i:19663565 original size:32 final size:32
Alignment explanation
Indices: 19663523--19663588 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
19663513 TGTTTTAGAC
*
19663523 TTCTTTTAAAGTCTTTCCAAGATGGAGGAAGT
1 TTCTTCTAAAGTCTTTCCAAGATGGAGGAAGT
19663555 TTCTTCTAAAGTCTTTCCAAGATGGAGGAAGT
1 TTCTTCTAAAGTCTTTCCAAGATGGAGGAAGT
19663587 TT
1 TT
19663589 GTCTATTGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (32 bp):
TTCTTCTAAAGTCTTTCCAAGATGGAGGAAGT
Found at i:19664371 original size:30 final size:28
Alignment explanation
Indices: 19664337--19664416 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 28
19664327 TTTTTTAAAT
*
19664337 TACATTTTGACCTTTAAAATTTCAAAAAAG
1 TACATTTTGACC-CTAAAATTTC-AAAAAG
* * *
19664367 TACATTTTGACCCCTAAACTTTCTAAAAT
1 TACATTTTGA-CCCTAAAATTTCAAAAAG
19664396 TACATTTTGACCCTAAAATTT
1 TACATTTTGACCCTAAAATTT
19664417 TGAAAAATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
28 10 0.23
29 14 0.32
30 18 0.41
31 2 0.05
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.39
Consensus pattern (28 bp):
TACATTTTGACCCTAAAATTTCAAAAAG
Found at i:19664403 original size:29 final size:30
Alignment explanation
Indices: 19664333--19664428 Score: 115
Period size: 29 Copynumber: 3.3 Consensus size: 30
19664323 TTATTTTTTT
**
19664333 AAATTACATTTTGACCTTTAAAATTTCAAA
1 AAATTACATTTTGACCCCTAAAATTTCAAA
* * *
19664363 AAAGTACATTTTGACCCCTAAACTTTC-TA
1 AAATTACATTTTGACCCCTAAAATTTCAAA
**
19664392 AAATTACATTTTGA-CCCTAAAATTTTGAA
1 AAATTACATTTTGACCCCTAAAATTTCAAA
19664421 AAATTACA
1 AAATTACA
19664429 CTTTAGCCCT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
28 10 0.18
29 23 0.41
30 23 0.41
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (30 bp):
AAATTACATTTTGACCCCTAAAATTTCAAA
Found at i:19664438 original size:29 final size:30
Alignment explanation
Indices: 19664333--19664448 Score: 78
Period size: 29 Copynumber: 3.9 Consensus size: 30
19664323 TTATTTTTTT
* * **
19664333 AAATTACATTTTGA-CCTTTAAAATTTCAAA
1 AAATTACATTTAGACCCTAT-AAATTTTGAA
* * * * **
19664363 AAAGTACATTTTGACCC-CTAAACTTTCTA
1 AAATTACATTTAGACCCTATAAATTTTGAA
*
19664392 AAATTACATTTTGACCCTA-AAATTTTGAA
1 AAATTACATTTAGACCCTATAAATTTTGAA
*
19664421 AAATTACACTTTAG-CCCTATAAGTTTTG
1 AAATTACA-TTTAGACCCTATAAATTTTG
19664449 CTACATTTAC
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
29 42 0.61
30 25 0.36
31 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (30 bp):
AAATTACATTTAGACCCTATAAATTTTGAA
Found at i:19664784 original size:17 final size:17
Alignment explanation
Indices: 19664727--19664786 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
19664717 AAGGGGACGG
* *
19664727 CGACGTGAAGGAGACGA
1 CGACGTAAAGGAGGCGA
* * * *
19664744 CAACGTGAAGGAGGTGG
1 CGACGTAAAGGAGGCGA
*
19664761 CGGCGTAAAGGAGGCGA
1 CGACGTAAAGGAGGCGA
19664778 CGACGTAAA
1 CGACGTAAA
19664787 CTAGAGCAAG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.42, T:0.08
Consensus pattern (17 bp):
