Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 154 of 199
Found at i:46052294 original size:21 final size:23
Alignment explanation
Indices: 46052268--46052312 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
46052258 AAAGAGTATC
*
46052268 TACAAATTAA-ATC-TCTAAGAT
1 TACAAAATAATATCTTCTAAGAT
46052289 TACAAAATAATATCTTCTAAGAT
1 TACAAAATAATATCTTCTAAGAT
46052312 T
1 T
46052313 GTATATATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 3 0.14
23 9 0.43
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (23 bp):
TACAAAATAATATCTTCTAAGAT
Found at i:46052333 original size:21 final size:21
Alignment explanation
Indices: 46052304--46052379 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
46052294 AATAATATCT
46052304 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
* *
46052325 TCTAGGATTGCATATATCATA
1 TCTAAGATTGTATATATCATA
**
46052346 TCTAAGATTG--CGTATCATA
1 TCTAAGATTGTATATATCATA
*
46052365 TCTGAGATTGTATAT
1 TCTAAGATTGTATAT
46052380 CCTCGAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.36
21 29 0.64
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:46052339 original size:19 final size:19
Alignment explanation
Indices: 46052317--46052380 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
46052307 AAGATTGTAT
46052317 ATATCATATCTAGGATTGC
1 ATATCATATCTAGGATTGC
*
46052336 ATATATCATATCTAAGATTGC
1 --ATATCATATCTAGGATTGC
* *
46052357 GTATCATATCT-GAGATTGT
1 ATATCATATCTAG-GATTGC
46052376 ATATC
1 ATATC
46052381 CTCGAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 19 0.51
21 18 0.49
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAGGATTGC
Found at i:46052766 original size:44 final size:44
Alignment explanation
Indices: 46052690--46053199 Score: 186
Period size: 44 Copynumber: 11.8 Consensus size: 44
46052680 CTCTAATCCA
* * * * *
46052690 CTCCACTACAACTT-AGGGAGACAGGATTTGTTTATTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
46052733 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGTTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGTTTACTTAGTCTG
* * * * *
46052777 CTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-TCTT
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
* * ** * *
46052818 CT-CTCTGCAACTTCAGAGAGATAAGATCCAAGGTT--TT-GATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA--CTTGTTTACTTAG-TCTG
* * *** * *
46052861 CTCCACTGCAACTTCAGGGAGATAGGA-TTATCGGCTCTAATATG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACT-TAGTCTG
* * ** *
46052905 CTCCACTGCAACTTTAGGGAGATAAGATTTG-CCATCTTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTA-CTT-AGTCTG
* * * * *
46052950 C-CTCACTACAACTTCA-GGAGGATAAGACTTGCTTGCTGAGTCTA
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGTTTACTTAGTCTG
* * * *
46052994 CTCCACTGCAACTTTAGGGAGATAAGACTAG-ATACGT--TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
* * ** * *
46053035 CT-CTCTGCAACTTCAGAGAGATAAGATCCAAGGTT--TTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA--CTTGTTTACTTAGTCTG
* * * * * *
46053078 CTCCACTGCAACTTCAAGAAGATAGGATTATCGGTT--TTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACT-T-GTTTACTTAGTCTG
* * * * ** *
46053122 CTCTACTGCAACTTCCGAGAGATAAGATTTG-CCATCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTA-CTT-AGTCTG
*
46053167 CCCCACTGCAACTTCA-GGAGGATAAGACTTGTT
1 CTCCACTGCAACTTCAGGGA-GATAAGACTTGTT
46053200 GGCTTAAATC
Statistics
Matches: 349, Mismatches: 80, Indels: 73
0.70 0.16 0.15
Matches are distributed among these distances:
40 43 0.12
41 11 0.03
42 9 0.03
43 32 0.09
44 186 0.53
45 68 0.19
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
Found at i:46053108 original size:217 final size:217
Alignment explanation
Indices: 46052727--46053197 Score: 735
Period size: 217 Copynumber: 2.2 Consensus size: 217
46052717 TTGTTTATTT
* * *
46052727 AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTTC
1 AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTGAGTCTACTCCACTGCAACTTC
* * *
46052792 AGGGAGATAAGACTAGATGCGATCTTCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
66 AGGGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
* * *
46052857 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTCTAATATGCTCCACTGCAACTTTAG
131 TCCGCTCCACTGCAACTTCAAGAAGATAGGATTATCGGCTCTAATATGCTCCACTGCAACTTCAG
*
46052922 GGAGATAAGATTTGCCATCTTC
196 AGAGATAAGATTTGCCATCTTC
* * * *
46052944 AGTCTACCTCACTACAACTTCAGGAGGATAAGACTTGCTTGCTGAGTCTACTCCACTGCAACTTT
1 AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTGAGTCTACTCCACTGCAACTTC
*
46053009 AGGGAGATAAGACTAGATACGTTCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
66 AGGGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
* * * * * *
46053074 TCTGCTCCACTGCAACTTCAAGAAGATAGGATTATCGGTTTTAATCTGCTCTACTGCAACTTCCG
131 TCCGCTCCACTGCAACTTCAAGAAGATAGGATTATCGGCTCTAATATGCTCCACTGCAACTTCAG
46053139 AGAGATAAGATTTGCCATCTTC
196 AGAGATAAGATTTGCCATCTTC
* *
46053161 AATCTGCCCCACTGCAACTTCAGGAGGATAAGACTTG
1 AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTG
46053198 TTGGCTTAAA
Statistics
Matches: 229, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
217 229 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTGAGTCTACTCCACTGCAACTTC
AGGGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
TCCGCTCCACTGCAACTTCAAGAAGATAGGATTATCGGCTCTAATATGCTCCACTGCAACTTCAG
AGAGATAAGATTTGCCATCTTC
Found at i:46053210 original size:45 final size:44
Alignment explanation
Indices: 46053072--46053213 Score: 124
Period size: 45 Copynumber: 3.2 Consensus size: 44
46053062 CCAAGGTTTT
* * * * *
46053072 AATCTGCTCCACTGCAACTTCAAGAAGATAGGATTATCGGTTTT
1 AATCTGCTCCACTGCAACTTCAAGAGGATAAGATTGTCGGCTTA
* * * ** *
46053116 AATCTGCTCTACTGCAACTTC-CGAGAGATAAGATTTGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAAGAG-GATAAGA-TTGTCGGCTTA
* * *
46053161 AATCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGTTGGCTTA
1 AATCTGCTCCACTGCAACTTCAAGAGGATAAGA-TTGTCGGCTTA
46053206 AATCTGCT
1 AATCTGCT
46053214 TCCCACTATC
Statistics
Matches: 75, Mismatches: 20, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
43 2 0.03
44 26 0.35
45 44 0.59
46 3 0.04
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAAGAGGATAAGATTGTCGGCTTA
Found at i:46053278 original size:44 final size:44
Alignment explanation
Indices: 46053140--46053414 Score: 132
Period size: 44 Copynumber: 6.2 Consensus size: 44
46053130 CAACTTCCGA
* * * **
46053140 GAGATAAGATTTGCCATCTTCAATCTGCCCCACTGCAACTTCA-G
1 GAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT-AGG
* ** * *
46053184 GAGGATAAGACTTGTTGGCTTAAATCTGCTTCCCACTA-T-CTT-GG
1 GA-GATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG
* *
46053228 AAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGG
1 -GAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGG
* * ** * * * * * *
46053273 GAGATAAGATCTACAATCTTTAACCTACTCCGCTGCTGCTCAGG
1 GAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGG
* ** ** * * *
46053317 GAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GAA
1 GAGATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAG-G
* * *
46053361 AAGATAAGATTTGCCGTCTTCGATCTGTTCCACTACTGCTTAGG
1 GAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGG
46053405 GAGATAAGAT
1 GAGATAAGAT
46053415 CTACAATCTT
Statistics
Matches: 161, Mismatches: 56, Indels: 28
0.66 0.23 0.11
Matches are distributed among these distances:
42 12 0.07
43 5 0.03
44 106 0.66
45 29 0.18
46 4 0.02
47 5 0.03
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
GAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGG
Found at i:46053346 original size:132 final size:132
Alignment explanation
Indices: 46053194--46053464 Score: 488
Period size: 132 Copynumber: 2.1 Consensus size: 132
46053184 GAGGATAAGA
* *
46053194 CTTGTTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATAAGATTTGCCGTCTTCGATCTGCTC
*
46053259 CACTACTGCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCACTGCTGCTCAGGGAGACAA
46053324 GG
131 GG
*
46053326 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATAAGATTTGCCGTCTTCGATCTGTTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATAAGATTTGCCGTCTTCGATCTGCTC
*
46053391 CACTACTGCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCATTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCACTGCTGCTCAGGGAGACAA
46053456 GG
131 GG
*
46053458 TTTGGTG
1 CTTGGTG
46053465 TTTCACCGGT
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (132 bp):
CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATAAGATTTGCCGTCTTCGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCACTGCTGCTCAGGGAGACAA
GG
Found at i:46054720 original size:8 final size:8
Alignment explanation
Indices: 46054707--46054732 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
46054697 TCCATTTTAC
46054707 TTTTTCAT
1 TTTTTCAT
46054715 TTTTTCAT
1 TTTTTCAT
46054723 TTTTTCAT
1 TTTTTCAT
46054731 TT
1 TT
46054733 CGTCATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:46055132 original size:26 final size:26
Alignment explanation
Indices: 46055102--46055155 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
46055092 ACTCAGAGAG
46055102 AAAGAATCTCGTCTTCAATAAGCAAA
1 AAAGAATCTCGTCTTCAATAAGCAAA
46055128 AAAGAATCTCGTCTTCAATAAGCAAA
1 AAAGAATCTCGTCTTCAATAAGCAAA
46055154 AA
1 AA
46055156 CCGCGATGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (26 bp):
AAAGAATCTCGTCTTCAATAAGCAAA
Found at i:46060650 original size:19 final size:19
Alignment explanation
Indices: 46060628--46060670 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
46060618 AATATTGTAT
46060628 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
*
46060647 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
46060666 ATATC
1 ATATC
46060671 CTCGAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:46068547 original size:21 final size:19
Alignment explanation
Indices: 46068514--46068556 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
46068504 TTAAATTCTA
46068514 AGTTTAAAGTTTATTCGATTT
1 AGTTTAAAGTTTA--CGATTT
**
46068535 AGTTTAACTTTTACGATTT
1 AGTTTAAAGTTTACGATTT
46068554 AGT
1 AGT
46068557 CCATGTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (19 bp):
AGTTTAAAGTTTACGATTT
Found at i:46075402 original size:13 final size:13
Alignment explanation
Indices: 46075384--46075475 Score: 57
Period size: 13 Copynumber: 6.7 Consensus size: 13
46075374 TTAATTTAAA
46075384 ATATATATATTAT
1 ATATATATATTAT
46075397 ATATATACGTAATTA-
1 ATATATA--T-ATTAT
*
46075412 ATGAT-TATGTT-T
1 AT-ATATATATTAT
*
46075424 TTATATTATATTAT
1 ATATA-TATATTAT
46075438 -TATTAATATATTAT
1 ATA-T-ATATATTAT
46075452 ATTATATTATATTAT
1 A-TATA-TATATTAT
46075467 ATATATATA
1 ATATATATA
46075476 ACAAAAGAGA
Statistics
Matches: 63, Mismatches: 3, Indels: 26
0.68 0.03 0.28
