Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 14 of 218
Found at i:5123357 original size:87 final size:86
Alignment explanation
Indices: 5123239--5123403 Score: 197
Period size: 87 Copynumber: 1.9 Consensus size: 86
5123229 AATACACATT
* * *
5123239 ACTTACATAGCATACATAACTTACACAACTTAAATAA-TACATAACTTACATAACTTACATAACC
1 ACTTACATAACATACATAACTTACACAACTTAAATAACTACATAA--TACACAACTTAAATAACC
5123303 TACATAATACATAATAACTTACA
64 TACATAATACATAATAACTTACA
* ** * * * *
5123326 ACTTACATAACATACATTACTTTGATAACTTACATAACTTACATAATACACAACTTAAATAGCTT
1 ACTTACATAACATACATAACTTACACAACTTAAATAAC-TACATAATACACAACTTAAATAACCT
*
5123391 ACTTAATACATAA
65 ACATAATACATAA
5123404 CTTACATAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 58 0.89
89 7 0.11
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.31
Consensus pattern (86 bp):
ACTTACATAACATACATAACTTACACAACTTAAATAACTACATAATACACAACTTAAATAACCTA
CATAATACATAATAACTTACA
Found at i:5123375 original size:34 final size:33
Alignment explanation
Indices: 5123254--5123439 Score: 149
Period size: 34 Copynumber: 5.7 Consensus size: 33
5123244 CATAGCATAC
* *
5123254 ATAACTTACACAACTTAAATAATACATAACTTA
1 ATAACTTACATAACTTACATAATACATAACTTA
*
5123287 CATAACTTACATAACCTACATAATAC---A--TA
1 -ATAACTTACATAACTTACATAATACATAACTTA
* *
5123316 ATAACTTAC--AACTTACATAACATACATTACTTTG
1 ATAACTTACATAACTTACAT-A-ATACATAAC-TTA
*
5123350 ATAACTTACATAACTTACATAATACACAACTTAA
1 ATAACTTACATAACTTACATAATACATAACTT-A
* *
5123384 ATAGCTTACTTAA--TACATAACTTACATAACTT-
1 ATAACTTACATAACTTACATAA--TACATAACTTA
*
5123416 ATACACGTACATAACTTACATAAT
1 ATA-ACTTACATAACTTACATAAT
5123440 TGACTTAATA
Statistics
Matches: 122, Mismatches: 14, Indels: 33
0.72 0.08 0.20
Matches are distributed among these distances:
26 8 0.07
27 1 0.01
28 13 0.11
29 2 0.02
31 2 0.02
32 10 0.08
33 10 0.08
34 59 0.48
35 8 0.07
36 9 0.07
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (33 bp):
ATAACTTACATAACTTACATAATACATAACTTA
Found at i:5123391 original size:25 final size:25
Alignment explanation
Indices: 5123276--5123451 Score: 106
Period size: 25 Copynumber: 6.8 Consensus size: 25
5123266 ACTTAAATAA
* *
5123276 TACATAACTTACATAACTTACATAACC
1 TACATAACTTACATAA--TACACAACT
5123303 TACATAA--TACATAATAACTTACAACT
1 TACATAACTTACATAAT-AC--ACAACT
* * ** *
5123329 TACATAACATACATTACTTTGATAACT
1 TACATAACTTACA-TA-ATACACAACT
5123356 TACATAACTTACATAATACACAACT
1 TACATAACTTACATAATACACAACT
* * * *
5123381 TAAATAGCTTACTTAATACATAACT
1 TACATAACTTACATAATACACAACT
* * * *
5123406 TACATAACTTATACACGTACATAACT
1 TACATAACTTACATA-ATACACAACT
*
5123432 TACATAA-TTGACTTAATACA
1 TACATAACTT-ACATAATACA
5123452 TAAATATATA
Statistics
Matches: 115, Mismatches: 25, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
23 1 0.01
24 2 0.02
25 50 0.43
26 31 0.27
27 24 0.21
28 4 0.03
29 2 0.02
30 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.32
Consensus pattern (25 bp):
TACATAACTTACATAATACACAACT
Found at i:5129472 original size:42 final size:42
Alignment explanation
Indices: 5129420--5129617 Score: 305
Period size: 42 Copynumber: 4.8 Consensus size: 42
5129410 TAAGAATAAA
* *
5129420 CGCCGTTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* *
5129462 CGTCGCTAAAGAACATGGTCTTTAGCGGCATTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
5129504 CGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTTTCTAAG
*
5129547 CGCCGCTAAAG-A-AT--TCTTTAGCGGCGTTTTTTTCAAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
5129585 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT
5129618 GTTTGTAAAC
Statistics
Matches: 142, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
38 22 0.15
39 12 0.08
40 2 0.01
41 2 0.01
42 81 0.57
43 23 0.16
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:5129592 original size:81 final size:84
Alignment explanation
Indices: 5129420--5129617 Score: 305
Period size: 81 Copynumber: 2.4 Consensus size: 84
5129410 TAAGAATAAA
* * *
5129420 CGCCGTTAAAGAACATGATCTTTAGCGGCG-TTTTTTTCTAAGCGTCGCTAAAGAACATGGTCTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACAT-GTCTT
*
5129484 TAGCGGCATTTTTTTCTAAG
65 TAGCGGCATTTTTTTCAAAG
*
5129504 CGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTTCTAAGCGCCGCTAAAG-A-AT-TCTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATGTCTTT
*
5129566 AGCGGCGTTTTTTTCAAAG
66 AGCGGCATTTTTTTCAAAG
5129585 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT
5129618 GTTTGTAAAC
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
81 54 0.51
83 2 0.02
84 28 0.26
85 22 0.21
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (84 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATGTCTTT
AGCGGCATTTTTTTCAAAG
Found at i:5129739 original size:21 final size:21
Alignment explanation
Indices: 5129696--5129739 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5129686 TTAGTGGCGT
* *
5129696 TAAAAAGCGCCGCTAAAGGCC
1 TAAAAAACGCCGCTAAAGACC
*
5129717 TAAAAAACGCCGCTAGAGACC
1 TAAAAAACGCCGCTAAAGACC
5129738 TA
1 TA
5129740 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.27, G:0.20, T:0.11
Consensus pattern (21 bp):
TAAAAAACGCCGCTAAAGACC
Found at i:5132053 original size:19 final size:21
Alignment explanation
Indices: 5132019--5132059 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
5132009 CTCCAAATCC
5132019 TAATTTAAAGATTATTATGAA
1 TAATTTAAAGATTATTATGAA
5132040 TAATTT-AA-ATTATTATGAA
1 TAATTTAAAGATTATTATGAA
5132059 T
1 T
5132060 TTGACAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (21 bp):
TAATTTAAAGATTATTATGAA
Found at i:5134001 original size:77 final size:77
Alignment explanation
Indices: 5133874--5134027 Score: 299
Period size: 77 Copynumber: 2.0 Consensus size: 77
5133864 AATTATAAAG
*
5133874 CGCTGGATCAAAATTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
1 CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
5133939 CTCATGTAACAT
66 CTCATGTAACAT
5133951 CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
1 CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
5134016 CTCATGTAACAT
66 CTCATGTAACAT
5134028 GAGGGGGCGG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (77 bp):
CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
CTCATGTAACAT
Found at i:5139007 original size:2 final size:2
Alignment explanation
Indices: 5139002--5139038 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5138992 GCAGAGAGTT
5139002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5139039 CAGATATCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5142228 original size:78 final size:78
Alignment explanation
Indices: 5142099--5142249 Score: 266
Period size: 78 Copynumber: 1.9 Consensus size: 78
5142089 GTCGTGACTT
* *
5142099 GTAGGATATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAAGTTGTGCACAAGAGACAAC
1 GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAACTTGTGCACAAGAGACAAC
5142164 AACTATGCAACTC
66 AACTATGCAACTC
* *
5142177 GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAATTCATTGAACTTGTGCACAAGAGACAAC
1 GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAACTTGTGCACAAGAGACAAC
5142242 AACTATGC
66 AACTATGC
5142250 CAGGAGTACT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (78 bp):
GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAACTTGTGCACAAGAGACAAC
AACTATGCAACTC
Found at i:5147850 original size:18 final size:18
Alignment explanation
Indices: 5147759--5147879 Score: 61
Period size: 18 Copynumber: 6.6 Consensus size: 18
5147749 TATACCCTTT
5147759 TACATATATATTTTT-TA
1 TACATATATATTTTTATA
** **
5147776 TATTTCATA-ATTCATATA
1 TACAT-ATATATTTTTATA
*
5147794 CACATATAT-TTTTTATA
1 TACATATATATTTTTATA
* * *
5147811 TATATTTTACAATTTATATATA
1 TACA-TATA-TATTT-T-TATA
5147833 TACATATATATTTTTATA
1 TACATATATATTTTTATA
* **
5147851 TAC-TTTATAATTTCCATA
1 TACATATAT-ATTTTTATA
5147869 TACATATATAT
1 TACATATATAT
5147880 ATACATATTT
Statistics
Matches: 74, Mismatches: 20, Indels: 19
0.65 0.18 0.17
Matches are distributed among these distances:
17 22 0.30
18 29 0.39
19 5 0.07
20 7 0.09
21 4 0.05
22 7 0.09
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (18 bp):
TACATATATATTTTTATA
Found at i:5149536 original size:19 final size:18
Alignment explanation
Indices: 5149487--5149536 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
5149477 TATAAAAATA
5149487 TTATATTA-ATTATATAT
1 TTATATTATATTATATAT
* *
5149504 TTAAATAATAATTATATAT
1 TTATATTAT-ATTATATAT
5149523 TTATATTTATATTA
1 TTATA-TTATATTA
5149537 AATCACGAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.23
19 17 0.65
20 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATATTATATTATATAT
Found at i:5150599 original size:50 final size:50
Alignment explanation
Indices: 5150536--5150643 Score: 171
Period size: 50 Copynumber: 2.2 Consensus size: 50
5150526 CCGAAATGAT
* * * *
5150536 ATTTTTTTTATGGCGCCTATCTGAGAGGCGCCAATGATTATTTTGTATTA
1 ATTTTTTTAATGGCGCCTATCTGAGAGGCGCCAATGAATATTATATATTA
*
5150586 ATTTTTTTAATGGCGCCTATCTGATAGGCGCCAATGAATATTATATATTA
1 ATTTTTTTAATGGCGCCTATCTGAGAGGCGCCAATGAATATTATATATTA
5150636 ATTTTTTT
1 ATTTTTTT
5150644 TCTTTTAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (50 bp):
ATTTTTTTAATGGCGCCTATCTGAGAGGCGCCAATGAATATTATATATTA
Found at i:5151071 original size:21 final size:20
Alignment explanation
Indices: 5151047--5151085 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5151037 ATTTTTTTGC
5151047 ATTTCGAAAACTGTTTTAAGA
1 ATTTCGAAAA-TGTTTTAAGA
* *
5151068 ATTTTGAAAATTTTTTAA
1 ATTTCGAAAATGTTTTAA
5151086 CATATCTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (20 bp):
ATTTCGAAAATGTTTTAAGA
Found at i:5157926 original size:15 final size:15
Alignment explanation
Indices: 5157908--5157947 Score: 71
Period size: 16 Copynumber: 2.6 Consensus size: 15
5157898 TAAAAATCAA
5157908 ATAAAATTACATTAT
1 ATAAAATTACATTAT
5157923 ATAAAAATTACATTAT
1 AT-AAAATTACATTAT
5157939 ATAAAATTA
1 ATAAAATTA
5157948 AATGAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATTACATTAT
Found at i:5158262 original size:56 final size:55
Alignment explanation
Indices: 5158192--5158305 Score: 158
Period size: 55 Copynumber: 2.1 Consensus size: 55
5158182 TTATTTAAAC
* *
5158192 AAAAAAAATATTTTTAATATAAAAAATTAATTCGCGCCTGTTAGGTAGGCGCGATT
1 AAAAAAAATATTTTTAATAT-AAAAATTAATTCGCGCCTGTCAGATAGGCGCGATT
* * *
5158248 AAAAAATAAT-TTTTTAATATAAAACTTTATTCGCGTCTGTCAGATAGGCGCGATT
1 AAAAAA-AATATTTTTAATATAAAAATTAATTCGCGCCTGTCAGATAGGCGCGATT
5158303 AAA
1 AAA
5158306 TTTTTTTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
55 33 0.63
56 16 0.31
57 3 0.06
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (55 bp):
AAAAAAAATATTTTTAATATAAAAATTAATTCGCGCCTGTCAGATAGGCGCGATT
Found at i:5158706 original size:60 final size:60
Alignment explanation
Indices: 5158613--5158731 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
5158603 ATACTAAACT
* * * *
5158613 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAAATAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAAATAATTATAAAATAATTAC
*
5158673 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAAATAATTATAAAATAATTA
5158732 TTAAAAGCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAAATAATTATAAAATAATTAC
Found at i:5158929 original size:17 final size:16
Alignment explanation
Indices: 5158899--5158932 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5158889 ACATTACCTT
5158899 TTTTTATTCTTTCTTC
1 TTTTTATTCTTTCTTC
*
5158915 TTTTTCTTCTCTTCTTC
1 TTTTTATTCT-TTCTTC
5158932 T
1 T
5158933 CCTTTCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTATTCTTTCTTC
Found at i:5162313 original size:44 final size:44
Alignment explanation
Indices: 5162172--5162329 Score: 148
Period size: 44 Copynumber: 3.7 Consensus size: 44
5162162 TCTCGTACAT
* * *
5162172 TGCCAACGTCCCAAACGTGGTCTTACATGT--ATTCAAATAACGA
1 TGCCAATGTCCCAAACATGGTCTTACACGTAAATTCAAAT-ACGA
* * * * *
5162215 TGCCACTGTCCCAGATAGGGTCTTACACG-AAATT-ATATACGA
1 TGCCAATGTCCCAAACATGGTCTTACACGTAAATTCAAATACGA
* *
5162257 TGTCGATGTCCCAAACATGGTCTTACACGTAAATCTCAAAT-CGA
1 TGCCAATGTCCCAAACATGGTCTTACACGTAAAT-TCAAATACGA
*
5162301 TGCCAAAGTCCCAAA-AGTGGTCTTACACG
1 TGCCAATGTCCCAAACA-TGGTCTTACACG
5162330 ATATCACATA
Statistics
Matches: 91, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
42 27 0.30
43 30 0.33
44 31 0.34
45 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (44 bp):
TGCCAATGTCCCAAACATGGTCTTACACGTAAATTCAAATACGA
Found at i:5163575 original size:22 final size:22
Alignment explanation
Indices: 5163542--5163602 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
5163532 GCCCGGCCCG
* *
5163542 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
5163565 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
5163587 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
5163603 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:5163615 original size:16 final size:16
Alignment explanation
Indices: 5163578--5163617 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5163568 TTAATAAAAT
* *
5163578 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
5163594 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
5163610 TAAAATTA
1 TAAAATTA
5163618 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:5163696 original size:59 final size:59
Alignment explanation
Indices: 5163628--5163767 Score: 262
Period size: 59 Copynumber: 2.4 Consensus size: 59
5163618 TCAAATTATT
*
5163628 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
5163687 AATTATTAATTGTATTAATTATTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
5163746 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
5163768 ATTAATTGTT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 78 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:5163761 original size:9 final size:9
Alignment explanation
Indices: 5163749--5163776 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5163739 TTTATCAAAT
5163749 TATTAATTG
1 TATTAATTG
5163758 TATTAATTG
1 TATTAATTG
5163767 TATTAATTG
1 TATTAATTG
5163776 T
1 T
5163777 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:5163902 original size:24 final size:23
Alignment explanation
Indices: 5163873--5163917 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
5163863 AAATAAACTT
*
5163873 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAAATA-TATATTTTA
5163897 AAAATAAAAAAATATATATTT
1 AAAATAAAAAAATATATATTT
5163918 AATATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATAAAAAAATATATATTTTA
Found at i:5164917 original size:43 final size:43
Alignment explanation
Indices: 5164856--5165056 Score: 278
Period size: 43 Copynumber: 4.7 Consensus size: 43
5164846 ATGTTCCAAT
5164856 ATCGATTTGAGATTTCGTGTAAGACCATAGCTAGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTAGGCTATTGGC
* * *
5164899 ATCGATTTGAGATTTCGTGTAAGACCATAGTTGGGCTATTAG-
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTAGGCTATTGGC
* * *
5164941 AGTCAATCTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
1 A-TCGATTTGAGATTTCGTGTAAGACCATAGCTAGGCTATTGGC
**
5164985 ATCGATTTGAGATTTCGTGTAAGACCATAGCTAAACTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTAGGCTATTGGC
** *
5165028 ATCGATACGAGATTTCCATGTAAGACCAT
1 ATCGATTTGAGATTT-CGTGTAAGACCAT
5165057 GTTTGGGACA
Statistics
Matches: 140, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 126 0.90
44 13 0.09
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
ATCGATTTGAGATTTCGTGTAAGACCATAGCTAGGCTATTGGC
Found at i:5167522 original size:2 final size:2
Alignment explanation
Indices: 5167517--5167543 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5167507 ACACACACAC
5167517 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5167544 ATTTTAGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5177710 original size:15 final size:17
Alignment explanation
Indices: 5177685--5177716 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5177675 AAATTATTAA
5177685 AAAACTTAT-AAATTTT
1 AAAACTTATAAAATTTT
5177701 AAAA-TTATAAAATTTT
1 AAAACTTATAAAATTTT
5177717 TATTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAACTTATAAAATTTT
Found at i:5177858 original size:44 final size:46
Alignment explanation
Indices: 5177812--5177900 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 46
5177802 ATATTGTTAT
* *
5177812 TTTTAATAAAA-TT-TTTGTAATTT-TGTAATTTTTAA-AACTTTTA
1 TTTT-ATAAAATTTGTTTATAATTTCTATAATTTTTAATAACTTTTA
*
5177855 TTTTATAAAATTTGTTTATAATTTCTATGATTTTTAATAACTTTTA
1 TTTTATAAAATTTGTTTATAATTTCTATAATTTTTAATAACTTTTA
5177901 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
42 6 0.15
43 6 0.15
44 9 0.23
45 10 0.26
46 8 0.21
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.58
Consensus pattern (46 bp):
TTTTATAAAATTTGTTTATAATTTCTATAATTTTTAATAACTTTTA
Found at i:5191238 original size:14 final size:14
Alignment explanation
Indices: 5191218--5191252 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5191208 GATCACAATT
*
5191218 TAAAAAAA-ATAAA
1 TAAAAAAATAAAAA
5191231 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
5191245 TAAAAAAA
1 TAAAAAAA
5191253 GGTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:5191469 original size:21 final size:22
Alignment explanation
Indices: 5191417--5191469 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
5191407 TATAAAATTT
*
5191417 AAATTTATTATTATATTTTTTG
1 AAATTTTTTATTATATTTTTTG
* *
5191439 AAAATATTTATGTA-ATTTTTTG
1 AAATTTTTTAT-TATATTTTTTG
5191461 -AATTTTTTA
1 AAATTTTTTA
5191470 GAATAAGGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 7 0.28
22 16 0.64
23 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (22 bp):
AAATTTTTTATTATATTTTTTG
Found at i:5193786 original size:21 final size:21
Alignment explanation
Indices: 5193761--5193801 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5193751 ACAGAAAAAT
5193761 GTCATATCGTCAAAGAGGGAG
1 GTCATATCGTCAAAGAGGGAG
*
5193782 GTCATATTGTCAAAGAGGGA
1 GTCATATCGTCAAAGAGGGA
5193802 ATAATCGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (21 bp):
GTCATATCGTCAAAGAGGGAG
Found at i:5194470 original size:30 final size:27
Alignment explanation
Indices: 5194427--5194487 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 27
5194417 AAAAGTATTT
*
5194427 TTTTTTTAAATTTACCGAAATGGGCCA
1 TTTTTTTAAATTTACCGAAATGAGCCA
*
5194454 CTTTTTTTAATTATTTACCGGAATGAGCCA
1 -TTTTTTTAA--ATTTACCGAAATGAGCCA
5194484 TTTT
1 TTTT
5194488 CCGTGAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.31
29 4 0.14
30 16 0.55
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (27 bp):
TTTTTTTAAATTTACCGAAATGAGCCA
Found at i:5195077 original size:14 final size:15
Alignment explanation
Indices: 5195060--5195093 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5195050 AATAATTATC
5195060 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
5195074 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
5195089 TAAAA
1 TAAAA
5195094 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:5195247 original size:29 final size:29
Alignment explanation
Indices: 5195184--5195240 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
5195174 TTGAAAATAT
*
5195184 TAAAATTA-TTAAAATTATTTTTAAAAAA
1 TAAAAATATTTAAAATTATTTTTAAAAAA
5195212 TAAAAATATTTAAAATT-TTCTTTAAAAAA
1 TAAAAATATTTAAAATTATT-TTTAAAAAA
5195241 ATGAAATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TAAAAATATTTAAAATTATTTTTAAAAAA
Found at i:5195301 original size:22 final size:21
Alignment explanation
Indices: 5195276--5195326 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
5195266 TAATATGGAT
*
5195276 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
*
5195298 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
5195320 TTGAGAG
1 TTGAGAG
5195327 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:5195349 original size:52 final size:52
Alignment explanation
Indices: 5195279--5195378 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
5195269 TATGGATTTG
* * * *
5195279 AGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTTA
5195331 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
5195379 AATATTTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTTA
Found at i:5195395 original size:24 final size:22
Alignment explanation
Indices: 5195331--5195386 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
5195321 TGAGAGTTTA
5195331 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
5195353 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
5195375 AGAGAATATTTG
1 AGAGAAT-TTTG
5195387 TTTGTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.29
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:5196952 original size:337 final size:337
Alignment explanation
Indices: 5196337--5197014 Score: 1356
Period size: 337 Copynumber: 2.0 Consensus size: 337
5196327 AGGAGAAACA
5196337 CAATTTTTTTGGAAATTTTTAAATGTGAAATAATTTTTTTTTAATTTTCAAAATAAGAATGGCTT
1 CAATTTTTTTGGAAATTTTTAAATGTGAAATAATTTTTTTTTAATTTTCAAAATAAGAATGGCTT
5196402 ATATTAACATTAAGTTTTATTTTCTTTAAATTTGAGTTTGATGTAAGTCGATTGTCTTTTGTCTT
66 ATATTAACATTAAGTTTTATTTTCTTTAAATTTGAGTTTGATGTAAGTCGATTGTCTTTTGTCTT
5196467 TGAGAGATTCTTGGGTCACAAGAAAATACATACCCAAGAATCGTTAAGAAAATTACTGCGGACAG
131 TGAGAGATTCTTGGGTCACAAGAAAATACATACCCAAGAATCGTTAAGAAAATTACTGCGGACAG
5196532 AAAATGCAGTTGATTATATTACCAAGTAATGTAGTTGATTTATATTGATTGGAATCTTGAAATTA
196 AAAATGCAGTTGATTATATTACCAAGTAATGTAGTTGATTTATATTGATTGGAATCTTGAAATTA
5196597 ACTTGGCAGACCTTTGTAAATAATTTAGTTAATTAAAATTTGAACATATTATCTATAATTTAAGC
261 ACTTGGCAGACCTTTGTAAATAATTTAGTTAATTAAAATTTGAACATATTATCTATAATTTAAGC
5196662 TCGATAAGAATG
326 TCGATAAGAATG
5196674 CAATTTTTTTGGAAATTTTTAAATGTGAAATAATTTTTTTTTAATTTTCAAAATAAGAATGGCTT
1 CAATTTTTTTGGAAATTTTTAAATGTGAAATAATTTTTTTTTAATTTTCAAAATAAGAATGGCTT
5196739 ATATTAACATTAAGTTTTATTTTCTTTAAATTTGAGTTTGATGTAAGTCGATTGTCTTTTGTCTT
66 ATATTAACATTAAGTTTTATTTTCTTTAAATTTGAGTTTGATGTAAGTCGATTGTCTTTTGTCTT
5196804 TGAGAGATTCTTGGGTCACAAGAAAATACATACCCAAGAATCGTTAAGAAAATTACTGCGGACAG
131 TGAGAGATTCTTGGGTCACAAGAAAATACATACCCAAGAATCGTTAAGAAAATTACTGCGGACAG
5196869 AAAATGCAGTTGATTATATTACCAAGTAATGTAGTTGATTTATATTGATTGGAATCTTGAAATTA
196 AAAATGCAGTTGATTATATTACCAAGTAATGTAGTTGATTTATATTGATTGGAATCTTGAAATTA
5196934 ACTTGGCAGACCTTTGTAAATAATTTAGTTAATTAAAATTTGAACATATTATCTATAATTTAAGC
261 ACTTGGCAGACCTTTGTAAATAATTTAGTTAATTAAAATTTGAACATATTATCTATAATTTAAGC
5196999 TCGATAAGAATG
326 TCGATAAGAATG
5197011 CAAT
1 CAAT
5197015 GTACTAAATT
Statistics
Matches: 341, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
337 341 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.40
Consensus pattern (337 bp):
CAATTTTTTTGGAAATTTTTAAATGTGAAATAATTTTTTTTTAATTTTCAAAATAAGAATGGCTT
ATATTAACATTAAGTTTTATTTTCTTTAAATTTGAGTTTGATGTAAGTCGATTGTCTTTTGTCTT
TGAGAGATTCTTGGGTCACAAGAAAATACATACCCAAGAATCGTTAAGAAAATTACTGCGGACAG
AAAATGCAGTTGATTATATTACCAAGTAATGTAGTTGATTTATATTGATTGGAATCTTGAAATTA
ACTTGGCAGACCTTTGTAAATAATTTAGTTAATTAAAATTTGAACATATTATCTATAATTTAAGC
TCGATAAGAATG
Found at i:5202987 original size:7 final size:7
Alignment explanation
Indices: 5202975--5202999 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5202965 AAATAAATTA
5202975 ACTTTTC
1 ACTTTTC
5202982 ACTTTTC
