Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 130 of 290
Found at i:44063721 original size:7 final size:7
Alignment explanation
Indices: 44063709--44063738 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
44063699 CATTCACTCC
44063709 AAATATA
1 AAATATA
44063716 AAATATA
1 AAATATA
44063723 AAATATA
1 AAATATA
44063730 AAATATA
1 AAATATA
44063737 AA
1 AA
44063739 TATTATCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATATA
Found at i:44069305 original size:15 final size:15
Alignment explanation
Indices: 44069281--44069322 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
44069271 TGAATATTGT
*
44069281 AATAATATATTAAGC
1 AATAACATATTAAGC
44069296 AATAACATATTAAGC
1 AATAACATATTAAGC
44069311 AATAACATATTA
1 AATAACATATTA
44069323 GGAAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.31
Consensus pattern (15 bp):
AATAACATATTAAGC
Found at i:44076619 original size:10 final size:10
Alignment explanation
Indices: 44076604--44076642 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
44076594 ATGTTCTTCC
44076604 TTCTTTT-TCT
1 TTCTTTTAT-T
44076614 TTCTTTTATT
1 TTCTTTTATT
44076624 TTCTTTTATT
1 TTCTTTTATT
44076634 TTCTATTTA
1 TTCT-TTTA
44076643 ATTTGCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 22 0.81
11 5 0.19
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (10 bp):
TTCTTTTATT
Found at i:44076776 original size:29 final size:29
Alignment explanation
Indices: 44076709--44076780 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 29
44076699 TATATATTAT
* * **
44076709 ATATTATATAATACATATACATACTTTTA
1 ATATAATATAATATATATACATAAGTTTA
* *
44076738 ATTTATTATAATATATATA-ATAAGTTTA
1 ATATAATATAATATATATACATAAGTTTA
44076766 CATATAATAT-ATATA
1 -ATATAATATAATATA
44076781 CTTCATTAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
28 12 0.35
29 22 0.65
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (29 bp):
ATATAATATAATATATATACATAAGTTTA
Found at i:44077616 original size:23 final size:21
Alignment explanation
Indices: 44077583--44077629 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
44077573 ATTTATCCCA
* *
44077583 TTTTGTTTTTACTTTAATACTTT
1 TTTTGTATTTAATTTAA-A-TTT
44077606 TTTTGTATTTAATTTAAATTT
1 TTTTGTATTTAATTTAAATTT
44077627 TTT
1 TTT
44077630 ATTCTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 1 0.05
23 15 0.68
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTGTATTTAATTTAAATTT
Found at i:44080808 original size:17 final size:18
Alignment explanation
Indices: 44080774--44080807 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44080764 TTTAAAATTA
44080774 ATTTTTCAAAAATATTTT
1 ATTTTTCAAAAATATTTT
44080792 ATTTTT-AAAAAT-TTTT
1 ATTTTTCAAAAATATTTT
44080808 TGGATTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTCAAAAATATTTT
Found at i:44097298 original size:42 final size:42
Alignment explanation
Indices: 44097251--44097357 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 42
44097241 GAGTTACATG
*
44097251 GCCTGGCCAAACGCCCATGTCCTTACCCATGTGGCTCACACA
1 GCCTGGCCAAACGCCCATGTCCTTACCCATGAGGCTCACACA
* * ** * *
44097293 GCCTGGGCAGACATCCTTGTCCTTACCCATGAGGCTCACACG
1 GCCTGGCCAAACGCCCATGTCCTTACCCATGAGGCTCACACA
* *
44097335 GCCTGGTCACACGCCCATG-CCTT
1 GCCTGGCCAAACGCCCATGTCCTT
44097358 GGCCGCGTGG
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 4 0.08
42 49 0.92
ACGTcount: A:0.19, C:0.39, G:0.21, T:0.21
Consensus pattern (42 bp):
GCCTGGCCAAACGCCCATGTCCTTACCCATGAGGCTCACACA
Found at i:44099079 original size:28 final size:28
Alignment explanation
Indices: 44099009--44099081 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
44098999 GCTTGGCGCG
*
44099009 AATATTATATTTTAAA-AACAATTATATT
1 AATATT-TATATTAAATAACAATTATATT
* * *
44099037 AATTATATATGTTAAATAATAATTATATT
1 AA-TATTTATATTAAATAACAATTATATT
*
44099066 TATATTTATATTAAAT
1 AATATTTATATTAAAT
44099082 CACTAACCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 22 0.59
29 15 0.41
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
AATATTTATATTAAATAACAATTATATT
Found at i:44102296 original size:17 final size:17
Alignment explanation
Indices: 44102274--44102378 Score: 54
Period size: 19 Copynumber: 5.9 Consensus size: 17
44102264 TGATATGTAG
*
44102274 TAAAAAATTATAAACTA
1 TAAAAAATTATAAAATA
*
44102291 T-AAAAATCAATAAAATA
1 TAAAAAAT-TATAAAATA
* *
44102308 TATAAAAATTATTAAATTT
1 TA-AAAAATTA-TAAAATA
44102327 TAATAAAA--ATAAAATTTA
1 TAA-AAAATTATAAAA--TA
* * *
44102345 TTAAAAATTAGAAAAAA
1 TAAAAAATTATAAAATA
*
44102362 TATAAAAATTGTAAAAT
1 TA-AAAAATTATAAAAT
44102379 TTTGTAAAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 19
0.66 0.14 0.20
Matches are distributed among these distances:
16 10 0.16
17 16 0.25
18 16 0.25
19 22 0.34
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
TAAAAAATTATAAAATA
Found at i:44102338 original size:26 final size:26
Alignment explanation
Indices: 44102309--44102389 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
44102299 AATAAAATAT
44102309 ATAAAAATTATTAAATTTTAATAAAA
1 ATAAAAATTATTAAATTTTAATAAAA
* ** *
44102335 ATAAAATTTATTAAAAATTAGAAAAAA
1 ATAAAAATTATTAAATTTTA-ATAAAA
* * *
44102362 TATAAAAATTGTAAAATTTT-GTAAAA
1 -ATAAAAATTATTAAATTTTAATAAAA
44102388 AT
1 AT
44102390 CATTAGAAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
25 2 0.05
26 21 0.50
27 5 0.12
28 14 0.33
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (26 bp):
ATAAAAATTATTAAATTTTAATAAAA
Found at i:44102359 original size:19 final size:19
Alignment explanation
Indices: 44102336--44102389 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
44102326 TTAATAAAAA
44102336 TAAAATTTATTAAAAATTAG
1 TAAAATTTATTAAAAATT-G
**
44102356 -AAAAAATA-TAAAAATTG
1 TAAAATTTATTAAAAATTG
44102373 TAAAATTT-TGTAAAAAT
1 TAAAATTTAT-TAAAAAT
44102390 CATTAGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
17 1 0.04
18 13 0.48
19 13 0.48
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (19 bp):
TAAAATTTATTAAAAATTG
Found at i:44103108 original size:89 final size:87
Alignment explanation
Indices: 44102976--44103138 Score: 222
Period size: 89 Copynumber: 1.9 Consensus size: 87
44102966 AAGGGGCTTA
* *
44102976 AATTATTATTTTTTAAATTTGAGGGTCTTTTTTATGCATTTTGAAAGTTTAAGTACCCAATTTGA
1 AATTATTATTTTTTAAATTTGAGGGTCTTTTTTATGCAATTTGAAAATTTAAGTACCCAATTT-A
44103041 GT-AAAAAATAGAGTAAGGACTT
65 GTGAAAAAATAGAGTAAGGACTT
* * * *
44103063 AATTATCTTTTTTTTAAGTTTTGAGGGT-TTTTTTGATGCAATTTGAAAATTTAATTACCTAATT
1 AATTAT-TATTTTTTAA-ATTTGAGGGTCTTTTTT-ATGCAATTTGAAAATTTAAGTACCCAATT
44103127 TAGTGAAAAAAT
63 TAGTGAAAAAAT
44103139 GCAAGAACTT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
87 6 0.09
88 18 0.27
89 42 0.64
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (87 bp):
AATTATTATTTTTTAAATTTGAGGGTCTTTTTTATGCAATTTGAAAATTTAAGTACCCAATTTAG
TGAAAAAATAGAGTAAGGACTT
Found at i:44103161 original size:89 final size:85
Alignment explanation
Indices: 44102976--44103183 Score: 217
Period size: 89 Copynumber: 2.4 Consensus size: 85
44102966 AAGGGGCTTA
* * * *
44102976 AATTAT-TATTTTTTAAATTTGAGGGTCTTTTTTATGCATTTTGAAAGTTTAAGTACCCAATTTG
1 AATTATCTTTTTTTTAAGTTTGAGGGT-TTTTTTATGCAATTTGAAAATTTAAGTACCCAATTTG
* *
44103040 AGTAAAAAATAGAGTAAGGACTT
65 AGTAAAAAAT--AGCAAGAACTT
* *
44103063 AATTATCTTTTTTTTAAGTTTTGAGGGTTTTTTTGATGCAATTTGAAAATTTAATTACCTAATTT
1 AATTATCTTTTTTTTAAG-TTTGAGGGTTTTTTT-ATGCAATTTGAAAATTTAAGTACCCAATTT
44103128 -AGTGAAAAAAT-GCAAGAACTT
64 GAGT-AAAAAATAGCAAGAACTT
*
44103149 AATTAAT-TTCTTTTATAGAAGTTTGAGGGTTTTTT
1 AATT-ATCTT-TTTT-T-TAAGTTTGAGGGTTTTTT
44103184 ACACTCTTAA
Statistics
Matches: 104, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
86 14 0.13
87 12 0.12
88 33 0.32
89 45 0.43
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (85 bp):
AATTATCTTTTTTTTAAGTTTGAGGGTTTTTTTATGCAATTTGAAAATTTAAGTACCCAATTTGA
GTAAAAAATAGCAAGAACTT
Found at i:44108217 original size:20 final size:21
Alignment explanation
Indices: 44108183--44108236 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
44108173 TGATGATAAT
*
44108183 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
44108204 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
44108224 TTTTATTATTTTA
1 TTATATTATTTTA
44108237 TTATTATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:44108240 original size:3 final size:3
Alignment explanation
Indices: 44108222--44108270 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
44108212 TTTAATGAGA
*
44108222 TAT T-T TAT TAT T-T TAT TAT TAT T-T CAT TAT TAT T-T TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
44108267 TAT T
1 TAT T
44108271 TAGTATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:44108242 original size:11 final size:11
Alignment explanation
Indices: 44108226--44108264 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
44108216 ATGAGATATT
44108226 TTATTATTTTA
1 TTATTATTTTA
*
44108237 TTATTATTTCA
1 TTATTATTTTA
44108248 TTATTATTTTA
1 TTATTATTTTA
44108259 TTATTA
1 TTATTA
44108265 ATTATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:44108250 original size:19 final size:19
Alignment explanation
Indices: 44108222--44108263 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
44108212 TTTAATGAGA
*
44108222 TATTTTATTATT-TTATTAT
1 TATTTCATTATTATT-TTAT
44108241 TATTTCATTATTATTTTAT
1 TATTTCATTATTATTTTAT
44108260 TATT
1 TATT
44108264 AATTATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTCATTATTATTTTAT
Found at i:44108681 original size:219 final size:219
Alignment explanation
Indices: 44108302--44108738 Score: 865
Period size: 219 Copynumber: 2.0 Consensus size: 219
44108292 TGAAGAATTT
44108302 TCATCATCTTTCCATGCATGCAACCAACATTAGAAGAGAAGGAAAAGAAAGAAATTTTCTTTTCT