CGACGTAAAGGAGGCGA
Found at i:19664816 original size:10 final size:10
Alignment explanation
Indices: 19664798--19664872 Score: 70
Period size: 10 Copynumber: 7.8 Consensus size: 10
19664788 TAGAGCAAGG
19664798 AGAAAGAAGA
1 AGAAAGAAGA
*
19664808 AGAATGAAGGA
1 AGAAAGAA-GA
*
19664819 AAAAAGAAGA
1 AGAAAGAAGA
19664829 AGAAAGAAGA
1 AGAAAGAAGA
19664839 AGGAAAGAA-A
1 A-GAAAGAAGA
19664849 AGAAA-AA-A
1 AGAAAGAAGA
*
19664857 ATAAA-AA-A
1 AGAAAGAAGA
19664865 AGAAAGAA
1 AGAAAGAA
19664873 AAAAATATCA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
8 14 0.25
9 6 0.11
10 21 0.38
11 15 0.27
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (10 bp):
AGAAAGAAGA
Found at i:19664840 original size:24 final size:23
Alignment explanation
Indices: 19664800--19664852 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
19664790 GAGCAAGGAG
19664800 AAAGAAGAAGAATGAAGGAAAAA
1 AAAGAAGAAGAATGAAGGAAAAA
*
19664823 AGAAGAAGAAAGAA-GAAGGAAAGA
1 A-AAGAAG-AAGAATGAAGGAAAAA
19664847 AAAGAA
1 AAAGAA
19664853 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 6 0.22
24 16 0.59
25 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (23 bp):
AAAGAAGAAGAATGAAGGAAAAA
Found at i:19664845 original size:21 final size:21
Alignment explanation
Indices: 19664794--19664853 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
19664784 AAACTAGAGC
*
19664794 AAGG-AGAAAGAAGAAGAATG
1 AAGGAAGAAAGAAGAAGAAAG
*
19664814 AAGGAAAAAAGAAGAAGAAAG
1 AAGGAAGAAAGAAGAAGAAAG
19664835 AA-GAAGGAAAGAA-AAGAAA
1 AAGGAA-GAAAGAAGAAGAAA
19664854 AAAATAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (21 bp):
AAGGAAGAAAGAAGAAGAAAG
Found at i:19664846 original size:18 final size:17
Alignment explanation
Indices: 19664798--19664847 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 17
19664788 TAGAGCAAGG
*
19664798 AGAAAGAAGAAGAATGA
1 AGAAAGAAGAAGAAAGA
*
19664815 AGGAA-AA-AAG-AAGA
1 AGAAAGAAGAAGAAAGA
19664829 AGAAAGAAGAAGGAAAGA
1 AGAAAGAAGAA-GAAAGA
19664847 A
1 A
19664848 AAGAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
14 7 0.27
15 5 0.19
16 4 0.15
17 5 0.19
18 5 0.19
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (17 bp):
AGAAAGAAGAAGAAAGA
Found at i:19665124 original size:28 final size:28
Alignment explanation
Indices: 19665075--19665128 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
19665065 GGCCCAAACT
** *
19665075 AGCAGGCTAGTGCCTGGTCCAACAGCAC
1 AGCAGGCTAGCACCTGGCCCAACAGCAC
*
19665103 AGCAGGCTAGCACTTGGCCCAACAGC
1 AGCAGGCTAGCACCTGGCCCAACAGC
19665129 CAACAGCCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.26, C:0.33, G:0.28, T:0.13
Consensus pattern (28 bp):
AGCAGGCTAGCACCTGGCCCAACAGCAC
Found at i:19674475 original size:78 final size:77
Alignment explanation
Indices: 19674192--19675321 Score: 1259
Period size: 78 Copynumber: 14.6 Consensus size: 77
19674182 TCTTTTTATG
*
19674192 TTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACG-CGAGGTATTT
