Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 117 of 344
Found at i:39761259 original size:30 final size:30
Alignment explanation
Indices: 39761225--39761285 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39761215 TCCTTAACTC
39761225 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
39761255 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
39761285 A
1 A
39761286 GGCTCGAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:39765934 original size:15 final size:15
Alignment explanation
Indices: 39765911--39765950 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
39765901 CAAGCCCAGA
39765911 ATAAGGAAATCCAAG
1 ATAAGGAAATCCAAG
* *
39765926 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
39765941 ATAAGGAAAT
1 ATAAGGAAAT
39765951 ACCATTTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:39767554 original size:20 final size:20
Alignment explanation
Indices: 39767508--39767554 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
39767498 AGCTCGTTTC
*
39767508 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
39767528 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
39767548 CAGCTCA
1 CAGCTCA
39767555 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:39772127 original size:47 final size:49
Alignment explanation
Indices: 39772012--39772280 Score: 172
Period size: 46 Copynumber: 5.7 Consensus size: 49
39772002 GGGTAAGGTT
* * * *
39772012 CCGATGCCATGTCCCAGACATGGTCTTACACT-G-TCTCATATCTAAAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCGAAGG
* * * * *
39772059 TCGATGCCATGCCCCAAACATGGTCTTACACTAACTATCATCTCGTA-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCGAAGG
* * * * *
39772107 CCGATG-CATGTCCTAGACAT-GTTTTACACTGGCT-TACGTGTCG-AGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTAT-CATCTCGAAGG
* * * *
39772153 CCAATG-CATTTCCTAGACAT-GTCTTACACTAGC-ACTCATCTC-AATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTA-TCATCTCGAAGG
* ** * * **
39772199 CCAATGCCATGTCCCAGACATGGTCTTACACGGGCTCTC-T-TAGTGTGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCG-AAGG
*
39772247 CCGATG-CAGGTCCCAGACAT-GTCTTACACTAGCT
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCT
39772281 CACAATAACC
Statistics
Matches: 173, Mismatches: 37, Indels: 25
0.74 0.16 0.11
Matches are distributed among these distances:
45 2 0.01
46 71 0.41
47 67 0.39
48 25 0.14
49 8 0.05
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (49 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCGAAGG
Found at i:39789877 original size:14 final size:14
Alignment explanation
Indices: 39789855--39789902 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
39789845 ACCTAAACCG
* *
39789855 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
39789869 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
39789883 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
39789897 ACCATT
1 ACCATT
39789903 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:39790905 original size:21 final size:20
Alignment explanation
Indices: 39790866--39790905 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
39790856 CACTTGACAC
*
39790866 AAGGGCACACGCCCATGTGG
1 AAGGGCACACACCCATGTGG
*
39790886 AAGGGCAACACACCCGTGTG
1 AAGGGC-ACACACCCATGTG
39790906 ACCATTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.30, G:0.33, T:0.10
Consensus pattern (20 bp):
AAGGGCACACACCCATGTGG
Found at i:39802278 original size:40 final size:42
Alignment explanation
Indices: 39802222--39802393 Score: 251
Period size: 42 Copynumber: 4.1 Consensus size: 42
39802212 TCGATATAAT
* *
39802222 ATATATATATCTGGGTTAAATCTCGCAGGCTTCATGCTGGT-
1 ATATATATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTA
*
39802263 A-ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
1 ATATATATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTA
* *
39802304 ATATATATATACGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
1 ATATATATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTA
*
39802346 ATATATATATCCGGGTTAAATCCTGCAGGCTT-AGTGCTGGTA
1 ATATATATATCCGGGTTAAATCCCGCAGGCTTCA-TGCTGGTA
*
39802388 CTATAT
1 ATATAT
39802394 CCGGACTTAG
Statistics
Matches: 120, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
40 36 0.30
41 2 0.02
42 82 0.68
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (42 bp):
ATATATATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTA
Found at i:39806461 original size:21 final size:22
Alignment explanation
Indices: 39806435--39806497 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
39806425 TTGGTATTTG
39806435 GGAATTGGTACGAAATGGTAT-
1 GGAATTGGTACGAAATGGTATA
*
39806456 GGAATTGGTATGAAATGGTATA
1 GGAATTGGTACGAAATGGTATA
* * *
39806478 GTATTTGGTACGAATTGGTA
1 GGAATTGGTACGAAATGGTA
39806498 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 20 0.56
22 16 0.44
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (22 bp):
GGAATTGGTACGAAATGGTATA
Found at i:39808800 original size:16 final size:17
Alignment explanation
Indices: 39808761--39808798 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
39808751 TTTCACTTTC
39808761 TTTTTCTTTGATATTGT
1 TTTTTCTTTGATATTGT
39808778 TTTTTCTTTGATATTGT
1 TTTTTCTTTGATATTGT
39808795 TTTT
1 TTTT
39808799 CTCACAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.05, G:0.11, T:0.74
Consensus pattern (17 bp):
TTTTTCTTTGATATTGT
Found at i:39811016 original size:13 final size:13
Alignment explanation
Indices: 39810984--39811020 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
39810974 AAATTTTGGA
39810984 AATTTTTTTTTTC
1 AATTTTTTTTTTC
*
39810997 AAATTTTTTTTTC
1 AATTTTTTTTTTC
39811010 --TTTTTTTTTTC
1 AATTTTTTTTTTC
39811021 GAACTCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
13 12 0.55
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (13 bp):
AATTTTTTTTTTC
Found at i:39811031 original size:25 final size:24
Alignment explanation
Indices: 39810986--39811033 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
39810976 ATTTTGGAAA
**
39810986 TTTTTTTTTTCAAATTTTTTTTTC
1 TTTTTTTTTTCAAATCCTTTTTTC
*
39811010 TTTTTTTTTTCGAACTCCTTTTTT
1 TTTTTTTTTTC-AAATCCTTTTTT
39811034 TTACGTACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTTTTTTTCAAATCCTTTTTTC
Found at i:39811360 original size:21 final size:21
Alignment explanation
Indices: 39811334--39811396 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
39811324 TTGGTATTTG
39811334 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
39811355 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
39811376 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
39811397 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:39816512 original size:42 final size:42
Alignment explanation
Indices: 39816465--39816596 Score: 214
Period size: 42 Copynumber: 3.2 Consensus size: 42
39816455 GCTCTCGATA
39816465 TAATATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGG
1 TAATATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGG
39816507 T-A-ATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGG
1 TAATATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGG
* * *
39816547 TAATATATATATCCGGGTTAAATCCCGCATGCTTAGTGCTGG
1 TAATATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGG
*
39816589 TACTATAT
1 TAATATAT
39816597 CCAGACTTAG
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
40 39 0.46
41 2 0.02
42 43 0.51
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (42 bp):
TAATATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGG
Found at i:39816513 original size:40 final size:40
Alignment explanation
Indices: 39816469--39816596 Score: 202
Period size: 40 Copynumber: 3.1 Consensus size: 40
39816459 TCGATATAAT
39816469 ATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGTA
1 ATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGTA
39816509 ATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGTAA
1 ATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGT-A
* * *
39816550 TATATATATCCGGGTTAAATCCCGCATGCTTAGTGCTGGTA
1 -ATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGTA
*
39816591 CTATAT
1 ATATAT
39816597 CCAGACTTAG
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
40 44 0.54
41 2 0.02
42 36 0.44
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (40 bp):
ATATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGTA
Found at i:39817518 original size:18 final size:17
Alignment explanation
Indices: 39817488--39817548 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
39817478 AAGAATCTGT
39817488 AGAAAAAGCAAAAGAAAA
1 AGAAAAAG-AAAAGAAAA
*
39817506 AGAACAAGAAAA-AAAGA
1 AGAAAAAGAAAAGAAA-A
* *
39817523 TTGAAAAAGAAAAAAGAAA
1 -AGAAAAAGAAAAGA-AAA
39817542 AGAAAAA
1 AGAAAAA
39817549 CGAGAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 3 0.09
17 5 0.14
18 23 0.66
19 2 0.06
20 2 0.06
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (17 bp):
AGAAAAAGAAAAGAAAA
Found at i:39817529 original size:36 final size:37
Alignment explanation
Indices: 39817489--39817559 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
39817479 AGAATCTGTA