1 TCATCATCTTTCCATGCATGCAACCAACATTAGAAGAGAAGGAAAAGAAAGAAATTTTCTTTTCT
44108367 TTACAATTTGGTCCTTCCACCAAAAATTCACCATTTTCATCTAGAAATCAAAAGAATTTCCATAG
66 TTACAATTTGGTCCTTCCACCAAAAATTCACCATTTTCATCTAGAAATCAAAAGAATTTCCATAG
44108432 CTAATAAGAGAGAAAAATGTTAAGGAGACCATGGGGAGTTAGAATATCAAGTTGTATTTAAGAAA
131 CTAATAAGAGAGAAAAATGTTAAGGAGACCATGGGGAGTTAGAATATCAAGTTGTATTTAAGAAA
44108497 TAGAAGCTGGAGGAGAGAGAAAAA
196 TAGAAGCTGGAGGAGAGAGAAAAA
*
44108521 TCATCATTTTTCCATGCATGCAACCAACATTAGAAGAGAAGGAAAAGAAAGAAATTTTCTTTTCT
1 TCATCATCTTTCCATGCATGCAACCAACATTAGAAGAGAAGGAAAAGAAAGAAATTTTCTTTTCT
44108586 TTACAATTTGGTCCTTCCACCAAAAATTCACCATTTTCATCTAGAAATCAAAAGAATTTCCATAG
66 TTACAATTTGGTCCTTCCACCAAAAATTCACCATTTTCATCTAGAAATCAAAAGAATTTCCATAG
44108651 CTAATAAGAGAGAAAAATGTTAAGGAGACCATGGGGAGTTAGAATATCAAGTTGTATTTAAGAAA
131 CTAATAAGAGAGAAAAATGTTAAGGAGACCATGGGGAGTTAGAATATCAAGTTGTATTTAAGAAA
44108716 TAGAAGCTGGAGGAGAGAGAAAA
196 TAGAAGCTGGAGGAGAGAGAAAA
44108739 TCAAGTTAAA
Statistics
Matches: 217, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
219 217 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (219 bp):
TCATCATCTTTCCATGCATGCAACCAACATTAGAAGAGAAGGAAAAGAAAGAAATTTTCTTTTCT
TTACAATTTGGTCCTTCCACCAAAAATTCACCATTTTCATCTAGAAATCAAAAGAATTTCCATAG
CTAATAAGAGAGAAAAATGTTAAGGAGACCATGGGGAGTTAGAATATCAAGTTGTATTTAAGAAA
TAGAAGCTGGAGGAGAGAGAAAAA
Found at i:44124908 original size:32 final size:32
Alignment explanation
Indices: 44124867--44124928 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
44124857 AGAGCCCACC
*
44124867 TCAATCTATTTTCGTTCCCAAATCAATGCACT
1 TCAATCTATTTTCATTCCCAAATCAATGCACT
44124899 TCAATCTATTTTCATTCCCAAATCAATGCA
1 TCAATCTATTTTCATTCCCAAATCAATGCA
44124929 AACTTGGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (32 bp):
TCAATCTATTTTCATTCCCAAATCAATGCACT
Found at i:44136805 original size:21 final size:23
Alignment explanation
Indices: 44136779--44136822 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
44136769 ACCACACGGG
*
44136779 TGTGTGATA-AC-TGGGCCAAGC
1 TGTGTGATATACATGGGCAAAGC
44136800 TGTGTGATATACATGGGCAAAGC
1 TGTGTGATATACATGGGCAAAGC
44136823 CAGTTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (23 bp):
TGTGTGATATACATGGGCAAAGC
Found at i:44137409 original size:39 final size:40
Alignment explanation
Indices: 44137334--44137412 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 40
44137324 CTGTATACAT
**
44137334 ACTGTATCTAAGATGGGCTAAGGCCTAATTTATATCTGAA
1 ACTGTATCTAAGATGGGCTAAGGCCTAAACTATATCTGAA
* *
44137374 ACTGTATTTAA-ATGGGCTAAGGCCTAAACTGTATCTGAA
1 ACTGTATCTAAGATGGGCTAAGGCCTAAACTATATCTGAA
44137413 TATGTGATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 25 0.71
40 10 0.29
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (40 bp):
ACTGTATCTAAGATGGGCTAAGGCCTAAACTATATCTGAA
Found at i:44140535 original size:24 final size:21
Alignment explanation
Indices: 44140496--44140554 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
44140486 ATGTAATCCT
* *
44140496 AGATATAATATGTAATCTTTAAA
1 AGATATGATTTGTAATC-TT-AA
44140519 AGATATGACTTTGTAATCTTAA
1 AGATATGA-TTTGTAATCTTAA
*
44140541 AGATTTGATTTGTA
1 AGATATGATTTGTA
44140555 GATAGCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 6 0.19
22 9 0.28
23 9 0.28
24 8 0.25
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (21 bp):
AGATATGATTTGTAATCTTAA
Found at i:44140554 original size:21 final size:24
Alignment explanation
Indices: 44140506--44140554 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
44140496 AGATATAATA
44140506 TGTAATCTTTAAAAGATATGACTT
1 TGTAATCTTTAAAAGATATGACTT
*
44140530 TGTAATC-TT-AAAGATTTGA-TT
1 TGTAATCTTTAAAAGATATGACTT
44140551 TGTA
1 TGTA
44140555 GATAGCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 6 0.25
22 9 0.38
23 2 0.08
24 7 0.29
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (24 bp):
TGTAATCTTTAAAAGATATGACTT
Found at i:44140717 original size:13 final size:13
Alignment explanation
Indices: 44140699--44140723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44140689 AATTGATATC
44140699 TGTGAAAATTTTG
1 TGTGAAAATTTTG
44140712 TGTGAAAATTTT
1 TGTGAAAATTTT
44140724 ATCGTTTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
TGTGAAAATTTTG
Found at i:44141877 original size:44 final size:42
Alignment explanation
Indices: 44141810--44141932 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
44141800 TTTCGATATG
* * * ** *
44141810 TGATTTTGTGTAAGACTACGTCTGAGATGTTGGCATCG-ATT
1 TGATTTCGTGTAAGACCATGTCTGAGACATCGGCATCGTATT
*
44141851 TGAGATTTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATT
1 T--GATTT-CGTGTAAGACCATGTCTGAGACATCGGCATCGTATT
*
44141896 TGATTTCGTGTAAGACCCTGTCTGAGACAGT-GGCATC
1 TGATTTCGTGTAAGACCATGTCTGAGACA-TCGGCATC
44141933 AATATTGGAT
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
41 1 0.01
42 27 0.40
43 11 0.16
44 25 0.37
45 4 0.06
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTGAGACATCGGCATCGTATT
Found at i:44149225 original size:42 final size:41
Alignment explanation
Indices: 44149117--44149225 Score: 103
Period size: 44 Copynumber: 2.6 Consensus size: 41
44149107 TTTCGATATG
* * * *
44149117 TGATTTCGTGTAAGACTAC-GTCTGGGACGTAGTCATCGATT
1 TGATTTCGTGTAAGAC-CCTGTCTAGGACATAGACATCGATT
* * *
44149158 TGAGATTTACGTGTAAGGCCATGTCTAGGACATCGACATCGTATT
1 T--GATTT-CGTGTAAGACCCTGTCTAGGACATAGACATCG-ATT
44149203 TGATTTCGTGTAAGACCCTGTCT
1 TGATTTCGTGTAAGACCCTGTCT
44149226 GAGACAGTGG
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
41 1 0.02
42 15 0.28
43 10 0.19
44 24 0.44
45 4 0.07
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCCTGTCTAGGACATAGACATCGATT
Found at i:44158714 original size:21 final size:20
Alignment explanation
Indices: 44158685--44158725 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
44158675 ACAAAACTTG
44158685 TATAACTATCATCAAACATT
1 TATAACTATCATCAAACATT
*
44158705 TATAATCTATCATCAATCATT
1 TATAA-CTATCATCAAACATT
44158726 AAAATACGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (20 bp):
TATAACTATCATCAAACATT
Found at i:44159743 original size:29 final size:31
Alignment explanation
Indices: 44159685--44159741 Score: 84
Period size: 28 Copynumber: 1.9 Consensus size: 31
44159675 GTAACAGCTT
*
44159685 ACAAAAGAAAGCAAAAAGAAAATAGAAAACA
1 ACAAAAGAAAGCAAAAAGAAAAGAGAAAACA
44159716 ACAAAAG-AAG-AAAAAG-AAAGAGAAAA
1 ACAAAAGAAAGCAAAAAGAAAAGAGAAAA
44159742 ACGTTAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 6 0.24
30 3 0.12
31 7 0.28
ACGTcount: A:0.75, C:0.07, G:0.16, T:0.02
Consensus pattern (31 bp):
ACAAAAGAAAGCAAAAAGAAAAGAGAAAACA
Found at i:44185459 original size:9 final size:8
Alignment explanation
Indices: 44185434--44185458 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
44185424 CTCCAACTAC
44185434 ATAAAAAA
1 ATAAAAAA
44185442 ATAAAAAA
1 ATAAAAAA
44185450 ATAAAAAA
1 ATAAAAAA
44185458 A
1 A
44185459 AAACATTTTT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Found at i:44186089 original size:68 final size:69
Alignment explanation
Indices: 44186008--44186145 Score: 174
Period size: 70 Copynumber: 2.0 Consensus size: 69
44185998 CCCTGGAAAC
*
44186008 CTCAAACATACCAT-TTCAATATTTAATTAG-TTTTTTATACTAATTAAGT-AAGAAGCATACAA
1 CTCAAACATACCATCTT-AATATTTAATTAGTTTTTTTATACTAATTAAGTGAA-AAACATACAA
44186070 ATAAAT
64 ATAAAT
* * * * *
44186076 CTCAAATATACCATCTTAGTATTTATTTAGTTTTTTTTATAGTACTTAAGTGAAAAACATACAAA
1 CTCAAACATACCATCTTAATATTTAATTAG-TTTTTTTATACTAATTAAGTGAAAAACATACAAA
44186141 TAAAT
65 TAAAT
44186146 AATACTCCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
68 24 0.40
69 2 0.03
70 32 0.53
71 2 0.03
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (69 bp):
CTCAAACATACCATCTTAATATTTAATTAGTTTTTTTATACTAATTAAGTGAAAAACATACAAAT
AAAT
Found at i:44194570 original size:58 final size:58
Alignment explanation
Indices: 44194442--44194584 Score: 155
Period size: 58 Copynumber: 2.5 Consensus size: 58
44194432 AATTATTAAT
* **
44194442 AATTAAGTAATTCCTAAAATATAAAAGAGTTACTTAAAACATGAAAATATTTCCACAA
1 AATTAAGTAATTCATAAAATATAAAAGAAATACTTAAAACATGAAAATATTTCCACAA
* * * ** * *
44194500 AACTAAGCAATTCGTAAAATATAAAAGAAATGTTTAAAACATGATAAA-GTTTCTA-AGA
1 AATTAAGTAATTCATAAAATATAAAAGAAATACTTAAAACATGA-AAATATTTCCACA-A
*
44194558 AATTAAGTAATTCATAAAACATAAAAG
1 AATTAAGTAATTCATAAAATATAAAAG
44194585 TGTTCTAAGA
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
57 1 0.01
58 66 0.94
59 3 0.04
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.28
Consensus pattern (58 bp):
AATTAAGTAATTCATAAAATATAAAAGAAATACTTAAAACATGAAAATATTTCCACAA
Found at i:44194652 original size:53 final size:53
Alignment explanation
Indices: 44194572--44194705 Score: 162
Period size: 53 Copynumber: 2.5 Consensus size: 53
44194562 AAGTAATTCA
* * *
44194572 TAAAACATAAAAGTGTTCTAAGAAATTAAT-TTTCGACAGATGAAAGAATTACT
1 TAAAACATAAAAGAGTTCTAAGAAATTAATCTAT-GACAGAAGAAAGAATTACT
* ***
44194625 TAAAACATGAAAGAGTTCTAAGAAATTAATCTATGATTTAAGAAAGAATTACT
1 TAAAACATAAAAGAGTTCTAAGAAATTAATCTATGACAGAAGAAAGAATTACT
* *
44194678 TAAAACATAAAAAGATTTCAAAGAAATT
1 TAAAACAT-AAAAGAGTTCTAAGAAATT
44194706 TTGTAATTCA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
53 51 0.74
54 18 0.26
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (53 bp):
TAAAACATAAAAGAGTTCTAAGAAATTAATCTATGACAGAAGAAAGAATTACT
Found at i:44194857 original size:20 final size:20
Alignment explanation
Indices: 44194828--44194882 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
44194818 TTAAATATTT
*
44194828 CATAATACATGAAAAAATTA
1 CATAAAACATGAAAAAATTA
*
44194848 CATAAAACATAAAAAAATTA
1 CATAAAACATGAAAAAATTA
*
44194868 C-TTAAACTATGAAAA
1 CATAAAAC-ATGAAAA