19674257 TTCAATTTCTATTT
65 TTCAATTTCTA-TT
* * *
19674271 TTTTTCAAAACTCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGATCGCACGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGC-GAGGTATTT
*
19674336 TTTAATTTCTA--
65 TTCAATTTCTATT
* * **
19674347 TTTTTCAAAAATCAACTCATAATGCGAGAGATCAGTTGAGCCTCGGGTCACACGTCGAACTATTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACG-CGAGGTATTT
19674412 TTCAATTTCTATT
65 TTCAATTTCTATT
* * * * * *
19674425 TTTTTTAAAACTCAACTCATAATGCCAGAGGTGAGTTGAGCCACGAGTCACACGCTGATGTATTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGC-GAGGTATTT
*
19674490 TTCAA-TT-TATG
65 TTCAATTTCTATT
* * * *
19674501 TTTTTCAAAAAAATCAACACATAATGCGAGAGGTGAGTTGAGACTAGGGTCACACGCTAAGGTAT
1 TTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGC-GAGGTAT
*
19674566 TTTTCAATTTCTATA
63 TTTTCAATTTCTATT
* * *
19674581 TTTTTCAAAAATCAACTTATAATACGAGAGGTGAGTTGAGCCTAGGGTCACACGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGC-GAGGTATTT
*
19674646 TTCAATTTCTGTT
65 TTCAATTTCTATT
* *
19674659 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGTCGCACGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGC-GAGGTATTT
*
19674724 TTCAA-TT-TATG
65 TTCAATTTCTATT
* *
19674735 TTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTAAGCCTCGGGTCGCACGCCGAGGTAT
1 TTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACG-CGAGGTAT
19674800 TTTTCAA-TT-TATGT
63 TTTTCAATTTCTAT-T
* * *
19674814 TTTTTCAAAAAAAATCAACTCATAATGCGAGATGTGAGTTGAGCCTCGAGTTACACGTCGAGGTA
1 TTTTTC---AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACG-CGAGGTA
* *
19674879 TTTTTGAA-TT-TATG
62 TTTTTCAATTTCTATT
* * *
19674893 TTTTTCAAAAATATCAGCTCATAATGCGAGAGGTGAGTT-ATGCCTCGGGTCGCACGTTGAGGTA
1 TTTTTC-AAAA-ATCAACTCATAATGCGAGAGGTGAGTTGA-GCCTCGGGTCACACG-CGAGGTA
*
19674957 TTTTTCAATTTC--TG
62 TTTTTCAATTTCTATT
* *
19674971 TTTTTCAAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CACATGCCGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACG-CGAGGTATTT
*
19675035 TTCAATTTCCA-T
65 TTCAATTTCTATT
** * * *
19675047 TTTTTCAAAAATCAACTCATAATATGATAGGTGAGTTGAGCCTCGGG-CAAATGCCGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACG-CGAGGTATTT
*
19675111 TTCAA-TT-TATG
65 TTCAATTTCTATT
* * *
19675122 TTTTTCAAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCGCGCTGAGG-A-
1 TTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGC-GAGGTAT
*
19675185 TTTTCAATTTC--TG
63 TTTTCAATTTCTATT
* * * * * * *
19675198 TTCTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCTTTGGGTCGCGCGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGC-GAGGTATTT
*
19675263 TT-AATTTC--TG
65 TTCAATTTCTATT
* *
19675273 TTTTTCAAAGATCAACTCATAAT-CTGAGAGGTGAGTTGAGCTTCGGGTC
1 TTTTTCAAAAATCAACTCATAATGC-GAGAGGTGAGTTGAGCCTCGGGTC
19675322 GTACCCTGAG
Statistics
Matches: 928, Mismatches: 92, Indels: 66
0.85 0.08 0.06
Matches are distributed among these distances:
