Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 18
Found at i:2219549 original size:65 final size:63
Alignment explanation
Indices: 2219480--2219602 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 63
2219470 TGCATTACCC
* * *
2219480 ATGCATCGATACACAAATTACCTTTGATGTTTTCATT-TTTAAAGGGATGCATCGATGCACTCTT
1 ATGCATCGATACACAAATTACATTCGATG-TTTC-TTCTTTAAAGAG-TGCATCGATGCACTCTT
2219544 T
63 T
* * * *
2219545 ATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGAGTGTATCGATGCAC
1 ATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGAGTGCATCGATGCAC
2219603 ATTGATGCAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
63 14 0.28
64 12 0.24
65 24 0.48
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (63 bp):
ATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGAGTGCATCGATGCACTCTTT
Found at i:2228444 original size:19 final size:18
Alignment explanation
Indices: 2228408--2228446 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2228398 GGGTGGATTA
2228408 TGCCATAACAAATTTTTT
1 TGCCATAACAAATTTTTT
2228426 TGCCATAACAAATTTTTT
1 TGCCATAACAAATTTTTT
2228444 TGC
1 TGC
2228447 AGAAGCCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.44
Consensus pattern (18 bp):
TGCCATAACAAATTTTTT
Found at i:2228950 original size:12 final size:12
Alignment explanation
Indices: 2228935--2228985 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
2228925 CCTGAAAAAG
*
2228935 ACAAGGAAAATA
1 ACAAGTAAAATA
2228947 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
*
2228960 TACAA-AAAAATGA
1 -ACAAGTAAAAT-A
2228973 ACAAGTAAAATA
1 ACAAGTAAAATA
2228985 A
1 A
2228986 AAATGCTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 16 0.50
13 12 0.38
14 4 0.12
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.14
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:2230680 original size:18 final size:18
Alignment explanation
Indices: 2230653--2230705 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
2230643 AGGGATTATC
* *
2230653 AGTGGACCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
*
2230671 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
* *
2230689 TGTGGTCTTTCGGGACA
1 AGTGGTCCTTCGGGACA
2230706 AATATTCAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2264187 original size:64 final size:64
Alignment explanation
Indices: 2264119--2264275 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 64
2264109 TTGAAGGTGT
** *
2264119 ATCGATGCACAGGTAGTGCATCGATGCATT-CTTTTAA-AATAAAGAGATCGAATGCA-ATTAGT
1 ATCGATGCACAGGTAGTGCATCGATGCATTAC-AATAATAATAAA-ACATCGAATGCATATTA-T
2264181 GC
63 GC
* * *
2264183 ATCGATGCATAAGGCA-TGCATCGATGCATTACAATAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCATTACAATAATAATAAAACATCGAATGCATATTATGC
* *
2264247 ACCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACAGGTAGTGCATCGATGCAT
2264276 ACCTTCATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
63 3 0.04
64 61 0.78
65 14 0.18
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATTACAATAATAATAAAACATCGAATGCATATTATGC
Found at i:2264828 original size:15 final size:15
Alignment explanation
Indices: 2264804--2264841 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2264794 GAGGGTATAA
2264804 TAGTCATTCGGGACG
1 TAGTCATTCGGGACG
* *
2264819 TAGTCCTTCGGGATG
1 TAGTCATTCGGGACG
2264834 TAGT-ATTC
1 TAGTCATTC
2264842 CTACGGGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.34
Consensus pattern (15 bp):
TAGTCATTCGGGACG
Found at i:2268720 original size:25 final size:25
Alignment explanation
Indices: 2268692--2268760 Score: 138
Period size: 25 Copynumber: 2.8 Consensus size: 25
2268682 TATATATATA
2268692 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
2268717 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
2268742 TCCCGAAGGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
2268761 CCCTCTACCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:2269255 original size:20 final size:20
Alignment explanation
Indices: 2269227--2269267 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2269217 TTTTTATATG
*
2269227 GGGGAATCGGTTCCCCCCTA
1 GGGGAATCGATTCCCCCCTA
* *
2269247 GGGGTATCGATTCCCCTCTA
1 GGGGAATCGATTCCCCCCTA
2269267 G
1 G
2269268 CATTCTGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.24
Consensus pattern (20 bp):
GGGGAATCGATTCCCCCCTA
Found at i:2272173 original size:64 final size:64
Alignment explanation
Indices: 2272020--2272173 Score: 179
Period size: 64 Copynumber: 2.4 Consensus size: 64
2272010 AAGGTGTATT
* * * * * *
2272020 GATGCACAGGTAGTGCATCGATGCACTCTTTTCAAATAAAGATATCGAATGCAATTAGTGCATC
1 GATGCACAAGTAGTGCATCGATGCATTCTATTAAAATAAAGACATCGAATGCAATTAGTGCACC
* * *
2272084 GATGCATAAGGCA-TGCATCGATGCATTCTATTAATAATAAA-ACATCGAATGCATTTTA-TGCA
1 GATGCACAA-GTAGTGCATCGATGCATTCTATTAA-AATAAAGACATCGAATGCA-ATTAGTGCA
2272146 CC
63 CC
2272148 GATGCACAAGTAGTGCATCGATGCAT
1 GATGCACAAGTAGTGCATCGATGCAT
2272174 ACCTTCATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
63 2 0.03
64 62 0.83
65 11 0.15
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (64 bp):
GATGCACAAGTAGTGCATCGATGCATTCTATTAAAATAAAGACATCGAATGCAATTAGTGCACC
Found at i:2287783 original size:243 final size:244
Alignment explanation
Indices: 2287260--2287769 Score: 943
Period size: 243 Copynumber: 2.1 Consensus size: 244
2287250 TACATCAAAT
2287260 AAATTATTAATATAAAAATTAATTTATTTAAATTTATAATACTTCTGATACTCGAAAAGATAGTG
1 AAATTATTAATATAAAAATTAATTTATTTAAATTTATAATACTTCTGATACTCGAAAAGATAGTG
2287325 TGAATATTATATAAACATTTGTAAAATGATTTAATAAAAAATATATACAAAATATAAGATAATTT
66 TGAATATTATATAAACATTTGTAAAATGATTTAATAAAAAATATATACAAAATATAAGATAATTT
2287390 AAGATATGATGCATAATAAAAAAAAATTCCGAATTGCACCACCATGATAAGCTAAATATAATATA
131 AAGATATGATGCATAATAAAAAAAAATTCCGAATTGCACCACCATGATAAGCTAAATATAATATA
2287455 ATATAATAATAATTCACAAATGCATACGCAACTCCAAACTGTCATATAA
196 ATATAATAATAATTCACAAATGCATACGCAACTCCAAACTGTCATATAA
2287504 AAATTATTAATAT-AAAATTAATTTATTTAAATTTATAATACTTCTGATACTCGAAAAGATAGTG
1 AAATTATTAATATAAAAATTAATTTATTTAAATTTATAATACTTCTGATACTCGAAAAGATAGTG
2287568 TGAATATTATATAAACATTTGTAAAATGATTTAATAAAAAATATATACAAAATATAAGATAATTT
66 TGAATATTATATAAACATTTGTAAAATGATTTAATAAAAAATATATACAAAATATAAGATAATTT
*
2287633 AAGATATGATGCATAAT-AAAAAAAATTCTGAATTGCACCACCATGATAAGCTAAATATAATATA
131 AAGATATGATGCATAATAAAAAAAAATTCCGAATTGCACCACCATGATAAGCTAAATATAATATA
*
2287697 ATATAATAATAATTCACAAATGCATATGCAACTCCAAACTGTCATATAA
196 ATATAATAATAATTCACAAATGCATACGCAACTCCAAACTGTCATATAA
* *
2287746 CAATTTCTTAATATGTAAAAATTA
1 -AAATTATTAATA--TAAAAATTA
2287770 TATATTAATT
Statistics
Matches: 258, Mismatches: 4, Indels: 6
0.96 0.01 0.02
Matches are distributed among these distances:
242 94 0.36
243 143 0.55
244 13 0.05
245 1 0.00
246 7 0.03
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (244 bp):
AAATTATTAATATAAAAATTAATTTATTTAAATTTATAATACTTCTGATACTCGAAAAGATAGTG
TGAATATTATATAAACATTTGTAAAATGATTTAATAAAAAATATATACAAAATATAAGATAATTT
AAGATATGATGCATAATAAAAAAAAATTCCGAATTGCACCACCATGATAAGCTAAATATAATATA
ATATAATAATAATTCACAAATGCATACGCAACTCCAAACTGTCATATAA
Found at i:2288106 original size:20 final size:20
Alignment explanation
Indices: 2288081--2288119 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2288071 CTAAAATTTA
*
2288081 AAATTTTTAATTTATTCATT
1 AAATTTTTAATTTACTCATT
2288101 AAATTTTTAATTTACTCAT
1 AAATTTTTAATTTACTCAT
2288120 ATTTTGATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATTTTTAATTTACTCATT
Found at i:2288719 original size:7 final size:7
Alignment explanation
Indices: 2288676--2288720 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
2288666 ATTTCGTCCT
2288676 TATATTA
1 TATATTA
*
2288683 TATAATA
1 TATATTA
2288690 TATATT-
1 TATATTA
2288696 TATATTA
1 TATATTA
*
2288703 TA-AAT-
1 TATATTA
2288708 TATATTA
1 TATATTA
2288715 TATATT
1 TATATT
2288721 TATTCATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
5 2 0.06
6 10 0.32
7 19 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATTA
Found at i:2288723 original size:20 final size:20
Alignment explanation
Indices: 2288675--2288720 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2288665 AATTTCGTCC
2288675 TTATATTATATAATATATAT
1 TTATATTATATAATATATAT
2288695 TTATATTATA-AAT-TATAT
1 TTATATTATATAATATATAT
2288713 TATATATT
1 T-TATATT
2288721 TATTCATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.24
19 9 0.36
20 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATATTATATAATATATAT
Found at i:2290003 original size:57 final size:57
Alignment explanation
Indices: 2289893--2290006 Score: 133
Period size: 57 Copynumber: 2.0 Consensus size: 57
2289883 ATCATTATTA
* * * **
2289893 TTTTTTTTACTATTTACGTATAAATATATTATCATTATTTTTTTCTTTTTTTTCCTC
1 TTTTTATTACTATTAACGTATAAATATATTATCATTATTTTTTTATTGGTTTTCCTC
* *
2289950 TTTTTATTACTATTAACGTATATATATA-TATTC-TTTTGTTTTTTATTGGTTTTCCTC
1 TTTTTATTACTATTAACGTATAAATATATTA-TCATTAT-TTTTTTATTGGTTTTCCTC
2290007 ATGATTAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
56 5 0.10
57 43 0.90
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.63
Consensus pattern (57 bp):
TTTTTATTACTATTAACGTATAAATATATTATCATTATTTTTTTATTGGTTTTCCTC
Found at i:2290170 original size:2 final size:2
Alignment explanation
Indices: 2290163--2290198 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2290153 AAATATTTAT
2290163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2290199 GTTTACATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2292959 original size:30 final size:30
Alignment explanation
