Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 18 of 352
Found at i:5743100 original size:177 final size:172
Alignment explanation
Indices: 5742565--5743231 Score: 483
Period size: 177 Copynumber: 3.9 Consensus size: 172
5742555 TACTGCCACT
*
5742565 TCAGAGAGATAAGAT--TTTTTTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATGTC
1 TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TATGTC
* * * * *
5742628 TTTAATCTGCTCCGCTGTAACCTCA-GGAGATAAGATCTGCAAT-TCTTC-GTCTACTCCGCTGT
65 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-TAC-ATGTCTTCAATCTACTCCACTGT
* * *
5742690 AACCTCAGGGAAATAAGACCTGATGCGATCTACTCTATTGTAA-C
128 AACCTCAGGGAAATAAGATCTGATGCGATCTACTCCACTGTAATC
*
5742734 TTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAACTTCAGGGAGATAGGATAGTGA
1 -TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATA-TG-
* ** * * * * * * *
5742799 CTTCGCTTCCATCTATTCC-AT-TACAACTTTAGGG-GAATAAGATT-CGTTTTTTCAATCTATT
63 --T--CTTCAATCTGCTCCGCTGTA-ATC-TCAGGGAG-ATAAGATTACATGTCTTCAATCTACT
* * * * ** *
5742860 CCACTGCATCTTCAGGGAAATAAGA-CTTGATGCGACCTACTCTGCTGTAACC
121 CCACTGTAACCTCAGGGAAATAAGATC-TGATGCGATCTACTCCACTGTAATC
* *
5742912 TCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAACTTCGGGGAGATAGGATAGTGTC
1 TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATA-TGTC
* * *
5742977 TTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-C-TGGCTTCAATCTGCTCCACTGTA
65 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-TACATGTCTTCAATCTACTCCACTGTA
* * **
5743040 ACCTCAGGGAAATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATC
129 ACCTCAGGGAAATAAGATCTG--ATGC---GATCTACTCCACTGTAATC
* * * * ** * * * *
5743089 TCAGGGAGATAAGA-CC-TGA-TGTGATCTTCTCTACTGTAACTTCAGAGAGATACG--AT-CCT
1 TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATATGTCT
* * ** * * ** * * *
5743148 TTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTAC-TGTCTTTGATCTGCTCCGCTGTAAT
66 TCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACATGTCTTCAATCTACTCCACTGTAAC
*
5743212 CTCAGGGAGATAAGATCTGA
131 CTCAGGGAAATAAGATCTGA
5743232 AATTCTTTGG
Statistics
Matches: 401, Mismatches: 69, Indels: 56
0.76 0.13 0.11
Matches are distributed among these distances:
168 1 0.00
169 1 0.00
170 85 0.21
171 3 0.01
172 99 0.25
173 7 0.02
174 33 0.08
175 6 0.01
176 11 0.03
177 145 0.36
178 10 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (172 bp):
TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATATGTCT
TCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACATGTCTTCAATCTACTCCACTGTAAC
CTCAGGGAAATAAGATCTGATGCGATCTACTCCACTGTAATC
Found at i:5748500 original size:15 final size:16
Alignment explanation
Indices: 5748480--5748521 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
5748470 AAACGGCCCT
5748480 TCTTCTCGCTT-GTTC
1 TCTTCTCGCTTCGTTC
* *
5748495 TCTTCTCACTTCTTTC
1 TCTTCTCGCTTCGTTC
5748511 TCTTCT-GCTTC
1 TCTTCTCGCTTC
5748522 ATGCAGGCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.02, C:0.36, G:0.07, T:0.55
Consensus pattern (16 bp):
TCTTCTCGCTTCGTTC
Found at i:5755532 original size:16 final size:16
Alignment explanation
Indices: 5755511--5755541 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5755501 AAGAAACGAT
*
5755511 AAATATGTATATATAA
1 AAATATGTACATATAA
5755527 AAATATGTACATATA
1 AAATATGTACATATA
5755542 TATGGGTGTA
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:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
AAATATGTACATATAA
Found at i:5756123 original size:3 final size:3
Alignment explanation
Indices: 5756074--5756105 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
5756064 AACATAAACA
5756074 AAT AAGT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT A
5756106 GAATAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5757315 original size:27 final size:27
Alignment explanation
Indices: 5757275--5757343 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
5757265 TTTTTTTGTT
*
5757275 TTGGGTT-TTGGGCTGAGGGTAGGCTA
1 TTGGGTTATTGGGCTAAGGGTAGGCTA
5757301 TTGGGTTATTGGGCTAAGGGTAGGCTA
1 TTGGGTTATTGGGCTAAGGGTAGGCTA
5757328 TTGGGTTATTGGGCTA
1 TTGGGTTATTGGGCTA
5757344 GTGGTTCTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 7 0.17
27 34 0.83
ACGTcount: A:0.14, C:0.07, G:0.42, T:0.36
Consensus pattern (27 bp):
TTGGGTTATTGGGCTAAGGGTAGGCTA
Found at i:5759864 original size:29 final size:30
Alignment explanation
Indices: 5759805--5759862 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5759795 TCCGAGCCTT
*
5759805 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
5759835 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
5759863 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:5760092 original size:13 final size:13
Alignment explanation
Indices: 5760074--5760105 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5760064 TTTCCAGCAA
5760074 TTATGAATTTATT
1 TTATGAATTTATT
5760087 TTATGAATTTATT
1 TTATGAATTTATT
*
5760100 TGATGA
1 TTATGA
5760106 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:5760329 original size:50 final size:50
Alignment explanation
Indices: 5760200--5760440 Score: 279
Period size: 50 Copynumber: 4.7 Consensus size: 50
5760190 ATTTGGGTAA
* * *
5760200 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCAT-TGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
5760255 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
5760305 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
5760355 AGAGGTCCCCTATAAGACCATGTCTAGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
5760405 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
5760441 TTTGGCATGT
Statistics
Matches: 163, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 90 0.55
51 28 0.17
52 1 0.01
53 3 0.02
55 37 0.23
56 3 0.02
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:5760385 original size:100 final size:103
Alignment explanation
Indices: 5760200--5760448 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 103
5760190 ATTTGGGTAA
5760200 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATT-GCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* * *
5760264 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTAGGACATGGCATGGGCACC-ATCACG
* * *
5760305 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
5760367 TAAGACCATGTCTAGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTAGGACATGGCATGGGCACCATCACG
* *
5760405 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
5760449 GTTATTATCA
Statistics
Matches: 131, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 39 0.30
105 38 0.29
106 3 0.02
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTAGGACATGGCATGGGCACCATCACG
Found at i:5770010 original size:30 final size:29
Alignment explanation
Indices: 5769976--5770043 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
5769966 AATTTATATA
5769976 TTTATTATTTCTAAAAGATTAAAAT-AAATT
1 TTTATTATTTCTAAAAG-TTAAAATGAAA-T
* * * *
5770006 TTTATCATTTTTGAAAGTTAAAATGTAAT
1 TTTATTATTTCTAAAAGTTAAAATGAAAT
5770035 TTTATTATT
1 TTTATTATT
5770044 AAAATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (29 bp):
TTTATTATTTCTAAAAGTTAAAATGAAAT
Found at i:5773152 original size:17 final size:18
Alignment explanation
Indices: 5773116--5773153 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5773106 TCTTTTTAAT
*
5773116 TTATTTTATATAATAAAA
1 TTATTTTATATAAAAAAA
*
5773134 TTATTTTTTA-AAAAAAA
1 TTATTTTATATAAAAAAA
5773151 TTA
1 TTA
5773154 ATATAAGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATTTTATATAAAAAAA
Found at i:5773903 original size:30 final size:30
Alignment explanation
Indices: 5773867--5773924 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
5773857 GATTAAAGAT
*
5773867 GAGTAATTTTATCTCGTATCTTAATAATGA
1 GAGTAATTTAATCTCGTATCTTAATAATGA
*
5773897 GAGTAATTTAATCTCGTATCTTATTAAT
1 GAGTAATTTAATCTCGTATCTTAATAAT
5773925 AATGGGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (30 bp):
GAGTAATTTAATCTCGTATCTTAATAATGA
Found at i:5773983 original size:20 final size:20
Alignment explanation
Indices: 5773960--5773998 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5773950 ATATTATTAC
5773960 TGTTCACGACATGACCCTAA
1 TGTTCACGACATGACCCTAA
* *
5773980 TGTTCATGACTTGACCCTA