44194883 TATTCCTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.62, C:0.11, G:0.04, T:0.24
Consensus pattern (20 bp):
CATAAAACATGAAAAAATTA
Found at i:44202438 original size:17 final size:18
Alignment explanation
Indices: 44202409--44202442 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
44202399 TGTGGTTTAC
44202409 CCGTGTGGGCCCACATGT
1 CCGTGTGGGCCCACATGT
44202427 CCGTGT-GGCCCACATG
1 CCGTGTGGGCCCACATG
44202443 ACCTAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.12, C:0.35, G:0.32, T:0.21
Consensus pattern (18 bp):
CCGTGTGGGCCCACATGT
Found at i:44203885 original size:28 final size:27
Alignment explanation
Indices: 44203784--44203885 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 27
44203774 TCAGTGTTAA
* *
44203784 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
44203812 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTATC--A--AT
*
44203844 ATTGGGCCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
44203872 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
44203886 TATTACAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 27 0.46
30 2 0.03
32 16 0.27
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:44203905 original size:60 final size:59
Alignment explanation
Indices: 44203785--44203921 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
44203775 CAGTGTTAAC
* *
44203785 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG-ATCAGAGTATAT
* *
44203846 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TATAT
* *
44203906 TGGGTCTTGCCCATAT
1 TGGGCCTAGCCCATAT
44203922 TAACACAGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
59 4 0.06
60 52 0.78
61 11 0.16
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGATCAGAGTATAT
Found at i:44206323 original size:15 final size:15
Alignment explanation
Indices: 44206286--44206314 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
44206276 TTTCCCTATC
44206286 TAATAATAATAATTA
1 TAATAATAATAATTA
44206301 TAATAATAATAATT
1 TAATAATAATAATT
44206315 TTATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:44206436 original size:19 final size:18
Alignment explanation
Indices: 44206403--44206446 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
44206393 ATACATGCAG
44206403 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
44206420 TAATAATTTTATCTAATAA
1 TAATAATTTT-TCTAATAA
*
44206439 TACTAATT
1 TAATAATT
44206447 AAAATTTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.21
19 15 0.62
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:44208998 original size:6 final size:6
Alignment explanation
Indices: 44208980--44209088 Score: 98
Period size: 6 Copynumber: 17.7 Consensus size: 6
44208970 AAGAAACATT
*
44208980 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATACAGA ATCAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA AT-CAGA ATCAGA ATCAGA
* * *
44209029 ATCAGT ATCAGGTA A-CAGA ATCAGA ATCAAA ATCAGT ATCAGGTA A-CAGA
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
*
44209079 ATCAAA ATCA
1 ATCAGA ATCA
44209089 AAATGTGAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
5 5 0.06
6 65 0.76
7 13 0.15
8 2 0.02
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:44209022 original size:25 final size:24
Alignment explanation
Indices: 44208980--44209088 Score: 98
Period size: 25 Copynumber: 4.4 Consensus size: 24
44208970 AAGAAACATT
44208980 ATCAGAA-CTAGAATCAGAATCAGA
1 ATCAGAATC-AGAATCAGAATCAGA
*
44209004 ATCAGAATACAGAATCAGAATCAAA
1 ATCAGAAT-CAGAATCAGAATCAGA
*
44209029 ATCAGTATCAGGTAA-CAGAATCAGA
1 ATCAGAATCA-G-AATCAGAATCAGA
* *
44209054 ATCAAAATCAGTATCAGGTAA-CAGA
1 ATCAGAATCAGAATCA-G-AATCAGA
*
44209079 ATCAAAATCA
1 ATCAGAATCA
44209089 AAATGTGAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
23 1 0.01
24 12 0.17
25 54 0.75
26 5 0.07
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (24 bp):
ATCAGAATCAGAATCAGAATCAGA
Found at i:44209026 original size:31 final size:31
Alignment explanation
Indices: 44208989--44209092 Score: 156
Period size: 31 Copynumber: 3.4 Consensus size: 31
44208979 TATCAGAACT
* * *
44208989 AGAATCAGAATCAGAATCA-GAATACAGAATC
1 AGAATCAAAATCAGTATCAGGTA-ACAGAATC
44209020 AGAATCAAAATCAGTATCAGGTAACAGAATC
1 AGAATCAAAATCAGTATCAGGTAACAGAATC
44209051 AGAATCAAAATCAGTATCAGGTAACAGAATC
1 AGAATCAAAATCAGTATCAGGTAACAGAATC
*
44209082 AAAATCAAAAT
1 AGAATCAAAAT
44209093 GTGAATGCAA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 66 0.97
32 2 0.03
ACGTcount: A:0.52, C:0.15, G:0.14, T:0.18
Consensus pattern (31 bp):
AGAATCAAAATCAGTATCAGGTAACAGAATC
Found at i:44209262 original size:28 final size:26
Alignment explanation
Indices: 44209207--44209288 Score: 92
Period size: 28 Copynumber: 3.0 Consensus size: 26
44209197 AGCATTGCTG
* * *
44209207 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGGCAAAGCCA
*
44209233 CCAGATACAGATATTTGTGGCATAGCCA
1 CCAGA-ACAGATA-TTGTGGCAAAGCCA
*
44209261 CCAGAATCAGATAATGTGGCAAAGCCA
1 CCAGAA-CAGATATTGTGGCAAAGCCA
44209288 C
1 C
44209289 TTAACAGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
26 5 0.10
27 21 0.44
28 22 0.46
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAAAGCCA
Found at i:44209479 original size:22 final size:22
Alignment explanation
Indices: 44209447--44209504 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
44209437 TAAATACGTT
*
44209447 TGGCACGAAGCCATAGTCAGGA
1 TGGCACAAAGCCATAGTCAGGA
* * *
44209469 TGGCACAAAGCCATATTTAGGT
1 TGGCACAAAGCCATAGTCAGGA
*
44209491 TGGCACAGAGCCAT
1 TGGCACAAAGCCAT
44209505 CGATAACGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (22 bp):
TGGCACAAAGCCATAGTCAGGA
Found at i:44210083 original size:27 final size:27
Alignment explanation
Indices: 44209941--44210090 Score: 158
Period size: 27 Copynumber: 5.6 Consensus size: 27
44209931 CCCCCCACAA
* * * * *
44209941 GGTATCTCGGTAATTCCACCATACAAG
1 GGTATTTCAGTAATTCTACCCTACAGG
* *
44209968 GGTATTTTAGTAATTCTACCCTATAGG
1 GGTATTTCAGTAATTCTACCCTACAGG
* *
44209995 GGTATTGC-GATAATTTTACCCTACAGG
1 GGTATTTCAG-TAATTCTACCCTACAGG
**
44210022 GGTATTTTGGTAATTCTACCCTACAGG
1 GGTATTTCAGTAATTCTACCCTACAGG
* *
44210049 GGTATTTCAGTATTTCTACCCTACAAG
1 GGTATTTCAGTAATTCTACCCTACAGG
*
44210076 GGTATTTCGGTAATT
1 GGTATTTCAGTAATT
44210091 TTGTAAATCG
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
26 1 0.01
27 99 0.98
28 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (27 bp):
GGTATTTCAGTAATTCTACCCTACAGG
Found at i:44210088 original size:54 final size:54
Alignment explanation
Indices: 44209962--44210090 Score: 181
Period size: 54 Copynumber: 2.4 Consensus size: 54
44209952 AATTCCACCA
* *
44209962 TACAAGGGTATTTTAGTAATTCTACCCTATAGGGGTATTGCGATAATTTTACCC
1 TACAAGGGTATTTTGGTAATTCTACCCTACAGGGGTATTGCGATAATTTTACCC
* *
44210016 TACAGGGGTATTTTGGTAATTCTACCCTACAGGGGTATTTC-AGT-ATTTCTACCC
1 TACAAGGGTATTTTGGTAATTCTACCCTACAGGGGTATTGCGA-TAATTT-TACCC
*
44210070 TACAAGGGTATTTCGGTAATT
1 TACAAGGGTATTTTGGTAATT
44210091 TTGTAAATCG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
53 5 0.07
54 62 0.93
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (54 bp):
TACAAGGGTATTTTGGTAATTCTACCCTACAGGGGTATTGCGATAATTTTACCC
Found at i:44210141 original size:27 final size:27
Alignment explanation
Indices: 44210111--44210521 Score: 423
Period size: 27 Copynumber: 15.3 Consensus size: 27
44210101 AGGGTAAAAC
* * * *
44210111 GGTAATTCTATAAATCAAGGGTACTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
* *
44210138 GGTAATTTTACAAGTCGAA-GGTATTTT
1 GGTAATTTTACAA-ACCAAGGGTATTTT
** *** * *
44210165 AATAATTTTACAGGTCGAGGGTATTTC
1 GGTAATTTTACAAACCAAGGGTATTTT
* * * *
44210192 AGTAATTTCACAAATCAGGGGTATTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
* * *
44210219 GGTAATTTTATAAACTAGGGGTATTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
* * *
44210246 GATAATTTTACAAACCAGGGGTACTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
*
44210273 GGTAATTTTACAAACCAGGGGTATTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
* *
44210300 GGTAATTTTATAAACAAAGGGTATTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
* *
44210327 AGT-ATTTTACAAACCAGGGGTATTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
**
44210353 GGTAATTTTGTAAACCAAGGGTATTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
*
44210380 GGTAATTTTACAAACCAGGGGTATTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
* * *
44210407 GGTGATTTTATAAACCAAGGGTGTTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
* *
44210434 AGTAATTTTACAAACCAGGGGTATTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
*** * *
44210461 GGTAATTTGGTAAACTAA-AGTATTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
44210487 GGTAATTTTACAAACCAAGGGTATTTT
1 GGTAATTTTACAAACCAAGGGTATTTT
44210514 GGTAATTT
1 GGTAATTT
44210522 GGTAAACTAA
Statistics
Matches: 313, Mismatches: 67, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
26 44 0.14
27 267 0.85
28 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (27 bp):
GGTAATTTTACAAACCAAGGGTATTTT
Found at i:44210375 original size:107 final size:108
Alignment explanation
Indices: 44210210--44210521 Score: 475
Period size: 107 Copynumber: 2.9 Consensus size: 108
44210200 CACAAATCAG
* * * * ** * *
44210210 GGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTGATAATTTTACAAACCAGGGGTACTTTGG
1 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGG
44210275 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAAA
66 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAAA
44210318 GGGTATTTTAGT-ATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGG
1 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGG
* *
44210382 TAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAACCAA
66 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAAA
* * * *
44210425 GGGTGTTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAAACTAA-AGTATTTTGG
1 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGG
*
44210489 TAATTTTACAAACCAAGGGTATTTTGGTAATTT
66 TAATTTTACAAACCAGGGGTATTTTGGTAATTT
44210522 GGTAAACTAA
Statistics
Matches: 187, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
107 137 0.73
108 50 0.27
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (108 bp):
GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGG
TAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAAA
Found at i:44211272 original size:20 final size:20
Alignment explanation
Indices: 44211249--44211292 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
44211239 AAAATGATGA
44211249 AACGACAGAGAAGCAAAACT
1 AACGACAGAGAAGCAAAACT
44211269 AACGACAGAGAAGCAAAACT
1 AACGACAGAGAAGCAAAACT
44211289 AACG
1 AACG
44211293 TCAGGTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.55, C:0.20, G:0.20, T:0.05
Consensus pattern (20 bp):
AACGACAGAGAAGCAAAACT
Found at i:44212801 original size:38 final size:39
Alignment explanation
Indices: 44212717--44212851 Score: 107
Period size: 39 Copynumber: 3.4 Consensus size: 39
44212707 ACCAATATGG
*
44212717 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * * *
44212756 CCCCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
44212794 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
44212835 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
44212852 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:44214796 original size:33 final size:34
Alignment explanation
Indices: 44214732--44214801 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
44214722 ATCAATTAAG
*
44214732 TAATCATAATAATTTAATATAAAACTATAATA-A
1 TAATCATAATAATATAATATAAAACTATAATATA
* * *
44214765 TAATCATTATAATATATATATATAA-TTTAATATA
1 TAATCATAATAATATA-ATATAAAACTATAATATA
44214799 TAA
1 TAA
44214802 AACCTAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
33 20 0.65
34 11 0.35
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (34 bp):
TAATCATAATAATATAATATAAAACTATAATATA
Found at i:44218400 original size:59 final size:59
Alignment explanation
Indices: 44218308--44218419 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
44218298 TAATACATGT
*
44218308 TAGGGTTCAGGTGCTTTTGAGTAACCCCGTTGAGAGGCATGTGATTATGTGATAAATGC
1 TAGGGTTCAGGTGCTTTTGAGTAACCCCGTTGAGAGCCATGTGATTATGTGATAAATGC
* * *
44218367 TAGGGTTCGGGTGCTTTTGAGTAGCCCCGTTGAGAGCCATGTGATTCTGTGAT
1 TAGGGTTCAGGTGCTTTTGAGTAACCCCGTTGAGAGCCATGTGATTATGTGAT
44218420 CTGTGGCACT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.33
Consensus pattern (59 bp):
TAGGGTTCAGGTGCTTTTGAGTAACCCCGTTGAGAGCCATGTGATTATGTGATAAATGC
Found at i:44224967 original size:22 final size:22
Alignment explanation
Indices: 44224942--44224983 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
44224932 CATAAAATTA
44224942 AAAAAGAA-AAATGAATCAATCC
1 AAAAAGAATAAA-GAATCAATCC
*
44224964 AAAAATAATAAAGAATCAAT
1 AAAAAGAATAAAGAATCAAT
44224984 TCATTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (22 bp):
AAAAAGAATAAAGAATCAATCC
Found at i:44235130 original size:42 final size:42
Alignment explanation
Indices: 44235071--44235154 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
44235061 AATGTCCTAC
44235071 TGATGATTAAGGTCATGTATTTGTTACGAACTCTCCACAGCT
1 TGATGATTAAGGTCATGTATTTGTTACGAACTCTCCACAGCT
* * *
44235113 TGATGATTGAGGTCATGTATTTGTTATGAATTCTCCACAGCT
1 TGATGATTAAGGTCATGTATTTGTTACGAACTCTCCACAGCT
44235155 CGTGTGAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (42 bp):
TGATGATTAAGGTCATGTATTTGTTACGAACTCTCCACAGCT
Found at i:44240599 original size:31 final size:31
Alignment explanation
Indices: 44240561--44240623 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
44240551 CCTAACCCAA
44240561 ACCCATTTTAGGCCCGCCAGTATTGGTTTTT
1 ACCCATTTTAGGCCCGCCAGTATTGGTTTTT
*
44240592 ACCCATTTTAGGCCCGCCCGTATTGGTTTTT
1 ACCCATTTTAGGCCCGCCAGTATTGGTTTTT
44240623 A
1 A
44240624 AATTTTTGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (31 bp):
ACCCATTTTAGGCCCGCCAGTATTGGTTTTT
Found at i:44241082 original size:60 final size:60
Alignment explanation
Indices: 44240952--44241082 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 60
44240942 TACAAAATTG
* * **
44240952 AATAGTTGGGTGACCATTTAGTAACTTTTCATAGTTAGGTGACCAAAAAAGAATTTTACT
1 AATAGTTGGGTAACCATTTAGTAACTTTTCATAATTAGGTGACCAAAAAAGAATAGTACT
** *
44241012 AATAACTGGGTAACCATTTTGTAACTTTTCATAATT-GTGTGACCAAAAAAGAAATAGT-CT
1 AATAGTTGGGTAACCATTTAGTAACTTTTCATAATTAG-GTGACCAAAAAAG-AATAGTACT
44241072 AATAGTTGGGT
1 AATAGTTGGGT
44241083 GACTATTAGT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 1 0.02
60 55 0.92
61 4 0.07
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (60 bp):
AATAGTTGGGTAACCATTTAGTAACTTTTCATAATTAGGTGACCAAAAAAGAATAGTACT
Found at i:44245373 original size:8 final size:8
Alignment explanation
Indices: 44245360--44245385 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
44245350 AAGTTTTTAT
44245360 TTAAATCA
1 TTAAATCA
44245368 TTAAATCA
1 TTAAATCA
44245376 TTAAATCA
1 TTAAATCA
44245384 TT
1 TT
44245386 CAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (8 bp):
TTAAATCA
Found at i:44253961 original size:21 final size:21
Alignment explanation
Indices: 44253935--44253975 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44253925 AGACGAGCAA
* *
44253935 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
44253956 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
44253976 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:44255914 original size:16 final size:16
Alignment explanation
Indices: 44255881--44255914 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44255871 GGAGATTGTT
* *
44255881 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
44255897 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
44255913 AA
1 AA
44255915 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:44256679 original size:26 final size:24
Alignment explanation
Indices: 44256638--44256685 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
44256628 ATTTTTAGCC
*
44256638 TTTATTTTTAAGTTTTTTGTTTCT
1 TTTATTTTTAAGTTTTTGGTTTCT
*
44256662 TTTATCTTTTCAATTTTTTGGTTT
1 TTTAT-TTTT-AAGTTTTTGGTTT
44256686 TGTTTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 4 0.20
26 11 0.55
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.73
Consensus pattern (24 bp):
TTTATTTTTAAGTTTTTGGTTTCT
Found at i:44257850 original size:31 final size:31
Alignment explanation
Indices: 44257812--44257873 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
44257802 ACAAAAGTGT
44257812 AAGAAAAATGAGGAATTTTTTACTCCAACAA
1 AAGAAAAATGAGGAATTTTTTACTCCAACAA
44257843 AAGAAAAATGAGGAATTTTTTACTCCAACAA
1 AAGAAAAATGAGGAATTTTTTACTCCAACAA
44257874 CCTAGGTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (31 bp):
AAGAAAAATGAGGAATTTTTTACTCCAACAA
Found at i:44258728 original size:11 final size:11
Alignment explanation
Indices: 44258709--44258742 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
44258699 TTGGGCCTAG
44258709 AACAAAAAATA
1 AACAAAAAATA
*
44258720 AACAGAAAAT-
1 AACAAAAAATA
44258730 AACAAAAAATA
1 AACAAAAAATA
44258741 AA
1 AA
44258743 TAGTCCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (11 bp):
AACAAAAAATA
Found at i:44259752 original size:4 final size:4
Alignment explanation
Indices: 44259743--44259845 Score: 56
Period size: 4 Copynumber: 26.5 Consensus size: 4
44259733 TTTATAAATC
* * * *
44259743 TATT TATT TATT TGTT AATT TA-T TATT TATT TA-T TCTT TGTT TATTT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TA-TT
* * * * *
44259790 TATT T-TT TATT GA-G TATG TATT TTTT TATCAT TA-T TA-T TATT TATG
1 TATT TATT TATT TATT TATT TATT TATT TAT--T TATT TATT TATT TATT
44259836 TATT TATT TA
1 TATT TATT TA
44259846 CAAATTGCTC
Statistics
Matches: 76, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
3 15 0.20
4 54 0.71
5 4 0.05
6 3 0.04
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:44259774 original size:27 final size:27
Alignment explanation
Indices: 44259743--44259800 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
44259733 TTTATAAATC
44259743 TATTTATTTATTTG-TTAATTTATTATT
1 TATTTA-TTATTTGTTTAATTTATTATT
* * *
44259770 TATTTATTCTTTGTTTATTTTATTTTT
1 TATTTATTATTTGTTTAATTTATTATT
44259797 TATT
1 TATT
44259801 GAGTATGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (27 bp):
TATTTATTATTTGTTTAATTTATTATT
Found at i:44267517 original size:81 final size:83
Alignment explanation
Indices: 44267368--44267527 Score: 191
Period size: 81 Copynumber: 2.0 Consensus size: 83
44267358 CATTGTGTGC
* ** * * **
44267368 AAATATTCTTTATTCTTTCCATTCATAATTACATTATACAGACAATTATTTTTAGACTCTTTTGT
1 AAATATTCTTTATTCTTTCCATTCATAATCACACCATACAAACAATTATTCTTAGACTCTTTCAT
*
44267433 TCTTTGGA-CTTTCCTTT
66 TCTTTCGATCTTTCCTTT
* * *
44267450 AAATATTCCTTTATTC-TT-CATTCATAATCATACCATACAAATAATTATTCTTAGATTCTTTCA
1 AAATATT-CTTTATTCTTTCCATTCATAATCACACCATACAAACAATTATTCTTAGACTCTTTCA
44267513 TTCTTTCGATCTTTC
65 TTCTTTCGATCTTTC
44267528 ATTCGCCTCC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
81 43 0.66
82 14 0.22
83 8 0.12
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.49
Consensus pattern (83 bp):
AAATATTCTTTATTCTTTCCATTCATAATCACACCATACAAACAATTATTCTTAGACTCTTTCAT
TCTTTCGATCTTTCCTTT
Found at i:44278213 original size:8 final size:8
Alignment explanation
Indices: 44278200--44278238 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
44278190 AATAAAAATG
44278200 TAATTTTA
1 TAATTTTA
44278208 TAATTTTA
