Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 105 of 125
Found at i:31740008 original size:2 final size:2
Alignment explanation
Indices: 31740001--31740041 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
31739991 CTATTAAAGG
31740001 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
31740042 CTTTTCCCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:31743347 original size:31 final size:30
Alignment explanation
Indices: 31743294--31743355 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
31743284 ACCCAAATAT
31743294 TATGTTATAAAACAATATTATATTAATTATA
1 TATGTTATAAAACAATATTATA-TAATTATA
*
31743325 TATGTTA-AATAACAAT-TATATATAGTTATA
1 TATGTTATAA-AACAATAT-TATATAATTATA
31743355 T
1 T
31743356 TTATATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (30 bp):
TATGTTATAAAACAATATTATATAATTATA
Found at i:31751322 original size:2 final size:2
Alignment explanation
Indices: 31751315--31751340 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31751305 GCTGCTGCTG
31751315 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
31751341 TTAATTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:31753158 original size:17 final size:17
Alignment explanation
Indices: 31753133--31753171 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
31753123 TTTTTATTAA
*
31753133 CTTTATTTTCTCCCTTT
1 CTTTATTTTCTACCTTT
* *
31753150 CTTTCTTTTCTATCTTT
1 CTTTATTTTCTACCTTT
31753167 CTTTA
1 CTTTA
31753172 AATTATTTCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.67
Consensus pattern (17 bp):
CTTTATTTTCTACCTTT
Found at i:31754123 original size:32 final size:32
Alignment explanation
Indices: 31754065--31754136 Score: 78
Period size: 32 Copynumber: 2.2 Consensus size: 32
31754055 TCGAAAAGTT
*
31754065 AATATTTTTTAGTTTTTGGATGAATTTGTAT-AA
1 AATATTTTTTAGTTTTTGGA-GAATTTCT-TGAA
31754098 AATATTTTTTA-TTGTTTGGCA-AATTTCTTGAA
1 AATATTTTTTAGTT-TTTGG-AGAATTTCTTGAA
31754130 AATATTT
1 AATATTT
31754137 CATAAAAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
31 1 0.03
32 17 0.49
33 16 0.46
34 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (32 bp):
AATATTTTTTAGTTTTTGGAGAATTTCTTGAA
Found at i:31755024 original size:15 final size:14
Alignment explanation
Indices: 31755004--31755047 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
31754994 CAGAAAAGGT
*
31755004 TAAAAATATTTTCTG
1 TAAAAA-ATTTTATG
*
31755019 TAAAAACTTTTATG
1 TAAAAAATTTTATG
*
31755033 TAAAAACTTTTATG
1 TAAAAAATTTTATG
31755047 T
1 T
31755048 TGAAACAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 21 0.78
15 6 0.22
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TAAAAAATTTTATG
Found at i:31755053 original size:14 final size:14
Alignment explanation
Indices: 31755012--31755047 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
31755002 GTTAAAAATA
*
31755012 TTTTCTGTAAAAAC
1 TTTTATGTAAAAAC
31755026 TTTTATGTAAAAAC
1 TTTTATGTAAAAAC
31755040 TTTTATGT
1 TTTTATGT
31755048 TGAAACAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (14 bp):
TTTTATGTAAAAAC
Found at i:31763307 original size:10 final size:10
Alignment explanation
Indices: 31763234--31763381 Score: 78
Period size: 10 Copynumber: 14.9 Consensus size: 10
31763224 GATATAAACT
31763234 TATAAAAACTA
1 TATAAAAA-TA
31763245 TA-AAAAAT-
1 TATAAAAATA
* * *
31763253 TTTAATAATT
1 TATAAAAATA
31763263 TATAAAAAT-
1 TATAAAAATA
*
31763272 TATAAAATTA
1 TATAAAAATA
31763282 -ATAAAATATA
1 TATAAAA-ATA
*
31763292 TTTAAAAATA
1 TATAAAAATA
31763302 TATAAAATATA
1 TATAAAA-ATA
* *
31763313 TATTAAAATTC
1 TA-TAAAAATA
31763324 TATAAAAA-A
1 TATAAAAATA
31763333 TCATAAAAAGTA
1 T-ATAAAAA-TA
*
31763345 T-TAAAATTGA
1 TATAAAAAT-A
**
31763355 TATAAACTTA
1 TATAAAAATA
31763365 T-TAAAAA-A
1 TATAAAAATA
*
31763373 TAAAAAAAT
1 TATAAAAAT
31763382 CATTAAAACT
Statistics
Matches: 106, Mismatches: 17, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
8 3 0.03
9 31 0.29
10 44 0.42
11 21 0.20
12 7 0.07
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (10 bp):
TATAAAAATA
Found at i:31763321 original size:12 final size:12
Alignment explanation
Indices: 31763283--31763321 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 12
31763273 ATAAAATTAA
31763283 TAAAATATAT-T
1 TAAAATATATAT
31763294 TAAAA-ATATA-
1 TAAAATATATAT
31763304 TAAAATATATAT
1 TAAAATATATAT
31763316 TAAAAT
1 TAAAAT
31763322 TCTATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.36
11 10 0.40
12 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAATATATAT
Found at i:31763858 original size:9 final size:9
Alignment explanation
Indices: 31763832--31763963 Score: 66
Period size: 9 Copynumber: 15.1 Consensus size: 9
31763822 TTAATTTTAA
*
31763832 ATAAGTTTT
1 ATAATTTTT
31763841 ATTAA-TTTT
1 A-TAATTTTT
31763850 ATAATTTTT
1 ATAATTTTT
31763859 AT-A-TTTT
1 ATAATTTTT
** *
31763866 ATAACATTA
1 ATAATTTTT
31763875 ATAATGTTTT
1 ATAAT-TTTT
*
31763885 ATAATTTTA
1 ATAATTTTT
*
31763894 ATAA-GTTT
1 ATAATTTTT
31763902 ATCAA-TTTT
1 AT-AATTTTT
31763911 AGT-A-TTTT
1 A-TAATTTTT
*
31763919 -TAATATTTA
1 ATAAT-TTTT
*
31763928 ATATTTTTT
1 ATAATTTTT
31763937 ATAATTTTT
1 ATAATTTTT
*
31763946 -CAATTTTT
1 ATAATTTTT
*
31763954 ATGATTTTT
1 ATAATTTTT
31763963 A
1 A
31763964 AATATTCTTA
Statistics
Matches: 95, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
6 1 0.01
7 7 0.07
8 21 0.22
9 52 0.55
10 14 0.15
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (9 bp):
ATAATTTTT
Found at i:31763908 original size:18 final size:19
Alignment explanation
Indices: 31763846--31763944 Score: 65
Period size: 19 Copynumber: 5.6 Consensus size: 19
31763836 GTTTTATTAA
*
31763846 TTTTATAATTTT--T-ATA
1 TTTTATAATTTTAATAATG
**
31763862 TTTTATAACATTAATAATG
1 TTTTATAATTTTAATAATG
31763881 TTTTATAATTTTAATAA-G
1 TTTTATAATTTTAATAATG
*
31763899 -TTTATCAATTTTAGT-A--
1 TTTTAT-AATTTTAATAATG
*
31763915 TTTT-TAATATTTAAT-ATT
1 TTTTATAAT-TTTAATAATG
31763933 TTTTATAATTTT
1 TTTTATAATTTT
31763945 TCAATTTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.04
16 17 0.25
17 9 0.13
18 17 0.25
19 21 0.31
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTATAATTTTAATAATG
Found at i:31763911 original size:52 final size:52
Alignment explanation
Indices: 31763832--31763944 Score: 133
Period size: 52 Copynumber: 2.2 Consensus size: 52
31763822 TTAATTTTAA
* *
31763832 ATAAGTTTTATTAATTTTATAATTTTTA-TATTTTATAACA-TTAATAATGTTTT
1 ATAA-TTTTAATAAGTTTATAATTTTTAGTATTTT-TAACATTTAAT-ATGTTTT
* *
31763885 ATAATTTTAATAAGTTTATCAA-TTTTAGTATTTTTAATATTTAATATTTTTT
1 ATAATTTTAATAAGTTTAT-AATTTTTAGTATTTTTAACATTTAATATGTTTT
31763937 ATAATTTT
1 ATAATTTT
31763945 TCAATTTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
52 36 0.68
53 17 0.32
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (52 bp):
ATAATTTTAATAAGTTTATAATTTTTAGTATTTTTAACATTTAATATGTTTT
Found at i:31763941 original size:62 final size:63
Alignment explanation
Indices: 31763810--31763930 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 63
31763800 TTAAGAATTC
* * *
31763810 TAAT-ATGTTGTTTTAATTTTAAATAAGTTTTATTAATTTTATAATTTTTATATTTTATAACAT
1 TAATAATGTT-TTATAATTTTAAATAAGTTTTATCAATTTTATAATTTTTATATTTAATAACAT
31763873 TAATAATGTTTTATAATTTT-AATAAG-TTTATCAATTTTAGT-ATTTTTAATATTTAATA