1 TGTTCACGACATGACCCTA
5773999 CTATTTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (20 bp):
TGTTCACGACATGACCCTAA
Found at i:5775191 original size:21 final size:20
Alignment explanation
Indices: 5775167--5775212 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5775157 TACAAATGTG
5775167 TTAATATTTAATTGAAAATAT
1 TTAATATTTAATT-AAAATAT
* *
5775188 TTAATGATTTTATTTAAATAT
1 TTAAT-ATTTAATTAAAATAT
5775209 TTAA
1 TTAA
5775213 AATATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TTAATATTTAATTAAAATAT
Found at i:5778449 original size:12 final size:13
Alignment explanation
Indices: 5778425--5778455 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
5778415 TCGAACCATT
5778425 AAACCTCGAACCC
1 AAACCTCGAACCC
5778438 AAACCT-GAACCC
1 AAACCTCGAACCC
5778450 AAACCT
1 AAACCT
5778456 AAATCCTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.42, C:0.42, G:0.06, T:0.10
Consensus pattern (13 bp):
AAACCTCGAACCC
Found at i:5779681 original size:30 final size:31
Alignment explanation
Indices: 5779646--5779706 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
5779636 TATTTTATTA
*
5779646 TTAA-TTTTGTTATTATTTTAAAGACATTTG
1 TTAATTTTTATTATTATTTTAAAGACATTTG
5779676 TTAATTTTTATTATTATTTTAAAGACATTTG
1 TTAATTTTTATTATTATTTTAAAGACATTTG
5779707 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.57
Consensus pattern (31 bp):
TTAATTTTTATTATTATTTTAAAGACATTTG
Found at i:5780652 original size:20 final size:18
Alignment explanation
Indices: 5780624--5780669 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
5780614 ATTGAATGAT
5780624 AAATGAAAAGAAAATAATA
1 AAATGAAAAGAAAATAA-A
* *
5780643 AAATTGAAAATATAATAAA
1 AAA-TGAAAAGAAAATAAA
5780662 AAATGAAA
1 AAATGAAA
5780670 TTCTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 7 0.29
20 12 0.50
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.20
Consensus pattern (18 bp):
AAATGAAAAGAAAATAAA
Found at i:5780686 original size:8 final size:8
Alignment explanation
Indices: 5780673--5780697 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5780663 AATGAAATTC
5780673 TAAATTAT
1 TAAATTAT
5780681 TAAATTAT
1 TAAATTAT
5780689 TAAATTAT
1 TAAATTAT
5780697 T
1 T
5780698 TTAATTATAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TAAATTAT
Found at i:5780744 original size:31 final size:33
Alignment explanation
Indices: 5780679--5780749 Score: 103
Period size: 31 Copynumber: 2.2 Consensus size: 33
5780669 ATTCTAAATT
5780679 ATTAAATTATTAAATTATTTTAATTATACTTAA
1 ATTAAATTATTAAATTATTTTAATTATACTTAA
*
5780712 ATTAAATTATT-AATT-TTTCTATTTA-ACTTAA
1 ATTAAATTATTAAATTATTT-TAATTATACTTAA
5780743 ATTAAAT
1 ATTAAAT
5780750 AATAATAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 16 0.44
32 9 0.25
33 11 0.31
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (33 bp):
ATTAAATTATTAAATTATTTTAATTATACTTAA
Found at i:5781348 original size:89 final size:90
Alignment explanation
Indices: 5781226--5781724 Score: 358
Period size: 89 Copynumber: 5.5 Consensus size: 90
5781216 TGCAATAAAA
* * * * *
5781226 ATTTTTCAGACTAATTATAATAATTGCTATTTATTTTATTTATTTTTCGAGACATTTAAGTTTGA
1 ATTTTTTAGAATAATTATAATAATTACTATTTATTTTATTTATTTTTCGAGACATTTAAGCTTAA
5781291 GTATGATGTTACAACAATATTATTT
66 GTATGATGTTACAACAATATTATTT
* * * *
5781316 -TTTTTTAGAATAATTATTATAATTACTATTTATTTTATTTCTTTTTCGAGACATTTGGAG-TTG
1 ATTTTTTAGAATAATTATAATAATTACTATTTATTTTATTTATTTTTCGAGACATTT-AAGCTTA
* * * * *
5781379 AGCATGCA--ATA-ATA-TATTTGTTTTT
65 AGTATG-ATGTTACA-ACAATAT-TATTT
** * * *
5781404 ATTTTTTAGAATAATTATAATAATTTTTATTTATTTTATTTATTTTTCAGGGTAC--TGAGGCTT
1 ATTTTTTAGAATAATTATAATAATTACTATTTATTTTATTTATTTTTC-GAG-ACATTTAAGCTT
* * * * *
5781467 AAGT-TTAGTGCTATAACATTTTTATTTT
64 AAGTATGA-TGTTACAACAATATTA-TTT
* * * * * * * * *
5781495 ATTTTTTCGTAATATTTATAACAATTATTATTTATTTTATTTCTTTTTCGGGGCACTTAAGCTTG
1 ATTTTTTAG-AATAATTATAATAATTACTATTTATTTTATTTATTTTTCGAGACATTTAAGCTTA
* * *
5781560 AGTCTAATGTTGCAACAATATT-TTT
65 AGTATGATGTTACAACAATATTATTT
* * * ** * *
5781585 -CTTTTTAGAATATTTATAATAATTACTATTCATTTTATTTCGTTTTC-AGATACTTAAGCTTAA
1 ATTTTTTAGAATAATTATAATAATTACTATTTATTTTATTTATTTTTCGAGACATTTAAGCTTAA
**
5781648 GTATGATGTTGTAACAATATT-TTT
66 GTATGATGTTACAACAATATTATTT
** *
5781672 ATTATTGTCCGAAATAATTATAATAATTACTATGTATTTTATTTCATTTTTCG
1 ATT-TT-TTAG-AATAATTATAATAATTACTATTTATTTTATTT-ATTTTTCG
5781725 GATTAATTGA
Statistics
Matches: 323, Mismatches: 62, Indels: 45
0.75 0.14 0.10
Matches are distributed among these distances:
87 38 0.12
88 45 0.14
89 115 0.36
90 15 0.05
91 49 0.15
92 59 0.18
93 2 0.01
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (90 bp):
ATTTTTTAGAATAATTATAATAATTACTATTTATTTTATTTATTTTTCGAGACATTTAAGCTTAA
GTATGATGTTACAACAATATTATTT
Found at i:5793085 original size:28 final size:28
Alignment explanation
Indices: 5793012--5793085 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
5793002 TCGAATCCTG
*
5793012 AACCCTGAACCTTAAATCCTAAACATTA
1 AACCCTAAACCTTAAATCCTAAACATTA
* * *
5793040 AACTCAAAATCC-TAAATCTTAAACATTA
1 AACCCTAAA-CCTTAAATCCTAAACATTA
*
5793068 AACCCTAAACCTTGAATC
1 AACCCTAAACCTTAAATC
5793086 AATTGTTCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 2 0.05
28 33 0.89
29 2 0.05
ACGTcount: A:0.45, C:0.27, G:0.03, T:0.26
Consensus pattern (28 bp):
AACCCTAAACCTTAAATCCTAAACATTA
Found at i:5793211 original size:14 final size:14
Alignment explanation
Indices: 5793170--5793226 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
5793160 GTCGGAGTCG
*
5793170 AGATTCAAGGTTTA
1 AGATTCAAGATTTA
*
5793184 AG-TTCAAAATTTA
1 AGATTCAAGATTTA
*
5793197 AGATTCGAGATTTA
1 AGATTCAAGATTTA
* *
5793211 AGATTGAAGGTTTA
1 AGATTCAAGATTTA
5793225 AG
1 AG
5793227 TTTAAATTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
13 11 0.31
14 24 0.69
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (14 bp):
AGATTCAAGATTTA
Found at i:5795592 original size:21 final size:20
Alignment explanation
Indices: 5795548--5795585 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5795538 ATTGCAATTC
5795548 TAAAAATATAAATAATTTTA
1 TAAAAATATAAATAATTTTA
*
5795568 TAAAAA-ATTAATAATTTT
1 TAAAAATATAAATAATTTT
5795586 GATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAAATATAAATAATTTTA
Found at i:5802462 original size:22 final size:22
Alignment explanation
Indices: 5802434--5802477 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5802424 AAGGTGAAAG
5802434 TTGATTCTTAAACAACACTAAA
1 TTGATTCTTAAACAACACTAAA
5802456 TTGATTCTTAAACAACACTAAA
1 TTGATTCTTAAACAACACTAAA
5802478 AAAAAGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (22 bp):
TTGATTCTTAAACAACACTAAA
Found at i:5805508 original size:20 final size:21
Alignment explanation
Indices: 5805471--5805510 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5805461 CGTGTTTGCT
*
5805471 TTCCGTTCAACTCTTATGAGC
1 TTCCGTTCAACTCATATGAGC
5805492 TTCCGTT-AACTCATATGAG
1 TTCCGTTCAACTCATATGAG
5805511 TTTCAGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (21 bp):
TTCCGTTCAACTCATATGAGC
Found at i:5806626 original size:81 final size:81
Alignment explanation
Indices: 5806491--5806734 Score: 409
Period size: 81 Copynumber: 3.0 Consensus size: 81
5806481 ACTAAACTAA
* * *
5806491 ATGAAGTAGAAAATAGTATGATATAGTTGATGCATGATATGTTACATGAATATAGTATGAACCAT
1 ATGAAGTAGAAAATAGTATGATATAGTTGATGCATGATATGTGATATGAATATAGAATGAACCAT
5806556 GCTATGTGATATTGGG
66 GCTATGTGATATTGGG
* *
5806572 ATGAAGTAGAAAATAGCATGATATAGTTGATGCATGATATGTGATATGACTATAGAATGAACCAT
1 ATGAAGTAGAAAATAGTATGATATAGTTGATGCATGATATGTGATATGAATATAGAATGAACCAT
*
5806637 GCTTTGTGATATTGGG
66 GCTATGTGATATTGGG
*
5806653 ATGAAGTAGAAAATAGTATGATGTAGTTGATGCGA-GATATGTGATATGAATATAGAATGAACCA
1 ATGAAGTAGAAAATAGTATGATATAGTTGATGC-ATGATATGTGATATGAATATAGAATGAACCA
5806717 TGCTATGTGATATTGGG
65 TGCTATGTGATATTGGG
5806734 A
1 A
5806735 ATATATGAAG
Statistics
Matches: 152, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
81 151 0.99
82 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (81 bp):
ATGAAGTAGAAAATAGTATGATATAGTTGATGCATGATATGTGATATGAATATAGAATGAACCAT
GCTATGTGATATTGGG
Found at i:5808649 original size:13 final size:13
Alignment explanation
Indices: 5808631--5808660 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5808621 TGCTTTCACA
5808631 AAGAGTGTATAAT
1 AAGAGTGTATAAT