* *
39817489 GAAAAAG-CAAAAGAAAAAGAACAA-GAAAAAAAGATT
1 GAAAAAGAAAAAAG-AAAAGAAAAACGAAAAAAAGATT
*
39817525 GAAAAAGAAAAAAGAAAAGAAAAACGAGAAAAAGA
1 GAAAAAGAAAAAAGAAAAGAAAAACGAAAAAAAGA
39817560 AAGGAAGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 16 0.53
37 14 0.47
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.03
Consensus pattern (37 bp):
GAAAAAGAAAAAAGAAAAGAAAAACGAAAAAAAGATT
Found at i:39817574 original size:21 final size:20
Alignment explanation
Indices: 39817525--39817561 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39817515 AAAAAAGATT
39817525 GAAAAA-GA-AAAAAGAAAA
1 GAAAAACGAGAAAAAGAAAA
39817543 GAAAAACGAGAAAAAGAAA
1 GAAAAACGAGAAAAAGAAA
39817562 GGAAGAAGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (20 bp):
GAAAAACGAGAAAAAGAAAA
Found at i:39822412 original size:27 final size:26
Alignment explanation
Indices: 39822377--39822478 Score: 123
Period size: 27 Copynumber: 3.8 Consensus size: 26
39822367 AGCATGGATG
* *
39822377 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
39822403 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
* *
39822431 CTAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
*
39822458 CCAGATCAGATAATTGTGGCA
1 CCAGAACAGATAA-TGTGGCA
39822479 AGTCCAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.09
27 43 0.66
28 16 0.25
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:39823173 original size:24 final size:24
Alignment explanation
Indices: 39823146--39823192 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
39823136 CTAGATTTCC
**
39823146 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
39823170 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
39823193 CTCCTGACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.02, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:39839354 original size:17 final size:19
Alignment explanation
Indices: 39839325--39839359 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39839315 GATCTTTCTC
39839325 ACGCTTCTACCT-CTCAGT
1 ACGCTTCTACCTCCTCAGT
39839343 ACGCTT-TACCTCCTCAG
1 ACGCTTCTACCTCCTCAG
39839360 CTATCTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.17, C:0.40, G:0.11, T:0.31
Consensus pattern (19 bp):
ACGCTTCTACCTCCTCAGT
Found at i:39840304 original size:11 final size:10
Alignment explanation
Indices: 39840284--39840318 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
39840274 AGTACAGACA
39840284 AATAATTCAG
1 AATAATTCAG
39840294 AATATATTCAG
1 AATA-ATTCAG
*
39840305 AAAAATTCAG
1 AATAATTCAG
39840315 AATA
1 AATA
39840319 CTTACAGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.29
Consensus pattern (10 bp):
AATAATTCAG
Found at i:39841406 original size:27 final size:27
Alignment explanation
Indices: 39841373--39841476 Score: 124
Period size: 27 Copynumber: 3.9 Consensus size: 27
39841363 GCTGCCAGAA
* *
39841373 AGATAATGTGACAGAGTCACCAGATAC
1 AGATAATGTGGCAGAGCCACCAGATAC
39841400 AGATAATCGTGGCAGAGCCACCAGA-AC
1 AGATAAT-GTGGCAGAGCCACCAGATAC
*
39841427 AGAAATATGTGGCAGAGCCACCAGAT-C
1 AGATA-ATGTGGCAGAGCCACCAGATAC
*
39841454 AGATAAT-TGTGCATAGCCACCAG
1 AGATAATGTG-GCAGAGCCACCAG
39841477 GACGCTTCCT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
25 2 0.03
26 14 0.21
27 35 0.51
28 17 0.25
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (27 bp):
AGATAATGTGGCAGAGCCACCAGATAC
Found at i:39842897 original size:24 final size:24
Alignment explanation
Indices: 39842870--39842940 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
39842860 CTAGATTTCC
**
39842870 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
39842894 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
39842918 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
39842941 CTCCTGACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.38, G:0.01, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:39845684 original size:43 final size:43
Alignment explanation
Indices: 39845636--39845746 Score: 109
Period size: 43 Copynumber: 2.6 Consensus size: 43
39845626 TCCTAGATAT
* *
39845636 GGTCTTACATGTTATCACATATCGATGCCACTGTCCCATACAA
1 GGTCTTACATGTTATCACATATCGATGCCAATGTCCCAGACAA
* ** * * * *
39845679 GGTCTTACACGAAATCA-AAATACAATGCCAATGTCCTAGACAT
1 GGTCTTACATGTTATCACATAT-CGATGCCAATGTCCCAGACAA
39845722 GGTCTTACAT-TTAATCACATATCGA
1 GGTCTTACATGTT-ATCACATATCGA
39845747 GTCGATGCCA
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
42 3 0.06
43 45 0.88
44 3 0.06
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (43 bp):
GGTCTTACATGTTATCACATATCGATGCCAATGTCCCAGACAA
Found at i:39845775 original size:47 final size:49
Alignment explanation
Indices: 39845703--39845924 Score: 163
Period size: 50 Copynumber: 4.6 Consensus size: 49
39845693 TCAAAATACA
* * * *
39845703 ATGCCAATGTCCTAGACATGGTCTTACATTTAATCAC-ATATCGA-GTCG
1 ATGCC-ATGTCCCAGACATGGTCTTACACTGAATCACTATATCGAGGCCG
* * *
39845751 ATGCCATGTCCCAGACATGATCTTACACTGACTCTCTTATATCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGAATCAC-TATATCGAGGCCG
* * * ** * * * *
39845801 ATGCTATATCCCAGACATGGTCTTACACCGGCTCTCCTCTTTTCGTA--CTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGAATC-ACT-ATATCG-AGGCCG
* *
39845851 ATGCAATGTCCCAGACATGGTCTTACACTG-A-CAC-ATATC-AAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGAATCACTATATCGAGGCCG
* *
39845896 AGGCCATGTCCTAGACATGGTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
39845925 AGCTCACATG
Statistics
Matches: 139, Mismatches: 27, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
43 1 0.01
45 31 0.22
47 26 0.19
48 6 0.04
49 7 0.05
50 62 0.45
51 5 0.04
52 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGAATCACTATATCGAGGCCG
Found at i:39848860 original size:44 final size:44
Alignment explanation
Indices: 39848795--39848881 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
39848785 TTGATATCTC
* * *
39848795 AAAGTCCATGGTTGTACCATGGTAATTAAGGAAGAATTGACAGA
1 AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATTGACAGA
* *
39848839 AAAGTCCAT-GTTCATAACATGGCATTTAAGGAGGAATTGACAG
1 AAAGTCCATGGTT-ATAACATGGCAATTAAGGAAGAATTGACAG
39848882 TTAAGGATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
43 3 0.08
44 34 0.92
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (44 bp):
AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATTGACAGA
Found at i:39849069 original size:47 final size:47
Alignment explanation
Indices: 39849018--39849138 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
39849008 GCATTGGCAA
*
39849018 AAGACAAGGATACCATGTAAGACCATGTTTGGAACATTGCATTTGGT
1 AAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGT
* *
39849065 AAGACAAGGATACCACGTAAGATCATGTTTGGAACATGGCATTTGGT
1 AAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGT
* **
39849112 AAGATAAGGATTTCATGTAAGACCATG
1 AAGACAAGGATACCATGTAAGACCATG
39849139 CCGAGGCATG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (47 bp):
AAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGT
Found at i:39849246 original size:55 final size:54
Alignment explanation
Indices: 39849125--39849310 Score: 207
Period size: 55 Copynumber: 3.4 Consensus size: 54
39849115 ATAAGGATTT
* * * * * *
39849125 CATGTAAGACCATGCCGAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAAT
1 CATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGCAAGGATAC
*
39849179 CATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGG-TCC
1 CATGTAAGACCATGTCAAGACATGGCATTGATGAGTT-CTATAAGGC-AAGGATAC
* * *
39849234 CATGTAAGACCATG-CTAAGGCATGGTATTGGTGAGTTC-ATAAGGCAAGGATAC
1 CATGTAAGACCATGTC-AAGACATGGCATTGATGAGTTCTATAAGGCAAGGATAC
** *
39849287 CACATAAGATCATGTCAAGACATG
1 CATGTAAGACCATGTCAAGACATG
39849311 ACAATGGTAA
Statistics
Matches: 112, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
52 4 0.04
53 27 0.24
54 36 0.32
55 41 0.37
56 4 0.04
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (54 bp):
CATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGCAAGGATAC
Found at i:39852018 original size:16 final size:17
Alignment explanation
Indices: 39851986--39852018 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39851976 TTGACAATAA
39851986 GATCTGTATGATGTTAAT
1 GATCTGTAT-ATGTTAAT
39852004 GATCTGTAT-TGTTAA
1 GATCTGTATATGTTAA
39852019 CTATTGCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.45
Consensus pattern (17 bp):
GATCTGTATATGTTAAT
Found at i:39852983 original size:37 final size:37
Alignment explanation
Indices: 39852942--39853014 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
39852932 CCAAGTTGTC
39852942 TGATTGTTAAGGTCCTCATTGTATGAAGTTTAGTTTT
1 TGATTGTTAAGGTCCTCATTGTATGAAGTTTAGTTTT
*
39852979 TGATTGTTAAGGTTCTCATTGTATGAAGTTTAGTTT
1 TGATTGTTAAGGTCCTCATTGTATGAAGTTTAGTTT
39853015 GGCTTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.49
Consensus pattern (37 bp):
TGATTGTTAAGGTCCTCATTGTATGAAGTTTAGTTTT
Found at i:39855537 original size:44 final size:44
Alignment explanation
Indices: 39855472--39855556 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
39855462 TTGATATCTC
* *
39855472 AAATTCCATGGTTGTACCATGGCAATTAAGG-GAGAATTGACGGA
1 AAATTCCATGGTTATAACATGGCAATTAAGGAG-GAATTGACGGA
*
