Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008881.1 Hibiscus syriacus cultivar Beakdansim tig00112127_pilon, whole genome shotgun sequence
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: 608427
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 3
Found at i:323113 original size:31 final size:31
Alignment explanation
Indices: 323075--323196 Score: 131
Period size: 31 Copynumber: 3.9 Consensus size: 31
323065 CCTCGGCAAC
* *
323075 TGTCCATAGGTTCCGAAGAACCTAGGTAAAT
1 TGTCCATATGTTCCGAAGAACATAGGTAAAT
** * *
323106 TGTCCATATGTTCCTTAGAACATAGGTATAC
1 TGTCCATATGTTCCGAAGAACATAGGTAAAT
*
323137 TGTCCATATG-TCTCGAA-AGACATAGGTAATT
1 TGTCCATATGTTC-CGAAGA-ACATAGGTAAAT
*
323168 CTGTCCATATGTTCCGTAGAACATAGGTA
1 -TGTCCATATGTTCCGAAGAACATAGGTA
323197 TACCCTCGAC
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
30 3 0.04
31 46 0.62
32 22 0.30
33 3 0.04
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
TGTCCATATGTTCCGAAGAACATAGGTAAAT
Found at i:327922 original size:30 final size:30
Alignment explanation
Indices: 327882--327953 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
327872 TCCGAAGGAC
* * *
327882 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCATCGGCAA
327912 CTATCCAGAGGTCATAAAGATCATCGGCAA
1 CTATCCAGAGGTCATAAAGATCATCGGCAA
* *
327942 CTGTCCATAGGT
1 CTATCCAGAGGT
327954 TCCGAAGAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCATCGGCAA
Found at i:328011 original size:31 final size:31
Alignment explanation
Indices: 327945--328067 Score: 97
Period size: 31 Copynumber: 3.9 Consensus size: 31
327935 TCGGCAACTG
* * * * *
327945 TCCATAGGTTCCGA-AGAACCTAGGTAAATTG
1 TCCATATGTTCC-ATAGAACATAGGTATACTA
* *
327976 TCCATATATTCCTTAGAACATAGGTATACTA
1 TCCATATGTTCCATAGAACATAGGTATACTA
* * * *
328007 TCCATATGTCTCGAAAG-ACATAGGTAATTCTG
1 TCCATATGT-TCCATAGAACATAGGT-ATACTA
*
328039 TCCATATGTTCCGTAGAACATAGGTATAC
1 TCCATATGTTCCATAGAACATAGGTATAC
328068 CCTCGACTCT
Statistics
Matches: 71, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
31 46 0.65
32 25 0.35
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (31 bp):
TCCATATGTTCCATAGAACATAGGTATACTA
Found at i:331785 original size:3 final size:3
Alignment explanation
Indices: 331779--331809 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
331769 AATAATAATA
331779 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
331810 CTCAAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:333960 original size:7 final size:7
Alignment explanation
Indices: 333944--333976 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
333934 TTGCCTTGTA
333944 TTTTCTTT
1 TTTTC-TT
333952 TTTTCTT
1 TTTTCTT
333959 TTTTCTT
1 TTTTCTT
333966 TTTTCTT
1 TTTTCTT
333973 TTTT
1 TTTT
333977 GAATTAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:336538 original size:2 final size:2
Alignment explanation
Indices: 336531--336568 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
336521 TGATTTAAAA
336531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
336569 TAATTTCGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:342548 original size:15 final size:16
Alignment explanation
Indices: 342508--342551 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
342498 TAGGGTAAGT
*
342508 TTAAAT-TTATAAAGA
1 TTAAATATTAAAAAGA
342523 TTAAATAATTAAAAAGA
1 TTAAAT-ATTAAAAAGA
342540 -TAAATATTAAAA
1 TTAAATATTAAAA
342552 TAATTCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 13 0.50
16 5 0.19
17 8 0.31
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (16 bp):
TTAAATATTAAAAAGA
Found at i:343929 original size:16 final size:16
Alignment explanation
Indices: 343873--343991 Score: 67
Period size: 16 Copynumber: 7.4 Consensus size: 16
343863 GATTAAATTT
*
343873 GGTTCGGGCTGCTTTC
1 GGTTCGGGTTGCTTTC
* * ** *
343889 AGATCGGGTTAATTTT
1 GGTTCGGGTTGCTTTC
* *
343905 AGTTTGGGTTGCTTTC
1 GGTTCGGGTTGCTTTC
**
343921 GGTTCGGGTTAATTTC
1 GGTTCGGGTTGCTTTC
* *
343937 GGTTCGGGATGCTTTT
1 GGTTCGGGTTGCTTTC
* **
343953 GGTTCAGGTTAATTTC
1 GGTTCGGGTTGCTTTC
* * * *
343969 TGTTTGAGTTGCTCTC
1 GGTTCGGGTTGCTTTC
343985 GGTTCGG
1 GGTTCGG
343992 ATTATTTTCA
Statistics
Matches: 69, Mismatches: 34, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
16 69 1.00
ACGTcount: A:0.10, C:0.14, G:0.32, T:0.44
Consensus pattern (16 bp):
GGTTCGGGTTGCTTTC
Found at i:343941 original size:64 final size:64
Alignment explanation
Indices: 343863--344018 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 64
343853 TTTTGGGTCA
* * * *
343863 GATTAAATTT-GGTTCGGGCTGCTTTCAGATCGGGTTAATTT-TAGTTTGGGTTGCTTTCGGTTC
1 GATT-AATTTCGGTTCGGGATGCTTTCAGATCAGGTTAATTTCT-GTTTGAGTTGCTCTCGGTTC
343926 G
64 G
* ** *
343927 GGTTAATTTCGGTTCGGGATGCTTTTGGTTCAGGTTAATTTCTGTTTGAGTTGCTCTCGGTTCG
1 GATTAATTTCGGTTCGGGATGCTTTCAGATCAGGTTAATTTCTGTTTGAGTTGCTCTCGGTTCG
* **
343991 GATTATTTTCAATTC-GGATTGCTTTCAG
1 GATTAATTTCGGTTCGGGA-TGCTTTCAG
344019 TTTCGCTAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
63 8 0.11
64 66 0.88
65 1 0.01
ACGTcount: A:0.14, C:0.13, G:0.28, T:0.45
Consensus pattern (64 bp):
GATTAATTTCGGTTCGGGATGCTTTCAGATCAGGTTAATTTCTGTTTGAGTTGCTCTCGGTTCG
Found at i:343950 original size:32 final size:32
Alignment explanation
Indices: 343868--344016 Score: 129
Period size: 32 Copynumber: 4.7 Consensus size: 32
343858 GGTCAGATTA
* * *
343868 AATTT-GGTTCGGGCTGCTTTCAGATCGGGTT
1 AATTTCGGTTCGGGTTGCTTTCGGTTCGGGTT
** *
343899 AATTTTAGTTTGGGTTGCTTTCGGTTCGGGTT
1 AATTTCGGTTCGGGTTGCTTTCGGTTCGGGTT
* * *
343931 AATTTCGGTTCGGGATGCTTTTGGTTCAGGTT
1 AATTTCGGTTCGGGTTGCTTTCGGTTCGGGTT
* * * * *
343963 AATTTCTGTTTGAGTTGCTCTCGGTTCGGATT
1 AATTTCGGTTCGGGTTGCTTTCGGTTCGGGTT
* ** *
343995 ATTTTCAATTCGGATTGCTTTC
1 AATTTCGGTTCGGGTTGCTTTC
344017 AGTTTCGCTA
Statistics
Matches: 91, Mismatches: 26, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
31 5 0.05
32 86 0.95
ACGTcount: A:0.13, C:0.14, G:0.28, T:0.46
Consensus pattern (32 bp):
AATTTCGGTTCGGGTTGCTTTCGGTTCGGGTT
Found at i:347379 original size:20 final size:20
Alignment explanation
Indices: 347346--347385 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
347336 ATTGTTCATG
*
347346 TTTGAACTTTAATCAAGTTA
1 TTTGAACTTCAATCAAGTTA
* *
347366 TTTGAGCTTCAATCGAGTTA
1 TTTGAACTTCAATCAAGTTA
347386 AATATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (20 bp):
TTTGAACTTCAATCAAGTTA
Found at i:349876 original size:12 final size:12
Alignment explanation
Indices: 349859--349889 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
349849 GAACACTAAA
349859 TGAACATGTTCG
1 TGAACATGTTCG
*
349871 TGAACACGTTCG
1 TGAACATGTTCG
349883 TGAACAT
1 TGAACAT
349890 ATAAACGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (12 bp):
TGAACATGTTCG
Found at i:349899 original size:24 final size:23
Alignment explanation
Indices: 349872--349922 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
349862 ACATGTTCGT
*
349872 GAACACGTTCGTGAACATATAAAC
1 GAACACGCTCGTGAACAT-TAAAC
*
349896 GAACATGCTCGTGAACATTAAAC
1 GAACACGCTCGTGAACATTAAAC
349919 GAAC
1 GAAC
349923 GCTAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (23 bp):
GAACACGCTCGTGAACATTAAAC
Found at i:349935 original size:34 final size:34
Alignment explanation
Indices: 349891--349956 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
349881 CGTGAACATA
* *
349891 TAAACGAACATGCTCGTGAACATTAAACGAACGC
1 TAAACAAACATGCTCGCGAACATTAAACGAACGC
* *
349925 TAAACAAACATGTTCGCGAACATTAAATGAAC
1 TAAACAAACATGCTCGCGAACATTAAACGAAC
349957 ATGTTCGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (34 bp):
TAAACAAACATGCTCGCGAACATTAAACGAACGC
Found at i:349944 original size:23 final size:23
Alignment explanation
Indices: 349918--349963 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
349908 GAACATTAAA
*
349918 CGAACGCTAAACAAACATGTTCG
1 CGAACACTAAACAAACATGTTCG
* **
349941 CGAACATTAAATGAACATGTTCG
1 CGAACACTAAACAAACATGTTCG
349964 TGAATAATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (23 bp):
CGAACACTAAACAAACATGTTCG
Found at i:349974 original size:23 final size:23
Alignment explanation
Indices: 349931--349975 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
349921 ACGCTAAACA
*
349931 AACATGTTCGCGAACATTAAATG
1 AACATGTTCGCGAACAATAAATG
* *
349954 AACATGTTCGTGAATAATAAAT
1 AACATGTTCGCGAACAATAAAT
349976 AAACGAACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (23 bp):
AACATGTTCGCGAACAATAAATG
Found at i:358750 original size:84 final size:84
Alignment explanation
Indices: 358262--358852 Score: 428
Period size: 84 Copynumber: 7.1 Consensus size: 84
358252 TACTTTGGCC
* * * * *
358262 TCTTCAACAG-C-T-TTCTTAGTTTCTTCT-GCAATCCTCTTTTGCTCCTCTGCCTTAGCCAT-T
1 TCTTCAACAGCCTTCTTCTTAGTTTCTT-TAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCT
* **
358322 GC-AAGCTCAGCTTGTTTT-CT
65 -CTAA-ATCAGCACGTTTTCCT
* * ** * * * *
358342 TACTTCAACAGCCTTCTTCAT-GTTTTCTTCAGCAATCTTAGTTTGCTCCGCTGCTTCAGCCATC
1 T-CTTCAACAGCCTTCTTCTTAG-TTTCTTTAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATC
* *
358406 TCTAAATCAGCATGTTTTCTT
64 TCTAAATCAGCACGTTTTCCT
* * *
358427 TCTTCAACGGCCTTCTTCTTAGTTTCTTTAGCAACCCTCCTCTGCTTCTCTGCTTTAGCCATCTC
1 TCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTC
* * *
358492 TGAATCGGCAC-ATTTCCTT
66 TAAATCAGCACGTTTTCC-T
* * * * *
358511 TCATCAACAGCCTTTTTCTTAGTTTCTTCT-GCAATCTTCCTTTGCTCCTCTGCCTTAGCCATCT
1 TCTTCAACAGCCTTCTTCTTAGTTTCTT-TAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCT
**
358575 C-AAACTCAGCTTGTTTT-CT
65 CTAAA-TCAGCACGTTTTCCT
* * * * * * *
358594 TACTTCAAAAGCATTTTTCAT-GTTTTCTTCAGCAATCTTCCTTTG-TTCTGCTGCTTCAGCCAT
1 T-CTTCAACAGCCTTCTTCTTAG-TTTCTTTAGCAATCTTCCTCTGCTTCT-CTGCTTTAGCCAT
358657 CTCTAAATCAGCACGTTTTCCT
63 CTCTAAATCAGCACGTTTTCCT
* * *
358679 TCTTCAGCAGCCTTCTTCTTAGTTTCTTTAGCAACCTTCCTCTGCTTCTCCGCTTTAGCCATCTC
1 TCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTC
** * *
358744 CGAATCAACACATTTT-CT
66 TAAATCAGCACGTTTTCCT
* * ** *
358762 ATCGTCAACAGCCTGT-TTCTTAGTTT-TTTCTGCAATCTTCCTCAAC-TCCCTTGCTTTAGCCA
1 -TCTTCAACAGCCT-TCTTCTTAGTTTCTTT-AGCAATCTTCCTCTGCTTCTC-TGCTTTAGCCA
* * *
358824 TTTCTAAATC-GACAAGTTTTCTT
62 TCTCTAAATCAG-CACGTTTTCCT
358847 TCTTCA
1 TCTTCA
358853 CCTGCCTTTT
Statistics
Matches: 403, Mismatches: 80, Indels: 52
0.75 0.15 0.10
Matches are distributed among these distances:
80 1 0.00
81 9 0.02
82 1 0.00
83 22 0.05
84 347 0.86
85 23 0.06
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.42