5808644 AAGAGTGTATAAT
1 AAGAGTGTATAAT
5808657 AAGA
1 AAGA
5808661 AGTTTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (13 bp):
AAGAGTGTATAAT
Found at i:5820168 original size:6 final size:6
Alignment explanation
Indices: 5820157--5820183 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5820147 TTGGGTTCTA
5820157 TTTTGT TTTTGT TTTTGT TTTTGT TTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTT
5820184 CTTTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:5821269 original size:6 final size:6
Alignment explanation
Indices: 5821258--5821294 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
5821248 AATGCTGAGA
*
5821258 GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GCTGCT G
1 GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT G
5821295 ACTGCATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.19, G:0.35, T:0.46
Consensus pattern (6 bp):
GTTGCT
Found at i:5827967 original size:21 final size:21
Alignment explanation
Indices: 5827943--5827986 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5827933 CAAAGGTTAA
*
5827943 TCGATAGCTACTCACAATCTT
1 TCGATAACTACTCACAATCTT
5827964 TCGATAACTACTCACAATCTT
1 TCGATAACTACTCACAATCTT
5827985 TC
1 TC
5827987 AATATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.34
Consensus pattern (21 bp):
TCGATAACTACTCACAATCTT
Found at i:5830236 original size:25 final size:23
Alignment explanation
Indices: 5830161--5830288 Score: 120
Period size: 25 Copynumber: 5.4 Consensus size: 23
5830151 CACTAATGAA
*
5830161 CAGAGAGCACTGAAGTGCT-ATA-
1 CAGAGAGCACT-ACGTGCTAATAT
* *
5830183 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCAC-TACGTGCTAATAT
5830205 CAGAGAGCACTCACGTGCTAAATAT
1 CAGAGAGCACT-ACGTGCT-AATAT
5830230 CAGAGAGCACTAGCGTGCTAATAAT
1 CAGAGAGCACTA-CGTGCTAAT-AT
*
5830255 CAGAGAGCACTGGCGTGCTAATATT
1 CAGAGAGCACT-ACGTGCTAATA-T
5830280 CAGAGAGCA
1 CAGAGAGCA
5830289 TGCTGAGGTC
Statistics
Matches: 91, Mismatches: 5, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
21 1 0.01
22 33 0.36
24 6 0.07
25 51 0.56
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (23 bp):
CAGAGAGCACTACGTGCTAATAT
Found at i:5834634 original size:16 final size:16
Alignment explanation
Indices: 5834610--5834643 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5834600 TTATTAATTT
5834610 ATGTGATTAATT-GAA
1 ATGTGATTAATTGGAA
5834625 ATGTGTATTAATTGGAA
1 ATGTG-ATTAATTGGAA
5834642 AT
1 AT
5834644 TGAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (16 bp):
ATGTGATTAATTGGAA
Found at i:5834967 original size:18 final size:18
Alignment explanation
Indices: 5834944--5835031 Score: 122
Period size: 18 Copynumber: 4.9 Consensus size: 18
5834934 TAAAAGTACT
* *
5834944 GAATAACTGACTGTTACA
1 GAATAATTGATTGTTACA
*
5834962 GAATAATTAATTGTTACA
1 GAATAATTGATTGTTACA
*
5834980 GAATAATTGATTGCTACA
1 GAATAATTGATTGTTACA
* *
5834998 GAATAATTGATTGCTACT
1 GAATAATTGATTGTTACA
5835016 GAATAATTGATTGTTA
1 GAATAATTGATTGTTA
5835032 TTGAGTAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (18 bp):
GAATAATTGATTGTTACA
Found at i:5837523 original size:23 final size:22
Alignment explanation
Indices: 5837496--5837545 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
5837486 TGCCTAAAAT
5837496 GACACACGAGGTGCCTG-ATAC
1 GACACACGAGGTGCCTGAATAC
5837517 GACACACGAGGTGCCTGAAATAC
1 GACACACGAGGTGCCTG-AATAC
5837540 GACACA
1 GACACA
5837546 TAAAGTGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.63
23 10 0.37
ACGTcount: A:0.34, C:0.28, G:0.26, T:0.12
Consensus pattern (22 bp):
GACACACGAGGTGCCTGAATAC
Found at i:5837553 original size:23 final size:23
Alignment explanation
Indices: 5837471--5837557 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
5837461 CCTGATCAGT
*
5837471 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* * *
5837493 A-ATGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
5837513 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
5837536 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
5837558 TCAGTAGCCG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 32 0.60
22 1 0.02
23 19 0.36
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:5838063 original size:27 final size:30
Alignment explanation
Indices: 5838018--5838072 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 30
5838008 GCTCGAATGC
*
5838018 TTTCTGTTCTCTTTTCTCT-ATTCTTTTTG
1 TTTCTGTTCTCTTTACTCTGATTCTTTTTG
*
5838047 TTTCT-TT-TCTTTACTCTGTTTCTTTT
1 TTTCTGTTCTCTTTACTCTGATTCTTTT
5838073 ATTCACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 9 0.39
29 5 0.22
ACGTcount: A:0.04, C:0.20, G:0.05, T:0.71
Consensus pattern (30 bp):
TTTCTGTTCTCTTTACTCTGATTCTTTTTG
Found at i:5844402 original size:21 final size:22
Alignment explanation
Indices: 5844378--5844426 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
5844368 GCCTAAAACC
*
5844378 ACACACGAGGTGTCTG-ATACG
1 ACACACGAGGTGCCTGAATACG
5844399 ACACACGAGGTGCCTGAAATACG
1 ACACACGAGGTGCCTG-AATACG
5844422 ACACA
1 ACACA
5844427 TAAAGTGCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 15 0.60
23 10 0.40
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (22 bp):
ACACACGAGGTGCCTGAATACG
Found at i:5844434 original size:23 final size:23
Alignment explanation
Indices: 5844356--5844438 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 23
5844346 ATCAGTATAT
*
5844356 GACACATAAAGTGCCT-AAA-AC
1 GACACACAAAGTGCCTGAAATAC
* * * *
5844377 CACACACGAGGTGTCTG--ATAC
1 GACACACAAAGTGCCTGAAATAC
* *
5844398 GACACACGAGGTGCCTGAAATAC
1 GACACACAAAGTGCCTGAAATAC
*
5844421 GACACATAAAGTGCCTGA
1 GACACACAAAGTGCCTGA
5844439 TCAGTAAAGC
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.02
21 28 0.58
23 19 0.40
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (23 bp):
GACACACAAAGTGCCTGAAATAC
Found at i:5844945 original size:27 final size:30
Alignment explanation
Indices: 5844900--5844954 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 30
5844890 GCTCGAATGC
*
5844900 TTTCTGTTCTCTTTTCTCT-ATTCTTTTTG
1 TTTCTGTTCTCTTTACTCTGATTCTTTTTG
*
5844929 TTTCT-TT-TCTTTACTCTGTTTCTTTT
1 TTTCTGTTCTCTTTACTCTGATTCTTTT
5844955 ATTCACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 9 0.39
29 5 0.22
ACGTcount: A:0.04, C:0.20, G:0.05, T:0.71
Consensus pattern (30 bp):
TTTCTGTTCTCTTTACTCTGATTCTTTTTG
Found at i:5851760 original size:21 final size:23
Alignment explanation
Indices: 5851728--5851769 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5851718 AATCATAACA
5851728 TTTTTATGAATAAATA-TATTAT
1 TTTTTATGAATAAATAGTATTAT
*
5851750 TTTTTAT-AATATATAGTATT
1 TTTTTATGAATAAATAGTATT
5851770 GGCACTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTTTATGAATAAATAGTATTAT
Found at i:5853452 original size:5 final size:5
Alignment explanation
Indices: 5853426--5853483 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
5853416 ATGTGTTAAA
* *
5853426 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
5853475 ATATT ATAT
1 ATATT ATAT
5853484 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:5853462 original size:10 final size:9
Alignment explanation
Indices: 5853427--5853484 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
5853417 TGTGTTAAAA
5853427 TATATATAT
1 TATATATAT
*
5853436 TAAAT-TAT
1 TATATATAT
5853444 TAT-TATAT
1 TATATATAT
5853452 TATAGTATAT
1 TATA-TATAT
5853462 TATAT-TA-
1 TATATATAT
5853469 TATATTATAT
1 TATA-TATAT
5853479 TATATA
1 TATATA
5853485 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:5853474 original size:12 final size:12
Alignment explanation
Indices: 5853429--5853484 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
5853419 TGTTAAAATA
*
5853429 TATATATTAAAT
1 TATATATTATAT
5853441 TAT-TATTATATT
1 TATATATTATA-T
5853453 ATAGTATATTATAT
1 -TA-TATATTATAT
5853467 TATATATTATAT
1 TATATATTATAT
5853479 TATATA
1 TATATA
5853485 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:5853858 original size:18 final size:19
Alignment explanation
Indices: 5853835--5853873 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5853825 ATATATAGAT
5853835 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
5853853 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
5853872 AT
1 AT