1 TAATAATGTTTTATAATTTTAAATAAGTTTTATCAATTTTA-TAATTTTT-ATATTTAATA
31763931 TTTTTTATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
61 18 0.35
62 16 0.31
63 13 0.25
64 5 0.10
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (63 bp):
TAATAATGTTTTATAATTTTAAATAAGTTTTATCAATTTTATAATTTTTATATTTAATAACAT
Found at i:31763963 original size:52 final size:51
Alignment explanation
Indices: 31763845--31763963 Score: 120
Period size: 52 Copynumber: 2.3 Consensus size: 51
31763835 AGTTTTATTA
31763845 ATTTTATAATTTTTATATTTTATAACATTAATAATGTTTTATAATTTTAAT
1 ATTTTATAATTTTTATATTTTATAACATTAATAATGTTTTATAATTTTAAT
* * *
31763896 AAGTTTATCAA-TTTTAGTATTTT-TAATATTTAAT-ATTTTTTATAATTTTTCAAT
1 -ATTTTAT-AATTTTTA-TATTTTATAACA-TTAATAATGTTTTATAA-TTTT-AAT
*
31763950 -TTTTATGATTTTTA
1 ATTTTATAATTTTTA
31763964 AATATTCTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
51 1 0.02
52 35 0.62
53 17 0.30
54 3 0.05
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (51 bp):
ATTTTATAATTTTTATATTTTATAACATTAATAATGTTTTATAATTTTAAT
Found at i:31763976 original size:19 final size:17
Alignment explanation
Indices: 31763932--31763976 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
31763922 TATTTAATAT
* *
31763932 TTTTTATAATTTTTCAA
1 TTTTTATGATTTTTAAA
31763949 TTTTTATGATTTTTAAA
1 TTTTTATGATTTTTAAA
31763966 TATTCTTATGA
1 T-TT-TTATGA
31763977 AAAAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 16 0.67
18 2 0.08
19 6 0.25
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTTTATGATTTTTAAA
Found at i:31764208 original size:3 final size:3
Alignment explanation
Indices: 31764200--31764230 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31764190 ACTAAATCGG
31764200 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31764231 TAAAATTACA
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:31765281 original size:1 final size:1
Alignment explanation
Indices: 31765275--31765315 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
31765265 TGTTTAGGGC
31765275 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
31765316 TTGTGGCCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:31768077 original size:24 final size:24
Alignment explanation
Indices: 31768030--31768077 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31768020 ATGGATGTTC
* *
31768030 AACCTTTCATCTCCCTTGAGCTTT
1 AACCTTTCATCTCCCTTAACCTTT
* *
31768054 AACCTTTCATCTTCTTTAACCTTT
1 AACCTTTCATCTCCCTTAACCTTT
31768078 CATATTTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.04, T:0.46
Consensus pattern (24 bp):
AACCTTTCATCTCCCTTAACCTTT
Found at i:31771858 original size:2 final size:2
Alignment explanation
Indices: 31771851--31771903 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
31771841 TCCCTAATAC
31771851 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31771893 AG AG AG AG AG A
1 AG AG AG AG AG A
31771904 TGATGAGGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31772461 original size:20 final size:20
Alignment explanation
Indices: 31772425--31772462 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31772415 GTATTTGGGA
* *
31772425 TTTAAGTTTAGGGTTTAGAG
1 TTTAAGTTTAAGATTTAGAG
31772445 TTTAAGTTTAAGATTTAG
1 TTTAAGTTTAAGATTTAG
31772463 GATTGGGGAT
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:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (20 bp):
TTTAAGTTTAAGATTTAGAG
Found at i:31789239 original size:31 final size:31
Alignment explanation
Indices: 31789173--31789257 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 31
31789163 TATTATCGCA
* *
31789173 AATTTAGTTTTTCTA--TTTT-AATTTAATTT
1 AATTTAGTTTTTATATTTTTTGAA-TTAATTC
31789202 AATTTAGTTTTTATATTTTTTGAATTAATTC
1 AATTTAGTTTTTATATTTTTTGAATTAATTC
* **
31789233 ATTTTAG-TTTTGCATTTTTTGAATT
1 AATTTAGTTTTTATATTTTTTGAATT
31789258 TTAAAGTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
29 14 0.29
30 16 0.33
31 16 0.33
32 2 0.04
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.64
Consensus pattern (31 bp):
AATTTAGTTTTTATATTTTTTGAATTAATTC
Found at i:31802360 original size:16 final size:16
Alignment explanation
Indices: 31802335--31802365 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31802325 TGCAAAGCAC
31802335 TCCTTCAGTTCTACTT
1 TCCTTCAGTTCTACTT
*
31802351 TCCTTGAGTTCTACT
1 TCCTTCAGTTCTACT
31802366 ACAGTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.29, G:0.10, T:0.48
Consensus pattern (16 bp):
TCCTTCAGTTCTACTT
Found at i:31807182 original size:12 final size:12
Alignment explanation
Indices: 31807160--31807199 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
31807150 TAATTTTCTC
31807160 TATTTTT-AATT
1 TATTTTTAAATT
31807171 TATTTTTAAATT
1 TATTTTTAAATT
31807183 TATATTTTAAA-T
1 TAT-TTTTAAATT
31807195 TATTT
1 TATTT
31807200 AATCAAACCG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.33
12 11 0.41
13 7 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTTTAAATT
Found at i:31807944 original size:25 final size:24
Alignment explanation
Indices: 31807916--31807974 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
31807906 TATTTCTTAT
31807916 ATTATTAAAAATTAAATAAATTTAA
1 ATTATTAAAAATTAAA-AAATTTAA
*
31807941 ATTA-TAACAAATTAAAACATTTAA
1 ATTATTAA-AAATTAAAAAATTTAA
* *
31807965 TTTATGAAAA
1 ATTATTAAAA
31807975 GTATCTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (24 bp):
ATTATTAAAAATTAAAAAATTTAA
Found at i:31812818 original size:14 final size:14
Alignment explanation
Indices: 31812778--31812824 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
31812768 TTAAAATAAT
*
31812778 ATATAAAATATTAA
1 ATATAAAATATTTA
* *
31812792 ATGT-AAATTTTTA
1 ATATAAAATATTTA
31812805 ATATAAAATATTTA
1 ATATAAAATATTTA
*
31812819 AAATAA
1 ATATAA
31812825 GAGTAAACAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
ATATAAAATATTTA
Found at i:31812859 original size:23 final size:23
Alignment explanation
Indices: 31812833--31812878 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
31812823 AAGAGTAAAC
31812833 ATTTAATATAAATGTTATCTTTA
1 ATTTAATATAAATGTTATCTTTA
* *
31812856 ATTTGATATAAATGTTTTCTTTA
1 ATTTAATATAAATGTTATCTTTA
31812879 TTTCTTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
ATTTAATATAAATGTTATCTTTA
Found at i:31819503 original size:31 final size:29
Alignment explanation
Indices: 31819468--31819532 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 29
31819458 AAATCTCAAA
*
31819468 ATACATTAACTATGATTTAATGTGTAATTAT
1 ATACATGAACTATGATTT--TGTGTAATTAT
* *
31819499 ATACATGAACTTTGATTTTGTGTAATTTT
1 ATACATGAACTATGATTTTGTGTAATTAT
31819528 ATACA
1 ATACA
31819533 AGAAATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 15 0.48
31 16 0.52
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (29 bp):
ATACATGAACTATGATTTTGTGTAATTAT
Found at i:31819530 original size:29 final size:29
Alignment explanation
Indices: 31819468--31819555 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
31819458 AAATCTCAAA
* *
31819468 ATACATTAACTATGATTTAATGTGTAATTAT
1 ATACATGAACTTTGATTT--TGTGTAATTAT
*
31819499 ATACATGAACTTTGATTTTGTGTAATTTT
1 ATACATGAACTTTGATTTTGTGTAATTAT
* * * *
31819528 ATACAAGAAATTTTGATTTGGTCTAATT
1 ATACATG-AACTTTGATTTTGTGTAATT