Consensus pattern (84 bp):
TCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTC
TAAATCAGCACGTTTTCCT
Found at i:358824 original size:252 final size:252
Alignment explanation
Indices: 358273--358803 Score: 830
Period size: 252 Copynumber: 2.1 Consensus size: 252
358263 CTTCAACAGC
* * *
358273 TTTCTTAGTTTCTTCTGCAATCCTCTTTTGCTCCTCTGCCTTAGCCATTGCAAGCTCAGCTTGTT
1 TTTCTTAGTTTCTTCTGCAATCTTCCTTTGCTCCTCTGCCTTAGCCATTGCAAACTCAGCTTGTT
* * *
358338 TTCTTACTTCAACAGCCTTCTTCATGTTTTCTTCAGCAATCTTAGTTTGCTCCGCTGCTTCAGCC
66 TTCTTACTTCAAAAGCATTCTTCATGTTTTCTTCAGCAATCTTACTTTGCTCCGCTGCTTCAGCC
* * *
358403 ATCTCTAAATCAGCATGTTTTCTTTCTTCAACGGCCTTCTTCTTAGTTTCTTTAGCAACCCTCCT
131 ATCTCTAAATCAGCACGTTTTCCTTCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAACCCTCCT
* * ** * *
358468 CTGCTTCTCTGCTTTAGCCATCTCTGAATCGGCACATTTCCTTTCATCAACAGCCTT
196 CTGCTTCTCCGCTTTAGCCATCTCCGAATCAACACATTTCCTATCATCAACAGCCTG
358525 TTTCTTAGTTTCTTCTGCAATCTTCCTTTGCTCCTCTGCCTTAGCCATCT-CAAACTCAGCTTGT
1 TTTCTTAGTTTCTTCTGCAATCTTCCTTTGCTCCTCTGCCTTAGCCAT-TGCAAACTCAGCTTGT
* * * *
358589 TTTCTTACTTCAAAAGCATTTTTCATGTTTTCTTCAGCAATCTTCCTTTGTTCTGCTGCTTCAGC
65 TTTCTTACTTCAAAAGCATTCTTCATGTTTTCTTCAGCAATCTTACTTTGCTCCGCTGCTTCAGC
* *
358654 CATCTCTAAATCAGCACGTTTTCCTTCTTCAGCAGCCTTCTTCTTAGTTTCTTTAGCAACCTTCC
130 CATCTCTAAATCAGCACGTTTTCCTTCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAACCCTCC
* *
358719 TCTGCTTCTCCGCTTTAGCCATCTCCGAATCAACACATTTTCTATCGTCAACAGCCTG
195 TCTGCTTCTCCGCTTTAGCCATCTCCGAATCAACACATTTCCTATCATCAACAGCCTG
*
358777 TTTCTTAGTTTTTTCTGCAATCTTCCT
1 TTTCTTAGTTTCTTCTGCAATCTTCCT
358804 CAACTCCCTT
Statistics
Matches: 254, Mismatches: 24, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
252 253 1.00
253 1 0.00
ACGTcount: A:0.16, C:0.30, G:0.11, T:0.42
Consensus pattern (252 bp):
TTTCTTAGTTTCTTCTGCAATCTTCCTTTGCTCCTCTGCCTTAGCCATTGCAAACTCAGCTTGTT
TTCTTACTTCAAAAGCATTCTTCATGTTTTCTTCAGCAATCTTACTTTGCTCCGCTGCTTCAGCC
ATCTCTAAATCAGCACGTTTTCCTTCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAACCCTCCT
CTGCTTCTCCGCTTTAGCCATCTCCGAATCAACACATTTCCTATCATCAACAGCCTG
Found at i:360588 original size:38 final size:39
Alignment explanation
Indices: 360537--360613 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
360527 GATATGGCAA
360537 TGACATAAAATTAGTAAGCTG-TTTTTTATATAACCATC
1 TGACATAAAATTAGTAAGCTGTTTTTTTATATAACCATC
* *
360575 TGACATTAAATTAGTAAGTTGTTTTTTTTATATAACCAT
1 TGACATAAAATTAGTAAGCTG-TTTTTTTATATAACCAT
360614 ATGAAGTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 19 0.54
40 16 0.46
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (39 bp):
TGACATAAAATTAGTAAGCTGTTTTTTTATATAACCATC
Found at i:365103 original size:19 final size:20
Alignment explanation
Indices: 365081--365124 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
365071 TTTTTTTAGT
*
365081 AAATTTAAATATAA-TTTAA
1 AAATATAAATATAATTTTAA
**
365100 AAATATATTTATAATTTTAA
1 AAATATAAATATAATTTTAA
365120 AAATA
1 AAATA
365125 AATTTATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATATAAATATAATTTTAA
Found at i:365120 original size:20 final size:19
Alignment explanation
Indices: 365090--365131 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
365080 TAAATTTAAA
*
365090 TATAATTTAAAAATATATT
1 TATAATTTAAAAATAAATT
365109 TATAATTTTAAAAATAAATT
1 TATAA-TTTAAAAATAAATT
365129 TAT
1 TAT
365132 GAAATTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATAATTTAAAAATAAATT
Found at i:366929 original size:18 final size:18
Alignment explanation
Indices: 366896--366930 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
366886 TGAAGAAGAA
**
366896 CAAGATGTGATTCCTCCG
1 CAAGATGTGAACCCTCCG
366914 CAAGATGTGAACCCTCC
1 CAAGATGTGAACCCTCC
366931 ATAGGATATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
CAAGATGTGAACCCTCCG
Found at i:375082 original size:30 final size:30
Alignment explanation
Indices: 375018--375086 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
375008 TATTTTTTAT
* *
375018 AAAAAATTAAACAAGCCCTCAAACTTTCTA
1 AAAAAATCAAACAAGCCCTCAAACTTACTA
* *
375048 AAAAAATCAAACAAGCCCTCAAACTTAGTC
1 AAAAAATCAAACAAGCCCTCAAACTTACTA
375078 AAAAAATCA
1 AAAAAATCA
375087 GTTAAACCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.54, C:0.23, G:0.04, T:0.19
Consensus pattern (30 bp):
AAAAAATCAAACAAGCCCTCAAACTTACTA
Found at i:377031 original size:23 final size:23
Alignment explanation
Indices: 376997--377057 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
376987 CTCGTATAAA
*
376997 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
377020 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
377043 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
377058 TACAAGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:377586 original size:12 final size:13
Alignment explanation
Indices: 377562--377595 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
377552 TAACACATAG
*
377562 ATTCTTATTTCAT
1 ATTCTTATATCAT
377575 ATT-TTATATCAT
1 ATTCTTATATCAT
377587 ATTCTTATA
1 ATTCTTATA
377596 CCACTAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTCTTATATCAT
Found at i:387357 original size:3 final size:3
Alignment explanation
Indices: 387334--387394 Score: 79
Period size: 3 Copynumber: 20.3 Consensus size: 3
387324 AGCCTGCAAA
* * *
387334 AAT AAT ATT AAT AGT ATT AAT AAT -AT AAT AAT AAT AAGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
387379 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
387395 TATATATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:387763 original size:84 final size:84
Alignment explanation
Indices: 387640--387901 Score: 355
Period size: 84 Copynumber: 3.1 Consensus size: 84
387630 CGAACTCATC
* * *
387640 AGGTCTTTGGTTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCTCGGAGC
1 AGGTCTTTGGTTGGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
*
387705 TGAGCGTAGTCAAACTCGA
66 TGAGCGTAGTCGAACTCGA
* * * * *
387724 AGGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTACCTTGGAGC
1 AGGTCTTTGGTTGGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
*
387789 TGAGCGTAGTCGAACTCAA
66 TGAGCGTAGTCGAACTCGA
* * * *
387808 AGGTCTTTGGTTGG-AAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATGTGCCTTAGAG
1 AGGTCTTTGGTTGGCAA-ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAG
* *
387872 CTGAGCGTAATCGAACTCGG
65 CTGAGCGTAGTCGAACTCGA
*
387892 GGGTCTTTGG
1 AGGTCTTTGG
387902 CAGATAGCCT
Statistics
Matches: 154, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
83 2 0.01
84 152 0.99
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (84 bp):
AGGTCTTTGGTTGGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
TGAGCGTAGTCGAACTCGA
Found at i:388236 original size:105 final size:106
Alignment explanation
Indices: 387936--388746 Score: 1227
Period size: 105 Copynumber: 7.7 Consensus size: 106
387926 TCCTTCGTCG
* * *
387936 TGAAGTTGA-AAGTTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * * * *
388000 CTTGAGTTCAATATCCTTTGCTATGAAGTTGAAATTGACTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * *
388041 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
388106 CTGGAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
388147 TGAAATTGAGAAGTTGTTTGTTGACAACCAGC-GTCCCTTCGTCATGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
388211 CTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * * * * *
388252 TGATATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACATACGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
388317 CTGGAGTCCAATATCCTTCGTTGTGAAGTT-AAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * * * *
388357 TGATATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
388422 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
388463 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTG-AGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
388527 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
388568 TAAAATTGAGAAGTTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
388632 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * * * ** * *
388673 TGAAATTGGGCAGTTATTTTTTTTGACAACCAGTAGTCCCTTCTTCGTGAAGTTGAACTTGTGTT
1 TGAAATTGAGAAG-T-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
*
388738 GTCTCGAGT
64 GTCTGGAGT
388747 GGCATGATAT
Statistics
Matches: 656, Mismatches: 43, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
104 30 0.05
105 345 0.53
106 231 0.35
107 1 0.00
108 49 0.07
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
Found at i:388332 original size:211 final size:212
Alignment explanation
Indices: 387936--388746 Score: 1256
Period size: 211 Copynumber: 3.8 Consensus size: 212
387926 TCCTTCGTCG
* * *
387936 TGAAGTTGA-AAGTTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * * * * *
388000 CTTGAGTTCAATATCCTTTGCTATGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGA
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGA
* *
388065 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTTGCTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
388130 GAAGTTGAAATTGGCTC
196 GAAGTTGAAATTGGCTC
*
388147 TGAAATTGAGAAGTTGTTTGTTGACAACCAGC-GTCCCTTCGTCATGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * *
388211 CTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTGTTGA
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGA
* * *
388276 CAACCAGCGGTCCCTTCGTTGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
388341 GAAGTT-AAATTGGCTC
196 GAAGTTGAAATTGGCTC
* * * * *
388357 TGATATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
388422 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGA
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGA
388487 CAACCAGCGGTCCCTTCGTCGTG-AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
388551 GAAGTTGAAATTGGCTC
196 GAAGTTGAAATTGGCTC
*
388568 TAAAATTGAGAAGTTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
388632 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGCAGTTATT-TTTTT
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG-A--AATTGTTTGT
** * * *
388696 TGACAACCAGTAGTCCCTTCTTCGTGAAGTTGAACTTGTGTTGTCTCGAGT
128 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
388747 GGCATGATAT
Statistics
Matches: 547, Mismatches: 46, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
210 180 0.33
211 296 0.54
212 47 0.09
213 24 0.04
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (212 bp):
TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGA
CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
GAAGTTGAAATTGGCTC
Found at i:388536 original size:316 final size:317
Alignment explanation
Indices: 387943--388730 Score: 1260
Period size: 316 Copynumber: 2.5 Consensus size: 317
387933 TCGTGAAGTT
* * * *
387943 GAAAGTTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTT
1 GAAA-TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
* * *
388008 CAATATCCTTTGCTATGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGC
65 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGC
* * *
388073 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTTGCTGTGAAGTTGA
130 GGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGA
388138 AATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGTCCCTTCGTCATGAAGTTGAACT
195 AATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGTCCCTTCGTCATGAAGTTGAACT
* * *
388203 TGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGG
260 TGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGA
* * *
388261 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACATACGTTGTCTGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
388326 AATATCCTTCGTTGTGAAGTT-AAATTGGCTCTGATATTGGGAAATTGTTTGTTGACAACCAGCG
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCG
388390 GTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAA
131 GTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAA
*
388455 ATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTG-AGTTGAACT
196 ATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGC-GTCCCTTCGTCATGAAGTTGAACT
*
388519 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGA
260 TGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGA
*
388577 GAAGTTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
388641 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGCAGTTATT-TTTTTTGACAACCA
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG-A--AATTGTTTATTGACAACCA
** *
388705 GTAGTCCCTTCTTCGTGAAGTTGAAC
128 GCGGTCCCTTCGTCGTGAAGTTGAAC
388731 TTGTGTTGTC
Statistics
Matches: 433, Mismatches: 32, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
315 74 0.17
316 230 0.53
317 86 0.20
318 40 0.09
319 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (317 bp):
GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCG
GTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAA
ATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGTCCCTTCGTCATGAAGTTGAACTT
GCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGA
Found at i:394036 original size:3 final size:3
Alignment explanation
Indices: 394013--394084 Score: 94
Period size: 3 Copynumber: 24.3 Consensus size: 3
394003 AGCCTGCAAA
* * *
394013 AAT AAT ATT AAT AGT ATT AAT AAT -AT AAT AAT AAT AAT AAGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
394058 AAT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
394085 TATTATTTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
2 4 0.07
3 54 0.89
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:401419 original size:23 final size:23
Alignment explanation
Indices: 401390--401452 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
401380 ACCCCCATGA
*
401390 GGGAACCGATTCCCCTTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
401413 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
401436 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
401453 AGGGGAATCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.32, G:0.25, T:0.22
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:401472 original size:20 final size:19
Alignment explanation
Indices: 401411--401476 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
401401 CCCCTTTTGA
*
401411 AGGGGAACCGATTCCCCCTTT
1 AGGGGAACCGA-TCCCCC-CT
*
401432 GAAGGGGAACCGATTCCCCCT
1 --AGGGGAACCGATCCCCCCT
*
401453 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
401473 -GGGG
1 AGGGG
401477 TTCTGGTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 15 0.39
20 6 0.16
21 1 0.03
22 5 0.13
23 11 0.29
ACGTcount: A:0.21, C:0.32, G:0.30, T:0.17
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:413291 original size:60 final size:59
Alignment explanation
Indices: 413181--413309 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 59
413171 ATTGAATGAC
* * * *
413181 CATTTTATAACTTTTAATAGTCGTAAGACTTAACAAAACAATATCTTATAATCAAGAGAT
1 CATTTTATAACATATAATAGTCGTAAGACTCAAAAAAACAATATCTTATAATCAAG-GAT
* **
413241 CATTTTATAACATATAATAGTC-TGAAGACTCAAAAAAATAATAATC-TATAATTGAGGAT
1 CATTTTATAACATATAATAGTCGT-AAGACTCAAAAAAACAAT-ATCTTATAATCAAGGAT
413300 CATTTGTATA
1 CATTT-TATA
413310 CTTTATCCTA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 9 0.15
60 47 0.80
61 3 0.05
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (59 bp):
CATTTTATAACATATAATAGTCGTAAGACTCAAAAAAACAATATCTTATAATCAAGGAT
Found at i:413649 original size:6 final size:6
Alignment explanation
Indices: 413638--413686 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
413628 GCCAAAACTC
*
413638 GTGGCT GTGGCT GT-GCT GTGGTT GTGG-T G-GGCT GTGGGCT GTGGCT
1 GTGGCT GTGGCT GTGGCT GTGGCT GTGGCT GTGGCT GT-GGCT GTGGCT
413684 GTG
1 GTG
413687 CTTTCTGCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
4 2 0.05
5 9 0.24
6 21 0.55
7 6 0.16
ACGTcount: A:0.00, C:0.12, G:0.53, T:0.35
Consensus pattern (6 bp):
GTGGCT
Found at i:413657 original size:11 final size:11
Alignment explanation
Indices: 413641--413688 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
413631 AAAACTCGTG
413641 GCTGTGGCTGT
1 GCTGTGGCTGT
*
413652 GCTGTGGTTGT
1 GCTGTGGCTGT
*
413663 GGTG-GGCTGT
1 GCTGTGGCTGT
413673 GGGCTGTGGCTGT
1 --GCTGTGGCTGT
413686 GCT
1 GCT
413689 TTCTGCTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 5 0.17
11 16 0.53
12 3 0.10
13 6 0.20
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (11 bp):
GCTGTGGCTGT
Found at i:420782 original size:128 final size:127
Alignment explanation
Indices: 420484--420783 Score: 293
Period size: 127 Copynumber: 2.3 Consensus size: 127
420474 ACTGGTTCGT
* * * * *
420484 TTATATATCTATCACTACAACAAAATTGAAAATTGCAGAAATC-TATGATTGTCAAAAGGTAGCG
1 TTATATATCCATCACTACAACAAAATTGAAAATTGCAG-GACCATATGATCGTCAAAAGGTAGCA
* ** * * *
420548 TCACCAACCATTCATGCTTAAAAAACATGTTTTTTTATCTAAGACAAATCAATATCAGTTTGA
65 TCACCAACAATTCATGCTTAAAAAACATGTCCTTTTACCCAAGACAAATCAACATCAGTTTGA
* * ** *
420611 TTATATATCCGTAACTACAACAAAATAAAAAATTGTATGGACCATATGCA-CGTCAAAAGGTAGC
1 TTATATATCCATCACTACAACAAAATTGAAAATTGCA-GGACCATATG-ATCGTCAAAAGGTAGC
* * * ** * ** *
420675 ATTATCAACAATTCCTGCTTAAATCACATG-CCTTTTCCCCAAGGTAAATCAACATCAG-TTGG
64 ATCACCAACAATTCATGCTTAAAAAACATGTCCTTTTACCCAAGACAAATCAACATCAGTTTGA
420737 TTCATATATCCATCACTAACAACAAAATTGAAAATTGCAGCGACCAT
1 TT-ATATATCCATCACT-ACAACAAAATTGAAAATTGCAG-GACCAT
420784 CATCAAGTAT
Statistics
Matches: 137, Mismatches: 30, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
126 5 0.04
127 66 0.48
128 65 0.47
129 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (127 bp):
TTATATATCCATCACTACAACAAAATTGAAAATTGCAGGACCATATGATCGTCAAAAGGTAGCAT
CACCAACAATTCATGCTTAAAAAACATGTCCTTTTACCCAAGACAAATCAACATCAGTTTGA
Found at i:424291 original size:30 final size:30
Alignment explanation
Indices: 424252--424451 Score: 283
Period size: 30 Copynumber: 6.7 Consensus size: 30
424242 AAGCCCAAGG
*
424252 AACCAGAGAAGCCGAAAGAGGCTGAGAAGA
1 AACCAGAGAAGCCGAAAGAGGCCGAGAAGA
* * *
424282 AACCCGAGAAGCCTAAAGAGGCTGAGAAGA
1 AACCAGAGAAGCCGAAAGAGGCCGAGAAGA
* * *
424312 AACCCGAGCAGCCTAAAGAGGCCGAGAAGA
1 AACCAGAGAAGCCGAAAGAGGCCGAGAAGA
* *
424342 AATCTGAGAAGCCGAAAGAGGCCGAGAAGA
1 AACCAGAGAAGCCGAAAGAGGCCGAGAAGA
*
424372 AGCCAGAGAAGCCGAAAGAGGCCGAGAAGA
1 AACCAGAGAAGCCGAAAGAGGCCGAGAAGA
*
424402 AGCCAGAGAAGCCGAAAGAGGCCGAGAAGA
1 AACCAGAGAAGCCGAAAGAGGCCGAGAAGA
* *
424432 AACCGGAGAAGCCTAAAGAG
1 AACCAGAGAAGCCGAAAGAG
424452 TCTGGGGAGA
Statistics
Matches: 156, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 156 1.00
ACGTcount: A:0.43, C:0.20, G:0.33, T:0.04
Consensus pattern (30 bp):
AACCAGAGAAGCCGAAAGAGGCCGAGAAGA
Found at i:424382 original size:12 final size:11
Alignment explanation
Indices: 424348--424442 Score: 96
Period size: 10 Copynumber: 9.2 Consensus size: 11
424338 AAGAAATCTG
424348 AGAAGCCGA-A
1 AGAAGCCGAGA
*
424358 AGAGGCCGAGA
1 AGAAGCCGAGA
424369 AGAAGCC-AG-
1 AGAAGCCGAGA
424378 AGAAGCCGA-A
1 AGAAGCCGAGA
*
424388 AGAGGCCGAGA
1 AGAAGCCGAGA
424399 AGAAGCC-AG-
1 AGAAGCCGAGA
424408 AGAAGCCGA-A
1 AGAAGCCGAGA
*
424418 AGAGGCCGAGA
1 AGAAGCCGAGA
*
424429 AGAAACCGGAGA
1 AGAAGCC-GAGA
424441 AG
1 AG
424443 CCTAAAGAGT
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
9 14 0.20
10 30 0.43
11 20 0.29
12 6 0.09
ACGTcount: A:0.44, C:0.19, G:0.37, T:0.00
Consensus pattern (11 bp):
AGAAGCCGAGA
Found at i:424488 original size:18 final size:18
Alignment explanation
Indices: 424465--424527 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
424455 GGGGAGAAGA
*
424465 AGGCTGATAAACCAAAAG
1 AGGCTGAGAAACCAAAAG
* *
424483 AGGCTGAGAAGCCTAAAG
1 AGGCTGAGAAACCAAAAG
* *
424501 AGGGTGGGGAGAAACCCAAAG
1 AGGCT---GAGAAACCAAAAG
424522 AGGCTG
1 AGGCTG
424528 CTCCGGCGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 20 0.57
21 15 0.43
ACGTcount: A:0.40, C:0.16, G:0.35, T:0.10
Consensus pattern (18 bp):
AGGCTGAGAAACCAAAAG
Found at i:424493 original size:90 final size:87
Alignment explanation
Indices: 424252--424495 Score: 227
Period size: 90 Copynumber: 2.7 Consensus size: 87
424242 AAGCCCAAGG
* * * * * * *
424252 AACCAGAGAAGCCGAAAGAGGCTGAGAAGAAACCCGAGAAGCCTAAAGAGGCTGAGAAGAAACCC
1 AACCGGAGAAGCCGAAAGAGGCCGAGAAGAAGCCAGAGAAACCAAAAGAGGCTGAGAAG---CCA
* *
424317 GAGCAGCCTAAAGAGGCCGAGAAGA
63 GAGAAGCCGAAAGAGGCCGAGAAGA
* * * * *
424342 AATCTGAGAAGCCGAAAGAGGCCGAGAAGAAGCCAGAGAAGCCGAAAGAGGCCGAGAAGAAGCCA
1 AACCGGAGAAGCCGAAAGAGGCCGAGAAGAAGCCAGAGAAACCAAAAGAGG-C-TG-AGAAGCCA
424407 GAGAAGCCGAAAGAGGCCGAGAAGA
63 GAGAAGCCGAAAGAGGCCGAGAAGA
* ** * * *
424432 AACCGGAGAAGCCTAAAGAGTCTGGGGAGAAGAAGGCTGATAAACCAAAAGAGGCTGAGAAGCC
1 AACCGGAGAAGCCGAAAGAG---GCCGAGAAGAAGCCAGAGAAACCAAAAGAGGCTGAGAAGCC
424496 TAAAGAGGGT
Statistics
Matches: 127, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
90 94 0.74
91 2 0.02
92 2 0.02
93 29 0.23
ACGTcount: A:0.43, C:0.19, G:0.33, T:0.05
Consensus pattern (87 bp):
AACCGGAGAAGCCGAAAGAGGCCGAGAAGAAGCCAGAGAAACCAAAAGAGGCTGAGAAGCCAGAG