Indices: 2292925--2292983 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
2292915 AAGATAAAGT
*
2292925 AGACAAATTAGAAAGAGAGCAGAAAAGAGC
1 AGACAAACTAGAAAGAGAGCAGAAAAGAGC
*
2292955 AGACAAACTGGAAAGAGAGCAGAAAAGAG
1 AGACAAACTAGAAAGAGAGCAGAAAAGAG
2292984 TTCGTTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.56, C:0.10, G:0.29, T:0.05
Consensus pattern (30 bp):
AGACAAACTAGAAAGAGAGCAGAAAAGAGC
Found at i:2309318 original size:6 final size:6
Alignment explanation
Indices: 2309307--2309362 Score: 51
Period size: 6 Copynumber: 8.5 Consensus size: 6
2309297 TAAATTGAAG
2309307 AAAGAA AAAGAAA AAGAGAA AAAGAAA AAAGAACA AAAGAA AAA-AGA
1 AAAGAA AAAG-AA AA-AGAA AAAG-AA AAAG-A-A AAAGAA AAAGA-A
2309354 AAAGAA AAA
1 AAAGAA AAA
2309363 TAAGGTGGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
5 1 0.02
6 18 0.41
7 18 0.41
8 7 0.16
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:2309321 original size:63 final size:64
Alignment explanation
Indices: 2309207--2309331 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 64
2309197 AGTACTTCGC
* ** *
2309207 TTAGGATGAAAACCCGAGAGGGCGTTCTAAGTTGAAAAAAAAGAGAAAAAAAGA-AAAAGATGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAGAGAAAAAAAGAGAAAAGATGT
* * *
2309270 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAGAAAGAAAAAGAAAAAGAGA-AAAAGA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAA-AAA-AAAGAGAAAAAAAGAGAAAAGA
2309332 AAAAAGAACA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
63 31 0.58
64 3 0.06
65 19 0.36
ACGTcount: A:0.52, C:0.10, G:0.26, T:0.13
Consensus pattern (64 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAGAGAAAAAAAGAGAAAAGATGT
Found at i:2309328 original size:8 final size:7
Alignment explanation
Indices: 2309307--2309356 Score: 68
Period size: 7 Copynumber: 7.1 Consensus size: 7
2309297 TAAATTGAAG
2309307 AAAG-AA
1 AAAGAAA
2309313 AAAG-AA
1 AAAGAAA
2309319 AAAGAGAA
1 AAAGA-AA
2309327 AAAGAAA
1 AAAGAAA
2309334 AAAGAACA
1 AAAGAA-A
2309342 AAAGAAA
1 AAAGAAA
2309349 AAAGAAA
1 AAAGAAA
2309356 A
1 A
2309357 GAAAAATAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
6 10 0.24
7 17 0.41
8 14 0.34
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:2309354 original size:15 final size:14
Alignment explanation
Indices: 2309307--2309356 Score: 68
Period size: 15 Copynumber: 3.6 Consensus size: 14
2309297 TAAATTGAAG
2309307 AAAG-AAAAAG-AA
1 AAAGAAAAAAGAAA
2309319 AAAGAGAAAAAGAAA
1 AAAGA-AAAAAGAAA
2309334 AAAGAACAAAAGAAA
1 AAAGAA-AAAAGAAA
2309349 AAAGAAAA
1 AAAGAAAA
2309357 GAAAAATAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.12
14 9 0.26
15 21 0.62
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAGAAA
Found at i:2310636 original size:98 final size:97
Alignment explanation
Indices: 2310494--2310675 Score: 273
Period size: 98 Copynumber: 1.9 Consensus size: 97
2310484 AATTTCAAAC
*
2310494 CAATTTCAACTTCACAGTAAGGATATTGGAACCAAGCAACACAAGCTCAACTTCAC-GACGAAGG
1 CAATTTCAACTTCACAGTAAGGATATTAGAACCAAGCAACACAAGCTCAACTTCACAG-CGAAGG
*
2310558 GGCGGCTGATTGTCAACAAACAACTTTCAGAGT
65 GGCGGCTGACTGTCAACAAACAACTTTCAGAGT
2310591 CAATTTCAACTTCACAACG-AAGGATATTAG-ACTCAAG-ACACACAAGCTCAACTTCACAGCGA
1 CAATTTCAACTTCAC-A-GTAAGGATATTAGAAC-CAAGCA-ACACAAGCTCAACTTCACAGCGA
2310653 AGGGGCGGCTGACTGTCAACAAA
62 AGGGGCGGCTGACTGTCAACAAA
2310676 TAATTTCCCA
Statistics
Matches: 78, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
97 18 0.23
98 58 0.74
99 2 0.03
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (97 bp):
CAATTTCAACTTCACAGTAAGGATATTAGAACCAAGCAACACAAGCTCAACTTCACAGCGAAGGG
GCGGCTGACTGTCAACAAACAACTTTCAGAGT
Found at i:2311488 original size:7 final size:7
Alignment explanation
Indices: 2311445--2311489 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
2311435 ATTTCATCCT
2311445 TATATTA
1 TATATTA
*
2311452 TATAATA
1 TATATTA
2311459 TATATT-
1 TATATTA
2311465 TATATTA
1 TATATTA
*
2311472 TA-AAT-
1 TATATTA
2311477 TATATTA
1 TATATTA
2311484 TATATT
1 TATATT
2311490 TATTCACATT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
5 2 0.06
6 10 0.32
7 19 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATTA
Found at i:2311492 original size:20 final size:20
Alignment explanation
Indices: 2311444--2311489 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2311434 AATTTCATCC
2311444 TTATATTATATAATATATAT
1 TTATATTATATAATATATAT
2311464 TTATATTATA-AAT-TATAT
1 TTATATTATATAATATATAT
2311482 TATATATT
1 T-TATATT
2311490 TATTCACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.24
19 9 0.36
20 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATATTATATAATATATAT
Found at i:2313391 original size:18 final size:18
Alignment explanation
Indices: 2313358--2313430 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 18
2313348 TATTTATTTA
2313358 TTTATCTTCTCTTTATTTTT
1 TTTAT-TTC-CTTTATTTTT
*
2313378 TTTATTTCCTTTATCTTTGA
1 TTTATTTCCTTTAT-TTT-T
* *
2313398 TTTATTTAC-TCATTTTT
1 TTTATTTCCTTTATTTTT
*
2313415 ATTTA-TTCATTTATTT
1 -TTTATTTCCTTTATTT
2313431 ATGTATATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
17 2 0.05
18 18 0.43
19 9 0.21
20 13 0.31
ACGTcount: A:0.16, C:0.12, G:0.01, T:0.70
Consensus pattern (18 bp):
TTTATTTCCTTTATTTTT
Found at i:2313401 original size:20 final size:19
Alignment explanation
Indices: 2313350--2313421 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 19
2313340 TTATTTATTA
2313350 TTTA-TTTATTTATCTTCTC
1 TTTATTTTATTTAT-TTCTC
*
2313369 TTTATTTTTTTTATTTC-C
1 TTTATTTTATTTATTTCTC
2313387 TTTATCTTTGATTTATTTACTC
1 TTTAT-TTT-ATTTATTT-CTC
*
2313409 -AT-TTTTATTTATT
1 TTTATTTTATTTATT
2313422 CATTTATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
18 13 0.29
19 13 0.29
20 16 0.36
21 2 0.04
22 1 0.02
ACGTcount: A:0.17, C:0.11, G:0.01, T:0.71
Consensus pattern (19 bp):
TTTATTTTATTTATTTCTC
Found at i:2317292 original size:88 final size:92
Alignment explanation
Indices: 2317156--2317321 Score: 259
Period size: 89 Copynumber: 1.8 Consensus size: 92
2317146 CAGTCAATAT
* * *
2317156 TGTGTGAACTAAGCAAAGACCTTTTCTCTCTTAACAAAGGAATGAGT-AACATTTACAAGACATC
1 TGTGTGAACTAAGCAAAGACCTTTTCACTCTTAACAAAGGAATAAGTAAAAATTTACAAGACATC
2317220 AAAAGTCCTCGTTTTACACTCGAATGC
66 AAAAGTCCTCGTTTTACACTCGAATGC
* *
2317247 TGTGTGAACTAAG-AAAGACC-TTT-ACTCTTGACAAAGGAATAAGTAAAAATTTATAAGACATC
1 TGTGTGAACTAAGCAAAGACCTTTTCACTCTTAACAAAGGAATAAGTAAAAATTTACAAGACATC
2317309 AAAAGTCCTCGTT
66 AAAAGTCCTCGTT
2317322 GGAAAAACTT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
88 18 0.26
89 31 0.45
90 7 0.10
91 13 0.19
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (92 bp):
TGTGTGAACTAAGCAAAGACCTTTTCACTCTTAACAAAGGAATAAGTAAAAATTTACAAGACATC
AAAAGTCCTCGTTTTACACTCGAATGC
Found at i:2321269 original size:3 final size:3
Alignment explanation
Indices: 2321261--2321314 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
2321251 ACAGGAAAAC
2321261 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2321309 ATT ATT
1 ATT ATT
2321315 TAACACAGGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2345600 original size:21 final size:21
Alignment explanation
Indices: 2345576--2345615 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2345566 TTCTGCTGTA
*
2345576 GTGGTTTGCTCTGGTGGGGAT
1 GTGGGTTGCTCTGGTGGGGAT
*
2345597 GTGGGTTGTTCTGGTGGGG
1 GTGGGTTGCTCTGGTGGGG
2345616 TGGCTGGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.07, G:0.53, T:0.38
Consensus pattern (21 bp):
GTGGGTTGCTCTGGTGGGGAT
Found at i:2345987 original size:31 final size:31
Alignment explanation
Indices: 2345952--2346015 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
2345942 TTTGTCATGT
*
2345952 TAGTTTGTTTTTGGAATGTTAGGGGATTTAA
1 TAGTTTGTTTTTGGAATGTTAAGGGATTTAA
*
2345983 TAGTTTGTTTTTGGAATGTTAAGGTATTTAA
1 TAGTTTGTTTTTGGAATGTTAAGGGATTTAA
2346014 TA
1 TA
2346016 ATCATCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (31 bp):
TAGTTTGTTTTTGGAATGTTAAGGGATTTAA
Found at i:2349860 original size:12 final size:11
Alignment explanation
Indices: 2349839--2349870 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2349829 TTTAGAGATG
2349839 TTAATTTTTTT
1 TTAATTTTTTT
*
2349850 TAAATTTTTTT
1 TTAATTTTTTT
2349861 TTAATTTTTT
1 TTAATTTTTT
2349871 AAAATAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTAATTTTTTT
Found at i:2352719 original size:60 final size:59
Alignment explanation
Indices: 2352626--2352763 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 59
2352616 AGCATAATGA
* * * * * * *
2352626 ATAGTCGAGTGATCATTTTGTAATTTTTAATAGTC-AGGGGATTCAACAAAGCA-ACTCCCT
1 ATAGTCGAGGGACCATTTTATAACTTTTAATAGTCGA-CGAACTCAACAAAGCATA-T-CCT
*
2352686 ATAGTTGAGGGACCATTTTATAACTTTTAATAGTCGACGAACTCAACAAAGCATTATCCT
1 ATAGTCGAGGGACCATTTTATAACTTTTAATAGTCGACGAACTCAACAAAGCA-TATCCT
2352746 ATAGTCGAGGGACCATTT
1 ATAGTCGAGGGACCATTT
2352764 GCATACTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
60 63 0.95
61 2 0.03
62 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (59 bp):
ATAGTCGAGGGACCATTTTATAACTTTTAATAGTCGACGAACTCAACAAAGCATATCCT
Found at i:2352847 original size:14 final size:14
Alignment explanation
Indices: 2352828--2352857 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2352818 AGTATTATAT
2352828 AAAATATTATTTTA
1 AAAATATTATTTTA
*
2352842 AAAATATTCTTTTA
1 AAAATATTATTTTA
2352856 AA
1 AA
2352858 GCAGCGGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAATATTATTTTA
Found at i:2360396 original size:36 final size:36
Alignment explanation
Indices: 2360343--2360524 Score: 217