31819556 CTTGTAATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 16 0.33
30 17 0.35
31 16 0.33
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (29 bp):
ATACATGAACTTTGATTTTGTGTAATTAT
Found at i:31832501 original size:33 final size:32
Alignment explanation
Indices: 31832431--31832492 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
31832421 TCGAATTAAA
*
31832431 CGAATCGAGTTGAATTTTTTCGAATTTCGAGTT
1 CGAATCGAGTTGAA-TTTTTCGAATTTCGAATT
31832464 CGAATCGAGTTGAA-TTTTCGAATTT-GAAT
1 CGAATCGAGTTGAATTTTTCGAATTTCGAAT
31832493 AACTCGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 3 0.11
31 11 0.39
33 14 0.50
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.40
Consensus pattern (32 bp):
CGAATCGAGTTGAATTTTTCGAATTTCGAATT
Found at i:31832704 original size:34 final size:34
Alignment explanation
Indices: 31832659--31832742 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 34
31832649 CGTAAACTAA
*
31832659 ACCCAAATATTTTTAATTTTTTACCTTTTATCTT
1 ACCCAAATATTTTTAATTTTTTACCTTTTACCTT
* **
31832693 ATCCAAATATTTTTAATTTTTTATTTTTTACCTT
1 ACCCAAATATTTTTAATTTTTTACCTTTTACCTT
31832727 ACCCAAATATTGTTTA
1 ACCCAAATATT-TTTA
31832743 CTTGGACTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 40 0.91
35 4 0.09
ACGTcount: A:0.29, C:0.15, G:0.01, T:0.55
Consensus pattern (34 bp):
ACCCAAATATTTTTAATTTTTTACCTTTTACCTT
Found at i:31839723 original size:32 final size:32
Alignment explanation
Indices: 31839687--31839750 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
31839677 TACAATGGTA
31839687 GAGGCTTTCCATATGAAGATACTCGACAACAT
1 GAGGCTTTCCATATGAAGATACTCGACAACAT
31839719 GAGGCTTTCCATATGAAGATACTCGACAACAT
1 GAGGCTTTCCATATGAAGATACTCGACAACAT
31839751 CAATCTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (32 bp):
GAGGCTTTCCATATGAAGATACTCGACAACAT
Found at i:31852985 original size:19 final size:19
Alignment explanation
Indices: 31852961--31853041 Score: 89
Period size: 19 Copynumber: 4.4 Consensus size: 19
31852951 ATCATTAATA
*
31852961 ATTCAATTTTAATATAAAT
1 ATTCAATATTAATATAAAT
31852980 ATTCAATATT-AT-T-AAT
1 ATTCAATATTAATATAAAT
*
31852996 AATTCAATTTTAATATAAAT
1 -ATTCAATATTAATATAAAT
* *
31853016 ATTCAATATTATTA-AAAA
1 ATTCAATATTAATATAAAT
31853034 ATTCAATA
1 ATTCAATA
31853042 ATATAAATAG
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
16 3 0.06
17 10 0.19
18 15 0.28
19 22 0.42
20 3 0.06
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTCAATATTAATATAAAT
Found at i:31852994 original size:36 final size:36
Alignment explanation
Indices: 31852954--31853040 Score: 156
Period size: 36 Copynumber: 2.4 Consensus size: 36
31852944 TTGTGGTATC
31852954 ATTAATAATTCAATTTTAATATAAATATTCAATATT
1 ATTAATAATTCAATTTTAATATAAATATTCAATATT
31852990 ATTAATAATTCAATTTTAATATAAATATTCAATATT
1 ATTAATAATTCAATTTTAATATAAATATTCAATATT
*
31853026 ATTAAAAAATTCAAT
1 ATT-AATAATTCAAT
31853041 AATATAAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 39 0.80
37 10 0.20
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (36 bp):
ATTAATAATTCAATTTTAATATAAATATTCAATATT
Found at i:31853048 original size:17 final size:16
Alignment explanation
Indices: 31852970--31853048 Score: 59
Period size: 18 Copynumber: 4.6 Consensus size: 16
31852960 AATTCAATTT
*
31852970 TAATATAAATATTCAA
1 TAATATAAAAATTCAA
* *
31852986 TATTATTAATAATTCAA
1 TAATA-TAAAAATTCAA
*
31853003 TTTTAATATAAATATTCAA
1 ---TAATATAAAAATTCAA
*
31853022 TATTATTAAAAAATTCAA
1 TAATA-T-AAAAATTCAA
31853040 TAATATAAA
1 TAATATAAA
31853049 TAGTAAAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
16 11 0.23
17 11 0.23
18 13 0.27
19 9 0.19
20 4 0.08
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAAAAATTCAA
Found at i:31853687 original size:24 final size:24
Alignment explanation
Indices: 31853626--31853680 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
31853616 TATTCGAGTT
31853626 ATTCGAATTTGAAAACTCAACTCG
1 ATTCGAATTTGAAAACTCAACTCG
31853650 ATTCGAATTTGAAAACTCAACTCG
1 ATTCGAATTTGAAAACTCAACTCG
31853674 ATTCGAA
1 ATTCGAA
31853681 CTCGAAATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (24 bp):
ATTCGAATTTGAAAACTCAACTCG
Found at i:31853956 original size:13 final size:11
Alignment explanation
Indices: 31853924--31853951 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
31853914 AATATTAAAT
31853924 TTTTTATATTA
1 TTTTTATATTA
31853935 TTTTTATATTA
1 TTTTTATATTA
31853946 TTTTTA
1 TTTTTA
31853952 AATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:31854004 original size:25 final size:24
Alignment explanation
Indices: 31853976--31854023 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
31853966 ATTAAAAATA
31853976 CTAAAAACATT-AAAATAAATATTTC
1 CTAAAAA-ATTAAAAATAAA-ATTTC
*
31854001 CTAACAAATTAAAAATAAAATTT
1 CTAAAAAATTAAAAATAAAATTT
31854024 TAAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.31
Consensus pattern (24 bp):
CTAAAAAATTAAAAATAAAATTTC
Found at i:31859978 original size:7 final size:7
Alignment explanation
Indices: 31859966--31859994 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
31859956 TCGGTCTACC
31859966 ATGATTG
1 ATGATTG
31859973 ATGATTG
1 ATGATTG
31859980 ATGATTG
1 ATGATTG
31859987 ATGATTG
1 ATGATTG
31859994 A
1 A
31859995 AAGGAAACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (7 bp):
ATGATTG
Found at i:31861703 original size:19 final size:18
Alignment explanation
Indices: 31861679--31861743 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
31861669 TAATATAATT
31861679 TATTTTAATTATGTAAAAA
1 TATTTTAATTAT-TAAAAA
* *
31861698 TATTTTCATAATT-AAAA
1 TATTTTAATTATTAAAAA
* *
31861715 TAATTTATATTATTTAAAAG
1 TATTTTA-ATTA-TTAAAAA
31861735 TATTTTAAT
1 TATTTTAAT
31861744 ATTTTCATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
17 9 0.25
18 4 0.11
19 14 0.39
20 9 0.25
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (18 bp):
TATTTTAATTATTAAAAA
Found at i:31863439 original size:34 final size:34
Alignment explanation
Indices: 31863400--31863470 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
31863390 TCTTTTCTGT
* *
31863400 TAATTCAGTCTTCTCCTTTACAATTGACCCTAAA
1 TAATTCAGTCTTCTCCATTACAATCGACCCTAAA
31863434 TAATTCAGTCTTCTCCATTACAATCGACCCTAAA
1 TAATTCAGTCTTCTCCATTACAATCGACCCTAAA
31863468 TAA
1 TAA
31863471 AAACTATGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (34 bp):
TAATTCAGTCTTCTCCATTACAATCGACCCTAAA
Found at i:31868756 original size:20 final size:21
Alignment explanation
Indices: 31868731--31868780 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
31868721 AATTTCTATA
*
31868731 TAAATTTTAT-TAAATGCTTT
1 TAAATTTTATATAAATGATTT
* *
31868751 TAAATTATATATAACTGATTT
1 TAAATTTTATATAAATGATTT
*
31868772 TTAATTTTA
1 TAAATTTTA
31868781 GTCATGTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (21 bp):
TAAATTTTATATAAATGATTT
Found at i:31869403 original size:17 final size:18
Alignment explanation
Indices: 31869381--31869422 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
31869371 TATAGATTGC
31869381 ATATTTTGAATT-TT-TAT
1 ATATTTT-AATTATTATAT
31869398 ATA-TTTAATTATTATAT
1 ATATTTTAATTATTATAT
31869415 ATATTTTA
1 ATATTTTA
31869423 GAGTTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.18
16 5 0.23
17 9 0.41
18 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATATTTTAATTATTATAT
Found at i:31869516 original size:19 final size:19
Alignment explanation
Indices: 31869472--31869556 Score: 68
Period size: 19 Copynumber: 4.4 Consensus size: 19
31869462 ATAATTTAAC
*
31869472 ATATATTTTTA-GATTTTAT
1 ATATATTTTTATAATTTT-T
*
31869491 ATTTATTTTTATAATTTTT
1 ATATATTTTTATAATTTTT
*
31869510 ATATATTTATT-TCTATTTCTT
1 ATATATTT-TTAT-AATTT-TT
* *
31869531 ATA-ATTTTTAAAATTTGT
1 ATATATTTTTATAATTTTT
31869549 ATATATTT
1 ATATATTT
31869557 AATAAAATAA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
18 4 0.08
19 29 0.55
20 15 0.28
21 5 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
ATATATTTTTATAATTTTT
Found at i:31869535 original size:30 final size:28
Alignment explanation
Indices: 31869476--31869540 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 28
31869466 TTTAACATAT
31869476 ATTTTTAGATTTTATATTTATTTTTATA
1 ATTTTTAGATTTTATATTTATTTTTATA
*
31869504 ATTTTTATATATTTAT-TTCTATTTCTTATA
1 ATTTTTAGAT-TTTATATT-TATTT-TTATA
31869534 ATTTTTA
1 ATTTTTA
31869541 AAATTTGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 11 0.33
29 10 0.30
30 12 0.36
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.68
Consensus pattern (28 bp):
ATTTTTAGATTTTATATTTATTTTTATA
Found at i:31870502 original size:71 final size:71
Alignment explanation
Indices: 31870426--31870579 Score: 245
Period size: 71 Copynumber: 2.2 Consensus size: 71
31870416 AGCCTTCCAG
* *
31870426 GTATCGGTAGAAGTCCCAGGCCACAACTTCTTAACTCTCTGGAGTTTGTTTTACCGATAGAACTC
1 GTATCGGTAGAAGTCCCAGGCCACAACTTCTTAACTCTCAGGAGTTTGTTCTACCGATAGAACTC
31870491 TTGGTT
66 TTGGTT
* ** * *
31870497 GTATCGGTAGAAGTCCTAGGCCACAACTTCTTTGCTCTCAGGAGTTTGTTCTACCGATAGAAGTT
1 GTATCGGTAGAAGTCCCAGGCCACAACTTCTTAACTCTCAGGAGTTTGTTCTACCGATAGAACTC
31870562 TTGGTT
66 TTGGTT
31870568 GTATCGGTAGAA
1 GTATCGGTAGAA
31870580 TCAAGACATG
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 76 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (71 bp):
GTATCGGTAGAAGTCCCAGGCCACAACTTCTTAACTCTCAGGAGTTTGTTCTACCGATAGAACTC
TTGGTT
Found at i:31891954 original size:23 final size:23
Alignment explanation
Indices: 31891928--31891973 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31891918 AAAATTCGAA
**
31891928 ATTCGAATTATTCGAATCGAGTT
1 ATTCGAATTAAACGAATCGAGTT
*
31891951 ATTCGAGTTAAACGAATCGAGTT
1 ATTCGAATTAAACGAATCGAGTT
31891974 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (23 bp):
ATTCGAATTAAACGAATCGAGTT
Found at i:31892247 original size:57 final size:58
Alignment explanation
Indices: 31892184--31892302 Score: 188
Period size: 57 Copynumber: 2.1 Consensus size: 58
31892174 ACCCATTAAC
*
31892184 AAACTAAACCCAAATATTTTAAAACACAAATATAA-TTTATTCTTCAAA-AACACTCAT
1 AAACTAAACCCAAATATTTTAAAACACAAATATAATTTTATTCCT-AAATAACACTCAT
* *
31892241 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTAAAACACAAATATAATTTTATTCCTAAATAACACTCAT
31892299 AAAC
1 AAAC
31892303 AACTCCTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 36 0.63
58 21 0.37
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTAAAACACAAATATAATTTTATTCCTAAATAACACTCAT
Found at i:31892662 original size:18 final size:19
Alignment explanation
Indices: 31892639--31892674 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
31892629 ATTGTGTTAT
*
31892639 TGTTG-TTACTTGGATTTA
1 TGTTGTTTACTTGAATTTA
31892657 TGTTGTTTACTTGAATTT
1 TGTTGTTTACTTGAATTT
31892675 TTGCTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.17, C:0.06, G:0.19, T:0.58
Consensus pattern (19 bp):
TGTTGTTTACTTGAATTTA
Found at i:31895148 original size:13 final size:14
Alignment explanation
Indices: 31895130--31895191 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 14
31895120 TAAATTAAAC
31895130 TTTTCAAAAGCA-T
1 TTTTCAAAAGCACT
*
31895143 TTTTCAAAAGTACT
1 TTTTCAAAAGCACT
* **
31895157 TTTCCACCA-CA-T
1 TTTTCAAAAGCACT
*
31895169 TTTTTAAAAGCACT
1 TTTTCAAAAGCACT
31895183 TTTT-AAAAG
1 TTTTCAAAAG
31895192 TAACGTTAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
12 6 0.16
13 19 0.51
14 12 0.32
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.40
Consensus pattern (14 bp):
TTTTCAAAAGCACT
Found at i:31902623 original size:23 final size:23
Alignment explanation
Indices: 31902577--31902625 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
31902567 TTAAATAGTG
* *
31902577 ATTTAAGTATTTTTTTTTACATT
1 ATTTAAGAATTTTTTTATACATT
31902600 ATTTAAGAATTTTTTTAT-CTATT
1 ATTTAAGAATTTTTTTATAC-ATT
31902623 ATT
1 ATT
31902626 ATCTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (23 bp):
ATTTAAGAATTTTTTTATACATT
Found at i:31903762 original size:5 final size:5
Alignment explanation
Indices: 31903754--31903782 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
31903744 AAATAAAATT
31903754 ACAAC ACAAC ACAAC ACAAC ACAAC ACAA
1 ACAAC ACAAC ACAAC ACAAC ACAAC ACAA
31903783 AGGCAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
ACAAC
Found at i:31904703 original size:3 final size:3
Alignment explanation
Indices: 31904695--31904720 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31904685 GCTTCGCATT
31904695 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
31904721 CATAAGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:31905638 original size:2 final size:2
Alignment explanation
Indices: 31905631--31905669 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
31905621 TCTAAAACGA
31905631 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
31905670 ATATGGCGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31908992 original size:26 final size:26
Alignment explanation
Indices: 31908962--31909016 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
31908952 GTCATATACA
31908962 TATATGATTTATTGTCGACCCTAAAC
1 TATATGATTTATTGTCGACCCTAAAC
31908988 TATATGATTTATTGTCGACCCTAAAC
1 TATATGATTTATTGTCGACCCTAAAC
31909014 TAT
1 TAT
31909017 TTTATATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (26 bp):
TATATGATTTATTGTCGACCCTAAAC
Found at i:31911210 original size:30 final size:29
Alignment explanation
Indices: 31911176--31911238 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
31911166 AATTTACAAG
*
31911176 AATTGAATC-AAATCAAAATTTCATGTATAC
1 AATTGAA-CAAAATC-AAAGTTCATGTATAC
*
31911206 AATTGCACAAAATCAAAGTTCATGTATAC
1 AATTGAACAAAATCAAAGTTCATGTATAC
31911235 AATT
1 AATT
31911239 ACACATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (29 bp):
AATTGAACAAAATCAAAGTTCATGTATAC
Found at i:31911228 original size:29 final size:30
Alignment explanation
Indices: 31911185--31911243 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
31911175 GAATTGAATC
* *
31911185 AAATCAAAATTTCATGTATACAATTGCACA
1 AAATCAAAAGTTCATGTATACAATTACACA
31911215 AAATC-AAAGTTCATGTATACAATTACACA
1 AAATCAAAAGTTCATGTATACAATTACACA
31911244 TTAAACTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATACAATTACACA
Found at i:31915459 original size:36 final size:35
Alignment explanation
Indices: 31915370--31915460 Score: 87
Period size: 36 Copynumber: 2.6 Consensus size: 35
31915360 TGTCTCTAAA
31915370 ATAATAGCAAAAT-TAACAATAAAATAAAAGTAAT
1 ATAATAGCAAAATCTAACAATAAAATAAAAGTAAT
* * * * *
31915404 ACAATATCCAAACA-ATAACAGTAAAATAATAGTAAT
1 ATAATA-GCAAA-ATCTAACAATAAAATAAAAGTAAT
*