74 53 0.06
75 84 0.09
76 197 0.21
77 59 0.06
78 376 0.41
79 86 0.09
80 73 0.08
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (77 bp):
TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCGAGGTATTTT
TCAATTTCTATT
Found at i:19674585 original size:156 final size:154
Alignment explanation
Indices: 19674186--19675358 Score: 1421
Period size: 156 Copynumber: 7.6 Consensus size: 154
19674176 ACCATTTCTT
* *
19674186 TTTATGTTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAG
1 TTTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAG
* *
19674251 GTATTTTTCAATTTCTATTTTTTTTCAAAACTCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
66 GTATTTTTCAATTTCTA-TGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
* *
19674316 GATCGCACGCTGAGGTATTTTTTAA
130 GGTCGCACGCTGAGGTATTTTTCAA
* * * *
19674341 TTTCTATTTTTCAAAAATCAACTCATAATGCGAGAGATCAGTTGAGCCTCGGGTCACACG-TCGA
1 TTTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCT-GA
** * * * * *
19674405 ACTATTTTTCAATTTCTATTTTTTTTAAAACTCAACTCATAATGCCAGAGGTGAGTTGAGCCACG
65 GGTATTTTTCAATTTCTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
* * *
19674470 AGTCACACGCTGATGTATTTTTCAA
130 GGTCGCACGCTGAGGTATTTTTCAA
* * * *
19674495 TTTATGTTTTTCAAAAAAATCAACACATAATGCGAGAGGTGAGTTGAGACTAGGGTCACACGCTA
1 TTTATGTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
* * * *
19674560 AGGTATTTTTCAATTTCTATATTTTTCAAAAATCAACTTATAATACGAGAGGTGAGTTGAGCCTA
64 AGGTATTTTTCAATTTCTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
*
19674625 GGGTCACACGCTGAGGTATTTTTCAA
129 GGGTCGCACGCTGAGGTATTTTTCAA
* * *
19674651 TTTCTGTTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGTCGCACGCTG
1 TTTATG--TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
*
19674716 AGGTATTTTTCAA-TT-TATGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTAAGCC
64 AGGTATTTTTCAATTTCTATGTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCC
*
19674779 TCGGGTCGCACGCCGAGGTATTTTTCAA
127 TCGGGTCGCACGCTGAGGTATTTTTCAA
* * *
19674807 TTTATGTTTTTTCAAAAAAAATCAACTCATAATGCGAGATGTGAGTTGAGCCTCGAGTTACACG-
1 TTTATG-TTTTTC---AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGC
* *
19674871 TCGAGGTATTTTTGAA-TT-TATGTTTTTCAAAAATATCAGCTCATAATGCGAGAGGTGAGTT-A
62 T-GAGGTATTTTTCAATTTCTATGTTTTTC-AAAA-ATCAACTCATAATGCGAGAGGTGAGTTGA
*
19674933 TGCCTCGGGTCGCACGTTGAGGTATTTTTCAA
124 -GCCTCGGGTCGCACGCTGAGGTATTTTTCAA
* * * *
19674965 TTTCTGTTTTTCAAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CACATGCCGAG
1 TTTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAG
* ** *
19675029 GTATTTTTCAATTTCCAT-TTTTTCAAAAATCAACTCATAATATGATAGGTGAGTTGAGCCTCGG
66 GTATTTTTCAATTTCTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
** * *
19675093 G-CAAATGCCGAGGTATTTTTCAA
131 GTCGCACGCTGAGGTATTTTTCAA
* * *
19675116 TTTATGTTTTTCAAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCGCGCTG
1 TTTATGTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