1 TAATTTTA
*
44278216 -ATAGTTTA
1 TA-ATTTTA
44278224 TAATTTTA
1 TAATTTTA
44278232 TAATTTT
1 TAATTTT
44278239 TAAAGGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 1 0.04
8 25 0.93
9 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (8 bp):
TAATTTTA
Found at i:44283271 original size:25 final size:25
Alignment explanation
Indices: 44283237--44283289 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
44283227 ATCTGTTACT
44283237 TATTCATGATTGAGGTAAGCCACAC
1 TATTCATGATTGAGGTAAGCCACAC
44283262 TATTCATGATTGAGGTAAGCCACAC
1 TATTCATGATTGAGGTAAGCCACAC
44283287 TAT
1 TAT
44283290 GAACGTCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (25 bp):
TATTCATGATTGAGGTAAGCCACAC
Found at i:44285669 original size:6 final size:6
Alignment explanation
Indices: 44285653--44285697 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
44285643 TGATTTTCTC
* * *
44285653 AAAATG GAAATG AAAATG CAAACG AAAATG AAAATG AAAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG -AAAATG AA
44285698 TTCATTTAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.64, C:0.04, G:0.18, T:0.13
Consensus pattern (6 bp):
AAAATG
Found at i:44285725 original size:73 final size:75
Alignment explanation
Indices: 44285590--44285729 Score: 180
Period size: 73 Copynumber: 1.9 Consensus size: 75
44285580 GGTAGTCTCC
* ** *
44285590 AAAATGAAAATGAAAATGAAAATGGAGAAAAGTGAATCATTAAGAAATGAACGTGATTTTCTCAA
1 AAAATGAAAACGAAAATGAAAATGGAGAAAAGTGAATCATTAAGAAATGAACAAGATATTCTCAA
44285655 AATGGAAATG
66 AATGGAAATG
* *
44285665 AAAATGCAAACGAAAATGAAAAT-GA-AAAA-TGAATTCATTTAGAAATGAACAAAGA-ATTCTC
1 AAAATGAAAACGAAAATGAAAATGGAGAAAAGTGAA-TCATTAAGAAATGAAC-AAGATATTCTC
44285726 AAAA
64 AAAA
44285730 ATGATCGAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
72 4 0.07
73 28 0.49
74 4 0.07
75 21 0.37
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.21
Consensus pattern (75 bp):
AAAATGAAAACGAAAATGAAAATGGAGAAAAGTGAATCATTAAGAAATGAACAAGATATTCTCAA
AATGGAAATG
Found at i:44285848 original size:99 final size:99
Alignment explanation
Indices: 44285726--44285923 Score: 308
Period size: 99 Copynumber: 2.0 Consensus size: 99
44285716 AAGAATTCTC
44285726 AAAAATGATCGAAAGATTGAGTTTATGTTTTAGAGCTATTTTAAACCCCAAAAATGAAAATAAAC
1 AAAAATGATCGAAAGATTGAGTTTATGTTTTAGAGCTATTTTAAACCCCAAAAATGAAAATAAAC
* * *
44285791 TATATGGTCATAGTGAACAAGTTGA-ATGGTGAAA
66 CATAAGATCATAGTGAACAAGTT-ACATGGTGAAA
* * * * *
44285825 AAAAATGATCGGAAGATTGAGTTTATGTTTTTGAGCTATTTTAAAGCTCGAAAATGAAAATAAAC
1 AAAAATGATCGAAAGATTGAGTTTATGTTTTAGAGCTATTTTAAACCCCAAAAATGAAAATAAAC
44285890 CATAAGATCATAGTGAACAAGTTACATGGTGAAA
66 CATAAGATCATAGTGAACAAGTTACATGGTGAAA
44285924 TATTAAATAT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 1 0.01
99 89 0.99
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (99 bp):
AAAAATGATCGAAAGATTGAGTTTATGTTTTAGAGCTATTTTAAACCCCAAAAATGAAAATAAAC
CATAAGATCATAGTGAACAAGTTACATGGTGAAA
Found at i:44287368 original size:5 final size:5
Alignment explanation
Indices: 44287358--44287394 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
44287348 ATTTAAGTAA
*
44287358 ATATT ATATT ATATT ATATT ATATT ATATT GTATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
44287395 TATAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:44287490 original size:16 final size:17
Alignment explanation
Indices: 44287442--44287509 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
44287432 AAAAGATTAG
44287442 AAAA-AGAAAGAACAAGA
1 AAAAGAGAAAGAA-AAGA
* *
44287459 AAAAAACGAAACAGAAAGGA
1 AAAAGA-G-AA-AGAAAAGA
44287479 AAAAG-GAAAGAAAAGA
1 AAAAGAGAAAGAAAAGA
44287495 AAAAGAGAAAGAAAA
1 AAAAGAGAAAGAAAA
44287510 AGGAGAAAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
16 12 0.28
17 15 0.35
18 2 0.05
19 1 0.02
20 9 0.21
21 4 0.09
ACGTcount: A:0.75, C:0.04, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAGAGAAAGAAAAGA
Found at i:44287510 original size:13 final size:12
Alignment explanation
Indices: 44287485--44287518 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
44287475 AGGAAAAAGG
44287485 AAAGA-AAAGAA
1 AAAGAGAAAGAA
44287496 AAAGAGAAAGAA
1 AAAGAGAAAGAA
44287508 AAAGGAGAAAG
1 AAA-GAGAAAG
44287519 CGAGGGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 9 0.43
13 7 0.33
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAAGAGAAAGAA
Found at i:44295188 original size:39 final size:39
Alignment explanation
Indices: 44295145--44295227 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 39
44295135 AAAAGGGTTA
44295145 AGTTATAGGTTATTATTAAGGGGAAAATTAAGAAAAAAT
1 AGTTATAGGTTATTATTAAGGGGAAAATTAAGAAAAAAT
*
44295184 AGTTATGGGTTATTATTAAGGGGAAAATTAAGAAAAAAT
1 AGTTATAGGTTATTATTAAGGGGAAAATTAAGAAAAAAT
44295223 AGTTA
1 AGTTA
44295228 AGGCCCAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (39 bp):
AGTTATAGGTTATTATTAAGGGGAAAATTAAGAAAAAAT
Found at i:44308718 original size:803 final size:803
Alignment explanation
Indices: 44307174--44308778 Score: 3201
Period size: 803 Copynumber: 2.0 Consensus size: 803
44307164 TGGTGCTCTG
44307174 AAGTAAGGCGCAAATTGCGGTGGCTGGTGGTGGTGGTGGTGATGGAAGTAGAGGTCCGTGGTGTG
1 AAGTAAGGCGCAAATTGCGGTGGCTGGTGGTGGTGGTGGTGATGGAAGTAGAGGTCCGTGGTGTG
*
44307239 GATGGAGTTTGGGGAGCCAAGCTCAGATTCCTTGCGGTGGAAGTTACGGTGGCAGTTACAAGCCG
66 GACGGAGTTTGGGGAGCCAAGCTCAGATTCCTTGCGGTGGAAGTTACGGTGGCAGTTACAAGCCG
44307304 CGCATTTGAGAGCGTCGAGGGTGCCTTCAGTTCCAGCCGGCATGAACTCACCGCAACCGTCGAGA
131 CGCATTTGAGAGCGTCGAGGGTGCCTTCAGTTCCAGCCGGCATGAACTCACCGCAACCGTCGAGA
44307369 GCGTGACCGCCGATCCCCACCGCATGGTTCTTCAAACACTCCCTATACCTAGGCTTCCTCTGCTG
196 GCGTGACCGCCGATCCCCACCGCATGGTTCTTCAAACACTCCCTATACCTAGGCTTCCTCTGCTG
44307434 CTGCTGCTGCTGCTGACCCGTTGGAGTTACTGAACCAGGTTCAACACCTGACATTTTGAGTCTAG
261 CTGCTGCTGCTGCTGACCCGTTGGAGTTACTGAACCAGGTTCAACACCTGACATTTTGAGTCTAG
44307499 ACGAGTTTCCCAGCGAGTCATAACTCGGTGTCAAACCCATCTCTTCTTCCTGCTCTTCTTGATCC
326 ACGAGTTTCCCAGCGAGTCATAACTCGGTGTCAAACCCATCTCTTCTTCCTGCTCTTCTTGATCC
44307564 TCAAACTCCATTTCCCCTCCCTTCAACAGGAATTATGTAATTTTAATAAAAAAAATTCAACAGTT
391 TCAAACTCCATTTCCCCTCCCTTCAACAGGAATTATGTAATTTTAATAAAAAAAATTCAACAGTT
44307629 TTTTTTCCTAATTAATAGAGAAGAAGAAGACGAAGATAAGAGGAATAAGAGAGTGTGGCCATAAA
456 TTTTTTCCTAATTAATAGAGAAGAAGAAGACGAAGATAAGAGGAATAAGAGAGTGTGGCCATAAA
44307694 TTTTGTTTTTTGGGTAATTTCTTCCCTTTATATCTGCAAAAAGAAAGCTGTTTCTGTGTCTGTGT
521 TTTTGTTTTTTGGGTAATTTCTTCCCTTTATATCTGCAAAAAGAAAGCTGTTTCTGTGTCTGTGT
44307759 GTGTGTGTGTGTGTGTGTTTTGGTTTCAAAGGGGGGCGTTGAGACCGTCTTGATATAAGCCTTCC
586 GTGTGTGTGTGTGTGTGTTTTGGTTTCAAAGGGGGGCGTTGAGACCGTCTTGATATAAGCCTTCC
44307824 CCCTTCCTCTGAAATCAAATCACTTGATAGCTGCTTCTCTAATTGATTTTTACTGCGCTGTAAAA
651 CCCTTCCTCTGAAATCAAATCACTTGATAGCTGCTTCTCTAATTGATTTTTACTGCGCTGTAAAA
44307889 TATAATTTTAACCTTTTGTTTTTTTACCGTGAAGCGAACAAGAGTGTGGCTACAGTGATGATAGC
716 TATAATTTTAACCTTTTGTTTTTTTACCGTGAAGCGAACAAGAGTGTGGCTACAGTGATGATAGC
44307954 AGGGATTGGGTTTGGGGTTTGGA
781 AGGGATTGGGTTTGGGGTTTGGA
44307977 AAGTAAGGCGCAAATTGCGGTGGCTGGTGGTGGTGGTGGTGATGGAAGTAGAGGTCCGTGGTGTG
1 AAGTAAGGCGCAAATTGCGGTGGCTGGTGGTGGTGGTGGTGATGGAAGTAGAGGTCCGTGGTGTG
44308042 GACGGAGTTTGGGGAGCCAAGCTCAGATTCCTTGCGGTGGAAGTTACGGTGGCAGTTACAAGCCG
66 GACGGAGTTTGGGGAGCCAAGCTCAGATTCCTTGCGGTGGAAGTTACGGTGGCAGTTACAAGCCG
44308107 CGCATTTGAGAGCGTCGAGGGTGCCTTCAGTTCCAGCCGGCATGAACTCACCGCAACCGTCGAGA
131 CGCATTTGAGAGCGTCGAGGGTGCCTTCAGTTCCAGCCGGCATGAACTCACCGCAACCGTCGAGA
44308172 GCGTGACCGCCGATCCCCACCGCATGGTTCTTCAAACACTCCCTATACCTAGGCTTCCTCTGCTG
196 GCGTGACCGCCGATCCCCACCGCATGGTTCTTCAAACACTCCCTATACCTAGGCTTCCTCTGCTG
44308237 CTGCTGCTGCTGCTGACCCGTTGGAGTTACTGAACCAGGTTCAACACCTGACATTTTGAGTCTAG
261 CTGCTGCTGCTGCTGACCCGTTGGAGTTACTGAACCAGGTTCAACACCTGACATTTTGAGTCTAG
44308302 ACGAGTTTCCCAGCGAGTCATAACTCGGTGTCAAACCCATCTCTTCTTCCTGCTCTTCTTGATCC
326 ACGAGTTTCCCAGCGAGTCATAACTCGGTGTCAAACCCATCTCTTCTTCCTGCTCTTCTTGATCC
44308367 TCAAACTCCATTTCCCCTCCCTTCAACAGGAATTATGTAATTTTAATAAAAAAAATTCAACAGTT
391 TCAAACTCCATTTCCCCTCCCTTCAACAGGAATTATGTAATTTTAATAAAAAAAATTCAACAGTT
44308432 TTTTTTCCTAATTAATAGAGAAGAAGAAGACGAAGATAAGAGGAATAAGAGAGTGTGGCCATAAA
456 TTTTTTCCTAATTAATAGAGAAGAAGAAGACGAAGATAAGAGGAATAAGAGAGTGTGGCCATAAA
44308497 TTTTGTTTTTTGGGTAATTTCTTCCCTTTATATCTGCAAAAAGAAAGCTGTTTCTGTGTCTGTGT
521 TTTTGTTTTTTGGGTAATTTCTTCCCTTTATATCTGCAAAAAGAAAGCTGTTTCTGTGTCTGTGT
44308562 GTGTGTGTGTGTGTGTGTTTTGGTTTCAAAGGGGGGCGTTGAGACCGTCTTGATATAAGCCTTCC
586 GTGTGTGTGTGTGTGTGTTTTGGTTTCAAAGGGGGGCGTTGAGACCGTCTTGATATAAGCCTTCC
44308627 CCCTTCCTCTGAAATCAAATCACTTGATAGCTGCTTCTCTAATTGATTTTTACTGCGCTGTAAAA
651 CCCTTCCTCTGAAATCAAATCACTTGATAGCTGCTTCTCTAATTGATTTTTACTGCGCTGTAAAA
44308692 TATAATTTTAACCTTTTGTTTTTTTACCGTGAAGCGAACAAGAGTGTGGCTACAGTGATGATAGC
716 TATAATTTTAACCTTTTGTTTTTTTACCGTGAAGCGAACAAGAGTGTGGCTACAGTGATGATAGC
44308757 AGGGATTGGGTTTGGGGTTTGG
781 AGGGATTGGGTTTGGGGTTTGG
44308779 CCATTATTGG
Statistics
Matches: 801, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
803 801 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (803 bp):
AAGTAAGGCGCAAATTGCGGTGGCTGGTGGTGGTGGTGGTGATGGAAGTAGAGGTCCGTGGTGTG
GACGGAGTTTGGGGAGCCAAGCTCAGATTCCTTGCGGTGGAAGTTACGGTGGCAGTTACAAGCCG
CGCATTTGAGAGCGTCGAGGGTGCCTTCAGTTCCAGCCGGCATGAACTCACCGCAACCGTCGAGA
GCGTGACCGCCGATCCCCACCGCATGGTTCTTCAAACACTCCCTATACCTAGGCTTCCTCTGCTG
CTGCTGCTGCTGCTGACCCGTTGGAGTTACTGAACCAGGTTCAACACCTGACATTTTGAGTCTAG
ACGAGTTTCCCAGCGAGTCATAACTCGGTGTCAAACCCATCTCTTCTTCCTGCTCTTCTTGATCC
TCAAACTCCATTTCCCCTCCCTTCAACAGGAATTATGTAATTTTAATAAAAAAAATTCAACAGTT
TTTTTTCCTAATTAATAGAGAAGAAGAAGACGAAGATAAGAGGAATAAGAGAGTGTGGCCATAAA
TTTTGTTTTTTGGGTAATTTCTTCCCTTTATATCTGCAAAAAGAAAGCTGTTTCTGTGTCTGTGT
GTGTGTGTGTGTGTGTGTTTTGGTTTCAAAGGGGGGCGTTGAGACCGTCTTGATATAAGCCTTCC
CCCTTCCTCTGAAATCAAATCACTTGATAGCTGCTTCTCTAATTGATTTTTACTGCGCTGTAAAA
