Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold158
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: 1811518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:290512 original size:24 final size:24
Alignment explanation
Indices: 290480--290566 Score: 106
Period size: 24 Copynumber: 3.5 Consensus size: 24
290470 AAAACCAAAT
290480 AAACAAAAA-AAAGAAGAAAAAACA
1 AAACAAAAACAAAGAA-AAAAAACA
290504 AAACAAAAACAAA-AAACAAAAACA
1 AAACAAAAACAAAGAAA-AAAAACA
290528 AAACAAAAAACAAAGAAAAAAAAACAA
1 AAAC-AAAAACAAAG-AAAAAAAAC-A
*
290555 AAACAACAACAA
1 AAACAAAAACAA
290567 CAAAAAGGGT
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
23 1 0.02
24 22 0.39
25 12 0.21
26 13 0.23
27 8 0.14
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (24 bp):
AAACAAAAACAAAGAAAAAAAACA
Found at i:290549 original size:19 final size:18
Alignment explanation
Indices: 290466--290560 Score: 109
Period size: 18 Copynumber: 5.1 Consensus size: 18
290456 CGTCCTCCAC
*
290466 AAAAAAAACCAAATAAACA
1 AAAAAAAAACAAA-AAACA
*
290485 AAAAAAAGAAGAAAAAACA
1 AAAAAAA-AACAAAAAACA
*
290504 AAACAAAAACAAAAAACA
1 AAAAAAAAACAAAAAACA
*
290522 AAAACAAAACAAAAAACA
1 AAAAAAAAACAAAAAACA
*
290540 AAGAAAAAAAAACAAAAACA
1 AA-AAAAAAACA-AAAAACA
290560 A
1 A
290561 CAACAACAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
18 28 0.43
19 25 0.38
20 12 0.18
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.01
Consensus pattern (18 bp):
AAAAAAAAACAAAAAACA
Found at i:292090 original size:34 final size:30
Alignment explanation
Indices: 292079--292643 Score: 799
Period size: 29 Copynumber: 19.1 Consensus size: 30
292069 GCACCTTTTT
292079 CTTTT-CAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
292108 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* *
292138 CTTTTCCAAAGCTCACAAGTCAGTGGCA-T
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
*
292167 CTTTTCAAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* * *
292197 TTTTTCCAAAGCCCACAAGTCAATGGCA-T
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* *
292226 CTTTTCAAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
*
292255 CTTTTCAAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* *
292285 CTTTTCCAAAGCCCATAAGTCAGTGGCA-T
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
292314 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* *
292344 CTTTTCCAAAGCCCACAAGTCAATGGCA-T
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
*
292373 CTTTTCAAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
*
292403 CTTTTCCAAAGCCCACAAGTTAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* * *
292433 CTTTTACAAAGCCCACAAGTCAGTGGTA-T
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* * *
292462 CTTTTCAAAAGCCCACAAGTCAGTGGTA-T
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
*
292491 CTTTTCAAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
*
292521 CTTTTCCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
*
292550 CTTTTCCAAAGCCCACAAGTTAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* *
292580 CTTTTTCCAAAGCCCACAAGTCAGTGGTA-T
1 C-TTTTCCAAAGCCCACAAGTCAGTGGCACC
* *
292610 CTTTTCAAAAGCCCACAAGTCAGTGGCAAC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
292640 CTTT
1 CTTT
292644 AAAAGCATAC
Statistics
Matches: 484, Mismatches: 43, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
29 244 0.50
30 215 0.44
31 25 0.05
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (30 bp):
CTTTTCCAAAGCCCACAAGTCAGTGGCACC
Found at i:292180 original size:59 final size:59
Alignment explanation
Indices: 292078--292643 Score: 852
Period size: 59 Copynumber: 9.6 Consensus size: 59
292068 GGCACCTTTT
292078 TCTTTT-CAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
* * * *
292136 CCCTTTTCCAAAGCTCACAAGTCAGTGGCA-TCTTTTCAAAAGCCCACAAGTCAGTGGCA
1 -TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
* * * *
292195 CCTTTTTCCAAAGCCCACAAGTCAATGGCA-TCTTTTCAAAAGCCCACAAGTCAGTGGCA
1 TC-TTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
* *
292254 TCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCATAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
*
292313 TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAATGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
* *
292372 TCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTTAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
* * * * * *
292431 CCCTTTTACAAAGCCCACAAGTCAGTGGTA-TCTTTTCAAAAGCCCACAAGTCAGTGGTA
1 -TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
*
292490 TCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
* *
292549 TCTTTTCCAAAGCCCACAAGTTAGTGGCACCCTTTTTCCAAAGCCCACAAGTCAGTGGTA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCACCC-TTTTCCAAAGCCCACAAGTCAGTGGCA
* *
292609 TCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTT
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTT
292644 AAAAGCATAC
Statistics
Matches: 462, Mismatches: 39, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
58 52 0.11
59 309 0.67
60 101 0.22
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (59 bp):
TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
Found at i:292700 original size:88 final size:87
Alignment explanation
Indices: 292078--292683 Score: 709
Period size: 88 Copynumber: 6.9 Consensus size: 87
292068 GGCACCTTTT
* *
292078 TCTTTTC-AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTT
1 TCTTTTCAAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAAGCCCACAAGTCAGTGGCACCC-TT
* *
292142 TCCAAAGCTCACAAGTCAGTGGCA
64 TCAAAAGCCCACAAGTCAGTGGCA
* * * *
292166 TCTTTTCAAAAGCCCACAAGTCAGTGGCA-CCTTTTTCCAAAGCCCACAAGTCAATGGCATCTTT
1 TCTTTTCAAAAGCCCACAAGTCAGTGGCATCC--TTTCAAAAGCCCACAAGTCAGTGGCACCCTT
292230 TCAAAAGCCCACAAGTCAGTGGCA
64 TCAAAAGCCCACAAGTCAGTGGCA
* * * * *
292254 TCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCATAAGTCAGTGGCATCTTTT
1 TCTTTTCAAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAAGCCCACAAGTCAGTGGCACCCTTT
*
292319 CCAAAGCCCACAAGTCAGTGGCA
65 CAAAAGCCCACAAGTCAGTGGCA
* * * *
292342 CCCTTTTCCAAAGCCCACAAGTCAATGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTT
1 -TCTTTTCAAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAGTGGCACCC-TT
* *
292407 TCCAAAGCCCACAAGTTAGTGGCA
64 TCAAAAGCCCACAAGTCAGTGGCA
* * * * * *
292431 CCCTTTT-ACAAAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGGTATCTTT
1 -TCTTTTCA-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAGTGGCACCCTT
292495 TCAAAAGCCCACAAGTCAGTGGCA
64 TCAAAAGCCCACAAGTCAGTGGCA
* * * * *
292519 CCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTTAGTGGCACCCTTT
1 -TCTTTTCAAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAGTGGCACCC--T
* *
292584 TTCCAAAGCCCACAAGTCAGTGGTA
63 TTCAAAAGCCCACAAGTCAGTGGCA
* ** ** *
292609 TCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTT-AAAAGCATACAAGTTGGT-ACAACCCTTT
1 TCTTTTCAAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAGTGGC-ACCCTTT
292672 CAAAAGCCCACA
65 CAAAAGCCCACA
292684 CAAGTTGATG
Statistics
Matches: 463, Mismatches: 45, Indels: 22
0.87 0.08 0.04
Matches are distributed among these distances:
86 14 0.03
87 1 0.00
88 236 0.51
89 188 0.41
90 24 0.05
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.24
Consensus pattern (87 bp):
TCTTTTCAAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTC
AAAAGCCCACAAGTCAGTGGCA
Found at i:292869 original size:98 final size:97
Alignment explanation
Indices: 292710--293089 Score: 340
Period size: 98 Copynumber: 3.8 Consensus size: 97
292700 TCTTCTAAGT
* * * *
292710 CCAATATCGCTAGCCTTGAATCAGCACATTGGCA--C--CTTTAAGTCCAATATCGTTGGTCTTG
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCTTCTTTAAGTCCAATGTCGCTGGCCTTG
* *
292771 AATTAGCATATTGGCACCTTCATCTTTAAAAC
66 AATCAGCACATTGGCACCTTCATCTTTAAAAC
* * * * *
292803 CCAAATGTCGTTGGCCTTGAATCAACACACTGGCATTCTTCTTTAAGTCCAATGTCACTGGCCTT
1 CC-AATATCGCTGGCCTTGAATCAGCACATTGGCATTCTTCTTTAAGTCCAATGTCGCTGGCCTT
**
292868 GAATCAGCACATTGGCACCTTCATCTTT-AAGT
65 GAATCAGCACATTGGCACCTTCATCTTTAAAAC
* *
292900 CCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTT-TGTCACCTTTTAAGTCCAATGTCGCT
1 CCAATATCGCTGGCCTTGAATCAGCACATT-G-GCATTCT-T---C-TTTAAGTCCAATGTCGCT
*
292964 GGCCTTGAATCAGCACATTGGCACCTTTATCTTTAACATTCCTAAGC
59 GGCCTTGAATCAGCACATTGGCACCTTCATCTTT-A-A-----AA-C
* * ** * * ** *
293011 CCGATGTCGCTGGCCTTGCCTCAGCACATTGGCATTTTTCTTCAAGTTTAAATGTCGCTGGCCAT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCTTCTTTAAG-TCCAATGTCGCTGGCCTT
293076 GAATCAGCACATTG
65 GAATCAGCACATTG
293090 TTATTTTCGC
Statistics
Matches: 231, Mismatches: 33, Indels: 33
0.78 0.11 0.11
Matches are distributed among these distances:
93 2 0.01
94 27 0.12
96 24 0.10
97 6 0.03
98 52 0.23
101 1 0.00
102 50 0.22
105 6 0.03
106 30 0.13
109 5 0.02
110 3 0.01
111 25 0.11
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.32
Consensus pattern (97 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCTTCTTTAAGTCCAATGTCGCTGGCCTTG
AATCAGCACATTGGCACCTTCATCTTTAAAAC
Found at i:292913 original size:49 final size:49
Alignment explanation
Indices: 292700--292999 Score: 301
Period size: 49 Copynumber: 6.1 Consensus size: 49
292690 GATGGCATCT
*
292700 TCTTCTAAGTCCAATATCGCTAGCCTTGAATCAGCACATTGGCA----C-
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
292745 -CTTTAAGTCCAATATCGTTGGTCTTGAATTAGCATATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
** * * * * *
292793 TCTTTAAAACCCAAATGTCGTTGGCCTTGAATCAACACACTGGCA--TTCT
1 TCTTT-AAGTCC-AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
292842 TCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* **
292891 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCA
* * *
292943 CCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTA
1 TC-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
292993 TCTTTAA
1 TCTTTAA
293000 CATTCCTAAG
Statistics
Matches: 208, Mismatches: 33, Indels: 24
0.78 0.12 0.09
Matches are distributed among these distances:
43 34 0.16
44 3 0.01
47 29 0.14
48 4 0.02
49 60 0.29
50 7 0.03
51 28 0.13
52 4 0.02
53 39 0.19
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (49 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:293899 original size:13 final size:13
Alignment explanation
Indices: 293881--293937 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
293871 CATAAAGTGT
293881 TGTATCGATACAA
1 TGTATCGATACAA
*
293894 TGTATCGACACATAA
1 TGTATCGATAC--AA
293909 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
293926 TGTATCGATACA
1 TGTATCGATACA
293938 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:293916 original size:32 final size:32
Alignment explanation
Indices: 293863--293961 Score: 171
Period size: 32 Copynumber: 3.1 Consensus size: 32
293853 CAACGATTTA
293863 TATCGATACATAAAGTGTTGTATCGATACAATG
1 TATCGATACAT-AAGTGTTGTATCGATACAATG
*
293896 TATCGACACATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
*
293928 TATCGATACATAAGTTTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
293960 TA
1 TA
293962 AGCTACTGCC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 53 0.84
33 10 0.16
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATG
Found at i:293950 original size:19 final size:18
Alignment explanation
Indices: 293863--293956 Score: 73