1 ACTTTTC
5202989 ACTTTTC
1 ACTTTTC
5202996 ACTT
1 ACTT
5203000 GATGAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (7 bp):
ACTTTTC
Found at i:5204565 original size:23 final size:23
Alignment explanation
Indices: 5204519--5204562 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5204509 CCAACTAAAC
*
5204519 TAAACCATAATATATATTTATTA
1 TAAACCATAATAAATATTTATTA
*
5204542 TAAATCATAATAAAT-TTTATT
1 TAAACCATAATAAATATTTATT
5204563 TATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAACCATAATAAATATTTATTA
Found at i:5209250 original size:12 final size:14
Alignment explanation
Indices: 5209223--5209254 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
5209213 GTTTTGGAAG
5209223 AATAAAAGTCAAAA
1 AATAAAAGTCAAAA
5209237 AATAAAA-T-AAAA
1 AATAAAAGTCAAAA
5209249 AATAAA
1 AATAAA
5209255 GTAATGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (14 bp):
AATAAAAGTCAAAA
Found at i:5211950 original size:36 final size:36
Alignment explanation
Indices: 5211885--5212483 Score: 557
Period size: 37 Copynumber: 16.4 Consensus size: 36
5211875 AAAAATGGAA
*
5211885 TACTGATTCTATTG-AAGTGCTCAACAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * *
5211920 TACTGATACTATTGAAAGTGCTCAATAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * * **
5211956 TACTGATCCTACTGAATGAGCTCAA-ATGAGCAATGCC
1 TACTGATTCTACTGAAAGTGCTCAACA--AGCAATATC
* * *
5211993 TATTGGTTCTACTGAAAGTGCTCAAACAAGCAATACC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* * *
5212030 TATTGATACTACTGAAAGTGCTCAAATAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* * * * *
5212067 TATTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* **
5212104 TACTTATTCTACTGAAAGTGCTCAA-AAG-AGCATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * * *
5212138 TACTGATCCTACTAAAAGTGCTCAACGAGCAATGTC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* *
5212174 TACTGATTCTACTGAAAGTGCTAAAACGAGCAATATC
1 TACTGATTCTACTGAAAGTGCT-CAACAAGCAATATC
* * * *
5212211 TACT-AGTTCTATTGGAAGTGCTTAACGAGCAATATC
1 TACTGA-TTCTACTGAAAGTGCTCAACAAGCAATATC
* * *
5212247 TATTGGTCCTACTGAAAGTGCTCAACAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * * *
5212283 TACTAATCCTACT-AAATGTGCTCAAACGAGCAATGTC
1 TACTGATTCTACTGAAA-GTGCTC-AACAAGCAATATC
* *
5212320 TACTAATTCTACTG-AAGTGCTCAAACGAGCAATATC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* *
5212356 TACTAATTCTACTGAAAGTGCTCAACGAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * * *
5212392 TACT-AGTCCTACTGAATGTGCTCAAACAAGTAATGTC
1 TACTGA-TTCTACTGAAAGTGCTC-AACAAGCAATATC
*
5212429 TACTGATTCTACTAAATAGTTGCTCAAACAAGCAATATC
1 TACTGATTCTACTGAA-AG-TGCTC-AACAAGCAATATC
*
5212468 TACTGATTTTACTGAA
1 TACTGATTCTACTGAA
5212484 TAGTTACTCA
Statistics
Matches: 474, Mismatches: 71, Indels: 34
0.82 0.12 0.06
Matches are distributed among these distances:
34 25 0.05
35 22 0.05
36 189 0.40
37 202 0.43
38 4 0.01
39 32 0.07
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (36 bp):
TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
Found at i:5212304 original size:109 final size:110
Alignment explanation
Indices: 5211898--5212540 Score: 683
Period size: 109 Copynumber: 5.8 Consensus size: 110
5211888 TGATTCTATT
* * *
5211898 GAAGTGCTC-AACAAGCAATATCTACTGATACTATTGAAAGTGCTCAATAAGCAATATCTACTGA
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* * * * *
5211962 TCCTACTGAATGAGCTCAAATGAGCAATGCCTATTGGTTCTACTG
66 TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
* * * * * *
5212007 AAAGTGCTCAAACAAGCAATACCTATTGATACTACTGAAAGTGCTCAAATAAGCAATATCTATTG
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTC-AACAAGCAATATCTACTG
5212072 ATCCTACTGAATGTGCTCAAACGAGCAATGTCTACTTA-TTCTACTG
65 ATCCTACTGAATGTGCTCAAACGAGCAATGTCTAC-TAGTTCTACTG
* * * * * *
5212118 AAAGTGCTCAAAAGAGC---ATCTACTGATCCTACTAAAAGTGCTCAACGAGCAATGTCTACTGA
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* * * * *
5212180 TTCTACTGAAAGTGCTAAAACGAGCAATATCTACTAGTTCTATTG
66 TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
* * * * *
5212225 GAAGTGCT-TAACGAGCAATATCTATTGGTCCTACTGAAAGTGCTCAACAAGCAATATCTACTAA
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* *
5212289 TCCTACTAAATGTGCTCAAACGAGCAATGTCTACTAATTCTACT-
66 TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
* * *
5212333 GAAGTGCTCAAACGAGCAATATCTACTAATTCTACTGAAAGTGCTCAACGAGCAATATCTACT-A
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* * *
5212397 GTCCTACTGAATGTGCTCAAACAAGTAATGTCTACT-GATTCTACTA
66 -TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAG-TTCTACTG
* * ** * * * *
5212443 AATAGTTGCTCAAACAAGCAATATCTACTGATTTTACTGAATAGTTACTCAAACGAGAAATATCC
1 GA-AG-TGCTCAAACGAGCAATATCTACTGATACTACTGAA-AG-TGCTC-AACAAGCAATATCT
** *
5212508 ACTGATTATAATGAATGCGTGCTCAAACGAGCA
61 ACTGATCCTACTGAAT--GTGCTCAAACGAGCA
5212541 TTATCCACTG
Statistics
Matches: 452, Mismatches: 63, Indels: 30
0.83 0.12 0.06
Matches are distributed among these distances:
106 8 0.02
107 59 0.13
108 31 0.07
109 171 0.38
110 34 0.08
111 73 0.16
112 33 0.07
113 2 0.00
114 4 0.01
115 23 0.05
116 1 0.00
117 13 0.03
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (110 bp):
GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
Found at i:5212523 original size:39 final size:39
Alignment explanation
Indices: 5212301--5212556 Score: 172
Period size: 39 Copynumber: 6.8 Consensus size: 39
5212291 CTACTAAATG
* * * * *
5212301 TGCTCAAACGAGCAATGTCTACTAATTCTACTG-A-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATAATGAATAGT
* * * *
5212337 TGCTCAAACGAGCAATATCTACTAATTCTACTGAA-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATAATGAATAGT
* ** *
5212374 TGCTC-AACGAGCAATATCTACT-AGTCCTACTGAAT-G-
1 TGCTCAAACGAGCAATATCCACTGA-TTATAATGAATAGT
* * * * * * *
5212410 TGCTCAAACAAGTAATGTCTACTGATTCTACTAAATAGT
1 TGCTCAAACGAGCAATATCCACTGATTATAATGAATAGT
* * * *
5212449 TGCTCAAACAAGCAATATCTACTGATTTTACTGAATAGT
1 TGCTCAAACGAGCAATATCCACTGATTATAATGAATAGT
* * *
5212488 TACTCAAACGAGAAATATCCACTGATTATAATGAAT-GCG
1 TGCTCAAACGAGCAATATCCACTGATTATAATGAATAG-T
*
5212527 TGCTCAAACGAGCATTATCCACTGATTATA
1 TGCTCAAACGAGCAATATCCACTGATTATA
5212557 CTCAATAAGA
Statistics
Matches: 191, Mismatches: 21, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
35 1 0.01
36 64 0.34
37 31 0.16
38 3 0.02
39 92 0.48
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (39 bp):
TGCTCAAACGAGCAATATCCACTGATTATAATGAATAGT
Found at i:5212533 original size:78 final size:76
Alignment explanation
Indices: 5211885--5212563 Score: 500
Period size: 73 Copynumber: 9.2 Consensus size: 76
5211875 AAAAATGGAA
* * * * * *
5211885 TACTGATTCTATTG-A-AGTGCTC-AACAAGCAATATCTACTGATACTATTGAA-AGTGCTCAAT
1 TACTGATTCTACTGAATAGTGCTCAAACGAGAAATATCTACTGATTCTACTGAATGGTGCTCAA-
5211946 A--AGCAATATC
65 ACGAGCAATATC
* * * * ** * * *
5211956 TACTGATCCTACTGAAT-GAGCTCAAATGAGCAATGCCTATTGGTTCTACTGAA-AGTGCTCAAA
1 TACTGATTCTACTGAATAGTGCTCAAACGAGAAATATCTACTGATTCTACTGAATGGTGCTCAAA
* *
5212019 CAAGCAATACC
66 CGAGCAATATC
* * ** * * *
5212030 TATTGATACTACTGAA-AGTGCTCAAATAAGCAATATCTATTGATCCTACTGAAT-GTGCTCAAA
1 TACTGATTCTACTGAATAGTGCTCAAACGAGAAATATCTACTGATTCTACTGAATGGTGCTCAAA
*
5212093 CGAGCAATGTC
66 CGAGCAATATC
* ** * **
5212104 TACTTATTCTACTGAA-AGTGCTCAAA--AG-AGCATCTACTGATCCTACT-AAAAGTGCTC-AA
1 TACTGATTCTACTGAATAGTGCTCAAACGAGAAATATCTACTGATTCTACTGAATGGTGCTCAAA
*
5212163 CGAGCAATGTC
66 CGAGCAATATC
* * * *
5212174 TACTGATTCTACTGAA-AGTGCTAAAACGAGCAATATCTACT-AGTTCTATTGGAA--GTGCT-T
1 TACTGATTCTACTGAATAGTGCTCAAACGAGAAATATCTACTGA-TTCTACT-GAATGGTGCTCA
5212234 AACGAGCAATATC
64 AACGAGCAATATC
* * * * * * * *
5212247 TATTGGTCCTACTGAA-AGTGCTC-AACAAGCAATATCTACTAATCCTACTAAAT-GTGCTCAAA
1 TACTGATTCTACTGAATAGTGCTCAAACGAGAAATATCTACTGATTCTACTGAATGGTGCTCAAA
*
5212309 CGAGCAATGTC
66 CGAGCAATATC
* * * *
5212320 TACTAATTCTACTG-A-AGTGCTCAAACGAGCAATATCTACTAATTCTACTGAA-AGTGCTC-AA
1 TACTGATTCTACTGAATAGTGCTCAAACGAGAAATATCTACTGATTCTACTGAATGGTGCTCAAA
5212381 CGAGCAATATC
66 CGAGCAATATC
* * * * * *
5212392 TACT-AGTCCTACTGAAT-GTGCTCAAACAAGTAATGTCTACTGATTCTACTAAATAGTTGCTCA
1 TACTGA-TTCTACTGAATAGTGCTCAAACGAGAAATATCTACTGATTCTACTGAAT-GGTGCTCA
*
5212455 AACAAGCAATATC
64 AACGAGCAATATC
* * * * *
5212468 TACTGATTTTACTGAATAGTTACTCAAACGAGAAATATCCACTGATTATAATGAATGCGTGCTCA
1 TACTGATTCTACTGAATAG-TGCTCAAACGAGAAATATCTACTGATTCTACTGAATG-GTGCTCA
*
5212533 AACGAGCATTATC
64 AACGAGCAATATC
* * *
5212546 CACTGATTATACTCAATA
1 TACTGATTCTACTGAATA
5212564 AGATTTTCTG
Statistics
Matches: 498, Mismatches: 80, Indels: 53
0.79 0.13 0.08
Matches are distributed among these distances:
70 39 0.08
71 37 0.07
72 69 0.14
73 166 0.33
74 92 0.18
75 7 0.01
76 25 0.05
77 3 0.01
78 60 0.12
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (76 bp):
TACTGATTCTACTGAATAGTGCTCAAACGAGAAATATCTACTGATTCTACTGAATGGTGCTCAAA
CGAGCAATATC
Found at i:5218002 original size:21 final size:21
Alignment explanation
Indices: 5217969--5218008 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5217959 TTACAACCAA
* *
5217969 TACGAATAATAGTATAAAACT
1 TACGAACAATAGTAAAAAACT
*
5217990 TACGAACATTAGTAAAAAA
1 TACGAACAATAGTAAAAAA
5218009 AATTATTCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (21 bp):
TACGAACAATAGTAAAAAACT
Found at i:5218858 original size:31 final size:29
Alignment explanation
Indices: 5218800--5218862 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
5218790 AATTTTAACG
*
5218800 ATGAACAAAGAAAGAAATTAAGAACCAATA
1 ATGAACAAAGAAAGAAAATAAGAACCAA-A
5218830 ATGAACTAAAGAAAGAAAATAATG-ACCAAA
1 ATGAAC-AAAGAAAGAAAATAA-GAACCAAA
5218860 ATG
1 ATG
5218863 TGAATTAGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 10 0.33
31 19 0.63
32 1 0.03
ACGTcount: A:0.62, C:0.10, G:0.14, T:0.14
Consensus pattern (29 bp):
ATGAACAAAGAAAGAAAATAAGAACCAAA
Found at i:5236510 original size:105 final size:106
Alignment explanation
Indices: 5236334--5236533 Score: 375
Period size: 105 Copynumber: 1.9 Consensus size: 106
5236324 AAGCTTTAAG
*
5236334 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGTACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGA
5236399 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
66 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
*
5236440 AGGATATTTGGCTATTTGGTCGAACGAGAAATC-AAACCCAGCACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGA
5236504 TTTTCCAAACGCGAAATATTGCCTTATTTA
66 TTTTCCAAACGCGAAATATTGCCTTATTTA
5236534 GAAAATTTCC
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
105 60 0.65
106 32 0.35
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (106 bp):
AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGA
TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
Found at i:5237052 original size:38 final size:38
Alignment explanation
Indices: 5236993--5237098 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
5236983 TATTTTTAAG
*
5236993 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
5237030 AATATGTATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
5237068 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
5237099 TGTCACGGAC
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:5237632 original size:48 final size:48
Alignment explanation
Indices: 5237559--5237652 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
5237549 AGGGAATTCT
* *
5237559 GTTGAATCCTTTATTGTTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
*
5237607 GTTGAATCCATTATTGGTG-GAAGTTGGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCATTATTGGTGCG-AGTTGAGCTGACTTAGGCGTTTTTA
5237653 AGCCAAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