5853874 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:5854001 original size:16 final size:16
Alignment explanation
Indices: 5853975--5854007 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5853965 TTATGAATTT
5853975 ATGTGATTGATT-AAA
1 ATGTGATTGATTGAAA
5853990 ATGTGTATTGATTGAAA
1 ATGTG-ATTGATTGAAA
5854007 A
1 A
5854008 AAATCGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (16 bp):
ATGTGATTGATTGAAA
Found at i:5854222 original size:39 final size:39
Alignment explanation
Indices: 5854112--5854246 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
5854102 GACCTCGAGT
* * * *
5854112 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
5854153 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
5854191 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
5854230 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
5854247 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:5854390 original size:18 final size:19
Alignment explanation
Indices: 5854369--5854409 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5854359 AATGAAATGA
5854369 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
5854387 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
5854406 GAAA
1 GAAA
5854410 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:5855354 original size:16 final size:17
Alignment explanation
Indices: 5855318--5855355 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5855308 TTCTAATTTA
5855318 TTATGGAAGAAAATCTCT
1 TTATGGAAGAAAA-CTCT
*
5855336 TTATGTAAGAAAA-TCT
1 TTATGGAAGAAAACTCT
5855352 TTAT
1 TTAT
5855356 TTAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (17 bp):
TTATGGAAGAAAACTCT
Found at i:5855734 original size:12 final size:12
Alignment explanation
Indices: 5855717--5855753 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5855707 TACAACAATT
5855717 AAATTAAATAAA
1 AAATTAAATAAA
*
5855729 AAATTAAATATA
1 AAATTAAATAAA
*
5855741 AAATTATATAAA
1 AAATTAAATAAA
5855753 A
1 A
5855754 TTAAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTAAATAAA
Found at i:5855756 original size:22 final size:22
Alignment explanation
Indices: 5855728--5855773 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5855718 AATTAAATAA
5855728 AAAATT-AAATATAAAATTATAT
1 AAAATTAAAAT-TAAAATTATAT
5855750 AAAATTAAAATTAAAATTATAT
1 AAAATTAAAATTAAAATTATAT
5855772 AA
1 AA
5855774 GCGAGGCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATTAAAATTAAAATTATAT
Found at i:5855764 original size:12 final size:11
Alignment explanation
Indices: 5855713--5855768 Score: 53
Period size: 12 Copynumber: 5.0 Consensus size: 11
5855703 AATTTACAAC
5855713 AATT-AAATTA
1 AATTAAAATTA
*
5855723 AATAAAAAATTA
1 AAT-TAAAATTA
5855735 AATATAAAATTA
1 AAT-TAAAATTA
*
5855747 TA-TAAAATTAA
1 AATTAAAATT-A
5855758 AATTAAAATTA
1 AATTAAAATTA
5855769 TATAAGCGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 10 0.26
11 3 0.08
12 25 0.66
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATTAAAATTA
Found at i:5856351 original size:17 final size:19
Alignment explanation
Indices: 5856315--5856353 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
5856305 TTTTGCTTTG
*
5856315 TTTGTTGATTCAATGTGTT
1 TTTGTTGATTCAATGGGTT
5856334 TTTGTT-ATTC-ATGGGTT
1 TTTGTTGATTCAATGGGTT
5856351 TTT
1 TTT
5856354 TTTGTCTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.13, C:0.05, G:0.21, T:0.62
Consensus pattern (19 bp):
TTTGTTGATTCAATGGGTT
Found at i:5863433 original size:99 final size:99
Alignment explanation
Indices: 5863262--5863456 Score: 345
Period size: 99 Copynumber: 2.0 Consensus size: 99
5863252 TTTCAAAGTG
* *
5863262 TGAAACAAATAGTCCCTGCCACATTTGACAATTTTGCAGTAATAATGTCATCACCATAATTGCTG
1 TGAAACAAATAGTCACTGCCACATTTGACAATTTTGCAGTAATAATGTCATCACCAAAATTGCTG
5863327 CATATCATATACTGCTATTACTTACAATCAAATT
66 CATATCATATACTGCTATTACTTACAATCAAATT
* *
5863361 TGAAACAGATAGTCACTGCCACATTTGACAATTTTGCAGTAATAATGTCTTCACCAAAATTGCTG
1 TGAAACAAATAGTCACTGCCACATTTGACAATTTTGCAGTAATAATGTCATCACCAAAATTGCTG
*
5863426 CATATCATATACTTCTATTACTTACAATCAA
66 CATATCATATACTGCTATTACTTACAATCAA
5863457 CCTATCATCT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 91 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.33
Consensus pattern (99 bp):
TGAAACAAATAGTCACTGCCACATTTGACAATTTTGCAGTAATAATGTCATCACCAAAATTGCTG
CATATCATATACTGCTATTACTTACAATCAAATT
Found at i:5869608 original size:21 final size:21
Alignment explanation
Indices: 5869570--5869612 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5869560 AATGTTATTT
*
5869570 TAACATGAATTTTGATTATAA
1 TAACATGAAATTTGATTATAA
5869591 TAACAT-AAATTTGAATTATAA
1 TAACATGAAATTTG-ATTATAA
5869612 T
1 T
5869613 TGAATCAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
TAACATGAAATTTGATTATAA
Found at i:5870002 original size:35 final size:35
Alignment explanation
Indices: 5869956--5870036 Score: 153
Period size: 35 Copynumber: 2.3 Consensus size: 35
5869946 AGGTTTGCTC
*
5869956 GAAAAATGAGAGGATTTGGGTAAAAATATAAGCTT
1 GAAAAATGAGAGGATTTGGGTAAAAATATAAACTT
5869991 GAAAAATGAGAGGATTTGGGTAAAAATATAAACTT
1 GAAAAATGAGAGGATTTGGGTAAAAATATAAACTT
5870026 GAAAAATGAGA
1 GAAAAATGAGA
5870037 TTAAACAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.23
Consensus pattern (35 bp):
GAAAAATGAGAGGATTTGGGTAAAAATATAAACTT
Found at i:5872259 original size:25 final size:24
Alignment explanation
Indices: 5872214--5872266 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
5872204 TTAATAATAT
*
5872214 ATATTATATATTTATAAGCCCAAC
1 ATATTATATATATATAAGCCCAAC
*
5872238 ATATTATATTATATATAAGCCCAAT
1 ATATTATA-TATATATAAGCCCAAC
5872263 ATAT
1 ATAT
5872267 GACCTAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (24 bp):
ATATTATATATATATAAGCCCAAC
Found at i:5876313 original size:23 final size:23
Alignment explanation
Indices: 5876270--5876314 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5876260 TTTCAATTTT
*
5876270 TTATTTTAATAAGTGTCATCTCC
1 TTATTTTAATAAGTCTCATCTCC
* *
5876293 TTATTTTACTAAGTCTTATCTC
1 TTATTTTAATAAGTCTCATCTC
5876315 AATTGACATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (23 bp):
TTATTTTAATAAGTCTCATCTCC
Found at i:5883229 original size:22 final size:20
Alignment explanation
Indices: 5883204--5883247 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
5883194 TTTAAATTCA
5883204 TAATTATTTTAAATAGTGTTTT
1 TAATTATTTTAAAT--TGTTTT
*
5883226 TAATTATTTTTAATTGTTTT
1 TAATTATTTTAAATTGTTTT
5883246 TA
1 TA
5883248 TATAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
TAATTATTTTAAATTGTTTT
Found at i:5886404 original size:106 final size:105
Alignment explanation
Indices: 5886242--5886455 Score: 401
Period size: 106 Copynumber: 2.0 Consensus size: 105
5886232 TCTTTTTAGT
5886242 AAATGAATTAACGTTATCTATGGAGGAAATGATGTCATGATTTTTAATCAATGAGCAGGAGCCCT
1 AAATGAATTAACGTTATCTATGGAGGAAATGATGTCATGATTTTTAATCAATGAGCAGGAGCCCT
5886307 ATATTCCTACTTTTCCTCCTAAAATGAAAAAAACGAAAAGA
66 ATATTCCTACTTTTCCTCCTAAAATG-AAAAAACGAAAAGA
5886348 AAATGAATTAACGTTATCTATGGAGGAAATGATGTCATGATTTTTAATCAATGAGCAGGAGCCCT
1 AAATGAATTAACGTTATCTATGGAGGAAATGATGTCATGATTTTTAATCAATGAGCAGGAGCCCT
* *
5886413 ATATTCCTTCTTTTCCTCCTAACATGAAAAAACGAAAAGA
66 ATATTCCTACTTTTCCTCCTAAAATGAAAAAACGAAAAGA
5886453 AAA
1 AAA
5886456 AAAGGAGGAA
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
105 17 0.16
106 89 0.84
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (105 bp):
AAATGAATTAACGTTATCTATGGAGGAAATGATGTCATGATTTTTAATCAATGAGCAGGAGCCCT
ATATTCCTACTTTTCCTCCTAAAATGAAAAAACGAAAAGA
Found at i:5888379 original size:7 final size:7
Alignment explanation
Indices: 5888367--5888392 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5888357 GTCCTTTAAA
5888367 AAATTTT
1 AAATTTT
5888374 AAATTTT
1 AAATTTT
5888381 AAATTTT
1 AAATTTT
5888388 AAATT
1 AAATT
5888393 AGTAAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:5889642 original size:16 final size:16
Alignment explanation
Indices: 5889621--5889651 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5889611 AAATTAATAT
5889621 AAAATAACATAAATTC
1 AAAATAACATAAATTC
*
5889637 AAAATAACCTAAATT
1 AAAATAACATAAATT
5889652 TGAAACAATT
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:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACATAAATTC
Found at i:5897189 original size:65 final size:65