Period size: 19 Copynumber: 5.6 Consensus size: 18
293853 CAACGATTTA
293863 TATCGATACATAAAGTGTTG
1 TATCGATACAT-AAGT-TTG
293883 TATCGATAC--AA---TG
1 TATCGATACATAAGTTTG
*
293896 TATCGACACATAAGTGTTG
1 TATCGATACATAAGT-TTG
293915 TATCGATAC--AA---TG
1 TATCGATACATAAGTTTG
293928 TATCGATACATAAGTTTTG
1 TATCGATACATAAG-TTTG
293947 TATCGATACA
1 TATCGATACA
293957 ATGTAAGCTA
Statistics
Matches: 60, Mismatches: 2, Indels: 25
0.69 0.02 0.29
Matches are distributed among these distances:
13 21 0.35
15 4 0.07
17 4 0.07
19 22 0.37
20 9 0.15
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
TATCGATACATAAGTTTG
Found at i:294017 original size:13 final size:13
Alignment explanation
Indices: 293999--294023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
293989 ATTACTCAAA
293999 TGTATCGATACAT
1 TGTATCGATACAT
294012 TGTATCGATACA
1 TGTATCGATACA
294024 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:294076 original size:52 final size:52
Alignment explanation
Indices: 294032--294162 Score: 253
Period size: 52 Copynumber: 2.5 Consensus size: 52
294022 CACTGATCTT
294032 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
294084 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
294136 TGTATCGATACATGCAGGCAAATTTGC
1 TGTATCGATACATGCAGGCAAATTTGC
294163 ATATTTCGGG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 78 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:299626 original size:19 final size:21
Alignment explanation
Indices: 299587--299627 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
299577 AGAGAGTATT
299587 AAATATTTATTAAGGGGGAGAA
1 AAATATTTATTAA-GGGGAGAA
299609 AAAT-TTTATTAA-GGGAGAA
1 AAATATTTATTAAGGGGAGAA
299628 TATTTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
21 8 0.42
22 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (21 bp):
AAATATTTATTAAGGGGAGAA
Found at i:300416 original size:20 final size:21
Alignment explanation
Indices: 300374--300422 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
300364 ACTCACTCAA
*
300374 TATCGATACATACTTGAATTG
1 TATCGATACATACGTGAATTG
*
300395 TATCGATACATA-GTGCATTG
1 TATCGATACATACGTGAATTG
300415 TATCGATA
1 TATCGATA
300423 TATTGAGCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (21 bp):
TATCGATACATACGTGAATTG
Found at i:303231 original size:22 final size:21
Alignment explanation
Indices: 303205--303249 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
303195 TGATAACTAT
*
303205 TATTACAAAGTATATAAAATTA
1 TATTACAAACTATA-AAAATTA
* *
303227 TATTATAAACTATAAATATTA
1 TATTACAAACTATAAAAATTA
303248 TA
1 TA
303250 ATAAAAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (21 bp):
TATTACAAACTATAAAAATTA
Found at i:303253 original size:19 final size:19
Alignment explanation
Indices: 303217--303254 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
303207 TTACAAAGTA
303217 TATAAAATTATATTATAAAC
1 TATAAAATTATA-TATAAAC
303237 TATAAATATTATA-ATAAA
1 TATAAA-ATTATATATAAA
303255 AATGGGCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TATAAAATTATATATAAAC
Found at i:303882 original size:13 final size:15
Alignment explanation
Indices: 303853--303882 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
303843 ATTAAAATTT
303853 TATTTTATATTTATA
1 TATTTTATATTTATA
*
303868 TATTTTATTTTTATA
1 TATTTTATATTTATA
303883 ATTAATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTATATTTATA
Found at i:304251 original size:2 final size:2
Alignment explanation
Indices: 304244--304277 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
304234 TTAAATAGTT
304244 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
304278 GTATGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:304265 original size:15 final size:15
Alignment explanation
Indices: 304245--304274 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
304235 TAAATAGTTT
304245 ATATATATATATATA
1 ATATATATATATATA
304260 ATATATATATATATA
1 ATATATATATATATA
304275 TATGTATGTT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:304266 original size:17 final size:17
Alignment explanation
Indices: 304244--304276 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
304234 TTAAATAGTT
304244 TATATATATATATATAA
1 TATATATATATATATAA
304261 TATATATATATATATA
1 TATATATATATATATA
304277 TGTATGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATATATATATAA
Found at i:305264 original size:3 final size:3
Alignment explanation
Indices: 305256--305289 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
305246 TATAGAACCT
305256 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
305290 TTCTACCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:306090 original size:14 final size:13
Alignment explanation
Indices: 306055--306110 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
306045 TTGCTATCAA
306055 TTTTAAATATTTT
1 TTTTAAATATTTT
*
306068 TAATT-AATATTATT
1 T-TTTAAATATT-TT
306082 TTTTAAATATTTAT
1 TTTTAAATATTT-T
*
306096 ATTTAAA-ATTTT
1 TTTTAAATATTTT
306108 TTT
1 TTT
306111 ACTATTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
12 3 0.09
13 14 0.40
14 18 0.51
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTAAATATTTT
Found at i:306090 original size:27 final size:26
Alignment explanation
Indices: 306055--306110 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
306045 TTGCTATCAA
* *
306055 TTTTAAATATTTTTAATTAATATTATT
1 TTTTAAATATTTATAATTAAAATT-TT
*
306082 TTTTAAATATTTATATTTAAAATTTT
1 TTTTAAATATTTATAATTAAAATTTT
306108 TTT
1 TTT
306111 ACTATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTTAAATATTTATAATTAAAATTTT
Found at i:307419 original size:15 final size:14
Alignment explanation
Indices: 307399--307438 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
307389 TTTATAATAA
307399 TAATAAATTTATAGT
1 TAATAAATTTATA-T
*
307414 TAATAAATATATAT
1 TAATAAATTTATAT
*
307428 AAATAAATTTA
1 TAATAAATTTA
307439 AAATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TAATAAATTTATAT
Found at i:307429 original size:34 final size:36
Alignment explanation
Indices: 307338--307429 Score: 82
Period size: 34 Copynumber: 2.6 Consensus size: 36
307328 AAAAAATAAA
* * *
307338 ATAGTGAATAATTATATATTAATAATATAATAGATAT
1 ATAGTTAATAAATATATA-TAATAATATAATAAATAT
* * * *
307375 AAAATTAA-AAATA-AT-TTATAATAATAATAAATTT
1 ATAGTTAATAAATATATATAATAAT-ATAATAAATAT
307409 ATAGTTAATAAATATATATAA
1 ATAGTTAATAAATATATATAA
307430 ATAAATTTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
33 6 0.15
34 15 0.37
35 7 0.17
36 6 0.15
37 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (36 bp):
ATAGTTAATAAATATATATAATAATATAATAAATAT
Found at i:308252 original size:13 final size:15
Alignment explanation
Indices: 308208--308253 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
308198 TCAGAATAAA
* *
308208 AATAAAGTTATATTT
1 AATAATGTTTTATTT
308223 AATAATGTTTTATTTT
1 AATAATGTTTTA-TTT
308239 AAT-AT-TTTTATTT
1 AATAATGTTTTATTT
308252 AA
1 AA
308254 AATAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 5 0.18
14 5 0.18
15 12 0.43
16 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (15 bp):
AATAATGTTTTATTT
Found at i:308263 original size:9 final size:9
Alignment explanation
Indices: 308251--308289 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
308241 TATTTTTATT
308251 TAAAATAAA
1 TAAAATAAA
308260 TAAAATAAA
1 TAAAATAAA
308269 TAAAATTAATA
1 TAAAA-TAA-A
308280 TAAAA-AAA
1 TAAAATAAA
308288 TA
1 TA
308290 CAAGTGCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 3 0.11
9 16 0.57
10 3 0.11
11 6 0.21
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
TAAAATAAA
Found at i:308855 original size:15 final size:15
Alignment explanation
Indices: 308837--308868 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
308827 ATTTTTTAAT
*
308837 TTTTTTATAAAAATA
1 TTTTTTAAAAAAATA
308852 TTTTTTAAAAAAATA
1 TTTTTTAAAAAAATA
308867 TT
1 TT
308869 CAGCTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTTTAAAAAAATA
Found at i:314352 original size:22 final size:22
Alignment explanation
Indices: 314324--314366 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
314314 ATTAAAAGTT
314324 AGGGATTACA-AACTAATCCCTA
1 AGGGATTACAGAA-TAATCCCTA
314346 AGGGATTACAGAATAATCCCT
1 AGGGATTACAGAATAATCCCT
314367 GAAAATCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (22 bp):
AGGGATTACAGAATAATCCCTA
Found at i:314994 original size:2 final size:2
Alignment explanation
Indices: 314989--315028 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
314979 GGGTATGTGC
314989 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
315029 TCTTGATAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:318240 original size:6 final size:6
Alignment explanation
Indices: 318230--318288 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
318220 TTCTATATGC
* * * * * *
318230 ATATAT TTATAT ATATAT GTATAC ATGTAT ATATAT ATGTAT ATATGT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
318278 ATACAT ATATA
1 ATATAT ATATA
318289 CACACACACA
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (6 bp):
ATATAT
Found at i:318241 original size:8 final size:8
Alignment explanation
Indices: 318230--318288 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 8
318220 TTCTATATGC
*
318230 ATATATTT
1 ATATATAT
318238 ATATATAT
1 ATATATAT
* *
318246 ATGTATAC
1 ATATATAT
*
318254 ATGTATAT
1 ATATATAT
*
318262 ATATATGT
1 ATATATAT
*
318270 ATATATGT
1 ATATATAT
*
318278 ATACATAT
1 ATATATAT
318286 ATA
1 ATA
318289 CACACACACA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (8 bp):
ATATATAT
Found at i:318248 original size:20 final size:20
Alignment explanation
Indices: 318223--318287 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
318213 TGTTTTTTTC
* *
318223 TATATGCATATATTTATATA
1 TATATGTATATATGTATATA
*
318243 TATATGTATACATGTATATA
1 TATATGTATATATGTATATA
*
318263 TATATGTATATATGTATACA
1 TATATGTATATATGTATATA
318283 TATAT
1 TATAT
318288 ACACACACAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.48
Consensus pattern (20 bp):
TATATGTATATATGTATATA
Found at i:319662 original size:7 final size:8
Alignment explanation
Indices: 319636--319661 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
319626 TTCCTTTCTA
319636 TTTCTTTT
1 TTTCTTTT
319644 TTTCTTTT
1 TTTCTTTT
319652 TTTCTTTT
1 TTTCTTTT
319660 TT
1 TT
319662 CATCTTCTCG
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTCTTTT
Found at i:322206 original size:2 final size:2
Alignment explanation
Indices: 322199--322223 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
322189 TTATTATAAT
322199 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
322224 TAACAGACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:325278 original size:20 final size:19
Alignment explanation
Indices: 325256--325323 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
325246 CTATTATATA
325256 ATATAAATATAATAAAAAT
1 ATATAAATATAATAAAAAT
* *
325275 AATAAAAATATAAT-ATAAT
1 -ATATAAATATAATAAAAAT
* *
325294 ATA-AAAAATAATATAAAT
1 ATATAAATATAATAAAAAT
325312 ATATAAAATATA
1 ATAT-AAATATA
325324 TCAAAATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 8 0.21
18 9 0.23
19 4 0.10
20 18 0.46
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
ATATAAATATAATAAAAAT
Found at i:325292 original size:25 final size:23
Alignment explanation