Period size: 36 Copynumber: 5.1 Consensus size: 36
2360333 GTTTCATGAG
* * *
2360343 AACGATCTCGAGGGAGACAAAATTTGTTTCAAGAGA
1 AACGATCTCAAGAGAGACAAAATTTGTTTCAAGGGA
* * *
2360379 AACGATCTCAAGTGAGACAAAATATATTTCAAGGGA
1 AACGATCTCAAGAGAGACAAAATTTGTTTCAAGGGA
2360415 AACTG-TCTCAAGAGAGACAAAATTTGTTTCAAGGG-
1 AAC-GATCTCAAGAGAGACAAAATTTGTTTCAAGGGA
* * *
2360450 AACTG-TCTCAAGAGAGTCAAAATTCGTTCCAAGGGA
1 AAC-GATCTCAAGAGAGACAAAATTTGTTTCAAGGGA
* **
2360486 AACTATCTCAAGAGAGACAAAATTCATTTCAAGGGA
1 AACGATCTCAAGAGAGACAAAATTTGTTTCAAGGGA
2360522 AAC
1 AAC
2360525 ATTTTCAAAG
Statistics
Matches: 128, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
35 32 0.25
36 95 0.74
37 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
AACGATCTCAAGAGAGACAAAATTTGTTTCAAGGGA
Found at i:2360485 original size:71 final size:71
Alignment explanation
Indices: 2360356--2360609 Score: 256
Period size: 71 Copynumber: 3.6 Consensus size: 71
2360346 GATCTCGAGG
* * *
2360356 GAGACAAAATTTGTTTCAAGAGAAAC-GATCTCAAGTGAGACAAAATATATTTCAAGGGAAACTG
1 GAGACAAAATTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAAT-TGTTTCAAGGGAAACTG
2360420 TCTCAAGA
64 TCTCAAGA
* * *
2360428 GAGACAAAATTTGTTTCAAGGG-AACTGTCTCAAGAGAGTCAAAATTCGTTCCAAGGGAAACTAT
1 GAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT-GTTTCAAGGGAAACTGT
2360492 CTCAAGA
65 CTCAAGA
** * *** **
2360499 GAGACAAAATTCATTTCAAGGGAAACAT-TTTC-A-A-AG--TTTA-TGTTTCAAAAGAAACTGT
1 GAGACAAAATTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATTGTTTCAAGGGAAACTGT
*
2360557 CTCAAGG
65 CTCAAGA
*
2360564 GAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 GAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
2360610 CTTTCTTTAA
Statistics
Matches: 147, Mismatches: 24, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
65 29 0.20
66 19 0.13
67 2 0.01
69 4 0.03
70 2 0.01
71 62 0.42
72 28 0.19
73 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25
Consensus pattern (71 bp):
GAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTGTTTCAAGGGAAACTGTC
TCAAGA
Found at i:2360580 original size:37 final size:38
Alignment explanation
Indices: 2360530--2360609 Score: 126
Period size: 37 Copynumber: 2.1 Consensus size: 38
2360520 GAAACATTTT
*
2360530 CAAAGTTTATGTTTCAAAAGAAACTGTCTCAAGGGAGA
1 CAAAATTTATGTTTCAAAAGAAACTGTCTCAAGGGAGA
**
2360568 CAAAATTT-TGTTTCAAGGGAAACTGTCTCAAGGGAGA
1 CAAAATTTATGTTTCAAAAGAAACTGTCTCAAGGGAGA
2360605 CAAAA
1 CAAAA
2360610 CTTTCTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 32 0.82
38 7 0.18
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (38 bp):
CAAAATTTATGTTTCAAAAGAAACTGTCTCAAGGGAGA
Found at i:2361173 original size:64 final size:64
Alignment explanation
Indices: 2361080--2361246 Score: 255
Period size: 64 Copynumber: 2.6 Consensus size: 64
2361070 GCATCGTTTC
* *
2361080 GAGTCCAAAATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAA-GTTGTTGGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATAAAACT-GAAATGTTGTTGGTT
* * * * *
2361144 GAGTCCAATATCTTTCGCTCTGAAATTGAAATTGACTCTGAATAAAACTGAAATGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATAAAACTGAAATGTTGTTGGTT
2361208 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
2361247 AAAAGCTGAA
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
63 4 0.04
64 87 0.96
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35
Consensus pattern (64 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATAAAACTGAAATGTTGTTGGTT
Found at i:2364776 original size:3 final size:3
Alignment explanation
Indices: 2364770--2364809 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
2364760 GGTTGGTTTA
2364770 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2364810 ATAAATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2371609 original size:23 final size:23
Alignment explanation
Indices: 2371579--2371623 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2371569 CATATAAATG
2371579 CACCGAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
**
2371602 CACCGAAGTGCCGTGTAGAATT
1 CACCGAAGTGCCACGTAGAATT
2371624 GCACATATAA
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:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:2372390 original size:64 final size:64
Alignment explanation
Indices: 2372297--2372418 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
2372287 CGGTATATCC
* * * * *
2372297 CATTCGATGTTTGTATTTTAAGGGGGTGCATCGATGCACTACTTGTGCATCGATACACTGATGG
1 CATTCAATGTTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTGATGG
* * *
2372361 CATTCAATGTTTTTATTTTAAAGGAGTGCATTGATACACTTCATGTGCATCGATACAC
1 CATTCAATGTTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACAC
2372419 CTTGAACAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (64 bp):
CATTCAATGTTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTGATGG
Found at i:2381107 original size:153 final size:153
Alignment explanation
Indices: 2380807--2381094 Score: 558
Period size: 153 Copynumber: 1.9 Consensus size: 153
2380797 GTCCTTCGGG
*
2380807 ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCTCTAGTATAT
1 ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
*
2380872 GTATATTATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
66 GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
2380937 TTCTAAGCGGTCATTCGGGATAT
131 TTCTAAGCGGTCATTCGGGATAT
2380960 ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
1 ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
2381025 GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
66 GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
2381090 TTCTA
131 TTCTA
2381095 CGTGGCACTT
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 133 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (153 bp):
ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
TTCTAAGCGGTCATTCGGGATAT
Found at i:2381108 original size:23 final size:23
Alignment explanation
Indices: 2381074--2381119 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2381064 CATTATTATA
*
2381074 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
2381097 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
2381120 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:2383671 original size:23 final size:23
Alignment explanation
Indices: 2383645--2383689 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2383635 CACCACAGCT
* *
2383645 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
*
2383668 CGTAGAATTGCACCAAAGTGCC
1 CGTAGAAATGCACCAAAGTGCC
2383690 GCGTGGAATT
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:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:2383711 original size:23 final size:23
Alignment explanation
Indices: 2383653--2383702 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2383643 CTCGTATAAA
*
2383653 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
* *
2383676 TGCACCAAAGTGCCGCGTGGAAT
1 TGCACCAAAGTGCCACGTAGAAT
2383699 TGCA
1 TGCA
2383703 TCGTAGTGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCAAAGTGCCACGTAGAAT
Found at i:2384430 original size:64 final size:64
Alignment explanation
Indices: 2384362--2384483 Score: 190
Period size: 64 Copynumber: 1.9 Consensus size: 64
2384352 ACATAAATCC
* * * *
2384362 CATTCGATGTTTGTATTTTAAGGGGGTGCATCGATGCACTACTTGTGCATCGATACACTGATGG
1 CATTCGATGTTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTGATGG
* *
2384426 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATACACTTCATGTGCATCGATACAC
1 CATTCGATGTTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACAC
2384484 CTTGAACAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTGATGG
Found at i:2384570 original size:21 final size:21
Alignment explanation
Indices: 2384514--2384562 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
2384504 TTACCCTTGA
2384514 TGCATCGGTACACATTGAATG
1 TGCATCGGTACACATTGAATG
2384535 TGCATCGGTACACATTGAATG
1 TGCATCGGTACACATTGAATG
2384556 TGCATCG
1 TGCATCG
2384563 ATGCACATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCATCGGTACACATTGAATG
Found at i:2389319 original size:35 final size:35
Alignment explanation
Indices: 2389273--2389349 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
2389263 GTTGGGTATG
*
2389273 TAATTGAAGTATTTTGGAATTTGAGGTTTAGAATA
1 TAATTGAAGTATTTTGGAATTTGAGGTTTAAAATA
* *
2389308 TAATTGAAGTATTTTGGATTTTGGGGTTTAAAATA
1 TAATTGAAGTATTTTGGAATTTGAGGTTTAAAATA
2389343 TAATTGA
1 TAATTGA
2389350 TGATTGTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (35 bp):
TAATTGAAGTATTTTGGAATTTGAGGTTTAAAATA
Found at i:2390352 original size:20 final size:21
Alignment explanation
Indices: 2390324--2390366 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2390314 TAGTAAAAAA
* *
2390324 TTACTTAAAATATTAAT-TTT
1 TTACCTAAAAAATTAATGTTT
2390344 TTACCTAAAAAATTAATGTTT
1 TTACCTAAAAAATTAATGTTT
2390365 TT
1 TT
2390367 TAACATTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
TTACCTAAAAAATTAATGTTT
Found at i:2390865 original size:2 final size:2
Alignment explanation
Indices: 2390858--2390891 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2390848 CAAAGCCCAG
2390858 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2390892 GCTACTAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2401628 original size:168 final size:164
Alignment explanation
Indices: 2401312--2401642 Score: 626
Period size: 168 Copynumber: 2.0 Consensus size: 164
2401302 TGGTTAGGAA
2401312 AAACAACATTGAAGAAGTATTCCCATAAAGTAGGCTACTGTTAACATGAGCACATAAAATTGAAG