TATAATTTTAACCTTTTGTTTTTTTACCGTGAAGCGAACAAGAGTGTGGCTACAGTGATGATAGC
AGGGATTGGGTTTGGGGTTTGGA
Found at i:44310429 original size:38 final size:38
Alignment explanation
Indices: 44310345--44310444 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 38
44310335 ATAACCTAAA
* * *
44310345 AATCTGCAACAAGGCTAGATCTTGTTAAATCACTAGAG
1 AATCTGCAACAAGGCTAGATCTTATTAAATAACCAGAG
* * *
44310383 AATTTGCAACAAGGCTAGATCTTATTAAGTAACCCGAG
1 AATCTGCAACAAGGCTAGATCTTATTAAATAACCAGAG
* *
44310421 AGTCTGCAACAAATGCTAGATCTT
1 AATCTGCAAC-AAGGCTAGATCTT
44310445 TTTATAAACT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
38 40 0.77
39 12 0.23
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (38 bp):
AATCTGCAACAAGGCTAGATCTTATTAAATAACCAGAG
Found at i:44312166 original size:33 final size:33
Alignment explanation
Indices: 44312126--44312197 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
44312116 CGACTTTGAG
*
44312126 ATTATTTTAGAGAATAGTATGGCTCAAACACTT
1 ATTATTTTAGAGAAGAGTATGGCTCAAACACTT
44312159 ATTATTTTAGAGAAGAGTATGGCTCAAACACTT
1 ATTATTTTAGAGAAGAGTATGGCTCAAACACTT
44312192 ATTATT
1 ATTATT
44312198 GAATTGCTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (33 bp):
ATTATTTTAGAGAAGAGTATGGCTCAAACACTT
Found at i:44320475 original size:12 final size:12
Alignment explanation
Indices: 44320458--44320482 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44320448 CAGAGGCTAT
44320458 TAACAATATTTA
1 TAACAATATTTA
44320470 TAACAATATTTA
1 TAACAATATTTA
44320482 T
1 T
44320483 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:44322469 original size:12 final size:12
Alignment explanation
Indices: 44322452--44322476 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44322442 CAGAGGCTAT
44322452 TAACAATATTTA
1 TAACAATATTTA
44322464 TAACAATATTTA
1 TAACAATATTTA
44322476 T
1 T
44322477 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:44323930 original size:66 final size:66
Alignment explanation
Indices: 44323822--44323949 Score: 195
Period size: 66 Copynumber: 1.9 Consensus size: 66
44323812 TACCAATTAT
* * *
44323822 ATGAAGGAATGAGCTCTAGTGTATAAAGAGGACCTCACTGTTTAAGAAGTAA-CAGTAGAAACTT
1 ATGAAAGAATGAGCTCCAGTGTATAAAGAGGACCTCACTGTTTAAAAAGTAACCA-TAGAAACTT
44323886 AA
65 AA
* *
44323888 ATGAAAGAATGAGCTCCGGTGTATAAAGAGGACCTCATTGTTTAAAAAGTAACCATAGAAAC
1 ATGAAAGAATGAGCTCCAGTGTATAAAGAGGACCTCACTGTTTAAAAAGTAACCATAGAAAC
44323950 GATGGAACCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 54 0.96
67 2 0.04
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.23
Consensus pattern (66 bp):
ATGAAAGAATGAGCTCCAGTGTATAAAGAGGACCTCACTGTTTAAAAAGTAACCATAGAAACTTA
A
Found at i:44325473 original size:17 final size:17
Alignment explanation
Indices: 44325451--44325487 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
44325441 GAATTTACTA
* *
44325451 AAATTTTATTTTTTTTT
1 AAATTTTATGTGTTTTT
44325468 AAATTTTATGTGTTTTT
1 AAATTTTATGTGTTTTT
44325485 AAA
1 AAA
44325488 AAAAAATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (17 bp):
AAATTTTATGTGTTTTT
Found at i:44325567 original size:20 final size:20
Alignment explanation
Indices: 44325527--44325567 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
44325517 TTTACTAAAA
* *
44325527 TAATTAGATTTTTATTTTGT
1 TAATTAGATTTTAATTGTGT
44325547 TAATTAGATTTTAATTGTGT
1 TAATTAGATTTTAATTGTGT
44325567 T
1 T
44325568 GAAAAGGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (20 bp):
TAATTAGATTTTAATTGTGT
Found at i:44326479 original size:15 final size:15
Alignment explanation
Indices: 44326455--44326493 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
44326445 TAAATTCTAC
* *
44326455 ACTTAATTTTTGAGT
1 ACTTATTTTTTCAGT
44326470 ACTTATTTTTTCAGT
1 ACTTATTTTTTCAGT
*
44326485 ACTAATTTT
1 ACTTATTTT
44326494 CTTTTTAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (15 bp):
ACTTATTTTTTCAGT
Found at i:44338423 original size:33 final size:33
Alignment explanation
Indices: 44338386--44338482 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
44338376 GTTTGAGTGA
*
44338386 GAGTGTTTGGTTGCTAGACAGGAGCTGGAATAG
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATAG
*
44338419 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATTG
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATAG
* * *
44338452 AAGTGTTTGGTTGTTGGACAAGAGCTGGAAT
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAAT
44338483 GTCAAGAAGA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.23, C:0.08, G:0.39, T:0.30
Consensus pattern (33 bp):
GAGTGTTTGGTTGCTGGACAGGAGCTGGAATAG
Found at i:44350053 original size:3 final size:3
Alignment explanation
Indices: 44350045--44350084 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
44350035 AGTTACTATT
*
44350045 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44350085 GGGAGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44351739 original size:50 final size:50
Alignment explanation
Indices: 44351680--44351778 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 50
44351670 CAGGACTTAG
** *
44351680 TGTTATAGTTTC-ATCTTGCTCCATTGTAACTTTAAGG-AGATAAGATTTGT
1 TGTTATAGTTTCAATC-TAATCCACTGTAAC-TTAAGGAAGATAAGATTTGT
* *
44351730 TGTTGTAGTTTCAATCTAATCCACTGTAACTTCAGGAAGATAAGATTTG
1 TGTTATAGTTTCAATCTAATCCACTGTAACTTAAGGAAGATAAGATTTG
44351779 GGACTATAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
49 5 0.12
50 34 0.81
51 3 0.07
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (50 bp):
TGTTATAGTTTCAATCTAATCCACTGTAACTTAAGGAAGATAAGATTTGT
Found at i:44351984 original size:93 final size:94
Alignment explanation
Indices: 44351844--44352101 Score: 274
Period size: 93 Copynumber: 2.8 Consensus size: 94
44351834 TCATCTTATT
* * * *
44351844 CCACTGCAACTTCAAGGAG-ATA-AGACTTGTAACTTCAATCTGCTCCACTGCAACTTGAGGGAG
1 CCACTACAACTTCAAGG-GTATAGA-ATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAG
* *
44351907 ATAAGATTCGCCACT-ATAGTTTCAAT-CAAC
64 ATAAGATTCACCA-TGATAGATTCAATCCAAC
* * * * * * ** *
44351937 CCATTGCAACTTCAAGGTTATAGAATTTGTAGC-TCTATTTTGTTCCACTATAACTTCAGAGAGA
1 CCACTACAACTTCAAGGGTATAGAATTTGTAGCTTC-AATCTGCTCCACTGCAACTTCAGGGAGA
* *
44352001 TAAGATTCACTATGATAGATTCAATCCGAC
65 TAAGATTCACCATGATAGATTCAATCCAAC
* *
44352031 CCACTACAACTTCAGGGGTATAGAATTTTTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGAT
1 CCACTACAACTTCAAGGGTATAGAATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGAT
44352096 AAGATT
66 AAGATT
44352102 TGCTATGGTG
Statistics
Matches: 133, Mismatches: 26, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
92 3 0.02
93 67 0.50
94 61 0.46
95 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (94 bp):
CCACTACAACTTCAAGGGTATAGAATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGAT
AAGATTCACCATGATAGATTCAATCCAAC
Found at i:44352078 original size:94 final size:94
Alignment explanation
Indices: 44351870--44352145 Score: 290
Period size: 94 Copynumber: 2.9 Consensus size: 94
44351860 GAGATAAGAC
* * * *
44351870 TTGTAACTTCAATCTGCTCCACTGCAACTTGAGGGAGATAAGATTCGCCACT-ATAGTTTCAAT-
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTA-TGATAGATTCAATC
* * * *
44351933 CAACCCATTGCAACTTCAAGGTTATAGAAT
65 CGACCCATTACAACTTCAGGGGTATAGAAT
* * * ** * *
44351963 TTGTAGC-TCTATTTTGTTCCACTATAACTTCAGAGAGATAAGATTCACTATGATAGATTCAATC
1 TTGTAGCTTC-AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGATAGATTCAATC
*
44352027 CGACCCACTACAACTTCAGGGGTATAGAAT
65 CGACCCATTACAACTTCAGGGGTATAGAAT
* * *
44352057 TTTTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATGGT-GATTTCAATC
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGATAGA-TTCAATC
* * * *
44352121 TGAACCATTACAACTTTAGAGGTAT
65 CGACCCATTACAACTTCAGGGGTAT
44352146 GAGATTTATG
Statistics
Matches: 147, Mismatches: 31, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
92 3 0.02
93 49 0.33
94 93 0.63
95 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (94 bp):
TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGATAGATTCAATCC
GACCCATTACAACTTCAGGGGTATAGAAT
Found at i:44366530 original size:18 final size:19
Alignment explanation
Indices: 44366504--44366548 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
44366494 CGATGCTATG
*
44366504 AAAACTTTC-AATATGATT
1 AAAATTTTCTAATATGATT
*
44366522 AAAATTTTCTTATATGATT
1 AAAATTTTCTAATATGATT
44366541 AAAATTTT
1 AAAATTTT
44366549 TTATTTGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (19 bp):
AAAATTTTCTAATATGATT
Found at i:44366538 original size:19 final size:18
Alignment explanation
Indices: 44366514--44366552 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
44366504 AAAACTTTCA
44366514 ATATGATTAAAATTTTCTT
1 ATATGATTAAAATTTT-TT
44366533 ATATGATTAAAATTTTTT
1 ATATGATTAAAATTTTTT
44366551 AT
1 AT
44366553 TTGCAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (18 bp):
ATATGATTAAAATTTTTT
Found at i:44371359 original size:73 final size:73
Alignment explanation
Indices: 44371240--44371385 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
44371230 TGTCCACGAG
44371240 ACATCTCAACAAAGAAATAGCAAATATGGTTTGGATAATAATAATTCTATCGATTAGAAGAAACA
1 ACATCTCAACAAAGAAATAGCAAATATGGTTTGGATAATAATAATTCTATCGATTAGAAGAAACA
44371305 AGAATATA
66 AGAATATA
44371313 ACATCTCAACAAAGAAATAGCAAATATGGTTTGGATAATAATAATTCTATCGATTAGAAGAAACA
1 ACATCTCAACAAAGAAATAGCAAATATGGTTTGGATAATAATAATTCTATCGATTAGAAGAAACA
44371378 AGAATATA
66 AGAATATA
44371386 CTTTCAGTTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (73 bp):
ACATCTCAACAAAGAAATAGCAAATATGGTTTGGATAATAATAATTCTATCGATTAGAAGAAACA
AGAATATA
Found at i:44373403 original size:17 final size:17
Alignment explanation
Indices: 44373381--44373415 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