AAGCCGAAAGAGGCCGAGAAGA
Found at i:432905 original size:8 final size:8
Alignment explanation
Indices: 432892--432916 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
432882 GACATGTCAA
432892 TTTTTAAT
1 TTTTTAAT
432900 TTTTTAAT
1 TTTTTAAT
432908 TTTTTAAT
1 TTTTTAAT
432916 T
1 T
432917 ACCACATCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTAAT
Found at i:433589 original size:18 final size:19
Alignment explanation
Indices: 433517--433601 Score: 75
Period size: 19 Copynumber: 4.4 Consensus size: 19
433507 TACAATATTA
* *
433517 TTTAAAATTAAATATACAA
1 TTTAAAAATAAATATACAT
433536 TTTAAAAAT-AATATA-AT
1 TTTAAAAATAAATATACAT
*
433553 TTTAAATAAATAAATAATATAAT
1 TTT-AA-AAATAAAT-ATA-CAT
* *
433576 TTTAAAAATAAATAAATAT
1 TTTAAAAATAAATATACAT
433595 TTTAAAA
1 TTTAAAA
433602 TATTTTCATA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
17 4 0.07
18 8 0.14
19 21 0.38
20 5 0.09
21 11 0.20
22 2 0.04
23 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTAAAAATAAATATACAT
Found at i:433592 original size:25 final size:23
Alignment explanation
Indices: 433541--433600 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
433531 TACAATTTAA
433541 AAATAATATAATTTTAAATAAAT
1 AAATAATATAATTTTAAATAAAT
433564 AAATAATATAATTTT-AA-AAAT
1 AAATAATATAATTTTAAATAAAT
433585 AAATAA-AT-ATTTTAAA
1 AAATAATATAATTTTAAA
433601 ATATTTTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.14
20 4 0.11
21 10 0.28
22 2 0.06
23 15 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATAATATAATTTTAAATAAAT
Found at i:433603 original size:39 final size:36
Alignment explanation
Indices: 433517--433603 Score: 86
Period size: 39 Copynumber: 2.2 Consensus size: 36
433507 TACAATATTA
433517 TTTAAAATTAAATATACAATTTAAAAATAATATAATT
1 TTTAAAA-TAAATATACAATTTAAAAATAATATAATT
* *
433554 TTAAATAAATAAATAATATAATTTTAAAAATAA-ATAAATAT
1 TT-TA-AAATAAAT-ATACAA-TTTAAAAATAATAT-AAT-T
433595 TTTAAAATA
1 TTTAAAATA
433604 TTTTCATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
37 2 0.05
38 6 0.15
39 15 0.37
40 15 0.37
41 3 0.07
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (36 bp):
TTTAAAATAAATATACAATTTAAAAATAATATAATT
Found at i:436472 original size:19 final size:19
Alignment explanation
Indices: 436448--436489 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
436438 TGCATTGGAT
436448 AGGTGGTTAG-TCTGTTAAG
1 AGGTGGTTAGAT-TGTTAAG
436467 AGGTGGTTAGATTGTTAAG
1 AGGTGGTTAGATTGTTAAG
436486 AGGT
1 AGGT
436490 TAGCTAAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.24, C:0.02, G:0.38, T:0.36
Consensus pattern (19 bp):
AGGTGGTTAGATTGTTAAG
Found at i:441059 original size:19 final size:19
Alignment explanation
Indices: 441035--441076 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
441025 TGCATTGGAT
441035 AGGTGGTTAG-TCTGTTAAG
1 AGGTGGTTAGAT-TGTTAAG
441054 AGGTGGTTAGATTGTTAAG
1 AGGTGGTTAGATTGTTAAG
441073 AGGT
1 AGGT
441077 TAGCTAAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.24, C:0.02, G:0.38, T:0.36
Consensus pattern (19 bp):
AGGTGGTTAGATTGTTAAG
Found at i:446569 original size:7 final size:7
Alignment explanation
Indices: 446552--446585 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
446542 AGGAGGAAGC
446552 TCAGG-T
1 TCAGGCT
446558 TCAGGCT
1 TCAGGCT
446565 TCAGGCT
1 TCAGGCT
446572 TCAGGCT
1 TCAGGCT
446579 TCAGGCT
1 TCAGGCT
446586 CAAGCTGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
TCAGGCT
Found at i:449126 original size:21 final size:21
Alignment explanation
Indices: 449100--449140 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
449090 AATGCTCCAC
**
449100 CATTTCCGTTTGGTATATCAT
1 CATTTCCACTTGGTATATCAT
449121 CATTTCCACTTGGTATATCA
1 CATTTCCACTTGGTATATCA
449141 AGTCATCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (21 bp):
CATTTCCACTTGGTATATCAT
Found at i:453629 original size:14 final size:14
Alignment explanation
Indices: 453610--453642 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
453600 TGCTGGGCAT
453610 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
453624 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
453638 ACGAG
1 CCGAG
453643 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:453676 original size:33 final size:33
Alignment explanation
Indices: 453624--453708 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
453614 GGCCATCCGA
* * * *
453624 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
453657 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
*
453690 CCGAGGGCAACCGTGCGAG
1 CCGAGGGCAACCGAGCGAG
453709 GGTAGGTCAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.38, T:0.09
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:453804 original size:10 final size:10
Alignment explanation
Indices: 453783--453909 Score: 74
Period size: 10 Copynumber: 12.1 Consensus size: 10
453773 CCTACCCTCG
*
453783 CTCGGTTGCC
1 CTCGGATGCC
*
453793 CTCGGATTCC
1 CTCGGATGCC
*
453803 CTCGCATAGCTC
1 CTCGGAT-GC-C
453815 GCTCGGATGCC
1 -CTCGGATGCC
453826 CTCGGATGCC
1 CTCGGATGCC
**
453836 CTCACATAGCTC
1 CTCGGAT-GC-C
* *
453848 GTTCGGATGGC
1 -CTCGGATGCC
*
453859 CTCGGATGCT
1 CTCGGATGCC
*
453869 CTCGGATGGC
1 CTCGGATGCC
* * *
453879 ATCGAATGCT
1 CTCGGATGCC
* *
453889 TTCGGATGGC
1 CTCGGATGCC
453899 CTCGGATGCC
1 CTCGGATGCC
453909 C
1 C
453910 AGCGTGTTGG
Statistics
Matches: 85, Mismatches: 26, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
10 65 0.76
11 5 0.06
12 5 0.06
13 10 0.12
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.25
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:453820 original size:33 final size:33
Alignment explanation
Indices: 453779--453867 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
453769 GCGACCTACC
* * *
453779 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCACATAG
453812 CTCGCTCGGATGCCCTCGGATGCCCTCACATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCACATAG
* *
453845 CTCGTTCGGATGGCCTCGGATGC
1 CTCGCTCGGATGCCCTCGGATGC
453868 TCTCGGATGG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.11, C:0.37, G:0.27, T:0.25
Consensus pattern (33 bp):
CTCGCTCGGATGCCCTCGGATGCCCTCACATAG
Found at i:453875 original size:20 final size:20
Alignment explanation
Indices: 453816--453907 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
453806 GCATAGCTCG
* *
453816 CTCGGATGCCCTCGGATGCC
1 CTCGGATGCTCTCGGATGGC
**
453836 CTCACATAGCTCGTTCGGATGGC
1 CTCGGAT-GCTC--TCGGATGGC
453859 CTCGGATGCTCTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
* * *
453879 ATCGAATGCTTTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
453899 CTCGGATGC
1 CTCGGATGC
453908 CCAGCGTGTT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
20 38 0.66
21 3 0.05
22 4 0.07
23 13 0.22
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.25
Consensus pattern (20 bp):
CTCGGATGCTCTCGGATGGC
Found at i:454239 original size:29 final size:29
Alignment explanation
Indices: 454197--454285 Score: 160
Period size: 29 Copynumber: 3.1 Consensus size: 29
454187 AACACCCCAC
*
454197 AGGTCGCTCGGATGTCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
*
454226 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
454255 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
454284 AG
1 AG
454286 CTCACTGTAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.18, C:0.34, G:0.31, T:0.17
Consensus pattern (29 bp):
AGGTCGCTCGGATGCCATGGCGACCTCCA
Found at i:458036 original size:6 final size:6
Alignment explanation
Indices: 458027--458055 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
458017 TATTTGTTCT
458027 ATATGC ATATGC ATATGC ATATGC ATATG
1 ATATGC ATATGC ATATGC ATATGC ATATG
458056 TAAATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (6 bp):
ATATGC
Found at i:458856 original size:17 final size:18
Alignment explanation
Indices: 458834--458873 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
458824 CTCCTAAAAT
458834 TTTTAAA-TTCTTTTATA
1 TTTTAAATTTCTTTTATA
*
458851 TTTTAAATTTTTTTTATA
1 TTTTAAATTTCTTTTATA
458869 TTTTA
1 TTTTA
458874 TTGATATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTAAATTTCTTTTATA
Found at i:475767 original size:333 final size:333
Alignment explanation
Indices: 475123--475788 Score: 1250
Period size: 333 Copynumber: 2.0 Consensus size: 333
475113 GTTAATAATT
475123 TTAAATACCTTATCAACATACATGTCTTTCATAGTAAGCTAACCAGAATTGACCACAAAAATAAA
1 TTAAATACCTTATCAACATACATGTCTTTCATAGTAAGCTAACCAGAATTGACCACAAAAATAAA
*
475188 GAATTAGATAGAGAAAATAAGGAATACCTGGCCTTTATGCTCCACATTCTTGGTCTGGTAAAATC
66 GAATTAGATAGAGAAAAAAAGGAATACCTGGCCTTTATGCTCCACATTCTTGGTCTGGTAAAATC
475253 CTTTACGATTATCTTTATAAACTCGAATAAAAAAGGTGAGAGAAATGAAGTGAATAAATCGATGA
131 CTTTACGATTATCTTTATAAACTCGAATAAAAAAGGTGAGAGAAATGAAGTGAATAAATCGATGA
475318 AGTAAATTACGAAAGAAGAAGAAAAATGAAAATGAAACTTTTTTAATGACCTCGTCGGCTTTCTT
196 AGTAAATTACGAAAGAAGAAGAAAAATGAAAATGAAACTTTTTTAATGACCTCGTCGGCTTTCTT
475383 AGCTGCATCGACTGCAGTGGCCAAGAACTCTTCATGGGAACCTGAAAATCCATAGAATTTACGAA
261 AGCTGCATCGACTGCAGTGGCCAAGAACTCTTCATGGGAACCTGAAAATCCATAGAATTTACGAA
475448 AGAAAAAG
326 AGAAAAAG
475456 TTAAATACCTTATCAACATACATGTCTTTCATAGTAAGCTAACCAGAATTGACCACAAAAATAAA
1 TTAAATACCTTATCAACATACATGTCTTTCATAGTAAGCTAACCAGAATTGACCACAAAAATAAA
475521 GAATTAGATAGAGAAAAAAAGGAA-ACCTGGCCTTTATGCTCCACATTCTTGGTCTGGTAAAATC
66 GAATTAGATAGAGAAAAAAAGGAATACCTGGCCTTTATGCTCCACATTCTTGGTCTGGTAAAATC
475585 CTTTACGGATTATCTTTATAAACATCGAAT-AAAAAGGTGAGAGAAATGAAGTGAATAAATCGAT
131 CTTTAC-GATTATCTTTATAAAC-TCGAATAAAAAAGGTGAGAGAAATGAAGTGAATAAATCGAT
*
475649 GAAGTAAATTACGAAAGAAGAAG-AAAATGAAAATGAAACTTTTTTTAATGAATCTCGTCGGCTT
194 GAAGTAAATTACGAAAGAAGAAGAAAAATGAAAATGAAAC-TTTTTTAATG-ACCTCGTCGGCTT
475713 TCTTAGCTGCATCGACTGCAGTGGCCAAGAACTCTTCATGGGAACCTG-AAATCCATAGAATTTA
257 TCTTAGCTGCATCGACTGCAGTGGCCAAGAACTCTTCATGGGAACCTGAAAATCCATAGAATTTA
475777 CGAAAGAAAAAG
322 CGAAAGAAAAAG
475789 GATTATGAAT
Statistics
Matches: 327, Mismatches: 2, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
332 62 0.19
333 199 0.61
334 66 0.20
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (333 bp):
TTAAATACCTTATCAACATACATGTCTTTCATAGTAAGCTAACCAGAATTGACCACAAAAATAAA
GAATTAGATAGAGAAAAAAAGGAATACCTGGCCTTTATGCTCCACATTCTTGGTCTGGTAAAATC
CTTTACGATTATCTTTATAAACTCGAATAAAAAAGGTGAGAGAAATGAAGTGAATAAATCGATGA
AGTAAATTACGAAAGAAGAAGAAAAATGAAAATGAAACTTTTTTAATGACCTCGTCGGCTTTCTT
AGCTGCATCGACTGCAGTGGCCAAGAACTCTTCATGGGAACCTGAAAATCCATAGAATTTACGAA