47 1 0.02
48 41 0.98
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
Found at i:5240567 original size:22 final size:23
Alignment explanation
Indices: 5240511--5240567 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
5240501 AGTTTAAAAT
5240511 AAAATATATAAAAGAAAGTCTTA
1 AAAATATATAAAAGAAAGTCTTA
*
5240534 AATAATA-A-AAAAGACAGT-TTA
1 AA-AATATATAAAAGAAAGTCTTA
5240555 AAAATATATAAAA
1 AAAATATATAAAA
5240568 ATAGTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 13 0.43
23 3 0.10
24 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAATATATAAAAGAAAGTCTTA
Found at i:5241299 original size:13 final size:13
Alignment explanation
Indices: 5241281--5241305 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5241271 AAATGCGTAG
5241281 ATAAATAAATGAA
1 ATAAATAAATGAA
5241294 ATAAATAAATGA
1 ATAAATAAATGA
5241306 TAGATGATAA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
ATAAATAAATGAA
Found at i:5243993 original size:21 final size:20
Alignment explanation
Indices: 5243960--5243998 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5243950 TTGTGCAGCA
*
5243960 AGTTTTGCTGATGTTGCTTG
1 AGTTTTGCTGATGGTGCTTG
*
5243980 AGTTTCTGGTGATGGTGCT
1 AGTTT-TGCTGATGGTGCT
5243999 GATACCACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.10, C:0.10, G:0.33, T:0.46
Consensus pattern (20 bp):
AGTTTTGCTGATGGTGCTTG
Found at i:5245546 original size:30 final size:30
Alignment explanation
Indices: 5245510--5245568 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5245500 AGATATAAAA
*
5245510 TAACACAAACACAATATTAATATACAAATT
1 TAACACAAACAAAATATTAATATACAAATT
*
5245540 TAACACAAACAAAATGTTAATATACAAAT
1 TAACACAAACAAAATATTAATATACAAAT
5245569 CTAATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (30 bp):
TAACACAAACAAAATATTAATATACAAATT
Found at i:5246327 original size:27 final size:29
Alignment explanation
Indices: 5246296--5246351 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 29
5246286 TCTCCTGCTA
*
5246296 GTTAGGGTTTT-GGGTTTTT-GGTTTAAG
1 GTTAGGGTTTTAGGATTTTTAGGTTTAAG
5246323 GTTAGGGTTTTAGGATTTTTAGGTTTAAG
1 GTTAGGGTTTTAGGATTTTTAGGTTTAAG
5246352 ATTTTAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 11 0.42
28 7 0.27
29 8 0.31
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (29 bp):
GTTAGGGTTTTAGGATTTTTAGGTTTAAG
Found at i:5246652 original size:97 final size:95
Alignment explanation
Indices: 5246404--5246678 Score: 315
Period size: 95 Copynumber: 2.9 Consensus size: 95
5246394 GTTTTTTAAT
* * * *
5246404 TAAATTAATTATAAAATTTTCAAAATTAGATTA-GGTTTCGTGTTTATGGTTTTTAAAGAAAAA-
1 TAAATTAATTATAAAATTTTAAAAAATAGATTAGGGTTTAGTGTTTAGGGTTTTTAAAGAAAAAT
*
5246467 AATCAATTAAATT-AGGGTTAGGGTTACTTGAG
66 AA--AA-TAAATTAAGGTTTAGGGTTACTTGAG
*** * ** *
5246499 TAAATTAATTA-AAAAAAATAAAAAATCATATTAGGGTTTAGTGTGAAGGGTTTTTAAGGAAAAA
1 TAAATTAATTATAAAATTTTAAAAAAT-AGATTAGGGTTTAGTGTTTAGGGTTTTTAAAGAAAAA
5246563 TAAAATAAATTAAGGTTTAGGGTTACTTGAG
65 TAAAATAAATTAAGGTTTAGGGTTACTTGAG
**
5246594 TAAATTAATTATAATTTTTTTTAAAAAATAGATTAGGGTTTAGTGTTTAGGGTTTTTAAAGAAAA
1 TAAATTAATTATAA--AATTTTAAAAAATAGATTAGGGTTTAGTGTTTAGGGTTTTTAAAGAAAA
* *
5246659 ATTCAAATAAATTACGGTTT
64 A-TAAAATAAATTAAGGTTT
5246679 GGAGTTTAGG
Statistics
Matches: 149, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
94 16 0.11
95 47 0.32
96 27 0.18
97 35 0.23
98 24 0.16
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.39
Consensus pattern (95 bp):
TAAATTAATTATAAAATTTTAAAAAATAGATTAGGGTTTAGTGTTTAGGGTTTTTAAAGAAAAAT
AAAATAAATTAAGGTTTAGGGTTACTTGAG
Found at i:5248082 original size:12 final size:12
Alignment explanation
Indices: 5248065--5248096 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
5248055 ATAATAATAT
5248065 AATATAATTTAC
1 AATATAATTTAC
5248077 AATATAATTTAC
1 AATATAATTTAC
5248089 AATATAAT
1 AATATAAT
5248097 AAAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (12 bp):
AATATAATTTAC
Found at i:5250031 original size:12 final size:11
Alignment explanation
Indices: 5249994--5250045 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
5249984 GCTTTTTTTA
*
5249994 AGAGGAATTTG
1 AGAGAAATTTG
*
5250005 AGATG-AATTTA
1 AGA-GAAATTTG
5250016 AGAGAATATTTG
1 AGAGAA-ATTTG
5250028 AGAGAAA-TTG
1 AGAGAAATTTG
5250038 AGAGAAAT
1 AGAGAAAT
5250046 GATTTAGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 11 0.31
11 13 0.37
12 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (11 bp):
AGAGAAATTTG
Found at i:5250466 original size:22 final size:23
Alignment explanation
Indices: 5250441--5250487 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5250431 TAAAGCTTTT
* *
5250441 TTTAAGAGGA-ATTTGAGAGGAA
1 TTTAAGAGAATATTTGAGAGAAA
5250463 TTTAAGAGAATATTTGAGAGAAA
1 TTTAAGAGAATATTTGAGAGAAA
5250486 TT
1 TT
5250488 GAGAGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.32
Consensus pattern (23 bp):
TTTAAGAGAATATTTGAGAGAAA
Found at i:5250481 original size:23 final size:22
Alignment explanation
Indices: 5250441--5250496 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
5250431 TAAAGCTTTT
* *
5250441 TTTAAGAGGAATTTGAGAGGAA
1 TTTAAGAGAAATTTGAGAGAAA
5250463 TTTAAGAGAATATTTGAGAGAAA
1 TTTAAGAGAA-ATTTGAGAGAAA
*
5250486 -TTGAGAGAAAT
1 TTTAAGAGAAAT
5250497 GATTTAGGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.07
22 17 0.57
23 11 0.37
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.29
Consensus pattern (22 bp):
TTTAAGAGAAATTTGAGAGAAA
Found at i:5250482 original size:12 final size:11
Alignment explanation
Indices: 5250445--5250496 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
5250435 GCTTTTTTTA
*
5250445 AGAGGAATTTG
1 AGAGAAATTTG
* *
5250456 AGAGGAATTTA
1 AGAGAAATTTG
5250467 AGAGAATATTTG
1 AGAGAA-ATTTG
5250479 AGAGAAA-TTG
1 AGAGAAATTTG
5250489 AGAGAAAT
1 AGAGAAAT
5250497 GATTTAGGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 10 0.28
11 16 0.44
12 10 0.28
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.25
Consensus pattern (11 bp):
AGAGAAATTTG
Found at i:5250819 original size:21 final size:21
Alignment explanation
Indices: 5250795--5250842 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5250785 AGGCTGAGAT
*
5250795 TATTTTGAGTGAT-TTTATAAA
1 TATTTTGA-TGATAATTATAAA
*
5250816 TATTTTGATTATAATTATAAA
1 TATTTTGATGATAATTATAAA
5250837 TATTTT
1 TATTTT
5250843 TAGGGATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.56
Consensus pattern (21 bp):
TATTTTGATGATAATTATAAA
Found at i:5250901 original size:31 final size:29
Alignment explanation
Indices: 5250866--5250931 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
5250856 CAAAATTATG
*
5250866 CATGAACTATGGTTTAATGTGCAATTGTATA
1 CATGAACTATGATTT--TGTGCAATTGTATA
* * *
5250897 CATGAATTTTGATTTTGTGCAATTTTATA
1 CATGAACTATGATTTTGTGCAATTGTATA
5250926 CATGAA
1 CATGAA
5250932 ATTTTGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 19 0.61
31 12 0.39
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (29 bp):
CATGAACTATGATTTTGTGCAATTGTATA
Found at i:5250915 original size:29 final size:30
Alignment explanation
Indices: 5250883--5250941 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
5250873 TATGGTTTAA
5250883 TGTGCAATTGTATACATG-AATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
*
5250912 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
5250942 GATCAAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAATTTTGATTT
Found at i:5252985 original size:44 final size:45
Alignment explanation
Indices: 5252930--5253025 Score: 158
Period size: 44 Copynumber: 2.2 Consensus size: 45
5252920 CAAGTATAAT
* *
5252930 ATTATAATACGGATTGTTCTAGTAATCATAAAGTA-TAACAAACA
1 ATTACAATACGGATTGTTCTAGTAATCATAAAGTAGGAACAAACA
*
5252974 ATTACAATACGGATTGTTCTAGTAATCATAAAGTAGGATCAAACA
1 ATTACAATACGGATTGTTCTAGTAATCATAAAGTAGGAACAAACA
5253019 ATTACAA
1 ATTACAA
5253026 GCACAAACAG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 34 0.71
45 14 0.29
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (45 bp):
ATTACAATACGGATTGTTCTAGTAATCATAAAGTAGGAACAAACA
Found at i:5257098 original size:57 final size:56
Alignment explanation
Indices: 5256982--5257116 Score: 155
Period size: 57 Copynumber: 2.3 Consensus size: 56
5256972 AATAAGATTA
* * *
5256982 TTAATAAAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAAT-AAAATAATATATAATTTAATAAAATTTTAACATAATTATTATT-AATATAAT
* *
5257040 TTAATAAAATAATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATATATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AAT
* *
5257097 TTACTAAAATCATAATATAA
1 TTAATAAAATAAT-ATATAA
5257117 AATACTATAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
56 4 0.06
57 37 0.55
58 26 0.39
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (56 bp):
TTAATAAAATAATATATAATTTAATAAAATTTTAACATAATTATTATTAATATAAT
Found at i:5260041 original size:34 final size:34
Alignment explanation
Indices: 5260002--5260071 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
5259992 TGGATGGCAC
*
5260002 CAAATGTAAGTAAGAACCAACTCGCAATTGTACA
1 CAAATGTAAGTAAGAACCAACTCACAATTGTACA
5260036 CAAATGTAAGTAAGAACCAACTCACAATTGTACA
1 CAAATGTAAGTAAGAACCAACTCACAATTGTACA
5260070 CA
1 CA
5260072 TTTGCAACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.20
Consensus pattern (34 bp):
CAAATGTAAGTAAGAACCAACTCACAATTGTACA
Found at i:5261633 original size:16 final size:16
Alignment explanation
Indices: 5261609--5261641 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5261599 GGGAATAACC
5261609 CAGAGCACAATCTAAA
1 CAGAGCACAATCTAAA
*
5261625 CAGATCACAATCTAAA
1 CAGAGCACAATCTAAA
5261641 C
1 C
5261642 TTCATGCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.27, G:0.09, T:0.15
Consensus pattern (16 bp):
CAGAGCACAATCTAAA
Found at i:5266375 original size:41 final size:41
Alignment explanation
Indices: 5266317--5266429 Score: 129
Period size: 41 Copynumber: 2.8 Consensus size: 41
5266307 TGATTCGGTA
* * *
5266317 CACCGGCTTTTAA-CCTGCTAGACATATAGTCCGAAATGTAT
1 CACCGGC-ATTAAGCCTGCTAGACATAAAGTCCGAAATATAT
* * *
5266358 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCCGAAATATAT
* **
5266399 CACCGGCATCAAGTGTGCTAGACATAAAGTC
1 CACCGGCATTAAGCCTGCTAGACATAAAGTC
5266430 TGTATTACAT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 4 0.06
41 58 0.94
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATAAAGTCCGAAATATAT
Found at i:5266430 original size:41 final size:41
Alignment explanation
Indices: 5266330--5266436 Score: 133
Period size: 41 Copynumber: 2.6 Consensus size: 41
5266320 CGGCTTTTAA
* * * * *
5266330 CCTGCTAGACATATAGTCCGAAATGTATCACCGGCATTAAG
1 CCTGCTAGACATAAAGTCTGAATTATATCACCGGCATCAAG
*
5266371 CCTGCTAGACATAAAGTCTGAATTATTTCACCGGCATCAAG
1 CCTGCTAGACATAAAGTCTGAATTATATCACCGGCATCAAG
** *
5266412 TGTGCTAGACATAAAGTCTGTATTA
1 CCTGCTAGACATAAAGTCTGAATTA
5266437 CATTCGATCA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (41 bp):
CCTGCTAGACATAAAGTCTGAATTATATCACCGGCATCAAG
Found at i:5266626 original size:17 final size:16
Alignment explanation
Indices: 5266606--5266658 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 16
5266596 AATCAAACCT
5266606 CATATATAAATGTTATA
1 CATATATAAAT-TTATA
5266623 CATACCT-TAAATTTATA
1 CATA--TATAAATTTATA
5266640 CA-A-A-AAATTTATA
1 CATATATAAATTTATA
5266653 CATATA
1 CATATA
5266659 CAACATTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
13 11 0.35
14 1 0.03
15 1 0.03
16 1 0.03
17 11 0.35
18 5 0.16
19 1 0.03
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (16 bp):
CATATATAAATTTATA
Found at i:5266708 original size:12 final size:12
Alignment explanation