Matches are distributed among these distances:
11 2 0.03
12 3 0.05
13 19 0.30
14 15 0.24
15 16 0.25
16 8 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:46075434 original size:5 final size:5
Alignment explanation
Indices: 46075424--46075474 Score: 70
Period size: 5 Copynumber: 10.2 Consensus size: 5
46075414 GATTATGTTT
46075424 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA TTATA TATATA
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA T-TATA
46075474 T
1 T
46075475 AACAAAAGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 28 0.67
6 10 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:46075449 original size:19 final size:20
Alignment explanation
Indices: 46075424--46075474 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 20
46075414 GATTATGTTT
46075424 TTATATTATATTATTATTA-A
1 TTATATTATATTA-TATTATA
46075444 -TATATTATATTATATTATA
1 TTATATTATATTATATTATA
46075463 TTATATATATAT
1 TTATAT-TATAT
46075475 AACAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.18
19 13 0.46
20 5 0.18
21 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATATTATATTATATTATA
Found at i:46075451 original size:24 final size:24
Alignment explanation
Indices: 46075424--46075472 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
46075414 GATTATGTTT
46075424 TTATATTATATTATTATTA-ATATA
1 TTATATTATATTA-TATTATATATA
46075448 TTATATTATATTATATTATATATA
1 TTATATTATATTATATTATATATA
46075472 T
1 T
46075473 ATAACAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATATTATATTATATTATATATA
Found at i:46075555 original size:17 final size:17
Alignment explanation
Indices: 46075530--46075563 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46075520 ACGAAACAGA
*
46075530 GAAGGAAAGAAAGAAAG
1 GAAGAAAAGAAAGAAAG
46075547 GAAGAAAAGAAAGAAAG
1 GAAGAAAAGAAAGAAAG
46075564 AAAAGGGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
GAAGAAAAGAAAGAAAG
Found at i:46075567 original size:13 final size:13
Alignment explanation
Indices: 46075529--46075568 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
46075519 AACGAAACAG
*
46075529 AGAAGGAAAG-AA
1 AGAAAGAAAGAAA
*
46075541 AGAAAGGAAGAAA
1 AGAAAGAAAGAAA
46075554 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
46075567 AG
1 AG
46075569 GGGAAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGAAA
Found at i:46076392 original size:19 final size:19
Alignment explanation
Indices: 46076368--46076442 Score: 68
Period size: 19 Copynumber: 4.0 Consensus size: 19
46076358 TTATGTGTGA
46076368 ATATGTGAATTGTGAATTG
1 ATATGTGAATTGTGAATTG
*
46076387 ATATGTGAATTG-GAAATCG
1 ATATGTGAATTGTG-AATTG
* *
46076406 AGATATGAGATT-TGAA--G
1 ATATGTGA-ATTGTGAATTG
46076423 ATATGTGAATATGTGAATTG
1 ATATGTGAAT-TGTGAATTG
46076443 TGTATTGATT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
16 2 0.05
17 8 0.18
18 5 0.11
19 24 0.55
20 5 0.11
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.36
Consensus pattern (19 bp):
ATATGTGAATTGTGAATTG
Found at i:46078850 original size:33 final size:34
Alignment explanation
Indices: 46078799--46079006 Score: 118
Period size: 33 Copynumber: 5.7 Consensus size: 34
46078789 TTATCCGTTA
* *
46078799 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGGTGGAATCAGCACTTAGCAACCACCAATGAT
**
46078833 TCGG-GGAATCAGCACTTAGCAACCCTTTTCACAGTCAAAAAT
1 TCGGTGGAATCAGCACTTAGCAA--C----CAC---CAATGAT
* * *
46078875 ACGGTAGAATCAGCAC-TAGCAACCACCAATGAA
1 TCGGTGGAATCAGCACTTAGCAACCACCAATGAT
* * * *
46078908 TCAG-GGAATCAACACTTAGCAACCCCTTTCACTTTTAAGAT
1 TCGGTGGAATCAGCACTTAGCAACCAC---CA-----ATGAT
* *
46078949 ACGGTGGGATCAGCACTTAGCAACCACCAATGAT
1 TCGGTGGAATCAGCACTTAGCAACCACCAATGAT
46078983 TCGG-GGAATCAGCACTTAGCAACC
1 TCGGTGGAATCAGCACTTAGCAACC
46079007 CCGTTCACAT
Statistics
Matches: 130, Mismatches: 24, Indels: 41
0.67 0.12 0.21
Matches are distributed among these distances:
32 9 0.07
33 51 0.39
34 11 0.08
35 1 0.01
36 5 0.04
39 5 0.04
40 1 0.01
41 5 0.04
42 32 0.25
43 10 0.08
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (34 bp):
TCGGTGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:46078938 original size:75 final size:74
Alignment explanation
Indices: 46078800--46079047 Score: 345
Period size: 75 Copynumber: 3.3 Consensus size: 74
46078790 TATCCGTTAT
* * *
46078800 CGGTGGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCTTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
46078865 AGTCAAAAATA
66 A-T-TAAAATA
* * * *
46078876 CGGTAGAATCAGCAC-TAGCAACCACCAATGAATCAGGGAATCAACACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
* *
46078940 TTTTAAGATA
66 -ATTAAAATA
* *
46078950 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCGTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
46079015 ATTTAAATA
66 ATTAAAATA
46079024 CGGTGGAATCAGCACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACC
46079048 CCTTTATATT
Statistics
Matches: 150, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
74 47 0.31
75 90 0.60
76 13 0.09
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (74 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTAAAATA
Found at i:46086504 original size:16 final size:16
Alignment explanation
Indices: 46086483--46086534 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
46086473 TTTGGTTCGC
46086483 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
46086499 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
46086515 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
46086531 TGTA
1 TGTA
46086535 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:46086787 original size:16 final size:16
Alignment explanation
Indices: 46086750--46086791 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
46086740 TTAATCATAT
*
46086750 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
46086766 TT-AAATATATTATAA
1 TTAAAATATATTATAA
46086781 TTAAAATATAT
1 TTAAAATATAT
46086792 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:46086798 original size:14 final size:15
Alignment explanation
Indices: 46086759--46086800 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
46086749 TTTAAACATA
*
46086759 ATTATTATTAAATAT
1 ATTATAATTAAATAT
46086774 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
46086788 A-TATAATTTAATA
1 ATTATAATTAAATA
46086801 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:46086872 original size:107 final size:108
Alignment explanation
Indices: 46086748--46086958 Score: 370
Period size: 107 Copynumber: 2.0 Consensus size: 108
46086738 ATTTAATCAT
*
46086748 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
* *
46086813 ATTAATATTCTTATATGAATTTACTCAAATCATAATATAGATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATAGATA
*
46086856 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAGTTATTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
*
46086920 ATCAATATTCTTATATGAATTTACTAAAATTATAATATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATA
46086959 TAATACTATA
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 94 0.96
108 4 0.04
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (108 bp):
ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
ATCAATATTCTTATATGAATTTACTAAAATCATAATATAGATA
Found at i:46086896 original size:16 final size:16
Alignment explanation
Indices: 46086853--46086898 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
46086843 CATAATATAG
*
46086853 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
46086869 ATTATT-AAATATATT
1 ATAATTAAAATATATT
46086884 ATAATTAAAATATAT
1 ATAATTAAAATATAT
46086899 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:46086905 original size:14 final size:15
Alignment explanation
Indices: 46086853--46086907 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
46086843 CATAATATAG
46086853 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
46086869 ATTATTAAATATATT
1 ATAATTAAATATATT
46086884 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
46086897 ATAATTTAATA
1 ATAATTAAATA
46086908 AAGTTATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:46087009 original size:107 final size:107
Alignment explanation
Indices: 46086751--46087014 Score: 326
Period size: 107 Copynumber: 2.5 Consensus size: 107
46086741 TAATCATATT
* * * *
46086751 TAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
1 TAAA-ATAATAATTATGAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATC
* * *
46086816 AATATTCTTATATGAATTTACTCAAATCATAATATAGATAATT
65 AATATTCTTATATGAATTTACTAAAATCATAATATAAATAATA
* * * *
46086859 TAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAGTTATTAATAATCA
1 TAAAATAATAATTATGAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCA
* *
46086924 ATATTCTTATATGAATTTACTAAAATTATAATATATAATACTA
66 ATATTCTTATATGAATTTACTAAAATCATAATATA-AATAATA
46086967 TAAAAT-ATAATT-TGAAATA-ATTA-ATATT-AAATATAT--TTTAATTAAAAT
1 TAAAATAATAATTATGAAATATATTATA-ATTAAAATATATAATTTAA-TAAAAT
46087015 ATATGATTTA
Statistics
Matches: 140, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
102 5 0.04
103 5 0.04
104 9 0.06
105 7 0.05
106 6 0.04
107 96 0.69
108 12 0.09
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (107 bp):
TAAAATAATAATTATGAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCA
ATATTCTTATATGAATTTACTAAAATCATAATATAAATAATA
Found at i:46087029 original size:59 final size:58
Alignment explanation
Indices: 46086853--46087031 Score: 152
Period size: 59 Copynumber: 3.0 Consensus size: 58
46086843 CATAATATAG
* * *
46086853 ATAATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAGT
1 ATAATTTAA-ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAAT
* ** * *
46086912 -T-A-TT-AATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATAATACT-ATAAAA
1 ATAATTTAAATAATTAATATT-AAATAT--ATTT--T--AATTAAAATATATAAT-TTAATAAAA
46086972 T
58 T
*
46086973 ATAATTTGAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAAT
1 ATAATTT-AAATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAAT
46087032 TTAAAATAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 2 0.02
57 4 0.04
58 2 0.02
59 22 0.24
61 22 0.24
62 2 0.02
63 5 0.05
64 2 0.02
65 4 0.04
66 12 0.13
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (58 bp):
ATAATTTAAATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAAT
Found at i:46090477 original size:13 final size:12
Alignment explanation
Indices: 46090436--46090500 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 12
46090426 AGATTTTTCC
46090436 TAAATATTATCA
1 TAAATATTATCA
* * *
46090448 CAAA-ATAATCC
1 TAAATATTATCA
46090459 TAAATATTATCAA
1 TAAATATTATC-A
*
46090472 TAAATAAT-TC-
1 TAAATATTATCA
46090482 TAAATATTATCA
1 TAAATATTATCA
46090494 CTAAATA
1 -TAAATA
46090501 ATTTAAAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
10 7 0.17
11 10 0.25
12 10 0.25