Indices: 325255--325319 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 23
325245 ACTATTATAT
325255 AATATAAATATAATAAAAATAATAAA
1 AATAT-AATATAATAAAAA-AAT-AA
325281 AATATAATATAATATAAAAAATAA
1 AATATAATATAATA-AAAAAATAA
*
325305 TATA-AATAT-ATAAAA
1 AATATAATATAATAAAA
325320 TATATCAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 3 0.08
22 3 0.08
23 5 0.14
24 5 0.14
25 12 0.32
26 9 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AATATAATATAATAAAAAAATAA
Found at i:325320 original size:9 final size:9
Alignment explanation
Indices: 325256--325425 Score: 75
Period size: 9 Copynumber: 18.0 Consensus size: 9
325246 CTATTATATA
325256 ATAT-AAAT
1 ATATAAAAT
325264 ATAATAAAA-
1 AT-ATAAAAT
325273 ATAATAAAA-
1 AT-ATAAAAT
*
325282 ATATAATAT
1 ATATAAAAT
*
325291 AATATAAAAA
1 -ATATAAAAT
325301 ATAATATAAAT
1 AT-ATA-AAAT
325312 ATATAAAAT
1 ATATAAAAT
325321 ATATCAAAATTT
1 ATAT-AAAA--T
*
325333 ATTTAAAAT
1 ATATAAAAT
*
325342 AAATTAATTAAT
1 ATA-TAA--AAT
*
325354 -TAT-TAAT
1 ATATAAAAT
325361 ATATTAAAAT
1 ATA-TAAAAT
*
325371 TTATATAAAT
1 ATATA-AAAT
*
325381 ATGTAAAAT
1 ATATAAAAT
*
325390 ATTTAAAAT
1 ATATAAAAT
325399 ATTATAATAAT
1 A-TATAA-AAT
*
325410 AT-TAAAAG
1 ATATAAAAT
325418 ATA-AAAAT
1 ATATAAAAT
325426 TAATTATGAT
Statistics
Matches: 126, Mismatches: 17, Indels: 38
0.70 0.09 0.21
Matches are distributed among these distances:
7 3 0.02
8 17 0.13
9 44 0.35
10 41 0.33
11 14 0.11
12 7 0.06
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (9 bp):
ATATAAAAT
Found at i:325330 original size:19 final size:18
Alignment explanation
Indices: 325256--325425 Score: 75
Period size: 19 Copynumber: 9.0 Consensus size: 18
325246 CTATTATATA
325256 ATAT-AAATATAATAAAA-
1 ATATAAAATAT-ATAAAAT
*
325273 ATAATAAAA-ATATAATAT
1 AT-ATAAAATATATAAAAT
*
325291 AATATAAAAAATAATATAAAT
1 -ATATAAAATAT-ATA-AAAT
325312 ATATAAAATATATCAAAATTT
1 ATATAAAATATAT-AAAA--T
* *
325333 ATTTAAAATAAATTAATTAAT
1 ATATAAAATATA-TAA--AAT
*
325354 -TAT-TAATATATTAAAAT
1 ATATAAAATATA-TAAAAT
* *
325371 TTATATAAATATGTAAAAT
1 ATATA-AAATATATAAAAT
*
325390 ATTTAAAATATTATAATAAT
1 ATATAAAATA-TATAA-AAT
*
325410 AT-TAAAAGATA-AAAAT
1 ATATAAAATATATAAAAT
325426 TAATTATGAT
Statistics
Matches: 121, Mismatches: 14, Indels: 37
0.70 0.08 0.22
Matches are distributed among these distances:
16 3 0.02
17 12 0.10
18 20 0.17
19 40 0.33
20 26 0.21
21 17 0.14
22 1 0.01
23 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (18 bp):
ATATAAAATATATAAAAT
Found at i:325403 original size:29 final size:28
Alignment explanation
Indices: 325358--325416 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
325348 ATTAATTATT
325358 AATATATTAAAATTTAT-ATAAATATGTAA
1 AATATATTAAAATTTATAAT-AATAT-TAA
325387 AATAT-TTAAAATATTATAATAATATTAA
1 AATATATTAAAAT-TTATAATAATATTAA
325415 AA
1 AA
325417 GATAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 12 0.43
29 14 0.50
30 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (28 bp):
AATATATTAAAATTTATAATAATATTAA
Found at i:325412 original size:11 final size:10
Alignment explanation
Indices: 325260--325413 Score: 53
Period size: 10 Copynumber: 15.8 Consensus size: 10
325250 TATATAATAT
*
325260 AAATATAATA
1 AAATATTATA
*
325270 AAA-ATAATA
1 AAATATTATA
325279 AAA-A-TATA
1 AAATATTATA
* *
325287 ATATAATATA
1 AAATATTATA
* *
325297 AAAAATAATA
1 AAATATTATA
325307 TAAATA-TATA
1 -AAATATTATA
325317 AAATA-TATCA
1 AAATATTAT-A
325327 AAAT-TTATTTA
1 AAATATTA--TA
* *
325338 AAATA-AATT
1 AAATATTATA
*
325347 AATTAATTAT-
1 AAAT-ATTATA
*
325357 TAATA-TATTA
1 AAATATTA-TA
325367 AAAT-TTATA
1 AAATATTATA
*
325376 TAAATA-TGTA
1 -AAATATTATA
325386 AAATATT-TA
1 AAATATTATA
325395 AAATATTATA
1 AAATATTATA
325405 ATAATATTA
1 A-AATATTA
325414 AAAGATAAAA
Statistics
Matches: 110, Mismatches: 16, Indels: 35
0.68 0.10 0.22
Matches are distributed among these distances:
8 7 0.06
9 41 0.37
10 42 0.38
11 19 0.17
12 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (10 bp):
AAATATTATA
Found at i:335127 original size:20 final size:19
Alignment explanation
Indices: 335082--335138 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
335072 TCTATCGATA
*
335082 CATTGTATCAATACATGAT
1 CATTGTATCGATACATGAT
335101 CATTGTATCGATACATGCA-
1 CATTGTATCGATACATG-AT
335120 CAATTGTATCGATACATGA
1 C-ATTGTATCGATACATGA
335139 AACTGGCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:340796 original size:19 final size:18
Alignment explanation
Indices: 340771--340833 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
340761 TTTTATCGAT
340771 ACATTGTATCGATACATG
1 ACATTGTATCGATACATG
*
340789 ATCATTGTATCGAGACATG
1 A-CATTGTATCGATACATG
340808 CACAATTGTATCGATACATG
1 -AC-ATTGTATCGATACATG
*
340828 AAATTG
1 ACATTG
340834 GCAGTAGCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.13
19 18 0.46
20 16 0.41
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:342352 original size:43 final size:43
Alignment explanation
Indices: 342291--342376 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
342281 CTTTACGATT
342291 AATCAGGAACCTATATTGAGTATTTGTTATTAATATGGATAGC
1 AATCAGGAACCTATATTGAGTATTTGTTATTAATATGGATAGC
342334 AATCAGGAACCTATATTGAGTATTTGTTATTAATATGGATAGC
1 AATCAGGAACCTATATTGAGTATTTGTTATTAATATGGATAGC
342377 TTTTCTTGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (43 bp):
AATCAGGAACCTATATTGAGTATTTGTTATTAATATGGATAGC
Found at i:346763 original size:21 final size:22
Alignment explanation
Indices: 346739--346780 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
346729 ATTTTCAACT
*
346739 AAAATAAAATATA-TTTAGTTA
1 AAAATAAAATAAATTTTAGTTA
*
346760 AAAATAAGATAAATTTTAGTT
1 AAAATAAAATAAATTTTAGTT
346781 TTATTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (22 bp):
AAAATAAAATAAATTTTAGTTA
Found at i:347696 original size:38 final size:38
Alignment explanation
Indices: 347631--347733 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 38
347621 ATTTCAAACT
* *
347631 ATGCCACC-GGTTAAGAATAATGATTTTTGTATCGAACC
1 ATGCCACCGGGTTAA-AATAGTAATTTTTGTATCGAACC
* * * * *
347669 GTGCCACTGGTTTAAAATAGTAGTTTTTGTTTCGAACC
1 ATGCCACCGGGTTAAAATAGTAATTTTTGTATCGAACC
*
347707 ATGCTACCGGGTTAAAATAGTAATTTT
1 ATGCCACCGGGTTAAAATAGTAATTTT
347734 CGTTATCGTG
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
38 47 0.90
39 5 0.10
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (38 bp):
ATGCCACCGGGTTAAAATAGTAATTTTTGTATCGAACC
Found at i:352281 original size:20 final size:20
Alignment explanation
Indices: 352242--352282 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
352232 CTTGGCCATT
* *
352242 CATATTTTAGTAAATTTTTA
1 CATATTTTAATAAATATTTA
*
352262 CATATTTTAATATATATTTA
1 CATATTTTAATAAATATTTA
352282 C
1 C
352283 GAATTTATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (20 bp):
CATATTTTAATAAATATTTA
Found at i:356420 original size:20 final size:20
Alignment explanation
Indices: 356395--356442 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
356385 TTCCCAGATG
356395 TATCGATACAAAG-ATCAATA
1 TATCGATACAAAGAAT-AATA
**
356415 TATCGATACATTGAATAATA
1 TATCGATACAAAGAATAATA
356435 TATCGATA
1 TATCGATA
356443 TATTTCATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
TATCGATACAAAGAATAATA
Found at i:356504 original size:19 final size:19
Alignment explanation
Indices: 356476--356538 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
356466 AGCGATACAT
*
356476 TGTATTGATACAACACTTA
1 TGTATCGATACAACACTTA
356495 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
356508 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
356527 TGTATCGATACA
1 TGTATCGATACA
356539 GTTACTGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 20 0.54
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:356509 original size:32 final size:32
Alignment explanation
Indices: 356463--356538 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
356453 GCAGTAGCTT
* *
356463 TGTAGCGATACATTGTATTGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
356495 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
356527 TGTATCGATACA
1 TGTATCGATACA
356539 GTTACTGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:356513 original size:13 final size:13
Alignment explanation
Indices: 356495--356519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
356485 ACAACACTTA
356495 TGTATCGATACAT
1 TGTATCGATACAT
356508 TGTATCGATACA
1 TGTATCGATACA
356520 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:358717 original size:21 final size:21
Alignment explanation
Indices: 358691--358743 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
358681 TTTTAATATA
*
358691 TTTATATATT-TATATCATA-
1 TTTATATATTATATATCAAAT
*
358710 TTTATATAATTATTTATCAAAT
1 TTTATAT-ATTATATATCAAAT
*
358732 TTTATATCTTAT
1 TTTATATATTAT
358744 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 7 0.25
20 3 0.11
21 11 0.39
22 7 0.25
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTATATATTATATATCAAAT
Found at i:359018 original size:18 final size:18
Alignment explanation
Indices: 358968--359021 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
358958 TTAGTAAAAG
358968 TTAAATTTAAAAAATTTGA
1 TTAAATTTAAAAAATTT-A
* *
358987 -T-ACTTTAACTAAATTTA
1 TTAAATTTAA-AAAATTTA
359004 TTAAATTTAAAAAATTTA
1 TTAAATTTAAAAAATTTA
359022 AATGATCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
17 7 0.25
18 15 0.54
19 6 0.21
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAAATTTAAAAAATTTA
Found at i:360979 original size:24 final size:23
Alignment explanation
Indices: 360952--361009 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
360942 TATACTTATT
360952 TATTTAATTTTTAAAAATTTTAAA
1 TATTTAATTTTTAAAAA-TTTAAA
* * *
360976 TATTAAATATTTATAAATTTAAA
1 TATTTAATTTTTAAAAATTTAAA
360999 -ATTTATATTTT
1 TATTTA-ATTTT
361010 GACAAAACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 4 0.14
23 10 0.36
24 14 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTTAATTTTTAAAAATTTAAA
Found at i:360981 original size:16 final size:16
Alignment explanation
Indices: 360961--361005 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
360951 TTATTTAATT
360961 TTTAAAAATTT-TAAA
1 TTTAAAAATTTATAAA
*
360976 TATTAAATATTTATAAA
1 T-TTAAAAATTTATAAA
360993 TTT-AAAATTTATA
1 TTTAAAAATTTATA
361006 TTTTGACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 10 0.38
16 11 0.42
17 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAAAAATTTATAAA
Found at i:361002 original size:15 final size:16
Alignment explanation
Indices: 360965--361005 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
360955 TTAATTTTTA
360965 AAAATTT-TAAATATT
1 AAAATTTATAAATATT
360980 AAATATTTATAAAT-TT
1 AAA-ATTTATAAATATT
360996 AAAATTTATA
1 AAAATTTATA
361006 TTTTGACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.42
16 9 0.38
17 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAATTTATAAATATT
Found at i:367812 original size:21 final size:21
Alignment explanation
Indices: 367768--367841 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
367758 ATTTAAAATG
* *
367768 ATATTAAAATATTAAATTTTTT
1 ATATTAATAT-TTAAATATTTT
*
367790 ATATTAATATTTATATATTTT
1 ATATTAATATTTAAATATTTT
*
367811 ATAATTAA-ATATAAATAATTTT
1 AT-ATTAATATTTAAAT-ATTTT
*
367833 TTATTAATA
1 ATATTAATA
367842 AATAATAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 22 0.51
22 21 0.49