AGAAAAAG
Found at i:476096 original size:43 final size:43
Alignment explanation
Indices: 476031--476113 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
476021 ATAGTTAATT
* *
476031 ATAATTTAGTCTTTATATTTTAGGGTATTTATAAGATTAAATC
1 ATAATTTAGTCATTATACTTTAGGGTATTTATAAGATTAAATC
476074 ATAATTTAGTCATTATACTTTAGGGTATTTATAAGATTAA
1 ATAATTTAGTCATTATACTTTAGGGTATTTATAAGATTAA
476114 TTCTTAAGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (43 bp):
ATAATTTAGTCATTATACTTTAGGGTATTTATAAGATTAAATC
Found at i:482718 original size:20 final size:20
Alignment explanation
Indices: 482693--482827 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
482683 AATTGGGAAA
482693 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
482713 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
482733 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
482754 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
482774 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* ** *
482794 TTCGCAGCGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
482814 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
482828 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 65 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:482755 original size:61 final size:61
Alignment explanation
Indices: 482690--482827 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
482680 ACGAATTGGG
* * *
482690 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * * *
482751 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAGCGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
482812 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
482828 TTTCAAAGCG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:483023 original size:22 final size:22
Alignment explanation
Indices: 482995--483038 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
482985 CACTCTCTCA
482995 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
483017 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
483039 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:483355 original size:20 final size:20
Alignment explanation
Indices: 483301--483359 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
483291 GCGATTCTCT
* **
483301 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCATTTTCG
483321 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
483341 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
483360 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:499223 original size:31 final size:31
Alignment explanation
Indices: 499188--499266 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
499178 ATGATAGTGG
**
499188 AGTGACTATTTTGTTATAAATTGATAATATT
1 AGTGACTATTTTGTTATAAATCAATAATATT
*
499219 AGTGAGC-ATTTTGATATAAATCAATAATATT
1 AGTGA-CTATTTTGTTATAAATCAATAATATT
*
499250 AGTGACTAATTTGTTAT
1 AGTGACTATTTTGTTAT
499267 TTTAAAACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.02
31 39 0.95
32 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (31 bp):
AGTGACTATTTTGTTATAAATCAATAATATT
Found at i:501496 original size:43 final size:43
Alignment explanation
Indices: 501447--501592 Score: 193
Period size: 43 Copynumber: 3.4 Consensus size: 43
501437 CGTTAAACAT
* * * *
501447 CACCTATTGCGGCGTTTGTCTTAAAAATGCTGCTAAATATCAA
1 CACCTATTGCGGCGTTTGTCTCACAAACGCCGCTAAATATCAA
* * * *
501490 CACCTATTGTGGCGTTTTTCTGACAAACGCCACTAAATATCAA
1 CACCTATTGCGGCGTTTGTCTCACAAACGCCGCTAAATATCAA
*
501533 CACCTATTGCGGCGTTTGTCACACAAACGCCGCTAAATATCAA
1 CACCTATTGCGGCGTTTGTCTCACAAACGCCGCTAAATATCAA
* *
501576 TACCTATTGCGGTGTTT
1 CACCTATTGCGGCGTTT
501593 TTTGTTAAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (43 bp):
CACCTATTGCGGCGTTTGTCTCACAAACGCCGCTAAATATCAA
Found at i:503913 original size:20 final size:18
Alignment explanation
Indices: 503872--503920 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
503862 TATTATTTTA
503872 ATAAATTATATTTTTATC
1 ATAAATTATATTTTTATC
503890 ATAATATTAT-TTTTTACCTC
1 ATAA-ATTATATTTTTA--TC
503910 ATAAAATTATA
1 AT-AAATTATA
503921 ATTAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 10 0.38
19 5 0.19
20 9 0.35
21 2 0.08
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAAATTATATTTTTATC
Found at i:509816 original size:2 final size:2
Alignment explanation
Indices: 509807--510091 Score: 100
Period size: 2 Copynumber: 145.0 Consensus size: 2
509797 TTGAAAAAAT
*
509807 TA TA -A TA TA T- TA -A TA TA TA TA TA TA TA TA TA TA CA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
509845 TA TA TA -A T- TA TA TA -A TA TG TA TA AA CTA TA TA GTT TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * * *
509886 TA TA TA CTA TGG TA TA TA AA CTA TA TA TG T- TA TA AA T- TA TA
1 TA TA TA -TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * *
509927 TA TA AA CA -A TA TA GTA TA TA AA CTA TA TA -A T- TT TT TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * * * *
509968 GTT TA TA TT TA TA TA T- TA TG TA AA AA TA CA TA TA AA CTA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
510011 TA -A AA T- TA TA TA TT TA TA TT TA TA TA CTA TG TA TA -A AA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
*
510052 TA TA GTT 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 TA
510092 CAATATACTT
Statistics
Matches: 210, Mismatches: 44, Indels: 58
0.67 0.14 0.19
Matches are distributed among these distances:
1 17 0.08
2 178 0.85
3 15 0.07
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:509928 original size:27 final size:27
Alignment explanation
Indices: 509898--509955 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
509888 TATACTATGG
* *
509898 TATATAAACTATATATGT-TATAAATTA
1 TATATAAACAATATA-GTATATAAACTA
509925 TATATAAACAATATAGTATATAAACTA
1 TATATAAACAATATAGTATATAAACTA
509952 TATA
1 TATA
509956 ATTTTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (27 bp):
TATATAAACAATATAGTATATAAACTA
Found at i:510040 original size:33 final size:34
Alignment explanation
Indices: 509997--510078 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 34
509987 GTAAAAATAC
* *
509997 ATATAAACTATATATAAAATTATATA-TTTATAT
1 ATATATACTATATATAAAACTATATAGTTTATAT
* *
510030 TTATATACTATGTATAAAACTATATAGTTTATAT
1 ATATATACTATATATAAAACTATATAGTTTATAT
510064 ATATATA-TATATATA
1 ATATATACTATATATA
510079 TATATATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 29 0.69
34 13 0.31
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (34 bp):
ATATATACTATATATAAAACTATATAGTTTATAT
Found at i:510063 original size:54 final size:55
Alignment explanation
Indices: 509942--510085 Score: 150
Period size: 54 Copynumber: 2.6 Consensus size: 55
509932 ACAATATAGT
*** *
509942 ATATAAACTATATA-ATTTTTTATATAGTTTATATTTATATATTATGTAAAAATAC
1 ATATAAACTATATATATAAATTATATA-TTTATATTTATATACTATGTAAAAATAC
*
509997 ATATAAACTATATATA-AAATTATATATTTATATTTATATACTATGTATAAA-AC
1 ATATAAACTATATATATAAATTATATATTTATATTTATATACTATGTAAAAATAC
*** * *
510050 TATATAGTTTATATATATATATATATATATATATAT
1 -ATATAAACTATATATATAAAT-TATATATTTATAT
510086 AATATACAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
53 2 0.03
54 36 0.48
55 24 0.32
56 13 0.17
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (55 bp):
ATATAAACTATATATATAAATTATATATTTATATTTATATACTATGTAAAAATAC
Found at i:510217 original size:27 final size:27
Alignment explanation
Indices: 510187--510240 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
510177 TGTATGTAAG
*
510187 TATATAT-TATACTTATGAGTATATATA
1 TATATATATATA-ATATGAGTATATATA
*
510214 TATATATATATAATATTAGTATATATA
1 TATATATATATAATATGAGTATATATA
510241 CAAGTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (27 bp):
TATATATATATAATATGAGTATATATA
Found at i:523310 original size:20 final size:20
Alignment explanation
Indices: 523285--523324 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
523275 TTCAAGAAGA
523285 ATGAAGAGTCCGAGCAACAT
1 ATGAAGAGTCCGAGCAACAT
**
523305 ATGAAGAGTTTGAGCAACAT
1 ATGAAGAGTCCGAGCAACAT
523325 CGGTTCACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (20 bp):
ATGAAGAGTCCGAGCAACAT
Found at i:524228 original size:41 final size:42
Alignment explanation
Indices: 524171--524254 Score: 161
Period size: 41 Copynumber: 2.0 Consensus size: 42
524161 TTGTCGTTTA
524171 AGTTCTTTAAGAAACTAAAACGT-AAACATGAATGATAAATG
1 AGTTCTTTAAGAAACTAAAACGTAAAACATGAATGATAAATG
524212 AGTTCTTTAAGAAACTAAAACGTAAAACATGAATGATAAATG
1 AGTTCTTTAAGAAACTAAAACGTAAAACATGAATGATAAATG
524254 A
1 A
524255 CATCTCTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 23 0.55
42 19 0.45
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (42 bp):
AGTTCTTTAAGAAACTAAAACGTAAAACATGAATGATAAATG
Found at i:531481 original size:30 final size:30
Alignment explanation
Indices: 531445--531512 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
531435 TTAGTCCTTA
531445 AGCTTCAACTATAAATACCCTAGCTCATTT
1 AGCTTCAACTATAAATACCCTAGCTCATTT
531475 AGCTTCAACTATAAATACCCTAGCTCATTT
1 AGCTTCAACTATAAATACCCTAGCTCATTT
531505 AGCTTCAA
1 AGCTTCAA
531513 AACCATCCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.32
Consensus pattern (30 bp):
AGCTTCAACTATAAATACCCTAGCTCATTT
Found at i:534852 original size:29 final size:29
Alignment explanation
Indices: 534810--534913 Score: 163
Period size: 29 Copynumber: 3.6 Consensus size: 29
534800 AATTCTACAG
* * *
534810 TGGCATCCGGGCGAGCTTGGAGATCGCCA
1 TGGCATCCGAGCGACCTTGGAGGTCGCCA
534839 TGGCATCCGAGCGACCTTGGAGGTCGCCA
1 TGGCATCCGAGCGACCTTGGAGGTCGCCA
*
534868 TGGCATCCGGGCGACCTTGGAGGTCGCCA
1 TGGCATCCGAGCGACCTTGGAGGTCGCCA
*
534897 TGACATCCGAGCGACCT
1 TGGCATCCGAGCGACCT
534914 GTGCGGTGTT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.17, C:0.31, G:0.35, T:0.17
Consensus pattern (29 bp):
TGGCATCCGAGCGACCTTGGAGGTCGCCA
Found at i:535022 original size:20 final size:20
Alignment explanation
Indices: 534999--535036 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
534989 TGGGATGCAT
*
534999 GTGGGAGCTGTGCATGGGAC
1 GTGGGAACTGTGCATGGGAC
*
535019 GTGGGAACTGTTCATGGG
1 GTGGGAACTGTGCATGGG
535037 CCATGCACGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.13, G:0.47, T:0.24
Consensus pattern (20 bp):
GTGGGAACTGTGCATGGGAC
Found at i:535175 original size:21 final size:21
Alignment explanation
Indices: 535149--535220 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
535139 GGGAGATTCC
535149 TGCATCCGTAGCTGCATGCGT
1 TGCATCCGTAGCTGCATGCGT
* * * *