* * * * *
19675181 AGG-A-TTTTCAATTTC--TGTTCTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCTTT
64 AGGTATTTTTCAATTTCTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
*
19675242 GGGTCGCGCGCTGAGGTATTTTT-AA
129 GGGTCGCACGCTGAGGTATTTTTCAA
* * * ** *
19675267 TTTCTGTTTTTCAAAGATCAACTCATAAT-CTGAGAGGTGAGTTGAGCTTCGGGTCGTACCCTGA
1 TTTATGTTTTTCAAAAATCAACTCATAATGC-GAGAGGTGAGTTGAGCCTCGGGTCACACGCTGA
* *
19675331 GCTATTTTT-GATTTC--TGTTTTTCAAAAA
65 GGTATTTTTCAATTTCTATGTTTTTCAAAAA
19675359 AAAATTTAGA
Statistics
Matches: 886, Mismatches: 106, Indels: 57
0.84 0.10 0.05
Matches are distributed among these distances:
148 1 0.00
149 46 0.05
150 18 0.02
151 85 0.10
152 56 0.06
153 62 0.07
154 137 0.15
155 84 0.09
156 249 0.28
157 14 0.02
158 134 0.15
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (154 bp):
TTTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAG
GTATTTTTCAATTTCTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
GTCGCACGCTGAGGTATTTTTCAA
Found at i:19675530 original size:29 final size:30
Alignment explanation
Indices: 19675486--19675639 Score: 172
Period size: 29 Copynumber: 5.2 Consensus size: 30
19675476 ATTTTTTTAT
* * *
19675486 AATTACATTTTGACCCCTAAATTTTCCTAA
1 AATTACATTTTAACCCTTAAACTTTCCTAA
*
19675516 AATTA-GTTTTAACCCTTAAACTTTCCTAA
1 AATTACATTTTAACCCTTAAACTTTCCTAA
* *
19675545 AATTGCATTTTGA-CCTTGAAACTTTCCTAA
1 AATTACATTTTAACCCTT-AAACTTTCCTAA
*
19675575 AATTACATTTTAACCCTTAAAC-TTCTTAA
1 AATTACATTTTAACCCTTAAACTTTCCTAA
* * * *
19675604 AACTACATTTTAA-CCATAAATTTTCCAAA
1 AATTACATTTTAACCCTTAAACTTTCCTAA
19675633 AATTACA
1 AATTACA
19675640 CTTTGGCACC
Statistics
Matches: 104, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
28 6 0.06
29 57 0.55
30 37 0.36
31 4 0.04
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (30 bp):
AATTACATTTTAACCCTTAAACTTTCCTAA
Found at i:19675605 original size:59 final size:59
Alignment explanation
Indices: 19675486--19675639 Score: 195
Period size: 59 Copynumber: 2.6 Consensus size: 59
19675476 ATTTTTTTAT
* *
19675486 AATTACATTTTGACCCCTAAATTTTCCTAAAATTA-GTTTTAACCCTTAAACTTTCCTAA
1 AATTACATTTTGA-CCATAAATTTTCCTAAAATTACATTTTAACCCTTAAACTTTCCTAA
* * * *
19675545 AATTGCATTTTGACCTTGAAACTTTCCTAAAATTACATTTTAACCCTTAAAC-TTCTTAA
1 AATTACATTTTGACCAT-AAATTTTCCTAAAATTACATTTTAACCCTTAAACTTTCCTAA
* * *
19675604 AACTACATTTTAACCATAAATTTTCCAAAAATTACA
1 AATTACATTTTGACCATAAATTTTCCTAAAATTACA
19675640 CTTTGGCACC
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 20 0.24
59 47 0.57
60 15 0.18
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (59 bp):
AATTACATTTTGACCATAAATTTTCCTAAAATTACATTTTAACCCTTAAACTTTCCTAA
Found at i:19676033 original size:19 final size:19
Alignment explanation
Indices: 19675996--19676033 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19675986 TAGGAGAAAG
* *
19675996 AAGAAGAAGGAAGGGAAAA
1 AAGAAGAAGGAAAGAAAAA
19676015 AAGAAGAAGGAAAGAAAAA