13 13 0.32
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAATATTATCA
Found at i:46090503 original size:23 final size:23
Alignment explanation
Indices: 46090435--46090507 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
46090425 TAGATTTTTC
* *
46090435 CTAAATATTATCACAAAATAATC
1 CTAAATATTATCACTAAATAATT
*
46090458 CTAAATATTATCAATAAATAATT
1 CTAAATATTATCACTAAATAATT
46090481 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
46090504 -TAAA
1 CTAAA
46090508 AATCAAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 4 0.09
23 42 0.91
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:46102979 original size:90 final size:90
Alignment explanation
Indices: 46102855--46103024 Score: 313
Period size: 90 Copynumber: 1.9 Consensus size: 90
46102845 TAATTTGATT
46102855 AAAACATAGTTAAATAAGTAAATTAAAGTTAATTAACAAACTAATCTTAGTATAAAAGTGAAATT
1 AAAACATAGTTAAATAAGTAAATTAAAGTTAATTAACAAACTAATCTTAGTATAAAAGTGAAATT
*
46102920 TGTGGATAGAGAGATCCAAGTTACC
66 GGTGGATAGAGAGATCCAAGTTACC
*
46102945 AAAACATAGTTAAATAAGTAAATTAAGGTTAATTAACAAACTAATCTTAGTATAAAAGTGAAATT
1 AAAACATAGTTAAATAAGTAAATTAAAGTTAATTAACAAACTAATCTTAGTATAAAAGTGAAATT
*
46103010 GGTGGATGGAGAGAT
66 GGTGGATAGAGAGAT
46103025 GATATATCAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 77 1.00
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (90 bp):
AAAACATAGTTAAATAAGTAAATTAAAGTTAATTAACAAACTAATCTTAGTATAAAAGTGAAATT
GGTGGATAGAGAGATCCAAGTTACC
Found at i:46104452 original size:18 final size:17
Alignment explanation
Indices: 46104401--46104453 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
46104391 TTCTCGTGAA
46104401 AAATCAAAA-TAAAATTG
1 AAAT-AAAAGTAAAATTG
*
46104418 AAATAAAAGTTACAATTG
1 AAATAAAAG-TAAAATTG
46104436 AAAGTAAAAGTAAAATTG
1 AAA-TAAAAGTAAAATTG
46104454 TAACATCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 17 0.55
19 6 0.19
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.25
Consensus pattern (17 bp):
AAATAAAAGTAAAATTG
Found at i:46109097 original size:62 final size:63
Alignment explanation
Indices: 46109029--46109149 Score: 183
Period size: 62 Copynumber: 1.9 Consensus size: 63
46109019 CCCACATGGA
* ** *
46109029 CTGGACACACGCCCATGTCTCTGGCTTGTGT-GACTCTAATTC-CAAACAGTGAGTTACACGAC
1 CTGGACACACGCCCATGTCCCTGGCCCGTGTAAAC-CTAATTCACAAACAGTGAGTTACACGAC
46109091 CTGGACACACGCCCATGTCCCTGGCCCGTGTAAACCTAATTCACAAACAGTGAGTTACA
1 CTGGACACACGCCCATGTCCCTGGCCCGTGTAAACCTAATTCACAAACAGTGAGTTACA
46109150 TAGCCTGTCA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
62 35 0.66
63 18 0.34
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (63 bp):
CTGGACACACGCCCATGTCCCTGGCCCGTGTAAACCTAATTCACAAACAGTGAGTTACACGAC
Found at i:46119470 original size:13 final size:13
Alignment explanation
Indices: 46119452--46119482 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
46119442 CACTCAATCG
46119452 GTTAATGTATCAT
1 GTTAATGTATCAT
46119465 GTTAATGTATCAT
1 GTTAATGTATCAT
46119478 GTTAA
1 GTTAA
46119483 AAAATAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.45
Consensus pattern (13 bp):
GTTAATGTATCAT
Found at i:46119530 original size:24 final size:24
Alignment explanation
Indices: 46119502--46119556 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
46119492 TAGACTAATT
46119502 GGTTAATGTATCATGTTAGCAATC
1 GGTTAATGTATCATGTTAGCAATC
46119526 GGTTAATGTATCATGTTAGCAATC
1 GGTTAATGTATCATGTTAGCAATC
*
46119550 GATTAAT
1 GGTTAAT
46119557 CAAAACAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (24 bp):
GGTTAATGTATCATGTTAGCAATC
Found at i:46120406 original size:15 final size:15
Alignment explanation
Indices: 46120367--46120406 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
46120357 CCATTTTTTA
46120367 TTTTTT-AAATTAAT
1 TTTTTTAAAATTAAT
46120381 TTTATTTAAAATTAAT
1 TTT-TTTAAAATTAAT
46120397 TTTTTTAAAA
1 TTTTTTAAAA
46120407 AAAATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.12
15 10 0.42
16 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTTAAAATTAAT
Found at i:46123757 original size:17 final size:16
Alignment explanation
Indices: 46123735--46123768 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
46123725 CGACCCACCC
46123735 ATATTAAAATTTTTTTT
1 ATATT-AAATTTTTTTT
*
46123752 ATATTATATTTTTTTT
1 ATATTAAATTTTTTTT
46123768 A
1 A
46123769 CATAATTTTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATTAAATTTTTTTT
Found at i:46128843 original size:17 final size:16
Alignment explanation
Indices: 46128816--46128849 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
46128806 CACTTTTGAG
*
46128816 CATATATCACATTACA
1 CATATATCACATAACA
46128832 CATATAATCACATAACA
1 CATAT-ATCACATAACA
46128849 C
1 C
46128850 TTAAGCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
CATATATCACATAACA
Found at i:46128857 original size:39 final size:39
Alignment explanation
Indices: 46128814--46128989 Score: 228
Period size: 39 Copynumber: 4.5 Consensus size: 39
46128804 TCCACTTTTG
* *
46128814 AGCATATATCACATTACACATATAATCACATAACACTT-A
1 AGCATATATCACAATACTCATATAATCACATAACA-TTCA
* *
46128853 AGCATATATCACAATACTCATATAATTACATAACGTTCA
1 AGCATATATCACAATACTCATATAATCACATAACATTCA
* * * *
46128892 AGCACATATCGCAATATTCATATGATCACATAACATTCA
1 AGCATATATCACAATACTCATATAATCACATAACATTCA
**
46128931 AGCATATATCGTAATACTCATATAATCACATAACATTCA
1 AGCATATATCACAATACTCATATAATCACATAACATTCA
* *
46128970 AGCATATGTCGCAATACTCA
1 AGCATATATCACAATACTCA
46128990 AAAACATGTT
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
38 2 0.02
39 118 0.98
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (39 bp):
AGCATATATCACAATACTCATATAATCACATAACATTCA
Found at i:46145626 original size:3 final size:3
Alignment explanation
Indices: 46145620--46145649 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
46145610 ATAATAATAA
46145620 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
46145650 TATTCGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:46145642 original size:17 final size:16
Alignment explanation
Indices: 46145620--46145653 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
46145610 ATAATAATAA
46145620 TATTATTATTATATTAT
1 TATTATTATTAT-TTAT
46145637 TATTATTATTATTTAT
1 TATTATTATTATTTAT
46145653 T
1 T
46145654 CGGTTACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTATTATTATTTAT
Found at i:46156678 original size:18 final size:17
Alignment explanation
Indices: 46156657--46156698 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
46156647 TTATAATCTT
46156657 ATTTAATAAAAATGTTAA
1 ATTTAATAAAAAT-TTAA
*
46156675 ATTTAA-AGAAATTTAA
1 ATTTAATAAAAATTTAA
46156691 A-TTAATAA
1 ATTTAATAA
46156699 TTTATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 4 0.19
16 6 0.29
17 5 0.24
18 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
ATTTAATAAAAATTTAA
Found at i:46157451 original size:20 final size:20
Alignment explanation
Indices: 46157410--46157452 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
46157400 ATTAAAACTT
* *
46157410 TATTTTAATTTTATTATGCA
1 TATTTTAATTATATTATACA
46157430 TATTTT-ATTATATCTATACA
1 TATTTTAATTATAT-TATACA
46157450 TAT
1 TAT
46157453 ATTTTCTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTTTAATTATATTATACA
Found at i:46159533 original size:54 final size:54
Alignment explanation
Indices: 46159469--46159578 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
46159459 ACATAAATGC
46159469 ACAACATAACCCGCATAAAAGATACACCAAATTGCATCCCAAACATTGCATATA
1 ACAACATAACCCGCATAAAAGATACACCAAATTGCATCCCAAACATTGCATATA
*
46159523 ACAACATAACCTGCATAAAAGATACACCAAATTGCATCCCAAACATTGCATATA
1 ACAACATAACCCGCATAAAAGATACACCAAATTGCATCCCAAACATTGCATATA
46159577 AC
1 AC
46159579 CATTACCAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.46, C:0.27, G:0.07, T:0.19
Consensus pattern (54 bp):
ACAACATAACCCGCATAAAAGATACACCAAATTGCATCCCAAACATTGCATATA
Found at i:46161521 original size:22 final size:22
Alignment explanation
Indices: 46161477--46161521 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
46161467 CGAGTCGTTA
* * *
46161477 CACCATGCTTTAATGTGATGAC
1 CACCATGATTTAATGTCACGAC
*
46161499 CACCATGATTTCATGTCACGAC
1 CACCATGATTTAATGTCACGAC
46161521 C
1 C
46161522 TGAGTTGTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (22 bp):
CACCATGATTTAATGTCACGAC
Found at i:46162156 original size:41 final size:41
Alignment explanation
Indices: 46162099--46162418 Score: 213
Period size: 41 Copynumber: 7.8 Consensus size: 41
46162089 ATTTTTAAAC
* *
46162099 CTTTAGCGGCGTTTTTATTTTAGCGCCACTAATTCTCCGAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCCGAT
* **
46162140 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGT-TCTGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAAT-TCTCCGAT
* * *
46162181 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCT-CGTAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCCG-AT
* * * * * * *
46162222 CATTAGTGGCGTTATTGTCTGAGCGCCAGTAATTCTCTGTT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCCGAT
* * * * **
46162263 CTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGTTTTTTTG-T
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACT-AA--TTCTCCGAT
* * * * * **
46162306 TTTTAGTGGCGTTTTTATCTGAGAGCCACTAATACTCTGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCCGAT
* * * * *
46162347 CTTTAGCGGCGTTTTATATGTAAGCGCCGCTAATGCT---AC
1 CTTTAGCGGCGTTTT-TATCTGAGCGCCACTAATTCTCCGAT
* *
46162386 CTTTAGCGGCGTTTTT-TCCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTATCTG-AGCGCCACTAAT
46162419 AGTAACAAAA
Statistics
Matches: 218, Mismatches: 51, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
37 1 0.00
38 13 0.06
39 16 0.07
40 5 0.02
41 131 0.60
42 22 0.10
43 25 0.11
44 5 0.02
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCCGAT
Found at i:46162243 original size:82 final size:81
Alignment explanation
Indices: 46162098--46162383 Score: 313
Period size: 82 Copynumber: 3.5 Consensus size: 81
46162088 GATTTTTAAA
* * * * *
46162098 CCTTTAGCGGCGTTTTTATTTTAGCGCCACTAATTCTCCG-ATCTTTAGCGGCGTTTTTATCTGA
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCT-CGTATCTTTAGTGGCGTTTTTATCTGA
46162162 GCGCCACTAATGTTCTGG
65 GCGCCACTAAT-TTCTGG
* * *
46162180 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTATTGTCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
* *
46162245 CGCCAGTAATTCTCTGT
66 CGCCACTAATT-TCTGG
* * ** ** * *
46162262 TCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGTTTTTTTGTTTTTAGTGGCGTTTTTATCTG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCT-AA-TGCTCGTATCTTTAGTGGCGTTTTTATCTG
* *
46162327 AGAGCCACTAATACTCTGG
64 AGCGCCACTAAT-TTCTGG
*
46162346 CCTTTAGCGGCGTTTTATATGTAAGCGCCGCTAATGCT
1 CCTTTAGCGGCGTTTT-TATCTAAGCGCCGCTAATGCT
46162384 ACCTTTAGCG
Statistics
Matches: 168, Mismatches: 30, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