44373371 TTTATATGTC
44373381 AATGAAAGTTGATTTTT
1 AATGAAAGTTGATTTTT
44373398 AATGAAAGTTGATTTTT
1 AATGAAAGTTGATTTTT
44373415 A
1 A
44373416 GAGGTGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (17 bp):
AATGAAAGTTGATTTTT
Found at i:44374729 original size:158 final size:158
Alignment explanation
Indices: 44374441--44374756 Score: 605
Period size: 158 Copynumber: 2.0 Consensus size: 158
44374431 CTTTACTAAT
44374441 TTATAATTTTAAAAATTTTAAAAGATCAAAATGAAAAATTGAGTCGGGACCCCTGCCAATCCCCT
1 TTATAATTTTAAAAATTTTAAAAGATCAAAATGAAAAATTGAGTCGGGACCCCTGCCAATCCCCT
44374506 TAGATTCGCCCCTGTTGATGCCTCAAAATTTGAAGACAAACATGCTATCGAGGTTGGCGGTGGTT
66 TAGATTCGCCCCTGTTGATGCCTCAAAATTTGAAGACAAACATGCTATCGAGGTTGGCGGTGGTT
44374571 ATTCGCGACAATCATGGTCACCTAGTAA
131 ATTCGCGACAATCATGGTCACCTAGTAA
*
44374599 TTATAATTTTAAAAATTTTAAAAGATCAAAATGAAAAATTGAGTCGGGACCCCTGCCAATCTCCT
1 TTATAATTTTAAAAATTTTAAAAGATCAAAATGAAAAATTGAGTCGGGACCCCTGCCAATCCCCT
* *
44374664 TAGATTCGCCCTTGTTGATGCCTCAAATTTTGAAGACAAACATGCTATCGAGGTTGGCGGTGGTT
66 TAGATTCGCCCCTGTTGATGCCTCAAAATTTGAAGACAAACATGCTATCGAGGTTGGCGGTGGTT
44374729 ATTCGCGACAATCATGGTCACCTAGTAA
131 ATTCGCGACAATCATGGTCACCTAGTAA
44374757 AAGGCCTTAC
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
158 155 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (158 bp):
TTATAATTTTAAAAATTTTAAAAGATCAAAATGAAAAATTGAGTCGGGACCCCTGCCAATCCCCT
TAGATTCGCCCCTGTTGATGCCTCAAAATTTGAAGACAAACATGCTATCGAGGTTGGCGGTGGTT
ATTCGCGACAATCATGGTCACCTAGTAA
Found at i:44378757 original size:40 final size:40
Alignment explanation
Indices: 44378683--44378904 Score: 394
Period size: 40 Copynumber: 5.6 Consensus size: 40
44378673 AACCCAAGTA
* *
44378683 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
44378722 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
44378762 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
44378802 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
44378842 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
44378882 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
44378905 CATTCGAATA
Statistics
Matches: 177, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
39 12 0.07
40 164 0.93
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:44388120 original size:40 final size:40
Alignment explanation
Indices: 44388050--44388267 Score: 350
Period size: 40 Copynumber: 5.5 Consensus size: 40
44388040 CAAGTACCTC
* *
44388050 CGGGATTTAG-CCGGATATAG-CGACTCGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTT
* * * *
44388089 CGAGTCTTAGCCCGGATATAGTCAATAGCACAAAAGCCTT
1 CGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTT
*
44388129 CGGGACTTAGCCCGAATATAGTCACTAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTT
44388169 CGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTT
44388209 CGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTT
44388249 CGGGACTTAGCCCGGATAT
1 CGGGACTTAGCCCGGATAT
44388268 CATTCGAATA
Statistics
Matches: 165, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
39 7 0.04
40 157 0.95
41 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (40 bp):
CGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTT
Found at i:44390134 original size:8 final size:9
Alignment explanation
Indices: 44390114--44390142 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
44390104 CTTTAACATA
44390114 AAACATAAC
1 AAACATAAC
44390123 AAACAT-AC
1 AAACATAAC
44390131 AAACATAAC
1 AAACATAAC
44390140 AAA
1 AAA
44390143 GATTACACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.69, C:0.21, G:0.00, T:0.10
Consensus pattern (9 bp):
AAACATAAC
Found at i:44390136 original size:17 final size:16
Alignment explanation
Indices: 44390108--44390142 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
44390098 AATATTCTTT
44390108 AACATAAAACATAACA
1 AACATAAAACATAACA
44390124 AACATACAAACATAACA
1 AACATA-AAACATAACA
44390141 AA
1 AA
44390143 GATTACACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.69, C:0.20, G:0.00, T:0.11
Consensus pattern (16 bp):
AACATAAAACATAACA
Found at i:44394140 original size:12 final size:12
Alignment explanation
Indices: 44394125--44394149 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44394115 TCATCCTCTC
44394125 CATCAGATTCAT
1 CATCAGATTCAT
44394137 CATCAGATTCAT
1 CATCAGATTCAT
44394149 C
1 C
44394150 CCTCGATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (12 bp):
CATCAGATTCAT
Found at i:44399131 original size:21 final size:21
Alignment explanation
Indices: 44399105--44399146 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
44399095 ACTTCAAGTG
44399105 GATATGGCAAACCAAATCATT
1 GATATGGCAAACCAAATCATT
44399126 GATATGGCAAACCAAATCATT
1 GATATGGCAAACCAAATCATT
44399147 TAAACATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (21 bp):
GATATGGCAAACCAAATCATT
Found at i:44399272 original size:15 final size:15
Alignment explanation
Indices: 44399247--44399283 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
44399237 ATCTATGTGC
*
44399247 AAATTAATTATTTAA
1 AAATAAATTATTTAA
*
44399262 AAGTAAATTATTTAA
1 AAATAAATTATTTAA
44399277 AAATAAA
1 AAATAAA
44399284 AAAACTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AAATAAATTATTTAA
Found at i:44399571 original size:13 final size:13
Alignment explanation
Indices: 44399523--44399571 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
44399513 TTTTTCTCCT
44399523 TTTTATTTATATAA
1 TTTTA-TTATATAA
* *
44399537 TTTTTTTATAAATA
1 TTTTATTATATA-A
44399551 TATTTATTATATAA
1 T-TTTATTATATAA
44399565 TTTTATT
1 TTTTATT
44399572 CTTCAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 12 0.41
14 8 0.28
15 9 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTATTATATAA
Found at i:44403979 original size:12 final size:11
Alignment explanation
Indices: 44403960--44404071 Score: 53
Period size: 11 Copynumber: 10.4 Consensus size: 11
44403950 ATTGTCATTA
44403960 TTATTATTTAT
1 TTATTATTTAT
44403971 TTATCTATTTAT
1 TTAT-TATTTAT
***
44403983 TTATTACCCAT
1 TTATTATTTAT
44403994 TT-TGTATTTAT
1 TTAT-TATTTAT
44404005 ATATATTATTCTAAT
1 -T-TATTATT-T-AT
*
44404020 TT-CTA-TTA-
1 TTATTATTTAT
44404028 TTATTA-TTA-
1 TTATTATTTAT
44404037 TTATTA-TTA-
1 TTATTATTTAT
44404046 TTATTA-TTATT
1 TTATTATTTA-T
*
44404057 TTATTATTTGT
1 TTATTATTTAT
44404068 TTAT
1 TTAT
44404072 ACATTTTATT
Statistics
Matches: 81, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
8 2 0.02
9 24 0.30
10 2 0.02
11 26 0.32
12 16 0.20
13 6 0.07
14 3 0.04
15 2 0.02
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (11 bp):
TTATTATTTAT
Found at i:44404029 original size:3 final size:3
Alignment explanation
Indices: 44404023--44404064 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
44404013 TTCTAATTTC
44404023 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
44404065 TGTTTATACA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:44404071 original size:11 final size:11
Alignment explanation
Indices: 44404018--44404064 Score: 67
Period size: 12 Copynumber: 4.0 Consensus size: 11
44404008 TATTATTCTA
44404018 ATTTCTATTATT
1 ATTT-TATTATT
44404030 ATTATTATTATT
1 ATT-TTATTATT
44404042 ATTATTATTATT
1 ATT-TTATTATT
44404054 ATTTTATTATT
1 ATTTTATTATT
44404065 TGTTTATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.24
12 25 0.74
13 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:44405887 original size:31 final size:31
Alignment explanation
Indices: 44405852--44405918 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
44405842 CTTCCTGCAT
* * *
44405852 TAAAATCCAACCAAATACAACAAATATAGTA
1 TAAAATCCAACAAAAAACAACAAATATAGCA
* * *
44405883 TAAAATGCAGCAAAAAACAACAAATTTAGCA
1 TAAAATCCAACAAAAAACAACAAATATAGCA
44405914 TAAAA
1 TAAAA
44405919 AATACAACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.60, C:0.16, G:0.06, T:0.18
Consensus pattern (31 bp):
TAAAATCCAACAAAAAACAACAAATATAGCA
Found at i:44406190 original size:21 final size:21
Alignment explanation
Indices: 44406166--44406262 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
44406156 TCTGCTGCCA
44406166 TCGCTGCTGCCTCTGCCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
* *
44406187 TCGCT-CGTGCCTTTGCATCCC
1 TCGCTGC-TGCCTCTGCCTCCC
* ** *
44406208 TTGCTGCTATCGCTGCCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
* *
44406229 TCGCTACTGCCGCTGCCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
*
44406250 TCTCTGCTGCCTC
1 TCGCTGCTGCCTC
44406263 GGCTCTAAGT
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 1 0.02
21 57 0.97
22 1 0.02
ACGTcount: A:0.03, C:0.47, G:0.19, T:0.31
Consensus pattern (21 bp):
TCGCTGCTGCCTCTGCCTCCC
Found at i:44406702 original size:13 final size:14
Alignment explanation
Indices: 44406677--44406705 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44406667 TGATGAATTG
44406677 AATTAAACAATTAT
1 AATTAAACAATTAT
44406691 AATTAAAC-ATTAT
1 AATTAAACAATTAT
44406704 AA
1 AA
44406706 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:44406889 original size:18 final size:18
Alignment explanation
Indices: 44406857--44406894 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
44406847 TACAATATAG
44406857 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
44406876 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
44406893 TA
1 TA
44406895 TTTGAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:44410039 original size:12 final size:12
Alignment explanation
Indices: 44410024--44410048 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44410014 TCATCCTCTC
44410024 CATCAGATTCAT
1 CATCAGATTCAT
44410036 CATCAGATTCAT
1 CATCAGATTCAT
44410048 C
1 C