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTAATATTTAAATATTTT
Found at i:370119 original size:2 final size:2
Alignment explanation
Indices: 370112--370141 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
370102 ATCAAACATA
370112 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
370142 CAAAACTACA
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:371278 original size:16 final size:16
Alignment explanation
Indices: 371257--371328 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
371247 TATTATTATA
371257 ATTAATTATAATAAAT
1 ATTAATTATAATAAAT
371273 ATTAA-T-T-ATAAAT
1 ATTAATTATAATAAAT
*
371286 ATTAATAATAA-AAA-
1 ATTAATTATAATAAAT
371300 ATTAAAATTAT-A-AAAT
1 ATT--AATTATAATAAAT
*
371316 AATAATTATAATA
1 ATTAATTATAATA
371329 TTATTTAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
13 11 0.24
14 10 0.22
15 10 0.22
16 14 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAATTATAATAAAT
Found at i:371314 original size:14 final size:15
Alignment explanation
Indices: 371259--371331 Score: 71
Period size: 14 Copynumber: 4.9 Consensus size: 15
371249 TTATTATAAT
* *
371259 TAATTATAATAAATAT
1 TAATTATAA-AATTAA
371275 TAATTATAAATATTAA
1 TAATTATAAA-ATTAA
*
371291 TAA-TAAAAAATTAA
1 TAATTATAAAATTAA
371305 -AATTATAAAA-TAA
1 TAATTATAAAATTAA
*
371318 TAATTATAATATTA
1 TAATTATAAAATTA
371332 TTTAAATCCG
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.10
14 20 0.42
15 8 0.17
16 15 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATTATAAAATTAA
Found at i:378009 original size:19 final size:20
Alignment explanation
Indices: 377964--378015 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
377954 TTACAAGCCA
*
377964 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
*
377984 ATGTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
378004 -TGTATCGATACA
1 ATGTATCGATACA
378016 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:378457 original size:33 final size:33
Alignment explanation
Indices: 378420--378486 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
378410 TTCAACGATT
378420 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
378453 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
378486 T
1 T
378487 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:378458 original size:13 final size:13
Alignment explanation
Indices: 378440--378464 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
378430 CATAAAATGT
378440 TGTATCGATACAA
1 TGTATCGATACAA
378453 TGTATCGATACA
1 TGTATCGATACA
378465 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:378545 original size:13 final size:13
Alignment explanation
Indices: 378527--378551 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
378517 ATTACTCAAA
378527 TGTATCGATACAT
1 TGTATCGATACAT
378540 TGTATCGATACA
1 TGTATCGATACA
378552 CTAATATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:386973 original size:19 final size:20
Alignment explanation
Indices: 386928--386979 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
386918 TTACAAGCCA
*
386928 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
*
386948 ATGTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
386968 -TGTATCGATACA
1 ATGTATCGATACA
386980 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:387072 original size:20 final size:21
Alignment explanation
Indices: 387021--387073 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
387011 GCCAATGACC
*
387021 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTATACA
* *
387042 AGTATCAATACATT-TGAT-CA
1 TGTATCGATACATTCT-ATACA
387062 TGTATCGATACA
1 TGTATCGATACA
387074 ATGTATCGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTATACA
Found at i:387077 original size:13 final size:13
Alignment explanation
Indices: 387061--387085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
387051 ACATTTGATC
387061 ATGTATCGATACA
1 ATGTATCGATACA
387074 ATGTATCGATAC
1 ATGTATCGATAC
387086 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:387080 original size:33 final size:31
Alignment explanation
Indices: 387038--387106 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 31
387028 ATACATTCTT
*
387038 TACAAGTATCAATACATTTG-ATCATGTATCGA
1 TACAAGTATCAATAC-TGTGAATC-TGTATCGA
*
387070 TACAATGTATCGATACTGTGCAATCTGTATCGA
1 TACAA-GTATCAATACTGTG-AATCTGTATCGA
387103 TACA
1 TACA
387107 TTTGAAGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 8 0.25
33 21 0.66
34 3 0.09
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (31 bp):
TACAAGTATCAATACTGTGAATCTGTATCGA
Found at i:387632 original size:52 final size:52
Alignment explanation
Indices: 387554--387805 Score: 177
Period size: 52 Copynumber: 4.8 Consensus size: 52
387544 GATGAGAAGA
* * *
387554 GTGCTAATGTGCTGATTCAAGGCCAGCGACATTTGACTTAAAAATGATAAAG
1 GTGCTAATATGATGATTCAAGGCCAGCGACATTGGACTTAAAAATGATAAAG
* * *
387606 GTGCTAATATGATGATTCAATGCCAGCGACATTGGGCTTAAAAATGA-GAAG
1 GTGCTAATATGATGATTCAAGGCCAGCGACATTGGACTTAAAAATGATAAAG
* * * ** ** ** * * *
387657 AATGCCAATGTTCTGATTCAAGATCAGTAATATTGGGCTTAAAAATGATAAAT
1 -GTGCTAATATGATGATTCAAGGCCAGCGACATTGGACTTAAAAATGATAAAG
* * * * ** * * *
387710 GTGCCT-ATATGCTAATTCGAGGCCAGCGATATCAGACTTAAAGATAATAAGG
1 GTG-CTAATATGATGATTCAAGGCCAGCGACATTGGACTTAAAAATGATAAAG
* * * *
387762 GTGCTAATGTGCTGATTCAAGGCTAGCAACATTAGG-CTTAAAAA
1 GTGCTAATATGATGATTCAAGGCCAGCGACATT-GGACTTAAAAA
387806 AGGCCAGCAA
Statistics
Matches: 150, Mismatches: 45, Indels: 10
0.73 0.22 0.05
Matches are distributed among these distances:
51 5 0.03
52 141 0.94
53 4 0.03
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (52 bp):
GTGCTAATATGATGATTCAAGGCCAGCGACATTGGACTTAAAAATGATAAAG
Found at i:387735 original size:104 final size:104
Alignment explanation
Indices: 387545--387805 Score: 247
Period size: 104 Copynumber: 2.5 Consensus size: 104
387535 GTTGATAAGG
* * * * *
387545 ATGAGAAGAGTGCTAATGTGCTGATTCAAGGCCAGCGACATTTGACTTAAAAATGATAAAGGTGC
1 ATGAGAAGAATGCCAATGTGCTGATTCAAGACCAGCAACATTGGACTTAAAAATGATAAAGGTGC
* *
387610 TAATATGATGATTCAATGCCAGCGACATTGGGCTTAAAA
66 TAATATGATAATTCAAGGCCAGCGACATTGGGCTTAAAA
* * * * * *
387649 ATGAGAAGAATGCCAATGTTCTGATTCAAGATCAGTAATATTGGGCTTAAAAATGATAAATGTGC
1 ATGAGAAGAATGCCAATGTGCTGATTCAAGACCAGCAACATTGGACTTAAAAATGATAAAGGTG-
* * * ** * *
387714 CT-ATATGCTAATTCGAGGCCAGCGATATCAGACTTAAAG
65 CTAATATGATAATTCAAGGCCAGCGACATTGGGCTTAAAA
* * ** * * *
387753 ATAATAAGGGTGCTAATGTGCTGATTCAAGGCTAGCAACATTAGG-CTTAAAAA
1 ATGAGAAGAATGCCAATGTGCTGATTCAAGACCAGCAACATT-GGACTTAAAAA
387806 AGGCCAGCAA
Statistics
Matches: 124, Mismatches: 31, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
104 120 0.97
105 4 0.03
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (104 bp):
ATGAGAAGAATGCCAATGTGCTGATTCAAGACCAGCAACATTGGACTTAAAAATGATAAAGGTGC
TAATATGATAATTCAAGGCCAGCGACATTGGGCTTAAAA
Found at i:388120 original size:52 final size:53
Alignment explanation
Indices: 388046--388200 Score: 154
Period size: 52 Copynumber: 3.0 Consensus size: 53
388036 TTAGGCTTTG
* * * * *
388046 GAATGATAAAGATGCCAGTATGCTAATTCAAGGCTAACGATATTGGACTTAAA
1 GAATGAAAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAA
* * * *
388099 G-ATGACAAAGGTGCCAATATGCTGATTCAAGGGC-AGCAATATTAGA-TTTAA
1 GAATGAAAAAGGTGCCAATATGCTGATTCAA-GGCTAGCGATATTGGACTTAAA
* * * * *
388150 GAAAGAAAAATGTGCCAATATGCTGATTCAAGACTAGTGACATTGGACTTA
1 GAATGAAAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTA
388201 GAAAGAGATG
Statistics
Matches: 81, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
51 7 0.09
52 68 0.84
53 6 0.07
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.26
Consensus pattern (53 bp):
GAATGAAAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAA
Found at i:388349 original size:33 final size:32
Alignment explanation
Indices: 388268--388603 Score: 363
Period size: 32 Copynumber: 10.5 Consensus size: 32
388258 TAAAAGGAGA
* *
388268 TGCCATCGACTTGTGTGGGCTTTTGAGAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAAGGGT
*
388300 TGCCA-CAACTTGTGTGGGCTTTTGAAAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAA-GGGT
*
388332 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAAGGGT
* * *
388364 TACCACCGACTTGTGTGGGCTTTAGCAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAAGGGT
** *
388396 TGCCACCGACTTGTGTGAACTTTCGAAAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAA-GGGT
* **
388429 TGCCACCAACTTGTGTGGGCTTTAAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAAGGGT
* ** * *
388461 TGCCACTGACTTGTGTGAAC-TTTAAAAGTGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAAGGGT
* * *
388492 TGCCACCAACTTGTGTGGGCTTTAGGGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT-TGAAAGGGT
* * * *
388525 TGCTACCGACTTATGTGGGCTTTAGAGAAGGAT
1 TGCCACCGACTTGTGTGGGCTTTTGA-AAGGGT
* * *
388558 TGCCATCGACTTGTGTAGGC-TTTAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAAGGGT
388589 TGCCACCGACTTGTG
1 TGCCACCGACTTGTG
388604 GAGTTTAAGA
Statistics
Matches: 254, Mismatches: 44, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
31 64 0.25
32 97 0.38
33 93 0.37
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.30
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTTGAAAGGGT
Found at i:388433 original size:97 final size:96
Alignment explanation
Indices: 388252--388603 Score: 415
Period size: 97 Copynumber: 3.7 Consensus size: 96
388242 CCAACGACAT
* * * *
388252 TGGGC-TTA-AAAGGAGATGCCATCGACTTGTGTGGGCTTTTGAGAGGGTTGCCA-CAACTTGTG
1 TGGGCTTTAGAAAGG-GTTGCCACCGACTTGTGTGGGC-TTTAAAAGGGTTGCCACCAACTTGTG
*
388314 TGGGCTTTTGAAAGGGGTTGCCACCGACTTGTG
64 TGGGCTTTCGAAAGGGGTTGCCACCGACTTGTG
* * *
388347 TGGGCTTTAGAAAGGGTTACCACCGACTTGTGTGGGCTTTAGCAAGGGTTGCCACCGACTTGTGT
1 TGGGCTTTAGAAAGGGTTGCCACCGACTTGTGTGGGCTTTA-AAAGGGTTGCCACCAACTTGTGT
** *
388412 GAACTTTCGAAAGGGGTTGCCACCAACTTGTG
65 GGGCTTTCGAAAGGGGTTGCCACCGACTTGTG
* * ** *
388444 TGGGCTTTAAAAAGGGTTGCCACTGACTTGTGTGAACTTTAAAAGTGTTGCCACCAACTTGTGTG
1 TGGGCTTTAGAAAGGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTTGCCACCAACTTGTGTG
* * * *
388509 GGCTTTAGGGAA-GGGTTGCTACCGACTTATG
66 GGCTTT-CGAAAGGGGTTGCCACCGACTTGTG
* * * *
388540 TGGGCTTTAGAGAAGGATTGCCATCGACTTGTGTAGGCTTTAAAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-AAGGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTTGCCACCAACTTGTG
388604 GAGTTTAAGA
Statistics
Matches: 216, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
95 8 0.04
96 83 0.38
97 125 0.58
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.30
Consensus pattern (96 bp):
TGGGCTTTAGAAAGGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTTGCCACCAACTTGTGTG
GGCTTTCGAAAGGGGTTGCCACCGACTTGTG
Found at i:388692 original size:34 final size:32
Alignment explanation
Indices: 388613--388695 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 32
388603 GGAGTTTAAG
* * * *
388613 AAAGGGTGCCATGGAGTTGCAGACTTAAAAGA
1 AAAGGGTGCAACGGAGTTACAGACTTAAAAAA
*
388645 AAA-GGTGCAACGGAGTTATAGACTTAAAAATAA
1 AAAGGGTGCAACGGAGTTACAGACTT-AAAA-AA
*
388678 AAAGGGTGCTACGGAGTT
1 AAAGGGTGCAACGGAGTT
388696 GTGGACTTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
31 18 0.43
32 7 0.17
33 4 0.10
34 13 0.31
ACGTcount: A:0.40, C:0.11, G:0.29, T:0.20
Consensus pattern (32 bp):
AAAGGGTGCAACGGAGTTACAGACTTAAAAAA
Found at i:388703 original size:34 final size:32
Alignment explanation