1 AAACAACATTGAAGAAGTATTCCCATAAAGTAGGCTACTGTTAACATGAGCACATAAAATTGAAG
2401377 AAGTTATTCCAATAAAGTTGAACCAATTCAAACTCAAACACAATTTTAGTTTTGAATAAACAAAA
66 AAGTTATTCCAATAAAGTTGAACCAATTCAAACTCAAACACAATTTTAGTTTTGAATAAACAAAA
2401442 ACCTAGTAGACAATAATATGTGGTATCGATTTGT
131 ACCTAGTAGACAATAATATGTGGTATCGATTTGT
2401476 AAACAACATTGAAGAAGTTATTCCCATAAAGTAGGCTACTGTTAACATGAGCACATAAAATTGAA
1 AAACAACATTGAAGAAG-TATTCCCATAAAGTAGGCTACTGTTAACATGAGCACATAAAATTGAA
2401541 GAAGTTATTCCAATAAAGTAAATGAACCAATTCAAACTCAAACACAATTTTAGTTTTGAATAAAC
65 GAAGTTATTCCAATAAAGT---TGAACCAATTCAAACTCAAACACAATTTTAGTTTTGAATAAAC
2401606 AAAAACCTAGTAGACAATAATATGTGGTATCGATTTG
127 AAAAACCTAGTAGACAATAATATGTGGTATCGATTTG
2401643 AACAAGGCAT
Statistics
Matches: 163, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
164 17 0.10
165 66 0.40
168 80 0.49
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.28
Consensus pattern (164 bp):
AAACAACATTGAAGAAGTATTCCCATAAAGTAGGCTACTGTTAACATGAGCACATAAAATTGAAG
AAGTTATTCCAATAAAGTTGAACCAATTCAAACTCAAACACAATTTTAGTTTTGAATAAACAAAA
ACCTAGTAGACAATAATATGTGGTATCGATTTGT
Found at i:2403286 original size:2 final size:2
Alignment explanation
Indices: 2403279--2403304 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2403269 TCAATATTTA
2403279 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2403305 TTAAAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2403706 original size:20 final size:20
Alignment explanation
Indices: 2403669--2403708 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2403659 TTTATTAAAA
*
2403669 ATTAATATAATTTCTAAGAT
1 ATTAATATAATTTATAAGAT
**
2403689 ATTAATATTTTTTATAAGAT
1 ATTAATATAATTTATAAGAT
2403709 TATATATTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTAATATAATTTATAAGAT
Found at i:2403796 original size:38 final size:38
Alignment explanation
Indices: 2403745--2403830 Score: 172
Period size: 38 Copynumber: 2.3 Consensus size: 38
2403735 AAAATATATT
2403745 AATTTTTAAATTAATTAAATTAAAGACATGTTAACGCA
1 AATTTTTAAATTAATTAAATTAAAGACATGTTAACGCA
2403783 AATTTTTAAATTAATTAAATTAAAGACATGTTAACGCA
1 AATTTTTAAATTAATTAAATTAAAGACATGTTAACGCA
2403821 AATTTTTAAA
1 AATTTTTAAA
2403831 AGTCGTCTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (38 bp):
AATTTTTAAATTAATTAAATTAAAGACATGTTAACGCA
Found at i:2404458 original size:19 final size:18
Alignment explanation
Indices: 2404436--2404484 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
2404426 TAGTTTAAGT
*
2404436 TTATATTTATAAATTTTTA
1 TTATATTT-TAAATATTTA
* *
2404455 TTATAATTTTATATATTTC
1 TTAT-ATTTTAAATATTTA
2404474 TTATATTTTAA
1 TTATATTTTAA
2404485 TAAAATTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATATTTTAAATATTTA
Found at i:2404597 original size:28 final size:31
Alignment explanation
Indices: 2404538--2404601 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 31
2404528 AAAGATCTAC
*
2404538 ATAAAATTATGTTAATAATTTAATTATCAAT
1 ATAAAATTATGTTAATAATTTAATTATAAAT
* *
2404569 ATAAAA-TATTTTAA-AA-TTAATTTTAAAT
1 ATAAAATTATGTTAATAATTTAATTATAAAT
2404597 A-AAAA
1 ATAAAA
2404602 CCATAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 4 0.13
28 11 0.37
29 2 0.07
30 7 0.23
31 6 0.20
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
ATAAAATTATGTTAATAATTTAATTATAAAT
Found at i:2404833 original size:15 final size:17
Alignment explanation
Indices: 2404813--2404849 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2404803 TGTTCCTTTC
2404813 ATTTTT-ATAAAAAA-T
1 ATTTTTAATAAAAAATT
2404828 ATTTTTAAATAAAAAATT
1 ATTTTT-AATAAAAAATT
2404846 ATTT
1 ATTT
2404850 CCTAACGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
17 8 0.42
18 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTTTAATAAAAAATT
Found at i:2405219 original size:33 final size:33
Alignment explanation
Indices: 2405177--2405246 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
2405167 TCGCTGCCAC
2405177 CCCACCGGTGACCTACACATTGGTTGCTTCTTA
1 CCCACCGGTGACCTACACATTGGTTGCTTCTTA
2405210 CCCACCGGTGACCTACACATTGGTTGCTTCTTA
1 CCCACCGGTGACCTACACATTGGTTGCTTCTTA
2405243 CCCA
1 CCCA
2405247 TTCACAGGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.19, C:0.36, G:0.17, T:0.29
Consensus pattern (33 bp):
CCCACCGGTGACCTACACATTGGTTGCTTCTTA
Found at i:2407037 original size:5 final size:5
Alignment explanation
Indices: 2407027--2407057 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2407017 AATGTTAGGT
2407027 AATAA AATAA AAT-A AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA
2407058 AAGAACAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:2407046 original size:14 final size:14
Alignment explanation
Indices: 2407027--2407056 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2407017 AATGTTAGGT
2407027 AATAAAATAAAATA
1 AATAAAATAAAATA
2407041 AATAAAATAAAATA
1 AATAAAATAAAATA
2407055 AA
1 AA
2407057 AAAGAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AATAAAATAAAATA
Found at i:2408342 original size:13 final size:13
Alignment explanation
Indices: 2408324--2408351 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2408314 ATAGTGCCGC
2408324 GTGAACAGTTACA
1 GTGAACAGTTACA
2408337 GTGAACAGTTACA
1 GTGAACAGTTACA
2408350 GT
1 GT
2408352 AACTGCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (13 bp):
GTGAACAGTTACA
Found at i:2408977 original size:59 final size:59
Alignment explanation
Indices: 2408885--2409016 Score: 194
Period size: 59 Copynumber: 2.3 Consensus size: 59
2408875 CGTAGTGTTA
* **
2408885 TCCCGAATATGACACATAAGGTCGTGCCCACCATCTGTACTAGGTATCCTTAACTGCAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAACTGCAG
* * * *
2408944 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAACTGCAG
2409003 TCCCGAATAT-ACAC
1 TCCCGAATATGACAC
2409017 CTGCTGCTGG
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
58 4 0.06
59 62 0.94
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAACTGCAG
Found at i:2411145 original size:21 final size:21
Alignment explanation
Indices: 2411078--2411145 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
2411068 ATAATAAGCT
*
2411078 TAATATATATTTAAAAATCTATA
1 TAATATAT-TTTGAAAAT-TATA
* * * *
2411101 TATTATATTTTTAAAATCACA
1 TAATATATTTTGAAAATTATA
*
2411122 TAATATGTTTTGAAAATTATA
1 TAATATATTTTGAAAATTATA
2411143 TAA
1 TAA
2411146 CAATATGTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 21 0.58
22 8 0.22
23 7 0.19
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (21 bp):
TAATATATTTTGAAAATTATA
Found at i:2414518 original size:44 final size:45
Alignment explanation
Indices: 2414436--2414539 Score: 133
Period size: 44 Copynumber: 2.3 Consensus size: 45
2414426 CCATTCAACA
* **
2414436 GGTACCGATACCCTCTAATACGAGAAAATTTTAGAATGTCAT-AGG
1 GGTACCGATACCCCCTAATACGAGAAAATTACAGAATGTCATGA-G
*
2414481 GGTACCGATACCCCCTTGA-ACGA-AAAATTACAGAATGTCATGAG
1 GGTACCGATACCCCC-TAATACGAGAAAATTACAGAATGTCATGAG
2414525 GGTACCGATACCCCC
1 GGTACCGATACCCCC
2414540 AGTAGGGTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
44 32 0.60
45 19 0.36
46 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (45 bp):
GGTACCGATACCCCCTAATACGAGAAAATTACAGAATGTCATGAG
Found at i:2416377 original size:23 final size:23
Alignment explanation
Indices: 2416351--2416408 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
2416341 GACACTTCGA
2416351 TGCATTTCTACGTGGCACTACGG
1 TGCATTTCTACGTGGCACTACGG
* * * **
2416374 TGCAATTCTATGTGGCATTTTGG
1 TGCATTTCTACGTGGCACTACGG
*
2416397 TGCATTTATACG
1 TGCATTTCTACG
2416409 AGTTGTGGTG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (23 bp):
TGCATTTCTACGTGGCACTACGG
Found at i:2420981 original size:24 final size:20
Alignment explanation
Indices: 2420954--2421011 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
2420944 GCATGGGTAG
2420954 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
2420978 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
2420998 TTCATCGATGCACT
1 TGCATCGATGCACT
2421012 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:2421344 original size:10 final size:10
Alignment explanation
Indices: 2421317--2421350 Score: 54
Period size: 9 Copynumber: 3.6 Consensus size: 10
2421307 GTGTTTGTTA
2421317 TGATTATATG
1 TGATTATATG
2421327 TG-TTATATG
1 TGATTATATG
2421336 TGATTATATG
1 TGATTATATG
2421346 T-ATTA
1 TGATTA
2421351 CATTAATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.57
10 10 0.43
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (10 bp):
TGATTATATG
Found at i:2421503 original size:2 final size:2
Alignment explanation
Indices: 2421498--2421561 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
2421488 TATATATATA
2421498 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2421540 TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG
2421562 AACAAAAGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2423669 original size:18 final size:20
Alignment explanation
Indices: 2423633--2423669 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
2423623 ATTTAATAAA
*
2423633 AAAAACTCTCCTCACCTCTC
1 AAAAACTCTCCTCAACTCTC
2423653 AAAAAC-CT-CTCAACTCT
1 AAAAACTCTCCTCAACTCT
2423670 TCCTAACTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 2 0.12
20 6 0.38
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAACTCTCCTCAACTCTC
Found at i:2424575 original size:21 final size:21
Alignment explanation
Indices: 2424541--2424725 Score: 85
Period size: 21 Copynumber: 8.3 Consensus size: 21
2424531 TAAGCTTAAT
**
2424541 ATATATTTAAAAAACTATATA
1 ATATATTTTCAAAACTATATA
*
2424562 TTATATTTTCAAAA-TCATATA