Alignment explanation
Indices: 5897110--5897241 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
5897100 AAAATACAAT
5897110 GCTTGCTTAATTAATATGTTTCAATGGTAGTGTGCTCCGAAATCCACTGTTCCCAACAAGGATTA
1 GCTTGCTTAATTAATATGTTTCAATGGTAGTGTGCTCCGAAATCCACTGTTCCCAACAAGGATTA
5897175 GCTTGCTTAATTAATATGTTTCAATGGTAGTGTGCTCCGAAATCCACTGTTCCCAACAAGGATTA
1 GCTTGCTTAATTAATATGTTTCAATGGTAGTGTGCTCCGAAATCCACTGTTCCCAACAAGGATTA
5897240 GC
1 GC
5897242 ACCATTGAAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (65 bp):
GCTTGCTTAATTAATATGTTTCAATGGTAGTGTGCTCCGAAATCCACTGTTCCCAACAAGGATTA
Found at i:5899635 original size:13 final size:14
Alignment explanation
Indices: 5899602--5899641 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
5899592 ATTACTTATG
5899602 TATAAAAT-TATAT
1 TATAAAATATATAT
5899615 TA-AAAATATAT-T
1 TATAAAATATATAT
*
5899627 TATAAAATATTTAT
1 TATAAAATATATAT
5899641 T
1 T
5899642 CATTTAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 8 0.35
13 13 0.57
14 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATAAAATATATAT
Found at i:5906755 original size:13 final size:13
Alignment explanation
Indices: 5906737--5906766 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5906727 CGGCTGAGGC
5906737 AGCCGTGTACATA
1 AGCCGTGTACATA
5906750 AGCCGTGTACATA
1 AGCCGTGTACATA
5906763 AGCC
1 AGCC
5906767 ATCCACCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (13 bp):
AGCCGTGTACATA
Found at i:5907775 original size:11 final size:14
Alignment explanation
Indices: 5907743--5907775 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
5907733 TTGAAGAATG
5907743 ATATTATTGTAATT
1 ATATTATTGTAATT
5907757 ATATTATTGTAATT
1 ATATTATTGTAATT
5907771 ATATT
1 ATATT
5907776 TGTATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (14 bp):
ATATTATTGTAATT
Found at i:5915845 original size:20 final size:20
Alignment explanation
Indices: 5915822--5915874 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
5915812 AAAAAATTCA
**
5915822 AAAAATATATAAATATTTTT
1 AAAAATATATAAATAAATTT
*
5915842 AAAAAAAT-TATAATAAATTT
1 AAAAATATATA-AATAAATTT
5915862 AAAAATATATAAA
1 AAAAATATATAAA
5915875 AATGAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATATATAAATAAATTT
Found at i:5915882 original size:17 final size:18
Alignment explanation
Indices: 5915844--5915887 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5915834 ATATTTTTAA
*
5915844 AAAAATTATAATAAATTT
1 AAAAATTATAATAAATTG
5915862 AAAAATATATAA-AAA-TG
1 AAAAAT-TATAATAAATTG
5915879 AAAAATTAT
1 AAAAATTAT
5915888 TGTTGACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 7 0.29
18 9 0.38
19 5 0.21
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAAATTATAATAAATTG
Found at i:5915980 original size:17 final size:18
Alignment explanation
Indices: 5915941--5915978 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5915931 AATTAAATAT
5915941 TTTAAAAAATATAATAAA
1 TTTAAAAAATATAATAAA
*
5915959 TTTAAAATAA-ATATTAAA
1 TTTAAAA-AATATAATAAA
5915977 TT
1 TT
5915979 AATAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAAAAAATATAATAAA
Found at i:5916354 original size:23 final size:23
Alignment explanation
Indices: 5916328--5916381 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5916318 CTGGGATTGG
* *
5916328 GGTGGGGGAGGGGTAGGGATGAT
1 GGTGGGGGAGGGGGAGGGACGAT
* * *
5916351 GGTGGAGGTGGGGGAGGGACGGT
1 GGTGGGGGAGGGGGAGGGACGAT
5916374 GGTGGGGG
1 GGTGGGGG
5916382 TAGGTTCGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.13, C:0.02, G:0.70, T:0.15
Consensus pattern (23 bp):
GGTGGGGGAGGGGGAGGGACGAT
Found at i:5916467 original size:20 final size:21
Alignment explanation
Indices: 5916440--5916509 Score: 85
Period size: 20 Copynumber: 3.4 Consensus size: 21
5916430 ATTTAATATA
5916440 ATTATATTTTTAAAATATTTT
1 ATTATATTTTTAAAATATTTT
*
5916461 -TTTTATTTTTAAAAT-TTATT
1 ATTATATTTTTAAAATATT-TT
5916481 ATTATATTTTTTAAAATA-TTT
1 ATTATA-TTTTTAAAATATTTT
5916502 A-TATATTT
1 ATTATATTT
5916510 ATATATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
19 5 0.12
20 20 0.47
21 7 0.16
22 11 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATATTTTTAAAATATTTT
Found at i:5937090 original size:15 final size:15
Alignment explanation
Indices: 5937072--5937125 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
5937062 TCCAAGACAG
5937072 AGAAACCCAGAATAA
1 AGAAACCCAGAATAA
*
5937087 AGAAATCCAGAATAA
1 AGAAACCCAGAATAA
* * * *
5937102 AGAGATCTAGGATAA
1 AGAAACCCAGAATAA
5937117 AGAAACCCA
1 AGAAACCCA
5937126 AGATATGATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.56, C:0.17, G:0.17, T:0.11
Consensus pattern (15 bp):
AGAAACCCAGAATAA
Found at i:5937130 original size:15 final size:15
Alignment explanation
Indices: 5937054--5937130 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
5937044 CAAGAAAACC
5937054 TAAAGAAATCCAAGA
1 TAAAGAAATCCAAGA
* * *
5937069 CAGAGAAA-CCCAGAA
1 TAAAGAAATCCAAG-A
5937084 TAAAGAAATCC-AGAA
1 TAAAGAAATCCAAG-A
* * *
5937099 TAAAGAGATCTAGGA
1 TAAAGAAATCCAAGA
*
5937114 TAAAGAAACCCAAGA
1 TAAAGAAATCCAAGA
5937129 TA
1 TA
5937131 TGATACTATG
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
14 4 0.09
15 40 0.85
16 3 0.06
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
TAAAGAAATCCAAGA
Found at i:5940152 original size:93 final size:93
Alignment explanation
Indices: 5940046--5940216 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
5940036 GCCCATAAGT
* * * *
5940046 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTAAACGAGCTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
5940111 CGAGTTCGGATGCCTAGTTACATTTCTC
66 CGAGTTCGGATGCCTAGTTACATTTCTC
*
5940139 GAACTCGGACTCAACTAAACGAGTTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTAAACGAGCTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
5940204 CGAGTTCGGATGC
66 CGAGTTCGGATGC
5940217 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTAAACGAGCTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCTC
Found at i:5940213 original size:46 final size:45
Alignment explanation
Indices: 5940038--5940213 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 45
5940028 TGCAACCCGC
* *
5940038 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAC-TTTGCAT
* * *
5940084 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CTTTGCAT
* *** *
5940130 ACATTTCTCGAACTCGGACTCAACTAAACGAGTTCGGACATTTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGAC-TTTGCAT
*
5940177 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5940214 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
45 1 0.01
46 69 0.65
47 35 0.33
48 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACTTTGCAT
Found at i:5942598 original size:12 final size:13
Alignment explanation
Indices: 5942581--5942610 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5942571 AAAAAACTAT
5942581 ATTAT-AAAAAAA
1 ATTATAAAAAAAA
5942593 ATTATAAAAAAAA
1 ATTATAAAAAAAA
5942606 ATTAT
1 ATTAT
5942611 GCAACAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATTATAAAAAAAA
Found at i:5946082 original size:11 final size:11
Alignment explanation
Indices: 5946068--5946125 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
5946058 TTGATGTTGA
*
5946068 TTTGTTATTGT
1 TTTGTTATTAT
* *
5946079 TTTGCTACTAT
1 TTTGTTATTAT
*
5946090 TTTGCTATTAT
1 TTTGTTATTAT
5946101 ATATTGTTATTAT
1 -T-TTGTTATTAT
*
5946114 TTTGTTGTTAT
1 TTTGTTATTAT
5946125 T
1 T
5946126 ATTTGGATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 28 0.72
12 2 0.05
13 9 0.23
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.66
Consensus pattern (11 bp):
TTTGTTATTAT
Found at i:5946826 original size:25 final size:26
Alignment explanation
Indices: 5946797--5946850 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 26
5946787 AATTTAATTC
*
5946797 ATTAAAAATTATAAAAATATA-AGTT
1 ATTAAAAATGATAAAAATATATAGTT
* *
5946822 ATT-AAAATGATAAAATTATATATTT
1 ATTAAAAATGATAAAAATATATAGTT
5946847 ATTA
1 ATTA
5946851 TAGTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
ATTAAAAATGATAAAAATATATAGTT
Found at i:5946834 original size:24 final size:25
Alignment explanation
Indices: 5946801--5946865 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 25
5946791 TAATTCATTA
*
5946801 AAAATTATAAAAATATA-AGTTATT