Indices: 5266691--5266744 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
5266681 CTCAAAAACT
5266691 TATATATATACA
1 TATATATATACA
*
5266703 TATATATATTCGA
1 TATATATATAC-A
*
5266716 GTATTATACATACA
1 -TA-TATATATACA
5266730 TATATATATACA
1 TATATATATACA
5266742 TAT
1 TAT
5266745 CTTTGACTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 22 0.63
13 3 0.09
14 3 0.09
15 7 0.20
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (12 bp):
TATATATATACA
Found at i:5268914 original size:41 final size:41
Alignment explanation
Indices: 5268846--5269046 Score: 305
Period size: 41 Copynumber: 4.9 Consensus size: 41
5268836 TGACTTTTCG
* *
5268846 TGGGCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTC
1 TGGGATTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTC
5268887 TGGGATTTAGCGGCGTTTTGT-TTTAAGCGCCGCTAATGTTC
1 TGGGATTTAGCGGCGTTTT-TATTTAAGCGCCGCTAATGTTC
*
5268928 TGGGATTTAGCGGCATTTTTATTTAAGCGCCGCTAATGTTC
1 TGGGATTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTC
* * *
5268969 TGGGATTTAGTGGCATTTTTAATTAAGCGCCGCTAATGTTC
1 TGGGATTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTC
* * *
5269010 TGGGCTTTAGCGGCGTTTTTATTGATGCGCCGCTAAT
1 TGGGATTTAGCGGCGTTTTTATTTAAGCGCCGCTAAT
5269047 TCGCAGGCCT
Statistics
Matches: 147, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 1 0.01
41 145 0.99
42 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.38
Consensus pattern (41 bp):
TGGGATTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTC
Found at i:5269100 original size:123 final size:123
Alignment explanation
Indices: 5268851--5269111 Score: 298
Period size: 123 Copynumber: 2.1 Consensus size: 123
5268841 TTTCGTGGGC
* * *
5268851 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGCGGCGTTTTGTTTTAAGCG
1 TTTAGTGGCATTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGCGGCGTTTTGTTTGAAGCG
* * * ** * * *
5268916 CCGCTAATGTTCTGGGATTTAGCGGCATTTTTATTTAAGCGCCGCTAATGTTCTGGGA
66 CCGCTAATGTGCAGGCATTTAGCGGCATTTTTATAAAAACGCCGCTAATGCTCTGGCA
* *
5268974 TTTAGTGGCATTTTTAAT-TAAGCGCCGCTAATGTTCTGGGCTTTAGCGGCGTTTT-TATTGATG
1 TTTAGTGGCATTTTT-ATGTAAGCGCCGCTAATGTTCTGGGATTTAGCGGCGTTTTGT-TTGAAG
* * *
5269037 CGCCGCTAAT-TCGCAGGCCTTTAGCGGCGCTTTTT-TAAAAAACGCCGCTAATGCTCT-TCA
64 CGCCGCTAATGT-GCAGGCATTTAGCGGC-ATTTTTAT-AAAAACGCCGCTAATGCTCTGGCA
5269097 TTTAGTGGCATTTTT
1 TTTAGTGGCATTTTT
5269112 GGAAAGAGCC
Statistics
Matches: 117, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
122 2 0.02
123 92 0.79
124 23 0.20
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (123 bp):
TTTAGTGGCATTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGCGGCGTTTTGTTTGAAGCG
CCGCTAATGTGCAGGCATTTAGCGGCATTTTTATAAAAACGCCGCTAATGCTCTGGCA
Found at i:5269503 original size:16 final size:16
Alignment explanation
Indices: 5269482--5269551 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
5269472 CTATAGTATG
5269482 TAGTTTAAGGGTTTTA
1 TAGTTTAAGGGTTTTA
*
5269498 TAGTTTAA-GGTTTAA
1 TAGTTTAAGGGTTTTA
** * *
5269513 T-GTTTACTATAG-TATG
1 TAGTTTA--AGGGTTTTA
5269529 TAGTTTAAGGGTTTTA
1 TAGTTTAAGGGTTTTA
5269545 TAGTTTA
1 TAGTTTA
5269552 TGGTTTAGGG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
14 5 0.12
15 9 0.22
16 20 0.50
17 6 0.15
ACGTcount: A:0.27, C:0.01, G:0.21, T:0.50
Consensus pattern (16 bp):
TAGTTTAAGGGTTTTA
Found at i:5269510 original size:23 final size:23
Alignment explanation
Indices: 5269484--5269564 Score: 80
Period size: 23 Copynumber: 3.5 Consensus size: 23
5269474 ATAGTATGTA
5269484 GTTTAAGGGTTTTATAGTTTAAG
1 GTTTAAGGGTTTTATAGTTTAAG
*
5269507 GTTTAA-TGTTTACTATAGTATGT-A-
1 GTTTAAGGGTTT--TATAGT-T-TAAG
*
5269531 GTTTAAGGGTTTTATAGTTTATG
1 GTTTAAGGGTTTTATAGTTTAAG
5269554 GTTT-AGGGTTT
1 GTTTAAGGGTTT
5269565 GTTATATTGG
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
21 1 0.02
22 12 0.25
23 16 0.33
24 12 0.25
25 6 0.12
26 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.25, T:0.51
Consensus pattern (23 bp):
GTTTAAGGGTTTTATAGTTTAAG
Found at i:5269600 original size:22 final size:21
Alignment explanation
Indices: 5269575--5269615 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
5269565 GTTATATTGG
5269575 GTTTGTGA-TTTAGTGTTTTAAA
1 GTTTG-GAGTTTAGT-TTTTAAA
5269597 GTTTGGAGTTTAGTTTTTA
1 GTTTGGAGTTTAGTTTTTA
5269616 TAGTCAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (21 bp):
GTTTGGAGTTTAGTTTTTAAA
Found at i:5274289 original size:66 final size:66
Alignment explanation
Indices: 5274219--5274354 Score: 227
Period size: 66 Copynumber: 2.1 Consensus size: 66
5274209 GACCACAGTT
* * *
5274219 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAGAGCAGATGCGGCAGCGAGAGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCAGATGCGGCAGCCAGAGAAGC
5274284 A
66 A
* *
5274285 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCTGATGCGGCATCCAGAGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCAGATGCGGCAGCCAGAGAAGC
5274350 A
66 A
5274351 GAGG
1 GAGG
5274355 CTGCAGCGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.14
Consensus pattern (66 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCAGATGCGGCAGCCAGAGAAGC
A
Found at i:5274751 original size:43 final size:43
Alignment explanation
Indices: 5274703--5274835 Score: 198
Period size: 43 Copynumber: 3.1 Consensus size: 43
5274693 AACAAAAAGT
*
5274703 GGCGTTTGTGAAAAAAGCGCCGCTAAAGAACAT-TAGCTTTAGC
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAGAACATGT-TCTTTAGC
*
5274746 GGCGTTTGTGTAAAAAGCGCCGCTAAAGAACATGTTCTTTAGC
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAGAACATGTTCTTTAGC
* *
5274789 GGCGTTTGT-ATAAAATGTGCCGCTAAAGAACATGTTCTTTAGC
1 GGCGTTTGTGA-AAAAAGCGCCGCTAAAGAACATGTTCTTTAGC
5274832 GGCG
1 GGCG
5274836 CTTTTAAAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
43 82 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
GGCGTTTGTGAAAAAAGCGCCGCTAAAGAACATGTTCTTTAGC
Found at i:5280501 original size:19 final size:20
Alignment explanation
Indices: 5280470--5280514 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
5280460 TTGGAAGATT
5280470 ATTGA-AATAAAAATCATTC
1 ATTGAGAATAAAAATCATTC
5280489 ATTGAGAATAAAAATCATTC
1 ATTGAGAATAAAAATCATTC
5280509 ATTGAG
1 ATTGAG
5280515 CGAAACTCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (20 bp):
ATTGAGAATAAAAATCATTC
Found at i:5288376 original size:2 final size:2
Alignment explanation
Indices: 5288369--5288395 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5288359 AAGGAAAGGA
5288369 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
5288396 TAATAATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5290397 original size:22 final size:21
Alignment explanation
Indices: 5290361--5290405 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
5290351 ATATATATTT
** *
5290361 TAAAATTTTTTATTAATTTTTA
1 TAAAATTTTAAATT-ATTTATA
5290383 TAAAATTTTAAATTATTTATA
1 TAAAATTTTAAATTATTTATA
5290404 TA
1 TA
5290406 CTTATTGTTA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TAAAATTTTAAATTATTTATA
Found at i:5290400 original size:21 final size:21
Alignment explanation
Indices: 5290344--5290405 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
5290334 GAACTAATTT
*
5290344 ATTTTTAATATATATTT-TAAA
1 ATTTTTAAT-TATTTTTATAAA
*
5290365 ATTTTTTATTAATTTTTATAAA
1 ATTTTTAATT-ATTTTTATAAA
* *
5290387 ATTTTAAATTATTTATATA
1 ATTTTTAATTATTTTTATA
5290406 CTTATTGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.03
21 21 0.62
22 12 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAATTATTTTTATAAA
Found at i:5297090 original size:27 final size:27
Alignment explanation
Indices: 5297042--5297100 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
5297032 AATAGCAGAA
*
5297042 ATATACATGAATCAAATAAATA-AAGAT
1 ATATACATGAATAAAATAAATAGAA-AT
*
5297069 ATATATATGAATTAAAAT-AATAGAAAT
1 ATATACATGAA-TAAAATAAATAGAAAT
5297096 ATATA
1 ATATA
5297101 AAAACATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (27 bp):
ATATACATGAATAAAATAAATAGAAAT
Found at i:5297115 original size:16 final size:16
Alignment explanation
Indices: 5297094--5297132 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5297084 AATAATAGAA
5297094 ATATATAAAAACATGT
1 ATATATAAAAACATGT
* **
5297110 ATATATGAAAGTATGT
1 ATATATAAAAACATGT
5297126 ATATATA
1 ATATATA
5297133 TAGATGAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:5297252 original size:3 final size:3
Alignment explanation
Indices: 5297215--5297239 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5297205 TAAATGCAAC
5297215 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5297240 GGTTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5298882 original size:44 final size:44
Alignment explanation
Indices: 5298831--5299027 Score: 134
Period size: 44 Copynumber: 4.5 Consensus size: 44
5298821 CTTCGATCTG
5298831 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
* * * * *
5298875 CTCCACTACTGCTTAGGGTGATAGGA-CT--AATGGCTTAAATCTG
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAAT--CTTCAACCTA
* * * * * * * * * ** * *
5298918 CTTCTCCACTG-TATTGGGAAGATAAGATTC-ACCATCTTTGATCTG
1 CTCCACTACTGCT-TAGGG-TGA-CAGAATCTGCAATCTTCAACCTA
* *
5298963 CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTA
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
5299007 CTCCACTACTGCTTAGGGTGA
1 CTCCACTACTGCTTAGGGTGA
5299028 TAGGACTAAT
Statistics
Matches: 114, Mismatches: 29, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 26 0.23
44 58 0.51
45 22 0.19
46 2 0.02
47 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
Found at i:5298913 original size:132 final size:132
Alignment explanation
Indices: 5298691--5299118 Score: 739
Period size: 132 Copynumber: 3.2 Consensus size: 132
5298681 TTCGTTATTG
* * * * * * *
5298691 TTGATTTGCTCCATTACTGCTTAGGGGGACAGAATCTACAGTCTTTGACCTACTCCACTACTGCT
1 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCT
5298756 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
66 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
5298821 CT
131 CT
* * *
5298823 TCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCT
1 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCT
5298888 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
66 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
5298953 CT
131 CT
5298955 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCT
1 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCT
* *
5299020 TAGGGTGATAGGACTAATGGCTTAAATATGTTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
66 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
5299085 CT
131 CT
5299087 TTGATCATGCTCCACTACTGATTAGGGTGACA
1 TTGATC-TGCTCCACTACTGATTAGGGTGACA
5299119 AGACTAATGG
Statistics
Matches: 282, Mismatches: 13, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
132 257 0.91
133 25 0.09
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (132 bp):
TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCT
TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
CT
Found at i:5299126 original size:221 final size:220
Alignment explanation
Indices: 5298875--5299338 Score: 795
Period size: 221 Copynumber: 2.1 Consensus size: 220
5298865 CTTCAACCTA
* *
5298875 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGACAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
*
5298940 TAAGATTCACCATCTTTGATCTGCTCCACTACTG-ATTAGGGTGACAGAATCTGCAATCTTCGAC
66 TAAGATTCACCATCTTTGATCTGCTCCACTACTGCA-TAGGGTGACAGAATCTGCAATCTTCAAC
* * **
5299004 CTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATATGTTTCTCCACTGTATTGGGA
130 CTACTCCACTACTGCTTAGGGTGATAAGACAAATGGCTTAAATATACTTCTCCACTGTATTGGGA
*
5299069 AGATAAGATTCACCATCTTTGATCATG
195 AGATAAGATTCACCATCTTCGATC-TG
*
5299096 CTCCACTACTGATTAGGGTGACAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGACAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
* *
5299161 TAAGATTCACCATCTTTGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGTAATTTTCAACC
66 TAAGATTCACCATCTTTGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGCAATCTTCAACC
*
5299226 TACTCCACTACTGCTTAGGGTGATAAGACAAATGGCTTAAATCTACTTCTCCACTGTATTGGGAA
131 TACTCCACTACTGCTTAGGGTGATAAGACAAATGGCTTAAATATACTTCTCCACTGTATTGGGAA
5299291 GATAAGATTCACCATCTTCGATCTG
196 GATAAGATTCACCATCTTCGATCTG
5299316 CTCCACTACTGCTTAGGGTGACA
1 CTCCACTACTGCTTAGGGTGACA
5299339 GAATCTGATT
Statistics
Matches: 229, Mismatches: 13, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
220 24 0.10
221 204 0.89
222 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (220 bp):
CTCCACTACTGCTTAGGGTGACAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
TAAGATTCACCATCTTTGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGCAATCTTCAACC
TACTCCACTACTGCTTAGGGTGATAAGACAAATGGCTTAAATATACTTCTCCACTGTATTGGGAA
GATAAGATTCACCATCTTCGATCTG
Found at i:5299158 original size:89 final size:88
Alignment explanation
Indices: 5299007--5299206 Score: 330
Period size: 89 Copynumber: 2.3 Consensus size: 88
5298997 CTTCGACCTA
* * * *
5299007 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATATGTTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGATTAGGGTGACAAGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGA
5299072 TAAGATTCACCATCTTTGATCATG
66 TAAGATTCACCATCTTTGATC-TG
*
5299096 CTCCACTACTGATTAGGGTGACAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGATTAGGGTGACAAGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGA
5299161 TAAGATTCACCATCTTTGATCTG
66 TAAGATTCACCATCTTTGATCTG
5299184 CTCCACTACTGCA-TAGGGTGACA
1 CTCCACTACTG-ATTAGGGTGACA
5299207 GAATCTGTAA
Statistics
Matches: 105, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
88 23 0.22
89 82 0.78
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (88 bp):
CTCCACTACTGATTAGGGTGACAAGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGA
TAAGATTCACCATCTTTGATCTG
Found at i:5299185 original size:45 final size:45
Alignment explanation
Indices: 5299051--5299185 Score: 127
Period size: 45 Copynumber: 3.0 Consensus size: 45
5299041 TTAAATATGT
5299051 TTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTTGATCATGC
1 TTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTTGATC-TGC
* * * * * * **
5299097 TCCACTACTG-ATTAGGG-TGACAAGACT-A--ATGGCTTAAATCTGC
1 TTCTCCACTGTATT-GGGAAGATAAGATTCACCAT--CTTTGATCTGC
5299140 TTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTTGATCTGC
1 TTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTTGATCTGC
5299185 T
1 T
5299186 CCACTACTGC
Statistics
Matches: 65, Mismatches: 16, Indels: 17
0.66 0.16 0.17
Matches are distributed among these distances:
42 2 0.03
43 13 0.20
44 17 0.26
45 21 0.32
46 10 0.15
47 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (45 bp):
TTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTTGATCTGC
Found at i:5299333 original size:132 final size:132
Alignment explanation
Indices: 5299096--5299345 Score: 446
Period size: 132 Copynumber: 1.9 Consensus size: 132
5299086 TTTGATCATG
* *
5299096 CTCCACTACTGATTAGGGTGACAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGATTAGGGTGACAAGACAAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGA
*
5299161 TAAGATTCACCATCTTTGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGTAATTTTCAACC
66 TAAGATTCACCATCTTCGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGTAATTTTCAACC
5299226 TA
131 TA
* *
5299228 CTCCACTACTGCTTAGGGTGATAAGACAAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGATTAGGGTGACAAGACAAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGA
*
5299293 TAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTG
66 TAAGATTCACCATCTTCGATCTGCTCCACTACTGCATAGGGTGACAGAATCTG
5299346 ATTCGTAGCT
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 112 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (132 bp):
CTCCACTACTGATTAGGGTGACAAGACAAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAGA
TAAGATTCACCATCTTCGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGTAATTTTCAACC
TA
Found at i:5300088 original size:114 final size:114
Alignment explanation
Indices: 5299886--5300115 Score: 288
Period size: 114 Copynumber: 2.0 Consensus size: 114
5299876 AAGATTCGCT
*
5299886 GTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAAAGTAAGATTCGTCGTTGTGGCCTCAAT
1 GTCGTAGCTTCAATCTATTCCACTACACCGCCAGGG-AAGTAAGATTCGTCGTTGTAGCCTCAAT
*
5299951 CTATTTAACCATAATGTCGGGGAAACAAGATTCGCTATTGTAGCTTCAATC
65 CTATTTAA-CATAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATC
* * * *
5300002 GTCGTAGCTTCAATCTATTCC-GTCGCATCGCCTGGG-AGTAAGATTCGTCGTTGTAGCCTCAAT
1 GTCGTAGCTTCAATCTATTCCACT-ACACCGCCAGGGAAGTAAGATTCGTCGTTGTAGCCTCAAT
* * * *
5300065 CT-TTTAA-ATTGCTATGTTGGGGAAACAGGATTCGCCGTTGTAGCTTCAATC
65 CTATTTAACA-T--AATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATC
5300116 TGTTCCGCTG
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
111 1 0.01
112 1 0.01
113 5 0.05
114 62 0.62
115 1 0.01
116 30 0.30
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (114 bp):
GTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATTCGTCGTTGTAGCCTCAATC
TATTTAACATAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATC
Found at i:5300147 original size:50 final size:49
Alignment explanation
Indices: 5300093--5300962 Score: 414
Period size: 50 Copynumber: 17.5 Consensus size: 49
5300083 GGGGAAACAG
* * *
5300093 GATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCCTGAAAGGTAA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACGCCTGGAA-GTAA
* ** * ** *
5300143 GATTCACCGTTGTAGCTTCAATCT-TTGAAACTGCAATGTCGAGGAAGCAA
1 GATTCGCCGTTGTAGCTTCAATCTGTT-CCACTGCAACG-CCTGGAAGTAA
* * * * * *
5300193 GATTCGCCGTCGTAGTTTTAATCTGTTCCGCTACATCGCCTGGAAGTAA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACGCCTGGAAGTAA
* * ** * * * **
5300242 GATTCACCGTTGTGGCTTCAATCT-TTTAATTCCAATGTCGGGGAAGTGAA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACG-CCTGGAAGT-AA
* * * * *
5300292 -ATTTGCCATCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACGCCT-GGAAGTAA
* ** * * * ** *
5300341 GATTCGCCGTTGTGGCTTCAATCT-TTTAATTGTAATGTCGGGGAAGTGA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACG-CCTGGAAGTAA
* * * * *
5300390 GATTCGCCATCGTTGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACGCCT-GGAAGTAA
* * * * ** * * ** **
5300440 GATTCACCGTTGTGGCTTCGATCTTTTTAATTGCAATGTCGAGGAAGGGA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACG-CCTGGAAGTAA
* * * * *
5300490 GATTCGCCGTCGTAGTTTCAATCTATTCCACTTCATCGCCTGGGAAGTAA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACGCCT-GGAAGTAA
* * * ** * * ** *
5300540 GATTCGCCGTTGTGGCTTCGATCTTTTGAATTGCAATGTCAGGGAAGTGA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACG-CCTGGAAGTAA
* * * * * * *
5300590 GATTCGCTGTCGTAACTTTAATCTGTTCCGCTGCACCGCCTGAAAGGTAA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACGCCTGGAA-GTAA
* * ** * * **
5300640 GATTCGCCGTTGTAGCTTCGATCTTTTTAATTGCAATGTCAGGGAAGTAA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACG-CCTGGAAGTAA
* ** *
5300690 GATCCGTTGTTGTAGCTTCAATCTGTTACACTGCAACG-CTAGGAAAGTAA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACGCCT-GG-AAGTAA
* * ** * * *
5300740 GATCCGCTGTTGTAGCTTCAATCT-TCTTAATTGCAATG-TTAGGGAAGTAA
1 GATTCGCCGTTGTAGCTTCAATCTGT-TCCACTGCAACGCCT--GGAAGTAA
* * *
5300790 GATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAATAA
1 GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACGCCT-GG-AAGTAA
* ** * * * * *
5300840 GA-TCTGCTGTTGTAGCTTCAATCT-TTTAATTGCAATGTCAGAGAATTAA
1 GATTC-GCCGTTGTAGCTTCAATCTGTTCCACTGCAACGCCTG-GAAGTAA
* * * *
5300889 GA-TCTGCTGTTGAAGCTTCAATCTGTTCCACTGCAATG-CTAAGAAAGTAA
1 GATTC-GCCGTTGTAGCTTCAATCTGTTCCACTGCAACGCCT--GGAAGTAA
*
5300939 GATTCGCTGTTGTAGCTTCAATCT
1 GATTCGCCGTTGTAGCTTCAATCT
5300963 ATCATGTTGT
Statistics
Matches: 595, Mismatches: 196, Indels: 58
0.70 0.23 0.07
Matches are distributed among these distances:
48 6 0.01
49 142 0.24
50 429 0.72
51 18 0.03
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (49 bp):
GATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAACGCCTGGAAGTAA
Found at i:5300197 original size:100 final size:99
Alignment explanation
Indices: 5300001--5300962 Score: 957
Period size: 100 Copynumber: 9.7 Consensus size: 99
5299991 TAGCTTCAAT
* * * *
5300001 CGTCGTAGCTTCAATCTATTCCG-TCGCATCGCCTGG-GAGTAAGATTCGTCGTTGTAGCCTCAA
1 CGTCGTAGCTTCAATCTGTTCCGCT-GCATCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAA
* * * ** *
5300064 TCTTTTAAATTGCTATGTTGGGGAAACAGGATTCGC
65 TCTTTT-AATTGCAATGTCGAGGAAGTAAGATTCGC
* * *
5300100 CGTTGTAGCTTCAATCTGTTCCGCTGCACCGCCT-GAAAGGTAAGATTCACCGTTGTAGCTTCAA
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAA-GTAAGATTCGCCGTTGTAGCTTCAA
* * *
5300164 TCTTTGAAACTGCAATGTCGAGGAAGCAAGATTCGC
65 TCTTT-TAATTGCAATGTCGAGGAAGTAAGATTCGC
* * * * *
5300200 CGTCGTAGTTTTAATCTGTTCCGCTACATCGCCTGG-AAGTAAGATTCACCGTTGTGGCTTCAAT
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAAT
* * *
5300264 CTTTTAATTCCAATGTCGGGGAAGTGAA-ATTTGC
66 CTTTTAATTGCAATGTCGAGGAAGT-AAGATTCGC
* * *
5300298 CATCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAAT
* * *
5300363 CTTTTAATTGTAATGTCGGGGAAGTGAGATTCGC
66 CTTTTAATTGCAATGTCGAGGAAGTAAGATTCGC
* * * * * *
5300397 CATCGTTGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCGAT
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAAT
**
5300462 CTTTTTAATTGCAATGTCGAGGAAGGGAGATTCGC
66 C-TTTTAATTGCAATGTCGAGGAAGTAAGATTCGC
* * * * * * *
5300497 CGTCGTAGTTTCAATCTATTCCACTTCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCGAT
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAAT
*
5300562 CTTTTGAATTGCAATGTC-AGGGAAGTGAGATTCGC
66 CTTTT-AATTGCAATGTCGA-GGAAGTAAGATTCGC
* * * * *
5300597 TGTCGTAACTTTAATCTGTTCCGCTGCACCGCCT-GAAAGGTAAGATTCGCCGTTGTAGCTTCGA
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAA-GTAAGATTCGCCGTTGTAGCTTCAA
* *
5300661 TCTTTTTAATTGCAATGTC-AGGGAAGTAAGATCCGT
65 TC-TTTTAATTGCAATGTCGA-GGAAGTAAGATTCGC
* * * * * * *
5300697 TGTTGTAGCTTCAATCTGTTACACTGCAACG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAA
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-GGAAAGTAAGATTCGCCGTTGTAGCTTCAA
* *
5300761 TCTTCTTAATTGCAATGT-TAGGGAAGTAAGATCCGC
65 TCTT-TTAATTGCAATGTCGA-GGAAGTAAGATTCGC
* * * * * *
5300797 TGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAATAAGA-TCTGCTGTTGTAGCTTCA
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-GGAAAGTAAGATTC-GCCGTTGTAGCTTCA
*
5300860 ATCTTTTAATTGCAATGTC-AGAGAATTAAGA-TCTGC
64 ATCTTTTAATTGCAATGTCGAG-GAAGTAAGATTC-GC
* * * * * *
5300896 TGTTGAAGCTTCAATCTGTTCCACTGCAAT-G-CTAAGAAAGTAAGATTCGCTGTTGTAGCTTCA
1 CGTCGTAGCTTCAATCTGTTCCGCTGC-ATCGCCT-GGAAAGTAAGATTCGCCGTTGTAGCTTCA
5300959 ATCT
64 ATCT
5300963 ATCATGTTGT
Statistics
Matches: 759, Mismatches: 81, Indels: 46
0.86 0.09 0.05
Matches are distributed among these distances:
98 57 0.08
99 274 0.36
100 419 0.55
101 9 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (99 bp):
CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAAT
CTTTTAATTGCAATGTCGAGGAAGTAAGATTCGC
Found at i:5300670 original size:200 final size:199
Alignment explanation
Indices: 5300001--5300962 Score: 977