81 3 0.02
82 96 0.57
83 4 0.02
84 52 0.31
85 13 0.08
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (81 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
CGCCACTAATTTCTGG
Found at i:46164688 original size:10 final size:10
Alignment explanation
Indices: 46164673--46164717 Score: 76
Period size: 10 Copynumber: 4.7 Consensus size: 10
46164663 TATTTTTACT
46164673 TATATATGGA
1 TATATATGGA
46164683 TATATATGGA
1 TATATATGGA
46164693 TATATATGGA
1 TATATATGGA
46164703 TATATAT--A
1 TATATATGGA
46164711 TATATAT
1 TATATAT
46164718 ATAGTTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.23
10 27 0.77
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (10 bp):
TATATATGGA
Found at i:46164826 original size:27 final size:27
Alignment explanation
Indices: 46164785--46164836 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
46164775 AATAAACAAA
* *
46164785 TAAATAAGTTAGTAATTATTTATTTGT
1 TAAATAAATTAGTAATTAATTATTTGT
*
46164812 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATTAGTAATTAATTATTT
46164837 AAAAGTAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (27 bp):
TAAATAAATTAGTAATTAATTATTTGT
Found at i:46166111 original size:25 final size:25
Alignment explanation
Indices: 46166082--46166147 Score: 132
Period size: 25 Copynumber: 2.6 Consensus size: 25
46166072 ATCATTATAT
46166082 GTAAGATTTTACGAATAATGATGTA
1 GTAAGATTTTACGAATAATGATGTA
46166107 GTAAGATTTTACGAATAATGATGTA
1 GTAAGATTTTACGAATAATGATGTA
46166132 GTAAGATTTTACGAAT
1 GTAAGATTTTACGAAT
46166148 GTTTAATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (25 bp):
GTAAGATTTTACGAATAATGATGTA
Found at i:46167837 original size:21 final size:21
Alignment explanation
Indices: 46167811--46167855 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
46167801 CAACTTAAAA
*
46167811 CAGAGG-CGACAGCGAGGGAAG
1 CAGAGGCCG-CAGCGAGAGAAG
46167832 CAGAGGCCGCAGCGAGAGAAG
1 CAGAGGCCGCAGCGAGAGAAG
46167853 CAG
1 CAG
46167856 CAAGAGAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.33, C:0.22, G:0.44, T:0.00
Consensus pattern (21 bp):
CAGAGGCCGCAGCGAGAGAAG
Found at i:46168336 original size:43 final size:43
Alignment explanation
Indices: 46168289--46168403 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 43
46168279 ATCATATAGT
*
46168289 GGCGTTTCTGAAAT-AAGCGCCGCTAAAGCACACTACTTTTAGC
1 GGCGTTTCT-AAATAAAGCGCCGCTAAAGAACACTACTTTTAGC
* * **
46168332 GGCGTTTGTAGATAAAGCGCCGCTAAAGAACTTTACTTTTAGC
1 GGCGTTTCTAAATAAAGCGCCGCTAAAGAACACTACTTTTAGC
* *
46168375 GGCATTT-T-ATTCACAAGCGCCGCTAAAGA
1 GGCGTTTCTAAAT-A-AAGCGCCGCTAAAGA
46168404 TCATGGTCTG
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.02
42 5 0.08
43 55 0.90
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (43 bp):
GGCGTTTCTAAATAAAGCGCCGCTAAAGAACACTACTTTTAGC
Found at i:46168418 original size:43 final size:43
Alignment explanation
Indices: 46168346--46168568 Score: 283
Period size: 43 Copynumber: 5.2 Consensus size: 43
46168336 TTTGTAGATA
* * * *
46168346 AAGCGCCGCTAAAGAACTTTA-CTTTTAGCGGCATTTTATTCAC-
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTTTC-CT
* * *
46168389 AAGCGCCGCTAAAGATCATGGTCTGTAGCGGCGTTTTTTT-CT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCT
*
46168431 AAGCGCCGCTAAAGAACATGATCTTTAACGGCGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCT
*
46168474 AAGCGCCGCTAAGGAACATGATCTTTAGCGGCGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCT
* * *
46168517 AAGCGCCGCTAAAGAACATGACCTTTACCGGCG-TTTTTTCTGT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC-CT
46168560 AAGCGCCGC
1 AAGCGCCGC
46168569 AAAAAGTTAG
Statistics
Matches: 159, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
41 1 0.01
42 43 0.27
43 114 0.72
44 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (43 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCT
Found at i:46168481 original size:85 final size:86
Alignment explanation
Indices: 46168346--46168568 Score: 283
Period size: 85 Copynumber: 2.6 Consensus size: 86
46168336 TTTGTAGATA
* * * * * * *
46168346 AAGCGCCGCTAAAGAACTTTACTTTTAGCGGCATTTTATTCAC-AAGCGCCGCTAAAGATCATGG
1 AAGCGCCGCTAAAGAACATGAC-TTTAACGGCGTTTTTTTCACTAAGCGCCGCTAAAGAACATGA
46168410 TCTGTAGCGGCGTTTTTTT-CT
65 TCTGTAGCGGCGTTTTTTTCCT
*
46168431 AAGCGCCGCTAAAGAACATGATCTTTAACGGCGTTTTTTTC-CTAAGCGCCGCTAAGGAACATGA
1 AAGCGCCGCTAAAGAACATGA-CTTTAACGGCGTTTTTTTCACTAAGCGCCGCTAAAGAACATGA
*
46168495 TCTTTAGCGGCGTTTTTTTCCT
65 TCTGTAGCGGCGTTTTTTTCCT
* **
46168517 AAGCGCCGCTAAAGAACATGACCTTTACCGGCG-TTTTTTCTGTAAGCGCCGC
1 AAGCGCCGCTAAAGAACATGA-CTTTAACGGCGTTTTTTTCACTAAGCGCCGC
46168569 AAAAAGTTAG
Statistics
Matches: 122, Mismatches: 12, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
84 1 0.01
85 77 0.63
86 44 0.36
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (86 bp):
AAGCGCCGCTAAAGAACATGACTTTAACGGCGTTTTTTTCACTAAGCGCCGCTAAAGAACATGAT
CTGTAGCGGCGTTTTTTTCCT
Found at i:46169532 original size:12 final size:13
Alignment explanation
Indices: 46169496--46169532 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
46169486 TTTAAACTAA
*
46169496 ACTTCTCAAAAAC
1 ACTTTTCAAAAAC
46169509 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
46169522 ACTTTTCAAAA
1 ACTTTTCAAAA
46169533 GCATTGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:46172423 original size:47 final size:47
Alignment explanation
Indices: 46172369--46172461 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
46172359 ATCAAGCTCA
* * *
46172369 CCTAGAAGGCTAAATGGAACTCGCCAGGTAAAGTATAAGTAAATCCG
1 CCTAGAAGGCTAAATGGAACTCACCAGGTAAAGCATAAATAAATCCG
*
46172416 CCTAGAAGGCTAAATGGAGCTCACCAGGTAAAGCATAAATAAATCC
1 CCTAGAAGGCTAAATGGAACTCACCAGGTAAAGCATAAATAAATCC
46172462 AAATTATACT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (47 bp):
CCTAGAAGGCTAAATGGAACTCACCAGGTAAAGCATAAATAAATCCG
Found at i:46174185 original size:19 final size:19
Alignment explanation
Indices: 46174161--46174198 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
46174151 ACCAAATGGT
46174161 AAGCCAATTTACTCAACCA
1 AAGCCAATTTACTCAACCA
46174180 AAGCCAATTTACTCAACCA
1 AAGCCAATTTACTCAACCA
46174199 TTCAACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.05, T:0.21
Consensus pattern (19 bp):
AAGCCAATTTACTCAACCA
Found at i:46182169 original size:26 final size:27
Alignment explanation
Indices: 46182130--46182217 Score: 75
Period size: 25 Copynumber: 3.5 Consensus size: 27
46182120 AAATTGGTGC
*
46182130 TTAATTGCTATCCATTTTTTGAGCATA
1 TTAATTGCTGTCCATTTTTTGAGCATA
**
46182157 TTAA-TGCTGTCCA--AATTGATGC---
1 TTAATTGCTGTCCATTTTTTGA-GCATA
*
46182179 TTAATTGCTGTCCATTTTTT-AGTATA
1 TTAATTGCTGTCCATTTTTTGAGCATA
46182205 TTAA-TGCTGTCCA
1 TTAATTGCTGTCCA
46182218 AATTGGTGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
22 4 0.08
23 10 0.21
24 5 0.10
25 13 0.27
26 12 0.25
27 4 0.08
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (27 bp):
TTAATTGCTGTCCATTTTTTGAGCATA
Found at i:46182190 original size:23 final size:22
Alignment explanation
Indices: 46182157--46182240 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 22
46182147 TTTGAGCATA
46182157 TTAATGCTGTCCAAATTGATGC
1 TTAATGCTGTCCAAATTGATGC
** *
46182179 TTAATTGCTGTCCATTTTTTAGTAT-A
1 TTAA-TGCTGTCCA--AATT-G-ATGC
*
46182205 TTAATGCTGTCCAAATTGGTGC
1 TTAATGCTGTCCAAATTGATGC
46182227 TTAAATGCTGTCCA
1 TT-AATGCTGTCCA
46182241 TTTTTGTACA
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
21 1 0.02
22 7 0.15
23 22 0.46
25 11 0.23
26 5 0.10
27 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (22 bp):
TTAATGCTGTCCAAATTGATGC
Found at i:46182259 original size:48 final size:48
Alignment explanation
Indices: 46182115--46182264 Score: 221
Period size: 48 Copynumber: 3.1 Consensus size: 48
46182105 GATAATATGT
*
46182115 TGTCCAAATTGGTGCTTAATTGCTATCCATTTTTTGAGCATATTAATGC
1 TGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTT-AGCATATTAATGC
* *
46182164 TGTCCAAATTGATGCTTAATTGCTGTCCATTTTTTAGTATATTAATGC
1 TGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTAATGC
* * *
46182212 TGTCCAAATTGGTGCTTAAATGCTGTCCATTTTTGTA-CAAATCAATGC
1 TGTCCAAATTGGTGCTTAATTGCTGTCCATTTTT-TAGCATATTAATGC
46182260 TGTCC
1 TGTCC
46182265 GAATGTTGTT
Statistics
Matches: 92, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
48 57 0.62
49 35 0.38
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (48 bp):
TGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTAATGC
Found at i:46193263 original size:13 final size:13
Alignment explanation
Indices: 46193227--46193266 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
46193217 AGTTTGGCAA
46193227 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
46193240 TG-TTGTAGAAAAG
1 TGCTT-TTGAAAAG
46193253 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
46193266 T
1 T
46193267 TTGGTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 2 0.09
13 19 0.83
14 2 0.09
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:46194201 original size:24 final size:24
Alignment explanation
Indices: 46194169--46194219 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
46194159 CACCCTTAAA
46194169 ACCATTTCCACAGCTCCTCTCTTC
1 ACCATTTCCACAGCTCCTCTCTTC
46194193 ACCATTTCCACAGCTCCTCTCTTC
1 ACCATTTCCACAGCTCCTCTCTTC
46194217 ACC
1 ACC
46194220 CTATCAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.18, C:0.47, G:0.04, T:0.31
Consensus pattern (24 bp):
ACCATTTCCACAGCTCCTCTCTTC
Found at i:46195266 original size:15 final size:15
Alignment explanation
Indices: 46195246--46195275 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
46195236 TTTCAAATTG
46195246 GTGTTCAAGACTTGT
1 GTGTTCAAGACTTGT
46195261 GTGTTCAAGACTTGT
1 GTGTTCAAGACTTGT
46195276 TCTGTTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (15 bp):
GTGTTCAAGACTTGT
Found at i:46201291 original size:22 final size:22
Alignment explanation
Indices: 46201262--46201323 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
46201252 TTGCTCAGGT
46201262 AATTTCTGCTTCTTCTTCCATC
1 AATTTCTGCTTCTTCTTCCATC
*
46201284 GATTTCTGCTTCTTCTTCCATC
1 AATTTCTGCTTCTTCTTCCATC
*
46201306 AATTTCTACTTCTTCTTC
1 AATTTCTGCTTCTTCTTC
46201324 TTCTAACAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.13, C:0.31, G:0.05, T:0.52
Consensus pattern (22 bp):
AATTTCTGCTTCTTCTTCCATC
Found at i:46202748 original size:4 final size:4
Alignment explanation
Indices: 46202739--46202825 Score: 156
Period size: 4 Copynumber: 21.8 Consensus size: 4
46202729 TATAAACTAA
* *
46202739 ATAC ATAC ATGC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
46202787 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
46202826 TATGAACATC
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 81 1.00
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:46204497 original size:31 final size:30