1 ATATATTTTCAAAACT-ATATA
* *
2424583 ATATGTTTTCAAAATTATATAACA
1 ATATATTTTCAAAACTATAT---A
* *
2424607 ATATGTTTTTAAAAACTATACT-
1 ATAT-ATTTTCAAAACTATA-TA
2424629 ATATATTTTCAAAAACTATATA
1 ATATATTTTC-AAAACTATATA
* *
2424651 TTATATGTTTTTTTTTAAAAACTATATA
1 --ATA-----TATTTTCAAAACTATATA
*
2424679 ATATGTTTTCAAAA--ACTAT-
1 ATATATTTTCAAAACTA-TATA
*
2424698 ATATATTTTCAAAAAT-TATA
1 ATATATTTTCAAAACTATATA
2424718 TATATATT
1 -ATATATT
2424726 ATATATTTTT
Statistics
Matches: 128, Mismatches: 15, Indels: 42
0.69 0.08 0.23
Matches are distributed among these distances:
19 17 0.13
20 4 0.03
21 53 0.41
22 14 0.11
24 8 0.06
25 12 0.09
26 4 0.03
28 11 0.09
29 5 0.04
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATATTTTCAAAACTATATA
Found at i:2424609 original size:24 final size:21
Alignment explanation
Indices: 2424557--2424711 Score: 73
Period size: 22 Copynumber: 6.9 Consensus size: 21
2424547 TTAAAAAACT
* *
2424557 ATATATTATATTTTCAAAATC
1 ATATAATATGTTTTCAAAATC
*
2424578 ATATAATATGTTTTCAAAATT
1 ATATAATATGTTTTCAAAATC
* *
2424599 ATATAACAATATGTTTTTAAAAAC
1 ATAT---AATATGTTTTCAAAATC
* *
2424623 -TATACTATATATTTTCAAAAAC
1 ATATA--ATATGTTTTCAAAATC
* *
2424645 TATATATTATATGTTTTTTTTTAAAAAC
1 -ATATA--ATATG----TTTTCAAAATC
*
2424673 TATATAATATGTTTTCAAAAAC
1 -ATATAATATGTTTTCAAAATC
*
2424695 -TAT-ATATATTTTCAAAA
1 ATATAATATGTTTTCAAAA
2424712 ATTATATATA
Statistics
Matches: 110, Mismatches: 13, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
19 13 0.12
20 4 0.04
21 22 0.20
22 24 0.22
23 3 0.03
24 23 0.21
26 5 0.05
28 16 0.15
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (21 bp):
ATATAATATGTTTTCAAAATC
Found at i:2424717 original size:17 final size:19
Alignment explanation
Indices: 2424662--2424722 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
2424652 TATATGTTTT
*
2424662 TTTTTAAAAACTATATAATA
1 TTTTCAAAAACTATAT-ATA
2424682 TGTTTTCAAAAACTATATATA
1 --TTTTCAAAAACTATATATA
*
2424703 TTTTCAAAAATTATATATA
1 TTTTCAAAAACTATATATA
2424722 T
1 T
2424723 ATTATATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 19 0.51
21 3 0.08
22 15 0.41
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTTCAAAAACTATATATA
Found at i:2425662 original size:206 final size:205
Alignment explanation
Indices: 2425307--2425709 Score: 716
Period size: 206 Copynumber: 2.0 Consensus size: 205
2425297 AAAAGAAAAT
*
2425307 AAAAGAAGAAGAAGATTACGGTGGCAACAAGGTAGGAAGAATGGAGCAAGAATTTTTATCTTATT
1 AAAAGAAGAAGAAGATTACGGTGGCAACAAGGTAGGAAGAATGGAGCAAGAATTATTATCTTATT
* *
2425372 TTTGCTCGTGATTTTTTTGGAATAGTATAAGATGGTTACAAGAAAGAGTATAATGGAACTAGGAT
66 TTTGCTCGTGATTTTTTTGGAATAGTATAAGATGGTTACAAGAAAGAGCAGAATGGAACTAGGAT
*
2425437 GAAATTATGGGAGGTGCCAAGTTTCTTATCCTTTAAACTATCAAGTTTCTAAAAGGTAATTAAAT
131 GAAATTATGGGAGGTGCCAAGTTGCTTATCCTTTAAACTATCAAGTTTCTAAAAGGTAATTAAAT
2425502 CATAGAAGAA
196 CATAGAAGAA
* *
2425512 AAAAGAAGAAGAAGATTACGGTGGTAACAAGGTGGGAAGAATGGAGCAAGAATTATTATCTTATT
1 AAAAGAAGAAGAAGATTACGGTGGCAACAAGGTAGGAAGAATGGAGCAAGAATTATTATCTTATT
* *
2425577 TTTGCTTGTGATTGTTTTTGGAATAGTATGAGATGGTTACAAGAAAGAGCAGAATGGAACTAGGA
66 TTTGCTCGTGATT-TTTTTGGAATAGTATAAGATGGTTACAAGAAAGAGCAGAATGGAACTAGGA
*
2425642 TGAAATTATGGGAGGTGCCAAGTTGCTTATCCTTTAAACTATCAAGTTTTTAAAAGGTAATTAAA
130 TGAAATTATGGGAGGTGCCAAGTTGCTTATCCTTTAAACTATCAAGTTTCTAAAAGGTAATTAAA
2425707 TCA
195 TCA
2425710 CAAAAAATAG
Statistics
Matches: 188, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
205 74 0.39
206 114 0.61
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (205 bp):
AAAAGAAGAAGAAGATTACGGTGGCAACAAGGTAGGAAGAATGGAGCAAGAATTATTATCTTATT
TTTGCTCGTGATTTTTTTGGAATAGTATAAGATGGTTACAAGAAAGAGCAGAATGGAACTAGGAT
GAAATTATGGGAGGTGCCAAGTTGCTTATCCTTTAAACTATCAAGTTTCTAAAAGGTAATTAAAT
CATAGAAGAA
Found at i:2429667 original size:6 final size:6
Alignment explanation
Indices: 2429656--2429680 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2429646 AAATGAAATG
2429656 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
2429681 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:2431963 original size:43 final size:43
Alignment explanation
Indices: 2431902--2432190 Score: 142
Period size: 43 Copynumber: 6.4 Consensus size: 43
2431892 ACTCATATGC
* * *
2431902 GATGAAGAGGTCTGGTCATCTAAGGGTGACTCAGCTCCTACGT
1 GATGAAGAGATCTGGTCATCTAAGGGTGACACGGCTCCTACGT
* *
2431945 GATGAAGAGATCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCT
1 GATGAAGAGATCTGGTCATC--T---AAGGGTG---ACACGGCTCCTACG-T
* * *
2431997 -ATG-AG-GACTACTGATTATCTAGGGGTGACACGGCTCCTACGT
1 GATGAAGAGA-T-CTGGTCATCTAAGGGTGACACGGCTCCTACGT
** * *
2432039 GATGAAGAGATCTGGTC-GGT--GGATGACACGGCTCATACGT
1 GATGAAGAGATCTGGTCATCTAAGGGTGACACGGCTCCTACGT
* * *
2432079 GATGAAGAGTTCTGGTCATCTTTAGGAAGGGCGATAACACGGTTCCTACGT
1 GATGAAGAGATCTGGTCATC--T---AA-GG-G-TGACACGGCTCCTACGT
* * * * * * * *
2432130 GATGAGGATGGT-TGATTATCTATGGTTGACATGGCTCATACGT
1 GATGAAGA-GATCTGGTCATCTAAGGGTGACACGGCTCCTACGT
2432173 GATGAAGAGATCTGGTCA
1 GATGAAGAGATCTGGTCA
2432191 GGGGATGACA
Statistics
Matches: 184, Mismatches: 35, Indels: 54
0.67 0.13 0.20
Matches are distributed among these distances:
40 34 0.18
42 4 0.02
43 63 0.34
44 3 0.02
45 5 0.03
46 7 0.04
48 7 0.04
49 6 0.03
50 3 0.02
51 49 0.27
52 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.27
Consensus pattern (43 bp):
GATGAAGAGATCTGGTCATCTAAGGGTGACACGGCTCCTACGT
Found at i:2432135 original size:134 final size:134
Alignment explanation
Indices: 2431935--2432215 Score: 415
Period size: 134 Copynumber: 2.1 Consensus size: 134
2431925 GGGTGACTCA
* *
2431935 GCTCCTACGTGATGAAGAGATCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCTATG
1 GCTCCTACGTGATGAAGAGATCTGGTCATCTTTAGGAAGGGCGATAACACGGTTCCTACGCTATG
*
2432000 AGGACT-ACTGATTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTC-GGTGGAT
66 AGGA-TGACTGATTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGG-GGAT
2432063 GACACG
129 GACACG
* *
2432069 GCTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGCGATAACACGGTTCCTACG-TGAT
1 GCTCCTACGTGATGAAGAGATCTGGTCATCTTTAGGAAGGGCGATAACACGGTTCCTACGCT-AT
** * * *
2432133 GAGGATGGTTGATTATCTATGGTTGACATGGCTCATACGTGATGAAGAGATCTGGTCAGGGGATG
65 GAGGATGACTGATTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGGATG
2432198 ACACG
130 ACACG
*
2432203 GTTCCTACGTGAT
1 GCTCCTACGTGAT
2432216 AAGGAAGGCT
Statistics
Matches: 132, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
133 2 0.02
134 128 0.97
135 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (134 bp):
GCTCCTACGTGATGAAGAGATCTGGTCATCTTTAGGAAGGGCGATAACACGGTTCCTACGCTATG
AGGATGACTGATTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGGATGA
CACG
Found at i:2432287 original size:28 final size:28
Alignment explanation
Indices: 2432247--2432301 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2432237 GTGATTATGG
** *
2432247 TTTCAAGGGAAACCGACTCAAAGATTTA
1 TTTCAAGAAAAACAGACTCAAAGATTTA
*
2432275 TTTCAAGAAAAACATACTCAAAGATTT
1 TTTCAAGAAAAACAGACTCAAAGATTT
2432302 TGTTTGTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (28 bp):
TTTCAAGAAAAACAGACTCAAAGATTTA
Found at i:2432662 original size:31 final size:31
Alignment explanation
Indices: 2432580--2432654 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
2432570 AAAAAATTCG
* *
2432580 TTTCAAGGGAAAC-GACTCAAAGATAGTTTTA
1 TTTCAAGAGAAACAAACTCAAAGATA-TTTTA
2432611 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAACAAACTCAAAGATATTT-TA
*
2432642 TTTCCAGAGAAAC
1 TTTCAAGAGAAAC
2432655 TGCCTCAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.67
32 10 0.26
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (31 bp):
TTTCAAGAGAAACAAACTCAAAGATATTTTA
Found at i:2433378 original size:36 final size:36
Alignment explanation
Indices: 2433337--2433474 Score: 131
Period size: 36 Copynumber: 3.8 Consensus size: 36
2433327 TCAATTTGGA
2433337 AAATTGTCTCAAGTAAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGTAAGACAACATTTGTTTTTAGAG
* * *
2433373 AAATTGTCTCAA-AAGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGTA-AGACAACATTTGTTTTTAGAG
** *
2433409 AAATTGTCTCAAGCGAGACAA-AGTTTGTTTTT-GAA
1 AAATTGTCTCAAGTAAGACAACA-TTTGTTTTTAGAG
** *
2433444 AAAACGATCTCAAGTGAGATCAAC-TTTGTTT
1 AAATTG-TCTCAAGTAAGA-CAACATTTGTTT
2433475 AATGTGAACA
Statistics
Matches: 86, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
35 8 0.09
36 75 0.87
37 3 0.03
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (36 bp):
AAATTGTCTCAAGTAAGACAACATTTGTTTTTAGAG
Found at i:2433616 original size:106 final size:106
Alignment explanation
Indices: 2433441--2433656 Score: 287
Period size: 107 Copynumber: 2.0 Consensus size: 106
2433431 GTTTGTTTTT
* *
2433441 GAAAAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTGAACAAATTCGAAATTTGTATTCTCA
1 GAAAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAACAAATTCGAAATTTGTATTATCA
2433506 AAGG-AAAAATGCCTCAAACAAGACAAAATTTGTTTTGAA-A
66 AAGGAAAAAATGCCTCAAACAAGACAAAATTTGTTTT-AAGA
* * *
2433546 GAAACAACAATCTCAAGTGAGATTAATTTTTGTTTCAA-GTGAATCAAATTCGAAATTTGTA-TA
1 GAAAAAACAATCTCAAGTGAGATCAA-CTTTGTTT-AATGTGAA-CAAATTCGAAATTTGTATTA
* * * *
2433609 TCAAAGGAAAAAATGTCTCAAGCAAGACGAAGTTTGTTTTAAGA
63 TCAAAGGAAAAAATGCCTCAAACAAGACAAAATTTGTTTTAAGA
2433653 GAAA
1 GAAA
2433657 TTGTCTTAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
105 23 0.24
106 22 0.23
107 52 0.54
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (106 bp):
GAAAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAACAAATTCGAAATTTGTATTATCA
AAGGAAAAAATGCCTCAAACAAGACAAAATTTGTTTTAAGA
Found at i:2433845 original size:100 final size:102
Alignment explanation
Indices: 2433739--2433930 Score: 219
Period size: 100 Copynumber: 1.9 Consensus size: 102
2433729 AATTTTGAAA
* * * * * * * * *
2433739 ATCTCAAGTAAGATTAATTTTGTTTCAA-GTACAACAAATT-TAAATTTTTATTTC-ATGAAAAA
1 ATCTCAAATAAGATCAACTTTATTT-AATGTAAAACAAATTCGAAATTTGTATCTCAAGGAAAAA
* * *
2433801 TGTCTTAAGCGAGACGAAGTTTGTTTTTTTAGAAAGCG
65 TGTCTCAAGCGAGACGAAATTTATTTTTTTAGAAAGCG
*
2433839 ATCTCAAATGAGATCAACTTTATTTAATGTAAAACAAATTCGAAATTTGTATCTCAAAGGAAAAA
1 ATCTCAAATAAGATCAACTTTATTTAATGTAAAACAAATTCGAAATTTGTATCTC-AAGGAAAAA
*
2433904 TGTCTCAAGTGAGACGAAATTTATTTT
65 TGTCTCAAGCGAGACGAAATTTATTTT
2433931 GAAATAAATT
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
99 2 0.03
100 31 0.42
101 11 0.15
103 30 0.41
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (102 bp):
ATCTCAAATAAGATCAACTTTATTTAATGTAAAACAAATTCGAAATTTGTATCTCAAGGAAAAAT
GTCTCAAGCGAGACGAAATTTATTTTTTTAGAAAGCG
Found at i:2433981 original size:71 final size:72
Alignment explanation
Indices: 2433898--2434038 Score: 196
Period size: 71 Copynumber: 2.0 Consensus size: 72
2433888 TATCTCAAAG
* * *
2433898 GAAAAATGTCTCAAGTGAGACGAAATTTATTTTGAAATAAATTATCTCCAA-CGAGAC-AAAATT
1 GAAAAATGTCTCAAGCGAGACAAAATTTATTTTGAAAGAAATTATCT-CAAGCGAGACAAAAATT
2433961 TGTTTTTA
65 TGTTTTTA
* * * *
2433969 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAAAAATTT
1 GAAAAATGTCTCAAGCGAGACAAAATTTATTTTGAAAGAAATTATCTCAAGCGAGACAAAAATTT
2434034 GTTTT
66 GTTTT
2434039 AAAATTCTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
70 3 0.05
71 46 0.75
72 12 0.20
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (72 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTATTTTGAAAGAAATTATCTCAAGCGAGACAAAAATTT
GTTTTTA
Found at i:2433990 original size:35 final size:36
Alignment explanation
Indices: 2433904--2434038 Score: 166
Period size: 36 Copynumber: 3.8 Consensus size: 36
2433894 AAAGGAAAAA
* * * * *
2433904 TGTCTCAAGTGAGACGAAATTTATTTTGAAATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAAT
* * *
2433940 TATCTCCAA-CGAGACAAAATTTGTTTTTAGA-AAAC
1 TGTCT-CAAGCGAGACAAAATTTGTTTTGAGAGAAAT
2433975 TGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAAT
2434011 TGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGAC-AAAATTTGTTTT
2434039 AAAATTCTCA
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
34 3 0.04
35 28 0.33
36 39 0.46
37 15 0.18
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAAT
Found at i:2435617 original size:24 final size:24
Alignment explanation
Indices: 2435589--2435637 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2435579 CGAGAGACTC
2435589 TTTG-TCTGTGCTTCTTGTTTTCTT
1 TTTGTTCTGTGCTT-TTGTTTTCTT
* *
2435613 TTTGTTCTTTGCTTTTTTTTTCTT
1 TTTGTTCTGTGCTTTTGTTTTCTT
2435637 T
1 T
2435638 GCTTTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.00, C:0.14, G:0.12, T:0.73
Consensus pattern (24 bp):
TTTGTTCTGTGCTTTTGTTTTCTT
Found at i:2435629 original size:14 final size:13
Alignment explanation
Indices: 2435610--2435699 Score: 83
Period size: 14 Copynumber: 6.5 Consensus size: 13
2435600 TTCTTGTTTT
2435610 CTTTTTGTTCTTTG
1 CTTTTT-TTCTTTG
2435624 CTTTTTTTTTCTTTG
1 C--TTTTTTTCTTTG
2435639 CTTTTTTTCTTTG
1 CTTTTTTTCTTTG
*
2435652 TTGTTTTTTCTTTG
1 CT-TTTTTTCTTTG
*
2435666 CTTCTTTCTCTTTG
1 CTT-TTTTTCTTTG
*
2435680 -TTATTTGCTCTTTG
1 CTT-TTT-TTCTTTG
2435694 CTTTTT
1 CTTTTT
2435700 CCTTTGTTGT
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
13 19 0.29
14 32 0.48
15 10 0.15
16 5 0.08
ACGTcount: A:0.01, C:0.16, G:0.10, T:0.73
Consensus pattern (13 bp):
CTTTTTTTCTTTG
Found at i:2435651 original size:28 final size:27
Alignment explanation
Indices: 2435610--2435707 Score: 108
Period size: 28 Copynumber: 3.6 Consensus size: 27
2435600 TTCTTGTTTT
*
2435610 CTTTTTGTTCTTTGCTTTTTTTTTCTTTG
1 CTTTTT-TTCTTTG-TTATTTTTTCTTTG
*
2435639 CTTTTTTTCTTTGTTGTTTTTTCTTTG
1 CTTTTTTTCTTTGTTATTTTTTCTTTG
* **
2435666 CTTCTTTCTCTTTGTTATTTGCTCTTTG
1 CTT-TTTTTCTTTGTTATTTTTTCTTTG
*
2435694 C-TTTTTCCTTTGTT
1 CTTTTTTTCTTTGTT
2435708 GTGACTTGAT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
26 10 0.16
27 17 0.28
28 28 0.46
29 6 0.10
ACGTcount: A:0.01, C:0.16, G:0.10, T:0.72
Consensus pattern (27 bp):
CTTTTTTTCTTTGTTATTTTTTCTTTG
Found at i:2435692 original size:42 final size:43
Alignment explanation
Indices: 2435612--2435693 Score: 98
Period size: 41 Copynumber: 1.9 Consensus size: 43
2435602 CTTGTTTTCT
* * *
2435612 TTTTGTTCTTTGCTTTTTTTTTCTTTGCTTTTTTTCTTTGTTG
1 TTTTGTTCTTTGCTTTCTTTCTCTTTGCTTTTTCTCTTTGTTG
2435655 TTTT-TTCTTTGC-TTCTTTCTCTTTG-TTATTTGCTCTTTG
1 TTTTGTTCTTTGCTTTCTTTCTCTTTGCTT-TTT-CTCTTTG
2435694 CTTTTTCCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 2 0.06
41 14 0.41
42 14 0.41
43 4 0.12
ACGTcount: A:0.01, C:0.15, G:0.11, T:0.73
Consensus pattern (43 bp):
TTTTGTTCTTTGCTTTCTTTCTCTTTGCTTTTTCTCTTTGTTG
Found at i:2435989 original size:30 final size:30
Alignment explanation
Indices: 2435953--2436018 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
2435943 AACCGATAAA
* * *
2435953 GAACCGGTTGAAAACTGGGAAAATCGGGGT
1 GAACCGGCTGAAAACCGGCAAAATCGGGGT
**
2435983 GAACCGGCTGAAAACCGGCAAAATCGGTTT
1 GAACCGGCTGAAAACCGGCAAAATCGGGGT
2436013 GAACCG
1 GAACCG
2436019 CCGGTTCACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.32, T:0.15
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGGCAAAATCGGGGT
Found at i:2438563 original size:14 final size:14
Alignment explanation
Indices: 2438544--2438575 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2438534 TATTACACGA
*
2438544 TCCTCGAGCAAGTC
1 TCCTCGAGCAAGCC
2438558 TCCTCGAGCAAGCC
1 TCCTCGAGCAAGCC
2438572 TCCT
1 TCCT
2438576 TCTTGTACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.41, G:0.19, T:0.22
Consensus pattern (14 bp):
TCCTCGAGCAAGCC
Found at i:2440483 original size:10 final size:10
Alignment explanation
Indices: 2440470--2440496 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2440460 AAAAATAAAT
2440470 ATGAAATGAA
1 ATGAAATGAA
2440480 ATGAAATGAA
1 ATGAAATGAA
2440490 ATGAAAT
1 ATGAAAT
2440497 ATAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (10 bp):
ATGAAATGAA
Found at i:2443386 original size:2 final size:2
Alignment explanation
Indices: 2443374--2443413 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
2443364 TCTAATTTAA
2443374 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2443414 AAATCCTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2446633 original size:28 final size:28
Alignment explanation
Indices: 2446593--2446648 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2446583 AAAGAAAGGT
2446593 AAGCAGATTGATTCTATCCCAAATGAAA
1 AAGCAGATTGATTCTATCCCAAATGAAA
2446621 AAGCAGATTGATTCTATCCCAAATGAAA
1 AAGCAGATTGATTCTATCCCAAATGAAA
2446649 CCAGTAACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (28 bp):
AAGCAGATTGATTCTATCCCAAATGAAA
Found at i:2447888 original size:86 final size:86
Alignment explanation
Indices: 2447743--2447914 Score: 335
Period size: 86 Copynumber: 2.0 Consensus size: 86
2447733 CGCCCTTCCC
*
2447743 TTGTTTATGCACTCAAATGTGAAGTTCCAGTTAAGGTCTAAACGACCCTTTTCACCTTTAATCAT
1 TTGTTTATGCACTCAAATGTGAAGTTCCAATTAAGGTCTAAACGACCCTTTTCACCTTTAATCAT
2447808 TTTTGTTTGTAGATGAACATG
66 TTTTGTTTGTAGATGAACATG
2447829 TTGTTTATGCACTCAAATGTGAAGTTCCAATTAAGGTCTAAACGACCCTTTTCACCTTTAATCAT
1 TTGTTTATGCACTCAAATGTGAAGTTCCAATTAAGGTCTAAACGACCCTTTTCACCTTTAATCAT
2447894 TTTTGTTTGTAGATGAACATG
66 TTTTGTTTGTAGATGAACATG
2447915 AACCTCCCAG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (86 bp):
TTGTTTATGCACTCAAATGTGAAGTTCCAATTAAGGTCTAAACGACCCTTTTCACCTTTAATCAT
TTTTGTTTGTAGATGAACATG
Found at i:2451648 original size:40 final size:41
Alignment explanation
Indices: 2451604--2451786 Score: 124
Period size: 40 Copynumber: 4.4 Consensus size: 41
2451594 ATGACCCGAC
*
2451604 TCCTTCGTGATGAGGAGTTCTGATTGGT-AGATGACATTGT
1 TCCTTCGTGATGAGGAGTTCTGATTGGTCAGATAACATTGT
** * * *
2451644 TCCTTCGTGATGAGGACATCTGGTCATCT-TTGAGATAACATAGT
1 TCCTTCGTGATGAGGAGTTCT-G--AT-TGGTCAGATAACATTGT
* * ** * *
2451688 TCCTTCGTGATGAGG-GCGTCTGGTTATCTCAGGATAACA-CGAC
1 TCCTTCGTGATGAGGAG-TTCTGATT-GGTCA-GATAACATTG-T
* *
2451731 TCCTTTGTGATGAGGAGTTCTGATTGGT-AGATGACATTGT
1 TCCTTCGTGATGAGGAGTTCTGATTGGTCAGATAACATTGT
*
2451771 TCCTTCGTGATAAGGA
1 TCCTTCGTGATGAGGA
2451787 CATCTGGTTA
Statistics
Matches: 109, Mismatches: 22, Indels: 24
0.70 0.14 0.15
Matches are distributed among these distances:
40 40 0.37
41 4 0.04
42 4 0.04
43 31 0.28
44 30 0.28
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.34
Consensus pattern (41 bp):
TCCTTCGTGATGAGGAGTTCTGATTGGTCAGATAACATTGT
Found at i:2451710 original size:44 final size:44
Alignment explanation
Indices: 2451632--2451843 Score: 195
Period size: 44 Copynumber: 4.9 Consensus size: 44
2451622 TCTGATTGGT
* * *
2451632 AGATGACATTGTTCCTTCGTGATGAGGACATCTGGTCATCTTTG
1 AGATAACATAGTTCCTTCGTGATGAGGACATCTGGTTATCTTTG
* * **
2451676 AGATAACATAGTTCCTTCGTGATGAGGGCGTCTGGTTATCTCAG
1 AGATAACATAGTTCCTTCGTGATGAGGACATCTGGTTATCTTTG
* * * ** *
2451720 -GATAACA-CGACTCCTTTGTGATGAGGAGTTCT-G--A--TTGG
1 AGATAACATAG-TTCCTTCGTGATGAGGACATCTGGTTATCTTTG
* * *
2451758 TAGATGACATTGTTCCTTCGTGATAAGGACATCTGGTTATCTTTG
1 -AGATAACATAGTTCCTTCGTGATGAGGACATCTGGTTATCTTTG
* *
2451803 AGATAACATAGTTCCTTCGTGATGAGAACTTCTGGTTATCT
1 AGATAACATAGTTCCTTCGTGATGAGGACATCTGGTTATCT
2451844 AAGGATTTTT
Statistics