1 AAAATGATAAAAATATATAGTTATT
* *
5946825 AAAATGATAAAATTATATATTTATT
1 AAAATGATAAAAATATATAGTTATT
*
5946850 -ATA-G-TAAAAATATATA
1 AAAATGATAAAAATATATA
5946866 ATTTAATTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 11 0.31
23 1 0.03
24 17 0.49
25 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (25 bp):
AAAATGATAAAAATATATAGTTATT
Found at i:5947907 original size:9 final size:9
Alignment explanation
Indices: 5947893--5947921 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
5947883 ATTTTTATTT
5947893 TTTAAAATA
1 TTTAAAATA
5947902 TTTAAAATA
1 TTTAAAATA
5947911 TTTAAAATA
1 TTTAAAATA
5947920 TT
1 TT
5947922 ATAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAAAATA
Found at i:5947933 original size:24 final size:27
Alignment explanation
Indices: 5947901--5947950 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 27
5947891 TTTTTAAAAT
5947901 ATTTAAAATA-T-TTAAA-ATATTATA
1 ATTTAAAATATTATTAAATATATTATA
*
5947925 ATTTTAAATATTATTAAATATATTAT
1 ATTTAAAATATTATTAAATATATTAT
5947951 TTATATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 1 0.05
26 5 0.23
27 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTTAAAATATTATTAAATATATTATA
Found at i:5962053 original size:15 final size:15
Alignment explanation
Indices: 5962028--5962062 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5962018 TGACTTTAAA
*
5962028 AAATAATTAAAATTT
1 AAATAACTAAAATTT
*
5962043 TAATAACTAAAATTT
1 AAATAACTAAAATTT
5962058 AAATA
1 AAATA
5962063 TAATTTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATAACTAAAATTT
Found at i:5964065 original size:14 final size:14
Alignment explanation
Indices: 5964041--5964078 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
5964031 AAAATATGAG
5964041 TTAATTATAAAAAT
1 TTAATTATAAAAAT
5964055 ATTAA-TATAAAAAT
1 -TTAATTATAAAAAT
5964069 TTAATTATAA
1 TTAATTATAA
5964079 GTAATTGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 14 0.64
15 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAATTATAAAAAT
Found at i:5964784 original size:18 final size:19
Alignment explanation
Indices: 5964761--5964798 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5964751 AAATAATATC
5964761 ATATTTAAATATATT-TTT
1 ATATTTAAATATATTATTT
*
5964779 ATATTTATATATATTATTT
1 ATATTTAAATATATTATTT
5964798 A
1 A
5964799 CTTTCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTAAATATATTATTT
Found at i:5966087 original size:31 final size:31
Alignment explanation
Indices: 5966046--5966120 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
5966036 AAAAAAACTT
*
5966046 AATAACTCAATGACCTAAATAAAAACCTTCA
1 AATAATTCAATGACCTAAATAAAAACCTTCA
* ** * ** *
5966077 AATAATTCAATAATTTAAATGAAAATTTTTA
1 AATAATTCAATGACCTAAATAAAAACCTTCA
5966108 AATAATTCAATGA
1 AATAATTCAATGA
5966121 TCATTTTGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (31 bp):
AATAATTCAATGACCTAAATAAAAACCTTCA
Found at i:5977751 original size:132 final size:132
Alignment explanation
Indices: 5977514--5977764 Score: 353
Period size: 132 Copynumber: 1.9 Consensus size: 132
5977504 CTTTCCCACC
* * * *
5977514 GATTCGGATTTCACCTTGCTCGAATCATAATAGTGTACACCAGGCACAGTTTTTTCAGATTGCAA
1 GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
* * *
5977579 TGAACGAAAGGAGTTAGAACTCTTATGATCATCAATGGGATG-TTTGAAGGAAGATTTGCTTCTC
66 CGAACGAAAGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTG-AGGAAGATTTGCTTCTC
5977643 ACT
130 ACT
* * *
5977646 GATTCAGATTTCACCTTACTCGAGTCATAATAGTGTGCACCAGGCACAGGTTTTTCATATTCCAA
1 GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
* * *
5977711 CGAAGCG-ATGGAATCAGAAGTCTTATGATCATCGATGGGATGCTTTGAGGAAGA
66 CGAA-CGAAAGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGA
5977765 CTTGATTGCA
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
132 98 0.94
133 6 0.06
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (132 bp):
GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
CGAACGAAAGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGATTTGCTTCTCA
CT
Found at i:5977937 original size:150 final size:150
Alignment explanation
Indices: 5977646--5977981 Score: 399
Period size: 150 Copynumber: 2.2 Consensus size: 150
5977636 GCTTCTCACT
* * * * *
5977646 GATTCAGATTTCACCTTACTCGAGTCATAATAGTGTGCACCAGGCACAGGTTTTTCATATTCCAA
1 GATTCGGATTTCACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTTTTCATATTCCAA
* * *
5977711 CGAAGCGATGGAATCAGAAGTCTTATGATCATCGATGGGATGCTTTGAGGAAGACTTGATTGCAG
66 CGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGATTGCAG
* * *
5977776 TTGTCAGAATCTTTCCCACC
131 CTGCCAAAATCTTTCCCACC
* *
5977796 GATTCGGATTTTACCTTACTAGAATCATAATAGTGTACACCAGACACA-GTTTGTTCGTATTCCA
1 GATTCGGATTTCACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTT-TTCATATTCCA
* ** * * *
5977860 ATGAAGCAATGGAATTGGAACTCTTATGGTCATCAATGGGATG-TTTGAAGGAAGATTTGCTTGC
65 ACGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTG-AGGAAGACTTGATTG-
**
5977924 CA-CTGCCAAAATCTTTCCCGTC
128 CAGCTGCCAAAATCTTTCCCACC
* * * *
5977946 AATTCGGATTTCATCTTGCTTGAATCATAATAGTGT
1 GATTCGGATTTCACCTTACTAGAATCATAATAGTGT
5977982 TTTGCTATAT
Statistics
Matches: 157, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
149 8 0.05
150 147 0.94
151 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (150 bp):
GATTCGGATTTCACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTTTTCATATTCCAA
CGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGATTGCAG
CTGCCAAAATCTTTCCCACC
Found at i:5979189 original size:14 final size:14
Alignment explanation
Indices: 5979172--5979210 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5979162 CTCTTTTCTT
*
5979172 TTTCTTTTTTTTCC
1 TTTCTTTTTTTTAC
*
5979186 TTTCTTTCTTTTAC
1 TTTCTTTTTTTTAC
*
5979200 TTTATTTTTTT
1 TTTCTTTTTTT
5979211 GTTTCCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTTTTTTTAC
Found at i:5981579 original size:5 final size:5
Alignment explanation
Indices: 5981571--5981636 Score: 50
Period size: 5 Copynumber: 14.0 Consensus size: 5
5981561 AAAATAAAAT
* * * * *
5981571 TTAAG TTAAA TTAAA TTGAG TAAAA TT-AT TTAAA TTAAA TTAAA --AAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
*
5981618 TTAAA -TATA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA
5981637 ATTTTATTAC
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
3 3 0.07
4 6 0.13
5 37 0.80
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (5 bp):
TTAAA
Found at i:5981613 original size:10 final size:10
Alignment explanation
Indices: 5981548--5981636 Score: 51
Period size: 10 Copynumber: 9.2 Consensus size: 10
5981538 AATTTTTTAT
**
5981548 AATTAAATCG
1 AATTAAATTA
* *
5981558 AATAAAATAA
1 AATTAAATTA
*
5981568 AATTTAAGTTA
1 AA-TTAAATTA
*
5981579 AATTAAATTG
1 AATTAAATTA
* *
5981589 AGTAAAATT-
1 AATTAAATTA
*
5981598 ATTTAAATTA
1 AATTAAATTA
5981608 AATTAAA--A
1 AATTAAATTA
5981616 AATTAAA-TA
1 AATTAAATTA
*
5981625 TATTAAATTA
1 AATTAAATTA
5981635 AA
1 AA
5981637 ATTTTATTAC
Statistics
Matches: 60, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
8 8 0.13
9 14 0.23
10 31 0.52
11 7 0.12
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (10 bp):
AATTAAATTA
Found at i:5981620 original size:22 final size:22
Alignment explanation
Indices: 5981566--5981637 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
5981556 CGAATAAAAT
*
5981566 AAAATTTAAGTTAAATTAAATTGA
1 AAAAATTAA-TTAAATTAAATT-A
* *
5981590 GTAAAATTATTTAAATTAAATTA
1 -AAAAATTAATTAAATTAAATTA
* *
5981613 AAAAATTAAATATATTAAATTA
1 AAAAATTAATTAAATTAAATTA
5981635 AAA
1 AAA
5981638 TTTTATTACA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
22 21 0.52
23 1 0.03
24 12 0.30
25 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAAATTAATTAAATTAAATTA
Found at i:5984518 original size:28 final size:29
Alignment explanation
Indices: 5984473--5984534 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
5984463 GTATTTTTGA
*
5984473 TAAAAAAGTGAAATTTAAATTTTATAT-T
1 TAAAAAAGTGAAAATTAAATTTTATATCT
* * *
5984501 TAAAAAATTTAAAATTAAATTTTTTATCT
1 TAAAAAAGTGAAAATTAAATTTTATATCT
5984530 TAAAA
1 TAAAA
5984535 TTTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (29 bp):
TAAAAAAGTGAAAATTAAATTTTATATCT
Found at i:5984539 original size:21 final size:22
Alignment explanation