39855516 AAATTCCAT-GTTCATAACATGGCATTTAAGGAGGAATTGAC
1 AAATTCCATGGTT-ATAACATGGCAATTAAGGAGGAATTGAC
39855557 TGTTAAGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 3 0.08
44 32 0.89
45 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (44 bp):
AAATTCCATGGTTATAACATGGCAATTAAGGAGGAATTGACGGA
Found at i:39855679 original size:47 final size:46
Alignment explanation
Indices: 39855560--39855769 Score: 169
Period size: 47 Copynumber: 4.5 Consensus size: 46
39855550 AATTGACTGT
* *
39855560 TAAGGATGCCATGTAAGACCATGTCAAGACATGGCATCGGTA-AGGA
1 TAAGGATACCATGTAAGACCATGTCAAGACATGGCATCGGCATA-GA
** *
39855606 -AAGGAT-CTTGTGTAAGACCATGTCAAGACATGGCATCGGCATTGA
1 TAAGGATAC-CATGTAAGACCATGTCAAGACATGGCATCGGCATAGA
** ** *
39855651 TTAAGGACT-CCATGTAAGACCACATCAAGATGTGGCATTGGCATAAGA
1 -TAAGGA-TACCATGTAAGACCATGTCAAGACATGGCATCGGCAT-AGA
* *** **
39855699 CAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGC-TAAGA
1 TAAGGATACCATGTAAGACCATGTCAAG-ACATGGCATCGGCAT-AGA
*
39855746 CAAGGATACCATGTAAGACCATGT
1 TAAGGATACCATGTAAGACCATGT
39855770 TTGGAACATG
Statistics
Matches: 135, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
44 1 0.01
45 38 0.28
46 1 0.01
47 81 0.60
48 14 0.10
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (46 bp):
TAAGGATACCATGTAAGACCATGTCAAGACATGGCATCGGCATAGA
Found at i:39855770 original size:47 final size:47
Alignment explanation
Indices: 39855683--39855815 Score: 203
Period size: 47 Copynumber: 2.8 Consensus size: 47
39855673 CATCAAGATG
*
39855683 TGGCATTGGCATAAGACAAGGATACCATGTAAGACCATGTTTGGAACA
1 TGGCATTTGC-TAAGACAAGGATACCATGTAAGACCATGTTTGGAACA
39855731 TGGCATTTGCTAAGACAAGGATACCATGTAAGACCATGTTTGGAACA
1 TGGCATTTGCTAAGACAAGGATACCATGTAAGACCATGTTTGGAACA
* * * * *
39855778 TGGCATTTGGTAAGATAATGATATCATGTAAGGCCATG
1 TGGCATTTGCTAAGACAAGGATACCATGTAAGACCATG
39855816 CCAAGGCAGG
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 70 0.89
48 9 0.11
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (47 bp):
TGGCATTTGCTAAGACAAGGATACCATGTAAGACCATGTTTGGAACA
Found at i:39855977 original size:53 final size:54
Alignment explanation
Indices: 39855797--39856001 Score: 162
Period size: 53 Copynumber: 3.8 Consensus size: 54
39855787 GTAAGATAAT
* * * * *
39855797 GATATCATGTAAGGCCATGCCAAGGCAGGGCATTGATAAATTCTATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAG
* *** *** * * *
39855851 GAAATTGTGTAAGACCACATCAAGACATGGCATTGATGAGTTACTATAAGACAAAT
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTATAAGGC-AAG
* * * *
39855907 G-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAG
* * * * *
39855959 GATACCACGTAAGACCATGTCAAGACATGACAATGGTAAGTTC
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTC
39856002 AAAAAGGAAA
Statistics
Matches: 116, Mismatches: 32, Indels: 7
0.75 0.21 0.05
Matches are distributed among these distances:
52 3 0.03
53 40 0.34
54 32 0.28
55 38 0.33
56 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAG
Found at i:39864367 original size:67 final size:67
Alignment explanation
Indices: 39864259--39864395 Score: 238
Period size: 67 Copynumber: 2.0 Consensus size: 67
39864249 CTATTTGAAT
* **
39864259 TCATAGGATACGAGTGACTTGTGACTAGGGTTTTCGATTTGGTCGAGCTCCTGCATTTGTTGCGG
1 TCATAGGATACGAGTGACTTGTCACTAGGGTTACCGATTTGGTCGAGCTCCTGCATTTGTTGCGG
39864324 AC
66 AC
*
39864326 TCATAGGATACGAGTGACTTGTCACTAGGGTTACCGATTTGGTTGAGCTCCTGCATTTGTTGCGG
1 TCATAGGATACGAGTGACTTGTCACTAGGGTTACCGATTTGGTCGAGCTCCTGCATTTGTTGCGG
39864391 AC
66 AC
39864393 TCA
1 TCA
39864396 CCACAGCTCA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (67 bp):
TCATAGGATACGAGTGACTTGTCACTAGGGTTACCGATTTGGTCGAGCTCCTGCATTTGTTGCGG
AC
Found at i:39864522 original size:23 final size:23
Alignment explanation
Indices: 39864459--39864533 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
39864449 CAGCTAATTG
* *
39864459 GAGCTCACCGTTTTAGCTCG-TA
1 GAGCTTACCGTTTCAGCTCGATA
* *
39864481 TGATCTTACTG-TTCAGCTCGATA
1 -GAGCTTACCGTTTCAGCTCGATA
*
39864504 GAGCTTACCGTTTCAGCTCAATA
1 GAGCTTACCGTTTCAGCTCGATA
39864527 GAGCTTA
1 GAGCTTA
39864534 TTGATCATCA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 16 0.37
23 27 0.63
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCGATA
Found at i:39871542 original size:40 final size:40
Alignment explanation
Indices: 39871396--39871579 Score: 193
Period size: 40 Copynumber: 4.6 Consensus size: 40
39871386 ACTCGATATC
* * * *
39871396 TCGCACACTAAGTGCCAATACATAGTCGAAGCTATTATAATT
1 TCGCACACTAAGTGCC-ATATATAGCCGAAGCTA-TCTAAGT
* *
39871438 TCGCACACTAAGTGCCTTACATAGCCGAAGCTATCTAAGT
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTAAGT
39871478 CTCGCACACCT---TGCCATATATAGCCGAAGCTATTCTGAA-T
1 -TCGCACA-CTAAGTGCCATATATAGCCGAAGCTA-TCT-AAGT
39871518 T-GCACACTAAGTGCCATATATAGCCGAAGCTATCTCGAA--
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCT--AAGT
39871557 TCGCACACTAAGTGCCATATATA
1 TCGCACACTAAGTGCCATATATA
39871580 TATCTGAATC
Statistics
Matches: 127, Mismatches: 6, Indels: 20
0.83 0.04 0.13
Matches are distributed among these distances:
37 2 0.02
38 5 0.04
39 24 0.19
40 54 0.43
41 24 0.19
42 18 0.14
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTAAGT
Found at i:39871779 original size:21 final size:22
Alignment explanation
Indices: 39871753--39871793 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
39871743 ATCCTAATCC
*
39871753 GAATTCTGTTTTT-CTTGATTT
1 GAATTCTATTTTTGCTTGATTT
39871774 GAATTCTATTTTTGCTTGAT
1 GAATTCTATTTTTGCTTGAT
39871794 CTAAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.59
Consensus pattern (22 bp):
GAATTCTATTTTTGCTTGATTT
Found at i:39878226 original size:25 final size:25
Alignment explanation
Indices: 39878198--39878246 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39878188 TTATAATATG
* * *
39878198 AAAAATGACTGTTTTGCCCCTAGGT
1 AAAAATGACCGTTATACCCCTAGGT
39878223 AAAAATGACCGTTATACCCCTAGG
1 AAAAATGACCGTTATACCCCTAGG
39878247 GTTTAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (25 bp):
AAAAATGACCGTTATACCCCTAGGT
Found at i:39878319 original size:20 final size:21
Alignment explanation
Indices: 39878283--39878330 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
39878273 ATTTTGATAT
*
39878283 ACATGATGTGATATGATATGC
1 ACATGATATGATATGATATGC
39878304 ACATGATATG-TATGATATGC
1 ACATGATATGATATGATATGC
*
39878324 GCATGAT
1 ACATGAT
39878331 GTATTCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (21 bp):
ACATGATATGATATGATATGC
Found at i:39878407 original size:26 final size:25
Alignment explanation
Indices: 39878378--39878445 Score: 91
Period size: 26 Copynumber: 2.7 Consensus size: 25
39878368 GAGAAAGTGC
* *
39878378 AAAAGGGATATGCCCCAATTTACCGA
1 AAAAGGGCTTTGCCCCAATTTACC-A
* *
39878404 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAATTTACCA
39878429 AAAAGGGCTTTGCCCCA
1 AAAAGGGCTTTGCCCCA
39878446 GTTATTATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
25 18 0.47
26 20 0.53
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAATTTACCA
Found at i:39878446 original size:25 final size:26
Alignment explanation
Indices: 39878378--39878448 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 26
39878368 GAGAAAGTGC
* * *
39878378 AAAAGGGATATGCCCCAATTTACCGA
1 AAAAGGGCTTTGCCCCAGTTTACCGA
*
39878404 AAAAGGGCTTTGCCCCAGTTTATC-A
1 AAAAGGGCTTTGCCCCAGTTTACCGA
39878429 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
39878449 ATTATAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 21 0.51
26 20 0.49
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (26 bp):
AAAAGGGCTTTGCCCCAGTTTACCGA
Found at i:39878707 original size:31 final size:29
Alignment explanation
Indices: 39878669--39878752 Score: 109
Period size: 29 Copynumber: 2.8 Consensus size: 29
39878659 CGTTTACAGT
*
39878669 AAAGGCTTCAGCCCAGTGATATGATTT-ATG
1 AAAGGCTTCGGCCCAGT-ATATG-TTTAATG
39878699 AAAAGGCTTCGGCCCAGTA-ATCGTTTAATG
1 -AAAGGCTTCGGCCCAGTATAT-GTTTAATG
39878729 AAAGGCTTCGGCCCAGTATATGTT
1 AAAGGCTTCGGCCCAGTATATGTT
39878753 GAGATTGATT
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
29 26 0.53
30 7 0.14
31 16 0.33
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (29 bp):
AAAGGCTTCGGCCCAGTATATGTTTAATG
Found at i:39885849 original size:11 final size:10
Alignment explanation
Indices: 39885817--39885862 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
39885807 CATGAGATTT
39885817 TGATAT-ACA
1 TGATATGACA
*
39885826 TGATTTGACA
1 TGATATGACA
39885836 TGATATGCACA
1 TGATATG-ACA
*
39885847 TGATATG-TA
1 TGATATGACA
39885856 TGATATG
1 TGATATG
39885863 CGCATGATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 13 0.41
10 9 0.28
11 10 0.31
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (10 bp):
TGATATGACA
Found at i:39885946 original size:25 final size:26
Alignment explanation
Indices: 39885918--39885989 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
39885908 GAGGAAGTGC
* *
39885918 AAAAGGGCTATGCCCTAGTTTACCGAA
1 AAAAGGGCTTTGCCCCAGTTTACC-AA
* *
39885945 AAAAGGTCTTTGCCCCAGTTTATC-A
1 AAAAGGGCTTTGCCCCAGTTTACCAA
39885970 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
39885990 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 20 0.50