Matches: 131, Mismatches: 28, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
38 2 0.02
40 24 0.18
41 2 0.02
42 2 0.02
43 25 0.19
44 73 0.56
45 3 0.02
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (44 bp):
AGATAACATAGTTCCTTCGTGATGAGGACATCTGGTTATCTTTG
Found at i:2451771 original size:127 final size:127
Alignment explanation
Indices: 2451552--2451849 Score: 506
Period size: 127 Copynumber: 2.3 Consensus size: 127
2451542 ATATTTGAAC
* * *
2451552 TAACATGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGACCCGACTCCTTCGTGATGA
1 TAACATAGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATAACACGACTCCTTCGTGATGA
*
2451617 GGAGTTCTGATTGGTAGATGACATTGTTCCTTCGTGATGAGGACATCTGGTCATCTTTGAGA
66 GGAGTTCTGATTGGTAGATGACATTGTTCCTTCGTGATAAGGACATCTGGTCATCTTTGAGA
* * *
2451679 TAACATAGTTCCTTCGTGATGAGGGCGTCTGGTTATCTCAGGATAACACGACTCCTTTGTGATGA
1 TAACATAGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATAACACGACTCCTTCGTGATGA
*
2451744 GGAGTTCTGATTGGTAGATGACATTGTTCCTTCGTGATAAGGACATCTGGTTATCTTTGAGA
66 GGAGTTCTGATTGGTAGATGACATTGTTCCTTCGTGATAAGGACATCTGGTCATCTTTGAGA
* *
2451806 TAACATAGTTCCTTCGTGATGAGAACTTCTGGTTATCTAAGGAT
1 TAACATAGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGAT
2451850 TTTTGTTTCT
Statistics
Matches: 159, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
127 159 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (127 bp):
TAACATAGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATAACACGACTCCTTCGTGATGA
GGAGTTCTGATTGGTAGATGACATTGTTCCTTCGTGATAAGGACATCTGGTCATCTTTGAGA
Found at i:2454792 original size:21 final size:21
Alignment explanation
Indices: 2454766--2454810 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2454756 GATTTCTGGG
* *
2454766 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2454787 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2454808 CAA
1 CAA
2454811 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2456199 original size:31 final size:31
Alignment explanation
Indices: 2456112--2456212 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
2456102 AGAGTCGAGG
*
2456112 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* ***
2456143 GTTTTACCTTTG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAAGGA-ACATATGGACA
*
2456175 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
2456206 GTTTACC
1 GTTTACC
2456213 GATGATCTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 31 0.54
32 26 0.46
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:2456244 original size:30 final size:30
Alignment explanation
Indices: 2456200--2456293 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
2456190 AAGGAACATA
*
2456200 TGGACAGTTTACCGATGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
2456231 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
2456261 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2456290 TGGA
1 TGGA
2456294 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 17 0.29
30 34 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:2459461 original size:21 final size:21
Alignment explanation
Indices: 2459435--2459479 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2459425 GATTTCTGGG
* *
2459435 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2459456 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2459477 CAA
1 CAA
2459480 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2460823 original size:32 final size:32
Alignment explanation
Indices: 2460782--2460878 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
2460772 GAGTCGAGGG
2460782 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
2460814 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
2460845 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
2460877 TT
1 TT
2460879 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:2460854 original size:31 final size:31
Alignment explanation
Indices: 2460781--2460881 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
2460771 AGAGTCGAGG
2460781 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
2460812 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
2460844 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
2460875 GTTTACC
1 GTTTACC
2460882 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:2460913 original size:30 final size:30
Alignment explanation
Indices: 2460869--2460962 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
2460859 AAGGAACATA
2460869 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
2460900 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
2460930 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2460959 TGGA
1 TGGA
2460963 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.29
30 35 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:2467473 original size:15 final size:16
Alignment explanation
Indices: 2467453--2467484 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2467443 TTGCAAAAAA
2467453 ATAATAATGC-TAAAT
1 ATAATAATGCATAAAT
2467468 ATAATAATGCATAAAT
1 ATAATAATGCATAAAT
2467484 A
1 A
2467485 AAATGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (16 bp):
ATAATAATGCATAAAT
Found at i:2481362 original size:32 final size:32
Alignment explanation
Indices: 2481326--2481397 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
2481316 GAAATAAAAT
2481326 TAAAAAATTACATAATTTTTAATTATTATTAA
1 TAAAAAATTACATAATTTTTAATTATTATTAA
*
2481358 TAAAAAATTATATAATTTTTAATTATTATTAA
1 TAAAAAATTACATAATTTTTAATTATTATTAA
2481390 TAAAAAAT
1 TAAAAAAT
2481398 AATTTTAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (32 bp):
TAAAAAATTACATAATTTTTAATTATTATTAA
Found at i:2493423 original size:84 final size:84
Alignment explanation
Indices: 2493282--2493449 Score: 311
Period size: 84 Copynumber: 2.0 Consensus size: 84
2493272 GTATGCATAG
*
2493282 GAGCGGACAACATGGTGCATCTCCTGTGTATGATGTTACAAAACTGACTAGACCACACTTTTGTT
1 GAGCGGACAACATGGTGCATCTCCTGTGTATGATATTACAAAACTGACTAGACCACACTTTTGTT
2493347 GATGACGTTCAATGATGAT
66 GATGACGTTCAATGATGAT
2493366 GAGCGGACAACATAGG-GCATCTCCTGTGTATGATATTACAAAACTGACTAGACCACACTTTTGT
1 GAGCGGACAACAT-GGTGCATCTCCTGTGTATGATATTACAAAACTGACTAGACCACACTTTTGT
2493430 TGATGACGTTCAATGATGAT
65 TGATGACGTTCAATGATGAT
2493450 TATGATCTTT
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
84 80 0.98
85 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (84 bp):
GAGCGGACAACATGGTGCATCTCCTGTGTATGATATTACAAAACTGACTAGACCACACTTTTGTT
GATGACGTTCAATGATGAT
Found at i:2494592 original size:99 final size:99
Alignment explanation
Indices: 2494482--2494681 Score: 400
Period size: 99 Copynumber: 2.0 Consensus size: 99
2494472 GAAAAAGAAT
2494482 AAGCGATCTTGAAGCATATTATAACATCCCAACCCGTATCCGACCCGAATACGAATCTGAAGTGT
1 AAGCGATCTTGAAGCATATTATAACATCCCAACCCGTATCCGACCCGAATACGAATCTGAAGTGT
2494547 CACATTGATTTTTCAAAGCTCGTACATTTATAAA
66 CACATTGATTTTTCAAAGCTCGTACATTTATAAA
2494581 AAGCGATCTTGAAGCATATTATAACATCCCAACCCGTATCCGACCCGAATACGAATCTGAAGTGT
1 AAGCGATCTTGAAGCATATTATAACATCCCAACCCGTATCCGACCCGAATACGAATCTGAAGTGT
2494646 CACATTGATTTTTCAAAGCTCGTACATTTATAAA
66 CACATTGATTTTTCAAAGCTCGTACATTTATAAA
2494680 AA
1 AA
2494682 CCATAGTAAA
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (99 bp):
AAGCGATCTTGAAGCATATTATAACATCCCAACCCGTATCCGACCCGAATACGAATCTGAAGTGT
CACATTGATTTTTCAAAGCTCGTACATTTATAAA
Found at i:2495162 original size:21 final size:21
Alignment explanation
Indices: 2495136--2495176 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2495126 CATATGAGTT
2495136 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
*
2495157 TTGTCCTGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
2495177 AACCCTCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:2495890 original size:44 final size:45
Alignment explanation
Indices: 2495778--2495897 Score: 161
Period size: 44 Copynumber: 2.7 Consensus size: 45
2495768 GCACTAACTA
* *
2495778 TGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAATGGG
1 TGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGGGG
* *
2495823 TGCATTGATACACAAATTACATTCGATGTTTTCA-TTTTAAGGGG
1 TGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGGGG
* ** *
2495867 TGCATCGATGCACTTATTGCATTCGATGTTT
1 TGCATCGATACACAAATTACATTCGATGTTT
2495898 ATTTATTTGA
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
44 35 0.53
45 31 0.47
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (45 bp):
TGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGGGG
Found at i:2501914 original size:19 final size:19
Alignment explanation
Indices: 2501890--2501942 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
2501880 AGTTTTAATG
2501890 TGTGCATCGATACACTTCC
1 TGTGCATCGATACACTTCC
* *
2501909 TGTGCATTGATACACTTTC
1 TGTGCATCGATACACTTCC
2501928 TGTGCATCGATACAC
1 TGTGCATCGATACAC
2501943 AAATTACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (19 bp):
TGTGCATCGATACACTTCC
Found at i:2502949 original size:19 final size:19
Alignment explanation
Indices: 2502925--2502977 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
2502915 ATTTTTAATG
2502925 TGTGCATCGATACACTTCC
1 TGTGCATCGATACACTTCC
* *
2502944 TGTGCATTGATACACTTTC
1 TGTGCATCGATACACTTCC
2502963 TGTGCATCGATACAC
1 TGTGCATCGATACAC
2502978 AAATTACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (19 bp):
TGTGCATCGATACACTTCC
Found at i:2503033 original size:19 final size:19
Alignment explanation
Indices: 2503009--2503060 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
2502999 TTTTAAGGGG
2503009 TGCATCGATGCACTCCCTA