Indices: 5984509--5984568 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 22
5984499 TTTAAAAAAT
5984509 TTAAAA-TTAAATTTTTTATC-
1 TTAAAATTTAAATTTTTTATCA
*
5984529 TTAAAATTTAAA--TTTAATCA
1 TTAAAATTTAAATTTTTTATCA
5984549 TTAAAATTGTAAAGTTTTTT
1 TTAAAATT-TAAA-TTTTTT
5984569 TTTTAAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 6 0.19
20 14 0.44
21 9 0.28
24 3 0.09
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (22 bp):
TTAAAATTTAAATTTTTTATCA
Found at i:5987635 original size:16 final size:17
Alignment explanation
Indices: 5987614--5987648 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5987604 TTTAAATTTT
5987614 TTAAAATAATTA-AAAA
1 TTAAAATAATTATAAAA
*
5987630 TTAAAATATTTATAAAA
1 TTAAAATAATTATAAAA
5987647 TT
1 TT
5987649 CCAAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAATAATTATAAAA
Found at i:5987681 original size:10 final size:9
Alignment explanation
Indices: 5987613--5987702 Score: 51
Period size: 9 Copynumber: 9.8 Consensus size: 9
5987603 TTTTAAATTT
5987613 TTTAAAATA
1 TTTAAAATA
*
5987622 ATTAAAA-A
1 TTTAAAATA
5987630 -TTAAAATA
1 TTTAAAATA
5987638 TTTATAAA-A
1 TTTA-AAATA
** *
5987647 TTCCAAATT
1 TTTAAAATA
*
5987656 TTTATATATA
1 TTTA-AAATA
5987666 TTTAAAATA
1 TTTAAAATA
*
5987675 TTATAAAAATC
1 TT-T-AAAATA
*
5987686 TTTAAAAAA
1 TTTAAAATA
5987695 TTCTAAAA
1 TT-TAAAA
5987703 AATATATTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
7 6 0.10
8 5 0.08
9 26 0.43
10 17 0.28
11 7 0.11
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (9 bp):
TTTAAAATA
Found at i:5987691 original size:20 final size:20
Alignment explanation
Indices: 5987666--5987703 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5987656 TTTATATATA
*
5987666 TTTAAAATATTATAAAAATC
1 TTTAAAAAATTATAAAAATC
*
5987686 TTTAAAAAATTCTAAAAA
1 TTTAAAAAATTATAAAAA
5987704 ATATATTAAA
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:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTAAAAAATTATAAAAATC
Found at i:5988873 original size:16 final size:16
Alignment explanation
Indices: 5988852--5988887 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
5988842 GCAGGCTGCA
5988852 ATCAGTCCAGATGGAG
1 ATCAGTCCAGATGGAG
5988868 ATCAGTCCAGATGGAG
1 ATCAGTCCAGATGGAG
5988884 ATCA
1 ATCA
5988888 CGTATTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.19
Consensus pattern (16 bp):
ATCAGTCCAGATGGAG
Found at i:5997635 original size:32 final size:32
Alignment explanation
Indices: 5997594--5997660 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
5997584 TTATATGGGC
5997594 ATAGGAATGCTTTAAAGTTAACCTGAGATCAA
1 ATAGGAATGCTTTAAAGTTAACCTGAGATCAA
*
5997626 ATAGGAATGCTTTAAAGTTAACCTGAGATCGA
1 ATAGGAATGCTTTAAAGTTAACCTGAGATCAA
5997658 ATA
1 ATA
5997661 AGAACTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (32 bp):
ATAGGAATGCTTTAAAGTTAACCTGAGATCAA
Found at i:5998353 original size:23 final size:23
Alignment explanation
Indices: 5998340--5998392 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
5998330 AATCAAGCAT
*
5998340 ATTCAAGGATCAAACTCAAGAAC
1 ATTCAAAGATCAAACTCAAGAAC
5998363 ATTCAAAGATCAAACTCAAGAAC
1 ATTCAAAGATCAAACTCAAGAAC
5998386 ATTCAAA
1 ATTCAAA
5998393 TTAAGCACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.51, C:0.21, G:0.09, T:0.19
Consensus pattern (23 bp):
ATTCAAAGATCAAACTCAAGAAC
Found at i:5999347 original size:5 final size:5
Alignment explanation
Indices: 5999337--5999372 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
5999327 AATAATTAAG
5999337 TATAT TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
5999373 ATAAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:5999434 original size:31 final size:30
Alignment explanation
Indices: 5999399--5999460 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
5999389 AGTTAAAAGA
*
5999399 AGAAAGCAAACGAAAC-AGAGAAGAACAGGGG
1 AGAAAG-AAACGAAACAAGA-AAGAAAAGGGG
* *
5999430 AGAAAGAAAGGAAAGAAGAAAGAAAAGGGG
1 AGAAAGAAACGAAACAAGAAAGAAAAGGGG
5999460 A
1 A
5999461 AATAAGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.60, C:0.06, G:0.34, T:0.00
Consensus pattern (30 bp):
AGAAAGAAACGAAACAAGAAAGAAAAGGGG
Found at i:6007766 original size:22 final size:22
Alignment explanation
Indices: 6007739--6007784 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
6007729 GTATATTTAT
6007739 TTTAGGTTTAATATTTGATGAA
1 TTTAGGTTTAATATTTGATGAA
6007761 TTTAGGTTTAATATTTGATGAA
1 TTTAGGTTTAATATTTGATGAA
6007783 TT
1 TT
6007785 GTGACACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (22 bp):
TTTAGGTTTAATATTTGATGAA
Found at i:6007896 original size:14 final size:14
Alignment explanation
Indices: 6007873--6007913 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
6007863 GATTATAATG
*
6007873 TTTAGATATTTTAT
1 TTTAAATATTTTAT
*
6007887 TTTAATTATTTTA-
1 TTTAAATATTTTAT
6007900 TTTAAATATTTTAT
1 TTTAAATATTTTAT
6007914 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTAAATATTTTAT
Found at i:6007909 original size:13 final size:13
Alignment explanation
Indices: 6007873--6007918 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
6007863 GATTATAATG
*
6007873 TTTAGATATTTTA
1 TTTAAATATTTTA
*
6007886 TTTTAATTATTTTA
1 -TTTAAATATTTTA
6007900 TTTAAATATTTTA
1 TTTAAATATTTTA
*
6007913 TATAAA
1 TTTAAA
6007919 AATAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTAAATATTTTA
Found at i:6010127 original size:23 final size:23
Alignment explanation
Indices: 6010100--6010144 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6010090 AATTGTAAAA
*
6010100 TTAAATGTTTAAAATTTATTATG
1 TTAAAAGTTTAAAATTTATTATG
*
6010123 TTAAAAGTTTAAATTTTATTAT
1 TTAAAAGTTTAAAATTTATTAT
6010145 TGATGAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (23 bp):
TTAAAAGTTTAAAATTTATTATG
Found at i:6013731 original size:31 final size:29
Alignment explanation
Indices: 6013670--6013729 Score: 75
Period size: 32 Copynumber: 2.0 Consensus size: 29
6013660 TTAAAATTTT
*
6013670 TTATATTAATTTTATTATTTTAATTAAAA
1 TTATATTAATTTTATTATTTTAAATAAAA
*
6013699 TTATATTTAATTTTTATATTTTTTAAATAAA
1 TTATA-TTAA-TTTTAT-TATTTTAAATAAA
6013730 TTTGTTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 6 0.23
32 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TTATATTAATTTTATTATTTTAAATAAAA
Found at i:6013972 original size:17 final size:16
Alignment explanation
Indices: 6013950--6013991 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
6013940 AGTAAAAATG
6013950 TAATTTTATTATTTTAA
1 TAATTTTATT-TTTTAA
*
6013967 TAATTTATATTTTTTTA
1 TAATTT-TATTTTTTAA
6013984 TAATTTTA
1 TAATTTTA
6013992 AAAGATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 17 0.74
18 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TAATTTTATTTTTTAA
Found at i:6013984 original size:23 final size:24
Alignment explanation
Indices: 6013921--6013984 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 24
6013911 GGAGGGTTAG
*
6013921 AAATTTATATTTTTATATTAGTAA
1 AAATTTATATTTTTTTATTAGTAA
* * *
6013945 AAATGTA-ATTTTATTATT-TTAA
1 AAATTTATATTTTTTTATTAGTAA
*
6013967 TAATTTATATTTTTTTAT
1 AAATTTATATTTTTTTAT
6013985 AATTTTAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 8 0.25
23 18 0.56
24 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (24 bp):
AAATTTATATTTTTTTATTAGTAA
Found at i:6020256 original size:9 final size:8
Alignment explanation
Indices: 6020226--6020255 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
6020216 GATTAATTTT
6020226 TTTTTTAA
1 TTTTTTAA
6020234 TTTTTTAA
1 TTTTTTAA
*
6020242 ATTTTTAA
1 TTTTTTAA
6020250 TTTTTT
1 TTTTTT
6020256 TTCTCTTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTAA
Found at i:6021410 original size:102 final size:100
Alignment explanation
Indices: 6021231--6021518 Score: 305
Period size: 102 Copynumber: 2.8 Consensus size: 100
6021221 TTAAATTGCT
* * * *
6021231 TATTTTAAATCTGTTTTTACGTATTATTT-TTTTAAAAAATAGTTTTAT-TACTTAGTTTAAATT
1 TATTTTAAAT-TG-TTTTACATATTATTTATCTT--AAACT-GTTTTATATACTTACTTTAAATT
*
6021294 GTTCTATATATTATTTATCTTTAAAATGTTTTGTATATTATG
61 GTT-TATATATTATTTAT-TTTAAAATGCTTTGTATATTATG
*
6021336 TATTTTAAATTTCTTTTTACATATTATTTATCTTAAACT-TTTTATATA-TTACTTTAAATTGTC
1 TATTTTAAA-TT-GTTTTACATATTATTTATCTTAAACTGTTTTATATACTTACTTTAAATTGT-
* *
6021399 TTATATATTATTTATTTTAAATTGCTTTGTATATTATT
63 TTATATATTATTTATTTTAAAATGCTTTGTATATTATG