31915440 ATAATAGCGAAATCGTAACAA
1 ATAATAGCAAAATC-TAACAA
31915461 AACAACAACA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
34 6 0.14
35 7 0.16
36 30 0.70
ACGTcount: A:0.59, C:0.11, G:0.08, T:0.22
Consensus pattern (35 bp):
ATAATAGCAAAATCTAACAATAAAATAAAAGTAAT
Found at i:31921136 original size:19 final size:19
Alignment explanation
Indices: 31921092--31921136 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
31921082 CCCCAAATTA
31921092 AAATTTTAGAAAAATTTGG
1 AAATTTTAGAAAAATTTGG
* * * *
31921111 AACTTTTATAAATATTTTG
1 AAATTTTAGAAAAATTTGG
31921130 AAATTTT
1 AAATTTT
31921137 TGTTAAGAGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (19 bp):
AAATTTTAGAAAAATTTGG
Found at i:31924723 original size:15 final size:15
Alignment explanation
Indices: 31924705--31924752 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
31924695 TTTTCTCAAA
31924705 TTATATTTTAATTAT
1 TTATATTTTAATTAT
*
31924720 TTATATTTGAA--AT
1 TTATATTTTAATTAT
*
31924733 GTTATATATTAATTAT
1 -TTATATTTTAATTAT
31924749 TTAT
1 TTAT
31924753 GTTATCGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
15 14 0.52
16 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:31927111 original size:1 final size:1
Alignment explanation
Indices: 31927100--31927129 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
31927090 TAGTTAGACG
*
31927100 CCCCCCTCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
31927130 AAAGGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:31930217 original size:21 final size:21
Alignment explanation
Indices: 31930191--31930230 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31930181 AGTGGCCAAC
*
31930191 CTGTACACATATTTATATAAG
1 CTGTACACATATATATATAAG
*
31930212 CTGTACATATATATATATA
1 CTGTACACATATATATATA
31930231 TATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (21 bp):
CTGTACACATATATATATAAG
Found at i:31930223 original size:2 final size:2
Alignment explanation
Indices: 31930218--31930250 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31930208 TAAGCTGTAC
31930218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31930251 AGCTTGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31933352 original size:26 final size:28
Alignment explanation
Indices: 31933297--31933357 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
31933287 ATTCTTATTG
31933297 AAAATATAAAAATGTTAATAAAACTATA
1 AAAATATAAAAATGTTAATAAAACTATA
* *
31933325 AAAATATATAATTGCTTAA-AAAA-T-TA
1 AAAATATAAAAATG-TTAATAAAACTATA
31933351 AAAATAT
1 AAAATAT
31933358 GTTAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 9 0.30
27 1 0.03
28 16 0.53
29 4 0.13
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAATATAAAAATGTTAATAAAACTATA
Found at i:31933362 original size:19 final size:18
Alignment explanation
Indices: 31933334--31933383 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
31933324 AAAAATATAT
31933334 AATTGCTTAAAAAATTAAA
1 AATTG-TTAAAAAATTAAA
**
31933353 AATATGTTAAAATTTTAAA
1 AAT-TGTTAAAAAATTAAA
31933372 AATTG-TAAAAAA
1 AATTGTTAAAAAA
31933384 CAATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 5 0.19
18 2 0.08
19 17 0.65
20 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (18 bp):
AATTGTTAAAAAATTAAA
Found at i:31933390 original size:27 final size:27
Alignment explanation
Indices: 31933360--31933437 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 27
31933350 AAAAATATGT
*
31933360 TAAAATTTTAAAAATTGTAAAAAACAA
1 TAAAATATTAAAAATTGTAAAAAACAA
* * *
31933387 TAAAATATT-AAAATTATAAAAAATAT
1 TAAAATATTAAAAATTGTAAAAAACAA
* *
31933413 TAAAATGATTAGAAATTGAAAAAAA
1 TAAAAT-ATTAAAAATTGTAAAAAA
31933438 TATTGTGAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 20 0.48
27 11 0.26
28 11 0.26
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (27 bp):
TAAAATATTAAAAATTGTAAAAAACAA
Found at i:31933398 original size:18 final size:18
Alignment explanation
Indices: 31933377--31933418 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
31933367 TTAAAAATTG
31933377 TAAAA-AACAATAAAATAT
1 TAAAATAACAA-AAAATAT
* *
31933395 TAAAATTATAAAAAATAT
1 TAAAATAACAAAAAATAT
31933413 TAAAAT
1 TAAAAT
31933419 GATTAGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAATAACAAAAAATAT
Found at i:31934509 original size:23 final size:23
Alignment explanation
Indices: 31934473--31934530 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
31934463 TTAAAATTTT
*
31934473 ATTTTTCAACAAAAA-TACATA-A
1 ATTTTT-AAAAAAAACTACATACA
31934495 GATTTTATAAAAAAAACTACATACA
1 -ATTTT-TAAAAAAAACTACATACA
31934520 ATTTTTAAAAA
1 ATTTTTAAAAA
31934531 TATTTATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 18 0.58
24 12 0.39
25 1 0.03
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (23 bp):
ATTTTTAAAAAAAACTACATACA
Found at i:31938760 original size:1 final size:1
Alignment explanation
Indices: 31938754--31938784 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
31938744 CAAAGTTTAT
31938754 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
31938785 CAGGGTGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:31950828 original size:17 final size:17
Alignment explanation
Indices: 31950806--31950850 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
31950796 TAGCTTCAGA
31950806 TAAACAAAAAATCAAAT
1 TAAACAAAAAATCAAAT
*
31950823 TAAACAAAAAATGAAAT
1 TAAACAAAAAATCAAAT
31950840 TAAACAAAAAA
1 TAAACAAAAAA
31950851 AAAAGGATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (17 bp):
TAAACAAAAAATCAAAT
Found at i:31951168 original size:31 final size:31
Alignment explanation
Indices: 31951133--31951192 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
31951123 CATTAATGGA
*
31951133 TTTTTTAGATT-AGTCATCCCCAAACTATTTC
1 TTTTTTA-ATTAAATCATCCCCAAACTATTTC
**
31951164 TTTTTTAATTAAATTGTCCCCAAACTATT
1 TTTTTTAATTAAATCATCCCCAAACTATT
31951193 AAATGGAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTTTTAATTAAATCATCCCCAAACTATTTC
Found at i:31959322 original size:21 final size:19
Alignment explanation
Indices: 31959300--31959345 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
31959290 TAGTGTATAT
*
31959300 ATATATATATATATTAGAC
1 ATATATATATATTTTAGAC
31959319 ATAT-TACTATATTTTAGAC
1 ATATATA-TATATTTTAGAC
*
31959338 ACATATAT
1 ATATATAT
31959346 TACACAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (19 bp):
ATATATATATATTTTAGAC
Found at i:31963177 original size:14 final size:16
Alignment explanation
Indices: 31963146--31963194 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
31963136 TATGTGAAAC
31963146 ATTTAAATATATATTT
1 ATTTAAATATATATTT
31963162 ATTTAAATA-A-ATTT
1 ATTTAAATATATATTT
* *
31963176 ATCTAAAATTTATATTT
1 AT-TTAAATATATATTT
31963193 AT
1 AT
31963195 ATTTATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 6 0.21
15 6 0.21
16 10 0.36
17 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTAAATATATATTT
Found at i:31963254 original size:20 final size:20
Alignment explanation
Indices: 31963229--31963275 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
31963219 GTTGGACTAC
*
31963229 TTTATATTTGTGTATTTAAT
1 TTTATATTTGGGTATTTAAT
*
31963249 TTTATATTTGGGTATTTAGT
1 TTTATATTTGGGTATTTAAT
31963269 TTTATAT
1 TTTATAT