Indices: 388613--388703 Score: 94
Period size: 34 Copynumber: 2.8 Consensus size: 32
388603 GGAGTTTAAG
* * * *
388613 AAAGGGTGCCATGGAGTTGCAGACTTAAAAGA
1 AAAGGGTGCAACGGAGTTGTAGACTTAAAAAA
*
388645 AAA-GGTGCAACGGAGTTATAGACTTAAAAATAA
1 AAAGGGTGCAACGGAGTTGTAGACTT-AAAA-AA
* *
388678 AAAGGGTGCTACGGAGTTGTGGACTT
1 AAAGGGTGCAACGGAGTTGTAGACTT
388704 TGGGAAGAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
31 18 0.38
32 7 0.15
33 4 0.08
34 19 0.40
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (32 bp):
AAAGGGTGCAACGGAGTTGTAGACTTAAAAAA
Found at i:388732 original size:30 final size:30
Alignment explanation
Indices: 388691--388793 Score: 127
Period size: 30 Copynumber: 3.5 Consensus size: 30
388681 GGGTGCTACG
*
388691 GAGTTGTGGACTTTGGGAAGAGATGCCACT
1 GAGTCGTGGACTTTGGGAAGAGATGCCACT
* * * *
388721 AAGTCGTGGACTTTGAGAAGGGA-GCGACT
1 GAGTCGTGGACTTTGGGAAGAGATGCCACT
* * *
388750 GAGTCATGGACTTTGGGAAAAGATGCCATT
1 GAGTCGTGGACTTTGGGAAGAGATGCCACT
388780 GAGTCGTGGACTTT
1 GAGTCGTGGACTTT
388794 AAAAAAAGTG
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
29 23 0.39
30 36 0.61
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.26
Consensus pattern (30 bp):
GAGTCGTGGACTTTGGGAAGAGATGCCACT
Found at i:388801 original size:30 final size:29
Alignment explanation
Indices: 388714--388895 Score: 94
Period size: 33 Copynumber: 6.0 Consensus size: 29
388704 TGGGAAGAGA
* * * **
388714 TGCCACTAAGTCGTGGACTTTGAGAAGGG
1 TGCCACTGAGTCGTGGACTTTAAAAAAAG
* * * ***
388743 AGCGACTGAGTCATGGACTTTGGGAAAAG
1 TGCCACTGAGTCGTGGACTTTAAAAAAAG
*
388772 ATGCCATTGAGTCGTGGACTTTAAAAAAAG
1 -TGCCACTGAGTCGTGGACTTTAAAAAAAG
* *
388802 TGCCACGGAGTTGTGGACTTTTGGAGAAAAAAG
1 TGCCACTGAGTCGTGGAC-TTT--A-AAAAAAG
* * * *
388835 TGTCACGGATTTGTGGACTTTAAAAGAGAAAGG
1 TGCCACTGAGTCGTGGACTTT-AAA-A-AAA-G
* **
388868 TGCCACGGAGTTATGGACTTTAAAAAAA
1 TGCCACTGAGTCGTGGACTTTAAAAAAA
388896 AAAGGGTCCC
Statistics
Matches: 122, Mismatches: 23, Indels: 15
0.76 0.14 0.09
Matches are distributed among these distances:
29 37 0.30
30 30 0.25
31 3 0.02
32 10 0.08
33 42 0.34
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (29 bp):
TGCCACTGAGTCGTGGACTTTAAAAAAAG
Found at i:388819 original size:59 final size:59
Alignment explanation
Indices: 388683--388888 Score: 178
Period size: 59 Copynumber: 3.4 Consensus size: 59
388673 AATAAAAAGG
* * * * * * **
388683 GTGCTACGGAGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCGTGGACTTTGAGAAGG
1 GTGCCACGGAGTTATGGACTTTGGGAAAAGATGCCACTGAGTCGTGGACTTTAAAAAAA
* * * * *
388742 GAGCGACTGAGTCATGGACTTTGGGAAAAGATGCCATTGAGTCGTGGACTTTAAAAAAA
1 GTGCCACGGAGTTATGGACTTTGGGAAAAGATGCCACTGAGTCGTGGACTTTAAAAAAA
* * * * * *
388801 GTGCCACGGAGTTGTGGACTTTTGGAGAAAAAAGTGTCACGGATTTGTGGACTTTAAAAGAGAAA
1 GTGCCACGGAGTTATGGAC-TTTGG-GAAAAGA-TGCCACTGAGTCGTGGACTTT-AAA-A-AAA
388866 GGTGCCACGGAGTTATGGACTTT
1 -GTGCCACGGAGTTATGGACTTT
388889 AAAAAAAAAA
Statistics
Matches: 116, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
59 61 0.53
60 5 0.04
61 6 0.05
62 16 0.14
63 3 0.03
64 1 0.01
65 6 0.05
66 18 0.16
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.26
Consensus pattern (59 bp):
GTGCCACGGAGTTATGGACTTTGGGAAAAGATGCCACTGAGTCGTGGACTTTAAAAAAA
Found at i:388842 original size:33 final size:33
Alignment explanation
Indices: 388795--388926 Score: 131
Period size: 33 Copynumber: 4.0 Consensus size: 33
388785 GTGGACTTTA
***
388795 AAAAAAGTGCCACGGAGTTGTGGACTTTTGGAG
1 AAAAAAGTGCCACGGAGTTGTGGACTTTAAAAG
* *
388828 AAAAAAGTGTCACGGATTTGTGGACTTTAAAAG
1 AAAAAAGTGCCACGGAGTTGTGGACTTTAAAAG
* * *
388861 AGAAAGGTGCCACGGAGTTATGGACTTTAAAA-
1 AAAAAAGTGCCACGGAGTTGTGGACTTTAAAAG
* * **
388893 AAAAAAGGGTCCCATGGAGTCATGGACTTTAAAA
1 AAAAAA--GTGCCACGGAGTTGTGGACTTTAAAA
388927 AGAAGGAGAA
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
32 4 0.05
33 55 0.67
34 23 0.28
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.23
Consensus pattern (33 bp):
AAAAAAGTGCCACGGAGTTGTGGACTTTAAAAG
Found at i:388918 original size:34 final size:33
Alignment explanation
Indices: 388848--388927 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 33
388838 CACGGATTTG
* * * *
388848 TGGACTTTAAAAGAGAAAGGTGCCACGGAGTTA
1 TGGACTTTAAAAAAAAAAGGTCCCACGGAGTCA
*
388881 TGGACTTTAAAAAAAAAAGGGTCCCATGGAGTCA
1 TGGACTTTAAAAAAAAAA-GGTCCCACGGAGTCA
388915 TGGACTTTAAAAA
1 TGGACTTTAAAAA
388928 GAAGGAGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 16 0.39
34 25 0.61
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (33 bp):
TGGACTTTAAAAAAAAAAGGTCCCACGGAGTCA
Found at i:393322 original size:162 final size:161
Alignment explanation
Indices: 393145--393600 Score: 673
Period size: 161 Copynumber: 2.8 Consensus size: 161
393135 AAAATTAAAT
393145 AATATTTATTTTTTCTAATCTTTTATATTCTTATGGGCATCCGTAGAGGTATAAAAGATTTCAAA
1 AATATTTATTTTTTCTAATCTTTTATATTCTTATGGGCATCCGTAGAGGTATAAAAGATTTCAAA
* * * *
393210 AACCTTTTGTATTCTTTCAGGCTTCCGTTAGGATATGAAATAATATTTTCAAAAATAAATAAAAT
66 AACCTTTTATATTCTTTC-GGCTTCCATTAGGGTATGAAATAGTATTTTCAAAAATAAATAAAAT
393275 TAACTTAAATTGGTATTATTGAGATAAATTCC
130 TAACTTAAATTGGTATTATTGAGATAAATTCC
* * *
393307 AATATTT-TATTTTTCTAATCTTTTATATTCTTATAGGCATCTGTAGGGGTATAAAAGATTTCAA
1 AATATTTAT-TTTTTCTAATCTTTTATATTCTTATGGGCATCCGTAGAGGTATAAAAGATTTCAA
*
393371 AAACCTTTCATATTCTTTCGAGCTTCCATTAGGGTATGAAATAGTATTTTCAAAAATAAAT-AAA
65 AAACCTTTTATATTCTTTCG-GCTTCCATTAGGGTATGAAATAGTATTTTCAAAAATAAATAAAA
* * * * *
393435 TAAATTTAAATTGGTGTTATTGGGATAAATTCT
129 TTAACTTAAATTGGTATTATTGAGATAAATTCC
* * *
393468 AATATTTATTTTTTCTATTTTTTTATATTCCTATGGGCATCCGTAGAGGTATAAAAGATTTCAAA
1 AATATTTATTTTTTCTAATCTTTTATATTCTTATGGGCATCCGTAGAGGTATAAAAGATTTCAAA
* * * * *
393533 ACCCTTTTATATTCTTTCGGGCTTCCATTAGGGTACGAAATGGTATTTTTAAAAGTAAATAAAAT
66 AACCTTTTATATTCTTTC-GGCTTCCATTAGGGTATGAAATAGTATTTTCAAAAATAAATAAAAT
393598 TAA
130 TAA
393601 ATTGAATTAA
Statistics
Matches: 263, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
161 142 0.54
162 121 0.46
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (161 bp):
AATATTTATTTTTTCTAATCTTTTATATTCTTATGGGCATCCGTAGAGGTATAAAAGATTTCAAA
AACCTTTTATATTCTTTCGGCTTCCATTAGGGTATGAAATAGTATTTTCAAAAATAAATAAAATT
AACTTAAATTGGTATTATTGAGATAAATTCC
Found at i:397901 original size:13 final size:13
Alignment explanation
Indices: 397883--397907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
397873 ATTTTGCTTA
397883 GTATCGATACATT
1 GTATCGATACATT
397896 GTATCGATACAT
1 GTATCGATACAT
397908 AAACTAGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:398026 original size:17 final size:17
Alignment explanation
Indices: 398000--398035 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
397990 TATCGATACA
398000 TCACTATTCATCACTGT
1 TCACTATTCATCACTGT
*
398017 TCACTGTTCATCACTGT
1 TCACTATTCATCACTGT
398034 TC
1 TC
398036 GCGTATCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.31, G:0.08, T:0.42
Consensus pattern (17 bp):
TCACTATTCATCACTGT
Found at i:398030 original size:10 final size:10
Alignment explanation
Indices: 397998--398061 Score: 53
Period size: 10 Copynumber: 6.3 Consensus size: 10
397988 AGTATCGATA
*
397998 CATCACTATT
1 CATCACTGTT
398008 CATCACTG-T
1 CATCACTGTT
398017 --TCACTGTT
1 CATCACTGTT
398025 CATCACTGTT
1 CATCACTGTT
*
398035 CGCGTATCACTATT
1 --C--ATCACTGTT
398049 CATCACTGTT
1 CATCACTGTT
398059 CAT
1 CAT
398062 GTATCGATAC
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
7 6 0.14
8 1 0.02
9 1 0.02
10 26 0.59
12 2 0.05
14 8 0.18
ACGTcount: A:0.22, C:0.30, G:0.09, T:0.39
Consensus pattern (10 bp):
CATCACTGTT
Found at i:398065 original size:24 final size:24
Alignment explanation
Indices: 398017--398066 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
398007 TCATCACTGT
* *
398017 TCACTGTTCATCACTGTTCGCGTA
1 TCACTATTCATCACTGTTCACGTA
*
398041 TCACTATTCATCACTGTTCATGTA
1 TCACTATTCATCACTGTTCACGTA
398065 TC
1 TC
398067 GATACATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.40
Consensus pattern (24 bp):
TCACTATTCATCACTGTTCACGTA
Found at i:400147 original size:17 final size:15
Alignment explanation
Indices: 400113--400159 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
400103 AGTTATTAGT
400113 TAAAAAAACAAAAAA
1 TAAAAAAACAAAAAA
*
400128 TAAAATAAATAAATAAA
1 TAAAA-AAACAAA-AAA
*
400145 TAAAAACA-AAAAAA
1 TAAAAAAACAAAAAA
400159 T
1 T
400160 TAAGTCTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 8 0.29
17 8 0.29
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (15 bp):
TAAAAAAACAAAAAA
Found at i:402961 original size:13 final size:13
Alignment explanation
Indices: 402943--402972 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
402933 ACAATTCATC
402943 ATGTATCGATACA
1 ATGTATCGATACA
402956 ATGTATCGATACA
1 ATGTATCGATACA
402969 ATGT
1 ATGT
402973 GCTATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:402964 original size:33 final size:33
Alignment explanation
Indices: 402922--402989 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
402912 CATTTGAAAT
402922 AATGTATCGATACAAT-T-CATCATGTATCGATAC
1 AATGTATCGATACAATGTGC-T-ATGTATCGATAC
402955 AATGTATCGATACAATGTGCTATGTATCGATAC
1 AATGTATCGATACAATGTGCTATGTATCGATAC
402988 AA
1 AA
402990 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.91
34 2 0.06
35 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
AATGTATCGATACAATGTGCTATGTATCGATAC
Found at i:403684 original size:28 final size:28
Alignment explanation
Indices: 403644--403754 Score: 177
Period size: 28 Copynumber: 3.9 Consensus size: 28
403634 TTCCCTTTGA
403644 TAAAAAATTTCTCCCCCTTGATAATCGG
1 TAAAAAATTTCTCCCCCTTGATAATCGG
403672 TAAAAAATTTCTCCCCCTTGATAATCGG
1 TAAAAAATTTCTCCCCCTTGATAATCGG
* *
403700 CAAAAAATTTCTCCCCCTTGATAATCGAT
1 TAAAAAATTTCTCCCCCTTGATAATCG-G
403729 TAAAAAGATTTTCTCCCCCTTGATAA
1 TAAAAA-A-TTTCTCCCCCTTGATAA
403755 AAATTTATTT
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
28 54 0.70
29 5 0.06
30 1 0.01
31 17 0.22
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.32
Consensus pattern (28 bp):
TAAAAAATTTCTCCCCCTTGATAATCGG
Found at i:405066 original size:20 final size:22
Alignment explanation
Indices: 405027--405071 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
405017 GCAGTGGGTG
* *
405027 TGGGAGTTGCCCGATTGCGAGC
1 TGGGAGTTGCCCGATCGCGACC
405049 TGGGAG-TG-CCGATCGCGACC
1 TGGGAGTTGCCCGATCGCGACC
405069 TGG
1 TGG
405072 AGGTGGCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.13, C:0.24, G:0.42, T:0.20
Consensus pattern (22 bp):
TGGGAGTTGCCCGATCGCGACC
Found at i:410066 original size:3 final size:3
Alignment explanation
Indices: 410058--410127 Score: 104
Period size: 3 Copynumber: 23.3 Consensus size: 3
410048 TCCGAGTCAC
*
410058 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT TAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
* * *
410106 CAC CAT CAT CAT TAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT C
410128 GTCTTTGATG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (3 bp):
CAT
Found at i:411735 original size:13 final size:13
Alignment explanation
Indices: 411717--411749 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
411707 GCCGTTTCAA
411717 ACAATGTATCGAT
1 ACAATGTATCGAT
411730 ACAATGTATCGAT
1 ACAATGTATCGAT
411743 ACAATGT
1 ACAATGT
411750 GCCATGTATC
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:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:411820 original size:20 final size:19