Alignment explanation
Indices: 46204462--46204617 Score: 78
Period size: 31 Copynumber: 5.2 Consensus size: 30
46204452 TCATATAAGA
46204462 ATATTTAATATTAAGAATTTTATTAAATTAT
1 ATATTTAATATT-AGAATTTTATTAAATTAT
* * *
46204493 ATATTT--TATTA-AATTATATTTAATAAT
1 ATATTTAATATTAGAATTTTATTAAATTAT
* *
46204520 AATTATGTTAA-ATTA-TATTTTA-TAGTATTAT
1 -A-TAT-TTAATATTAGAATTTTATTA-AATTAT
* * *
46204551 ATATTATGATTTTAGTAATTTAATATT-AA-GA-
1 ATATT-TAATATTAG-AATTT--TATTAAATTAT
*
46204582 ATATCTAATATTAAGAATTTTATTAAATTAT
1 ATATTTAATATT-AGAATTTTATTAAATTAT
46204613 ATATT
1 ATATT
46204618 ATTAAATTAT
Statistics
Matches: 90, Mismatches: 18, Indels: 34
0.63 0.13 0.24
Matches are distributed among these distances:
27 13 0.14
28 7 0.08
29 14 0.16
30 18 0.20
31 29 0.32
32 5 0.06
33 1 0.01
34 2 0.02
35 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (30 bp):
ATATTTAATATTAGAATTTTATTAAATTAT
Found at i:46204498 original size:17 final size:17
Alignment explanation
Indices: 46204478--46204511 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
46204468 AATATTAAGA
46204478 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
46204495 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
46204512 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:46204519 original size:119 final size:120
Alignment explanation
Indices: 46204363--46204649 Score: 508
Period size: 119 Copynumber: 2.4 Consensus size: 120
46204353 CAAACTTTAG
*
46204363 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
1 ATTAAATTATATA-TTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
* *
46204428 TTATATATTATGATTTTAGTAAATTCATA-TAAGAATATTTAATATTAAGAATTTT
65 TTATATATTATGATTTTAGTAAATTAATATTAAGAATATCTAATATTAAGAATTTT
46204483 ATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
1 ATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
*
46204548 TATATATTATGATTTTAGTAATTTAATATTAAGAATATCTAATATTAAGAATTTT
66 TATATATTATGATTTTAGTAAATTAATATTAAGAATATCTAATATTAAGAATTTT
46204603 ATTAAATTATATA--TTATTAAATTATATTTAATAATAATTATGTTAAA
1 ATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAAA
46204650 ATATGATTAA
Statistics
Matches: 162, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
118 34 0.21
119 77 0.48
120 51 0.31
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
ATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
TATATATTATGATTTTAGTAAATTAATATTAAGAATATCTAATATTAAGAATTTT
Found at i:46204576 original size:22 final size:21
Alignment explanation
Indices: 46204527--46204578 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
46204517 AATAATTATG
*
46204527 TTAA-ATTATATTTTATAGTA
1 TTAATATTATATTTTATAATA
46204547 TTATATATTATGATTTTAGTAAT-
1 TTA-ATATTAT-ATTTTA-TAATA
46204570 TTAATATTA
1 TTAATATTA
46204579 AGAATATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.11
21 1 0.04
22 11 0.41
23 9 0.33
24 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (21 bp):
TTAATATTATATTTTATAATA
Found at i:46204621 original size:15 final size:15
Alignment explanation
Indices: 46204601--46204629 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46204591 ATTAAGAATT
46204601 TTATTAAATTATATA
1 TTATTAAATTATATA
46204616 TTATTAAATTATAT
1 TTATTAAATTATAT
46204630 TTAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATTAAATTATATA
Found at i:46204622 original size:43 final size:42
Alignment explanation
Indices: 46204457--46204622 Score: 122
Period size: 43 Copynumber: 4.1 Consensus size: 42
46204447 TAAATTCATA
46204457 TAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAT
1 TAAGAATA-TTAATATTAAGAATTTTATTAAATTATATA--TTAT
* * * * *
46204502 TAA-ATTATATT--TAATAATAATTATGTTAAATTATATTTTA-
1 TAAGA--ATATTAATATTAAGAATTTTATTAAATTATATATTAT
* *
46204542 T-AG--TATTATATATTATG-ATTTTAGT-AATT-TA-A-TAT
1 TAAGAATATTA-ATATTAAGAATTTTATTAAATTATATATTAT
46204577 TAAGAATATCTAATATTAAGAATTTTATTAAATTATATATTAT
1 TAAGAATAT-TAATATTAAGAATTTTATTAAATTATATATTAT
46204620 TAA
1 TAA
46204623 ATTATATTTA
Statistics
Matches: 91, Mismatches: 14, Indels: 34
0.65 0.10 0.24
Matches are distributed among these distances:
34 2 0.02
35 1 0.01
36 8 0.09
37 4 0.04
38 15 0.16
39 14 0.15
40 5 0.05
41 5 0.05
42 1 0.01
43 27 0.30
44 1 0.01
45 5 0.05
46 3 0.03
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.51
Consensus pattern (42 bp):
TAAGAATATTAATATTAAGAATTTTATTAAATTATATATTAT
Found at i:46204876 original size:45 final size:44
Alignment explanation
Indices: 46204790--46204884 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 44
46204780 ATTACAACAT
* *
46204790 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
1 CATTACATTCAACCAAACACAAGAATACTATTACGCATCTATTC
* *
46204834 CATTACATTCAACCAAACA-ATTGAATTGCTATTACGCATCTATTC
1 CATTACATTCAACCAAACACA-AGAA-TACTATTACGCATCTATTC
46204879 CATTAC
1 CATTAC
46204885 GCCTCTATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.47
45 23 0.51
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTACATTCAACCAAACACAAGAATACTATTACGCATCTATTC
Found at i:46204885 original size:16 final size:16
Alignment explanation
Indices: 46204864--46204897 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
46204854 TTGAATTGCT
46204864 ATTACGCATCTATTCC
1 ATTACGCATCTATTCC
*
46204880 ATTACGCCTCTATTCC
1 ATTACGCATCTATTCC
46204896 AT
1 AT
46204898 AAATTGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.32, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:46207713 original size:66 final size:68
Alignment explanation
Indices: 46207607--46207742 Score: 240
Period size: 66 Copynumber: 2.0 Consensus size: 68
46207597 GCTGCCAAGC
46207607 TAATATGAAATTCCTGGTGCGTAGGACAATGTTATAAGCAAAACTGTCA-T-TGACAAACAGTGA
1 TAATATGAAATTCCTGGTGCGTAGGACAATGTTATAAGCAAAACTGTCATTATGACAAACAGTGA
46207670 CAT
66 CAT
46207673 TAATATGAAATTCCTGGTGCGTAGGACAATGTTATAAGCAAAACTGTCATTTAGTGACAAACAGT
1 TAATATGAAATTCCTGGTGCGTAGGACAATGTTATAAGCAAAACTGTCA-TTA-TGACAAACAGT
46207738 GACAT
64 GACAT
46207743 GTCATGTTGA
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
66 49 0.74
68 1 0.02
70 16 0.24
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (68 bp):
TAATATGAAATTCCTGGTGCGTAGGACAATGTTATAAGCAAAACTGTCATTATGACAAACAGTGA
CAT
Found at i:46207799 original size:21 final size:23
Alignment explanation
Indices: 46207773--46207822 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
46207763 TTAACTCAAG
46207773 CAAAAT-GAG-TAGAATTTTTAA
1 CAAAATAGAGATAGAATTTTTAA
*
46207794 CAAAATAAATAGATAGAATTTTTAA
1 CAAAAT--AGAGATAGAATTTTTAA
46207819 CAAA
1 CAAA
46207823 CGGTGGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.25
24 2 0.08
25 16 0.67
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.30
Consensus pattern (23 bp):
CAAAATAGAGATAGAATTTTTAA
Found at i:46219668 original size:15 final size:17
Alignment explanation
Indices: 46219648--46219679 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
46219638 ACAAAATGAG
46219648 AATAA-TTAAT-ACAAA
1 AATAATTTAATCACAAA
46219663 AATAATTTAATCACAAA
1 AATAATTTAATCACAAA
46219680 TAAACCAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAATTTAATCACAAA
Found at i:46221577 original size:44 final size:44
Alignment explanation
Indices: 46221529--46222984 Score: 311
Period size: 44 Copynumber: 33.2 Consensus size: 44
46221519 GCAACTTCAA
* *
46221529 GGAGATAGGATTACTAGCTTTAATCTGCTCCGCTGTAATCTCAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* ** ** *
46221573 GGAGATAAGATCTGA-AATTTTTCGGTCTGTTCCACTGTAATCTCAG
1 GGAGATAAGAT-T-ACTAGCTTT-AATCTGCTCCACTGTAATCTCAG
* *** * * *
46221619 GGAGATAAGA-T-CT-GATGCGATCTACTCTACTGTAA-CTTTAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATC-TCAG
* * * * * *
46221660 AGAGATAAGATCCT-TTA-TTTTAATTTGCTCTACTGTAATCTTAG
1 GGAGATAAGAT--TACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * * *
46221704 GGAGATAGGATTACTAGCTTCAATCTGTTCCGCTGTAATCTCAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * ** *
46221748 GGAGATAAGATCTGA-AATTCTTTGGTCTGTTCCACTGTAATCTCAG
1 GGAGATAAGAT-T-ACTA-GCTTTAATCTGCTCCACTGTAATCTCAG
* * *** * *
46221794 GGAGATAAGA--CCT-GATGCGATCTACTCTACTGTAA-CTTCAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATC-TCAG
* * * *
46221835 AGAGATAAGATCCT-TTA-TTTTAATCTGCTCTACTGTAATCTCAG
1 GGAGATAAGAT--TACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * * * * *
46221879 GGAGATATGATTACTAGCTTCAATCCGCTCCGCTGTAATCTTAA
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * * *** * *
46221923 AGAGATAAGATCTGA-AATTCTTCGGTCTGTTCCACTGTAATCTCAA
1 GGAGATAAGAT-T-ACTA-GCTTTAATCTGCTCCACTGTAATCTCAG
* * *** * *
46221969 GGAGATAAGA--CCT-GATGCGATCTACTCTACTGTAA-CTTCAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATC-TCAG
** * * *
46222010 ATAGATAAGATCCT-TTA-TTTTAATCTGCTCCACTATAATCTCAG
1 GGAGATAAGAT--TACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * * * *
46222054 AGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAA
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * *** *
46222098 GGAGATAAGATCTGAAATATCTTCGGTCTGTTCCACTGTAATCTCAG
1 GGAGATAAGAT-T--ACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * *** * * *
46222145 GGAGATAAGA--CCT-GATGCGATCTACTCTACTGTAA-CTTTAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATC-TCAG
* * * *
46222186 AGAGATAAGATCCT-TTA-TTTTAATCCGCTCCACTGTAATCTCAG
1 GGAGATAAGAT--TACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * * * *
46222230 GGAGATAGGATTACTAGCTTCAACCTGCTCCGCTGTAAGCTCAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * *** * *
46222274 GGAGATAAGATCTGA-AATTCTTCGGTCTGTTCTACTGTAATCTCAG
1 GGAGATAAGAT-T-ACTA-GCTTTAATCTGCTCCACTGTAATCTCAG
* * *** * *
46222320 GGAGATAAGA--CCT-GATGCGATCTACTCTACTGTAA-CTTCAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATC-TCAG
* * * * *
46222361 AGAGATAAGATCCT-TTA-TTTTAATCCGCTCTACTGTAATCTCAG
1 GGAGATAAGAT--TACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * * * * *
46222405 GAAGATAGGATTACTAGCTTCAAGCTGCTTCGCTGTAATCTCAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * ** *
46222449 GGAGATAAGATCTGA-AATTCTTTGGTCTGTTCCACTGTAATCTCAG
1 GGAGATAAGAT-T-ACTA-GCTTTAATCTGCTCCACTGTAATCTCAG
* * *** * * *
46222495 GGAGATAAGA--CCT-GATGCGATCTACTCTACTGTAA-CTTTAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATC-TCAG
* * * * ** *
46222536 AGAGATAAGATCCT-TTA-TTTTAATCCGCTTTACTGTAATCTTAG
1 GGAGATAAGAT--TACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * * * *
46222580 GGAGATAGGATTACTAGCTTCAATCCGCTCCGCTGTAATCTCAA
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATCTCAG
** ** ** * *
46222624 GGAGATAAGATCTAAAATTTTTCGGTCTGTTCCACTGTAATCTCAA
1 GGAGATAAGAT-TACTAGCTTT-AATCTGCTCCACTGTAATCTCAG
* * *** * *
46222670 GGAGATAAGA--CCT-GATGCGATCTACTCTACTGTAA-CTTCAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATC-TCAG
* * * * * * *
46222711 AGAGATAAGATCCT-TTA-TTTTAATCCGCTCCATTGTAATATCAA