31963276 GTGAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (20 bp):
TTTATATTTGGGTATTTAAT
Found at i:31978358 original size:13 final size:13
Alignment explanation
Indices: 31978342--31978382 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
31978332 CAGTTAATAG
*
31978342 AATCAGTTGATCA
1 AATCAATTGATCA
* *
31978355 AATCAATTAATAA
1 AATCAATTGATCA
31978368 AATCAATTGATCA
1 AATCAATTGATCA
31978381 AA
1 AA
31978383 ACAACCACTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (13 bp):
AATCAATTGATCA
Found at i:31979382 original size:27 final size:27
Alignment explanation
Indices: 31979351--31979411 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
31979341 ATGATATTTG
*
31979351 TTATTTTATAAAATAAATAAAT-TTTAA
1 TTATTTT-CAAAATAAATAAATATTTAA
* *
31979378 TTATTGTTCAAACTAAATTAATATTTAA
1 TTATT-TTCAAAATAAATAAATATTTAA
31979406 TTATTT
1 TTATTT
31979412 CGTAGCACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (27 bp):
TTATTTTCAAAATAAATAAATATTTAA
Found at i:31980252 original size:8 final size:7
Alignment explanation
Indices: 31980226--31980250 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31980216 CTCAACAATG
31980226 TTTTATT
1 TTTTATT
31980233 TTTTATT
1 TTTTATT
31980240 TTTTATT
1 TTTTATT
31980247 TTTT
1 TTTT
31980251 TAATAGTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:31993142 original size:22 final size:22
Alignment explanation
Indices: 31993099--31993142 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31993089 ATAAATTAGT
* *
31993099 AAAATTATATTTTGATTCTAAA
1 AAAATTATAATTTAATTCTAAA
*
31993121 AAAATTATAATTTAATTTTAAA
1 AAAATTATAATTTAATTCTAAA
31993143 CCCTTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
AAAATTATAATTTAATTCTAAA
Found at i:31994364 original size:26 final size:28
Alignment explanation
Indices: 31994325--31994381 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
31994315 AAACTATGAC
31994325 AAAAATAATTGTTT-GTG-CCAAAATGAAA
1 AAAAATAA-TGTTTAG-GACCAAAATGAAA
*
31994353 AAAAATAA-GTTTAGGATCAAAATGAAA
1 AAAAATAATGTTTAGGACCAAAATGAAA
31994380 AA
1 AA
31994382 TGAGTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 5 0.19
27 13 0.50
28 8 0.31
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.25
Consensus pattern (28 bp):
AAAAATAATGTTTAGGACCAAAATGAAA
Found at i:31996646 original size:28 final size:28
Alignment explanation
Indices: 31996615--31996671 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
31996605 CAAGGTATGA
31996615 GATTTAAAGTTCAAAGTCTAAGATTTAG
1 GATTTAAAGTTCAAAGTCTAAGATTTAG
* * *
31996643 GATTTAAAGTTTAAAGTCTAGGGTTTAG
1 GATTTAAAGTTCAAAGTCTAAGATTTAG
31996671 G
1 G
31996672 GTTAATCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (28 bp):
GATTTAAAGTTCAAAGTCTAAGATTTAG
Found at i:31997118 original size:32 final size:32
Alignment explanation
Indices: 31997075--31997135 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
31997065 ATACGTATGA
*
31997075 TTAAATCAAAAATTAAAATTTTAAATATATAT
1 TTAAATCAAAAATTAAAATTCTAAATATATAT
* *
31997107 TTAAATTAAAAATTAAAATTCTACATATA
1 TTAAATCAAAAATTAAAATTCTAAATATA
31997136 AAAATACATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (32 bp):
TTAAATCAAAAATTAAAATTCTAAATATATAT
Found at i:31997555 original size:6 final size:6
Alignment explanation
Indices: 31997546--31997580 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
31997536 CTTTCTCTGT
31997546 ACTCCA ACTCCA ACTCCA ACTCCA ACTCCA ACTCC
1 ACTCCA ACTCCA ACTCCA ACTCCA ACTCCA ACTCC
31997581 GCCCTCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.51, G:0.00, T:0.17
Consensus pattern (6 bp):
ACTCCA
Found at i:32000020 original size:4 final size:4
Alignment explanation
Indices: 32000013--32000048 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
32000003 AGGATATATA
* *
32000013 TATG TATG TATG TATG TATG TATG TCTG TGTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
32000049 CATGGTTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:32006770 original size:21 final size:19
Alignment explanation
Indices: 32006741--32006781 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
32006731 TCAAGCGGCT
32006741 TGAGTTGTTGTTGGTTTTGA
1 TGAG-TGTTGTTGGTTTTGA
32006761 TGA-TGTTGTTGGTTTTGA
1 TGAGTGTTGTTGGTTTTGA
32006779 TGA
1 TGA
32006782 TGATGATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.86
20 3 0.14
ACGTcount: A:0.12, C:0.00, G:0.34, T:0.54
Consensus pattern (19 bp):
TGAGTGTTGTTGGTTTTGA
Found at i:32006786 original size:21 final size:18
Alignment explanation
Indices: 32006746--32006783 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
32006736 CGGCTTGAGT
32006746 TGTTGTTGGTTTTGATGA
1 TGTTGTTGGTTTTGATGA
32006764 TGTTGTTGGTTTTGATGA
1 TGTTGTTGGTTTTGATGA
32006782 TG
1 TG
32006784 ATGATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.55
Consensus pattern (18 bp):
TGTTGTTGGTTTTGATGA
Found at i:32038954 original size:22 final size:22
Alignment explanation
Indices: 32038929--32038977 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 22
32038919 ATTTTGGAAA
*
32038929 ATTAATGTAAATATATTATTAT
1 ATTAATGTAAATAAATTATTAT
32038951 ATT-A--TAAATAAATTATTAT
1 ATTAATGTAAATAAATTATTAT
*
32038970 AGTAATGT
1 ATTAATGT
32038978 TACTTTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
19 16 0.73
20 1 0.05
21 1 0.05
22 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (22 bp):
ATTAATGTAAATAAATTATTAT
Found at i:32039439 original size:110 final size:110
Alignment explanation
Indices: 32039196--32039403 Score: 319
Period size: 110 Copynumber: 1.9 Consensus size: 110
32039186 AAAATTTACG
* ** *
32039196 ATCTAAAAACTCTAAGGATCTTATATGTAAATTTTTCGTTTTAATTGACAGCTGAAAAACGCTTC
1 ATCTAAAAACTCAAACCACCTTATATGTAAATTTTTCGTTTTAATTGACAGCTGAAAAACGCTTC
32039261 AAGGTGCCGCTTGACAGTATGGCGGCACCAAATTAAAATGTGATA
66 AAGGTGCCGCTTGACAGTATGGCGGCACCAAATTAAAATGTGATA
* **
32039306 ATCTAAAAACTCCAAGGACCTTATATGTAAATTTTTCGTTTTAATTGACAGCTGAAAAAACGCTT
1 ATCTAAAAACTCAAACCACCTTATATGTAAATTTTTCGTTTTAATTGACAGCTG-AAAAACGCTT
*
32039371 CAAGGTGCCG-TCTGATAGTATGGCGGCACCAAA
65 CAAGGTGCCGCT-TGACAGTATGGCGGCACCAAA
32039404 CTTTAAAAGG
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
110 53 0.57
111 40 0.43
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (110 bp):
ATCTAAAAACTCAAACCACCTTATATGTAAATTTTTCGTTTTAATTGACAGCTGAAAAACGCTTC
AAGGTGCCGCTTGACAGTATGGCGGCACCAAATTAAAATGTGATA
Found at i:32041018 original size:17 final size:18
Alignment explanation
Indices: 32040988--32041021 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
32040978 TGGGCTGAAG
32040988 TTTTATAAACATAATTAT
1 TTTTATAAACATAATTAT
*
32041006 TTTTA-AAATATAATTA
1 TTTTATAAACATAATTA
32041022 ATAAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTATAAACATAATTAT
Found at i:32048725 original size:52 final size:52
Alignment explanation
Indices: 32048655--32048759 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
32048645 CTTTGAGGTG
* * *
32048655 ACCTAACTTCTTACTATAGCGACACTTTTTGTCTCGTTTCTTTGATGCTACC
1 ACCTAACTTCTTACTATAGCGACACCTTTTGTCTCGTTTCTTTAATACTACC
* *
32048707 ACCTAACTTCTTATTATAGCGACACCTTTTGTTTCGTTTCTTTAATACTACC
1 ACCTAACTTCTTACTATAGCGACACCTTTTGTCTCGTTTCTTTAATACTACC
32048759 A
1 A
32048760 AAACGGAAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.43