535170 TGCATCCATAGCTGGGAGATTC-C
1 TGCATCCGTAGCT--G-CATGCGT
*
535193 TGCATCCGTAGCTGCATGTGT
1 TGCATCCGTAGCTGCATGCGT
535214 TGCATCC
1 TGCATCC
535221 ATAGTTGCGT
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
20 2 0.05
21 20 0.53
23 13 0.34
24 3 0.08
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (21 bp):
TGCATCCGTAGCTGCATGCGT
Found at i:535197 original size:44 final size:44
Alignment explanation
Indices: 535134--535224 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
535124 AGCTAGATTC
535134 TAGCTGGGAGATTCCTGCATCCGTAGCTGCATGCGTTGCATCCA
1 TAGCTGGGAGATTCCTGCATCCGTAGCTGCATGCGTTGCATCCA
*
535178 TAGCTGGGAGATTCCTGCATCCGTAGCTGCATGTGTTGCATCCA
1 TAGCTGGGAGATTCCTGCATCCGTAGCTGCATGCGTTGCATCCA
535222 TAG
1 TAG
535225 TTGCGTTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (44 bp):
TAGCTGGGAGATTCCTGCATCCGTAGCTGCATGCGTTGCATCCA
Found at i:535198 original size:23 final size:23
Alignment explanation
Indices: 535134--535206 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
535124 AGCTAGATTC
535134 TAGCTGGGAGATTCCTGCATCCG
1 TAGCTGGGAGATTCCTGCATCCG
* * * *
535157 TAGCT--G-CATGCGTTGCATCCA
1 TAGCTGGGAGATTC-CTGCATCCG
535178 TAGCTGGGAGATTCCTGCATCCG
1 TAGCTGGGAGATTCCTGCATCCG
535201 TAGCTG
1 TAGCTG
535207 CATGTGTTGC
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.08
21 13 0.34
23 19 0.50
24 3 0.08
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (23 bp):
TAGCTGGGAGATTCCTGCATCCG
Found at i:535625 original size:21 final size:21
Alignment explanation
Indices: 535600--535643 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
535590 AATCTAGTTA
535600 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
535621 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
535642 AT
1 AT
535644 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:535653 original size:28 final size:30
Alignment explanation
Indices: 535620--535682 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
535610 TAGTATAAAT
*
535620 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
535648 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
535678 TATTA
1 TATTA
535683 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:535743 original size:43 final size:48
Alignment explanation
Indices: 535643--535755 Score: 128
Period size: 50 Copynumber: 2.4 Consensus size: 48
535633 GTTTAAGTTA
*
535643 TATTATATTAGTTTATTAGTTTAAGTTATATATTATATTATATAAAAAAT
1 TATTA-ATTAGTTTATTAGTTTAAGTTATATA-TATATTATATAAAAAAG
*
535693 TAGTTAATTAGTTTCTTAGTTTAAGTTAT-TA-A-A-TATA-AAAAAAG
1 TA-TTAATTAGTTTATTAGTTTAAGTTATATATATATTATATAAAAAAG
* *
535737 TATTAATTAATTTGTTAGT
1 TATTAATTAGTTTATTAGT
535756 GTCTTTAAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
43 15 0.26
44 8 0.14
45 4 0.07
46 1 0.02
47 1 0.02
49 2 0.03
50 24 0.41
51 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.50
Consensus pattern (48 bp):
TATTAATTAGTTTATTAGTTTAAGTTATATATATATTATATAAAAAAG
Found at i:536205 original size:17 final size:16
Alignment explanation
Indices: 536172--536228 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
536162 TAATTTTCGT
536172 TTTAAAAAATATTGTG
1 TTTAAAAAATATTGTG
*
536188 TTTAAAAACATTTAGTGTTG
1 TTTAAAAA-A--TATTG-TG
* *
536208 TTTTAAAAATATTTTG
1 TTTAAAAAATATTGTG
536224 TTTAA
1 TTTAA
536229 TTTACATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
16 14 0.44
17 4 0.12
19 5 0.16
20 9 0.28
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.49
Consensus pattern (16 bp):
TTTAAAAAATATTGTG
Found at i:539451 original size:26 final size:26
Alignment explanation
Indices: 539422--539718 Score: 203
Period size: 26 Copynumber: 12.2 Consensus size: 26
539412 TTTGATGATT
539422 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
539448 TAGTAATGATTTGATAATAATCA-TA
1 TAGTAATGATTTGATAATAATCATTA
* *
539473 TAATAAT--TTT-AGTAATAATTATTA
1 TAGTAATGATTTGA-TAATAATCATTA
* *
539497 TA-AAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
539518 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
539542 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
539568 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
539594 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
* *
539620 TA-AAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
539641 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
539665 TAGTAATGATTTGATAATAATCA-TA
1 TAGTAATGATTTGATAATAATCATTA
* * *
539690 TAATAATGATTTTATAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
539715 TAGT
1 TAGT
539719 TATTATTTAG
Statistics
Matches: 224, Mismatches: 23, Indels: 49
0.76 0.08 0.17
Matches are distributed among these distances:
19 2 0.01
20 10 0.04
21 4 0.02
22 23 0.10
23 16 0.07
24 27 0.12
25 47 0.21
26 83 0.37
27 12 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:539516 original size:11 final size:11
Alignment explanation
Indices: 539485--539770 Score: 84
Period size: 11 Copynumber: 23.6 Consensus size: 11
539475 ATAATTTTAG
*
539485 TAATAATTATT
1 TAATAATGATT
539496 ATAA-AATGATT
1 -TAATAATGATT
539507 TAATAATGATT
1 TAATAATGATT
539518 T-A-AAT-ATT
1 TAATAATGATT
539526 TAATGATTTGATGATT
1 TAAT-A----ATGATT
*
539542 TAGTAATGATTT
1 TAATAATGA-TT
*
539554 GATAATAATCATT
1 --TAATAATGATT
*
539567 ATAGTAATGATTT
1 -TAATAATGA-TT
*
539580 GATAATAATCATT
1 --TAATAATGATT
539593 ATAATAATGATTT
1 -TAATAATGA-TT
*
539606 AGTAATAATCATT
1 --TAATAATGATT
539619 ATAA-AATGATT
1 -TAATAATGATT
539630 TAATAATGATT
1 TAATAATGATT
539641 T-A-AAT-ATT
1 TAATAATGATT
539649 TAATGATTTGATGATT
1 TAAT-A----ATGATT
*
539665 TAGTAATGATTT
1 TAATAATGA-TT
* *
539677 GATAATAATCATA
1 --TAATAATGATT
539690 TAATAATGATTTT
1 TAATAATGA--TT
539703 ATAATAATGATT
1 -TAATAATGATT
* * *
539715 TAGTTATTATT
1 TAATAATGATT
* *
539726 TAGTAATTATTT
1 TAATAATGA-TT
539738 ATAATAATGATT
1 -TAATAATGATT
539750 TAATACTAATGATT
1 T-A-A-TAATGATT
539764 TAATAAT
1 TAATAAT
539771 TATTACTAAT
Statistics
Matches: 213, Mismatches: 25, Indels: 73
0.68 0.08 0.23
Matches are distributed among these distances:
8 8 0.04
9 8 0.04
10 8 0.04
11 67 0.31
12 35 0.16
13 21 0.10
14 48 0.23
15 6 0.03
16 12 0.06
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (11 bp):
TAATAATGATT
Found at i:539598 original size:12 final size:12
Alignment explanation
Indices: 539555--539636 Score: 78
Period size: 12 Copynumber: 6.7 Consensus size: 12
539545 TAATGATTTG
539555 ATAATAATCATT
1 ATAATAATCATT
* *
539567 ATAGTAATGATTT
1 ATAATAATCA-TT
539580 GATAATAATCATT
1 -ATAATAATCATT
*
539593 ATAATAATGATTT
1 ATAATAATCA-TT
539606 AGTAATAATCATT
1 A-TAATAATCATT
*
539619 ATAA-AATGATT
1 ATAATAATCATT
539630 -TAATAAT
1 ATAATAAT
539637 GATTTAAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
10 3 0.05
11 9 0.16
12 20 0.34
13 10 0.17
14 16 0.28
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (12 bp):
ATAATAATCATT
Found at i:539654 original size:123 final size:122
Alignment explanation
Indices: 539369--539754 Score: 608
Period size: 120 Copynumber: 3.2 Consensus size: 122
539359 ATGTATTTAT
*
539369 TAATCATTATAAAAATTATTT-ATAATGA-TTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTAT-AAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
539432 TTGATAATAATCATTATAGTAATGATTTGATAATAATCA-TATAATAAT-TTTAGTAA
65 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATATTTAGTAA
*
539488 TAATTATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
1 TAATCATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
539553 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAAT-ATTTAGTAA
539611 TAATCATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
1 TAATCATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
* * * * *
539676 TGATAATAATCA-TATAATAATGATTTTATAATAATGATT-TAGTTATTATTTAGTAA
66 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATA-ATAATATTTAGTAA
*
539732 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAA-AATGATTTAATA
539755 CTAATGATTT
Statistics
Matches: 251, Mismatches: 9, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
118 9 0.04
119 22 0.09
120 86 0.34
121 23 0.09
122 27 0.11
123 84 0.33
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.46
Consensus pattern (122 bp):
TAATCATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATATTTAGTAA
Found at i:539657 original size:52 final size:51
Alignment explanation
Indices: 539426--539759 Score: 183
Period size: 49 Copynumber: 6.8 Consensus size: 51
539416 ATGATTTAGT
* *
539426 AATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCA-TATA-A
1 AATGATTTAATAATAAT-ATTATAATAATGATTTGATAATAATCATTATAGA
* *
539476 TAAT--TTTAGTAATAATTATTATAA-AATGA-TT--TAATAATGATT-T--A
1 -AATGATTTAATAATAA-TATTATAATAATGATTTGATAATAATCATTATAGA
* * * *
539520 AAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAATCATTATAGT
1 AATGATTTAAT-A-ATAAT-ATTATAATAATGATTTGATAATAATCATTATAGA
*
539572 AATGATTTGATAATAATCATTATAATAATGATTT-AGTAATAATCATTATA-A
1 AATGATTTAATAATAAT-ATTATAATAATGATTTGA-TAATAATCATTATAGA
* * * * * * * *
539623 AATGATTTAATAATGAT-TTA-AATATTTA-ATGAT-TTGATGATT-TAGT
1 AATGATTTAATAATAATATTATAATAATGATTTGATAATAATCATTATAGA
* * * *
539669 AATGATTTGATAATAATCA-TATAATAATGATTTTATAATAATGATT-TAGT
1 AATGATTTAATAATAAT-ATTATAATAATGATTTGATAATAATCATTATAGA
* * * * * *
539719 TATTATTTAGTAATTAT-TTATAATAATGATTTAATACTAAT
1 AATGATTTAATAATAATATTATAATAATGATTTGATAATAAT
539760 GATTTAATAA
Statistics
Matches: 219, Mismatches: 40, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
43 3 0.01
44 6 0.03
45 15 0.07
46 32 0.15
47 8 0.04
48 18 0.08
49 52 0.24
50 25 0.11
51 25 0.11
52 29 0.13
53 6 0.03
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (51 bp):
AATGATTTAATAATAATATTATAATAATGATTTGATAATAATCATTATAGA
Found at i:539726 original size:25 final size:25
Alignment explanation
Indices: 539416--539770 Score: 194
Period size: 26 Copynumber: 14.5 Consensus size: 25
539406 TAATGATTTG
539416 ATGATTTAGTAATGATTTGATAATA
1 ATGATTTAGTAATGATTTGATAATA
*
539441 ATCATTATAGTAATGATTTGATAATA
1 ATGATT-TAGTAATGATTTGATAATA
* * *
539467 ATCA--TA-TAATAATTTTAGTAATA
1 ATGATTTAGTAATGATTTGA-TAATA
* *
539490 ATTATTATA-AAATGA-TT--TAATA
1 ATGATT-TAGTAATGATTTGATAATA
* * *
539512 ATGATTTA--AAT-ATTTAATGATTTG
1 ATGATTTAGTAATGATTTGAT-A-ATA
539536 ATGATTTAGTAATGATTTGATAATA
1 ATGATTTAGTAATGATTTGATAATA
*
539561 ATCATTATAGTAATGATTTGATAATA
1 ATGATT-TAGTAATGATTTGATAATA
* *
539587 ATCATTATAATAATGATTT-AGTAATA
1 ATGATT-TAGTAATGATTTGA-TAATA
* *