1 GGAGATAAGAT--TACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * * * * *
46222755 AGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTTAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * * *** *
46222799 GGATATAAGATCTGAAATATCTTCGGTCTGTTCCACTGTAATCTCAG
1 GGAGATAAGAT-T--ACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * *** * * *
46222846 GGAGATAAGA--CCT-GATGCGATCTACTCTACTGTAA-CTTTAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATC-TCAG
* * * * * *
46222887 AGAG-TTAGATCCT-TTA-TTTTAATCCGGTCCACTGTAATCTCAG
1 GGAGATAAGAT--TACTAGCTTTAATCTGCTCCACTGTAATCTCAG
* * ****
46222930 GGAGATAGGATTACTAGCTTCAATCTGCTATGTTGTAATCTCAG
1 GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATCTCAG
46222974 GGAGATAAGAT
1 GGAGATAAGAT
46222985 CTGAAATATT
Statistics
Matches: 994, Mismatches: 318, Indels: 200
0.66 0.21 0.13
Matches are distributed among these distances:
40 12 0.01
41 206 0.21
42 12 0.01
43 36 0.04
44 449 0.45
45 26 0.03
46 185 0.19
47 68 0.07
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
GGAGATAAGATTACTAGCTTTAATCTGCTCCACTGTAATCTCAG
Found at i:46222826 original size:701 final size:701
Alignment explanation
Indices: 46221477--46222991 Score: 2586
Period size: 701 Copynumber: 2.2 Consensus size: 701
46221467 GCCCCTCTGC
* ** * * * * * *
46221477 AACTTCAGAGAGATGGGATCCATCATTTTGATCCGCTCCAATGCAA-CTTCAAGGAGATAGGATT
1 AACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC-TCAGGGAGATAGGATT
* *
46221541 ACTAGCTTTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTTTTCGGTCTGTTCC
65 ACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCC
* *
46221606 ACTGTAATCTCAGGGAGATAAGATCTGATGCGATCTACTCTACTGTAACTTTAGAGAGATAAGAT
130 ACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT
** * * *
46221671 CCTTTATTTTAATTTGCTCTACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGTTCCG
195 CCTTTATTTTAATCCGCTCTACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAAGCTGTTCCG
46221736 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATA
260 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATA
*
46221801 AGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCT
325 AGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCT
* *
46221866 ACTGTAATCTCAGGGAGATATGATTACTAGCTTCAATCCGCTCCGCTGTAATCTTAAAGAGATAA
390 ACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCCGCTCCGCTGTAATCTCAAAGAGATAA
*
46221931 GATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTC
455 GATCTAAAATTCTTCGGTCTGTTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTC
* * * *
46221996 TACTGTAACTTCAGATAGATAAGATCCTTTATTTTAATCTGCTCCACTATAATCTCAGAGAGATA
520 TACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATATCAAAGAGATA
*
46222061 GGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGATCTGAAATATCTTCGGTC
585 GGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAAGGAGATAAGATCTGAAATATCTTCGGTC
46222126 TGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
650 TGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
46222178 AACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
1 AACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
* * *
46222243 CTAGCTTCAACCTGCTCCGCTGTAAGCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCTA
66 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCA
46222308 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
131 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
46222373 CTTTATTTTAATCCGCTCTACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAAGCTGCTT-CG
196 CTTTATTTTAATCCGCTCTACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAAGCTG-TTCCG
46222437 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATA
260 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATA
* *
46222502 AGACCTGATGCGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTTT
325 AGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCT
* *
46222567 ACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCCGCTCCGCTGTAATCTCAAGGAGATAA
390 ACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCCGCTCCGCTGTAATCTCAAAGAGATAA
*
46222632 GATCTAAAATTTTTCGGTCTGTTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTC
455 GATCTAAAATTCTTCGGTCTGTTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTC
* *
46222697 TACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCATTGTAATATCAAAGAGATA
520 TACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATATCAAAGAGATA
* * *
46222762 GGATTACTAGCTTCAATCTACTCCGCTGTAATCTTAGGGATATAAGATCTGAAATATCTTCGGTC
585 GGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAAGGAGATAAGATCTGAAATATCTTCGGTC
46222827 TGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
650 TGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
* *
46222879 AACTTTAGAGAG-TTAGATCCTTTATTTTAATCCGGTCCACTGTAATCTCAGGGAGATAGGATTA
1 AACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
** *
46222943 CTAGCTTCAATCTGCTATGTTGTAATCTCAGGGAGATAAGATCTGAAAT
66 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
46222992 ATTCACTGAT
Statistics
Matches: 765, Mismatches: 47, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
700 94 0.12
701 668 0.87
702 3 0.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (701 bp):
AACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCA
CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
CTTTATTTTAATCCGCTCTACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAAGCTGTTCCGC
TGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAA
GACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCTA
CTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCCGCTCCGCTGTAATCTCAAAGAGATAAG
ATCTAAAATTCTTCGGTCTGTTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCT
ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATATCAAAGAGATAG
GATTACTAGCTTCAATCTACTCCGCTGTAATCTCAAGGAGATAAGATCTGAAATATCTTCGGTCT
GTTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
Found at i:46222993 original size:175 final size:175
Alignment explanation
Indices: 46221477--46222991 Score: 2431
Period size: 175 Copynumber: 8.7 Consensus size: 175
46221467 GCCCCTCTGC
** * * * * * *
46221477 AACTTCAGAGAGATGGGATCCATCATTTTGATCCGCTCCAATGCAA-CTTCAAGGAGATAGGATT
1 AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC-TCAGGGAGATAGGATT
* *
46221541 ACTAGCTTTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTTTTCGGTCTGTTCC
65 ACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCC
*
46221606 ACTGTAATCTCAGGGAGATAAGATCTGATGCGATCTACTCTACTGT
130 ACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
* ** * *
46221652 AACTTTAGAGAGATAAGATCCTTTATTTTAATTTGCTCTACTGTAATCTTAGGGAGATAGGATTA
1 AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
* *
46221717 CTAGCTTCAATCTGTTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCA
66 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCA
46221782 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
131 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
* * *
46221827 AACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCTACTGTAATCTCAGGGAGATATGATTA
1 AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
* * **
46221892 CTAGCTTCAATCCGCTCCGCTGTAATCTTAAAGAGATAAGATCTGAAATTCTTCGGTCTGTTCCA
66 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCA
*
46221957 CTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGT
131 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
* * * *
46222002 AACTTCAGATAGATAAGATCCTTTATTTTAATCTGCTCCACTATAATCTCAGAGAGATAGGATTA
1 AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
*
46222067 CTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGATCTGAAATATCTTCGGTCTGTTCC
66 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT-TCTTCGGTCTGTTCC
46222132 ACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
130 ACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
*
46222178 AACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
1 AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
* * *
46222243 CTAGCTTCAACCTGCTCCGCTGTAAGCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCTA
66 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCA
46222308 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
131 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
* *
46222353 AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCTACTGTAATCTCAGGAAGATAGGATTA
1 AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
* * *
46222418 CTAGCTTCAAGCTGCTTCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCA
66 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCA
46222483 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
131 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
* ** *
46222528 AACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTTTACTGTAATCTTAGGGAGATAGGATTA
1 AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
* * * *
46222593 CTAGCTTCAATCCGCTCCGCTGTAATCTCAAGGAGATAAGATCTAAAATTTTTCGGTCTGTTCCA
66 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCA
*
46222658 CTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGT
131 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
* * **
46222703 AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCATTGTAATATCAAAGAGATAGGATTA
1 AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
* * *
46222768 CTAGCTTCAATCTACTCCGCTGTAATCTTAGGGATATAAGATCTGAAATATCTTCGGTCTGTTCC
66 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT-TCTTCGGTCTGTTCC
46222833 ACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
130 ACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
* * *
46222879 AACTTTAGAGAG-TTAGATCCTTTATTTTAATCCGGTCCACTGTAATCTCAGGGAGATAGGATTA
1 AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
** *
46222943 CTAGCTTCAATCTGCTATGTTGTAATCTCAGGGAGATAAGATCTGAAAT
66 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
46222992 ATTCACTGAT
Statistics
Matches: 1241, Mismatches: 96, Indels: 6
0.92 0.07 0.00
Matches are distributed among these distances:
175 1004 0.81
176 237 0.19
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (175 bp):
AACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTA
CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCA
CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
Found at i:46231569 original size:27 final size:27
Alignment explanation
Indices: 46231506--46231578 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
46231496 CTATACGTAT
* *
46231506 ATATATTATAAAATATGGAAGATATAAC
1 ATATACTATAAAATAT-AAAGATATAAC
46231534 A-ATACTATAAAATATAAATG-TATATAC
1 ATATACTATAAAATATAAA-GATATA-AC
*
46231561 ATATA-TATAAACTATAAA
1 ATATACTATAAAATATAAA
46231579 AATGAATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 6 0.15