Consensus pattern (52 bp):
ACCTAACTTCTTACTATAGCGACACCTTTTGTCTCGTTTCTTTAATACTACC
Found at i:32052465 original size:30 final size:30
Alignment explanation
Indices: 32052430--32052491 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
32052420 TATTTTATTG
*
32052430 TTAATTTTATTATTATTTTAGAGGCATTTA
1 TTAATTTTATTACTATTTTAGAGGCATTTA
* *
32052460 TTAATTTTGTTACTATTTTATAGGCATTTA
1 TTAATTTTATTACTATTTTAGAGGCATTTA
32052490 TT
1 TT
32052492 TGTTATGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTACTATTTTAGAGGCATTTA
Found at i:32054436 original size:14 final size:14
Alignment explanation
Indices: 32054417--32054447 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
32054407 ATCCAAACAA
32054417 TAACAATAAAATAG
1 TAACAATAAAATAG
*
32054431 TAACAATATAATAG
1 TAACAATAAAATAG
32054445 TAA
1 TAA
32054448 AATGACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (14 bp):
TAACAATAAAATAG
Found at i:32055229 original size:16 final size:16
Alignment explanation
Indices: 32055208--32055251 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
32055198 TATAAAAATT
*
32055208 ATTTTTTACAATATAA
1 ATTTTTTAAAATATAA
32055224 ATTTTTTAAAATATAA
1 ATTTTTTAAAATATAA
* *
32055240 AATTATTAAAAT
1 ATTTTTTAAAAT
32055252 TATTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTTTTAAAATATAA
Found at i:32059342 original size:14 final size:14
Alignment explanation
Indices: 32059319--32059352 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
32059309 TACAATATCC
32059319 AAATAATAACAATA
1 AAATAATAACAATA
*
32059333 AAATAGTAACAATA
1 AAATAATAACAATA
*
32059347 TAATAA
1 AAATAA
32059353 CGAAACGACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:32059390 original size:22 final size:23
Alignment explanation
Indices: 32059365--32059407 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
32059355 AAACGACACC
*
32059365 AAAACAAC-AACAAAAACAATGG
1 AAAACAACAAAAAAAAACAATGG
32059387 AAAACAACAAAAAAAAACAAT
1 AAAACAACAAAAAAAAACAAT
32059408 ATTTTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.74, C:0.16, G:0.05, T:0.05
Consensus pattern (23 bp):
AAAACAACAAAAAAAAACAATGG
Found at i:32060274 original size:22 final size:23
Alignment explanation
Indices: 32060242--32060290 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
32060232 TAAAAATATA
*
32060242 TATATTATTAAAAT-GTTAAAAT
1 TATATTATTAAAATCGTAAAAAT
* *
32060264 TATATTTTTAATATCGTAAAAAT
1 TATATTATTAAAATCGTAAAAAT
32060287 TATA
1 TATA
32060291 ATTTAATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
TATATTATTAAAATCGTAAAAAT
Found at i:32060289 original size:23 final size:24
Alignment explanation
Indices: 32060227--32060290 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 24
32060217 AAATCATTTA
32060227 AAAAT-TAAAAATATATATATTATT
1 AAAATGTAAAAAT-TATATATTATT
*
32060251 AAAATGTTAAAATTATAT-TT-TT
1 AAAATGTAAAAATTATATATTATT
*
32060273 AATATCGTAAAAATTATA
1 AAAAT-GTAAAAATTATA
32060291 ATTTAATTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 6 0.17
23 13 0.37
24 10 0.29
25 6 0.17
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (24 bp):
AAAATGTAAAAATTATATATTATT
Found at i:32061878 original size:21 final size:21
Alignment explanation
Indices: 32061854--32061893 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
32061844 GCAGGTAAAT
32061854 TTGATGTTATTGCTTCTTGAA
1 TTGATGTTATTGCTTCTTGAA
* *
32061875 TTGATTTTATTGTTTCTTG
1 TTGATGTTATTGCTTCTTG
32061894 TGAAGGTAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.07, G:0.17, T:0.60
Consensus pattern (21 bp):
TTGATGTTATTGCTTCTTGAA
Found at i:32061952 original size:16 final size:16
Alignment explanation
Indices: 32061933--32061987 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
32061923 TGAATAGCTT
32061933 CTTCATGGAGGAAGTA
1 CTTCATGGAGGAAGTA
* *
32061949 CTTCATGGAGGTCTATTGTT
1 CTTCATGGAGG---A-AGTA
32061969 CTTCATGGAGGAAGTA
1 CTTCATGGAGGAAGTA
32061985 CTT
1 CTT
32061988 TTTAGGCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 16 0.52
17 1 0.03
19 1 0.03
20 13 0.42
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.35
Consensus pattern (16 bp):
CTTCATGGAGGAAGTA
Found at i:32077799 original size:2 final size:2
Alignment explanation
Indices: 32077792--32077819 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32077782 AGTATATTCA
32077792 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
32077820 CTTAACTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32079057 original size:39 final size:39
Alignment explanation
Indices: 32079000--32079083 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
32078990 AAATATTTTT
*
32079000 ATAATTTTTAGTAATTTTAATGA-TTTT-TAATTTTAAAAA
1 ATAATTTTTAGTAATTTTAA--ACTTTTAGAATTTTAAAAA
*
32079039 ATAATTTTTA-TATTTTTTAAACTTTTAGAATTTTAAAAA
1 ATAATTTTTAGTA-ATTTTAAACTTTTAGAATTTTAAAAA
*
32079078 TTAATT
1 ATAATT
32079084 AAATGTTGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
37 1 0.03
38 6 0.15
39 32 0.82
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (39 bp):
ATAATTTTTAGTAATTTTAAACTTTTAGAATTTTAAAAA
Found at i:32079229 original size:12 final size:12
Alignment explanation
Indices: 32079212--32079238 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
32079202 ATTAAAAATA
32079212 AAATAAATAATT
1 AAATAAATAATT
32079224 AAATAAATAATT
1 AAATAAATAATT
32079236 AAA
1 AAA
32079239 ATAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAAATAATT
Found at i:32082239 original size:12 final size:12
Alignment explanation
Indices: 32082222--32082266 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
32082212 AATCTTATTT
*
32082222 TGTCTGTCTGTA
1 TGTCTGTATGTA
32082234 TGTCTGTATGTA
1 TGTCTGTATGTA
*
32082246 TGTATGTATGTA
1 TGTCTGTATGTA
*
32082258 TGTATGTAT
1 TGTCTGTAT
32082267 ACATTTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.18, C:0.07, G:0.24, T:0.51
Consensus pattern (12 bp):
TGTCTGTATGTA
Found at i:32082245 original size:4 final size:4
Alignment explanation
Indices: 32082230--32082266 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
32082220 TTTGTCTGTC
*
32082230 TGTA TGTC TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
32082267 ACATTTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.22, C:0.03, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:32087243 original size:3 final size:3
Alignment explanation
Indices: 32087235--32087266 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
32087225 AGCGTTTGAG
32087235 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
32087267 GATGATGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:32090979 original size:26 final size:25
Alignment explanation
Indices: 32090949--32091038 Score: 67
Period size: 26 Copynumber: 3.4 Consensus size: 25
32090939 TTCGGACTTA
32090949 TATTTATAATTGTATTATATTTATTT
1 TATTTATAATTGTATTAT-TTTATTT
* *
32090975 TATTTAAAAAAT-TATTATTTTTAATTT
1 TATTT-ATAATTGTATTA-TTTT-ATTT
* * *
32091002 TATTTTTAATATAGAATTATTTTATAT
1 TATTTATAAT-T-GTATTATTTTATTT
32091029 T-TTTATAATT
1 TATTTATAATT
32091039 TTTTAAAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
25 1 0.02
26 22 0.44
27 19 0.38
28 4 0.08
29 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TATTTATAATTGTATTATTTTATTT
Found at i:32091817 original size:24 final size:24