539613 ATCATTATA-AAATGA-TT--TAATA
1 ATGATT-TAGTAATGATTTGATAATA
* * *
539635 ATGATTTA--AAT-ATTTAATGATTTG
1 ATGATTTAGTAATGATTTGAT-A-ATA
539659 ATGATTTAGTAATGATTTGATAATA
1 ATGATTTAGTAATGATTTGATAATA
* * * *
539684 ATCATATAATAATGATTTTATAATA
1 ATGATTTAGTAATGATTTGATAATA
* * *
539709 ATGATTTAGTTATTATTT-AGTAATT
1 ATGATTTAGTAATGATTTGA-TAATA
* * *
539734 AT--TTATAATAATGATTTAATACTA
1 ATGATT-TAGTAATGATTTGATAATA
*
539758 ATGATTTAATAAT
1 ATGATTTAGTAAT
539771 TATTACTAAT
Statistics
Matches: 266, Mismatches: 36, Indels: 56
0.74 0.10 0.16
Matches are distributed among these distances:
19 2 0.01
20 10 0.04
21 4 0.02
22 31 0.12
23 14 0.05
24 35 0.13
25 68 0.26
26 90 0.34
27 12 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (25 bp):
ATGATTTAGTAATGATTTGATAATA
Found at i:539761 original size:14 final size:14
Alignment explanation
Indices: 539425--539770 Score: 110
Period size: 14 Copynumber: 26.1 Consensus size: 14
539415 GATGATTTAG
*
539425 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
539439 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
539451 TAATGATTTGATAA
1 TAATGATTTAATAA
*
539465 TAATCA--T-ATAA
1 TAATGATTTAATAA
*
539476 TAAT--TTTAGTAA
1 TAATGATTTAATAA
*
539488 TAATTA-TT-ATAA
1 TAATGATTTAATAA
539500 -AATGA-TT--TAA
1 TAATGATTTAATAA
*
539510 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
539526 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
539545 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
539559 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
539571 TAATGATTTGATAA
1 TAATGATTTAATAA
*
539585 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
539597 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
539611 TAATCA-TT-ATAA
1 TAATGATTTAATAA
539623 -AATGA-TT--TAA
1 TAATGATTTAATAA
*
539633 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
539649 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
539668 TAATGATTTGATAA
1 TAATGATTTAATAA
*
539682 TAATCA--T-ATAA
1 TAATGATTTAATAA
*
539693 TAATGATTTTATAA
1 TAATGATTTAATAA
*
539707 TAATGATTTAGT--
1 TAATGATTTAATAA
* *
539719 T-ATTATTTAGTAA
1 TAATGATTTAATAA
539732 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
539742 TAATGATTTAATAC
1 TAATGATTTAATAA
539756 TAATGATTTAATAA
1 TAATGATTTAATAA
539770 T
1 T
539771 TATTACTAAT
Statistics
Matches: 256, Mismatches: 36, Indels: 80
0.69 0.10 0.22
Matches are distributed among these distances:
10 10 0.04
11 53 0.21
12 47 0.18
13 22 0.09
14 74 0.29
15 4 0.02
16 22 0.09
18 2 0.01
19 18 0.07
20 4 0.02
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:539793 original size:38 final size:38
Alignment explanation
Indices: 539723--539796 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
539713 TTTAGTTATT
* **
539723 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
539761 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
539797 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:540002 original size:17 final size:17
Alignment explanation
Indices: 539977--540009 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
539967 ACTAAATATT
*
539977 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
539994 TAATGATTTGATACTA
1 TAATGATTTGATACTA
540010 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:540002 original size:25 final size:24
Alignment explanation
Indices: 539927--540002 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
539917 TTATTGTTAT
539927 ATTTAATTATTTGATAC--TAATG
1 ATTTAATTATTTGATACTATAATG
* *
539949 ATTTAAAATAGTTGATTTACTA-AAT-
1 ATTT-AATTATTTGA--TACTATAATG
539974 ATTTAATTATTTGATACTAGTAATG
1 ATTTAATTATTTGATACTA-TAATG
539999 ATTT
1 ATTT
540003 GATACTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
22 9 0.21
23 8 0.19
24 11 0.26
25 11 0.26
26 3 0.07
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTTAATTATTTGATACTATAATG
Found at i:542436 original size:46 final size:48
Alignment explanation
Indices: 542359--542450 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
542349 CAACAAACAA
*
542359 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAACTTAACTATTTAACTAAAACAAACTAATTAAAT-ATTTTTTTT
*
542408 ATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAACTATTTTTT
1 ATATAACTTAACTATTTAACTAAAACAAACTAATTAAATATTTTTT
542451 AACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 7 0.17
46 16 0.39
47 5 0.12
48 6 0.15
49 7 0.17
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAAAACAAACTAATTAAATATTTTTTTT
Found at i:542461 original size:47 final size:48
Alignment explanation
Indices: 542359--542463 Score: 135
Period size: 46 Copynumber: 2.2 Consensus size: 48
542349 CAACAAACAA
* *
542359 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTCT
*
542408 ATATAACTAACTA-TTAAC-AAAACAAACTAATTAACT-ATTTTTTAACT
1 ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTT--CT
542455 ATATAACTA
1 ATATAACTA
542464 TCAAACATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
45 7 0.14
46 16 0.31
47 15 0.29
48 6 0.12
49 7 0.14
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (48 bp):
ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTCT
Found at i:543048 original size:29 final size:29
Alignment explanation
Indices: 543015--543090 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
543005 TCGTGAGCTA
** *
543015 GGACTACATGGCGACCTACTTGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCC
543044 GGACTACATGGCGACCTACAAGGTCGCCC
1 GGACTACATGGCGACCTACAAGGTCGCCC
* *
543073 AGACTGCATGGCGACCTA
1 GGACTACATGGCGACCTA
543091 TCCATTGGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.22, C:0.32, G:0.29, T:0.17
Consensus pattern (29 bp):
GGACTACATGGCGACCTACAAGGTCGCCC
Found at i:543110 original size:9 final size:9
Alignment explanation
Indices: 543096--543134 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
543086 ACCTATCCAT
543096 TGGCTCGTA
1 TGGCTCGTA
543105 TGGCTCGTATA
1 TGGCTCG--TA
*
543116 TGGCTTGTA
1 TGGCTCGTA
543125 TGGCTCGTA
1 TGGCTCGTA
543134 T
1 T
543135 TCGTATGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 18 0.69
11 8 0.31
ACGTcount: A:0.13, C:0.18, G:0.31, T:0.38
Consensus pattern (9 bp):
TGGCTCGTA
Found at i:543125 original size:20 final size:20
Alignment explanation
Indices: 543096--543134 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
543086 ACCTATCCAT
543096 TGGCTCGTATGGCTCGTATA
1 TGGCTCGTATGGCTCGTATA
*
543116 TGGCTTGTATGGCTCGTAT
1 TGGCTCGTATGGCTCGTAT
543135 TCGTATGTCA
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:0.13, C:0.18, G:0.31, T:0.38
Consensus pattern (20 bp):
TGGCTCGTATGGCTCGTATA
Found at i:546924 original size:24 final size:23
Alignment explanation
Indices: 546897--546947 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
546887 GTTTCCCGAG
546897 CATCAGACAATGTTACTTTTATGT
1 CATCAGA-AATGTTACTTTTATGT
** **
546921 CATCCTAGTTGTTACTTTTATGT
1 CATCAGAAATGTTACTTTTATGT
546944 CATC
1 CATC
546948 CTAGTTGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.45
Consensus pattern (23 bp):
CATCAGAAATGTTACTTTTATGT
Found at i:546933 original size:23 final size:23
Alignment explanation
Indices: 546907--546957 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
546897 CATCAGACAA
546907 TGTTACTTTTATGTCATCCTAGT
1 TGTTACTTTTATGTCATCCTAGT
546930 TGTTACTTTTATGTCATCCTAGT
1 TGTTACTTTTATGTCATCCTAGT
546953 TGTTA
1 TGTTA
546958 TTGTTTCTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.53
Consensus pattern (23 bp):
TGTTACTTTTATGTCATCCTAGT
Found at i:548247 original size:24 final size:24
Alignment explanation
Indices: 548220--548275 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
548210 CAAACTCAAA
* ** *
548220 CATTTTAATTTTGGTAAAACGTTT
1 CATTTCAATTTTACTAAAACATTT
548244 CATTTCAATTTTACTAAAACATTT
1 CATTTCAATTTTACTAAAACATTT
548268 CATTTCAA
1 CATTTCAA
548276 GACAAAAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.46
Consensus pattern (24 bp):
CATTTCAATTTTACTAAAACATTT
Found at i:553306 original size:19 final size:19
Alignment explanation
Indices: 553282--553358 Score: 100
Period size: 19 Copynumber: 4.1 Consensus size: 19
553272 TATGCATTAG
*
553282 GCTATGAATTTGAAAATAA
1 GCTATGAATCTGAAAATAA
* *
553301 GCTATGACTTTGAAAATAA
1 GCTATGAATCTGAAAATAA
* *
553320 GCTATGAATCTGACAGTAA
1 GCTATGAATCTGAAAATAA
*
553339 GCTATGAGTCTGAAAATAA
1 GCTATGAATCTGAAAATAA
553358 G
1 G
553359 TTTTGATTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:553340 original size:38 final size:38
Alignment explanation
Indices: 553282--553376 Score: 109
Period size: 38 Copynumber: 2.5 Consensus size: 38
553272 TATGCATTAG
* *
553282 GCTATGAATTTGAAAATAAGCTATGACTTTGAAAATAA
1 GCTATGAATCTGAAAATAAGCTATGACTCTGAAAATAA
* * *
553320 GCTATGAATCTGACAGTAAGCTATGAGTCTGAAAATAA
1 GCTATGAATCTGAAAATAAGCTATGACTCTGAAAATAA
* * * *
553358 GTTTTGATTCAGAAAATAA
1 GCTATGAATCTGAAAATAA
553377 ATTCTAAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (38 bp):
GCTATGAATCTGAAAATAAGCTATGACTCTGAAAATAA
Found at i:570290 original size:23 final size:23
Alignment explanation
Indices: 570264--570315 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
570254 TTATTGGCTC
570264 AGGAAGTAGTTAGGGGATATTCT
1 AGGAAGTAGTTAGGGGATATTCT
570287 AGGAAGTAGTTAGGGGATATTCT
1 AGGAAGTAGTTAGGGGATATTCT
570310 AGGAAG
1 AGGAAG
570316 AACCTTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.33, C:0.04, G:0.37, T:0.27
Consensus pattern (23 bp):
AGGAAGTAGTTAGGGGATATTCT
Found at i:574058 original size:20 final size:21
Alignment explanation
Indices: 574020--574059 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
574010 CATACGAATA
* *
574020 TTTTACCATTTTCTTTTATTT
1 TTTTACCATTTACTATTATTT
574041 TTTTACCA-TTACTATTATT
1 TTTTACCATTTACTATTATT
574060 ATTATTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTACCATTTACTATTATTT
Found at i:574125 original size:13 final size:14
Alignment explanation
Indices: 574100--574131 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
574090 GTATATATCA
574100 TTTTATTTGTTTAT
1 TTTTATTTGTTTAT
574114 TTTTATTT-TTTAT
1 TTTTATTTGTTTAT
574127 TTTTA
1 TTTTA
574132 CAAATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTATTTGTTTAT
Found at i:574144 original size:16 final size:15
Alignment explanation
Indices: 574121--574163 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
574111 TATTTTTATT
574121 TTTTATTTTTACAAA
1 TTTTATTTTTACAAA
* *
574136 TTATTATTTATACATA
1 TT-TTATTTTTACAAA
574152 TTTTATCTTTTA
1 TTTTAT-TTTTA