27 20 0.50
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTTGCCCCAGTTTACCAA
Found at i:39886002 original size:24 final size:23
Alignment explanation
Indices: 39885944--39886016 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 23
39885934 AGTTTACCGA
39885944 AAAAAGGTCTTTGCCCCAGTTTATC
1 AAAAAGG-CTTTGCCCCAG-TTATC
*
39885969 AAAAAGGGCTTTGCCCCAGTTATT
1 AAAAA-GGCTTTGCCCCAGTTATC
**
39885993 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAA-AGGCTTTGCC-CCAGTTAT
39886017 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 15 0.36
25 25 0.60
26 2 0.05
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (23 bp):
AAAAAGGCTTTGCCCCAGTTATC
Found at i:39886283 original size:29 final size:30
Alignment explanation
Indices: 39886211--39886292 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 30
39886201 CGTTTACAGT
* *
39886211 AAAGGCTTCAGCCCAGTGATATGAATTATGA
1 AAAGGCTTCGGCCCAGT-ATATCAATTATGA
* *
39886242 AAAGGCTTTGGCCCAGTA-ATCATTTAATG-
1 AAAGGCTTCGGCCCAGTATATCAATT-ATGA
39886271 AAAGGCTTCGGCCCAGTATATC
1 AAAGGCTTCGGCCCAGTATATC
39886293 TCGAGACTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 22 0.50
30 7 0.16
31 15 0.34
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTATATCAATTATGA
Found at i:39889173 original size:48 final size:48
Alignment explanation
Indices: 39889099--39889195 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
39889089 AATATAAATG
*
39889099 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
39889147 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATGTGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
39889195 T
1 T
39889196 ATTGTCGCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
Found at i:39889379 original size:37 final size:37
Alignment explanation
Indices: 39889329--39889400 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
39889319 GAAATATATT
*
39889329 CCGGGTAAGACCCGATGGCTACGTGTGGAGATTATGC
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGC
*
39889366 CCGGGTAAGACCCGATGACTACGTGTGGGGATTAT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTAT
39889401 TCGAGCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGC
Found at i:39894372 original size:44 final size:41
Alignment explanation
Indices: 39894316--39894467 Score: 128
Period size: 43 Copynumber: 3.6 Consensus size: 41
39894306 GATTTCGTAC
*
39894316 AAGACCACGTCTGGGACGTTGGCATCAATTTGTGATTTGTGTGT
1 AAGACCACGTCTGGGACGTTGGCATC-ATATGTGA-TT-TGTGT
* * * * *
39894360 AAGACCATGTCTGGGACATTGGCATCGTATATGAGCTTGTGT
1 AAGACCACGTCTGGGACGTTGGCATCATATGTGA-TTTGTGT
* * **
39894402 AAGACC-CTATCTGGGACAG-TGGCATCGAGATGTGATTACATGT
1 AAGACCAC-GTCTGGGAC-GTTGGCATC-ATATGTGATT-TGTGT
39894445 AAGACCACGTCTGGGACGTTGGC
1 AAGACCACGTCTGGGACGTTGGC
39894468 GTTGTACGAG
Statistics
Matches: 85, Mismatches: 17, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
42 28 0.33
43 32 0.38
44 25 0.29
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (41 bp):
AAGACCACGTCTGGGACGTTGGCATCATATGTGATTTGTGT
Found at i:39896776 original size:39 final size:39
Alignment explanation
Indices: 39896682--39896785 Score: 122
Period size: 39 Copynumber: 2.7 Consensus size: 39
39896672 GAGGAATTGT
* **
39896682 ATCCGGGCTTAAAGACCCGCAGGCTATATCTGGAATGTT
1 ATCCGGGCTTAAAGACCCGCAGGCTATATCTAGAATGCC
*
39896721 ATCCGGGCTTAAAGACCCGCAGGCT-TCGTGCTAGAATGCC
1 ATCCGGGCTTAAAGACCCGCAGGCTAT-AT-CTAGAATGCC
* *
39896761 ATCCGGGC-TAGAGACCCCCAGGCTA
1 ATCCGGGCTTAAAGACCCGCAGGCTA
39896786 CGAGCTGGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
38 1 0.02
39 40 0.71
40 15 0.27
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (39 bp):
ATCCGGGCTTAAAGACCCGCAGGCTATATCTAGAATGCC
Found at i:39898825 original size:12 final size:12
Alignment explanation
Indices: 39898808--39898833 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39898798 CATTCCGAAG
39898808 TATATATATACA
1 TATATATATACA
39898820 TATATATATACA
1 TATATATATACA
39898832 TA
1 TA
39898834 AGTATGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:39899346 original size:27 final size:27
Alignment explanation
Indices: 39899315--39899492 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39899305 TAAATTGTAC
39899315 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
39899342 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39899368 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
39899396 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
39899424 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39899451 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39899478 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39899493 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39899429 original size:82 final size:81
Alignment explanation
Indices: 39899316--39899471 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39899306 AAATTGTACA
* *
39899316 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39899380 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
39899397 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39899462 TGCGAGTTGA
65 TGCGAATTGA
39899472 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39899483 original size:82 final size:81
Alignment explanation
Indices: 39899312--39899492 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
39899302 GATTAAATTG
* *
39899312 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39899377 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
39899393 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39899457 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39899475 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39899493 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39914305 original size:27 final size:25
Alignment explanation
Indices: 39914274--39914439 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 25
39914264 TAAATTGTAC
39914274 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACT-AGTGTGCGA-TTGACTATGT
* * *
39914301 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACT-AGTGTGCG-ATTGACTATGT
* *
39914327 ATGCACTAGTGTGCGAATGACCATG-
1 A-GCACTAGTGTGCGATTGACTATGT
* *
39914352 CGCACTAG-GTGCGGTTGACTATGT
1 AGCACTAGTGTGCGATTGACTATGT
*
39914376 AGCA-TAGTGTGCGATTGA-TACGT
1 AGCACTAGTGTGCGATTGACTATGT
*
39914399 AGCACTAAGTGTGCGAGTTGATTAT-T
1 AGCACT-AGTGTGCGA-TTGACTATGT
39914425 AGCACTGAGTGTGCG
1 AGCACT-AGTGTGCG
39914440 GACTCAATAT
Statistics
Matches: 116, Mismatches: 15, Indels: 17
0.78 0.10 0.11
Matches are distributed among these distances:
23 23 0.20
24 20 0.17
25 17 0.15
26 27 0.23
27 28 0.24
28 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.29
Consensus pattern (25 bp):
AGCACTAGTGTGCGATTGACTATGT
Found at i:39914427 original size:26 final size:24
Alignment explanation
Indices: 39914274--39914439 Score: 113
Period size: 26 Copynumber: 6.6 Consensus size: 24
39914264 TAAATTGTAC
39914274 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACT-AGTGTGCGA-TTGACTAT-T
* * * *
39914301 TGCACTAAGTGTGCGAAATGAATATG
1 AGCACT-AGTGTGCG-ATTGACTATT
* * *
39914327 ATGCACTAGTGTGCGAATGACCATG
1 A-GCACTAGTGTGCGATTGACTATT
* *
39914352 CGCACTAG-GTGCGGTTGACTATGT
1 AGCACTAGTGTGCGATTGACTAT-T
*
39914376 AGCA-TAGTGTGCGATTGA-TACGT
1 AGCACTAGTGTGCGATTGACTA-TT
*
39914399 AGCACTAAGTGTGCGAGTTGATTATT
1 AGCACT-AGTGTGCGA-TTGACTATT
39914425 AGCACTGAGTGTGCG
1 AGCACT-AGTGTGCG
39914440 GACTCAATAT
Statistics
Matches: 113, Mismatches: 17, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
23 21 0.19
24 20 0.18
25 17 0.15
26 27 0.24
27 27 0.24
28 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.29
Consensus pattern (24 bp):
AGCACTAGTGTGCGATTGACTATT
Found at i:39921769 original size:12 final size:12
Alignment explanation
Indices: 39921752--39921777 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39921742 CATTCCGAAG
39921752 TATATATATACA
1 TATATATATACA
39921764 TATATATATACA
1 TATATATATACA
39921776 TA
1 TA
39921778 AGTATGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:39922290 original size:27 final size:27
Alignment explanation
Indices: 39922259--39922436 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39922249 TAAATTGTAC
39922259 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
39922286 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39922312 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
39922340 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
39922368 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39922395 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39922422 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39922437 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39922373 original size:82 final size:81
Alignment explanation
Indices: 39922260--39922415 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39922250 AAATTGTACA
* *
39922260 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39922324 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
39922341 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39922406 TGCGAGTTGA
65 TGCGAATTGA