Alignment explanation
Indices: 32091781--32091826 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
32091771 CCAATTAGGG
32091781 AATTACTGTTTAG-ATTTAATTCT
1 AATTACTGTTTAGAATTTAATTCT
*
32091804 AATTATCTTTTTAGAATTTAATT
1 AATTA-CTGTTTAGAATTTAATT
32091827 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (24 bp):
AATTACTGTTTAGAATTTAATTCT
Found at i:32095274 original size:24 final size:24
Alignment explanation
Indices: 32095228--32095274 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
32095218 CACATGGCAT
* * *
32095228 TTTTTCAAATTAAATTATGTGGTA
1 TTTTTAAAATAAAAATATGTGGTA
*
32095252 TTTTTAAAATAAAAATATTTGGT
1 TTTTTAAAATAAAAATATGTGGT
32095275 CAATGGTCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTTTAAAATAAAAATATGTGGTA
Found at i:32097869 original size:22 final size:21
Alignment explanation
Indices: 32097842--32097891 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
32097832 AAAGCTCTTT
* *
32097842 AAAATTCAACAATGTAAAAAA
1 AAAATTCAAAAATATAAAAAA
*
32097863 AACAATTTTAAAAATATAAAAAA
1 AA-AA-TTCAAAAATATAAAAAA
32097886 AAAATT
1 AAAATT
32097892 TGAAATCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 4 0.17
22 4 0.17
23 16 0.67
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATTCAAAAATATAAAAAA
Found at i:32098408 original size:23 final size:23
Alignment explanation
Indices: 32098370--32098420 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
32098360 AGTTCAAAGT
*
32098370 AAATAAATTATTAAAAAAT-TAA
1 AAATAAAATATTAAAAAATATAA
32098392 AAATAAAAATATTAAAAAATCATAA
1 AAAT-AAAATATTAAAAAAT-ATAA
32098417 AAAT
1 AAAT
32098421 CGATTCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 4 0.16
23 14 0.56
25 7 0.28
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATAAAATATTAAAAAATATAA
Found at i:32100281 original size:31 final size:31
Alignment explanation
Indices: 32100244--32100323 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
32100234 TTTGGGATCC
* * * *
32100244 AATTTGGTACTTAAATTTGA-TACTTTTTTCT
1 AATTTGGTACTTAAACTTCACGAATTTTTT-T
*
32100275 AATTTGGTACCTAAACTTCACGAATTTTTTT
1 AATTTGGTACTTAAACTTCACGAATTTTTTT
*
32100306 AAGTTGGTACTTAAACTT
1 AATTTGGTACTTAAACTT
32100324 TTTGGGATCC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 34 0.83
32 7 0.17
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.47
Consensus pattern (31 bp):
AATTTGGTACTTAAACTTCACGAATTTTTTT
Found at i:32100701 original size:58 final size:56
Alignment explanation
Indices: 32100543--32100701 Score: 160
Period size: 59 Copynumber: 2.7 Consensus size: 56
32100533 AAATTAAATC
* *
32100543 TAAAAAAAGCTTAGGTACCAAATTAGGAAAAAAATTGTCAAGTTCAGTACCAACTTGGA
1 TAAAAAAAGTTTAGGTACCAAATTA--AAAAAAA-TGTCAAATTCAGTACCAACTTGGA
** *
32100602 TAAAAAAAGTTTAGGTATTAAATTAAGAAAAAGTGTCAAATTCATGTACCATA-TT-GA
1 TAAAAAAAGTTTAGGTACCAAATTAA-AAAAAATGTCAAATTCA-GTACCA-ACTTGGA
* * *
32100659 GTCAAAAAAAATTTAGATACCAAATTAAAAAAAATGTAAAATT
1 -T-AAAAAAAGTTTAGGTACCAAATTAAAAAAAATGTCAAATT
32100702 TGGATACCAA
Statistics
Matches: 84, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
57 13 0.15
58 27 0.32
59 44 0.52
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.27
Consensus pattern (56 bp):
TAAAAAAAGTTTAGGTACCAAATTAAAAAAAATGTCAAATTCAGTACCAACTTGGA
Found at i:32103647 original size:2 final size:2
Alignment explanation
Indices: 32103640--32103667 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32103630 GGGGGAAGGG
32103640 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
32103668 CGAAAATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32107749 original size:15 final size:15
Alignment explanation
Indices: 32107732--32107783 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
32107722 AAAAAATAAT
*
32107732 TTAAAATTAACCAAT
1 TTAAAATTAACCAAA
32107747 TTAAAA--AACTCAAAA
1 TTAAAATTAAC-C-AAA
*
32107762 TTAAAATTGACCAAA
1 TTAAAATTAACCAAA
32107777 TTAAAAT
1 TTAAAAT
32107784 ATAAACACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 3 0.10
14 1 0.03
15 24 0.77
16 1 0.03
17 2 0.06
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.29
Consensus pattern (15 bp):
TTAAAATTAACCAAA
Found at i:32111233 original size:20 final size:20
Alignment explanation
Indices: 32111209--32111256 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
32111199 AATTATGTTT
*
32111209 AAAAATAAATAAAAATTATAG
1 AAAAATAAATAAAAATTA-AA
*
32111230 AAAAAT-AGTAAAAATTAAA
1 AAAAATAAATAAAAATTAAA
32111249 AAAAATAA
1 AAAAATAA
32111257 CCCTAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.29
20 11 0.46
21 6 0.25
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (20 bp):
AAAAATAAATAAAAATTAAA
Found at i:32133225 original size:2 final size:2
Alignment explanation
Indices: 32133218--32133252 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
32133208 ACCCCACCAT
*
32133218 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32133253 GTAACTGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:32134935 original size:12 final size:13
Alignment explanation
Indices: 32134908--32134937 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
32134898 GTTCATTGCG
32134908 AATTAATAATTAA
1 AATTAATAATTAA
32134921 AATTAATAA-TAA
1 AATTAATAATTAA
32134933 AATTA
1 AATTA
32134938 CCATTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATTAATAATTAA
Found at i:32135249 original size:22 final size:22
Alignment explanation
Indices: 32135211--32135253 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
32135201 CACCCACCTT
*
32135211 TATTTTTTTAATTTTTTATATA
1 TATTTTTTTAATATTTTATATA
32135233 TATTTTTTT-ATAATTTTATAT
1 TATTTTTTTAAT-ATTTTATAT
32135254 TTTATAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTTTTTTAATATTTTATATA
Found at i:32135264 original size:24 final size:23
Alignment explanation
Indices: 32135237--32135281 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
32135227 TATATATATT
* *
32135237 TTTTTATAATTTTATATTTTATAG
1 TTTTCATAATTTAAT-TTTTATAG
32135261 TTTTCATAATTTAATTTTTAT
1 TTTTCATAATTTAATTTTTAT
32135282 CTCATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTCATAATTTAATTTTTATAG
Found at i:32135333 original size:15 final size:15
Alignment explanation
Indices: 32135302--32135335 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
32135292 TATTGAGTTG
*
32135302 TTTTATTTTTATGAT
1 TTTTATTTTTATAAT
*
32135317 TTTTATTTTTTTAAT
1 TTTTATTTTTATAAT
32135332 TTTT
1 TTTT
32135336 TATAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTATTTTTATAAT
Found at i:32136324 original size:7 final size:7
Alignment explanation
Indices: 32136312--32136339 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
32136302 ATCCTATTGG
32136312 AGGAAAT
1 AGGAAAT
32136319 AGGAAAT
1 AGGAAAT
32136326 AGGAAAT
1 AGGAAAT
32136333 AGGAAAT
1 AGGAAAT
32136340 TCATAGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (7 bp):
AGGAAAT
Found at i:32144198 original size:6 final size:6
Alignment explanation
Indices: 32144189--32144228 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
32144179 CCATATTCTG
32144189 ATTCCA ATTCCA ATTCCA ATTCCA ATTCCA ATTCCA ATTC
1 ATTCCA ATTCCA ATTCCA ATTCCA ATTCCA ATTCCA ATTC
32144229 AAGGTATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTCCA
Done.