27 29 0.74
28 4 0.10
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (27 bp):
ATATACTATAAAATATAAAGATATAAC
Found at i:46231779 original size:3 final size:3
Alignment explanation
Indices: 46231703--46231764 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
46231693 GTATAACAAG
* * **
46231703 AAT AAT AAGT TAT -AT AAT AAT AAT GATT AAT AAT GGT AAT AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
46231749 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
46231765 GAATGTCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 2 0.04
3 43 0.88
4 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:46233890 original size:45 final size:45
Alignment explanation
Indices: 46233742--46233958 Score: 195
Period size: 45 Copynumber: 4.9 Consensus size: 45
46233732 GTACATGAAA
* *
46233742 ACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAG
1 ACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAGTACGGGAAG
* * * * * * * * **
46233787 GCAAGATCTGGTATCTCTGATTTACTTC-ACGCCAATACATGAAG
1 ACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAGTACGGGAAG
* * *
46233831 ACAAAATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAG
1 ACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAGTACGGGAAG
* * * * * *
46233876 GCAAGATTTGCTTTCTTCGATCTACTTCACCACCTGTACGGGGAG
1 ACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAGTACGGGAAG
* * * *
46233921 ACAAGATCTGGTATCTATGATCTACTTC-ACACCAGTAC
1 ACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAGTAC
46233959 ATGACGATAG
Statistics
Matches: 129, Mismatches: 42, Indels: 3
0.74 0.24 0.02
Matches are distributed among these distances:
44 39 0.30
45 90 0.70
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (45 bp):
ACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAGTACGGGAAG
Found at i:46233902 original size:89 final size:89
Alignment explanation
Indices: 46233708--46233905 Score: 281
Period size: 89 Copynumber: 2.2 Consensus size: 89
46233698 ACAGGACCTA
* ** ** *
46233708 CTATCTTTGATCTGTTTCACGCCGGTACATGAAAACAAGATCTGCTTTCTTTGATCTGCTTCGCC
1 CTATCTCTGATCTACTTCACGCCAATACATGAAAACAAAATCTGCTTTCTTTGATCTGCTTCGCC
46233773 ACCAGTATGGGAAGGCAAGATCTG
66 ACCAGTATGGGAAGGCAAGATCTG
* * *
46233797 GTATCTCTGATTTACTTCACGCCAATACATGAAGACAAAATCTGCTTTCTTTGATCTGCTTCGCC
1 CTATCTCTGATCTACTTCACGCCAATACATGAAAACAAAATCTGCTTTCTTTGATCTGCTTCGCC
*
46233862 ACCAGTATGGGAAGGCAAGATTTG
66 ACCAGTATGGGAAGGCAAGATCTG
*
46233886 CTTTCT-TCGATCTACTTCAC
1 CTATCTCT-GATCTACTTCAC
46233906 CACCTGTACG
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 1 0.01
89 94 0.99
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (89 bp):
CTATCTCTGATCTACTTCACGCCAATACATGAAAACAAAATCTGCTTTCTTTGATCTGCTTCGCC
ACCAGTATGGGAAGGCAAGATCTG
Found at i:46233954 original size:89 final size:89
Alignment explanation
Indices: 46233733--46233957 Score: 256
Period size: 89 Copynumber: 2.5 Consensus size: 89
46233723 TTCACGCCGG
* * *
46233733 TACATGAAAACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGG
1 TACAGGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGC
* *
46233798 TATCTCTGATTTACTTCACGCCAA
66 TATCTCTGATCTACTTCACACCAA
* * *
46233822 TACATGAAGACAAAATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATTTGC
1 TACAGGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGC
* **
46233887 TTTCT-TCGATCTACTTCACCACCTG
66 TATCTCT-GATCTACTTCA-CACCAA
* * * * * * *
46233912 TACGGGGAGACAAGATCTGGTATCTATGATCTACTTC-ACACCAGTA
1 TACAGGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTA
46233958 CATGACGATA
Statistics
Matches: 116, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
88 1 0.01
89 83 0.72
90 32 0.28
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (89 bp):
TACAGGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGC
TATCTCTGATCTACTTCACACCAA
Found at i:46244348 original size:45 final size:45
Alignment explanation
Indices: 46244298--46244390 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
46244288 CGAGTTAAAT
46244298 TAAAAAAATTAAACATGTCAAATTAAAATCTTGTTACAATATACC
1 TAAAAAAATTAAACATGTCAAATTAAAATCTTGTTACAATATACC
46244343 TAAAAAAATTAAACATGTCAAATTAAAATCTTGTTACAATATACC
1 TAAAAAAATTAAACATGTCAAATTAAAATCTTGTTACAATATACC
46244388 TAA
1 TAA
46244391 TTCCATGTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.31
Consensus pattern (45 bp):
TAAAAAAATTAAACATGTCAAATTAAAATCTTGTTACAATATACC
Found at i:46244764 original size:19 final size:20
Alignment explanation
Indices: 46244740--46244787 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
46244730 AAAATTATTA
46244740 TTTTAGAAAATTTT-TAATT
1 TTTTAGAAAATTTTATAATT
**
46244759 TTTTAG-ATTTTTTATAATT
1 TTTTAGAAAATTTTATAATT
46244778 TTTTA-AAAAT
1 TTTTAGAAAAT
46244788 AAAAATTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTAGAAAATTTTATAATT
Found at i:46244831 original size:18 final size:20
Alignment explanation
Indices: 46244804--46244845 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
46244794 TTTGGAATTT
*
46244804 TTTTATAAA-TATTTTG-AA
1 TTTTAAAAATTATTTTGTAA
46244822 TTTTAAAAATTATTTTGTAA
1 TTTTAAAAATTATTTTGTAA
46244842 TTTT
1 TTTT
46244846 TGTTGAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGTAA
Found at i:46245441 original size:19 final size:21
Alignment explanation
Indices: 46245400--46245442 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
46245390 AAATTATTAA
* *
46245400 ATATTAATTTACAAATAATAT
1 ATATTAATTTACAAAAAAAAT
46245421 ATATT-ATTTA-AAAAAAAAT
1 ATATTAATTTACAAAAAAAAT
46245440 ATA
1 ATA
46245443 AGACCAGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 5 0.25
21 5 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATTAATTTACAAAAAAAAT
Found at i:46250768 original size:2 final size:2
Alignment explanation
Indices: 46250761--46250787 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46250751 AATTTCCTTC
46250761 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
46250788 GTGAACAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46251995 original size:38 final size:38
Alignment explanation
Indices: 46251940--46252036 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 38
46251930 GTTAACCTTT
* * *
46251940 ATAACACC-GACAATAAGCCTGTTAGGCACTAAGCCTAA
1 ATAACACCAG-CACTAAGCCTGCTAGGCACAAAGCCTAA
* *
46251978 ATAACACCAGCACTAAGCCTACTAGGCACAAAGCCTGA
1 ATAACACCAGCACTAAGCCTGCTAGGCACAAAGCCTAA
* *
46252016 ATAACACCAACACAAAGCCTG
1 ATAACACCAGCACTAAGCCTG
46252037 AATAACACCG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
38 49 0.98
39 1 0.02
ACGTcount: A:0.41, C:0.30, G:0.14, T:0.14
Consensus pattern (38 bp):
ATAACACCAGCACTAAGCCTGCTAGGCACAAAGCCTAA
Found at i:46252032 original size:22 final size:22
Alignment explanation
Indices: 46252004--46252058 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
46251994 GCCTACTAGG
46252004 CACAAAGCCTGAATAACACCAA
1 CACAAAGCCTGAATAACACCAA
*
46252026 CACAAAGCCTGAATAACACCGA
1 CACAAAGCCTGAATAACACCAA
*
46252048 CACTAAGCCTG
1 CACAAAGCCTG
46252059 CTAGGCACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.33, G:0.13, T:0.11
Consensus pattern (22 bp):
CACAAAGCCTGAATAACACCAA
Found at i:46256447 original size:20 final size:20
Alignment explanation
Indices: 46256415--46256452 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46256405 AAAATTTATA
46256415 TATATAAAATCATAAAAACT
1 TATATAAAATCATAAAAACT
46256435 TATA-AAAATTCATAAAAA
1 TATATAAAA-TCATAAAAA
46256453 ATAGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (20 bp):
TATATAAAATCATAAAAACT
Found at i:46256460 original size:19 final size:19
Alignment explanation
Indices: 46256420--46256461 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
46256410 TTATATATAT
* *
46256420 AAAATCATAAAAACTTATA
1 AAAATCATAAAAACATAGA
46256439 AAAATTCATAAAAA-ATAGA
1 AAAA-TCATAAAAACATAGA
46256458 AAAA
1 AAAA
46256462 AGGCACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATCATAAAAACATAGA
Found at i:46256994 original size:18 final size:18
Alignment explanation
Indices: 46256973--46257019 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
46256963 TGGTTTTTCA
* *
46256973 AATTTTATAGATTTATAT
1 AATTTTATAAAATTATAT
*
46256991 AATTTTAAAAAATTATAT
1 AATTTTATAAAATTATAT
*
46257009 AAATTTATAAA
1 AATTTTATAAA
46257020 CTTCTTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
AATTTTATAAAATTATAT
Found at i:46262185 original size:2 final size:2
Alignment explanation
Indices: 46262178--46262207 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46262168 TGTTGTTGAA
46262178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46262208 GATTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46274893 original size:12 final size:12
Alignment explanation
Indices: 46274876--46274901 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46274866 ATACATATAT
46274876 TTGTCACTTCAA
1 TTGTCACTTCAA
46274888 TTGTCACTTCAA
1 TTGTCACTTCAA
46274900 TT
1 TT
46274902 ATCTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (12 bp):
TTGTCACTTCAA
Found at i:46275309 original size:26 final size:27
Alignment explanation
Indices: 46275279--46275329 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
46275269 AGCCACATTG
*
46275279 GGAAGCTCACAAAGAGCC-TTTAATCA
1 GGAAGATCACAAAGAGCCATTTAATCA
* *
46275305 GGAAGATTACGAAGAGCCATTTAAT
1 GGAAGATCACAAAGAGCCATTTAAT
46275330 GGGACGCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (27 bp):
GGAAGATCACAAAGAGCCATTTAATCA
Found at i:46277300 original size:13 final size:13
Alignment explanation
Indices: 46277282--46277313 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
46277272 ATTTTATATT
46277282 ATTAAAATTTTTA
1 ATTAAAATTTTTA
46277295 ATT-AAATTTTTA
1 ATTAAAATTTTTA
46277307 ATTAAAA
1 ATTAAAA
46277314 GTATAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTAAAATTTTTA
Found at i:46277380 original size:3 final size:3
Alignment explanation
Indices: 46277372--46277404 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
46277362 AACATTTTCT
46277372 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
46277405 ATACTCCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:46277486 original size:13 final size:13
Alignment explanation
Indices: 46277468--46277500 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
46277458 GCTTTGGGTC
46277468 TTCAATTGGTTAG
1 TTCAATTGGTTAG
46277481 TTCAATTGGTTAG
1 TTCAATTGGTTAG
46277494 TTCAATT
1 TTCAATT
46277501 TAGTCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (13 bp):
TTCAATTGGTTAG
Found at i:46279303 original size:37 final size:37
Alignment explanation
Indices: 46279247--46279331 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
46279237 CTATTGATCC
* *
46279247 TACTGAATGAAGCTCAATTGAGCAAATCTTA-TCATTA
1 TACTGAATGAAGCTAAATTGAGCAAATCGTACT-ATTA
* *
46279284 TACTAAATGAAGCTAAATTGAGTAAATCGTACTATTA