39922416 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39922427 original size:82 final size:81
Alignment explanation
Indices: 39922256--39922436 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
39922246 GATTAAATTG
* *
39922256 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39922321 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
39922337 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39922401 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39922419 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39922437 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39926942 original size:39 final size:40
Alignment explanation
Indices: 39926825--39927008 Score: 252
Period size: 39 Copynumber: 4.7 Consensus size: 40
39926815 GCTCCTCGTT
* *
39926825 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39926865 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39926905 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39926944 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
39926983 CAAATGCCTTC-GGATCTTAGTCCGGA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA
39927009 TATTGTCACT
Statistics
Matches: 133, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
38 2 0.02
39 73 0.55
40 56 0.42
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:39927002 original size:79 final size:80
Alignment explanation
Indices: 39926825--39927008 Score: 250
Period size: 79 Copynumber: 2.3 Consensus size: 80
39926815 GCTCCTCGTT
* *
39926825 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTC-GGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
*
39926889 GATTTAGTAACTCGCA
65 GAATTAGTAACTCGCA
* *
39926905 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGACTTAGCCCGGAATATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCCG
*
39926967 GAATTAGTATCTCGCA
65 GAATTAGTAACTCGCA
*
39926983 CAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGA-CTTAGCCCGGA
39927009 TATTGTCACT
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
78 37 0.40
79 44 0.47
80 12 0.13
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCA
Found at i:39930582 original size:40 final size:40
Alignment explanation
Indices: 39930538--39930799 Score: 310
Period size: 39 Copynumber: 6.7 Consensus size: 40
39930528 GCTCCTCGTT
* *
39930538 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39930578 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
39930618 CAAATGCCTTAGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39930657 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
39930696 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
39930735 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
39930776 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39930800 CATCATTCAA
Statistics
Matches: 200, Mismatches: 14, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 125 0.62
40 62 0.31
41 11 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:39933361 original size:47 final size:47
Alignment explanation
Indices: 39933260--39933363 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 47
39933250 CACAATCGAT
* *
39933260 AAATACCTATACCATAGCCCATAGCCAAATCAAGGTAACTTATCCCA
1 AAATACCTATACCATAGCCCATAGCCAAATCAAGGGAACTCATCCCA
* * * * * * * *
39933307 GAGTACCTATACCGTGGCCCGTAGCCAAATCAAGGGAGCTCCTCTCA
1 AAATACCTATACCATAGCCCATAGCCAAATCAAGGGAACTCATCCCA
39933354 AAATACCTAT
1 AAATACCTAT
39933364 GTTGTAATAT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.21
Consensus pattern (47 bp):
AAATACCTATACCATAGCCCATAGCCAAATCAAGGGAACTCATCCCA
Found at i:39934348 original size:93 final size:93
Alignment explanation
Indices: 39934189--39934359 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
39934179 GGATGGTTGA
* *
39934189 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
39934254 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
39934282 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
*
39934347 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
39934360 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:39934362 original size:46 final size:46
Alignment explanation
Indices: 39934193--39934364 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
39934183 GGTTGAGCAT
* * *
39934193 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * * *
39934239 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
39934284 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
39934332 CCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
39934365 GGGGCGGTGT
Statistics
Matches: 104, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
45 2 0.02
46 59 0.57
47 28 0.27
48 4 0.04
50 3 0.03
51 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:39935854 original size:40 final size:40
Alignment explanation
Indices: 39935754--39935925 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
39935744 GCTCCTCGTT
* * *
39935754 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
39935794 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
39935833 CGAATGCCTTCGGGACTTAACCCAGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
39935873 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
39935913 CAAATGCCTTCGG
1 CAAATGCCTTCGG
39935926 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 35 0.30
40 78 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:39943648 original size:40 final size:40
Alignment explanation
Indices: 39943548--39943719 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
39943538 GCTCCTCGTT
* * *
39943548 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
39943588 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
39943627 CGAATGCCTTCGGGACTTAACCCAGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
39943667 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
39943707 CAAATGCCTTCGG
1 CAAATGCCTTCGG
39943720 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 35 0.30
40 78 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:39947200 original size:29 final size:28
Alignment explanation
Indices: 39947158--39947222 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 28
39947148 TTTTCATTTA
* *
39947158 TTTCACAATTTAACCCCTCAATTTACACT
1 TTTCTCAATTTAACCCCT-AATTGACACT
*
39947187 TTTCTCAATTTAACCCCTAATTGACATT
1 TTTCTCAATTTAACCCCTAATTGACACT
*
39947215 TTTATCAA
1 TTTCTCAA
39947223 AAATAACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.31, C:0.26, G:0.02, T:0.42
Consensus pattern (28 bp):
TTTCTCAATTTAACCCCTAATTGACACT
Found at i:39947222 original size:28 final size:29
Alignment explanation
Indices: 39947163--39947222 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
39947153 ATTTATTTCA
* *
39947163 CAATTTAACCCCTCAATTTACACTTTTCT
1 CAATTTAACCCCTCAATTGACACTTTTAT
*
39947192 CAATTTAACCCCT-AATTGACATTTTTAT
1 CAATTTAACCCCTCAATTGACACTTTTAT
39947220 CAA
1 CAA
39947223 AAATAACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.40
Consensus pattern (29 bp):
CAATTTAACCCCTCAATTGACACTTTTAT
Found at i:39953760 original size:46 final size:44
Alignment explanation
Indices: 39953666--39953779 Score: 153
Period size: 46 Copynumber: 2.6 Consensus size: 44
39953656 CGGCATTTCA
* *
39953666 CCTGCTAGGCTCG--AGGCCCGATATCATTTCACCGGCATTATAG
1 CCTGCTAGGCTCGAAAGGCCCGA-ATAATTTCACCGGCATAATAG
39953709 CCTGCTAGGCTCGAAAGGCCCGAATAATGTCTCACCGGCATAATAG
1 CCTGCTAGGCTCGAAAGGCCCGAATAAT-T-TCACCGGCATAATAG
*
39953755 TCTGCTAGGCTC-AAAGGCCCGAATA
1 CCTGCTAGGCTCGAAAGGCCCGAATA
39953780 TAATACCAGC
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
43 13 0.20
44 4 0.06
45 22 0.34
46 25 0.39
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (44 bp):
CCTGCTAGGCTCGAAAGGCCCGAATAATTTCACCGGCATAATAG
Found at i:39953829 original size:38 final size:38
Alignment explanation
Indices: 39953772--39954008 Score: 366
Period size: 38 Copynumber: 6.2 Consensus size: 38
39953762 GGCTCAAAGG
* * *
39953772 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
39953810 CCCGGATATAATACTAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * *
39953848 CCTGGATATATTACCAGCACGAAGCTTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
39953886 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
39953924 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTGAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * *
39953962 TCCGGATATATTACCAGCACGAAGCCTGCAGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
39954000 CCCGGATAT
1 CCCGGATAT
39954009 CATATTTCGA
Statistics
Matches: 182, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 182 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:39958722 original size:24 final size:24
Alignment explanation
Indices: 39958695--39958796 Score: 159
Period size: 24 Copynumber: 4.2 Consensus size: 24
39958685 AAGGCTGTCA
39958695 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
*
39958719 GGAGATGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
39958743 GGAGAGGATGTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
39958767 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAAGATTTAGGAGCTGATAAG
39958791 GGAGAA
1 GGAGAA
39958797 CGGTGTTGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.34, C:0.04, G:0.41, T:0.21
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:39958794 original size:12 final size:12
Alignment explanation
Indices: 39958707--39958794 Score: 56
Period size: 12 Copynumber: 7.3 Consensus size: 12
39958697 AGAAGATTTA
*
39958707 GGAGCTGATAAG
1 GGAGCTGATTAG
*
39958719 GGAGATGATTTA-
1 GGAGCTGA-TTAG
*
39958731 GGAGCTGATAAG
1 GGAGCTGATTAG
**
39958743 GGAGAGGATGTA-
1 GGAGCTGAT-TAG
*
39958755 GGAGCTGATAAG
1 GGAGCTGATTAG
**
39958767 GGAGAGGATTTA-
1 GGAGCTGA-TTAG
39958779 GGAGCTGATTAG
1 GGAGCTGATTAG
39958791 GGAG
1 GGAG
39958795 AACGGTGTTG
Statistics
Matches: 55, Mismatches: 15, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
11 6 0.11
12 44 0.80
13 5 0.09
ACGTcount: A:0.32, C:0.05, G:0.43, T:0.20
Consensus pattern (12 bp):
GGAGCTGATTAG
Found at i:39960268 original size:27 final size:27
Alignment explanation
Indices: 39960228--39960292 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
39960218 AGGAAGCGTC
39960228 CTGGTGGCTA-TGCCACA-ATTATCTGAT
1 CTGGTGGC-ACTGCCACATA-TATCTGAT
*
39960255 CTGGTGGCACTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACATATATCTGAT
*
39960282 CTGGTGACACT
1 CTGGTGGCACT
39960293 ATCACATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 1 0.03
27 32 0.94
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACATATATCTGAT
Found at i:39960298 original size:27 final size:26
Alignment explanation
Indices: 39960240--39960311 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
39960230 GGTGGCTATG
* * *
39960240 CCACAATTATCTGATCTGGTGGCACTG
1 CCAC-ATTATCTGTTCTGGTGACACTA
39960267 CCACATATATCTGTTCTGGTGACACTA
1 CCACAT-TATCTGTTCTGGTGACACTA
* *
39960294 TCACATTATCTATTCTGG
1 CCACATTATCTGTTCTGG
39960312 CAGCTATGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 13 0.33
27 26 0.67
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.35
Consensus pattern (26 bp):
CCACATTATCTGTTCTGGTGACACTA
Found at i:39967872 original size:27 final size:27
Alignment explanation
Indices: 39967842--39968019 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39967832 ATATTGAGTC
* * * *
39967842 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39967869 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39967896 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39967924 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39967951 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39967978 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39968005 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39968020 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39967981 original size:82 final size:81
Alignment explanation
Indices: 39967863--39968018 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39967853 TGCTATATAA
* *
39967863 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
39967928 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39967945 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
39968009 CACTTAGTGC
65 CACTTAGTGC
39968019 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39969871 original size:24 final size:24
Alignment explanation
Indices: 39969844--39969945 Score: 168
Period size: 24 Copynumber: 4.2 Consensus size: 24
39969834 AAGGCTGTCA
39969844 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
*
39969868 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
39969892 GGAGAGGATGTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
*
39969916 GGAGAAGATTTAGGAGCTGATTAG
1 GGAGAAGATTTAGGAGCTGATAAG
39969940 GGAGAA
1 GGAGAA
39969946 CGGTGTTGGT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.35, C:0.04, G:0.41, T:0.20
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:39971453 original size:27 final size:27
Alignment explanation
Indices: 39971375--39971457 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
39971365 AGGAAGCATC
* **
39971375 CTGGTGGCTATGCCACAATTATCTAAT
1 CTGGTGGCTCTGCCACAATTATCTGTT
*
39971402 CTGGTGGCACTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGTT
39971429 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGTT
39971456 CT
1 CT
39971458 AGTGACACTG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 45 0.92
28 2 0.04
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGTT
Found at i:39971467 original size:54 final size:53
Alignment explanation
Indices: 39971375--39971486 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 53
39971365 AGGAAGCATC
* * *
39971375 CTGGTGGCTATGCCACAATTATCTAATCTGGTGGCACTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTAATCTAGTGACACTGCCACAT-TATCAGTT
* ** *
39971429 CTGGTGGCTCTGCCACAATTATCTGTTCTAGTGACACTGTCACATTATCAGTT
1 CTGGTGGCTATGCCACAATTATCTAATCTAGTGACACTGCCACATTATCAGTT
*
39971482 TTGGT
1 CTGGT
39971487 AGCCATGCTG
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
53 11 0.22
54 39 0.78
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTAATCTAGTGACACTGCCACATTATCAGTT
Found at i:39971472 original size:27 final size:26
Alignment explanation
Indices: 39971375--39971486 Score: 109
Period size: 27 Copynumber: 4.2 Consensus size: 26
39971365 AGGAAGCATC
**
39971375 CTGGTGGCTA-TGCCACAATTATCTAAT
1 CTGGTGGC-ACTGCCAC-ATTATCTGTT
39971402 CTGGTGGCACTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAT-TATCTGTT
*
39971429 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCACTGCCAC-ATTATCTGTT
* * * *
39971456 CTAGTGACACTGTCACATTATCAGTT
1 CTGGTGGCACTGCCACATTATCTGTT
*
39971482 TTGGT
1 CTGGT
39971487 AGCCATGCTG
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 15 0.21
27 55 0.76
28 2 0.03
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (26 bp):
CTGGTGGCACTGCCACATTATCTGTT
Found at i:39980440 original size:18 final size:18
Alignment explanation
Indices: 39980417--39980451 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
39980407 GTTTCAATTT
39980417 CAGAAACTCTTTATGTTC
1 CAGAAACTCTTTATGTTC
39980435 CAGAAACTCTTTATGTT
1 CAGAAACTCTTTATGTT
39980452 TCTGATCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (18 bp):
CAGAAACTCTTTATGTTC
Found at i:39985763 original size:30 final size:30
Alignment explanation
Indices: 39985697--39985765 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
39985687 TTTGTTTCAA
*
39985697 TTTCTTTTTCACTCTCGAATTTCTTTTCGT
1 TTTCTTTTTCAATCTCGAATTTCTTTTCGT
* * *
39985727 TCTCTTTTTCAATCTC-ATTTTCTTTTTCTT
1 TTTCTTTTTCAATCTCGAATTTC-TTTTCGT
39985757 TTTCTTTTT
1 TTTCTTTTT
39985766 GCTTTTCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.09, C:0.22, G:0.03, T:0.67
Consensus pattern (30 bp):
TTTCTTTTTCAATCTCGAATTTCTTTTCGT
Found at i:39985783 original size:12 final size:12
Alignment explanation
Indices: 39985768--39985810 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
39985758 TTCTTTTTGC
39985768 TTTTCAAAGGCT
1 TTTTCAAAGGCT
39985780 TTTTCAAAGGCT
1 TTTTCAAAGGCT
39985792 TTTTCAAAGGCT
1 TTTTCAAAGGCT
39985804 TTTTCAA
1 TTTTCAA
39985811 GTTCTCTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:39985883 original size:20 final size:21
Alignment explanation
Indices: 39985858--39985909 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
39985848 CTCTTGCCTA
39985858 TCTTTTTTTTTATTTTG-TTT
1 TCTTTTTTTTTATTTTGCTTT
*
39985878 TC-TTTTTCTTATTTTGCTTTT
1 TCTTTTTTTTTATTTTGC-TTT
*
39985899 TCTTTTCTTTT
1 TCTTTTTTTTT
39985910 CTCTGTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 13 0.50
20 2 0.08
21 5 0.19
22 6 0.23
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.81
Consensus pattern (21 bp):
TCTTTTTTTTTATTTTGCTTT
Found at i:39985923 original size:21 final size:20
Alignment explanation
Indices: 39985862--39985924 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
39985852 TGCCTATCTT
*
39985862 TTTTTTTATTTTGTTTTCT-
1 TTTTCTTATTTTGTTTTCTC
39985881 TTTTCTTATTTTGCTTTT-TC
1 TTTTCTTATTTTG-TTTTCTC
39985901 TTTTCTT-TTCTCTGTTTTCTC
1 TTTTCTTATT-T-TGTTTTCTC
39985922 TTT
1 TTT
39985925 ACAAGAATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 15 0.39
20 16 0.42
21 7 0.18
ACGTcount: A:0.03, C:0.14, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTCTTATTTTGTTTTCTC
Found at i:39990423 original size:15 final size:16
Alignment explanation
Indices: 39990402--39990441 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
39990392 ATAAAACACC
39990402 TTTTTTTATTTCAAAA
1 TTTTTTTATTTCAAAA
*
39990418 TTTTTTTATTTC-TAA
1 TTTTTTTATTTCAAAA
39990433 TTTTTTTAT
1 TTTTTTTAT
39990442 ATACTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTTATTTCAAAA
Found at i:39997965 original size:56 final size:56
Alignment explanation
Indices: 39997879--39997994 Score: 214
Period size: 56 Copynumber: 2.1 Consensus size: 56
39997869 ACAAAGGGTG
39997879 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
39997935 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGCAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
39997991 ATGG
1 ATGG
39997995 ACAATAAACT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:39999523 original size:39 final size:40