1 AAGAAGAAGGAAAGAAAAA
19676034 GAAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (19 bp):
AAGAAGAAGGAAAGAAAAA
Found at i:19676310 original size:28 final size:28
Alignment explanation
Indices: 19676274--19676327 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
19676264 AGCCCAAACT
19676274 AGCAAGCCAGCACCTGGCCCAACAGCAC
1 AGCAAGCCAGCACCTGGCCCAACAGCAC
* *
19676302 AGCAGGCCAGCACTTGGCCCAACAGC
1 AGCAAGCCAGCACCTGGCCCAACAGC
19676328 TAGCAACCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.41, G:0.24, T:0.06
Consensus pattern (28 bp):
AGCAAGCCAGCACCTGGCCCAACAGCAC
Found at i:19681300 original size:41 final size:41
Alignment explanation
Indices: 19681233--19681329 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
19681223 AATACACCTA
* * *
19681233 CATTAAACCTGCTAGACGTAAGGTCTGAAATATTTCACCGG
1 CATTAAGCCTGCTAGAAGTAAAGTCTGAAATATTTCACCGG
*
19681274 CATTAAGCCTGCTAGAAGTAAAGTCTGAAATATTTCACTGG
1 CATTAAGCCTGCTAGAAGTAAAGTCTGAAATATTTCACCGG
19681315 CATTAAGCCTGCTAG
1 CATTAAGCCTGCTAG
19681330 GCACAAAGCC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (41 bp):
CATTAAGCCTGCTAGAAGTAAAGTCTGAAATATTTCACCGG
Found at i:19681343 original size:41 final size:41
Alignment explanation
Indices: 19681233--19681344 Score: 127
Period size: 41 Copynumber: 2.7 Consensus size: 41
19681223 AATACACCTA
* * * * *
19681233 CATTAAACCTGCTAGACGTAAGGTCTGAAATATTTCACCGG
1 CATTAAGCCTGCTAGAAGCAAAGCCTGAAATATTTCACCGG
* * *
19681274 CATTAAGCCTGCTAGAAGTAAAGTCTGAAATATTTCACTGG
1 CATTAAGCCTGCTAGAAGCAAAGCCTGAAATATTTCACCGG
*
19681315 CATTAAGCCTGCTAGGCA-CAAAGCCTGAAA
1 CATTAAGCCTGCTA-GAAGCAAAGCCTGAAA
19681345 ATCACATATA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
41 61 0.97
42 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (41 bp):
CATTAAGCCTGCTAGAAGCAAAGCCTGAAATATTTCACCGG
Found at i:19681633 original size:71 final size:65
Alignment explanation
Indices: 19681487--19681648 Score: 175
Period size: 65 Copynumber: 2.4 Consensus size: 65
19681477 AATTCACGAC
* * *
19681487 TTTAACTTCAGCTCAAGGAATTTGTAACTAATATTCGAACCTCATATGTATATAAAATTCATACA
1 TTTAAATTCAGCTCAAGAAACTTGTAACTAATATTCGAACCTCATATGTATATAAAATTCATACA
* *
19681552 TTAAAATTCAGCTCAAGAAACTTGTAACCT-ATATTCGAACCATATATATATGTATATATGAAAT
1 TTTAAATTCAGCTCAAGAAACTTGTAA-CTAATATTCGAACC---T-CATATGTATATA--AAAT
19681616 TCATA-A
59 TCATACA
* *
19681622 TATTAAGTTCAGCTCAATAAACTTGTA
1 T-TTAAATTCAGCTCAAGAAACTTGTA
19681649 TCATACATTC
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
65 34 0.42
66 2 0.02
68 1 0.01
69 11 0.14
70 2 0.02
71 31 0.38
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.35
Consensus pattern (65 bp):
TTTAAATTCAGCTCAAGAAACTTGTAACTAATATTCGAACCTCATATGTATATAAAATTCATACA
Found at i:19681659 original size:71 final size:69
Alignment explanation
Indices: 19681530--19681661 Score: 176
Period size: 71 Copynumber: 1.9 Consensus size: 69
19681520 TTCGAACCTC
* *