Alignment explanation
Indices: 411795--411867 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
411785 CTGCTAGTTT
**
411795 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
411815 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
*
411834 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
411855 -ATGTATCGATACA
1 CATGTATCGATACA
411868 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:411839 original size:19 final size:20
Alignment explanation
Indices: 411795--411848 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
411785 CTGCTAGTTT
**
411795 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
411815 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGAA
411834 CATGTATCGATACAA
1 CATGTATCGATACAA
411849 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:412288 original size:47 final size:47
Alignment explanation
Indices: 412227--412596 Score: 284
Period size: 47 Copynumber: 7.8 Consensus size: 47
412217 TTTTCATCTT
* *
412227 CGTTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTTTTTCTTC
1 CGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTTTTTCCTC
* *
412274 CATTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTTTCTCAC-C
1 CGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTTTTTC-CTC
** * * * *
412321 CTAGTTTGACTATATTTACGTTAAGACCTAGTCAAACTCTCTTATCCTC
1 C--GTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTTTTTCCTC
* * *
412370 TGTTTGACTATATTAGCGTTAGGACCTGATCAAACT-TTATTTTCCTC
1 CGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTT-TTTTCCTC
* * * * *
412417 TGTTTAACTGTATTGGCATTA-GACCTGGTCAAACTCTCTCTTTCACTC
1 CGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCT-TTTTTC-CTC
* * * * * * *
412465 TTGTTTGACTGTATTAGTGTTA-AACTTGGTCAAACT-TTCTTTTCCGC
1 -CGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTT-TTTTCCTC
* * * ** *
412512 CTTGTTTGACTATATTGGCATTAGGACATGATCAAACTCCTTTTAACAT-
1 C--GTTTGACTATATTGGCGTTAGGACCTGGTCAAACT-CTTTTTTCCTC
** * *
412561 TATTTAACTATGTTGGCGTTAGGACCTGGTCAAACT
1 CGTTTGACTATATTGGCGTTAGGACCTGGTCAAACT
412597 TTTCTCACCA
Statistics
Matches: 256, Mismatches: 52, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
46 14 0.05
47 134 0.52
48 26 0.10
49 77 0.30
50 3 0.01
51 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.40
Consensus pattern (47 bp):
CGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTTTTTCCTC
Found at i:412392 original size:96 final size:95
Alignment explanation
Indices: 412228--412642 Score: 326
Period size: 96 Copynumber: 4.4 Consensus size: 95
412218 TTTCATCTTC
* * * * * * * *
412228 GTTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTTTTTCTTCCATTTGACTATATTGGCGT
1 GTTTGACTATATTGGCATTAAGACCTGGTCAAACTCTCTTATCCTCTATTTGACTATATTAGCGT
*
412293 TAGGACCTGGTCAAACTCTTTTCTCACCCTA
66 TAGGACCTGGTCAAACTCTTTTCTC-CCCTT
** * * *
412324 GTTTGACTATATTTACGTTAAGACCTAGTCAAACTCTCTTATCCTCTGTTTGACTATATTAGCGT
1 GTTTGACTATATTGGCATTAAGACCTGGTCAAACTCTCTTATCCTCTATTTGACTATATTAGCGT
* * *
412389 TAGGACCTGATCAAACT-TTATTTTCCTC-T
66 TAGGACCTGGTCAAACTCTT-TTCTCCCCTT
* * * * *
412418 GTTTAACTGTATTGGCATT-AGACCTGGTCAAACTCTCTCTTTCACTCTTGTTTGACTGTATTAG
1 GTTTGACTATATTGGCATTAAGACCTGGTCAAACTCTCT-TATC-CTC-TATTTGACTATATTAG
* * * *
412482 TGTTA-AACTTGGTCAAACTTTCTTTTC-CGCCTT
63 CGTTAGGACCTGGTCAAAC--TCTTTTCTCCCCTT
* * * * * * * * *
412515 GTTTGACTATATTGGCATTAGGACATGATCAAACTCCTTTTAACAT-TATTTAACTATGTTGGCG
1 GTTTGACTATATTGGCATTAAGACCTGGTCAAACT-CTCTTATCCTCTATTTGACTATATTAGCG
*
412579 TTAGGACCTGGTCAAA--CTTTTCTCACCATT
65 TTAGGACCTGGTCAAACTCTTTTCTC-CCCTT
* * * *
412609 GTTTGATTGTATTAGCATT-AGTCCTGGTCAAACT
1 GTTTGACTATATTGGCATTAAGACCTGGTCAAACT
412643 GTTTTCCTCT
Statistics
Matches: 250, Mismatches: 56, Indels: 29
0.75 0.17 0.09
Matches are distributed among these distances:
92 6 0.02
93 30 0.12
94 36 0.14
95 32 0.13
96 105 0.42
97 22 0.09
98 16 0.06
99 3 0.01
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (95 bp):
GTTTGACTATATTGGCATTAAGACCTGGTCAAACTCTCTTATCCTCTATTTGACTATATTAGCGT
TAGGACCTGGTCAAACTCTTTTCTCCCCTT
Found at i:412471 original size:143 final size:144
Alignment explanation
Indices: 412228--412642 Score: 407
Period size: 143 Copynumber: 2.9 Consensus size: 144
412218 TTTCATCTTC
* * * * *
412228 GTTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTTTTTCTTCCATTTGACTATATTGGCGT
1 GTTTGACTATATTGGCGTTAGGACCTGATCAAACTCTTTTTTCCTCCATTTAACTATATTGGCAT
412293 TAGGACCTGGTCAAACTCTTTTCTCACCCTAGTTTGACTATATTTA-CGTTAAGACCTAGTCAAA
66 TAGGACCTGGTCAAACTCTTTTCTCACCCTAGTTTGACTATA-TTAGCGTTAA-ACCTAGTCAAA
*
412357 CTCTCTTATCC-TC-T
129 CTCTCTTATCCGCCTT
* ** *
412371 GTTTGACTATATTAGCGTTAGGACCTGATCAAACT-TTATTTTCCTCTGTTTAACTGTATTGGCA
1 GTTTGACTATATTGGCGTTAGGACCTGATCAAACTCTT-TTTTCCTCCATTTAACTATATTGGCA
* * * * * *
412435 TTA-GACCTGGTCAAACTCTCTCTT-TCACTCTTGTTTGACTGTATTAGTGTTAAACTTGGTCAA
65 TTAGGACCTGGTCAAACTCT-T-TTCTCACCCTAGTTTGACTATATTAGCGTTAAACCTAGTCAA
* *
412498 ACTTTCTTTTCCGCCTT
128 ACTCTCTTATCCGCCTT
* * ** * * * *
412515 GTTTGACTATATTGGCATTAGGACATGATCAAACTCCTTTTAACAT-TATTTAACTATGTTGGCG
1 GTTTGACTATATTGGCGTTAGGACCTGATCAAACT-CTTTTTTCCTCCATTTAACTATATTGGCA
* * * * * ** *
412579 TTAGGACCTGGTCAAA--CTTTTCTCACCATTGTTTGATTGTATTAGCATTAGTCCTGGTCAAAC
65 TTAGGACCTGGTCAAACTCTTTTCTCACCCTAGTTTGACTATATTAGCGTTAAACCTAGTCAAAC
412642 T
130 T
412643 GTTTTCCTCT
Statistics
Matches: 226, Mismatches: 36, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
141 2 0.01
142 74 0.33
143 80 0.35
144 52 0.23
145 16 0.07
146 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (144 bp):
GTTTGACTATATTGGCGTTAGGACCTGATCAAACTCTTTTTTCCTCCATTTAACTATATTGGCAT
TAGGACCTGGTCAAACTCTTTTCTCACCCTAGTTTGACTATATTAGCGTTAAACCTAGTCAAACT
CTCTTATCCGCCTT
Found at i:412521 original size:48 final size:47
Alignment explanation
Indices: 412217--412642 Score: 253
Period size: 47 Copynumber: 8.9 Consensus size: 47
412207 CAAATAAACT
* * *
412217 TTTTCATCTTCGTTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTT-
1 TTTTCCTCTT-GTTTGACTATATTAGCGTTA-GACCTGGTCAAACT-TTC
* ** *
412266 TTTTCTTC-CATTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTT-
1 TTTTCCTCTTGTTTGACTATATTAGCGTTA-GACCTGGTCAAACT-TTC
* * * * *
412313 TTCTCACCCTAGTTTGACTATATTTA-CGTTAAGACCTAGTCAAACTCTC
1 TTTTC-CTCTTGTTTGACTATA-TTAGCGTT-AGACCTGGTCAAACTTTC
* * *
412362 TTATCCTC-TGTTTGACTATATTAGCGTTAGGACCTGATCAAACTTTA
1 TTTTCCTCTTGTTTGACTATATTAGCGTTA-GACCTGGTCAAACTTTC
* * * * *
412409 TTTTCCTC-TGTTTAACTGTATTGGCATTAGACCTGGTCAAACTCTC
1 TTTTCCTCTTGTTTGACTATATTAGCGTTAGACCTGGTCAAACTTTC
* * * *
412455 TCTTTCACTCTTGTTTGACTGTATTAGTGTTAAACTTGGTCAAACTTTC
1 T-TTTC-CTCTTGTTTGACTATATTAGCGTTAGACCTGGTCAAACTTTC
* * * * * *
412504 TTTTCCGCCTTGTTTGACTATATTGGCATTAGGACATGATCAAAC-TCC
1 TTTTCC-TCTTGTTTGACTATATTAGCGTTA-GACCTGGTCAAACTTTC
* * * * * *
412552 TTTTAAC-ATTATTTAACTATGTTGGCGTTAGGACCTGGTCAAAC-TT-
1 TTTT-CCTCTTGTTTGACTATATTAGCGTTA-GACCTGGTCAAACTTTC
* * * * *
412598 TTCTCAC-CATTGTTTGATTGTATTAGCATTAGTCCTGGTCAAACT
1 TTTTC-CTC-TTGTTTGACTATATTAGCGTTAGACCTGGTCAAACT
412643 GTTTTCCTCT
Statistics
Matches: 298, Mismatches: 63, Indels: 34
0.75 0.16 0.09
Matches are distributed among these distances:
46 35 0.12
47 143 0.48
48 36 0.12
49 81 0.27
50 3 0.01
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (47 bp):
TTTTCCTCTTGTTTGACTATATTAGCGTTAGACCTGGTCAAACTTTC
Found at i:412887 original size:84 final size:84
Alignment explanation
Indices: 412723--413233 Score: 573
Period size: 84 Copynumber: 6.1 Consensus size: 84
412713 TTTTTCATCT
* * * * * *
412723 TTGTTTAACTATCCGCTCAGT-CCTCGGTAAACCCATTACCTTTATGGTGACCTGCCAGCTTAGT
1 TTGTTTACCTATCGGCTTAGTCCCT-GGTAAACCCATTACCCTTATGGTGACCTGTCAGCTCAGT
* *
412787 CT-TCGTTCAACTTTCATCCA
65 CTCT-GGTCAACCTTCATCCA
* * *
412807 TTATTTACCTGTCGGCTTAGTCCCTGGTAAACCCATTACCCTTATGGTGACCTATCAGCTCAGTC
1 TTGTTTACCTATCGGCTTAGTCCCTGGTAAACCCATTACCCTTATGGTGACCTGTCAGCTCAGTC
*
412872 TCTGGTCAACCTTCATCTA
66 TCTGGTCAACCTTCATCCA
* * * * *
412891 TTATTTACCTATCGGCTCAGTCCCCGGTAAACCTATTACCCTTATGGTGACCTGTCAGCTCAATC
1 TTGTTTACCTATCGGCTTAGTCCCTGGTAAACCCATTACCCTTATGGTGACCTGTCAGCTCAGTC
* *
412956 TCCGGTCAACCTTTATCCA
66 TCTGGTCAACCTTCATCCA
* * * * * *
412975 TTGTTTACCTATCAGTTTAATCCCTGGTAAACCC-TTTCTCTCCT-TGGTGACCTGTCAGCTTAG
1 TTGTTTACCTATCGGCTTAGTCCCTGGTAAACCCATTAC-C-CTTATGGTGACCTGTCAGCTCAG
* *
413038 TCTCCGGTCAACTTTCATCCA
64 TCTCTGGTCAACCTTCATCCA
* * * * *
413059 TTGTTTACTTGTTGG-TTAGTCCCTAGTAAACCCATTACCCTTATGGTGACCTGTCAGCTTAGTC
1 TTGTTTACCTATCGGCTTAGTCCCTGGTAAACCCATTACCCTTATGGTGACCTGTCAGCTCAGTC
*
413123 TCTGGTCAACTTTCATCCA
66 TCTGGTCAACCTTCATCCA
* * * * * * *
413142 TTGTTTACCTATCGACCTAGTCCCTAGTAAACCTATTACCCTTATAGTGACCTATTAGCTCAGTC
1 TTGTTTACCTATCGGCTTAGTCCCTGGTAAACCCATTACCCTTATGGTGACCTGTCAGCTCAGTC
* *
413207 TCTGGTTAACCTCCATCCA
66 TCTGGTCAACCTTCATCCA
413226 TTGTTTAC
1 TTGTTTAC
413234 TTGTCAGCTC
Statistics
Matches: 364, Mismatches: 56, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
82 2 0.01
83 70 0.19
84 286 0.79
85 6 0.02
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.36
Consensus pattern (84 bp):
TTGTTTACCTATCGGCTTAGTCCCTGGTAAACCCATTACCCTTATGGTGACCTGTCAGCTCAGTC
TCTGGTCAACCTTCATCCA
Found at i:412901 original size:41 final size:41
Alignment explanation
Indices: 412778--412989 Score: 135
Period size: 41 Copynumber: 5.1 Consensus size: 41
412768 GGTGACCTGC
* * * *
412778 CAGCTTAGTCTTCGTTCAA-CTTTCATCCATTATTTACCTGT
1 CAGCTCAGTCTCCGGTCAACCTTT-ATCCATTATTTACCTAT
* * * * * *
412819 CGGCTTAGTC-CCTGGTAAACCCATTA-CCCTTATGGTGACCTAT
1 CAGCTCAGTCTCC-GGTCAA-CCTTTATCCATTAT--TTACCTAT
* * *
412862 CAGCTCAGTCTCTGGTCAACCTTCATCTATTATTTACCTAT
1 CAGCTCAGTCTCCGGTCAACCTTTATCCATTATTTACCTAT
* * * * * *
412903 CGGCTCAGTCCCCGGTAAACCTATTA-CCCTTATGGTGACCTGT
1 CAGCTCAGTCTCCGGTCAACCT-TTATCCATTAT--TTACCTAT
* *
412946 CAGCTCAATCTCCGGTCAACCTTTATCCATTGTTTACCTAT
1 CAGCTCAGTCTCCGGTCAACCTTTATCCATTATTTACCTAT
412987 CAG
1 CAG
412990 TTTAATCCCT
Statistics
Matches: 126, Mismatches: 34, Indels: 22
0.69 0.19 0.12
Matches are distributed among these distances:
40 1 0.01
41 58 0.46
42 10 0.08
43 56 0.44
44 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (41 bp):
CAGCTCAGTCTCCGGTCAACCTTTATCCATTATTTACCTAT
Found at i:412961 original size:43 final size:43
Alignment explanation
Indices: 412832--412967 Score: 134
Period size: 43 Copynumber: 3.2 Consensus size: 43
412822 CTTAGTCCCT
* *
412832 GGTAAACCCATTACCCTTATGGTGACCTATCAGCTCAGTCTCT
1 GGTAAACCTATTACCCTTATGGTGACCTATCAGCTCAGTCTCC
* * ** * * *
412875 GGTCAACCT-TCATCTATTAT--TTACCTATCGGCTCAGTCCCC
1 GGTAAACCTATTA-CCCTTATGGTGACCTATCAGCTCAGTCTCC
* *
412916 GGTAAACCTATTACCCTTATGGTGACCTGTCAGCTCAATCTCC
1 GGTAAACCTATTACCCTTATGGTGACCTATCAGCTCAGTCTCC
*
412959 GGTCAACCT
1 GGTAAACCT
412968 TTATCCATTG
Statistics
Matches: 70, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
41 30 0.43
42 4 0.06
43 36 0.51
ACGTcount: A:0.22, C:0.32, G:0.15, T:0.31
Consensus pattern (43 bp):
GGTAAACCTATTACCCTTATGGTGACCTATCAGCTCAGTCTCC
Found at i:413174 original size:251 final size:255
Alignment explanation
Indices: 412767--413293 Score: 740
Period size: 251 Copynumber: 2.1 Consensus size: 255
412757 ATTACCTTTA
* * *
412767 TGGTGACCTGCCAGCTTAGTCTTCGTTCAACTTTCATCCATTATTTACCTGTCGGCTTAGTCCCT