Alignment explanation
Indices: 39999423--39999607 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
39999413 TCGAATGATG
* * *
39999423 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
39999462 ATCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
39999503 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
39999542 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
39999581 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
39999608 AATGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 36 0.29
40 78 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:39999563 original size:79 final size:81
Alignment explanation
Indices: 39999423--39999607 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
39999413 TCGAATGATG
* *
39999423 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCTGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
39999487 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
39999502 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
39999564 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
39999582 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39999608 AATGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:39999629 original size:79 final size:79
Alignment explanation
Indices: 39999476--39999640 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
39999466 GGACTAAGAT
* **
39999476 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
39999541 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
39999555 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
39999618 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
39999634 CCGAAGG
1 CCGAAGG
39999641 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:40006161 original size:56 final size:56
Alignment explanation
Indices: 40006075--40006190 Score: 223
Period size: 56 Copynumber: 2.1 Consensus size: 56
40006065 ACAAAGGGTG
40006075 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
40006131 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40006187 ATGG
1 ATGG
40006191 ACAATAAACT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:40007756 original size:79 final size:81
Alignment explanation
Indices: 40007620--40007804 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
40007610 TCGAATGATG
*
40007620 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
40007684 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
40007699 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
* *
40007761 TTTGTGTGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
40007779 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40007805 AATGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:40007811 original size:40 final size:40
Alignment explanation
Indices: 40007620--40007804 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
40007610 TCGAATGATG
* * * *
40007620 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACTAAA
* * * *
40007660 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGTGAGTTACTAAA
*
40007700 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAA
*
40007739 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTA-AA
*
40007780 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40007805 AATGAGTAGC
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 35 0.28
40 81 0.65
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAA
Found at i:40007826 original size:79 final size:79
Alignment explanation
Indices: 40007673--40007837 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
40007663 GGACTAAGAT
* **
40007673 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
40007738 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * * *
40007752 CCGAAGGCATTTGTGTGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
40007815 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
40007831 CCGAAGG
1 CCGAAGG
40007838 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 24 0.33
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:40013309 original size:20 final size:21
Alignment explanation
Indices: 40013275--40013315 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
40013265 ATGATTTCAT
*
40013275 GAAATTTTTTTTATGTGTTTG
1 GAAATTTTTTATATGTGTTTG
40013296 GAAA-TTTTTATATGTGTTTG
1 GAAATTTTTTATATGTGTTTG
40013316 ATTTAGTCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.59
Consensus pattern (21 bp):
GAAATTTTTTATATGTGTTTG
Found at i:40016896 original size:16 final size:16
Alignment explanation
Indices: 40016877--40016913 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
40016867 GTAAATCGGC
*
40016877 AAAAGCCGAAATGTCG
1 AAAAGCCGAAATGCCG
40016893 AAAAGCCGAAATGCCG
1 AAAAGCCGAAATGCCG
40016909 AAAAG
1 AAAAG
40016914 TCAAAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.19, G:0.24, T:0.08
Consensus pattern (16 bp):
AAAAGCCGAAATGCCG
Found at i:40017213 original size:29 final size:29
Alignment explanation
Indices: 40017131--40017246 Score: 137
Period size: 29 Copynumber: 4.1 Consensus size: 29
40017121 GTGAGCATGA
* *
40017131 ATAT-AATGTGATTTGGGCCAAATGGGCC
1 ATATGAATGTGAATTGGGCCTAATGGGCC
* * *
40017159 ATATAAATGAG-GTTGGGCCTAATGGGCC
1 ATATGAATGTGAATTGGGCCTAATGGGCC
*
40017187 ATATGAATGTGAATTGGGCCTGATGGGCC
1 ATATGAATGTGAATTGGGCCTAATGGGCC
* * *
40017216 ATATGAACGTGAATTGGGCATGATGGGCC
1 ATATGAATGTGAATTGGGCCTAATGGGCC
40017245 AT
1 AT
40017247 CTAAATGAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
28 28 0.36
29 49 0.64
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.27
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTAATGGGCC
Found at i:40020943 original size:26 final size:26
Alignment explanation
Indices: 40020905--40020978 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
40020895 CTCTTTTAGT
40020905 AACTGGGGTAAAAGCCCTTTTTGATA
1 AACTGGGGTAAAAGCCCTTTTTGATA
* * * *
40020931 AATTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGTAAAAGCCCTTTTTGATA
40020957 AACTGGGGTAAAAGCCCTTTTT
1 AACTGGGGTAAAAGCCCTTTTT
40020979 ACACTTCCTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (26 bp):
AACTGGGGTAAAAGCCCTTTTTGATA
Found at i:40022014 original size:25 final size:25
Alignment explanation
Indices: 40021980--40022030 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
40021970 CGCTTTAGAA
40021980 TACGAACACTTACCACAGTCTCTCT
1 TACGAACACTTACCACAGTCTCTCT
40022005 TACGAACACTTACCACAGTCTCTCT
1 TACGAACACTTACCACAGTCTCTCT
40022030 T
1 T
40022031 CTTGAATCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.35, G:0.08, T:0.29
Consensus pattern (25 bp):
TACGAACACTTACCACAGTCTCTCT
Found at i:40024791 original size:93 final size:93
Alignment explanation
Indices: 40024684--40024854 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
40024674 GCCCCTAAGT
* * *
40024684 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTTGCATCCATAAGTGAACTCGGCCTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40024748 ACGAGTTCGGATGCCTAGTTACATTTCAC
65 ACGAGTTCGGATGCCTAGTTACATTTCAC
*
40024777 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40024842 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40024855 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40024849 original size:46 final size:45
Alignment explanation
Indices: 40024679--40024851 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 45
40024669 AACCCGCCCC
* *
40024679 TAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGAC-ATTGCATCCA
* * *
40024725 TAAGTGAACTCGGCCTCAACTCAACGAGTTCGGATGCCTAGTTACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTGCATCCA
* *
40024773 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCA
40024818 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40024852 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 4 0.04
46 58 0.55
47 28 0.27
48 2 0.02
49 1 0.01
50 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCA
Found at i:40025312 original size:30 final size:30
Alignment explanation
Indices: 40025278--40025337 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
40025268 ATTTAATACG
40025278 AACTTTAGAAAAATTACACTTTTGCCCCTA
1 AACTTTAGAAAAATTACACTTTTGCCCCTA
* * * *
40025308 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTAGAAAAATTACACTTTTGCCCCTA
40025338 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTAGAAAAATTACACTTTTGCCCCTA
Found at i:40027217 original size:23 final size:23
Alignment explanation
Indices: 40027155--40027218 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
40027145 TGAAAAAACA
* *
40027155 AAATCAAAAGAAAAAGAAAAGAG
1 AAATAAAAAGAAAAAGGAAAGAG
*
40027178 CAATAAAAAGAAAAAGGAAAGAG
1 AAATAAAAAGAAAAAGGAAAGAG
40027201 AAATAAAAAGAAAAAGGA
1 AAATAAAAAGAAAAAGGA
40027219 GTTTAAGGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.05
Consensus pattern (23 bp):
AAATAAAAAGAAAAAGGAAAGAG
Found at i:40029120 original size:27 final size:27
Alignment explanation
Indices: 40029090--40029267 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40029080 ATATTGAGTC
* * * *