19681530 ATATGTATATAAAATTCATACATTAAAATTCAGCTCAAGAAACTTGTAACCTATATTCGAACCAT
1 ATATGTATATAAAATTCATACATTAAAATTCAGCTCAAGAAACTTGTAACATACATTCGAACCAT
19681595 ATAT
66 ATAT
* * * *
19681599 ATATGTATATATGAAATTCATA-ATATTAAGTTCAGCTCAATAAACTTGTATCATACATTCGAA
1 ATATGTATATA--AAATTCATACAT-TAAAATTCAGCTCAAGAAACTTGTAACATACATTCGAA
19681662 ATTTAACCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
69 11 0.20
70 2 0.04
71 41 0.76
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.35
Consensus pattern (69 bp):
ATATGTATATAAAATTCATACATTAAAATTCAGCTCAAGAAACTTGTAACATACATTCGAACCAT
ATAT
Found at i:19688595 original size:6 final size:6
Alignment explanation
Indices: 19688584--19688656 Score: 53
Period size: 6 Copynumber: 11.8 Consensus size: 6
19688574 CGCAATGAAC
* **
19688584 AAAAAG AAAAAG AAAAAG -AGAAG AAATGTG AAAGAAG -AAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG AAA-AAG AAAAAG AAAAAG
19688632 AAGAACA- AAAGAAG AAAAAG AAAAA
1 AA-AA-AG AAA-AAG AAAAAG AAAAA
19688657 ACGTTAAAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
5 7 0.13
6 32 0.60
7 13 0.25
8 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.21, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:19688609 original size:17 final size:18
Alignment explanation
Indices: 19688587--19688654 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 18
19688577 AATGAACAAA
19688587 AAGAAAAAGAAA-AAGAG
1 AAGAAAAAGAAACAAGAG
** * *
19688604 AAGAAATGTGAAAGAAGAA
1 AAGAAA-AAGAAACAAGAG
*
19688623 AAGAAAAAGAAGAACAAAAG
1 AAGAAAAAG-A-AACAAGAG
19688643 AAGAAAAAGAAA
1 AAGAAAAAGAAA
19688655 AAACGTTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
17 6 0.15
18 7 0.18
19 12 0.31
20 14 0.36
ACGTcount: A:0.74, C:0.01, G:0.22, T:0.03
Consensus pattern (18 bp):
AAGAAAAAGAAACAAGAG
Found at i:19689889 original size:138 final size:138
Alignment explanation
Indices: 19689638--19689908 Score: 413
Period size: 138 Copynumber: 2.0 Consensus size: 138
19689628 TAACAAGTTT
* *
19689638 ACTAGAAGGACATTGTCCAATTGGAGTCAAATGGATGTACAAGACAAAGACCAACAAAAAAGGAA
1 ACTAGAAGGACATAGTCCAATTGAAGTCAAATGGATGTACAAGACAAAGACCAACAAAAAAGGAA
* *
19689703 AAGTGGAGAAATACAAAGCAAGACTGATTGCAAAGGGCTTCAAGTAAAGAC-ATAGAGTGGACTA
66 AAGTGGAGAAATACAAAGCAAGACTGATTGCAAAAGGCTACAAGTAAAGACAAT-GAGTGGACTA
19689767 TGATGAAGG
130 TGATGAAGG
* * *
19689776 ACTAGAAGGACATAGTCCAATTGAAGTCAAAT-GAGTGTACAAGACAAATACTAACAAAGAAGGA
1 ACTAGAAGGACATAGTCCAATTGAAGTCAAATGGA-TGTACAAGACAAAGACCAACAAAAAAGGA
* *
19689840 AAATTGGAGAAATACAAAGCAAGACT-AGTTGCAAAAGGCTACAATTAAAGACAATGAGTGGACT
65 AAAGTGGAGAAATACAAAGCAAGACTGA-TTGCAAAAGGCTACAAGTAAAGACAATGAGTGGACT
19689904 ATGAT
129 ATGAT
19689909 TGAGTATTTA
Statistics
Matches: 121, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
137 3 0.02
138 116 0.96
139 2 0.02
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.18
Consensus pattern (138 bp):
ACTAGAAGGACATAGTCCAATTGAAGTCAAATGGATGTACAAGACAAAGACCAACAAAAAAGGAA