1 TGCATCGATGCACTCCCTA
2503028 TGCATCGATGCACTCCCTA
1 TGCATCGATGCACTCCCTA
2503047 TGCATCGATGCACT
1 TGCATCGATGCACT
2503061 TATTGCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.35, G:0.17, T:0.27
Consensus pattern (19 bp):
TGCATCGATGCACTCCCTA
Found at i:2504931 original size:42 final size:40
Alignment explanation
Indices: 2504884--2504977 Score: 107
Period size: 42 Copynumber: 2.3 Consensus size: 40
2504874 TAGTAAGTCT
* * *
2504884 TTCGGGCCATTAGTAAGTCTTTCGAGCATGATGCTTAAACCC
1 TTCGGGCCATT-GTAAGCCTTTCGAGCAAGATG-ATAAACCC
* **
2504926 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCC
1 TTCGGGCCAT-TGTAAGCCTTTCGAGCAAGATGATAAACCC
2504967 TTCGGGCCATT
1 TTCGGGCCATT
2504978 CATAAGATCT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 1 0.02
41 14 0.32
42 28 0.64
43 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (40 bp):
TTCGGGCCATTGTAAGCCTTTCGAGCAAGATGATAAACCC
Found at i:2505185 original size:225 final size:225
Alignment explanation
Indices: 2504794--2505234 Score: 679
Period size: 225 Copynumber: 2.0 Consensus size: 225
2504784 TTATGAAATG
2504794 AAATGAGAAAGATTTCTCATTAAAATCTGAAATTTGAAAAGTAAGAAAGATTTCTTACCTAGTAA
1 AAATGAGAAAGATTTCTCATTAAAATCTGAAATTTGAAAAGTAAGAAAGATTTCTTACCTAGTAA
* * * * *
2504859 ATTATTTCCAAAACTTAGTAAGTCTTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGCTTAAAC
66 ATTATTTCCAAAACTGAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAAC
* *
2504924 CCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTCATAAGATCTT
131 CATTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTCATAAGACCTT
**
2504989 TGGGCAGGATGTTTTCACATGTCTATTGAA
196 CAGGCAGGATGTTTTCACATGTCTATTGAA
2505019 AAATGAGAAAGATTTCTCATTAAAATCTGAAGATTTGAAAAGTAAGAAATG-TTTCTTACCTAGT
1 AAATGAGAAAGATTTCTCATTAAAATCTGAA-ATTTGAAAAGTAAGAAA-GATTTCTTACCTAGT
* *
2505083 AAATTGTTTCCAAAACTGA-TAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCGTGATGATTAA
64 AAATTATTTCCAAAACTGAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAA
** * * * * *
2505147 ATTATTCGGGTTATCTGTAAGCCTTTTGAGTAAGATGATAAGTTCTTTGGGCCATTCATAAGACC
129 ACCATTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTCATAAGACC
*
2505212 TTCAGGTAGGATGTTTTCACATG
194 TTCAGGCAGGATGTTTTCACATG
2505235 ATGTTTTAAG
Statistics
Matches: 195, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
225 147 0.75
226 47 0.24
227 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (225 bp):
AAATGAGAAAGATTTCTCATTAAAATCTGAAATTTGAAAAGTAAGAAAGATTTCTTACCTAGTAA
ATTATTTCCAAAACTGAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAAC
CATTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTCATAAGACCTT
CAGGCAGGATGTTTTCACATGTCTATTGAA
Found at i:2505373 original size:42 final size:39
Alignment explanation
Indices: 2505301--2505408 Score: 99
Period size: 42 Copynumber: 2.6 Consensus size: 39
2505291 ACTTAGTAAG
* *
2505301 TCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGC-ATCA-TAAGCCTTTCGAGCAAGATGA-TAAA
* *
2505343 TCCTTCGGGTCATCTATAAGCCTTTTGAGCAAGATGATAAG
1 TCCTTCGGG-CATC-ATAAGCCTTTCGAGCAAGATGATAAA
*
2505384 TCCTTCGAGCCATCCATAAGACCTT
1 TCCTTCG-GGCAT-CATAAG-CCTT
2505409 CGGGTAGGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
41 18 0.32
42 36 0.64
43 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (39 bp):
TCCTTCGGGCATCATAAGCCTTTCGAGCAAGATGATAAA
Found at i:2505535 original size:38 final size:38
Alignment explanation
Indices: 2505456--2505599 Score: 227
Period size: 38 Copynumber: 3.8 Consensus size: 38
2505446 CTAGGCCAGC
* *
2505456 TTAAGCCTTCACCGAAGAATAGTGAAGC-AAATCCATT
1 TTAAGCCTTCACCGAAGAGTAGTGAAGCAAAATCAATT
*
2505493 TTAAGCCTTAACCGAAGAGTAGTGAAGCAAAATCAATT
1 TTAAGCCTTCACCGAAGAGTAGTGAAGCAAAATCAATT
*
2505531 TTAAGCCTTCACCGAAGAGTAGTGAAGCAAAATCAATC
1 TTAAGCCTTCACCGAAGAGTAGTGAAGCAAAATCAATT
* *
2505569 TTAAGCCTTCACAGAAGAGTAGTGAAACAAA
1 TTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
2505600 TCCATCTCTT
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
37 26 0.26
38 73 0.74
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (38 bp):
TTAAGCCTTCACCGAAGAGTAGTGAAGCAAAATCAATT
Found at i:2505630 original size:76 final size:73
Alignment explanation
Indices: 2505473--2505639 Score: 160
Period size: 76 Copynumber: 2.2 Consensus size: 73
2505463 TTCACCGAAG
* * * * *
2505473 AATAGTGAAGCAAATCCATTTTAAGCCTTAACCGAAGAGTAGTGAAGCAAAATCAATTTTAAGCC
1 AATAGTGAAGCAAATCAATCTTAAGCCTTAACAGAAGAGTAGTGAAACAAAATCAATTTTAACCC
* *
2505538 TTCACCGA
66 CTCACAGA
* *
2505546 AGAGTAGTGAAGCAAAATCAATCTTAAGCCTTCACAGAAGAGTAGTGAAAC-AAATCCATCTCTT
1 A-A-TAGTGAAGC-AAATCAATCTTAAGCCTTAACAGAAGAGTAGTGAAACAAAATCAAT-T-TT
2505610 ATATCCCCT-ACAGA
61 A-A-CCCCTCACAGA
2505624 AATAGTGGAA-CAAATC
1 AATAGT-GAAGCAAATC
2505640 CCTTATCAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
73 1 0.01
74 1 0.01
75 21 0.27
76 38 0.49
77 7 0.09
78 6 0.08
79 3 0.04
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (73 bp):
AATAGTGAAGCAAATCAATCTTAAGCCTTAACAGAAGAGTAGTGAAACAAAATCAATTTTAACCC
CTCACAGA
Found at i:2506233 original size:30 final size:30
Alignment explanation
Indices: 2506147--2506234 Score: 140
Period size: 30 Copynumber: 2.9 Consensus size: 30
2506137 ATAAGGTTAT
* *
2506147 TTATTTTAAAATAAATTATTATAAAAGAAT
1 TTATTTTAAAATAAATTATTATAAAATAAA
* *
2506177 TTATTTTAAAAGAATTTATTATAAAATAAA
1 TTATTTTAAAATAAATTATTATAAAATAAA
2506207 TTATTTTAAAATAAATTATTATAAAATA
1 TTATTTTAAAATAAATTATTATAAAATA
2506235 TGGATTGATT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
TTATTTTAAAATAAATTATTATAAAATAAA
Found at i:2506262 original size:15 final size:14
Alignment explanation
Indices: 2506242--2506309 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 14
2506232 ATATGGATTG
2506242 ATTTATTTTAAAATA
1 ATTTATTTT-AAATA
2506257 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* * *
2506271 ATTTATTAGTATGGATTG
1 ATTTATT--T-T-AAATA
2506289 ATTTATTTTAAATA
1 ATTTATTTTAAATA
2506303 ATTTATT
1 ATTTATT
2506310 AGTATGGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
14 21 0.49
15 10 0.23
16 2 0.05
17 1 0.02
18 9 0.21
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:2506271 original size:14 final size:15
Alignment explanation
Indices: 2506145--2506277 Score: 124
Period size: 15 Copynumber: 8.5 Consensus size: 15
2506135 TAATAAGGTT
2506145 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* * *
2506160 AATTATTATAAAAGA
1 ATTTATTTTAAAATA
*
2506175 ATTTATTTTAAAAGA
1 ATTTATTTTAAAATA
*
2506190 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
2506205 AATTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
2506220 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
2506239 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
2506257 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
2506271 ATTTATT
1 ATTTATT
2506278 AGTATGGATT
Statistics
Matches: 99, Mismatches: 12, Indels: 15
0.79 0.10 0.12
Matches are distributed among these distances:
14 12 0.12
15 67 0.68
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.06
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:2506287 original size:47 final size:52
Alignment explanation
Indices: 2506190--2506511 Score: 212
Period size: 54 Copynumber: 6.1 Consensus size: 52
2506180 TTTTAAAAGA
* *
2506190 ATTTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGATTG
* *
2506242 ATTTATTTTAAAATAATTTATTTT-AAAT-AA-T-TTAT-TAGTATGGATTG
1 ATTTATTTTAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGATTG
** * * * *
2506289 ATTTATTTT-AAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATT--T-TAAAATAAATTATTATAAAATATGGATTG
** * * * * *
2506343 ATTTATTTT-AAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATAATTTATT--T-TAAAATAAATTATTATAAAATATGGATTG
** * * * * *
2506397 ATTTATTTT-AAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATAATTTATT--T-TAAAATAAATTATTATAAAATATGGATTG
* * * * *
2506451 ATTTATTTT-AAATAATTTATTAGTAATGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATT-TTAA--AATAAATTATTATAAAATATGGATTG
2506505 ATTTATT
1 ATTTATT
2506512 ATTGTAGTTG
Statistics
Matches: 244, Mismatches: 16, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
46 12 0.05
47 19 0.08
48 5 0.02
49 2 0.01
50 4 0.02
51 5 0.02
52 24 0.10
53 3 0.01
54 170 0.70
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (52 bp):
ATTTATTTTAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGATTG
Found at i:2506295 original size:32 final size:32
Alignment explanation
Indices: 2506257--2506494 Score: 250
Period size: 32 Copynumber: 8.4 Consensus size: 32
2506247 TTTTAAAATA
2506257 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2506289 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2506321 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2506343 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2506375 ATTTATTTT--A-AA---A-TA-TA--GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2506397 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2506429 ATTTATTTT--A-AA---A-TA-TA--GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2506451 ATTTATTTTAAATAATTTATTAGTAAT-GATTG
1 ATTTATTTTAAATAATTTATTAGT-ATGGATTG
2506483 ATTTATTTTAAA
1 ATTTATTTTAAA
2506495 ATATGGATTG
Statistics
Matches: 176, Mismatches: 0, Indels: 60
0.75 0.00 0.25
Matches are distributed among these distances:
22 42 0.24
23 4 0.02
24 6 0.03
25 9 0.05
26 5 0.03
28 5 0.03
29 9 0.05
30 5 0.03
31 5 0.03
32 86 0.49
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Done.