1 TACTGAATGAAGCTAAATTGAGCAAATCGTACTATTA
46279321 TACTGAATGAA
1 TACTGAATGAA
46279332 ACTCAGGCGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 41 0.98
38 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (37 bp):
TACTGAATGAAGCTAAATTGAGCAAATCGTACTATTA
Found at i:46295797 original size:6 final size:6
Alignment explanation
Indices: 46295782--46295844 Score: 85
Period size: 6 Copynumber: 10.7 Consensus size: 6
46295772 GTGTATTTTG
*
46295782 TTTT-A TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
*
46295829 TGTTT-A TTTTTA TTTT
1 T-TTTAA TTTTAA TTTT
46295845 CTTCTATTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
5 7 0.13
6 44 0.81
7 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTAA
Found at i:46297339 original size:13 final size:13
Alignment explanation
Indices: 46297310--46297350 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
46297300 CCAATGCATG
46297310 ATTATTTATG-G-
1 ATTATTTATGAGA
46297321 ATTATTT-TGAGA
1 ATTATTTATGAGA
46297333 TATTATTTATGAGA
1 -ATTATTTATGAGA
46297347 ATTA
1 ATTA
46297351 CAAATTGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.08
11 8 0.31
13 11 0.42
14 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (13 bp):
ATTATTTATGAGA
Found at i:46297653 original size:30 final size:30
Alignment explanation
Indices: 46297617--46297674 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
46297607 TTTCCAAGTT
*
46297617 CCACACGAGCTGGCCACACACCCGTGTGAG
1 CCACACGAGCTGGCCACACACCCATGTGAG
* * *
46297647 CCACACGGGTTGGCCACACGCCCATGTG
1 CCACACGAGCTGGCCACACACCCATGTG
46297675 TTAGCCCGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.21, C:0.40, G:0.28, T:0.12
Consensus pattern (30 bp):
CCACACGAGCTGGCCACACACCCATGTGAG
Found at i:46307978 original size:22 final size:21
Alignment explanation
Indices: 46307948--46308005 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
46307938 GAATGGTATC
46307948 TACAAATCAAATCTCTAAGAT
1 TACAAATCAAATCTCTAAGAT
*
46307969 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCAAATC-TCTAAGAT
* *
46307992 TGCATATCAAATCT
1 TACAAATCAAATCT
46308006 ACGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.55
23 10 0.32
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
TACAAATCAAATCTCTAAGAT
Found at i:46307999 original size:17 final size:17
Alignment explanation
Indices: 46307977--46308028 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
46307967 ATTACAAAAT
*
46307977 CATATCTTCTAAGATTG
1 CATATCATCTAAGATTG
*
46307994 CATATCAAATCTACGATTG
1 CATATC--ATCTAAGATTG
* *
46308013 CATATCCTCGAAGATT
1 CATATCATCTAAGATT
46308029 ATGTTTCCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 13 0.46
19 15 0.54
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (17 bp):
CATATCATCTAAGATTG
Found at i:46310542 original size:26 final size:27
Alignment explanation
Indices: 46310486--46310550 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
46310476 AGTAAGCTTG
* * * *
46310486 GCGAGCTGGTGTACGCCAGTAGGTTTG
1 GCGAGCTGGTGTACGACAGAAGGTCTA
46310513 GCGAGCTGGTGTAC-ACAGAAGGTCTA
1 GCGAGCTGGTGTACGACAGAAGGTCTA
*
46310539 GCGAGTTGGTGT
1 GCGAGCTGGTGT
46310551 TCGCCAATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
26 19 0.58
27 14 0.42
ACGTcount: A:0.18, C:0.17, G:0.40, T:0.25
Consensus pattern (27 bp):
GCGAGCTGGTGTACGACAGAAGGTCTA
Found at i:46318727 original size:189 final size:186
Alignment explanation
Indices: 46318407--46318785 Score: 677
Period size: 189 Copynumber: 2.0 Consensus size: 186
46318397 GAAAATTTTC
46318407 TACTTGAAACCTTTGTTTAGATGGTTTTTGCACATGAATTATGAGTGTGTGCATGCATGTGACAA
1 TACTTGAAACCTTTGTTTAGATGGTTTTTGCACATGAATTATGAGTGTGTGCATGCATGTGACAA
* *
46318472 TTGATGGAATCAAAAGCGGGAATATTTTGTTAGTTGAGCTCTGAATTATTGACTTGCAATTATCA
66 TTGATGGAACCAAAAGCGGGAATATTTTGTTAGTTGAGCTCTGAATTATAGACTTGCAATTATCA
46318537 TTATTGACTTAAGATATAAGTGATATTAAGAAGCCTAACATATTTCTTCTAAGGGTCTT
131 TTATTGACTTAAGATATAAGTGATATTAAGAAGCCTAACATA--T-TTCTAAGGGTCTT
* *
46318596 TACTTGAAACCTTTGTTTAGATGGTTTTTGCACATGAATTTTGAGTGTGTGCATGCATGTGAGAA
1 TACTTGAAACCTTTGTTTAGATGGTTTTTGCACATGAATTATGAGTGTGTGCATGCATGTGACAA
*
46318661 TTGATGGAACCAAAAGGGGGAATATTTTGTTAGTTGAGCTCTGAATTATAGACTTGCAATTATCA
66 TTGATGGAACCAAAAGCGGGAATATTTTGTTAGTTGAGCTCTGAATTATAGACTTGCAATTATCA
*
46318726 TTATTGACTTAAGATATAAGTGATATTAAGAAGCCTGACATATTTCTAAGGGTCTT
131 TTATTGACTTAAGATATAAGTGATATTAAGAAGCCTAACATATTTCTAAGGGTCTT
46318782 TACT
1 TACT
46318786 GTCTAGCTCT
Statistics
Matches: 184, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
186 17 0.09
187 1 0.01
189 166 0.90
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (186 bp):
TACTTGAAACCTTTGTTTAGATGGTTTTTGCACATGAATTATGAGTGTGTGCATGCATGTGACAA
TTGATGGAACCAAAAGCGGGAATATTTTGTTAGTTGAGCTCTGAATTATAGACTTGCAATTATCA
TTATTGACTTAAGATATAAGTGATATTAAGAAGCCTAACATATTTCTAAGGGTCTT
Found at i:46327862 original size:30 final size:30
Alignment explanation
Indices: 46327828--46327885 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
46327818 CATATGGATG
46327828 ATCTCATCATGGTTCTGCAAAGTTTCAAAC
1 ATCTCATCATGGTTCTGCAAAGTTTCAAAC
46327858 ATCTCATCATGGTTCTGCAAAGTTTCAA
1 ATCTCATCATGGTTCTGCAAAGTTTCAA
46327886 GCAATGGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (30 bp):
ATCTCATCATGGTTCTGCAAAGTTTCAAAC
Found at i:46338532 original size:18 final size:18
Alignment explanation
Indices: 46338509--46338546 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
46338499 AATTAATATG
*
46338509 AATAAAGGTTATAAAAAT
1 AATAAAAGTTATAAAAAT
*
46338527 AATAAAAGTTATAATAAT
1 AATAAAAGTTATAAAAAT
46338545 AA
1 AA
46338547 AAGAAAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (18 bp):
AATAAAAGTTATAAAAAT
Found at i:46343738 original size:21 final size:23
Alignment explanation
Indices: 46343713--46343758 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
46343703 TAAACAATTC
46343713 AAATT-ATAA-TCAAACATATAT
1 AAATTCATAATTCAAACATATAT
**
46343734 AAATTCATAATTCAATTATATAT
1 AAATTCATAATTCAAACATATAT
46343757 AA
1 AA
46343759 TAATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 4 0.19
23 12 0.57
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (23 bp):
AAATTCATAATTCAAACATATAT
Found at i:46346281 original size:6 final size:6
Alignment explanation
Indices: 46346253--46346283 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
46346243 AAGGAAAATG
*
46346253 GAAATA GAAAAA GAAAAA GAAAAA GAAAAA G
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G
46346284 CAAATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:46351057 original size:12 final size:12
Alignment explanation
Indices: 46351022--46351060 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
46351012 ACTTAATCAC
46351022 TTTAATATTAAA
1 TTTAATATTAAA
*
46351034 TTCATTATATTAAA
1 TT--TAATATTAAA
46351048 TTTAATATTAAA
1 TTTAATATTAAA
46351060 T
1 T
46351061 CTTATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 12 0.52
14 11 0.48
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:46353735 original size:12 final size:12
Alignment explanation
Indices: 46353718--46353742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46353708 TATTGATATA
46353718 TATACATATCAT
1 TATACATATCAT
46353730 TATACATATCAT
1 TATACATATCAT
46353742 T
1 T
46353743 CTCTTACTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TATACATATCAT
Found at i:46353882 original size:21 final size:21
Alignment explanation
Indices: 46353853--46354019 Score: 142
Period size: 21 Copynumber: 8.0 Consensus size: 21
46353843 GCTCGTAAGC
* *
46353853 TGAAAAGAAACTCTTAAGAGT
1 TGAACAGAAACTCATAAGAGT
*
46353874 TGAACAGAAGCTCATAAGAGT
1 TGAACAGAAACTCATAAGAGT
*
46353895 TGAACAAAAACTCATAAGAGT
1 TGAACAGAAACTCATAAGAGT
** *
46353916 TGAACA-AAAGCTTGTAAGAGC
1 TGAACAGAAA-CTCATAAGAGT
* * * *
46353937 TAAACAAAAACTCGTATGAGT
1 TGAACAGAAACTCATAAGAGT
* * * *
46353958 TAAATAGGAACT-AGTAAGAGC
1 TGAACAGAAACTCA-TAAGAGT
*
46353979 TGAACAGAAACTCATAATAGT
1 TGAACAGAAACTCATAAGAGT
46354000 TGAACA-AAAGCTCATAAGAG
1 TGAACAGAAA-CTCATAAGAG
46354020 CTAAACTGAA
Statistics
Matches: 117, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
20 6 0.05
21 107 0.91
22 4 0.03
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.20
Consensus pattern (21 bp):
TGAACAGAAACTCATAAGAGT
Found at i:46353913 original size:42 final size:42
Alignment explanation
Indices: 46353836--46354021 Score: 184
Period size: 42 Copynumber: 4.5 Consensus size: 42
46353826 GTACATCGTT
* *
46353836 AACAGAAGCTCGT-A-AGCTGAA-AAGAAACTCTTAAGAGTTG
1 AACAGAAGCTCATAAGAGCTGAACAA-AAACTCATAAGAGTTG
*
46353876 AACAGAAGCTCATAAGAGTTGAACAAAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGTTG
* ** * * * *
46353918 AACAAAAGCTTGTAAGAGCTAAACAAAAACTCGTATGAGTTA
1 AACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGTTG
* * *
46353960 AATAGGAA-CT-AGTAAGAGCTGAACAGAAACTCATAATAGTTG
1 AACA-GAAGCTCA-TAAGAGCTGAACAAAAACTCATAAGAGTTG
*
46354002 AACAAAAGCTCATAAGAGCT
1 AACAGAAGCTCATAAGAGCT
46354022 AAACTGAAAG
Statistics
Matches: 117, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
40 12 0.10
41 3 0.03
42 97 0.83
43 5 0.04
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGTTG
Found at i:46360909 original size:27 final size:25
Alignment explanation
Indices: 46360879--46360960 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
46360869 CATAAACAGA
46360879 AAGCTCTCTCGCGAGCCATATAACGGG
1 AAGCTC-CT-GCGAGCCATATAACGGG
* * *
46360906 AAGCTCGTGTGAGCCATGTAACGGG
1 AAGCTCCTGCGAGCCATATAACGGG
* ** *
46360931 AAGCTCATAAGAGCCATA-ATCGGG
1 AAGCTCCTGCGAGCCATATAACGGG
46360955 AAGCTC
1 AAGCTC
46360961 ATACGAGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
24 11 0.23
25 29 0.62
26 1 0.02
27 6 0.13
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.18
Consensus pattern (25 bp):
AAGCTCCTGCGAGCCATATAACGGG
Found at i:46360921 original size:25 final size:25
Alignment explanation
Indices: 46360891--46360963 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 25
46360881 GCTCTCTCGC
* **
46360891 GAGCCATATAACGGGAAGCTCGTGT
1 GAGCCATATAACGGGAAGCTCATAA
*
46360916 GAGCCATGTAACGGGAAGCTCATAA
1 GAGCCATATAACGGGAAGCTCATAA
*
46360941 GAGCCATA-ATCGGGAAGCTCATA
1 GAGCCATATAACGGGAAGCTCATA
46360964 CGAGAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 14 0.33
25 28 0.67
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.18
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATAA
Found at i:46368097 original size:12 final size:12
Alignment explanation
Indices: 46368080--46368121 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
46368070 CTTGACATTA
46368080 AATAAATAATGG
1 AATAAATAATGG
**
46368092 AATAAA-ACATTA
1 AATAAATA-ATGG
46368104 AATAAATAATGG
1 AATAAATAATGG
46368116 AATAAA
1 AATAAA
46368122 ACATACCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (12 bp):
AATAAATAATGG
Done.