1 TGGTGACCTGTCAGCTTAGTCTCCGGTCAACTTTCATCCATTATTTACCTGTCGGCTTAGTCCCT
* *
412832 GGTAAACCCATTACCCTTATGGTGACCTATCAGCTCAGTCTCTGGTCAACCTTCATCTATTATTT
66 AGTAAACCCATTACCCTTATGGTGACCTATCAGCTCAGTCTCTGGTCAACCTTCATCCATTATTT
* * * *
412897 ACCTATCGGCTCAGTCCCCGGTAAACCTATTACCCTTATGGTGACCTGTCAGCTCAATCTCCGGT
131 ACCTATCGCCTCAGTCCCCAGTAAACCTATTACCCTTATAGTGACCTATCAGCTCAATCTCCGGT
** * * **
412962 CAACCTTTATCCATTGTTTACCTATCAGTTTAATCCCTGGTAAACCCTTTC-T-C-TCCT
196 CAACCTCCATCCATTGTTTACCTATCAGCTCAATCCCCAGTAAACCCTTTCTTCCTTCCT
* * *
413019 TGGTGACCTGTCAGCTTAGTCTCCGGTCAACTTTCATCCATTGTTTACTTGTTGG-TTAGTCCCT
1 TGGTGACCTGTCAGCTTAGTCTCCGGTCAACTTTCATCCATTATTTACCTGTCGGCTTAGTCCCT
* * * *
413083 AGTAAACCCATTACCCTTATGGTGACCTGTCAGCTTAGTCTCTGGTCAACTTTCATCCATTGTTT
66 AGTAAACCCATTACCCTTATGGTGACCTATCAGCTCAGTCTCTGGTCAACCTTCATCCATTATTT
* * * *
413148 ACCTATCGACCT-AGTCCCTAGTAAACCTATTACCCTTATAGTGACCTATTAGCTCAGTCTCTGG
131 ACCTATCG-CCTCAGTCCCCAGTAAACCTATTACCCTTATAGTGACCTATCAGCTCAATCTCCGG
* * *
413212 TTAACCTCCATCCATTGTTTACTTGTCAGCTCAATCCCCAGTAAACCCTTTCTTCCTTCCT
195 TCAACCTCCATCCATTGTTTACCTATCAGCTCAATCCCCAGTAAACCCTTTCTTCCTTCCT
*
413273 TGGTGACCTGTCGGCTTAGTC
1 TGGTGACCTGTCAGCTTAGTC
413294 CCAGCTCCCT
Statistics
Matches: 241, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
251 164 0.68
252 52 0.22
253 1 0.00
254 24 0.10
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.36
Consensus pattern (255 bp):
TGGTGACCTGTCAGCTTAGTCTCCGGTCAACTTTCATCCATTATTTACCTGTCGGCTTAGTCCCT
AGTAAACCCATTACCCTTATGGTGACCTATCAGCTCAGTCTCTGGTCAACCTTCATCCATTATTT
ACCTATCGCCTCAGTCCCCAGTAAACCTATTACCCTTATAGTGACCTATCAGCTCAATCTCCGGT
CAACCTCCATCCATTGTTTACCTATCAGCTCAATCCCCAGTAAACCCTTTCTTCCTTCCT
Found at i:414555 original size:165 final size:163
Alignment explanation
Indices: 414308--415033 Score: 783
Period size: 165 Copynumber: 4.4 Consensus size: 163
414298 GAATTTTTTA
* * * * * * *
414308 TTTTTCCTTGAAGTTTTCATTTTTTTCAAAATA-CGAGTTTTTTA-TCCATAAATTTTTTAGAG-
1 TTTTTCCTTGAAATCTTC--TTTTTTCAAAATATGGAGTTTTCTACTTCGTAAATTTTTTCGAGA
* * * * * *
414370 GGATTTTT-TTGGAATTTTAATTTTCAAAATTTATCAAAAT-TTATTATTTAATTCACATAAAAT
64 GGATTTTTCTT-G-TTTTTAATTTTCAAAATTTAT-AAAATATTATTATTTATTTTATATTAATT
* ** *
414433 CAGTTCTCAAAAATTTGTTCATTTTCATAAAATTTTGAT
126 CAGTTTTCAAAAATTCATTCATTTCCAT-AAATTTTGAT
** * *
414472 TTTTTCCTTGAAAT-TTCTTTTTTTGAAATATGGAGTTTTCTACCTTTGTAATTTTTTTCGAGAG
1 TTTTTCCTTGAAATCTTCTTTTTTCAAAATATGGAGTTTTCTA-CTTCGTAAATTTTTTCGAGAG
* * *
414536 GATTTTTCTTCGTTTTTAATTTTCAAAATTCATAAAATATTATTATTTATTTTATATTAACTCAA
65 GATTTTTCTT-GTTTTTAATTTTCAAAATTTATAAAATATTATTATTTATTTTATATTAATTCAG
414601 TTTTCAAAAATTCATTCATTTCCATAAATTTTGAAT
129 TTTTCAAAAATTCATTCATTTCCATAAATTTTG-AT
* * * * *
414637 TTTTTTCTTGAAATC-TCATTTTTTCAAAATATGGAGTTTTCTACTTCATAAATTCTTTCGGGAA
1 TTTTTCCTTGAAATCTTC-TTTTTTCAAAATATGGAGTTTTCTACTTCGTAAATTTTTTCGAGAG
* * *
414701 GATTTTTCTTGTTTTTTGATATTT-AAAATTTATCAAATATTATTATCTATTTTATATTAATTCA
65 GATTTTTCTTG-TTTTTAAT-TTTCAAAATTTATAAAATATTATTATTTATTTTATATTAATTCA
* *
414765 GTTTTCAAAAATTCATTCATTTTCATAAATTTTAAAT
128 GTTTTCAAAAATTCATTCATTTCCATAAATTTT-GAT
* * *
414802 TTTTT-CTTGAAATCTTCTTTTTTCAAAATATGGAGTTTTCTACTCCGTAAATTGTTTCG-GGGA
1 TTTTTCCTTGAAATCTTCTTTTTTCAAAATATGGAGTTTTCTACTTCGTAAATTTTTTCGAGAG-
* * * *
414865 GAGTTTTCTTGGTTTTTGATTTTTAAAATTAATAAAATATTATTATTTATTTTATATTAATTCAG
65 GATTTTTCTT-GTTTTTAATTTTCAAAATTTATAAAATATTATTATTTATTTTATATTAATTCAG
* * *
414930 TTTTCGAATATTCATTCATTTCCATAAATTTTGAA
129 TTTTCAAAAATTCATTCATTTCCATAAATTTTGAT
* *** *
414965 TTTTTCCTTGAAATCTT-TTTTTTCGAAATACAAAGTTTT-TACTTCGTAAATTTTTTCGAGGGG
1 TTTTTCCTTGAAATCTTCTTTTTTCAAAATATGGAGTTTTCTACTTCGTAAATTTTTTCGAGAGG
*
415028 ACTTTT
66 ATTTTT
415034 AAAATTTATA
Statistics
Matches: 483, Mismatches: 61, Indels: 38
0.83 0.10 0.07
Matches are distributed among these distances:
161 11 0.02
162 32 0.07
163 34 0.07
164 183 0.38
165 194 0.40
166 29 0.06
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.51
Consensus pattern (163 bp):
TTTTTCCTTGAAATCTTCTTTTTTCAAAATATGGAGTTTTCTACTTCGTAAATTTTTTCGAGAGG
ATTTTTCTTGTTTTTAATTTTCAAAATTTATAAAATATTATTATTTATTTTATATTAATTCAGTT
TTCAAAAATTCATTCATTTCCATAAATTTTGAT
Found at i:414789 original size:18 final size:19
Alignment explanation
Indices: 414760--414795 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
414750 TTTTATATTA
414760 ATTCAGTTTTCAAAAATTC
1 ATTCAGTTTTCAAAAATTC
*
414779 ATTCA-TTTTCATAAATT
1 ATTCAGTTTTCAAAAATT
414796 TTAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTCAGTTTTCAAAAATTC
Found at i:414883 original size:164 final size:164
Alignment explanation
Indices: 414287--415022 Score: 794
Period size: 164 Copynumber: 4.5 Consensus size: 164
414277 TGATTTTTTT
* ** * * * * *
414287 TTCATTTTCATGAATTTTTTATTTTTCCTTGAAGTTTTCATTTTTTTCAAAATA-CGAGTTTTTT
1 TTCATTTTCATAAATTTTAAATTTTTTCTTGAAATCTTC--TTTTTTCAAAATATGGAGTTTTCT
* * * * *
414351 A-TCCATAAATTTTTTAGAGG-GATTTTT-TTGGAATTTTAATTTTCAAAATTTATCAAAAT-TT
64 ACTTCGTAAATTTTTTCGGGGAGATTTTTCTTGG-TTTTTAATTTTCAAAATTTAT-AAAATATT
* * * * * * **
414412 ATTATTTAATTCACATAAAATCAGTTCTCAAAAATTTG
127 ATTATTTATTTTATATTAATTCAGTTTTCAAAAATTCA
* **
414450 TTCATTTTCATAAAATTTT-GATTTTTTCCTTGAAAT-TTCTTTTTTTGAAATATGGAGTTTTCT
1 TTCATTTTCAT-AAATTTTAAATTTTTT-CTTGAAATCTTCTTTTTTCAAAATATGGAGTTTTCT
* * * * *
414513 ACCTTTGTAATTTTTTTC-GAGAGGATTTTTCTTCGTTTTTAATTTTCAAAATTCATAAAATATT
64 A-CTTCGTAAATTTTTTCGGGGA-GATTTTTCTTGGTTTTTAATTTTCAAAATTTATAAAATATT
* *
414577 ATTATTTATTTTATATTAACTCAATTTTCAAAAATTCA
127 ATTATTTATTTTATATTAATTCAGTTTTCAAAAATTCA
* *
414615 TTCATTTCCATAAATTTTGAATTTTTTTCTTGAAATC-TCATTTTTTCAAAATATGGAGTTTTCT
1 TTCATTTTCATAAATTTT-AAATTTTTTCTTGAAATCTTC-TTTTTTCAAAATATGGAGTTTTCT
* * * * * *
414679 ACTTCATAAATTCTTTCGGGAAGATTTTTCTTGTTTTTTGATATTT-AAAATTTATCAAATATTA
64 ACTTCGTAAATTTTTTCGGGGAGATTTTTCTTGGTTTTTAAT-TTTCAAAATTTATAAAATATTA
*
414743 TTATCTATTTTATATTAATTCAGTTTTCAAAAATTCA
128 TTATTTATTTTATATTAATTCAGTTTTCAAAAATTCA
414780 TTCATTTTCATAAATTTTAAATTTTTTCTTGAAATCTTCTTTTTTCAAAATATGGAGTTTTCTAC
1 TTCATTTTCATAAATTTTAAATTTTTTCTTGAAATCTTCTTTTTTCAAAATATGGAGTTTTCTAC
* * * * * *
414845 TCCGTAAATTGTTTCGGGGAGAGTTTTCTTGGTTTTTGATTTTTAAAATTAATAAAATATTATTA
66 TTCGTAAATTTTTTCGGGGAGATTTTTCTTGGTTTTTAATTTTCAAAATTTATAAAATATTATTA
* *
414910 TTTATTTTATATTAATTCAGTTTTCGAATATTCA
131 TTTATTTTATATTAATTCAGTTTTCAAAAATTCA
* * * * ***
414944 TTCATTTCCATAAATTTTGAATTTTTCCTTGAAATCTT-TTTTTTCGAAATACAAAGTTTT-TAC
1 TTCATTTTCATAAATTTTAAATTTTTTCTTGAAATCTTCTTTTTTCAAAATATGGAGTTTTCTAC
415007 TTCGTAAATTTTTTCG
66 TTCGTAAATTTTTTCG
415023 AGGGGACTTT
Statistics
Matches: 488, Mismatches: 68, Indels: 35
0.83 0.12 0.06
Matches are distributed among these distances:
161 11 0.02
162 26 0.05
163 42 0.09
164 197 0.40
165 175 0.36
166 37 0.08
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (164 bp):
TTCATTTTCATAAATTTTAAATTTTTTCTTGAAATCTTCTTTTTTCAAAATATGGAGTTTTCTAC
TTCGTAAATTTTTTCGGGGAGATTTTTCTTGGTTTTTAATTTTCAAAATTTATAAAATATTATTA
TTTATTTTATATTAATTCAGTTTTCAAAAATTCA
Found at i:414964 original size:329 final size:327
Alignment explanation
Indices: 414395--415022 Score: 852
Period size: 329 Copynumber: 1.9 Consensus size: 327
414385 TTTAATTTTC
* **
414395 AAAATTTATCAAAATTTATTATTTAATTCACATAAAATCAGTTCTCAAAAATTTGTTCATTTTCA
1 AAAATTTATCAAAATTTATTATCTAATTCACATAAAATCAGTTCTCAAAAATTCATTCATTTTCA
* ** ** *
414460 TAAAATTTTGATTTTTTCCTTGAAATTTCTTTTTTTGAAATATGGAGTTTTCTACCTTTGTAATT
66 TAAAATTTTAATTTTTTCCTTGAAATTTCTTTTTTCAAAATATGGAGTTTTCTACCTCCGTAAAT
* * *
414525 TTTTTCGAGAGGATTTTTCTTCGTTTTTAATTTTCAAAATTCATAAAATATTATTATTTATTTTA
131 TGTTTCGAGAGGAGTTTTCTTCGTTTTTAATTTTCAAAATTAATAAAATATTATTATTTATTTTA
*
414590 TATTAACTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTGAATTTTTTTCTTGAAATCTCA
196 TATTAACTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTGAA-TTTTTCCTTGAAATCT-A
***
414655 TTTTTTCAAAATATGGAGTTTTCTACTTCATAAATTCTTTCGGGAAGATTTTTCTTGTTTTTTGA
259 TTTTTTCAAAATACAAAGTTTT-TACTTCATAAATTCTTTCGGGAAGATTTTTCTTGTTTTTTGA
414720 TATTT
323 TATTT
* * * * * *
414725 AAAATTTATC-AAATATTATTATCTATTTTATATTAATTCAGTTTTCAAAAATTCATTCATTTTC
1 AAAATTTATCAAAAT-TTATTATCTAATTCACATAAAATCAGTTCTCAAAAATTCATTCATTTTC
414789 AT-AAATTTTAAATTTTTT-CTTGAAATCTTCTTTTTTCAAAATATGGAGTTTTCTA-CTCCGTA
65 ATAAAATTTT-AATTTTTTCCTTGAAAT-TTCTTTTTTCAAAATATGGAGTTTTCTACCTCCGTA
* * * *
414851 AATTGTTTCG-GGGAGAGTTTTCTTGGTTTTTGATTTTTAAAATTAATAAAATATTATTATTTAT
128 AATTGTTTCGAGAG-GAGTTTTCTTCGTTTTTAATTTTCAAAATTAATAAAATATTATTATTTAT
* * * *
414915 TTTATATTAATTCAGTTTTCGAATATTCATTCATTTCCATAAATTTTGAATTTTTCCTTGAAATC
192 TTTATATTAACTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTGAATTTTTCCTTGAAATC
* * * *
414980 TTTTTTTTCGAAATACAAAGTTTTTACTTCGTAAATTTTTTCG
257 TATTTTTTCAAAATACAAAGTTTTTACTTCATAAATTCTTTCG
415023 AGGGGACTTT
Statistics
Matches: 260, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
326 17 0.07
327 18 0.07
328 17 0.07
329 123 0.47
330 85 0.33
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (327 bp):
AAAATTTATCAAAATTTATTATCTAATTCACATAAAATCAGTTCTCAAAAATTCATTCATTTTCA
TAAAATTTTAATTTTTTCCTTGAAATTTCTTTTTTCAAAATATGGAGTTTTCTACCTCCGTAAAT
TGTTTCGAGAGGAGTTTTCTTCGTTTTTAATTTTCAAAATTAATAAAATATTATTATTTATTTTA
TATTAACTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTGAATTTTTCCTTGAAATCTATT
TTTTCAAAATACAAAGTTTTTACTTCATAAATTCTTTCGGGAAGATTTTTCTTGTTTTTTGATAT
TT
Found at i:415037 original size:145 final size:148
Alignment explanation
Indices: 414885--415174 Score: 387
Period size: 145 Copynumber: 2.0 Consensus size: 148
414875 GGTTTTTGAT
* *
414885 TTTTAAAATTAATAAAATATTATTATTTATTTTATATTAATT-CAGTTTTCGA-ATA-TTCATTC
1 TTTTAAAATTAATAAAATATTATTATTTATTTCATATTAATTCCA-TTTTC-ATAAAGTT-ATTC
414947 ATTTCCATAAATTTTGAATTTTTCCTTGAAA-TCTT-TTTTTTCGAAATACAAAGTTTT-TACTT
63 ATTTCCATAAATTTTGAATTTTTCCTTGAAATTCTTATTTTTTCGAAATACAAAGTTTTCTACTT
415009 CGTAAATTT-TTTCGAGGGGAC
128 CGT-AATTTCTTTCGAGGGGAC
*
415030 TTTTAAAATTTATAAAATATTATTATTTATTTCATATTAATTCCATTTTCATAAAGTTATTCATT
1 TTTTAAAATTAATAAAATATTATTATTTATTTCATATTAATTCCATTTTCATAAAGTTATTCATT
*** * * * * * *
415095 TCCATGTTTTTTGAATTTTTTCTTGAAATTTTTATTTTTTTGAAATACGAAGTTTTCTTCTTTGT
66 TCCATAAATTTTGAATTTTTCCTTGAAATTCTTATTTTTTCGAAATACAAAGTTTTCTACTTCGT
415160 AATTTCTTTCGAGGG
131 AATTTCTTTCGAGGG
415175 ATTTTTTTAT
Statistics
Matches: 126, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
144 1 0.01
145 78 0.62
146 7 0.06
147 25 0.20
148 15 0.12
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (148 bp):
TTTTAAAATTAATAAAATATTATTATTTATTTCATATTAATTCCATTTTCATAAAGTTATTCATT
TCCATAAATTTTGAATTTTTCCTTGAAATTCTTATTTTTTCGAAATACAAAGTTTTCTACTTCGT
AATTTCTTTCGAGGGGAC
Found at i:415999 original size:36 final size:34
Alignment explanation
Indices: 415954--416061 Score: 114
Period size: 36 Copynumber: 3.1 Consensus size: 34
415944 AAATAAAAAT
*
415954 AATTTAAAAAATCCAAAGAAAAATAAAAAATCAAAG
1 AATTCAAAAAAT-CAAA-AAAAATAAAAAATCAAAG
415990 AATTCAAAAAATTTCAAAAAAAATAAAAAAAT-AAA-
1 AATTCAAAAAA--TCAAAAAAAAT-AAAAAATCAAAG
*
416025 AAATCAAAGAAATCAAAACAAAA-AAAAAATCAAAG
1 AATTCAAA-AAATCAAAA-AAAATAAAAAATCAAAG
416060 AA
1 AA
416062 AGAAAAAAAG
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
33 7 0.11
34 9 0.14
35 13 0.21
36 22 0.35
37 11 0.17
38 1 0.02
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.15
Consensus pattern (34 bp):
AATTCAAAAAATCAAAAAAAATAAAAAATCAAAG
Found at i:416017 original size:19 final size:18