Period size: 199 Copynumber: 4.8 Consensus size: 199
5299991 TAGCTTCAAT
* * * *
5300001 CGTCGTAGCTTCAATCTATTCCG-TCGCATCGCCTGG-GAGTAAGATTCGTCGTTGTAGCCTCAA
1 CGTCGTAGCTTCAATCTGTTCCGCT-GCATCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAA
* * * * ** * *
5300064 TCTTTTAAATTGCTATGTTGGGGAA-ACAGGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCA
65 TCTTTTTAATTGCAATGTCGAGGAAGTGA-GATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCA
* * * * *
5300128 CCGCCT-GAAAGGTAAGATTCACCGTTGTAGCTTCAATCTTTGAAACTGCAATGTC-GAGGAAGC
129 TCGCCTGGAAA-GTAAGATTCGCCGTTGTAGCTTCAATCTTT-TAATTGCAATGTCAG-GGAAGT
5300191 AAGATTCGC
191 AAGATTCGC
* * * * *
5300200 CGTCGTAGTTTTAATCTGTTCCGCTACATCGCCTGG-AAGTAAGATTCACCGTTGTGGCTTCAAT
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAAT
* * * * * *
5300264 C-TTTTAATTCCAATGTCGGGGAAGTGAAATTTGCCATCGTAGCTTCAATCTGTTCCGCTGCATC
66 CTTTTTAATTGCAATGTCGAGGAAGTGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCATC
* * * * *
5300328 GCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTGTAATGTCGGGGAAGTGAGAT
131 GCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAATTGCAATGTCAGGGAAGTAAGAT
5300393 TCGC
196 TCGC
* * * * * *
5300397 CATCGTTGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCGAT
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAAT
* * * *
5300462 CTTTTTAATTGCAATGTCGAGGAAGGGAGATTCGCCGTCGTAGTTTCAATCTATTCCACTTCATC
66 CTTTTTAATTGCAATGTCGAGGAAGTGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCATC
* * * *
5300527 GCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTGAATTGCAATGTCAGGGAAGTGAGA
131 GCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTT-AATTGCAATGTCAGGGAAGTAAGA
5300592 TTCGC
195 TTCGC
* * * * *
5300597 TGTCGTAACTTTAATCTGTTCCGCTGCACCGCCT-GAAAGGTAAGATTCGCCGTTGTAGCTTCGA
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAA-GTAAGATTCGCCGTTGTAGCTTCAA
* * ** * *
5300661 TCTTTTTAATTGCAATGTC-AGGGAAGTAAGATCCGTTGTTGTAGCTTCAATCTGTTACACTGCA
65 TCTTTTTAATTGCAATGTCGA-GGAAGTGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCA
* * * *
5300725 ACG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTTAGGGAAGTA
129 TCGCCT-GGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTT-TTAATTGCAATGTCAGGGAAGTA
*
5300789 AGATCCGC
192 AGATTCGC
* * * * * *
5300797 TGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAATAAGA-TCTGCTGTTGTAGCTTCA
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-GGAAAGTAAGATTC-GCCGTTGTAGCTTCA
* * * * *
5300860 ATC-TTTTAATTGCAATGTC-AGAGAATTAAGA-TCTGCTGTTGAAGCTTCAATCTGTTCCACTG
64 ATCTTTTTAATTGCAATGTCGAG-GAAGTGAGATTC-GCCGTCGTAGCTTCAATCTGTTCCACTG
* *
5300922 CAAT-G-CTAAGAAAGTAAGATTCGCTGTTGTAGCTTCAATCT
127 C-ATCGCCT-GGAAAGTAAGATTCGCCGTTGTAGCTTCAATCT
5300963 ATCATGTTGT
Statistics
Matches: 655, Mismatches: 91, Indels: 34
0.84 0.12 0.04
Matches are distributed among these distances:
197 54 0.08
198 113 0.17
199 246 0.38
200 236 0.36
201 6 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (199 bp):
CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAAT
CTTTTTAATTGCAATGTCGAGGAAGTGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCATC
GCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAATTGCAATGTCAGGGAAGTAAGAT
TCGC
Found at i:5301202 original size:45 final size:44
Alignment explanation
Indices: 5301151--5301985 Score: 251
Period size: 44 Copynumber: 19.0 Consensus size: 44
5301141 GTAAGGCTTG
*
5301151 TGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGTAAGATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAATG-AGGAAGGTAAGATCTTT
* * ** * * * *
5301196 TGTCTTCAACCAGC-TC-CATCACAACCGA-GAGAGGCAAGGT-TTG
1 TGTCTTCGACCTGCTTCGC-TGTCAA-TGAGGA-AGGTAAGATCTTT
5301239 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGTAAGATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAATG-AGGAAGGTAAGATCTTT
* * ** * ** * *
5301284 TGTCTTCAACCAGC-TC-CATCACAACCGA-GAGAGACAAGGT-TTG
1 TGTCTTCGACCTGCTTCGC-TGTCAA-TGAGGA-AGGTAAGATCTTT
* * *
5301327 TGTCTTCGACCTGCTTCACTGTCAGTGTAGGAAGGCAAGATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAATG-AGGAAGGTAAGATCTTT
* * ** ** * * * *
5301372 TGTCTTCAACCAGC-TCTATCACAACCGA-GAGAGGCAAGGT-TTG
1 TGTCTTCGACCTGCTTCGCTGTCAA-TGAGGA-AGGTAAGATCTTT
* *
5301415 TGTCTTCGACCTACTTCGCTGTCAATGCAGGAAGGCAAGATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAATG-AGGAAGGTAAGATCTTT
* * ** * * * *
5301460 TGTCTTCAACCAGC-TC-CATCACAACCGA-GAGAGGCAAGGT-TTG
1 TGTCTTCGACCTGCTTCGC-TGTCAA-TGAGGA-AGGTAAGATCTTT
*
5301503 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAATG-AGGAAGGTAAGATCTTT
* * ** ** * * * *
5301548 TGTCTTCAACCAGC-TCTATCACAACCGA-GAGAGGCAAGGT-TTG
1 TGTCTTCGACCTGCTTCGCTGTCAA-TGAGGA-AGGTAAGATCTTT
* * *
5301591 TGTCTTCGACCTGCTTCGCTGTCAATCCAAGAAGGCAAGATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAAT-GAGGAAGGTAAGATCTTT
* * ** * * * *
5301636 TATCTTCAACCTGC-TC-CATCACAACCGAGAGAA-GCAAGGT-TTG
1 TGTCTTCGACCTGCTTCGC-TGTCAA-TGAG-GAAGGTAAGATCTTT
* * * *
5301679 TGTCTTCGACATGCTTCGCTGTCAATACAGGAAGGCAAAATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAAT-GAGGAAGGTAAGATCTTT
* * ** * * *
5301724 TGTCTTCAACCAGC-TC-CATCACAACCGA-GAGAGGTAAGGT-TTG
1 TGTCTTCGACCTGCTTCGC-TGTCAA-TGAGGA-AGGTAAGATCTTT
* * *
5301767 TGTCTTCGACCTGCTTCGCTGTTAATACAGGAAGATAAGATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAAT-GAGGAAGGTAAGATCTTT
* * ** ** * * *
5301812 TGTCTTCTACCAGC-TCTATCACAACCGA-GAGAGGTAAGGT-TTG
1 TGTCTTCGACCTGCTTCGCTGTCAA-TGAGGA-AGGTAAGATCTTT
* * *
5301855 TGTCTTCGACCTGCTTCGCTATCAATACAGGAAGGCAAGATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAAT-GAGGAAGGTAAGATCTTT
* * ** * * * *
5301900 TGTCTTCAACCAGC-TC-CATCACAACCGA-GAGAGGCAAGGT-TTG
1 TGTCTTCGACCTGCTTCGC-TGTCAA-TGAGGA-AGGTAAGATCTTT
*
5301943 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 TGTCTTCGACCTGCTTCGCTGTCAATG-AGGAAGGTAAGATCT
5301986 GCAACTTTAT
Statistics
Matches: 558, Mismatches: 166, Indels: 132
0.65 0.19 0.15
Matches are distributed among these distances:
43 154 0.28
44 252 0.45
45 152 0.27
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (44 bp):
TGTCTTCGACCTGCTTCGCTGTCAATGAGGAAGGTAAGATCTTT
Found at i:5301244 original size:88 final size:88
Alignment explanation
Indices: 5301130--5301985 Score: 1433
Period size: 88 Copynumber: 9.7 Consensus size: 88
5301120 TTTCCACTTA
* * * * *
5301130 AACCGAGAGAGGTAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGTAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
5301195 TTGTCTTCAACCAGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
*
5301218 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGTAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
5301283 TTGTCTTCAACCAGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
* * * *
5301306 AACCGAGAGAGACAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAGTGTAGGAAGGCAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
*
5301371 TTGTCTTCAACCAGCTCTATCAC
66 TTGTCTTCAACCAGCTCCATCAC
*
5301394 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTACTTCGCTGTCAATGCAGGAAGGCAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
5301459 TTGTCTTCAACCAGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
5301482 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
*
5301547 TTGTCTTCAACCAGCTCTATCAC
66 TTGTCTTCAACCAGCTCCATCAC
* *
5301570 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATCCAAGAAGGCAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
* *
5301635 TTATCTTCAACCTGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
* * * *
5301658 AACCGAGAGAAGCAAGGTTTGTGTCTTCGACATGCTTCGCTGTCAATACAGGAAGGCAAAATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
5301723 TTGTCTTCAACCAGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
* * * **
5301746 AACCGAGAGAGGTAAGGTTTGTGTCTTCGACCTGCTTCGCTGTTAATACAGGAAGATAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
* *
5301811 TTGTCTTCTACCAGCTCTATCAC
66 TTGTCTTCAACCAGCTCCATCAC
* * *
5301834 AACCGAGAGAGGTAAGGTTTGTGTCTTCGACCTGCTTCGCTATCAATACAGGAAGGCAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
5301899 TTGTCTTCAACCAGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
5301922 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
5301986 GCAACTTTAT
Statistics
Matches: 720, Mismatches: 48, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 720 1.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (88 bp):
AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
TTGTCTTCAACCAGCTCCATCAC
Found at i:5303093 original size:21 final size:21
Alignment explanation
Indices: 5303067--5303110 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5303057 GGTATAGCAA
5303067 GATCACCACATGCCCCAATCT
1 GATCACCACATGCCCCAATCT
** *
5303088 GATCACTTCATGCCCCATTCT
1 GATCACCACATGCCCCAATCT
5303109 GA
1 GA
5303111 ACAAATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.39, G:0.11, T:0.25
Consensus pattern (21 bp):
GATCACCACATGCCCCAATCT
Found at i:5303213 original size:6 final size:7
Alignment explanation
Indices: 5303199--5303242 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
5303189 TTAGCCTCTC
5303199 CATTTTT
1 CATTTTT
5303206 CA-TTTT
1 CATTTTT
5303212 CATTTTT
1 CATTTTT
*
5303219 TATTTTT
1 CATTTTT
*
5303226 CA-TTCT
1 CATTTTT
5303232 CATTTTT
1 CATTTTT
5303239 CATT
1 CATT
5303243 CGTTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:5303223 original size:20 final size:20
Alignment explanation
Indices: 5303200--5303238 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5303190 TAGCCTCTCC
*
5303200 ATTTTTCATTTTCATTTTTT
1 ATTTTTCATTCTCATTTTTT
5303220 ATTTTTCATTCTCATTTTT
1 ATTTTTCATTCTCATTTTT
5303239 CATTCGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTCATTCTCATTTTTT
Found at i:5308236 original size:16 final size:16
Alignment explanation
Indices: 5308215--5308253 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5308205 AATAATAGAA
5308215 ATATATAAAAACATGT
1 ATATATAAAAACATGT
* **
5308231 ATATATGAAAGTATGT
1 ATATATAAAAACATGT
5308247 ATATATA
1 ATATATA
5308254 TAGATGAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:5308385 original size:3 final size:3
Alignment explanation
Indices: 5308348--5308372 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5308338 CAACAACAAC
5308348 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5308373 GGCTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5308395 original size:17 final size:18
Alignment explanation
Indices: 5308360--5308397 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5308350 TAATAATAAT
5308360 AATAATAATAATAGGCTA
1 AATAATAATAATAGGCTA
5308378 AATAATAA-AA-AGGGCTA
1 AATAATAATAATA-GGCTA
5308395 AAT
1 AAT
5308398 TGAAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.05
17 10 0.53
18 8 0.42
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24
Consensus pattern (18 bp):
AATAATAATAATAGGCTA
Found at i:5312021 original size:67 final size:67
Alignment explanation
Indices: 5311913--5312041 Score: 240
Period size: 67 Copynumber: 1.9 Consensus size: 67
5311903 TCAAATTCAG
*
5311913 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGTTAAATCCCCTACA
1 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTACA
5311978 AA
66 AA
*
5311980 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACTAGTCCAGGCTAAATCCCCT
1 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCT
5312042 GTAATATAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (67 bp):
AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTACA
AA