* * * * *
6021437 TGTTTTAAATTGTTTTACATATTATTTATTTTAAATTGTTTTATACTATTTACTTCAAATTGTTT
1 TATTTTAAATTGTTTTACATATTATTTATCTTAAACTGTTTTATA-TACTTACTTTAAATTG-TT
*
6021502 TATACATTATTTTATTT
64 TATATATTA-TTTATTT
6021519 CATTTTCTTT
Statistics
Matches: 159, Mismatches: 14, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
99 23 0.14
100 9 0.06
101 30 0.19
102 54 0.34
103 11 0.07
104 4 0.03
105 24 0.15
106 4 0.03
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (100 bp):
TATTTTAAATTGTTTTACATATTATTTATCTTAAACTGTTTTATATACTTACTTTAAATTGTTTA
TATATTATTTATTTTAAAATGCTTTGTATATTATG
Found at i:6021415 original size:75 final size:74
Alignment explanation
Indices: 6021312--6021464 Score: 184
Period size: 75 Copynumber: 2.1 Consensus size: 74
6021302 TATTATTTAT
* * * *
6021312 CTTTAAAATGTTTTGTATATTATGTATTTTAAATTTCTTTTTACATATTATTTATCTTAAACT-T
1 CTTTAAAATGTCTTATATATTATGTATTTTAAATTGCTTTGT--ATATTATTTATCTTAAACTGT
*
6021376 TTTATATATTA
64 TTTACATATTA
* * * * *
6021387 CTTTAAATTGTCTTATATATTATTTATTTTAAATTGCTTTGTATATTATTTGTTTTAAATTGTTT
1 CTTTAAAATGTCTTATATATTATGTATTTTAAATTGCTTTGTATATTATTTATCTTAAACTGTTT
6021452 TACATATTA
66 TACATATTA
6021461 -TTTA
1 CTTTA
6021465 TTTTAAATTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
73 20 0.30
74 11 0.16
75 36 0.54
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.59
Consensus pattern (74 bp):
CTTTAAAATGTCTTATATATTATGTATTTTAAATTGCTTTGTATATTATTTATCTTAAACTGTTT
TACATATTA
Found at i:6021418 original size:26 final size:25
Alignment explanation
Indices: 6021276--6021518 Score: 199
Period size: 26 Copynumber: 9.5 Consensus size: 25
6021266 AAAATAGTTT
* *
6021276 TATTACTTAGTTTAAATTGTTCTATA
1 TATTATTTATTTTAAATTGTT-TATA
* *
6021302 TATTATTTATCTTTAAAATGTTTTGTA
1 TATTATTTAT-TTTAAATTG-TTTATA
* * *
6021329 TATTATGTATTTTAAATTTCTTTTTACA
1 TATTATTTATTTTAAA--T-TGTTTATA
* *
6021357 TATTATTTATCTTAAACT-TTT-TA
1 TATTATTTATTTTAAATTGTTTATA
*
6021380 TA-TA-TTACTTTAAATTGTCTTATA
1 TATTATTTATTTTAAATTGT-TTATA
*
6021404 TATTATTTATTTTAAATTGCTTTGTA
1 TATTATTTATTTTAAATTG-TTTATA
* *
6021430 TATTATTTGTTTTAAATTGTTTTACA
1 TATTATTTATTTTAAATTG-TTTATA
6021456 TATTATTTATTTTAAATTGTTT-TA
1 TATTATTTATTTTAAATTGTTTATA
* * *
6021480 TACTATTTACTTCAAATTGTTTTATA
1 TATTATTTATTTTAAATTG-TTTATA
*
6021506 CATTATTTTATTT
1 TATTA-TTTATTT
6021519 CATTTTCTTT
Statistics
Matches: 173, Mismatches: 30, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
21 9 0.05
22 3 0.02
23 5 0.03
24 24 0.14
25 9 0.05
26 75 0.43
27 27 0.16
28 20 0.12
29 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (25 bp):
TATTATTTATTTTAAATTGTTTATA
Found at i:6021460 original size:52 final size:52
Alignment explanation
Indices: 6021276--6021518 Score: 239
Period size: 50 Copynumber: 4.7 Consensus size: 52
6021266 AAAATAGTTT
* * * * *
6021276 TATTACTTAGTTTAAATTGTTCTATATATTATTTATCTTTAAAATGTTTTGTA
1 TATTATTTACTTTAAATTGTTTTATATATTATTTAT-TTTAAATTGCTTTGTA
* * * * * *
6021329 TATTATGTATTTTAAATTTCTTTTTACATATTATTTATCTTAAA---CTTTTTA
1 TATTATTTACTTTAAA-TT-GTTTTATATATTATTTATTTTAAATTGCTTTGTA
*
6021380 TA-TA-TTACTTTAAATTGTCTTATATATTATTTATTTTAAATTGCTTTGTA
1 TATTATTTACTTTAAATTGTTTTATATATTATTTATTTTAAATTGCTTTGTA
** *
6021430 TATTATTTGTTTTAAATTGTTTTACATATTATTTATTTTAAATTG-TTT-TA
1 TATTATTTACTTTAAATTGTTTTATATATTATTTATTTTAAATTGCTTTGTA
* * *
6021480 TACTATTTACTTCAAATTGTTTTATACATTATTTTATTT
1 TATTATTTACTTTAAATTGTTTTATATATTA-TTTATTT
6021519 CATTTTCTTT
Statistics
Matches: 156, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
47 20 0.13
48 2 0.01
49 8 0.05
50 37 0.24
51 19 0.12
52 35 0.22
53 13 0.08
54 7 0.04
55 15 0.10
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (52 bp):
TATTATTTACTTTAAATTGTTTTATATATTATTTATTTTAAATTGCTTTGTA
Found at i:6042338 original size:96 final size:96
Alignment explanation
Indices: 6042147--6042331 Score: 264
Period size: 96 Copynumber: 1.9 Consensus size: 96
6042137 GGGGCTGTTG
* * * * * *
6042147 CTGCTGTGTAGGAGGCATTGGGAAGTGTTGACTTGGAGCCTCCTGAGTTTGGCCAGGTGGTGTAT
1 CTGCTGAGTAGGAGGCATAGGGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGGGGAGTAT
*
6042212 AGTAAGCATCTCGCTGAGGGACAGATGGAAC
66 AGTAAGCATCTCGCTGAGCGACAGATGGAAC
* * *
6042243 CTGCTGAGTAGGAGGCATAGGGAATTGCTGACTTGGAATCTCCTGAGTTTGGGCAGGGGGAGTAT
1 CTGCTGAGTAGGAGGCATAGGGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGGGGAGTAT
6042308 AGTAAGCATCTC-CTTGAGCGACAG
66 AGTAAGCATCTCGC-TGAGCGACAG
6042332 GAGGAACTTG
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 1 0.01
96 77 0.99
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (96 bp):
CTGCTGAGTAGGAGGCATAGGGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGGGGAGTAT
AGTAAGCATCTCGCTGAGCGACAGATGGAAC
Found at i:6046333 original size:17 final size:16
Alignment explanation
Indices: 6046307--6046347 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
6046297 AGAAATAAGA
6046307 TTTT-TATTTTTTACT
1 TTTTCTATTTTTTACT
*
6046322 TTTTGCTATTTTTTAGT
1 TTTT-CTATTTTTTACT
6046339 TTTTCTATT
1 TTTTCTATT
6046348 CTATCACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 5 0.22
17 14 0.61
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTTCTATTTTTTACT
Found at i:6047013 original size:24 final size:24
Alignment explanation
Indices: 6046962--6047015 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
6046952 TTTATTTTTG
*
6046962 AATTTTATATATATTAATTTTTTA
1 AATTTTATATATATTAATTTCTTA
6046986 AATTTTATA-ATA-TATATTTCTTA
1 AATTTTATATATATTA-ATTTCTTA
6047009 TAATTTT
1 -AATTTT
6047016 TCTGGAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 10 0.37
24 15 0.56
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
AATTTTATATATATTAATTTCTTA
Found at i:6050504 original size:17 final size:17
Alignment explanation
Indices: 6050478--6050511 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6050468 ATATTTAATT
*
6050478 TTTAAGATTAAATTTTA
1 TTTAAAATTAAATTTTA
6050495 TTTAAAATTAAATTTTA
1 TTTAAAATTAAATTTTA
6050512 AAAATGCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAAATTAAATTTTA
Found at i:6051391 original size:21 final size:22
Alignment explanation
Indices: 6051339--6051391 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
6051329 TTTATTGTTG
*
6051339 AAAATATTATATTAAAATAATT
1 AAAATATTATATGAAAATAATT
* *
6051361 AAAATAATTAT-TGAATATATTT
1 AAAAT-ATTATATGAAAATAATT
6051383 AAAATATTA
1 AAAATATTA
6051392 AATGTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 18 0.67
23 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAATATTATATGAAAATAATT
Found at i:6053488 original size:11 final size:11
Alignment explanation
Indices: 6053472--6053510 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6053462 TATCTCATTA
*
6053472 TTATTTTATTG
1 TTATTTTGTTG
*
6053483 TTATTTCGTTG
1 TTATTTTGTTG
6053494 TTATTTTGTTG
1 TTATTTTGTTG
*
6053505 TCATTT
1 TTATTT
6053511 CATTATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.13, C:0.05, G:0.13, T:0.69
Consensus pattern (11 bp):
TTATTTTGTTG
Found at i:6053519 original size:22 final size:22
Alignment explanation
Indices: 6053466--6053519 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
6053456 TTTTACTATC
*
6053466 TCATTATTATTTTATTGTTATT
1 TCATTATTATTTTATTGTCATT
* * *
6053488 TCGTTGTTATTTTGTTGTCATT
1 TCATTATTATTTTATTGTCATT
6053510 TCATTATTAT
1 TCATTATTAT
6053520 AAAGTTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.07, G:0.09, T:0.65
Consensus pattern (22 bp):
TCATTATTATTTTATTGTCATT
Found at i:6053921 original size:91 final size:91
Alignment explanation
Indices: 6053766--6053947 Score: 283
Period size: 91 Copynumber: 2.0 Consensus size: 91
6053756 TTTTTTTTTA
* *
6053766 AATATGGACAGGTCGTATCAAGCTCAAATTTAGCATTTTTAATCTAGTTCAAGTTTGGACAAAAT
1 AATATGGACAGGTCGTATCAAGCTCAAATTTAGCATTTTTAATCTAGTTCAAATTTAGACAAAAT
6053831 TTTAGGCCCATTTTTCGACCCGAATC
66 TTTAGGCCCATTTTTCGACCCGAATC
* * * * *
6053857 AATATGGGCAGGTCTTATTAAGCTCGAATTTAGCATTTTTAATCTAGTTTAAATTTAGACAAAAT
1 AATATGGACAGGTCGTATCAAGCTCAAATTTAGCATTTTTAATCTAGTTCAAATTTAGACAAAAT
* *
6053922 TTTAGGCCTATTTTTCGACCTGAATC
66 TTTAGGCCCATTTTTCGACCCGAATC
6053948 CGAGTCTGAA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (91 bp):
AATATGGACAGGTCGTATCAAGCTCAAATTTAGCATTTTTAATCTAGTTCAAATTTAGACAAAAT
TTTAGGCCCATTTTTCGACCCGAATC
Done.