Alignment explanation
Indices: 415958--416019 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
415948 AAAAATAATT
*
415958 TAAAAAATCCAAAGAAAAA
1 TAAAAAATTCAAA-AAAAA
* *
415977 TAAAAAA-TC-AAAGAAT
1 TAAAAAATTCAAAAAAAA
415993 TCAAAAAATTTCAAAAAAAA
1 T-AAAAAA-TTCAAAAAAAA
416013 TAAAAAA
1 TAAAAAA
416020 ATAAAAAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.12
17 8 0.24
18 1 0.03
19 15 0.44
20 6 0.18
ACGTcount: A:0.73, C:0.08, G:0.03, T:0.16
Consensus pattern (18 bp):
TAAAAAATTCAAAAAAAA
Found at i:416051 original size:26 final size:24
Alignment explanation
Indices: 416010--416070 Score: 86
Period size: 26 Copynumber: 2.5 Consensus size: 24
416000 ATTTCAAAAA
*
416010 AAATAAAAAAATAAAAAATCAAAG
1 AAATAAAAAAAAAAAAAATCAAAG
416034 AAATCAAAACAAAAAAAAAATCAAAG
1 AAAT-AAAA-AAAAAAAAAATCAAAG
*
416060 AAAGAAAAAAA
1 AAATAAAAAAA
416071 GAGAAAACGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 7 0.21
25 8 0.24
26 18 0.55
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.08
Consensus pattern (24 bp):
AAATAAAAAAAAAAAAAATCAAAG
Found at i:416070 original size:44 final size:43
Alignment explanation
Indices: 415935--416070 Score: 125
Period size: 44 Copynumber: 3.1 Consensus size: 43
415925 TAATAAGTAG
* * **
415935 AAATCAAAAAAATAAAAATAATTTAAAAAATCCAAAGAAAAATAAA
1 AAATCAAAGAAATCAAAA-AATAAAAAAAAT-CAAAGAAAAA-AAA
* *
415981 AAATCAAAGAATTCAAAAAATTTCAAAAAAAAT-AAA-AAAATAAA
1 AAATCAAAGAAATCAAAAAA--T-AAAAAAAATCAAAGAAAAAAAA
*
416025 AAATCAAAGAAATCAAAACAA-AAAAAAAATCAAAGAAAGAAAA
1 AAATCAAAGAAATCAAAA-AATAAAAAAAATCAAAGAAAAAAAA
416068 AAA
1 AAA
416071 GAGAAAACGT
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
41 9 0.12
42 3 0.04
43 9 0.12
44 20 0.27
45 8 0.11
46 18 0.24
47 1 0.01
48 7 0.09
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.14
Consensus pattern (43 bp):
AAATCAAAGAAATCAAAAAATAAAAAAAATCAAAGAAAAAAAA
Found at i:416901 original size:30 final size:30
Alignment explanation
Indices: 416867--416924 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
416857 AAAGTCACAT
*
416867 TTTTACCCAAATGTATCGATAAATTTTTTC
1 TTTTACCCAAATGTATCAATAAATTTTTTC
* *
416897 TTTTACCCAGATGTATCAATACATTTTT
1 TTTTACCCAAATGTATCAATAAATTTTT
416925 CAATGTATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (30 bp):
TTTTACCCAAATGTATCAATAAATTTTTTC
Found at i:416932 original size:20 final size:20
Alignment explanation
Indices: 416907--416973 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
416897 TTTTACCCAG
416907 ATGTATCAATACATTTTTCA
1 ATGTATCAATACATTTTTCA
* * *
416927 ATGTATCAATACATGTATGA
1 ATGTATCAATACATTTTTCA
* *
416947 ATGTATCGATACATTCTTCA
1 ATGTATCAATACATTTTTCA
416967 ATGTATC
1 ATGTATC
416974 GATGCATTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (20 bp):
ATGTATCAATACATTTTTCA
Found at i:416974 original size:20 final size:20
Alignment explanation
Indices: 416907--416983 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
416897 TTTTACCCAG
*
416907 ATGTATCAATACATTTTTCA
1 ATGTATCAATACATTCTTCA
* *
416927 ATGTATCAATACATGT-ATGA
1 ATGTATCAATACAT-TCTTCA
*
416947 ATGTATCGATACATTCTTCA
1 ATGTATCAATACATTCTTCA
* *
416967 ATGTATCGATGCATTCT
1 ATGTATCAATACATTCT
416984 GTCTTTTTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCAATACATTCTTCA
Found at i:422118 original size:48 final size:48
Alignment explanation
Indices: 422047--422314 Score: 407
Period size: 48 Copynumber: 5.5 Consensus size: 48
422037 CAATATGCCA
* *
422047 ATTCAAGGCCAACGACATCGAGCTAAGGGAAAAGTGGACAATGTGCTG
1 ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
*
422095 ATTCAAGGCTAGCGACATTGAGCTAAGGGAAAA-TGGACAATGTGCTG
1 ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
422142 ATTCAAGGCCAGC-AGCATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
1 ATTCAAGGCCAGCGA-CATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
*
422190 ATTCAAGGCCAGCGACATTGAGCTAATAAAGGGAAAA-TGAACAATGTGCTG
1 ATTCAAGGCCAGCGACATTGAGC---T-AAGGGAAAAGTGGACAATGTGCTG
* *
422241 ATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAGTGGATAATGTGCTG
1 ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
*
422289 ATTCAAGGCTAGCGACATTGAGCTAA
1 ATTCAAGGCCAGCGACATTGAGCTAA
422315 TAAAGGTGCC
Statistics
Matches: 202, Mismatches: 10, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
46 1 0.00
47 53 0.26
48 102 0.50
49 1 0.00
51 36 0.18
52 9 0.04
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.20
Consensus pattern (48 bp):
ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
Found at i:422273 original size:99 final size:99
Alignment explanation
Indices: 422047--422320 Score: 457
Period size: 99 Copynumber: 2.8 Consensus size: 99
422037 CAATATGCCA
* * *
422047 ATTCAAGGCCAACGACATCGAGCTAAGGGAAAAGTGGACAATGTGCTGATTCAAGGCTAGCGACA
1 ATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAGTGGACAATGTGCTGATTCAAGGCTAGCGACA
*
422112 TTGAGC---T-AAGGGAAAATGGACAATGTGCTG
66 TTGAGCTAATAAAGGGAAAATGAACAATGTGCTG
* *
422142 ATTCAAGGCCAGCAGCATTGAGCTAAGGGAAAAGTGGACAATGTGCTGATTCAAGGCCAGCGACA
1 ATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAGTGGACAATGTGCTGATTCAAGGCTAGCGACA
422207 TTGAGCTAATAAAGGGAAAATGAACAATGTGCTG
66 TTGAGCTAATAAAGGGAAAATGAACAATGTGCTG
*
422241 ATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAGTGGATAATGTGCTGATTCAAGGCTAGCGACA
1 ATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAGTGGACAATGTGCTGATTCAAGGCTAGCGACA
422306 TTGAGCTAATAAAGG
66 TTGAGCTAATAAAGG
422321 TGCCAATATG
Statistics
Matches: 166, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
95 66 0.40
98 1 0.01
99 99 0.60
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (99 bp):
ATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAGTGGACAATGTGCTGATTCAAGGCTAGCGACA
TTGAGCTAATAAAGGGAAAATGAACAATGTGCTG
Found at i:422485 original size:28 final size:28
Alignment explanation
Indices: 422439--422764 Score: 251
Period size: 28 Copynumber: 11.1 Consensus size: 28
422429 CACTAAATTG
422439 TGTGGGCTTTG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
*
422467 TGTGGGCTTTGGAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
422495 CGTGGGCTTTGAAAAGTTACCACTGACG
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** * *
422523 CATGGGCTTTGAAAAGTTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
422551 TGTGGGCTTGGAAAGGATGCCA-TAGACT
1 TGTGGGCTTTGAAAGGATGCCACT-GACT
* * *
422579 TGTGGGCTTCGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * **
422607 TCTGGGCTTTGAAAAGATGCCACAAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
422635 TGTGGGCTTTGAAATGGGTTGCCACCGACTT
1 TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* *
422666 GTGTGGGCTTTGAAATAGGTTGCCACCGACTT
1 -TGTGGGCTTTG-AA-AGGATGCCACTGAC-T
* **
422698 GTGTGGGCTTTGAAATGGGTTGCCACCAACTT
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* *
422730 ATGTGGGCTTTGAAATGAGTTGCCACCGACT
1 -TGTGGGCTTTGAAA-G-GATGCCACTGACT
422761 TGTG
1 TGTG
422765 TGGGCTTTAA
Statistics
Matches: 254, Mismatches: 32, Indels: 22
0.82 0.10 0.07
Matches are distributed among these distances:
27 1 0.00
28 150 0.59
29 4 0.02
30 14 0.06
31 5 0.02
32 77 0.30
33 2 0.01
34 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:422518 original size:56 final size:57
Alignment explanation
Indices: 422440--422764 Score: 280
Period size: 56 Copynumber: 5.5 Consensus size: 57
422430 ACTAAATTGT
* * *
422440 GTGGGCTTTGAAGAGATGCCACTGACTTGTGGGCTTTGGAAGGATGCCACTGAC-TC
1 GTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGTTGCCACTGACTTC
* * *** *
422496 GTGGGCTTTGAAAAGTTACCACTGACGCATGGGCTTTGAAAAGTTGCCACTGACTT-
1 GTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGTTGCCACTGACTTC
* * * * *
422552 GTGGGCTTGGAAAGGATGCCA-TAGACTTGTGGGCTTCGAAAGGGTGCCATTGACTTC
1 GTGGGCTTTGAAAAGATGCCACT-GACTTGTGGGCTTTGAAAGGTTGCCACTGACTTC
** * *
422609 -TGGGCTTTGAAAAGATGCCACAAACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
1 GTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAA--GGTTGCCACTGACTT-C
* * ** *
422668 GTGGGCTTTGAAATAGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTAT
1 GTGGGCTTTGAAA-A-GATGCCACTGAC-T-TGTGGGCTTTGAAA--GGTTGCCACTGACTT-C
* *
422732 GTGGGCTTTGAAATGAGTTGCCACCGACTTGTG
1 GTGGGCTTTGAAA--AGATGCCACTGACTTGTG
422765 TGGGCTTTAA
Statistics
Matches: 221, Mismatches: 35, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
55 1 0.00
56 122 0.55
57 1 0.00
58 12 0.05
60 12 0.05
61 1 0.00
62 13 0.06
63 2 0.01
64 56 0.25
65 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.29
Consensus pattern (57 bp):
GTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGTTGCCACTGACTTC
Found at i:423215 original size:32 final size:32
Alignment explanation
Indices: 422635--423198 Score: 831
Period size: 32 Copynumber: 17.6 Consensus size: 32
422625 GCCACAAACT
*
422635 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
422667 TGTGGGCTTTGAAATAGGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
422699 TGTGGGCTTTGAAATGGGTTGCCACCAACTTA
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
422731 TGTGGGCTTTGAAATGAGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* **
422763 TGTGGGCTTTAAAATGACTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
422795 TGCGGGCTTTAAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
422827 TGTGGGCTTTGAAATAGGTTGTCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * * * * *
422859 TGTAGGCTTTAAAATGGGTTACTACCAATTTA
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * * *
422891 TGTGGGCTTTCAAATGAGTTACTACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
422923 TGTGGGCTTTGAAATGGGTTGCCACTAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
422955 TGTGGGGTTTCAAATGAGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
422987 TGTGGGCTTTAAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
423019 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
423051 TGTGGGCTTTGAAATGGGTTGCTACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
423083 TGTGGGCTTTGAAATAGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
423115 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
423147 TGTGGGCTTTCAAATGAGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
423179 TGTGGGCTTTAAAATGGGTT
1 TGTGGGCTTTGAAATGGGTT
423199 ACCATCGACT
Statistics
Matches: 481, Mismatches: 51, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 481 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (32 bp):
TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
Found at i:423304 original size:28 final size:27
Alignment explanation
Indices: 423259--423443 Score: 219
Period size: 28 Copynumber: 6.7 Consensus size: 27
423249 TAGAAGGGAA
* * *
423259 TGCCACTGACTTGCGGACTTAAAAAGGG
1 TGCCACGGAGTTGTGGACTT-AAAAGGG
*
423287 TGCCA-TGATGTTGTGGACTTAAAAGGG
1 TGCCACGGA-GTTGTGGACTTAAAAGGG
*
423314 TGCCACAGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
**
423342 TGCCATAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
423369 TGCCACGGAGTTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
423397 TGCCACGAAATTGTGGACTCTAAAAGGG
1 TGCCACGGAGTTGTGGACT-TAAAAGGG
*
423425 TGCCACAGAGTTGTGGACT
1 TGCCACGGAGTTGTGGACT
423444 GTTGTGGACT
Statistics
Matches: 139, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
27 50 0.36
28 89 0.64
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Done.