Found at i:5312257 original size:57 final size:60
Alignment explanation
Indices: 5312164--5312311 Score: 198
Period size: 57 Copynumber: 2.5 Consensus size: 60
5312154 ACCCTAATTC
* * *
5312164 GGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTC-GAGAGGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCAG-GAGGGCTATATCGATA
5312222 -GATCACCCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCAGGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCAGGAGGGCTATATC--GATA
5312283 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTTT
5312312 ACCGTCAATT
Statistics
Matches: 79, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
56 6 0.08
57 43 0.54
58 1 0.01
60 1 0.01
61 1 0.01
62 21 0.27
63 6 0.08
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCAGGAGGGCTATATCGATA
Found at i:5315176 original size:30 final size:31
Alignment explanation
Indices: 5315119--5315182 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
5315109 AATATTACTT
* *
5315119 TTATTATTATCATATAATATTATTAATA-AA
1 TTATTATTATAATATAATATTAATAATATAA
*
5315149 TTATTATTATAATGTCAAT-TTAATAATATAA
1 TTATTATTATAATAT-AATATTAATAATATAA
5315180 TTA
1 TTA
5315183 ATAATAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (31 bp):
TTATTATTATAATATAATATTAATAATATAA
Found at i:5319895 original size:11 final size:11
Alignment explanation
Indices: 5319879--5319906 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5319869 GTCGCCTCTT
5319879 CCTTCGTTCTA
1 CCTTCGTTCTA
5319890 CCTTCGTTCTA
1 CCTTCGTTCTA
5319901 CCTTCG
1 CCTTCG
5319907 CCTCTCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.39, G:0.11, T:0.43
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:5323423 original size:18 final size:18
Alignment explanation
Indices: 5323395--5323445 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
5323385 ATTATTAAGA
5323395 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
5323412 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
*
5323428 A-TTTAATAATAATTATAT
1 ATTTTAATTA-AATTATAT
5323446 TAATTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 7 0.24
16 7 0.24
17 5 0.17
18 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:5323498 original size:120 final size:120
Alignment explanation
Indices: 5323345--5323563 Score: 429
Period size: 120 Copynumber: 1.8 Consensus size: 120
5323335 TTGGTCCAAT
*
5323345 TCATATATTATGATTTGAGTCAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
1 TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
5323410 ATATTTTAATTAAAATATATTTAATAATAATTATATTAATTTATATTTTACAGTA
66 ATATTTTAATTAAAATATATTTAATAATAATTATATTAATTTATATTTTACAGTA
5323465 TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
1 TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
5323530 ATATTTTAATTAAAATATATTTAATAATAATTAT
66 ATATTTTAATTAAAATATATTTAATAATAATTAT
5323564 GTTTAAATAT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 98 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (120 bp):
TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
ATATTTTAATTAAAATATATTTAATAATAATTATATTAATTTATATTTTACAGTA
Found at i:5323543 original size:18 final size:17
Alignment explanation
Indices: 5323515--5323549 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5323505 ATTATTAAGA
*
5323515 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
5323532 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
5323550 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:5323779 original size:44 final size:45
Alignment explanation
Indices: 5323714--5323804 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
5323704 ACCTCTATTC
* * *
5323714 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
5323758 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
5323803 CA
1 CA
5323805 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:5323806 original size:16 final size:16
Alignment explanation
Indices: 5323785--5323853 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
5323775 GATTAGCTAT
5323785 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5323801 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
5323818 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
5323834 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
5323850 TACA
1 TACA
5323854 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:5323827 original size:33 final size:32
Alignment explanation
Indices: 5323785--5323853 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
5323775 GATTAGCTAT
5323785 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
5323818 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
5323850 TACA
1 TACA
5323854 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:5325571 original size:20 final size:20
Alignment explanation
Indices: 5325530--5325571 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
5325520 TCTCTTAAAA
* *
5325530 TTTTTGTGTTAAAAGCATTT
1 TTTTTGTGTTAAAAACACTT
5325550 TTTTTGTCG-TAAAAACACTT
1 TTTTTGT-GTTAAAAACACTT
5325570 TT
1 TT
5325572 GAGAAACACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (20 bp):
TTTTTGTGTTAAAAACACTT
Found at i:5326830 original size:12 final size:12
Alignment explanation
Indices: 5326815--5326844 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5326805 GTGTACCTCC
5326815 TTTTCCTTTTTA
1 TTTTCCTTTTTA
*
5326827 TTTTCTTTTTTA
1 TTTTCCTTTTTA
5326839 TTTTCC
1 TTTTCC
5326845 CTCCTCTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCCTTTTTA
Found at i:5355427 original size:778 final size:777
Alignment explanation
Indices: 5353934--5355492 Score: 2956
Period size: 778 Copynumber: 2.0 Consensus size: 777
5353924 GGTGGTGTTG
5353934 AAGACAAGGCAAGTAATGGACTGATGTTTGTGGATATCATCGTGGCAGACAAGAAATTGAATGCC
1 AAGACAAGGCAAGTAATGGACTGATGTTTGTGGATATCATCGTGGCAGACAAGAAATTGAATGCC
* * *
5353999 CTTGTTGATACTGGCGCATCCGATTTGTTCATATCTAAAGAGTTGGCAAATGAACTCGGTCTGAA
66 CTTGTTGATACTGGCGCATCCGATTTGGTCATATCTAAAGAGATGGCAAAGGAACTCGGTCTGAA
5354064 AGTGGAAGAAGATGCGGGTCGACTCAAAACGGTAAACTCAGAAAGTATTCCCATAACAGGTGTGG
131 AGTGGAAGAAGATGCGGGTCGACTCAAAACGGTAAACTCAGAAAGTATTCCCATAACAGGTGTGG
*
5354129 CTAAAGGGGTGAACTCAAACTTGGCGAGTGGACAGGCAATGCAACCATTAAGGTAATCCCACTTG
196 CTAAAGGGGTGAACTCAAACTTGGCGAGTAGACAGGCAATGCAACCATTAAGGTAATCCCACTTG
5354194 ATGATTATGATTTTGTGGTAGGATTGAGTTTGCTTGACCGACTTAATGCGGATATTCACTCTTCC
261 ATGATTATGATTTTGTGGTAGGATTGAGTTTGCTTGACCGACTTAATGCGGATATTCACTCTTCC
5354259 GAGAATTACATGACGATCTCTGATTCGAACCATCGATATATGGTGCGAATGAAAAGAAAGGGAAA
326 GAGAATTACATGACGATCTCTGATTCGAACCATCGATATATGGTGCGAATGAAAAGAAAGGGAAA
*
5354324 CATGGAAGGCAAAACATTGTCGGCAATCCAATTTGCCAAAAGAGTACGTAGAAACGAAGTCTTCT
391 CATGGAAGGCAAAACATTGTCGGCAATCCAATTTGCCAAAAGAGTACGTAGAAACGAAGTCTCCT
*
5354389 ATTTAGCCACCTTAAGGGACAATGTGGAGGAGAAATTTGAGGGGGAAATTCCAAAGGAAGTGAAG
456 ATTTAGCCACCTTAAGGGACAATGTGGAGGAGAAATTCGAGGGGGAAATTCCAAAGGAAGTGAAG
*
5354454 CAGCTGTTGCAGTCTTTTCAAGATGTAATGCCCACGGAGTTGCCCAAGACATTGTCACCAAAGAG
521 CAGCTGTTGCAGTCTTTTCAAGATGTAATGCCCACGGAGTTGCCCAAGACATTGCCACCAAAGAG
*
5354519 GGAGGTGGATCACAAGATTGAGTTGTTGCCTAATACTGAGCCGCCAGCAAGGGCACCATATTGAA
586 GGAGGTGGATCACAAGATTGAGTTGTTGCCTAATACTGAGCCGCCAGCAAGGGCACCATATCGAA
* * *
5354584 TGTCCCTGCCTGAGTTGGAGGAATTGTGGAAGCAGTTAAGGGAACTTCTAGATGCCGGGTTCATT
651 TGTCCCCGCCTGAGTTGGAGAAATTGCGGAAGCAGTTAAGGGAACTTCTAGATGCCGGGTTCATT
* *
5354649 AAACCTTCCAAAGCCCCATTTGGTGCGCCAGTGTTATTCTAAAGGAAGCATGATGGGTCCTT
716 AAACCTTCAAAAGCCCCATTTGGTGCGCCAGTGTTATTCCAAAGGAAGCATGATGGGTCCTT
*
5354711 AAGACAAGGCAAGTAATGGACTGATGTTTGTGGATATCATTGTGGCAGACAAGAAATTGAATGCC
1 AAGACAAGGCAAGTAATGGACTGATGTTTGTGGATATCATCGTGGCAGACAAGAAATTGAATGCC
5354776 CTTGTTGATACTGGCGCATCCGATTTGGTCATATCTAAAGAGATGGCAAAGGAACTCGGTCTGAA
66 CTTGTTGATACTGGCGCATCCGATTTGGTCATATCTAAAGAGATGGCAAAGGAACTCGGTCTGAA
* *
5354841 AGTGGAAGAAGATGCGGGTCGACTCAAAACGGTGAACTCAGAAAGTATTCCCATAACGGGTGTGG
131 AGTGGAAGAAGATGCGGGTCGACTCAAAACGGTAAACTCAGAAAGTATTCCCATAACAGGTGTGG
5354906 CTAAAGGGGTGGAACTCAAACTTGGCGAGTAGACAGGCAATGCAACCATTAAGGTAATCCCACTT
196 CTAAAGGGGT-GAACTCAAACTTGGCGAGTAGACAGGCAATGCAACCATTAAGGTAATCCCACTT
5354971 GATGATTATGATTTTGTGGTAGGATTGAGTTTGCTTGACCGACTTAATGCGGATATTCACTCTTC
260 GATGATTATGATTTTGTGGTAGGATTGAGTTTGCTTGACCGACTTAATGCGGATATTCACTCTTC
5355036 CGAGAATTACATGACGATCTCTGATTCGAACCATCGATATATGGTGCGAATGAAAAGAAAGGGAA
325 CGAGAATTACATGACGATCTCTGATTCGAACCATCGATATATGGTGCGAATGAAAAGAAAGGGAA
*
5355101 ACATGGAAGGCAAAACATTGTCGGCAATCCAATTTGCCAAAGGAGTACGTAGAAACGAAGTCTCC
390 ACATGGAAGGCAAAACATTGTCGGCAATCCAATTTGCCAAAAGAGTACGTAGAAACGAAGTCTCC
5355166 TATTTAGCCACCTTAAGGGACAATGTGGAGGAGAAATTCGAGGGGGAAATTCCAAAGGAAGTGAA
455 TATTTAGCCACCTTAAGGGACAATGTGGAGGAGAAATTCGAGGGGGAAATTCCAAAGGAAGTGAA
5355231 GCAGCTGTTGCAGTCTTTTCAAGATGTAATGCCCACGGAGTTGCCCAAGACATTGCCACCAAAGA
520 GCAGCTGTTGCAGTCTTTTCAAGATGTAATGCCCACGGAGTTGCCCAAGACATTGCCACCAAAGA
5355296 GGGAGGTGGATCACAAGATTGAGTTGTTGCCTAATACTGAGCCGCCAGCAAGGGCACCATATCGA
585 GGGAGGTGGATCACAAGATTGAGTTGTTGCCTAATACTGAGCCGCCAGCAAGGGCACCATATCGA
5355361 ATGTCCCCGCCTGAGTTGGAGAAATTGCGGAAGCAGTTAAGGGAACTTCTAGATGCCGGGTTCAT
650 ATGTCCCCGCCTGAGTTGGAGAAATTGCGGAAGCAGTTAAGGGAACTTCTAGATGCCGGGTTCAT
5355426 TAAACCTTCAAAAGCCCCATTTGGTGCGCCAGTGTTATTCCAAAGGAAGCATGATGGGTCCTT
715 TAAACCTTCAAAAGCCCCATTTGGTGCGCCAGTGTTATTCCAAAGGAAGCATGATGGGTCCTT
5355489 AAGA
1 AAGA
5355493 TTGTGCATTG
Statistics
Matches: 764, Mismatches: 17, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
777 199 0.26
778 565 0.74
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (777 bp):
AAGACAAGGCAAGTAATGGACTGATGTTTGTGGATATCATCGTGGCAGACAAGAAATTGAATGCC
CTTGTTGATACTGGCGCATCCGATTTGGTCATATCTAAAGAGATGGCAAAGGAACTCGGTCTGAA
AGTGGAAGAAGATGCGGGTCGACTCAAAACGGTAAACTCAGAAAGTATTCCCATAACAGGTGTGG
CTAAAGGGGTGAACTCAAACTTGGCGAGTAGACAGGCAATGCAACCATTAAGGTAATCCCACTTG
ATGATTATGATTTTGTGGTAGGATTGAGTTTGCTTGACCGACTTAATGCGGATATTCACTCTTCC
GAGAATTACATGACGATCTCTGATTCGAACCATCGATATATGGTGCGAATGAAAAGAAAGGGAAA
CATGGAAGGCAAAACATTGTCGGCAATCCAATTTGCCAAAAGAGTACGTAGAAACGAAGTCTCCT
ATTTAGCCACCTTAAGGGACAATGTGGAGGAGAAATTCGAGGGGGAAATTCCAAAGGAAGTGAAG
CAGCTGTTGCAGTCTTTTCAAGATGTAATGCCCACGGAGTTGCCCAAGACATTGCCACCAAAGAG
GGAGGTGGATCACAAGATTGAGTTGTTGCCTAATACTGAGCCGCCAGCAAGGGCACCATATCGAA
TGTCCCCGCCTGAGTTGGAGAAATTGCGGAAGCAGTTAAGGGAACTTCTAGATGCCGGGTTCATT
AAACCTTCAAAAGCCCCATTTGGTGCGCCAGTGTTATTCCAAAGGAAGCATGATGGGTCCTT
Found at i:5358283 original size:22 final size:21
Alignment explanation
Indices: 5358253--5358310 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
5358243 ATACAATCGT
*
5358253 AGATTTGATATGTAATCTTAG
1 AGATTTGATTTGTAATCTTAG
*
5358274 AAGATATGATTTTGTAATCTTAG
1 -AGATTTGA-TTTGTAATCTTAG
5358297 AGATTTGATTTGTA
1 AGATTTGATTTGTA
5358311 GATACTATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 14 0.44
23 12 0.38
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:5358293 original size:23 final size:22
Alignment explanation
Indices: 5358263--5358307 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
5358253 AGATTTGATA
5358263 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAG-AGATATGATTT
*
5358286 TGTAATCTTAGAGATTTGATTT
1 TGTAATCTTAGAGATATGATTT
5358308 GTAGATACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (22 bp):
TGTAATCTTAGAGATATGATTT
Found at i:5359699 original size:15 final size:15
Alignment explanation
Indices: 5359679--5359711 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5359669 AATTGGACCT
5359679 AAATTTTAAAATCTA
1 AAATTTTAAAATCTA
5359694 AAATTTTAAAATCTA
1 AAATTTTAAAATCTA
5359709 AAA
1 AAA
5359712 AGTAGAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATTTTAAAATCTA
Done.