44410049 CCTCGATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (12 bp):
CATCAGATTCAT
Found at i:44411924 original size:9 final size:9
Alignment explanation
Indices: 44411910--44412206 Score: 277
Period size: 9 Copynumber: 33.8 Consensus size: 9
44411900 TATTTAAGTA
*
44411910 TTATGTAAG
1 TTATATAAG
*
44411919 TTATGTAAG
1 TTATATAAG
*
44411928 TTATGATATG
1 TTAT-ATAAG
* * *
44411938 ATACAT-AT
1 TTATATAAG
*
44411946 TTATGTAAG
1 TTATATAAG
*
44411955 TTATAT-AT
1 TTATATAAG
*
44411963 TTATCTAAG
1 TTATATAAG
44411972 TTATATAAG
1 TTATATAAG
*
44411981 TTATGTAAG
1 TTATATAAG
*
44411990 TTATGTAAG
1 TTATATAAG
*
44411999 TTATAT-AT
1 TTATATAAG
*
44412007 TTATCTAAG
1 TTATATAAG
44412016 TTATATAAG
1 TTATATAAG
*
44412025 TTATGTAAG
1 TTATATAAG
*
44412034 TTATGTAAG
1 TTATATAAG
*
44412043 TTATAT-AT
1 TTATATAAG
*
44412051 TTATCTAA-
1 TTATATAAG
44412059 TTATATAAG
1 TTATATAAG
*
44412068 TTATCTAAG
1 TTATATAAG
*
44412077 TTATAT-AT
1 TTATATAAG
*
44412085 TTATCTAAG
1 TTATATAAG
*
44412094 TTATCTAAG
1 TTATATAAG
*
44412103 TTATAT-AT
1 TTATATAAG
*
44412111 TTATCTAAG
1 TTATATAAG
44412120 TTATATAAG
1 TTATATAAG
*
44412129 TTATGTAAG
1 TTATATAAG
*
44412138 TTATGTAAG
1 TTATATAAG
*
44412147 TTATAT-AT
1 TTATATAAG
*
44412155 TTATCTAAG
1 TTATATAAG
44412164 TTATATAAG
1 TTATATAAG
44412173 TTATATAAG
1 TTATATAAG
*
44412182 TTATGTAAG
1 TTATATAAG
44412191 TTATATAAG
1 TTATATAAG
44412200 TTATATA
1 TTATATA
44412207 TTTATCTGTT
Statistics
Matches: 235, Mismatches: 44, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
8 46 0.20
9 184 0.78
10 5 0.02
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48
Consensus pattern (9 bp):
TTATATAAG
Found at i:44411994 original size:44 final size:45
Alignment explanation
Indices: 44411946--44412203 Score: 332
Period size: 44 Copynumber: 5.9 Consensus size: 45
44411936 TGATACATAT
* * *
44411946 TTATGTAAGTTATAT-ATTTATCTAAGTTATATAAGTTATGTAAG
1 TTATATAAGTTATATAAGTTATCTAAGTTATATAAGTTATCTAAG
* * *
44411990 TTATGTAAGTTATAT-ATTTATCTAAGTTATATAAGTTATGTAAG
1 TTATATAAGTTATATAAGTTATCTAAGTTATATAAGTTATCTAAG
* *
44412034 TTATGTAAGTTATAT-ATTTATCTAA-TTATATAAGTTATCTAAG
1 TTATATAAGTTATATAAGTTATCTAAGTTATATAAGTTATCTAAG
* * *
44412077 TTATAT-ATTTATCTAAGTTATCTAAGTTATAT-ATTTATCTAAG
1 TTATATAAGTTATATAAGTTATCTAAGTTATATAAGTTATCTAAG
* * *
44412120 TTATATAAGTTATGTAAGTTATGTAAGTTATAT-ATTTATCTAAG
1 TTATATAAGTTATATAAGTTATCTAAGTTATATAAGTTATCTAAG
*
44412164 TTATATAAGTTATATAAGTTATGTAAGTTATATAAGTTAT
1 TTATATAAGTTATATAAGTTATCTAAGTTATATAAGTTAT
44412204 ATATTTATCT
Statistics
Matches: 199, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
42 6 0.03
43 47 0.24
44 141 0.71
45 5 0.03
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48
Consensus pattern (45 bp):
TTATATAAGTTATATAAGTTATCTAAGTTATATAAGTTATCTAAG
Found at i:44412277 original size:7 final size:7
Alignment explanation
Indices: 44412265--44412304 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
44412255 ACGTATAAAC
44412265 GCAAAAA
1 GCAAAAA
44412272 GCAAAAA
1 GCAAAAA
44412279 GCAAAAA
1 GCAAAAA
44412286 GCAAAAA
1 GCAAAAA
44412293 GCAAAAA
1 GCAAAAA
44412300 GCAAA
1 GCAAA
44412305 TCTATAAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.70, C:0.15, G:0.15, T:0.00
Consensus pattern (7 bp):
GCAAAAA
Found at i:44414132 original size:19 final size:19
Alignment explanation
Indices: 44414108--44414145 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
44414098 GGTCGTCCAC
44414108 TCGGAGTCTTCAACGGCAG
1 TCGGAGTCTTCAACGGCAG
44414127 TCGGAGTCTTCAACGGCAG
1 TCGGAGTCTTCAACGGCAG
44414146 AAGGATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (19 bp):
TCGGAGTCTTCAACGGCAG
Found at i:44414210 original size:19 final size:20
Alignment explanation
Indices: 44414168--44414214 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
44414158 ATTTTGATTC
* *
44414168 GGGGAAATATTTAGGGACTA
1 GGGGAAATAGTTAAGGACTA
*
44414188 GGGGAAA-AGTTAAGGACTT
1 GGGGAAATAGTTAAGGACTA
44414207 GGGGAAAT
1 GGGGAAAT
44414215 TTGGGTGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.36, C:0.04, G:0.38, T:0.21
Consensus pattern (20 bp):
GGGGAAATAGTTAAGGACTA
Found at i:44415489 original size:92 final size:92
Alignment explanation
Indices: 44415322--44415490 Score: 268
Period size: 92 Copynumber: 1.8 Consensus size: 92
44415312 GGTTTATAGG
*
44415322 TCATGGGTTATGATTTAGGGGTTAGGCTTTATATTTTAGGGTTTAAAGCAATTTAAGGTTTTAGG
1 TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAAGCAATTTAAGGTTTTAGG
*
44415387 ATATCGCTTTAGAGTTTAGGGTTTAGA
66 ATAGCGCTTTAGAGTTTAGGGTTTAGA
* * * *
44415414 TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAGGTAGTTTAAGGTTTTGGG
1 TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAAGCAATTTAAGGTTTTAGG
44415479 ATTAGC-CTTTAG
66 A-TAGCGCTTTAG
44415491 GGGCAAAATT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 67 0.96
93 3 0.04
ACGTcount: A:0.23, C:0.06, G:0.28, T:0.43
Consensus pattern (92 bp):
TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAAGCAATTTAAGGTTTTAGG
ATAGCGCTTTAGAGTTTAGGGTTTAGA
Found at i:44416065 original size:80 final size:81
Alignment explanation
Indices: 44415958--44416155 Score: 210
Period size: 80 Copynumber: 2.4 Consensus size: 81
44415948 ATAATAAATA
* * *
44415958 TTAGCGGCGCTTTT-ACAAAAACGCCACTATAGCTCTA-CCTTTTGTGGC-GTTTGGAAAT-AAA
1 TTAGCGGCG-TTTTGACAAAAATGCCACTATTGCTC-AGCCTTTTGCGGCAGTTTGG--ATGAAA
*
44416019 GCGCCACTA-TATCTTAGTTT
62 ACGCCACTATTA-CTTAGTTT
* * ** *
44416039 TTTGCGGCGTTTTGA-AAAAATGCCACTATTTCTCAGTTTTTTGCGGCATTTTGGATGAAAACGC
1 TTAGCGGCGTTTTGACAAAAATGCCACTATTGCTCAGCCTTTTGCGGCAGTTTGGATGAAAACGC
44416103 CACTATTACTTAGTTT
66 CACTATTACTTAGTTT
*
44416119 TTAGCGGCGTTTTGGATAAAAATGCCACTATTGCTCA
1 TTAGCGGCGTTTT-GACAAAAATGCCACTATTGCTCA
44416156 ATTTTTAGCG
Statistics
Matches: 99, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
79 3 0.03
80 59 0.60
81 18 0.18
82 19 0.19
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (81 bp):
TTAGCGGCGTTTTGACAAAAATGCCACTATTGCTCAGCCTTTTGCGGCAGTTTGGATGAAAACGC
CACTATTACTTAGTTT
Found at i:44416077 original size:39 final size:40
Alignment explanation
Indices: 44415997--44416173 Score: 178
Period size: 41 Copynumber: 4.4 Consensus size: 40
44415987 TAGCTCTACC
* * * *
44415997 TTTTGTGGCGTTTGGA-AATAAAGCGCCACTATATCTTAGTT
1 TTTTGCGGCGTTTTGATAA-AAA-CGCCACTATTTCTCAGTT
*
44416038 TTTTGCGGCGTTTTGA-AAAAATGCCACTATTTCTCAGTT
1 TTTTGCGGCGTTTTGATAAAAACGCCACTATTTCTCAGTT
* * * *
44416077 TTTTGCGGCATTTTGGATGAAAACGCCACTATTACTTAGTT
1 TTTTGCGGCGTTTT-GATAAAAACGCCACTATTTCTCAGTT
* * * *
44416118 TTTAGCGGCGTTTTGGATAAAAATGCCACTATTGCTCAATT
1 TTTTGCGGCGTTTT-GATAAAAACGCCACTATTTCTCAGTT
*
44416159 TTTAGCGGCGTTTTG
1 TTTTGCGGCGTTTTG
44416174 TTTCAAACGC
Statistics
Matches: 117, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
39 28 0.24
40 6 0.05
41 83 0.71
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (40 bp):
TTTTGCGGCGTTTTGATAAAAACGCCACTATTTCTCAGTT
Found at i:44416172 original size:41 final size:41
Alignment explanation
Indices: 44416021--44416173 Score: 186
Period size: 41 Copynumber: 3.8 Consensus size: 41
44416011 GAAATAAAGC
* *
44416021 GCCACTA-TATCTTAGTTTTTTGCGGCGTTTT-GA-AAAAAT
1 GCCACTATTA-CTCAGTTTTTAGCGGCGTTTTGGATAAAAAT
* * * * *
44416060 GCCACTATTTCTCAGTTTTTTGCGGCATTTTGGATGAAAAC
1 GCCACTATTACTCAGTTTTTAGCGGCGTTTTGGATAAAAAT
*
44416101 GCCACTATTACTTAGTTTTTAGCGGCGTTTTGGATAAAAAT
1 GCCACTATTACTCAGTTTTTAGCGGCGTTTTGGATAAAAAT
* *
44416142 GCCACTATTGCTCAATTTTTAGCGGCGTTTTG
1 GCCACTATTACTCAGTTTTTAGCGGCGTTTTG
44416174 TTTCAAACGC
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
39 26 0.27
40 3 0.03
41 68 0.70
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.40
Consensus pattern (41 bp):
GCCACTATTACTCAGTTTTTAGCGGCGTTTTGGATAAAAAT
Found at i:44416173 original size:82 final size:80
Alignment explanation
Indices: 44416020--44416173 Score: 229
Period size: 82 Copynumber: 1.9 Consensus size: 80
44416010 GGAAATAAAG
* * * *
44416020 CGCCACTATATCTTAGTTTTTTGCGGCGTTTTGAAAAAATGCCACTATTTCTCAGTTTTTTGCGG
1 CGCCACTATATCTTAGTTTTTAGCGGCGTTTTGAAAAAATGCCACTATTGCTCAATTTTTAGCGG
44416085 CATTTTGGATGAAAA
66 CATTTTGGATGAAAA
44416100 CGCCACTAT-TACTTAGTTTTTAGCGGCGTTTTGGATAAAAATGCCACTATTGCTCAATTTTTAG
1 CGCCACTATAT-CTTAGTTTTTAGCGGCGTTTT-GA-AAAAATGCCACTATTGCTCAATTTTTAG
*
44416164 CGGCGTTTTG
63 CGGCATTTTG
44416174 TTTCAAACGC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
79 1 0.02
80 29 0.44
81 2 0.03
82 34 0.52
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (80 bp):
CGCCACTATATCTTAGTTTTTAGCGGCGTTTTGAAAAAATGCCACTATTGCTCAATTTTTAGCGG
CATTTTGGATGAAAA
Found at i:44431087 original size:21 final size:23
Alignment explanation
Indices: 44431045--44431089 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
44431035 TTAGATAATA
*
44431045 TGTTTTGATATAACAAATTAAAG
1 TGTTTTGATATAACAAAGTAAAG
*
44431068 TGTTTTTATAT-A-AAAGTAAAG
1 TGTTTTGATATAACAAAGTAAAG
44431089 T
1 T
44431090 TCAGCAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 1 0.05
23 10 0.50
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.42
Consensus pattern (23 bp):
TGTTTTGATATAACAAAGTAAAG
Found at i:44433360 original size:40 final size:40
Alignment explanation
Indices: 44433262--44433381 Score: 179
Period size: 40 Copynumber: 3.0 Consensus size: 40
44433252 TCCTCGTTCA
* * * *
44433262 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
44433301 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
44433341 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
44433381 A
1 A
44433382 CTACAAGATC
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 34 0.47
40 39 0.53
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Done.