40029090 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40029117 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40029144 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40029172 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40029199 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40029226 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40029253 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40029268 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40029229 original size:82 final size:81
Alignment explanation
Indices: 40029111--40029266 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40029101 TGCTATATAA
* *
40029111 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40029176 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40029193 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40029257 CACTTAGTGC
65 CACTTAGTGC
40029267 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40029281 original size:82 final size:83
Alignment explanation
Indices: 40029090--40029281 Score: 216
Period size: 82 Copynumber: 2.3 Consensus size: 83
40029080 ATATTGAGTC
* * * * *
40029090 CGCACACTCAGTGCTATATAA-TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTA
1 CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
*
40029154 GTGCTACATAGTCAAACT
66 GTGCAACATAGTCAAACT
* * **
40029172 CGCACACTTAGTGCCG--C-ATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACAC
1 CGCACACTTAGTGCTGTACAAT--TCAATTCGCACACTTAGTGCTA-CATAATCAAATCGCACAC
40029233 TTAGTGCAACATAGTCAAA-T
63 TTAGTGCAACATAGTCAAACT
*
40029253 CGCACACTTAGTGCTGTACAATTTAATTC
1 CGCACACTTAGTGCTGTACAATTCAATTC
40029282 CCGCGCACTT
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
79 1 0.01
81 17 0.19
82 70 0.77
83 1 0.01
84 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (83 bp):
CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
GTGCAACATAGTCAAACT
Found at i:40031709 original size:43 final size:43
Alignment explanation
Indices: 40031648--40031731 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
40031638 AAAAAAGTCA
40031648 TTTAATTTGATAAAAGAACGACTCACCAATGCTCCATTATTCC
1 TTTAATTTGATAAAAGAACGACTCACCAATGCTCCATTATTCC
*
40031691 TTTAATTTGATAAAAGAACGACTCACCAATGCTCTATTATT
1 TTTAATTTGATAAAAGAACGACTCACCAATGCTCCATTATT
40031732 AGCTTTACTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.35
Consensus pattern (43 bp):
TTTAATTTGATAAAAGAACGACTCACCAATGCTCCATTATTCC
Found at i:40031744 original size:43 final size:43
Alignment explanation
Indices: 40031648--40031744 Score: 142
Period size: 43 Copynumber: 2.3 Consensus size: 43
40031638 AAAAAAGTCA
*
40031648 TTTAATTTGATAAAAGAACGACTCACCAATGCTCCATTATTCC
1 TTTAACTTGATAAAAGAACGACTCACCAATGCTCCATTATTCC
* * *
40031691 TTTAATTTGATAAAAGAACGACTCACCAATGCTCTATTATTAGC
1 TTTAACTTGATAAAAGAACGACTCACCAATGCTCCATTATT-CC
40031735 TTT-ACTTGAT
1 TTTAACTTGAT
40031745 TTTACTAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
43 46 0.92
44 4 0.08
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (43 bp):
TTTAACTTGATAAAAGAACGACTCACCAATGCTCCATTATTCC
Found at i:40033365 original size:18 final size:18
Alignment explanation
Indices: 40033308--40033366 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
40033298 TAGCCCATTT
*
40033308 CAGTAATAGTAATCAG-A
1 CAGTAACAGTAATCAGTA
* *
40033325 GCAGTAACCA-TGATCAATA
1 -CAGTAA-CAGTAATCAGTA
*
40033344 CAGTAACAGTAATCAGTC
1 CAGTAACAGTAATCAGTA
40033362 CAGTA
1 CAGTA
40033367 TGCAAACAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
17 2 0.06
18 28 0.88
19 2 0.06
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (18 bp):
CAGTAACAGTAATCAGTA
Found at i:40033673 original size:23 final size:23
Alignment explanation
Indices: 40033618--40033673 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
40033608 TATGCCACCC
40033618 CATGCAATGCAACATAATAATATA
1 CATGC-ATGCAACATAATAATATA
*
40033642 CATGGATGCAACATACAT-ATA-A
1 CATGCATGCAACATA-ATAATATA
40033664 CATCGCATGC
1 CAT-GCATGC
40033674 TCAAATATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 4 0.14
23 18 0.64
24 6 0.21
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.23
Consensus pattern (23 bp):
CATGCATGCAACATAATAATATA
Found at i:40033754 original size:27 final size:27
Alignment explanation
Indices: 40033708--40033905 Score: 204
Period size: 27 Copynumber: 7.3 Consensus size: 27
40033698 GAACAAATCT
* ** *
40033708 GTCATTTTACCTTACCGGGGTATTACA
1 GTCATTTTACCCTATAGGGGTATTTCA
*
40033735 GTCATTTTACCCTACAGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTCA
* *
40033762 GTCATTTTACCCTACACGGGTATTAT-A
1 GTCATTTTACCCTATAGGGGTATT-TCA
* *
40033789 GTCATTTTACCTTATAGCGGTATTTC-
1 GTCATTTTACCCTATAGGGGTATTTCA
* **
40033815 GATCATTTTACCCTATGGGGGTATTTTG
1 G-TCATTTTACCCTATAGGGGTATTTCA
* *
40033843 GTCATTTTACCTTATGGGGGTATTTC-
1 GTCATTTTACCCTATAGGGGTATTTCA
* *
40033869 GATCATTTTACCCTATGGGGGTATTTCG
1 G-TCATTTTACCCTATAGGGGTATTTCA
40033897 GTCATTTTA
1 GTCATTTTA
40033906 TCATATAAGG
Statistics
Matches: 150, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
26 3 0.02
27 144 0.96
28 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTCA
Found at i:40033771 original size:54 final size:54
Alignment explanation
Indices: 40033709--40033905 Score: 227
Period size: 54 Copynumber: 3.6 Consensus size: 54
40033699 AACAAATCTG
* * *
40033709 TCATTTTACCTTACCGGGGTATTACAGTCATTTTACCCTACAGGGGTATTTC-A
1 TCATTTTACCCTACCGGGGTATTACAGTCATTTTACCTTATAGGGGTATTTCGA
* *
40033762 GTCATTTTACCCTACAC-GGGTATTATAGTCATTTTACCTTATAGCGGTATTTCGA
1 -TCATTTTACCCTAC-CGGGGTATTACAGTCATTTTACCTTATAGGGGTATTTCGA
** *** *
40033817 TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATGGGGGTATTTCGA
1 TCATTTTACCCTACCGGGGTATTACAGTCATTTTACCTTATAGGGGTATTTCGA
** * *
40033871 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTA
1 TCATTTTACCCTACCGGGGTATTACAGTCATTTTA
40033906 TCATATAAGG
Statistics
Matches: 128, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
54 126 0.98
55 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (54 bp):
TCATTTTACCCTACCGGGGTATTACAGTCATTTTACCTTATAGGGGTATTTCGA
Found at i:40033930 original size:27 final size:27
Alignment explanation
Indices: 40033897--40033997 Score: 157
Period size: 27 Copynumber: 3.7 Consensus size: 27
40033887 GGGTATTTCG
*
40033897 GTCATTTTATCATATAAGGGCAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
*
40033924 GTTATTTTATCACATAAGGGCAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
* *
40033951 GTCATTTTATCACCTTAGGGCAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
*
40033978 ATCATTTTATCACATAAGGG
1 GTCATTTTATCACATAAGGG
40033998 TTCAGGTACG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (27 bp):
GTCATTTTATCACATAAGGGCAAAATC
Found at i:40033931 original size:54 final size:54
Alignment explanation
Indices: 40033813--40033932 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 54
40033803 TAGCGGTATT
* * * ** **
40033813 TCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATGGGGGTATT
1 TCGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCATATAGGGCAAAA
*
40033867 TCGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCATATAAGGGCAAAA
1 TCGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCATAT-AGGGCAAAA
*
40033922 TCG-TTATTTTA
1 TCGATCATTTTA
40033933 TCACATAAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 49 0.88
55 7 0.12
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (54 bp):
TCGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCATATAGGGCAAAA
Found at i:40036762 original size:28 final size:28
Alignment explanation
Indices: 40036722--40036780 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
40036712 CATGTGATAG
40036722 TTTGATTAGTTTGAACAAACTCTTCAAT
1 TTTGATTAGTTTGAACAAACTCTTCAAT
*
40036750 TTTGGTTAGTTTGAACAAACTCTTCAAT
1 TTTGATTAGTTTGAACAAACTCTTCAAT
40036778 TTT
1 TTT
40036781 TAATTAAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.46
Consensus pattern (28 bp):
TTTGATTAGTTTGAACAAACTCTTCAAT
Found at i:40040041 original size:79 final size:81
Alignment explanation
Indices: 40039905--40040089 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
40039895 TTGAATGATG
* *
40039905 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
*
40039969 TGTGTGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
40039984 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
40040046 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
40040064 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40040090 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:40040096 original size:40 final size:40
Alignment explanation
Indices: 40039905--40040089 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
40039895 TTGAATGATG
* * * *
40039905 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
40039945 TCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
40039985 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40040024 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40040065 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40040090 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 34 0.28
40 80 0.65
41 9 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Done.