AAGTGGAGAAATACAAAGCAAGACTGATTGCAAAAGGCTACAAGTAAAGACAATGAGTGGACTAT
GATGAAGG
Found at i:19691664 original size:3 final size:3
Alignment explanation
Indices: 19691656--19691708 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
19691646 GTGTGAGTAA
19691656 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
19691704 AAG AA
1 AAG AA
19691709 AGACTATGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19701622 original size:15 final size:15
Alignment explanation
Indices: 19701602--19701636 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
19701592 ATCAATACGG
19701602 CCCAATTAGCCTAAA
1 CCCAATTAGCCTAAA
* *
19701617 CCCAATTAGCTTTAA
1 CCCAATTAGCCTAAA
19701632 CCCAA
1 CCCAA
19701637 ACTCTAGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.34, G:0.06, T:0.23
Consensus pattern (15 bp):
CCCAATTAGCCTAAA
Found at i:19709479 original size:75 final size:75
Alignment explanation
Indices: 19709386--19709532 Score: 249
Period size: 75 Copynumber: 2.0 Consensus size: 75
19709376 TCTTAATTTA
*
19709386 TAGTAGGATTTTCAAGAGTCAAATTAAAACTGGAAAAATCGCGCGTACCAAATCGTAAAACGCTC
1 TAGTAGGATTTTCAAGAGTCAAATTAAAACTGGAAAAATCGCGCATACCAAATCGTAAAACGCTC
19709451 GATCGCTTTC
66 GATCGCTTTC
** * *
19709461 TAGTAGGATTTTCAAGAGTTGAATTAAAACTGGAAAATTCGCGCATACCAAATCGTAAAGCGCTC
1 TAGTAGGATTTTCAAGAGTCAAATTAAAACTGGAAAAATCGCGCATACCAAATCGTAAAACGCTC
19709526 GATCGCT
66 GATCGCT
19709533 CGTTCGATGC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (75 bp):
TAGTAGGATTTTCAAGAGTCAAATTAAAACTGGAAAAATCGCGCATACCAAATCGTAAAACGCTC
GATCGCTTTC
Found at i:19710868 original size:14 final size:14
Alignment explanation
Indices: 19710851--19710878 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19710841 TCTTTTTATT
19710851 TTATTTTCTTTTAA
1 TTATTTTCTTTTAA
19710865 TTATTTTCTTTTAA
1 TTATTTTCTTTTAA
19710879 CTTTCATTTT
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:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTTTCTTTTAA
Found at i:19713048 original size:27 final size:27
Alignment explanation
Indices: 19713010--19713069 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
19713000 ACTGTGATAA
19713010 GTCCTACTGCTGAGGACTTCTAGGATT
1 GTCCTACTGCTGAGGACTTCTAGGATT
19713037 GTCCTACTGCTGAGGACTTCTAGGATT
1 GTCCTACTGCTGAGGACTTCTAGGATT
*
19713064 ATCCTA
1 GTCCTA
19713070 AGTAACTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (27 bp):
GTCCTACTGCTGAGGACTTCTAGGATT
Found at i:19718292 original size:30 final size:31
Alignment explanation
Indices: 19718235--19718294 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
19718225 AGGGAGGAGA
*
19718235 TGGGAGAGAAGTAAAAGTTTTTGGGGAAAAG
1 TGGGAGAGAAGTAAAAGATTTTGGGGAAAAG
*
19718266 TGGGAGGGAA-TAAAA-ATTTTGAGGGAAAA
1 TGGGAGAGAAGTAAAAGATTTTG-GGGAAAA
19718295 TAAAAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.19
30 12 0.46
31 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.22
Consensus pattern (31 bp):
TGGGAGAGAAGTAAAAGATTTTGGGGAAAAG
Done.