574164 TTTTCATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTATTTTTACAAA
Found at i:577589 original size:9 final size:8
Alignment explanation
Indices: 577565--577630 Score: 55
Period size: 8 Copynumber: 8.2 Consensus size: 8
577555 TCCAATCAAG
*
577565 AAGAAAAG
1 AAGAAAAA
*
577573 AAGCAAAA
1 AAGAAAAA
577581 AAGCAAAAA
1 AAG-AAAAA
577590 AA-AAAAA
1 AAGAAAAA
577597 CAAGAAAAA
1 -AAGAAAAA
* *
577606 GAG-AAAC
1 AAGAAAAA
*
577613 AAGAACAA
1 AAGAAAAA
577621 AAGAAAAA
1 AAGAAAAA
577629 AA
1 AA
577631 AGCAAAAAGC
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
7 10 0.22
8 24 0.53
9 11 0.24
ACGTcount: A:0.79, C:0.08, G:0.14, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:577604 original size:15 final size:15
Alignment explanation
Indices: 577586--577638 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
577576 CAAAAAAGCA
577586 AAAAAAAAAAACAAG
1 AAAAAAAAAAACAAG
* *
577601 AAAAAGAGAAACAAG
1 AAAAAAAAAAACAAG
*
577616 AACAAAAGAAAAAAAAG
1 AA-AAAA-AAAAACAAG
577633 CAAAAA
1 -AAAAA
577639 GCAAAAAGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 15 0.50
16 3 0.10
17 10 0.33
18 2 0.07
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAACAAG
Found at i:577629 original size:7 final size:7
Alignment explanation
Indices: 577565--577658 Score: 62
Period size: 7 Copynumber: 12.1 Consensus size: 7
577555 TCCAATCAAG
577565 AAGAAAA
1 AAGAAAA
577572 GAAGCAAAA
1 -AAG-AAAA
577581 AAGCAAAAA
1 AAG--AAAA
*
577590 AAAAAAA
1 AAGAAAA
577597 CAAGAAAA
1 -AAGAAAA
*
577605 AGAGAAAC
1 A-AGAAAA
577613 AAGAACAA
1 AAGAA-AA
577621 AAGAAAAAA
1 AAG--AAAA
*
577630 AAGCAAA
1 AAGAAAA
*
577637 AAGCAAA
1 AAGAAAA
*
577644 AAGCAAA
1 AAGAAAA
577651 AAGAAAA
1 AAGAAAA
577658 A
1 A
577659 GGGACAAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
7 33 0.46
8 22 0.31
9 15 0.21
10 2 0.03
ACGTcount: A:0.78, C:0.09, G:0.14, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:578305 original size:22 final size:22
Alignment explanation
Indices: 578280--578350 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
578270 CCATCAATCT
*
578280 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
578302 TTTGAGCATCAAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
*
578324 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGTCAAACC
578346 TTTGA
1 TTTGA
578351 CCAAACACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (22 bp):
TTTGAGCATCAAATGTCAAACC
Found at i:579086 original size:105 final size:105
Alignment explanation
Indices: 578946--579200 Score: 483
Period size: 105 Copynumber: 2.4 Consensus size: 105
578936 GCTTTAGAGT
578946 CAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAA
1 CAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAA
579011 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
579051 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCGGAGCCAA
1 CAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAA
579116 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
579156 CAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACA
1 CAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAACA
579201 AGTTCGATTT
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 146 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (105 bp):
CAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAA
TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:579369 original size:43 final size:43
Alignment explanation
Indices: 579308--579557 Score: 185
Period size: 43 Copynumber: 5.4 Consensus size: 43
579298 CAGAGCCAAT
579308 TTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAG
*** ** * * * *
579351 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAAACA---ACGCAAG
579402 TTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAG
*** ** * * * *
579445 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAAACA---ACGCAAG
*
579496 TTCAACTTCACAACGAAGGATATTTGACTCCAAACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAG
579539 TTCAACTTCACAACGAAGG
1 TTCAACTTCACAACGAAGG
579558 GACCGCTGGT
Statistics
Matches: 154, Mismatches: 37, Indels: 32
0.69 0.17 0.14
Matches are distributed among these distances:
43 61 0.40
44 6 0.04
45 6 0.04
46 14 0.09
48 14 0.09
49 5 0.03
50 6 0.04
51 42 0.27
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAG
Found at i:579369 original size:191 final size:192
Alignment explanation
Indices: 579007--579603 Score: 870
Period size: 188 Copynumber: 3.1 Consensus size: 192
578997 AAATTCAGAG
*
579007 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAA
579072 GGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCGGAGCCAATTTCAACTTCACAACGAAGGA
66 GGGACCGCTGGTTGT---C-AAC--TTCTCAAATTC-GAGCCAATTTCAACTTCACAACGAAGGA
* * *
579137 TATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACAA
124 TATTGGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAA
579202 G-TT
189 GTTT
* ***
579205 -CGATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAA
**
579269 GGGACCGCTGACTGTCAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 GGGACCGCTGGTTGTCAACTTCTCAAATTC-GAGCCAATTTCAACTTCACAACGAAGGATATTGG
579334 ACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAAC-AGTTT
130 ACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAAGTTT
*
579396 CCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA-ACAACGCAAGTTCAACTTCACAACG
1 -CCAATTTCAACTTCACAACGAAGGATATTGGACT-CAAGACAACGCAAGTTCAACTTCACGACG
*** ** *
579460 AAGGGACCGCTGGTTGTCAA-TAAACAGTTTC---CCAATTTCAACTTCACAACGAAGGATATTT
64 AAGGGACCGCTGGTTGTCAACTTCTCAAATTCGAGCCAATTTCAACTTCACAACGAAGGATATTG
579521 GACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAAC-AGTTT
129 GACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAAGTTT
*
579584 CCCAATTTCAGCTTCACAAC
1 -CCAATTTCAACTTCACAAC
579604 AAAGTATCTT
Statistics
Matches: 370, Mismatches: 25, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
188 111 0.30
190 2 0.01
191 101 0.27
192 6 0.02
193 74 0.20
194 4 0.01
197 72 0.19
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (192 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAACTTCTCAAATTCGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
CTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAAGTTT
Found at i:579412 original size:51 final size:51
Alignment explanation
Indices: 579351--579603 Score: 223
Period size: 51 Copynumber: 5.3 Consensus size: 51
579341 ACAACGCAAG
579351 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAAT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAAT
*** ** * * * *
579402 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAAACA---ACGCAAG
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAAT
579445 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAAT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAAT
** * *** * * *
579496 TTCAACTTCACAACGAA-GGA----TATTTGACTCCAAACA---ACGCAAG
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAAT
579539 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAAT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAAT
*
579590 TTCAGCTTCACAAC
1 TTCAACTTCACAAC
579604 AAAGTATCTT
Statistics
Matches: 149, Mismatches: 37, Indels: 32
0.68 0.17 0.15
Matches are distributed among these distances:
43 42 0.28
44 6 0.04
45 3 0.02
46 17 0.11
48 17 0.11
49 3 0.02
50 6 0.04
51 55 0.37
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (51 bp):
TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAAT
Found at i:579436 original size:94 final size:94
Alignment explanation
Indices: 579112--579603 Score: 740
Period size: 94 Copynumber: 5.2 Consensus size: 94
579102 AAATTCGGAG
* * *
579112 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAACGAA
579177 GGGACCGCTGGTTGTCAATAAACAAG-TT-
66 GGGACCGCTGGTTGTCAATAAAC-AGTTTC
* *** *
579205 -CGATTTCAACTTCACAACGAAGGATATTGGACT-CAAGACAGTACAAGTTCAACTTCACGACGA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA-ACAACGCAAGTTCAACTTCACAACGA
** *** **
579268 AGGGACCGCTGACTGTCAACTTCTCAAATTC
65 AGGGACCGCTGGTTGTCAA-TAAACAGTTTC
579299 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAA
579364 CGAAGGGACCGCTGGTTGTCAATAAACAGTTTC
62 CGAAGGGACCGCTGGTTGTCAATAAACAGTTTC
579397 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAACGAA
579462 GGGACCGCTGGTTGTCAATAAACAGTTTC
66 GGGACCGCTGGTTGTCAATAAACAGTTTC
*
579491 CCAATTTCAACTTCACAACGAAGGATATTTGACTCCAAACAACGCAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAACGAA
579556 GGGACCGCTGGTTGTCAATAAACAGTTTC
66 GGGACCGCTGGTTGTCAATAAACAGTTTC
*
579585 CCAATTTCAGCTTCACAAC
1 CCAATTTCAACTTCACAAC
579604 AAAGTATCTT
Statistics
Matches: 363, Mismatches: 26, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
91 2 0.01
92 72 0.20
93 4 0.01
94 205 0.56
98 6 0.02
99 71 0.20
100 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (94 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAACGAA
GGGACCGCTGGTTGTCAATAAACAGTTTC
Found at i:579677 original size:20 final size:20
Alignment explanation
Indices: 579652--579693 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
579642 CCAGAACTCT
579652 GAGTTCGATTTCAACTTCAC
1 GAGTTCGATTTCAACTTCAC
* *
579672 GAGTTCGTTTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
579692 GA
1 GA
579694 CGAAGGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:581161 original size:20 final size:21
Alignment explanation
Indices: 581123--581162 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
581113 CATACGAATA
* *
581123 TTTTACCATTTTCTTTTATTT
1 TTTTACCATTTACTATTATTT
581144 TTTTACCA-TTACTATTATT
1 TTTTACCATTTACTATTATT
581163 ATTATTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTACCATTTACTATTATTT
Found at i:581228 original size:13 final size:14
Alignment explanation
Indices: 581203--581234 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
581193 GTATATATCA
581203 TTTTATTTGTTTAT
1 TTTTATTTGTTTAT
581217 TTTTATTT-TTTAT
1 TTTTATTTGTTTAT
581230 TTTTA
1 TTTTA
581235 CAAATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTATTTGTTTAT
Found at i:581247 original size:16 final size:15
Alignment explanation
Indices: 581224--581266 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
581214 TATTTTTATT
581224 TTTTATTTTTACAAA
1 TTTTATTTTTACAAA
* *
581239 TTATTATTTATACATA
1 TT-TTATTTTTACAAA
581255 TTTTATCTTTTA
1 TTTTAT-TTTTA
581267 TTTTCATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTATTTTTACAAA
Done.